The Gender Minority Stress and Resilience Measure: Psychometric Validity for Use in Spanish.

Purpose: Stigma is a fundamental driver of HIV disparities among transgender women (TW). The gender minority stress and resilience (GMSR) measure has not been validated in Spanish-speaking, resource-limited settings. We examined the psychometric properties of a translated and abbreviated GMSR among TW in Tijuana, Mexico. Methods: From 2020 to 2021, 152 participants were recruited through social media and venue-based sampling. We collected information on the abbreviated GMSR, psychosocial factors (e.g., depressive symptoms), and sociodemographics. The abbreviated GMSR assessed 7 factors (Discrimination, Rejection, Internalized Transphobia, Negative Expectations, Nondisclosure, Pride, and Community Connectedness). Confirmatory factor analysis, Cronbach's alphas, and McDonald's omegas assessed structural validity. Pearson's partial correlations assessed criterion, convergent, and discriminant validities. Results: The 7-factor structure solution had acceptable fit (root mean square error of approximation [95% confidence interval]=0.05 [0.05-0.06]; comparative fit index/Tucker-Lewis index=0.92/0.91); and internal reliability (α=0.62-0.89; ω=0.62-0.89). Depressive (r=0.22-0.43; p<0.001-0.007), post-traumatic stress disorder (PTSD; r=0.20-0.34; p<0.001-0.017) symptoms, and perceived stress (r=0.19-0.41; p≤0.001-0.030) were all positively associated with all stress factors (e.g., Discrimination, Rejection, Internalized Transphobia, Negative Expectations, and Nondisclosure). The resilience factor Pride was associated with fewer PTSD symptoms (r=-0.18; p=0.027), lower perceived life stress (r=-0.21; p=0.012), and greater general resilience (r=0.26; p=0.002). The Community Connectedness resilience factor was associated with fewer depressive symptoms (r=-0.22; p=0.007). Constructs were conceptually distinct with factor correlations below 0.60. Conclusion: Findings suggest that the Spanish-translated, abbreviated GMSR is a reliable and valid measure. These data expand the usability of the GMSR to TW in a Latin American, Spanish-speaking context.

Behavior and Use of Quaternary Ammonium-Based Disinfectants in Biosafety Protocols Against Fusarium oxysporum f. sp. cubense Race 1 and Tropical Race 4.

The banana is one of Colombia's main export products. However, production is seriously affected by Fusarium wilt of banana, which is the most destructive disease caused by the fungus Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4). Currently, management strategies focus on containment and biosecurity protocols to prevent its spread to territories that are free of this disease. This study aimed to evaluate nine quaternary ammonium-based disinfectants (i.e., quaternary ammonium compounds [QACs]) in vitro in Colombia on reproductive (microconidia and macroconidia) and resistance structures (chlamydospores) of Foc race 1 (R1) and tropical race 4 (TR4), with and without soil, to determine the influence of organic matter and soil texture on the action of QACs. A method for inhibiting the action of QACs was standardized and evaluated at 1,200 ppm with a contact time of ≤30 s while evaluating the soil-inoculum and soil-disinfectant interactions. In the soil-inoculum interaction, the efficacy of QACs was 100% in the reproductive and resistance structures of Foc R1 and TR4 without soil. However, in the soil-disinfectant interaction, only QAC4 controlled the pathogen at 100%. The presence of organic matter influenced the biocidal action of the QACs, and fine textures had a greater reducing effect on the concentration. The soil decreased the efficacy of the QACs and, therefore, must be removed from contaminated boots before treatments are applied.

Vertical Immobilization Method for Time-Lapse Microscopy Analysis in Filamentous Cyanobacteria.

