GOCompare: An R package to compare functional enrichment analysis between two species.

Functional enrichment analysis is a cornerstone in bioinformatics as it makes possible to identify functional information by using a gene list as source. Different tools are available to compare gene ontology (GO) terms, based on a directed acyclic graph structure or content-based algorithms which are time-consuming and require a priori information of GO terms. Nevertheless, quantitative procedures to compare GO terms among gene lists and species are not available. Here we present a computational procedure, implemented in R, to infer functional information derived from comparative strategies. GOCompare provides a framework for functional comparative genomics starting from comparable lists from GO terms. The program uses functional enrichment analysis (FEA) results and implement graph theory to identify statistically relevant GO terms for both, GO categories and analyzed species. Thus, GOCompare allows finding new functional information complementing current FEA approaches and extending their use to a comparative perspective. To test our approach GO terms were obtained for a list of aluminum tolerance-associated genes in Oryza sativa subsp. japonica and their orthologues in Arabidopsis thaliana. GOCompare was able to detect functional similarities for reactive oxygen species and ion binding capabilities which are common in plants as molecular mechanisms to tolerate aluminum toxicity. Consequently, the R package exhibited a good performance when implemented in complex datasets, allowing to establish hypothesis that might explain a biological process from a functional perspective, and narrowing down the possible landscapes to design wet lab experiments.

[Clinical and microbiological characteristics of bloodstream infections in adult neutropenic patients]. / Características clínicas y microbiológicas de infecciones del torrente sanguíneo en pacientes adultos neutropénicos.

Bloodstream infections (BI) are relevant in neutropenic patients because they are associated with an increased number of complications and death. The objective was determinate the epidemiologic and microbiologic features of the BI in neutropenic patients with solid neoplasm (SN) and hematologic neoplasm (HN). Retrospective study in two third level hospitals between 2009 and 2016. They were included all the patients older than 18 years-old with active oncologic disease and neutropenia, who had BI. Patients with dermatologic cancer other than melanoma where excluded. A total of 143 BI in neutropenic were observed, of which 80.4% occurred in HN. Around 97.9% of the patients had a high-risk neutropenia without differences between both groups. The most frequent site of BI was primary bacteremia (46.9%) and catheter-associated infection (21%), without significant differences between the two groups. The gram negatives bacilli (GNB) predominated over the gram positive cocci (GPC) and they represented 74.1% of the isolated bacteria, being Escherichia coli the most frequent (32.8%). Among the gram positive cocci, Staphylococcus aureus (28.1%) was the most frequent isolated, followed by coagulase-negative Staphylococci (CNS). There were no differences in microbiological isolates between both groups. With regard to the antimicrobial susceptibility 67.5% of the CNS, 17.6% of the E. coli and 27.6% of the Klebsiella pneumoniae were multiresistant with no differences between both groups. Only 11.1% of S. aureus isolates were methicillin resistant. In conclusion BI of the neutropenic patients where most frequents within patients with HN, GNB were the main microbiological isolates. High mortality was observed in neutropenic patients with BI.

State of ex situ conservation of landrace groups of 25 major crops.

Crop landraces have unique local agroecological and societal functions and offer important genetic resources for plant breeding. Recognition of the value of landrace diversity and concern about its erosion on farms have led to sustained efforts to establish ex situ collections worldwide. The degree to which these efforts have succeeded in conserving landraces has not been comprehensively assessed. Here we modelled the potential distributions of eco-geographically distinguishable groups of landraces of 25 cereal, pulse and starchy root/tuber/fruit crops within their geographic regions of diversity. We then analysed the extent to which these landrace groups are represented in genebank collections, using geographic and ecological coverage metrics as a proxy for genetic diversity. We find that ex situ conservation of landrace groups is currently moderately comprehensive on average, with substantial variation among crops; a mean of 63% ± 12.6% of distributions is currently represented in genebanks. Breadfruit, bananas and plantains, lentils, common beans, chickpeas, barley and bread wheat landrace groups are among the most fully represented, whereas the largest conservation gaps persist for pearl millet, yams, finger millet, groundnut, potatoes and peas. Geographic regions prioritized for further collection of landrace groups for ex situ conservation include South Asia, the Mediterranean and West Asia, Mesoamerica, sub-Saharan Africa, the Andean mountains of South America and Central to East Asia. With further progress to fill these gaps, a high degree of representation of landrace group diversity in genebanks is feasible globally, thus fulfilling international targets for their ex situ conservation.

