bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete genome analysis of a virulent Vibrio scophthalmi strain VSc190401 isolated from diseased marine fish half-smooth tongue sole, Cynoglossus semilaevis
Authors: Zhang Zheng , Yu Yong-xiang , Wang Yin-geng , Liu Xiao , Wang Li-fang , Zhang Hao , Liao Mei-jie , Li Bin 
Published: November 2020

Abstract
Background
Vibrio scophthalmi is an opportunistic bacterial pathogen, which is widely distributed in the marine environment. Earlier studies have suggested that it is a normal microorganism in the turbot gut. However, recent studies have confirmed that this bacterial strain can cause diseases in many different marine animals. Therefore, it is necessary to investigate its whole genome for better understanding its physiological and pathogenic mechanisms.

Results
In the present study, we obtained a pathogenic strain of V. scophthalmi from diseased half-smooth tongue sole (Cynoglossus semilaevis) and sequenced its whole genome. Its genome contained two circular chromosomes and two plasmids with a total size of 3,541,838 bp, which harbored 3185 coding genes. Among these genes, 2648, 2298, and 1915 genes could be found through annotation information in COG, Blast2GO, and KEGG databases, respectively. Moreover, 10 genomic islands were predicted to exist in the chromosome I through IslandViewer online system. Comparison analysis in VFDB and PHI databases showed that this strain had 334 potential virulence-related genes and 518 pathogen-host interaction-related genes. Although it contained genes related to four secretion systems of T1SS, T2SS, T4SS, and T6SS, there was only one complete T2SS secretion system. Based on CARD database blast results, 180 drug resistance genes belonging to 27 antibiotic resistance categories were found in the whole genome of such strain. However, there were many differences between the phenotype and genotype of drug resistance.

Conclusions
Based on the whole genome analysis, the pathogenic V. scophthalmi strain contained many types of genes related to pathogenicity and drug resistance. Moreover, it showed inconsistency between phenotype and genotype on drug resistance. These results suggested that the physiological mechanism seemed to be complex.
Identifying candidate Aspergillus pathogenicity factors by annotation frequency
Authors: Pennerman Kayla K. , Yin Guohua , Glenn Anthony E. , Bennett Joan W. 
Published: November 2020

Abstract

Background
Members of the genus Aspergillus display a variety of lifestyles, ranging from saprobic to pathogenic on plants and/or animals. Increased genome sequencing of economically important members of the genus permits effective use of “-omics” comparisons between closely related species and strains to identify candidate genes that may contribute to phenotypes of interest, especially relating to pathogenicity. Protein-coding genes were predicted from 216 genomes of 12 Aspergillus species, and the frequencies of various structural aspects (exon count and length, intron count and length, GC content, and codon usage) and functional annotations (InterPro, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes terms) were compared.

Results
Using principal component analyses, the three sets of functional annotations for each strain were clustered by species. The species clusters appeared to separate by pathogenicity on plants along the first dimensions, which accounted for over 20% of the variance. More annotations for genes encoding pectinases and secondary metabolite biosynthetic enzymes were assigned to phytopathogenic strains from species such as Aspergillus flavus. In contrast, Aspergillus fumigatus strains, which are pathogenic to animals but not plants, were assigned relatively more terms related to phosphate transferases, and carbohydrate and amino-sugar metabolism. Analyses of publicly available RNA-Seq data indicated that one A. fumigatus protein among 17 amino-sugar processing candidates, a hexokinase, was up-regulated during co-culturing with human immune system cells.

Conclusion
Genes encoding hexokinases and other proteins of interest may be subject to future manipulations to further refine understanding of Aspergillus pathogenicity factors.
Risk factors for Keshan disease: a prospective cohort study protocol of gut flora
Authors: Li Zhenzhen , Wei Jin , Zhang Yanping , Li Gaopeng , Zhu Huange , Lei Na , He Qian , Geng Yan , Zhu Jianhong 
Published: November 2020

Abstract
Background
Keshan disease is an endemic cardiomyopathy of undefined causes. Being involved in the unclear pathogenesis of Keshan disease, a clear diagnosis, and effective treatment cannot be initiated. However, the rapid development of gut flora in cardiovascular disease combined with omics and big data platforms may promote the discovery of new diagnostic markers and provide new therapeutic options. This study aims to identify biomarkers for the early diagnosis and further explore new therapeutic targets for Keshan disease.

