bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global characterization of interferon regulatory factor (IRF) genes in vertebrates: Glimpse of the diversification in evolution
Authors: Huang Bei , Qi Zhi T , Xu Zhen , Nie Pin 
Published: June 2010

Abstract

Background
Interferon regulatory factors (IRFs), which can be identified based on a unique helix-turn-helix DNA-binding domain (DBD) are a large family of transcription factors involved in host immune response, haemotopoietic differentiation and immunomodulation. Despite the identification of ten IRF family members in mammals, and some recent effort to identify these members in fish, relatively little is known in the composition of these members in other classes of vertebrates, and the evolution and probably the origin of the IRF family have not been investigated in vertebrates.

Results
Genome data mining has been performed to identify any possible IRF family members in human, mouse, dog, chicken, anole lizard, frog, and some teleost fish, mainly zebrafish and stickleback, and also in non-vertebrate deuterostomes including the hemichordate, cephalochordate, urochordate and echinoderm. In vertebrates, all ten IRF family members, i.e. IRF-1 to IRF-10 were identified, with two genes of IRF-4 and IRF-6 identified in fish and frog, respectively, except that in zebrafish exist three IRF-4 genes. Surprisingly, an additional member in the IRF family, IRF-11 was found in teleost fish. A range of two to ten IRF-like genes were detected in the non-vertebrate deuterostomes, and they had little similarity to those IRF family members in vertebrates as revealed in genomic structure and in phylogenetic analysis. However, the ten IRF family members, IRF-1 to IRF-10 showed certain degrees of conservation in terms of genomic structure and gene synteny. In particular, IRF-1, IRF-2, IRF-6, IRF-8 are quite conserved in their genomic structure in all vertebrates, and to a less degree, some IRF family members, such as IRF-5 and IRF-9 are comparable in the structure. Synteny analysis revealed that the gene loci for the ten IRF family members in vertebrates were also quite conservative, but in zebrafish conserved genes were distributed in a much longer distance in chromosomes. Furthermore, all ten different members are clustered in respectively different clades; but the IRF-11 was clustered with one in sea urchin.

Conclusions
In vertebrates, the ten well-characterized IRF family members shared a relatively high degree of similarity in genomic structure and syntenic gene arrangement, implying that they might have been evolved in a similar pattern and with similar selective pressure in different classes of vertebrates. Genome and/or gene duplication, and probably gene shuffling or gene loss might have occurred during the evolution of these IRF family members, but arrangement of chromosome or its segment might have taken place in zebrafish. However, the ten IRF family members in vertebrates and those IRF-like genes in non-vertebrate deuterostomes were quite different in those analyzed characters, as they might have undergone different patterns of evolution.
Pharmacokinetic-pharmacodynamic profiling of four antimicrobials against Gram-negative bacteria collected from Shenyang, China
Authors: Chu Yun Zhuo , Tian Su Fei , Chen Bai Yi , Nian Hua , Shang Hong , Sun Guo Quan 
Published: June 2010

Abstract

Background
To examine common antimicrobial regimens used in eradicating certain nosocomial Gram-negative pathogens and determine which ones are likely to be the most suitable as empirical choices in Shenyang, China.

Methods
A 5000-subject Monte Carlo simulation was conducted to determine the cumulative fraction of response (CFR) for meropenem, imipenem, cefepime, piperacillin/tazobactam and levofloxacin against Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae, Acinetobacter baumannii and Pseudomonas aeruginosa collected in 2006 and 2007 from Shenyang.

Results
Meropenem and imipenem had the highest CFRs against the Enterobacteriaceae (97%-100%), followed by cefepime. No antibiotic simulated regimen achieved optimal CFR against P. aeruginosa and A. baumannii. Piperacillin/tazobactam dosed at 4.5 g q8h achieved the lowest CFR against all bacteria.

Conclusions
This study suggests that the carbapenems provide the greatest likelihood of clinical success for the Enterobacteriaceae, and combination therapy might be needed when choosing empirical therapy, especially when A. baumannii or P. aeruginosa are suspected.
The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature
Authors: Zhao Jianhua , Li Mingyao , Bradfield Jonathan P , Zhang Haitao , Mentch Frank D , Wang Kai , Sleiman Patrick M , Kim Cecilia E , Glessner Joseph T , Hou Cuiping , Keating Brendan J , Thomas Kelly A , Garris Maria L , Deliard Sandra , Frackelton Edward C , Otieno F George , Chiavacci Rosetta M , Berkowitz Robert I , Hakonarson Hakon , Grant Struan FA 
Published: June 2010

Abstract

Background
Human height is considered highly heritable and correlated with certain disorders, such as type 2 diabetes and cancer. Despite environmental influences, genetic factors are known to play an important role in stature determination. A number of genetic determinants of adult height have already been established through genome wide association studies.

Methods
To examine 51 single nucleotide polymorphisms (SNPs) corresponding to the 46 previously reported genomic loci for height in 8,184 European American children with height measurements. We leveraged genotyping data from our ongoing GWA study of height variation in children in order to query the 51 SNPs in this pediatric cohort.

