bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data Archive for the BRAIN Initiative (DABI)
Authors: Duncan Dominique , Garner Rachael , Brinkerhoff Sarah , Walker Harrison C. , Pouratian Nader , Toga Arthur W. 
Published: February 2023

AbstractData sharing is becoming ubiquitous and can be advantageous for most biomedical research. However, some data are inherently more amenable to sharing than others. For example, human intracranial neurophysiology recordings and associated multimodal data have unique features that warrant special considerations. The associated data are heterogeneous, difficult to compare, highly specific, and collected from small cohorts with treatment resistant conditions, posing additional complications when attempting to perform generalizable analyses across projects. We present the Data Archive for the BRAIN Initiative (DABI) and describe features of the platform that are designed to overcome these and other challenges. DABI is a data repository and portal for BRAIN Initiative projects that collect human and animal intracranial recordings, and it allows users to search, visualize, and analyze multimodal data from these projects. The data providers maintain full control of data sharing privileges and can organize and manage their data with a user-friendly and intuitive interface. We discuss data privacy and security concerns, example analyses from two DABI datasets, and future goals for DABI.
Mortality among acute myocardial infarction patients admitted to hospitals on weekends as compared with weekdays in Taiwan
Authors: Liu Sheng-Fu , Lai Chao-Lun , Kuo Raymond Nien-Chen , Wang Ting-Chuan , Lin Ting-Tse , Chan K. Arnold 
Published: February 2023

AbstractWeekend effect has been considered to be associated with poorer quality of care and patient’s survival. For acute myocardial infarction (AMI) patients, the question of whether patients admitted during off-hours have worse outcomes as compared with patients admitted during on-hours is still inconclusive. We conducted this study to explore the weekend effect in AMI patients, using a nationwide insurance database in Taiwan. Using Taiwan National Health Insurance (NHI) claims database, we designed a retrospective cohort study, and extracted 184,769 incident cases of AMI through the NHI claims database between January 2006 and December 2014. We divided the patients into weekend admission group and weekday admission group. Patients were stratified as ST elevation/non-ST elevation AMI and receiving/not receiving percutaneous coronary intervention (PCI). We used a logistic regression model to examine the relative risk of in-hospital mortality and 1-year mortality which were obtained from the Taiwan National Death Registry between study groups. We found no difference between weekend group and weekday group for risk of in-hospital mortality (15.8% vs 16.2%, standardized difference 0.0118) and risk of 1-year mortality (30.2% vs 30.9%, standardized difference 0.0164). There was no statistically significant difference among all the comparisons through the multivariate logistic regression analysis adjusting for all the covariates and stratifying by the subtypes of AMI and whether or not executing PCI during hospitalization. As for AMI patients in Taiwan, admission on weekends or weekdays did not have a significant impact on either in-hospital mortality or 1-year cumulative mortality.
Prescient diagnostic analysis for boron nutritional status in soy crops
Authors: Traspadini Edilaine Istéfani Franklin , Wadt Paulo Guilherme Salvador , de Mello Prado Renato , Roque Cassiano Garcia , Wassolowski Carlos Roberto 
Published: February 2023

AbstractBoron is the most limiting micronutrient for soybean yield; therefore, accurate identification of its nutritional status is important for adequate fertilization management and maximize soybean yield potential. Currently, tools for nutritional status interpretation of B, such as the CND and DRIS are used; however, their efficacy is not considered to identify the true nutritional status of B. In this research, we investigated the efficacy of these methods to identify the nutritional status of B in 140 commercial soybean crops to obtain nutritional standards for the DRIS and CND methods. In addition, an experiment of B dose calibration (0, 300, 600, 1200 and 1800 g ha−1) was installed to assess the quality of nutritional diagnoses using the PDA. The experimental approach tested the limits of 0.25, 0.50, and 1.00 for the NRr and values of 1%, 5%, or 10% for YR. The DRIS method was more effective, and, on average, its variations increased yield by 27% compared to CND, with the best performance of DRIS when NRr = 1.00 was adopted with 10% for YR. This study highlights the need for reliable and accurate diagnostic methods with global implications for crop sustainability by improving the efficacy of B fertilization programs and crop yield.
Quantifying the feeding behavior and trophic impact of a widespread oceanic ctenophore
Authors: Potter Betsy , Corrales-Ugalde Marco , Townsend James P. , Colin Sean P. , Sutherland Kelly R. , Costello John H. , Collins Richard , Gemmell Brad J. 
Published: February 2023

