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Sequence Determinants Of In Cell Condensate Morphology, Dynamics, And Oligomerization As Measured By Number And Brightness Analysis, Ryan J Emenecker, Alex S Holehouse, Lucia C Strader Jun 2021

Sequence Determinants Of In Cell Condensate Morphology, Dynamics, And Oligomerization As Measured By Number And Brightness Analysis, Ryan J Emenecker, Alex S Holehouse, Lucia C Strader

2020-Current year OA Pubs

BACKGROUND: Biomolecular condensates are non-stoichiometric assemblies that are characterized by their capacity to spatially concentrate biomolecules and play a key role in cellular organization. Proteins that drive the formation of biomolecular condensates frequently contain oligomerization domains and intrinsically disordered regions (IDRs), both of which can contribute multivalent interactions that drive higher-order assembly. Our understanding of the relative and temporal contribution of oligomerization domains and IDRs to the material properties of in vivo biomolecular condensates is limited. Similarly, the spatial and temporal dependence of protein oligomeric state inside condensates has been largely unexplored in vivo.

METHODS: In this study, we combined …


The Azithromycin To Prevent Wheezing Following Severe Rsv Bronchiolitis-Ii Clinical Trial: Rationale, Study Design, Methods, And Characteristics Of Study Population, Mythili Srinivasan, Leonard B Bacharier, Charles W Goss, Yanjiao Zhou, Jonathan Boomer, Sarah Bram, Dana Burgdorf, Carey-Ann Burnham, Timothy Casper, Mario Castro, Andrea Coverstone, Matthew Haslam, Watcharoot Kanchongkittiphon, Cadence Kuklinski, Qinghua Lian, Kenneth Schechtman, Gregory A Storch, Kelly True, Meghan A Wallace, Huiqing Yin-Declue, Elizabeth Ahrens, Jinli Wang, Avraham Beigelman Jun 2021

The Azithromycin To Prevent Wheezing Following Severe Rsv Bronchiolitis-Ii Clinical Trial: Rationale, Study Design, Methods, And Characteristics Of Study Population, Mythili Srinivasan, Leonard B Bacharier, Charles W Goss, Yanjiao Zhou, Jonathan Boomer, Sarah Bram, Dana Burgdorf, Carey-Ann Burnham, Timothy Casper, Mario Castro, Andrea Coverstone, Matthew Haslam, Watcharoot Kanchongkittiphon, Cadence Kuklinski, Qinghua Lian, Kenneth Schechtman, Gregory A Storch, Kelly True, Meghan A Wallace, Huiqing Yin-Declue, Elizabeth Ahrens, Jinli Wang, Avraham Beigelman

2020-Current year OA Pubs

Severe respiratory syncytial virus (RSV) bronchiolitis in early life is a significant risk factor for future recurrent wheeze (RW) and asthma. The goal of the Azithromycin to Prevent Wheezing following severe RSV bronchiolitis II (APW-RSV II) clinical trial is to evaluate if azithromycin treatment in infants hospitalized with RSV bronchiolitis reduces the occurrence of RW during the preschool years. The APW-RSV II clinical trial is a double-blind, placebo-controlled, parallel-group, randomized trial, including otherwise healthy participants, ages 30 days-18 months, who are hospitalized due to RSV bronchiolitis. The study includes an active randomized treatment phase with azithromycin or placebo for 2 …


A Peptide-Based Checkpoint Immunomodulator Alleviates Immune Dysfunction In Murine Polymicrobial Sepsis, Timothy W Phares, Vinayaka Kotraiah, Chun-Shiang Chung, Jacqueline Unsinger, Monty Mazer, Kenneth E. Remy, Cecille D. Browne, Peter Buontempo, Marc Mansour, James Pannucci, Alfred Ayala, Richard S. Hotchkiss, Gabriel M. Gutierrez Jun 2021

A Peptide-Based Checkpoint Immunomodulator Alleviates Immune Dysfunction In Murine Polymicrobial Sepsis, Timothy W Phares, Vinayaka Kotraiah, Chun-Shiang Chung, Jacqueline Unsinger, Monty Mazer, Kenneth E. Remy, Cecille D. Browne, Peter Buontempo, Marc Mansour, James Pannucci, Alfred Ayala, Richard S. Hotchkiss, Gabriel M. Gutierrez

2020-Current year OA Pubs

Sepsis-induced immunosuppression involves both innate and adaptive immunity and is associated with the increased expression of checkpoint inhibitors, such as programmed cell-death protein 1 (PD-1). The expression of PD-1 is associated with poor outcomes in septic patients, and in models of sepsis, blocking PD-1 or its ligands with antibodies increased survival and alleviated immune suppression. While inhibitory antibodies are effective, they can lead to immune-related adverse events (irAEs), in part due to continual blockade of the PD-1 pathway, resulting in hyperactivation of the immune response. Peptide-based therapeutics are an alternative drug modality that provide a rapid pharmacokinetic profile, reducing the …


