research support information network (resin) · 2019/12/03 · irb orra iacuc oris hipaa tri...

Research Support Information

Network (RESIN)

December 3, 2019

Agenda

Updates & Timely Information from Research Support

Office of the VCR COIRSC Office of General CounselIRB ORRAIACUC ORISHIPAA TRI

Library Core Facilities Biomedical Informatics

212/3/2019

New PubMed & JANESusan Steelman, MLIS, AHIP – Head of Education & Research – UAMS Library

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New PubMed - HEADS UP

– Things will be fluid for a while

• New features being added

• Current features are being tweaked

• Expect unusual

– UAMS Library Full Text Access

• Use Legacy Version


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• Journal/Author Name Estimator [JANE]

http://jane.biosemantics.org/

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http://jane.biosemantics.org/


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WANT TO LEARN MORE…Library’s Education & Research Services Offers

– Presentations

– Classes

– House Calls

501-686-6734

[email protected]

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mailto:[email protected]

Why does UAMS have an IP policy?

• Exploitation of intellectual property (IP) for public benefit

• Assist faculty, students, and staff with IP matters

• Provide an environment that encourages disclosure and development of IP

• Obtain proper benefits for inventors and authors

• Apply royalties from IP to future research

Updates to UA Board of Trustees Patent & Copyright Policy (210.1) Nathan P. Chaney, JD, Assoc.

General Counsel, Office of General Counsel, Research Contracts Div.

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Who does the policy apply to?

• All persons employed, compensated, or appointed by the University

• Faculty, staff, and students

– High school students and undergrads excluded unless paid by or through University in connection with sponsored research

• Anyone using facilities owned, operated, or controlled by the University

– Includes non-employees absent an agreement to the contrary



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What IP is covered?

• University research

– Any R&D related to duties, responsibilities, or field of work

– Facilities owned, operated, or controlled by the University are used

• excludes nonessential facilities like meeting rooms and nonessential equipment like phones

• IP financed by the University



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What are some examples of IP?• Invention – any material capable of legal protection arising out of University research

– discovery, process, know-how, trade secret, design, model, computer software (if patentable), strain, cultivar, or culture of an organism

– Any portion, modification, translation, or extension of these items• Work — Original work of authorship arising of out University research

– books, software, computer programs, videos, multimedia products, etc.• Tangible Research Property — tangible items produced in University research

– biological materials, engineering drawings, computer databases, prototype devices, and equipment, etc.

• Research Data — means all information, both physical and electronic, collected and/or generated in the course of University Research– data, analytical programs, procedures, and records necessary for the reconstruction and

evaluation of the results of research– data contained in laboratory notebooks– data collected using instrumentation or systems and stored in an electronic format– case report forms and source documentation for human participant research studies



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What does the policy mean?

• All inventions and works of authorship must be disclosed to the Patent & Copyright Committee

• IP is automatically assigned to the University– Exception for sponsored research where rights are

negotiated by separate agreement– Exceptions for approved independent work or consulting

activities– University can waive rights and reassign IP rights to

inventor/author



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What about consulting agreements?

• External consulting work can’t conflict with contractual, teaching, or research obligations to the University

• Employees should provide notice to the external party about their obligations to the University

• Employee must:– obtain campus authorization prior to starting the consulting or

business activity;– abide by all applicable Conflict of Interest and Conflict of

Commitment policies; and– develop or create IP without the use of (a) facilities owned,

operated, or controlled by the University, (b) a pre-existing Invention owned by the University, or (c) University Research.



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How are inventions/works disclosed?

• Online form available at https://apps.uams.edu/CopyrightPatents/Submissions.aspx

• Err on the side of disclosure



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https://apps.uams.edu/CopyrightPatents/Submissions.aspx

When should an invention/work be disclosed?

• Promptly after creation

• Legal imperatives/benefits for prompt filing



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Other Topics in IP Policy

• Publication

• Sponsored research

• Inventor’s share in royalties

• Procedures for patent and copyright committees



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Link to IP Policy:

• https://www.uasys.edu/wp-content/uploads/sites/16/2019/08/BP-210.1-Patent-and-Copyright-Policy-8.21.19.pdf



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https://www.uasys.edu/wp-content/uploads/sites/16/2019/08/BP-210.1-Patent-and-Copyright-Policy-8.21.19.pdf

Being Open: Reproducibly sharing data and methods.

