Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystal Structure of Pyrococcus furiosus Phosphoglucose Isomerase

Phosphoglucose isomerase (PGI) catalyzes the reversible isomerization between d-fructose 6-phosphate and d-glucose 6-phosphate as part of the glycolytic pathway. PGI from the Archaea Pyrococcus furiosus (Pfu) was crystallized, and its structure was determined by x-ray diffraction to a 2-Å resolution. Structural comparison of this archaeal PGI with the previously solved structures of bacterial and eukaryotic PGIs reveals a completely different structure. Each subunit of the homodimeric Pfu PGI consists of a cupin domain, for which the overall structure is similar to other cupin domain-containing proteins, and includes a conserved transition metal-binding site. Biochemical data on the recombinant enzyme suggests that Fe2+ is bound to Pfu PGI. However, as catalytic activity is not strongly influenced either by the replacement of Fe2+ by a range of transition metals or by the presence or absence of the bound metal ion, we suggest that the metal may not be directly involved in catalysis but rather may be implicated in substrate recognition.
How Hierarchical Topics Evolve in Large Text Corpora

Using a sequence of topic trees to organize documents is a popular way to represent hierarchical and evolving topics in text corpora. However, following evolving topics in the context of topic trees remains difficult for users. To address this issue, we present an interactive visual text analysis approach to allow users to progressively explore and analyze the complex evolutionary patterns of hierarchical topics. The key idea behind our approach is to exploit a tree cut to approximate each tree and allow users to interactively modify the tree cuts based on their interests. In particular, we propose an incremental evolutionary tree cut algorithm with the goal of balancing 1) the fitness of each tree cut and the smoothness between adjacent tree cuts; 2) the historical and new information related to user interests. A time-based visualization is designed to illustrate the evolving topics over time. To preserve the mental map, we develop a stable layout algorithm. As a result, our approach can quickly guide users to progressively gain profound insights into evolving hierarchical topics. We evaluate the effectiveness of the proposed method on Amazon's Mechanical Turk and real-world news data. The results show that users are able to successfully analyze evolving topics in text data.
Transformation Invariance in Hand Shape Recognition

In hand shape recognition, transformation invariance is key for successful recognition. We propose a system that is invariant to small scale, translation and shape variations. This is achieved by using a-priori knowledge to create a transformation subspace for each hand shape. Transformation subspaces are created by performing principal component analysis (PCA) on images produced using computer animation. A method to increase the efficiency of the system is outlined. This is achieved using a technique of grouping subspaces based on their origin and then organising them into a hierarchical decision tree. We compare the accuracy of this technique with that of the tangent distance technique and display the results
Insulin-sensitive targeting of the GLUT4 glucose transporter in L6 myoblasts is conferred by its COOH-terminal cytoplasmic tail

The GLUT4 glucose transporter appears to be targeted to a unique insulin-sensitive intracellular membrane compartment in fat and muscle cells. Insulin stimulates glucose transport in these cell types by mediating the partial redistribution of GLUT4 from this intracellular compartment to the plasma membrane. The structural basis for the unique targeting behavior of GLUT4 was investigated in the insulin-sensitive L6 myoblast cell line. Analysis of immunogold-labeled cells of independent clonal lines by electron microscopy indicated that 51-53% of GLUT1 was present in the plasma membrane in the basal state. Insulin did not significantly affect this distribution. In contrast, only 4.2- 6.1% of GLUT4 was present in the plasma membrane of basal L6 cells and insulin increased this percentage by 3.7-6.1-fold. Under basal conditions and after insulin treatment, GLUT4 was detected in tubulovesicular structures, often clustered near Golgi stacks, and in endosome-like vesicles. Analysis of 25 chimeric transporters consisting of reciprocal domains of GLUT1 and GLUT4 by confocal immunofluorescence microscopy indicated that only the final 25 amino acids of the COOH- terminal cytoplasmic tail of GLUT4 were both necessary and sufficient for the targeting pattern observed for GLUT4. A dileucine motif present in the COOH-terminal tail of GLUT4 was found to be necessary, but not sufficient, for intracellular targeting. Contrary to previous studies, the NH2 terminus of GLUT4 did not affect the subcellular distribution of chimeras. Analysis of a chimera containing the COOH-terminal tail of GLUT4 by immunogold electron microscopy indicated that its subcellular distribution in basal cells was very similar to that of wild-type GLUT4 and that its content in the plasma membrane increased 6.8-10.5-fold in the presence of insulin. Furthermore, only the chimera containing the COOH terminus of GLUT4 enhanced insulin responsive 2-deoxyglucose uptake. GLUT1 and two other chimeras lacking the COOH terminus of GLUT4 were studied by immunogold electron microscopy and did not demonstrate insulin-mediated changes in subcellular distribution. The NH2-terminal cytoplasmic tail of GLUT4 did not confer intracellular sequestration and did not cause altered subcellular distribution in the presence of insulin. Intracellular targeting of one chimera to non-insulin- sensitive compartments was also observed. We conclude that the COOH terminus of GLUT4 is both necessary and sufficient to confer insulin- sensitive subcellular targeting of chimeric glucose transporters in L6 myoblasts.
4-Channel asynchronous bio-potential recording system

