bluuebunny/crossref_metadata_2025_split huggingface dataset:
FAIR in action - a flexible framework to guide FAIRification
Authors: Welter Danielle , Juty Nick , Rocca-Serra Philippe , Xu Fuqi , Henderson David , Gu Wei , Strubel Jolanda , Giessmann Robert T. , Emam Ibrahim , Gadiya Yojana , Abbassi-Daloii Tooba , Alharbi Ebtisam , Gray Alasdair J. G. , Courtot Melanie , Gribbon Philip , Ioannidis Vassilios , Reilly Dorothy S. , Lynch Nick , Boiten Jan-Willem , Satagopam Venkata , Goble Carole , Sansone Susanna-Assunta , Burdett Tony 
Published: May 2023

AbstractThe COVID-19 pandemic has highlighted the need for FAIR (Findable, Accessible, Interoperable, and Reusable) data more than any other scientific challenge to date. We developed a flexible, multi-level, domain-agnostic FAIRification framework, providing practical guidance to improve the FAIRness for both existing and future clinical and molecular datasets. We validated the framework in collaboration with several major public-private partnership projects, demonstrating and delivering improvements across all aspects of FAIR and across a variety of datasets and their contexts. We therefore managed to establish the reproducibility and far-reaching applicability of our approach to FAIRification tasks.
iOBPdb A Database for Experimentally Determined Functional Characterization of Insect Odorant Binding Proteins
Authors: Shukla Shalabh , Nakano-Baker Oliver , Godin Dennis , MacKenzie Devin , Sarikaya Mehmet 
Published: May 2023

AbstractOdorant binding proteins (OBPs) are extra-cellular proteins that solubilize and transport volatile organic compounds (VOCs). Thousands of OBPs have been identified through genome sequencing, and hundreds have been characterized by fluorescence ligand binding assays in individual studies. There is a limited understanding of the comparative structure-function relations of OBPs, primarily due to a lack of a centralized database that relates OBP binding affinity and structure. Combining 181 functional studies containing 382 unique OBPs from 91 insect species, we present a database, iOBPdb, of OBP binding affinities for 622 individual VOC targets. This initial database provides powerful search and associative capabilities for retrieving and analyzing OBP-VOC binding interaction data. We have validated this dataset using phylogenetic mapping to determine the authenticity of the collected sequences and whether they cluster according to their assigned subfamilies. Potential applications include developing molecular probes for biosensors, novel bioassays and drugs, targeted pesticides that inhibit VOC/OBP interactions, and understanding odor sensing and perception in the brain.
Race and ethnicity data for first, middle, and surnames
Authors: Rosenman Evan T. R. , Olivella Santiago , Imai Kosuke 
Published: May 2023

AbstractWe provide the largest compiled publicly available dictionaries of first, middle, and surnames for the purpose of imputing race and ethnicity using, for example, Bayesian Improved Surname Geocoding (BISG). The dictionaries are based on the voter files of six U.S. Southern States that collect self-reported racial data upon voter registration. Our data cover the racial make-up of a larger set of names than any comparable dataset, containing 136 thousand first names, 125 thousand middle names, and 338 thousand surnames. Individuals are categorized into five mutually exclusive racial and ethnic groups — White, Black, Hispanic, Asian, and Other — and racial/ethnic probabilities by name are provided for every name in each dictionary. We provide both probabilities of the form ℙ(race|name) and ℙ(name|race), and conditions under which they can be assumed to be representative of a given target population. These conditional probabilities can then be deployed for imputation in a data analytic task for which self-reported racial and ethnic data is not available.
The chromosome-level genome assembly and genes involved in biosynthesis of nervonic acid of Malania oleifera
Authors: Yang Tianquan , Zhang Rengang , Tian Xiaoling , Yao Gang , Shen Yuanting , Wang Sihai , Mao Jianfeng , Li Guangyuan , Liu Aizhong , Sun Weibang , Ma Yongpeng 
Published: May 2023