AbstractOceanic ctenophores are widespread predators on pelagic zooplankton. While data on coastal ctenophores often show strong top-down predatory impacts in their ecosystems, differing morphologies, prey capture mechanisms and behaviors of oceanic species preclude the use of coastal data to draw conclusion on oceanic species. We used high-resolution imaging methods both in situ and in the laboratory to quantify interactions of Ocyropsis spp. with natural copepod prey. We confirmed that Ocyropsis spp. uses muscular lobe contraction and a prehensile mouth to capture prey, which is unique amongst ctenophores. This feeding mechanism results in high overall capture success whether encountering single or multiple prey between the lobes (71 and 81% respectively). However, multiple prey require several attempts for successful capture whereas single prey are often captured on the first attempt. Digestion of adult copepods takes 44 min at 25 °C and does not vary with ctenophore size. At high natural densities, we estimate that Ocyropsis spp. consume up to 40% of the daily copepod standing stock. This suggests that, when numerous, Ocyropsis spp. can exert strong top-down control on oceanic copepod populations. At more common densities, these animals consume only a small proportion of the daily copepod standing stock. However, compared to data from pelagic fishes and oceanic medusae, Ocyropsis spp. appears to be the dominant copepod predator in this habitat.
Biventricular shape modes discriminate pulmonary valve replacement in tetralogy of Fallot better than imaging indices
Authors: Govil Sachin , Mauger Charlène , Hegde Sanjeet , Occleshaw Christopher J. , Yu Xiaoyang , Perry James C. , Young Alistair A. , Omens Jeffrey H. , McCulloch Andrew D. 
Published: February 2023

AbstractCurrent indications for pulmonary valve replacement (PVR) in repaired tetralogy of Fallot (rTOF) rely on cardiovascular magnetic resonance (CMR) image-based indices but are inconsistently applied, lead to mixed outcomes, and remain debated. This study aimed to test the hypothesis that specific markers of biventricular shape may discriminate differences between rTOF patients who did and did not require subsequent PVR better than standard imaging indices. In this cross-sectional retrospective study, biventricular shape models were customized to CMR images from 84 rTOF patients. A statistical atlas of end-diastolic shape was constructed using principal component analysis. Multivariate regression was used to quantify shape mode and imaging index associations with subsequent intervention status (PVR, n = 48 vs. No-PVR, n = 36), while accounting for confounders. Clustering analysis was used to test the ability of the most significant shape modes and imaging indices to discriminate PVR status as evaluated by a Matthews correlation coefficient (MCC). Geometric strain analysis was also conducted to assess shape mode associations with systolic function. PVR status correlated significantly with shape modes associated with right ventricular (RV) apical dilation and left ventricular (LV) dilation (p < 0.01), RV basal bulging and LV conicity (p < 0.05), and pulmonary valve dilation (p < 0.01). PVR status also correlated significantly with RV ejection fraction (p < 0.05) and correlated marginally with LV end-systolic volume index (p < 0.07). Shape modes discriminated subsequent PVR better than standard imaging indices (MCC = 0.49 and MCC = 0.28, respectively) and were significantly associated with RV and LV radial systolic strain. Biventricular shape modes discriminated differences between patients who did and did not require subsequent PVR better than standard imaging indices in current use. These regional features of cardiac morphology may provide insight into adaptive vs. maladaptive types of structural remodeling and point toward an improved quantitative, patient-specific assessment tool for clinical use.
Dressed jeff-1/2 objects in mixed-valence lacunar spinel molybdates
Authors: Petersen Thorben , Prodan Lilian , Geirhos Korbinian , Nakamura Hiroyuki , Kézsmárki István , Hozoi Liviu 
Published: February 2023

