Development of an automated amplicon-based next-generation sequencing pipeline for rapid detection of bacteria and fungi directly from clinical specimens.

The timely identification of microbial pathogens is essential to guide targeted antimicrobial therapy and ultimately, successful treatment of an infection. However, the yield of standard microbiology testing (SMT) is directly related to the duration of antecedent antimicrobial therapy as SMT culture methods are dependent on the recovery of viable organisms, the fastidious nature of certain pathogens, and other pre-analytic factors. In the last decade, metagenomic next-generation sequencing (mNGS) has been successfully utilized as a diagnostic tool for various applications within the clinical laboratory. However, mNGS is resource, time, and labor-intensive-requiring extensive laborious preliminary benchwork, followed by complex bioinformatic analysis. We aimed to address these shortcomings by developing a largely Automated targeted Metagenomic next-generation sequencing (tmNGS) PipeLine for rapId inFectIous disEase Diagnosis (AMPLIFIED) to detect bacteria and fungi directly from clinical specimens. Therefore, AMPLIFIED may serve as an adjunctive approach to complement SMT. This tmNGS pipeline requires less than 1 hour of hands-on time before sequencing and less than 2 hours of total processing time, including bioinformatic analysis. We performed tmNGS on 50 clinical specimens with concomitant cultures to assess feasibility and performance in the hospital laboratory. Of the 50 specimens, 34 (68%) were from true clinical infections. Specimens from cases of true infection were more often tmNGS positive compared to those from the non-infected group (82.4% vs 43.8%, respectively, P = 0.0087). Overall, the clinical sensitivity of AMPLIFIED was 54.6% with 85.7% specificity, equating to 70.6% and 75% negative and positive predictive values, respectively. AMPLIFIED represents a rapid supplementary approach to SMT; the typical time from specimen receipt to identification of potential pathogens by AMPLIFIED is roughly 24 hours which is markedly faster than the days, weeks, and months required to recover bacterial, fungal, and mycobacterial pathogens by culture, respectively. IMPORTANCE: To our knowledge, this represents the first application of an automated sequencing and bioinformatics pipeline in an exclusively pediatric population. Next-generation sequencing is time-consuming, labor-intensive, and requires experienced personnel; perhaps contributing to hesitancy among clinical laboratories to adopt such a test. Here, we report a strong case for use by removing these barriers through near-total automation of our sequencing pipeline.

A novel remote TSST procedure reliably increases stress reactivity in cannabis users: A pilot study.

The Trier Social Stress Test (TSST) is a standard laboratory stressor comprised of a speech and arithmetic tasks that reliably induces physiological and psychological stress. It is traditionally administered in a room where the participant takes part in the TSST in front of two "committee" members. However, due to the recent Coronavirus disease (COVID-19) pandemic, in-person research study procedures have been limited due to potential exposure risks. Since stress reactivity is associated with drug use and the TSST reliably increases stress reactivity among cannabis users, the present pilot study examined a "remote" version of the TSST using the cloud-based virtual video communications platform, Zoom, among cannabis-using individuals (N = 15). The use of a remote platform such as Zoom allowed the participant and the committee to interact in real time while limiting in-person contact. The primary aim of this study was to test the feasibility of a remote version of the TSST in producing an increase in subjective stress response, cannabis craving, and cardiovascular stress in individuals who use cannabis. Participants completed subjective effects questionnaires and had blood pressure (BP) assessed before (baseline) and at various time points after the TSST. Heart rate (HR) was continuously measured throughout the session. This remote version of the TSST significantly and robustly increased State Anxiety and Perceived Stress scores, BP, and HR compared to baseline. There was no effect of the remote TSST on cannabis craving. Overall, the remote version of the TSST appears to be an effective laboratory stressor for future stress reactivity studies. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Uso de la técnica de economía de fichas para incrementar conductas de tratamiento en adultos mayores con sarcopenia / Use of a token economy to increase target behaviors in older people with sarcopenia

