Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural studies of sugar binding proteins

Binding proteins, which are themselves non-enzymatic, play an important role in enzymatic reactions as well as non-enzymatic processes by providing a binding platform for the specific recognition of particular molecules. For example, periplasmic binding proteins play a vital role in nutrient uptake in Gram-negative bacteria. In the present study, three sugar binding proteins, including two periplasmic binding proteins and a β-glucan binding protein, are described. The glucose/galactose binding protein in complex with (2R)-glyceryl-β-D-galactopyranoside, another physiologically relevant ligand for the protein, was revealed. The structure was solved using the molecular replacement method and refined to 1.87 A with R and R free values 17% and 22%. The structure displays the closest form among the available glucose/galactose binding protein structures with three additional binding residues, which are conserved among the group. We also present three different conformations of E. coli xylose binding protein structures, open ligand free, open liganded and closed liganded. This is the first structure of the open liganded form in the pentose/hexose sugar-binding cluster. The structures were solved using molecular replacement method and refined to 2.15 A, 2.1 A and to 2.2 A respectively. The new family of antimicrobial protein, secreted upon fungal attacks from Pinus sylvestris was present here with the binding and activity assays. The inhibition of vegetative growth and the spore germination of the causative agent of the disease, root and butt rot was proved with low concentrations of the peptide. The assays determined its ability to bind with β-(1,3)-D-glucans. The homology model was made using the PDB structure 1C01, the antimicrobial protein from Macadamia integrifolia, which has 64% sequence identity.
Dyadobacter arcticus sp. nov., isolated from Arctic soil.

A psychrotolerant, Gram-negative, rod-shaped, yellow-pigmented bacterium, designated strain R-S7-29(T), was isolated from a soil sample collected from the Svalbard Archipelago in Norway (78° N). Cells were non-motile, aerobic, and catalase- and oxidase-positive. Growth occurred at 4-28 °C (optimum, 18 °C). A phylogenetic tree based on 16S rRNA gene sequences showed that strain R-S7-29(T) belongs to the genus Dyadobacter (family 'Flexibacteraceae') with sequence similarity to related members of the genus ranging from 95.2 to 96.7 %. The major fatty acids were C16 : 1ω5c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and the predominant respiratory quinone was MK-7. The DNA G+C content of strain R-S7-29(T) was 50 mol%. On the basis of its phenotypic, phylogenetic and chemotaxonomic properties, strain R-S7-29(T) represents a novel species of the genus Dyadobacter, for which the name Dyadobacter arcticus sp. nov. is proposed. The type strain is R-S7-29(T) ( = CCTCC AB 2011022(T) = NRRL B-59659(T)).
Magnetization transfer histogram methodology: its clinical and neuropsychological correlates.

OBJECTIVE To review studies on the assessment of correlations between magnetization transfer ratio (MTR) histogram analysis and measures of clinical and neuropsychological function. BACKGROUND Since its recent introduction, MTR histogram analysis has attracted attention in the field of multiple sclerosis (MS). METHODS In this paper, studies are discussed that deal with MTR histogram analysis. The principles of MTR, application of MTR methodology as regional and volumetric MTR analysis, clinical and neuropsychological correlates, and potential use of MTR histogram analysis as an estimate of cerebral lesion load in MS are discussed respectively. RESULTS In several preliminary studies, it has been shown that in MS patients, measures derived from MTR histograms correlate with measures of clinical and particularly neuropsychological function. CONCLUSION MTR histogram analysis is a promising method to estimate cerebral lesion load in MS patients. Before it can be routinely used as an outcome measure in clinical trials, a number of questions about this technique have to be addressed.
Relative Duration of Transmitted Mitral A Wave as a Measure of Left Ventricular End‐Diastolic Pressure and Stiffness

