bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tracheostomy tube manometry: evaluation of speaking valves, capping and need for downsizing
Authors: Johnson Douglas Clark , Campbell Stacy Lynn , Rabkin Judith Dawn 
Published: October 2008

AbstractIntroduction:  Readiness to speak is a major problem for many tracheostomized patients. Evaluation for tracheostomy tube capping or speaking valve is often subjective.Objectives:  We first wanted to assess whether there were differences among speaking valves. We developed a care pathway for tracheostomy tube evaluation and management including manometry, which we wanted to evaluate.Methods:  Three different speaking valves were assessed using manometry and measuring dyspnea in 21 patients. Subsequently, 100 consecutive patients referred for tracheostomy tube evaluation in a long‐term acute‐care rehabilitation hospital were studied using our care pathway with manometry before and after tracheostomy tube changes.Results:  Inspiratory pressures differed among the speaking valves. Borg scale was higher among patients with high expiratory pressures. Of the 100 patients, following our care pathway, speech (speaking valve or capping) was recommended for 78 patients with their initial tube, and for 93 patients within 2 days of their initial evaluation. Tracheostomy tube downsizing was recommended in 94 patients. Downsizing led to significant reductions in airway pressures. Capping was initially recommended for 12 patients and for 71 following downsizing. Women had higher pressures than men for the same size tubes.Conclusion:  Tracheostomy tube manometry is very helpful in objectively guiding recommendations for speaking valve use, capping, and changing tracheostomy tubes. Speech is an early recommendation for most patients.Please cite this paper as: Johnson DC, Campbell SL and Rabkin JD. Tracheostomy tube manometry: evaluation of speaking valves, capping and need for downsizing. The Clinical Respiratory Journal 2009; 3: 8–14.
Giant solitary fibrous tumour of the pleura: a rare but usually benign intrathoracic neoplasm
Authors: Bodtger Uffe , Pedersen Jesper Holst , Skov Birgit Guldhammer , Clementsen Paul 
Published: October 2008

AbstractBackground:  Low forced expiratory volume (FEV1) and low performance status usually preclude surgical treatment of lung neoplasms. Earlier case reports have suggested that curative, safe surgery is possible in extrapulmonal intrathoracic neoplasms.Methods:  A case report of an 83‐year‐old women with progressing dyspnoea secondary to a huge left‐side neoplasm.Results:  Work‐up reveal an FEV1 of 0.4 L, and a giant solitary fibrous tumor of the pleura. The tumor was surgically removed in toto without complications: weighting approximately 3 kg, and benign histology. The patient was without dyspnoea at discharge and at 1‐year follow‐up.Conclusion:  Safe and curative surgery is possible in patients with extrapulmonal neoplasm despite poor FEV1.Please cite this paper as: Bodtger U, Pedersen JH, Skov BG and Clementsen P. Giant solitary fibrous tumour of the pleura: a rare but usually benign intrathoracic neoplasm. The Clinical Respiratory Journal 2009; 3: 109–111.
Stable bronchiectasis is associated with low serum L‐ficolin concentrations
Authors: Kilpatrick David Chalmers , Chalmers James Duncan , MacDonald Shirley Lynn , Murray Maeve , Mohammed Ali , Hart Simon Paul , Matsushita Misao , Hill Adam 
Published: October 2008