We present a 4-channel bio-potential recording system using asynchronous delta analog-to-digital converter. The system is designed to reduce the amount of data in neuro-physiological sensors. The circuit includes low-power low-noise amplifiers with asynchronous delta modulators. The analog front end offers a gain of 53dB within bandwidth of 200Hz-20kHz. In this asynchronous data converter, the minimum input-referred delta resolution is 4μV. The input-referred rms noise is 2μV. T h e system was fabricated with AMI 0. 5μm CMOS technology. The chip size is 1.5mm by 1.5mm. The power consumption of the 4-channel system with 3.3V supply is 118. 8μW in static state and 501. 6μW with 240kbps data conversion rate. A graphic user interface was developed to monitor the transmitted signal in real time.
Entropy and Compression Capture Different Complexity Features: The Case of Fetal Heart Rate

Entropy and compression have been used to distinguish fetuses at risk of hypoxia from their healthy counterparts through the analysis of Fetal Heart Rate (FHR). Low correlation that was observed between these two approaches suggests that they capture different complexity features. This study aims at characterizing the complexity of FHR features captured by entropy and compression, using as reference international guidelines. Single and multi-scale approaches were considered in the computation of entropy and compression. The following physiologic-based features were considered: FHR baseline; percentage of abnormal long (%abLTV) and short (%abSTV) term variability; average short term variability; and, number of acceleration and decelerations. All of the features were computed on a set of 68 intrapartum FHR tracings, divided as normal, mildly, and moderately-severely acidemic born fetuses. The correlation between entropy/compression features and the physiologic-based features was assessed. There were correlations between compressions and accelerations and decelerations, but neither accelerations nor decelerations were significantly correlated with entropies. The %abSTV was significantly correlated with entropies (ranging between −0.54 and −0.62), and to a higher extent with compression (ranging between −0.80 and −0.94). Distinction between groups was clearer in the lower scales using entropy and in the higher scales using compression. Entropy and compression are complementary complexity measures.
Behavior Classification based Self-learning Mobile Malware Detection

More and more mobile malware appears on mobile internet and pose great threat to mobile users. It is difficult for traditional signature-based anti-malware system to detect the polymorphic and metamorphic mobile malware. A mobile malware behavior analysis method based on behavior classification and self-learning data mining is proposed to detect the malicious network behavior of the unknown or metamorphic mobile malware. A network behavior classification module is used to divide the network behavior data of mobile malware into different categories according to the behavior characteristic in the training and detection phase. Three types of network behavior data of mobile malware and normal network access are employed to train the different Naive Bayesian classifier respectively. Those classifiers are used to analyze the corresponding type of network behavior to detect the new or metamorphic mobile malware. An incremental self- learning method is adopted to gradually optimize those Naive Bayesian Classifiers for different behavior. The simulation results showed that those Naive Bayesian Classifiers based on behavior classification have better accuracy rate of analysis on mobile malware network behavior. Performance simulation results showed that the network behavior analysis system based on the proposed method can analyze the mobile malware on mobile internet in real time.
A Fuzzy Approach for Evaluation of Maintainability of Object Oriented Software System

