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Spatiotemporal regulation of gene expression is controlled by transcription factor (TF) binding to regulatory elements, resulting in a plethora of cell types and cell states from the same genetic information. Due to the importance of regulatory elements, various sequencing methods have been developed to localise them in genomes, for example using ChIP-seq profiling of the histone mark H3K27ac that marks active regulatory regions. Moreover, multiple tools have been developed to predict TF binding to these regulatory elements based on DNA sequence. As altered gene expression is a hallmark of disease phenotypes, identifying TFs driving such gene expression programs is critical for the identification of novel drug targets.In this study, we curated 84 chromatin profiling experiments (H3K27ac ChIP-seq) where TFs were perturbed through e.g., genetic knockout or overexpression. We ran nine published tools to prioritize TFs using these real-world datasets and evaluated the performance of the methods in identifying the perturbed TFs. This allowed the nomination of three frontrunner tools, namely RcisTarget, MEIRLOP and monaLisa. Our analyses revealed opportunities and commonalities of tools that will help to guide further improvements and developments in the field.

Objetivo. evaluar la evolución de la empatía y sus dimensiones en dos períodos anuales diferentes y determinar las fortalezas y las deficiencias observadas en la empatía y en sus dimensiones. Material y Métodos. estudio no experimental, descriptivo y transversal. La población la conforman estudiantes colombianos de odontología. La muestra se conformó de dos cohortes: n=326 estudiantes, 100% de la población (cohorte 2016) y n=207 estudiantes, 87,34 % de la población (cohorte 2022). La empatía fue medida por el instrumento JES-HPS. Se aplicó un análisis factorial confirmatorio, fiabilidad e invarianza. Las comparaciones de empatía entre las cohortes se realizaron mediante un análisis de la varianza factorial. Resultados. se cumplió el modelo teórico de tres dimensiones de la empatía en ambas cohortes estudiadas. Los niveles de confiabilidad fueron aceptables. No se encontraron diferencias estadísticas relevantes entre las cohortes y se observa una declinación en el segundo y quinto curso de la empatía y de las dimensiones en general. Conclusiones. los valores de la empatía y sus dimensiones se han mantenido sin cambios en el tiempo y la empatía clasifico como “nivel medio” Como consecuencia de lo anterior, los niveles medios de la empatía podrían asociase a un déficit en la capacidad de entender la subjetividad del pensamiento del paciente y, esta situación, complica una actitud empática normal.

Objectives This study aimed to evaluate pulmonary diffusing capacity for nitric oxide (DLNO) and pulmonary diffusing capacity for carbon monoxide (DLCO) in Mexican Hispanics born and raised at 2240 m altitude (midlanders) compared with those born and raised at sea level (lowlanders). It also aimed to assess the effectiveness of race-specific reference equations for pulmonary diffusing capacity (white people vs Mexican Hispanics) in minimising root mean square errors (RMSE) compared with race-neutral equations.Methods DLNO, DLCO, alveolar volume (VA) and gas transfer coefficients (KNO and KCO) were measured in 392 Mexican Hispanics (5 to 78 years) and compared with 1056 white subjects (5 to 95 years). Reference equations were developed using segmented linear regression (DLNO, DLCO and VA) and multiple linear regression (KNO and KCO) and validated with Least Absolute Shrinkage and Selection Operator. RMSE comparisons between race-specific and race-neutral models were conducted using repeated k-fold cross-validation and random forests.Results Midlanders exhibited higher DLCO (mean difference: +4 mL/min/mm Hg), DLNO (mean difference: +7 mL/min/mm Hg) and VA (mean difference: +0.17 L) compared with lowlanders. The Bayesian information criterion favoured race-specific models and excluding race as a covariate increased RMSE by 61% (DLNO), 18% (DLCO) and 4% (KNO). RMSE values for VA and KCO were comparable between race-specific and race-neutral models. For DLCO and DLNO, race-neutral equations resulted in 3% to 6% false positive rates (FPRs) in Mexican Hispanics and 20% to 49% false negative rates (FNRs) in white subjects compared with race-specific equations.Conclusions Mexican Hispanics born and raised at 2240 m exhibit higher DLCO and DLNO compared with lowlanders. Including race as a covariate in reference equations lowers the RMSE for DLNO, DLCO and KNO and reduces FPR and FNR compared with race-neutral models. This study highlights the need for altitude-specific and race-specific reference equations to improve pulmonary function assessments across diverse populations.