Michael S. Robeson II, Ph.D., Assistant Professor, Dept. of Biomedical Informatics.

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“What we observe is not nature itself, but nature exposed to our method of questioning.”

- Werner Heisenberg (1962)

Being Open: Reproducibly sharing data and methods Michael S. Robeson II, Ph.D., Assistant Professor, Dept. of Biomedical Informatics

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Reproducibility vs. Replicability

What do these terms mean?


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Reproducibility: as the ability to recompute data analytic results given an observed dataset and knowledge of the data analysis pipeline.

Replicability: is the chance that an independent experiment targeting the same scientific question will produce a consistent result.

• Leek & Peng (2015) “Opinion: Reproducible Research Can Still Be Wrong: Adopting a Prevention Approach.” PNAS 112 (6): 1645–46.

• Schloss (2018) “Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research”, mBio 9:e00525-18


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Reproducibility vs. Replicability


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Poussin et al. (2018) “Interrogating the Microbiome: Experimental and Computational Considerations in Support of Study Reproducibility.” Drug Discovery Today 23 (9): 1644–57.


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Prinz et al. (2011). “Believe It or Not: How Much Can We Rely on Published Data on Potential Drug Targets?” Nature Reviews. Drug Discovery 10 (August): 712.


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“Reproducing, adapting or even repeating a bioinformatics workflow in any environment requires substantial technical knowledge of the workflow execution environment, resolving analysis assumptions and rigorous compliance with reproducibility requirements.”

-Kanwal et al. 2017

• Garijo et al. (2013) “Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome.” PloS One 8 (11): e80278.

• Kanwal et al. 2017. “Investigating Reproducibility and Tracking Provenance - A Genomic Workflow Case Study.” BMC Bioinformatics 18 (1): 337.

Being Open: Reproducibly sharing data and methods Michael S. Robeson II,

Ph.D., Assistant Professor, Dept. of Biomedical Informatics

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Why is there a lack of effort to make research reproducible or replicable?

1. Takes time.2. Work required to support additional users.

• e.g. formatting metadata for sharing3. May require additional skills to make the data available

• e.g. Github, GenBank SRA, etc…4. Not considered for promotion / tenure.

• though this is changing e.g. Pre-Print servers, BioRxiv, • Data storage services: DataDryad, figshare, …

5. If others don’t do it why should I?6. many other reasons …


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“Available upon Request: Not Good Enough for Microbiome Data!”Langille et al. (2018) Microbiome 6 (1): 8.

Being Open: Reproducibly sharing data and methods. Michael S. Robeson II, Ph.D., Assistant Professor, Dept. of Biomedical Informatics.

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Collins et al. (2014) “Policy: NIH Plans to Enhance Reproducibility.” Nature 505 (7485): 612–13.


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A variety of services being made available to help make your data more easily shareable and accessible. Make use of them!

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https://www.springernature.com/gp/authors/research-data/research-data-support

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https://www.springernature.com/gp/authors/research-data/research-data-support


It may be a lot of work. But you’ll never have to worry about where you stored your data & meta data. Just send the BioProject Accession to anyone that requests the data.

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https://www.protocols.io/groups/earth-microbiome-project


https://www.protocols.io/

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Editorial Policy Checklisthttps ://www.nature.com/nature/for-authors /initial-


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“I particularly liked the focus on changes in community structure through time with a strong focus on immigration, rather than relying on single snapshots -- a limitation of much empirical community structure work in the past. I was also very impressed with the transparency of the analysis (all code is well organized on github and even comes with a tutorial to understand the analytical approach!), which sets a standard that new submissions should strive to match.”

- Referee #1


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Can I still be open and reproducible, even if I can’t share my data? Yes!

