Miracle-dz/UniFAR-FTUs huggingface dataset:
2p24.2 (rs7552) is a susceptibility locus for nonsyndromic cleft lip with or without cleft palate in the Brazilian population

The population of Brazil is highly admixed, with each individual showing variable levels of Amerindian, European and African ancestry, which may interfere in the genetic susceptibility of known risk loci to nonsyndromic cleft lip with or without cleft palate (NSCL±P). Here, we investigated 5 reported genome‐wide loci for NSCL±P in an ancestry‐structured case‐control study containing 1697 Brazilian participants (831 NSCL±P and 866 healthy controls). SNPs rs7552 in 2q24.2, rs8049367 in 16p13.3, rs1880646, rs7406226, rs9891446 in 17p13, rs1588366 in 17q23.2 and rs73039426 in 19q13.11 were genotyped using TaqMan allelic discrimination assays and genomic ancestry was estimated using a panel of 40 biallelic short insertion/deletion polymorphic markers informative of the Brazilian population. Logistic regression analysis of the single‐markers revealed rs7552 in 2p24.2 as a susceptibility risk marker for NSCL±P, yielding an odds ratio (OR) of 1.71 (95% confidence interval (CI): 1.31‐2.24, P = 9 × 10−6) in the homozygous state. Several SNP‐SNP interactions containing rs7552 reached significance after adjustment for multiple tests (both Bonferroni assumption and 1000 permutation test), with the most significant interaction involving the 3‐loci among rs7552, rs9891446 and rs73039426 (P = 6.1 × 10−9 and p1000 permutation = 0.001). Our study is the first to support the association of rs7552 in 2p24.2 with NSCL±P in the highly admixed Brazilian population.
Interconnect networks for memristor crossbar

As the down-scaling of CMOS technology reaches inherent physical device limits, major challenges arise such as reliability, power consumption, etc. Novel technologies are under investigation as an alternative for next-generation VLSI circuits. Memristor is one of the promising candidates due to its scalability, non-volatility, practically zero leakage, high integration density, etc. Several applications have been proposed for the memristor crossbar architecture; examples are neuromophic, memories and logic circuits. This paper proposes a generic and flexible interconnect network for memristor-based logic circuits within a crossbar architecture. The scheme is based on the use of reserved memristors (within the crossbar) and the execution of copy operations from and/or to the reserved memristors; it can be applied both at intra-tile as well as inter-tile level, where a tile is a basic block performing a simple logic function. To illustrate the potential of the proposed scheme, two intra-tile and one inter-tile case study are evaluated using SPICE simulation, and their incurred costs are analyzed; the case studies consist of interconnect networks for (a) a specific function within a tile (i.e., the matrix transpose), (b) generic logic functions within a tile, and (c) communication between tiles.
Identification and Characterization of C-type Lectins in Ostrinia furnacalis (Lepidoptera: Pyralidae)

Abstract C-type lectins (CTLs) are a large family of calcium-dependent carbohydrate-binding proteins. They function primarily in cell adhesion and immunity by recognizing various glycoconjugates. We identified 14 transcripts encoding proteins with one or two CTL domains from the transcriptome from Asian corn borer, Ostrinia furnacalis (Guenée; Lepidoptera: Pyralidae). Among them, five (OfCTL-S1 through S5) only contain one CTL domain, the remaining nine (OfIML-1 through 9) have two tandem CTL domains. Five CTL-Ss and six OfIMLs have a signal peptide are likely extracellular while another two OfIMLs might be cytoplasmic. Phylogenetic analysis indicated that OfCTL-Ss had 1:1 orthologs in Lepidoptera, Diptera, Coleoptera and Hymenoptera species, but OfIMLs only clustered with immulectins (IMLs) from Lepidopteran. Structural modeling revealed that the 22 CTL domains adopt a similar double-loop fold consisting of β-sheets and α-helices. The key residues for calcium-dependent or independent binding of specific carbohydrates by CTL domains were predicted with homology modeling. Expression profiles assay showed distinct expression pattern of 14 CTLs: the expression and induction were related to the developmental stages and infected microorganisms. Overall, our work including the gene identification, sequence alignment, phylogenetic analysis, structural modeling, and expression profile assay would provide a valuable basis for the further functional studies of O. furnacalis CTLs.
PopNet: A Markov Clustering Approach to Study Population Genetic Structure

