bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient construction and utilization of k-ordered FM-indexes with kISS for ultra-fast read mapping in large genomes
Authors: Yang Zheng-Dao , Kuo Hsuan-Yu , Hsieh Po-Wei , Hung Jui-Hung 
Published: June 2024

Abstract

Motivation
The Full-text index in Minute space (FM-index) is a memory-efficient data structure widely used in bioinformatics for solving the fundamental pattern-matching task of searching for short patterns within a long reference. With the demand for short query patterns, the k-ordered concept has been proposed for FM-indexes. However, few construction algorithms in the state of the art fully exploit this idea to achieve significant speedups in the pan-genome era.

Results
We introduce the k-ordered induced suffix sorting (kISS) for efficient construction and utilization of k-ordered FM-indexes. We present an algorithmic workflow for building k-ordered suffix arrays, incorporating two novel strategies to improve time and memory efficiency. We also demonstrate the compatibility of integrating k-ordered FM-indexes with locate operations in FMtree. Experiments show that kISS can improve the construction time, and the generated k-ordered suffix array can also be applied to FMtree without any additional in computation or memory usage.

Availability and implementation
https://github.com/jhhung/kISS.
International study on prevalence of itch: examining the role of itch as a major global public health problem
Authors: Yosipovitch Gil , Skayem Charbel , Aroman Marketa Saint , Taieb Charles , Inane Medhi , Hayoun Yaron Ben , Cullel Nuria Perez , Baissac Catherine , Halioua Bruno , Richard Marie Aleth , Misery Laurent 
Published: June 2024

Abstract

Background
Very few studies have evaluated the global prevalence of pruritus.

Objectives
To assess its prevalence according to age, sex, ethnicity and geographic region.

Methods
An international cross-sectional study was conducted in 20 countries from January to April 2023. Participants were asked to complete a questionnaire on sociodemographics, and to confirm the presence or absence of a skin disease in the last 12 months and the presence or absence of pruritus in the last 7 days.

Results
The studied sample included 50 552 individuals. The worldwide prevalence of pruritus was 39.8%. The age group ≥ 65 years had the highest prevalence (43.3%). The prevalence was 40.7% among women and 38.9% among men (P &lt; 0.001). There was no significant difference between ethnicities (P = 0.14). Compared with North America (41.2%), the prevalence of pruritus was significantly lower in Europe (35.9%, P &lt; 0.001), Australia (38.4%, P = 0.017), East Asia (40.2%, P = 0.04) and Latin America (36.5%, P &lt; 0.001), and higher in Africa (45.7%, P = 0.007). No significant difference was found with the Middle East (40.2%, P = 0.36). The prevalence of pruritus in BRICS countries (40.3%) was significantly higher than that in developed countries (38.7%) (P &lt; 10–3).

Conclusions
Out analysis is limited because there is no information about the severity or type (acute, chronic) of pruritus. The global prevalence of pruritus revealed age, sex and geographic region differences, with no ethnic differences.
Preoperative prediction of renal fibrous capsule invasion in clear cell renal cell carcinoma using CT-based radiomics model
Authors: Zhang Yaodan , Zhao Jinkun , Li Zhijun , Yang Meng , Ye Zhaoxiang 
Published: June 2024

Abstract

Objectives
To develop radiomics-based classifiers for preoperative prediction of fibrous capsule invasion in renal cell carcinoma (RCC) patients by CT images.

Methods
In this study, clear cell RCC (ccRCC) patients who underwent both preoperative abdominal contrast-enhanced CT and nephrectomy surgery at our hospital were analysed. By transfer learning, we used base model obtained from Kidney Tumour Segmentation challenge dataset to semi-automatically segment kidney and tumours from corticomedullary phase (CMP) CT images. Dice similarity coefficient (DSC) was measured to evaluate the performance of segmentation models. Ten machine learning classifiers were compared in our study. Performance of the models was assessed by their accuracy, precision, recall, and area under the receiver operating characteristic curve (AUC). The reporting and methodological quality of our study was assessed by the CLEAR checklist and METRICS score.

