bluuebunny/crossref_metadata_2025_split huggingface dataset:
External features enriched model for biomedical question answering
Authors: Xu Gezheng , Rong Wenge , Wang Yanmeng , Ouyang Yuanxin , Xiong Zhang 
Published: May 2021

AbstractBackgroundBiomedical question answering (QA) is a sub-task of natural language processing in a specific domain, which aims to answer a question in the biomedical field based on one or more related passages and can provide people with accurate healthcare-related information. Recently, a lot of approaches based on the neural network and large scale pre-trained language model have largely improved its performance. However, considering the lexical characteristics of biomedical corpus and its small scale dataset, there is still much improvement room for biomedical QA tasks.ResultsInspired by the importance of syntactic and lexical features in the biomedical corpus, we proposed a new framework to extract external features, such as part-of-speech and named-entity recognition, and fused them with the original text representation encoded by pre-trained language model, to enhance the biomedical question answering performance. Our model achieves an overall improvement of all three metrics on BioASQ 6b, 7b, and 8b factoid question answering tasks.ConclusionsThe experiments on BioASQ question answering dataset demonstrated the effectiveness of our external feature-enriched framework. It is proven by the experiments conducted that external lexical and syntactic features can improve Pre-trained Language Model’s performance in biomedical domain question answering task.
Lantern: an integrative repository of functional annotations for lncRNAs in the human genome
Authors: Daulatabad Swapna Vidhur , Srivastava Rajneesh , Janga Sarath Chandra 
Published: May 2021

Abstract
Background
With advancements in omics technologies, the range of biological processes where long non-coding RNAs (lncRNAs) are involved, is expanding extensively, thereby generating the need to develop lncRNA annotation resources. Although, there are a plethora of resources for annotating genes, despite the extensive corpus of lncRNA literature, the available resources with lncRNA ontology annotations are rare.

Results
We present a lncRNA annotation extractor and repository (Lantern), developed using PubMed’s abstract retrieval engine and NCBO’s recommender annotation system. Lantern’s annotations were benchmarked against lncRNAdb’s manually curated free text. Benchmarking analysis suggested that Lantern has a recall of 0.62 against lncRNAdb for 182 lncRNAs and precision of 0.8. Additionally, we also annotated lncRNAs with multiple omics annotations, including predicted cis-regulatory TFs, interactions with RBPs, tissue-specific expression profiles, protein co-expression networks, coding potential, sub-cellular localization, and SNPs for ~ 11,000 lncRNAs in the human genome, providing a one-stop dynamic visualization platform.

Conclusions
Lantern integrates a novel, accurate semi-automatic ontology annotation engine derived annotations combined with a variety of multi-omics annotations for lncRNAs, to provide a central web resource for dissecting the functional dynamics of long non-coding RNAs and to facilitate future hypothesis-driven experiments. The annotation pipeline and a web resource with current annotations for human lncRNAs are freely available on sysbio.lab.iupui.edu/lantern.
Identification of cis-regulatory motifs in first introns and the prediction of intron-mediated enhancement of gene expression in Arabidopsis thaliana
Authors: Back Georg , Walther Dirk 
Published: May 2021

