EMVC-2: an efficient single-nucleotide variant caller based on expectation maximization.

MOTIVATION: Single-nucleotide variants (SNVs) are the most common type of genetic variation in the human genome. Accurate and efficient detection of SNVs from next-generation sequencing (NGS) data is essential for various applications in genomics and personalized medicine. However, SNV calling methods usually suffer from high computational complexity and limited accuracy. In this context, there is a need for new methods that overcome these limitations and provide fast reliable results. RESULTS: We present EMVC-2, a novel method for SNV calling from NGS data. EMVC-2 uses a multi-class ensemble classification approach based on the expectation-maximization algorithm that infers at each locus the most likely genotype from multiple labels provided by different learners. The inferred variants are then validated by a decision tree that filters out unlikely ones. We evaluate EMVC-2 on several publicly available real human NGS data for which the set of SNVs is available, and demonstrate that it outperforms state-of-the-art variant callers in terms of accuracy and speed, on average. AVAILABILITY AND IMPLEMENTATION: EMVC-2 is coded in C and Python, and is freely available for download at: https://github.com/guilledufort/EMVC-2. EMVC-2 is also available in Bioconda.

RENANO: a REference-based compressor for NANOpore FASTQ files.

MOTIVATION: Nanopore sequencing technologies are rapidly gaining popularity, in part, due to the massive amounts of genomic data they produce in short periods of time (up to 8.5 TB of data in <72 h). To reduce the costs of transmission and storage, efficient compression methods for this type of data are needed. RESULTS: We introduce RENANO, a reference-based lossless data compressor specifically tailored to FASTQ files generated with nanopore sequencing technologies. RENANO improves on its predecessor ENANO, currently the state of the art, by providing a more efficient base call sequence compression component. Two compression algorithms are introduced, corresponding to the following scenarios: (1) a reference genome is available without cost to both the compressor and the decompressor and (2) the reference genome is available only on the compressor side, and a compacted version of the reference is included in the compressed file. We compare the compression performance of RENANO against ENANO on several publicly available nanopore datasets. RENANO improves the base call sequences compression of ENANO by 39.8% in scenario (1), and by 33.5% in scenario (2), on average, over all the datasets. As for total file compression, the average improvements are 12.7% and 10.6%, respectively. We also show that RENANO consistently outperforms the recent general-purpose genomic compressor Genozip. AVAILABILITY AND IMPLEMENTATION: RENANO is freely available for download at: https://github.com/guilledufort/RENANO. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Latino Health Access: Comparative Effectiveness of a Community-Initiated Promotor/a-Led Diabetes Self-management Education Program.

Community-initiated health interventions fill important gaps in access to health services. This study examines the effectiveness of a community-initiated health intervention to improve diabetes management in an underserved community of color using a retrospective observational study, comparing a study intervention, the Latino Health Access Diabetes Self-Management Program (LHA-DSMP), with usual care. The LHA-DSMP is a 12-session community health worker (promotor/a) intervention developed and implemented by a community-based organization in a medically underserved area. Usual care was delivered at a federally qualified health center in the same geographic area. Participants were 688 predominantly Spanish-speaking Latinx adults with type 2 diabetes. The main outcome was change in glycemic control (glycosylated hemoglobin [HbA1c]) from baseline to follow-up. At 14-week follow-up, mean (95% CI) HbA1c decrease was -1.1 (-1.3 to -0.9; P < .001) in the LHA-DSMP cohort compared with -0.3 (-0.4 to -0.2; P < .001) in the comparison cohort. Controlling for baseline differences between cohorts, the adjusted difference-in-differences value in HbA1c was -0.6 (-0.8 to -0.3; P < .001) favoring the LHA-DSMP. A community-initiated promotor/a-led educational program for diabetes self-management is associated with clinically significant improvement in blood sugar control, superior to what was observed with usual medical care.

Efficacy and safety comparative study of dexrabeprazole vs. esomeprazole for the treatment of gastroesophageal reflux disease.

