bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fluoroscopy During Removal of 50 Upper Arm Venous Ports
Authors: Burbridge Brent , Sinclair Nicolette , Stoneham Grant , Otani Robert , Szkup Peter 
Published: November 2013

Abstract
Background: The Cook Vital Port system was observed with fluoroscopy before elective removal. A previous publication noted that catheter fracture with this device occurred at the entry of the catheter into the vein used for catheter deployment. We hypothesized that catheter rupture at the vein entry site may be due to ballooning of the catheter during injection, or possibly due to angulation of the catheter during arm movements.
Methods: Port system contrast injection and fluoroscopy was performed for 50 consecutive patients who attended for elective arm vein port removal. Assessment of the angle of entry of the catheter into the arm vein was performed with the arm in anatomic position and during arm movements.
Results: There was no evidence of catheter ballooning or distortion during contrast injection. There was no evidence of fibrin sheath formation at the catheter tip. One catheter was observed to leak at the vein entry site with the injection of contrast. The only arm movement that affected the angle of the catheter at the vein entry site was flexion at the elbow. The average change in the angle of the catheter between anatomic position and full elbow flexion was 22.4°C.
Conclusions: The hypothesis of ballooning of the catheter at the vein entry site during injection was not confirmed. We observed a wide variation in catheter angulation with elbow flexion. The exact cause for catheter fracture remains unknown.
The Need for Comparative Data in Vascular Access: The Rationale and Design of the PICC Registry
Authors: Girgenti Constance , Moureau Nancy L. 
Published: November 2013

Abstract
Approximately 4.3 million peripherally inserted central catheters (PICCs) are placed each year. Currently, there are no national-level comparative data registries to gather information regarding PICC placement, care, or maintenance, and there are no benchmarks or quality measures for vascular access specialists. As the specialty of vascular access evolves from placing peripheral intravenous catheters and administering infusions to the placement of more advanced devices such as PICCs and other central venous access devices, the lack of national comparative data becomes more significant. Without consistent, comparative data, vascular access specialists cannot demonstrate the high level of clinical outcomes provided for patients or justify the value of the specialty to hospital administrators or third-party payers. Data collection must evolve to improve quality and show cost-effectiveness. National-level comparative data collection has been used for decades by physicians to implement quality initiatives and improve patient care. Comparative data can now easily be provided using informatics technologies like the Internet to collect and analyze data for improved clinical outcomes. Vascular access teams must begin using data registries for collecting comparative data, allowing the development of benchmarks and improved quality measures.
The Effects of 3 Peripherally Inserted Central Catheter Insertion Techniques in Chinese Patients With Different Vascular Status
Authors: Yuan Ling , Fu Rong , Li Rong-Mei , Guo Miao-Miao , Chen Xiang-Yu 
Published: November 2013

Abstract
Objective: To provide evidence for selecting an appropriate peripherally inserted central catheter (PICC) insertion technique by comparing the insertion success rate and the incidence of complications with 3 PICC insertion techniques.
Methods: We assigned enrolled patients to 3 groups according to the insertion technique selected by the individual patient: Group A, usual insertion technique (traditional, blind insertion); Group B, Modified Seldinger Technique (MST) insertion without ultrasound guidance; and group C, ultrasound-guided MST insertion. We compared the insertion success rate and the incidence of complications among these groups.
Results: When comparing these 3 PICC insertion techniques, no significant difference was seen with respect to the insertion success rate and the incidence of catheter malposition (P &gt; 0.05), although a significant difference existed in the incidence of bleeding at the insertion site after the PICC procedure (P &lt; 0.05), with the ultrasound-guided MST insertion technique superior to the other 2 techniques; the incidence of mechanical phlebitis and catheter occlusion during the use of PICC had no significant difference among the 3 groups (P &gt; 0.05); but a significant difference was seen in the incidence of thrombosis and catheter-related infections (P &lt; 0.05), with a lower incidence in the ultrasound-guided MST insertion group than that in the other 2 groups.
Conclusions: Ultrasound-guided MST insertion technique may address the problems occurring in patients with poor vascular access during the PICC procedure, whereas the usual insertion technique is the best choice for patients with good vascular access and poor economic status. Therefore, the selection of an appropriate insertion technique should be based on the economic and vascular status of the individual patient in clinical practice.
Initial Affect of Introducing Ultrasound Guided—Long Lines to the All Wales Cystic Fibrosis Centre
Authors: Marson Ben Arthur , Davies Carole , Lee Jonathan , Ketchell Robert Ian , Duckers Jamie 
Published: November 2013

