Medical Specialties Commons^™

A Machine Learning-Based Method For Automatically Identifying Novel Cells In Annotating Single-Cell Rna-Seq Data, Ziyi Li, Yizhuo Wang, Irene Ganan-Gomez, Simona Colla, Kim-Anh Do

Faculty, Staff and Student Publications

MOTIVATION: Single-cell RNA sequencing (scRNA-seq) has been widely used to decompose complex tissues into functionally distinct cell types. The first and usually the most important step of scRNA-seq data analysis is to accurately annotate the cell labels. In recent years, many supervised annotation methods have been developed and shown to be more convenient and accurate than unsupervised cell clustering. One challenge faced by all the supervised annotation methods is the identification of the novel cell type, which is defined as the cell type that is not present in the training data, only exists in the testing data. Existing methods usually …

Standards In Semen Examination: Publishing Reproducible And Reliable Data Based On High-Quality Methodology, Lars Björndahl, Christopher L R Barratt, David Mortimer, Ashok Agarwal, Robert J Aitken, Juan G Alvarez, Natalie Aneck-Hahn, Stefan Arver, Elisabetta Baldi, Lluís Bassas, Florence Boitrelle, Riana Bornman, Douglas T Carrell, José A Castilla, Gerardo Cerezo Parra, Jerome H Check, Patricia S Cuasnicu, Sally Perreault Darney, Christiaan De Jager, Christopher J De Jonge, Joël R Drevet, Erma Z Drobnis, Stefan S Du Plessis, Michael L Eisenberg, Sandro C Esteves, Evangelini A Evgeni, Alberto Ferlin, Nicolas Garrido, Aleksander Giwercman, Ilse G F Goovaerts, Trine B Haugen, Ralf Henkel, Lars Henningsohn, Marie-Claude Hofmann, James M Hotaling, Piotr Jedrzejczak, Pierre Jouannet, Niels Jørgensen, Jackson C Kirkman Brown, Csilla Krausz, Maciej Kurpisz, Ulrik Kvist, Dolores J Lamb, Hagai Levine, Kate L Loveland, Robert I Mclachlan, Ali Mahran, Liana Maree, Sarah Martins Da Silva, Michael T Mbizvo, Andreas Meinhardt, Roelof Menkveld, Sharon T Mortimer, Sergey Moskovtsev, Charles H Muller, Maria José Munuce, Monica Muratori, Craig Niederberger, Cristian O'Flaherty, Rafael Oliva, Willem Ombelet, Allan A Pacey, Michael A Palladino, Ranjith Ramasamy, Liliana Ramos, Nathalie Rives, Eduardo Rs Roldan, Susan Rothmann, Denny Sakkas, Andrea Salonia, Maria Cristina Sánchez-Pozo, Rosanna Sapiro, Stefan Schlatt, Peter N Schlegel, Hans-Christian Schuppe, Rupin Shah, Niels E Skakkebæk, Katja Teerds, Igor Toskin, Herman Tournaye, Paul J Turek, Gerhard Van Der Horst, Monica Vazquez-Levin, Christina Wang, Alex Wetzels, Theodosia Zeginiadou, Armand Zini

Faculty, Staff and Student Publications

Biomedical science is rapidly developing in terms of more transparency, openness and reproducibility of scientific publications. This is even more important for all studies that are based on results from basic semen examination. Recently two concordant documents have been published: the 6th edition of the WHO Laboratory Manual for the Examination and Processing of Human Semen, and the International Standard ISO 23162:2021. With these tools, we propose that authors should be instructed to follow these laboratory methods in order to publish studies in peer-reviewed journals, preferable by using a checklist as suggested in an Appendix to this article.

The Risks Of Birth Defects And Childhood Cancer With Conception By Assisted Reproductive Technology, Barbara Luke, Morton B Brown, Ethan Wantman, Maria J Schymura, Marilyn L Browne, Sarah C Fisher, Nina E Forestieri, Chandrika Rao, Hazel B Nichols, Mahsa M Yazdy, Susan T Gershman, Caitlin R Sacha, Melanie Williams, Mary K Ethen, Mark A Canfield, Kevin J Doody, Michael L Eisenberg, Valerie L Baker, Carrie Williams, Alastair G Sutcliffe, Melissa A Richard, Philip J Lupo

Center for Medical Ethics and Health Policy Staff Publications

Study question: Is there an association between fertility status, method of conception and the risks of birth defects and childhood cancer?

Summary answer: The risk of childhood cancer had two independent components: (i) method of conception and (ii) presence, type and number of birth defects.

