bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of Noroviruses GII in wastewater samples of Bhopal, India, using Droplet Digital PCR
Authors: Nema R K , Nagar J , Singh A K , Tandekar A , Singh S , Rahman A , Sharma O P , Tiwari R R , Sarma D K , Mishra P K 
Published: December 2023

AbstractNoroviruses are a significant cause of global gastroenteritis outbreaks, underscoring the importance of effective surveillance. Wastewater-based epidemiology helps identify viral pathogens in communities. Recent advancements in wastewater-based molecular surveillance have shown that viruses can be detected in feces and urine early, making sewage monitoring an essential tool for tracking viral presence. We aimed to create and validate a new method for detecting and monitoring Noroviruses GII in Bhopal’s wastewater using Automated Droplet Digital PCR (ddPCR) technology. In this study, a ddPCR assay targeting the ORF1-2 region of Norovirus GII was developed, allowing viral nucleic acid quantification without a standard curve. A total of 27 samples from five Sewage Treatment Plants located in Bhopal city were collected during the summer season (April and May 2023) at fortnightly intervals and analyzed for the presence of Norovirus using the novel ddPCR assay. Among the samples tested, 33% tested positive for Norovirus, with the highest detection rate observed as 72.72%, followed by 25%. The concentrations of Noroviruses GII in positive samples ranged from 0.06 to 6.60 copies/µl. These findings indicate a potentially higher patient population within Bansal Hospital’s catchment area than the other STPs in the Bhopal region. The study underscores Norovirus’s varying prevalence and distribution in wastewater across different STPs in Bhopal. Moreover, it demonstrates the utility of wastewater surveillance and digital PCR in accurately and specifically detecting Norovirus in wastewater. The practical application of this wastewater surveillance strategy could serve as an early warning system for communities, enabling timely preparedness for impending viral outbreaks, implementation of effective administrative containment measures, and intensified vaccination campaigns.
Pain, inconvenience, and blame - Defining work-related injuries in the veterinary workplace
Authors: Furtado Tamzin , Whiting Martin , Schofield Imogen , Jackson Rebecca , Tulloch John S.P. 
Published: December 2023

AbstractObjectivesThe veterinary workplace carries a high risk of staff accidents and injuries, yet there is scant research exploring it in comparison with other comparable fields, such as human medicine. The aim of this study was to understand how veterinary professionals define injuries and to understand what injuries they do, or do not, deem reportable.MethodsA cross-sectional survey comprising demographic questions and open-text questions was shared with veterinary practice staff across the United Kingdom. Data were analysed descriptively and using an inductive content analysis.ResultsThere were 740 respondents, who were broadly representative of the veterinary profession. There were differences in how injuries were defined; for example, small animal veterinarians expected injuries to involve blood, while equine and production animal veterinarians were more likely to expect injuries to reduce their ability to perform work and result in time off work. Many suggested that “all” workplace injuries should be reported, however “minor” injuries were often overlooked, for example needlestick injuries did not always meet the criteria of being an “injury”. Injuries caused by staff themselves (e.g. trips) were less likely to be reported than injuries that could be blamed on an external factor (e.g. dog bite).ConclusionsCollectively, the data suggest a wide-ranging perception of risk of injury in practice, with some harms seen as “everyday norms”. Veterinary practices should interpret their injury statistics with a high degree of caution. They should explore the microcultures within their practices relating to worker perception of risk, injury and barriers to reporting.What is already known on this topicThe veterinary industry has one of the highest case rates of non-fatal occupation injuries and illnesses per full time worker. In the USA, no other industry is higher; it is almost five times higher than the national average. Yet, little research has explored how injuries are perceived nor their context.What this study addsThis study shows clear divisions within different veterinary sectors, and job roles, in how injuries are perceived. In particular, that equine and production animal veterinarians have a high threshold before acknowledging that an incident is a work-related injury.How this study might affect research, practice or policyTo contextualise any epidemiological research into veterinary workplace injuries, one needs to understand how injuries are perceived. The discordance in definition needs to be accounted for when interpreting company or national injury reporting figures.
Multiscale predictability of Cutaneous Leishmaniasis in Morocco and Tunisia through the AMO-NAO coupling and its modulation of regional rainfall
Authors: San-José Adrià , Aoun Karim , Lemrani Meryem , Idis Mhaidi , Bouratbine Aida , Paul Richard , Rodó Xavier 
Published: December 2023