La sarcopenia está caracterizada por la baja masa y fuerza muscular en los adultos mayores. La implementación de técnicas de modificación de la conducta como la técnica de economía de fichas (TEF) puede fungir como estrategia para mejorar la adherencia al tratamiento. El objetivo fue evaluar el efecto de la TEF sobre las conductas de tratamiento: realizar la rutina de ejercicio de resistencia, consumir el suplemento de proteína y consumir el suplemento de vitamina D. Se realizó un estudio de caso de múltiples sujetos en ocho adultos mayores con sarcopenia. El estudio estuvo conformado por tres fases: pre-intervención, intervención conductual y post-intervención conductual. Se evaluó la frecuencia de las conductas de tratamiento en las tres fases, además de los cambios en masa y fuerza muscular. El análisis de los datos se realizó por medio de estadística descriptiva. Los resultados mostraron que la frecuencia de las conductas de tratamiento aumentó en el 100% de los participantes en la etapa de intervención conductual al comparar con la fase pre-intervención, valores que no regresaron a cero en la fase post-intervención conductual. El 83.3 % de los participantes dejaron de tener el diagnóstico de sarcopenia con base en los cambios de masa y fuerza muscular.

Sarcopenia is characterized by low muscle mass and strength in older adults. It is caused by decreased physical activity and quality of dietary intake. Therefore, the implementation of behavior modification techniques such as the token economy technique can serve as a strategy to improve treatment. The aim of the current study was to evaluate the effect of the token economy technique on treatment behaviors. A multiple case studies with an ABC-type design was conducted in eight older adults with sarcopenia. The intervention consisted of modification of treatment-related behaviors; in addition, changes in muscle mass and strength were assessed. The results showed that the frequency of target behaviors increased in 100% of the participants in the intervention stage compared to baseline. The frequency of the target behaviors did not return to the obtained baseline compared to the maintenance stage. 83.3% of the participants changed their sarcopenia diagnosis.

Evaluation of Taste Aversion Learning Procedure for the Generalization of Aversion Using Palatable Foods / Evaluación del procedimiento aprendizaje aversivo gustativo para la generalización de la aversión con dos alimentos palatables

Abstract An experiment to evaluate the effectiveness of the taste aversion conditioning paradigm in the generalization of aversion with palatable foods was performed. Ten experimentally naive females Wistar rats and three types of foods were used: a) standard purina rodent chow, b) vanilla flavor cookies and c) chocolate-flavored cookies. Subjects were divided into two groups, five subjects per group. Using the taste aversion conditioning paradigm protocol, subjects were exposed to the types of food keeping an intake record. The experiment demonstrated that rats can acquire an aversion to palatable foods accompanied by a tendency to generalize, when using elements that share characteristics such as nutritional content and texture. In addition, the intake of a food that does not share the characteristics of texture, taste, smell and energy content with the one used for conditioning was not been affected. These findings indicate that the aversion generalization seems to depend on the properties of the food used.

Resumen Se evaluó experimentalmente la efectividad del paradigma de aprendizaje aversivo gustativo en la generalización de la aversión utilizando alimentos palatables. Se utilizaron diez ratas Wistar hembras experimentalmente ingenuas y tres tipos de alimentos: a) purina comida estándar para roedores, b) galletas con sabor a vainilla y c) galletas con sabor a chocolate. Los sujetos fueron divididos en dos grupos, cinco sujetos en cada uno. Usando el paradigma de condicionamiento de aversión al sabor, los sujetos fueron expuestos a los tipos de alimentos manteniendo un registro de ingesta. El experimento demostró que las ratas pueden adquirir una aversión a los alimentos palatables acompañados por una tendencia a generalizarse, cuando se utilizan elementos que comparten características como el contenido nutricional y la textura. Además, la ingesta de un alimento que no comparte características como la textura, sabor, olor y contenido energético como el utilizado para el condicionamiento no se vio afectada. Estos hallazgos demuestran que la generalización de la aversión parece depender de las propiedades de los alimentos utilizados.

Voluntary vs forced physical activity, which is more effective in reducing body weight gain from sucrose consumption?

