bluuebunny/crossref_metadata_2025 huggingface dataset:
HCPrune: A Hierarchical Classification Pruning Method Based on Receptive Field Size
Authors: Zhang Ruixuan , Zhao Yufeng , Zhang Wenlong
Published: October 2024

Model pruning, as an optimisation algorithm for convolutional neural network (CNN) models, can effectively compress and accelerate various complex CNN models. Recent network pruning algorithms usually focus on removing unimportant and redundant convolutional kernels or channels in the network. This paper propose a hierarchical pruning algorithm, HCPrune, which classifies and then prunes the convolutional layers of a CNN model to improve the model prediction accuracy while reducing the number of parameters and FLOPs. In this paper, the CNN convolutional layers are divided in terms of the size relationship between the receptive field of each layer of the network and the resolution of the input image, and use the VGG and Resnet series of networks based on some popular pruning methods to conduct experiments on the CIFAR10 and CIFAR100 datasets and ensure that the same number of parameters and FLOPs compared with the basic pruning methods. The VGG16 network improves the accuracy by 0.42% in CIFAR10 and 0.47% in CIFAR100, and the ResNet164 improves the accuracy by about 0.2% in the same configuration.
Modulation Measurement Profilometry Based on One-Dimensional Frequency-Guided S-Transform
Authors: Zhong Min , Hu Zhengyan , Duan Peng , Zan Junmu , Cao Weiwei
Published: October 2024

The modulation measurement profilometry employs the principle of vertical measurement, where the projection optical axis and the observation optical axis are aligned. This technique effectively avoids the limitations of shadows and occlusions inherent in optical 3D sensing methods based on the triangulation principle. To further enhance the accuracy of modulation information extraction, a one-dimensional frequency-guided S-transform method (1D-FGST) is introduced, which incorporates the parameter p to control the width of the Gaussian window, offering better time-frequency analysis characteristics compared to the traditional one-dimensional S-transform method (1D-ST). It can extract high-frequency detailed information about object, achieving a root mean square (RMS) error of 4.24 μm within a depth range of 1100 μm.
An Image Distortion Correction Method Based on Distortion Centre and Parameter Estimation
Authors: Zhao Wenhuang , Liu Xing , Zhang Yinhuan
Published: October 2024

We propose a radial distortion correction method based on straight-line feature calibration to address the challenge of image radial distortion when measuring mechanical motion parameters using computer vision technology. This method first independently estimates the distortion center, and then transforms the distortion parameter estimation into an arc fitting problem. The least squares optimization algorithm is applied to quickly and accurately estimate the arc parameter of distorted lines, ultimately achieving precise correction of distortion in wide-angle camera images. This method can reduce lens distortion by 89% to 92%, laying a solid foundation for the application of computer vision technology in the field of mechanical motion parameter measurement.
The thrust balance model during the dragonfly hovering flight
Authors: Zhang Kaixuan , Su Xiaohui , Zhao Yong
Published: October 2024

In recent years, the micro air vehicle (MAV) oscillations caused by thrust imbalances have received more attention. This paper proposes a dual-wing thrust balance model (DTBM) that can solve the above problem by iterating the modified rotation angle formula. The core control parameter of the DTBM model is the au angle, which refers to the angle between the wing surface and the stroke plane at the mid-stroke position during the upstroke. For each degree change in the au angle, the range of variation in the dimensionless average thrust coefficient is between 0.0225–0.0268. A thrust coefficient of 0.0225 causes the dragonfly to move forward by 9.037 cm in one second, which is equivalent to 1.29 times its body length. By using DTBM, the average thrust coefficient can be reduced to below 0.001 in just a few iterations. No matter how complex the motion pattern is, the DTBM can achieve thrust balance within 0.278 s. Through our research, when selecting the deviation angle motion of real dragonflies, the dual-wing au angles exhibit a highly linear correlation with wing spacing, called linear motion. In contrast, the nonlinear variation of the au angle appears in the hindwing of the no-deviation motion and the forewing of the elliptical deviation motion. All of the nonlinear changes are referred to as nonlinear motion. Nonlinear variation of the au angle arises from larger disturbances of the lateral force during the upstroke. The stronger lateral force is closely related to the flapping trajectory. When the flapping trajectory causes the dual-wing to closely approach each other in the mid-stroke, a continuous positive pressure zone forms between the dual-wing. The collision of the leading-edge vortex and the shedding of the trailing-edge vortex is the special flow field structure in the nonlinear motion. Guided by the DTBM, future designs of MAVs will be able to better achieve thrust balance during hovering flight, requiring only the embedding of the iteration algorithm and prediction function of the DTBM in the internal chip.
Increasing summertime low-level cloud cover associated with increasing vegetation in China from 2003 to 2022
Authors: Zhang Chenqi , Zhao Defeng , Gao Yanhong , Song Zhen , Zhao Bin , Wang Guoyin
Published: October 2024

