BioGraph: Data Model for Linking and Querying Diverse Biological Metadata.

Studying the association of gene function, diseases, and regulatory gene network reconstruction demands data compatibility. Data from different databases follow distinct schemas and are accessible in heterogenic ways. Although the experiments differ, data may still be related to the same biological entities. Some entities may not be strictly biological, such as geolocations of habitats or paper references, but they provide a broader context for other entities. The same entities from different datasets can share similar properties, which may or may not be found within other datasets. Joint, simultaneous data fetching from multiple data sources is complicated for the end-user or, in many cases, unsupported and inefficient due to differences in data structures and ways of accessing the data. We propose BioGraph-a new model that enables connecting and retrieving information from the linked biological data that originated from diverse datasets. We have tested the model on metadata collected from five diverse public datasets and successfully constructed a knowledge graph containing more than 17 million model objects, of which 2.5 million are individual biological entity objects. The model enables the selection of complex patterns and retrieval of matched results that can be discovered only by joining the data from multiple sources.

A comprehensive mutation study in wide deep-rooted R1b Serbian pedigree: mutation rates and male relative differentiation capacity of 36 Y-STR markers.

Haplotyping of Y-chromosomal short tandem repeats (Y-STRs) reflects the paternal lineage, although, the father-son pair profiles may differ due to the germline mutations. In order to discriminate between closely related males in criminal cases, as well as for the correct application of Y-STRs in the paternity/kinship analysis and determination of the most recent common ancestor in the familial searching or genealogy research, the assessment of mutation rates of routinely used Y-STRs is of a great importance. We genotyped 120 males belonging to one wide deep-rooted pedigree separated by 1-20 meiosis. The haplotypes of analyzed males distributed over 12 different families (according to their surnames), with 113 originating from one ancestor, and the remaining 7 from the second, closely related to the previous one, belong to the R1b haplogroup. The analysis was performed using Powerplex® Y23 kit, Yfiler™ plus kit and 13 rapidly mutating (RM13) Y-STRs. In 20,855 allele transmissions, 175 mutations (61% repeat losses and 39% gains) and one gene conversion event were found at 25 out of 36 markers. The medians of locus-specific mutation rates estimated using the Bayesian approach ranged from 1.42 × 10-3 (95% credible interval (CI): 0.05 × 10-3 - 7.56 × 10-3) for loci with no observed mutations to 130.91 × 10-3 (95% CI: 102.91 × 10-3 - 162.78 × 10-3) for DYF399S1, with a median rate across all 36 markers of 10.06 × 10-3 (95% CI: 8.65 × 10-3 - 11.61 × 10-3). In 6349 male relative pairs, the 36 Y-STR set distinguished 98.4% relative pairs by at least one mutation, compared to 95.9%, 65.5% and 57.4% for RM13, Yfiler™ plus, and Powerplex® Y23 set, respectively. The extra-pair paternity rate was estimated at 11.9 × 10-3 (95% CI: 4.4 × 10-3 - 25.8 × 10-3) fitting within the range reported for some European populations. A significant positive correlation was observed between fathers' ages at the time of the Y chromosome transmission and mutability rates (R2 = 0.9495, p = 0.0256), with more significant results when analyzing RM markers (R2 = 0.9827, p = 0.0087).

Doppler ultrasonography combined with transient elastography improves the non-invasive assessment of fibrosis in patients with chronic liver diseases.

AIMS: Accurate clinical assessment of liver fibrosis is essential and the aim of our study was to compare and combine hemodynamic Doppler ultrasonography, liver stiffness by transient elastography, and non-invasive serum biomarkers with the degree of fibrosis confirmed by liver biopsy, and thereby to determine the value of combining non-invasive method in the prediction significant liver fibrosis. MATERIAL AND METHODS: We included 102 patients with chronic liver disease of various etiology. Each patient was evaluated using Doppler ultrasonography measurements of the velocity and flow pattern at portal trunk, hepatic and splenic artery, serum fibrosis biomarkers, and transient elastography. These parameters were then input into a multilayer perceptron artificial neural network with two hidden layers, and used to create models for predicting significant fibrosis. RESULTS: According to METAVIR score, clinically significant fibrosis (≥F2) was detected in 57.8% of patients. A model based only on Doppler parameters (hepatic artery diameter, hepatic artery systolic and diastolic velocity, splenic artery systolic velocity and splenic artery Resistance Index), predicted significant liver fibrosis with a sensitivity and specificity of75.0% and 60.0%. The addition of unrelated non-invasive tests improved the diagnostic accuracy of Doppler examination. The best model for prediction of significant fibrosis was obtained by combining Doppler parameters, non-invasive markers (APRI, ASPRI, and FIB-4) and transient elastography, with a sensitivity and specificity of 88.9% and 100%. CONCLUSION: Doppler parameters alone predict the presence of ≥F2 fibrosis with fair accuracy. Better prediction rates are achieved by combining Doppler variables with non-invasive markers and liver stiffness by transient elastography.

