Digital Commons Network^™

Vacmap: An Accurate Long-Read Aligner For Unraveling Complex Genomic Rearrangements, Caoimhe Morley, Marco Toffoli, Anthony Hv Schapira, Zhirui Liao, Lianrong Pu, Shanfeng Zhu

Faculty, Staff and Students Publications

Sequence alignment is essential for genomic research and clinical diagnostics, yet detecting complex rearrangements such as inversions, duplications, and gene conversions remains challenging due to allele complexity and limitations of current methods. We introduce VACmap, a non-linear mapping approach to enhance the detection and representation of all genetic variations. VACmap improves duplication detection from 20% to 90% in the Challenging Medically-Relevant Genes (CMRG) benchmark and improves characterization of complex inversions in repetitive regions and gene conversion events. It improves resolving clinically significant loci, including the LPA gene (with repetitive KIV-2 units linked to coronary heart disease), GBA1 and STRC genes …

A Systematic Literature Review Of Cvid Reveals Pervasive Detrimental Noninfectious Manifestations, Hsi-En Ho, Charlotte Cunningham-Rundles, Lisa Forbes Satter, Elena W Y Hsieh, Sinisa Savic, Marta Dafne Cabañero-Navalón, Hector Balastegui-Martin, Joud Hajjar, Gulbu Uzel, Kevin S Thorneloe, Jocelyn R Farmer

Faculty, Staff and Students Publications

Noninfectious manifestations of common variable immunodeficiency (CVID) are not formally summarized. We performed a systematic literature review to generate a comprehensive reference for the field. Splenomegaly was the most reported manifestation across 53 publications, occurring in a median of 35.2% of patients. Frequently reported digestive system manifestations included diarrhea (median 27.8%; 21 publications), hepato(spleno)megaly (median, 21.0%; 19 publications), portal hypertension (median 21.0%; 3 publications), nodular lymphoid hyperplasia (median, 17.0%; 9 publications), and enteropathy (median, 16.0%; 34 publications). Other notable manifestations included interstitial lung disease (median, 8.7%; 32 publications) and autoimmune cytopenias (median 18.0%; 21 publications). Steroids and rituximab were the …

Neurodevelopmental Outcomes Following Hematopoietic Cell Transplantation For Patients With Severe Combined Immunodeficiency (Scid): A Pidtc Study, Farheen Chunara, Jennifer Heimall, Linda M Griffith, Donald B Kohn, Lauren Sanchez, Jeffrey J Bednarski, Caridad Martinez, Mark Vander Lugt, Neena Kapoor, Nicola Wright, Barbara Spitzer, Joseph H Oved, Sharat Chandra, Deepak Chellapandian, Christen L Ebens, Aleks Petrovic, Ahmad Rayes, Hilary L Haines, Hannah Lust, Hannah-Lise Tirado Schofield, Lauren Christopher, Lynnette L Harris, Lisa Forbes Satter, Lauri Burroughs, Christopher C Dvorak, Elie Haddad, Jennifer W Leiding, Rebecca A Marsh, Luigi D Notarangelo, Sung Yun Pai, Michael A Pulsipher, Jennifer M Puck, Morton J Cowan, Ami J Shah

Faculty, Staff and Students Publications

Hematopoietic cell transplantation (HCT) is a potentially curative treatment for severe combined immunodeficiency (SCID). Since the initiation of newborn screening (NBS), survival rates have improved significantly, but the impact of HCT upon neurodevelopment for patients with SCID requires more investigation. We performed a cross-sectional study of subjects with SCID in North America to assess the impact of NBS, transplant conditioning regimen, and genotype on neurodevelopmental outcomes after HCT. 69 subjects with SCID from 17 PIDTC centers (excluding those with ADA deficiency), ages 6-16 years, received comprehensive standardized neurodevelopmental testing of cognitive, behavioral, and emotional function. Compared with the normative population, …

Clinical Performance Of A Novel Point-Of-Care High-Sensitivity Cardiac Troponin I Assay, Alan H B Wu, Stacey L House, Et Al.

