Digital Commons Network^™

Understanding The Health-Related Quality Of Life Of People Living With Hiv Based On Sexual Orientation, Rico Januar Sitorus, Nyoman Yudi Antara, Reymart Sangalang, Merry Natalia Panjaitan, Nelsensius Klau Fauk

Kesmas

Human immunodeficiency virus (HIV) infection has detrimental impacts on the lives of different population groups living with HIV, including men who have sex with men (MSM). Using the World Health Organization Quality of Life questionnaire, this study aimed to assess the health-related quality of life of men living with HIV with different sexual orientations and to determine the dominant influential factors. This cross-sectional study involved 206 men living with HIV. They were recruited from the Sriwijaya Plus Foundation and a medical facility that provided antiretroviral therapy. The data were analyzed using Chi-square and binomial logistic regression. The analysis showed that …

Structural Model Of The Technological Process Of Storage And Processing Of Oil Raw Materials, N.A Kabulov

Chemical Technology, Control and Management

The technological method of storing and processing oilseed raw materials is structurally modelled in the article. Additionally, it is suggested that the generalized structure be presented as a three-part scheme, consisting of a raw material department, a processing shop, and transportation networks. On the basis of a thorough examination of the characteristics of the constituent parts of the technological complex, a practical model for the problem of the general characteristics of the technological complex is proposed.

Jaml Immunotherapy Targets Recently Activated Tumor-Infiltrating Cd8+ T Cells, Simon Eschweiler, Alice Wang, Ciro Ramírez-Suástegui, Adrian Von Witzleben, Yingcong Li, Serena J Chee, Hayley Simon, Monalisa Mondal, Matthew Ellis, Gareth J Thomas, Vivek Chandra, Christian H Ottensmeier, Pandurangan Vijayanand

Faculty, Staff and Student Publications

Junctional adhesion molecule-like protein (JAML) serves as a co-stimulatory molecule in γδ T cells. While it has recently been described as a cancer immunotherapy target in mice, its potential to cause toxicity, specific mode of action with regard to its cellular targets, and whether it can be targeted in humans remain unknown. Here, we show that JAML is induced by T cell receptor engagement, reveal that this induction is linked to cis-regulatory interactions between the CD3D and JAML gene loci. When compared with other immunotherapy targets plagued by low target specificity and end-organ toxicity, we find JAML to be mostly …

Recovering False Negatives In Crispr Fitness Screens With Jloe, Merve Dede, Traver Hart

Faculty, Staff and Student Publications

It is widely accepted that pooled library CRISPR knockout screens offer greater sensitivity and specificity than prior technologies in detecting genes whose disruption leads to fitness defects, a critical step in identifying candidate cancer targets. However, the assumption that CRISPR screens are saturating has been largely untested. Through integrated analysis of screen data in cancer cell lines generated by the Cancer Dependency Map, we show that a typical CRISPR screen has a ∼20% false negative rate, in addition to library-specific false negatives. Replicability falls sharply as gene expression decreases, while cancer subtype-specific genes within a tissue show distinct profiles compared …

Prognostic Significance Of Acellular Mucin In Patients Undergoing Cytoreductive Surgery And Hyperthermic Intraperitoneal Chemotherapy (Crs/Hipec) For Appendiceal Neoplasms, Derek J Erstad, Kristen A Robinson, Karen Beaty, Safia Rafeeq, Yi-Ju Chiang, Kanwal Raghav, John P Shen, Michael J Overman, Wai Chin Foo, Melissa W Taggart, Paul F Mansfield, Richard E Royal, Keith F Fournier, Christopher P Scally

Faculty, Staff and Student Publications

Introduction: Appendiceal neoplasms have a propensity for peritoneal dissemination. The standard of care for select individuals is CRS/HIPEC. In the current 8th AJCC Staging system, a finding of only intraperitoneal acellular mucin (M1a) is classified as Stage IVa. There is concern that the current AJCC system may over-stage patients.