INTRODUCTION: A national survey in the general population showed that gastroesophageal reflux disease (GERD) is highly prevalent in Mexico. OBJECTIVE: To compare the efficacy and safety of two isomers, dexrabeprazole (10 mg) vs. esomeprazole (20 mg), in the treatment of GERD for four weeks. METHODS: Randomized, multicenter, prospective, double-blind phase III clinical trial in two groups that included 230 patients. RESULTS: A statistically significant decrease in the severity of GERD symptoms (heartburn, regurgitation, epigastric pain and dysphagia), evaluated using a visual analogue scale, was observed with both treatments. Mean score for dexrabeprazole on Carlsson-Dent questionnaire at 28 days was 2.12, and for esomeprazole, 3.02. Both treatments were effective, with no statistically significant difference being recorded (p < 0.05). On SF-36 health questionnaire, both were observed to improve the quality-of-life score, with no significant difference being identified. Both drugs were well tolerated, and the adverse event incidence profile was low. CONCLUSIONS: In the treatment of non-erosive GERD, the use of dexrabeprazole at 10 mg/day is as effective as esomeprazole 20 mg/day, with the advantage that the dose is lower with an appropriate safety profile.

INTRODUCCIÓN: Una encuesta nacional en población abierta mostró que la enfermedad por reflujo gastroesofágico (ERGE) tiene alta prevalencia en México. OBJETIVO: Comparar la eficacia y seguridad de dos isómeros, dexrabeprazol (10 mg) versus esomeprazol (20 mg), en el tratamiento de la ERGE durante cuatro semanas. MÉTODOS: Ensayo clínico fase III, aleatorizado, multicéntrico, prospectivo, doble ciego, en dos grupos que incluyeron 230 pacientes. RESULTADOS: Con ambos tratamientos se observó disminución estadísticamente significativa en la severidad de los síntomas de ERGE (pirosis, regurgitación, dolor epigástrico y disfagia), evaluados mediante una escala visual análoga. La puntuación promedio de dexrabeprazol en el Cuestionario de Carlsson-Dent a los 28 días fue de 2.12 y la de esomeprazol de 3.02. Ambos tratamientos fueron efectivos, sin diferencia estadísticamente significativa (p < 0.05). En el Cuestionario de Salud SF-36 se observó que ambos mejoraron la puntuación en la calidad de vida, sin diferencia significativa. Ambos medicamentos fueron bien tolerados y el perfil de incidencia de eventos adversos fue bajo. CONCLUSIONES: En el tratamiento de ERGE no erosiva, el uso de 10 mg/día de dexrabeprazol es tan efectivo como 20 mg/día de esomeprazol, con la ventaja de que la dosis es menor con un adecuado perfil de seguridad.

ENANO: Encoder for NANOpore FASTQ files.

MOTIVATION: The amount of genomic data generated globally is seeing explosive growth, leading to increasing needs for processing, storage and transmission resources, which motivates the development of efficient compression tools for these data. Work so far has focused mainly on the compression of data generated by short-read technologies. However, nanopore sequencing technologies are rapidly gaining popularity due to the advantages offered by the large increase in the average size of the produced reads, the reduction in their cost and the portability of the sequencing technology. We present ENANO (Encoder for NANOpore), a novel lossless compression algorithm especially designed for nanopore sequencing FASTQ files. RESULTS: The main focus of ENANO is on the compression of the quality scores, as they dominate the size of the compressed file. ENANO offers two modes, Maximum Compression and Fast (default), which trade-off compression efficiency and speed. We tested ENANO, the current state-of-the-art compressor SPRING and the general compressor pigz on several publicly available nanopore datasets. The results show that the proposed algorithm consistently achieves the best compression performance (in both modes) on every considered nanopore dataset, with an average improvement over pigz and SPRING of >24.7% and 6.3%, respectively. In addition, in terms of encoding and decoding speeds, ENANO is 2.9× and 1.7× times faster than SPRING, respectively, with memory consumption up to 0.2 GB. AVAILABILITY AND IMPLEMENTATION: ENANO is freely available for download at: https://github.com/guilledufort/EnanoFASTQ. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

An intrapancreatic bronchogenic cyst simulating a mucinous cystadenoma. A case report.

We present the case of a 61-year-old male with a long-term epigastric mass and pain, high CA 19.9 levels and no weight loss. A computerized tomography was performed and a solid-cystic pancreatic mass was observed. The lesion measured 10 x 8 cm with well-defined margins, a macroscopic calcification and an enhanced solid component.

Genetic variants in COL13A1, ADIPOQ and SAMM50, in addition to the PNPLA3 gene, confer susceptibility to elevated transaminase levels in an admixed Mexican population.

