bluuebunny/crossref_metadata_2025_split huggingface dataset:
Research Letter: Application of GPT-4 to select next-step antidepressant treatment in major depression
Authors: Perlis Roy H. 
Published: April 2023

AbstractIntroductionLarge language models perform well on a range of academic tasks including medical examinations. The performance of this class of models in psychopharmacology has not been explored.MethodChat GPT-plus, implementing the GPT-4 large language model, was presented with each of 10 previously-studied antidepressant prescribing vignettes in randomized order, with results regenerated 5 times to evaluate stability of responses. Results were compared to expert consensus.ResultsAt least one of the optimal medication choices was included among the best choices in 38/50 (76%) vignettes: 5/5 for 7 vignettes, 3/5 for 1, and 0/5 for 2. At least one of the poor choice or contraindicated medications was included among the choices considered optimal or good in 24/50 (48%) of vignettes. The model provided as rationale for treatment selection multiple heuristics including avoiding prior unsuccessful medications, avoiding adverse effects based on comorbidities, and generalizing within medication class.ConclusionThe model appeared to identify and apply a number of heuristics commonly applied in psychopharmacologic clinical practice. However, the inclusion of less optimal recommendations indicates that large language models may pose a substantial risk if routinely applied to guide psychopharmacologic treatment without further monitoring.
Understanding the Impact of Comorbidity-Interaction in Patients Undergoing Transcatheter Edge-to-Edge Mitral Valve Repair on Outcomes
Authors: Agrawal Ankit , Ramu Shivabalan Kathavarayan , Shekhar Shashank , Isogai Toshiaki , Bansal Agam , Yun James , Reed Grant W. , Puri Rishi , Krishnaswamy Amar , Kapadia Samir R. 
Published: April 2023

ABSTRACTBACKGROUNDTranscatheter Edge-to-Edge Mitral Valve Repair (M-TEER) is an accepted procedure for high-risk surgical patients with degenerative and functional mitral regurgitation. Non-cardiovascular comorbidities (NCCs) are highly prevalent in patients undergoing M-TEER. Although the impact of mitral valve anatomy and cardiac comorbidities in determination of M-TEER outcomes has been studied, precise understanding of the effect of the burden of NCCs on patients undergoing M-TEER remains unclear for acute outcomes. Our objective was to identify the association of NCC comorbidity-interaction patterns in patients undergoing M-TEER on length of stay (LOS), cost of care, and in-hospital major adverse cardiovascular events (MACE).METHODS9 245 admissions from the Nationwide Readmission Database that underwent M-TEER between 2015 and 2018 were included in the study. Patients were categorized by the overall burden of non-cardiovascular comorbidities (0, 1, 2, and ≥ 3). NCC included chronic liver disease, chronic lung disease, obesity, diabetes mellitus, dementia, major depressive disorder, chronic anemia, chronic kidney disease including end-stage renal disease (ESRD) on dialysis, and malignancy. Logistic Regression and Machine Learning (ML) algorithms were used to assess associations between comorbidity burden and in-hospital MACE.RESULTSOut of 9 245 index admissions, in-hospital MACE was recorded in a total of 504 (5.3 %). Of these, the majority (30.4%) had one NCC (n = 2 861). Patients with at least three NCCs had the longest median LOS [3.0, IQR (1.0 – 11.0)] and highest median cost of hospital care [$47 275, IQR (34 175.8 – 71 149.4)]. The Gradient Boosting (GB) classifier performed the best in predicting MACE with an AUROC of 96 % (95% CI: 0.95 – 0.97). The top features of importance that predicted in-hospital MACE were admission type, number of NCCs, and age in descending order.CONCLUSIONSCalibrated GB classifier identified patients with three NCCs as the subset of admission having the highest probability of a positive MACE outcome.
A Tool for Low-Cost, Quantitative Assessment of Shoulder Function Using Machine Learning
Authors: Darevsky David M. , Hu Daniel A. , Gomez Francisco A. , Davies Michael R. , Liu Xuhui , Feeley Brian T. 
Published: April 2023

