Temporal genetic structure patterns in tropical maize populations under reciprocal recurrent selection.

In order to investigate the effect of long term recurrent selection on the pattern of gene diversity, thirty randomly-selected individuals from the progenitors (p) and four selection cycles (C0, C3, C6 and C11) were sampled for DNA analysis from the tropical maize (Zea mays L.) breeding populations, Atherton 1 (AT1) and Atherton 2 (AT2). Fifteen polymorphic Simple Sequence Repeat markers amplified a total of 284 and 257 alleles in AT1 and AT2 populations, respectively. Reductions in the number of alleles were observed at advanced selection cycles. About 11 and 12% of the alleles in AT1 and AT2 populations respectively, were near to fixation. However, a higher number of alleles (37% in AT1 and 33% in AT2) were close to extinction. Fisher's exact test and analysis of molecular variance (AMOVA) showed significant population differentiations. Gene diversity estimates and AMOVA revealed increased genetic differentiations at the expense of loss of heterozygosity. Population differentiations were mainly due to fixation of complementary alleles at a locus in the two breeding populations. The estimates of effective population at an advanced selection cycle were close to the population size predicted by the breeding method.

Efficient search for statistically significant dependency rules in binary data

Analyzing statistical dependencies is a fundamental problem in all empirical science. Dependencies help us understand causes and effects, create new scientific theories, and invent cures to problems. Nowadays, large amounts of data is available, but efficient computational tools for analyzing the data are missing. In this research, we develop efficient algorithms for a commonly occurring search problem - searching for the statistically most significant dependency rules in binary data. We consider dependency rules of the form X->A or X->not A, where X is a set of positive-valued attributes and A is a single attribute. Such rules describe which factors either increase or decrease the probability of the consequent A. A classical example are genetic and environmental factors, which can either cause or prevent a disease. The emphasis in this research is that the discovered dependencies should be genuine - i.e. they should also hold in future data. This is an important distinction from the traditional association rules, which - in spite of their name and a similar appearance to dependency rules - do not necessarily represent statistical dependencies at all or represent only spurious connections, which occur by chance. Therefore, the principal objective is to search for the rules with statistical significance measures. Another important objective is to search for only non-redundant rules, which express the real causes of dependence, without any occasional extra factors. The extra factors do not add any new information on the dependence, but can only blur it and make it less accurate in future data. The problem is computationally very demanding, because the number of all possible rules increases exponentially with the number of attributes. In addition, neither the statistical dependency nor the statistical significance are monotonic properties, which means that the traditional pruning techniques do not work. As a solution, we first derive the mathematical basis for pruning the search space with any well-behaving statistical significance measures. The mathematical theory is complemented by a new algorithmic invention, which enables an efficient search without any heuristic restrictions. The resulting algorithm can be used to search for both positive and negative dependencies with any commonly used statistical measures, like Fisher's exact test, the chi-squared measure, mutual information, and z scores. According to our experiments, the algorithm is well-scalable, especially with Fisher's exact test. It can easily handle even the densest data sets with 10000-20000 attributes. Still, the results are globally optimal, which is a remarkable improvement over the existing solutions. In practice, this means that the user does not have to worry whether the dependencies hold in future data or if the data still contains better, but undiscovered dependencies.

Improving outcome of childhood bacterial meningitis by simplified treatment : Experience from Angola

