bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide association studies of ionomic and agronomic traits in USDA mini core collection of rice and comparative analyses of different mapping methods
Authors: Liu Shuai , Zhong Hua , Meng Xiaoxi , Sun Tong , Li Yangsheng , Pinson Shannon R. M. , Chang Sam K. C. , Peng Zhaohua 
Published: September 2020

Abstract
Background
Rice is an important human staple food vulnerable to heavy metal contamination leading to serious concerns. High yield with low heavy metal contamination is a common but highly challenging goal for rice breeders worldwide due to lack of genetic knowledge and markers.

Results
To identify candidate QTLs and develop molecular markers for rice yield and heavy metal content, a total of 191 accessions from the USDA Rice mini-core collection with over 3.2 million SNPs were employed to investigate the QTLs. Sixteen ionomic and thirteen agronomic traits were analyzed utilizing two univariate (GLM and MLM) and two multivariate (MLMM and FarmCPU) GWAS methods. 106, 47, and 97 QTLs were identified for ionomics flooded, ionomics unflooded, and agronomic traits, respectively, with the criterium of p-value < 1.53 × 10− 8, which was determined by the Bonferroni correction for p-value of 0.05. While 49 (~ 20%) of the 250 QTLs were coinciding with previously reported QTLs/genes, about 201 (~ 80%) were new. In addition, several new candidate genes involved in ionomic and agronomic traits control were identified by analyzing the DNA sequence, gene expression, and the homologs of the QTL regions. Our results further showed that each of the four GWAS methods can identify unique as well as common QTLs, suggesting that using multiple GWAS methods can complement each other in QTL identification, especially by combining univariate and multivariate methods.

Conclusions
While 49 previously reported QTLs/genes were rediscovered, over 200 new QTLs for ionomic and agronomic traits were found in the rice genome. Moreover, multiple new candidate genes for agronomic and ionomic traits were identified. This research provides novel insights into the genetic basis of both ionomic and agronomic variations in rice, establishing the foundation for marker development in breeding and further investigation on reducing heavy-metal contamination and improving crop yields. Finally, the comparative analysis of the GWAS methods showed that each method has unique features and different methods can complement each other.
Factors affecting the fruit and vegetable intake in Nepal and its association with history of self-reported major cardiovascular events
Authors: Nepali Sajama , Rijal Anupa , Olsen Michael Hecht , McLachlan Craig S. , Kallestrup Per , Neupane Dinesh 
Published: September 2020

Abstract
Background
The World Health Organization recommends consumption of a minimum of 400 g of fruits and vegetables per day for prevention of cardiovascular disease. Low fruit and vegetable intake is associated with an increased risk of stroke by 11% and ischemic heart disease by 31%. The present study aims to explore factors affecting the fruit and vegetable intake in Nepal and its association with history of self-reported major cardiovascular events (myocardial infarction and stroke).

Method
Data for this cross-sectional study were collected as part of the study “Community Based Management of Hypertension in Nepal” initiated in the Lekhnath Municipality in 2013. Demographic and nutrition information were collected using the WHO STEPwise approach to a surveillance tool. Descriptive statistics identified the frequency and percentage of fruit and vegetable intake. A Chi-square test examined the association between fruit and vegetable intake and history of self-reported cardiovascular events, socio-demographic and cardiovascular risk factors. Binary logistic regression analysis identified odds ratio with 95% confidence intervals between fruit and vegetable intake and history of self-reported cardiovascular events.

Results
The mean and median intake of fruits and vegetables were 3.3 ± 0.79 and 3 servings respectively. Of the 2815 respondents, 2% (59) reported having a history of major cardiovascular events. The adjusted odds of having a history of major cardiovascular events was 2.22 (95%CI, 1.06–4.66) for those who consumed < 3 servings compared to those who consumed ≥3 servings of fruits and vegetables a day.