demand for efficient software system is increasing day by day. Maintainability is considered as an important quality factor for developing the efficient software system. Recent trends show that mostly software systems are using object- oriented technique to develop the quality software products. Object-oriented approach enhances the maintainability of software system. In literature there are no well defined criteria to evaluate maintainability. This paper proposes a fuzzy model to quantify maintainability of object-oriented software system. The model takes object-oriented projects and evaluates its maintainability. The value obtained by fuzzy model is validated by using analytical hierarchy processing technique.
Automatically Detecting Vulnerable Websites Before They Turn Malicious

Significant recent research advances have made it possible to design systems that can automatically determine with high accuracy the maliciousness of a target website. While highly useful, such systems are reactive by nature. In this paper, we take a complementary approach, and attempt to design, implement, and evaluate a novel classification system which predicts, whether a given, not yet compromised website will become malicious in the future. We adapt several techniques from data mining and machine learning which are particularly well-suited for this problem. A key aspect of our system is that the set of features it relies on is automatically extracted from the data it acquires; this allows us to be able to detect new attack trends relatively quickly. We evaluate our implementation on a corpus of 444,519 websites, containing a total of 4,916,203 webpages, and show that we manage to achieve good detection accuracy over a one-year horizon; that is, we generally manage to correctly predict that currently benign websites will become compromised within a year.
Antigenic variation of varicella zoster virus Fc receptor gE: loss of a major B cell epitope in the ectodomain.

Varicella zoster virus (VZV) is considered to possess a genetically stable genome; only one serotype is recognized around the world. The 125-kbp genome contains approximately 70 open reading frames. One that has received particular attention is open reading frame 68, which codes for glycoprotein gE, the predominant 623-residue viral envelope product that harbors both B and T cell epitopes. This report describes the initial characterization of a community-acquired VZV isolate that was a distinguishable second serotype (i.e., it had lost a major B cell epitope defined on the gE ectodomain by a murine monoclonal antibody called mAb 3B3). The mAb 3B3 epitope was found not only on the prototype sequenced Dumas strain from Holland and all previously tested North American isolates but also on the varicella vaccine Oka strain originally attenuated in Japan. Sequencing of the mutated gE ectodomain demonstrated that codon 150 exhibited a single base change that led to an amino acid change (aspartic acid to asparagine). Observation of the monolayers infected with the mutant VZV strain also led to the surprising discovery that the topography of egress was altered. Wild-type VZV emerges along distinctive viral highways, whereas the mutant strain virions were nearly uniformly distributed over the cell surface in a pattern more closely resembling egress of herpes simplex virus 1. The mutant VZV strain was designated VZV-MSP because it was isolated in Minnesota.
NMPP: a user-customized NimbleGen microarray data processing pipeline

UNLABELLED NMPP package is a bundle of user-customized tools based on established algorithms and methods to process self-designed NimbleGen microarray data. It features a command-line-based integrative processing procedure that comprises five major functional components, namely the raw microarray data parsing and integrating module, the array spatial effect smoothing and visualization module, the probe-level multi-array normalization module, the gene expression intensity summarization module and the gene expression status inference module. AVAILABILITY http://plantgenomics.biology. yale.edu/nmpp
Aryl Diazonium Chemistry for the Surface Functionalization of Glassy Biosensors

