Protein sequence threading, the alignment problem, and a two-step strategy

Conventionally, protein structure prediction via threading relies on some nonoptimal method to align a protein sequence to each member of a library of known structures. We show how a score function (force field) can be modified so as to allow the direct application of a dynamic programming algorithm to the problem. This involves an approximation whose damage can be minimized by an optimization process during score function parameter determination. The method is compared to sequence to structure alignments using a more conventional pair-wise score function and the frozen approximation. The new method produces results comparable to the frozen approximation, but is faster and has fewer adjustable parameters. It is also free of memory of the template's original amino acid sequence, and does not suffer from a problem of nonconvergence, which can be shown to occur with the frozen approximation. Alignments generated by the simplified score function can then be ranked using a second score function with the approximations removed. (C) 1999 John Wiley & Sons, Inc.

Two-step tuberculin skin test and booster phenomenon prevalence among Brazilian medical students

SETTING: Five medical schools in three cities in Rio de Janeiro State, Brazil, with different tuberculosis (TB) incidence rates. OBJECTIVE: To evaluate the prevalence of the booster phenomenon and its associated factors in a voting universally BCG-vaccinated TB-exposed population. DESIGN: A two-step tuberculin skin test (TST) was performed among undergraduate medical students. Boosting was defined as an induration >= 10 mm in the second TST (TST2), with an increase of at least 6 mm over the first TST (TST1). The association of boosting with independent variables was evaluated using multivariate analysis. RESULTS: Of the 764 participants (mean age 21.9 +/- 2.7 years), 672 (87.9%) had a BCG scar. The overall booster SUMMARY phenomenon prevalence was 8.4% (95%CI 6.5-10.6). Boosting was associated with TST1 reactions of 1-9 mm (aOR 2.5, 95%CI 1.04-5.9) and with BCG vaccination, mostly after infancy, i.e., after age two years (aOR 9.1, 95%,CI 1.2-70.7). CONCLUSION: The prevalence of the booster phenomenon was high. A two-step TST in young BCG-vaccinated populations, especially in those with TST1 reactions of 1-9 mm, can avoid misdiagnosis as a false conversion and potentially reduce unnecessary treatment for latent TB infection.

Durability of Enamel Bonding Using One-step Self-etch Systems on Ground and Unground Enamel

Objective: To examine the morphological, early and long-term microtensile bond strengths (mu TBS) of one-step self-etch systems to unground and ground enamel. Materials and Methods: Resin composite (Filtek Z250) buildups were bonded to the buccal and lingual enamel surfaces (unground, bur-cut or SiC-roughened enamel) of third molars after adhesive application using the following adhesives: Clearfil S(3) Bond (CS3); Adper Prompt L-Pop (ADP); iBond (iB) and, as the control, Clearfil SE Bond (CSE). Six tooth halves were assigned for each condition. After storage in water (24 hours/37 degrees C), the bonded specimens were sectioned into beams (0.8 mm(2)) and subjected to pTBS (0.5 mm/min) either immediately (IM) or after six (6M) or 12 months (12M) of water storage. The data were analyzed by three-way repeated measures ANOVA and Tukey`s test (alpha=0.05). Surface conditioning was observed under scanning electron microscopy (SEM). Results: The mu TBS in the Si-C paper and diamond bur groups were similar and higher than the unground group. No significant difference was observed among the different storage periods, except for CS3, which showed an increase in the pTBS after 12M. The etching pattern was more retentive on ground enamel. Conclusions: One-step self-etch adhesives showed higher bond strengths on ground enamel and no reductions in resin-enamel bonds were observed after 12M of water storage.