AbstractBackground and Aims:  Bronchiectasis is a common chronic respiratory condition with recurrent cough and sputum production and recurrent chest infections. It is characterised by pathological dilatation of the bronchi thought to result from infection and inflammation. It was hypothesised that impaired innate immunity might influence susceptibility to this disease process. The aim of the present study was to look for an association between bronchiectasis and insufficiency of either mannan‐binding lectin (MBL) or L‐ficolin.Materials and Methods:  MBL and L‐ficolin were measured by Enzyme‐linked Immunosorbent Assay (ELISA) in sera from 119 clinically stable bronchiectasis patients, and compared with 43 age‐matched disease controls admitted to hospital with community‐acquired pneumonia, as well as healthy blood donors (168 for L‐ficolin and 564 for MBL).Results:  Average (mean and median) serum L‐ficolin concentrations were lower in the bronchiectasis patients (P < 0.04), but average MBL values did not differ significantly between the three groups. Relative L‐ficolin deficiency was more frequent in bronchiectasis patients compared with blood donors (P ≤ 0.002), whereas MBL insufficiency was associated with pneumonia.Conclusion:  A relative lack of serum L‐ficolin might predispose to the development of bronchiectasis, although other explanations for the observed association are possible.Please cite this paper as: Kilpatrick DC, Chalmers JD, MacDonald SL, Murray M, Mohammed A, Hart SP, Matsushita M and Hill A. Stable bronchiectasis is associated with low serum L‐ficolin concentrations. The Clinical Respiratory Journal 2009; 3: 29–33.
Cytokine Adjuvanation of Therapeutic Anti‐tumor Immunity Targeted to Cancer Mucosa Antigens
Authors: Snook Adam E. , Huang Lan , Schulz Stephanie , Eisenlohr Laurence C. , Waldman Scott A. 
Published: October 2008

AbstractColorectal cancer immunotherapy is limited by the paucity of available target antigens fulfilling the necessary criteria of tumor‐specificity, sufficient immunogenicity and universal association with disease. A novel class of immune targets, cancer mucosa antigens (CMAs), whose expression normally is confined to mucosae but maintained during neoplastic transformation, promises to overcome these imitations, enjoying the advantage of immune compartmentalization, preventing autoimmune disease, while permitting therapeutic anti‐tumor responses. Indeed, therapeutic immunization against the model CMA guanylyl cyclase c (GCC) extends survival in mouse models of established parenchymal colorectal cancer metastases with antitumor efficacy superior to currently available antigens. Here adjuvanation of therapeutic antitumor immunity to GCC was explored employing the cytokines IL‐2 and GM‐CSF in a mouse model of metastatic colorectal cancer. Combining plasmids expressing murine IL‐2 or GM‐CSF with recombinant viral vector immunization to GCC enhanced antitumor efficacy beyond viral vector immunization alone. These studies support the incorporation of IL‐2 and GM‐CSF in CMA‐targeted immunization regimens for established colorectal cancer metastases.
BPSI2.0: a C/C++ interface program for species identification via DNA barcoding with a BP‐neural network by calling the Matlab engine
Authors: ZHANG A. B. , SAVOLAINEN P. 
Published: October 2008

AbstractBP‐Species Identification (BPSI2.0) is a computer program that performs species identification by training a Back‐Propagation Neural Network. A short DNA barcoding segment is used as input for training a three‐layer BP network. The trained network can assign an unknown query sequence to a known species in the user's database, and provide the corresponding subvector value of the output vector as a relative probability value.
Correlation between vision‐ and health‐related quality of life scores
Authors: Swamy Brighu N. , Chia Ee‐Munn , Wang Jie Jin , Rochtchina Elena , Mitchell Paul 
Published: October 2008

