bluuebunny/crossref_metadata_2025_split huggingface dataset:
Network rewiring promotes cooperation in an aspirational learning model
Authors: Pal Anuran , Sengupta Supratim 
Published: September 2021

We analyze a cooperative decision-making model that is based on individual aspiration levels using the framework of a public goods game in static and dynamic networks. Sensitivity to differences in payoff and dynamic aspiration levels modulate individual satisfaction and affects subsequent behavior. The collective outcome of such strategy changes depends on the efficiency with which aspiration levels are updated. Below a threshold learning efficiency, cooperators dominate despite short-term fluctuations in strategy fractions. Categorizing players based on their satisfaction level and the resulting strategy reveal periodic cycling between the different categories. We explain the distinct dynamics in the two phases in terms of differences in the dominant cyclic transitions between different categories of cooperators and defectors. Allowing even a small fraction of nodes to restructure their connections can promote cooperation across almost the entire range of values of learning efficiency. Our work reinforces the usefulness of an internal criterion for strategy updates, together with network restructuring, in ensuring the dominance of altruistic strategies over long time-scales.Maintaining a public resource requires sustained cooperation through contributions by community members who benefit from it. Yet, a selfish individual who refuses to contribute can enjoy the benefits without paying the cost of sustaining the public good. If however, too many members of the community act selfishly, the public resource collapses to the detriment of all. The public goods game highlights such a social dilemma and provides a framework for exploring different mechanisms of strategic decision-making that allow cooperation and consequently the public good to be sustained. Among many mechanisms, the reorganization of social ties has been shown to be effective in promoting cooperation in PGG. However, the efficacy of most mechanisms in sustaining cooperation rely on individuals updating their strategy on the basis of information about the contributions of other members of the community. Often such information is either not forthcoming or cannot be effectively utilized. An alternative low-information model of behavioral updating relies on a comparison between the actual benefit received and the benefit aspired for. Individuals tend to retain their strategy if they are satisfied with the benefit received and change their strategy if they are unsatisfied. We show that such a simple reinforcement learning model along with modest restructuring of social ties over time can allow cooperation to be sustained. Our work shows that a low-information strategy-update model can be very effective in ensuring dominance of cooperators in social dilemmas.
Body mass index and childhood symptoms of depression, anxiety, and attention-deficit hyperactivity disorder: a within-family Mendelian randomization study
Authors: Hughes Amanda M , Sanderson Eleanor , Morris Tim , Ayorech Ziada , Tesli Martin , Ask Helga , Reichborn-Kjennerud Ted , Andreassen Ole A. , Magnus Per , Helgeland Øyvind , Johansson Stefan , Njølstad Pål , Davey Smith George , Havdahl Alexandra , Howe Laura D , Davies Neil M 
Published: September 2021

AbstractBackgroundHigher BMI in childhood is associated with emotional and behavioural problems, but these associations may not be causal. Results of previous genetic studies imply causal effects but may reflect influence of demography and the family environment.MethodsThis study used data on 40,949 8-year-old children and their parents from the Norwegian Mother, Father and Child Cohort Study (MoBa) and Medical Birth Registry of Norway (MBRN). We investigated the impact of BMI on symptoms of depression, anxiety, and attention-deficit hyperactivity disorder (ADHD) at age 8. We applied within-family Mendelian randomization, which accounts for familial effects by controlling for parental genotype.ResultsWithin-family Mendelian randomization estimates using genetic variants associated with BMI in adults suggested that a child’s own BMI increased their depressive symptoms (per 5kg/m2increase in BMI, beta=0.26 S.D., CI=-0.01,0.52, p=0.06) and ADHD symptoms (beta= 0.38 S.D., CI=0.09,0.63, p=0.009). These estimates also suggested maternal BMI, or related factors, may independently affect a child’s depressive symptoms (per 5kg/m2increase in maternal BMI, beta=0.11 S.D., CI:0.02,0.09, p=0.01). However, within-family Mendelian randomization using genetic variants associated with retrospectively-reported childhood body size did not support an impact of BMI on these outcomes. There was little evidence from any estimate that the parents’ BMI affected the child’s ADHD symptoms, or that the child’s or parents’ BMI affected the child’s anxiety symptoms.ConclusionsWe found inconsistent evidence that a child’s BMI affected their depressive and ADHD symptoms, and little evidence that a child’s BMI affected their anxiety symptoms. There was limited evidence of an influence of parents’ BMI. Genetic studies in samples of unrelated individuals, or using genetic variants associated with adult BMI, may have overestimated the causal effects of a child’s own BMI.FundingThis research was funded by the Health Foundation. It is part of the HARVEST collaboration, supported by the Research Council of Norway. Individual co-author funding: the European Research Council, the South-Eastern Norway Regional Health Authority, the Research Council of Norway, Helse Vest, the Novo Nordisk Foundation, the University of Bergen, the South-Eastern Norway Regional Health Authority, the Trond Mohn Foundation, the Western Norway Regional Health Authority, the Norwegian Diabetes Association, the UK Medical Research Council. The Medical Research Council (MRC) and the University of Bristol support the MRC Integrative Epidemiology Unit.
The proportion of seizure onset zone contacts resected is not associated with outcome following SEEG-guided resective epilepsy surgery in children
Authors: Khan Mehdi , Chari Aswin , Seunarine Kiran , Eltze Christin , Moeller Friederike , D’Arco Felice , Thornton Rachel , Das Krishna , Boyd Stewart , Cross J Helen , Tahir M Zubair , Tisdall Martin M 
Published: September 2021

