bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening.
Authors: Cramer Grant R. , Cochetel Noé , Ghan Ryan , Destrac-Irvine Agnès , Delrot Serge 
Published: January 2020

Abstract
Background Grape berry ripening is influenced by climate, the main component of the “terroir” of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition. Results To better understand the effect of “place” on berry ripening, transcript abundances in Cabernet Sauvignon berries grown in Bordeaux were compared to those in Reno during the late stages of berry development at similar berry sugar levels (19 to 26 °Brix, total soluble solids (TSS)). Day lengths were similar in both locations but day temperatures were warmer and night temperatures were cooler in Reno. TSS was lower in Bordeaux berries compared to Reno at maturity levels considered optimum for harvest. RNA-seq analysis identified 4,455 differentially expressed genes (DEGs) between Bordeaux and Reno grape skins at 22°Brix. Top DEG gene ontology categories involved response to stimulus (1464 genes), biosynthesis (1260 genes) and response to stress (834 genes). Some DEGS included genes encoding terpene synthases, cell wall enzymes, kinases, transporters, transcription factors and photoreceptors. Most circadian clock genes had higher transcript abundance in Bordeaux. The plant temperature sensor phytochrome B was linked with Reveille 1 expression, which is part of the circadian clock output pathway that affects seed dormancy. Bordeaux berries had higher transcript abundance with DEGs associated with seed dormancy, light, auxin, ethylene signaling, powdery mildew infection, phenylpropanoid, carotenoid and terpenoid metabolism, whereas Reno berries were enriched with DEGs involved in water deprivation, cold response, ABA signaling and Fe homeostasis. Conclusions Transcript abundance profiles in the berry skins at maturity were highly dynamic. RNA-seq analysis identified a common core set of ripening genes that do not depend on rootstock, vineyard management, plant age, soil and climatic conditions. Most DEGs could be associated with different environmental conditions that affected the berries in the two locations and may be potentially controlled in different ways by the vinegrower to adjust final berry composition and reach a desired result. Temperature, light, water status and fungal infection were identified to be some of the most influential factors that affected differential gene expression and the quality trait pathways associated with them.
Genome-wide identification and expression analysis of PUB genes in cotton
Authors: Lu Xuke , Shu Na , Wang Delong , Wang Junjuan , Chen Xiugui , Zhang Binglei , Wang Shuai , Guo Lixue , Chen Chao , Ye Wuwei 
Published: January 2020

Abstract
Background: The U-box gene encodes a ubiquitin ligase that contain U-box domain. The plant U-box gene (PUB) plays an important role in the response to stress, but few reports about PUBs in cotton were available. Therefore research on PUBs is of great importance and is a necessity when studying the mechanism of stress tolerance in cotton.

Results: In this study, we identified 93, 96, 185 and 208 PUBs from four sequenced cotton species G. raimondii (D5), G. arboreum (A2), G. hirsutum (AD1) and G. barbadense (AD2), respectively. Prediction analysis of subcellular localization showed that the PUBs in cotton were widely distributed in cells, but primarily in the nucleus. The PUBs in cotton were divided into six subfamilies (A-F) on the basis of phylogenetic analysis, and the intron/exon structure was comparatively conserved within each subfamily. Location analysis showed that cotton PUBs were unevenly anchored on all chromosomes, varying from 1 to 14 per chromosome. Through multiple sequence alignment, 3 tandem duplications and 28 segmental duplications in cotton genome D5, 2 tandem duplications and 25 segmental duplications in A2, and 143 homologous gene pairs shared in A2 and D5 were found; however no tandem duplication region in A2 or D5 was found. Additionally, 105, 14 and 17 homologous gene pairs were found in the intra-subgenome of At and Dt, the At subgenome and the Dt subgenome of allotetraploid cotton, respectively. Functional analysis of GhPUB85A and GhPUB45D showed that these genes positively responded to abiotic stresses, but the expression patterns were different. In addition, although the expression levels of these two homologous genes were similar, their contributions were different when responding to stresses, specifically showing different responses to abiotic stresses and functional differences between the two subgenomes of G. hirsutum.

