bluuebunny/crossref_metadata_2025_split huggingface dataset:
linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type
Authors: Kalinka Alex T. , Tomancak Pavel 
Published: May 2011

Abstract
Summary: An essential element when analysing the structure, function, and dynamics of biological networks is the identification of communities of related nodes. An algorithm proposed recently enhances this process by clustering the links between nodes, rather than the nodes themselves, thereby allowing each node to belong to multiple overlapping or nested communities. The R package ‘linkcomm’ implements this algorithm and extends it in several aspects: (i) the clustering algorithm handles networks that are weighted, directed, or both weighted and directed; (ii) several visualization methods are implemented that facilitate the representation of the link communities and their relationships; (iii) a suite of functions are included for the downstream analysis of the link communities including novel community-based measures of node centrality; (iv) the main algorithm is written in C++ and designed to handle networks of any size; and (v) several clustering methods are available for networks that can be handled in memory, and the number of communities can be adjusted by the user.
Availability: The program is freely available from the Comprehensive R Archive Network (http://cran.r-project.org/) under the terms of the GNU General Public License (version 2 or later).
Contact: kalinka@mpi-cbg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Positional integratomic approach in identification of genomic candidate regions for Parkinson's disease
Authors: Maver Ales , Peterlin Borut 
Published: May 2011

Abstract
Motivation: Recent abundance of data from studies employing high-throughput technologies to reveal alterations in human disease on genomic, transcriptomic, proteomic and other levels, offer the possibility to integrate this information into a comprehensive picture of molecular events occurring in human disease. Diversity of data originating from these studies presents a methodological obstacle in the integration process, also due to difficulties in choosing the optimal unified denominator that would allow inclusion of variables from various types of studies. We present a novel approach for integration of such multi-origin data based on positions of genetic alterations occurring in human diseases. Parkinson's disease (PD) was chosen as a model for evaluation of our methodology.
Methods: Datasets from various types of studies in PD (linkage, genome-wide association, transcriptomic and proteomic studies) were obtained from online repositories or were extracted from available research papers. Subsequently, human genome assembly was subdivided into 10 kb regions, and significant signals from aforementioned studies were arranged into their corresponding regions according to their genomic position. For each region, rank product values were calculated and significance values were estimated by permuting the original dataset.
Results: Altogether, 179 regions (representing 33 contiguous genomic regions) had significant accumulation of signals when P-value cut-off was set at 0.0001. Identified regions with significant accumulation of signals contained 29 plausible candidate genes for PD. In conclusion, we present a novel approach for identification of candidate regions and genes for various human disorders, based on the positional integration of data across various types of omic studies.
Contact: ales.maver@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Pregabalin Suppresses Spinal Neuronal Hyperexcitability and Visceral Hypersensitivity in the Absence of Peripheral Pathophysiology
Authors: Bannister Kirsty , Sikandar Shafaq , Bauer Claudia S. , Dolphin Annette C. , Porreca Frank , Dickenson Anthony H. 
Published: May 2011

Background
Opioid-induced hyperalgesia is recognized in the laboratory and the clinic, generating central hyperexcitability in the absence of peripheral pathology. We investigated pregabalin, indicated for neuropathic pain, and ondansetron, a drug that disrupts descending serotonergic processing in the central nervous system, on spinal neuronal hyperexcitability and visceral hypersensitivity in a rat model of opioid-induced hyperalgesia.

Methods
Male Sprague-Dawley rats (180-200 g) were implanted with osmotic mini-pumps filled with morphine (90 μg · μl⁻¹ · h⁻¹) or saline (0.9% w/v). On days 7-10 in isoflurane anesthetized animals, we evaluated the effects of (1) systemic pregabalin on spinal neuronal and visceromotor responses, and (2) spinal ondansetron on dorsal horn neuronal response. Messenger ribonucleic acid concentrations of α2δ-1, 5HT3A, and μ-opioid receptor in the dorsal root ganglia of all animals were analyzed.

