bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heterogeneous graph embedding model for predicting interactions between TF and target gene
Authors: Huang Yu-An , Pan Gui-Qing , Wang Jia , Li Jian-Qiang , Chen Jie , Wu Yang-Han 
Published: March 2022

AbstractMotivationIdentifying the target genes of transcription factors (TFs) is of great significance for biomedical researches. However, using biological experiments to identify TF–target gene interactions is still time consuming, expensive and limited to small scale. Existing computational methods for predicting underlying genes for TF to target is mainly proposed for their binding sites rather than the direct interaction. To bridge this gap, we in this work proposed a deep learning prediction model, named HGETGI, to identify the new TF–target gene interaction. Specifically, the proposed HGETGI model learns the patterns of the known interaction between TF and target gene complemented with their involvement in different human disease mechanisms. It performs prediction based on random walk for meta-path sampling and node embedding in a skip-gram manner.ResultsWe evaluated the prediction performance of the proposed method on a real dataset and the experimental results show that it can achieve the average area under the curve of 0.8519 ± 0.0731 in fivefold cross validation. Besides, we conducted case studies on the prediction of two important kinds of TF, NFKB1 and TP53. As a result, 33 and 32 in the top-40 ranking lists of NFKB1 and TP53 were successfully confirmed by looking up another public database (hTftarget). It is envisioned that the proposed HGETGI method is feasible and effective for predicting TF–target gene interactions on a large scale.Availability and implementationThe source code and dataset are available at https://github.com/PGTSING/HGETGI.Supplementary informationSupplementary data are available at Bioinformatics online.
GenRisk: a tool for comprehensive genetic risk modeling
Authors: Aldisi Rana , Hassanin Emadeldin , Sivalingam Sugirthan , Buness Andreas , Klinkhammer Hannah , Mayr Andreas , Fröhlich Holger , Krawitz Peter , Maj Carlo 
Published: March 2022

AbstractSummaryThe genetic architecture of complex traits can be influenced by both many common regulatory variants with small effect sizes and rare deleterious variants in coding regions with larger effect sizes. However, the two kinds of genetic contributions are typically analyzed independently. Here, we present GenRisk, a python package for the computation and the integration of gene scores based on the burden of rare deleterious variants and common-variants-based polygenic risk scores. The derived scores can be analyzed within GenRisk to perform association tests or to derive phenotype prediction models by testing multiple classification and regression approaches. GenRisk is compatible with VCF input file formats.Availability and implementationGenRisk is an open source publicly available python package that can be downloaded or installed from Github (https://github.com/AldisiRana/GenRisk).Supplementary informationSupplementary data are available at Bioinformatics online.
Agile Emotion Practices: Findings from an Ethnographic Study of Children and Families Social Work
Authors: O’Connor Louise 
Published: March 2022

Abstract
Social work is intrinsically relational, centred on interpersonal encounters between practitioners, service users and other professionals. Emotions are a core element in these encounters. Yet, despite a substantial focus on relationship-based practice there is limited research into the everyday experience and functions of practitioners’ emotions in socio-legal organisational environments. This article reports on findings from an ethnographic study of a Local Authority Children and Families Referral and Assessment Service in England. It explores how practitioners constructed and used their emotions in everyday practice. The construct of ‘agile emotion practices’ was generated from analysing observations of teams, home visits, systemic group supervision, interviews and diaries. Informed by social constructionist and psychosocial theories, the characteristics of agile emotion practices are outlined. This article suggests there is merit in recognising practitioners’ emotions as functional practices, which inform relational practice, analysis and assessment. Data are specific to the organisation, context and timeframe. However, valuable insights are provided into the ‘doing’ of emotions in social work, including some of the factors that facilitate and hinder agile emotion practices. The analysis offers new empirically based knowledge, applicable to diverse social work settings, education and research.
The Unheld Child: Social Work, Social Distancing and the Possibilities and Limits to Child Protection during the COVID-19 Pandemic
Authors: Ferguson Harry , Pink Sarah , Kelly Laura 
Published: March 2022

