ITI PUBLICATIONS FOR JANUARY 2014 (74)

1)Am J Nucl Med Mol Imaging. 2013 Dec 15;4(1):89-95.American Journal of Nuclear Medicine and Molecular Imaging: Editorial Board (2014) e-Century Publishing Corporation.Seto B1, Jacobs PM2, Mach RH3, Bulte JW4, Cai W5, Alavi A6, Divgi CR7, Wu JC8.Author information

PMID: 24380049 [PubMed] PMCID: PMC3867733--2)Proc Natl Acad Sci USA. 2013 Dec 30. [Epub ahead of print]High-throughput platform for real-time monitoring of biological processes by multicolor single-molecule fluorescence.Chen J, Dalal RV, Petrov AN, Tsai A, O'Leary SE, Chapin K, Cheng J, Ewan M, Hsiung PL, Lundquist P, Turner SW, Hsu DR, Puglisi JD.Author information

Zero-mode waveguides provide a powerful technology for studying single-molecule real-time dynamics of biological systems at physiological ligand concentrations. We customized a commercial zero-mode waveguide-based DNA sequencer for use as a versatile instrument for single-molecule fluorescence detection and showed that the system provides long fluorophore lifetimes with good signal to noise and low spectral cross-talk. We then used a ribosomal translation assay to show real-time fluidic delivery during data acquisition, showing it is possible to follow the conformation and composition of thousands of single biomolecules simultaneously through four spectral channels. This instrument allows high-throughput multiplexed dynamics of single-molecule biological processes over long timescales. The instrumentation presented here has broad applications to single-molecule studies of biological systems and is easily accessible to the biophysical community.PMID: 24379388 [PubMed - as supplied by publisher]--3)Hepatology. 2013 Dec 25. doi: 10.1002/hep.26986. [Epub ahead of print]Nonalcoholic steatohepatitis is the most rapidly growing indication for liver transplantation in patients with hepatocellular carcinoma in the U.S.Wong RJ, Cheung R, Ahmed A.

Nonalcoholic steatohepatitis (NASH) is currently the third leading indication for liver transplantation (LT) in the U.S. and is predicted to become the leading indication for LT in the near future. The trends in NASH-related hepatocellular carcinoma (HCC) among LT recipients in the U.S. remain undefined. We performed a retrospective cohort study to evaluate trends in the etiology of HCC among adult LT recipients in the U.S. from 2002 to 2012, utilizing national data from the United Network for Organ Sharing registry. From 2002-2012, there were 61,868 adults who underwent LT in the U.S., including 10,061 patients HCC. The total number and proportion of HCC LT recipients demonstrated a significant increase following the implementation of the model for end stage liver disease (MELD) scoring system in 2002 (3.3%, n=143 in 2000 vs. 12.2%, n=714 in 2005 vs. 23.3%, n=1336 in 2012). The proportion of HCV-related HCC increased steadily from 2002 to 2012, and HCV remained the leading etiology of HCC throughout the MELD era (43.4% in 2002 vs. 46.3% in 2007 vs. 49.9% in 2012). NASH-related

HCC also increased significantly, and NASH is the second leading etiology of HCC-related LT (8.3% in 2002 vs. 10.3% in 2007 vs. 13.5% in 2012). From 2002 to 2012, the number of patients undergoing LT for HCC secondary to NASH increased by nearly 4-fold, and the number of LT patients with HCC secondary to HCV increased by 2-fold. Conclusion: NASH is the second leading etiology of HCC leading to LT in the U.S. More importantly, NASH is currently the most rapidly growing indication for LT in patients with HCC in the U.S. (Hepatology 2013;).Copyright © 2013 American Association for the Study of Liver Diseases.KEYWORDS:UNOS, alcoholic liver disease, fatty liver, hepatitis C virus, liver cancerPMID: 24375711 [PubMed - as supplied by publisher]--4)Reprod Toxicol. 2013 Dec 26. pii: S0890-6238(13)00386-9. doi: 10.1016/j.reprotox.2013.12.005. [Epub ahead of print]Investigation of maternal environmental exposures in association with self-reported preterm birth.Patel CJ1, Yang T2, Hu Z2, Wen Q2, Sung J3, El-Sayed YY3, Cohen H4, Gould J5, Stevenson DK5, Shaw GM5, Ling XB6, Butte AJ7; on behalf of the March of Dimes Prematurity Research Center at Stanford University School of Medicine.

Identification of maternal environmental factors influencing preterm birth risks is important to understand the reasons for the increase in prematurity since 1990. Here, we utilized a health survey, the US National Health and Nutrition Examination Survey (NHANES) to search for personal environmental factors associated with preterm birth. 201 urine and blood markers of environmental factors, such as allergens, pollutants, and nutrients were assayed in mothers (range of N: 49 to 724) who answered questions about any children born preterm (delivery <37 weeks). We screened each of the 201 factors for association with any child born preterm adjusting by age, race/ethnicity, education, and household income. We attempted to verify the top finding, urinary bisphenol A, in an independent study of pregnant women attending Lucile Packard Children's Hospital. We conclude that the association between maternal urinary levels of bisphenol A and preterm birth should be evaluated in a larger epidemiological investigation.Copyright © 2013. Published by Elsevier Inc.KEYWORDS:CDC, Centers for Disease Control and Prevention, EWAS, Environment-wide association study, FDR, LPCH, Lucile Packard Children's Hospital, NCHS, NHANES, National Centers for Health Statistics, National Health and Nutrition Examination Survey, SES, environment-wide association study, environmental exposure, false discovery rate, preterm birth, socioeconomic statusPMID: 24373932 [PubMed - as supplied by publisher]--5)Neurochem Int. 2013 Dec 25. pii: S0197-0186(13)00324-0. doi: 10.1016/j.neuint.2013.12.006. [Epub ahead of print]microRNAs affect BCL-2 family proteins in the setting of cerebral ischemia.Ouyang YB1, Giffard RG2.

The BCL-2 family is centrally involved in the mechanism of cell death after cerebral ischemia. It is well known that the proteins of the BCL-2 family are key regulators of apoptosis through controlling mitochondrial outer membrane permeabilization. Recent findings suggest that many BCL-2 family members are also directly involved in controlling transmission of Ca2+ from the

endoplasmic reticulum (ER) to mitochondria through a specialization called the mitochondria-associated ER membrane (MAM). Increasing evidence supports the involvement of microRNAs (miRNAs), some of them targeting BCL-2 family proteins, in the regulation of cerebral ischemia. In this mini-review, after highlighting current knowledge about the multiple functions of BCL-2 family proteins and summarizing their relationship to outcome from cerebral ischemia, we focus on the regulation of BCL-2 family proteins by miRNAs, especially miR-29 which targets multiple BCL-2 family proteins.Copyright © 2013. Published by Elsevier Ltd.KEYWORDS:BCL-2, Cerebral ischemia, Stroke, miR-29, microRNAPMID: 24373752 [PubMed - as supplied by publisher]--6)Biol Blood Marrow Transplant. 2013 Dec 23. pii: S1083-8791(13)01161-0. doi: 10.1016/j.bbmt.2013.12.564. [Epub ahead of print]Unrelated Donor Allogeneic Hematopoietic Stem Cell Transplant for Patients with Hemoglobinopathies using a Reduced Intensity Conditioning Regimen and Third-party Mesenchymal Stromal Cells.Kharbanda S1, Smith AR2, Hutchinson SK3, McKenna DH2, Ball JB4, Lamb LS Jr4, Agarwal R3, Weinberg KI3, Wagner JE Jr2.

Allogeneic hematopoietic stem cell transplantation (HSCT) for patients with a hemoglobinopathy can be curative but is limited by donor availability. While positive results are frequently observed in those with a HLA matched sibling donor, the use of unrelated donors has been complicated by poor engraftment, excessive regimen-related toxicity and graft-versus-host disease (GVHD). As a potential strategy to address these obstacles, a pilot study was designed that incorporated both a reduced intensity conditioning (RIC) and mesenchymal stromal cells (MSCs). Six patients were enrolled including four with high risk Sickle Cell Disease (SCD) and two with transfusion dependent thalassemia major. Conditioning consisted of Fludarabine (150mg/m2), Melphalan (140mg/m2), and Alemtuzumab (60mg for patients weighing >30kg and 0.9mg/kg for patients weighing <30kg). Two patients received a HLA 7/8 allele matched bone marrow and four received 4-5/6 HLA matched umbilical cord blood (UCB) as the source of HSCs. MSCs were of bone marrow origin and derived from a parent in one patient and unrelated third party donor in the remaining five patients. GVHD prophylaxis consisted of cyclosporine A (CSA) and mycophenolate mofetil (MMF). One patient had neutropenic graft failure, two had autologous hematopoietic recovery and three had hematopoietic recovery with complete chimerism. The two SCD patients with autologous hematopoietic recovery are alive. The remaining four died either from opportunistic infection, GVHD, or intracranial hemorrhage. While there was no infusion-related toxicity, the co-transplantation of MSCs was not sufficient for reliable engraftment in patients with advanced hemoglobinopathy. While poor engraftment has been observed in nearly all such trials to date in this patient population, there was no evidence to suggest that MSC had any positive impact on engraftment. Due to lack of improved engraftment and unacceptably high transplant-related mortality, the study was prematurely terminated. Further investigations into understanding the mechanisms of graft resistance and development of strategies to overcome this barrier are needed to move this field forward.Copyright © 2013 American Society for Blood and Marrow Transplantation. Published by Elsevier Inc. All rights reserved.

KEYWORDS:Hemoglobinopathies, bone marrow, engraftment, graft-versus-host disease, hematopoietic stem cell transplant, mesenchymal stromal cells, reduced intensity conditioning, sickle cell disease, thalassemia, umbilical cordPMID: 24370862 [PubMed - as supplied by publisher]--7)Clin J Am Soc Nephrol. 2014 Jan;9(1):73-81. doi: 10.2215/CJN.04200413. Epub 2013 Dec 26.Comparison of Hospitalization Rates among For-Profit and Nonprofit Dialysis Facilities.Dalrymple LS, Johansen KL, Romano PS, Chertow GM, Mu Y, Ishida JH, Grimes B, Kaysen GA, Nguyen DV.

BACKGROUND AND OBJECTIVES:The vast majority of US dialysis facilities are for-profit and profit status has been associated with processes of care and outcomes in patients on dialysis. This study examined whether dialysis facility profit status was associated with the rate of hospitalization in patients starting dialysis.DESIGN, SETTING, PARTICIPANTS, & METHODS:This was a retrospective cohort study of Medicare beneficiaries starting dialysis between 2005 and 2008 using data from the US Renal Data System. All-cause hospitalization was examined and compared between for-profit and nonprofit dialysis facilities through 2009 using Poisson regression. Companion analyses of cause-specific hospitalization that are likely to be influenced by dialysis facility practices including hospitalizations for heart failure and volume overload, access complications, or hyperkalemia were conducted.RESULTS:The cohort included 150,642 patients. Of these, 12,985 (9%) were receiving care in nonprofit dialysis facilities. In adjusted models, patients receiving hemodialysis in for-profit facilities had a 15% (95% confidence interval [95% CI], 13% to 18%) higher relative rate of hospitalization compared with those in nonprofit facilities. Among patients receiving peritoneal dialysis, the rate of hospitalization in for-profit versus nonprofit facilities was not significantly different (relative rate, 1.07; 95% CI, 0.97 to 1.17). Patients on hemodialysis receiving care in for-profit dialysis facilities had a 37% (95% CI, 31% to 44%) higher rate of hospitalization for heart failure or volume overload and a 15% (95% CI, 11% to 20%) higher rate of hospitalization for vascular access complications.CONCLUSIONS:Hospitalization rates were significantly higher for patients receiving hemodialysis in for-profit compared with nonprofit dialysis facilities.PMID: 24370770 [PubMed - in process]--8)J Perinatol. 2013 Dec 26. doi: 10.1038/jp.2013.162. [Epub ahead of print]Outcomes of extremely preterm infants following severe intracranial hemorrhage.Davis AS1, Hintz SR1, Goldstein RF2, Ambalavanan N3, Bann CM4, Stoll BJ5, Bell EF6, Shankaran S7, Laptook AR8, Walsh MC9, Hale EC5, Newman NS9, Das A10, Higgins RD11.

Objective:Severe intracranial hemorrhage (ICH) is an important prognostic variable in extremely preterm (EPT) infants. We examined imaging and clinical variables that predict outcomes in EPT infants with severe ICH.Study design:Retrospective analysis of 353 EPT infants with severe ICH. Outcomes were compared by examining: (i) unilateral vs bilateral ICH; and (ii) presence vs absence of hemorrhagic parenchymal infarction (HPI). Regression analyses identified variables associated with death or neurodevelopmental impairment (NDI).Result:Bilateral ICH and HPI had higher rates of adverse outcomes and were independently associated with death/NDI. HPI

was the most important variable for infants of lower birth weight, and bilateral ICH for larger infants. For infants surviving to 36 weeks, shunt placement was most associated with death/NDI.Conclusion:Bilateral ICH and the presence of HPI in EPT infants with severe ICH are associated with death/NDI, though the importance depends on birth weight and survival to 36 weeks.Journal of Perinatology advance online publication, 26 December 2013; doi:10.1038/jp.2013.162.PMID: 24370654 [PubMed - as supplied by publisher]--9)Onco Targets Ther. 2013 Dec 17;7:13-21. doi: 10.2147/OTT.S53348.Management of cytopenias in patients with myelofibrosis treated with ruxolitinib and effect of dose modifications on efficacy outcomes.Verstovsek S1, Gotlib J2, Gupta V3, Atallah E4, Mascarenhas J5, Quintas-Cardama A1, Sun W6, Sarlis NJ6, Sandor V6, Levy RS6, Kantarjian HM1, Mesa RA7.

PURPOSE:Ruxolitinib is an oral Janus kinase (JAK) 1/JAK2 inhibitor approved in the US for the treatment of intermediate-or high-risk myelofibrosis (MF). Because thrombopoietin and erythropoietin signal through JAK2, dose-dependent cytopenias are expected with treatment. In the COMFORT-I (COntrolled Myelofibrosis study with ORal JAK inhibitor Treatment I) trial, these cytopenias were effectively managed with dose adjustments. These analyses were conducted to evaluate the relationship between ruxolitinib titrated doses and changes in platelet count and hemoglobin level as well as efficacy measures.PATIENTS AND METHODS:COMFORT-I was a randomized, placebo-controlled trial in 309 patients with intermediate-2 or high-risk MF and a platelet count ≥100 × 10(9)/L. Ruxolitinib starting doses were 15 and 20 mg twice daily (bis in die [BID]) for patients with baseline platelet counts of 100-200 × 10(9)/L and >200 × 10(9)/L, respectively. Percentage changes from baseline to week 24 in spleen volume and MF-related symptoms were assessed in subgroups defined by final titrated dose (average daily dose during weeks 21 to 24).RESULTS:The median final titrated doses for patients starting at doses of 15 and 20 mg BID were 10 and 20 mg BID, respectively, at week 24. Most dose reductions occurred in the first 8-12 weeks of treatment and coincided with decreases in platelet count and hemoglobin level. Subsequently, platelet counts stabilized and hemoglobin levels gradually returned to near baseline levels (red blood cell transfusion rates followed a similar trend). Final titrated doses of ≥10 mg BID were associated with clinically meaningful improvements in MF-related symptoms that were comparable across doses, while marginally greater reductions in spleen volume were observed at higher doses.CONCLUSION:This COMFORT-I analysis shows that dose-dependent cytopenias were effectively managed with ruxolitinib dose adjustments, and titrated doses of ≥10 mg BID were associated with clinically meaningful reductions in spleen volume and symptom improvement at week 24.KEYWORDS:COMFORT-I, JAK2 inhibitor, dose titration, myelofibrosis, ruxolitinib, treatment-related cytopeniasPMID: 24368888 [PubMed] PMCID: PMC3869911--10)JAMA. 2013 Dec 25;310(24):2640-9. doi: 10.1001/jama.2013.282833.Effect of nortriptyline on symptoms of idiopathic gastroparesis: the NORIG randomized clinical trial.

