bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing GPT-3.5 and GPT-4 in Generating International Classification of Diseases Billing Codes
Authors: Soroush Ali , Glicksberg Benjamin S. , Zimlichman Eyal , Barash Yiftach , Freeman Robert , Charney Alexander W. , Nadkarni Girish N , Klang Eyal 
Published: July 2023

BackgroundLarge Language Models (LLMs) like GPT-3.5 and GPT-4 are increasingly entering the healthcare domain as a proposed means to assist with administrative tasks. To ensure safe and effective use with billing coding tasks, it is crucial to assess these models’ ability to generate the correct International Classification of Diseases (ICD) codes from text descriptions.ObjectivesWe aimed to evaluate GPT-3.5 and GPT-4’s capability to generate correct ICD billing codes, using the ICD-9-CM (2014) and ICD-10-CM and PCS (2023) systems.MethodsWe randomly selected 100 unique codes from each of the most recent versions of the ICD-9-CM, ICD-10-CM, and ICD-10-PCS billing code sets published by the Centers for Medicare and Medicaid Services. Using the ChatGPT interface (GPT-3.5 and GPT-4), we prompted for the ICD codes that corresponding to each provided code description. Outputs were compared with the actual billing codes across several performance measures. Errors were qualitatively and quantitatively assessed for any underlying patterns.ResultsGPT-4 and GPT-3.5 demonstrated varied performance across each ICD system. In ICD-9-CM, GPT-4 and GPT-3.5 achieved an exact match rate of 22% and 10%, respectively. 13% (GPT-4) and 10% (GPT-3.5) of generated ICD-10-CM codes were exact matches. Notably, both models struggled considerably with the procedurally focused ICD-10-PCS, with neither GPT-4 or GPT-3.5 producing any exactly matched codes. A substantial number of incorrect codes had semantic similarity with the actual codes for ICD-9-CM (GPT-4: 60.3%, GPT-3.5: 51.1%) and ICD-10-CM (GPT-4: 70.1%, GPT-3.5: 61.1%), in contrast to ICD-10-PCS (GPT-4: 30.0%, GPT-3.5: 16.0%).ConclusionOur evaluation of GPT-3.5 and GPT-4’s proficiency in generating ICD billing codes from ICD-9-CM, ICD-10-CM and ICD-10-PCS code descriptions reveals an inadequate level of performance. While the models appear to exhibit a general conceptual understanding of the codes and their descriptions, they have a propensity for hallucinating key details, suggesting underlying technological limitations of the base LLMs. This suggests a need for more rigorous LLM augmentation strategies and validation prior to their implementation in healthcare contexts, particularly in tasks such as ICD coding which require significant digit-level precision.
Prognostic value of advanced lung cancer inflammation index (ALI) combined with geriatric nutritional risk index (GNRI) in patients with chronic heart failure
Authors: Shi Tao , Wang Yan , Peng Yunzhu , Wang Meifen , Zhou Yanji , Gu Wenyi , Li Yanyan , Zou Jie , Zhu Na , Chen Lixing 
Published: July 2023

BackgroundThis study was undertaken to explore the predictive value of the advanced lung cancer inflammation index (ALI) combined with the geriatric nutritional risk index (GNRI) for all‐cause mortality in patients with CHF.Methods and ResultsWe enrolled 1123 patients with HF admitted to our cardiology department from January 2017 to October 2021. Patients were divided into Group 1 (ALI<24.60 and GNRI<94.41), Group 2 (ALI<24.60 and GNRI≥94.41), Group 3 (ALI≥24.60 and GNRI<94.41) and Group 4 (ALI≥24.60 and GNRI≥94.41), according to the median ALI and GNRI. From the analysis of the relationship between the ALI and GNRI, we concluded that there was a mild positive linear correlation (r= 0.348, p< 0.001) and no interaction (p=0.140) between the ALI and GNRI. Kaplan‒Meier analysis showed that the cumulative incidence of all‐cause mortality in patients with CHF was highest in Group 1 (log‐rank χ2126.244, p<0.001). Multivariate Cox proportional hazards analysis revealed that ALI and GNRI were independent predictors of all‐cause mortality in CHF patients (ALI: HR 0.313, 95% CI 0.228‐0.430, p <0.001; GNRI: HR 0.966, 95% CI 0.953‐0.979, p <0.001). The area under the curve (AUC) for ALI combined with GNRI was 0.711 (p<0.001), according to the time‐dependent ROC curve.ConclusionALI and GNRI were independent predictors of all‐cause mortality in CHF patients. Patients with CHF had the highest risk of all‐cause mortality when the ALI was <24.60 and the GNRI was <94.41. ALI combined with the GNRI has good predictive value for the prognosis of CHF patients.
From colonial clusters to colonial sheaths: analysis ofMicrocystismorphospecies in mesocosm by imaging flow cytometry
Authors: Zhumakhanova Adina , Mirasbekov Yersultan , Malashenkov Dmitry V. , Davidson Thomas A. , Levi Eti Ester , Jeppesen Erik , Barteneva Natasha S. 
Published: July 2023

