bluuebunny/crossref_metadata_2025 huggingface dataset:
CONSORT-TM: Text classification models for assessing the completeness of randomized controlled trial publications
Authors: Jiang Lan , Lan Mengfei , Menke Joe D. , Vorland Colby J , Kilicoglu Halil
Published: April 2024

Objective

To develop text classification models for determining whether the checklist items in the CONSORT reporting guidelines are reported in randomized controlled trial publications.

Materials and Methods

Using a corpus annotated at the sentence level with 37 fine-grained CONSORT items, we trained several sentence classification models (PubMedBERT fine-tuning, BioGPT fine-tuning, and in-context learning with GPT-4) and compared their performance. To address the problem of small training dataset, we used several data augmentation methods (EDA, UMLS-EDA, text generation and rephrasing with GPT-4) and assessed their impact on the fine-tuned PubMedBERT model. We also fine-tuned PubMedBERT models limited to checklist items associated with specific sections (e.g., Methods) to evaluate whether such models could improve performance compared to the single full model. We performed 5-fold cross-validation and report precision, recall, F1 score, and area under curve (AUC).

Results

Fine-tuned PubMedBERT model that takes as input the sentence and the surrounding sentence representations and uses section headers yielded the best overall performance (0.71 micro-F1, 0.64 macro-F1). Data augmentation had limited positive effect, UMLS-EDA yielding slightly better results than data augmentation using GPT-4. BioGPT fine-tuning and GPT-4 in-context learning exhibited suboptimal results. Methods-specific model yielded higher performance for methodology items, other section-specific models did not have significant impact.

Conclusion

Most CONSORT checklist items can be recognized reasonably well with the fine-tuned PubMedBERT model but there is room for improvement. Improved models can underpin the journal editorial workflows and CONSORT adherence checks and can help authors in improving the reporting quality and completeness of their manuscripts.
Maternal health in rural Pakistan: An analysis of knowledge and practices of antenatal care using the socio-ecological model
Authors: Agha Nadia , Rind Rahim Dad , Mahar Shoukat Ali , Channa Moomal Mendhri , Ansar Fizza , Bhanbhro Sadiq
Published: April 2024

Background: Pakistan carries a heavy burden of maternal and child health vulnerabilities. Maternal health can be prevented with culturally specific interventions and women’s enhanced access to healthcare facilities, yet women in rural areas in Pakistan are deprived of such interventions. In this study, we assessed the prevalent knowledge and practices of antenatal care and the impact of low-income and gender inequalities on maternal health in rural areas of Pakistan. Methods: We conducted a cross-sectional study using the Socio-Ecological Model (SEM) in five villages in the Sindh province of Pakistan. We tested hypotheses using descriptive reliability and regression techniques. Results: Findings show that the socio-geographical and cultural factors influencing maternal health were embedded within the different levels of SEM. The prevalence of Maternal Health Vulnerabilities (MHV) was high in villages where women had limited literacy and awareness. Of the 352 participants, 173 (49%) women were not literate and could not read pregnancy-related information imparted through leaflets or brochures. Data showed that women consumed less milk, multivitamins, and proper food due to poverty. At the same time, they had restricted access to health facilities: 119 (34%) women had lost their babies after birth. In this study, poverty and gender inequality correlate with MHV (significant 65.60% and .000 and 10.50% and .000, respectively) and exacerbate the situation by complementing each other. Conclusion: Culturally appropriate and evidence-based interventions are needed to reduce gender inequality and prioritise women’s and girls’ maternal health needs. This study has considered cultural, social, geographical, and economic factors influencing maternal health. It provides a nuanced account of a complex web of barriers to attaining Sustainable Development Goals (SDGs), particularly goals 3, ‘Good health and well-being’ and 5 ‘, Gender equality’.
Predictors of Postoperative pharyngeal complaints in children undergoing surgery under general anesthesia at Hawassa university comprehensive specialized hospital, aprospective observational study
Authors: Legasse Adanech Shifarew , Mossie Addisu , Besha Aschalew , Mohammed Nesra
Published: April 2024

Background

Postoperative pharyngeal complaints are common but minor complications following surgery and are commonly reported during postoperative visits. These complaints includes sore throat, dysphagia, and hoarseness, which can significantly impact a child’s comfort, overall well-being and satisfaction after surgery. Identifying and understanding the predictors of these postoperative pharyngeal complaints is crucial to improve the overall outcomes in children undergoing surgery. This study aimed to assess the predictors of postoperative pharyngeal complaints in children undergoing surgery under general anesthesia.

Methods

A prospective observational study was conducted among children aged 6 to 16 years who underwent emergency and elective surgical procedures under general anesthesia. The data was entered and analyzed using SPSS version 26 software packages. Univariate and multivariate analyses were performed to investigate the independent predictors of postoperative pharyngeal complaint. The postoperative pharyngeal complaints (Sore throat, dysphagia and hoarseness) were assessed at 2nd, 6th, 12th, and 24th hours postoperatively.

Result

A total of 102 patients were included in this study, of which 68 of them male. The result of this study showed the overall incidence of postoperative pharyngeal complaints was 32.4%; whereas the incidence of postoperative sore throat 26.5%, cough 5.9%, Postoperative hoarseness 2.9% and dysphagia 4.9% of participants. Endotracheal intubation was identified as the only independent predictors of postoperative pharyngeal complaints with p-values of 0.01 (AOR-3.846, 95% CI [1.385-10.682]).