Parkman HP1, Van Natta ML2, Abell TL3, McCallum RW4, Sarosiek I4, Nguyen L5, Snape WJ6, Koch KL7, Hasler WL8, Farrugia G9, Lee L2, Unalp-Arida A2, Tonascia J2, Hamilton F10, Pasricha PJ11.

IMPORTANCE:Gastroparesis remains a challenging syndrome to manage, with few effective treatments and a lack of rigorously controlled trials. Tricyclic antidepressants are often used to treat refractory symptoms of nausea, vomiting, and abdominal pain. Evidence from well-designed studies for this use is lacking.OBJECTIVE:To determine whether treatment with nortriptyline results in symptomatic improvement in patients with idiopathic gastroparesis.DESIGN, SETTING, AND PARTICIPANTS:The NORIG (Nortriptyline for Idiopathic Gastroparesis) trial, a 15-week multicenter, parallel-group, placebo-controlled, double-masked, randomized clinical trial from the National Institute of Diabetes and Digestive and Kidney Diseases Gastroparesis Clinical Research Consortium (GpCRC), comparing nortriptyline with placebo for symptomatic relief in idiopathic gastroparesis. One hundred thirty patients with idiopathic gastroparesis were enrolled between March 2009 and June 2012 at 7 US academic medical centers. Patient follow-up was completed in October 2012. Inclusion criteria included delayed gastric emptying and moderate to severe symptom scores using the Gastroparesis Cardinal Symptom Index (GCSI). INTERVENTIONS Nortriptyline vs placebo. Study drug dose was increased at 3-week intervals (10, 25, 50, 75 mg) up to 75 mg at 12 weeks.MAIN OUTCOMES AND MEASURES:The primary outcome measure of symptomatic improvement was a decrease from the patient's baseline GCSI score of at least 50% on 2 consecutive 3-week GCSI assessments during 15 weeks of treatment.RESULTS:The primary symptomatic improvement outcome did not differ between 65 patients randomized to nortriptyline vs 65 patients randomized to placebo: 15 (23% [95% CI, 14%-35%]) in the nortriptyline group vs 14 (21% [95% CI, 12%-34%]) in the placebo group (P = .86). Treatment was stopped more often in the nortriptyline group (19 [29% {95% CI, 19%-42%}]) than in the placebo group (6 [9%] {95% CI, 3%-19%}]) (P = .007), but numbers of adverse events were not different (27 [95% CI, 18-39] vs 28 [95% CI, 19-40]) (P = .89).CONCLUSIONS AND RELEVANCE:Among patients with idiopathic gastroparesis, the use of nortriptyline compared with placebo for 15 weeks did not result in improvement in overall symptoms. These findings do not support the use of nortriptyline for idiopathic gastroparesis.TRIAL REGISTRATION:clinicaltrials.gov Identifier: NCT00765895.PMID: 24368464 [PubMed - indexed for MEDLINE]--11)Proc Natl Acad Sci USA. 2013 Dec 23. [Epub ahead of print]Systems analysis of sex differences reveals an immunosuppressive role for testosterone in the response to influenza vaccination.Furman D, Hejblum BP, Simon N, Jojic V, Dekker CL, Thiébaut R, Tibshirani RJ, Davis MM.

Females have generally more robust immune responses than males for reasons that are not well-understood. Here we used a systems analysis to investigate these differences by analyzing the neutralizing antibody response to a trivalent inactivated seasonal influenza vaccine (TIV) and a large number of immune system components, including serum cytokines and chemokines, blood cell subset frequencies, genome-wide gene expression, and cellular responses to diverse in vitro stimuli, in 53 females and 34 males of different ages. We found elevated antibody responses to

TIV and expression of inflammatory cytokines in the serum of females compared with males regardless of age. This inflammatory profile correlated with the levels of phosphorylated STAT3 proteins in monocytes but not with the serological response to the vaccine. In contrast, using a machine learning approach, we identified a cluster of genes involved in lipid biosynthesis and previously shown to be up-regulated by testosterone that correlated with poor virus-neutralizing activity in men. Moreover, men with elevated serum testosterone levels and associated gene signatures exhibited the lowest antibody responses to TIV. These results demonstrate a strong association between androgens and genes involved in lipid metabolism, suggesting that these could be important drivers of the differences in immune responses between males and females.KEYWORDS:aging, gender, immuno-endocrine, immunosenescence, sexual dimorphismPMID: 24367114 [PubMed - as supplied by publisher]--12)Lymphat Res Biol. 2013 Dec;11(4):195. doi: 10.1089/lrb.2013.1141.Tissue changes, bioimpedance, and acquired lymphedema.Rockson SG.

PMID: 24364841 [PubMed - in process]--13)Clin Gastroenterol Hepatol. 2013 Dec 17. pii: S1542-3565(13)01939-3. doi: 10.1016/j.cgh.2013.11.038. [Epub ahead of print]Histologic Changes in Liver Tissues from Patients with Chronic Hepatitis B and Minimal Increases in Levels of Alanine Aminotransferase: a Meta-analysis and Systematic Review.Nguyen LH1, Chao D2, Lim JK3, Ayoub W4, Nguyen MH5.

BACKGROUND & AIMS:Level of alanine aminotransferase (ALT) is a marker of hepatitis B severity and response to treatment. However, measurements ALT level may be of limited utility during the immune clearance phase of chronic hepatitis B (CHB), and can be affected by age, weight, and concomitant liver disease. We performed a literature review to determine the proportion of CHB patients with levels of ALT 1-2-fold the upper limit of normal who also had significant underlying liver fibrosis (stage ≥ 2).METHODS:We performed Medline search of original manuscripts published before June 2012, their references; we also searched abstracts from the 2010 and 2011 Annual Meetings of the AASLD and 2011 and 2012 Digestive Disease Weeks. Studies were included that had ≥20 consecutive treatment-naïve CHB patients with ≥6 months follow up, histologic data, and levels of ALT 1-2-fold the upper limit of normal. Study heterogeneity was assessed by Forest plot and Q and I2 analyses. Sensitivity was measured using 1-study removed analysis.RESULTS:Our analysis included 8 manuscripts and 1 abstract, comprising 683 patients. Based on random-effects modeling, 48% of patients had stage ≥ 2 fibrosis (95% confidence interval, 36%-61%). Upon sensitivity analysis, exclusion of the study that caused the greatest deflection of the pooled estimate produced a revised estimate of 43%. A subgroup of hepatitis B e-antigen-positive and -negative patients (n=168 and 170, respectively) revealed similar rates of fibrosis (41% vs 47%, P=non-significant).CONCLUSION:Despite heterogeneity in the literature, a substantial proportion of patients with slight increases in level of ALT have significant fibrosis. Given the possibility of advanced liver disease, the threshold for antiviral treatment must be individualized. Further studies are needed to investigate patients with modest increases in ALT.

Copyright © 2013 AGA Institute. Published by Elsevier Inc. All rights reserved.KEYWORDS:HBV, HBeAg, cirrhosis, patient managementPMID: 24361419 [PubMed - as supplied by publisher]--14)Clin Gatroenterol Hepatol. 2013 Dec 17. pii: S1542-3565(13)01934-4. doi: 10.1016/j.cgh.2013.12.008. [Epub ahead of print]Increased Long-Term Survival Among Patients with Hepatocellular Carcinoma After Implementation of Model for End-Stage Liver Disease Score.Wong RJ1, Devaki P2, Nguyen L3, Cheung R1, Cho-Phan C4, Nguyen MH5.

BACKGROUND & AIMS:Assignment of model for end-stage liver disease (MELD) exception points to patients with hepatocellular carcinoma (HCC) who fall within Milan criteria, which began in 2003, increases their priority on liver transplantation waitlists. However, little is known about how this change affected survival of all patients with HCC (transplant eligible and ineligible). We compared long-term survival of HCC patients before and after this change.METHODS:We performed a large population-based cohort study using the Surveillance, Epidemiology, and End Results cancer registry to investigate survival times of patients with HCC before those who met the Milan criteria were given MELD exception points (1998-2003) and afterward (2004-2010), using Kaplan Meier methods. Multivariate Cox proportional hazards models evaluated independent predictors of survival.RESULTS:During 2004-2010, a significantly higher percentage of patients with HCC survived for 5 years compared to 1998-2003 (21.9% vs 13.0%, P<.001). This difference remained significant among all treatment groups (no therapy: 15.2% vs 10.2%, P<0.001; local tumor destruction: 37.6% vs 22.1%, P<0.001; resection: 55.5% vs 39.2%, P<0.001; transplantation: 77.2% vs 73.1%, P =0.12). Multivariate Cox proportional hazards models, inclusive of sex, age, ethnicity, Milan criteria, number and stage of tumor, and time period, showed increased survival of patients during 2004-2010 (hazard ratio [HR], 0.87; 95% confidence interval, 0.83-0.91; P<.001). Compared to non-Hispanic whites, Asians (HR, 0.81; 95% CI, 0.77-0.86; P<.001) and Hispanics (HR, 0.89, 95% CI, 0.84-0.95; P<.001) had longer survival times, whereas blacks had a trend toward shorter survival times (HR, 1.05; 95% CI 0.98-1.13; P=.16).CONCLUSIONS:Patients with HCC who met Milan criteria had significantly longer survival times after implementation of the MELD exception points, regardless of sex or ethnicity. Blacks continued to have the lowest rates of 5 year survival.Copyright © 2013 AGA Institute. Published by Elsevier Inc. All rights reserved.KEYWORDS:CI, HCC, HR, MELD, SEER, TACE, UNOS, United Network for Organ Sharing, and end results, confidence interval, epidemiology, hazard ratio, hepatocellular carcinoma, liver cancer, model for end stage liver disease, racial disparities, resource allocation, surveillance, transarterial chemoembolizationPMID: 24361414 [PubMed - as supplied by publisher]--15)Diagn Microbiol Infect Dis. 2013 Nov 21. pii: S0732-8893(13)00598-1. doi: 10.1016/j.diagmicrobio.2013.11.013. [Epub ahead of print]Application of a non-amplification-based technology to detect invasive fungal pathogens.Hsu JL1, Binkley J2, Clemons KV3, Stevens DA3, Nicolls MR4, Holodniy M5.

Current diagnostic techniques for fungal diseases could be improved with respect to sensitivity, specificity, and timeliness. To address this clinical need, we adapted a non-amplification-based nucleic acid detection technology to identify fungal pathogens. We demonstrate a high-specificity, detection sensitivity, reproducibility, and multiplex capacity for detecting fungal strains.Copyright © 2013 Elsevier Inc. All rights reserved.KEYWORDS:Aspergillus, Candida, Diagnosis, Invasive fungal disease, nCounter analysis systemPMID: 24359934 [PubMed - as supplied by publisher]--16)Antioxid Redox Signal. 2013 Dec 20. [Epub ahead of print]The use of microRNAs to modulate redox and immune response to stroke.Giffard RG, Ouyang YB, Stary CM, White RE.

Significance: Cerebral ischemia is a major cause of death and disability throughout the world, yet therapeutic options remain limited. The interplay between cellular redox state and the immune response plays a critical role in determining the extent of neural cell injury after ischemia and reperfusion. Excessive amounts of reactive oxygen species (ROS) generated by mitochondria and other sources act both as triggers and effectors of inflammation. This review will focus on the interplay between these two mechanisms. Recent Advances: MicroRNAs (miRNAs) are important post-transcriptional regulators that interact with multiple target messenger RNAs (mRNAs) coordinately regulating target genes including those involved in controlling mitochondrial function, redox state, and inflammatory pathways. This review will focus on the regulation of mitochondria, ROS, and inflammation by miRNAs in the chain of deleterious intra- and intercellular events that lead to brain cell death after cerebral ischemia. Critical Issues: Although pretreatment using miRNAs was effective in cerebral ischemia in rodents, testing treatment after the onset of ischemia is an essential next step in the development of acute stroke treatment. In addition, miRNA formulation and delivery into the CNS remain a challenge in the clinical translation of miRNA therapy. Future Directions: Future research should focus on post-treatment and potential clinical use of miRNAs.PMID: 24359188 [PubMed - as supplied by publisher]--17)PLoS One. 2013 Dec 16;8(12):e82153. doi: 10.1371/journal.pone.0082153.Identification of common blood gene signatures for the diagnosis of renal and cardiac acute allograft rejection.Li L1, Khush K2, Hsieh SC3, Ying L1, Luikart H2, Sigdel T3, Roedder S3, Yang A2, Valantine H2, Sarwal MM3.

To test, whether 10 genes, diagnostic of renal allograft rejection in blood, are able to diagnose and predict cardiac allograft rejection, we analyzed 250 blood samples from heart transplant recipients with and without acute rejection (AR) and with cytomegalovirus (CMV) infection by QPCR. A QPCR-based logistic regression model was built on 5 of these 10 genes (AR threshold composite score>37% = AR) and tested for AR prediction in an independent set of 109 samples, where it correctly diagnosed AR with 89% accuracy, with no misclassifications for AR ISHLT grade 1b. CMV infection did not confound the AR score. The genes correctly diagnosed AR in a blood sample within 6 months prior to biopsy diagnosis with 80% sensitivity and untreated grade 1b AR episodes had persistently elevated scores until 6 months after biopsy diagnosis. The gene

score was also correlated with presence or absence of cardiac allograft vasculopathy (CAV) irrespective of rejection grade. In conclusion, there is a common transcriptional axis of immunological trafficking in peripheral blood in both renal and cardiac organ transplant rejection, across a diverse recipient age range. A common gene signature, initially identified in the setting of renal transplant rejection, can be utilized serially after cardiac transplantation, to diagnose and predict biopsy confirmed acute heart transplant rejection.PMID: 24358149 [PubMed - in process] PMCID: PMC3864873--18)J Clin Rheumatol. 2014 Jan;20(1):1-10. doi: 10.1097/RHU.0000000000000053.Effect of golimumab on carotid atherosclerotic disease measures and cardiovascular events in inflammatory arthritides.Wasko MC, Hsia EC, Kirkham B, Touboul PJ, Fleischmann R, Genovese MC, Matteson EL, Lu J, Xu W, Rahman MU.

