Codon usage variability determines the correlation between proteome and transcriptome fold changes

Background: The availability of high throughput experimental methods has made possible to observe the relationships between proteome and transcirptome. The protein abundances show a positive but weak correlation with the concentrations of their cognate mRNAs. This weak correlation implies that there are other crucial effects involved in the regulation of protein translation, different from the sole availability of mRNA. It is well known that ribosome and tRNA concentrations are sources of variation in protein levels. Thus, by using integrated analysis of omics data, genomic information, transcriptome and proteome, we aim to unravel important variables affecting translation. Results: We identified how much of the variability in the correlation between protein and mRNA concentrations can be attributed to the gene codon frequencies. We propose the hypothesis that the influence of codon frequency is due to the competition of cognate and near-cognate tRNA binding; which in turn is a function of the tRNA concentrations. Transcriptome and proteome data were combined in two analytical steps; first, we used Self-Organizing Maps (SOM) to identify similarities among genes, based on their codon frequencies, grouping them into different clusters; and second, we calculated the variance in the protein mRNA correlation in the sampled genes from each cluster. This procedure is justified within a mathematical framework. Conclusions: With the proposed method we observed that in all the six studied cases most of the variability in the relation protein-transcript could be explained by the variation in codon composition

Simulación de la Implementación de un variador de velocidad en un motor mediante software especializado

The electrical systems are in constant evolution, a lot changes are occurring precipitously in this days. Parallel to these events, technology is evolving in a dramatic way. In this scenario, the development of tools that allow optimizing and improving the simulation of large electrical systems has become the subject of numerous recent investigations. The induction motor is up today the most economical and efficient electric motor in industrial applications, making it the most popular in this area. The speed drives for electric motors can greatly support the reduction of energy consumption in industrial processes and extend the useful life of equipment.  Los sistemas eléctricos viven tiempos de constante evolución, numerosos cambios se están presentando precipitadamente en los últimos tiempos. Paralelamente a estos sucesos, la tecnología está evolucionando de una manera dramática. En este escenario, el desarrollo de herramientas que permitan optimizar y mejorar la simulación de sistemas eléctricos de gran dimensión se ha convertido en objeto de numerosas investigaciones recientes. El motor de inducción es a la fecha el motor eléctrico más económico y eficiente en aplicaciones industriales, por lo que es el más popular en dicha rama. Los variadores de velocidad para motores eléctricos pueden apoyar en gran medida a la reducción de consumo energético de los procesos industriales y prolongar la vida útil en los equipos

Validación de método analítico para la cuantificación de compuestos de fermentación por HPLC–RI–UV

La producción de bioetanol a partir de biomasa lignocelulósica sigue ganando importancia, además de su principal uso como bio–combustible, el etanol es considerado un importante químico de plataforma, debido a su alto volumen de producción esperado. Durante el pretratamiento de los materiales lignocelulósicos se producen compuestos furfurales, tales como el furfural y el hidroximetilfurfural (HMF), los cuales inhiben el proceso de fermentación, y he ahí la importancia de detectarlos y cuantificarlos. El presente trabajo se enfocó en establecer y validar un método de cromatografía liquida de alta resolución (HPLC) para cuantificar glucosa, etanol, ácido fórmico y acético, así como HMF y furfural, en un solo análisis. Esto se logró en un sistema isocrático de HPLC con dos detectores, índice de refracción (RI) y ultravioleta (UV220) acoplados en serie. El método mostro ser preciso y lineal hasta los 10 mg/mL con R2 ≥ 0.98 y límites de detección de partes por millón.The production of bioethanol from lignocellulosic biomass continues to gain importance, in addition to its main use as a bio–fuel the ethanol is considered an important building block chemical, due to its high expected production volume. During pretreatment of lignocellulosic materials, furfural compounds are produced, such as furfural and hydroxymethylfurfural (HMF), which inhibit the fermentation process, hence the importance of detecting and quantifying them. The present study was focused on establishing and validating a high-performance liquid chromatography (HPLC) method to quantify glucose, ethanol, formic and acetic acid, as well as HMF and furfural, in a single analysis. This was achieved in an isocratic HPLC system with two detectors, refractive index (RI) and ultraviolet (UV220) coupled in series. The method proved to be accurate and linear up to 10 mg/mL with R2 ≥ 0.98 and detection limits in the order of parts per million

El comercio de anfibios y la presencia de Batrachochytrium dendrobatidis en vida libre: ¿dispersión en círculo vicioso?

