bluuebunny/crossref_metadata_2025 huggingface dataset:
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

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

Background

Intron 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.

Results

Based 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.

Conclusions

Exploiting 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

Background

Individuals 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.

Methods

We 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.

Results

152 (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.

Conclusions

Our 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

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

Background

The 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).

Methods

Interventional 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.

Results

383 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).

Conclusion

Providing 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

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

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

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

Introduction

The 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.

Method

Molecular 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.

Result

Molecular 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.

Conclusion

These 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.
Correction to: Mulberry leaf extract improves glycaemic response and insulaemic response to sucrose in healthy subjects: results of a randomized, double blind, placebo‑controlled study
Authors: Thondre Pariyarath Sangeetha , Lightowler Helen , Ahlstrom Lis , Gallagher Andrew
Published: May 2021

An amendment to this paper has been published and can be accessed via the original article.
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

Background

Ethnobotanical 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.

Methods

We 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.

Results

The 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.

Conclusion

It 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.
Determinants of breastfeeding practice in Pujehun district, southern Sierra Leone: a mixed-method study
Authors: van Breevoort Dorothee , Tognon Francesca , Beguin Arne , Ngegbai Amara S. , Putoto Giovanni , van den Broek Ankie
Published: May 2021

Background

It is well established that exclusive breastfeeding can play a critical role in reducing child morbidity and mortality. Limited research has been done thus far on the practice and perceptions of breastfeeding in Sierra Leone, where more than 10 % of children die before the age of five. This study aimed to gain understanding into and explore both matters in order to develop recommendations for effective strategies to promote breastfeeding practice in Pujehun District, Southern Sierra Leone.

Methods

This exploratory mixed-method study included a cross-sectional survey of 194 mothers, semi-structured interviews and focus group discussions. Logistic regression analysis was used calculated odds ratios of factors associated with primarily breastfeeding practice, defined as ‘Children under six months of age who are fed with breast milk only and children older than six months of age that were exclusively breastfed up to six months’, based on recall from birth. Exclusive breastfeeding rate was based on breastfeeding practice 24 h prior to the survey. Qualitative data was analysed through a deductive approach, using a pre-determined framework on determinants of breastfeeding.

Results

This study revealed an exclusive breastfeeding rate of 62.8% (95% CI 53.9, 71.7); dropping from 74% in the 0–1-month age group to 33% in the 4–5 months group. Triangulation of qualitative and quantitative data revealed enabling factors for primarily breastfeeding practice included mothers receiving support during their first breastfeed, pregnant women being provided with information on the benefits of the practice, counselling by nurses, support from husbands, and women’s awareness of how their friends and family members fed their own babies. The main barriers were a lack of encouragement by husbands, women’s perception that their infants’ stools were abnormal or that they were not producing enough breast milk.

Conclusions

Although the exclusive breastfeeding may have risen over recent years, a gap remains compared to World Health Organization recommendations. According to the breastfeeding determinants identified in this study, promotion of counselling by a nurse, encouragement of husbands’ support, and improve knowledge of mothers on breastfeeding are recommended to be incorporated in the design of future health programs.
Utility of modified Laboratory Risk Indicator for Necrotizing Fasciitis (MLRINEC) score in distinguishing necrotizing from non-necrotizing soft tissue infections
Authors: Wu Po-Han , Wu Kai-Hsiang , Hsiao Cheng-Ting , Wu Shu-Ruei , Chang Chia-Peng
Published: May 2021

Background

We conducted this study to promote a modified Laboratory Risk Indicator for Necrotizing Fasciitis (MLRINEC) score and evaluate the utility in distinguishing necrotizing fasciitis (NF) from other soft-tissue infections.

Method

A retrospective cohort study of hospitalized patients with NF diagnosed by surgical finding was conducted in two tertiary hospital in southern Taiwan between January 2015 and January 2020. Another group was matched by controls with non-necrotizing soft tissue infections based on time, demographics, and immune status. Data such as infectious location, comorbidities, and laboratory findings were recorded and compared. Logistics regression were used to determine the association with NF after adjustment for confounders and MLRINEC score was developed by then. Receiver operating curve (ROC) and the area under the curve (AUC) were used to evaluate its discriminating ability.

Result

A total of 303 patients were included; 101 in NF group and 202 in non-NF group. We added serum lactate and comorbid liver disease to the original LRINEC score and re-defined the cut-off values for 3 variables to develop the MLRINEC score. The cut-off value for MLRINEC score was 12 points with corresponding sensitivity of 91.8% and a specificity of 88.4%, and the area under ROC (AUC) was 0.893 (95% CI, 0.723 to 0.948; p < 0.01).