ABSTRACT The organoleptic characteristics of sucrose encourage its consumption in excessive amounts that result in increased body weight and possible involvement of other health indicators. In contrast, physical activity reduces body weight and promotes health and well-being, however the question remains as to what type of physical activity is the most effective to achieve those goals. The objective of the current study was to compare the effect of voluntary (VA) vs forced physical activity (FA) on body weight in organisms that consume sucrose daily. Twenty, three-month-old Wistar female rats were assigned either VA or FA; both groups were exposed to beverages with 8% sucrose concentration. The results showed that consuming sucrose daily increased body weight, despite being an active organism. However, this increase was by 11% in the VA group and 8.4% among the FA group. Therefore, although neither type of physical activity proposed in this study was effective to reduce body weight, FA influenced body weight gain less. Another interesting result was that VA registered a greater effect by reducing the consumption of sucrose. In conclusion, performing physical activity delays, but does not reverse, body weight gain from sucrose consumption.

RESUMEN Las características organolépticas de la sacarosa incentivan su consumo en cantidades excesivas que tienen como resultado el incremento del peso corporal y la posible afectación de otros indicadores de salud. En contraparte, la realización de actividad física reduce el peso corporal y favorece la salud y bienestar, pero ¿cuál es la manera más efectiva de realizar actividad física para lograr esos objetivos? Se planteó como objetivo comparar el efecto de la actividad física voluntaria (AV) contra el de la actividad física forzada (AF) sobre el peso corporal en organismos que consumen diariamente sacarosa. Se utilizaron veinte ratas hembras de la cepa Wistar de tres meses de edad, agrupadas en: (1) actividad voluntaria; (2) actividad forzada. Ambos expuestos a una bebida al 8% de concentración de sacarosa. Los resultados mostraron que consumir sacarosa diariamente incrementa el peso corporal, a pesar de ser un organismo activo. Sin embargo, este aumento fue en un 11% en AV y del 8.4% en AF. Por lo que, si bien ningún tipo de actividad física propuesto en este estudio fue efectivo para reducir el peso corporal, realizar actividad física de forma forzada influye en que la ganancia de el peso corporal sea menor. Otro resultado de interés, fue que realizar actividad física voluntaria registró un mayor efecto al reducir el consumo de sacarosa. En conclusión, realizar actividad fisica retrasa, pero no revierte la ganancia de peso corporal ante el consumo de sacarosa.

[Socioeconomic and sociodemographic determinants associated with fruit and vegetable consumption among mothers and homes of schoolchildren in Jalisco]. / Determinantes socioeconómicos y sociodemográficos asociados al consumo de frutas y verduras de las madres de familia y los hogares de escolares de Jalisco.

INTRODUCTION: Introduction: increasing fruit and vegetable consumption is a priority. It has been prioritized as a fundamental objective of public policies worldwide. Given that such consumption in schoolchildren in Jalisco (Mexico) is below the dietary recommendations it is crucial to identify the determinants that influence this consumption to promote the development of contextualized actions that improve it. Objective: to identify the socioeconomic and sociodemographic determinants of fruit and vegetable consumption among mothers and households of schoolchildren in Jalisco, Mexico. Method: an analytical, cross-sectional study carried out during the first quarter of 2020. A validated food consumption frequency and a questionnaire on sociodemographic and socioeconomic factors were used for its development. Results: a lower educational level of the mothers of schoolchildren was associated with a lower consumption of vegetables by schoolchildren. In turn, a lower household income level was associated with a lower consumption of fruits in schoolchildren. Conclusions: a low educational level of mothers and a low household income were determinants associated with fruit and vegetable consumption in schoolchildren. However, there were differences in the determinants for fruits and vegetables. It is essential to consider these factors and their differences in order to plan actions that contribute to improving fruit and vegetable intake in the school population.