AbstractBackgroundIntron mediated enhancement (IME) is the potential of introns to enhance the expression of its respective gene. This essential function of introns has been observed in a wide range of species, including fungi, plants, and animals. However, the mechanisms underlying the enhancement are as of yet poorly understood. The goal of this study was to identify potential IME-related sequence motifs and genomic features in first introns of genes inArabidopsis thaliana.ResultsBased on the rationale that functional sequence motifs are evolutionarily conserved, we exploited the deep sequencing information available forArabidopsis thaliana, covering more than one thousand Arabidopsis accessions, and identified 81 candidate hexamer motifs with increased conservation across all accessions that also exhibit positional occurrence preferences. Of those, 71 were found associated with increased correlation of gene expression of genes harboring them, suggesting a cis-regulatory role. Filtering further for effect on gene expression correlation yielded a set of 16 hexamer motifs, corresponding to five consensus motifs. While all five motifs represent new motif definitions, two are similar to the two previously reported IME-motifs, whereas three are altogether novel. Both consensus and hexamer motifs were found associated with higher expression of alleles harboring them as compared to alleles containing mutated motif variants as found in naturally occurring Arabidopsis accessions. To identify additional IME-related genomic features, Random Forest models were trained for the classification of gene expression level based on an array of sequence-related features. The results indicate that introns contain information with regard to gene expression level and suggest sequence-compositional features as most informative, while position-related features, thought to be of central importance before, were found with lower than expected relevance.ConclusionsExploiting deep sequencing and broad gene expression information and on a genome-wide scale, this study confirmed the regulatory role on first-introns, characterized their intra-species conservation, and identified a set of novel sequence motifs located in first introns of genes in the genome of the plantArabidopsis thalianathat may play a role in inducing high and correlated gene expression of the genes harboring them.
Outcomes of patients with end stage kidney disease on dialysis with COVID-19 in Abu Dhabi, United Arab Emirates; from PCR to antibody
Authors: Ahmed Wasim , Al Obaidli Ali Abdul Kareem , Joseph Princy , Smith Edward R. , Khan Ayaz Ahmad , Anwar Siddiq , Chandrasekar Thangavelu , Al Madani Ayman Kamal , Dastoor Hormazdiar Dara , Zahid Imran , Costales Freddie Agbayani , Boobes Yousef Abdul Rahim , Al Kindi Fatima , Issa Salah Eldin Khalil , Hassan Mohamed H. , George Abraham , Holt Stephen Geoffrey 
Published: May 2021

AbstractBackgroundIndividuals with end-stage kidney disease (ESKD) on dialysis are vulnerable to contracting COVID-19 infection, with mortality as high as 31 % in this group. Population demographics in the UAE are dissimilar to many other countries and data on antibody responses to COVID-19 is also limited. The objective of this study was to describe the characteristics of patients who developed COVID-19, the impact of the screening strategy, and to assess the antibody response to a subset of dialysis patients.MethodsWe retrospectively examined the outcomes of COVID19 infection in all our haemodialysis patients, who were tested regularly for COVID 19, whether symptomatic or asymptomatic. In addition, IgG antibody serology was also performed to assess response to COVID-19 in a subset of patients.Results152 (13 %) of 1180 dialysis patients developed COVID-19 during the study period from 1st of March to the 1st of July 2020. Of these 81 % were male, average age of 52​ years and 95 % were on in-centre haemodialysis. Family and community contact was most likely source of infection in most patients. Fever (49 %) and cough (48 %) were the most common presenting symptoms, when present. Comorbidities in infected individuals included hypertension (93 %), diabetes (49 %), ischaemic heart disease (30 %). The majority (68 %) developed mild disease, whilst 13 % required critical care. Combinations of drugs including hydroxychloroquine, favipiravir, lopinavir, ritonavir, camostat, tocilizumab and steroids were used based on local guidelines. The median time to viral clearance defined by two negative PCR tests was 15 days [IQR 6–25]. Overall mortality in our cohort was 9.2 %, but ICU mortality was 65 %. COVID-19 IgG antibody serology was performed in a subset (n = 87) but 26 % of PCR positive patients (n = 23) did not develop a significant antibody response.ConclusionsOur study reports a lower mortality in this patient group compared with many published series. Asymptomatic PCR positivity was present in 40 %. Rapid isolation of positive patients may have contributed to the relative lack of spread of COVID-19 within our dialysis units. The lack of antibody response in a few patients is concerning.
Association between mode of delivery and body mass index at 4-5 years in White British and Pakistani children: the Born in Bradford birth cohort
Authors: Ralphs Eleanor , Pembrey Lucy , West Jane , Santorelli Gillian 
Published: May 2021

Abstract
Background
Globally, it is becoming more common for pregnant women to deliver by caesarean section (CS). In 2020, 31% of births in England were CS, surpassing the recommended prevalence of CS. Concerns have been raised regarding potential unknown consequences of this mode of delivery.
Childhood adiposity is also an increasing concern. Previous research provides inconsistent conclusions on the association between CS and childhood adiposity. More studies are needed to investigate the consequences of CS in different populations and ethnicities. Therefore, this study investigates the association between mode of delivery and BMI, in children of 4–5 years and if this differs between White British (WB) and Pakistani ethnicities, in Bradford UK.

