Digital Commons Network^™

Efficacy And Safety Of Eluxadoline In Patients With Irritable Bowel Syndrome With Diarrhea Who Report Inadequate Symptom Control With Loperamide: Relief Phase 4 Study, Darren M. Brenner, Gregory S. Sayuk, Catherine R. Gutman, Esther Jo, Steven J. R. Elmes, Louis W. C. Liu, Brooks D. Cash

Open Access Publications

No abstract provided.

Determining Population Stratification And Subgroup Effects In Association Studies Of Rare Genetic Variants For Nicotine Dependence, Ai-Ru Hsieh, Li-Shiun Chen, Ying-Ju Li, Cathy S. J. Fann

Open Access Publications

No abstract provided.

Challenges To Curing Primary Brain Tumours, Kenneth Aldape, David H. Gutmann, Et Al.

Open Access Publications

No abstract provided.

Clinical Performance Of A Novel Fully Synthetic Dura Substitute, Umang Khandpur, Wilson Ray, Matthew Macewan

Open Access Publications

No abstract provided.

A Strategy For Building And Using A Human Reference Pangenome, Bastien Llamas, Allison Regier, Et Al

Open Access Publications

In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and standards for a usable human pangenome as well as to build relevant tools for genome graph infrastructures. During the meeting, the group held several intense and productive discussions covering a diverse set of topics, including advantages of graph genomes over a linear reference representation, design of new methods that can leverage graph-based data structures, and novel visualization and annotation approaches for pangenomes. Additionally, the …

Somatosensory Predictors Of Response To Pregabalin In Painful Chemotherapy-Induced Peripheral Neuropathy: A Randomized, Placebo-Controlled, Crossover Study, Alexander Hincker, Karen Frey, Lesley Rao, Nina Wagner-Johnston, Arbi Ben Abdallah, Benjamin Tan, Manik Amin, Tanya Wildes, Rajiv Shah, Pall Karlsson, Kristopher Bakos, Katarzyna Kosicka, Leonid Kagan, Simon Haroutounian

Open Access Publications

No abstract provided.

Differential In Vitro Infection Of Neural Cells By Astroviruses, Andrew B. Janowski, Robyn S. Klein, David Wang

Open Access Publications

No abstract provided.

Aberrant Structural And Functional Connectivity And Neurodevelopmental Impairment In Preterm Children, Cynthia E Rogers, Rachel E Lean, Muriah D Wheelock, Christopher D Smyser

Open Access Publications

BACKGROUND: Despite advances in antenatal and neonatal care, preterm birth remains a leading cause of neurological disabilities in children. Infants born prematurely, particularly those delivered at the earliest gestational ages, commonly demonstrate increased rates of impairment across multiple neurodevelopmental domains. Indeed, the current literature establishes that preterm birth is a leading risk factor for cerebral palsy, is associated with executive function deficits, increases risk for impaired receptive and expressive language skills, and is linked with higher rates of co-occurring attention deficit hyperactivity disorder, anxiety, and autism spectrum disorders. These same infants also demonstrate elevated rates of aberrant cerebral structural and …

Association Of Alcohol Consumption After Development Of Heart Failure With Survival Among Older Adults In The Cardiovascular Health Study, Justin S. Sadhu, Eric Novak, Kenneth J. Mukamal, Jorge R. Kizer, Bruce M. Psaty, Phyllis K. Stein, David L. Brown

Open Access Publications

Importance: More than 1 million older adults develop heart failure annually. The association of alcohol consumption with survival among these individuals after diagnosis is unknown.

Objective: To determine whether alcohol use is associated with increased survival among older adults with incident heart failure.

Design, Setting, and Participants: This prospective cohort study included 5888 community-dwelling adults aged 65 years or older who were recruited to participate in the Cardiovascular Health Study between June 12, 1989, and June 1993, from 4 US sites. Of the total participants, 393 individuals had a new diagnosis of heart failure within the first 9 years of …

Lrrk1 Regulation Of Actin Assembly In Osteoclasts Involves Serine 5 Phosphorylation Of L-Plastin, Mingjue Si, Helen Goodluck, Canjun Zeng, Songqin Pan, Elizabeth M Todd, Sharon Celeste Morley, Xuezhong Qin, Subburaman Mohan, Weirong Xing