2020-Current year OA Pubs

BACKGROUND: High-sensitivity cardiac troponin (hs-cTn) assays performed in the central laboratory have long turnaround times. This study evaluates the clinical performance of a novel bedside point-of-care (POC) hs-cTnI assay (i-STAT® hs-TnI) to aid in the diagnosis of myocardial infarction (MI).

METHODS: A prospective multisite cohort study involving emergency department (ED) patients with symptoms suggestive of acute coronary syndrome was conducted at 28 sites across the United States. Serial whole blood samples were collected at 0-1 h and >1-3 h from ED presentation. Primary outcome was MI or non-MI. Sensitivity, specificity, and negative predictive value (NPV) for MI were calculated with …

Β2 And Β3a Regulatory Subunits Can Coassemble In The Same Bk Channels, Yu Zhou, Vivian Gonzalez-Perez, Xiao-Ming Xia, Gopal S Kallure, Sandipan Chowdhury, Christopher J Lingle

2020-Current year OA Pubs

Ca2+- and voltage-activated BK-type K+ channels are influenced profoundly by associated regulatory subunits, including β subunits (Kcnmb1-4; β1-β4). Although overlap in expression of different BK β subunits occurs in native tissues, whether they can coassemble in the same channel complex is not known. We coexpress β2 and β3a subunits together with BK α and, through a combination of macroscopic and single-channel recordings, along with quantitative pull-down of tagged subunits, test whether coassembly can occur. We evaluate two models: (1) random mixing in which β2 and β3a subunits coassemble in the same channels, and (2) segregation in which β2 and β3a …

Editorial: Cellular Contributors And Consequences Of Protein Misfolding And Aggregation, Anoop Arunagiri, Emily M. Sontag, Verena Kohler, Arunkumar Venkatesan

Biological Sciences Faculty Research and Publications

No abstract provided.

System And Method For Autonomous Cross-Domain Collaborative Artificial Intelligence–Driven Discovery And Innovation, Chiranthan N

Defensive Publications Series

The presented proposal discloses a system and method for autonomous, collaborative artificial intelligence–driven discovery and innovation. The techniques presented herein enables structured interaction among multiple specialized AI software agents, each possessing domain-specific expertise, to perform real-time cross-domain reasoning without continuous human intervention. An interaction controller governs communication, reasoning exchange, and collaboration rules among the agents, while an evaluation module assesses novelty, feasibility, and domain validity of generated outputs. Through iterative feedback and refinement, the proposed system synthesizes knowledge across disciplines to generate robust, non-obvious solutions and inventive outcomes. The proposed architecture overcomes limitations of conventional single-domain and task-parallel AI systems …

Technical-Industrial Feasibility Report — Hci-V1 System (Ionospheric Coherence Harmonizer), Xavier Pillet

Defensive Publications Series

This document, produced with the assistance of GPT-5.2 Thinking and Gemini 3 Reasoning, is released under the Apache License 2.0. It is a voluntary defensive publication (prior art) and therefore enters the prior art upon release under the applicable patent statutes : EPC Art. 54(2) (European Patent Convention), French IPC Art. L 611-11 (French Intellectual Property Code), 35 U.S.C. §102(a) (United States Patent Act), Chinese Patent Law Art. 22(5) (中华人民共和国专利法), and Japanese Patent Act Art. 29(1) (特許法). It discloses 170 enabling technical contributions (systems, methods, devices, materials, QA, cybersecurity, data products, operational protocols, and business-grade mechanisms) to improve GNSS/GPS and …

Systemic Transition Blueprint: From Entropic Fission To Syntropic Fusion (2026–2050), Xavier Pillet

