bluuebunny/crossref_metadata_2025_split huggingface dataset:
Which Role for Muscle-Sparing Posterolateral Thoracotomy in the Treatment of Spontaneous Pneumothorax?
Authors: Issoufou Ibrahim , Sani Rabiou , Amadou Daouda , Alio Kadre , Adamou-Nouhou Kaled , Lakranbi Marouane , Sani Rachid , Ouadnouni Yassine , Abarchi Habibou , Smahi Mohamed 
Published: December 2023

Abstract
Objective This study aims to show the place of muscle-sparing posterolateral thoracotomy in the treatment of spontaneous pneumothorax.
Methods It was a single-center study performed in the Department of Thoracic Surgery of Teaching hospital Hassan II of Fez for 8 years. We adopted the nosological definition, which classifies spontaneous pneumothorax into three categories. We included patients over 15 years of age with primary or secondary spontaneous pneumothorax operated by posterolateral thoracotomy without muscle section, and we analyzed the specific indications of this approach. It included 49 patients with primary or secondary spontaneous pneumothorax, operated by muscle-sparing posterolateral thoracotomy. Data were collected from regularly updated computer files of patients, entered by Excel 2013, and analyzed using SPSS.20 software. These data are: epidemiological, clinical, radiological, surgical exploration, surgical procedure, the result of the surgery and the evolution.
Results The average age was 42 years. Smoking was found in 61% of cases and pulmonary tuberculosis in 10% of cases. Thoracic computed tomography (CT) showed bullae and blebs in 31% of cases, pleural adhesions and pachypleuritis in 50% of cases, and hydropneumothorax with pachypleuritis in 37% of cases. There is a statistical correlation between pleuropulmonary decortication and pachypleuritis (p = 0.002) or hydropneumothorax (p = 0.001) on CT. Bullae and blebs resection was performed in 53% of cases and pleuropulmonary decortication in 63% of cases. A right pleuropneumonectomy was performed in one case. The follow-up was uneventful in 82% of cases.
Conclusion Muscle-sparing posterolateral thoracotomy remains the best approach and leads to good results.
Two-dimensional investigation of characteristic parameters and their gradients for the self-generated electric and magnetic fields of laser-induced zirconium plasma
Authors: SAJID Tayyaba , BASHIR Shazia , AKRAM Mahreen , RAZZAQ Maira , MAHMOOD Khaliq 
Published: December 2023

Abstract
Two-dimensional diagnosis of laser-induced zirconium (Zr) plasma has been experimentally performed using the time-of-flight method by employing Faraday cups in addition to electric and magnetic probes. The characteristic parameters of laser-induced Zr plasma have been evaluated as a function of different laser irradiances ranging from 4.5 to 11.7 GW cm−2 at different axial positions of 1–4 cm with a fixed radial distance of 2 cm. A well-supporting correlation between the plume parameters and the laser-plasma-produced spontaneous electric and magnetic (E and B) fields was established. The measurements of the characteristic parameters and spontaneously induced fields were observed to have an increasing trend with the increasing laser irradiance. However, when increasing the spatial distance in both the axial and radial directions, the plasma parameters (electron/ion number density, temperature and kinetic energy) did not show either continuously increasing or decreasing trends due to various kinetic and dynamic processes during the spatial evolution of the plume. However, the E and B fields were observed to be always diffusing away from the target. The radial component of electron number densities remained higher than the axial number density component, whereas the axial ion number density at all laser irradiances and axial distances remained higher than the radial ion number density. The higher axial self-generated electric field (SGEF) values than radial SGEF values are correlated with the effective charge-separation mechanism of electrons and ions. The generation of a self-generated magnetic field is observed dominantly in the radial direction at increasing laser irradiance as compared to the axial one due to the deflection of fast-moving electrons and the persistence of two-electron temperature on the radial axis.
Machine learning reveals singing rhythms of male Pacific field crickets are clock controlled
Authors: Westwood Mary L , Geissmann Quentin , O’Donnell Aidan J , Rayner Jack , Schneider Will , Zuk Marlene , Bailey Nathan W , Reece Sarah E 
Published: December 2023

