Miracle-dz/UniFAR-FTUs huggingface dataset:
Comprehensive review and annotation of susceptibility SNPs associated with obesity‐related traits

We aimed to summarize the results of genetic association studies for obesity and provide a comprehensive annotation of all susceptibility single nucleotide polymorphisms (SNPs). A total of 72 studies were summarized, resulting in 90,361 susceptibility SNPs (738 index SNPs and 89,623 linkage disequilibrium SNPs). Over 90% of the susceptibility SNPs are located in non‐coding regions, and it is challenging to understand their functional significance. Therefore, we annotated these SNPs by using various functional databases. We identified 24,623 functional SNPs, including 4 nonsense SNPs, 479 missense SNPs, 399 untranslated region SNPs which might affect microRNA binding, 262 promoter and 5,492 enhancer SNPs which might affect transcription factor binding, 7 splicing sites, 76 SNPs which might affect gene methylation levels, 1,839 SNPs under natural selection and 17,351 SNPs which might modify histone binding. Expression quantitative trait loci analyses for functional SNPs identified 98 target genes, including 69 protein coding genes, 27 long non‐coding RNAs and 3 processed transcripts. The percentage of protein coding genes that could be correlated with obesity‐related pathways directly or through gene–gene interaction is 75.36 (52/69). Our results may serve as an encyclopaedia of obesity susceptibility SNPs and offer guide for functional experiments.
Are cervical vertebrae suitable for age estimation?

BACKGROUND The ability of cervical vertebrae (CV) staging to contribute in forensic age estimation is being discussed controversially. The large variability of CV geometries in the end stage of development might be the reason for not reaching a performance competitive to hand or third molar methods. Here we study the geometry of adult CV and demonstrate that the description of their "typical" appearance is often not met. MATERIALS AND METHODS Lateral cephalograms from clinical routine of 320 subjects aged 20 years or above (median 24 years, 52% female) were evaluated. The criteria for the end stage of CV development (Hassel-Farman, Baccetti) were examined by assessing them in terms of metric measurements: (1) rectangular shape of C3/C4, (2) at least one of the height-width ratios of C3/C4 > 1 (both not <1), (3) significant concavities at the inferior margin of C2, C3 and C4. Metric data of the adults were also compared to those of 100 children aged 8-10 years (50% female). RESULTS Adult CV often violated the criteria of rectangular shape (44% C3, 36% C4), of height-width ratio (16% C3, 35% C4) and inferior concavity (10% C2, 10% C3, 19% C4). All of the criteria for adult CV were fulfilled in only 24% of the subjects (95%CI 19-28%). The variability of measures of the CV shapes was large; e.g., the 95% reference ranges for the height-width ratios were 0.81-1.19 (C3) and 0.77-1.14 (C4). There was a material overlap of ranges of CV measures of adults and children. CONCLUSION While hand bones and teeth have well-defined appearances in the end stage of development, adult CV have a large biological variance of shapes; it is hard to define their "typical" appearance. Moreover, measures of CV geometry do not strictly separate adults from children. These facts might reason the limited usefulness of CV in age estimation.
Comparison of computational and semi-empirical aerodynamics tools for making fit-for-purpose modelling decisions

It was found that CFD++ produced the lowest errors of all the tools tested, highlighting the applicability of the tool to all tested flow regimes, and is recommended for use where the highest fidelity solution is desired and the result is not highly time critical. The results for Cart3D showed that it may be used to obtain a solution for supersonic cases where a small margin for error in the results is acceptable. However, the accuracy was lower for other flow regimes, especially the transonic regime where Cart3D produced erroneous results. Missile Datcom produced erroneous results for the non-conventional geometry tested, however it was able to produce medium fidelity results for conventional air to air missile shapes. The ability of Missile Datcom to produce results very quickly highlights its utility for quick-look analysis of conventional air to air systems.
EEG-based classification of learning strategies : Model-based and model-free reinforcement learning

