bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial Pattern in Chronic Sinusitis and Cystic Fibrosis
Authors: Godoy Jose M. , Godoy Andres N. , Ribalta Gloria , Largo Isabel 
Published: April 2011

ObjectiveTo assess the association between pathogenic bacteria found in bronchoalveolar lavages and paranasal cavity cultures in patients with cystic fibrosis (CF) who underwent endonasal endoscopic sinus surgery. The authors hypothesized that the pathogenic bacterial pattern of the upper airway would be associated with that of the lower airway.Study DesignProspective case series with planned data collection.SettingTertiary referral center.Subjects and MethodsA group of 16 patients with diagnosis of CF who underwent endonasal endoscopic sinus surgery from July 2001 to August 2009 participated in the study. Culture samples were obtained from bronchoalveolar lavages and paranasal cavities. A Fisher exact test was performed to examine the significance of the association between upper airway and lower airway cultures.ResultsThe most frequent microorganisms in cultures of para‐nasal cavities and bronchoalveolar lavages were Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus viridans. Statistical analysis revealed a significant association between upper airway cultures (paranasal cavities) and lower airway cavities (bronchoalveolar lavages) for the 2 most frequent microorganisms, P aeruginosa and S aureus (P =. 007 and P =. 030, respectively).ConclusionThe authors confirmed their initial hypothesis that a significant association between bronchoalveolar lavages and sinus cultures was established, once more confirming the idea of a unified airway. They found chronic rhinosinusitis with polyps to be a common clinical presentation in patients with CF. Further studies are required to indicate the role of antibiotics and the pathogenesis of the microorganisms as a manifestation of clinical severity.
Complementary and Alternative Medicine Use in the Thyroid Patients of a Head and Neck Practice
Authors: Brake Maria K. , Bartlett Clark , Hart Robert D. , Trites Jonathon R. B. , Taylor S. Mark 
Published: April 2011

ObjectiveTo investigate the prevalence of complementary and alternative medicine (CAM) use among patients being investigated for thyroid nodules in a head and neck oncology practice. Subsequently, to determine whether the common therapies used were likely to interfere with the planned patient’s care and whether the predominance was significant to warrant inclusion in routine history assessments.Study DesignCross‐sectional survey.SettingDalhousie University, Halifax, Nova Scotia, Canada.Subjects and MethodsA survey regarding CAM use was completed by 100 patients being investigated for thyroid nodules upon their initial presentation to a head and neck oncology practice.ResultsPreliminary results showed that 79% of participants have a history of CAM use and 51% of participants were actively using oral supplements. Thirty‐one percent of participants reported using supplements known to have hemostasis‐affecting properties.ConclusionMedical professionals should incorporate CAM questioning in any thyroid patient assessment to reduce patient risk and optimize medical and surgical outcomes.
Pretreatment with phosphatase and tensin homolog deleted on chromosome 10 (PTEN) inhibitor SF1670 augments the efficacy of granulocyte transfusion in a clinically relevant mouse model
Authors: Li Yitang , Prasad Amit , Jia Yonghui , Roy Saurabh Ghosh , Loison Fabien , Mondal Subhanjan , Kocjan Paulina , Silberstein Leslie E. , Ding Sheng , Luo Hongbo R. 
Published: April 2011

AbstractThe clinical outcome of granulocyte transfusion therapy is often hampered by short ex vivo shelf life, inefficiency of recruitment to sites of inflammation, and poor pathogen-killing capability of transplanted neutrophils. Here, using a recently developed mouse granulocyte transfusion model, we revealed that the efficacy of granulocyte transfusion can be significantly increased by elevating intracellular phosphatidylinositol (3,4,5)-trisphosphate signaling with a specific phosphatase and tensin homolog deleted on chromosome 10 (PTEN) inhibitor SF1670. Neutrophils treated with SF1670 were much sensitive to chemoattractant stimulation. Neutrophil functions, such as phagocytosis, oxidative burst, polarization, and chemotaxis, were augmented after SF1670 treatment. The recruitment of SF1670-pretreated transfused neutrophils to the inflamed peritoneal cavity and lungs was significantly elevated. In addition, transfusion with SF1670-treated neutrophils led to augmented bacteria-killing capability (decreased bacterial burden) in neutropenic recipient mice in both peritonitis and bacterial pneumonia. Consequently, this alleviated the severity of and decreased the mortality of neutropenia-related pneumonia. Together, these observations demonstrate that the innate immune responses can be enhanced and the severity of neutropenia-related infection can be alleviated by augmenting phosphatidylinositol (3,4,5)-trisphosphate in transfused neutrophils with PTEN inhibitor SF1670, providing a therapeutic strategy for improving the efficacy of granulocyte transfusion.
Inhibition of β-TrcP–dependent ubiquitination of p53 by HIV-1 Vpu promotes p53–mediated apoptosis in human T cells
Authors: Verma Sachin , Ali Amjad , Arora Sakshi , Banerjea Akhil C. 
Published: April 2011