Conclusion: This study reports the genome-wide identification, structure, evolution and expression analysis of PUBs in cotton, and the results showed that the PUBs were highly conserved throughout the evolutionary history of cotton. All PUB genes were involved in response to abiotic stresses (including those genes induced by salt, drought, hot and cold) to varying degrees.
Prevalence of modifiable cardiovascular risk factors in Yazd inner-city municipalities
Authors: Mirzaei Mohsen , Mirzaei Masoud , Sarsangi Ali Reza , Bagheri Nasser 
Published: January 2020

Abstract
Background:Cardiovascular disease (CVD) is the leading cause of death in the world. With effective intervention and control of cardiovascular risk factors, mortality rates may be reduced.The aim of this study was to investigate the prevalence of modifiable risk factors across five municipalities in Yazd city. Methods:10,000 residents of the Yazd greater area aged 20-69 years were selected using cluster random sampling method.Overall, 200 clusters were randomly selected based on the postcodes of residents who lived in the five municipalities of Yazd.Those who lived in Yazd annexed cities and rural areas were excluded. A valid questionnaire was completed and physical examination performed as done (94.9% response rate). Instances of self-reported diabetes mellitus, high blood cholesterol, tobacco smoking, and unhealthy diet were recorded. Blood pressure, height, and weight were measured and physical activity was classified by International Physical Activity Questionnaire (IPAQ). A chi-square test was used to analyze the differences in variables across municipalities. Statistical analyses were performed using SPSS V. 16. Results:We analyzed 8749 participants’ data from Yazd city. The prevalence of diabetes mellitus, hypercholesterolemia, and hypertension were 14.1, 16.7 and 18.6%, respectively. One in every four people consumed the recommended five servings of vegetables per day. Fish consumption was less than 5% at least once a week among participants. An unhealthy diet (85.7%); low physical activity (52.2%), hypertension (36.7%) and obesity (26.3%) were the most common cardiovascular risk factors. Only 2.1% of adults had no risk factors for CVD, and almost 75% of people had more than one risk factor. The prevalence of risk factors (excluding hypertension) was significantly different across the municipalities. Residents of region three had the highest prevalence of all risk factors aside from inactivity and unhealthy diet. Conclusion:unhealthy dietary habits and inactivity are the most common modifiable risk factors of CVD in Yazd.Spatial variations of cardiovascular risk factors observed. This geographic health inequality requires more attention from policymakers to control CVD risk factors across different municipalities accordingly. Promoting healthy lifestyle is the top priority of health intervention programs. It is recommended to increase access to sport arenas and restrict access to tobacconist in high-risk areas.
Association between maternal sleep duration and quality, and the risk of preterm birth: a systematic review and meta-analysis of observational studies
Authors: wang ling , Jin Feng 
Published: January 2020

Abstract
Study Objectives: To assess the association between sleep duration and quality, and the risk of preterm birth.Methods: Relevant studies were retrieved from the PubMed and Web of Science databases up to September 30, 2018. The reference lists of the retrieved articles were reviewed. Random effects models were applied to estimate summarized relative risks (RRs) and 95% confidence intervals (CIs).Results: Ten identified studies (nine cohort studies and one case-controlled study) examined the associations between sleep duration and quality and the risk of preterm birth. As compared with women with the longest sleep duration, the summary RR was 1.23 (95% CI = 1.01–1.50) for women with the shortest sleep duration, with moderate between-study heterogeneity (I2 = 57.4%). Additionally, as compared with women with good sleep quality, the summary RR was 1.54 (95% CI = 1.18–2.01) for women with poor sleep quality (Pittsburgh Sleep Quality Index > 5), with high between-study heterogeneity (I2 = 76.7%). The results of stratified analysis by trimester, geographical location, study design, type of preterm birth, and adjustment for potential confounders were comparable to those of the main meta-analysis. Funnel plots as well as the Egger’s and Begg’s tests showed no evidence of publication bias.
Conclusions: This systematic review and meta-analysis revealed that short sleep duration and poor sleep quality may be associated with an increased risk of preterm birth.
Ups and downs of drug rehab among women: a qualitative study
Authors: boroumandfar zahra , kianpour masoud , afshari maryam 
Published: January 2020