AbstractNervonic acid (C24:1 Δ15, NA) is a very long-chain monounsaturated fatty acid, a clinically indispensable resource in maintaining the brain and nerve cells development and regeneration. Till now, NA has been found in 38 plant species, among which the garlic-fruit tree (Malania oleifera) has been evaluated to be the best candidate for NA production. Here, we generated a high-quality chromosome-scale assembly of M. oleifera employing PacBio long-read, short-read Illumina as well as Hi-C sequencing data. The genome assembly consisted of 1.5 Gb with a contig N50 of ~4.9 Mb and a scaffold N50 of ~112.6 Mb. ~98.2% of the assembly was anchored into 13 pseudo-chromosomes. It contains ~1123 Mb repeat sequences, and 27,638 protein-coding genes, 568 tRNAs, 230 rRNAs and 352 other non-coding RNAs. Additionally, we documented candidate genes involved in NA biosynthesis including 20 KCSs, 4 KCRs, 1 HCD and 1 ECR, and profiled the expression patterns of these genes in developing seeds. The high-quality assembly of the genome provides insights into the genome evolution of the M. oleifera genome and candidate genes involved in NA biosynthesis in the seeds of this important woody tree.
Vegetation photosynthetic phenology dataset in northern terrestrial ecosystems
Authors: Fang Jing , Li Xing , Xiao Jingfeng , Yan Xiaodong , Li Bolun , Liu Feng 
Published: May 2023

AbstractVegetation phenology can profoundly modulate the climate-biosphere interactions and thus plays a crucial role in regulating the terrestrial carbon cycle and the climate. However, most previous phenology studies rely on traditional vegetation indices, which are inadequate to characterize the seasonal activity of photosynthesis. Here, we generated an annual vegetation photosynthetic phenology dataset with a spatial resolution of 0.05 degrees from 2001 to 2020, using the latest gross primary productivity product based on solar-induced chlorophyll fluorescence (GOSIF-GPP). We combined smoothing splines with multiple change-point detection to retrieve the phenology metrics: start of the growing season (SOS), end of the growing season (EOS), and length of growing season (LOS) for terrestrial ecosystems above 30° N latitude (Northern Biomes). Our phenology product can be used to validate and develop phenology or carbon cycle models and monitor the climate change impacts on terrestrial ecosystems.
A global dataset of sequence, diversity and biosafety recommendation of arbovirus and arthropod-specific virus
Authors: Huang Ying , Wang Shunlong , Liu Hong , Atoni Evans , Wang Fei , Chen Wei , Li Zhaolin , Rodriguez Sergio , Yuan Zhiming , Ming Zhaoyan , Xia Han 
Published: May 2023

AbstractArthropod-borne virus (arbovirus) and arthropod-specific virus (ASV) are viruses circulating amongst hematophagous arthropods that are broadly transmitted in ecological systems. Arbovirus may replicate in both vertebrates and invertebrates and some are known to be pathogenic to animals or humans. ASV only replicate in invertebrate arthropods yet they are basal to many types of arboviruses. We built a comprehensive dataset of arbovirus and ASV by curating globally available data from the Arbovirus Catalog, the arbovirus list in Section VIII-F of the Biosafety in Microbiological and Biomedical Laboratories 6th edition, Virus Metadata Resource of International Committee on Taxonomy of Viruses, and GenBank. Revealing the diversity, distribution and biosafety recommendation of arbovirus and ASV at a global scale is essential to the understanding of potential interactions, evolution, and risks associated with these viruses. Moreover, the genomic sequences associated with the dataset will enable the investigation of genetic patterns distinguishing the two groups, as well as aid in predicting the vector/host relationships of the newly discovered viruses.
Invasive alien species of policy concerns show widespread patterns of invasion and potential pressure across European ecosystems
Authors: Polce Chiara , Cardoso Ana Cristina , Deriu Ivan , Gervasini Eugenio , Tsiamis Konstantinos , Vigiak Olga , Zulian Grazia , Maes Joachim 
Published: May 2023

AbstractAnimals, plants, and other organisms unintentionally or deliberately brought into a natural environment where they are not normally found, and where they cause harmful effects on that environment, are known also as invasive alien species (IAS). They represent a major threat to native biodiversity and ecosystem functioning, and can affect negatively human health and the economy. We assessed the presence and potential pressure by IAS on terrestrial and freshwater ecosystems across 27 European countries, for 66 IAS of policy concern. We computed a spatial indicator that accounts for the number of IAS present in an area and the extent of the ecosystems affected; for each ecosystem, we also looked at the pattern of invasions in the different biogeographical regions. We found disproportionally greater invasion in the Atlantic region, followed by Continental and Mediterranean regions, possibly related to historical patterns of first introductions. Urban and freshwater ecosystems were the most invaded (nearly 68% and ca. 52% of their extent respectively), followed by forest and woodland (nearly 44%). The average potential pressure of IAS was greater across cropland and forests, where we also found the lowest coefficient of variation. This assessment can be repeated over time to derive trends and monitor progress towards environmental policy objectives.
The association between dietary diabetic risk reduction score with anthropometric and body composition variables in overweight and obese women: a cross-sectional study
Authors: Karimi Mehdi , Shiraseb Farideh , Mofidi Maryam , Khadem Alireza , Ebrahimi Sara , Mirzaei Khadijeh 
Published: May 2023

