bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reverse Transcriptase Genotypes in Pediatric Patients Failing Initial Antiretroviral Therapy in Gaborone, Botswana
Authors: Tolle Michael , Howard Leigh , Kirk Brianna , Gomila Andres , Schwarzwald Heidi , Anabwani Gabriel 
Published: October 2011

Background Limited data are available on patterns of resistance mutations in pediatric patients in southern Africa, where HIV-1 subtype C (HIV-1C) predominates. Methods Retrospective chart review of pediatric patients. Nucleoside reverse transcriptase inhibitor (NRTI)- and nonnucleoside reverse transcriptase inhibitor (NNRTI)-associated resistance mutations quantified from population-based sequencing genotypic resistance assay results taken at time of first-line antiretroviral therapy (ART) failure (first-line ART = stavudine [d4T] or zidovudine [ZDV] + lamivudine [3TC] + nevirapine [NVP] or efavirenz [EFV]). Results Total number of patients with resistance assays analyzed is 45. Nucleoside reverse transcriptase inhibitor-associated mutation frequencies noted were M184V (n = 41; 91.1%); thymidine analogue mutations (TAMs; n = 20; 44.4%); >1 TAM (n = 9; 20%); TAM-2 pathway (n = 10; 22.2%); TAM-1 pathway (n = 7; 15.6%); TAM-1 and TAM-2 pathways (n = 3; 6.7%); K65R (n = 2; 4.4%); Q151M (n = 1; 2.2%); and L74V (n = 0; 0%). Nonnucleoside reverse transcriptase inhibitor-associated mutation frequencies noted were associated with notable resistance to either/both NVP and EFV (n = 40; 88.9%); K103N (n = 15; 33.3%); ≥1 mutations associated with etravirine (ETR) failure (K101E, Y181C, and G190A; n =20; 44.4%); and ≥2 notable NNRTI mutations (n = 12; 26.7%). Conclusions In this cohort, low-genetic barrier mutations were common, as were TAMs, including more than 1 TAM. Mutations compromising nonthymidine analogue backbones were rare, suggesting that it is likely that children who fail first-line NRTI backbones containing d4T or ZDV/3TC would still respond to abacavir (ABC), didanosine (ddI), and, for adolescents, tenofovir (TDF). Our data support the empiric continuation of 3TC in second-line regimens.
Emergency granulopoiesis promotes neutrophil-dendritic cell encounters that prevent mouse lung allograft acceptance
Authors: Kreisel Daniel , Sugimoto Seiichiro , Zhu Jihong , Nava Ruben , Li Wenjun , Okazaki Mikio , Yamamoto Sumiharu , Ibrahim Mohsen , Huang Howard J. , Toth Kelsey A. , Ritter Jon H. , Krupnick Alexander S. , Miller Mark J. , Gelman Andrew E. 
Published: October 2011

AbstractThe mechanisms by which innate immune signals regulate alloimmune responses remain poorly understood. In the present study, we show by intravital 2-photon microscopy direct interactions between graft-infiltrating neutrophils and donor CD11c+ dendritic cells (DCs) within orthotopic lung allografts immediately after reperfusion. Neutrophils isolated from the airways of lung transplantation recipients stimulate donor DCs in a contact-dependent fashion to augment their production of IL-12 and expand alloantigen-specific IFN-γ+ T cells. DC IL-12 expression is largely regulated by degranulation and induced by TNF-α associated with the neutrophil plasma membrane. Extended cold ischemic graft storage enhances G-CSF–mediated granulopoiesis and neutrophil graft infiltration, resulting in exacerbation of ischemia-reperfusion injury after lung transplantation. Ischemia reperfusion injury prevents immunosuppression-mediated acceptance of mouse lung allografts unless G-CSF–mediated granulopoiesis is inhibited. Our findings identify granulopoiesis-mediated augmentation of alloimmunity as a novel link between innate and adaptive immune responses after organ transplantation.
Evaluation of epithelial mesenchymal transition in patients with chronic obstructive pulmonary disease
Authors: Sohal Sukhwinder S , Reid David , Soltani Amir , Ward Chris , Weston Steven , Muller H Konrad , Wood-Baker Richard , Walters E Haydn 
Published: October 2011

Abstract

Background
The reticular basement membrane (Rbm) in smokers and especially smokers with COPD is fragmented with "clefts" containing cells staining for the collagenase matrix-metalloproteinase-9 (MMP-9) and fibroblast protein, S100A4. These cells are also present in the basal epithelium. Such changes are likely hallmarks of epithelial mesenchymal transition (EMT). We aimed to confirm the epithelial origin of these Rbm cells, and to exclude potential confounding by infiltrating inflammatory cells.