Vegetation impacts on cloud physical properties and climate. The rapid greening in China in the past two decades, which contributed the most to global greening, may influence clouds in the region. However, due to the influence of a rapid concomitant decline in aerosol levels in China and of global warming, such influence of vegetation change is yet to be clarified. By utilizing observation data from satellite, we explored the impact of vegetation change on summertime low-level cloud cover in China from 2003 to 2022. After excluding the influence of changing aerosol and temperature on clouds, we revealed a significant positive correlation between vegetation changes and low-level cloud cover. Moreover, we explored the underlying mechanisms through which vegetation exerts its influence on clouds. We found that such influence is mediated through enhancing surface water vapor content by vegetation as well as altering net surface radiation and sensible heat flux.
Transient opto-thermal simulation analysis and experimental validation of LERP systems
Authors: Chatzizyrli Elisavet , Afentaki Angeliki , Hinkelmann Moritz , Lachmayer Roland , Neumann Jörg , Kracht Dietmar
Published: October 2024

Solid-state technology has revolutionized the lighting industry. However, efficiency-droop-limited light emitting diodes (LEDs) introduce constraints to the luminances achieved, and as a result, laser diodes (LDs) are replacing them in the remote phosphor setup. This introduces a new family of lighting solutions, laser-excited remote phosphor (LERP) systems, which can outperform cutting-edge LEDs. LERP systems however have not yet reached their full potential as the high intensity laser beam induces high temperatures within the phosphor material whose emission characteristics heavily depend on temperature. For this reason, a simulation framework has been developed that combines optical and thermal analysis in order to study and optimize these systems and derive their temperature thresholds for sustainable long-term usage. The focus here is on transient analysis, where the interplay between optical and thermal effects can be accounted for and the time dynamics of the system can be investigated. This enables the study of operation points near or at the thermal quenching regime. Furthermore, advanced material models have been developed in order to incorporate the temperature-dependence. The experimental validation of the model has shown that experimental and simulated results are in good agreement.
Cavitation erosion behaviour of MAB-CU4 alloy: influences of cavitation number, attack angle, time, and stand-off distance
Authors: Tini Sedat Can , Zeren Adalet , Yıldıran Avcu Yasemin , Abakay Eray , Guney Mert , Avcu Egemen
Published: October 2024

The present study comprehensively examines the cavitation erosion behaviour of a manganese aluminium bronze alloy (MAB-CU4 alloy) as a function of several parameters (i.e., cavitation angle, cavitation number, time, and stand-off distance), particularly focusing on the influences of cavitation angle on the surface morphology and topography of the alloy. According to the design of experiment (Taguchi experimental design) analysis, mass loss increased with cavitation number and attack angle, while increasing the stand-off distance resulted in a decrease in mass loss and an increase in the surface area affected by cavitation erosion. Cavitation erosion behaviour was most affected by the cavitation attack angle, with the cavitation attack angle contributing 69.1% to total erosion, according to variance analysis. At 90° cavitation attack angle, MAB-CU4’s erosion rate was 64% greater than that at 30°. Scanning electron microscopy and optical profilometry revealed that cavitation erosion damage at 90° occurred mostly in the grain interiors as cavitation pits due to severe plastic deformation and surface corrosion, whereas pit formation was restricted around the hard secondary phases at the grain boundaries. At 30°, deep cavitation pits were limited, the erosion crater expanded, and the number of pits was reduced. Overall, finer microstructures with more grain boundaries and secondary phases may improve cavitation erosion resistance at 90°. The present study is the first to comprehensively capture erosion damage at the microstructural scale and analyse the impact of microstructural features on the erosion damage during the cavitation erosion of MAB-CU4 alloy.
First-principles insights into thermoelectric behavior of XNiAs (X = Sc, Y) half-Heusler compounds
Authors: Giri Ashesh , Khatri Prakash , Neupane Hari Krishna , Adhikari Narayan Prasad
Published: October 2024

Half-Heusler (HH) compounds are regarded as potential candidates for thermoelectric devices to convert waste heat energy into electrical power, which could help mitigate the ongoing energy crisis. In this study, we investigate the structural, electronic, magnetic, and thermoelectric properties of HH compounds XNiAs (X = Sc, Y) using Density Functional Theory (DFT) and semi-classical Boltzmann transport theory (BTE). The compounds are non-magnetic semiconductors with an indirect band gap of 0.48 ( 0.50) eV for ScNiAs (YNiAs) respectively. Both materials show dynamic and mechanical stability, with ScNiAs displaying brittleness and YNiAs exhibiting ductility. At room temperature, the lattice thermal conductivity (κ

l
) for ScNiAs is 28.67 W/mK, while for YNiAs, it is 15.21 W/mK and both decrease as the temperature rises. The highest value of power factors is 29.03 μW/cmK2 and 29.74 μW/cmK2 for ScNiAs and YNiAs respectively at 1100 K for n-type doping. The optimal values of the figure of merit (zT) for n-type doping are 0.33 for ScNiAs and 0.58 for YNiAs at 1100 K. Both compounds exhibit better thermoelectric performance for n-type doping compared to p-type doping. The presence of flat bands and higher κ
l limits these materials from achieving higher zT values.
Analysis of anticipatory and compensatory postural adjustment in women of different age groups using surface electromyography
Authors: Moura Luan de Almeida , Scardovelli Terigi Augusto , Fernandes da Silva André Roberto , da Palma Valério Mariana , Barreto Campos Higor , de Camargo Matheus Leonardo Alves , Moraes Isabella Titico , Martini Silvia Cristina , da Silva Boschi Silvia Regina Matos , de Oliveira Gonzalez Tabajara , Pereira da Silva Alessandro
Published: October 2024