ABSTRACT Clostridia are abundant in the human gut and comprise families associated with host health such as Oscillospiraceae, which has been correlated with leanness. However, culturing bacteria within this family is challenging, leading to their detection primarily through 16S rRNA amplicon sequencing, which has a limited ability to unravel diversity at low taxonomic levels, or by shotgun metagenomics, which is hindered by its high costs and complexity. In this cross-sectional study involving 114 Colombian adults, we used an amplicon-based sequencing strategy with alternative markers—gyrase subunit B (gyrB) and DNA K chaperone heat protein 70 (dnaK)—that evolve faster than the 16S rRNA gene. Comparing the diversity and abundance observed with the three markers in our cohort, we found a reduction in the diversity of Clostridia, particularly within Lachnospiraceae and Oscillospiraceae among obese individuals [as measured by the body mass index (BMI)]. Within Lachnospiraceae, the diversity of Ruminococcus_A negatively correlated with BMI. Within Oscillospiraceae, the genera CAG-170 and Vescimonas also exhibited this negative correlation. In addition, the abundance of Vescimonas was negatively correlated with BMI. Leveraging shotgun metagenomic data, we conducted a phylogenetic and genomic characterization of 120 metagenome-assembled genomes from Vescimonas obtained from a larger sample of the same cohort. We identified 17 of the 72 reported species. The functional annotation of these genomes showed the presence of multiple carbohydrate-active enzymes, particularly glycosyl transferases and glycoside hydrolases, suggesting potential beneficial roles in fiber degradation, carbohydrate metabolism, and butyrate production.IMPORTANCEThe gut microbiota is diverse across various taxonomic levels. At the intra-species level, it comprises multiple strains, some of which may be host-specific. However, our understanding of fine-grained diversity has been hindered by the use of the conserved 16S rRNA gene. While shotgun metagenomics offers higher resolution, it remains costly, may fail to identify specific microbes in complex samples, and requires extensive computational resources and expertise. To address this, we employed a simple and cost-effective analysis of alternative genetic markers to explore diversity within Clostridia, a crucial group within the human gut microbiota whose diversity may be underestimated. We found high intra-species diversity for certain groups and associations with obesity. Notably, we identified Vescimonas, an understudied group. Making use of metagenomic data, we inferred functionality, uncovering potential beneficial roles in dietary fiber and carbohydrate degradation, as well as in short-chain fatty acid production.

Abstract Background Psychometric studies of the FACES III scale in Spanish-speaking countries show a lack of agreement on the factorial structure of the scale. In addition, most of the studies have only performed exploratory analyses of its factorial structure. Objective The objective of the present study was to confirm the structure and factorial invariance of the FACES III scale in nursing and obstetric students from Chile, Colombia, Peru, and Mexico. Methods A total of 3303 students from the four countries participated in this study (Colombia = 1559, Chile = 1224, Peru = 215, Mexico = 305). Results The results of the study showed that the Bi-factor model presents the best-fit indexes to the data from Colombia, Chile, and Mexico, but not from Peru. In addition, it was found that this model showed evidence of being strictly invariant among the three countries in the sequence of the invariance models proposed: metric invariance (ΔRMSEA = .000), scalar (ΔRMSEA = .008), and strict (ΔRMSEA = .008). The bi-factor model also showed adequate reliability indexes in the three countries. Conclusion It is concluded that the FACES III scale shows adequate psychometric performance under a bi-factor model in nursing and obstetric students from Colombia, Chile, and Mexico. The lack of fit of the model in Peru could be associated with the small sample size.

In recent years, the fast growth of computational power has allowed the application of computational fluid dynamics (CFD) in a wide range of areas of interest, such as gas–solid unit operations. In this context, the multiphase particle-in-cell (MP-PIC) method appears as an option to represent fluid–particle and particle–particle interactions, avoiding the complexity of tracking each particle and the high computational cost derived from this. The MP-PIC method can represent the particles as a group with the same characteristics, allowing the simulation of gas–solid systems at different scales. To achieve this, the particle–particle interactions are simplified using the solid stress tensor to represent them; this does not require explicit expressions. This approach has a low computational cost, allowing the simulation of industrial cases using just workstations. This paper provides a review of the literature on the solid stress tensor and its commercial and non-commercial applications, including its historical and mathematical development in the description of particle–particle interactions. In addition, to consolidate the knowledge and advancing understanding in this crucial aspect of multiphase flow simulations, this review identifies the current challenges and opportunities for future research in multiphase systems based on the solid stress tensor. In addition, this review identifies the current challenges and opportunities for future research in multiphase systems based on the solid stress tensor.

Introduction: Empathy is a complex and multidimensional attribute. Attempts have been made to explain empathic behavior based on other variables. Empirical evidence shows that empathy could be the product of the influence of several factors. One of these factors could be resilience. There is still no developed theory and consistent empirical evidence demonstrating that empathy depends on resilience. Objective: The aim of this study is to determine if resilience can predict empathic behavior. Methodology: This study is non-experimental and ex post facto with a cross-sectional design. Variables. Dependent: Empathy; Independent: Resilience. Population: Medical students belonging to the Faculty of Health Sciences of the Universidad Autónoma de Santa Ana (UNASA), Santa Ana, El Salvador (N=579). The sample (n=465) consisted of students (both sexes). Convenience sampling. Jefferson Scale of Empathy for Healthcare Professionals, student version (JSE-HPS). Trait Resilience Scale (EEA). A Structural Equation Modelling (SEM) model was used. Additionally, the Comparative Fit Index (CFI) (>0.95), Tucker-Lewis Index (TLI) (>0.95), Root Mean Square Error of Approximation (RMSEA) (

