Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing.

Antimicrobial resistance (AMR) is a growing threat to public health and farming at large. In clinical and veterinary practice, timely characterization of the antibiotic susceptibility profile of bacterial infections is a crucial step in optimizing treatment. High-throughput sequencing is a promising option for clinical point-of-care and ecological surveillance, opening the opportunity to develop genotyping-based AMR determination as a possibly faster alternative to phenotypic testing. In the present work, we compare the performance of state-of-the-art methods for detection of AMR using high-throughput sequencing data from clinical settings. We consider five computational approaches based on alignment (AMRPlusPlus), deep learning (DeepARG), k-mer genomic signatures (KARGA, ResFinder) or hidden Markov models (Meta-MARC). We use an extensive collection of 585 isolates with available AMR resistance profiles determined by phenotypic tests across nine antibiotic classes. We show how the prediction landscape of AMR classifiers is highly heterogeneous, with balanced accuracy varying from 0.40 to 0.92. Although some algorithms-ResFinder, KARGA and AMRPlusPlus-exhibit overall better balanced accuracy than others, the high per-AMR-class variance and related findings suggest that: (1) all algorithms might be subject to sampling bias both in data repositories used for training and experimental/clinical settings; and (2) a portion of clinical samples might contain uncharacterized AMR genes that the algorithms-mostly trained on known AMR genes-fail to generalize upon. These results lead us to formulate practical advice for software configuration and application, and give suggestions for future study designs to further develop AMR prediction tools from proof-of-concept to bedside.

Avances de la bioinformática en Costa Rica: vista retrospectiva y perspectivas / Bioinformatics advances in Costa Rica: retrospective view and perspectives

Resumen Introducción: La disciplina científica de la bioinformática tiene el potencial de generar aplicaciones innovadoras para las sociedades humanas. Costa Rica, pequeña en tamaño y población en comparación con otros países de América Latina, ha ido adoptando la disciplina de manera progresiva. El reconocer los avances permite determinar hacia dónde puede dirigirse el país en este campo, así como su contribución a la región latinoamericana. Objetivo: En este manuscrito se reporta evidencia de la evolución de la bioinformática en Costa Rica, para identificar debilidades y fortalezas que permitan definir acciones a futuro. Métodos: Se realizaron búsquedas en bases de datos de publicaciones científicas y repositorios de secuencias, así como información de actividades de capacitación, redes, infraestructura, páginas web y fuentes de financiamiento. Resultados: Se observan avances importantes desde el 2010, incluyendo un aumento en oportunidades de entrenamiento y número de publicaciones, aportes significativos a las bases de datos de secuencias y conexiones por medio de redes. Sin embargo, ciertas áreas, como la masa crítica y la financiación requieren más desarrollo. La comunidad científica y sus patrocinadores deben promover la investigación basada en bioinformática, invertir en la formación de estudiantes de posgrado, aumentar la formación de profesionales, crear oportunidades laborales para carreras en bioinformática y promover colaboraciones internacionales a través de redes. Conclusiones: Se sugiere que para experimentar los beneficios de las aplicaciones de la bioinformática se deben fortalecer tres aspectos clave: la comunidad científica, la infraestructura de investigación y las oportunidades de financiamiento. El impacto de tal inversión sería el desarrollo de proyectos ambiciosos pero factibles y colaboraciones extendidas dentro de la región latinoamericana. Esto permitiría realizar contribuciones significativas para abordar los desafíos globales y la aplicación de nuevos enfoques de investigación, innovación y transferencia de conocimiento para el desarrollo de la economía, dentro de un marco de ética de la investigación.

Abstract Introduction: The scientific discipline of bioinformatics has the potential to generate innovative applications for human societies. Costa Rica, small in size and population compared to other Latin American countries, has been progressively adopting the discipline. Recognizing progress makes it possible to determine where the country can go in this field, as well as its contribution to the Latin American region. Objective: This manuscript reports evidence of the evolution of bioinformatics in Costa Rica, to identify weaknesses and strengths allowing future actions plans. Methods: We searched databases of scientific publications and sequence repositories, as well as information on training activities, networks, infrastructure, web pages and funding sources. Results: Important advances have been observed since 2010, such as increases in training opportunities and the number of publications, significant contributions to the sequence databases and connections through networks. However, areas such as critical mass and financing require further development. The scientific community and its sponsors should promote bioinformatics-based research, invest in graduate student training, increase professional training, create career opportunities in bioinformatics, and promote international collaborations through networks. Conclusions: It is suggested that in order to experience the benefits of bioinformatics applications, three key aspects must be strengthened: the scientific community, the research infrastructure, and funding opportunities. The impact of such investment would be the development of ambitious but feasible projects and extended collaborations within the Latin American region and abroad. This would allow significant contributions to address global challenges and the implementation of new approaches to research, innovation and knowledge transfer for the development of the economy, within an ethics of research framework.