Methods
Data were obtained from the Born in Bradford (BiB) cohort, which recruited pregnant women at the Bradford Royal Infirmary, between 2007 and 2010. For these analyses, a sub-sample (n = 6410) of the BiB cohort (n = 13,858) was used.
Linear regression models determined the association between mode of delivery (vaginal or CS) and BMI z-scores at 4–5 years. Children were categorised as underweight/healthy weight, overweight and obese, and logistic regression models determined the odds of adiposity. Effect modification by ethnicity was also explored.

Results
Multivariable analysis found no evidence for a difference in BMI z-score between children of CS and vaginal delivery (0.005 kg/m2, 95% CI = − 0.062–0.072, p = 0.88). Neither was there evidence of CS affecting the odds of being overweight (OR = 1.05, 95% CI = 0.86–1.28, p = 0.65), or obese (OR = 0.98, 95% CI = 0.74–1.29, p = 0.87). There was no evidence that ethnicity was an effect modifier of these associations (p = 0.97).

Conclusion
Having CS, compared to a vaginal delivery, was not associated with greater adiposity in children of 4–5 years in this population. Concerns over CS increasing adiposity in children are not supported by the findings reported here using the BiB study population, of both WB and Pakistani families.
Comparison of cervical cancer screening by self-sampling papillomavirus test versus pap-smear in underprivileged women in France
Authors: Reques Laura , Rolland Camille , Lallemand Anne , Lahmidi Najat , Aranda-Fernández Ezequiel , Lazzarino Antonio , Bottero Julie , Hamers Françoise , Bergeron Christine , Haguenoer Ken , Launoy Guy , Luhmann Niklas 
Published: May 2021

AbstractBackgroundThe purpose of this study was to compare cervical cancer screening by pap smear (PS) versus preliminary HPV testing based on self-collected samples (SC-HPV).MethodsInterventional study among underprivileged women from 25 to 65 years old in four French cities. The control group (CG) was referred for a PS. The experimental group (EG) conducted a SC-HPV test followed by a PS in case of positivity. Differences on screening completion and cytological abnormalities were analysed by logistic and Cox regression.Results383 women were assigned to the EG and 304 to the CG. The screening completion proportion was 39.5% in the CG compared to 71.3% in the EG (HR = 2.48 (CI 95% [1.99–3.08];p < 0.001). The proportion of cytological abnormalities was 2.0% in the CG and 2.3% in the EG (OR = 1.20 (CI 95% [0.42–3.40]; p = 0.7). The proportion of participants lost to follow-up was 60.5% in the CG and 63.2% in the EG HPV positive (p = 0.18).ConclusionProviding an SC-HPV-test increased the participation of underprivileged women in CCS. Nevertheless, the significant number of lost to follow-up in both groups can undermine the initial benefits of the strategy for HPV positive women.Registration: Clinicaltrials.gov: NCT03118258.
“I came to escort someone”: Men’s experiences of antenatal care services in urban Ghana—a qualitative study
Authors: Ampim Gloria Abena , Blystad Astrid , Kpoor Albert , Haukanes Haldis 
Published: May 2021

Abstract
Background
Male involvement in maternal healthcare has been widely recognized as essential for positive health outcomes for expectant mothers and their unborn babies. However, few studies have explored men’s experiences of maternal health services. The purpose of this paper is to explore men’s involvement in antenatal care in urban Ghana and to discuss how men navigate their roles in a space that has been constructed as feminine. The study draws upon theories of space, place, and gender.

Methods
A qualitative exploratory study using semistructured interviews, focus group discussion, and observation was conducted in Accra, Ghana. Expectant fathers and health workers were interviewed, and observation was conducted at a selected public hospital in Accra.

Results
The findings suggest that the few men who attend antenatal care with their expecting partners become involved to a limited extent in the clinic’s activities. Beyond a few who take an active role, most men stay on the outskirts of the hospital grounds and rarely participate in consultations with their partner and midwife. Men still view their presence as necessary to acquire knowledge and as sources of emotional, financial, and physical support for their partners. On the health workers’ side, the study found no clear agenda for engaging men at the clinic, and nurses/midwives felt there was a lack of staff who could engage more directly with the men.

