bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole genome sequencing and comparative genomic analysis of oleaginous red yeast Sporobolomyces pararoseus NGR identifies candidate genes for biotechnological potential and ballistospores-shooting
Authors: Li Chun-Ji , Zhao Die , Li Bing-Xue , Zhang Ning , Yan Jian-Yu , Zou Hong-Tao 
Published: February 2020

Abstract
Background
Sporobolomyces pararoseus is regarded as an oleaginous red yeast, which synthesizes numerous valuable compounds with wide industrial usages. This species hold biotechnological interests in biodiesel, food and cosmetics industries. Moreover, the ballistospores-shooting promotes the colonizing of S. pararoseus in most terrestrial and marine ecosystems. However, very little is known about the basic genomic features of S. pararoseus. To assess the biotechnological potential and ballistospores-shooting mechanism of S. pararoseus on genome-scale, the whole genome sequencing was performed by next-generation sequencing technology.

Results
Here, we used Illumina Hiseq platform to firstly assemble S. pararoseus genome into 20.9 Mb containing 54 scaffolds and 5963 predicted genes with a N50 length of 2,038,020 bp and GC content of 47.59%. Genome completeness (BUSCO alignment: 95.4%) and RNA-seq analysis (expressed genes: 98.68%) indicated the high-quality features of the current genome. Through the annotation information of the genome, we screened many key genes involved in carotenoids, lipids, carbohydrate metabolism and signal transduction pathways. A phylogenetic assessment suggested that the evolutionary trajectory of the order Sporidiobolales species was evolved from genus Sporobolomyces to Rhodotorula through the mediator Rhodosporidiobolus. Compared to the lacking ballistospores Rhodotorula toruloides and Saccharomyces cerevisiae, we found genes enriched for spore germination and sugar metabolism. These genes might be responsible for the ballistospores-shooting in S. pararoseus NGR.

Conclusion
These results greatly advance our understanding of S. pararoseus NGR in biotechnological potential and ballistospores-shooting, which help further research of genetic manipulation, metabolic engineering as well as its evolutionary direction.
Development and validation of algorithms to classify type 1 and 2 diabetes according to age at diagnosis using electronic health records
Authors: Ke Calvin , Stukel Thérèse A. , Luk Andrea , Shah Baiju R. , Jha Prabhat , Lau Eric , Ma Ronald C. W. , So Wing-Yee , Kong Alice P. , Chow Elaine , Chan Juliana C. N. 
Published: February 2020

Abstract
Background
Validated algorithms to classify type 1 and 2 diabetes (T1D, T2D) are mostly limited to white pediatric populations. We conducted a large study in Hong Kong among children and adults with diabetes to develop and validate algorithms using electronic health records (EHRs) to classify diabetes type against clinical assessment as the reference standard, and to evaluate performance by age at diagnosis.

Methods
We included all people with diabetes (age at diagnosis 1.5–100 years during 2002–15) in the Hong Kong Diabetes Register and randomized them to derivation and validation cohorts. We developed candidate algorithms to identify diabetes types using encounter codes, prescriptions, and combinations of these criteria (“combination algorithms”). We identified 3 algorithms with the highest sensitivity, positive predictive value (PPV), and kappa coefficient, and evaluated performance by age at diagnosis in the validation cohort.

Results
There were 10,196 (T1D n = 60, T2D n = 10,136) and 5101 (T1D n = 43, T2D n = 5058) people in the derivation and validation cohorts (mean age at diagnosis 22.7, 55.9 years; 53.3, 43.9% female; for T1D and T2D respectively). Algorithms using codes or prescriptions classified T1D well for age at diagnosis < 20 years, but sensitivity and PPV dropped for older ages at diagnosis. Combination algorithms maximized sensitivity or PPV, but not both. The “high sensitivity for type 1” algorithm (ratio of type 1 to type 2 codes ≥ 4, or at least 1 insulin prescription within 90 days) had a sensitivity of 95.3% (95% confidence interval 84.2–99.4%; PPV 12.8%, 9.3–16.9%), while the “high PPV for type 1” algorithm (ratio of type 1 to type 2 codes ≥ 4, and multiple daily injections with no other glucose-lowering medication prescription) had a PPV of 100.0% (79.4–100.0%; sensitivity 37.2%, 23.0–53.3%), and the “optimized” algorithm (ratio of type 1 to type 2 codes ≥ 4, and at least 1 insulin prescription within 90 days) had a sensitivity of 65.1% (49.1–79.0%) and PPV of 75.7% (58.8–88.2%) across all ages. Accuracy of T2D classification was high for all algorithms.