Postural balance is crucial for daily activities, relying on the coordination of sensory systems. Balance impairment, common in the elderly, is a leading cause of mortality in this population. To analyze balance, methods like postural adjustment analysis using electromyography (EMG) have been developed. With age, women tend to experience reduced mobility and greater muscle loss compared to men. However, few studies have focused on postural adjustments in women of different ages using EMG of the lower limbs during laterolateral and anteroposterior movements. This gap could reveal a decrease in muscle activation time with aging, as activation time is vital for postural adjustments. This study aimed to analyze muscle activation times in women of different ages during postural adjustments. Thirty women were divided into two groups: young and older women. A controlled biaxial force platform was used for static and dynamic balance tests while recording lower limb muscle activity using EMG. Data analysis focused on identifying muscle activation points and analyzing postural adjustment times. Results showed significant differences in muscle activation times between the two groups across various muscles and platform tilt conditions. Younger women had longer muscle activation times than older women, particularly during laterolateral platform inclinations. In anteroposterior movements, older women exhibited longer activation times compared to their laterolateral performance, with fewer differences between the groups. Overall, older women had shorter muscle activation times than younger women, suggesting a potential indicator of imbalance and increased fall risk.
Gendered vulnerabilities in climate shocks: the role of social protection interventions
Authors: Dasgupta Aparajita
Published: October 2024

This review explores how climate change exacerbates gender inequalities and the potential of social protection programs to alleviate these impacts. It examines how women disproportionately bear the brunt of climate shocks and discusses pathways through which programs like public works initiatives, cash transfers, and social insurance can bolster women’s resilience in this framework. Despite the potential of these programs, challenges such as implementation gaps and limited engagement of women in program design hinder the effectiveness of social protection programs. Limited research on the gendered effects of social insurance underscores the need for further investigation and gender-responsive policy interventions.
Intersectionality shapes the access to various adaptive resources in climate-vulnerable contexts
Authors: Ahmed Saleh , Eklund Elizabeth
Published: October 2024

Intersectional approaches are becoming essential to understanding the differential impacts of climate change and the heterogeneity of adaptive capacities. Varying factors of social and economic privileges and inequalities synergistically shape the local power structure, ultimately determining disproportionality and unequal access to adaptive resources. Using empirical data from coastal Bangladesh, which is part of the Ganges Delta, and one of the world’s -most climate-vulnerable regions, this study shows how religion, gender, and ethnicity intersect with patterns in (i) farm and non-farm incomes, (ii) land conflicts, (iii) the size of farms, and (iv) access to critical sources of weather information. The study highlights that multilayered identity, which is shaped by various structural determinants, including local power structure, can determine gendered dimensions of access to various adaptation resources. It also shows that if policymakers and development partners partially understand or do not understand the complex landscape of local vulnerability or unequal power structures including the adaptive capacity of the vulnerable populations, they would not be able to provide critical support in times of crisis. The concept of intersectionality is therefore critical in addressing adaptation and risk management challenges for regions like the Ganges Delta and other parts of the world, where people are struggling with similar social and environmental challenges.
Large deviations for perturbed Gaussian processes and logarithmic asymptotic estimates for some exit probabilities
Authors: Macci Claudio , Pacchiarotti Barbara
Published: October 2024

The main results in this paper concern large deviations for families of non-Gaussian processes obtained as suitable perturbations of continuous centered multivariate Gaussian processes which satisfy a large deviation principle. We present some corollaries and, as a consequence, we obtain logarithmic asymptotic estimates for exit probabilities from suitable halfspaces and quadrants.
Asymptotic normality of estimators for all parameters in the Vasicek model by discrete observations
Authors: Prykhodko Olha , Ralchenko Kostiantyn
Published: October 2024

We continue to study the joint estimation of all three parameters of the Vasicek model, based on equidistant observations of a trajectory. We consider strongly consistent estimators previously constructed in Prykhodko and Ralchenko (2022) and establish their joint asymptotic normality. The theoretical results are illustrated by a numerical study that confirms our theoretical findings.
Smoothness and Lévy concentration function inequalities for distributions of random diagonal sums
Authors: Roos Bero
Published: October 2024

We present new explicit upper bounds for the smoothness of the distribution of the random diagonal sum

S
n

=

∑

j
=
1

n

X

j
,
π
(
j
)

S_n=\sum _{j=1}^nX_{j,\pi (j)}

of a random

n
×
n

n\times n

matrix

X
=
(

X

j
,
r

)

X=(X_{j,r})

, where

X

j
,
r

X_{j,r}

are independent integer valued random variables, and

π
\pi

denotes a uniformly distributed random permutation on

{
1
,
…
,
n
}

\{1,\dots ,n\}

independent of

X
X

. As a measure of smoothness, we consider the total variation distance between the distributions of