A main event in bacterial cell division is the septation process, where the protein FtsZ is the key element. FtsZ polymerizes forming a ring-like structure (Z-ring) in the middle of the cell that serves as a scaffold for other division proteins. Super-resolution microscopy in bacterial models Escherichia coli and Bacillus subtilis showed that the Z-ring is discontinuous, while live cell imaging studies demonstrated that FtsZ moves along the ring by a mechanism known as treadmilling. To study the dynamics of FtsZ in vivo, a special cell placement in a vertical position is necessary for imaging the complete structure of the ring in the XY plane. In the case of FtsZ imaging in multicellular cyanobacteria, such as Anabaena sp. PCC7120, maintaining the filaments in a vertical position is challenging because of the size of the cells and the filaments' length. In this article, we describe a method that allows the vertical immobilization of Anabaena sp. PCC 7120 filaments using low melting point agarose and syringes, to record the Z-ring in a mutant that expresses a FtsZ-sfGFP fusion protein. This method is a rapid and inexpensive way to register protein dynamics at the division site using confocal microscopy.

Suicide prevention programming across ecological levels: Recommendations from Latinx immigrant origin youth and their parents.

INTRODUCTION: Latinx immigrant-origin youth (IOY) have unique risks for suicidal thoughts and behaviors. It has been suggested that these risks should be addressed from an ecological perspective, addressing cultural and family context as well as structural and systemic barriers to prevention. This study sought to explore perspectives of immigrant-origin Latinx adolescents and their caregivers on suicide and its prevention, including the potential impact of stressors specific to immigrant status. METHOD: Focus groups were conducted in 2018-2019 with Latinx immigrant-origin caregivers (N = 41, 97.5% female) and adolescents (ages = 14-19, N = 56, 50% female). Participants were recruited from community-based organizations in two different cities. A codebook approach to thematic analysis was used to identify themes, which were subsequently mapped onto levels of the Center for Disease Control's Social-Ecological Framework for Violence Prevention. RESULTS: Participants identified both contributors to suicidal behavior and potential components of prevention programming across ecological levels. Specific recommendations for suicide prevention included engaging in recreation, parenting education and support, enhancing academic supports for adolescents, and enhancing school-family communication. Structural barriers (e.g., caregiver work schedules) to implementing recommendations were described. DISCUSSION: Our results highlight the potential role of access to school and community-based supports as public health-oriented suicide prevention strategies and suggest a need to address barriers faced by immigrant families in accessing these supports alongside addressing barriers to mental health treatment. Policies impacting immigrant families' financial stability and increasing the availability of recreational and academic opportunities may promote mental health and prevent suicidal thoughts and behavior among IOY. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Incidencia e historia natural de la enfermedad inflamatoria intestinal en Castilla y León: estudio prospectivo, multicéntrico y poblacional / Incidence, and natural history of inflammatory bowel disease in Castilla y León: Prospective and multicenter epidemiological study

Introducción: La incidencia de la enfermedad inflamatoria intestinal (EII) está aumentando en todo el mundo. Objetivos: Evaluar la incidencia de EII en la comunidad autónoma de Castilla y León y describir las características clínicas de los pacientes al diagnóstico, el tipo de tratamiento recibido y la evolución clínica durante el primer año. Material y métodos: Estudio prospectivo, multicéntrico y poblacional en el que se incluyeron pacientes adultos diagnosticados de EII (enfermedad de Crohn [EC], colitis ulcerosa [CU] o colitis indeterminada [CI]) durante el año 2017 procedentes de 8 centros de Castilla y León. Se incluyeron variables epidemiológicas, clínicas y terapéuticas. Se calculó la incidencia global y por enfermedades. Resultados: Doscientos noventa pacientes fueron diagnosticados de EII (54,5% de CU, 45.2% de EC y 0,3% de CI), con una mediana de seguimiento de 9 meses (rango 8-11). La tasa de incidencia fue de 16,6 casos/100.000 habitantes-año (9/105 casos de CU y 7,5/105 casos de EC), con una proporción CU/EC de 1,2:1. Los pacientes con EC recibieron significativamente más corticoides sistémicos (47% vs. 30%; p=0,002), más tratamiento inmunomodulador (81% vs. 19%; p=0,000), más tratamiento biológico (29% vs. 8%; p=0,000) y mayor necesidad de cirugía (11% vs. 2%; p=0,000). Conclusiones: La incidencia de pacientes con CU en nuestro medio se incrementa, mientras que la de EC se mantiene estable, con una historia natural de la enfermedad peor (uso de corticoides, inmunosupresores, biológicos y cirugía) para los pacientes con EC comparado con los pacientes con CU en el primer año de seguimiento.(AU)

