Digital Commons Network^™

Opportunities For Helicobacter Pylori Eradication Beyond Conventional Antibiotics, Camilia Metadea Aji Savitri, Kartika Afrida Fauzia, Ricky Indra Alfaray, Hafeza Aftab, Ari Fahrial Syam, Masrul Lubis, Yoshio Yamaoka, Muhammad Miftahussurur

Faculty, Staff and Students Publications

Helicobacter pylori (H. pylori) is a bacterium known to be associated with a significant risk of gastric cancer in addition to chronic gastritis, peptic ulcer, and MALT lymphoma. Although only a small percentage of patients infected with H. pylori develop gastric cancer, Gastric cancer causes more than 750,000 deaths worldwide, with 90% of cases being caused by H. pylori. The eradication of this bacterium rests on multiple drug regimens as guided by various consensus. However, the efficacy of empirical therapy is decreasing due to antimicrobial resistance. In addition, biofilm formation complicates eradication. As the search for new antibiotics …

A Framework For Human Evaluation Of Large Language Models In Healthcare Derived From Literature Review, Thomas Yu Chow Tam, Sonish Sivarajkumar, Sumit Kapoor, Alisa V Stolyar, Katelyn Polanska, Karleigh R Mccarthy, Hunter Osterhoudt, Xizhi Wu, Shyam Visweswaran, Sunyang Fu, Piyush Mathur, Giovanni E Cacciamani, Cong Sun, Yifan Peng, Yanshan Wang

Faculty, Staff and Student Publications

With generative artificial intelligence (GenAI), particularly large language models (LLMs), continuing to make inroads in healthcare, assessing LLMs with human evaluations is essential to assuring safety and effectiveness. This study reviews existing literature on human evaluation methodologies for LLMs in healthcare across various medical specialties and addresses factors such as evaluation dimensions, sample types and sizes, selection, and recruitment of evaluators, frameworks and metrics, evaluation process, and statistical analysis type. Our literature review of 142 studies shows gaps in reliability, generalizability, and applicability of current human evaluation practices. To overcome such significant obstacles to healthcare LLM developments and deployments, we …

Effect Of An In-Home Palivizumab Administration Program For Children With Medical Complexity, Hina Emanuel, Aravind Yadav, Julie C Eapan, Maria Caldas-Vasquez, Tomika S Harris, Katrina Mcbeth, Fatima Boricha, Janice John, Ivan G Magana Ceballos, Giuseppe N Colasurdo, Maria E Tellez, Tina Reddy, Wilfredo De Jesús-Rojas, Ricardo A Mosquera

Faculty, Staff and Student Publications

Background: In-home palivizumab administration programs (PH) have shown promise in reducing RSV-associated infections. These programs may be particularly beneficial for children with medical complexity (CMC) by limiting their exposure to healthcare-associated infections (HAIs) from non-RSV-related pathogens during transportation and visits to medical facilities.

Methods: In this prospective study, 41 children with CMC less than 2 years of age were randomized by their health insurance to receive PH or in the clinic (PC) during the RSV season (October 2018-April 2019). Patients were stratified by home ventilation. The primary outcome was the total number of face-to-face encounters. Secondary outcomes were unscheduled clinic …

Molecular Testing Of Environmental Samples As A Potential Source To Estimate Parasite Infection, Rojelio Mejia, Barton Slatko, Cristina Almazan, Ruben Cimino, Alejandro Krolewiecki, Natalia Montellano Duran, Jacob Edwin Valera Aspetty, Paola Andrea Vargas, Chiara Cássia Oliveira Amorim, Stefan Michael Geiger, Ricardo Toshio Fujiwara, Juan David Ramirez, Luz Marina Llangarí-Arizo, Irene Guadalupe, Liliana E Villanueva-Lizama, Julio Vladimir Cruz-Chan, María Leticia Ojeda, Eva Mereles Aranda, Sandra Ocampos Benedetti, Maritza Dalí Camones Rivera, Eddyson Montalvo Sabino, Carlos Pineda, Eric J Wetzel, Philip J Cooper