AbstractThe development of effective Early Warning Systems (EWS) for climate-driven zoonotic diseases has been hindered by a lack of predictors with adequate lead time for effective interventions. Atmosphere-Ocean coupled phenomena present predictability beyond the atmospheric deterministic limits and therefore are potentially useful climate drivers to be integrated in mathematical models. While the El Niño-Southern Oscillation (ENSO) has been used to forecast disease dynamics in equatorial and tropical regions, there is a lack of similar applications for temperate areas, likely because of the perceived unpredictability of atmospheric systems such as the North Atlantic Oscillation (NAO). This study challenges this notion by establishing a connection between the NAO and its oceanic counterpart, the Atlantic Multidecadal Oscillation (AMO), revealing common low-frequency components that strongly modulate Cutaneous Leishmaniasis (CL) in Northern Africa. We demonstrate not only short-term couplings, such as the known NAO’s impact on seasonal rainfall, which subsequently affects CL incidence, but we also uncover a significant lagged effect of approximately three years on rainfall and four years on CL incidence. Our findings reveal a unified, multiscale mechanism that influences CL epidemiology across different time scales, underscoring the predictive skill for short and long term time frames, which should be integrated in CL forecasting models.
Diagnostic Accuracy of the Abbot BinaxNOW COVID-19 Antigen Card Test, Puerto Rico
Authors: Madewell Zachary J. , Major Chelsea G. , Graff Nathan , Adams Cameron , Rodriguez Dania M. , Morales Tatiana , Medina Lopes Nicole A. , Tosado Rafael , Sánchez-González Liliana , Perez-Padilla Janice , Volkman Hannah R. , Bertran Jorge , Sainz Diego , Munoz-Jordan Jorge , Santiago Gilberto A. , Lorenzi Olga , Rivera-Amill Vanessa , Rolfes Melissa A. , Paz-Bailey Gabriela , Adams Laura E. , Wong Joshua M. ,   PRESCA Study Team
Published: December 2023

AbstractBackgroundThe COVID-19 pandemic underscored the need for rapid and accurate diagnostic tools. In August 2020, the Abbot BinaxNOW COVID-19 Antigen Card test became available as a timely and affordable alternative for SARS-CoV-2 molecular testing, but its performance may vary due to factors including timing and symptomatology. This study evaluates BinaxNOW diagnostic performance in diverse epidemiological contexts.MethodsUsing RT-PCR as reference, we assessed performance of the BinaxNOW COVID-19 test for SARS-CoV-2 detection in anterior nasal swabs from participants of two studies in Puerto Rico from December 2020 to May 2023. Test performance was assessed by days post symptom onset, collection strategy, vaccination status, symptomatology, repeated testing, and RT-PCR cycle threshold (Ct) values.ResultsBinaxNOW demonstrated an overall sensitivity of 84.1% and specificity of 98.8%. Sensitivity peaked within 1–6 days after symptom onset (93.2%) and was higher for symptomatic (86.3%) than asymptomatic (67.3%) participants. Sensitivity declined over the course of infection, dropping from 96.3% in the initial test to 48.4% in testing performed 7–14 days later. BinaxNOW showed 99.5% sensitivity in participants with low Ct values (≤25) but lower sensitivity (18.2%) for participants with higher Cts (36–40).ConclusionsBinaxNOW demonstrated high sensitivity and specificity, particularly in early-stage infections and symptomatic participants. In situations where test sensitivity is crucial for clinical decision- making, nucleic acid amplification tests are preferred. These findings highlight the importance of considering clinical and epidemiological context when interpreting test results and emphasize the need for ongoing research to adapt testing strategies to emerging SARS-CoV-2 variants.
GPT for RCTs?: Using AI to determine adherence to reporting guidelines
Authors: Wrightson J.G. , Blazey P. , Moher D. , Khan K.M. , Ardern C.L. 
Published: December 2023

