bluuebunny/crossref_metadata_2025_split huggingface dataset:
PROTRIDER: Protein abundance outlier detection from mass spectrometry-based proteomics data with a conditional autoencoder
Authors: Scheller Ines F. , Klaproth-Andrade Daniela , Loipfinger Stefan , Mertes Christian , Smirnov Dmitrii , Prokisch Holger , Yépez Vicente A. , Gagneur Julien 
Published: February 2025

Structured abstractMotivationDetection of gene regulatory aberrations enhances our ability to interpret the impact of inherited and acquired genetic variation for rare disease diagnostics and tumor characterization. While numerous methods for calling RNA expression outliers from RNA-sequencing data have been proposed, the establishment of protein expression outliers from mass spectrometry data is lacking.ResultsHere we propose and assess various modeling approaches to call protein expression outliers across three datasets from rare disease diagnostics and oncology. We use as independent evidence the enrichment for outlier calls in matched RNA-seq samples and the enrichment for rare variants likely disrupting protein expression. We show that controlling for hidden confounders and technical covariates is largely beneficial and can be achieved using conditional autoencoders. Moreover, we find that the differences between experimental and fitted log-transformed intensities by such models exhibit heavy tails that are poorly captured with the Gaussian distribution and report stronger statistical calibration when instead using the Student’s t-distribution. Our resulting method, PROTRIDER, outperformed baseline approaches based on raw log-intensities Z-scores or on differential expression analysis with limma. The application of PROTRIDER reveals significant enrichments of AlphaMissense pathogenic variants in protein expression outliers. Overall, PROTRIDER provides a method to confidently identify aberrantly expressed proteins applicable to rare disease diagnostics and cancer proteomics.Availability and ImplementationPROTRIDER is freely available atgithub.com/gagneurlab/PROTRIDER.ContactJulien Gagneur: gagneur at in.tum.de
Mortality prediction by Carotid Intimal Medial Thickness with a novel Life Table Statistical Model
Authors: Rembold Christopher M 
Published: February 2025

ABSTRACTCarotid Intimal Medial Thickness (CIMT) is an ultrasound estimate of preclinical atherosclerosis. The Charlottesville CIMT trial entered 1470 subjects from 1995 to 2011 and assessed total mortality in 2024 with a mean 15-year follow-up. In those subjects who reported no smoking or coronary disease, Cox statistics revealed that the presence of plaque and 4thquartile common, bulb and internal CIMT measurements predicted total mortality (compared to the 1stquartile). Age-normalized CIMT quartiles were less predictive. The age of subjects in the 4thquartile was 15 years higher than the 1stquartile. To correct for different ages, a novel life table model was created to analyze clinical data from a cohort who entered a trial at varying ages. This life table model allowed inclusion of subjects lost to follow-up. With this life table model, age-normalized 4thand 3rdquartile common, bulb and internal CIMT predicted total mortality. These data show the utility of measuring CIMT to predict mortality and the benefit of the life table model. The output statistic of the life table model, Age Difference, is an easily understandable and relevant measure of effect size.
Utilization of Genomic Services Among Physicians in Kenya
Authors: Sigilai Hillary , Ogola Elijah , Ilovi Syokau 
Published: February 2025