AbstractPurposeChildren undergoing stereoelectroencephalography (SEEG)-guided epilepsy surgery represent a complex cohort. We aimed to determine whether the proportion of putative seizure onset zone (SOZ) contacts resected associates with seizure outcome in a cohort of children undergoing SEEG-guided resective epilepsy surgery.MethodsPatients who underwent SEEG-guided resective surgery over a six-year period were included. The proportion of SOZ contacts resected was determined by co-registration of pre- and post-operative imaging. Seizure outcomes were classified as seizure free (SF, Engel class I) or not seizure-free (NSF, Engel class II-IV) at last clinical follow-up.ResultsOf 94 patients undergoing SEEG, 29 underwent subsequent focal resection of whom 22 had sufficient imaging data to be included in the primary analysis (median age at surgery of 10 years, range 5-18). Fifteen (68.2%) were SF and 7 (31.8%) NSF at median follow-up of 19.5 months (range 12-46). On univariate analysis, histopathology, was the only significant factor associated with SF (p<0.05). The percentage of defined SOZ contacts resected ranged from 25-100% and was not associated with SF (p=0.89). In a binary logistic regression model, it was highly likely that histology was the only independent predictor of outcome, although the interpretation was limited by pseudo-complete separation of the data.ConclusionHistopathology is a significant predictor of surgical outcomes in children undergoing SEEG-guided resective epilepsy surgery. The percentage of SOZ contacts resected was not associated with SF. Factors such as spatial organisation of the epileptogenic zone, neurophysiological biomarkers and the prospective identification of pathological tissue may therefore play an important role.
Identification of REM Sleep Behavior Disorder by Magnetic Resonance Imaging and Machine Learning
Authors: Mei Jie , Rahayel Shady , Desrosiers Christian , Postuma Ronald B. , Montplaisir Jacques , Carrier Julie , Monchi Oury , Frasnelli Johannes , Gagnon Jean-François 
Published: September 2021