AbstractBackgroundAdherence to established reporting guidelines can improve clinical trial reporting standards, but attempts to improve adherence have produced mixed results. This exploratory study aimed to determine how accurate a Large Language Model generative AI system (AI-LLM) was for determining reporting guideline compliance in a sample of sports medicine clinical trial reports.Design and MethodsThis study was an exploratory retrospective data analysis. The OpenAI GPT-4 and Meta LLama2 AI-LLMa were evaluated for their ability to determine reporting guideline adherence in a sample of 113 published sports medicine and exercise science clinical trial reports. For each paper, the GPT-4-Turbo and Llama 2 70B models were prompted to answer a series of nine reporting guideline questions about the text of the article. The GPT-4-Vision model was prompted to answer two additional reporting guideline questions about the participant flow diagram in a subset of articles. The dataset was randomly split (80/20) into a TRAIN and TEST dataset. Hyperparameter and fine-tuning were performed using the TRAIN dataset. The Llama2 model was fine-tuned using the data from the GPT-4-Turbo analysis of the TRAIN dataset. Primary outcome measure: Model performance (F1-score, classification accuracy) was assessed using the TEST dataset.ResultsAcross all questions about the article text, the GPT-4-Turbo AI-LLM demonstrated acceptable performance (F1-score = 0.89, accuracy[95% CI] = 90%[85-94%]). Accuracy for all reporting guidelines was > 80%. The Llama2 model accuracy was initially poor (F1-score = 0.63, accuracy[95%CI] = 64%[57-71%]), and improved with fine-tuning (F1-score = 0.84, accuracy[95%CI] = 83%[77-88%]). The GPT-4-Vision model accurately identified all participant flow diagrams (accuracy[95% CI] = 100%[89-100%]) but was less accurate at identifying when details were missing from the flow diagram (accuracy[95% CI] = 57%[39-73%]).ConclusionsBoth the GPT-4 and fine-tuned Llama2 AI-LLMs showed promise as tools for assessing reporting guideline compliance. Next steps should include developing an efficent, open-source AI-LLM and exploring methods to improve model accuracy.
Online cognitive behavioural therapy as an initial treatment for psychological distress in patients waiting for therapy: Study protocol
Authors: Guiney Hayley , Mahoney Alison , Morgan Andie , Elders Anna , David Charlie , Howell Zahra , Codyre David , Rapsey Charlene , Poulton Richie 
Published: December 2023

AbstractBackgroundWait times for mental health treatment are long. This protocol describes a trial to test whether engaging in a self-directed online cognitive behavioural therapy tool (called ‘Just a Thought’) while waiting for psychological therapy is an acceptable and effective intervention for help-seeking patients. The trial will be conducted within the context of a large psychological service in Auckland, New Zealand.MethodsIn this parallel group, pragmatic randomised controlled trial, consenting patients with at least five weeks to wait for their first therapy appointment will be randomly assigned to receive Just a Thought (intervention) or waitlist-as-usual conditions plus generic wellbeing information (control) while they wait. Mental health, general health and wellbeing, and treatment satisfaction will be measured across the first ten weeks of the trial, and at 8 months.OutcomesThe primary outcomes are the acceptability and effectiveness of Just a Thought as an initial treatment. Acceptability will be assessed as participants’ satisfaction, and effectiveness as change in psychological distress over time (relative to control). We hypothesise that participants will be more satisfied with Just a Thought than generic wellbeing information and that those who engage in Just a Thought will show greater reductions in psychological distress than those in the waiting-as-usual group.ConclusionsOnline cognitive behavioural therapy is efficacious and has the potential to provide people experiencing psychological distress with fast access to evidence-based psychological treatment. This study will provide insight into its potential as an acceptable and effective pre-treatment for people seeking psychological help.
Portable Cerebral Blood Flow Monitor to Detect Large Vessel Occlusion in Suspected Stroke Patients
Authors: Favilla Christopher G. , Baird Grayson L. , Grama Kedar , Konecky Soren , Carter Sarah , Smith Wendy , Gitlevich Rebecca , Lebron-Cruz Alexa , Yodh Arjun G. , McTaggert Ryan A. 
Published: December 2023