Whitaker (2017) “Publishing a reproducible paper” https://figshare.com/articles/Publishing_a_reproducible_paper/5440621


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https://www.maqc2020.org/

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https://www.maqc2020.org/

Gut microbiome changes among delirious and non-delirious patientsSangam Kandel1,2, Thidathip Wongsurawat2, Piroon Jenjaroenpun2, Intawat Nookaew2, Michael S. Robeson II2, David Ussery2, Anne Sofie Andreasen 2,3

1Department of Bioinformatics, University of Arkansas at Little Rock, Little Rock, AR 722052Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205

3Department of Anesthesiology and Intensive Care, University Hospital Herlev, Copenhagen, Denmark

BACKGROUND

• Temporary state of mental confusion characterized by a lack of focus,

reduced awareness of environment, hallucinations.

• It a clinical syndrome, rather than one specific disease.

• Previous microbiome studies have shown dynamic changes in gut

microbiota of ICU patients in the acute phase of critical illness [1].

• But there are no any reported studies about the changes in the

composition of the gut microbiota during the development of delirium

in critical illness.

• An understanding of the association of changes in gut microbiota and

critical illness and related conditions could eventually lead to new

prevention and treatments strategies.

Methods

• Rectal swab samples collected from the patients admitted at ICU

• Healthy nurses working in ICU as positive controls.

• 16S rDNA sequencing performed in Illumina Hi-Seq platform.

• Taxonomic classification and microbial diversity analyzed using

QIIME2 [2].

Conclusion

References

Acknowledgements

1. Ojima, Masahiro, et al. "Metagenomic analysis reveals dynamic changes of whole gut microbiota in the acute phase of intensive care unit patients." Digestive diseases and

sciences 61.6 (2016): 1628-1634.

2. Bolyen, Evan, et al. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. No. e27295v1. P eerJ Preprints

• There is significant difference in microbial composition and diversity between control and

diseased groups.

• Microbial diversity is less in D2 as compared to D1.

• Patients that develop delirium in ICU have different gut microbiome compared to the patients

admitted at ICU (D2 and D1).

• There is no microbiome change in the ICU patients that developed delirium and the ICU patients

that did not develop delirium (D2 and ND2).

Thanks to Dr. Michael S Robeson, Dr. Thidathip Wongsurawat, all collaborators for their valuable suggestions. This research was

supported by NIH/NIGMS grant 1P20GM121293 and from the Helen Adams & Arkansas Research Alliance Endowment in the Department

of Biomedical Informatics, College of Medicine at UAMS.

OTUs

Data filtering

Denoising

Demultiplexing

Raw sequences

Illumina sequencing

DNA extraction

Sample Collection

Taxonomy, Diversity

WORKFLOW

Taxonomic classification

Alpha diversity

Beta diversity

PCoA plot based on Weighted UniFrac distance

PCoA plot based on Weighted UniFrac distancePCoA plots based on Bray Curtis

0

500

1000

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4500

5000

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9000

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10000

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11500

12000

12500

Firmicutes Bacteroidetes Proteobacteria Actinobacteria Fusobacteria Synergistetes Tenericutes

Average counts at Phylum level in D1 and D2

D1 D2

Relative frequency in D1-D2

p=0.014 p=0.002 p=0.002 p=0.438 p=0.636p=0.205 p=0.268

* * ** * * ******

Hypothesis

There is a difference in composition in the gut microbiota in patients

that develop delirium during critical illness as compared to those that do

not.

Objective

To investigate if there is change in the gut microbiome among delirious

and non-delirious patients admitted in hospital ICU.

*

**

p<0.0020

p>0.007

D1: Patients at time of admission that later developed delirium (time point 1)

D2: Patients that developed delirium (time point 2)

ND1: Patients at time of admission that later did not develop delirium (time point 1)

ND2: Patients that did not develop delirium (time point 2)

Time point 1 Time point 2

No. of samples Group No. of samples Group

Controls 10 C 10 C

Delirium 21 D1 21 D2

Non-Delirium 19 ND1 19 ND2

Total 100

Samples collected at two time points

Bacterial diversity will have a noticeable relationship with hatching success.

Certain bacterial taxa will have higher appearance rates in clutches with lower success rates.

Hypothesis

Introduction16S rRNA Sequence data was obtained from the paper

“Bacterial density rather than

diversity correlates with

hatching success across

different avian species.”

The authors monitored 600 nest boxes as well as several wild nests. Eggs were swabbed at the start of incubation and after the clutch was completed.

The final dataset included 157 clutches from 17 bird species.

