bluuebunny/crossref_metadata_2025_split huggingface dataset:
Partial Mastectomy and M. Latissimus Dorsi Reconstruction for Radiation‐induced Fibrosis After Breast‐conserving Cancer Therapy
Authors: van Geel Albertus N. , Lans Titia E. , Haen Roel , Tjong Joe Wai Rudi , Menke‐Pluijmers Marian B. E. 
Published: December 2010

AbstractBackgroundPatients with severe complaints of radiation‐induced fibrosis after breast‐conserving therapy and not responding to conservative therapy, were treated by partial mastectomy and m. latissimus dorsi reconstruction.MethodTo determine the feasibility and outcome of this approach, a retrospective study of nine patients was carried out.ResultsAfter a mean follow‐up of 46 months, eight of the nine patients experienced improvement of their complaints and shape of the breast. In only one case did the procedure fail, as evidenced by continuation of all complaints.ConclusionsPartial mastectomy and m. latissimus dorsi reconstruction is the ultimate option in the treatment of radiation fibrosis. The procedure is safe with satisfying results.
Chromosome Segment Substitution Lines: A Powerful Tool for the Introgression of Valuable Genes from Oryza Wild Species into Cultivated Rice (O. sativa)
Authors: Ali M. Liakat , Sanchez Paul L. , Yu Si-bin , Lorieux Mathias , Eizenga Georgia C. 
Published: December 2010

AbstractWild species of rice (genusOryza) contain many useful genes but a vast majority of these genes remain untapped to date because it is often difficult to transfer these genes into cultivated rice (Oryza sativaL.). Chromosome segment substitution lines (CSSLs) and backcross inbred lines (BILs) are powerful tools for identifying these naturally occurring, favorable alleles in unadapted germplasm. In this paper, we present an overview of the research involving CSSLs and BILs in the introgression of quantitative trait loci (QTLs) associated with the improved performance of rice including resistance to various biotic and abiotic stresses, and even high yield from wild relatives of rice and other unadapted germplasm into the genetic background of adapted rice cultivars. The CSSLs can be used to dissect quantitative traits into the component genetic factors and evaluate gene action as single factors (monogenic loci). CSSLs have the potential to uncover new alleles from the unadapted, non-productive wild rice accessions, develop genome-wide genetic stocks, and clone genes identified in QTL studies for functional genomics research. Recent development of high-density single-nucleotide polymorphism (SNP) arrays in rice and availability of custom-designed medium- and low-density SNP arrays will enhance the CSSL development process with smaller marker-defined segment introgressions from unadapted germplasm.
Molecular marks for epigenetic identification of developmental and cancer stem cells
Authors: Patra Samir Kumar , Deb Moonmoon , Patra Aditi 
Published: December 2010

AbstractEpigenetic regulations of genes by reversible methylation of DNA (at the carbon-5 of cytosine) and numerous reversible modifications of histones play important roles in normal physiology and development, and epigenetic deregulations are associated with developmental disorders and various disease states, including cancer. Stem cells have the capacity to self-renew indefinitely. Similar to stem cells, some malignant cells have the capacity to divide indefinitely and are referred to as cancer stem cells. In recent times, direct correlation between epigenetic modifications and reprogramming of stem cell and cancer stem cell is emerging. Major discoveries were made with investigations on reprogramming gene products, also known as master regulators of totipotency and inducer of pluoripotency, namely, OCT4, NANOG, cMYC, SOX2, Klf4, and LIN28. The challenge to induce pluripotency is the insertion of four reprogramming genes (Oct4, Sox2, Klf4, and c-Myc) into the genome. There are always risks of silencing of these genes by epigenetic modifications in the host cells, particularly, when introduced through retroviral techniques. In this contribution, we will discuss some of the major discoveries on epigenetic modifications within the chromatin of various genes associated with cancer progression and cancer stem cells in comparison to normal development of stem cell. These modifications may be considered as molecular signatures for predicting disorders of development and for identifying disease states.
An overview of sarcopenia: facts and numbers on prevalence and clinical impact
Authors: von Haehling Stephan , Morley John E. , Anker Stefan D. 
Published: December 2010