ABSTRACTBackgroundEarly detection of large vessel occlusion (LVO) facilitates triage to a comprehensive or thrombectomy-capable stroke center to reduce treatment times and improve outcomes. Prehospital stroke scales, however, are not sufficiently sensitive, so here we investigate the ability of the portable Openwater optical blood flow monitor to detect LVO in patients undergoing acute stroke evaluation.MethodsPatients were prospectively enrolled at two comprehensive stroke centers during acute stroke evaluation within 24 hours of symptom onset with NIHSS ≥2. Each patient underwent a 60-second bedside optical blood flow evaluation with the Openwater instrument. The Openwater instrument generates cerebral blood flow waveforms based on relative changes in speckle contrast. Anterior circulation LVO was deteremined based on CT angiographic imaging and defined as occlusion of the ICA, or first/second segment of the MCA. A deep learning model, based on a transformer architecture trained on all patient data using fivefold cross-validation and learned discriminative representations from the raw speckle contrast waveform data. ROC analysis compared the Openwater diagnostic performance (i.e., LVO detection) with performance of prehospital stroke scales.ResultsAmongst 135 patients, the median NIHSS was 8 (IQR: 4-14), and 52 (39%) had an anterior circulation LVO based on CT angiogram. The Openwater instrument had 79% sensitivity and 84% specificity for the detection of LVO. The RACE scale had 60% sensitivity and 81% specificity. LAMS had 50% sensitivity and 81% specificity. In the ROC analysis, the binary Openwater classification (high-likelihood vs low-likelihood) had an AUC of 0.82 (95%CI: 0.75-0.88), which outperformed RACE (AUC: 0.70; 95%CI: 0.62-0.78; p=0.04) and LAMS (AUC: 0.65; 95% CI: 0.57-0.73; p=0.002).ConclusionsThe Openwater optical blood flow monitor outperformed prehospital stroke scales for the detection of LVO in patients who presented to the Emergency Department for acute stroke evaluation. These encouraging findings need to be validated in the prehospital environment.
Airway epithelial cells as a novel intracellular host reservoir forCryptococcusspores
Authors: Ortiz Sébastien C. , Fortune-Grant Rachael , Davies Joshua , May Robin C. , Drummond Rebecca A. , Bertuzzi Margherita 
Published: December 2023

AbstractHuman fungal pathogens cause an estimated 1.5 million annual deaths andCryptococcus neoformans, an inhaled facultative intracellular pathogen, is at the top of the WHO’s priority list of fungal pathogens.Cryptococcuscauses disease when it disseminates out of the lung and into the brain which can occur years after initial exposure. However, the mechanisms of bothCryptococcusdissemination and latency are still unclear. One potential reason that these mechanisms remain unknown is that the morphotype used for the vast majority of studies is the yeast form and not the dormant and stress resistant spore morphotype. The inhalation ofCryptococcusspores initiates infections and recent evidencein vivohas shown that spores display unique host-pathogen interactions and are able to escape the lung and disseminate to the brain more readily than yeast. Due to the difficulties associated working with these spores, little is known about how they interact with host cells.AirwayEpithelialCells (AECs), which cover the entire alveolar surface and comprise 24% of all cells in the human lung parenchyma, likely have instant and extensive contact with inhaled spores. In this study, we demonstrated thatCryptococcusspores can invade AECs bothin vitroandin vivo. Once inside spores can germinate and subsequently replicate, persist and/or escape. This ability to enter AECs correlates with a preferential ability of spore to cross AEC barriers. Together our work indicates AECs may serve as a previously ignored intracellular host reservoir and challenges the current paradigms of bothCryptococcusdissemination and latency.
Path analysis reveals combined winter climate and pollution effects on the survival of a marine top predator
Authors: Layton-Matthews Kate , Erikstad Kjell E. , Sandvik Hanno , Ballesteros Manuel , Hodges Kevin , Mesquita Michael d.S. , Reiertsen Tone K. , Yoccoz Nigel G. , Bustnes Jan Ove 
Published: December 2023

AbstractMarine ecosystems are experiencing growing pressure from multiple threats caused by human activities, with far-reaching consequences for marine food webs. Determining the effects of multiple stressors is complex, in part, as they can affect different levels of biological organisation (behaviour, individual traits, demographic rates). Knowledge of the cumulative effects of stressors is key to predict the consequences for threatened populations’ viability under global change. Due to their position in the food chain, top predators such as seabirds are considered more sensitive to environmental changes. Climate change is affecting the prey resources available for seabirds, through bottom-up effects, while organic pollutants can bioaccumulate in food chains with the greatest impacts on top predators. However, knowledge of their combined effects on seabird population dynamics is lacking. Using a path analysis, we quantify the effects of both climate change and pollution, via an effect on body mass, on the survival of adult great black-backed gulls. Warmer ocean temperatures in gulls’ winter foraging areas in the North Sea were correlated with higher survival, potentially explained by shifts in prey availability associated with global climate change. We also found support for indirect negative effects of organochlorines, highly toxic pollutants to seabirds, on survival acting through a negative effect on body mass. The results from this path analysis highlight how, even for such long-lived species where variance in survival tends to be limited, two stressors still have had a marked influence on adult survival and illustrate the potential of such models to improve predictions of population variability under multiple stressors.
Conformational Space Profile Enhances Generic Molecular Representation Learning
Authors: Wang Lin , Wang Shihang , Yang Hao , Li Shiwei , Wang Xinyu , Zhou Yongqi , Tian Siyuan , Liu Lu , Bai Fang 
Published: December 2023

