Miracle-dz/UniFAR-FTUs huggingface dataset:
A cell type-specific expression signature predicts haploinsufficient autism-susceptibility genes

Recent studies have identified many genes with rare de novo mutations in autism, but a limited number of these have been conclusively established as disease-susceptibility genes due to lack of recurrence and confounding background mutations. Such extreme genetic heterogeneity severely limits recurrence-based statistical power even in studies with a large sample size. In addition, the cellular contexts in which these genomic lesions confer disease risks remain poorly understood. Here we investigate the use of cell-type specific expression profiles to differentiate mutations in autism patients or unaffected siblings. Using 24 distinct cell types isolated from the mouse central nervous system, we identified an expression signature shared by genes with likely gene disrupting (LGD) mutations detected by exome-sequencing in autism cases. The signature reflects haploinsufficiency of risk genes enriched in transcriptional and post-transcriptional regulators, with the strongest positive associations with specific types of neurons in different brain regions, including cortical neurons, cerebellar granule cells, and striatal medium spiny neurons. Based on this signature, we assigned a D score to all human genes to prioritize candidate autism-susceptibility genes. When applied to genes with only a single LGD mutation in cases, the D score achieved a precision of 40% as compared to the 15% baseline with a minimal loss in sensitivity. Further improvement was made by combining D score and mutation intolerance metrics from ExAC which were derived from orthogonal data sources. The ensemble model achieved precision of 60% and predicted 117 high-priority candidates. These prioritized lists can facilitate identification of additional autism-susceptibility genes.
Behavioural Vigilance in Schizophrenia

Background Despite 30 years of research, some surprisingly fundamental gaps remain in our understanding of schizophrenic input dysfunctions. Method In a provisional test of a ‘hyperattention’ hypothesis, schizophrenic patients and control subjects performed a behavioural test that was adapted from a paradigm originally developed for characterising vigilance or sustained attention in animals. On this computerised operant testing procedure, subjects discriminated between signals of various salience and non-signal presentations. Hits and correct rejections resulted in monetary rewards while misses and false alarms entailed monetary costs. Results Data from in-patients with schizophrenia and age, education and gender-matched controls support hypotheses not only about hyperattentional dysfunctions in schizophrenia with respect to overall signal detectability but also in terms of resistance to the vigilance decrement that normally occurs over trials. Conclusions The theoretical importance of impairments of this sort are discussed with respect to the cognitive and perceptual consequences of hypervigilance and ‘input dysfunction’.
Bayesian analysis improves pulse secretion characterization in reproductive hormones

ABSTRACT Pulsatile secretion of hormones in the hypothalamic-pituitary-gonadal axis is critical for normal functioning of the reproductive system. Thus, appropriate characterization of pulsatile secretion is important for identifying the (patho)physiology of reproductive conditions. Existing analysis methods often fail to adequately characterize pulsatility, especially when the signal-to-noise ratio is low. Newer Bayesian analysis methods for pulsatile hormones may offer improved secretion quantification in noisier data. The objective of this study was to extensively validate a Bayesian analysis approach for analyzing pulsatile hormones in settings that occur in reproductive studies. An investigative approach was chosen so that clinical research teams will have the knowledge to adopt this newer analysis approach in practice. Three experimental conditions were investigated: luteinizing hormone (LH) profiles in ovariectomized ewes (N=6; high signal-to-noise setting), LH profiles in young ovulating women (N=12; lower signal-to-noise setting), and computer-simulated scenarios (N=200). For each experimental condition, differences in luteinizing hormone pulse outcomes (pulse number, average pulse size, hormone half-life, and non-pulse secretion) were obtained and compared between non-Bayesian and Bayesian analysis pulse analysis methods. For the ewe model, the estimated pulse number and mass were comparable between the Bayesian and non-Bayesian analyses. For the human model, only 4 of 12 subjects could be fitted with the non-Bayesian analysis compared to 10 of the 12 with Bayesian analysis. In general, the Bayesian analysis had lower false negative rates (<4.5%) compared to the non-Bayesian analysis while maintaining a high specificity (false positive rate <2.5%). The Bayesian analysis also had less biased estimates of all pulse features. In conclusion, Bayesian analysis provides a more reliable pulse characterization in low signal-to-noise experiments and should be used for the analysis of reproductive physiology studies of pulsatile hormones. Software is available at www.github. com/BayesPulse. Abbreviations: LH: luteinizing hormone; FSH: follicle stimulating hormone; GnRH: gonadotropin-releasing hormone; FP: false positive; FN: false negative
Response to Kawada: Sleep habits and non‐alcoholic fatty liver disease: Risk assessment by adjusting confounders

