bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species
Authors: Nielsen Erica S. , Henriques Romina , Beger Maria , Toonen Robert J. , von der Heyden Sophie 
Published: September 2020

AbstractBackgroundAs global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species’ potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare putative environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin (Parechinus angulosus), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis).ResultsUsing pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, onlyS. granularisshowed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation inC. punctatusandP. angulosus. Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts forS. granularisandP. angulosus, but not forC. punctatus.ConclusionThe findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses may be better predictors of evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.
Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes
Authors: Duarte-Delgado Diana , Dadshani Said , Schoof Heiko , Oyiga Benedict C. , Schneider Michael , Mathew Boby , Léon Jens , Ballvora Agim 
Published: September 2020

AbstractBackgroundBread wheat is one of the most important crops for the human diet, but the increasing soil salinization is causing yield reductions worldwide. Improving salt stress tolerance in wheat requires the elucidation of the mechanistic basis of plant response to this abiotic stress factor. Although several studies have been performed to analyze wheat adaptation to salt stress, there are still some gaps to fully understand the molecular mechanisms from initial signal perception to the onset of responsive tolerance pathways. The main objective of this study is to exploit the dynamic salt stress transcriptome in underlying QTL regions to uncover candidate genes controlling salt stress tolerance in bread wheat. The massive analysis of 3′-ends sequencing protocol was used to analyze leave samples at osmotic and ionic phases. Afterward, stress-responsive genes overlapping QTL for salt stress-related traits in two mapping populations were identified.ResultsAmong the over-represented salt-responsive gene categories, the early up-regulation of calcium-binding and cell wall synthesis genes found in the tolerant genotype are presumably strategies to cope with the salt-related osmotic stress. On the other hand, the down-regulation of photosynthesis-related and calcium-binding genes, and the increased oxidative stress response in the susceptible genotype are linked with the greater photosynthesis inhibition at the osmotic phase. The specific up-regulation of some ABC transporters and Na+/Ca2+exchangers in the tolerant genotype at the ionic stage indicates their involvement in mechanisms of sodium exclusion and homeostasis. Moreover, genes related to protein synthesis and breakdown were identified at both stress phases. Based on the linkage disequilibrium blocks, salt-responsive genes within QTL intervals were identified as potential components operating in pathways leading to salt stress tolerance. Furthermore, this study conferred evidence of novel regions with transcription in bread wheat.ConclusionThe dynamic transcriptome analysis allowed the comparison of osmotic and ionic phases of the salt stress response and gave insights into key molecular mechanisms involved in the salt stress adaptation of contrasting bread wheat genotypes. The leveraging of the highly contiguous chromosome-level reference genome sequence assembly facilitated the QTL dissection by targeting novel candidate genes for salt tolerance.
Comparative analysis of maca (Lepidium meyenii) proteome profiles reveals insights into response mechanisms of herbal plants to high-temperature stress
Authors: Wang Zhan Qi , Zhao Qi Ming , Zhong Xueting , Xiao Li , Ma Li Xuan , Wu Chou Fei , Zhang Zhongshan , Zhang Li Qin , Tian Yang , Fan Wei 
Published: September 2020

AbstractBackgroundHigh-temperature stress (HTS) is one of the main environmental stresses that limit plant growth and crop production in agricultural systems. Maca (Lepidium meyenii) is an important high-altitude herbaceous plant adapted to a wide range of environmental stimuli such as cold, strong wind and UV-B exposure. However, it is an extremely HTS-sensitive plant species. Thus far, there is limited information about gene/protein regulation and signaling pathways related to the heat stress responses in maca. In this study, proteome profiles of maca seedlings exposed to HTS for 12 h were investigated using a tandem mass tag (TMT)-based proteomic approach.ResultsIn total, 6966 proteins were identified, of which 300 showed significant alterations in expression following HTS. Bioinformatics analyses indicated that protein processing in endoplasmic reticulum was the most significantly up-regulated metabolic pathway following HTS. Quantitative RT-PCR (qRT-PCR) analysis showed that the expression levels of 19 genes encoding proteins mapped to this pathway were significantly up-regulated under HTS. These results show that protein processing in the endoplasmic reticulum may play a crucial role in the responses of maca to HTS.ConclusionsOur proteomic data can be a good resource for functional proteomics of maca and our results may provide useful insights into the molecular response mechanisms underlying herbal plants to HTS.
A nationwide survey of intraoperative management for one-lung ventilation in Taiwan: time to accountable for diversity in protective lung ventilation
Authors: Kuo Chuan-Yi , Liu Ying-Tung , Chen Tzu-Shan , Lam Chen-Fuh , Wu Ming-Cheng 
Published: September 2020

Abstract
Background
There is a major paradigm shift for intraoperative mechanical ventilator support by the introduction of lung protective ventilation strategies to reduce postoperative pulmonary complications and improve overall clinical outcomes in non-thoracic surgeries. However, there is currently a lack of standardized practice guideline for lung protection during thoracic surgeries that require one-lung ventilation (OLV). This study aimed to collect the expert opinions of the thoracic anesthesiologists in perioperative care for OLV surgery in Taiwan.