Methods
This cohort study consists of two parts. Though the first part includes 300 participants, however, recruiting will be continued for the eligible participants. After rigorous screening, the blood samples, stools, electrocardiograms, and ultrasonic cardiogram data would be collected from participants to elucidate the relationship between gut flora and host. The second part includes a prospective follow-up study for every 6 months within 2 years. Finally, deep mining of big data and rapid machine learning will be employed to analyze the baseline data, experimental data, and clinical data to seek out the new biomarkers to predict the pathogenesis of Keshan disease.

Discussion
Our study will clarify the distribution of gut flora in patients with Keshan disease and the abundance and population changes of gut flora in different stages of the disease. Through the big data platform analyze the relationship between environmental factors, clinical factors, and gut flora, the main factors affecting the occurrence of Keshan disease were identified, and the changed molecular pathways of gut flora were predicted. Finally, the specific gut flora and molecular pathways affecting Keshan disease were identified by metagenomics combined with metabonomic analysis.
Trial registration: ChiCTR1900026639. Registered on 16 October 2019.
Exploring person-centred care in relation to resource utilization, resident quality of life and staff job strain – findings from the SWENIS study
Authors: Sköldunger Anders , Sandman Per-Olof , Backman Annica 
Published: November 2020

AbstractBackgroundA critical challenge facing elderly care systems throughout the world is to meet the complex care needs of a growing population of older persons. Although person-centred care has been advocated as the “gold standard” and a key component of high-quality care, the significance of care utilisation in person-centred units as well as the impact of person-centred care on resident quality of life and staff job strain in nursing home care has yet to be explored.The aim of this study was to explore person-centred care and its association to resource use, resident quality of life, and staff job strain.DesignA cross-sectional national survey.MethodsData on 4831 residents and 3605 staff were collected by staff working in nursing homes in 35 randomly selected Swedish municipalities in 2014. Descriptive statistics and regression modelling were used to explore associations between person-centred care and resource use, resident quality of life, and staff job strain.ResultsNo association was found between person-centred care and resource use. Person-centred care was positively associated with resident quality of life and was negatively associated with staff perception of job strain.ConclusionPerson-centred care does not increase resource utilisation in nursing homes, but beneficially impacts resident quality of life and alleviates the care burden in terms job strain among staff.
Association between self-reported walking speed and calcaneal stiffness index in postmenopausal Japanese women
Authors: Tomita Yoshihito , Arima Kazuhiko , Mizukami Satoshi , Tsujimoto Ritsu , Kawashiri Shin-ya , Nishimura Takayuki , Okabe Takuhiro , Tanaka Natsumi , Honda Yuzo , Nakahara Kazumi , Yamamoto Naoko , Ohmachi Izumi , Goto Hisashi , Hasegawa Maiko , Sou Youko , Horiguchi Itsuko , Kanagae Mitsuo , Abe Yasuyo , Nonaka Fumiaki , Tamai Mami , Yamanashi Hirotomo , Nagata Yasuhiro , Kawakami Atsushi , Maeda Takahiro , Aoyagi Kiyoshi 
Published: November 2020

Abstract

Background
Osteoporosis and related fractures, a worldwide public health issue of growing concern, is characterized by compromised bone strength and an increased risk of fracture. Here we show an association between self-reported walking speed and bone mass among community-dwelling postmenopausal Japanese women aged 50 years and older.

Design; cross-sectional study
Setting and Participants; The survey population included 1008 postmenopausal women 50–92 years of age residing in rural communities.

Methods
Self-reported walking speed was ascertained by asking the participants: “Is your walking speed faster than others of the same age and sex?” to which participants responded “yes (faster)” or “no (moderate/slower).” Calcaneal stiffness index was measured.

