bluuebunny/crossref_metadata_2025_split huggingface dataset:
A review of the effectiveness and experiences of welfare advice services co-located in health settings: a critical narrative systematic review
Authors: Reece Sian , Sheldon Trevor A , Dickerson Josie , Pickett Kate E 
Published: October 2021

ABSTRACTThe links between financial insecurity and poor health and wellbeing are well established. Individuals experiencing financial insecurity are also more likely to face challenges in accessing the support services they need. There is evidence of unequal uptake of welfare support and benefits, particularly in some ethnic minority groups. The COVID-19 pandemic has further exacerbated financial insecurity for the most vulnerable and action is needed to improve the support provided for those affected during the recovery from the pandemic.One approach to improving uptake of benefits has been to deliver welfare services within health settings. This has the potential to increase income and possibly improve health. We conducted systematic review with a critical narrative synthesis to assess the health, social and financial impacts of welfare advice services co-located in health settings and explore the facilitators and barriers to successful implementation of these services, in order to guide future policy and practice.The review identified 14 studies published in the UK from 2010. The services provided generated on average £27 of social, economic and environmental return on investment per £1 invested. Individuals on average benefitted from an additional £2,757 household income per annum and cost savings for the NHS were demonstrated. The review demonstrated that improvements to health were made by addressing key social determinants of health, thereby reducing health inequalities. Co-located welfare services actively incorporated elements of proportionate universalism and targeted those, who due to predominately health needs, were most in need of this support. The nature of the welfare advice service, how it operates within a health setting, and how visible and accessible this service is to participants and professionals referring into the service, were seen as important facilitators. Co-production during service development and ongoing enhanced multi-disciplinary collaboration were also considered vital to the success of co-located services.
Visual space curves before eye movements
Authors: Adeyefa-Olasupo Ifedayo-EmmanuEL , Xiao Zixuan 
Published: October 2021

ABSTRACTIn most experiments within the field of cognitive and systems neuroscience, fixation is often required prior to the onset of an experimental trial. However, the term “fixation” is rather misleading since our eyes are constantly moving. One type of transient miniature movement ubiquitously observed during fixation is commonly referred to as fixational eye movements or microsaccades. Perimicrosaccadic compression of visual space — the ability of retinotopic cells to transiently exhibit predictive spatiotemporal retinotopic compressive shifts toward the target of an impending microsaccade — is known to dramatically alter visual perception. However, whether perimicrosaccadic compressive shifts can become spatially asymmetric, that is, continuously directed toward a specific foveal region over another (e.g., an upper over a lower region in the fovea) and for what purpose, remains poorly understood. Assuming that these transient shifts are indeed asymmetric under certain conditions, the perceptual and oculomotor consequences such asymmetricity might accompany across visual space is poorly understood. Equally unaccounted for is a mechanistic account of the neural computation and architecture that could support these transient asymmetric shifts while the visual system actively maintains retinotopic organization. Here, we systematically measured visual sensitivity in human subjects to faint probes presented during fixation and around the time of saccadic eye movement at geometrically symmetric retinotopic locations in the foveal, parafoveal, and peripheral regions of visual space. Remarkably, we observed transient local asymmetric visual sensitivity differences between these symmetric retinotopic locations where none should be observed. Equally surprising, we observed the trajectories of saccadic eye movements, which are expected to travel along a linear path, routinely deviate along a curved path toward orthogonal eccentric locations. To provide a mechanistic account of the neural computation and architecture that may explain our results, we proposed a novel neurobiologically inspired phenomenological force field model in which underlying attentional and oculomotor signals are modulated by transient eccentric error signals that manifest as temporally overlapping predictive forces and impinge on the retinotopic visual cortex. These forces, which transiently bias putative population sensitivity toward an orthogonal retinotopic foveal region and, around the time of a saccadic eye movement, along an axis orthogonal to the saccade direction toward a mislocalized peripheral region, succinctly capture the essence of our empirical observations.
Exome sequencing as a first-tier test for copy number variant detection : retrospective evaluation and prospective screening in 2418 cases
Authors: Testard Quentin , Vanhoye Xavier , Yauy Kevin , Naud Marie-Emmanuelle , Vieville Gaelle , Rousseau Francis , Dauriat Benjamin , Marquet Valentine , Bourthoumieu Sylvie , Genevieve David , Gatinois Vincent , Wells Constance , Willems Marjolaine , Coubes Christine , Pinson Lucile , Dard Rodolphe , Tessier Aude , Hervé Bérénice , Vialard François , Harzallah Ines , Touraine Renaud , Cogné Benjamin , Deb Wallid , Besnard Thomas , Pichon OIivier , Laudier Béatrice , Mesnard Laurent , Doreille Alice , Busa Tiffany , Missirian Chantal , Satre Véronique , Coutton Charles , Celse Tristan , Harbuz Radu , Raymond Laure , Taly Jean-François , Thevenon Julien 
Published: October 2021

