bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Analysis of Decision Trees on Two COVID-19 Symptom Datasets
Authors: Saengamnatdej Somchai , Molee Phuangphet Waree , Warnnissorn Prateep 
Published: June 2023

AbstractObjectiveThis study compares decision trees on two COVID-19 symptom datasets to assess their performance and feature importance in predicting and understanding infection patterns.MethodsWe created decision trees on Israeli and Swedish COVID-19 infection datasets. Performance metrics were used to assess their predictive capabilities, and feature importance analysis identified significant variables in the decision-making process.ResultsThe study observed different performance levels of decision trees on the COVID-19 datasets. The Swedish dataset achieved high accuracy and F1-score without hyperparameter tuning, while the Israeli dataset improved significantly with Extreme Gradient Boosting. Dataset characteristics impact the selection of an optimal decision tree algorithm. The key variable in both datasets was sore throat.ConclusionThis study compares decision trees on COVID-19 infection datasets, emphasizing the importance of dataset characteristics in selecting an optimal algorithm. Identifying significant features enhances understanding of infection patterns, benefiting decision-making and prediction accuracy in infectious disease analysis.
Estimation of introduction and transmission rates of SARS-CoV-2 in a prospective household study
Authors: van Boven Michiel , van Dorp Christiaan H. , Westerhof Ilse , Jaddoe Vincent , Heuvelman Valerie , Duijts Liesbeth , Fourie Elandri , Sluiter-Post Judith , van Houten Marlies A. , Badoux Paul , Euser Sjoerd , Herpers Bjorn , Eggink Dirk , de Hoog Marieke , Boom Trisja , Wildenbeest Joanne , Bont Louis , Rozhnova Ganna , Bonten Marc J. , Kretzschmar Mirjam E. , Bruijning-Verhagen Patricia 
Published: June 2023

AbstractHousehold studies provide an efficient means to study transmission of infectious diseases, enabling estimation of individual susceptibility and infectivity. A main inclusion criterion in such studies is often the presence of an infected person. This precludes estimation of the hazards of pathogen introduction into the household. Here we use data from a prospective household-based study to estimate SARS-CoV-2 age- and time-dependent household introduction hazards together with within household transmission rates in the Netherlands from August 2020 to August 2021. Introduction hazards and within-household transmission rates are estimated with penalized splines and stochastic epidemic models, respectively. The estimated hazard of introduction of SARS-CoV-2 in the households was lower for children (0-12 years) than for adults (relative hazard: 0.62; 95%CrI: 0.34-1.0). Estimated introduction hazards peaked in mid October 2020, mid December 2020, and mid April 2021, preceding peaks in hospital admissions by 1-2 weeks. The best fitting transmission models include increased infectivity of children relative to adults and adolescents, such that the estimated child-to-child transmission probability (0.62; 95%CrI: 0.40-0.81) was considerably higher than the adult-to-adult transmission probability (0.12; 95%CrI: 0.057-0.19). Scenario analyses show that vaccination of adults could have strongly reduced infection attack rates in households and that adding adolescent vaccination would have offered limited added benefit.
Tau accumulation and its spatial progression across the Alzheimer’s disease spectrum
Authors: St-Onge Frédéric , Chapleau Marianne , Breitner John CS , Villeneuve Sylvia , Binette Alexa Pichet ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: June 2023