Introduction: The incidence of inflammatory bowel disease (IBD) is increasing worldwide. Objectives: To evaluate the incidence of IBD in Castilla y León describing clinical characteristics of the patients at diagnosis, the type of treatment received and their clinical course during the first year. Materials and methods: Prospective, multicenter and population-based incidence cohort study. Patients aged >18 years diagnosed during 2017 with IBD (Crohn's disease [CD], ulcerative colitis [UC] and indeterminate colitis [IC]) were included from 8 hospitals in Castilla y León. Epidemiological, clinical, and therapeutic variables were registered. The global incidence and disease incidence were calculated.Results290 patients were diagnosed with IBD (54.5% UC, 45.2% CD, and 0.3% IC), with a median follow-up of 9 months (range 8−11). The incidence rate of IBD in Castilla y Leon in 2017 was 16.6 cases per 10,000 inhabitants-year (9/105 UC cases and 7.5/105 CD cases), with a UC/CD ratio of 1.2:1. Use of systemic corticosteroids (47% vs 30%; P=.002), immunomodulatory therapy (81% vs 19%; P=.000), biological therapy (29% vs 8%; P=.000), and surgery (11% vs 2%; p=.000) were significatively higher among patients with CD comparing with those with UC. Conclusions: The incidence of patients with UC in our population increases while the incidence of patients with CD remains stable. Patients with CD present a worse natural history of the disease (use of corticosteroids, immunomodulatory therapy, biological therapy and surgery) compared to patients with UC in the first year of follow-up.(AU)

Incidence, and natural history of inflammatory bowel disease in Castilla y León: Prospective and multicenter epidemiological study. / Incidencia e historia natural de la enfermedad inflamatoria intestinal en Castilla y León: estudio prospectivo, multicéntrico y poblacional.

INTRODUCTION: The incidence of inflammatory bowel disease (IBD) is increasing worldwide. OBJECTIVES: To evaluate the incidence of IBD in Castilla y León describing clinical characteristics of the patients at diagnosis, the type of treatment received and their clinical course during the first year. MATERIALS AND METHODS: Prospective, multicenter and population-based incidence cohort study. Patients aged >18 years diagnosed during 2017 with IBD (Crohn's disease [CD], ulcerative colitis [UC] and indeterminate colitis [IC]) were included from 8 hospitals in Castilla y León. Epidemiological, clinical, and therapeutic variables were registered. The global incidence and disease incidence were calculated. RESULTS: 290 patients were diagnosed with IBD (54.5% UC, 45.2% CD, and 0.3% IC), with a median follow-up of 9 months (range 8-11). The incidence rate of IBD in Castilla y Leon in 2017 was 16.6 cases per 10,000 inhabitants-year (9/105 UC cases and 7.5/105 CD cases), with a UC/CD ratio of 1.2:1. Use of systemic corticosteroids (47% vs 30%; P=.002), immunomodulatory therapy (81% vs 19%; P=.000), biological therapy (29% vs 8%; P=.000), and surgery (11% vs 2%; p=.000) were significatively higher among patients with CD comparing with those with UC. CONCLUSIONS: The incidence of patients with UC in our population increases while the incidence of patients with CD remains stable. Patients with CD present a worse natural history of the disease (use of corticosteroids, immunomodulatory therapy, biological therapy and surgery) compared to patients with UC in the first year of follow-up.

Club cell secretory protein and lung function in children with cystic fibrosis.

