bluuebunny/crossref_metadata_2025_split huggingface dataset:
Community-acquired and healthcare-associated Staphylococcus aureus infections in a pediatric hospital in southern Brazil over 8 years: how common is MRSA?
Authors: Fassbind Derrick Alexandre , Rezende Raíssa Queiroz , Dias Cícero Armídio Gomes , Motta Fabrizio 
Published: June 2023

BackgroundsBoth healthcare-associated and community-acquired methicillin-resistant Staphylococcus aureus (MRSA) infections are relevant in children. The objective of our study was to evaluate their impact in a pediatric hospital in southern Brazil.MethodsData from patients under 18 years of age with S. aureus infections between January 2013 and December 2020 were retrospectively analyzed. Data were collected regarding infection site, infection type (community-acquired or healthcare-associated), susceptibility to oxacillin [methicillin-susceptible S. aureus (MSSA) or MRSA] and other antimicrobials. We analyzed the evolution of the susceptibility rates for the isolates over this period.ResultsA total of 563 patients were included, among whom the prevalences of community- and hospital-acquired MRSA infections were 46.1% and 8.1%, respectively. No significant change occurred in these prevalences over the study period. In community-acquired infections, MSSA was significantly more associated with osteoarticular infections and MRSA was more associated with respiratory and intra-abdominal infections. In healthcare-associated infections, there was an association between MSSA and primary bloodstream infections and between MRSA, skin/soft tissue infections, and respiratory infections. Community-acquired MRSA were highly susceptible to trimethoprim-sulfamethoxazole (96.1%), clindamycin (88.4%), and doxycycline (99.0%).ConclusionOur study draws attention to the high rates of MRSA in community-acquired staphylococcal infections in this population, indicating a need to review initial protocols for severe staphylococcal infections according to local epidemiology.
Constructing a cancer stem cell related prognostic model for predicting immune landscape and drug sensitivity in colorectal cancer
Authors: Chen Jianfang , Wu Shuang , Peng Yu , Zhao Yang , Dong Yan , Ran Fengwei , Geng Haofei , Zhang Kang , Li Jianjun , Huang Shuo , Wang Zhe 
Published: June 2023

Background: Colorectal cancer (CRC) ranks the second malignancy with high incidence and mortality worldwide. Cancer stem cells (CSCs) function critically in cancer progression and metastasis via the interplay with immune cells in tumor microenvironment. This study aimed to identify important CSC marker genes and parsed the role of these marker genes in CRC.Materials and methods: CRC samples’ single-cell RNA sequencing data and bulk transcriptome data were utilized. Seurat R package annotated CSCs and identified CSC marker genes. Consensus clustering subtyped CRC samples based on CSC marker genes. Immune microenvironment, pathway and oxidative stress analysis was performed using ESTIMATE, MCP-counter analysis and ssGSEA analysis. A prognostic model was established by Lasso and stepAIC. Sensitivity to chemotherapeutic drugs was determined by the biochemical half maximal inhibitory concentration with pRRophetic R package.Results: We identified a total of 29 CSC marker genes related to disease-specific survival (DSS). Two clusters (CSC1 and CSC2) were determined, and CSC2 showed shorter DSS, a larger proportion of late-stage samples, and higher oxidative stress response. Two clusters exhibited differential activation of biological pathways associated with immune response and oncogenic signaling. Drug sensitivity analysis showed that 44 chemotherapy drugs were more sensitive to CSC2 that those in CSC1. We constructed a seven-gene prognostic model (DRD4, DPP7, UCN, INHBA, SFTA2, SYNPO2, and NXPH4) that was effectively to distinguish high-risk and low-risk patients. 14 chemotherapy drugs were more sensitive to high-risk group and 13 chemotherapy drugs were more sensitive to low-risk group. Combination of higher oxidative stress and risk score indicated dismal prognosis.Conclusion: The CSC marker genes we identified may help to further decipher the role of CSCs in CRC development and progression. The seven-gene prognostic model could serve as an indicator for predicting the response to immunotherapy and chemotherapy as well as prognosis of CRC patients.
Based on cuproptosis-related lncRNAs, a novel prognostic signature for colon adenocarcinoma prognosis, immunotherapy, and chemotherapy response
Authors: Li Chong , Zhang Keqian , Gong Yuzhu , Wu Qinan , Zhang Yanyan , Dong Yan , Li Dejia , Wang Zhe 
Published: June 2023

