Miracle-dz/UniFAR-FTUs huggingface dataset:
Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding

Motivation: Experimental techniques for measuring chromatin accessibility are expensive and time consuming, appealing for the development of computational approaches to predict open chromatin regions from DNA sequences. Along this direction, existing methods fall into two classes: one based on handcrafted k‐mer features and the other based on convolutional neural networks. Although both categories have shown good performance in specific applications thus far, there still lacks a comprehensive framework to integrate useful k‐mer co‐occurrence information with recent advances in deep learning. Results: We fill this gap by addressing the problem of chromatin accessibility prediction with a convolutional Long Short‐Term Memory (LSTM) network with k‐mer embedding. We first split DNA sequences into k‐mers and pre‐train k‐mer embedding vectors based on the co‐occurrence matrix of k‐mers by using an unsupervised representation learning approach. We then construct a supervised deep learning architecture comprised of an embedding layer, three convolutional layers and a Bidirectional LSTM (BLSTM) layer for feature learning and classification. We demonstrate that our method gains high‐quality fixed‐length features from variable‐length sequences and consistently outperforms baseline methods. We show that k‐mer embedding can effectively enhance model performance by exploring different embedding strategies. We also prove the efficacy of both the convolution and the BLSTM layers by comparing two variations of the network architecture. We confirm the robustness of our model to hyper‐parameters by performing sensitivity analysis. We hope our method can eventually reinforce our understanding of employing deep learning in genomic studies and shed light on research regarding mechanisms of chromatin accessibility. Availability and implementation: The source code can be downloaded from https://github.com/minxueric/ismb2017_lstm. Contact: tingchen@tsinghua.edu. cn or ruijiang@tsinghua.edu. cn Supplementary information: Supplementary materials are available at Bioinformatics online.
Distributed K-Median Clustering with Application to Image Clustering

Developing algorithms suitable for distributed environments is important as data becomes more distributed. This paper proposes a distributed KMedian clustering algorithm for use in a distributed environment with centralized server, such as the Napster model in a peer-to-peer environment. Several approximate methods for computing the median in a distributed environment are proposed and analyzed in the context of the iterative KMedian algorithm. The proposed algorithm allows the clustering of multivariate data while ensuring that each cluster representative remains an item in the collection. This facilitates exploratory analysis where retaining a representative in the collection is important, such as imaging applications. Introduction and Background ● K-Means clustering is a well known and popular clustering technique. – Creates a new mean vector, which may not be meaningful in many applications ● Using the centroid of a cluster rather than the mean is one variation to the basic K-Means algorithm. – This is also known as the L1 Multivariate Median ● Dhillon and Modha first proposed a distributed KMeans clustering algorithm. – Computing the distributed median is more complicated At each Peer, P: For each image, x i , at P, Distributed K-Median Clustering Algorithm Select Initial Cluster Centers: Center(C G ) Calculate distance: from image, x i , to cluster center, Center(C G ) For each cluster, C Assign x i to cluster C, where Dist(x i ,Center(C G )) is minimized Select representatives to communicate, X P (C) Server communicates to peers For each cluster C: Calculate new center as an approximate Global Median: Median(C G ) = WMedian({X P (C)| P}) where X P (C) = {(x i ,w i )| x i is a representative image at peer P, w i is the number of items at P that x i represents}
Development of Hybrid Calcium Carbonate for High Loading Paper (II) - Comparison with GCC -

In filler loaded paper, the size of the filler affects its strength, optical and surface properties. As the size of the filler increases, tensile strength and bulk usually increases, opacity decreases, and smoothness becomes worse. Pre-flocculation of GCC (grounded calcium carbonate) makes large diameter flocs at aqueous medium that consists of multiple GCC particles, but they collapse to 2-dimensional shape in dried paper and makes low bulk paper. The hybrid calcium carbonate (HCC) that was made by in-situ formation between GCC in aqueous medium made high bulk paper without harming tensile strength, bulk, opacity, and smoothness. The GCC that has equivalent size as HCC failed to make high opacity and smoothness as much as HCC.
Effect of electro-acupuncture on the BDNF-TrkB pathway in the spinal cord of CCI rats

