bluuebunny/crossref_metadata_2025_split huggingface dataset:
Introduction to deep learning methods for multi‐species predictions
Authors: Hu Yuqing , Si‐Moussi Sara , Thuiller Wilfried 
Published: November 2024

Abstract

Predicting species distributions and entire communities is crucial for ecologists, to enhance our understanding of the drivers behind species distributions and community assembly and to provide quantitative data for conservation efforts.

Popular species distribution models use statistical and machine learning methods but face limitations with multi‐species predictions at the community level, hindered by scalability and data imbalance sensitivity. This paper explores the potential of deep learning methods to overcome these challenges and provide more accurate multi‐species predictions.

Specifically, we introduced four distinct deep learning models that use site × species community data but differ in their internal structure or on the input environmental data structure: (1) a multi‐layer perceptron (MLP) model for tabular data (e.g. in‐situ/raster climate or soil data), (2) a convolutional neural network (CNN) and (3) a vision transformer (ViT) models tailored for image data (e.g. aerial ortho‐photographs, satellite imagery), and a multimodal model that integrates both tabular and image data. We also show how adapted loss functions can address imbalance issues.

We applied these deep learning models to a plant community dataset comprising 130,582 vegetation surveys encompassing 2522 species located in the French Alps. The tabular environmental data consisted of climate, terrain and soil information, while the images were derived from aerial photographs. All models achieved approximately 70% true skill statistics on hold‐out data, demonstrating high predictive capacity for community data, the multimodal model being the best performing one. Additionally, we showcased how interpretability tools can illuminate community structure as seen by deep learning models.

Deep learning models offer a broad array of features for predicting entire species communities. They handle imbalance issues and accommodate various data types, from tabular datasets to images, while also being equipped with insightful interpretation tools. The versatility extends to tabular datasets and images, with no clear superiority between the two. The last hidden layers can provide valuable features for modelling other species, and the trained models can be used to support transfer learning to related tasks. The field of ecology now possesses an additional, potent tool in its arsenal that can foster basic and fundamental research.
Prenatal exposure to maternal hypertension and higher body mass index and risks of neurodevelopmental and psychiatric disorders during childhood
Authors: Nivins Samson , Kumar Parvin , Chen Xinxia , Gissler Mika , Lavebratt Catharina 
Published: November 2024

AbstractIntroductionHypertensive disorders of pregnancy (HDP) or prepregnancy overweight/obesity are independently associated with the risk for certain neurodevelopmental and psychiatric disorders in offspring. These two conditions often co‐exist but the risk from combined exposure is unknown. We investigated whether specific subtypes of maternal HDP, along with prepregnancy overweight/obesity, were associated with the distinct risk of neurodevelopmental and psychiatric disorders in offspring during childhood.Material and MethodsThis prospective, population‐based cohort study used data from 652 732 singleton children born alive in Finland between 2004 and 2014 and followed until 2018. The Cox proportional hazards model was used to estimate adjusted hazard ratios (aHR) and 95% confidence intervals (95% CI).ResultsChildren exposed to both chronic hypertension and obesity exhibited a 2.4–3.5‐fold higher risk for mood disorders, specific developmental disorder, autism spectrum disorders, and attention‐deficit/hyperactivity disorders. Similarly, exposure to both gestational hypertension and overweight increased the risk for anxiety disorders and attention‐deficit hyperactivity disorders by 2.4‐fold. Meanwhile, combined exposure to preeclampsia and overweight increased the risk of mood and anxiety disorders, specific developmental disorders, and other behavioral disorders, by 1.8–2.2‐fold. The effect size of combined exposure to HDP and overweight/obesity was greater than that of the individual exposure to HDP subtypes or overweight/obesity. Furthermore, overweight/obesity synergistically modified these associations between the HDP subtype exposure and offspring mental disorders, except for specific developmental disorders.ConclusionsOur findings suggest that combined exposure to different subtypes of HDP and higher prepregnancy BMI have distinct impacts on the mental health of offspring. Notably, a more pronounced effect was observed in cases where chronic hypertension and obesity coexisted. Future research should focus on exploring dose‐related relationships rather than amalgamating maternal HDP for investigating the offspring outcomes.
Cognitive biases and research miscitations
Authors: Simmering Marcia J. , Fuller Christie M. , Leonard Stephanie R. , Simmering Vanessa R. 
Published: November 2024