Conclusion

This study revealed the overall incidence of postoperative pharyngeal complaints was 32.4%. Endotracheal intubation was identified as the only independent predictors of postoperative pharyngeal complaints in children in this study.
Evaluating the Sex Dependent Influence of Sarcospan on Cardiometabolic Disease Traits in Mice
Authors: Kahmini Aida Rahimi , Valera Isela C. , Samarah Luaye , Crawford Rhiannon Q. , Elsheikh Salma , Kanashiro-Takeuchi Rosemeire M. , Olateju Bolade S. , Matthews Aaron R. , Mohammadipoor Nazanin , Parvatiyar Michelle S.
Published: April 2024

Numerous genes including sarcospan (SSPN) have been designated as obesity-susceptibility genes by human genome-wide association studies. Variants in the sarcospan (SSPN) gene locus have been associated with obesity traits with a stronger effect in women. To date this association has not been tested in vivo, therefore, we assessed the susceptibility of young (2 month) global SSPN-deficient (SSPN-/-) mice to diet-induced obesity by feeding them high fat diet (HFD) or control diet (CD) for 16 weeks. Anthropometric measurements were used to assess outcomes to the diets including weight change, glucose handling, fat distribution, adipocyte size and effects on cardiac function. To assess the age-dependent impact of SSPN deletion we also compared the response of (13 month) male and female mice to HFD, which were aged by study completion. SSPN deficiency offered modest protection from weight gain in all groups studied, which was not attributable to reduced food consumption. Aging revealed glucose intolerance for SSPN-/-CD mice, which was significant in females. Young female mice had low % Fat and less visceral adipose tissue accumulation that remained relatively unchanged in HFD groups. However, this protection was lost with aging. SSPN-/-mice did not exhibit decrements in cardiac function in response to HFD. However, aged male SSPN-/-CD mice had significantly increased left ventricular mass (LVM) and signs of ventricular remodeling in response to HFD. These studies suggest that SSPN influences phenotype in a sex dependent manner and participates in a network of metabolic genes.

New & Noteworthy

In this study the association of the sarcospan protein with human obesity is assessed using in vivo models. Sarcospan-deficient mice of both sexes show an age- dependent influence on adipose tissue biology and glucose handling in response to control and high fat diet. The effect of sarcospan deletion was more pronounced effects in females. Aging reveals susceptibility of SSPN-deficient male mice to increased left ventricular mass.
Anatomy of the mandibular symphysis of extant cercopithecids: taxonomy and variation
Authors: Pallas Laurent , Nakatsukasa Masato , Kunimatsu Yutaka
Published: April 2024

The symphyseal anatomy of extant and fossil cercopithecids has not yet been demonstrated as a useful tool for taxonomic discrimination, and the source of variation in cercopithecid symphysis has not been addressed on a broad taxonomic scale. Here, we used linear and angular dimensions to quantify symphysis shape. Using univariate, multivariate data and allometric regressions (partial least squares and phylogenetic generalized least square regressions), we addressed the hypothesis that extant cercopithecids can be distinguished by symphysis shape. Significant differences in univariate and multivariate data and allometric regressions permitted to distinguish cercopithecids at the subfamilial, tribal, and genus levels. We showed that multivariate data followed the distribution expected under Brownian Motion and significantly discriminates taxa at different taxonomic levels. Colobine symphysis are characterized by developed inferior transverse tori, short planum alveolare, and short symphysis, whereas cercopithecine symphysis are characterized by developed superior transverse tori, long planum alveolare, and long symphysis. Exceptions to this pattern exist within each subfamily, and this study underlines the particular anatomy ofColobusandPresbytisamong the colobines,Allenopithecusamong the Cercopithecini, andTheropithecusandLophocebusamong the Papionini. We also demonstrate that the relative development of the transverse tori, the relative length of the planum alveolare and symphyseal inclination are dimorphic traits. Specifically, we show that the symphysis ofProcolobus verus,Nasalis larvatus, andPapio anubisis strongly dimorphic.
UVREK: Development and analysis of an expression profile knowledgebase of biomolecules induced by ultraviolet radiation exposure
Authors: Baskaran Shanmuga Priya , Ravichandran Janani , Shree Priya , Thengumthottathil Vinayak , Karthikeyan Bagavathy Shanmugam , Samal Areejit
Published: April 2024

Humans encounter diverse environmental factors which can have impact on their health. One such environmental factor is the ultraviolet (UV) radiation, which is part of the physical component of the exposome. UV radiation is the leading cause of skin cancer and is a significant global health concern. A large body of published research has been conducted to uncover the mechanisms underlying the adverse outcomes of UV radiation exposure on living beings. These studies involve identifying the biomolecules induced upon UV radiation exposure. A few previous efforts have attempted to compile this information in the form of a database, but such earlier efforts have certain limitations. To fill this gap, we present a structured database named UVREK, containing manually curated data on biomolecules induced by UV radiation exposure from published literature. UVREK has compiled information on 985 genes, 470 proteins, 54 metabolites and 77 miRNAs along with their metadata. Thereafter, an enrichment analysis performed on the human gene set of UVREK database showed the importance of transcription related processes in UV related response, and enrichment of pathways involved in cancer and aging. While significantly contributing towards characterizing the physical component of the exposome, we expect the compiled data in UVREK will serve as a valuable resource for development of better UV protection mechanisms such as UV sensors and sunscreens. Noteworthy, UVREK is the only resource to date, compiling varied types of biomolecular responses to UV radiation with corresponding metadata. UVREK is openly accessible at:https://cb.imsc.res.in/uvrek/.
Carbohydrate Hydrolytic Activity, Antibiotic Resistance and Stress Tolerance ofLacticaseibacillus paracaseiBCRC-16100 andLacticaseibacillus paracaseiZFM54 for Probiotics Using Genomic and Biochemical Approaches
Authors: Icalia Gann Peter James , Fabia Jimmbeth Zenila P. , Pagurayan Althea Gay B. , Agcaoili Ma. Joy Theresa , Pascual Ryan James J. , Baranda Suerte M. , Racho Arc Josam J. , Olivar Marvielyn P. , Cariaga Jayson F. , Domingo Alvin , Bucao Dionisio S. , Agrupis Shirley C.
Published: April 2024

