bluuebunny/crossref_metadata_2025_split huggingface dataset:
A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio
Authors: Leung Henry C. M. , Yiu S. M. , Yang Bin , Peng Yu , Wang Yi , Liu Zhihua , Chen Jingchi , Qin Junjie , Li Ruiqiang , Chin Francis Y. L. 
Published: April 2011

Abstract
Motivation: With the rapid development of next-generation sequencing techniques, metagenomics, also known as environmental genomics, has emerged as an exciting research area that enables us to analyze the microbial environment in which we live. An important step for metagenomic data analysis is the identification and taxonomic characterization of DNA fragments (reads or contigs) resulting from sequencing a sample of mixed species. This step is referred to as ‘binning’. Binning algorithms that are based on sequence similarity and sequence composition markers rely heavily on the reference genomes of known microorganisms or phylogenetic markers. Due to the limited availability of reference genomes and the bias and low availability of markers, these algorithms may not be applicable in all cases. Unsupervised binning algorithms which can handle fragments from unknown species provide an alternative approach. However, existing unsupervised binning algorithms only work on datasets either with balanced species abundance ratios or rather different abundance ratios, but not both.
Results: In this article, we present MetaCluster 3.0, an integrated binning method based on the unsupervised top–down separation and bottom–up merging strategy, which can bin metagenomic fragments of species with very balanced abundance ratios (say 1:1) to very different abundance ratios (e.g. 1:24) with consistently higher accuracy than existing methods.
Availability: MetaCluster 3.0 can be downloaded at http://i.cs.hku.hk/~alse/MetaCluster/.
Contact: cmleung2@cs.hku.hk; chin@cs.hku.hk
RING: networking interacting residues, evolutionary information and energetics in protein structures
Authors: Martin Alberto J. M. , Vidotto Michele , Boscariol Filippo , Di Domenico Tomàs , Walsh Ian , Tosatto Silvio C. E. 
Published: April 2011

Abstract
Motivation: Residue interaction networks (RINs) have been used in the literature to describe the protein 3D structure as a graph where nodes represent residues and edges physico–chemical interactions, e.g. hydrogen bonds or van-der-Waals contacts. Topological network parameters can be calculated over RINs and have been correlated with various aspects of protein structure and function. Here we present a novel web server, RING, to construct physico–chemically valid RINs interactively from PDB files for subsequent visualization in the Cytoscape platform. The additional structure-based parameters secondary structure, solvent accessibility and experimental uncertainty can be combined with information regarding residue conservation, mutual information and residue-based energy scoring functions. Different visualization styles are provided to facilitate visualization and standard plugins can be used to calculate topological parameters in Cytoscape. A sample use case analyzing the active site of glutathione peroxidase is presented.
Availability: The RING server, supplementary methods, examples and tutorials are available for non-commercial use at URL: http://protein.bio.unipd.it/ring/.
Contact: silvio.tosatto@unipd.it
Identifying indicators of the effects of fishing using alternative models, uncertainty, and aggregation error
Authors: Metcalf Sarah J. , Pember Matthew B. , Bellchambers Lynda M. 
Published: April 2011

Abstract
Metcalf, S. J., Pember, M. B., and Bellchambers, L. M. 2011. Identifying indicators of the effects of fishing using alternative models, uncertainty, and aggregation error. – ICES Journal of Marine Science, 68: 1417–1425. The identification of indicators of the indirect effects of fishing is often an issue for fisheries management, particularly if just commercial catch data are available. Complex, intermediate, and simplified qualitative models were produced for a fishery case study off Western Australia to identify potential indicators of ecosystem change attributable to western rock lobster (Panulirus cygnus) extraction and bait input. Models of intermediate complexity were used to identify indicators because they produced the least aggregation error. Structural uncertainty was considered through a series of structurally different intermediate models. These alternate models consistently predicted that extraction of rock lobster may positively impact small fish of low economic value, such as old wife (Enoplosus armatus), footballer sweep (Neatypus obliquus), and king wrasse (Coris auricularis). These small fish were therefore identified as potential indicators of the effects of rock lobster extraction. Small crustaceans (amphipods and isopods) also displayed positive impacts attributable to bait input from the rock lobster fishery and were identified as potential indicators of bait effects. Monitoring of these indicators may aid the detection of ecosystem change caused by the rock lobster fishery.
Distinct cellular and therapeutic effects of obatoclax in rituximab‐sensitive and ‐resistant lymphomas
Authors: Brem Elizabeth A. , Thudium Karen , Khubchandani Sapna , Tsai Ping‐Chiao , Olejniczak Scott H. , Bhat Seema , Riaz Wasif , Gu Jenny , Iqbal Arshad , Campagna Ryan , Knight Joy , Mavis Cory , Hoskin Paul , Deeb George , Gibbs John F. , Fetterly Gerald , Czuczman Myron S. , Hernandez‐Ilizaliturri Francisco J. 
Published: April 2011