BACKGROUND: Club cell secretory protein (CC16) exerts anti-inflammatory functions in lung disease. We sought to determine the relation of serum CC16 deficits and genetic variants that control serum CC16 to lung function among children with cystic fibrosis (CF). METHODS: We used longitudinal data from CF children (EPIC Study) with no positive cultures for Pseudomonas aeruginosa prior to enrollment. Circulating levels of CC16 and an inflammatory score (generated from CRP, SAA, calprotectin, G-CSF) were compared between participants with the lowest and highest FEV1 levels in adolescence (LLF and HLF groups, respectively; N = 130-per-group). Single nucleotide variants (SNVs) in the SCGB1A1, EHF-APIP loci were tested for association with circulating CC16 and with decline of FEV1 and FEV1/FVC% predicted levels between ages 7-16 using mixed models. RESULTS: Compared with the HLF group, the LLF group had lower levels of CC16 (geometric means: 8.2 vs 6.5 ng/ml, respectively; p = 0.0002) and higher levels of the normalized inflammatory score (-0.21 vs 0.21, p = 0.0007). Participants in the lowest CC16 and highest inflammation tertile had the highest odds for having LLF (p<0.0001 for comparison with participants in the highest CC16 and lowest inflammation tertile). Among seven SNVs associated with circulating CC16, the top SNV rs3741240 was associated with decline of FEV1/FVC and, marginally, FEV1 (p = 0.003 and 0.025, respectively; N = 611 participants, 20,801 lung function observations). CONCLUSIONS: Serum CC16 deficits are strongly associated with severity of CF lung disease and their effects are additive with systemic inflammation. The rs3741240 A allele is associated with low circulating CC16 and, possibly, accelerated lung function decline in CF.

El aprendizaje basado en problemas en el internado rotatorio de la Carrera de Medicina del Hospital Univalle / The learning based on problems in the rotary boarding school of the Univalle Hospital Medicine career

OBJETIVO: en la formación del estudiante de medicina, el internado rotatorio es un puente al inicio de su carrera profesional bajo una continua relación con los docentes instructores y los pacientes, esto implica un nexo entre la teoría de años previos y la aplicación práctica de su último año de pregrado; el objetivo de este trabajo se basó en determinar si esta relación se favorece con la aplicación del Aprendizaje Basado en Problemas (ABP). MÉTODOS: una primera etapa corresponde al diagnóstico de necesidades, sobre la base de una encuesta y una entrevista a grupo focal. En una segunda etapa de Investigación-Acción, se aplicó la metodología del ABP y se evaluó la misma con un cuestionario de guías de Co y Auto-evaluación y además con una guía de observación directa. RESULTADOS: los estudiantes manifestaron que los docentes están preparados y que el Hospital Univalle cuenta con buena estructura, sin embargo bajo un trabajo excesivo, de difícil adaptación y hasta con una mala relación con el docente, admitieron otras limitantes, como el cansancio de algunos pacientes por tantos periodos de anamnesis, el poco interés de los propios docentes y la aplicación de castigos por algunas fallas, asociados a una posición imponente de los docentes, generando temor. Citaron estrategias de evaluación como el repaso diario, los exámenes orales o escritos, la resolución de casos clínicos. Se destacó que el ABP es un método productivo, innovador y creativo que despierta la curiosidad e interés; además el uso de conocimientos previos y nuevos permite la reflexión en forma permanente e incentiva al discernimiento, sin ningún tipo de presión ni temor a ser castigados. CONCLUSIÓN: la aplicación del ABP en los procesos educativos es recomendable, con horarios accesibles, con adecuada estructura y un cronograma de trabajo, donde se debe instruir, preparar al estudiante y docentes. Toda esta innovación, permite la articulación de la teoría y la práctica, algunas limitaciones son la dificultad en el cumplimiento de la planificación, falta de hábito de los estudiantes y docentes, prefiriendo en muchas oportunidades las clases magistrales. En este momento de inminente proceso de renovación, de los paradigmas antiguos con la enseñanza conductual, es imperioso implementar diseños curriculares que tomen en cuenta estrategias de enseñanza y aprendizaje activos y con mucha auto-reflexión. (AU)