AbstractDietary diabetes risk reduction score (DDRRs) is inversely associated with a lower risk of type 2 diabetes. Given the importance of the association between body fat and insulin resistance and the effect of diet on these parameters, this study aimed to investigate the association between DDRRS and body composition parameters, including the visceral adiposity index (VAI), lipid accumulation product (LAP), and skeletal muscle mass (SMM). This study was conducted on 291 overweight and obese women aged 18–48 years old recruited from 20 Tehran Health Centers in 2018. The anthropometric indices, biochemical parameters, and body composition were measured. A semi-quantitative food frequency questionnaire (FFQ) was used to calculate DDRRs. Linear regression analysis was used to examine the association between DDRRs and body composition indicators. The mean (SD) age of participants was 36.67 (9.10) years. After adjustment for potential confounders, VAI (β = 0.27, 95% CI = − 0.73, 1.27, Ptrend = 0.052), LAP (β = 8.14, 95% CI = − 10.54, 26.82, Ptrend = 0.069), TF (β = − 1.41, 95% CI = 11.45, 17.30, Ptrend = 0.027), trunk fat percent (TF%) (β = − 21.55, 95% CI = − 44.51, 1.61, Ptrend = 0.074), body fat mass (BFM) (β = − 3.26, 95% CI = − 6.08, − 0.44, Ptrend = 0.026), visceral fat area (VFA) (β = − 45.75, 95% CI = − 86.10, − 5.41, Ptrend = 0.026), waist-to-hip ratio (WHtR) (β = − 0.014, 95% CI = − 0.031, 0.004, Ptrend = 0.066), visceral fat level (VFL) (β = − 0.38, 95% CI = − 5.89, 5.12, Ptrend = 0.064), fat mass index (FMI) (β = − 1.15, 95% CI = − 2.28, − 0.02, Ptrend = 0.048) decreased significantly over tertiles of DDRRs, and also there was no significant association between SMM and DDRRs tertiles (β = − 0.57, 95% CI = − 1.69, 0.53, Ptrend = 0.322). The findings of this study demonstrated that participants with higher adherence to the DDRRs had lower VAI (β = 0.78 vs 0.27) and LAP (β = 20.73 vs 8.14). However, there was no significant association between DDRRs and VAI, LAP and SMM, which are mentioned as the primary outcomes. Future studies with larger sample of both genders are needed to investigate our findings.
Rare variant contribution to cholestatic liver disease in a South Asian population in the United Kingdom
Authors: Zöllner Julia , Finer Sarah , Linton Kenneth J. ,   Genes and Health Research Team, Akhtar Shaheen , Anwar Mohammad , Arciero Elena , Ashraf Samina , Bidi Saeed , Breen Gerome , Broster James , Chung Raymond , Collier David , Curtis Charles J. , Chaudhary Shabana , Clinch Megan , Colligan Grainne , Deloukas Panos , Durham Ceri , Durrani Faiza , Eto Fabiola , Finer Sarah , Gafton Joseph , Garcia Ana Angel , Griffiths Chris , Harvey Joanne , Heng Teng , Hodgson Sam , Huang Qin Qin , Hurles Matt , Hunt Karen A. , Hussain Shapna , Islam Kamrul , Iyer Vivek , Jacobs Ben , Khan Ahsan , Lavery Cath , Lee Sang Hyuck , Lerner Robin , MacArthur Daniel , Malawsky Daniel , Martin Hilary , Mason Dan , Mathur Rohini , Mazid Mohammed Bodrul , McDermott John , Morton Caroline , Newman Bill , Owor Elizabeth , Qureshi Asma , Rahman Samiha , Ramachandrappa Shwetha , Reza Mehru , Russell Jessry , Safa Nishat , Samuel Miriam , Simpson Michael , Solly John , Spreckley Marie , Stow Daniel , Taylor Michael , Trembath Richard C. , Tricker Karen , Uddin Nasir , van Heel David A. , Walter Klaudia , Winckley Caroline , Wood Suzanne , Wright John , Zöllner Julia , van Heel David A. , Williamson Catherine , Dixon Peter H. 
Published: May 2023

