Automated scoring of AFLPs using RawGeno v 2.0, a free R CRAN library.

Amplified Fragment Length Polymorphisms (AFLPs) are a cheap and efficient protocol for generating large sets of genetic markers. This technique has become increasingly used during the last decade in various fields of biology, including population genomics, phylogeography, and genome mapping. Here, we present RawGeno, an R library dedicated to the automated scoring of AFLPs (i.e., the coding of electropherogram signals into ready-to-use datasets). Our program includes a complete suite of tools for binning, editing, visualizing, and exporting results obtained from AFLP experiments. RawGeno can either be used with command lines and program analysis routines or through a user-friendly graphical user interface. We describe the whole RawGeno pipeline along with recommendations for (a) setting the analysis of electropherograms in combination with PeakScanner, a program freely distributed by Applied Biosystems; (b) performing quality checks; (c) defining bins and proceeding to scoring; (d) filtering nonoptimal bins; and (e) exporting results in different formats.

Crystal structures of reduced and oxidized DsbA: investigation of domain motion and thiolate stabilization

Background: The redox proteins that incorporate a thioredoxin fold have diverse properties and functions. The bacterial protein-folding factor DsbA is the most oxidizing of the thioredoxin family. DsbA catalyzes disulfide-bond formation during the folding of secreted proteins, The extremely oxidizing nature of DsbA has been proposed to result from either domain motion or stabilizing active-site interactions in the reduced form. In the domain motion model, hinge bending between the two domains of DsbA occurs as a result of redox-related conformational changes. Results: We have determined the crystal structures of reduced and oxidized DsbA in the same crystal form and at the same pH (5.6). The crystal structure of a lower pH form of oxidized DsbA has also been determined (pH 5.0). These new crystal structures of DsbA, and the previously determined structure of oxidized DsbA at pH 6.5, provide the foundation for analysis of structural changes that occur upon reduction of the active-site disulfide bond. Conclusions: The structures of reduced and oxidized DsbA reveal that hinge bending motions do occur between the two domains. These motions are independent of redox state, however, and therefore do not contribute to the energetic differences between the two redox states, instead, the observed domain motion is proposed to be a consequence of substrate binding. Furthermore, DsbA's highly oxidizing nature is a result of hydrogen bond, electrostatic and helix-dipole interactions that favour the thiolate over the disulfide at the active site.

Structure of TcpG, the DsbA protein folding catalyst from Vibrio cholerae

The efficient and correct folding of bacterial disulfide bonded proteins in vivo is dependent upon a class of periplasmic oxidoreductase proteins called DsbA, after the Escherichia coli enzyme. In the pathogenic bacterium Vibrio cholerae, the DsbA homolog (TcpG) is responsible for the folding, maturation and secretion of virulence factors. Mutants in which the tcpg gene has been inactivated are avirulent; they no longer produce functional colonisation pill and they no longer secrete cholera toxin. TcpG is thus a suitable target for inhibitors that could counteract the virulence of this organism, thereby preventing the symptoms of cholera. The crystal structure of oxidized TcpG (refined at a resolution of 2.1 Angstrom) serves as a starting point for the rational design of such inhibitors. As expected, TcpG has the same fold as E. coli DsbA, with which it shares similar to 40% sequence identity. Ln addition, the characteristic surface features of DsbA are present in TcpG, supporting the notion that these features play a functional role. While the overall architecture of TcpG and DsbA is similar and the surface features are retained in TcpG, there are significant differences. For example, the kinked active site helix results from a three-residue loop in DsbA, but is caused by a proline in TcpG (making TcpG more similar to thioredoxin in this respect). Furthermore, the proposed peptide binding groove of TcpG is substantially shortened compared with that of DsbA due to a six-residue deletion. Also, the hydrophobic pocket of TcpG is more shallow and the acidic patch is much less extensive than that of E. coli DsbA. The identification of the structural and surface features that are retained or are divergent in TcpG provides a useful assessment of their functional importance in these protein folding catalysts and is an important prerequisite for the design of TcpG inhibitors. (C) 1997 Academic Press Limited.

