bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction and analysis of metagenomic operons via MetaRon: a pipeline for prediction of Metagenome and whole-genome opeRons
Authors: Zaidi Syed Shujaat Ali , Kayani Masood Ur Rehman , Zhang Xuegong , Ouyang Younan , Shamsi Imran Haider 
Published: January 2021

Abstract
Background
Efficient regulation of bacterial genes in response to the environmental stimulus results in unique gene clusters known as operons. Lack of complete operonic reference and functional information makes the prediction of metagenomic operons a challenging task; thus, opening new perspectives on the interpretation of the host-microbe interactions.

Results
In this work, we identified whole-genome and metagenomic operons via MetaRon (Metagenome and whole-genome opeRon prediction pipeline). MetaRon identifies operons without any experimental or functional information. MetaRon was implemented on datasets with different levels of complexity and information. Starting from its application on whole-genome to simulated mixture of three whole-genomes (E. coli MG1655, Mycobacterium tuberculosis H37Rv and Bacillus subtilis str. 16), E. coli c20 draft genome extracted from chicken gut and finally on 145 whole-metagenome data samples from human gut. MetaRon consistently achieved high operon prediction sensitivity, specificity and accuracy across E. coli whole-genome (97.8, 94.1 and 92.4%), simulated genome (93.7, 75.5 and 88.1%) and E. coli c20 (87, 91 and 88%,), respectively. Finally, we identified 1,232,407 unique operons from 145 paired-end human gut metagenome samples. We also report strong association of type 2 diabetes with Maltose phosphorylase (K00691), 3-deoxy-D-glycero-D-galacto-nononate 9-phosphate synthase (K21279) and an uncharacterized protein (K07101).

Conclusion
With MetaRon, we were able to remove two notable limitations of existing whole-genome operon prediction methods: (1) generalizability (ability to predict operons in unrelated bacterial genomes), and (2) whole-genome and metagenomic data management. We also demonstrate the use of operons as a subset to represent the trends of secondary metabolites in whole-metagenome data and the role of secondary metabolites in the occurrence of disease condition. Using operonic data from metagenome to study secondary metabolic trends will significantly reduce the data volume to more precise data. Furthermore, the identification of metabolic pathways associated with the occurrence of type 2 diabetes (T2D) also presents another dimension of analyzing the human gut metagenome. Presumably, this study is the first organized effort to predict metagenomic operons and perform a detailed analysis in association with a disease, in this case type 2 diabetes. The application of MetaRon to metagenomic data at diverse scale will be beneficial to understand the gene regulation and therapeutic metagenomics.
Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines
Authors: Weißbach Stephan , Sys Stanislav , Hewel Charlotte , Todorov Hristo , Schweiger Susann , Winter Jennifer , Pfenninger Markus , Torkamani Ali , Evans Doug , Burger Joachim , Everschor-Sitte Karin , May-Simera Helen Louise , Gerber Susanne 
Published: January 2021

Abstract
Background
Next Generation Sequencing (NGS) is the fundament of various studies, providing insights into questions from biology and medicine. Nevertheless, integrating data from different experimental backgrounds can introduce strong biases. In order to methodically investigate the magnitude of systematic errors in single nucleotide variant calls, we performed a cross-sectional observational study on a genomic cohort of 99 subjects each sequenced via (i) Illumina HiSeq X, (ii) Illumina HiSeq, and (iii) Complete Genomics and processed with the respective bioinformatic pipeline. We also repeated variant calling for the Illumina cohorts with GATK, which allowed us to investigate the effect of the bioinformatics analysis strategy separately from the sequencing platform’s impact.

Results
The number of detected variants/variant classes per individual was highly dependent on the experimental setup. We observed a statistically significant overrepresentation of variants uniquely called by a single setup, indicating potential systematic biases. Insertion/deletion polymorphisms (indels) were associated with decreased concordance compared to single nucleotide polymorphisms (SNPs). The discrepancies in indel absolute numbers were particularly prominent in introns, Alu elements, simple repeats, and regions with medium GC content. Notably, reprocessing sequencing data following the best practice recommendations of GATK considerably improved concordance between the respective setups.

