bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole genomic comparative analysis of Streptococcus pneumoniae serotype 1 isolates causing invasive and non-invasive infections among children under 5 years in Casablanca, Morocco
Authors: Nzoyikorera Néhémie , Diawara Idrissa , Fresia Pablo , Maaloum Fakhreddine , Katfy Khalid , Nayme Kaotar , Maaloum Mossaab , Cornick Jennifer , Chaguza Chrispin , Timinouni Mohammed , Belabess Houria , Zerouali Khalid , Elmdaghri Naima 
Published: January 2021

Abstract
Background
Streptococcus pneumoniae serotype 1 remains a leading cause of invasive pneumococcal diseases, even in countries with PCV-10/PCV-13 vaccine implementation. The main objective of this study, which is part of the Pneumococcal African Genome project (PAGe), was to determine the phylogenetic relationships of serotype 1 isolates recovered from children patients in Casablanca (Morocco), compared to these from other African countries; and to investigate the contribution of accessory genes and recombination events to the genetic diversity of this serotype.

Results
The genome average size of the six-pneumococcus serotype 1 from Casablanca was 2,227,119 bp, and the average content of coding sequences was 2113, ranging from 2041 to 2161. Pangenome analysis of the 80 genomes used in this study revealed 1685 core genes and 1805 accessory genes. The phylogenetic tree based on core genes and the hierarchical bayesian clustering analysis revealed five sublineages with a phylogeographic structure by country. The Moroccan strains cluster in two different lineages, the five invasive strains clusters altogether in a divergent clade distantly related to the non-invasive strain, that cluster with all the serotype 1 genomes from Africa.

Conclusions
The whole genome sequencing provides increased resolution analysis of the highly virulent serotype 1 in Casablanca, Morocco. Our results are concordant with previous works, showing that the phylogeography of S. pneumoniae serotype 1 is structured by country, and despite the small size (six isolates) of the Moroccan sample, our analysis shows the genetic cohesion of the Moroccan invasive isolates.
Analysis across diverse fish species highlights no conserved transcriptome signature for proactive behaviour
Authors: Rey Sonia , Jin Xingkun , Damsgård Børge , Bégout Marie-Laure , Mackenzie Simon 
Published: January 2021

Abstract
Background
Consistent individual differences in behaviour, known as animal personalities, have been demonstrated within and across species. In fish, studies applying an animal personality approach have been used to resolve variation in physiological and molecular data suggesting a linkage, genotype-phenotype, between behaviour and transcriptome regulation. In this study, using three fish species (zebrafish; Danio rerio, Atlantic salmon; Salmo salar and European sea bass; Dicentrarchus labrax), we firstly address whether personality-specific mRNA transcript abundances are transferrable across distantly-related fish species and secondly whether a proactive transcriptome signature is conserved across all three species.

Results
Previous zebrafish transcriptome data was used as a foundation to produce a curated list of mRNA transcripts related to animal personality across all three species. mRNA transcript copy numbers for selected gene targets show that differential mRNA transcript abundance in the brain appears to be partially conserved across species relative to personality type. Secondly, we performed RNA-Seq using whole brains from S. salar and D. labrax scoring positively for both behavioural and molecular assays for proactive behaviour. We further enriched this dataset by incorporating a zebrafish brain transcriptome dataset specific to the proactive phenotype. Our results indicate that cross-species molecular signatures related to proactive behaviour are functionally conserved where shared functional pathways suggest that evolutionary convergence may be more important than individual mRNAs.

Conclusions
Our data supports the proposition that highly polygenic clusters of genes, with small additive effects, likely support the underpinning molecular variation related to the animal personalities in the fish used in this study. The polygenic nature of the proactive brain transcriptome across all three species questions the existence of specific molecular signatures for proactive behaviour, at least at the granularity of specific regulatory gene modules, level of genes, gene networks and molecular functions.
Antimicrobial activity screening of rhizosphere soil bacteria from tomato and genome-based analysis of their antimicrobial biosynthetic potential
Authors: Zhou Lu , Song Chunxu , Li Zhibo , Kuipers Oscar P. 
Published: January 2021

Abstract
Background
Tomato plant growth is frequently hampered by a high susceptibility to pests and diseases. Traditional chemical control causes a serious impact on both the environment and human health. Therefore, seeking environment-friendly and cost-effective green methods in agricultural production becomes crucial nowadays. Plant Growth Promoting Rhizobacteria (PGPR) can promote plant growth through biological activity. Their use is considered to be a promising sustainable approach for crop growth. Moreover, a vast number of biosynthetic gene clusters (BGCs) for secondary metabolite production are being revealed in PGPR, which helps to find potential anti-microbial activities for tomato disease control.

