Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhancement of Speech Signals Under Multiple Hypotheses using an Indicator for Transient Noise Presence

In this paper, we formulate a speech enhancement problem under multiple hypotheses, assuming an indicator or detector for the transient noise presence is available in the short-time Fourier transform (STFT) domain. Hypothetical presence of speech or transient noise is considered in the observed spectral coefficients, and cost parameters control the trade-off between speech distortion and residual transient noise. An optimal estimator, which minimizes the mean-square error of the log-spectral amplitude, is derived, while taking into account the probability of erroneous detection. Experimental results demonstrate the improved performance in transient noise suppression, compared to using the optimally-modified log-spectral amplitude estimator.
Improving data reduction for 3D shape preserving

A novel 3D shape preserving data reduction technique for managing the amount of data acquired by laser scanning is presented that overcomes the shortcomings of existing filter-based methods. The technique is based on a discrete Gaussian image of the scanned points which is obtained by estimating surface normals and projecting them into a Gaussian sphere. The discrete Gaussian image is then used to partition the points into cells. In each cell, a reference point and its neighbours are used to determine the cell representative point and all other points are removed. The performance of the proposed method is illustrated using a range of point clouds scanned from typical engineering surfaces.
Computational Methods for Prediction of Protein-Protein Interaction Sites

Studies of protein-protein interactions play a central role in understanding protein function in biological systems, closing the gap between large-scale sequencing efforts and medically relevant outcomes. Increasingly, protein interaction interfaces that mediate communication between proteins are becoming targets for therapeutics, offering a possibility to disrupt critical interactions and specifically attenuate function (Fletcher and Hamilton, 2007; Fry, 2006).
Co-Expression of SERCA Isoforms, Phospholamban and Sarcolipin in Human Skeletal Muscle Fibers

Sarcolipin (SLN) and phospholamban (PLN) inhibit the activity of sarco(endo)plasmic reticulum Ca2+-ATPases (SERCAs) by reducing their apparent affinity for Ca2+. A ternary complex between SLN, PLN, and SERCAs results in super-inhibition of SERCA activity. Analysis of skeletal muscle homogenate has limited our current understanding of whether SLN and PLN regulate SERCA1a, SERCA2a, or both in skeletal muscle and whether SLN and PLN are co-expressed in skeletal muscle fibers. Biopsies from human vastus lateralis were analyzed through single fiber Western blotting and immunohisto/fluorescence staining to circumvent this limitation. With a newly generated SLN antibody, we report for the first time that SLN protein is present in human skeletal muscle. Addition of the SLN antibody (50 µg) to vastus lateralis homogenates increased the apparent Ca2+ affinity of SERCA (K Ca, pCa units) (-Ab, 5.85 ± 0.02 vs. +Ab, 5.95 ± 0.02) and maximal SERCA activity (μmol/g protein/min) (-Ab, 122 ± 6.4 vs. +Ab, 159 ± 11) demonstrating a functional interaction between SLN and SERCAs in human vastus lateralis. Specifically, our results suggest that although SLN and PLN may preferentially regulate SERCA1a, and SERCA2a, respectively, physiologically they both may regulate either SERCA isoform. Furthermore, we show that SLN and PLN co-immunoprecipitate in human vastus lateralis homogenate and are simultaneously expressed in 81% of the fibers analyzed with Western blotting which implies that super-inhibition of SERCA may exist in human skeletal muscle. Finally, we demonstrate unequivocally that mouse soleus contains PLN protein suggesting that super-inhibition of SERCA may also be important physiologically in rodent skeletal muscle.
Extremely Randomized Machine Learning Methods for Compound Activity Prediction

Speed, a relatively low requirement for computational resources and high effectiveness of the evaluation of the bioactivity of compounds have caused a rapid growth of interest in the application of machine learning methods to virtual screening tasks. However, due to the growth of the amount of data also in cheminformatics and related fields, the aim of research has shifted not only towards the development of algorithms of high predictive power but also towards the simplification of previously existing methods to obtain results more quickly. In the study, we tested two approaches belonging to the group of so-called ‘extremely randomized methods’—Extreme Entropy Machine and Extremely Randomized Trees—for their ability to properly identify compounds that have activity towards particular protein targets. These methods were compared with their ‘non-extreme’ competitors, i.e., Support Vector Machine and Random Forest. The extreme approaches were not only found out to improve the efficiency of the classification of bioactive compounds, but they were also proved to be less computationally complex, requiring fewer steps to perform an optimization procedure.
Entwicklung des akutmaßes zur erfassung von erholung und beanspruchung im sport