OBJECTIVE:The objective of this study was to assess the effect of golimumab on carotid ultrasound measures and cardiovascular serious adverse events (SAEs) in patients with inflammatory arthritides.METHODS:An exploratory carotid artery ultrasound substudy was performed in the GO-BEFORE study of methotrexate (MTX)-naive rheumatoid arthritis patients, with ultrasounds performed at weeks 0, 24, and 52 to measure common carotid artery intima-media thickness, distensibility coefficient, interadventitial diameter, and plaque count. Cardiovascular SAEs reported over 2 years of follow-up were assessed in 5 golimumab phase 3 clinical trials of patients with rheumatoid arthritis (GO-BEFORE, GO-FORWARD, and GO-AFTER), psoriatic arthritis (GO-REVEAL), and ankylosing spondylitis (GO-RAISE). In GO-BEFORE and GO-FORWARD, patients received placebo + MTX, golimumab 50 mg + MTX, or golimumab 100 mg +/- MTX at baseline and every 4 weeks; in the other 3 trials, patients received placebo or golimumab 50 or 100 mg.RESULTS:The carotid ultrasound substudy showed inconsistent changes in common carotid artery intima-media thickness in the golimumab + MTX groups over time, and there was large variability in the measurements. Increases in interadventitial diameter were observed in the golimumab 100 mg + placebo group, but not in the golimumab + MTX groups. There were no significant differences in the distensibility coefficient and plaque count between the golimumab and placebo groups. Very few patients overall experienced a cardiovascular SAE, and the incidence of cardiovascular SAEs was not statistically different between the golimumab and placebo groups.CONCLUSIONS:The results of the carotid ultrasound substudy were inconclusive, and no increase or decrease in cardiovascular SAEs was observed following 2 years of treatment with golimumab with or without MTX.PMID: 24356481 [PubMed - in process]--19)Sci Transl Med. 2013 Dec 18;5(216):216ra176. doi: 10.1126/scitranslmed.3007762.CD4+ T Cell Autoimmunity to Hypocretin/Orexin and Cross-Reactivity to a 2009 H1N1 Influenza A Epitope in Narcolepsy.De la Herrán-Arita AK, Kornum BR, Mahlios J, Jiang W, Lin L, Hou T, Macaubas C, Einen M, Plazzi G, Crowe C, Newell EW, Davis MM, Mellins ED, Mignot E.

Narcolepsy, a disorder strongly associated with human leukocyte antigen (HLA)-DQA1*01:02/DQB1*06:02 (DQ0602), is characterized by excessive daytime sleepiness, cataplexy, and rapid eye movement sleep abnormalities. It is caused by the loss of ~70,000 posterior hypothalamic neurons that produce the wake-promoting neuropeptide hypocretin (HCRT) (orexin). We identified two DQ0602-binding HCRT epitopes, HCRT56-68 and HCRT87-99, that activated a subpopulation of CD4(+) T cells in narcolepsy patients but not in DQ0602-positive healthy control subjects. Because of the established association of narcolepsy with the 2009 H1N1 influenza A strain (pH1N1), we administered a seasonal influenza vaccine (containing pH1N1) to patients with narcolepsy and found an increased frequency of circulating HCRT56-68- and HCRT87-99-reactive T cells. We also identified a hemagglutinin (HA) pHA1 epitope specific to the 2009 H1N1 strain, pHA1275-287, with homology to HCRT56-68 and HCRT87-99. In vitro stimulation of narcolepsy CD4(+) T cells with pH1N1 proteins or pHA1275-287 increased the frequency of HCRT56-68- and HCRT87-99-reactive T cells. Our data indicate the presence of CD4(+) T cells that are reactive to HCRT in narcolepsy patients and possible molecular mimicry between HCRT and a similar epitope in influenza pH1N1, pHA1275-287. PMID: 24353159 [PubMed - in process]--20)Nat Immunol. 2013 Dec 18;15(1):1. doi: 10.1038/ni.2791.Leonard a. Herzenberg 1931-2013.Nolan GP.

PMID: 24352313 [PubMed - in process]--21)Mol Ther. 2013 Dec 19. doi: 10.1038/mt.2013.285. [Epub ahead of print]Recombinant AAV as a Platform for Translating the Therapeutic Potential of RNA Interference.Borel F1, Kay MA2, Mueller C3.

RNA interference has become a ubiquitous biological tool, and is being harnessed for therapeutic purposes as well. Therapeutic post-transcriptional gene silencing takes advantage of the endogenous RNAi pathway through delivery of either chemically-synthesized siRNAs, or transgenes expressing hairpin-based inhibitory RNAs (<i>e.g.</i> shRNAs and artificial miRNAs). RNAi has expanded the field of viral gene therapy from gene replacement to gene knockdown. Here we review various non-coding RNAs such as shRNAs, miRNAs, and miRNA decoys which can be utilized for therapeutic applications when expressed from recombinant AAV vectors, and present examples of their basic design. In addition the basis of exploiting cellular miRNA profiles for de-targeting AAV expression from specific cells is described. Finally an overview of AAV-mediated RNAi preclinical studies is presented, and current RNAi-based clinical trials are reviewed.Molecular Therapy (2013); doi:10.1038/mt.2013.285.PMID: 24352214 [PubMed - as supplied by publisher]--22)Autophagy. 2013 Dec 17;10(2). [Epub ahead of print]The glycolytic enzyme PFKFB3/phosphofructokinase regulates autophagy.Yang Z, Goronzy JJ, Weyand CM.

T lymphocytes, the master regulators of immunity, have an unusual lifestyle. Equipped with a clonally distributed receptor they remain resting for long periods of time but go into overdrive when encountering antigen. Antigen recognition triggers an activation program that results in massive proliferation, differentiation into effector/memory cells, egress from lymphoid storage sites, and production of an array of cytokines. To adapt to the sudden demand for energy and biosynthetic macromolecules, T cells resort to aerobic glycolysis, relying on the Warburg effect to provide sufficient ATP and precursor molecules. Metabolic adaptation to the biosynthetic needs includes upregulation of autophagy, a catabolic process resulting in the degradation of cytoplasmic contents. The close connection between a metabolic switch, proliferative expansion, and functional differentiation connects the metabolic conditions in the cell to normal and pathogenic immunity.KEYWORDS:NADPH, PFKFB3, ROS, autophagy, glycolysisPMID: 24351650 [PubMed - as supplied by publisher]--23)PLoS One. 2013 Dec 12;8(12):e80579. doi: 10.1371/journal.pone.0080579.ESAT-6 (EsxA) and TB10.4 (EsxH) Based Vaccines for Pre- and Post-Exposure Tuberculosis Vaccination.Hoang T1, Aagaard C1, Dietrich J2, Cassidy JP3, Dolganov G4, Schoolnik GK4, Lundberg CV5, Agger EM1, Andersen P1.

The ESX systems from Mycobacterium tuberculosis are responsible for the secretion of highly immunogenic proteins of key importance for bacterial survival and growth. The two prototypic proteins, ESAT-6 (EsxA from ESX-1) and TB10.4 (EsxH from ESX-3) share a lot of characteristics regarding genome organization, size, antigenic properties, and vaccine potential but the two molecules clearly have very different roles in bacterial physiology. To further investigate the role of ESAT-6 and TB10.4 as preventive and post-exposure tuberculosis vaccines, we evaluated four different fusion-protein vaccines; H1, H4, H56 and H28, that differ only in these two components. We found that all of these vaccines give rise to protection in a conventional prophylactic vaccination model. In contrast, only the ESAT-6-containing vaccines resulted in significant protection against reactivation, when administered post-exposure. This difference in post-exposure activity did not correlate with a difference in gene expression during infection or a differential magnitude or quality of the vaccine-specific CD4 T cells induced by ESAT-6 versus TB10.4-containing vaccines. The post-exposure effect of the ESAT-6 based vaccines was found to be influenced by the infectious load at the time-point of vaccination and was abolished in chronically infected animals with high bacterial loads at the onset of vaccination. Our data demonstrate that there are specific requirements for the immune system to target an already established tuberculosis infection and that ESAT-6 has a unique potential in post-exposure vaccination strategies.PMID: 24349004 [PubMed - in process] PMCID: PMC3861245--24)Int J Epidemiol. 2013 Dec 16. [Epub ahead of print]Systematic evaluation of environmental and behavioural factors associated with all-cause mortality in the United States National Health and Nutrition Examination Survey.Patel CJ, Rehkopf DH, Leppert JT, Bortz WM, Cullen MR, Chertow GM, Ioannidis JP.

BACKGROUND:Environmental and behavioural factors are thought to contribute to all-cause mortality. Here, we develop a method to systematically screen and validate the potential independent contributions to all-cause mortality of 249 environmental and behavioural factors in the National Health and Nutrition Examination Survey (NHANES).METHODS:We used Cox proportional hazards regression to associate 249 factors with all-cause mortality while adjusting for sociodemographic factors on data in the 1999-2000 and 2001-02 surveys (median 5.5 follow-up years). We controlled for multiple comparisons with the false discovery rate (FDR) and validated significant findings in the 2003-04 survey (median 2.8 follow-up years). We selected 249 factors from a set of all possible factors based on their presence in both the 1999-2002 and 2003-04 surveys and linkage with at least 20 deceased participants. We evaluated the correlation pattern of validated factors and built a multivariable model to identify their independent contribution to mortality.RESULTS:We identified seven environmental and behavioural factors associated with all-cause mortality, including serum and urinary cadmium, serum lycopene levels, smoking (3-level factor) and physical activity. In a multivariable model, only physical activity, past smoking, smoking in participant's home and lycopene were independently associated with mortality. These three factors explained 2.1% of the variance of all-cause mortality after adjusting for demographic and socio-economic factors.CONCLUSIONS:Our association study suggests that, of the set of 249 factors in NHANES, physical activity, smoking, serum lycopene and serum/urinary cadmium are associated with all-cause mortality as identified in previous studies and after controlling for multiple hypotheses and validation in an independent survey. Whereas other NHANES factors may be associated with mortality, they may require larger cohorts with longer time of follow-up to detect. It is possible to use a systematic association study to prioritize risk factors for further investigation.KEYWORDS:All-cause mortality, behaviour, environment-wide association study, exposurePMID: 24345851 [PubMed - as supplied by publisher]--25)Mol Cell Biol. 2013 Dec 16. [Epub ahead of print]The Apoptosis Repressor with a CARD Domain (ARC) is a Direct HIF1 Target Gene and Promotes Survival and Proliferation of VHL Deficient Renal Cancer Cells.Razorenova OV, Castellini L, Colavitti R, Edgington LE, Nicolau M, Huang X, Bedogni B, Mills EM, Bogyo M, Giaccia AJ.

The induction of hypoxia inducible factors (HIFs) is essential for the adaptation of tumor cells to a low oxygen environment. We found that the expression of the apoptosis inhibitor ARC was induced by hypoxia in a variety of cancer cell types and its induction is primarily HIF1 dependent. Chromatin immunoprecipitation (ChIP) and reporter assays also indicate that the ARC gene is regulated by direct binding of HIF1 to a hypoxia response element (HRE) located at -190 bp upstream of the transcription start site. HIFs play an essential role in the pathogenesis of renal cell carcinoma (RCC) under normoxic conditions, through the loss of the Von Hippel Lindau (VHL) gene. Accordingly, our results show that ARC is not expressed in normal renal tissue, but is highly expressed in 65% of RCC tumors, which also express high levels of Carbonic Anhydrase IX (CAIX), a HIF1-dependent gene. Compared to controls, ARC-deficient RCCs exhibited decreased colony formation and increased apoptosis in vitro. In addition, loss of ARC resulted in a dramatic reduction of RCC tumor growth in SCID mice in vivo. Thus, HIF-

mediated increased expression of ARC in RCC can explain how loss of VHL can promote survival early in tumor formation.PMID: 24344197 [PubMed - as supplied by publisher]--26)Clin Gastroenterol Hepatol. 2013 Dec 13. pii: S1542-3565(13)01892-2. doi: 10.1016/j.cgh.2013.11.036. [Epub ahead of print]Mutations in HBV DNA Polymerase Associated with Nucleos(t)ide resistance are Rare in Treatment-naïve Patients.Vutien P1, Trinh HN2, Garcia RT2, Nguyen HA3, Levitt BS3, Nguyen K3, da Silveira E3, Daugherty T4, Ahmed A4, Garcia G4, Lutchman GA4, Nguyen MH5.

BACKGROUND & AIMS:Prior studies have detected hepatitis B virus (HBV) DNA polymerase mutations in treatment naïve patients. However, most of these studies used either direct PCR sequencing, which detects these mutations with low levels of sensitivity, or patient cohorts that were not well characterized. We investigated the prevalence of HBV mutations in DNA polymerase using a line probe assay.METHODS:In a prospective, cross-sectional study, we enrolled 198 treatment-naïve patients with chronic hepatitis B (52.5% male, mean age 41 y), from February 2009 through May 2011, from 3 gastroenterology and liver clinics in Northern California. Exclusion criteria included infection with hepatitis C or D viruses or HIV. All patients completed a questionnaire (to determine demographics, history of liver disease, prior treatments, family medical history, drug and alcohol use, and environmental risk factors for hepatitis) that was administered by a research coordinator; mutations in HBV DNA polymerase were detected using the INNO-LiPA HBV DR v.3 assay.RESULTS:Most patients were Vietnamese (48.5%) or Chinese (36.4%), and were infected with HBV genotypes B (67.5%) or C (24.2%). Mutations in HBV DNA polymerase were found in 2 patients (1%): rtI233V (n = 1) and rtM250M/L (n = 1).CONCLUSION:In a multicenter prospective study of treatment-naïve patients with chronic hepatitis B, we detected mutations in HBV DNA polymerase in only 1%. Given the low prevalence of these mutations and the uncertain clinical significance of such quasi-species, routine HBV DNA polymerase mutation analysis cannot be recommended before initiation of antiviral therapy for treatment-naïve patients with chronic hepatitis B. The analysis requires further molecular and clinical studies. Copyright © 2013 AGA Institute. Published by Elsevier Inc. All rights reserved.KEYWORDS:ADV, CHB, ETV, HBV, LAM, NA, TDF, adefovir, baseline, entecavir, hepatitis B virus, lamivudine, nucleos(t)ide analogue, reverse, reverse transcriptase, rt, tenofovir, transcriptasePMID: 24342744 [PubMed - as supplied by publisher]--27)J Immunol. 2014 Jan 15;192(2):603-11. doi: 10.4049/jimmunol.1301384. Epub 2013 Dec 11.Effects of Aging, Cytomegalovirus Infection, and EBV Infection on Human B Cell Repertoires.Wang C, Liu Y, Xu LT, Jackson KJ, Roskin KM, Pham TD, Laserson J, Marshall EL, Seo K, Lee JY, Furman D, Koller D, Dekker CL, Davis MM, Fire AZ, Boyd SD.

Elderly humans show decreased humoral immunity to pathogens and vaccines, yet the effects of aging on B cells are not fully known. Chronic viral infection by CMV is implicated as a driver of

clonal T cell proliferations in some aging humans, but whether CMV or EBV infection contributes to alterations in the B cell repertoire with age is unclear. We have used high-throughput DNA sequencing of IGH gene rearrangements to study the BCR repertoires over two successive years in 27 individuals ranging in age from 20 to 89 y. Some features of the B cell repertoire remain stable with age, but elderly subjects show increased numbers of B cells with long CDR3 regions, a trend toward accumulation of more highly mutated IgM and IgG Ig genes, and persistent clonal B cell populations in the blood. Seropositivity for CMV or EBV infection alters B cell repertoires, regardless of the individual's age: EBV infection correlates with the presence of persistent clonal B cell expansions, whereas CMV infection correlates with the proportion of highly mutated Ab genes. These findings isolate effects of aging from those of chronic viral infection on B cell repertoires and provide a baseline for understanding human B cell responses to vaccination or infectious stimuli.PMID: 24337376 [PubMed - in process]--28)Neuro Oncol. 2014 Jan;16(1):21-8. doi: 10.1093/neuonc/not149. Epub 2013 Dec 10.Blockade of SDF-1 after irradiation inhibits tumor recurrences of autochthonous brain tumors in rats.Liu SC, Alomran R, Chernikova SB, Lartey F, Stafford J, Jang T, Merchant M, Zboralski D, Zöllner S, Kruschinski A, Klussmann S, Recht L, Brown JM.