Methods: This was a single-institution retrospective review of 164 cases of mucinous appendiceal neoplasm. Patients undergoing CRS/HIPEC with M1a disease were compared to patients with peritoneal deposits containing tumor cells (well-differentiated adenocarcinoma; low-grade mucinous carcinoma peritonei-M1b,G1). Overall and recurrence-free survival were assessed.

Results: Median age was 51 years, 70% were female, …

Cedar: Incorporating Cell Type Hierarchy Improves Cell Type-Specific Differential Analyses In Bulk Omics Data, Luxiao Chen, Ziyi Li, Hao Wu

Faculty, Staff and Student Publications

Bulk high-throughput omics data contain signals from a mixture of cell types. Recent developments of deconvolution methods facilitate cell type-specific inferences from bulk data. Our real data exploration suggests that differential expression or methylation status is often correlated among cell types. Based on this observation, we develop a novel statistical method named CeDAR to incorporate the cell type hierarchy in cell type-specific differential analyses of bulk data. Extensive simulation and real data analyses demonstrate that this approach significantly improves the accuracy and power in detecting cell type-specific differential signals compared with existing methods, especially in low-abundance cell types.

Allosteric Autoregulation Of Dna Binding Via A Dna-Mimicking Protein Domain: A Biophysical Study Of Znf410-Dna Interaction Using Small Angle X-Ray Scattering, Gundeep Kaur, Ren Ren, Michal Hammel, John R Horton, Jie Yang, Yu Cao, Chenxi He, Fei Lan, Xianjiang Lan, Gerd A Blobel, Robert M Blumenthal, Xing Zhang, Xiaodong Cheng

Faculty, Staff and Student Publications

ZNF410 is a highly-conserved transcription factor, remarkable in that it recognizes a 15-base pair DNA element but has just a single responsive target gene in mammalian erythroid cells. ZNF410 includes a tandem array of five zinc-fingers (ZFs), surrounded by uncharacterized N- and C-terminal regions. Unexpectedly, full-length ZNF410 has reduced DNA binding affinity, compared to that of the isolated DNA binding ZF array, both in vitro and in cells. AlphaFold predicts a partially-folded N-terminal subdomain that includes a 30-residue long helix, preceded by a hairpin loop rich in acidic (aspartate/glutamate) and serine/threonine residues. This hairpin loop is predicted by AlphaFold to …

Determinants And Mechanisms Of The Low Fusogenicity And High Dependence On Endosomal Entry Of Omicron Subvariants, Panke Qu, John P Evans, Chaitanya Kurhade, Cong Zeng, Yi-Min Zheng, Kai Xu, Pei-Yong Shi, Xuping Xie, Shan-Lu Liu

Faculty, Staff and Student Publications

The rapid spread and strong immune evasion of the SARS-CoV-2 Omicron subvariants has raised serious concerns for the global COVID-19 pandemic. These new variants exhibit generally reduced fusogenicity and increased endosomal entry pathway utilization compared to the ancestral D614G variant, the underlying mechanisms of which remain elusive. Here, we show that the C-terminal S1 mutations of the BA.1.1 subvariant, H655Y and T547K, critically govern the low fusogenicity of Omicron. Notably, H655Y also dictates the enhanced endosome entry pathway utilization. Mechanistically, T547K and H655Y likely stabilize the spike trimer conformation as suggested by increased molecular interactions in structural modeling and enhanced …

Low-Altitude Uav Imaging Accurately Quantifies Eelgrass Wasting Disease From Alaska To California, Bo Yang, Timothy L. Hawthorne, Lillian Aoki, Deanna S. Beatty, Tyler Copeland, Lia K. Domke, Ginny L. Eckert, Carla P. Gomes, Olivia J. Graham, C. Drew Harvell, Kevin A. Hovel, Margot Hessing-Lewis, Leah Harper, Ryan S. Mueller, Brendan Rappazzo, Luba Reshitnyk, John J. Stachowicz, Fiona Tomas, J. Emmett Duffy