Faculty, Staff and Students Publications

We discuss the potential usefulness of molecular testing of soil, dust, and water samples to detect medically important parasites, and where such testing could be used to supplement stool sampling in humans. A wide variety of parasites including protozoa and helminths, many of which are zoonotic, have an important infection reservoir in the environment. In some cases, this environmental period is essential for further parasite development. We describe the progress in implementing methods for the molecular detection of these parasites in soil across eight collaborating centers in Latin America and represent a variety of potential applications in improving our understanding …

A Review Of Studies On Hiv Pre-Exposure Prophylaxis In Community Pharmacies In States With Restrictive Pharmacist Prescription Authority In The United States, Hongmei Wang, Dominique Guinn, Xavier Roshitha Ramisetty, Thomas P Giordano, Ivy O Poon

Faculty, Staff and Students Publications

Community pharmacies have unparalleled potential to increase access to pre-exposure prophylaxis medications (PrEP) for HIV prevention; however, only 17 out of 50 states in the United States have statewide authority for pharmacists to provide PrEP at community pharmacies. Few studies have reported on how pharmacists overcome the legislative barrier and provide PrEP services in restrictive pharmacy prescription states. The objective of this article is to identify the existing primary literature describing pharmacist PrEP services in the community in states with restrictive prescription authority. Methods: A systemic literature review was conducted to identify the primary literature that involved community pharmacy service …

Mta-Cooperative Prmt5 Inhibitors Enhance T Cell-Mediated Antitumor Activity In Mtap-Loss Tumors, Si Chen, Jiakai Hou, Roshni Jaffery, Ashley Guerrero, Rongjie Fu, Leilei Shi, Ningbo Zheng, Ritu Bohat, Nicholas A Egan, Chengtai Yu, Sana Sharif, Yue Lu, Wei He, Shuyue Wang, Donjeta Gjuka, Everett M Stone, Pooja Anil Shah, Jordi Rodon Ahnert, Taiping Chen, Xinli Liu, Mark T Bedford, Han Xu, Weiyi Peng

Faculty, Staff and Student Publications

BACKGROUND: Hyperactivated protein arginine methyltransferases (PRMTs) are implicated in human cancers. Inhibiting tumor intrinsic PRMT5 was reported to potentiate antitumor immune responses, highlighting the possibility of combining PRMT5 inhibitors (PRMT5i) with cancer immunotherapy. However, global suppression of PRMT5 activity impairs the effector functions of immune cells. Here, we sought to identify strategies to specifically inhibit PRMT5 activity in tumor tissues and develop effective PRMT5i-based immuno-oncology (IO) combinations for cancer treatment, particularly for methylthioadenosine phosphorylase (MTAP)-loss cancer.

METHODS: Isogeneic tumor lines with and without MTAP loss were generated by CRISPR/Cas9 knockout. The effects of two PRMT5 inhibitors (GSK3326595 and MRTX1719) were …

Humoral Immunity And Antibody Responses Against Diphtheria, Tetanus, And Pneumococcus After Immune Effector Cell Therapies: A Prospective Study, Georgios Angelidakis, Roy F Chemaly, Pranoti V Sahasrabhojane, Oscar Morado-Aramburo, Ying Jiang, Micah M Bhatti, Elizabeth Shpall, Chitra Hosing, Preetesh Jain, Kris Michael Mahadeo, Fareed Khawaja, Peter Elhajj, Jennifer A Wargo, Robert R Jenq, Nadim J Ajami, Partow Kebriaei, Ella J Ariza-Heredia

Faculty, Staff and Student Publications

Patients undergoing immune effector cell therapy (IECT) are at high risk for infections. We assessed seropositivity against pneumococcus, tetanus, and diphtheria in patients before and after IECT and the patients' response to vaccination. We enrolled patients who underwent IECT from January 2020 to March 2022. Antibody levels for diphtheria, tetanus, and pneumococcus were measured before IECT, at 1 month, and 3-6 months after. Eligible patients were vaccinated after IECT. In non-seroprotected patients, we discontinued testing. Before IECT, most patients had seroprotective antibody levels against tetanus (68/69, 99%) and diphtheria (65/69, 94%), but fewer did against pneumococcus (24/67, 36%). After IECT, …

