bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo assembly of transcriptome and genome-wide identification reveal GA3 stress-responsive WRKY transcription factors involved in fiber formation in jute (Corchorus capsularis)
Authors: Zhang Lilan , Wan Xuebei , Xu Yi , Niyitanga Sylvain , Qi Jianmin , Zhang Liwu 
Published: September 2020

Abstract
Background
WRKY is a group of transcription factors (TFs) that play a vital role in plant growth, development, and stress tolerance. To date, none of jute WRKY (CcWRKY) genes have been identified, even if jute (Corchorus capsularis) is one of the most important natural fiber crops in the world. Little information about the WRKY genes in jute is far from sufficient to understand the molecular mechanism of bast fiber biosynthesis.

Results
A total of 244,489,479 clean reads were generated using Illumina paired-end sequencing. De novo assembly yielded 90,982 unigenes with an average length of 714 bp. By sequence similarity searching for known proteins, 48,896 (53.74%) unigenes were annotated. To mine the CcWRKY TFs and identify their potential function, the search for CcWRKYs against the transcriptome data of jute was performed, and a total of 43 CcWRKYs were identified in this study. The gene structure, phylogeny, conserved domain and three-dimensional structure of protein were analyzed by bioinformatics tools of GSDS2.0, MEGA7.0, DNAMAN5.0, WebLogo 3 and SWISS-MODEL respectively. Phylogenetic analysis showed that 43 CcWRKYs were divided into three groups: I, II and III, containing 9, 28, and 6 members respectively, according to the WRKY conserved domain features and the evolution analysis with Arabidopsis thaliana. Gene structure analysis indicated that the number of exons of these CcWRKYs varied from 3 to 11. Among the 43 CcWRKYs, 10, 2, 2, and 14 genes showed higher expression in leaves, stem sticks, stem barks, and roots at the vigorous vegetative growth stage, respectively. Moreover, the expression of 21 of 43 CcWRKYs was regulated significantly with secondary cell wall biosynthesis genes using FPKM and RT-qPCR by GA3 stress to a typical GA3 sensitive dwarf germplasm in comparison to an elite cultivar in jute. The Cis-element analysis showed that promoters of these 21 CcWRKYs had 1 to 4 cis-elements involved in gibberellin-responsiveness, suggesting that they might regulate the development of bast fiber in response to GA3 stress.

Conclusions
A total of 43 CcWRKYs were identified in jute for the first time. Analysis of phylogenetic relationship and gene structure revealed that these CcWRKYs might have a functional diversity. Expression analysis showed 21 TFs as GA3 stress responsive genes. The identification of these CcWRKYs and the characterization of their expression pattern will provide a basis for future clarification of their functions in bast fiber development in jute.
Feasibility of containing shigellosis in Hubei Province, China: a modelling study
Authors: Rui Jia , Chen Qi , Chen Qiuping , Hu Qingqing , Hannah Mikah Ngwanguong , Zhao Zeyu , Wang Yao , Liu Xingchun , Lei Zhao , Yu Shanshan , Chiang Yi-Chen , Zhao Benhua , Su Yanhua , Zhao Bin , Chen Tianmu 
Published: September 2020

AbstractBackgroundThe transmission features and the feasibility of containing shigellosis remain unclear among a population-based study in China.MethodsA population–based Susceptible – Exposed – Infectious / Asymptomatic – Recovered (SEIAR) model was built including decreasing the infectious period (DIP) or isolation of shigellosis cases. We analyzed the distribution of the reported shigellosis cases in Hubei Province, China from January 2005 to December 2017, and divided the time series into several stages according to the heterogeneity of reported incidence during the period. In each stage, an epidemic season was selected for the modelling and assessing the effectiveness of DIP and case isolation.ResultsA total of 130,770 shigellosis cases were reported in Hubei Province. The median ofReffwas 1.13 (range: 0.86–1.21), 1.10 (range: 0.91–1.13), 1.09 (range: 0.92–1.92), and 1.03 (range: 0.94–1.22) in 2005–2006 season, 2010–2011 season, 2013–2014 season, and 2016–2017 season, respectively. The reported incidence decreased significantly (trendχ2 = 8260.41,P <  0.001) among four stages. The incidence of shigellosis decreased sharply when DIP implemented in three scenarios (γ = 0.1, 0.1429, 0.3333) and when proportion of case isolation increased.ConclusionsYear heterogeneity of reported shigellosis incidence exists in Hubei Province. It is feasible to contain the transmission by implementing DIP and case isolation.
Using Q-methodology to understand the perspectives and practical experiences of dermatologists about treatment difficulties of cutaneous leishmaniasis
Authors: Qurtas Dindar S. , Shabila Nazar Pauls 
Published: September 2020