AbstractThis study assessed the contribution of five genes previously known to be involved in cholestatic liver disease in British Bangladeshi and Pakistani people. Five genes (ABCB4,ABCB11,ATP8B1,NR1H4,TJP2) were interrogated by exome sequencing data of 5236 volunteers. Included were non-synonymous or loss of function (LoF) variants with a minor allele frequency < 5%. Variants were filtered, and annotated to perform rare variant burden analysis, protein structure, and modelling analysisin-silico. Out of 314 non-synonymous variants, 180 fulfilled the inclusion criteria and were mostly heterozygous unless specified. 90 were novel and of those variants, 22 were considered likely pathogenic and 9 pathogenic. We identified variants in volunteers with gallstone disease (n = 31), intrahepatic cholestasis of pregnancy (ICP, n = 16), cholangiocarcinoma and cirrhosis (n = 2). Fourteen novel LoF variants were identified: 7 frameshift, 5 introduction of premature stop codon and 2 splice acceptor variants. The rare variant burden was significantly increased inABCB11. Protein modelling demonstrated variants that appeared to likely cause significant structural alterations. This study highlights the significant genetic burden contributing to cholestatic liver disease. Novel likely pathogenic and pathogenic variants were identified addressing the underrepresentation of diverse ancestry groups in genomic research.
Correcting bias in cardiac geometries derived from multimodal images using spatiotemporal mapping
Authors: Zhao Debbie , Mauger Charlène A. , Gilbert Kathleen , Wang Vicky Y. , Quill Gina M. , Sutton Timothy M. , Lowe Boris S. , Legget Malcolm E. , Ruygrok Peter N. , Doughty Robert N. , Pedrosa João , D’hooge Jan , Young Alistair A. , Nash Martyn P. 
Published: May 2023

AbstractCardiovascular imaging studies provide a multitude of structural and functional data to better understand disease mechanisms. While pooling data across studies enables more powerful and broader applications, performing quantitative comparisons across datasets with varying acquisition or analysis methods is problematic due to inherent measurement biases specific to each protocol. We show how dynamic time warping and partial least squares regression can be applied to effectively map between left ventricular geometries derived from different imaging modalities and analysis protocols to account for such differences. To demonstrate this method, paired real-time 3D echocardiography (3DE) and cardiac magnetic resonance (CMR) sequences from 138 subjects were used to construct a mapping function between the two modalities to correct for biases in left ventricular clinical cardiac indices, as well as regional shape. Leave-one-out cross-validation revealed a significant reduction in mean bias, narrower limits of agreement, and higher intraclass correlation coefficients for all functional indices between CMR and 3DE geometries after spatiotemporal mapping. Meanwhile, average root mean squared errors between surface coordinates of 3DE and CMR geometries across the cardiac cycle decreased from 7 ± 1 to 4 ± 1 mm for the total study population. Our generalised method for mapping between time-varying cardiac geometries obtained using different acquisition and analysis protocols enables the pooling of data between modalities and the potential for smaller studies to leverage large population databases for quantitative comparisons.
Mapping soil organic carbon stocks in Nepal’s forests
Authors: Khanal Shiva , Nolan Rachael H. , Medlyn Belinda E. , Boer Matthias M. 
Published: May 2023

AbstractComprehensive forest carbon accounting requires reliable estimation of soil organic carbon (SOC) stocks. Despite being an important carbon pool, limited information is available on SOC stocks in global forests, particularly for forests in mountainous regions, such as the Central Himalayas. The availability of consistently measured new field data enabled us to accurately estimate forest soil organic carbon (SOC) stocks in Nepal, addressing a previously existing knowledge gap. Our method involved modelling plot-based estimates of forest SOC using covariates related to climate, soil, and topographic position. Our quantile random forest model resulted in the high spatial resolution prediction of Nepal’s national forest SOC stock together with prediction uncertainties. Our spatially explicit forest SOC map showed the high SOC levels in high-elevation forests and a significant underrepresentation of these stocks in global-scale assessments. Our results offer an improved baseline on the distribution of total carbon in the forests of the Central Himalayas. The benchmark maps of predicted forest SOC and associated errors, along with our estimate of 494 million tonnes (SE = 16) of total SOC in the topsoil (0–30 cm) of forested areas in Nepal, carry important implications for understanding the spatial variability of forest SOC in mountainous regions with complex terrains.
Baseline P2Y12 reactivity, kidney function, and CYP2C19 genotype determine clopidogrel responsiveness in acute stroke
Authors: Lee Yi-Chung , Liao Yi-Chu , Lin Chun-Jen , Chung Chih-Ping 
Published: May 2023