What is known already: The rarity of the co-occurrence of birth defects, cancer and ART makes studying their association challenging. Prior studies have indicated that infertility and ART are associated with an increased risk of birth defects or cancer but have been limited by small sample size and inadequate statistical power, failure to adjust for …

Steroid Receptor Coactivator-3 Inhibition Generates Breast Cancer Antitumor Immune Microenvironment, Sang Jun Han, Nuri Sung, Jin Wang, Bert W O'Malley, David M Lonard

Faculty, Staff and Students Publications

BACKGROUND: The tumor immune microenvironment (TIME) generated by cancer-infiltrating immune cells has a crucial role in promoting or suppressing breast cancer progression. However, whether the steroid receptor coactivator-3 (SRC-3) modulates TIME to progress breast cancer is unclear. Therefore, the present study evaluates whether SRC-3 generates a tumor-promoting TIME in breast tumors using a syngeneic immune-intact mouse model of breast cancer.

METHODS: We employed E0771 and 4T1 breast cancer in immune-intact syngeneic female C57BL/6 and BALB/c mice, respectively. SI-2, a specific small-molecule inhibitor of SRC-3, was administered daily (2.5 mg/kg) to E0771 and 4T1 breast tumor-bearing immune-intact mice. In addition, SRC-3 …

The Importance Of An Early Onset Of Migraine Preventive Disease Control: A Roundtable Discussion, Christopher Gottschalk, Anirban Basu, Andrew Blumenfeld, Bradley Torphy, Michael J. Marmura, Jelena M. Pavlovic, Paula K. Dumas, Nim Lalvani, Dawn C. Buse

Department of Jefferson Headache Center Papers and Presentations

Background: Newly approved migraine preventive therapies have allowed for rapid control of migraine activity, offering potential to minimize the burden of migraine. This report summarizes a roundtable discussion convened to analyze evidence for early onset of prevention, ascertain its clinical relevance, and provide guidance for healthcare professionals in crafting goals and treatment expectations for patients with migraine initiating preventive therapy.

Methods: A virtual roundtable meeting of migraine clinicians, researchers, and patient advocates convened in October 2020. Participants reviewed and discussed data summarizing patient and healthcare professional perceptions of migraine prevention and evidence from the peer-reviewed and gray literature to develop …

Developing A Virtual Global Dermatology Curriculum: Qualitative Analysis Based On A Pilot Study In Ethiopia, Rishab Revankar, Aditya Sood, Heli Patel, Kassahun Bilcha, Annisa Befekadu, Howa Yeung, Benjamin Stoff

Department of Dermatology and Cutaneous Biology Faculty Papers

No abstract provided.

Quantification Of Pulmonary Artery Configuration After The Arterial Switch Operation: A Pilot Study, Thomas Martens, Gillian Claeys, Joachim De Groote, Meletios Kanakis, Martin Kostolny, Victor Tsang, Marina Hughes

Faculty, Staff and Student Publications

BACKGROUND: The arterial switch operation (ASO) is the preferred treatment for d-transposition of the great arteries (TGA). Freedom from reintervention is mainly determined by the performance of the arterial outflow tracts, with variable incidence of pulmonary artery stenosis (PAS), possibly related to aspects of surgical technique. This pilot study attempts to describe pulmonary artery (PA) configuration through several measurements using three-dimensional data from cardiac magnetic resonance (CMR) imaging and assesses whether PA configuration is associated with PAS.

METHODS: A retrospective, single-centre analysis of paediatric patients undergoing CMR after ASO. The geometry of the pulmonary arteries was compared between patients with …

Successful Long-Term Anticoagulation With Low Molecular Weight Heparin In A Patient With Mechanical Mitral Valve And Atrial Flutter, Narjis Aljaziri, Meshail Saleh Alkhaleel, Norah Alrajhi, Mohammed Alghamdi, Ahmed Aljizeeri

Journal of the Saudi Heart Association

Mechanical heart valves are associated with high risk of thrombosis and thromboembolic complications. Vitamin K antagonist is the only approved oral medication for the anticoagulation in cases of mechanical heart valves. This poses a challenge in cases where vitamin K antagonists are contraindicated. Although temporary anticoagulation with low molecular weight heparin is common among pregnant patients with mechanical heart valves, data about long term anticoagulation with low molecular weight heparin is limited. We report a successful long-term anticoagulation with low molecular weight heparin in a patient with mechanical mitral valve and atrial flutter.