Open Access Publications

Mice with disruption of Lrrk1 and patients with nonfunctional mutant Lrrk1 exhibit severe osteopetrosis phenotypes because of osteoclast cytoskeletal dysfunction. To understand how Lrrk1 regulates osteoclast function by modulating cytoskeleton rearrangement, we examined the proteins that are differentially phosphorylated in wild-type mice and Lrrk1-deficient osteoclasts by metal affinity purification coupled liquid chromatography/mass spectrometry (LC/MS) analyses. One of the candidates that we identified by LC/MS is L-plastin, an actin bundling protein. We found that phosphorylation of L-plastin at serine (Ser) residues 5 was present in wild-type osteoclasts but not in Lrrk1-deficient cells. Western blot analyses with antibodies specific for Ser5 phosphorylated …

Reengineering Workflow For Curation Of Dicom Datasets, William Bennett, Kirk Smith, Quasar Jarosz, Tracy Nolan, Walter Bosch

Open Access Publications

Reusable, publicly available data is a pillar of open science and rapid advancement of cancer imaging research. Sharing data from completed research studies not only saves research dollars required to collect data, but also helps insure that studies are both replicable and reproducible. The Cancer Imaging Archive (TCIA) is a global shared repository for imaging data related to cancer. Insuring the consistency, scientific utility, and anonymity of data stored in TCIA is of utmost importance. As the rate of submission to TCIA has been increasing, both in volume and complexity of DICOM objects stored, the process of curation of collections …

What About The Partner? -Factors Associated With Patient-Perceived Partner Dyspareunia In Men With Peyronie's Disease, Yifan Meng, David Y Yang, Kevin M Hebert, Josh B Savage, Manaf Alom, Tobias S Kohler, Landon Trost

Open Access Publications

Background: Limited data are available on how partners of men with Peyronie's disease (PD) are affected by the disease. We sought to characterize PD patients whose curvatures result in pain for their partners during penetrative intercourse.

Methods: We queried a database of all men undergoing initial evaluation for PD at a single clinic between March 2014 and June 2016. Patients were administered a questionnaire regarding sexual health concerns with domains including erectile dysfunction, ejaculatory dysfunction, libido, and penile curvature. In the penile curvature section, patients were specifically asked: "Does the curvature cause your partner any pain during penetrative intercourse? (Y/N)." …

A Prospective Adaptive Utility Trial To Validate Performance Of A Novel Urine Exosome Gene Expression Assay To Predict High-Grade Prostate Cancer In Patients With Prostate-Specific Antigen 2-10ng/Ml At Initial Biopsy, James Mckiernan, Michael J Donovan, Eric Margolis, Alan Partin, Ballentine Carter, Gordon Brown, Phillipp Torkler, Mikkel Noerholm, Johan Skog, Neal Shore, Gerry Andriole, Ian Thompson, Peter Carroll

Open Access Publications

BACKGROUND: Discriminating indolent from clinically significant prostate cancer (PCa) in the initial biopsy setting remains an important issue. Prospectively evaluated diagnostic assays are necessary to ensure efficacy and clinical adoption.

OBJECTIVE: Performance and utility assessment of ExoDx Prostate (IntelliScore) (EPI) urine exosome gene expression assay versus standard clinical parameters for discriminating Grade Group (GG) ≥2 PCa from GG1 PCa and benign disease on initial biopsy.

DESIGN, SETTING, AND PARTICIPANTS: A two-phase adaptive clinical utility study (NCT03031418) comparing EPI results with biopsy outcomes in men, with age ≥50 yr and prostate-specific antigen (PSA) 2-10ng/ml, scheduled for initial prostate biopsy. After EPI …

In Vivo Characterization Of Connective Tissue Remodeling Using Infrared Photoacoustic Spectra, Yuan Qu, Peng Hu, Junhui Shi, Konstantin Maslov, Peinan Zhao, Chiye Li, Jun Ma, Alejandro Garcia-Uribe, Karen Meyers, Emily Diveley, Stephanie Pizzella, Lisa Muench, Nina Punyamurthy, Naomi Goldstein, Oji Onwumere, Mariana Alisio, Kaytelyn Meyenburg, Jennifer Maynard, Kristi Helm, Emma Altieri, Janessia Slaughter, Sabrina Barber, Tracy Burger, Christine Kramer, Jessica Chubiz, Monica Anderson, Ronald Mccarthy, Sarah K England, George A Macones, Molly J Stout, Methodius Tuuli, Lihong V Wang

