bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV-1 infection among women in Israel, 2010–2018
Authors: Wagner Tali , Olshtain-Pops Karen , Wax Marina , Horwitz Olivia , Shirazi Rachel , Gozlan Yael , Volnowitz Hadar , Mendelson Ella , Levy Itzchak , Mor Orna 
Published: September 2020

Abstract
Introduction
Although women comprise 33% of the HIV-1-carriers in Israel, they have not previously been considered a risk group requiring special attention. Immigration waves from countries in Africa and in East Europe may have changed the local landscape of women diagnosed with HIV-1. Here, we aimed to assess viral and demographic characteristics of HIV-1-positive women identified in Israel between 2010 and 2018.

Methods
All > 16 year-old, HIV-1-infected women, diagnosed in Israel in 2010–2018, (n = 763) registered in the National HIV reference laboratory were included in this cross-sectional study. Demographic and clinical characteristics were extracted from the database. Viral subtypes and transmitted drug resistance mutations (TDRM) were determined in 337 (44.2%) randomly selected samples collected from treatment-naive women.

Results
Median age at diagnosis was 38 years. Most (73.3%) women were immigrants from the former Soviet Union (FSU) (41.2%, 314) or sub-Saharan Africa (SSA) (32.2%, 246) and carried subtype A (79.7%) or C (90.3%), respectively. Only 11.4% (87) were Israeli-born women. Over the years, the prevalence of women from SSA decreased while that of women from FSU increased significantly (p < 0.001). The median CD4+ cell count was 263 cells/mm3, and higher (391 cells/mm3) in Israeli-born women. TDRM were identified in 10.4% of the tested samples; 1.8, 3 and 7.1% had protease inhibitors (PI), nucleotide reverse transcriptase inhibitors (NRTI) and non-nucleoside reverse transcriptase inhibitors (NNRTI) TDRM, respectively. The prevalence of women with NNRTI TDRM significantly increased from 4.9% in 2010–2012 to 13.3% in 2016–2018. Israeli-born women had the highest prevalence (16.3%) of NNRTI TDRM (p = 0.014). NRTI A62 (5.6%), NNRTI E138 and K103 (5.6 and 4.2%, respectively) were the most prominent mutated sites.

Conclusions
Most HIV-1-positive women diagnosed in Israel in 2010–2018 were immigrants, with the relative ratio of FSU immigrants increasing in recent years. The high proportion of women diagnosed with resistance mutations, particularly, the yearly increase in the frequency of NNRTI mutations, support the national policy of resistance testing at baseline.
Prevalence and risk factors for chronic kidney disease of unknown cause in Malawi: a cross-sectional analysis in a rural and urban population
Authors: Hamilton Sophie A. , Nakanga Wisdom P. , Prynn Josephine E. , Crampin Amelia C. , Fecht Daniela , Vineis Paolo , Caplin Ben , Pearce Neil , Nyirenda Moffat J. 
Published: September 2020

Abstract
Background
An epidemic of chronic kidney disease of unknown cause (CKDu) is occurring in rural communities in tropical regions of low-and middle-income countries in South America and India. Little information is available from Southern African countries which have similar climatic and occupational characteristics to CKDu-endemic countries. We investigated whether CKDu is prevalent in Malawi and identified its potential risk factors in this setting.

Methods
We conducted a cross-sectional study from January–August 2018 collecting bio samples and anthropometric data in two Malawian populations. The sample comprised adults > 18 years (n = 821) without diabetes, hypertension, and proteinuria. Estimates of glomerular filtration rate (eGFR) were calculated using the CKD-EPI equation. Linear and logistic regression models were applied with potential risk factors, to estimate risk of reduced eGFR.

Results
The mean eGFR was 117.1 ± 16.0 ml/min per 1.73m2 and the mean participant age was 33.5 ± 12.7 years. The prevalence of eGFR< 60 was 0.2% (95% confidence interval (95% CI) 0.1, 0.9); the prevalence of eGFR< 90 was 5% (95% CI =3.2, 6.3). We observed a higher prevalence in the rural population (5% (3.6, 7.8)), versus urban (3% (1.4, 6.7)). Age and BMI were associated with reduced eGFR< 90 [Odds ratio (OR) (95%CI) =3.59 (2.58, 5.21) per ten-year increment]; [OR (95%CI) =2.01 (1.27, 3.43) per 5 kg/m2 increment] respectively. No increased risk of eGFR < 90 was observed for rural participants [OR (95%CI) =1.75 (0.50, 6.30)].

Conclusions
Reduced kidney function consistent with the definition of CKDu is not common in the areas of Malawi sampled, compared to that observed in other tropical or sub-tropical countries in Central America and South Asia. Reduced eGFR< 90 was related to age, BMI, and was more common in rural areas. These findings are important as they contradict some current hypothesis that CKDu is endemic across tropical and sub-tropical countries. This study has enabled standardized comparisons of impaired kidney function between and within tropical/subtropical regions of the world and will help form the basis for further etiological research, surveillance strategies, and the implementation and evaluation of interventions.
Effect of nipple shield use on milk removal: a mechanistic study
Authors: Coentro Viviane Silva , Perrella Sharon Lisa , Lai Ching Tat , Rea Alethea , Murray Kevin , Geddes Donna Tracy 
Published: September 2020

Abstract
Background
Concerns about reduced milk transfer with nipple shield (NS) use are based on evidence from studies with methodological flaws. Milk removal during breastfeeding can be impacted by infant and maternal factors other than NS use. The aim of this study was to control electric breast pump vacuum strength, pattern and duration across multiple study sessions to determine if NS use reduces milk removal from the breast.

Methods
A within-subject study with two groups of breastfeeding mothers (infants < 6 months) were recruited; Control Group (CG): no breastfeeding difficulties; Pain Group (PG) used NS for persistent nipple pain. Mothers completed three randomised 15 min pumping sessions using the Symphony vacuum curve (Medela AG); no NS, fitted NS, and a small NS. Sessions were considered valid where the applied vacuum was within 20 mmHg of the set vacuum. Milk removal was considered as pumped milk volume, and also percentage of available milk removed (PAMR), which is calculated as the pumped volume divided by the estimated milk volume stored in the breast immediately prior to pumping.

Results
Of 62 sessions (all: n = 31 paired sessions) a total of 11 paired sessions from both PG (n = 03) and CG (n = 08) were valid (subset) with and without a fitted NS. Only 2 small shield sessions were valid and so all small shield measurements were excluded. Both pumped volumes and PAMR were significantly lower with NS use for all data but not for subset data. (All: Volume and PAMR median: no NS: 76.5 mL, 69%, Fitted NS: 32.1 mL, 41% respectively (volume p = 0.002, PAMR p = 0.002); Subset: Volume and PAMR median: no NS: 83.8 mL, 72%; Fitted NS: 35.2 mL, 40% (volume p = 0.111 and PAMR p = 0.045). The difference in PAMR, but not volume, was statistically significant when analysed by linear mixed modelling. A decrease of 10 mmHg was associated with a 4.4% increase in PAMR (p = 0.017).

Conclusions
This experimental data suggests that nipple shield use may reduce milk removal. Close clinical monitoring of breastfeeding mothers using nipple shields is warranted.
MassARRAY-based single nucleotide polymorphism analysis in breast cancer of north Indian population
Authors: Bakshi Divya , Nagpal Ashna , Sharma Varun , Sharma Indu , Shah Ruchi , Sharma Bhanu , Bhat Amrita , Verma Sonali , Bhat Gh. Rasool , Abrol Deepak , Sharma Rahul , Vaishnavi Samantha , Kumar Rakesh 
Published: September 2020

Abstract
Background
Breast Cancer (BC) is associated with inherited gene mutations. High throughput genotyping of BC samples has led to the identification and characterization of biomarkers for the diagnosis of BC. The most common genetic variants studied are SNPs (Single Nucleotide Polymorphisms) that determine susceptibility to an array of diseases thus serving as a potential tool for identifying the underlying causes of breast carcinogenesis.