Introduction: Colon adenocarcinoma (COAD) is a special pathological subtype of colorectal cancer (CRC) with highly heterogeneous solid tumors with poor prognosis, and novel biomarkers are urgently required to guide its prognosis.Material and methods: RNA-Seq data of COAD were downloaded through The Cancer Genome Atlas (TCGA) database to determine cuproptosis-related lncRNAs (CRLs) using weighted gene co-expression network analysis (WGCNA). The scores of the pathways were calculated by single-sample gene set enrichment analysis (ssGSEA). CRLs that affected prognoses were determined via the univariate COX regression analysis to develop a prognostic model using multivariate COX regression analysis and LASSO regression analysis. The model was assessed by applying Kaplan–Meier (K-M) survival analysis and receiver operating characteristic curves and validated in GSE39582 and GSE17538. The tumor microenvironment (TME), single nucleotide variants (SNV), and immunotherapy response/chemotherapy sensitivity were assessed in high- and low-score subgroups. Finally, the construction of a nomogram was adopted to predict survival rates of COAD patients during years 1, 3, and 5.Results: We found that a high cuproptosis score reduced the survival rates of COAD significantly. A total of five CRLs affecting prognosis were identified, containing AC008494.3, EIF3J-DT, AC016027.1, AL731533.2, and ZEB1-AS1. The ROC curve showed that RiskScore could perform well in predicting the prognosis of COAD. Meanwhile, we found that RiskScore showed good ability in assessing immunotherapy and chemotherapy sensitivity. Finally, the nomogram and decision curves showed that RiskScore would be a powerful predictor for COAD.Conclusion: A novel prognostic model was constructed using CRLs in COAD, and the CRLs in the model were probably a potential therapeutic target. Based on this study, RiskScore was an independent predictor factor, immunotherapy response, and chemotherapy sensitivity for COAD, providing a new scientific basis for COAD prognosis management.
3D data-augmentation methods for semantic segmentation of tomato plant parts
Authors: Xin Bolai , Sun Ji , Bartholomeus Harm , Kootstra Gert 
Published: June 2023

Introduction3D semantic segmentation of plant point clouds is an important step towards automatic plant phenotyping and crop modeling. Since traditional hand-designed methods for point-cloud processing face challenges in generalisation, current methods are based on deep neural network that learn to perform the 3D segmentation based on training data. However, these methods require a large annotated training set to perform well. Especially for 3D semantic segmentation, the collection of training data is highly labour intensitive and time consuming. Data augmentation has been shown to improve training on small training sets. However, it is unclear which data-augmentation methods are effective for 3D plant-part segmentation.MethodsIn the proposed work, five novel data-augmentation methods (global cropping, brightness adjustment, leaf translation, leaf rotation, and leaf crossover) were proposed and compared to five existing methods (online down sampling, global jittering, global scaling, global rotation, and global translation). The methods were applied to PointNet++ for 3D semantic segmentation of the point clouds of three cultivars of tomato plants (Merlice, Brioso, and Gardener Delight). The point clouds were segmented into soil base, stick, stemwork, and other bio-structures.Results and disccusionAmong the data augmentation methods being proposed in this paper, leaf crossover indicated the most promising result which outperformed the existing ones. Leaf rotation (around Z axis), leaf translation, and cropping also performed well on the 3D tomato plant point clouds, which outperformed most of the existing work apart from global jittering. The proposed 3D data augmentation approaches significantly improve the overfitting caused by the limited training data. The improved plant-part segmentation further enables a more accurate reconstruction of the plant architecture.
Transcriptomic and metabolomic analyses reveal the potential mechanism of waterlogging resistance in cotton (Gossypium hirsutum L.)
Authors: Owusu Anane Gideon , Lv Yin-Ping , Liu Man , Wu Yong , Li Cheng-Lin , Guo Ning , Li Da-Hui , Gao Jun-Shan 
Published: June 2023