Abstract.Purpose:  To examine the correlation between health‐related quality of life (HRQOL) scores [assessed using the generic Short Form Health Survey (SF‐36) questionnaire] and vision‐related quality of life (VRQOL) scores [assessed using the National Eye Institute Visual Function Questionnaire (NEI‐VFQ25)].Methods:  Cross‐sectional analytic study. All surviving participants of the Blue Mountains Eye Study (n = 1952, aged 60 years and older) were invited to attend comprehensive eye examinations 10 years after baseline examinations and were asked to complete both questionnaires.Results:  Complete data were available for 1436 participants. After controlling for age, sex and the presence of either unilateral or bilateral visual impairment, the number of hospital admissions, chronic medical conditions and disabilities, we found that the composite NEI‐VFQ score was significantly associated with the two main domains of the SF‐36 survey: the summary physical component score (P < 0.001) and the mental component score (P < 0.001). There was relatively low correlation (r < 0.3) between the NEI‐VFQ25 subscales and SF‐36 subscales including the physical and mental composite scores.Conclusion:  VRQOL is influenced by both general health and HRQOL. However, there is a relatively low correlation between the individual subscales of these two quality of life questionnaires.
Development of an Optimized Dose for Coformulation of Zidovudine with Drugs That Select for the K65R Mutation Using a Population Pharmacokinetic and Enzyme Kinetic Simulation Model
Authors: Hurwitz Selwyn J. , Asif Ghazia , Kivel Nancy M. , Schinazi Raymond F. 
Published: October 2008

ABSTRACTIn vitro selection studies and data from large genotype databases from clinical studies have demonstrated that tenofovir disoproxil fumarate and abacavir sulfate select for the K65R mutation in the human immunodeficiency virus type 1 polymerase region. Furthermore, other novel non-thymine nucleoside reverse transcriptase (RT) inhibitors also select for this mutation in vitro. Studies performed in vitro and in humans suggest that viruses containing the K65R mutation remained susceptible to zidovudine (ZDV) and other thymine nucleoside antiretroviral agents. Therefore, ZDV could be coformulated with these agents as a “resistance repellent” agent for the K65R mutation. The approved ZDV oral dose is 300 mg twice a day (b.i.d.) and is commonly associated with bone marrow toxicity thought to be secondary to ZDV-5′-monophosphate (ZDV-MP) accumulation. A simulation study was performed in silico to optimize the ZDV dose for b.i.d. administration with K65R-selecting antiretroviral agents in virtual subjects using the population pharmacokinetic and cellular enzyme kinetic parameters of ZDV. These simulations predicted that a reduction in the ZDV dose from 300 to 200 mg b.i.d. should produce similar amounts of ZDV-5′-triphosphate (ZDV-TP) associated with antiviral efficacy (>97% overlap) and reduced plasma ZDV and cellular amounts of ZDV-MP associated with toxicity. The simulations also predicted reduced peak and trough amounts of cellular ZDV-TP after treatment with 600 mg ZDV once a day (q.d.) rather than 300 or 200 mg ZDV b.i.d., indicating that q.d. dosing with ZDV should be avoided. These in silico predictions suggest that 200 mg ZDV b.i.d. is an efficacious and safe dose that could delay the emergence of the K65R mutation.
Impact of Self-Assembly Properties on Antibacterial Activity of Short Acyl-Lysine Oligomers
Authors: Sarig Hadar , Rotem Shahar , Ziserman Lior , Danino Dganit , Mor Amram 
Published: October 2008

ABSTRACT

We investigated both the structural and functional consequences of modifying the hydrophobic, lipopeptide-mimetic oligo-acyl-lysine (OAK) N
α
-hexadecanoyl-
l
-lysyl-
l
-lysyl-aminododecanoyl-
l
-lysyl-amide (c
16
KKc
12
K) to its unsaturated analog hexadecenoyl-KKc
12
K [c
16(ω7)
KKc
12
K]. Despite similar tendencies for self-assembly in solution (critical aggregation concentrations, ∼10 μM), the analogous OAKs displayed dissimilar antibacterial properties (e.g., bactericidal kinetics taking minutes versus hours). Diverse experimental evidence provided insight into these discrepancies: whereas c
16(ω7)
KKc
12
K created wiry interconnected nanofiber networks, c
16
KKc
12
K formed both wider and stiffer fibers which displayed distinct binding properties to phospholipid membranes. Unsaturation also shifted their gel-to-liquid transition temperatures and altered their light-scattering properties, suggesting the disassembly of c
16(ω7)
KKc
12
K in the presence of bacteria. Collectively, the data indicated that the higher efficiency in interfering with bacterial viability emanated from a wobbly packing imposed by a single double bond. This suggests that similar strategies might improve hydrophobic OAKs and related lipopeptide antibiotics.
Comparison of Disk Diffusion and Agar Dilution Methods for Erythromycin, Ciprofloxacin, and Tetracycline Susceptibility Testing of
Campylobacter coli
and for Tetracycline Susceptibility Testing of
Campylobacter jejuni
subsp.
jejuni
Authors: Gaudreau Christiane , Girouard Yves , Gilbert Huguette , Gagnon Josée , Bekal Sadjia 
Published: October 2008