AbstractTears within the stabilizing muscles of the shoulder, known as the rotator cuff (RC), are the most common cause of shoulder pain—often presenting in older patients and requiring expensive, advanced imaging for diagnosis1–4. Despite the high prevalence of RC tears within the elderly population, there are no accessible and low-cost methods to assess shoulder function which can eschew the barrier of an in-person physical exam or imaging study. Here we show that a simple string pulling behavior task, where subjects pull a string using hand-over-hand motions, provides a reliable readout of shoulder health across animals and humans. We find that both mice and humans with RC tears exhibit decreased movement amplitude, prolonged movement time, and quantitative changes in waveform shape during string pulling task performance. In rodents, we further note the degradation of low dimensional, temporally coordinated movements after injury. Furthermore, a predictive model built on our biomarker ensemble succeeds in classifying human patients as having a RC tear with >90% accuracy. Our results demonstrate how a combined framework bridging task kinematics, machine learning, and algorithmic assessment of movement quality enables future development of smartphone-based, at-home diagnostic tests for shoulder injury.
Fluid restrictive resuscitation with high molecular weight hyaluronan infusion in early peritonitis-sepsis
Authors: Barrueta Tenhunen Annelie , van der Heijden Jaap , Skorup Paul , Maccarana Marco , Larsson Anders , Larsson Anders , Perchiazzi Gaetano , Tenhunen Jyrki 
Published: April 2023

AbstractSepsis is a condition with high morbidity and mortality. Prompt recognition and initiation of treatment is essential. Despite forming an integral part of sepsis management, fluid resuscitation may also lead to volume overload, which in turn is associated with increased mortality. The optimal fluid strategy in sepsis resuscitation is yet to be defined. Hyaluronan, an endogenous glycosaminoglycan with high affinity to water is an important constituent of the endothelial glycocalyx. We hypothesized that exogenously administered hyaluronan would contribute to endothelial glycocalyx integrity and counteract intravascular volume depletion in a fluid restrictive model of peritonitis. In a prospective, blinded model of porcine peritonitis-sepsis, we randomized animals to intervention with hyaluronan (n=8) or 0.9% saline (n=8). The animals received an infusion of 0.1% hyaluronan 6 ml/kg/h, or the same volume of saline, during the first two hours of peritonitis. Stroke volume variation and hemoconcentration were comparable in the two groups throughout the experiment. Cardiac output (p=0.008 and p=0.017) and diastolic blood pressure (p=0.015 and p=0.019) were higher in the intervention group during the infusion of hyaluronan, but these effects disappeared as the experiment proceeded. The increase in lactate was more pronounced in the intervention group (p=0.041) throughout the experiment, while concentrations of surrogate markers of glycocalyx damage; syndecan 1 (0.6 ± 0.2 ng/ml vs 0.5 ± 0.2 ng/ml, p=0.292), heparan sulphate (1.23 ± 0.2 vs 1.4 ± 0.3 ng/ml, p=0.211) and vascular adhesion protein 1 (7.0 ± 4.1 vs 8.2 ± 2.3 ng/ml, p=0.492) were comparable in the two groups at the end of the experiment. In conclusion, hyaluronan did not counteract intravascular volume depletion in early peritonitis sepsis. The intervention was associated with higher cardiac output and diastolic blood pressure, than placebo, during the infusion. However, the increase in lactate throughout the experiment was more pronounced in the intervention group.
Precision Gestational Diabetes Treatment: Systematic review and Meta-analyses
Authors: Benham Jamie L , Gingras Véronique , McLennan Niamh-Maire , Most Jasper , Yamamoto Jennifer M , Aiken Catherine E , Ozanne Susan E , Reynolds RM 
Published: April 2023

