bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification, evolution, expression, and docking studies of fatty acid desaturase genes in wheat (Triticum aestivum L.)
Authors: Hajiahmadi Zahra , Abedi Amin , Wei Hui , Sun Weibo , Ruan Honghua , Zhuge Qiang , Movahedi Ali 
Published: November 2020

AbstractBackgroundsFatty acid desaturases (FADs) introduce a double bond into the fatty acids acyl chain resulting in unsaturated fatty acids that have essential roles in plant development and response to biotic and abiotic stresses. Wheat germ oil, one of the important by-products of wheat, can be a good alternative for edible oils with clinical advantages due to the high amount of unsaturated fatty acids. Therefore, we performed a genome-wide analysis of the wheatFADgene family (TaFADs).Results68FADgenes were identified from the wheat genome. Based on the phylogenetic analysis, wheatFADsclustered into five subfamilies, includingFAB2,FAD2/FAD6,FAD4,DES/SLD, andFAD3/FAD7/FAD8. TheTaFADswere distributed on chromosomes 2A-7B with 0 to 10 introns. The Ka/Ks ratio was less than one for most of the duplicated pair genes revealed that the function of the genes had been maintained during the evolution. Several cis-acting elements related to hormones and stresses in theTaFADs promoters indicated the role of these genes in plant development and responses to environmental stresses. Likewise, 72 SSRs and 91 miRNAs in 36 and 47TaFADs have been identified. According to RNA-seq data analysis, the highest expression in all developmental stages and tissues was related toTaFAB2.5,TaFAB2.12,TaFAB2.15,TaFAB2.17,TaFAB2.20,TaFAD2.1,TaFAD2.6, andTaFAD2.8genes while the highest expression in response to temperature stress was related toTaFAD2.6,TaFAD2.8,TaFAB2.15,TaFAB2.17, andTaFAB2.20. Furthermore, docking simulations revealed several residues in the active site of TaFAD2.6 and TaFAD2.8 in close contact with the docked oleic acid that could be useful in future site-directed mutagenesis studies to increase the catalytic efficiency of them and subsequently improve agronomic quality and tolerance of wheat against environmental stresses.ConclusionsThis study provides comprehensive information that can lead to the detection of candidate genes for wheat genetic modification.
Genome-wide survey of sucrose non-fermenting 1-related protein kinase 2 in Rosaceae and expression analysis of PbrSnRK2 in response to ABA stress
Authors: Chen Guodong , Wang Jizhong , Qiao Xin , Jin Cong , Duan Weike , Sun Xiaochuan , Wu Juyou 
Published: November 2020

Abstract

Background
The members of the sucrose non-fermenting 1-related protein kinase 2 (SnRK2) family are specific serine/threonine protein kinases in plants that play important roles in stress signal transduction and adaptation. Because of their positive regulatory roles in response to adverse conditions, the genes encoding thes proteins are considered potential candidates for breeding of plants for disease resistance and genetic improvement. However, there is far less information about this kinase family, and the function of these genes has not been explored in Rosaceae.

Results
A genome-wide survey and analysis of the genes encoding members of the SnRK2 family were performed in pear (Pyrus bretschneideri) and seven other Rosaceae species. A total of 71 SnRK2 genes were identified from the eight Rosaceae species and classified into three subgroups based on phylogenetic analysis and structural characteristics. Purifying selection played a crucial role in the evolution of SnRK2 genes, and whole-genome duplication and dispersed duplication were the primary forces underlying the characteristics of the SnRK2 gene family in Rosaceae. Transcriptome data and qRT-PCR assay results revealed that the distribution of PbrSnRK2s was very extensive, including across the roots, leaves, pollen, styles, and flowers, although most of them were mainly expressed in leaves. In addition, under stress conditions, the transcript levels of some of the genes were upregulated in leaves in response to ABA treatment.