SummaryBcl‐2 proteins represent a rheostat that controls cellular viability. Obatoclax, a BH3‐mimetic, has been designed to specifically target and counteract anti‐apoptotic Bcl‐2 proteins. We evaluated the biological effects of obatoclax on the anti‐tumour activity of rituximab and chemotherapy agents. Obatoclax induced cell death of rituximab/chemotherapy‐sensitive (RSCL), ‐resistant cell lines (RRCL) and primary tumour‐cells derived from patients with B‐cell lymphomas (N = 39). Obatoclax also enhanced the activity of rituximab and had synergistic activity when combined with chemotherapy agents. The ability of Obatoclax to induce PARP cleavage varied between patient samples and was not observed in some RRCL. Inhibition of caspase activity did not affect obatoclax activity, suggesting the existence of caspase‐independent death pathways. Autophagy was detected by LC3 conversion and/or electron microscopy in RRCL and in patient‐derived tumour cells. Moreover, obatoclax activity was inhibited by Beclin‐1 knockdown. In summary, obatoclax is an active Bcl‐2 inhibitor that potentiates the activity of chemotherapy agents and, to a lesser degree, rituximab. Defining the molecular events triggered by obatoclax is necessary to further its clinical development and identify potential biomarkers that are predictive of response.
Modification and testing of the chronic disease compliance instrument to measure treatment compliance in adolescents with diabetes
Authors: Fernandes Ralston , Wales Sandra , Crisp Jackie , Kyngas Helvi 
Published: April 2011

Aims and objectives.  To examine the factor structure and internal consistency of the Chronic Disease Compliance Instrument–Diabetes in an Australian sample of adolescents with diabetes, to modify the instrument and re‐examine factor structure and internal consistency of subsequent scales and to examine the relationship between compliance behaviour and theoretically relevant explanatory factors.Background.  Compliance is a key challenge for adolescents with a chronic disease; however, valid and reliable self‐report measures of compliance behaviour and explanatory factors for diabetes remain elusive, particularly applied in an Australian setting.Design.  Correlational design.Methods.  Participants were 133 adolescents (12–17 years) diagnosed with diabetes and receiving treatment at several health care settings in New South Wales. Participants voluntarily completed the self‐report instrument while waiting to see their Physician/Clinical Nurse Consultant/Diabetes Educator.Results.  On logical modification of the instrument based on exploratory factor analysis and thorough review of item content, the instrument was shown to have sufficient factor structure and internal consistency. Further, eight of the 11 explanatory factor scales were significantly related to compliance behaviour (accounting for 31% of variance).Conclusions.  The present study represents the first application of an established instrument to measure compliance to diabetes treatment among adolescents in an Australian sample and demonstrates that the instrument has sufficient factor structure and internal consistency in this setting. Findings provide a list of relevant factors for explaining compliance, which may be employed to guide the development of initiatives to increase the level of compliance to treatment among Australian adolescents with diabetes.Relevance to clinical practice.  The Chronic Disease Compliance Instrument–Diabetes is a tool that can help nurses with their clinical practice by allowing for more efficient identification of adolescent compliance to diabetes treatment, which may be used in conjunction with HbA1c values already employed.
Global computer‐assisted appraisal of osteoporosis risk in Asian women: an innovative study
Authors: Chang Shu F , Hong Chin M , Yang Rong S 
Published: April 2011

