Miracle-dz/UniFAR-FTUs huggingface dataset:
InterPro, progress and status in 2005

InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIRSF and SUPERFAMILY. Signatures are manually integrated into InterPro entries that are curated to provide biological and functional information. Annotation is provided in an abstract, Gene Ontology mapping and links to specialized databases. New features of InterPro include extended protein match views, taxonomic range information and protein 3D structure data. One of the new match views is the InterPro Domain Architecture view, which shows the domain composition of protein matches. Two new entry types were introduced to better describe InterPro entries: these are active site and binding site. PIRSF and the structure-based SUPERFAMILY are the latest member databases to join InterPro, and CATH and PANTHER are soon to be integrated. InterPro release 8.0 contains 11 007 entries, representing 2573 domains, 8166 families, 201 repeats, 26 active sites, 21 binding sites and 20 post-translational modification sites. InterPro covers over 78% of all proteins in the Swiss-Prot and TrEMBL components of UniProt. The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro).
Service Identification Based on Quality Metrics - Object-Oriented Legacy System Migration Towards SOA

Migrating towards Service Oriented Architecture SOA has become a major topic of interest during the recent years. Since emerging service technologies have forced non-service based software systems to become legacy, many efforts and researches have been carried out to enable these legacy systems to survive. In this context, several service identification solutions have been proposed. These approaches are either manual, thus considered expensive, or rely on ad-hoc criteria that fail to identify relevant services. In this paper, within the big picture of migrating object-oriented legacy systems towards SOA, we address automatic service identification from source code based on service quality characteristics. To achieve this, we propose a quality measurement model where characteristics of services are refined to measurable metrics.
Current status of research on osteoporosis in COPD: a systematic review

Patients with chronic obstructive pulmonary disease (COPD) are at increased risk of osteoporosis. However, the prevalence, correlates and effectiveness of treatment of osteoporosis in COPD patients remain unclear. We performed a systematic review of the literature to answer three questions. 1) What is the prevalence of osteoporosis in COPD? 2) What are identified correlates of osteoporosis in COPD? 3) What are the effects of treatment of osteoporosis in COPD? A computerised literature search in MEDLINE/PubMed and the Cochrane database was carried out. In addition, reference lists were searched by hand and authors were contacted if necessary. The prevalence of osteoporosis and osteopenia varied 9–69% and 27–67%, respectively. Prevalence of osteoporosis was generally higher than in healthy subjects and some other chronic lung diseases. Correlates of osteoporosis in COPD are mainly measures of body composition, disease severity and the use of corticosteroids, although causality has not been proven. Effects of treatment of osteoporosis have not been investigated in samples consisting of COPD patients only. Longitudinal follow-up to assess determinants of osteoporosis in COPD and randomised placebo-controlled trials on the effects of treatment of osteoporosis in patients with COPD only are warranted.
A simple method for the quantitative analysis of tyrosol by HPLC in liquid Czapek cultures from endophytic fungi.

®ODS (250 × 4,6 mm, 5 µm) a 25 °C foi utilizada. Extracao liquido-liquido de 0,5 mL do meio (pH 7,0) com acetato de etila e injecao de 20 µL apos concentracao do solvente sob ar comprimido originou bons resultados. Os parâmetros validados foram: linearidade 0,0125-5,0 µg mL -1 (r = 0,9967), limite de quantificacao 0,0125 µg mL -1 obtidos pela media das analises; %CV (precisao) e %E (exatidao) com valores abaixo de 15% e recuperacao de cerca de 80%. Alem disso, o metodo desenvolvido apresentou valores de validacao satisfatorios demonstrando eficiencia na analise do tirosol em meio liquido Czapek. Tyrosol is a possible quorum sensing molecule in endophytic fungi. High-performance liquid chromatography (HPLC) coupled with diode array detector (DAD) was used for the analysis of tyrosol in liquid Czapek fungal cultures. The optimized conditions were gradient mobile phase, in linear mode, consisting initially of acetonitrile/water (1:9 v/v) and increasing up to acetonitrile (100%) in 30 minutes at a flow rate of 1 mL min -1 . The column used was a ZORBAX  ODS o C. Liquid-liquid extraction of 0.5 mL medium (pH 7.0) with ethyl acetate and injection of 20 µL after solvent evaporation under air flow gave good results. Some validation parameters obtained were: linearity 0.0125-5.0 µg mL -1 medium (r = 0.9967), quantification limit of 0.0125 µg mL -1 medium, %CV (precision) and %E (accuracy) bellow 15% and recovery around 80%. Therefore, the developed method presented satisfactory validation parameters and it was efficient for the analysis of tyrosol in Czapek medium.
Uncertainty Estimation for the Optical System of Optical Measuring Machines

