bluuebunny/crossref_metadata_2025_split huggingface dataset:
The school environment and bullying victimization among seventh graders with autism spectrum disorder: a cohort study
Authors: Lu Hsin-Hui , Chen Duan-Rung , Chou An-Kuo 
Published: March 2022

Abstract
Background
There is strong evidence to support the association between bullying and the onset of mental health conditions in students with ASD (autism spectrum disorder). In Taiwan, the seventh grade marks the first year of middle school, following elementary school. This period is also when peers tend to perform bullying behaviours to establish status among the peer group. Therefore, seventh grade is considered one of the most challenging times for students with ASD due to several changes within the school environment and the developmental changes that arise at this age. This study aims to assess the association between the school environment and bullying victimization among students with autism spectrum disorder (ASD) enrolled in regular classes in their first year of middle school.

Methods
Data were obtained from the Special Needs Education Longitudinal Study database located in the Survey Research Data Archive of Academia Sinica. The analysis included one hundred eighty-four seventh graders with ASD who were in regular classes across Taiwan. The primary variables under study were whether the participants had experienced social exclusion, insults or teasing, extortion, or sexual harassment over the past semester.

Results
Participants with a higher positive friendship quality (P = 0.027) and who had received more peer support upon encountering difficulties in school (P = 0.041) were less likely to experience social exclusion. Participants with a higher positive friendship quality (P = 0.001) and a more positive classroom learning environment (P = 0.031) were less likely to have experienced insults or teasing. However, participants with more friends were more likely to be extorted (P = 0.015) and sexually harassed (P = 0.001) than those with fewer friends. Furthermore, participants in regular classes on a part-time basis were 2.59 times more likely to report sexual harassment than those in regular classes on a full-time basis (P = 0.021).

Conclusions
This study suggests that a supportive school environment reduces the likelihood that seventh-graders with ASD will be bullied. Clinicians should consider the association between the school environment and bullying victimization among adolescents with ASD in regular classes during their first year of middle school.
Radiomics predicts the prognosis of patients with locally advanced breast cancer by reflecting the heterogeneity of tumor cells and the tumor microenvironment
Authors: Wang Xuanyi , Xie Tiansong , Luo Jurui , Zhou Zhengrong , Yu Xiaoli , Guo Xiaomao 
Published: March 2022

Abstract
Background
This study investigated the efficacy of radiomics to predict survival outcome for locally advanced breast cancer (LABC) patients and the association of radiomics with tumor heterogeneity and microenvironment.

Methods
Patients with LABC from 2010 to 2015 were retrospectively reviewed. Radiomics features were extracted from enhanced MRI. We constructed the radiomics score using lasso and assessed its prognostic value. An external validation cohort from The Cancer Imaging Archive was used to assess phenotype reproducibility. Sequencing data from TCGA and our center were applied to reveal genomic landscape of different radiomics score groups. Tumor infiltrating lymphocytes map and bioinformatics methods were applied to evaluate the heterogeneity of tumor microenvironment. Computational histopathology was also applied.

Results
A total of 278 patients were divided into training cohort and validation cohort. Radiomics score was constructed and significantly associated with disease-free survival (DFS) of the patients in training cohort, validation cohort and external validation cohort (p < 0.001, p = 0.014 and p = 0.041, respectively). The radiomics-based nomogram showed better predictive performance of DFS compared with TNM model. Distinct gene expression patterns were identified. Immunophenotype and immune cell composition was different in each radiomics score group. The link between radiomics and computational histopathology was revealed.

Conclusions
The radiomics score could effectively predict prognosis of LABC after neoadjuvant chemotherapy and radiotherapy. Radiomics revealed heterogeneity of tumor cell and tumor microenvironment and holds great potential to facilitate individualized DFS estimation and guide personalized care.
Developmental transcriptomics throughout the embryonic developmental process of Rhipicephalus turanicus reveals stage-specific gene expression profiles
Authors: Ruiling Zhang , Wenjuan Liu , Kexin Zhang , Xuejun Wang , Zhong Zhang 
Published: March 2022

Abstract
Background
Ticks are important vectors and transmit diverse pathogens, including protozoa, viruses, and bacteria. Tick-borne diseases can cause damage to both human health and the livestock industries. The control and prevention of ticks and tick-borne diseases has relied heavily on acaricides.

