bluuebunny/crossref_metadata_2025_split huggingface dataset:
Humans display interindividual differences in the latent mechanisms underlying fear generalization behaviour
Authors: Yu Kenny , Tuerlinckx Francis , Vanpaemel Wolf , Zaman Jonas 
Published: August 2023

AbstractHuman generalization research aims to understand the processes underlying the transfer of prior experiences to new contexts. Generalization research predominantly relies on descriptive statistics, assumes a single generalization mechanism, interprets generalization from mono-source data, and disregards individual differences. Unfortunately, such an approach fails to disentangle various mechanisms underlying generalization behaviour and can readily result in biased conclusions regarding generalization tendencies. Therefore, we combined a computational model with multi-source data to mechanistically investigate human generalization behaviour. By simultaneously modelling learning, perceptual and generalization data at the individual level, we revealed meaningful variations in how different mechanisms contribute to generalization behaviour. The current research suggests the need for revising the theoretical and analytic foundations in the field to shift the attention away from forecasting group-level generalization behaviour and toward understanding how such phenomena emerge at the individual level. This raises the question for future research whether a mechanism-specific differential diagnosis may be beneficial for generalization-related psychiatric disorders.
Functional Nasal Surgery in a Compromised Soft Tissue Envelope
Authors: Dunn Brandyn S. , Madorsky Simon 
Published: August 2023

AbstractFunctional nasal surgery in the setting of a compromised soft tissue envelope (STE) requires significant planning and preparation. Proper preoperative evaluation is imperative to assess the degree of STE compromise and determine the best surgical approach. Alternative approaches to functional nasal surgery, such as limited access surgical approaches, should be considered to minimize complications while achieving functional improvement. Given the increased risk of ischemia and necrosis in individuals with a history of a compromised STE, a comprehensive postoperative treatment algorithm is necessary to identify and treat signs of early vascular compromise.
The transhistorical, transcultural life of sausages: From medieval morescas to New Mexican Matachines with Aby Warburg
Authors: Drury Lindsey 
Published: August 2023

AbstractNew Mexican Matachines dances have long been discussed as descendent dances of medieval morescas. This article explores this ‘ancestral relation’, beginning on New Year’s Day in 1896 at the colonial outpost of Cubero, New Mexico. There, the German art historian Aby Warburg met a local shepherd who endeavoured to explain the pantomimic killing of a bull in the dance drama by saying the blood was ‘good for making sausages.’ Accordingly, this article investigates Warburg’s lifelong exploration of Matachines antecedents in the margins of his research on early Italian Renaissance images of medieval festive drama, and ‘headhuntress’ figures, such as Judith and Salome. Warburg’s thoughts on New Mexican Matachines meandered over the course of his life from Aztec sacrifice to medieval morescas, to the Mithras cult. Through these explorations, Warburg pursued a cultural evolutionary theory that would situate New Mexican Matachines as a descendent of antique pagan blood ceremony.
Modeling of surface damage at the Si/SiO2-interface of irradiated MOS-capacitors
Authors: Akchurin N. , Altopp G. , Burkle B. , Frey W.D. , Heintz U. , Hinton N. , Hoeferkamp M. , Kazhykarim Y. , Kuryatkov V. , Mengke T. , Peltola T. , Seidel S. , Spencer E. , Tripathi M. , Voelker J. 
Published: August 2023

