bluuebunny/crossref_metadata_2025_split huggingface dataset:
iBBiG: iterative binary bi-clustering of gene sets
Authors: Gusenleitner Daniel , Howe Eleanor A. , Bentink Stefan , Quackenbush John , Culhane Aedín C. 
Published: July 2012

AbstractMotivation: Meta-analysis of genomics data seeks to identify genes associated with a biological phenotype across multiple datasets; however, merging data from different platforms by their features (genes) is challenging. Meta-analysis using functionally or biologically characterized gene sets simplifies data integration is biologically intuitive and is seen as having great potential, but is an emerging field with few established statistical methods.Results: We transform gene expression profiles into binary gene set profiles by discretizing results of gene set enrichment analyses and apply a new iterative bi-clustering algorithm (iBBiG) to identify groups of gene sets that are coordinately associated with groups of phenotypes across multiple studies. iBBiG is optimized for meta-analysis of large numbers of diverse genomics data that may have unmatched samples. It does not require prior knowledge of the number or size of clusters. When applied to simulated data, it outperforms commonly used clustering methods, discovers overlapping clusters of diverse sizes and is robust in the presence of noise. We apply it to meta-analysis of breast cancer studies, where iBBiG extracted novel gene set—phenotype association that predicted tumor metastases within tumor subtypes.Availability: Implemented in the Bioconductor package iBBiGContact: aedin@jimmy.harvard.edu
Divorced mothers' self‐perception of their divorce‐related communication with their children
Authors: Cohen Orna , Leichtentritt Ronit Dina , Volpin Netta 
Published: July 2012

ABSTRACTThis is a qualitative study of divorce‐related communication between mothers and children, as recounted by 20 Jewish Israeli mothers. We adopt the communication privacy management theory, focusing on mothers' subjective experiences of communication, their management of dialectic tension between concealment and disclosure – namely, not only what mothers choose to disclose to and hide from their children, but also the feelings, concerns and perceptions that drove their communication. The mothers' reports convey the challenges and dilemmas they faced when communicating with their children about their divorce and its repercussions; the main one being their obligation to maintain a good father image and their wish to preserve a strong maternal figure. The ‘child's well‐being’ was the dominant criterion in the mothers' decision to reveal or conceal divorce‐related information. Clinical suggestions are made.
Pro‐inflammatory and Th2‐type cytokine responses in PBMC in infants are associated with parental smoking
Authors: Linnamaa P. , Nieminen K. , Koulu L. , Tuomasjukka S. , Kallio H. , Yang B. , Tahvonen R. , Savolainen J. 
Published: July 2012

AbstractBackgroundDuring infancy, a disturbed cytokine balance leads to an atopic immune response. Many risk factors have been associated with the development of atopy. These include parental smoking, elevated cord blood IgE, early exposure to pets and family history of atopy, but the knowledge of their impact on cytokine balance is limited.ObjectiveTo assess the cytokines induced by mitogen in peripheral blood mononuclear cells (PBMC) of infants at 3 months and 12 months of age and their potential association with fatty acid (FA) intervention, parental atopy, atopic dermatitis and parental smoking.MethodsInfants from an intervention study using black currant seed oil (BCSO, n = 34) or placebo (n = 34) were included. PBMC samples were taken at the age of 3 and 12 months. Signs of atopic dermatitis and parental smoking were registered. PBMC were isolated from heparinized blood samples, stimulated with ConcanavalinA mitogen and the cytokine responses were detected at 72 h of stimulation by Luminex technology.ResultsChildren of smoking parents had elevated levels of IL‐4 (P = 0.0004), IL‐5 (P = 0.0002), IFN‐γ (P = 0.039) and TNF (P = 0.0003) at 12 months of age. Children who had atopic dermatitis by the age of 3 months showed elevated levels of IL‐5 at 3 months (P = 0.0027) and 12 months of age (P = 0.022). The production of TNF at the age of 3 months was higher (P = 0.010) and the production of IL‐12 at the age of 12 months was lower (P = 0.025) in infants whose parents were atopic. BCSO intervention did not have any effect on any cytokine production or mRNA expression.ConclusionChildren of smoking parents had highly significantly elevated levels of Th2‐type cytokines IL‐4, IL‐5 and pro‐inflammatory cytokine TNF. The detrimental effects of parental smoking on the child's immune function should lead us to pay more attention to supporting parents to stop smoking.
Endocrinopathies in transfusion‐associated iron overload
Authors: Kim Mee Kyoung , Lee Jong Wook , Baek Ki Hyun , Song Ki Ho , Kwon Hyuk Sang , Oh Ki Won , Jang Eun Hee , Kang Moo Il , Lee Kwang Woo 
Published: July 2012