Microglia, which comprise a sensor for pathological events in the central nervous system, may be triggered by nerve injury and transformed from a quiescent state into an activated state; ionised calcium binding adaptor molecule 1 (Iba1) is a sensitive marker associated with activated microglia. Accumulated evidence suggests that spinal activated microglia and the brain-derived neurotrophic factor (BDNF)-tyrosine kinase receptor B (TrkB) signalling pathway play major roles in the production and development of neuropathic pain. Electro-acupuncture (EA) has a positive effect on relieving chronic neuropathic pain; however, the underlying mechanisms remain unclear. To determine the significance of EA in the treatment of neuropathic pain mediated by activated microglia and the BDNF-TrkB signalling pathway in the spinal cord, the mechanical withdrawal threshold (MWT) and thermal withdrawal latency (TWL) values were recorded to assess hyperalgesia and allodynia. In addition, the amount of activated microglia and BDNF were assessed via immunofluorescence. Iba1, BDNF and TrkB mRNA expression levels were examined using qPCR; the protein levels of BDNF, p-TrkB and TrkB in the spinal cord were analysed via western blotting. The present study demonstrated that EA treatment increased the MWT and TWL values. EA significantly inhibited the proportion of activated microglia and BDNF expression in the spinal cord after chronic constrictive injury (CCI). Furthermore, EA decreased the expression of BDNF and TrkB at both the mRNA and protein levels in the spinal cord of CCI rats. These findings suggest that the analgesic effect of EA may be achieved by inhibiting the activation of spinal microglia and subsequently blocking the BDNF-TrkB signalling pathway.
FARKLI PUZOLANK KATKILARIN ÇMENTO HARÇLARININ MEKANK ÖZELLKLER ÜZERNE ETKS THE EFFECT OF DIFFERENT PUZZOLANIC ADDITIVES ON MECHANICAL PROPERTIES OF CEMENT MORTARS

In this study, cement mortar samples containing fly ash obtained from Soma Power Plant, two different types of natural pozzolan supplied from Yeniehir and Bilecik and silica fume from Antalya Ferrocrom Industry partial replacement of cement clinker. The strength of the mortars prepared by these mixtures were investigated. The mixtures were prepared by using 10% fly ash and 5% silica fume and the trass contents varied as 30%, 35%, and 40%. Chemical analyses of these mixtures were carried out and Blaine specific surface area values were measured. In performed tests, the highest strength values were noticed in mortars containing natural puzzolan from Bilecik which has high fineness.
Tumor necrosis factor‐α‐mediated hepatocyte apoptosis stimulates fibrosis in the steatotic liver in mice