AbstractThe alarming increase in the frequency of blooms ofMicrocystisin freshwater lakes and reservoirs occurs worldwide, with major implications for their ecosystem functioning and water quality. We applied FlowCAM-based imaging flow cytometry together with PCR and sequencing to get a comprehensive picture of the seasonal development ofMicrocystiscommunity in a long-term running lake mesocosm experiment. The IFC analysis with manual taxonomic classification confirmed early findings with a machine learning algorithm that someMicrocystismorphospecies completely disappeared and re-appeared along the mesocosm experiment timeline. This observation supports the hypothesis of the main transition pathways of colonialMicrocystis. For the first time, colonial mucilaginous envelopes or sheaths were reported as separate entities, and not as a part ofMicrocystiscolonies. The colonial sheaths may contain a few single Microcystis cells and reach significant numbers (thousands) during a cyanobacterial bloom. We also found that non-identifiable colonial small clusters ofMicrocystiscells are an important stage in the complex mosaic of aMicrocystisbloom and are associated with the development of colonial forms. Our findings were validated by the principal component analysis coupled with the constructed associative matrices. We hypothesize that colonial sheaths may be crucial atMicrocystisspp. dispersal and represent one of the stages of colonies development.
Modeling the seasonal variation of windborne transmission of porcine reproductive and respiratory syndrome virus between swine farms
Authors: Lim Seunghyun , Perez Andres M. , Kanankege Kaushi S. T. 
Published: July 2023

AbstractModeling windborne transmission of aerosolized pathogens is challenging. We adapted an atmospheric dispersion model named Hybrid Single-Particle Lagrangian Integrated Trajectory model (HYSPLIT) to simulate windborne dispersion of porcine reproductive and respiratory syndrome virus (PRRSv) between swine farms and incorporated the findings into an outbreak investigation. The risk was estimated semi-quantitatively based on the cumulative daily deposition of windborne particles, and the distance to closest emitting farm with an ongoing outbreak. Five years of data (2014 : 2018) were used to study seasonal differences of deposition thresholds of the airborne particles containing PRRSv and to evaluate model in relation to risk prediction and barn air filtration. When considered the 14-day cumulative deposition, in Winter, above threshold particle depositions would reach up to 30 km from emitting farms with 84% of them being within 10km. Long-distance pathogen transmission was highest in Winter and Fall, lower in Spring, and least in Summer. The model successfully replicated the observed seasonality of PRRSv where Fall and Winter posing a higher risk for outbreaks. Reaching the humidity and temperature thresholds tolerated by the virus in Spring and Summer reduced the survival and infectivity of aerosols beyond 10 -20 km. Within in the data limitations of voluntary participation, when assumed wind as the sole route of PRRSv transmission, the predictive performance of the model was fair with >0.64 AUC. Barn air filtration was associated with fewer outbreaks, particularly when exposed to high levels of viral particles. The study confirms the usefulness of HYSPLIT models as a tool when determining seasonal effects, distances, and inform near real-time risk of windborne PRRSv transmission that can be useful in future outbreak investigations and implementing timely control measures.
Preserved striatal innervation and motor function despite severe loss of nigral dopamine neurons following mitochondrial dysfunction induced by mtDNA mutations
Authors: Paß Thomas , Ricke Konrad M. , Hofmann Pierre , Chowdhury Roy , Nie Yu , Chinnery Patrick , Endepols Heike , Neumaier Bernd , Carvalho André , Rigoux Lionel , Steculorum Sophie , Prudent Julien , Riemer Trine , Aswendt Markus , Brachvogel Bent , Wiesner Rudolf J. 
Published: July 2023

