bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outdoor Physical Activity as a Confounder for Vitamin D Status: A Scoping Review Protocol
Authors: Corr Patrick G. , Badawi Alia M. , Vu Stephanie H. , Frame Leigh A. 
Published: February 2023

AbstractBackgroundVitamin D (vitD) has been correlated with a number of health outcomes and disease states; however, these relationships are likely confounded by the role of outdoor physical activity (PA). Currently, there are few studies that consider confounders to vitD status and the potentially spurious relationships between PA and vitD status.MethodsThis scoping review will employ Arksey and O’Malley’s five-stage approach. Publications will be identified through five databases (CINAHL, Cochrane Library, PubMed, Scopus, and SportDISCUS) and reviewed in Covidence.ResultsThe findings are expected to help identify what information is presently available regarding the correlation between outdoor PA and vitD status. The results of this scoping review will help to inform a quantitative analysis of the National Institutes of Health (NIH) All of Us database.DiscussionIt is unclear what effect outdoor PA may have on the relationship between vitD status and health outcomes and if any portion of this relationship is spurious. This scoping review will initiate an exploration of the relationship between vitD and PA to determine the strength and magnitude of potential confounders. Ultimately, we seek to reassess previous findings and determine the true effect of vitD alone by isolating the effect of outdoor PA.
Autonomous Screening for Laser Photocoagulation in Fundus Images Using Deep Learning
Authors: Bressler Idan , Aviv Rachelle , Margalit Danny , Rom Yovel , Ianchulev Sean , Dvey-Aharon Zack 
Published: February 2023

AbstractBackgroundDiabetic retinopathy is a leading cause of blindness in adults worldwide. AI with autonomous deep learning algorithms has been increasingly used in the analysis of retinal images particularly for the screening of referrable DR. An established treatment for proliferative DR is pan-retinal or focal laser photocoagulation. Training AI autonomous models to discern laser patterns can be important in disease management and follow-up.MethodsA deep learning model was trained for laser treatment detection using the EyePACs dataset. Data was randomly assigned, by participant, into development (n= 18,945) and validation (n= 2,105) sets. Analysis was conducted at the single image, eye, and patient levels. The model was then used to filter input images for three independent AI models for various retinal indications, and changes in model efficacy were measured using AUC and MAE.FindingsOn the task of laser photocoagulation detection: AUC of 0.981 (CI 95% 0.971-0.87) was achieved at the patient level. AUC of 0.950 (CI 95% 0.943-0.956) was achieved at the image level. AUC of 0.979 (CI 95% 0.972-0.984) was achieved at the eye level.When analyzing independent AI models, efficacy was shown to improve across the board on images of untreated eyes. DME detection on images with artifacts was AUC 0.932 (CI 95% 0.905-0.951) vs. AUC 0.955 (CI 95% 0.948-0.961) on those without. Participant sex detection on images with artifacts was AUC 0.872 (CI 95% 0.830-0.903) compared to AUC 0.922 (CI 95% 0.916-0.927) on those without. Participant age detection on images with artifacts was MAE 5.33 vs. MAE 3.81 on those without.InterpretationThe proposed model for laser treatment detection achieved high performance on all analysis metrics and has been demonstrated to positively affect the efficacy of different AI models, suggesting that laser detection can generally improve AI powered applications for fundus images.FundingProvided by AEYE Health Inc.
A systematic review on machine learning approaches in the diagnosis of rare genetic diseases
Authors: Roman-Naranjo P , Parra-Perez AM , Lopez-Escamez JA 
Published: February 2023