Hepatocyte apoptosis has been implicated in the progression of nonalcoholic steatohepatitis. However, it is unclear whether the induction of tumor necrosis factor (TNF)‐α‐mediated hepatocyte apoptosis in the simple fatty liver triggers liver fibrosis. To address this question, high‐fat diet‐fed mice were repeatedly administered D‐galactosamine, which increases the sensitivity of hepatocytes to TNF‐α‐mediated apoptosis. In mice treated with a high‐fat diet plus D‐galactosamine, hepatocyte apoptosis and liver fibrosis were induced, whereas both apoptosis and fibrosis were inhibited in these mice following gut sterilization with antimicrobials or knockout of TNF‐α. Furthermore, liver fibrosis was diminished when hepatocyte apoptosis was inhibited by expressing a constitutively active inhibitor of nuclear factor κB kinase subunit β. Thus, hepatocyte apoptosis induced by intestinal dysbiosis or TNF‐α up‐regulation in the steatotic liver caused fibrosis. Organ fibrosis, including liver fibrosis, involves the interaction of cyclic adenosine monophosphate‐response element‐binding protein‐binding protein (CBP) and β‐catenin. Here, hepatocyte‐specific CBP‐knockout mice showed reduced liver fibrosis accompanied by hepatocyte apoptosis diminution; notably, liver fibrosis was also decreased in mice in which CBP was specifically knocked out in collagen‐producing cells because the activation of these cells was now suppressed. Conclusion: TNF‐α‐mediated hepatocyte apoptosis induced fibrosis in the steatotic liver, and inhibition of CBP/β‐catenin signaling attenuated the liver fibrosis due to the reduction of hepatocyte apoptosis and suppression of the activation of collagen‐producing cells. Thus, targeting CBP/β‐catenin may represent a new therapeutic strategy for treating fibrosis in nonalcoholic steatohepatitis. (Hepatology Communications 2018;2:407‐420)
Throughput and robustness guaranteed beam tracking for mmWave wireless networks

With the increasing demand of ultra-high-speed wireless communications and the existing low frequency band (e.g., sub-6GHz) becomes more and more crowded, millimeter-wave (mmWave) with large spectra available is considered as the most promising frequency band for future wireless communications. Since the mmWave suffers a serious path-loss, beam-forming techniques shall be adopted to concentrate the transmit power and receive region on a narrow beam for achieving long distance communications. However, the mobility of users will bring frequent beam handoff, which will decrease the quality of experience (QoE). Therefore, efficient beam tracking mechanism should be carefully researched. However, the existing beam tracking mechanisms concentrate on system throughput maximization without considering beam handoff and link robustness. This paper proposes a throughput and robustness guaranteed beam tracking mechanism for mobile mmWave communication systems which takes account of both system throughput and handoff probability. Simulation results show that the proposed throughput and robustness guaranteed beam tracking mechanism can provide better performance than the other beam tracking mechanisms.
A 12-camera body scanning system based on close-range photogrammetry for precise applications

ABSTRACT A precise 3D body scanning system, designed for applications in the medical and biomedical field, is described. The system consists of 12 digital cameras, mounted on a rigid frame which maintains the B/H ratio constant. An LED lighting system, integrated with the rigid frame, ensures a homogenous illumination of the subject. A modified firmware installed on each device enables the synchronised remote release driven by remote control. Data transmission to the computer is carried out wirelessly. A process for the estimation of the extrinsic camera parameters has been implemented with the aim of obtaining a 3D model in 1:1 scale. Analyses have been performed in order to state the repeatability of the process used to estimate the external camera calibration parameters as well as the precision of the 3D digital models of a body obtained for a mannequin and for a live human subject.
Point-of-care tests for STIs: the way forward

It has been over 10 years since the WHO Sexually Transmitted Diseases Diagnostics Initiative (SDI) published a full supplement in this journal on rapid diagnostic testing for STIs,1 making the case for quality-assured rapid STI tests to help countries achieve their Millennium Development Goals and decrease the STI burden worldwide. The supplement introduced the ASSURED criteria to assess whether diagnostics were appropriate for disease control needs, namely: Affordable, Sensitive, Specific, User-friendly, Rapid and robust, Equipment-free and Deliverable to end users.2 This ASSURED approach has broadened the paradigm of STI testing from rapid to point-of-care testing (POCT) or near-patient testing. Testing and delivering the results rapidly and conveniently to the patient will increase the likelihood of appropriate and immediate treatment and decrease the chances of onward transmission and development of reproductive sequelae. The most recent WHO estimates found that in 2012, among people aged 15–49 years, there were an estimated 6 million new cases of syphilis each year, 78 million cases of gonorrhoea, 131 million cases of chlamydial infection and 142 million cases of trichomoniasis—the four most common curable STIs.3 A separate literature review, including a modelling analysis, suggested that in 2012, 417 million people 15–49 years of age were living with herpes simplex virus type 2 infection worldwide,4 and 291 million women with genital human papillomavirus (HPV) infection.5 These pandemics, and the growing number of STIs caused by other pathogens have a profound impact on the health and lives of children, adolescents and adults worldwide.6 To achieve a sustainable decrease of STI infections globally, the new WHO STI health sector strategy reaffirms the need for early diagnosis of STIs, …
Effects of small conductance calcium activated potassium channels in cardiac myocytes