Association Between Non-Injection Drug Use And Hepatitis C Infection Among Hiv-Negative Men Who Have Sex With Men, Jing Zhao, Charles Green, Christine Markham, Kayo Fujimoto, Alan G Nyitray, Lu-Yu Hwang

Faculty, Staff and Student Publications

Background: Prior research predominantly examined the association between HIV-positive men who have sex with men (MSM) or those using injection drugs and hepatitis C virus (HCV) infection. However, limited attention has been given to understanding the association among HIV-negative MSM who do not inject drugs. This gap leaves apportion of the population unexamined, potentially overlooking important factor that may contribute to the transmission and prevalence of HCV. This study aims to investigate the relationship between non-injection drug use and HCV infection in this population.

Methods: In this cross-sectional study, we analyzed data on 118 MSM who reported use of non-injection …

Gut Phageome In Mexican Americans: A Population At High Risk For Metabolic Dysfunction-Associated Steatotic Liver Disease And Diabetes, Suet-Ying Kwan, Caroline M Sabotta, Lorenzo R Cruz, Matthew C Wong, Nadim J Ajami, Joseph B Mccormick, Susan P Fisher-Hoch, Laura Beretta

Faculty, Staff and Student Publications

Mexican Americans are disproportionally affected by metabolic dysfunction-associated steatotic liver disease (MASLD), which often co-occurs with diabetes. Despite extensive evidence on the causative role of the gut microbiome in MASLD, studies determining the involvement of the gut phageome are scarce. In this cross-sectional study, we characterized the gut phageome in Mexican Americans of South Texas by stool shotgun metagenomic sequencing of 340 subjects, concurrently screened for liver steatosis by transient elastography. Inter-individual variations in the phageome were associated with gender, country of birth, diabetes, and liver steatosis. The phage signatures for diabetes and liver steatosis were subsequently determined. Enrichment of …

Development Of A Maturity Assessment Tool To Evaluate And Strengthen National Immunization Technical Advisory Groups (Nitags), Eliza Dryer, Abigail Shefer, Shalini Desai, Lance Rodewald, Magdalena Bastías, Nathalie El Omeiri, Sidy Ndiaye, Kori Cook, Louise Henaff, Erin Kennedy

Staff and Researcher Publications

As dozens of new National Immunization Technical Advisory Groups (NITAGs) were established worldwide in the past decade, and as existing NITAGs continued to play an important role in vaccine policy, global NITAG partners recognized a need for a standardized assessment tool to evaluate and strengthen their functions. This article describes the development of the NITAG Maturity Assessment Tool (NMAT), a stepwise evaluation tool that assesses NITAGs on seven key indicators of structure and process. A draft tool was developed through an iterative, consensus-based process with an expert working group before it was piloted with an economically and geographically diverse convenience …

Comparison Of Multi-Parallel Quantitative Real-Time Pcrs Targeting Different Dna Regions And Detecting Soil-Transmitted Helminths In Stool, Marina Papaiakovou, Rubén O Cimino, Nils Pilotte, Julia Dunn, D Timothy J Littlewood, Steven A Williams, Alejandro J Krolewiecki, Rojelio Mejia

Faculty, Staff and Students Publications

BACKGROUND: Soil-transmitted helminths infect an estimated 18% of the world's population, causing a significant health burden. Microscopy has been the primary tool for diagnosing eggs from fecal samples, but its sensitivity drops in low-prevalence settings. Quantitative real-time polymerase chain reaction (qPCR) is slowly increasing in research and clinical settings. However, there is still no consensus on preferred qPCR targets.

