TransNeT-CGP: A cluster-based comorbid gene prioritization by integrating transcriptomics and network-topological features.

The local disruptions caused by the genes of one disease can influence the pathways associated with the other diseases resulting in comorbidity. For gene therapies, it is necessary to prioritize the key genes that regulate common biological mechanisms to tackle the issues caused by overlapping diseases. This work proposes a clustering-based computational approach for prioritising the comorbid genes within the overlapping disease modules by analyzing Protein-Protein Interaction networks. For this, a sub-network with gene interactions of the disease pair was extracted from the interactome. The edge weights are assigned by combining the pairwise gene expression correlation and betweenness centrality scores. Further, a weighted graph clustering algorithm is applied and dominant nodes of high-density clusters are ranked based on clustering coefficients and neighborhood connectivity. Case studies based on neurodegenerative diseases such as Amyotrophic Lateral Sclerosis- Spinal Muscular Atrophy (ALS-SMA) pair and cancers such as Ovarian Carcinoma-Invasive Ductal Breast Carcinoma (OC-IDBC) pair were conducted to examine the efficacy of the proposed method. To identify the mechanistic role of top-ranked genes, we used Functional and Pathway enrichment analysis, connectivity analysis with leave-one-out (LOO) method, analysis of associated disease-related protein complexes, and prioritization tools such as TOPPGENE and Heml2.0. From pathway analysis, it was observed that the top 10 genes obtained using the proposed method were associated with 10 pathways in ALS-SMA comorbidity and 15 in the case of OC-IDBC, while that in similar methods like SAPDSB and S2B were 4, 6 respectively for ALS-SMA and 9, 10 respectively for OC-IDBC. In both case studies, 70 % of the disease-specific benchmark protein complexes were linked to top-ranked genes of the proposed method while that of SAPDSB and S2B were 55 % and 60 % respectively. Additionally, it was found that the removal of the top 10 genes disconnect the network into 14 distinct components in the case of ALS-SMA and 9 in the case of OC-IDBC. The experimental results shows that the proposed method can be effectively used for identifying key genes in comorbidity and can offer insights about the intricate molecular relationship driving comorbid diseases.

Pectoralis major myocutaneous flap for head and neck reconstruction: risk factors for fistula formation.

The pectoralis major myocutaneous flap (PMMF) is a safe and versatile flap used widely for head and neck cancer reconstructions, but one of the major and most feared complications is oro- or pharyngocutaneous fistula. Herein, we attempt to establish risk factors for fistula formation in reconstructions of mucosal defects in the head and neck using PMMF through retrospective analysis of PMMF performed during 3 years at a single institution, with a total of 84 procedures. There were 69 men and 15 women, with a mean age of 59.5 years. There were 15 cases of partial flap loss, two total flap losses and 31 fistulas. The independent risk factors for fistula formation were preoperative serum hemoglobin < 13 g/dl, preoperative serum albumin < 3.4 g/dl and hypopharynx reconstruction. The PMMF is still a very useful flap and this is the first multivariate analysis analysing risk factors for fistula formation. These findings are helpful in selecting patients with elevated risk of fistula formation, and therefore preventive measures can be undertaken to avoid potentially serious complications.

Superantigen gene complement of Streptococcus pyogenes--relationship with other typing methods and short-term stability.

