Digital Commons Network^™

Xatlas: Scalable Small Variant Calling Across Heterogeneous Next-Generation Sequencing Experiments, Jesse Farek, Daniel Hughes, William Salerno, Yiming Zhu, Aishwarya Pisupati, Adam Mansfield, Olga Krasheninina, Adam C English, Ginger Metcalf, Eric Boerwinkle, Donna M Muzny, Richard Gibbs, Ziad Khan, Fritz J Sedlazeck

Faculty, Staff and Students Publications

Background: The growing volume and heterogeneity of next-generation sequencing (NGS) data complicate the further optimization of identifying DNA variation, especially considering that curated high-confidence variant call sets frequently used to validate these methods are generally developed from the analysis of comparatively small and homogeneous sample sets.

Findings: We have developed xAtlas, a single-sample variant caller for single-nucleotide variants (SNVs) and small insertions and deletions (indels) in NGS data. xAtlas features rapid runtimes, support for CRAM and gVCF file formats, and retraining capabilities. xAtlas reports SNVs with 99.11% recall and 98.43% precision across a reference HG002 sample at 60× whole-genome coverage …

An Rna Interference (Rnai) Toolkit And Its Utility For Functional Genetic Analysis Of Leishmania (Viannia), Lon-Fye Lye, Katherine L Owens, Soojin Jang, Joseph E Marcus, Erin A Brettmann, Stephen M Beverley

2020-Current year OA Pubs

RNA interference (RNAi) is a powerful tool whose efficacy against a broad range of targets enables functional genetic tests individually or systematically. However, the RNAi pathway has been lost in evolution by a variety of eukaryotes including most Leishmania sp. RNAi was retained in species of the

Correction: Evidence For The Effects Of Decommissioning Man-Made Structures On Marine Ecosystems Globally: A Systematic Map (Environmental Evidence, (2022), 11, 1, (35), 10.1186/S13750-022-00285-9), Anaëlle J. Lemasson, Paul J. Somerfield, Michaela Schratzberger, Caroline Louise Mcneill, Joana Nunes, Christine Pascoe, Stephen C.L. Watson, Murray S.A. Thompson, Elena Couce, Antony M. Knights

School of Biological and Marine Sciences

In the original publication of the article [1], the authors identified that the caption of the Additional files 3 and 4 has been swapped. Correct captions are: Additional file 3. Lists of articles included, unobtainable or excluded at full text screening with reasons for exclusion. Additional file 4. DREAMS systematic map database. The Original article has been corrected.

Interventions To Treat And Prevent Postpartum Depression: A Protocol For Systematic Review Of The Literature And Parallel Network Meta-Analyses, David Thomas Monks, Basavaraj Ankalagi, Preet Mohinder Singh, Ebony Carter, Michelle Doering, Meg Guard, Shannon Lenze

2020-Current year OA Pubs

INTRODUCTION: Postpartum depression has costly consequences for the mother, baby, and society. Numerous pharmacological and non-pharmacological interventions are available for the prevention and treatment of postpartum depression. To date, no attempt has been made to synthesize the evidence from comparisons of interventions both within and across these categories.

METHODS: We will perform a systematic review of the literature and perform network meta-analysis of interventions to (a) prevent and (b) treat postpartum depression. This review will include studies of primiparous or multiparous women during pregnancy or within 12 months of delivery of their baby that assess either interventions initiated during pregnancy …

Socioecological Predictors Of Breastfeeding Practices In Rural Eastern Ethiopia, Marina Magalhães, Amanda Ojeda, Karah Mechlowitz, Kaitlin Brittain, Jenna Daniel, Kedir Teji Roba, Jemal Yousuf Hassen, Mark J Manary, Wondwossen A Gebreyes, Arie H Havelaar, Sarah L Mckune

2020-Current year OA Pubs

BACKGROUND: Estimates by the World Health Organization indicate that over 800,000 global neonatal deaths each year are attributed to deviations from recommended best practices in infant feeding. Identifying factors promoting ideal breastfeeding practices may facilitate efforts to decrease neonatal and infant death rates and progress towards achieving the Sustainable Development Goals set for 2030. Though numerous studies have identified the benefits of breastfeeding in reducing the risk of childhood undernutrition, infection and illness, and mortality in low- and middle-income countries, no studies have explored predictors of breastfeeding practices in rural eastern Ethiopia, where undernutrition is widespread. The aim of this …

Forest Therapy For Anxiety, Fiteh Yelekal, Nipa Doshi

Transformative Medicine

No abstract provided.