Results
We isolated 181 Bacillus-like strains from healthy tomato, rhizosphere soil, and tomato tissues. In vitro antagonistic assays revealed that 34 Bacillus strains have antimicrobial activity against Erwinia carotovora, Pseudomonas syringae; Rhizoctonia solani; Botrytis cinerea; Verticillium dahliae and Phytophthora infestans. The genomes of 10 Bacillus and Paenibacillus strains with good antagonistic activity were sequenced. Via genome mining approaches, we identified 120 BGCs encoding NRPs, PKs-NRPs, PKs, terpenes and bacteriocins, including known compounds such as fengycin, surfactin, bacillibactin, subtilin, etc. In addition, several novel BGCs were identified. We discovered that the NRPs and PKs-NRPs BGCs in Bacillus species are encoding highly conserved known compounds as well as various novel variants.

Conclusions
This study highlights the great number of varieties of BGCs in Bacillus strains. These findings pave the road for future usage of Bacillus strains as biocontrol agents for tomato disease control and are a resource arsenal for novel antimicrobial discovery.
Plasma membrane vesicles from cauliflower meristematic tissue and their role in water passage
Authors: Garcia-Ibañez Paula , Nicolas-Espinosa Juan , Carvajal Micaela 
Published: January 2021

Abstract
Background
Cauliflower (Brassica oleracea L. var. botrytis) inflorescences are composed mainly of meristematic tissue, which has a high cellular proliferation. This considerable cellular density makes the inflorescence an organ with a large proportion of membranes. However, little is known about the specific role of the lipid and protein composition of the plasma membrane present in this organ.

Results
In this work, we analyzed the lipids and proteins present in plasma membrane from two different stages of development of cauliflower inflorescence and compared them with leaf plasma membrane. For this purpose, plasma membrane vesicles were obtained by centrifugation for each sample and the vesicular diameter and osmotic permeability (Pf) were analyzed by dynamic light scattering and the stopped-flow technique, respectively. In addition, fatty acids and sterols were analyzed by gas chromatography and HPLC. The protein composition of the inflorescences and leaves was characterized by HPLC-ESI-QTOF-MS and the data obtained were compared with Brassicaceae proteins present in the UniProt database in relation to the presence of aquaporins determined by western blot analysis. The highest Pf value was found in 90 day inflorescences-derived plasma membrane vesicles (61.4 ± 4.14 μms− 1). For sterols and fatty acids, the concentrations varied according to the organ of origin. The protein profile revealed the presence of aquaporins from the PIP1 and PIP2 subfamilies in both inflorescences and leaves.

Conclusion
This study shows that the composition of the sterols, the degree of unsaturation of the fatty acids, and the proteins present in the membranes analyzed give them high functionality for water passage. This represents an important addition to the limited information available in this field.
Genome-wide association study of yield and related traits in common wheat under salt-stress conditions
Authors: Hu Pan , Zheng Qi , Luo Qiaoling , Teng Wan , Li Hongwei , Li Bin , Li Zhensheng 
Published: January 2021

Abstract
Background
Soil salinization is a major threat to wheat production. It is essential to understand the genetic basis of salt tolerance for breeding and selecting new salt-tolerant cultivars that have the potential to increase wheat yield.