METHODS: We aimed to compare soil-transmitted helminth (STH) DNA detection methods by testing naïve stool samples spiked with known quantities of STH eggs and larvae. DNA extracts from spiked samples were tested using independent quantitative realtime PCR (qPCR) assays targeting ribosomal …

Expanding The Crispr Base Editing Toolbox In Drosophila Melanogaster, Michael Clark, Christina Nguyen, Hung Nguyen, Aidan Tay, Samuel J Beach, Maciej Maselko, Víctor López Del Amo

Faculty, Staff and Student Publications

CRISPR base editors can introduce point mutations into DNA precisely, and cytosine base editors (CBEs) catalyze C to T transitions. While CBEs have been thoroughly explored in cell culture and organisms such as mice, little is known about DNA base editing in insects. In this study, we evaluated germline editing rates of three different CBEs expressed under actin (ubiquitous) or nanos (germline) promoters utilizing Drosophila melanogaster. The original Rattus norvegicus-derived cytosine deaminase APOBEC1 (rAPO-1) displayed high base editing rates (~99%) with undetectable indel formation. Additionally, we show that base editors can be used for generating male sterility and female lethality. …

Role Of Poly(A)-Binding Protein Cytoplasmic 1, A Trna-Derived Rna Fragment-Bound Protein, In Respiratory Syncytial Virus Infection, Devin V Davis, Eun-Jin Choi, Deena Ismail, Miranda L Hernandez, Jong Min Choi, Ke Zhang, Kashish Khatkar, Sung Yun Jung, Wenzhe Wu, Xiaoyong Bao

Faculty, Staff and Students Publications

Respiratory Syncytial Virus (RSV) is a significant cause of lower respiratory tract infections (LRTI) across all demographics, with increasing mortality and morbidity among high-risk groups such as infants under two years old, the elderly, and immunocompromised individuals. Although newly approved vaccines and treatments have substantially reduced RSV hospitalizations, accessibility remains limited, and response to treatment varies. This underscores the importance of comprehensive studies on host-RSV interactions. tRNA-derived RNA fragments (tRFs) are recently discovered non-coding RNAs, notable for their regulatory roles in diseases, including viral infections. Our prior work demonstrated that RSV infection induces tRFs, primarily derived from the 5'-end of …

Synthesis And Optimization Of Small Molecule Inhibitors Of Prostate Specific Antigen, Jeffery A Erickson, Ravikumar Jimmidi, Prashanth Anamthathmakula, Xuan Qin, Jian Wang, Leyi Gong, Jaehyeon Park, Gary Koolpe, Caitlin Tan, Martin M Matzuk, Feng Li, Srinivas Chamakuri, Wipawee Winuthayanon

Faculty, Staff and Students Publications

Semen liquefaction is a postejaculation process that transforms semen from a gel-like (coagulated) form to a water-like consistency (liquefied). This process is primarily regulated by serine proteases from the prostate gland, most prominently, prostate-specific antigen (PSA; KLK3). Inhibiting PSA activity has the potential to impede liquefaction of human semen, presenting a promising target for nonhormonal contraception in the female reproductive tract. This study employed triazole B1 as a starting compound. Through systematic design, synthesis, and optimization, we identified compound 20 (CDD-3290) as a 216 nM inhibitor of PSA with better stability in media than triazole B1. Further, we also evaluated …

Persistent Tailoring Of Msc Activation Through Genetic Priming, Michael A Beauregard, Guy C Bedford, Daniel A Brenner, Leonardo D Sanchez Solis, Tomoki Nishiguchi, Abhimanyu, Santiago Carrero Longlax, Barun Mahata, Omid Veiseh, Pamela L Wenzel, Andrew R Dinardo, Isaac B Hilton, Michael R Diehl