Abstract
Background: due to the increasing importance of addicted women and the need to pay particular attention to this vulnerable group, and more awareness of women-specific addiction prevention and rehab programs among authorities. Objectives: In this content analysis of qualitative study we explored experiences of the women’s experience of the ups and downs of drug rehab Methods: 30 participants (addicted women) were selected through purposive and theoretical sampling until data saturation. Data collection was conducted through semi structured interviews. Conventional content analysis was utilized to analyze the transcribed interviews. Results: Based on analysis of the obtained results, the experience of women from the ups and downs of leaving the drug abuse yielded two themes and nine sub-themes. The themes were “the need for emancipation” and “Sinking factors”. Conclusions: It is concluded that addiction rehab strategies can only lead the addicted women to a brighter life when, along with open-hearted assistance by the families, women-specific rehab centers are established to help them meet their specific needs. Keywords: Substance Use, Lived Experience, Addiction disorders, Women's Health, qualitative study
Side Effect Concerns and their Impact on Women’s Uptake of Modern Family Planning Methods in Rural Ghana: A Mixed Methods Study
Authors: Schrumpf Leah A. , Stephens Maya J. , Nsarko Nathaniel E. , Akosah Eric , Baumgartner Joy Noel , Ohemeng-Dapaah Seth , Watt Melissa H. 
Published: January 2020

Abstract
Background: Despite availability of modern contraceptive methods and documented unmet need for family planning in Ghana, many women still report forgoing modern contraceptive use due to anticipated side effects. The goal of this study was to examine the use of modern family planning, in particular hormonal methods, in one district in rural Ghana, and to understand the role that side effects play in women’s decisions to start or continue use. Methods: This exploratory mixed-methods study included 281 surveys and 33 in-depth interviews of women 18-49 years old in the Amansie West District of Ghana between May and July 2018. The survey assessed contraceptive use and potential predictors of use. In-depth interviews examined the context around uptake and continuation of contraceptive use, with a particular focus on the role of perceived and experienced side effects. Results: The prevalence of unmet need for modern family planning among sexually active women who wanted to avoid pregnancy (n=135) was 68.9%. No factors were found to be significantly different in comparing those with a met need and unmet for modern family planning. Qualitative interviews revealed significant concerns about side effects stemming from previous method experiences and/or rumors regarding short-term impacts and perceived long-term consequences of family planning use. Side effects mentioned include menstrual changes (heavier bleeding, amenorrhea or oligomenorrhea), infertility and childbirth complications. Conclusion: As programs have improved women’s ability to access modern family planning, it is paramount to address patient-level barriers to uptake, in particular information about side effects and misconceptions about long-term use. Unintended pregnancies can be reduced through comprehensive counseling about contraceptive options including accurate information about side effects, and the development of new contraceptive technologies that meet women’s needs in low-income countries.
GC-PROM: Validation of a patient-reported outcomes measure for Chinese patients with gastric cancer
Authors: Hu Xiaojuan , Zhao Fen , Yu Hongmei , Luo Yanhong , Liu Jinchun , Zhang Yanbo 
Published: January 2020

Abstract
Background: There is increasing recognition that PROs are important in the estimation of the burden of long-term survival among patients with gastric cancer. The study aimed to develop a disease-specific instrument to assess patient-reported outcomes for Chinese patients with gastric cancer.
Method: Following the FDA’s draft guidance for patient-reported outcome, conceptual framework and item pool were defined based on relevant existing work. A draft scale was formed after revising some items based on feedback from experts and Chinese patients with gastric cancer. The pre-survey and formal survey were conducted in eight different hospitals in Shanxi Province, and two item-selection process based on classical test theory and item response theory. Finally, the patient-reported outcomes measure for Chinese patients with gastric cancer (GC-PROM) was validated in terms of reliability, validity, and feasibility. The minimal clinically important difference was determined by distribution-based method.
Results: The final GC-PROM consisted of 38 items, 13 subdomains, and 4 domains. Reliability was verified by Cronbach’s alpha coefficient for four domains and 13 subdomains respectively. The validity results showed that the multidimensional scale fulfilled expectations. In the formal survey, the completion rate was 96.16%, and the average filling time was less than half an hour. The values of the minimal clinically important difference were 4.14, 3.41, 3.37, and 3.28 in the four domains.
Conclusions: The GC-PROM had good reliability, validity, and feasibility and thus can be considered an effective clinical evaluation instrument for Chinese patients with gastric cancer.
Effect Of Smoking On Treatment Outcome Among Tuberculosis Patients In Malaysia; A Multicentre Study
Authors: Khan Amer Hayat , Sulaiman Syed Azhar Syed , Hassali Mohamed Azmi , Khan Kashif Ullah , Ming Long Chiau , Mateen Umer , Malik Obaid Ullah 
Published: January 2020