Methods

The ratios of common bacterial taxa are similar between

species regardless of their hatching success rates. Imported into

QIIME2

Closed Reference

OTU picking

(Greengenes)

Filtered

mitochondria,

archaea, and low

frequency OTUs

Align to tree

Core Metrics

Taxa Barplot

Deblur

Trim Length 100

Sonya Utecht, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR

How Bacterial Diversity Impacts the Hatching Success of Eur opean Birds

Athene noctua

Little Owl

100%

Turdus merula

Common Blackbird

89.2%Discussion

Research with negative results or small effect sizes can still contribute to the field.

Reproducibility should always be a major focus in scientific papers.

Hirundo rustica

Barn Swallow

95.0%

Results

Beta Diversity

significance

Unweighted Unifrac

Hatching Success

Unweighted Unifrac distances of nest communities with darker colors representing higher hatching success rates.

Box and whisker graph showing how 100% hatching rate nests are nearly as similar to each other as they are to every other nest.

OTU community samples by host bird species

A total of 609 sequences were obtained.


Fundamentals of the Human Microbiome

BMIG 6202 - Spring 2020

Course Description:

This graduate course will provide students with

foundational knowledge and practical analytical

skills required for analyzing microbiome data.

The course will explore the microbial inhabitants

of the human body, with an emphasis on how the

microbiome affects human health and disease

progression.

We will make use of current leading-edge

microbial community analysis tools to investiga te

the interactions microbiota have with each other

and their human hosts.

‣ Review foundational research.

‣ Host-microbiome interactions.

‣ Learn how to plan a microbiome study.

‣ Learn how to analyze microbiome data.

Location: Education Bldg. II, Room G110A

Times: Tu 9:00 - 09:50 AM (Lecture)

Thu 9:00 - 10:50 AM (Computer Lab)

Prerequisites: BMIG 5002, 5003, 5101 or

commensurate experience.

Contact: [email protected]

[email protected]

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KL2 Scholar Program- RFA Open SoonMiesha Hall, MHA, CHAA, KL2 Program Manager, TRI

Program Basics

– Mentored Career Research and Development Program offered through the Translational Research Institute (TRI)

– Goal: Increase the number and quality of independently funded clinical and translational research investigators at UAMS.

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Program Basics (cont.)

– Targets early career faculty committed to developing a career in translational research.

– Provides 2 years of salary support (75%) plus $25K/year in research funding

– Includes mentored research and career/research development training

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Eligibility

– Early Career Faculty (Instructors or Assistant Professors)

– Doctoral level degree (MD, PhD, PharmD, DrPH, etc.)

– Must be a citizen of the U.S. or non-citizen national

– May not have been PI of an RO1, the leader of a PO1 component, or recipient of a K23, K08, K01, or equivalent grant award.

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RFA Release- January 6

Info Session- Jan 16/17 (TBD- stay tuned!)

Department Pre-Approvals- March 6

Applications Due- March 20

Awardees Announced- May 1

Scholar Start Date- August 1

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Pam ChristieSr. Project Manager, UAMS Translational Research Institute

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Research & InnovationShuk-Mei Ho, Ph.D., Vice Chancellor of Research & Innovation

• New Employees in Research– Office of Research & Innovation

• Ashley Gregory, Business Manager, (501) 686-5322

• [email protected]

– Office of Sponsored Programs Administrative Network (OSPAN)• Ty Stephens, CPA, MBA, Director

(501) 526-7452

• [email protected]

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Showcase for Medical Discoveries - CancerLinda Williams, M.S., Research Liaison, Office of Research

• Bone Research Showcase

– Reception

– Wednesday, January 22, 2020

– 4:30 – 6:00 p.m.

– 10th floor Winthrop P. Rockefeller Cancer Institute

– Posters (contact me if interested) [email protected]

– New Technology (Sign-in tablets)

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RESIN Meeting

• Next RESIN

– January 7, 2020 @ 12:00 p.m.

– Location - Walton Auditorium, Winthrop P. Rockefeller Cancer Institute, 10th floor

– All RESIN presentations archived on the UAMS Research website

• http://www.uams.edu/research/RESIN_Achive.asp

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http://www.uams.edu/research/RESIN_Achive.asp

research support information network (resin) · 2019/12/03 · irb orra iacuc oris hipaa tri...

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