bluuebunny/crossref_metadata_2025_split huggingface dataset:
The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events
Authors: Macciotta Nicolo P. P. , Colli Licia , Cesarani Alberto , Ajmone-Marsan Paolo , Low Wai Y. , Tearle Rick , Williams John L. 
Published: February 2021

Abstract
Background
Water buffalo is one of the most important livestock species in the world. Two types of water buffalo exist: river buffalo (Bubalus bubalis bubalis) and swamp buffalo (Bubalus bubalis carabanensis). The buffalo genome has been recently sequenced, and thus a new 90 K single nucleotide polymorphism (SNP) bead chip has been developed. In this study, we investigated the genomic population structure and the level of inbreeding of 185 river and 153 swamp buffaloes using runs of homozygosity (ROH). Analyses were carried out jointly and separately for the two buffalo types.

Results
The SNP bead chip detected in swamp about one-third of the SNPs identified in the river type. In total, 18,116 ROH were detected in the combined data set (17,784 SNPs), and 16,251 of these were unique. ROH were present in both buffalo types mostly detected (~ 59%) in swamp buffalo. The number of ROH per animal was larger and genomic inbreeding was higher in swamp than river buffalo. In the separated datasets (46,891 and 17,690 SNPs for river and swamp type, respectively), 19,760 and 10,581 ROH were found in river and swamp, respectively. The genes that map to the ROH islands are associated with the adaptation to the environment, fitness traits and reproduction.

Conclusions
Analysis of ROH features in the genome of the two water buffalo types allowed their genomic characterization and highlighted differences between buffalo types and between breeds. A large ROH island on chromosome 2 was shared between river and swamp buffaloes and contained genes that are involved in environmental adaptation and reproduction.
The small molecule ZY-214-4 may reduce the virulence of Staphylococcus aureus by inhibiting pigment production
Authors: Yu Jingyi , Rao Lulin , Zhan Lingling , Wang Bingjie , Zhan Qing , Xu Yanlei , Zhao Huilin , Wang Xinyi , Zhou Yan , Guo Yinjuan , Wu Xiaocui , Song Zengqiang , Yu Fangyou 
Published: February 2021

Abstract
Background
In recent years, clinical Staphylococcus aureus isolates have become highly resistant to antibiotics, which has raised concerns about the ability to control infections by these organisms. The aim of this study was to clarify the effect of a new small molecule, ZY-214-4 (C19H11BrNO4), on S. aureus pigment production.

Results
At the concentration of 4 μg/mL, ZY-214-4 exerted a significant inhibitory effect on S. aureus pigment synthesis, without affecting its growth or inducing a toxic effect on the silkworm. An oxidant sensitivity test and a whole-blood killing test indicated that the S. aureus survival rate decreased significantly with ZY-214-4 treatment. Additionally, ZY-214-4 administration significantly reduced the expression of a pigment synthesis-related gene (crtM) and the superoxide dismutase genes (sodA) as determined by real-time quantitative polymerase chain reaction (RT-qPCR) analysis. ZY-214-4 treatment also improved the survival rate of S. aureus-infected silkworm larvae.

Conclusions
The small molecule ZY-214-4 has potential for the prevention of S. aureus infections by reducing the virulence associated with this bacterium.
Non-target metabolomics revealed the differences between Rh. tanguticum plants growing under canopy and open habitats
Authors: Xiong Feng , Nie Xiuqing , Yang Lucun , Wang Lingling , Li Jingjing , Zhou Guoying 
Published: February 2021