The amphibian trade has an important role in Batrachochytrium dendrobatidis (Bd) persistence, for at least 28 amphibian species can serve as vectors. The objectives of this work are to evaluate the presence and prevalence of Bd in amphibian traded in two petshops in Mexico City, as well as to verify their presence in wild amphibian populations of species traded. It was found that 92% of amphibians sold in the two petshops were captured free-living, and 37.3% of these animals were infected with Bd, according to histological analysis. The prevalence of 30.8% of Bd in wild amphibians at the wild capture sites was detected by means of DNA amplification. No significant differences were found between prevalence of wild and trade amphibians, but the trend was higher for trade amphibians. The importance of amphibian management and conservation plans has been growing in the last years. The pet trade and its capture from the wild turn these trade routes and their captive management into means of pathogenic dispersion, which may increase the risk of disease outbreaks.Keywords: Chytridiomycosis, pet trade, optical microscopy, nested PCR.El comercio de anfibios tiene un papel importante en la persistencia del Batrachochytrium dendrobatidis (Bd), ya que al menos 28 especies pueden servir como vectores. Los objetivos de este trabajo fueron evaluar la presencia de Bd en anfibios comercializados en dos mercados de mascotas en la Ciudad de México; además verificamos su presencia en poblaciones silvestres de las especies comerciadas. Se encontró que el 92% de los anfibios comercializados fueron capturados de vida libre, y el 37.3% estuvieron infectados con Bd de acuerdo con análisis histológicos. La prevalencia de 30.8% de Bd en anfibios silvestres fue detectada por amplificación de ADN. No hubo diferencias significativas entre las prevalencias de los anfibios silvestres y de comercio, pero la tendencia es mayor para los anfibios de comercio. La importancia de los planes de conservación de anfibios a nivel mundial ha crecido en los últimos años. El mercado de mascotas y la captura de individuos de vida libre hacen que las rutas de comercio y el manejo de individuos para estos fines sea una forma de dispersión de patógenos y un gran riesgo de brotes de las enfermedades.Palabras claves: Quitridiomicosis, mercado de mascotas, microscopia óptica, PCR anidado

Combining Substrate Specificity Analysis with Support Vector Classifiers Reveals Feruloyl Esterase as a Phylogenetically Informative Protein Group

Our understanding of how fungi evolved to develop a variety of ecological niches, is limited but of fundamental biological importance. Specifically, the evolution of enzymes affects how well species can adapt to new environmental conditions. Feruloyl esterases (FAEs) are enzymes able to hydrolyze the ester bonds linking ferulic acid to plant cell wall polysaccharides. The diversity of substrate specificities found in the FAE family shows that this family is old enough to have experienced the emergence and loss of many activities. In this study we evaluate the relative activity of FAEs against a variety of model substrates as a novel predictive tool for Ascomycota taxonomic classification. Our approach consists of two analytical steps; (1) an initial unsupervised analysis to cluster the FAEs substrate specificity data which were generated by cultivation of 34 Ascomycota strains and then an analysis of the produced enzyme cocktail against 10 substituted cinnamate and phenylalkanoate methyl esters, (2) a second, supervised analysis for training a predictor built on these substrate activities. By applying both linear and non-linear models we were able to correctly predict the taxonomic Class (∼86% correct classification), Order (∼88% correct classification) and Family (∼88% correct classification) that the 34 Ascomycota belong to, using the activity profiles of the FAEs. The good correlation with the FAEs substrate specificities that we have defined via our phylogenetic analysis not only suggests that FAEs are phylogenetically informative proteins but it is also a considerable step towards improved FAEs functional prediction.published_or_final_versio

Recent Progress and Next Steps for the MATHUSLA LLP Detector

We report on recent progress and next steps in the design of the proposed MATHUSLA Long Lived Particle (LLP) detector for the HL-LHC as part of the Snowmass 2021 process. Our understanding of backgrounds has greatly improved, aided by detailed simulation studies, and significant R&D has been performed on designing the scintillator detectors and understanding their performance. The collaboration is on track to complete a Technical Design Report, and there are many opportunities for interested new members to contribute towards the goal of designing and constructing MATHUSLA in time for HL-LHC collisions, which would increase the sensitivity to a large variety of highly motivated LLP signals by orders of magnitude.Comment: Contribution to Snowmass 2021 (EF09, EF10, IF6, IF9), 18 pages, 12 figures. v2: included additional endorser

Risk factors associated with adverse fetal outcomes in pregnancies affected by Coronavirus disease 2019 (COVID-19): a secondary analysis of the WAPM study on COVID-19.