AbstractThe spread of tau abnormality in sporadic Alzheimer’s disease is believed typically to follow neuropathologically defined Braak staging. Recentin-vivopositron emission tomography (PET) evidence challenges this belief, however, as spreading patterns for tau appear heterogenous among individuals with varying clinical expression of Alzheimer’s disease. We therefore sought better understanding of the spatial distribution of tau in the preclinical and clinical phases of sporadic Alzheimer’s disease and its association with cognitive decline.Longitudinal tau-PET data (1,370 scans) from 832 participants (463 cognitively unimpaired, 277 with mild cognitive impairment (MCI) and 92 with Alzheimer’s disease dementia) were obtained from the Alzheimer’s Disease Neuroimaging Initiative. Among these, we defined thresholds of abnormal tau deposition in 70 brain regions from the Desikan atlas, and for each group of regions characteristic of Braak staging. We summed each scan’s number of regions with abnormal tau deposition to form a spatial extent index. We then examined patterns of tau pathology cross-sectionally and longitudinally and assessed their heterogeneity. Finally, we compared our spatial extent index of tau uptake with a temporal meta region of interest—a commonly used proxy of tau burden—assessing their association with cognitive scores and clinical progression.More than 80% of amyloid-beta positive participants across diagnostic groups followed typical Braak staging, both cross-sectionally and longitudinally. Within each Braak stage, however, the pattern of abnormality demonstrated significant heterogeneity such that overlap of abnormal regions across participants averaged less than 50%. The annual rate of change in number of abnormal tau-PET regions was similar among individuals without cognitive impairment and those with Alzheimer’s disease dementia. Spread of disease progressed more rapidly, however, among participants with MCI. The latter’s change on our spatial extent measure amounted to 2.5 newly abnormal regions per year, as contrasted with 1 region/year among the other groups. Comparing the association of tau pathology and cognitive performance in MCI and Alzheimer’s disease dementia, our spatial extent index was superior to the temporal meta-ROI for measures of executive function.Thus, while participants broadly followed Braak stages, significant individual regional heterogeneity of tau binding was observed at each clinical stage. Progression of spatial extent of tau pathology appears to be fastest in persons with MCI. Exploring the spatial distribution of tau deposits throughout the entire brain may uncover further pathological variations and their correlation with impairments in cognitive functions beyond memory.
Assessing regional intracortical myelination in schizophrenia spectrum and bipolar disorders using the optimized T1w/T2w-ratio
Authors: Jørgensen Kjetil Nordbø , Nerland Stener , Slapø Nora Berz , Norbom Linn B. , Mørch-Johnsen Lynn , Wortinger Laura Anne , Barth Claudia , Andreou Dimitrios , Maximov Ivan I. , Geier Oliver M. , Andreassen Ole A. , Jönsson Erik G. , Agartz Ingrid 
Published: June 2023

AbstractBackgroundDysmyelination could be part of the pathophysiology of schizophrenia spectrum (SCZ) and bipolar disorders (BPD), yet few studies have examined myelination of the cerebral cortex. The ratio of T1- and T2-weighted magnetic resonance images (MRI) correlates with intracortical myelin. We investigated the T1w/T2w-ratio and its age trajectories in patients and healthy controls (CTR) and explored associations with antipsychotic medication use and psychotic symptoms.MethodsPatients with SCZ (n=64; mean age = 30.4 years, SD=9.8), BPD (n=91; mean age 31.0 years, SD=10.2), and CTR (n=155; mean age = 31.9 years, SD=9.1) who participated in the TOP study (NORMENT, University of Oslo, Norway) were clinically assessed and scanned using a General Electric 3T MRI system. T1w/T2w-ratio images were computed using an optimized pipeline with intensity normalization and field inhomogeneity correction. Vertex-wise regression models were used to compare groups and examine group × age interactions. In regions showing significant differences, we explored associations with antipsychotic medication use and psychotic symptoms.ResultsNo main effect of diagnosis was found. However, age slopes of the T1w/T2w-ratio differed significantly between SCZ and CTR, predominantly in frontal and temporal lobe regions: Lower T1w/T2w-ratio values with higher age were found in CTR, but not in SCZ. Follow-up analyses revealed a more positive age slope in patients who were using antipsychotics and patients using higher chlorpromazine-equivalent doses.ConclusionsWhile we found no evidence of reduced intracortical myelin in SCZ or BPD relative to CTR, different regional age trajectories in SCZ may suggest a promyelinating effect of antipsychotic medication.
Causal Interactions in Brain Networks Predict Pain Levels in Trigeminal Neuralgia
Authors: Liang Yun , Zhao Qing , Neubert John K. , Ding Mingzhou 
Published: June 2023

