Miracle-dz/UniFAR-FTUs huggingface dataset:
Piecewise linear approximation of protein structures using the principle of minimum message length

Simple and concise representations of protein-folding patterns provide powerful abstractions for visualizations, comparisons, classifications, searching and aligning structural data. Structures are often abstracted by replacing standard secondary structural features—that is, helices and strands of sheet—by vectors or linear segments. Relying solely on standard secondary structure may result in a significant loss of structural information. Further, traditional methods of simplification crucially depend on the consistency and accuracy of external methods to assign secondary structures to protein coordinate data. Although many methods exist automatically to identify secondary structure, the impreciseness of definitions, along with errors and inconsistencies in experimental structure data, drastically limit their applicability to generate reliable simplified representations, especially for structural comparison. This article introduces a mathematically rigorous algorithm to delineate protein structure using the elegant statistical and inductive inference framework of minimum message length (MML). Our method generates consistent and statistically robust piecewise linear explanations of protein coordinate data, resulting in a powerful and concise representation of the structure. The delineation is completely independent of the approaches of using hydrogen-bonding patterns or inspecting local substructural geometry that the current methods use. Indeed, as is common with applications of the MML criterion, this method is free of parameters and thresholds, in striking contrast to the existing programs which are often beset by them. The analysis of results over a large number of proteins suggests that the method produces consistent delineation of structures that encompasses, among others, the segments corresponding to standard secondary structure. Availability: http://www.csse. monash.edu. au/~karun/pmml. Contact: arun.konagurthu@monash.edu; lloyd.allison@monesh.edu
Dimensionality Estimation and Manifold Learning using Tensor Voting

We address instance-based learning from a perceptual organization standpoint using tensor voting. The goal of instance-based learning is to learn the underlying relationships between observations, which are points in an N -D continuous space, under the assumption that they lie in a limited part of the N -D space, typically a manifold, the dimensionality of which is an indication of the degrees of freedom of the underlying system. We pose the problem of instance-based learning in an equivalent form: manifold learning from observations. Unlike traditional manifold learning approaches, we do not perform dimensionality reduction, which would limit the class of datasets we are able to process, but instead perform all operations in the original input space. To this end we apply tensor voting, a perceptual organization framework that has mostly been applied to computer vision problems, after modifying it to make its implementation in high-dimensional spaces practical. We are able to estimate local dimensionality and structure for datasets that cannot be handled by current state-of-the-art approaches. We first show that we can obtain reliable dimensionality estimates at each point, instead of a global average estimate for the entire dataset, which is a major advantage over competing methods. We then present a quantitative evaluation of our results in the estimation of local manifold structure using synthetic datasets with known ground truth. Our software is available to the scientific community at http://iris.usc. edu/home/iris/medioni/User.html.
What’s in a Message?

In this paper we present the first step in a larger series of experiments for the induction of predicate/argument structures. The structures that we are inducing are very similar to the conceptual structures that are used in Frame Semantics (such as FrameNet). Those structures are called messages and they were previously used in the context of a multi-document summarization system of evolving events. The series of experiments that we are proposing are essentially composed from two stages. In the first stage we are trying to extract a representative vocabulary of words. This vocabulary is later used in the second stage, during which we apply to it various clustering approaches in order to identify the clusters of predicates and arguments---or frames and semantic roles, to use the jargon of Frame Semantics. This paper presents in detail and evaluates the first stage.
An O(sqrt(n)) Approximation and Integrality Gap for Disjoint Paths and Unsplittable Flow

We consider the maximization version of the edge-disjoint path problem (EDP). In undirected graphs and directed acyclic graphs, we obtain an O( p n) upper bound on the approximation ratio where n is the number of nodes in the graph. We show this by es- tablishing the upper bound on the integrality gap of the natural relaxation based on mul- ticommodity flows. Our upper bound matches within a constant factor a lower bound of Ω( p n) that is known for both undirected and directed acyclic graphs. The best previous upper bounds on the integrality gaps were O(min{n 2/3 , p m}) for undirected graphs and O(min{ p n log n, p m}) for directed acyclic graphs; here m is the number of edges in the graph. These bounds are also the best known approximation ratios for these problems. Our bound also extends to the unsplittable flow problem (UFP) when the maximum demand is at most the minimum capacity.
Investigation on people living with Paro at home

Questionnaires have been conducted to the owners of Paro in order to investigate people living with Paro at home. Although service robots such as AIBO have been commercialized and tend to be familiar with us, researches on owners' background are few. The owners of Paro answered the questionnaires and 85 feedbacks were obtained. The results showed that majority of the owners were females and have kept pets before, but cannot keep pets currently. Important factors for females to keep Paro seem to be not only “Can touch and hug” but also “Tactile texture”. In addition, although animal preference seems to influence the way to touch Paro; it does not influence the evaluation of Paro. This tendency seems to be due to different playing style. This paper presents the analyzed data of the effects of owners' sex difference and animal preference on interaction with Paro.
Fertility and Age in the Domestic Fowl.