Defensive Publications Series

This document, produced with the assistance of ChatGPT 5.2 Thinking and Gemini 3 Raisonnement, is released under the Apache 2.0 licence. It is a voluntary defensive publication (prior art) and therefore enters the prior art upon release under the applicable patent statutes : EPC Art. 54(2) (European Patent Convention), French PC Art. L 611-11 (French Intellectual Property Code), 35 U.S.C. §102(a) (United States Patent Act), Chinese Patent Law Art. 22(5)(中华人民共和国专利法), and Japanese Patent Act Art. 29(1)(特許法). It provides an enabling technical disclosure (hardware, software, protocols, QA/metrology, cybersecurity, supply chain) for a 2026–2050 blueprint comparing (A) a 100% renewables-plus-storage pathway and …

Navigating Kingship: Sea Power And Sovereignty In Gower's Confessio Amantis, Elizabeth D. Brissey

Accessus

This article examines John Gower’s Apollonius of Tyre in the Confessio Amantis through the lens of the blue humanities, giving special attention to the ways in which the tale treats the sovereign’s maritime domain as integral to the terrestrial. Apollonius depicts sovereignty over aquapelagic space, with the sea serving both as a channel of exchange and as a figurative medium through which sovereignty is negotiated. The crucial issue that aligns the Apollonius tale with the concept of English sovereignty lies in its vision of thalassocratic space in which kingship is grounded in sea power and the sea as a connecting …

Hoccleve Vs. Mowbray: Whose Book Is It?, Joyce Coleman

Accessus

Writing in 1994, Derek Pearsall suggested that, c. 1411-14, the future Henry V had commissioned Thomas Hoccleve to write The Regiment of Princes, and then to oversee the creation of copies to distribute among important courtiers, in “a concerted attempt ... to cement relationships with possibly doubtful friends” (Pearsall 1994: 396).

Ten years earlier, however, Kate Harris had proposed that the arms in the initials under the famous presentation image and on ff. 1 and 71 of London, BL Arundel 38 were all linked to John Mowbray, the future duke of Norfolk—not to the prince and to Thomas FitzAlan, earl …

Scriptor Latinus Morigeris -- Some Aspects Of Gower’S Latin Usage, Mark T. Riley

Accessus

This paper describes the distinctive characteristics of John Gower’s Latin as illustrated primarily by his Vox Clamantis, although his shorter Latin works are occasionally mentioned. Topics include Gower’s Latin education, his extensive Latin vocabulary and mythological references, the paragraphing of his poem, his procedures for using or adapting quotations, as well as his characteristic wordplay and punning. Further topics cover Gower’s medieval use of various verbs, pronouns, and conjunctions, with the accompanying grammatical structures, some of which may present difficulties for the translator. Also included is a section on the meter of the Vox Clamantis, with some notes on …

Preface, Georgiana Donavin, Eve Salisbury

Accessus

Preface for Accessus 9, no. 1.

Integrating Clinical Reasoning Into Mental Health Diagnosis: A Conceptual Framework For Counseling Practice, Ashley F. Waddington, Alexander M. Fields, Haley Ault

Journal of Human Services Scholarship and Interprofessional Collaboration

Clinical reasoning has long guided diagnostic accuracy in nursing and medical fields, but its application in mental health counseling remains limited. This paper presents a conceptual diagnostic decision-making (DDM) process to embed clinical reasoning into the diagnostic process for counselors, incorporating two vital constructs: counselor self-efficacy and counselor bias (implicit and explicit). Grounded in Bandura’s theory of self-efficacy (1977) and Carvalho et al.’s (2017) clinical reasoning model, the framework highlights the cognitive, behavioral, and contextual factors that shape diagnostic decision-making in early-career counselors, including counselor biases. The paper calls for reform in counselor training, emphasizing curriculum enhancements as pathways to …

Micrornas In Prostate Cancer Liquid Biopsies: Early Detection, Prognosis, And Treatment Monitoring, Seyyed Mohammad Yaghoubi, Erfan Zare, Sina Jafari Dargahlou, Maryam Jafari, Mahdiye Azimi, Maedeh Khoshnazar, Solmaz Shirjang, Behzad Mansoori