Among the different potassium channels present in cardiac myocytes, the small conductance Ca2+ activated potassium channels (SK channels) are particular because they are affected by changes in intracellular calcium. The functional role of these channels in cardiac electrophysiology is still under intense debate. While they do not seem to play an important role in healthy hearts — their associated current, IKCa, is smaller than other potassium currents —, there is increasing evidence that they may become relevant under pathological conditions. In fact, both pro- and anti-arrhythmic effects have been assigned to these channels, depending on the clinical situation. In this work, we have incorporated the current through SK channels, IKCa, into an electrophysiological ionic model of human atria myocyte. This allows us to evaluate changes in the action potential under different parameters affecting the kinetics of these channels. We observe a large dependence of the action potential duration with the conductance and gate dynamics of the channel. The dependence of SK channels with changes in intracellular calcium dynamics helps decreasing the pro-arrhythmic effect of spontaneous calcium release events.
Mining revision histories to detect cross-language clones without intermediates

To attract more users on different platforms, many projects release their versions in multiple programming languages (e.g., Java and C#). They typically have many code snippets that implement similar functionalities, i.e., cross-language clones. Programmers often need to track and modify cross-language clones consistently to maintain similar functionalities across different language implementations. In literature, researchers have proposed approaches to detect cross-language clones, mostly for languages that share a common intermediate language (such as the .NET language family) so that techniques for detecting single-language clones can be applied. As a result, those approaches cannot detect cross-language clones for many projects that are not implemented in a . NET language. To overcome the limitation, in this paper, we propose a novel approach, CLCMiner, that detects cross-language clones automatically without the need of an intermediate language. Our approach mines such clones from revision histories, which reflect how programmers maintain cross-language clones in practice. We have implemented a prototype tool for our approach and conducted an evaluation on five open source projects that have versions in Java and C#. The results show that CLCMiner achieves high accuracy and point to promising future work.
Evaluation of the Model for Analysing

Phishing takes advantage of the way humans interact with computers or interpret messages. A security ceremony is one way of extending the reach of current methods for social, technical and contextual analysis of security protocols to include humans. It is an extension of the concept of network security protocol and includes user interface and human-protocol interaction. We propose a model with which anti-phishing authentication ceremonies can be examined not only with a technical focus but by including the human into the analysis. The model examines anti-phishing authentication tasks that a human needs to apply, how users process these additional authentication tasks and how these tasks impact the human’s decision outcome. We outline the evaluation of the model and propose a ceremony called MultiStep Mutual Authentication (MSMA) that combines PIN, text password and dynamic image feedback as a help to foil phishing attacks. The MSMA ceremony is used as part of the evaluation of the model.
Testing the Long-Memory Features in Return and Volatility of NSE Index

Long-term memory of stock markets is a topic that has not received its due attention from academics. Posting the assertion made by Fama, 1970 [1] about markets being efficient, no one can consistently outrun it for a longer duration. Handful of papers checked the efficiency in emerging markets to see if the efficiency proposition held true. Furthering the literature in this study we test for the long-term memory of National Stock Exchange (NSE) index, Nifty and NSE_500 which are a collection of 50 and 500 listed firms respectively in India. The duration of the data for study is roughly eight years over the period from 2006-06-29 to 2012-09-13, a total of 1545 observations. We observe that long-term memory does exist in the context of Indian stock market index.
Inter-Network Interactions: Impact of Connections between Oscillatory Neuronal Networks on Oscillation Frequency and Pattern