This paper presents the problem of optical measuring machine calibration, emphasizing the calibration of the "optical system", omitting the calibration of the "machine system". The calibration of an optical measuring machine is the first step before using the instrument for any application. For this purpose, a mathematical model has been developed to transform the coordinates of a point in space (3D) into coordinates of a point in an image (2D). Using this camera model, a calibration procedure has been developed using a grid distortion pattern. Finally, a procedure for calculating the uncertainty of the camera and geometric distortion parameters based on the Monte Carlo method has been developed.
A coordinated Jacobian transpose control for mobile multi-limbed robotic systems

This analytic and experimental study proposes a control algorithm based on Jacobian control for coordinated position and force control for autonomous multi-limbed mobile robotic systems. The technique is called coordinated Jacobian transpose control, or CJTC. Such position/force control algorithms will be required if future robotic systems are to operate effectively in unstructured environments. Generalized control variables, GCV's, express in a consistent and coordinated manner the desired behavior of the forces exerted by the multi-limbed robot on the environment and a system's motions. The effectiveness of this algorithm is demonstrated in simulation and laboratory experiments on a climbing system. <<ETX>>
Extracting Reusable Funtions by Flow Graph-Based Program Slicing

An alternative approach to developing reusable components from scratch is to recover them from existing systems. We apply program slicing, a program decomposition method, to the problem of extracting reusable functions from ill structured programs. As with conventional slicing first described by M. Weiser (1984), a slice is obtained by iteratively solving data flow equations based on a program flow graph. We extend the definition of program slice to a transform slice, one that includes statements which contribute directly or indirectly to transform a set of input variables into a set of output variables. Unlike conventional program slicing, these statements do not include either the statements necessary to get input data or the statements which test the binding conditions of the function. Transform slicing presupposes the knowledge that a function is performed in the code and its partial specification, only in terms of input and output data. Using domain knowledge we discuss how to formulate expectations of the functions implemented in the code. In addition to the input/output parameters of the function, the slicing criterion depends on an initial statement, which is difficult to obtain for large programs. Using the notions of decomposition slice and concept validation we show how to produce a set of candidate functions, which are independent of line numbers but must be evaluated with respect to the expected behavior. Although human interaction is required, the limited size of candidate functions makes this task easier than looking for the last function instruction in the original source code.
Morphological features and prognostic significance of tip variant of focal segmental glomerulosclerosis: Study of an Indian cohort.

CONTEXT Several attempts have been made to formulate a morphologic classification of focal segmental glomerulosclerosis (FSGS) variants with therapeutic and prognostic implications. Differences in study populations such as racial profile or therapy offered have hampered attempts to define prognostic variables in FSGS. Literature reveals conflicting results regarding the prognostic significance of tip variant of FSGS in different populations. AIMS To study the clinical and pathologic parameters in tip and not otherwise specified (NOS) variants of FSGS, in subjects from the Indian subcontinent with prognostic significance. MATERIALS AND METHODS First we performed a retrospective analysis of patients with biopsy proven primary FSGS, diagnosed between January 2004 and December 2008. Twenty cases of tip variant were encountered in adult population and similar numbers of adult cases of NOS variant were randomly selected. Renal biopsies were studied using light and immunofluorescence microscopy. Medical records for clinical data at presentation, biopsy and three monthly follow-up intervals were reviewed and compared between two groups. RESULTS At presentation, clinical profiles for the two groups were similar; however, significant differences in histological parameters and clinical outcome in tip and NOS variant cases were noted. Interstitial fibrosis and tubular atrophy were significantly higher in NOS variant. Greater response rate to steroid therapy was observed in tip variant cases while higher proportion of NOS variant cases showed renal failure. CONCLUSION Analysis of histological parameters is important in assessing the outcome of tip and NOS variants. Tip variant signifies a better prognostic subset for a population of Indian origin affected by FSGS.
Plasma Renin Activity Predicts the Improvement in Resistant Hypertension after Percutaneous Transluminal Renal Artery Angioplasty

