Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystal Structures of Escherichia coli ATP-Dependent Glucokinase and Its Complex with Glucose

ABSTRACT Intracellular glucose in Escherichia coli cells imported by phosphoenolpyruvate-dependent phosphotransferase system-independent uptake is phosphorylated by glucokinase by using ATP to yield glucose-6-phosphate. Glucokinases (EC 2.7.1.2) are functionally distinct from hexokinases (EC 2.7.1.1) with respect to their narrow specificity for glucose as a substrate. While structural information is available for ADP-dependent glucokinases from Archaea, no structural information exists for the large sequence family of eubacterial ATP-dependent glucokinases. Here we report the first structure determination of a microbial ATP-dependent glucokinase, that from E. coli O157:H7. The crystal structure of E. coli glucokinase has been determined to a 2.3-Å resolution (apo form) and refined to final Rwork/Rfree factors of 0.200/0.271 and to 2.2-Å resolution (glucose complex) with final Rwork/Rfree factors of 0.193/0.265. E. coli GlK is a homodimer of 321 amino acid residues. Each monomer folds into two domains, a small α/β domain (residues 2 to 110 and 301 to 321) and a larger α+β domain (residues 111 to 300). The active site is situated in a deep cleft between the two domains. E. coli GlK is structurally similar to Saccharomyces cerevisiae hexokinase and human brain hexokinase I but is distinct from the ADP-dependent GlKs. Bound glucose forms hydrogen bonds with the residues Asn99, Asp100, Glu157, His160, and Glu187, all of which, except His160, are structurally conserved in human hexokinase 1. Glucose binding results in a closure of the small domains, with a maximal Cα shift of ∼10 Å. A catalytic mechanism is proposed that is consistent with Asp100 functioning as the general base, abstracting a proton from the O6 hydroxyl of glucose, followed by nucleophilic attack at the γ-phosphoryl group of ATP, yielding glucose-6-phosphate as the product.
Interactive Cuts through 3‐Dimensional Soft Tissue

We describe a physically based framework for interactive modeling and cutting of 3‐dimensional soft tissue that can be used for surgery simulation. Unlike existing approaches which are mostly designed for tensorproduct grids our methods operate on tetrahedral decompositions giving more topological and geometric flexibility for the efficient modeling of complex anatomical structures. We start from an initial tetrahedralization such as being provided by any conventional meshing method. In order to track topological changes tetrahedra intersected by the virtual scalpel are split into substructures whose connectivity follows the trajectory of the cut, which can be arbitrary. For the efficient computation of collisions between the scalpel and individual tetrahedra we devised a local collision detection algorithm. The underlying physics is approximated through masses and springs attached to each tetrahedral vertex and edge. A hierarchical Runge‐Kutta iteration computes the relaxation of the system by traversing the designed data structures in a breadth‐first order. The framework includes a force‐feedback interface and uses real‐time texture mapping to enhance the visual realism.
Detecting distributed denial-of-service attacks by analyzing TCP SYN packets statistically

Distributed denial-of-service attacks on public servers have recently become more serious. More are SYN flood attacks, since the malicious attackers can easily exploit the TCP specification to generate traffic making public servers unavailable. To assure that network services will not be interrupted, we need faster and more accurate defense mechanisms against malicious traffic, especially SYN floods. One of the problems in detecting SYN flood traffic is that server nodes or firewalls cannot distinguish the SYN packets of normal TCP connections from those of SYN flood attack. Moreover, since the rate of normal network traffic may vary, we cannot use an explicit threshold of SYN arrival rates to detect SYN flood traffic. In this paper we introduce a mechanism for detecting SYN flood traffic more accurately by taking into consideration the the time variation of arrival traffic. We first investigate the statistics of the arrival rates of both normal TCP SYN packets and SYN flood attack packets. We then describe our new detection mechanism based on the statistics of SYN arrival rates. Our analytical results show that the arrival rate of normal TCP SYN packets can be modeled by a normal distribution and that our proposed mechanism can detect SYN flood traffic quickly and accurately regardless of time variance of the traffic.
Micronutrients and the pathogenesis of human immunodeficiency virus infection