The profiling of the superantigen (SAg) encoding genes has been frequently used as a complementary typing method for group A streptococci (GAS), but a confusing gene nomenclature and a large diversity of primers used in screening has led to some conflicting results. The aim of this work was to develop a polymerase chain reaction (PCR) method capable of efficiently amplifying all the known allelic variants of these genes, and to evaluate the congruence of this methodology with other commonly used molecular typing methods. The presence of the 11 known SAg genes and two other exotoxin-encoding genes (speB and speF) was tested in a collection of 480 clinical GAS isolates, using two multiplex PCR reactions. The SAg gene profile was compared with other typing methods. Four naturally occurring deletions involving the genes speB, speF, and rgg were characterized, two of which were found among invasive isolates. The absence of the chromosomally encoded genes speG and smeZ was supported by Southern blot hybridization and associated with specific GAS lineages, while the presence of phage-encoded genes was more variable. Positive associations between SAg genes or between SAg profiles and emm types or pulsed-field gel electrophoresis (PFGE) clusters were observed. The results suggest that the SAg profile diversifies faster than other properties commonly used for molecular typing, such as emm type and multilocus sequence typing (MLST) sequence types (STs), and can be a useful complement in GAS molecular epidemiology. Still, the short-term stability of the SAg gene profile among prevalent genetic lineages may largely explain the observed associations between SAg genes.

Influence of chlorine added to drinking water during the preslaughter feed withdrawal on microbiology and morphology of the broiler gastrointestinal tract.

The objective of this experiment was to test the effects of the addition of chlorine to broiler drinking water during a 12-h preslaughter feed withdrawal period on reduction of the quantities of microorganisms, such as Escherichia coli and enterococci, in broiler crops and ceca. Reduction of these microorganisms would likely also reduce contamination of broiler meat by pathogenic bacteria during processing. It was also investigated if the chlorine caused some intestinal damage that could disseminate the microorganisms to the carcass. A total of 40 Cobb male broilers were used. Samples of crop and cecal content were collected for microbiological analysis, and duodenum and jejunum were used for morphological analysis from 10 birds in each treatment. The most probable number (MPN) of E. coli and enterococci in the collected samples of crop and ceca and the measure of the free residual chlorine in water were determined. The scanning electron microscopy from duodenum and jejunum was used to illustrate the mucosa integrity. The chlorine added to water was efficient in reducing the quantities of microorganisms in broiler crops and improved the integrity of the mucosa. Therefore, preslaughter feed withdrawal should be coupled with crop disinfection, because preslaughter feed withdrawal increases the MPN of enterococci and E. coli in broiler crops. So, it presents a higher risk for carcass contamination during slaughterhouse processing and, consequently, a higher risk for public health.

Perfil microbiológico de peixes e água de cultivo em pesque-pagues situados na região nordeste do estado de São Paulo / Microbiological profile of fish and pond water in fee-fishing located in the northeast region of São Paulo state, Brazil

O objetivo deste trabalho foi determinar o número de coliformes totais, termotolerantes, Staphylococcus coagulase positivo e a presença de bactéria do gênero Salmonella no músculo, no tecido superficial, no trato gastrintestinal de peixes e na água de cultivo de pesque-pagues situados na microbacia do Córrego Rico, SP. Não foi detectado Staphylococcus coagulase positivo em nenhuma amostra de água e peixe. O número mais provável (NMP) de coliformes totais no peixe variou de 2,0 x 10 a >1,1 x 104 NMP.100 mL-1, na água de cultivo variou de 4,2 x 104 a > 2,4 x 105 NMP.100 mL-1. A contagem de coliformes termotolerantes no peixe variou de < 3 a 5,1 x 103 NMP.g-1, na água de cultivo variou de 3,8 x 102 a 2,0 x 104 NMP.100 mL-1. Não houve diferença estatística (P > 0,05) entre as populações de micro-organismos pesquisados na água, pele e trato gastrintestinal, o que reflete uma relação entre a presença dos micro-organismos na água e nesses dois locais analisados. Foi isolada Salmonella sp. em uma amostra de músculo e em duas amostras de trato gastrintestinal. O pescado pode ser veículo de contaminação cruzada, tendo como fonte dos micro-organismos a pele e o trato gastrintestinal para sua própria musculatura. Portanto, o monitoramento da qualidade da água é de suma importância para garantir a produção de peixes com boa qualidade.

