bluuebunny/crossref_metadata_2025_split huggingface dataset:
Internal Validation of Automated Visual Evaluation (AVE) on Smartphone Images for Cervical Cancer Screening in a Prospective Study in Zambia
Authors: Hu Liming , Mwanahamuntu Mulindi H. , Sahasrabuddhe Vikrant V. , Barrett Caroline , Horning Matthew P. , Shah Ishan , Laverriere Zohreh , Banik Dipayan , Ji Ye , Shibemba Aaron Lunda , Chisele Samson , Munalula Mukatimui Kalima , Kaunga Friday , Musonda Francis , Malyangu Evans , Hariharan Karen Milch , Parham Groesbeck P. 
Published: July 2023

I.AbstractObjectivesVisual inspection with acetic acid (VIA) is a low-cost approach for cervical cancer screening used in most low- and middle-income countries (LMICs) but, similar to other visual tests like histopathology, is subjective and requires sustained training and quality assurance. We developed, trained, and validated an artificial-intelligence-based “Automated Visual Evaluation” (AVE) tool that can be adapted to run on smartphones to assess smartphone-captured images of the cervix and identify precancerous lesions, helping augment performance of VIA.DesignProspective study.SettingEight public health facilities in Zambia.Participants8,204 women aged 25-55.InterventionsCervical images captured on commonly used low-cost smartphone models were matched with key clinical information including human immunodeficiency virus (HIV) and human papillomavirus (HPV) status, plus histopathology analysis (where applicable), to develop and train an AVE algorithm and evaluate its performance for use as a primary screen and triage test for women who are HPV positive.Main outcome measuresArea under the receiver operating curve (AUC); sensitivity; specificity.ResultsAs a general population screening for cervical precancerous lesions, AVE identified cases of cervical precancerous and cancerous (CIN2+) lesions with high performance (AUC = 0.91, 95% confidence interval [CI] = 0.89 to 0.93), which translates to a sensitivity of 85% (95% CI = 81% to 90%) and specificity of 86% (95% CI = 84% to 88%) based on maximizing the Youden’s index. This represents a considerable improvement over VIA, which a meta-analysis by the World Health Organization (WHO) estimates to have sensitivity of 66% and specificity of 87%. For women living with HIV, the AUC of AVE was 0.91 (95% CI = 0.88 to 0.93), and among those testing positive for high-risk HPV types, the AUC was 0.87 (95% CI = 0.83 to 0.91).ConclusionsThese results demonstrate the feasibility of utilizing AVE on images captured using a commonly available smartphone by screening nurses and support our transition to clinical evaluation of AVE’s sensitivity, specificity, feasibility, and acceptability across a broader range of settings. The performance of the algorithm as reported may be inflated, as biopsies were obtained only from study participants with visible aceto-white cervical lesions, which can lead to verification bias; and the images and data sets used for testing of the model, although “unseen” by the algorithm during training, were acquired from the same set of patients and devices, limiting the study to that of an internal validation of the AVE algorithm.
Development and Validation of a Computable Phenotype for Turner Syndrome Utilizing Electronic Health Records from a National Pediatric Network
Authors: Huang Sarah D. , Bamba Vaneeta , Bothwell Samantha , Fechner Patricia Y. , Furniss Anna , Ikomi Chijioke , Nahata Leena , Nokoff Natalie J , Pyle Laura , Seyoum Helina , Davis Shanlee M 
Published: July 2023

ABSTRACTTurner syndrome (TS) is a genetic condition occurring in ∼1 in 2,000 females characterized by the complete or partial absence of the second sex chromosome. TS research faces similar challenges to many other pediatric rare disease conditions, with homogenous, single-center, underpowered studies. Secondary data analyses utilizing Electronic Health Record (EHR) have the potential to address these limitations, however, an algorithm to accurately identify TS cases in EHR data is needed. We developed a computable phenotype to identify patients with TS using PEDSnet, a pediatric research network. This computable phenotype was validated through chart review; true positives and negatives and false positives and negatives were used to assess accuracy at both primary and external validation sites. The optimal algorithm consisted of the following criteria: female sex, ≥1 outpatient encounter, and ≥3 encounters with a diagnosis code that maps to TS, yielding average sensitivity 0.97, specificity 0.88, and C-statistic 0.93 across all sites. The accuracy of any estradiol prescriptions yielded an average C-statistic of 0.91 across sites and 0.80 for transdermal and oral formulations separately. PEDSnet and computable phenotyping are powerful tools in providing large, diverse samples to pragmatically study rare pediatric conditions like TS.
Dysregulation of gut microbiota composition in individuals with personality disorders: A systemic review and meta-analysis
Authors: Imran Rangraze , Khan Shehla 
Published: July 2023