Results
Women with a faster self-reported walking speed were younger and had a lower BMI, higher stiffness index, and higher grip strength than women with a slower walking speed. Multiple linear regression analysis adjusted for age, BMI, grip strength, comorbidity, current smoking, and alcohol drinking status showed a significant association between faster self-reported walking speed and higher calcaneal stiffness index (p <  0.001).

Conclusions
Our findings suggest that questionnaires of walking speed may be useful for predicting bone mass and that a fast self-reported walking may benefit bone health in postmenopausal women.
First identification of Anaplasma phagocytophilum in both a biting tick Ixodes nipponensis and a patient in Korea: a case report
Authors: Lee Seung Hun , Shin Na-Ri , Kim Choon-Mee , Park Sungdo , Yun Na Ra , Kim Dong-Min , Jung Dong Sik 
Published: November 2020

Abstract

Background
Human granulocytic anaplasmosis (HGA) is a tick-borne infectious disease caused by Anaplasma phagocytophilum. To date, there have been no reported cases of A. phagocytophilum infection found in both the biting tick and the patient following a tick bite.

Case presentation
An 81-year-old woman presented with fever following a tick bite, with the tick still intact on her body. The patient was diagnosed with HGA. The tick was identified as Ixodes nipponensis by morphological and molecular biological detection methods targeting the 16S rRNA gene. The patient’s blood was cultured after inoculation into the human promyelocytic leukemia cell line HL-60. A. phagocytophilum growth was confirmed via culture and isolation. A. phagocytophilum was identified in both the tick and the patient’s blood by Anaplasma-specific groEL- and ankA-based nested polymerase chain reaction followed by sequencing. Moreover, a four-fold elevation in antibodies was observed in the patient’s blood.

Conclusion
We report a case of a patient diagnosed with HGA following admission for fever due to a tick bite. A. phagocytophilum was identified in both the tick and the patient, and A. phagocytophilum was successfully cultured. The present study suggests the need to investigate the possible incrimination of I. nipponensis as a vector for HGA in Korea.
Simultaneous disseminated infections with intracellular pathogens: an intriguing case report of adult-onset immunodeficiency with anti-interferon-gamma autoantibodies
Authors: Roerden Malte , Döffinger Rainer , Barcenas-Morales Gabriela , Forchhammer Stephan , Döbele Stefanie , Berg Christoph P. 
Published: November 2020

Abstract
Background
Severe and disseminated non-tuberculous mycobacterial (NTM) infections are frequently linked to a genetic predisposition but acquired defects of the interferon gamma (IFNγ) / interleukin 12 (IL-12) pathway need to be considered in adult patients with persistent or recurrent infections. Neutralizing anti-IFNγ autoantibodies disrupting IFNγ signalling have been identified as the cause of a severe and unique acquired immunodeficiency syndrome with increased susceptibility to NTM and other intracellular pathogens.

Case presentation
An adult Asian female with a previous history of recurrent NTM infections presented with persistent diarrhea, abdominal pain, night sweats and weight loss. Severe colitis due to a simultaneous infection with cytomegalovirus (CMV) and Salmonella typhimurium was diagnosed, with both pathogens also detectable in blood samples. Imaging studies further revealed thoracic as well as abdominal lymphadenopathy and a disseminated Mycobacterium intracellulare infection was diagnosed after a lymph node biopsy. Further diagnostics revealed the presence of high-titer neutralizing anti-IFNγ autoantibodies, allowing for the diagnosis of adult-onset immunodeficiency with anti-IFNγ autoantibodies (AIIA).

Conclusions
We here present a severe case of acquired immunodeficiency with anti-IFNγ autoantibodies with simultaneous, disseminated infections with both viral and microbial pathogens. The case illustrates how the diagnosis can cause considerable difficulties and is often delayed due to unusual presentations. Histological studies in our patient give further insight into the pathophysiological significance of impaired IFNγ signalling. B-cell-depleting therapy with rituximab offers a targeted treatment approach in AIIA.
Comparison of practicability and effectiveness between unassisted HIV self-testing and directly assisted HIV self-testing in the Democratic Republic of the Congo: a randomized feasibility trial
Authors: Tonen-Wolyec Serge , Kayembe Tshilumba Charles , Batina-Agasa Salomon , Marini Djang’eing’a Roland , Hayette Marie-Pierre , Belec Laurent 
Published: November 2020

Abstract

Background
HIV self-testing (HIVST) can be performed using directly assisted and unassisted approaches in facilities or communities to reach different populations. The aim of this study was to compare the practicability and effectiveness of the two delivery approaches for HIVST, unassisted HIVST (UH) and directly assisted HIVST (DAH), in the field setting of Kisangani, the Democratic Republic of the Congo (DRC).

