bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tetrasodium EDTA as a Novel Central Venous Catheter Lock Solution Against Biofilm
Authors: Percival Steven L. , Kite Peter , Eastwood Kerrie , Murga Ricardo , Carr Janice , Arduino Matthew J. , Donlan Rodney M. 
Published: April 2006

AbstractBackground:Central venous catheter (CVC)-related bloodstream infections (BSIs) are known to increase rates of morbidity and mortality in both inpatients and outpatients, including hematology-oncology patients and those undergoing hemodialysis or home infusion therapy. Biofilm-associated organisms on the lumens of these catheters have reduced susceptibility to antimicrobial chemotherapy. This study tested the efficacy of tetrasodium EDTA as a catheter lock solution on biofilms of several clinically relevant microorganisms.Methods:Biofilms ofStaphylococcus epidermidis, methicillin-resistantS. aureus, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, andCandida albicanswere grown to levels of approximately 1 × 105colony-forming units (CFU)/cm−1on CVC segments in a model system, then subjected to the tetrasodium EDTA lock treatment.Results:Comparisons of biofilms before and after exposure to the 40-mg/mL−1tetrasodium EDTA lock for 21 hours showed that the biofilm viable cell counts of all organisms tested were significantly reduced (P< .05) after exposure to the treatment.Conclusion:Antimicrobial lock treatment using 40 mg/mL−1of tetrasodium EDTA for at least 21 hours could significantly reduce or potentially eradicate CVC-associated bio-films of clinically relevant microorganisms (Infect Control Hosp Epidemiol2005;26:515-519).
Why Is It That Internists Do Not Follow Guidelines for Preventing Intravascular Catheter Infections?
Authors: Rubinson Lewis , Wu Albert W. , Haponik Edward F. , Diette Gregory B. 
Published: April 2006

AbstractBackground and Objective:High morbidity of CVC-related infections has led to national guidelines for their prevention. Despite recommendations for the use of maximal barrier precautions (mask, sterile gloves, gown, and large drape) and skin antisepsis with 2% Chlorhexidine gluconate during CVC insertion, internists in the United States are not implementing these practices frequently. This study sought to identify and characterize the obstacles to and potential opportunities for improving adherence.Design:Cross-sectional survey.Participants:One thousand randomly selected physician-members of the American College of Physicians-American Society of Internal Medicine.Methods:Several potential determinants of adherence to maximal barrier precautions were assessed, including awareness of, agreement with, and ability to implement the recommendation, as well as the practice and training characteristics of the respondents. Factors influencing antiseptic selection were also recorded.Results:Of 526 respondents, 178 (34%) had recently inserted CVCs. Clinician experience and subspecialty, awareness of CDC guidelines, and external influences (eg, time to collect equipment) did not affect maximal barrier precautions adherence. The only independent predictor of adherence was high outcome expectancy for the use of large sterile drapes (OR, 5.3; CI95, 2.2-12.6). Availability had the greatest influence on internists' selection of specific antiseptic agents, whereas cost was the least important determinant.Conclusions:Despite established efficacy, use of maximal barrier precautions and Chlorhexidine gluconate is low among internists. Because improved adherence to these practices will require increased outcome expectancy for maximal barrier precautions and availability of Chlorhexidine gluconate, targeting these areas through focused education and systems modifications is essential (Infect Control Hosp Epidemiol2005;26:525-533).
Excess Mortality, Hospital Stay, and Cost Due to Candidemia: A Case-Control Study Using Data From Population-Based Candidemia Surveillance
Authors: Morgan Juliette , Meltzer Martin I. , Plikaytis Brian D. , Sofair Andre N. , Huie-White Sharon , Wilcox Steven , Harrison Lee H. , Seaberg Eric C. , Hajjeh Rana A. , Teutsch Steven M. 
Published: April 2006