Objectives To evaluate the strength of association between maternal and pregnancy characteristics and the risk of adverse perinatal outcomes in pregnancies with laboratory confirmed COVID-19. Methods Secondary analysis of a multinational, cohort study on all consecutive pregnant women with laboratory-confirmed COVID-19 from February 1, 2020 to April 30, 2020 from 73 centers from 22 different countries. A confirmed case of COVID-19 was defined as a positive result on real-time reverse-transcriptase-polymerase-chain-reaction (RT-PCR) assay of nasal and pharyngeal swab specimens. The primary outcome was a composite adverse fetal outcome, defined as the presence of either abortion (pregnancy loss before 22 weeks of gestations), stillbirth (intrauterine fetal death after 22 weeks of gestation), neonatal death (death of a live-born infant within the first 28 days of life), and perinatal death (either stillbirth or neonatal death). Logistic regression analysis was performed to evaluate parameters independently associated with the primary outcome. Logistic regression was reported as odds ratio (OR) with 95% confidence interval (CI). Results Mean gestational age at diagnosis was 30.6+/-9.5 weeks, with 8.0% of women being diagnosed in the first, 22.2% in the second and 69.8% in the third trimester of pregnancy. There were six miscarriage (2.3%), six intrauterine device (IUD) (2.3) and 5 (2.0%) neonatal deaths, with an overall rate of perinatal death of 4.2% (11/265), thus resulting into 17 cases experiencing and 226 not experiencing composite adverse fetal outcome. Neither stillbirths nor neonatal deaths had congenital anomalies found at antenatal or postnatal evaluation. Furthermore, none of the cases experiencing IUD had signs of impending demise at arterial or venous Doppler. Neonatal deaths were all considered as prematurity-related adverse events. Of the 250 live-born neonates, one (0.4%) was found positive at RT-PCR pharyngeal swabs performed after delivery. The mother was tested positive during the third trimester of pregnancy. The newborn was asymptomatic and had negative RT-PCR test after 14 days of life. At logistic regression analysis, gestational age at diagnosis (OR: 0.85, 95% CI 0.8-0.9 per week increase; pPeer reviewe

Association Between Preexisting Versus Newly Identified Atrial Fibrillation and Outcomes of Patients With Acute Pulmonary Embolism

Background Atrial fibrillation (AF) may exist before or occur early in the course of pulmonary embolism (PE). We determined the PE outcomes based on the presence and timing of AF. Methods and Results Using the data from a multicenter PE registry, we identified 3 groups: (1) those with preexisting AF, (2) patients with new AF within 2 days from acute PE (incident AF), and (3) patients without AF. We assessed the 90-day and 1-year risk of mortality and stroke in patients with AF, compared with those without AF (reference group). Among 16 497 patients with PE, 792 had preexisting AF. These patients had increased odds of 90-day all-cause (odds ratio [OR], 2.81; 95% CI, 2.33-3.38) and PE-related mortality (OR, 2.38; 95% CI, 1.37-4.14) and increased 1-year hazard for ischemic stroke (hazard ratio, 5.48; 95% CI, 3.10-9.69) compared with those without AF. After multivariable adjustment, preexisting AF was associated with significantly increased odds of all-cause mortality (OR, 1.91; 95% CI, 1.57-2.32) but not PE-related mortality (OR, 1.50; 95% CI, 0.85-2.66). Among 16 497 patients with PE, 445 developed new incident AF within 2 days of acute PE. Incident AF was associated with increased odds of 90-day all-cause (OR, 2.28; 95% CI, 1.75-2.97) and PE-related (OR, 3.64; 95% CI, 2.01-6.59) mortality but not stroke. Findings were similar in multivariable analyses. Conclusions In patients with acute symptomatic PE, both preexisting AF and incident AF predict adverse clinical outcomes. The type of adverse outcomes may differ depending on the timing of AF onset.info:eu-repo/semantics/publishedVersio

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements