Miracle-dz/UniFAR-FTUs huggingface dataset:
PROF_ PAT 1.3: Updated database of patterns used to detect local similarities

MOTIVATION When analysing novel protein sequences, it is now essential to extend search strategies to include a range of 'secondary' databases. Pattern databases have become vital tools for identifying distant relationships in sequences, and hence for predicting protein function and structure. The main drawback of such methods is the relatively small representation of proteins in trial samples at the time of their construction. Therefore, a negative result of an amino acid sequence comparison with such a databank forces a researcher to search for similarities in the original protein banks. We developed a database of patterns constructed for groups of related proteins with maximum representation of amino acid sequences of SWISS-PROT in the groups. RESULTS Software tools and a new method have been designed to construct patterns of protein families. By using such method, a new version of databank of protein family patterns, PROF_ PAT 1.3, is produced. This bank is based on SWISS-PROT (r1.38) and TrEMBL (r1.11), and contains patterns of more than 13 000 groups of related proteins in a format similar to that of the PROSITE. Motifs of patterns, which had the minimum level of probability to be found in random sequences, were selected. Flexible fast search program accompanies the bank. The researcher can specify a similarity matrix (the type PAM, BLOSUM and other). Variable levels of similarity can be set (permitting search strategies ranging from exact matches to increasing levels of 'fuzziness'). AVAILABILITY The Internet address for comparing sequences with the bank is: http://wwwmgs.bionet. nsc.ru/mgs/programs/prof_pat/. The local version of the bank and search programs (approximately 50 Mb) is available via ftp: ftp://ftp.bionet. nsc. ru/pub/biology/vector/prof_pat/, and ftp://ftp.ebi. ac. uk/pub/databases/prof_pat/. Another appropriate way for its external use is to mail amino acid sequences to bachin@vector.nsc.ru for comparison with PROF_ PAT 1.3.
The Effect of Physical Activity on Children With ADHD: A Quantitative Review of the Literature

ABSTRACT Research on the effects of physical activity on children with attention deficit hyperactivity disorder is promising, yet no attempt has been made to integrate current findings using meta-analytic techniques. Using a meta-regression, the present study examined the effectives of physical activity for children with attention deficit hyperactivity disorder on a number of cognitive, behavioral, and emotional outcomes. From 20 empirical studies, 164 effect sizes quantifying the effectiveness of physical activity for children with attention deficit hyperactivity disorder were extracted from 22 independent samples. Results indicated an overall moderate-to-large effect for physical activity on children with attention deficit hyperactivity disorder, with a significant effect for emotion/mood. Limitations of the study, future directions, and implications for school professionals are discussed.
Beliefs Are Not Behavior

Abstract. Compensatory health beliefs (CHBs), defined as belief that an unhealthy behavior can be compensated by engaging in another healthy behavior, are negatively predictive of health-behavior change intentions and behavior. However, CHBs have to be distinguished from compensatory health behavior (CBs), which is defined as compensatory behavior that an individual engages in. As it has not been investigated to date, the aim of this study was to systematically examine the distinction between CHBs and CBs in the context of alcohol consumption. The baseline sample consisted of 898 participants (mainly students, mean age = 23.57 years). For running exploratory and confirmatory factor analyses on CHBs and CBs, the split-half sample method was used. Moreover, the relationships of CHBs and CBs with health-related variables were assessed by regression analyses. The cross-sectional analyses supported the distinction between CHBs and CBs. In contrast to the CHBs, CBs were positively predictive of the intention to.
CAPD::RedHom - Reduction heuristics for homology algorithms

We present an efficient software package for computing homology of sets, maps and filtrations represented as cubical, simplicial and regular CW complexes. The core homology computation is based on classical Smith diagonalization, but the efficiency of our approach comes from applying several geometric and algebraic reduction techniques combined with smart implementation.
Quality Evaluation for Robust Wavelet Zerotree Image Coders