Faculty, Staff and Student Publications

Mesenchymal stem/stromal cells (MSCs) are an attractive platform for cell therapy due to their safety profile and unique ability to secrete broad arrays of immunomodulatory and regenerative molecules. Yet, MSCs are well known to require preconditioning or priming to boost their therapeutic efficacy. Current priming methods offer limited control over MSC activation, yield transient effects, and often induce the expression of pro-inflammatory effectors that can potentiate immunogenicity. Here, we describe a genetic priming method that can both selectively and sustainably boost MSC potency via the controlled expression of the inflammatory-stimulus-responsive transcription factor interferon response factor 1 (IRF1). MSCs engineered to …

Sensory Dysfunction, Microbial Infections, And Host Responses In Alzheimer's Disease, Praveen Bathini, Emanuele Brai, Brian J Balin, Lynn Bimler, David B Corry, Davangere P Devanand, Richard L Doty, Garth D Ehrlich, William A Eimer, Tamas Fulop, David L Hahn, Christine J Hammond, Joseph Infanti, Ruth Itzhaki, Richard Lathe, Christopher Scott Little, Rima Mcleod, Shima T Moein, Amy R Nelson, George Perry, Or A Shemesh, Rudolph E Tanzi, Wilmore C Webley, Nikki M Schultek, Lavinia Alberi Auber

Faculty, Staff and Students Publications

Sensory functions of organs of the head and neck allow humans to interact with the environment and establish social bonds. With aging, smell, taste, vision, and hearing decline. Evidence suggests that accelerated impairment in sensory abilities can reflect a shift from healthy to pathological aging, including the development of Alzheimer's disease (AD) and other neurological disorders. While the drivers of early sensory alteration in AD are not elucidated, insults such as trauma and infections can affect sensory function. Herein, we review the involvement of the major head and neck sensory systems in AD, with emphasis on microbes exploiting sensory pathways …

Reimagining Critical Care: Trends And Shifts In 21st Century Medicine, Sai Doppalapudi, Bilal Khan, Muhammad Adrish

Faculty, Staff and Students Publications

Critical care medicine has undergone significant evaluation in the 21st century, primarily driven by advancements in technology, changes in healthcare delivery, and a deeper understanding of disease processes. Advancements in technology have revolutionized patient monitoring, diagnosis, and treatment in the critical care setting. From minimally invasive procedures to advances imaging techniques, clinicians now have access to a wide array of tools to assess and manage critically ill patients more effectively. In this editorial we comment on the review article published by Padte S et al wherein they concisely describe the latest developments in critical care medicine.

Identification Of A Clade-Specific Hla-C*03:02 Ctl Epitope Gy9 Derived From The Hiv-1 P17 Matrix Protein, Samuel Kyobe, Savannah Mwesigwa, Gyaviira Nkurunungi, Gaone Retshabile, Moses Egesa, Eric Katagirya, Marion Amujal, Busisiwe C Mlotshwa, Lesedi Williams, Hakim Sendagire, On Behalf Of The Cafgen Consortium, Dithan Kiragga, Graeme Mardon, Mogomotsi Matshaba, Neil A Hanchard, Jacqueline Kyosiimire-Lugemwa, David Robinson

Faculty, Staff and Students Publications

Efforts towards an effective HIV-1 vaccine have remained mainly unsuccessful. There is increasing evidence for a potential role of HLA-C-restricted CD8+ T cell responses in HIV-1 control, including our recent report of HLA-C*03:02 among African children. However, there are no documented optimal HIV-1 CD8+ T cell epitopes restricted by HLA-C*03:02; additionally, the structural influence of HLA-C*03:02 on epitope binding is undetermined. Immunoinformatics approaches provide a fast and inexpensive method to discover HLA-restricted epitopes. Here, we employed immunopeptidomics to identify HLA-C*03:02 CD8+ T cell epitopes. We identified a clade-specific Gag-derived GY9 (GTEELRSLY) HIV-1 p17 matrix epitope potentially restricted to HLA-C*03:02. Residues …

Parasitic Contamination Of Soil In The Southern United States, Christine Crudo Blackburn, Sally Mingshuang Yan, David Mccormick, Lauren Nicholas Herrera, Roumen Borilov Iordanov, Mark Daniel Bailey, Maria Elena Bottazzi, Peter J Hotez, Rojelio Mejia