With the advent of low cost, high-throughput genome sequencing technology, population genomic data sets are being generated for hundreds of species of pathogenic, industrial, and agricultural importance. The challenge is how best to analyze and visually display these complex data sets to yield intuitive representations capable of capturing complex evolutionary relationships. Here we present PopNet, a novel computational method that identifies regions of shared ancestry in the chromosomes of related strains through clustering patterns of genetic variation. These relationships are subsequently visualized within a network by a novel implementation of chromosome painting. We apply PopNet to three diverse populations that feature differential rates of recombination and demonstrate its ability to capture evolutionary relationships as well as associate traits to specific loci. Compared with existing tools, PopNet provides substantial advances by both removing the need to predefine a single reference genome that can bias interpretation of population structure, as well as its ability to visualize multiple evolutionary relationships, such as recombination events and shared ancestry, across hundreds of strains.
Local and global convergence of on-line learning.

We study the performance of an on-line algorithm for learning di-chotomies, with a dynamical error-dependent learning rate. The asymp-totic scaling form of the solution to the associated Markov equations is derived, assuming certain smoothness conditions. We show that the system converges to the optimal solution and the generalization error vanishes inversely with the number of examples. The system is capable of escaping from local minima, and adapts rapidly to shifts in the target function. The general theory is illustrated for the perceptron and committee machine. Much of learning theory has analyzed the paradigm of batch learning, in which the learner has free access to a xed set of examples stored in memory. This paradigm leads naturally to an equilibrium statistical mechanical approach based on an energy function that is the learner's error on the training set. The theoretical advantage of this equilibrium formulation is that the learner's performance as a function of the number of examples can be studied without addressing the complex dynamic aspects of learning. The disadvantage is that it gives no information about the learner's performance as a function of training time. Many learning phenomena, especially biological ones, t more naturally in an on-line learning paradigm, rather than a batch one. At each time step, the learner receives a single new example drawn at random, and is unable to store previous examples in memory (see e.g. 1]{{4]). In the simplest cases, the change in the learner depends only on the new example and its current state. Hence training time is proportional to the number of examples. Interesting theoretical results have been derived for on-line learning of functions that are smooth functions of the system's parameters, using stochastic approximation theoryy5] and statistical mechanical methodss1]{{4]. In this Letter , we focus on learning of dichotomies, to which most of this existing theory 1
Modification of oxide inclusions present in aluminum-killed low carbon steel by addition of calcium

The increasing demand in recent years for high-quality steel products has led to the continuous improvement of steelmaking practices. There is a special interest in the control of non-metallic inclusions due to their harmful effect on the subsequent stages and their great influence on the properties of the final product. Through the control of the amount, size and chemical composition of the inclusions it is possible to obtain a final product of good quality. The control of the formation of non-metallic inclusions and the identification of their constituent phases are of extreme importance for the obtaining of clean steels. In this work, samples collected in a steelmaking process are analyzed and it is demonstrated that by comparing the total calcium and oxygen contents in the steel, it is possible to have an overview of the types of oxide inclusions present.
Investigation of cardiac fibroblasts using myocardial slices