AbstractBackgroundTransfusional iron overload primarily results in reticuloendothelial iron accumulation, which is considered to be less harmful than parenchymal iron accumulation. However, systematic and comprehensive data on endocrine function in transfusion‐associated haemochromatosis are limited.MethodsWe examined 25 aplastic anaemia patients (11 men and 14 women) diagnosed with transfusion‐associated haemochromatosis at a single institution. Pituitary function was determined with a combined pituitary function test. On a different day, a 75‐g oral glucose tolerance test was performed. The bone mineral density (BMD) of the lumbar spine and total hip was assessed with dual‐energy X‐ray absorptiometry.ResultsTwenty‐two (88%) of these 25 patients had at least one endocrine abnormality, and 12 had more than one abnormality. The most common pituitary hormonal deficiency involved the pituitary–gonadal axis; 54% of the total subjects had hypogonadotropic hypogonadism. Two patients had an insufficient cortisol response to corticotrophin‐releasing hormone stimulation. No patient had a deficiency of growth hormone or thyroid‐stimulating hormone. Twelve (48%) had diabetes mellitus, and these patients tended to have higher concentrations of ferritin, alanine aminotransferase and γ‐glutamyl transferase. Osteoporosis (T‐score <−2·5 SD) was observed in 48% of patients. The reduction in BMD was more pronounced in the lumbar spine than in the total hip. The patients with osteoporosis were accompanied by hypogonadism, which predominantly affected the trabecular bone.ConclusionsOur observations suggest that endocrinopathies are common in transfusion‐associated haemochromatosis.
Polymorphisms in the interferon‐induced helicase (IFIH1) locus and susceptibility to Addison's disease
Authors: Żurawek Magdalena , Fichna Marta , Januszkiewicz Danuta , Fichna Piotr , Nowak Jerzy 
Published: July 2012

AbstractObjectiveThe interferon‐induced helicase C domain‐containing protein 1 (IFIH1) gene encodes a sensor for double‐stranded RNA that initiates antiviral activity against enteroviruses. Previous investigations have indicated a role for IFIH1 in autoimmunity, as common and rare polymorphisms in this gene have been associated with type 1 diabetes. We hypothesized that polymorphisms in the IFIH1 locus may play a role in the pathogenesis of autoimmune Addison's disease (AAD).DesignWe analysed the association of rs3747517, rs1990760, rs2111485 and rs13422767 single‐nucleotide polymorphisms (SNPs) in the IFIH1 gene and intergenic region with AAD in a Polish cohort. The study comprised 120 patients with AAD and 689 healthy control individuals. Genotyping was performed using TaqMan genotyping assays.ResultsThe major AA genotype of the coding SNP rs1990760 appeared significantly more frequently in AAD compared with healthy individuals (AG vs AA OR 0·62, 95%CI 0·40–0·95, P = 0·03). We also observed a significant difference in the distribution of the rs13422767 SNP alleles. The major G allele was more frequent in the AAD group (A vs G OR 0·65, 95%CI 0·43–0·98, P = 0·04). Both statistically significant differences, for rs1990760 and rs13422767 SNPs, did not survive the Bonferroni correction (P = 0·11 and P = 0·15, for AA genotype and G allele, respectively). Subsequently, a meta‐analysis of 519 patients with AAD and 1362 controls from three different European populations was performed. Under a fixed‐effect model, a pooled OR for A allele and AA genotype of rs1990760 did not display any significant increase among AAD (OR = 1·05, P = 0·56 and OR = 1·08, P = 0·50, respectively).ConclusionThe IFIH1 locus polymorphisms are unlikely to be associated with Addison's disease
Effects of functional groups and species richness on biomass constituents relevant for combustion: results from a grassland diversity experiment
Authors: Khalsa J. , Fricke T. , Weisser W. W. , Weigelt A. , Wachendorf M. 
Published: July 2012