ABSTRACTWe hypothesized that a precision medicine approach could be a tool for risk-stratification of women to streamline successful GDM management. With the relatively short timeframe available to treat GDM, commencing effective therapy earlier, with more rapid normalization of hyperglycaemia, could have benefits for both mother and fetus. We conducted two systematic reviews, to identify precision markers that may predict effective lifestyle and pharmacological interventions. There were a paucity of studies examining precision lifestyle-based interventions for GDM highlighting the pressing need for further research in this area. We found a number of precision markers identified from routine clinical measures that may enable earlier identification of those requiring escalation of pharmacological therapy. Whether there are other sensitive markers that could be identified using more complex individual-level data, such as ‘omics’, and if these can be implemented in clinical practice remains unknown. These will be important to consider in future studies.
Enhanced Peer-Group strategies to support prevention of Mother-to-Child HIV transmission leads to increased retention in care in Uganda: A Randomized controlled trial
Authors: Amone Alexander , Gabagaya Grace , Wavamunno Priscilla , Rukundo Gordon , Namale-Matovu Joyce , Malamba Samuel S. , Lubega Irene , Homsy Jaco , King Rachel , Nakabiito Clemensia , Namukwaya Zikulah , Fowler Mary Glenn , Musoke Philippa 
Published: April 2023

AbstractIntroduction:Despite scale up of Option B+, long-term retention of women in HIV care during pregnancy and the postpartum period remains an important challenge. We compared adherence to clinic appointments and antiretroviral therapy (ART) at different follow-up time points between enrolment and 24 months postpartum among pregnant women living with HIV and initiating Option B+ randomized to a peer group support, community-based drug distribution and income-generating intervention called “Friends for Life Circles” (FLCs) versus the standard of care (SOC).Methods:Between 16 May 2016 and 12 September 2017, 540 ART-naïve pregnant women living with HIV at urban and rural health facilities in Uganda were enrolled in the study. Participants were randomized 1:1 to the FLC intervention or SOC and assessed for adherence to prevention of mother to child HIV transmission (PMTCT) clinic appointments at 6 weeks, 12 and 24 months postpartum, self-reported adherence to ART at 6 weeks, 6 and 24 months postpartum validated by plasma HIV-1 RNA viral load (VL) measured at the same time points, and HIV status and HIV-free survival of infants at 18 months postpartum. We used Log-rank and Chi-Square p-values to test the equality of Kaplan-Meier survival probabilities and hazard rates (HR) for failure to retain in care for any reason by study arm.Results:There was no significant difference in adherence to PMTCT clinic visits or to ART or in median viral loads between FLC and SOC arms at any follow-up time points. Retention in care through the end of study was high in both arms but significantly higher among participants randomized to FLC (86.7%) compared to SOC (79.3%), p=0.022. The adjusted HR of visit dropout was 2.5 times greater among participants randomized to SOC compared to FLC (aHR=2.498, 95% CI: 1.417 – 4.406, p=0.002). Median VL remained < 400 copies/ml in both arms at 6 weeks, 6 and 24 months postpartum.Conclusions:Our findings suggest that programmatic interventions that provide group support, community based ART distribution and income-generation activities may contribute to retention in PMTCT care, HIV-free survival of children born to women living with HIV, and to the elimination of mother to child HIV transmission (MTCT).
Effect of nasal carriage ofBacillusspecies on COVID-19 severity: A cross-sectional study
Authors: Fowora Muinah A. , Aiyedogbon Adenike , Omolopo Ibilola , Tajudeen Ahmed O. , Olanlege Abdul-Lateef , Abioye Adefunke , Akintunde Grace B. , Folayan Morenike O. , Salako Babatunde L. 
Published: April 2023

