Miracle-dz/UniFAR-FTUs huggingface dataset:
Domain Interaction Footprint: a multi-classification approach to predict domain-peptide interactions

MOTIVATION The flow of information within cellular pathways largely relies on specific protein-protein interactions. Discovering such interactions that are mostly mediated by peptide recognition modules (PRM) is therefore a fundamental step towards unravelling the complexity of varying pathways. Since peptides can be recognized by more than one PRM and high-throughput experiments are both time consuming and expensive, it would be preferable to narrow down all potential peptide ligands for one specific PRM by a computational method. We at first present Domain Interaction Footprint (DIF) a new approach to predict binding peptides to PRMs merely based on the sequence of the peptides. Second, we show that our method is able to create a multi-classification model that assesses the binding specificity of a given peptide to all examined PRMs at once. RESULTS We first applied our approach to a previously investigated dataset of different SH3 domains and predicted their appropriate peptide ligands with an exceptionally high accuracy. This result outperforms all recent methods trained on the same dataset. Furthermore, we used our technique to build two multi-classification models (SH3 and PDZ domains) to predict the interaction preference between a peptide and every single domain in the corresponding domain family at once. Predicting the domain specificity most reliably, our proposed approach can be seen as a first step towards a complete multi-domain classification model comprised of all domains of one family. Such a comprehensive domain specificity model would benefit the quest for highly specific peptide ligands interacting solely with the domain of choice. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Online Social Media and Police in India: Behavior, Perceptions, Challenges

Police agencies across the globe are increasingly using Online Social Media (OSM) to acquire intelligence and connect with citizens. Developed nations have well thought of strategies to use OSM for policing. However, developing nations like India are exploring and evolving OSM as a policing solution. India, in recent years, experienced many events where rumors and fake content on OSM instigated communal violence. In contrast to traditional media (e.g. television and print media) used by Indian police departments, OSM offers velocity, variety, veracity and large volume of information. These introduce new challenges for police like platforms selection, secure usage strategy, developing trust, handling offensive comments, and security / privacy implication of information shared through OSM. Success of police initiatives on OSM to maintain law and order depends both on their understanding of OSM and citizen's acceptance / participation on these platforms. This study provides multidimensional understanding of behavior, perceptions, interactions, and expectation regarding policing through OSM. First, we examined recent updates from four different police pages- Delhi, Bangalore, Uttar Pradesh and Chennai to comprehend various dimensions of police interaction with citizens on OSM. Second, we conducted 20 interviews with IPS officers (Indian Police Service) and 17 interviews with citizens to understand decision rationales and expectation gaps between two stakeholders (police and citizens); this was followed up with 445 policemen surveys and 204 citizen surveys. We also present differences between police expectations of Indian and police departments in developed countries.
Functional implications of K63-linked ubiquitination in the iron deficiency response of Arabidopsis roots

Iron is an essential micronutrient that plays important roles as a redox cofactor in a variety of processes, many of which are related to DNA metabolism. The E2 ubiquitin conjugase UBC13, the only E2 protein that is capable of catalyzing the formation of non-canonical K63-linked ubiquitin chains, has been associated with the DNA damage tolerance pathway in eukaryotes, critical for maintenance of genome stability and integrity. We previously showed that UBC13 and an interacting E3 ubiquitin ligase, RGLG, affect the differentiation of root epidermal cells in Arabidopsis. When grown on iron-free media, Arabidopsis plants develops root hairs that are branched at their base, a response that has been interpreted as an adaption to reduced iron availability. Mutations in UBC13A abolished the branched root hair phenotype. Unexpectedly, mutations in RGLG genes caused constitutive root hair branching. Based on recent results that link endocytotic turnover of plasma membrane-bound PIN transporters to K63-linked ubiquitination, we reinterpreted our results in a context that classifies the root hair phenotype of iron-deficient plants as a consequence of altered auxin distribution. We show here that UBC13A/B and RGLG1/2 are involved in DNA damage repair and hypothesize that UBC13 protein becomes limited under iron-deficient conditions to prioritize DNA metabolism. The data suggest that genes involved in combating detrimental effects on genome stability may represent essential components in the plant’s stress response.
1 0 M ay 2 00 0 First Steps in Glass Theory

This paper is an introduction to some of the main present issues in the theory of structural glasses. After recalling a few experimental facts, it gives a short account of the analogy between fragile glasses and the mean field discontinuous spin glasses. The many valley picture is presented, and a brief account of recent attempts to obtain quantitative results from first principle computations is summarised.
Towards 3D Communications: Real Time Emotion Driven 3D Virtual Facial Animation