AbstractBackgroundIdiopathic rapid eye movement sleep behavior disorder (iRBD) is a major risk factor for synucleinopathies, and patients often present with clinical signs and morphological brain changes. However, there is a heterogeneity in the presentation and progression of these alterations, and brain regions that are more vulnerable to neurodegeneration remain to be determined.ObjectivesTo assess the feasibility of morphology-based machine learning in the identification and subtyping of iRBD.MethodsFor the classification tasks [iRBD (n=48) vs controls (n=41); iRBD vs Parkinson’s disease (n=29); iRBD with mild cognitive impairment (n=16) vs without mild cognitive impairment (n=32)], machine learning models were trained with morphometric measurements (thickness, surface area, volume, and deformation) extracted from T1-weighted structural magnetic resonance imaging. Model performance and the most discriminative brain regions were analyzed and identified.ResultsA high accuracy was reported for iRBD vs controls (79.6%, deformation of the caudal middle frontal gyrus and putamen, thinning of the superior frontal gyrus, and reduced volume of the inferior parietal cortex and insula), iRBD vs Parkinson’s disease (82%, smaller volume and surface area of the insula, lower thinning of the entorhinal cortex and lingual gyrus, and greater volume of the fusiform gyrus), and iRBD with vs without mild cognitive impairment (84.8%, thinning of the pars triangularis, superior temporal gyrus, transverse temporal cortex, larger surface area of the superior temporal gyrus, and deformation of isthmus of the cingulate gyrus).ConclusionsMorphology-based machine learning approaches may allow for detection and subtyping of iRBD, potentially enabling efficient preclinical identification of synucleinopathies.
Novel protein-altering variants associated with serum apolipoprotein and lipid levels
Authors: Sandholm Niina , Hotakainen Ronja , Haukka Jani K , Sigfrids Fanny Jansson , Dahlström Emma H , Antikainen Anni , Valo Erkka , Syreeni Anna , Kilpeläinen Elina , Kytölä Anastasia , Palotie Aarno , Harjutsalo Valma , Forsblom Carol , Groop Per-Henrik 
Published: September 2021

AbstractDyslipidemia is a major risk factor for cardiovascular disease. While common genetic variants are known to modestly affect the serum lipid concentrations, rare genetic mutations can cause monogenic forms of hypercholesteremia and other genetic disorders of lipid metabolism. Aiming to identify low-frequency protein-altering variants (PAVs) affecting lipoprotein and lipid traits, we analyzed whole-exome and whole-genome sequencing data of 481 and 573 individuals with type 1 diabetes, respectively. The phenotypic data consisted of 97 serum lipid, apolipoprotein, or other metabolic phenotypes obtained with clinical laboratory measurements and nuclear magnetic resonance (NMR) technology. Single variant analysis identified a novel association between LIPC p.Thr405Met (rs113298164) and serum apolipoprotein-A1 levels (p=7.8×10−8). In the APOB gene, we identified novel associations at two protein-truncating variants (PTVs) resulting in lower serum apolipoprotein B levels (p=5.6×10−4). The burden of PAVs was significantly associated with lipid phenotypes in LIPC, RBM47, TRMT5, and GTF3C5 (p<2.9×10−6). The RBM47 gene is required for apolipoprotein-B post-translational modifications, and in our data, the association between RBM47 and apolipoprotein C-III levels was led by a rare 21 base pair Ala496-Ala502 deletion; as replication, the burden of rare deleterious variants in RBM47 was associated with TG-to-HDLC ratio in WES of 20,917 individuals (p=0.0093). Two PAVs in GTF3C5 were highly Finnish-enriched and associated with cardiovascular phenotypes in external data, whereby the TRMT5 p.Ser185Cys lead variant was associated with stroke phenotypes. Altogether, we identified both novel variant associations in known lipid genes, as well as novel genes implicated in lipoprotein metabolism.
RNA-extraction-free diagnostic method to detect SARS-CoV-2: an assessment from two States, India
Authors: Jayaprakasam Madhumathi , Aggarwal Sumit , Mane Arati , Saxena Vandana , Rao Amrita , Bandopadhyay Bhaswati , Chakraborty Banya , Guha Subhasish Kamal , Taraphdar Mekhala , Acharya Alisha , Gupta Bishal , Deb Sonia , Chowdhury Aparna , Singh Kh Jitenkumar , Tapase Prashant , Pandey Ravindra M , Bhargava Balram , Panda Samiran 
Published: September 2021

SummaryWith increasing demand for large numbers of testing during COVID-19 pandemic, came alternative protocols with shortened turn-around time. We evaluated the performance of such an approach wherein 1138 consecutive clinic attendees were enrolled; 584 and 554 respectively from two independent study sites in the cities of Pune and Kolkata. Paired nasopharyngeal and oropharyngeal swabs were tested by using both reference and index methods in blinded fashion. Prior to conducting RT-PCR, swabs collected in viral transport medium (VTM) were processed for RNA extraction (reference method) and swabs collected in dry tube without VTM were incubated in Tris-EDTA-Proteinase K buffer for 30 minutes and heat inactivated at 98°C for 6 minutes (index method). Overall sensitivity and specificity of the index method were 78.9% (95% CI 71% to 86%) and 99 % (95% CI 98% to 99.6%) respectively. Agreement between the index and reference method was 96.8 % (k = 0.83, SE=0.030). The reference method exhibited enhanced detection of viral genes (E, N and RdRP) with lower Ct values compared to the index method. The index method can be used for detecting SARS-CoV-2 infection with appropriately chosen primer-probe set and heat treatment approach in pressing time; low sensitivity constrains its potential wider use.
Role of Lateral Inhibition on Visual Number Sense
Authors: Zhou Yiwei , Chen Huanwen , Wang Yijun 
Published: September 2021

