Miracle-dz/UniFAR-FTUs huggingface dataset:
BiPPred: Combined sequence‐ and structure‐based prediction of peptide binding to the Hsp70 chaperone BiP

Substrate binding to Hsp70 chaperones is involved in many biological processes, and the identification of potential substrates is important for a comprehensive understanding of these events. We present a multi‐scale pipeline for an accurate, yet efficient prediction of peptides binding to the Hsp70 chaperone BiP by combining sequence‐based prediction with molecular docking and MMPBSA calculations. First, we measured the binding of 15mer peptides from known substrate proteins of BiP by peptide array (PA) experiments and performed an accuracy assessment of the PA data by fluorescence anisotropy studies. Several sequence‐based prediction models were fitted using this and other peptide binding data. A structure‐based position‐specific scoring matrix (SB‐PSSM) derived solely from structural modeling data forms the core of all models. The matrix elements are based on a combination of binding energy estimations, molecular dynamics simulations, and analysis of the BiP binding site, which led to new insights into the peptide binding specificities of the chaperone. Using this SB‐PSSM, peptide binders could be predicted with high selectivity even without training of the model on experimental data. Additional training further increased the prediction accuracies. Subsequent molecular docking (DynaDock) and MMGBSA/MMPBSA‐based binding affinity estimations for predicted binders allowed the identification of the correct binding mode of the peptides as well as the calculation of nearly quantitative binding affinities. The general concept behind the developed multi‐scale pipeline can readily be applied to other protein‐peptide complexes with linearly bound peptides, for which sufficient experimental binding data for the training of classical sequence‐based prediction models is not available. Proteins 2016; 84:1390–1407. © 2016 Wiley Periodicals, Inc.
A comparative study of various magnetic design topologies for a semi-dynamic EV charging application

The aim of this paper is to present a comparative study between various combinations of primary and secondary pad topologies, when used to charge a vehicle on the move. In order to ensure a fair comparison it is important to use the designs for each topology that are dimensionally comparable to each other. This is achieved by exploiting the ability of the Bi-Polar Pad (BPP), a hybrid flux pad topology, to be operated in different modes. This way the same design can be used not only to attain the results for a multi-coil/2-phase topology, but also the equivalent results achievable by similarly sized single-phase parallel (Double-D Pad or DDP) or perpendicular flux only pad (Rectangular Pad or RP) topologies. In order to evaluate and compare the effectiveness of the various cases, considered here, it is assumed that continuous transfer of power along the whole length of the track is desirable.
The effect of processing parameters on the performance of cotton-fabric-based MEMS fabricated using stamped silver nanoparticles

In this study, silver nanoparticles (AgNPs) were being transferred onto fabric by stamping to produce different conductive regions. The resistive part acts as the transducer of the device using piezoresistive effects. The scope of this project is to investigate the effect of stamping processing parameters to the fabricated textile-based Micro Electro Mechanical System (MEMS). We show that the force applied during stamping procedure and the amount of AgNPs will affect the performance of the sensor. We calculated the gauge factor in order to investigate the sensitivity of the sensor with different processing parameters. We found that there are optimum values for both the applied force, i.e. about 15N, and the applied AgNPs amount, i.e. 0.5 μl, such that the sensitivity of the textile-based MEMS strain sensing is maximum.
Performance analysis of FFH-FDMA satellite communication system using partial processing Dehop-Rehop Transponder (DRT) under jamming

This paper presents simulation results which illustrate the performance of a fast frequency hopped - frequency division multiple access (FFH-FDMA) satellite communication system using a partial processing Dehop-Rehop Transponder (DRT) under jamming. In the simulated system, convolutional coded symbols (using rates 1/2 or 1/4) are hopped with time diversity to enhance the anti-jamming (AJ) capacity. This study examines the combined effect of time diversity and channel coding under the influence of TWTA nonlinearity, jammer strength and up/down link channel noises on the end-to-end bit error rate (BER) of the DRT system. The simulated results show that under the considered jamming environments of partial band noise jamming (PBNJ) and band multi-tone jamming (BMTJ), excessive TWTA input back-off (IBOF) does not necessarily enhance the performance; rather, it greatly degrades the BER, particularly when channel noise is non-negligible. It was also verified that under the same conditions, time diversity and convolutional coding must be carefully combined to avoid possible degradation in FH-FDMA satellite channel.
A sparse coding approach for the efficient representation and segmentation of white matter fibers

A sparse coding method is proposed for the representation and segmentation of multi-subject white matter fiber tracts. Instead of representing bundles as a single centroid, this method learns a compact dictionary of training fibers, capable of describing the whole dataset, and encodes bundles as a sparse combination of dictionary prototypes. This provides an efficient and accurate way to segment new fiber data, without explicitly embedding fibers. A strategy based on the Nyström method is used to approximate the pairwise similarities of training fibers. Experiments using dMRI data from the Human Connectome Project show the ability of our method to identify white matter bundles across subjects, and illustrates the impact of sparsity on the performance of the proposed method.
Study of Electrolyte pH in Production of Cu–Co–Ni Ternary Alloys and Its Effect on Microstructural and Magnetic Properties