The output of wavelet zerotree-style coders is typically very sensitive to channel errors, and several strategies have been proposed in the literature for combatting this problem. In particular, the two solutions of forward error correction and error-resilient packetization, produce images with very diierent types of degradations (global blurrines versus more localized distortions), making comparison diicult. In this work, we compare the output of these coders by having human observers use the images in a recognition task, and also rate the images subjectively. The results indicate that the localized distortions produced by the error-resilient packe-tization allow recognition of the image content at lower PSNR, and are also more subjectively pleasing at the same PSNR.
Brain Development, Intelligence and Cognitive Outcome in Children Born Small for Gestational Age

Intrauterine growth restriction (IUGR) can lead to infants being born small for gestational age (SGA). SGA is associated with increased neonatal morbidity and mortality as well as short stature, cardiovascular disease, insulin resistance, diabetes mellitus type 2, dyslipidemia and end-stage renal disease in adulthood. In addition, SGA children have decreased levels of intelligence and cognition, although the effects are mostly subtle. The overall outcome of each child is the result of a complex interaction between intrauterine and extrauterine factors. Animal and human studies show structural alterations in the brains of individuals with IUGR/SGA. The presence of growth hormone (GH) receptors in the brain implies that the brain is also a target for GH. Exogenous GH theoretically has the ability to act on the brain. This is exemplified by the effects of GH on cognition in GH-deficient adults. In SGA children, data on the effect of exogenous GH on intelligence and cognition are scant and contradictory.
Role of the carotid body in metabolic disturbances

O trabalho apresentado nesta tese foi realizado no CEDOC – Centro de Estudos de Doencas Cronicas da FCM|NOVA MEDICAL SCHOOL, da Universidade Nova de Lisboa e foi financiado por fundos FEDER atraves do Programa Operacional Fatores de Competitividade – COMPETE e por Fundos Nacionais atraves da FCT – Fundacao para a Ciencia e a Tecnologia no âmbito do projeto PTDC/SAU-ORG/111417/ 2009. A candidata realizou o trabalho experimental com o apoio de uma bolsa de investigacao da FCT com a referencia SFRH/BD/88983/2012.
Upgrade of Conventional Positional Systems into High-Precision Tracking Systems Using Sliding Mode Controlled Active Digital Compensators

—The paper offers a possibility of upgrading conventional PD controlled positional systems into high-precision tracking systems using active compensators. For improving of tracking as well as disturbance rejection capabilities of these systems, two digital active compensators are used. The first one is feedforward improvement of tracking, whereas the second one represents feedback compensation of disturbances. The introduced compensators contain active sliding mode controlled subsystems. The proposed solution does not require any additional sensors. The proposed control extension is described as well as digital sliding mode controller design procedures. Also, simulation results in case of dc motor servo-system are presented.
Negotiating language, literacy and identity: A sociocultural perspective on children’s learning strategies in a multilingual ESL classroom in Singapore

This article reports on part of a larger study investigating children’s language learning strategies (LLSs) for bringing to bear on the range and patterns of such strategies for enhancing children’s self-regulated engagement in biliteracy learning. Taking a case study approach, the study describes the process of the language learning activities in order to answer two research questions: (1) Do elementary schoolchildren use LLSs in meaningful interaction? (2) If they do, how do they negotiate language, literacy and identity in this process? A cloze passage task was set for 36 children to complete in groups of 5 each.Two methods were used in tandem in data analysis – data reduction and interpretation and connecting the inter-relationships and offering explanations. Results show that children use LLSs, as do adults, although the level of cognitive engagement differs; and that ‘successful’ and ‘less successful’ learners contribute to the meaningful interaction in different ways. Counting LLSs is not as significant as scrutinising learners’ effort for negotiating language, literacy and identity. I conclude that there is a need to nestle and reframe a cognitive view of language acquisition within a socially-imbedded system so that these commonly used constructs are not treated in isolation but in osmosis so that they are understood as “interactionally open and ecologically situated” (Canangarajah 2007: 936). Pedagogical implications of context-sensitive and culturally suitable strategiesbased instruction are also discussed.
The practice of physical activity related to self-esteem and academical performance in students of basic education