[Bloodstream infections in cancer patients]. / Infecciones del torrente sanguíneo en pacientes oncológicos.

Bloodstream infections (BI) are an important cause of morbidity and mortality in cancer patients. A retrospective study was performed in two hospitals aimed to evaluate characteristics of BI episodes occurred in adult patients with hematologic (HN) and solid (SN) neoplasia other than non-melanoma skin cancers in the period 2009-2016. A total of 467 episodes of bacteremia and 16 of fungemia were identified. A total of 200 (41.4%) bacteremias occurred in patients with HN and 283 (58.6%) in patients with SN. The most frequent SN and HN were colon cancer (18.7%) and non-Hodgkin lymphoma (27%), respectively. The main risk factors for BI were a previous surgical procedure in SN and chemotherapy in the previous 30 days and use of central venous catheter in HN. Infections were mainly acquired in the hospital environment and the most frequent presentation was bacteremia without focus, mostly in HN (38% vs. 20.8%, p < 0.001). Gram negative bacilli (GNB) were isolated in 336 (69.5%) episodes and predominated over Gram positive cocci (GPC) in both groups. Escherichia coli was the most frequent GNB isolated in both SN (24.7%) and HN patients (20.5%). The most frequent GPC was Staphylococcus aureus. Multidrug-resistance was found in 15% of the isolates in SN and 18% in HN. The overall mortality was 40.5% in patients with HN and 37.5% in patients with SN, with the majority of deaths occurring in the first 30 days.

Las infecciones del torrente sanguíneo (ITS) son una importante causa de morbimortalidad en pacientes oncológicos. Los objetivos del estudio fueron evaluar las características de las ITS en pacientes con neoplasia hematológica (NH) y sólida (NS) en un estudio retrospectivo realizado en dos hospitales, entre 2009 y 2016. Fueron incluidos todos los episodios de ITS en adultos con neoplasias activas, excepto cáncer de piel no melanoma. Fueron identificados 467 episodios de bacteriemia y 16 de fungemia. Un total de 200 (41.4%) bacteriemias ocurrieron en pacientes con NH y 283 (58.6%) en pacientes con NS. Las NS y NH más frecuentes fueron cáncer de colon (18.7%) y linfoma no Hodgkin (27%), respectivamente. Los principales factores de riesgo de ITS fueron el antecedente de procedimiento quirúrgico para NS y quimioterapia en los 30 días previos y uso de catéter venoso central para NH. Las infecciones fueron adquiridas principalmente en el medio intrahospitalario y la presentación más frecuente fue la bacteriemia sin foco, fundamentalmente en NH (38.0% vs. 20.8%, p < 0.001). En un total de 336 (69.5%) aislamientos predominaron bacilos Gram negativos (BGN) sobre cocos Gram positivos (CGP) sin diferencias entre grupos. Escherichia coli fue el BGN más frecuente en NS (24.7%) y NH (20.5%). El CGP más frecuente fue Staphylococcus aureus. El 15% y el 18% de los aislamientos fue multirresistente en NS y NH, respectivamente. La mortalidad global fue 40.5% en pacientes con NH y 37.5% en pacientes con NS. La mayoría de las muertes ocurrió en los primeros 30 días.

Data for the calculation of an indicator of the comprehensiveness of conservation of useful wild plants.