AbstractBackgroundDuring the outbreak of cutaneous leishmaniasis in the Kurdistan Region of Iraq that started in 2015, the course of the disease and the treatment were not consistent with the available literature. Physicians, particularly dermatologists, faced challenges with treating the cutaneous leishmaniasis lesions with high rates of treatment failure and resistance to treatment. We used Q-methodology to understand the range and diversities of opinions and the practical experiences of dermatologists about the treatment difficulties of cutaneous leishmaniasis.MethodsThis Q-methodology study was carried out in Erbil, Kurdistan Region of Iraq, and involved 37 dermatologists. A set of 40 statements related to different aspects of difficulties and uncertainties of treating cutaneous leishmaniasis was prepared. The dermatologists were requested to distribute the 40 statements into a scaled grid of nine piles from least agree to most agree. We applied by-person factor analysis using PQMethod 2.35 for the data analysis.ResultsThe analysis revealed two different viewpoints about the treatment of cutaneous leishmaniasis and a consensus viewpoint. The first viewpoint emphasized the use of sodium stibogluconate-based combination therapy, concerns with treatment failure, and lack of compliance with the treatment. The second viewpoint emphasized the lack of standard treatment and advances in the treatment of cutaneous leishmaniasis. There was a consensus between both groups of respondents about many aspects of the treatment of cutaneous leishmaniasis, including considering sodium stibogluconate the first drug of choice for cutaneous leishmaniasis treatment.ConclusionsThis study revealed a diversity of viewpoints and uncertainties about the effectiveness of the available treatment modalities and treatment difficulties and failure. Interrupted supply and poor quality of the available drugs and lack of a standard and advanced treatment are the main problems facing the treatment of cutaneous leishmaniasis. More research is required to determine the best treatment modalities for the different types of cutaneous leishmaniasis. There is a need for the development of treatment guidelines specific to the Iraqi context with a particular focus on the treatment of the resistant and atypical cases of cutaneous leishmaniasis.
Effect of donor non-muscle myosin heavy chain (MYH9) gene polymorphisms on clinically relevant kidney allograft dysfunction
Authors: Pazik Joanna , Oldak Monika , Oziębło Dominika , Materkowska Dominika Dęborska , Sadowska Anna , Malejczyk Jacek , Durlik Magdalena 
Published: September 2020

Abstract
Background
Despite its established association with chronic kidney disease (CKD) the role of myosin-9 (MYH9) gene variation on transplanted kidney function remains unknown. This study aimed at evaluating the effect of donor MYH9 nephrogenic variants on renal allograft function within the first post transplantation year.

Methods
In the longitudinal kidney transplant study 207 deceased donors were genotyped for previously known risk MYH9 single nucleotide polymorphisms (SNPs). The predictor was MYH9 high–risk variants status. The primary outcome was mean eGFR found in low vs. high risk MYH9 genotypes between third and twelfth post-transplant month, the secondary outcome was the risk of proteinuria.

Results
Distribution of genotypes remained in Hardy-Weinberg equilibrium. The T allele of rs3752462 (dominant model, TT or TC vs. CC) was associated with higher filtration rate (P = 0.05) in a multivariate analysis after adjusting for delayed graft function and donor sex. Two G alleles of rs136211 (recessive model, GG vs. GA or AA) resulted in doubling the risk of proteinuria (OR = 2.22; 95% CI = 1.18–4.37, P = 0.017) after adjusting for donor and recipient sex.