Open Access Publications

Premature cervical remodeling is a critical precursor of spontaneous preterm birth, and the remodeling process is characterized by an increase in tissue hydration. Nevertheless, current clinical measurements of cervical remodeling are subjective and detect only late events, such as cervical effacement and dilation. Here, we present a photoacoustic endoscope that can quantify tissue hydration by measuring near-infrared cervical spectra. We quantify the water contents of tissue-mimicking hydrogel phantoms as an analog of cervical connective tissue. Applying this method to pregnant women in vivo, we observed an increase in the water content of the cervix throughout pregnancy. The application of this …

Unilateral, 3d Arm Movement Kinematics Are Encoded In Ipsilateral Human Cortex, David T. Bundy, Nicholas Szrama, Mrinal Pahwa, Eric C. Leuthardt

Open Access Publications

There is increasing evidence that the hemisphere ipsilateral to a moving limb plays a role in planning and executing movements. However, the exact relationship between cortical activity and ipsilateral limb movements is uncertain. We sought to determine whether 3D arm movement kinematics (speed, velocity, and position) could be decoded from cortical signals recorded from the hemisphere ipsilateral to the moving limb. By having invasively monitored patients perform unilateral reaches with each arm, we also compared the encoding of contralateral and ipsilateral limb kinematics from a single cortical hemisphere. In four motor-intact human patients (three male, one female) implanted with electrocorticography …

Novel Pleiotropic Risk Loci For Melanoma And Nevus Density Implicate Multiple Biological Pathways, David L Duffy, Gu Zhu, Xin Li, Marianna Sanna, Mark M Iles, Leonie C Jacobs, David M Evans, Seyhan Yazar, Jonathan Beesley, Matthew H Law, Peter Kraft, Alessia Visconti, John C Taylor, Fan Liu, Margaret J Wright, Anjali K Henders, Lisa Bowdler, Dan Glass, M Arfan Ikram, André G Uitterlinden, Pamela A Madden, Andrew C Heath, Elliot C Nelson, Adele C Green, Stephen Chanock, Jennifer H Barrett, Matthew A Brown, Nicholas K Hayward, Stuart Macgregor, Richard A Sturm, Alex W Hewitt, Manfred Kayser, David J Hunter, Julia A Newton Bishop, Timothy D Spector, Grant W Montgomery, David A Mackey, George Davey Smith, Tamar E Nijsten, D Timothy Bishop, Veronique Bataille, Mario Falchi, Jiali Han, Nicholas G Martin

Open Access Publications

No abstract provided.

A Web-Based Calculator For The Prediction Of Severe Neurodevelopmental Impairment In Preterm Infants Using Clinical And Imaging Characteristics, Zachary A Vesoulis, Nathalie M El Ters, Maja Herco, Halana V Whitehead, Amit M Mathur

Open Access Publications

Although the most common forms of brain injury in preterm infants have been associated with adverse neurodevelopmental outcomes, existing MRI scoring systems lack specificity, do not incorporate clinical factors, and are technically challenging to perform. The objective of this study was to develop a web-based, clinically-focused prediction system which differentiates severe neurodevelopmental outcomes from normal-moderate outcomes at two years. Infants were retrospectively identified as those who were born ≤30 weeks gestation and who had MRI imaging at term-equivalent age and neurodevelopmental testing at 18⁻24 months. Each MRI was scored on injury in three domains (intraventricular hemorrhage, white matter injury, and …

Lymph Nodes Go With The Flow, Rafael S. Czepielewski, Gwendalyn J. Randolph

Open Access Publications

In this issue, Bovay et al. (https://doi.org/10.1084/jem.20180217) invoke a compelling model of interplay between the venous and lymphatic vasculature in regulating the developmental genesis and early expansion of LNs. This work supports an emerging model that lymph-venous crosstalk supports LN functionality at all stages.

Changes In The Us Burden Of Chronic Kidney Disease From 2002 To 2016: An Analysis Of The Global Burden Of Disease Study, Benjamin Bowe, Yan Xie, Tingting Li, Ali H. Mokdad, Hong Xian, Yan Yan, Geetha Maddukuri, Ziyad Al-Aly

Open Access Publications

Introduction: Over the past 15 years, changes in demographic, social, and epidemiologic trends occurred in the United States. These changes likely contributed to changes in chronic kidney disease (CKD) epidemiology.

Objective: To describe the change in burden of CKD at the US state level from 2002 to 2016.

Design, Setting, and Participants: This systematic analysis used data and methodologies from the 2016 Global Burden of Disease study in the United States. Data on CKD from 2002 to 2016 were examined at the state level.