Conclusion
The respondents who consumed < 3 servings of fruits and vegetables a day had higher odds of a history of major cardiovascular events in comparison to those who consumed ≥3 servings. This finding may carry a policy recommendation for those settings where the current recommendation of having ≥5 servings of fruits and vegetables a day is not possible. Our findings also suggest that surviving a major cardiovascular event was not enough in itself to modify nutritional intake. As many Nepali consumes low amount of fruits and vegetables, appropriate measures should be taken to increase this consumption to prevent cardiovascular morbidity and mortality.
Integrating trials into a whole-population cohort of children and parents: statement of intent (trials) for the Generation Victoria (GenV) cohort
Authors: Wake Melissa , Hu Yanhong Jessika , Warren Hayley , Danchin Margie , Fahey Michael , Orsini Francesca , Pacilli Maurizio , Perrett Kirsten P. , Saffery Richard , Davidson Andrew 
Published: September 2020

Abstract
Background
Very large cohorts that span an entire population raise new prospects for the conduct of multiple trials that speed up advances in prevention or treatment while reducing participant, financial and regulatory burden. However, a review of literature reveals no blueprint to guide this systematically in practice. This Statement of Intent proposes how diverse trials may be integrated within or alongside Generation Victoria (GenV), a whole-of-state Australian birth cohort in planning, and delineates potential processes and opportunities.

Methods
Parents of all newborns (estimated 160,000) in the state of Victoria, Australia, will be approached for two full years from 2021. The cohort design comprises four elements: (1) consent soon after birth to follow the child and parent/s until study end or withdrawal; retrospective and prospective (2) linkage to clinical and administrative datasets and (3) banking of universal and clinical biosamples; and (4) GenV-collected biosamples and data. GenV-collected data will focus on overarching outcome and phenotypic measures using low-burden, universal-capable electronic interfaces, with funding-dependent face-to-face assessments tailored to universal settings during the early childhood, school and/or adult years.

Results
For population or registry-type trials within GenV, GenV will provide all outcomes data and consent via traditional, waiver, or Trials Within Cohorts models. Trials alongside GenV consent their own participants born within the GenV window; GenV may help identify potential participants via opt-in or opt-out expression of interest. Data sharing enriches trials with outcomes, prior data, and/or access to linked data contingent on custodian’s agreements, and supports modeling of causal effects to the population and between-trials comparisons of costs, benefits and utility. Data access will operate under the Findability, Accessibility, Interoperability, and Reusability (FAIR) and Care and Five Safes Principles. We consider governance, ethical and shared trial oversight, and expectations that trials will adhere to the best practice of the day.

Conclusions
Children and younger adults can access fewer trials than older adults. Integrating trials into mega-cohorts should improve health and well-being by generating faster, larger-scale evidence on a longer and/or broader horizon than previously possible. GenV will explore the limits and details of this approach over the coming years.
Knowledge, attitudes, and practices of primary health care physicians regarding the pre-travel counselling of patients with type 2 diabetes in Riyadh, Saudi Arabia
Authors: Alduraibi Rabia Khalid , Almigbal Turky H. , Alrasheed Abdullah A. , Batais Mohammed Ali 
Published: September 2020

Abstract
Background
Travel has become an integral part of Saudi life. People with diabetes face many challenges while travelling that can have detrimental effects on glycaemic control. However, no previous studies have investigated pre-travel counselling in Saudi Arabia. This study aims to assess the knowledge, attitudes and practices of primary health care (PHC) physicians regarding pre-travel counselling for patients with type 2 diabetes.

Methods
This cross-sectional study was conducted in PHC centres under the Ministry of Health in Riyadh, Saudi Arabia, during the period 2018–2019. A cluster multistage random sampling technique was used to recruit physicians. The data were collected through a self-administered questionnaire.

Results
Three hundred and eighty-five primary health care physicians were recruited. This study showed that more than half (57.9%) of PHC physicians had poor knowledge scores. Additionally, the following characteristics were significantly associated with poor knowledge: being younger in age, being male, being Saudi, being a general practitioner, and having limited (0–5 years) experience. A total of 183 (47.5%) subjects showed disagreement attitudes towards the importance of pre-travel counselling among patients with diabetes. Furthermore, these disagreement attitudes were significantly associated with being older and having more years of experience. The majority (62.6%) of the physicians had poor practice scores. Poor practices were detected among physicians who were younger, male, and Saudi and who had a general practitioner specialty and degree.