Methods
Endobronchial biopsy sections from 17 COPD current smokers, with documented Rbm splitting and cellularity were stained for neutrophil elastase (neutrophil marker), CD68 (macrophage/mature fibroblasts), CD4+/CD8+ T lymphocytes, CD19 (B-cells), CD11c (dendritic cells/inflammatory cells), and S100 (Langerhans cells). The number of cells in the Rbm and epithelium staining for these "inflammatory" cell markers were then compared to numbers staining for S100A4, "a documented EMT epitope". Slides were double stained for S100A4 and cytokeratin(s).

Results
In the basal epithelium significantly more cells stained for S100A4 compared to infiltrating macrophages, fibroblasts or immune cells: median, 26 (21.3 - 37.3) versus 0 (0 - 9.6) per mm, p < 0.003. Markedly more S100A4 staining cells were also observed in the Rbm compared to infiltrating macrophages, neutrophils, fibroblasts or immune cells or any sub-type: 58 (37.3 - 92.6) versus 0 (0 - 4.8) cells/mm Rbm, p < 0.003. Cells in the basal epithelium 26 (21.3 - 37.3) per mm) and Rbm (5.9 (2.3 - 13.8) per mm) frequently double stained for both cytokeratin and S100A4.

Conclusions
These data provide additional support for active EMT in COPD airways.
The evolution of the tape measure protein: units, duplications and losses
Authors: Belcaid Mahdi , Bergeron Anne , Poisson Guylaine 
Published: October 2011

AbstractBackgroundA large family of viruses that infect bacteria, calledphages, is characterized by long tails used to inject DNA into their victims' cells. Thetape measure proteingot its name because the length of the corresponding gene is proportional to the length of the phage's tail: a fact shown by actually copying or splicing out parts of DNA in exemplar species. A natural question is whether there existunitsfor these tape measures, and if different tape measures have different units and lengths. Such units would allow us to retrace the evolution of tape measure proteins using their duplication/loss history. The vast number of sequenced phages genomes allows us to attack this problem with a comparative genomics approach.ResultsHere we describe a subset of phages whose tape measure proteins contain variable numbers of an 11 amino acids sequence repeat, aligned with sequence similarity, structural properties, and simple arithmetics. This subset provides a unique opportunity for the combinatorial study of phage evolution, without the added uncertainties of multiple alignments, which are trivial in this case, or of protein functions, that are well established. We give a heuristic that reconstructs the duplication history of these sequences, using divergent strains to discriminate between mutations that occurred before and after speciation, or lineage divergence. The heuristic is based on an efficient algorithm that gives an exhaustive enumeration of all possible parsimonious reconstructions of the duplication/speciation history of a single nucleotide. Finally, we present a method that allows, when possible, to discriminate between duplication and loss events.ConclusionsEstablishing the evolutionary history of viruses is difficult, in part due to extensive recombinations and gene transfers, and high mutation rates that often erase detectable similarity between homologous genes. In this paper, we introduce new tools to address this problem.
Application of latent semantic analysis for open-ended responses in a large, epidemiologic study
Authors: Leleu Travis D , Jacobson Isabel G , LeardMann Cynthia A , Smith Besa , Foltz Peter W , Amoroso Paul J , Derr Marcia A , Ryan Margaret AK , Smith Tyler C ,   the Millennium Cohort Study Team
Published: October 2011

Abstract

Background
The Millennium Cohort Study is a longitudinal cohort study designed in the late 1990s to evaluate how military service may affect long-term health. The purpose of this investigation was to examine characteristics of Millennium Cohort Study participants who responded to the open-ended question, and to identify and investigate the most commonly reported areas of concern.

Methods
Participants who responded during the 2001-2003 and 2004-2006 questionnaire cycles were included in this study (n = 108,129). To perform these analyses, Latent Semantic Analysis (LSA) was applied to a broad open-ended question asking the participant if there were any additional health concerns. Multivariable logistic regression was performed to examine the adjusted odds of responding to the open-text field, and cluster analysis was executed to understand the major areas of concern for participants providing open-ended responses.

Results
Participants who provided information in the open-ended text field (n = 27,916), had significantly lower self-reported general health compared with those who did not provide information in the open-ended text field. The bulk of responses concerned a finite number of topics, most notably illness/injury, exposure, and exercise.