Conclusion
We provide empirical evidence of systematic heterogeneity in variant calls between alternative experimental and data analysis setups. Furthermore, our results demonstrate the benefit of reprocessing genomic data with harmonized pipelines when integrating data from different studies.
The semi-dwarfing gene Rht-dp from dwarf polish wheat (Triticum polonicum L.) is the "Green Revolution” gene Rht-B1b
Authors: Chai Songyue , Yao Qin , Zhang Xu , Xiao Xue , Fan Xing , Zeng Jian , Sha Lina , Kang Houyang , Zhang Haiqin , Li Jun , Zhou Yonghong , Wang Yi 
Published: January 2021

Abstract
Background
The wheat dwarfing gene increases lodging resistance, the grain number per spike and harvest index. Dwarf Polish wheat (Triticum polonicum L., 2n = 4x = 28, AABB, DPW), initially collected from Tulufan, Xinjiang, China, carries a semi-dwarfing gene Rht-dp on chromosome 4BS. However, Rht-dp and its dwarfing mechanism are unknown.

Results
Homologous cloning and mapping revealed that Rht-dp is the ‘Green Revolution’ gene Rht-B1b. A haplotype analysis in 59 tetraploid wheat accessions showed that Rht-B1b was only present in T. polonicum. Transcriptomic analysis of two pairs of near-isogenic lines (NILs) of DPW × Tall Polish wheat (Triticum polonicum L., 2n = 4x = 28, AABB, TPW) revealed 41 differentially expressed genes (DEGs) as potential dwarfism-related genes. Among them, 28 functionally annotated DEGs were classed into five sub-groups: hormone-related signalling transduction genes, transcription factor genes, cell wall structure-related genes, reactive oxygen-related genes, and nitrogen regulation-related genes.

Conclusions
These results indicated that Rht-dp is Rht-B1b, which regulates pathways related to hormones, reactive oxygen species, and nitrogen assimilation to modify the cell wall structure, and then limits cell wall loosening and inhibits cell elongation, thereby causing dwarfism in DPW.
Deciphering the miRNA transcriptome of breast muscle from the embryonic to post-hatching periods in chickens
Authors: Liu Jie , Li Fuwei , Hu Xin , Cao Dingguo , Liu Wei , Han Haixia , Zhou Yan , Lei Qiuxia 
Published: January 2021

Abstract
Background
miRNAs play critical roles in growth and development. Various studies of chicken muscle development have focused on identifying miRNAs that are important for embryo or adult muscle development. However, little is known about the role of miRNAs in the whole muscle development process from embryonic to post-hatching periods. Here, we present a comprehensive investigation of miRNA transcriptomes at 12-day embryo (E12), E17, and day 1 (D1), D14, D56 and D98 post-hatching stages.

Results
We identified 337 differentially expressed miRNAs (DE-miRNAs) during muscle development. A Short Time-Series Expression Miner analysis identified two significantly different expression profiles. Profile 4 with downregulated pattern contained 106 DE-miRNAs, while profile 21 with upregulated pattern contained 44 DE-miRNAs. The DE-miRNAs with the upregulated pattern mainly played regulatory roles in cellular turnover, such as pyrimidine metabolism, DNA replication, and cell cycle, whereas DE-miRNAs with the downregulated pattern directly or indirectly contributed to protein turnover metabolism such as glycolysis/gluconeogenesis, pyruvate metabolism and biosynthesis of amino acids.

Conclusions
The main functional miRNAs during chicken muscle development differ between embryonic and post-hatching stages. miRNAs with an upregulated pattern were mainly involved in cellular turnover, while miRNAs with a downregulated pattern mainly played a regulatory role in protein turnover metabolism. These findings enrich information about the regulatory mechanisms involved in muscle development at the miRNA expression level, and provide several candidates for future studies concerning miRNA-target function in regulation of chicken muscle development.
Lipases of germinating jojoba seeds efficiently hydrolyze triacylglycerols and wax esters and display wax ester-synthesizing activity
Authors: Kawiński Adam , Miklaszewska Magdalena , Stelter Szymon , Głąb Bartosz , Banaś Antoni 
Published: January 2021

Abstract
Background
Simmondsia chinensis (jojoba) is the only plant known to store wax esters instead of triacylglycerols in its seeds. Wax esters are composed of very-long-chain monounsaturated fatty acids and fatty alcohols and constitute up to 60% of the jojoba seed weight. During jojoba germination, the first step of wax ester mobilization is catalyzed by lipases. To date, none of the jojoba lipase-encoding genes have been cloned and characterized. In this study, we monitored mobilization of storage reserves during germination of jojoba seeds and performed detailed characterization of the jojoba lipases using microsomal fractions isolated from germinating seeds.