Faculty Research, Scholarly, and Creative Activity

Declines in eelgrass, an important and widespread coastal habitat, are associated with wasting disease in recent outbreaks on the Pacific coast of North America. This study presents a novel method for mapping and predicting wasting disease using Unoccupied Aerial Vehicle (UAV) with low-altitude autonomous imaging of visible bands. We conducted UAV mapping and sampling in intertidal eelgrass beds across multiple sites in Alaska, British Columbia, and California. We designed and implemented a UAV low-altitude mapping protocol to detect disease prevalence and validated against in situ results. Our analysis revealed that green leaf area index derived from UAV imagery was a …

Association Of IsvSa3 With Multidrug Resistance In Salmonella Enterica Isolates From Cattle (Bos Taurus), Gentry L. Lewis, Robert J. Fenton, Etsuko Moriyama, John Dustin Loy, Rodney A. Moxley

School of Veterinary and Biomedical Sciences: Faculty Publications

Salmonella enterica is, globally, an important cause of human illness with beef being a significant attributable source. In the human patient, systemic Salmonella infection requires antibiotic therapy, and when strains are multidrug resistant (MDR), no effective treatment may be available. MDR in bacteria is often associated with the presence of mobile genetic elements (MGE) that mediate horizontal spread of antimicrobial resistance (AMR) genes. In this study, we sought to determine the potential relationship of MDR in bovine Salmonella isolates with MGE. The present study involved 111 bovine Salmonella isolates obtained collectively from specimens derived from healthy cattle or their environments …

Multifunctional Microgel-Based Cream Hydrogels For Postoperative Abdominal Adhesion Prevention, Bo Liu, Yunfan Kong, Olawale A. Alimi, Mitchell Kuss, Huiyin Tu, Wenfeng Hu, Abu Rafay, Kumar Vikas, Wen Shi, Megan Lerner, William L. Berry, Yulong Li, Mark A. Carlson, Bin Duan

Department of Mechanical and Materials Engineering: Faculty Publications

Postoperative abdominal adhesions are a common problem after surgery and can produce serious complications. Current anti-adhesive strategies focus mostly on physical barriers and are unsatisfactory and inefficient. In this study, we designed and synthesized advanced injectable cream-like hydrogels with multiple functionalities, including rapid gelation, self-healing, anti-oxidation, anti-inflammation, and anti-cellular adhesion. The multifunctional hydrogels were facilely formed by the conjugation reaction of epigallocatechin gallate (EGCG) and hyaluronic acid (HA)-based microgels and polyvinyl alcohol (PVA) based on the dynamic boronic ester bond. The physicochemical properties of the hydrogels including anti-oxidative and anti-inflammatory activities were systematically characterized. A mouse cecum-abdominal wall adhesion model …

Survey Of Mastery Of Basic Skills Of Playing Futsal In 15-17 Year Old Futsal Athletes, Mustofa Aji Prasetyo, Supriatna Supriatna, Taufik Taufik

Indonesian Journal of Research in Physical Education, Sport, and Health

This study aims to determine the level of physical condition of Vasco Futsal Academy players in Lamongan Regency. This research is a type of quantitative descriptive research. The subjects of this study were Vasco Futsal Academy players, totaling 20 people. The data collection process was taken using one FIK Jogja battery tes instrumen which included passing, dribbling, and shooting. Overall, the results of the Vasco Futsal Academy's basic futsal tes results showed 10% “very good”, 15% “good”, 40% “moderate” and 30% “poor”, and 5% “very poor”. The conclusion obtained in this study is that the level of mastery of the …

Single Cell Preparations Of Mycobacterium Tuberculosis Damage The Mycobacterial Envelope And Disrupt Macrophage Interactions, Ekansh Mittal, Andrew T Roth, Anushree Seth, Srikanth Singamaneni, Wandy Beatty, Jennifer A Philips

2020-Current year OA Pubs

For decades, investigators have studied the interaction of

Spectral Sensitivity Near Exceptional Points As A Resource For Hardware Encryption, Minye Yang, Liang Zhu, Qi Zhong, Ramy El-Ganainy, Pai Yen Chen