Oscillations in electrical activity are a characteristic feature of many brain networks and display a wide variety of temporal patterns. A network may express a single oscillation frequency, alternate between two or more distinct frequencies, or continually express multiple frequencies. In addition, oscillation amplitude may fluctuate over time. The origin of this complex repertoire of activity remains unclear. Different cortical layers often produce distinct oscillation frequencies. To investigate whether interactions between different networks could contribute to the variety of oscillation patterns, we created two model networks, one generating on its own a relatively slow frequency (20 Hz; slow network) and one generating a fast frequency (32 Hz; fast network). Taking either the slow or the fast network as source network projecting connections to the other, or target, network, we systematically investigated how type and strength of inter-network connections affected target network activity. For high inter-network connection strengths, we found that the slow network was more effective at completely imposing its rhythm on the fast network than the other way around. The strongest entrainment occurred when excitatory cells of the slow network projected to excitatory or inhibitory cells of the fast network. The fast network most strongly imposed its rhythm on the slow network when its excitatory cells projected to excitatory cells of the slow network. Interestingly, for lower inter-network connection strengths, multiple frequencies coexisted in the target network. Just as observed in rat prefrontal cortex, the target network could express multiple frequencies at the same time, alternate between two distinct oscillation frequencies, or express a single frequency with alternating episodes of high and low amplitude. Together, our results suggest that input from other oscillating networks may markedly alter a network's frequency spectrum and may partly be responsible for the rich repertoire of temporal oscillation patterns observed in the brain.
Hydrogen Peroxide-Induced Root Ca2+ and K+ Fluxes Correlate with Salt Tolerance in Cereals: Towards the Cell-Based Phenotyping

Salinity stress-induced production of reactive oxygen species (ROS) and associated oxidative damage is one of the major factors limiting crop production in saline soils. However, the causal link between ROS production and stress tolerance is not as straightforward as one may expect, as ROS may also play an important signaling role in plant adaptive responses. In this study, the causal relationship between salinity and oxidative stress tolerance in two cereal crops—barley (Hordeum vulgare) and wheat (Triticum aestivum)—was investigated by measuring the magnitude of ROS-induced net K+ and Ca2+ fluxes from various root tissues and correlating them with overall whole-plant responses to salinity. We have found that the association between flux responses to oxidative stress and salinity stress tolerance was highly tissue specific, and was also dependent on the type of ROS applied. No correlation was found between root responses to hydroxyl radicals and the salinity tolerance. However, when oxidative stress was administered via H2O2 treatment, a significant positive correlation was found for the magnitude of ROS-induced K+ efflux and Ca2+ uptake in barley and the overall salinity stress tolerance, but only for mature zone and not the root apex. The same trends were found for wheat. These results indicate high tissue specificity of root ion fluxes response to ROS and suggest that measuring the magnitude of H2O2-induced net K+ and Ca2+ fluxes from mature root zone may be used as a tool for cell-based phenotyping in breeding programs aimed to improve salinity stress tolerance in cereals.
Moving emotional labor beyond surface and deep acting

Emotional labor (EL) is the process by which employees manage their true feelings in order to express organizationally desired emotional displays. We develop and test components of an organizing framework for emotional labor wherein various aspects of emotional labor are understood through the underlying discordance versus congruence in felt versus displayed emotions. Meta-analytic results from 109 independent studies (total N = 36,619) demonstrate that discordant emotional labor states are associated with a range of harmful consequences (health-, attitudinal-, and performance-related), whereas congruent emotional labor states do not incur these harmful consequences. We identify different patterns of worker- and work-related correlates on the basis of emotional discordance–congruence, as well as interesting occupational differences in these relationships. Lastly, we find discordant forms of emotional labor partially mediate the effects of organizational display rules on burnout, whereas congruent states do not mediate this relationship.