Micronutrient deficiencies may be common during human immunodeficiency virus (HIV) infection. Insufficient dietary intake, malabsorption, diarrhoea, and impaired storage and altered metabolism of micronutrients can contribute to the development of micronutrient deficiencies. Low plasma or serum levels of vitamins A, E, B6, B12 and C, carotenoids, Se, and Zn are common in many HIV-infected populations. Micronutrient deficiencies may contribute to the pathogenesis of HIV infection through increased oxidative stress and compromised immunity. Low levels or intakes of micronutrients such as vitamins A, E, B6 and B12, Zn and Se have been associated with adverse clinical outcomes during HIV infection, and new studies are emerging which suggest that micronutrient supplementation may help reduce morbidity and mortality during HIV infection.
A Data-Driven Deployment Approach for Persistent Monitoring in Aquatic Environments

Processes of scientific interest in the aquatic environment occur across multiple spatio-temporal time scales. To properly assess and understand these processes, we must observe aquatic ecosystems over long time periods. This requires examination of the problem of deploying multiple, inexpensive, and minimally-actuated drifting vehicles. We aim to utilize these persistent assets to explore all locations on the water surface, and examine the entirety an underwater environment through the visibility of downward-facing cameras. In this work, we propose a data-driven approach for the deployment of drifters that creates a stochastic model, finds the generalized flow pattern of the water, and studies the long-term behavior of an aquatic environment from a flow point-of-view. Given the long-term behavior of the environment, our approach finds attractors and their transient groups as the domains of attractions. We then determine a minimum number of deployment locations for the drifters using these attractors and their transient groups. Our simulation results based on actual ocean model prediction data demonstrate the applicability of our approach.
Mechanical Vibration Test of a REBCO Coil Designed for Application to the Maglev

We have been developing on-board REBCO magnets for maglev. Because of the running vibration, the on-board magnets receive vibration acceleration up to 10 G (98 m/s2). For the realization of the on-board REBCO magnet, we carried out mechanical vibration tests with a real-scale REBCO coil. The REBCO coil is racetrack-shaped (1070 mm wide, 500 mm high), and its magnetomotive force is 700 kA. The upper limit temperature of the excitation is approximately 39 K. The REBCO coil was excited and vibrated for 20 min for the evaluation of durability and heat load. Any mechanical damage on the REBCO coil was not observed, although the vibration acceleration in the experiments exceeded 10 G. The heat load was small enough compared to the static heat load.
Chronic testosterone administration improves cardiac contractility and has a beneficial effect on the haemostatic system by enhancing fibrinolytic activity and inducing hypocoagulation in healthy rats

Abstract This study investigated the effects of chronic supraphysiological dose of testosterone propionate administration cardiovascular function in rats from the perspective of haemostatic function including platelet functions, coagulation, and fibrinolysis. Testosterone significantly enhanced cardiac contractility by enhancing LVSP (10%), dp/dtmax (36.7%), dp/dtmin (14.6%) without altering heart rate, diastolic function, and serum lipid profile. While it has no effect on platelets count, thromboxane B2 levels, and platelet aggregation, testosterone significantly enhanced bleeding time and increased circulatory and thoracic aorta mRNA and protein levels of tPA (46.5%, 58.2%, and 74.3%, respectively) and significantly decreased those of PAI-1 (29.3%, 26.4%, and 32.8%, respectively). While there were no significant changes in PT and aPTT, mRNA and protein levels of prothrombin and factor VII were downregulated in the livers of the testosterone-treated rats (57.7% and 64.9%, respectively). Overall, chronic testosterone administration in rats may act as a cardio-protective agent by modulating haemostasis in rats.
A fast image stitching algorithm based on SURF