Methods
In the present study, using a high-throughput RNA sequencing (RNA-Seq) technique, we performed a comprehensive time-series transcriptomic analysis throughout the embryogenesis period of Rhipicephalus turanicus.

Results
Altogether, 127,157 unigenes were assembled and clustered. Gene expression differences among the embryonic stages demonstrated that the most differentially expressed genes (DEGs) were observed in the comparisons of early embryonic stages (RTE5 vs. RTE10, 9726 genes), and there were far fewer DEGs in later stages (RTE25 vs. RTE30, 2751 genes). Furthermore, 16 distinct gene modules were identified according to weighted gene co-expression network analysis (WGCNA), and genes in different modules displayed stage-specific characteristics. Gene Ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment suggested that some genes involved in organ and tissue formation were significantly upregulated in the early embryonic developmental stages, whereas metabolism-related pathways were more enriched in the later embryonic developmental stages.

Conclusions
These transcriptome studies revealed gene expression profiles at different stages of embryonic development, which would be useful for interrupting the embryonic development of ticks and disrupting the transmission of tick-borne diseases.

Graphical Abstract
Determinants of apprehension to return to sport after reconstruction of the anterior cruciate ligament: an exploratory observational retrospective study
Authors: Martini Alexandre , Ayala Anne , Lechable Marc , Rannou François , Lefèvre-Colau Marie-Martine , Nguyen Christelle 
Published: March 2022

Abstract
Background
Only 65% of people return to a level of sport equivalent to that before after anterior cruciate ligament (ACL) surgery. Persisting apprehension may in part explain this observation. We aimed to describe characteristics of people with ACL-Return to Sport after Injury (RSI) scores ≥ 60/100 (low apprehension) at 6 months after injury and to identify variables independently associated with low apprehension at 6 months.

Methods
We conducted a single-center retrospective study. People who had surgery for an ACL rupture and who participated in an outpatient post-operative rehabilitation program were included consecutively. The ACL-RSI questionnaire was self-administered at 6 months after injury. Baseline characteristics of people with ACL-RSI scores ≥ 60/100 and < 60/100 were described. Multiple logistic regression was performed to identify baseline variables associated with low apprehension at 6 months.

Results
We included 37 participants: 13/37 (35.1%) were women and mean age was 27.2 (9.2) years. At 6 months, 21/37 (56.8%) had an ACL-RSI score ≥ 60/100. Participants who had an ACL-RSI score ≥ 60/100 more often received a preoperative rehabilitation (16/21 [76.2%] vs 5/16 [31.2%]), and had less often knee pain (7/21 [33.3%] vs 7/16 [43.7%]) and effusion (5/21 [23.8%] vs 8/16 [50.0%]) at 1 month after surgery, than participants who had an ACL-RSI score < 60/100. In the multivariate analysis, preoperative rehabilitation was associated with low apprehension at 6 months (OR [95% CI] = 0.107 [0.023 to 0.488], p = 0.002).

Conclusions
Preoperative rehabilitation was independently associated with low apprehension at 6 months.
Trial registration. Not applicable.
Pancoast tumor presenting with multiple joint pains: a case report
Authors: Mohamud Safia , Oyawusi Mosunmola , Weir Roger L. , Halbert Etuajie O. , Millis Richard M. , Gebremedhin Teddy , Dehkordi Ozra 
Published: March 2022

Abstract
Background
Pancoast tumors represent a unique subset of lung cancers wherein a primary neoplasm arises in the lung’s apex and invades the surrounding soft tissues. One of the main challenges in the diagnosis and treatment of these apical lung cancers is that they are usually not visualized on initial chest x-ray and, by the time the patient presents with symptoms, the tumor has almost always invaded nearby structures.