AbstractBackgroundAnxiety disorders are the most frequent mental comorbidity in people with functional GI difficulties, and abdominal discomfort is one of the most known physical signs of sadness. Successful top-down treatments using antidepressants and psychosocial therapies in the treatment of irritable bowel syndrome (IBS) further define personality illnesses as more than merely CNS disorders, but disorders with highly extensive systemic interconnections.Therefore, we recently conducted a systematic review of the observational literature comparing the gut microbiota composition of persons with personality difficulties with healthy control.MethodsThis review was written according to the guidelines established by Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Not a single rule was broken, yet a more thorough search strategy did provide more relevant results. Pubmed, Scopus, Embase, Web of Science, Ovid, Global Health, PsycINFO, etc. were searched thoroughly using the phrases “gut microbiota, psychological disorders, personality disorders, composition, major depressive disorder, bipolar disorders, schizophrenia, etc.”ResultsResearchers did discover widespread differences in the gut microbiota of patients and controls under each category of personality disorder. They also found that there are distinct bacterial taxa that had differing abundances in patients with these three psychiatric illnesses compared to healthy controls. They found a great deal of variation in study designs and reporting, such as in the inclusion and exclusion of study populations, sampling feces for study of gut microbiota; taking into account or adjusting for important factors known to impact gut microbiota composition; storing feces; processing feces; analyzing feces.ConclusionOur systematic review did find that psychological disorders appeared to exhibit different overall compositional differences compared to controls. There was a general trend toward the finding of increased abundances of bacteria involved in glutamate and GABA metabolism, and lower abundances of butyrate-producing bacteria in psychological disorders
Social Cohesion and Covid-19: an integrative review
Authors: Ware Paul 
Published: July 2023

AbstractBackgroundNations of considerable wealth and sophisticated healthcare infrastructures have seen high rates of illness and death from Covid-19. Others with limited economic means and less developed healthcare infrastructures have achieved much lower burdens. In order to build a full understanding, an appraisal of the contribution of social relationships is necessary. Social cohesion represents a promising conceptual tool.ObjectiveThe aim was to examine scholarship on social cohesion during the Covid-19 pandemic: specifically – the constructions of social cohesion deployed, how it was measured, and the effects of and on social cohesion reported.MethodsThe Pubmed, Scopus and JSTOR databases were searched for relevant journal articles and grey literature. 66 studies met the inclusion criteria. Data were extracted and analysed from these using spreadsheet software.ResultsSeveral constructions of social cohesion were found. These concerned interpersonal relationships; sameness and difference; collective action; perceptions/emotions of group members; structures and institutions of governance; local or cultural specificity; and hybrid/multidimensional models. Social cohesion was reported as influential on health outcomes, health behaviours, and resilience and emotional wellbeing; but also that there was some potential for it to drive undesirable outcomes. Scholarship reported increases or decreases in quantitative measures of social cohesion, a temporary ‘rally round the flag’ effect early in the pandemic, the variable impacts of policy on cohesion, and changing interpersonal relationships due to pandemic conditions. There are numerous issues with the literature that reflect the well-documented limitations of popular versions of the social cohesion concept.ConclusionsSocial cohesion has been used to express a range of different aspects of relationships during the pandemic. It is said to promote better health outcomes, more engagement with positive health behaviours, and greater resilience and emotional wellbeing. The literature presents a range of ways in which it has been altered by the pandemic conditions.
Covid-19 related cognitive, structural and functional brain changes among Italian adolescents and young adults: a multimodal longitudinal case-control study
Authors: Invernizzi Azzurra , Renzetti Stefano , van Thriel Christoph , Rechtman Elza , Patrono Alessandra , Ambrosi Claudia , Mascaro Lorella , Cagna Giuseppa , Gasparotti Roberto , Reichenberg Abraham , Tang Cheuk Y. , Lucchini Roberto G. , Wright Robert O. , Placidi Donatella , Horton Megan K. 
Published: July 2023

