bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prioritization of oligogenic variant combinations in whole exomes
Authors: Gravel Barbara , Renaux Alexandre , Papadimitriou Sofia , Smits Guillaume , Nowé Ann , Lenaerts Tom 
Published: April 2024

Abstract

Motivation
Whole exome sequencing (WES) has emerged as a powerful tool for genetic research, enabling the collection of a tremendous amount of data about human genetic variation. However, properly identifying which variants are causative of a genetic disease remains an important challenge, often due to the number of variants that need to be screened. Expanding the screening to combinations of variants in two or more genes, as would be required under the oligogenic inheritance model, simply blows this problem out of proportion.

Results
We present here the High-throughput oligogenic prioritizer (Hop), a novel prioritization method that uses direct oligogenic information at the variant, gene and gene pair level to detect digenic variant combinations in WES data. This method leverages information from a knowledge graph, together with specialized pathogenicity predictions in order to effectively rank variant combinations based on how likely they are to explain the patient’s phenotype. The performance of Hop is evaluated in cross-validation on 36 120 synthetic exomes for training and 14 280 additional synthetic exomes for independent testing. Whereas the known pathogenic variant combinations are found in the top 20 in approximately 60% of the cross-validation exomes, 71% are found in the same ranking range when considering the independent set. These results provide a significant improvement over alternative approaches that depend simply on a monogenic assessment of pathogenicity, including early attempts for digenic ranking using monogenic pathogenicity scores.

Availability and implementation
Hop is available at https://github.com/oligogenic/HOP.
pyaging: a Python-based compendium of GPU-optimized aging clocks
Authors: de Lima Camillo Lucas Paulo 
Published: April 2024

Abstract

Motivation
Aging is intricately linked to diseases and mortality. It is reflected in molecular changes across various tissues which can be leveraged for the development of biomarkers of aging using machine learning models, known as aging clocks. Despite advancements in the field, a significant challenge remains: the lack of robust, Python-based software tools for integrating and comparing these diverse models. This gap highlights the need for comprehensive solutions that can handle the complexity and variety of data in aging research.

Results
To address this gap, I introduce pyaging, a comprehensive open-source Python package designed to facilitate aging research. pyaging harmonizes dozens of aging clocks, covering a range of molecular data types such as DNA methylation, transcriptomics, histone mark ChIP-Seq, and ATAC-Seq. The package is not limited to traditional model types; it features a diverse array, from linear and principal component models to neural networks and automatic relevance determination models. Thanks to a PyTorch-based backend that enables GPU acceleration, pyaging is capable of rapid inference, even when dealing with large datasets and complex models. In addition, the package’s support for multi-species analysis extends its utility across various organisms, including humans, various mammals, and Caenorhabditis elegans.

Availability and implementation
pyaging is accessible on GitHub, at https://github.com/rsinghlab/pyaging, and the distribution is available on PyPi, at https://pypi.org/project/pyaging/. The software is also archived on Zenodo, at https://zenodo.org/doi/10.5281/zenodo.10335011.
Sharp symbolic nonparametric bounds for measures of benefit in observational and imperfect randomized studies with ordinal outcomes
Authors: Gabriel Erin E , Sachs Michael C , Jensen Andreas Kryger 
Published: April 2024

Abstract
The probability of benefit can be a valuable and meaningful measure of treatment effect. Particularly for an ordinal outcome, it can have an intuitive interpretation. Unfortunately, this measure, and variations of it, are not identifiable even in randomized trials with perfect compliance. There is, for this reason, a long literature on nonparametric bounds for unidentifiable measures of benefit. These have primarily focused on perfect randomized trial settings and one or two specific estimands. We expand these bounds to observational settings with unmeasured confounders and imperfect randomized trials for all three estimands considered in the literature: the probability of benefit, the probability of no harm and the relative treatment effect.
The Iconic Apache: Early 1900s Paris and the Making of a Criminal Bogeyman
Authors: Beauchez Jérôme 
Published: April 2024