Michigan Tech Publications, Part 1

The spectral sensitivity near exceptional points (EPs) has been recently explored as an avenue for building sensors with enhanced sensitivity. However, to date, it is not clear whether this class of sensors does indeed outperform traditional sensors in terms of signal-to-noise ratio. In this work, we investigate the spectral sensitivity associated with EPs under a different lens and propose to utilize it as a resource for hardware security. In particular, we introduce a physically unclonable function (PUF) based on analogue electronic circuits that benefit from the drastic eigenvalues bifurcation near a divergent exceptional point to enhance the stochastic entropy caused …

Unpacking The Proteome And Metaproteome Of The Black Soldier Fly Larvae: Efficacy And Complementarity Of Multiple Protein Extraction Protocols, Utpal Bose, Angela Juhasz, Sally Stockwell, Sophia Escobar-Correas, Anna Marcora, Cate Paull, James A. Broadbent, Gene Wijffels

Research outputs 2022 to 2026

The larvae of the black soldier fly (BSF), Hermetia illucens (Diptera: Stratiomyidae), have demonstrated the ability to efficiently bioconvert organic waste into a sustainable source of food and feed, but fundamental biology remains to be discovered to exploit their full biodegradative potential. Herein, LC-MS/MS was used to assess the efficiency of eight differing extraction protocols to build foundational knowledge regarding the proteome landscape of both the BSF larvae body and gut. Each protocol yielded complementary information to improve BSF proteome coverage. Protocol 8 (liquid nitrogen, defatting, and urea/thiourea/chaps) was better than all other protocols for the protein extraction from larvae …

Quantitative Phosphoproteomic Analysis Reveals Unique Camp Signaling Pools Emanating From Ac2 And Ac6 In Human Airway Smooth Muscle Cells, Isabella Cattani-Cavalieri, Yue Li, Jordyn Margolis, Amy S. Bogard, Moom R. Roosan, Rennolds S. Ostrom

Pharmacy Faculty Articles and Research

Human airway smooth muscle (HASM) is the primary target of ßAR agonists used to control airway hypercontractility in asthma and chronic obstructive pulmonary disease (COPD). ßAR agonists induce the production of cAMP by adenylyl cyclases (ACs), activate PKA and cause bronchodilation. Several other G-protein coupled receptors (GPCR) expressed in human airway smooth muscle cells transduce extracellular signals through cAMP but these receptors elicit different cellular responses. Some G-protein coupled receptors couple to distinct adenylyl cyclases isoforms with different localization, partly explaining this compartmentation, but little is known about the downstream networks that result. We used quantitative phosphoproteomics to define the …

The Er Protein Translocation Channel Subunit Sbh1 Controls Virulence Of Cryptococcus Neoformans, Felipe H. Santiago-Tirado, Thomas Hurtaux, Jennifer Geddes-Mcalister, Duy Nguyen, Volkhard Helms, Tamara L Doering, Karin Römisch

2020-Current year OA Pubs

The fungal pathogen Cryptococcus neoformans is distinguished by a cell-wall-anchored polysaccharide capsule that is critical for virulence. Biogenesis of both cell wall and capsule relies on the secretory pathway. Protein secretion begins with polypeptide translocation across the endoplasmic reticulum (ER) membrane through a highly conserved channel formed by three proteins: Sec61, Sbh1, and Sss1. Sbh1, the most divergent, contains multiple phosphorylation sites, which may allow it to regulate entry into the secretory pathway in a species- and protein-specific manner. Absence of

Impact Of Duodenal Pathology On Oral Drug Bioavailability And Disease Outcomes In Pediatric Crohn's Disease., Rebecca Casini, Carrie A. Vyhlidal, Julia M. Bracken, Ashley K. Sherman, Atif Ahmed, Vivekanand Singh, Veronica Williams, Valentina Shakhnovich

Manuscripts, Articles, Book Chapters and Other Papers

Background: Crohn's disease with upper gastrointestinal tract involvement occurs more often in children than adults and has the potential to interfere with oral drug absorption. We aimed to compare disease outcomes in children receiving oral azathioprine for the treatment of Crohn's disease with (DP) and without (NDP) duodenal pathology at diagnosis.