Background Tumor irradiation blocks local angiogenesis, forcing any recurrent tumor to form new vessels from circulating cells. We have previously demonstrated that the post-irradiation recurrence of human glioblastomas in the brains of nude mice can be delayed or prevented by inhibiting circulating blood vessel-forming cells by blocking the interaction of CXCR4 with its ligand stromal cell-derived factor (SDF)-1 (CXCL12). In the present study we test this strategy by directly neutralizing SDF-1 in a clinically relevant model using autochthonous brain tumors in immune competent hosts. Methods We used NOX-A12, an l-enantiomeric RNA oligonucleotide that binds and inhibits SDF-1 with high affinity. We tested the effect of this inhibitor on the response to irradiation of brain tumors in rat induced by n-ethyl-N-nitrosourea. Results Rats treated in utero with N-ethyl-N-nitrosourea began to die of brain tumors from approximately 120 days of age. We delivered a single dose of whole brain irradiation (20 Gy) on day 115 of age, began treatment with NOX-A12 immediately following irradiation, and continued with either 5 or 20 mg/kg for 4 or 8 weeks, doses and times equivalent to well-tolerated human exposures. We found a marked prolongation of rat life span that was dependent on both drug dose and duration of treatment. In addition we treated tumors only when they were visible by MRI and demonstrated complete regression of the tumors that was not achieved by irradiation alone or with the addition of temozolomide. Conclusions Inhibition of SDF-1 following tumor irradiation is a powerful way of improving tumor response of glioblastoma multiforme.KEYWORDS:CXCL12, CXCR4, CXCR7, ENU-induced tumors, NOX-A12, SDF-1, angiogenesis, glioblastoma, irradiation, vasculogenesisPMID: 24335554 [PubMed - in process] PMCID: PMC3870826

--29)Contraception. 2013 Nov 12. pii: S0010-7824(13)00690-2. doi: 10.1016/j.contraception.2013.11.003. [Epub ahead of print]

Integrating family planning and prevention of mother to child HIV transmission in Zimbabwe.Sarnquist CC1, Moyo P2, Stranix-Chibanda L3, Chipato T3, Kang JL4, Maldonado YA4.

OBJECTIVE:The objective was to integrate enhanced family planning (FP) and prevention of mother-to-child HIV transmission services in order to help HIV-positive Zimbabwean women achieve their desired family size and spacing as well as to maximize maternal and child health.STUDY DESIGN:HIV-positive pregnant women were enrolled into a standard-of-care (SOC, n=33) or intervention (n=65) cohort, based on study entry date, and followed for 3 months postpartum. The intervention cohort received education sessions aimed at increasing FP use and negotiation power. Both groups received care from nurses with enhanced FP training. Outcomes included FP use, FP knowledge and HIV disclosure, and were assessed with Fisher's Exact Tests, binomial tests and t tests.RESULTS:The intervention cohort reported increased control over condom use (p=.002), increased knowledge about IUDs (p=.002), increased relationship power (p=.01) and increased likelihood of disclosing their HIV status to a partner (p=.04) and having that partner disclose to them (p=.04) when compared to the SOC cohort. Long-acting reversible contraception (LARC) use in both groups increased from ~2% at baseline to >80% at 3 months postpartum (p<.001).CONCLUSIONS:FP and sexual negotiation skills and knowledge, as well as HIV disclosure, increased significantly in the intervention cohort. LARC uptake increased significantly in both the intervention and SOC cohorts, likely because both groups received care from nurses with enhanced FP training. Successful service integration models are needed to maximize health outcomes in resource-constrained environments; this intervention is such a model that should be replicable in other settings in sub-Saharan Africa and beyond.IMPLICATIONS:This study provides a rigorously evaluated intervention to integrate FP education into ante- and postnatal care for HIV-positive women and also to train providers on FP. Results suggest that this intervention had significant effects on contraception use and communication with sexual partners. This intervention should be adaptable to other areas.Copyright © 2013 Elsevier Inc. All rights reserved.KEYWORDS:Contraception, HIV/AIDS, Intervention, Maternal child health, Prevention education, Provider trainingPMID: 24332254 [PubMed - as supplied by publisher]--30)Cell Host Microbe. 2013 Dec 11;14(6):631-40. doi: 10.1016/j.chom.2013.11.005.Nasal Microenvironments and Interspecific Interactions Influence Nasal Microbiota Complexity and S. aureus Carriage.Yan M1, Pamp SJ1, Fukuyama J2, Hwang PH3, Cho DY3, Holmes S2, Relman DA4.

The indigenous microbiota of the nasal cavity plays important roles in human health and disease. Patterns of spatial variation in microbiota composition may help explain Staphylococcus aureus colonization and reveal interspecies and species-host interactions. To assess the biogeography of the nasal microbiota, we sampled healthy subjects, representing both S. aureus carriers and noncarriers at three nasal sites (anterior naris, middle meatus, and sphenoethmoidal recess). Phylogenetic compositional and sparse linear discriminant analyses revealed communities that differed according to site epithelium type and S. aureus culture-based carriage status. Corynebacterium accolens and C. pseudodiphtheriticum were identified as the most important

microbial community determinants of S. aureus carriage, and competitive interactions were only evident at sites with ciliated pseudostratified columnar epithelium. In vitro cocultivation experiments provided supporting evidence of interactions among these species. These results highlight spatial variation in nasal microbial communities and differences in community composition between S. aureus carriers and noncarriers.Copyright © 2013 Elsevier Inc. All rights reserved. PMID: 24331461 [PubMed - in process]--31)BMC Biol. 2013 Dec 13;11:119. doi: 10.1186/1741-7007-11-119.Why are bacteria different from eukaryotes?Theriot JA.

PMID: 24330667 [PubMed - in process] PMCID: PMC3874686--32)Blood. 2013 Dec 10. [Epub ahead of print]Anti-KIR antibody enhancement of anti-lymphoma activity of natural killer cells as monotherapy and in combination with anti-CD20 antibodies.Kohrt HE, Thielens A, Marabelle A, Sagiv-Barfi I, Sola C, Chanuc F, Fuseri N, Bonnafous C, Czerwinski D, Rajapaksa A, Waller E, Ugolini S, Vivier E, Romagné F, Levy R, Bléry M, André P.

Natural killer (NK) cells mediate anti-lymphoma activity by spontaneous cytotoxicity and antibody-dependent cell-mediated cytotoxicity (ADCC) when triggered by rituximab, an anti-CD20 monoclonal antibody (mAb) used to treat patients with B cell lymphomas. The balance of inhibitory and activating signals determines the magnitude of NK cell's efficacy by spontaneous cytoxicity. Here, using a killer cell immunoglobulin-like receptor (KIR) transgenic murine model, we show that blockade of the interface of inhibitory KIRs with MHC class I antigens on lymphoma by anti-KIR antibodies prevents a tolerogenic interaction and augments NK cell spontaneous cytotoxicity. In combination with anti-CD20 mAbs, anti-KIR treatment induces enhanced NK cell-mediated, rituximab-dependent cytotoxicity against lymphoma in vitro and in vivo in KIR transgenic and syngeneic murine lymphoma models. These results support a therapeutic strategy of combination, rituximab and KIR blockade through lirilumab, illustrating the potential efficacy of combining a tumor targeting therapy with an NK cell agonist thus stimulating the post-rituximab anti-lymphoma immune response. PMID: 24326534 [PubMed - as supplied by publisher]--33)Transl Stroke Res. 2013 Dec;4(6):693-703. doi: 10.1007/s12975-013-0280-3. Epub 2013 Aug 17.MicroRNAs Regulate the Chaperone Network in Cerebral Ischemia.Ouyang YB, Giffard RG.

The highly evolutionarily conserved 70 kDa heat shock protein (HSP70) family was first understood for its role in protein folding and response to stress. Subsequently, additional functions have been identified for it in regulation of organelle interaction, of the inflammatory response, and of cell death and survival. Overexpression of HSP70 family members is associated with increased resistance to and improved recovery from cerebral ischemia. MicroRNAs (miRNAs) are important posttranscriptional regulators that interact with multiple target

messenger RNAs (mRNA) coordinately regulating target genes, including chaperones. The members of the HSP70 family are now appreciated to work together as networks to facilitate organelle communication and regulate inflammatory signaling and cell survival after cerebral ischemia. This review will focus on the new concept of the role of the chaperone network in the organelle network and its novel regulation by miRNA. PMID: 24323423 [PubMed - in process] PMCID: PMC3864745 [Available on 2014/12/1]--34)Pediatr Res. 2013 Dec 9. doi: 10.1038/pr.2013.235. [Epub ahead of print]Apolipoprotein E genotype and outcome in infants with hypoxic-ischemic encephalopathy.Cotten CM1, Goldstein RF1, McDonald SA2, Goldberg RN1, Salhab WA3, Carlo WA4, Tyson JE5, Finer NN6, Walsh MC7, Ehrenkranz RA8, Laptook AR9, Guillet R10, Schibler K11, Van Meurs KP12, Poindexter BB13, Stoll BJ14, O'Shea TM15, Duara S16, Das A17, Higgins RD18, Shankaran S19.

Background:Adults with the apolipoprotein E (APOE) gene alleles e4 and e2 are at high risk of poor neurological outcome after brain injury. The e4 allele has been associated with cerebral palsy (CP), and the e2 allele has been associated with worse neurological outcome with congenital heart disease. This study was done to test the hypothesis that the APOE genotype is associated with outcome among neonates who survive after hypoxic-ischemic encephalopathy (HIE).Methods:We conducted a cohort study of infants who survived HIE and had 18-22 mo standardized neurodevelopmental evaluations to assess associations between disability and the APOE genotypes e3/e3, e4/-, and e2/-.Results:A total of 139 survivors were genotyped. Of these, 86 (62%) were of the e3/e3, 41 (29%) were of the e4/-, and 14 (10%) were of the e2/- genotypes. One hundred and twenty-nine infants had genotype and follow-up data; 26% had moderate or severe disabilities. Disability prevalence was 30 and 19% among those with and without the e3/e3 genotype, 25 and 26% among those with and without the e2 allele, and 18 and 29% among those with and without the e4 allele, respectively. None of the differences were statistically significant. CP prevalence was also similar among genotype groups.Conclusion:Disability was not associated with the APOE genotype in this cohort of HIE survivors.Pediatric Research (2014); doi:10.1038/pr.2013.235.PMID: 24322171 [PubMed - as supplied by publisher]--35)J Undergrad Neurosci Educ. 2013 Oct 15;12(1):E6-E10.Science Communication to the General Public: Why We Need to Teach Undergraduate and Graduate Students this Skill as Part of Their Formal Scientific Training.Brownell SE, Price JV, Steinman L.

PMID: 24319399 [PubMed] PMCID: PMC3852879

--36)Oncogene. 2013 Dec 9. doi: 10.1038/onc.2013.523. [Epub ahead of print]Upregulation of the microRNA cluster at the Dlk1-Dio3 locus in lung adenocarcinoma.Valdmanis PN, Roy-Chaudhuri B, Kim HK, Sayles LC, Zheng Y, Chuang CH, Caswell DR, Chu K, Zhang Y, Winslow MM, Sweet-Cordero EA, Kay MA.

Mice in which lung epithelial cells can be induced to express an oncogenic KrasG12D develop lung adenocarcinomas in a manner analogous to humans. A myriad of genetic changes

accompany lung adenocarcinomas, many of which are poorly understood. To get a comprehensive understanding of both the transcriptional and post-transcriptional changes that accompany lung adenocarcinomas, we took an omics approach in profiling both the coding genes and the non-coding small RNAs in an induced mouse model of lung adenocarcinoma. RNAseq transcriptome analysis of KrasG12D tumors from F1 hybrid mice revealed features specific to tumor samples. This includes the repression of a network of GTPase-related genes (Prkg1, Gnao1 and Rgs9) in tumor samples and an enrichment of Apobec1-mediated cytosine to uridine RNA editing. Furthermore, analysis of known single-nucleotide polymorphisms revealed not only a change in expression of Cd22 but also that its expression became allele specific in tumors. The most salient finding, however, came from small RNA sequencing of the tumor samples, which revealed that a cluster of ∼53 microRNAs and mRNAs at the Dlk1-Dio3 locus on mouse chromosome 12qF1 was markedly and consistently increased in tumors. Activation of this locus occurred specifically in sorted tumor-originating cancer cells. Interestingly, the 12qF1 RNAs were repressed in cultured KrasG12D tumor cells but reactivated when transplanted in vivo. These microRNAs have been implicated in stem cell pleuripotency and proteins targeted by these microRNAs are involved in key pathways in cancer as well as embryogenesis. Taken together, our results strongly imply that these microRNAs represent key targets in unraveling the mechanism of lung oncogenesis.Oncogene advance online publication, 9 December 2013; doi:10.1038/onc.2013.523.PMID: 24317514 [PubMed - as supplied by publisher]--37)JAMA. 2013 Nov 20;310(19):2039-40. doi: 10.1001/jama.2013.282409.Patient-specific stem cells and cardiovascular drug discovery.Mordwinkin NM, Lee AS, Wu JC.

PMID: 24240927 [PubMed - indexed for MEDLINE]--38)N Engl J Med. 2013 Nov 14;369(20):e26. doi: 10.1056/NEJMvcm0909669.Videos in clinical medicine: Laryngeal mask airway in medical emergencies.Lighthall G, Harrison TK, Chu LF.

This video demonstrates the placement of a laryngeal mask airway, an alternative airway device that is both efficacious and easy to place. The laryngeal mask airway is routinely used for patients receiving general anesthesia and, increasingly, in patient resuscitation.

PMID: 24224639 [PubMed - indexed for MEDLINE]--39)N Engl J Med. 2013 Dec 26;369(26):2492-503. doi: 10.1056/NEJMoa1306033. Epub 2013 Nov 9.Bardoxolone methyl in type 2 diabetes and stage 4 chronic kidney disease.de Zeeuw D, Akizawa T, Audhya P, Bakris GL, Chin M, Christ-Schmidt H, Goldsberry A, Houser M, Krauth M, Lambers Heerspink HJ, McMurray JJ, Meyer CJ, Parving HH, Remuzzi G, Toto RD, Vaziri ND, Wanner C, Wittes J, Wrolstad D, Chertow GM; BEACON Trial Investigators.Collaborators (347)

BACKGROUND:Although inhibitors of the renin-angiotensin-aldosterone system can slow the progression of diabetic kidney disease, the residual risk is high. Whether nuclear 1 factor (erythroid-derived 2)-related factor 2 activators further reduce this risk is unknown.METHODS:We randomly assigned 2185 patients with type 2 diabetes mellitus and stage 4 chronic kidney disease (estimated glomerular filtration rate [GFR], 15 to <30 ml per minute per 1.73 m(2) of body-surface area) to bardoxolone methyl, at a daily dose of 20 mg, or placebo. The primary composite outcome was end-stage renal disease (ESRD) or death from cardiovascular causes.RESULTS:The sponsor and the steering committee terminated the trial on the recommendation of the independent data and safety monitoring committee; the median follow-up was 9 months. A total of 69 of 1088 patients (6%) randomly assigned to bardoxolone methyl and 69 of 1097 (6%) randomly assigned to placebo had a primary composite outcome (hazard ratio in the bardoxolone methyl group vs. the placebo group, 0.98; 95% confidence interval [CI], 0.70 to 1.37; P=0.92). In the bardoxolone methyl group, ESRD developed in 43 patients, and 27 patients died from cardiovascular causes; in the placebo group, ESRD developed in 51 patients, and 19 patients died from cardiovascular causes. A total of 96 patients in the bardoxolone methyl group were hospitalized for heart failure or died from heart failure, as compared with 55 in the placebo group (hazard ratio, 1.83; 95% CI, 1.32 to 2.55; P<0.001). Estimated GFR, blood pressure, and the urinary albumin-to-creatinine ratio increased significantly and body weight decreased significantly in the bardoxolone methyl group, as compared with the placebo group.CONCLUSIONS:Among patients with type 2 diabetes mellitus and stage 4 chronic kidney disease, bardoxolone methyl did not reduce the risk of ESRD or death from cardiovascular causes. A higher rate of cardiovascular events with bardoxolone methyl than with placebo prompted termination of the trial. (Funded by Reata Pharmaceuticals; BEACON ClinicalTrials.gov number, NCT01351675.).Comment in New therapies for diabetic kidney disease. [N Engl J Med. 2013]PMID: 24206459 [PubMed - indexed for MEDLINE]--40)Proc Natl Acad Sci USA. 2013 Nov 5;110(45):18244-9. doi: 10.1073/pnas.1312782110. Epub 2013 Oct 21.Ferrous iron-dependent drug delivery enables controlled and selective release of therapeutic agents in vivo.Deu E, Chen IT, Lauterwasser EM, Valderramos J, Li H, Edgington LE, Renslo AR, Bogyo M.