Multiparametric Early Detection And Prediction Of Cardiotoxicity Using Myocardial Strain, T1 And T2 Mapping, And Biochemical Markers: A Longitudinal Cardiac Resonance Imaging Study During 2 Years Of Follow-Up, Sorin Giusca, Grigorios Korosoglou, Moritz Montenbruck, Blaž Geršak, Arne Kristian Schwarz, Sebastian Esch, Sebastian Kelle, Pia Wülfing, Susan Dent, Daniel Lenihan, Henning Steen Jun 2021

Multiparametric Early Detection And Prediction Of Cardiotoxicity Using Myocardial Strain, T1 And T2 Mapping, And Biochemical Markers: A Longitudinal Cardiac Resonance Imaging Study During 2 Years Of Follow-Up, Sorin Giusca, Grigorios Korosoglou, Moritz Montenbruck, Blaž Geršak, Arne Kristian Schwarz, Sebastian Esch, Sebastian Kelle, Pia Wülfing, Susan Dent, Daniel Lenihan, Henning Steen

2020-Current year OA Pubs

BACKGROUND: Our goal was to evaluate the ability of cardiovascular magnetic resonance for detecting and predicting cardiac dysfunction in patients receiving cancer therapy. Left ventricular ejection fraction, global and regional strain utilizing fast-strain-encoded, T1 and T2 mapping, and cardiac biomarkers (troponin and BNP [brain natriuretic peptide]) were analyzed.

METHODS: Sixty-one patients (47 with breast cancer, 11 with non-Hodgkin lymphoma, and 3 with Hodgkin lymphoma) underwent cardiovascular magnetic resonance scans at baseline and at regular intervals during 2 years of follow-up. The percentage of all left ventricular myocardial segments with strain ≤-17% (normal myocardium [%]) was analyzed. Clinical cardiotoxicity (CTX) and …


Sars-Cov-2 Detection Among International Air Travellers To Ghana During Mandatory Quarantine, Bright Adu, Joseph K H Bonney, John K Odoom, Evelyn Y A Bonney, Evangeline Obodai, Ivy A Asante, James Aboagye, Mildred A Adusei-Poku, Lawrence Lartey, Ernest K Asiedu, William K Ampofo, George B Kyei Jun 2021

Sars-Cov-2 Detection Among International Air Travellers To Ghana During Mandatory Quarantine, Bright Adu, Joseph K H Bonney, John K Odoom, Evelyn Y A Bonney, Evangeline Obodai, Ivy A Asante, James Aboagye, Mildred A Adusei-Poku, Lawrence Lartey, Ernest K Asiedu, William K Ampofo, George B Kyei

2020-Current year OA Pubs

OBJECTIVES: To determine the prevalence of SARS-CoV-2 detection among international travellers to Ghana during mandatory quarantine.

DESIGN: A retrospective cross-sectional study.

SETTING: Air travellers to Ghana on 21

PARTICIPANTS: On 21

MAIN OUTCOME MEASURE: Positivity for SARS-CoV-2 by polymerase chain reaction.

RESULTS: The initial testing at the beginning of quarantine found 79 (7.7%) individuals to be positive for SARS-CoV-2. In the exit screening after 12 to 13 days of quarantine, it was discovered that 26 of those who tested negative for SARS-CoV-2 in the initial screening subsequently tested positive.

CONCLUSIONS: Ghana likely averted an early community spread of COVID-19 through …


Integration Of Immunotherapy Into Adjuvant Therapy For Resected Non-Small-Cell Lung Cancer: Alchemist Chemo-Io (Accio), Jacob M Sands, Ramaswamy Govindan, Jhanelle Gray, Et Al Jun 2021

Integration Of Immunotherapy Into Adjuvant Therapy For Resected Non-Small-Cell Lung Cancer: Alchemist Chemo-Io (Accio), Jacob M Sands, Ramaswamy Govindan, Jhanelle Gray, Et Al

2020-Current year OA Pubs

Non-small-cell lung cancer (NSCLC) causes significant mortality each year. After successful resection of disease stage IB (>4 cm) to IIIA (per AJCC 7), adjuvant platinum-based chemotherapy improves median overall survival and is the standard of care, but many patients still experience recurrence of disease. An adjuvant regimen with greater efficacy could substantially improve outcomes. Pembrolizumab, a programmed cell death-1 inhibitor, has become an important option in the treatment of metastatic NSCLC. ALCHEMIST is a clinical trial platform of the National Cancer Institute that includes biomarker analysis for resected NSCLC and supports therapeutic trials including A081801 (ACCIO), a three-arm study …


Elevated Mrna Expression And Defective Processing Of Cathepsin D In Hela Cells Lacking The Mannose 6-Phosphate Pathway, Lin Liu, Balraj Doray Jun 2021