IntroductionCotton (Gossypium hirsutum L.) is susceptible to long-term waterlogging stress; however, genomic information of cotton response mechanisms toward long days of waterlogging is quite elusive.MethodsHere, we combined the transcriptome and metabolome expression level changes in cotton roots after 10 and 20 days of waterlogging stress treatment pertaining to potential resistance mechanisms in two cotton genotypes.Results and discussionNumerous adventitious roots and hypertrophic lenticels were induced in CJ1831056 and CJ1831072. Transcriptome analysis revealed 101,599 differentially expressed genes in cotton roots with higher gene expression after 20 days of stress. Reactive oxygen species (ROS) generating genes, antioxidant enzyme genes, and transcription factor genes (AP2, MYB, WRKY, and bZIP) were highly responsive to waterlogging stress among the two genotypes. Metabolomics results showed higher expressions of stress-resistant metabolites sinapyl alcohol, L-glutamic acid, galactaric acid, glucose 1-phosphate, L-valine, L-asparagine, and melibiose in CJ1831056 than CJ1831072. Differentially expressed metabolites (adenosine, galactaric acid, sinapyl alcohol, L-valine, L-asparagine, and melibiose) significantly correlated with the differentially expressed PRX52, PER1, PER64, and BGLU11 transcripts. This investigation reveals genes for targeted genetic engineering to improve waterlogging stress resistance to enhance abiotic stress regulatory mechanisms in cotton at the transcript and metabolic levels of study.
Effectiveness of exercise intervention on improving fundamental motor skills in children with autism spectrum disorder: a systematic review and meta-analysis
Authors: Ji Yu-Qin , Tian Hao , Zheng Ze-Yu , Ye Zhuo-Yan , Ye Qiang 
Published: June 2023

BackgroundAutism spectrum disorder (ASD) is a severe public health concern, and most of the children with ASD experience a substantial delay in FMS. This study aimed to investigate the effectiveness of exercise interventions in improving FMS in children with ASD, and provide evidence to support the scientific use of exercise interventions in practice.MethodsWe searched seven online databases (PubMed, Scopus, Web of Science, Embase, EBSCO, Clinical Trials, and The Cochrane Library) from inception to May 20, 2022. We included randomized control trials of exercise interventions for FMS in children with ASD. The methodological quality of the included studies was assessed using the Physiotherapy Evidence Database Scale. Stata 14.0 software was used for meta-analysis, forest plotting, subgroup analysis, heterogeneity analysis, and meta-regression.ResultsThirteen studies underwent systematic review (541 participants), of which 10 underwent meta-analysis (297 participants). Overall, exercise interventions significantly improved overall FMS in children with ASD. Regarding the three categories of FMS, exercise interventions significantly improved LMS (SMD = 1.07; 95% CI 0.73 to 1.41, p &lt; 0.001), OCS (SMD = 0.79; 95% CI 0.32 to 1.26, p = 0.001), and SS (SMD = 0.72; 95% CI 0.45 to 0.98, p &lt; 0.0001).Conclusionexercise interventions can effectively improve the FMS of children with ASD. The effects on LMS are considered as large effect sizes, while the effects on OCS and SS are considered as moderate effect sizes. These findings can inform clinical practice.Systematic review registrationhttps://inplasy.com/inplasy-2022-12-0013/.
Mobile health in the specific management of first-episode psychosis: a systematic literature review
Authors: Maechling Claire , Yrondi Antoine , Cambon Amandine 
Published: June 2023

PurposeThe purpose of this systematic literature review is to assess the therapeutic efficacy of mobile health methods in the management of patients with first-episode psychosis (FEP).MethodThe participants are patients with FEP. The interventions are smartphone applications. The studies assess the preliminary efficacy of various types of application.ResultsOne study found that monitoring symptoms minimized relapses, visits to A&amp;E and hospital admissions, while one study showed a decrease in positive psychotic symptoms. One study found an improvement in anxiety symptoms and two studies noted an improvement in psychotic symptoms. One study demonstrated its efficacy in helping participants return to studying and employment and one study reported improved motivation.ConclusionThe studies suggest that mobile applications have potential value in the management of young patients with FEP through the use of various assessment and intervention tools. This systematic review has several limitations due to the lack of randomized controlled studies available in the literature.
Breath-centered virtual mind-body medicine reduces COVID-related stress in women healthcare workers of the Regional Integrated Support for Education in Northern Ireland: a single group study
Authors: Gerbarg Patricia L. , Dickson Felicity , Conte Vincent A. , Brown Richard P. 
Published: June 2023