The precise targeting of cytotoxic agents to specific cell types or cellular compartments is of significant interest in medicine, with particular relevance for infectious diseases and cancer. Here, we describe a method to exploit aberrant levels of mobile ferrous iron (Fe(II)) for selective drug delivery in vivo. This approach makes use of a 1,2,4-trioxolane moiety, which serves as an Fe(II)-sensitive "trigger," making drug release contingent on Fe(II)-promoted trioxolane fragmentation. We demonstrate in vivo validation of this approach with the Plasmodium berghei model of murine malaria. Malaria parasites produce high concentrations of mobile ferrous iron as a consequence of their catabolism of host hemoglobin in the infected erythrocyte. Using activity-based probes, we successfully demonstrate the Fe(II)-dependent and parasite-selective delivery of a potent dipeptidyl aminopeptidase inhibitor. We find that delivery of the compound in its Fe(II)-targeted form leads to more sustained target inhibition with greatly reduced off-target inhibition of mammalian cathepsins. This selective drug delivery translates into improved

efficacy and tolerability. These findings demonstrate the utility of a purely chemical means to achieve selective drug targeting in vivo. This approach may find useful application in parasitic infections and more broadly in any disease state characterized by aberrant production of reactive ferrous iron.KEYWORDS:combination therapy, dipeptidyl peptidase, iron-mediated delivery, targeted prodrugs

PMID: 24145449 [PubMed - indexed for MEDLINE] PMCID: PMC3831501 [Available on 2014/5/5]--41)Circulation. 2013 Sep 10;128(11 Suppl 1):S42-9. doi: 10.1161/CIRCULATIONAHA.112.000230.Comparison of transendocardial and intracoronary CD34+ cell transplantation in patients with nonischemic dilated cardiomyopathy.Vrtovec B, Poglajen G, Lezaic L, Sever M, Socan A, Domanovic D, Cernelc P, Torre-Amione G, Haddad F, Wu JC.

BACKGROUND:In an open-label blinded study, we compared intracoronary and transendocardial CD34(+) cell transplantation in patients with nonischemic dilated cardiomyopathy.METHODS AND RESULTS:Of the 40 patients with dilated cardiomyopathy, 20 were randomized to receive intracoronary injection and 20 received transendocardial CD34(+) cell delivery. In both groups, CD34(+) cells were mobilized by filgrastim, collected via apheresis, and labeled with technetium-99m radioisotope for single-photon emission computed tomographic imaging. In the intracoronary group, cells were injected intracoronarily in the artery supplying segments of greater perfusion defect on myocardial perfusion scintigraphy. In the transendocardial group, electroanatomic mapping was used to identify viable but dysfunctional myocardium, and transendocardial cell injections were performed. Nuclear single-photon emission computed tomographic imaging for quantification of myocardial retention was performed 18 hours thereafter. At baseline, groups did not differ in age, sex, left ventricular ejection fraction, or N-terminal pro-brain natriuretic peptide levels. The number of CD34(+) cells was also comparable (105 ± 31 × 10(6) in the transendocardial group versus 103 ± 27 × 10(6) in the intracoronary group, P=0.62). At 18 hours after procedure, myocardial retention was higher in the transendocardial group (19.2 ± 4.8%) than in the intracoronary group (4.4 ± 1.2%, P<0.01). At 6 months, left ventricular ejection fraction improved more in the transendocardial group (+8.1 ± 4.3%) than in the intracoronary group (+4.2 ± 2.3%, P=0.03). The same pattern was observed for the 6-minute walk test distance (+125 ± 33 m in the transendocardial group versus +86 ± 13 m in the intracoronary group, P=0.03) and N-terminal pro-brain natriuretic peptide (-628 ± 211 versus -315 ± 133 pg/mL, P=0.04).CONCLUSIONS:In patients with dilated cardiomyopathy, transendocardial CD34(+) cell transplantation is associated with higher myocardial retention rates and greater improvement in ventricular function, N-terminal pro-brain natriuretic peptide, and exercise capacity compared with intracoronary route.CLINICAL TRIAL REGISTRATION URL:http://www.clinicaltrials.gov. Unique identifier: NCT01350310.KEYWORDS:cardiomyopathy, dilated, heart failure, stem cells

PMID: 24030420 [PubMed - indexed for MEDLINE]--42)Circulation. 2013 Sep 10;128(11 Suppl 1):S3-13. doi: 10.1161/CIRCULATIONAHA.112.000570.Screening drug-induced arrhythmia events using human induced pluripotent stem cell-derived cardiomyocytes and low-impedance microelectrode arrays.Navarrete EG, Liang P, Lan F, Sanchez-Freire V, Simmons C, Gong T, Sharma A, Burridge PW, Patlolla B, Lee AS, Wu H, Beygui RE, Wu SM, Robbins RC, Bers DM, Wu JC.

BACKGROUND:Drug-induced arrhythmia is one of the most common causes of drug development failure and withdrawal from market. This study tested whether human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) combined with a low-impedance microelectrode array (MEA) system could improve on industry-standard preclinical cardiotoxicity screening methods, identify the effects of well-characterized drugs, and elucidate underlying risk factors for drug-induced arrhythmia. hiPSC-CMs may be advantageous over immortalized cell lines because they possess similar functional characteristics as primary human cardiomyocytes and can be generated in unlimited quantities.METHODS AND RESULTS:Pharmacological responses of beating embryoid bodies exposed to a comprehensive panel of drugs at 65 to 95 days postinduction were determined. Responses of hiPSC-CMs to drugs were qualitatively and quantitatively consistent with the reported drug effects in literature. Torsadogenic hERG blockers, such as sotalol and quinidine, produced statistically and physiologically significant effects, consistent with patch-clamp studies, on human embryonic stem cell-derived cardiomyocytes hESC-CMs. False-negative and false-positive hERG blockers were identified accurately. Consistent with published studies using animal models, early afterdepolarizations and ectopic beats were observed in 33% and 40% of embryoid bodies treated with sotalol and quinidine, respectively, compared with negligible early afterdepolarizations and ectopic beats in untreated controls.CONCLUSIONS:We found that drug-induced arrhythmias can be recapitulated in hiPSC-CMs and documented with low impedance MEA. Our data indicate that the MEA/hiPSC-CM assay is a sensitive, robust, and efficient platform for testing drug effectiveness and for arrhythmia screening. This system may hold great potential for reducing drug development costs and may provide significant advantages over current industry standard assays that use immortalized cell lines or animal models.KEYWORDS:arrhythmias, cardiac, genomics, myocytes, cardiac, pharmacogenetics, pharmacology, stem cellsPMID: 24030418 [PubMed - indexed for MEDLINE] PMCID: PMC3855862 [Available on 2014/9/10]--43)J Exp Med. 2013 Oct 21;210(11):2205-21. doi: 10.1084/jem.20122709. Epub 2013 Oct 14.A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation.Khatri P, Roedder S, Kimura N, De Vusser K, Morgan AA, Gong Y, Fischbein MP, Robbins RC, Naesens M, Butte AJ, Sarwal MM.

Using meta-analysis of eight independent transplant datasets (236 graft biopsy samples) from four organs, we identified a common rejection module (CRM) consisting of 11 genes that were significantly overexpressed in acute rejection (AR) across all transplanted organs. The CRM genes could diagnose AR with high specificity and sensitivity in three additional independent cohorts (794 samples). In another two independent cohorts (151 renal transplant biopsies), the CRM genes correlated with the extent of graft injury and predicted future injury to a graft using protocol biopsies. Inferred drug mechanisms from the literature suggested that two FDA-approved drugs (atorvastatin and dasatinib), approved for nontransplant indications, could regulate specific CRM genes and reduce the number of graft-infiltrating cells during AR. We treated mice with HLA-mismatched mouse cardiac transplant with atorvastatin and dasatinib and showed reduction of the CRM genes, significant reduction of graft-infiltrating cells, and extended graft survival. We further validated the beneficial effect of atorvastatin on graft survival by retrospective analysis of electronic medical records of a single-center cohort of 2,515 renal transplant patients followed for up to 22 yr. In conclusion, we identified a CRM in transplantation that provides new opportunities for diagnosis, drug repositioning, and rational drug design.PMID: 24127489 [PubMed - indexed for MEDLINE] PMCID: PMC3804941 [Available on 2014/4/21]--44)Nat Immunol. 2013 Nov;14(11):1166-72. doi: 10.1038/ni.2730. Epub 2013 Sep 29.Defective sphingosine 1-phosphate receptor 1 (S1P1) phosphorylation exacerbates TH17-mediated autoimmune neuroinflammation.Garris CS, Wu L, Acharya S, Arac A, Blaho VA, Huang Y, Moon BS, Axtell RC, Ho PP, Steinberg GK, Lewis DB, Sobel RA, Han DK, Steinman L, Snyder MP, Hla T, Han MH.

Sphingosine 1-phosphate (S1P) signaling regulates lymphocyte egress from lymphoid organs into systemic circulation. The sphingosine phosphate receptor 1 (S1P1) agonist FTY-720 (Gilenya) arrests immune trafficking and prevents multiple sclerosis (MS) relapses. However, alternative mechanisms of S1P-S1P1 signaling have been reported. Phosphoproteomic analysis of MS brain lesions revealed S1P1 phosphorylation on S351, a residue crucial for receptor internalization. Mutant mice harboring an S1pr1 gene encoding phosphorylation-deficient receptors (S1P1(S5A)) developed severe experimental autoimmune encephalomyelitis (EAE) due to autoimmunity mediated by interleukin 17 (IL-17)-producing helper T cells (TH17 cells) in the peripheral immune and nervous system. S1P1 directly activated the Jak-STAT3 signal-transduction pathway via IL-6. Impaired S1P1 phosphorylation enhances TH17 polarization and exacerbates autoimmune neuroinflammation. These mechanisms may be pathogenic in MS.PMID: 24076635 [PubMed - indexed for MEDLINE]--45)Proc Natl Acad Sci USA. 2013 Oct 15;110(42):17059-64. doi: 10.1073/pnas.1306070110. Epub 2013 Sep 23.Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota.Kashyap PC, Marcobal A, Ursell LK, Smits SA, Sonnenburg ED, Costello EK, Higginbottom SK, Domino SE, Holmes SP, Relman DA, Knight R, Gordon JI, Sonnenburg JL.

We investigate how host mucus glycan composition interacts with dietary carbohydrate content to influence the composition and expressed functions of a human gut community. The

humanized gnotobiotic mice mimic humans with a nonsecretor phenotype due to knockout of their α1-2 fucosyltransferase (Fut2) gene. The fecal microbiota of Fut2(-) mice that lack fucosylated host glycans show decreased alpha diversity relative to Fut2(+) mice and exhibit significant differences in community composition. A glucose-rich plant polysaccharide-deficient (PD) diet exerted a strong effect on the microbiota membership but eliminated the effect of Fut2 genotype. Additionally fecal metabolites predicted host genotype in mice on a polysaccharide-rich standard diet but not on a PD diet. A more detailed mechanistic analysis of these interactions involved colonization of gnotobiotic Fut2(+) and Fut2(-) mice with Bacteroides thetaiotaomicron, a prominent member of the human gut microbiota known to adaptively forage host mucosal glycans when dietary polysaccharides are absent. Within Fut2(-) mice, the B. thetaiotaomicron fucose catabolic pathway was markedly down-regulated, whereas BT4241-4247, an operon responsive to terminal β-galactose, the precursor that accumulates in the Fut2(-) mice, was significantly up-regulated. These changes in B. thetaiotaomicron gene expression were only evident in mice fed a PD diet, wherein B. thetaiotaomicron relies on host mucus consumption. Furthermore, up-regulation of the BT4241-4247 operon was also seen in humanized Fut2(-) mice. Together, these data demonstrate that differences in host genotype that affect the carbohydrate landscape of the distal gut interact with diet to alter the composition and function of resident microbes in a diet-dependent manner.KEYWORDS:host–microbial mutualism, intestinal microbiota, metabolomicsPMID: 24062455 [PubMed - indexed for MEDLINE] PMCID: PMC3800993 [Available on 2014/4/15]--46)Curr Opin Immunol. 2013 Aug;25(4):484-94. doi: 10.1016/j.coi.2013.07.004. Epub 2013 Aug 31.Single-cell mass cytometry for analysis of immune system functional states.Bjornson ZB, Nolan GP, Fantl WJ.

Mass cytometry facilitates high-dimensional, quantitative analysis of the effects of bioactive molecules on cell populations at single-cell resolution. Datasets are generated with panels of up to 45 antibodies. Each antibody is conjugated to a polymer chelated with a stable metal isotope, usually in the lanthanide series of the periodic table. Antibody panels recognize surface markers to delineate cell types simultaneously with intracellular signaling molecules to measure biological functions, such as metabolism, survival, DNA damage, cell cycle and apoptosis, to provide an overall determination of the network state of an individual cell. This review will cover the basics of mass cytometry as well as outline assays developed for the platform that enhance the immunologist's analytical arsenal. Copyright © 2013 Elsevier Ltd. All rights reserved.PMID: 23999316 [PubMed - indexed for MEDLINE] PMCID: PMC3835664 [Available on 2014/8/31]--47)Nat Cell Biol. 2013 Oct;15(10):1244-52. doi: 10.1038/ncb2835. Epub 2013 Sep 1.Early role for IL-6 signalling during generation of induced pluripotent stem cells revealed by heterokaryon RNA-Seq.Brady JJ, Li M, Suthram S, Jiang H, Wong WH, Blau HM.

Molecular insights into somatic cell reprogramming to induced pluripotent stem cells (iPS) would aid regenerative medicine, but are difficult to elucidate in iPS because of their

heterogeneity, as relatively few cells undergo reprogramming (0.1-1%; refs , ). To identify early acting regulators, we capitalized on non-dividing heterokaryons (mouse embryonic stem cells fused to human fibroblasts), in which reprogramming towards pluripotency is efficient and rapid, enabling the identification of transient regulators required at the onset. We used bi-species transcriptome-wide RNA-seq to quantify transcriptional changes in the human somatic nucleus during reprogramming towards pluripotency in heterokaryons. During heterokaryon reprogramming, the cytokine interleukin 6 (IL6), which is not detectable at significant levels in embryonic stem cells, was induced 50-fold. A 4-day culture with IL6 at the onset of iPS reprogramming replaced stably transduced oncogenic c-Myc such that transduction of only Oct4, Klf4 and Sox2 was required. IL6 also activated another Jak/Stat target, the serine/threonine kinase gene Pim1, which accounted for the IL6-mediated twofold increase in iPS frequency. In contrast, LIF, another induced GP130 ligand, failed to increase iPS frequency or activate c-Myc or Pim1, thereby revealing a differential role for the two Jak/Stat inducers in iPS generation. These findings demonstrate the power of heterokaryon bi-species global RNA-seq to identify early acting regulators of reprogramming, for example, extrinsic replacements for stably transduced transcription factors such as the potent oncogene c-Myc.PMID: 23995732 [PubMed - indexed for MEDLINE]--48)Curr Opin Immunol. 2013 Aug;25(4):511-5. doi: 10.1016/j.coi.2013.07.007. Epub 2013 Aug 28.Human lymphocyte repertoires in ageing.Boyd SD, Liu Y, Wang C, Martin V, Dunn-Walters DK.