Conclusion

MLRINEC score shows a high sensitivity and specificity in distinguishing NF from non-necrotizing soft-tissue infections. Patients with a MLRINEC score > 12 points should be highly suspected of presence of necrotizing fasciitis.
Histological and ultrastructural degenerative findings in the gluteus medius tendon after hip arthroplasty
Authors: Ibrahim Mustafa , Hedlundh Urban , Sernert Ninni , Meknas Khaled , Haag Lars , Movin Tomas , Papadogiannakis Nikos , Kartus Jüri-Toomas
Published: May 2021

Background

Despite gluteus medius (GMED) tendinosis being relatively common, its presence in association with hip osteoarthritis (OA) or total hip arthroplasty (THA) is not well studied. It was hypothesized that more tendon degeneration would be found in patients with OA of the hip and in those that had undergone THA than that in a control group.

Methods

One hundred patients were included between 2016 and 2019 and were included into 4 groups; the patients were undergoing revision surgery in two groups and primary THA in the other two groups; 22 patients had previously undergone primary THA through a direct lateral approach (involving sectioning of the GMED tendon), 24 patients had previously undergone primary THA through a posterior approach (leaving the GMED tendon intact), 29 patients had primary hip OA, and 25 patients who suffered a femoral neck fracture served as controls. Biopsies from the GMED tendon were obtained at the time of the primary THA or the hip revision surgery. The tendon biopsies were examined ultrastructurally and histologically.

Results

Ultrastructurally, the direct lateral and posterior revision groups had statistically significantly more collagen fibrils with smaller diameters compared with the fracture and primary THA groups. Moreover, the direct lateral revision group had more collagen fibrils with smaller diameters compared with the posterior revision group.

Histologically, the direct lateral revision group had a higher total degeneration score (TDS) compared with the primary hip OA group.

Conclusions

The GMED tendon shows more ultrastructural degeneration in patients who undergo hip revision arthroplasty than in patients with primary OA of the hip and control patients, who had suffered a femoral neck fracture. Furthermore, patients who had previously undergone primary THA through a direct lateral approach revealed more histological GMED tendon degeneration than patients who suffer primary hip OA.
A systematic and meta-analysis review on the diagnostic accuracy of antibodies in the serological diagnosis of COVID-19
Authors: Vengesai Arthur , Midzi Herald , Kasambala Maritha , Mutandadzi Hamlet , Mduluza-Jokonya Tariro L. , Rusakaniko Simbarashe , Mutapi Francisca , Naicker Thajasvarie , Mduluza Takafira
Published: May 2021

Background

Serological testing based on different antibody types are an alternative method being used to diagnose SARS-CoV-2 and has the potential of having higher diagnostic accuracy compared to the current gold standard rRT-PCR. Therefore, the objective of this review was to evaluate the diagnostic accuracy of IgG and IgM based point-of-care (POC) lateral flow immunoassay (LFIA), chemiluminescence enzyme immunoassay (CLIA), fluorescence enzyme-linked immunoassay (FIA) and ELISA systems that detect SARS-CoV-2 antigens.

Method

A systematic literature search was carried out in PubMed, Medline complete and MedRxiv. Studies evaluating the diagnostic accuracy of serological assays for SARS-CoV-2 were eligible. Study selection and data-extraction were performed by two authors independently. QUADAS-2 checklist tool was used to assess the quality of the studies. The bivariate model and the hierarchical summary receiver operating characteristic curve model were performed to evaluate the diagnostic accuracy of the serological tests. Subgroup meta-analysis was performed to explore the heterogeneity.

Results

The pooled sensitivity for IgG (n = 17), IgM (n = 16) and IgG-IgM (n = 24) based LFIA tests were 0.5856, 0.4637 and 0.6886, respectively compared to rRT-PCR method. The pooled sensitivity for IgG (n = 9) and IgM (n = 10) based CLIA tests were 0.9311 and 0.8516, respectively compared to rRT-PCR. The pooled sensitivity the IgG (n = 10), IgM (n = 11) and IgG-IgM (n = 5) based ELISA tests were 0.8292, 0.8388 and 0.8531 respectively compared to rRT-PCR. All tests displayed high specificities ranging from 0.9693 to 0.9991. Amongst the evaluated tests, IgG based CLIA expressed the highest sensitivity signifying its accurate detection of the largest proportion of infections identified by rRT-PCR. ELISA and CLIA tests performed better in terms of sensitivity compared to LFIA. IgG based tests performed better compared to IgM except for the ELISA.