Objective: The present study was aimed to relate physical activity in the formation of self-concept, self-esteem and school performance in children of of basic education. We had a sample of 531 students of the municipalities of Santarem, Torres Novas, Entroncamento and Tomar (Portugal), of which 295 students (55.6%) for males and 236 students (44.4%) than females, with a mean age of the sample of 9.13 years, ranging from a minimum of 8 years and a maximum of 10 years. From this sample, 394 students (74%) have the practice of physical activity at least one formal character extracurricular and 137 students (26%) of the total sample reported no physical activity. Methods: As an instrument of data collection used the concept of the Self Susan Harter validated for the Portuguese population (Martins, Peixoto, Mata & Monteiro, 1995), where we analyzed descriptive and inferential data in order to confront levels average self-concept in the areas of scholastic competence, social acceptance, athletic competence, physical appearance, behaviour, and global self-esteem. Were also recorded income school students study the subject areas of Mathematics, English and Sciences Studies. Results: The practice of regular physical activity not decisively proved a significant factor in the level of self-concept, self-esteem and academic performance of students. However, the variable self seems to assume an evolution with increasing number of sessions per week of physical activity, as apparently the practice of at least one sport elevates levels of self-esteem. Conclusions: Students with the highest number of weekly hours of physical activity regularly reveal a level of academic achievement significantly higher, compared to students with less hours without registration or practice regular physical activity weekly.
Novel Form of Curcumin Improves Endothelial Function in Young, Healthy Individuals: A Double-Blind Placebo Controlled Study

Curcumin, a turmeric extract, may protect against cardiovascular diseases by enhancing endothelial function. In this randomized controlled double-blind parallel prospective study, fifty-nine healthy adults were assigned to placebo, 50 mg (50 mg), or 200 mg (200 mg) curcumin, for 8 weeks. The higher curcumin (200 mg) supplementation produced a dose-mediated improvement in endothelial function measured by flow-mediated dilation (FMD). The outcome was a clinically substantial 3.0% increase (90% CI 0.7 to 5.3%, p = 0.032; benefit : harm odds ratio 546 : 1) with the 200 mg dose, relative to placebo. The 50 mg dose also increased FMD relative to placebo by 1.7% (−0.6 to 4.0%, p = 0.23; 25 : 1), but the outcome was not clinically decisive. In apparently healthy adults, 8 weeks of 200 mg oral curcumin supplementation resulted in a clinically meaningful improvement in endothelial function as measured by FMD. Oral curcumin supplementation may present a simple lifestyle strategy for decreasing the risk of cardiovascular diseases. This trial was registered at ISRCTN registry (ISRCTN90184217).
THE INTENSITY PROFILE OF THE SOLAR SUPERGRANULATION

We have measured the average radial (cell center to network boundary) profile of the continuum intensity contrast associated with supergranular flows using data from the Precision Solar Photometric Telescope at the Mauna Loa Solar Observatory. After removing the contribution of the network flux elements by the application of masks based on Ca ii K intensity and averaging over more than 105 supergranular cells, we find a ∼0.1% decrease in red and blue continuum intensity from the supergranular cell centers outward, corresponding to a ∼1.0 K decrease in brightness temperature across the cells. The radial intensity profile may be caused either by the thermal signal associated with the supergranular flows or a variation in the packing density of unresolved magnetic flux elements. These are not unambiguously distinguished by the observations, and we raise the possibility that the network magnetic fields play an active role in supergranular scale selection by enhancing the radiative cooling of the deep photosphere at the cell boundaries.
Chamnamul [Pimpinella brachycarpa (Kom.) Nakai] ameliorates hyperglycemia and improves antioxidant status in mice fed a high-fat, high-sucrose diet