ABSTRACT

With disk diffusion, the following zone diameters are suggested to be resistant and susceptible breakpoints, respectively: for susceptibility testing of
Campylobacter coli
, no inhibition zone and 15 mm or more for erythromycin, and 20 mm or less and 25 mm or more for ciprofloxacin, in the absence or presence of an inhibition zone around the nalidixic acid disk; and for susceptibility testing of
C. coli
and
Campylobacter jejuni
, 20 mm or less and 26 mm or more for tetracycline.
Drug Resistance Mutation Profile and Accumulation Kinetics in Human Immunodeficiency Virus-Positive Individuals Infected with Subtypes B and F Failing Highly Active Antiretroviral Therapy Are Influenced by Different Viral Codon Usage Patterns
Authors: Waléria-Aleixo A. , Martins A. N. , Arruda M. B. , Brindeiro R. M. , Da-Silva R. M. , Nobre F. F. , Greco D. B. , Tanuri A. 
Published: October 2008

ABSTRACTThe major human immunodeficiency virus type 1 subtype circulating in Brazil is B, followed by F and C. We have genotyped 882 samples from Brazilian patients for whom highly active antiretroviral therapy failed, and we found subtype B and the unique recombinant B/F1 forms circulating. Due to codon usage variation, there is a significantly lower incidence of the substitutions L210W, Q151M, and F116Y in subtype F1 isolates than in the subtype B counterparts.
Incidence and Characteristics of Vancomycin Nonsusceptible Strains of Methicillin-ResistantStaphylococcus aureusat Hershey Medical Center
Authors: Kosowska-Shick Klaudia , Ednie Lois M. , McGhee Pamela , Smith Kathy , Todd Cynthia D. , Wehler Amanda , Appelbaum Peter C. 
Published: October 2008

ABSTRACTAll 982 methicillin-resistantStaphylococcus aureusstrains collected from August 2006 to December 2007 were tested for vancomycin susceptibility by using 3-μg/ml vancomycin brain heart infusion screening plates, a vancomycin Etest, and a vancomycin/teicoplanin macro Etest. Three vancomycin-intermediateStaphylococcus aureus(VISA) (0.3%) and two heterogeneous VISA (0.2%) isolates were identified. The screening method yielded 895 cases of ≤1 colony and 87 positive results (with growth of >1 colony after 48 h); further Etests showed 82/87 isolates with growth on screening plates to be false positive. Repeat testing showed a false-positivity rate of only 15 of the original 87 isolates by plate screening.
Porphyromonas gingivalis, Gamma Interferon, and a Proapoptotic Fibronectin Matrix Form a Synergistic Trio That Induces c-Jun N-Terminal Kinase 1-Mediated Nitric Oxide Generation and Cell Death
Authors: Ghosh Abhijit , Park Ji Young , Fenno Christopher , Kapila Yvonne L. 
Published: October 2008