The objective of this study was to determine the number of total and thermotolerant coliforms, coagulase-positive Staphylococcus, and the presence of bacteria of the genus Salmonella in the muscle, surface tissue, and gastrointestinal tract of fish, and in the pond water of fee-fishing establishments located in the Córrego Rico microwatershed in the state of São Paulo, Brazil. Coagulase-positive Staphylococcus was not detected in any sample of pond water or fish. The most probable number (MPN) of total coliforms in fish ranged from 2.0 x 10 to > 1.1 x 104 NMP.100 mL-1, while in pond water it ranged from 4.2 x 104 to > 2.4 x 105 NMP.100 mL-1. The count of thermotolerant coliforms in fish ranged from < 3 to 5.1 x 103 NMP.g-1, while in pond water it ranged from 3.8 x 102 to 2.0 x 104 NMP.100 mL-1. There was no statistical difference (P > 0.05) among the studied populations of microorganisms in pond water, surface tissue and gastrointestinal tract, which reflects a relationship between the presence of microorganisms in the water and in the two tissues analyzed. Salmonella sp. was isolated in one sample of muscle and in two samples of gastrointestinal tract. The fish can be a vehicle for cross contamination, having the gastrointestinal tract and the surface tissue as a source of microorganisms for its muscles. Therefore, monitoring the water quality is important to ensure the production of fish with good quality.

Ocorrência de Aeromonas spp. em abatedouro bovino e sensibilidade a antimicrobianos / Occurrence of Aeromonas spp. in bovine abattoir and antimicrobial sensitivity

O gênero Aeromonas compreende espécies consideradas importantes patógenos para os seres humanos, sendo as gastroenterites as infecções mais comumente atribuídas a estas bactérias. Tendo em vista sua importância como patógeno de origem alimentar, a ocorrência deAeromonas spp. foi estudada em carcaças bovinas e ambiente do abatedouro em uma indústria do Estado de São Paulo. Foram colhidas 285 amostras de 19 locais. Foi realizada a contagem direta por semeadura em meio seletivo, caracterização bioquímica das espécies após enriquecimento seletivo e teste de sensibilidade a antimicrobianos. A contagem direta permitiu a quantificação dessas bactérias em apenas 12 amostras, variando de 0,5 a 9,2 x 100 UFC/cm2, sendo cinco delas de ambiente, com populações que variaram de 1,0 x 100 a 3,0 x 100 UFC/placa. Entretanto, após o enriquecimento seletivo, Aeromonas spp. foram isoladas de 38 amostras que, somadas às amostras de ambiente não submetidas ao enriquecimento, forneceram 62 isolados para análise. A caracterização bioquímica das espécies permitiu verificar a ocorrência de 59 isolados de A. caviae, um de A. sobria, um de A. trota e um de A. schubertii. O teste com antimicrobianos revelou resistência de todos os isolados pela ampicilina e cefalotina, enquanto, para os demais antimicrobianos, esta foi variável. A resistência da totalidade dos isolados a determinados antimicrobianos indica que estes devem ser utilizados criteriosamente com a finalidade de evitar o surgimento precoce de cepas deAeromonas spp. multirresistentes. Ainda, a maior prevalência deA. caviae deve ser considerada relevante, pois trata-se de uma das espécies causadoras de gastroenterite em humanos.

The genus Aeromonas comprises important human pathogens, gastroenteritis being the most common type of infection attributed to these bacteria. Considering their importance as foodborne pathogens, the occurrence of Aeromonas spp. was studied on bovine carcasses and the environment of a slaughterhouse in São Paulo State, Brazil. A total of 285 samples were collected from 19 points. Direct counting was carried out by seeding on selective medium, with biochemical characterization of the species after selective enrichment and antimicrobial sensitivity testing. The direct count permitted bacteria quantification only in 12 samples ranging from 0.5 to 9.2 x 100 CFU/ cm2, of which 5 were from environment, ranging from 1.0 x 100 to 3.0 x 100 CFU/plate. However, after selective enrichment,Aeromonas spp. was isolated from 38 samples, which when added to the environmental samples not subjected to the enrichment provided 62 isolates for analysis. Biochemical characterization allowed for the verification of the occurrence of 59 isolates of A. caviae, 1 ofA. sobria, 1 ofA. trota and 1 ofA. schubertii. Antimicrobial testing revealed that all isolates were resistant to ampicillin and cephalotin, while the results for the other antimicrobials were variable. Resistance of all isolates to some antimicrobials indicates that these must be used carefully to avoid early development of multiresistantAeromonas spp. Also, the greatest prevalence of A. caviae must be considered relevant because it is one of the causative species of human gastroenteritis.