AbstractDegeneration of dopamine neurons in the substantia nigra and their striatal axon terminals causes cardinal motor symptoms of Parkinson’s disease (PD). In idiopathic cases, high levels of mitochondrial DNA (mtDNA) mutations associated with mitochondrial dysfunction are a central feature of these vulnerable neurons. Here we present a mouse model expressing the K320E-variant of the mitochondrial helicase Twinkle in dopamine neurons, leading to accelerated mtDNA ageing. K320E-TwinkleDaNmice showed normal motor function at 20 months of age, although already ∼70% of nigral dopamine neurons had perished. The remaining neuron population still preserved ∼75% of axon terminals in the dorsal striatum, which enabled normal dopamine release. Transcriptome analysis and viral tracing confirmed compensatory axonal sprouting of surviving nigral dopamine neurons. We conclude that a small population of substantia nigra neurons can adapt to mtDNA mutations and maintain motor control in mice, holding chances for new treatment strategies in PD patients.
Towards establishing a 24-hour, microplate-based, transcriptomics assay for rainbow trout embryos
Authors: Basu Niladri , Marshall Aylish , Marchand Hugo , Boulanger Emily , Mittal Krittika , Head Jessica 
Published: July 2023

ABSTRACTThere is interest in the development of early-life stage (ELS) tests with fish embryo models that are high-throughput and can generate transcriptomics point of departure (tPOD) values. The objective of this study was to establish a method in rainbow trout (Oncorhynchus mykiss) hatchlings that could satisfy both of these interests. We based our pilot method on recent efforts by U.S. EPA researchers to establish a larval fathead minnow high throughput transcriptomics assay. Here, 1-2 day post hatch trout were assayed in 24-well plates in which they were exposed for 24 hours to 12 different concentrations of test chemicals, including a negative control (DMSO, culture water). Test concentrations were anchored with a chemical’s LC50 data from the US EPA ECOTOX database and EnviroTox database, and from this, concentrations were spaced on a half-log basis that spanned 6-7 orders of magnitude. In pilot study 1 we tested 3,4-dichloroaniline, CuSO4(0.34 mg/L), and ethinylestradiol. In pilot study 2 we tested 3,4-dichloroaniline (58.5 mg/L), CuSO4(0.34 and 0.41 mg/L), ethinylestradiol (>10 µg/L), permethrin (>10 µg/L), malathion (0.61 mg/L), 6PPD quinone (5.6 µg/L), acetaldehyde (41.2 mg/L), 4-fluoroaniline (242.7 mg/L), glyphosate (∼150 mg/L), ethanol (>1 g/L), thiamethoxam (>300 mg/L), and allyl alcohol (>30 mg/L). In both pilot studies derived LC50 values are provided in parentheses. Repeated studies of CuSO4yielded consistent LC50 values (0.34, 0.34, 0.41 mg/L). The correlation between LC50s from the current study for rainbow trout embryos versus those from the literature on adult rainbow trout for 7 chemicals was r2= 0.91. Work is underway to optimize transcriptomics assays from these samples using EcoToxChips and UPXome, with the ultimate goal to be able to derive transcriptomics points of departure. Taken together these results provide a foundation towards establishing a novel testing platform for chemical and environmental risk assessment that is much quicker (24 hrs), ethical (non-protected life stages), resource efficient (e.g., microplate-based, small volumes of chemicals), and more informative (molecular clues into MOA) than traditional bioassay approaches.
Genetic approaches reveal a healthy population and an unexpectedly recent origin for an isolated desert spring fish
Authors: Sidlauskas Brian L. , Mathur Samarth , Aydoğan Hakan , Monzyk Fred R. , Black Andrew N. 
Published: July 2023

AbstractFoskett Spring in Oregon’s desert harbors a historically threatened population of Western Speckled Dace (Rhinichthys klamathensis). Though recently delisted, the dace’s recruitment depends upon regular removal of encroaching vegetation. Previous studies assumed that Foskett Dace separated from others in the Warner Valley about 10,000 years ago, thereby framing an enigma about the population’s surprising ability to persist for so long in a tiny habitat easily overrun by plants. To investigate the phenomenon of persistence and the effectiveness of interventions to augment population size, we assessed genetic diversity among daces inhabiting Foskett Spring, a refuge at Dace Spring, and three nearby streams. Analysis revealed a robust effective population size (Ne) of nearly 5,000 within Foskett Spring, though Nein the Dace Spring refuge is just 10% of that value. Heterozygosity is slightly lower than expected based on random mating at all five sites, indicating mild inbreeding, but not at a level of concern. These results confirm the genetic health of Foskett Dace. Unexpectedly, genetic differentiation reveals closer similarity between Foskett Dace and a newly discovered population from Nevada’s Coleman Creek than between Foskett Dace and dace elsewhere in Oregon. Demographic modeling inferred Coleman Creek as the ancestral source of Foskett Dace just 600 years ago, much more recently than previously suspected and coincident with the arrival of large herbivores whose grazing may have maintained open water suitable for reproduction. These results solve the enigma of persistence by greatly shortening the duration over which Foskett Dace have inhabited their isolated spring.
Human complement Factor H and Properdin act as soluble pattern recognition receptors and differentially modulate SARS-CoV-2 Infection
Authors: Beirag Nazar , Varghese Praveen M , Kumar Chandan , Idicula-Thomas Susan , Neto Martin Mayora , Khan Haseeb A. , Sim Robert B. , Madan Taruna , Temperton Nigel , Kishore Uday 
Published: July 2023