We thank Tomoyuki Kawada for his comments in response to our recent article in the Journal of Diabetes entitled “Short sleep duration and longer daytime napping are associated with non-alcoholic fatty liver disease in Chinese adults,” in which we assessed the association between sleep habit and nonalcoholic fatty liver disease (NAFLD). Kawada commented on the conclusions and confounding factors in the article. We appreciate the opportunity to discuss these issues. According to current categories of nightly sleep duration (≤6.0, 6.1–7, 7.1–8, 8.1–9, and >9 h [reference group]), shorter sleep durations tend to be associated with higher risk of prevalent NAFLD. In addition, when fatty liver index (FLI)-diagnosed NAFLD (i.e. FLI ≥60) was used as the outcome, an increased risk of prevalent NAFLD was only associated with 6.1–7 and <6 h sleep duration. We did not specify the “short” nightly sleep duration that increased the risk of NAFLD in the study’s conclusion because a different study population structure could generate different nightly sleep patterns, including sleep duration. Therefore, considering the effects of ethnicity and population structure on sleep patterns, whether there is a negative correlation between sleep duration and prevalent NAFLD needs to be investigated in different populations. Previous studies have provided some insight into the potential roles of inflammatory cytokines, such as interleukin (IL)-6, enhanced by sleep disturbance, in the pathogenesis of NAFLD. However, we did not provide any data regarding IL-6 in our study, but we do speculate that inflammatory cytokines may be an intermediate factor associated with sleep duration and NAFLD. We agree with Kawada that it is important to consider ethnicity when evaluating the risk factors for NAFLD. The population in our study was confined to community-based middle-aged and elderly Chinese with similar customs and lifestyles. As noted by Kawada, the relationship between NAFLD and type 2 diabetes mellitus (T2DM) is bidirectional. These conditions share insulin resistance as a common pathophysiological mechanism. A metaanalysis has indicated an association between sleep duration and diabetes. To reduce the effect of diabetes, we conducted stratified analysis according to insulin resistance status (yes/no). However, the results showed that the associations between short sleep durations and NAFLD were generally similar across subgroups. We agree with Kawada that there may be a synergistic effect between prolonged napping and short nightly sleep duration. Specifically, the association between daytime napping and NAFLD remained after adjustment for nightly sleep duration and other covariates, suggesting an independent contribution of daytime napping to NAFLD, as reported in our article. In conclusion, given the existence of confounding factors, future prospective or mechanistic studies are warranted to elucidate the associations of nightly sleep duration and daytime napping with NAFLD.
A systematic analysis of nature inspired workflow scheduling algorithm in heterogeneous cloud environment

Cloud computing is the new form of distributed system to store and compute the large amount of data and solve complex computational problems. The size of data and computational complexity is increasing day by day. It leads us to find out an efficient solution to scheduled and dispose them properly in large cloud computing environment. The major demand to analyze large scientific issues is Workflow. In workflow scheduling, the problem is divided into the smaller dependent tasks, solve individually in either sequential or parallel mode and finally combined to leads the desired output. Workflow scheduling is NPC (NP Complete) problem, which attracts researchers to explore the solution. In this paper, we propose a extensive and systematic analysis of nature inspired workflow scheduling algorithms in heterogeneous cloud environment. Moreover, it gives a classification of nature inspired algorithms and highlights their aim, properties and their limitations. Finally, we desire to furnish a comprehensive and complete perceptive of current nature inspired literature and assist researchers by equipping them an observation into future trends and unsolved issues.
Herpes Simplex Virus and Langerhans Cell Histiocytosis.