Desmoglein-2 Is Important For Islet Function And Β-Cell Survival, Kay K. Myo Min, Darling Rojas-Canales, Daniella Penko, Mark Denichilo, Michaelia P. Cockshell, Charlie B. Ffrench, Emma J. Thompson, Olof Asplund, Christopher J. Drogemuller, Rashmi B. Prasad, Leif Groop, Shane T Grey, Helen E. Thomas, Thomas Loudovaris, Thomas W. Kay, My G. Mahoney, Claire F. Jessup, P. Toby Coates, Claudine S. Bonder

Department of Dermatology and Cutaneous Biology Faculty Papers

Type 1 diabetes is a complex disease characterized by the lack of endogenous insulin secreted from the pancreatic β-cells. Although β-cell targeted autoimmune processes and β-cell dysfunction are known to occur in type 1 diabetes, a complete understanding of the cell-to-cell interactions that support pancreatic function is still lacking. To characterize the pancreatic endocrine compartment, we studied pancreata from healthy adult donors and investigated a single cell surface adhesion molecule, desmoglein-2 (DSG2). Genetically-modified mice lacking Dsg2 were examined for islet cell mass, insulin production, responses to glucose, susceptibility to a streptozotocin-induced mouse model of hyperglycaemia, and ability to cure diabetes …

Improv-Ing The Forensic Interview, Nina E. Ross, Karen B. Rosenbaum, Charles L. Scott, Jeffrey Guina, Kendall Genre

Conference Presentation Abstracts

No abstract provided.

Inhibition Of Colorectal Cancer Tumorigenesis By Ursolic Acid And Doxorubicin Is Mediated By Targeting The Akt Signaling Pathway And Activating The Hippo Signaling Pathway, Masashi Fujita, Mei-Ju May Chen, Doris Rieko Siwak, Shota Sasagawa, Ayako Oosawa-Tatsuguchi, Koji Arihiro, Atsushi Ono, Ryoichi Miura, Kazuhiro Maejima, Hiroshi Aikata, Masaki Ueno, Shinya Hayami, Hiroki Yamaue, Kazuaki Chayama, Ju-Seog Lee, Yiling Lu, Gordon B Mills, Han Liang, Satoshi S Nishizuka, Hidewaki Nakagawa

Faculty, Staff and Student Publications

Primary liver cancer is a heterogeneous disease in terms of its etiology, histology, and therapeutic response. Concurrent proteomic and genomic characterization of a large set of clinical liver cancer samples can help elucidate the molecular basis of heterogeneity and thus serve as a valuable resource for personalized liver cancer treatment. In this study, we perform proteomic profiling of ~300 proteins on 259 primary liver cancer tissues with reverse-phase protein arrays, mutational analysis using whole genome sequencing and transcriptional analysis with RNA-Seq. Patients are of Japanese ethnic background and mainly HBV or HCV positive, providing insight into this important liver cancer …

Proteo-Genomic Characterization Of Virus-Associated Liver Cancers Reveals Potential Subtypes And Therapeutic Targets, Masashi Fujita, Mei-Ju May Chen, Doris Rieko Siwak, Shota Sasagawa, Ayako Oosawa-Tatsuguchi, Koji Arihiro, Atsushi Ono, Ryoichi Miura, Kazuhiro Maejima, Hiroshi Aikata, Masaki Ueno, Shinya Hayami, Hiroki Yamaue, Kazuaki Chayama, Ju-Seog Lee, Yiling Lu, Gordon B Mills, Han Liang, Satoshi S Nishizuka, Hidewaki Nakagawa

Faculty, Staff and Student Publications

Primary liver cancer is a heterogeneous disease in terms of its etiology, histology, and therapeutic response. Concurrent proteomic and genomic characterization of a large set of clinical liver cancer samples can help elucidate the molecular basis of heterogeneity and thus serve as a valuable resource for personalized liver cancer treatment. In this study, we perform proteomic profiling of ~300 proteins on 259 primary liver cancer tissues with reverse-phase protein arrays, mutational analysis using whole genome sequencing and transcriptional analysis with RNA-Seq. Patients are of Japanese ethnic background and mainly HBV or HCV positive, providing insight into this important liver cancer …

Patient Satisfaction & Usgpiv, Joey Nguyen

St. Joseph Hospital, Orange, CA. Evidence Based Practice Conference

No abstract provided.

Oncology Referral To Chemotherapy Initiation: Improving Timely Access To Care In Infusion Clinic, Kathy A. Keener

St. Joseph Hospital, Orange, CA. Evidence Based Practice Conference

No abstract provided.

Quality Outcomes Of Alternative Therapies For Treating Depression, Makenna Tsao

St. Joseph Hospital, Orange, CA. Evidence Based Practice Conference

No abstract provided.