Abstract
Circadian rhythms are ubiquitous in nature and endogenous circadian clocks drive the daily expression of many fitness-related behaviors. However, little is known about whether such traits are targets of selection imposed by natural enemies. In Hawaiian populations of the nocturnally active Pacific field cricket (Teleogryllus oceanicus), males sing to attract mates, yet sexually selected singing rhythms are also subject to natural selection from the acoustically orienting and deadly parasitoid fly, Ormia ochracea. Here, we use T. oceanicus to test whether singing rhythms are endogenous and scheduled by circadian clocks, making them possible targets of selection imposed by flies. We also develop a novel audio-to-circadian analysis pipeline, capable of extracting useful parameters from which to train machine learning algorithms and process large quantities of audio data. Singing rhythms fulfilled all criteria for endogenous circadian clock control, including being driven by photoschedule, self-sustained periodicity of approximately 24 h, and being robust to variation in temperature. Furthermore, singing rhythms varied across individuals, which might suggest genetic variation on which natural and sexual selection pressures can act. Sexual signals and ornaments are well-known targets of selection by natural enemies, but our findings indicate that the circadian timing of those traits’ expression may also determine fitness.
Batch correction of single-cell sequencing data via an autoencoder architecture
Authors: Danino Reut , Nachman Iftach , Sharan Roded 
Published: December 2023

Abstract

Motivation
Technical differences between gene expression sequencing experiments can cause variations in the data in the form of batch effect biases. These do not represent true biological variations between samples and can lead to false conclusions or hinder the ability to integrate multiple datasets. Since there is a growing need for the joint analysis of single-cell sequencing datasets from different sources, there is also a need to correct the resulting batch effects while maintaining the true biological variations in the data.

Results
We developed a semi-supervised deep learning architecture called Autoencoder-based Batch Correction (ABC) for integrating single-cell sequencing datasets. Our method removes batch effects through a guided process of data compression using supervised cell type classifier branches for biological signal retention. It aligns the different batches using an adversarial training approach. We comprehensively evaluate the performance of our method using four single-cell sequencing datasets and multiple measures for batch effect removal and biological variation conservation. ABC outperforms 10 state-of-the-art methods for this task including Seurat, scGen, ComBat, scanorama, scVI, scANVI, AutoClass, Harmony, scDREAMER, and CLEAR, correcting various types of batch effects while preserving intricate biological variations.
MHCSeqNet2—improved peptide-class I MHC binding prediction for alleles with low data
Authors: Wongklaew Patiphan , Sriswasdi Sira , Chuangsuwanich Ekapol 
Published: December 2023

Abstract

Motivation
The binding of a peptide antigen to a Class I major histocompatibility complex (MHC) protein is part of a key process that lets the immune system recognize an infected cell or a cancer cell. This mechanism enabled the development of peptide-based vaccines that can activate the patient’s immune response to treat cancers. Hence, the ability of accurately predict peptide-MHC binding is an essential component for prioritizing the best peptides for each patient. However, peptide-MHC binding experimental data for many MHC alleles are still lacking, which limited the accuracy of existing prediction models.

Results
In this study, we presented an improved version of MHCSeqNet that utilized sub-word-level peptide features, a 3D structure embedding for MHC alleles, and an expanded training dataset to achieve better generalizability on MHC alleles with small amounts of data. Visualization of MHC allele embeddings confirms that the model was able to group alleles with similar binding specificity, including those with no peptide ligand in the training dataset. Furthermore, an external evaluation suggests that MHCSeqNet2 can improve the prioritization of T cell epitopes for MHC alleles with small amount of training data.