AbstractHIV-1 viral protein U (Vpu) is involved in ubiquitination and degradation of BM stromal cell Ag 2 and surface receptor CD4 through their recruitment to SCFβ-TrcP (Skp1/Cul1/F-box) ubiquitin ligase (SCF) complex. Here, we show that specific interaction of wild-type Vpu protein with SCF complex leads to inhibition of ubiquitination and proteasomal degradation of p53 protein in a β-TrcP–dependent manner. Successful interaction of SCFβ-TrcP complex with β-TrcP binding motif (DS52GNES56) present in Vpu is essential because mutant Vpu possessing specific alanine substitutions (DA52GNEA56) in the β-TrcP binding motif not only failed to stabilize p53 protein but was also unable to inhibit ubiquitination of p53 protein. Furthermore, Vpu competes efficiently with the interaction of p53 protein with the β-TrcP subunit of the SCF complex and inhibits subsequent ubiquitination of p53 proteins in a dose-dependent manner. We also observed potent apoptotic activity in a p53 null cell line (H-1299) that was cotransfected with p53 and Vpu-expressing plasmids. Furthermore, MOLT-3 (human T-lymphoblast) cells when infected with vesicular stomatitis virus glycoprotein–pseudotypic HIV-1 possessing wild-type vpu gene exhibited maximum activation of p53/Bax proteins and p53-mediated cell death. These findings establish a novel function of Vpu in modulating the stability of p53 protein that correlates positively with apoptosis during late stages of HIV-1 infection.
Prevention of bronchial hyperreactivity in a rat model of precapillary pulmonary hypertension
Authors: Habre Walid , Albu Gergely , Janosi Tibor Z , Fontao Fabienne , von Ungern-Sternberg Britta S , Beghetti Maurice , Petak Ferenc 
Published: April 2011

AbstractBackgroundThe development of bronchial hyperreactivity (BHR) subsequent to precapillary pulmonary hypertension (PHT) was prevented by acting on the major signalling pathways (endothelin, nitric oxide, vasoactive intestine peptide (VIP) and prostacyclin) involved in the control of the pulmonary vascular and bronchial tones.MethodsFive groups of rats underwent surgery to prepare an aorta-caval shunt (ACS) to induce sustained precapillary PHT for 4 weeks. During this period, no treatment was applied in one group (ACS controls), while the other groups were pretreated with VIP, iloprost, tezosentan via an intraperitoneally implemented osmotic pump, or by orally administered sildenafil. An additional group underwent sham surgery. Four weeks later, the lung responsiveness to increasing doses of an intravenous infusion of methacholine (2, 4, 8 12 and 24 μg/kg/min) was determined by using the forced oscillation technique to assess the airway resistance (Raw).ResultsBHR developed in the untreated rats, as reflected by a significant decrease in ED50, the equivalent dose of methacholine required to cause a 50% increase in Raw. All drugs tested prevented the development of BHR, iloprost being the most effective in reducing both the systolic pulmonary arterial pressure (Ppa; 28%, p = 0.035) and BHR (ED50= 9.9 ± 1.7 vs. 43 ± 11 μg/kg in ACS control and iloprost-treated rats, respectively, p = 0.008). Significant correlations were found between the levels of Ppa and ED50(R = -0.59, p = 0.016), indicating that mechanical interdependence is primarily responsible for the development of BHR.ConclusionsThe efficiency of such treatment demonstrates that re-establishment of the balance of constrictor/dilator mediators via various signalling pathways involved in PHT is of potential benefit for the avoidance of the development of BHR.
Stochastic sequence-level model of coupled transcription and translation in prokaryotes
Authors: Mäkelä Jarno , Lloyd-Price Jason , Yli-Harja Olli , Ribeiro Andre S 
Published: April 2011