Nanostring resonator and fiber-optics-based biosensors are of interest as they offer high sensitivity, real-time measurements and the ability to integrate with electronics. However, these devices are somewhat impaired by issues related to surface modification. Both nanostring resonators and photonic sensors employ glassy materials, which are incompatible with electrochemistry. A surface chemistry approach providing strong and stable adhesion to glassy surfaces is thus required. In this work, a diazonium salt induced aryl film grafting process is employed to modify a novel SiCN glassy material. Sandwich rabbit IgG binding assays are performed on the diazonium treated SiCN surfaces. Fluorescently labelled anti-rabbit IgG and anti-rabbit IgG conjugated gold nanoparticles were used as markers to demonstrate the absorption of anti-rabbit IgG and therefore verify the successful grafting of the aryl film. The results of the experiments support the effectiveness of diazonium chemistry for the surface functionalization of SiCN surfaces. This method is applicable to other types of glassy materials and potentially can be expanded to various nanomechanical and optical biosensors.
UML as an Ontology Modelling Language

Current tools and techniques for ontology development are based on the traditions of AI knowledge representation research. This research has led to popular formalisms such as KIF and KL-ONE style languages. However, these representations are little known outside AI research laboratories. In contrast, commercial interest has resulted in ideas from the object-oriented programming community maturing into industry standards and powerful tools for object-oriented analysis, design and implementation. These standards and tools have a wide and rapidly growing user community. This paper examines the potential for object-oriented standards to be used for ontology modelling, and in particular presents an ontology representation language based on a subset of the Unified Modeling Language together with its associated Object Constraint Language.
Class 1 Integron-Borne, Multiple-Antibiotic Resistance Encoded by a 150-Kilobase Conjugative Plasmid in Epidemic Vibrio cholerae O1 Strains Isolated in Guinea-Bissau

ABSTRACT In the 1996–1997 cholera epidemic in Guinea-Bissau, surveillance for antimicrobial resistance showed the emergence of a multidrug-resistant strain of Vibrio cholerae O1 during the course of the epidemic. The strain was resistant to ampicillin, erythromycin, tetracycline, furazolidone, aminoglycosides, trimethoprim, and sulfamethoxazole. Concomitant with the emergence of this strain, we observed a resurgence in the number of registered cholera cases as well as an increase in the case fatality rate from 1.0% before the emergence of the multiple-drug-resistant strain to 5.3% after the emergence of the strain. Our study shows that the strain contained a 150-kb conjugative multiple-antibiotic resistance plasmid with class 1 integron-borne gene cassettes encoding resistance to trimethoprim (dhfrXII) and aminoglycosides [ant(3")-1a]). The finding of transferable resistance to almost all of the antibiotics commonly used to treat cholera is of great public health concern. Studies should be carried out to determine to what extent the strain or its resistance genes have been spread to other areas where cholera is endemic.
Head pose estimation and movement analysis for speech scene

Public speaking is an essential skill for a large variety of professions and in everyday life. However, it is difficult to master the skills. This paper focuses on the automatic assessment of nonverbal facial behavior of public speaking and proposes simple and efficient method of head pose estimation and motion analysis. We collected nine speech scenes of the recitation contest in a Japanese high school, and applied the proposed method to evaluate the performance. As for the head pose estimation, our method was obtained acceptable accuracy for the speech scene. Proposed motion analysis method can be calculated frequencies and moving ranges of head motion. As the result, it was found that there is correlation between the moving range and eye contact score.
Lightweight Adaptive Filtering for Efficient Learning and Updating of Probabilistic Models

Adaptive software systems are designed to cope with unpredictable and evolving usage behaviors and environmental conditions. For these systems reasoning mechanisms are needed to drive evolution, which are usually based on models capturing relevant aspects of the running software. The continuous update of these models in evolving environments requires efficient learning procedures, having low overhead and being robust to changes. Most of the available approaches achieve one of these goals at the price of the other. In this paper we propose a lightweight adaptive filter to accurately learn time-varying transition probabilities of discrete time Markov models, which provides robustness to noise and fast adaptation to changes with a very low overhead. A formal stability, unbiasedness and consistency assessment of the learning approach is provided, as well as an experimental comparison with state-of-the-art alternatives.
Medical diagnostics using terahertz pulsed spectroscopy