Result
In this study, a panel of 191 wheat accessions was subjected to genome wide association study (GWAS) to identify SNP markers linked with adult-stage characters. The population was genotyped by Wheat660K SNP array and eight phenotype traits were investigated under low and high salinity environments for three consecutive years. A total of 389 SNPs representing 11 QTLs were significantly associated with plant height, spike number, spike length, grain number, thousand kernels weight, yield and biological mass under different salt treatments, with the phenotypic explanation rate (R2) ranging from 9.14 to 50.45%. Of these, repetitive and pleiotropic loci on chromosomes 4A, 5A, 5B and 7A were significantly linked to yield and yield related traits such as thousand kernels weight, spike number, spike length, grain number and so on under low salinity conditions. Spike length-related loci were mainly located on chromosomes 1B, 3B, 5B and 7A under different salt treatments. Two loci on chromosome 4D and 5A were related with plant height in low and high salinity environment, respectively. Three salt-tolerant related loci were confirmed to be important in two bi-parental populations. Distribution of favorable haplotypes indicated that superior haplotypes of pleiotropic loci on group-5 chromosomes were strongly selected and had potential for increasing wheat salt tolerance. A total of 14 KASP markers were developed for nine loci associating with yield and related traits to improve the selection efficiency of wheat salt-tolerance breeding.

Conclusion
Utilizing a Wheat660K SNPs chip, QTLs for yield and its related traits were detected under salt treatment in a natural wheat population. Important salt-tolerant related loci were validated in RIL and DH populations. This study provided reliable molecular markers that could be crucial for marker-assisted selection in wheat salt tolerance breeding programs.
Characterization and functional analysis of phytoene synthase gene family in tobacco
Authors: Wang Zhaojun , Zhang Lin , Dong Chen , Guo Jinggong , Jin Lifeng , Wei Pan , Li Feng , Zhang Xiaoquan , Wang Ran 
Published: January 2021

Abstract
Background
Carotenoids play important roles in photosynthesis, hormone signaling, and secondary metabolism. Phytoene synthase (PSY) catalyzes the first step of the carotenoid biosynthetic pathway. In this study, we aimed to characterize the PSY genes in tobacco and analyze their function.

Results
In this study, we identified three groups of PSY genes, namely PSY1, PSY2, and PSY3, in four Nicotiana species; phylogenetic analysis indicated that these genes shared a high similarity with those in tomato but not with those in monocots such as rice and maize. The expression levels of PSY1 and PSY2 were observed to be highest in leaves compared to other tissues, and they could be elevated by treatment with certain phytohormones and exposure to strong light. No PSY3 expression was detected under these conditions. We constructed virus-induced PSY1 and PSY2 silencing in tobacco and found that the newly emerged leaves in these plants were characterized by severe bleaching and markedly decreased carotenoid and chlorophyll content. Thylakoid membrane protein complex levels in the gene-silenced plants were also less than those in the control plants. The chlorophyll fluorescence parameters such as Fv/Fm, ΦPSII, qP, and NPQ, which reflect photosynthetic system activities, of the gene-silenced plants were also significantly decreased. We further performed RNA-Seq and metabonomics analysis between gene-silenced tobacco and control plants. RNA-Seq results showed that abiotic stress, isoprenoid compounds, and amino acid catabolic processes were upregulated, whereas the biosynthesis of cell wall components was downregulated. Metabolic analysis results were consistent with the RNA-Seq. We also found the downstream genes in carotenoid biosynthesis pathways were upregulated, and putative transcription factors that regulate carotenoid biosynthesis were identified.

Conclusions
Our results suggest that PSY can regulate carotenoid contents not only by controlling the first biosynthesis step but also by exerting effects on the expression of downstream genes, which would thereby affect photosynthetic activity. Meanwhile, PSY may affect other processes such as amino acid catabolism and cell wall organization. The information we report here may aid further research on PSY genes and carotenoid biosynthesis.
The prevalence of hypercholesterolemia and associated risk factors in Al-Kharj population, Saudi Arabia: a cross-sectional survey
Authors: Al-Zahrani Jamaan , Shubair Mamdouh M. , Al-Ghamdi Sameer , Alrasheed Abdullah A. , Alduraywish Abdulrahman A. , Alreshidi Fayez Saud , Alshahrani Saeed Mastour , Alsalamah Majid , Al-Khateeb Badr F. , Ashathri Aljawharah Ibraheem , El-Metwally Ashraf , Aldossari Khaled K. 
Published: January 2021

Abstract
Background
Hypercholesterolemia (HC) is an important precursor to many cardiovascular, cerebrovascular, and peripheral vascular diseases. A report conducted by the American Heart Association showed the prevalence of HC to be 11.9%, with around 28.5 million adults age ≥ 20 years having high cholesterol levels. This study aimed to evaluate the prevalence of HC and its associated risk factors among the general population of Al-Kharj, Saudi Arabia.

