bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk of major labour-related complications for pregnancies progressing to 42 weeks or beyond
Authors: Lindquist Anthea C. , Hastie Roxanne M. , Hiscock Richard J. , Pritchard Natasha L. , Walker Susan P. , Tong Stephen 
Published: May 2021

Abstract
Background
Post-term gestation beyond 41+6 completed weeks of gestation is known to be associated with a sharp increase in the risk of stillbirth and perinatal mortality. However, the risk of common adverse outcomes related to labour, such as shoulder dystocia and post-partum haemorrhage for those delivering at this advanced gestation, remains poorly characterised. The objective of this study was to examine the risk of adverse, labour-related outcomes for women progressing to 42 weeks gestation or beyond, compared with those giving birth at 39 completed weeks.

Methods
We performed a state-wide cohort study using routinely collected perinatal data in Australia. Comparing the two gestation cohorts, we examined the adjusted relative risk of clinically significant labour-related adverse outcomes, including macrosomia (≥ 4500 at birth), post-partum haemorrhage (≥1000 ml), shoulder dystocia, 3rd or 4th degree perineal tear and unplanned caesarean section. Parity, maternal age and mode of birth were adjusted for using logistic regression.

Results
The study cohort included 91,314 women who birthed at 39 completed weeks and 4317 at ≥42 completed weeks. Compared to 39 weeks gestation, those giving birth ≥42 weeks gestation had an adjusted relative risk (aRR) of 1.85 (95% CI 1.55–2.20) for post-partum haemorrhage following vaginal birth, 2.29 (95% CI 1.89–2.78) following instrumental birth and 1.44 (95% CI 1.17–1.78) following emergency caesarean section; 1.43 (95% CI 1.16–1.77) for shoulder dystocia (for non-macrosomic babies); and 1.22 (95% CI 1.03–1.45) for 3rd or 4th degree perineal tear (all women). The adjusted relative risk of giving birth to a macrosomic baby was 10.19 (95% CI 8.26–12.57) among nulliparous women and 4.71 (95% CI 3.90–5.68) among multiparous women. The risk of unplanned caesarean section was 1.96 (95% CI 1.86–2.06) following any labour and 1.47 (95% CI 1.38–1.56) following induction of labour.

Conclusions
Giving birth at ≥42 weeks gestation may be an under-recognised risk factor for several important, labour-related adverse outcomes. Clinicians should be aware that labour at this advanced gestation incurs a higher risk of adverse outcomes. In addition to known perinatal risks, the risk of obstetric complications should be considered in the counselling of women labouring at post-term gestation.
Impact of 2017 ACC/AHA guideline on prevalence, awareness, treatment, control, and determinants of hypertension: a population-based cross-sectional study in southwest of Iran
Authors: Sadeghi Fatemeh , Cheraghian Bahman , Mohammadi Zahra , Sepanlou Sadaf G. , Masoudi Sahar , Rahimi Zahra , Danehchin Leila , Paridar Yousef , Abolnezhadian Farhad , Noori Mohammad , Mard Seyed Ali , Shayesteh Ali Akbar , Poustchi Hossein 
Published: May 2021

Abstract
Background
In 2017, the American College of Cardiology/American Heart Association (ACC/AHA) provided a new guideline for hypertension prevention and management. We aimed to update the prevalence, awareness, control, and determinants of hypertension based on this guideline in Khuzestan province, southwest of Iran, and to estimate the number of people who are eligible for non-pharmacologic and pharmacologic intervention.

Methods
This population-based cross-sectional study was conducted in Khuzestan, a large province in the southwest of Iran. Comprehensive information about the potential relating factors of hypertension was collected, blood pressure was measured, and anthropometric measurements were obtained. Moreover, the dietary pattern was evaluated in 2830 individuals, using a qualitative food frequency questionnaire.

Results
Among 30,506 participants, 30,424 individuals aged 20–65 years were eligible for the study. In comparison with the previous guideline released by the Joint National Committee (JNC8), the prevalence of hypertension in Khuzestan dramatically increased from 15.81 to 42.85% after implementation of the ACC/AHA guideline, which was more dominant in the male population and the 45–54 age group. The sex and age adjustment of the hypertension prevalence was estimated to be 39.40%. The percentage of hypertension awareness, treatment, and control were 45.85%, 35.42%, and 59.63%, which dropped to 22.72%, 26.37%, and 28.94% after implementation of new guideline, respectively.