BackgroundDuring the COVID-19 pandemic, healthcare workers endured prolonged stress affecting their psychological well-being. Objectives: (1) Evaluate the effects of the Breath-Body-Mind Introductory Course (BBMIC) on COVID-related stress among employees of the Regional Integrated Support for Education, Northern Ireland, (2) Reduce the risk of adverse effects from COVID-related stress, and (3) Evaluate the effects of BBMIC on indicators of psychophysiological states and the consistency with hypothesized mechanisms of action.MethodsIn this single group study, a convenience sample of 39 female healthcare workers completed informed consent and baseline measures: Perceived Stress Scale (PSS), Stress Overload Scale-Short (SOS-S), and Exercise-Induced Feelings Inventory (EFI). Following the online BBMIC 4 h/day for 3 days and the 6 week solo (20 min/day) and group practice (45 min weekly), repeat testing plus the Indicators of Psychophysiological State (IPSS) and Program Evaluation were obtained.ResultsBaseline (T1) mean PSS score was significantly elevated compared to a normative sample: PSS = 18.2 vs. 13.7 (p &lt; 0.001) and improved significantly 11 weeks post-BBMIC (T4). SOS-S mean score declined from 10.7(T1) to 9.7 at 6 week post-test (T3). The SOS-S proportion of High Risk scores found in 22/29 participants (T1), dropped to 7/29 (T3). EFI mean subscale scores improved significantly from T1 to T2 and T3 for Revitalization (p &lt; 0.001); Exhaustion (p &lt; 0.002); and Tranquility (p &lt; 0.001); but not Engagement (p &lt; 0.289).ConclusionAmong RISE NI healthcare workers affected by COVID-related stress, participation in the BBMIC significantly reduced scores for Perceived Stress, Stress Overload, and Exhaustion. EFI Revitalization and Tranquility scores significantly improved. More than 60% of participants reported moderate to very strong improvements in 22 indicators of psychophysiological state, e.g., tension, mood, sleep, mental focus, anger, connectedness, awareness, hopefulness, and empathy. These results are consistent with the hypothesized mechanisms of action whereby voluntarily regulated breathing exercises change interoceptive messaging to brain regulatory networks that shift psychophysiological states of distress and defense to states of calmness and connection. These positive findings warrant validation in larger, controlled studies to extend the understanding of how breath-centered Mind-body Medicine practices could mitigate adverse effects of stress.
Preventive health examinations: protocol for a prospective cross-sectional study of German employees aged 45 to 59 years (Ü45-check)
Authors: Kalski Linda , Greiß Franziska , Hartung Johannes J. , Hafermann Lorena , Hofmann Maja A. , Wolfarth Bernd 
Published: June 2023

ObjectiveEarly identification of health-related risk factors is of great importance for maintaining workability. Screening examinations can help to detect diseases at an early stage and provide more needs-based recommendations. This study aims (1) to assess the individual need for prevention or rehabilitation based on preventive health examinations compared to a questionnaire survey, (2) to assess the results of the preventive health examinations compared to the Risk Index – Disability Pension (RI-DP), (3) to assess the results of the questionnaire survey compared to the RI-DP, (4) to assess the general health status of the sample (target population &gt; 1,000) in German employees aged 45–59, (5) to identify the most common medical conditions. A further study question aims, and (6) to investigate the general health status of the specific occupational groups.MethodsComprehensive diagnostics including medical examination, anamnesis, anthropometric measurements, bioelectrical impedance analysis (BIA), handgrip strength, resting electrocardiogram (ECG), resting blood pressure, pulse wave velocity (PWV), and laboratory blood analyses added by a questionnaire are conducted. The research questions are analyzed in an exploratory manner.Results and conclusionWe expect that the results will allow us to formulate recommendations regarding screening for prevention and rehabilitation needs on a more evidence-based level.Clinical Trial Registration: DRKS ID: DRKS00030982.
Repurposing agricultural waste as low-cost cultured meat scaffolds
Authors: Perreault Luke R. , Thyden Richard , Kloster Jack , Jones Jordan D. , Nunes Jordan , Patmanidis Andriana A. , Reddig David , Dominko Tanja , Gaudette Glenn R. 
Published: June 2023