Abstract Aims Cardiac fibroblasts (CFs) are considered the principal regulators of cardiac fibrosis. Factors that influence CF activity are difficult to determine. When isolated and cultured in vitro, CFs undergo rapid phenotypic changes including increased expression of α-SMA. Here we describe a new model to study CFs and their response to pharmacological and mechanical stimuli using in vitro cultured mouse, dog and human myocardial slices. Methods and results Unloading of myocardial slices induced CF proliferation without α-SMA expression up to 7 days in culture. CFs migrating onto the culture plastic support or cultured on glass expressed αSMA within 3 days. The cells on the slice remained αSMA(−) despite transforming growth factor-β (20 ng/ml) or angiotensin II (200 µM) stimulation. When diastolic load was applied to myocardial slices using A-shaped stretchers, CF proliferation was significantly prevented at Days 3 and 7 (P < 0.001). Conclusions Myocardial slices allow the study of CFs in a multicellular environment and may be used to effectively study mechanisms of cardiac fibrosis and potential targets.
The Impact of Stress at Different Life Stages on Physical Health and the Buffering Effects of Maternal Sensitivity

Objective: Many studies indicate that early life stress leads to negative health outcomes in adulthood, and some suggest that high-quality parenting might buffer these effects. Most prior research, however, has relied on cross-sectional retrospective reports of stress and parenting. Our study tests how coder-rated stress and parenting quality assessed at different life stages predict adult health outcomes in a prospective, longitudinal study. Method: Participants were 163 individuals in the Minnesota Longitudinal Study of Risk and Adaptation studied since birth. Physical health was assessed at age 32 with body mass index, self-reports of symptoms and illnesses experienced, and self-ratings of overall physical health. Stress was assessed by coder-rated interviews involving participants or their mothers at 16 time points partitioned into 5 life stages: early childhood, middle childhood, adolescence, young adulthood, and at age 32 (when health was assessed). Parenting quality was measured by coder ratings of each mother’s provision of sensitive, responsive support at 7 time points between birth and age 13. Results: Early childhood, adolescent, and concurrent stress predicted adult health outcomes at age 32. Early childhood and adolescent stress, and adolescent and concurrent stress, both showed a “dual-risk” pattern, such that experiencing higher stress at both of these life stages predicted the worst health outcomes. Higher maternal sensitivity, however, buffered these deleterious effects. Conclusion: Our prospective data reveal that early childhood and adolescence are important developmental periods during which stress is influential for adult physical health. However, parenting interventions that promote greater sensitivity may help children in high-stress environments avoid negative adult health outcomes.
OR-PCA with dynamic feature selection for robust background subtraction

Background modeling and foreground object detection is the first step in visual surveillance system. The task becomes more difficult when the background scene contains significant variations, such as water surface, waving trees and sudden illumination conditions, etc. Recently, subspace learning model such as Robust Principal Component Analysis (RPCA) provides a very nice framework for separating the moving objects from the stationary scenes. However, due to its batch optimization process, high dimensional data should be processed. As a result, huge computational complexity and memory problems occur in traditional RPCA based approaches. In contrast, Online Robust PCA (OR-PCA) has the ability to process such large dimensional data via stochastic manners. OR-PCA processes one frame per time instance and updates the subspace basis accordingly when a new frame arrives. However, due to the lack of features, the sparse component of OR-PCA is not always ro-bust to handle various background modeling challenges. As a consequence, the system shows a very weak performance, which is not desirable for real applications. To handle these challenges, this paper presents a multi-feature based OR-PCA scheme. A multi-feature model is able to build a ro-bust low-rank background model of the scene. In addition, a very nice feature selection process is designed to dynamically select a useful set of features frame by frame, according to the weighted sum of total features. Experimental results on challenging datasets such as Wallflower, I2R and BMC 2012 show that the proposed scheme outperforms the state of the art approaches for the background subtraction task.
Epithelial chloride channel. Development of inhibitory ligands