Human reinforcement learning (RL) has been known to utilize two distinctive learning strategies, model-based (MB) and model-free (MF) RL. The process of arbitration between MB and MF is thought to be located in the ventrolateral prefrontal cortex and frontopolar cortex. These loci are near the cortex, so we expect the related information can be represented in EEG signals. However, EEG signal patterns considering the arbitration of RL has not been investigated. In this paper, we tested a EEG-based classification model to separate these two different types of trials, each of which is meant to promote MB and MF RL. We found, for the first time, firm evidence to indicate that information pertaining to learning strategies is represented in prefrontal EEG signals.
One-and Two-dimenisonal Compressive Edge Spectrum Sensing

Future industrial radio systems for Industry 4.0 applications will heavily rely on the management of shared spectrum to provide coexistence of different wireless communication systems and unknown wireless transmitters. A crucial component for successful coexistence management is the estimation of the spectrum of interest to identify active wireless systems and potential interference sources. Monitoring large bandwidths can be very costly in terms of the required bandwidth if classical Shannon-Nyquist signal acquisition is pursued at a sampling rate at least the bandwidth of the signal of interest. For fast and accurate spectrum estimation, we propose a novel approach called Compressive Edge Spectrum Sensing (CES) that allows for a sampling down to 5% of the Nyquist rate without losses in the detection accuracy of occupied and unoccupied spectrum regions.
Multi-Step Time Series Forecasting with an Ensemble of Varied Length Mixture Models

Many real-world problems require modeling and forecasting of time series, such as weather temperature, electricity demand, stock prices and foreign exchange (FX) rates. Often, the tasks involve predicting over a long-term period, e.g. several weeks or months. Most existing time series models are inheritably for one-step prediction, that is, predicting one time point ahead. Multi-step or long-term prediction is difficult and challenging due to the lack of information and uncertainty or error accumulation. The main existing approaches, iterative and independent, either use one-step model recursively or treat the multi-step task as an independent model. They generally perform poorly in practical applications. In this paper, as an extension of the self-organizing mixture autoregressive (AR) model, the varied length mixture (VLM) models are proposed to model and forecast time series over multi-steps. The key idea is to preserve the dependencies between the time points within the prediction horizon. Training data are segmented to various lengths corresponding to various forecasting horizons, and the VLM models are trained in a self-organizing fashion on these segments to capture these dependencies in its component AR models of various predicting horizons. The VLM models form a probabilistic mixture of these varied length models. A combination of short and long VLM models and an ensemble of them are proposed to further enhance the prediction performance. The effectiveness of the proposed methods and their marked improvements over the existing methods are demonstrated through a number of experiments on synthetic data, real-world FX rates and weather temperatures.
Identification and characterization of antibodies elicited by human cystatin C fragment

Amyloid formation is associated with a number of neurodegenerative diseases that affect the independence and quality of life of aging populations. One of rather atypical, occurring at a young age amyloidosis is hereditary cystatin C amyloid angiopathy (HCCAA) related to aggregation of L68Q variant of human cystatin C (hCC). Human cystatin C plays a very important role in many aspects of human health; however, its amyloidogenic properties manifested in HCCAA present a real, lethal threat to some populations and any work on factors that can affect possible influencing hCC aggregation is not to overestimate. It was proved that interaction of hCC with monoclonal antibodies suppresses significantly hCC dimerization process. Therefore, immunotherapy seems to be the right approach toward possible HCCAA treatment. In this work, the hCC fragment encompassing residue 60‐70 (in 2 variants: linear peptide and multiple antigenic peptide) was used as an immunogen in rabbit immunization. As a result, specific anti‐hCC antibodies were found in both rabbit sera. Surprisingly, rabbit antibodies were obtained after immunization with only a short peptide. The obtained antibodies were characterized, and their influence on the aggregation propensity of the hCC molecules was evaluated. The antibodies turned out not to have any significant influence on the cystatin C dimerization process. Nevertheless, we hope that antibodies elicited in rabbits by other hCC fragments could lead to elaboration of effective treatment against HCCAA.
Switching and loss of cellular cytokine producing capacity characterize in vivo viral infection and malignant transformation in human T- lymphotropic virus type 1 infection