Methods: Duodenal villous length, body mass index (BMI), and laboratory studies were compared in DP vs. NDP during the first year post-diagnosis, using parametric/nonparametric tests and regression analysis (SAS v9.4); the data are reported as the median (interquartile range) or the mean ± standard deviation. Thiopurine metabolite concentration (pmol/8 …

Excess Folic Acid Intake Increases Dna De Novo Point Mutations, Xuanye Cao, Jianfeng Xu, Ying L Lin, Robert M Cabrera, Qiuying Chen, Chaofan Zhang, John W Steele, Xiao Han, Steven S Gross, Bogdan J Wlodarczyk, James R Lupski, Wei Li, Hongyan Wang, Richard H Finnell, Yunping Lei

Faculty, Staff and Students Publications

No abstract provided.

Does The Potocki-Lupski Syndrome Convey The Autism Spectrum Disorder Phenotype? Case Report And Scoping Review, Oksana I Talantseva, Galina V Portnova, Raisa S Romanova, Daria A Martynova, Olga V Sysoeva, Elena L Grigorenko

Faculty, Staff and Students Publications

Potocki-Lupski Syndrome (PTLS) is a rare condition associated with a duplication of 17p11.2 that may underlie a wide range of congenital abnormalities and heterogeneous behavioral phenotypes. Along with developmental delay and intellectual disability, autism-specific traits are often reported to be the most common among patients with PTLS. To contribute to the discussion of the role of autism spectrum disorder (ASD) in the PTLS phenotype, we present a case of a female adolescent with a de novo dup(17) (p11.2p11.2) without ASD features, focusing on in-depth clinical, behavioral, and electrophysiological (EEG) evaluations. Among EEG features, we found the atypical peak-slow wave patterns …

Clic And Membrane Wound Repair Pathways Enable Pandemic Norovirus Entry And Infection, B Vijayalakshmi Ayyar, Khalil Ettayebi, Wilhelm Salmen, Umesh C Karandikar, Frederick H Neill, Victoria R Tenge, Sue E Crawford, Erhard Bieberich, B V Venkataram Prasad, Robert L Atmar, Mary K Estes

Faculty, Staff and Students Publications

Globally, most cases of gastroenteritis are caused by pandemic GII.4 human norovirus (HuNoV) strains with no approved therapies or vaccines available. The cellular pathways that these strains exploit for cell entry and internalization are unknown. Here, using nontransformed human jejunal enteroids (HIEs) that recapitulate the physiology of the gastrointestinal tract, we show that infectious GII.4 virions and virus-like particles are endocytosed using a unique combination of endosomal acidification-dependent clathrin-independent carriers (CLIC), acid sphingomyelinase (ASM)-mediated lysosomal exocytosis, and membrane wound repair pathways. We found that besides the known interaction of the viral capsid Protruding (P) domain with host glycans, the Shell …

Can Undergraduate Artists With No Training In Forensic Art Produce Accurate Age Progressions?, William B. Erickson, James Lampinen, Charlie Frowd, Gregory Mahoney

International Journal of Missing Persons

When children go missing and remain missing for long periods of time, authorities sometimes retain forensic artists to age progress the last known picture to provide an estimate of the current appearance. In the present research, undergraduate artists with no training in forensic art were asked to age progress images of children to an adult appearance. Similarity of age progressions produced by undergraduate artists were as similar to the corresponding targets as were age progressions produced by practicing forensic artists. However, age progressions produced by undergraduate artists were rated as being more similar to description matched foils than were the …

Supporting Mental, Emotional, And Sexual Wellness For Lgbtq+ College Students: A Special Commentary, Devyn Savitsky, Madeleine Stevens, Mahmoud Yacoub

Journal of Counseling Sexology & Sexual Wellness: Research, Practice, and Education