Conclusions
In the ACC/AHA guideline, a higher number of individuals with the pre-hypertension condition were shifted into the hypertension category and the level of awareness, treatment, and control were dramatically decreased, which highlight a great need to expand the public health infrastructure for further managing the substantial increased burden on healthcare system. However, further studies with population over 65 years are required to estimate the eligibility for antihypertensive treatment in this province after implementation of new guideline.
Gene Ontology Meta Annotator for Plants (GOMAP)
Authors: Wimalanathan Kokulapalan , Lawrence-Dill Carolyn J. 
Published: May 2021

AbstractAnnotating gene structures and functions to genome assemblies is necessary to make assembly resources useful for biological inference. Gene Ontology (GO) term assignment is the most used functional annotation system, and new methods for GO assignment have improved the quality of GO-based function predictions. The Gene Ontology Meta Annotator for Plants (GOMAP) is an optimized, high-throughput, and reproducible pipeline for genome-scale GO annotation of plants. We containerized GOMAP to increase portability and reproducibility and also optimized its performance for HPC environments. Here we report on the pipeline’s availability and performance for annotating large, repetitive plant genomes and describe how GOMAP was used to annotate multiple maize genomes as a test case. Assessment shows that GOMAP expands and improves the number of genes annotated and annotations assigned per gene as well as the quality (based on $$F_{max}$$

F

max

) of GO assignments in maize. GOMAP has been deployed to annotate other species including wheat, rice, barley, cotton, and soy. Instructions and access to the GOMAP Singularity container are freely available online at https://bioinformapping.com/gomap/. A list of annotated genomes and links to data is maintained at https://dill-picl.org/projects/gomap/.
COVID-19 among patients with orthopedic surgery: our experience from the Middle East
Authors: Bagherifard Abolfazl , Arasteh Peyman , Salehpour Mostafa , Zadeh Hooman Shariat , Mazhar Farid Najd , Ghandhari Hasan , Bahaeddini Mohammad Reza , Tabrizian Pouria , Askari Alireza 
Published: May 2021

Abstract
Background
We report our experiences with COVID-19 in one of the largest referral orthopedic centers in the Middle East and aimed to describe the epidemiology and clinical characteristics of these patients.

Methods
During February 20 and April 20, 2020, patients who underwent orthopedic surgery and healthcare staff who were in contact with these patients were screened for COVID-19. To identify patients who were in the incubation period of COVID-19 during their hospital stay, all patients were tested again for COVID-19 4 weeks after discharge.

Results
Overall, 1244 patients underwent orthopedic surgery (1123 emergency and 121 elective) during the study period. Overall, 17 patients were diagnosed with COVID-19 during hospital admission and seven after discharge. Among the total 24 patients with COVID-19, 15 were (62.5%) males with a mean (SD) age of 47.0±1.6 years old. Emergency surgeries were performed in 20 (83.3%) patients, and elective surgery was done in the remaining 4 patients which included one case of posterior spinal fusion, spondylolisthesis, acromioclavicular joint dislocation, and one case of leg necrosis. A considerable number of infections occurred in patients with intertrochanteric fractures (n=7, 29.2%), followed by pelvic fractures (n=2, 8.3%), humerus fractures (n=2, 8.3%), and tibial plateau fractures (n=2, 8.3%). Fever (n=11, 45.8%) and cough (n=10, 37.5%) were the most common symptoms among patients. Laboratory examinations showed leukopenia in 2 patients (8.3%) and lymphopenia in 4 (16.7%) patients. One patient with a history of cancer died 2 weeks after discharge due to myocardial infarction.
Among hospital staff, 26 individuals contracted COVID-19 during the study period, which included 13 (50%) males. Physicians were the most commonly infected group (n = 11), followed by operation room technicians (n = 5), nurses (n = 4), and paramedics (n = 4).

