Caipirini: using gene sets to rank literature

<p>Abstract</p> <p>Background</p> <p>Keeping up-to-date with bioscience literature is becoming increasingly challenging. Several recent methods help meet this challenge by allowing literature search to be launched based on lists of abstracts that the user judges to be 'interesting'. Some methods go further by allowing the user to provide a second input set of 'uninteresting' abstracts; these two input sets are then used to search and rank literature by relevance. In this work we present the service 'Caipirini' (<url>http://caipirini.org</url>) that also allows two input sets, but takes the novel approach of allowing ranking of literature based on one or more sets of genes.</p> <p>Results</p> <p>To evaluate the usefulness of Caipirini, we used two test cases, one related to the human cell cycle, and a second related to disease defense mechanisms in <it>Arabidopsis thaliana</it>. In both cases, the new method achieved high precision in finding literature related to the biological mechanisms underlying the input data sets.</p> <p>Conclusions</p> <p>To our knowledge Caipirini is the first service enabling literature search directly based on biological relevance to gene sets; thus, Caipirini gives the research community a new way to unlock hidden knowledge from gene sets derived via high-throughput experiments.</p

Doença de Hirschsprung: experiência com uma série de 55 casos Hirschsprung's disease: experiment with a serie of 55 cases

OBJETIVOS: analisar aspectos clínicos de pacientes com Doença de Hirschprung (DH). MÉTODOS: realizou-se estudo de caso institucional, retrospectivo, via revisão de prontuários de pacientes com DH atendidos no Instituto Fernandes Figueira entre 1993 e 2003. RESULTADOS: Em um total de 55 pacientes, 98% apresentaram sintomas neonatais, sendo 47,2% diagnosticados nesse período; em 88,9% o enema baritado foi conclusivo; 69% tinham DH de segmento curto; 16,3% síndrome de Down; 15,2% outras anomalias congênitas; 40% foram rastreados para mutações RET associadas a neoplasias endócrinas múltiplas (MEN2A), não sendo detectada nenhuma; 63,6% fizeram abaixamento estagiado do colon/íleo; 12,72% abaixamento endoretal transanal primário; as principais complicações cirúrgicas foram sepse, enterocolite e obstrução intestinal; distúrbios da defecação foram detectados anos pós-cirurgia; a taxa de letalidade foi 9,25%; os óbitos relacionaram-se a enterocolite e sepse pós-operatórias. CONCLUSÃO: embora apresentasse sintomas neonatais, a maioria dos pacientes foi diagnosticada tardiamente. Enterocolite foi a principal causa de morbimortalidade. Distúrbios da defecação ocorrem com frequência, demandando follow-up prolongado. Embora rara, a associação com MEN2A precisa ser investigada devido à agressividade da doença. A heterogeneidade clínica e genética da DH exige atuação de equipe multidisciplinar.<br>OBJECTIVES: to analyze clinical features of patients with Hirschprung's Disease (HD). METHODS: a retrospective institutional case study was carried out using the medical records of patients with HD attending the Fernandes Figueira Institute between 1993 and 2003. RESULTS: out of a total of 55 patients, 98% presented symptoms on birth, 47.2% of whom were diagnosed during the neonatal period; in 88.9% of cases the barium enema was conclusive; 69% had short segment HD; 16.3% Down's Syndrome; 15.2% other congenital anomalies; 40% were screened for RET mutations associated with multiple endocrine neoplasias (MEN2A), although none were detected; 63.6% had staged pull-through surgery on the colon or ileum; 12.72% primary transanal endorectal pull-through surgery; the main complications arising from surgery were sepsis, enterocolitis and obstruction of the intestines; abnormal bowel movements were detected years after the surgery; the mortality rate was 9.25%, the causes of death being post-operal enterocolitis and sepsis. CONCLUSION: although patients presented symptoms on birth, most were diagnosed at a later stage. Enterocolitis was the main cause of death. Abnormal bowel movements frequently occurred, requiring prolonged follow-up. Although rare, the association with MEN2A needs to be investigated owing to the highly aggressive nature of the disease. The clinical and genetic heterogeneity of HD necessitates the involvement of a multidisciplinary team