Durability of enamel bonding using two-step self-etch systems on ground and unground enamel

This study examined the early and long-term microtensile bond strengths (mu TBS) and interfacial enamel gap formation (IGW) of two-step selfetch systems to unground and ground enamel. Resin composite (Filtek Z250) buildups were bonded to proximal enamel surfaces (unground, bur-cut or SiC-treated enamel) of third molars after the application of four self-etch adhesives: a mild (Clearfil SE Bond [SE]), two moderate (Optibond Solo Plus Self-Etch Primer [SO] and AdheSE [AD]) and a strong adhesive (Tyrian Self Priming Etchant + One Step Plus [TY]) and two etch-and-rinse adhesive systems (Single Bond [SB] and Scotchbond Multi-Purpose Plus [SBMP]). Ten tooth halves were assigned for each adhesive. After storage in water (24 hours/37 degrees C), the bonded specimens were sectioned into beams (0.9 mm(2)) and subjected to mu TBS (0.5 mm/minute) or interfacial gap width measurement (stereomicroscope at 400x) either immediately (IM) or after 12 months (12M) of water storage. The data were analyzed by three-way repeated measures ANOVA and Tukey`s test (alpha=0.05). No gap formation was observed in any experimental condition. The mu TBS in the Si-C paper and diamond bur groups were similar and greater than the unground group only for the moderate self-etch systems (SO and AD). No reductions in bond strength values were observed after 12 months of water storage, regardless of the adhesive evaluated.

A Randomized Clinical Evaluation of a One- and Two-step Self-etch Adhesive Over 24 Months

Objective: To evaluate the performance of All Bond SE used in a one- or two-step protocol in a 24-month randomized clinical study. Methods: Thirty-three patients with two similarly sized non-carious cervical lesions participated in this study. A total of 66 restorations were placed, half using the one-step All Bond SE protocol (SE-1) and the other half using the two-step All Bond SE protocol (SE-2). The restorations were evaluated at baseline and after 6, 12 and 24 months following the modified USPHS criteria and analyzed by the McNemar`s test and Fisher`s exact test (alpha=0.05). Results: After 24 months, six SE-1 and four SE-2 restorations were rated as Bravo in marginal discoloration The retention rates for SE-1 and SE-2 were 84.8% and 90.9%, respectively, after 24 months. Compared to baseline, the retention rate for SE-1 was statistically lower. Conclusions: All Bond SE used in the one- or two-step protocol resulted in high retention rates after 24 months.

Formation of cumulenes, triple-bonded, and related compounds by flash vacuum thermolysis of five-membered heterocycles

Flash vacuum thermolysis of a large variety of heterocyclic compounds is a useful means of production of ketenes, ketenimines, thioketenes, allenes, iminopropadienones, bis(imino)propadienes, iminopropadienethiones, carbodiimides, isothiocyanates, acetylenes, fulminic acid, nitrile imines and nitrile ylides, nitriles, cyanamides, cyanates, and other compounds, often in preparatively useful yields.

Heat transfer and flow behind a step in high enthalpy superorbital flow

Heat transfer levels have been investigated behind a rearward-facing step in a superorbital expansion tube. The heat transfer was measured along a flat plate and behind 2 and 3mm steps with the same length to step height ratio. Results were obtained with air as the test gas at speeds of 6.76kms(-1) and 9-60kms(-1) corresponding to stagnation enthalpies of 26MJ/kg and 48MJ/kg respectively. A laminar boundary layer was established on the flat plate and measured heat transfer levels were consistent with classical empirical correlations. In the case of flow behind a step, the measurements showed a gradual rise in heat transfer from the rear of the step to a plateau several step heights downstream for both flow conditions. Reattachment distance was estimated to be approximately 1.6 step heights downstream of the 2mm step at the low enthalpy condition through the use of flow visualisation.

Sustainable Tourism and Eradication of Poverty (Step): impact assessment of a tourism development program in Brazil

This paper aims to evaluate the social impacts of the Tourism Development Program (Prodetur) in the northeastern town of Porto Seguro, Bahia, Brazil. The method used is based on the difference in difference technique applied to the 1991 and 2000 Census microdata. The results suggest social advances following from poverty relief based on income - where the benefits are distributed, generally, in a relatively equal manner between the native and migrant population. There is a relative deterioration in the sanitary situation, which consists of a very serious problem in the mid- and long-term, whose costs are mostly borne by the native population. Therefore, maintaining the natural capital is the main aspect that distances Porto Seguro’s tourism supply from the concept of sustainability. The article also relies on difference in difference estimators to assess the impacts of local public policies related to the sector.