The datasets and code presented in this article are related to the research article entitled "Comprehensiveness of conservation of useful wild plants: an operational indicator for biodiversity and sustainable development targets"1. The indicator methodology includes five main steps, each requiring and producing data, which are fully described and available here. These data include: species taxonomy, uses, and general geographic information (dataset 1); species occurrence data (dataset 2); global administrative areas data (dataset 3); eco-geographic predictors used in species distribution modeling (dataset 4); a world map raster file (dataset 5); species spatial distribution modeling outputs (dataset 6); ecoregion spatial data used in conservation analyses (dataset 7); protected area spatial data used in conservation analyses (dataset 8); and countries, sub-regions, and regions classifications data (dataset 9). These data are available at http://dx.doi.org/10.17632/2jxj4k32m2.1. In combination with the openly accessible methodology code (https://github.com/CIAT-DAPA/UsefulPlants-Indicator), these data facilitate indicator assessments and serve as a baseline against which future calculations of the indicator can be measured. The data can also contribute to other species distribution modeling, ecological research, and conservation analysis purposes.

La potencia de los espacios colectivos como estrategia frente a la vulneración de derechos / O poder dos espaços coletivos como estratégia contra a violação de direitos / The power of collective spaces as a strategy against the violation of rights

Resumen Se propone desarrollar la articulación entre los aportes teórico-metodológicos de la terapia ocupacional social y la experiencia de los proyectos Timbó em Movimento y ResisTO, dentro del núcleo de la Rede Metuia perteneciente a la Universidad Federal de Paraíba, Brasil. Se reconoce la importancia de las prácticas territoriales y del campo de la terapia ocupacional social para el fortalecimiento y acompañamiento a poblaciones con diversas condiciones de vulnerabilidad. Se articula lo observado en los proyectos Timbó em Movimento y ResisTO con conceptos como la interseccionalidad de los marcadores sociales de diferencia, sus implicancias en el derecho a la ciudad y sus efectos en el cotidiano de los jóvenes. Se desarrolla la implicancia de los marcadores sociales en los cotidianos de les participantes, así como el potencial de los espacios colectivos de referencia y la articulación intersectorial para enfrentar las violencias. Se concluye que los espacios de pertenencia poseen gran relevancia para el abordaje de conflictos en el campo social, potenciando la participación de les sujetes y el ejercicio de ciudadanía, rechazando la tendencia de buscar soluciones individuales a problemáticas colectivas. Se identifica el desafío de llevar estos diálogos a los contextos cotidianos en que las violencias tienen lugar, incorporando actores que también puedan estar involucrados en su reproducción.

Resumo Propõe-se desenvolver a articulação entre as contribuições teórico-metodológicas da terapia ocupacional social e a experiência dos projetos Timbó em Movimento e ResisTO, dentro do núcleo da Rede Metuia pertencente à Universidade Federal da Paraíba, Brasil. Reconhece-se a importância das práticas territoriais e do campo da terapia ocupacional social para o fortalecimento e acompanhamento de populações com diversas condições de vulnerabilidade. Articula-se a prática dos projetos Timbó em Movimento e ResisTO com conceitos como a interseccionalidade dos marcadores sociais da diferença, suas implicações para o direito à cidade e seus efeitos no cotidiano dos jovens. Desenvolve-se a implicação dos marcadores sociais nos cotidianos dos participantes, assim como o potencial dos espaços coletivos de referência e a articulação intersetorial para o enfrentamento das violências. Conclui-se que os espaços de pertencimento têm grande relevância para o enfrentamento de conflitos no campo social, promovendo a participação dos sujeitos e o exercício da cidadania, rejeitando a tendência de buscar soluções individuais para problemas coletivos. Identifica-se o desafio de levar esses diálogos aos contextos cotidianos em que as violências ocorrem, incorporando atores que também podem estar envolvidos em sua reprodução.

Abstract This paper articulates the theoretical-methodological contributions of social occupational therapy and the experience of "Timbó em Movimento'' and "ResisTO" projects, which are part of the Rede Metuia nucleus belonging to the Federal University of Paraíba (UFPB), Brazil. It recognizes the importance of territorial practices and the social occupational therapy field for the strengthening and support of populations with diverse conditions of vulnerability. Articulation of what was observed in the Timbó em Movimento and ResisTO projects with concepts such as the intersectionality of social markers of difference, their implications for the right to the city and their effects in the daily life of youths. The article elaborates the implications of social markers in the daily life of the participants, as well as the potential of collective reference spaces and intersectoral articulation to confront violence. It is concluded that the spaces of belonging have great relevance for addressing conflicts in the social field, promoting the participation of people and the exercise of citizenship, rejecting the tendency to seek individual solutions to collective problems. Remains the challenge of taking these dialogues to the daily contexts in which violence takes place, incorporating actors that may also be involved in its reproduction.