Book Review Essay: Korean “Comfort Women”: Military Brothels, Brutality, And The Redress Movement, Ñusta Carranza Ko

Journal of International Women's Studies

No abstract provided.

Listen To The Voices Of The Women, Judith Mirkinson

Journal of International Women's Studies

Using survivor testimonies, military records and statements from human rights organizations, this paper lays out the undeniable truth of the “comfort women” system. This truth is recognized by the international community and maintains that the Japanese government and Japanese Imperial Army instituted and maintained the largest system of sexual slavery in the 20th century. These testimonies provide the factual counterpoint to the historical denialism of Harvard Professor J. Mark Ramseyer as well as the Japanese government. The “comfort women” survivors’ experiences, since breaking a 40-year silence in the 1990s, manifest a resilience and sense of purpose in demanding an accounting …

Ramseyer, The Japanese Right-Wing And The “History Wars”, Tomomi Yamaguchi

Journal of International Women's Studies

J. Mark Ramseyer’s publications on the topics of wartime “comfort women” and Japan’s minorities have become the focus of intense controversy. His article on “comfort women” in the International Review of Law and Economics gained global scrutiny following its coverage in Japan’s right-wing newspaper, Sankei Shimbun, and its English-language publication, Japan Forward. Ramseyer claims that “comfort women” willingly entered into sex-work contracts, denying responsibility by Japan’s military and government for the “comfort station” system. He also insists that naming this system “sexual slavery” is “pure fiction” – a stance shared by Japanese history denialists in Japan. Since the controversy over …

Ramseyer’S History Denialism And The Efforts To “Save Ramseyer”: Focusing On Critique Of “A Response To My Critics” (2022), Sung Hyun Kang

Journal of International Women's Studies

This article focuses on Ramseyer’s “Contracting for Sex in the Pacific War: A Response to My Critics.” Ramseyer did not accept critiques that evaluated his claims, logic, and empirical methods for denialism in document analysis as lacking academic integrity and research sincerity. His response is mostly limited to the issue of “contractual structure at the wartime ‘comfort stations,’” and addressing the idea that women were never “forcibly conscripted at gunpoint or hauled away against their will.” He continues to argue that women were not “forcibly conscripted” because they agreed on “indentured servitude” contracts based on “credible commitments,” which represent “choices” …

My Response To Ramseyer’S Effort To Deny The History Of Japanese Military Sexual Slavery, Pyong Gap Min

Journal of International Women's Studies

The main objective of this paper is to critically evaluate as many of Ramseyer’s arguments as possible included in his 2022 paper. It consists of three sections in addition to the introduction and concluding remarks. The first section summarizes the expanded literature that interpreted the “comfort women” system as sexual slavery, judgments, and recommendations to the Japanese government given by scholars, international human rights organizations and the legislative branches of four Western countries. Since Ramseyer published his article denying the “comfort women” system as sexual slavery without introducing this literature, we cannot consider his article as an academic work. The …

Introduction: A Critical Evaluation Of Mark Ramseyer’S Arguments For “Comfort Women” As Voluntary Prostitutes With Labor Contracts, Pyong Gap Min

Journal of International Women's Studies

No abstract provided.