AbstractThe lacunar-spinel chalcogenides exhibit magnetic centers in the form of transition-metal tetrahedra. On the basis of density-functional computations, the electronic ground state of an Mo413+ tetrahedron has been postulated as single-configuration a12 e4 t25, where a1, e, and t2 are symmetry-adapted linear combinations of single-site Mo t2g atomic orbitals. Here we unveil the many-body tetramer wave-function: we show that sizable correlations yield a weight of only 62% for the a12 e4 t25 configuration. While spin–orbit coupling within the peculiar valence orbital manifold is still effective, the expectation value of the spin–orbit operator and the g factors deviate from figures describing nominal t5jeff = 1/2 moments. As such, our data documents the dressing of a spin–orbit jeff = 1/2 object with intra-tetramer excitations. Our results on the internal degrees of freedom of these magnetic moments provide a solid theoretical starting point in addressing the intriguing phase transitions observed at low temperatures in these materials.
Reduced glucosinolate content in oilseed rape (Brassica napus L.) by random mutagenesis of BnMYB28 and BnCYP79F1 genes
Authors: Jhingan Srijan , Harloff Hans-Joachim , Abbadi Amine , Welsch Claudia , Blümel Martina , Tasdemir Deniz , Jung Christian 
Published: February 2023

AbstractThe presence of anti-nutritive compounds like glucosinolates (GSLs) in the rapeseed meal severely restricts its utilization as animal feed. Therefore, reducing the GSL content to < 18 µmol/g dry weight in the seeds is a major breeding target. While candidate genes involved in the biosynthesis of GSLs have been described in rapeseed, comprehensive functional analyses are missing. By knocking out the aliphatic GSL biosynthesis genes BnMYB28 and BnCYP79F1 encoding an R2R3 MYB transcription factor and a cytochrome P450 enzyme, respectively, we aimed to reduce the seed GSL content in rapeseed. After expression analyses on single paralogs, we used an ethyl methanesulfonate (EMS) treated population of the inbred winter rapeseed ‘Express617’ to detect functional mutations in the two gene families. Our results provide the first functional analysis by knock-out for the two GSL biosynthesis genes in winter rapeseed. We demonstrate that independent knock-out mutants of the two genes possessed significantly reduced seed aliphatic GSLs, primarily progoitrin. Compared to the wildtype Express617 control plants (36.3 µmol/g DW), progoitrin levels were decreased by 55.3% and 32.4% in functional mutants of BnMYB28 (16.20 µmol/g DW) and BnCYP79F1 (24.5 µmol/g DW), respectively. Our study provides a strong basis for breeding rapeseed with improved meal quality in the future.
A deconvolution approach to modelling surges in COVID-19 cases and deaths
Authors: Melnyk Adam , Kozarov Lena , Wachsmann-Hogiu Sebastian 
Published: February 2023

AbstractThe COVID-19 pandemic continues to emphasize the importance of epidemiological modelling in guiding timely and systematic responses to public health threats. Nonetheless, the predictive qualities of these models remain limited by their underlying assumptions of the factors and determinants shaping national and regional disease landscapes. Here, we introduce epidemiological feature detection, a novel latent variable mixture modelling approach to extracting and parameterizing distinct and localized features of real-world trends in daily COVID-19 cases and deaths. In this approach, we combine methods of peak deconvolution that are commonly used in spectroscopy with the susceptible-infected-recovered-deceased model of disease transmission. We analyze the second wave of the COVID-19 pandemic in Israel, Canada, and Germany and find that the lag time between reported cases and deaths, which we term case-death latency, is closely correlated with adjusted case fatality rates across these countries. Our findings illustrate the spatiotemporal variability of both these disease metrics within and between different disease landscapes. They also highlight the complex relationship between case-death latency, adjusted case fatality rate, and COVID-19 management across various degrees of decentralized governments and administrative structures, which provides a retrospective framework for responding to future pandemics and disease outbreaks.
Development and validation of a decision model for the evaluation of novel lung cancer treatments in the Netherlands
Authors: Mfumbilwa Zakile A. , Wilschut Janneke A. , Simons Martijn J. H. G. , Ramaekers Bram , Joore Manuela , Retèl Valesca , der Welle Christine M. Cramer-van , Schramel Franz M. N. H. , van de Garde Ewoudt M. W. , Coupé Veerle M. H. 
Published: February 2023