The effect of R-plasmid RP1 on the properties of Proteus mirabilis

A clinical isolate of Proteus mirabilis containing R-plasmid RP1 (R+ cells), grown in both iron- and carbon- limited chemically defined media in mixed culture with plasmid-free (R- cells), did not disappear as expected, due to adherence of R+ cells to the wall of the chemostat vessel. Plasmid RP1 promoted adherence to glass and to medical prostheses. The hydrophobicity and surface charge of R+ cells were different from those of R- cells and both factors may contribute to the adherence of R+ cells to surfaces. The mode of cultivation of the cells, whether batch or continuous culture, were also found to affect the result. Antibodies raised against homologous cells increased the surface hydrophobicity of both R+ and R- cells and eliminated the differences between them. Results for surface hydrophobicity varied with the method used for measuring it. R+ cells were more sensitive than R- cells to tbe bacteridical action of normal serum and whole blood and to phagocytosis as measured by chemiluminescence. No clear differences were revealed in the protein antigens of R+ and R- cells by both SDS PAGE gels and immunoblots reacted with homologous antibodies. However, lectins revealed differences in the sugars exposed on the cell surfaces. Chemical analysis of R&43 and R- cells also revealed differences in the content of 2-keto-3-deoxy-D-manno-2-octulosonate, lipopolysaccharide and total fatty acids, when cells were grown in media containing added iron; however, no qualitative differences in the lipopolysaccharide were found. Removal of iron from the medium was found to have considerable effects on the chemical structure of R+ cells but not of R- ones. Adhesion to prostheses and to leucocytes is discussed in the light of the results and the clinical relevance outlined with respect to the initiation of infection and the association of virulence with antibiotic resistance.

Avaliação do amaciamento de carne bovina de dianteiro (Triceps brachii) pelos métodos de maturação, estimulação elétrica, injeção de ácidos e tenderização mecânica

Twenty-two Triceps brachii muscle obtained from 11 cows aged 3 and 4 years , killed in an experimental slaughter plant, were submitted to mechanical tenderization, injection with acetic acid 0,1M and lactic acid 0,2M, ageing for 9 and 14 days and electrical stimulation (250v - 60Hz - 90s), some of them were reserved as a control group, without treatment. The 14 days ageing time presented 21% of increase in subjective tenderness and 12% of reduction in shear force, these values were similar to the electrical stimulated meat. However the injection with acids and the ageing time 9 days did not present significant effect in the texture. Although the shear force values of mechanical tenderized meat was the shortest among all treatments, suspect of superestimation because of the fractures plan created by this process. Another analyses were carried out: pH reduction curve, R value; colour analysis; weight losses by cooking and by treatment; and microbiological analysis.

Synthesis of [Cu-2(Me-2[9]aneN(2)S)(2)(OH)(2)] (PF6)(2), a hydroxo-bridged copper(II) complex of N,N '-dimethyl-1-thia-4,7-diazacyclononane (Me-2[9]aneN(2)S). X-ray structural analysis, magnetic susceptibility, EPR and visible spectroscopy