INTRODUCCIÓN: Introducción: incrementar el consumo de frutas y verduras es una prioridad, objetivo fundamental en las políticas públicas a nivel mundial. Dado que dicho consumo en los escolares de Jalisco (México) se encuentra por debajo de las recomendaciones alimentarias, es esencial identificar los determinantes que influyen en su consumo de frutas y verduras, para promover el desarrollo de acciones que contribuyan a mejorarlo. Objetivo: identificar los determinantes socioeconómicos y sociodemográficos del consumo de frutas y verduras en las madres de familia y los hogares de escolares de Jalisco, México. Método: estudio transversal analítico, realizado durante el primer trimestre del año 2020 utilizando una frecuencia de consumo de alimentos validada y un cuestionario sobre factores sociodemográficos y socioeconómicos. Resultados: el bajo nivel educativo de las madres de los escolares se asoció con un menor consumo de verduras y el bajo nivel de ingresos en el hogar se asoció con un menor consumo de frutas por los escolares. Conclusiones: el bajo nivel educativo de las madres y el bajo nivel de ingresos de los hogares fueron determinantes asociados al consumo de frutas y verduras de los escolares. Sin embargo, se presentaron diferencias en cuanto a los determinantes para las frutas y para las verduras. Estos factores y sus diferencias deben de tenerse en cuenta para la planificación de acciones que contribuyan a mejorar la ingesta de frutas y verduras en la población escolar.

Dysfunctional Patterns of Food Intake by Anxiety during Isolation by COVID-19 in Chile, Colombia and Mexico.

The aim of this research was to compare food intake dysfunctional patterns score with the subjective perception of anxiety and sociodemographic characteristics of the participants in isolation by COVID-19 from Chile, Colombia, and Mexico. A cross-sectional research was carried out, with a virtual questionnaire of subjective perception of anxiety and the questionnaire of three 18-item feeding factors. 958 people of both sexes participated (F = 83%, M = 17%), mainly in the 18 to 35 age range. Dysfunctional eating patterns presented high scores in people who perceived anxiety, as well as in participants from Chile. Additionally, it was found that women present greater cognitive restriction and emotional intake, and college students showed greater disinhibition. In conclusion, the scores of the three dysfunctional eating patterns were higher in people with subjective perception of anxiety during social isolation due to COVID-19, and there were also differences according to country, sex, and educational level.

El objetivo de esta investigación fue comparar el puntaje de los patrones disfuncionales de la ingesta con la percepción subjetiva de la ansiedad y características sociodemográficas de los participantes en aislamiento por COVID-19 de Chile, Colombia y México. Se realizó una investigación de tipo transversal, con un cuestionario virtual de percepción subjetiva de la ansiedad y el cuestionario de tres factores de alimentación 18-items. Participaron 958 personas de ambos sexos (F = 83%, M = 17%), principalmente en el rango de edad de 18 35 años. Los patrones disfuncionales de la ingesta presentaron puntajes altos en personas que percibieron ansiedad y en participantes de Chile. Adicionalmente, se encontró que las mujeres presentan mayor restricción cognitiva e ingesta emocional y los estudiantes universitarios mostraron mayor desinhibición. En conclusión, los puntajes de los tres patrones disfuncionales de la ingesta fueron más altos en las personas con percepción subjetiva de ansiedad durante el aislamiento social por COVID-19 y así mismo se presentaron diferencias de acuerdo al país, sexo y nivel educativo.

Actividad física como conducta auto-reguladora de ansiedad percibida y patrones disfuncionales de la ingesta en época de aislamiento por COVID-19 en latinoamericanos

RESUMEN La actividad física es considerada una conducta reguladora de ansiedad y ha demostrado efectividad para reducir esta condición emocional. Debido a la pandemia del coronavirus (COVID-19), en Latinoamérica los gobiernos han aplicado estrategias de aislamiento para reducir la probabilidad de contagio y de esta manera controlar las afectaciones a la salud; sin embargo, un efecto desfavorable de esta situación es el incremento en los niveles de ansiedad que puede afectar la ingesta de alimentos. El objetivo fue analizar la asociación entre la actividad física y la percepción subjetiva de la ansiedad, y las diferencias de estas variables con los patrones disfuncionales de la ingesta en personas latinoamericanas que se encontraban en aislamiento. Se aplicó un cuestionario a 1.035 personas de diferentes países, a partir del cual se identificó que aquellas personas que realizaban actividad física presentaron una probabilidad 50% menor de percibir ansiedad. Adicionalmente, los sujetos que realizaban actividad física presentaron mayor restricción cognitiva y los que no realizaban actividad física, registraron mayor nivel de desinhibición e ingesta emocional. Finalmente, se concluye que la actividad física es una conducta reguladora de la ansiedad en esta época de aislamiento o cuarentena y tiene influencia positiva en los individuos, ya que reduce la desinhibición y la ingesta emocional, por lo que podría prevenir el incremento de peso y el posible desarrollo de patologías alimentarias. Este hallazgo es importante para la promoción de la actividad física en esta época de aislamiento y en situaciones similares, además es útil para las intervenciones en sujetos con alimentación emocional.