Background Acute bacterial meningitis (BM) continues to be an important cause of childhood mortality and morbidity, especially in developing countries. Prognostic scales and the identification of risk factors for adverse outcome both aid in assessing disease severity. New antimicrobial agents or adjunctive treatments - except for oral glycerol - have essentially failed to improve BM prognosis. A retrospective observational analysis found paracetamol beneficial in adult bacteraemic patients, and some experts recommend slow β-lactam infusion. We examined these treatments in a prospective, double-blind, placebo-controlled clinical trial. Patients and methods A retrospective analysis included 555 children treated for BM in 2004 in the infectious disease ward of the Paediatric Hospital of Luanda, Angola. Our prospective study randomised 723 children into four groups, to receive a combination of cefotaxime infusion or boluses every 6 hours for the first 24 hours and oral paracetamol or placebo for 48 hours. The primary endpoints were 1) death or severe neurological sequelae (SeNeSe), and 2) deafness. Results In the retrospective study, the mortality of children with blood transfusion was 23% (30 of 128) vs. without blood transfusion 39% (109 of 282; p=0.004). In the prospective study, 272 (38%) of the children died. Of those 451 surviving, 68 (15%) showed SeNeSe, and 12% (45 of 374) were deaf. Whereas no difference between treatment groups was observable in primary endpoints, the early mortality in the infusion-paracetamol group was lower, with the difference (Fisher s exact test) from the other groups at 24, 48, and 72 hours being significant (p=0.041, 0.0005, and 0.005, respectively). Prognostic factors for adverse outcomes were impaired consciousness, dyspnoea, seizures, delayed presentation, and absence of electricity at home (Simple Luanda Scale, SLS); the Bayesian Luanda Scale (BLS) also included abnormally low or high blood glucose. Conclusions New studies concerning the possible beneficial effect of blood transfusion, and concerning longer treatment with cefotaxime infusion and oral paracetamol, and a study to validate our simple prognostic scales are warranted.

Expressão de marcadores imuno-histoquímicos em biópsias renais de pacientes transplantados

A partir da década de 60, com a utilização do transplante renal em larga escala como terapia substitutiva para pacientes com falência do órgão, surgiu a preocupação quanto ao desenvolvimento do processo de rejeição do enxerto. Tal intercorrência, em geral, cursa com sinais e sintomas clínicos apenas quando o evento está bem estabelecido, ou mesmo quando lesões irreversíveis já se instalaram. Assim, é fundamental um acompanhamento rigoroso, visando detectar os casos subclínicos. O presente trabalho, a fim de fornecer novas ferramentas que auxiliem o diagnóstico precoce de rejeição do enxerto, avaliou a expressão imuno-histoquímica dos anticorpos CD3, CD5, CD20, CD68, CD25, FoxP3 e C4d em biópsias renais realizadas entre os anos de 2007 e 2009 em pacientes transplantados acompanhados pelo Serviço de Nefrologia do Hospital Universitário Pedro Ernesto, UERJ - RJ, correlacionando os resultados obtidos com o diagnóstico histológico. Para tal, as biópsias foram reavaliadas por três médicos patologistas que as classificaram, segundo Critérios de Banff 2007, quanto à presença ou não de rejeição do enxerto e seu tipo, aguda ou crônica. A partir de então, os blocos de parafina foram processados pela técnica Tissue Microarray for all (Pires, ARC. e cols.) e submetidos à imuno-histoquímica. A positividade dos marcadores foi avaliada e graduada e os resultados encontrados foram correlacionados, em um primeiro momento, com a presença ou ausência de rejeição. Posteriormente, os casos com diagnóstico histológico de rejeição tiveram seu perfil imuno-histoquímico analisado em função da positividade para C4d, marcador definidor de rejeição humoral. Neste momento, buscou-se averiguar se os anticorpos estudados seriam úteis em detectar, neste grupo, rejeição humoral e celular. Após a análise estatística, realizada pelo Teste Exato de Fisher, pode-se, então, concluir que o comportamento do marcador CD3 é capaz de inferir a presença de rejeição e que os anticorpos CD5 e CD25 permitem sugerir rejeição celular e humoral, respectivamente. Foi observado também que casos sem diagnóstico histológico de rejeição podem apresentar marcação para C4d em mais de 10% de seus capilares peritubulares.