Conclusions
This study provides useful information and a theoretical introduction for the study of the evolution, expression, and functions of the SnRK2 gene family in plants.
Membrane and lipid metabolism plays an important role in desiccation resistance in the yeast Saccharomyces cerevisiae
Authors: Ren Qun , Brenner Rebecca , Boothby Thomas C. , Zhang Zhaojie 
Published: November 2020

Abstract

Background
Anhydrobiotes, such as the yeast Saccharomyces cerevisiae, are capable of surviving almost total loss of water. Desiccation tolerance requires an interplay of multiple events, including preserving the protein function and membrane integrity, preventing and mitigating oxidative stress, maintaining certain level of energy required for cellular activities in the desiccated state. Many of these crucial processes can be controlled and modulated at the level of organelle morphology and dynamics. However, little is understood about what organelle perturbations manifest in desiccation-sensitive cells as a consequence of drying or how this differs from organelle biology in desiccation-tolerant organisms undergoing anhydrobiosis.

Results
In this study, electron and optical microscopy was used to examine the dynamic changes of yeast cells during the desiccation process. Dramatic structural changes were observed during the desiccation process, including the diminishing of vacuoles, decrease of lipid droplets, decrease in mitochondrial cristae and increase of ER membrane, which is likely caused by ER stress and unfolded protein response. The survival rate was significantly decreased in mutants that are defective in lipid droplet biosynthesis, or cells treated with cerulenin, an inhibitor of fatty acid synthesis.

Conclusion
Our study suggests that the metabolism of lipid droplets and membrane may play an important role in yeast desiccation tolerance by providing cells with energy and possibly metabolic water. Additionally, the decrease in mitochondrial cristae coupled with a decrease in lipid droplets is indicative of a cellular response to reduce the production of reactive oxygen species.
Adaptive response to iterative passages of five Lactobacillus species in simulated vaginal fluid
Authors: Brandt Katelyn , Barrangou Rodolphe 
Published: November 2020

AbstractBackgroundMicrobiome and metagenomic studies have given rise to a new understanding of microbial colonization of various human tissues and their ability to impact our health. One human microbiome growing in notoriety, the vaginal microbiome, stands out given its importance for women’s health, and is peculiar in terms of its relative bacterial composition, including its simplicity and typical domination by a small number ofLactobacillusspecies. The loss ofLactobacillusdominance is associated with disorders such as bacterial vaginosis, and efforts are now underway to understand the ability ofLactobacillusspecies to colonize the vaginal tract and adapt to this dynamic and acidic environment. Here, we investigate how variousLactobacillusspecies often isolated from the vaginal and intestinal cavities genomically and transcriptionally respond to iterative growth in simulated vaginal fluid.ResultsWe determined the genomes and transcriptomes ofL. acidophilus, L. crispatus, L. fermentum, L. gasseri,andL. jenseniiand compared profiles after 50, 100, 500, and 1000 generations of iterative passages in synthetic vaginal fluid. In general, we identified relatively few genetic changes consisting of single nucleotide polymorphisms, with higher counts occurring more frequently in non-vaginal isolated species. Transcriptional profiles were more impacted over time and tended to be more extensive for species that typically do not dominate the vaginal tract, reflecting a more extensive need to adapt to a less familiar environment.ConclusionsThis study provides insights into how vaginal and non-vaginalLactobacillusspecies respond and adapt to a simulated vaginal environment. Overall, trends indicate high genomic stability for all species involved, with more variability in the transcriptome especially for non-dominant species of the vaginal tract.
Cardiac damage in patients with the severe type of coronavirus disease 2019 (COVID-19)
Authors: Li Jing , Zhang Yinghua , Wang Fang , Liu Bing , Li Hui , Tang Guodong , Chang Zhigang , Liu Aihua , Fu Chunyi , Lv You , Gao Jing , Li Jing 
Published: November 2020

Abstract

Background
Coronavirus disease 2019 (COVID-19) has become a global pandemic. Studies showed COVID-19 affected not only the lung but also other organs. In this study, we aimed to explore the cardiac damage in patients with COVID-19.