Probiotics are microorganisms infused in products for health benefits including acceleration of nutrient digestion, however, it is also important to ensure the safety prior to incorporation. Here, we present evidence of the ability of two probiotic isolates,Lacticaseibacillus paracaseiBCRC-16100 andLacticaseibacillus paracaseiZFM54, in the (1) enhancement of carbohydrate digestion, (2) tolerance to stress, and (3) antibiotic resistance. Approaches include whole genome sequence (WGS) analysis and bioactivity assays. WGS revealed genes suggesting the ability of the two isolates to promote carbohydrate digestion, tolerance to stress and antibiotic resistance. Carbohydrate digestive ability was confirmed through a biochemical assay where the two isolates cause glucose release from starch. The two isolates also showed versatility in a range of temperature and alcohol concentration. For antibiotic resistance particularly on vancomycin, there are three mechanisms namely transporter control, transcriptional regulation, and efflux pump. Furthermore, promoter and transposable element analysis showed that some of the active antibiotic resistant (AbR) genes can be laterally transferred. Altogether, we show the potential of two probiotic isolates to be incorporated in products for improved carbohydrate digestion and the need to address the removal of active and mobile antibiotic resistance genes that may compromise safety.
Anatomy of the mandibular corpus of extant cercopithecids : taxonomy and variation
Authors: Pallas Laurent , Nakatsukasa Masato , Kunimatsu Yutaka
Published: April 2024

This study aims to discriminate cercopithecid taxa of higher taxonomic levels (subfamily, tribe, subtribe, and genus) on the basis of corpus shape in transverse cross-section at the M1-M2junction and to assess its variation using 2D geometric morphometrics. Specifically, we evaluated the effect of allometry and sexual dimorphism on differences in corpus shape at interspecific and intraspecific levels, respectively. We also investigated whether corpus variation among cercopithecids was following Brownian motion using Pagel’s λ. Taxonomic discrimination and sexual dimorphism were established using Analysis of Variance on Principal Component scores. Allometry was studied using phylogenetic least-squares regressions and partial least-squares regressions. We demonstrated that, using corpus shape, extant cercopithecids can be significantly discriminated at the subfamilial, tribal, and subtribal levels. In addition, the main axis of variation of the Principal Component Analysis follows a distribution expected under Brownian motion, validating the presence of a phylogenetic signal in corpus shape. Colobines exhibit a robust corpus (superoinferiorly short and transversely broad) with large lateral prominences while cercopithecines have a gracile corpus (superoinferiorly long and transversely thin in its distal portion) with marked corpus fossae in African papionins. Exception to the typical subfamilial or tribal shape pattern exist, with the best examples beingTrachypithecus,PresbytisandPygathrixwithin colobines,Allenopithecuswithin Cercopithecini, andMacaca,TheropithecusandCercocebuswithin Papionini. Sexual dimorphism is a confounding factor in shape discrimination, as there are significant differences between sexes, notably inPapio anubis,Nasalis larvatusandProcolobus verus. Intriguingly, sexual dimorphism in corpus shape does not seem to follow the dimorphism deduced in canine and molar crown dimensions. This discrepancy is illustrated by the low degree of dimorphism in corpus shape inPiliocolobus badius, despite dimorphic canine and molar dimensions. Overall, our findings concerning corpus shape variation in cercopithecids will greatly benefit to paleontological studies that seek to identify taxa in the fossil record, and to neontological studies aiming to explore the ecomorphological value of the cercopithecid mandible.
A sneak peek at the high altitude adaptation of the Ladakh populations
Authors: Chorol Urgyan , Choudhury Bhagyashree , Norboo Tsering , Wangchuk Nony P. , Chaubey Gyaneshwer , Mallick Chandana Basu
Published: April 2024

The physiological response to high-altitude stress (for individuals living at 2,400m and above sea level) has been evident. However, recent advances in genomics have allowed us to explore the molecular genetic basis of these adaptive responses and their relationship with physiological responses. In the current study, we focused on thirteen biological parameters to understand the adaptive response to the high altitude of populations living across regions of Sakti, Korzok, Hanle, Aryan and Zanskar valleys of Ladakh and to understand the variation between and across individuals. Interestingly, we found a negative correlation between haemoglobin levels and partial oxygen pressure, thereby testifying to higher haemoglobin levels as an adaptive response in these individuals. The lipid profiles, including cholesterol, triglyceride, LDL and HDL levels, varied significantly across the five regions studied. Notably, individuals from Sakti Valley showed higher LDL (>140) and cholesterol values. These variations in health parameters and lipid profiles may be attributed to diet and altitude adaptations specific to the region. Overall, the study provides valuable insights into the adaptations of highlanders living at different altitudes in the Ladakh region. The findings can have implications for better understanding the molecular mechanism of physiological responses of humans to high-altitude environments.
Cellular uptake and viability switch in the properties of lipid-coated carbon quantum dots for potential bioimaging and therapeutics
Authors: Jain Sweny , Sahu Nidhi , Bhatia Dhiraj , Yadav Pankaj
Published: April 2024