Results
During 26 days of germination, we observed a 60–70% decrease in wax ester content in the seeds, which was accompanied by the reduction of oleosin amounts and increase in glucose content. The activity of jojoba lipases in the seed microsomal fractions increased in the first 50 days of germination. The enzymes showed higher activity towards triacylglycerols than towards wax esters. The maximum lipase activity was observed at 60 °C and pH around 7 for triacylglycerols and 6.5–8 for wax esters. The enzyme efficiently hydrolyzed various wax esters containing saturated and unsaturated acyl and alcohol moieties. We also demonstrated that jojoba lipases possess wax ester-synthesizing activity when free fatty alcohols and different acyl donors, including triacylglycerols and free fatty acids, are used as substrates. For esterification reactions, the enzyme utilized both saturated and unsaturated fatty alcohols, with the preference towards long chain and very long chain compounds.

Conclusions
In in vitro assays, jojoba lipases catalyzed hydrolysis of triacylglycerols and different wax esters in a broad range of temperatures. In addition, the enzymes had the ability to synthesize wax esters in the backward reaction. Our data suggest that jojoba lipases may be more similar to other plant lipases than previously assumed.
Exogenous application of xanthine and uric acid and nucleobase-ascorbate transporter MdNAT7 expression regulate salinity tolerance in apple
Authors: Sun Tingting , Pei Tingting , Yang Lulu , Zhang Zhijun , Li Mingjun , Liu Yuerong , Ma Fengwang , Liu Changhai 
Published: January 2021

Abstract
Background
Soil salinity is a critical threat to global agriculture. In plants, the accumulation of xanthine activates xanthine dehydrogenase (XDH), which catalyses the oxidation/conversion of xanthine to uric acid to remove excess reactive oxygen species (ROS). The nucleobase-ascorbate transporter (NAT) family is also known as the nucleobase-cation symporter (NCS) or AzgA-like family. NAT is known to transport xanthine and uric acid in plants. The expression of MdNAT is influenced by salinity stress in apple.

Results
In this study, we discovered that exogenous application of xanthine and uric acid enhanced the resistance of apple plants to salinity stress. In addition, MdNAT7 overexpression transgenic apple plants showed enhanced xanthine and uric acid concentrations and improved tolerance to salinity stress compared with nontransgenic plants, while opposite phenotypes were observed for MdNAT7 RNAi plants. These differences were probably due to the enhancement or impairment of ROS scavenging and ion homeostasis abilities.

Conclusion
Our results demonstrate that xanthine and uric acid have potential uses in salt stress alleviation, and MdNAT7 can be utilized as a candidate gene to engineer resistance to salt stress in plants.
Evaluation of a novel Cardiac Peri-Operative Transfusion Trigger Scoring system in patients with coronary artery disease
Authors: Ma Hai-Ping , Zhang Lei , Chen Chun-ling , Li Jin , Ma Zhi Tong , Jiang Qiao Qiao , Liang Yuan Yuan , Li Shan Shan , Long Fei , Zheng Hong 
Published: January 2021

Abstract
Background
A simple and accurate scoring system to guide perioperative blood transfusion in patients with coronary artery disease (CAD) undergoing cardiac surgery is lacking. The trigger point for blood transfusions for these patients may be different from existing transfusion guidelines. This study aimed to evaluate the safety and efficacy of a new scoring strategy for use in guiding transfusion decisions in patients with CAD.

Methods
A multicenter randomized controlled trial was conducted at three third-level grade-A hospitals from January 2015 to May 2018. Data of 254 patients in a Cardiac Peri-Operative Transfusion Trigger Score (cPOTTS) group and 246 patients in a group receiving conventional evaluation of the need for transfusion (conventional group) were analysed. The requirements for transfusion and the per capita consumption of red blood cells (RBCs) were compared between groups.

Results
Baseline characteristics of the two groups were comparable. Logistic regression analyses revealed no significant differences between the two groups in primary outcomes (1-year mortality and perioperative ischemic cardiac events), secondary outcomes (shock, infections, and renal impairment), ICU admission, and ICU stay duration. However, patients in the cPOTTS group had significantly shorter hospital stays, lower hospital costs, lower utilization rate and lower per capita consumption of transfused RBCs than controls. Stratified analyses revealed no significant differences between groups in associations between baseline characteristics and perioperative ischemic cardiac events, except for hemofiltration or dialysis and NYHA class in I.

