bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pair-barcode high-throughput sequencing for large-scale multiplexed sample analysis
Authors: Tu Jing , Ge Qinyu , Wang Shengqin , Wang Lei , Sun Beili , Yang Qi , Bai Yunfei , Lu Zuhong 
Published: January 2012

AbstractBackgroundThe multiplexing becomes the major limitation of the next-generation sequencing (NGS) in application to low complexity samples. Physical space segregation allows limited multiplexing, while the existing barcode approach only permits simultaneously analysis of up to several dozen samples.ResultsHere we introduce pair-barcode sequencing (PBS), an economic and flexible barcoding technique that permits parallel analysis of large-scale multiplexed samples. In two pilot runs using SOLiD sequencer (Applied Biosystems Inc.), 32 independent pair-barcoded miRNA libraries were simultaneously discovered by the combination of 4 unique forward barcodes and 8 unique reverse barcodes. Over 174,000,000 reads were generated and about 64% of them are assigned to both of the barcodes. After mapping all reads to pre-miRNAs in miRBase, different miRNA expression patterns are captured from the two clinical groups. The strong correlation using different barcode pairs and the high consistency of miRNA expression in two independent runs demonstrates that PBS approach is valid.ConclusionsBy employing PBS approach in NGS, large-scale multiplexed pooled samples could be practically analyzed in parallel so that high-throughput sequencing economically meets the requirements of samples which are low sequencing throughput demand.
Triggers for an episode of sudden onset low back pain: study protocol
Authors: Steffens Daniel , Ferreira Manuela L , Maher Christopher G , Latimer Jane , Koes Bart W , Blyth Fiona M , Ferreira Paulo H 
Published: January 2012

Abstract

Background
Most research on risk factors for low back pain has focused on long term exposures rather than factors immediately preceding the onset of low back pain. The aim of this study is to quantify the transient increase in risk of a sudden episode of low back pain associated with acute exposure to a range of common physical and psychological factors.

Methods/design
This study uses a case-crossover design. One thousand adults with a sudden onset of low back pain presenting to primary care clinicians will be recruited. Basic demographic and clinical information including exposure to putative triggers will be collected using a questionnaire. These triggers include exposure to hazardous manual tasks, physical activity, a slip/trip or fall, consumption of alcohol, sexual activity, being distracted, and being fatigued or tired. Exposures in the case window (0-2 hours from the time when participants first notice their back pain) will be compared to exposures in two control time-windows (one 24-26 hours and another 48-50 hours before the case window).

Discussion
The completion of this study will provide the first-research based estimates of the increase in risk of a sudden episode of acute low back pain associated with transient exposure to a range of common factors thought to trigger low back pain.
Exploiting the Campylobacter jejuni protein glycosylation system for glycoengineering vaccines and diagnostic tools directed against brucellosis
Authors: Iwashkiw Jeremy A , Fentabil Messele A , Faridmoayer Amirreza , Mills Dominic C , Peppler Mark , Czibener Cecilia , Ciocchini Andres E , Comerci Diego J , Ugalde Juan E , Feldman Mario F 
Published: January 2012

Abstract

Background
Immune responses directed towards surface polysaccharides conjugated to proteins are effective in preventing colonization and infection of bacterial pathogens. Presently, the production of these conjugate vaccines requires intricate synthetic chemistry for obtaining, activating, and attaching the polysaccharides to protein carriers. Glycoproteins generated by engineering bacterial glycosylation machineries have been proposed to be a viable alternative to traditional conjugation methods.

Results
In this work we expressed the C. jejuni oligosaccharyltansferase (OTase) PglB, responsible for N-linked protein glycosylation together with a suitable acceptor protein (AcrA) in Yersinia enterocolitica O9 cells. MS analysis of the acceptor protein demonstrated the transfer of a polymer of N-formylperosamine to AcrA in vivo. Because Y. enterocolitica O9 and Brucella abortus share an identical O polysaccharide structure, we explored the application of the resulting glycoprotein in vaccinology and diagnostics of brucellosis, one of the most common zoonotic diseases with over half a million new cases annually. Injection of the glycoprotein into mice generated an IgG response that recognized the O antigen of Brucella, although this response was not protective against a challenge with a virulent B. abortus strain. The recombinant glycoprotein coated onto magnetic beads was efficient in differentiating between naïve and infected bovine sera.