Abstract

Background
In prokaryotes, transcription and translation are dynamically coupled, as the latter starts before the former is complete. Also, from one transcript, several translation events occur in parallel. To study how events in transcription elongation affect translation elongation and fluctuations in protein levels, we propose a delayed stochastic model of prokaryotic transcription and translation at the nucleotide and codon level that includes the promoter open complex formation and alternative pathways to elongation, namely pausing, arrests, editing, pyrophosphorolysis, RNA polymerase traffic, and premature termination. Stepwise translation can start after the ribosome binding site is formed and accounts for variable codon translation rates, ribosome traffic, back-translocation, drop-off, and trans-translation.

Results
First, we show that the model accurately matches measurements of sequence-dependent translation elongation dynamics. Next, we characterize the degree of coupling between fluctuations in RNA and protein levels, and its dependence on the rates of transcription and translation initiation. Finally, modeling sequence-specific transcriptional pauses, we find that these affect protein noise levels.

Conclusions
For parameter values within realistic intervals, transcription and translation are found to be tightly coupled in Escherichia coli, as the noise in protein levels is mostly determined by the underlying noise in RNA levels. Sequence-dependent events in transcription elongation, e.g. pauses, are found to cause tangible effects in the degree of fluctuations in protein levels.
Reversal to air-driven sound production revealed by a molecular phylogeny of tongueless frogs, family Pipidae
Authors: Irisarri Iker , Vences Miguel , San Mauro Diego , Glaw Frank , Zardoya Rafael 
Published: April 2011

AbstractBackgroundEvolutionary novelties often appear by conferring completely new functions to pre-existing structures or by innovating the mechanism through which a particular function is performed. Sound production plays a central role in the behavior of frogs, which use their calls to delimit territories and attract mates. Therefore, frogs have evolved complex vocal structures capable of producing a wide variety of advertising sounds. It is generally acknowledged that most frogs call by moving an air column from the lungs through the glottis with the remarkable exception of the family Pipidae, whose members share a highly specialized sound production mechanism independent of air movement.ResultsHere, we performed behavioral observations in the poorly known African pipid genusPseudhymenochirusand document that the sound production in this aquatic frog is almost certainly air-driven. However, morphological comparisons revealed an indisputable pipid nature ofPseudhymenochiruslarynx. To place this paradoxical pattern into an evolutionary framework, we reconstructed robust molecular phylogenies of pipids based on complete mitochondrial genomes and nine nuclear protein-coding genes that coincided in placingPseudhymenochirusnested among other pipids.ConclusionsWe conclude that althoughPseudhymenochirusprobably has evolved a reversal to the ancestral non-pipid condition of air-driven sound production, the mechanism through which it occurs is an evolutionary innovation based on the derived larynx of pipids. This strengthens the idea that evolutionary solutions to functional problems often emerge based on previous structures, and for this reason, innovations largely depend on possibilities and constraints predefined by the particular history of each lineage.
Empirical evaluations of analytical issues arising from predicting HLA alleles using multiple SNPs
Authors: Zhang Xinyi Cindy , Li Shuying Sue , Wang Hongwei , Hansen John A , Zhao Lue Ping 
Published: April 2011