Carbon quantum dots derived from mango leaves exhibited bright red fluorescence. These negatively charged particles underwent coating with the positively charged lipid molecule N-[1-(2,3-dioleyloxy) propyl]-N,N,N-trimethylammonium chloride (DOTMA). However, the bioconjugate displayed reduced uptake compared to the standalone mQDs in cancer cells (SUM 159A), and increased uptake in the case of epithelial (RPE-1) cells. Upon in vitro testing, the bioconjugate demonstrated a mitigating effect on the individual toxicity of both DOTMA and mQDs in SUM-159A (cancerous cells) and of DOTMA in RPE-1 cells. Conversely, it exhibited a proliferative effect on RPE-1 (epithelial cells). Surface modifications of QDs with lipids thus enhances their compatibility with biological systems, reducing systemic toxicity, minimizing off-site effects, sustaining drug release, and modulating cellular viability through various mechanisms (for example, apoptosis), which is, therefore, crucial for multiple applications such as targeted therapeutics.

TOC

Red emitting, fluorescent carbon quantum dots synthesized using mango leaves(mQDs) showed enhanced cellular uptake and reduced cell viability in the case of cancer cells when compared with lipid-coated mQDs. However, in the case of non-cancerous cells, the lipid-coated mQDs showed enhanced cellular uptake and cell viability when compared with mQDs alone.
High affinity chimeric antigen receptor signaling induces an inflammatory program in human regulatory T cells
Authors: Cochrane Russell W. , Robino Rob A. , Granger Bryan , Allen Eva , Vaena Silvia , Romeo Martin J. , de Cubas Aguirre A. , Berto Stefano , Ferreira Leonardo M.R.
Published: April 2024

Regulatory T cells (Tregs) are promising cellular therapies to induce immune tolerance in organ transplantation and autoimmune disease. The success of chimeric antigen receptor (CAR) T-cell therapy for cancer has sparked interest in using CARs to generate antigen-specific Tregs. Here, we compared CAR with endogenous T cell receptor (TCR)/CD28 activation in human Tregs. Strikingly, CAR Tregs displayed increased cytotoxicity and diminished suppression of antigen-presenting cells and effector T (Teff) cells compared with TCR/CD28 activated Tregs. RNA sequencing revealed that CAR Tregs activate Teff cell gene programs. Indeed, CAR Tregs secreted high levels of inflammatory cytokines, with a subset of FOXP3+CAR Tregs uniquely acquiring CD40L surface expression and producing IFNγ. Interestingly, decreasing CAR antigen affinity reduced Teff cell gene expression and inflammatory cytokine production by CAR Tregs. Our findings showcase the impact of engineered receptor activation on Treg biology and support tailoring CAR constructs to Tregs for maximal therapeutic efficacy.

Graphical Abstract
Discovering cancer stem-like cells using Spatial transcriptomic analysis: Nuclear factor I X as a novel therapeutic target for gastric cancer
Authors: Ishikawa Akira , Fukui Takafumi , Kido Aya , Katsuya Narutaka , Kuraoka Kazuya , Uraoka Naohiro , Suzuki Takahisa , Oka Shiro , Kotachi Takahiro , Ashktorab Hassan , Smoot Duane , Yasui Wataru
Published: April 2024

Background

Gastric cancer (GC) is characterized by significant intratumoral heterogeneity and stem cells presenting as promising therapeutic targets. Despite advancements in spatial transcriptome analysis, unexplored targets for addressing cancer stemness remain unknown. This study aims to identify Nuclear Factor IX (NFIX) as a critical regulator of cancer stemness in GC and evaluate its clinicopathological significance and function.

Methods

Spatial transcriptome analysis was conducted on GC. NFIX expression’s correlation with clinicopathological factors and prognosis was assessed through immunostaining in 127 GC cases. Functional analyses in cancer cell lines validated these findings.

Results

Spatial transcriptome analysis stratified GC tissues based on genetic profiles, pinpointing CSC-like cells and further refined the classification to identify and highlight the NFIX’s significance, validated by Monocle 3 and CytoTRACE analyses. Knockdown experiments in cancer cell lines demonstrated the involvement of NFIX in cancer cell proliferation and kinase activity.