S
n

S_n

and

1
+

S
n

1+S_n

. Our approach uses new auxiliary inequalities for a generalized normalized matrix hafnian and for inverse moments of non-negative random variables, which could be of independent interest. This approach is also used to prove upper bounds of the Lévy concentration function of

S
n

S_n

in the case of independent real valued random variables

X

j
,
r

X_{j,r}

.
Strong laws of large numbers for weighted sums of 𝑑-dimensional arrays of random variables and applications to marked point processes
Authors: Son Ta , Cuong Tran , Dung Le , Dung Le
Published: October 2024

The aim of this paper is twofold. Firstly, we give equivalent conditions for the convergence of each of three series in the Kolmogorov-type three-series theorem for random variables with multidimensional indices. Our results extend the results of Sung (2011) for multi-indexed sums. Secondly, by using these results, we develop almost sure convergence for weighted sums of

d
d

-dimensional arrays of random variables. We obtain the Jajte type strong law of large number for these arrays of random variables. As an application, the almost sure asymptotic behavior for sums generated by marked point processes is investigated.
On Lamperti transformation and AR(1) type characterisations of discrete random fields
Authors: Voutilainen Marko , Viitasaari Lauri , Ilmonen Pauliina
Published: October 2024

In this article we characterise discrete time stationary fields by difference equations involving stationary increment fields and self-similar fields. This gives connections between stationary fields, stationary increment fields and, through Lamperti transformation, self-similar fields. Our contribution is a natural generalisation of recently proved results covering the case of stationary processes.
Regulating transport efficiency through the nuclear pore complex: The role of binding affinity with FG-Nups
Authors: Matsuda Atsushi , Mofrad Mohammad R. K.
Published: October 2024

Macromolecules are transported through the nuclear pore complex (NPC) via a series of transient binding and unbinding events with FG-Nups, which are intrinsically disordered proteins anchored to the pore's inner wall. Prior studies suggest that the weak and transient nature of this binding is crucial for maintaining the transported molecules’ diffusivity. In this study, we explored the relationship between binding kinetics and transport efficiency using Brownian dynamics simulations. Our results indicate that the duration of binding is a critical factor in regulating transport efficiency. Specifically, excessively short binding durations insufficiently facilitate transport, while overly long durations impede molecular movement. We calculated the optimal binding duration for efficient molecular transport and found that it aligns with other theoretical predictions. Additionally, the calculated value is comparable to experimental measurements of the association timescale between nuclear transport receptors and FG-Nups at a single binding site. Our study provides a quantitative framework that bridges local molecular interactions with overall transport dynamics through the NPC, offering valuable insights into the mechanisms governing selective molecular transport.
After their membrane assembly, Sec18 (NSF) and Sec17 (SNAP) promote membrane fusion
Authors: Song Hongki , Lopes Karina , Orr Amy , Wickner William
Published: October 2024

The energy that drives membrane fusion can come from either complete SNARE zippering, from Sec17 and Sec18, or both. Sec17 and Sec18 initially form a complex which binds membranes. Sec17, Sec18, and the apolarity of a loop on the N-domain of Sec17 are required for their interdependent membrane association. To determine whether Sec18 and the Sec17 loop apolarity are still required for fusion after their membrane arrival, a hydrophobic transmembrane (TM) anchor was affixed to the N-terminus of Sec17, forming TM-Sec17. Fusion without energy from complete SNARE zippering requires Sec18 as well as either Sec17 or TM-Sec17. Even without the need for membrane targeting, the TM-Sec17 apolar loop strongly stimulates Sec17/18-driven fusion. Thus, Sec18 and the Sec17 apolar loop are first required for membrane targeting, and once bound, drive rapid fusion. Each of these variables—the absence or presence of Sec17, its N-loop apolarity, addition or omission of Sec18, and unimpeded or diminished energy from SNARE zippering—has almost no effect on the amount of trans-SNARE complex, but instead regulates the capacity of docked membranes to fuse.
Luther, the National Socialist
Authors: Hayden-Roy Patrick
Published: October 2024

The early years of Nazi rule saw an explosion of literature that portrayed in outlandish fashion Luther as a supporter of National Socialist ideals. Books by Hans Preuß, Alfred Rosenberg, and Wolf Meyer-Erlach, among others, published at the outset of the regime took as their main thesis the proposition that Luther’s Reformation aimed to achieve what the Nazis were now bringing to fulfilment; in doing so, they portray Luther as a fundamental supporter of National Socialism, and accuse those who resist such continuity between Luther’s religiosity and fascist politics of betraying his legacy. The chapter highlights the extremities of the image of Luther that emerged in the context of the new order in Germany.
Associations Among Experiences With Racial Discrimination, Religion/Spirituality, and Cigarette Smoking Among African American Adults: The Jackson Heart Study
Authors: Cottrell-Daniels Cherell , Aycock Dawn M , Pecháček Terry F , Sims Mario , Spears Claire A
Published: October 2024

Background

African American adults exhibit disproportionately high rates of tobacco-related diseases and associated death. Experiences with racial discrimination contribute to health disparities among African Americans, but more research is needed to understand associations between perceived discrimination and tobacco use as well as potential protective factors.