Methods
SNP genotyping employing the Agena MassARRAY offers a robust, sensitive, cost-effective method to assess multiple SNPs and samples simultaneously. In this present study, we analyzed 15 SNPs of 14 genes in 550 samples (150 cases and 400 controls). We identified four SNPs of genes TCF21, SLC19A1, DCC, and ERCC1 showing significant association with BC in the population under study.

Results
The SNPs were rs12190287 (TCF21) having OR 1.713 (1.08–2.716 at 95% CI) p-value 0.022 (dominant), rs1051266 (SLC19A1) having OR 3.461 (2.136–5.609 at 95% CI) p-value 0.000000466 (dominant), rs2229080 (DCC) having OR 0.6867 (0.5123–0.9205 at 95% CI) p-value 0.0116 (allelic) and rs2298881 (ERCC1) having OR 0.669 (0.46–0.973 at 95% CI), p-value 0.035 (additive) respectively. The in-silico analysis was further used to fortify the above findings.

Conclusion
It is further anticipated that the variants should be evaluated in other population groups that may aid in understanding the genetic complexity and bridge the missing heritability.
Association between sexual violence and unintended pregnancy among adolescent girls and young women in South Africa
Authors: Ajayi Anthony Idowu , Ezegbe Henrietta Chinelo 
Published: September 2020

Abstract
Background
Unintended pregnancy has dire consequences on the health and socioeconomic wellbeing of adolescent girls and young women (AGYW) (aged 15–24 years). While most studies tend to focus on lack of access to contraceptive information and services, and poverty as the main contributing factor to early-unintended pregnancies, the influence of sexual violence has received limited attention. Understanding the link between sexual violence and unintended pregnancy is critical towards developing a multifaceted intervention to reduce unintended pregnancies among AGYW in South Africa, a country with high teenage pregnancy rate. Thus, we estimated the magnitude of unintended pregnancy among AGYW and also examined the effect of sexual violence on unintended pregnancy.

Methods
Our study adopted a cross-sectional design, and data were obtained from AGYW in a South African university between June and November 2018. A final sample of 451 girls aged 17–24 years, selected using stratified sampling, were included in the analysis. We used adjusted and unadjusted logistic regression analysis to examine the effect of sexual violence on unintended pregnancy.

Results
The analysis shows that 41.9% of all respondents had experienced an unintended pregnancy, and 26.3% of those unintended pregnancies ended in abortions. Unintended pregnancy was higher among survivors of sexual violence (54.4%) compared to those who never experienced sexual abuse (34.3%). In the multivariable analysis, sexual violence was consistently and robustly associated with increased odds of having an unintended pregnancy (AOR:1.70; 95% CI: 1.08–2.68).

Conclusion
Our study found a huge magnitude of unintended pregnancy among AGYW. Sexual violence is an important predictor of unintended pregnancy in this age cohort. Thus, addressing unintended pregnancies among AGYW in South Africa requires interventions that not only increase access to contraceptive information and services but also reduce sexual violence and cater for survivors.
Smartphone and medical application use among dentists in China
Authors: Zhang Chao , Fan Lin , Chai Zhaowu , Yu Cong , Song Jinlin 
Published: September 2020

Abstract
Background
With the development of information technology, an increasing number of healthcare professionals are using smartphones and mobile medical applications (apps) in their clinical practice. The objective of this study was to survey the use of smartphone-based medical apps among dentists in China and determine dentists’ perceptions of such apps.

Methods
All data were collected using anonymous questionnaires. The questionnaires for this cross-sectional study were randomly sent to dentists by email, and 379 dentists responded. Dentists’ demographics and perceptions of WeChat, QQ (the most popular social media apps in China) and other medical apps were assessed; the questionnaire including questions on the purpose, frequency, daily use, and opinion of the apps they used. Questions were answered using a Likert scale (1 = strongly agree, 2 = agree, 3 = not sure, 4 = disagree, and 5 = strongly disagree).