seems definitely confined to the class of plants combining the tunicate and ramosa characters. The cauliflower character, which in itself would seem more nearly related to ramosa than to tunicate, is somewhat more definitely associated with the ramosa than with the tunicate character of the tassels. There were 22 plants with pure cauliflower ears. Twenty of these had tassels in which both tunicate and ramosa characters were obvious. The other two were classed as having ramosa tassels. Of the 13 plants with partial cauliflower ears 11 had ramosa tassels in which no tunicate characters were observed, and two showed evidence of both tunicate and ramosa in their tassels. If the second-generation plants are examined for each of the parental types separately, there is seen to have been a simple 1 to 3 segregation in both instances. One-fourth of the total number of plants are ramosa and three-fourths non-ramosa (observed 79 to 247, expected 81.5 to 244.5). One-fourth are non-tunicate and three-fourths tunicate (observed 80 to 246, expected 81.5 to 244.5). The distinction between halfand full-tunicate could not be made when these characters were combined with the ramosa character. The various combinations of parental characters, occurring as they do in the normal di-hybrid ratios, show that the tunicate and ramosa characters are not genetically correlated. The extended publication will appear in the Journal of Agricultural Research.
Decision Analytic Markov Model Weighting Expected Benefits and Current Limitations of First-Generation Bioresorbable Vascular Scaffolds: Implications for Manufacturers and Next Device Iterations

Background— Relative benefits of bioresorbable vascular scaffolds (BVS) compared with everolimus-eluting stents (EES) are expected to accrue after complete bioresorption. Methods and Results— We built a decision analytic Markov model comparing BVS and EES for a contemporary percutaneous coronary intervention population. Procedure-related morbidity and outcome data from the available literature were used to derive model probabilities. The net benefit of BVS and EES was estimated in terms of quality-adjusted life expectancy. Under the assumption of no risk for device thrombosis and target lesion revascularization with BVS beyond 3 years, the equipoise in quality-adjusted life expectancy (12.86) between BVS and EES was achieved 19 years after implantation. The maximum tolerable excess risk of 3-year BVS thrombosis equalizing the model-predicted quality-adjusted life expectancy of BVS and EES at 10 years was 1.40, corresponding to an absolute tolerable rate of 1.45%. Conclusions— At the currently observed relative increase in device thrombosis and under the extreme hypothesis of no scaffold thrombosis and target lesion revascularization beyond 3 years, the incremental benefit of BVS over EES becomes apparent only after 19 years. This simulation suggests that there is a small degree of benefit that clinicians and decision-makers may expect from the first-generation BVS at the current risk of device thrombosis. Manufacturers should target scaffold thrombosis rates <1.45% at 3 years to make their technologies attractive during a 10-year horizon.
Obesity, regional body fat distribution, and the metabolic syndrome in older men and women.

BACKGROUND The metabolic syndrome is a disorder that includes dyslipidemia, insulin resistance, and hypertension and is associated with an increased risk of diabetes and cardiovascular disease. We determined whether patterns of regional fat deposition are associated with metabolic syndrome in older adults. METHODS A cross-sectional study was performed that included a random, population-based, volunteer sample of Medicare-eligible adults within the general communities of Pittsburgh, Pa, and Memphis, Tenn. The subjects consisted of 3035 men and women aged 70 to 79 years, of whom 41.7% were black. Metabolic syndrome was defined by Adult Treatment Panel III criteria, including serum triglyceride level, high-density lipoprotein cholesterol level, glucose level, blood pressure, and waist circumference. Visceral, subcutaneous abdominal, intermuscular, and subcutaneous thigh adipose tissue was measured by computed tomography. RESULTS Visceral adipose tissue was associated with the metabolic syndrome in men who were of normal weight (odds ratio, 95% confidence interval: 2.1, 1.6-2.9), overweight (1.8, 1.5-2.1), and obese (1.2, 1.0-1.5), and in women who were of normal weight (3.3, 2.4-4.6), overweight (2.4, 2.0-3.0), and obese (1.7, 1.4-2.1), adjusting for race. Subcutaneous abdominal adipose tissue was associated with the metabolic syndrome only in normal-weight men (1.3, 1.1-1.7). Intermuscular adipose tissue was associated with the metabolic syndrome in normal-weight (2.3, 1.6-3.5) and overweight (1.2, 1.1-1.4) men. In contrast, subcutaneous thigh adipose tissue was inversely associated with the metabolic syndrome in obese men (0.9, 0.8-1.0) and women (0.9, 0.9-1.0). CONCLUSION In addition to general obesity, the distribution of body fat is independently associated with the metabolic syndrome in older men and women, particularly among those of normal body weight.
Computational Predictions of Rear Surface Velocities for Metal Plates under Ballistic Impact