Introducción: La empatía es uno de los componentes de la estructura de la humanización en la atención de los pacientes. Los médicos especialistas deben tener altos niveles de empatía. Objetivo. El objetivo del presente trabajo es describir los niveles de empatía en médicos que trabajan en un hospital de alta complejidad y explorar diferencias entre las especialidades estudiadas. Métodos: Muestra por conveniencia de 237 médicos que representa el 53,55 % del total poblacional (N=443). La empatía fue medida mediante la Escala de Empatía para Profesionales de la Salud. Se realizó análisis factorial confirmatorio y análisis multigrupo para examinar la invarianza del modelo entre los sexos y análisis de confiabilidad (α de Cronbach, coeficiente de correlación intraclase y ω de McDonald). Resultados: La especialidad de pediatría tuvo los niveles más altos en la empatía general y en las dimensiones Cuidado con compasión y “Caminando en los zapatos del paciente”, no así en la dimensión Toma de perspectiva donde presenta niveles semejantes a las especialidades de anestesiología, medicina crítica y terapia intensiva, y ginecología. Conclusión: Los valores de la empatía y los valores en las subescalas Cuidado con compasión y “Caminando en los zapatos del paciente” fueron (en valores absolutos, pero no estadísticos) mayores en la especialidad de Pediatría. En la subescala Toma de perspectiva, las especialidades de Pediatría, Anestesiología, Cirugía y Clínica se observaron puntuaciones prácticamente iguales. Se requieren otros estudios que permita arribar a una explicación que permita entender por qué algunas especialidades tienen valores de empatía mayores que otras.

Abstract Background A psychometric study of the Family Adaptability and Cohesion Scale (FACES III) has been conducted in Spanish-speaking countries from the perspective of the classical test theory. However, this approach has limitations that affect the psychometric understanding of this scale. Objective Accordingly, this study used the item response theory to investigate the psychometric performance of the items. Furthermore, it evaluated the differential performance of the items for Colombia and Chile. Method For this purpose, 518 health science students from both countries participated. Confirmatory Factor Analysis was used. Results The study results revealed that the cohesion and adaptability items presented adequate discrimination and difficulty indices. In addition, items 5, 8, 13, 17, and 19 of cohesion indicated differential functioning between students from both countries, with Chilean students exhibiting a greater discriminatory power. Further, the Colombian group exhibited a greater discriminatory power for item 18 of adaptability. Conclusions The study concluded that the items of FACES III indicated adequate psychometric performance in terms of their discriminative capacity and difficulty in Chile and Colombia.

Background: Empathy is an attribute that plays an essential role in the dentist–patient therapeutic relationship, clinical care, and treatment adherence, along with providing other benefits. The main objective of this research was to establish the validity, reliability, and invariance of the Jefferson Scale of Empathy and then characterize the empathy levels of students and teachers at a dental school. Materials and Methods: An observational and cross-sectional study analyzed a sample of undergraduate students and professors from the Universidad Andrés Bello Faculty of Dentistry (Chile) (n = 1727 and n = 267, respectively). The Empathy Scale for Health Professionals (HP) and the same scale for students (HPS) were applied. Results: The Jefferson Empathy Scale presents adequate psychometric properties. The empathy measure has adequate reliability and construct validity, confirming a fit of the three-factor empathy model to the data. The measurement is invariant within the university campus, the sex of the student, and between teacher and student. Teachers present greater empathy than students except in the Perspective Adoption dimension. Conclusions: The Jefferson Empathy Scale is reliable, valid, and invariant among Chilean dental students and professors. Students do not differ from their professors in the cognitive component of empathy, but they present a lower score in the affective component and global empathy. It is inferred that students can develop the affective component of empathy in their interactions with their professors, increasing their overall empathy. Understanding and fostering empathy in dental students and professors can significantly improve patient care and treatment adherence and increase patient and dentist satisfaction.

The selective detection of halides in aqueous samples is crucial for addressing environmental and physiological concerns. Consequently, the development of an affordable, portable, and user-friendly sensing platform for rapid halide detection holds substantial promise. In this study, we present a novel paper-based nanosensor as an appealing alternative for selectively detecting halides in water. This nanosensor leverages the optical properties of silver nanoparticles (ranging from 50 to 250 nm) embedded in epoxy resin and printed on filter paper. We elucidate the colorimetric behavior of this nanosensor in response to specific halides (chloride, bromide, and iodide) upon contact. Importantly, this sensor discerns, through a single measurement, the presence of these halides in aqueous media with remarkable selectivity. The nanosensor manifests distinct color changes in reaction to different halides, particularly at elevated concentrations (ranging from 2 to 400 mM), surpassing the saturation levels observed in other proposed sensors. These discernible color changes are due to the oxidation of silver nanoparticles, changing their morphology and aggregation density, and can be readily detected and analyzed directly from a captured image. Consequently, it demonstrates considerable potential for integration into automated qualitative monitoring devices based on chromaticity analysis.

Objetivo. El objetivo del estudio es caracterizar psicométricamente los datos de empatía y sus dimensiones, así como determinar la distribución empática entre las áreas académicas en el proceso de formación de estudiantes de pregrado de enfermería. Métodos. Este es un estudio comparativo, no experimental y transversal. La muestra estudiada fue de 365 estudiantes de enfermería de ambos sexos pertenecientes a la Facultad de Enfermería de la Universidad Veracruzana, México. El total de la población fue de 425 estudiantes y la muestra constituyó el 85,88% del total de estudiantes (mayo a julio de 2022). Se estudiaron las propiedades psicométricas de la escala de Empatía para Profesionales de la Salud, versión estudiantes (fiabilidad, validez de constructo e invarianza del modelo). Para describir y comparar los grupos se utilizaron estadísticos descriptivos, análisis de varianza y gráficos de las medias con barras que representaban el intervalo de confianza al 95%. Resultados. La medida de empatía alcanza coeficientes de fiabilidad satisfactorios y presenta adecuados indicadores de validez de constructo, resultando una medida invariante según área académica y sexo. Se encontró la existencia de déficits en algunas de las dimensiones de empatía. Conclusión. El análisis psicométrico (modelo de dimensiones subyacentes e invarianza), previa a la estimación de los parámetros de la empatía, constituye una necesitad metodológica que garantiza teóricamente la estimación de los niveles de empatía y de la comparación entre grupos. La distribución de los niveles de empatía entre las áreas académicas se caracterizó por un déficit en las dimensiones cuidado con compasión y “caminar en los zapatos del paciente”

In Amazonia, small-oriented family businesses or communities cultivate freshwater organisms as a source of income. Although effective management is fundamental for optimizing cultivated stocks, Amazonian aquaculture belittles the importance of genetic diversity, relying primarily on phenotypical characteristics during breeders’ selection. To provide a “proof of concept” built on the premise that implementing modern technologies is crucial to optimizing fish stocks in rural Amazonian fish farms, we conducted a pilot study assessing genetic diversity on cultivated Piaractus brachypomus from Caquetá, Colombia. We used mitochondrial control region (CR) sequences to evaluate heterogeneity. Our data revealed low genetic diversity and suggested that most sampled individuals probably originated from a single maternal lineage. Haplotype diversification resulted from discrete point mutations not associated with geographical location. Polymorphisms accumulate in non-conserved CR regions, yet the most divergent haplotypes display mutations in conserved CR sequences with roles in mitochondrial metabolisms and proliferation. Overall, our results indicate a need in the local industry to design breeding strategies to enhance diversity to avoid deleterious effects caused by inbreeding and domestication.

Antecedentes: Las ventajas de la cirugía mínimamente invasiva debido a las incisiones pequeñas en comparación con la cirugía tradicional están descritas en la literatura, sin embargo, no existe una medida establecida en cuanto al tamaño de la herida en cirugía tradicional. Objetivo: Comparar el tamaño de las incisiones quirúrgicas entre distintos abordajes. Método: Estudio observacional, transversal, retrospectivo. Medición de incisiones quirúrgicas en fotografías clínicas de 182 pacientes operados con técnica tradicional de 2015 a 2017. Resultados: El promedio obtenido para un nivel de fijación y artrodesis fue de 6.64 cm con una muestra del 51.09% de la población. Con cirugía solo descompresiva es de 3 cm en promedio. Dos niveles, 8.5 cm, con 32.4%, 3 niveles 9.34 cm con 9.8%, 4 niveles 13.1 cm con 4.39% y para 5 niveles 15cm. El tamaño de la herida está relacionado con el diagnóstico (r = 0.392) p = 0001, mientras que el tamaño de la herida está relacionado con los segmentos operados (r = 0.695) p = 0001. Conclusiones: El tamaño de la incisión obtenida en cirugía tradicional no actúa como desventaja en comparación con múltiples incisiones realizadas en cirugía mínimamente invasiva, considerando que varios procedimientos se realizan a través de una sola incisión.

