bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovering and visualizing indirect associations between biomedical concepts
Authors: Tsuruoka Yoshimasa , Miwa Makoto , Hamamoto Kaisei , Tsujii Jun'ichi , Ananiadou Sophia 
Published: June 2011

AbstractMotivation: Discovering useful associations between biomedical concepts has been one of the main goals in biomedical text-mining, and understanding their biomedical contexts is crucial in the discovery process. Hence, we need a text-mining system that helps users explore various types of (possibly hidden) associations in an easy and comprehensible manner.Results: This article describes FACTA+, a real-time text-mining system for finding and visualizing indirect associations between biomedical concepts from MEDLINE abstracts. The system can be used as a text search engine like PubMed with additional features to help users discover and visualize indirect associations between important biomedical concepts such as genes, diseases and chemical compounds. FACTA+ inherits all functionality from its predecessor, FACTA, and extends it by incorporating three new features: (i) detecting biomolecular events in text using a machine learning model, (ii) discovering hidden associations using co-occurrence statistics between concepts, and (iii) visualizing associations to improve the interpretability of the output. To the best of our knowledge, FACTA+ is the first real-time web application that offers the functionality of finding concepts involving biomolecular events and visualizing indirect associations of concepts with both their categories and importance.Availability: FACTA+ is available as a web application at http://refine1-nactem.mc.man.ac.uk/facta/, and its visualizer is available at http://refine1-nactem.mc.man.ac.uk/facta-visualizer/.Contact: tsuruoka@jaist.ac.jp
Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs
Authors: Kam-Thong Tony , Pütz Benno , Karbalai Nazanin , Müller−Myhsok Bertram , Borgwardt Karsten 
Published: June 2011

Abstract
Motivation: In recent years, numerous genome-wide association studies have been conducted to identify genetic makeup that explains phenotypic differences observed in human population. Analytical tests on single loci are readily available and embedded in common genome analysis software toolset. The search for significant epistasis (gene–gene interactions) still poses as a computational challenge for modern day computing systems, due to the large number of hypotheses that have to be tested.
Results: In this article, we present an approach to epistasis detection by exhaustive testing of all possible SNP pairs. The search strategy based on the Hilbert–Schmidt Independence Criterion can help delineate various forms of statistical dependence between the genetic markers and the phenotype. The actual implementation of this search is done on the highly parallelized architecture available on graphics processing units rendering the completion of the full search feasible within a day.
Availability:The program is available at http://www.mpipsykl.mpg.de/epigpuhsic/.
Contact: tony@mpipsykl.mpg.de
Environment specific substitution tables improve membrane protein alignment
Authors: Hill Jamie R. , Kelm Sebastian , Shi Jiye , Deane Charlotte M. 
Published: June 2011

Abstract
Motivation: Membrane proteins are both abundant and important in cells, but the small number of solved structures restricts our understanding of them. Here we consider whether membrane proteins undergo different substitutions from their soluble counterparts and whether these can be used to improve membrane protein alignments, and therefore improve prediction of their structure.
Results: We construct substitution tables for different environments within membrane proteins. As data is scarce, we develop a general metric to assess the quality of these asymmetric tables. Membrane proteins show markedly different substitution preferences from soluble proteins. For example, substitution preferences in lipid tail-contacting parts of membrane proteins are found to be distinct from all environments in soluble proteins, including buried residues. A principal component analysis of the tables identifies the greatest variation in substitution preferences to be due to changes in hydrophobicity; the second largest variation relates to secondary structure. We demonstrate the use of our tables in pairwise sequence-to-structure alignments (also known as ‘threading’) of membrane proteins using the FUGUE alignment program. On average, in the 10–25% sequence identity range, alignments are improved by 28 correctly aligned residues compared with alignments made using FUGUE's default substitution tables. Our alignments also lead to improved structural models.
Availability: Substitution tables are available at: http://www.stats.ox.ac.uk/proteins/resources.
Contact: deane@stats.ox.ac.uk
A method for probing the mutational landscape of amyloid structure
Authors: O'Donnell Charles W. , Waldispühl Jérôme , Lis Mieszko , Halfmann Randal , Devadas Srinivas , Lindquist Susan , Berger Bonnie 
Published: June 2011