AbstractBackgroundThe diagnosis of rare genetic diseases is often challenging due to the complexity of the genetic underpinnings of these conditions and the limited availability of diagnostic tools. Machine learning (ML) algorithms have the potential to improve the accuracy and speed of diagnosis by analyzing large amounts of genomic data and identifying complex multiallelic patterns that may be associated with specific diseases. In this systematic review, we aimed to identify the methodological trends and the ML application areas in rare genetic diseases.MethodsWe performed a systematic review of the literature following the PRISMA guidelines to search studies that used ML approaches to enhance the diagnosis of rare genetic diseases. Studies that used DNA-based sequencing data and a variety of ML algorithms were included, summarized, and analyzed using bibliometric methods, visualization tools, and a feature co-occurrence analysis.FindingsOur search identified 22 studies that met the inclusion criteria. We found that exome sequencing was the most frequently used sequencing technology (59%), and rare neoplastic diseases were the most prevalent disease scenario (59%). In rare neoplasms, the most frequent applications of ML models were the differential diagnosis or stratification of patients (38.5%) and the identification of somatic mutations (30.8%). In other rare diseases, the most frequent goals were the prioritization of rare variants or genes (55.5%) and the identification of biallelic or digenic inheritance (33.3%). The most employed method was the random forest algorithm (54.5%). In addition, the features of the datasets needed for training these algorithms were distinctive depending on the goal pursued, including the mutational load in each gene for the differential diagnosis of patients, or the combination of genotype features and sequence-derived features (such as GC-content) for the identification of somatic mutations.ConclusionsML algorithms based on sequencing data are mainly used for the diagnosis of rare neoplastic diseases, with random forest being the most common approach. We identified key features in the datasets used for training these ML models according to the objective pursued. These features can support the development of future ML models in the diagnosis of rare genetic diseases.
Coinfection withStrongyloidesand SARS-CoV-2: protocol for a systematic review
Authors: Rosca Elena C , Heneghan Carl , Spencer Elizabeth A , Plüddemann Annette , Maltoni Susanna , Gandini Sara , Onakpoya Igho J , Evans David H , Conly John M , Jefferson Tom 
Published: February 2023

AbstractRationale for the reviewCOVID-19 treatment can worsen parasitic disease in patients with coinfection. Consequently, there is a need to investigate the infection with SARS-CoV-2 andStrongyloides. We aim to systematically review clinical and laboratory features of COVID-19 andStrongyloidescoinfection, to investigate possible interventions and outcomes in this pathology. Also, we aim to identify difficulties in managing the parasitic disease manifestations in this context and to emphasize research gaps requiring further attention.MethodsWe will search two electronic databases – LitCOVID, and WHO COVID-19 and will include studies on SARS-CoV-2 andStrongyloidescoinfection. We will adapt the WHO-UMC system for standardized case causality assessment to evaluate if using corticosteroids or other immunosuppressive drugs in COVID-19 patients determined acute strongyloidiasis manifestations.Expected resultsWe will present the evidence in three distinct packages: study description, methodological quality assessment and data extracted. We will summarize the evidence and will draw conclusions as to the quality of the evidence.
Spatial enhancer activation determines inhibitory neuron identity
Authors: Dvoretskova Elena , Ho May C. , Kittke Volker , Neuhaus Florian , Vitali Ilaria , Lam Daniel D. , Delgado Irene , Feng Chao , Torres Miguel , Winkelmann Juliane , Mayer Christian 
Published: February 2023

AbstractThe mammalian telencephalon contains a tremendous diversity of GABAergic projection neuron and interneuron types, that originate in a germinal zone of the embryonic basal ganglia. How genetic information in this transient structure is transformed into different cell types is not yet fully understood. Using a combination ofin vivoCRISPR perturbation, lineage tracing, and ChIP-seq in mice, we found that the transcription factor MEIS2 favors the development of projection neurons through genomic binding sites in regulatory enhancers of projection neuron specific genes. MEIS2 requires the presence of the homeodomain transcription factor DLX5 to direct its functional activity towards these sites. In interneuron precursors, the activation of projection neuron specific enhancers by MEIS2 and DLX5 is repressed by the transcription factor LHX6. When MEIS2 carries a mutation associated with intellectual disability in humans, it is less effective at activating enhancers involved in projection neuron development. This suggests that GABAergic differentiation may be impaired in patients carrying this mutation. Our research supports a model (“Differential Binding‘) where the spatial specific composition of transcription factors atcis-regulatory elements determines differential gene expression and cell fate decisions in the ganglionic eminence.
Human Abdominal Subcutaneous-Derived Active Beige Adipocytes CarryingFTOrs1421085 Obesity-Risk Alleles Exert Lower Thermogenic Capacity
Authors: Vámos Attila , Arianti Rini , Vinnai Boglárka Ágnes , Alrifai Rahaf , Shaw Abhirup , Póliska Szilárd , Guba Andrea , Csősz Éva , Csomós István , Mocsár Gábor , Lányi Cecilia , Balajthy Zoltán , Fésüs László , Kristóf Endre 
Published: February 2023