Conclusions
It could be concluded that a gap was detected in the knowledge and practices of primary health care physicians regarding pre-travel counselling for people with type 2 diabetes. Therefore, it is necessary to create easily accessible travel medicine education programmes for Saudi PHC providers to improve the management of travellers with diabetes.
Mechanical Thrombectomy of COVID-19 positive acute ischemic stroke patient: a case report and call for preparedness
Authors: Mansour Ossama Yassin , Malik Amer M. , Linfante Italo 
Published: September 2020

Abstract
Background
The novel coronavirus (COVID-19) global pandemic is associated with an increased incidence of acute ischemic stroke (AIS) secondary to large vessel occlusion (LVO). The treatment of these patients poses unique and significant challenges to health care providers requiring changes in existing protocols.

Case presentation
A 54-year-old COVID-19 positive patient developed sudden onset left hemiparesis secondary to an acute right middle cerebral artery occlusion (National Institutes of Health Stroke Scale (NIHSS) score = 11). Mechanical thrombectomy (MT) was performed under a new protocol specifically designed to maximize protective measures for the team involved in the care of the patient. Mechanical Thrombectomy was performed successfully under general anesthesia resulting in TICI 3 recanalization. With regards to time metrics, time from door to reperfusion was 60 mins. The 24-h NIHSS score decreased to 2. Patient was discharged after 19 days after improvement of her pulmonary status with modified Rankin Scale = 1.

Conclusion
Patients infected by COVID-19 can develop LVO that is multifactorial in etiology. Mechanical thrombectomy in a COVID-19 confirmed patient presenting with AIS due to LVO is feasible with current mechanical thrombectomy devices. A change in stroke workflow and protocols is now necessary in order to deliver the appropriate life-saving therapy for COVID-19 positive patients while protecting medical providers.
An immunotherapy effect analysis in Rasmussen encephalitis
Authors: Liba Zuzana , Vaskova Martina , Zamecnik Josef , Kayserova Jana , Nohejlova Hana , Ebel Matyas , Sanda Jan , Ramos-Rivera Gonzalo Alonso , Brozova Klara , Liby Petr , Tichy Michal , Krsek Pavel 
Published: September 2020

Abstract
Background
Immune-mediated mechanisms substantially contribute to the Rasmussen encephalitis (RE) pathology, but for unknown reasons, immunotherapy is generally ineffective in patients who have already developed intractable epilepsy; overall laboratory data regarding the effect of immunotherapy on patients with RE are limited. We analyzed multiple samples from seven differently treated children with RE and evaluated the effects of immunotherapies on neuroinflammation. Immunotherapy was introduced to all patients at the time of intractable epilepsy and they all had to undergo hemispherothomy.

Methods
Immunohistochemistry, flow cytometry, Luminex multiplex bead and enzyme-linked immunosorbent assay techniques were combined to determine: 1) inflammatory changes and lymphocyte subpopulations in 45 brain tissues; 2) lymphocyte subpopulations and the levels of 12 chemokines/cytokines in 24 cerebrospinal fluid (CSF) samples and 30 blood samples; and 3) the dynamics of these parameters in four RE patients from whom multiple samples were collected.

Results
Sustained T cell-targeted therapy with cyclophosphamide, natalizumab, alemtuzumab, and intrathecal methotrexate (ITMTX), but not with azathioprine, substantially reduced inflammation in brain tissues. Despite the therapy, the distributions of CD8+ T cells and the levels of C-X-C motif ligand (CXCL) 10, CXCL13, and B cell activating factor (BAFF) in patients’ CSF remained increased compared to controls. A therapeutic approach combining alemtuzumab and ITMTX was the most effective in producing simultaneous reductions in histopathological inflammatory findings and in the numbers of activated CD8+ T cells in the brain tissue, as well as in the overall CD8+ T cell population and chemokine/cytokine production in the CSF.