AbstractLateral inhibition is a basic principle of information processing and widely exists in the human and animal nervous systems. Lateral inhibition is also involved in processing visual information because it travels through the retina, primary visual cortex, and visual nervous system. This finding suggests that lateral inhibition is associated with visual number sense in humans and animals. Here, we show a number-sensing neural network model based on lateral inhibition. The model can reproduce the size and distance effects of the output response of human and animal number-sensing neurons when the network connection weights are set randomly without adjustment. The number sense of the model disappears when lateral inhibition is removed. Our study shows that the first effect of lateral inhibition is to strengthen the linear correlation between the total response intensity of the input layer and the number of objects. The second one is to allow the output cells to prefer different numbers. Results indicate that lateral inhibition plays an indispensable role in untrained spontaneous number sense.
Genomic Heritability: A Ragged Diagonal Between Bias and Variance
Authors: Feldmann Mitchell J. , Piepho Hans-Peter , Knapp Steven J. 
Published: September 2021

ABSTRACTMany important traits in plants, animals, and microbes are polygenic and are therefore difficult to improve through traditional marker-assisted selection. Genomic prediction addresses this by enabling the inclusion of all genetic data in a mixed model framework. The main method for predicting breeding values is genomic best linear unbiased prediction (GBLUP), which uses the realized genomic relationship or kinship matrix (K) to connect genotype to phenotype. The use of relationship matrices allows information to be shared for estimating the genetic values for observed entries and predicting genetic values for unobserved entries. One of the key parameters of such models is genomic heritability, or the variance of a trait associated with a genome-wide sample of DNA polymorphisms. Here we discuss the relationship between several common methods for calculating the genomic relationship matrix and propose a new matrix based on the average semivariance that yields accurate estimates of genomic variance in the observed population regardless of the focal population quality as well as accurate breeding value predictions in unobserved samples. Notably, our proposed method is highly similar to the approach presented by Legarra (2016) despite different mathematical derivations and statistical perspectives and only deviates from the classic approach presented in VanRaden (2008) by a scaling factor. With current approaches, we found that the genomic heritability tends to be either over- or underestimated depending on the scaling and centering applied to the marker matrix (Z), the value of the average diagonal element ofK, and the assortment of alleles and heterozygosity (H) in the observed population and that, unlike its predecessors, our newly proposed kinship matrixKASVyields accurate estimates ofin the observed population, generalizes to larger populations, and produces BLUPs equivalent to common methods in plants and animals.
Genome-wide meta-analysis of iron status biomarkers and the effect of iron on all-cause mortality in HUNT
Authors: Moksnes Marta R , Hansen Ailin Falkmo , Graham Sarah E , Gagliano Taliun Sarah A , Wu Kuan-Han , Zhou Wei , Thorstensen Ketil , Fritsche Lars G , Gill Dipender , Mason Amy , Cucca Francesco , Schlessinger David , Abecasis Gonçalo R. , Burgess Stephen , Åsvold Bjørn Olav , Nielsen Jonas B , Hveem Kristian , Willer Cristen J , Brumpton Ben M 
Published: September 2021