Conclusions
Our validated set of algorithms accurately classifies T1D and T2D using EHRs for Hong Kong residents enrolled in a diabetes register. The choice of algorithm should be tailored to the unique requirements of each study question.
A randomized controlled trial study of the acceptability, feasibility, and preliminary impact of SITA (SMS as an Incentive To Adhere): a mobile technology-based intervention informed by behavioral economics to improve ART adherence among youth in Uganda
Authors: MacCarthy Sarah , Wagner Zachary , Mendoza-Graf Alexandra , Gutierrez Carlos Ignacio , Samba Clare , Birungi Josephine , Okoboi Stephen , Linnemayr Sebastian 
Published: February 2020

AbstractBackgroundStudies report serious adherence problems among youth (individuals age 15–24 years of age) in Uganda. Recent growth in mobile phone ownership has highlighted the potential of using text-based interventions to improve antiretroviral treatment (ART) adherence among Ugandan youth. We piloted a randomized controlled trial of a text-based intervention providing weekly real-time antiretroviral adherence feedback, based on information from a smart pill box, to HIV-positive Ugandan youth. In this paper, we report the acceptability, feasibility, and preliminary impact of the intervention.MethodsWe randomized participants to a control group, or to receive messages with information on either their own adherence levels (Treatment 1 - T1), or their own adherence and peer adherence levels (Treatment 2 – T2). We conducted six focus groups from December 2016 to March 2017 with providers and youth ages 15–24, double coded 130 excerpts, and achieved a pooled Cohen’s Kappa of 0.79 and 0.80 based on 34 randomly selected excerpts.ResultsThe quantitative and qualitative data show that the intervention was deemed acceptable and feasible. After controlling for baseline adherence, the T1 group had 3.8 percentage point lower adherence than the control group (95% CI -9.9, 2.3) and the T2 group had 2.4 percentage points higher adherence than the control group (95% CI -3.0, 7.9). However, there was an increasing treatment effect over time for the T2 group with the largest effect towards the end of the study; a 2.5 percentage point increase in the initial 9-weeks that grows steadily to 9.0 percentage points by the last 9-weeks of the study. We find negative treatment effects for T1 in 3 of the 4 9-week intervals. This pilot study was not designed to detect statistically significant differences.ConclusionsImproving youth’s adherence by supplementing information about their adherence with information about the adherence of peers is a promising new strategy that should be further evaluated in a fully-powered study. Providing one’s own adherence information alone appears to have less potential.Trial registrationNCT0251435607/30/2015.
Association of ABO polymorphisms and pancreatic Cancer/ Cardiocerebrovascular disease: a meta-analysis
Authors: Li Yanxia , Liu Luyang , Huang Yubei , Zheng Hong , Li Lian 
Published: February 2020

Abstract
Background
ABO gene polymorphisms have been reported to be associated with the risk of multiple cancers and cardiocerebrovascular diseases. However, the results remained controversial. In this study, we conducted a systematic review and meta-analysis to clarify the association between two SNPs (rs505922 and rs657152) in ABO gene and cancers/cardiocerebrovascular diseases.

Method
All eligible case-control studies come from PubMed, Embase and Web of Science up to Jan. 1, 2019. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the corresponding associations. Sensitivity analysis, publication bias assessment, and heterogeneity test were performed using STATA 12.0.

Results
A total of nineteen articles involving twenty-two case-control populations were included according to inclusion and exclusion criteria. Twelve populations (20,820 cases and 27,837 controls) were used to evaluate the relationship between rs505922 and overall cancers and nine populations (22,275 cases and 71,549 controls) were included to assess the association between rs505922 and cardiocerebrovascular diseases. The results showed a significant association between the rs505922 polymorphism and cancers (CvsT: OR = 1.13, 95%CI = 1.05–1.22, P = 0.001), and cardiocerebrovascular diseases (OR = 1.36, 95%CI = 1.19–1.57, P < 0.001). Five populations (8660 cases and 10,618 controls) were included to evaluate association between rs657152 and cancers and five populations (8105 cases and 6712 controls) were included to estimate the relationship between rs657152 and cardiocerebrovascular diseases. The result of meta-analysis reveals that rs657152 was significantly associated with cancers (OR = 1.18, 95%CI = 1.13–1.23, P < 0.001) and cardiocerebrovascular diseases (OR = 1.54, 95%CI = 1.24–1.92, P < 0.001).