Results
In morphine-treated animals, evoked spinal neuronal responses were enhanced to a subset of thermal and mechanical stimuli. This activity was attenuated by pregabalin (by at least 71%) and ondansetron (37%); the visceromotor response to a subset of colorectal distension pressures was attenuated by pregabalin (52.8%; n = 8 for all measures, P < 0.05). Messenger ribonucleic acid concentrations were unchanged.

Conclusions
The inhibitory action of pregabalin in opioid-induced hyperalgesia animals is neither neuropathy-dependent nor reliant on up-regulation of the α₂δ-1 subunit of voltage-gated calcium channels-mechanisms proposed as being essential for pregabalin's efficacy in neuropathy. In opioid-induced hyperalgesia, which extends to colonic distension, a serotonergic facilitatory system may be up-regulated, creating an environment that is permissive for pregabalin-mediated analgesia without peripheral pathology.
Leaf Rolling Controlled by the Homeodomain Leucine Zipper Class IV GeneRoc5in Rice
Authors: Zou Liang-ping , Sun Xue-hui , Zhang Zhi-guo , Liu Peng , Wu Jin-xia , Tian Cai-juan , Qiu Jin-long , Lu Tie-gang 
Published: May 2011

AbstractLeaf rolling is considered an important agronomic trait in rice (Oryza sativa) breeding. To understand the molecular mechanism controlling leaf rolling, we screened a rice T-DNA insertion population and isolated the outcurved leaf1 (oul1) mutant showing abaxial leaf rolling. The phenotypes were caused by knockout of Rice outermost cell-specific gene5 (Roc5), an ortholog of the Arabidopsis (Arabidopsis thaliana) homeodomain leucine zipper class IV gene GLABRA2. Interestingly, overexpression of Roc5 led to adaxially rolled leaves, whereas cosuppression of Roc5 resulted in abaxial leaf rolling. Bulliform cell number and size increased in oul1 and Roc5 cosuppression plants but were reduced in Roc5-overexpressing lines. The data indicate that Roc5 negatively regulates bulliform cell fate and development. Gene expression profiling, quantitative polymerase chain reaction, and RNA interference (RNAi) analyses revealed that Protodermal Factor Like (PFL) was probably down-regulated in oul1. The mRNA level of PFL was increased in Roc5-overexpressing lines, and PFL-RNAi transgenic plants exhibit reversely rolling leaves by reason of increases of bulliform cell number and size, indicating that Roc5 may have a conserved function. These are, to our knowledge, the first functional data for a gene encoding a homeodomain leucine zipper class IV transcriptional factor in rice that modulates leaf rolling.
Characterisation of Slovenian honeys on the basis of sensory and physicochemical analysis with a chemometric approach
Authors: Bertoncelj Jasna , Golob Terezija , Kropf Urška , Korošec Mojca 
Published: May 2011

SummaryThe purpose of this study was sensory and physicochemical characterisation of Slovenian honeys with a chemometric approach. Honey samples were obtained from the beekeepers in different natural geographical macroregions of Slovenia. The sensory characteristics of the seven main types of Slovenian honeys are described, together with the physicochemical analyses. The average results of electrical conductivity (0.19–1.61 mS cm−1), pH (4.01–5.51), free acidity (13.3–30.9 meq kg−1), proline content (317–558 mg kg−1), protein content (1.70–3.53 g kg−1), optical rotation (–19.6 to 12.6), phenolic content (44.9–232.5 mg GAE kg−1) and antioxidant activity [69.6–456.4 μm Fe(II)] show wide variability among analysed honey types. Statistically significant differences were obtained among different honey types, generally lower values of the analysed parameters were determined in the light honeys, as the acacia, linden and multifloral honeys, while the higher values are characteristic for darker honeys, as the chestnut, fir, spruce and forest honeys. Linear discriminant analysis was performed to classify the honey samples according to their botanical origin and proved that physicochemical parameters analysed can provide enough information for the classification and distinction of acacia, linden, multifloral and chestnut honeys, and the group of honeydew honeys (fir, spruce and forest honeys).
Terbinafine pharmacokinetics after single dose oral administration in the dog
Authors: Sakai Mary R. , May Elizabeth R. , Imerman Paula M. , Felz Charles , Day Timothy A. , Carlson Steve A. , Noxon James O. 
Published: May 2011