Deterioration of adaptive immunity with ageing may reflect changes in the repertoire of T cells and B cells available to respond to antigenic challenges, due to altered proportions and absolute numbers of lymphocyte subpopulations as well as changes in the repertoire of antigen receptor genes expressed by these cells. High-throughput DNA sequencing (HTS) now facilitates examination of immunoglobulin and T cell receptor gene rearrangements, and initial studies using these methods to study immune system ageing in humans have demonstrated age-related alterations in the receptor populations within lymphocyte subsets, as well as in repertoires responding to vaccination. Accurate measurement of repertoire diversity remains an experimental challenge. Studies of larger numbers of human subjects, analysis of defined lymphocyte subpopulations including antigen-specific populations, and controlling for factors such as chronic viral infections, will be important for gaining additional understanding of the impact of ageing on human lymphocyte populations.Copyright © 2013 Elsevier Ltd. All rights reserved.PMID: 23992996 [PubMed - indexed for MEDLINE]--49)J Allergy Clin Immunol. 2013 Oct;132(4):881-8.e1-11. doi: 10.1016/j.jaci.2013.06.008. Epub 2013 Aug 1.Selective ablation of mast cells or basophils reduces peanut-induced anaphylaxis in mice.Reber LL, Marichal T, Mukai K, Kita Y, Tokuoka SM, Roers A, Hartmann K, Karasuyama H, Nadeau KC, Tsai M, Galli SJ.

BACKGROUND:Studies with c-kit mutant mast cell (MC)-deficient mice and antibody-mediated depletion of basophils suggest that both MCs and basophils can contribute to peanut-induced anaphylaxis (PIA). However, interpretation of data obtained by using such approaches is

complicated because c-kit mutant mice have several phenotypic abnormalities in addition to MC deficiency and because basophil-depleting antibodies can also react with MCs.OBJECTIVE:We analyzed (1) the changes in the features of PIA in mice after the selective and inducible ablation of MCs or basophils and (2) the possible importance of effector cells other than MCs and basophils in the PIA response.METHODS:Wild-type and various mutant mice were orally sensitized with peanut extract and cholera toxin weekly for 4 weeks and challenged intraperitoneally with peanut extract 2 weeks later.RESULTS:Peanut-challenged, MC-deficient Kit(W-sh/W-sh) mice had reduced immediate hypothermia, as well as a late-phase decrease in body temperature that was abrogated by antibody-mediated depletion of neutrophils. Diphtheria toxin-mediated selective depletion of MCs or basophils in Mcpt5-Cre;iDTR and Mcpt8(DTR) mice, respectively, and treatment of wild-type mice with the basophil-depleting antibody Ba103 significantly reduced peanut-induced hypothermia. Non-c-kit mutant MC- and basophil-deficient Cpa3-Cre;Mcl-1(fl/fl) mice had reduced but still significant responses to peanut.CONCLUSION:Inducible and selective ablation of MCs or basophils in non-c-kit mutant mice can significantly reduce PIA, but partial responses to peanut can still be observed in the virtual absence of both cell types. The neutrophilia in Kit(W-sh/W-sh) mice might influence the responses of these mice in this PIA model.Copyright © 2013 American Academy of Allergy, Asthma & Immunology. Published by Mosby, Inc. All rights reserved.KEYWORDS:BMCMC, Bone marrow–derived cultured mast cell, CTMC, Carboxypeptidase A3, Connective tissue–type mast cells, Cpa3, DT, DTR, Diphtheria toxin, Diphtheria toxin receptor, Kit(W-sh/W-sh), MC, MMC, Mast cell, Mast cell protease, Mcpt, Mucosal mast cell, PAF, PIA, PSA, Passive systemic anaphylaxis, Peanut, Peanut-induced anaphylaxis, Platelet-activating factor, WT, Wild-type, allergy, anaphylaxis, basophils, carboxypeptidase A3, diphtheria toxin, mast cell protease 5, mast cells, neutrophilsPMID: 23915716 [PubMed - indexed for MEDLINE] PMCID: PMC3794715 [Available on 2014/10/1]--50)Clin Pharmacol Ther. 2013 Oct;94(4):452-8. doi: 10.1038/clpt.2013.134. Epub 2013 Jul 31.CD34+ stem cell therapy in nonischemic dilated cardiomyopathy patients.Vrtovec B, Poglajen G, Sever M, Lezaic L, Socan A, Haddad F, Wu JC.

Recent trends indicate that patients with nonischemic dilated cardiomyopathy represent the largest subpopulation of heart failure patients with a significant need for alternative treatment modalities. Similar to patients with ischemic cardiomyopathy, patients with nonischemic dilated cardiomyopathy have been found to have myocardial regions with flow abnormalities, which may represent targets for neoangiogenic therapies. CD34(+) stem cells might contribute to the formation of new blood vessels from existing vascular structures in ischemic tissues by the direct incorporation of injected cells into the newly developing vasculature or by the production and secretion of angiogenic cytokines. This review summarizes the long-term clinical effects and potential underlying mechanisms of CD34(+) cell therapy in patients with nonischemic dilated cardiomyopathy.PMID: 23903668 [PubMed - indexed for MEDLINE]--

51)Proc Natl Acad Sci USA. 2013 Jul 30;110(31):12643-8. doi: 10.1073/pnas.1310212110. Epub 2013 Jul 15.Clonal precursor of bone, cartilage, and hematopoietic niche stromal cells.Chan CK, Lindau P, Jiang W, Chen JY, Zhang LF, Chen CC, Seita J, Sahoo D, Kim JB, Lee A, Park S, Nag D, Gong Y, Kulkarni S, Luppen CA, Theologis AA, Wan DC, DeBoer A, Seo EY, Vincent-Tompkins JD, Loh K, Walmsley GG, Kraft DL, Wu JC, Longaker MT, Weissman IL.

Organs are composites of tissue types with diverse developmental origins, and they rely on distinct stem and progenitor cells to meet physiological demands for cellular production and homeostasis. How diverse stem cell activity is coordinated within organs is not well understood. Here we describe a lineage-restricted, self-renewing common skeletal progenitor (bone, cartilage, stromal progenitor; BCSP) isolated from limb bones and bone marrow tissue of fetal, neonatal, and adult mice. The BCSP clonally produces chondrocytes (cartilage-forming) and osteogenic (bone-forming) cells and at least three subsets of stromal cells that exhibit differential expression of cell surface markers, including CD105 (or endoglin), Thy1 [or CD90 (cluster of differentiation 90)], and 6C3 [ENPEP glutamyl aminopeptidase (aminopeptidase A)]. These three stromal subsets exhibit differential capacities to support hematopoietic (blood-forming) stem and progenitor cells. Although the 6C3-expressing subset demonstrates functional stem cell niche activity by maintaining primitive hematopoietic stem cell (HSC) renewal in vitro, the other stromal populations promote HSC differentiation to more committed lines of hematopoiesis, such as the B-cell lineage. Gene expression analysis and microscopic studies further reveal a microenvironment in which CD105-, Thy1-, and 6C3-expressing marrow stroma collaborate to provide cytokine signaling to HSCs and more committed hematopoietic progenitors. As a result, within the context of bone as a blood-forming organ, the BCSP plays a critical role in supporting hematopoiesis through its generation of diverse osteogenic and hematopoietic-promoting stroma, including HSC supportive 6C3(+) niche cells.KEYWORDS:endochondral ossification, lymphopoiesisPMID: 23858471 [PubMed - indexed for MEDLINE] PMCID: PMC3732968 [Available on 2014/1/30]--52)Am J Transplant. 2013 Aug;13(8):2035-43. doi: 10.1111/ajt.12328. Epub 2013 Jul 10.PI3Kδ inhibition augments the efficacy of rapamycin in suppressing proliferation of Epstein-Barr virus (EBV)+ B cell lymphomas.Furukawa S, Wei L, Krams SM, Esquivel CO, Martinez OM.

Posttransplant lymphoproliferative disorder (PTLD) continues to be a devastating and potentially life-threatening complication in organ transplant recipients. PTLD is associated with EBV infection and can result in malignant B cell lymphomas. Here we demonstrate that the PI3K/Akt/mTOR pathway is highly activated in EBV+ B cell lymphoma lines derived from patients with PTLD. Treatment with the mTORC1 inhibitor Rapamycin (RAPA) partially inhibited the proliferation of EBV+ B cell lines. Resistance to RAPA treatment correlated with high levels of Akt phosphorylation. An mTORC1/2 inhibitor and a PI3K/mTOR dual inhibitor suppressed Akt phosphorylation and showed a greater anti-proliferative effect on EBV+ B lymphoma lines compared to RAPA. EBV+ B cell lymphoma lines expressed high levels of PI3Kδ. We demonstrate that PI3Kδ is responsible for Akt activation in EBV+ B cell lymphomas, and that selective inhibition of PI3Kδ by either siRNA, or a small molecule inhibitor, augmented

the anti-proliferative effect of RAPA on EBV+ B cell lymphomas. These results suggest that PI3Kδ is a novel, potential therapeutic target for the treatment of EBV-associated PTLD and that combined blockade of PI3Kδ and mTOR provides increased efficacy in inhibiting proliferation of EBV+ B cell lymphomas. © Copyright 2013 The American Society of Transplantation and the American Society of Transplant Surgeons.KEYWORDS:Epstein−Barr Virus, PI3kinase/Akt pathway, mTOR, posttransplant lymphoproliferative disorderPMID: 23841834 [PubMed - indexed for MEDLINE]--53)J Allergy Clin Immunol. 2013 Oct;132(4):922-32.e1-16. doi: 10.1016/j.jaci.2013.05.004. Epub 2013 Jun 26.Rapid desensitization induces internalization of antigen-specific IgE on mouse mast cells.Oka T, Rios EJ, Tsai M, Kalesnikoff J, Galli SJ.

BACKGROUND:Rapid desensitization transiently prevents severe allergic reactions, allowing administration of life-saving therapies in previously sensitized patients. However, the mechanisms underlying successful rapid desensitization are not fully understood.OBJECTIVES:We sought to investigate whether the mast cell (MC) is an important target of rapid desensitization in mice sensitized to exhibit IgE-dependent passive systemic anaphylaxis in vivo and to investigate the antigen specificity and underlying mechanisms of rapid desensitization in our mouse model.METHODS:C57BL/6 mice (in vivo) or primary isolated C57BL/6 mouse peritoneal mast cells (PMCs; in vitro) were passively sensitized with antigen-specific anti-2,4-dinitrophenyl IgE, anti-ovalbumin IgE, or both. MCs were exposed over a short period of time to increasing amounts of antigen (2,4-dinitrophenyl-human serum albumin or ovalbumin) in the presence of extracellular calcium in vitro or by means of intravenous administration to sensitized mice in vivo before challenging the mice with or exposing the PMCs to optimal amounts of specific or irrelevant antigen.RESULTS:Rapidly exposing mice or PMCs to progressively increasing amounts of specific antigen inhibited the development of antigen-induced hypothermia in sensitized mice in vivo and inhibited antigen-induced PMC degranulation and prostaglandin D2 synthesis in vitro. Such MC hyporesponsiveness was induced antigen-specifically and was associated with a significant reduction in antigen-specific IgE levels on MC surfaces.CONCLUSIONS:Rapidly exposing MCs to progressively increasing amounts of antigen can both enhance the internalization of antigen-specific IgE on the MC surface and also desensitize these cells in an antigen-specific manner in vivo and in vitro.Copyright © 2013 American Academy of Allergy, Asthma & Immunology. Published by Mosby, Inc. All rights reserved.KEYWORDS:2,4-Dinitrophenyl, Anaphylaxis, BMCMC, Bone marrow–derived cultured mast cell, DNP, FITC, Fluorescein isothiocyanate, HSA, Human serum albumin, IgE, MC, MCPT-1, MFI, Mast cell, Mast cell protease 1, Mean fluorescence intensity, OVA, Ovalbumin, PGD(2), PMC, PSA, Passive systemic anaphylaxis, Peritoneal mast cell, Prostaglandin D(2), STAT6, Signal transducer and activator of transcription 6, antigen, basophil, degranulation, desensitization, mast cell, rapid desensitization, receptor internalization, rush desensitizationPMID: 23810240 [PubMed - indexed for MEDLINE] PMCID: PMC3789647 [Available on 2014/10/1]

--54)Clin Exp Immunol. 2013 Oct;174(1):27-37. doi: 10.1111/cei.12163.B6.g7 mice reconstituted with BDC2·5 non-obese diabetic (BDC2·5NOD) stem cells do not develop autoimmune diabetes.Rajasekaran N, Wang N, Hang Y, Macaubas C, Rinderknecht C, Beilhack GF, Shizuru JA, Mellins ED.

In BDC2·5 non-obese diabetic (BDC2·5NOD) mice, a spontaneous model of type 1 diabetes, CD4(+) T cells express a transgene-encoded T cell receptor (TCR) with reactivity against a pancreatic antigen, chromogranin. This leads to massive infiltration and destruction of the pancreatic islets and subsequent diabetes. When we reconstituted lethally irradiated, lymphocyte-deficient B6.g7 (I-A(g7+)) Rag(-/-) mice with BDC2·5NOD haematopoietic stem and progenitor cells (HSPC; ckit(+)Lin(-)Sca-1(hi)), the recipients exhibited hyperglycaemia and succumbed to diabetes. Surprisingly, lymphocyte-sufficient B6.g7 mice reconstituted with BDC2·5NOD HSPCs were protected from diabetes. In this study, we investigated the factors responsible for attenuation of diabetes in the B6.g7 recipients. Analysis of chimerism in the B6.g7 recipients showed that, although B cells and myeloid cells were 98% donor-derived, the CD4(+) T cell compartment contained ∼50% host-derived cells. These host-derived CD4(+) T cells were enriched for conventional regulatory T cells (Tregs ) (CD25(+) forkhead box protein 3 (FoxP3)(+)] and also for host- derived CD4(+)CD25(-)FoxP3(-) T cells that express markers of suppressive function, CD73, FR4 and CD39. Although negative selection did not eliminate donor-derived CD4(+) T cells in the B6.g7 recipients, these cells were functionally suppressed. Thus, host-derived CD4(+) T cells that emerge in mice following myeloablation exhibit a regulatory phenoytpe and probably attenuate autoimmune diabetes. These cells may provide new therapeutic strategies to suppress autoimmunity.© 2013 British Society for Immunology.KEYWORDS:BDC2·5NOD, CD73, Tregs, radio-resistant T cells, type 1 diabetesPMID: 23795893 [PubMed - indexed for MEDLINE] PMCID: PMC3784210 [Available on 2014/10/1]--55)Arthritis Rheum. 2013 Sep;65(9):2424-9. doi: 10.1002/art.38038.Interferon-α induction and detection of anti-ro, anti-la, anti-sm, and anti-rnp autoantibodies by autoantigen microarray analysis in juvenile dermatomyositis.Balboni I, Niewold TB, Morgan G, Limb C, Eloranta ML, Rönnblom L, Utz PJ, Pachman LM.

