bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic and evolutionary features of two AHPND positive Vibrio parahaemolyticus strains isolated from shrimp (Penaeus monodon) of south-west Bangladesh
Authors: Ahmmed Shawon , Khan Md. Abdullah-Al-Kamran , Eshik Md. Mostavi Enan , Punom Nusrat Jahan , Islam Abul Bashar Mir Md. Khademul , Rahman Mohammad Shamsur 
Published: December 2019

Abstract
Background
Due to its rapid lethal effect in the early development stage of shrimp, acute hepatopancreatic necrosis disease (AHPND) has been causing great economic losses, since its first outbreak in southeast China in 2009. Vibrio parahaemolyticus, carrying the pirA and pirB toxin genes is known to cause AHPND in shrimp. The overall objective of this study was to sequence the whole genome of AHPND positive V. parahaemolyticus strains isolated from shrimp (Peneaus monodon) of the south-west region of Bangladesh in 2016 and 2017 and characterize the genomic features and emergence pattern of this marine pathogen.

Results
Two targeted AHPND positive V. parahaemolyticus strains were confirmed using PCR with 16S rRNA, ldh, AP3 and AP4 primers. The assembled genomes of strain MSR16 and MSR17 were comprised of a total of 5,393,740 bp and 5,241,592 bp, respectively. From annotation, several virulence genes involved in chemotaxis and motility, EPS type II secretion system, Type III secretion system-1 (T3SS-1) and its secreted effectors, thermolabile hemolysin were found in both strains. Importantly, the ~ 69 kb plasmid was identified in both MSR16 and MSR17 strains containing the two toxin genes pirA and pirB. Antibiotic resistance genes were predicted against β-lactam, fluoroquinolone, tetracycline and macrolide groups in both MSR16 and MSR17 strains.

Conclusions
The findings of this research may facilitate the tracking of pathogenic and/or antibiotic-resistant V. parahaemolyticus isolates between production sites, and the identification of candidate strains for the production of vaccines as an aid to control of this devastating disease. Also, the emergence pattern of this pathogen can be highlighted to determine the characteristic differences of other strains found all over the world.
A whole canopy gas exchange system for the targeted manipulation of grapevine source-sink relations using sub-ambient CO2
Authors: Smith Jason P. , Edwards Everard J. , Walker Amanda R. , Gouot Julia C. , Barril Celia , Holzapfel Bruno P. 
Published: December 2019

AbstractBackgroundElucidating the effect of source-sink relations on berry composition is of interest for wine grape production as it represents a mechanistic link between yield, photosynthetic capacity and wine quality. However, the specific effects of carbohydrate supply on berry composition are difficult to study in isolation as leaf area or crop adjustments can also change fruit exposure, or lead to compensatory growth or photosynthetic responses. A new experimental system was therefore devised to slow berry sugar accumulation without changing canopy structure or yield. This consisted of six transparent 1.2 m3chambers to enclose large pot-grown grapevines, and large soda-lime filled scrubbers that reduced carbon dioxide (CO2) concentration of day-time supply air by approximately 200 ppm below ambient.ResultsIn the first full scale test of the system, the chambers were installed on mature Shiraz grapevines for 14 days from the onset of berry sugar accumulation. Three chambers were run at sub-ambient CO2for 10 days before returning to ambient. Canopy gas exchange, and juice hexose concentrations were determined. Net CO2exchange was reduced from 65.2 to 30 g vine− 1 day− 1, or 54%, by the sub-ambient treatment. At the end of the 10 day period, total sugar concentration was reduced from 95 to 77 g L− 1from an average starting value of 23 g L− 1, representing a 25% reduction. Scaling to a per vine basis, it was estimated that 223 g of berry sugars accumulated under ambient supply compared to 166 g under sub-ambient, an amount equivalent to 50 and 72% of total C assimilated.ConclusionsThrough supply of sub-ambient CO2using whole canopy gas exchange chambers system, an effective method was developed for reducing photosynthesis and slowing the rate of berry sugar accumulation without modifying yield or leaf area. While in this case developed for further investigations of grape and wine composition, the system has broader applications for the manipulation and of study of grapevine source-sink relations.
Time to shape up – assessment and reporting standards for data quality in clinical research using echocardiographic imaging techniques require improvement
Authors: Hensel Kai O. 
Published: December 2019