Background and objectives: The mitral A wave is transmitted to the left ventricular (LV) outflow tract where it is registered as Ar wave. We have related its transit time to the LV late diastolic stiffness. We also observed incidentally that the duration of the transmitted Ar wave exhibited marked variability and hence investigated its hemodynamic correlates. Methods and results: Mitral A wave and the Ar wave in the LV outflow tract were recorded using pulsed wave Doppler technique simultaneous with high fidelity LV pressure recordings in 20 patients undergoing cardiac catheterization. A high‐speed contrast left ventriculogram was obtained as well. The duration of both these wave forms were measured and A wave duration minus the Ar wave duration was measured. The A minus Ar wave duration (range 0–95 ms) correlated with LV end‐diastolic pressure (r = 0.54, P = 0.014, range 4–32 mmHg), LV late diastolic stiffness (r = 0.62, P = 0.004, range 0.1–1.6 mmHg/ml) and the amount of LV pressure rise with atrial contraction (r = 0.67, P = 0.001, range 2–13 mmHg). Conclusion: A minus Ar wave duration is an easily obtainable Doppler parameter that is related to LV late diastolic filling pressures and stiffness and gives insights into aspects of LV diastolic function. (ECHOCARDIOGRAPHY, Volume 21, January 2004)
Chronic ethanol consumption impairs the circadian rhythm of pro‐opiomelanocortin and period genes mRNA expression in the hypothalamus of the male rat

Certain psychiatric disorders are known to alter the body's biological rhythms. However, currently, very little information is known about the effect of chronic ethanol administration on the circadian clock or the rhythm of β‐endorphin‐containing neurons that participate in the control of the reward and reinforcement of alcohol drinking. Here, we report that administration of ethanol, via a liquid diet paradigm for a period of 2 weeks, abolishes the circadian rhythm of pro‐opiomelanocortin mRNA expression of β‐endorphin neurons in the arcuate nucleus of the hypothalamus. The circadian expression of the clock governing rat period genes (rPeriod1 mRNA and rPeriod2 mRNA) in the arcuate nucleus was significantly altered, suggesting that ethanol administration disrupted the internal clock. Moreover, ethanol consumption altered the circadian rhythms of rPeriod2 and rPeriod3 mRNA levels in the suprachiasmatic nucleus, suggesting that ethanol also affected the function of the central pacemaker. Our findings identified the vulnerability of the body's clock machinery and its opioidergic system to chronic alcohol drinking.
Suspended Spiral Inductor and Band-Pass Filter on Thick Anodized Aluminum Oxide

We make suspended inductors and 2.45 GHz BPFs on the selectively anodized aluminum. The thick anodized alumina is used as the supporting dielectric and it is easily removed by using chemical wet-etching. The thickness of anodized alumina is 80 mum and the depth of the total air-cavity is 200 mum. The fabricated inductor over an air cavity has a 25% greater Q factor and 21% higher inductance at 2 GHz compared to an inductor on anodized aluminum. The 2.45 GHz BPF adjusting the suspended inductors has 2.8 dB of insertion loss with a narrow bandwidth.
Magnetic and half-metallic properties of Cr-doped /spl beta/-SiC

Using ab initio ultrasoft pseudopotential plane wave method, the effect of Cr doping concentration on the magnetic properties of /spl beta/-SiC (SiC:Cr) was investigated quantitatively. It is found that the total magnetic moment of SiC:Cr is independent of the substitution site and amount of doping concentration. Using the density of states calculation, it is shown that SiC:Cr has half-metallic properties for selected doping concentrations of 1.56%, 3.13%, and 6.25%, irrespective of substitution site. The conduction electron mobility of SiC:Cr/sub C/ was expected to be higher than that of SiC:Cr/sub Si/. On the contrary, SiC:Cr/sub Si/ has a wider spin band gap compared to SiC:Cr/sub C/. It is predicted that SiC with 6.25% Cr doping represents desirable characteristics for realizing spintronic devices. These include half-metallic properties, high electron mobility, and a wide spin band gap with the Fermi level located at the center of the gap.
Enhancing the Performance of Motor Imagery EEG Classification Using Phase Features

An electroencephalogram recognition system considering phase features is proposed to enhance the performance of motor imagery classification in this study. It mainly consists of feature extraction, feature selection and classification. Surface Laplacian filter is used for background removal. Several potential features, including phase features, are then extracted to enhance the classification accuracy. Next, genetic algorithm is used to select sub-features from feature combination. Finally, selected features are classified by extreme learning machine. Compared with “without phase features” and linear discriminant analysis on motor imagery data from 2 data sets, the results denote that the proposed system achieves enhanced performance, which is suitable for the brain–computer interface applications.
Genetic deficit of KCa3.1 channels protects against pulmonary circulatory collapse induced by TRPV4 channel activation