Conclusion
Our study suggested that ABO polymorphisms might serve as a risk factor of pancreatic cancers and cardiocerebrovascular diseases.
Gestational weight gain charts for twin pregnancies in Southeast China
Authors: Lin Lihua , Lin Juan , Mao Xiaodan , Xu Libo , Zhang Ronghua , Luo Jinying , Lin Yingying , Yan Jianying 
Published: February 2020

Abstract
Background
To establish age-standardized charts of weight gain for term twin pregnancies in Southeast China.

Methods
We designed a retrospective study on data from women pregnant with twins, a gestational age beyond 36 weeks and an average weight ≥ 2500 g. We established hierarchical linear regression models to express gestational weight gain patterns.

Results
We analyzed data from 884 women pregnant with twins (151 underweight, 597 normal weight, and 136 overweight). Our final models fit the crude weight measurement data well. The means of weight gain generally decreased as the pre-pregnancy BMI increased. For each BMI category, the mean weight gains increased with the gestational age and the standard deviation increased slightly. The mean weight gains were 18.82 ± 6.73, 18.53 ± 6.74, and 16.97 ± 6.95 kg at 37 weeks in underweight, normal weight, and overweight women, respectively.

Conclusion
The weight gain chart can be used to estimate maternal weight gain to be gestational age–standardized z scores by pre-pregnancy BMI and may serve as an innovative tool for perinatal care providers to guide the weight gain of women pregnant with twins.
Essential newborn care utilization and associated factors in Ethiopia: a systematic review and meta-analysis
Authors: Alamneh Yoseph , Adane Fentahun , Yirga Tadesse , Desta Melaku 
Published: February 2020

Abstract
Background
Globally, newborn death accounted for 46% of under-five deaths and more than 80% of newborn deaths are the result of preventable and treatable conditions. Findings on the prevalence and associated factors of essential newborn care utilization are highly variable and inconsistent across Ethiopia. Therefore, this systematic review and meta-analysis aimed to estimate the pooled prevalence of essential newborn care utilization and associated factors in Ethiopia.

Methods
The international databases accessed included MEDLINE/PubMed, EMBASE, Web of Sciences, Scopus, and Grey literature databases, Google Scholar, Science Direct and Cochrane library were scientifically explored. We considered all primary studies reporting the prevalence of essential newborn care utilization and associated factors in Ethiopia. We retrieved all necessary data by using a standardized data extraction format spreadsheet. STATA 14 statistical software was used to analyze the data and Cochrane Q test statistics and I2 test was used to assess the heterogeneity between the studies. There significant heterogeneity between the studies so a random effect model was employed.

Results
The pooled estimate of essential newborn care utilization from 11 studies in Ethiopia was 48.77% (95% CI: 27.89, 69.65). Residence [OR = 2.50 (95% CI: 1.64, 3.88)], Postnatal care [OR = 5.53, 95% CI = (3.02, 10.13], counseling during pregnancy and delivery [OR = 4.39, 95% CI = (2.99, 6.45], antenatal care follows up (OR = 6.84; 95% CI: 1.15, 4.70) and maternal educational status [OR = 1.63 (95% CI: 1.12, 2.37)] were identified as associated factors of essential newborn care utilization.

Conclusion
Based on the current study essential newborn care utilization in Ethiopia was significantly low in comparison with the current global recommendation on essential newborn care utilization. Place of residence, Postnatal care, counseling during pregnancy and delivery, antenatal care follow up, and maternal educational status were associated risk factors. Therefore, on the basis of the results, it is suggested that special attention should be given to attempts to ensure that education should focus on women during ante and postnatal follow-up, counseling during pregnancy and delivery, as well as rural and illiterate mothers. Finally, appropriate newborn services at health facilities and raising mother’s level of awareness about newborn care practices are imperative in addressing the gaps in essential newborn care utilization in Ethiopia.
Maternal serum glycosylated fibronectin as a short-term predictor of preeclampsia: a prospective cohort study
Authors: Huhn Evelyn A. , Hoffmann Ina , Martinez De Tejada Begoña , Lange Soeren , Sage Kylie M. , Roberts Charles T. , Gravett Michael G. , Nagalla Srinivasa R. , Lapaire Olav 
Published: February 2020

Abstract
Background
Preeclampsia is a major pregnancy complication that results in significant maternal and infant mortality, most of which occurs in low and middle-income countries. The accurate and timely diagnosis of preeclampsia is critical in management of affected pregnancies to reduce maternal and fetal/neonatal morbidity and mortality, yet difficulties remain in establishing the rigorous diagnosis of preeclampsia based on clinical parameters alone. Biomarkers that detect biochemical disease have been proposed as complements or alternatives to clinical criteria to improve diagnostic accuracy. This cohort study assessed the performance of several biomarkers, including glycosylated fibronectin (GlyFn), to rule-in or rule-out preeclampsia within 4 weeks in a cohort of women at increased risk for preeclampsia.