Zusammenfassung. In dem vom Bundesinstitut fur Sportwissenschaft geforderten Verbundprojekt REGman wird mit der Entwicklung des Akutmases zur Erfassung von Erholung und Beanspruchung im Sport (AEB) dem Wunsch der Sportpraxis nach einem kompakten und sensitiven psychometrischen Messinstrument zur Quantifizierung von Erholung und Beanspruchung nachgegangen. Nach einer Expertenbefragung wurde eine erste Fragebogenversion an Sportstudierenden (N = 257) getestet. Basierend auf den Ergebnissen einer exploratorischen Faktoren- und Reliabilitatsanalyse wurde jeweils ein Modell fur Erholung und fur Beanspruchung mit insgesamt 32 Adjektiven erstellt. Zur Uberprufung dieser Modelle durch eine konfirmatorische Faktorenanalyse wurde die uberarbeitete Version zunachst an einer Gruppe leistungsorientierter Sportlerinnen und Sportler (N = 429) getestet, leicht modifiziert und anschliesend an einer Gruppe von Leistungssportlerinnen und -sportlern (N = 574) konfirmatorisch validiert. Es zeigten sich gute Fit-Indizes sowie .
Channel assignment in cellular radio

Some heuristic channel-assignment algorithms for cellular systems are described. These algorithms have yielded optimal, or near-optimal assignments, in many cases. The channel-assignment problem can be viewed as a generalized graph-coloring problem, and these algorithms have been developed, in part, by suitably adapting some of the ideas previously introduced in heuristic graph-coloring algorithms. The channel-assignment problem is formulated as a minimum-span problem, i.e. a problem wherein the requirement is to find the minimum bandwidth necessary to satisfy a given demand. Examples are presented, and algorithm performance results are discussed. <<ETX>>
Characterization of a novel meiosis-specific protein within the central element of the synaptonemal complex

During the first meiotic prophase, alignment and synapsis of the homologous chromosomes are mediated by the synaptonemal complex. Incorrect assembly of this complex results in cell death, impaired meiotic recombination and formation of aneuploid germ cells. We have identified a novel mouse meiosis-specific protein, TEX12, and shown it to be a component of the central element structure of the synaptonemal complex at synapsed homologous chromosomes. Only two other central element proteins, SYCE1 and SYCE2, have been identified to date and, using several mouse knockout models, we show that these proteins and TEX12 specifically depend on the synaptonemal transverse filament protein SYCP1 for localization to the meiotic chromosomes. Additionally, we show that TEX12 exactly co-localized with SYCE2, having the same, often punctate, localization pattern. SYCE1, on the other hand, co-localized with SYCP1 and these proteins displayed the same more continuous expression pattern. These co-localization studies were confirmed by co-immunoprecipitation experiments that showed that TEX12 specifically co-precipitated with SYCE2. Our results suggest a molecular network within the central elements, in which TEX12 and SYCE2 form a complex that interacts with SYCE1. SYCE1 interacts more directly with SYCP1 and could thus anchor the central element proteins to the transverse filaments.
Primate motor cortex and free arm movements to visual targets in three- dimensional space. II. Coding of the direction of movement by a neuronal population

We describe a code by which a population of motor cortical neurons could determine uniquely the direction of reaching movements in three- dimensional space. The population consisted of 475 directionally tuned cells whose functional properties are described in the preceding paper (Schwartz et al., 1988). Each cell discharged at the highest rate with movements in its “preferred direction” and at progressively lower rates with movements in directions away from the preferred one. The neuronal population code assumes that for a particular movement direction each cell makes a vectorial contribution (“votes”) with direction in the cell's preferred direction and magnitude proportional to the change in the cell's discharge rate associated with the particular direction of movement. The vector sum of these contributions is the outcome of the population code (the “neuronal population vector”) and points in the direction of movement in space well before the movement begins.
Modeling Regional Interdependencies using a Global Error-Correcting Macroeconometric Model 1

Financial institutions are ultimately exposed to macroeconomic fluctuations in the global economy. This paper proposes and builds a compact global model capable of generating forecasts for a core set of macroeconomic factors (or variables) across a number of countries. The model explicitly allows for the interdependencies that exist between national and international factors. Individual region-specific vector error-correcting models are estimated, where the domestic variables are related to corresponding foreign variables constructed exclusively to match the international trade pattern of the country under consideration. The individual country models are then linked in a consistent and cohesive manner to generate forecasts for all the variables in the world economy simultaneously. The global model is estimated for 26 countries grouped into 11 regions using quarterly data over 1979Q1-99Q1. The degree of regional interdependencies is investigated via generalized impulse responses where the effects of shocks to a given variable in a given country on the rest of the world are provided. The model is then used to investigate the effects of various global risk scenarios on a bank’s loan portfolio.
Trunk Control as an Early Predictor of Comprehensive Activities of Daily Living Function in Stroke Patients