Abstract
Surface damage caused by ionizing radiation in SiO2
passivated silicon particle detectors consists mainly of the
accumulation of a positively charged layer along with
trapped-oxide-charge and interface traps inside the oxide and close
to the Si/SiO2-interface. High density positive interface net
charge can be detrimental to the operation of a multi-channel
n-on-p sensor since the inversion layer generated under the
Si/SiO2-interface can cause loss of position resolution by
creating a conduction channel between the electrodes. In the
investigation of the radiation-induced accumulation of oxide charge
and interface traps, a capacitance-voltage characterization study of
n/γ- and γ-irradiated Metal-Oxide-Semiconductor (MOS)
capacitors showed that close agreement between measurement and
simulation were possible when oxide charge density was complemented
by both acceptor- and donor-type deep interface traps with densities
comparable to the oxide charges. Corresponding inter-strip
resistance simulations of a n-on-p sensor with the tuned oxide
charge density and interface traps show close agreement with
experimental results. The beneficial impact of radiation-induced
accumulation of deep interface traps on inter-electrode isolation
may be considered in the optimization of the processing parameters
of isolation implants on n-on-p sensors for the extreme
radiation environments.
Reduction of radioactive impurities in liquid scintillator by using metal scavengers
Authors: Kamei Y. , Shimizu I. , Teraoka Y. , Yamamura T. , Shirasaki K. 
Published: August 2023

Abstract
Development of radio-purification for the large-volume
liquid scintillator detector is a key to enhance search
sensitivities in neutrino physics. In this paper, we describe
laboratory studies on the radio-purification of the liquid
scintillator detector by using the metal scavenger, aiming at the
improved search for the neutrinoless double beta decay in
KamLAND-Zen. In the purification tests, the 210Pb reduction
efficiency was evaluated. Based on the purification performance in
small-scale system, we designed a large adsorption column for the
metal scavenging applicable to the KamLAND purification system. We
produced the column and constructed a purification test bench, and
confirmed the 212Pb reduction efficiency, the process speed,
the LS contamination and quality changes, and the stability of
chemical components in the Xe-LS. We found that the metal scavenging
is a practical method for the large-volume LS purification, and will
be effective to reduce metallic radioactive elements.
Total economic costs of climate change at different discount rates for market and non-market values
Authors: Oda Takahiro , Takakura Jun’ya , Tang Longlong , Iizumi Toshichika , Itsubo Norihiro , Ohashi Haruka , Kiguchi Masashi , Kumano Naoko , Takahashi Kiyoshi , Tanoue Masahiro , Tamura Makoto , Zhou Qian , Hanasaki Naota , Hasegawa Tomoko , Park Chan , Hijioka Yasuaki , Hirabayashi Yukiko , Fujimori Shinichiro , Honda Yasushi , Matsui Tetsuya , Matsuda Hiroyuki , Yokoki Hiromune , Oki Taikan 
Published: August 2023

Abstract
What will be the aggregated cost of climate change in achieving the Paris Agreement, including mitigation, adaptation, and residual impacts? Several studies estimated the aggregated cost but did not always consider the critical issues. Some do not address non-market values such as biodiversity and human health, and most do not address differentiating discount rates. In this study, we estimate the aggregated cost of climate change using an integrated assessment model linked with detailed-process-based climate impact models and different discount rates for market and non-market values. The analysis reveals that a climate policy with minimal aggregated cost is sensitive to socioeconomic scenarios and the way discount rates are applied. The results elucidate that a lower discount rate to non-market value—that is, a higher estimate of future value—makes the aggregated cost of achieving the Paris Agreement economically reasonable.
KOMPUTE: imputing summary statistics of missing phenotypes in high-throughput model organism data
Authors: Warkentin Coby , O’Connell Michael J , Lee Donghyung 
Published: August 2023

Abstract

Motivation
The International Mouse Phenotyping Consortium (IMPC) is striving to build a comprehensive functional catalog of mammalian protein-coding genes by systematically producing and phenotyping gene-knockout mice for almost every protein-coding gene in the mouse genome and by testing associations between gene loss-of-function and phenotype. To date, the IMPC has identified over 90 000 gene–phenotype associations, but many phenotypes have not yet been measured for each gene, resulting in largely incomplete data; ∼75.6% of association summary statistics are still missing in the latest IMPC summary statistics dataset (IMPC release version 16).