AbstractPrior research on miscitations in academic literatures have painted a dismal picture of high rates of inaccuracy. While this issue and the problems that stem from inaccurate citations have been reviewed, the attention given to the causes of such inaccuracies has so far been narrow. The primary rationale given for citation errors is author lack of motivation. In the current manuscript, we suggest that examining the potential for cognitive biases to also contribute to miscitations can add conceptual nuance to this question as well as provide additional recommendations for practice. We argue that even when authors are motivated to cite research correctly, that the cognitive biases of source confusion, gist memory, and repetition effects may lead to miscitations. We explore these ideas with a systematic review of over 1400 papers in which we found that the rates of miscitation are high (44.8%). Additionally, evidence from the review provides some support that cognitive biases may produce miscitations. Recommendations to authors, reviewers, and editors are provided.
Coronary Artery Disease and Major Adverse Cardiovascular Events in People With Hepatic Steatosis at Low Atherosclerotic Cardiovascular Disease Risk
Authors: Karady Julia , Mayrhofer Thomas , Foldyna Borek , Lu Michael T. , Meyersohn Nandini , Hoffmann Udo , Balogon Oluwafemi , Pagidipati Neha , Shah Svati , Douglas Pamela S. , Ferencik Maros , Corey Kathleen 
Published: November 2024

ABSTRACTBackgroundHepatic steatosis (HS) and 10‐year atherosclerotic cardiovascular disease (ASCVD) risk ≥ 7.5% are associated with increased risk for cardiovascular events.AimTo assess underlying coronary artery disease (CAD) and major adverse cardiovascular event (MACE) among those with and without HS at different ASCVD risk.MethodsWe evaluated stable chest pain patients receiving coronary computed tomography (CT) in the PROMISE trial. HS and CAD endpoints were defined on coronary CT. MACE was defined as unstable angina, non‐fatal myocardial infarction, and all‐cause death. Multivariable Cox regression, adjusting for CAD characteristics, assessed the association of HS with MACE for ASCVD < 7.5%.ResultsOne thousand two hundred and four of 3702 (32.5%) patients were at ASCVD < 7.5% and 20.3% (244/1204) of them had HS. Individuals with HS were younger (54.3 ± 5.2 vs. 55.8 ± 5.2; p < 0.001), more often males (40.2% [98/244] vs. 27.1% [260/960]; p < 0.001), had more risk factors/person (2.06 ± 0.89 vs. 1.93 ± 0.91; p = 0.047). CAD characteristics were similar between HS vs. non‐HS patients at ASCVD < 7.5% and ASCVD ≥ 7.5% (all p > 0.05). Patients with HS had greater MACE rate compared to non‐HS patients (ASCVD < 7.5%: 3.75%[9/244] vs. 1.5% [14/960]; p = 0.027 and ASCVD ≥ 7.5%: 4.7% [33/696] vs. 3.1% [56/1802]; p = 0.043). In patients without HS, MACE rate was higher in the ASCVD ≥ 7.5% vs. < 7.5% (3.1% [56/1802] vs. 1.5% [14/960]; p = 0.011). In patients with HS, MACE rates were not significantly different between ASCVD ≥ 7.5% vs. < 7.5% (4.7% [33/696] vs. 3.7% [9/244]; p = 0.484). In ASCVD < 7.5%, HS predicted MACE (aHR:2.34, 95%CI:1.01–5.43; p = 0.048), independent of CAD characteristics.ConclusionsIndividuals with HS at ASCVD < 7.5% risk had similar CAD characteristics as patients without HS at < 7.5% ASCVD risk, yet experienced comparable MACE rates as those at ASCVD ≥ 7.5%.
Effects of the Scopist's Skills on the Perioperative Outcomes of Laparoscopic Liver Resection
Authors: Kimura Taku , Nitta Hiroyuki , Katagiri Hirokatsu , Kanno Shoji , Umemura Akira , Takeda Daiki , Ando Taro , Amano Satoshi , Kawashima Toma , Kikuchi Koji , Kuchida Shuta , Sasaki Akira 
Published: November 2024