Abstract
Background: The insertion of a long line can be a dreaded aspect of receiving courses of intravenous antibiotics for respiratory exacerbations associated with cystic fibrosis. Our study evaluates the use of ultrasound guidance in a pilot scheme to improve the experience of line insertion.
Methods: Fifty-five patients commencing intravenous antibiotics for respiratory exacerbation had a long line inserted using conventional Seldinger technique, whereas 18 patients had a line inserted after the introduction of ultrasound guidance. Patients completed a questionnaire to score their satisfaction with line placement and longevity. Complication rates of the lines inserted were recorded prospectively.
Results: No significant difference was found in satisfaction with line placement, line longevity, or number of attempts required to insert the line. Qualitative assessment suggests that patients preferred the use of ultrasound.
Conclusions: Our study shows that routine ultrasound guidance is not associated with improvement in clinical variables, but it does have a role in the management of cystic fibrosis in adult patients.
Finding consistent disease subnetworks using PFSNet
Authors: Lim Kevin , Wong Limsoon 
Published: November 2013

Abstract
Motivation: Microarray data analysis is often applied to characterize disease populations by identifying individual genes linked to the disease. In recent years, efforts have shifted to focus on sets of genes known to perform related biological functions (i.e. in the same pathways). Evaluating gene sets reduces the need to correct for false positives in multiple hypothesis testing. However, pathways are often large, and genes in the same pathway that do not contribute to the disease can cause a method to miss the pathway. In addition, large pathways may not give much insight to the cause of the disease. Moreover, when such a method is applied independently to two datasets of the same disease phenotypes, the two resulting lists of significant pathways often have low agreement.
Results: We present a powerful method, PFSNet, that identifies smaller parts of pathways (which we call subnetworks), and show that significant subnetworks (and the genes therein) discovered by PFSNet are up to 51% (64%) more consistent across independent datasets of the same disease phenotypes, even for datasets based on different platforms, than previously published methods. We further show that those methods which initially declared some large pathways to be insignificant would declare subnetworks detected by PFSNet in those large pathways to be significant, if they were given those subnetworks as input instead of the entire large pathways.
Availability: http://compbio.ddns.comp.nus.edu.sg:8080/pfsnet/
Contact: kevinl@comp.nus.edu.sg
Supplementary Information: Supplementary data are available at Bioinformatics online.
Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets
Authors: Rahmatallah Yasir , Emmert-Streib Frank , Glazko Galina 
Published: December 2013

Abstract
Motivation: To date, gene set analysis approaches primarily focus on identifying differentially expressed gene sets (pathways). Methods for identifying differentially coexpressed pathways also exist but are mostly based on aggregated pairwise correlations or other pairwise measures of coexpression. Instead, we propose Gene Sets Net Correlations Analysis (GSNCA), a multivariate differential coexpression test that accounts for the complete correlation structure between genes.
Results: In GSNCA, weight factors are assigned to genes in proportion to the genes’ cross-correlations (intergene correlations). The problem of finding the weight vectors is formulated as an eigenvector problem with a unique solution. GSNCA tests the null hypothesis that for a gene set there is no difference in the weight vectors of the genes between two conditions. In simulation studies and the analyses of experimental data, we demonstrate that GSNCA captures changes in the structure of genes’ cross-correlations rather than differences in the averaged pairwise correlations. Thus, GSNCA infers differences in coexpression networks, however, bypassing method-dependent steps of network inference. As an additional result from GSNCA, we define hub genes as genes with the largest weights and show that these genes correspond frequently to major and specific pathway regulators, as well as to genes that are most affected by the biological difference between two conditions. In summary, GSNCA is a new approach for the analysis of differentially coexpressed pathways that also evaluates the importance of the genes in the pathways, thus providing unique information that may result in the generation of novel biological hypotheses.
Availability and implementation: Implementation of the GSNCA test in R is available upon request from the authors.
Contact: YRahmatallah@uams.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Accessibility of microRNA binding sites in metastable RNA secondary structures in the presence of SNPs
Authors: Day Luke , Abdelhadi Ep Souki Ouala , Albrecht Andreas A. , Steinhöfel Kathleen 
Published: December 2013