Main Outcomes and Measures: Disability-adjusted life years (DALYs) and death due to CKD.

Results: In this …

Association Between Health Insurance Literacy And Avoidance Of Health Care Services Owing To Cost, Renuka Tipirneni, Mary C. Politi, Jeffrey T. Kullgren, Edith C. Kieffer, Susan D. Goold, Aaron M. Scherer

Open Access Publications

Importance: Navigating health insurance and health care choices requires considerable health insurance literacy. Although recommended preventive services are exempt from out-of-pocket costs under the Affordable Care Act, many people may remain unaware of this provision and its effect on their required payment. Little is known about the association between individuals' health insurance literacy and their use of preventive or nonpreventive health care services.

Objective: To assess the association between health insurance literacy and self-reported avoidance of health care services owing to cost.

Design, Setting, and Participants: In this survey study, a US national, geographically diverse, nonprobability sample of 506 US …

Dietary Protein Restriction Reduces Circulating Vldl Triglyceride Levels Via Crebh-Apoa5-Dependent And -Independent Mechanisms, J Humberto Treviño-Villarreal, Valeria Tosti, Nicola Veronese, Beatrice Bertozzi, Arnold D Bullock, Robert S Figenshau, Gerald L Andriole, Luigi Fontana, Et Al

Open Access Publications

Hypertriglyceridemia is an independent risk factor for cardiovascular disease. Dietary interventions based on protein restriction (PR) reduce circulating triglycerides (TGs), but underlying mechanisms and clinical relevance remain unclear. Here, we show that 1 week of a protein-free diet without enforced calorie restriction significantly lowered circulating TGs in both lean and diet-induced obese mice. Mechanistically, the TG-lowering effect of PR was due, in part, to changes in very low-density lipoprotein (VLDL) metabolism both in liver and peripheral tissues. In the periphery, PR stimulated VLDL-TG consumption by increasing VLDL-bound APOA5 expression and promoting VLDL-TG hydrolysis and clearance from circulation. The PR-mediated increase …

Glasdegib In Combination With Cytarabine And Daunorubicin In Patients With Aml Or High-Risk Mds: Phase 2 Study Results, Jorge E Cortes, Mark A Schroeder, Et Al

Open Access Publications

Glasdegib is a Hedgehog pathway inhibitor. This ongoing, open-label, phase 2 study (NCT01546038) evaluated glasdegib plus cytarabine/daunorubicin in patients with untreated acute myeloid leukemia (AML) or high-risk myelodysplastic syndromes (MDS). Patients received glasdegib 100 mg orally, once daily in continuous 28-day cycles from day -3, with intravenous cytarabine 100 mg/m

Adapting Crowdsourced Clinical Cancer Curation In Civic To The Clingen Minimum Variant Level Data Community-Driven Standards, Arpad M Danos, Alex H Wagner, Kilannin Krysiak, Erica K Barnell, Joshua F Mcmichael, Susanna Kiwala, Adam C Coffman, Lynzey Kujan, Malachi Griffith, Obi L Griffith, Et Al

Open Access Publications

Harmonization of cancer variant representation, efficient communication, and free distribution of clinical variant-associated knowledge are central problems that arise with increased usage of clinical next-generation sequencing. The Clinical Genome Resource (ClinGen) Somatic Working Group (WG) developed a minimal variant level data (MVLD) representation of cancer variants, and has an ongoing collaboration with Clinical Interpretations of Variants in Cancer (CIViC), an open-source platform supporting crowdsourced and expert-moderated cancer variant curation. Harmonization between MVLD and CIViC variant formats was assessed by formal field-by-field analysis. Adjustments to the CIViC format were made to harmonize with MVLD and support ClinGen Somatic WG curation activities, …

Testing A Brief Web-Based Intervention To Increase Recognition Of Tobacco Constituents, Elizabeth G Klein, Amanda J Quisenberry, Abigail B Shoben, Tiffany Thomson, Susandi Htut, Randi E Foraker, Albert M Lai, Michael D Slater

Open Access Publications

Objective: We examined website formats to increase smokers' recognition of harmful and potentially harmful constituents (HPHCs) in cigarettes.

