Improving the sensitivity of the sequence profile method.

The sequence profile method (Gribskov M, McLachlan AD, Eisenberg D, 1987, Proc Natl Acad Sci USA 84:4355-4358) is a powerful tool to detect distant relationships between amino acid sequences. A profile is a table of position-specific scores and gap penalties, providing a generalized description of a protein motif, which can be used for sequence alignments and database searches instead of an individual sequence. A sequence profile is derived from a multiple sequence alignment. We have found 2 ways to improve the sensitivity of sequence profiles: (1) Sequence weights: Usage of individual weights for each sequence avoids bias toward closely related sequences. These weights are automatically assigned based on the distance of the sequences using a published procedure (Sibbald PR, Argos P, 1990, J Mol Biol 216:813-818). (2) Amino acid substitution table: In addition to the alignment, the construction of a profile also needs an amino acid substitution table. We have found that in some cases a new table, the BLOSUM45 table (Henikoff S, Henikoff JG, 1992, Proc Natl Acad Sci USA 89:10915-10919), is more sensitive than the original Dayhoff table or the modified Dayhoff table used in the current implementation. Profiles derived by the improved method are more sensitive and selective in a number of cases where previous methods have failed to completely separate true members from false positives.

An analysis of the accounting principles applied by the European Farm Accountancy Data Network

In spite of its relative importance in the economy of many countriesand its growing interrelationships with other sectors, agriculture has traditionally been excluded from accounting standards. Nevertheless, to support its Common Agricultural Policy, for years the European Commission has been making an effort to obtain standardized information on the financial performance and condition of farms. Through the Farm Accountancy Data Network (FADN), every year data are gathered from a rotating sample of 60.000 professional farms across all member states. FADN data collection is not structured as an accounting cycle but as an extensive questionnaire. This questionnaire refers to assets, liabilities, revenues and expenses, and seems to try to obtain a "true and fair view" of the financial performance and condition of the farms it surveys. However, the definitions used in the questionnaire and the way data is aggregated often appear flawed from an accounting perspective. The objective of this paper is to contrast the accounting principles implicit in the FADN questionnaire with generally accepted accounting principles, particularly those found in the IVth Directive of the European Union, on the one hand, and those recently proposed by the International Accounting Standards Committee’s Steering Committeeon Agriculture in its Draft Statement of Principles, on the other hand. There are two reasons why this is useful. First, it allows to make suggestions how the information provided by FADN could be more in accordance with the accepted accounting framework, and become a more valuable tool for policy makers, farmers, and other stakeholders. Second, it helps assessing the suitability of FADN to become the starting point for a European accounting standard on agriculture.

Use of high-frequency jet ventilation for percutaneous tumor ablation.

PURPOSE: To report feasibility and potential benefits of high-frequency jet ventilation (HFJV) in tumor ablations techniques in liver, kidney, and lung lesions. METHODS: This prospective study included 51 patients (14 women, mean age 66 years) bearing 66 tumors (56 hepatic, 5 pulmonary, 5 renal tumors) with a median size of 16 ± 8.7 mm, referred for tumor ablation in an intention-to-treat fashion before preoperative anesthesiology visit. Cancellation and complications of HFJV were prospectively recorded. Anesthesia and procedure duration, as well as mean CO2 capnea, were recorded. When computed tomography guidance was used, 3D spacial coordinates of an anatomical target <2 mm in diameter on 8 slabs of 4 slices of 3.75-mm slice thickness were registered. RESULTS: HFJV was used in 41 of 51 patients. Of the ten patients who were not candidate for HFJV, two patients had contraindication to HFJV (severe COPD), three had lesions invisible under HFJV requiring deep inspiration apnea for tumor targeting, and five patients could not have HFJV because of unavailability of a trained anesthetic team. No specific complication or hypercapnia related to HFJV were observed despite a mean anesthetic duration of 2 h and ventilation performed in procubitus (n = 4) or lateral decubitus (n = 6). Measured internal target movement was 0.3 mm in x- and y-axis and below the slice thickness of 3.75 mm in the z-axis in 11 patients. CONCLUSIONS: HFJV is feasible in 80 % of patients allowing for near immobility of internal organs during liver, kidney, and lung tumor ablation.