ABSTRACTIntranasal sprays containingBacillusspecies are being researched for treating viral respiratory tract infections. The aim of this study was to assess the relationship between the nasal carriage ofBacillusand COVID-19 severity. This was a cross-sectional study that collected nasopharyngeal samples from adults 18 years and above visiting two COVID-19 testing centers in Lagos, Nigeria between September 2020 and September 2021.Bacillusspecies were cultured from the respiratory samples and confirmed using molecular methods. The dependent variable was COVID-19 status classified as negative, asymptomatic, mild, or severe. The independent variable was the nasal carriage ofBacillusspecies. Multinomial regression analysis was done to determine the association between nasal carriage ofBacillusand COVID-19 severity after adjusting for age, sex, and co-morbidity status. About 388 participants were included in the study with a mean (standard deviation) age of 40.05 (13.563) years. The majority (61.1%) of the participants were male, 100 (25.8%) had severe COVID-19, 130 (33.5%) had pre-existing comorbidity, and 76 (19.6%) hadBacilluscultured from their nasopharyngeal specimen. Bacillus species presence was significantly associated with higher odds of severe COVID-19 compared to having a negative COVID-19 status. However, the presence ofBacillusspecies was significantly associated with lower odds of severe COVID-19 compared to having a mild COVID-19 status. The study suggests that nasal carriage ofBacillusspecies may substantially impact the clinical course of COVID-19. This study supports the exploration ofBacillusspecies in the prevention and management of viral respiratory tract infections.IMPORTANCEWith the introduction of intranasal spray containingBacillusspecies for the treatment of viral respiratory tract infections, such as COVID-19 and respiratory syncytial virus, identifying the association between the nasal carriage ofBacillusspecies and COVID-19 susceptibility and severity will help further substantiate the investigation of these bacteria for COVID-19 prevention and treatment. This study evaluated the association between the carriage ofBacillusspecies in the nasopharyngeal tract and COVID-19 severity and found that the presence ofBacillusspecies in the nasopharynx may significantly impact the clinical course of COVID-19.
Symptom persistence and biomarkers in post-COVID-19/chronic fatigue syndrome – results from a prospective observational cohort
Authors: Legler A. F. , Meyer-Arndt L. , Mödl L. , Kedor C. , Freitag H. , Stein E. , Hoppmann U. , Rust R. , Konietschke Frank , Thiel A. , Paul F. , Scheibenbogen C. , Bellmann-Strobl J. 
Published: April 2023

AbstractIntroductionPost-COVID-19 syndrome (PCS) is characterized by a wide range of symptoms, predominantly fatigue and exertional intolerance. While disease courses during the first year post infection have been repeatedly described, little is known about long-term health consequences.MethodsWe assessed symptom severity and various biomarkers at three time points post infection (3-8 months (mo), 9-16mo, 17-20mo) in 106 PCS patients with moderate to severe fatigue and exertional intolerance. A subset of patients fulfilled diagnostic criteria of myalgic encephalomyelitis/chronic fatigue syndrome (PCS-ME/CFS) based on the Canadian Consensus Criteria.ResultsWhile PCS-ME/CFS patients showed persisting symptom severity and disability up to 20mo post infection, PCS patients reported an overall health improvement. Inflammatory biomarkers equally decreased in both groups. Lower hand grip force at onset correlated with symptom persistence especially in PCS-ME/CFS.DiscussionDebilitating PCS may persist beyond 20mo post infection, particularly in patients fulfilling diagnostic criteria for ME/CFS.
Human airway ex vivo models: new tools to study the airway epithelial cell response to SARS-CoV-2 infection
Authors: Assou Said , Ahmed Engi , Morichon Lisa , Nasri Amel , Foisset Florent , Bourdais Carine , Gros Nathalie , Wong Sonia , Petit Aurelie , Vachier Isabelle , Muriaux Delphine , Bourdin Arnaud , De Vos John 
Published: April 2023