Abstract
The COVID-19 pandemic changed dramatically the ways social workers engaged with children and families. This article presents findings from our research into the effects of COVID-19 on social work and child protection in England during the first nine months of the pandemic. Our aim is to provide new knowledge to enable realistic expectations of what it was possible for social workers to achieve and particularly the limits to child protection. Such perspective has become more important than ever due to knowledge of children who died tragically from abuse despite social work involvement during the pandemic. Our research findings show how some practitioners got physically close to some children, whilst being distanced from others. We examine the dynamics that shaped closeness and distance and identify seven influences that created limits to child protection and the problem of ‘the unheld child’. The article provides new understandings of child protection as embodied, multi-sensorial practices and the ways anxiety and experiences of bodily self-alienation limit practitioners’ capacities to think about and get close to children. Whilst social workers creatively improvised to achieve their goals, coronavirus and social distancing imposed limits to child protection that no amount of innovative practice could overcome in all cases.
Machine prescription for chronic migraine
Authors: Stubberud Anker , Gray Robert , Tronvik Erling , Matharu Manjit , Nachev Parashkev 
Published: March 2022

Abstract
Responsive to treatment individually, chronic migraine remains strikingly resistant collectively, incurring the second-highest population burden of disability worldwide. A heterogeneity of responsiveness, requiring prolonged—currently heuristic—individual evaluation of available treatments, may reflect a diversity of causal mechanisms, or the failure to identify the most important, single causal factor. Distinguishing between these possibilities, now possible through the application of complex modelling to large-scale data, is critical to determine the optimal approach to identify new interventions in migraine and making the best use of existing ones. Examining a richly phenotyped cohort of 1446 consecutive unselected patients with chronic migraine, here we use causal multitask Gaussian process models to estimate individual treatment effects across 10 classes of preventatives. Such modelling enables us to quantify the accessibility of heterogeneous responsiveness to high-dimensional modelling, to infer the likely scale of the underlying causal diversity. We calculate the treatment effects in the overall population, and the conditional treatment effects among those modelled to respond and compare the true response rates between these two groups. Identifying a difference in response rates between the groups supports a diversity of causal mechanisms. Moreover, we propose a data-driven machine prescription policy, estimating the time-to-response when sequentially trialling preventatives by individualized treatment effects and comparing it to expert guideline sequences. All model performances are quantified out-of-sample. We identify significantly higher true response rates among individuals modelled to respond, compared with the overall population (mean difference of 0.034; 95% confidence interval 0.003–0.065; P = 0.033), supporting significant heterogeneity of responsiveness and diverse causal mechanisms. The machine prescription policy yields an estimated 35% reduction in time-to-response (3.750 months; 95% confidence interval 3.507–3.993; P &lt; 0.0001) compared with expert guidelines, with no substantive increase in expense per patient. We conclude that the highly distributed mode of causation in chronic migraine necessitates high-dimensional modelling for optimal management. Machine prescription should be considered an essential clinical decision-support tool in the future management of chronic migraine.
CD155 expression impairs anti-PD1 therapy response in non-small cell lung cancer
Authors: Jiang Chang , Qu Xiaodie , Ma Li , Yi Ling , Cheng Xu , Gao Xiang , Wang Jinghui , Che Nanying , Zhang Hongtao , Zhang Shucai 
Published: March 2022

Abstract
CD155 is an immune checkpoint protein expressed in tumor cells that interacts with its ligand TIGIT, and inhibition of this point presents a new and novel way for cancer therapy. At present, whether the expression of CD155 affects the response to anti(α)-PD1 treatment in non-small cell lung cancer (NSCLC) patients is unclear. This observational study characterizes the expression of CD155 in NSCLC patients and its responses to PD1 inhibitors. We retrospectively detected the expression of CD155 and tumor-infiltrated lymphocyte (TIL) TIGIT by immunohistochemistry in advanced NSCLC patients who had received αPD1 therapy. The patients with CD155 positive had a significantly worse response to αPD1 therapy compared with CD155-negative patients (ORR: 25.6% vs 54.8%, P &lt; 0.01; median PFS: 5.1 vs 7.1 months, HR = 2.322; 95% CI 1.396–3.861, P = 0.001). This effect is more prominent in PD-L1 positive patients. In PD-L1-positive patients, CD155 expression is associated with a poor response to αPD1 therapy in both LUAC (lung adenocarcinoma) and LUSC (lung squamous cell carcinoma); meanwhile, the expression of CD155 was associated with a poor response to the first-line αPD1 therapy, posterior-line αPD1 therapy, and αPD1 combination therapy. Furthermore, the expression of TIGIT was not correlated with the therapeutic effect of αPD1. Our pilot study suggests that CD155 expression attenuates the therapeutic effect of αPD1 therapy and is associated with a higher risk of progression. The CD155 pathway may be a promising immunotherapeutic target and simultaneously targeting CD155/TIGIT and PD1/PD-L1 can improve the effect of immunotherapy.
Interhemispheric functional brain connectivity predicts new language learning success in adults
Authors: Sander Kaija , Chai Xiaoqian , Barbeau Elise B , Kousaie Shanna , Petrides Michael , Baum Shari , Klein Denise 
Published: March 2022