Conclusion
These findings suggest generalized topic areas, as well as identify subgroups who are more likely to provide additional information in their response that may add insight into future epidemiologic and military research.
Gene expression profile of circulating tumor cells in breast cancer by RT-qPCR
Authors: Strati Areti , Markou Athina , Parisi Cleo , Politaki Eleni , Mavroudis Dimitris , Georgoulias Vasilis , Lianidou Evi 
Published: October 2011

Abstract

Background
Circulating tumor cells (CTCs) have been associated with prognosis especially in breast cancer and have been proposed as a liquid biopsy for repeated follow up examinations. Molecular characterization of CTCs is difficult to address since they are very rare and the amount of available sample is very limited.

Methods
We quantified by RT-qPCR CK-19, MAGE-A3, HER-2, TWIST1, hTERT α+β+, and mammaglobin gene transcripts in immunomagnetically positively selected CTCs from 92 breast cancer patients, and 28 healthy individuals. We also compared our results with the CellSearch system in 33 of these patients with early breast cancer.

Results
RT-qPCR is highly sensitive and specific and can detect the expression of each individual gene at the one cell level. None of the genes tested was detected in the group of healthy donors. In 66 operable breast cancer patients, CK-19 was detected in 42.4%, HER-2 in 13.6%, MAGE-A3 in 21.2%, hMAM in 13.6%, TWIST-1 in 42.4%, and hTERT α+β+ in 10.2%. In 26 patients with verified metastasis, CK-19 was detected in 53.8%, HER-2 in 19.2%, MAGE-A3 in 15.4%, hMAM in 30.8%, TWIST-1 in 38.5% and hTERT α+β+in 19.2%. Our preliminary data on the comparison between RT-qPCR and CellSearch in 33 early breast cancer patients showed that RT-qPCR gives more positive results in respect to CellSearch.

Conclusions
Molecular characterization of CTCs has revealed a remarkable heterogeneity of gene expression between breast cancer patients. In a small percentage of patients, CTCs were positive for all six genes tested, while in some patients only one of these genes was expressed. The clinical significance of these findings in early breast cancer remains to be elucidated when the clinical outcome for these patients is known.
Implementation and first-year screening results of an ocular telehealth system for diabetic retinopathy in China
Authors: Peng Jinjuan , Zou Haidong , Wang Weiwei , Fu Jiong , Shen Bingjie , Bai Xuelin , Xu Xun , Zhang Xi 
Published: October 2011

Abstract

Background
To describe implementation and first-year screening results of the first Chinese telehealth system for diabetic retinopathy (DR) - the Beixinjing Community Diabetic Retinopathy Telehealth system (BCDRT).

Methods
BCDRT implementation was based on the acquisition of adequate digital retinographs, secure digital transmission, storage and retrieval of participants' data and reader-generated medical reports. Local diabetic residents meeting inclusion criteria were enrolled into the BCDRT system beginning in 2009. Participants recommended for further in-person examination with ophthalmologists were followed, and the consistencies in diagnoses between BCDRT and ophthalmologists for DR or macular edema were calculated.

Results
A total of 471 diabetic residents participated in BCDRT screening in 2009. The proportions of total DR, proliferative DR, and diabetic macular edema were 24.42% (115 patients), 2.12% (10 patients) and 6.47% (24 patients), respectively: 56 patients consulted ophthalmologists for further in-person retinal examination with funduscopy after pupil dilation. High rates of consistency between BCDRT screening and ophthalmologists were observed for macular edema (Kappa = 0.81), moderate or severe non-proliferative DR grade (Kappa = 0.92), and other DR grades (Kappa = 1). A total of 456 (96.82%) patients were willing to participate in the next BCDRT screening.

Conclusions
BCDRT was a reliable and valid system for DR screening, and offers the potential to increase DR annual screening rates in local residents.
Lipopolysaccharide modulates astrocytic S100B secretion: a study in cerebrospinal fluid and astrocyte cultures from rats
Authors: Guerra Maria Cristina , Tortorelli Lucas S , Galland Fabiana , Da Ré Carollina , Negri Elisa , Engelke Douglas S , Rodrigues Letícia , Leite Marina C , Gonçalves Carlos-Alberto 
Published: October 2011

Abstract

Background
Inflammatory responses in brain are primarily mediated by microglia, but growing evidence suggests a crucial importance of astrocytes. S100B, a calcium-binding protein secreted by astrocytes, has properties of a neurotrophic or an inflammatory cytokine. However, it is not known whether primary signals occurring during induction of an inflammatory response (e.g. lipopolysaccharide, LPS) directly modulate S100B.

Methods
In this work, we evaluated whether S100B levels in cerebrospinal fluid (CSF) and serum of Wistar rats are affected by LPS administered by intraperitoneal (IP) or intracerebroventricular (ICV) injection, as well as whether primary astrocyte cultures respond directly to lipopolysaccharide.