Purpose

This study examined associations between perceived racial discrimination and cigarette smoking, as well as religion and spirituality as moderators of any associations.

Methods

Cross-sectional data were drawn from the Jackson Heart Study, a study of cardiovascular disease risk factors among African American adults in Jackson, MS. Measures included perceived everyday discrimination and major life events discrimination that was attributed to race. Participants also reported religious attendance, prayer, spirituality, and whether they prayed in response to discriminatory experiences. Logistic regression models tested associations between perceived racial discrimination and cigarette smoking status, and interactions between religiosity/spirituality and discrimination in predicting smoking status.

Results

A total of 2,972 participants were included in the analysis (62.7% female, mean age 55.1 years). Thirteen percent reported currently smoking cigarettes. Everyday racial discrimination was associated with a higher likelihood of current smoking (p = .01). The association between lifetime racial discrimination and current smoking status was weaker for those who reported prayer as a reaction compared to those who did not report prayer as a reaction (adjusted odds ratio = 0.32, 95% confidence interval: 0.11 to 0.91) while adjusting for demographics and covariates.

Conclusions

Stressful experiences with racial discrimination may create risks for health behaviors like smoking. However, prayer may act as a coping strategy to help buffer the effects of racial discrimination on smoking behavior.
The case of the kid sister: adapting Enola Holmes for a new generation
Authors: West Nancy
Published: October 2024

In adapting the Enola Holmes book series, the Netflix films rework the figure of the girl sleuth to suit a new generation of feminist viewers. They also provide a deeper exploration of power and the risks of trying to improve a world resistant to change. Netflix also amplifies the stories’ feminism by rehabilitating the ‘toxic’ male figure of Holmes himself.
Methodological challenges and actionable recommendations in studying the health effects of high-concentration THC products
Authors: Li Tianjing , Wang George Sam , Brooks-Russell Ashley , Tung Gregory , Leslie Louis , Rittiphairoj Thanitsara , Oberste Jean-Pierre , Yim Tsz Wing , Bero Lisa , Samet Jonathan M
Published: October 2024

In conducting a scoping review on the health effects of high-concentration cannabis products, we have uncovered pervasive methodological shortcomings within the cannabis literature. This paper begins by defining the ‘causal effect’ of interest for public health and delineating the desirable features of study design that can address crucial questions pertaining to public health and policy. We further delve into the methodological complexities inherent in studying the health effects of high-concentration cannabis products, describing challenges associated with the measurement of exposures and outcomes, confounding, selection bias, and the generalizability of findings. We introduce causal inference methods to mitigate potential biases in observational cannabis use studies. We identify specific areas that necessitate further development and investigation to deepen our understanding of this topic. Finally, this paper extends actionable recommendations, serving as a roadmap for upcoming research initiatives in this domain.
Exon nomenclature and classification of transcripts database (ENACTdb): a resource for analyzing alternative splicing mediated proteome diversity
Authors: Verma Paras , Thakur Deeksha , Pandit Shashi B
Published: October 2024

Motivation

Gene transcripts are distinguished by the composition of their exons, and this different exon composition may contribute to advancing proteome complexity. Despite the availability of alternative splicing information documented in various databases, a ready association of exonic variations to the protein sequence remains a mammoth task.

Results

To associate exonic variation(s) with the protein systematically, we designed the Exon Nomenclature and Classification of Transcripts (ENACT) framework for uniquely annotating exons that tracks their loci in gene architecture context with encapsulating variations in splice site(s) and amino acid coding status. After ENACT annotation, predicted protein features (secondary structure/disorder/Pfam domains) are mapped to exon attributes. Thus, ENACTdb provides trackable exonic variation(s) association to isoform(s) and protein features, enabling the assessment of functional variation due to changes in exon composition. Such analyses can be readily performed through multiple views supported by the server. The exon-centric visualizations of ENACT annotated isoforms could provide insights on the functional repertoire of genes due to alternative splicing and its related processes and can serve as an important resource for the research community.

Availability and implementation

The database is publicly available at https://www.iscbglab.in/enactdb/. It contains protein-coding genes and isoforms for Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Mus musculus, and Homo sapiens.
AAclust: k-optimized clustering for selecting redundancy-reduced sets of amino acid scales
Authors: Breimann Stephan , Frishman Dmitrij
Published: October 2024

Amino acid scales are crucial for sequence-based protein prediction tasks, yet no gold standard scale set or simple scale selection methods exist. We developed AAclust, a wrapper for clustering models that require a pre-defined number of clusters k, such as k-means. AAclust obtains redundancy-reduced scale sets by clustering and selecting one representative scale per cluster, where k can either be optimized by AAclust or defined by the user. The utility of AAclust scale selections was assessed by applying machine learning models to 24 protein benchmark datasets. We found that top-performing scale sets were different for each benchmark dataset and significantly outperformed scale sets used in previous studies. Noteworthy is the strong dependence of the model performance on the scale set size. AAclust enables a systematic optimization of scale-based feature engineering in machine learning applications.