Chronic consumption of a high-fat, high-sucrose (HFHS) diet increases insulin resistance and results in type 2 diabetes mellitus in C57BL/6J mice. Hyperglycemia in diabetics increases oxidative stress, which is associated with a high risk of diabetic complications. The purpose of this study was to examine the hypoglycemic and antioxidant effects of chamnamul [Pimpinella brachycarpa (Kom.) Nakai] in an animal model of type 2 diabetes. The α-glucosidase inhibitory activity of a 70% ethanol extract of chamnamul was measured in vitro. Five-week-old male C57BL/6J mice were fed a basal or HFHS diet with or without a 70% ethanol extract of chamnamul at a 0.5% level of the diet for 12 weeks after 1 week of adaptation. After sacrifice, serum glucose, insulin, adiponectin, and lipid profiles, and lipid peroxidation of the liver were determined. Homeostasis model assessment for insulin resistance (HOMA-IR) was determined. Chamnamul extract inhibited α-glucosidase by 26.7%, which was 78.3% the strength of inhibition by acarbose at a concentration of 0.5 mg/mL. Serum glucose, insulin, and cholesterol levels, as well as HOMA-IR values, were significantly lower in the chamnamul group than in the HFHS group. Chamnamul extract significantly decreased the level of thiobarbituric acid reactive substances and increased the activities of superoxide dismutase, catalase, and glutathione peroxidase in the liver compared with the HFHS group. These findings suggest that chamnamul may be useful in prevention of hyperglycemia and reduction of oxidative stress in mice fed a HFHS diet.
Initial results for a ballbot driven with a spherical induction motor

We give a system overview and initial experimental results for SIMbot (spherical induction motor based ballbot), a human-sized dynamically stable mobile robot with only two active moving parts. SIMbot is a qualitatively new kind of robot with the potential to drastically reduce mechanical complexity in human-sized mobile robots. SIMbot uses a novel spherical induction motor as its drive mechanism, which is mechanically simpler than other ballbot drive mechanisms. We demonstrate the feasibility of this innovation with experimental results for balancing, stationkeeping, short point-to-point motions, and recovery from initial lean angles.
No Place to Hide: Football Players' and Coaches' Perceptions of the Psychological Factors Influencing Video Feedback

The purpose of this two-part study was to examine the role of psychological factors within the delivery of video feedback in elite youth football. Interviews were conducted with 11 coaches and 12 players. A thematic content analysis yielded data relating to three general dimensions: (a) the psychological responses engaged during delivery; (b) the impact of using a range of delivery strategies; and (c) the impact of the delivery climate surrounding practice. The findings suggest that a greater appreciation of these factors would add significant value to the way coaches, sport scientists, and athletes currently use video technology for performance enhancement.
A balanced logic routing block for Factorial-DLL based Frequency Generation

This paper presents the design of a balanced logic block that can act as either a delay line or a ring oscillator, with the addition of a voltage controlled element to pave the way for flexibility and tunability. This block is the key element of a Factorial Delay Locked Loop (F-DLL), and its balanced nature allows to significantly reduce the reference frequency-related spurious that are generated within the spectrum of a frequency generation unit when the latter is based on DLL. Once compared to the classical implementations of F-DLL logic block a Boolean routing is substituted to the switches. This allows a constant loading to the delay elements regardless the selected functionality of the logic block, namely delay line or ring oscillator. Doing so, the classical discrepancy that occurs in propagation delays in the two different modes is cancelled or at least minimized. The reference frequency-related error is therefore repealed.
The Proteomics Identifications database: 2010 update