Comparison Of Bone Thickness In Infrazygomatic Crest Area At Various Miniscrew Insertion Angles: A Cone-Beam Computed Tomographic Study, Rajju Dangal, Rabindra Man Shrestha, Jyoti Dhakal, Sujita Shrestha, Alka Gupta, Shreya Shah

Taiwanese Journal of Orthodontics

Introduction: The infrazygomatic crest (IZC) is an alternative site for miniscrew anchorage. It is important to analyze the anatomy of the region during preoperative planning to minimize the risk of unwanted tooth movement and injury to the vital structures. The literatures on the clinical application of miniscrew in IZC is scarce. Objective: To determine bone thickness, height and angle of insertion of miniscrew in the IZC region. Materials and methods: This cross-sectional observational comparative study included 44 patients above18 years. IZC bone thickness and height of miniscrew insertion were measured on cone-beam computed tomographic (CBCT) records. Student t-test was done …

2022-12-27_Michiganoverview_Covidlongtermcare, Michigan Department Of Health & Human Services

Michigan COVID-19 Long Term Care Data

The COVID Long Term Care Facilities page was obtained from Michigan's COVID-19 data page: https://www.michigan.gov/coronavirus/stats/data-about-places/long-term-care-data.

This report is created by the Michigan Department of Health & Human Services from data self-reported by long-term care facilities into EMResource. Data for all reporting facilities is posted weekly each Monday.

The information below represents COVID-19 data reported directly to MDHHS by licensed and operating Skilled Nursing, Home for the Aged and Adult Foster Care facilities (licensed to serve 13 or more individuals) in Michigan from January 1, 2020. All long-term care facilities additionally have an obligation to report COVID-positive residents and/or staff …

Netact: A Computational Platform To Construct Core Transcription Factor Regulatory Networks Using Gene Activity., Kenong Su, Ataur Katebi, Vivek Kohar, Benjamin Clauss, Danya Gordin, Zhaohui S Qin, Radha Krishna Murthy Karuturi, Sheng Li, Mingyang Lu

Faculty Research 2023

A major question in systems biology is how to identify the core gene regulatory circuit that governs the decision-making of a biological process. Here, we develop a computational platform, named NetAct, for constructing core transcription factor regulatory networks using both transcriptomics data and literature-based transcription factor-target databases. NetAct robustly infers regulators' activity using target expression, constructs networks based on transcriptional activity, and integrates mathematical modeling for validation. Our in silico benchmark test shows that NetAct outperforms existing algorithms in inferring transcriptional activity and gene networks. We illustrate the application of NetAct to model networks driving TGF-β-induced epithelial-mesenchymal transition and macrophage …

2022-12-27_Michiganoverview_Covidstats, Michigan Department Of Health & Human Services

Cumulative Michigan COVID-19 Data

The COVID Overview page was obtained from Michigan's main COVID-19 page: https://www.michigan.gov/coronavirus/stats.

The State of Michigan is working around the clock to test and treat COVID-19 patients. Below is the most recent data healthcare experts across the state have compiled. COVID case and testing data will be posted once a week on Tuesdays.

This report is provisional and subject to change. City of Detroit and Wayne County are reported separately. MDHHS began tracking probable cases April 5, 2020. FCI indicates federal correctional institute. MDOC indicates Michigan Department of Corrections. Diagnostic tests, including nucleic acid amplification/real-time polymerase chain reaction (NAAT/RT-PCR) …

2022-12-27_Michiganoverview_Covidcounts, Michigan Department Of Health & Human Services

Michigan COVID-19 Confirmed Cases by Date of Onset Data

Data was downloaded as an Excel spreadsheet which appeared in the Public Use Datasets section under the Cumulative Data link of Michigan's Coronavirus webpage, under the url https://www.michigan.gov/coronavirus/stats.

Cases are aggregated by the date of onset of COVID-19 symptoms, if known, otherwise by laboratory specimen date if known, otherwise by case referral date. Deaths are aggregated by the date of death if known, otherwise by the last date of a change to the case status.

Keithrollin Thompson V. Septa

2022 Decisions

USDC for the Eastern District of Pennsylvania

Prinyah Godiah Payne El-Bey V. Amazon Llc

2022 Decisions

USDC for the District of New Jersey

2022-12-27_Michiganoverview_Isdreporting, Michigan Department Of Health & Human Services

Michigan COVID-19 Outbreak Reports

The K-12 Aged ISD Reporting page was obtained from Michigan's COVID-19 data page: https://www.michigan.gov/coronavirus/stats/k-to-12-aged-isd-reporting.