AbstractSevere cases of SARS-CoV-2 infection are characterised by an imbalanced immune response, excessive inflammation, and the development of acute respiratory distress syndrome, which can lead to multiorgan failure and death. Several studies have demonstrated dysregulated complement activity as an indicator of immunopathogenesis in the SARS-CoV-2 infection. Notably, the complement alternative pathway has been implicated in driving the excessive inflammation during severe SARS-CoV-2 infection. Reduced levels of factor H (FH), a down-regulator of the alternative pathway, and increased levels of properdin (Factor P/FP), the only known up-regulator of the alternative pathway, have been observed in individuals with severe COVID-19 infection. The present study investigated the complement activation-independent, and a more direct role of FH and FP against SARS-CoV-2 infection. Using direct ELISA, the interactions of FH and FP with the SARS-CoV-2 spike (S) and receptor binding domain (RBD) were assessed. Using S protein expressing lentiviral pseudotypes, the cell binding and luciferase-based virus entry assays were employed to assess the potential modulatory effects of FH, FP, and recombinant thrombospondin repeats 4 and 5 (TSR4+5) on SARS-CoV-2 cell entry. We also evaluated the immunomodulatory functions of FH and FP in the cytokine response triggered by SARS-CoV-2 pseudotypes via RT-qPCR. SARS-CoV-2 S and RBD proteins were found to bind both FH and FP. Treatment of A549 cells expressing human ACE2 and TMPRSS2 with FP or TSR4+5 resulted in increased cell entry and binding of SARS-CoV-2 pseudotypes. In silico studies revealed that FP increases affinity between SARS-CoV-2 and host ACE2. The impact of FP on viral cell entry and binding was reversed by anti-FP antibody treatment in A549-hACE2+TMPRSS2 cells. However, FH treatment reduced the cell entry and binding of SARS-CoV-2 lentiviral pseudotypes. Furthermore, the A549-hACE2+TMPRSS2 cells challenged with SARS-CoV-2 spike, envelope, nucleoprotein, and membrane protein expressing alphaviral pseudotypes pre-treated with FP or TSR4+5, exhibited upregulation of the transcripts of pro-inflammatory cytokines, such as IL-1β, IL-8, IL-6, TNF-α, IFN-α and RANTES (as well as NF-κB). Conversely, FH pre-treatment downregulated the expression of these pro-inflammatory cytokines. Treatment of A549-hACE2+TMPRSS2 cells with FP increased S protein-mediated NF-κB activation, while FH treatment reduced it. These findings suggest that FH may act as an inhibitor of SARS-CoV-2 cell entry and binding, thereby attenuating the infection-associated inflammatory response in a complement activation-independent manner. FP may contribute to viral cell entry, binding, and exacerbating the immune response. That may result in potentially influencing the severity of the infection.
Molossus molossus bats encompass at least two distinct genera of totivirus-like
Authors: Silva Couto Roseane da , Foro Ramos Endrya do Socorro , Abreu Wandercleyson Uchôa , Ribeiro Rodrigues Luis Reginaldo , Marinho Luis Fernando , Santos Morais Vanessa dos , Villanova Fabiola , Pandey Ramendra Pati , Deng Xutao , Delwart Eric , da Costa Antonio Charlys , Leal Elcio 
Published: July 2023