AbstractBackgroundNumerous immune-mediated diseases have been associated with the class I and II HLA genes located within the major histocompatibility complex (MHC) consisting of highly polymorphic alleles encoded by the HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1 loci. Genotyping for HLA alleles is complex and relatively expensive. Recent studies have demonstrated the feasibility of predicting HLA alleles, using MHC SNPs inside and outside of HLA that are typically included in SNP arrays and are commonly available in genome-wide association studies (GWAS). We have recently described a novel method that is complementary to the previous methods, for accurately predicting HLA alleles using unphased flanking SNPs genotypes. In this manuscript, we address several practical issues relevant to the application of this methodology.ResultsApplying this new methodology to three large independent study cohorts, we have evaluated the performance of the predictive models in ethnically diverse populations. Specifically, we have found that utilizing imputed in addition to genotyped SNPs generally yields comparable if not better performance in prediction accuracies. Our evaluation also supports the idea that predictive models trained on one population are transferable to other populations of the same ethnicity. Further, when the training set includes multi-ethnic populations, the resulting models are reliable and perform well for the same subpopulations across all HLA genes. In contrast, the predictive models built from single ethnic populations have superior performance within the same ethnic population, but are not likely to perform well in other ethnic populations.ConclusionsThe empirical explorations reported here provide further evidence in support of the application of this approach for predicting HLA alleles with GWAS-derived SNP data. Utilizing all available samples, we have built "state of the art" predictive models for HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1. The HLA allele predictive models, along with the program used to carry out the prediction, are available on our website.
Identification of ovule transcripts from the Apospory-Specific Genomic Region (ASGR)-carrier chromosome
Authors: Zeng Yajuan , Conner Joann , Ozias-Akins Peggy 
Published: April 2011

Abstract

Background
Apomixis, asexual seed production in plants, holds great potential for agriculture as a means to fix hybrid vigor. Apospory is a form of apomixis where the embryo develops from an unreduced egg that is derived from a somatic nucellar cell, the aposporous initial, via mitosis. Understanding the molecular mechanism regulating aposporous initial specification will be a critical step toward elucidation of apomixis and also provide insight into developmental regulation and downstream signaling that results in apomixis. To discover candidate transcripts for regulating aposporous initial specification in P. squamulatum, we compared two transcriptomes derived from microdissected ovules at the stage of aposporous initial formation between the apomictic donor parent, P. squamulatum (accession PS26), and an apomictic derived backcross 8 (BC8) line containing only the Apospory-Specific Genomic Region (ASGR)-carrier chromosome from P. squamulatum. Toward this end, two transcriptomes derived from ovules of an apomictic donor parent and its apomictic backcross derivative at the stage of apospory initiation, were sequenced using 454-FLX technology.

Results
Using 454-FLX technology, we generated 332,567 reads with an average read length of 147 base pairs (bp) for the PS26 ovule transcriptome library and 363,637 reads with an average read length of 142 bp for the BC8 ovule transcriptome library. A total of 33,977 contigs from the PS26 ovule transcriptome library and 26,576 contigs from the BC8 ovule transcriptome library were assembled using the Multifunctional Inertial Reference Assembly program. Using stringent in silico parameters, 61 transcripts were predicted to map to the ASGR-carrier chromosome, of which 49 transcripts were verified as ASGR-carrier chromosome specific. One of the alien expressed genes could be assigned as tightly linked to the ASGR by screening of apomictic and sexual F1s. Only one transcript, which did not map to the ASGR, showed expression primarily in reproductive tissue.

Conclusions
Our results suggest that a strategy of comparative sequencing of transcriptomes between donor parent and backcross lines containing an alien chromosome of interest can be an efficient method of identifying transcripts derived from an alien chromosome in a chromosome addition line.
Introgression of Swertia mussotii gene into Bupleurum scorzonerifoliumvia somatic hybridization
Authors: Wang Junfeng , Zhao Cuizhu , Liu Chang , Xia Guangmin , Xiang Fengning 
Published: April 2011

Abstract

Background
The wild herb Swertia mussotii is a source of the anti-hepatitis compounds swertiamarin, mangiferin and gentiopicroside. Its over-exploitation has raised the priority of producing these compounds heterologously. Somatic hybridization represents a novel approach for introgressing Swertia mussotii genes into a less endangered species.

Results
Protoplasts derived from calli of Bupleurum scorzonerifolium and S. mussotii were fused to produce 194 putative hybrid cell lines, of which three (all derived from fusions where the S. mussotii protoplasts were pre-treated for 30 s with UV light) later differentiated into green plants. The hybridity of the calli was confirmed by a combination of isozyme, RAPD and chromosomal analysis. The hybrid calli genomes were predominantly B. scorzonerifolium. GISH analysis of mitotic chromosomes confirmed that the irradiation of donor protoplasts increased the frequency of chromosome elimination and fragmentation. RFLP analysis of organellar DNA revealed that mitochondrial and chloroplast DNA of both parents coexisted and recombined in some hybrid cell lines. Some of the hybrid calli contained SmG10H from donor, and produced swertiamarin, mangiferin and certain volatile compounds characteristic of S. mussotii. The expression of SmG10H (geraniol 10-hydroxylase) was associated with the heterologous accumulation of swertiamarin.