Background and objective Langerhans cell histiocytosis (LCH) is a rare histiocytic proliferative disorder of unknown etiology and mainly affects young children. The histological feature is granuloma-like proliferation of langerhans-type dendritic cells. Although the possible role of viruses such as Epstein-Barr virus (EBV, Human Herpes virus -4), Human Herpes virus-6 (HHV-6), Herpes Simplex virus (HSV) types 1 and 2 and Cytomegalovirus (CMV, Human Herpes virus-5) is suggested in the pathogenesis of LCH by some investigators, its exact pathophysiology has not been cleared yet. In this study, we investigated the presence of HSV types 1 and 2 in Iranian children with LCH. Methods In this retrospective study, we investigated the prevalence of presence of HSV types 1 and 2 (in 30 patients with LCH), using paraffin-embedded tissue samples and 30 age and tissue-matched controls (operated for reasons other than infectious diseases) from the Department of Pediatric Pathology, Tehran, Iran, by nested Polymerase Chain reaction method. No ethical issues arose in the study, because only the pathology reports were reviewed and patients were anonymous. Results We failed to find HSV types 1 and 2 DNA in any of the 30 patients with LCH or the control group. Conclusion According to our findings, HSV types 1 and 2 do not appear to have any etiologic role in the pathogenesis of LCH in Iranian children. These results are in accordance with previous investigations with negative findings.
Gene Interaction in DNA Microarray Data Is Decomposed by Information Geometric Measure

MOTIVATION Given the vast amount of gene expression data, it is essential to develop a simple and reliable method of investigating the fine structure of gene interaction. We show how an information geometric measure achieves this. RESULTS We introduce an information geometric measure of binary random vectors and show how this measure reveals the fine structure of gene interaction. In particular, we propose an iterative procedure by using this measure (called IPIG). The procedure finds higher-order dependencies which may underlie the interaction between two genes of interest. To demonstrate the method, we investigate the interaction between the two genes of interest in the data from human acute lymphoblastic leukemia cells. The method successfully discovered biologically known findings and also selected other genes as hidden causes that constitute the interaction. AVAILABILITY Softwares are currently not available but are possibly made available in future at http://www.mns. brain.riken. go.jp/~nakahara/DNA_pub. html where all the related information is also linked.
Circular markers for camera pose estimation

This papers presents a new system using circular markers to estimate the pose of a camera. Contrary to most markersbased systems using square markers, we advocate the use of circular markers, as we believe that they are easier to detect and provide a pose estimate that is more robust to noise. Unlike existing systems using circular markers, our method computes the exact pose from one single circular marker, and do not need specific points being explicitly shown on the marker (like center, or axes orientation). Indeed, the center and orientation is encoded directly in the markers code. We can thus use the entire marker surface for the code design. After solving the back projection problem for one conic correspondence, we end up with two possible poses. We show how to find the markers code, rotation and final pose in one single step, by using a pyramidal cross-correlation optimizer. The marker tracker runs at 100 frames/second on a desktop PC and 30 frames/second on a hand-held UMPC.
Phloem Girdling of Norway Spruce Alters Quantity and Quality of Wood Formation in Roots Particularly Under Drought