AbstractCoronavirus disease 2019 (COVID-19) has been associated with brain functional, structural, and cognitive changes that persist months after infection. Most studies of the neurologic outcomes related to COVID-19 focus on severe infection and aging populations. Here, we investigated the neural activities underlying COVID-19 related outcomes in a case-control study of mildly infected youth enrolled in a longitudinal study in Lombardy, Italy, a global hotspot of COVID-19. All participants (13 cases, 27 controls, mean age 24 years) completed resting state functional (fMRI), structural MRI, cognitive assessments (CANTAB spatial working memory) at baseline (pre-COVID) and follow-up (post-COVID). Using graph theory eigenvector centrality (EC) and data-driven statistical methods, we examined differences in ECdelta(i.e., the difference in EC values pre- and post-COVID-19) and volumetricdelta(i.e., the difference in cortical volume of cortical and subcortical areas pre- and post-COVID) between COVID-19 cases and controls. We found that ECdeltasignificantly between COVID-19 and healthy participants in five brain regions; right intracalcarine cortex, right lingual gyrus, left hippocampus, left amygdala, left frontal orbital cortex. The left hippocampus showed a significant decrease in volumetricdeltabetween groups (p=0.041). The reduced ECdeltain the right amygdala associated with COVID-19 status mediated the association between COVID-19 and disrupted spatial working memory. Our results show persistent structural, functional and cognitive brain changes in key brain areas associated with olfaction and cognition. These results may guide treatment efforts to assess the longevity, reversibility and impact of the observed brain and cognitive changes following COVID-19.
Multiple Biomarkers to Predict Major Adverse Cardiovascular Events in Patients With Coronary Chronic Total Occlusions
Authors: Adusumalli Srikanth , Mohebi Reza , McCarthy Cian P. , Megaret Craig A. , Rhyne Rhonda F. , Jaffer Farouc A. , Januzzi James L. 
Published: July 2023

AbstractBackgroundThere are limited tools available to predict the long-term prognosis of persons with coronary chronic total occlusions (CTO).ObjectivesWe evaluated performance of a blood biomarker panel to predict cardiovascular (CV) events in patients with CTO.MethodsFrom 1251 patients in the CASABLANCA study, 241 participants with a CTO were followed for an average of 4 years for occurrence of major adverse CV events (MACE, CV death, non-fatal myocardial infarction or stroke) and CV death/heart failure (HF) hospitalization. Results of a biomarker panel (kidney injury molecule-1, N-terminal pro-B-type natriuretic peptide, osteopontin, and tissue inhibitor of metalloproteinase-1) from baseline samples were expressed as low-, moderate-, and high-risk.ResultsBy 4 years, a total of 67 (27.8%) MACE events and 56 (23.2%) CV death/HF hospitalization events occurred. The C-statistic of the panel for MACE through 4 years was 0.79. Considering patients in the low-risk group as a reference, the hazard ratio of MACE by 4 years was 6.65 (95% confidence interval [CI]: 2.98-14.8) and 12.4 (95% CI:5.17-29.6) for the moderate and high-risk groups (both P <0.001). The C-statistic for CVD/HF hospitalization by 4 years was 0.84. Compared to the low-risk score group, the moderate and high-risk groups had hazard ratios of 5.61 (95% CI: 2.33-13.5) and 15.6 (95% CI: 6.18, 39.2; both P value <0.001).ConclusionA multiple biomarker panel assists in evaluating the risk of adverse outcomes in patients with coronary CTO. These results may have implications for patient care and could have a role for clinical trial enrichment.Clinical TrialCASABLANCA,ClinicalTrials.govIdentifier:NCT00842868
Prevalence of Chronic Rhinosinusitis in Rajavithi Hospital Workers, Bangkok, Thailand
Authors: Chitsuthipakorn Wirach , Naphapunsakul Suphitsara , Korwattanamongkol Patlada , Mongkolkul Kittichai , Chindavijak Somjin 
Published: July 2023