AbstractTrigeminal neuralgia (TN) is a highly debilitating facial pain condition. Magnetic resonance imaging (MRI) is the main method for generating insights into the central mechanisms of TN pain in humans. Studies have found both structural and functional abnormalities in various brain structures in TN patients as compared with healthy controls. Whereas studies have also examined aberrations in brain networks in TN, no studies have to date investigated causal interactions in these brain networks and related these causal interactions to the levels of TN pain. We recorded fMRI data from 39 TN patients who either rested comfortably in the scanner during the resting state session or tracked their pain levels during the pain tracking session. Applying Granger causality to analyze the data and requiring consistent findings across the two scanning sessions, we found 5 causal interactions, including: (1) Thalamus → dACC, (2) Caudate → Inferior temporal gyrus, (3) Precentral gyrus → Inferior temporal gyrus, (4) Supramarginal gyrus → Inferior temporal gyrus, and (5) Bankssts → Inferior temporal gyrus, that were consistently associated with the levels of pain experienced by the patients. Utilizing these 5 causal interactions as predictor variables and the pain score as the predicted variable in a linear multiple regression model, we found that in both pain tracking and resting state sessions, the model was able to explain ∼36% of the variance in pain levels, and importantly, the model trained on the 5 causal interaction values from one session was able to predict pain levels using the 5 causal interaction values from the other session, thereby cross-validating the models. These results, obtained by applying novel analytical methods to neuroimaging data, provide important insights into the pathophysiology of TN and could inform future studies aimed at developing innovative therapies for treating TN.
Combined GWAS and single cell transcriptomics uncover the underlying genes and cell types in disorders of gut-brain interaction
Authors: Majd Alireza , Richter Mikayla N , Samuel Ryan M , Cesiulis Andrius , Ghazizadeh Zaniar , Wang Jeffrey , Fattahi Faranak 
Published: June 2023

AbstractDisorders of gut-brain interaction (DGBIs), formerly known as functional gastrointestinal disorders, are extremely common and historically difficult to manage. This is largely because their cellular and molecular mechanisms have remained poorly understood and understudied. One approach to unravel the molecular underpinnings of complex disorders such as DGBIs is performing genome wide association studies (GWASs). However, due to the heterogenous and non-specific nature of GI symptoms, it has been difficult to accurately classify cases and controls. Thus, to perform reliable studies, we need to access large patient populations which has been difficult to date. Here, we leveraged the UK Biobank (UKBB) database, containing genetic and medical record data of over half a million individuals, to perform GWAS for five DGBI categories: functional chest pain, functional diarrhea, functional dyspepsia, functional dysphagia, and functional fecal incontinence. By applying strict inclusion and exclusion criteria, we resolved patient populations and identified genes significantly associated with each condition. Leveraging multiple human single-cell RNA-sequencing datasets, we found that the disease associated genes were highly expressed in enteric neurons, which innervate and control GI functions. Further expression and association testing-based analyses revealed specific enteric neuron subtypes consistently linked with each DGBI. Furthermore, protein-protein interaction analysis of each of the disease associated genes revealed protein networks specific to each DGBI, including hedgehog signaling for functional chest pain and neuronal function and neurotransmission for functional diarrhea and functional dyspepsia. Finally, through retrospective medical record analysis we found that drugs that inhibit these networks are associated with an increased disease risk, including serine/threonine kinase 32B drugs for functional chest pain, solute carrier organic anion transporter family member 4C1, mitogen-activated protein kinase 6, and dual serine/threonine and tyrosine protein kinase drugs for functional dyspepsia, and serotonin transporter drugs for functional diarrhea. This study presents a robust strategy for uncovering the tissues, cell types, and genes involved in DGBIs, presenting novel predictions of the mechanisms underlying these historically intractable and poorly understood diseases.
Hypertension diagnosis, treatment, and control in India: nationally representative results from 1.69 million adults, 2019-2021
Authors: Varghese Jithin Sam , Venkateshmurthy Nikhil Srinivasapura , Sudharsanan Nikkil , Jeemon Panniyammakal , Patel Shivani A , Thirumurthy Harsha , Roy Ambuj , Tandon Nikhil , Narayan KM Venkat , Prabhakaran Dorairaj , Ali Mohammed K. 
Published: June 2023