OBJECTIVE:To evaluate serum interferon-α (IFNα) activity in the context of autoantibody profiles in patients with juvenile dermatomyositis (JDM).METHODS:Sera from 36 patients with JDM were analyzed. Autoantibody profiles were determined by probing microarrays, which were fabricated with ∼80 distinct autoantigens, with serum and a Cy3-conjugated secondary antibody. Arrays were scanned and analyzed to determine antigen reactivity. Serum IFNα activity was measured using a functional reporter cell assay. Sera were assayed alone or in combination with cellular material released from necrotic U937 cells to stimulate peripheral blood mononuclear cells from healthy donors in vitro, and IFNα production in culture was measured by a dissociation-enhanced lanthanide fluoroimmunoassay (DELFIA).RESULTS:Reactivity against at least 1 of 41 autoantigens on the microarray, including Ro 52, Ro 60, La, Sm, and RNP, was observed in 75% of the serum samples from patients with JDM.

IFNα activity was detected in 7 samples by reporter cell assay. The reporter cell assay showed a significant association of reactivity against Ro, La, Sm, and proliferating cell nuclear antigen with serum IFNα activity (P = 0.005). Significance Analysis of Microarrays (SAM) identified increased reactivity against Sm, RNP, Ro 52, U1-C, and Mi-2 in these sera. Sixteen samples induced IFNα production as measured by DELFIA, and there was a significant association of reactivity against Ro, La, Sm, and RNP with the induction of IFNα by serum and necrotic cell material (P = 0.034). SAM identified increased reactivity against Ro 60 in these sera.CONCLUSION:These data support the hypothesis that nucleic acid-associated autoantibodies, including the Ro/La and Sm/RNP complexes, may stimulate the production of active IFNα in children with JDM. Copyright © 2013 by the American College of Rheumatology.PMID: 23740815 [PubMed - indexed for MEDLINE]--56)Bioinformatics. 2013 Aug 1;29(15):1922-4. doi: 10.1093/bioinformatics/btt316. Epub 2013 Jun 3.Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool.Auerbach RK, Chen B, Butte AJ.

MOTIVATION:Biological analysis has shifted from identifying genes and transcripts to mapping these genes and transcripts to biological functions. The ENCODE Project has generated hundreds of ChIP-Seq experiments spanning multiple transcription factors and cell lines for public use, but tools for a biomedical scientist to analyze these data are either non-existent or tailored to narrow biological questions. We present the ENCODE ChIP-Seq Significance Tool, a flexible web application leveraging public ENCODE data to identify enriched transcription factors in a gene or transcript list for comparative analyses.IMPLEMENTATION:The ENCODE ChIP-Seq Significance Tool is written in JavaScript on the client side and has been tested on Google Chrome, Apple Safari and Mozilla Firefox browsers. Server-side scripts are written in PHP and leverage R and a MySQL database. The tool is available at http://encodeqt.stanford.edu.CONTACT:abutte@stanford.eduSUPPLEMENTARY INFORMATION:Supplementary material is available at Bioinformatics online. PMID: 23732275 [PubMed - indexed for MEDLINE] PMCID: PMC3712221--57)PLoS One. 2013 May 22;8(5):e64503. doi: 10.1371/journal.pone.0064503. Print 2013.Induced pluripotency of human prostatic epithelial cells.Zhao H, Sun N, Young SR, Nolley R, Santos J, Wu JC, Peehl DM.

Induced pluripotent stem (iPS) cells are a valuable resource for discovery of epigenetic changes critical to cell type-specific differentiation. Although iPS cells have been generated from other terminally differentiated cells, the reprogramming of normal adult human basal prostatic epithelial (E-PZ) cells to a pluripotent state has not been reported. Here, we attempted to reprogram E-PZ cells by forced expression of Oct4, Sox2, c-Myc, and Klf4 using lentiviral vectors and obtained embryonic stem cell (ESC)-like colonies at a frequency of 0.01%. These E-PZ-iPS-like cells with normal karyotype gained expression of pluripotent genes typical of iPS cells (Tra-1-81, SSEA-3, Nanog, Sox2, and Oct4) and lost gene expression characteristic of basal prostatic epithelial cells (CK5, CK14, and p63). E-PZ-iPS-like cells demonstrated pluripotency

by differentiating into ectodermal, mesodermal, and endodermal cells in vitro, although lack of teratoma formation in vivo and incomplete demethylation of pluripotency genes suggested only partial reprogramming. Importantly, E-PZ-iPS-like cells re-expressed basal epithelial cell markers (CD44, p63, MAO-A) in response to prostate-specific medium in spheroid culture. Androgen induced expression of androgen receptor (AR), and co-culture with rat urogenital sinus further induced expression of prostate-specific antigen (PSA), a hallmark of secretory cells, suggesting that E-PZ-iPS-like cells have the capacity to differentiate into prostatic basal and secretory epithelial cells. Finally, when injected into mice, E-PZ-iPS-like cells expressed basal epithelial cell markers including CD44 and p63. When co-injected with rat urogenital mesenchyme, E-PZ-iPS-like cells expressed AR and expression of p63 and CD44 was repressed. DNA methylation profiling identified epigenetic changes in key pathways and genes involved in prostatic differentiation as E-PZ-iPS-like cells converted to differentiated AR- and PSA-expressing cells. Our results suggest that iPS-like cells derived from prostatic epithelial cells are pluripotent and capable of prostatic differentiation; therefore, provide a novel model for investigating epigenetic changes involved in prostate cell lineage specification.PMID: 23717621 [PubMed - indexed for MEDLINE] PMCID: PMC3661502--58)Diabetes Care. 2013 Jun;36(6):1789-96. doi: 10.2337/dc12-1235.Ethnic differences in the relationship between insulin sensitivity and insulin response: a systematic review and meta-analysis.Kodama K, Tojjar D, Yamada S, Toda K, Patel CJ, Butte AJ.

OBJECTIVE:Human blood glucose levels have likely evolved toward their current point of stability over hundreds of thousands of years. The robust population stability of this trait is called canalization. It has been represented by a hyperbolic function of two variables: insulin sensitivity and insulin response. Environmental changes due to global migration may have pushed some human subpopulations to different points of stability. We hypothesized that there may be ethnic differences in the optimal states in the relationship between insulin sensitivity and insulin response.RESEARCH DESIGN AND METHODS:We identified studies that measured the insulin sensitivity index (SI) and acute insulin response to glucose (AIRg) in three major ethnic groups: Africans, Caucasians, and East Asians. We identified 74 study cohorts comprising 3,813 individuals (19 African cohorts, 31 Caucasian, and 24 East Asian). We calculated the hyperbolic relationship using the mean values of SI and AIRg in the healthy cohorts with normal glucose tolerance.RESULTS:We found that Caucasian subpopulations were located around the middle point of the hyperbola, while African and East Asian subpopulations are located around unstable extreme points, where a small change in one variable is associated with a large nonlinear change in the other variable.CONCLUSIONS:Our findings suggest that the genetic background of Africans and East Asians makes them more and differentially susceptible to diabetes than Caucasians. This ethnic stratification could be implicated in the different natural courses of diabetes onset.PMID: 23704681 [PubMed - indexed for MEDLINE] PMCID: PMC3661854 [Available on 2014/6/1]--59)PLoS Pathog. 2013;9(5):e1003331. doi: 10.1371/journal.ppat.1003331. Epub 2013 May 2.

A nucleotide sugar transporter involved in glycosylation of the Toxoplasma tissue cyst wall is required for efficient persistence of bradyzoites.Caffaro CE, Koshy AA, Liu L, Zeiner GM, Hirschberg CB, Boothroyd JC.

Toxoplasma gondii is an intracellular parasite that transitions from acute infection to a chronic infective state in its intermediate host via encystation, which enables the parasite to evade immune detection and clearance. It is widely accepted that the tissue cyst perimeter is highly and specifically decorated with glycan modifications; however, the role of these modifications in the establishment and persistence of chronic infection has not been investigated. Here we identify and biochemically and biologically characterize a Toxoplasma nucleotide-sugar transporter (TgNST1) that is required for cyst wall glycosylation. Toxoplasma strains deleted for the TgNST1 gene (Δnst1) form cyst-like structures in vitro but no longer interact with lectins, suggesting that Δnst1 strains are deficient in the transport and use of sugars for the biosynthesis of cyst-wall structures. In vivo infection experiments demonstrate that the lack of TgNST1 activity does not detectably impact the acute (tachyzoite) stages of an infection or tropism of the parasite for the brain but that Δnst1 parasites are severely defective in persistence during the chronic stages of the infection. These results demonstrate for the first time the critical role of parasite glycoconjugates in the persistence of Toxoplasma tissue cysts.PMID: 23658519 [PubMed - indexed for MEDLINE] PMCID: PMC3642066--60)Analyst. 2013 Jul 7;138(13):3660-6. doi: 10.1039/c3an00259d.An AC electrokinetics facilitated biosensor cassette for rapid pathogen identification.Ouyang M, Mohan R, Lu Y, Liu T, Mach KE, Sin ML, McComb M, Joshi J, Gau V, Wong PK, Liao JC.

To develop a portable point-of-care system based on biosensors for common infectious diseases such as urinary tract infection, the sensing process needs to be implemented within an enclosed fluidic system. On chip sample preparation of clinical samples remains a significant obstacle to achieving robust sensor performance. Herein AC electrokinetics is applied in an electrochemical biosensor cassette to enhance molecular convection and hybridization efficiency through electrokinetics induced fluid motion and Joule heating induced temperature elevation. Using E. coli as an exemplary pathogen, we determined the optimal electrokinetic parameters for detecting bacterial 16S rRNA in the biosensor cassette based on the current output, signal-to-noise ratio, and limit of detection. In addition, a panel of six probe sets targeting common uropathogenic bacteria was demonstrated. The optimized parameters were also validated using patient-derived clinical urine samples. The effectiveness of electrokinetics for on chip sample preparation will facilitate the implementation of point-of-care diagnosis of urinary tract infection in the future. PMID: 23626988 [PubMed - indexed for MEDLINE]PMCID: PMC3709570 [Available on 2014/6/4]--61)J Transl Med. 2013 Apr 9;11:93. doi: 10.1186/1479-5876-11-93.Daily cytokine fluctuations, driven by leptin, are associated with fatigue severity in chronic fatigue syndrome: evidence of inflammatory pathology.Stringer EA, Baker KS, Carroll IR, Montoya JG, Chu L, Maecker HT, Younger JW.

BACKGROUND:Chronic fatigue syndrome (CFS) is a debilitating disorder characterized by persistent fatigue that is not alleviated by rest. The lack of a clearly identified underlying mechanism has hindered the development of effective treatments. Studies have demonstrated elevated levels of inflammatory factors in patients with CFS, but findings are contradictory across studies and no biomarkers have been consistently supported. Single time-point approaches potentially overlook important features of CFS, such as fluctuations in fatigue severity. We have observed that individuals with CFS demonstrate significant day-to-day variability in their fatigue severity.METHODS:Therefore, to complement previous studies, we implemented a novel longitudinal study design to investigate the role of cytokines in CFS pathophysiology. Ten women meeting the Fukuda diagnostic criteria for CFS and ten healthy age- and body mass index (BMI)-matched women underwent 25 consecutive days of blood draws and self-reporting of symptom severity. A 51-plex cytokine panel via Luminex was performed for each of the 500 serum samples collected. Our primary hypothesis was that daily fatigue severity would be significantly correlated with the inflammatory adipokine leptin, in the women with CFS and not in the healthy control women. As a post-hoc analysis, a machine learning algorithm using all 51 cytokines was implemented to determine whether immune factors could distinguish high from low fatigue days.RESULTS:Self-reported fatigue severity was significantly correlated with leptin levels in six of the participants with CFS and one healthy control, supporting our primary hypothesis. The machine learning algorithm distinguished high from low fatigue days in the CFS group with 78.3% accuracy.CONCLUSIONS:Our results support the role of cytokines in the pathophysiology of CFS.PMID: 23570606 [PubMed - indexed for MEDLINE] PMCID: PMC3637529

--62)Aliment Pharmacol Ther. 2013 May;37(10):921-36. doi: 10.1111/apt.12300. Epub 2013 Apr 5.Systematic review: Asian patients with chronic hepatitis C infection.Nguyen LH, Nguyen MH.

BACKGROUND:Chronic hepatitis C (CHC) infection is a risk factor for both the development of end-stage liver disease and hepatocellular carcinoma (HCC). Globally, approximately 170 million people are chronically infected with the hepatitis C virus (HCV), and the majority of these individuals come from the western Pacific and Southeast Asia regions (94.6 million persons combined). CHC is an understudied and underappreciated health problem in many Asian countries and in the US, where Asians represent one of the fastest growing groups of new Americans.AIM:To perform a systematic review of the current literature on the epidemiology, diagnosis and screening, clinical characteristics and response to anti-viral therapy of Asians with CHC.METHODS:Using a PubMed search of 'hepatitis C' and 'Asia,' 341 original manuscripts published in peer-reviewed journals were identified, and 99 were selected based on their relevance.RESULTS:Many Asian CHC patients do not have easily identifiable risk factors and may be underdiagnosed. Rates of HCV infection in Asians on community screening in the US are unexpectedly high, and there is a high prevalence of HCV genotype 6 in Southeast Asia and Southern China. HCV-infected Asians tend to present at older age and may have higher risk of

HCC; however, they respond better to anti-viral therapy than non-Asians across all HCV genotypes.CONCLUSIONS:Given the high HCV endemicity in Asia, lack of identifiable risk factors and favourable treatment response rates in Asians, we advocate the screening for HCV infection of all Asians who come from areas where HCV prevalence is ≥2%.© 2013 Blackwell Publishing Ltd.PMID: 23557103 [PubMed - indexed for MEDLINE]--63)Adv Physiol Educ. 2013 Mar;37(1):70-9. doi: 10.1152/advan.00138.2012.A writing-intensive course improves biology undergraduates' perception and confidence of their abilities to read scientific literature and communicate science.Brownell SE, Price JV, Steinman L.

Most scientists agree that comprehension of primary scientific papers and communication of scientific concepts are two of the most important skills that we can teach, but few undergraduate biology courses make these explicit course goals. We designed an undergraduate neuroimmunology course that uses a writing-intensive format. Using a mixture of primary literature, writing assignments directed toward a layperson and scientist audience, and in-class discussions, we aimed to improve the ability of students to 1) comprehend primary scientific papers, 2) communicate science to a scientific audience, and 3) communicate science to a layperson audience. We offered the course for three consecutive years and evaluated its impact on student perception and confidence using a combination of pre- and postcourse survey questions and coded open-ended responses. Students showed gains in both the perception of their understanding of primary scientific papers and of their abilities to communicate science to scientific and layperson audiences. These results indicate that this unique format can teach both communication skills and basic science to undergraduate biology students. We urge others to adopt a similar format for undergraduate biology courses to teach process skills in addition to content, thus broadening and strengthening the impact of undergraduate courses.PMID: 23471252 [PubMed - indexed for MEDLINE]--64)J Pain. 2013 May;14(5):516-24. doi: 10.1016/j.jpain.2013.01.004. Epub 2013 Feb 28.Changes resembling complex regional pain syndrome following surgery and immobilization.Pepper A, Li W, Kingery WS, Angst MS, Curtin CM, Clark JD.