Methods
151 women with risk factors for or clinical signs and symptoms of preeclampsia were selected from a prospective cohort. Maternal serum samples were collected between 20 and 37 weeks of gestation. Clinical suspicion of preeclampsia was defined as presence of new-onset proteinuria, or clinical symptoms of preeclampsia. Subjects with a clinical diagnosis of preeclampsia at the time of enrollment were excluded. GlyFn, pregnancy-associated plasma protein-A2 (PAPPA2), placental growth factor (PlGF), and soluble fms-like tyrosine kinase-1 (sFlt-1) were measured by immunoassay. GlyFn was also determined using a rapid point-of care (POC) test format. Receiver-operating characteristic (ROC) curves derived from logistic regression analysis were used to determine the classification performance for each analyte.

Results
32 of 151 (21%) women developed a clinical diagnosis of preeclampsia within 4 weeks. All biomarkers exhibited good classification performance [GlyFn (area under the curve (AUROC) = 0.94, 91% sensitivity, 86% specificity); PAPPA2 AUC = 0.92, 87% sensitivity, 77% specificity; PlGF AUC = 0.90, 81% sensitivity, 83% specificity; sFlt-1 AUC = 0.92, 84% sensitivity, 91% specificity. The GlyFn immunoassay and the rapid POC test showed a correlation of r = 0.966.

Conclusions
In this prospective cohort, serum biomarkers of biochemical disease were effective in short-term prediction of preeclampsia, and the performance of GlyFn in particular as a POC test may meet the needs of rapid and accurate triage and intervention.
Why do pregnant women in Iringa region in Tanzania start antenatal care late? A qualitative analysis
Authors: Maluka Stephen Oswald , Joseph Chakupewa , Fitzgerald Sian , Salim Robert , Kamuzora Peter 
Published: February 2020

Abstract
Background
When started early in pregnancy and continued up till childbirth, antenatal care (ANC) can be effective in reducing adverse pregnancy outcomes. While the proportion of women who attend ANC at least once in low income countries is high, most pregnant women attend their first ANC late. In Tanzania, while over 51% of pregnant women complete ≥4 visits, only 24% start within the first trimester. This study aimed to understand the factors that lead to delay in seeking ANC services among pregnant women in Tanzania.

Methods
This qualitative descriptive case study was conducted in two rural districts in Iringa Region in Tanzania. A total of 40 focus group discussions (FGDs) were conducted involving both male and female participants in 20 villages. In addition, 36 semi-structured interviews were carried out with health care workers, members of health facility committees and community health workers. Initial findings were further validated during 10 stakeholders’ meetings held at ward level in which 450 people participated. Data were analysed using thematic approach.

Results
Key individual and social factors for late ANC attendance included lack of knowledge of the importance of early visiting ANC, previous birth with good outcome, traditional gender roles, fear of shame and stigma, and cultural beliefs about pregnancy. Main factors which inhibit early ANC attendance in Kilolo and Mufindi districts include spouse accompany policy, rude language of health personnel and shortage of health care providers.

Conclusions
Traditional gender roles and cultural beliefs about pregnancy as well as health system factors continue to influence the timing of ANC attendance. Improving early ANC attendance, therefore, requires integrated interventions that address both community and health systems barriers. Health education on the timing and importance of early antenatal care should also be strengthened in the communities. Additionally, while spouse accompany policy is important, the implementation of this policy should not infringe women’s rights to access ANC services.
Heterogeneous components of lung adenocarcinomas confer distinct EGFR mutation and PD-L1 expression
Authors: Cai Yiran , Wu Hongbo , Shi Xiaoqin , Dong Yujie , Chang Xiujun , Zhang Li , Zhou Lijuan , Su Dan , Yang Ming 
Published: February 2020

Abstract
Background
Lung adenocarcinoma (LAC) is composed of lepidic, papillary, mucinous, micropapillary and solid components in its parenchyma. Complex responses to therapeutics result from intratumoral heterogeneity. However, it remains confused that what components in a mixed LAC tumor are responsible to the heterogeneous EGFR mutation and PD-L1 expression.

