bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV infection and sexual risk behaviour among youth who have experienced orphanhood: systematic review and meta‐analysis
Authors: Operario Don , Underhill Kristen , Chuong Carolyn , Cluver Lucie 
Published: May 2011

BackgroundPrevious research has suggested that orphaned children and adolescents might have elevated risk for HIV infection. We examined the state of evidence regarding the association between orphan status and HIV risk in studies of youth aged 24 years and younger.MethodsUsing systematic review methodology, we identified 10 studies reporting data from 12 countries comparing orphaned and non‐orphaned youth on HIV‐related risk indicators, including HIV serostatus, other sexually transmitted infections, pregnancy and sexual behaviours. We meta‐analyzed data from six studies reporting prevalence data on the association between orphan status and HIV serostatus, and we qualitatively summarized data from all studies on behavioural risk factors for HIV among orphaned youth.ResultsMeta‐analysis of HIV testing data from 19,140 participants indicated significantly greater HIV seroprevalence among orphaned (10.8%) compared with non‐orphaned youth (5.9%) (odds ratio = 1.97; 95% confidence interval = 1.41‐2.75). Trends across studies showed evidence for greater sexual risk behaviour in orphaned youth.ConclusionsStudies on HIV risk in orphaned populations, which mostly include samples from sub‐Saharan Africa, show nearly two‐fold greater odds of HIV infection among orphaned youth and higher levels of sexual risk behaviour than among their non‐orphaned peers. Interventions to reduce risk for HIV transmission in orphaned youth are needed to address the sequelae of parental illness and death that might contribute to sexual risk and HIV infection.
18q deletion in a cystic fibrosis infant, increased morbidity and challenge for correct treatment choices: a case report
Authors: Spinelli Elide , Timpano Silviana , Fogazzi Annalisa , Dester Silvia , Milianti Susanna , Padoan Rita 
Published: May 2011

AbstractCystic Fibrosis (CF) is the most frequent recessive disease of Caucasian patients. Association with other diseases or syndromes has previously been reported. Co-morbidity may be a challenge for clinicians, who have to face more severe problems.We have described a CF infant, F508del homozygote, diagnosed by neonatal screening, who also had a chromosome 18q terminal deletion [del (18)(q22-qter)]. Some clinical features of the 18q deletion: e.g., cardiopathy, gastro-oesophageal reflux and severe muscular hypotonia, worsened the CF clinical picture and his quality of life, with repeated pulmonary exacerbations and failure to thrive in the first six months of life. The treatment strategy was chosen following an accurate multi-disciplinary team study of overlapping chromosome syndrome and CF symptoms. The use of a gastrostomy device for enteral nutrition together with a new device (Ez-PAP) for chest physiotherapy led to normal growth, a notably reduced hospitalization rate and improved quality of life.This case shows how co-morbidities worsening the clinical course of a "complicated patient" can be faced thanks to unconventional therapies that represent a challenge for clinicians.
Integration and publication of heterogeneous text-mined relationships on the Semantic Web
Authors: Coulet Adrien , Garten Yael , Dumontier Michel , Altman Russ B , Musen Mark A , Shah Nigam H 
Published: May 2011

Abstract
Background
Advances in Natural Language Processing (NLP) techniques enable the extraction of fine-grained relationships mentioned in biomedical text. The variability and the complexity of natural language in expressing similar relationships causes the extracted relationships to be highly heterogeneous, which makes the construction of knowledge bases difficult and poses a challenge in using these for data mining or question answering.

Results
We report on the semi-automatic construction of the PHARE relationship ontology (the PHArmacogenomic RElationships Ontology) consisting of 200 curated relations from over 40,000 heterogeneous relationships extracted via text-mining. These heterogeneous relations are then mapped to the PHARE ontology using synonyms, entity descriptions and hierarchies of entities and roles. Once mapped, relationships can be normalized and compared using the structure of the ontology to identify relationships that have similar semantics but different syntax. We compare and contrast the manual procedure with a fully automated approach using WordNet to quantify the degree of integration enabled by iterative curation and refinement of the PHARE ontology. The result of such integration is a repository of normalized biomedical relationships, named PHARE-KB, which can be queried using Semantic Web technologies such as SPARQL and can be visualized in the form of a biological network.

