bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multilocus sequence analysis for the taxonomic updating and identification of the genus Proteus and reclassification of Proteus genospecies 5 O’Hara et al. 2000, Proteus cibarius Hyun et al. 2016 as later heterotypic synonyms of Proteus terrae Behrendt et al. 2015
Authors: Dai Hang , Lu Binghuai , Li Zhenpeng , Huang Zhenzhou , Cai Hongyan , Yu Keyi , Wang Duochun 
Published: June 2020

Abstract
Background
Members of the genus Proteus are mostly opportunistic pathogens that cause a variety of infections in humans. The molecular evolutionary characteristics and genetic relationships among Proteus species have not been elucidated to date. In this study, we developed a multilocus sequence analysis (MLSA) approach based on five housekeeping genes (HKGs) to delineate phylogenetic relationships of species within the genus Proteus.

Results
Of all 223 Proteus strains collected in the current study, the phylogenetic tree of five concatenated HKGs (dnaJ, mdh, pyrC, recA and rpoD) divided 223 strains into eleven clusters, which were representative of 11 species of Proteus. Meanwhile, the phylogenetic trees of the five individual HKGs also corresponded to that of the concatenated tree, except for recA, which clustered four strains at an independent cluster. The evaluation of inter- and intraspecies distances of HKG concatenation indicated that all interspecies distances were significantly different from intraspecies distances, which revealed that these HKG concatenations can be used as gene markers to distinguish different Proteus species. Further web-based DNA-DNA hybridization estimated by genome of type strains confirmed the validity of the MLSA, and each of eleven clusters was congruent with the most abundant Proteus species. In addition, we used the established MLSA method to identify the randomly collected Proteus and found that P. mirabilis is the most abundant species. However, the second most abundant species is P. terrae but not P. vulgaris. Combined with the genetic, genomic and phenotypic characteristics, these findings indicate that three species, P. terrae, P. cibarius and Proteus genospecies 5, should be regarded as heterotypic synonyms, and the species should be renamed P. terrae, while Proteus genospecies 5 has not been named to date.

Conclusions
This study suggested that MLSA is a powerful method for the discrimination and classification of Proteus at the species level. The MLSA scheme provides a rapid and inexpensive means of identifying Proteus strains. The identification of Proteus species determined by the MLSA approach plays an important role in the clinical diagnosis and treatment of Proteus infection.
Transcriptome and metabolite analysis reveal the drought tolerance of foxtail millet significantly correlated with phenylpropanoids-related pathways during germination process under PEG stress
Authors: Yu Aili , Zhao Jinfeng , Wang Zhenhua , Cheng Kai , Zhang Peng , Tian Gang , Liu Xin , Guo Erhu , Du Yanwei , Wang Yuwen 
Published: June 2020

Abstract
Background
Foxtail millet [Setaria italica (L.) P. Beauv.] is an excellent crop known for its superior level of drought tolerance across the world. Especially, less water is needed during its germination period than the other cereal crops. However, the knowledge of the mechanisms underlying the abiotic stress effects on seed germination of foxtail millet is largely unknown.

Results
The water uptake pattern of foxtail millet seeds was ploted during germination period, according to which the germination time course of millet was separated into three phases. We sequenced the transcriptome of foxtail millet seeds, which were treated by PEG during different germination phases after sowing. The transcriptional studies revealed that more DEGs were identified during the further increase in water uptake period (phase III) than during the rapid initial uptake period (phase I) and the plateau period (phase II) under PEG stress. The pathway analysis of DEGs showed that the highly enriched categories were related to phenylpropanoid biosynthesis, plant hormone signal transduction and phenylalanine metabolism during phase III. The 20 phenylpropanoids-related genes of germinating foxtail millet were found to be down-regulated during the further increase in water uptake period under PEG stress. Further expression analysis identified 4 genes of phenylalanine ammonia-lyase, 4-coumarate-CoA ligase 3, cinnamoyl-CoA reductase 1, cationic peroxidase SPC4 in phenylpropanoids-related pathway, which played important roles in foxtail millet in response to PEG stress during different germination periods. The studies of metabolites in phenylpropanoid biosynthesis pathway revealed that higher amount of cinnamic acid was accumulated in germinating seeds under PEG stress, while the contents of p-coumaric acid, caffeic acid, ferulic acid and sinapic acid were decreased. And the effects of five phenolic compounds on germination and growth of foxtail millet showed that 1 mM concentration of cinnamic acid inhibited shoot and root growth, especially root development. Ferulic acid, caffeic acid, sinapic acid and p-coumaric acid could increase the root length and root/sprout in lower concentration.