AbstractObjective:To determine the mortality, hospital stay, and total hospital charges and cost of hospitalization attributable to candidemia by comparing patients with candidemia with control-patients who have otherwise similar illnesses. Prior studies lack broad patient and hospital representation or cost-related information that accurately reflects current medical practices.Design:Our case-control study included case-patients with candidemia and their cost-related data, ascertained from laboratory-based candidemia surveillance conducted among all residents of Connecticut and Baltimore and Baltimore County, Maryland, during 1998 to 2000. Control-patients were matched on age, hospital type, admission year, discharge diagnoses, and duration of hospitalization prior to candidemia onset.Results:We identified 214 and 529 sets of matched case-patients and control-patients from the two locations, respectively. Mortality attributable to candidemia ranged between 19% and 24%. On multivariable analysis, candidemia was associated with mortality (OR, 5.3 for Connecticut and 8.5 for Baltimore and Baltimore County;P< .05), whereas receiving adequate treatment was protective (OR, 0.5 and 0.4 for the two locations, respectively;P< .05). Candidemia itself did not increase the total hospital charges and cost of hospitalization; when treatment status was accounted for, having received adequate treatment for candidemia significantly increased the total hospital charges and cost of hospitalization ($6,000 to $29,000 and $3,000 to $22,000, respectively) and the length of stay (3 to 13 days).Conclusion:Our findings underscore the burden of candidemia, particularly regarding the risk of death, length of hospitalization, and cost associated with treatment (Infect Control Hosp Epidemiol2005;26:540-547).
Dynamics of Hemodialysis Catheter Colonization by Coagulase-Negative Staphylococci
Authors: Fux Christoph A. , Uehlinger Dominik , Bodmer Thomas , Droz Sara , Zellweger Claudine , Mühlemann Kathrin 
Published: April 2006

AbstractObjectives:Catheter colonization is a necessary but poorly characterized step in the pathogenesis of catheter-related infections. Colonization dynamics of central venous hemodialysis catheters were studied with emphasis on coagulase-negative staphylococci (CoNS) and their population genetics, antibiotic resistance, and biofilm formation. The homogeneity of CoNS colony morphotypes was evaluated.Design:Prospective, longitudinal study during 1,158 catheter-days with microbiological analysis of skin swabs, weekly catheter blood and brush samples, and catheter tips.Setting:Hemodialysis unit of a university hospital.Patients:Twenty-six patients with 24 non-tunneled and 5 tunneled catheters.Results:Nineteen (65.5%) of the catheters became colonized, 17 by CoNS. CoNS colonization of the inner lumen was observed in 17.2% of the catheters and was first detectable after 3 weeks. Colonization of the outer surface occurred in 44.8% of the catheters within a minimum of 2 weeks. PFGE of 53 CoNS revealed 10 clones and 20 unique isolates. Isolates from clones were more frequent in catheter blood and brush cultures than were unique isolates (41% vs 15%), were resistant to more antibiotics (median, 7 vs 2), and tended to more often carry theicaAgene (64.1% vs 40%). Four (23.5%) of the catheters showed colonization with a mixture of CoNS based on PFGE. The time from catheter insertion to such mixed CoNS colonization was longer than that for colonization with one CoNS PFGE pattern only (42 vs 25 days).Conclusions:Colonization of hemodialysis catheters is dominated by multidrug-resistant,icaA-positive CoNS clones. Mixed CoNS colonization occurs, but is delayed, suggesting a process of sequential superinfection (Infect Control Hosp Epidemiol2005;26:567-574).
Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules
Authors: Zhu Shanfeng , Udaka Keiko , Sidney John , Sette Alessandro , Aoki-Kinoshita Kiyoko F. , Mamitsuka Hiroshi 
Published: April 2006

Abstract
Motivation: Various computational methods have been proposed to tackle the problem of predicting the peptide binding ability for a specific MHC molecule. These methods are based on known binding peptide sequences. However, current available peptide databases do not have very abundant amounts of examples and are highly redundant. Existing studies show that MHC molecules can be classified into supertypes in terms of peptide-binding specificities. Therefore, we first give a method for reducing the redundancy in a given dataset based on information entropy, then present a novel approach for prediction by learning a predictive model from a dataset of binders for not only the molecule of interest but also for other MHC molecules.
Results: We experimented on the HLA-A family with the binding nonamers of A1 supertype (HLA-A*0101, A*2601, A*2902, A*3002), A2 supertype (A*0201, A*0202, A*0203, A*0206, A*6802), A3 supertype (A*0301, A*1101, A*3101, A*3301, A*6801) and A24 supertype (A*2301 and A*2402), whose data were collected from six publicly available peptide databases and two private sources. The results show that our approach significantly improves the prediction accuracy of peptides that bind a specific HLA molecule when we combine binding data of HLA molecules in the same supertype. Our approach can thus be used to help find new binders for MHC molecules.
Contact: mami@kuicr.kyoto-u.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster
Authors: Adryan Boris , Teichmann Sarah A. 
Published: April 2006