Methods
We investigated EGFR status via laser microdissection to capture spatially separated cancer cell subpopulations and digital droplet PCR to determine the abundance of EGFR sensitizing mutation and naïve T790M. Whilst, PD-L1 expression level via tumor proportion score (TPS) was evaluated by Ventana immunohistochemistry using SP263 antibody. PD-L1 expression levels were tiered in < 1, 1–49% and > =50% groups.

Results
EGFR mutation harbored in 154 (59%) of 261 LAC patients and more frequently occurred in papillary, lepidic and micropapillary constituents. Higher levels of PD-L1 were found in LACs at stage III and IV (68.3%) versus those at stage I and II (31.7%) (P = 0.04). Solid predominant LACs (41.3%) expressed PD-L1 with TPS > =50%, versus mucinous and lepidic LACs (P < 0.01). LACs with solid constituents also had more positive proportion of PD-L1 protein. Cut-offs < 1, 1–49% or > =50% were associated with patients’ progression-free survival and longer in the < 1% group (22.9 month, 95% CI 17.6–28.2) (P < 0.05). LACs consisting of two constituents with PD-L1 TPS < 1% had a better prognosis than the groups with single component and more than two components (P < 0.05). Eighteen LACs (6.9%) had concomitantly deletion in exon 19 or L858R and naïve T790M mutation. The abundance of T790M varied diversely with sensitizing mutation. PD-L1 expression was not concordant in same components and usually negative in the EGFR-mutated constituents. Heterogeneous PD-L1 expression occurred in the vicinity of stromal tissues. 58.8, 29.4 and 11.8% in ALK positive LACs (N = 17) were found PD-L1 expression via cutoffs of < 1, 1–49% and > =50%, respectively (P > 0.05).

Conclusion
Intratumoral genetic heterogeneity of LACs was demonstrated associated with histological patterns. Heterogeneous PD-L1 expression in higher level usually occurred in solid component both in EGFR mutated and EGFR wild-typed LACs. EGFR mutated LACs heterogeneously had sensitizing and resistant mutation and was accompanied with PD-L1 expression, but discordant among histological constituents. Immune checkpoint inhibitor combined with third generation EGFR tyrosine kinase inhibitor should be more effective to these LACs.
Temporal changes in gut microbiota profile in children with acute lymphoblastic leukemia prior to commencement-, during-, and post-cessation of chemotherapy
Authors: Chua Ling Ling , Rajasuriar Reena , Lim Yvonne Ai Lian , Woo Yin Ling , Loke P’ng , Ariffin Hany 
Published: February 2020

AbstractBackgroundAlteration in gut microbiota has been recently linked with childhood leukemia and the use of chemotherapy. Whether the perturbed microbiota community is restored after disease remission and cessation of cancer treatment has not been evaluated. This study examines the chronological changes of gut microbiota in children with acute lymphoblastic leukemia (ALL) prior to the start-, during-, and following cessation of chemotherapy.MethodologyWe conducted a longitudinal observational study in gut microbiota profile in a group of paediatric patients diagnosed with ALL using 16 s ribosomal RNA sequencing and compared these patients’ microbiota pattern with age and ethnicity-matched healthy children. Temporal changes of gut microbiota in these patients with ALL were also examined at different time-points in relation to chemotherapy.ResultsPrior to commencement of chemotherapy, gut microbiota in children with ALL had larger inter-individual variability compared to healthy controls and was enriched with bacteria belonging toBacteroidetesphylum andBacteroidesgenus.The relative abundance ofBacteroidesdecreased upon commencement of chemotherapy. Restitution of gut microbiota composition to resemble that of healthy controls occurred after cessation of chemotherapy. However, the microbiota composition (beta diversity) remained distinctive and a few bacteria were different in abundance among the patients with ALL compared to controls despite completion of chemotherapy and presumed restoration of normal health.ConclusionOur findings in this pilot study is the first to suggest that gut microbiota profile in children with ALL remains marginally different from healthy controls even after cessation of chemotherapy. These persistent microbiota changes may have a role in the long-term wellbeing in childhood cancer survivors but the impact of these changes in subsequent health perturbations in these survivors remain unexplored.