Chloride channels are present in the majority of epithelial cells, where they mediate absorption or secretion of NaCl. Although the absorptive and secretory channels are well characterized in terms of their electrophysiological behavior, there is a lack of pharmacological ligands that can aid us in further functional and eventually molecular characterization. To obtain such ligands, we prepared membrane vesicles from bovine kidney cortex and apical membrane vesicles from trachea and found that they contain a chloride transport process that is electrically conductive. This conductance was reduced by preincubating the vesicles in media containing ATP or ATP-gamma-S, but not beta- methylene ATP, which suggests that the membranes contain a kinase that can close the channels. We then screened compounds derived from three classes: indanyloxyacetic acid (IAA), anthranilic acid (AA), and ethacrynic acid. We identified potent inhibitors from the IAA and the AA series. We tritiated IAA-94 and measured binding of this ligand to the kidney cortex membrane vesicles and found a high-affinity binding site whose dissociation constant (0.6 microM) was similar to the inhibition constant (1 microM). There was a good correlation between the inhibitory potency of several IAA derivatives and their efficacy in displacing [3H]IAA-94 from its binding site. Further, other chloride channel inhibitors, including AA derivatives, ethacrynic acid, bumetanide, and DIDS, also displaced the ligand from its binding site. A similar conductance was found in apical membrane vesicles from bovine trachea that was also inhibited by IAA-94 and AA-130B, but the inhibitory effects of these compounds were weaker than their effects on the renal cortex channel. The two drugs were also less potent in displacing [3H]IAA-94 from the tracheal binding site.
Alu exaptation enriches the human transcriptome by introducing new gene ends

ABSTRACT In mammals, transposable elements are largely silenced, but under fortuitous circumstances may be co-opted to play a functional role. Here, we show that when Alu elements are inserted within or nearby genes in sense orientation, they may contribute to the transcriptome diversity by forming new cleavage and polyadenylation sites. We mapped these new gene ends in human onto the Alu sequence and identified three hotspots of cleavage and polyadenylation site formation. Interestingly, the native Alu sequence does not contain any canonical polyadenylation signal. We therefore studied what evolutionary processes might explain the formation of these specific hotspots of novel gene ends. We show that two of the three hotspots might have emerged from mutational processes that turned sequences that resemble polyadenylation signals into full-blown canonical signals, whereas one hotspot is tightly linked to the process of Alu insertion into the genome. Overall, Alu elements may lie behind the formation of 302 new gene end variants, affecting a total of 243 genes. Intergenic Alu elements may elongate genes by creating a downstream cleavage site, intronic Alu elements may lead to gene variants which code for truncated proteins, and 3′UTR Alu elements may result in gene variants with alternative 3′UTR.
MOWAD: Automation-based Detection of Malicious OfferWall Android Apps

Misusing of advertising platforms by developers, which cause the emergence of malicious advertising fraud in Android apps, has become a serious and concrete threat for the users' interests. OfferWall is a new type of advertising, it offers some tasks for the users to complete. Malicious OfferWall apps are the apps induce or force users to complete the tasks within the OfferWall and it is a kind of advertising fraud. In this paper, we propose malicious OfferWall apps detector (MOWAD), a comprehensive and practical system, which contains four parts including pre-filtering, automatically running, classification and behavior analysis. The key idea of MOWAD is the analysis on malicious behavior of the apps, and it leveraged machine learning techniques. Results attained on real-world Android apps show that the MOWAD could distinguish malicious OfferWall apps with high accuracy (0.8915 of F1-score). Moreover, our experimental results show the chaos of misusing of advertising platform in Android apps.
Acute embryotoxic effects but no long‐term reproductive effects of in ovo methylmercury exposure in zebra finches (Taeniopygia guttata)