AbstractWhite adipocytes store lipids, have a large lipid droplet and few mitochondria. Brown and beige adipocytes, which produce heat, are characterized by high expression of uncoupling protein (UCP) 1, multilocular lipid droplets, and large amounts of mitochondria. The rs1421085 T-to-C single-nucleotide polymorphism (SNP) of the humanFTOgene interrupts a conserved motif for ARID5B repressor, resulting in adipocyte type shift from beige to white. We obtained abdominal subcutaneous adipose tissue from donors carryingFTOrs1421085 TT (risk-free) or CC (obesity-risk) genotypes, isolated and differentiated their preadipocytes into beige adipocytes (driven by the PPARγ agonist rosiglitazone for 14 days), and activated them with dibutyryl-cAMP for 4 hours. Then, either the same culture conditions were applied for additional 14 days (active beige adipocytes) or it was replaced by a white differentiation medium (inactive beige adipocytes). White adipocytes were differentiated by their medium for 28 days. RNA-sequencing was performed to investigate the gene expression pattern of adipocytes carrying differentFTOalleles and found that active beige adipocytes had higher brown adipocyte content and browning capacity compared to white or inactive beige ones when the cells were obtained from risk-free TT but not from obesity-risk CC genotype carriers. Active beige adipocytes carryingFTOCC had lower thermogenic gene (e.g.,UCP1, PM20D1, CIDEA) expression and thermogenesis measured by proton leak respiration as compared to TT carriers. In addition, active beige adipocytes with CC alleles exerted lower expression of ASC1 neutral amino acid transporter (encoded bySLC7A10) and less consumption of Ala, Ser, Cys, and Gly as compared to risk-free carriers. We did not observe any influence of theFTOrs1421085 SNP on white and inactive beige adipocytes highlighting its exclusive and critical effect when adipocytes were activated for thermogenesis.
Delayed normalization model captures disparate nonlinear neural dynamics measured with different techniques in macaque and human V1
Authors: Zhou Jingyang , Whitmire Matt , Chen Yuzhi , Seidemann Eyal 
Published: February 2023

SummaryNeuronal representations throughout the primate visual system display a wide range of nonlinear dynamics in response to static visual stimuli. To understand the neural basis of visual perception, it is important to quantify these nonlinearities and to develop general models that allow one to predict response dynamics to visual stimuli with arbitrary temporal waveform.Voltage-sensitive dye imaging (VSDI) is a powerful method for measuring neural population responses from the cortex of awake, behaving, subjects. Here we used VSDI to measure the dynamics of neural population responses in macaque V1 to visual stimuli with a wide range of time courses.We found that beyond clear nonlinearities for briefly presented visual stimuli, stimulus-evoked VSDI responses are surprisingly near additive in time. These results are qualitatively different from neural dynamics to similar stimuli previously measured in human visual cortex using fMRI and electrocorticography (ECoG), which show strong sub-additivity in time.To test whether this discrepancy is specific to VSDI, a signal dominated by subthreshold neural activity, we repeated our measurements using a genetically encoded calcium indicator (GCaMP), a signal dominated by spiking activity. We found that GCaMP signals in macaque V1 are also near-additive. Therefore, the discrepancies in the degree of additivity between these different measurements are not attributed to the difference between sub- and supra-threshold neural response.Finally, we show that a simple yet flexible delayed normalization model can capture the dynamics of all of these measurements, suggesting that dynamic gain-control is an important mechanism contributing to neural processing in the brain.
Chemical defences indicate distinct colour patterns with reduced variability in aposematic nudibranchs
Authors: van den Berg Cedric P. , Santon Matteo , Endler John A. , Drummond Leon , Dawson Bethany R. , Santiago Carl , Weber Nathalie , Cheney Karen L. 
Published: February 2023