AbstractRecent discoveries in molecular diagnostics and drug treatments have improved the treatment of patients with advanced (inoperable) non-squamous non-small cell lung cancer (NSCLC) from solely platinum-based chemotherapy to more personalized treatment, including targeted therapies and immunotherapies. However, these improvements come at considerable costs, highlighting the need to assess their cost-effectiveness in order to optimize lung cancer care. Traditionally, cost-effectiveness models for the evaluation of new lung cancer treatments were based on the findings of the randomized control trials (RCTs). However, the strict RCT inclusion criteria make RCT patients not representative of patients in the real-world. Patients in RCTs have a better prognosis than patients in a real-world setting. Therefore, in this study, we developed and validated a diagnosis-treatment decision model for patients with advanced (inoperable) non-squamous NSCLC based on real-world data in the Netherlands. The model is a patient-level microsimulation model implemented as discrete event simulation with five health events. Patients are simulated from diagnosis to death, including at most three treatment lines. The base-model (non-personalized strategy) was populated using real-world data of patients treated with platinum-based chemotherapy between 2008 and 2014 in one of six Dutch teaching hospitals. To simulate personalized care, molecular tumor characteristics were incorporated in the model based on the literature. The impact of novel targeted treatments and immunotherapies was included based on published RCTs. To validate the model, we compared survival under a personalized treatment strategy with observed real-world survival. This model can be used for health-care evaluation of personalized treatment for patients with advanced (inoperable) NSCLC in the Netherlands.
Empirical investigations into Kruskal-Wallis power studies utilizing Bernstein fits, simulations and medical study datasets
Authors: Clark Jeremy S. C. , Kulig Piotr , Podsiadło Konrad , Rydzewska Kamila , Arabski Krzysztof , Białecka Monika , Safranow Krzysztof , Ciechanowicz Andrzej 
Published: February 2023

AbstractBernstein fits implemented into R allow another route for Kruskal-Wallis power-study tool development. Monte-Carlo Kruskal-Wallis power studies were compared with measured power, a Monte-Carlo ANOVA equivalent and with an analytical method, with or without normalization, using four simulated runs, each with 60–100 populations (each population with N = 30,000 from a set of Pearson-type ranges): random selection gave 6300 samples analyzed for predictive power. Three medical-study datasets (Dialysis/systolic blood pressure; Diabetes/sleep-hours; Marital-status/high-density-lipoprotein cholesterol) were also analyzed. In three from four simulated runs (run_one, run_one_relaxed, and run_three) with Pearson types pooled, Monte-Carlo Kruskal-Wallis gave predicted sample sizes significantly slightly lower than measured but more accurate than with ANOVA methods; the latter gave high sample-size predictions. Populations (run_one_relaxed) with ANOVA assumptions invalid gave Kruskal-Wallis predictions similar to those measured. In two from three medical studies, Kruskal-Wallis predictions (Dialysis: similar predictions; Marital: higher than measured) were more accurate than ANOVA (both higher than measured) but in one (Diabetes) the reverse was found (Kruskal-Wallis: lower; Monte-Carlo ANOVA: similar to measured). These preliminary studies appear to show that Monte-Carlo Kruskal-Wallis power studies, based on Bernstein fits, might perform better than ANOVA equivalents in many settings (and provide reasonable results when ANOVA cannot be used); and both Monte-Carlo methods appeared to be considerably more accurate than the analytical version analyzed.
Information extraction from German radiological reports for general clinical text and language understanding
Authors: Jantscher Michael , Gunzer Felix , Kern Roman , Hassler Eva , Tschauner Sebastian , Reishofer Gernot 
Published: February 2023