AbstractAdvanced echocardiography techniques such as speckle tracking imaging are sensitive diagnostic tools frequently used in various clinical and scientific scenarios. Importantly, imperfect reproducibility and dependence of post-processing algorithms on echocardiographic image quality are potential methodological limitations. Therefore, meticulous assessment of data quality and detailed reporting of study methodology, sample specifics, technical peculiarities and measurement conditions are crucial. Unfortunately, despite the recognized importance of this, there is still no broadly accepted standard for assessing the quality of echocardiographic images in clinical research reports. This article quintessentially highlights important shortcomings of data quality assessment and methodological study design, commonly occurring in clinical research reports using advanced echocardiography techniques. Finally, suggestions are made as to how researchers, scientific communities and biomedical journals can contribute to the ever-lasting process of improving the quality of clinical research in cardiovascular imaging.
Determinants of first line antiretroviral therapy treatment failure among adult patients on ART at central Ethiopia: un-matched case control study
Authors: Mulisa Diriba , Tesfa Mulugeta , Mullu Kassa Getachew , Tolossa Tadesse 
Published: December 2019

AbstractBackgroundIn 2018 in Ethiopia, magnitude of human immunodeficiency virus Acquired Immunodeficiency Syndrome treatment failure was 15.9% and currently the number of patient receiving second line antiretroviral therapy (ART) is more increasing than those taking first line ART. Little is known about the predictors of treatment failure in the study area. Therefore; more factors that can be risk for first line ART failure have to identified to make the patients stay on first line ART for long times. Consequently, the aim of this study was to identify determinants of first line ART treatment failure among patients on ART at St. Luke referral hospital and Tulubolo General Hospital, 2019.MethodsA 1:2 un-matched case-control study was conducted among adult patients on active follow up. One new group variables was formed as group 1 for cases and group 0 for controls and then data was entered in to Epi data version 3 and exported to STATA SE version 14 for analysis. From binary logistic regression variables withpvalue ≤0.25 were a candidate for multiple logistic regression. At the end variables with ap-value ≤0.05 were considered as statistically significant.ResultA total of 350 (117 cases and 233 controls) patients were participated in the study. Starting ART after 2 years of being confirmed HIV positive (AOR = 3.82 95% CI 1.37,10.6), nevirapine (NVP) based initial ART (AOR = 2.77,95%CI 1.22,6.28) having history of lost to follow up (AOR 3.66,95%CI 1.44,9.27) and base line opportunistic infection (AOR = 1.97,95%CI 1.06,3.63), staying on first line ART for greater than 5 years (AOR = 3.42,95%CI 1.63,7.19) and CD4 less than100cell/ul (AOR = 2.72,95%CI 1.46,5.07) were independent determinants of first line ART treatment failure.ConclusionLost to follow up, staying on first line ART for greater than 5 years, presence of opportunistic infections, NVP based NNRT, late initiation of ART are determinant factors for first line ART treatment failure. The concerned bodies have to focus and act on those identified factors to maintain the patient on first line ART.
“They turn to you first for everything”: insights into midwives’ perspectives of providing physical activity advice and guidance to pregnant women
Authors: De Vivo Marlize , Mills Hayley 
Published: December 2019

Abstract
Background
The antenatal period is associated with a decline in physical activity among women. Midwives are viewed central to the dissemination of information during pregnancy, however, there is little research relating to their promotion of physical activity. The purpose of this study was to gain insight into midwives’ perspectives of providing physical activity advice and guidance to pregnant women

Methods
Community midwives (N = 10) from ten randomly selected antenatal clinics in England took part in semi-structured interviews which were audio recorded, transcribed and analysed thematically

Results
In relation to perceived role and responsibilities in providing physical activity advice and guidance, midwives emphasised the extent to which their profession has evolved, the perceived burden of responsibility, and the tick box approach to physical activity discussion. Midwives identified a lack of training, knowledge, confidence, time, resources, and perceptions of vulnerability as barriers to effective physical activity promotion. Despite these issues midwives proposed eight opportunities to facilitate pregnant women’s physical activity engagement: (1) recognising and addressing barriers in the uptake and maintenance of physical activities, (2) professional development, (3) inter-professional collaboration, (4) communicating effectively through simple, reliable resources, (5) improved access, availability, and awareness of suitable activities in the local community, (6) encouraging a support network, (7) “selling” physical activity by challenging misconceptions and focusing on benefits, and (8) suitable motivation, incentives and reward.