This report is created from data reported by the Michigan Disease Surveillance System (MDSS) the Michigan Department of Health and Human Services' web-based communicable disease reporting system. Data is updated every week.

The purpose of the dashboard is to report the 7 day average of COVID-19 cases in Michigan school students aged 5 through 18 at the intermediate school district and school district levels, as well as display trends over time to better illustrate the changing nature of the COVID-19 pandemic. Cases are attributed to …

Prostate Cancer Malignancy Detection And Localization From Mpmri Using Auto-Deep Learning As One Step Closer To Clinical Utilization, Weiwei Zong, Eric Carver, Simeng Zhu, Eric Schaff, Daniel Chapman, Joon K. Lee, Hassan Bagher-Ebadian, Benjamin Movsas, Winston Wen, Tarik Alafif, Xiangyun Zong

Radiation Oncology Articles

Automatic diagnosis of malignant prostate cancer patients from mpMRI has been studied heavily in the past years. Model interpretation and domain drift have been the main road blocks for clinical utilization. As an extension from our previous work we trained on a public cohort with 201 patients and the cropped 2.5D slices of the prostate glands were used as the input, and the optimal model were searched in the model space using autoKeras. As an innovative move, peripheral zone (PZ) and central gland (CG) were trained and tested separately, the PZ detector and CG detector were demonstrated effective in highlighting …

Tourist Accommodation Demand Vs. Blue Flag Award: Review And A Simple Empirical Approach To Bivariate Trends In The South-East Of Spain, Javier Alarcon

Journal of Mediterranean Tourism Research

An analytical review of the literature on the effect of the Blue Flag eco-label on tourism demand reveals clear divergences. Certain free sources provide valuable panel data to study trends over time in Blue Flag awards to beaches, on one side, and the demand for accommodation in bathing season, on the other. These data also serve as a basis for the construction of correlation models, such as the simple approach tested here in a representative territory of sun&beach tourism, on the south and east coasts of Spain. As a result, these two variables follow a similar trend, and the Blue …

Aspen Leaves As A "Chemical Landscape" For Fungal Endophyte Diversity - Can Nitrogen And Herbivory Shape The Community Composition In Controlled Conditions?, Johanna Witzell, Vicki Huizu Guo Decker, Marta Agostinelli, Carmen Romeralo Tapia, Michelle Cleary, Benedicte Riber Albrectsen

Aspen Bibliography

The endophytic microbiome may influence the ecological performance of plants, including forest trees. Various abiotic and biotic factors may shape the endophyte communities directly but also indirectly, by modifying the quality of host plants as a substrate. We hypothesized that potentially antifungal or fungistatic condensed tannins (CTs) would determine the quality of aspen (Populus tremula) leaves as a substrate for endophytic fungi. By subjecting the plants to nitrogen fertilization (N) or herbivory (H; leaf beetles) we aimed to change the internal “chemical landscape”, especially the CT levels, in aspen leaves. We expected that this would lead to changes in the …

Financing Benefits And Barriers To Routine Hiv Screening In Clinical Settings In The United States: A Scoping Review, Hani Serag, Isabel Clark, Cherith Naig, David Lakey, Yordanos M. Tiruneh

School of Medicine Faculty Publications and Presentations

The Centers for Disease Control and Prevention recommends everyone between 13--64 years be tested for HIV at least once as a routine procedure. Routine HIV screening is reimbursable by Medicare, Medicaid, expanded Medicaid, and most commercial insurance plans. Yet, scaling-up HIV routine screening remains a challenge. We conducted a scoping review for studies on financial benefits and barriers associated with HIV screening in clinical settings in the U.S. to inform an evidence-based strategy to scale-up routine HIV screening. We searched Ovid MEDLINE®, Cochrane, and Scopus for studies published between 2006-2020 in English. The search identified 383 Citations; we screened 220 …

Sr Flip-Flop Based Physical Unclonable Functions For Hardware Security, Srinivas Katkoori, Rohith Prasad Challa, Sheikh Ariful Islam