Aims and objective.  To develop a computer‐assisted appraisal system of osteoporosis that can predict osteoporosis health risk in community‐dwelling women and to use it in an empirical analysis of the risk in Asian women.Background.  As the literature indicates, health risk assessment tools are generally applied in clinical practice for patient diagnosis. However, few studies have explored how to assist community‐dwelling women to understand the risk of osteoporosis without invasive data.Design.  A longitudinal, evidence‐based study.Method.  The first stage of this study is to establish a system that combines expertise in nursing, medicine and information technology. This part includes information from random samples (n = 700), including data on bone mineral density, osteoporosis risk factors, knowledge, beliefs and behaviour, which are used as the health risk appraisal system database. The second stage is to apply an empirical study. The relative risks of osteoporosis of the participants (n = 300) were determined with the system. The participants that were classified as at‐risk were randomly grouped into experimental and control groups. Each group was treated using different nursing intervention methods.Results.  The sensitivity and specificity of the analytical tools was 75%. In empirical study, analysis results indicate that the prevalence of osteoporosis was 14·0%. Data indicate that strategic application of multiple nursing interventions can promote osteoporosis prevention knowledge in high‐risk women and enhance the effectiveness of preventive action.Conclusions.  The system can also provide people in remote areas or with insufficient medical resources a simple and effective means of managing health risk and implement the idea of self‐evaluation and self‐caring among community‐dwelling women at home to achieve the final goal of early detection and early treatment of osteoporosis.Relevance to clinical practice.  This study developed a useful approach for providing Asia women with a reliable, valid, convenient and economical self‐health management model. Health care professionals can explore the use of advanced information systems and nursing interventions to increase the effectiveness of osteoporosis prevention programmes for women.
Risk factors for workplace violence in clinical registered nurses in Taiwan
Authors: Pai Hsiang‐Chu , Lee Sheuan 
Published: April 2011

Aims and objectives.  The purpose of this study was to determine the risk factors and mental health consequences of physical and psychological violence for clinical nurses working in healthcare settings in Taiwan.Background.  Registered nurses working in hospitals in Taiwan report high incidences of workplace violence. However, previous studies rarely report psychological abuse among nursing staff, while the relationships between personal factors and workplace violence remain unclear.Design.  This is a cross‐sectional study.Methods.  Participants were invited to complete the Workplace Violence Questionnaire, an instrument designed to assess types of workplace violence (physical violence, verbal abuse, bullying/mobbing and sexual harassment), the characteristics of perpetrators and victims and victims’ reactions to their abuse.Results.  A total of 521 nurses completed the questionnaire. Of the participants, 102 (19·6%) indicated that they had experienced physical violence, 268 (51·4%) had experienced verbal abuse, 155 (29·8%) had experienced bullying/mobbing and 67 (12·9%) had experienced sexual harassment. Multiple logistic analyses indicated that age under 30 years (odds ratio = 2·4; 95% confidence interval = 1·34–4·46) and anxiety (odds ratio = 4·7; 95% confidence interval = 1·24–18·12) increased the odds of verbal abuse, while bullying was associated with anxiety (odds ratio = 2·7, 95% confidence interval = 1·09–6·93). Night work shift increased the odds of experiencing sexual harassment (odds ratio = 2·3, 95% confidence interval = 1·29–4·16), while physical violence was associated with bachelor’s degree (odds ratio = 2·8, 95% confidence interval = 1·20–6·73). The most serious psychological harm was post‐traumatic stress disorder.Conclusions.  Exposure to psychological violence often has a great impact on clinical nurses.Relevance to clinical practice.  For violence prevention, interventions should be sensitive to personal factors. Healthcare institutions should initiate counselling programs to help nurses cope with the stress related to workplace violence.
Readiness of Chinese frail old age home residents towards end‐of‐life care decision making
Authors: Chan Helen YL , Pang Samantha MC 
Published: April 2011