Decrease in macrolide resistance and clonal instability among Streptococcus pyogenes in Portugal.

Macrolide resistance among Streptococcus pyogenes (group A streptococci) in Portugal was stable during 1998-2003, but a rapid inversion in the dominant phenotypes was noted in the same period, with a sharp decrease in the proportion of isolates presenting the MLS(B) phenotype and a concomitant increase in isolates presenting the M phenotype. The characterization of group A streptococci recovered during 2004-2006, which is reported here, revealed that resistance was not stable during this period and that the decline in erythromycin resistance observed during 2004-2006 was due to a decrease in the prevalence of isolates presenting the M phenotype, while the proportion of isolates expressing the MLS(B) phenotype remained stable. Characterization by emm typing, T serotyping, pulsed-field gel electrophoresis (PFGE) profiling and multilocus sequence typing revealed a very diverse population. Several of the major PFGE clusters identified had already been found in the 1998-2003 study period, but others were found for the first time, e.g. T11/emm11/ST403, carrying the erm(B) gene, and T3/13/emm3/ST315, carrying the mef(A) gene. The clone defined as T12/emm12/ST36, previously found to be associated with mef(A), was now found to be predominantly associated with erm(B). The clonal dynamics of macrolide-resistant group A streptococci emphasizes the importance of considering factors other than antibiotic consumption in explaining the prevalence of resistant isolates.

Changes in Streptococcus pneumoniae serotypes causing invasive disease with non-universal vaccination coverage of the seven-valent conjugate vaccine.

The pneumococcal seven-valent conjugate vaccine (PCV7) has been administered in Portugal since late 2001 through the private sector. To evaluate the impact of PCV7 use, the serotypes and antimicrobial susceptibility of pneumococci causing invasive disease in Portugal during 2003-2005 were determined and compared with available data for the period 1999-2002. Changes in serotype distribution compatible with the introduction of PCV7 were shown for children

Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes.

The studies that correlate the results obtained by different typing methodologies rely solely on qualitative comparisons of the groups defined by each methodology. We propose a framework of measures for the quantitative assessment of correspondences between different typing methods as a first step to the global mapping of type equivalences. A collection of 325 macrolide-resistant Streptococcus pyogenes isolates associated with pharyngitis cases in Portugal was used to benchmark the proposed measures. All isolates were characterized by macrolide resistance phenotyping, T serotyping, emm sequence typing, and pulsed-field gel electrophoresis (PFGE), using SmaI or Cfr9I and SfiI. A subset of 41 isolates, representing each PFGE cluster, was also characterized by multilocus sequence typing (MLST). The application of Adjusted Rand and Wallace indices allowed the evaluation of the strength and the directionality of the correspondences between the various typing methods and showed that if PFGE or MLST data are available one can confidently predict the emm type (Wallace coefficients of 0.952 for both methods). In contrast, emm typing was a poor predictor of PFGE cluster or MLST sequence type (Wallace coefficients of 0.803 and 0.655, respectively). This was confirmed by the analysis of the larger data set available from http://spyogenes.mlst.net and underscores the necessity of performing PFGE or MLST to unambiguously define clones in S. pyogenes.

Assessment of band-based similarity coefficients for automatic type and subtype classification of microbial isolates analyzed by pulsed-field gel electrophoresis.

