A sentence sliding window approach to extract protein annotations from biomedical articles

From A critical assessment of text mining methods in molecular biology[Background] Within the emerging field of text mining and statistical natural language processing (NLP) applied to biomedical articles, a broad variety of techniques have been developed during the past years. Nevertheless, there is still a great ned of comparative assessment of the performance of the proposed methods and the development of common evaluation criteria. This issue was addressed by the Critical Assessment of Text Mining Methods in Molecular Biology (BioCreative) contest. The aim of this contest was to assess the performance of text mining systems applied to biomedical texts including tools which recognize named entities such as genes and proteins, and tools which automatically extract protein annotations.[Results] The "sentence sliding window" approach proposed here was found to efficiently extract text fragments from full text articles containing annotations on proteins, providing the highest number of correctly predicted annotations. Moreover, the number of correct extractions of individual entities (i.e. proteins and GO terms) involved in the relationships used for the annotations was significantly higher than the correct extractions of the complete annotations (protein-function relations).[Conclusion] We explored the use of averaging sentence sliding windows for information extraction, especially in a context where conventional training data is unavailable. The combination of our approach with more refined statistical estimators and machine learning techniques might be a way to improve annotation extraction for future biomedical text mining applications.This work was sponsored by DOC, the doctoral scholarship programme of the Austrian Academy of Sciences and the ORIEL (IST-2001-32688) and TEMBLOR (QLRT-2001-00015) projects.Peer reviewe

SAP, Change Management and Process Development Effetiveness (II): Case Study

Last year, at AIS ́98 (Pérez and Rojas, 1998), a series of variables was presented to measure the influence of change management on the effectiveness of the Information Systems development process. This proposal was based on the analysis of possible factors, which affect the Process Effectiveness dimension. The Process Effectiveness dimension is one of the four dimensions included in the Systemic Global Quality vision. The other dimensions included in that vision is: Product Effectiveness, Product Efficiency and Process Efficiency (Callaos and Callaos, 1996). This paper presents the results of a case study performed in a company of the oil- producing sector and is focused on measuring Process Effectiveness in the implementation of three SAP/r3 modules (Sales, Materials and Finance). The results participating in the process in roles such as the Leaders and End Users. No evidence was found on the rest of the showed that there is a correlation between the Change Management factor and Process Effectiveness in the personnel personnel - the technicians and functional users. This research represented a contribution to the organization subject to the study on the improvement of the Process Effectiveness for the development of its Information Systems

La percepción vecinal acerca de los grandes proyectos inmobiliarios: el caso de Ciudad Progresiva en Xoco

121 páginas. Maestría en Planeación y Políticas Metropolitanas.En el presente trabajo se desarrolla un estudio de caso, que tiene como escenario uno de los pueblos urbanos que aún existen en la Ciudad de México: Xoco. Este territorio posee una de las 11 zonas patrimoniales localizadas en la Delegación Benito Juárez que, a pesar de las continuas transformaciones urbanas, aún conserva su riqueza identitaria y su valor histórico. El periodo de tiempo en el que se contextualiza este trabajo es, de la década de 1980, a la fecha, ya que desde entonces, este territorio ha recibido una fuerte presión de cambio de uso del suelo que, progresivamente ha promovido su destrucción física, simbólica y social. Fue en el año 2000, Xoco se convirtió en un escenario importante de grandes proyectos urbanos, derivados de la globalización, que pretendieron revalorizar el suelo, al generar un cambio en las densidades y usos de la zona. En este tenor, en 2008 llega el megaproyecto Ciudad Progresiva, cuyo principal objetivo fue desarrollar una Torre de 60 niveles, destinada a promover vivienda, oficinas, comercios y servicios de lujo, acción que detonó un fuerte conflicto urbano entre los habitantes de la zona y los desarrolladores del proyecto que, a la fecha no ha podido ser conciliado por las autoridades de la ciudad. El presente trabajo describe el impacto físico, social y simbólico en espacios locales e intenta comprender ¿Por qué hay un rechazo ciudadano a la construcción de megaproyectos? Partiendo del supuesto de que las identidades colectivas marcan pautas de aprobación y desaprobación hacia tendencias de la globalización. El aporte de este trabajo es que, a pesar de que Xoco posee una identidad fragmentada y compleja, producto de la globalización económica, que ha avanzado en detrimento de las identidades colectivas tradicionales, también ha inducido el surgimiento de identidades modernas interesadas en conformarse como una ciudadanía activa, informada e interesada en lo público y en la exigibilidad y el cumplimiento de los derechos ciudadanos, capaz de incidir en la creación de mecanismos de inclusión social y transparencia en la toma de decisiones en materia de desarrollo urbano