Aims.  To identify different approaches to end‐of‐life care decision‐making among Chinese frail old age home residents.Background.  Advance care planning has been recently introduced to older people, family members and health care providers in the local community with the intention of better preparing them for end‐of‐life care. However, promoting the concept is challenging as the customary beliefs and previous research findings provide little reassurance that Chinese frail older people are ready for this potentially sensitive discussion.Design.  Qualitative study.Method.  Semi‐structured interviews were used to evaluate the process of advance care planning and the readiness of the participants for such planning.Results.  The findings revealed five approaches towards end‐of‐life care decision‐making among the frail old age home residents: holding on to life, planning ahead, weighing benefits, avoiding and deferring.Conclusions.  The various approaches to end‐of‐life care decision‐making, which affect the older person’s level of engagement in advance care planning, are largely related to individual personal values, beliefs and experiences. The level of readiness of frail residents for advance care planning can be explained as a continuum and has to be interpreted in the personal context.Relevance to clinical practice.  The purpose of identifying various approaches is not to be able to screen for individuals who are more likely to undertake advance care planning. Rather, it is to provide insights into the different responses among frail older people with regard to advance care planning and hence the possible ways of devising a specific emphasis and strategies for engaging individuals in the planning process.
The relationships among social capital, organisational commitment and customer‐oriented prosocial behaviour of hospital nurses
Authors: Hsu Chiu‐Ping , Chang Chia‐Wen , Huang Heng‐Chiang , Chiang Chi‐Yun 
Published: April 2011

Aims.  This study examines the perceptions of registered nurses of social capital, organisational commitment and customer‐oriented prosocial behaviour. Additionally, this study also addresses a conceptual model for testing how registered nurses’ perceptions of three types of social capital influence their organisational commitment, in turn intensifying customer‐oriented prosocial behaviour, including role‐prescribed customer service and extra‐role customer service.Background.  Customer‐oriented prosocial behaviour explains differences in job satisfaction and job performance. However, the critical role of customer orientation in the hospital setting has yet to be explored.Design.  Survey.Methods.  The survey was conducted to obtain data from registered nurses working for a large Taiwanese medical centre, yielding 797 usable responses and a satisfactory response rate of 86·7%. The partial least squares method was adopted to obtain parameter estimates and test proposed hypotheses.Results.  The study measurements display satisfactory reliability, as well as both convergent and discriminant validities. All hypotheses were supported. Empirical results indicate that registered nurses’ perceptions of social capital were significantly impacted the extent of organisational commitment, which in turn significantly influenced customer‐oriented prosocial behaviour.Conclusion.  By stimulating nursing staff commitment, health care providers can urge them to pursue organisational goals and provide high quality customer service. To enhance organisational commitment, health care managers should endeavour to create interpersonal interaction platforms in addition to simply offering material rewards.Relevance to clinical practice.  Nurses act as contact employees for their patient customers in the hospital, and they are required to provide patient safety and service quality. This study shows that nurses with high organisational commitment are willing to provide customer‐oriented prosocial activities, which in turn enhances patient satisfaction.
Association of aggressive behaviours with psychiatric disorders, age, sex and degree of intellectual disability: a large‐scale survey
Authors: Tsiouris J. A. , Kim S. Y. , Brown W. T. , Cohen I. L. 
Published: April 2011

AbstractBackground  The link between aggression and mental disorders has been the focus of diverse studies in persons with and without intellectual disabilities (ID). Because of discrepancies in the finding of studies in persons with ID to date, and because of differences in research design, instruments used and the population studied, more research is needed. The purpose of this study was to delineate any significant association between certain psychiatric disorders and specific domains of aggressive behaviours in a large sample of persons with ID controlling for sex, age, autism and degree of ID.Method  Data from the present study were obtained from 47% of all persons with ID receiving services from New York State agencies, using the Institute for Basic Research – Modified Overt Aggression Scale (IBR‐MOAS between 2006 and 2007). The IBR‐MOAS was completed by the chief psychologists of 14 agencies based on information from the participants' files. Demographic information obtained included the psychiatric diagnosis made by the treating psychiatrist as well as information on age, sex and degree of ID. Data from 4069 participants were analysed.Results  Impulse control disorder and bipolar disorder were strongly associated with all five domains of aggressive behaviour in the IBR‐MOAS. Psychotic disorder was highly associated with four domains except for physical aggression against self (PASLF), which was of borderline significance. Anxiety was most associated with PASLF and verbal aggression against self (VASLF); depression with VASLF; obsessive compulsive disorder with physical aggression against objects (PAOBJ); personality disorders with verbal aggression against others (VAOTH), VASLF and PASLF; and autism with physical aggression against others (PAOTH), PAOBJ and PASLF. Mild to moderate ID was associated with VAOTH and VASLF and severe to profound ID with PAOBJ and PASLF. Female sex was most associated with VASLF.Conclusions  Impulse control, mood dysregulation and perceived threat appear to underlie most of the aggressive behaviours reported. Psychosis and depression appeared to have been over‐diagnosed in persons with mild to moderate ID and under‐diagnosed in persons with severe and profound ID. These findings replicate and extend findings from previous studies. The pattern of associations reported can be used as helpful indicators by professionals involved in the treatment of aggressive behaviours in persons with ID.
The effect of pathogen reduction technology (Mirasol) on platelet quality when treated in additive solution with low plasma carryover
Authors: Johnson L. , Winter K. M. , Reid S. , Hartkopf‐Theis T. , Marschner S. , Goodrich R. P , Marks D. C. 
Published: April 2011