Conclusions

We report that IgG-IgM based ELISA tests have the best overall diagnostic test accuracy. Moreover, irrespective of the method, a combined IgG/IgM test seems to be a better choice in terms of sensitivity than measuring either antibody type independently. Given the poor performances of the current LFIA devices, there is a need for more research on the development of highly sensitivity and specific POC LFIA that are adequate for most individual patient applications and attractive for large sero-prevalence studies.

Systematic review registration

PROSPERO CRD42020179112
An accurate approach based on the orthonormal shifted discrete Legendre polynomials for variable-order fractional Sobolev equation
Authors: Heydari M. H. , Atangana A.
Published: May 2021

This paper applies the Heydari–Hosseininia nonsingular fractional derivative for defining a variable-order fractional version of the Sobolev equation. The orthonormal shifted discrete Legendre polynomials, as an appropriate family of basis functions, are employed to generate an operational matrix method for this equation. A new fractional operational matrix related to these polynomials is extracted and employed to construct the presented method. Using this approach, an algebraic system of equations is obtained instead of the original variable-order equation. The numerical solution of this system can be found easily. Some numerical examples are provided for verifying the accuracy of the generated approach.
Adapting a neuroscience-informed intervention to alter reward mechanisms of anorexia nervosa: a novel direction for future research
Authors: Haynos Ann F. , Anderson Lisa M. , Askew Autumn J. , Craske Michelle G. , Peterson Carol B.
Published: May 2021

Accumulating psychobiological data implicate reward disturbances in the persistence of anorexia nervosa (AN). Evidence suggests that individuals with AN demonstrate decision-making deficits similar to those with mood and anxiety disorders that cause them to under-respond to many conventionally rewarding experiences (e.g., eating, interacting socially). In contrast, unlike individuals with other psychiatric disorders, individuals with AN simultaneously over-respond to rewards associated with eating-disorder behaviors (e.g., restrictive eating, exercising). This pattern of reward processing likely perpetuates eating-disorder symptoms, as the rewards derived from eating-disorder behaviors provide temporary relief from the anhedonia associated with limited responsivity to other rewards. Positive Affect Treatment (PAT) is a cognitive-behavioral intervention designed to target reward deficits that contribute to anhedonia in mood and anxiety disorders, including problems with reward anticipation, experiencing, and learning. PAT has been found to promote reward responsivity and clinical improvement in mood and anxiety disorders. This manuscript will: (1) present empirical evidence supporting the promise of PAT as an intervention for AN; (2) highlight nuances in the maintaining processes of AN that necessitate adaptations of PAT for this population; and (3) suggest future directions in research on PAT and other reward-based treatments that aim to enhance clinical outcomes for AN.
The landscape of bispecific T cell engager in cancer treatment
Authors: Zhou Shujie , Liu Mingguo , Ren Fei , Meng Xiangjiao , Yu Jinming
Published: May 2021

T cell-based immunotherapies have revolutionized treatment paradigms in various cancers, however, limited response rates secondary to lack of significant T-cell infiltration in the tumor site remain a major problem. To address this limitation, strategies for redirecting T cells to treat cancer are being intensively investigated, while the bispecific T cell engager (BiTE) therapy constitutes one of the most promising therapeutic approaches. BiTE is a bispecific antibody construct with a unique function, simultaneously binding an antigen on tumor cells and a surface molecule on T cells to induce tumor lysis. BiTE therapy represented by blinatumomab has achieved impressive efficacy in the treatment of B cell malignancies. However, major mechanisms of resistance to BiTE therapy are associated with antigen loss and immunosuppressive factors such as the upregulation of immune checkpoints. Thus, modification of antibody constructs and searching for combination strategies designed to further enhance treatment efficacy as well as reduce toxicity has become an urgent issue, especially for solid tumors in which response to BiTE therapy is always poor. In particular, immunotherapies focusing on innate immunity have attracted increasing interest and have shown promising anti-tumor activity by engaging innate cells or innate-like cells, which can be used alone or complement current therapies. In this review, we depict the landscape of BiTE therapy, including clinical advances with potential response predictors, challenges of treatment toxicity and resistance, and developments of novel immune cell-based engager therapy.
Interspecific and intraspecific foraging differentiation of neighbouring tropical seabirds
Authors: Austin R. E. , De Pascalis F. , Votier S. C. , Haakonsson J. , Arnould J. P. Y. , Ebanks-Petrie G. , Newton J. , Harvey J. , Green J. A.
Published: May 2021

Background

Social interactions, reproductive demands and intrinsic constraints all influence foraging decisions in animals. Understanding the relative importance of these factors in shaping the way that coexisting species within communities use and partition resources is central to knowledge of ecological and evolutionary processes. However, in marine environments, our understanding of the mechanisms that lead to and allow coexistence is limited, particularly in the tropics.