AbstractTerbinafine is an allylamine antifungal prescribed for the treatment of mycoses in humans. It is increasingly being used in veterinary patients. The purpose of this study was to evaluate the pharmacokinetic properties of terbinafine in dogs after a single oral dose. Ten healthy adult dogs were included in the study. A single dose of terbinafine (30–35 mg/kg) was administered orally, and blood samples were periodically collected over a 24 h period during which dogs were monitored for adverse effects. Two of 10 dogs developed transient ocular changes. A high‐performance liquid chromatography assay was developed and used to determine plasma terbinafine concentrations. Pharmacokinetic analysis was performed using PK Solutions®computer software. Area under the curve (AUC) from time 0 to 24 h was 15.4 μg·h/mL (range 5–27), maximal plasma concentration (Cmax) was 3.5 μg/mL (range 3–4.9 μg/mL) and time toCmax(Tmax) was 3.6 h (range 2–6 h). The time above minimal inhibitory concentration (T > MIC) as well as AUC/MIC was calculated for important invasive fungal pathogens and dermatophytes. TheT > MIC was 17–18 h forBlastomyces dermatitidis,Histoplasma capsulatumand dermatophytes (Microsporumspp. andTrichophyton mentagrophytes), while the MIC forSporothrix schenckiiandCoccidioides immitiswas exceeded for 9.5–11 h. The AUC/MIC values ranged from 9 to 13 μg h/mL for these fungi. Our results provide evidence supporting the use of terbinafine as an oral therapeutic agent for treating systemic and subcutaneous mycoses in dogs.
Analysis of associations between the patterns of global DNA hypomethylation and expression of DNA methyltransferase in patients with systemic lupus erythematosus
Authors: Zhu Xiaohua , Liang Jun , Li Feng , Yang Yongsheng , Xiang Leihong , Xu Jinhua 
Published: May 2011

AbstractObjectives To analyze associations between the patterns of global DNA hypomethylation and expression of DNA methyltransferase (DNMT1, DNMT3A, and DNMT3B) in patients with systemic lupus erythematosus (SLE) and to obtain a deeper understanding of the role that epigenetic mechanism may have on SLE.Methods The global DNA methylation profile in T cells from 34 patients with SLE and 23 healthy controls was assessed by the specific monoclonal antibodies to 5‐methylcytosine and was analyzed quantitatively by flow cytometry. Real‐time reverse transcription–polymerase chain reaction was applied to analyze DNMTs (DNMT1, DNMT3A, and DNMT3B) mRNA levels in T cells from patients and controls.Results Patients with SLE had significantly global DNA hypomethylation than that in controls (P = 0.004), and the global DNA methylation was inverse correlated with the SLE Disease Activity Index (P < 0.0005). Patients with SLE had significantly lower levels of DNMT1 mRNA than that in controls (P < 0.0005), and there was no correlation between the level of DNMT1 mRNA and SLE Disease Activity Index, neither the correlation between the levels of DNMT1 mRNA and global DNA methylation. There was no statistical difference in levels of DNMT3A mRNA between the patients with SLE and normal controls. The levels of DNMT3B mRNA were very low, and there was no difference in patients with SLE and normal controls.Conclusions Global DNA hypomethylation plays an important role in the pathogenesis of SLE. Lower expression of DNMT1 mRNA may play a role in the pathogenesis of SLE, which is not the exclusive regulation factor of global DNA methylation of SLE. The mechanism of global DNA hypomethylation in patients with SLE was complicated. Enzymes that participate in DNA methylation and demethylation events should be studied further.
Basal cell carcinoma: evidence‐based medicine and review of treatment modalities
Authors: Kwasniak Laura A. , Garcia‐Zuazaga Jorge 
Published: May 2011