Conclusions
We provide evidence that various T cell-targeted immunotherapies reduced inflammation in the brains of RE patients. The observation that intractable epilepsy persisted in all of the patients suggests a relative independence of seizure activity on the presence of T cells in the brain later in the disease course. Thus, new therapeutic targets must be identified. CXCL10, CXCL13 and BAFF levels were substantially increased in CSF from all patients and their significance in RE pathology remains to be addressed.
Determinants for choice of home birth over health facility birth among women of reproductive age in Tanzania: an analysis of data from the 2015-16 Tanzania demographic and health survey and malaria indicator survey
Authors: Moshi Fabiola V. , Mbotwa Christopher H. 
Published: September 2020

Abstract
Background
While evidence has shown an association between place of birth and birth outcomes, factors contributing to the choice of home birth have not been adequately investigated in Tanzania while more than 30% of deliveries occur outside of health care facilities, and more than 95% of those deliveries are assisted by non-medical providers who are often unskilled. The use of unskilled birth attendants has been cited as a factor contributing to the high maternal and neonatal mortalities in low-resources countries. This study aimed to identify determinants of choice for home birth over health care facility birth in Tanzania.

Method:
This study used the 2015-16 Tanzania Demographic and Health Survey and Malaria Indicator Survey (2015-16 TDHS-MIS) dataset. A total of 2286 women of reproductive age (15–49 years) who gave birth within one year preceding the survey were included in the analysis. Both univariate and multivariable regression analyses were used to determine predictors for the choice of home-based childbirth over health care facility delivery.

Results
A total of 805 (35.2%) women had a home birth. After adjusting for confounders, the determinants for choice of home birth were: the level of education (primary education [AOR = 0.666; p = 0.001]; secondary and higher education [AOR = 0.417; p < 0.001]), in reference to no formal education; not owning a mobile phone (AOR = 1.312; p = 0.018); parity (parity 2–4 [AOR = 1.594; p = 0.004], parity 5 and above [AOR = 2.158; p < 0.001] in reference to parity 1); inadequate antenatal visits (AOR = 1.406; p = 0.001); wealth index (poorest (AOR = 9.395, p < 0.001); poorer (AOR = 7.701; p < 0.001); middle (AOR = 5.961; p < 0.001); richer (AOR = 2.557; p < 0.001)] in reference to richest women; and Zones (Southern Highlands, [AOR = 0.189; p < 0.001]; Southern, [AOR = 0.225; p < 0.001]; Zanzibar, [AOR = 2.55; p < 0.001]) in reference to Western zone.

Conclusions
A large proportion of women birth at home. Unskilled providers such as traditional birth attendants (TBAs), relatives or friends attend most of them. Predictors for home-based childbirth included lack of formal education, poor access to telecommunication, poor uptake of antenatal visits, low socio-economic status, and geographical zone. Innovative strategies targeting these groups are needed to increase the use of health care facilities for childbirth, thereby reducing maternal and neonatal mortality in Tanzania.
HLA-DPA1 gene is a potential predictor with prognostic values in multiple myeloma
Authors: Yang Jie , Wang Fei , Chen Baoan 
Published: September 2020

Abstract
Background
Multiple myeloma (MM) is an incurable hematological tumor, which is closely related to hypoxic bone marrow microenvironment. However, the underlying mechanisms are still far from fully understood. We took integrated bioinformatics analysis with expression profile GSE110113 downloaded from National Center for Biotechnology Information-Gene Expression Omnibus (NCBI-GEO) database, and screened out major histocompatibility complex, class II, DP alpha 1 (HLA-DPA1) as a hub gene related to hypoxia in MM.

Methods
Differentially expressed genes (DEGs) were filtrated with R package “limma”. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were performed using “clusterProfiler” package in R. Then, protein-protein interaction (PPI) network was established. Hub genes were screened out according to Maximal Clique Centrality (MCC). PrognoScan evaluated all the significant hub genes for survival analysis. ScanGEO was used for visualization of gene expression in different clinical studies. P and Cox p value < 0.05 was considered to be statistical significance.

Results
HLA-DPA1 was finally picked out as a hub gene in MM related to hypoxia. MM patients with down-regulated expression of HLA-DPA1 has statistically significantly shorter disease specific survival (DSS) (COX p = 0.005411). Based on the clinical data of GSE47552 dataset, HLA-DPA1 expression showed significantly lower in MM patients than that in healthy donors (HDs) (p = 0.017).