Human muscle undergoes constant changes. After about age 50, muscle mass decreases at an annual rate of 1–2%. Muscle strength declines by 1.5% between ages 50 and 60 and by 3% thereafter. The reasons for these changes include denervation of motor units and a net conversion of fast type II muscle fibers into slow type I fibers with resulting loss in muscle power necessary for activities of daily living. In addition, lipids are deposited in the muscle, but these changes do not usually lead to a loss in body weight. Once muscle mass in elderly subjects falls below 2 standard deviations of the mean of a young control cohort and the gait speed falls below 0.8 m/s, a clinical diagnosis of sarcopenia can be reached. Assessment of muscle strength using tests such as the short physical performance battery test, the timed get‐up‐and‐go test, or the stair climb power test may also be helpful in establishing the diagnosis. Sarcopenia is one of the four main reasons for loss of muscle mass. On average, it is estimated that 5–13% of elderly people aged 60–70 years are affected by sarcopenia. The numbers increase to 11–50% for those aged 80 or above. Sarcopenia may lead to frailty, but not all patients with sarcopenia are frail—sarcopenia is about twice as common as frailty. Several studies have shown that the risk of falls is significantly elevated in subjects with reduced muscle strength. Treatment of sarcopenia remains challenging, but promising results have been obtained using progressive resistance training, testosterone, estrogens, growth hormone, vitamin D, and angiotensin‐converting enzyme inhibitors. Interesting nutritional interventions include high‐caloric nutritional supplements and essential amino acids that support muscle fiber synthesis.
Soil phytoliths from miombo woodlands in Mozambique
Authors: Mercader Julio , Bennett Tim , Esselmont Chris , Simpson Steven , Walde Dale 
Published: December 2010

AbstractThis paper describes topsoil phytolith assemblages from 25 loci underneath miombo woodlands on an eco-transect intersecting the Mozambican Rift along a geographical, altitudinal, climatic and botanical gradient. We provide the first comprehensive overview of the phytolith spectrum that defines northern Mozambique's Zambezian floristic zone. Our classifying criteria derive from comparison with previously described and quantified reference collections of trees and grasses growing in the study area. We characterize the sedimentological and soil features of the matrices where phytoliths are found, establishing correlation among geo-edaphic variables and phytoliths. Descriptive statistics along with nonparametric and parametric statistical analyses evaluate phytolith grouping criteria, variation, robustness, and membership. From a taphonomic perspective, we attest that topsoil phytolith assemblages are polygenic and do not represent an episodic snapshot of extant vegetation, but a palimpsest from plants representing various disturbance episodes, succession stages, and ecological trends. Phytoliths retrieved from Mozambican miombo soils do not seem to trace altitudinal, temperature, or precipitation gradients, and no significant differences exist between highland and lowland phytolith assemblages. This article provides a phytolith analog for woodland environments that can guide future paleoenvironmental research. It also confirms that phytolith analysis is able to detect shifts in the woodland/grassland interface.
Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics
Authors: Weber Marc , Teeling Hanno , Huang Sixing , Waldmann Jost , Kassabgy Mariette , Fuchs Bernhard M , Klindworth Anna , Klockow Christine , Wichels Antje , Gerdts Gunnar , Amann Rudolf , Glöckner Frank Oliver 
Published: December 2010