OBJECTIVE: in the training of the medical student, the rotary internship is a bridge at the beginning of his professional career under a continuous relationship with the teaching teachers and the patients, this implies a link between the theory of previous years and the practical application of his last year undergraduate; The objective of this work was based on determining if this relationship favors the application of Problem Based Learning (ABP). Methods METHODS: a first stage corresponds to the diagnosis of needs, based on a survey and a focus group interview. In a second stage of Research-Action, the ABP methodology was applied and it was evaluated with a questionnaire of Co and Self-evaluation guides and also with a direct observation guide. Results: : the students stated that the teachers are prepared and that the Univalle Hospital has a good structure, nevertheless under excessive work, difficult to adapt and even with a bad relationship with the teacher;,admitted other limitations, such as the fatigue of some patients for so many periods of history, the lack of interest of the teachers themselves and the application of punishment for some failures, associated with an imposing position of teachers, generating fear. They cited evaluation strategies such as daily review, oral or written exams, and the resolution of clinical cases. It was emphasized that the ABP is a productive, innovative and creative method that arouses curiosity and interest; In addition, the use of prior and new knowledge allows permanent reflection and encourages discernment, without any pressure or fear of being punished. CONCLUSION: the application of ABP in educational processes is recommended, with accessible schedules, with adequate structure and a work schedule, where you must instruct, prepare the student and teachers. All this innovation allows the articulation of theory and practice, Some limitations are the difficulty in fulfilling the planning, lack of habit of the students and teachers, preferring many times the master classes. In this moment of imminent process of renewal, of the old paradigms with behavioral teaching, it is imperative to implement curricular designs that take into account active teaching and learning strategies and with a lot of self-reflection.

Serum levels of L1-ORF1p and airflow limitation.

In a population-based study, higher circulating levels of L1-ORF1p were associated with lower lung function levels and increased risk for airflow limitation among former smokers http://bit.ly/2ZEIjNv.

High-efficiency nuclear transformation of the microalgae Nannochloropsis oceanica using Tn5 Transposome for the generation of altered lipid accumulation phenotypes.

BACKGROUND: One of the major problems in the production of lipids for biotechnological purposes using microalgae is maintaining a high productivity of these molecules without reducing cellular biomass. High production rates are usually obtained by cultivating microalgae under different stress conditions. However, many of these changes usually result in lower biomass productivity. Therefore, the optimization of the culture conditions and genetic modification techniques in these organisms is needed to generate robust new strains for profitable economic use. RESULTS: In this work, we describe a new strategy for random mutation of genomic DNA in the microalgae Nannochloropsis oceanica by insertion of a Transposome complex Tn5. This complex contains an antibiotic-resistance cassette commanded by a CMV viral promoter that allows high efficiency of transformation and the generation of mutants. This strategy, complemented with a large-scale identification and selection system for mutants, such as flow cytometry with cell selection, allowed us to obtain clonal cultures of mutants with altered phenotypes in the accumulation of intracellular lipids. The characterization of some of these mutants uncovered new genes that are likely to be involved in the regulation of lipid synthesis, revealing possible cellular responses that influence the intracellular homeostasis of lipids. CONCLUSION: The strategies proposed here are easy to implement in different types of microalgae and provide a promising scenario for improving biotechnological applications.

Even non-experts identify non-dysplastic lesions in inflammatory bowel disease via chromoendoscopy: results of a screening program in real-life.

Background and study aims Chromoendoscopy with targeted biopsy is the technique of choice for colorectal cancer screening in longstanding inflammatory bowel disease. We aimed to analyze results of a chromoendoscopy screening program and to assess the possibility of identifying low-risk dysplastic lesions by their endoscopic appearance in order to avoid histological analysis. Materials and methods We retrospectively reviewed chromoendoscopies performed between February 2011 and June 2017 in seven Spanish hospitals in a standardized fashion. We analyzed the findings and the diagnostic yield of the Kudo pit pattern for predicting dysplasia. Results A total of 709 chromoendoscopies (569 patients) were reviewed. Median duration of disease was 16.7 years (SD 8.1); 80.4 % had ulcerative colitis. A total of 2025 lesions (3.56 lesions per patient) were found; two hundred and thirty-two lesions were neoplastic (11.5 %) (223 were LGD (96.1 %), eight were HGD (3.4 %), and one was colorectal cancer (0.5 %). The correlation between dysplasia and Kudo pit patterns predictors of dysplasia (≥ III) was low, with an area under the curve of 0.649. Kudo I and II lesions were correctly identified with a high negative predictive value (92 %), even by non-experts. Endoscopic activity, Paris 0-Is classification, and right colon localization were risk factors for dysplasia detection, while rectum or sigmoid localization were protective against dysplasia. Conclusions Chromoendoscopy in the real-life setting detected 11 % of dysplastic lesions with a low correlation with Kudo pit pattern. A high negative predictive value would prevent Kudo I and, probably, Kudo II biopsies in the left colon, reducing procedure time and avoiding complications.