Adult T-cell leukaemia/lymphoma (ATL) arises from chronic non-malignant human T lymphotropic virus type-1 (HTLV-1) infection which is characterized by high plasma pro-inflammatory cytokines whereas ATL is characterized by high plasma anti-inflammatory (IL-10) concentrations. The poor prognosis of ATL is partly ascribed to disease-associated immune suppression. ATL cells have a CD4+CCR4+CD26-CD7- immunophenotype but infected cells with this immunophenotype (‘ATL-like’ cells) are also present in non-malignant HTLV-1 infection. We hypothesized that ‘ATL-like’ and ATL cells have distinct cytokine producing capacity and a switch in the cytokines produced occurs during leukemogenesis. Seventeen asymptomatic carriers (ACs), 28 patients with HTLV-1-associated myelopathy (HAM) and 28 with ATL were studied. Plasma IL-10 concentration and the absolute frequency of IL-10-producing CD4+ T cells were significantly higher in patients with ATL compared to AC. IL-10-producing ATL cells were significantly more frequent than ‘ATL-like’ cells. The cytokine-producing cells were only a small fraction of ATL cells. Clonality analysis revealed that even in patients with ATL the ATL cells were composed not only of a single dominant clone (putative ATL cells) but also tens of non-dominant infected clones (‘ATL-like’ cells). The frequency of cytokine-producing cells showed a strong inverse correlation with the relative abundance of the largest clone in ATL cells suggesting that the putative ATL cells were cytokine non-producing and that the ‘ATL-like’ cells were the primary cytokine producers. These findings were confirmed by RNAseq with cytokine mRNA expression in ATL cells in patients with ATL (confirmed to be composed of both putative ATL and ‘ATL-like’ cells by TCR analysis) significantly lower compared to ‘ATL-like’ cells in patients with non-malignant HTLV-1 infection (confirmed to be composed of hundreds of non-dominant clones by TCR analysis). A significant inverse correlation between the relative abundance of the largest clone and cytokine mRNA expression was also confirmed. Finally, ‘ATL-like’ cells produced less pro- and more anti-inflammatory cytokines than non ‘ATL-like’ CD4+ cells (which are predominantly HTLV uninfected). In summary, HTLV-1 infection of CD4+ T cells is associated with a change in cytokine producing capacity and dominant malignant clonal growth is associated with loss of cytokine producing capacity. Non-dominant clones with ‘ATL-like’ cells contribute to plasma cytokine profile in patients with non-malignant HTLV-1 infection and are also present in patient with ATL.
Celebrity-endorsed e-cigarette brand Instagram advertisements: Effects on young adults’ attitudes towards e-cigarettes and smoking intentions

Celebrities endorsing e-cigarette brands on social media may exert a strong influence on e-cigarette uptake. Using a between-subject experiment, this study examines the effects of endorser type (celebrities, non-celebrities and products only) in e-cigarette brand Instagram advertisements on e-cigarette attitudes and smoking intentions. Results showed that celebrity endorsers significantly increased positive attitudes towards e-cigarettes and smoking intentions, compared to non-celebrities or products only. Celebrity endorsers also rated significantly higher on trustworthiness, expertise, goodwill and attractiveness, compared to non-celebrities. Additionally, identification, social comparison, health consciousness and social networking site use moderated between endorser type and key dependent measures. Implications for e-cigarette marketing regulation are discussed.
Dopaminergic and behavioural changes in a loss‐of‐imprinting model of Cdkn1c

The imprinted gene Cdkn1c is expressed exclusively from the maternally inherited allele as a consequences of epigenetic regulation. Cdkn1c exemplifies many of the functional characteristics of imprinted genes, playing a role in foetal growth and placental development. However, Cdkn1c also plays an important role in the brain, being key to the appropriate proliferation and differentiation of midbrain dopaminergic neurons. Using a transgenic model (Cdkn1cBACx1) with a twofold elevation in Cdkn1c expression that mimics loss‐of‐imprinting, we show that increased expression of Cdkn1c in the brain gives rise to neurobiological and behavioural changes indicative of a functionally altered dopaminergic system. Cdkn1cBACX1 mice displayed altered expression of dopamine system‐related genes, increased tyrosine hydroxylase (Th) staining and increased tissue content of dopamine in the striatum. In addition, Cdkn1cBACx1 animals were hypersensitive to amphetamine as showed by c‐fos expression in the nucleus accumbens. Cdkn1cBACX1 mice had significant changes in behaviours that are dependent on the mesolimbic dopaminergic system. Specifically, increased motivation for palatable food stuffs, as indexed on a progressive ratio task. In addition, Cdkn1cBACX1 mice displayed enhanced social dominance. These data show, for the first time, the consequence of elevated Cdkn1c expression on dopamine‐related behaviours highlighting the importance of correct dosage of this imprinted gene in the brain. This work has significant relevance for deepening our understanding of the epigenetic factors that can shape neurobiology and behaviour.
Positive and Negative Affect Is Related to Experiencing Chest Pain During Exercise-Induced Myocardial Ischemia