Frequency and Type of Side Effects of Immunomodulating Medication in the Swiss Inflammatory Bowel Disease Cohort

Background: Medical treatment of inflammatory bowel disease (IBD) is becoming more and more complex, as several classes of immuno-modulating drugs (IMD) are often used simultaneously. Thus, the probability of adverse effects is greatly increased. Most studies reporting on adverse effects focus on single therapy, and studies providing a global survey of side effects for multiple treatments are lacking. Aim: To assess the type and frequency of adverse events in IBD patients treated with single and multiple IMD therapy. Methods: Analysis of data from the Swiss IBD Cohort Study (SIBDCS) that collects data on a large sample of IBD patients from hospitals and private practices across Switzerland. The following IMD categories were analyzed: 5-ASA, azathioprine (Aza), 6-mercaptopurine (6-MP), methotrexate (MTX), anti-TNF (infliximab, adalimumab, certolizumab-pegol), cyclosporine, tacrolimus, and steroids. The following side effects were assessed: hepatitis, pancreatitis, leucopenia, thrombopenia, nephritis, allergic reaction, pneumonitis, infections (including tuberculosis), osteoporosis, abdominal pain/diarrhea (unrelated to IBD activity), cataract, diabetes, exanthema, hirsutism, lupus-like syndrome, myalgias, depression/psychosis, tumor development. Results: A total of 1,961 patients were analyzed (977 [50%] female, mean age 42.1 ± 14.4 years): 1,119 with Crohn's disease (CD), 800 with ulcerative colitis (UC), and 42 with indeterminate colitis (IC). Three-hundred eighteen (16.2%) patients were not treated with any of the above-mentioned medications, while 650 (33.2%), 569 (29%) and 424 (21.6%) patients had one-, two-, and three- or more- IMD therapy, respectively. Of the 1,643 patients treated with IMD, 535 (32.6%) patients reported at least one side effect. We found a significant correlation between the number of drugs used by a patient and the frequency of side effects (17.4% side effects for one drug, 29% for 2 drugs, and 60.6% for three or more drugs, p < 0.001). The frequency of side effects for the different IMD classes were as follows: 5-ASA (n = 980 treated patients) 10.8%, Aza/6-MP (n = 636) 51.9% (pancreatitis in 57 = 9%, hepatitis in 17 = 2.7% of treated patients), MTX (n = 146) 42.5% (hepatitis in 4 = 2.7% of treated patients), anti-TNF (n = 255) 23.1%, cyclosporine (n = 49) 10.2%, tacrolimus (n = 5) 20%, steroids (systemic or topical, n = 1,150) 9.6%. Conclusion: IBD treatment is associated with a significant number of side effects. A direct correlation between the number of IMD used simultaneously and the frequency of side effects was observed. The results of this study indicate that treating physicians should be vigilant for the occurrence of side effects in IBD patients under single and/or multiple drug therapy.

Análisis de la estructura poblacional y las capturas de merluza (Merluccius gayi peruanus) en Agosto de 1995

Analiza la evolución de la estructura por tallas y edades del recurso merluza durante el año 1995, período en el cual se observa un disminución de las tallas medias de las capturas de merluza, con una alta inicdencia de ejemplares menores que la talla mínima legal.

Differentiation of focal liver lesions: usefulness of parametric imaging with contrast-enhanced US.

Purpose: To evaluate whether parametric imaging with contrast material-enhanced ultrasonography (US) is superior to visual assessment for the differential diagnosis of focal liver lesions (FLLs). Materials and Methods: This study had institutional review board approval, and verbal patient informed consent was obtained. Between August 2005 and October 2008, 146 FLLs in 145 patients (63 women, 82 men; mean age, 62.5 years; age range, 22-89 years) were imaged with real-time low-mechanical-index contrast-enhanced US after a bolus injection of 2.4 mL of a second-generation contrast agent. Clips showing contrast agent uptake kinetics (including arterial, portal, and late phases) were recorded and subsequently analyzed off-line with dedicated image processing software. Analysis of the dynamic vascular patterns (DVPs) of lesions with respect to adjacent parenchyma allowed mapping DVP signatures on a single parametric image. Cine loops of contrast-enhanced US and results from parametric imaging of DVP were assessed separately by three independent off-site readers who classified each lesion as benign, malignant, or indeterminate. Sensitivity, specificity, accuracy, and positive and negative predictive values were calculated for both techniques. Interobserver agreement (κ statistics) was determined. Results: Sensitivities for visual interpretation of cine loops for the three readers were 85.0%, 77.9%, and 87.6%, which improved significantly to 96.5%, 97.3%, and 96.5% for parametric imaging, respectively (P < .05, McNemar test), while retaining high specificity (90.9% for all three readers). Accuracy scores of parametric imaging were higher than those of conventional contrast-enhanced US for all three readers (P < .001, McNemar test). Interobserver agreement increased with DVP parametric imaging compared with conventional contrast-enhanced US (change of κ from 0.54 to 0.99). Conclusion: Parametric imaging of DVP improves diagnostic performance of contrast-enhanced US in the differentiation between malignant and benign FLLs; it also provides excellent interobserver agreement.