Case presentation
Herein we report a case of a 58-year-old nonsmoking African American male who presented to the neurology clinic with a history of multiple chronic joint pains. The patient complained of shoulder pain that traveled into his right arm and right finger and had worsened over the past 9 months. The patient also reported decreased right proximal strength and swelling of his right hand. Magnetic resonance imaging of the shoulder and cervical region showed mild cervical spondylosis and a questionable right apical mass. A subsequent high-resolution computed tomography scan of the chest revealed a large right apical lung mass, with chest wall invasion and erosion of the adjacent ribs. Biopsy of the mass confirmed poorly differentiated non-small cell lung cancer. Radiation therapy was initiated, and the patient’s pain improved significantly. Given the size of the tumor, chemotherapy was recommended by the oncology team. The patient decided against chemotherapy.

Conclusion
This case highlights the importance of early diagnosis by expanding the differential diagnosis in patients presenting with weakness, sensory loss, and shoulder pain beyond radiculopathy or joint-related diseases. A comprehensive history and careful examination may lead to an earlier diagnosis, more appropriate treatment, and better outcome in cases of Pancoast tumor presenting with neuropathic or musculoskeletal pain.
Rapid and robust derivation of mesenchymal stem cells from human pluripotent stem cells via temporal induction of neuralized ectoderm
Authors: Jin Wei , He Yi , Li Tuo , Long Fei , Qin Xin , Yuan Yuan , Gao Ge , Shakhawat Hosen Md , Liu Xinguang , Jin Guoxiang , Zhou Zhongjun 
Published: March 2022

Abstract
Background
Mesenchymal stem cells (MSCs) are emerging as the mainstay of regenerative medicine because of their ability to differentiate into multiple cell lineages. The infinite proliferative potential of human pluripotent stem cells (PSCs) grants an unlimited supply of MSCs. Despite their great potential in therapeutic applications, several drawbacks have hindered its clinical translation, including limited number of replication, compromised potential and altered function in late passages. The aim of this study is to establish an efficient method for the production of MSCs from pluripotent stem cells for potential clinical application in rare human disease Hutchinson-Gilford progeria syndrome.

Results
We established a robust method allowing rapid derivation of MSCs from both human iPSCs and ESCs via a temporal induction of neural ectoderm in chemically defined media. The iPSC- and ESC-derived MSCs satisfy the standard criteria of surface markers. They exhibited a high tri-lineage differentiation potential with over 90% transcriptional similarity to the primary MSCs derived from bone marrow. To evaluate the potential application of this method in disease modeling, MSCs were generated from iPSCs derived from a patient with Hutchinson-Gilford progeria syndrome (HGPS-MSCs) and from mutation-rectified HGPS-iPSCs (cHGPS-MSCs). HGPS-MSCs manifested accelerated senescence whereas mutation rectification rescued cellular senescence in HGPS-MSCs.

Conclusions
The robust method of MSC derivation from ESCs and iPSCs provides an efficient approach to rapidly generate sufficient MSCs for in vitro disease modeling and clinical applications.
TSLP regulates mitochondrial ROS-induced mitophagy via histone modification in human monocytes
Authors: Lin Yi-Ching , Lin Yu-Chih , Tsai Mei-Lan , Liao Wei-Ting , Hung Chih-Hsing 
Published: March 2022

Abstract
Background
Thymic stromal lymphopoietin (TSLP) is a Th2-like cytokine involved in asthma pathogenesis. Excessive reactive oxygen species (ROS) production can lead to airway inflammation, hyperresponsiveness and remodeling. Mitophagy, followed by ROS production, is the selective degradation of mitochondria by autophagy and often occurs in defective mitochondria. In the present study, we aimed to examine the effects of TSLP on ROS production and mitophagy in human monocytes and to investigate the underlying mechanisms, including epigenetic regulation.