Conclusions
The PHARE ontology serves as a common semantic framework to integrate more than 40,000 relationships pertinent to pharmacogenomics. The PHARE ontology forms the foundation of a knowledge base named PHARE-KB. Once populated with relationships, PHARE-KB (i) can be visualized in the form of a biological network to guide human tasks such as database curation and (ii) can be queried programmatically to guide bioinformatics applications such as the prediction of molecular interactions. PHARE is available at http://purl.bioontology.org/ontology/PHARE.
HyQue: evaluating hypotheses using Semantic Web technologies
Authors: Callahan Alison , Dumontier Michel , Shah Nigam H 
Published: May 2011

AbstractBackgroundKey to the success of e-Science is the ability to computationally evaluate expert-composed hypotheses for validity against experimental data. Researchers face the challenge of collecting, evaluating and integrating large amounts of diverse information to compose and evaluate a hypothesis. Confronted with rapidly accumulating data, researchers currently do not have the software tools to undertake the required information integration tasks.ResultsWe present HyQue, a Semantic Web tool for querying scientific knowledge bases with the purpose of evaluating user submitted hypotheses. HyQue features a knowledge model to accommodate diverse hypotheses structured as events and represented using Semantic Web languages (RDF/OWL). Hypothesis validity is evaluated against experimental and literature-sourced evidence through a combination of SPARQL queries and evaluation rules. Inference over OWL ontologies (for type specifications, subclass assertions and parthood relations) and retrieval of facts stored as Bio2RDF linked data provide support for a given hypothesis. We evaluate hypotheses of varying levels of detail about the genetic network controlling galactose metabolism inSaccharomyces cerevisiaeto demonstrate the feasibility of deploying such semantic computing tools over a growing body of structured knowledge in Bio2RDF.ConclusionsHyQue is a query-based hypothesis evaluation system that can currently evaluate hypotheses about the galactose metabolism inS. cerevisiae. Hypotheses as well as the supporting or refuting data are represented in RDF and directly linked to one another allowing scientists to browse from data to hypothesis andvice versa.HyQue hypotheses and data are available athttp://semanticscience.org/projects/hyque.
Scalable representations of diseases in biomedical ontologies
Authors: Schulz Stefan , Spackman Kent , James Andrew , Cocos Cristian , Boeker Martin 
Published: May 2011

Abstract
Background
The realm of pathological entities can be subdivided into pathological dispositions, pathological processes, and pathological structures. The latter are the bearer of dispositions, which can then be realized by their manifestations — pathologic processes. Despite its ontological soundness, implementing this model via purpose-oriented domain ontologies will likely require considerable effort, both in ontology construction and maintenance, which constitutes a considerable problem for SNOMED CT, presently the largest biomedical ontology.

Results
We describe an ontology design pattern which allows ontologists to make assertions that blur the distinctions between dispositions, processes, and structures until necessary. Based on the domain upper-level ontology BioTop, it permits ascriptions of location and participation in the definition of pathological phenomena even without an ontological commitment to a distinction between these three categories. An analysis of SNOMED CT revealed that numerous classes in the findings/disease hierarchy are ambiguous with respect to process vs. disposition. Here our proposed approach can easily be applied to create unambiguous classes. No ambiguities could be defined regarding the distinction of structure and non-structure classes, but here we have found problematic duplications.

Conclusions
We defend a judicious use of disjunctive, and therefore ambiguous, classes in biomedical ontologies during the process of ontology construction and in the practice of ontology application. The use of these classes is permitted to span across several top-level categories, provided it contributes to ontology simplification and supports the intended reasoning scenarios.
Developing a kidney and urinary pathway knowledge base
Authors: Jupp Simon , Klein Julie , Schanstra Joost , Stevens Robert 
Published: May 2011

Abstract
Background
Chronic renal disease is a global health problem. The identification of suitable biomarkers could facilitate early detection and diagnosis and allow better understanding of the underlying pathology. One of the challenges in meeting this goal is the necessary integration of experimental results from multiple biological levels for further analysis by data mining. Data integration in the life science is still a struggle, and many groups are looking to the benefits promised by the Semantic Web for data integration.