Carbon (C) availability plays an essential role in tree growth and wood formation. We evaluated the hypothesis that a decrease in C availability (i) triggers mobilization of C reserves in the coarse roots of Picea abies to maintain growth and (ii) causes modification of wood structure notably under drought. The 6-year-old saplings were subjected to two levels of soil moisture (watered versus drought conditions) and root C status was manipulated by physically blocking phloem transport in the stem at three girdling dates (GDs). Stem girdling was done before the onset of bud break [day of the year (doy) 77], during vigorous aboveground shoot and radial stem growth (GD doy 138), and after cessation of shoot growth (GD doy 190). The effect of blockage of C transport on root growth, root phenology, and wood anatomical traits [cell lumen diameter (CLD) and cell wall thickness (CWT)] in earlywood (EW) and latewood (LW) was determined. To evaluate changes in belowground C status caused by girdling, non-structural carbohydrates (soluble sugars and starch) in coarse roots were determined at the time of girdling and after the growing season. Although fine root mass significantly decreased in response to blockage of phloem C transport, the phenology of root elongation growth was not affected. Surprisingly, radial root growth and CLD of EW tracheids in coarse roots were strikingly increased in drought-stressed trees, when girdling occurred before bud break or during aboveground stem growth. In watered trees, the growth response to girdling was less distinct, but the CWT of EW significantly increased. Starch reserves in the roots of girdled trees significantly decreased in both soil moisture treatments and at all GDs. We conclude that (i) radial growth and wood development in coarse roots of P. abies saplings are not only dependent on current photosynthates, and (ii) blockage of phloem transport induces physiological changes that outweigh drought effects imposed on root cambial activity and cell differentiation.
Associations between frequency of food shopping at different store types and diet and weight outcomes: findings from the NEWPATH study

Abstract Objective The present study aimed to: (i) examine associations between food store patronage and diet and weight-related outcomes; and (ii) explore consumer motivations for visiting different types of food store. Design A stratified probability sample of residents completed household and individual-level surveys in 2009/2010 on food purchasing patterns and motivations, dietary intake, waist circumference (WC), weight and height. Diet quality was calculated using the Healthy Eating Index for Canada from a subset of participants (n 1362). Generalized estimating equations were created in 2015 to examine how frequency of patronizing different types of food store was associated with diet quality, intake of fruits and vegetable, mean intake of energy (kcal) sodium and saturated fat, WC and BMI. Setting Three mid-sized urban municipalities in Ontario, Canada. Subjects A representative sample of residents (n 4574). Results Participants who shopped frequently at food co-ops had significantly better diet quality (β=5·3; 99 % CI 0·3, 10·2) than those who did not. BMI and WC were significantly lower among those who frequently shopped at specialty shops (BMI, β=−2·1; 99 % CI −3·0, −1·1; WC, β=−4·8; 99 % CI −7·0, −2·5) and farmers’ markets (BMI, β=−1·4; 99 % CI −2·3, −0·5; WC, β=−3·8; 99 % CI −6·0, −1·6) compared with those who did not. Relative importance of reasons for food outlet selection differed by large (price, food quality) v. small (proximity, convenient hours) shopping trip and by outlet type. Conclusions Findings contribute to our understanding of food store selection and have implications for potentially relevant retail food intervention settings.
Modeling and Predicting Learning Behavior in MOOCs

Massive Open Online Courses (MOOCs), which collect complete records of all student interactions in an online learning environment, offer us an unprecedented opportunity to analyze students' learning behavior at a very fine granularity than ever before. Using dataset from xuetangX, one of the largest MOOCs from China, we analyze key factors that influence students' engagement in MOOCs and study to what extent we could infer a student's learning effectiveness. We observe significant behavioral heterogeneity in students' course selection as well as their learning patterns. For example, students who exert higher effort and ask more questions are not necessarily more likely to get certificates. Additionally, the probability that a student obtains the course certificate increases dramatically (3 x higher) when she has one or more "certificate friends". Moreover, we develop a unified model to predict students' learning effectiveness, by incorporating user demographics, forum activities, and learning behavior. We demonstrate that the proposed model significantly outperforms (+2.03-9.03% by F1-score) several alternative methods in predicting students' performance on assignments and course certificates. The model is flexible and can be applied to various settings. For example, we are deploying a new feature into xuetangX to help teachers dynamically optimize the teaching process.
Recent applications of ultra performance liquid chromatography (UPLC) in pharmaceutical analysis