Conclusion
We identified HLA-DPA1 as a hub gene in MM related to hypoxia. HLA-DPA1 down-regulated expression was associated with MM patients’ poor outcome. Further functional and mechanistic studies are need to investigate HLA-DPA1 as potential therapeutic target.
Consumer perception of food variety in the UK: an exploratory mixed-methods analysis
Authors: Embling Rochelle , Pink Aimee E. , Lee Michelle D. , Price Menna , Wilkinson Laura L. 
Published: September 2020

Abstract
Background
‘Food variety’ is a key term that is frequently used in dietary guidelines around the world. Consuming a variety of foods – be it within a meal, across meals, or as part of the whole diet – is one factor that has been shown to increase food intake. However, little is known about consumer understanding of variety, and this may be a potential barrier to the success of dietary guidelines in today’s ‘obesogenic’ environment. This research sought to explore 1) consumer recognition of different forms of variety, and 2) consumer definitions of variety.

Methods
In an online study (N = 240), participants were asked to discuss a range of photographs depicting different forms of variety, and to directly define the term ‘food variety’. They were unaware of the research aim.

Results
Using a mixed methods approach, directed content analysis of these data showed that individuals referenced multiple forms of variety in the presence of food photographs. However, when asked to define variety, participants tended to only discuss variety in the context of the whole diet.

Conclusions
These findings emphasise a need to educate consumers about variety to encourage adherence to dietary guidelines and help consumers better manage their own food intake.
Risky injection practices and HCV awareness in Chiang Mai Province, Thailand: a respondent-driven sampling study of people who inject drugs
Authors: Prouté Myrtille , Le Coeur Sophie , Tiv Métrey H. , Dub Timothée , Jongpaijitsakul Parinya , Ratnamhin Anantika , Angkurawaranon Chaisiri , Aramrattana Apinun , Lallemant Marc 
Published: September 2020

Abstract
Background
People who inject drugs (PWID) are the most exposed to hepatitis C virus (HCV). In Thailand, drug use is highly criminalized, and harm reduction services are scarce. This study estimates risky injection practices and assesses the proportion of HCV awareness and screening in the PWID population in Northern Thailand.

Methods
We used respondent-driven sampling (RDS) to recruit PWID in Chiang Mai Province. Social and behavioural data were collected through face-to-face interviews at an addiction treatment facility. Weighted population estimates were calculated to limit biases related to the non-random sampling method. Univariate and multivariate analyses were performed to study factors associated with HCV awareness and screening.

Results
One hundred seventy-one PWID were recruited between April 2016 and January 2017. Median age was 33 (Interquartile range: 26–40) years, 12.2% were women, and 49.4% belonged to a minority ethnic group. Among participants, 76.8% injected heroin, 20.7% methadone, and 20.7% methamphetamine. We estimate that 22.1% [95% CI: 15.7–28.6] of the population had shared needles in the last 6 months and that 32.0% [95% CI: 23.6–40.4] had shared injection material. Only 26.6% [95% CI: 17.6–35.6] had heard of HCV. Factors independently associated with knowledge of HCV included belonging to a harm reduction organization (adjusted odds ratio (aOR) = 5.5 [95% CI: 2.0–15.3]) and voluntary participation in a drug rehabilitation programme (aOR = 4.3 [95% CI: 1.3–13.9]), while Lahu ethnicity was negatively associated (aOR = 0.3 [95% CI: 0.1–0.9]). We estimate that 5% of the PWID population were screened for HCV; the only factor independently associated with being screened was membership of a harm reduction organization (aOR = 5.7 [95% CI: 1.6–19.9]).

Conclusion
Our study reveals that the PWID population is poorly informed and rarely screened for HCV, despite widespread risky injection practices. A public health approach aimed at reducing the incidence of HCV should target the PWID population and combine harm reduction measures with information and destigmatization campaigns. Civil society organizations working with PWID are a major asset for the success of such an approach, based on their current positive interventions promoting awareness of and screening for HCV.