AbstractBackgroundRheum tanguticum(Rh. tanguticum) is an important traditional Chinese medicine plant, “Dahuang”, which contains productive metabolites and occupies wide habitats on the Qinghai-Tibet plateau. Plants occupying wide habitats usually vary in phenotypes such as in morphology and metabolism, thereby developing into different ecotypes. Under canopy and open habitats are a pair of dissimilar habitats which possessRh. tanguticumplants. However, few studies have focused on the effect of habitats onRh. tanguticumgrowth, particularly combining morphological and metabolic changes. This study focused onRh. tanguticumplants growing in under canopy and open habitats where morphology and metabolism changes were quantified using non-target metabolism methods.ResultsThe obtained results indicated that the two dissimilar habitats led toRh. tanguticumdeveloping into two distinct ecotypes where the morphology and metabolism were simultaneously changed. Under canopy habitats bred morphologically smallerRh. tanguticumplants which had a higher level of metabolites (22 out of 31) which included five flavonoids, four isoflavonoids, and three anthracenes. On the other hand, the open habitats produced morphologically largerRh. tanguticumplants having a higher level of metabolites (9 out of 31) including four flavonoids. 6 of the 31 metabolites were predicted to have effect targets, include 4 represent for under canopy habitats and 2 for open habitats. Totally, 208 targets were connected, among which 42 were communal targets for both under canopy and open habitats represent compounds, and 100 and 66 were unique targets for under canopy superior compounds and open habitats superior compounds, respectively. In addition, aloe-emodin, emodin, chrysophanol, physcion, sennoside A and sennoside B were all more accumulated in under canopy habitats, and among which aloe-emodin, emodin, chrysophanol and physcion were significantly higher in under canopy habitats.ConclusionsThis study determined thatRh. tanguticumgrowing in under canopy and in open habitats developed into two distinct ecotypes with morphological and metabolic differences. Results of network pharmacology study has indicated that “Dahuang” coming from different habitats, such as under canopy and open habitats, are different in effect targets and thus may have different medicinal use. According to target metabolomics, under canopy habitats may grow better “Dahuang”.
A patient-centered framework for health systems engineering in gastroenterology: improving inpatient colonoscopy bowel preparation
Authors: Strauss Alexandra T. , Yeh Jennifer , Martinez Diego A. , Yenokyan Gayane , Yoder Janet , Nehra Ravi , Feller Tara , Bull-Henry Kathy , Stein Ellen , Hsu Lawrence C. H. , Al-Grain Haitham , Zabko Candice , Fain Christopher 
Published: February 2021

AbstractBackgroundInpatient colonoscopy bowel preparation (ICBP) is frequently inadequate and can lead to adverse events, delayed or repeated procedures, and negative patient outcomes. Guidelines to overcome the complex factors in this setting are not well established. Our aims were to use health systems engineering principles to comprehensively evaluate the ICBP process, create an ICBP protocol, increase adequate ICBP, and decrease length of stay. Our goal was to provide adaptable tools for other institutions and procedural specialties.MethodsPatients admitted to our tertiary care academic hospital that underwent inpatient colonoscopy between July 3, 2017 to June 8, 2018 were included. Our multi-disciplinary team created a protocol employing health systems engineering techniques (i.e., process mapping, cause-effect diagrams, and plan-do-study-act cycles). We collected demographic and colonoscopy data. Our outcome measures were adequate preparation and length of stay. We compared pre-intervention (120 ICBP) vs. post-intervention (129 ICBP) outcomes using generalized linear regression models. Our new ICBP protocol included: split-dose 6-L polyethylene glycol-electrolyte solution, a gastroenterology electronic note template, and an education plan for patients, nurses, and physicians.ResultsThe percent of adequate ICBPs significantly increased with the intervention from 61% pre-intervention to 74% post-intervention (adjusted odds ratio of 1.87,pvalue = 0.023). The median length of stay decreased by approximately 25%, from 4 days pre-intervention to 3 days post-intervention (pvalue  = 0.11).ConclusionsBy addressing issues at patient, provider, and system levels with health systems engineering principles, we addressed patient safety and quality of care provided by improving rates of adequate ICBP.
Social factors influencing utilization of home care in community-dwelling older adults: a scoping review
Authors: Mah Jasmine C. , Stevens Susan J. , Keefe Janice M. , Rockwood Kenneth , Andrew Melissa K. 
Published: February 2021

Abstract
Background
Older adults want to live at home as long as possible, even in the face of circumstances that limit their autonomy. Home care services reflect this emergent preference, allowing older adults to ‘age in place’ in familiar settings rather than receiving care for chronic health conditions or ageing needs in an institutionalized setting. Numerous social factors, generally studied in isolation, have been associated with home care utilization. Even so, social circumstances are complex and how these factors collectively influence home care use patterns remains unclear.