Conclusion
The study indicates that most expecting fathers feel too shy and uncomfortable to locate themselves in the female space that makes up antenatal care/maternity wards. Health workers do not feel they have the necessary resources to involve men fruitfully. Thus, men do not engage in the activity as hoped but rather remain on the outskirts of the maternity clinic. However, if men continue to negotiate their involvement at the clinic and become more assertive in their roles, the maternity clinic as a female space could, with time, be transformed into a space in which both expecting mothers and fathers can actively participate and be engaged to the benefit of all.
Early union, ‘disgrasya’, and prior adversity and disadvantage: pathways to adolescent pregnancy among Filipino youth
Authors: Habito Christine Marie , Morgan Alison , Vaughan Cathy 
Published: May 2021

Abstract
Background
Few studies explore what it means to be an adolescent parent in the Philippines from the young parents’ perspective. This study sought to improve understanding of how adolescent mothers and young fathers experienced pregnancy in Palawan, Philippines.

Methods
We conducted narrative analysis of 27 semi-structured interviews with 15 Filipino young parents.

Findings
Our findings point to three pathways to adolescent pregnancy differentiated by life circumstances and perceived self-efficacy: through early unions, through ‘disgrasya’ (accident) in romantic relationships, and when pregnancy is directly related to adversity and disadvantage. Some young people adopted agentic narratives and had intended pregnancies within early unions. Young people who had unintended pregnancies in romantic relationships recounted constrained choice narratives, taking responsibility for their decisions while emphasising external factors’ influence on their decision-making. Other young mothers described the ways that prior adversity and disadvantage gave rise to unfavourable circumstances—including sexual violence—that led to unintended pregnancy but shared narratives showing how they had reclaimed agency in their lives.

Conclusion
Our findings highlight the need to (1) address underlying poverty and structural inequalities that limit Filipino young people’s life choices and contribute to their pathways to adolescent pregnancy; (2) provide Filipino young people with access to essential sexual and reproductive health information, services, and supplies; and (3) change social norms to rectify gender-based power imbalances and sexual violence.
Epidural cerebellar stimulation drives widespread neural synchrony in the intact and stroke perilesional cortex
Authors: Abbasi Aamir , Danielsen Nathan P. , Leung Jennifer , Muhammad A. K. M. G. , Patel Saahil , Gulati Tanuj 
Published: May 2021

Abstract
Background
Cerebellar electrical stimulation has shown promise in improving motor recovery post-stroke in both rodent and human studies. Past studies have used motor evoked potentials (MEPs) to evaluate how cerebellar stimulation modulates ongoing activity in the cortex, but the underlying mechanisms are incompletely understood. Here we used invasive electrophysiological recordings from the intact and stroke-injured rodent primary motor cortex (M1) to assess how epidural cerebellar stimulation modulates neural dynamics at the level of single neurons as well as at the level of mesoscale dynamics.

Methods
We recorded single unit spiking and local field potentials (LFPs) in both the intact and acutely stroke-injured M1 contralateral to the stimulated cerebellum in adult Long-Evans rats under anesthesia. We analyzed changes in the firing rates of single units, the extent of synchronous spiking and power spectral density (PSD) changes in LFPs during and post-stimulation.

Results
Our results show that post-stimulation, the firing rates of a majority of M1 neurons changed significantly with respect to their baseline rates. These firing rate changes were diverse in character, as the firing rate of some neurons increased while others decreased. Additionally, these changes started to set in during stimulation. Furthermore, cross-correlation analysis showed a significant increase in coincident firing amongst neuronal pairs. Interestingly, this increase in synchrony was unrelated to the direction of firing rate change. We also found that neuronal ensembles derived through principal component analysis were more active post-stimulation. Lastly, these changes occurred without a significant change in the overall spectral power of LFPs post-stimulation.