Crítica a la idea de Infancia y proyecto educativo en las políticas públicas de Colombia / Criticism of the idea of childhood and educational project in the public policies of Colombia / Crítica da ideia de Infância e projeto educativo nas políticas públicas da Colômbia

Resumen (analítico): En este artículo se comprende el sentido de algunos lineamientos nacionales e internacionales sobre la infancia y su relación con el proyecto educativo para Colombia. Se hizo un estudio cualitativo, de tipo descriptivo, analítico y documental. La metodología empleada fue el análisis de contenido de tipo semántico, en tanto que la población estuvo conformada por un conjunto de documentos oficiales que orientan lineamientos para la formulación de políticas públicas en Colombia y Latinoamérica. Se concluyó que la infancia es solo una estrategia de inversión para contribuir al desarrollo económico del país, como una inversión que tiene su tasa de retorno en la etapa adulta. De este modo, la idea de desarrollo infantil se sustenta en una propuesta educativa instrumental, ligada a la lógica neoliberal del capital humano.

Abstract (analytical): This article explores the meaning of national and international guidelines on childhood and their relation with educational projects in Colombia. A qualitative study was carried out using documentary, descriptive and analytical approaches. The methodology used was semantic content analysis, while the population consisted of official documents that have the purpose of providing guidelines for the formulation of public policies in Colombia and Latin America. The conclusion of the researchers was that childhood is only considered as an investment strategy that contributes to a country's economic development in the future, an investment for which the return comes when these children reach adulthood. Subsequently, the idea of childhood development is based on an instrumental educational proposal that is associated with a neoliberal logic based on human capital.

Resumo (analítico): Este artigo teve como objetivo compreender o significado de algumas diretrizes nacionais e internacionais sobre as crianças e sua relação com o projeto educacional para Colômbia. Por tanto realizou-se um estudo descritivo-analítico, qualitativo e documental. A metodologia utilizada foi a análise do conteúdo do tipo semântico e a população foi conformada por documentos oficiais que orientam diretrizes para a formulação de políticas públicas na Colômbia e na América Latina. Concluiu-se que a infância uma estratégia de investimento para contribuir ou contribuir para o desenvolvimento econômico dos países para o futuro, como um investimento que tem seu retorno na fase adulta. Desta forma, a idéia de desenvolvimento infantil baseia-se em uma proposta instrumental educacional, associada à lógica neoliberal do capital humano.

Genomic Features for Desiccation Tolerance and Sugar Biosynthesis in the Extremophile Gloeocapsopsis sp. UTEX B3054.

For tolerating extreme desiccation, cyanobacteria are known to produce both compatible solutes at intracellular level and a copious amount of exopolysaccharides as a protective coat. However, these molecules make cyanobacterial cells refractory to a broad spectrum of cell disruption methods, hindering genome sequencing, and molecular studies. In fact, few genomes are already available from cyanobacteria from extremely desiccated environments such as deserts. In this work, we report the 5.4 Mbp draft genome (with 100% of completeness in 105 contigs) of Gloeocapsopsis sp. UTEX B3054 (subsection I; Order Chroococcales), a cultivable sugar-rich and hardly breakable hypolithic cyanobacterium from the Atacama Desert. Our in silico analyses focused on genomic features related to sugar-biosynthesis and adaptation to dryness. Among other findings, screening of Gloeocapsopsis genome revealed a unique genetic potential related to the biosynthesis and regulation of compatible solutes and polysaccharides. For instance, our findings showed for the first time a novel genomic arrangement exclusive of Chroococcaceae cyanobacteria associated with the recycling of trehalose, a compatible solute involved in desiccation tolerance. Additionally, we performed a comparative genome survey and analyses to entirely predict the highly diverse pool of glycosyltransferases enzymes, key players in polysaccharide biosynthesis and the formation of a protective coat to dryness. We expect that this work will set the fundamental genomic framework for further research on microbial tolerance to desiccation and to a wide range of other extreme environmental conditions. The study of microorganisms like Gloeocapsopsis sp. UTEX B3054 will contribute to expand our limited understanding regarding water optimization and molecular mechanisms allowing extremophiles to thrive in xeric environments such as the Atacama Desert.