Results
This retrospective study enrolled 163 ccRCC patients. The semiautomatic segmentation model using CMP CT images obtained DSCs of 0.98 in the training cohort and 0.96 in the test cohort for kidney segmentation, and DSCs of 0.94 and 0.86 for tumour segmentation in the training and test set, respectively. For preoperative prediction of renal capsule invasion, the AdaBoost had the best performance in batch 1, with accuracy, precision, recall, and F1-score equal to 0.8571, 0.8333, 0.9091, and 0.8696, respectively; and the same classifier was also the most suitable for this classification in batch 2. The AUCs of AdaBoost for batch 1 and batch 2 were 0.83 (95% CI: 0.68-0.98) and 0.74 (95% CI: 0.51-0.97), respectively. Nine common significant features for classification were found from 2 independent batch datasets, including morphological and texture features.

Conclusions
The CT-based radiomics classifiers performed well for the preoperative prediction of fibrous capsule invasion in ccRCC.

Advances in knowledge
Noninvasive prediction of renal fibrous capsule invasion in RCC is rather difficult by abdominal CT images before surgery. A machine learning classifier integrated with radiomics features shows a promising potential to assist surgical treatment options for RCC patients.
The Visibility of a Socio-Economic Dimension in Day-to-Day Child and Family Social Work Practice in Wales
Authors: Elliott Martin , Smith Philip , Scourfield Jonathan 
Published: June 2024

Abstract
This study explored how day-to-day social work practice with children and families in Wales responds to poverty, building on case studies already published in the other three UK nations. A case study design was used. The sites were locality teams in two local authorities, differing in their children looked after rates and trajectories of these over time. Qualitative research methods included practice observations; interviews with staff; focus groups; mapping of decision-making processes; and a sample of family case narratives. In one local authority, the range of data was similar to the other UK nation case studies. However, in the second, data collection was adapted to the coronavirus disease-19 (COVID-19) lockdown context. Some evidence was found of narratives that emphasised the cultural, rather than material, aspect of poverty, and blamed parents for making inappropriate spending choices. Poverty alleviation was generally seen as outside of social workers’ control and requiring earlier help before social services involvement. In one of the local authorities, there was some awareness shown of the impact of poverty on parenting. In the other, that took part in the study during 2020, the exacerbating effects of families in lockdown were described, including the lack of family support due to pandemic restrictions.
Engineered nanovesicles from activated neutrophils with enriched bactericidal proteins have molecular debridement ability and promote infectious wound healing
Authors: Jin Hangfei , Wen Xiao , Sun Ran , Yu Yanzhen , Guo Zaiwen , Yang Yunxi , Li Linbin , Sun Bingwei 
Published: June 2024

Abstract

Background
Bacterial infections pose a considerable threat to skin wounds, particularly in the case of challenging-to-treat diabetic wounds. Systemic antibiotics often struggle to penetrate deep wound tissues and topically applied antibiotics may lead to sensitization, necessitating the development of novel approaches for effectively treating germs in deep wound tissues. Neutrophils, the predominant immune cells in the bloodstream, rapidly release an abundance of molecules via degranulation upon activation, which possess the ability to directly eliminate pathogens. This study was designed to develop novel neutrophil cell engineered nanovesicles (NVs) with high production and explore their bactericidal properties and application in promoting infectious wound healing.

Methods
Neutrophils were isolated from peripheral blood and activated in vitro via phorbol myristate acetate (PMA) stimulation. Engineered NVs were prepared by sequentially extruding activated neutrophils followed by ultracentrifugation and were compared with neutrophil-derived exosomes in terms of morphology, size distribution and protein contents. The bactericidal effect of NVs in vitro was evaluated using the spread plate technique, LIVE/DEAD backlight bacteria assay and observation of bacterial morphology. The therapeutic effects of NVs in vivo were evaluated using wound contraction area measurements, histopathological examinations, assessments of inflammatory factors and immunochemical staining.

Results
Activated neutrophils stimulated with PMA in vitro promptly release a substantial amount of bactericidal proteins. NVs are similar to exosomes in terms of morphology and particle size, but they exhibit a significantly higher enrichment of bactericidal proteins. In vitro, NVs demonstrated a significant bactericidal effect, presumably mediated by the enrichment of bactericidal proteins such as lysozyme. These NVs significantly accelerated wound healing, leading to a marked reduction in bacterial load, downregulation of inflammatory factors and enhanced collagen deposition in a full-thickness infectious skin defect model.

Conclusions
We developed engineered NVs derived from activated neutrophils to serve as a novel debridement method targeting bacteria in deep tissues, ultimately promoting infectious wound healing.
Compensatory thickening of cortical thickness in early stage of schizophrenia
Authors: Wang Yujue , Fan Lejia , He Ying , Yuan Liu , Li Zongchang , Zheng Wenxiao , Tang Jinsong , Li Chunwang , Jin Ke , Liu Weiqing , Chen Xiaogang , Ouyang Lijun , Ma Xiaoqian 
Published: June 2024

Abstract
Brain structural abnormality has been observed in the prodromal and early stages of schizophrenia, but the mechanism behind it is not clear. In this study, to explore the association between cortical abnormalities, metabolite levels, inflammation levels and clinical symptoms of schizophrenia, 51 drug-naive first-episode schizophrenia (FES) patients, 51 ultra-high risk for psychosis (UHR), and 51 healthy controls (HC) were recruited. We estimated gray matter volume (GMV), cortical thickness (CT), concentrations of different metabolites, and inflammatory marks among four groups (UHR converted to psychosis [UHR-C], UHR unconverted to psychosis [UHR-NC], FES, HC). UHR-C group had more CT in the right lateral occipital cortex and the right medial orbito-frontal cortex (rMOF), while a significant reduction in CT of the right fusiform cortex was observed in FES group. UHR-C group had significantly higher concentration of IL-6, while IL-17 could significantly predict CT of the right fusiform and IL-4 and IL-17 were significant predictors of CT in the rMOF. To conclude, it is reasonable to speculate that the increased CT in UHR-C group is related to the inflammatory response, and may participate in some compensatory mechanism, but might become exhaustive with the progress of the disease due to potential neurotoxic effects.
Verbal semantic expertise is associated with reduced functional connectivity between left and right anterior temporal lobes
Authors: Wu Wei , Hoffman Paul 
Published: June 2024

Abstract
The left and right anterior temporal lobes (ATLs) encode semantic representations. They show graded hemispheric specialization in function, with the left ATL contributing preferentially to verbal semantic processing. We investigated the cognitive correlates of this organization, using resting-state functional connectivity as a measure of functional segregation between ATLs. We analyzed two independent resting-state fMRI datasets (n = 86 and n = 642) in which participants’ verbal semantic expertise was measured using vocabulary tests. In both datasets, people with more advanced verbal semantic knowledge showed weaker functional connectivity between left and right ventral ATLs. This effect was highly specific. It was not observed for within-hemisphere connections between semantic regions (ventral ATL and inferior frontal gyrus (IFG), though it was found for left–right IFG connectivity in one dataset). Effects were not found for tasks probing semantic control, nonsemantic cognition, or face recognition. Our results suggest that hemispheric specialization in the ATLs is not an innate property but rather emerges as people develop highly detailed verbal semantic representations. We speculate that this effect is a consequence of the left ATL’s greater connectivity with left-lateralized written word recognition regions, which causes it to preferentially represent meaning for advanced vocabulary acquired primarily through reading.
DMLS: an automated pipeline to extract the Drosophila modular transcription regulators and targets from massive literature articles
Authors: Yang Tzu-Hsien , Yu Yu-Huai , Wu Sheng-Hang , Chang Fang-Yuan , Tsai Hsiu-Chun , Yang Ya-Chiao 
Published: June 2024

Abstract
Transcription regulation in multicellular species is mediated by modular transcription factor (TF) binding site combinations termed cis-regulatory modules (CRMs). Such CRM-mediated transcription regulation determines the gene expression patterns during development. Biologists frequently investigate CRM transcription regulation on gene expressions. However, the knowledge of the target genes and regulatory TFs participating in the CRMs under study is mostly fragmentary throughout the literature. Researchers need to afford tremendous human resources to fully surf through the articles deposited in biomedical literature databases in order to obtain the information. Although several novel text-mining systems are now available for literature triaging, these tools do not specifically focus on CRM-related literature prescreening, failing to correctly extract the information of the CRM target genes and regulatory TFs from the literature. For this reason, we constructed a supportive auto-literature prescreener called Drosophila Modular transcription-regulation Literature Screener (DMLS) that achieves the following: (i) prescreens articles describing experiments on modular transcription regulation, (ii) identifies the described target genes and TFs of the CRMs under study for each modular transcription-regulation-describing article and (iii) features an automated and extendable pipeline to perform the task. We demonstrated that the final performance of DMLS in extracting the described target gene and regulatory TF lists of CRMs under study for given articles achieved test macro area under the ROC curve (auROC) = 89.7% and area under the precision-recall curve (auPRC) = 77.6%, outperforming the intuitive gene name-occurrence-counting method by at least 19.9% in auROC and 30.5% in auPRC. The web service and the command line versions of DMLS are available at https://cobis.bme.ncku.edu.tw/DMLS/ and https://github.com/cobisLab/DMLS/, respectively.
Database Tool URL: https://cobis.bme.ncku.edu.tw/DMLS/
Unveiling the reliability of left atrial strain measurement: a dedicated speckle tracking software perspective in controls and cases
Authors: Mandoli G E , Pastore M C , Procopio M C , Pica A , Vigna M , Benfari G , Diviggiano E E , Martini L , Lunghetti S , Focardi M , Henein M Y , Cameli M 
Published: June 2024

Abstract

Aims
Speckle tracking echocardiography increasingly supports left atrial (LA) strain (LAS) analysis for diagnosis and prognosis of various clinical conditions. Prior limitations, such as the absence of dedicated software, have been overcome by validated ventricular-based software. A newly automated real-time and offline LA-specific software have now become available on echocardiographs and dedicated workstations. This study aimed at comparing LA strain measures obtained from new fully automated software vs. traditional semi-automated ventricular-based methods in different groups of patients.

Methods and results
Two operators acquired LA images in a mixed population of healthy individuals and patients with pressure overload (hypertension and aortic stenosis) or pressure–volume overload (mitral regurgitation and heart failure). Subjects with prosthetic valves, heart transplant, or atrial fibrillation were excluded. Strain analysis was performed twice by old semi-automated software and new LA dedicated. LAS was then measured online on the scanning echocardiograph. Overall, 100 patients were analysed (41 healthy subjects, 28 pressure overload, 31 volume overload). LAS proved to be highly reproducible with both software. The dedicated method exhibited slightly superior inter- and intra-operator reproducibility. The online software results showed a nearly perfect reproducibility with offline software [intraclass correlation coefficient = 0.99 [0.99; 1.00]] in addition to being able to save an average of ∼30 s.

Conclusion
The recently developed fully automated software for dedicated LAS analysis demonstrates excellent inter- and intra-operator reproducibility, making it a reliable and efficient strain calculation method in routine clinical practice. Another advantage of online LAS calculation is time efficiency.
Molecular diagnosis and phylogenetic analysis of a Middle East respiratory syndrome coronavirus human case in Jordan
Authors: Abu-Basha Ehab A , Ismail Zuhair B , Alboom Mohammad H , Alkofahi Ayesha , Amarneh Basil H , Al-Omari Omar , Fahmawi Alaa , Alshammari Abdullah , Lakaideh Mais , Shaban Shereen , Al-Omari Bilal , Talafha Hani , Hijazeen Zaidoun , Daradkeh Yasmin , El-Shesheny Rabeh , Kayali Ghazi , Bagge Whitney , Karesh William B 
Published: June 2024

Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is an important zoonotic pathogen. The aim of this paper is to report one polymerase chain reaction (PCR)-positive case of MERS-CoV in a 27-year-old man who was involved in a nationwide longitudinal surveillance study of certain zoonotic diseases in Jordan including MERS-CoV. Whole-blood and nasal swab samples were collected from the man and five camels in the vicinity of his living area. The samples were subjected to enzyme-linked immunosorbent assay (ELISA) and real-time reverse-transcription PCR (RT-PCR) to detect MERS-CoV-specific antibodies and MERS-CoV genetic material, respectively. Genomic sequencing and phylogenetic analysis were also performed to detect similarities with known strains of the virus in the region. In January 2021, an ongoing surveillance study detected a MERS-CoV-positive nasal swab sample from an asymptomatic male and camels using RT-PCR. Phylogenetically, the MERS-CoV isolated in this case belonged to clade B and is clustered with other strains originating in the Arabian Peninsula. The case report represents the first PCR-positive case of MERS-CoV in an asymptomatic individual in Jordan, indicating active circulation of the virus within the population.
Digest: Asymmetrical introgression of belly coloration across a manakin hybrid zone in Panama
Authors: Ottenburghs Jente 
Published: June 2024