This paper proposes a fast image stitching algorithm with a new way to determine feature searching area. Consider that flat area, such as ground, of an image has less information, and features always mainly gather on other objects. So in this paper we set the region of interest (ROI) by finding a set of potential feature points. We use an algorithm model to identify candidate feature points, and set up a ROI searching area. After setting the ROI we use speeded up robust feature (SURF) descriptor to achieve image registration. Finally, we compare the proposed algorithm with other stitching algorithms. The result of the experiment indicates that the proposed algorithm improves the computational speed while maintaining the accuracy of splicing.
A personalized committee classification approach to improving prediction of breast cancer metastasis

MOTIVATION Metastasis prediction is a well-known problem in breast cancer research. As breast cancer is a complex and heterogeneous disease with many molecular subtypes, predictive models trained for one cohort often perform poorly on other cohorts, and a combined model may be suboptimal for individual patients. Furthermore, attempting to develop subtype-specific models is hindered by the ambiguity and stereotypical definitions of subtypes. RESULTS Here, we propose a personalized approach by relaxing the definition of breast cancer subtypes. We assume that each patient belongs to a distinct subtype, defined implicitly by a set of patients with similar molecular characteristics, and construct a different predictive model for each patient, using as training data, only the patients defining the subtype. To increase robustness, we also develop a committee-based prediction method by pooling together multiple personalized models. Using both intra- and inter-dataset validations, we show that our approach can significantly improve the prediction accuracy of breast cancer metastasis compared with several popular approaches, especially on those hard-to-learn cases. Furthermore, we find that breast cancer patients belonging to different canonical subtypes tend to have different predictive models and gene signatures, suggesting that metastasis in different canonical subtypes are likely governed by different molecular mechanisms. AVAILABILITY AND IMPLEMENTATION Source code implemented in MATLAB and Java available at www.cs. utsa.edu/∼jruan/PCC/.
Self-Organization and Artificial Life: A Review

Self-organization has been an important concept within a number of disciplines, which Artificial Life (ALife) also has heavily utilized since its inception. The term and its implications, however, are often confusing or misinterpreted. In this work, we provide a mini-review of self-organization and its relationship with ALife, aiming at initiating discussions on this important topic with the interested audience. We first articulate some fundamental aspects of self-organization, outline its usage, and review its applications to ALife within its soft, hard, and wet domains. We also provide perspectives for further research.
The 2011 October Draconids outburst-II. Meteoroid chemical abundances from fireball spectroscopy

We acknowledge support from the Spanish Ministry of Science and Innovation (projects AYA2009-13227, AYA2009-14000-C03-01 and AYA2011-26522), Junta de Andalucia (project P09-FQM-4555) and CSIC (grant # 201050I043).
Adsorption of Enamel Matrix Derivative to Bone Grafts: Is the Devil in the Details

Cite this article: Yufeng Z. Adsorption of Enamel Matrix Derivative to Bone Grafts: Is the Devil in the Details. J Dent Cl Res. 2014. Volume 1, Issue 1: 003 Over 15 years has now passed since enamel matrix derivative (EMD) was shown to facilitate periodontal regeneration by stimulating new cementum, alveolar bone and periodontal ligament formation [1-4]. The major component of EMD is a family of hydrophobic proteins, amelogenins, which account for more than 95% of the total protein content of the enamel matrix [5]. Other proteins found in the enamel matrix include enamelin, ameloblastin (also called amelin or sheathlin), amelotin, apin, and various proteinases [6, 7]. Despite the ability for EMD to facilitate periodontal regeneration, many clinicians have combined EMD with various bone grafting materials in order to improve the outcomes by preventing a flap collapse and improving blood clot formation [8-14]. Recently, the effects of EMD in combination with a bone grafting material were investigated in a systematic review [15]. It was found that while EMD was able to improve the regeneration with certain bone grafts, other types of materials have failed to improve clinical outcomes [15]. Thus, direct evidence supporting the combination approach is still missing and further investigation is required.
Analysis and Comparison of Energy Efficiency of Commercially Available Battery Electric Buses