Paediatric out-of-hospital resuscitation in an area with scattered population (Galicia-Spain).

BACKGROUND: Cardiorespiratory arrest (CRA) is a rare event in childhood. Our objective was to determine the characteristics of paediatric CRA and the immediate results of cardiopulmonary resuscitation (CPR) in Galicia, a community with a very scattered population. METHODS: All children (aged from newborn to 16 years old) who suffered an out-of-hospital CRA in Galicia and were assisted by the Public Foundation Medical Emergencies of Galicia-061 staff, from June 2002 to February 2005, were included in the study. Data were prospectively recorded following the Utstein's style guidelines. RESULTS: Thirty-one cases were analyzed (3.4 CRA annual cases per 100,000 paediatric population). The arrest was respiratory in 16.1% and cardiac in 83.9% of cases. CRA occurred at home in 58.1% of instances. Time CRA to initiation of CPR was shorter than 10 minutes in 32.2% and longer than 20 minutes in 29.0% of cases. 22.6% of children received bystander CPR. The first recorded rhythm was asystole in 67.7% of cases. Bag-mask ventilation was used in 67.7% and in 83.8% oro-tracheal intubation was done. A peripheral venous access was achieved in 67.7% and intraosseous access was used in 16.1% of patients. 93.5% of children were treated with adrenaline. After initial CPR, sustained restoration of spontaneous circulation was achieved in 38.7% of cases. Six children (19.4%) survived until hospital discharge. Four of 5 children with respiratory arrest survived, whereas only 2 of 26 children with cardiac arrest survived until hospital discharge. CONCLUSION: Despite the handicap of a highly disseminated population, paediatric CRA characteristics and CPR results in Galicia are comparable to references from other communities. Programs to increase bystander CPR, equip laypeople with basic CPR skills and to update life support knowledge of health staff are needed to improve outcomes.

Cost-efficiency assessment of Advanced Life Support (ALS) courses based on the comparison of advanced simulators with conventional manikins.

BACKGROUND: Simulation is an essential tool in modern medical education. The object of this study was to assess, in cost-effective measures, the introduction of new generation simulators in an adult life support (ALS) education program. METHODS: Two hundred fifty primary care physicians and nurses were admitted to ten ALS courses (25 students per course). Students were distributed at random in two groups (125 each). Group A candidates were trained and tested with standard ALS manikins and Group B ones with new generation emergency and life support integrated simulator systems. RESULTS: In group A, 98 (78%) candidates passed the course, compared with 110 (88%) in group B (p < 0.01). The total cost of conventional courses was euro 7689 per course and the cost of the advanced simulator courses was euro 29034 per course (p < 0.001). Cost per passed student was euro 392 in group A and euro 1320 in group B (p < 0.001). CONCLUSION: Although ALS advanced simulator systems may slightly increase the rate of students who pass the course, the cost-effectiveness of ALS courses with standard manikins is clearly superior.

Características clínicas y microbiológicas de infecciones del torrente sanguíneo en pacientes adultos neutropénicos / Clinical and microbiological characteristics of bloodstream infections in adult neutropenic patients