Abstract
Motivation: Proteins of all kinds can self-assemble into highly ordered β-sheet aggregates known as amyloid fibrils, important both biologically and clinically. However, the specific molecular structure of a fibril can vary dramatically depending on sequence and environmental conditions, and mutations can drastically alter amyloid function and pathogenicity. Experimental structure determination has proven extremely difficult with only a handful of NMR-based models proposed, suggesting a need for computational methods.
Results: We present AmyloidMutants, a statistical mechanics approach for de novo prediction and analysis of wild-type and mutant amyloid structures. Based on the premise of protein mutational landscapes, AmyloidMutants energetically quantifies the effects of sequence mutation on fibril conformation and stability. Tested on non-mutant, full-length amyloid structures with known chemical shift data, AmyloidMutants offers roughly 2-fold improvement in prediction accuracy over existing tools. Moreover, AmyloidMutants is the only method to predict complete super-secondary structures, enabling accurate discrimination of topologically dissimilar amyloid conformations that correspond to the same sequence locations. Applied to mutant prediction, AmyloidMutants identifies a global conformational switch between Aβ and its highly-toxic ‘Iowa’ mutant in agreement with a recent experimental model based on partial chemical shift data. Predictions on mutant, yeast-toxic strains of HET-s suggest similar alternate folds. When applied to HET-s and a HET-s mutant with core asparagines replaced by glutamines (both highly amyloidogenic chemically similar residues abundant in many amyloids), AmyloidMutants surprisingly predicts a greatly reduced capacity of the glutamine mutant to form amyloid. We confirm this finding by conducting mutagenesis experiments.
Availability: Our tool is publically available on the web at http://amyloid.csail.mit.edu/.
Contact: lindquist_admin@wi.mit.edu; bab@csail.mit.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin
Authors: Savol Andrej J. , Burger Virginia M. , Agarwal Pratul K. , Ramanathan Arvind , Chennubhotla Chakra S. 
Published: June 2011

Abstract
Motivation: Molecular dynamics (MD) simulations have dramatically improved the atomistic understanding of protein motions, energetics and function. These growing datasets have necessitated a corresponding emphasis on trajectory analysis methods for characterizing simulation data, particularly since functional protein motions and transitions are often rare and/or intricate events. Observing that such events give rise to long-tailed spatial distributions, we recently developed a higher-order statistics based dimensionality reduction method, called quasi-anharmonic analysis (QAA), for identifying biophysically-relevant reaction coordinates and substates within MD simulations. Further characterization of conformation space should consider the temporal dynamics specific to each identified substate.
Results: Our model uses hierarchical clustering to learn energetically coherent substates and dynamic modes of motion from a 0.5 μs ubiqutin simulation. Autoregressive (AR) modeling within and between states enables a compact and generative description of the conformational landscape as it relates to functional transitions between binding poses. Lacking a predictive component, QAA is extended here within a general AR model appreciative of the trajectory's temporal dependencies and the specific, local dynamics accessible to a protein within identified energy wells. These metastable states and their transition rates are extracted within a QAA-derived subspace using hierarchical Markov clustering to provide parameter sets for the second-order AR model. We show the learned model can be extrapolated to synthesize trajectories of arbitrary length.
Contact: ramanathana@ornl.gov; chakracs@pitt.edu
Parenting conditions in the midst of suspicion of child sexual abuse (CSA)
Authors: Søftestad Siri , Toverud Ruth 
Published: June 2011

ABSTRACTThis paper presents the findings of an exploratory study on parenting in the midst of suspicion of child sexual abuse (CSA). Data were drawn from in‐depth interviews with 19 parents. Five of these had been accused of CSA. Study methods followed guidelines of grounded theory approaches. Specific parenting conditions during CSA suspicion were identified. Six analytic categories were developed: uncertainty concerning abuse, dilemmas on protection, changes in parent–child relationships, changes in the natural support network, dependency upon professional competence and severe emotional strain. The results are suggested as a tool for identifying themes in order to support and strengthen parenting in ensuring the safety and well‐being of children in these kinds of situations. The current paper contributes to the field by exploring the perspectives of both suspected and non‐suspected parents.
Pain and psychological well‐being of older persons living in nursing homes: an exploratory study in planning patient‐centred intervention
Authors: Tse Mimi , Leung Rincy , Ho Suki 
Published: June 2011