The study of complex regional pain syndrome (CRPS) in humans is complicated by inhomogeneities in available study cohorts. We hoped to characterize early CRPS-like features in patients undergoing hand surgery. Forty-three patients were recruited from a hand surgery clinic that had elective surgeries followed by cast immobilization. On the day of cast removal, patients were assessed for vasomotor, sudomotor, and trophic changes, and edema and pain sensitization using quantitative sensory testing. Pain intensity was assessed at the time of cast removal and after 1 additional month, as was the nature of the pain using the Leeds Assessment of Neuropathic Symptoms and Signs (LANSS). Skin biopsies were harvested for the analysis of expression of inflammatory mediators. We identified vascular and trophic changes in the surgical hands of most patients. Increased sensitivity to punctate, pressure, and cold stimuli were observed commonly as well. Moreover, levels of IL-6, TNF-alpha, and the mast cell marker

tryptase were elevated in the skin of hands ipsilateral to surgery. Moderate-to-severe pain persisted in the surgical hands for up to 1 month after cast removal. Exploratory analyses suggested interrelationships between the physical, quantitative sensory testing, and gene expression changes and pain-related outcomes.PERSPECTIVE:This study has identified CPRS-like features in the limbs of patients undergoing surgery followed by immobilization. Further studies using this population may be useful in refining our understanding of CRPS mechanisms and treatments for this condition.Published by Elsevier Inc.PMID: 23453564 [PubMed - indexed for MEDLINE] PMCID: PMC3644418 [Available on 2014/5/1]--65)Pac Symp Biocomput. 2013:224-35.Systematic identification of risk factors for Alzheimer's disease through shared genetic architecture and electronic medical records.Li L, Ruau D, Chen R, Weber S, Butte AJ.

Alzheimer's disease (AD) is one of the leading causes of death for older people in US with rapidly increasing incidence. AD irreversibly and progressively damages the brain, but there are treatments in clinical trials to potentially slow the development of AD. We hypothesize that the presence of clinical traits, sharing common genetic variants with AD, could be used as a non-invasive means to predict AD or trigger for administration of preventative therapeutics. We developed a method to compare the genetic architecture between AD and traits from prior GWAS studies. Six clinical traits were significantly associated with AD, capturing 5 known risk factors and 1 novel association: erythrocyte sedimentation rate (ESR). The association of ESR with AD was then validated using Electronic Medical Records (EMR) collected from Stanford Hospital and Clinics. We found that female patients and with abnormally elevated ESR were significantly associated with higher risk of AD diagnosis (OR: 1.85 [1.32-2.61], p=0.003), within 1 year prior to AD diagnosis (OR: 2.31 [1.06-5.01], p=0.032), and within 1 year after AD diagnosis (OR: 3.49 [1.93-6.31], p<0.0001). Additionally, significantly higher ESR values persist for all time courses analyzed. Our results suggest that ESR should be tested in a specific longitudinal study for association with AD diagnosis, and if positive, could be used as a prognostic marker.PMID: 23424127 [PubMed - indexed for MEDLINE]--66)Am J Transplant. 2013 Apr;13(4):851-60. doi: 10.1111/ajt.12140. Epub 2013 Feb 7.Dynamic challenges inhibiting optimal adoption of kidney paired donation: findings of a consensus conference.Melcher ML, Blosser CD, Baxter-Lowe LA, Delmonico FL, Gentry SE, Leishman R, Knoll GA, Leffell MS, Leichtman AB, Mast DA, Nickerson PW, Reed EF, Rees MA, Rodrigue JR, Segev DL, Serur D, Tullius SG, Zavala EY, Feng S.

While kidney paired donation (KPD) enables the utilization of living donor kidneys from healthy and willing donors incompatible with their intended recipients, the strategy poses complex challenges that have limited its adoption in United States and Canada. A consensus conference was convened March 29-30, 2012 to address the dynamic challenges and complexities of KPD that inhibit optimal implementation. Stakeholders considered donor evaluation and care, histocompatibility testing, allocation algorithms, financing, geographic challenges and

implementation strategies with the goal to safely maximize KPD at every transplant center. Best practices, knowledge gaps and research goals were identified and summarized in this document.

No claim to original US government works Journal compilation © 2013 The American Society of Transplantation and the American Society of Transplant Surgeons.Comment in Response to "dynamic challenges inhibiting optimal adoption of kidney paired donation: findings of a consensus conference" by Melcher et al. [Am J Transplant. 2013]PMID: 23398969 [PubMed - indexed for MEDLINE]--67)Am J Transplant. 2013 Apr;13(4):883-90. doi: 10.1111/ajt.12137. Epub 2013 Feb 7.Syk-induced phosphatidylinositol-3-kinase activation in Epstein-Barr virus posttransplant lymphoproliferative disorder.Hatton O, Lambert SL, Phillips LK, Vaysberg M, Natkunam Y, Esquivel CO, Krams SM, Martinez OM.

Posttransplant lymphoproliferative disorder (PTLD)-associated Epstein-Barr virus (EBV)+ B cell lymphomas are serious complications of solid organ and bone marrow transplantation. The EBV protein LMP2a, a B cell receptor (BCR) mimic, provides survival signals to virally infected cells through Syk tyrosine kinase. Therefore, we explored whether Syk inhibition is a viable therapeutic strategy for EBV-associated PTLD. We have shown that R406, the active metabolite of the Syk inhibitor fostamatinib, induces apoptosis and cell cycle arrest while decreasing downstream phosphatidylinositol-3'-kinase (PI3K)/Akt signaling in EBV+ B cell lymphoma PTLD lines in vitro. However, Syk inhibition did not inhibit or delay the in vivo growth of solid tumors established from EBV-infected B cell lines. Instead, we observed tumor growth in adjacent inguinal lymph nodes exclusively in fostamatinib-treated animals. In contrast, direct inhibition of PI3K/Akt significantly reduced tumor burden in a xenogeneic mouse model of PTLD without evidence of tumor growth in adjacent inguinal lymph nodes. Taken together, our data indicate that Syk activates PI3K/Akt signaling which is required for survival of EBV+ B cell lymphomas. PI3K/Akt signaling may be a promising therapeutic target for PTLD, and other EBV-associated malignancies.© Copyright 2013 The American Society of Transplantation and the American Society of Transplant Surgeons.PMID: 23398911 [PubMed - indexed for MEDLINE]--68)Trends Immunol. 2013 Apr;34(4):151-4. doi: 10.1016/j.it.2012.11.004. Epub 2012 Dec 22.The natural and the inducible: interleukin (IL)-17-producing γδ T cells.Chien YH, Zeng X, Prinz I.

γδ T cells are the major initial interleukin (IL)-17 producers in acute infections. Recent studies have indicated that some γδ T cells have IL-17-producing capabilities without explicit induction of an immune response. They are preferentially localized in barrier tissues and are likely to originate from fetal γδ thymocytes. In addition, γδ T cells present in the secondary lymphoid organs will mature and differentiate to produce IL-17 after antigen encounter in an immune response. Based on these studies, we propose that there are two different sets of IL-17-producing γδ T cells (Tγδ17) referred to as the 'natural' and the 'inducible' Tγδ17 cells. This review focuses on recent publications leading to the delineation of these two types of cells and their implied roles in host immune defense.

Copyright © 2012 Elsevier Ltd. All rights reserved.PMID: 23266231 [PubMed - indexed for MEDLINE] PMCID: PMC3622789 [Available on 2014/4/1]--69)Neurosurgery. 2013 Apr;72(4):573-89; discussion 588-9. doi: 10.1227/NEU.0b013e318283c9c2.Cavernous malformation of brainstem, thalamus, and basal ganglia: a series of 176 patients.Pandey P, Westbroek EM, Gooderham PA, Steinberg GK.

BACKGROUND:Cavernous malformations (CMs) in deep locations account for 9% to 35% of brain malformations and are surgically challenging.OBJECTIVE:To study the clinical features and outcomes following surgery for deep CMs and the complication of hypertrophic olivary degeneration (HOD).METHODS:Clinical records, radiological findings, operative details, and complications of 176 patients with deep CMs were reviewed retrospectively.RESULTS:Of 176 patients with 179 CMs, 136 CMs were in the brainstem, 27 in the basal ganglia, and 16 in the thalamus. Cranial nerve deficits (51.1%), hemiparesis (40.9%), numbness (34.7%), and cerebellar symptoms (38.6%) presented most commonly. Hemorrhage presented in 172 patients (70 single, 102 multiple). The annual retrospective hemorrhage rate was 5.1% (assuming CMs are congenital with uniform hemorrhage risk throughout life); the rebleed rate was 31.5%/patient per year. Surgical approach depended on the proximity of the CM to the pial or ependymal surface. Postoperatively, 121 patients (68.8%) had no new neurological deficits. Follow-up occurred in 170 patients. Delayed postoperative HOD developed in 9/134 (6.7%) patients with brainstem CMs. HOD occurred predominantly following surgery for pontine CMs (9/10 patients). Three patients with HOD had palatal myoclonus, nystagmus, and oscillopsia, whereas 1 patient each had limb tremor and hemiballismus. At follow-up, 105 patients (61.8%) improved, 44 (25.9%) were unchanged, and 19 (11.2%) worsened neurologically. Good preoperative modified Rankin Score (98.2% vs 54.5%, P = .001) and single hemorrhage (89% vs 77.3%, P < .05) were predictive of good long-term outcome.CONCLUSION:Symptomatic deep CMs can be resected with acceptable morbidity and outcomes. Good preoperative modified Rankin Score and single hemorrhage are predictors of good long-term outcome.PMID: 23262564 [PubMed - indexed for MEDLINE]--70)Transfusion. 2013 Oct;53(10):2152-7. doi: 10.1111/trf.12027. Epub 2012 Dec 12.Anti-Ge3 causes late-onset hemolytic disease of the newborn: the fourth case in three Hispanic families.Pate LL, Myers JC, Palma JP, Viele M, Galel SA, Ferrer Z, Gonzalez CL, Benitz WE, Garratty G, Fontaine MJ.

BACKGROUND:The Gerbich (Ge) blood group system consists of 11 antigens carried on red blood cell (RBC) membrane glycophorins C and D; of these, Ge:3 antigen is of high prevalence, and the anti-Ge3 is found to be clinically significant.CASE REPORT:A 34-week neonate born to a Hispanic mother with anti-Ge3 developed late-onset hemolysis with hyperbilirubinemia and was successfully treated with transfusions from her

mother. Relevant clinical findings and laboratory results for this case are summarized and compared to three other previously reported cases; all babies were born from a mother of Hispanic ethnicity.CONCLUSION:Hemolytic disease of the fetus and new born associated with anti-Ge3 is rare but should be considered when working up a broadly reactive RBC antibody screen in women of Hispanic ethnicity. Early identification of pregnant women with anti-Ge3 is recommended for prenatal transfusion planning and close monitoring of the newborn infant for evidence of late-onset anemia. © 2012 American Association of Blood Banks.Comment in Glycophorin C ligation: another biochemical pathway in red blood cell senescence? [Transfusion. 2013]PMID: 23241141 [PubMed - indexed for MEDLINE]--71)Neurosurgery. 2013 Jun;72(2 Suppl Operative):onsE245-50; discussion onsE250-1. doi: 10.1227/NEU.0b013e31827fc9be.Delayed retraction of the pipeline embolization device and corking failure: pitfalls of pipeline embolization device placement in the setting of a ruptured aneurysm.McTaggart RA, Santarelli JG, Marcellus ML, Steinberg GK, Dodd RL, Do HM, Marks MP.

BACKGROUND AND IMPORTANCE:The safety of flow-diverting stents for the treatment of ruptured intracranial aneurysms is unknown.CLINICAL PRESENTATION:A 35-year-old woman with a ruptured dissecting aneurysm of the intradural right vertebral artery and incorporating the right posterior inferior cerebellar artery was treated with a Pipeline Embolization Device (PED). Five days after reconstruction of the diseased right vertebral segment, she was treated for vasospasm, and retraction of the PED was observed, leaving her dissecting aneurysm unprotected. A second PED was placed with coverage of the aneurysm, but vasospasm complicated optimal positioning of the device.CONCLUSION:In addition to the potential risks of dual antiplatelet therapy in these patients, this case illustrates 2 pitfalls of flow-diverting devices in vessels in vasospasm: delayed retraction of the device and difficulty positioning the device for deployment in the setting of vasospasm. PMID: 23190640 [PubMed - indexed for MEDLINE]--72)Anal Chem. 2012 Nov 6;84(21):9572-8. doi: 10.1021/ac302436y. Epub 2012 Oct 23.High-performance binary protein interaction screening in a microfluidic format.Meier M, Sit R, Pan W, Quake SR.

The standard procedure to increase microfluidic chip performance is to grow the number of parallel test systems on the chip. This process is accompanied by miniaturizing biochemical workflows and micromechanical elements, which is often a major challenge for both engineering fields. In this work, we show that it is possible to substantially increase the runtime performance of a microfluidic affinity assay for protein interactions by simultaneously engineering fluid logics and assay chemistry. For this, synergistic effects between the micro- and chemical architecture of the chip are exploited. The presented strategy of reducing the runtime rather than size and volume of the mechanical elements and biological reagent compartments will, in general, be of importance for future analytical test systems on microfluidic chips to overcome performance barriers.

PMID: 23051662 [PubMed - indexed for MEDLINE] PMCID: PMC3533494--73)Cell Transplant. 2013;22(5):881-92.Imaging neural stem cell graft-induced structural repair in stroke.Daadi MM, Hu S, Klausner J, Li Z, Sofilos M, Sun G, Wu JC, Steinberg GK.

Stem cell therapy ameliorates motor deficits in experimental stroke model. Multimodal molecular imaging enables real-time longitudinal monitoring of infarct location, size, and transplant survival. In the present study, we used magnetic resonance imaging (MRI) and positron emission tomography (PET) to track the infarct evolution,tissue repair, and the fate of grafted cells. We genetically engineered embryonic stem cell-derived neural stem cells (NSCs) with a triple fusion reporter gene to express monomeric red fluorescence protein and herpes simplex virus-truncated thymidine kinase for multimodal molecular imaging and SPIO labeled for MRI. The infarct size as well as fate and function of grafted cells were tracked in real time for 3 months using MRI and PET. We report that grafted NSCs reduced the infarct size in animals with less than 0.1 cm(3) initial infarct in a dose-dependent manner, while larger stroke was not amenable to such beneficial effects. PET imaging revealed increased metabolic activity in grafted animals and visualized functioning grafted cells in vivo. Immunohistopathological analysis demonstrated that, after a 3-month survival period, grafted NSCs dispersed in the stroke-lesioned parenchyma and differentiated into neurons, astrocytes, and oligodendrocytes. Longitudinal multimodal imaging provides insights into time course dose-dependent interactions between NSC grafts and structural changes in infarcted tissue.PMID: 23044338 [PubMed - indexed for MEDLINE]--74)Pac Symp Biocomput. 2012:213-24.Comparisons of distance methods for combining covariates and abundances in microbiome studies.Fukuyama J, McMurdie PJ, Dethlefsen L, Relman DA, Holmes S.

This article compares different methods for combining abundance data, phylogenetic trees and clinical covariates in a nonparametric setting. In particular we study the output from the principal coordinates analysis on UNIFRAC and WEIGHTED UNIFRAC distances and the output from a double principal coordinate analyses DPCOA using distances computed on the phylogenetic tree. We also present power comparisons for some of the standard tests of phylogenetic signal between different types of samples. These methods are compared both on simulated and real data sets. Our study shows that DPCoA is less robust to outliers, and more robust to small noisy fluctuations around zero.PMID: 22174277 [PubMed - indexed for MEDLINE]