Battery electric buses have been tested in Helsinki region to gain experience on the actual energy consumption and how well they suit for the Finnish climate. Measurements were performed on a chassis dynamometer with various driving cycles and gross vehicle weights in order to be able to analyse the buses in detail. The measurements reveal significant differences in the energy consumption of the buses. The sensitivity to different cycles and loads also varies greatly. The observed differences can partly be explained by the different curb weights of the buses. Another reason for the differences is the regeneration rate, which was as low as 15% for some buses, while the best bus was able to regenerate over 35% of the energy.
A privacy-preserving interactive messaging scheme based on users credibility over online social networks

Due to the tremendous growth in user population over online social networks (OSNs), interactive messaging traffic has experienced exponential increase, which consequently elevates the privacy leakage. Malicious users may utilize camouflage, phishing and other unconventional techniques to lure ordinary users to reveal their sensitive attributes in their interactive messages, when they least expect that the other sides are malicious. Therefore, it is very important to identify malicious users quickly and successfully when socializing over OSNs. In this paper, we propose a privacy-preserving interactive messaging scheme by relying on user credibility, which characterizes users' reputation through users' social behaviors, and use the item response theory in psychometrics to assess the risk levels of users' interactive messages. We have conducted extensive studies by sending interactive messages with sensitive attributes and have observed that the success rate of identifying malicious users based on user credibility is significantly higher and our scheme can effectively lower the risk of privacy leakage in our interactive messaging system.
challenges for cross-cloud applications

Federated clouds can expose the Internet as a homogeneous compute fabric. There is an opportunity for developing cross-cloud applications that can be deployed pervasively over the Internet, dynamically adapting their internal topology to their needs. In this paper we explore the main challenges for fully realizing the potential of cross-cloud applications. First, we focus on the networking dimension of these applications. We evaluate what support is needed from the infrastructure, and what are the further implications of opening the networking side. On a second part, we examine the impact of a distributed deployment for applications, assessing the implications from a management perspective, and how it affects the delivery of quality of service and non-functional requirements.
Task-Related Modulations of BOLD Low-Frequency Fluctuations within the Default Mode Network

Spontaneous low-frequency Blood-Oxygenation Level-Dependent (BOLD) signals acquired during resting state are characterized by spatial patterns of synchronous fluctuations, ultimately leading to the identification of robust brain networks. The resting-state brain networks, including the Default Mode Network (DMN), are demonstrated to persist during sustained task execution, but the exact features of task-related changes of network properties are still not well characterized. In this work we sought to examine in a group of 20 healthy volunteers (age 33 ± 6 years, 8 F/12 M) the relationship between changes of spectral and spatiotemporal features of one prominent resting-state network, namely the DMN, during the continuous execution of a working memory n-back task. We found that task execution impacted on both functional connectivity and amplitude of BOLD fluctuations within large parts of the DMN, but these changes correlated between each other only in a small area of the posterior cingulate. We conclude that combined analysis of multiple parameters related to connectivity, and their changes during the transition from resting state to continuous task execution, can contribute to a better understanding of how brain networks rearrange themselves in response to a task.
Lead and carbon monoxide effects on human atrial action potential. In silico study