Anti-DFS70 Antibodies Among Patient and Healthy Population Cohorts in China: Results From a Multicenter Training Program Showing Spontaneous Abortion and Pediatric Systemic Autoimmune Rheumatic Diseases Are Common in Anti-DFS70 Positive Patients.

Objective: Anti-DFS70 antibodies correlating with the nuclear dense fine speckled (DFS) pattern in the HEp-2 indirect immunofluorescence assay (IFA) are less common in patients with systemic autoimmune rheumatic disease (SARD) than in healthy subjects and their clinical associations remain elusive. We hosted a multi-center HEp-2 IFA training program to improve the ability of clinical laboratories to recognize the DFS pattern and to investigate the prevalence and relevance of anti-DFS70 antibodies. Methods: DFS pattern sera identified by HEp-2 IFA in 29 centers in China were redirected to a central laboratory for anti-DFS70 testing by line immunoblot assay (LIA), enzyme-linked immunosorbent assay (ELISA), and IFA with HEp-2 ELITE/DFS70-KO substrate. Anti-extractable nuclear antigen antibodies were measured by LIA and the clinical relevance was examined in adult and pediatric patients. Results: HEp-2 IFA positive rate and DFS pattern in positive sera were 36.2% (34,417/95,131) and 1.7% (582/34,417) in the patient cohort, and 10.0% (423/4,234) and 7.8% (33/423) in a healthy population, respectively. Anti-DFS70 prevalence among sera presenting the DFS pattern was 96.0, 93.7, and 49.6% by ELISA, LIA, and HEp-2 ELITE, respectively. 15.5% (52/336) of adult and 50.0% (20/40) of pediatric anti-DFS70 positive patients were diagnosed with SARD. Diseases most common in anti-DFS70 positive patients were spontaneous abortion (28.0%) in adults and juvenile idiopathic arthritis (22.5%) in pediatric patients. Conclusion: Accurate DFS pattern identification increased the detection rate of anti-DFS70 antibodies by ELISA and LIA. Anti-DFS70 antibodies are remarkably high in cases of spontaneous abortion and in pediatric SARD patients, but not prevalent in adult SARD patients.

Establishment of international autoantibody reference standards for the detection of autoantibodies directed against PML bodies, GW bodies, and NuMA protein.

Objectives: Reference materials are important in the standardization of autoantibody testing and only a few are freely available for many known autoantibodies. Our goal was to develop three reference materials for antibodies to PML bodies/multiple nuclear dots (MND), antibodies to GW bodies (GWB), and antibodies to the nuclear mitotic apparatus (NuMA). Methods: Reference materials for identifying autoantibodies to MND (MND-REF), GWB (GWB-REF), and NuMA (NuMA-REF) were obtained from three donors and validated independently by seven laboratories. The sera were characterized using indirect immunofluorescence assay (IFA) on HEp-2 cell substrates including two-color immunofluorescence using antigen-specific markers, western blot (WB), immunoprecipitation (IP), line immunoassay (LIA), addressable laser bead immunoassay (ALBIA), enzyme-linked immunosorbent assay (ELISA), and immunoprecipitation-mass spectrometry (IP-MS). Results: MND-REF stained 6-20 discrete nuclear dots that colocalized with PML bodies. Antibodies to Sp100 and PML were detected by LIA and antibodies to Sp100 were also detected by ELISA. GWB-REF stained discrete cytoplasmic dots in interphase cells, which were confirmed to be GWB using two-color immunofluorescence. Anti-Ge-1 antibodies were identified in GWB-REF by ALBIA, IP, and IP-MS. All reference materials produced patterns at dilutions of 1:160 or greater. NuMA-REF produced fine speckled nuclear staining in interphase cells and staining of spindle fibers and spindle poles. The presence of antibodies to NuMA was verified by IP, WB, ALBIA, and IP-MS. Conclusions: MND-REF, GWB-REF, and NuMA-REF are suitable reference materials for the corresponding antinuclear antibodies staining patterns and will be accessible to qualified laboratories.

Using adaptive genetic algorithms combined with high sensitivity single cell-based technology to detect bladder cancer in urine and provide a potential noninvasive marker for response to anti-PD1 immunotherapy.