Mercury bioaccumulates in terrestrial ecosystems as methylmercury (MeHg), yet little is known about its effects on terrestrial organisms, including songbirds. The authors used a model songbird species, the zebra finch (Taeniopygia guttata), to assess short‐term embryotoxic effects of in ovo MeHg exposure on hatching success and posthatching growth and nestling survival, as well as longer‐term effects on mating behavior and reproduction. Egg treatment groups included a low‐MeHg dose of 0.2 μg Hg g−1 egg (n = 36), a high‐MeHg dose of 3.2 μg Hg g−1 egg (n = 49), and a control (n = 34). Doses were dissolved in nanopure filtered water and injected into the albumen on the day eggs showed signs of viability (3 d incubation). In ovo exposure to MeHg significantly reduced hatching success (53% in the high‐MeHg dose group vs 94% in vehicle controls). Among hatched chicks, however, no effects of MeHg on growth, hematological variables, or nestling survival were detected. While the in ovo injection method resulted in a dose‐dependent pattern of MeHg concentrations in blood of surviving chicks at 15 d and 30 d posthatching, there was evidence of rapid excretion of MeHg with nestling age during that growth period. At reproductive maturity (90 d of age), no long‐term effects of in ovo exposure to MeHg on female mating behavior, reproductive effort (egg or clutch size), or growth and survivorship of offspring were observed. Environ Toxicol Chem 2016;35:1534–1540. © 2015 SETAC
A smart composite-piezoelectric one-dimensional finite element model for vibration damping analysis

A one-dimensional finite element method for generally layered smart beams is presented in this paper. The model implements the first-order shear deformation beam theory and is based on the preliminary analytical condensation of the electric state to the mechanical state. This allows us to establish an effective mechanical beam kinematically equivalent to the original smart beam including the effects of electro-elastic couplings. The contributions of the external electric loads are included in both the equivalent stiffness properties and the equivalent mechanical boundary conditions. Hermite shape functions, which depend on parameters representative of the staking sequence through the equivalent electro-elastic stiffness coefficients, are used to formulate the finite element method. The state space representation is then invoked for the assembled smart beam finite element model to favor its implementation in a block diagram environment for multi-domain simulation. Validation results and solutions for passive and active vibrations damping system are presented last.
Evaluation Method of Delayed Fracture Property of High Strength Steels

Synopsis : To evaluate delayed fracture properties of martensitic bolt steels containing Cr,Mo,and V, the relationship between critical content for delayed fracture [Hc] and environmentally absorbed content [HE] in diffusible hydrogen have been investigated. The critical value [Hc] and the environmental value [HE] were determined by accelerated delayed fracture tests under constant applied load using specimens with uniformly distributed hydrogen and by cyclic corrosion tests in 5% NaCl aqueous solution as an environmental condition, respectively. The diffusible hydrogen was detected by hydrogen thermal desorption analysis after respective tests. On the other hand, the delayed fracture resistance was defined as fracture ratio [F] of bolts exposed in the seaside testing site. Based on the result that ( [Hc] [HE]) / [Hc] increases monotonically with a decrease in fracture ratio [F] , it is proposed that the parameter ( [Hc] [HE] ) / [Hc] would be a quantitative indication showing delayed fracture susceptibility of high strength steels in service environment.
PrivateHunt

Recently, for-hire vehicle services (FHV, e.g., Uber and Lyft) have become essential to people's daily transportation. Similar to taxis, how to effectively dispatch these FHV based on demand and supply is important for both FHV passengers and drivers. Based on real-world multi-source data, we identify two new challenges for FHV dispatching: (i) diverse demand: FHV passengers are a mix of passengers previously using taxis, buses, subways, or private vehicles; (ii) uncertain supply: FHV drivers join and leave the FHV system with spatiotemporal dynamics. As a result, the state-of-the-art taxi dispatching techniques cannot be applied to FHV systems. In this paper, we design the first FHV dispatching system PrivateHunt based on extremely large-scale urban transportation data from New York City and Shenzhen in China. In particular, we present (i) a passenger demand model based on taxi, bus, subway, and private vehicle data; (ii) a driver supply model based on small-scale FHV data; (iii) a dispatching technique for FHV vehicles based on proposed demand/supply models to reduce idle driving time. We implement PrivateHunt based on 14 thousand taxis, 13 thousand buses, and 8-line subway system and 10 thousand private vehicles. The experimental results show that our data-driven dispatching strategy significantly outperforms the state-of-the-art dispatching strategies without data-driven FHV insights.