Conclusions

This study underscores spatial transcriptome analysis’s role in refining GC tissue classification and identifying therapeutic targets, highlighting NFIX as pivotal. NFIX expression correlates with poor prognosis and drives GC progression, suggesting its potential as a novel therapeutic target for personalized GC therapies.
A Robust Statistical Approach for Finding Informative Spatially Associated Pathways
Authors: Tian Leqi , Xiao Jiashun , Yu Tianwei
Published: April 2024

Spatial transcriptomics offers insights into functional localization of cells by mapping gene expression to spatial locations. Traditional focus on selecting spatially variable genes often misses the complexity of biological pathways and biological network dynamics. We introduce a novel framework that shifts the focus towards identifying functional pathways associated with spatial variability, by adapting the Brownian distance covariance test to explore the heterogeneity of biological functions over space. The statistical approach is free of parameter selection. It allows for a deeper understanding of how cells coordinate their activities across different spatial domains through biological processes. By analyzing real human and mouse datasets, the method found significant pathways that were associated with spatial variation, as well as different pathway patterns among inner- and edge-cancer regions. This innovative framework offers a new perspective on analyzing spatial transcriptomic data, contributing to our understanding of tissue architecture and disease pathology.
EAP: a versatile cloud-based platform for comprehensive and interactive analysis of large-scale ChIP/ATAC-seq data sets
Authors: Chen Haojie , Huang Tao , Guo Zhijie , Zheng Anqin , Chen Weiran , Ma Liangxiao , Tu Shiqi , Zheng Guangyong , Li Yixue , Shao Zhen
Published: April 2024

Epigenome profiling techniques such as ChIP-seq and ATAC-seq have revolutionized our understanding of gene expression regulation in tissue development and disease progression. However, increasing amount of ChIP/ATAC-seq data poses challenges in computational resources, and the absence of systematic tools for epigenomic analysis underscores the necessity for an efficient analysis platform. To address these issues, we developed the Epigenomic Analysis Platform (EAP,https://www.biosino.org/epigenetics), a scalable cloud-based tool that efficiently analyzes large-scale ChIP/ATAC-seq data sets. EAP employs advanced computational algorithms to derive biologically meaningful insights from heterogeneous datasets and automatically generates publication-ready figures and tabular results, enabling comprehensive epigenomic analysis and data mining in areas like cancer subtyping and therapeutic target discovery.
Bellymount-Pulsed Tracking: A Novel Approach for Real-Time In vivo Imaging of Drosophila Abdominal Tissues
Authors: Balachandra Shruthi , Amodeo Amanda A
Published: April 2024

Quantitative live imaging is a valuable tool that offers insights into cellular dynamics. However, many fundamental biological processes are incompatible with current live imaging modalities. Drosophila oogenesis is a well-studied system that has provided molecular insights into a range of cellular and developmental processes. The length of the oogenesis coupled with the requirement for inputs from multiple tissues has made long-term culture challenging. Here, we have developed Bellymount-Pulsed Tracking (Bellymount-PT), which allows continuous, non-invasive live imaging of Drosophila oogenesis inside the female abdomen for up to 16 hours. Bellymount-PT improves upon the existing Bellymount technique by adding pulsed anesthesia with periods of feeding that support the long-term survival of females during imaging. Using Bellymount-PT we measure key events of oogenesis including egg chamber growth, yolk uptake, and transfer of specific proteins to the oocyte during nurse cell dumping with high spatiotemporal precision within the abdomen of a live female.
A paired analysis of mercury among non-invasive tissues to inform bat conservation monitoring
Authors: Simonis Molly C , Whitmore Kimberlee , Dyer Kristin E , Allira Meagan , Demory Bret , Chumchal Matthew M , Becker Daniel J
Published: April 2024

Contaminant exposure can harm wildlife. However, measuring contaminant exposure in wildlife can be challenging due to accessibility of species and/or sampling tissue matrices needed to answer research questions regarding exposure. For example, in bats and other taxa that roost, it may be best to collect pooled feces from colonies for minimal disturbance to species of conservation concern, but fecal contaminant concentrations do not provide contaminant bioaccumulation estimates. Thus, there is a need for quantifying relationships between sample matrices for measuring contaminant exposure to answer research questions pertaining to wildlife health and addressing conservation needs. Our goal was to determine relationships between fecal and fur total mercury (THg). To do so, we collected paired feces and fur from Mexican free-tailed bats (Tadarida brasiliensis) in summer 2023 in western Oklahoma at a maternity roost with no known Hg point source. We analyzed THg in each sample matrix for each individual (n = 48). We found no relationship between individual fecal and fur THg. However, when averaged, fur THg was 6.11 times greater than fecal THg. This factor can be used as a screening-level risk assessment of under-roost feces, which could then be followed by direct assessments of fur THg concentrations and health impacts. We encourage the use of this conversion factor across other insectivorous bat species and sites for estimating initial risks of contaminant exposure with minimal disturbance to species of conservation concern, when timely research for conservation actions are needed, and when a contaminant point source is not yet known.

Graphical Abstract

Graphical abstract created in BioRender under a free subscription. Cave icon created by artist Freepik athttps://www.flaticon.com/free-icons/cave.

Highlights

Under-roost sampling for contaminant exposure minimizes species disturbance

Contaminant exposure relationships in tissues can aide in measuring wildlife health

We sampledTadarida brasilliensisfor paired fecal and fur total Hg (THg)

THg in fur averaged 6.11 times greater than feces

This factor can be used as an initial risk assessment for under-roost fecal sampling

More invasive follow-up sampling (bat fur) can be justified following risk assessment
Artificial Intelligence for Hemodynamic Monitoring with a Wearable Electrocardiogram Monitor
Authors: Schlesinger Daphne E. , Alam Ridwan , Ringel Roey , Pomerantsev Eugene , Devireddy Srikanth , Shah Pinak , Garasic Joseph , Stultz Collin M.
Published: April 2024

Background

The ability to non-invasively measure left atrial pressure would facilitate the identification of patients at risk of pulmonary congestion and guide proactive heart failure care. Wearable cardiac monitors, which record single-lead electrocardiogram data, provide information that can be leveraged to infer left atrial pressures.