Abstract
Motivation: We study microRNA (miRNA) bindings to metastable RNA secondary structures close to minimum free energy conformations in the context of single nucleotide polymorphisms (SNPs) and messenger RNA (mRNA) concentration levels, i.e. whether features of miRNA bindings to metastable conformations could provide additional information supporting the differences in expression levels of the two sequences defined by a SNP. In our study, the instances [mRNA/3′UTR; SNP; miRNA] were selected based on strong expression level analyses, SNP locations within binding regions and the computationally feasible identification of metastable conformations.
Results: We identified 14 basic cases [mRNA; SNP; miRNA] of 3′ UTR-lengths ranging from 124 up to 1078 nt reported in recent literature, and we analyzed the number, structure and miRNA binding to metastable conformations within an energy offset above mfe conformations. For each of the 14 instances, the miRNA binding characteristics are determined by the corresponding STarMir output. Among the different parameters we introduced and analyzed, we found that three of them, related to the average depth and average opening energy of metastable conformations, may provide supporting information for a stronger separation between miRNA bindings to the two alleles defined by a given SNP.
Availability and implementation: At http://kks.inf.kcl.ac.uk/MSbind.html the MSbind tool is available for calculating features of metastable conformations determined by putative miRNA binding sites.
Contact: kathleen.steinhofel@kcl.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
A mathematical model describing the mechanical kinetics of kinesin stepping
Authors: Khataee Hamidreza , Wee-Chung Liew Alan 
Published: December 2013

Abstract
Motivation: Kinesin is a smart motor protein that steps processively forward and backward along microtubules (MTs). The mechanical kinetics of kinesin affecting its stepping behavior is not fully understood. Here, we propose a mathematical model to study the mechanical kinetics of forward and backward stepping of kinesin motor based on the four-state discrete stochastic model of the motor.
Results: Results show that the probabilities of forward and backward stepping can be modeled using the mean probabilities of forward and backward kinetic transitions, respectively. We show that the backward stepping of kinesin motor starts when the probability of adenosine diphosphate (ADP) binding to the motor is much higher than that of adenosine triphosphate (ATP) binding. Furthermore, our results indicate that the backward stepping is related to both ATP hydrolysis and synthesis with rate limiting factor being ATP synthesis. Low rate of ATP synthesis under high backward loads above 10 pN is also suggested as a reason for the detachment of kinesin motor from MT in the kinetic state MTċKinesinċADPċPi.
Availability and implementation: The code for this work is written in Visual C# and is available by request from the authors.
Contact: a.liew@griffith.edu.au
GPU linear and non-linear Poisson–Boltzmann solver module for DelPhi
Authors: Colmenares José , Ortiz Jesús , Rocchia Walter 
Published: December 2013

Abstract
Summary: In this work, we present a CUDA-based GPU implementation of a Poisson–Boltzmann equation solver, in both the linear and non-linear versions, using double precision. A finite difference scheme is adopted and made suitable for the GPU architecture. The resulting code was interfaced with the electrostatics software for biomolecules DelPhi, which is widely used in the computational biology community. The algorithm has been implemented using CUDA and tested over a few representative cases of biological interest. Details of the implementation and performance test results are illustrated. A speedup of ∼10 times was achieved both in the linear and non-linear cases.
Availability and implementation: The module is open-source and available at http://www.electrostaticszone.eu/index.php/downloads.
Contact: walter.rocchia@iit.it
Supplementary information: Supplementary data are available at Bioinformatics online
RNASurface: fast and accurate detection of locally optimal potentially structured RNA segments
Authors: Soldatov Ruslan A. , Vinogradova Svetlana V. , Mironov Andrey A. 
Published: November 2013