OBJECTIVE: To use adaptive genetic algorithms (AGA) in combination with single-cell flow cytometry technology to develop a noninvasive test to detect bladder cancer. MATERIALS AND METHODS: Fifty high grade, cystoscopy confirmed, superficial bladder cancer patients, and 15 healthy donor early morning urine samples were collected in an optimized urine collection media. These samples were then used to develop an assay to distinguish healthy from cancer patients' urine using AGA in combination with single-cell flow cytometry technology. Cell recovery and test performance were verified based on cystoscopy and histology for both bladder cancer determination and PD-L1 status. RESULTS: Bladder cancer patients had a significantly higher percentage of white blood cells with substantial PD-L1 expression (P< 0.0001), significantly increased post-G1 epithelial cells (P < 0.005) and a significantly higher DNA index above 1.05 (P < 0.05). AGA allowed parameter optimization to differentiate normal from malignant cells with high accuracy. The resulting prediction model showed 98% sensitivity and 87% specificity with a high area under the ROC value (90%). CONCLUSIONS: Using single-cell technology and machine learning; we developed a new assay to distinguish bladder cancer from healthy patients. Future studies are planned to validate this assay.

Pandemia y ansiedad social / Pandemic and social anxiety

La pandemia del COVID-19 ha generado una crisis en el ser humano y en su contexto de cómo vivir ante lo desconocido, estableciendo parámetros de un desequilibrio de la salud mental y una reinvención de sostenimiento imaginario de lo incomprensible, desarticulando los esquemas socialmente aceptados y articulando modelos nuevos que le permitan al hombre continuar con la vida, encontrando formas de fortalecer al Eros y disminuir la proliferación de Thanatos. (AU)

The COVID-19 pandemic has generated a crisis in the human being and in its context of how to live in the face of the unknown, establishing parameters of an imbalance of mental health and a reinvention of imaginary maintenance of the incomprehensible, disarticulating socially accepted schemes and articulating new models that allow man to continue with life, finding ways to strengthen Eros and decrease the proliferation of Thanatos (AU)

¿El siglo de las luces? / The lights century?

El siglo de las luces es una reflexión sobre el excesivo racionalismo de la medicina actual frente a los problemas del inconsciente dejando de lado el análisis del inconsciente del sujeto y la posibilidad del sujeto de mirarse así mismo.

This paper is a reflection about the excessive rationalism of current medici-ne against the unconscious problems leaving aside the analysis of the un-conscious of the person and the possibility of the person to look at himself.

Establishment of an international autoantibody reference standard for human anti-DFS70 antibodies: proof-of-concept study for a novel Megapool strategy by pooling individual specific sera.

Background International autoantibody standards, traditionally based on material obtained from plasmapheresis of single subjects, represent individual immune response and may not comprehend the heterogeneity of the general population. The anti-DFS70 autoantibody yields a characteristic dense fine speckled (DFS) nuclear pattern on indirect immunofluorescence assay on HEp-2 cells (HEp-2 IFA) and speaks against autoimmunity. We propose a novel strategy for developing autoantibody reference standards, based on stepwise pooling of serum samples from hundreds of individuals with anti-DFS70 antibodies. Methods Within a 2-year period, serum samples were selected from routine HEp-2 IFA according to the following criteria: DFS HEp-2 IFA pattern at titer ≥1:640; anti-DFS70 reactivity in three analyte-specific tests (Western blot [WB], enzyme-linked immunosorbent assay [ELISA] and chemiluminescent immunoassay [CLIA]). Aliquots of individual samples were combined into progressively larger pools with stepwise validation of intermediary pools as for individual samples. Validated intermediary pools were merged into a final pool for lyophilization. Results A total of 741 validated samples yielded a 750 mL final pool that was lyophilized into thousands of 200 µL-aliquots. Reconstituted aliquots yielded the expected anti-DFS70 reactivity in ELISA, CLIA and WB, as well as high-titer DFS HEp-2 IFA pattern. The appropriate anti-DFS70 reactivity of the lyophilized pool was confirmed by seven international expert centers, using HEp-2 IFA, ELISA, WB and immunoprecipitation. Conclusions This proof-of-concept study provides an innovative and efficient strategy to build serum reference standards for autoantibody testing. The anti-DFS70 standard will integrate the panel of standards of Autoantibody Standardization Committee (ASC, www.autoab.org), contributing to education for proper assay validation and interpretation of the DFS pattern and other HEp-2 IFA patterns.

Emerging microRNAs in cancer diagnosis, progression, and immune surveillance.