AbstractNon‐melanoma skin cancers (NMSCs) are the most common type of human cancer, with basal cell carcinomas representing the majority of these cancers. The following article will focus on a review of the current knowledge regarding incidence, risk factors, and pathogenesis, including genetics, clinical features, and treatment options of basal cell carcinomas.
Update on nephrogenic systemic fibrosis: are we making progress?
Authors: Haemel Anna K. , Sadowski Elizabeth A. , Shafer Martin M. , Djamali Arjang 
Published: May 2011

AbstractNephrogenic systemic fibrosis is a rare fibrosing disorder associated with the use of gadolinium‐based contrast agents in patients with renal dysfunction. However, only a small proportion of at‐risk patients develops the disorder, and the exact determinants of disease are still not completely clear. Here, we present an update on emerging evidence for the role of gadolinium‐based contrast agents, renal dysfunction, and background inflammation in disease expression, with a focus on current experimental models. Based on these findings, significant progress has been made in our understanding of the pathophysiology of this disorder over the last few years. This review provides a summary of these developments with discussion of the implications for clinical practice and directions for additional study.
Intestinal transplantation: Current status and future directions
Authors: Garg Mayur , Jones Robert M , Vaughan Rhys B , Testro Adam G 
Published: May 2011

AbstractThree decades after the first intestinal transplant was performed in humans, this life‐saving procedure has come of age and now offers hope of long‐term survival in a small group of patients with life‐threatening complications of intestinal failure and parenteral nutrition. Success rates have greatly improved, largely through advances in immunosuppression protocols, improved surgical technique and postoperative care, and accumulated experience. Management of the intestinal transplant recipient entails careful surveillance, prevention, and treatment of rejection and infection, as well as optimization of feeding and nutrition. With this approach, survival and quality of life are demonstrably improved, such that intestinal transplantation is now an established and accepted procedure for this very select group of highly‐complex patients.
Palliative day care: A qualitative study of service users' experiences in the United Kingdom
Authors: Hyde Val , Skirton Heather , Richardson Janet 
Published: May 2011

AbstractIn many countries, specialist palliative day care for patients with life‐limiting conditions is provided by specific teams of professionals from a range of relevant disciplines. During 2006 to 2007, the day care services at a hospice in the UK were redesigned so that specialist palliative care sessions replaced the existing long‐established, traditional day care model. The purpose of this study was to enhance the understanding of those aspects of the service that the users valued most (the “X‐factor”). Qualitative data were collected via semistructured interviews with 29 patients and eight carers. These data were subjected to a framework analysis. The users of the service used poignant and powerful words to describe the special qualities that they valued, some phrasing it as the X‐factor. The data are presented under three themes: the quality of the staff; the sense of community; and relationships. Of these, the relationships between and within the staff and patient groups held the greatest significance for the patients. Service providers need to recognize that opportunities for the formation of relationships between the patients, staff, and carers are of utmost importance when designing palliative day care services.
Realistic evaluation of an emergency department‐based mental health nurse practitioner outpatient service in Australia
Authors: Wand Timothy , White Kathryn , Patching Joanna 
Published: May 2011