Background and Purpose— Prediction of activities of daily living (ADL) functions at an early stage after a stroke is critical because it enables clinicians to set treatment programs and goals. The objective of this study was to assess the relationship between trunk control at an early stage and comprehensive ADL function (as assessed by combining basic ADL and instrumental ADL [IADL]) in patients at 6 months after stroke. Methods— A total of 169 stroke patients participated in this prospective study. Trunk control was measured with the use of the trunk control items of the Postural Assessment Scale for Stroke Patients (PASS-TC). In addition to the PASS-TC score, age, sex, type of stroke, side of hemiparesis, urinary incontinence, limb paresis (measured by the Fugl-Meyer motor test), balance (measured by the Fugl-Meyer balance test), and basic ADL (measured by the Barthel Index) were also selected as predictor variables. These variables were assessed at 14 days after stroke or earlier. The Barthel Index and Frenchay Activities Index (measuring IADL) were administered at 6 months after stroke. The sum of the standardized Barthel Index and standardized Frenchay Activities Index scores was used to assess comprehensive ADL function. Results— Multivariable stepwise linear regression analysis showed that PASS-TC score, age, Fugl-Meyer motor test score, and Barthel Index score (listed by the order of forward selection) were the strongest predictors of comprehensive ADL function. These results were internally validated with the use of the bootstrap resampling technique. The PASS-TC score alone accounted for 45% of the variance in predicting comprehensive ADL function. Results also indicated that the PASS-TC score had slightly more power in predicting comprehensive ADL function than either the Fugl-Meyer motor test score or Barthel Index score. Conclusions— The findings of this study provide strong evidence of the predictive value of trunk control on comprehensive ADL function in stroke patients. The results imply that early assessment and management of trunk control after stroke should be emphasized.
Fast and accurate predictions of binding free energies using MM‐PBSA and MM‐GBSA

In the drug discovery process, accurate methods of computing the affinity of small molecules with a biological target are strongly needed. This is particularly true for molecular docking and virtual screening methods, which use approximated scoring functions and struggle in estimating binding energies in correlation with experimental values. Among the various methods, MM‐PBSA and MM‐GBSA are emerging as useful and effective approaches. Although these methods are typically applied to large collections of equilibrated structures of protein‐ligand complexes sampled during molecular dynamics in water, the possibility to reliably estimate ligand affinity using a single energy‐minimized structure and implicit solvation models has not been explored in sufficient detail. Herein, we thoroughly investigate this hypothesis by comparing different methods for the generation of protein‐ligand complexes and diverse methods for free energy prediction for their ability to correlate with experimental values. The methods were tested on a series of structurally diverse inhibitors of Plasmodium falciparum DHFR with known binding mode and measured affinities. The results showed that correlations between MM‐PBSA or MM‐GBSA binding free energies with experimental affinities were in most cases excellent. Importantly, we found that correlations obtained with the use of a single protein‐ligand minimized structure and with implicit solvation models were similar to those obtained after averaging over multiple MD snapshots with explicit water molecules, with consequent save of computing time without loss of accuracy. When applied to a virtual screening experiment, such an approach proved to discriminate between true binders and decoy molecules and yielded significantly better enrichment curves. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
Improved State Aggregation with Growing Neural Gas in Multidimensional State Spaces

Q-Learning is a widely used method for dealing with reinforcement learning problems. However, the conditions for its convergence include an exact representation and sufficiently (in theory even infinitely) many visits of each state-action pair—requirements that raise problems for large or continuous state spaces. To speed up learning and to exploit gained experience more efficiently it is highly beneficial to add generalization to Q-Learning and thus enabling the transfer of experience to unseen but similar states. In this paper, we report on improvements for GNG-Q, an algorithm that solves reinforcement learning problems with continuous state spaces and simultaneously learns a proper abstract state space. This approach combines Q-Learning and growing neural gas (an adaptive vector quantizer) to compute a state space abstraction. It starts with a coarse resolution that is gradually refined based on information achieved during learning. We improve the dealing with the non-determinism that may emerge in abstracted state spaces, suggest a new refinement strategy and propose a new criterion to decide when a refinement is necessary. Furthermore, we argue that this criterion offers an implicit local stopping condition for changes made to the approximation. Additionally, we employ eligibility traces to speed up learning. We evaluate the improved method in continuous state spaces with up to four dimensions and compare the results with several approaches from literature. Our experiments confirm that the modifications highly improve the efficiency of the abstract state space and that our approach is well competitive with existing methods.
Parabens Accelerate Ovarian Dysfunction in a 4-Vinylcyclohexene Diepoxide-Induced Ovarian Failure Model