Conclusions
These opportunities identified by midwives provide foundations from which improvements in practice can result. Whilst midwives are ideally placed to promote physical activity as part of a healthy pregnancy, this is likely to be most effective as part of a wider network of practitioners that share consistent and confident messages regarding physical activity engagement. This notion has far reaching implications for practice, policy, research and the normalisation of active pregnancies in the wider population.
Identification of recurrence marker associated with immune infiltration in prostate cancer with radical resection and build prognostic nomogram
Authors: Rui Xin , Shao Siliang , Wang Li , Leng Jiangyong 
Published: December 2019

AbstractBackgroundSome historic breakthroughs have been made in immunotherapy of advanced cancer. However, there is still little research on immunotherapy in prostate cancer. We explored the relationship between immune cell infiltration and prostate cancer recurrence and tried to provide new ideas for the treatment of prostate cancer.MethodsProstate cancer RNA-seq data and clinical information were downloaded from the TCGA database and GEO database. The infiltration of 24 immune cells in tissues was quantified by ssGSEA. Univariate Cox regression analysis was used to screen for immune cell types associated with tumor recurrence, weighted gene co-expression network analysis (WGCNA) and LASSO were used to identify hub genes which regulate prognosis in patients through immune infiltration. Then, the nomogram was constructed based on the hub gene to predict the recurrence of prostate cancer, and the decision curve analysis (DCA) was used to compare the accuracy with the PSA and Gleason prediction models.ResultAnalysis showed that Th2 cells and Tcm related to prostate cancer recurrence after radical prostatectomy, and they are independent protective factors for recurrence. Through WGCNA and Lasso, we identified that NDUFA13, UQCR11, and USP34 involved in the infiltration of Th2 cells and Tcm in tumor tissues, and the expression of genes is related to the recurrence of patients. Based on the above findings, we constructed a clinical prediction model and mapped a nomogram, which has better sensitivity and specificity for prostate cancer recurrence prediction, and performed better in comparison with PSA and Gleason’s predictions.ConclusionThe immune cells Th2 cells and Tcm are associated with recurrence of PCa. Moreover, the genes NDUFA13, UQCR11, and USP34 may affect the recurrence of PCa by affecting the infiltration of Th2 cells and Tcm. Moreover, nomogram can make prediction effectively.
The Therapeutic Engagement Questionnaire (TEQ): a service user-focused mental health nursing outcome metric
Authors: Chambers Mary , McAndrew Sue , Nolan Fiona , Thomas Ben , Watts Paul , Grant Robert , Kantaris Xenya 
Published: December 2019