Conclusion
Bacterial engineered glycoproteins show promising applications for the development on an array of diagnostics and immunoprotective opportunities in the future.
Perioperative dynamic alterations in peripheral regulatory T and B cells in patients with hepatocellular carcinoma
Authors: Chen Tianxiang , Song Dongli , Min Zhihui , Wang Xiangdong , Gu Yu , Wei Bajin , Yao Jia , Chen Kangjie , Jiang Zhijun , Xie Haiyang , Zhou Lin , Zheng Shusen 
Published: January 2012

AbstractBackgroundIntratumoral and circulating regulatory T cells (Tregs) have been shown to be critical in the pathogenesis of hepatocellular carcinoma (HCC). However there is limited knowledge on the alterations of regulatory B cells (Bregs). We here investigated perioperative dynamic alterations of peripheral circulating Tregs and Bregs in HCC patients to reveal the relationship between regulatory lymphocytes and its clinical implications.Methods36 patients with HCC, 6 with chronic hepatitis B infection and 10 healthy donors were enrolled for this study. Frequencies of peripheral Tregs and Bregs were measured by flow cytometry with antibodies against CD4, CD25, CD127, CD19 and IL-10 before, and after radical surgery. Then, clinical informatics of HCC patients was achieved through Digital Evaluation Score System (DESS) for the assessment of disease severity. Finally, we analysed correlations between digitalized clinical features and kinetics of circulating regulatory lymphocytes.ResultsLevel of circulating CD4+CD25+CD127-Tregs in HCC patients was significantly lower than that in healthy donors and patients with chronic hepatitis B infection before surgery, but was increased after surgery. Preoperative level of CD19+IL-10+Bregs in HCC patients was also significantly lower than the other groups. However it dramatically was elevated right after surgery and remained elevated compared to controls (about 7 days after surgery,P= 0.04). Frequency of circulating Tregs was correlated with circulating leukocytes, ferritin, and clinical features suggesting tumor aggressiveness including portal vein thrombosis, hepatic vein involvement and advanced clinical stages. Frequency of circulating Bregs was associated with Hepatitis B e Antigen (HBeAg) and Hepatitis B virus (HBV) DNA copy number. In addition, DESS was significantly and positively correlated with other staging systems.ConclusionFrequencies of peripheral Tregs and Bregs in HCC patients increased after surgery. These results suggest that a postoperative combination of therapies against Tregs and Bregs may be beneficial for better outcome of HCC patients after resection.
Highly selective fluorescent chemosensor for Zn2+ derived from inorganic-organic hybrid magnetic core/shell Fe3O4@SiO2 nanoparticles
Authors: Wang Yujiao , Peng Xiaohong , Shi Jinmin , Tang Xiaoliang , Jiang Jie , Liu Weisheng 
Published: January 2012

Abstract
Magnetic nanoparticles with attractive optical properties have been proposed for applications in such areas as separation and magnetic resonance imaging. In this paper, a simple and novel fluorescent sensor of Zn2+ was designed with 3,5-di-tert-butyl-2-hydroxybenzaldehyde [DTH] covalently grafted onto the surface of magnetic core/shell Fe3O4@SiO2 nanoparticles [NPs] (DTH-Fe3O4@SiO2 NPs) using the silanol hydrolysis approach. The DTH-Fe3O4@SiO2 inorganic-organic hybrid material was characterized by transmission electron microscopy, dynamic light scattering, X-ray power diffraction, diffuse reflectance infrared Fourier transform, UV-visible absorption and emission spectrometry. The compound DTH exhibited fluorescence response towards Zn2+ and Mg2+ ions, but the DTH-Fe3O4@SiO2 NPs only effectively recognized Zn2+ ion by significant fluorescent enhancement in the presence of various ions, which is due to the restriction of the N-C rotation of DTH-Fe3O4@SiO2 NPs and the formation of the rigid plane with conjugation when the DTH-Fe3O4@SiO2 is coordinated with Zn2+. Moreover, this DTH-Fe3O4@SiO2 fluorescent chemosensor also displayed superparamagnetic properties, and thus, it can be recycled by magnetic attraction.
Coupled coincidence point theorems for contractions without commutative condition in intuitionistic fuzzy normed spaces
Authors: Sintunavarat Wutiphol , Cho Yeol Je , Kumam Poom 
Published: January 2012