Background and Objectives  Pathogen reduction technologies (PRT) for platelets are now compatible with both plasma and platelet additive solutions (PAS). The aim of this study was to examine the effect of PRT on the platelet storage lesion, in the presence of PAS with low plasma carryover.Materials and Methods  PRT‐treated (Mirasol) and untreated buffy coat‐derived platelet concentrates prepared in 28% plasma/PAS‐IIIM were evaluated using in vitro cell quality parameters on days 1, 2, 5, and 7 post‐collection.Results  At day 5, there were no significant differences between control and PRT treated platelets for swirl, viability, pO2, pCO2, mean platelet volume and adenosine diphosphate‐induced aggregation. PRT treatment did not affect the functional integrity of the mitochondria. However, PRT resulted in a decrease in pH and enhancement of platelet glycolysis and activation, evidenced by increased glucose consumption and lactate production rates, increased expression of CD62P, CD63, annexin V staining and increased secretion of cytokines (P < 0·05). Hypotonic shock response and aggregation in response to collagen were also significantly reduced in PRT treated platelets (P < 0·05).Conclusion  Despite the observed differences in platelet metabolism and activation observed following PRT treatment in PAS and low plasma carryover, the results suggest that treatment and storage of platelets in PAS is no more detrimental to platelets than treatment and storage in plasma.
Effect of X‐irradiation on the quality of red cell concentrates
Authors: Bashir S. , Naik F. , Cardigan R. , Thomas S. 
Published: April 2011

Introduction  The irradiation of blood components is used to inactivate T‐lymphocytes to prevent transfusion‐associated graft‐versus‐host (GVH) disease in susceptible recipients. X‐irradiation can be used as an alternative to gamma irradiation and does not involve the use of a radioactive source. This study investigated the effect of X‐irradiation on the quality of various red cell concentrates (RCC).Methods  Whole blood units were processed into RCC in additive solution (SAG‐M) or RCC in plasma suitable for intra‐uterine (IUT) or neonatal exchange transfusion. RCC‐SAG‐M were irradiated at day 14 and sampled before and 0, 7 and 14 days following irradiation. RCC‐IUT and RCC‐Exchange were irradiated on day 4 and sampled before and 0 and 24 h following irradiation. Extracellular potassium levels and free plasma haemoglobin (haemolysis) were compared in X or gamma‐irradiated units during storage.Results  X‐irradiation of RCC in SAG‐M, or RCC for IUT or Exchange resulted in haemolysis comparable with gamma irradiation and levels were below the current UK/CE limit of 0·8% at the end of shelf life. X‐irradiation of RCC‐SAG‐M or RCC‐IUT with haematocrit of 75% and 85% resulted in potassium leakage comparable with gamma‐irradiation. However, X‐irradiation of RCC for neonatal exchange transfusion showed statistically significantly higher supernatant potassium levels after 24 h than gamma irradiation, although this difference is considered to be clinically insignificant.Conclusion  X‐irradiation of RCC in SAG‐M or IUT or RCC in plasma suitable for neonatal exchange transfusion resulted in acceptable levels of haemolysis and potassium leakage compared with the current process of gamma irradiation.