Conclusion
Deceased donor kidneys of European descent harboring MYH9 SNPs rs3752462 T allele show significantly superior estimated filtration rate while those of rs136211 GG genotype excessive risk of proteinuria. These findings, if replicated, may further inform and improve individualization of allocation and treatment policies.
Brain hypoperfusion and nigrostriatal dopaminergic dysfunction in primary familial brain calcification caused by novel MYORG variants: case report
Authors: Chen Shih-Ying , Lin Wei-Che , Chang Yung-Yee , Lin Tsu-Kung , Lan Min-Yu 
Published: September 2020

Abstract
Background
Primary familial brain calcification (PFBC) is a rare inherited disease characterized by multiple calcified foci in the brain parenchyma. MYORG is the first gene found to be associated with autosomal recessive PFBC. The precise pathogenic mechanism of neurodegeneration in PFBC remains unclear. The clinical phenotypes of PFBC are variable, and there is no clear correlation between clinical manifestations and radiological and pathological features of calcification.

Case presentation
Two sisters in a Taiwanese family presented with young-onset Parkinsonism and multifocal dystonia. Their brain CTs showed multiple intracerebral calcifications. The genetic study detected two heterozygous novel variants, c.104 T > A (p.Met35Lys) and c.850 T > C (p.Cys284Arg) in the MYORG gene. In both patients, MR susceptibility weighted images revealed calcification of the deep medullary veins. Tc99m ECD SPECT demonstrated a significant decrease of tracer uptake in the brain cortex and subcortical gray matter. Tc99m TRODAT-1 SPECT revealed decreased tracer uptake in the bilateral striatum.

Conclusion
Two novel MYORG variants were identified in Taiwanese family members presenting with PFBC. Abnormalities in the brain perfusion and dopamine transporter SPECTs suggest that cerebral ischemia due to extensive calcified vasculopathy, disruption of the basal ganglia-thalamo-cortical circuit, and nigrostriatal dopaminergic dysfunction are plausible pathogenic mechanisms of neurodegeneration in PFBC patients. Further investigation into the correlations between the pathogenicity-implicated imaging findings and the clinical phenotype are recommended.
Increased neutrophil-to-lymphocyte ratio predicts the development of post-stroke infections in patients with acute ischemic stroke
Authors: He Lanying , Wang Jian , Wang Feng , Zhang Lili , Zhang Lijuan , Zhao Wang 
Published: September 2020

Abstract
Background
Infections could increase the risk of poor outcome in patients with acute ischemic stroke (AIS). The peripheral neutrophil-to-lymphocyte ratio (NLR) is an important indicator of inflammation. The purpose of our study was to investigate the association increased NLR with post stroke infections (PSI) in AIS.

Methods
In this study, we included 606 consecutive patients with AIS within 24 h. The NLR was calculated by dividing absolute neutrophil counts by absolute lymphocyte counts. Receiver operating characteristic (ROC) curve was performed to identify the optimal cut point of NLR for PSI. The relationship between NLR and PSI was analyzed by multivariable analysis.

Results
We assessed 606 consecutive patients with AIS. ROC curve analysis showed that the optimal cut point of NLR for PSI was NLR ≥ 5.79. Compared with no PSI, patients with PSI have higher NLR, older age, higher NIHSS, higher PCT, higher percentage of nasogastric tube feeding and indwelling urinary catheter (P < 0.05). Multivariable analysis showed that NLR ≥ 5.79 [adjusted odds ratio (aOR),4.52; 95% confidence interval (CI),3.02–6.76; P < 0.001], older age (aOR,1.03; 95% CI, 1.00–1.05; P = 0.009), higher admission NIHSS (aOR,1.13; 95%CI, 1.07–1.18; P < 0.001), indwelling urinary catheter (aOR1.83; 95%CI, 1.08–3.10; P = 0.026], and nasogastric tube feeding (aOR2.52; 95%CI, 1.38–4.59; P = 0.003) were associated with increased risk of PSI.

Conclusions
Higher NLR can predict PSI in AIS patients. The NLR may help to select high-risk patients to start intervention in time.
Antenatal depression and anxiety and early pregnancy BMI among White British and South Asian women: retrospective analysis of data from the Born in Bradford cohort
Authors: Insan Nafisa , Slack Emma , Heslehurst Nicola , Rankin Judith 
Published: September 2020

Abstract
Background
Maternal obesity has severe physical impacts such as increased chances of pre-eclampsia and gestational diabetes. However, mental health impacts are given less attention within antenatal care. Evidence suggests that women with obesity carry increased risk of maternal depression and anxiety, however, this association is not well researched amongst South Asian women in the UK who are vulnerable to both. The aim of this study was to investigate the association between antenatal depression and anxiety and early pregnancy BMI, within and between White British and South Asian women, using data from the Born in Bradford cohort.