USF Patents

The present disclosure presents various systems and methods for implementing a physical unclonable function device. One such method comprises providing an integrated circuit having a plurality of set/reset flip flop logic circuits, wherein each of the set/reset flip flop logic circuits enters a metastable state for a particular input sequence. The method includes varying circuit parameters for each of the plurality of set/reset flip flop logic circuits to account for manufacturing variations in the set/reset flip flop logic circuits and enable generating a stable but random output in response to the particular input sequence. Thus, by applying the particular input …

Modified Ube3a Gene For A Gene Therapy Approach For Angelman Syndrome, Kevin Ron Nash, Edwin John Weeber, Jennifer Leigh Daily

USF Patents

Angelman Syndrome (AS) is a genetic disorder occurring in approximately one in every 15,000 births. It is characterized by severe mental retardation, seizures, difficulty speaking and ataxia. The gene responsible for AS was discovered to be UBE3A and encodes for E6-AP, an ubiquitin ligase. A unique feature of this gene is that it undergoes maternal imprinting in a neuron-specific manner. In the majority of AS cases, there is a mutation or deletion in the maternally inherited UBE3A gene, although other cases are the result of uniparental disomy or mismethylation of the maternal gene. While most human disorders characterized by severe …

Structure-Based Rational Design Of Small Α-Helical Peptides With Broad-Spectrum Activity Against Multidrug-Resistant Pathogens, Sandeep Lohan, Anastasia G. Konshina, Roman G. Efremov, Innokentiy Maslennikov, Keykavous Parang

Pharmacy Faculty Articles and Research

A series of small (7–12 mer) amphipathic cationic peptides were designed and synthesized to create short helical peptides with broad-range bactericidal activity and selectivity toward the bacterial cells. The analysis identified a lead 12-mer peptide 8b with broad-spectrum activity against Gram-positive (MIC = 3.1–6.2 μg/mL) and Gram-negative (MIC = 6.2–12.5 μg/mL) bacteria and selectivity toward prokaryotic versus eukaryotic cells (HC50 = 280 μg/mL, >75% cell viability at 150 μg/mL). The rapid membranolytic action of 8b was demonstrated by a calcein dye leakage assay and confirmed using scanning electron microscopy. According to circular dichroism and NMR spectroscopy, the peptides have an …

Leadership Doctorates Newsletter: Volume 8, Number 4, Larry Starr, Phd

Leadership Doctorates Newsletter (Formerly Strategic Leadership Newsletter)

In this Issue:

• Congratulations to Dr. Andrew Braverman and Dr. Michael Jones
• Complex and Strategic Leaders who have Graduated with DMgt or PhD Degree
• Emerging Complex and Strategic Leaders Working Toward Degree Completion
• Updated Doctoral Candidate Status
• Our New Home is the School of Business in the College of Design, Engineering and Commerce About the
• Academic Appointments Update: Larry Starr
• Strategic Leadership and Complex Systems Leadership Alumni
• Alumni Profiles : Reverend Dr. Valerie Andrews
• Research Project: Reverend Dr. Valerie Andrews
• Research Project: Carol Haines
• Congratulations to Derek Hunsberger

Do Academic Supervisors Know What Their Employees Want From Work?, Emily Faulconer, John Griffith

Publications

This research has meaning to higher education learning institutions regarding faculty and staff motivation. Effectively motivating employees has captivated management theorists in search of higher morale and higher productivity. This study challenges the assumption by Hersey and Blanchard (1993) based on Lindahl’s (1949) study that supervisors do not know what their employees want from work.

Taking Action: Turning Evolutionary Theory Into Preventive Policies, Orsolya Molnár, Marina Knickel, Christine Marizzi

MANTER: Journal of Parasite Biodiversity

The emerging infectious disease (EID) crisis has been challenging global health security for decades, dealing substantial damage to all socioeconomic landscapes. Control measures have failed to prevent or even mitigate damages from an accelerating wave of EIDs, leading to the emergence and devastation caused by the COVID-19 pandemic. In the wake of the pandemic, we must critically review our public health policies and approaches. Current health security measures are based on the evolutionary theorem of host-parasite coevolution, which falsely deems EIDs as rare and unpredictable. The DAMA protocol (Document, Assess, Monitor, Act) is nested in a novel evolutionary framework that …