Results
To overcome these challenges, we propose KOMPUTE, a novel method for imputing missing summary statistics in the IMPC dataset. Using conditional distribution properties of multivariate normal, KOMPUTE estimates the association Z-scores of unmeasured phenotypes for a particular gene as a conditional expectation given the Z-scores of measured phenotypes. Our evaluation of the method using simulated and real-world datasets demonstrates its superiority over the singular value decomposition matrix completion method in various scenarios.

Availability and implementation
An R package for KOMPUTE is publicly available at https://github.com/statsleelab/kompute, along with usage examples and results for different phenotype domains at https://statsleelab.github.io/komputeExamples.
ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization
Authors: Yang Chen , Mai Jiahao , Cao Xuan , Burberry Aaron , Cominelli Fabio , Zhang Liangliang 
Published: August 2023

Abstract

Summary
Microbiome research is now moving beyond the compositional analysis of microbial taxa in a sample. Increasing evidence from large human microbiome studies suggests that functional consequences of changes in the intestinal microbiome may provide more power for studying their impact on inflammation and immune responses. Although 16S rRNA analysis is one of the most popular and a cost-effective method to profile the microbial compositions, marker-gene sequencing cannot provide direct information about the functional genes that are present in the genomes of community members. Bioinformatic tools have been developed to predict microbiome function with 16S rRNA gene data. Among them, PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) has become one of the most popular functional profile prediction tools, which generates community-wide pathway abundances. However, no state-of-art inference tools are available to test the differences in pathway abundances between comparison groups. We have developed ggpicrust2, an R package, for analyzing functional profiles derived from 16S rRNA sequencing. This powerful tool enables researchers to conduct extensive differential abundance analyses and generate visually appealing visualizations that effectively highlight functional signals. With ggpicrust2, users can obtain publishable results and gain deeper insights into the functional composition of their microbial communities.

Availability and implementation
The package is open-source under the MIT and file license and is available at CRAN and https://github.com/cafferychen777/ggpicrust2. Its shiny web is available at https://a95dps-caffery-chen.shinyapps.io/ggpicrust2_shiny/.
MIX-TPI: a flexible prediction framework for TCR–pMHC interactions based on multimodal representations
Authors: Yang Minghao , Huang Zhi-An , Zhou Wei , Ji Junkai , Zhang Jun , He Shan , Zhu Zexuan 
Published: August 2023

Abstract

Motivation
The interactions between T-cell receptors (TCR) and peptide-major histocompatibility complex (pMHC) are essential for the adaptive immune system. However, identifying these interactions can be challenging due to the limited availability of experimental data, sequence data heterogeneity, and high experimental validation costs.

Results
To address this issue, we develop a novel computational framework, named MIX-TPI, to predict TCR–pMHC interactions using amino acid sequences and physicochemical properties. Based on convolutional neural networks, MIX-TPI incorporates sequence-based and physicochemical-based extractors to refine the representations of TCR–pMHC interactions. Each modality is projected into modality-invariant and modality-specific representations to capture the uniformity and diversities between different features. A self-attention fusion layer is then adopted to form the classification module. Experimental results demonstrate the effectiveness of MIX-TPI in comparison with other state-of-the-art methods. MIX-TPI also shows good generalization capability on mutual exclusive evaluation datasets and a paired TCR dataset.

Availability and implementation
The source code of MIX-TPI and the test data are available at: https://github.com/Wolverinerine/MIX-TPI.
Short-read aligner performance in germline variant identification
Authors: Wilton Richard , Szalay Alexander S 
Published: August 2023

Abstract

Motivation
Read alignment is an essential first step in the characterization of DNA sequence variation. The accuracy of variant-calling results depends not only on the quality of read alignment and variant-calling software but also on the interaction between these complex software tools.