Objective Silent myocardial ischemia is thought to be associated with worse cardiovascular outcomes due to a lack of perception of pain cues that initiate treatment seeking. Negative affect (NA) has been associated with increased pain reporting and positive affect (PA) with decreased pain reporting, but these psychological factors have not been examined within the context of myocardial ischemia. This study evaluated the associations between PA, NA, and chest pain reporting in patients with and without ischemia during exercise testing. Methods A total of 246 patients referred for myocardial perfusion single-photon emission computed tomography exercise stress testing completed the positive and negative affect schedule-expanded version, a measure of PA and NA. Presence of chest pain and myocardial ischemia were evaluated using standardized protocols. Results Logistic regression analyses revealed that for every 1-point increase in NA, there was a 13% higher chance for ischemic patients (odds ratio [OR] = 1.13; 95% confidence interval [CI] = 1.02 to 1.26) and an 11% higher chance in nonischemic patients (OR = 1.11; 95% CI = 1.03 to 1.19) to report chest pain. A significant interaction of PA and NA on chest pain reporting (&bgr; = 0.02; 95% CI = 0.002 to 0.031) was also observed; nonischemic patients with high NA and PA reported more chest pain (57%) versus patients with low NA and low PA (13%), with high NA and low PA (17%), and with high PA and low NA (7%). Conclusions Patients who experience higher NA are more likely to report experiencing chest pain. In patients without ischemia, high NA and PA was also associated with a higher likelihood of reporting chest pain. Results suggest that high levels of PA as well as NA may increase the experience and/or reporting of chest pain.
Shared and Unique Patterns of Embryo Development in Extremophile Poeciliids

Background Closely related lineages of livebearing fishes have independently adapted to two extreme environmental factors: toxic hydrogen sulphide (H2S) and perpetual darkness. Previous work has demonstrated in adult specimens that fish from these extreme habitats convergently evolved drastically increased head and offspring size, while cave fish are further characterized by reduced pigmentation and eye size. Here, we traced the development of these (and other) divergent traits in embryos of Poecilia mexicana from benign surface habitats (“surface mollies”) and a sulphidic cave (“cave mollies”), as well as in embryos of the sister taxon, Poecilia sulphuraria from a sulphidic surface spring (“sulphur mollies”). We asked at which points during development changes in the timing of the involved processes (i.e., heterochrony) would be detectible. Methods and Results Data were extracted from digital photographs taken of representative embryos for each stage of development and each type of molly. Embryo mass decreased in convergent fashion, but we found patterns of embryonic fat content and ovum/embryo diameter to be divergent among all three types of mollies. The intensity of yellow colouration of the yolk (a proxy for carotenoid content) was significantly lower in cave mollies throughout development. Moreover, while relative head size decreased through development in surface mollies, it increased in both types of extremophile mollies, and eye growth was arrested in mid-stage embryos of cave mollies but not in surface or sulphur mollies. Conclusion Our results clearly demonstrate that even among sister taxa convergence in phenotypic traits is not always achieved by the same processes during embryo development. Furthermore, teleost development is crucially dependent on sufficient carotenoid stores in the yolk, and so we discuss how the apparent ability of cave mollies to overcome this carotenoid-dependency may represent another potential mechanism explaining the lack of gene flow between surface and cave mollies.
Characterization of Head Transcriptome and Analysis of Gene Expression Involved in Caste Differentiation and Aggression in Odontotermes formosanus (Shiraki)