AbstractBackgroundWith advancement of genetic technology and mainstreaming of genetics into all specialties of medicine, physicians will be required to play a pivotal role in the coordination and provision of primary genetic services.ObjectiveTo describe the delivery of basic genetic services among physicians in Kenya and factors affecting integration of genomic medicine into their practice.Materials and MethodsAn online descriptive cross-sectional study was conducted among registered physicians practicing within Kenya and physicians in training at University of Nairobi. A self-administered online close-ended questionnaire that assessed the following domains: delivery of genetic services, attitude and perceptions towards genetics, barriers to delivery of genomic services, knowledge of genetics and physician demographics. Simple random sampling method was used to recruit participants into the study. Interview of participants was conducted using an online close-ended questionnaire. Descriptive analysis methods were used for data analysis. The data was summarized using frequencies and proportions.ResultsThe response rate was 41% with 190 of the eligible 464 physicians completing the survey. Eighty-seven percent of respondents had not received formal training in genetics, with 80% reporting involvement in evaluation of genetic patients. Physician involvement in genetic testing and pharmacogenomics was low at 31% and 29% respectively. Sixty-four percent of the respondents graded their graded their knowledge of genetics as moderate. Participants identified limited access to medical geneticist (80%), lack of referral guidelines (86%), high cost of genetic services (93%), inadequate knowledge of genetics as barriers to genetic service delivery.ConclusionUptake of genetic service provision to patients by physician remains low due to inadequate genetics training, limited genetic specialists and prohibitive costs of genetic testing. Mitigation of these factors is required to improve genetic access to care.
Impact of prolonged video viewing on physical and mental stress: An analysis of autonomic nervous system activity and salivary stress markers
Authors: Matsui Hiroki , Tanabe Rina , Mogi Rikako , Sugiura Yuka , Yokomachi Hana , Yokoyama Tomoyuki 
Published: February 2025

AbstractIn recent years, online lectures and conferences have become widespread, but problems such as stress and adjustment disorders caused by watching long videos have become a problem. Few studies have objectively evaluated the minute changes in stress associated with such prolonged viewing. This study aimed to determine the effects of prolonged video viewing on physical and mental stress.Twenty-six students (10 males and 16 females, aged 21–24) from University A participated in this study. The subjects watched both a high-interest and a low-interest video for 90 minutes each and then subjectively evaluated the video content. Heart rate variability analysis was used to assess heart rate and autonomic nervous system changes during video viewing and saliva samples were collected before, during, and after viewing the videos to measure the concentration of stress markers in the saliva. This study was approved by the Gunma University Medical Ethics Review Committee for Human Subjects.The results of the subjective evaluation showed that scores for concentration, comprehension, and interest were significantly higher, while the fatigue score was lower for the high-interest video than for the low-interest video. Both videos caused a decrease in heart rate and low sympathetic nerve activity, and an increase in parasympathetic nerve activity; however, the changes were more pronounced with the high-interest video. In addition, the differences in subjective scores between the high- and low-interest videos were more pronounced in women, with salivary chromogranin A also showing opposite trends for the two videos.This study demonstrates that watching two different types of videos for extended periods affects autonomic nervous system activity, heart rate, and stress hormones in saliva. Since trends differ depending on the type of video and the participant’s sex, attention should be paid to the video content and the individual subject when examining stress during video viewing.
Diffusion-based size determination of solute particles: a method adapted for PSD proteins
Authors: Szabó András László , Nagy-Kanta Eszter , Jáger Edit Andrea , Pongor Csaba István , Laki Mária , Laki András József , Gáspári Zoltán 
Published: February 2025

AbstractThe postsynaptic density (PSD) is a complex, multi-layered protein network largely situated on the internal surface of the postsynaptic membrane, with receptor proteins extending it across the membrane. It is the first processing unit for incoming synaptic transmissions, and changes in its internal structure exhibit a strong correlation with synaptic strength and plasticity. These structural changes are largely governed by multivalent interactions between its components, which leads to complex forming and, under certain circumstances, protein phase separation. Here we present an experimental method for detecting specific PSD proteins as well as their complexes via their diffusion. The method requires a fluorescent labelling technique that does not disrupt the function of labelled proteins, a microfluidic device that can maintain laminar flow for labelled protein solutions, a microscope that can record the fluorescent signal emitted by these solutions, and an analytic software package that can process the collected experimental data and convert them into approximate particle sizes.
BabyPy: a brain-age model for infancy, childhood, and adolescence
Authors: Biondo Francesca , O’Muircheartaigh Jonathan , Bethlehem Richard A.I. , Seidlitz Jakob , Alexander-Bloch Aaron , Elison Jed T. , D’Sa Viren , Deoni Sean C.L. , Bruchhage Muriel M.K. , Cole James H. 
Published: February 2025