Elevated Mrna Expression And Defective Processing Of Cathepsin D In Hela Cells Lacking The Mannose 6-Phosphate Pathway, Lin Liu, Balraj Doray

2020-Current year OA Pubs

Disruption of the mannose 6-phosphate (M-6-P) pathway in HeLa cells by inactivation of the GNPTAB gene, which encodes the α/β subunits of GlcNAc-1-phosphotransferase, results in missorting of newly synthesized lysosomal acid hydrolases to the cell culture media instead of transport to the endolysosomal system. We previously demonstrated that the majority of the lysosomal aspartyl protease, cathepsin D, is secreted in these GNPTAB


Association Of Clinical Factors And Recent Anticancer Therapy With Covid-19 Severity Among Patients With Cancer: A Report From The Covid-19 And Cancer Consortium, P Grivas, K E Stockerl-Goldstein, A Y Zhou, Et Al. Jun 2021

Association Of Clinical Factors And Recent Anticancer Therapy With Covid-19 Severity Among Patients With Cancer: A Report From The Covid-19 And Cancer Consortium, P Grivas, K E Stockerl-Goldstein, A Y Zhou, Et Al.

2020-Current year OA Pubs

BACKGROUND: Patients with cancer may be at high risk of adverse outcomes from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We analyzed a cohort of patients with cancer and coronavirus 2019 (COVID-19) reported to the COVID-19 and Cancer Consortium (CCC19) to identify prognostic clinical factors, including laboratory measurements and anticancer therapies.

PATIENTS AND METHODS: Patients with active or historical cancer and a laboratory-confirmed SARS-CoV-2 diagnosis recorded between 17 March and 18 November 2020 were included. The primary outcome was COVID-19 severity measured on an ordinal scale (uncomplicated, hospitalized, admitted to intensive care unit, mechanically ventilated, died within 30 days). …


Addressing Cancer Survivors' Cardiovascular Health Using The Automated Heart Health Assessment (Ah-Ha) Ehr Tool: Initial Protocol And Modifications To Address Covid-19 Challenges, Randi E Foraker, Eleanor C Davidson, Emily V Dressler, Brian J Wells, Simon Craddock Lee, Heidi D Klepin, Karen M Winkfield, W Gregory Hundley, Philip R O Payne, Albert M Lai, Glenn J Lesser, Kathryn E Weaver Jun 2021

Addressing Cancer Survivors' Cardiovascular Health Using The Automated Heart Health Assessment (Ah-Ha) Ehr Tool: Initial Protocol And Modifications To Address Covid-19 Challenges, Randi E Foraker, Eleanor C Davidson, Emily V Dressler, Brian J Wells, Simon Craddock Lee, Heidi D Klepin, Karen M Winkfield, W Gregory Hundley, Philip R O Payne, Albert M Lai, Glenn J Lesser, Kathryn E Weaver

2020-Current year OA Pubs

BACKGROUND: The purpose of this paper is to describe the Automated Heart-Health Assessment (AH-HA) study protocol, which demonstrates an agile approach to cancer care delivery research. This study aims to assess the effect of a clinical decision support tool for cancer survivors on cardiovascular health (CVH) discussions, referrals, completed visits with primary care providers and cardiologists, and control of modifiable CVH factors and behaviors. The COVID-19 pandemic has caused widespread disruption to clinical trial accrual and operations. Studies conducted with potentially vulnerable populations, including cancer survivors, must shift towards virtual consent, data collection, and study visits to reduce risk for …


A Case Of Hepatic Cyst-Induced Internal Jugular Venous Thrombosis, Tuyen V Le, Thai Truong, Tam N M Ngo, Quoc Bui, Cassady Palmer, Vien T Truong, Duc H Nguyen Jun 2021

A Case Of Hepatic Cyst-Induced Internal Jugular Venous Thrombosis, Tuyen V Le, Thai Truong, Tam N M Ngo, Quoc Bui, Cassady Palmer, Vien T Truong, Duc H Nguyen

2020-Current year OA Pubs

• Echocardiography can demonstrate hepatic cyst–induced right atrial compression. • Hepatic cyst–induced blood flow stasis can cause internal jugular venous thrombus. • Laparoscopic deroofing of hepatic cysts is a safe and effective treatment.


Report Dose-To-Medium In Clinical Trials Where Available; A Consensus From The Global Harmonisation Group To Maximize Consistency, Stephen F Kry, Jeff Michalski, Et Al. Jun 2021

Report Dose-To-Medium In Clinical Trials Where Available; A Consensus From The Global Harmonisation Group To Maximize Consistency, Stephen F Kry, Jeff Michalski, Et Al.

2020-Current year OA Pubs

PURPOSE: To promote consistency in clinical trials by recommending a uniform framework as it relates to radiation transport and dose calculation in water versus in medium.