Availability and implementation
The source code and installation instruction for MHCSeqNet2 are available at https://github.com/cmb-chula/MHCSeqNet2.
Covariate-guided Bayesian mixture of spline experts for the analysis of multivariate high-density longitudinal data
Authors: Fu Haoyi , Tang Lu , Rosen Ori , Hipwell Alison E , Huppert Theodore J , Krafty Robert T 
Published: December 2023

Summary
With rapid development of techniques to measure brain activity and structure, statistical methods for analyzing modern brain-imaging data play an important role in the advancement of science. Imaging data that measure brain function are usually multivariate high-density longitudinal data and are heterogeneous across both imaging sources and subjects, which lead to various statistical and computational challenges. In this article, we propose a group-based method to cluster a collection of multivariate high-density longitudinal data via a Bayesian mixture of smoothing splines. Our method assumes each multivariate high-density longitudinal trajectory is a mixture of multiple components with different mixing weights. Time-independent covariates are assumed to be associated with the mixture components and are incorporated via logistic weights of a mixture-of-experts model. We formulate this approach under a fully Bayesian framework using Gibbs sampling where the number of components is selected based on a deviance information criterion. The proposed method is compared to existing methods via simulation studies and is applied to a study on functional near-infrared spectroscopy, which aims to understand infant emotional reactivity and recovery from stress. The results reveal distinct patterns of brain activity, as well as associations between these patterns and selected covariates.
Biallelic NUDT2 variants defective in mRNA decapping cause a neurodevelopmental disease
Authors: Husain Ralf A , Jiao Xinfu , Hennings J Christopher , Giesecke Jan , Palsule Geeta , Beck-Wödl Stefanie , Osmanović Dina , Bjørgo Kathrine , Mir Asif , Ilyas Muhammad , Abbasi Saad M , Efthymiou Stephanie , Dominik Natalia , Maroofian Reza , Houlden Henry , Rankin Julia , Pagnamenta Alistair T , Nashabat Marwan , Altwaijri Waleed , Alfadhel Majid , Umair Muhammad , Khouj Ebtissal , Reardon William , El-Hattab Ayman W , Mekki Mohammed , Houge Gunnar , Beetz Christian , Bauer Peter , Putoux Audrey , Lesca Gaetan , Sanlaville Damien , Alkuraya Fowzan S , Taylor Robert W , Mentzel Hans-Joachim , Hübner Christian A , Huppke Peter , Hart Ronald P , Haack Tobias B , Kiledjian Megerditch , Rubio Ignacio 
Published: December 2023

Abstract
Dysfunctional RNA processing caused by genetic defects in RNA processing enzymes has a profound impact on the nervous system, resulting in neurodevelopmental conditions. We characterized a recessive neurological disorder in 18 children and young adults from 10 independent families typified by intellectual disability, motor developmental delay and gait disturbance.
In some patients peripheral neuropathy, corpus callosum abnormalities and progressive basal ganglia deposits were present. The disorder is associated with rare variants in NUDT2, a mRNA decapping and Ap4A hydrolysing enzyme, including novel missense and in-frame deletion variants. We show that these NUDT2 variants lead to a marked loss of enzymatic activity, strongly implicating loss of NUDT2 function as the cause of the disorder. NUDT2-deficient patient fibroblasts exhibit a markedly altered transcriptome, accompanied by changes in mRNA half-life and stability. Amongst the most up-regulated mRNAs in NUDT2-deficient cells, we identified host response and interferon-responsive genes. Importantly, add-back experiments using an Ap4A hydrolase defective in mRNA decapping highlighted loss of NUDT2 decapping as the activity implicated in altered mRNA homeostasis.
Our results confirm that reduction or loss of NUDT2 hydrolase activity is associated with a neurological disease, highlighting the importance of a physiologically balanced mRNA processing machinery for neuronal development and homeostasis.
Baseline Serum and Stool Microbiome Biomarkers Predict Clinical Efficacy and Tissue Molecular Response After Ritlecitinib Induction Therapy in Ulcerative Colitis
Authors: Hassan-Zahraee Mina , Ye Zhan , Xi Li , Dushin Elizabeth , Lee Julie , Romatowski Jacek , Leszczyszyn Jaroslaw , Danese Silvio , Sandborn William J , Banfield Christopher , Gale Jeremy D , Peeva Elena , Longman Randy S , Hyde Craig L , Hung Kenneth E 
Published: December 2023

Abstract

Background and Aims
Ritlecitinib, an oral JAK3/TEC family kinase inhibitor, was well-tolerated and efficacious in the phase 2b VIBRATO study in participants with moderate-to-severe ulcerative colitis [UC]. The aim of this study was to identify baseline serum and microbiome markers that predict subsequent clinical efficacy and to develop noninvasive serum signatures as potential real-time noninvasive surrogates of clinical efficacy after ritlecitinib.