The intermediate conductance calcium/calmodulin‐regulated K+ channel KCa3.1 produces hyperpolarizing K+ currents that counteract depolarizing currents carried by transient receptor potential (TRP) channels, and provide the electrochemical driving force for Cl− and fluid movements. We investigated whether a deficiency in KCa3.1 (KCa3.1−/−) protects against fatal pulmonary circulatory collapse in mice after pharmacological activation of the calcium‐permeable TRP subfamily vanilloid type 4 (TRPV4) channels.
Management of Congenital Talipes Equinovarus by Joshi's External Stabilizing System

Introduction: Joshi’s external stabilizing system (JESS) is a useful option to correct the deformities in patients who present to the orthopedic department with neglected congenital talipes equinovarus, Plaster of Paris (POP) drop out cases, or failed surgical procedures. Purpose: We aimed to analyze a short term follow-up study of 16 patients with 4 bilateral cases treated with JESS at the Department of Orthopedics, JJM Medical College, Davangere, in terms of cosmetic, functional, and anatomical outcome. Methods: A total of 16 children underwent 20 JESS procedures at the Department of Orthopaedics, JJM Medical College, affiliated to Chigateri Government Hospital, Davangere and Bapuji Hospital, Davangere, during the period from September 2008 to September 2010. Patients were followed up regularly. Three-dimensional corrections were achieved by the use of the distractor device. Results: Excellent results were obtained in 15 feet, good results in two feet, fair in one foot, and poor in one foot. The most common complication we encountered was pin tract infection which eventually healed on an outpatient basis without any residual sequelae. Conclusion: The Joshi’s external stabilization system frame is ideally suited for children in whom clubfoot deformities remain uncorrected by POP cast manipulations as well as recurrent/relapsed clubfoot. The procedure is minimally invasive, and the results are good irrespective of the severity of the deformity.
Analysis of Flow-Through Entities Using Social Network Analysis Techniques

The tax law allows flow-through tax treatment for certain legal entities so that income is subject to tax only once—at the partner or shareholder level. The information return that flow-through entities file includes a Schedule K-1 that shows income, deductions, credits, and other items that are allocated to the owners. Flow-through treatment introduces complexity in auditing tax returns as flow-through entities can be associated with many owners and vice versa. A flowthrough entity can also be associated with many other flow-through entities. Additionally, the financial flows can vary across owners—both in type and magnitude. For example, owners can receive different types of income and deductions from a flow-through entity, and each owner may not receive the same proportion of the income and deductions. Due to this complexity, there is a need to represent the associations between different types of entities and the related financial flows in a form that is quantifiable and that can be used to evaluate these associations for tax compliance risk. This is especially important considering that more than 20 million Schedule K-1s are issued every year.
Comparison of inhibitors of superoxide generation in vascular smooth muscle cells

Background and purpose: We compared the dose‐dependent reductions in cellular superoxide anion (O2‐) by catalytic agents: superoxide dismutase (SOD), polyethylene glycol (PEG)‐SOD and the nitroxide 4‐hydroxy‐2,2,6,6,‐tetramethylpiperidine‐1‐oxyl (tempol) with uncharacterized antioxidants: 5,10,15,20‐tetrakis (4‐sulphonatophenyl) porphyrinate iron (III)(Fe‐TTPS), (‐)‐cis‐3,3′,4′,5,7‐pentahydroxyflavane (2R,3R)‐2‐(3,4‐dihydroxyphenyl)‐3,4‐dihydro‐1(2H)‐benzopyran‐3,5,7‐triol (‐epicatechin), 2‐phenyl‐1,2‐benzisoselenazol‐3(2H)‐one (ebselen) and N‐acetyl‐L‐cysteine (NAC) with the spin trap nitroblue tetrazolium (NBT) and with the vitamins or their analogues: ascorbate, α‐tocopherol and 6‐hydroxy‐2,5,7,8‐tetramethylkroman‐2‐carboxy acid (trolox).
THE EFFECTS OF RUNNING SPEED ON THE METABOLIC AND MECHANICAL ENERGY COSTS OF RUNNING