METHODS: The Global Quality Assurance of Radiation Therapy Clinical Trials Harmonisation Group (GHG; www.rtqaharmonization.org) compared the differences between dose to water in water (D

RESULTS: No framework was found to be ideal or perfect given the history, complexity, and current status of radiation therapy. Nevertheless, based on the evidence available, the GHG established a recommendation preferring dose to medium in medium (D

CONCLUSIONS: Dose to medium in medium (D


Outcomes And Risk Factors Associated With Sars-Cov-2 Infection In A North American Registry Of Patients With Multiple Sclerosis, Amber Salter, Robert J Fox, Scott D Newsome, June Halper, David K B Li, Pamela Kanellis, Kathleen Costello, Bruce Bebo, Kottil Rammohan, Gary R Cutter, Anne H Cross Jun 2021

Outcomes And Risk Factors Associated With Sars-Cov-2 Infection In A North American Registry Of Patients With Multiple Sclerosis, Amber Salter, Robert J Fox, Scott D Newsome, June Halper, David K B Li, Pamela Kanellis, Kathleen Costello, Bruce Bebo, Kottil Rammohan, Gary R Cutter, Anne H Cross

2020-Current year OA Pubs

Importance: Emergence of SARS-CoV-2 causing COVID-19 prompted the need to gather information on clinical outcomes and risk factors associated with morbidity and mortality in patients with multiple sclerosis (MS) and concomitant SARS-CoV-2 infections.

Objective: To examine outcomes and risk factors associated with COVID-19 clinical severity in a large, diverse cohort of North American patients with MS.

Design, Setting, and Participants: This analysis used deidentified, cross-sectional data on patients with MS and SARS-CoV-2 infection reported by health care professionals in North American academic and community practices between April 1, 2020, and December 12, 2020, in the COVID-19 Infections in MS Registry. …


Brain-Responsive Neurostimulation For The Treatment Of Adults With Epilepsy In Tuberous Sclerosis Complex: A Case Series, Danielle S Mcdermott, Emily A Mirro, Kirsten Fetrow, David E Burdette, Stephanie Chen, Jennifer Hopp, Todd Masel, Emily A Johnson, Felicia M K Elefant, Scheherazade Le, Sanjay E Patra, Mesha-Gay Brown, Zulfi Haneef Jun 2021

Brain-Responsive Neurostimulation For The Treatment Of Adults With Epilepsy In Tuberous Sclerosis Complex: A Case Series, Danielle S Mcdermott, Emily A Mirro, Kirsten Fetrow, David E Burdette, Stephanie Chen, Jennifer Hopp, Todd Masel, Emily A Johnson, Felicia M K Elefant, Scheherazade Le, Sanjay E Patra, Mesha-Gay Brown, Zulfi Haneef

2020-Current year OA Pubs

OBJECTIVE: Tuberous sclerosis complex (TSC) is a genetic disorder primarily characterized by the development of multisystem benign tumors. Epilepsy is the most common neurologic manifestation, affecting 80%-90% of TSC patients. The diffuse structural brain abnormalities and the multifocal nature of epilepsy in TSC pose diagnostic challenges when evaluating patients for epilepsy surgery.

METHODS: We retrospectively reviewed the safety experience and efficacy outcomes of five adult TSC patients who were treated with direct brain-responsive neurostimulation (RNS System, NeuroPace, Inc).

RESULTS: The average follow-up duration was 20 months. All five patients were responders (≥50% disabling seizure reduction) at last follow-up. The median …


Transfer Transcriptomic Signatures For Infectious Diseases, Julia Di Iulio, Istvan Bartha, Roberto Spreafico, Herbert W Virgin, Amalio Telenti Jun 2021

Transfer Transcriptomic Signatures For Infectious Diseases, Julia Di Iulio, Istvan Bartha, Roberto Spreafico, Herbert W Virgin, Amalio Telenti

2020-Current year OA Pubs

The modulation of the transcriptome is among the earliest responses to infection. However, defining the transcriptomic signatures of disease is challenging because logistic, technical, and cost factors limit the size and representativeness of samples in clinical studies. These limitations lead to a poor performance of signatures when applied to new datasets. Although the study focuses on infection, the central hypothesis of the work is the generalization of sets of signatures across diseases. We use a machine learning approach to identify common elements in datasets and then test empirically whether they are informative about a second dataset from a disease or …


Malda, Accelerating Malaria Drug Discovery, Tuo Yang, Eva S. Istvan, Daniel E. Goldberg, Et Al. Jun 2021

Malda, Accelerating Malaria Drug Discovery, Tuo Yang, Eva S. Istvan, Daniel E. Goldberg, Et Al.