Methods
Tissue and peripheral blood proteomics, transcriptomics, and faecal metagenomics were performed on samples before and after 8 weeks of oral ritlecitinib induction therapy [20 mg, 70 mg, 200 mg, or placebo once daily, N = 39, 41, 33, and 18, respectively]. Linear mixed models were used to identify baseline and longitudinal protein markers associated with efficacy. The combined predictivity of these proteins was evaluated using a logistic model with permuted efficacy data. Differential expression of faecal metagenomics was used to differentiate responders and nonresponders.

Results
Peripheral blood serum proteomics identified four baseline serum markers [LTA, CCL21, HLA-E, MEGF10] predictive of modified clinical remission [MR], endoscopic improvement [EI], histological remission [HR], and integrative score of tissue molecular improvement. In responders, 37 serum proteins significantly changed at Week 8 compared with baseline [false discovery rate of &lt;0.05]; of these, changes in four [IL4R, TNFRSF4, SPINK4, and LAIR-1] predicted concurrent EI and HR responses. Faecal metagenomics analysis revealed baseline and treatment response signatures that correlated with EI, MR, and tissue molecular improvement.

Conclusions
Blood and microbiome biomarkers stratify endoscopic, histological, and tissue molecular responses to ritlecitinib, which may help guide future precision medicine approaches to UC treatment. ClinicalTrials.gov NCT02958865
Sex-limited experimental evolution drives transcriptomic divergence in a hermaphrodite
Authors: Cīrulis Aivars , Nordén Anna K , Churcher Allison M , Ramm Steven A , Zadesenets Kira S , Abbott Jessica K 
Published: December 2023

Abstract
The evolution of gonochorism from hermaphroditism is linked with the formation of sex chromosomes, as well as the evolution of sex-biased and sex-specific gene expression to allow both sexes to reach their fitness optimum. There is evidence that sexual selection drives the evolution of male-biased gene expression in particular. However, previous research in this area in animals comes from either theoretical models or comparative studies of already old sex chromosomes. We therefore investigated changes in gene expression under 3 different selection regimes for the simultaneous hermaphrodite Macrostomum lignano subjected to sex-limited experimental evolution (i.e. selection for fitness via eggs, sperm, or a control regime allowing both). After 21 and 22 generations of selection for male-specific or female-specific fitness, we characterized changes in whole-organism gene expression. We found that female-selected lines had changed the most in their gene expression. Although annotation for this species is limited, gene ontology term and Kyoto Encyclopedia of Genes and Genomes pathway analyses suggest that metabolic changes (e.g. biosynthesis of amino acids and carbon metabolism) are an important adaptive component. As predicted, we found that the expression of genes previously identified as testis-biased candidates tended to be downregulated in the female-selected lines. We did not find any significant expression differences for previously identified candidates of other sex-specific organs, but this may simply reflect that few transcripts have been characterized in this way. In conclusion, our experiment suggests that changes in testis-biased gene expression are important in the early evolution of sex chromosomes and gonochorism.
Hazardous Alcohol Use Among Community-Dwelling Older Adults With Persistent or Recurrent Pain: Findings From the Health and Retirement Study
Authors: LaRowe Lisa R , Miller Angela , Shah Sachin J , Ritchie Christine S 
Published: December 2023

Abstract

Background
Although pain and alcohol use are highly prevalent and associated with deleterious health outcomes among older adults, a paucity of literature has examined hazardous drinking among older adults with pain. We aimed to examine the prevalence of hazardous drinking among a nationally representative sample of older adults with persistent or recurrent pain.