Results
A total of 379 valid responses were received; the respondents had a median age of 33.6 years old (63.3% female). All subjects (100%) owned a smartphone, and all of them installed and used WeChat or QQ in their clinical practice. Only 76% of subjects installed medical apps (other than WeChat and QQ) on their smartphones. Male dentists were more likely to install medical apps than female dentists (p < 0.05). With increasing age, the percentage of dentists who installed medical apps decreased (p < 0.001). The frequency and daily use were higher for WeChat and QQ than for medical apps. Medical apps were positively perceived, with dentists reporting that they recommend these medical apps to their peers (Likert score: 1.67 ± 0.68).

Conclusion
Medical apps were perceived to have a positive impact on clinical practice, education and patient care in dentistry by providing relevant medical information. However, there will still be much room for improvement in the future.
The influence of patient race on the use of diagnostic imaging in United States emergency departments: data from the National Hospital Ambulatory Medical Care survey
Authors: Ross Andrew B. , Kalia Vivek , Chan Brian Y. , Li Geng 
Published: September 2020

Abstract
Background
An established body of literature has shown evidence of implicit bias in the health care system on the basis of patient race and ethnicity that contributes to well documented disparities in outcomes. However, little is known about the influence of patient race and ethnicity on the decision to order diagnostic radiology exams in the acute care setting. This study examines the role of patient race and ethnicity on the likelihood of diagnostic imaging exams being ordered during United States emergency department encounters.

Methods
Publicly available data from the National Hospital Ambulatory Medical Care Survey Emergency Department sample for the years 2006–2016 was compiled. The proportion of patient encounters where diagnostic imaging was ordered was tabulated by race/ethnicity, sub-divided by imaging modality. A multivariable logistic regression model was used to evaluate the influence of patient race/ethnicity on the ordering of diagnostic imaging controlling for other patient and hospital characteristics. Survey weighting variables were used to formulate national-level estimates.

Results
Using the weighted data, an average of 131,558,553 patient encounters were included each year for the 11-year study period. Imaging was used at 46% of all visits although this varied significantly by patient race and ethnicity with white patients receiving medical imaging at 49% of visits and non-white patients at 41% of visits (p < 0.001). This effect persisted in the controlled regression model and across all imaging modalities with the exception of ultrasound. Other factors with a significant influence on imaging use included patient age, gender, insurance status, number of co-morbidities, hospital setting (urban vs non-urban) and hospital region. There was no evidence to suggest that the disparate use of imaging by patient race and ethnicity changed over the 11-year study time period.

Conclusion
The likelihood that a diagnostic imaging exam will be ordered during United States emergency department encounters differs significantly by patient race and ethnicity even when controlling for other patient and hospital characteristics. Further work must be done to understand and mitigate what may represent systematic bias and ensure equitable use of health care resources.
Malignant transformation and genetic alterations are uncoupled in early colorectal cancer progression
Authors: Mamlouk Soulafa , Simon Tincy , Tomás Laura , Wedge David C. , Arnold Alexander , Menne Andrea , Horst David , Capper David , Morkel Markus , Posada David , Sers Christine , Bläker Hendrik 
Published: September 2020

Abstract
Background
Colorectal cancer (CRC) development is generally accepted as a sequential process, with genetic mutations determining phenotypic tumor progression. However, matching genetic profiles with histological transition requires the analyses of temporal samples from the same patient at key stages of progression.

Results
Here, we compared the genetic profiles of 34 early carcinomas with their respective adenomatous precursors to assess timing and heterogeneity of driver alterations accompanying the switch from benign adenoma to malignant carcinoma. In almost half of the cases, driver mutations specific to the carcinoma stage were not observed. In samples where carcinoma-specific alterations were present, TP53 mutations and chromosome 20 copy gains commonly accompanied the switch from adenomatous tissue to carcinoma. Remarkably, 40% and 50% of high-grade adenomas shared TP53 mutations and chromosome 20 gains, respectively, with their matched carcinomas. In addition, multi-regional analyses revealed greater heterogeneity of driver mutations in adenomas compared to their matched carcinomas.