2020-Current year OA Pubs

The Malaria Drug Accelerator (MalDA) is a consortium of 15 leading scientific laboratories. The aim of MalDA is to improve and accelerate the early antimalarial drug discovery process by identifying new, essential, druggable targets. In addition, it seeks to produce early lead inhibitors that may be advanced into drug candidates suitable for preclinical development and subsequent clinical testing in humans. By sharing resources, including expertise, knowledge, materials, and reagents, the consortium strives to eliminate the structural barriers often encountered in the drug discovery process. Here we discuss the mission of the consortium and its scientific achievements, including the identification of …


Effects Of Pathogen Reduction Technology And Storage Duration On The Ability Of Cryoprecipitate To Rescue Induced Coagulopathies In Vitro, Kimberly A Thomas, Susan M Shea, Philip C Spinella Jun 2021

Effects Of Pathogen Reduction Technology And Storage Duration On The Ability Of Cryoprecipitate To Rescue Induced Coagulopathies In Vitro, Kimberly A Thomas, Susan M Shea, Philip C Spinella

2020-Current year OA Pubs

BACKGROUND: Fibrinogen concentrates and cryoprecipitate are currently used for fibrinogen supplementation in bleeding patients with dysfibrinogenemia. Both products provide an abundant source of fibrinogen but take greater than 10 min to prepare for administration. Fibrinogen concentrates lack coagulation factors (i.e., factor VIII [FVIII], factor XIII [FXIII], von Willebrand factor [VWF]) important for robust hemostatic function. Cryoprecipitate products contain these factors but have short shelf lives (<6 h). Pathogen reduction (PR) of cryoprecipitate would provide a shelf-stable immediately available adjunct containing factors important for rescuing hemostatic dysfunction.

STUDY DESIGN AND METHODS: Hemostatic adjunct study products were psoralen-treated PR-cryoprecipitated fibrinogen complex (PR-Cryo FC), cryoprecipitate (Cryo), and fibrinogen concentrates (FibCon). PR-Cryo FC and Cryo were stored for 10 days at 20-24°C. Adjuncts were …


Clinical Epigenomics: Genome-Wide Dna Methylation Analysis For The Diagnosis Of Mendelian Disorders, Bekim Sadikovic, Jorge L Granadillo, Et Al. Jun 2021

Clinical Epigenomics: Genome-Wide Dna Methylation Analysis For The Diagnosis Of Mendelian Disorders, Bekim Sadikovic, Jorge L Granadillo, Et Al.

2020-Current year OA Pubs

PURPOSE: We describe the clinical implementation of genome-wide DNA methylation analysis in rare disorders across the EpiSign diagnostic laboratory network and the assessment of results and clinical impact in the first subjects tested.

METHODS: We outline the logistics and data flow between an integrated network of clinical diagnostics laboratories in Europe, the United States, and Canada. We describe the clinical validation of EpiSign using 211 specimens and assess the test performance and diagnostic yield in the first 207 subjects tested involving two patient subgroups: the targeted cohort (subjects with previous ambiguous/inconclusive genetic findings including genetic variants of unknown clinical significance) …


Commonalities Across Computational Workflows For Uncovering Explanatory Variants In Undiagnosed Cases, Shilpa Nadimpalli Kobren, Dustin Baldridge, Daniel J Wegner, Alexander J Paul, Et Al. Jun 2021

Commonalities Across Computational Workflows For Uncovering Explanatory Variants In Undiagnosed Cases, Shilpa Nadimpalli Kobren, Dustin Baldridge, Daniel J Wegner, Alexander J Paul, Et Al.

2020-Current year OA Pubs

PURPOSE: Genomic sequencing has become an increasingly powerful and relevant tool to be leveraged for the discovery of genetic aberrations underlying rare, Mendelian conditions. Although the computational tools incorporated into diagnostic workflows for this task are continually evolving and improving, we nevertheless sought to investigate commonalities across sequencing processing workflows to reveal consensus and standard practice tools and highlight exploratory analyses where technical and theoretical method improvements would be most impactful.

METHODS: We collected details regarding the computational approaches used by a genetic testing laboratory and 11 clinical research sites in the United States participating in the Undiagnosed Diseases Network …


Randomized Trial Of The Efficacy And Safety Of Berotralstat (Bcx7353) As An Oral Prophylactic Therapy For Hereditary Angioedema: Results Of Apex-2 Through 48 Weeks (Part 2), H James Wedner, Et Al. Jun 2021

Randomized Trial Of The Efficacy And Safety Of Berotralstat (Bcx7353) As An Oral Prophylactic Therapy For Hereditary Angioedema: Results Of Apex-2 Through 48 Weeks (Part 2), H James Wedner, Et Al.

2020-Current year OA Pubs

BACKGROUND: Berotralstat (BCX7353) is a recently approved, oral, once-daily kallikrein inhibitor for hereditary angioedema (HAE) prophylaxis. In the APeX-2 trial, berotralstat reduced HAE attack rates over 24 weeks, with a favorable safety and tolerability profile.