AbstractClopidogrel is the most-widely used platelet P2Y12-inhibitor for secondary-prevention of ischemic stroke. Platelet P2Y12 reactivity before and after inhibitors can be measured with blood sampling by commercialized system. We aimed to evaluate (1) whether high-on-clopidogrel platelet P2Y12 reactivity (HCPR) is associated with short-term vascular events and (2) the predictors of HCPR in acute stroke. The inclusion criterion was patients with acute stroke who received clopidogrel within 12–48 h after the onset. Platelet reactivity was assayed at baseline and after clopidogrel treatment using the VerifyNow system. The primary endpoint was recurrent ischemic events within 21 days after stroke. Among 190 patients, 32(16.9%) had recurrent ischemic stroke. Multivariate analyses showed that HCPR was significantly associated with the short-term events with an odds-ratio of 2.5 (95% CI 1.1–5.7, p = 0.027). Patients with HCPR had significantly higher frequencies of high baseline platelet P2Y12 reactivity, impaired kidney function, and carrying one or two CYP2C19 loss-of-function alleles. A poor clopidogrel response score combining these factors was developed. Ten percent of patients with score 0, 20.3% of those with score 1, 38.3% of those with score 2, and 66.7% of those with score 3 had HCPR (χ2-test, p < 0.001). Multivariate analyses showed that, compared with the score-0 group, the score-2 and -3 groups had higher risks of HCPR with hazard-ratios of 5.4 (95% CI 1.5–20.3, p = 0.012) and 17.4 (95% CI 3.4–88.9, p = 0.001) for developing recurrent ischemic strokes. The study emphasized the role of HCPR in ischemic stroke. We also developed an HCPR risk score, which could be used in clinical practice or trials, potentially with more precision, to weigh the clinical benefit of a tailored antiplatelet-strategy for patients with stroke.
Amplification of ammonia sensing performance through gate induced carrier modulation in Cur-rGO Silk-FET
Authors: Sett Avik , Sarkar Lisa , Majumder Santanab , Bhattacharyya Tarun Kanti 
Published: May 2023

AbstractUncontrolled human and industrial activities lead to the increase in demand for selective gas sensors for detection of poisonous gases in our environment. Conventional resistive gas sensors suffer from predetermined sensitivity and poor selectivity among gases. This paper demonstrates curcumin reduced graphene oxide-silk field effect transistor for selective and sensitive detection of ammonia in air. The sensing layer was characterized by X-ray diffraction, FESEM and HRTEM to confirm its structural and morphological features. Raman spectroscopy, Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy was carried out to analyze the functional moieties present in the sensing layer. Curcumin reduced graphene oxide introduces sufficient hydroxyl groups in the sensing layer to provide high degree of selectivity towards ammonia vapors. The performance of the sensor device was evaluated at positive, negative and zero gate voltage. Carrier modulation in the channel through gate electrostatics revealed that the minority carriers (electrons) in p-type reduced graphene oxide plays a pivotal role in enhancement of sensitivity of the sensor device. The sensor response was enhanced to 634% for 50 ppm ammonia at 0.6 V gate voltage compared to 23.2% and 39.3% at 0 V and − 3 V respectively. The sensor exhibited faster response and recovery at 0.6 V owing to higher mobility of electrons and quick charge transfer mechanism. The sensor exhibited satisfactory humidity resistant characteristics and high stability. Hence, curcumin reduced graphene oxide-silk field effect transistor device with proper gate bias elucidates excellent ammonia detection and may be a potential candidate for future room temperature, low power, portable gas detection system.
Adsorption behavior of furan at Ge(100) surface
Authors: Nam Jeong-Woo , Lee Han-Koo , Kim Byeong-Seon , Gwag Jin Seog , Kim Youngsoo , Youn Young-Sang 
Published: May 2023

AbstractThe adsorption behavior of furan on the Ge(100) surface was studied using a combination of high-resolution photoemission spectroscopy (HRPES) and density functional theory (DFT) calculations. We identified the two adsorption species produced by the [4 + 2] cycloaddition and deoxygenation reactions of furan with the Ge(100) surface in a ratio of approximately 76:24 at the surveyed coverages, via an analysis of the binding energies and relative area proportions of all the peaks in the C 1s and O 1s core-level spectra. The DFT simulation results revealed that the [4 + 2] cycloaddition and deoxygenation adducts are thermodynamically preferred by the reaction of furan with the Ge(100) surface compared with others, which is consistent with the HRPES results. The findings will further our understanding of the surface reactions of five-membered heterocyclic molecules.