Conclusions
This novel scoring system offered a practical and straightforward guideline of perioperative blood transfusion in patients with CAD.
Trial registration chiCTR1800016561(2017/7/19).
Utilization of serum D-dimer assays prior to computed tomography pulmonary angiography scans in the diagnosis of pulmonary embolism among emergency department physicians: a retrospective observational study
Authors: Salehi Leila , Phalpher Prashant , Yu Hubert , Jaskolka Jeffrey , Ossip Marc , Meaney Christopher , Valani Rahim , Mercuri Mathew 
Published: January 2021

Abstract
Background
A variety of evidence-based algorithms and decision rules using D-Dimer testing have been proposed as instruments to allow physicians to safely rule out a pulmonary embolism (PE) in low-risk patients.

Objective
To describe the prevalence of D-Dimer utilization among emergency department (ED) physicians and its impact on positive yields and utilization rates of Computed Tomography Pulmonary Angiography (CTPA).

Methods
Data was collected on all CTPA studies ordered by ED physicians at three sites during a 2-year period. Using a chi-square test, we compared the diagnostic yield for those patients who had a D-Dimer prior to their CTPA and those who did not. Secondary analysis was done to examine the impact of D-Dimer testing prior to CTPA on individual physician diagnostic yield or utilization rate.

Results
A total of 2811 CTPAs were included in the analysis. Of these, 964 CTPAs (34.3%) were ordered without a D-Dimer, and 343 (18.7%) underwent a CTPA despite a negative D-Dimer. Those CTPAs preceded by a D-Dimer showed no significant difference in positive yields when compared to those ordered without a D-Dimer (9.9% versus 11.3%, p = 0.26). At the individual physician level, no statistically significant relationship was found between D-Dimer utilization and CTPA utilization rate or diagnostic yield.

Conclusion
This study provides evidence of suboptimal adherence to guidelines in terms of D-Dimer screening prior to CTPA, and forgoing CTPAs in patients with negative D-Dimers. However, the lack of a positive impact of D-Dimer testing on either CTPA diagnostic yield or utilization rate is indicative of issues relating to the high false-positive rates associated with D-Dimer screening.
Geriatrician perspectives on perioperative care: a qualitative study
Authors: Thillainadesan Janani , Jansen Jesse , Close Jacqui , Hilmer Sarah , Naganathan Vasi 
Published: January 2021

AbstractBackgroundPerioperative medicine services for older surgical patients are being developed across several countries. This qualitative study aims to explore geriatricians’ perspectives on challenges and opportunities for developing and delivering integrated geriatrics perioperative medicine services.MethodsA qualitative phenomenological semi-structured interview design. All geriatric medicine departments in acute public hospitals across Australia and New Zealand (n = 81) were approached. Interviews were conducted with 38 geriatricians. Data were analysed thematically using a framework approach.ResultsGeriatricians identified several system level barriers to developing geriatrics perioperative medicine services. These included lack of funding for staffing, encroaching on existing consultative services, and competing clinical priorities. The key barrier at the healthcare professional level was the current lack of clarity of roles within the perioperative care team. Key facilitators were perceived unmet patient needs, existing support for geriatrician involvement from surgical and anaesthetic colleagues, and the unique skills geriatricians can bring to perioperative care. Despite reporting barriers, geriatricians are contemplating and implementing integrated proactive perioperative medicine services. Geriatricians identified a need to support other specialties gain clinical experience in geriatric medicine and called for pragmatic research to inform service development.ConclusionsGeriatricians perceive several challenges at the system and healthcare professional levels that are impacting current development of geriatrics perioperative medicine services. Yet their strong belief that patient needs can be met with their specialty skills and their high regard for team-based care, has created opportunities to implement innovative multidisciplinary models of care for older surgical patients. The barriers and evidence gaps highlighted in this study may be addressed by qualitative and implementation science research. Future work in this area may include application of patient-reported measures and qualitative research with patients to inform patient-centred perioperative care.
The risk factors associated with COVID-19-Related death among patients with end‐stage renal disease
Authors: Rastad Hadith , Ejtahed Hanieh-Sadat , Shafiee Gita , Safari Anis , Shahrestanaki Ehsan , Khodaparast Zeinab , Hassani Neda Shafiabadi , Rezaei Mohammad , Nazari Morteza , Zakani Akram , Niksima Mohammad Mahdi , Azimzadeh Mehdi , Karimi Fatemeh , Tajbakhsh Ramin , Qorbani Mostafa 
Published: January 2021