Methods
We collected data of 100 patients diagnosed as severe type of COVID-19 from February 8 to April 10, 2020, including demographics, illness history, physical examination, laboratory test, and treatment. In-hospital mortality were observed. Cardiac damage was defined as plasma hypersensitive troponin I (hsTnI) over 34.2 pg/ml and/or N-terminal-pro brain natriuretic peptide (NTproBNP) above 450 pg/ml at the age < 50, above 900 pg/ml at the age < 75, or above 1800 pg/ml at the age ≥ 75.

Results
The median age of the patients was 62.0 years old. 69 (69.0%) had comorbidities, mainly presenting hypertension, diabetes, and cardiovascular disease. Fever (69 [69.0%]), cough (63 [63.0%]), chest distress (13 [13.0%]), and fatigue (12 [12.0%]) were the common initial symptoms. Cardiac damage occurred in 25 patients. In the subgroups, hsTnI was significantly higher in elder patients (≥ 60 years) than in the young (median [IQR], 5.2 [2.2–12.8] vs. 1.9 [1.9–6.2], p = 0.018) and was higher in men than in women (4.2 [1.9–12.8] vs. 2.9 [1.9–7.4], p = 0.018). The prevalence of increased NTproBNP was significantly higher in men than in women (32.1% vs. 9.1%, p = 0.006), but was similar between the elder and young patients (20.0% vs. 25.0%, p = 0.554). After multivariable analysis, male and hypertension were the risk factors of cardiac damage. The mortality was 4.0%.

Conclusions
Cardiac damage exists in patients with the severe type of COVID-19, especially in male patients with hypertension. Clinicians should pay more attention to cardiac damage.
Transitioning to Aboriginal community control of primary health care: the process and strategies of one community-controlled health organisation in Queensland
Authors: Jongen Crystal , Campbell Sandra , McCalman Janya , Fagan Ruth , Pearson Kingsley , Andrews Suzanne 
Published: November 2020

Abstract

Background
Aboriginal Community Controlled Health Services (ACCHSs) play a critical role in providing culturally appropriate, accessible primary healthcare (PHC) for Aboriginal and Torres Strait Islander peoples in Australia. The success of many ACCHSs has led to increased policy support for their growth and development, including the transition of state government administered PHC services to Aboriginal community control in select communities. However, there is minimal published literature available which evaluates such transitions. This paper reports on an evaluation of one ACCHS (Gurriny Yealamucka Health Service)‘s experience of transitioning local PHC services to community control in Yarrabah, Queensland, with a focus on the processes and strategies which were implemented to achieve successful transition.

Methods
Data was collected from interviews with key personnel involved in the transition and organisational documents from the evaluation period. Face-to-face or telephone interviews were conducted with 14 key stakeholders, audio-recorded and transcribed with written consent. Historical organisational documents were provided by Gurriny. All interview transcripts and documents were imported into NVIVO, coded and analysed using grounded theory methods.

Results
Gurriny’s journey of achieving community control of PHC in Yarrabah entailed an almost 30 year process of building and demonstrating organisational capacity. The first stage (1986 to 2004) was focused on establishing and developing a community-controlled health service and the second stage (2005–14) on preparing for the transition. Formal handover occurred in June 2014. Stage one strategies included: addressing community social and emotional wellbeing; consulting the community; collaborating with researchers; and, strategically building services, organisation capacity and stakeholder trust. Stage two strategies were: communicating and engaging with stakeholders; ensuring strong governance; planning and developing the services and workforce; assuring quality; and, financial planning, management and modelling.

Conclusion
Achieving successful transition to community control of PHC for Gurriny entailed a lengthy process of substantial, ongoing organisational growth and development. Gurriny’s experience provides a framework for both governments and the ACCHS sector to inform future transitions of PHC services to Aboriginal community control.
The effects of resistant starches on inflammatory bowel disease in preclinical and clinical settings: a systematic review and meta-analysis
Authors: Montroy Joshua , Berjawi Rania , Lalu Manoj M. , Podolsky Eyal , Peixoto Cayden , Sahin Levent , Stintzi Alain , Mack David , Fergusson Dean A. 
Published: November 2020

Abstract

Background
Inflammatory bowel disease (IBD) is a debilitating chronic disease with limited treatment options. Resistant starches may represent a novel treatment for IBD. However, its efficacy and safety remain unclear. Our objective was to perform a systematic review to summarize the preclinical and clinical effects of resistant starch, which may help guide future studies.