ABSTRACTIntroductionLaparoscopic liver resection (LLR) is a difficult procedure that requires the scopist to have a high skill level. Scopists play an important role in ensuring an appropriate surgical field. This is the first study that focuses on the scopist's skills in perioperative outcomes of LLR.Materials and MethodsPatients who underwent LLR from April 2018 to March 2023 were included in this study. The scopists were separated into expert (≥ 10 LLR procedures as a scopist) and beginner (< 10 LLR procedures as a scopist) groups. The effects of the scopists' skills on the perioperative outcomes of LLR between the two groups were examined retrospectively. In addition to listing baseline characteristics and perioperative outcomes, this study viewed video recordings to list intraoperative surgical manipulation factors as new attempts.ResultsNo significant differences were observed in the baseline characteristics or perioperative outcomes between the two groups. The duration of the time during which the surgical procedure was interrupted due to scope operation errors during the Pringle maneuver was significantly longer in the beginner group (71 vs. 198 s, p < 0.001).ConclusionThe scope manipulation by the less experienced LLR scopists sometimes hindered the progress of the surgery. The scopist's skills may lead to an increased psychological burden on the surgeon and prolonged operative times.
Exploring the factors associated with difficulties in extracting tablets or capsules from press‐through‐package sheets
Authors: Tsuchiya Masami , Imai Shungo , Asano Masaki , Shimizu Yuri , Kizaki Hayato , Ito Yukiko , Tsuchiya Makoto , Kuriyama Ryoko , Yoshida Nao , Shimada Masanori , Sando Takanori , Ishijima Tomo , Hori Satoko 
Published: November 2024

AbstractExploring factors related to difficulties in extracting tablets or capsules from press‐through‐packages is essential for optimizing the dosage form. To achieve this, the involvement of patient insight is important. In the present study, the preferences of patients regarding drugs that are difficult to extract from their packaging were collected using an electronic medication notebook (‘harmo®’) based on dispensing data. We found that approximately 30% of respondents had difficulty removing tablets or capsules from their packaging, with 125 specific drugs identified as ‘hard to push out’. Independent factors related to ‘hard‐to‐push‐out’ drugs were female sex and feeling of weakness in the hands or fingers. Furthermore, several ‘hard‐to‐push‐out’ drugs had characteristics such as a spherical shape or small major axis or small major axis drug‐to‐pocket size ratio. The findings of this study may help improve the quality of drug packaging, thus enhancing the patients' medication experience.
A successful clinical trial ecosystem offers equal opportunities for all citizens
Authors: El‐Galaly Tarec Christoffer , Roug Anne Stidsholt , Kristensen Daniel Tuyet 
Published: November 2024

An inclusive clinical trial ecosystem is essential to obtain scientific results that can be generalized to a broad patient population. When possible, all efforts should be made to remove geographic, demographic, cultural and ethnic barriers for enrolment in clinical trials. However, to do this effectively, we need more knowledge about factors influencing clinical trial participation and practical frameworks to enhance diversity in clinical trials.Commentary on: Jones et al. Inequalities in geographic barriers and patient representation in lymphoma clinical trials across England. Br J Haematol 2025; 206:531‐540.
Glial cell line derived neurotrophic factor (GDNF) induces mucosal healing via intestinal stem cell niche activation
Authors: Hörner Marius , Burkard Natalie , Kelm Matthias , Leist Antonia , Selig Thekla , Kollmann Catherine , Meir Michael , Otto Christoph , Germer Christoph‐Thomas , Kretzschmar Kai , Flemming Sven , Schlegel Nicolas 
Published: November 2024

AbstractMucosal healing is critical to maintain and restore intestinal homeostasis in inflammation. Previous data provide evidence that glial cell line‐derived neurotrophic factor (GDNF) restores epithelial integrity by largely undefined mechanisms. Here, we assessed the role of GDNF for mucosal healing. In dextran sodium sulphate (DSS)‐induced colitis in mice application of GDNF enhanced recovery as revealed by reduced disease activity index and histological inflammation scores. In biopsy‐based wounding experiments GDNF application in mice improved healing of the intestinal mucosa. GDNF‐induced epithelial recovery was also evident in wound assays from intestinal organoids and Caco2 cells. These observations were accompanied by an increased number of Ki67‐positive cells in vivo after GDNF treatment, which were present along elongated proliferative areas within the crypts. In addition, the intestinal stem cell marker and R‐spondin receptor LGR5 was significantly upregulated following GDNF treatment in all experimental models. The effects of GDNF on cell proliferation, LGR5 and Ki67 upregulation were blocked using the RET‐specific inhibitor BLU‐667. Downstream of RET‐phosphorylation, activation of Src kinase was involved to mediate GDNF effects. GDNF promotes intestinal wound healing by promoting cell proliferation. This is mediated by RET‐dependent activation of Src kinase with consecutive LGR5 upregulation, indicating activation of the stem cell niche.
VEXAS Syndrome: Histiocytoid Cells With Feathery Cytoplasm as a Clue to the Diagnosis
Authors: Ko Christine J. , Odell Ian , Gehlhausen Jeffrey R. , Leventhal Jonathan , McNiff Jennifer M. , Zubek Amanda 
Published: November 2024