Parabens are widely used preservatives in basic necessities such as cosmetic and pharmaceutical products. In previous studies, xenoestrogenic actions of parabens were reported in an immature rat model and a rat pituitary cell line (GH3 cells). The relationship between parabens and ovarian failure has not been described. In the present study, the influence of parabens on ovarian folliculogenesis and steroidogenesis was investigated. A disruptor of ovarian small pre-antral follicles, 4-vinylcyclohexene diepoxide (VCD, 40 mg/kg), was used to induce premature ovarian failure (POF). Methylparaben (MP, 100 mg/kg), propylparaben (PP, 100 mg/kg), and butylparaben (BP, 100 mg/kg) dissolved in corn oil were treated in female 8-week-old Sprague-Dawley rat for 5 weeks. Estrus cycle status was checked daily by vaginal smear test. Ovarian follicle development and steroid synthesis were investigated through real-time PCR and histological analyses. Diestrus phases in the VCD, PP, and BP groups were longer than that in the vehicle group. VCD significantly decreased mRNA level of folliculogenesis-related genes (Foxl2, Kitl and Amh). All parabens significantly increased the Amh mRNA level but unchanged Foxl2 and Kitlg acting in primordial follicles. VCD and MP slightly increased Star and Cyp11a1 levels, which are related to an initial step in steroidogenesis. VCD and parabens induced an increase in FSH levels in serum and significantly decreased the total number of follicles. Increased FSH implies impairment in ovarian function due to VCD or parabens. These results suggest that VCD may suppress both formation and development of follicles. In particular, combined administration of VCD and parabens accelerated inhibition of the follicle-developmental process through elevated AMH level in small antral follicles.
Cryptanalysis of an ElGamal-Like Cryptosystem for Enciphering Large Messages

In 2002, Hwang et al. propose an asymmetric cryptosystem in which a large message is broken into smaller plaintexts which are then encrypted efficiently. They claim that based on the assumption of the intractability of the discrete logarithm problem, their cryptosystem is secure in the sense that even knowing some pairs of plaintext-ciphertext does not allow an intruder to acquire other plaintexts easily. This paper disproves this claim. Key-Words: Asymmetric cryptosystem, ElGamal cryptosystem, Cryptanalysis, Discrete logarithm, Order of element.
Efficient query construction for large scale data

In recent years, a number of open databases have emerged on the Web, providing Web users with platforms to collaboratively create structured information. As these databases are intended to accommodate heterogeneous information and knowledge, they usually comprise a very large schema and billions of instances. Browsing and searching data on such a scale is not an easy task for a Web user. In this context, interactive query construction offers an intuitive interface for novice users to retrieve information from databases neither requiring any knowledge of structured query languages, nor any prior knowledge of the database schema. However, the existing mechanisms do not scale well on large scale datasets. This paper presents a set of techniques to boost the scalability of interactive query construction, from the perspective of both, user interaction cost and performance. We connect an abstract ontology layer to the database schema to shorten the process of user-computer interaction. We also introduce a search mechanism to enable efficient exploration of query interpretation spaces over large scale data. Extensive experiments show that our approach scales well on Freebase - an open database containing more than 7,000 relational tables in more than 100 domains.
Validation of an instrument to measure inter-organisational linkages in general practice

Purpose Linkages between general medical practices and external services are important for high quality chronic disease care. The purpose of this research is to describe the development, evaluation and use of a brief tool that measures the comprehensiveness and quality of a general practice's linkages with external providers for the management of patients with chronic disease. In this study, clinical linkages are defined as the communication, support, and referral arrangements between services for the care and assistance of patients with chronic disease. Methods An interview to measure surgery-level (rather than individual clinician-level) clinical linkages was developed, piloted, reviewed, and evaluated with 97 Australian general practices. Two validated survey instruments were posted to patients, and a survey of locally available services was developed and posted to participating Divisions of General Practice (support organisations). Hypotheses regarding internal validity, association with local services, and patient satisfaction were tested using factor analysis, logistic regression and multilevel regression models. Results The resulting General Practice Clinical Linkages Interview (GP-CLI) is a nine-item tool with three underlying factors: referral and advice linkages, shared care and care planning linkages, and community access and awareness linkages. Local availability of chronic disease services has no affect on the comprehensiveness of services with which practices link, however, comprehensiveness of clinical linkages has an association with patient assessment of access, receptionist services, and of continuity of care in their general practice. Conclusions The GP-CLI may be useful to researchers examining comparable health care systems for measuring the comprehensiveness and quality of linkages at a general practice-level with related services, possessing both internal and external validity. The tool can be used with large samples exploring the impact, outcomes, and facilitators of high quality clinical linkages in general practice.