The bis(mu-hydroxo) complex [Cu-2(Me-2[9]aneN(2)S)(2)(OH)(2)](PF6)(2) (Me-2[9]aneN(2)S = N,N'-dimethyl-1-thia-4,7-diazacyclononane) results after reaction of [Cu(Me-2[9]aneN(2)S)(MeCN)] (PF6) with dioxygen at -78 degrees C in acetonitrile. The complex has been characterized by X-ray crystallography: orthorhombic, space group Pnma, with a 18.710(3), b 16.758(2), c 9.593(2) Angstrom, and Z = 4. The structure refined to a final R value of 0.051. The complex contains two copper(II) ions bridged by two hydroxo groups with Cu ... Cu 2.866(1) Angstrom. The solid-state magnetic susceptibility study reveals ferromagnetic coupling, the fitting parameters being J = +46+/-5 cm(-1), g = 2.01+/-0.01 and theta = -0.58+/-0.03 K. The frozen-solution e.p.r. spectrum in dimethyl sulfoxide is characteristic of a monomeric copper(II) ion (g(parallel to) 2.300, g(perpendicular to) 2.063; A(parallel to) 156.2 x 10(-4) cm(-1), A(perpendicular to) 9.0 x 10(-4) cm(-1)) with an N2O2 donor set. Thioether coordination to the copper(II) in solution is supported by the presence of an intense absorption assigned to a sigma(S)-->Cu-II LMCT transition at c. 34000 cm(-1). The single-crystal spectrum of [Cu-2(Me-2[9]aneN(2)S)(2)(OH)(2)] (PF6)(2) (273 K) reveals d-->d transitions at 14500 and 18300 cm(-1) and a weak pi(S)-->Cu-II charge-transfer band at approximately 25000 cm(-1).

Desenvolvimento e análise de uma rede neural artificial para estimativa da erosividade da chuva para o Estado de São Paulo

O conhecimento do valor da erosividade da chuva (R) de determinada localidade é fundamental para a estimativa das perdas de solo feitas a partir da Equação Universal de Perdas de Solo, sendo, portanto, de grande importância no planejamento conservacionista. A fim de obter estimativas do valor de R para localidades onde este é desconhecido, desenvolveu-se uma rede neural artificial (RNA) e analisou-se a acurácia desta com o método de interpolação "Inverso de uma Potência da Distância" (ID). Comparando a RNA desenvolvida com o método de interpolação ID, verificou-se que a primeira apresentou menor erro relativo médio na estimativa de R e melhor índice de confiança, classificado como "Ótimo", podendo, portanto, ser utilizada no planejamento de uso, manejo e conservação do solo no Estado de São Paulo.

Lesões da substância branca por ressonância magnética: uma avaliação entre as ponderações DWI e T2 FLAIR

RESUMO: Objetivos – Determinar a sensibilidade e especificidade das ponderações Difusão (DWI) e T2 Fluid-Attenuated Inversion Recovery (FLAIR) na avaliação de lesões da substância branca (SB) e verificar em que medida se complementam, por forma a criar um conjunto de boas práticas na RM cranioencefálica de rotina. Metodologia – Recorrendo-se a uma metodologia quantitativa, efetuou-se uma análise retrospetiva da qual foram selecionados 30 pacientes, 10 sem patologia e 20 com patologia (2 com EM, 7 com Leucoencefalopatia, 6 com doença microangiopática e 5 com patologia da substância branca indefinida). Obteve-se uma amostra de 60 imagens, nomeadamente: 30 imagens ponderadas em DWI e 30 em T2 FLAIR. Recorrendo ao programa Viewdex®, três observadores avaliaram um conjunto de imagens segundo sete critérios: visibilidade, deteção, homogeneidade, localização, margens e dimensões da lesão e capacidade de diagnóstico. Com os resultados obtidos recorreu-se ao cálculo de sensibilidade e especificidade pelas Curvas ROC, bem como à análise estatística, nomeadamente, Teste-T, Índice de Concordância Kappa e coeficiente de correlação de Pearson entre as variáveis em estudo. Resultados – Os resultados de sensibilidade e de especificidade obtidos para a ponderação T2 FLAIR foram superiores (0,915 e 0,038, respetivamente) aos da ponderação DWI (0,08 e 0,100, respetivamente). Não se verificaram variâncias populacionais significativas. Obteve-se uma elevada correlação linear entre as variáveis com um valor r situado entre 0,8 e 0,99. Verificou-se também uma variabilidade considerável entre os observadores. Conclusões – Dados os baixos valores de sensibilidade e especificidade obtidos para a DWI, sugere-se que esta deva ser incluída no protocolo de rotina de crânio como auxiliar no diagnóstico diferencial com outras patologias.