AbstractBackgroundTherapeutic engagement (TE) has been described as the crux of mental health nursing but despite its perceived importance, to date, there is no measurement tool that captures it. As a result, there is no way of determining the contribution of mental health nursing interaction to service user recovery, in acute inpatient mental health settings or the wider care quality agenda.MethodsTo develop and validate a TE measurement tool in partnership with Service Users (SUs) and Registered Mental Health Nurses (RMHNs). The TEQ was developed in 3 stages: 1) item generation (and pre-testing), 2) item reduction using Principal Component Analysis (PCA), and 3) validation across Mental Health Trusts in England.ResultsThe final questionnaire has two versions, (SU and RMHN version), each scored within two contexts (1–1 SU-RMHN interactions and overall environment and atmosphere of the ward) and includes 20 items with two sub-scales (care interactions and care delivery). Psychometric evaluation of the TEQ shows high inter-scale correlations (0.66–0.95 SU; 0.57–0.90 RMHN), sound sub-scale internal consistency (> 0.95), concurrent validity (> 0.60) and adequate score variability for both versions of the TEQ. In summary, the TEQ behaves well as a measurement tool.ConclusionsThe TEQ can determine the collaborative and empathic nature of RMHN-SU interactions, capture if SUs are treated with dignity and respect and recognise that the principles of the recovery approach are being respected. The TEQ can also provide robust monitoring of nursing activity, offer opportunity for transparency of activity, feed into healthcare organizations’ key performance indicators and provide reassurance about the nature and quality of nurses’ work.
Prevalence of asymptomatic malaria parasitaemia following mass testing and treatment in Pakro sub-district of Ghana
Authors: Ndong Ignatius Cheng , Okyere Daniel , Enos Juliana Yartey , Mensah Benedicta A. , Nyarko Alexander , Abuaku Benjamin , Amambua-Ngwa Alfred , Merle Corinne Simone C. , Koram Kwadwo Ansah , Ahorlu Collins Stephen 
Published: December 2019

Abstract
Background
Global efforts to scale-up malaria control interventions are gaining steam. These include the use of Long-Lasting Insecticide Nets, Indoor Residual Spraying, Intermittent Preventive Treatment and Test, Treat and Track. Despite these, the drive for malaria elimination is far from being realistic in endemic communities in Africa. This is partly due to the fact that asymptomatic parasite carriage, not specifically targeted by most interventions, remains the bedrock that fuels transmission. This has led to mass testing, treatment and tracking (MTTT) as an alternative strategy to target asymptomatic individuals. We report the impact of MTTT on the prevalence of asymptomatic malaria parasitaemia over a one-year period in Ghana, hypothesizing that implementing MTTT could reduce the rate of asymptomatic parasitaemia.

Methods
A population of about 5000 individuals in seven communities in the Pakro sub-district of Ghana participated in this study. A register was developed for each community following a census. MTTT engaged trained community-based health volunteers who conducted house-to-house testing using RDTs every 4 months and treated positive cases with Artemisinin–based Combination Therapy. Between interventions, community-based management of malaria was implemented for symptomatic cases.

Results
MTTT Coverage was 98.8% in July 2017 and 79.3% in July 2018. Of those tested, asymptomatic infection with malaria parasites reduced from 36.3% (1795/4941) in July 2017 to 32.9% (1303/3966) in July 2018 (p = 0.001). Prevalence of asymptomatic parasitaemia among children under 15 years declined from 52.6% (1043/1984) in July 2017 to 47.5% (820/1728) in July 2018 (p = 0.002). Implementing MTTT significantly reduced asymptomatic parasitaemia by 24% from July 2017 to July 2018 after adjusting for age, ITN use and axillary temperature (OR = 0.76, CI = 0.67, 0.85 p ≤ 0.001).

Conclusion
This study has demonstrated that implementing MTTT is feasible and could reduce the prevalence of asymptomatic malaria parasitaemia in children under 15 years of age. Furthermore, the use of community-based health volunteers could ensure high coverage at lower cost of implementation.

Trial registration
NCT04167566, Date 14/11/2019. Retrospective registration.
Development of a high-precision bladder hyperthermic intracavitary chemotherapy device for bladder cancer and pharmacokinetic study
Authors: Ba Mingchen , Cui Shuzhong , Long Hui , Gong Yuanfeng , Wu Yinbing , Lin Kunpeng , Tu Yinuo , Zhang Bahuo , Wu Wanbo 
Published: December 2019

Abstract
Background
Bladder hyperthermic intracavitary chemotherapy (HIVEC) has good effectiveness for bladder cancer, but conventional HIVEC systems lack precision and convenient application. To test the safety of a new HIVEC device (BR-TRG-II-type) in pigs and to perform a preliminary clinical trial in patients with bladder cancer.

Methods
This device was tested on six pigs to optimize the temperature and time parameters. Then, 165 patients (HIVEC after transurethral resection (TUR), n = 128; or HIVEC, n = 37) treated between December 2006 and December 2016 were recruited. Mitomycin C (MMC) was the chemotherapeutic agent. A serum pharmacokinetic study was performed. The primary endpoints were tumor recurrence, disease-free survival (DFS), and cumulative incidence rate (CIR) during follow-up. The adverse effects were graded.