tse m., leung r. & ho s. (2012) Pain and psychological well‐being of older persons living in nursing homes: an exploratory study in planning patient‐centred intervention. Journal of Advanced Nursing 68(2), 312–321.AbstractAim.  This article is a report on a study to examine the pain situation, the use of oral analgesics and non‐pharmacological strategies and the psychological well‐being of older patients living in nursing homes; the relationships between pain and psychological well‐being were also explored.Background.  Pain is common among older adults world‐wide, and tends to be under‐treated. Indeed, the high prevalence of pain may further hinder the fulfilment of psychological needs in a Maslow hierarchy of needs model.Method.  It was a quantitative cross‐sectional study; older adults from six nursing homes were invited to join the study in 2007–2009, with a response rate of 100%. Pain was measured using the Geriatric Pain Assessment, happiness using the Subjective Happiness Scale, life satisfaction using the Life Satisfaction Index – A Form, loneliness using the Revised UCLA Loneliness Scale and depression was measured using the Geriatric Depression Scale.Results.  A convenience sample of 302 older patients (213 females and 89 males aged from 60 to 101, mean age of 84·99) joined the study. The majority of them had experienced pain in the previous 3 months, with a pain intensity of 4·51 on a 10‐point scale. Pain sites were mainly the knee, back, shoulder and musculoskeletal areas. Only 50% of them took oral analgesics, and 70% used non‐pharmacological measures for pain relief. The pain group reported significantly more loneliness and depression when compared with their no‐pain counterparts.Conclusions.  As the number of older patients increases, so does the need for alternative accommodation; thus, pain management education is urgently needed for staff and nursing home residents.
Evolutionary development: a model for the design, implementation, and evaluation of ICT for education programmes
Authors: Rodríguez P. , Nussbaum M. , Dombrovskaia L. 
Published: June 2011

AbstractThe impact of information and communication technology (ICT) in primary and secondary education is still an open question. Following review of the available literature, we classify the causes of the lack of impact on students' attainment in four dimensions: (1) the design and implementation of ICT in educational settings; (2) the evaluation of its impact; (3) the scaling up of these kinds of innovations; and (4) the cost‐effectiveness of technology‐enhanced learning environments. Based on this evidence, we proposed the evolutionary development model (EDM), which aims to produce a cost‐effective and sustainable ICT for education (ICT4E) programme in three steps: efficacy, effectiveness, and efficiency. In each step, one component of the programme is built and validated in real educational settings. Therefore, the resultant ICT4E programme is ready to be replicated across the school system. We also show how the EDM guided the development of a programme based on mobile computer supported collaborative learning, known as Eduinnova. Finally, we discuss how EDM can serve as an analysis tool for researchers and policy makers.
A P5 cancer medicine approach: why personalized medicine cannot ignore psychology
Authors: Pravettoni Gabriella , Gorini Alessandra 
Published: June 2011

AbstractA system approach termed P4 medicine has recently been proposed in the field of oncology. This approach has been advanced as an extension of what is usually called ‘personalized’ or ‘genomic medicine’. P4 medicine creates effective predictive, personalized, preventive and participatory models to treat patients. In order to give more relevance to the behavioural component that impinges on the way individuals act to prevent, cope and react to illnesses, how they decide between different therapeutic options and interact with physicians and adhere to treatment, we propose that P4 medicine should be transformed into P5 medicine. The fifth P represents the psycho‐cognitive aspects to be considered in order to empower the patient, increase his/her quality of life and transform him/her from a passive recipient into an active decision‐maker in the treatment process.
Colorectal neoplasms in relation to non‐alcoholic fatty liver disease in Korean women: A retrospective cohort study
Authors: Lee Young In , Lim Young‐Suk , Park Hye Soon 
Published: June 2011

AbstractBackground and Aim:  Metabolic syndrome has been associated with an increased risk for colorectal cancer. Non‐alcoholic fatty liver disease (NAFLD) is regarded as a hepatic manifestation of metabolic syndrome. We investigated whether NAFLD is associated with colorectal neoplasms in Korean women.Methods:  This retrospective cohort study included data from 5517 women, aged 35–80 years, who underwent life insurance company health examinations between July 2002 and June 2006. Fatty liver disease was assessed by abdominal ultrasound, with NAFLD defined as fatty liver disease in the absence of alcohol use of > 40 g/week or other secondary causes. The incidence of colorectal neoplasms through December 2008 was obtained through medical certificate codes for insurance claims. The association between NAFLD and the risk of colorectal neoplasms was estimated using standard Cox proportional hazards models.Results:  Of the study population, 15.1% were diagnosed with NAFLD. During follow‐up, 65 women were verified as having adenomatous polyps and 15 as having colorectal cancer. Adjusted relative risks (95% confidence interval [CI]) for adenomatous polyps by age, low high‐density lipoprotein‐cholesterol, and NAFLD were 1.12 (95% CI 1.09–1.15), 2.56 (95% CI 1.53–4.28) and 1.94 (95% CI 1.11–3.40). Adjusted relative risks (95% CI) for colorectal cancer by age and NAFLD were 1.23 (95% CI 1.17–1.29) and 3.08 (95% CI 1.02–9.34).Conclusions:  Our findings demonstrate a significant relationship between NAFLD and colorectal neoplasms. Among the various manifestations of metabolic syndrome, NAFLD may predict the development of colorectal neoplasms in Korean women.
The need for capacity building for biomonitoring of lakes and streams in Asia
Authors: Goulden Clyde E. 
Published: June 2011