ABSTRACTVEXAS (Vacuoles, E1‐ubiquitin activating enzyme UBA1 variant, X‐linked, Autoinflammatory, Somatic) syndrome was initially described as having mature neutrophil‐predominant infiltrates. More recent reports suggest that infiltrates can be composed of variable cell types. We report three cases of VEXAS syndrome with seven total biopsies having in common histiocytoid cells with feathery cytoplasm; these cells may be a potential clue to the diagnosis.
Impact of ‘street’ benzodiazepines on drug‐related deaths in England, Wales and Northern Ireland
Authors: Rock Kirsten L. , Frinculescu Anca , Shine Trevor , Kalk Nicola J. , Copeland Caroline S. 
Published: November 2024

AbstractIntroduction‘Street’ benzodiazepines (BZD) are structurally and pharmacologically related to BZDs licensed for human use. In this study we investigated how street BZDs contribute to overall BZD use and death prevalences in England, Wales and Northern Ireland.MethodsData were analysed from deaths reported to the National Programme on Substance Use Mortality with post‐mortem BZD detections (1999–2021), BZDs seized from music festivals (2017–2021) and drug samples with BZD detections submitted to Welsh Emerging Drugs and Identification of Novel Substances (WEDINOS) (2017–2021).ResultsAbout 14,837 deaths with BZD detections were identified, with polydrug use evident in 99.3% of cases (n = 14,733/14,837). Deaths following BZD use increased by over 200% from 2010 (n = 556) to 2020 (n = 1245). Most BZD detections were of those available via NHS prescription (96.2%), although in most cases (61.9%) the BZD—majority diazepam (77.3% of detections)—had been illicitly sourced. While street BZD deaths represented only 8.5% of overall BZD deaths, street BZD deaths increased by over 1200% between 2015 (n = 26) and 2020 (n = 326). There were increasing proportions of street BZD deaths in each geographical region but was more marked in Northern Ireland. The proportion of individual BZDs seized at music festivals and submitted to WEDINOS largely reflected that of individual BZDs detected in deaths.Discussion and ConclusionsWhile deaths following street BZD use are increasing, most BZDs detected in deaths were prescribable BZDs that were often illicitly sourced. The types of BZD detected in post‐mortem samples, festival seizures and WEDINOS submissions has evolved over time to reflect changes in BZD prevalence on the illicit drug market.
Development of a predictive model for gastrointestinal side effects of metformin treatment in Chinese individuals with type 2 diabetes based on four randomised clinical trials
Authors: Wang Weihao , Han Yujia , Jiang Xun , Shao Jian , Zhang Jia , Zhou Kaixin , Yang Wenying , Pan Qi , Nie Zedong , Guo Lixin 
Published: November 2024

AbstractAimsThis study aimed to build a model‐based predictive approach to evaluate the gastrointestinal side effects following an initial metformin medication.Materials and MethodsThe model was developed from data from four randomised clinical cohorts. A prediction model was established using integrated or simplified indicators. Ten machine learning models were used for the construction of predictive models. The Shapley values were used to report the features' contribution.ResultsFour randomised clinical trial cohorts, including 1736 patients with type 2 diabetes, were first included in the analysis. Seventy percent of participants (1216) were allocated to the training set, 15% (260) were assigned to the internal validation set and 15% (260) were assigned to the test set. The Extra Tree model had the highest area under curve (AUC) (0.87) in the validation and test set. The top five crucial indicators were blood urea nitrogen (BUN), sex, triglyceride (TG), high‐density lipoprotein‐cholesterol (HDL‐C) and total cholesterol (TC), and these five indicators were selected for constructing a simplified predictive model (AUC = 0.76). An online web‐based tool was established based on the predictive model with integrated 17 features and top five indicators.ConclusionsTo predict gastrointestinal side effects in diabetic patients for initial use of metformin, a few easily obtained features are needed to establish the model. The model can be applied to the Chinese population in clinical practice.
Breastfeeding and contrast agents—A critical review and presentation of new aspects
Authors: Lemmenmeier Sina , Boehm Ingrid 
Published: November 2024