Results
We present a Semantic Web approach to developing a knowledge base that integrates data from high-throughput experiments on kidney and urine. A specialised KUP ontology is used to tie the various layers together, whilst background knowledge from external databases is incorporated by conversion into RDF. Using SPARQL as a query mechanism, we are able to query for proteins expressed in urine and place these back into the context of genes expressed in regions of the kidney.

Conclusions
The KUPKB gives KUP biologists the means to ask queries across many resources in order to aggregate knowledge that is necessary for answering biological questions. The Semantic Web technologies we use, together with the background knowledge from the domain’s ontologies, allows both rapid conversion and integration of this knowledge base. The KUPKB is still relatively small, but questions remain about scalability, maintenance and availability of the knowledge itself.

Availability
The KUPKB may be accessed via http://www.e-lico.eu/kupkb.
C-reactive protein in critically ill cancer patients with sepsis: influence of neutropenia
Authors: Póvoa Pedro , Souza-Dantas Vicente Ces , Soares Márcio , Salluh Jorge IF 
Published: May 2011

Abstract
Introduction
Several biomarkers have been studied in febrile neutropenia. Our aim was to assess C-reactive protein (CRP) concentration in septic critically ill cancer patients and to compare those with and without neutropenia.

Methods
A secondary analysis of a matched case-control study conducted at an oncologic medical-surgical intensive care unit (ICU) was performed, segregating patients with severe sepsis/septic shock. The impact of neutropenia on CRP concentrations at admission and during the first week of ICU stay was assessed.

Results
A total of 154 critically ill septic cancer patients, 86 with neutropenia and 68 without, were included in the present study. At ICU admission, the CRP concentration of neutropenic patients was significantly higher than in non-neutropenic patients, 25.9 ± 11.2 mg/dL vs. 19.7 ± 11.4 mg/dL (P = 0.009). Among neutropenic patients, CRP concentrations at ICU admission were not influenced by the severity of neutropenia (< 100/mm3 vs. ≥ 100/mm3 neutrophils), 25.1 ± 11.6 mg/dL vs. 26.9 ± 10.9 mg/dL (P = 0.527). Time dependent analysis of CRP from Day 1 to Day 7 of antibiotic therapy showed an almost parallel decrease in both groups (P = 0.335), though CRP of neutropenic patients was, on average, always higher in comparison to that of non-neutropenic patients.

Conclusions
In septic critically ill cancer patients CRP concentrations are more elevated in those with neutropenia. However, the CRP course seems to be independent from the presence or absence of neutropenia.
Outcomes of Nordic mental health systems: life expectancy of patients with mental disorders
Authors: Wahlbeck Kristian , Westman Jeanette , Nordentoft Merete , Gissler Mika , Laursen Thomas Munk 
Published: May 2011

BackgroundPeople with mental disorders evince excess mortality due to natural and unnatural deaths. The relative life expectancy of people with mental disorders is a proxy measure of effectiveness of social policy and health service provision.AimsTo evaluate trends in health outcomes of people with serious mental disorders.MethodWe examined nationwide 5-year consecutive cohorts of people admitted to hospital for mental disorders in Denmark, Finland and Sweden in 1987–2006. In each country the risk population was identified from hospital discharge registers and mortality data were retrieved from cause-of-death registers. The main outcome measure was life expectancy at age 15 years.ResultsPeople admitted to hospital for a mental disorder had a two- to threefold higher mortality than the general population in all three countries studied. This gap in life expectancy was more pronounced for men than for women. The gap decreased between 1987 and 2006 in these countries, especially for women. The notable exception was Swedish men with mental disorders. In spite of the positive general trend, men with mental disorders still live 20 years less, and women 15 years less, than the general population.ConclusionsDuring the era of deinstitutionalisation the life expectancy gap for people with mental disorders has somewhat diminished in the three Nordic countries. Our results support further development of the Nordic welfare state model, i.e. tax-funded community-based public services and social protection. Health promotion actions, improved access to healthcare and prevention of suicides and violence are needed to further reduce the life expectancy gap.
War exposure, 5-HTTLPR genotype and lifetime risk of
depression
Authors: Artero Sylvaine , Touchon Jacques , Dupuy Anne-Marie , Malafosse Alain , Ritchie Karen 
Published: May 2011