ABSTRACTBackgroundHypertension is a major cause of morbidity and mortality worldwide. Previous efforts to characterize gaps in the hypertension care continuum in India –including diagnosis, treatment, and control– did not assess district level variation. Local data are critical for planning, implementation, and monitoring efforts to curb hypertension burdens. Our objective is to characterize the hypertension care continuum in India among individuals aged 18-98 years old at national, state, and district levels and by socio-demographic group.MethodsData were from 1,895,297 individuals in the nationally representative Fifth National Family Health Survey (NFHS-5), 2019-21. Hypertension was defined as self-reported diagnosis or newly measured blood pressure ≥140/90 mmHg. Among those with hypertension, we calculated the proportion diagnosed (self-reported). Among those with diagnosed hypertension, we computed the proportion treated (self-reported medication use). Among those treated, we calculated the proportion controlled (BP <140/90 mmHg [20-80 years] or <150/90 mmHg [>80 years]) based on national guidelines. Estimates were also provided among the total with hypertension. To assess differences in the care continuum between or within states (i.e. between districts), we partitioned the variance at both levels using linear mixed models.ResultsAmong 1,691,109 adult respondents nationally (52.6% female; mean age: 41.6 years), 28.2% [95%CI: 28.0-28.4] had hypertension, of whom, 36.7% [36.3-37.2] were diagnosed. Among those diagnosed, 44.7% [44.1-45.3] reported taking medication (17.7% [17.5-17.9] of total with hypertension). Among those treated, 52.3% [51.4-53.1] had blood pressure control (9.1% [8.9-9.2] of total with hypertension). There were substantial variations across districts in diagnosis [range: 6.3–77.5%], treatment [8.7–97.1%] and control [2.7–76.6%]. Notably, large proportions of the variation in hypertension diagnosis (53.7%), treatment (32.8%), and control (57.7%) were within states, not just between states.ConclusionsIn India, more than 1 in 4 people have hypertension, and of these, only 1 in 3 are diagnosed, less than 1 in 5 are treated, and only 1 in 11 controlled. National averages hide considerable state- and district-level variation in the care continuum, implying the need for targeted, decentralized solutions to improve the hypertension care continuum in India.
Dynamic phytomeric growth contributes to local adaptation in barley
Authors: Huang Yongyu , Maurer Andreas , Giehl Ricardo F. H. , Zhao Shuangshuang , Golan Guy , Thirulogachandar Venkatasubbu , Li Guoliang , Zhao Yusheng , Trautewig Corinna , Himmelbach Axel , Börner Andreas , Jayakodi Murukarthick , Stein Nils , Mascher Martin , Pillen Klaus , Schnurbusch Thorsten 
Published: June 2023

SummaryVascular plants segment their body axis with iterative nodes of lateral branches and internodes. Appropriate node initiation and internode elongation are fundamental to plant fitness and crop yield formation; but how they are spatiotemporally coordinated remains elusive. We show that in barley (Hordeum vulgareL.), selections under domestication have extended the apical meristematic phase to promote node initiation, but constrained subsequent internode elongation. In both vegetative and reproductive axes, internode elongation displays a dynamic proximal – distal gradient, and among subpopulations of domesticated barleys at the global range, node initiation and proximal internode elongation are associated with latitudinal and longitudinal gradients, respectively. Genetic and functional analysis suggest that, in addition to their converging roles in node initiation, flowering time genes are repurposed to specify the dynamic internode elongation. Our study provides an integrated view of barley node initiation and internode elongation, and suggests that plant architecture has to be recognized as dynamic phytomeric units in the context of crop evolution.
LORA, Lipid Over-Representation Analysis based on structural information
Authors: Vondrackova Michaela , Kopczynski Dominik , Hoffmann Nils , Kuda Ondrej 
Published: June 2023

