Algorithms for Highly Symmetric Linear and Integer Programs

This paper deals with exploiting symmetry for solving linear and integer programming problems. Basic properties of linear representations of finite groups can be used to reduce symmetric linear programming to solving linear programs of lower dimension. Combining this approach with knowledge of the geometry of feasible integer solutions yields an algorithm for solving highly symmetric integer linear programs which only takes time which is linear in the number of constraints and quadratic in the dimension.Comment: 21 pages, 1 figure; some references and further comments added, title slightly change

RegenBase: a knowledge base of spinal cord injury biology for translational research.

Spinal cord injury (SCI) research is a data-rich field that aims to identify the biological mechanisms resulting in loss of function and mobility after SCI, as well as develop therapies that promote recovery after injury. SCI experimental methods, data and domain knowledge are locked in the largely unstructured text of scientific publications, making large scale integration with existing bioinformatics resources and subsequent analysis infeasible. The lack of standard reporting for experiment variables and results also makes experiment replicability a significant challenge. To address these challenges, we have developed RegenBase, a knowledge base of SCI biology. RegenBase integrates curated literature-sourced facts and experimental details, raw assay data profiling the effect of compounds on enzyme activity and cell growth, and structured SCI domain knowledge in the form of the first ontology for SCI, using Semantic Web representation languages and frameworks. RegenBase uses consistent identifier schemes and data representations that enable automated linking among RegenBase statements and also to other biological databases and electronic resources. By querying RegenBase, we have identified novel biological hypotheses linking the effects of perturbagens to observed behavioral outcomes after SCI. RegenBase is publicly available for browsing, querying and download.Database URL:http://regenbase.org

De los Mayas a la planificación familiar: demografía del Istmo

El Istmo centroamericano es una de las regiones más heterogéneas del mundo y una región muy importante desde el punto de vista demográfico, social y ambiental. Históricamente, el Istmo fue habitado por una de las poblaciones precolombinas más grandes de América, la cual experimentó una disminución devastadora durante y después de la Conquista. Desde entonces, el Istmo ha recibido oleadas de inmigrantes de Europa y de otras regiones, además de una considerable migración interna. En años recientes, algunos países del Istmo han generado también importantes flujos de emigración, especialmente hacia los países de Norteamérica. Durante las últimas décadas, un país del Istmo, Costa Rica, tuvo una de las tasas más altas de crecimiento de población observada históricamente, seguido por una de las diminuciones más rápidas de fecundidad. Otros países de la región también han experimentado diminuciones considerables de fecundidad, aún cuando hay una variación grande en las tasas de fecundidad entre países de la región en los años noventa. Aunque la mayoría de los países del Istmo han experimentado diminuciones importantes en la mortalidad, persisten en algunos de ellos unas de las más altas tasas de mortalidad del continente. Varios países del Istmo también se enfrentan a problemas del medio ambiente, a consecuencia de la sobrexplotación de la tierra, la industrialización descontrolada y la tala de las selvas por compañías madereras y por hogares buscando leña. Los problemas sociales y ambientales en algunos países han empeorado por las crisis económicas y las guerras civiles. Sin embargo, el Istmo centroamericano es una región rica en recursos, incluyendo recursos humanos. La experiencia demográfica del Istmo provee lecciones importantes para otras regiones. Las investigaciones demográficas del Istmo centroamericano han cambiado dramáticamente durante los últimos 25 años, como lo demuestran los capítulos de este volumen. En parte ello se debe al aumento en la disponibilidad de datos. En 1970, los censos nacionales y los sistemas de registro civil eran las fuentes principales de datos demográficos, sociales y económicos. Aunque se realizaron muchos censos en períodos anteriores, los programas de censos generalmente comenzaron alrededor de 1960 con el apoyo técnico de las Naciones Unidas. La mayoría de los países también llevaron a cabo un censo en la década de los años setentas y en cada decenio desde entonces. Los censos han proporcionado información muy importante, aunque limitada, acerca del tamaño y estructura por edad, sexo y etnicidad de la población además de características del hogar, niveles de ingreso y educación. Un cambio importante comenzó en los años setenta, inicialmente con la Encuesta Mundial de Fecundidad y subsiguientemente con las Encuestas de Prevalencia Anticonceptiva y las Encuestas Demográficas y de Salud. Estas encuestas han hecho disponibles abundantes datos demográficos acerca de países del Istmo. Además, algunos países han desarrollado una capacidad importante en el diseño de encuestas y métodos de trabajo de campo y han empezado a realizar encuestas aparte de los programas internacionales. A consecuencia del gran número de encuestas de fecundidad llevadas a cabo durante los últimos 25 años en el Istmo, conocemos mucho mejor los patrones de fecundidad y uso de anticonceptivos. La mayoría de encuestas demográficas recientes también han proveído información importante de salud y mortalidad infantil. Sin embargo, las encuestas han contenido solo información muy limitada de la migración, una variable muy importante para el futuro. A pesar de la creciente disponibilidad de datos y de conocimiento acerca de la situación demográfica de la región, quedan todavía varios obstáculos importantes para la investigación demográfica en el Istmo centroamericano. El primero es que existen pocos centros para investigaciones demográficas en la región y la mayoría de los centros que existen no tienen fondos adecuados. Muchos participantes en el Seminario expresaron su frustración en relación con la dificultad de buscar empleo en el área de demografía y están preocupados por la posibilidad de una diminución en la disponibilidad de fondos para realizar investigaciones. Un segundo obstáculo ha sido la falta de acceso a los datos de las encuestas y de los censos de parte de investigadores. Los participantes mencionaron dos problemas principales:(1) la falta de una fuente central disponible para los datos de las encuestas y (2) algunos gobiernos están poco dispuestos a proveer acceso a los datos del censo a investigadores fuera del gobierno. Una parte de este problema será solucionado por el Archivo de Datos Centroamericanos organizado por el Programa Centroamericano de Población de la Universidad de Costa Rica. El archivo proporcionará acceso a la mayoría de las encuestas realizadas en el Istmo durante los últimos 20 años. Un tercer obstáculo mencionado por algunos participantes es la falta de comparabilidad completa entre las encuestas realizadas en la región. En algunos casos, la falta de comparabilidad ha hecho difícil el análisis comparativo entre países del Istmo. Otra limitación para la investigación demográfica en el Istmo es que la mayoría ha estado enfocada estrechamente al área de fecundidad y planificación familiar, aún cuando hay más investigaciones de salud infantil en años recientes. Como se muestra en los capítulos de este libro, las áreas en las cuales se realizan investigaciones demográficas se están extendiendo a nuevos territorios. Este cambio ocurre, cuando menos, de dos maneras. Primero, se extienden las investigaciones de fecundidad y planificación familiar de manera innovadora. Buenos ejemplos de esta tendencia son el capítulo por Arodys Robles de la relación entre el uso de anticonceptivos y conocimientos de salud, el capítulo por Hubacher et al. que investiga la importancia de anticonceptivos tradicionales en Honduras, y el capítulo por Luis Rosero Bixby que introduce el análisis espacial al estudio de la oferta de planificación familiar. Segundo, en términos substantivos los investigadores están incursionando en áreas nuevas. Ejemplos de ello son los capítulos por Hoover-Castañeda, Bilsborrow, Stupp y Patrinos. Se espera que los capítulos de este libro generarán ideas en otros investigadores con interés en el Istmo centroamericano y fomentarán la investigación en un rango amplio de temas demográficos y variables conexas.UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Sociales::Centro Centroamericano de Población (CCP