AbstractRecently, Gordji et al. [Math. Comput. Model. 54, 1897-1906 (2011)] prove the coupled coincidence point theorems for nonlinear contraction mappings satisfying commutative condition in intuitionistic fuzzy normed spaces. The aim of this article is to extend and improve some coupled coincidence point theorems of Gordji et al. Also, we give an example of a nonlinear contraction mapping which is not applied by the results of Gordji et al., but can be applied to our results.2000 MSC: primary 47H10; secondary 54H25; 34B15.
Loss of Niemann Pick type C proteins 1 and 2 greatly enhances HIV infectivity and is associated with accumulation of HIV Gag and cholesterol in late endosomes/lysosomes
Authors: Coleman Ebony M , Walker Tiffany N , Hildreth James EK 
Published: January 2012

Abstract

Background
Cholesterol pathways play an important role at multiple stages during the HIV-1 infection cycle. Here, we investigated the role of cholesterol trafficking in HIV-1 replication utilizing Niemann-Pick Type C disease (NPCD) cells as a model system.

Results
We used a unique NPC2-deficient cell line (NPCD55) that exhibited Gag accumulation as well as decreased NPC1 expression after HIV infection. Virus release efficiency from NPCD55 cells was similar to that from control cells. However, we observed a 3 to 4-fold enhancement in the infectivity of virus released from these cells. Fluorescence microscopy revealed accumulation and co-localization of Gag proteins with cholesterol in late endosomal/lysosomal (LE/L) compartments of these cells. Virion-associated cholesterol was 4-fold higher in virions produced in NPCD55 cells relative to virus produced in control cells. Treatment of infected NPCD55 cells with the cholesterol efflux-inducing drug TO-9013171 reduced virus infectivity to control levels.

Conclusions
These results suggest cholesterol trafficking and localization can profoundly affect HIV-1 infectivity by modulating the cholesterol content of the virions.
Gastric malignant schwannoma presenting with upper gastrointestinal bleeding: a case report
Authors: Takemura Masashi , Yoshida Kayo , Takii Mamiko , Sakurai Katsunobu , Kanazawa Akishige 
Published: January 2012

Abstract

Introduction
We report a case of gastric malignant schwannoma presenting with gastrointestinal bleeding.

Case presentation
A 70-year-old Japanese man presented with gastrointestinal bleeding to our hospital. Gastrointestinal endoscopy revealed a protruding lesion in the gastric body. Hematoxylin and eosin staining of biopsy specimens from this lesion revealed sheets of spindle cells. Immunohistochemistry revealed that these cells were positive for S-100 protein and negative for c-Kit and smooth muscle actin. Because mitosis was diffusely visible, this tumor was diagnosed as a gastric malignant schwannoma. Distal gastrectomy with lymph node dissection was performed and the patient's postoperative course was uneventful. However, five months after the surgery, he died from multiple liver metastases.

Conclusion
Cases of gastric malignant schwannoma have rarely been reported. The efficacy of surgical resection and postoperative prognosis continues to remain unclear and should be investigated further.
Paratesticular desmoplastic small round cell tumour: an unusual tumour with an unusual fusion; cytogenetic and molecular genetic analysis combining RT-PCR and COBRA-FISH
Authors: Cliteur Vincent PM , Szuhai Károly , Baelde Hans J , van Dam Jurriaan , Gelderblom Hans , Hogendoorn Pancras CW 
Published: January 2012