Measurement error correction in the least absolute shrinkage and selection operator model when validation data are available.

Measurement of serum biomarkers by multiplex assays may be more variable as compared to single biomarker assays. Measurement error in these data may bias parameter estimates in regression analysis, which could mask true associations of serum biomarkers with an outcome. The Least Absolute Shrinkage and Selection Operator (LASSO) can be used for variable selection in these high-dimensional data. Furthermore, when the distribution of measurement error is assumed to be known or estimated with replication data, a simple measurement error correction method can be applied to the LASSO method. However, in practice the distribution of the measurement error is unknown and is expensive to estimate through replication both in monetary cost and need for greater amount of sample which is often limited in quantity. We adapt an existing bias correction approach by estimating the measurement error using validation data in which a subset of serum biomarkers are re-measured on a random subset of the study sample. We evaluate this method using simulated data and data from the Tucson Epidemiological Study of Airway Obstructive Disease (TESAOD). We show that the bias in parameter estimation is reduced and variable selection is improved.

Draft genome sequences of Cylindrospermopsis raciborskii strains CS-508 and MVCC14, isolated from freshwater bloom events in Australia and Uruguay.

Members of the genus Cylindrospermopsis represent an important environmental and health concern. Strains CS-508 and MVCC14 of C. raciborskii were isolated from freshwater reservoirs located in Australia and Uruguay, respectively. While CS-508 has been reported as non-toxic, MVCC14 is a saxitoxin (STX) producer. We annotated the draft genomes of these C. raciborskii strains using the assembly of reads obtained from Illumina MiSeq sequencing. The final assemblies resulted in genome sizes close to 3.6 Mbp for both strains and included 3202 ORFs for CS-508 (in 163 contigs) and 3560 ORFs for MVCC14 (in 99 contigs). Finally, both the average nucleotide identity (ANI) and the similarity of gene content indicate that these two genomes should be considered as strains of the C. raciborskii species.

Diurnal Changes in Active Carbon and Nitrogen Pathways Along the Temperature Gradient in Porcelana Hot Spring Microbial Mat.

Composition, carbon and nitrogen uptake, and gene transcription of microbial mat communities in Porcelana neutral hot spring (Northern Chilean Patagonia) were analyzed using metagenomics, metatranscriptomics and isotopically labeled carbon (H13CO3) and nitrogen (15NH4Cl and K15NO3) assimilation rates. The microbial mat community included 31 phyla, of which only Cyanobacteria and Chloroflexi were dominant. At 58°C both phyla co-occurred, with similar contributions in relative abundances in metagenomes and total transcriptional activity. At 66°C, filamentous anoxygenic phototrophic Chloroflexi were >90% responsible for the total transcriptional activity recovered, while Cyanobacteria contributed most metagenomics and metatranscriptomics reads at 48°C. According to such reads, phototrophy was carried out both through oxygenic photosynthesis by Cyanobacteria (mostly Mastigocladus) and anoxygenic phototrophy due mainly to Chloroflexi. Inorganic carbon assimilation through the Calvin-Benson cycle was almost exclusively due to Mastigocladus, which was the main primary producer at lower temperatures. Two other CO2 fixation pathways were active at certain times and temperatures as indicated by transcripts: 3-hydroxypropionate (3-HP) bi-cycle due to Chloroflexi and 3-hydroxypropionate-4-hydroxybutyrate (HH) cycle carried out by Thaumarchaeota. The active transcription of the genes involved in these C-fixation pathways correlated with high in situ determined carbon fixation rates. In situ measurements of ammonia assimilation and nitrogen fixation (exclusively attributed to Cyanobacteria and mostly to Mastigocladus sp.) showed these were the most important nitrogen acquisition pathways at 58 and 48°C. At 66°C ammonia oxidation genes were actively transcribed (mostly due to Thaumarchaeota). Reads indicated that denitrification was present as a nitrogen sink at all temperatures and that dissimilatory nitrate reduction to ammonia (DNRA) contributed very little. The combination of metagenomic and metatranscriptomic analysis with in situ assimilation rates, allowed the reconstruction of day and night carbon and nitrogen assimilation pathways together with the contribution of keystone microorganisms in this natural hot spring microbial mat.