Abstract
Summary: We present a manually annotated catalogue of site-specific transcription factors (TFs) in the fruit fly Drosophila melanogaster. These were identified from a list of candidate proteins with transcription-related Gene Ontology (Go) annotation as well as structural DNA-binding domain assignments. For all 1052 candidate proteins, a defined set of rules was applied to classify information from the literature and computational data sources with respect to both DNA-binding and transcriptional regulatory properties. We propose a set of 753 TFs in the fruit fly, of which 23 are confident novel predictions of this function for previously uncharacterized proteins.
Availability:
Contact: boris@mrc-lmb.cam.ac.uk
Supplementary information: Supplementary data are available at
Ribosomal RNA as molecular barcodes: a simple correlation analysis without sequence alignment
Authors: Chu K. H. , Li C. P. , Qi J. 
Published: April 2006

Abstract
Motivation: We explored the feasibility of using unaligned rRNA gene sequences as DNA barcodes, based on correlation analysis of composition vectors (CVs) derived from nucleotide strings. We tested this method with seven rRNA (including 12, 16, 18, 26 and 28S) datasets from a wide variety of organisms (from archaea to tetrapods) at taxonomic levels ranging from class to species.
Result: Our results indicate that grouping of taxa based on CV analysis is always in good agreement with the phylogenetic trees generated by traditional approaches, although in some cases the relationships among the higher systemic groups may differ. The effectiveness of our analysis might be related to the length and divergence among sequences in a dataset. Nevertheless, the correct grouping of sequences and accurate assignment of unknown taxa make our analysis a reliable and convenient approach in analyzing unaligned sequence datasets of various rRNAs for barcoding purposes.
Availability: The newly designed software (CVTree 1.0) is publicly available at the Composition Vector Tree (CVTree) web server
Contact: kahouchu@cuhk.edu.hk
Molecular strategies for detection and quantitation of clonal cytotoxic T-cell responses in aplastic anemia and myelodysplastic syndrome
Authors: Wlodarski Marcin W. , Gondek Lukasz P. , Nearman Zachary P. , Plasilova Magdalena , Kalaycio Matt , Hsi Eric D. , Maciejewski Jaroslaw P. 
Published: April 2006

AbstractImmune mechanisms are involved in the pathophysiology of aplastic anemia (AA) and myelodysplastic syndrome (MDS). Immune inhibition can result from cytotoxic T cell (CTL) attack against normal hematopoiesis or reflect immune surveillance. We used clonally unique T-cell receptor (TCR) variable β-chain (VB) CDR3 regions as markers of pathogenic CTL responses and show that while marrow failure syndromes are characterized by polyclonal expansions, overexpanded clones exist in these diseases and can serve as investigative tools. To test the applicability of clonotypic assays, we developed rational molecular methods for the detection of immunodominant clonotypes in blood and in historic marrow biopsies of 35 AA, 37 MDS, and 21 paroxysmal nocturnal hemoglobinuria (PNH) patients, in whom specific CDR3 sequences and clonal sizes were determined. CTL expansions were detected in 81% and 97% of AA and MDS patients, respectively. In total, 81 immunodominant signature clonotypes were identified. Based on the sequence of immunodominant CDR3 clonotypes, we designed quantitative assays for monitoring corresponding clones, including clonotypic Taqman polymerase chain reaction (PCR) and clonotype-specific sequencing. No correlation was found between clonality and disease severity but in patients treated with immunosuppression, truly pathogenic clones were identified based on the decline that paralleled hematologic response. We conclude that immunodominant clonotypes associated with marrow failure may be used to monitor immunosuppressive therapy.
Bcr-Abl resistance screening predicts a limited spectrum of point mutations to be associated with clinical resistance to the Abl kinase inhibitor nilotinib (AMN107)
Authors: von Bubnoff Nikolas , Manley Paul W. , Mestan Jurgen , Sanger Jana , Peschel Christian , Duyster Justus 
Published: April 2006