Background The subterranean termite Odontotermes formosanus (Shiraki) is a serious insect pest of trees and dams in China. To date, very little is known about genomic or transcriptomic data for caste differentiation and aggression in O. formosanus. Hence, studies on transcriptome and gene expression profiling are helpful to better understand molecular basis underlying caste differentiation and aggressive behavior in O. formosanus. Methodology and Principal Findings Using the Illumina sequencing, we obtained more than 57 million sequencing reads derived from the heads of O. formosanus. These reads were assembled into 116,885 unique sequences (mean size = 536 bp). Of the unigenes, 30,646 (26.22%) had significant similarity with proteins in the NCBI nonredundant protein database and Swiss-Prot database (E-value<10−5). Of these annotated unigenes, 10,409 and 9,009 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. In total, 19,611 (25.52%) unigenes were mapped onto 242 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). A total of 11,661 simple sequence repeats (SSRs) were predicted from the current transcriptome database. Moreover, we detected seven putative genes involved in caste differentiation and six putative genes involved in aggression. The qPCR analysis showed that there were significant differences in the expression levels of the three putative genes hexamerin 2, β-glycosidase and bicaudal D involved in caste differentiation and one putative gene Cyp6a20 involved in aggression among workers, soldiers and larvae of O. formosanus. Conclusions To our knowledge, this is the first study to characterize the complete head transcriptome of a higher fungus-cultivating termite using high-throughput sequencing. Our study has provided the comprehensive sequence resources available for elucidating molecular basis underlying caste differentiation and aggressive behavior in O. formosanus.
A test of basic psychological needs theory in young soccer players: time‐lagged design at the individual and team levels

Within the framework of basic psychological needs theory (Deci & Ryan, 2000), multilevel structural equation modeling (MSEM) with a time‐lagged design was used to test a mediation model examining the relationship between perceptions of coaches’ interpersonal styles (autonomy supportive and controlling), athletes’ basic psychological needs (satisfaction and thwarting), and indicators of well‐being (subjective vitality) and ill‐being (burnout), estimating separately between and within effects. The participants were 597 Spanish male soccer players aged between 11 and 14 years (M = 12.57, SD = 0.54) from 40 teams who completed a questionnaire package at two time points in a competitive season. Results revealed that at the individual level, athletes’ perceptions of autonomy support positively predicted athletes’ need satisfaction (autonomy, competence, and relatedness), whereas athletes’ perceptions of controlling style positively predicted athletes’ need thwarting (autonomy, competence, and relatedness). In turn, all three athletes’ need satisfaction dimensions predicted athletes’ subjective vitality and burnout (positively and negatively, respectively), whereas competence thwarting negatively predicted subjective vitality and competence and relatedness positively predicted burnout. At the team level, team perceptions of autonomy supportive style positively predicted team autonomy and relatedness satisfaction. Mediation effects only appeared at the individual level.
A Model for Analyzing the Performance of Wireless Multi-Hop Networks using a Contention-based CSMA/CA Strategy

Multi-hop networks are a low-setup-cost solution for enlarging an area of network coverage through multi-hop routing. Carrier sense multiple access with collision avoidance (CSMA/CA) is frequently used in multi-hop networks. Multi-hop networks face multiple problems, such as a rise in contention for the medium, and packet loss under heavy-load, saturated conditions, which consumes more bandwidth due to re-transmissions. The number of re-transmissions carried out in a multi-hop network plays a major role in the achievable quality of service (QoS). This paper presents a statistical, analytical model for the end-to-end delay of contention-based medium access control (MAC) strategies. These strategies schedule a packet before performing the back-off contention for both differentiated heterogeneous data and homogeneous data under saturation conditions. The analytical model is an application of Markov chain theory and queuing theory. The M/M/1 model is used to derive access queue waiting times, and an absorbing Markov chain is used to determine the expected number of re-transmissions in a multi-hop scenario. This is then used to calculate the expected end-to-end delay. The prediction by the proposed model is compared to the simulation results, and shows close correlation for the different test cases with different arrival rates.