AbstractBackgroundThere are discrepancies between guidelines of scientific societies and information of the package inserts of contrast media concerning breastfeeding following the application of a contrast agent to the mother.ObjectivesThe contents of different review articles reflect the opinion of scientific societies. Consequently, in clinical routine settings it is difficult to find the optimal advice for a breastfeeding woman and her baby.MethodsTherefore, the paper carefully summarized important information dealing with the topic ‘breastfeeding and contrast media’ from the literature. Among other things, the paper focuses on topics that are not yet taken into account in other reviews (e.g. approval for breastfeeding women, contrast agents that have been analysed in human breast milk).ResultsIn this way, the review shows new aspects. It has been revealed that data concerning the amount of contrast agents in human breast milk as well as contrast medium absorption by the infants' intestine are sparse. Instead of them, a lot of speculations and incorrect conclusions do exist in the literature. Because studies are rare or missing, contrast media are not approved for breastfeeding women (off‐label‐use).ConclusionAlthough breastfeeding women 100% prefers a break from breastfeeding, in current decision‐making processes, their preference plays a minor role. However, this should change in the future. In addition, it would be very important to inform breastfeeding women in the future about the missing data concerning ‘breastfeeding and contrast media’.
Net Mixture Effects on Nutritive Value in Lucerne‐Grass Swards of Varied Composition and Diversity
Authors: Glowacki Sebastian Christoph , Komainda Martin , Leisen Edmund , Hummel Jürgen , Isselstein Johannes 
Published: November 2024

ABSTRACTClimate change and associated risks of extreme weather has led to growing interest in drought‐tolerant species such as lucerne (Medicago sativa L.), tall fescue (Festuca arundinacea Schreb.) and cocksfoot (Dactylis glomerata L.) in mixed grass‐legume forage production in North‐Western Europe. Lucerne and grasses have distinct nutritive value that can be combined when grown in mixtures. The extent of a ‘net mixture effect’ (NE) on the nutritive value, that is the deviations of the mixture quality from the expected one derived from the pure stands, has not been studied in any depth and requires further investigation in the context of climate change. The present study was conducted at four sites during two main cropping years with the aim of comparing potentially drought‐tolerant mixtures against pure stands. With significant sward type × site × year interactions, nutritive value of the mixed swards often differed significantly from pure stands, ranging intermediate between the component pure stand nutritive value. The concentration of water‐soluble carbohydrate (WSC) did not differ between mixtures and lucerne pure stands. Significant NE were found, with larger measured concentrations in mixtures compared to those predicted, for neutral and acid detergent fibre and the crude protein:WSC ratio. The concentrations of WSC and metabolizable energy were smaller than expected. The NE was not influenced by sward type or species number, except for WSC at a few sites. The results show that improved knowledge of positive mixing effects could be used to specifically enhance the nutritive value in grasses‐lucerne mixtures irrespective of sward diversity.
Exploring the use and usability of the Physiotherapy Evidence Database (PEDro) ‘Evidence in your inbox’ e‐mail alert service
Authors: Wong Jeremy Joelin , Sharma Sweekriti , Wong Alfred , Moseley Anne M. , Ilhan Emre 
Published: November 2024

AbstractObjectiveTo evaluate the use and useability of the Physiotherapy Evidence Database's ‘Evidence in your inbox’ e‐mail alert service.Materials and MethodsAn explanatory sequential design consisting of a usage evaluation, cross‐sectional survey, and semi‐structured interviews. Usage was evaluated using routinely collected data from October 2015 to March 2021: number of subscribers, number of articles, open rates, and click‐through rates. Subscribers were subdivided by level of engagement. All subscribers were invited to participate in a 17‐question online survey. Semi‐structured interviews were conducted with a subgroup of participants who completed the survey.ResultsThe service sent a minimum of 121 or a maximum of 431 articles, on average, each month across 15 feeds to 16,556 subscribers. Overtime, the rate of opening and clicking on links within e‐mails decreased. Low engagers (62%) subscribed to 3.5 (95% CI 3.7–3.4) more feeds than high engagers (23%) and 2.8 (95% CI 3.0–2.6) more than moderate engagers (15%). Seventy‐one subscribers completed the survey, 89% of whom were satisfied with the service and who thought it was an efficient way to be updated on evidence (98%). Six subscribers participated in semi‐structured interviews. Thematic analysis of interviews identified five facilitators and four barriers to using the service, with three potential solutions to aid useability.Discussion and ConclusionThe format and structure of the service may facilitate its use and usability. Addressing barriers of having too few or too many articles, and lack of time to read full articles may enhance the usability of ‘Evidence in your inbox’.