Methods

We developed a deep neural network using single-lead electrocardiogram data to determine when the left atrial pressure is elevated. The model was developed and internally evaluated using a cohort of 6739 samples from the Massachusetts General Hospital (MGH) and externally validated on a cohort of 4620 samples from a second institution. We then evaluated model on patch-monitor electrocardiographic data on a small prospective cohort.

Results

The model achieves an area under the receiver operating characteristic curve of 0.80 for detecting elevated left atrial pressures on an internal holdout dataset from MGH and 0.76 on an external validation set from a second institution. A further prospective dataset was obtained using single-lead electrocardiogram data with a patch-monitor from patients who underwent right heart catheterization at MGH. Evaluation of the model on this dataset yielded an area under the receiver operating characteristic curve of 0.875 for identifying elevated left atrial pressures for electrocardiogram signals acquired close to the time of the right heart catheterization procedure.

Conclusions

These results demonstrate the utility and the potential of ambulatory cardiac hemodynamic monitoring with electrocardiogram patch-monitors.

Plain Language Summary

Heart failure is a prevalent disorder that is challenging to manage. Part of what makes heart failure management challenging is that the onset of symptoms can be insidious as there are few robust tools that a clinical can leverage to estimate when a patient is likely to experience an episode of acute heart failure. While elevated intracardiac pressures are a reliable harbinger of worsening heart failure, these pressures are typically measured using an invasive, gold-standard approach, which can only be performed in an inpatient setting. A non-invasive method for detecting higher pressures inside of heart would be especially helpful for identifying worsening heart failure in an expeditious manner in the home environment. For this reason, we developed an artificial intelligence model to detect elevated pressures inside the heart using a non-invasive signal, the electrocardiogram (ECG, or EKG), which can be acquired from a wearable patch monitor device. Our results demonstrate that the model provides a reliable platform for the non-invasive assessment of cardiac pressures using data that can be obtained in the outpatient setting.
Barriers influencing the care of survivors of gender-based violence in the context of forced displacement in Kaya, Burkina Faso: a qualitative study
Authors: Bayoulou Souleymane , Ngangue Patrice , Kaboré Soutongnoma Safiata , Nteungue Boris Arnaud Kouomogne , Pafadnam Yacouba , Yopa Danièle Sandra , Seu Josiane , Kiki Gbètogo Maxime
Published: April 2024

Gender-based violence (GBV) is a serious international health problem that challenges fundamental human rights. In addition to violating fundamental rights, it is an attack on the principles of gender equality. GBV is exacerbated in situations of conflict and forced displacement because of the vulnerability it engenders, particularly among women and children. Therefore, caring for victims of GBV in the context of a humanitarian crisis is special because of the specific nature of the context itself. This study aimed to explore the factors that negatively influence the care of survivors of GBV in the context of forced displacement. This was a descriptive and analytical-qualitative study. A total of 26 participants participated in the individual interviews. Most participants were healthcare workers (53,8%). The findings show that barriers to care are sociocultural (fear of stigmatization, ignorance of the benefits of seeking appropriate care and support, self-censorship among GBV survivors, fear or risk of reprisal, honor denied, fear of the aggressor punishment, shame and fear of being repudiated), institutional (lack of qualified human resources to care for GBV survivors, insufficient information on the availability of care services, geographical inaccessibility of care services, lack of confidentiality from service providers, inadequate health care and support systems, low availability of care services, poor quality of care) and financial. Bringing all care services together in one place, such as a one-stop center, is imperative to overcome these obstacles. In this way, it will be possible to improve accessibility to services and enhance the quality of care through effective coordination.
CovTransformer: A transformer model for SARS-CoV-2 lineage frequency forecasting
Authors: Feng Yinan , Goldberg Emma E , Kupperman Michael , Zhang Xitong , Lin Youzuo , Ke Ruian
Published: April 2024

With hundreds of SARS-CoV-2 lineages circulating in the global population, there is an urgent need for forecasting lineage frequencies and thus identifying rapidly expanding lineages. To address this need, we constructed a framework for SARS-CoV-2 lineage frequency forecasting (CovTransformer), based on the transformer architecture. We designed our framework to navigate challenges such as a limited amount of data with high levels of noise and bias. We first trained and tested the model using data from the UK and the US, and then tested the generalization ability of the model on data collected across the globe. Remarkably, the model makes predictions two months into the future with high levels of accuracy in 31 countries. Finally, we show that our model performed substantially better than the current gold-standard, i.e. a regression-based model implemented in Nextstrain. Overall, our work demonstrates transformer models represent a promising approach for lineage forecasting and pandemic monitoring.
BENEFITS OF PALLIATIVE CARE IN ADULTS WITH A DIAGNOSIS OF HEART FAILURE: AN EXPLORATORY LITERATURE REVIEW
Authors: Herrera Obando Aura Cristina , Larrañaga Guerrero Jhaina Isabella , Mejia Montehermoso William Antonio , Giraldo Oliveros Simon Andres
Published: April 2024

Introduction

Heart Failure is a clinical syndrome characterized by a series of symptoms such as dyspnea, orthopnea and edema in the lower limbs. This pathology continues to have a high prevalence despite advances in pharmacotherapy and device therapy and given that it is a pathology that significantly impairs the quality of life of patients, the implementation of care is of vital importance. However, these are underused due to lack of knowledge on the part of health personnel and also due to poor implementation in the different health providers.