Association between Sociodemographic Factors and Abuse by a Parent or Intimate Partner Violence among Haitian Women: A Population-Based Study

One in three Haitian women, and two in three Haitian children, experience physical abuse. This study aims to assess characteristics of abused Haitian women and identify effective sources of support. This cross-sectional study used multiple logistic regression models to analyze sociodemographic characteristics of Haitian women, associations with abuse-exposure from a parent/intimate partner (IPV)/any perpetrator, and impacts of seeking help for abuse, from police/doctors/family. About 9.1% experienced abuse by a parent, 8.6% from IPV. Women abused by a parent were less likely to be employed (OR = 0.74, [95% CI = 0.59–0.93]) and more likely to have an often-drunk partner (2.10, [1.54–2.87]). IPV-exposed women were more likely to have primary education (1.56, [1.12–2.16]), an often-drunk partner (3.07, [2.24–4.22]) and less likely to live rurally (0.65, [0.47–0.89]). Seeking help from own family for IPV exposure was strongly associated with having a job (2.00, [1.04–3.89]) (P for interaction = 0.039) and seeking help from partner’s family for IPV was strongly associated with having an often-drunk husband (8.80, [3.07–25.23]) (p for interaction <0.001). We recommend family-based interventions targeting men’s perceptions about abuse and their alcohol consumption, introducing programs/policies integrating women into the workforce, and havens for abuse victims to confidentially receive individualized support.S

Track My Ride

Cycling has become more and more popular as a healthy activity and a transport option across many countries. This is not different in Ireland, a country where in April 2016, 56,837 people cycled to work; an increase of 43% since 2011 (Central statistics office, 2017). Irish Government “committed to developing cycling as one of the most desirable modes of travel by 2020” as it plays an indispensable role in people’s lives (Sustainable transport division - department of transport, tourism and sport, 2009). The “Balance” team managed to visualize that a strong cycling culture was becoming important in Ireland. Hence our team was seeking to develop a mobile application called “Track my Ride” to contribute to the cycling community whilst by answering a crucial question: How can a cyclist manage and store its bike details? Answering that question, we have intended provide tools where the cyclists could discard common concerns such as: ● Is this second-hand bike reported as missing? ● Is there any bike parking space near a specific location? ● How can I warn people if my bike goes missing? Track My Ride is a bike management tool for bike-users, previous and/or future bike owners. Our main objective is to facilitate the way people manage and use their bikes, enhancing the cyclists experience while building an active online and collaborative cycling community

KLRF1, a novel marker of CD56bright NK cells, predicts improved survival for patients with locally advanced bladder cancer

Background Bladder tumor-infiltrating CD56bright NK cells are more tumor cytotoxic than their CD56dim counterparts. Identification of NK cell subsets is labor-intensive and has limited utility in the clinical setting. Here, we sought to identify a surrogate marker of bladder CD56bright NK cells and to test its prognostic significance. Methods CD56bright and CD56dim NK cells were characterized with the multiparametric flow (n = 20) and mass cytometry (n = 21) in human bladder tumors. Transcriptome data from bladder tumors (n = 351) profiled by The Cancer Genome Atlas (TCGA) were analyzed. The expression levels of individual markers in intratumoral CD56bright and CD56dim NK cells were visualized in tSNE plots. Expressions of activation markers were also compared between Killer Cell Lectin-Like Receptor Subfamily F Member 1 (KLRF1)+ and KLRF1− NK cells. Results Intratumoral CD56bright NK cells displayed a more activated phenotype compared to the CD56dim subset. Multiple intratumoral cell types expressed CD56, including bladder tumor cells and nonspecific intratumoral CD56 expression was associated with worse patient survival. Thus, an alternative to CD56 as a marker of CD56bright NK cells was sought. The activation receptor KLRF1 was significantly increased on CD56bright but not on CD56dim NK cells. Intratumoral KLRF1+ NK cells were more activated and expressed higher levels of activation molecules compared with KLRF1− NK cells, analogous to the distinct effector function of NK cells across CD56 expression. High intratumoral KLRF1 was associated with improved recurrence-free survival (hazard ratio [HR] 0.53, p = 0.01), cancer-specific survival (HR 0.47, p = 0.02), and overall survival (HR 0.54, p = 0.02) on multivariable analyses that adjusted for clinical and pathologic variables. Conclusions KLRF1 is a promising prognostic marker in bladder cancer and may guide treatment decisions upon validation

La imagen y la narrativa como herramientas para el abordaje psicosocial de los escenarios de violencia. Municipios de Córdoba y Sucre