Abstract : We are interested in temporally and spatially resolving the rear surface velocity of a plate under ballistic impact as a function of materials, impact velocity, and the ratio of plate thickness to impactor diameter. There are a variety of applications for which these details are useful: material model validation, ballistic limit (V50) characterization, and mechanics of layered systems, for example. Rapacki1 used free-surface bulging to quantify the remaining armor value of rolled homogeneous armor (RHA). Most previous work however has been related to developing or advancing analytic penetration models. The Walker-Anderson2 model, which describes long-rod penetrators into semi-infinite targets, is of particular note. However, it is only applicable until the targets rear surface affects the penetration process. Ravid et al.3 extended the model by accounting for target bulging and failure. Separately, Walker4 derived a velocity field for the back surface bulge to augment their original model. Chocron et al.5 also extended the Walker-Anderson model to account for different failure criteria in part to accurately capture the ballistic limit for several targets.
Perspectives on Sexual and Reproductive Health Sexually Transmitted Diseases among American Youth: Incidence and Prevalence Estimates, 2000

Sexually transmitted diseases (STDs) are among the most common infections in the United States. According to national estimates for 1996, more than 15 million new STD cases occur each year. 1 However, the annual STD incidence among young Americans is not known, even though 15–24-year-olds represent 25% of the sexually experienced population aged 15–44. 2 Accurately monitoring the incidence and prevalence of STDs among the population, and particularly among young people, is important in measuring the effects of disease control and prevention efforts. However, a major obstacle to the diagnosis, treatment and surveillance of STDs is that many of these infections—including chlamydia, genital her-pes, trichomoniasis and human papillomavirus (HPV) in-fection—have few, if any, recognizable symptoms. If STDs are not detected because infected persons have no symptoms and therefore do not get tested, these infections cannot be reported and counted. Even when STDs are diagnosed, health care providers may not always report nationally no-tifiable ones, such as syphilis, gonorrhea and chlamydia. Furthermore, some STDs, such as genital herpes, trichomoniasis and HPV infection, are not nationally reportable; our knowledge about these infections is based on prevalence surveys conducted among various populations that may not be representative of the general population. As a result of expanded screening programs and improved detection tests, the ability to monitor the occurrence of STDs, especially asymptomatic infections, has increased since 1996. In this article, we examine available evidence and provide estimates for the incidence and prevalence of STDs among 15–24-year-olds in the United States in 2000. METHODS We studied relevant data and estimates of STD incidence and prevalence in the available literature, focusing on the eight main STDs. For each STD, we adjusted the available information to estimate the incidence and prevalence among 15–24-year-olds in the United States for the year 2000. Sources were case reports of nationally notifiable diseases, national surveys, literature reviews and the World Health Organization (WHO). Building on prior efforts, 3 we categorized the quality and reliability of our estimates as good (level I), fair (level II) or poor (level III). Table 1 summarizes the criteria for these ratings. Our estimates were made using the available information with the highest-quality evidence. RESULTS Chlamydia Chlamydia trachomatis infection is the most commonly reported notifiable disease in the United States. In 2000—the year in which all 50 states and the District of Columbia required that cases of chlamydia be reported—the Centers for Disease Control and Prevention …
Nonlinear function controller: a simple alternative to fuzzy logic controller for a power electronic converter

Recently, there has been an increase in the application of fuzzy logic controllers (FLCs) for control of power electronic converters. Due to the FLCs' complex algorithm, their realization often calls for a compromise between cost and performance. In this paper, it is shown that the rule table of most of the two-input FLCs used with power converters can be approximated into a single nonlinearity. This allows the controller to be easily realized using simple, fast, and inexpensive analog circuits. The simplified "nonlinear function controller (NLFC)" developed in this manner is shown to be equivalent in performance to the original FLC through simulations. The NLFC concept is then applied to PI-FLC, a type of FLC popular in power converter control applications. This results in the PI-FLC being replaced by a simple "nonlinear PI controller (NPIC)". Using this simplification, the design of NPICs to obtain good dynamic performance in power converters is explained. An example design of NPIC for controlling a dc-dc boost power converter is presented. Experimental results are also presented to demonstrate the superior dynamic performance of the converter with NPIC versus that of a linear-PI controller.
Disease Rescue and Increased Lifespan in a Model of Cardiomyopathy and Muscular Dystrophy by Combined AAV Treatments