Abstract
This article describes the creation of a criminal icon, the Paris Apache, brandished as a threat by the press and conservative politicians alike at the turn of the twentieth century in France. Archival analysis points to the theory that this figure of street crime was turned into a criminal ‘bogeyman’. The iconic Apache bogeyman allowed those manipulating it to focus the general public’s fears and attention on factual violence (crimes, assaults and misdemeanours) of which the structural causes (political instability and socio-economic inequalities) were masked by framing the criminal icon as solely responsible. This bogeyman role, embodied by the Apache in the past, is also examined in the present and analysed critically from the perspective of cultural criminology.
A shift between bee and wasp pollinators explains floral divergence in the Duvernoia clade of Justicia (Acanthaceae)
Authors: Adit Arjun , Johnson Steven D 
Published: April 2024

Abstract
Floral divergence among sister taxa can arise from pollinator shifts and play a role in speciation. We investigate a potential case of pollinator-driven divergence in the Duvernoia clade of Justicia (Acanthaceae), which includes two species with markedly divergent floral morphology. Pollinator observations and pollen load analyses showed that Justicia aconitiflora is pollinated by vespid wasps, while its sister taxon Justicia adhatodoides is confirmed to be pollinated exclusively by large carpenter bees. Reciprocal nectar-feeding experiments show that wasps and bees are not deterred by the taste of nectar of non-preferred species. Floral morphology matches body and tongue morphology of these two insect groups, and this phenotypic matching mediates pollen transfer and physical access to nectar. Controlled pollination experiments showed that both species are self-compatible, yet dependent on pollinator visits for fruit-set. Historical reconstruction of pollination system evolution in Justicia indicates that the direction of the shift in the Duvernoia clade was from bee to wasp pollinators. This study provides a compelling example of a transition between bee and wasp pollination, and highlights the effects of floral architecture on specialization in plant pollination systems.
Memory deficit in patients with cerebral small vessel disease: evidence from eye tracking technology
Authors: Huang Kailing , Zhao Tingting , Sun Weifeng , Feng Li , Wang Quan , Feng Jie 
Published: April 2024

Abstract
Cerebral small vessel disease is the one of the most prevalent causes of vascular cognitive impairment. We aimed to find objective and process-based indicators related to memory function to assist in the detection of memory impairment in patients with cerebral small vessel disease. Thirty-nine cerebral small vessel disease patients and 22 healthy controls were invited to complete neurological examinations, neuropsychological assessments, and eye tracking tasks. Eye tracking indicators were recorded and analyzed in combination with imaging features. The cerebral small vessel disease patients scored lower on traditional memory task and performed worse on eye tracking memory task performance compared to the healthy controls. The cerebral small vessel disease patients exhibited longer visit duration and more visit count within areas of interest and targets and decreased percentage value of total visit duration on target images to total visit duration on areas of interest during decoding stage among all levels. Our results demonstrated the cerebral small vessel disease patients performed worse in memory scale and eye tracking memory task, potentially due to their heightened attentional allocation to nontarget images during the retrieval stage. The eye tracking memory task could provide process-based indicators to be a beneficial complement to memory assessment and new insights into mechanism of memory impairment in cerebral small vessel disease patients.
Noninvasive brain stimulations modulated brain modular interactions to ameliorate working memory in community-dwelling older adults
Authors: Fan Dongqiong , Che Xianwei , Jiang Yang , He Qinghua , Yu Jing , Zhao Haichao 
Published: April 2024

