Miracle-dz/UniFAR-FTUs huggingface dataset:
Improving sequence-based fold recognition by using 3D model quality assessment

MOTIVATION The ability of a simple method (MODCHECK) to determine the sequence-structure compatibility of a set of structural models generated by fold recognition is tested in a thorough benchmark analysis. Four Model Quality Assessment Programs (MQAPs) were tested on 188 targets from the latest LiveBench-9 automated structure evaluation experiment. We systematically test and evaluate whether the MQAP methods can successfully detect native-like models. RESULTS We show that compared with the other three methods tested MODCHECK is the most reliable method for consistently performing the best top model selection and for ranking the models. In addition, we show that the choice of model similarity score used to assess a model's similarity to the experimental structure can influence the overall performance of these tools. Although these MQAP methods fail to improve the model selection performance for methods that already incorporate protein three dimension (3D) structural information, an improvement is observed for methods that are purely sequence-based, including the best profile-profile methods. This suggests that even the best sequence-based fold recognition methods can still be improved by taking into account the 3D structural information. CONTACT d.jones@cs.ucl. ac.uk
Thyroid hormone deficiency before the onset of hearing causes irreversible damage to peripheral and central auditory systems.

Both a genetic or acquired neonatal thyroid hormone (TH) deficiency may result in a profound mental disability that is often accompanied by deafness. The existence of various TH-sensitive periods during inner ear development and general success of delayed, corrective TH treatment was investigated by treating pregnant and lactating rats with the goitrogen methimazole (MMI). We observed that for the establishment of normal hearing ability, maternal TH, before fetal thyroid gland function on estrus days 17-18, is obviously not required. Within a crucial time between the onset of fetal thyroid gland function and the onset of hearing at postnatal day 12 (P12), any postponement in the rise of TH-plasma levels, as can be brought about by treating lactating mothers with MMI, leads to permanent hearing defects of the adult offspring. The severity of hearing defects that were measured in 3- to 9-mo-old offspring could be increased with each additional day of TH deficiency during this critical period. Unexpectedly, the active cochlear process, assayed by distortion product otoacoustic emissions (DPOAE) measurements, and speed of auditory brain stem responses, which both until now were not thought to be controlled by TH, proved to be TH-dependent processes that were damaged by a delay of TH supply within this critical time. In contrast, no significant differences in the gross morphology and innervation of the organ of Corti or myelin gene expression in the auditory system, detected as myelin basic protein (MBP) and proteolipid protein (PLP) mRNA using Northern blot approach, were observed when TH supply was delayed for few days. These classical TH-dependent processes, however, were damaged when TH supply was delayed for several weeks. These surprising results may suggest the existence of different TH-dependent processes in the auditory system: those that respond to corrective TH supply (e.g., innervation and morphogenesis of the organ of Corti) and those that do not, but require T3 activity during a very tight time window (e.g. , active cochlear process, central processes).
A portable, extensible and fast stochastic volatility model calibration using multi and many‐core processors

Financial markets change precipitously, and on‐demand pricing and risk models must be constantly recalibrated to reduce risk. However, certain classes of models are computationally intensive to robustly calibrate to intraday prices – stochastic volatility models being an archetypal example due to the non‐convexity of the objective function. In order to accelerate this procedure through parallel implementation, financial application developers are faced with an ever growing plethora of low‐level high‐performance computing frameworks such as Open Multi‐Processing, Open Computing Language, compute unified device architecture, or single instruction multiple data intrinsics, and forced to make a trade‐off between performance versus the portability, flexibility, and modularity of the code required to facilitate rapid in‐house model development and productionisation. This paper describes the acceleration of stochastic volatility model calibration on multi‐core CPUs and graphics processing units (GPUs) using the Xcelerit platform. By adopting a simple programming model, the Xcelerit platform enables the application developer to write sequential, high‐level C++ code, without concern for low‐level high‐performance computing frameworks. This platform provides the portability, flexibility, and modularity required by application developers. Speedups of up to 30x and 293x are respectively achieved on an Intel Xeon CPU and NVIDIA Tesla K40 GPU, compared with a sequential CPU implementation. The Xcelerit platform implementation is further shown to be equivalent in performance to a low‐level compute unified device architecture version. Overall, we are able to reduce the entire calibration process time of the sequential implementation from 6189 to 183.8 and 17.8 s on the CPU and GPU, respectively, without requiring the developer to reimplement in low‐level high‐performance computing frameworks. Copyright © 2015 John Wiley & Sons, Ltd.
Variations in the use of health care services: why are more studies needed?