Faculty, Staff and Students Publications

Parasites are generally associated with lower income countries in tropical and subtropical areas. Still, they are also prevalent in low-income communities in the southern United States. Studies characterizing the epidemiology of parasites in the United States are limited, resulting in little comprehensive understanding of the problem. This study investigated the environmental contamination of parasites in the southern United States by determining each parasite's contamination rate and burden in five low-income communities. A total of 499 soil samples of approximately 50 g were collected from public parks and private residences in Alabama, Louisiana, Mississippi, South Carolina, and Texas. A technique using …

Human Papillomavirus Vaccination And Human Papillomavirus-Related Cancer Rates, Victor Adekanmbi, Itunu Sokale, Fangjian Guo, Jessica Ngo, Thao N Hoang, Christine D Hsu, Abiodun Oluyomi, Abbey B Berenson

Faculty, Staff and Students Publications

IMPORTANCE: To inform the design and implementation of targeted interventions to reduce the future burden of human papillomavirus (HPV)-related cancers in Texas, it is necessary to examine the county and health service region (HSR) levels of (1) the proportion of children and teenagers aged 9 to 17 years who initiated and were up to date for HPV vaccination series and (2) HPV-related cancer incidence rates (IRs).

OBJECTIVE: To evaluate temporal trends and geospatial patterns of HPV vaccination initiation and up-to-date status as well as HPV-related cancer rates at county and HSR levels in Texas.

DESIGN, SETTING, AND PARTICIPANTS: This population-based …

Panel Stacking Is A Threat To Consensus Statement Validity, Kasper P Kepp, Preben Aavitsland, Marcel Ballin, Francois Balloux, Stefan Baral, Kevin Bardosh, Howard Bauchner, Eran Bendavid, Raj Bhopal, Daniel T Blumstein, Paolo Boffetta, Florence Bourgeois, Adam Brufsky, Peter J Collignon, Sally Cripps, Ioana A Cristea, Nigel Curtis, Benjamin Djulbegovic, Oliver Faude, Maria Elena Flacco, Gordon H Guyatt, George Hajishengallis, Lars G Hemkens, Tammy Hoffmann, Ari R Joffe, Terry P Klassen, Despina Koletsi, Dimitrios P Kontoyiannis, Ellen Kuhl, Carlo La Vecchia, Tea Lallukka, John Lambris, Michael Levitt, Spyros Makridakis, Helena C Maltezou, Lamberto Manzoli, Ana Marusic, Clio Mavragani, David Moher, Ben W Mol, Taulant Muka, Florian Naudet, Paul W Noble, Anna Nordström, Peter Nordström, Nikolaos Pandis, Stefania Papatheodorou, Chirag J Patel, Irene Petersen, Stefan Pilz, Nikolaus Plesnila, Anne-Louise Ponsonby, Manuel A Rivas, Andrea Saltelli, Manuel Schabus, Michaéla C Schippers, Holger Schünemann, Marco Solmi, Andreas Stang, Hendrik Streeck, Joachim P Sturmberg, Lehana Thabane, Brett D Thombs, Athanasios Tsakris, Simon N Wood, John P A Ioannidis

Faculty, Staff and Student Publications

Consensus statements can be very influential in medicine and public health. Some of these statements use systematic evidence synthesis but others fail on this front. Many consensus statements use panels of experts to deduce perceived consensus through Delphi processes. We argue that stacking of panel members toward one particular position or narrative is a major threat, especially in absence of systematic evidence review. Stacking may involve financial conflicts of interest, but nonfinancial conflicts of strong advocacy can also cause major bias. Given their emerging importance, we describe here how such consensus statements may be misleading, by analyzing in depth a …

Generative Large Language Models Are All-Purpose Text Analytics Engines: Text-To-Text Learning Is All Your Need, Cheng Peng, Xi Yang, Aokun Chen, Zehao Yu, Kaleb E Smith, Anthony B Costa, Mona G Flores, Jiang Bian, Yonghui Wu

Faculty, Staff and Student Publications

Objective: To solve major clinical natural language processing (NLP) tasks using a unified text-to-text learning architecture based on a generative large language model (LLM) via prompt tuning.