Conclusions
These findings suggest that key genes and metabolites of foxtail millet related with phenylpropanoids pathway may play prominent roles in the regulation of resistance to drought during germination. Foxtail millet can probably avoid drought by regulating the levels of endogenous allelochemicals.
Mining the stable quantitative trait loci for agronomic traits in wheat (Triticum aestivum L.) based on an introgression line population
Authors: Chen Weiguo , Sun Daizhen , Li Runzhi , Wang Shuguang , Shi Yugang , Zhang Wenjun , Jing Ruilian 
Published: June 2020

Abstract
Background
Human demand for wheat will continue to increase together with the continuous global population growth. Agronomic traits in wheat are susceptible to environmental conditions. Therefore, in breeding practice, priority is given to QTLs of agronomic traits that can be stably detected across multiple environments and over many years.

Results
In this study, QTL analysis was conducted for eight agronomic traits using an introgression line population across eight environments (drought stressed and well-watered) for 5 years. In total, 44 additive QTLs for the above agronomic traits were detected on 15 chromosomes. Among these, qPH-6A, qHD-1A, qSL-2A, qHD-2D and qSL-6A were detected across seven, six, five, five and four environments, respectively. The means in the phenotypic variation explained by these five QTLs were 12.26, 9.51, 7.77, 7.23, and 8.49%, respectively.

Conclusions
We identified five stable QTLs, which includes qPH-6A, qHD-1A, qSL-2A, qHD-2D and qSL-6A. They play a critical role in wheat agronomic traits. One of the dwarf genes Rht14, Rht16, Rht18 and Rht25 on chromosome 6A might be the candidate gene for qPH-6A. The qHD-1A and qHD-2D were novel stable QTLs for heading date and they differed from known vernalization genes, photoperiod genes and earliness per se genes.
Prognosis evaluation of universal acute coronary syndrome: the interplay between SYNTAX score and ApoB/ApoA1
Authors: Wang Xiaotong , Wang Zhongyu , Li Bing , Yang Ping 
Published: June 2020

Abstract
Background
Acute coronary syndrome (ACS) is a group of clinical syndromes associated with substantial morbidity and mortality rate. SYNTAX and SYNTAX II score used to be a reference for surgical selection of coronary revascularization and prognosis evaluation in patients with 3-vessel or left main artery disease. In addition, apoB/apoA1 is an important predictor of ACS risk. This study aims to assess the prognosis value of different kinds of SYNTAX score together with apoB/apoA1 in universal ACS patients (Regardless of ACS type, lesion location and vessel numbers).

Method
Three hundred ninety-six patients with ACS undergoing percutaneous coronary intervention(PCI)and coronary stenting from 2013 to 2014 were chosen and recorded the major adverse cardiovascular and cerebrovascular events (MACCE) and quality of life during the next 5 years. According to SYNTAX and SYNTAX II score, the patients were divided into low-risk, medium-risk and high-risk groups, and the clinical features, MACCE incidence and EQ-5D score at each time points were compared. And the predictive factors of MACCE incidence were analyzed.