A one-shot Prisoners’ Dilemma with procedural utility

This article introduces a model of rationality that combines procedural utility over actions with consequential utility over payoffs. It applies the model to the Prisoners Dilemma and shows that empirically observed cooperative behaviors can be rationally explained by a procedural utility for cooperation. The model characterizes the situations in which cooperation emerges as a Nash equilibrium. When rational individuals are not solely concerned by the consequences of their behavior but also care for the process by which these consequences are obtained, there is no one single rational solution to a Prisoners Dilemma. Rational behavior depends on the payoffs at stake and on the procedural utility of individuals. In this manner, this model of procedural utility reflects how ethical considerations, social norms or emotions can transform a game of consequences.

Conhecimento de Estudantes da Universitários sobre a Transmissão das IST/VIH-SIDA e o uso do Preservativo

Introdução: A infecção pelo vírus da imunodeficiência humana é um flagelo das sociedades modernas, que acarreta enormes custos sociais, económicos e pessoais. Têm sido utilizados fundos públicos e comunitários em acções de prevenção e educação populacional. Objectivos: proceder a uma descrição do conhecimento e comportamento sexual dos universitários e a frequência do uso do preservativo Método: Estudo transversal com uso de questionário estruturado autoaplicavél, onde participaram 893 estudantes universitários provenientes da Universidade privada Jean Piaget da Ilha de Santiago, Cabo Verde. Resultados: O perfil predominante dos adolescentes investigados foi ser do sexo feminino, solteiro, católico maioritariamente sem renda individual mensal, e coabitando com os familiares. Quanto aos comportamentos sexuais, verificou-se que a idade média da primeira relação foi de 16,5 anos e destes mais de 50% dos universitários referiram não ter usado preservativo na sua primeira relação. Dos sexualmente activos, mais de metade 56,3% não usou preservativo no seu último contacto sexual. Apenas 4,6% afirmam já ter tido alguma IST, apesar da elevada frequência de múltiplos parceiros (41,4% referem 3 ou mais parceiros na vida e 67,1%, 1 a 2 no último ano). No que concerne ao nível de conhecimento verificouse que os sujeitos da pesquisa apresentaram um grau de conhecimento sobre IST/VIH/SIDA, inferior ao que se esperaria do seu grau de escolaridade pois a média de acerto foi de 64% e mediana de 61,9%. Assim, percebe-se que a implementação da saúde sexual e reprodutiva na adolescência e nas universidades deve ser considerada uma acção prioritária para eliminar os riscos a que os jovens estão propensos

Evaluación de la población del percebes Pollicipes elegans en las islas Lobos de Afuera (18 - 20 julio 2001)

Presenta los resultados de la evaluación poblacional de percebes Pollicipes elegans en las islas Lobos de Afuera con el fin de estimar la magnitud del stock y determinar las características del recurso en relación al ambiente marino, como base para la toma de decisiones en su ordenamiento pesquero.

Situación actual y perspectivas de explotación del recurso potencial caracol bola Malea ringens en las islas Lobos de Afuera, Lambayeque

Presenta por primera vez en el Perú algunos aspectos biológico-pesqueros del caracol bola, así como su distribución espacial local, los mismos que contribuirán en una futura dación de normas para su regulación y ordenamiento pesquero, a fin de preservar una extracción sostenida.

Sociedade de Informação em Cabo Verde Metas e Desafios

O trabalho que se segue, ciente das actividades desenvolvidas na maioria dos países com vista a aproveitar as vantagens das Tecnologias de Informação e Comunicação, trás a questão para a realidade de Cabo Verde. A realidade vista em outros países junta ao termo Tecnologias de Informação e Comunicação a um conjunto de problemas de implicação social que origina um novo conceito ou realidade que é a Sociedade de Informação. Deste modo o trabalho encara a Sociedade de Informação como um contexto estimulante que deverá “obrigatoriamente” ser tratada em Cabo Verde, na vontade de desenvolver o país. A obrigatoriedade é tratada no sentido de Cabo Verde se ver cada vez mais introduzido num processo de desenvolvimento que exige uma outra visão perante os recursos e situação vivida neste momento. Neste sentido é que os aspectos sociais deverão ser abordados de formas distintas através de uma análise comparativa com o futuro que já se faz ver noutros países desenvolvidos. A abordagem do tema Sociedade de Informação por si só suscita debates, pois apesar da associação feita, tecnologias e aspectos sociais, o conceito de sociedade nunca deixará de ser outra diferente, porém adaptada sempre salvaguardando as origens. Portanto aspecto técnicos (infra-estruturas tecnológicas), novos meios (Internet e multimédia) e intervenientes (sector privado e sociedade civil) serão sempre tratados tendo em vista a sociedade no seu todo. Ao longo deste trabalho então, teremos a oportunidade de acompanhar, sempre de forma crítica, os valores e/ ou aspectos menos bons que eventualmente surgem nos planos do Estado, pois o tema sociedade já careta um amplo esforço no sentido de se ter um desenvolvimento sustentado e justo. E a essa justiça, que visamos sempre, a ideia de Sociedade em Rede como o fim de todas as iniciativas.