BackgroundIn 1962 approximately 1.5 million French people living in Algeria were
repatriated to France in very poor and often life-threatening conditions.
These people constitute a cohort for the study of the long-term impact of
gene–environment interaction on depression.AimsTo examine the interaction between a highly stressful life event and
subsequent depression, and its modulation by a length polymorphism of the
serotonin transporter gene (5–HTTLPR).MethodA community sample of people aged 65 years and over residing in the
Montpellier region of the south of France was randomly recruited from
electoral rolls. Genotyping was performed on 248 repatriated persons and
632 controls. Current and lifetime major and minor depressive disorders
were assessed according to DSM-IV criteria.ResultsA significant relationship was observed between exposure to repatriation
and subsequent depression (P<0.002), but there was no
significant effect of gene alone (P = 0.62). After
controlling for age, gender, education, disability, recent life events
and cognitive function, the gene–environment interaction
(repatriation×5-HTTLPR) was globally significant
(P<0.002; OR = 3.21, 95% CI 2.48–5.12). Individuals
carrying the two short (s) alleles of 5-HTTLPR were observed to be at
higher risk (P<0.005; OR = 2.34, 95% CI 1.24–4.32),
particularly when repatriation occurred before age 35 years
(P<0.002; OR = 2.91, 95% CI 1.44–5.88), but this
did not reach significance in those who were older at the time of the
event (P = 0.067).ConclusionsThe association between depression and war repatriation was significantly
modulated by 5-HTTLPR genotype but this appeared to occur only in people
who were younger at the time of exposure.
Intact Primary Mitochondrial Function in Myotubes Established from Women with PCOS
Authors: Eriksen Mette Brandt , Minet Ariane Denise , Glintborg Dorte , Gaster Michael 
Published: May 2011

Abstract

Context:
Polycystic ovary syndrome (PCOS) affects 5–8% of fertile women and is often accompanied by insulin resistance, leading to increased risk of developing type 2 diabetes. Skeletal muscle from insulin-resistant PCOS subjects display reduced expression of nuclear encoded genes involved in mitochondrial oxidative metabolism.

Objective:
We aimed to investigate whether there was a primary mitochondrial dysfunction or difference in mitochondria content that might contribute to the in vivo detected insulin resistance.

Design:
The ATP synthesis with and without ATP use and the mitochondrial mass was determined in mitochondria isolated from myotubes established from PCOS subjects and control subjects.

Patients:
Myotubes were established from eight insulin-resistant PCOS subjects (verified by euglycemic hyperinsulinemic clamp) and eight healthy weight- and age-matched controls.

Results:
Mitochondrial mass and measurable mitochondrial ATP synthesis, with and without ATP use, were not different between PCOS subjects and control subjects.

Conclusion:
We found no evidence for a primary impaired mitochondrial function or content in myotubes established from PCOS subjects, and our results suggest that reduced expression of oxidative genes in PCOS subjects is an adaptive trait.
OR PRACTICE—Production Planning with Patterns: A Problem from Processed Food Manufacturing
Authors: Mehrotra Mili , Dawande Milind , Gavirneni Srinagesh , Demirci Mehmet , Tayur Sridhar 
Published: May 2011