In this paper, we provide a novel algorithm for building real time 3D virtual facial animation of avatar by drawing facial expression features of real characters. This algorithm first (automatically) labels the feature points of user's facial imagines drew from camera. Then sequentially estimates the emotional state of user's face expressions by Hidden Markov Model. At last construct the avatar's facial animation according to these emotional states. We explore the complex expression space by outputting synthetic facial animations blended by 6 standard facial expressions.
CHANNEL NORMALISATION USING PHASE-CORRECTED

Recently, we proposed an extension to the classical RASTA technique. The new method consists of classical RASTA ltering followed by a phase correction operation. In this manner, the innuence of the communication channel is as eeectively removed as with classical RASTA. However, our proposal does not introduce a left-context dependency like classical RASTA. Therefore the new method is better suited for automatic speech recognition based on context-independent modeling with Gaussian mixture hidden Markov models. In this paper we introduce an implementation of phase-corrected RASTA suited for real-time processing. In the context of connected digit recognition over the phone using context independent phone-based models, we show that word error rate for this implementation is more than 20% lower compared to a real-time implementation of the cepstrum mean subtraction channel normalisation method.
Nutritional supplementation in Down syndrome: theoretical considerations and current status

Down syndrome (DS) is the most common inherited cause of learning disability1, and affected individuals are more prone to infections, leukaemia, congenital heart disease and other anomalies, thyroid dysfunction, early senescence and Alzheimer’s disease2. These complications create a heavy burden for carers of individuals with DS and the social and health services. Consequently, any intervention that ameliorates some of these complications will have a significant impact on the quality of life of individuals with DS and their carers. However, before investing resources in interventions, it is important to ascertain their scientific validity. The Internet and the lay press make many claims that certain expensive nutritional supplements improve the outcome in DS. These claims have left some health professionals confused and parents of children with DS vulnerable to pressures to spend large amounts of money on nutritional supplements whose benefits have not been proved. This review was undertaken firstly, to determine whether there is a theoretical basis to expect that nutritional supplements may improve the pathology of DS, and secondly, to critically examine published trials of nutritional supplements in DS to determine whether the existing evidence supports claims that nutritional supplements improve the outcome in DS.
Composite control of periodic-review just-in-time inventory systems with asymmetric costs

In this paper, the problem of inventory management in production-inventory systems is addressed from the control-theoretic perspective. We analyze the systems in which customers (or retailers) are served from a common distribution point. The stock at the distribution center used to satisfy an unknown, time-varying customers' demand is replenished with delay from a supply source which is subject to capacity limitations. The purpose of the control action is to keep the stock level close to zero despite unpredictable demand variations. In this way we minimize the costs of holding inventory at the distribution center imposed by a positive stock level, and reduce the shortage costs generated when customers need to wait for the ordered goods since not all of the demand can be satisfied from the readily available resources and the stock level is negative. Since, typically, the holding and shortage costs are not equal to each other (asymmetric costs), a different controller should be used depending on the sign of the stock level. For this purpose we propose a composite control structure consisting of two linear-quadratic (LQ) optimal controllers. It is shown that under the proposed policy the stock level is finite and converges to zero asymptotically with nonoscillatory ordering signal.
High speed implementation of symmetric block cipher on GPU

Recently, GPU is widely accepted in research community as an effective accelerator to many existing algorithms. In this paper, we contribute to the cryptography research community by presenting high speed implementation of symmetric block ciphers in GPU platform. We implemented Camellia, CAST5 and SEED in NVIDIA GTX680 and present the details of implementation techniques together with benchmarking results against existing solutions. According to the evaluation result, we are able to achieve throughput of 61.1 Gbps, 45.5 Gbps and 47.4 Gbps for Camellia, CAST5 and SEED accordingly, without considering the data transfer between CPU and GPU. By considering the data transfer, the throughput for Camellia, CAST5 and SEED dropped to 44.9 Gbps, 40.5 Gbps and 38.6 Gbps accordingly.
RESONANT ABSORPTION AND THE SPECTRUM OF 5-MIN OSCILLATIONS OF THE SUN

We studied influence of magnetic field on the spectrum of 5-min solar oscillations. The calculations were made within a two-layer shell model. The lower non-magnetized layer is characterized by a linear decrease in temperature with height while in the upper layer (with an inhomogeneous horizontal magnetic field) the temperature increases and reaches the coronal value at a height of about 2500 km. The fine structure of the spectrum of 5-min oscillations was calculated for f-, p1and p2modes for large k.
Postprandial Lipoprotein Changes in Patients Taking Antiretroviral Therapy for HIV Infection