AbstractThe molecular representation model is a neural network that converts molecular representations (SMILES, Graph) into feature vectors, that carries the potential to be applied across a wide scope of drug discovery scenarios. However, current molecular representation models have been limited to 2D or static 3D structures, overlooking the dynamic nature of small molecules in solution and their ability to adopt flexible conformational changes crucial for drug-target interactions. To address this limitation, we propose a novel strategy that incorporates the conformational space profile into molecular representation learning. By capturing the intricate interplay between molecular structure and conformational space, our strategy enhances the representational capacity of our model named GeminiMol. Consequently, when pre-trained on a miniaturized molecular dataset, the GeminiMol model demonstrates a balanced and superior performance not only on traditional molecular property prediction tasks but also on zero-shot learning tasks, including virtual screening and target identification. By capturing the dynamic behavior of small molecules, our strategy paves the way for rapid exploration of chemical space, facilitating the transformation of drug design paradigms.
Deep MALDI-MS Spatial ‘Omics guided by Quantum Cascade Laser Mid-infrared Imaging Microscopy
Authors: Gruber Lars , Schmidt Stefan , Enzlein Thomas , Vo Huong Giang , Cairns James Lucas , Ucal Yasemin , Keller Florian , Abu Sammour Denis , Rudolf Rüdiger , Eckhardt Matthias , Iakab Stefania Alexandra , Bindila Laura , Hopf Carsten 
Published: December 2023

AbstractIn spatial ‘omics, highly confident molecular identifications are indispensable for the investigation of complex biology and for spatial biomarker discovery. However, current mass spectrometry (MS)-based spatial ‘omics must compromise between data acquisition speed and biochemical profiling depth, thus often leading to only “putative” molecular identifications. Here, we introduce fast quantum cascade laser mid-infrared imaging microscopy to guide MS imaging to confined tissue areas of high interest,e.g.,multicellular spheroid cores or kidney glomeruli, for spatial lipidomics profiling at maximized analytical depth utilizing magnetic resonance-MS imaging at >106resolution or prm-PASEF-MS2fragmentation imaging. Instigating selective sulfatide accumulation in arylsulfatase A-deficient mice as ground truth concept, we demonstrate that deep QCL-infrared-guidedon-tissuespatial ‘omics unequivocally identifies 120 sulfatides. This approach enables identifications of odd-chain sulfatides and studies of structure-ion mobility-relationships that provide chemical rationales for improvements to current ion mobility prediction algorithms. Workflows and data processing tools are provided as community resources.
Connecting species-specific extents of genome reduction in mitochondria and plastids
Authors: Giannakis Konstantinos , Richards Luke , Dauda Kazeem A. , Johnston Iain G. 
Published: December 2023

AbstractMitochondria and plastids have both dramatically reduced their genomes since the endosymbiotic events that created them. The similarities and differences in the evolution of the two organelle genome types has been the target of discussion and investigation for decades. Ongoing work has suggested that similar mechanisms may modulate the reductive evolution of the two organelles in a given species, but quantitative data and statistical analyses exploring this picture remain limited outside of some specific cases like parasitism. Here, we use cross-eukaryote organelle genome data to explore evidence for coevolution of mitochondrial and chloroplast genome reduction. Controlling for differences between clades and pseudoreplication due to relatedness, we find that mtDNA and ptDNA gene retention are related across taxa, in a generally positive correlation that appears to differ quantitatively across eukaryotes, for example, between algal and non-algal species. We find limited evidence for coevolution of specific mtDNA and ptDNA gene pairs, suggesting that the similarities between the two organelle types may be due mainly to independent responses to consistent evolutionary drivers.