THE EFFECTS OF RUNNING SPEED ON THE METABOLIC AND MECHANICAL ENERGY COSTS OF RUNNING. Chad Harris, Mark Debeliso, Kent J. Adams. JEPonline. 2003;6(3):28-37. This study assessed the influence of speed on the metabolic and the mechanical cost to run a given distance. Trained male runners (n=12) performed 2 treadmill run trials of 8 min duration at each of 6 speeds (range 2.33 to 4.0 m/s). Oxygen uptake values were normalized for running speed providing a metabolic task cost variable (MBTC, ml/kg/m). Mechanical work was calculated from digitized video records using three different algorithms. Values were normalized for running speed giving mechanical task cost variables (MTC, J/kg/m). No change in the group mean metabolic task cost was found across speeds (p=0.25). In contrast, mechanical task cost decreased as running speed increased (p<0.001). The three mechanical work algorithms resulted in MTC characteristics that were significantly different from each other (p<0.001). This study suggests that metabolic cost per distance remains relatively constant across running speeds while mechanical cost per distance decreases as speed increases.
Water‐immersion wrinkling is due to vasoconstriction

The underlying mechanism of the water‐immersion skin wrinkling test, which is used as a test of sympathetic nerve function, remains elusive. We investigated changes of blood circulation in the hand occurring with water‐immersion wrinkling by measuring the velocity of ulnar and digital artery blood flow, and of digit skin blood flow, in healthy subjects before and during wrinkling. Wrinkling was accompanied by significant reduction in blood flow velocity in all vessels, with a maximum in digital vessels. Our data show that water‐immersion wrinkling is a function of digit pulp vasoconstriction. This test of sympathetic function can now be quantified using parameters of blood flow velocity, enabling its more widespread and accurate use. Muscle Nerve 27: 307–311, 2003
Practice Strategies for Elective Red Blood Cell Transfusion

more specific guidelines are given in various exhibits, and a general management strategy is outlined in algorithm form. The background paper is the analytic component of the guideline, and as such it contains information that is not presented in the clinical guideline. These two documents should thus be viewed as complementing each other. Readers are invited to comment on this new format for the Clinical Efficacy Assessment Project (CEAP) clinical guidelines. Comments should be sent to the authors or to the Department of Scientific Policy, American College of Physicians. The following clinical guideline is based on the background paper "Prudent Strategies for Elective Red Blood Cell Transfusion, "published in this issue of Annals. The goal of presenting the guideline in this format is to enhance clarity and promote use in daily clinical practice. The information provided in the various exhibits and algorithms can be found in the background paper (the numbers in brackets correspond to specific paragraphs of the background paper). The clinical guideline is structured in the following way: First, general therapeutic principles are introduced in a concise manner. Then,
Object Based Key Frame Selection for Hand Gesture Recognition

The sign language recognition is the most popular research area involving computer vision, pattern recognition and image processing. It enhances communication capabilities of the mute person. In this paper, we present an object based key frame selection. , Hausdorff distance, Forward Algorithm and Euclidean distance are used for shape similarity for hand gesture recognition. We proposed use to the hidden markov model and nonlinear time alignment model with key frame selection facility and gesture trajectory features for hand gesture recognition. Experimental results demonstrate the effectiveness of our proposed scheme for recognizing American Sign Language.
SarcasmBot: An open-source sarcasm-generation module for chatbots

Sarcasm detection is a recent innovation in sentiment analysis research. However, there has been no attention to sar-casm generation. We present a sarcasm-generation module for chatbots. The uniqueness of ‘ SarcasmBot ’ is that it generates a sarcastic response for a user input. SarcasmBot is a sarcasm generation module that implements eight rule-based sarcasm generators, each of which generates a certain type of sarcastic expression. One of these sarcasm generators is selected at run-time, based on properties of user input such as question type, number of entities, etc. We evaluate our sarcasm-generation module in two ways: (a) a qualitative evaluation on three parameters: coherence, grammatical correctness and sarcastic nature, where all scores are above 0.69 out of 1, and (b) a comparative evaluation between SarcasmBot and ALICE, where a majority of our human evaluators are able to identify the output of SarcasmBot among two outputs, in 70.97% of test examples.
A parallelized multilevel Green's function interpolation method for open and closed objects

A parallelized multilevel Green's function interpolation method (MLGFIM) based on extended combined field integral equation is developed for the analysis of electromagnetic problems involving composite open and closed conductors. The parallelized MLGFIM is developed using message passing interface technique on distributed-memory computer. Some issues for the achievement of an efficient parallelized MLGFIM are discussed. Numerical results demonstrate the accuracy and efficiency of this algorithm.
Fast Intra Prediction Mode Decision for High Efficiency Video Coding