Objective— Dyslipidemia is common among patients receiving antiretroviral therapy for HIV infection. The purpose of this study was to determine whether postprandial lipemia contributes to the dyslipidemia observed in HIV-positive patients taking antiretroviral therapy. Methods and Results— A standardized fat load was administered to 65 subjects (group 1 35 HIV-positive subjects receiving protease inhibitors [PIs]; group 2 20 HIV-positive subjects not receiving PIs; group 3 10 HIV-negative controls). Serum triglycerides, retinyl palmitate, and lipoproteins were measured using enzymatic and nuclear magnetic resonance spectroscopic techniques. Compared with HIV-negative controls, peak postprandial retinyl palmitate and large very low-density lipoprotein (VLDL) levels occurred later in both HIV-positive groups, and a delayed decrease in serum triglycerides was observed. However, postprandial areas under the curve (AUCs) for triglycerides, retinyl palmitate, chylomicrons, and large VLDL were similar. Postprandial AUCs for intermediate-density lipoproteins (IDLs) and low-density lipoproteins (LDLs) were higher in group 1 than groups 2 and 3 (all P<0.035). Conclusions— Postprandial clearance of triglyceride-rich lipoproteins is delayed in HIV-positive individuals receiving antiretroviral therapy. Compared with HIV-positive individuals not on PIs, those taking PIs do not have increased postprandial triglyceride-rich lipoproteins but do have increased postprandial IDLs and LDLs.
Nitric Oxide Prevents Aortic Neointimal Hyperplasia by Controlling Macrophage Polarization

Objective— Nitric oxide synthase 3 (NOS3) prevents neointima hyperplasia by still unknown mechanisms. To demonstrate the significance of endothelial nitric oxide in the polarization of infiltrated macrophages through the expression of matrix metalloproteinase (MMP)-13 in neointima formation. Approach and Results— After aortic endothelial denudation, NOS3 null mice show elevated neointima formation, detecting increased mobilization of LSK (lineage-negative [Lin]-stem-cell antigen 1 [SCA1]+KIT+) progenitor cells, and high ratios of M1 (proinflammatory) to M2 (resolving) macrophages, accompanied by high expression of interleukin-5, interleukin-6, MCP-1 (monocyte chemoattractant protein), VEGF (vascular endothelial growth factor), GM-CSF (granulocyte-macrophage colony stimulating factor), interleukin-1&bgr;, and interferon-&ggr;. In conditional c-Myc knockout mice, in which M2 polarization is defective, denuded aortas showed extensive wall thickening as well. Conditioned medium from NOS3-deficient endothelium induced extensive repolarization of M2 macrophages to an M1 phenotype, and vascular smooth muscle cells proliferated and migrated faster in conditioned medium from M1 macrophages. Among the different proteins participating in cell migration, MMP-13 was preferentially expressed by M1 macrophages. M1-mediated vascular smooth muscle cell migration was inhibited when macrophages were isolated from MMP-13–deficient mice, whereas exogenous administration of MMP-13 to vascular smooth muscle cell fully restored migration. Excess vessel wall thickening in mice lacking NOS3 was partially reversed by simultaneous deletion of MMP-13, indicating that NOS3 prevents neointimal hyperplasia by preventing MMP-13 activity. An excess of M1-polarized macrophages that coexpress MMP-13 was also detected in human carotid samples from endarterectomized patients. Conclusions— These findings indicate that at least M1 macrophage-mediated expression of MMP-13 in NOS3 null mice induces neointima formation after vascular injury, suggesting that MMP-13 may represent a new promising target in vascular disease.
PARTICLE CREATION IN AN OSCILLATING SPHERICAL CAVITY

We study the creation of massless scalar particles from the quantum vacuum due to the dynamical Casimir effect by spherical shell with oscillating radius. In the case of a small amplitude of the oscillation, to solve the infinite set of coupled differential equations for the instantaneous basis expansion coefficients we use the method based on the time-dependent perturbation theory of the quantum mechanics. To the first order of the amplitude we derive the expressions for the number of the created particles for both parametric resonance and non-resonance cases.
School Counseling Toward an LGBTQ-Inclusive School Climate: Implementing the SCEARE Model

ABSTRACT The school environment is often perceived as hostile by sexual minority youth. Lesbian, gay, bisexual, transgender, queer (LGBTQ) students experience high rates of bullying and suicidal ideation yet are often underserved by school counselors. School counselors are uniquely situated to facilitate systemic change within a school. The proposed School Counselors: Educate, Affirm, Respond, and Empower (SCEARE, pronounced SKEER) model outlines components of an LGBTQ-inclusive school climate. It is designed to be a practical tool for helping school counselors conceptualize their interventions, and a theory of how systemic change might occur. It empowers school counselors to be catalysts of change toward an LGBTQ-inclusive school climate.
Interactive normal reconstruction from a single image

We present an interactive system for reconstructing surface normals from a single image. Our approach has two complementary contributions. First, we introduce a novel shape-from-shading algorithm (SfS) that produces faithful normal reconstruction for local image region (high-frequency component), but it fails to faithfully recover the overall global structure (low-frequency component). Our second contribution consists of an approach that corrects low-frequency error using a simple markup procedure. This approach, aptly called rotation palette, allows the user to specify large scale corrections of surface normals by drawing simple stroke correspondences between the normal map and a sphere image which represents rotation directions. Combining these two approaches, we can produce high-quality surfaces quickly from single images.
A cross sectional study on determinants of quality of life in ALS