Associação das variáveis socieconômicas, laborais e de saúde relacionadas à insegurança alimentar em trabalhadores dos Restaurantes Populares do município do Rio de Janeiro

Apesar das diversas ações governamentais nas questões relacionadas a alimentação, a insegurança alimentar faz parte da realidade brasileira. Esta pode ocorrer em diversos níveis: primeiramente a preocupação com a oferta de alimentos e a qualidade dos mesmos, em seguida, redução da qualidade e quantidade de alimentos entre os adultos e por fim em um nível mais elevado, a redução ocorre entre as crianças, até mesmo a fome, quando não há nada para comer no domicilio. É direito de todos terem acesso a alimentos seguros e nutritivos, desta forma a alimentação e nutrição é uma condição para proteção da saúde. Trata-se de um estudo seccional, com 273 trabalhadores de sete restaurantes localizados no município do Rio de Janeiro. A avaliação da insegurança alimentar foi realizada utilizando a Escala Brasileira de Insegurança Alimentar (EBIA) classificando a população em segurança alimentar e insegurança alimentar. As análises foram desenvolvidas aplicando-se o teste qui quadrado ou o teste exato de Fisher quando apropriado (p<0,20) e a regressão logística foi efetuada considerando três blocos de variáveis: socioeconômicas, laborais e de saúde. A prevalência de insegurança alimentar foi de 53,7%. A maioria da população estudada era do sexo masculino (57,9%), eram negros ou pardos (81,7%), com nove anos de escolaridade (57,1%), casados (58,2%), com filhos (70,1%), possuíam moradia própria (73,6%), eram ASGs ou copeiras (54,6%), quanto ao tempo gasto do deslocamento de casa para o trabalho, 67,6% dispendem mais de 40 minutos neste trajeto. As variáveis: escolaridade (OR-2,39; IC-95% 1,38 - 4,16), opinião sobre a falta de condições financeiras para manter alimentação saudável (OR-2,24; IC-95% 1,25 4,00), tempo de trabalho em cozinhas <29 meses (OR-2,72; IC-95% 1,44 5,16) e opinião da composição e regularidade da alimentação (OR- 2,01; IC-95% 1,12 3,57) associaram-se significativamente com a insegurança alimentar. Estes trabalhadores mesmo inseridos em um equipamento destinado a ofertar alimentação de qualidade, não tem a percepção da garantia ao acesso de forma satisfatória aos alimentos tanto quantitativamente como qualitativamente.

Associação de componentes dietéticos com desordens alimentares e seus agravos em adolescentes atletas tenistas e não atletas