The paper contains recent results of studying the ability of human body disease diagnosis with terahertz time-domain spectroscopy. In vitro skin cancer samples (squamous cell carcinoma, epithelioid cell melanoma, infiltrating carcinoma) were studied experimentally with terahertz pulsed spectrometer. The parametrical in vitro images of skin cancers are presented. The ability to make early tooth cariosity diagnosis with terahertz time-domain spectroscopy was also shown experimentally. The results of studying the in vitro tooth samples are presented and discussed.
SFLASHv3, a fast asymmetric signature scheme

Note: SFLASH is one of the three asymmetric signature schemes recommended by the Nessie European consortium for low-cost smart cards [19, 14]. The latest implementation report shows that SFLASH is the fastest signature scheme known, see [1]. Recent results on solving random systems of quadratic equations over fields of the form GF (2) (see [2]) suggest that the parameters of SFLASH should be increased. We also improve the hashing procedure, as suggested by Nessie evaluation reports. The new version is called SFLASH and is fully specified in the present document. This is therefore the only official version of SFLASH and we do no longer recommend SFLASH. In the appendix of the present document we summarize all the changes in SFLASH, for readers and developers that are acquainted with the previous version(s).
Postsynaptic Expression of Homeostatic Plasticity at Neocortical Synapses

Synaptic scaling is a form of homeostatic plasticity that scales synaptic strengths up or down to compensate for prolonged changes in activity. It has been controversial whether this plasticity is expressed presynaptically, postsynaptically, or both. Here we describe in detail the homeostatic changes that take place at excitatory synapses in visual cortical cultures after 1 or 2 d of activity blockade. After 7-10 d in vitro, activity blockade significantly increased postsynaptic accumulation of synaptic AMPA receptors via proportional increases in glutamate receptor 1 (GluR1) and GluR2. Time-lapse imaging of enhanced green fluorescent protein-tagged AMPA receptors revealed that receptor accumulation increased progressively over 2 d of activity blockade and affected the entire population of imaged synapses. The strength of synaptic connections between pyramidal neurons was more than doubled after activity blockade without affecting short-term depression or the coefficient of variation of the postsynaptic responses. Furthermore, uptake of the fluorescent styryl dye FM1-43 (N-(3-triethylammoniumpropyl)-4-[4-(dibutylamino)styryl] pyridinium dibromide) by presynaptic terminals was not different at control and activity-blocked synapses. In addition to the increased accumulation of postsynaptic AMPA receptors, boosting of dendritic AMPA currents by sodium channels was increased by activity blockade. These data indicate that, at young neocortical synapses, synaptic scaling has a predominantly postsynaptic locus and functions as a gain control mechanism to regulate neuronal activity without affecting the dynamics of synaptic transmission.
The boundary integral equation (boundary element) method in engineering stress analysis

Abstract The principles of the boundary integral equation (BIE) or boundary element method (BEM) are discussed in a non-mathematical way. The technique is compared with other numerical methods, particularly the finite element method (FEM), on the basis of computational efficiency, and the main advantages and disadvantages of the BIE approach are outlined.
rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea

A dramatic exception to the general pattern of single-copy genes in bacterial and archaeal genomes is the presence of 1–15 copies of each ribosomal RNA encoding gene. The original version of the Ribosomal RNA Database (rrnDB) cataloged estimates of the number of 16S rRNA-encoding genes; the database now includes the number of genes encoding each of the rRNAs (5S, 16S and 23S), an internally transcribed spacer region, and the number of tRNA genes. The rrnDB has been used largely by microbiologists to predict the relative rate at which microbial populations respond to favorable growth conditions, and to interpret 16S rRNA-based surveys of microbial communities. To expand the functionality of the rrnDB (http://ribosome.mmg.msu.edu/rrndb/index.php), the search engine has been redesigned to allow database searches based on 16S rRNA gene copy number, specific organisms or taxonomic subsets of organisms. The revamped database also computes average gene copy numbers for any collection of entries selected. Curation tools now permit rapid updates, resulting in an expansion of the database to include data for 785 bacterial and 69 archaeal strains. The rrnDB continues to serve as the authoritative, curated source that documents the phylogenetic distribution of rRNA and tRNA genes in microbial genomes.