Conclusions
Patients who undergo surgical treatment for orthopedic problems, particularly lower limb fractures with limited ambulation, are at a higher risk of acquiring COVID-19 infections, although they may not be at higher risks for death compared to the general population. Orthopedic surgeons in particular and other hospital staff who are in close contact with these patients must be adequately trained and given appropriate personal protective equipment during the COVID-19 outbreak.
GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization
Authors: Lee Da-Inn , Roy Sushmita 
Published: May 2021

AbstractHigh-throughput chromosome conformation capture assays, such as Hi-C, have shown that the genome is organized into organizational units such as topologically associating domains (TADs), which can impact gene regulatory processes. The sparsity of Hi-C matrices poses a challenge for reliable detection of these units. We present GRiNCH, a constrained matrix-factorization-based approach for simultaneous smoothing and discovery of TADs from sparse contact count matrices. GRiNCH shows superior performance against seven TAD-calling methods and three smoothing methods. GRiNCH is applicable to multiple platforms including SPRITE and HiChIP and can predict novel boundary factors with potential roles in genome organization.
Clinical and epigenetic features of colorectal cancer patients with somatic POLE proofreading mutations
Authors: Kawai Takashi , Nyuya Akihiro , Mori Yoshiko , Tanaka Takehiro , Tanioka Hiroaki , Yasui Kazuya , Toshima Toshiaki , Taniguchi Fumitaka , Shigeyasu Kunitoshi , Umeda Yuzo , Fujiwara Toshiyoshi , Okawaki Makoto , Yamaguchi Yoshiyuki , Goel Ajay , Nagasaka Takeshi 
Published: May 2021

Abstract
Background
Mutations in the POLE gene result in an ultra-hypermutated phenotype in colorectal cancer (CRC); however, the molecular characterisation of epigenetic alterations remains unclear. We examined the genetic and epigenetic profiles of POLE-mutant CRC to elucidate the clinicopathological features of the associated genetic and epigenetic alterations.

Results
Tumour tissues (1,013) obtained from a cohort of patients with CRC were analysed to determine associations between the proofreading domain mutations of POLE with various clinicopathological variables, microsatellite instability (MSI) status, BRAF and KRAS mutations, and the methylation status of key regions of MLH1, MGMT, and SFRP2 promoters by calculating the methylation scores (range 0–6). Only four cases (0.4%) exhibited pathogenic POLE hotspot mutations (two p.P286R [c.857C > G], one p.V411L [c.1231G > C], and p.S459F [c.1376C > T] each), which were mutually exclusive to BRAF and KRAS mutations and MSI. CRC patients were divided into four subgroups: patients with POLE mutations (POLE, 0.4%, n = 4), patients with both MSI and extensive methylation in MLH1 (MSI-M, 2.9%, n = 29), patients with MSI but no extensive methylation in MLH1 (MSI-U, 3.6%, n = 36), and patients without MSI (non-MSI, 93.2%, n = 944). The POLE group was younger at diagnosis (median 52 years, P < 0.0001), with frequent right-sided tumour localisation (frequency of tumours located in the right colon was 100%, 93.1%, 36.1%, and 29.9% in POLE, MSI-M, MSI-U, and non-MSI, respectively; P < 0.0001), and was diagnosed at an earlier stage (frequency of stages I–II was 100%, 72.4%, 77.8%, and 46.6% in POLE, MSI-M, MSI-U, and non-MSI, respectively, P < 0.0001). The mean methylation score in POLE was not different from that in MSI-U and non-MSI, but the methylation signature was distinct from that of the other subgroups. Additionally, although the examined number of POLE-mutant tumours was small, the number of CD8-positive cells increased in tumours with partial methylation in the MLH1 gene.

Conclusions
CRC patients with POLE proofreading mutations are rare. Such mutations are observed in younger individuals, and tumours are primarily located in the right colon. Diagnosis occurs at an earlier stage, and distinct epigenetic alterations may be associated with CD8 cell infiltration.
SYNCRIP facilitates porcine parvovirus viral DNA replication through the alternative splicing of NS1 mRNA to promote NS2 mRNA formation
Authors: Chen Songbiao , Miao Bichen , Chen Nannan , Chen Caiyi , Shao Ting , Zhang Xuezhi , Chang Lingling , Zhang Xiujuan , Du Qian , Huang Yong , Tong Dewen 
Published: May 2021