Objectives
To provide a broad and comprehensive overview of the social factors influencing home care utilization; and to evaluate the influence of discrete social factors on patterns of home care utilization in community-dwelling older adults in high-income countries.

Methods
A scoping review was conducted of six electronic databases for records published between 2010 and 2020; additional records were obtained from hand searching review articles, reference lists of included studies and documents from international organisations. A narrative synthesis was presented, complemented by vote counting per social factor, harvest plots and an evaluation of aggregated findings to determine consistency across studies.

Results
A total of 2,365 records were identified, of which 66 met inclusion criteria. There were 35 discrete social factors grouped into four levels of influence using a socio-ecological model (individual, relationship, community and societal levels) and grouped according to outcome of interest (home care propensity and intensity). Across all studies, social factors consistently showing any association (positive, negative, or equivocal in pattern) with home care propensity were: age, ethnicity/race, self-assessed health, insurance, housing ownership, housing problems, marital status, household income, children, informal caregiving, social networks and urban/rural area. Age, education, personal finances, living arrangements and housing ownership were associated with home care intensity, also with variable patterns in utilization. Additional community and societal level factors were identified as relevant but lacking consistency across the literature; these included rurality, availability of community services, methods of financing home care systems, and cultural determinants.

Conclusion
This is the first literature review bringing together a wide range of reported social factors that influence home care utilization. It confirms social factors do influence home care utilization in complex interactions, distinguishes level of influences at which these factors affect patterns of use and discusses policy implications for home care reform.
Prevention of AcuTe admIssioN algorithm (PATINA): study protocol of a stepped wedge randomized controlled trial
Authors: Fournaise Anders , Lauridsen Jørgen T. , Bech Mickael , Wiil Uffe K. , Rasmussen Jesper B. , Kidholm Kristian , Espersen Kurt , Andersen-Ranberg Karen 
Published: February 2021

Abstract
Background
The challenges imposed by ageing populations will confront health care systems in the years to come. Hospital owners are concerned about the increasing number of acute admissions of older citizens and preventive measures such as integrated care models have been introduced in primary care. Yet, acute admission can be appropriate and lifesaving, but may also in itself lead to adverse health outcome, such as patient anxiety, functional loss and hospital-acquired infections. Timely identification of older citizens at increased risk of acute admission is therefore needed.
We present the protocol for the PATINA study, which aims at assessing the effect of the ‘PATINA algorithm and decision support tool’, designed to alert community nurses of older citizens showing subtle signs of declining health and at increased risk of acute admission. This paper describes the methods, design and intervention of the study.

Methods
We use a stepped-wedge cluster randomized controlled trial (SW-RCT). The PATINA algorithm and decision support tool will be implemented in 20 individual area home care teams across three Danish municipalities (Kerteminde, Odense and Svendborg). The study population includes all home care receiving community-dwelling citizens aged 65 years and above (around 6500 citizens). An algorithm based on home care use triggers an alert based on relative increase in home care use. Community nurses will use the decision support tool to systematically assess health related changes for citizens with increased risk of acute hospital admission.
The primary outcome is acute admission. Secondary outcomes are readmissions, preventable admissions, death, and costs of health care utilization. Barriers and facilitators for community nurse’s acceptance and use of the algorithm will be explored too.

Discussion
This ‘PATINA algorithm and decision support tool’ is expected to positively influence the care for older community-dwelling citizens, by improving nurses’ awareness of citizens at increased risk, and by supporting their clinical decision-making. This may increase preventive measures in primary care and reduce use of secondary health care. Further, the study will increase our knowledge of barriers and facilitators to implementing algorithms and decision support in a community care setup.