Abstract
Next-generation sequencing (NGS) technologies have enabled the application of broad-scale sequencing in microbial biodiversity and metagenome studies. Biodiversity is usually targeted by classifying 16S ribosomal RNA genes, while metagenomic approaches target metabolic genes. However, both approaches remain isolated, as long as the taxonomic and functional information cannot be interrelated. Techniques like self-organizing maps (SOMs) have been applied to cluster metagenomes into taxon-specific bins in order to link biodiversity with functions, but have not been applied to broad-scale NGS-based metagenomics yet. Here, we provide a novel implementation, demonstrate its potential and practicability, and provide a web-based service for public usage. Evaluation with published data sets mimicking varyingly complex habitats resulted into classification specificities and sensitivities of close to 100% to above 90% from phylum to genus level for assemblies exceeding 8 kb for low and medium complexity data. When applied to five real-world metagenomes of medium complexity from direct pyrosequencing of marine subsurface waters, classifications of assemblies above 2.5 kb were in good agreement with fluorescence in situ hybridizations, indicating that biodiversity was mostly retained within the metagenomes, and confirming high classification specificities. This was validated by two protein-based classifications (PBCs) methods. SOMs were able to retrieve the relevant taxa down to the genus level, while surpassing PBCs in resolution. In order to make the approach accessible to a broad audience, we implemented a feature-rich web-based SOM application named TaxSOM, which is freely available at http://www.megx.net/toolbox/taxsom. TaxSOM can classify reads or assemblies exceeding 2.5 kb with high accuracy and thus assists in linking biodiversity and functions in metagenome studies, which is a precondition to study microbial ecology in a holistic fashion.
Ontology-Based Queries over Cancer Data
Authors: Gonzalez-Beltran Alejandra 
Published: December 2010

AbstractThe ever-increasing amount of data in biomedical research, and in cancer research in particular, needs to be managed to support efficient data access, exchange and integration. Existing software infrastructures, such as caGrid, support access to distributed information annotated with a domain ontology. However, caGrid's current querying functionality depends on the structure of individual data resources without exploiting the semantic annotations. In this paper, we present the design and development of an ontology-based querying functionality that consists of: the generation of OWL2 ontologies from the underlying data resources’ metadata and a query rewriting and translation process based on reasoning, which converts a query at the domain ontology level into queries at the software infrastructure level. We present a detailed analysis of our approach as well as an extensive performance evaluation. While the implementation and evaluation was performed for the caGrid infrastructure, the approach could be applicable to other model and metadata-driven environments for data sharing.
Variable selection for discriminant analysis with Markov random field priors for the analysis of microarray data
Authors: Stingo Francesco C. , Vannucci Marina 
Published: December 2010

Abstract
Motivation: Discriminant analysis is an effective tool for the classification of experimental units into groups. Here, we consider the typical problem of classifying subjects according to phenotypes via gene expression data and propose a method that incorporates variable selection into the inferential procedure, for the identification of the important biomarkers. To achieve this goal, we build upon a conjugate normal discriminant model, both linear and quadratic, and include a stochastic search variable selection procedure via an MCMC algorithm. Furthermore, we incorporate into the model prior information on the relationships among the genes as described by a gene–gene network. We use a Markov random field (MRF) prior to map the network connections among genes. Our prior model assumes that neighboring genes in the network are more likely to have a joint effect on the relevant biological processes.
Results: We use simulated data to assess performances of our method. In particular, we compare the MRF prior to a situation where independent Bernoulli priors are chosen for the individual predictors. We also illustrate the method on benchmark datasets for gene expression. Our simulation studies show that employing the MRF prior improves on selection accuracy. In real data applications, in addition to identifying markers and improving prediction accuracy, we show how the integration of existing biological knowledge into the prior model results in an increased ability to identify genes with strong discriminatory power and also aids the interpretation of the results.
Contact: marina@rice.edu
The Smoking Abstinence Questionnaire: measurement of smokers' abstinence‐related expectancies
Authors: Hendricks Peter S. , Wood Sabrina B. , Baker Majel R. , Delucchi Kevin L. , Hall Sharon M. 
Published: December 2010