ABSTRACTBackgroundThe prevalence of chronic rhinosinusitis (CRS) has been reported to range from 5% to 12% in different parts of the world. However, the prevalence of CRS in Thailand has not been investigated. Our objective was to determine the prevalence of CRS among hospital workers and identify any potential problems encountered during the survey.MethodAdult workers (>18 years) of Rajavithi Hospital, a tertiary hospital in Bangkok, Thailand, were recruited. This cross-sectional survey was conducted from September 2021 to September 2022. The participants were given a link to online questionnaires asking if they had nasal obstruction, discharge, decreased smell sensation, or facial pain and their respective duration. Phone numbers and email were asked for contact when needed. The participants who fulfilled the symptom and duration according to the European position paper on rhinosinusitis and nasal polyp 2020 were counted as symptom-based CRS patients. These patients were then contacted for nasal endoscopy. The endoscopic-based diagnosis of CRS was made after positive endoscopy findings.ResultA total of 1,025 participants (mean age of 33.7 years) were recruited. Of total, there were 34 (3.3%) and 6 (0.58%) participants fulfilled symptom- and endoscopy-based diagnoses, respectively. Fourteen participants did not respond to calls or emails. Five patients refused to visit the clinic due to inconveniences. One patient refused nasal endoscopy because of the expenses.ConclusionThe overall prevalence of chronic rhinosinusitis in workers of Rajavithi Hospital, was 3.3% and 0.58% by symptom- and endoscopy-based criteria, respectively. Difficulty reaching the participants for nasal endoscopy was the leading survey problem.
DIMPLE: AN R PACKAGE TO QUANTIFY, VISUALIZE, AND MODEL SPATIAL CELLULAR INTERACTIONS FROM MULTIPLEX IMAGING WITH DISTANCE MATRICES
Authors: Masotti Maria , Osher Nathaniel , Eliason Joel , Rao Arvind , Baladandayuthapani Veerabhadran 
Published: July 2023

AbstractThe tumor microenvironment (TME) is a complex ecosystem containing tumor cells, other surrounding cells, blood vessels, and extracellular matrix. Recent advances in multiplexed imaging technologies allow researchers to map several cellular markers in the TME at the single cell level while preserving their spatial locations. Evidence is mounting that cellular interactions in the TME can promote or inhibit tumor development and contribute to drug resistance. Current statistical approaches to quantify cell-cell interactions do not readily scale to the outputs of new imaging technologies which can distinguish many unique cell phenotypes in one image. We propose a scalable analytical framework and accompanying R package, DIMPLE, to quantify, visualize, and model cell-cell interactions in the TME. In application of DIMPLE to publicly available MI data, we uncover statistically significant associations between image-level measures of cell-cell interactions and patient-level covariates.
Cellular proliferation biases clonal lineage tracing and trajectory inference
Authors: Bonham-Carter Becca , Schiebinger Geoffrey 
Published: July 2023

AbstractWe identify a fundamental statistical phenomenon in single-cell time courses with clone-based lineage tracing. Through simple probabilistic arguments, we show how the relative growth rates of cells influence the probability that they will be sampled in clones observed across multiple time points. We support these arguments with a simple simulation study and a time-course of T-cell development, and we demonstrate that this bias can impact fate probability predictions from trajectory inference methods. Finally, we explore how to develop trajectory inference methods which are robust to this bias. In particular, we show how to extendLineageOT[1] to use data from clones observed across multiple time points.
Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon
Authors: Brealey Jaelle C. , Kodama Miyako , Rasmussen Jacob A. , Hansen Søren B. , Santos-Bay Luisa , Lecaudey Laurène A. , Hansen Martin , Fjære Even , Myrmel Lene S. , Madsen Lise , Bernhard Annette , Sveier Harald , Kristiansen Karsten , Gilbert M. Thomas P. , Martin Michael D. , Limborg Morten T. 
Published: July 2023