Method
A cross-sectional study was conducted on the general population of Al-Kharj, Saudi Arabia in 2016. The representative sample consisted of 1019 individuals, who all participated on a voluntary basis. The statistical analysis was performed using SPSS version 25.

Results
The results of this study showed the prevalence of HC in the sample to be 12.5%. There was a significant moderate positive association between increasing age and the prevalence of HC (r = 0.240, P < 0.0001). Males had a significantly higher prevalence of HC (56.7%) compared to their female counterparts (43.3%) (X2 = 23.093, P ≤ 0.0001). BMI was positively and significantly associated with high cholesterol status. Participants in the overweight category had a significantly higher risk of HC (OR = 1.727; 95% CI = 1.58–1.914; P = 0.046). The non-obese (< 25 kg/m2) participants had an inverse significant association with the risk of hypercholesterolemia. (OR = 0.411; 95% CI = 0.216–0.783; P = 0.007).

Conclusion
In this population-based study, the predominant risk factors of HC in Al-Kharj region were being of a Saudi nationality, male, having obesity, being unemployed, and being a civilian worker. There is a clear need for future screening studies of HC, as most previous studies have reported contradictory prevalence data (because they were conducted in different regions of KSA). Furthermore, well-designed prospective cohort studies are needed in the future to assess how the association between lifestyle behavioural factors such as dietary intake patterns and levels of physical activity may affect the relative risk of HC status.
Health care providers’ perception of the frequent emergency department user issue and of targeted case management interventions: a cross-sectional national survey in Switzerland
Authors: Chastonay Oriane J. , Lemoine Melissa , Grazioli Véronique S. , Canepa Allen Marina , Kasztura Miriam , Moullin Joanna C. , Daeppen Jean-Bernard , Hugli Olivier , Bodenmann Patrick 
Published: January 2021

AbstractBackgroundFrequent users of emergency departments (FUEDs) (≥5 ED visits/year) represent a vulnerable population with complex needs accounting for a significant number of emergency department (ED) consultations, thus contributing to EDs overcrowding. Research exploring ED staff perceptions of FUEDs is scarce.ObjectivesThe current study aimed to evaluate in ED staff a) the extent to which FUEDs are perceived as an issue; b) their perceived levels of knowledge and understanding of FUEDs; c) levels of perceived usefulness of case management (CM) and interest in implementing this intervention in their ED service.MethodsHead physicians of the EDs at all public hospitals in Switzerland (of various level of specialization) were sent a 19-item web-based survey, pilot tested prior to its dissemination. The head physicians were asked to forward the survey to ED staff members from different health professional backgrounds.ResultsThe hospital response rate was 81% (85/106). The exploitable hospital response rate was 71% (75/106 hospitals) including 208 responding health professionals. Issues and difficulties around FUEDs were perceived as important by 64% of respondents. The perceived frequency of being confronted with FUEDs was higher among nurses in more specialized EDs. In total, 64% of respondents felt poorly informed about FUEDs, nurses feeling less informed than physicians. The understanding of FUEDs was lower in the French-Italian-speaking parts (FISP) of Switzerland than in the German-speaking part. Eighty-one percent of respondents had no precise knowledge of FUED-related interventions. The perceived usefulness of CM interventions after receiving explanations about it was high (92%). However, the overall level of interest for CM implementation was 59%. The interest in CM by physicians was low across all regions and ED categories. Nurses, on the other hand, showed more interest, especially those in EDs of high specialization.ConclusionsThe majority of ED staff reported being confronted with FUEDs on a regular basis. Staff perceived FUEDs as a vulnerable population, yet, they felt poorly informed about how to manage the issue. The majority of ED staff thought a CM intervention would be useful for FUEDs, however there appears to be a gap in their desire or willingness to implement such interventions.
Sedation practices for routine gastrointestinal endoscopy: a systematic review of recommendations
Authors: Dossa Fahima , Megetto Olivia , Yakubu Mafo , Zhang David D. Q. , Baxter Nancy N. 
Published: January 2021