Trial registration
ClinicalTrials.gov, identifier: NCT04398797. Registered 13 May 2020.
The clinical profiles and outcomes of HIV-negative cryptococcal meningitis patients in type II diabetes mellitus
Authors: Li Hang , Li Xiaojing , Zhang Lei , Fang Wenjie , Zhang Keming , Arastehfar Amir , Ilkit Macit , Hu Dongying , Chen Xianzhen , Wang Huiwei , Ling Liyan , Lin Jianjun , Xu Bin , Liao Wanqing , Pan Weihua , Zhang Qilong 
Published: February 2021

AbstractBackgroundThe clinical profiles and outcomes of cryptococcal meningitis have been shown to vary depending on the underlying condition. The aim of this study was to investigate clinical characteristics and outcomes in patients with and without type II diabetes mellitus.MethodsA retrospective study was performed. Clinical data of HIV-negative cryptococcal meningitis patients with type II diabetes mellitus (n = 26) and without type II diabetes mellitus (n = 52) referring to the Jiangxi Chest Hospital between January 2012 to December 2018 were analyzed. The data were analyzed using chi square, none-parametric tests, and logistic regression.P-values < 0.05 were considered significant.ResultsIn this study, cryptococcal meningitis patients suffering from type II diabetes mellitus had a higher mortality (23.08% vs. 7.69%;P = 0.055), and required longer hospitalization (59.58 vs. 42.88 days;P = 0.132). Moreover, cerebrospinal fluid examinations revealed that cryptococcal meningitis patients with type II diabetes mellitus had higher opening pressure (271.54 vs. 234.23 mmH2O;P = 0.125).The results of multivariate regression analysis revealed that cryptococcal meningitis patients with type II diabetes were more often presented with visual disorders (28.54% vs. 11.54%; [95% CI 0.056–0.705];p = 0.012), and had higher cerebrospinal fluid protein levels (1027.62 ± 594.16 vs. 705.72 ± 373.88 mg/l; [95% CI 1.000–1.002];p = 0.016). Among patients with type II diabetes mellitus, nausea and vomiting was more frequent at the initial visit in those died (100% vs. 50%;p = 0.027), and 66% of died type II diabetes mellitus patients were poorly controlled blood glucose level, compared with 30% in survival type II diabetes mellitus patients.ConclusionThis study suggests that cryptococcal meningitis patients with type II diabetes mellitus differ significantly from cryptococcal meningitis patients without type II diabetes mellitus with respect to clinical symptoms such as visual disorders and cerebrospinal fluid examination. The presence of nausea and vomiting among type II diabetes mellitus patients could have implication in mortality.
Effect of oxidative stress and calcium deregulation on FAM26F (CALHM6) expression during hepatitis B virus infection
Authors: Jabeen Kehkshan , Malik Uzma , Mansoor Sajid , Shahzad Shaheen , Zahid Saadia , Javed Aneela 
Published: February 2021

AbstractBackgroundFamily with sequence similarity 26, member F (FAM26F) is an important innate immunity modulator playing a significant role in diverse immune responses, however, the association of FAM26F expression with HBV infection is not yet known. Thus, the current study aims to explore the differential expression of FAM26F in vitro in HepAD38 and HepG2 cell lines upon HBV infection, and in vivo in HBV infected individuals. The effects of antioxidant and calcium inhibitors on the regulation of FAM26F expression were also evaluated. The expression of FAM26F was simultaneously determined with well-established HBV infection markers: IRF3, and IFN-β.MethodsThe expression of FAM26F and marker genes was analyzed through Real-time qPCR and western blot.ResultsOur results indicate that the differential expression of FAM26F followed the same trend as that of IRF3 and IFN-β. The in vitro study revealed that, in both HBV infected cell lines, FAM26F expression was significantly down-regulated as compared to uninfected control cells. Treatment of cells with N-acetyl-L-cysteine (NAC), EGTA-AM, BAPTA-AM, and Ru360 significantly upregulated the expression of FAM26F in both the cell lines. Moreover, in in vivo study, FAM26F expression was significantly downregulated in all HBV infected groups as compared to controls (p = 0.0007). The expression was higher in the HBV recovered cases, probably due to the decrease in infection and increase in the immunity of these individuals.ConclusionOur study is the first to show the association of FAM26F with HBV infection. It is proposed that FAM26F expression could be an early predictive marker for HBV infection, and thus is worthy of further investigation.
The role of smart monitoring digital health care system based on smartphone application and personal health record platform for patients diagnosed with coronavirus disease 2019
Authors: Kim Jong Hun , Choi Won Suk , Song Joon Young , Yoon Young Kyung , Kim Min Ja , Sohn Jang Wook 
Published: February 2021

