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.

Estudio comparativo de eficacia y seguridad de dexrabeprazol versus esomeprazol en el tratamiento de la enfermedad por reflujo gastroesofágico / Efficacy and safety comparative study of dexrabeprazole vs. esomeprazole for the treatment of gastroesophageal reflux disease

Resumen 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.

Abstract 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.

[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.

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? / 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?

Antecedentes y objetivos: Cada vez es más frecuente la asistencia de los pacientes de más edad en las unidades de cuidados intensivos (UCI).Describir las características de los pacientes mayores ingresados en la UCI y analizar los factores asociados a la mortalidad.Pacientes y métodos: Estudio transversal retrospectivo, con pacientes ≥80 años, admitidos en la UCI del Hospital Universitario Rey Juan Carlos, desde marzo 2012 a diciembre 2018. Se recogieron variables demográficas, comorbilidades y mortalidad en la UCI, en hospital y al año, analizadas mediante análisis univariante y regresión logística binaria.Resultados: Seiscientos veinte pacientes, edad media 83,6 años (DE: 3,25), el 31% precisó ventilación mecánica invasiva (VMI), el 25% vasopresores y el 29% terapia renal sustitutiva (TRS) por fracaso renal agudo (FRA). El 60% fueron ingresos de origen médico. La mortalidad intrahospitalaria fue de 156 pacientes (25%), 91 fallecieron en la UCI y 65 en planta, siendo las estancias en la UCI más breves de los supervivientes (2,72; DE: 0,22) respecto a los fallecidos (3,74; DE: 0,38), con diferencias estadísticamente significativa. El 63% permanecieron vivos un año después del alta de la UCI.Se obtuvo un modelo explicativo de mortalidad en la UCI mediante regresión logística que incluía los siguientes factores: VMI (OR: 5,78; IC 95%: 2,73-12,22), vasopresores (OR: 2,54; IC 95%: 1,24-5,19), FRA/TRS (OR: 2,69; IC 95%: 1.35-5.35), ingreso médico (OR: 2,88; IC 95%: 1,40-5,92), ingreso urgente (OR: 2,33; IC 95%: 1,30-4,18) y limitación de soporte vital (LTSV) (OR: 47,35; IC 95%: 22,96-97,68). Los días en la UCI (OR: 0,93; IC 95%: 0,87-0,99) se relacionarían inversamente con la mortalidad.Conclusiones: En los pacientes mayores no hay un aumento de la mortalidad con una supervivencia al año >63%. La necesidad de VMI, el uso de fármacos vasopresores y FRA/TRS, fueron factores asociados a la mortalidad en el análisis multivariante. (AU)

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. (AU)

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.

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.

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.

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.

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.

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.

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.

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.

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.

Individual variations and sex differences in hemodynamics with percutaneous arterial oxygen saturation (SpO2) in young Andean highlanders in Bolivia.

BACKGROUND: Many studies have reported specific adaptations to high altitude, but few studies have focused on physiological variations in high-altitude adaptation in Andean highlanders. This study aimed to investigate the relationships between SpO2 and related factors, including individual variations and sex differences, in Andean highlanders. METHODS: The participants were community-dwelling people in La Paz, Bolivia, aged 20 years and over (age range 20-34 years). A total of 50 men and 50 women participated in this study. Height, weight, SpO2, hemoglobin concentration, finger temperature, heart rate, and blood pressure were measured. Information about lifestyle was also obtained by interview. RESULTS: There were individual variations of SpO2 both in men (mean 89.9%, range 84.0-95.0%) and women (mean 91.0%, range 84.0-96.0%). On Student's t test, men had significantly lower heart rate (p = 0.046) and SpO2 (p = 0.030) than women. On the other hand, men had significantly higher SBP (p < 0.001), hemoglobin (p < 0.001), and finger temperature (p = 0.004). In men, multiple stepwise regression analysis showed that a higher SpO2 was correlated with a lower heart rate (ß = - 0.089, p = 0.007) and a higher finger temperature (ß = 0.308, p = 0.030) (r2 for model = 0.18). In women, a higher SpO2 was significantly correlated with a higher finger temperature (ß = 0.391, p = 0.015) (r2 for model = 0.12). A higher SpO2 was related to a higher finger temperature (ß = 0.286, p = 0.014) and a lower heart rate (ß = - 0.052, p = 0.029) in all participants (r2 for model = 0.21). Residual analysis showed that individual SpO2 values were randomly plotted. CONCLUSION: Random plots of SpO2 on residual analysis indicated that these variations were random error, such as biological variation. A higher SpO2 was related to a lower heart rate and finger temperature in men, but a higher SpO2 was related to finger temperature in women. These results suggest that there are individual variations and sex differences in the hemodynamic responses of high-altitude adaptation in Andean highlanders.

Dyslipidemia as a risk factor for liver fibrosis progression in a multicentric population with non-alcoholic steatohepatitis.

Background: Nonalcoholic fatty liver disease (NAFLD) is a serious worldwide health problem, with an estimated global prevalence of 24%; it has a notable relationship with other metabolic disorders, like obesity and type 2 diabetes mellitus (T2DM). Nonalcoholic steatohepatitis (NASH) is one of the most important clinical entities of NAFLD, which is associated with an increased risk of progression to liver cirrhosis and hepatocellular carcinoma (HCC). Mexico is one of the countries with the highest prevalence of metabolic diseases; therefore, we sought to investigate the impact that these clinical entities have in the progression to advanced fibrosis in Mexican patients with NASH. Methods: We performed a multicenter retrospective cross-sectional study, from January 2012 to December 2017. A total of 215 patients with biopsy-proven NASH and fibrosis were enrolled. NASH was diagnosed according NAS score and liver fibrosis was staged by the Kleiner scoring system. For comparing the risk of liver fibrosis progression, we divided our sample into two groups. Those patients with stage F0-F2 liver fibrosis were included in the group with non-significant liver fibrosis (n=178) and those individuals with F3-F4 fibrosis were included in the significant fibrosis group (n=37). We carried out a multivariate analysis to find risk factors associated with liver fibrosis progression. Results: From the 215 patients included, 37 had significant liver fibrosis (F3-4). After logistic regression analysis T2DM (p=0.044), systemic arterial hypertension (p=0.014), cholesterol (p=0.041) and triglycerides (p=0.015) were the main predictor of advanced liver fibrosis. Conclusions: In a Mexican population, dyslipidemia was the most important risk factor associated with advanced liver fibrosis and cirrhosis.

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.

A Histoarchitectural Approach to Skeletal Muscle Injury: Searching for a Common Nomenclature.

In recent years, different classifications for muscle injuries have been proposed based on the topographic location of the injury within the bone-tendon-muscle chain. We hereby propose that in addition to the topographic classification of muscle injuries, a histoarchitectonic (description of the damage to connective tissue structures) definition of the injury be included within the nomenclature. Thus, the nomenclature should focus not only on the macroscopic anatomy but also on the histoarchitectonic features of the injury.