Non-alcoholic fatty liver disease (NAFLD) is the accumulation of extra fat in liver cells not caused by alcohol. Elevated transaminase levels are common indicators of liver disease, including NAFLD. Previously, we demonstrated that PNPLA3 (rs738409), LYPLAL1 (rs12137855), PPP1R3B (rs4240624), and GCKR (rs780094) are associated with elevated transaminase levels in overweight/obese Mexican adults. We investigated the association between 288 SNPs identified in genome-wide association studies and risk of elevated transaminase levels in an admixed Mexican-Mestizo sample of 178 cases of NAFLD and 454 healthy controls. The rs2896019, rs12483959, and rs3810622 SNPs in PNPLA3 and rs1227756 in COL13A1 were associated with elevated alanine aminotransferase (ALT, ≥40IU/L). A polygenic risk score (PRS) based on six SNPs in the ADIPOQ, COL13A1, PNPLA3, and SAMM50 genes was also associated with elevated ALT. Individuals carrying 9-12 risk alleles had 65.8% and 48.5% higher ALT and aspartate aminotransferase (AST) levels, respectively, than those with 1-4 risk alleles. The PRS showed the greatest risk of elevated ALT levels, with a higher level of significance than the individual variants. Our findings suggest a significant association between variants in COL13A1, ADIPOQ, SAMM50, and PNPLA3, and risk of NAFLD/elevated transaminase levels in Mexican adults with an admixed ancestry. This is the first study to examine high-density single nucleotide screening for genetic variations in a Mexican-Mestizo population. The extent of the effect of these variations on the development and progression of NAFLD in Latino populations requires further analysis.

Helicobacter pylori Activates and Expands Lgr5(+) Stem Cells Through Direct Colonization of the Gastric Glands.

BACKGROUND & AIMS: Helicobacter pylori infection is the main risk factor for gastric cancer. We characterized the interactions of H pylori with gastric epithelial progenitor and stem cells in humans and mice and investigated how these interactions contribute to H pylori-induced pathology. METHODS: We used quantitative confocal microscopy and 3-dimensional reconstruction of entire gastric glands to determine the localizations of H pylori in stomach tissues from humans and infected mice. Using lineage tracing to mark cells derived from leucine-rich repeat-containing G-protein coupled receptor 5-positive (Lgr5(+)) stem cells (Lgr5-eGFP-IRES-CreERT2/Rosa26-TdTomato mice) and in situ hybridization, we analyzed gastric stem cell responses to infection. Isogenic H pylori mutants were used to determine the role of specific virulence factors in stem cell activation and pathology. RESULTS: H pylori grow as distinct bacterial microcolonies deep in the stomach glands and interact directly with gastric progenitor and stem cells in tissues from mice and humans. These gland-associated bacteria activate stem cells, increasing the number of stem cells, accelerating Lgr5(+) stem cell proliferation, and up-regulating expression of stem cell-related genes. Mutant bacteria with defects in chemotaxis that are able to colonize the stomach surface but not the antral glands in mice do not activate stem cells. In addition, bacteria that are unable to inject the contact-dependent virulence factor CagA into the epithelium colonized stomach glands in mice, but did not activate stem cells or produce hyperplasia to the same extent as wild-type H pylori. CONCLUSIONS: H pylori colonize and manipulate the progenitor and stem cell compartments, which alters turnover kinetics and glandular hyperplasia. Bacterial ability to alter the stem cells has important implications for gastrointestinal stem cell biology and H pylori-induced gastric pathology.

Association between PNPLA3 (rs738409), LYPLAL1 (rs12137855), PPP1R3B (rs4240624), GCKR (rs780094), and elevated transaminase levels in overweight/obese Mexican adults.

There is scarce information about the link between specific single-nucleotide polymorphisms (SNPs) and risk of liver disease among Latinos, despite the disproportionate burden of disease among this population. Our aim was to investigate nine SNPs in or near the following genes: PNPLA3, LYPLAL1, PPP1R3B, GCKR, NCAN, IRS1, PPARG, and ADIPOR2 and examine their association with persistently elevated alanine aminotransferase (ALT) or aspartate aminotransferase (AST) levels in Mexican adults. Data and samples were collected from 741 participants in the Mexican Health Worker Cohort Study, in Cuernavaca, Mexico. We identified 207 cases who had persistently elevated levels of ALT or AST (≥40 U/L) and 534 controls with at least two consecutive normal ALT or AST results in a 6 month period, during 2004-2006 and 2011-2013. TaqMan assays were used to genotype the SNPs. The risk allele of PNPLA3 rs738409 was found to be associated with persistently elevated levels of ALT or AST, adjusting for age, sex, BMI, type 2 diabetes, and ancestry: (OR 2.28, 95 % CI 1.13, 4.58). A significant association was found between the LYPLAL1, PPP1R3B, and GCKR risk alleles and elevated ALT or AST levels among overweight/obese adults. These results suggest that among Mexicans, the PNPLA3 (rs738409), LYPLAL1 (rs12137855), PPP1R3B (rs4240624), and GCKR (rs780094) polymorphisms may be associated with a greater risk of chronic liver disease among overweight adults. This study is the first to examine these nine SNPs in a sample of adults in Mexico.

A 3-Arm Randomized Trial for Achilles Tendinopathy: Eccentric Training, Eccentric Training Plus a Dietary Supplement Containing Mucopolysaccharides, or Passive Stretching Plus a Dietary Supplement Containing Mucopolysaccharides.

BACKGROUND: Tendinopathy is an overuse tendon injury that occurs in loaded tendons and results in pain and functional impairment. Although many treatments for painful tendons are described, the scientific evidence for most of the conservative and surgical treatments is not always conclusive. OBJECTIVES: This study was designed to evaluate the efficacy of 3 different interventions in patients with Achilles tendinopathy. The interventions include the combination of 2 physical therapy programs (eccentric training [EC] or passive stretching [PS]) with a supplement containing mucopolisaccharides. The efficacy of the interventions was evaluated depending on the stage of the disease. METHODS: Fifty-nine patients were randomly assigned to 1 of 3 treatment groups, and classified according to the disease stage: reactive versus degenerative tendinopathy. Treatment groups were EC; EC + a dietary supplement containing mucopolisaccharides, type I collagen, and vitamin C (MCVC); and a passive stretching program + MCVC. Patients were evaluated at baseline, 6 weeks, and 12 weeks with the Victorian Institute of Sports Assessment-Achilles questionnaire for function, a visual analog scale for pain, and ultrasound characterization for the evolution of tendon structure. RESULTS: A significant improvement in Victorian Institute of Sports Assessment-Achilles questionnaire score, pain at rest, and pain during activity were detected in all 3 treatment groups at 6 and 12 weeks' follow-up when compared with baseline. In patients with reactive tendinopathy, the reduction in pain at rest was greater in the groups who took the supplemental MCVC than in the EC alone group (P < 0.05). CONCLUSIONS: MCVC seems to be therapeutically useful for management of tendinopathies, providing some additional benefit to physical therapy. This is especially evident in early stages of the disease, when the tendon does not present severe matrix and vascular changes. CLINICALTRIALSGOV IDENTIFIER: NCT01691716.

Predictive markers of response to neoadjuvant therapy in rectal cancer.

BACKGROUND: Neoadjuvant therapy followed by radical surgery is the standard treatment in locally advanced rectal cancer. It is important to predict the response because the treatment has side effects and is costly. The aim of this study was to establish the relationship among clinical, pathologic, and molecular biomarkers and the response to neoadjuvant therapy. METHOD: A total of 130 patients with locally advanced mid and low rectal cancer who underwent long-course radiotherapy with 5-FU based chemotherapy followed by radical surgical resection were included in the study. Clinical and pathologic data were collected. Paraffin-embedded sections obtained in diagnostic biopsies were assessed by immunohistochemical staining for molecular markers and classified using a semiquantitative method. Results were related with T-downstaging and tumor regression grade using Mandard scoring system on surgical specimens. RESULTS: Pathologic complete response was found in 19 patients (14.6%), while in another 18 (13.8%) only minor residual disease was seen in the rectal wall. T-downstaging was observed in 63 (48.5%). The average of lymph node retrieval in the surgical specimens was 9.4. Regarding predictive markers of response, there was significant correlation between the expression of B-cell lymphoma 2 (P = 0.005), ß-catenin (P = 0.03), vascular endothelial growth factor (P = 0.048) and apoptotic protease activating factor 1 (P = 0.03), tumor differentiation grade (P < 0.001), and response in the univariate analysis. T-downstaging was associated with vascular endothelial growth factor expression (P = 0.03) and tumor differentiation grade (P < 0.001). Significant parameters found in the multivariate analysis were tumor differentiation grade and Bcl-2 expression. CONCLUSIONS: Pathologic and molecular biomarkers in the diagnostic biopsies may help us predict tumor response to chemoradiation in rectal cancer patients.