ABSTRACTBumblebees are important pollinators in natural ecosystems and agriculture, but many species are declining. Temperate-zone bumblebees have host-specific and beneficial gut microbiomes, which may have a role in mediating the effects of stressors. However, there is almost no published information on the gut microbiomes of tropical bumblebees. As temperate and tropical bumblebees encounter different floral resources and environmental conditions, their microbiomes could differ. Here, we characterized the gut microbiomes of four neotropical Bombus species and, for comparison, co-occurring solitary bees (genus Thygater). We collected wild-foraging bees from multiple sites in central Colombia and used 16S rRNA gene sequencing to characterize their gut microbiomes. DNA barcoding and morphology were used to identify bumblebee species. We found that the microbiomes of neotropical bumblebees cluster with those of closely related temperate-zone species, in agreement with a model of bumblebee-symbiont codiversification. There was no evidence of geographic differences in microbiome composition between neotropical and temperate-zone bumblebees. These results suggest that the microbiome was conserved during bumblebee dispersal from North America, despite major shifts in ecology and life history. As previously observed in temperate-zone species, some neotropical bumblebees have highly disrupted microbiomes, in which conserved gut bacterial symbionts are replaced by environmental microbes. In these individuals, the gut microbial profile is more like that of solitary bees than of conspecifics. The gut parasites Nosema and Crithidia are also prevalent and associated with microbiome disruption. Our findings provide insights into the biogeography of bee microbiomes and a foundation for studying bee-microbe-stressor interactions in the neotropics.IMPORTANCESocial bees are an important model for the ecology and evolution of gut microbiomes. These bees harbor ancient, specific, and beneficial gut microbiomes and are crucial pollinators. However, most of the research has concentrated on managed honeybees and bumblebees in the temperate zone. Here we used 16S rRNA gene sequencing to characterize gut microbiomes in wild neotropical bumblebee communities from Colombia. We also analyzed drivers of microbiome structure across our data and previously published data from temperate bumblebees. Our results show that lineages of neotropical bumblebees not only retained their ancient gut bacterial symbionts during dispersal from North America but also are prone to major disruption, a shift that is strongly associated with parasite infection. Finally, we also found that microbiomes are much more strongly structured by host phylogeny than by geography, despite the very different environmental conditions and plant communities in the two regions.

Objetivo: determinar los niveles de empatía en profesionales de enfermería de un hospital de alta complejidad, relacionar la edad con la empatía (y cada una de sus dimensiones), y establecer si existen diferencias entre estos niveles según el tipo de jornada laboral. Método: diseño comparativo, correlacional y transversal. La muestra utilizada (n=271) constituyó el 40,9% del total de profesionales de enfermería. Se estudiaron las propiedades psicométricas de la Escala de Empatía de Jefferson para Profesionales de la Salud. Se calcularon estadísticos descriptivos: media y desviación estándar. La asociación entre empatía y edad se estimó mediante ecuaciones de regresión y significancia estadística de los coeficientes de regresión, luego de evaluar el tipo de curva mediante análisis de varianza. Resultados: se identificó el modelo subyacente de las tres dimensiones de la empatía. Los valores de los estadísticos descriptivos observados fueron relativamente bajos en empatía y sus dimensiones. Los niveles de empatía no se asociaron con el rango de edad. No se encontraron diferencias en la empatía entre los tipos de horarios de trabajo. Se encontró variabilidad en las dimensiones: “cuidado compasivo” y “ponerse en los zapatos del paciente”. Conclusión: estos resultados muestran que los niveles de empatía observados pueden implicar un desempeño deficiente en el cuidado empático de los pacientes.

ABSTRACT Vibrio parahaemolyticus is a bacterial pathogen that becomes lethal to Penaeus shrimps when acquiring the pVA1-type plasmid carrying the PirABvp genes, causing acute hepatopancreatic necrosis disease (AHPND). This disease causes significant losses across the world, with outbreaks reported in Southeast Asia, Mexico, and South America. Virulence level and mortality differences have been reported in isolates from different locations, and whether this phenomenon is caused by plasmid-related elements or genomic-related elements from the bacteria remains unclear. Here, nine genomes of South American AHPND-causing V. parahaemolyticus (VPAHPND) isolates were assembled and analyzed using a comparative genomics approach at (i) whole-genome, (ii) secretion system, and (iii) plasmid level, and then included for a phylogenomic analysis with another 86 strains. Two main results were obtained from our analyses. First, all isolates contained pVA1-type plasmids harboring the toxin coding genes, and with high similarity with the prototypical sequence of Mexican-like origin, while phylogenomic analysis showed some level of heterogeneity with discrete clusters and wide diversity compared to other available genomes. Second, although a high genomic similarity was observed, variation in virulence genes and clusters was observed, which might be relevant in the expression of the disease. Overall, our results suggest that South American pathogenic isolates are derived from various genetic lineages which appear to have acquired the plasmid through horizontal gene transfer. Furthermore, pathogenicity seems to be a multifactorial trait where the degree of virulence could be altered by the presence or variations of several virulence factors. IMPORTANCE AHPND have caused losses of over $2.6 billion to the aquaculture industry around the world due to its high mortality rate in shrimp farming. The most common etiological agent is V. parahaemolyticus strains possessing the pVA1-type plasmid carrying the PirABvp toxin. Nevertheless, complete understanding of the role of genetic elements and their impact in the virulence of this pathogen remains unclear. In this work, we analyzed nine South American AHPND-causing V. parahaemolyticus isolates at a genomic level, and assessed their evolutionary relationship with other 86 strains. We found that all our isolates were highly similar and possessed the Mexican-type plasmid, but their genomic content did not cluster with other Mexican strains, but instead were spread across all isolates. These results suggest that South American VPAHPND have different genetic backgrounds, and probably proceed from diverse geographical locations, and acquire the pVA1-type plasmid via horizontal gene transfer at different times.