Pulsed-field gel electrophoresis (PFGE) has been the typing method of choice for strain identification in epidemiological studies of several bacterial species of medical importance. The usual procedure for the comparison of strains and assignment of strain type and subtype relies on visual assessment of band difference number, followed by an incremental assignment to the group hosting the most similar type previously seen. Band-based similarity coefficients, such as the Dice or the Jaccard coefficient, are then used for dendrogram construction, which provides a quantitative assessment of strain similarity. PFGE type assignment is based on the definition of a threshold linkage value, below which strains are assigned to the same group. This is typically performed empirically by inspecting the hierarchical cluster analysis dendrogram containing the strains of interest. This approach has the problem that the threshold value selected is dependent on the linkage method used for dendrogram construction. Furthermore, the use of a linkage method skews the original similarity values between strains. In this paper we assess the goodness of classification of several band-based similarity coefficients by comparing it with the band difference number for PFGE type and subtype classification using receiver operating characteristic curves. The procedure described was applied to a collection of PFGE results for 1,798 isolates of Streptococcus pneumoniae, which documented 96 types and 396 subtypes. The band-based similarity coefficients were found to perform equally well for type classification, but with different proportions of false-positive and false-negative classifications in their minimal false discovery rate when they were used for subtype classification.

Local correlation of expression profiles with gene annotations--proof of concept for a general conciliatory method.

MOTIVATION: Integrated analysis of expression data and gene ontology annotations is a prime example of biological data that need co-explanatory interpretation. This particular application is used to validate a new method for integrated analysis of varied biological information. RESULTS: The proposed method consists of determining local correlation coefficients and the corresponding P-values calculated per biological entity. This measure considers the combined intensity and significance of the agreement or disagreement, between two data sources about the same biological entity. The method is applied to the integrated analysis of gene expression and annotation of two gene sets, one from yeast and other from mouse. The potential of the method to generate accurate mechanistic hypothesis is also demonstrated. Specially, negative correlation results pose a new kind of biological hypothesis. Method performance was compared with annotation enrichment methods, and optimal conditions for the superiority of local correlation results are discussed.

[Cervical perforating foreign body: case report]. / Corpo estranho perfurante cervical: relato de caso.

BACKGROUND: Neck perforations by foreign bodies are uncommon. The surgical approach depends on the extension of visceral wounds and the development of cervical or mediastinal infection. PURPOSE: The objective of this paper is to report a neck perforation trauma by a piece of wire, with associated laryngeal and hypopharyngeal wounds and extensive cervico-mediastinal emphysema. Anatomic and clinical correlations are discussed, as well as the management of the case. MATERIAL AND METHODS: A 28-year-old male patient suffered a perforating trauma in his neck by a piece of wire. This foreign body was laid in the retropharyngeal space, at the level of the sixth cervical vertebra, after perforating the larynx and hypopharynx. There are no similar cases previously reported. The imaging tests are presented. Despite the potential severity of the lesions, the patient had a favorable outcome, and no surgical approach was necessary. CONCLUSIONS: This case illustrates, by the imaging tests, the complex anatomy of the cervical fasciae and deep neck spaces, and confirms the possibility of conservative management in a great number of laryngeal and hypopharyngeal traumatic lesions.

Corpo estranho perfurante cervical: relato de caso / Cervical perforating foreign body: case report