[Factors related to a suboptimal bowel preparation for colonoscopy]. / Factores relacionados a una subóptima preparación intestinal para la colonoscopía.

INTRODUCTION: Colonoscopy is the standard method for the evaluation of the colon. A suitable intestinal cleaning is critical for the effectiveness and security of the procedure, but unfortunately there is a high proportion of suboptimal bowel preparation. OBJECTIVE: To identify factors related to suboptimal bowel preparation. METHODS: We performed an analytic, observational, cross-sectional and prospective study. We included all outpatients scheduled for colonoscopy in the Peruvian-Japanese Health Center between January and July 2012. We excluded patients with a complete or partial colonic resection. In patients with two or more colonoscopies during the study interval, only the first procedure was considered. Aronchick scale was used in assessment of bowel cleaning. The variables studied with relationship to bowel preparation were: age, sex, grade ofeducation, body mass index, time of examination, history (diabetes mellitus, stroke, cirrhosis, use of antidepressants/anxiolytics, number of bowel movements per week, abdominal surgery, personal history of previous colonoscopy, polyps and colon cancer, family history of colon cancer), received purgative, additional laxative, indication for colonoscopy and adverse effects of the preparation. Statistical analysis was made with SPSS v.160. For the categorical variables we used chi square test or Fisher exact test, whereas for continuous variables the Mann Whitney test was used. The variables significantly associated with suboptimal preparation in the univariated analysis were included in a multivariate analysis using logistic regression. RESULTS: We included 841 patients. The bowel preparation was suboptimal in 438 patients (52.1%). The univariate analysis showed that the factors related to suboptimal preparation were age (P = 0.023) and body mass index ≥ 30 kg/m2 (P = 0.021). The multivariate analysis confirmed that age ≥ 70 years old (P = 0.001) and body mass index ≥ 30 kg/m2 (P = 0.010) were the variables related to suboptimal bowel preparation. CONCLUSIONS: Age greater than 70 years old and obesity are factors related to suboptimal bowel preparation.

[Analysis of the factors involved in the evolution of patients over 80 years of age admitted to the intensive care unit: Should we change our procedure?] / Análisis de los factores implicados en la evolución de los pacientes mayores de 80 años, ingresados en la unidad de cuidados intensivos: ¿debemos cambiar nuestro proceder?

BACKGROUND AND OBJECTIVES: The care of older patients in intensive care units (ICU) is becoming more frequent. To describe characteristics of elderly patients admitted to the ICU and to analyze the factors associated with mortality. PATIENTS AND METHODS: Retrospective cross-sectional study, with patients ≥80 years, admitted to the ICU of the Rey Juan Carlos University Hospital, from March 2012 to December 2018. Demographic variables, comorbidities and mortality in the ICU, in hospital and at one year were collected, analyzed by univariate analysis and binary logistic regression. RESULTS: Six hundred twenty patients, mean age 83.6 years (SD: 3.25), 31% required invasive mechanical ventilation (IMV), 25% vasopressors and 29% renal replacement therapy (RRT) due to acute renal failure (ARF). The 60% were admissions of medical origin. In-hospital mortality was 156 patients (25%), 91 died in the ICU and 65 on the ward, with shorter ICU stays for the survivors (2.72; SD: 0.22) compared to the deceased (3.74; SD: 0.38), with statistically significant differences. 63% remained alive one year after ICU discharge. An explanatory model of ICU mortality was obtained by logistic regression that included the following factors: IMV (OR: 5.78, 95% CI 2.73-12.22), vasopressors (OR: 2.54, 95% CI 1.24-5.19), AKI/TRS (OR: 2.69, 95% CI 1.35-5.35), medical admission (OR: 2.88, 95% CI 1.40-5.92), urgent admission (OR: 2.33, 95% CI 1.30-4.18) and limitation of life support (LTSV) (OR: 47.35, 95% CI 22.96-97.68). The days in the ICU (OR: 0.93, 95% CI 0.87-0.99) would be inversely related to mortality. CONCLUSIONS: In older patients, there is no increase in mortality, with a 1-year survival >63%. The need for IMV, the use of vasopressor drugs and ARF/RTS were factors associated with mortality in the multivariate analysis.