Methods
This prospective cross-sectional study was undertaken in 16 tertiary hospitals in Taiwan from January to February 2019. A structured survey form was distributed across the participating hospitals and the thoracic anesthesiologists were invited to complete the form voluntarily. The survey form consisted of three parts, including the basic information of the institutional anesthesia care standards, ventilatory settings for a proposed patient receiving OLV surgery and expert opinions on OLV.

Results
A total of 71 thoracic anesthesiologists responded to the survey. Double-lumen tubes are the most commonly used (93.8%) airway devices for OLV. The most commonly recommended ventilator setting during OLV is a tidal volume of 6–7 ml/kg PBW (67.6%) and a PEEP level of 4–6 cmH2O (73.5%). Dual controlled ventilator modes are used by 44.1% of the anesthesiologists. During OLV, high oxygen fraction (FiO2 > 0.8) is more commonly supplemented to achieve an oxygen saturation higher than 94%. The consensus of anesthesiologists on the indices for lung protection in thoracic surgery is considerably low. Large majority of the anesthesiologists (91.5%) highly recommend that an international clinical practice guideline on the protective lung ventilation strategy for thoracic anesthesia should be established.

Conclusions
This study found that the thoracic anesthesiologists in Taiwan share certain common practices in ventilator support during OLV. However, they are concerned about the lack of fundamental clinical evidences to support the beneficial outcomes of the current lung protective strategies applicable to OLV. Large-scale trials are needed to form an evidence-based clinical practice guideline for thoracic anesthesia.
Investigation of the underlying genes and mechanism of familial hypercholesterolemia through bioinformatics analysis
Authors: Wang Dinghui , Liu Bin , Xiong Tianhua , Yu Wenlong , She Qiang 
Published: September 2020

Abstract
Background
Familial hypercholesterolemia (FH) is one of the commonest inherited metabolic disorders. Abnormally high level of low-density lipoprotein cholesterol (LDL-C) in blood leads to premature atherosclerosis onset and a high risk of cardiovascular disease (CVD). However, the specific mechanisms of the progression process are still unclear. Our study aimed to investigate the potential differently expressed genes (DEGs) and mechanism of FH using various bioinformatic tools.

Methods
GSE13985 and GSE6054 were downloaded from the Gene Expression Omnibus (GEO) database for bioinformatic analysis in this study. First, limma package of R was used to identify DEGs between blood samples of patients with FH and those from healthy individuals. Then, the functional annotation of DEGs was carried out by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and Gene Ontology (GO) analysis. Based on Search Tool for the Retrieval of Interacting Genes (STRING) tool, we constructed the Protein-Protein Interactions (PPIs) network among DEGs and mined the core genes as well.

Results
A total of 102 communal DEGs (49 up-regulated and 53 down-regulated) are identified in FH samples compared with control samples. The functional changes of DEGs are mainly associated with the focal adhere and glucagon signaling pathway. Ten genes (ITGAL, TLN1, POLR2A, CD69, GZMA, VASP, HNRNPUL1, SF1, SRRM2, ITGAV) were identified as core genes. Bioinformatic analysis showed that the core genes are mainly enriched in numerous processes related to cell adhesion, integrin-mediated signaling pathway and cell-matrix adhesion. In the transcription factor (TF) target regulating network, 219 nodes were detected, including 214 DEGs and 5 TFs (SP1, EGR3, CREB, SEF1, HOX13). In conclusion, the DEGs and hub genes identified in this study may help us understand the potential etiology of the occurrence and development of AS.

Conclusion
Up-regulated ITGAL, TLN1, POLR2A, VASP, HNRNPUL1, SF1, SRRM2, and down-regulated CD69, GZMA and ITGAV performed important promotional effects for the formation of atherosclerotic plaques those suffering from FH. Moreover, SP1, EGR3, CREB, SEF1 and HOX13 were the potential transcription factors for DEGs and could serve as underlying targets for AS rupture prevention. These findings provide a theoretical basis for us to understand the potential etiology of the occurrence and development of AS in FH patients and we may be able to find potential diagnostic and therapeutic targets.
Modeling socio-demographic and clinical factors influencing psychiatric inpatient service use: a comparison of models for zero-Inflated and overdispersed count data
Authors: Sharker Sharmin , Balbuena Lloyd , Marcoux Gene , Feng Cindy Xin 
Published: September 2020