Adolescentes apresentam rápido crescimento e intensas mudanças corporais que os tornam vulneráveis em termos nutricionais. A prática de restrições alimentares, bastante comum entre adolescentes, pode levar a inadequações nutricionais que parecem ser o primeiro sinal para o início de uma desordem alimentar (DA). A participação feminina no esporte e o número de casos de DA em adolescentes atletas de modalidades que exigem exposição do corpo, agilidade e leveza dos movimentos, como o tênis, têm aumentado nos últimos anos. As DA podem levar a complicações de saúde como irregularidades menstruais (IM) e baixa densidade mineral óssea (DMO), caracterizando a Tríade da Mulher Atleta (TMA). Desta forma, acredita-se que alguns componentes dietéticos podem ter associação com DA e seus agravos. O objetivo do presente estudo foi avaliar a associação de componentes dietéticos com desordens alimentares, irregularidades menstruais e composição corporal em adolescentes atletas tenistas e não atletas do sexo feminino. Trata-se de estudo do tipo transversal. Foram realizadas avaliações do desenvolvimento puberal pela auto-aplicação dos critérios de Tanner; da composição corporal pela absortometria radiológica de dupla energia (DXA); dos parâmetros dietéticos por registro alimentar de três dias alternados; das DA pela aplicação de três questionários validados (Eating Attitudes Test - EAT-26, Bulimic Investigatory Test, Edinburgh- BITE e o Body Shape Questionnaire - BSQ); do ciclo menstrual por questionário validado e da DMO também pelo DXA. A Tríade da Mulher Atleta (TMA) foi estabelecida pela presença concomitante de DA e/ou baixa disponibilidade de energia (BDE), IM e baixa DMO. Foram realizadas associações por meio de correlações de Spearman entre as variáveis numéricas de componentes dietéticos com DA e composição corporal. Também foram realizadas associações por meio do teste qui-quadrado, teste exato de Fisher ou prova binomial para as variáveis categóricas de adequação dos componentes dietéticos com DA e seus agravos. Participaram do estudo 75 adolescentes (25 tenistas, 50 não atletas) apresentando desenvolvimento puberal similar. Atletas obtiveram melhor perfil da composição corporal quanto ao tecido adiposo. Quanto à ingestão de macronutrientes, os carboidratos merecem destaque. Em ambos os grupos, a maioria das participantes apresentaram baixa ingestão de carboidratos, sendo este percentual de inadequação significativamente maior para as atletas. Os micronutrientes que obtiveram maior percentual de inadequação foram folato e cálcio em ambos os grupos. Verificou-se que 92%, 32% e 24% das atletas e 72%, 8% e 30% das não atletas preencheram critérios para DA e/ou BDE, IM e baixa massa óssea, respectivamente. Apesar de adolescentes atletas tenistas e não atletas apresentarem prevalência de DA similares, as não atletas apresentaram maior insatisfação com a imagem corporal pelo teste BSQ. No entanto, as atletas parecem estar em situação mais grave uma vez que apresentaram maior prevalência de BDE e de IM. A DMO e a prevalência de TMA foram similares entre os grupos. Foi verificada associação inversa e significativa entre alguns componentes dietéticos (principalmente energia e carboidratos) e os escores do teste BSQ. Foi possível concluir que a baixa ingestão de alguns componentes dietéticos, principalmente energia e carboidratos, podem funcionar como marcadores para desordens alimentares em ambos os grupos a fim de previnir posteriores consequências à saúde

Características sociodemográficas e ocupacional dos egressos do curso de graduação em enfermagem

Trata-se de um estudo cujo objeto foi a caracterização sociodemográfica e ocupacional dos egressos da Faculdade de Enfermagem da Universidade do Estado do Rio de Janeiro (ENF/UERJ). Objetivos: a) Caracterizar os egressos do curso de graduação em enfermagem da ENF/UERJ com relação às situações sociodemográfica e ocupacional e b) analisar os resultados acerca das caracterizações sociodemográfica e ocupacional dos egressos de enfermagem da ENF/UERJ. Método: Pesquisa quantitativa, transversal e observacional, cujo projeto foi aprovado pelo Comitê de Ética e Pesquisa sob o número 360.021. A coleta de dados ocorreu no período de dezembro de 2013 a maio de 2014 e foi realizada com egressos das turmas graduadas entre o primeiro semestre de 2000 e o segundo semestre de 2010. Para coleta de dados foram utilizadas as estratégias presencial e on-line, através de um questionário autoaplicável. Após aplicação do questionário, no formato impresso ou por meio do envio aos e-mails dos egressos, obtiveram-se 147 questionários respondidos. Para análise dos dados, aplicou-se o teste exato de Fisher, considerando valor de p significativo ≤ 0,05. A população foi dividida em dois grupos (G1 e G2), tomando-se por base a divisão equilibrada das 22 turmas pesquisadas (11 turmas no G1 e 11 no G2). Resultados: População com o predomínio do sexo feminino (88,4%), média de idade de 32 anos ( 1), maioria residindo no Estado do Rio de Janeiro (96,6%), com renda familiar ≥ 3 salários mínimos (96,6%) e até três dependentes da renda (81%). A maioria possuía mais de um emprego (53,7%) e cumpria carga horária de trabalho semanal superior a 30 horas (80,3%). Não houve diferença quantitativa entre os grupos em relação às escalas de trabalho diurna e noturna. Sobre as diferenças entre os grupos G1 e G2, verificou-se aumento significativo dos egressos com vínculos laborais não celetista e não estatutário (p = 0,0244) no G2; redução do salário dos enfermeiros que constituíram o G2 (p = 0,0015); e aumento da atuação na área hospitalar dos egressos inseridos no G2 (p = 0,0018) quando comparados à saúde pública, à pesquisa e ao ensino. Conclusão: A área hospitalar ainda é o grande empregador de enfermeiros, apesar de haver uma política governamental para aquecer a área de enfermagem em Atenção Básica. Os efeitos do neoliberalismo e a consequente precarização das condições de trabalho impactaram negativamente nos participantes do estudo. Isso porque houve aumento de vínculos não convencionais entre os grupos, no decorrer do tempo, e, apesar da multiplicidade de vínculos, a renda como enfermeiro, entre os grupos de egressos, foi reduzida. Verificou-se ainda um absentismo significativa nos grupos (24%), em especial por motivo de doença, fato que preocupa, considerando que os egressos investigados eram jovens, em plena fase produtiva e com expectativa de pouca ou nenhuma morbidade.