AbstractInvestigating interhemispheric interactions between homologous cortical regions during language processing is of interest. Despite prevalent left hemisphere lateralization of language, the right hemisphere also plays an important role and interhemispheric connectivity is influenced by language experience and is implicated in second language (L2) acquisition. Regions involved in language processing have differential connectivity to other cortical regions and to each other, and play specific roles in language. We examined the interhemispheric interactions of subregions of the inferior frontal gyrus (areas 44 and 45), the adjacent area 9/46v in the middle frontal gyrus, the superior temporal gyrus (STG), and the posterior inferior parietal lobule (pIPL) in relation to distinct and specific aspects of L2 learning success. The results indicated that the connectivity between left and right areas 44 and 9/46v predicted improvement in sentence repetition, connectivity between left and right area 45 and mid-STG predicted improvement in auditory comprehension, and connectivity between left and right pIPL predicted improvement in reading speed. We show interhemispheric interactions in the specific context of facilitating performance in adult L2 acquisition that follow an anterior to posterior gradient in the brain, and are consistent with the respective roles of these regions in language processing.
Effects of chitosan coatings fused with medicinal plant extracts on postharvest quality and storage stability of purple passion fruit (Passiflora edulisvar. Ester)
Authors: Nxumalo Kwanele A , Fawole Olaniyi A 
Published: March 2022

AbstractChitosan edible coating (Ch; 2%, mass concentration) enriched with 2% of 0.1 mg/L Bidens pilosa (Ch+B), Lippia javanica (Ch+L), Syzygium cordatum (Ch+S), or Ximenia caffra (Ch+X) was applied as a composite edible coating in alleviating shrivel and maintaining the quality of purple passion fruit (Passiflora edulis var. Ester). Treated fruit was dipped for 3 min in the coating solution, and control fruit was dipped in distilled water. The fruit were stored at (8±2) °C and 90%±5% relative humidity (RH) for 32 d. Sampling was done every 8 d plus 3 d ((20±2) °C and (50%±5%) RH) to simulate retail conditions. Efficacy of medicinal plant extracts in the chitosan matrix varied; lower ethylene production (82.42 µL C2H4/(kg·h)) was seen in fruit coated with Ch+S, and the lowest respiration rate (75 mL CO2/(kg·h)) was observed in fruit coated with Ch+B. The control fruit showed the highest ethylene production (84.90 µL C2H4/(kg·h)) and respiration rate (117.98 mL CO2/(kg·h)). Fruit coated with Ch+B had the lowest weight loss (41.67%), higher juice content (60.13%) and BrimA (3.31); while the control fruit had the highest weight loss (88.03%), lowest juice content (21.90%), and BrimA (2.49). Shrivel incidence was lowest (23.70%) on fruit coated with Ch+L and highest (83.30%) on the control fruit. Fruit coated with Ch+X had the lowest electrolyte leakage (71.40%), while the control fruit had the highest (91.97%). Fruit coated with chitosan alone performed better than the control fruit but did not exceed the quality of composite chitosan-coated fruit. Based on the principal component analysis, it can be concluded that passion fruit coated with Ch+B was more effective in alleviating shrivel incidence, better maintained the quality of passion fruit during storage, and shows potential for commercial applications.
Researchers or practitioners’ opinion of the possibilities for creating virtual safe social spaces for violence prevention interventions for young people
Authors: Ndungu Jane , Ngcobo-Sithole Magnolia , Gibbs Andrew 
Published: March 2022