Methods
Medline, EMBASE, and the Cochrane Central Register were searched. Included studies investigated the use of resistant starch therapy in in vivo animal models of IBD or human patients with IBD. Articles were screened, and data extracted, independently and in duplicate. The primary outcomes were clinical remission (clinical) and bowel mucosal damage (preclinical).

Results
21 preclinical (n = 989 animals) and seven clinical (n = 164 patients) studies met eligibility. Preclinically, resistant starch was associated with a significant reduction in bowel mucosal damage compared to placebo (standardized mean difference − 1.83, 95% CI − 2.45 to − 1.20). Clinically, five studies reported data on clinical remission but clinical and methodological heterogeneity precluded pooling. In all five, a positive effect was seen in patients who consumed resistant starch supplemented diets. The majority of studies in both the preclinical and clinical settings were at a high or unclear risk of bias due to poor methodological reporting.

Conclusions
Our review demonstrates that resistant starch is associated with reduced histology damage in animal studies, and improvements in clinical remission in IBD patients. These results need to be tempered by the risk of bias of included studies. Rigorously designed preclinical and clinical studies are warranted.
Trial registration
The review protocols were registered on PROSPERO (preclinical: CRD42019130896; clinical: CRD42019129513).
Association between apoptosis inhibitor of macrophage and microsatellite instability status in colorectal cancer
Authors: Huang Wen-juan , Wang Xin , Zhang Meng-lin , Li Li , Wang Rui-tao 
Published: November 2020

Abstract

Background
The microsatellite instability (MSI) in colorectal cancer (CRC) has a more favorable clinical outcome and is characterized by highly upregulated expression of various immunological checkpoints than microsatellite stable (MSS) tumors. Apoptosis inhibitor of macrophage (AIM) is a circulating protein and circulates throughout the body to remove cellular debris. The aim of this study was to evaluate the association between MSI status and AIM levels in CRC patients.

Methods
In this study, we evaluated the levels of AIM by Enzyme Linked Immuno-Sorbent Assay (ELISA) in serum of 430 CRC patients. All patients’ clinical and laboratory characteristics at initial diagnosis were collected. The relationship between AIM levels and MSI status was examined.

Results
64 patients (14.9%) were identified as having MSI-H (high-frequency MSI) and 366 casess (85.1%) having MSS. Patients with an MSI-H phenotype had lower AIM levels compared with MSS patients. Moreover, AIM levels were correlated with histological type and MSI status. Logistic regression analysis revealed that decreased AIM levels were independently associated with MSI-H phenotype after adjusting confounding factors.

Conclusion
Reduced AIM levels are associated with MSI-H subtyping of CRC. Further research on the involvement of AIM in MSI-H CRC is needed.
Folate levels in hepatocellular carcinoma patients with portal vein thrombosis
Authors: Malaguarnera Giulia , Catania Vito Emanuele , Latteri Saverio , Borzì Antonio Maria , Bertino Gaetano , Madeddu Roberto , Drago Filippo , Malaguarnera Michele 
Published: November 2020

Abstract

Background
Portal vein thrombosis (PVT) occurs frequently in hepatocellular carcinoma (HCC) and is often diagnosed in the course of a routine patient evaluation and surveillance for liver cancer. The purpose of this study is to investigate the relationship between folate status and portal vein thrombosis.

Methods
HCC with PVT patients were 78, HCC without PVT were 60 and control subjects were 70 randomly selected. We evaluate serum and red blood cellular folate, homocysteine, alpha fetal protein cholesterol, triglycerides, prothrombin time.