Abstract

Background : Smoking plays a key role in the development of tuberculosis (TB) infection and is also a predictor of poor TB treatment prognosis and outcomes. Objectives: To determine the prevalence of smoking and to assess the effects of smoking on treatment outcomes among TB patients. Methods : A multi-center retrospective study design was used to collect data from TB patients in four different states of Malaysia, namely Penang, Sabah, Sarawak, and Selangor. The study included medical records of TB patients admitted to the selected hospitals in the period from January 2006 to March 2009. Medical records with incomplete data were not included. Patient demographics and clinical data were collected using a validated data collection form. Results: Of all patients with TB (9337), the prevalence of smokers was 4313 (46.2%). Among smoker’s, 3584 (83.1%) were associated with pulmonary TB, while 729 (16.9%) were associated with Extra-pulmonary TB. Male gender (OR= 1.43, 95% CI 1.30-1.58), Chinese ethnicity (OR= 1.23, 95% CI 1.02-1.49), Sarawak indigenous ethnicity (OR= 0.74, 95% CI 0.58-0.95), urban residents (OR= 1.46, 95% CI 1.33-1.61), employed individuals (OR= 1.21, 95% CI 1.09-1.34), alcoholics (OR= 4.91, 95% CI 4.04-5.96), drug abusers (OR= 7.43, 95% CI 5.70-9.60) and presence of co-morbid condition (OR= 1.27, 95% CI 1.16-1.40) showed significant association with smoking habit. This study found that 3236 (75.0 %) patients were successfully treated in the smoker group, while 4004 (79.7 %) patients were non-smokers. The proportion of death rate 283 (6.6%), defaulters 284 (6.6%) and treatment interruption 204 (4.7%) was high in the smoker's group. Conclusions: Smoking had a strong influence on TB and is a major barrier towards treatment success (OR= 0.76, 95% CI 0.69-0.84, p< 0.001). Therefore, the findings point out that smoking cessations are an effective way to decrease treatment failure and drug resistance.
INTERGROWTH21st vs customized fetal growth curves in the assessment of the neonatal nutritional status: a retrospective cohort study of gestational diabetes
Authors: Alba Juan Jesus Fernández , Pazos Estefania Soto , Cortes Rocio Moreno , Sanchez Angel Vilar , Macias Carmen Gonzalez , Lara Maria Castillo , Corral Luis Moreno , Bueno Jose Antonio Sainz 
Published: January 2020

Abstract
Background
Gestational diabetes mellitus is associated with increased incidence of adverse perinatal outcomes including newborns large for gestational age, macrosomia, preeclampsia, polyhydramnios, stillbirth, and neonatal morbidity. Thus, fetal growth should be monitored by ultrasound to assess for fetal overnutrition, and thereby, its clinical consequence, macrosomia. However, it is not clear which reference curve to use to define the limits of normality. Our aim is to determine which method, INTERGROWTH21st or customized curves, better identifies the nutritional status of newborns of diabetic mothers.
Methods
This retrospective cohort study compared the risk of malnutrition in SGA newborns and the risk of overnutrition in LGA newborns using INTERGROWTH21st and customized birth weight references in gestational diabetes. Additionally, to determine the ability of both methods in the identification of neonatal malnutrition and overnutrition, we calculate sensitivity, specificity, positive predictive value, negative predictive value and likelihood ratios.
Results
231 pregnant women with GDM were included in the study. The rate of SGA indentified by INTERGROWTH21st was 4.7% vs 10.7% identified by the customized curves. The rate of LGA identified by INTERGROWTH21st was 25.6% vs 13.2% identified by the customized method. Newborns identified as SGA by the customized method showed a higher risk of malnutrition than those identified as SGA by INTERGROWTH21st. (RR 4.24 vs 2.5). LGA newborns according to the customized method also showed a higher risk of overnutrition than those classified as LGA according to INTERGROWTH21st. (RR 5.26 vs 3.57). In addition, the positive predictive value of the customized method was superior to that of INTERGROWTH21st in the identification of malnutrition (32% vs 27.27%), severe malnutrition (22.73% vs 20%), overnutrition (51.61% vs 32.20%) and severe overnutrition (28.57% vs 14.89%).
Conclusions
In pregnant women with DMG, the ability of personalized fetal growth curves to identify newborns with alterations in nutritional status could exceed that of INTERGROWTH21st.
Minimally invasive versus conventional fixation of tracer in robot-assisted pedicle screw insertion surgery: a randomized control trial
Authors: Yongqi Li , Dehua Zhang , Hongzi Wu , Ke Zhang , Rui Yang , Zhou Fang , Shaobo Wang , Liao yi 
Published: January 2020