Desde el diplomado de acompañamiento psicosocial en escenarios de violencia, se logró reconocer y observar de manera minuciosa y profunda las diferentes realidades en la que vivimos muchas poblaciones en diferentes territorios de nuestro país, por tanto a través del análisis de cada una de esas realidades, se comprendieron las diferentes problemáticas sociales que trae consigo la violencia, todo esto por medio de la herramienta foto voz, que accede y deja ver el problema desde afuera, también proporciona conocerlo desde adentro como si fuera propio, lo cual es muy importante porque da la posibilidad que, como psicólogos en formación se puedan analizar dichos contextos para así crear estrategias de acompañamiento psicosocial, las cuales son fundamentales para mitigar en gran manera ese daño o trauma psicosocial o sufrimiento emocional producido por la violencia pero también, de crear y potencializar recursos de afrontamiento que permiten superar la crisis de sufrimiento que le ha dejado este fenómeno. Desde este modo, y teniendo en cuenta la narrativa, se analiza el caso de Ana Ligia, una mujer que sufrió el desalojo, desplazamiento dos veces por la intimidación, el terror, la violencia, le toco vivir muchos momentos de estrés, angustia, de desesperación y miedo, pero esto no le impidió que tuviera una actitud resiliente y pudiera seguir adelante. Seguido, se analiza el caso de Peñas coloradas, donde se analizan los emergentes psicosociales que aún siguen latentes tras el hostigamiento de los grupos armados, pero a su vez se comparten acciones de apoyo las cuales les permitirán superar el impacto generado por el destierro que sufrió la población.From the psychosocial accompaniment course in scenes of violence, it was possible to recognize and observe in a meticulous and profound way the different realities in which many populations live in different territories of our country, therefore through the analysis of each one of these realities, the different social problems that violence brings with it were understood, all this through the photovoice tool, which accesses and allows the problem to be seen from the outside, it also provides knowledge of it from the inside as if it were ones own, which is very important because it gives the possibility that, as psychologists in training, these contexts can be analyzed in order to create psychosocial support strategies, which are essential to greatly mitigate that damage or psychosocial trauma or emotional suffering caused by violence, but also to create and potentiate support resources. Coping that allow to overcome the crisis of suffering that has left this phenomenon. From this way, and taking into account the narrative, the case of Ana Ligia is analyzed, a woman who suffered eviction, displacement twice due to intimidation, terror, violence, she had to experience many moments of stress, anguish, despair and fear, but this did not prevent him from having a resilient attitude and being able to move on. Next, the case of Peñas coloradas is analyzed, where the psychosocial emergents that are still latent after the harassment by the armed groups are analyzed, but at the same time support actions are shared which will allow them to overcome the impact generated by the exile they suffered. The population

Lung ultrasound as a translational approach for non-invasive assessment of heart failure with reduced or preserved ejection fraction in mice

Aims: Heart failure (HF) has become an epidemic and constitutes a major medical, social, and economic problem worldwide. Despite advances in medical treatment, HF prognosis remains poor. The development of efficient therapies is hampered by the lack of appropriate animal models in which HF can be reliably determined, particularly in mice. The development of HF in mice is often assumed based on the presence of cardiac dysfunction, but HF itself is seldom proved. Lung ultrasound (LUS) has become a helpful tool for lung congestion assessment in patients at all stages of HF. We aimed to apply this non-invasive imaging tool to evaluate HF in mouse models of both systolic and diastolic dysfunction. Methods and results: We used LUS to study HF in a mouse model of systolic dysfunction, dilated cardiomyopathy, and in a mouse model of diastolic dysfunction, diabetic cardiomyopathy. LUS proved to be a reliable and reproducible tool to detect pulmonary congestion in mice. The combination of LUS and echocardiography allowed discriminating those mice that develop HF from those that do not, even in the presence of evident cardiac dysfunction. The study showed that LUS can be used to identify the onset of HF decompensation and to evaluate the efficacy of therapies for this syndrome. Conclusions: This novel approach in mouse models of cardiac disease enables for the first time to adequately diagnose HF non-invasively in mice with preserved or reduced ejection fraction, and will pave the way to a better understanding of HF and to the development of new therapeutic approaches.This study was supported by grants from the Spanish Ministerio de Economia y Competitividad (SAF2015-65722-R), Comunidad Autonoma de Madrid (2010-BMD2321, FIBROTEAM Consortium), European Union's FP7 (CardioNeT-ITN-289600, CardioNext-ITN-608027) and the Spanish Instituto de Salud Carlos III (CPII14/00027 to E.L-P, RD12/0042/0054 to B.I. and RD12/0042/066 to P.G.-P. and E.L-P). This work was also supported by the Plan Estatal de I+D+I 2013-2016 - European Regional Development Fund (FEDER) "A way of making Europe", Spain. The CNIC is supported by the Ministry of Economy, Industry and Competitiveness (MINECO) and the Pro CNIC Foundation, and is a Severo Ochoa Center of Excellence (MINECO award SEV-2015-0505).S