RESUMEN Las infecciones del torrente sanguíneo (IS) en pacientes oncológicos neutropénicos constituyen una patología de relevancia y se asocian a un aumento de la morbimortalidad. El objetivo de este estudio fue determinar las características epidemiológicas y microbiológicas de los episodios de IS en pacientes adultos neutropénicos con neoplasias hematológicas (NH) y neoplasias sólidas (NS). Se realizó un estudio retrospectivo en dos hospitales de tercer nivel entre 2009 y 2016. Se incluyeron todos los pacientes neutropénicos mayores de 18años con NH y NS que presentaron episodios de IS. Se excluyeron aquellos con neoplasias dermatológicas no melanoma. Se identificaron 143 episodios de IS, de los cuales el 80,4% fueron en personas con NH. El 97,9% de los pacientes tuvieron neutropenia de alto riesgo, sin diferencia entre los grupos NH y NS. Los orígenes más frecuentes de IS fueron bacteriemia primaria (46,9%) e infección asociada a catéter (21%), sin diferencias significativas entre grupos. El 74,1% de los aislamientos fueron bacilos gram negativos yEscherichiacolifue el microorganismo más frecuente (32,1%). El coco gram positivo más frecuentemente aislado fueStaphylococcusaureus(28,1%), seguido del grupo de los estafilococos coagulasa negativos (ECN), sin diferencias entre ambos tipos de neoplasias. El 67,5% de los ECN fueron multirresistentes; solo el 11,1% de los aislamientos deS. aureusfue resistente a la meticilina. El 17,6% de los aislamientos deE. coliy el 27,6% de los deKlebsiellapneumoniaefueron multirresistentes. No hubo diferencias en la frecuencia de aislamientos multirresistentes al comparar entre ambos tipos de neoplasia. Como conclusión, las IS en pacientes neutropénicos fueron más frecuentes en pacientes con NH y las causaron, principalmente, bacilos gram negativos. Se observó una elevada mortalidad en los pacientes neutropénicos con IS.

ABSTRACT Bloodstream infections (BI) are relevant in neutropenic patients because they are associated with an increased number of complications and death. The objective was determinate the epidemiologic and microbiologic features of the BI in neutropenic patients with solid neoplasm (SN) and hematologic neoplasm (HN). Retrospective study in two third level hospitals between 2009 and 2016. They were included all the patients older than 18 years-old with active oncologic disease and neutropenia, who had BI. Patients with dermatologic cancer other than melanoma where excluded. A total of 143 BI in neutropenic were observed, of which 80.4% occurred in HN. Around 97.9% of the patients had a high-risk neutropenia without differences between both groups. The most frequent site of BI was primary bacteremia (46.9%) and catheter-associated infection (21%), without significant differences between the two groups. The gram negatives bacilli (GNB) predominated over the gram positive cocci (GPC) and they represented 74.1% of the isolated bacteria, beingEscherichia colithe most frequent (32.8%). Among the gram positive cocci,Staphylococcus aureus(28.1%) was the most frequent isolated, followed by coagulase-negativeStaphylococci(CNS). There were no differences in microbiological isolates between both groups. With regard to the antimicrobial susceptibility 67.5% of the CNS, 17.6% of theE. coliand 27.6% of theKlebsiella pneumoniaewere multiresistant with no differences between both groups. Only 11.1% of S. aureus isolates were methicillin resistant. In conclusion BI of the neutropenic patients where most frequents within patients with HN, GNB were the main microbiological isolates. High mortality was observed in neutropenic patients with BI.

Bloodstream infections in cancer patients / Artículo original

Resumen Las infecciones del torrente sanguíneo (ITS) son una importante causa de morbimortalidad en pacientes oncológicos. Los objetivos del estudio fueron evaluar las características de las ITS en pacientes con neoplasia hematológica (NH) y sólida (NS) en un estudio retrospectivo realizado en dos hospitales, entre 2009 y 2016. Fueron incluidos todos los episodios de ITS en adultos con neoplasias activas, excepto cáncer de piel no melanoma. Fueron identificados 467 episodios de bacteriemia y 16 de fungemia. Un total de 200 (41.4%) bacteriemias ocurrieron en pacientes con NH y 283 (58.6%) en pacientes con NS. Las NS y NH más frecuentes fueron cáncer de colon (18.7%) y linfoma no Hodgkin (27%), respectivamente. Los principales factores de riesgo de ITS fueron el antecedente de procedimiento quirúrgico para NS y quimioterapia en los 30 días previos y uso de catéter venoso central para NH. Las infecciones fueron adquiridas principalmente en el medio intrahospitalario y la presentación más frecuente fue la bacteriemia sin foco, fundamentalmente en NH (38.0% vs. 20.8%, p < 0.001). En un total de 336 (69.5%) aislamientos predominaron bacilos Gram negativos (BGN) sobre cocos Gram positivos (CGP) sin diferencias entre grupos. Escherichia coli fue el BGN más frecuente en NS (24.7%) y NH (20.5%). El CGP más frecuente fue Staphylococcus aureus. El 15% y el 18% de los aislamientos fue multirresistente en NS y NH, respectivamente. La mortalidad global fue 40.5% en pacientes con NH y 37.5% en pacientes con NS. La mayoría de las muertes ocurrió en los primeros 30 días.