AbstractGrassland biomass has been identified as a potential energy source. The combustion of mature and fibrous biomass, as occurs in extensive grasslands managed with low cutting frequencies, is one possible conversion technique. This study tested the relationship between plant diversity and biomass constituents relevant for combustion, as they determine energy content, energy yield and emission and corrosion risks. The biomass from a biodiversity experiment, with a species richness (SR) gradient of 1–60 species from Central European mesophilic grasslands divided into four functional groups (grasses, legumes, small and tall herbs), was harvested twice a year (in 2008 and 2009). The higher heating value (HHV) was estimated from carbon, hydrogen and oxygen contents to give insight into the energy potential of the species mixtures. The potential risk of emission and corrosion was assessed by analysing ash content, potassium, calcium, magnesium, nitrogen, sulphur and chloride content. HHV was independent of SR, and the overall mean was 18·13 MJ kg−1 DM. Biomass and gross energy (GE) yield were positively affected by SR. The presence of legumes in a mixture resulted in increased HHV, biomass yield and GE, irrespective of the level of SR. Annual GE varied between 59 (average of monocultures) and 152 GJ ha−1 year−1 (mixture of sixty species). The concentration of ash‐forming elements was generally high, suggesting a pre‐treatment of the biomass prior to combustion. Emission‐ and corrosion‐related constituents were clearly affected by the different functional groups, and sulphur and nitrogen both declined with SR. The results of this study show that high SR in experimental grassland communities is beneficial for the energy output and that legumes play a key role for the energy potential. However, identifying a functional group as being solely beneficial or disadvantageous for fuel quality was difficult.
Fine‐scale quantification of floral and faunal breaks and their geographic correlates, with an example from south‐eastern Australia
Authors: Di Virgilio Giovanni , Laffan Shawn W. , Ebach Malte C. 
Published: July 2012

AbstractAim  We introduce a method to quantify shared breaks in aggregate biotic distributions and their relationships to geographic variables. The method is based on quantification of distributional taxic and abiotic data that can be applied over multiple spatial scales. We aim to show biogeographic breaks and varying transition zones at a fine level of detail (5‐km resolution) and develop an approach to assess existing bioregionalization schemes.Location  Global applicability, using an example from New South Wales in south‐eastern Australia.Methods  Moving window analyses, rotated in 15° increments through 360°, are used to assess the degree of anisotropic spatial turnover between sets of gridded cells containing georeferenced species observations. Patterns of biotic turnover are compared with equivalent analyses for elevation and lithology. Identified breaks are assessed against an existing bioregionalization scheme (Interim Biogeographic Regionalisation of Australia, IBRA).Results  There was fine‐scale concordance between turnover patterns and several IBRA bioregions. Breaks in turnover of flora and fauna corresponded with the boundaries of the Hunter Valley and Sydney Basin regions, particularly the boundary between the Brigalow Belt South and Sydney Basin. Low‐turnover zones were quantified; prominent examples are the Sydney Cataract and Wyong bioregions. Turnover along many boundaries was gradational, confirming that mapped breaks are not abrupt. A previously unidentified break was identified in the South East Corner bioregion. Spatial turnover patterns were similar between biota and were reflected in mean correlation coefficients between turnover in each group: mammals–reptiles (r = 0.70, P << 0.01); mammals–flora (r = 0.56, P << 0.01); and reptiles–flora (r = 0.51, P << 0.01). Generally, patterns of abiotic turnover reflected biotic turnover, although mean turnover correlations were weaker than between biota.Main conclusions  Using this method we were able to characterize taxic breaks and overlaps in detail and at a spatially fine resolution. For our study region, we confirm the overall integrity of the IBRA framework, but suggest that it may benefit from revision in some respects.
Experiences of caregivers of people with Parkinson’s disease in Singapore: a qualitative analysis
Authors: Tan Siok Bee , Williams Allison F , Morris Meg E 
Published: July 2012