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries

<p>Abstract</p> <p>Background</p> <p>Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds.</p> <p>Results</p> <p>We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization.</p> <p>Conclusion</p> <p>EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.</p

MRI hip morphology is abnormal in unilateral DDH and increased lateral limbus thickness is associated with residual DDH at minimum 10-year follow-up.

PURPOSE The purpose of the study was to compare the post-reduction magnetic resonance imaging morphology for hips that developed residual acetabular dysplasia, hips without residual dysplasia, and uninvolved contralateral hips in patients with unilateral developmental dysplasia of the hip undergoing closed or open reduction and had a minimum 10-year follow-up. METHODS Retrospective study of patients with unilateral dysplasia of the hip who underwent open/closed hip reduction followed by post-reduction magnetic resonance imaging. Twenty-eight patients with a mean follow-up of 13 ± 3 years were included. In the treated hips, residual dysplasia was defined as subsequent surgery for residual acetabular dysplasia or for Severin grade > 2 at latest follow-up. On post-reduction, magnetic resonance imaging measurements were performed by two readers and compared between the hips with/without residual dysplasia and the contralateral uninvolved side. Magnetic resonance imaging measurements included acetabular version, coronal/ axial femoroacetabular distance, acetabular depth-width ratio, osseous/cartilaginous acetabular indices, and medial/lateral (limbus) cartilage thickness. RESULTS Fifteen (54%) and 13 (46%) hips were allocated to the "no residual dysplasia" group and to the "residual dysplasia" group, respectively. All eight magnetic resonance imaging parameters differed between hips with residual dysplasia and contralateral uninvolved hips (all p < 0.05). Six of eight parameters differed (all p < 0.05) between hips with and without residual dysplasia. Among these, increased limbus thickness had the largest effect (odds ratio = 12.5; p < 0.001) for increased likelihood of residual dysplasia. CONCLUSIONS We identified acetabular morphology and reduction quality parameters that can be reliably measured on the post-reduction magnetic resonance imaging to facilitate the differentiation between hips that develop with/without residual acetabular dysplasia at 10 years postoperatively. LEVEL OF EVIDENCE level III, prognostic case-control study

Long-term and recent trends in hypertension awareness, treatment and control in twelve high-income countries: an analysis of 123 nationally representative surveys