AbstractPorcine Parvovirus (PPV), a pathogen causing porcine reproductive disorders, encodes two capsid proteins (VP1 and VP2) and three nonstructural proteins (NS1, NS2 and SAT) in infected cells. The PPV NS2 mRNA is from NS1 mRNA after alternative splicing, yet the corresponding mechanism is unclear. In this study, we identified a PPV NS1 mRNA binding protein SYNCRIP, which belongs to the hnRNP family and has been identified to be involved in host pre-mRNA splicing by RNA-pulldown and mass spectrometry approaches. SYNCRIP was found to be significantly up-regulated by PPV infection in vivo and in vitro. We confirmed that it directly interacts with PPV NS1 mRNA and is co-localized at the cytoplasm in PPV-infected cells. Overexpression of SYNCRIP significantly reduced the NS1 mRNA and protein levels, whereas deletion of SYNCRIP significantly reduced NS2 mRNA and protein levels and the ratio of NS2 to NS1, and further impaired replication of the PPV. Furthermore, we found that SYNCRIP was able to bind the 3′-terminal site of NS1 mRNA to promote the cleavage of NS1 mRNA into NS2 mRNA. Taken together, the results presented here demonstrate that SYNCRIP is a critical molecule in the alternative splicing process of PPV mRNA, while revealing a novel function for this protein and providing a potential target of antiviral intervention for the control of porcine parvovirus disease.
Biofilm formation by Streptococcus mutans and its inhibition by green tea extracts
Authors: Zayed Sara Moataz , Aboulwafa Mohammad Mabrouk , Hashem Abdelgawad Mohamed , Saleh Sarra Ebrahim 
Published: May 2021

AbstractDental Caries is considered one of the most existing and worldwide common diseases related to the oral cavity affecting both children and adults. Streptococcus mutans is the main cariogenic microorganism involved in the dental caries progression. Natural products such as herbal plants were found to have less side effects and economic value than those of the chemically synthesized antibiofilm agents. This study aimed to isolate Streptococcus mutans from different oral samples taken from saliva and dental plaques specimens to determine their capability for biofilm formation and to evaluate the antibiofilm activity of aqueous and alcoholic green tea extracts. The results revealed that 35, 4 and 1% of recovered dental plaque isolates exhibited strong, moderate and weak biofilm formation capabilities versus 26, 12 and 2% for those recovered from saliva. Two green tea extracts (aqueous and alcoholic) were tested for their antibiofilm formation activity against some selected S. mutans isolates. The results showed that the minimum biofilm inhibitory concentrations (MBICs) of the alcoholic and aqueous green tea extracts were in the range of 3.1 to 12.5 mg/ml and 6.5 to 50 mg/ml, respectively. Accordingly, green tea extracts can be incorporated in various oral preparations for preventing dental caries.
Infectious events in patients with severe COVID-19: results of a cohort of patients with high prevalence of underlying immune defect
Authors: Saade Anastasia , Moratelli Giulia , Dumas Guillaume , Mabrouki Asma , Tudesq Jean-Jacques , Zafrani Lara , Azoulay Elie , Darmon Michael 
Published: May 2021

AbstractBackgroundEmpirical antibiotic has been considered in severe COVID-19 although little data are available regarding concomitant infections. This study aims to assess the frequency of infections, community and hospital-acquired infections, and risk factors for infections and mortality during severe COVID-19.MethodsRetrospective single-center study including consecutive patients admitted to the intensive care unit (ICU) for severe COVID-19. Competing-risk analyses were used to assess cumulative risk of infections. Time-dependent Cox and fine and gray models were used to assess risk factors for infections and mortality. Propensity score matching was performed to estimate the effect of dexamethasone.ResultsWe included 100 patients including 34 patients with underlying malignancies or organ transplantation. First infectious event was bacterial for 35 patients, and fungal for one. Cumulative incidence of infectious events was 27% [18–35] at 10 ICU-days. Prevalence of community-acquired infections was 7% [2.8–13.9]. Incidence density of hospital-acquired infections was 125 [91–200] events per 1000 ICU-days. Risk factors independently associated with hospital-acquired infections included MV. Patient’s severity and underlying malignancy were associated with mortality. Dexamethasone was associated with increased infections (36% [20–53] vs. 12% [4–20] cumulative incidence at day-10;p = 0.01). After matching, dexamethasone was associated with hospital-acquired infections (35% [18–52] vs. 13% [1–25] at 10 days, respectively,p = 0.03), except in the subset of patients requiring MV, and had no influence on mortality.ConclusionsIn this population of COVID-19 patients with high prevalence of underlying immune defect, a high risk of infections was noted. MV and use of steroids were independently associated with infection rate.
Facilitating rapid access to addiction treatment: a randomized controlled trial
Authors: Srivastava Anita , Clarke Sarah , Hardy Kate , Kahan Meldon 
Published: May 2021