Methods

Using simultaneous data from a suite of animal-borne data loggers (GPS, depth recorders, immersion and video), dietary samples and stable isotopes, we investigated interspecific and intraspecific differences in foraging of two closely-related seabird species (the red-footed booby and brown booby) from neighbouring colonies on the Cayman Islands in the Caribbean.

Results

The two species employed notably different foraging strategies, with marked spatial segregation, but limited evidence of interspecific dietary partitioning. The larger-bodied brown booby foraged within neritic waters, with the smaller-bodied red-footed booby travelling further offshore. Almost no sex differences were detected in foraging behaviour of red-footed boobies, while male and female brown boobies differed in their habitat use, foraging characteristics and dietary contributions. We suggest that these behavioural differences may relate to size dimorphism and competition: In the small brown booby population (n < 200 individuals), larger females showed a higher propensity to remain in coastal waters where they experienced kleptoparasitic attacks from magnificent frigatebirds, while smaller males that were never kleptoparasitised travelled further offshore, presumably into habitats with lower kleptoparasitic pressure. In weakly dimorphic red-footed boobies, these differences are less pronounced. Instead, density-dependent pressures on their large population (n > 2000 individuals) and avoidance of kleptoparasitism may be more prevalent in driving movements for both sexes.

Conclusions

Our results reveal how, in an environment where opportunities for prey diversification are limited, neighbouring seabird species segregate at-sea, while exhibiting differing degrees of sexual differentiation. While the mechanisms underlying observed patterns remain unclear, our data are consistent with the idea that multiple factors involving both conspecifics and heterospecifics, as well as reproductive pressures, may combine to influence foraging differences in these neighbouring tropical species.
Artificial intelligence paradigm for ligand-based virtual screening on the drug discovery of type 2 diabetes mellitus
Authors: Bustamam Alhadi , Hamzah Haris , Husna Nadya A. , Syarofina Sarah , Dwimantara Nalendra , Yanuar Arry , Sarwinda Devvi
Published: May 2021

Background

New dipeptidyl peptidase-4 (DPP-4) inhibitors need to be developed to be used as agents with low adverse effects for the treatment of type 2 diabetes mellitus. This study aims to build quantitative structure-activity relationship (QSAR) models using the artificial intelligence paradigm. Rotation Forest and Deep Neural Network (DNN) are used to predict QSAR models. We compared principal component analysis (PCA) with sparse PCA (SPCA) as methods for transforming Rotation Forest. K-modes clustering with Levenshtein distance was used for the selection method of molecules, and CatBoost was used for the feature selection method.

Results

The amount of the DPP-4 inhibitor molecules resulting from the selection process of molecules using K-Modes clustering algorithm is 1020 with logP range value of -1.6693 to 4.99044. Several fingerprint methods such as extended connectivity fingerprint and functional class fingerprint with diameters of 4 and 6 were used to construct four fingerprint datasets, ECFP_4, ECFP_6, FCFP_4, and FCFP_6. There are 1024 features from the four fingerprint datasets that are then selected using the CatBoost method. CatBoost can represent QSAR models with good performance for machine learning and deep learning methods respectively with evaluation metrics, such as Sensitivity, Specificity, Accuracy, and Matthew’s correlation coefficient, all valued above 70% with a feature importance level of 60%, 70%, 80%, and 90%.

Conclusion

The K-modes clustering algorithm can produce a representative subset of DPP-4 inhibitor molecules. Feature selection in the fingerprint dataset using CatBoost is best used before making QSAR Classification and QSAR Regression models. QSAR Classification using Machine Learning and QSAR Classification using Deep Learning, each of which has an accuracy of above 70%. The QSAR RFC-PCA and QSAR RFR-PCA models performed better than QSAR RFC-SPCA and QSAR RFR-SPCA models because QSAR RFC-PCA and QSAR RFR-PCA models have more effective time than the QSAR RFC-SPCA and QSAR RFR-SPCA models.
The pedagogy of experience complexity for smart learning: considerations for designing urban digital citizen learning activities
Authors: Lister Pen
Published: May 2021

The Pedagogy of Experience Complexity for Smart Learning (PECSL) is a four-tier model of considerations for the design and development of learning activities situated in real world hyperlocal locations, mediated by smart enough technologies. Learner experience is placed at the centre of learning design, focusing on the complex interrelated experiences that may be possible. A wider awareness of types of learning may enhance potential for gaining value for learners and offer more flexibility for instructors or others. Learning is considered as any potential object of vital interest for the learner, and may include making connections with others, dialogic space expansion between learners and wider relevance of topic or location as much as any intended learning outcome.