In this issue (see pages 1713 to 1719), Ms. Ruth E. Hall and Dr. Marsha M. Cohen present the results of their analysis of hysterectomy rates in Ontario. This carefully designed study shows a 2.7-fold variation in overall rates of hysterectomy among regions of the province. This level of geographic variation is comparable to that shown in other jurisdictions in North America and in other industrialized countries. "2 Indeed, hysterectomy is one of the surgical procedures for which variations in rates have most often been documented; such variations have previously been shown in Ontario,3'4 the setting for the study by Cohen and Hall. However, this study differs from earlier ones in that it shows variations not only in overall rates of hysterectomy but also in rates by specific indications. Such an analysis provides much more useful information to service providers and decision makers than do studies of variation in overall rates alone. Analysis by indication can indicate specifically where efforts are needed. Since Wennberg and Gittelsohns showed extensive geographic variation in surgical rates in New England, many studies have documented variations in all kinds of health care services, at all levels of aggregation (e.g., countries, provinces, states, counties, cities, hospital market areas and professional practices). ',7 Such analysis is interesting but of little use if it is limited to a general description of the phenomenon and if there is no attempt to answer two fundamental questions: What are the consequences of these variations? and What are their causes?
HISTOLOGICAL CHANGES IN SKELETAL MUSCLE AFTER TEMPORARY INDEPENDENT OCCLUSION OF ARTERIAL AND VENOUS SUPPLY

In both replantation and transplantation, circulation is restored to ischemic muscle by vascular anastomoses. As a result, the length of time that skeletal muscle will endure ischemia is important to know clinically. Using microsurgical techniques, we shut off the blood supply to the quadriceps femoris muscle in adult Wistar rats--by occluding the artery, the vein, or both for varying time intervals. The muscle was maintained in the animal for 48 hours, and then examined histologically. Our results indicate that the period of warm ischemia should be limited to about one hour, because a longer period of arterial ischemia produces severe histological changes in muscle. The limiting factor seems to be the arterial, rather than the venous supply. The possibility of muscle regeneration after such ischemic insults was not investigated.
Least Soft-thresold Squares Tracking

In this paper, we propose a generative tracking method based on a novel robust linear regression algorithm. In contrast to existing methods, the proposed Least Soft-thresold Squares (LSS) algorithm models the error term with the Gaussian-Laplacian distribution, which can be solved efficiently. Based on maximum joint likelihood of parameters, we derive a LSS distance to measure the difference between an observation sample and the dictionary. Compared with the distance derived from ordinary least squares methods, the proposed metric is more effective in dealing with outliers. In addition, we present an update scheme to capture the appearance change of the tracked target and ensure that the model is properly updated. Experimental results on several challenging image sequences demonstrate that the proposed tracker achieves more favorable performance than the state-of-the-art methods.
Constrained Gaussian mixture model framework for automatic segmentation of MR brain images

An automated algorithm for tissue segmentation of noisy, low-contrast magnetic resonance (MR) images of the brain is presented. A mixture model composed of a large number of Gaussians is used to represent the brain image. Each tissue is represented by a large number of Gaussian components to capture the complex tissue spatial layout. The intensity of a tissue is considered a global feature and is incorporated into the model through tying of all the related Gaussian parameters. The expectation-maximization (EM) algorithm is utilized to learn the parameter-tied, constrained Gaussian mixture model. An elaborate initialization scheme is suggested to link the set of Gaussians per tissue type, such that each Gaussian in the set has similar intensity characteristics with minimal overlapping spatial supports. Segmentation of the brain image is achieved by the affiliation of each voxel to the component of the model that maximized the a posteriori probability. The presented algorithm is used to segment three-dimensional, T1-weighted, simulated and real MR images of the brain into three different tissues, under varying noise conditions. Results are compared with state-of-the-art algorithms in the literature. The algorithm does not use an atlas for initialization or parameter learning. Registration processes are therefore not required and the applicability of the framework can be extended to diseased brains and neonatal brains
Brain activation in adults who stutter under delayed auditory feedback: An fMRI study

It is well known that some people who stutter (PWS) show an immediate reduction of stuttering when they speak under a condition of delayed auditory feedback (DAF). In the present study, to investigate cortical activations during speech production through the DAF effect, we performed functional magnetic resonance imaging (fMRI) experiments under the NAF (non-altered feedback) and DAF conditions for PWS and people who do not stutter (PWNS). The results are that (1) the PWS showed the higher activation in the right inferior frontal gyrus (Brodmann Area (BA)45) than the PWNS under the NAF condition; (2) the activations of the right superior temporal gyrus and the right middle temporal gyrus were higher under the DAF condition than the NAF in both PWNS and PWS groups; (3) the PWNS showed the higher activation in the right supplementary motor area and superior temporal gyrus than the PWS under both NAF and DAF conditions; (4) the PWNS showed the higher activation in the inferior frontal gyrus(the right BA45 and the bilateral BA46) under the DAF condition than the NAF. These results reconfirm most of the previous findings with some slightly different activation areas, and underscore the involvement of inferior frontal gyrus and superior temporal gyrus in dysfluency.
Kinanthropometric profile of Cuban women Olympic volleyball champions.

