Miracle-dz/UniFAR-FTUs huggingface dataset:
Studies of a Ring-Cleaving Dioxygenase Illuminate the Role of Cholesterol Metabolism in the Pathogenesis of Mycobacterium tuberculosis

Mycobacterium tuberculosis, the etiological agent of TB, possesses a cholesterol catabolic pathway implicated in pathogenesis. This pathway includes an iron-dependent extradiol dioxygenase, HsaC, that cleaves catechols. Immuno-compromised mice infected with a ΔhsaC mutant of M. tuberculosis H37Rv survived 50% longer than mice infected with the wild-type strain. In guinea pigs, the mutant disseminated more slowly to the spleen, persisted less successfully in the lung, and caused little pathology. These data establish that, while cholesterol metabolism by M. tuberculosis appears to be most important during the chronic stage of infection, it begins much earlier and may contribute to the pathogen's dissemination within the host. Purified HsaC efficiently cleaved the catecholic cholesterol metabolite, DHSA (3,4-dihydroxy-9,10-seconandrost-1,3,5(10)-triene-9,17-dione; k cat/K m = 14.4±0.5 µM−1 s−1), and was inactivated by a halogenated substrate analogue (partition coefficient<50). Remarkably, cholesterol caused loss of viability in the ΔhsaC mutant, consistent with catechol toxicity. Structures of HsaC:DHSA binary complexes at 2.1 Å revealed two catechol-binding modes: bidentate binding to the active site iron, as has been reported in similar enzymes, and, unexpectedly, monodentate binding. The position of the bicyclo-alkanone moiety of DHSA was very similar in the two binding modes, suggesting that this interaction is a determinant in the initial substrate-binding event. These data provide insights into the binding of catechols by extradiol dioxygenases and facilitate inhibitor design.
L1-Norm Kernel Discriminant Analysis Via Bayes Error Bound Optimization for Robust Feature Extraction

A novel discriminant analysis criterion is derived in this paper under the theoretical framework of Bayes optimality. In contrast to the conventional Fisher's discriminant criterion, the major novelty of the proposed one is the use of L1 norm rather than L2 norm, which makes it less sensitive to the outliers. With the L1-norm discriminant criterion, we propose a new linear discriminant analysis (L1-LDA) method for linear feature extraction problem. To solve the L1-LDA optimization problem, we propose an efficient iterative algorithm, in which a novel surrogate convex function is introduced such that the optimization problem in each iteration is to simply solve a convex programming problem and a close-form solution is guaranteed to this problem. Moreover, we also generalize the L1-LDA method to deal with the nonlinear robust feature extraction problems via the use of kernel trick, and hereafter proposed the L1-norm kernel discriminant analysis (L1-KDA) method. Extensive experiments on simulated and real data sets are conducted to evaluate the effectiveness of the proposed method in comparing with the state-of-the-art methods.
p . m . “ Negotiating with Labor under Financial Distress ”

We analyze how firms strategically renegotiate labor contracts to extract concessions from labor. While anecdotal evidence suggests that firms tend to renegotiate down wages in times of financial distress, there is no empirical evidence that documents such renegotiation, its determinants, and its magnitude. This paper attempts to fill this gap. Using a unique data set of airlines that includes detailed information on wages and pension plans we document an empirical link between airline financial distress, pension underfunding, and wage concessions. We show that airlines in financial distress obtain wage concession from employees whose pension plans are underfunded. As part of our identification strategy, we exploit the fact that pension plans in the U.S are partially insured by the Pension Benefit Guaranty Corporation (PBGC). Using variation in the degree of pension coverage provided by the PBGC, we show that employees’ outside option in bargaining is crucial in determining the degree of wage concessions during labor contract renegotiation. Our empirical evidence highlights the strategic use of pension underfunding by firms and the resultant wage cuts which employees endure as a result.
Chapter 1 Network of Sensor and Actuator Agents for Building Automation Systems

Due to at least two reasons, energy consumption for heating, ventilation, ir conditioning (HVAC) and domestic hot water (DHW) systems should be reduced. Firs t, the total energy consumption is high since nearly 20% of total energy in USA is accounted fo r HVAC systems. Sencond reason is exploitation of renevable energy sources, wh ich depend on current time and weather situation. Thus, the energy management should improve to eff ctive by managing currently available energy. For this purpose, the sensor acto r agent network is proposed with an example on domestic hot water heating, taking into accoun t several aspects including the occupant presence. The simulation model was used, wh re the water consumption affected system dynamics. The agent-based schema com bined with the simulator enables an occupant to choose the most subjectively desirable po licy of the DHW control mechanism.
Effect of Radial Shock Wave Therapy on Spasticity of the Upper Limb in Patients With Chronic Stroke