The study of viral communities has revealed the enormous diversity and impact these biological entities have on various ecosystems. These observations have sparked widespread interest in developing computational strategies that support the comprehensive characterisation of viral communities based on sequencing data. Here we introduce VIRify, a new computational pipeline designed to provide a user-friendly and accurate functional and taxonomic characterisation of viral communities. VIRify identifies viral contigs and prophages from metagenomic assemblies and annotates them using a collection of viral profile hidden Markov models (HMMs). These include our manually-curated profile HMMs, which serve as specific taxonomic markers for a wide range of prokaryotic and eukaryotic viral taxa and are thus used to reliably classify viral contigs. We tested VIRify on assemblies from two microbial mock communities, a large metagenomics study, and a collection of publicly available viral genomic sequences from the human gut. The results showed that VIRify could identify sequences from both prokaryotic and eukaryotic viruses, and provided taxonomic classifications from the genus to the family rank with an average accuracy of 86.6%. In addition, VIRify allowed the detection and taxonomic classification of a range of prokaryotic and eukaryotic viruses present in 243 marine metagenomic assemblies. Finally, the use of VIRify led to a large expansion in the number of taxonomically classified human gut viral sequences and the improvement of outdated and shallow taxonomic classifications. Overall, we demonstrate that VIRify is a novel and powerful resource that offers an enhanced capability to detect a broad range of viral contigs and taxonomically classify them.

DNA damage induces the activation of many different signals associated with repair or cell death, but it is also connected with physiological events, such as adult neurogenesis and B‐cell differentiation. DNA damage induces different signaling pathways, some of them linked to important metabolic changes. The mTORC1 pathway has a central role in the regulation of growth processes and cell division in response to environmental changes and also controls protein synthesis, lipid biogenesis, nucleotide synthesis, and expression of glycolytic genes. Here, we report that double‐strand breaks induced with etoposide affect the expression of genes encoding different enzymes associated with specific metabolic pathways in Ramos cells. We also analyzed the role of mTOR signaling, demonstrating that double‐strand breaks induce downregulation of mTOR signaling. Specific inhibition of mTORC1 using rapamycin also induced changes in the expression of metabolic genes. Finally, we demonstrated that DNA damage and rapamycin can regulate glucose uptake. In summary, our findings show that etoposide and rapamycin affect the expression of metabolic genes as well as apoptotic and proliferation markers in Ramos cells, increasing our understanding of cancer metabolism.

Objetivo. El objetivo del presente trabajo es determinar la existencia de diferencias de los niveles de empatía y de sus dimensiones entre las tipologías familiares en estudiantes de odontología. Metodología. Estudio cuantitativo y no experimental, con un diseño descriptivo transversal, una población de estudiantes de odontología de la Universidad Evangélica de El Salvador y una muestra por conveniencia. Fueron evaluados los niveles de empatía y el funcionamiento familiar mediante la Escala de Empatía de Jefferson para estudiantes de profesiones de la salud y la Escala Breve de Funcionamiento Familiar. Se estimó la validez de constructo de ambos instrumentos mediante Análisis Factorial Confirmatorio y la confiabilidad mediante omega de McDonald y alfa de Cronbach. Las comparaciones de la empatía y sus dimensiones entre las tipologías familiares fueron realizadas mediante análisis de varianza bifactorial. Resultados. No se observaron diferencias estadísticas en la empatía y en sus dimensiones en función de las tipologías familiares. Se encontró que las mujeres son más empáticas que los hombres. Este resultado no está en concordancia con otros estudios realizados en América Latina en estudiantes de odontología y medicina, evaluando la empatía y el funcionamiento familiar con los mismos instrumentos. Conclusiones. La distribución de los niveles de empatía y de sus dimensiones son semejantes entre las tipologías familiares estudiadas. Por lo tanto, no se constató que el funcionamiento familiar tenga un efecto sobre la empatía en la población estudiada. Es necesario continuar estos estudios para obtener mayor evidencia empírica respecto de la influencia del funcionamiento familiar en la empatía.

Huntington’s disease (HD) results from the abnormal expansion of CAG repeats in exon 1 of the HTT gene. Here, the authors show that orally available, brain penetrant molecule branaplam lowers HTT transcript by promoting inclusion of a poison exon or pseudoexon.

A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., “arboviruses”), infecting a certain type of host (e.g., “mycoviruses,” “bacteriophages”) or displaying specific pathogenicity (e.g., “human immunodeficiency viruses”), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent. Transforming an existing phenotypic classification of viruses into one based on evolutionary relationships that can accommodate the vast number of viruses characterized in metagenomics and environmental studies is an ongoing challenge. This Consensus View explains how such a taxonomy can be expanded to encapsulate viral diversity and to recognize independent biological origins of different virus groups.