AbstractIron is essential for many biological processes, but iron levels must be tightly regulated to avoid harmful effects of both iron deficiency and overload. Here, we perform genome-wide association studies on four iron related biomarkers (serum iron, serum ferritin, transferrin saturation, total iron binding capacity) in the Trøndelag Health Study (HUNT), the Michigan Genomics Initiative (MGI) and the SardiNIA study, followed by their meta-analysis with publicly available summary statistics, analyzing up to 257 953 individuals. We identify 127 genetic loci associated with iron traits. Among 19 novel protein-altering variants, we observe a rare missense variant (rs367731784) in HUNT, which suggests a role for DNAJC13 in transferrin recycling. We further validate the latest genetic risk scores for each biomarker in HUNT (6% variance in serum iron explained) and present linear and non-linear Mendelian randomization analyses of the traits on all-cause mortality. We find evidence of a harmful effect of increased serum iron and transferrin saturation in linear analyses that estimate population-averaged effects. However, there was weak evidence of a protective effect of increasing serum iron at the very low end of its distribution. Our findings contribute to our understanding of the genes affecting iron status and its consequences on human health.
Effects of myopia and glaucoma in the prelaminar neural canal and anterior lamina cribrosa using 1060-nm swept-source optical coherence tomography
Authors: Lee Sieun , Heisler Morgan , Ratra Dhanashree , Ratra Vineet , Mackenzie Paul J , Sarunic Marinko V , Beg Mirza Faisal 
Published: September 2021

AbstractPurposeInvestigate the effects of myopia and glaucoma in the prelaminar neural canal and anterior lamina cribrosa using 1060-nm swept-source optical coherence tomographyDesignRetrospective, cross-sectional studyMethodsSettingClinical practicePatient or study population19 controls (38 eyes); 38 glaucomatous subjects (63 eyes). Inclusion criteria for glaucomatous subjects: i) optic disc neural rim loss; ii) peripapillary nerve fibre layer (NFL) loss on spectral domain optical coherence tomography (SD-OCT); iii) glaucomatous visual field defect with an abnormal pattern standard deviation (P<.05); iv) stable SD-OCT, visual field, and optic disc clinical examination for 6 or more months. Inclusion criteria for control subjects: no evidence of retinal or optic nerve pathology. Exclusion criteria: i) retinal diseases or optic neuropathy other than primary open-angle glaucoma; ii) intraocular pressure less than 10 mmHg or higher than 20 mmHg; iii) ocular media opacities; iv) any surgery-related complication deemed inappropriate for the study.Intervention or observation proceduresSwept-source optical coherence tomographyMain Outcome Measure(s)Bruchs membrane opening (BMO) and anterior laminar insertion (ALI) dimension, prelaminar neural canal dimension, anterior lamina cribrosa surface (ALCS) depthResultsGlaucomatous eyes had more bowed and nasally rotated BMO and ALI, more horizontally skewed prelaminar neural canal, and deeper ALCS than the control eyes. Increased axial length was associated with a wider, longer, and more horizontally skewed neural canal, and decrease in the ALCS depth and curvature.ConclusionOur findings suggest that glaucomatous posterior bowing or cupping of lamina cribrosa can be significantly confounded by the myopic expansion of the neural canal. This may be related to higher glaucoma risk associated with myopia from decreased compliance and increased susceptibility to IOP-related damage of LC being pulled taut.
Anti-Bat Ultrasound Production in Moths is Globally and Phylogenetically Widespread
Authors: Barber JR , Plotkin D , Rubin JJ , Homziak NT , Leavell BC , Houlihan P , Miner KA , Breinholt JW , Quirk-Royal B , Padrón PS , Nunez M , Kawahara AY 
Published: September 2021

AbstractWarning signals are well known in the visual system, but rare in other modalities. Some moths produce ultrasonic sounds to warn bats of noxious taste or to mimic unpalatable models. Here we report results from a long-term study across the globe, assaying moth response to playback of bat echolocation. We tested 252 genera, spanning most families of large-bodied moths, and outline anti-bat ultrasound production in 52 genera, with eight new subfamily origins described. Based on acoustic analysis of ultrasonic emissions and palatability experiments with bats, it seems that acoustic warning and mimicry are theraison d’etrefor sound production in most moths. However, some moths use high-density ultrasound capable of jamming bat sonar. In fact, we find preliminary evidence of independent origins of sonar jamming in at least six subfamilies. Palatability data indicates that jamming and warning are not mutually exclusive strategies. To explore the possible organization of anti-bat warning sounds into acoustic mimicry rings, we intensively studied a community of moths in Ecuador and found five distinct acoustic clusters using machine learning algorithms. While these data represent an early understanding of acoustic aposematism and mimicry across this megadiverse insect order, it is likely that ultrasonically-signaling moths comprise one of the largest mimicry complexes on earth.