Exposure to air pollutants like lead (Pb ) and carbon monoxide (CO), promotes the occurrence of cardiovascular diseases. Experimental studies have shown that Pb++ and CO block the L-type calcium channels, decreasing the calcium current (ICaL) and the action potential duration (APD), favoring the initiation of atrial arrhythmias. Our goal is to study the effects of Pb++ and CO at different concentrations, on ICaL and action potential using computational simulation. For this, we developed mathematical models of the air pollutants effects on the atrial L-type calcium channel and they were incorporated in a mathematical model of human atrial cell and in a 2D model of atrial tissue. Our results suggest that the Pb++ and CO block the ICaL current in a fraction that increases as the concentration increases, generating an APD shortening. The combined effect of both air pollutants generated an APD shortening and a stable rotor, which is considered as a pro-arrhythmic effect. These results are consistent with experimental studies. In silico studies may contribute to a better understanding of the mechanisms by which air pollutants have unhealthy effects on cardiac system.
Kallikrein-Related Peptidase 5 Contributes to H3N2 Influenza Virus Infection in Human Lungs

ABSTRACT Hemagglutinin (HA) of influenza virus must be activated by proteolysis before the virus can become infectious. Previous studies indicated that HA cleavage is driven by membrane-bound or extracellular serine proteases in the respiratory tract. However, there is still uncertainty as to which proteases are critical for activating HAs of seasonal influenza A viruses (IAVs) in humans. This study focuses on human KLK1 and KLK5, 2 of the 15 serine proteases known as the kallikrein-related peptidases (KLKs). We find that their mRNA expression in primary human bronchial cells is stimulated by IAV infection. Both enzymes cleaved recombinant HA from several strains of the H1 and/or H3 virus subtype in vitro, but only KLK5 promoted the infectivity of A/Puerto Rico/8/34 (H1N1) and A/Scotland/20/74 (H3N2) virions in MDCK cells. We assessed the ability of treated viruses to initiate influenza in mice. The nasal instillation of only the KLK5-treated virus resulted in weight loss and lethal outcomes. The secretion of this protease in the human lower respiratory tract is enhanced during influenza. Moreover, we show that pretreatment of airway secretions with a KLK5-selective inhibitor significantly reduced the activation of influenza A/Scotland/20/74 virions, providing further evidence of its importance. Differently, increased KLK1 secretion appeared to be associated with the recruitment of inflammatory cells in human airways regardless of the origin of inflammation. Thus, our findings point to the involvement of KLK5 in the proteolytic activation and spread of seasonal influenza viruses in humans. IMPORTANCE Influenza A viruses (IAVs) cause acute infection of the respiratory tract that affects millions of people during seasonal outbreaks every year. Cleavage of the hemagglutinin precursor by host proteases is a critical step in the life cycle of these viruses. Consequently, host proteases that activate HA can be considered promising targets for the development of new antivirals. However, the specific proteases that activate seasonal influenza viruses, especially H3N2 viruses, in the human respiratory tract have remain undefined despite many years of work. Here we demonstrate that the secreted, extracellular protease KLK5 (kallikrein-related peptidase 5) is efficient in promoting the infectivity of H3N2 IAV in vitro and in vivo. Furthermore, we found that its secretion was selectively enhanced in the human lower respiratory tract during a seasonal outbreak dominated by an H3N2 virus. Collectively, our data support the clinical relevance of this protease in human influenza pathogenesis.
Therapeutic Use of Stem Cells for Myocardial Infarction

Myocardial infarction is a leading cause of morbidity and mortality worldwide. Although medical and surgical treatments can significantly improve patient outcomes, no treatment currently available is able to generate new contractile tissue or reverse ischemic myocardium. Driven by the recent/novel understanding that regenerative processes do exist in the myocardium—tissue previously thought not to possess regenerative properties—the use of stem cells has emerged as a promising therapeutic approach with high expectations. The literature describes the use of cells from various sources, categorizing them as either embryonic, induced pluripotent, or adult/tissue stem cells (mesenchymal, hematopoietic, skeletal myoblasts, cardiac stem cells). Many publications show the successful use of these cells to regenerate damaged myocardium in both animal and human models; however, more studies are needed to directly compare cells of various origins in efforts to draw conclusions on the ideal source. Although numerous challenges exist in this developing area of research and clinical practice, prospects are encouraging. The following aims to provide a concise review outlining the different types of stem cells used in patients after myocardial infarction.