Abstract
Motivation: During the past decade, new classes of non-coding RNAs (ncRNAs) and their unexpected functions were discovered. Stable secondary structure is the key feature of many non-coding RNAs. Taking into account huge amounts of genomic data, development of computational methods to survey genomes for structured RNAs remains an actual problem, especially when homologous sequences are not available for comparative analysis. Existing programs scan genomes with a fixed window by efficiently constructing a matrix of RNA minimum free energies. A wide range of lengths of structured RNAs necessitates the use of many different window lengths that substantially increases the output size and computational efforts.
Results: In this article, we present an algorithm RNASurface to efficiently scan genomes by constructing a matrix of significance of RNA secondary structures and to identify all locally optimal structured RNA segments up to a predefined size. RNASurface significantly improves precision of identification of known ncRNA in Bacillus subtilis.
Availability and implementation: RNASurface C source code is available from http://bioinf.fbb.msu.ru/RNASurface/downloads.html.
Contact: ruslansoldatov@gmail.com
Supplementary Information: Supplementary data are available at Bioinformatics online.
Chemical annotation of small and peptide-like molecules at the Protein Data Bank
Authors: Young Jasmine Y. , Feng Zukang , Dimitropoulos Dimitris , Sala Raul , Westbrook John , Zhuravleva Marina , Shao Chenghua , Quesada Martha , Peisach Ezra , Berman Helen M. 
Published: November 2013

Abstract
Over the past decade, the number of polymers and their complexes with small molecules in the Protein Data Bank archive (PDB) has continued to increase significantly. To support scientific advancements and ensure the best quality and completeness of the data files over the next 10 years and beyond, the Worldwide PDB partnership that manages the PDB archive is developing a new deposition and annotation system. This system focuses on efficient data capture across all supported experimental methods. The new deposition and annotation system is composed of four major modules that together support all of the processing requirements for a PDB entry. In this article, we describe one such module called the Chemical Component Annotation Tool. This tool uses information from both the Chemical Component Dictionary and Biologically Interesting molecule Reference Dictionary to aid in annotation. Benchmark studies have shown that the Chemical Component Annotation Tool provides significant improvements in processing efficiency and data quality. Database URL: http://wwpdb.org
When You Ain’t Got Nothin’, You Got Nothin’ to Lose…. Union Recognition Laws, Voluntarism and the Anglo Model
Authors: Doherty Michael 
Published: November 2013

Abstract
A number of recent works have assessed key outcomes of the third statutory union recognition procedure in Britain. A common feature of many of these is the concern that the machinery has failed to achieve positive collective bargaining outcomes for trade unions, due, in particular, to the wider policy environment into which the procedure has been inserted, and the inherent structural confines of the Anglo, ‘representational’, conception of collective bargaining. This article contributes further to this literature, by addressing these issues in the context of, and drawing comparisons with, Irish law on ‘the right to bargain’.
CXCR5+CD4+ follicular helper T cells accumulate in resting human lymph nodes and have superior B cell helper activity
Authors: Havenith Simone H. C. , Remmerswaal Ester B. M. , Idu Mirza M. , van Donselaar-van der Pant Karlijn A. M. I. , van der Bom Nelly , Bemelman Fréderike J. , van Leeuwen Ester M. M. , ten Berge Ineke J. M. , van Lier René A. W. 
Published: November 2013