Results
Our data suggest that S100B secretion in brain tissue is stimulated rapidly and persistently (for at least 24 h) by ICV LPS administration. This increase in CSF S100B was transient when LPS was IP administered. In contrast to these S100B results, we observed an increase in in TNFα levels in serum, but not in CSF, after IP administration of LPS. In isolated astrocytes and in acute hippocampal slices, we observed a direct stimulation of S100B secretion by LPS at a concentration of 10 μg/mL. An involvement of TLR4 was confirmed by use of specific inhibitors. However, lower levels of LPS in astrocyte cultures were able to induce a decrease in S100B secretion after 24 h, without significant change in intracellular content of S100B. In addition, after 24 h exposure to LPS, we observed a decrease in astrocytic glutathione and an increase in astrocytic glial fibrillary acidic protein.

Conclusions
Together, these data contribute to the understanding of the effects of LPS on astrocytes, particularly on S100B secretion, and help us to interpret cerebrospinal fluid and serum changes for this protein in neuroinflammatory diseases. Moreover, non-brain S100B-expressing tissues may be differentially regulated, since LPS administration did not lead to increased serum levels of S100B.
Comparative performance evaluation of hepatitis C virus genotyping based on the 5' untranslated region versus partial sequencing of the NS5B region of brazilian patients with chronic hepatitis C
Authors: Nakatani Sueli M , Santos Carlos A , Riediger Irina N , Krieger Marco A , Duarte Cesar AB , do Carmo Debur Maria , Carrilho Flair J , Ono Suzane K 
Published: October 2011

Abstract

Background
Genotyping of hepatitis C virus (HCV) has become an essential tool for prognosis and prediction of treatment duration. The aim of this study was to compare two HCV genotyping methods: reverse hybridization line probe assay (LiPA v.1) and partial sequencing of the NS5B region.

Methods
Plasma of 171 patients with chronic hepatitis C were screened using both a commercial method (LiPA HCV Versant, Siemens, Tarrytown, NY, USA) and different primers targeting the NS5B region for PCR amplification and sequencing analysis.

Results
Comparison of the HCV genotyping methods showed no difference in the classification at the genotype level. However, a total of 82/171 samples (47.9%) including misclassification, non-subtypable, discrepant and inconclusive results were not classified by LiPA at the subtype level but could be discriminated by NS5B sequencing. Of these samples, 34 samples of genotype 1a and 6 samples of genotype 1b were classified at the subtype level using sequencing of NS5B.

Conclusions
Sequence analysis of NS5B for genotyping HCV provides precise genotype and subtype identification and an accurate epidemiological representation of circulating viral strains.
Bayesian probit regression model for the diagnosis of pulmonary fibrosis: proof-of-principle
Authors: Meltzer Eric B , Barry William T , D'Amico Thomas A , Davis Robert D , Lin Shu S , Onaitis Mark W , Morrison Lake D , Sporn Thomas A , Steele Mark P , Noble Paul W 
Published: October 2011

Abstract

Background
The accurate diagnosis of idiopathic pulmonary fibrosis (IPF) is a major clinical challenge. We developed a model to diagnose IPF by applying Bayesian probit regression (BPR) modelling to gene expression profiles of whole lung tissue.

Methods
Whole lung tissue was obtained from patients with idiopathic pulmonary fibrosis (IPF) undergoing surgical lung biopsy or lung transplantation. Controls were obtained from normal organ donors. We performed cluster analyses to explore differences in our dataset. No significant difference was found between samples obtained from different lobes of the same patient. A significant difference was found between samples obtained at biopsy versus explant. Following preliminary analysis of the complete dataset, we selected three subsets for the development of diagnostic gene signatures: the first signature was developed from all IPF samples (as compared to controls); the second signature was developed from the subset of IPF samples obtained at biopsy; the third signature was developed from IPF explants. To assess the validity of each signature, we used an independent cohort of IPF and normal samples. Each signature was used to predict phenotype (IPF versus normal) in samples from the validation cohort. We compared the models' predictions to the true phenotype of each validation sample, and then calculated sensitivity, specificity and accuracy.

Results
Surprisingly, we found that all three signatures were reasonably valid predictors of diagnosis, with small differences in test sensitivity, specificity and overall accuracy.