Results
In this review, we evaluate short-read aligner performance with the goal of optimizing germline variant-calling accuracy. We examine the performance of three general-purpose short-read aligners—BWA-MEM, Bowtie 2, and Arioc—in conjunction with three germline variant callers: DeepVariant, FreeBayes, and GATK HaplotypeCaller. We discuss the behavior of the read aligners with regard to the data elements on which the variant callers rely, and illustrate how the runtime configurations of these software tools combine to affect variant-calling performance.
XGDAG: explainable gene–disease associations via graph neural networks
Authors: Mastropietro Andrea , De Carlo Gianluca , Anagnostopoulos Aris 
Published: August 2023

Abstract

Motivation
Disease gene prioritization consists in identifying genes that are likely to be involved in the mechanisms of a given disease, providing a ranking of such genes. Recently, the research community has used computational methods to uncover unknown gene–disease associations; these methods range from combinatorial to machine learning-based approaches. In particular, during the last years, approaches based on deep learning have provided superior results compared to more traditional ones. Yet, the problem with these is their inherent black-box structure, which prevents interpretability.

Results
We propose a new methodology for disease gene discovery, which leverages graph-structured data using graph neural networks (GNNs) along with an explainability phase for determining the ranking of candidate genes and understanding the model’s output. Our approach is based on a positive–unlabeled learning strategy, which outperforms existing gene discovery methods by exploiting GNNs in a non-black-box fashion. Our methodology is effective even in scenarios where a large number of associated genes need to be retrieved, in which gene prioritization methods often tend to lose their reliability.

Availability and implementation
The source code of XGDAG is available on GitHub at: https://github.com/GiDeCarlo/XGDAG. The data underlying this article are available at: https://www.disgenet.org/, https://thebiogrid.org/, https://doi.org/10.1371/journal.pcbi.1004120.s003, and https://doi.org/10.1371/journal.pcbi.1004120.s004.
The pericarp structure and histogenesis in Enkianthus: on the ancestral fruit type in Ericaceae family
Authors: Sorokin Alexey N , Yatsenko Olga V , Bobrov Alexey V F Ch , Romanov Mikhail S , Zdravchev Nikita S , Iovlev Petr S , Timchenko Anton S , Mikhaylova Anna A , Vasekha Natalia D , Kuptsov Kirill V 
Published: August 2023

Abstract
According to modern phylogenetic data, the monotypic subfamily Enkianthoideae is sister to all other subfamilies of the family Ericaceae s.l. Aiming to determine the peculiarities of development and structure of Enkianthus pericarp and to reveal the principal characters of its structure, which can be original for the Ericaceae, we have studied fruit anatomical structure at different stages of development in four species of the genus Enkianthus belonging to three sections: Meisteria, Enkiantella, Enkianthus. The pericarp of superior loculicidal capsule of Enkianthus is differentiated into three histogenetic zones: (i) one-layered exocarp, (ii) multilayered mesocarp differentiated into two histological zones: the peripheral parenchymatous one, and the inner sclerenchymatous one, and (iii) one-layered endocarp composed of tangentially elongated sclereids. It has been shown that the lignification of cells of the endocarp proceeds after the lignification of the inner zone of the mesocarp. Our investigation demonstrates that the superior loculicidal capsules of Enkianthus are capsules of Hamamelis type, which are recognized as the probable ancestral (plesiomorphic) fruit type for other subfamilies of Ericaceae. This fruit type is recognized as the original in several modes of morphogenetic transformations of fruit in Ericaceae family, from which other types of capsules, pyrenariums, and berries originated.
Sleep Quality Drives Next Day Pain and Fatigue in Adults With Inflammatory Bowel Disease: A Short Report
Authors: Guadagnoli Livia , Horrigan Jamie , Walentynowicz Marta , Salwen-Deremer Jessica K 
Published: August 2023

Abstract

Background and Aims
Poor sleep is prevalent in inflammatory bowel disease [IBD] and is associated with increased symptom severity and decreased quality of life. To date, research is mostly cross-sectional, limiting the ability to examine the causal direction between sleep and IBD symptoms. This short report aims to assess the temporal associations among sleep quality, pain, fatigue, and physical activity in adults with IBD.