Part I : Comparing derivatization methods for amino acids – one and two-step procedures using gas chromatography – flame ion detector (GC-FID) Part II: Story of an icon from its execution until its conservation

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Conservação e Restauro

Molecular characterization of two rocio flavivirus strains isolated during the encephalitis epidemic in são paulo state, brazil and the development of a one-step rt-pcr assay for diagnosis

Rocio virus (ROCV) was responsible for an explosive encephalitis epidemic in the 1970s affecting about 1,000 residents of 20 coastland counties in São Paulo State, Brazil. ROCV was first isolated in 1975 from the cerebellum of a fatal human case of encephalitis. Clinical manifestations of the illness are similar to those described for St. Louis encephalitis. ROCV shows intense antigenic cross-reactivity with Japanese encephalitis complex (JEC) viruses, particularly with Ilheus (ILHV), St. Louis encephalitis, Murray Valley and West Nile viruses. In this study, we report a specific RT-PCR assay for ROCV diagnosis and the molecular characterization of the SPAn37630 and SPH37623 strains. Partial nucleotide sequences of NS5 and E genes determined from both strains were used in phylogenetic analysis. The results indicated that these strains are closely related to JEC viruses, but forming a distinct subclade together with ILHV, in accordance with results recently reported by Medeiros et al. (2007).

Interlimb Coordination During Step-to-Step Transition and Gait Performance

Most energy spent in walking is due to step-to-step transitions. During this phase, the interlimb coordination assumes a crucial role to meet the demands of postural and movement control. The authors review studies that have been carried out regarding the interlimb coordination during gait, as well as the basic biomechanical and neurophysiological principles of interlimb coordination. The knowledge gathered from these studies is useful for understanding step-to-step transition during gait from a motor control perspective and for interpreting walking impairments and inefficiency related to pathologies, such as stroke. This review shows that unimpaired walking is characterized by a consistent and reciprocal interlimb influence that is supported by biomechanical models, and spinal and supraspinal mechanisms. This interlimb coordination is perturbed in subjects with stroke.

Step towards multiplatform framework for supporting pediatric and neonatology care unit decision process

Children are an especially vulnerable population, particularly in respect to drug administration. It is estimated that neonatal and pediatric patients are at least three times more vulnerable to damage due to adverse events and medication errors than adults are. With the development of this framework, it is intended the provision of a Clinical Decision Support System based on a prototype already tested in a real environment. The framework will include features such as preparation of Total Parenteral Nutrition prescriptions, table pediatric and neonatal emergency drugs, medical scales of morbidity and mortality, anthropometry percentiles (weight, length/height, head circumference and BMI), utilities for supporting medical decision on the treatment of neonatal jaundice and anemia and support for technical procedures and other calculators and widespread use tools. The solution in development means an extension of INTCare project. The main goal is to provide an approach to get the functionality at all times of clinical practice and outside the hospital environment for dissemination, education and simulation of hypothetical situations. The aim is also to develop an area for the study and analysis of information and extraction of knowledge from the data collected by the use of the system. This paper presents the architecture, their requirements and functionalities and a SWOT analysis of the solution proposed.

One-step in situ synthesis of polyamide microcapsules with inorganic payload and their transformation into responsive thermoplastic composite materials

Well-dispersed loads of finely powdered metals, metal oxides, several carbon allotropes or nanoclays are incorporated into highly porous polyamide 6 microcapsules in controllable amounts via an original one-step in situ fabrication technique. It is based on activated anionic polymerization (AAP) of ε-caprolactam in a hydrocarbon solvent performed in the presence of the respective micro- or nanosized loads. The forming microcapsules with typical diameters of 25-50 µm entrap up to 40 wt% of load. Their melt processing produces hybrid thermoplastic composites. Mechanical, electric conductivity and magnetic response measurements show that transforming of in situ loaded microcapsules into composites by melt processing (MP) is a facile and rapid method to fabricate materials with high mechanical resistance and electro-magnetic characteristics sufficient for many industrial applications. This novel concept requires low polymerization temperatures, no functionalization or compatibilization of the loads and it is easy to scale up at industrial production levels.