Conclusions
This study represents the first use of BPR on whole lung tissue; previously, BPR was primarily used to develop predictive models for cancer. This also represents the first report of an independently validated IPF gene expression signature. In summary, BPR is a promising tool for the development of gene expression signatures from non-neoplastic lung tissue. In the future, BPR might be used to develop definitive diagnostic gene signatures for IPF, prognostic gene signatures for IPF or gene signatures for other non-neoplastic lung disorders such as bronchiolitis obliterans.
Enhanced Toll-like receptor (TLR) responses of TNFR-associated factor 3 (TRAF3)-deficient B lymphocytes
Authors: Xie Ping , Poovassery Jayakumar , Stunz Laura L , Smith Sonja M , Schultz Mark L , Carlin Lindsey E , Bishop Gail A 
Published: October 2011

ABSTRACTThe key role of TRAF6 in TLR signaling pathways is well known. More recent evidence has implicated TRAF3 as another TRAF family member important to certain TLR responses of myeloid cells. Previous studies demonstrate that TRAF3 functions are highly context-dependent, displaying receptor and cell-type specificity. We thus examined the TLR responses of TRAF3−/−mouse B lymphocytes to test the hypothesis that TRAF3 plays distinct roles in such responses, depending on cell type. TRAF3−/− DC are known to have a defect in type 1 IFN production and here, showed diminished production of TNF and IL-10 and unaltered IL-6. In marked contrast, TRAF3−/− B cells made elevated amounts of TNF and IL-6 protein, as well as IL-10 and IP-10 mRNA, in response to TLR ligands. Also, in contrast to TRAF3−/− DC, the type 1 IFN pathway was elevated in TRAF3−/− B cells. Increased early responses of TRAF3−/− B cells to TLR signals were independent of cell survival or proliferation but associated with elevated canonical NF-κB activation. Additionally, TRAF3−/− B cells displayed enhanced TLR-mediated expression of AID and Ig isotype switching. Thus, TRAF3 plays varied and cell type-specific, biological roles in TLR responses.
Increased MMP-2 in healthy postmenopausal women
Authors: Muzzio María Luz , Miksztowicz Veronica , Repetto Esteban Martín , Brites Fernando , Berg Gabriela , Schreier Laura 
Published: October 2011

Background Matrix metalloproteases 2 (MMP-2) and 9 (MMP-9) are involved in the atherosclerosis process. The objective of the study was to evaluate MMP-2 and MMP-9 activities and other circulating inflammatory factors in healthy postmenopausal women (PMW) as a model of subclinical atherosclerosis. Methods Twenty-three PMW and 13 premenopausal women (PreMW) were selected following established criteria. The main measurements in plasma samples were: lipid–lipoprotein profile, high-sensitivity C-reactive protein (hs-CRP) (immunoturbidimetry), soluble vascular cellular adhesion molecules (sVCAM-1) enzyme-linked immunosorbent assay and MMP activity by zymography. Results The relative areas of MMP-2 were increased in PMW: 1.1 (0.1) versus 0.6 (0.05), P < 0.02. MMP-9 was only detected in three PMW and one PreMW. MMP-2 correlated with HDL-cholesterol ( r = −0.51), triglycerides ( r = 0.67), apolipoprotein B ( r = 0.47), hs-CRP ( r = 0.42), homeostasis model assessment ( r = 0.53) and waist circumference ( r = 0.40), at least P < 0.02. sVCAM-1 showed no difference between groups: 28.7 (5.5) versus 35.5 (20) ng/mL, but correlated with MMP-2 and hs-CRP ( r = 0.46 and r = 0.48 respectively, P < 0.05). Conclusions In postmenopause, the increase in MMP-2 reflects the systemic specific inflammatory process that accompanies atherogenesis.
Boceprevir and Telaprevir
Authors: Cada Dennis J. , Levien Terri L. , Baker Danial E. 
Published: October 2011

Each month, subscribers to The Formulary Monograph Service receive 5 to 6 well-documented monographs on drugs that are newly released or are in late phase 3 trials. The monographs are targeted to Pharmacy & Therapeutics Committees. Subscribers also receive monthly 1-page summary monographs on agents that are useful for agendas and pharmacy/nursing in-services. A comprehensive target drug utilization evaluation/medication use evaluation (DUE/MUE) is also provided each month. With a subscription, the monographs are sent in print and are also available on-line. Monographs can be customized to meet the needs of a facility. Subscribers to The Formulary Monograph Service also receive access to a pharmacy bulletin board, The Formulary Information Exchange (The F.I.X.). All topics pertinent to clinical and hospital pharmacy are discussed on The F.I.X. Through the cooperation of The Formulary, Hospital Pharmacy publishes selected reviews in this column. For more information about The Formulary Monograph Service or The F.I.X., call The Formulary at 800-322-4349. The October 2011 monograph topics are on ticagrelor, peginesatide, linaclotide, vemurafenib, and tafluprost. The DUE/MUE is on ticagrelor.