ABSTRACT Physical activity is considered an anxiety-regulating behavior and is effective in reducing this emotional condition. Due to the coronavirus pandemic (COVID-19), governments of Latin America have applied isolation strategies to reduce the probability of contagion and thus control health effects; however, an unfavorable effect of this situation has been the increase in anxiety levels that can affect food intake. The objective of the current study was to analyze the association between physical activity and differences in dysfunctional patterns of intake in Latin American people who were in isolation. A questionnaire was applied to 1.035 people from different countries. We observed that those performing physical activity presented a 50% lower probability of perceived anxiety. Additionally, the subjects who performed physical activity presented greater cognitive restriction, and those who did not perform physical activity registered a higher level of disinhibition and emotional intake. We conclude that physical activity is an anxiety-regulating behavior in this time of isolation or quarantine and has a positive influence on individuals, since it reduces disinhibition and emotional intake, and could prevent weight gain and possible development of food pathologies. This finding is important for the promotion of physical activity in this time of confinement and similar situations, and it is also useful for interventions on subjects with emotional feeding.

An in vitro vascularized micro-tumor model of human colorectal cancer recapitulates in vivo responses to standard-of-care therapy.

Around 95% of anti-cancer drugs that show promise during preclinical study fail to gain FDA-approval for clinical use. This failure of the preclinical pipeline highlights the need for improved, physiologically-relevant in vitro models that can better serve as reliable drug-screening and disease modeling tools. The vascularized micro-tumor (VMT) is a novel three-dimensional model system (tumor-on-a-chip) that recapitulates the complex human tumor microenvironment, including perfused vasculature, within a transparent microfluidic device, allowing real-time study of drug responses and tumor-stromal interactions. Here we have validated this microphysiological system (MPS) platform for the study of colorectal cancer (CRC), the second leading cause of cancer-related deaths, by showing that gene expression, tumor heterogeneity, and treatment responses in the VMT more closely model CRC tumor clinicopathology than current standard drug screening modalities, including 2-dimensional monolayer culture and 3-dimensional spheroids.

Computational Analysis of Electron Transfer Kinetics for CO2 Reduction with Organic Photoredox Catalysts.

We present a fundamental description of the electron transfer (ET) step from substituted oligo(p-phenylene) (OPP) radical anions to CO2, with the larger goal of assessing the viability of underexplored, organic photoredox routes for utilization of anthropogenic CO2. This work varies the electrophilicity of para-substituents to OPP and probes the dependence of rate coefficients and interfragment interactions on the substituent Hammett parameter, σp, using constrained density functional theory (CDFT) and energy decomposition analysis (EDA). Large electronic couplings across substituents indicates an adiabatic electron transfer process for reactants at contact. As one might intuitively expect, free energy changes dominate trends in ET rate coefficients in most cases, and rates increase with substituent electron-donating ability. However, we observe an unexpected dip in rate coefficients for the most electron-donating groups, due to the combined impact of flattening free energies and a steep increase in reorganization energies. Our analysis shows that, with decreasing σp, flattening OPP LUMO levels lower the marginal increase in free energy. EDA reveals trends in electrostatics and charge transfer interactions between the catalyst and substrate fragments that influence free energy changes across substituents. Reorganization energies do not exhibit a direct dependence on σp and are largely similar across systems, with the exception of substituents containing lone pairs of electrons that exhibit significant deformation upon electron transfer. Our study therefore suggests that while a wide range of ET rates are observed, there is an upper limit to rate enhancements achievable by only tuning the substituent electrophilicity.