Availability and implementation

The AAclust algorithm is part of AAanalysis, a Python-based framework for interpretable sequence-based protein prediction, which is documented and accessible at https://aaanalysis.readthedocs.io/en/latest and https://github.com/breimanntools/aaanalysis.
findGSEP: estimating genome size of polyploid species usingk-mer frequencies
Authors: Fu Laiyi , Xie Yanxin , Ling Shunkang , Wang Ying , Wang Binzhong , Du Hejun , Peng Qinke , Sun Hequan
Published: October 2024

Estimating genome size using k-mer frequencies, which plays a fundamental role in designing genome sequencing and analysis projects, has remained challenging for polyploid species, i.e., ploidy p > 2. To address this, we introduce “findGSEP,” which is designed based on iterative curve fitting of k-mer frequencies. Precisely, it first disentangles up to p normal distributions by analyzing k-mer frequencies in whole genome sequencing of the focal species. Second, it computes the sizes of genomic regions related to 1∼p (homologous) chromosome(s) using each respective curve fitting, from which it infers the full polyploid and average haploid genome size. “findGSEP” can handle any level of ploidy p, and infer more accurate genome size than other well-known tools, as shown by tests using simulated and real genomic sequencing data of various species including octoploids.

Availability and implementation

“findGSEP” was implemented as a web server, which is freely available at http://146.56.237.198:3838/findGSEP/. Also, “findGSEP” was implemented as an R package for parallel processing of multiple samples. Source code and tutorial on its installation and usage is available at https://github.com/sperfu/findGSEP.
Semi-supervised distribution learning
Authors: Wen Mengtao , Jia Yinxu , Ren Haojie , Wang Zhaojun , Zou Changliang
Published: October 2024

This study addresses the challenge of distribution estimation and inference in a semi-supervised setting. In contrast to prior research focusing on parameter inference, this work explores the complexities of semi-supervised distribution estimation, particularly the uniformity problem inherent in functional processes. To tackle this issue, we introduce a versatile framework designed to extract valuable information from unlabelled data by approximating a conditional distribution on covariates. The proposed estimator is derived using K-fold cross-fitting, and exhibits both consistency and asymptotic Gaussian process properties. Under mild conditions, the proposed estimator outperforms the empirical cumulative distribution function in terms of asymptotic efficiency. Several applications of the methodology are given, including parameter inference and goodness-of-fit tests.
Clustering computer mouse tracking data with informed hierarchical shrinkage partition priors
Authors: Song Ziyi , Shen Weining , Vannucci Marina , Baldizon Alexandria , Cinciripini Paul M , Versace Francesco , Guindani Michele
Published: October 2024

Mouse-tracking data, which record computer mouse trajectories while participants perform an experimental task, provide valuable insights into subjects’ underlying cognitive processes. Neuroscientists are interested in clustering the subjects’ responses during computer mouse-tracking tasks to reveal patterns of individual decision-making behaviors and identify population subgroups with similar neurobehavioral responses. These data can be combined with neuroimaging data to provide additional information for personalized interventions. In this article, we develop a novel hierarchical shrinkage partition (HSP) prior for clustering summary statistics derived from the trajectories of mouse-tracking data. The HSP model defines a subjects’ cluster as a set of subjects that gives rise to more similar (rather than identical) nested partitions of the conditions. The proposed model can incorporate prior information about the partitioning of either subjects or conditions to facilitate clustering, and it allows for deviations of the nested partitions within each subject group. These features distinguish the HSP model from other bi-clustering methods that typically create identical nested partitions of conditions within a subject group. Furthermore, it differs from existing nested clustering methods, which define clusters based on common parameters in the sampling model and identify subject groups by different distributions. We illustrate the unique features of the HSP model on a mouse tracking dataset from a pilot study and in simulation studies. Our results show the ability and effectiveness of the proposed exploratory framework in clustering and revealing possible different behavioral patterns across subject groups.
Coproducing recovery with people affected by substance use and criminalization
Authors: Buck Gillian , Pratt Emma , Yarwood Peter , Arnold Victoria , O’Mara Sarah
Published: October 2024

This study details the coproduction approach taken by Red Rose Recovery (RRR), a non-profit organization that coproduces recovery systems with people affected by substance use and criminalization. RRR is ‘lived-experience-led’ in that those who manage and work for the organization use their own experiences of recovery or desistance from crime to provide inspiration and hope to others. We explored people’s experiences of working with RRR using a ‘photovoice’ research design, where people use cameras to document their realities. Data were analysed collaboratively, offering a depth of insight into the perspectives of people involved. The images and words produced by photographers illustrate this article and indicate that, in contexts of pain, shame, exclusion, and disconnection, coproduced services can offer valued relationships, community, and a sense of belonging within built and natural environments.
Investigating the role of auditory cues in modulating motor timing: insights from EEG and deep learning
Authors: Jounghani Ali Rahimpour , Backer Kristina C , Vahid Amirali , Comstock Daniel C , Zamani Jafar , Hosseini Hadi , Balasubramaniam Ramesh , Bortfeld Heather
Published: October 2024