AbstractDespite warnings that clean fresh water is becoming increasingly scarce throughout the World, freshwater ecosystems continue to be under threat from economic development. The threat is worse in countries trying to build their economies and/or lack resources to protect their environment. Many economists have warned that economic development that destroys environmental resources is unsustainable. Local expertise needed to evaluate the water quality of lakes and flowing water systems is often missing. Many countries need capacity building programmes to help train young scientists in techniques commonly used to biomonitor aquatic ecosystems in the USA, Europe, Japan and South Korea. Biomonitoring of major groups of organisms can be less costly, relative to sophisticated instrumentation. Further, the presence of even tolerant biological organisms is more dependable than chemical concentrations that can vary continuously. The most effective groups of organisms for biomonitoring include the diatoms, which are often the dominant forms of algae in both lakes and riverine systems, aquatic insects, particularly mayflies, stoneflies and caddisflies, often referred to as the EPT and fishes. Biological methods can be used with an active adaptive management approach that provides guidance for remediation of polluted water systems by studying the levels of degradation or of recovery of ecosystems to or from a more normal state. This approach only can be effective as long the skills exist to understand ecosystems and properly identify lake and river flora and fauna.
Specialist resources are key to improving small mammal distribution models
Authors: HABY NERISSA A. , DELEAN STEVEN , BROOK BARRY W. 
Published: June 2011

AbstractSmall ground‐dwelling mammals can have complex ecological relationships with environmental factors that limit the usefulness of coarse data in predictive species distribution models. We investigated the relative importance of available abiotic and biotic, landscape‐ and quadrat‐scale data for predicting the distributions of four small mammals using data at three resolutions: 150 m, 500 m and 1000 m. At 150 m, the inclusion of landscape‐scale data to a climate‐only model improved the predicted occurrence of the wet heath specialist and woodland generalist, but not the two dense understorey species. Limited improvement was obtained with the inclusion of available quadrat‐scale data (possibly because of missing or insufficiently detailed descriptive variables). As the models of best fit were re‐applied to lower‐resolution environmental data (500 m and 1000 m), the variance explained decreased for the wet heath specialist and two dense understorey species. These trends corresponded with reduced variance explained predominantly by biotic variables or abiotic landscape variables respectively. In contrast, the resolution of environmental data had no effect on the woodland generalist species distribution models, indicating the habitat for this more mobile species was sufficiently represented at the lowest resolution (1000 m). These results highlight the potential value of landscape‐ and finer‐scale variables in modelling the distributions of small mammals. Where such variables are unavailable, higher‐resolution climate data could better represent resource availability (indirectly) or suitable microclimates (directly), especially for more vulnerable, above‐ground nesting species. We encourage the collection of additional detailed and high‐resolution environmental information to facilitate the development of more accurate models of the extent and distribution of small mammals.
Effect of antithyroid drug on chick embryos during the last week of development: Delayed hatching and decreased cerebellar acetylcholinesterase activity
Authors: Haba Gen , Nishigori Hidekazu , Tezuka Yu , Kagami Keisuke , Sugiyama Toru , Nishigori Hideo 
Published: June 2011

AbstractAim:  Hypothyroid state during embryogenesis disturbs normal growth and brain development, influencing later life. To evaluate the harmful consequences of the state during embryogenesis using an animal model, we inhibited thyroid hormone biosynthesis in chick embryos by using methimazole (MMI).Material and Methods:  Typically, embryos were treated with MMI (20 µmol/egg) on day 14, and examined on specific days.Results:  Of the control embryos, 94% hatched on day 21, whereas 0% and 60% of MMI‐treated embryos hatched on days 21 and 24, respectively. MMI retarded the rates of bodyweight gain as well as liver and heart development, and delayed hatching. However, the external differences in appearance and differences in the weights of the newly hatched control chicks on day 21 and the MMI‐treated chicks on day 24 were less obvious. Embryos treated with MMI exhibited increased mass in their brain parts on day 24. Most notably, the treatment resulted in a 1.35‐fold increase in cerebellum weight compared to that of the untreated animals. Acetylcholinesterase activity in the cerebellum on the day of hatching decreased significantly to 0.85‐fold that of the untreated controls. Thyroid hormone receptor β mRNA was detected from day 12 and dramatically expressed from day 19 to the day of hatching.Conclusion:  The ‘fertilized hen's egg‐chick embryo‐chick system’ is an appropriate animal model for investigating the hypothyroid state during embryogenesis. Decreased cerebellar acetylcholinesterase activity after MMI treatment was assumed to relate to a mechanism of motor and cognitive deficits in congenital hypothyroidism.