ABSTRACTWith the increasing number of lipidomic studies, there is a need for efficient and automated analysis of lipidomic data. One of the challenges faced by most existing approaches to lipidomic data analysis is lipid nomenclature. The systematic nomenclature of lipids contains all available information about the molecule, including its hierarchical representation, which can be used for statistical evaluation. The Lipid Over-Representation Analysis (LORA) web application (https://lora.metabolomics.fgu.cas.cz) analyzes this information using the Java-based Goslin framework, which translates lipid names into a standardized nomenclature. Goslin provides the level of lipid hierarchy, including information on headgroups, acyl chains, and their modifications, up to the ‘complete structure’ level. LORA allows the user to upload the experimental query and universe datasets, select a grammar for lipid name normalization, and then process the data. The user can then interactively explore the results and perform lipid overrepresentation analysis based on selected criteria. The results are graphically visualized according to the lipidome hierarchy. The lipids present in the most over-represented terms (lipids with the highest number of enriched shared structural features) are defined as Very Important Lipids (VILs). For example, the main result of a demo dataset is the information that the query is significantly enriched with ‘glycerophospholipids’ containing ‘acyl 20:4’ at ‘sn-2 position’. These terms define a set of VILs (e.g., PC 18:2/20:4;O and PE 16:0/20:4(5,8,10,14);OH). All results, graphs, and visualizations are summarized in a report. LORA is a tool focused on the smart mining of epilipidomics datasets to facilitate their interpretation at the molecular level.
Parallelized Acquisition of Orbitrap and Astral Analyzers Enables High-Throughput Quantitative Analysis
Authors: Stewart Hamish , Grinfeld Dmitry , Giannakopulos Anastassios , Petzoldt Johannes , Shanley Toby , Garland Matthew , Denisov Eduard , Peterson Amelia , Damoc Eugen , Zeller Martin , Arrey Tabiwang N. , Pashkova Anna , Renuse Santosh , Hakimi Amirmansoor , Kühn Andreas , Biel Matthias , Kreutzmann Arne , Hagedorn Bernd , Colonius Immo , Schütz Adrian , Stefes Arne , Dwivedi Ankit , Mourad Daniel , Hoek Max , Reitemeier Bastian , Cochems Philipp , Kholomeev Alexander , Ostermann Robert , Quiring Gregor , Ochmann Maximilian , Möhring Sascha , Wagner Alexander , Petker André , Kanngiesser Sebastian , Wiedemeyer Michael , Balschun Wilko , Hermanson Daniel , Zabrouskov Vlad , Makarov Alexander , Hock Christian 
Published: June 2023

AbstractThe growing trend towards high-throughput proteomics demands rapid liquid chromatography-mass spectrometry (LC-MS) cycles that limit the available time to gather the large numbers of MS/MS fragmentation spectra required for identification. Orbitrap analyzers scale performance with acquisition time, and necessarily sacrifice sensitivity and resolving power to deliver higher acquisition rates. We developed a new mass spectrometer that combines a mass resolving quadrupole, the Orbitrap and the novel Asymmetric Track Lossless (Astral) analyzer. The new hybrid instrument enables faster acquisition of high-resolution accurate mass (HRAM) MS/MS spectra compared to state-of-the-art mass spectrometers. Accordingly, new proteomics methods were developed that leverage the strengths of each HRAM analyzer, whereby the Orbitrap analyzer performs full scans with high dynamic range and resolution, synchronized with Astral analyzer’s acquisition of fast and sensitive HRAM MS/MS scans. Substantial improvements are demonstrated over previous methods using current state-of-the-art mass spectrometers.Abstract Figure
The PMA Phorbol Ester Tumor Promoter Increases Canonical Wnt Signaling Via Macropinocytosis
Authors: Tejeda-Muñoz Nydia , Azbazdar Yagmur , Monka Julia , Binder Grace , Dayrit Alex , Ayala Raul , O’Brien Neil , De Robertis Edward M. 
Published: June 2023

SummaryActivation of the Wnt pathway lies at the core of many human cancers. Wnt and macropinocytosis are often active in the same processes, and understanding how Wnt signaling and membrane trafficking cooperate should improve our understanding of embryonic development and cancer. Here we show that a macropinocytosis activator, the tumor promoter Phorbol 12-myristate 13-acetate (PMA), enhances Wnt signaling. Experiments using theXenopusembryo as an in vivo model showed marked cooperation between the PMA phorbol ester and Wnt signaling, which was blocked by inhibitors of macropinocytosis, Rac1 activity, and lysosome acidification. Human colorectal cancer tissue arrays and xenografts in mice showed a correlation of cancer progression with increased macropinocytosis/multivesicular body/lysosome markers and decreased GSK3 levels. The crosstalk between canonical Wnt, focal adhesions, lysosomes, and macropinocytosis suggests possible therapeutic targets for cancer progression in Wnt-driven cancers.