AbstractIntroBrain-age models quantify biological ageing by predicting a person’s age from neuroimaging data. In early life, brain-age can reflect underlying biological maturity (or immaturity), providing a candidate predictor of typical neurodevelopment versus deviation. Although widely used in adult research, the use of brain-age in early development has been limited due to data availability, heterogeneity and restricted model accessibility. Here, we introduce BabyPy, a shareable brain-age model for individuals aged 0–17 years that achieves accurate predictions despite substantial variability in site, scanner, and preprocessing pipelines.MethodsWe trained BabyPy on 4,021 structural T1-weighted MRI scans from multi-site datasets (ages 0–17 years). An external test set of 1,143 scans (ages 0–16 years) was used for validation. Coarse neuroimaging features - grey matter volume (GMV), white matter volume (WMV), and subcortical grey matter volume (sGMV) - along with sex, were the model inputs. An ensemble machine learning approach combined Extra Trees Regression, Support Vector Machine, and Multilayer Perceptron base models. Performance was evaluated via 5-fold cross-validation and external testing.ResultsThe ensemble meta-model explained 80% of the variance in age (training set, MAE = 1.55 years) and 46% of the variance in the external test set (MAE = 1.72 years).ConclusionBabyPy is a shareable framework that estimates brain-age across a broad developmental range, removing the need for separate age-specific models. Despite limitations due to data heterogeneity, it demonstrates robust predictive performance and supports cross-study comparisons. Future improvements in data harmonisation will further enhance the utility of generic brain-age models like BabyPy.KeypointsBroad developmental coverage:BabyPy provides a shareable brain-age model for individuals aged 0–17 years, removing the need for separate age-specific models in the primary developmental period.Minimal features, robust performance:Using just three coarse volumetric measures (GMV, WMV, sGMV) plus sex, BabyPy achieves good predictive accuracy (R2= 0.80, MAE = 1.55 years in training; R2= 0.46, MAE = 1.72 years in external validation) across diverse sites, scanners, and preprocessing protocols.Open Science contribution:BabyPy is freely available as a Python-based toolbox, facilitating easy adoption, reproducibility, and cross-study comparisons in developmental neuroimaging.
Mechanisms of transcription attenuation and condensation of RNA polymerase II by RECQ5
Authors: Sebesta M. , Skubnik K. , Morton W.S. , Kravec M. , Linhartova K. , Klapstova V. , Novacek J. , Kubicek K. , Bryja V. , Vacha R. , Stefl R. 
Published: February 2025

AbstractThe elongation rates of RNA polymerase II (RNAPII) require precise control to prevent transcriptional stress, which can impede co-transcriptional pre-mRNA processing and contribute to many age- or disease-associated molecular changes (e.g., loss of proteostasis)1–5. Additionally mesoscale organization of transcription is thought to control the transcriptional rates6and multiple factors have been reported to form biomolecular condensates and integrate RNAPII through the interaction with the C-terminal domain (CTD) of the largest subunit, RPB17–10. However, the structural organization of these condensates remains uncharacterized due to their small size and inherently dynamic nature. Here, we investigated the molecular mechanisms by which a general transcription factor – RECQ5 – associates with hyperphosphorylated RNAPII elongation complex (P-RNAPII EC) and controls translocation of RNAPII along genes. We combined biochemical reconstitution, electron cryomicroscopy, cryotomography, and coarse-grained simulations. We report two mechanisms by which RECQ5 modulates RNAPII transcription. At the atomic level, we demonstrate that RECQ5 uses the brake helix as a doorstop to control RNAPII translocation along DNA, attenuating transcription. At the mesoscale level, RECQ5 forms a condensate scaffold matrix, integrating P-RNAPII EC through a network of site-specific interactions, reinforcing the condensate’s structural integrity. Our integrative, multi-scale study provides insights into the structural basis of transcription attenuation and into the molecular architecture and biogenesis of a model RNAPII condensate.
Responses to oddball communication sequences in the bat frontal and auditory cortices
Authors: González-Palomares Eugenia , Wetekam Johannes , Malmierca Manuel S. , Hechavarria Julio C. 
Published: February 2025