Results
① Compared with SYNTAX low-risk group, MACCE incidence in 1 year significantly increased in medium/high risk group (p = 0.011). Compared with SYNTAX II low-risk group, MACCE incidence in 5 years significantly increased in medium and high-risk group (p = 0.032). ② Compared with SYNTAX II low-risk group, cardiovascular mortality in 3 and 5 years significantly elevated in high-risk group (p = 0.001, p<0.001 respectively). ③ Compared with SYNTAX II low and medium-risk group, EQ-5D score in 5 years significantly decreased in high-risk group (p = 0.019, p = 0.023 respectively). ④ ApoB/ApoA1 was more likely to be classified as high risk in SYNTAX/SYNTAX II medium and high-risk group (p = 0.023, p = 0.044 respectively). ⑤ Logistic regression analysis showed that apoB/apoA1 was an independent predictor of MACCE events in hospital and 5 years (p = 0.038, p = 0.016 respectively), SYNTAX score was an independent predictor of MACCE events in 1 year (medium-risk group: p = 0.02; high-risk group: p = 0.015) SYNTAX II score was an independent predictor of MACCE events in 5 yeasrs (p = 0.003).

Conclusions
① SYNTAX score has a high predictive value for short-term prognosis while SYNTAX II score is more predictive of long-term prognosis. ② SYNTAX II score is superior to SYNTAX score in predicting cardiovascular death. ③ The combination of apoB/apoA1 high-risk and SYNTAX II medium and high-risk group is the focus of clinical treatment and long-term follow-up observation.
Laplace approximation, penalized quasi-likelihood, and adaptive Gauss–Hermite quadrature for generalized linear mixed models: towards meta-analysis of binary outcome with sparse data
Authors: Ju Ke , Lin Lifeng , Chu Haitao , Cheng Liang-Liang , Xu Chang 
Published: June 2020

AbstractBackgroundIn meta-analyses of a binary outcome, double zero events in some studies cause a critical methodology problem. The generalized linear mixed model (GLMM) has been proposed as a valid statistical tool for pooling such data. Three parameter estimation methods, including the Laplace approximation (LA), penalized quasi-likelihood (PQL) and adaptive Gauss–Hermite quadrature (AGHQ) were frequently used in the GLMM. However, the performance of GLMM via these estimation methods is unclear in meta-analysis with zero events.MethodsA simulation study was conducted to compare the performance. We fitted five random-effects GLMMs and estimated the results through the LA, PQL and AGHQ methods, respectively. Each scenario conducted 20,000 simulation iterations. The data from Cochrane Database of Systematic Reviews were collected to form the simulation settings. The estimation methods were compared in terms of the convergence rate, bias, mean square error, and coverage probability.ResultsOur results suggested that when the total events were insufficient in either of the arms, the GLMMs did not show good point estimation to pool studies of rare events. The AGHQ method did not show better properties than the LA estimation in terms of convergence rate, bias, coverage, and possibility to produce very large odds ratios. In addition, although the PQL had some advantages, it was not the preferred option due to its low convergence rate in some situations, and the suboptimal point and variance estimation compared to the LA.ConclusionThe GLMM is an alternative for meta-analysis of rare events and is especially useful in the presence of zero-events studies, while at least 10 total events in both arms is recommended when employing GLMM for meta-analysis. The penalized quasi-likelihood and adaptive Gauss–Hermite quadrature are not superior to the Laplace approximation for rare events and thus they are not recommended.
Including ‘seldom heard’ views in research: opportunities, challenges and recommendations from focus groups with British South Asian people with type 2 diabetes
Authors: Prinjha Suman , Miah Nasima , Ali Ebrahim , Farmer Andrew 
Published: June 2020

Abstract
Background
The inclusion of ‘seldom heard’ groups in health and social care research is increasingly seen as important on scientific, policy and ethical grounds. British South Asians, the largest minority ethnic group in the United Kingdom (UK), are under-represented in health research yet over-represented in the incidence of certain conditions such as type 2 diabetes. With the growing requirement of patient involvement in research and the inclusion of diverse populations, methodological guidance on how to include, engage and conduct research with UK South Asian populations is essential if services and interventions are to be relevant and impactful. However, such guidance for researchers is limited.

Methods
The aim of the paper is to reflect on our experiences of conducting focus groups with UK South Asian communities with type 2 diabetes, which involved experienced community partners and researchers working closely together. We discuss the factors that aided the successful delivery of the project, the challenges that we encountered, how we dealt with these, and recommendations.