ABSTRACTDuring infection and inflammation, bacterial and inflammatory proteases break down extracellular matrices into macromolecular fragments. Fibronectin fragments are associated with disease severity in arthritis and periodontitis. The mechanisms by which these fragments contribute to disease pathogenesis are unclear. One likely mechanism is that fibronectin fragments induce apoptosis of resident cells, which can be further modulated by nitric oxide. Nitric oxide levels are increased at inflammatory sites in periodontitis patients. The aim of this study was to examine whether a proapoptotic fibronectin matrix (AFn) exerts its action by inducing nitric oxide and whether priming by bacterial and inflammatory components exacerbates this mechanism. Our data demonstrate that AFn increased the levels of nitric oxide and inducible nitric oxide synthase (iNOS) dose and time dependently in periodontal ligament (PDL) cells. These effects and apoptosis were inhibited by iNOS suppression and enhanced by iNOS overexpression. Nitric oxide and iNOS induction were paralleled by increased c-Jun N-terminal kinase 1 (JNK-1) phosphorylation. JNK-1 overexpression enhanced the expression of nitric oxide and iNOS, whereas inhibiting JNK-1 by small interfering RNA or a kinase mutant reversed these findings. Priming PDL cells withPorphyromonas gingivalis, its lipopolysaccharide (LPS), or gamma interferon (IFN-γ) further increased nitric oxide levels and apoptosis.Escherichia coliandStreptococcus mutansinduced lesser effects. Gingival fibroblasts and neutrophils responded to a lesser degree to these stimuli, whereas keratinocytes were resistant to apoptosis. Thus, proapoptotic matrices trigger nitric oxide release via JNK-1, promoting further apoptosis in host cells. LPS and IFN-γ accentuate this mechanism, suggesting that during inflammation, the affected matrices and bacterial and inflammatory components combined exert a greater pathogenic effect on host cells.
Primary Activation of Antigen-Specific Naive CD4+and CD8+T Cells following Intranasal Vaccination with Recombinant Bacteria
Authors: Ciabattini Annalisa , Pettini Elena , Andersen Peter , Pozzi Gianni , Medaglini Donata 
Published: October 2008

ABSTRACTThe primary activation of T-helper and T-cytotoxic cells following mucosal immunization with recombinantStreptococcus gordoniiwas studied in vivo by adoptive transfer of ovalbumin (OVA)-specific transgenic CD8+(OT-I) and CD4+(OT-II) T cells. A recombinant strain, expressing on the surface the vaccine antigen Ag85B-ESAT-6 fromMycobacterium tuberculosisfused to OVA T-helper and T-cytotoxic epitopes (peptides 323 to 339 and 257 to 264), was constructed and used to immunize C57BL/6 mice by the intranasal route. Recombinant, but not wild-type, bacteria induced OVA-specific CD4+and CD8+T-cell clonal expansion in cervical lymph nodes, lung, and spleen. OVA-specific CD4+and CD8+T-cell proliferation appeared first in cervical lymph nodes and later in the spleen, suggesting a possible migration of activated cells from the inductive site to the systemic district. A significant correlation between the percentages of CD4+and CD8+proliferating T cells was observed for each animal. The expression of CD69, CD44, and CD45RB on proliferating T lymphocytes changed as a function of the cell division number, confirming T-cell activation following the antigen encounter. These data indicate that intranasal immunization with recombinantS. gordoniiis capable of inducing primary activation of naive antigen-specific CD4+and CD8+T cells, both locally and systemically.
Hypothesis: huntingtin may function in membrane association and vesicular traffickingThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Membrane Proteins in Health and Disease.
Authors: Truant Ray , Atwal Randy , Burtnik Anjee 
Published: October 2008

