Searching for an optimal AUC estimation method: a never-ending task?
Ontology highlight
ABSTRACT:
SUBMITTER: Jawien W
PROVIDER: S-EPMC4225057 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundThe diagnostic process of pulmonary fibrosis (PF) is often challenging, requires a collaborative effort of several experts, and often requires bioptic material, which can be difficult to obtain, both in terms of quality and technique. The main procedures available to obtain such samples are transbronchial lung cryobiopsy (TBLC) and surgical lung biopsy (SLB).ObjectiveThe purpose of this paper is to review the evidence for the role of TBLC in the diagnostic-therapeutic process of PF.MethodsA comprehensive review was performed to identify articles to date that addressed the role of TBLC in the diagnostic-therapeutic process of PF using the PubMed® database.ResultsThe reasoned search identified 206 papers, including 21 manuscripts (three reviews, one systematic review, two guidelines, two prospective studies, three retrospective studies, one cross-sectional study, one original article, three editorials, three clinical trials, and two unclassifiable studies), which were included in the final review.ConclusionsTBLC is gaining increasing efficacy and improving safety profile; however, there are currently no clear data demonstrating its superiority over SLB. Therefore, the two techniques should be considered with careful rationalization on a case-by-case basis. Further research is needed to further optimize and standardize the procedure and to thoroughly study the histological and molecular characteristics of PF.
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Project description:The prevalence of non-alcoholic fatty liver disease (NAFLD) is increasing worldwide and parallels comorbidities such as obesity, metabolic syndrome, dyslipidemia, and diabetes. Recent studies describe the presence of NAFLD in non-obese individuals, with mechanisms partially independent from excessive caloric intake. Increasing evidences, in particular, point towards a close interaction between dietary and environmental factors (including food contaminants), gut, blood flow, and liver metabolism, with pathways involving intestinal permeability, the composition of gut microbiota, bacterial products, immunity, local, and systemic inflammation. These factors play a critical role in the maintenance of intestinal, liver, and metabolic homeostasis. An anomalous or imbalanced gut microbial composition may favor an increased intestinal permeability, predisposing to portal translocation of microorganisms, microbial products, and cell wall components. These components form microbial-associated molecular patterns (MAMPs) or pathogen-associated molecular patterns (PAMPs), with potentials to interact in the intestine lamina propria enriched in immune cells, and in the liver at the level of the immune cells, i.e., Kupffer cells and stellate cells. The resulting inflammatory environment ultimately leads to liver fibrosis with potentials to progression towards necrotic and fibrotic changes, cirrhosis. and hepatocellular carcinoma. By contrast, measures able to modulate the composition of gut microbiota and to preserve gut vascular barrier might prevent or reverse NAFLD.
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Project description:Background:We performed a review of published case studies of osteomyelitis associated with cat-scratch disease to consolidate existing information on clinical presentation, diagnostic tools, therapy, and outcome, as well as presenting a case of disseminated cat-scratch disease in a 12-year-old female with skull osteomyelitis and spleen involvement. Methods:A search for articles indexed in PubMed, Embase, and Google Scholar was performed with the search terms "Bartonella," "bone," "osteomyelitis," "osteolytic," and "cat-scratch disease" limited to the immunocompetent pediatric population and articles in English. Results:51 cases were identified. The average age was 7.8 years with equal sex distribution. Fever (84.3%), often with a prolonged course (64.7%), and osteoarticular pain (88.2%) were the most common clinical findings. Lymphadenopathy was present in 64.7% of patients. Vertebral body was mainly involved (51.9%). MRI (50%) and bone scintigraphy (48.1%) were favored to confirm osteomyelitis, while serology was the preferred microbiological diagnostic. Various antibiotics were prescribed in combined or sequential regimens, with median duration of therapy of 23 days. About 12.5% of patients did not receive any treatment. Most patients had excellent prognosis; in particular, all patients not receiving any therapy showed complete recovery and no recurrence of symptoms. Conclusions:Bartonella henselae should be considered in differential diagnosis of localized lymphadentitis. Osteoarticular pain or limitation during cat-scratch disease in children should always be investigated for bone spreading. Owing to good prognosis, invasive procedures to obtain the bone material should be avoided. Serology is the gold standard diagnostic tool and MRI is the best radiographic technique to define bone and surrounding tissue involvement. Treatment represents a never-ending dilemma: surgical intervention or use of antibiotics is still controversial, and more studies are needed to define the best antimicrobial regimen.
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Project description:The substitution rate in a gene can provide valuable information for understanding its functionality and evolution. A widely used method to estimate substitution rates is the maximum-likelihood method implemented in the CODEML program in the PAML package. A limited number of branch models, chosen based on a priori information or an interest in a particular lineage(s), are tested, whereas a large number of potential models are neglected. A complementary approach is also needed to test all or a large number of possible models to search for the globally optional model(s) of maximum likelihood. However, the computational time for this search even in a small number of sequences becomes impractically long. Thus, it is desirable to explore the most probable spaces to search for the optimal models. Using dynamic programming techniques, we developed a simple computational method for searching the most probable optimal branch-specific models in a practically feasible computational time. We propose three search methods to find the optimal models, which explored O(n) (method 1) to O(n(2)) (method 2 and method 3) models when the given phylogeny has n branches. In addition, we derived a formula to calculate the number of all possible models, revealing the complexity of finding the optimal branch-specific model. We show that in a reanalysis of over 50 previously published studies, the vast majority obtained better models with significantly higher likelihoods than the conventional hypothesis model methods.
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