Conclusions
Somatic hybrids between B. scorzonerifolium and S. mussotii were obtained, hybrids selected all contained introgressed nuclear and cytoplasmic DNA from S. mussotii; and some produced more mangiferin than the donor itself. The introgression of SmG10H was necessary for the accumulation of swertiamarin.
Performance of whole-blood interferon-gamma release assay in patients admitted to the emergency department with pulmonary infiltrates
Authors: Lee Yoon Jee , Lee Jaehee , Kim Yi Young , Won Dong Il , Cha Seung Ick , Park Jae Yong , Jung Tae Hoon , Kim Chang Ho 
Published: April 2011

Abstract

Background
This study was conducted to evaluate the performance of a whole-blood interferon-gamma release assay in inpatients who were admitted to the emergency department (ED) with pulmonary infiltrates who required a differential diagnosis with pulmonary tuberculosis (TB).

Methods
The patients with pulmonary infiltrates who received a QuantiFERON (QFT) test in the ED were included as an inpatient group and were divided into TB and non-TB group based on the final diagnosis. Patients with pulmonary TB who were tested in the outpatient department served as a control group.

Results
In total, 377 QFT tests were analyzed. Of the 284 inpatient QFT tests, 29.6% had an indeterminate result (35.2% in the 196 patients with non-TB and 17.0% in the 88 patients with TB). In contrast, only 1.1% of the 93 outpatients with TB returned an indeterminate result (p < 0.001). The indeterminate QFT results in the inpatient group were independently associated with lymphocytopenia, hypoalbuminemia, and high C-reactive protein levels. Non-positive QFT results in inpatients with TB were associated with lymphocytopenia and hypoalbuminemia, while non-positive QFT results in outpatients with TB were associated with high erythrocyte sedimentation rates and radiographically more severe diseases.

Conclusions
QFT tests in ED-based inpatients with pulmonary infiltrate return indeterminate results relatively frequently. In addition, inpatients and outpatients with pulmonary TB may differ in terms of the risk factors on non-positive QFT results.
Activities of colistin- and minocycline-based combinations against extensive drug resistant Acinetobacter baumannii isolates from intensive care unit patients
Authors: Liang Wang , Liu Xiao-fang , Huang Jun , Zhu De-mei , Li Jian , Zhang Jing 
Published: April 2011

Abstract

Background
Extensive drug resistance of Acinetobacter baumannii is a serious problem in the clinical setting. It is therefore important to find active antibiotic combinations that could be effective in the treatment of infections caused by this problematic 'superbug'. In this study, we analyzed the in vitro activities of three colistin-based combinations and a minocycline-based combination against clinically isolated extensive drug resistant Acinetobacter baumannii (XDR-AB) strains.

Methods
Fourteen XDR-AB clinical isolates were collected. The clonotypes were determined by polymerase chain reaction-based fingerprinting. Susceptibility testing was carried out according to the standards of the Clinical and Laboratory Standards Institute. Activities of drug combinations were investigated against four selected strains and analyzed by mean survival time over 12 hours (MST12 h) in a time-kill study.

Results
The time-kill studies indicated that the minimum inhibitory concentration (MIC) of colistin (0.5 or 0.25 μg/mL) completely killed all strains at 2 to 4 hours, but 0.5×MIC colistin showed no bactericidal activity. Meropenem (8 μg/mL), minocycline (1 μg/mL) or rifampicin (0.06 μg/mL) did not show bactericidal activity. However, combinations of colistin at 0.5×MIC (0.25 or 0.125 μg/mL) with each of the above were synergistic and shown bactericidal activities against all test isolates. A combination of meropenem (16 μg/mL) with minocycline (0.5×MIC, 4 or 2 μg/mL) was synergitic to all test isolates, but neither showed bactericidal activity alone. The MST12 h values of drug combinations (either colistin- or minocycline-based combinations) were significantly shorter than those of the single drugs (p < 0.01).

Conclusions
This study indicates that combinations of colistin/meropenem, colistin/rifampicin, colistin/minocycline and minocycline/meropenem are synergistic in vitro against XDR-AB strains.