AbstractAirway-liquid interface cultures of primary epithelial cells and of induced pluripotent stem cell-derived airway epithelial cells (ALI and iALI, respectively) are physiologically relevant models for respiratory virus infection studies because they can mimic thein vivohuman bronchial epithelium. Here, we investigated gene expression profiles in human airway cultures (ALI and iALI models) infected or not with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using publicly available and our own bulk and single-cell transcriptome datasets. SARS-CoV-2 infection significantly increased the expression of interferon-stimulated genes (IFI44,IFIT1,IFIT3,IFI35,IRF9,MX1,OAS1,OAS3andISG15) and inflammatory genes (NFKBIA,CSF1,FOSL1,IL32andCXCL10) at day 4 post-infection, indicating activation of the interferon and immune responses to the virus. Extracellular matrix genes (ITGB6,ITGB1andGJA1) also were altered in infected cells. Single-cell RNA sequencing data revealed that SARS-CoV-2 infection damaged the respiratory epithelium, particularly mature ciliated cells. The expression of genes encoding intercellular communication and adhesion proteins also was deregulated, suggesting a mechanism to promote shedding of infected epithelial cells. These data demonstrate that ALI/iALI models help to understand the airway epithelium response to SARS-CoV-2 infection and are a key tool for developing COVID-19 treatments.
SARS-CoV-2 shifts transcription of host gene to increase Spike acylation and boost infectivity
Authors: Mesquita Francisco S. , Abrami Laurence , Bracq Lucie , Panyain Nattawadee , Mercier Vincent , Kunz Béatrice , Chuat Audrey , Carlevaro-Fita Joana , Trono Didier , van der Goot F. Gisou 
Published: April 2023

ABSTRACTSARS-CoV-2 infection requires Spike protein mediating fusion between the viral and cellular membranes. The fusogenic activity of Spike requires its post-translational lipid modification by host S-acyltransferases, predominantly ZDHHC20. Previous observations indicate that SARS-CoV-2 infection augments the S-acylation of Spike when compared to transfection. Here, we find that SARS-CoV-2 infection triggers a change in the transcriptional start site of thezddhc20gene, both in cells and in anin vivoinfection model, resulting in a 67-amino–acid-long N-terminally extended protein with 37-times higher Spike acylating activity, leading to enhanced viral infectivity. Furthermore, we observed the same induced transcriptional change in response to other challenges, such as chemically induced colitis, indicating that SARS-CoV-2 hijacks an existing cell damage response pathway to generate more infectious viruses.
Rapid epidemic expansion of chikungunya virus-ECSA lineage in Paraguay
Authors: Giovanetti Marta , Vazquez Cynthia , Lima Mauricio , Castro Emerson , Rojas Analia , de la Fuente Andrea Gomez , Aquino Carolina , Cantero Cesar , Fleitas Fatima , Torales Juan , Barrios Julio , Ortega Maria Jose , Gamarra Maria Liz , Villalba Shirley , Alfonzo Tania , Xavier Joilson , Adelino Talita , Fritsch Hegger , Iani Felipe C. M. , Pereira Glauco Carvalho , de Oliveira Carla , Schuab Gabriel , Rodrigues Evandra Strazza , Kashima Simone , Leite Juliana , Gresh Lionel , Franco Leticia , Tegally Houriiyah , Van Voorhis Wesley C. , Lessels Richard , de Filippis Ana Maria Bispo , Ojeda Andrea , Sequera Guillermo , Montoya Romeo , Holmes Edward C. , de Oliveira Tulio , Rico Jairo Mendez , Lourenço José , Fonseca Vagner , Junior Alcantara Luiz Carlos 
Published: April 2023

AbstractThe spread of vector-borne viruses, such as CHIKV, is a significant public health concern in the Americas, with over 120,000 cases and 51 deaths in 2023, of which 46 occurred in Paraguay. Using a suite of genomic, phylodynamic, and epidemiological techniques, we characterized the ongoing large CHIKV epidemic in Paraguay.Article Summary LineGenomic and epidemiological characterization of the ongoing Chikungunya virus epidemic in Paraguay
Epidemiology of Syphilis infections among pregnant women in Tanzania: Analysis of the 2020 national representative sentinel surveillance
Authors: Sunguya Bruno , Mboya Erick , Mizinduko Mucho , Balandya Belinda , Sabasaba Amon , Amani Davis Elias , Kamori Doreen , Ruhago George , Mkumbwa Rebecca , Faustine Prosper , Maokola Werner , Sambu Veryeh , Mushi Jeremiah , Nyamuhagata Mukome , Jullu Boniphace S. , Juya Amiri , Rugemalila Joan , Mgomella George , Asiimwe Sarah , Pembe Andrea B. 
Published: April 2023