Abstract Bloodstream infections (BI) are an important cause of morbidity and mortality in cancer patients. A retrospective study was performed in two hospitals aimed to evaluate characteristics of BI episodes occurred in adult patients with hematologic (HN) and solid (SN) neoplasia other than non-melanoma skin cancers in the period 2009-2016. A total of 467 episodes of bacteremia and 16 of fungemia were identified. A total of 200 (41.4%) bacteremias occurred in patients with HN and 283 (58.6%) in patients with SN. The most frequent SN and HN were colon cancer (18.7%) and non-Hodgkin lymphoma (27%), respectively. The main risk factors for BI were a previous surgical procedure in SN and chemotherapy in the previous 30 days and use of central venous catheter in HN. Infections were mainly acquired in the hospital environment and the most frequent presentation was bacteremia without focus, mostly in HN (38% vs. 20.8%, p < 0.001). Gram negative bacilli (GNB) were isolated in 336 (69.5%) episodes and predominated over Gram positive cocci (GPC) in both groups. Escherichia coli was the most frequent GNB isolated in both SN (24.7%) and HN patients (20.5%). The most frequent GPC was Staphylococcus aureus. Multidrug-resistance was found in 15% of the isolates in SN and 18% in HN. The overall mortality was 40.5% in patients with HN and 37.5% in patients with SN, with the majority of deaths occurring in the first 30 days.

Hipoacusia neurosensorial adquirida asociada a alteraciones vestibulares y / o control postural / Neurosensorial acquired hypoacusia associated with vestibular alterations and / or postural control

La otitis media aguda es una infección del oído medio con alta prevalencia en población pediátrica, las complicaciones pueden generar desde hipoacusia neurosensorial de diverso grado hasta alteración vestibular y/o control postural, aunque de ello no existen mayores reportes ni investigaciones en Chile. Por lo anterior, el objetivo fue asociar la hipoacusia neurosensorial a alteraciones vestibulares y/o de control postural. Se evaluó a un sujeto de sexo femenino, 13 años de edad, quien presentó múltiples cuadros de Otitis Media Aguda y fue diagnosticada con hipoacusia neurosensorial bilateral grado moderado. Antes del estudio, reportó desequilibrio y aumento de riesgo de caída. Se aplicaron test auditivos (timpanometría y audiometría), vestibulares (evaluación del VIII par craneal) y de control postural (posturógrafo y tests "Time up and go", Romberg y Romberg en tándem). Se encontraron alteradas la prueba de integración sensorial, con predominancia del hemicuerpo derecho, igualmente predominancia a alteraciones auditivas en el oído derecho ante pruebas que valoraron oído medio. Se observó una relación directa entre las alteraciones posturales y de equilibrio con el tipo y grado de pérdida auditiva que presenta el sujeto de estudio.

The acute otitis media is a middle ear infection with high prevalence in pediatric population, the complications could generate from sensorineural hearing loss to vestibular alteration and/or postural control, although, there aren´t report or researches of it in Chile. Therefore, the objective was to associate sensorineural hearing loss with vestibular alterations and/or postural control. We evaluated a female subject presenting multiple events of acute otitis media and she was diagnosed with sensorineural hearing loss middle grade. Before this study, she reported imbalance and falling risk. Hearing (tympanometry and audiometry), vestibular (evaluation of the VIII cranial nerve) and postural control tests were applied (posturography and "Time up and go", Romberg and Romberg in tandem test). It was found altered the integration sensorial test, with predominance to half body right and predominance of hearing impairment in the right ear to the middle ear evaluated evidence. It was observed a direct relation between postural alterations and balance with the hearing loss type from the subject of study.