OBJECTIVE: Evaluate berotralstat safety, tolerability, and effectiveness over 48 weeks.

METHODS: APeX-2 is a phase 3, parallel-group, multicenter trial (NCT03485911) in patients with HAE due to C1 esterase inhibitor deficiency. Part 1 was double-blind and placebo-controlled, with patients randomized to 24 weeks of berotralstat 150 mg, 110 mg, or placebo. In part 2, patients continued berotralstat the same dose or, if initially randomized to placebo, …


Evaluation Of Serum-Derived Bovine Immunoglobulin Protein Isolate In Subjects With Decompensated Cirrhosis With Ascites, Matthew J. Stotts, Amanda Cheung, Muhammad B. Hammami, David J. Westrich Jr., Eric Anderson, Lauren Counts, Alex S. Befeler, Adrian M. Di Bisceglie, Charlene Prather Jun 2021

Evaluation Of Serum-Derived Bovine Immunoglobulin Protein Isolate In Subjects With Decompensated Cirrhosis With Ascites, Matthew J. Stotts, Amanda Cheung, Muhammad B. Hammami, David J. Westrich Jr., Eric Anderson, Lauren Counts, Alex S. Befeler, Adrian M. Di Bisceglie, Charlene Prather

2020-Current year OA Pubs

Background Bacterial translocation plays a pivotal role in the natural course of cirrhosis and its complications. Serum-derived bovine immunoglobulin (SBI) is an oral medical food that has been shown to both reduce inflammation in the intestines and neutralize bacteria. It represents a unique intervention that has not been studied in this population. Methodology We conducted a prospective open-label trial with an eight-week treatment phase of SBI. Individuals were assessed using lactulose breath testing, serum markers for enterocyte damage and bacterial translocation, and the Chronic Liver Disease Questionnaire (CLDQ) prior to and after completion of the treatment phase. Results We evaluated …


Safety And Efficacy Of Umbilical Cord-Derived Wharton's Jelly Compared To Hyaluronic Acid And Saline For Knee Osteoarthritis: Study Protocol For A Randomized, Controlled, Single-Blind, Multi-Center Trial, Ashim Gupta, Nicola Maffulli, Hugo C Rodriguez, Eric W Carson, Randa A Bascharon, Kristin Delfino, Howard J Levy, Saadiq F El-Amin May 2021

Safety And Efficacy Of Umbilical Cord-Derived Wharton's Jelly Compared To Hyaluronic Acid And Saline For Knee Osteoarthritis: Study Protocol For A Randomized, Controlled, Single-Blind, Multi-Center Trial, Ashim Gupta, Nicola Maffulli, Hugo C Rodriguez, Eric W Carson, Randa A Bascharon, Kristin Delfino, Howard J Levy, Saadiq F El-Amin

2020-Current year OA Pubs

BACKGROUND: Osteoarthritis (OA) is the most common joint disorder in the United States of America (USA) with a fast-rising prevalence. Current treatment modalities are limited, and total knee replacement surgeries have shown disadvantages, especially for grade II/III OA. The interest in the use of biologics, including umbilical cord (UC)-derived Wharton's jelly (WJ), has grown in recent years. The results from a preliminary study demonstrated the presence of essential components of regenerative medicine, namely growth factors, cytokines, hyaluronic acid (HA), and extracellular vesicles, including exosomes, in WJ. The proposed study aims to evaluate the safety and efficacy of intra-articular injection of …


Hypergraph Models Of Biological Networks To Identify Genes Critical To Pathogenic Viral Response, Song Feng, Larissa B Thackray, Qing Tan, Michael S Diamond, Et Al May 2021

Hypergraph Models Of Biological Networks To Identify Genes Critical To Pathogenic Viral Response, Song Feng, Larissa B Thackray, Qing Tan, Michael S Diamond, Et Al

2020-Current year OA Pubs

BACKGROUND: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems. Hypergraphs are generalizations of graphs that naturally model multi-way relationships and have shown promise in modeling systems such as protein complexes and metabolic reactions. In this paper we seek to understand how hypergraphs can more faithfully identify, and potentially predict, important genes based on complex relationships inferred from genomic expression data sets.