AbstractIn advanced-phase chronic myeloid leukemia (CML), resistance to imatinib mesylate is associated with point mutations in the BCR-ABL kinase domain. A new generation of potent ABL kinase inhibitors is undergoing clinical evaluation. It is important to generate specific resistance profiles for each of these compounds, which could translate into combinatorial and sequential treatment strategies. Having characterized nilotinib (AMN107) against a large panel of imatinib mesylate–resistant Bcr-Abl mutants, we investigated which mutants might arise under nilotinib therapy using a cell-based resistance screen. In contrast to imatinib mesylate, resistance to nilotinib was associated with a limited spectrum of Bcr-Abl kinase mutations. Among these were mutations affecting the P-loop and T315I. Rarely emerging resistant colonies at a concentration of 400 nM nilotinib exclusively expressed the T315I mutation. With the exception of T315I, all of the mutations that were identified were effectively suppressed when the nilotinib concentration was increased to 2000 nM, which falls within the peak-trough range in plasma levels (3.6-1.7 μM) measured in patients treated with 400 mg twice daily. Our findings suggest that nilotinib might be superior to imatinib mesylate in terms of the development of resistance. However, our study indicates that clinical resistance to nilotinib may be associated with the predominant emergence of T315I.
Evidence that phospholipase C-dependent, calcium-independent mechanisms are required for directional migration of T lymphocytes in response to the CCR4 ligands CCL17 and CCL22
Authors: Cronshaw Darran G , Kouroumalis Andreas , Parry Richard , Webb Adam , Brown Zarin , Ward Stephen G 
Published: April 2006

Abstract
Macrophage-derived chemokine [CC chemokine ligand 22 (CCL22)] and thymus- and activation-regulated chemokine (CCL17) mediate cellular effects, principally by binding to their receptor CC chemokine receptor 4 (CCR4) and together, constitute a multifunctional chemokine/receptor system with homeostatic and inflammatory roles within the body. This study demonstrates that CCL22 and CCL17 stimulate pertussis toxin-sensitive elevation of intracellular calcium in the CEM leukemic T cell line and human peripheral blood-derived T helper type 2 (Th2) cells. Inhibition of phospholipase C (PLC) resulted in the abrogation of chemokine-mediated calcium mobilization. Chemokine-stimulated calcium responses were also abrogated completely by the inhibition of inositol 1,4,5-trisphosphate [Ins(1,4,5)P3] receptor-mediated calcium release. Chemotactic responses of CEM and human Th2 cells to CCL17 and CCL22 were similarly abrogated by inhibition of PLC and inhibition of novel, Ca2+-independent/diacylglycerol-dependent protein kinase C (PKC) isoforms. Inhibition of Ins(1,4,5)P3 receptor-mediated calcium release from intracellular stores had no effect on chemotactic responses to CCR4 ligands. Taken together, this study provides compelling evidence of an important role for PLC and diacylglycerol-dependent effector mechanisms (most likely involving novel PKC isoforms) in CCL17- and CCL22-stimulated, directional cell migration. In this regard, CCL22 stimulates phosphatidylinositol-3 kinase-independent phosphorylation of the novel δ isoform of PKC at threonine 505, situated within its activation loop—an event closely associated with increased catalytic activity.
HIV regulation of the IL-7R: a viral mechanism for enhancing HIV-1 replication in human macrophages in vitro
Authors: Zhang Mingjie , Drenkow Jorg , Lankford Carla S R , Frucht David M , Rabin Ronald L , Gingeras Thomas R , Venkateshan Chettemegre , Schwartzkopff Franziska , Clouse Kathleen A , Dayton Andrew I 
Published: April 2006

Abstract
We report a novel mechanism, involving up-regulation of the interleukin (IL)-7 cytokine receptor, by which human immunodeficiency virus (HIV) enhances its own production in monocyte-derived macrophages (MDM) in vitro. HIV-1 infection or treatment of MDM cultures with exogenous HIV-1 Tat(86) protein up-regulates the IL-7 receptor (IL-7R) α-chain at the levels of steady-state RNA, protein, and functional IL-7R on the cell surface (as measured by ligand-induced receptor signaling). This IL-7R up-regulation is associated with increased amounts of HIV-1 virions in the supernatants of infected MDM cultures treated with exogenous IL-7 cytokine. The overall effect of IL-7 stimulation on HIV replication in MDM culture supernatants is typically in the range of one log and greater. The results are consistent with a model in which HIV infection produces the Tat protein, which in turn up-regulates IL-7R in a paracrine manner. This results in increased IL-7R signaling in response to the IL-7 cytokine, which ultimately promotes early events in HIV replication, including binding/entry and possibly other steps prior to reverse transcription. The results suggest that the effects of IL-7 on HIV replication in MDM should be considered when analyzing and designing clinical trials involving treatment of patients with IL-7 or Tat vaccines.
CPR Training and CPR Performance: Do CPR‐trained Bystanders Perform CPR?
Authors: Swor Robert , Khan Iftikhar , Domeier Robert , Honeycutt Linda , Chu Kevin , Compton Scott 
Published: April 2006