Methods
Depression and anxiety were assessed using the General Health Questionnaire (GHQ); a GHQ score of > 0 for the depression subscale and > 6 for anxiety. Mother’s BMI was stratified into six World Health Organisation BMI categories (underweight, recommended, overweight or obese class 1–3). To determine associations, univariate and multivariate logistic regression models (adjusting for maternal age, education, deprivation and smoking) were used.

Results
There were 7824 women included (3514 White British and 4310 South Asian). South Asian women were more likely to have depression than White British (43.3% vs 36.1% p < 0.0001) and less likely to have anxiety (45.3% vs 48.4% p < 0.01). There were no significant associations between BMI and depression or anxiety in South Asian women. White British women with an overweight BMI had higher odds of anxiety compared with women with a recommended BMI (Adjusted Odds Ratio 1.25, 95% Confidence Interval 1.05–1.47). No significant associations were observed for other BMI categories. Smoking was a risk factor for antenatal depression (AOR 1.32, 95% CI 1.12–1.56; AOR 2.08, 95% CI 1.49–2.91) and anxiety (AOR 1.34, 95% CI 1.14–1.57; (AOR 2.87, 95% CI 2.02–4.07) in both White British and South Asian women, respectively.

Conclusions
Although South Asian women have a higher prevalence of depression than White women in this cohort, the known associations between maternal obesity and anxiety do not appear to be present. More studies are needed using validated depression tools for South Asian pregnant women. Mental health screening during antenatal care is important for South Asian women, with factors such as smoking considered.
The Reproductive Agency Scale (RAS-17): development and validation in a cross-sectional study of pregnant Qatari and non-Qatari Arab Women
Authors: Yount Kathryn M. , James-Hawkins Laurie , Abdul Rahim Hanan F. 
Published: September 2020

AbstractBackgroundSustainable Development Goal (SDG) 5 prioritizes women’s empowerment and gender equality, alone and as drivers of other SDGs. Efforts to validate universal measures of women’s empowerment have eclipsed efforts to develop refined measures in local contexts and lifecycle stages. Measures of women’s empowerment across the reproductive lifecycle remain limited, including in the Arab Middle East.MethodsIn this sequential, mixed-methods study, we developed and validated the Reproductive Agency Scale 17 (RAS-17) in 684 women having a normal pregnancy and receiving prenatal care at Hamad Medical Corporation in Doha, Qatar. Participants varied in age (19–46 years), trimester, gravidity (M3.3[SD2.1], range 1–14), and parity (M2.1[SD1.5], range 0–7). Using qualitative research and questionnaire reviews, we developed 44 pregnancy-specific and non-pregnancy-specific agency items. We performed exploratory then confirmatory factor analyses (EFA/CFA) in random split-half samples and multiple-group CFA to assess measurement invariance of the scale across Qatari (n = 260) and non-Qatari Arab (n = 342) women.ResultsNon-Qatari women agreed more strongly than Qatari women that every woman should have university education, and working outside home benefitted women. Qatari women agreed more strongly than non-Qatari women that a woman should be free to sell her property. Qatari women reported more influence than non-Qatari women in decisions about spending their money (M4.6 versus M4.4), food they can eat (M4.4 versus M4.2), and rest during pregnancy (M4.5 versus M4.2). Qatari and non-Qatari women typically reported going most places with permission if accompanied. A 17-item, three-factor model measuring women’s intrinsic agency or awareness of economic rights (5 items) and instrumental agency in decision-making (5 items) and freedom of movement (7 items) had good fit and was partially invariant across groups.ConclusionsThe RAS-17 is a contextual, multidimensional measure of women’s reproductive agency validated in pregnant Qatari and non-Qatari Arab women. This scale integrates pregnancy-specific and non-pregnancy-specific items in dimensions of intrinsic agency and instrumental agency relevant to Arab women of reproductive age. The RAS-17 may be useful to screen for low reproductive agency as a predictor of maternal and perinatal outcomes. The RAS-17 should be validated in other samples to assess its full applicability across the reproductive life cycle.
Influence of electromagnetic radiation emitted by daily-use electronic devices on the Eyemate® system in-vitro: a feasibility study
Authors: Invernizzi Azzurra , Haykal Shereif , Lo Faro Valeria , Pennisi Vincenzo , Choritz Lars 
Published: September 2020