Ternary Cu-Co-Ni alloys were electrodeposited in the mediums that have different pH levels to investigate the microstructuremagnetic relationship. The electrolyte pH was considered as high (4.2) and low (2.5) levels. For both levels, the anomalous codeposition occurred in the deposition of the alloys. The face centered cubic crystalline structure was observed in the ternary alloys grown at high and low electrolyte pH levels. In addition, a significant decrease in average grain size of the crystallites, from 60 to 21 nm, occurred when the pH was reduced from 4.2 to 2.5. A dendritic structure was detected in the surface of the alloy deposited from electrolyte with the high pH level, whereas the alloy grown at the low pH has a surface without dendritic clumps. According to magnetic analysis, an increase in the saturation magnetization, caused by the increase of Co content, was detected when the pH was reduced. The coercivity Hc levels were 89 and 80 Oe for the alloys grown at high and low pH, respectively. The change of Hc was attributed to the changes in microstructural properties, i.e., different average grain sizes of the crystallites and surface morphologies, occurred when the electrolyte pH changed. The anisotropic magnetoresistance (AMR) was exhibited by the alloys and the AMR ratio was enhanced from ~3% to ~3.5%-4% when the pH decreased.
An Empirical Analysis for Technical Efficiency of Bioenergy Industry in EU28 Region Based on Data Envelopment Analysis Method

Over the last few years concerns have enhanced about the bioenergy industry as main source for renewable and sustainable energy in many countries. These concerns have been major magnitude for countries with joint green energy legislation such as European Union (EU) member states. A significant aspect to be considered when selecting a provided bioenergy is the efficiency involved in its production. In this context, the current study analyzes the technical efficiency components in bioenergy industry in EU28 region between 1990 and 2013. To this end, parametric and non-parametric frontier models are applied, where both are particularly appropriate in this special context due to their treatment of undesirable outputs. Results are presenting higher means for technical efficiency and pure technical efficiency in developing countries in compare with developed countries. In the other hand, scale efficiency mean presenting high value in developed countries in compare with developing ones. Keywords: Bioenergy industry; technical efficiency; EU28 Region JEL Classifications: Q4, D61
Quantitative Detection of Hepatitis B Virus DNA in Two International Reference Plasma Preparations

ABSTRACT Quantitative detection of hepatitis B virus (HBV) in serum or plasma is of significance for monitoring of therapy and establishment of the prognosis of the disease, as well as for infectivity assessment and quality control of the diagnosis. Unfortunately, various commercially available test kits for HBV DNA yielded conflicting quantitative results, with differences of up to a factor of 120. The Eurohep Pathobiology Group has established two reference samples of plasma from HBV carriers and determined as accurately as possible the number of HBV DNA molecules in these samples. Plasma donations from two single highly viremic carriers of HBV genotype A (HBV surface antigen subtype adw2) and genotype D (ayw2/3), respectively, were collected, and coded dilutions of these samples were analyzed by members of the Eurohep Pathobiology Group. Quantitative results from the seven laboratories reporting consistent results were initially divergent. Limiting dilution and nested PCR assays suffered from incomplete DNA extraction. Hybridization assays used inaccurately quantitated cloned DNA as a reference. Two hybridization assays could not be calibrated directly with cloned HBV DNA, because virion-derived DNA reacted much less efficiently. After identification and elimination of these problems, limiting-dilution assays from three laboratories and hybridization assays from two producers generated consistent and concordant results: 2.7 × 109 HBV DNA molecules/ml (range, 2.1 × 109 to 3.4 × 109 HBV DNA molecules/ml) in the plasma from the carrier of genotype A and 2.6 × 109 HBV DNA molecules/ml (range, 2.1 × 109 to 3.0 × 109 HBV DNA molecules/ml in the plasma from the carrier of genotype D. The two Eurohep reference plasma samples have already been used for the standardization of test kits and in quality control trials, and the plasma from the carrier of genotype A will probably be the basis of a World Health Organization reference sample.
Nature of the coupling between neural drive and force-generating capacity in the human quadriceps muscle