AbstractRecently, studies have reported that extracorporeal shock wave therapy (ESWT) is a safe, noninvasive, alternative treatment for spasticity. However, the effect of ESWT on spasticity cannot be determined, because most studies to date have enrolled small patient numbers and have lacked placebo-controlled groups and/or long-term follow-up. In addition, whether varying the number of ESWT sessions would affect the duration of the therapeutic effect has not been investigated in a single study. Hence, we performed a prospective, randomized, single blind, placebo-controlled study to investigate the long-term effect of radial ESWT (rESWT) in patients with poststroke spasticity and surveyed the outcome of functional activity.Sixty patients were randomized into 3 groups. Group A patients received 1 session of rESWT per week for 3 consecutive weeks; group B patients received a single session of rESWT; group C patients received one session of sham rESWT per week for 3 consecutive weeks. The primary outcome was Modified Ashworth Scale of hand and wrist, whereas the secondary outcomes were Fugl-Meyer Assessment of hand function and wrist control. Evaluations were performed before the first rESWT treatment and immediately 1, 4, 8, 12, and 16 weeks after the last session of rESWT.Compared to the control group, the significant reduction in spasticity of hand and wrist lasted at least 16 and 8 weeks in group A and B, respectively. Three sessions of rESWT had a longer-lasting effect than one session. Furthermore, the reduction in spasticity after 3 sessions of rESWT may be beneficial for hand function and wrist control and the effect was maintained for 16 and 12 weeks, respectively.rESWT may be valuable in decreasing spasticity of the hand and wrist with accompanying enhancement of wrist control and hand function in chronic stroke patients.
On-Line Supervisory Control Design for Maglev Transportation System via Total Sliding-Mode Approach and Particle Swarm Optimization

This study focuses on the design of an on-line levitation and propulsion control for a magnetic-levitation (maglev) transportation system. First, the dynamic model of a maglev transportation system including levitated electromagnets driven by linear servo amplifiers and a propulsive linear induction motor (LIM) based on the concepts of mechanical geometry and motion dynamics is developed. Then, a total sliding-mode (TS) control strategy is introduced, and the concept of TS control is incorporated into particle swarm optimization (PSO) to form an on-line TSPSO control framework with varied inertial weights for preserving the robust control characteristics and reducing the chattering control phenomena of TS control. In this TSPSO control scheme, a PSO control system is utilized to be the major controller, and the stability can be indirectly ensured by the concept of TS control without strict constraint and detailed system knowledge. In order to further directly stabilize the system states around a predefined bound region and effectively accelerate the searching speed of the PSO control, a supervisory mechanism is embedded into the TSPSO control to constitute a supervisory TSPSO (STSPSO) control strategy. The effectiveness of the proposed control schemes for the maglev transportation system is verified by numerical simulations and experimental results, and the superiority of the STSPSO control scheme is indicated in comparison with the adaptive fuzzy neural network, PSO-based proportional-integral-differential, TS and TSPSO control strategies.
A Linear Pendulum Experiment: Effects of Operator Intention on Damping Rate

An attractive pendulum consisting of a two-inch crystal ball sus- pended on a fused silica rod is the focus of an experiment to measure possible effects of conscious intention on an analog physical system. The pendulum is enclosed in a clear acrylic box, and provided with a computer controlled me- chanical system to release it from the same starting height in repeated runs. A high speed binary counter registers interruptions of photodiode beams, to measure velocities at the nadir of the pendulum arc with microsecond accura- cy. In runs of 100 swings, taking about three minutes, operators attempt to keep swings high, i.e. to decrease the damping rate (HI); to reduce swing am- plitude, i.e. to increase the damping rate (LO); or to take an undisturbed base- line (BL). Over a total of 1545 sets, generated by 42 operators, the HI - LO difference is significant in the direction of intention for five individuals, and the differ- ence between intention and baseline runs is significant and positive for five other operators. The overall HI - LO difference is reduced to non-signifi- cance by strong negative performances from several operators, four of whom have comparably large scores in the direction opposite to intention. Analysis of variance reveals significant internal structure in the database (main effects F4, 189= 2.845, p = .025). Subset comparisons indicate that male operators tend to score higher than females, and that randomly instructed trials tend to- ward higher scores than volitional trials, especially for male operators. Trials generated with the operator in a remote location have a larger effect size than the local trials. While direct comparisons are not straightforward, it appears that effects of operator intention on the pendulum damping rate may be similar in magni- tude and style to those in other human/machine interaction experiments. Al- though this result fails to support an experimental hypothesis that the analog nature of the pendulum experiment would engender larger effect sizes, it does confirm a basic similarity of consciousness effects across experiments using fundamentally different physical systems.
Supporting students’ mental health and wellbeing through the integration of companion animals into tutorial programmes at a teaching-led university

This paper considers the protocols and processes of a small-scale project involving final year students and the companion animals (dogs and guinea pigs) of tutors, aimed at improving student wellbeing and fostering relational learning. Narratives and survey data revealed a range of perceived benefits including those relating to the technique of distraction to reduce anxiety and improve student wellbeing. Also identified are possible further benefits including relational learning and improved attendance. The paper reflects on a range of other issues, such as the welfare of the animals, potential risks and objections from staff and students. Recommendations from the pilot project are provided and the potential for further research identified.
Improved blood pressure control associated with a large-scale hypertension program.