Abstract
Non-invasive brain stimulations have drawn attention in remediating memory decline in older adults. However, it remains unclear regarding the cognitive and neural mechanisms underpinning the neurostimulation effects on memory rehabilitation. We evaluated the intervention effects of 2-weeks of neurostimulations (high-definition transcranial direct current stimulation, HD-tDCS, and electroacupuncture, EA versus controls, CN) on brain activities and functional connectivity during a working memory task in normally cognitive older adults (age 60+, n = 60). Results showed that HD-tDCS and EA significantly improved the cognitive performance, potentiated the brain activities of overlapping neural substrates (i.e. hippocampus, dlPFC, and lingual gyrus) associated with explicit and implicit memory, and modulated the nodal topological properties and brain modular interactions manifesting as increased intramodular connection of the limbic-system dominated network, decreased intramodular connection of default-mode-like network, as well as stronger intermodular connection between frontal-dominated network and limbic-system–dominated network. Predictive model further identified the neuro-behavioral association between modular connections and working memory. This preliminary study provides evidence that noninvasive neurostimulations can improve older adults’ working memory through potentiating the brain activity of working memory-related areas and mediating the modular interactions of related brain networks. These findings have important implication for remediating older adults’ working memory and cognitive declines.
Volumetric analysis of age- and sex-related changes in the corpus striatum and thalamus in the 1–18 age group: a retrospective magnetic resonance imaging study
Authors: Işıklar Sefa , Sağlam Dilek 
Published: April 2024

Abstract
Studies of the development and asymmetry of the corpus striatum and thalamus in early childhood are rare. Studies investigating these structures across the lifespan have not presented their changes during childhood and adolescence in detail. For these reasons, this study investigated the effect of age and sex factors on the development and asymmetry of the corpus striatum and thalamus in the 1–18 age group. In this retrospective study, we included 652 individuals [362 (56%) males] aged 1–18 years with normal brain MRI between 2012 and 2021. Absolute and relative volumes of the corpus striatum and thalamus were obtained by segmentation of three-dimensional T1-weighted MRIs with volBrain1.0. We created age-specific volume data and month-based development models with the help of SPSS (ver.28). The corpus striatum and thalamus had cubic absolute volumetric developmental models. The relative volume of the caudate and thalamus (only males) is consistent with the decreasing “growth” model, the others with the decreasing cubic model. The absolute volumes of the males’ bilateral corpus striatum and thalamus and the relative volumes of the caudate and thalamus of the females were significantly larger (P &lt; 0.05). The caudate showed right &gt; left lateralization; putamen, globus pallidus, and thalamus showed left &gt; right lateralization.
Modeling refined differences of cortical folding patterns via spatial, morphological, and temporal fusion representations
Authors: Cao Chunhong , Li Yongquan , Hu Fang , Gao Xieping 
Published: April 2024

Abstract
The gyrus, a pivotal cortical folding pattern, is essential for integrating brain structure-function. This study focuses on 2-Hinge and 3-Hinge folds, characterized by the gyral convergence from various directions. Existing voxel-level studies may not adequately capture the precise spatial relationships within cortical folding patterns, especially when relying solely on local cortical characteristics due to their variable shapes and homogeneous frequency-specific features. To overcome these challenges, we introduced a novel model that combines spatial distribution, morphological structure, and functional magnetic resonance imaging data. We utilized spatio-morphological residual representations to enhance and extract subtle variations in cortical spatial distribution and morphological structure during blood oxygenation, integrating these with functional magnetic resonance imaging embeddings using self-attention for spatio-morphological-temporal representations. Testing these representations for identifying cortical folding patterns, including sulci, gyri, 2-Hinge, and 2-Hinge folds, and evaluating the impact of phenotypic data (e.g. stimulus) on recognition, our experimental results demonstrate the model’s superior performance, revealing significant differences in cortical folding patterns under various stimulus. These differences are also evident in the characteristics of sulci and gyri folds between genders, with 3-Hinge showing more variations. Our findings indicate that our representations of cortical folding patterns could serve as biomarkers for understanding brain structure-function correlations.
Assessing the Impact of the 2020 Council of State and Territorial Epidemiologists Case Definition for Pertussis on Reported Pertussis Cases
Authors: Rubis Amy B , Cole Matthew , Tondella M Lucia , Pawloski Lucia C , Youngkin Erin , Firmender Patricia , Aden Vanessa , Cruz Victor , Stanislawski Emma , Wester Rachel , Cieslak Paul R , Acosta Anna M , Skoff Tami H 
Published: April 2024

Abstract

Background
In 2020, the Council of State and Territorial Epidemiologists (CSTE) pertussis case definition was modified; the main change was classifying polymerase chain reaction (PCR)-positive cases as confirmed, regardless of cough duration. Pertussis data reported through Enhanced Pertussis Surveillance (EPS) in 7 sites and the National Notifiable Diseases Surveillance System (NNDSS) were used to evaluate the impact of the new case definition.