Nanopore quality score resolution can be reduced with little effect on downstream analysis.

Motivation: The use of high precision for representing quality scores in nanopore sequencing data makes these scores hard to compress and, thus, responsible for most of the information stored in losslessly compressed FASTQ files. This motivates the investigation of the effect of quality score information loss on downstream analysis from nanopore sequencing FASTQ files. Results: We polished de novo assemblies for a mock microbial community and a human genome, and we called variants on a human genome. We repeated these experiments using various pipelines, under various coverage level scenarios and various quality score quantizers. In all cases, we found that the quantization of quality scores causes little difference (or even sometimes improves) on the results obtained with the original (non-quantized) data. This suggests that the precision that is currently used for nanopore quality scores may be unnecessarily high, and motivates the use of lossy compression algorithms for this kind of data. Moreover, we show that even a non-specialized compressor, such as gzip, yields large storage space savings after the quantization of quality scores. Availability and supplementary information: Quantizers are freely available for download at: https://github.com/mrivarauy/QS-Quantizer.

Merging Brain-Computer Interface P300 speller datasets: Perspectives and pitfalls.

Background: In the last decades, the P300 Speller paradigm was replicated in many experiments, and collected data were released to the public domain to allow research groups, particularly those in the field of machine learning, to test and improve their algorithms for higher performances of brain-computer interface (BCI) systems. Training data is needed to learn the identification of brain activity. The more training data are available, the better the algorithms will perform. The availability of larger datasets is highly desirable, eventually obtained by merging datasets from different repositories. The main obstacle to such merging is that all public datasets are released in various file formats because no standard way is established to share these data. Additionally, all datasets necessitate reading documents or scientific papers to retrieve relevant information, which prevents automating the processing. In this study, we thus adopted a unique file format to demonstrate the importance of having a standard and to propose which information should be stored and why. Methods: We described our process to convert a dozen of P300 Speller datasets and reported the main encountered problems while converting them into the same file format. All the datasets are characterized by the same 6 × 6 matrix of alphanumeric symbols (characters and numbers or symbols) and by the same subset of acquired signals (8 EEG sensors at the same recording sites). Results and discussion: Nearly a million stimuli were converted, relative to about 7000 spelled characters and belonging to 127 subjects. The converted stimuli represent the most extensively available platform for training and testing new algorithms on the specific paradigm - the P300 Speller. The platform could potentially allow exploring transfer learning procedures to reduce or eliminate the time needed for training a classifier to improve the performance and accuracy of such BCI systems.

Danazol improves thrombocytopenia in HCV patients treated with peginterferon and ribavirin.

BACKGROUND: Thrombocytopenia is a common hematologic disorder observed in patients with chronic hepatitis C virus (HCV) infection. Combined peginterferon (PEG-INF) and ribavirin treatment may exacerbate thrombocytopenia in patients with HCV. OBJECTIVE: The aim of this pilot clinical trial was to assess the efficacy, tolerability and safety of Danazol in thrombocytopenia associated with PEG-INF and ribavirin treatment in patients with HCV. MATERIAL AND METHODS: We included patients whose platelets were < 90,000/mm³ and who were undergoing antiviral treatment. Danazol (300-600 mg/day) was administered during and until the end of antiviral therapy [7.6 months (2 to 11 months)]. The monitoring was performed through platelet analysis and liver function tests. A viral load test was done at the beginning and end of treatment. Fortynine patients receiving a combined therapy of PEG-INF, ribavirin and Danazol increased their platelet levels to 121,081/mm³ (46,000-216,000/mm³); 10.6% of patients gained > 100,000 platelets/mm³, and 71% of patients maintained their initial platelet levels. Sustained viral response (SVR) was achieved in 63% of patients. SVR rates were high in patients with genotype non 1 (78.7%) and decreased in patients with genotype 1 (60.1%). The increase in platelet levels was associated to an increase in fibrinogen levels and a decrease in the activity of ALT. By contrast, patients without SVR presented a delayed response to increased platelet levels and showed no significant improvement in liver function when they received Danazol. CONCLUSION: Danazol can be used along with PEG-INF and ribavirin to treat thrombocytopenia in patients with HCV.

[Quality indicators for colonoscopy in the Peruvian Japanese Policlinic: linked factors]. / Indicadores de calidad en colonoscopía en el Policlínico Peruano Japonés: factores relacionados.