INTRODUCTION Athletes' kinanthropometric profiles are widely addressed in the scientific literature. Such profiles are particularly important in volleyball because absolute size contributes a significant percentage of total variance associated with athletic success. As in other team sports, volleyball players' kinanthropometric attributes correlate with the game's tactical demands. From 1992 through 2000, the Cuban women's volleyball team achieved top global performance, winning first place in three successive Summer Olympic Games. OBJECTIVE Describe the kinanthropometric profiles of Cuban women Olympic volleyball champions during 1992-2000 and compare these by position played. METHODS Measurements were taken of body composition, somatotype, proportionality and several anthropometric indicators in 41 Cuban women volleyball players, grouped by playing position. All were members of the national team that participated in the Summer Olympic Games in Barcelona (1992), Atlanta (1996) and Sydney (2000). Mean and standard deviations were calculated for all study variables. Analysis of variance was used to compare means for different positions for the variables weight; height; percent adipose, muscle and bone mass; body mass index; and muscle-to-bone ratio. Discriminant analysis was performed to identify anthropometric dimensions differentiating playing positions (center, spiker and setter), using p<0.05 as significance threshold. Results were presented in tables and figures. RESULTS Centers presented greater absolute size and higher average adipose (22.8±1.7 kg) and bone (7.1±0.6 kg) mass. The mean somatotype of all volleyball players was balanced mesomorphic (2.7-3.6-2.9). Classified by position, centers (2.9-3.4-3.4) and spikers (2.8-3.6-2.9) presented an average mesomorphic-ectomorphic somatotype, and setters (2.6-3.7-2.6) were balanced mesomorphic. On assessing Somatotype Attitudinal Mean (SAM), centers and spikers showed more intrapositional homogeneity than that of setters. Centers were significantly taller (187.1±2.5 cm) than players in other positions. Centers' percent adipose tissue mass (28.9±2.7%) was significantly higher than that of setters (24.3±2.7%), who were leanest of all positions. CONCLUSIONS The kinanthropometric profile of Cuban women Olympic volleyball champions was defined by considerable muscular-skeletal development, with a predominantly mesomorphic somatotype and low endomorphy. Height and body composition varied significantly by playing position.
Unusual Manifestations of Vertebral Osteomyelitis: Intraosseous Lesions Mimicking Metastases

BACKGROUND AND PURPOSE: Vertebral osteomyelitis can have different imaging manifestations. The purpose of this study was to demonstrate the unusual MR imaging patterns of vertebral osteomyelitis with intraosseous lesions mimicking metastases. MATERIALS AND METHODS: From September 2000 to August 2007, 7 patients were selected from our data base of 214 patients with confirmed vertebral osteomyelitis and MR images. All of those having misinterpreted MR imaging reports and unusual imaging patterns were analyzed. The presence of a peripheral curvilinear area of low signal intensity in an osseous lesion (the rim sign) and a peripheral rim of high signal intensity on T2-weighted images around an osseous lesion (the halo sign) was evaluated. Follow-up MR imaging studies were performed in all patients. RESULTS: The patients were 5 men and 2 women, with an age range of 42–80 years. MR imaging findings of those with vertebral osteomyelitis showed a solitary lesion in 2 and multiple lesions in 5 patients. The intraosseous lesions revealed low signal intensity on T1-weighted images, mixed or high signal intensity on T2-weighted images, high signal intensity on short τ inversion recovery images, and global or marginal enhancement. The rim sign was found in 6 (86%) patients; halo sign, in 7 (100%); preserved intervertebral disks, in 7 (100%); and limited paraspinal or epidural inflammation, in 6 (86%). Images of all patients demonstrated healing or almost healed changes on the follow-up MR imaging studies. CONCLUSION: Vertebral osteomyelitis can have MR imaging patterns mimicking osseous metastases. Recognition of these unusual imaging manifestations, together with clinical and histopathologic analysis, may aid in reaching the correct diagnosis.
2 Goodness of Fit Statistics in GLMsIn

The possible discrepancy between a hypothesized model and the observed data is measured by so called Goodness of Fit Statistics. In order to decide whether the observed discrepancy is substantial, the distributions of these statistics under the hypothesised model are needed to perform a statistical test. Because of the diiculty to compute the exact distributions, just when the sample size is small, better approximations than provided by common asymptotic theory have to be found. In the case of a loglinear Poisson model we will do that by diierent bootstrap methods.
An Enlarged Pragmatist Inquiry Paradigm for Methodological Pluralism in Academic Design Research