High Efficiency Video Coding (HEVC) is the latest video compression standard for high resolution video content. It is said that HEVC promises the significant compression performance improvement compared to the H.264/AVC. However,it comes with the tremendous encoding complexity increase. It is necessary to decrease the computation complexity of coder. In this paper, after analysis of the coding unit and prediction unit algorithm, a fast mode decision scheme for intra prediction is proposed. This algorithm calculates firstly the texture complexity of coding unit, and set the rational threshold to select the size of coding unit fast; then a modified search process is used to decrease the number for candidate modes of prediction,finally early termination for rate-distortion optimized quantization(RDOQ) is used for Intra prediction. The simulation results showed that,compared with the recent HEVC conference software ,the proposed algorithm can reduce about 40.9% encoding time while suffers from a negligible on bit-rates performance and a negligible average PSNR loss. Keywords-High Efficiency Video Coding; HEVC; coding unit; prediction unit; context complexity; RDOQ
Rv2629 191A/C nucleotide change is not associated with rifampicin resistance in Mycobacterium tuberculosis

In 1972, rifampicin (RIF) was included in the treatment regimen as a first-line anti-tuberculosis (anti-TB) drug due to its exceptional bactericidal activity. Together with isoniazid, ethambutol and pyrazinamide, this drug forms an integral part of the current intensive and continuation phases of short-course treatment (1). Resistance to RIF is considered to be a reliable surrogate marker for multi-drug resistant TB (2). Therefore, identifying and understanding RIF resistance is of great importance and has led to the development of methods for the rapid identification of RIF resistance (2–4). These methods are based on the observation that 95% of RIF resistance can be attributed to mutations in the Rifampicin Resistance Determining Region (RRDR) of the Mycobacterium tuberculosis rpob gene (5). This suggests that other mechanisms or genes may be responsible for conferring RIF resistance in the remaining 5% of cases. In an attempt to discover such mechanisms, Wang et al. used a proteomic approach to identify overexpressed proteins specifically associated with RIF resistance (6). Sequencing of the gene Rv2629, encoding one of these overexpressed proteins, identified a nonsynonymous nucleotide polymorphism (nsSNP) at codon 191A/C. The authors demonstrated that this nsSNP was significantly associated with RIF resistance in M. tuberculosis (6) and thereby concluded that this nsSNP was a potential biomarker for the rapid detection of RIF resistance in M. tuberculosis. To test this hypothesis, 90 RIF-resistant and 67 RIFsusceptible M. tuberculosis clinical isolates were ran-
Novel Bacteriocinogenic Lactobacillus plantarum Strains and Their Differentiation by Sequence Analysis of 16S rDNA, 16S-23S and 23S-5S Intergenic Spacer Regions and Randomly Amplified Polymorphic DNA Analysis

Summary Six strains of bacteriocinogenic Lactobacillus plantarum (TL1, RG11, RS5, UL4, RG14 and RI11) isolated from Malaysian foods were investigated for their structural bacteriocin genes. A new combination of plantaricin EF and plantaricin W bacteriocin structural genes was successfully amplified from all studied strains, suggesting that they were novel bacteriocin-producing L. plantarum strains. A four-base pair variable region was detected in the short 16S-23S intergenic spacer regions of the studied strains by a comparative analysis with 17 L. plantarum strains deposited in the GenBank, implying they were new genotypes. The studied L. plantarum strains were subsequently differentiated into four groups on the basis of the detected four-base pair variable region of the short 16S-23S intergenic spacer region. Further analysis of the DNA sequence of 23S-5S intergenic spacer region revealed only one type of 23S-5S intergenic spacer region present in the studied strains, indicating it was highly conserved among the studied L. plantarum strains. Three randomly amplified polymorphic DNA experiments using three different combinations of arbitrary primers successfully differentiated the studied L. plantarum strains from each other, confirming they were different strains. In conclusion, the studied L. plantarum strains were shown to be novel bacteriocin producers and high level of strain discrimination could be achieved with a combination of randomly amplified polymorphic DNA analysis and the analysis of the variable region of short 16S-23S intergenic spacer region present in L. plantarum strains.