Prevent Vascular Access Complications By Adopting A Vascular Access Assessment Improvement Process In The Adultdialysis Unit, Ana Lopez Franco

St. Joseph Hospital, Orange, CA. Evidence Based Practice Conference

No abstract provided.

An Evidence-Based Skin Management Improvement Project In The Intensive Care Unit, Chelsea Lannoo

St. Joseph Hospital, Orange, CA. Evidence Based Practice Conference

No abstract provided.

Use Of Agitation Scale Decision Scoring Grid To Improve Care Of Agitated/Anxious Patients In Dsu, Angelica Taneca, Carmyle Seville

St. Joseph Hospital, Orange, CA. Evidence Based Practice Conference

No abstract provided.

Music Reduces Procedural Anxiety, Marijoyce Dimatulac

St. Joseph Hospital, Orange, CA. Evidence Based Practice Conference

No abstract provided.

Patient Outcomes: Stemi Diagnosis In The Emergency Care Center (Ecc) Resulting In Subsequent Pci Procedures, Laura Derr

St. Joseph Hospital, Orange, CA. Evidence Based Practice Conference

No abstract provided.

Contrast Induced Nephropathy, Tessa Cicchella

St. Joseph Hospital, Orange, CA. Evidence Based Practice Conference

No abstract provided.

Microalbuminuria And Hypertension Among Immigrants With Type 2 Diabetes: A Community-Based Cross-Sectional Study, Shiryn D. Sukhram, Gustavo G. Zarini, Lemia H. Shaban, Joan A. Vaccaro, Fatma G. Huffman

Publications and Research

Purpose: This study examined the association of microalbuminuria (MAU), as determined by albumin-to-creatinine ratio (ACR), with hypertension (HTN) among Turkish immigrants with type 2 diabetes (T2D) living in deprived neighborhoods of The Hague, Netherlands. Methods: A total of 110 participants, physician-diagnosed with T2D, aged ≥ 30 years were recruited from multiple sources from The Hague, Netherlands in a cross-sectional design. Systolic blood pressure (SBP) and diastolic blood pressure (DBP) were measured using automated office blood pressure equipment. Urine albumin was measured by immunoturbidimetric assay. Urine creatinine was determined using the Jaffe method. MAU was defined as ACR ≥ 3.5 mg/mmol …

Watch Your Back: The Risk Of Harm To The Forensic Psychiatrist, Kathleen L. Kruse, Nina E. Ross, Jeffrey Guina, Philip Saragoza, Drew Calhoun

Conference Presentation Abstracts

No abstract provided.

Range-Bounded Adaptive Therapy In Metastatic Prostate Cancer, Renee Brady-Nicholls, Heiko Enderling

Faculty, Staff and Student Publications

Adaptive therapy with abiraterone acetate (AA), whereby treatment is cycled on and off, has been presented as an alternative to continuous therapy for metastatic castration resistant prostate cancer (mCRPC). It is hypothesized that cycling through treatment allows sensitive cells to competitively suppress resistant cells, thereby increasing the amount of time that treatment is effective. It has been proposed that there exists a subset of patients for whom this competition can be enhanced through slight modifications. Here, we investigate how adaptive AA can be modified to extend time to progression using a simple mathematical model of stem cell, non-stem cell, and …

Characterization Of A Bioactive Peptide T14 In The Human And Rodent Substantia Nigra: Implications For Neurodegenerative Disease, Susan Adele Greenfield, Giovanni Ferrati, Clive W Coen, Auguste Vadisiute, Zoltan Molnár, Sara Garcia-Rates, Sally Frautschy, Gregory M Cole

Faculty, Staff and Student Publications

The substantia nigra is generally considered to show significant cell loss not only in Parkinson's but also in Alzheimer's disease, conditions that share several neuropathological traits. An interesting feature of this nucleus is that the pars compacta dopaminergic neurons contain acetylcholinesterase (AChE). Independent of its enzymatic role, this protein is released from pars reticulata dendrites, with effects that have been observed in vitro, ex vivo and in vivo. The part of the molecule responsible for these actions has been identified as a 14-mer peptide, T14, cleaved from the AChE C-terminus and acting at an allosteric site on alpha-7 nicotinic receptors, …

Implementation Of The Texas Community-Engaged Statewide Consortium For The Prevention Of Covid-19, Erika L Thompson, Bettina M Beech, Robert L Ferrer, Lorna H Mcneil, Jasmine J Opusunju, Rebecca A Seguin-Fowler, Emily E Spence, Luis Torres-Hostos, Christopher I Amos, Palak Desai, Jamboor K Vishwanatha