Human papillomavirus detection in women with and without human immunodeficiency virus infection in Colombia

Background: HIV infection leads to a decreasing immune response, thereby facilitating the appearance of other infections, one of the most important ones being HPV. However, studies are needed for determining associations between immunodeficiency caused by HIV and/or the presence of HPV during the course of cervical lesions and their degree of malignancy. This study describes the cytological findings revealed by the Papanicolaou test, laboratory characteristics and HPV molecular profile in women with and without HIV infection. Methods: A total of 216 HIV-positive and 1,159 HIV-negative women were invited to participate in the study; PCR was used for the molecular detection of HPV in cervical samples. Statistical analysis (such as percentages, Chi-square test and Fisher's exact test when applicable) determined human papillomavirus (HPV) infection frequency (single and multiple) and the distribution of six types of high-risk-HPV in women with and without HIV infection. Likewise, a logistic regression model was run to evaluate the relationship between HIV-HPV infection and different risk factors. Results: An association was found between the frequency of HPV infection and infection involving 2 or more HPV types (also known as multiple HPV infection) in HIV-positive women (69.0% and 54.2%, respectively); such frequency was greater than that found in HIV-negative women (44.3% and 22.7%, respectively). Statistically significant differences were observed between both groups (p = 0.001) regarding HPV presence (both in infection and multiple HPV infection). HPV-16 was the most prevalent type in the population being studied (p = 0.001); other viral types had variable distribution in both groups (HIV-positive and HIV-negative). HPV detection was associated with <500 cell/mm(3) CD4-count (p = 0.004) and higher HIV-viral-load (p = 0.001). HPV-DNA detection, <200 cell/mm(3) CD4-count (p = 0.001), and higher HIV-viral-load (p = 0.001) were associated with abnormal cytological findings. Conclusions: The HIV-1 positive population in this study had high multiple HPV infection prevalence. The results for this population group also suggested a greater association between HPV-DNA presence and cytological findings. HPV detection, together with low CD4 count, could represent useful tools for identifying HIV-positive women at risk of developing cervical lesions.

cpDNA-RFLP in Ceramium (Rhodophyta): Intraspecific polymorphism and species-level phylogeny