ABSTRACTAims  To develop and validate a measure of smokers' expectancies for the abstinence process upon quitting smoking: the Smoking Abstinence Questionnaire (SAQ).Design  Principal component analysis and other psychometric analyses of self‐report data.Setting  San Francisco, California.Participants  A total of 507 adult smokers of at least 10 cigarettes per day diverse in gender, sexual orientation and ethnoracial status.Measurements  The primary measure was a draft version of the SAQ. Additional measures assessed a variety of other smoking‐related constructs.Findings  Analyses yielded 10 scales of the SAQ: Withdrawal, Social Improvement/Non‐smoker Identity, Adverse Outcomes, Treatment Effectiveness, Common Reasons, Barriers to Treatment, Social Support, Optimistic Outcomes, Coffee Use and Weight Gain. The SAQ scales demonstrated internal consistencies ranging from 0.62 to 0.85 and were associated with tobacco dependence, motivation to quit, abstinence self‐efficacy, withdrawal symptoms, dietary restraint, shape and weight concern and tobacco use expectancies. The SAQ predicted smoking‐related constructs above and beyond tobacco use expectancies, suggesting that abstinence‐related expectancies and tobacco use expectancies are distinct from one another.Conclusions  A newly developed questionnaire, the Smoking Abstinence Questionnaire, appears to capture reliably smokers' expectancies for abstinence (Withdrawal, Social Improvement/Non‐smoker Identity, Adverse Outcomes, Common Reasons, Optimistic Outcomes, Coffee Use, and Weight Gain) and expectancies related to the success of a quit attempt (Treatment Effectiveness, Barriers to Treatment and Social Support). It remains to be seen how far any of these expectancies predict attempts to quit, withdrawal, treatment utilization and response and quitting success above and beyond existing measures.
Towards a national model for managing impaired driving offenders
Authors: Voas Robert B. , DuPont Robert L. , Talpins Stephen K. , Shea Corinne L. 
Published: December 2010

ABSTRACTAims  To describe a proposed national model for controlling the risk presented by offenders convicted of driving while impaired (DWI) and promoting behavioral change to reduce future recidivism.Setting  Traditional methods of controlling the risk they present to the driving public are not adequate, as indicated by the fact that approximately 1000 people are killed each year‐in alcohol‐related crashes involving drivers convicted of DWI in the previous three years. However, stimulated by the success of special drug courts for substance abusers and new technological methods for monitoring drug and alcohol use, new criminal justice programs for managing impaired driving offenders are emerging.Intervention  A national model for a comprehensive system applicable to both drug and alcohol impaired drivers is proposed. The program focuses on monitoring offender drinking or the offender driving employing vehicle interlocks with swift, sure but moderate penalties for non‐compliance in which the ultimate sanction is based on offender performance in meeting monitoring requirements.Findings  Several new court programs, such as the 24/7 Sobriety Project in South Dakota and North Dakota and the Hawaii's Opportunity Probation with Enforcement (HOPE) Project, which feature alcohol/drug consumption monitoring, have produced evidence that indicates even dependent drinkers can conform to abstinence monitoring requirements and avoid the short‐term jail consequence for failure.Conclusions  Based on the apparent success of emerging court monitoring systems, it appears that the cost of incarcerating driving‐while‐impaired offenders can be minimized by employing low‐cost community correction programs paid for by the offender.
The ecology and emergence of diseases in fresh waters
Authors: JOHNSON PIETER T. J. , PAULL SARA H. 
Published: December 2010

Summary1. Freshwater ecosystems, including ponds, lakes, streams and rivers, represent an interaction nexus between environmental change and a wide variety of infectious diseases, including human malaria, salmonid whirling disease, amphibian chytridiomycosis, crayfish plague and many others. However, few studies have explicitly examined patterns of disease in fresh waters and how they are changing over time.2. Freshwater environments can function as transmission foci for pathogens because of (i) the importance of fresh water for organism survival, (ii) the aquatic life histories of many vectors and intermediate hosts, (iii) the concentrated aggregations of species – both freshwater and terrestrial – in and around freshwater habitats and (iv) the highly altered condition of freshwater ecosystems, which can affect species interactions and disease pathology.3. To determine whether water‐related diseases in wildlife are increasing, we used generalised additive models to quantitatively assess trends in the scientific literature (1970–2009) for major freshwater groups, including amphibians, molluscs, crayfishes, fishes, mammals, reptiles and birds. We further examined what types of pathogens were primarily responsible for observed patterns and whether recurrent groups or transmission modes could be identified.4. After correcting for research effort and temporal autocorrelation, we find that reports of disease varied over time and across freshwater taxa, with significant increases in amphibians, fishes and crayfishes, a significant decrease in molluscs, and no significant change in freshwater reptiles, birds or mammals. The types and diversity of pathogens varied considerably among groups. Reports of infection in amphibians were dominated by helminths and a chytridiomycete, in crayfishes by viruses and fungi, in molluscs by digenetic trematodes, in birds, fishes and mammals by viruses, protists and helminths and in reptiles by helminths and bacteria.5. These results provide some of the first quantitative evidence indicative of a long‐term increase in disease‐related research for freshwater taxa. Managing freshwater ecosystems to reduce or minimise human and wildlife disease risk – arguably one of the most significant ecosystem services – will require enhanced incorporation of ecological approaches alongside medical and veterinary tools.
Falls in older hospital inpatients and the effect of cognitive impairment: a secondary analysis of prevalence studies
Authors: Härlein Jürgen , Halfens Ruud JG , Dassen Theo , Lahmann Nils A 
Published: December 2010