Results
HCC patients with PVT showed lower levels of serum folate, respect HCC patients without PVT, with an average difference of 1.6 nmol/l p < 0.01 (95% CI − 2.54 to − 0.66), red cell folate 33.6 nmol/l p < 0.001 (95% CI − 43.64 to − 23.55) and albumin 0.29 g/dl p < 0.001 (95% CI − 0.42 to − 0.15); PVT patients displayed higher levels of bilirubin 0.53 mg/dl p < 0.001 (95% CI 0.23 to 0.78), INR 0.91 p < 0.001 (95% CI 0.72 to 1.09), γGT 7.9 IU/l (95% CI 4.14 to 11.65) and homocysteine 4.6 μmol/l p < 0.05 (95% CI 0.32 to 8.87)

Conclusion
The low folate concentration and higher levels of homocysteine are associated with the loss of antithrombotic function, and with a more aggressive course of HCC and with a higher change of complications related to portal vein thrombosis
Expectations and experiences with physician care among patients receiving post-acute care in US skilled nursing facilities
Authors: Ryskina Kira L. , Foley Kierra A. , Karlawish Jason H. , Uy Joshua D. , Lott Briana , Goldberg Erica , Hodgson Nancy A. 
Published: November 2020

Abstract

Background
In the US, post-acute care in skilled nursing facilities (SNFs) is common and outcomes vary greatly across facilities. Little is known about the expectations of patients and their caregivers about physician care during the hospital to SNF transition. Our objectives were to (1) describe the experiences and expectations of patients and their caregivers with SNF physicians in SNFs, and (2) identify patterns that differed between patients with vs. without cognitive impairment.

Methods
This qualitative study used grounded theory approach to analyze data collected from semi-structured interviews at five SNFs in January–August 2018. Patients admitted for short-term SNF care 5–10 days prior were eligible to participate. Thematic analysis was performed to detect recurrent themes with a focus on modifiable aspects of physician care. Analysis was stratified by patient cognitive impairment (measured by the Montreal Cognitive Assessment at the time of the interview).

Results
Fifty patients and six caregivers were interviewed. Major themes were: (1) patients had poor awareness of the physician in charge of their care; (2) they were dissatisfied with the frequency of interaction with the physician; and (3) participants valued the perception of receiving individualized care from the physician. Less cognitively impaired patients were more concerned about limited interactions with the physicians and were more likely to report attempts to seek out the physician.

Conclusion
Patient and caregiver expectations of SNF physicians were not well aligned with their experiences. SNFs aiming to improve satisfaction with care may focus efforts in this area, such as facilitating frequent communication between physicians, patients and caregivers.
Factors associated with phylogenetic clustering of hepatitis C among people who inject drugs in Baltimore
Authors: Falade-Nwulia Oluwaseun , Hackman Jada , Mehta Shruti H. , McCormick Sean D. , Kirk Gregory D. , Sulkowski Mark , Thomas David , Latkin Carl , Laeyendecker Oliver , Ray Stuart C. 
Published: November 2020

Abstract

Background
The availability of effective, oral direct acting antivirals (DAAs) for hepatitis C virus (HCV) treatment has put elimination of HCV as a public health challenge within reach. However, little is known about the characteristics of transmission networks of people who inject drugs (PWID).

Methods
Sequencing of a segment of the HCV genome was performed on samples collected from a community-based cohort of PWID between August 2005 and December 2016. Phylogenetic trees were inferred, and clusters were identified (70% bootstrap threshold; 0.04 maximum genetic distance threshold). We describe sex, race, age difference, and HIV infection status of potential transmission partners. Logistic regression was used to assess factors associated with being in an HCV cluster.

Results
Of 508 HCV genotype 1 viremic PWID, 8% (n = 41) were grouped into 20 clusters, consisting of 19 pairs and 1 triad. In adjusted analyses, female sex (odds ratio [OR] 2.3 [95% confidence interval (CI) 1.2–4.5]) and HIV infection (OR 5.7 [CI 2.7–11.9]) remained independently associated with being in an HCV infection cluster.

Conclusions
Molecular epidemiological analysis reveals that, in this cohort of PWID in Baltimore, HIV infection and female sex were associated with HCV clustering. Combination HCV prevention interventions targeting HIV infected PWID and addressing HCV infection prevention needs of women have potential to advance HCV elimination efforts.