Correlação da Variação dos Níveis de NT-ProBNP com a Modificação da Capacidade Funcional em Doentes com Insuficiência Cardíaca Crónica

OBJECTIVE: We set out to evaluate whether changes in N-terminal pro-brain natriuretic peptide (proBNP) can predict changes in functional capacity, as determined by cardiopulmonary exercise testing (CPET), in patients with chronic heart failure (CHF) due to dilated cardiomyopathy (DCM). METHODS: We studied 37 patients with CHF due to DCM, 81% non-ischemic, 28 male, who performed symptom-limited treadmill CPET, with the modified Bruce protocol, in two consecutive evaluations, with determination of proBNP after 10 minutes rest prior to CPET. The time between evaluations was 9.6+/-5.5 months, and age at first evaluation was 41.1+/-13.9 years (21 to 67). RESULTS IN THE FIRST AND SECOND EVALUATIONS RESPECTIVELY WERE: NYHA functional class >II 51% and 16% (p<0.001), sinus rhythm 89% and 86.5% (NS), left ventricular ejection fraction 24.9+/-8.9% and 26.6+/-8.6% (NS), creatinine 1.03+/-0.25 and 1.09+/-0.42 mg/dl (NS), taking ACE inhibitors or ARBs 94.5% and 100% (NS), beta-blockers 73% and 97.3% (p<0.001), and spironolactone 89% and 89% (NS). We analyzed the absolute and percentage variation (AV and PV) in peak oxygen uptake (pVO2--ml/kg/min) and proBNP (pg/ml) between the two evaluations. RESULTS: (1) pVO2 AV: -17.4 to 15.2 (1.9+/-5.7); pVO2 PV: -56.1 to 84% (11.0+/-25.2); proBNP AV: -12850 to 5983 (-778.4+/-3332.5); proBNP PV: -99.0 to 379.5% (-8.8+/-86.3); (2) The correlations obtained--r value and p value [r (p)]--are shown in the table below; (3) We considered that a coefficient of variation of pVO2 PV of >10% represented a significant change in functional capacity. On ROC curve analysis, a proBNP PV value of 28% showed 80% sensitivity and 79% specificity for pVO2 PV of >10% (AUC=0.876, p=0.01, 95% CI 0.75 to 0.99). CONCLUSIONS: In patients with CHF due to DCM, changes in proBNP values correlate with variations in pVO2, as assessed by CPET. However, our results suggest that only a proBNP PV of >28% predicts a significant change in functional capacity.

Evaluation of DNA Recombinant Methodologies for the Diagnosis of Plasmodium falciparum and their Comparison with the Microscopy Assay

Since 1984, DNA tests based on the highly repeated subtelomeric sequences of Plasmodium falciparum (rep 20) have been frequently used in malaria diagnosis. Rep 20 is very specific for this parasite, and is made of 21 bp units, organized in repeated blocks with direct and inverted orientation. Based in this particular organization, we selected a unique consensus oligonucleotide (pf-21) to drive a PCR reaction coupled to hybridization to non-radioactive labeled probes. The pf-21 unique oligo PCR (pf-21-I) assay produced DNA amplification fingerprints when was applied on purified P. falciparum DNA samples (Brazil and Colombia), as well as in patient's blood samples from a large area of Venezuela. The performance of the Pf-21-I assay was compared against Giemsa stained thick blood smears from samples collected at a malaria endemic area of the Bolívar State, Venezuela, at the field station of Malariología in Tumeremo. Coupled to non-radioactive hybridization the pf-21-I performed better than the traditional microscopic method with a r=1.7:1. In the case of mixed infections the r value of P. falciparum detection increased to 2.5:1. The increased diagnostic sensitivity of the test produced with this homologous oligonucleotide could provide an alternative to the epidemiological diagnosis of P. falciparum being currently used in Venezuela endemic areas, where low parasitemia levels and asymptomatic malaria are frequent. In addition, the DNA fingerprint could be tested in molecular population studies

Indexes and boundaries for "quantitative significance" in statistical decisions.