Results
TSLP induced ROS generation, and the effects were reversed by the antioxidant N-acetylcysteine (NAC) in THP-1 cells. Transmission electron microscopy images showed donut-shaped mitochondria that lost the cristae ultrastructure after TSLP stimulation. A decrease in mitochondrial membrane potential, decreased MTCO2 expression, and increased mitochondrial DNA release after TSLP stimulation were found. TSLP enhanced mitochondrial complex I and complex II/III activity and increased mitochondrial copy numbers and the expression of the complex II SHDA gene. TSLP-induced SHDA expression was inhibited by the histone acetyltransferase inhibitor anacardic acid (AA) and the histone methyltransferase inhibitor methylthioadenosine (MTA), and chromatin immunoprecipitation assays revealed that TSLP enhanced H3 acetylation, H4 acetylation, and H3K4 and H3K36 trimethylation in the SHDA promoter. Confocal laser microscopy showed that TSLP treatment increased the signals of the mitophagy-related proteins PINK1, LC3, phospho-parkin and phospho-ubiquitin, and pretreatment with AA and MTA reduced TSLP-induced PINK1 and LC3 accumulation in mitochondria. Western blot analysis showed that TSLP significantly increased phosphor-AMPK signal intensity, and the effects were inhibited by the antioxidant NAC. The increased signal intensities of the mitophagy-related proteins PINK1, Parkin and LC3 I/II were decreased by dorsomorphin, an AMPK inhibitor. TSLP decreased M1-related cytokine CXCL-10 production and increased M2-related cytokine CCL-1 and CCL-22 production, which was suppressed by the mitophagy inhibitor Mdivi-1 and PINK1 gene knockdown.

Conclusions
Epithelial-derived TSLP regulates ROS production and mitophagy through AMPK activation and histone modification and alters M1/M2 chemokine expression in human monocytes.

Graphical Abstract
Clinical impact of ventilator-associated pneumonia in patients with the acute respiratory distress syndrome: a retrospective cohort study
Authors: Le Pape Marc , Besnard Céline , Acatrinei Camelia , Guinard Jérôme , Boutrot Maxime , Genève Claire , Boulain Thierry , Barbier François 
Published: March 2022

Abstract
Background
The clinical impact and outcomes of ventilator-associated pneumonia (VAP) have been scarcely investigated in patients with the acute respiratory distress syndrome (ARDS).

Methods
Patients admitted over an 18-month period in two intensive care units (ICU) of a university-affiliated hospital and meeting the Berlin criteria for ARDS were retrospectively included. The association between VAP and the probability of death at day 90 (primary endpoint) was appraised through a Cox proportional hazards model handling VAP as a delay entry variable. Secondary endpoints included (i) potential changes in the PaO2/FiO2 ratio and SOFA score values around VAP (linear mixed modelling), and (ii) mechanical ventilation (MV) duration, numbers of ventilator- and vasopressor-free days at day 28, and length of stay (LOS) in patients with and without VAP (median or absolute risk difference calculation). Subgroup analyses were performed in patients with COVID-19-related ARDS and those with ARDS from other causes.

Results
Among the 336 included patients (101 with COVID-19 and 235 with other ARDS), 176 (52.4%) experienced a first VAP. VAP induced a transient and moderate decline in the PaO2/FiO2 ratio without increase in SOFA score values. VAP was associated with less ventilator-free days (median difference and 95% CI, − 19 [− 20; − 13.5] days) and vasopressor-free days (− 5 [− 9; − 2] days) at day 28, and longer ICU (+ 13 [+ 9; + 15] days) and hospital (+ 11.5 [+ 7.5; + 17.5] days) LOS. These effects were observed in both subgroups. Overall day-90 mortality rates were 35.8% and 30.0% in patients with and without VAP, respectively (P = 0.30). In the whole cohort, VAP (adjusted HR 3.16, 95% CI 2.04–4.89, P < 0.0001), the SAPS-2 value at admission, chronic renal disease and an admission for cardiac arrest predicted death at day 90, while the COVID-19 status had no independent impact. When analysed separately, VAP predicted death in non-COVID-19 patients (aHR 3.43, 95% CI 2.11–5.58, P < 0.0001) but not in those with COVID-19 (aHR 1.19, 95% CI 0.32–4.49, P = 0.80).