Conclusion
Genetic alterations in TP53 and chromosome 20 occur at the earliest histological stage in colorectal carcinomas (pTis and pT1). However, high-grade adenomas can share these alterations despite their histological distinction. Based on the well-defined sequence of CRC development, we suggest that the timing of genetic changes during neoplastic progression is frequently uncoupled from histological progression.
24-h variations of blood serum metabolites in high yielding dairy cows and calves
Authors: Hussein Hussein Awad , Thurmann Jan-Peter , Staufenbiel Rudolf 
Published: September 2020

Abstract
Background
Blood profile testing is commonly used to monitor herd health status, diagnose disorders, and predict the risk of diseases in cows and calves, with subsequent optimization the production of dairy herds. By understanding the physiological ranges of serum metabolites relative to age, lactation stage, and the sampling time in healthy cows and calves, the dairy practitioners can accurately diagnose abnormalities with a blood test. The effect of sampling time on the variation of serum metabolites within 24 h were evaluated in 83 cattle. All animals were originated from a dairy herd, where the animals, based on their ages and lactation stages, were classified into eight groups. The blood samples were collected from each animal every 4 h within a day.

Results
The time of sampling within the day showed significant influences on the serum concentrations of glucose, β-hydroxybutyric acid (BHBA) and urea. BHBA was the most metabolite that showed day variation among cows’ groups. Furthermore, the concentrations of total cholesterol were the most stable metabolite in all groups. The mean values of albumin, total proteins, glucose, non-esterified fatty acids (NEFA), BHBA, total cholesterol, total bilirubin, urea, and creatinine revealed significant variations among the different studied groups.

Conclusions
A certain suitable time of blood sample collection cannot be recommended. However, care shall be taken for the time of sampling for measurements of glucose, NEFA, BHBA and urea, otherwise the comparative values of these metabolites at different sampling time points may differ significantly from each other’s, without a disease cause. It may be recommended, for metabolic assessment of dairy herds, classification the subjects into different groups based on lactation stages and ages of animals.
In vivo characterization of the activities of novel cyclodipeptide oxidases: new tools for increasing chemical diversity of bioproduced 2,5-diketopiperazines in Escherichia coli
Authors: Le Chevalier Fabien , Correia Isabelle , Matheron Lucrèce , Babin Morgan , Moutiez Mireille , Canu Nicolas , Gondry Muriel , Lequin Olivier , Belin Pascal 
Published: September 2020

Abstract
Background
Cyclodipeptide oxidases (CDOs) are enzymes involved in the biosynthesis of 2,5-diketopiperazines, a class of naturally occurring compounds with a large range of pharmaceutical activities. CDOs belong to cyclodipeptide synthase (CDPS)-dependent pathways, in which they play an early role in the chemical diversification of cyclodipeptides by introducing Cα-Cβ dehydrogenations. Although the activities of more than 100 CDPSs have been determined, the activities of only a few CDOs have been characterized. Furthermore, the assessment of the CDO activities on chemically-synthesized cyclodipeptides has shown these enzymes to be relatively promiscuous, making them interesting tools for cyclodipeptide chemical diversification. The purpose of this study is to provide the first completely microbial toolkit for the efficient bioproduction of a variety of dehydrogenated 2,5-diketopiperazines.

Results
We mined genomes for CDOs encoded in biosynthetic gene clusters of CDPS-dependent pathways and selected several for characterization. We co-expressed each with their associated CDPS in the pathway using Escherichia coli as a chassis and showed that the cyclodipeptides and the dehydrogenated derivatives were produced in the culture supernatants. We determined the biological activities of the six novel CDOs by solving the chemical structures of the biologically produced dehydrogenated cyclodipeptides. Then, we assessed the six novel CDOs plus two previously characterized CDOs in combinatorial engineering experiments in E. coli. We co-expressed each of the eight CDOs with each of 18 CDPSs selected for the diversity of cyclodipeptides they synthesize. We detected more than 50 dehydrogenated cyclodipeptides and determined the best CDPS/CDO combinations to optimize the production of 23.

Conclusions
Our study establishes the usefulness of CDPS and CDO for the bioproduction of dehydrogenated cyclodipeptides. It constitutes the first step toward the bioproduction of more complex and diverse 2,5-diketopiperazines.