Background The BIO14.6 hamster is an excellent animal model for inherited cardiomyopathy, because of its lethal and well-documented course, due to a spontaneous deletion of delta-sarcoglycan gene promoter and first exon. The muscle disease is progressive and average lifespan is 11 months, because heart slowly dilates towards heart failure. Methodology/Principal Findings Based on the ability of adeno-associated viral (AAV) vectors to transduce heart together with skeletal muscle following systemic administration, we delivered human delta-sarcoglycan cDNA into male BIO14.6 hamsters by testing different ages of injection, routes of administration and AAV serotypes. Body-wide restoration of delta-SG expression was associated with functional reconstitution of the sarcoglycan complex and with significant lowering of centralized nuclei and fibrosis in skeletal muscle. Motor ability and cardiac functions were completely rescued. However, BIO14.6 hamsters having less than 70% of fibers recovering sarcoglycan developed cardiomyopathy, even if the total rescued protein was normal. When we used serotype 2/8 in combination with serotype 2/1, lifespan was extended up to 22 months with sustained heart function improvement. Conclusions/Significance Our data support multiple systemic administrations of AAV as a general therapeutic strategy for clinical trials in cardiomyopathies and muscle disorders.
Reentrainment Impairs Spatial Working Memory until Both Activity Onset and Offset Reentrain

Compression of the active phase (α) during reentrainment to phase-shifted light-dark (LD) cycles is a common feature of circadian systems, but its functional consequences have not been investigated. This study tested whether α compression in Siberian hamsters (Phodopus sungorus) impaired their spatial working memory as assessed by spontaneous alternation (SA) behavior in a T-maze. Animals were exposed to a 1- or 3-h phase delay of the LD cycle (16 h light/8 h dark). SA behavior was tested at 4 multiday intervals after the phase shift, and α was quantified for those days. All animals failed at the SA task while α was decompressing but recovered spatial memory ability once α returned to baseline levels. A second experiment exposed hamsters to a 2-h light pulse either early or late at night to compress α without phase-shifting the LD cycle. SA behavior was impaired until α decompressed to baseline levels. In a third experiment, α was compressed by changing photoperiod (LD 16:8, 18:6, 20:4) to see if absolute differences in α were related to spatial memory ability. Animals performed the SA task successfully in all 3 photoperiods. These data show that the dynamic process of α compression and decompression impairs spatial working memory and suggests that α modulation is a potential biomarker for assessing the impact of transmeridian flight or shift work on memory.
Customizing treatment of chronic fatigue syndrome and fibromyalgia: the role of perpetuating factors.

BACKGROUND Syndromes characterized by chronic, medically unexplained fatigue, effort- and stress-intolerance, and widespread pain are highly prevalent in medicine. RESULTS In chronic fatigue syndrome (CFS) and fibromyalgia (FM), various perpetuating factors may impair patients' quality of life and functioning and impede recovery. Although cognitive-behavioral and graded-exercise therapy are evidence-based treatments, the effectiveness and acceptability of therapeutic interventions in CFS/FM may largely depend on a customized approach taking the heterogeneity of perpetuating factors into account. CONCLUSION Further research should clarify the aim and outcome of different treatment strategies in CFS/FM, as well as the underlying mechanisms of change, including those facilitating neurobiological recovery.
Cardiac inotropic, chronotropic, and dromotropic actions of subretrofacial neurons of cat RVLM.

The cardiac actions of microinjecting sodium glutamate (0.5-2 nmol) among sympathetic premotor neurons of the subretrofacial nucleus in the rostral ventrolateral medulla (RVLM) were studied in chloralose-anesthetized cats after bilateral vagotomy, sinoaortic denervation, adrenalectomy, and α1-receptor blockade. Glutamate microinjections increased heart rate by 25.9 ± 1.8 beats/min (17.5%), systolic rate of rise in left ventricular pressure (LVdP/d t) by 1,443 ± 110 mmHg/s (119%), and arterial blood pressure by 26.9 ± 1.7 mmHg (50%), whereas they shortened the electrocardiogram P-R interval in 85 of 103 cases by 7.5 ± 1.2 ms (11.4%), triggering junctional rhythms on five occasions. The increase in LVdP/d tusually led the rise in blood pressure, and its magnitude greatly exceeded any increase attributable to changes in heart rate, diastolic filling, or afterload. Right-sided microinjections caused significantly greater tachycardias than did left-sided microinjections, but only left-sided microinjections triggered junctional rhythms (5 of 52 vs. 0 of 51; P < 0.05), whereas microinjections on either side raised LVdP/d tequally. Subretrofacial neurons thus drive positive chronotropic, inotropic, and dromotropic actions via the cardiac sympathetic nerves, whereas subsets among them preferentially control different aspects of cardiac function.