AbstractEvaluation of new models of care requires consideration of the complexity inherent within health care programs and their sensitivity to local contextual factors as well as broader community, social and political influences. Evaluation frameworks that are flexible and responsive while maintaining research rigor are therefore required. Realistic evaluation was adopted as the methodology for the implementation and evaluation of an emergency department‐based mental health nurse practitioner outpatient service in Sydney, Australia. The aim of realistic evaluation is to generate, test and refine theories of how programs work within a given context. This paper represents the final methodological step from the completed evaluation. A summary of quantitative and qualitative findings from the mixed‐methods evaluation is presented, which is transformed into a set of overarching statements or “middle range theories”. Middle range theory statements seek to explain the success of a program and provide transferable lessons for practitioners wishing to implement similar programs elsewhere. For example, the research team consider that early consultation with key local stakeholders and emergency department ownership of the project was pivotal to the implementation process.
Barriers to and facilitators of coping with spinal cord injury for Iranian patients: A qualitative study
Authors: Babamohamadi Hassan , Negarandeh Reza , Dehghan‐Nayeri Nahid 
Published: May 2011

AbstractThe purpose of the present study was to explore the perspectives and experiences of Iranian patients regarding barriers and facilitators to their ability to cope with spinal cord injury (SCI). A qualitative design, based on the content analysis approach, was used to collect and analyze the experiences of 18 patients with spinal cord injury in two centers in Tehran, Iran. After using purposeful sampling for selection of the participants, semi‐structured interviews were held for data collection. Lack of “knowledge”, “financial resources”, “employment opportunities”, “suitable facilities and accessibility” as well as “societal acceptance and support” emerged as barriers; and having “self‐confidence”, “religious beliefs”, “support networks” and “positive thinking” emerged as facilitators in coping with spinal cord injury. Participants believed that with these hindering factors in place, adapting to their new condition had been difficult, therefore they can only manage to adapt partially to their situation. Additional multidisciplinary endeavors are needed to help this group cope adequately and further research is required to influence policy making and legislation processes efficiently.
Correlation between a self‐administered walk test and a standardised Six Minute Walk Test in adults
Authors: Du HuiYun , Davidson Patricia M. , Everett Bronwyn , Salamonson Yenna , Zecchin Robert , Rolley John Xavier , Newton Phillip J. , Macdonald Peter S. 
Published: May 2011

AbstractThis study was undertaken to assess the correlation between a self‐administered, adapted Six Minute Walk Test (the Home‐Heart‐Walk) and the standard Six Minute Walk Test based on the American Thoracic Society guideline. A correlational study was conducted at a university campus in Sydney, Australia. Thirteen healthy volunteers underwent the Home‐Heart‐Walk and the standard Six Minute Walk Test on a single occasion. The distance that participants walked during the two tests was assessed using Pearson's correlation. The correlation between the Home‐Heart‐Walk and the Six Minute Walk Test distance was 0.81. The Home‐Heart‐Walk distance was highly correlated to the standard Six Minute Walk Test distance in this study. This relationship provides confidence for further research in populations to facilitate monitoring and evaluation.
Perioperative management of children undergoing craniofacial reconstruction surgery: a practice survey
Authors: Stricker Paul A. , Cladis Franklyn P. , Fiadjoe John E. , McCloskey John J. , Maxwell Lynne G. 
Published: May 2011

SummaryObjective/Aims:  To assess current practices in the management of children undergoing craniofacial surgery and identify areas of significant practice variability with the intent to direct future research.Background:  The perioperative management of infants and children undergoing craniofacial reconstruction surgery can be challenging because of the routine occurrence of significant blood loss with associated morbidity. A variety of techniques have been described to improve the care for these children. It is presently unknown to what extent these practices are currently employed.Methods:  A web‐based survey was sent to representatives from 102 institutions. One individual per institution was surveyed to prevent larger institutions from being over‐represented in the results.Results:  Requests to complete the survey were sent to 102 institutions; 48 surveys were completed. The survey was composed of two parts: management of infants undergoing strip craniectomies, and management of children undergoing major craniofacial reconstruction.Conclusions:  Significant variability exists in the management of children undergoing these procedures; further study is required to determine the optimal management strategies. Clinical trials assessing the utility of central venous pressure and other hemodynamic monitoring modalities would enable evidence‐based decision‐making for monitoring in these children. The development of institutional transfusion thresholds should be encouraged, as there exists a body of evidence supporting their efficacy and safety.