RESULTS: We compiled a novel data set of transcriptional …


Exome Sequencing Revealed Pde11a As A Novel Candidate Gene For Early-Onset Alzheimer's Disease, Wei Qin, Aihong Zhou, Xiumei Zuo, Longfei Jia, Fangyu Li, Qi Wang, Ying Li, Yiping Wei, Hongmei Jin, Carlos Cruchaga, Bruno A Benitez, Jianping Jia May 2021

Exome Sequencing Revealed Pde11a As A Novel Candidate Gene For Early-Onset Alzheimer's Disease, Wei Qin, Aihong Zhou, Xiumei Zuo, Longfei Jia, Fangyu Li, Qi Wang, Ying Li, Yiping Wei, Hongmei Jin, Carlos Cruchaga, Bruno A Benitez, Jianping Jia

2020-Current year OA Pubs

To identify novel risk genes and better understand the molecular pathway underlying Alzheimer's disease (AD), whole-exome sequencing was performed in 215 early-onset AD (EOAD) patients and 255 unrelated healthy controls of Han Chinese ethnicity. Subsequent validation, computational annotation and in vitro functional studies were performed to evaluate the role of candidate variants in EOAD. We identified two rare missense variants in the phosphodiesterase 11A (PDE11A) gene in individuals with EOAD. Both variants are located in evolutionarily highly conserved amino acids, are predicted to alter the protein conformation and are classified as pathogenic. Furthermore, we found significantly decreased protein levels of …


Novel Autosegmentation Spatial Similarity Metrics Capture The Time Required To Correct Segmentations Better Than Traditional Metrics In A Thoracic Cavity Segmentation Workflow, Kendall J Kiser, Arko Barman, Sonja Stieb, Clifton D Fuller, Luca Giancardo May 2021

Novel Autosegmentation Spatial Similarity Metrics Capture The Time Required To Correct Segmentations Better Than Traditional Metrics In A Thoracic Cavity Segmentation Workflow, Kendall J Kiser, Arko Barman, Sonja Stieb, Clifton D Fuller, Luca Giancardo

2020-Current year OA Pubs

Automated segmentation templates can save clinicians time compared to de novo segmentation but may still take substantial time to review and correct. It has not been thoroughly investigated which automated segmentation-corrected segmentation similarity metrics best predict clinician correction time. Bilateral thoracic cavity volumes in 329 CT scans were segmented by a UNet-inspired deep learning segmentation tool and subsequently corrected by a fourth-year medical student. Eight spatial similarity metrics were calculated between the automated and corrected segmentations and associated with correction times using Spearman's rank correlation coefficients. Nine clinical variables were also associated with metrics and correction times using Spearman's rank …


Semi-Supervised Peak Calling With Span And Jbr Genome Browser, Oleg Shpynov, Aleksei Dievskii, Roman Chernyatchik, Petr Tsurinov, Maxim N Artyomov May 2021

Semi-Supervised Peak Calling With Span And Jbr Genome Browser, Oleg Shpynov, Aleksei Dievskii, Roman Chernyatchik, Petr Tsurinov, Maxim N Artyomov

2020-Current year OA Pubs

UNLABELLED: The widespread application of ChIP-seq led to a growing need for consistent analysis of multiple epigenetics profiles, for instance, in human studies where multiple replicates are a common element of design. Such multisamples experimental designs introduced analytical and computational challenges. For example, when peak calling is done independently for each sample, small differences in signal strength/quality lead to a very different number of peaks for individual samples, making group-level analysis difficult. On the other side, when samples are pooled together for joint analysis, individual-level statistical differences are averaged out. Recently we have demonstrated that a semi-supervised peak calling approach …


Electronic Clinical Decision Support For Children With Minor Head Trauma And Intracranial Injuries: A Sociotechnical Analysis, Jacob K Greenberg, Ayodamola Otun, Azzah Nasraddin, Ross C Brownson, Nathan Kuppermann, David D Limbrick, Po-Yin Yen, Randi E Foraker May 2021

Electronic Clinical Decision Support For Children With Minor Head Trauma And Intracranial Injuries: A Sociotechnical Analysis, Jacob K Greenberg, Ayodamola Otun, Azzah Nasraddin, Ross C Brownson, Nathan Kuppermann, David D Limbrick, Po-Yin Yen, Randi E Foraker

2020-Current year OA Pubs

BACKGROUND: Current management of children with minor head trauma (MHT) and intracranial injuries is not evidence-based and may place some children at risk of harm. Evidence-based electronic clinical decision support (CDS) for management of these children may improve patient safety and decrease resource use. To guide these efforts, we evaluated the sociotechnical environment impacting the implementation of electronic CDS, including workflow and communication, institutional culture, and hardware and software infrastructure, among other factors.

METHODS: Between March and May, 2020 semi-structured qualitative focus group interviews were conducted to identify sociotechnical influences on CDS implementation. Physicians from neurosurgery, emergency medicine, critical care, …


Tofacitinib, An Oral Janus Kinase Inhibitor: Analysis Of Malignancy (Excluding Nonmelanoma Skin Cancer) Events Across The Ulcerative Colitis Clinical Program, Gary R Lichtenstein, Gerhard Rogler, Matthew A Ciorba, Chinyu Su, Gary Chan, Ronald D Pedersen, Nervin Lawendy, Daniel Quirk, Chudy I Nduaka, Andrew J Thorpe, Julian Panés May 2021