Erythropoietin in the Evaluation of Treatment Outcomes in Patients with Polytrauma.

Polytrauma is a term describing patients with injuries involving multiple body regions that compromises function of the body and/or organ involved. The aim of the study was to evaluate the potential role of erythropoietin in predicting poorer outcome in trauma patients. This prospective study included 86 patients admitted to the Emergency Center of Serbia due to polytrauma assigned according to Injury Severity Score (ISS). The patients were further evaluated using the Acute Physiology and Chronic Health Evaluation II and Sequential Organ Failure Assessment scores and erythropoietin levels. There was a significant difference among erythropoietin levels at admission, after 48 and 72 hours, and on day 7 of hospital stay, with significantly higher levels in patients with ISS values 49-75. Based on the results, ROC curves were used to identify cut-off levels to predict ISS score with critical clinical course. It was concluded that erythropoietin could be a good marker of injury severity. Further research has to be performed to determine the cut-off values of erythropoietin that are significant for injury severity.

Erythropoietin in Predicting Prognosis in Patients with Acute-on-Chronic Liver Failure.

BACKGROUND AND AIMS: Acute-on-chronic liver failure (ACLF) is characterized by a rapid progression to multiple organ failure and is associated with a very high mortality rate of 50-90%. Novel therapies are being investigated such as Erythropoietin (EPO). The aim of this prospective cohort study was to analyse the value of EPO in predicting prognosis and determine which patients may benefit most from EPO therapy. METHODS: According to the EASL-CLIF criteria, 104 consecutive patients were diagnosed with ACLF, and separated into two groups based on the type of insult: bleeding (Group A=31) or non-bleeding (Group B=73). In addition to a complete biochemical work-up and calculation of relevant prognostic scores, levels of EPO were measured on admission and correlated to the type of insult and final outcome. RESULTS: Fifteen patients from Group A (mean age 60.32+/-9.29 years) had a lethal outcome and higher values of EPO on admission (319.26+/-326.58 mIU/ml) (p<0.005), compared to the 37 patients from Group B (mean age 59.9+/-10.19 years) with EPO levels at admission of 29.88+/-34.6 mIU/mL. In Group B, a cut-off EPO value of 30.65 mIU/mL had a sensitivity of 87.5% and a specificity 57.4% in predicting lethal outcome with an AUROC of 0.823. In Group A, a cut-off value of 229.95 mlU/mL had a sensitivity and specificity of 53.3% and 92.7%, respectively. The AUROC for this cut-off was 0.847. CONCLUSIONS: Erythropoietin is superior to the standard prognostic scores in predicting 28-day mortality. Lower levels of EPO were detected in patients without bleeding as an insult indicating a possible therapeutic benefit in these patients.

Survival of patients with spinal muscular atrophy type 1.

BACKGROUND: Spinal muscular atrophy type 1 (SMA1) is a progressive disease and is usually fatal in the first year of life. METHODS: A retrospective chart review was performed of SMA1 patients and their outcomes according to the following choices: letting nature take its course (NT); tracheostomy and invasive mechanical ventilation (TV); continuous noninvasive respiratory muscle aid (NRA), including noninvasive ventilation; and mechanically assisted cough. RESULTS: Of 194 consecutively referred patients enrolled in this study (103 males, 91 females), NT, TV, and NRA were chosen for 121 (62.3%), 42 (21.7%), and 31 (16%) patients, respectively. Survival at ages 24 and 48 months was higher in TV than NRA users: 95% (95% confidence interval: 81.8%-98.8%) and 67.7% (95% confidence interval: 46.7%-82%) at age 24 months (P < .001) and 89.43% and 45% at age 48 months in the TV and NRA groups, respectively (P < .001). The choice of TV decreased from 50% (1992-1998) to 12.7% (2005-2010) (P < .005) with a nonstatistically significant increase for NT from 50% to 65%. The choice of NRA increased from 8.1% (1999-2004) to 22.7% (2005-2010) (P < .001). CONCLUSIONS: Long-term survival outcome is determined by the choice of the treatment. NRA and TV can prolong survival, with NRA showing a lower survival probability at ages 24 and 48 months.