Methods
We compared the number of EPS cases with cough onset in 2020 to the number that would have been reported based on the prior (2014) CSTE case definition. To assess the impact of the change nationally, the proportion of EPS cases newly reportable under the 2020 CSTE case definition was applied to 2020 NNDSS data to estimate how many additional cases were captured nationally.

Results
Among 442 confirmed and probable cases reported to EPS states in 2020, 42 (9.5%) were newly reportable according to the 2020 case definition. Applying this proportion to the 6124 confirmed and probable cases reported nationally in 2020, we estimated that the new definition added 582 cases. Had the case definition not changed, reported cases in 2020 would have decreased by 70% from 2019; the observed decrease was 67%.

Conclusions
Despite a substantial decrease in reported pertussis cases in the setting of coronavirus disease 2019 (COVID-19), our data show that the 2020 pertussis case definition change resulted in additional case reporting compared with the previous case definition, providing greater opportunities for public health interventions such as prophylaxis of close contacts.
Effective corporate income taxation and its effect on capital accumulation: cross-country evidence
Authors: Goda Thomas 
Published: April 2024

Abstract
It is debated to what extent corporate taxation discourages capital formation, and the related empirical cross-country evidence is inconclusive. This paper provides new insights into this matter for a large sample of developed and developing countries. In the first step, national accounts data is used to calculate backward-looking effective corporate income tax rates (ECTR) for 77 countries during 1995–2018. In the second step, dynamic panel data regressions are used to estimate the effect of ECTR on aggregate corporate investment. The main findings of this exercise are that (i) statutory corporate income tax rates (SCTR), on average, are twice as high as ECTR, (ii) average ECTR has been relatively stable but show distinct dynamics across countries and (iii) no significant negative relationship exists between ECTR and investment. The latter finding is robust to different specifications and samples and when publicly available SCTR or forward-looking effective tax rate measures are used as alternative tax rate proxies.
Clinical Decision Making in Inflammatory Bowel Disease Mimics: Practice Management from Inflammatory Bowel Disease LIVE
Authors: Fiske Hannah W , Ward Christopher , Shah Samir A , Holubar Stefan D , Al-Bawardy Badr , Barnes Edward L , Binion David , Bohm Matthew , Brand Myron , Clarke Kofi , Cohen Benjamin L , Cross Raymond K , Dueker Jeffrey , Engels Michael , Farraye Francis A , Fine Sean , Forster Erin , Gaidos Jill , Ginsburg Philip , Goyal Alka , Hanson John , Herfath Hans , Hull Tracy , Kelly Colleen R , Lazarev Mark , Levy L Campbell , Melia Joanna , Philpott Jessica , Qazi Taha , Siegel Corey A , Watson Andrew , Wexner Steven D , Williams Emmanuelle D , Regueiro Miguel 
Published: April 2024

Abstract

Background
Since 2009, inflammatory bowel disease (IBD) specialists have utilized “IBD LIVE,” a weekly live video conference with a global audience, to discuss the multidisciplinary management of their most challenging cases. While most cases presented were confirmed IBD, a substantial number were diseases that mimic IBD. We have categorized all IBD LIVE cases and identified “IBD-mimics” with consequent clinical management implications.

Methods
Cases have been recorded/archived since May 2018; we reviewed all 371 cases from May 2018–February 2023. IBD-mimics were analyzed/categorized according to their diagnostic and therapeutic workup.

Results
Confirmed IBD cases made up 82.5% (306/371; 193 Crohn’s disease, 107 ulcerative colitis, and 6 IBD-unclassified). Sixty-five (17.5%) cases were found to be mimics, most commonly medication-induced (n = 8) or vasculitis (n = 7). The evaluations that ultimately resulted in correct diagnosis included additional endoscopic biopsies (n = 13, 21%), surgical exploration/pathology (n = 10, 16.5%), biopsies from outside the GI tract (n = 10, 16.5%), genetic/laboratory testing (n = 8, 13%), extensive review of patient history (n = 8, 13%), imaging (n = 5, 8%), balloon enteroscopy (n = 5, 8%), and capsule endoscopy (n = 2, 3%). Twenty-five patients (25/65, 38%) were treated with biologics for presumed IBD, 5 of whom subsequently experienced adverse events requiring discontinuation of the biologic. Many patients were prescribed steroids, azathioprine, mercaptopurine, or methotrexate, and 3 were trialed on tofacitinib.