ABSTRACTPurposeDespite exome (ES) or genome sequencing (GS) availability, chromosomal microarray (CMA) remains the first-line diagnostic tests in most rare disorders diagnostic work-up, looking for Copy-number variations (CNV), with a diagnostic yield of 10-20%. The question of the equivalence of CMA and ES in CNV calling is an organisational and economic question, especially when ordering a GS after a negative CMA and/or ES.MethodsThis work measures the equivalence between CMA and GATK4 exome sequencing depth of coverage method in detecting coding CNV on a retrospective cohort of 615 unrelated individuals. A prospective detection of ES CNV on a cohort of 2418 unrelated individuals, including the 615 individuals from the validation cohort, was performed.ResultsOn the retrospective validation cohort every CNV was accurately detected (64/64 events). In the prospective cohort, 32 diagnostics were performed among the 2418 individuals with CNVs ranging from 704bp to aneuploidy. An incidental finding was reported. The overall increase in diagnostic yield was of 1.7%, varying from 1.2% in individuals with multiple congenital anomalies to 1.9% in individuals with chronic kidney failure.ConclusionsCombining SNV and CNV detection increases the suitability of exome sequencing as a first-tier diagnostic test for suspected rare mendelian disorders. Before considering the prescription of a GS after a negative ES, a careful reanalysis with updated CNV calling and SNV annotation should be considered.
Microbiological Assessment of Health-Care Providers in Africa: Systematic Review and Meta-Analysis
Authors: Idris Abeer B. , Idris Alaa B. , Hasabo Elfatih A. , Badawi Marwan M. , Beirag Nazar 
Published: October 2021

AbstractBackgroundHealthcare workers (HCWs) are the safeguards that help prevent illnesses and eliminate them when they occur. This study aimed to scan the related literature and provide pooled data about the level of knowledge/attitude toward infections, vaccination status and infection prevalence among African HCWs to provide better evidence toward specific detailed determination of gaps to strengthen. A total of 11,038 published articles were identified from the search strategy. Among them, 163 articles met our inclusion criteria and passed the quality assessment procedure.ResultsThe prevalence of HBV was tested for 6,599 African HCWs;6.00% [95% Cl; 3.66, 8.33] were positive. The question Are you fully vaccinated against HBV?” was answered by 12,036 HCWs; 43.22% [95% Cl; 31.22, 55.21] answered yes. The most crucial local factor identified among respondents for the spread of antimicrobial resistance (AMR) was self-antibiotic prescription 42.00 % [18.79, 65.20]. The question “Does the infection prevention and control (IPC) guidelines available in your workplace?” was asked to 1,582 HCWs; 50.95% [95% Cl; 40.22, 61.67] answered yes.ConclusionThis study determined many weaknesses to be addressed for the sake of improving health in Africa. The current pooled data are critically significant to be implemented in planning governmental or NGOs strategies.
Sex steroid hormones and risk of breast cancer incidence and survival: A two-sample Mendelian randomization study
Authors: Nounu Aayah , Kar Siddhartha P , Relton Caroline L , Richmond Rebecca C 
Published: October 2021