Growing meat in vitro using tissue engineering and bioproduction techniques (cellular agriculture) has become an increasingly promising solution to the global food security challenge. Our lab has established methods to cultivate bovine muscle tissue on decellularized plants, representing a viable low-cost, sustainable method to grow meat on edible scaffolds. Most work in this area has focused on the use of edible plant materials (i.e., spinach leaves, apple, broccoli) with inherent economic value. Harvest waste such as corn husk or jackfruit represent abundant sources of cellulose for scaffold production and may be a viable alternative. The present study aims to investigate production of cultured meat through tissue engineering and bioproduction on decellularized, edible samples of corn husk and jackfruit rind. Corn husks and jackfruit rinds were exposed to immersion decellularization. DNA quantification and histological analysis demonstrated sufficient decellularization (0.17 ± 0.06 and 0.07 ± 0.00 ug DNA/g tissue for corn husk and jackfruit rinds, respectively). Following decellularization, corn husk scaffold stiffnesses decreased from 56.67±16.71 MPa to 12.95±2.43 MPa in fiber-aligned direction, while jackfruit decreased from 7.54 ±2.42 MPa to 2.47±1.47 MPa. Seeded scaffolds with bovine satellite cells (BSCs) (11.45±2.24 ug/ul lysate/Gram) and avian (QM7s) (12.90±1.99 ug/ul lysate/Gram) demonstrated increased protein yields on jackfruit scaffolds. QM7 cultured on corn husk scaffolds yielded increased protein but PBSCs seeded on corn husks did not yield protein content higher than controls (QM7 on corn husk: 16.28±3.55, PBSCs on corn husks: 9.57±1.56 ug/ul lysate/Gram, control: 6.35±1.43 ug/ul lysate/Gram). Additionally, cell transfer from scaffold to scaffold (bead-to-bead transfer) was observed on corn husk scaffolds in a dynamic environment. These results suggest that decellularized harvest waste scaffolds may aid in realization of cultured meat products that will contribute to a more robust and environmentally sustainable food supply.
How green is an urban tree? The impact of species selection in reducing the carbon footprint of park trees in Swedish cities
Authors: Lind Erik , Prade Thomas , Sjöman Deak Johanna , Levinsson Anna , Sjöman Henrik 
Published: June 2023

IntroductionPlanting trees in urban areas can mitigate some of the emissions generated in cities by carbon sequestration (annual uptake of CO2 through the process of photosynthesis) and carbon storage (amount of carbon stored in the tree's biomass throughout its lifespan). The aim of this study was to calculate the carbon footprint from nursery production to final establishment of different tree species grown for planting in urban parks in a northern European context.Material and methodsThe analysis included a cradle-to-gate approach and investigated the amount of carbon the adult trees needed to sequester in order to compensate for initial carbon emissions and which temporal perspectives are of concern. Greenhouse gas emissions were estimated based on an inventory of consumption of fuels, energy, materials and other production inputs during cultivation, delivery, planting and establishment of three different tree species in three different locations in Sweden. The tree species considered in the analysis (Salix alba, Quercus rubra, Pinus sylvestris) were selected due to significant differences in their growth rates. Salix alba is a competitive strategist in resource-rich habitats, and is proficient at converting these resources into vigorous growth. Pinus sylvestris is a pronounced stress strategist with good ability to handle resource-limited habitats, and invests in traits accordingly, resulting in significantly slower development. Quercus rubra has its main distribution in cool and moderately resource-rich habitats, but has relatively high stress tolerance and can be considered intermediate between the other two species in terms of growth rate.Results and discussionThe results showed that within 16 years of planting, all species in all three cities, except Pinus sylvestris planted in Umeå, compensated for initial carbon emissions, i.e. showed net absorption of CO2 after emissions from cultivation, delivery, planting and establishment of the trees had been deducted. There was a clear link between the time by which compensation of initial carbon emissions was achieved and growth rate of the different species, with the fast-growing Salix alba showing the best results. The single largest source of emissions among all activities carried out during cultivation, delivery and planting of all species, regardless of the city in which they were planted, was fuel consumption during tree planting.