AbstractRecent advances in deep learning and natural language processing (NLP) have opened many new opportunities for automatic text understanding and text processing in the medical field. This is of great benefit as many clinical downstream tasks rely on information from unstructured clinical documents. However, for low-resource languages like German, the use of modern text processing applications that require a large amount of training data proves to be difficult, as only few data sets are available mainly due to legal restrictions. In this study, we present an information extraction framework that was initially pre-trained on real-world computed tomographic (CT) reports of head examinations, followed by domain adaptive fine-tuning on reports from different imaging examinations. We show that in the pre-training phase, the semantic and contextual meaning of one clinical reporting domain can be captured and effectively transferred to foreign clinical imaging examinations. Moreover, we introduce an active learning approach with an intrinsic strategic sampling method to generate highly informative training data with low human annotation cost. We see that the model performance can be significantly improved by an appropriate selection of the data to be annotated, without the need to train the model on a specific downstream task. With a general annotation scheme that can be used not only in the radiology field but also in a broader clinical setting, we contribute to a more consistent labeling and annotation process that also facilitates the verification and evaluation of language models in the German clinical setting.
Accelerated degradation of plastic products via yeast enzyme treatment
Authors: Kitamoto Hiroko , Koitabashi Motoo , Sameshima-Yamashita Yuka , Ueda Hirokazu , Takeuchi Akihiko , Watanabe Takashi , Sato Shun , Saika Azusa , Fukuoka Tokuma 
Published: February 2023

AbstractBiodegradable plastics can solve the problem of unwanted plastics accumulating in the environment if they can be given the contradictory properties of durability in use and rapid degradation after use. Commercially available agricultural biodegradable mulch films are made from formulations containing polybutylene adipate-co-terephthalate (PBAT) to provide mechanical and UV resistance during the growing season. Although used films are ploughed into the soil using a tiller to promote decomposition, it is difficult if they remain durable. We showed that an enzyme produced by the leaf surface yeast Pseudozyma antarctica (PaE) degrades PBAT-containing films. In laboratory studies, PaE randomly cleaved the PBAT polymer chain and induced erosion of the film surface. In the field, commercial biodegradable films containing PBAT placed on ridges were weakened in both the warm and cold seasons by spraying the culture filtrate of P. antarctica. After the field was ploughed the next day, the size and total weight of residual film fragments decreased significantly (p < 0.05). Durable biodegradable plastics used in the field are degraded using PaE treatment and are broken down into small fragments by the plough. The resultant degradation products can then be more readily assimilated by many soil microorganisms.
Differential expression patterns of long noncoding RNAs in a pleiomorphic diatom and relation to hyposalinity
Authors: Debit Ahmed , Charton Florent , Pierre-Elies Priscillia , Bowler Chris , Cruz de Carvalho Helena 
Published: February 2023

AbstractLong non-coding (lnc)RNAs have been shown to have central roles in stress responses, cell identity and developmental processes in multicellular organisms as well as in unicellular fungi. Previous works have shown the occurrence of lncRNAs in diatoms, namely in Phaeodactylum tricornutum, many of which being expressed under specific stress conditions. Interestingly, P. tricornutum is the only known diatom that has a demonstrated morphological plasticity, occurring in three distinct morphotypes: fusiform, triradiate and oval. Although the morphotypes are interchangeable, the fusiform is the dominant one while both the triradiate and the oval forms are less common, the latter often being associated with stress conditions such as low salinity and solid culture media, amongst others. Nonetheless, the molecular basis underpinning morphotype identity in P. tricornutum remains elusive. Using twelve previously published transcriptomic datasets originating from the three morphotypes of P. tricornutum, we sought to investigate the expression patterns of lncRNAs (lincRNAs and NATs) in these distinct morphotypes, using pairwise comparisons, in order to explore the putative involvement of these noncoding molecules in morphotype identity. We found that differentially expressed lncRNAs cluster according to morphotype, indicating that lncRNAs are not randomly expressed, but rather seem to provide a specific (noncoding) transcriptomic signature of the morphotype. We also present evidence to suggest that the major differences in DE genes (both noncoding and coding) between the stress related oval morphotype and the most common fusiform morphotype could be due, to a large extent, to the hyposaline culture conditions rather than to the morphotype itself. However, several lncRNAs associated to each one of the three morphotypes were identified, which could have a potential role in morphotype (or cell) identity in P. tricornutum, similar to what has been found in both animals and plant development.