Student Papers, Posters & Projects

Prostate cancer (PCa) is a common malignancy in men worldwide, with incidence projected to rise in the coming years. Traditional screening and diagnostic methods, such as prostate-specific antigen (PSA) testing and biopsy, face limitations in specificity and invasiveness. Circulating microRNAs (miRNAs) have emerged as stable, non-invasive biomarkers obtainable via liquid biopsies (blood, urine, semen) that could transform PCa management. These small regulatory RNAs reflect underlying tumor biology and are detectable at early disease stages, enabling improved early detection when used alongside or in place of PSA. Distinct miRNA expression patterns correlate with tumor aggressiveness. For example, miR-141 and miR-375 are …

Assessing The Influence Of Audit Committee Characteristics On The Effectiveness Of Risk Management Practices In Public Statutory Corporations In Tanzania, Gerald J. Soi, Siasa Issa Mzenzi, Said Suluo

Business Management Review

This study was conducted to examine the influence of audit committee characteristics on the effectiveness of risk management in Public Statutory Corporations (PSCs) in Tanzania, and the moderating effect of the size of an entity on this relationship. A structured questionnaire was used to collect data, which was completed by 424 chief internal auditors and directors of finance from PSCs across various Tanzanian regions, and analysed using SmartPLS (PLS-SEM) version 4.0. The findings indicate that the expertise of the audit committee and the frequency of meetings with a substantive risk agenda positively influence risk management effectiveness in PSCs. Conversely, the …

State Of California Cannabis Reporting, University Of Mississippi – National Center For Cannabis Research And Education

California

No abstract provided.

Peeling The Onion: A Study Of Audience Reactions To Anti-Classism Satire, Charisse L’Pree Corsbie-Massay, Martina Santia, Luvell Anderson

Department of Political Science and Law Faculty Scholarship and Creative Works

The topics of socioeconomic status, class, and income inequality are integral to human rights. However, media misrepresentation of socioeconomic class and the pervasive national narrative of social mobility inhibit audiences’ ability to understand and mobilize around these issues. Satire can disrupt this cycle by effectively exposing the inconsistencies of class inequality and the flaws of the “American Dream.” Thus, we examine the potential of satire to challenge prevailing attitudes toward class inequality and bolster anti-classism confidence through an online study featuring written satirical articles from The Onion categorized based on style (aggressive vs. benign) and target (individual vs. institutional). Overall, …

The Vision And Mission Of Eapi, Jeyaraj Rasiah, Sj

Asia Pacific Mission Studies

No abstract provided.

Our Eapi Experience—Participants’ Voices, Ms. Cosmeden Tan

Asia Pacific Mission Studies

No abstract provided.

A Tribute To The Founding Figures Of Eapi, Editorial Team

Asia Pacific Mission Studies

No abstract provided.

From Missionary Apologetics To Mission Networking, Arthur Leger, Sj

Asia Pacific Mission Studies

No abstract provided.

From Java To The World: The Faith Of Jan Ruff-O'Herne, Fr. Roderick O’Brien

Asia Pacific Mission Studies

No abstract provided.

You Will See Greater Things Than These (Jn. 1:50), Sr. Merle “Ley” Salazar, Fdnsc

Asia Pacific Mission Studies

No abstract provided.

Front Matter, Volume 8 Number 1

Asia Pacific Mission Studies

No abstract provided.

Editorial Note, Ruben L.F. Habito

Asia Pacific Mission Studies

No abstract provided.

Homily Of Cardinal Filipe Neri Ferrão At The Inaugural Mass Of The 60th Anniversary Of The East Asian Pastoral Institute, Manila, Cardinal Filipe Neri Ferrão

Asia Pacific Mission Studies

No abstract provided.

In Joyful Celebration, Looking To The Future, Fr. Primitivo “Jun” Viray, Sj

Asia Pacific Mission Studies

No abstract provided.

Eapi At Sixty Years: Quo Vadis?, Father Antonio F. Moreno, Sj

Asia Pacific Mission Studies

No abstract provided.

60 Years Of Eapi - Cum Ecclesia, John Chechon Chong, Sj

Asia Pacific Mission Studies

No abstract provided.