Results
Our study suggests ways to involve and conduct focus groups with UK South Asian populations. Key considerations are categorised under four headings: co-working with community partners; linguistic competency; cultural competency and awareness; and reflexivity, power and acknowledgement. Having an experienced team of researchers and community experts – with the relevant linguistic and cultural competencies and different kinds of knowledge and skills – was key to the successful delivery of the study. Working collaboratively enabled us to recruit a diverse sample, to navigate the challenges of recruitment, to be present at every discussion which helped contribute to data richness, and to reflect on our own roles in the research process.

Conclusions
Focus groups with UK South Asian communities can be a useful way of exploring new topics and involving seldom heard views. While a useful method, focus groups are only one way of exploring a research topic and provide an insight into context-specific attitudes and views. Future research should explore British South Asian participants’ views on how they would like to be involved in research, including new methods of collecting data and coproducing research.
Symptom management strategies used by older community-dwelling people with multimorbidity and a high symptom burden - a qualitative study
Authors: Eckerblad Jeanette , Waldréus Nana , Stark Åsa Johansson , Jacobsson Lisa Ring 
Published: June 2020

Abstract
Background
Older community-dwelling people with multimorbidity are often not only vulnerable, but also suffer from several conditions that could produce a multiplicity of symptoms. This results in a high symptom burden and a reduced health-related quality of life. Even though these individuals often have frequent contact with healthcare providers they are expected to manage both appropriate disease control and symptoms by themselves or with the support of caregivers. The aim of this study was therefore to describe the symptom management strategies used by older community-dwelling people with multimorbidity and a high symptom burden.

Method
A qualitative descriptive design using face-to-face interviews with 20 community-dwelling older people with multimorbidity, a high healthcare consumption and a high symptom burden. People ≥75 years, who had been hospitalized ≥3 times during the previous year, ≥ 3 diagnoses in their medical records and lived at home were included. The participants were between 79 and 89 years old. Data were analysed using content analyses.

Result
Two main strategy categories were found: active symptom management and passive symptom management. The active strategies include the subcategories; to plan, to distract, to get assistance and to use facilitating techniques. An active strategy meant that participants took matters in their own hands, they could often describe the source of the symptoms and they felt that they had the power to do something to ease their symptoms. A passive symptom management strategy includes the subcategories to give in and to endure. These subcategories often reflected an inability to describe the source of the symptoms as well as the experience of having no alternative other than passively waiting it out.

Conclusions
These findings show that older people with multimorbidity and a high symptom burden employ various symptom management strategies on daily basis. They had adopted appropriate strategies based on their own experience and knowledge. Healthcare professionals might facilitate daily life for older people with multimorbidity by providing guidance on active management strategies with focus on patient’s own experience and preferences.
Influx of diverse, drug resistant and transmissible Plasmodium falciparum into a malaria-free setting in Qatar
Authors: Al-Rumhi Abir , Al-Hashami Zainab , Al-Hamidhi Salama , Gadalla Amal , Naeem Raeece , Ranford-Cartwright Lisa , Pain Arnab , Sultan Ali A. , Babiker Hamza A. 
Published: June 2020

Abstract
Background
Successful control programs have impeded local malaria transmission in almost all Gulf Cooperation Council (GCC) countries: Qatar, Bahrain, Kuwait, Oman, the United Arab Emirates (UAE) and Saudi Arabia. Nevertheless, a prodigious influx of imported malaria via migrant workers sustains the threat of local transmission. Here we examine the origin of imported malaria in Qatar, assess genetic diversity and the prevalence of drug resistance genes in imported Plasmodium falciparum, and finally, address the potential for the reintroduction of local transmission.

Methods
This study examined imported malaria cases reported in Qatar, between 2013 and 2016. We focused on P. falciparum infections and estimated both total parasite and gametocyte density, using qPCR and qRT-PCR, respectively. We also examined ten neutral microsatellites and four genes associated with drug resistance, Pfmrp1, Pfcrt, Pfmdr1, and Pfkelch13, to assess the genetic diversity of imported P. falciparum strains, and the potential for propagating drug resistance genotypes respectively.