The Proteomics Identifications database (PRIDE, http://www.ebi.ac.uk/pride) at the European Bioinformatics Institute has become one of the main repositories of mass spectrometry-derived proteomics data. For the last 2 years, PRIDE data holdings have grown substantially, comprising 60 different species, more than 2.5 million protein identifications, 11.5 million peptides and over 50 million spectra by September 2009. We here describe several new and improved features in PRIDE, including the revised submission process, which now includes direct submission of fragment ion annotations. Correspondingly, it is now possible to visualize spectrum fragmentation annotations on tandem mass spectra, a key feature for compliance with journal data submission requirements. We also describe recent developments in the PRIDE BioMart interface, which now allows integrative queries that can join PRIDE data to a growing number of biological resources such as Reactome, Ensembl, InterPro and UniProt. This ability to perform extremely powerful across-domain queries will certainly be a cornerstone of future bioinformatics analyses. Finally, we highlight the importance of data sharing in the proteomics field, and the corresponding integration of PRIDE with other databases in the ProteomExchange consortium.
Field Education in the Present Moment: Evaluating a 14-Week Pedagogical Model to Increase Mindfulness Practice

ABSTRACT Social work practitioners increasingly use mindfulness techniques, and research into the impact of this practice is being explored by multiple related disciplines, such as psychology and education. Cultivating the potential benefits of mindfulness at multiple practice levels necessitates curricular integration of mindfulness training. This article reports on the evaluation of a 14-week mindfulness-based pedagogical model implemented in two sections of social work field seminars. Using a pretest and posttest survey design that included an existing five-dimension mindfulness scale, students exhibited significant change in three facets of mindfulness: observing, nonjudgment of inner experience, and nonreactivity to inner experience. Implications for social work education and directions for future research are explored.
The effect of casein phosphopeptide amorphous calcium phosphate on the in vitro shear bond strength of orthodontic brackets

Objective The purpose of this study was to evaluate the effect of casein phosphopeptide amorphous calcium phosphate (CPP-ACP) on the shear bond strength (SBS) of brackets bonded to non-demineralized teeth with either phosphoric acid etching or self-etching primer. Methods Sixty human premolars were randomly assigned to 1 of 4 treatment groups (n = 15 each): phosphoric acid etching (group 1); self-etching primer (group 2); CPP-ACP for 2 weeks + phosphoric acid etching (group 3), and CPP-ACP for 2 weeks + self-etching primer (group 4). After bonding of the maxillary premolar metal brackets, specimens were subjected to shear forces in a testing machine. Scanning electron microscopy was used to observe etching patterns on the enamel surfaces of all teeth. A 2-way analysis of variance was used to test for effects of CPP-ACP and etching system on SBS. Results Significantly higher mean SBSs were observed in groups subjected to phosphoric acid etching (i.e., groups 1 and 3; p < 0.05). On the other hand, SBSs did not appear to be influenced by CPP-ACP (i.e., groups 3 and 4; p > 0.05). We observed a uniform and clear etched pattern on the enamel surface of the phosphoric acid etching groups. Conclusions CPP-ACP does not significantly affect the SBS of orthodontic brackets bonded to non-demineralized teeth, regardless of which adhesive method is used to bond the brackets.
Comparing the small sample performance of several variance estimators under competing risks

We examine several variance estimators for cumulative incidence estimators that have been proposed over time, some of which are derived from asymptotic martingale or counting process theory, and some of which are developed from the moments of the multinomial distribution. There is little published work comparing these variance estimators, largely because the variance estimators are algebraically complex and difficult to interpret and all but one have yet to be programmed for a standard statistical package. Through simulation and application to real data, we compare the performance of six variance estimators in relation to each other and the bootstrap in order to confirm earlier reports of their performance and to provide future direction toward their application. We find that the multinomial‐moment‐based estimators have performance close to that of the bootstrap, and are quite accurate for estimating the variance, even in samples of 20 subjects. All but one of the martingale theory‐based estimators tend to perform poorly in small samples, tending to either overestimate or underestimate the empirical variance in samples of fewer than 100 subjects. Copyright © 2006 John Wiley & Sons, Ltd.