Faculty, Staff and Students Publications

The Community Engagement Alliance (CEAL) Against COVID-19 Disparities aims to conduct community-engaged research and outreach. This paper describes the Texas CEAL Consortium's activities in the first year and evaluates progress. The Texas CEAL Consortium comprised seven projects. To evaluate the Texas CEAL Consortium's progress, we used components of the RE-AIM Framework. Evaluation included estimating the number of people reached for data collection and education activities (reach), individual project goals and progress (effectiveness), partnerships established and partner engagement (adoption), and outreach and education activities (implementation). During the one-year period, focus groups were conducted with 172 people and surveys with 2107 people …

Distinct Organization Of Two Cortico-Cortical Feedback Pathways, Shan Shen, Xiaolong Jiang, Federico Scala, Jiakun Fu, Paul Fahey, Dmitry Kobak, Zhenghuan Tan, Na Zhou, Jacob Reimer, Fabian Sinz, Andreas S Tolias

Duncan NRI Faculty and Staff Publications

Neocortical feedback is critical for attention, prediction, and learning. To mechanically understand its function requires deciphering its cell-type wiring. Recent studies revealed that feedback between primary motor to primary somatosensory areas in mice is disinhibitory, targeting vasoactive intestinal peptide-expressing interneurons, in addition to pyramidal cells. It is unknown whether this circuit motif represents a general cortico-cortical feedback organizing principle. Here we show that in contrast to this wiring rule, feedback between higher-order lateromedial visual area to primary visual cortex preferentially activates somatostatin-expressing interneurons. Functionally, both feedback circuits temporally sharpen feed-forward excitation eliciting a transient increase–followed by a prolonged decrease–in pyramidal …

Cluster Analysis Of Short Sensory Profile Data Reveals Sensory-Based Subgroups In Autism Spectrum Disorder, Ariel M Lyons-Warren, Michael F Wangler, Ying-Wooi Wan

Duncan NRI Faculty and Staff Publications

Autism spectrum disorder is a common, heterogeneous neurodevelopmental disorder lacking targeted treatments. Additional features include restricted, repetitive patterns of behaviors and differences in sensory processing. We hypothesized that detailed sensory features including modality specific hyper- and hypo-sensitivity could be used to identify clinically recognizable subgroups with unique underlying gene variants. Participants included 378 individuals with a clinical diagnosis of autism spectrum disorder who contributed Short Sensory Profile data assessing the frequency of sensory behaviors and whole genome sequencing results to the Autism Speaks’ MSSNG database. Sensory phenotypes in this cohort were not randomly distributed with 10 patterns describing 43% (162/378) …

The Impact Of Obesity And Adipokines On Breast And Gynecologic Malignancies, Surabhi Tewari, Roberto Vargas, Ofer Reizes

Faculty Scholarship

The link between obesity and multiple disease comorbidities is well established. In 2003, Calle and colleagues presented the relationship between obesity and several cancer types, including breast, ovarian, and endometrial malignancies. Nearly, 20% of cancer-related deaths in females can be accounted for by obesity. Identifying obesity as a risk factor for cancer led to a focus on the role of fat-secreted cytokines, known as adipokines, on carcinogenesis and tumor progression. Early studies indicated that the adipokine leptin increases cell proliferation, invasion, and inhibition of apoptosis in multiple cancer types. As a greater appreciation of the obesity–cancer link has amassed, we …

Challenges And Opportunities Associated With The Md Anderson Impact2 Randomized Study In Precision Oncology, Henry Hiep Vo, Siqing Fu, David S Hong, Daniel D Karp, Sarina Piha-Paul, Vivek Subbiah, Filip Janku, Aung Naing, Timothy A Yap, Jordi Rodon, Jaffer A Ajani, Carrie Cartwright, Amber Johnson, I-Wen Song, Jennifer Beck, Michael Kahle, Graciela M Nogueras-Gonzalez, Vincent Miller, Calvin Chao, David J Vining, Donald A Berry, Funda Meric-Bernstam, Apostolia-Maria Tsimberidou

Faculty, Staff and Student Publications

We investigated the challenges of conducting IMPACT2, an ongoing randomized study that evaluates molecular testing and targeted therapy (ClinicalTrials.gov: NCT02152254). Patients with metastatic cancer underwent tumor profiling and were randomized between the two arms when eligibility criteria were met (Part A). In Part B, patients who declined randomization could choose the study arm. In Part A, 69 (21.8%) of 317 patients were randomized; 78.2% were not randomized because of non-targetable alterations (39.8%), unavailability of clinical trial (21.8%), other reasons (12.6%), or availability of US Food and Drug Administration (FDA)-approved drugs for the indication (4.1%). In Part B, 32 (20.4%) of …