As perfurações cervicais por corpos estranhos são incomuns. Sua abordagem cirúrgica depende do grau de lesão das vísceras cervicais e do desenvolvimento de sinais e sintomas de infecção cérvico-mediastinal. OBJETIVO: O presente artigo objetiva registrar a ocorrência de trauma perfurante cervical por fragmento de arame com lesão de laringe e hipofaringe dando origem a extenso enfisema cérvico-mediastinal. Correlações anátomo-clínicas e a conduta adotada são discutidas MATERIAL E MÉTODOS: O caso relatado é o de um indivíduo de 28 anos, do sexo masculino, vítima de ferimento perfurante na região cervical anterior por fragmento de arame. O corpo estranho assestou-se no espaço retrofaríngeo do doente, ao nível da 6a vértebra cervical, após perfurar a laringe e a hipofaringe. Não há caso semelhante relatado na literatura. A documentação radiológica do caso é apresentada. Apesar da potencial gravidade das lesões, o doente evoluiu bem e não necessitou de tratamento cirúrgico. CONCLUSÕES: O caso em questão, além de ilustrar, através dos exames de imagem, a complexa anatomia das fáscias e dos espaços cervicais profundos, demonstra a possibilidade da aplicação do tratamento conservador em grande parte das lesões traumáticas de laringe e hipofaringe.

Os espaços cervicais profundos e seu interesse nas infecçoes da regiäo / Deep neck spaces and their interest in cervical infections

As infecçoes dos espaços cervicais profundos, embora raras, associam-se a alta morbi-mortalidade. A abordagem cirúrgica faz-se necessaria na maioria dos casos e se baseia no conhecimento da complexa anatomia das fascias cervicais e dos espaços cervicais profundos. Objetivo. Apresentar consideraçoes anatomicas de interese pratico sobre fascias e espaços do pescoço, sua conceituaçao e nomenclatura, relatando, a título de exemplo, quatro casos de infecçoes dos espaços cervicais profundos. Material e Método. Sao apresentados um caso de angina de Ludwig complicada com mediastinite, pericardite, pneumonia, empiema pleural, fístula esofagica e choque séptico, um caso de abscesso cervical espontâneo em paciente diabético, um caso de abscesso de loja submandibular e um caso de abscesso parafaríngeo iniciado após manipulaçao dentaria. Nos quatro casos, a documentaçao imagenológica é rica e, em dois deles, evidencia o comprometimento de mais e um espaço profundo do pescoço. Conclusoes. A literatura enfatiza morbidade e mortalidade elevadas, etiologia diversificada (infecçoes dentarias, uso de drogas endovenosas, infecçoes do trato aerodigestivo alto e outras), a necessidade de traqueostomia em cerca de 50 por cento dos casos e o emprego da terapêutica combinada (antibioticoterapia e abordagem cirúrgica do pescoço). Os métodos imagenológicos, como a tomografia computadorizada, sao imprescindíveis no estudo de infecçoes dos espaços profundos do pescoço, tanto para a avaliaçao do sítio e extensao da afecçao, como para o planejamento terapêutico.

[Deep neck spaces and their significance in cervical infections]. / Os espaços cervicais profundos e seu interesse nas infecções da região.

BACKGROUND: Although rare, deep neck space infections are associated with high morbidity and mortality rates. The surgical approach is necessary in the majority of the cases, and the surgeon must know the complex anatomy of the cervical fasciae and deep neck spaces. PURPOSE: The anatomy of the cervical fasciae and deep neck spaces in reviewed. As an illustration, a series of deep neck space infections is presented. MATERIAL AND METHOD: Four clinical cases are reported: 1) a case of Ludwig's angina with several complications (mediastinitis, pericarditis, pneumonia, pleural effusion and empyema, esophageal fistula and septic shock), 2) a case of cervical abscess that appeared without apparent cause, in a young diabetic patient, 3) a case of abscess of the submandibular triangle, and 4) a case of parapharyngeal abscess that came forth after a dental treatment. Data from history taking, physical examination, X-rays, echography, CT scan and treatment and the follow-up are presented. The image tests were valuable and, in two of the cases, they demonstrated that more than one deep neck space were affected. CONCLUSIONS: The literature reinforces the high mortality and morbidity rates, the diversified etiology (dental infection, intravenous drug abuse, infections of the upper aerodigestive tract and others), and the tracheostomy indication made in about half of the cases. It stresses also the need for combined therapy (antibiotics and surgery). Evaluation with CT scan and other radiologic methods is indispensable to determine the site and extent of the process and to plan properly the treatment.