Abstract
Desmoplastic small round cell tumour is a rare malignant tumour with a male to female ratio of 4:1. It manifests mostly at serosal sites. Here we present a case of a 28-year-old male patient, who presented with a fast growing paratesticular mass. On biopsy nests and cords of small round cells, without a clear morphological lineage of differentiation were seen. Occasionally desmoplatic small round cell tumour shows different lines of differentiation. An unequivocal histological diagnosis might be difficult in such cases. Here we demonstrate by a combination of methods the characteristic immunohistochemical profile and - albeit unusual - molecular background and discuss the eventual link with Ewing sarcoma.
Immunohistochemical studies showed a membranous staining of Keratine AE1/3 and a dot-like staining of Desmine, confirming its diagnosis. Using COBRA-FISH following a metaphase approach we demonstrated a balanced translocation, t(11;22)(p13;q12) and in RT-PCR formation of the EWSR1-WT1 fusion product, a specific translocation of desmoplastic round cell tumour. The fusion involves exon 9 of EWSR1 to exon 8 of WT1, an unusual fusion product, though earlier described in a case of a desmoplastic small round cell tumour of the hand. The EWSR1-WT1 chimera seems to function as an oncogenic transcription factor. Here the zinc finger domain of the WT1 acts with affinity with certain promoter domains influencing the expression of various downstream proteins such as: PDGFA, PAX2, insulin-like growth factor 1 receptor, epidermal growth factor receptor, IL2 receptor beta, BAIAP3, MLF1, TALLA-1, LRRC15 and ENT. We discuss their potential oncogenic roles and potential therapeutic consequences.
Identification of cytochrome P450 monooxygenase genes from the white-rot fungus Phlebia brevispora
Authors: Nakamura Ryoich , Kondo Ryuichiro , Shen Ming-hao , Ochiai Hideharu , Hisamatsu Shin , Sonoki Shigenori 
Published: January 2012

Abstract
Three cytochrome P450 monooxygenase (CYP) genes, designated pb-1, pb-2 and pb-3, were isolated from the white-rot fungus, Phlebia brevispora, using reverse transcription PCR with degenerate primers constructed based on the consensus amino acid sequence of eukaryotic CYPs in the O2-binding, meander and heme-binding regions. Individual full-length CYP cDNAs were cloned and sequenced, and the relative nucleotide sequence similarity of pb-1 (1788 bp), pb-2 (1881 bp) and pb-3 (1791 bp) was more than 58%. Alignment of the deduced amino acid (aa) sequences of pb-1-pb-3 showed that these three CYPs belong to the same family with > 40% aa sequence similarity, and pb-1 and pb-3 are in the same subfamily, with > 55% aa sequence similarity. Furthermore, pb-1-pb-3 appeared to be a subfamily of CYP63A (CYP63A1-CYP63A4), found in Phanerochaete chrysosporium. The phylogenetic tree constructed by 500 bootstrap replications using the neighbor-joining method showed that the evolutionary distance between pb-1 and pb-3 was shorter than that between pb-2 and pb-1 (or pb-3). Exon-intron analysis of pb-1 and pb-3 showed that both genes have nearly the same number, size and order of exons and the types of introns, also indicating both genes appear to be evolutionarily close. It is interesting that the transcription level of pb-3 was evidently increased above the pb-1 transcription level by exposure to 12 coplanar PCB congeners and 2,3,7,8-tetrachlorodibenzo-p-dioxin, though the two genes were evolutionarily close.
Restrictive pulmonary function is more prevalent in patients with ankylosing spondylitis than in matched population controls and is associated with impaired spinal mobility: a comparative study
Authors: Berdal Gunnhild , Halvorsen Silje , van der Heijde Désirée , Mowe Morten , Dagfinrud Hanne 
Published: January 2012

Abstract
Introduction
Pulmonary involvement is a known manifestation in patients with ankylosing spondylitis (AS). However, previous studies have been based on small samples and the reported prevalence and associations with typical clinical features vary. The purpose of this study was to compare pulmonary function (PF) in patients with AS and population controls, and to study associations between PF and disease related variables, cardio-respiratory fitness and demographic variables in patients with AS.