Methods
A randomized (1:1), non-blinded, non-inferiority trial using a blood-based and facility-based HIVST method was carried out in four facilities in Kisangani, the DRC, targeting populations at high risk for HIV infection. The primary outcome was the difference in the practicability of the HIV self-test between the two arms. Practicability was defined as successfully performing the test and correctly interpreting the result. Requests for assistance, positivity rate, linkage to care, and willingness to buy an HIV self-test kit constituted the secondary outcomes for HIVST effectiveness. The adjusted risk ratios (aRRs) were calculated using Poisson regression.

Results
The rate of successfully performing the test was same (93.2%) in the UH and DAH arms. The rate of correctly interpreting the results was 86.9% in the UH arm versus 93.2% in the DAH arm, for a difference of − 6.3%. After the follow-up 72 h later, participants in the UH arm had a significantly lower chance of correctly interpreting the test results than those in the DAH arm (aRR: 0.60; P = 0.019). Although the positivity rate was 3.4% among the participants in the DAH arm and 1.7% among those in the UH arm, no significant differences were found between the two arms in the positivity rate, requests for assistance, and linkage to care. Willingness to buy an HIV self-test was higher in the UH arm than in the DAH arm (92.3% versus 74.1%; aRR: 4.20; P < 0.001).

Conclusion
The results of this study indicate that UH is as practicable and effective as DAH among individuals at high risk for HIV infection in Kisangani, the DRC. However, additional support tools need to be assessed to improve the interpretation of the self-test results when using the UH approach.

Trial registration
PACTR201904546865585. Registered 03 April 2019 - Retrospectively registered, https://pactr.samrc.ac.za/TrialDisplay.aspx?TrialID=6032
Antiviral mechanism of carvacrol on HSV-2 infectivity through inhibition of RIP3-mediated programmed cell necrosis pathway and ubiquitin-proteasome system in BSC-1 cells
Authors: Wang Li , Wang Dan , Wu Xingan , Xu Rui , Li Yunlan 
Published: November 2020

Abstract

Background
Carvacrol, as the major components of aromatic plants used for treating human skin diseases including origanum, Satureja, thymus, and coridothymus species, presented a kind of antiviral activity. To explore the mechanisms of carvacrol against herpes simplex virus (HSV) in vitro.

Method
The BSC-1 cells model of HSV infection was established, and from the two aspects of viral replication level and cell death pathway, the antiviral effects of carvacrol on HSV infected cells were also evaluated by plaque assay under the three modes including prevention, treatment, and direct inactivation.

Results
In the three ways, the half-maximal effective concentration (EC50) of 2% true carvacrol solution on HSV-2 infected cells were severally 0.43, 0.19 and 0.51 mmol/L, and the corresponding therapeutic index (TI) were 4.02, 9.11 and 3.39, respectively. It’s the opposite of the increased levels caused by HSV-2 infection, that both the expressions at the transcription genes and protein levels of virus own replication key factors (including ICP4, ICP27, VP16, gB, and UL30) and cytokines (including RIP3, TNF-α, and MLKL) of infected cells treated with carvacrol were dose-dependently inhibited. Besides, HSV-2 infection can cause the decrease of intracellular protein ubiquitination level, and carvacrol can reverse the ubiquitination decrease level caused by HSV-2 infection.