AbstractStimulus-specific adaptation (SSA) is a ubiquitous phenomenon in the animal kingdom across sensory modalities, but this type of neural response has rarely been studied using natural sounds in the auditory brain. Here, we leveraged the well-documented acoustic repertoire of the bat speciesCarollia perspicillatato study adaptation in the bat brain using natural communication sounds. We searched for SSA in single neuron spiking activity measured in two brain areas simultaneously: the auditory cortex and the frontal auditory field. The stimuli consisted of natural distress syllables, a form of vocalization produced by bats under duress. Bat distress vocalizations signal different degrees of urgency based on their amplitude modulation pattern, without large differences in their spectral structure. These distress vocalizations make an ideal test case for exploring the limits of neural deviance detection when considering naturalistic soundscapes with low stimulus contrast. The results show limited evidence for stimulus-specific adaptation in response to natural sound sequences in the majority of neurons studied. Many neurons did show a prominent effect related to context-dependent changes, caused by the type of sounds that occurred most frequently within each oddball sequence. Context-dependent responses were strongest in frontal neurons. Decoding analysis showed the existence of neural populations in both frontal and auditory cortices, which could distinguish between deviants and standards occurring within the same sequence, without large changes in evoked spike counts. Taken together, our results highlight the diversity of neural mechanisms complementing classical stimulus-specific adaptation when encoding natural vocalizations that do not differ markedly in their spectral composition.
Complete classification and additional saddle-point solutions for high-order above-threshold ionization induced by a strong laser field
Authors: Habibović D. , Milošević D. B. 
Published: February 2025

Ionization of atoms by a strong laser field can be described using the improved strong-field approximation. The corresponding transition amplitude of high-order above-threshold ionization is presented in the form of a two-dimensional integral over the electron ionization time t0 and the rescattering time t. This integral can be solved using the saddle-point (SP) method and the resulting T-matrix element is expressed as a sum (over the SP times t0 and t) of the partial transition amplitudes. We address the problem of finding the solutions of the system of SP equations for the times t0 and t. For a bichromatic linearly polarized laser field with the frequencies rω and sω (r and s are integers, s>r, and ω is the fundamental frequency) we found that there are 8s2 SP solutions per optical cycle. For one half of them the velocity of the electron emitted in the laser field polarization direction changes the sign at the rescattering time (we call such solutions backward-scattering solutions), while for the other half this velocity remains unchanged (these solutions we call forward-scattering SP solutions). For very short (or even negative) electron travel time we call these solutions backward-like and forward-like scattering SP solutions. For these solutions the imaginary parts of the times t0 and t become large so that the concept of real electron trajectories becomes questionable. Having such a classification, we found additional SP solutions even for the simplest case of a monochromatic linearly polarized laser field. For a bichromatic linearly polarized laser field with s=2 and equal component intensities we presented a detailed analysis of all 32 solutions per optical cycle, showing how the SP times t0 and t and the corresponding differential ionization rates depend on the photoelectron energy. We have also analyzed the case where the intensity of the second component decreases while the sum of the component intensities remains fixed.

Published by the American Physical Society
2025
Put autistic women and girls at the heart: exploring the experiences of autistic women during diagnostic assessments in the UK
Authors: Trundle Grace , Alexander Zoe , Chester Verity 
Published: February 2025

Purpose
It is suggested that autism assessments are not sensitive to the female autism presentation. Autistic women are often misdiagnosed or delayed in receiving their diagnosis. More guidance for assessing clinicians is required to improve the validity and effectiveness of autism diagnostic assessments of women. This study aims to explore the experiences of autistic women during their diagnostic assessments and understand what they considered important for diagnostic assessments of females.

Design/methodology/approach
A focus group with four adult autistic women was conducted, exploring their experiences and recommendations. Thematic analysis was used to identify overarching themes.