Methods: Adult, daily smokers (N = 279) were randomized to view a brief, single-page study website showing HPHC names and uses. The intervention site was tailored + interactive, labeled by cigarette brand/subbrand showing color imagery and pop-up boxes; the generic + static website (control) was unbranded in greyscale. Eye tracking equipment measured attention (dwell time) to precise website features. Linear regression analyses compared attention to HPHC descriptions and the correct recognition of 15 HPHC chemicals. A randomly selected sub-sample (N = 30) …

Mouse Models Of Preterm Birth: Suggested Assessment And Reporting Guidelines, Ronald Mccarthy, Carmel Martin-Fairey, Dorothy K. Sojka, Erik D. Herzog, Emily S. Jungheim, Molly J. Stout, Justin C. Fay, Mala Mahendroo, Jeff Reese, Jennifer L. Herington, Erin J. Plosa, Elaine L. Shelton, Sarah K. England

Open Access Publications

Preterm birth affects approximately 1 out of every 10 births in the United States, leading to high rates of mortality and long-term negative health consequences. To investigate the mechanisms leading to preterm birth so as to develop prevention strategies, researchers have developed numerous mouse models of preterm birth. However, the lack of standard definitions for preterm birth in mice limits our field's ability to compare models and make inferences about preterm birth in humans. In this review, we discuss numerous mouse preterm birth models, propose guidelines for experiments and reporting, and suggest markers that can be used to assess whether …

Teenage Exercise Is Associated With Earlier Symptom Onset In Dysferlinopathy: A Retrospective Cohort Study, Ursula R Moore, Matthew Harms, Alan Pestronk, Et Al

Open Access Publications

No abstract provided.

Genome-Wide Association Study Of Brain Amyloid Deposition As Measured By Pittsburgh Compound-B (Pib)-Pet Imaging, Qi Yan, Jorge L Del-Aguila, Carlos Cruchaga, Et Al

Open Access Publications

Deposition of amyloid plaques in the brain is one of the two main pathological hallmarks of Alzheimer's disease (AD). Amyloid positron emission tomography (PET) is a neuroimaging tool that selectively detects in vivo amyloid deposition in the brain and is a reliable endophenotype for AD that complements cerebrospinal fluid biomarkers with regional information. We measured in vivo amyloid deposition in the brains of ~1000 subjects from three collaborative AD centers and ADNI using

Simulation Of Spontaneous G Protein Activation Reveals A New Intermediate Driving Gdp Unbinding, Xianqiang Sun, Sukrit Singh, Kendall J. Blumer, Gregory R. Bowman

Open Access Publications

Activation of heterotrimeric G proteins is a key step in many signaling cascades. However, a complete mechanism for this process, which requires allosteric communication between binding sites that are ~30 Å apart, remains elusive. We construct an atomically detailed model of G protein activation by combining three powerful computational methods: metadynamics, Markov state models (MSMs), and CARDS analysis of correlated motions. We uncover a mechanism that is consistent with a wide variety of structural and biochemical data. Surprisingly, the rate-limiting step for GDP release correlates with tilting rather than translation of the GPCR-binding helix 5. β-Strands 1 - 3 and …

Uncovering The Complex Genetics Of Human Character, Igor Zwir, Dragan M Svrakic, Sandor Rozsa, Maribel Martinez, C Robert Cloninger, Et Al

Open Access Publications

Human personality is 30-60% heritable according to twin and adoption studies. Hundreds of genetic variants are expected to influence its complex development, but few have been identified. We used a machine learning method for genome-wide association studies (GWAS) to uncover complex genotypic-phenotypic networks and environmental interactions. The Temperament and Character Inventory (TCI) measured the self-regulatory components of personality critical for health (i.e., the character traits of self-directedness, cooperativeness, and self-transcendence). In a discovery sample of 2149 healthy Finns, we identified sets of single-nucleotide polymorphisms (SNPs) that cluster within particular individuals (i.e., SNP sets) regardless of phenotype. Second, we identified five …

Uncovering The Complex Genetics Of Human Temperament, Igor Zwir, Javier Arnedo, Dragan M Svrakic, Sandor Rozsa, Maribel Martinez, C Robert Cloninger, Et Al

Open Access Publications

Experimental studies of learning suggest that human temperament may depend on the molecular mechanisms for associative conditioning, which are highly conserved in animals. The main genetic pathways for associative conditioning are known in experimental animals, but have not been identified in prior genome-wide association studies (GWAS) of human temperament. We used a data-driven machine learning method for GWAS to uncover the complex genotypic-phenotypic networks and environmental interactions related to human temperament. In a discovery sample of 2149 healthy Finns, we identified sets of single-nucleotide polymorphisms (SNPs) that cluster within particular individuals (i.e., SNP sets) regardless of phenotype. Second, we identified …