Methods
Adult IBD patients [N = 18] completed a structured electronic diary two times per day [morning and evening] over 14 consecutive days. Morning diary items assessed sleep [sleep quality, wake after sleep onset, number of awakenings] and evening diary items assessed daytime IBD symptoms [abdominal pain, fatigue]. An actigraph measured daily step count [physical activity]. Generalised estimating equation models evaluated the lagged temporal associations between sleep ratings and next day pain, fatigue, and physical activity as well as reverse lagged temporal associations between daytime symptoms and physical activity and subsequent sleep ratings.

Results
Poor self-reported sleep quality predicted increased next day abdominal pain and fatigue scores. Increased time awake during the night predicted decreased next day physical activity. In the reverse analyses, only the relationship between daytime abdominal pain and wake after sleep onset was significant.

Conclusions
Poor sleep appears to drive IBD-related outcomes, such as pain and fatigue. These findings are a first step in demonstrating the key role of sleep in the IBD patient experience, potentially resulting in a treatment target for intervention. Future research is needed to confirm results in a larger sample.
Early substance use disorders and subsequent NEET-not in education, employment or training—a national cohort study
Authors: Manhica Hélio , Yacamán-Méndez Diego , Sjöqvist Hugo , Lundin Andreas , Danielsson Anna-Karin 
Published: August 2023

Abstract

Background
Substance use problems have been associated with poor labour market outcomes. This study investigated whether substance use disorders (SUD) in emerging adulthood increase the likelihood of later being not in employment, education or training (NEET).

Methods
A national cohort study of 23 5295 males and 227 792 females born between 1981 and 1987. SUD was assessed between ages 17 and 24 years. Logistic regression models were used to estimate the odds ratios (ORs) of NEET, between ages 25–34. Sibling-comparison analysis was performed to account for potential shared genetic and environmental factors.

Results
Having been diagnosed with a SUD was associated with the likelihood of being NEET among males [OR = 1.37, 95% confidence interval (CI), 1.25–1.49] and females (1.19, 1.13–1.27) after adjusting for domicile, origin, psychiatric diagnosis and parental psychiatric diagnosis. Early SUD was also associated with a gradual increase in the ORs of accumulation of years being NEET. This was more evident among females. In the sibling-comparison analysis, we found a higher OR of NEET among same-sex sibling males 1.39 (1.06–1.82) and females 1.28 (0.99–1.66) with SUD. These risks were fully attenuated when another psychiatric diagnosis was adjusted for.

Conclusion
Early SUD was associated with an increased likelihood of being NEET in both males and females. Neither origin, domicile, psychiatric diagnoses nor parental psychiatric diagnoses did fully explain the association. The combination of unmeasured familial factors and having other psychiatric disorders largely explained these associations.
Evolutionary signatures of a trade-off in direct and indirect defenses across the wild grape genus, Vitis
Authors: Graham Carolyn D K , Forrestel Elisabeth J , Schilmiller Anthony L , Zemenick Ash T , Weber Marjorie G 
Published: August 2023

Abstract
Evolutionary correlations between chemical defense and protection by mutualist bodyguards have been long predicted, but tests of these patterns remain rare. We use a phylogenetic framework to test for evolutionary correlations indicative of trade-offs or synergisms between direct defense in the form of plant secondary metabolism and indirect defense in the form of leaf domatia, across 33 species in the wild grape genus, Vitis. We also performed a bioassay with a generalist herbivore to associate our chemical phenotypes with herbivore palatability. Finally, we tested whether defensive traits correlated with the average abiotic characteristics of each species’ contemporary range and whether these correlations were consistent with plant defense theory. We found a negative evolutionary correlation between domatia size and the diversity of secondary metabolites in Vitis leaf tissue across the genus, and also that leaves with a higher diversity and richness of secondary metabolites were less palatable to a generalist herbivore, consistent with a trade-off in chemical and mutualistic defense investment. Predictions from plant defense theory were not supported by associations between investment in defense phenotypes and abiotic variables. Our work demonstrates an evolutionary pattern indicative of a trade-off between indirect and direct defense strategies across the Vitis genus.