Findings
The main themes were 1) experience of the assessment; 2) gender-sensitive assessment content; and 3) clinician characteristics and skills. Participants made specific recommendations within these themes for how diagnostic assessments of females should be conducted.

Originality/value
This study differs from previous research by focusing on the experiences of autistic women specifically during diagnostic assessments and what they recommend for future assessments.
Leveraging social capital to build the cumulative triple-A supply chain sand cone model
Authors: Yang Lu , Huo Baofeng , Machuca Jose A.D. , Alfalla-Luque Rafaela , Gu Minhao 
Published: February 2025

PurposeDrawing on the cumulative capability perspective, this study tests the sand cone model of the triple-A supply chain (SC) (i.e. AAA: SC-alignment, SC-adaptability, SC-agility), including its financial performance implications. Besides, this study investigates social capital as AAA enabler.Design/methodology/approachStructural equation modeling and bootstrapping analysis are used to examine hypotheses using data from 216 companies in China that capture firms’ supply chain management practices in relation to their major suppliers.FindingsWe identified a cumulative sand cone sequence of three As: alignment-adaptability-agility to effectively develop a triple-A SC. Furthermore, based on this sequence, SC adaptability can enhance financial performance indirectly through SC agility, and SC alignment can improve financial performance indirectly through SC adaptability and SC agility, which directly and positively affects financial performance. Furthermore, cognitive, structural, and relational capital play different roles in improving AAA.Originality/valueThis study contributes to triple-A SC literature by identifying the cumulative sand cone sequence of alignment-adaptability-agility and thus further extends the cumulative capability perspective in operations and supply chain management. Besides, this study: (1) deepens our understanding of performance implications of triple-A SC capabilities based on the sand cone model; (2) contributes to revealing social capital as an important enabler of triple-A SC capabilities from the complex adaptive system perspective; (3) specifies difference in the pattern of triple-A SC sand cone model across different levels of market turbulence.
Disparity in sustainability competencies of business professionals and students: implications for lecturing as a teaching pedagogy
Authors: Shariq Samrah , Hameed Salman , Butt Adnan 
Published: February 2025

PurposeThis study aims to assess the level of sustainability competencies among full-time students and professional students, foresee any noteworthy change in students’ competencies after applying teaching pedagogy and determine whether lecturing is an effective teaching pedagogy for developing all five sustainability competencies in both cohorts.Design/methodology/approachThe presence and development of competencies after varying pedagogical practices are assessed using a pre-/post-test based on two case studies. This research approach of comparative case study is more advanced and is particularly useful when seeking to understand differences and similarities between distinct entities, which in our case were students of two different capacities. The study targets two cohorts: the first includes 15 professional students with considerable industry experience, while the second consists of 24 full-time students without industry exposure.FindingsThe study revealed that professional students have more sustainability competencies than full-time students. Also, lecturing is an effective pedagogical practice when all five sustainable competencies have to be enhanced in full-time students. In contrast, lecturing does not work for interpersonal competence in professional students.Research limitations/implicationsThere are certain limitations of the study that future researchers undermine. Firstly, the study was conducted only on business students at Bahria University. Secondly, the sample size for the study is small as the data were qualitative, and the researchers had time constraints. Thirdly, the effectiveness of only one teaching pedagogy has been gauged in the current research.Practical implicationsIt is recommended that higher educational institutions (HEIs) of Pakistan introduce sustainability courses or programs to its students to spread awareness among learners and develop sustainable competencies. All service and production industries in Pakistan should train their employees in sustainable practices so that hazardous impacts in the future can be reduced. It is a need of time for the country to move a step ahead towards sustainable development goals.Originality/valueThis research contributes to education for sustainable development (ESD) in Pakistan. Pakistan is a developing country that is far behind ESD. Therefore, this study identifies how sustainability education can become a part of the academic system. It also identifies the need for sustainable education not only for students but also for professionals. It also identifies teaching pedagogy required for developing sustainability competencies and is relevant to learners’ exposure.