Huntington’s disease is a progressive neurodegenerative genetic disorder that is caused by a CAG triplet-repeat expansion in the first exon of the IT15 gene. This CAG expansion results in polyglutamine expansion in the 350 kDa huntingtin protein. The exact function of huntingtin is unknown. Understanding the pathological triggers of mutant huntingtin, and distinguishing the cause of disease from downstream effects, is critical to designing therapeutic strategies and defining long- and short-term goals of therapy. Many studies that have sought to determine the functions of huntingtin by determining huntingtin’s protein–protein interactions have been published. Through these studies, huntingtin has been seen to interact with a large number of proteins, and is likely a scaffolding protein for protein–protein interactions. Recently, using imaging, integrative proteomics, and cell biology, huntingtin has been defined as a membrane-associated protein, with activities related to axonal trafficking of vesicles and mitochondria. These functions have also been attributed to some huntingtin-interacting proteins. Additionally, discoveries of a membrane association domain and a palmitoylation site in huntingtin reinforce the fact that huntingtin is membrane associated. In Huntington’s disease mouse and fly models, axonal vesicle trafficking is inhibited, and lack of proper uptake of neurotrophic factors may be an important pathological trigger leading to striatal cell death in Huntington’s disease. Here we discuss recent advances from many independent groups and methodologies that are starting to resolve the elusive function of huntingtin in vesicle transport, and evidence that suggests that huntingtin may be directly involved in membrane interactions.
Effects of site-directed mutations inEscherichia colisuccinate dehydrogenase on the enzyme activity and production of superoxide radicalsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Membrane Proteins in Health and Disease.
Authors: Zhao Zhongwei , Rothery Richard A. , Weiner Joel H. 
Published: October 2008

Escherichia coli succinate dehydrogenase (SdhCDAB) catalyzes the oxidation of succinate to fumarate in the Krebs cycle, and during turnover, it produces superoxide radicals. SdhCDAB is a good model system for the succinate dehydrogenase (Sdh) found in the mitochondrial respiratory chain (complex II), as the subunits are structural homologues. Although mutations in sdh genes are reportedly associated with a variety of mitochondria-related diseases, the molecular mechanism of these diseases is poorly understood. We have investigated the effects of site-directed mutations around the heme (SdhD-H71L and SdhC-H91L), and at the ubiquinone-binding site (Q site; SdhC-I28E), on enzyme activity and production of superoxide radicals. The mutations SdhD-H71L and SdhC-I28E, but not SdhC-H91L, significantly reduce the succinate–ubiquinone reductase activity of the enzyme. All 3 mutant enzymes produce more superoxide than the wild-type enzyme, indicating that disturbance of the heme or the Q site can enhance superoxide production. The presence of a Q-site inhibitor reduces superoxide production significantly. Furthermore, the yield of superoxide is substrate dependent and increases with succinate concentration from 0.1 to 10 mmol/L. Our results indicate that, in SdhCDAB, the Q site with bound ubiquinone is an important source of superoxide radicals.
The position of the Gly-xxx-Gly motif in transmembrane segments modulates dimer affinityThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Membrane Proteins in Health and Disease.
Authors: Johnson Rachel M. , Rath Arianna , Deber Charles M. 
Published: October 2008

Although the intrinsic low solubility of membrane proteins presents challenges to their high-resolution structure determination, insight into the amino acid sequence features and forces that stabilize their folds has been provided through study of sequence-dependent helix–helix interactions between single transmembrane (TM) helices. While the stability of helix–helix partnerships mediated by the Gly-xxx-Gly (GG4) motif is known to be generally modulated by distal interfacial residues, it has not been established whether the position of this motif, with respect to the ends of a given TM segment, affects dimer affinity. Here we examine the relationship between motif position and affinity in the homodimers of 2 single-spanning membrane protein TM sequences: glycophorin A (GpA) and bacteriophage M13 coat protein (MCP). Using the TOXCAT assay for dimer affinity on a series of GpA and MCP TM segments that have been modified with either 4 Leu residues at each end or with 8 Leu residues at the N-terminal end, we show that in each protein, centrally located GG4 motifs are capable of stronger helix–helix interactions than those proximal to TM helix ends, even when surrounding interfacial residues are maintained. The relative importance of GG4 motifs in stabilizing helix–helix interactions therefore must be considered not only in its specific residue context but also in terms of the location of the interactive surface relative to the N and C termini of α-helical TM segments.