Taking inspiration from digital artefact user centred design, the PECSL adopts a position of flexible layers of considerations that impact stages of design for complex smart learning activities. Each tier being interrelated to the others, these iteratively adapting as a result of decisions being made throughout the design and development process. Categories of learner experience variation derived from a phenomenographic study of smart learning journeys inform the foundation of the PECSL, providing concepts of experience relevance structures leading to related pedagogies, further pedagogical relevance considerations and deeper epistemological reflections. Acknowledging significance of the context, process and content of learning in these activities, considerations expand to enable pragmatic support for much of value towards effective learning. This paper seeks to provide a means for learners to learn from each other as much as any specified learning goals or assessment.
Successful surgical rescue of delayed onset diaphragmatic hernia following radiofrequency ablation using a thoracoscopic approach for hepatocellular carcinoma: a case report
Authors: Morito Atsushi , Nakagawa Shigeki , Imai Katsunori , Uemura Norio , Okabe Hirohisa , Hayashi Hiromitsu , Yamashita Yo-ichi , Chikamoto Akira , Baba Hideo
Published: May 2021

Background

Radiofrequency ablation (RFA) is widely used as a minimally invasive treatment for hepatocellular carcinoma (HCC). RFA has a low risk of complications, especially compared with liver resection. Nevertheless, various complications have been reported after RFA for HCC; however, diaphragmatic hernia (DH) is extremely rare.

Case presentation

A 78-year-old man underwent thoracoscopic RFA for HCC located at the medial segment adjacent to the diaphragm approximately 7 years before being transported to the emergency department due complaints of nausea and abdominal pain. Computed tomography revealed a prolapsed small intestine through a defect in the right diaphragm, and emergency surgery was performed. The cause of diaphragmatic hernia was the scar of RFA. We confirmed that the small intestine had prolapsed into the right diaphragm, and we resected the necrotic small intestine and repaired the right diaphragm. Herein, we report a case of ileal strangulation due to diaphragmatic hernia after thoracoscopic RFA.

Conclusions

Care should be taken when performing thoracoscopic RFA, especially for tumors located on the liver surface adjacent to the diaphragm. Patients should be carefully followed up for possible DH, even after a long postoperative interval.
Nutritional status and associated factors among people living with HIV/AIDS in Ghana: cross-sectional study of highly active antiretroviral therapy clients
Authors: Nanewortor Beauty Mawuenam , Saah Farrukh Ishaque , Appiah Prince Kubi , Amu Hubert , Kissah-Korsah Kwaku
Published: May 2021

Background

Nutrition among people living with HIV/AIDS (PLWHA) is essential in their care and management as it has implication for their immune function. We examined the nutritional status and associated factors among HIV positive clients accessing Highly Active Anti-Retroviral Therapy (HAART) at a public hospital in Ghana.

Methods

This was a descriptive cross-sectional study of 152 clients. Anthropometric measurements for weight and height were carried out in 2019. Data were analysed using SPSS 22.0. Descriptive and analytical statistics comprising frequency, percentage, and binary logistic regression were adopted in presenting the results.

Results

Seventy-nine percent and 74% of the clients had good nutrition knowledge and attitude, respectively. Also, 42% were malnourished (underweight = 13.8%, and overweight = 28.3%). Clients with primary (AOR = 0.36, 95% CI = 0.07–1.84), JSS/JHS (AOR = 0.26, 95% CI = 0.08–0.84), SSS/SHS (AOR = 0.22, 95% CI = 0.05–1.02) and tertiary (AOR = 0.26, 95% CI = 0.08–0.88) were less likely to be malnourished compared with those with no formal education. Those with good nutrition-related knowledge were 56% (AOR = 0.44, 95% CI = 0.18–1.09) less likely to be malnourished than those with poor knowledge; this was however, not statistically significant.

Conclusion

We found a high prevalence of malnutrition among the clients which militates against progress towards achieving the Sustainable Development Goal targets 3.3 and 3.4 of stopping AIDS epidemic and preventing premature deaths from malnutrition. Our findings justify the need for the implementation of innovative interventions by stakeholders in Ghana’s health industry to improve the nutritional status of people living with the disease.