Boundaries for delta, representing a "quantitatively significant" or "substantively impressive" distinction, have not been established, analogous to the boundary of alpha, usually set at 0.05, for the stochastic or probabilistic component of "statistical significance". To determine what boundaries are being used for the "quantitative" decisions, we reviewed pertinent articles in three general medical journals. For each contrast of two means, contrast of two rates, or correlation coefficient, we noted the investigators' decisions about stochastic significance, stated in P values or confidence intervals, and about quantitative significance, indicated by interpretive comments. The boundaries between impressive and unimpressive distinctions were best formed by a ratio of greater than or equal to 1.2 for the smaller to the larger mean in 546 comparisons, by a standardized increment of greater than or equal to 0.28 and odds ratio of greater than or equal to 2.2 in 392 comparisons of two rates; and by an r value of greater than or equal to 0.32 in 154 correlation coefficients. Additional boundaries were also identified for "substantially" and "highly" significant quantitative distinctions. Although the proposed boundaries should be kept flexible, indexes and boundaries for decisions about "quantitative significance" are particularly useful when a value of delta must be chosen for calculating sample size before the research is done, and when the "statistical significance" of completed research is appraised for its quantitative as well as stochastic components.

Use of Hy's law and a new composite algorithm to predict acute liver failure in patients with drug-induced liver injury.

BACKGROUND & AIMS Hy's Law, which states that hepatocellular drug-induced liver injury (DILI) with jaundice indicates a serious reaction, is used widely to determine risk for acute liver failure (ALF). We aimed to optimize the definition of Hy's Law and to develop a model for predicting ALF in patients with DILI. METHODS We collected data from 771 patients with DILI (805 episodes) from the Spanish DILI registry, from April 1994 through August 2012. We analyzed data collected at DILI recognition and at the time of peak levels of alanine aminotransferase (ALT) and total bilirubin (TBL). RESULTS Of the 771 patients with DILI, 32 developed ALF. Hepatocellular injury, female sex, high levels of TBL, and a high ratio of aspartate aminotransferase (AST):ALT were independent risk factors for ALF. We compared 3 ways to use Hy's Law to predict which patients would develop ALF; all included TBL greater than 2-fold the upper limit of normal (×ULN) and either ALT level greater than 3 × ULN, a ratio (R) value (ALT × ULN/alkaline phosphatase × ULN) of 5 or greater, or a new ratio (nR) value (ALT or AST, whichever produced the highest ×ULN/ alkaline phosphatase × ULN value) of 5 or greater. At recognition of DILI, the R- and nR-based models identified patients who developed ALF with 67% and 63% specificity, respectively, whereas use of only ALT level identified them with 44% specificity. However, the level of ALT and the nR model each identified patients who developed ALF with 90% sensitivity, whereas the R criteria identified them with 83% sensitivity. An equal number of patients who did and did not develop ALF had alkaline phosphatase levels greater than 2 × ULN. An algorithm based on AST level greater than 17.3 × ULN, TBL greater than 6.6 × ULN, and AST:ALT greater than 1.5 identified patients who developed ALF with 82% specificity and 80% sensitivity. CONCLUSIONS When applied at DILI recognition, the nR criteria for Hy's Law provides the best balance of sensitivity and specificity whereas our new composite algorithm provides additional specificity in predicting the ultimate development of ALF.

Better 6 months outcome for steroid refractory ulcerative colitis with infliximab rescue therapy compared to tacrolimus or cyclosporine: a Swiss IBD cohort retrospective analysis