AbstractBackgroundPsychiatric disorders may occur as a single episode or be persistent and relapsing, sometimes leading to suicidal behaviours. The exact causes of psychiatric disorders are hard to determine but easy access to health care services can help to reduce their severity. The aim of this study was to investigate the factors associated with repeated hospitalizations among the patients with psychiatric illness, which may help the policy makers to target the high-risk groups in a more focused manner.MethodsA large linked administrative database consisting of 200,537 patients with psychiatric diagnosis in the years of 2008-2012 was used in this analysis. Various counts regression models including zero-inflated and hurdle models were considered for analyzing the hospitalization rate among patients with psychiatric disorders within three months follow-up since their index visit dates. The covariates for this study consisted of socio-demographic and clinical characteristics of the patients.ResultsThe results show that the odds of hospitalization are significantly higher among registered Indians, male patients and younger patients. Hospitalization rate depends on the patients’ disease types. Having previously visited a general physician served a protective role for psychiatric hospitalization during the study period. Patients who had seen an outpatient psychiatrist were more likely to have a higher number of psychiatric hospitalizations. This may indicate that psychiatrists tend to see patients with more severe illnesses, who require hospital-based care for managing their illness.ConclusionsProviding easier access to registered Indian people and youth may reduce the need for hospital-based care. Patients with mental health conditions may benefit from greater and more timely access to primary care.
Extra-hepatic comorbidity burden significantly increases 90-day mortality in patients with cirrhosis and high model for endstage liver disease
Authors: Coppel Scott , Mathur Karan , Ekser Burcin , Patidar Kavish R. , Orman Eric , Desai Archita P. , Vilar-Gomez Eduardo , Kubal Chandrashekhar , Chalasani Naga , Nephew Lauren , Ghabril Marwan 
Published: September 2020

Abstract
Background
We examined how extra-hepatic comorbidity burden impacts mortality in patients with cirrhosis referred for liver transplantation (LT).

Methods
Adults with cirrhosis evaluated for their first LT in 2012 were followed through their clinical course with last follow up in 2019. Extra-hepatic comorbidity burden was measured using the Charlson Comorbidity Index (CCI). The endpoints were 90-day transplant free survival (Cox-Proportional Hazard regression), and overall mortality (competing risk analysis).

Results
The study included 340 patients, mean age 56 ± 11, 63% male and MELD-Na 17.2 ± 6.6. The CCI was 0 (no comorbidities) in 44%, 1–2 in 44% and > 2 (highest decile) in 12%, with no differences based on gender but higher CCI in patients with fatty and cryptogenic liver disease. Thirty-three (10%) of 332 patients not receiving LT within 90 days died. Beyond MELD-Na, the CCI was independently associated with 90-day mortality (hazard ratio (HR), 1.32 (95% confidence interval (CI) 1.02–1.72). Ninety-day mortality was specifically increased with higher CCI category and MELD ≥18 (12% (CCI = 0), 22% (CCI = 1–2) and 33% (CCI > 2), (p = 0.002)) but not MELD-Na ≤17. At last follow-up, 69 patients were alive, 100 underwent LT and 171 died without LT. CCI was associated with increased overall mortality in the competing risk analysis (Sub-HR 1.24, 95%CI 1.1–1.4).

Conclusions
Extra-hepatic comorbidity burden significantly impacts short-term mortality in patients with cirrhosis and high MELD-Na. This has implications in determining urgency of LT and mortality models in cirrhosis and LT waitlisting, especially with an ageing population with increasing prevalence of fatty liver disease.
Male gender and kidney illness are associated with an increased risk of severe laboratory-confirmed coronavirus disease
Authors: Murillo-Zamora Efrén , Trujillo Xóchitl , Huerta Miguel , Ríos-Silva Mónica , Mendoza-Cano Oliver 
Published: September 2020

AbstractBackgroundTo identify factors predicting severe coronavirus disease 2019 (COVID-19) in adolescent and adult patients with laboratory-positive (quantitative reverse-transcription polymerase chain reaction) infection.MethodA retrospective cohort study took place, and data from 740 subjects, from all 32 states of Mexico, were analyzed. The association between the studied factors and severe (dyspnea requiring hospital admission) COVID-19 was evaluated through risk ratios (RRs) and 95% confidence intervals (CIs).ResultsSevere illness was documented in 28% of participants. In multiple analysis, male gender (RR = 1.13, 95% CI 1.06–1.20), advanced age ([reference: 15–29 years old] 30–44, RR = 1.02, 95% CI 0.94–1.11; 45–59, RR = 1.26, 95% CI 1.15–1.38; 60 years or older, RR = 1.44, 95% CI 1.29–1.60), chronic kidney disease (RR = 1.31, 95% CI 1.04–1.64) and thoracic pain (RR = 1.16, 95% CI 1.10–1.24) were associated with an increased risk of severe disease.ConclusionsTo the best of our knowledge, this is the first study evaluating predictors of COVID-19 severity in a large subset of the Latin-American population. Male gender and kidney illness were independently associated with the risk of severe COVID-19. These results may be useful for health care protocols for the early detection and management of patients that may benefit from opportune and specialized supportive medical treatment.
Neonatal septicemia caused by a rare pathogen: Raoultella planticola - a report of four cases
Authors: Chen Xianrui , Guo Shaoqing , Liu Dengli , Zhong Meizhen 
Published: September 2020