Abstract
Although many relevant immune reactions are initiated in the lymph nodes, this compartment has not been systematically studied in humans. Analyses have been performed on immune cells derived from tonsils, but as this tissue is most often inflamed, generalization of these data is difficult. Here, we analyzed the phenotype and function of the human CD4+ T-cell subsets and lineages in paired resting lymph node and peripheral blood samples. Naive, central memory cells and effector memory cells as well as Th1, Th2, Th17 and Treg cells were equally represented in both compartments. On the other hand, cytotoxic CD4+ T cells were strikingly absent in the lymph nodes. CXCR5+CD4+ T cells, representing putative follicular Th (Tfh) cells were over-represented in lymph nodes and expressed higher levels of Tfh markers than their peripheral blood counterparts. Compared with the circulating pool, lymph-node-derived CXCR5+CD4+ T cells were superior in providing help to B cells. Thus, functionally competent Tfh cells accumulate in resting human lymph nodes, providing a swift induction of naive and memory antibody responses upon antigenic challenge.
RNA-dependent RNA polymerase of Japanese encephalitis virus binds the initiator nucleotide GTP to form a mechanistically important pre-initiation state
Authors: Surana Parag , Satchidanandam Vijaya , Nair Deepak T. 
Published: November 2013

Abstract
Flaviviral RNA-dependent RNA polymerases (RdRps) initiate replication of the single-stranded RNA genome in the absence of a primer. The template sequence 5′-CU-3′ at the 3′-end of the flaviviral genome is highly conserved. Surprisingly, flaviviral RdRps require high concentrations of the second incoming nucleotide GTP to catalyze de novo template-dependent RNA synthesis. We show that GTP stimulates de novo RNA synthesis by RdRp from Japanese encephalitis virus (jRdRp) also. Crystal structures of jRdRp complexed with GTP and ATP provide a basis for specific recognition of GTP. Comparison of the jRdRpGTP structure with other viral RdRp-GTP structures shows that GTP binds jRdRp in a novel conformation. Apo-jRdRp structure suggests that the conserved motif F of jRdRp occupies multiple conformations in absence of GTP. Motif F becomes ordered on GTP binding and occludes the nucleotide triphosphate entry tunnel. Mutational analysis of key residues that interact with GTP evinces that the jRdRpGTP structure represents a novel pre-initiation state. Also, binding studies show that GTP binding reduces affinity of RdRp for RNA, but the presence of the catalytic Mn2+ ion abolishes this inhibition. Collectively, these observations suggest that the observed pre-initiation state may serve as a checkpoint to prevent erroneous template-independent RNA synthesis by jRdRp during initiation.
Structural mechanism of transcription regulation of the Staphylococcus aureus multidrug efflux operon mepRA by the MarR family repressor MepR
Authors: Birukou Ivan , Seo Susan M. , Schindler Bryan D. , Kaatz Glenn W. , Brennan Richard G. 
Published: November 2013

Abstract
The multidrug efflux pump MepA is a major contributor to multidrug resistance in Staphylococcus aureus. MepR, a member of the multiple antibiotic resistance regulator (MarR) family, represses mepA and its own gene. Here, we report the structure of a MepR–mepR operator complex. Structural comparison of DNA-bound MepR with ‘induced’ apoMepR reveals the large conformational changes needed to allow the DNA-binding winged helix-turn-helix motifs to interact with the consecutive major and minor grooves of the GTTAG signature sequence. Intriguingly, MepR makes no hydrogen bonds to major groove nucleobases. Rather, recognition-helix residues Thr60, Gly61, Pro62 and Thr63 make sequence-specifying van der Waals contacts with the TTAG bases. Removing these contacts dramatically affects MepR–DNA binding activity. The wings insert into the flanking minor grooves, whereby residue Arg87, buttressed by Asp85, interacts with the O2 of T4 and O4′ ribosyl oxygens of A23 and T4. Mutating Asp85 and Arg87, both conserved throughout the MarR family, markedly affects MepR repressor activity. The His14′:Arg59 and Arg10′:His35:Phe108 interaction networks stabilize the DNA-binding conformation of MepR thereby contributing significantly to its high affinity binding. A structure-guided model of the MepR–mepA operator complex suggests that MepR dimers do not interact directly and cooperative binding is likely achieved by DNA-mediated allosteric effects.