INTRODUCTION: Colonoscopy is the gold standard for the diagnosis of diseases of the colon and rectum and the primary prevention test for colon cancer. The main indicators of quality in colonoscopy are the rate of complete colonoscopy and the rate of detected adenomas. OBJECTIVES: We aimed to know the rates of cecal intubation and detection of adenomas and to identify factors related to these two quality indicators in colonoscopies performed in the Peruvian Japanese Policlinic during 2007. MATERIAL AND METHODS: A correlational cross-sectional and retrospective study was performed. Data were collected from the colonoscopies performed by 10 endoscopists in the Peruvian Japanese Policlinic during 2007. RESULTS: We included 843 colonoscopies. Cecal intubation was achieved in 801 patients (95%). The multivariate analysis found that cecal intubation was correlated with the type of sedation/analgesia and the quality of bowel preparation. At least one adenoma was detected in 168 colonoscopies (19.9%). Multivariate analysis found that age, colonic cleansing and time of withdrawal were factors significantly associated with the detection of adenomas. CONCLUSIONS: The quality of colonoscopy depends on several factors: bowel preparation, type of sedation/analgesia and time of withdrawal. These are the targets on which we can act to improve performance.

Biomechanical Behavior Characterization and Constitutive Models of Porcine Trabecular Tibiae.

Customizing any trauma surgery requires prior planning by surgeons. Nowadays, the use of numerical tools is increasingly needed to facilitate this planning. The success of this analysis begins with the definition of all the mechanical constitutive models of the materials implied. Our target is the trabecular bone because almost all trauma surgeries are closely related to it. This work focuses on the experimental characterization of porcine trabecular tibiae and defining its best constitutive model. Therefore, different types of compression tests were performed with tibia samples. Once the potential constitutive models were defined, stress-strain state from numerical approaches were compared with the corresponding experimental results. Experimental results from uniaxial compression tests showed than trabecular bone exhibits clear anisotropy with more stiffness and strength when it is loaded in the tibia longitudinal direction. Results from confined compression tests confirmed that the plastic behavior of trabecular bone depends on the hydrostatic and deviatoric invariants, so an alternative formulation (crushable foam volumetric (CFV)) has been proposed to describe its behavior. A new method to obtain CFV characteristic parameters has been developed and validated. Predictions of the CFV model better describe trabecular bone mechanical behavior under confined conditions. In other cases, classical plasticity formulations work better.

A Functional Model for Unifying Brain Computer Interface Terminology.

Brain Computer Interface (BCI) technology is a critical area both for researchers and clinical practitioners. The IEEE P2731 working group is developing a comprehensive BCI lexicography and a functional model of BCI. The glossary and the functional model are inextricably intertwined. The functional model guides the development of the glossary. Terminology is developed from the basis of a BCI functional model. This paper provides the current status of the P2731 working group's progress towards developing a BCI terminology standard and functional model for the IEEE.

Effect of EGLN1 Genetic Polymorphisms on Hemoglobin Concentration in Andean Highlanders.

The physiological characteristics of Andean natives living at high altitudes have been investigated extensively, with many studies reporting that Andean highlanders have a higher hemoglobin (Hb) concentration than other highlander populations. It has previously been reported that positive natural selection has acted independently on the egl-9 family hypoxia inducible factor 1 (EGLN1) gene in Tibetan and Andean highlanders and is related to Hb concentration in Tibetans. However, no study has yet revealed the genetic determinants of Hb concentration in Andeans even though several single-nucleotide polymorphisms (SNPs) in EGLN1 have previously been examined. Therefore, we explored the relationship between hematological measurements and tag SNPs designed to cover the whole EGLN1 genomic region in Andean highlanders living in Bolivia. Our findings indicated that haplotype frequencies estimated from the EGLN1 SNPs were significantly correlated with Hb concentration in the Bolivian highlanders. Moreover, we found that an Andean-dominant haplotype related to high Hb level may have expanded rapidly in ancestral Andean highlander populations. Analysis of genotype data in an ~436.3 kb genomic region containing EGLN1 using public databases indicated that the population structure based on EGLN1 genetic markers in Andean highlanders was largely different from that in other human populations. This finding may be related to an intrinsic or adaptive physiological characteristic of Andean highlanders. In conclusion, the high Hb concentrations in Andean highlanders can be partly characterized by EGLN1 genetic variants.