The force produced by a muscle depends on both the neural drive it receives and several biomechanical factors. When multiple muscles act on a single joint, the nature of the relationship between the neural drive and force-generating capacity of the synergistic muscles is largely unknown. This study aimed to determine the relationship between the ratio of neural drive and the ratio of muscle force-generating capacity between two synergist muscles (vastus lateralis (VL) and vastus medialis (VM)) in humans. Twenty-one participants performed isometric knee extensions at 20 and 50% of maximal voluntary contractions (MVC). Myoelectric activity (surface electromyography (EMG)) provided an index of neural drive. Physiological cross-sectional area (PCSA) was estimated from measurements of muscle volume (magnetic resonance imaging) and muscle fascicle length (three-dimensional ultrasound imaging) to represent the muscles' force-generating capacities. Neither PCSA nor neural drive was balanced between VL and VM. There was a large (r = 0.68) and moderate (r = 0.43) correlation between the ratio of VL/VM EMG amplitude and the ratio of VL/VM PCSA at 20 and 50% of MVC, respectively. This study provides evidence that neural drive is biased by muscle force-generating capacity, the greater the force-generating capacity of VL compared with VM, the stronger bias of drive to the VL.
Evaluation of the quantitative insulin sensitivity check index as an estimate of insulin sensitivity in humans.

The goal of this study was to compare estimates of insulin resistance generated by the quantitative insulin sensitivity check index (QUICKI) with a direct measure of insulin-mediated glucose disposal in healthy, nondiabetic volunteers. For this purpose, the results of measurements of plasma glucose and insulin concentrations in 490 nondiabetic, healthy subjects were used to compute several surrogate estimates of insulin resistance, and these values were compared with a direct measure of insulin-mediated glucose disposal. The results of this analysis showed that estimates of insulin resistance derived from use of QUICKI were significantly correlated (r = -.60, P <.001) with direct measures of insulin-mediated glucose in the 490 subjects studied. It was also noted that QUICKI estimates of insulin resistance were highly correlated with fasting insulin concentrations (r = -.98) and the homeostasis model assessment for insulin resistance (HOMA-IR, r = -.99). On the other hand, the correlation between all 3 of the surrogate methods for estimating insulin resistance and the direct assessment of insulin-mediated glucose disposal was relatively weak, i.e., r =. 61, r =. 64, and r = -. 60) for fasting insulin concentration, HOMA-IR, and QUICKI, respectively. The results of these comparisons do not provide support for the superiority of QUICKI over other commonly used surrogate measures of insulin resistance based upon use of fasting insulin concentration or equations utilizing fasting insulin and glucose concentration. Furthermore, none of the 3 surrogate estimates can account for more than approximately 40% of the variability of the difference in insulin-mediated glucose disposal measured directly in 490 healthy, nondiabetic volunteers.
High-Quality Draft Genome Sequence of Francisella tularensis subsp. holarctica Strain 08T0073 Isolated from a Wild European Hare

ABSTRACT Here, we report a high-quality draft genome sequence of Francisella tularensis subsp. holarctica strain 08T0073, isolated from the cadaver of a wild European hare (Lepus europaeus) found near Helmstedt, Lower Saxony, Germany, in 2007. In Germany, infected hares are a major source of tularemia in humans.
The quagmire of stakeholder engagement in tourism planning: A case example from Australia

After its first election win in August 2001 since the Northern Territory of Australia (NT) was granted self-government (1978), the incoming NT Labor government released a new tourism plan, the Northern Territory Tourism Strategic Plan—2003–2007 in the following year. Turbulent events of 2001 that had a significant impact on the tourism industry in the NT and included the collapse of the Australian carrier Ansett Airlines and "September 11" provided the impetus for the new strategy. Purportedly, this plan was designed to direct and guide the NT tourism industry's future development based on sound research and extensive consultation with key stakeholders. Such a partnership approach was regarded as crucial for the success of future tourism in the Territory. This article specifically focuses on the formulation process of this Tourism Strategic Plan, exploring in particular the effectiveness of the underlying consultation process. Adopting a microperspective on tourism planning processes with the NT case example we portray a unique case that allows us to highlight not only the complex and dynamic nature of tourism planning during times of significant change in the Territory's political landscape, but also the often-experienced contradictions between tourism planning rhetoric and practice. Even though we explore a planning process that dates back about a decade, we believe that the findings of the study are relevant and inform current tourism policy and planning discourses.
Bi-clustering of gene expression microarray using coarse grained Parallel Genetic Algorithm(CgPGA) with migration

Bi-clustering of gene expression microarray data deals with creating a sub-matrix that shows a high similarity across both genes and conditions. Bi-clustering aims at identifying several bi-clusters that reveal potential local patterns from a microarray matrix. In this paper, evolutionary algorithm is used to find bi-clusters of large size which have mean squared residue less than a given threshold, δ. Attention is also given to find bi-clusters with minimum overlapping among themselves by assigning weights to the elements of microarray matrix. Initially, Genetic Algorithm (GA) is implemented to derive bi-clusters from microarray matrix. From numerical simulations, it is observed that GA took too much time to converge so as to meet the stopping criteria. To further improve the performance of GA, Parallel GA (PGA) is implemented with an objective, so as to efficiently handle the problem of slow convergence encountered in traditional GA. A framework of Coarse grained Parallel Genetic Algorithm (CgPGA) for bi-clustering is implemented in this paper. The results obtained from CgPGA are quite encouraging as CgPGA took very less time to meet the stopping criteria. The bi-clusters derived by CgPGA are larger in size, which is one of the primary objective of bi-clustering problem. The experiment was performed on microarray dataset i.e. yeast Saccharomyces cerevisiae cell cycle.
Physical Layer Impairment (PLI)-Aware RWA Algorithm Based on a Bidimensional QoS Framework