Summary: Bacteriophages, viruses specific to bacteria, coexist with their bacterial hosts with limited diversity fluctuations in the guts of healthy individuals where they replicate mostly via lysogenic replication. This favors ‘piggy-back-the-winner’ over ‘kill-the-winner’ dynamics which are driven by lytic bacteriophage replication. Revisiting the deep-viral sequencing data of a healthy individual sampled over 2.4 years, we explore how these dynamics occur. Prophages found in assembled bacterial metagenomes were also found extra-cellularly, as induced phage particles (iPPs), likely derived from prophage activation. These iPPs were diverse and continually present in low abundance, relative to the highly abundant but less diverse lytic phage population. The continuous detection of low levels of iPPs suggests that spontaneous induction regularly occurs in this healthy individual, possibly allowing prophages to maintain their ability to replicate and avoiding degradation and loss from the gut microbiota.

Abstract The microbiota in broiler chicken intestines affects the animals’ health, metabolism, and immunity both positively and negatively. Accordingly, it has a significant impact on animal productivity. Phages, host-specific parasites of bacterial cells, are a promising antimicrobial alternative that selectively target pathogens without disturbing the microbiota. The purpose of this study is to further characterize the commensal microbial community at production scale in broiler chickens treated with a Salmonella phage treatment. We evaluated the cecal microbiota of broilers reared in a commercial farming system where a phage cocktail against Salmonella, SalmoFree was supplied to animals. To do so, two field trials were conducted, incorporating three doses of phages in the broilers’ drinking water. Our results showed that the core microbiome (taxa that were present in more than 50% of samples) contained species that are key to microbiota adaptation in the last stage of the production cycle. Among these, there are some important degraders of complex polysaccharides and producers of short chain fatty acids (SCFA) such as Eisenbergiella and Lachnoclostridium. The phage cocktail did not affect the normal development of the microbiota’s structure. The addition of the phage cocktail resulted in a significant reduction in Campylobacter and an increase in Butyricimonas, Helicobacter and Rikenellaceae, which are common inhabitants in chicken gut with known negative and positive effects on their health and metabolism. Altogether, we consider that these results contribute valuable information to the implementation of large-scale phage therapy technologies.

ABSTRACT Phages and prophages are one of the principal modulators of microbial populations. However, much of their diversity is still poorly understood. Here, we extracted 33,624 prophages from 13,713 complete prokaryotic genomes to explore the prophage diversity and their relationships with their host. Our results reveal that prophages were present in 75% of the genomes studied. In addition, Enterobacterales were significantly enriched in prophages. We also found that pathogens are a significant reservoir of prophages. Finally, we determined that the prophage relatedness and the range of genomic hosts were delimited by the evolutionary relationships of their hosts. On a broader level, we got insights into the prophage population, identified in thousands of publicly available prokaryotic genomes, by comparing the prophage distribution and relatedness between them and their hosts. IMPORTANCE Phages and prophages play an essential role in controlling their host populations either by modulating the host abundance or providing them with genes that benefit the host. The constant growth in next-generation sequencing technology has caused the development of powerful computational tools to identify phages and prophages with high precision. Making it possible to explore the prophage populations integrated into host genomes on a large scale. However, it is still a new and under-explored area, and efforts are still required to identify prophage populations to understand their dynamics with their hosts.

Objective: To estimate and compare the levels of empathy between undergraduate dentistry students and professors at a university in the Dominican Republic. Material and Methods: Cross-sectional and descriptive study. The studied population consisted of two groups. The first: students of the Dentistry Career (N=520; n=335: 64.42% of total students) were distributed in two areas, basic-preclinical and clinical, while the second group corresponded of teachers who work in both areas (N=92; n=56; 60.87% of all teachers). The total sample was n = 391. The Jefferson Scale of Physician Empathy (S-Version) was used. Reliability was estimated using Cronbach's α and intraclass correlation coefficient, descriptive statistics, two-way analysis of variance, Tukey's test, effect size, and power of the test. Significance level: α ≤ 0.05 and β ≤ 0.20. Results: The empathy and dimension values were, in general, higher in the professors of the clinical area in relation to the other areas studied, with the exception of the compassionate care dimension. Conclusion: The finding that clinical teachers have a greater value of empathy is potentially an advantage for training students, especially in the clinical area.