Conclusions
VAP is an independent predictor of 90-day mortality in ARDS patients. This condition exerts a limited impact on oxygenation but correlates with extended MV duration, vasoactive support, and LOS.
MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations
Authors: Gregory Ann C. , Gerhardt Kenji , Zhong Zhi-Ping , Bolduc Benjamin , Temperton Ben , Konstantinidis Konstantinos T. , Sullivan Matthew B. 
Published: March 2022

Abstract
Background
Microbes and their viruses are hidden engines driving Earth’s ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter-(macrodiversity) and intra-(microdiversity) population variation, analytical tools to do so remain scattered or under-developed.

Results
Here, we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both the macro- and microdiversity levels. Macrodiversity estimates include population abundances and α- and β-diversity. Microdiversity calculations include identification of single nucleotide polymorphisms, novel codon-constrained linkage of SNPs, nucleotide diversity (π and θ), and selective pressures (pN/pS and Tajima’s D) within and fixation indices (FST) between populations. MetaPop will also identify genes with distinct codon usage. Following rigorous validation, we applied MetaPop to the gut viromes of autistic children that underwent fecal microbiota transfers and their neurotypical peers. The macrodiversity results confirmed our prior findings for viral populations (microbial shotgun metagenomes were not available) that diversity did not significantly differ between autistic and neurotypical children. However, by also quantifying microdiversity, MetaPop revealed lower average viral nucleotide diversity (π) in autistic children. Analysis of the percentage of genomes detected under positive selection was also lower among autistic children, suggesting that higher viral π in neurotypical children may be beneficial because it allows populations to better “bet hedge” in changing environments. Further, comparisons of microdiversity pre- and post-FMT in autistic children revealed that the delivery FMT method (oral versus rectal) may influence viral activity and engraftment of microdiverse viral populations, with children who received their FMT rectally having higher microdiversity post-FMT. Overall, these results show that analyses at the macro level alone can miss important biological differences.

Conclusions
These findings suggest that standardized population and genetic variation analyses will be invaluable for maximizing biological inference, and MetaPop provides a convenient tool package to explore the dual impact of macro- and microdiversity across microbial communities.
Socioeconomic disadvantage and ethnicity are associated with large differences in children’s working memory ability: analysis of a prospective birth cohort study following 13,500 children
Authors: Mooney Kate E. , Pickett Kate E. , Shire Katy , Allen Richard J. , Waterman Amanda H. 
Published: March 2022

AbstractWorking memory is a limited capacity system that stores and processes information over short time periods and is essential for learning new information. Some studies have investigated the associations between socioeconomic position and working memory, however none have examined this across potentially dissociable aspects of working memory. Further, there are very few studies about children’s working memory differences across and within different ethnic groups. Therefore, there is a need to understand the potential associations between socioeconomic position, ethnicity, and different aspects of children’s working memory. We investigated children’s working memory (n = 15,154) by socioeconomic group, using a latent class measure of family socioeconomic position, and then by ethnic group. To account for potential problems in applying socioeconomic measures across different ethnic groups, we then examined associations using an ethnic-specific socioeconomic measure within the ethnic majority group (White British) and the largest ethnic minority group (Pakistani). We found a strong association between socioeconomic group at birth and working memory at age 7–10 years, where the difference between the least and most deprived socioeconomic groups was equivalent to at least a 1-year age difference. We also found substantial differences in working memory between nine ethnic groups that varied by working memory task, where the difference between groups was equivalent to an age difference of between 6 and 24 months. Finally, we found evidence for a socioeconomic gradient in working memory for White British children, but this was considerably reduced in Pakistani children. These findings show the importance of separating out different ethnic groups when investigating associations between socioeconomic position and cognitive function, and that researchers need to be mindful when applying socioeconomic measures across ethnic groups. Where possible, ethnic-specific measures of socioeconomic position should be developed and applied for studies like these. Future research considering the possible mechanisms behind associations between ethnicity and working memory, and mechanisms by which socioeconomic position differentially influences working memory performance for different ethnic groups would shed further light on this important topic.