Abstract
Background
The massive outbreak of the novel coronavirus disease 2019 (COVID-19) in Daegu city and Gyeongsangbuk-do, Republic of Korea (ROK), caused the exponential increase in new cases exceeding 5000 within 6 weeks. Therefore, the community treatment center (CTC) with a digital health care monitoring system based on the smartphone application and personal health record platform (PHR) was implemented. Thus, we report our experience in one of the CTCs to investigate the role of CTC and the feasibility of the digital health care monitoring system in the COVID-19 pandemic.

Methods
The Gyeongbuk-Daegu 2 CTC was set up at the private residential facility. Admission criteria were 1) patients < 65 years with COVID-19, 2) patients without underlying medical comorbidities, and 3) COVID-19 disease severity of mild class. Admitted patients were placed under monitoring of vital signs and symptoms. Clinical information was collected using the smartphone application or telephone communication. Collected information was displayed on the PHR platform in a real-time fashion for close monitoring.

Results
From Mar 3, 2020, to Mar 26, 2020, there was a total of 290 patients admitted to the facility. Males were 104 (35.9%). The median age was 37 years. The median time between the COVID-19 diagnosis and admission was 7 days. Five patients were identified and were transferred to the designed COVID-19 treatment hospital for their urgent medical needs. The smartphone application usage to report vital signs and symptoms was noted in 96% of the patients. There were no deaths of the patients.

Conclusions
Our results suggest that implementation of the CTC using a commercial residence facility and digital health care technology may offer valuable solutions to the challenges posed by the COVID-19 outbreak.
The clinical application of Filmarray respiratory panel in children especially with severe respiratory tract infections
Authors: Pan Fen , Wang Bingjie , Zhang Hong , Shi Yingying , Xu Qi 
Published: February 2021

Abstract
Background
Respiratory tract infections (RTIs) are the common diseases in children and the routine detection methods frequently fail to identify the infectious pathogens especially for viruses. The Filmarray respiratory panel (FARP) can reliably and rapidly identify viruses and bacteria pathogens. This study is to evaluate the performance and clinical significance of FARP in children.

Methods
Children diagnosed with RTIs in pediatric intensive care unit (PICU) were enrolled in this study. Nasopharyngeal secretion (NPS) samples of these children were collected and the FARP assay for 17 pathogens and routine microbiological methods were performed. Clinical data of all patients was also collected and evaluated.

Results
A total of 90 children were enrolled into this study and 58 patients (64.4%) were positive for 13 pathogens by FARP, with 18 being detected positive with multiple-virus (31.3%, 18/58). Human rhinovirus/enterovirus (21.0%%, 17/58) were the predominant pathogen, followed by adenovirus (18.5%). Higher proportions of various pathogens were identified in the infant and toddler (0–2 years) groups with human rhinovirus/enterovirus being mostly virus. Adenovirus were common in the group aged 3–5 years, but only three pathogens including M.pneumoniae, respiratory syncytial virus, and adenovirus were also found in age group (6–14 years). Among 58 FARP positive patients, significant differences were found in antibiotic prescription and use of glucocorticoid between the single-organism-positive group and the multi-organism-positive group (P < 0.05). Furthermore, there was significant difference in use of anti-virus and usage of glucocorticoid between severe respiratory infections group and non severe respiratory infections group (P < 0.05).

Conclusions
This study demonstrated that FARP can provide the rapid detection of respiratory virus and atypical bacteria for children, especially with severe respiratory tract infections.