Cattle productivity depends on our ability to fully understand and manipulate the fermentation process of plant material that occurs in the bovine rumen, which ultimately leads to the improvement of animal health and increased productivity with a reduction in environmental impact. An essential step in this direction is the phylogenetic and functional characterization of the microbial species composing the ruminal microbiota. To address this challenge, we separated a ruminal fluid sample by size and density using a sucrose density gradient. We used the full sample and the smallest fraction (5%), allowing the enrichment of bacteria, to assemble metagenome-assembled genomes (MAGs). We obtained a total of 16 bacterial genomes, 15 of these enriched in the smallest fraction of the gradient. According to the recently proposed Genome Taxonomy Database (GTDB) taxonomy, these MAGs belong to Bacteroidota, Firmicutes_A, Firmicutes, Proteobacteria, and Spirochaetota phyla. Fifteen MAGs were novel at the species level and four at the genus level. The functional characterization of these MAGs suggests differences from what is currently known from the genomic potential of well-characterized members from this complex environment. Species of the phyla Bacteroidota and Spirochaetota show the potential for hydrolysis of complex polysaccharides in the plant cell wall and toward the production of B-complex vitamins and protein degradation in the rumen. Conversely, the MAGs belonging to Firmicutes and Alphaproteobacteria showed a reduction in several metabolic pathways; however, they have genes for lactate fermentation and the presence of hydrolases and esterases related to chitin degradation. Our results demonstrate that the separation of the rumen microbial community by size and density reduced the complexity of the ruminal fluid sample and enriched some poorly characterized ruminal bacteria allowing exploration of their genomic potential and their functional role in the rumen ecosystem.

DNA barcodes are standardized sequences that range between 400 and 800 bp, vary at different taxonomic levels, and make it possible to assign sequences to species that have been previously taxonomically characterized. Several DNA barcodes have been postulated for plants, nonetheless, their classification potential has not been evaluated for metabarcoding, and as a result, it would appear as none of them excels above the others in this area. One tool that has been widely used and served as a baseline when evaluating new approaches is Naïve Bayesian Classifiers (NBC). The present study aims at evaluating the classification power of several plant chloroplast genetic markers that have been proposed as barcodes (trnL, rpoB, rbcL, matK, psbA-trnH, and psbK) using an NBC. We performed the classification at different taxonomic levels, and identified problematic genera when resolution was desired. We propose matK and trnL as potential candidate markers with resolution up to genus level. Some problematic genera within certain families could lead to the misclassification no matter which marker is used (i.e., Aegilops, Gueldenstaedtia, Helianthus, Oryza, Shorea, Thysananthus, and Triticum). Finally, we suggest recommendations for the taxonomic identification of plants in samples with potential mixtures.

Empathy is a relevant competence in the study and practice of medicine whose development could depend on the functioning style of each family. This study aims to compare the distribution of empathy levels, about functionality or dysfunction, and the three styles, which can be derived from family functioning in the families of Argentine medical students. Previously providing evidence of the validity of the family functioning measure. As well as provide evidence of the validity of the measure of family functioning. Methods: Ex post facto design: 306 Argentine medical students who had already taken the Jefferson Scale of Empathy—Spanish Edition (JSE-S) and the abbreviated Spanish Family Adaptability and Cohesion Evaluation Scale (FACES-20). A gender-weighted linear regression analysis was made, establishing an ANOVA and multiple comparisons via DMS to determine the effect of functional and dysfunctional families’ balanced, intermediate and extreme functioning styles concerning empathy. Results: Students who presented dysfunction in familial cohesion and adaptability showed measures of empathy greater than those classified as functional. Differences of cohesion were statistically significant in compassionate care, perspective taking and general empathy. These components were significantly higher in students from families classified as extreme than balanced ones. Students classified within families with either extreme or dysfunctional styles showed greater levels of empathy than more adaptive and functional ones, except in the ‘walking in patient’s shoes’ component where differences were not observed. Conclusions: Individual resilience as an intervening variable in the presence of empathy is discussed. Implications: The study of empathy, its associated variables, and the conditions of its development remains a central theme in relation to students and professionals of the health sciences. To achieve an effective professional practice, it is necessary to develop human capacities such as empathy and personal resilience.

Profile hidden Markov models (HMMs) are a powerful way of modeling biological sequence diversity and constitute a very sensitive approach to detecting divergent sequences. Here, we report the development of protocols for the rational design of profile HMMs. These methods were implemented on TABAJARA, a program that can be used to either detect all biological sequences of a group or discriminate specific groups of sequences. By calculating position-specific information scores along a multiple sequence alignment, TABAJARA automatically identifies the most informative sequence motifs and uses them to construct profile HMMs. As a proof-of-principle, we applied TABAJARA to generate profile HMMs for the detection and classification of two viral groups presenting different evolutionary rates: bacteriophages of the Microviridae family and viruses of the Flavivirus genus. We obtained conserved models for the generic detection of any Microviridae or Flavivirus sequence, and profile HMMs that can specifically discriminate Microviridae subfamilies or Flavivirus species. In another application, we constructed Cas1 endonuclease-derived profile HMMs that can discriminate CRISPRs and casposons, two evolutionarily related transposable elements. We believe that the protocols described here, and implemented on TABAJARA, constitute a generic toolbox for generating profile HMMs for the highly sensitive and specific detection of sequence classes.