Objective Percutaneous transluminal renal artery angioplasty (PTRA) has been recommended for the treatment of renovascular resistant hypertension. However, large randomized trials have reported that PTRA did not improve the outcomes compared with optimal medical therapy in patients with renal artery stenosis (RAS). It is important to identify patients with renovascular hypertension who are likely to respond to PTRA. We herein examined whether or not the plasma renin activity (PRA) could predict the improvement in resistant hypertension after PTRA for RAS. Methods and Results A total of 40 patients (mean age: 63±15 years) with unilateral RAS who received PTRA for resistant hypertension were enrolled in this study. Twenty-two (55%) patients experienced a significant reduction in their blood pressure while using few antihypertensive agents at the 3-month follow up. The median PRA was significantly higher in patients using few antihypertensive agents than in those using more [4.2 ng/mL/hr, interquartile range (IQR) 2.6-8.0 vs. 0.8 ng/mL/hr, IQR 0.4-1.7, p<0.001]. To predict the improvement in hypertension after PTRA, a receiver operating characteristic analysis determined the optimal cut-off value of PRA to be 2.4 ng/mL/hr. A multivariate logistic regression analysis showed that higher PRA (>2.4 ng/mL/hr) was an independent predictor of the improvement in hypertension after PTRA (odds ratio: 22.3, 95% confidence interval: 2.17 to 65.6, p<0.01). Conclusion These findings suggest that the evaluation of preoperative PRA may be a useful tool for predicting the improvement in resistant hypertension after PTRA for patients with RAS.
Operating System Protection for Fine-Grained Programs

We present an operating system-level security model for controlling fine-grained programs, such as downloaded executable content, and compare this security model's implementation to that of language-based security models. Language-based security has well-known limitations, such as the lack of complete mediation (e.g., for compiled programs or race condition attacks) and faulty self-protection (effective security is unproven). Operating system-level models are capable of complete mediation and self-protection, but some researchers argue that operating system-level security models are unlikely to supplant such language-based models because they lack portability and performance. In this paper, we detail an operating system-level security model built on the Lava Nucleus, a minimal, fast µ-kernel operating system. We show how it can enforce security requirements for fine-grained programs and show that its performance overhead (with the additional security) can be virtually negligible when compared to language-based models. Given the sufficient performance and security, the portability issue should become moot because other vendors will have to meet the higher security and performance expectations of their customers.
Effect of glass transitions on the rheological properties of food polymers

The rheological properties of food products are highly dependent on the physical state of the structural matrix, which ranges from the glassy state, the glass-rubber transition region, the rubbery plateau region, the rubbery flow region, and viscous flow region. Depending upon the combination of temperature and/or moisture content, the viscosity could be anywhere from 1015 mPa.s for glassy material and 1 mPa.s for flowable, low viscosity liquid. During the glass transition range alone, the rheological properties can change as large as 1000 times. The rheological properties of ingredients, in-process intermediates, and finished products also affect the processing techniques, textural quality, physical and chemical stability during storage. In this paper, the similarity in rheological behaviors between synthetic and food polymers, as affected by degree of crystallinity, cross-linking, plasticization, and phase separation is reviewed. Various mathematical equations for modeling the changes in rheological properties during glass transitions are also discussed. The advantages and shortcomings of each model will also be compared.
Integrating different perspectives on design rationale: Supporting the emergence of design rationale from design communication