Tofacitinib, An Oral Janus Kinase Inhibitor: Analysis Of Malignancy (Excluding Nonmelanoma Skin Cancer) Events Across The Ulcerative Colitis Clinical Program, Gary R Lichtenstein, Gerhard Rogler, Matthew A Ciorba, Chinyu Su, Gary Chan, Ronald D Pedersen, Nervin Lawendy, Daniel Quirk, Chudy I Nduaka, Andrew J Thorpe, Julian Panés

2020-Current year OA Pubs

BACKGROUND: Tofacitinib is an oral, small molecule Janus kinase inhibitor for the treatment of ulcerative colitis (UC). Here, we performed an integrated analysis of malignancy events from the tofacitinib phase 3 UC clinical development program (excluding nonmelanoma skin cancer [NMSC]).

METHODS: Data (up to May 2019) were pooled from two phase 3 induction studies, a phase 3 maintenance study, and an ongoing, open-label, long-term extension (OLE) study, and analyzed as 3 cohorts: induction (N = 1139), maintenance (N = 592), and overall (induction, maintenance, and ongoing OLE study; N = 1124). Proportions and incidence rates (IRs; unique patients with events …


One-Year Urinary And Sexual Outcome Trajectories Among Prostate Cancer Patients Treated By Radical Prostatectomy: A Prospective Study, Lin Yang, Jung Ae Lee, Emily Heer, Claire Pernar, Graham A Colditz, Ratna Pakpahan, Kellie R Imm, Eric H Kim, Robert L Grubb 3rd, Kathleen Y Wolin, Adam S Kibel, Siobhan Sutcliffe May 2021

One-Year Urinary And Sexual Outcome Trajectories Among Prostate Cancer Patients Treated By Radical Prostatectomy: A Prospective Study, Lin Yang, Jung Ae Lee, Emily Heer, Claire Pernar, Graham A Colditz, Ratna Pakpahan, Kellie R Imm, Eric H Kim, Robert L Grubb 3rd, Kathleen Y Wolin, Adam S Kibel, Siobhan Sutcliffe

2020-Current year OA Pubs

BACKGROUND: To examine one-year trajectories of urinary and sexual outcomes, and correlates of these trajectories, among prostate cancer patients treated by radical prostatectomy (RP).

METHODS: Study participants were recruited from 2011 to 2014 at two US institutions. Self-reported urinary and sexual outcomes were measured at baseline before surgery, and 5 weeks, 6 months and 12 months after surgery, using the modified Expanded Prostate Cancer Index Composite-50 (EPIC-50). Changes in EPIC-50 scores from baseline were categorized as improved (beyond baseline), maintained, or impaired (below baseline), using previously-reported minimum clinically important differences.

RESULTS: Of the 426 eligible participants who completed the baseline …


Stroma-Targeting Strategies In Pancreatic Cancer: Past Lessons, Challenges And Prospects, Faran Polani, Patrick M Grierson, Kian-Huat Lim May 2021

Stroma-Targeting Strategies In Pancreatic Cancer: Past Lessons, Challenges And Prospects, Faran Polani, Patrick M Grierson, Kian-Huat Lim

2020-Current year OA Pubs

Pancreatic ductal adenocarcinoma (PDAC) is projected to emerge as the second leading cause of cancer-related death after 2030. Extreme treatment resistance is perhaps the most significant factor that underlies the poor prognosis of PDAC. To date, combination chemotherapy remains the mainstay of treatment for most PDAC patients. Compared to other cancer types, treatment response of PDAC tumors to similar chemotherapy regimens is clearly much lower and shorter-lived. Aside from typically harboring genetic alterations that to date remain un-druggable and are drivers of treatment resistance, PDAC tumors are uniquely characterized by a densely fibrotic stroma that has well-established roles in promoting …


Presepsin As A Diagnostic And Prognostic Biomarker In Sepsis, Dimitrios Velissaris, Nicholas Zareifopoulos, Vasileios Karamouzos, Evangelos Karanikolas, Charalampos Pierrakos, Ioanna Koniari, Menelaos Karanikolas May 2021

Presepsin As A Diagnostic And Prognostic Biomarker In Sepsis, Dimitrios Velissaris, Nicholas Zareifopoulos, Vasileios Karamouzos, Evangelos Karanikolas, Charalampos Pierrakos, Ioanna Koniari, Menelaos Karanikolas

2020-Current year OA Pubs

Sepsis is a condition characterized by high morbidity and mortality which is commonly encountered in an emergency and critical care setting. Despite a substantial body of research, the ideal biomarker for the diagnosis and prognostic stratification of septic patients remains unknown. This review aimed to summarize the publications referring to the validity of the biomarker presepsin when used for the detection, monitoring and prognosis in patients suffering with sepsis. This work is a narrative review based on a PubMed/Medline search conducted in order to identify all relevant publications referring to the use of presepsin in sepsis. Search was not limited …