In this paper, a bidimensional Quality of Service (QoS) differentiation framework, which considers both the physical layer impairments (PLIs) and the set-up delay as well as the impact of the former on the latter, is proposed to implement service differentiation in transparent optical networks. In addition, a new PLI-aware routing and wavelength assignment (RWA) algorithm based on the proposed framework is designed and simulation results show that the proposed algorithm can reduce the blocking probability (BP) of the network, guarantee the quality of transmission (QoT), and low set-up delay for multiservice offerings.
Regional Clustering of Shared Neutralization Determinants on Primary Isolates of Clade C Human Immunodeficiency Virus Type 1 from South Africa

ABSTRACT Clade C is one of the most prevalent genetic subtypes of human immunodeficiency virus type 1 (HIV-1) in the world today and one of the least studied with respect to neutralizing antibodies. Most information on HIV-1 serology as it relates to neutralization is derived from clade B. Clade C primary isolates of HIV-1 from South Africa and Malawi were shown here to resemble clade B isolates in their resistance to inhibition by soluble CD4 and their sensitivity to neutralization by human monoclonal antibody immunoglobulin G1b12 and, to a lesser extent, 2F5. Unlike clade B isolates, however, all 16 clade C isolates examined resisted neutralization by 2G12. Infection with clade C HIV-1 in a cohort of female sex workers in South Africa generated antibodies that neutralized the autologous clade C isolate and T-cell-line-adapted (TCLA) strains of clade B. Neutralization of clade B TCLA strains was much more sensitive to the presence of autologous gp120 V3 loop peptides compared to the neutralization of clade C isolates in most cases. Thus, the native structure of gp120 on primary isolates of clade C will likely pose a challenge for neutralizing antibody induction by candidate HIV-1 vaccines much the same as it has for clade B. The autologous neutralizing antibody response following primary infection with clade C HIV-1 in South Africa matured slowly, requiring at least 4 to 5 months to become detectable. Once detectable, extensive cross-neutralization of heterologous clade C isolates from South Africa was observed, suggesting an unusual degree of shared neutralization determinants at a regional level. This high frequency of cross-neutralization differed significantly from the ability of South African clade C serum samples to neutralize clade B isolates but did not differ significantly from results of other combinations of clade B and C reagents tested in checkerboard assays. Notably, two clade C serum samples obtained after less than 2 years of infection neutralized a broad spectrum of clade B and C isolates. Other individual serum samples showed a significant clade preference in their neutralizing activity. Our results suggest that clades B and C are each comprised of multiple neutralization serotypes, some of which are more clade specific than others. The clustering of shared neutralization determinants on clade C primary HIV-1 isolates from South Africa suggests that neutralizing antibodies induced by vaccines will have less epitope diversity to overcome at a regional level.
A Low Geriatric Nutrition Risk Index Is Associated with Progression to Dialysis in Patients with Chronic Kidney Disease

Evaluating nutritional status is crucial to detecting malnutrition in patients with chronic kidney disease (CKD). The Geriatric Nutritional Risk Index (GNRI) has been associated with overall and cardiovascular mortality in the dialysis population. The aim of this study was to evaluate whether the GNRI is associated with progression to dialysis in patients with moderate to advanced CKD. We enrolled 496 patients with stage 3–5 CKD who had received echocardiographic examinations, and categorized them according to baseline GNRI values calculated using the serum albumin level and body weight. The renal end-point was defined as the commencement of dialysis. During follow-up (mean, 25.2 ± 12.5 months; range, 3.3–50.1 months), 106 (21.4%) of the patients progressed to dialysis. The GNRI was positively correlated with the left ventricular ejection fraction (LVEF) (r = 0.111, p = 0.014), and negatively correlated with the left ventricular mass index (r = −0.116, p = 0.001), left ventricular hypertrophy (r = −0.095, p = 0.035), and LVEF < 50% (r = −0.138, p = 0.002). In multivariable Cox analysis, a low GNRI, female sex, high systolic blood pressure, high fasting glucose, and low estimated glomerular filtration rate were independently associated with progression to dialysis. A low GNRI was independently associated with progression to dialysis in our study cohort. The GNRI may be useful in predicting the risk of adverse renal outcomes in patients with CKD stages 3–5. Additional studies are needed to explore whether an improvement in GNRI delays CKD progression.