Restriction fragment length polymorphism (RFLP) analysis of chloroplast (cp) DNA is a powerful tool for the study of microevolutionary processes in land plants, yet has not previously been applied to seaweed populations. We used cpDNA-RFLP, detected on Southern blots using labeled total plastid DNA, to search for intraspecific and intrapopulational cpDNA RFLP polymorphism in two species of the common red algal genus Ceramium in Ireland and Britain. In C. botryocarpum one polymorphism was detected in one individual among 18 from two populations. Twenty-six individuals of C. virgatum from five populations at three locations exhibited a total of four haplotypes. One was frequent (80.8% of individuals); the others were rare (7.7, 7.7 and 4.2%) and were private to particular populations. Polymorphism was observed in two populations. The corrected mean was 2.26 +/- 0.36 haplotypes per population, which was within the typical range determined for higher plants using similar techniques. The spatial distribution of haplotypes was heterogeneous, with highly significant population differentiation (P = 0.00018; Fisher's exact test). Intraspecific polymorphism in C. virgatum had no impact on species-level phylogenetic reconstruction. This is the first unequivocal report of both intraspecific and intrapopulational cpDNA-RFLP polymorphism in algae.

Influence of test methodology and probe geometry on nanoscale fatigue mechanisms of diamond-like carbon thin film

The aim of this paper is to investigate the mechanism of nanoscale fatigue using nano-impact and multiple-loading cycle nanoindentation tests, and compare it to previously reported findings of nanoscale fatigue using integrated stiffness and depth sensing approach. Two different film loading mechanism, loading history and indenter shapes are compared to comprehend the influence of test methodology on the nanoscale fatigue failure mechanisms of DLC film. An amorphous 100 nm thick DLC film was deposited on a 500 μm silicon substrate using sputtering of graphite target in pure argon atmosphere. Nano-impact and multiple-load cycle indentations were performed in the load range of 100 μN to 1000 μN and 0.1 mN to 100 mN, respectively. Both test types were conducted using conical and Berkovich indenters. Results indicate that for the case of conical indenter, the combination of nano-impact and multiple-loading cycle nanoindentation tests provide information on the life and failure mechanism of DLC film, which is comparable to the previously reported findings using the integrated stiffness and depth sensing approach. However, the comparison of results is sensitive to the applied load, loading mechanism, test-type and probe geometry. The loading mechanism and load history is therefore critical which also leads to two different definitions of film failure. The choice of exact test methodology, load and probe geometry should therefore be dictated by the in-service tribological conditions, and where necessary both test methodologies can be used to provide better insights of failure mechanism. Molecular dynamics (MD) simulations of the elastic response of nanoindentation is reported, which indicates that the elastic modulus of the film measured using MD simulation was higher than that experimentally measured. This difference is attributed to the factors related to the presence of material defects, crystal structure, residual stress, indenter geometry and loading/unloading rate differences between the MD and experimental results.

The Cyclin D1 (CCND1) A870G polymorphism predicts clinical outcome to lapatinib and capecitabine in HER2-positive metastatic breast cancer

BACKGROUND: Lapatinib plus capecitabine emerged as an efficacious therapy in metastatic breast cancer (mBC). We aimed to identify germline single-nucleotide polymorphisms (SNPs) in genes involved in capecitabine catabolism and human epidermal receptor signaling that were associated with clinical outcome to assist in selecting patients likely to benefit from this combination.

PATIENTS AND METHODS: DNA was extracted from 240 of 399 patients enrolled in EGF100151 clinical trial (NCT00078572; clinicaltrials.gov) and SNPs were successfully evaluated in 234 patients. The associations between SNPs and clinical outcome were analyzed using Fisher's exact test, Kaplan-Meier curves, log-rank tests, likelihood ratio test within logistic or Cox regression model, as appropriate.

RESULTS: There were significant interactions between CCND1 A870G and clinical outcome. Patients carrying the A-allele were more likely to benefit from lapatinib plus capecitabine versus capecitabine when compared with patients harboring G/G (P = 0.022, 0.024 and 0.04, respectively). In patients with the A-allele, the response rate (RR) was significantly higher with lapatinib plus capecitabine (35%) compared with capecitabine (11%; P = 0.001) but not between treatments in patients with G/G (RR = 24% and 32%, respectively; P = 0.85). Time to tumor progression (TTP) was longer in patients with the A-allele treated with lapatinib plus capecitabine compared with capecitabine (median TTP = 7.9 and 3.4 months; P < 0.001), but not in patients with G/G (median TTP = 6.1 and 6.6 months; P = 0.92).