Methods: We formulated 7 key clinical NLP tasks as text-to-text learning and solved them using one unified generative clinical LLM, GatorTronGPT, developed using GPT-3 architecture and trained with up to 20 billion parameters. We adopted soft prompts (ie, trainable vectors) with frozen LLM, where the LLM parameters were not updated (ie, frozen) and only the vectors of soft prompts were updated, known as prompt tuning. We added additional soft prompts as a prefix …

Strategies For The Development Of Metalloimmunotherapies, Xiaoqi Sun, Xingwu Zhou, Xiaoyue Shi, Omar A Abed, Xinran An, Yu Leo Lei, James J Moon

Faculty, Staff and Student Publications

Metal ions play crucial roles in the regulation of immune pathways. In fact, metallodrugs have a long record of accomplishment as effective treatments for a wide range of diseases. Here we argue that the modulation of interactions of metal ions with molecules and cells involved in the immune system forms the basis of a new class of immunotherapies. By examining how metal ions modulate the innate and adaptive immune systems, as well as host-microbiota interactions, we discuss strategies for the development of such metalloimmunotherapies for the treatment of cancer and other immune-related diseases.

Determinant Of 30-Day Mortality Of Pulmonary Legionellosis: Do Coinfections Matter?, Takahiro Matsuo, Sebastian Wurster, Ying Jiang, Jeffrey Tarrand, Scott E Evans, Dimitrios P Kontoyiannis

Faculty, Staff and Student Publications

We retrospectively reviewed 64 cases of cancer with pulmonary legionellosis (Legionella pneumophila in 73%). Nearly all patients received Legionella-active antibiotics, yet 30-day mortality was 23%. Independent predictors of 30-day mortality were hyponatremia, bilateral lung involvement, and Sequential Organ Failure Assessment score ≥5. Lung coinfections were common (31%) but did not significantly increase mortality.

Refai: A Gpt-Powered Retrieval-Augmented Generative Tool For Biomedical Literature Recommendation And Summarization, Yiming Li, Jeff Zhao, Manqi Li, Yifang Dang, Evan Yu, Jianfu Li, Zenan Sun, Usama Hussein, Jianguo Wen, Ahmed M Abdelhameed, Junhua Mai, Shenduo Li, Yue Yu, Xinyue Hu, Daowei Yang, Jingna Feng, Zehan Li, Jianping He, Wei Tao, Tiehang Duan, Yanyan Lou, Fang Li, Cui Tao

Faculty, Staff and Student Publications

Objectives: Precise literature recommendation and summarization are crucial for biomedical professionals. While the latest iteration of generative pretrained transformer (GPT) incorporates 2 distinct modes-real-time search and pretrained model utilization-it encounters challenges in dealing with these tasks. Specifically, the real-time search can pinpoint some relevant articles but occasionally provides fabricated papers, whereas the pretrained model excels in generating well-structured summaries but struggles to cite specific sources. In response, this study introduces RefAI, an innovative retrieval-augmented generative tool designed to synergize the strengths of large language models (LLMs) while overcoming their limitations.

Materials and methods: RefAI utilized PubMed for systematic literature retrieval, …

Beneficial Effects Of Lactobacillus Plantarum On Growth Performance, Immune Status, Antioxidant Function And Intestinal Microbiota In Broilers, Xiao Xiao, Tiantian Cui, Songke Qin, Tao Wang, Jinsong Liu, Lihan Sa, Yanping Wu, Yifan Zhong, Caimei Yang

Faculty, Staff and Student Publications

Lactobacillus plantarum (L. plantarum) has been globally regarded as antibiotic alternative in animal farming in the past few years. However, the potential function of L. plantarum in broilers has not been systemically explored. In this study, a total of 560 one-day-old yellow-feathered broilers were randomly divided into 3 groups, fed with basal diet and drank with L. plantarum HJZW08 (LP) at the concentration of 0 (CON), 1000 × 10^5 (LP1000), and 2000 × 10^5 CFU/L (LP2000) for 70 d. Results showed that the body weight (BW), average daily …