Objective

An exploratory review of the literature was carried out regarding the benefits of palliative care in patients with advanced heart failure, in order to synthesize the available and updated evidence.

Methodology

Searched for articles published from 2017 to 2022 related to palliative care in patients with heart failure and using the PRISMA 2020 methodology for this study. This inquiry of articles was carried out in the following databases: UpToDate, PubMed, MESH, PMC (US National Library of Medicine National Institutes of health).

Results

A total of 5 articles were obtained, from which they concluded that palliative care has a positive impact on the quality of life of patients with heart failure, there was a lower rate of hospital readmissions, improvements in physical, psychological and existential.
Circulating biomarkers of kidney tumors in TSC (tuberous sclerosis complex) patients
Authors: Rubtsova Varvara I. , Chun Yujin , Kim Joohwan , Ramirez Cuauhtemoc B. , Jung Sunhee , Cassidy Elizabeth , Rushing Gabrielle , Aguiar Dean J. , Lau Wei Ling , Ahdoot Rebecca S. , Smith Moyra , Lee Sang-Guk , Jang Cholsoon , Lee Gina
Published: April 2024

Patients with tuberous sclerosis complex (TSC) develop an array of multi-organ disease manifestations, with angiomyolipomas (AML) and cysts in the kidneys being one of the most common and deadly. Early and regular AML/cyst detection and monitoring are vital in lowering TSC patient morbidity and mortality. However, current standard of care for imaging-based methods are not designed for rapid screening, posing challenges for early detection. To identify potential diagnostic screening biomarkers of AML/cysts, we performed global untargeted metabolomics in blood samples from 283 kidney AML/cyst-positive or -negative TSC patients using mass spectrometry. We identified seven highly sensitive chemical features, including octanoic acid, that predict kidney AML/cysts in TSC patients. Patients with elevated octanoic acid have lower levels of very long-chain fatty acids (VLCFAs), suggesting that dysregulated peroxisome activity leads to overproduction of octanoic acid via VLCFA oxidation. This study highlights serum metabolites as novel biomarkers for TSC kidney tumor diagnosis and offers valuable metabolic insights into the disease.
Laminar multi-contrast fMRI at 7T allows differentiation of neuronal excitation and inhibition underlying positive and negative BOLD responses
Authors: Shao Xingfeng , Guo Fanhua , Kim JungHwan , Ress David , Zhao Chenyang , Shou Qinyang , Jann Kay , Wang Danny JJ
Published: April 2024

A major challenge for human neuroimaging using functional MRI is the differentiation of neuronal excitation and inhibition which may induce positive and negative BOLD responses. Here we present an innovative multi-contrast laminar functional MRI technique that offers comprehensive and quantitative imaging of neurovascular (CBF, CBV, BOLD) and metabolic (CMRO2) responses across cortical layers at 7 Tesla. This technique was first validated through a finger-tapping experiment, revealing ’double-peak’ laminar activation patterns within the primary motor cortex. By employing a ring-shaped visual stimulus that elicited positive and negative BOLD responses, we further observed distinct neurovascular and metabolic responses across cortical layers and eccentricities in the primary visual cortex. This suggests potential feedback inhibition of neuronal activities in both superficial and deep cortical layers underlying the negative BOLD signals in the fovea, and also illustrates the neuronal activities in visual areas adjacent to the activated eccentricities.
TrajectoryViz: Interactive visualization of treatment trajectories
Authors: Pajusalu Maarja , Mooses Kerli , Oja Marek , Tamm Sirli , Haug Markus , Kolde Raivo
Published: April 2024

Background and objectives

With the proliferation of real-world or observational health data, there is increasing interest in studying treatment trajectories. The real-life treatment trajectories can be complex, and one has to simplify the patterns to draw any conclusions; however, oversimplification will cause the loss of essential details. Thus, the visualization challenge is to strike a balance between the two extremes.

Methods

We have implemented the observation of treatment trajectories starting from cohort definitions in cooperation with medical specialists, data processing, and then generating the interactive visualizations and detailed data tables within an open-source R package as a Shiny dashboard. The created R package called TrajectoryViz (https://github.com/HealthInformaticsUT/TrajectoryViz) enables reproducible visual analysis and visual content generation for various data investigations.

Results

We illustrate the use of the tool by assessing the sequence of events present within the data of cervical cancer prevention pathways, as well as the proportions of timely follow-up procedure events.

Conclusion

Building a toolset to access, manage, and analyze observational health data enables more accessible visual analysis of complicated data, adding time dimension to otherwise simplified event sequences that make up trajectories.
Pacemaker implantation after cardiac surgery: a contemporary, nationwide perspective
Authors: Taha Amar , David Alice , Ragnarsson Sigurdur , Szamlewski Piotr , Jamaly Shabbar , Smith J. Gustav , Nielsen Susanne J. , Jeppsson Anders , Martinsson Andreas
Published: April 2024

Background

Cardiac surgery entails an increased risk for brady-arrhythmias. Currently known rates for permanent pacemaker (PPM) implantation after cardiac surgery are derived from non-contemporary studies. This study aimed to explore the incidence and indications for PPM implantation at 30 days and one year after different cardiac surgical procedures in a modern cohort.

Methods

All first-time coronary artery bypass grafting (CABG) and/or valvular surgery patients in Sweden 2006 - 2020 without previous PPM or implantable cardioverter-defibrillator (ICD) (n= 76,447) were included in this nationwide population-based study using data from four national registries. Patients undergoing heart transplantation and those who subsequently received an ICD were excluded.