CONCLUSION: Our findings suggest that CCND1A870G may be useful in predicting clinical outcome in HER2-positive mBC patients treated with lapatinib plus capecitabine.

A let-7 microRNA-binding site polymorphism in 3'-untranslated region of KRAS gene predicts response in wild-type KRAS patients with metastatic colorectal cancer treated with cetuximab monotherapy

PURPOSE: recent studies have found that KRAS mutations predict resistance to monoclonal antibodies targeting the epidermal growth factor receptor in metastatic colorectal cancer (mCRC). A polymorphism in a let-7 microRNA complementary site (lcs6) in the KRAS 3' untranslated region (UTR) is associated with an increased cancer risk in non-small-cell lung cancer and reduced overall survival (OS) in oral cancers. We tested the hypothesis whether this polymorphism may be associated with clinical outcome in KRAS wild-type (KRASwt) mCRC patients treated with cetuximab monotherapy.

PATIENTS AND METHODS: the presence of KRAS let-7 lcs6 polymorphism was evaluated in 130 mCRC patients who were enrolled in a phase II study of cetuximab monotherapy (IMCL-0144). Genomic DNA was extracted from dissected formalin-fixed paraffin-embedded tumor tissue, KRAS mutation status and polymorphism were assessed using direct sequencing and PCR restriction fragment length polymorphism technique.

RESULTS: KRAS let-7 lcs6 polymorphism was found to be related to object response rate (ORR) in mCRC patients whose tumors had KRASwt. The 12 KRASwt patients harboring at least a variant G allele (TG or GG) had a 42% ORR compared with a 9% ORR in 55 KRASwt patients with let-7 lcs6 TT genotype (P = 0.02, Fisher's exact test). KRASwt patients with TG/GG genotypes had trend of longer median progression-free survival (3.9 versus 1.3 months) and OS (10.7 versus 6.4 months) compared to those with TT genotypes.

CONCLUSIONS: these results are the first to indicate that the KRAS 3'UTR polymorphism may predict for cetuximab responsiveness in KRASwt mCRC patients, which warrants validation in other clinical trials.

EGF61 polymorphism predicts complete pathologic response to cetuximab-based chemoradiation independent of KRAS status in locally advanced rectal cancer patients

BACKGROUND: Cetuximab has shown significant clinical activity in metastatic colon cancer. However, cetuximab-containing neoadjuvant chemoradiation has not been shown to improve tumor response in locally advanced rectal cancer patients in recent phase I/II trials. We evaluated functional germline polymorphisms of genes involved in epidermal growth factor receptor pathway, angiogenesis, antibody-dependent cell-mediated cytotoxicity, DNA repair, and drug metabolism, for their potential role as molecular predictors for clinical outcome in locally advanced rectal cancer patients treated with preoperative cetuximab-based chemoradiation.

METHODS: 130 patients (74 men and 56 women) with locally advanced rectal cancer (4 with stage II, 109 with stage III, and 15 with stage IV, 2 unknown) who were enrolled in phase I/II clinical trials treated with cetuximab-based chemoradiation in European cancer centers were included. Genomic DNA was extracted from formalin-fixed paraffin-embedded tumor samples and genotyping was done by using PCR-RFLP assays. Fisher's exact test was used to examine associations between polymorphisms and complete pathologic response (pCR) that was determined by a modified Dworak classification system (grade III vs. grade IV: complete response).

RESULTS: Patients with the epidermal growth factor (EGF) 61 G/G genotype had pCR of 45% (5/11), compared with 21% (11/53) in patients heterozygous, and 2% (1/54) in patients homozygous for the A/A allele (P < 0.001). In addition, this association between EGF 61 G allele and pCR remained significant (P = 0.019) in the 59 patients with wild-type KRAS.