Lessons Learnt From Broad-Spectrum Coronavirus Antiviral Drug Discovery, Andrew A Bolinger, Jun Li, Xuping Xie, Hongmin Li, Jia Zhou

Faculty, Staff and Student Publications

Introduction: Highly pathogenic coronaviruses (CoVs), such as severe acute respiratory syndrome CoV (SARS-CoV), Middle East respiratory syndrome CoV (MERS-CoV), and the most recent SARS-CoV-2 responsible for the COVID-19 pandemic, pose significant threats to human populations over the past two decades. These CoVs have caused a broad spectrum of clinical manifestations ranging from asymptomatic to severe distress syndromes (ARDS), resulting in high morbidity and mortality.

Areas covered: The accelerated advancements in antiviral drug discovery, spurred by the COVID-19 pandemic, have shed new light on the imperative to develop treatments effective against a broad spectrum of CoVs. This perspective discusses strategies and …

Determinant Of 30-Day Mortality Of Pulmonary Legionellosis: Do Coinfections Matter?, Takahiro Matsuo, Sebastian Wurster, Ying Jiang, Jeffrey Tarrand, Scott E Evans, Dimitrios P Kontoyiannis

Faculty, Staff and Student Publications

We retrospectively reviewed 64 cases of cancer with pulmonary legionellosis (Legionella pneumophila in 73%). Nearly all patients received Legionella-active antibiotics, yet 30-day mortality was 23%. Independent predictors of 30-day mortality were hyponatremia, bilateral lung involvement, and Sequential Organ Failure Assessment score ≥5. Lung coinfections were common (31%) but did not significantly increase mortality.

A Prospective Cohort Study Of Pregnancy Outcomes Following Antepartum Infection With Sars-Cov-2, James D Doss, Emily Diveley, Fan Zhang, Amy Scheffer, Ruizhi Huang, Daniel Jackson, Nandini Raghuraman, Ebony B Carter, Indira U Mysorekar, Jeannie C Kelly

Faculty, Staff and Students Publications

Objectives: Our study aimed to explore the impact of COVID-19 infection on pregnancy outcomes, accounting for the progression of variants, vaccines, and treatment modalities.

Study design: We performed a prospective longitudinal cohort study at two urban tertiary centers enrolling patients with a confirmed intrauterine singleton pregnancy from December 23, 2020 to July 18, 2022. Patients were evaluated for SARS-CoV-2 infection at enrollment and every trimester using serum antibody testing. The primary outcome was preterm birth. Symptom and treatment data were collected from pregnant patients with COVID-19 infections. Variant strain infection status was determined from local wastewater analysis.

Results: 448 patients …

Update On The Diagnosis Of Tuberculosis, Irina Kontsevaya, Andrea Maurizio Cabibbe, Daniela Maria Cirillo, Andrew R Dinardo, Nicole Frahm, Stephen H Gillespie, David Holtzman, Lennard Meiwes, Elisa Petruccioli, Maja Reimann, Morten Ruhwald, Wilber Sabiiti, Francesca Saluzzo, Elisa Tagliani, Delia Goletti

Faculty, Staff and Students Publications

Background: Tuberculosis (TB) remains a global public health threat, and the development of rapid and precise diagnostic tools is the key to enabling the early start of treatment, monitoring response to treatment, and preventing the spread of the disease.

Objectives: An overview of recent progress in host- and pathogen-based TB diagnostics.

Sources: We conducted a PubMed search of recent relevant articles and guidelines on TB screening and diagnosis.

Content: An overview of currently used methods and perspectives in the following areas of TB diagnostics is provided: immune-based diagnostics, X-ray, clinical symptoms and scores, cough detection, culture of Mycobacterium tuberculosis and …