Research on action-based timing has shed light on the temporal dynamics of sensorimotor coordination. This study investigates the neural mechanisms underlying action-based timing, particularly during finger-tapping tasks involving synchronized and syncopated patterns. Twelve healthy participants completed a continuation task, alternating between tapping in time with an auditory metronome (pacing) and continuing without it (continuation). Electroencephalography data were collected to explore how neural activity changes across these coordination modes and phases. We applied deep learning methods to classify single-trial electroencephalography data and predict behavioral timing conditions. Results showed significant classification accuracy for distinguishing between pacing and continuation phases, particularly during the presence of auditory cues, emphasizing the role of auditory input in motor timing. However, when auditory components were removed from the electroencephalography data, the differentiation between phases became inconclusive. Mean accuracy asynchrony, a measure of timing error, emerged as a superior predictor of performance variability compared to inter-response interval. These findings highlight the importance of auditory cues in modulating motor timing behaviors and present the challenges of isolating motor activation in the absence of auditory stimuli. Our study offers new insights into the neural dynamics of motor timing and demonstrates the utility of deep learning in analyzing single-trial electroencephalography data.
Mortality associated with the COVID-19 pandemic in the Swiss dialysis population beyond SARS-CoV-2 infection
Authors: Jaques David A , Hoessly Linard , Guidotti Rebecca , Koller Michael , Ponte Belen , Ambühl Patrice
Published: October 2024

Background

While SARS-CoV-2 infection has direct obvious consequences on patients undergoing dialysis, the COVID-19 pandemic also had an indirect impact on health systems. Therefore, we aimed to determine whether the COVID-19 era itself was associated with adverse consequences in the Swiss dialysis population as compared to the pre-COVID-19 era, while accounting for direct impact of SARS-CoV-2 infection.

Methods

We retrospectively included all patients recorded in the Swiss dialysis registry from January 2014 to December 2022. The pre-COVID-19 era and the COVID-19 era were defined based on the cut-off date of January 2020. Cox proportional hazard model was used with all-cause mortality as the primary outcome.

Results

The cohort consisted of 7837 patients from 97 dialysis centres. Median age was 68.6 years with 66.1% men. Crude mortality rates were 11.6% (11.0% to 12.2%) and 14.2% (13.4% to 14.9%) person-years for the pre-COVID-19 era and the COVID-19 era, respectively. In multivariable analysis, SARS-CoV-2 infection was associated with an increased risk of mortality (HR 4.26, 95% CI 3.65 to 4.97, P < .001) while the COVID-19 era itself was not (HR 0.98, 95% CI 0.88 to 1.08, P = .687).

Conclusions

The COVID-19 era was not associated with an excess of mortality in the Swiss dialysis population as compared to the pre-COVID-19 era when accounting for the direct effect of SARS-CoV-2 infection. This suggests that control measures established during the pandemic did not have a negative impact on dialysis patients at the national level. These results could inform health policy makers in the eventuality of future pandemics.
Navigating Reproductive Care in Patients With Inflammatory Bowel Disease: A Comprehensive Review
Authors: Sousa Paula , Gisbert Javier P , Julsgaard Mette , Selinger Christian Philipp , Chaparro María
Published: October 2024

Inflammatory bowel disease [IBD] is often diagnosed in patients during their reproductive years. It is crucial that both healthcare providers and patients are adequately informed to avoid misguided decisions regarding family planning.

One of the most important aspects during conception and pregnancy is to maintain disease remission, as disease activity is associated with adverse pregnancy outcomes. Apart from methotrexate, most conventional drugs used in IBD are considered low risk during conception and pregnancy. For newer agents, evidence is still limited. If needed, surgery must not be postponed and should ideally be performed in specialized centres.

In most patients, delivery should be vaginal except for patients with complex perianal disease, with an ileoanal pouch anastomosis, or if there is an obstetric contraindication.

In children exposed to biological treatments during pregnancy, the risk of infections appears to be low, and psychomotor development is probably not affected. Regarding immunizations, the standard vaccination schedule for inactivated vaccines should be followed for children exposed to biologics in utero. In the case of live vaccines, such as rotavirus, decisions should be individualized and take into consideration the risk–benefit ratio, particularly in developing countries.

In this review, we provide a comprehensive and updated overview of aspects related to fertility, pregnancy, breastfeeding, and the impact on the care of children born to mothers with IBD. Both the available evidence and areas of uncertainty are discussed, with the goal of assisting healthcare professionals caring for IBD patients during this important stage of their lives.
Epidemiology of Inflammatory Bowel Disease across the Ages in the Era of Advanced Therapies
Authors: Caron Bénédicte , Honap Sailish , Peyrin-Biroulet Laurent
Published: October 2024

Background and Aims

The incidence of inflammatory bowel diseases [IBD] has risen over the past decade to become a global issue. The objectives of this review were to describe the incidence and/or prevalence of IBD in the era of advanced therapies, and to describe the association between environmental risk factors and both pathogenesis and disease course across the ages.