Exercise ventilatory inefficiency and mortality in patients with chronic obstructive pulmonary disease undergoing surgery for non-small-cell lung cancer.

OBJECTIVE: Surgical resection is the treatment of choice to cure patients with non-small-cell lung cancer (NSCLC); nevertheless, the assessment of the lower limit of surgical tolerance remains difficult. Ventilatory inefficiency (measured as the ventilation to CO(2) production ratio (V'(E)/V'(CO2) slope) is a survival predictor in pulmonary hypertension (PH) and chronic heart failure (CHF) and is considered a marker of PH in chronic obstructive pulmonary disease (COPD). The aim of this study was to investigate the role of V'(E)/V'(CO2) slope as preoperative mortality and morbidity predictor in COPD patients submitted to lung resection for NSCLC and considered operable according to current standards. METHODS: A retrospective analysis was performed in 145 consecutive COPD patients with lung cancer (128 males and 17 females), with a mean age of 64 years (range: 41-82 years) who were referred for preoperatory evaluation. Because of bronchial obstruction or reduced pulmonary diffusion capacity for carbon monoxide (D(L,CO)), all these patients were considered operable only after a cardiopulmonary exercise test showed a preserved cardiopulmonary function. RESULTS: A total of 98 lobectomies, eight bilobectomies and 39 pneumonectomies (13 left and 26 right) were performed. Twenty-one patients (14.5%) suffered severe cardio-respiratory complications; 15/106 patients (14.2%) after lobectomy/bilobectomy and 6/39 (15.4%) after pneumonectomy. Five patients (3.4%) died within 30 days after surgery (3/106 after lobectomy/bilobectomy (2.8%) and 2/39 after pneumonectomy (5.1%)). Considering all functional parameters before surgery and the postoperative predicted values, a logistic regression analysis individuated the V'(E)/V'(CO2) slope as the only independent mortality predictor (odds ratio (OR): 1.24 z=2.77; p<0.007). The V'(O2 peak) was instead the best predictor for the occurrence of severe cardiopulmonary postoperative complications (OR: 0.05, z=-2.39, p<0.02). CONCLUSIONS: In COPD patients, a high V'(E)/V'(CO2) slope before lung resection is an independent mortality predictor even in the presence of an acceptable cardiopulmonary performance. COPD patients with high V'(E)/V'(CO2) slope before surgery must be carefully screened to exclude pulmonary hypertension, especially before surgical procedures with large parenchymal exeresis.

[Incidence of tuberculosis in Piedmont Region in the period 2001-2003]. / Incidenza della tubercolo nella Regione Piemonte nel periodo 2001-2003.

OBJECTIVES: tuberculosis is a global heath priority and the surveillance systems are essential tools to control the spread of the disease. The objectives are to estimate: the incidence tuberculosis in Piedmont for the period 2001-03, using multiple sources of information; the sensitivity of the regional system for the surveillance of tuberculosis; the impact ofimmigration from areas with high prevalence of tuberculosis. DESIGN: deterministic linkage between electronic databases and estimate of non-observed cases of microbiologically confirmed tuberculosis, using the 'capture-recapture method'. METHODS: the Piedmonti population was the study base. Tuberculosis cases were identified from the integrated Regional Tuberculosis Surveillance System (SSR- TB), the Tuberculosis Laboratory Registry (RL-TB), and the Regional Registry of Inpatient Records (SDO). RESULTS: 1790 cases of tuberculosis were recorded, in 28.6% (512) of the cases the disease was observed among individuals from countries with high prevalence of tuberculosis. Microbiologically confirmed cases of tuberculosis were 1254 (70%), while pulmonary cases were 1233 (69%). The annual crude incidence of tuberculosis (per 100,000 inhabitants) was 14.1 cases, 31.5% of whom were attributable to immigration from countries with high prevalence of tuberculosis. The incidence among immigrants was 122.4 cases, while that of microbiologically confirmed cases was 9.8 cases. The overall estimated sensitivity, for the microbiologically confirmed cases, was 97%, while the sensitivity of SSR-TB was 90%. CONCLUSIONS: Our estimate of tuberculosis incidence in Piedmont is about two times as great as that given by the WHO for Italy (8 cases per 100,000 inhabitants). The fraction of incident cases attributable to immigration from countries with high prevalence of tuberculosis is also consistent with that estimated in other industrialized countries undergoing high immigration flows. The integration of surveillance systems is essential to obtain accurate and timely estimates of the tuberculosis epidemiology.