Abstract Design rationale is a topic that implies different things to different people. To some it implies argumentation and frameworks for argumentation. To others it implies the documentation of design, like that required for many types of industrial or government work. Still others describe design rationale as the capture and potential reuse of normal communication about design. These perspectives of design rationale use different representations, which influence their ability to capture and to retrieve and use information. We propose an integrated approach to design rationale where design communication is captured and, over time, incrementally structured into argumentation and other formalisms to enable improved retrieval and use of this information. Two systems, PHIDIAS and the Hyper-Object Substrate, are used to demonstrate: (1) how to capture and integrate a variety of design information, (2) how to support the structuring of unstructured information, and (3) how to use design information to actively support design.
The Disintegrin ADAM9 Indirectly Contributes to the Physiological Processing of Cellular Prion by Modulating ADAM10 Activity*

The cellular prion protein (PrPc) is physiologically cleaved in the middle of its 106–126 amino acid neurotoxic region at the 110/111↓112 peptidyl bond, yielding an N-terminal fragment referred to as N1. We recently demonstrated that two disintegrins, namely ADAM10 and ADAM17 (TACE, tumor necrosis factor alpha converting enzyme) participated in both constitutive and protein kinase C-regulated generation of N1, respectively. These proteolytic events were strikingly reminiscent of those involved in the so-called “α-secretase pathway” that leads to the production of secreted sAPPα from βAPP. We show here, by transient and stable transfection analyses, that ADAM9 also participates in the constitutive secretion of N1 in HEK293 cells, TSM1 neurons, and mouse fibroblasts. Decreasing endogenous ADAM9 expression by an antisense approach drastically reduces both N1 and sAPPα recoveries. However, we establish that ADAM9 was unable to increase N1 and sAPPα productions after transient transfection in fibroblasts depleted of ADAM10. Accordingly, ADAM9 is unable to cleave a fluorimetric substrate of membrane-bound α-secretase activity in ADAM10-/- fibroblasts. However, we establish that co-expression of ADAM9 and ADAM10 in ADAM10-deficient fibroblasts leads to enhanced membrane-bound and released fluorimetric substrate hydrolyzing activity when compared with that observed after ADAM10 cDNA transfection alone in ADAM10-/- cells. Interestingly, we demonstrate that shedded ADAM10 displays the ability to cleave endogenous PrPc in fibroblasts. Altogether, these data provide evidence that ADAM9 is an important regulator of the physiological processing of PrPc and βAPP but that this enzyme acts indirectly, likely by contributing to the shedding of ADAM10. ADAM9 could therefore represent, besides ADAM10, another potential therapeutic target to enhance the breakdown of the 106–126 and Aβ toxic domains of the prion and βAPP proteins.
Initial Combination Therapy With Canagliflozin Plus Metformin Versus Each Component as Monotherapy for Drug-Naïve Type 2 Diabetes