Results
The animal experiment showed that 45 °C for 1 h was optimal. HIVEC was successful, with the infusion tube temperature stably controlled at about 45 °C, and outlet tube temperature of about 43 °C in all patients, for three sessions. Serum MMC levels gradually increased during HIVEC and decreased thereafter. The mean DFS was 39 ± 3.21 months (ranging from 8 to 78 months), and the DFS rate was 89.1% during follow-up. No adverse events occurred.

Conclusion
The use of the BR-TRG-II-type HIVEC device is feasible for the treatment of bladder cancer. Future clinical trials in patients with different stages of bladder cancer will further confirm the clinical usefulness of this device.

Trial registration
chictr.org.cn: ChiCTR1900022099 (registered on Mar. 252,019). Retrospectively registered.
Comparing dental plaque microbiome diversity of extrinsic black stain in the primary dentition using Illumina MiSeq sequencing technique
Authors: Chen Lulu , Zhang Qiong , Wang Yan , Zhang Keke , Zou Jing 
Published: December 2019

Abstract
Background
Extrinsic black stain (EBS) is characterized by discrete dark dots or lines on the tooth surface. The relationship between EBS and oral microbiota in children remains elusive. The aim of this study was to compare dental plaque microbiome in EBS children with that in EBS-free children in the primary dentition.

Methods
The Illumina MiSeq sequencing technique was utilized in the cross-sectional pilot study to investigate the diversity and composition of the supragingival plaque microbiota from 10 EBS-positive and 10 EBS-free children. The results were analysed with nonparametric Mann-Whitney U test, Pearson Chi-Square test, Fisher’s Exact test and one-way ANOVA tests.

Results
We identified 13 different phyla, 22 classes, 33 orders, 54 families, 105 genera, and 227 species from a total of 52,646 high-quality sequences. Between two groups, no statistical differences were observed in the estimators of community richness and diversity at 97% similarity, as well as in the Unweighted Unifrac principal co-ordinates analysis (PCoA). At the species level, higher level of relative abundance of Actinomyces naeslundii and lower level of relative abundance of a species belonging to Candidate_division_TM7 was observed in dental plaque of EBS-positive subjects, compared to dental plaque of EBS-free subjects (P < 0.05). This indicated that some species might be involved in the EBS process.

Conclusion
Changes in dental plaque microbiota is possibly relevant to the process of EBS in the primary dentition.
Patient perceptions in quality of care: report from university veterans clinic
Authors: Rai Nayanjot K. , Tyrrell Heidi , Carey Clifton , Tiwari Tamanna 
Published: December 2019

Abstract
Background
The Heroes Clinic is a unique dental clinic housed at the University of Colorado School of Dental Medicine that offers military veterans dental care at no or minimal cost. The aim of this study is to collect patient feedback on their perception of the quality of care they receive at the Heroes clinic.

Methods
A cross-sectional study design was used to gather patient feedback on empathy and quality of care using Service Quality Measures (SERVQUAL) and Dental Satisfaction Questionnaire (DSQ) frameworks. Mean scores were calculated to determine the average of positive or negative responses. Fisher’s exact test was conducted to test any significant differences between the patients’ perception of quality of care they receive at the Heroes clinic (outcome variable) and the SERVQUAL and DSQ independent variables.

Results
One hundred and seventy-seven veterans responded to the survey with a response rate of 35%. Over 50% of patients were between the ages of 20–35 years and 63% were students. The mean scores demonstrated high levels of all variables. Bivariate analysis for SERVQUAL data determined that veterans agreed to conditions demonstrated by four scales of empathy and all scales of responsiveness (p < 0.05). DSQ bivariate analysis revealed that veterans agreed to conditions demonstrated by four scales of quality of care, two scales of pain management, one scale of accessibility, and also general satisfaction pertaining to the received dental care (p < 0.05).

Conclusions
Heroes clinic has provided quality dental care to veterans as attested by the patients.