Abstract
Background This study evaluated the minimal invasiveness, safety, and accuracy of robot-assisted pedicle screw placement procedure using a modified tracer fixation device. Methods Patients were randomly assigned to conventional fixation group (25 patients) and modified fixation group (27 patients). Results No baseline statistical difference was observed between the groups ( P >0.05). The length of unnecessary incision, amount of bleeding, and fixation duration for tracer fixation respectively were 6.08±1.02 mm, 1.46±0.84 ml, and 1.56±0.32 min in the modified fixation group and 40.28±8.52 mm, 12.02±2.24 ml, and 5.08±1.06 min in the conventional group. The difference between both groups was significant ( P <0.05). However, no significant difference between the two groups was observed in terms of the accuracy of pedicle screw placement ( P >0.05). Conclusions The modified minimally invasive procedure for tracer fixation results in minimal trauma and is simple, reliable, and highly safe. Additionally, the procedure does not compromise the accuracy of pedicle screw placement. Thus, it has great clinical applicable value.
Identification of promoter elements in the Dolichospermum circinale AWQC131C saxitoxin gene cluster and the experimental analysis of their use for heterologous expression.
Authors: D'Agostino Paul Michael , Al-Sinawi Bakir , Mazmouz Rabia , Muenchhoff Julia , Neilan Brett Anthony , Moffitt Michelle 
Published: January 2020

Abstract
Background: Dolichospermum circinale is a filamentous bloom-forming cyanobacterium responsible for biosynthesis of the paralytic shellfish toxins (PST), including saxitoxin. PSTs are neurotoxins and in their purified form are important analytical standards for monitoring the quality of water and seafood and biomedical research tools for studying neuronal sodium channels. More recently, PSTs have been recognised for their utility as local anaesthetics. Characterisation of the transcriptional elements within the saxitoxin ( sxt ) biosynthetic gene cluster (BGC) is a first step towards accessing these molecules for biotechnology. Results: In D. circinale AWQC131C the sxt BGC is transcribed from two bidirectional promoter regions encoding five individual promoters. These promoters were identified experimentally using 5ʹ RACE and their activity assessed via coupling to a lux reporter system in E. coli and Synechocystis sp. PCC 6803. Transcription of the predicted drug/metabolite transporter (DMT) encoded by sxtPER was found to initiate from two promoters, P sxtPER1 and P sxtPER2 . In E. coli, strong expression of lux from P sxtP , P sxtD and sxtPER1 was observed while expression from P orf24 and P sxtPER2 was remarkably weaker. In contrast, heterologous expression in Synechocystis sp. PCC6803 showed that expression of lux from P sxtP , P sxtPER , and P orf24 promoters was statistically higher compared to the non-promoter control, while P sxtD showed poor activity under the described conditions. Conclusions: Both of the heterologous hosts investigated in this study exhibited high expression levels from three of the five sxt promoters. These results indicate that the majority of the native sxt promoters appear active in different heterologous hosts, simplifying initial cloning efforts. Therefore, heterologous expression of the sxt BGC in either E. coli or Synechocystis could be a viable first option for producing PSTs for industrial or biomedical purposes.