Abstract
Background
Obtaining timely access to addiction medicine treatment for patients with substance use disorders is challenging and patients often have to navigate complex referral pathways. This randomized controlled trial examines the effect of providing an expedited pathway to addiction medicine treatment on initial treatment engagement and health care utilization.

Methods
Individuals with possible alcohol or opioid use disorder were recruited from three residential withdrawal management services (WMS). Subjects randomized to the Delayed Intervention (DI) group were given contact information for a nearby addiction medicine clinic; those randomized to the Rapid Intervention (RI) group were given an appointment at the clinic within 2 days and were accompanied to their first appointment.

Results
Of the 174 individuals who were screened, 106 were randomized to either the DI or RI group. The two groups were similar in demographics, housing status, and substance use in the last 30 days. In the 6-month period following randomization, 85% of the RI group attended at least one clinic appointment, compared to only 29% in the DI group (p < 0.0001). The RI group had a mean of 6.39 ED visits per subject in the 12 months after randomization, while the DI group had a mean of 13.02 ED visits per subject in the same 12-month period (p = 0.0469). Other health utilization measures did not differ between the two groups.

Conclusion
Providing immediate facilitated access to an addiction medicine service resulted in greater initial engagement and reduced emergency department visits at 6 months.
Trial registration This trial is registered at the National Institutes of Health (ClinicalTrials.gov) under identifier #NCT01934751.
Are there any turning points for external debt in Malaysia? Case of adaptive neuro-fuzzy inference systems model
Authors: Karia Abdul Aziz Bin 
Published: May 2021

AbstractThis paper intends to investigate whether the turning points exist between tax revenue, gross domestic product, government expenditure, and gross domestic saving towards Malaysia’s total external debt. The researcher implements the adaptive neuro-fuzzy inference system model to forecast the total external debt in Malaysia. The total external debt prediction then projects the three-dimensional surface diagrams to depict whether the turning points exist among the variables. This study’s empirical finding reveals that the turning points are noticeable between the tax revenue, gross domestic product, and gross domestic saving toward external debt in Malaysia. However, government expenditure depicts a direct relationship with external debt. This finding demonstrates that the anomaly between the theories and scholarly activities. This study also recommends that the tax revenue be collected at maximum holding the government expenditure and gross domestic product are maximum statistics to reduce Malaysia’s external debt.
Epigenetics and microRNAs in UGT1As
Authors: Meng Cui-Lan , Zhao Wei , Zhong Dan-Ni 
Published: May 2021

AbstractUDP-glucuronosyltransferases (UGTs) are the main phase II drug-metabolizing enzymes mediating the most extensive glucuronidation-binding reaction in the human body. The UGT1A family is involved in more than half of glucuronidation reactions. However, significant differences exist in the distribution of UGT1As in vivo and the expression of UGT1As among individuals, and these differences are related to the occurrence of disease and differences in metabolism. In addition to genetic polymorphisms, there is now interest in the contribution of epigenetics and noncoding RNAs (especially miRNAs) to this differential change. Epigenetics regulates UGT1As pretranscriptionally through DNA methylation and histone modification, and miRNAs are considered the key mechanism of posttranscriptional regulation of UGT1As. Both epigenetic inheritance and miRNAs are involved in the differences in sex expression and in vivo distribution of UGT1As. Moreover, epigenetic changes early in life have been shown to affect gene expression throughout life. Here, we review and summarize the current regulatory role of epigenetics in the UGT1A family and discuss the relationship among epigenetics and UGT1A-related diseases and treatment, with references for future research.