AbstractIntimate partner violence (IPV) is a global concern. Interventions designed to prevent IPV are often participatory in nature, implemented in face-to-face settings and seek to create ‘safe social spaces’. We however do not fully understand how safe social spaces can be created in online spaces. Our study sought to understand the possibility of creating safe social spaces online, supportive of participatory interventions, from the perspective of those developing and implementing IPV prevention interventions. We conducted in-depth interviews with a global sample of 20 researchers and practitioners. Interviews were transcribed and analysed using thematic network analysis. We found mixed results about the possibility of creating safe social spaces online. Researchers and practitioners raised issues such as sharing of devices, the difficulties in developing trust and a sense of community online, challenges in having privacy and confidentiality online and difficulty in reading non-verbal cues as some of the key considerations when creating online safe social spaces. Younger researchers and practitioners were more optimistic about creating safe social spaces online. Our results show that the creation of safe social spaces online is complex and requires further investigation.
Rare complement factor I variants associated with reduced macular thickness and age-related macular degeneration in the UK Biobank
Authors: Tzoumas Nikolaos , Kavanagh David , Cordell Heather J , Lotery Andrew J , Patel Praveen J , Steel David H 
Published: March 2022

Abstract
To evaluate potential diagnostic and therapeutic biomarkers for age-related macular degeneration (AMD), we identified 8433 UK Biobank participants with rare complement Factor I gene (CFI) variants, 579 with optical coherence tomography-derived macular thickness data. We stratified these variants by predicted gene expression and measured their association with retinal pigment epithelium-Bruch’s membrane (RPE-BM) complex and retinal thicknesses at nine macular subfields, as well as AMD risk, using multivariable regression models adjusted for the common complement Factor H gene (CFH) p.Y402H and age-related maculopathy susceptibility protein 2 gene (ARMS2) p.A69S risk genotypes. CFI variants associated with low Factor I levels predicted a thinner mean RPE-BM (95% confidence interval [CI] −1.66 to −0.37 μm, P = 0.002) and retina (95% CI −5.88 to −0.13 μm, P = 0.04) and a higher AMD risk (odds ratio [OR] = 2.26, 95% CI 1.56 to 3.27, P &lt; 0.001). CFI variants associated with normal Factor I levels did not impact mean RPE-BM/retinal thickness (P = 0.28; P = 0.99) or AMD risk (P = 0.97). CFH p.Y402H was associated with a thinner RPE-BM (95% CI −0.31 to −0.18 μm, P &lt; 0.001 heterozygous; 95% CI −0.62 to −0.42 μm, P &lt; 0.001 homozygous) and retina (95% CI −0.73 to −0.12 μm, P = 0.007 heterozygous; 95% CI −1.08 to −0.21 μm, P = 0.004 homozygous). ARMS2 p.A69S did not influence RPE-BM (P = 0.80 heterozygous; P = 0.12 homozygous) or retinal thickness (P = 0.75 heterozygous; P = 0.07 homozygous). p.Y402H and p.A69S exhibited a significant allele–dose response with AMD risk. Thus, CFI rare variants associated with low Factor I levels are robust predictors of reduced macular thickness and AMD. The observed association between macular thickness and CFH p.Y402H, but not ARMS2 p.A69S, highlights the importance of complement dysregulation in early pathogenesis.
Optimal setting time and season increase the target and reduce the incidental catch in longline fisheries: a Bayesian beta mixed regression approach
Authors: Rodrigues Lucas dos Santos , Kinas Paul Gerhard , Cardoso Luis Gustavo 
Published: March 2022