AbstractBackgroundSedation is commonly used in gastrointestinal endoscopy; however, considerable variability in sedation practices has been reported. The objective of this review was to identify and synthesize existing recommendations on sedation practices for routine gastrointestinal endoscopy procedures.MethodsWe systematically reviewed guidelines and position statements identified through a search of PubMed, guidelines databases, and websites of relevant professional associations from January 1, 2005 to May 10, 2019. We included English-language guidelines/position statements with recommendations relating to sedation for adults undergoing routine gastrointestinal endoscopy. Documents with guidance only for complex endoscopic procedures were excluded.We extracted and synthesized recommendations relating to: 1) choice of sedatives, 2) sedation administration, 3) personnel responsible for monitoring sedated patients, 4) skills and training of individuals involved in sedation, and 5) equipment required for monitoring sedated patients. We assessed the quality of included documents using the Appraisal of Guidelines for Research & Evaluation (AGREE) II tool.ResultsWe identified 19 guidelines and 7 position statements meeting inclusion criteria. Documents generally agreed that a single, trained registered nurse can administer moderate sedation, monitor the patient, and assist with brief, interruptible tasks. Documents also agreed on the routine use of pulse oximetry and blood pressure monitoring during endoscopy. However, recommendations relating to the drugs to be used for sedation, the healthcare personnel capable of administering propofol and monitoring patients sedated with propofol, and the need for capnography when monitoring sedated patients varied. Only 9 documents provided a grade or level of evidence in support of their recommendations.ConclusionsRecommendations for sedation practices in routine gastrointestinal endoscopy differ across guidelines/position statements and often lack supporting evidence with potential implications for patient safety and procedural efficiency.
Clinical features and outcomes of combined hepatocellular carcinoma and cholangiocarcinoma versus hepatocellular carcinoma versus cholangiocarcinoma after surgical resection: a propensity score matching analysis
Authors: Lin Chih-Wen , Wu Tsung-Chin , Lin Hung-Yu , Hung Chao-Ming , Hsieh Pei-Min , Yeh Jen-Hao , Hsiao Pojen , Huang Ya-Ling , Li Yu-Chan , Wang Ya-Chin , Shu Chih-Wen , Chen Yaw-Sen 
Published: January 2021

AbstractBackgroundCombined hepatocellular carcinoma and cholangiocarcinoma (cHCC-CC) is an infrequent type of primary liver cancer that comprises hepatocellular carcinoma (HCC) and cholangiocarcinoma (CC). This study investigated the clinicopathological features and prognosis among cHCC-CC, HCC, and CC groups.MethodsWe prospectively collected the data of 608 patients who underwent surgical resection for liver cancer between 2011 and 2018 at E-Da Hospital, I-Shou University, Kaohsiung, Taiwan. Overall, 505 patients with cHCC-CC, HCC, and CC were included, and their clinicopathological features, overall survival (OS), and recurrence were recorded. OS and recurrence rates were analyzed using the Kaplan–Meier analysis.ResultsIn the entire cohort, the median age was 61 years and 80% were men. Thirty-five (7.0%) had cHCC-CC, 419 (82.9%) had HCC, and 51 (10.1%) had CC. The clinicopathological features of the cHCC-CC group were more identical to those of the HCC group than the CC group. OS was significantly lower in the cHCC-CC group than in the HCC group but was not significantly higher in the cHCC-CC group than in the CC group. The median OS of cHCC-CC, HCC, and CC groups was 50.1 months [95% confidence interval (CI): 38.7–61.2], 62.3 months (CI: 42.1–72.9), and 36.2 months (CI: 15.4–56.5), respectively. Cumulative OS rates at 1, 3, and 5 years in cHCC-CC, HCC, and CC groups were 88.5%, 62.2%, and 44.0%; 91.2%, 76.1%, and 68.0%; and 72.0%, 48.1%, and 34.5%, respectively. After propensity score matching (PSM), OS in the cHCC-CC group was not significantly different from that in the HCC or CC group. However, OS was significantly higher in the HCC group than in the CC group before and after PSM. Furthermore, the disease-free survival was not significantly different among cHCC-CC, HCC, and CC groups before and after PSM.ConclusionThe clinicopathological features of the cHCC-CC group were more identical to those of the HCC group than the CC group. The OS rate was significantly lower in the cHCC-CC group than the HCC group. However, after PSM, OS and disease-free survival in the cHCC-CC group were not significantly different from those in the HCC or CC group.