In this article we introduce modern statistical machine learning and bioinformatics approaches that have been used in learning statistical relationships from big data in medicine and behavioral science that typically include clinical, genomic (and proteomic) and environmental variables. Every year, data collected from biomedical and behavioral science is getting larger and more complicated. Thus, in medicine, we also need to be aware of this trend and understand the statistical tools that are available to analyze these datasets. Many statistical analyses that are aimed to analyze such big datasets have been introduced recently. However, given many different types of clinical, genomic, and environmental data, it is rather uncommon to see statistical methods that combine knowledge resulting from those different data types. To this extent, we will introduce big data in terms of clinical data, single nucleotide polymorphism and gene expression studies and their interactions with environment. In this article, we will introduce the concept of well-known regression analyses such as linear and logistic regressions that has been widely used in clinical data analyses and modern statistical models such as Bayesian networks that has been introduced to analyze more complicated data. Also we will discuss how to represent the interaction among clinical, genomic, and environmental data in using modern statistical models. We conclude this article with a promising modern statistical method called Bayesian networks that is suitable in analyzing big data sets that consists with different type of large data from clinical, genomic, and environmental data. Such statistical model form big data will provide us with more comprehensive understanding of human physiology and disease.
Bayes Theorem ; Behavioral Sciences ; Computational Biology ; Data Interpretation, Statistical ; Dataset ; Gene Expression ; Humans ; Learning ; Logistic Models ; Machine Learning* ; Models, Statistical ; Physiology ; Polymorphism, Single Nucleotide ; Statistics as Topic* ; Systems Biology

OBJECTIVE: To report the clinical presentation and oncologic outcomes of a series of patients who presented with an abdominal or pelvic mass and were diagnosed with a gastrointestinal stromal tumor (GIST). METHODS: Data were obtained on all patients who presented with an abdominal or pelvic mass between September 2007 and June 2010 and who were ultimately diagnosed with a GIST. The patients' medical records were reviewed. A literature review was also conducted. RESULTS: Six patients were identified who met the inclusion criteria. All six patients had a tumor in the intestinal tract arising from the small bowel. The mean tumor size was 12 cm (range, 6 to 22 cm). A complete resection was achieved in five of the six patients. There were no intraoperative complications; one patient had a postoperative complication. Two patients were treated with imatinib after surgery. The mean follow-up time was 32 months (range, 0.3 to 40 months). At the last follow-up, five of the six patients were without any evidence of disease. One patient died of an unrelated hepatic encephalopathy. The incidence in our institution is 3%. CONCLUSION: GISTs are uncommon; however, they should be considered in the differential diagnosis of patients presenting with an abdominal or pelvic mass.
Benzamides ; Diagnosis, Differential ; Follow-Up Studies ; Gastrointestinal Stromal Tumors ; Hepatic Encephalopathy ; Humans ; Imatinib Mesylate ; Incidence ; Incidental Findings ; Medical Records ; Ovarian Neoplasms ; Piperazines ; Postoperative Complications ; Pyrimidines

PURPOSE: To identify the factors affecting the surgical decisions of experienced physicians when treating patients with lower urinary tract symptoms that are suggestive of benign prostatic hyperplasia (LUTS/BPH). METHODS: Patients with LUTS/BPH treated by two physicians between October 2004 and August 2013 were included in this study. The causal Bayesian network (CBN) model was used to analyze factors influencing the surgical decisions of physicians and the actual performance of surgery. The accuracies of the established CBN models were verified using linear regression (LR) analysis. RESULTS: A total of 1,108 patients with LUTS/BPH were analyzed. The mean age and total prostate volume (TPV) were 66.2 (+/-7.3, standard deviation) years and 47.3 (+/-25.4) mL, respectively. Of the total 1,108 patients, 603 (54.4%) were treated by physician A and 505 (45.6%) were treated by physician B. Although surgery was recommended to 699 patients (63.1%), 589 (53.2%) actually underwent surgery. Our CBN model showed that the TPV (R=0.432), treating physician (R=0.370), bladder outlet obstruction (BOO) on urodynamic study (UDS) (R=0.324), and International Prostate Symptom Score (IPSS) question 3 (intermittency; R=0.141) were the factors directly influencing the surgical decision. The transition zone volume (R=0.396), treating physician (R=0.340), and BOO (R=0.300) directly affected the performance of surgery. Compared to the LR model, the area under the receiver operating characteristic curve of the CBN surgical decision model was slightly compromised (0.803 vs. 0.847, P<0.001), whereas that of the actual performance of surgery model was similar (0.801 vs. 0.820, P=0.063) to the LR model. CONCLUSIONS: The TPV, treating physician, BOO on UDS, and the IPSS item of intermittency were factors that directly influenced decision-making in physicians treating patients with LUTS/BPH.
Bayes Theorem ; Decision Making, Computer-Assisted ; Decision Support Techniques ; Humans ; Linear Models ; Lower Urinary Tract Symptoms* ; Prostate ; Prostatic Hyperplasia* ; ROC Curve ; Urinary Bladder Neck Obstruction ; Urodynamics

Lipomas are benign mesenchymal tumors that develop in areas of abundant adipose tissue. Due to the fatty composition of the breast, difficulties in diagnosis, treatment, and reconstruction are often encountered. We report a case of a 55-year-old female with a giant tumor of the right breast that comprised most of its mass, causing breast asymmetry. A thorough preoperative evaluation, followed by an uneventful difficult surgical resection and reconstruction, resulted in diagnosis of a benign lipoma. The case prompted this report because of its challenging size, location, diagnosis, and reconstructive solution.
Adipose Tissue ; Breast ; Breast Diseases ; Breast Neoplasms ; Female ; Humans ; Lipoma ; Mammaplasty