Methods

We performed a search of English language publications listed in PubMed regarding the epidemiology of IBD and key environmental factors implicated in IBD from January 2000 to December 2023.

Results

Annual incidence rates varied by geographical region with IBD estimates ranging from 10.5 to 46.14 per 100 000 in Europe, 1.37 to 1.5 per 100 000 in Asia and the Middle East, 23.67 to 39.8 per 100 000 in Oceania, 0.21 to 3.67 per 100 000 in South America, and 7.3 to 30.2 per 100 000 in North America. The burden of IBD among children and adolescents, and older people is rising globally. Key environmental factors implicated in IBD pathogenesis include exposure to tobacco smoking, antibiotics, non-steroidal anti-inflammatory drugs, oral contraceptives, infections, and ultra-high processed foods. Breastfeeding and a high-quality diet rich in fruit, vegetables, fish, and other fibre sources are important protective factors. Smoking has consistently been shown to negatively impact disease outcomes for Crohn’s disease.

Conclusion

The epidemiology of IBD has undergone considerable change in recent decades, with an increase in the burden of disease worldwide. Optimally studying and targeting environmental triggers in IBD may offer future opportunities for disease modification.
Considerations in Paediatric and Adolescent Inflammatory Bowel Disease
Authors: Vuijk Stephanie A , Camman Anouk E , de Ridder Lissy
Published: October 2024

The incidence of inflammatory bowel disease [IBD] is rising most rapidly among children and adolescents. Paediatric-onset IBD is associated with a more extensive and severe disease course compared to adult-onset IBD. At a young age, screening for underlying genetic and immunological disorders is important and may impact treatment management. Early and effective treatment is crucial to reach disease remission and prevent complications of ongoing active disease. In children with Crohn’s disease, exclusive enteral nutrition is an effective induction therapy. Other promising dietary therapies, such as the Crohn’s disease exclusion diet, are emerging. Within paediatric IBD, anti-tumour necrosis factor therapy is the only approved biological thus far and additional treatment options are crucially needed. Other biological therapies, such as vedolizumab and ustekinumab, are currently prescribed off-label in this population. A specific challenge in paediatric IBD is the unacceptable and major delay in approval of drugs for children with IBD. A guided transfer period of paediatric patients to adult care is associated with improved disease outcomes and is required. Major knowledge gaps and challenges within paediatric IBD include the aetiology, diagnostics, and monitoring of disease, tailoring of treatment, and both understanding and coping with the physical and psychological consequences of living with IBD. Challenges and research gaps in paediatrics should be addressed without any delay in comparison with the adult field, in order to ensure a high quality of care for all patients with IBD, irrespective of the age of onset.
Framework of IBD Care Delivery Across Ages
Authors: Delen Stefan , Jaghult Susanna , Blumenstein Irina , Pouillon Lieven , Bossuyt Peter
Published: October 2024

IBD care has gone through a real transformation over the last century, moving from the mere unidirectional interaction between the physician and the patient to a stronger framework with multiple stakeholders who interconnect and strengthen each other. The patient has evolved from a passive subject to the central pole in the care pathway. Key elements of the future framework include patient self-care and empowerment, and remote monitoring [eHealth]. This care will be delivered by a multidisciplinary team acknowledging the pivotal role of the IBD nurse, and emphasising and measuring the quality of its work. The big challenge for the future is to establish a financially viable model to make this evolution durable in the long term, and this by using the principles of value-based health care.
The Hypolimnas misippus Genome Supports a Common Origin of the W Chromosome in Lepidoptera
Authors: Orteu Anna , McCarthy Shane A , Hornett Emily A , Gemmell Matthew R , Reynolds Louise A , Warren Ian A , Gordon Ian J , Hurst Gregory D D , Durbin Richard , Martin Simon H , Jiggins Chris D
Published: October 2024

Moths and butterflies (Lepidoptera) have a heterogametic sex chromosome system with females carrying ZW chromosomes and males ZZ. The lack of W chromosomes in early-diverging lepidopteran lineages has led to the suggestion of an ancestral Z0 system in this clade and a B chromosome origin of the W. This contrasts with the canonical model of W chromosome evolution in which the W would have originated from the same homologous autosomal pair as the Z chromosome. Despite the distinct models proposed, the rapid evolution of the W chromosome has hindered the elucidation of its origin. Here, we present high-quality, chromosome-level genome assemblies of 2 Hypolimnas species (Hypolimnas misippus and Hypolimnas bolina) and use the H. misippus assembly to explore the evolution of W chromosomes in butterflies and moths. We show that in H. misippus, the W chromosome has higher similarity to the Z chromosome than any other chromosome, which could suggest a possible origin from the same homologous autosome pair as the Z chromosome. However, using genome assemblies of closely related species (ditrysian lineages) containing assembled W chromosomes, we present contrasting evidence suggesting that the W chromosome might have evolved from a B chromosome instead. Crucially, by using a synteny analysis to infer homology, we show that W chromosomes are likely to share a common evolutionary origin in Lepidoptera. This study highlights the difficulty of studying the evolution of W chromosomes and contributes to better understanding its evolutionary origins.