Design, Development and Initial Validation of a Wearable Particulate Matter Monitoring Solution

Air pollution in one of the main problems that big cities have nowadays. Traffic congestion, heaters, industrial activities, among others produce large quantities of Particulate Matter (PM) that have harmful effects on citizens health. This paper presents the design, development and initial validation of a wearable device for the detection of PM concentration, with communication capacity via WiFi and Bluetooth Low Energy and an end user interface. The results are promising due to the high accuracy of measurements collected by the developed device. This solution is a step forward in empowering citizens to prevent being exposed to high levels of air pollution and is the beginning of what could be a macro-network of air quality sensors within a Smart City. Document type: Part of book or chapter of boo

Activation of Serine One-Carbon Metabolism by Calcineurin A beta 1 Reduces Myocardial Hypertrophy and Improves Ventricular Function

BACKGROUND In response to pressure overload, the heart develops ventricular hypertrophy that progressively decompensates and leads to heart failure. This pathological hypertrophy is mediated, among others, by the phosphatase calcineurin and is characterized by metabolic changes that impair energy production by mitochondria. OBJECTIVES The authors aimed to determine the role of the calcineurin splicing variant CnA beta 1 in the context of cardiac hypertrophy and its mechanism of action. METHODS Transgenic mice overexpressing CnAb1 specifically in cardiomyocytes and mice lacking the unique C-terminal domain in CnA beta 1 (CnA beta 1(Delta i12) mice) were used. Pressure overload hypertrophy was induced by transaortic constriction. Cardiac function was measured by echocardiography. Mice were characterized using various molecular analyses. RESULTS In contrast to other calcineurin isoforms, the authors show here that cardiac-specific overexpression of CnA beta 1 in transgenic mice reduces cardiac hypertrophy and improves cardiac function. This effect is mediated by activation of serine and one-carbon metabolism, and the production of antioxidant mediators that prevent mitochondrial protein oxidation and preserve ATP production. The induction of enzymes involved in this metabolic pathway by CnAb1 is dependent on mTOR activity. Inhibition of serine and one-carbon metabolism blocks the beneficial effects of CnA beta 1. CnA beta 1(Delta i12) mice show increased cardiac hypertrophy and declined contractility. CONCLUSIONS The metabolic reprogramming induced by CnAb1 redefines the role of calcineurin in the heart and shows for the first time that activation of the serine and one-carbon pathway has beneficial effects on cardiac hypertrophy and function, paving the way for new therapeutic approaches. (J Am Coll Cardiol 2018; 71: 654-67) (C) 2018 The Authors. Published by Elsevier on behalf of the American College of Cardiology Foundation. This is an open access article under the CC BY-NC-ND license (http://creativecommons. org/licenses/by-nc-nd/4.0/).This work was supported by grants from the European Union (CardioNeT-ITN-289600 and CardioNext-608027 to Dr. Lara-Pezzi; Meet-ITN-317433 to Dr. Enriquez; UE0/MCA1108 to Dr. Acin-Perez), from the Spanish Ministry of Economy and Competitiveness (SAF2015-65722-R and SAF2012-31451 to Dr. Lara-Pezzi; SAF2015-71521-REDC, BFU2013-50448, and SAF2012-32776 to Dr. Enriquez; RyC-2011-07826 to Dr. Acin-Perez; BIO2012-37926 and BIO2015-67580-P to Dr. Vazquez), from the Spanish Carlos III Institute of Health (CPII14/00027 to Dr. Lara-Pezzi; RD12/0042/066 to Drs. Garcia-Pavia and Lara-Pezzi), from the Regional Government of Madrid (2010-BMD-2321 ``Fibroteam´´ to Dr. Lara-Pezzi; 2011-BMD-2402 ``Mitolab´´ to Dr. Enriquez) and the FIS-ISCIII (PRB2-IPT13/0001 and RD12/0042/0056-RIC-RETICS to Dr. Vazquez). This work was also supported by the Plan Estatal de IthornDthornI 2013-2016-European Regional Development Fund (FEDER) ``A way of making Europe,´´ Spain. The CNIC is supported by the Spanish Ministry of Economy and Competitiveness and by the Pro-CNIC Foundation and is a Severo Ochoa Center of Excellence (MINECO award SEV-2015-0505). Drs. Vazquez and Garcia-Pavia have served as consultants for VL39. All other authors have reported that they have no relationships relevant to the contents of this paper to disclose. Drs. Padron-Barthe, Villalba-Orero, and Gomez-Salinero contributed equally to this work and are joint first authors. Robyn Shaw, MD, PhD, served as Guest Editor for this paper.S