IMPORTANCE Hypertension control for large populations remains a major challenge. OBJECTIVE To describe a large-scale hypertension program in Northern California and to compare rates of hypertension control in that program with statewide and national estimates. DESIGN, SETTING, AND PATIENTS The Kaiser Permanente Northern California (KPNC) hypertension program included a multifaceted approach to blood pressure control. Patients identified as having hypertension within an integrated health care delivery system in Northern California from 2001-2009 were included. The comparison group comprised insured patients in California between 2006-2009 who were included in the Healthcare Effectiveness Data and Information Set (HEDIS) commercial measurement by California health insurance plans participating in the National Committee for Quality Assurance (NCQA) quality measure reporting process. A secondary comparison group was included to obtain the reported national mean NCQA HEDIS commercial rates of hypertension control between 2001-2009 from health plans that participated in the NCQA HEDIS quality measure reporting process. MAIN OUTCOMES AND MEASURES Hypertension control as defined by NCQA HEDIS. RESULTS The KPNC hypertension registry included 349,937 patients when established in 2001 and increased to 652,763 by 2009. The NCQA HEDIS commercial measurement for hypertension control within KPNC increased from 43.6% (95% CI, 39.4%-48.6%) to 80.4% (95% CI, 75.6%-84.4%) during the study period (P < .001 for trend). In contrast, the national mean NCQA HEDIS commercial measurement increased from 55.4% to 64.1%. California mean NCQA HEDIS commercial rates of hypertension were similar to those reported nationally from 2006-2009 (63.4% to 69.4%). CONCLUSIONS AND RELEVANCE Among adults diagnosed with hypertension, implementation of a large-scale hypertension program was associated with a significant increase in hypertension control compared with state and national control rates. Key elements of the program included a comprehensive hypertension registry, development and sharing of performance metrics, evidence-based guidelines, medical assistant visits for blood pressure measurement, and single-pill combination pharmacotherapy.
The contribution of hypersalience to the "jumping to conclusions" bias associated with delusions in schizophrenia.

BACKGROUND Previous schizophrenia research involving the "beads task" has suggested an association between delusions and 2 reasoning biases: (1) "jumping to conclusions" (JTC), whereby early, resolute decisions are formed on the basis of little evidence and (2) over-adjustment of probability estimates following a single instance of disconfirmatory evidence. In the current study, we used a novel JTC-style paradigm to provide new information about a cognitive operation common to these 2 reasoning biases. METHODS Using a task that required participants to rate the likelihood that a fisherman was catching a series of black or white fish from Lake A and not Lake B, and vice versa, we compared the responses of 4 groups (healthy, bipolar, nondelusional schizophrenia and delusional schizophrenia) when we manipulated 2 elements of the Bayesian formula: incoming data and prior odds. RESULTS Regardless of our manipulations of the Bayesian formula, the delusional schizophrenia group gave significantly higher likelihood ratings for the lake that best matched the colour of the presented fish, but the ratings for the nonmatching lake did not differ from the other groups. LIMITATIONS The limitations of this study include a small sample size for the group of severely delusional patients and a preponderance of men in the schizophrenia sample. CONCLUSION Delusions in schizophrenia are associated with hypersalience of evidence-hypothesis matches but normal salience of nonmatches. When the colour of the incoming data is uniform (fish of only one colour), this manifests as JTC early in a series, and when the colour of incoming data varies (both black and white fish), this manifests as an overadjustment midseries. This account can provide a unifying explanation for delusion-associated performance patterns previously observed in the beads task in schizophrenia.
Hidden Markov models (HMMs) isolated word recognizer with the optimization of acoustical analysis and modeling techniques