The application of Giemsa technique to stain compressed diaphragm samples obtained from rodents experimentally infected with Trichinella spiralis is described. Diaphragm samples from rats heavily infected with 20 muscle larvae per gram of body weight (20 ML/gbw) were cut into several pieces and stained with Giemsa; on the other hand, whole diaphragms from slightly infected mice (1 ML/gbw) were also stained with Giemsa. Besides, muscle samples were also stained with Giemsa. Observation at 10 x magnification revealed that both ML and nurse cells (NC) look as bluish structures clearly contrasting with the pinkish color of the non-infected muscle fibers. NC in the diaphragms of mice could be easily observed at naked eye as blue points contrasting with the pink surrounding areas formed by the non-infected muscle fibers. Among NC observed in the diaphragms of rats infected with 20 ML/gbw, 4.4% was multiple infection. These findings were confirmed in sectioned and hematoxylin-eosin stained specimens. This data could be usefulness for a rapid diagnosis of trichinellosis in post-mortem mammals without magnification procedures.
Animals ; Azure Stains/*chemistry ; Diaphragm/*parasitology ; Larva/ultrastructure ; Male ; Mice ; Rats ; Rats, Wistar ; Trichinella spiralis/*isolation & purification/ultrastructure ; Trichinosis/diagnosis/*parasitology

The application of Giemsa technique to stain compressed diaphragm samples obtained from rodents experimentally infected with Trichinella spiralis is described. Diaphragm samples from rats heavily infected with 20 muscle larvae per gram of body weight (20 ML/gbw) were cut into several pieces and stained with Giemsa; on the other hand, whole diaphragms from slightly infected mice (1 ML/gbw) were also stained with Giemsa. Besides, muscle samples were also stained with Giemsa. Observation at 10 x magnification revealed that both ML and nurse cells (NC) look as bluish structures clearly contrasting with the pinkish color of the non-infected muscle fibers. NC in the diaphragms of mice could be easily observed at naked eye as blue points contrasting with the pink surrounding areas formed by the non-infected muscle fibers. Among NC observed in the diaphragms of rats infected with 20 ML/gbw, 4.4% was multiple infection. These findings were confirmed in sectioned and hematoxylin-eosin stained specimens. This data could be usefulness for a rapid diagnosis of trichinellosis in post-mortem mammals without magnification procedures.
Animals ; Azure Stains/*chemistry ; Diaphragm/*parasitology ; Larva/ultrastructure ; Male ; Mice ; Rats ; Rats, Wistar ; Trichinella spiralis/*isolation & purification/ultrastructure ; Trichinosis/diagnosis/*parasitology

Background: Dengue is the most important human viral disease transmitted by arthropod vectors. The availability of random peptide libraries (RPL) displayed on phage has provided a powerful tool for selecting sequences that mimic epitopes from microorganisms that are useful for diagnostic and vaccine development purposes. In this paper, we describe peptides that resemble the antigenic structure of B-cell epitopes of dengue virus identified from a phage-peptide library using human sera containing polyclonal antibodies against dengue virus. Materials and Methods: Eighteen phage clones were isolated from the phage-display peptide library, J404, by affinity selection using human antisera against dengue virus type 3. These clones were tested for reactivity by ELISA with a panel of hyperimmune ascitic fluids (HAFs) containing antibodies either against all four dengue serotypes, West Nile virus (WNV) or Eastern equine encephalitis virus (EEEV) with control ascitic fluid (NAF) used as a negative control. Results: Eight clones were recognized by HAFs against the four dengue serotypes, of which four significantly inhibited binding of anti-dengue antibodies to the virus. Two peptides with similar sequences to regions of NS3 and NS4B non-structural dengue virus proteins were identified. Conclusion: Our results suggest that these peptides could be used for the development of diagnostic tools for the detection of dengue virus infection and for a potential vaccine against this pathogen.

BACKGROUND/AIMS: The development of therapeutic strategies for the treatment of cirrhosis has become an important focus for basic and clinical researchers. Adrenergic receptor antagonists have been evaluated as antifibrotic drugs in rodent models of carbon tetrachloride (CCl4)-induced cirrhosis. The aim of the present study was to evaluate the effects of carvedilol and doxazosin on fibrosis/cirrhosis in a hamster animal model. METHODS: Cirrhotic-induced hamsters were treated by daily administration of carvedilol and doxazosin for 6 weeks. Hepatic function and histological evaluation were conducted by measuring biochemical markers, including total bilirubin, aspartate aminotransferase, alanine aminotransferase and albumin, and liver tissue slices. Additionally, transforming growth factor beta (TGF-beta) immunohistochemistry was analyzed. RESULTS: Biochemical markers revealed that hepatic function was restored after treatment with doxazosin and carvedilol. Histological evaluation showed a decrease in collagen type I deposits and TGF-beta-secreting cells. CONCLUSIONS: Taken together, these results suggest that the decrease in collagen type I following treatment with doxazosin or carvedilol is achieved by decreasing the profibrotic activities of TGF-beta via the blockage of alpha1- and beta-adrenergic receptor. Consequently, a diminution of fibrotic tissue in the CCl4-induced model of cirrhosis is achieved.
Adrenergic alpha-1 Receptor Antagonists/*pharmacology ; Alanine Transaminase/blood ; Animals ; Aspartate Aminotransferases/blood ; Bilirubin/blood ; Carbazoles/*pharmacology ; Carbon Tetrachloride ; Collagen Type I/drug effects/metabolism ; Cricetinae ; Doxazosin/*pharmacology ; Liver/metabolism/pathology ; Liver Cirrhosis/blood/chemically induced/*drug therapy ; Liver Function Tests ; Propanolamines/*pharmacology ; Serum Albumin/analysis ; Transforming Growth Factor beta/blood/*drug effects