Background: Antihypertensive medicines are effective in reducing adverse cardiovascular events. Our aim was to compare hypertension awareness, treatment and control, and how they have changed over time, in high-income countries. Methods: We used data on 526,336 participants aged 40-79 years in 123 national health examination surveys from 1976 to 2017 in twelve high-income countries: Australia, Canada, Finland, Germany, Ireland, Italy, Japan, New Zealand, South Korea, Spain, the UK, and the USA. We calculated the percent of participants with hypertension – defined as systolic blood pressure ≥140 mmHg or diastolic blood pressure ≥90 mmHg or being on pharmacological treatment for hypertension – who were aware of their condition, who were treated, and whose hypertension was controlled (i.e. lower than 140/90 mmHg). Findings: Canada, South Korea, Australia and the UK have the lowest prevalence of hypertension, and Finland the highest. In the 1980s and early 1990s, treatment rates were at most 40% and control rates were below 25% in most countries and age-sex groups. Over time, hypertension awareness and treatment increased and control rate improved in all twelve countries, with South Korea and Germany experiencing the largest improvements. Most of the increase occurred in the 1990s and early-mid 2000s, having plateaued since in most countries. Canada, Germany, South Korea and the USA have the highest rates of awareness, treatment and control, while Finland, Ireland, Japan and Spain the lowest. Even in the best performing countries, treatment coverage was at most 80% and control rates were below 70%. Interpretation: Hypertension awareness, treatment and control have improved substantially in high-income countries since the 1980s and 1990s. However, control rates have plateaued in the past decade, at levels lower than those in high-quality hypertension programmes. There is substantial variation across countries in the rates of hypertension diagnosis, treatment an

Fixed-Parameter Algorithms in Analysis of Heuristics for Extracting Networks in Linear Programs

We consider the problem of extracting a maximum-size reflected network in a linear program. This problem has been studied before and a state-of-the-art SGA heuristic with two variations have been proposed. In this paper we apply a new approach to evaluate the quality of SGA\@. In particular, we solve majority of the instances in the testbed to optimality using a new fixed-parameter algorithm, i.e., an algorithm whose runtime is polynomial in the input size but exponential in terms of an additional parameter associated with the given problem. This analysis allows us to conclude that the the existing SGA heuristic, in fact, produces solutions of a very high quality and often reaches the optimal objective values. However, SGA contain two components which leave some space for improvement: building of a spanning tree and searching for an independent set in a graph. In the hope of obtaining even better heuristic, we tried to replace both of these components with some equivalent algorithms. We tried to use a fixed-parameter algorithm instead of a greedy one for searching of an independent set. But even the exact solution of this subproblem improved the whole heuristic insignificantly. Hence, the crucial part of SGA is building of a spanning tree. We tried three different algorithms, and it appears that the Depth-First search is clearly superior to the other ones in building of the spanning tree for SGA. Thereby, by application of fixed-parameter algorithms, we managed to check that the existing SGA heuristic is of a high quality and selected the component which required an improvement. This allowed us to intensify the research in a proper direction which yielded a superior variation of SGA

Heterogeneous contributions of change in population distribution of body mass index to change in obesity and underweight

From 1985 to 2016, the prevalence of underweight decreased, and that of obesity and severe obesity increased, in most regions, with significant variation in the magnitude of these changes across regions. We investigated how much change in mean body mass index (BMI) explains changes in the prevalence of underweight, obesity, and severe obesity in different regions using data from 2896 population-based studies with 187 million participants. Changes in the prevalence of underweight and total obesity, and to a lesser extent severe obesity, are largely driven by shifts in the distribution of BMI, with smaller contributions from changes in the shape of the distribution. In East and Southeast Asia and sub-Saharan Africa, the underweight tail of the BMI distribution was left behind as the distribution shifted. There is a need for policies that address all forms of malnutrition by making healthy foods accessible and affordable, while restricting unhealthy foods through fiscal and regulatory restrictions

A Strong B-cell Response Is Part of the Immune Landscape in Human High-Grade Serous Ovarian Metastases

In high-grade serous ovarian cancer (HGSOC), higher densities of both B cells and the CD8 + T-cell infiltrate were associated with a better prognosis. However, the precise role of B cells in the antitumor response remains unknown. As peritoneal metastases are often responsible for relapse, our aim was to characterize the role of B cells in the antitumor immune response in HGSOC metastases. Unmatched pre and post-chemotherapy HGSOC metastases were studied. B-cell localization was assessed by immunostaining. Their cytokines and chemokines were measured by a multiplex assay, and their phenotype was assessed by flow cytometry. Further in vitro and in vivo assays highlighted the role of B cells and plasma cell IgGs in the development of cytotoxic responses and dendritic cell activation. B cells mainly infiltrated lymphoid structures in the stroma of HGSOC metastases. There was a strong B-cell memory response directed at a restricted repertoire of antigens and production of tumor-specific IgGs by plasma cells. These responses were enhanced by chemotherapy. Interestingly, transcript levels of CD20 correlated with markers of immune cytolytic responses and immune complexes with tumor-derived IgGs stimulated the expression of the costimulatory molecule CD86 on antigen-presenting cells. A positive role for B cells in the antitumor response was also supported by B-cell depletion in a syngeneic mouse model of peritoneal metastasis. Our data showed that B cells infiltrating HGSOC omental metastases support the development of an antitumor response. Clin Cancer Res; 1-13. ©2016 AACR