AbstractThe Totiviridae family of viruses has a unique genome consisting of double-stranded RNA with two open reading frames that encode the capsid protein (Cap) and the RNA-dependent RNA polymerase (RdRp). Most virions in this family are isometric in shape, approximately 40 nm in diameter, and lack envelope. There are five genera within this family, including Totivirus,Victorivirus, Giardiavirus, Leishmaniavirus, andTrichomonasvirus. WhileTotivirusandVictorivirusprimarily infect fungi,Giardiavirus, Leishmaniavirus, andTrichomonasvirusinfect diverse hosts, including protists, insects, and vertebrates. Recently, new totivirus-like species have been discovered in fish and plant hosts, and through metagenomic analysis, a novel totivirus-like virus (named Tianjin totivirus) has been isolated from bat guano. Interestingly, Tianjin totivirus causes cytopathic effects in insect cells but cannot grow in mammalian cells, suggesting that it infects insects consumed by insectivorous bats. In this study, we used next-generation sequencing and identified totivirus-like viruses in liver tissue fromMolossus molossusbats () in the Amazon region of Brazil. Comparative phylogenetic analysis based on the RNA-dependent RNA polymerase region revealed that the viruses identified in Molossus bats belong to two distinct phylogenetic clades, possibly comprising different genera within the Totiviridae family. Notably, the mean similarity between Tianjin totivirus and the totiviruses identified in Molossus bats is less than 18%. These findings suggest that the diversity of totiviruses in bats is more extensive than previously recognized and highlight the potential for bats to serve as reservoirs for novel toti-like viruses.
Molecular Mechanism of a FRET Biosensor for the Cardiac Ryanodine Receptor Pathologically Leaky State
Authors: Svensson Bengt , Nitu Florentin R. , Rebbeck Robyn T. , McGurran Lindsey M. , Oda Tetsuro , Thomas David D. , Bers Donald M. , Cornea Razvan L. 
Published: July 2023

AbstractCa2+leak from cardiomyocyte sarcoplasmic reticulum (SR) via hyperactive resting cardiac ryanodine receptor channels (RyR2) is pro-arrhythmic. An exogenous peptide, (DPc10) detects leaky RyR2 in cardiomyocytes. Conversely, calmodulin (CaM) inhibits RyR2 leak. These observations have led to designing a FRET biosensor for drug discovery targeting RyR2. Here we used FRET to understand the molecular mechanism driving the DPc10-CaM interdependence when binding RyR2 in SR vesicles. We used donor-FKBP12.6 (D-FKBP) to resolve RyR2 binding of acceptor-CaM (A-CaM). In low nanomolar Ca2+, DPc10 decreased both FRETmax(under saturating [A-CaM]) and the CaM/RyR2 binding affinity. In micromolar Ca2+, DPc10 decreased FRETmaxwithout affecting CaM/RyR2 binding affinity. This correlates with analysis of fluorescence-lifetime-detected FRET indicating that DPc10 lowers occupancy of the RyR2 CaM-binding sites in nanomolar (not micromolar) Ca2+and lengthens D-FKBP/A-CaM distances independent of [Ca2+]. To observe DPc10/RyR2 binding, we used acceptor-DPc10 (A-DPc10). CaM weakens A-DPc10/RyR2 binding, this effect being larger in micromolar vs. nanomolar Ca2+. Moreover, A-DPc10/RyR2 binding is cooperative in CaM- and FKBP-dependent manner, suggesting that both endogenous modulators promote concerted structural changes between RyR2 protomers for channel regulation. Aided by analysis of cryo-EM structures, these insights inform further development of the DPc10-CaM paradigm for therapeutic discovery targeting RyR2.
DataPLAN: a web-based data management plan generator for the plant sciences
Authors: Zhou Xiao-Ran , Beier Sebastian , Brilhaus Dominik , Rodrigues Cristina Martins , Mühlhaus Timo , von Suchodoletz Dirk , Twyman Richard M. , Usadel Björn , Kranz Angela 
Published: July 2023

AbstractResearch Data Management (RDM) is a system for the effective handling of research data that enables scientists to structure their research questions and ensure best practices throughout the data lifecycle, from acquisition, computation and annotation to data publication and re-use. Data management plans (DMPs) are documents that formally set out the RDM of a project and are required by many funding bodies. DMPs help to organize and structure RDM strategies, thus promoting data findability, accessibility, interoperability and reusability (FAIR). Although DMPs incorporate methods and standards that can be reused by different research projects, the standardization of DMP content is not as evident as the standardization of RDM practices and data/metadata. To address this issue in the plant sciences, we developed DataPLAN – a tool that combines a questionnaire with pre-written standardized responses. We wrapped the questionnaire in a serverless single-page web application that can then generate standardized responses from DMP templates. The current templates cater to plant research grant proposals for Horizon 2020, Horizon Europe and the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG). In the future the range of templates will be extended to accommodate other funding schemes, thereby enabling more users to generate their own templates. The DataPLAN web application is open-source and does not require an internet connection. By utilizing DataPLAN, the workload associated with creating, updating, and adhering to DMPs is significantly reduced.