This brief commentary addresses the importance of campus-wide sexual health initiatives for lesbian, gay, bisexual, trans, queer, and other sexual and affectional identities (LGBTQ+) college students. LGBTQ+ college students in the emerging adulthood life stage are particularly susceptible to stigmatized, inequitable physical and mental healthcare, making the need for intentional and affirming support from college counselors, on-campus healthcare providers, and student affairs professionals essential. This article addresses LGBTQ+ friendly communication strategies, specific counseling modalities for work surrounding LGBTQ+ college student sexual health, implications for counselor education and supervision, as well as ongoing research priorities for college counselors. Because sexual health …

Incorporating Sexual Health Content Into The Rehabilitation Counseling Graduate Program Curriculum: A Special Commentary, Kenneth C. Hergenrather, Nichole Tichy, Maureen Mcguire-Kuletz

Journal of Counseling Sexology & Sexual Wellness: Research, Practice, and Education

Sexual health is considered a state of physical, emotional, mental, and social well-being (World Health Organization, 2006). Persons with disabilities are likely to be presumed as sexually inactive, asexual (Rico Alonso et al., 2021; Sant Angelo, 2000), or sexually deviant (Earle, 2001), often leading to their lack of sexual education, an increased risk of sexual exploitation, unwanted pregnancy, or sexually transmitted infections (STIs; Doughty et al., 2017). This commentary addresses three priorities for rehabilitation counseling graduate program curriculum. Clinical priorities should focus on providing persons with disabilities information and education regarding sexual health and wellness. Training priorities should focus on …

Can Tilt Be Used To Teach Study Tactics? A Case Study In A Biology Classroom, Anne Jacobs

Perspectives In Learning

Recently, there has been a movement encouraging instructors in higher education to use the Transparency in Teaching and Learning (TILT) framework when designing assignments. This framework helps instructors clarify their expectations and evaluation criteria. Making assignments more transparent may result in greater student success. However, it is less clear how this framework can be applied to classes that use exams as a main method of assessing student learning. One option might be to use a TILTed assignment to introduce students to learning tools to improve their studying. I did this by giving students in an introductory biology class an assignment …

Salty Genes: Rapid Discovery Of Salt Tolerance Genes In The Bacteria Kushneria, Andrew Jenkins, Brent Nielson, Jonathon T. Hill

Library/Life Sciences Undergraduate Poster Competition 2023

1st place poster design

Global rising levels of soil salinity have led researchers to seek microbial solutions to increase agricultural plant viability in high salt soils.

Kushneria increases growth of inoculated alfalfa in high salt soils, but little is known about how Kushneria survives in these environments1 or how it can be used to reduce the economic burden of salted soil.

An Investigation Of Gold Open Access Publications Of Stem Faculty At A Public University In The United States, Daniel G. Kipnis, Denise Brush

Libraries Scholarship

This study investigated Gold Open Access journal publication by science and engineering faculty at the authors’ university from 2013 to 2022. Specifically, did Gold Open Access (OA) by these faculty increase, and did the publication rate vary between disciplines? The authors found that Gold OA publication increased by 176% over the past 10 years, and that an important factor was the Libraries’ creation of an Open Access Publishing Fund in 2017. Disciplinary differences in publication rates were also notable, with life sciences research showing the highest rates of open access publication. An analysis of where our faculty are publishing found …

The Rider (2023-02-27), Verilu Infante

The Rider Archives

Vol.8 No.21

Geogenomics: Seeking Diamonds In The Desert, Matt Windsor

Browse All News

No abstract provided.

The Impact Of Transparent Instructions Upon Academic Confidence And Writing Performance, Ellen Cotter, Kerri Ann Battle, Cedarian Holsendolph, Jonathan Nguyen, Annabelle P. Smith

Perspectives In Learning

Recent demographic changes in college enrollment have led to an increased emphasis on retaining students. High-impact practices such as transparent assignments are one possible way to encourage student retention, but more empirical data related to student outcomes are needed. In this quasi-experimental study, students received either transparent or standard instructions for written assignments and completed a survey of academic confidence. A pre-test/post-test design was used to examine potential differences associated with instruction type. Results indicated no significant differences in essay scores or survey responses between conditions, and there were no consistent trends indicating improved performance in the transparent condition. Implications …