CONCLUSION: This study suggested EGF A+61G polymorphism to be a predictive marker for pCR, independent of KRAS mutation status, to cetuximab-based neoadjuvant chemoradiation of patients with locally advanced rectal cancer.

Possible potentiation of toxins from Prevotella intermedia, Prevotella nigrescens, and Porphyromonas gingivalis by cotinine

BACKGROUND: Smoking is a recognized risk factor for the initiation and progression of periodontitis. However, the mechanism by which smoking induces its negative effects on the periodontium is not clear. This study aimed to test the hypothesis that synergy may occur between cotinine and bacterial products isolated from 3 putative periodontopathogens.

METHODS: A chick embryo toxin assay was used to investigate bacterial toxins (cell-free extracellular toxins and cell-free cell lysates) from 5 species with and without cotinine. A total of 9 putative periodontopathogens (3 species) and 2 non-oral controls (2 species) were studied. The periodontal species were: Prevotella intermedia (n = 4), Prevotella nigrescens (n = 4), and Porphyromonas gingivalis (n = 1). The control species tested were: Staphylococcus aureus (n = 1) and Escherichia coli (n = 1).

RESULTS: The toxicity kill was significantly greater than expected by simple addition alone (P <0.05, Fisher's exact test) between cotinine (800 ng/ml) and 1) the cell-free extracellular toxins of P. nigrescens MH1 and 2) the cell-free cell lysates of P. intermedia MH2. Synergy occurred with cotinine plus the cell-free extracellular toxins in all but 3 periodontal isolates, and the cell-free cell lysates in all but 2 periodontal isolates. Cotinine significantly (P <0.05, Fisher's exact test) enhanced the effects of cell-free extracellular toxins and cell lysates from one control species (E. coli), but not the other (S. aureus).

CONCLUSIONS: These findings indicate that synergy in an in vitro assay can occur between cotinine and toxins from putative periodontopathogens. This may be one important mechanism by which smoking increases the severity of periodontitis.

Urinary thrombomodulin levels were significantly higher following occupational exposure to chemicals, in the presence of dipstick protein, but not in the presence of dipstick blood

Currently, there are no biomarkers which can identify patients with an increased risk of developing urothelial cancer as a result of occupational chemical exposure. The aim of this study was to evaluate the relationships between final diagnosis and 22 biomarkers measured in urine, serum and plasma collected from 156 hematuric patients. Fourteen of the 80 patients (17.5%) with urothelial cancer and 13/76 (17.1%) of the controls were deemed to have a history of chemical exposure. We applied Fisher's exact tests to explore associations between chemical exposure and final diagnosis, and tumor stage and grade, where applicable; ANOVA and t-test to compare age across patients with and without chemical exposure; and Zelen's exact test to evaluate relationships across final diagnosis, chemical exposure and smoking. Following pre-selection of biomarkers using Lasso, we identified biomarkers with differential levels across patients with and without chemical exposure using Welch's t-test. Using a one-sided t-test and considering multiple testing using FDR, we observed that TM levels in urine were significantly higher in samples from patients with a history of chemical exposure regardless of their diagnosis as control or urothelial cancer (one-sided t-test, p_UC = 0.014 and p_CTL = 0.043); in the presence of dipstick protein and when urinary pH levels ≤ 6 (p = 0.003), but not in the presence of dipstick blood (p = 0.115). Urothelial cancer patients with a history of chemical exposure were significantly younger (64.1 years) than those without chemical exposure (70.2 years) (one-sided t-test p-value = 0.012); and their tumors were higher grade (Fisher's exact test; p = 0.008). There was a strong association between a history of chemical exposure and smoking in urothelial cancer patients (Zelen's exact test; p = 0.025). Elevated urinary thrombomodulin levels could have the potential to identify chemical exposure in hematuric patients at high risk of developing urothelial cancer.