Aims and objectives.  To conduct an in‐depth qualitative examination of the experiences of Singaporean people caring for those with Parkinson’s disease (PD).Background.  The need to provide care for people with PD will increase with the extended life expectancy of Singaporeans. Caring for people with PD in their own homes for as long as possible is argued to provide psychosocial benefits as well as benefiting the community by delayed institutionalisation and reduced healthcare costs.Design.  This study reports the qualitative exploratory component of a large mixed method sequential explanatory design.Methods.  Caregivers were selected through a purposive sampling technique and stratified based on the Hoehn and Yahr disease staging. Twenty‐one semi‐structured interviews were conducted in the home setting. Interviews were audio‐taped and transcribed verbatim. The qualitative data were analysed using Ritchie and Spencer’s framework method of qualitative analysis (1994, Analyzing Qualitative Data, Routledge, London).Results.  Seventeen (81%) caregivers were women, and their ages ranged from 31 years to more than 71 years. The length of the interview ranged from 42–106 minutes. The interview transcriptions produced 1731 free nodes, and after careful scrutiny for redundancy, 11 sub‐themes were identified, which were organised into four key themes. These themes pertained to: (1) Coping and adaptation, (2) Challenges of caregiving, (3) Effects of caregiving on the caregivers and the (4) Need for better caregiver support.Conclusion.  The results of this study have provided insights into the coping and well‐being of caregivers of people with PD. The progressive nature of PD placed a significant burden on caregivers’ emotional well‐being. The findings of this study underscore the need for formal caregiver support and education to reduce strain in caregivers targeted at every stage of PD as there is no clear pattern of disease progression.Relevance to clinical practice.  This study has provided important findings that will inform the construction of interventional strategies to reduce caregiver burden and the provision of better support services for caregivers.
Tinkering and tailoring individual consultations: how practice nurses try to make cardiovascular risk communication meaningful
Authors: Boase Sue , Mason Dan , Sutton Stephen , Cohn Simon 
Published: July 2012

Aims and objectives.  To explore the perspectives of practice nurses in their role of communicating cardiovascular risk to patients.Background.  Nurses in primary care have for some time been engaged in cardiovascular risk discussions with patients. With the recent introduction of the NHS Health Checks, the focus on this work is set to increase.Design.  Qualitative using a framework approach.Methods.  Two focus groups and 16 semi‐structured interviews were conducted with nurses purposively sampled from those working in primary care.Results.  The nurses’ accounts revealed the need to develop a relationship of trust and establish a level of relevance with each individual patient whilst discussing cardiovascular risk. Potential aspects of these discussions were as follows: working within a highly structured data‐collecting task; time constraints and consideration of the individual’s context. We used the idea of tailoring to describe how nurses navigate and constantly modify and pitch their approach for each patient they see in response to these constraints.Conclusion.  We suggest that in order for risk to be made meaningful to patients, practice nurses recognise the need for such information to be embedded in the more reciprocal dynamics of nurse‐patient consultations. From their perspective, success is often as much about not saying something, or saying it in a particular way, as saying anything accurately or consistently.Relevance to clinical practice.  For practice nurses to be instrumental in the successful delivery of health prevention policy initiatives such as the NHS Health Checks, it is important to acknowledge their views and perspectives in undertaking this work. This study suggests that the nurses recognised the need for further skills and a refinement of approach for those health professionals involved.
Oppression and exposure as differentiating predictors of types of workplace violence for nurses
Authors: Rodwell John , Demir Defne 
Published: July 2012

Aims and objectives.  To extend a model of the antecedents of workplace bullying to apply to a wider range of types of workplace aggression, including bullying and several types of violence, among nurses.Background.  Research that has focused on workplace bullying has found that the Demand‐Control‐Support model, negative affectivity and certain demographic factors play important roles as antecedents of bullying.Design.  A cross‐sectional design.Methods.  A validated questionnaire was sent to the work addresses of all nursing and midwifery staff in a medium‐to‐large hospital in Australia. A total of 273 nurses and midwives returned their completed questionnaires. Ordinal regressions were conducted to assess the antecedents of workplace aggression across bullying and violence.Results.  Aspects of the Demand‐Control‐Support model and job tenure significantly predicted particular forms of violence, while negative affectivity and work schedule were significant for bullying.Conclusions.  The patterns of the results suggest key mechanisms that characterise certain forms of violence and distinguish between bullying and types of violence across the range of workplace aggression. In particular, oppression and exposure appear to differentiate types of workplace violence.Relevance to clinical practice.  The study suggests ways in which nursing and hospital managers may act to reduce the likelihood of certain forms of aggression, particularly violence, from occurring.
Lifestyle health promotion interventions for the nursing workforce: a systematic review
Authors: Chan Choi Wan , Perry Lin 
Published: July 2012