AbstractBackgroundSyphilis has detrimental effects on the health of the mother and that of the child when pregnant. Understanding its local epidemiology is essential for policies, planning, and implementation of targeted preventive interventions. Using data from the 2020 National Sentinel Surveillance of pregnant women attending antenatal clinics (ANCs) in Tanzania we determined the prevalence and determinants of Syphilis among pregnant women in Tanzania mainland.MethodologyThe ANC surveillance was conducted in 159 ANC sites from all 26 regions of Tanzania’s mainland from September to December 2020. It included all pregnant women older than 14 years on their first ANC visit in the current pregnancy during the survey period. Counselling for Syphilis was done using standard guidelines at the ANC and testing was done using rapid SD Bioline HIV/Syphilis Duo test kits. Analysis was done using both descriptive statistics to determine the prevalence and characteristics of syphilis, whereas, logistic regressions were used to examine the independent association between syphilis and dependent variables.ResultsA total of 38,783 women [median age (Interquartile range (IQR)) =25 (21-30) years] participated in the surveillance. Of them, 582 (1.4%) tested positive for Syphilis. A wide regional variation was observed with the highest burden in Kagera (4.5%) to the lowest burden in Kigoma (0.3%). The odds of Syphilis infections were higher among older women and those with no formal education. Compared with primigravids, women with 1-2, those with 3-4 and those with more than four previous pregnancies had 1.8 (aOR=1.8, 95% CI: 1.2-2.5), 2.1 (aOR=2.1, 95% CI: 1.4-3.1) and 2.6 (aOR=2.6, 95% CI: 1.7-3.9) higher odds of syphilis infection respectively.ConclusionSyphilis is still prevalent among pregnant women in Tanzania with a wide regional disparity. Efforts to prevent new infections, screen pregnant women, and treat those infected should be strategized to include all regions and renewed emphasis in regions with high burden, and importantly among women who are multipara, with the low level of education, and advanced age.
mitoSplitter: A mitochondrial variants-based method for efficient demultiplexing of pooled single-cell RNA-seq
Authors: Lin Xinrui , Chen Yingwen , Lin Li , Yin Kun , Cheng Rui , Wang Xiaoyu , Guo Ye , Wu Zhaorun , Zhang Yingkun , Li Jin , Yang Chaoyong , Song Jia 
Published: April 2023

AbstractSingle-cell RNA-seq (scRNA-seq) analysis of multiple samples separately can be costly and lead to batch effects. Exogenous barcodes or genome-wide RNA mutations can be used to demultiplex pooled scRNA-seq data, but they are experimentally or computationally challenging and limited in scope. Mitochondrial genomes are small but diverse, providing concise genotype information. We developed “mitoSplitter”, an algorithm that demultiplexes samples using mitochondrial RNA (mtRNA) variants, and demonstrated that mtRNA variants can be used to demultiplex large-scale scRNA-seq data. Using affordable computational resources, mitoSplitter can accurately analyze 10 samples and 60,000 cells in 6 hours. To avoid the batch effects from separated experiments, we applied mitoSplitter to analyze the responses of five non-small cell lung cancer (NSCLC) cell lines to BET chemical degradation in a multiplexed fashion. We found the synthetic lethality ofTOP2Ainhibition and BET chemical degradation in BET inhibitor-resistant cells. The result indicates that mitoSplitter can accelerate the application of scRNA-seq assays in biomedical research.