As part of a process of academic legitimization, design has made claims to be epistemologically and methodologically distinct from the Arts and Sciences. Among the multiple propositions that have been made about this distinctiveness little has been said about the fundamentally pragmatic nature of design research and practice. Pragmatism in both instrumental and critical forms is a robust epistemological and methodological terrain for design research, which architecture and built environment disciplines have explored as a basis for their methodological pluralism. In the newer design disciplines of industrial, interior, and communication design, theory fashions and the market (e.g. human-centred design, interaction design, retail design) predominate, and the rich heritage and relevance of pragmatism is poorly understood. An expanded pragmatist inquiry paradigm, incorporating visual and material argumentation and the opportunity for engagement with critical pragmatism, offers away beyond the current “conceits” of design. Such a theoretically and philosophically informed epistemology has particular relevance to the current debates about scholarship in design as it proposes a provisional metanarrative– pragmatism – as the broad epistemological and methodological base for methodological pluralism in design research and practice.
SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison

The proteome-wide characterization and analysis of protein ligand-binding sites and their interactions with ligands can provide pivotal information in understanding the structure, function and evolution of proteins and for designing safe and efficient therapeutics. The SMAP web service (SMAP-WS) meets this need through parallel computations designed for 3D ligand-binding site comparison and similarity searching on a structural proteome scale. SMAP-WS implements a shape descriptor (the Geometric Potential) that characterizes both local and global topological properties of the protein structure and which can be used to predict the likely ligand-binding pocket [Xie,L. and Bourne,P.E. (2007) A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand-binding sites. BMC bioinformatics, 8 (Suppl. 4.), S9. ]. Subsequently a sequence order independent profile–profile alignment (SOIPPA) algorithm is used to detect and align similar pockets thereby finding protein functional and evolutionary relationships across fold space [Xie, L. and Bourne, P.E. (2008) Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc. Natl Acad. Sci. USA, 105, 5441–5446]. An extreme value distribution model estimates the statistical significance of the match [Xie, L. , Xie, L. and Bourne, P.E. (2009) A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery. Bioinformatics, 25, i305–i312. ]. These algorithms have been extensively benchmarked and shown to outperform most existing algorithms. Moreover, several predictions resulting from SMAP-WS have been validated experimentally. Thus far SMAP-WS has been applied to predict drug side effects, and to repurpose existing drugs for new indications. SMAP-WS provides both a user-friendly web interface and programming API for scientists to address a wide range of compute intense questions in biology and drug discovery. AVAILABILITY SMAP-WS is available from the URL http://smap.nbcr. net.
Rapid and Sensitive Determination of Benzaldehyde Arising from Benzyl Alcohol Used as Preservative in an Injectable Formulation Solution Using Dispersive Liquid-Liquid Microextraction Followed by Gas Chromatography

A rapid and sensitive method has been developed for the determination of benzaldehyde, a toxic oxidation product of the widely used preservative and co-solvent benzyl alcohol in injectable formulations of non-steroidal anti-inflammatory drugs, diclofenac, vitamin B-complex and Voltaren injection solutions by using dispersive liquid-liquid microextraction followed by gas chromatography. This method involves the use of an appropriate mixture of extraction solvent (43.0 μL 1,2-dichloroethane) and disperser solvent (1.0 mL acetonitrile) for the formation of a cloudy solution in a 5.0-mL aqueous sample containing benzaldehyde. The linear range was 1.0 – 1000 μg L^−1, and the limit of detection was 0.2 μg L^−1 for benzaldehyde.
Multiple-Energy Carriers: Modeling of Production, Delivery, and Consumption

This paper presents a generic framework for the modeling of energy systems comprising multiple-energy carriers, such as electricity, heat, gas, biomass, etc. The modeling framework is based on the so-called energy hub approach. The core idea of the energy hub is the definition of a conversion matrix capable of describing the interactions of production, delivery, and consumption in multiple-energy carrier systems. Based on the energy hub concept a broad spectrum of modeling extensions and applications is presented, such as a multiple-energy carrier optimal power flow, risk management and investment analysis tools, agent-based control schemes for decentralized generation units as well as the possibility to analyze the influence of plug-in hybrid electric vehicles (PHEVs) on future energy systems. The paper is concluded with a section presenting the key benefits of the energy hub modeling framework, followed by a discussion on the main design principles generality, scalability, and modularity as well as a discussion on the possibility to follow top-down or bottom-up modeling strategies.