Ultra Performance Liquid Chromatography(UPLC) is a relatively new technique providing new possibili- ties in liquid chromatography,especially concerning decrease of time and solvent consumption.The ultra-fast sepa- rations were achieved thanks to ACQUITY BEH columns packed with 1. 7μm particles.This present paper reviewed recent applications of UPLC in pharmaceutical analysis.
Efecto de las fuerzas oclusales sobre el periodonto analizado por elementos finitos / Effect of occlusal forces over periodontium analyzed through finite elements

RESUMEN. Antecedentes: Los efectos biomecanicos de las cargas oclusales en los dientes se han evaluado tanto en el apretamiento como en la masticacion. Un efecto nocivo de la sobrecarga oclusal es la fractura dental, que se ha analizado mediante metodos como pruebas electricas de resistencia, fotoelasticidad y elementos finitos. Pese a que existen numerosos estudios que relacionan la oclusion con la enfermedad periodontal, aun no se ha sido estudiado suficientemente el papel biomecanico de las fuerzas sobre el periodonto. Objetivo: Evaluar el efecto que tienen las fuerzas oclusales normales, nocivas y fisiologicas en el periodonto normal por medio de elementos finitos. Metodos: El analisis de elementos finitos tuvo los siguientes pasos: especificacion de la geometria, tipo de elemento y propiedades del material, aplicacion de magnitudes de fuerzas en unidades Newton (de 150 N a 675 N con incrementos de 25 N) sobre el eje longitudinal del diente. Resultados: Se encontro una diferencia significativa entre la distribucion de esfuerzos en el ligamento periodontal, la dentina y hueso cortical de acuerdo con el tipo de diente (p = 0,000), pero no hubo una diferencia significativa en el hueso esponjoso (p = 0,166). Conclusion: la concentracion de estres se localizo en los tres dientes, incisivo, premolar y molar, en la zona cervical vestibular, donde se evidencio la mayor distribucion de esfuerzos en todas las magnitudes de fuerza aplicada.
Design and implementation of a novel software-defined wireless sensor network

Software defined wireless sensing network (SDWSN) has gained wide attention on account of overcoming the storage and computational restrictions. SDWSN, an ultramodern architecture, still has crippling roadblocks. One of the toughest aspects is energy confinement and imbalanced consumption. In this paper, we propose an energy efficient algorithm based on energy shell and dynamically adjusting communication radius. In our algorithm, nodes in higher energy shells have higher priority to relay data. Having several candidate nodes to relay data, nodes prefer to relay data through the nodes with the highest RSSI. Compared to most other algorithms the algorithm we are proposing performs better in reducing energy expenditure and balancing energy consumption.
DCE-MRI Pharmacokinetic-Based Phenotyping of Invasive Ductal Carcinoma: A Radiomic Study for Prediction of Histological Outcomes

Breast cancer is a disease affecting an increasing number of women worldwide. Several efforts have been made in the last years to identify imaging biomarker and to develop noninvasive diagnostic tools for breast tumor characterization and monitoring, which could help in patients' stratification, outcome prediction, and treatment personalization. In particular, radiomic approaches have paved the way to the study of the cancer imaging phenotypes. In this work, a group of 49 patients with diagnosis of invasive ductal carcinoma was studied. The purpose of this study was to select radiomic features extracted from a DCE-MRI pharmacokinetic protocol, including quantitative maps of ktrans, kep, ve, iAUC, and R1 and to construct predictive models for the discrimination of molecular receptor status (ER+/ER−, PR+/PR−, and HER2+/HER2−), triple negative (TN)/non-triple negative (NTN), ki67 levels, and tumor grade. A total of 163 features were obtained and, after feature set reduction step, followed by feature selection and prediction performance estimations, the predictive model coefficients were computed for each classification task. The AUC values obtained were 0.826 ± 0.006 for ER+/ER−, 0.875 ± 0.009 for PR+/PR−, 0.838 ± 0.006 for HER2+/HER2−, 0.876 ± 0.007 for TN/NTN, 0.811 ± 0.005 for ki67+/ki67−, and 0.895 ± 0.006 for lowGrade/highGrade. In conclusion, DCE-MRI pharmacokinetic-based phenotyping shows promising for discrimination of the histological outcomes.