Results

A PPM was implanted in 8.2% (n= 6,271) of the patients, 35% (n= 2,196) within the first 30 days and 46.3% (n= 2,647) at one year following surgery. The main indication of PPM implantation was atrioventricular block. Tricuspid valve surgery exhibited the highest cumulative incidence for PPM both at 30 days (6.8% (95% confidence interval 4.3 – 10.0)) and one year (8.8% (95% CI 6.0 – 12.0)) surpassing mitral valve surgery (30-day 5.3% (95% CI 4.7-6.0); one-year 6.5% (95% CI 5.8-7.3)), aortic valve surgery (30-day 4.8% (95% CI 4.5-5.1); one-year 6.0% (95% CI 5.6-6.3)) and CABG (30-day 0.74% (95% CI 0.66-0.83); one-year 1.3% (95% CI 1.2-1.35)). The incidence following combined operations (multiple valves and/or coronary surgery) was 6.5% (95% CI 6.0 – 6.9) and 8.1% (95% CI 7.7 – 8.6) at 30 days and one year respectively. Concomitant ablation surgery increased the risk even further (adjusted Hazard Ratio 9.20 (95% CI 7.96-10.64), p<0.001).

Conclusions

The need for PPM after cardiac surgery is common, primarily due to atrioventricular block. Tricuspid valve surgery is associated with the highest risk for PPM implantation amongst isolated procedures. Combined procedures and concomitant surgical ablation further increase that risk.

CLINICAL PERSPECTIVE

What is new?

Permanent pacemaker after cardiac surgery is not uncommon with atrioventricular blocking being the main indication.

Tricuspid valve surgery had the highest cumulative incidence at 30 days and one year, exceeding other isolated procedures.

Combined cardiac surgical procedures and concomitant ablation surgery increased the risk even further.

What are the clinical implications?

This information is valuable while informing individual patients awaiting cardiac surgery about potential post-operative complications.

Recognizing patients at higher risk enables targeted postoperative care, including closer monitoring for signs of conduction disturbances.

Studies investigating and identifying predictors of post-cardiac surgery bradyarrhythmias and subsequent need for permanent pacemakers are needed.
HHIP protein interactions in lung cells provide insight into COPD pathogenesis
Authors: Deritei Dávid , Inuzuka Hiroyuki , Castaldi Peter J. , Yun Jeong Hyun , Xu Zhonghui , Anamika Wardatul Jannat , Asara John M. , Guo Feng , Zhou Xiaobo , Glass Kimberly , Wei Wenyi , Silverman Edwin K.
Published: April 2024

Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide. The primary causes of COPD are environmental, including cigarette smoking; however, genetic susceptibility also contributes to COPD risk. Genome-Wide Association Studies (GWASes) have revealed more than 80 genetic loci associated with COPD, leading to the identification of multiple COPD GWAS genes. However, the biological relationships between the identified COPD susceptibility genes are largely unknown. Genes associated with a complex disease are often in close network proximity,i.e.their protein products often interact directly with each other and/or similar proteins. In this study, we use affinity purification mass spectrometry (AP-MS) to identify protein interactions withHHIP, a well-established COPD GWAS gene which is part of the sonic hedgehog pathway, in two disease-relevant lung cell lines (IMR90 and 16HBE). To better understand the network neighborhood ofHHIP, its proximity to the protein products of other COPD GWAS genes, and its functional role in COPD pathogenesis, we create HUBRIS, a protein-protein interaction network compiled from 8 publicly available databases. We identified both common and cell type-specific protein-protein interactors of HHIP. We find that our newly identified interactions shorten the network distance between HHIP and the protein products of several COPD GWAS genes, includingDSP, MFAP2, TET2, andFBLN5. These new shorter paths include proteins that are encoded by genes involved in extracellular matrix and tissue organization. We found and validated interactions to proteins that provide new insights into COPD pathobiology, including CAVIN1 (IMR90) and TP53 (16HBE). The newly discovered HHIP interactions with CAVIN1 and TP53 implicate HHIP in response to oxidative stress.
Explorative Discovery of Gene Signatures and Clinotypes in Glioblastoma Cancer Through GeneTerrain Knowledge Map Representation
Authors: Saghapour Ehsan , Yue Zongliang , Sharma Rahul , Kumar Sidharth , Sembay Zhandos , Willey Christopher D. , Chen Jake Y.
Published: April 2024

This study introduces the GeneTerrain Knowledge Map Representation (GTKM), a novel method for visualizing gene expression data in cancer research. GTKM leverages protein-protein interactions to graphically display differentially expressed genes (DEGs) on a 2-dimensional contour plot, offering a more nuanced understanding of gene interactions and expression patterns compared to traditional heatmap methods. The research demonstrates GTKM’s utility through four case studies on glioblastoma (GBM) datasets, focusing on survival analysis, subtype identification, IDH1 mutation analysis, and drug sensitivities of different tumor cell lines. Additionally, a prototype website has been developed to showcase these findings, indicating the method’s adaptability for various cancer types. The study reveals that GTKM effectively identifies gene patterns associated with different clinical outcomes in GBM, and its profiles enable the identification of sub-gene signature patterns crucial for predicting survival. The methodology promises significant advancements in precision medicine, providing a powerful tool for understanding complex gene interactions and identifying potential therapeutic targets in cancer treatment.