AbstractBackgroundBreast cancer (BC) is the cancer with the highest incidence and mortality in women worldwide. Observational epidemiological studies suggest a positive association between testosterone, estradiol, dehydroepiandrosterone sulphate (DHEAS) and both pre- and post-menopausal BC. Since previous studies may be prone to bias and confounding, we used a two-sample Mendelian randomization (MR) analysis to investigate this association.MethodsGenetic instruments for nine sex steroid hormones and sex hormone binding globulin (SHBG) were obtained from genome-wide association studies (GWAS) conducted in the UK Biobank (total testosterone (TT) N:230,454, bioavailable testosterone (BT) N: 188,507 and SHBG N: 189,473), The United Kingdom Household Longitudinal Study (DHEAS N: 9,722), the LIFE-Adult and LIFE-Heart cohorts (estradiol N: 2,607), the LIFE-Heart cohort only (androstenedione N: 711, aldosterone N: 685, progesterone N: 1,259 and 17-hydroxyprogesterone N: 711) and the CORtisol NETwork (CORNET) consortium (cortisol N: 25,314). GWAS summary statistics were also obtained from the Breast Cancer Association Consortium (BCAC) for overall BC risk (N: 122,977 cases and 105,974 controls) and BC mortality (96,661 BC cases and 7,697 BC-specific deaths). Subtype specific analysis were carried out for incidence of estrogen receptor (ER)+ BC, ER- BC, luminal A-like BC, luminal B-like BC, luminal B/HER2-negative-like BC, HER2-enriched-like BC, triple negative BC (TNBC) and BRCA1 mutated TNBC.ResultsUsing an inverse-variance weighted (IVW) approach, we found that a standard deviation (SD) increase in TT, BT and estradiol increased the risk of overall BC (OR: 1.14, 95% CI: 1.09-1.21, OR: 1.19, 95% CI: 1.07-1.33 and OR: 1.03, 95% CI: 1.01-1.06, respectively) and ER+ BC (OR: 1.19, 95% CI: 1.12-1.27, OR: 1.25, 95% CI: 1.11-1.40 and OR: 1.06, 95% CI: 1.03-1.09, respectively). A SD increase in DHEAS also increased ER+ BC risk (OR: 1.09, 95% CI: 1.03-1.09). Subtype specific analyses showed similar associations with ER+ expressing subtypes: luminal A-like BC, luminal B-like BC and luminal B/HER2-negative-like BC. A SD increase in cortisol was associated with poor survival after a diagnosis of ER-BC (HR: 2.35, 95% CI: 1.00-5.49).Discussion/ConclusionTT, BT, DHEAS and estradiol increase the risk of ER+ type BCs similar to observational studies, but none of these hormone measures are associated with BC survival. We found some evidence that cortisol reduced ER- BC survival. Stronger genetic instruments are required before definitive conclusions can be made about the role of other sex-steroid hormones in breast cancer. Understanding the role of sex steroid hormones in BC risk, particularly subtype-specific risks, highlights the potential importance of attempts to modify and/or monitor hormone levels in order to prevent BC.
Head and Neck Cancer Primary Tumor Auto Segmentation using Model Ensembling of Deep Learning in PET-CT Images
Authors: Naser Mohamed A. , Wahid Kareem A. , van Dijk Lisanne V. , He Renjie , Ab-delaal Moamen Abobakr , Dede Cem , Mohamed Abdallah S.R. , Fuller Clifton D. 
Published: October 2021