Aims and objectives.  The objective of this study was to compare fall rates in older hospital inpatients with and without cognitive impairment. Relationships between age, gender, mobility, cognitive impairment, care dependency, urinary incontinence and medical disciplines were investigated.Background.  Falls are common in older people with cognitive impairment, but studies in the hospital setting are rare.Design.  A secondary analysis of three nationwide prevalence studies in German hospitals from the years 2005, 2006 and 2007 was conducted.Method.  Trained staff nurses used a standardised instrument to collect data about accidental falls within the last two weeks in their institutions and about other patient characteristics. Data from 9246 patients aged 65 years or older from 37 hospitals were analysed.Results.  The fall rate for cognitively impaired patients was 12·9%, while only 4·2% of older persons without cognitive impairment experienced a fall. Comparison between medical disciplines showed great differences concerning fall risk for confused and non‐confused inpatients. In multivariate logistic regression analysis, the odds‐ratio association of cognitive impairment and falls was 2·1 (CI 1·7–2·7). Higher age (OR 1·5, CI 1·2–1·9), greater care dependency (OR 1·6, CI 1·1–2·1), reduced mobility (OR 2·6, CI 1·9–3·7) and being a patient on a geriatric ward (OR 1·8, CI 1·1–2·9) were also statistically significant predictors in this model.Conclusions.  Cognitively impaired older people constitute a high‐risk group for accidental falls in hospitals.Relevance to clinical practice.  Fall prevention strategies in the hospital setting should address cognitively impaired inpatients as an important high‐risk group.
Nurses’ clinical assessments of older clients who are suspected victims of abuse: an exploratory study in community care in Norway
Authors: Sandmoe Astrid , Kirkevold Marit 
Published: December 2010

Aim and objectives.  The aim of this study was to explore how nurses in community care experienced clinical assessment of suspected abuse cases and factors impacting on the assessment process.Background.  Elder abuse is a serious problem affecting an older person’s health and well‐being. A considerable number of older victims of abuse receive health care services. Health professionals, such as nurses in community care, will very likely meet clients suffering from abuse. In Scandinavia, research about older abuse is quite limited. This also applies to research into nurses’ clinical assessments of older, abused clients under community care services.Design.  Qualitative, hermeneutic approach.Method.  Ten nurses were recruited by purposeful sampling and interviewed in‐depth. The analysis process was guided by Gadamer’s recommendations on understanding and interpreting oral and written text.Results.  Three important phases in the clinical assessment were revealed, including the recognition of a possible abuse situation, an information gathering phase and, finally, judgement and conclusion. Two critical factors impacting on the process included the nurse’s ability to get into position to perform the necessary observations in the home and the quality of the information gathered about the client’s situation. In addition, factors related to the client and the community care organisation influenced the nurses’ work and thereby promoted, delayed or interrupted the clinical assessment.Conclusions.  Nurses’ opportunities to identify older, abused clients might fail unless certain conditions are present that facilitate the clinical assessment. In particular, the involvement of the manager is important, in addition to the presence of alliances in the assessment process.Relevance to clinical practice.  The findings indicate the need for a framework that may facilitate the systematic clinical assessment of suspected older, abused clients in community care. Such a framework might ensure the quality of the service provided to victims of abuse.