Background: Understanding the determinants of quality of life (QoL) in amyotrophic lateral sclerosis (ALS) has become increasingly important with the recent emphasis on the comprehensive management of patients. Objective: To evaluate the determinants of QoL in ALS using two scales with different theoretical constructs: the Schedule for the Evaluation of QoL-Direct Weighting (SEIQoL-DW), which evaluates subjective aspects of QoL, and the McGill QoL Questionnaire (MQOL), which evaluates both health related and non-health related factors of QoL. Methods: Eighty consecutive patients with ALS underwent a battery of tests evaluating QoL and a series of physical, emotional, psychological, and socioeconomic predictor variables. A stepwise linear regression model was used to compare QoL scores and explicatory variables. Results: SEIQoL-DW score was related to social support, depression, religiosity, and socioeconomic status. Total MQOL score was related to social support, socioeconomic status, and clinical status. MQOL single item score (MQOL-SIS) was related to social support, depression, social withdrawal, and socioeconomic status. SEIQoL-DW score was not related to total MQOL score. Conversely, a significant correlation was found between SEIQoL-DW and MQOL-SIS. Conclusions: With both QoL scales, the most important explicatory variable of QoL was the self perceived quality of social support. Physical status was not relevant in determining QoL. This study indicates that health related QoL measures are not adequate to assess QoL in patients with ALS, because their appreciation of QoL mainly relies on psychological, supportive, and spiritual factors. Therapeutic interventions should consider the psychological needs of patients and pay greater attention to caregivers’ issues.
Variable-rate Retransmissions for Incremental Redundancy Hybrid ARQ

The throughput achievable in truncated Hybrid ARQ protocol (HARQ) using incremental redundancy (IR) in analyzed when transmitting over a block-fading channel whose state is unknown at the transmitter. We allow the transmission lengths to vary, optimize them efficiently via dynamic programming, and show that such a variable-rate HARQ-IR provides gains with respect to a fixed-rate transmission in terms of increased throughput and decreased average number of transmissions, reducing at the same time the outage probability.
Rapid Assembly of Functional Presynaptic Boutons Triggered by Adhesive Contacts

CNS synapse assembly typically follows after stable contacts between “appropriate” axonal and dendritic membranes are made. We show that presynaptic boutons selectively form de novo following neuronal fiber adhesion to beads coated with poly-d-lysine (PDL), an artificial cationic polypeptide. As demonstrated by atomic force and live confocal microscopy, functional presynaptic boutons self-assemble as rapidly as 1 h after bead contact, and are found to contain a variety of proteins characteristic of presynaptic endings. Interestingly, presynaptic compartment assembly does not depend on the presence of a biological postsynaptic membrane surface. Rather, heparan sulfate proteoglycans, including syndecan-2, as well as others possibly adsorbed onto the bead matrix or expressed on the axon surface, are required for assembly to proceed by a mechanism dependent on the dynamic reorganization of F-actin. Our results indicate that certain (but not all) nonspecific cationic molecules like PDL, with presumably electrostatically mediated adhesive properties, can effectively bypass cognate and natural postsynaptic ligands to trigger presynaptic assembly in the absence of specific target recognition. In contrast, we find that postsynaptic compartment assembly depends on the prior presence of a mature presynaptic ending.
An Articial Volition Architecture for Autonomous Robotics

We introduce a new computational architecture capable of exhibiting an archetypal type of volition in a simplified modularized version of M. Minskys hive-mind. In this model, three relatively independent computational cores which themselves can also be whole multi-agent systems are engaged in an endless interaction each one representing the internal “imaginative” world, the external world interface and the arbitrator or Internal Observer. Volition then is expected to occur as the result of an endless antagonism for control between the internal and the external world models.
A new method for classification of events in noisy hydrophone data

In this paper a new method for classifying events in noisy hydrophone data is developed. The method takes an image processing approach to the 1D hydrophone data by first converting it into a log-frequency spectrogram image (cepstrum). This image is then filtered by reconstructing it based on mutual information (MI) criteria of the dominant orientation map. The features of the reconstructed cepstrum are then enhanced using a combination of edge-tracking and noise smoothing. Feature classification on the processed cepstrum is performed using a least-squares support vector machine (LS-SVM). The method showed event detection sensitivity in excess of 99% for rare events such as whale calls from noisy hydrophone recordings from the NEPTUNE Canada project, with in excess of 97% specificity and 98% overall accuracy. With relatively low computational cost and high accuracy, the proposed method is useful for automated long-term monitoring of a wide variety of marine mammals and human related activities from hydrophone data.