Methods
We conducted cross-sectional analyses of data collected from the 2018 wave of the Health and Retirement Study. Participants included 1  549 community-dwelling adults aged ≥65 with persistent or recurrent pain (ie, clinically significant pain present at 2 consecutive survey waves).

Results
More than one-quarter of older adults with persistent or recurrent pain reported regular alcohol use (≥weekly), nearly half of whom reported hazardous patterns of drinking. Specifically, 32% reported excessive drinking (ie, &gt;2 drinks per day for older men; &gt;1 drink per day for older women), and 22% reported binge drinking (ie, ≥4 drinks on one occasion). Exploratory analyses revealed a high prevalence of hazardous drinking among the subsample of older adults who used opioids (47%).

Conclusions
Hazardous alcohol use—including both excessive and binge drinking—is common among older adults with persistent or recurrent pain, including those who take opioids. Given that hazardous drinking can complicate pain management and increase the risk for adverse opioid effects (eg, overdose), the current findings underscore the importance of assessing and addressing hazardous patterns of alcohol use among older adults with persistent or recurrent pain.
Joint Association of Physical Frailty and Self-Rated Health With Mortality Among Community-Dwelling Older Adults
Authors: Wu Chenkai , Xu Yichen , Tang Junhan , Liu Hua , Xue Qian-Li 
Published: December 2023

Abstract

Background
The relationship between subjective and objective health is complex and not always matched. Although frailty and self-rated health (SRH) have been separately associated with adverse outcomes, their joint effects remained unclear.

Methods
Participants were 5 300 adults ≥60 years from the China Health and Retirement Longitudinal Study in 2011. Frailty, measured by the validated physical frailty phenotype approach, was classified as nonfrail, prefrail, and frail. SRH was categorized into 3 groups: excellent/very good/good, fair, and poor/very poor. We used the Cox models to examine the independent and joint association of frailty and SRH with mortality. We used the interaction approach to determine whether the association of SRH with mortality differed by frailty. Subgroup analyses were conducted by depression and cognitive impairment.

Results
About 8.1% of frail participants reported excellent/very good/good health; 21.2% of the nonfrail reported poor/very poor health. Prefrailty and frailty were associated with a 1.63- and 2.38-fold increase in the hazard of mortality than the nonfrail, respectively, after adjusting for SRH. Reporting fair and poor/very poor health was associated with a 29% and 100% increase in the hazard of mortality, respectively, after adjusting for frailty. No significant interaction was found. Prefrail and frail older adults with excellent/very good/good health had a similar mortality as the nonfrail with poor/very poor SRH. The association of SRH with mortality was less pronounced among individuals with depression or cognitive impairment.

Conclusions
SRH is a potential marker of resilience among people living with frailty that may be a target for ameliorating health risks induced by frailty.
A Frangi filter aided deep learning approach for palaeochannel recognition
Authors: Zhong Ding , Wang Jiaqi , Guo Yixiao , Liu Yicong , Chen Junyang , Xu Tianji 
Published: December 2023

SUMMARY
In view of the problem of identifying palaeochannels with high concealment and complex geological structures, this paper proposes an intelligent recognition method for palaeochannels based on Frangi filtering and deep learning. The methodology makes use of Maximum Entropy Wigner–Ville Distribution (MEWVD) method to process the original instantaneous amplitude data, which enhance the distinct features of micro palaeochannels in different sensitive frequency bands. The sample 2-D stratigraphic images generated from these data is labelled for the pre-training process of Attention R2U-Net neural network model. Subsequently, Frangi filter is used to identify and enhance the linear structures of river channels in target stratigraphic images, improving the identification effect of the neural network. Finally, RGB data fusion and 3-D visualization carving are performed on the identification data. This method not only eliminates redundant information using the Frangi filter but also proves that the Attention R2U-Net network model structure with attention mechanism and residual convolution structure can effectively improve the segmentation effect for river channels at different scales. Experimental examples show that this method achieves pixel-level feature segmentation of 3-D seismic data for palaeochannels, accurately depicting their shape, width, thickness, flow direction and other features, thus providing support for subsequent well deployment and horizontal well fracturing selection.