Conclusions
The diverse presentation of IBD and IBD-mimics necessitates periodic consideration of the differential diagnosis, and reassessment of treatment in presumed IBD patients without appropriate clinical response. The substantial differences and often conflicting treatment approaches to IBD versus IBD-mimics directly impact the quality and cost of patient care.
Apico-aortic conduit: a readily available technical modification
Authors: Wantiez Pauline , Flecher Erwan , Heautot Jean-François , Allain Geraldine 
Published: April 2024

Abstract
When neither surgical valve replacement nor transcatheter aortic valve implantation is possible, performing an apico-aortic conduit remains a therapeutic option. This procedure has become rare and the rigid angled apical connectors usually used to facilitate ventricular anastomosis are no longer commercially available. We described the technique that we performed on a 60-year-old patient with readily available material.
Weather shocks and pesticide purchases
Authors: Bareille François , Chakir Raja , Keles Derya 
Published: April 2024

Abstract
This paper investigates whether farmers adapt their pesticide use to cope with weather shocks. Using a unique, exhaustive dataset detailing all active substance purchases per zip code in France between 2014 and 2019, we econometrically explain abnormal pesticide purchase deviations by weather shocks. We identify heterogeneous weather impacts across pesticide types, seasons and locations. Because our analyses suggest limited year-to-year pesticide storage and farmers’ adaptation along other margins, we interpret our estimates as true weather impacts on pesticide use. Our preferred estimates suggest that, ceteris paribus, farmers increase pesticide use by seven to fifteen per cent in 2050 under a RCP4.5 climate change scenario.
Introduction to the special issue on bioeconomy innovation pipelines and supply chain shocks
Authors: Drabik Dušan , Wesseler Justus 
Published: April 2024

Abstract
This introduction presents five articles of the virtual issue on bioeconomy innovation pipelines and supply chain shocks. The presented cases use alternative methodological approaches with their own advantages and disadvantages. The conclusion we can draw is that the specificities of individual case studies make it difficult to generalise and many more cases would be needed to perform a meta-analysis. We encourage agricultural economists to provide further research on detailed cases, which will be particularly important for gaining a better understanding of the potential effects of the EU Green Deal.
Leaf surface microbiota transplantation confers resistance to coffee leaf rust in susceptible Coffea arabica
Authors: de Sousa Leandro Pio , Mondego Jorge Maurício Costa 
Published: April 2024

Abstract
Coffee leaf rust, caused by the fungus Hemileia vastatrix, has become a major concern for coffee-producing countries. Additionally, there has been an increase in the resistance of certain races of the fungus to fungicides and breeding cultivars, making producers use alternative control methods. In this work, we transplanted the leaf surface microbiota of rust-resistant coffee species (Coffea racemosa and Coffea stenophylla) to Coffea arabica and tested whether the new microbiota would be able to minimize the damage caused by H. vastatrix. It was seen that the transplant was successful in controlling rust, especially from C. stenophylla, but the protection depended on the concentration of the microbiota. Certain fungi, such as Acrocalymma, Bipolaris, Didymella, Nigrospora, Setophaeosphaeria, Simplicillium, Stagonospora and Torula, and bacteria, such as Chryseobacterium, Sphingobium and especially Enterobacter, had their populations increased and this may be related to the antagonism seen against H. vastatrix. Interestingly, the relative population of bacteria from genera Pantoea, Methylobacterium and Sphingomonas decreased after transplantation, suggesting a positive interaction between them and H. vastatrix development. Our findings may help to better understand the role of the microbiota in coffee leaf rust, as well as help to optimize the development of biocontrol agents.