Results
The majority of imported malaria cases were P. vivax, while P. falciparum and mixed species infections (P. falciparum / P. vivax) were less frequent. The primary origin of P. vivax infection was the Indian subcontinent, while P. falciparum was mostly presented by African expatriates. Imported P. falciparum strains were highly diverse, carrying multiple genotypes, and infections also presented with early- and late-stage gametocytes. We observed a high prevalence of mutations implicated in drug resistance among these strains, including novel SNPs in Pfkelch13.

Conclusions
The influx of genetically diverse P. falciparum, with multiple drug resistance markers and a high capacity for gametocyte production, represents a threat for the reestablishment of drug-resistant malaria into GCC countries. This scenario highlights the impact of mass international migration on the reintroduction of malaria to areas with absent or limited local transmission.
The correlations between Th1 and Th2 cytokines in human alveolar echinococcosis
Authors: Ma Xiao , Zhang Xuefei , Liu Jia , Liu Yufang , Zhao Cunzhe , Cai Huixia , Lei Wen , Ma Junying , Fan Haining , Zhou Jianye , Liu Na , Zhang Jingxiao , Wang Yongshun , Wang Wei , Zhan Peizhen , Zhang Xiongying , Zhang Qing , Shi Kemei , Liu Peiyun 
Published: June 2020

Abstract
Background
Alveolar echinococcosis (AE) is a zoonotic parasitic disease caused by Echinococcus multilocularis larval tapeworm infections in humans that severely impairs the health of affected patients in the northern hemisphere.

Methods
The expression levels of 20 cytokines associated with AE infection were measured by enzyme-linked immunosorbent assay, and the correlations between these cytokines were analysed in the R programming language.

Results
Serum cytokine levels differed among individuals in both the AE patient and healthy control groups. The results of the correlations among the cytokines showed obvious differences between the two groups. In the AE patients group, Th1 and Th2 cytokines formed a more complicated network than that in the healthy control group.

Conclusions
The altered correlations between Th1 and Th2 cytokines may be closely associated with AE infection, which may provide a new explanation for the essential differences between AE patients and healthy individuals.
Clinical and computed tomography features of extended-spectrum β-lactamase-producing Klebsiella pneumoniae liver abscess
Authors: Ren Yue , Wang Hairui , Chang Zhihui , Liu Zhaoyu 
Published: June 2020

Abstract
Background
Klebsiella pneumoniae (KP) is the primary pathogen associated with pyogenic liver abscesses (PLAs). Moreover, there has been an increase in the proportion of extended-spectrum beta-lactamase (ESBL)-producing KP. However, the clinical and computed tomography (CT) features of liver abscesses caused by ESBL-producing KP have not been separately described. We aimed to compare the clinical and CT features present in patients with ESBL-producing and non-ESBL-producing KP as well as to determine the risk factors for ESBL-producing KP liver abscesses (KPLAs).

Methods
We performed a retrospective analysis of data obtained from the medical records of patients with a first episode of KPLA admitted to Shengjing Hospital of China Medical University between May 2015 and May 2019. We compared the clinical and CT features between patients with ESBL-producing and non-ESBL-producing KPLA.

Results
We enrolled 100 patients with KPLA (14 and 86 in the ESBL-producing and non-ESBL-producing groups, respectively). There was no significant between-group difference in the proportion of patients with comorbid diabetes (71.43% vs. 66.2%, p = 0.086). The ESBL-producing KPLA group had a greater proportion of patients with a history of biliary disease (78.57% vs. 26.74%, p < 0.001) and gastrointestinal malignancy (50% vs. 6.98%, p < 0.001). Multivariate regression analysis showed that a history of biliary disease was an independent risk factor for ESBL-producing KPLA. Compared with the non-ESBL-producing KPLA group, the ESBL-producing KPLA group had a significantly higher intensive care unit (ICU) admission rate (28.57% vs. 2.33%, p < 0.001). All ESBL-producing KP isolates were susceptible to carbapenems and amikacin. Only the presence of multiloculation on CT was found to be significantly different between the groups (50% vs. 82.56%, p = 0.012).

Conclusions
The presence of biliary disease was an independent risk factor for ESBL-producing KPLA. Patients with ESBL-producing KPLA had a higher ICU admission rate, with only half of patients having evidence of multiloculation on CT.