Aims and objectives.  Study aims were to identify the efficacy of lifestyle health promotion interventions intended to improve behavioural health risk factors and/or behavioural or clinical outcomes of working‐age nurses.Background.  Nurses constitute around half the health workforce but global shortages and an ageing profile challenge future supply. The occupational hazards and stresses of nursing are well known. Health promotion, possibly workplace‐based, presents opportunities to safeguard the health of nurses.Design.  This was a systematic review undertaken in line with guidance for reviews in health care.Methods.  Seven electronic databases were searched from 2000–2011 and references of relevant papers. Two reviewers independently reviewed and critiqued retrieved papers and extracted data. Methodological features were described using the CONSORT checklists; risk of bias was assessed using the Cochrane Handbook classification.Results.  With design inclusion criteria relaxed to include an uncontrolled trial, only three intervention studies were retrieved, from the United States, Canada and Taiwan. All had limitations and high risk of bias, but benefits were reported. Outcomes included fewer cigarettes smoked during the intervention period, down from mean (SD) 20 (8)–12 (9) per day (p < 0·001); significantly reduced fat mass (0·68 vs. 0·07 kg; p = 0·028); and significant gains across a battery of fitness assessments. The paucity of work focused on nurses’ health behaviours was the important finding.Conclusion.  The workplace is a potentially fruitful location for health promotion intervention but nurses have seldom been recognised as a target participant group. Given the international priority ascribed to nursing workforce retention, this is a missed opportunity for occupational health planning. Potential benefits to nurses’ welfare and well‐being may accrue from well‐designed intervention studies.Relevance to clinical practice.  Nurse leaders have a key role in driving recognition, spearheading commitment and development of targeted, whole‐organisation programmes to promote health profile improvement for the nursing workforce.
Multiple rapid swallow responses segregate achalasia subtypes on high‐resolution manometry
Authors: Kushnir V. , Sayuk G. S. , Gyawali C. P. 
Published: July 2012

AbstractBackground  Multiple rapid swallows (MRS) inhibit esophageal peristalsis and lower esophageal sphincter (LES) tone; a rebound excitatory response then results in an exaggerated peristaltic sequence. Multiple rapid swallows responses are dependent on intact inhibitory and excitatory neural function and could vary by subtype in achalasia spectrum disorders.Methods  Consecutive subjects with incomplete LES relaxation on high‐resolution manometry (HRM) (Sierra Scientific, Los Angeles, CA, USA) in the absence of mechanical obstruction were prospectively identified. Achalasia spectrum disorders were classified and HRM plots reviewed according to Chicago criteria. Esophageal peristaltic performance and LES function were assessed after 10 wet swallows and MRS (five 2 mL water swallows 2–3 s apart). Findings were compared with 18 healthy controls (28.5 ± 0.6 years, 44% women).Key Results  A total of 46 subjects (57.1 ± 2.1 years, 52.2% women) met inclusion criteria. There was complete failure of peristalsis with MRS in all subjects with achalasia subtypes 1 and 2. In contrast, 80% of achalasia subtype 3 and incomplete LES relaxation (EGJ outflow obstruction) with preserved esophageal body peristalsis had a contractile response to MRS (P < 0.001 compared with subtypes 1 and 2); controls demonstrated 94.4% peristalsis. Percent decrease in LES residual pressure during MRS (compared to wet swallows) segregated achalasia subtypes; those with aperistalsis (subtypes 1 and 2) had a lesser decline (22.6%) compared to those with retained esophageal body peristalsis (40.5%) and controls (51.3%, P < 0.001 across groups).Conclusions & Inferences  Multiple rapid swallow responses segregate achalasia spectrum disorders into two patterns differentiated by presence or absence of esophageal body contraction response to wet swallows. These findings support subtyping of achalasia, with pathophysiologic implications.