Abstract
Background
Eyemate® is a system for the continual monitoring of intraocular pressure (IOP), composed of an intraocular sensor, and a hand-held reader device. As the eyemate®-IO sensor communicates with the hand-held reader telemetrically, some patients might fear that the electronic devices that they use on a daily basis might somehow interfere with this communication, leading to unreliable measurements of IOP. In this study, we investigated the effect of electromagnetic radiation produced by a number of everyday electronic devices on the measurements made by an eyemate®-IO sensor in-vitro, in an artificial and controlled environment.

Methods
The eyemate®-IO sensor was suspended in a sterile 0.9% sodium chloride solution and placed in a water bath at 37 °C. The antenna, connected to a laptop for recording the data, was positioned at a fixed distance of 1 cm from the sensor. Approximately 2 hrs of “quasi-continuous” measurements were recorded for the baseline and for a cordless phone, a smart-phone and a laptop. Repeated measures ANOVA was used to compare any possible differences between the baseline and the tested devices.

Results
For baseline measurements, the sensor maintained a steady-state, resulting in a flat profile at a mean pressure reading of 0.795 ± 0.45 hPa, with no apparent drift. No statistically significant difference (p = 0.332) was found between the fluctuations in the baseline and the tested devices (phone: 0.76 ± 0.41 hPa; cordless: 0.787 ± 0.26 hPa; laptop: 0.775 ± 0.39 hPa).

Conclusion
In our in-vitro environment, we found no evidence of signal drifts or fluctuations associated with the tested devices, thus showing a lack of electromagnetic interference with data transmission in the tested frequency ranges.
Outcomes of neonates with tracheostomy secondary to bronchopulmonary dysplasia
Authors: Upadhyay Kirtikumar , Vallarino Dario Antonio , Talati Ajay J. 
Published: September 2020

Abstract
Background
Bronchopulmonary dysplasia (BPD) is a disease that can affect preterm neonates. Infants with severe BPD may develop pulmonary hypertension (PHN) and may require chronic mechanical ventilation with tracheostomy. The outcomes of these infants have not been studied well. We proposed to review survival and outcomes of infants requiring tracheostomy secondary to severe BPD in our NICU at 24 months.

Methods
We reviewed infants’ charts who were diagnosed with BPD that underwent tracheostomy from January 2011 to May 2016 at our children’s hospital NICU. Data were recorded from hospital stay as well as from follow up clinics. Institutional review board approval was obtained prior to beginning of study.

Results
Forty-one babies (37 during initial hospitalization and 4 subsequently) requiring tracheostomy were identified from our database. Median gestational age at birth was 26 weeks (25–27 IQR), mean birthweight of 731 g (±245 SD) and 32% were small for gestational age (SGA). Median age of tracheostomy placement was 168 days (108–197 IQR), and median PMA 48 wks (40–56 IQR). 26% of infants requiring tracheostomy also had subglottic stenosis along with BPD. 34 infants (83%) survived to discharge from NICU. 66% (27/41) of our patients had a composite outcome of death, ventilator dependency and/or poor neurodevelopmental outcome at 2 years. We found that a higher respiratory severity score at the time of tracheostomy placement and later post-menstrual age at admission to level IV NICU was associated with a worse outcome. Small for gestational age infants were found to have worse outcomes as well. 41% (13/32) of infants had more than 3 hospital admissions after discharge.

Conclusions
In our cohort about 80% of infants with severe BPD and tracheostomy survived to discharge with need for prolonged home ventilation in more than half of the survivors. Later postmenstrual age at admission to level 4 NICU was associated with a worse outcome. Our retrospective data may be inadequate to determine the causal relationship between postmenstrual age at admission and outcome. These patients continue to have high morbidity and recurrent hospitalizations.