Methods
In a cross-sectional controlled study, 147 AS patients and 121 controls underwent examinations, including demographic variables, laboratory (C-reactive protein (CRP), erythrocyte sedimentation rate (ESR)) and clinical measures (disease activity (AS disease activity score, ASDAS), physical function (Bath ankylosing spondylitis functional index, BASFI), spinal mobility (Bath ankylosing spondylitis metrology index, BASMI), chest expansion, cardio-respiratory fitness (peak oxygen uptake, VO2peak) and pulmonary function test (PFT) (spirometry)). Cumulative probability plots were used to visualize associations between the ASDAS and BASMI scores and the corresponding forced vital capacity (FVC%, percentage of predicted value controlled for the influence of confounding factors) score for each patient. Univariate ANCOVAs were performed to explore group differences in PF adjusting for relevant variables, and a multiple regression model was used to estimate the explanatory power of independent variables (demographic, disease related, VO2peak) on restrictive ventilatory impairment (FVC%).

Results
AS patients showed significantly lower PF values compared with controls, and significantly more patients were categorized with restrictive pattern (18% vs. 0%, P < 0.001). Cumulative probability plots showed significant associations between spinal mobility measures (BASMI) and FVC% for individual patients. BASMI, chest expansion and male gender contributed significantly and independently in a multiple regression model predicting the variation of FVC% in AS patients, whereas disease activity, physical function and VO2peak did not contribute significantly. The final model explained 45% of the variance in FVC% (P < 0.001).

Conclusions
This study showed significantly impaired pulmonary function in the AS patients compared to controls and reference data, and demonstrated a clear relationship between reduced spinal mobility and restrictive PF in AS patients. The results support the assumption of an association between musculoskeletal limitations and restrictive respiratory impairment in AS, emphasizing the importance of maintaining spinal flexibility in the management of the disease. Further, patients with severely reduced spinal mobility should be referred for pulmonary function examination and relevant follow-up treatment.
Metastasis is an early event in mouse mammary carcinomas and is associated with cells bearing stem cell markers
Authors: Weng Desheng , Penzner Jeffrey H , Song Baizheng , Koido Shigeo , Calderwood Stuart K , Gong Jianlin 
Published: January 2012

Abstract
Introduction
It is still uncertain whether metastasis is predominantly an early or late event in tumor progression. The detection of early metastases and cells responsible for the dissemination may therefore have significant clinical implications.

Methods
Lung dissemination and/or metastasis were investigated in mice carrying the polyomavirus middle-T oncogene (PyMT) during different stages of mammary tumorigenesis using the colony forming assay. Immunocytochemical or immunohistochemical staining was used to identify subpopulations of cells responsible for lung dissemination and metastasis. Histological examination was used to show primary and metastatic tumors. The tumor-initiating and metastatic capacity of cells expressing stem cell markers was assessed in syngeneic wild-type (WT) mice whose mammary fat pads were injected with these cells.

Results
Metastatic mammary epithelial cells were detected in the lungs of mice carrying the PyMT oncogene (MMT mice). These cells were observed early in breast tumorigenesis when the mammary tree appeared by histological inspection to be normal (or at a premalignant stage), suggesting the possession of disseminating and metastatic capacity even before full malignant transformation. Some of the disseminated cells and lung metastases displayed surface stem cell markers. These findings suggest that stem cells from apparently precancerous primary lesions could be a source of metastasis. Indeed, injection of lung tissue cells from MMT mice into syngeneic WT mice resulted in the formation of mammary tumors. These tumors resembled their parent mammary tumors in the MMT donors as well as grafted tumors derived from mammary tumor cells. Furthermore, when we injected lung tissue cells from GFP MMT mice into the fat pads of recipient WT mice, disseminated or metastatic GFP-expressing cells were detected in the lungs, lymph nodes and blood of the recipient WT mice. We finally identified a subpopulation of mammary epithelial/tumor cells expressing CD44 and Sca1 that was largely responsible for dissemination and metastasis in MMT mice.

Conclusions
The tumorigenic and metastatic potential of a subpopulation of mammary epithelial/tumor cells in MMT mice is endowed relatively early in mammary neoplasms and suggests a potential role for cancer stem cell sub-populations in metastasis.