Conclusion
Carvacrol exhibits significant antiviral activity by inhibiting the HSV-2 proliferation process and HSV-2-induced TNF-α increasing levels, decreasing RIP3 and MLKL protein expressions through the intracellular RIP3-mediated programmed cell necrosis pathway. In addition, carvacrol also may exhibit anti-HSV-2 activity by reversing the ubiquitination decrease level caused by HSV-2 infection on the ubiquitin-proteasome system, which provides insights into the molecular mechanism.
A packaged intervention to improve viral load monitoring within a deeply rural health district of South Africa
Authors: Brijkumar J. , Johnson B. A. , Zhao Y. , Edwards J. , Moodley P. , Pathan K. , Pillay S. , Castro K. G. , Sunpath H. , Kuritzkes D. R. , Moosa M. Y. S. , Marconi V. C. 
Published: November 2020

Abstract

Background
The KwaZulu-Natal (KZN) province of South Africa has the highest prevalence of HIV infection in the world. Viral load (VL) testing is a crucial tool for clinical and programmatic monitoring. Within uMkhanyakude district, VL suppression rates were 91% among patients with VL data; however, VL performance rates averaged only 38·7%. The objective of this study was to determine if enhanced clinic processes and community outreach could improve VL monitoring within this district.

Methods
A packaged intervention was implemented at three rural clinics in the setting of the KZN HIV AIDS Drug Resistance Surveillance Study. This included file hygiene, outreach, a VL register and documentation revisions. Chart audits were used to assess fidelity. Outcome measures included percentage VL performed and suppressed. Each rural clinic was matched with a peri-urban clinic for comparison before and after the start of each phase of the intervention. Monthly sample proportions were modelled using quasi-likelihood regression methods for over-dispersed binomial data.

Results
Mkuze and Jozini clinics increased VL performance overall from 33·9% and 35·3% to 75·8% and 72·4%, respectively which was significantly greater than the increases in the comparison clinics (RR 1·86 and 1·68, p < 0·01). VL suppression rates similarly increased overall by 39·3% and 36·2% (RR 1·84 and 1·70, p < 0·01). The Chart Intervention phase showed significant increases in fidelity 16 months after implementation.

Conclusions
The packaged intervention improved VL performance and suppression rates overall but was significant in Mkuze and Jozini. Larger sustained efforts will be needed to have a similar impact throughout the province.
Aerobic exercise capacity is maintained over a 5-year period in mild-to-moderate chronic kidney disease: a longitudinal study
Authors: Wallin Helena , Jansson Eva , Wallquist Carin , Hylander Rössner Britta , Jacobson Stefan H. , Rickenlund Anette , Eriksson Maria J. 
Published: November 2020

AbstractBackgroundAerobic exercise capacity is reduced in non-dialysis chronic kidney disease (CKD), but the magnitude of changes in exercise capacity over time is less known. Our main hypothesis was that aerobic ExCap would decline over 5 years in individuals with mild-to-moderate CKD along with a decline in renal function. A secondary hypothesis was that such a decline in ExCap would be associated with a decline in muscle strength, cardiovascular function and physical activity.MethodsWe performed a 5-year-prospective study on individuals with mild-to-moderate CKD, who were closely monitored at a nephrology clinic. Fiftytwo individuals with CKD stage 2–3 and 54 age- and sex-matched healthy controls were included. Peak workload was assessed through a maximal cycle exercise test. Muscle strength and lean body mass, cardiac function, vascular stiffness, self-reported physical activity level, renal function and haemoglobin level were evaluated. Tests were repeated after 5 years. Statistical analysis of longitudinal data was performed using linear mixed models.ResultsExercise capacity did not change significantly over time in either the CKD group or controls, although the absolute workloads were significantly lower in the CKD group. Only in a CKD subgroup reporting low physical activity at baseline, exercise capacity declined. Renal function decreased in both groups, with a larger decline in CKD (p = 0.05 between groups). Peak heart rate, haemoglobin level, handgrip strength, lean body mass and cardiovascular function did not decrease significantly over time in CKD individuals.ConclusionsOn a group level, aerobic exercise capacity and peak heart rate were maintained over 5 years in patients with well-controlled mild-to-moderate CKD, despite a slight reduction in glomerular filtration rate. In line with the maintained exercise capacity, cardiovascular and muscular function were also preserved. In individuals with mild-to-moderate CKD, physical activity level at baseline seems to have a predictive value for exercise capacity at follow-up.