Next Generation Sequencing and mass spectrometry reveal high taxonomic diversity and complex phytoplankton-phycotoxins patterns in Southeastern Pacific fjords.

In fjord systems, Harmful Algal Blooms (HABs) not only constitute a serious problem when affecting the wildlife and ecosystems, but also human health and economic activities related to the marine environment. This is mostly due to a broad spectrum of toxic compounds produced by several members of the phytoplankton. Nevertheless, a deep coverage of the taxonomic diversity and composition of phytoplankton species and phycotoxin profiles in HAB prone areas are still lacking and little is known about the relationship between these fundamental elements for fjord ecosystems. In this study, a detailed molecular and microscopic characterization of plankton communities was performed, together with an analysis of the occurrence and spatial patterns of lipophilic toxins in a HAB prone area, located in the Southeastern Pacific fjord region. Microscopy and molecular analyses based on the 18S rRNA gene fragment indicated high diversity and taxonomic homogeneity among stations. Four toxigenic genera were identified: Pseudo-nitzschia, Dinophysis, Prorocentrum, and Alexandrium. In agreement with the detected species, liquid chromatography coupled with mass spectrometry revealed the presence of domoic acid (DA), pectenotoxin-2 (PTX-2), dinophysistoxin-2 (DTX-2), and 13-desmethyl spirolide C (SPX-1). Furthermore, a patchy distribution among DA in different net haul size fractions was found. Our results displayed a complex phytoplankton-phycotoxin pattern and for the first time contribute to the characterization of high-resolution phytoplankton community composition and phycotoxin distribution in fjords of the Southeastern Pacific region.

Regularized continuous-time Markov Model via elastic net.

Continuous-time Markov models are commonly used to analyze longitudinal transitions between multiple disease states in panel data, where participants' disease states are only observed at multiple time points, and the exact state paths between observations are unknown. However, when covariate effects are incorporated and allowed to vary for different transitions, the number of potential parameters to estimate can become large even when the number of covariates is moderate, and traditional maximum likelihood estimation and subset model selection procedures can easily become unstable due to overfitting. We propose a novel regularized continuous-time Markov model with the elastic net penalty, which is capable of simultaneous variable selection and estimation for large number of parameters. We derive an efficient coordinate descent algorithm to solve the penalized optimization problem, which is fully automatic and data driven. We further consider an extension where one of the states is death, and time of death is exactly known but the state path leading to death is unknown. The proposed method is extensively evaluated in a simulation study, and demonstrated in an application to real-world data on airflow limitation state transitions.

Persistent light to moderate alcohol intake and lung function: A longitudinal study.

Alcohol intake has been inconsistently associated with lung function levels in cross-sectional studies. The goal of our study was to determine whether longitudinally assessed light-to-moderate alcohol intake is associated with levels and decline of lung function. We examined data from 1333 adult participants in the population-based Tucson Epidemiological Study of Airway Obstructive Disease. Alcohol intake was assessed with four surveys between 1972 and 1992. Subjects who completed at least two surveys were classified into longitudinal drinking categories ("never", "inconsistent", or "persistent drinker"). Spirometric lung function was measured in up to 11 surveys between 1972 and 1992. Random coefficient models were used to test for differences in lung function by drinking categories. After adjustment for sex, age, height, education, BMI categories, smoking status, and pack-years, as compared to never-drinkers, persistent drinkers had higher FVC (coefficient: 157 mL, p < 0.001), but lower FEV1/FVC ratio (-2.3%, p < 0.001). Differences were due to a slower decline of FVC among persistent than among never-drinkers (p = 0.003), and these trends were present independent of smoking status. Inconsistent drinking showed similar, but weaker associations. After adjustment for potential confounders, light-to-moderate alcohol consumption was associated with a significantly decreased rate of FVC decline over adult life.