AbstractThe selective factors that shape phenotypic diversity in prey communities with aposematic animals are diverse and coincide with similar diversity in the strength of underlying secondary defences. However, quantitative assessments of colour pattern variation and the strength of chemical defences in assemblages of aposematic species are lacking. We quantified colour pattern diversity using Quantitative Colour Pattern Analysis (QCPA) in 13 Dorid nudibranch species (Infraorder: Doridoidei) that varied in the strength of their chemical defences. We accounted for the physiological properties of a potential predator’s visual system (a triggerfish,Rhinecanthus aculeatus) and modelled the appearance of nudibranchs from multiple viewing distances (2cm and 10cm). We identified distinct colour pattern properties associated with the presence and strength of chemical defences. Colour patterns were also less variable among species with chemical defences when compared to undefended species. This confirms correlations between secondary defences and diverse, bold colouration while showing that chemical defences coincide with decreased colour pattern variability among species. Our study suggests that complex spatiochromatic properties of colour patterns perceived by potential predators can be used to make inferences on the presence and strength of chemical defences.
Whole-genome comparisons identify repeated regulatory changes underlying convergent appendage evolution in diverse fish lineages
Authors: Chen Heidi I. , Turakhia Yatish , Bejerano Gill , Kingsley David M. 
Published: February 2023

AbstractFins are major functional appendages of fish that have been repeatedly modified in different lineages. To search for genomic changes underlying natural fin diversity, we compared the genomes of 36 wild fish species that either have complete or reduced pelvic and caudal fins. We identify 1,614 genomic regions that are well-conserved in fin-complete species but missing from multiple fin-reduced lineages. Recurrent deletions of conserved sequences (CONDELs) in wild fin-reduced species are enriched for functions related to appendage development, suggesting that convergent fin reduction at the organismal level is associated with repeated genomic deletions near fin-appendage development genes. We used sequencing and functional enhancer assays to confirm thatPelA, aPitx1enhancer previously linked to recurrent pelvic loss in sticklebacks, has also been independently deleted and may have contributed to the fin morphology in distantly related pelvic-reduced species. We also identify a novel enhancer that is conserved in the majority of percomorphs, drives caudal fin expression in transgenic stickleback, is missing in tetraodontiform,syngnathid, and synbranchid species with caudal fin reduction, and which alters caudal fin development when targeted by genome editing. Our study illustrates a general strategy for mapping phenotypes to genotypes across a tree of vertebrate species, and highlights notable new examples of regulatory genomic hotspots that have been used to evolve recurrent phenotypes during 100 million years of fish evolution.
TheOrshinarhythm in a colonial urochordate: recurrent aging/rejuvenation sequels
Authors: Ben-Hamo Oshrat , Izhaki Ido , Ben-Shlomo Rachel , Rinkevich Baruch 
Published: February 2023

AbstractWhen it comes to aging, some colonial invertebrates present disparate patterns from the customary aging phenomenon in unitary organisms, where a single senescence phenomenon along ontogeny culminates in their inevitable deaths. Here we studied aging processes in 81 colonies of the marine urochordateBotryllus schlosserieach followed from birth to death (over 720 days). The colonies were divided between three life history strategies, each distinct from the others based on the existence/absence of colonial fission: NF (no fission), FA (fission develops after the colony reaches maximal size), and FB (fission develops before the colony reaches maximal size). Results revealed that sexual reproductive statuses (hermaphroditism and male only settings), colonial vigorousness and sizes, represent coinciding and repeated rhythms of one or more emerged life/death ‘astogenic segments’ on the whole-genet level, each is termed asOrshina, and the sum of all segments as theOrshinarhythm. EachOrshinasegment lasts about three months (containing ca. 13 blastogenic cycles), ends by either the colonial death or rejuvenation, and manipulated by absence/existing of fission events in NF/FA/FB strategies. These findings indicate that reproduction, life span, death, rejuvenation and fission events are important scheduled biological components in the constructedOrshinarhythm, a novel aging phenomenon.
Generation time and seasonal migration explain variation in spatial population synchrony across European bird species
Authors: Martin Ellen C. , Hansen Brage Bremset , Lee Aline Magdalena , Herfindal Ivar 
Published: February 2023