MicroRNAs (miRNAs) are small noncoding RNAs that function in post-transcriptional regulation of gene expression. Dysregulation of miRNAs has been reported in different stages of cancer development and progression. This dysregulation results in different miRNA profiles between cancer and normal tissues. Many studies have shown a significant correlation between miRNA profile and cancer diagnosis and prognosis. Additionally, since a single miRNA regulates multiple mRNA targets, miRNAs dysregulation can affect several pathways involved in cancer development. Finally, due to their regulatory role in immune cell development, many recent studies have reported that certain miRNAs play key roles in cancer immunology. In this brief review, we discuss the role of miR-21 and miR-375 in the RAS pathway as well as their role in cancer diagnosis and progression, along with the role of other select miRNAs in cancer immune surveillance.

Implicancias en la actividad física y la salud del Programa CicloRecreoVía en Chile / Physical activity and health implications of the CicloRecreoVia program in Chile

Background: With approximately 66% of the population overweight and nearly 90% with sedentary lifestyles, obesity has become a major public health problem in Chile. Thus, in the last fifteen years health policies have promoted active lifestyles. An interesting initiative in this context is the CicloRecreoVia program, which closes a set of public streets on Sunday mornings, allowing people to carry out PA in streets free of vehicles. Aim: To characterize PA and mobility patterns of participants of the CicloRecreoVía program in Santiago. Material and Methods: 401 participants of five circuits of the CicloRecreoVia surveyed on the type, frequency and durantion of the PA carried out, their daily mobility habits, motivations for attending the CicloRecreoVia, self-perceived health condition, among other aspects. Results: Participants spent 113 minutes in the CicloRecreoVia, 77% declared walking or bicycling at least 10 minutes per day and 56.7% traveled actively (bicycling or walking) at least four times per week. Finally, 69.1% perceived their health condition "better" or "much better" than one year ago. In addition, it was noted that CicloRecreoVías attracted different type of participants depending on their location in the city. Conclusions: In line with previous studies, most users achieve about 75% of the weekly PA recommended by attending the CicloRecreoVía, and the main motivations to attend the program were to make PA, to be outdoor and to socialize. As a result, the CicloRecreoVía has the potential to become an effective public nationwide health policy to combat obesity.

Building a Personalized Cancer Treatment System.

This paper reports the process by which a personalized cancer treatment system was built, following a user-centered approach. We give some background on personalized cancer treatment, the particular tumor chemosensitivity assay supported by the system, as well as some quality and legal issues related to such health systems. We describe how Contextual Design was applied when building the system. Contextual design is a user-centered design technique involving seven steps. We also provide some details about the system implementation. Finally, we explain how the Think-Aloud protocol and Heuristic Evaluation methods were used to evaluate the system and report its results. A qualitative assessment from the users perspective is also provided. Results from the heuristic evaluation indicate that only one of ten heuristics was missing from the system, while five were partially covered and four were fully covered.

Outdoor gyms in Santiago: urban distribution and effects on physical activity

Abstract: Aims To put together a registry of the location of all existing outdoor gyms (OGs) in Santiago, Chile, and establish a profile of the users of these gyms. Methods: All OGs in Santiago located in public spaces were identified and geo-referenced, and an accessibility analysis of them was carried out. A total of 1,023 users of OGs were surveyed (71% men, average age 31.5 years old, SD =16.6), about the frequency of use of OGs, amount of time spent using them, transportation habits, motivation for usage, and their perceptions regarding their own health, among other questions. In addition, each person's neck circumference was measured. Results There are 1,981 OGs in the city squares, sidewalks and parks, mostly located in poorest areas of the city. Most OG users live less than one kilometer away from an OG. Discussion: In line with international studies, this research demonstrates that OGs have positive collateral effects, as they not only contribute to users to increase their physical activity, but also because they attract people with sedentary lifestyles to make physical activity. This, in turn, might contribute to make urban areas more livable and safer, for they bring new "eyes to the street" and permit to use cities' under-occupied public spaces. Conclusion: The proliferation of outdoor gyms should be regarded as an opportunity for public health policies aimed at tackling the obesity problem and increasing the physical activity of people.(AU)

Biopiracy of natural products and good bioprospecting practice.