BACKGROUND: C iclosporine ( CsA), Tacrolimus (Tcl) and Infliximab (IFX) are effective rescue therapies in steroidrefractory ulcerative colitis (UC). Comparative studies are however m issing. M ETHOD: T his i s the retrospective analysis of treatment outcome for oral Tcl (n=27, initially 0.05mg/Kg twice daily, aiming for serum trough levels of 5-10 n g/mL), i ntravenous C sA ( n=23, 2 mg/kg/daily a nd then o ral CsA 5mg/kg/daily) and IFX ( n=43, 5 mg/kg intravenously at week 0, 2, 6 and then every 8 weeks) in patients with s teroid r efractory moderate to s evere UC enrolled i n the SWISS IBD cohort s tudy. After successful rescue therapy with Tcl o r C sA, t hiopurine m aintenance therapy or maintenance therapy with Tcl (in Tcl pretreated patients) was introduced. The endpoints analyzed steroid free r emission r ate (on the basis of m odified Truelove- Witts severity index (MTWSI)) and number of colectomies after 6 m onths. R ESULTS: A t 6 months, 26% ( 7/27) o f patients treated with T cl r emained i n steroid free remission (MTWSI score ≤4) compared to 30 % (7/23) on 18 droplets to the same extend under the linoleic acid treat, whereas lipid hydrolysis or loss was significantly increased in Huh-7 WT cells after 24h. Conclusions: Chronic alcohol feeding in obese, insulin-resistant rats exerts significant and synergistic effects on PNPLA3 mRNA expression, which correlated with triglyceride content. In v itro experiments suggest that PNPLA3 expression depends on the t ypes of d ietary f atty acids with polyunsaturated fatty a cids i nducing a nd monounsaturated fatty a cids inhibiting PNPLA3 mRNA. I148M polymorphism of PNPLA3 l eads to attenuation o f lipolytic processes resulting in fat accumulation in the cell. 20 CsA and 58% ( 27/41) o f patients t reated w ith IFX ( Tcl & CsA vs I FX p = 0 .018). S ignificant m ore patients had primary non response, loss of response or severe adverse events i n the CsA cohort ( 61%, 1 4/23) c ompared to Tcl cohort (33.3 % , 9/27), and IFX cohort (30%, 1 3/43) (p= 0.037). Colectomy rate was significantly higher after CsA (17.4 %, 4/23) compared to Tcl (3.7 %, 1/27) or IFX (2.3 %, 1/43) (p= 0.047).CONCLUSION: After s ix m onth, rescue therapy with I FX h ad t he l owest c olectomy r ate, significantly h igher steroid free r emission rate, a nd t he lowest rate of non-response, loss of response and severe adverse events compared to CsA or Tcl rescue treatment.

Validation of the Addiction Severity Index in French-speaking alcoholic patients.

OBJECTIVE: Evaluation of a French translation of the Addiction Severity Index (ASI) in 100 (78 male) alcoholic patients. METHOD: Validity of the instrument was assessed by measuring test-retest and interrater reliability, internal consistency and convergence and discrimination between items and scales. Concurrent validity was assessed by comparing the scores from the ASI with those obtained from three other clinimetric instruments. RESULTS: Test-retest reliability of ASI scores (after a 10-day interval) was good (r = 0.63 to r = 0.95). Interrater reliability was evaluated using six video recordings of patient interviews. Severity ratings assigned by six rates were significantly different (p < .05), but 72% of the ratings assigned by those who viewed the videos were within two points of the interviewer's severity ratings. Cronbach alpha coefficient of internal consistency varied from 0.58 to 0.81 across scales. The average item-to-scale convergent validity (r value) was 0.49 (range 0.0 to 0.84) for composite scores and 0.35 (range 0.00 to 0.68) for severity ratings, whereas discriminant validity was 0.11 on average (range-0.19 to 0.46) for composite scores and 0.12 (range-0.20 to 0.52) for severity ratings. Finally, concurrent validity with the following instruments was assessed: Severity of Alcoholism Dependence Questionnaire (40% shared variance with ASI alcohol scale), Michigan Alcoholism Screening Test (2% shared variance with ASI alcohol scale) and Hamilton Depression Rating Scale (31% shared variance with ASI psychiatric scale). CONCLUSIONS: The Addiction Severity Index covers a large scope of problems encountered among alcoholics and quantifies need for treatment. This French version presents acceptable criteria of reliability and validity.