AbstractBackgroundThe extent to which patients with End-stage renal disease (ESRD) are at a higher risk of COVID-19-related death is still unclear. Therefore, the aim of this study was to identify the ESRD patients at increased risk of COVID-19 -related death and its associated factors.MethodsThis retrospective cohort study was conducted on 74 patients with ESRD and 446 patients without ESRD hospitalized for COVID-19 in Alborz province, Iran, from Feb 20 2020 to Apr 26 2020. Data on demographic factors, medical history, Covid-19- related symptoms, and blood tests were obtained from the medical records of patients with confirmed COVID-19. We fitted univariable and multivariable Cox regression models to assess the association of underlying condition ESRD with the COVID-19 in-hospital mortality. Results were presented as crude and adjusted Hazard Ratios (HRs) and 95% confidence intervals (CIs). In the ESRD subgroup, demographic factors, medical history, symptoms, and blood parameters on the admission of survivors were compared with non-survivors to identify factors that might predict a high risk of mortality.ResultsCOVID-19 patients with ESRD had in-hospital mortality of 37.8% compared to 11.9% for those without ESRD (Pvalue < 0.001). After adjusting for confounding factors, age, sex, and comorbidities, ESRD patients were more likely to experience in-hospital mortality compared to non-ESRD patients (Adjusted HR (95% CI): 2.59 (1.55–4.32)). The Log-rank test revealed that there was a significant difference between the ESRD and non-ESRD groups in terms of the survival distribution (χ2 (1) = 21.18,P-value < 0.001). In the ESRD subgroup, compared to survivors, non-survivors were older, and more likely to present with lack of consciousness or O2 saturation less than 93%; they also had lower lymphocyte but higher neutrophil counts and AST concentration at the presentation (allp–values < 0.05).ConclusionsOur findings suggested that the presence of ESRD would be regarded as an important risk factor for mortality in COVID-19 patients, especially in those who are older than age 65 years and presented with a lack of consciousness or O2 saturation less than 93%.
Hypothyroidism and risks of cerebrovascular complications among patients with head and neck cancer after radiotherapy
Authors: Liu Chi-Hung , Chang Joseph Tung-Chieh , Lee Tsong-Hai , Chang Pi-Yueh , Chang Chien-Hung , Wu Hsiu-Chuan , Chang Ting-Yu , Huang Kuo-Lun , Lin Chien-Yu , Fan Kang-Hsing , Chang Yeu-Jhy 
Published: January 2021

Abstract
Background
Hypothyroidism (HT) and carotid artery stenosis (CAS) are complications of radiotherapy (RT) in patients with head and neck cancer (HNC). The impact of post-RT HT on CAS progression remains unclear.

Methods
Between 2013 and 2014, HNC patients who had ever received RT and were under regular follow-up in our hospital were initially screened. Patients were categorized into euthyroid (EU) and HT groups. Details of RT and HNC were recorded. Total plaque scores and degrees of CAS were measured during annual extracranial duplex follow-up. Patients were monitored for CAS progression to > 50 % stenosis or ischemic stroke (IS). Cumulative time to CAS progression and IS between the 2 groups were compared. Data were further analyzed based on the use or nonuse of thyroxine of the HT group.

Results
333 HNC patients with RT history were screened. Finally, 216 patients were recruited (94 and 122 patients in the EU and HT groups). Patients of the HT group received higher mean RT doses (HT vs. EU; 7021.55 ± 401.67 vs. 6869.69 ± 425.32 centi-grays, p = 0.02). Multivariate Cox models showed comparable CAS progression (p = 0.24) and IS occurrence (p = 0.51) between the 2 groups. Moreover, no significant difference was observed in time to CAS progression (p = 0.49) or IS (p = 0.31) among patients with EU and HT using and not using thyroxine supplement.

Conclusions
Our results did not demonstrate significant effects of HT and thyroxine supplementation on CAS progression and IS incidence in patients with HNC after RT.