Based on our work with ConAgra Foods (http://www.conagrafoods.com), a leading U.S. food manufacturer, we study a large-scale production-planning problem. The problem incorporates several distinguishing characteristics of production in the processed-food industry, including (i) production patterns that define specific combinations of weeks in which products can be produced, (ii) food groups that classify products based on the allergens they contain, (iii) sequence-dependent setup times, and (iv) manufacture of a large number of products (typically, around 200–250) on multiple production lines (typically, around 15–20) in the presence of significant inventory holding costs and production setup costs. The objective is to obtain a minimum-cost four-week cyclic schedule to resolve three basic decisions: (a) the assignment of products to each line, (b) the partitioning of the demand of each product over the lines to which it is assigned, and (c) the sequence of production on each line. We show that the general problem is strongly NP-hard. To develop intuition via theoretical analysis, we first obtain a polynomially solvable special case by sacrificing as little of its structure as possible and then analyzing the impact of imposing production patterns. A mixed-integer programming model of the general problem allows us to assess the average impact of production patterns and production capacities on the cost of an optimal schedule. Next, to solve practical instances of the problem, we develop an easy-to-implement heuristic. We first demonstrate the effectiveness of the heuristic on a comprehensive test bed of instances; the average percentage gap of the heuristic solution from the optimum is about 3%. Then, we show savings of about 28% on a real-world instance (283 products, 17 production lines) by comparing the schedule obtained from the heuristic to one that was in use (at ConAgra) based on an earlier consultant's work. Finally, we discuss the IT infrastructure implemented to enable the incorporation of optimized (or near-optimized) solutions for ongoing use.
Quantifying the Impact of Layout on Productivity: An Analysis from Robotic-Cell Manufacturing
Authors: Rajapakshe Tharanga , Dawande Milind , Sriskandarajah Chelliah 
Published: May 2011

Although the impact of layout on the productivity of manufacturing systems is well recognized, a quantification of this impact is an issue that is often ignored or crudely approximated in practice. When evaluating competing layouts for a manufacturing system, the trade-off between their relative benefits and their relative costs underlines the need for a reasonably accurate comparison of the productivity offered by these potential layouts. In this paper, we argue for this approach by comparing the productivity of two well-known layouts in robotic-cell manufacturing: circular and linear. We consider the problem of optimizing throughput in single-gripper, bufferless robotic cells that produce identical parts under the free-pickup criterion and the additive-travel-time metric. For cells with a circular layout, we show that the problem of finding an optimal 1-unit cycle is NP-hard. Our main algorithmic result is a polynomial-time 5/3-approximation algorithm for this problem. We then demonstrate that our algorithm provides near-optimal solutions by compiling its performance on an extensive test bed of practically-relevant instances. Finally, we use the algorithm to assess the increase in throughput for cells with a circular layout over those with a linear layout. We show that a circular layout offers a significant improvement in productivity and demonstrate the robustness of this improvement by examining the sensitivity with respect to changes in the design parameters of the robotic cell. Thus, our work provides operations managers with a tool to trade off the resulting increase in revenue with the additional cost of acquiring and maintaining a robot that can exploit a circular layout.
Unintended Pregnancy Rates at the State Level
Authors: Finer Lawrence B. , Kost Kathryn 
Published: May 2011

CONTEXT: Unintended pregnancy is a key reproductive health indicator, but rates have never been calculated for all 50 states.
METHODS: State‐level estimates of unintended pregnancy rates in 2006 were calculated using data from several sources. The proportion of births resulting from unintended pregnancies was obtained from the Pregnancy Risk Assessment Monitoring System and similar state surveys, and the intention status of pregnancies ending in abortion from a national survey of abortion patients. These proportions were applied to birth and abortion counts for each state, and fetal losses were estimated. Rates of unintended pregnancy were obtained by dividing relevant figures by the number of women aged 15–44 in each state. Six states and the District of Columbia had no appropriate survey data; their rates were predicted using multivariate linear regression.
RESULTS: In 2006, the median state unintended pregnancy rate was 51 per 1,000 women aged 15–44. Most rates fell within a range of 40–65 unintended pregnancies per 1,000 women. The highest rate was in Mississippi (69); the lowest rate was in New Hampshire (36). Rates were generally highest in the South and Southwest, and in states with large urban populations. In 29 states and the District of Columbia, more than half of pregnancies were unintended; in nine, a consistent upward trend in unintended pregnancy rates between 2002 and 2006 was apparent; no state had a consistent decline.
CONCLUSIONS: These rates provide benchmarks for measuring the impact on unintended pregnancy of state policies and practices, such as those governing sex education and the funding of contraceptive services.