OBJECTIVE This study assessed the efficacy/safety of canagliflozin (CANA), a sodium–glucose cotransporter 2 (SGLT2) inhibitor, plus metformin extended-release (MET) initial therapy in drug-naïve type 2 diabetes. RESEARCH DESIGN AND METHODS This 26-week, double-blind, phase 3 study randomized 1,186 patients to CANA 100 mg (CANA100)/MET, CANA 300 mg (CANA300)/MET, CANA100, CANA300, or MET. Primary end point was change in HbA1c at week 26 for combinations versus monotherapies. Secondary end points included noninferiority in HbA1c lowering with CANA monotherapy versus MET; changes in fasting plasma glucose, body weight, and blood pressure; and proportion of patients achieving HbA1c <7.0% (<53 mmol/mol). RESULTS From mean baseline HbA1c of 8.8% (73 mmol/mol), CANA100/MET and CANA300/MET significantly lowered HbA1c versus MET (median dose, 2,000 mg/day) by –1.77%, –1.78%, and –1.30% (–19.3, –19.5, and –14.2 mmol/mol; differences of −0.46% and –0.48% [–5.0 and –5.2 mmol/mol]; P = 0.001) and versus CANA100 and CANA300 by –1.37% and –1.42% (–15.0 and –15.5 mmol/mol; differences of –0.40% and –0.36% [–4.4 and –3.9 mmol/mol]; P = 0.001). CANA100 and CANA300 monotherapy met noninferiority for HbA1c lowering and had significantly more weight loss versus MET (–2.8, –3.7, and –1.9 kg [–3.0%, –3.9%, and –2.1%]; P = 0.016 and P = 0.002). Greater attainment of HbA1c <7.0% (50%, 57%, and 43%) and significantly more weight loss (–3.2, –3.9, and –1.9 kg [–3.5%, –4.2%, and –2.1%]; P = 0.001) occurred with CANA100/MET and CANA300/MET versus MET. The incidence of adverse events (AEs) related to SGLT2 inhibition (genital mycotic infections, osmotic diuresis– and volume depletion–related AEs) was higher in the CANA arms (0.4–4.4%) versus MET (0–0.8%). AE-related discontinuation rates were 1.3–3.0% across groups. The incidence of hypoglycemia was 3.0–5.5% in the CANA arms and 4.6% with MET. CONCLUSIONS Initial therapy with CANA plus MET was more effective and generally well tolerated versus each monotherapy in drug-naïve type 2 diabetes. CANA monotherapy demonstrated noninferior HbA1c lowering versus MET.
The Bone-Muscle Relationship in Men and Women

Muscle forces are a strong determinant of bone structure, particularly during the process of growth and development. The gender divergence in the bone-muscle relationship becomes strongly evident during adolescence. In females, growth is characterized by increased estrogen levels and increased mass and strength of bone relative to that of muscle, whereas in men, increases in testosterone fuel large increases in muscle, resulting in muscle forces that coincide with a large growth in bone dimensions and strength. In adulthood, significant age-related losses are observed for both bone and muscle tissues. Large decrease in estrogen levels in women appears to diminish the skeleton's responsiveness to exercise more than in men. In contrast, the aging of the muscle-bone axis in men is a function of age related declines in both hormones. In addition to the well-known age related changes in the mechanical loading of bone by muscle, newer studies appear to provide evidence of age- and gender-related variations in molecular signaling between bone and muscle that are independent of purely mechanical interactions. In summary, gender differences in the acquisition and age-related loss in bone and muscle tissues may be important for developing gender-specific strategies for using exercise to reduce bone loss with aging.
A time-domain method for numerical noise analysis of oscillators

A numerical noise analysis method for oscillators is proposed. Noise sources are usually small and can be considered as perturbations to a large amplitude oscillation. Transfer functions from each noise source to the oscillator output can be calculated by modeling the oscillator as a linear periodic time-varying circuit. The proposed method is a time domain method and can be applied to strongly nonlinear circuits. Thermal noise, shot noise and flicker noise are considered as noise sources. Error in the time domain method is also discussed.
The Effects of Coarse Particles on Daily Mortality: A Case-Crossover Study in a Subtropical City, Taipei, Taiwan

Many studies have examined the effects of air pollution on daily mortality over the past two decades. However, information on the relationship between levels of coarse particles (PM2.5–10) and daily mortality is relatively sparse due to the limited availability of monitoring data. Furthermore, the results are inconsistent. In the current study, the association between coarse particle levels and daily mortality in Taipei, Taiwan’s largest city, which has a subtropical climate, was undertaken for the period 2006–2008 using a time-stratified case-crossover analysis. For the single pollutant model (without adjustment for other pollutants), PM2.5–10 showed statistically significant association with total mortality both on warm and cool days, with an interquartile range increase associated with a 11% (95% CI = 6%–17%) and 4% (95% CI = 1%–7%) rise in number of total deaths, respectively. In two-pollutant models, PM2.5–10 remained significant effects on total mortality after the inclusion of SO2 and O3 both on warm and cool days. We observed no significant associations between PM2.5–10 and daily mortality from respiratory diseases both on warm and cool days. For daily mortality from circulatory diseases, the effect of PM2.5–10 remained significant when SO2 or O3 was added in the regression model both on warm and cool days. Future studies of this type in cities with varying climates and cultures are needed.