AbstractSpatial population synchrony is common among populations of the same species and is an important predictor of extinction risk. Despite the potential consequences for metapopulation persistence, we still largely lack understanding of what makes one species more likely to be synchronized than another given the same environmental conditions.Generally, environmental conditions on a shared environment or a species’ sensitivity to the environment can explain the extent of synchrony. Populations that are closer together experience more similar fluctuations in their environments than those populations that are further apart and are therefore more synchronized. The relative importance of environmental and demographic stochasticity for population dynamics is strongly linked to species’ life history traits, such as pace of life, why may impact population synchrony. For populations that migrate, there may be multiple environmental conditions at different locations driving synchrony. However, the importance of life history and migration strategies in determining patterns of spatial population synchrony have rarely been explored empirically. We therefore hypothesize that generation time, a proxy for pace of life, and migration play an important role in determining spatial population synchrony.We used population abundance data on breeding birds from four countries to investigate patterns of spatial population synchrony in growth rate and abundance. We investigated differences in synchrony across a gradient of generation times in resident, short-distance migrant, and long-distance migrant bird species.Species with shorter generation times were more synchronized than species with longer generation times. Short-distance migrants were more synchronized than long-distance migrants and resident birds.Our results provide novel empirical links between spatial population synchrony and species traits known to be of key importance for population dynamics, generation time and migration characteristics. We show how these different mechanisms can be combined to understand species-specific causes of spatial population synchrony. Understanding these specific drivers of spatial population synchrony is important in the face of increasingly severe threats to biodiversity and could be key for successful future conservation outcomes.
USP8 inhibition promotes Parkin-independent mitophagy in theDrosophilabrain and in human neurons
Authors: Mauri Sofia , Bernardo Greta , Martinez Aitor , Favaro Mariavittoria , Trevisan Marta , Cobraiville Gael , Fillet Marienne , Caicci Federico , Whitworth Alexander J. , Ziviani Elena 
Published: February 2023

AbstractStress-induced mitophagy, a tightly regulated process that targets dysfunctional mitochondria for autophagy-dependent degradation, mainly relays on two proteins, PINK1 and Parkin, which genes are mutated in some forms of familiar Parkinson’s Disease (PD). Upon mitochondrial damage, the protein kinase PINK1 accumulates on the organelle surface where it controls the recruitment of the E3-ubiquitin ligase Parkin. On mitochondria, Parkin ubiquitinates a subset of mitochondrial resident proteins located on the outer mitochondrial membrane, leading to the recruitment of downstream cytosolic autophagic adaptors, and subsequent autophagosome formation.Importantly, PINK1/Parkin-independent mitophagy pathways also exist that can be counteracted by specific deubiquitinating enzymes (DUBs). Downregulation of these specific DUBs can presumably enhances basal mitophagy, and be beneficial in models in which accumulation of defective mitochondria is implicated. Among these DUBs, USP8 is an interesting target because of its role in the endosomal pathway and autophagy, and its beneficial effects, when inhibited, in models of neurodegeneration. Based on this, we evaluated autophagy and mitophagy levels when USP8 activity is altered. We used genetic approaches inD. melanogasterto measure autophagy and mitophagyin vivo, and complementaryin vitroapproaches to investigate the molecular pathway that regulates mitophagy via USP8.We found an inverse correlation between basal mitophagy and USP8 levels, in that inhibition of USP8 correlates with increased Parkin-independent mitophagy. These results suggest the existence of a yet uncharacterized mitophagic pathway that is inhibited by USP8.
Quantifying invasive pest dynamics through inference of a two-node epidemic network model
Authors: Wadkin Laura E , Golightly Andrew , Branson Julia , Hoppit Andrew , Parker Nick G , Baggaley Andrew W 
Published: February 2023

AbstractInvasive woodland pests are having a substantial ecological, economic and social impact, harming biodiversity and ecosystem services. Mathematical modelling informed by Bayesian inference can deepen our understanding of the fundamental behaviours of invasive pests and provide predictive tools for forecasting the future spread. A key invasive pest of concern in the UK is the oak processionary moth (OPM). OPM was established in the UK in 2006, is harmful to both oak trees and humans, and its infestation area is continually expanding. Here, we use a computational inference scheme to estimate the parameters for a two-node network epidemic model to describe the temporal dynamics of OPM in two geographically neighbouring parks (Bushy Park and Richmond Park, London). We show the applicability of such a network model to describing invasive pest dynamics and our results suggest that the infestation within Richmond Park has largely driven the infestation within Bushy Park.