AbstractAnimals and their associated microbiota share long evolutionary histories. Both host genotype and associated microbiota influence phenotypes such as growth and disease resilience. We applied a hologenomic approach to explore the relationship between host and microbiota in shaping lifetime growth and parasitic cestode infection in farmed Atlantic salmon. Genomes, transcriptomes, metabolomes and metagenomes were generated from the guts of 460 harvest-aged salmon, 82% of which were naturally infected with an intestinal cestode. One salmonid-specificMycoplasmadominated the gut microbiota of uninfected salmon. However, the microbiota was perturbed in smaller, parasitised fish, with increased abundance ofVibrionaceaeand otherMycoplasmaspecies previously linked to the cestode microbiota. The cestode-associatedMycoplasmacarry more virulence-associated genes than the salmonidMycoplasma. Colonisation by one cestode-associatedMycoplasmawas associated with a region of the salmon genome encoding several long noncoding RNA genes previously associated with host control of intestinal microbiota. Integrating the multiple omic datasets revealed coordinated changes in the salmon gut transcriptome and metabolome that correlated with shifts in the microbiota of smaller, parasitised fish. Our results suggest that cestode infections introduce new microbes and trigger host responses, altering the gut microbiota with increases in potentially pathogenic microbes. Establishment of these microbes is partially shaped by the genetic background of the host. Our study highlights the value of a hologenomic approach for gaining an in-depth understanding of trilateral interactions among host, microbiota and parasite.
Acetyl-CoA carboxylase 1-dependent lipogenesis drives breast cancer progression
Authors: Tan Keely , Owen Thomas , McEwen Holly P. , Simpson Peter , Hoy Andrew J. , James David E. , Don Anthony S. , Naylor Matthew J. 
Published: July 2023

AbstractDysregulation of cellular energetics, including lipid synthesis mediated through de novo lipogenesis, is a feature of many cancers. Here we report that acetyl-coenzyme A carboxylase (ACC) 1, the rate-limiting enzyme of de novo lipogenesis, is a key regulator of breast cancer progression and cancer cell phenotype. Mammary epithelial-specific deletion of ACC1 impaired tumour progression and decreased cancer cell proliferation in the PyMT model of breast cancerin vivo. ACC1 knockout in human breast cancer cell lines resulted in decreased cell number and altered cell and membrane morphology. Lipidomic profiling demonstrated reduced levels of acyl-carnitines (CARs) and several phospholipid (PL) classes, whilst also shifting the lipid profiles to exhibit more elongated and less saturated lipids in ACC1 knockout breast cancer cells. Palmitate rescue of ACC1 deletion phenotypes demonstrated a critical role for ACC1 driven de novo lipogenesis in breast cancer cell function. Analysis of human breast tumour-microarrays identified strong ACC1 expression at all breast cancer stages, grade and metastasis, compared to normal adjacent tissue. Together our data demonstrate a novel role for ACC1 in breast cancer progression and cancer cell function, mediated through its lipogenic role, that together with its expression profile, identify ACC1 as a potential therapeutic target in breast cancer.Statement of significanceThis study investigates the impact of ACC1 deletion in breast cancer progression, revealing the importance of ACC1-derived lipids in breast cancer cell phenotypes and identifies ACC1 as a potential novel therapeutic target.
Upregulated Fcrl5 disrupts B cell anergy and causes autoimmunity
Authors: Ono Chisato , Tanaka Shinya , Myouzen Keiko , Iwasaki Takeshi , Ueda Mahoko , Oda Yoshinao , Yamamoto Kazuhiko , Kochi Yuta , Baba Yoshihiro 
Published: July 2023

AbstractB cell anergy plays a critical role in maintaining self-tolerance by inhibiting autoreactive B cell activation to prevent autoimmune diseases. Here, we demonstrated that Fc receptor-like 5 (Fcrl5) upregulation contributes to autoimmune disease pathogenesis by disrupting B cell anergy. Fcrl5—a gene whose homologs are associated with human autoimmune diseases—is highly expressed in age/autoimmunity-associated B cells (ABCs), an autoreactive B cell subset. By generating B cell-specific Fcrl5 transgenic mice, we demonstrated that Fcrl5 overexpression in B cells caused systemic autoimmunity with age. Furthermore, Fcrl5 upregulation in B cells exacerbated the systemic lupus erythematosus-like disease model and increased the levels of ABCs and activated T cells. Mechanistically, an increase in Fcrl5 expression broke B cell anergy, activating autoreactive B cells in the presence of a self-antigen. Fcrl5 facilitated toll-like receptor signaling, reactivating anergic B cells. Thus, Fcrl5 is a potential regulator of B cell-mediated autoimmunity by regulating B cell anergy. This study provides important insights into the role of Fcrl5 in breaking B cell anergy and its effect on the pathogenesis of autoimmune diseases.