Abstract
Objectives:
To determine factors associated with cardiopulmonary resuscitation (CPR) provision by CPR‐trained bystanders and to determine factors associated with CPR performance by trained bystanders.
Methods:
The authors performed a prospective, observational study (January 1997 to May 2003) of individuals who called 911 (bystanders) at the time of an out‐of‐hospital cardiac arrest. A structured telephone interview of adult cardiac‐arrest bystanders was performed beginning two weeks after the incident. Elements gathered during interviews included bystander and patient demographics, identifying whether the bystander was CPR trained, when and by whom the CPR was performed, and describing the circumstances of the event. If CPR was not performed, we asked the bystanders why CPR was not performed. Logistic regression was used to calculate odds ratios and 95% confidence intervals (95% CI) for factors associated with CPR performance.
Results:
Of 868 cardiac arrests, 684 (78.1%) bystander interviews were completed. Of all bystanders interviewed, 69.6% were family members of the victims, 36.8% of the bystanders had more than a high‐school education, and 54.1% had been taught CPR at some time. In 21.2% of patients, the bystander immediately started CPR, and in 33.6% of cases, someone started CPR before the arrival of emergency medical services (EMS). Important overall predictors of CPR performance were the following: witnessed arrest (OR = 2.3; 95% CI = 1.4 to 3.8); bystander was CPR trained (OR = 6.6; 95% CI = 3.5 to 12.5); bystander had more than a high‐school education (OR = 2.0; 95% CI = 1.2 to 3.1), or arrest occurred in a public location (OR = 3.1; 95% CI = 1.7 to 5.8). These variables were significant predictors of CPR performance among CPR‐trained bystanders, as was CPR training within five years (OR = 4.5; 95% CI = 2.8 to 7.3). Common reasons that the CPR‐trained bystanders cited for not performing CPR were the following: 37.5% stated that they panicked, 9.1% perceived that they would not be able to do CPR correctly, and 1.1% thought that they would hurt the patient. Surprisingly, only 1.1% objected to performing mouth‐to‐mouth resuscitation.
Conclusions:
A minority of CPR‐trained bystanders performed CPR. CPR provision was more common in CPR‐trained bystanders with more than a high‐school education and when CPR training had been within five years. Previously espoused reasons for not doing CPR (mouth‐to‐mouth, infectious‐disease risk) were not the reasons that bystanders cited for not doing CPR. Further work is needed to maximize CPR provision after CPR training.
Processing Reflexives and Pronouns in Picture Noun Phrase
Authors: Runner Jeffrey T. , Sussman Rachel S. , Tanenhaus Michael K. 
Published: April 2006

AbstractBinding theory (e.g., Chomsky, 1981) has played a central role in both syntactic theory and models of language processing. Its constraints are designed to predict that the referential domains of pronouns and reflexives are nonoverlapping, that is, are complementary; these constraints are also thought to play a role in online reference resolution. The predictions of binding theory and its role in sentence processing were tested in four experiments that monitored participants' eye movements as they followed spoken instructions to have a doll touch a picture belonging to another doll. The instructions used pronouns and reflexives embedded in picture noun phrases (PNPs) containing possessor phrases (e.g., Pick up Ken. Have Ken touch Harry's picture of himself). Although the interpretations assigned to pronouns were generally consistent with binding theory, reflexives were frequently assigned interpretations that violated binding theory. In addition, the timing and pattern of eye movements were inconsistent with models of language processing that assume that binding theory acts as an early filter to restrict the referential domain. The interpretations assigned to reflexives in PNPs with possessors suggest that they are binding‐theory‐exempt logophors, a conclusion that unifies the treatment of reflexives in PNPs.
C–H Bond Activation by Ruthenium(0) Complexes. Isolation of an Active Intermediate in the Ruthenium Catalyzed Aldol and Michael Reactions
Authors: Mizuho Yuji , Kasuga Noriko , Komiya Sanshiro 
Published: April 2006

Abstract
Carbon-hydrogen bond oxidative addition of alkyl cyanoacetate to Ru(C2H4)(PPh3)3 in benzene at room temperature gives mer-RuH(NCCHCOOR)(NCCH2COOR)(PPh3)3 (R = Me, Et) accompanied by the liberation of ethylene. X-Ray structure analysis of the THF adduct (R = Me) reveals that NCCHCOOMe group bonds to ruthenium not through the methine carbon but the cyano group. These complexes react with benzaldehyde and methyl iodide to give alkyl (E)-1-cyanocinnamate and alkyl 2-cyanopropionate, respectively.