Conclusions
Our results show that cerebellar stimulation caused significant, long-lasting changes in the activity patterns of M1 neurons by altering firing rates, boosting neural synchrony and increasing neuronal assemblies’ activation strength. Our study provides evidence that cerebellar stimulation can directly modulate cortical dynamics. Since these results are present in the perilesional cortex, our data might also help explain the facilitatory effects of cerebellar stimulation post-stroke.
Inhibition of herpes simplex virus-1 infection by MBZM-N-IBT: in silico and in vitro studies
Authors: Kumar Abhishek , De Saikat , Moharana Alok Kumar , Nayak Tapas Kumar , Saswat Tanuja , Datey Ankita , Mamidi Prabhudutta , Mishra Priyadarsee , Subudhi Bharat Bhusan , Chattopadhyay Soma 
Published: May 2021

AbstractIntroductionThe emergence of drug resistance and cross-resistance to existing drugs has warranted the development of new antivirals for Herpes simplex viruses (HSV). Hence, we have designed this study to evaluate the anti-viral activity of 1-[(2-methyl benzimidazole-1-yl) methyl]-2-oxo-indolin-3-ylidene] amino] thiourea (MBZM-N-IBT), against HSV-1.MethodMolecular docking was performed to assess the affinity of MBZM-N-IBT for HSV-1 targets. This was validated by plaque assay, estimation of RNA and protein levels as well as time of addition experiments in vitro.ResultMolecular docking analysis suggested the inhibitory capacity of MBZM-N-IBT against HSV-1. This was supported by the abrogation of the HSV-1 infectious viral particle formation with the IC50value of 3.619 µM. Viral mRNA levels were also reduced by 72% and 84% for UL9 and gC respectively. MBZM-N-IBT also reduced the protein synthesis for gC and ICP8 significantly. While mRNA of ICP8 was not significantly affected, its protein synthesis was reduced by 47%. The time of addition experiment revealed the capacity of MBZM-N-IBT to inhibit HSV-1 at early as well as late stages of infection in the Vero cells. Similar effect of MBZM-N-IBT was also noticed in the Raw 264.7 and BHK 21 cells after HSV-1 infection. Supported by the in silico data, this can be attributed to possible interference with multiple HSV targets including the ICP8, ICP27, UL42, UL25, UL15 and gB proteins.ConclusionThese results along with the lack of acute oral toxicity and significant anti-inflammatory effects suggest its suitability for further evaluation as a non-nucleoside inhibitor of HSV.
Wild plants and the food-medicine continuum—an ethnobotanical survey in Chapada Diamantina (Northeastern Brazil)
Authors: de Medeiros Patrícia Muniz , Figueiredo Karina Ferreira , Gonçalves Paulo Henrique Santos , Caetano Roberta de Almeida , Santos Élida Monique da Costa , dos Santos Gabriela Maria Cota , Barbosa Déborah Monteiro , de Paula Marcelo , Mapeli Ana Maria 
Published: May 2021

AbstractBackgroundEthnobotanical research has demonstrated that several wild food plants (WFP) are used for medicinal purposes. Therefore, in addition to constituting an important source of nutrients, WFP can be used to help treat and avoid health problems. This study sought to characterize the traditional use of plants considered simultaneously as food and medicine by local specialists in the community of Caeté-Açu, which borders Chapada Diamantina National Park (NE Brazil). We also sought to identify the variables that influence the species’ cultural importance.MethodsWe selected local specialists based on a snowball sample and used a free-listing technique to register the wild plants they knew that are both edible and medicinal. Then, we asked the specialists to rank each plant component cited according to the following attributes: (1) ease of acquisition, (2) taste, (3) smell, (4) nutritional value, and (5) medicinal value. We used multiple regression to determine the variables that influence the cultural salience.ResultsThe most culturally salient species wasAnredera cordifolia(Ten.) Steenis.The main medicinal effects associated with this species were related to body strengthening, intestinal regulation, and stomach issues. The most salient used species were those that were easiest to acquire and had the highest perceived nutritional values.ConclusionIt is likely that the sociocultural backgrounds of the respondents (elders, former miners, or descendants of miners) and the historical importance of wild food plants to local diets increased the predictive power of the perceived nutritional importance and ease of acquisition of these plants.