AbstractSustainable fisheries' managers increasingly seek to implement measures that reduce the mortality of threatened species while maintaining or increasing catch of target species. Our study proposed a simple management option for optimizing fishing over daily and seasonal scales to maximize catch success while protecting non-target species in pelagic longline fisheries. We used Bayesian beta mixed regression models to describe the effects of setting times and seasonality on catches in a pelagic longline fishery in the southwest South Atlantic Ocean (SWAO). Targeted species (swordfish, blue shark, and albacore tuna) are typically captured in fully nocturnal sets (started between 16 and 00 h), whereas shortfin mako shark and loggerhead turtles are typically captured during partially nocturnal sets (started between 00 and 04 h); probably a response to hook depth and circadian behaviours. The results suggest that it is feasible to use only fully nocturnal sets to target preferred species while reducing incidental catch of non-target species. The catch of target species was higher in austral winter, explained by the northward displacement of the subtropical convergence in the SWAO during this season. These results provide a baseline for bycatch mitigation strategies in pelagic longline fisheries at regional and global scales.
Excess risk of subsequent infection in hospitalized children from a community cohort study in Cambodia and Madagascar
Authors: Rambliere Lison , Kermorvant-Duchemin Elsa , de Lauzanne Agathe , Collard Jean-Marc , Herindrainy Perlinot , Vray Muriel , Garin Benoit , Zo Andrianirina Zafitsara , Rasoanaivo Fanjalalaina , Rakotoarimanana Feno Manitra Jacob , Raheliarivao Tanjona Bodonirina , Diouf Jean-Baptiste Niokhhor , Ngo Véronique , Lach Siyin , Long Pring , Borand Laurence , Sok Touch , Abdou Armiya Youssouf , Padget Michael , Madec Yoann , Guillemot Didier , Delarocque-Astagneau Elisabeth , Huynh Bich-Tram 
Published: March 2022

Abstract

Background
Children in low- and middle-income countries are particularly vulnerable in the months following an initial health event (IHE), with increased risk of mortality caused mostly by infectious diseases. Due to exposure to a wide range of environmental stressors, hospitalization in itself might increase child vulnerability at discharge. The goal of this study was to disentangle the role of hospitalization on the risk of subsequent infection.

Methods
Data from a prospective, longitudinal, international, multicenter mother-and-child cohort were analysed. The main outcome assessed was the risk of subsequent infection within 3 months of initial care at hospital or primary healthcare facilities. First, risk factors for being hospitalized for the IHE (Step 1) and for having a subsequent infection (Step 2) were identified. Then, inpatients were matched with outpatients using propensity scores, considering the risk factors identified in Step 1. Finally, adjusted on the risk factors identified in Step 2, Cox regression models were performed on the matched data set to estimate the effect of hospitalization at the IHE on the risk of subsequent infection.

Results
Among the 1312 children presenting an IHE, 210 (16%) had a subsequent infection, mainly lower-respiratory infections. Although hospitalization did not increase the risk of subsequent diarrhoea or unspecified sepsis, inpatients were 1.7 (95% Confidence Intervals [1.0–2.8]) times more likely to develop a subsequent lower-respiratory infection than comparable outpatients.

Conclusion
For the first time, our findings suggest that hospitalization might increase the risk of subsequent lower-respiratory infection adjusted on severity and symptoms at IHE. This highlights the need for robust longitudinal follow-up of at-risk children and the importance of investigating underlying mechanisms driving vulnerability to infection.
How can the neglected tropical disease community be inclusive and equitable in programme delivery? Reaching refugees and internally displaced persons through integrating a ‘leave no one behind’ approach
Authors: Harvey Danny , Shu'aibu Joy , Debam Mark Terhemba , Aba Abraham Kwaghgee , Torres-Vitolas Carlos A 
Published: March 2022

Abstract
As directed by the Sustainable Development Goals, the principle of ‘leave no one behind’ is a pivotal approach to improving coverage and equity within neglected tropical disease (NTD) programme activities. Displaced populations are an at-risk group who are often excluded from treatment and services due to their mobility and marginalisation. This article reflects on the experiences of two countries within the Ascend programme, which responded to the need to strategise and implement approaches that lead to more inclusive and accessible programme activities for displaced populations. With the increasing rate of insecurity and the threat of natural disasters, which is resulting in the displacement of communities and persons eligible for NTD treatment, the ‘leave no one behind’ approach is needed to move closer towards the NTD elimination agenda and to ensure effective coverage thresholds are met.