BACKGROUND: Biopiracy mainly focuses on the use of biological resources and/or knowledge of indigenous tribes or communities without allowing them to share the revenues generated out of economic exploitation or other non-monetary incentives associated with the resource/knowledge. METHODS: Based on collaborations of scientists from five continents, we have created a communication platform to discuss not only scientific topics, but also more general issues with social relevance. This platform was termed 'PhytCancer -Phytotherapy to Fight Cancer' (www.phyt-cancer.uni-mainz.de). As a starting point, we have chosen the topic "biopiracy", since we feel this is of pragmatic significance for scientists working with medicinal plants. RESULTS: It was argued that the patenting of herbs or natural products by pharmaceutical corporations disregarded the ownership of the knowledge possessed by the indigenous communities on how these substances worked. Despite numerous court decisions in U.S.A. and Europe, several international treaties, (e.g. from United Nations, World Health Organization, World Trade Organization, the African Unity and others), sharing of a rational set of benefits amongst producers (mainly pharmaceutical companies) and indigenous communities is yet a distant reality. In this paper, we present an overview of the legal frameworks, discuss some exemplary cases of biopiracy and bioprospecting as excellent forms of utilization of natural resources. CONCLUSIONS: We suggest certain perspectives, by which we as scientists, may contribute towards prevention of biopiracy and also to foster the fair utilization of natural resources. We discuss ways, in which the interests of indigenous people especially from developing countries can be secured.

Percepción de la señalización y orientación espacial de los usuarios de tres complejos hospitalarios de Santiago, Chile / A survey about client orientation and wayfinding in Chilean hospitals

Background: Sense of orientation in hospitals can be tricky considering the large extension of buildings and the inadequate signage. Aim: To report some of the findings of a larger research project on wayfinding and patient navigation in Chilean hospitals. Material and Methods: Five hundred nine hospital users waiting for attention in three hospitals were contacted and asked to answer a survey that lasted 10 minutes, about wayfinding and sense of orientation within the hospital. Results: Users declared to have a good opinion of existing signage in the three hospitals analyzed as well as their architectural organization in terms of their capacity to orient people. However, the vast majority of users asked for directions to navigate within the hospital to staff and medical personnel. Conclusions: Patient navigation problems are imposing a great “hidden” cost to hospitals management due to missed appointments.

Where is my car? examining wayfinding behavior in a parking lot

This article examines wayfinding behavior in an extended parking lot belonging to one of the largest shopping malls in Santiago, Chile. About 500 people were followed while going to the mall and returning from it, and their trajectories were mapped and analyzed. The results indicate that inbound paths were, in average, 10% shorter that outbound paths, and that people stopped three times more frequently when leaving the mall than when accessing it. It is argued that these results are in line with previous research on the subject, which stress the importance of environmental information in shaping people`s behavior.

Internalization of Clostridium perfringens α-toxin leads to ERK activation and is involved on its cytotoxic effect.

Clostridium perfringens phospholipase C (CpPLC), also called α-toxin, plays a key role in the pathogenesis of gas gangrene. CpPLC may lead to cell lysis at concentrations that cause extensive degradation of plasma membrane phospholipids. However, at sublytic concentrations it induces cytotoxicity without inducing evident membrane damage. The results of this work demonstrate that CpPLC becomes internalized in cells by a dynamin-dependent mechanism and in a time progressive process: first, CpPLC colocalizes with caveolin both at the plasma membrane and in vesicles, and later it colocalizes with early and late endosomes and lysosomes. Lysosomal damage in the target cells is evident 9 h after CpPLC exposure. Our previous work demonstrated that CpPLCinduces ERK1/2 activation, which is involved in its cytotoxic effect. In this work we found that cholesterol sequestration, dynamin inhibition, as well as inhibition of actin polymerization, prevent CpPLC internalization and ERK1/2 activation, involving endocytosis in the signalling events required for CpPLC cytotoxic effect at sublytic concentrations. These results provide new insights about the mode of action of this bacterial phospholipase C, previously considered to act only locally on cell membrane.

[A survey about client orientation and wayfinding in Chilean hospitals]. / Percepción de la señalización y orientación espacial de los usuarios de tres complejos hospitalarios de Santiago, Chile.

BACKGROUND: Sense of orientation in hospitals can be tricky considering the large extension of buildings and the inadequate signage. AIM: To report some of the findings of a larger research project on wayfinding and patient navigation in Chilean hospitals. MATERIAL AND METHODS: Five hundred nine hospital users waiting for attention in three hospitals were contacted and asked to answer a survey that lasted 10 minutes, about wayfinding and sense of orientation within the hospital. RESULTS: Users declared to have a good opinion of existing signage in the three hospitals analyzed as well as their architectural organization in terms of their capacity to orient people. However, the vast majority of users asked for directions to navigate within the hospital to staff and medical personnel. CONCLUSIONS: Patient navigation problems are imposing a great "hidden" cost to hospitals management due to missed appointments.