NOx instrument intercomparison for laboratory biomass burning source studies and urban ambient measurements in Albuquerque, New Mexico.

Understanding nitrogen oxides (NOx = NO + NO2) measurement techniques is important as air-quality standards become more stringent, important sources change, and instrumentation develops. NOx observations are compared in two environments: source testing from the combustion of Southwestern biomass fuels, and urban, ambient NOx. The latter occurred in the urban core of Albuquerque, NM, at an EPA NCORE site during February-March 2017, a relatively clean photochemical environment with ozone (O3) <60 ppb for all but 6 hr. We compare two techniques used to measure NOx in biomass smoke during biomass burning source testing: light absorption at 405 nm and a traditional chemiluminescence monitor. Two additional oxides of nitrogen techniques were added in urban measurements: a cavity attenuated phase shift instrument for direct NO2, and the NOy chemiluminescence instrument (conversion of NOy to NO by molybdenum catalyst). We find agreement similar to laboratory standards for NOx, NO2, and NO comparing all four instruments (R2 > 0.97, slopes between 0.95 and 1.01, intercepts < 2 ppb for 1-hr averages) in the slowly varying ambient setting. Little evidence for significant interferences in NO2 measurements was observed in comparing techniques in late-winter urban Albuquerque. This was also confirmed by negligible NOz contributions as measured with an NOy instrument. For the rapidly varying (1-min) higher NOx concentrations in biomass smoke source testing, larger variability characterized chemiluminescence and absorption instruments. Differences between the two instruments were both positive and negative and occurred for total NOx, NO, and NO2. Nonetheless, integrating the NOx signals over an entire burn experiment and comparing 95 combustion experiments, showed little evidence for large systematic influences of possible interfering species biasing the methods. For concentrations of <2 ppm, a comparison of burn integrated NOx, NO2, and NO yielded slopes of 0.94 to 0.96, R2 of 0.83 to 0.93, and intercepts of 8 to 25 ppb. We attribute the latter, at least in part, to significant noise particularly at low NOx concentrations, resulting from short averaging times during highly dynamic lab burns. Discrepancies between instruments as indicated by the intercepts urge caution with oxides of nitrogen measurements at concentrations <50 ppb for rapidly changing conditions. Implications: Multiple NOx measurement methods were employed to measure NOx concentrations at an EPA NCORE site in Albuquerque, NM, and in smoke produced by the combustion of Southwestern biomass fuels. Agreement shown during intercomparison of these NOx techniques indicated little evidence of significant interfering species biasing the methods in these two environments. Instrument agreement is important to understand for accurately characterizing ambient NOx conditions in a range of environments.

How do I implement an automated screen for high-titer ABO antibody as an inventory management tool for ABO plasma-incompatible platelets?

BACKGROUND: Plasma volume reduction (PVR) may reduce the risk of hemolysis associated with transfusion of plateletpheresis blood products (PLTs) containing ABO-incompatible plasma. But PVR may delay PLT issue. In collaboration with our blood donor center we evaluated an automated screen of PLT for high-titer ABO antibody and to apply PVR to high-titer PLTs. STUDY DESIGN AND METHODS: At the donor center, plasma from PLT donors was tested using an automated microplate system (PK7300, Beckman). PK settings were set for a detection cutoff equivalent to 1 in 256 using a manual tube method. The donors associated with high-titer PLTs were characterized by sex and age. In the transfusion service, the number of PVR procedures was evaluated before and after implementation of the high-titer screen. RESULTS: During validation, 157 of 1008 PLT units (15%) were positive by the automated method versus 121 (12%) by manual method. After implementation, 2112 of 15,240 PLT units were high-titer, with higher frequency in donations from females versus males (18% vs. 12%, p < 0.0001). The PLT PVR rate was reduced by 50%. CONCLUSION: Implementation of an automated method to screen PLTs for high-titer ABO antibody at the donor center improves the inventory management of PLTs containing ABO-incompatible plasma at the hospital transfusion service.