Most state of the art automatic speech recognition (ASR) systems are typically based on continuous Hidden Markov Models (HMMs) as acoustic modeling technique. It has been shown that the performance of HMM speech recognizers may be affected by a bad choice of the type of acoustic feature parameters in the acoustic front end module. For these reasons, we propose in this paper a dedicated isolated word recognition system based on HMMs which was carefully optimized specifically at the acoustic analysis and HMM acoustical modeling levels. Such conception was tested and valued on Hidden Markov model toolkit platform (HTK). Systems performances were evaluated using the TIMIT database. One comparative study was carried out using two types of speech analysis: The cepstral method referred to as Mel frequency cepstral coefficients (MFCC) and the perceptual linear predictive (PLP) coding are used for different tests so as to evaluate and reinforce our conception. The frame shift duration effect of the acoustic analysis as well as the addition of the dynamic coefficients of the acoustic parameters (MFCC and PLP) were carefully tested in order to look for high accuracy for our optimized isolated word recognition (IWR) system. Finally, various experiments related to the HMM topology have been carried out in order to get better recognition accuracies. In fact, the effect of some modeling parameters of HMM on the recognition accuracy of the IWR system such as the number of states as well as the number of Gaussian mixtures were analyzed in order to get the optimal HMM topology.
Experimental determination of laws of color harmony. Part 5: The harmony content of the various hue triads

We, in 1956 the Department of Architecture at the Budapest University of Technology and Economics, decided to start an extensive color harmony experiment. The experimental work, the collation, and processing of the collected data, lasting 50 years, was completed in 2006. The experiments described in this article are based on earlier experimental results obtained from investigation into the harmony content of hue pairs. We then decided to search for a third hue, which in association with an existing pair, with high-color harmony, forms a hue triad with high-harmony content too. The compositions prepared for the experiment were composed in each case of three hues of four identical saturation but different brightness, forming a group of 12 colors. The color content of the compositions covered the color space uniformly. That was the first stage in the experiment, carried out with 60 compositions. In the second stage, we investigated the effect of the saturation content of the colors used in the composition, on the harmony content of the hue triads. For this experiment, we prepared 48 compositions. In these experiments, we applied the method of grading. We concluded that the level of the harmony content of the hue triads depends on the inclination between the hue planes in the Coloroid color space. We also concluded that to every hue, selected for starting point, six well-definable groups of hues can be ordered from the Coloroid color space, from which color triads with high harmony content, can be selected. It showed conclusively that the saturation level of the individual members of the triads has a significant influence on their harmony content. © 2010 Wiley Periodicals, Inc. Col Res Appl, 2011
Implications of hyperactivity in anorexia nervosa : from redefinition to clinical research

Anorexia nervosa is a serious and complex psychiatric pathology included in eating disorders. Its symptoms include physical hyperactivity, which has been associated by many with a worse clinical and therapeutic outcome. Much remains to be known and understood about physical activity, which is problematic in eating disorders, especially in anorexia nervosa. The aims of this thesis are to: 1) critically and exhaustively examine the literature published during the past 40 years (1975-2015). This is done in order to clarify the landscape and give general clinical and research perspectives for future studies. 2) Investigate the impact of different definitions of problematic physical activity, found in the literature, on its prevalence in a large sample of patients suffering from acute anorexia nervosa. We will examine the associations between these different definitions and core eating disorders symptoms, emotional profile and quality of life. 3) Investigate the impact of problematic physical activity on nutritional status (body mass index and body composition) of patients. This is done by taking into account clinical features. These features include anorexia nervosa subtypes (restricting or binge-eating/purging type), age at onset, illness duration, premenarchal anorexia nervosa, and presence of amenorrhea. Finally, we propose a comprehensive model of the development of problematic physical activity in anorexia nervosa. We highlight the fact that physical activity could be positively taken into account in global treatment programs. It could be integrated in these programs, in addition to their psychological, somatic and social dimensions. Problematic physical activity in anorexia nervosa is in need of immediate attention from clinicians and researchers.
The InterPro protein families database: the classification resource after 15 years

The InterPro database (http://www.ebi.ac.uk/interpro/) is a freely available resource that can be used to classify sequences into protein families and to predict the presence of important domains and sites. Central to the InterPro database are predictive models, known as signatures, from a range of different protein family databases that have different biological focuses and use different methodological approaches to classify protein families and domains. InterPro integrates these signatures, capitalizing on the respective strengths of the individual databases, to produce a powerful protein classification resource. Here, we report on the status of InterPro as it enters its 15th year of operation, and give an overview of new developments with the database and its associated Web interfaces and software. In particular, the new domain architecture search tool is described and the process of mapping of Gene Ontology terms to InterPro is outlined. We also discuss the challenges faced by the resource given the explosive growth in sequence data in recent years. InterPro (version 48.0) contains 36 766 member database signatures integrated into 26 238 InterPro entries, an increase of over 3993 entries (5081 signatures), since 2012.
Applied Techniques for High Bandwidth Data Transfers across Wide Area Networks

Large distributed systems such as Computational/Data Grids require large amounts of data to be co-located with the computing facilities for processing.From our work develogpin a scalable distributed network cache.we have gained experience with techniques necessary to achieve high data throughput over high bandwidth Wide Area Networks(WAN). In this paper,we discuss several hardware and software dsign techniques,and then describe their application to an implementation of an enhanced FTP protocol called GridFTP,We describe results from the Supercomputing 2000 conference.