Abstract
How does sexual selection impact introgression dynamics across a hybrid zone? Long et al. (2024) used historical (1989–1994) and contemporary (2017–2020) samples to quantify the stability of a Panamanian hybrid zone between golden-collared manakins (Manacus vitellinus) and white-collared manakins (M. candei). Their analyses revealed a spatially stable hybrid zone, except for one trait, belly plumage coloration, which has introgressed into the distribution of the white-collared manakin. This finding suggests possible sexual selection for this trait.
Examining First- and Second-Level Digital Divide at the Intersection of Race/Ethnicity, Gender, and Socioeconomic Status: An Analysis of the National Health and Aging Trends Study
Authors: Wang Kun , Chen Xiayu Summer , Gu Danan , Smith Brenda D , Dong Yanjun , Peet Jared Zak 
Published: June 2024

Abstract

Background and Objectives
Significant societal and technological changes in the 2010s called for an up-to-date understanding of the digital divide among older adults in the United States. This trend study aimed to examine the effects of race/ethnicity and the intersecting effects of race/ethnicity with other marginalized identities related to gender, income, education, and occupation on the first- and second-level digital divide.

Research Design and Methods
Utilizing a nationally representative sample of older community dwellers from the National Health and Aging Trends Study, we conducted weighted logistic regressions at 3 time points (2011/2013, 2015, and 2019). The first-level digital divide was measured by access to working phones or computers/laptops; the second-level divide was measured by 7 activities in personal task, social, and health-related Internet use.

Results
The first-level racial/ethnic digital divide became nonsignificant in 2019, whereas the disparities in all second-level measures persisted. The intersecting effects of race/ethnicity with low education and/or low income became nonsignificant in 2019 for personal-task use. However, the interactions with low education and/or low income became significant for social and health-related use in 2015 and/or 2019.

Discussion and Implications
This study highlights the persistence of the second-level racial/ethnic digital divide among older community dwellers in the United States, especially the exacerbated social and health-related digital divide for people of color with low socioeconomic status. By considering intersections of marginalized social identities, policymakers and stakeholders should develop targeted strategies to bridge the digital divide, promote health outcomes, and reduce health disparities.
Hybrid meshless-FEM method for 3-D magnetotelluric modelling using non-conformal discretization
Authors: Cao Jin , Liu Yunhe , Yin Changchun , Wang Haoman , Su Yang , Wang Luyuan , Ma Xinpeng , Zhang Bo 
Published: June 2024

SUMMARY
We propose a novel method for 3-D magnetotelluric (MT) forward modelling based on hybrid meshless and finite-element (FE) methods. This method divides the earth model into a central computational region and an expansion one. For the central region, we adopt scatter points to discretize the model, which can flexibly and accurately characterize the complex structures without generating unstructured mesh. The meshless method using compact support radial basis function is applied to simulate this area's electromagnetic field. While in the expansion region, to avoid the heavy time consumption and numerical error of the meshless method caused by non-uniform nodes, we adopt a node-based finite-element method with regular hexahedral mesh for stability. Finally, the two discretized systems are coupled at the interface nodes according to the continuity conditions of vector and scalar potentials. Considering that the normal electric field is discontinuous at the interface with resistivity discontinuity, while the shape functions for the meshless method are continuous, we further adopt the visibility criterion in constructing the support region. Numerical experiments on typical models show that using the same degree of freedom, the hybrid meshless-finite element method (FEM) algorithm has higher accuracy than the node-based FEM and meshless method. In addition, the electric field discontinuity at interfaces is well preserved, which proves the effectiveness of the visibility criterion method. In general, compared to the conventional grid-based method, this new approach does not need the complex mesh generation for complex structures and can achieve high accuracy, thus it has the potential to become a powerful 3-D MT forward modelling technique.