AbstractAuto-segmentation of primary tumors in oropharyngeal cancer using PET/CT images is an unmet need that has the potential to improve radiation oncology workflows. In this study, we develop a series of deep learning models based on a 3D Residual Unet (ResUnet) architecture that can segment oropharyngeal tumors with high performance as demonstrated through internal and external validation of large-scale datasets (training size = 224 patients, testing size = 101 patients) as part of the 2021 HECKTOR Challenge. Specifically, we leverage ResUNet models with either 256 or 512 bottleneck layer channels that are able to demonstrate internal validation (10-fold cross-validation) mean Dice similarity coefficient (DSC) up to 0.771 and median 95% Hausdorff distance (95% HD) as low as 2.919 mm. We employ label fusion ensemble approaches, including Simultaneous Truth and Performance Level Estimation (STAPLE) and a voxel-level threshold approach based on majority voting (AVERAGE), to generate consensus segmentations on the test data by combining the segmentations produced through different trained cross-validation models. We demonstrate that our best performing ensembling approach (256 channels AVERAGE) achieves a mean DSC of 0.770 and median 95% HD of 3.143 mm through independent external validation on the test set. Concordance of internal and external validation results suggests our models are robust and can generalize well to unseen PET/CT data. We advocate that ResUNet models coupled to label fusion ensembling approaches are promising candidates for PET/CT oropharyngeal primary tumors auto-segmentation, with future investigations targeting the ideal combination of channel combinations and label fusion strategies to maximize segmentation performance.
Metabolic disorders and the risk of head and neck cancer: a protocol for a systematic review and meta-analysis
Authors: Gormley Alexander , Richards Charlotte , Spiga Francesca , Gray Emily , Hooper Joanna , Main Barry G , Vincent Emma E , Richmond Rebecca C , Higgins Julian PT , Gormley Mark 
Published: October 2021

AbstractIntroductionHead and neck cancer squamous cell carcinoma (HNSCC) is the 6th most common cancer internationally. Established risk factors include smoking, alcohol and presence of human papillomavirus (HPV). The incidence rate of new disease continues to rise, despite falls in alcohol consumption and a reduction in smoking, the rising rates are unlikely to be solely attributed to HPV status alone. Obesity and its associated conditions such as type 2 diabetes (T2D) are implicated in the risk and progression of a variety of cancers but there is paucity of evidence regarding its role in HNSCC.Methods and analysisA systematic review of cohort studies, reporting a risk of incident head and neck squamous cell carcinoma will be included. A systematic search strategy has been developed, multiple databases will be searched from January 1966, including Cochrane Library, OVID SP versions of Medline and EMBASE. The primary outcome will be incident HNSCC based on exposures of type 2 diabetes, obesity, dyslipidemia and hypertension as defined by the World Health Organisation (WHO). A combined risk effect across studies will be calculated using meta-analysis, although depending on the heterogeneity in study design, exposure and outcome reporting this may not be possible.Ethics and disseminationNo ethical approval is required for this systematic review. The review will be published in a revelant peer-review journal and findings will be presented at scientific meetings in both poster and oral presentation form.Registration detailsThis study has been registered with the international prospective register of systematic reviews (PROSPERO) with study registration number CRD42021250520. This protocol has been developed in accordance with the preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) guidance statement.Article SummaryStrengths and limitations of this studyThis systematic review will be the first to comprehensively review the literature and provide a meta-analysis of the effect of metabolic disorders and the risk of incident HNSCC.The publication of this protocol provides a clear representation of the methods used in this review for transparency and to prevent future duplication.This systematic review will be one of the first to pilot the The ROBINS-E tool (Risk Of Bias In Non-randomised Studies - of Exposures).Despite the metabolic disorders being described as separate entities, the authors recognise the potential for disease processes to be related.Among cohort studies there is significant variability in terms of length of follow-up for the outcome of interest, HNSCC.
Reduced locus coeruleus integrity linked to response inhibition deficits in parkinsonian disorders
Authors: Ye Rong , Hezemans Frank H. , O’Callaghan Claire , Tsvetanov Kamen A. , Rua Catarina , Jones P. Simon , Holland Negin , Malpetti Maura , Murley Alexander G. , Barker Roger A. , Williams-Gray Caroline H. , Robbins Trevor W. , Passamonti Luca , Rowe James B. 
Published: October 2021