Abstract
Background
Raoultella planticola(R.planticola) is a very rare opportunistic pathogen and sometimes even associated with fatal infection in pediatric cases. Recently,the emergence of carbapenem resistance strains are constantly being reported and a growing source of concern for pediatricians.

Case presentation
We reported 4 cases of neonatal septicemia caused by Raoultella planticola. Their gestational age was 211 to 269 days, and their birth weight was 1490 to 3000 g.The R. planticola infections were detected on the 9th to 27th day after hospitalization and occured between May and June. They clinically manifested as poor mental response, recurrent cyanosis, apnea, decreased heart rate and blood oxygen, recurrent jaundice, fever or nonelevation of body temperature. The C-reactive protein and procalcitonin were elevated at significantly in the initial phase of the infection,and they had leukocytosis or leukopenia. Prior to R.planticola infection,all of them recevied at least one broad-spectrum antibiotic for 7-27d.All the R.planticola strains detected were only sensitive to amikacin, but resistant to other groups of drugs: cephalosporins (such as cefazolin, ceftetan,etc) and penicillins (such as ampicillin-sulbactam,piperacillin,etc),and even developed resistance to carbapenem. All the infants were clinically cured and discharged with overall good prognosis.

Conclusion
Neonatal septicemia caused by Raoultella planticola mostly occured in hot and humid summer, which lack specific clinical manifestations. Pediatricians should keep in mind that R. planticola can be a potential source of neonatal sepsis and even has the potential to acquire carbapenem-resistance. Preventing outbreaks of epidemics requires early detection, timely diagnosis and treatment, and active isolation.
Recovery of mobility function and life-space mobility after ischemic stroke: the MOBITEC-Stroke study protocol
Authors: Rössler R. , Bridenbaugh S. A. , Engelter S. T. , Weibel R. , Infanger D. , Giannouli E. , Sofios A. , Iendra L. , Portegijs E. , Rantanen T. , Streese L. , Hanssen H. , Roth R. , Schmidt-Trucksäss A. , Peters N. , Hinrichs T. 
Published: September 2020

Abstract
Background
Stroke is a major cause of disability and stroke incidence increases with age. Stroke frequently results in permanent limitations of mobility, and, consequently, the need for the help of others in activities of daily living. In order to optimize rehabilitative efforts and their functional outcomes, detailed knowledge of the functional recovery process, regarding mobility, is needed. Objectives of the MOBITEC-Stroke study are: 1.) To characterize mobility, including lower extremity physical function (LEPF) and life space (the geospatial extent of all of a person’s movements), and changes in mobility within the first year after stroke. 2.) To identify and characterize subgroups with different mobility trajectories. 3.) To evaluate whether changes in LEPF are associated with changes in life-space. 4.) To evaluate participants’ reasons for going outdoors, transportation use, and assistance needed for outdoor movement.

Methods
Patients with incident first stroke who live in their own homes (target N = 59, based on sample size calculation) will be included in this cohort study. At 3, 6, 9, and 12 months after stroke a battery of mobility tests will be performed at the study centre, including laboratory-based tests of balance and strength, and quantitative gait analysis. Life-space assessment (including 1-week GPS measurements) will be performed in participants’ real life. Semantic information on visited locations (reasons for going outdoors, transportation use, assistance needed) will be collected by using interactive digital maps. Linear mixed effects models will be used to model the trajectories of mobility measures for the total sample and for predefined subgroups. As an exploratory analysis, growth mixture models (GMMs) will be used to identify relevant subgroups with different trajectories. Linear mixed effect models will be used to test whether changes in LEPF parameters are associated with changes in life-space. Participants’ motivation for going outdoors, transportation use, and assistance needed for outdoor mobility will be analysed descriptively.

Discussion
A comprehensive and detailed knowledge of recovery patterns will enable the planning of targeted and adaptively tailored rehabilitation measures. Information about patients’ reasons for outdoor mobility will provide the opportunity to define individualized and patient-oriented rehabilitation goals.

Trial registration
ISRCTN85999967 (on 13 August 2020; retrospectively).