AbstractParkinson’s disease and progressive supranuclear palsy (PSP) both impair response inhibition, exacerbating impulsivity. Inhibitory control deficits vary across individuals, and have been linked with worse prognosis and lack of improvement on dopaminergic therapy. Motor and cognitive control are associated with noradrenergic innervation of the cortex, arising from the locus coeruleus noradrenergic system. Here we test the hypothesis that loss of structural integrity of the locus coeruleus explains response inhibition deficits in progressive supranuclear palsy and Parkinson’s disease. This cross-sectional observational study recruited 24 people with idiopathic Parkinson’s disease, 14 with PSP-Richardson’s syndrome, and 24 age- and sex-matched controls. All participants undertook a stop-signal task and ultrahigh field 7T-magnetic transfer weighted imaging of the locus coeruleus. Hierarchical Bayesian estimation of the parameters of ‘race models’ of go-versus stop-decisions was used to quantify the cognitive processes of response inhibition. We tested the multivariate relationship between locus coeruleus integrity and model parameters using partial least squares. Both disorders impaired response inhibition at the group level. Progressive supranuclear palsy caused a distinct pattern of abnormalities in inhibitory control, relative to Parkinson’s disease and healthy controls, with a paradoxically reduced threshold for go responses, but longer non-decision times, and more lapses of attention. The variation in response inhibition correlated with variation in the integrity of the locus coeruleus, across participants in both clinical groups. Structural imaging of the locus coeruleus, coupled with behavioural modelling in parkinsonian disorders, confirms that locus coeruleus integrity is associated with response inhibition and its degeneration contributes to neurobehavioural changes. The noradrenergic system is therefore a promising target to treat impulsivity in these conditions. The optimisation of noradrenergic treatment is likely to benefit from stratification according to locus coeruleus integrity.
Genetic associations of protein-coding variants in human disease
Authors: Sun Benjamin B. , Kurki Mitja I. , Foley Christopher N. , Mechakra Asma , Chen Chia-Yen , Marshall Eric , Wilk Jemma B. ,   Biogen Biobank Team, Chahine Mohamed , Chevalier Philippe , Christé Georges , FinnGen  , Palotie Aarno , Daly Mark J. , Runz Heiko 
Published: October 2021

AbstractGenome-wide association studies (GWAS) have identified thousands of genetic variants linked to the risk of human disease. However, GWAS have thus far remained largely underpowered to identify associations in the rare and low frequency allelic spectrum and have lacked the resolution to trace causal mechanisms to underlying genes. Here, we combined whole exome sequencing in 392,814 UK Biobank participants with imputed genotypes from 260,405 FinnGen participants (653,219 total individuals) to conduct association meta-analyses for 744 disease endpoints across the protein-coding allelic frequency spectrum, bridging the gap between common and rare variant studies. We identified 975 associations, with more than one-third of our findings not reported previously. We demonstrate population-level relevance for mutations previously ascribed to causing single-gene disorders, map GWAS associations to likely causal genes, explain disease mechanisms, and systematically relate disease associations to levels of 117 biomarkers and clinical-stage drug targets. Combining sequencing and genotyping in two population biobanks allowed us to benefit from increased power to detect and explain disease associations, validate findings through replication and propose medical actionability for rare genetic variants. Our study provides a compendium of protein-coding variant associations for future insights into disease biology and drug discovery.
Shell shape as an indicator of phenotypic stocks of Tehuelche scallop (Aequipecten tehuelchus) in Northern Patagonia, Argentina
Authors: Getino Mamet Leandro Nicolás , Soria Gaspar , Schejter Laura , Márquez Federico 
Published: October 2021

AbstractTehuelche scallop, Aequipecten tehuelchus, is a commercially exploited species in Northern Patagonia, Argentina. Without genetic differentiation at the species level, A. tehuelchus presents three morphotypes: tehuelchus, madrynensis, and a non-common variant felipponei. The main goal of this study was to analyze the shell shape variation of Tehuelche scallop to differentiate and identify the phenotypic stocks. The shape differences between and within the two main morphotypes (tehuelchus and madrynensis) were assessed using geometric morphometrics in nine localities. The shell shape presented variability at geographic scale, with the morphologic traits that maximized the differentiation among localities between the tehuelchus and madrynensis morphotypes. Scallops from madrynensis morphotype presented higher and circular shell discs with smaller auricles than those from tehuelchus morphotype. Morphometric differentiation was also detected among localities of each morphotype, wherein most of the variability was related to the disc circularity and the symmetry of the auricles. The presence of morphologic variation in San Matías and San José gulfs, wherein a single genetic pool is shared, evidenced the plastic nature of the species. Given the distribution of this resource in distinct provincial jurisdictions, the differentiation of phenotypic stocks has relevance in the context of fishery management, especially if zoning and rotational strategies are implemented.