Results
Sixteen of these SNPs yielded at least nominally significant association to height, representing fifteen different loci including EFEMP1-PNPT1, GPR126, C6orf173, SPAG17, Histone class 1, HLA class III and GDF5-UQCC. Other loci revealed no evidence for association, including HMGA1 and HMGA2. For the 16 associated variants, the genotype score explained 1.64% of the total variation for height z-score.

Conclusion
Among 46 loci that have been reported to associate with adult height to date, at least 15 also contribute to the determination of height in childhood.
Pim1 promotes human prostate cancer cell tumorigenicity and c-MYC transcriptional activity
Authors: Kim Jongchan , Roh Meejeon , Abdulkadir Sarki A 
Published: June 2010

Abstract

Background
The serine/threonine kinase PIM1 has been implicated as an oncogene in various human cancers including lymphomas, gastric, colorectal and prostate carcinomas. In mouse models, Pim1 is known to cooperate with c-Myc to promote tumorigenicity. However, there has been limited analysis of the tumorigenic potential of Pim1 overexpression in benign and malignant human prostate cancer cells in vivo.

Methods
We overexpressed Pim1 in three human prostate cell lines representing different disease stages including benign (RWPE1), androgen-dependent cancer (LNCaP) and androgen-independent cancer (DU145). We then analyzed in vitro and in vivo tumorigenicity as well as the effect of Pim1 overexpression on c-MYC transcriptional activity by reporter assays and gene expression profiling using an inducible MYC-ER system. To validate that Pim1 induces tumorigenicity and target gene expression by modulating c-MYC transcriptional activity, we inhibited c-MYC using a small molecule inhibitor (10058-F4) or RNA interference.

Results
Overexpression of Pim1 alone was not sufficient to convert the benign RWPE1 cell to malignancy although it enhanced their proliferation rates when grown as xenografts in vivo. However, Pim1 expression enhanced the in vitro and in vivo tumorigenic potentials of the human prostate cancer cell lines LNCaP and DU145. Reporter assays revealed increased c-MYC transcriptional activity in Pim1-expressing cells and mRNA expression profiling demonstrated that a large fraction of c-MYC target genes were also regulated by Pim1 expression. The c-MYC inhibitor 10058-F4 suppressed the tumorigenicity of Pim1-expressing prostate cancer cells. Interestingly, 10058-F4 treatment also led to a reduction of Pim1 protein but not mRNA. Knocking-down c-MYC using short hairpin RNA reversed the effects of Pim1 on Pim1/MYC target genes.

Conclusion
Our results suggest an in vivo role of Pim1 in promoting prostate tumorigenesis although it displayed distinct oncogenic activities depending on the disease stage of the cell line. Pim1 promotes tumorigenicity at least in part by enhancing c-MYC transcriptional activity. We also made the novel discovery that treatment of cells with the c-MYC inhibitor 10058-F4 leads to a reduction in Pim1 protein levels.
Identification of galectin-7 as a potential biomarker for esophageal squamous cell carcinoma by proteomic analysis
Authors: Zhu Xi , Ding Ming , Yu Mei-Lan , Feng Ming-Xiang , Tan Li-Jie , Zhao Fu-Kun 
Published: June 2010

Abstract

Background
Esophageal squamous cell carcinoma (ESCC) is one of the most common malignancies. Early diagnosis is critical for guiding the therapeutic management of ESCC. It is imperative to find more effective biomarkers of ESCC.

Methods
To identify novel biomarkers for esophageal squamous cell carcinoma (ESCC), specimens from 10 patients with ESCC were subjected to a comparative proteomic analysis. The proteomic patterns of ESCC samples and normal esophageal epithelial tissues (NEETs) were compared using two-dimensional gel electrophoresis. And differentially expressed proteins were identified using MALDI-TOF-MS/MS. For further identification of protein in selected spot, western blotting and immunohistochemistry were employed.

Results
Twelve proteins were up-regulated and fifteen proteins were down-regulated in the ESCC samples compared with the NEET samples. Up-regulation of galectin-7 was further confirmed by western blotting and immunohistochemistry. Furthermore, immunohistochemical staining of galectin-7 was performed on a tissue microarray containing ESCC samples (n = 50) and NEET samples (n = 10). The expression levels of galectin-7 were markedly higher in the ESCC samples than in the NEET samples (P = 0.012). In addition, tissue microarray analysis also showed that the expression level of galectin-7 was related to the differentiation of ESCC.

Conclusions
The present proteomics analysis revealed that galectin-7 was highly expressed in ESCC tissues. The alteration in the expression of galectin-7 was confirmed using a tissue microarray. These findings suggest that galectin-7 could be used as a potential biomarker for ESCC.
Acupuncture for chronic low back pain: protocol for a multicenter, randomized, sham-controlled trial
Authors: Lee Jun-Hwan , Park Hi-Joon , Lee Hyangsook , Shin Im Hee , Song Mi-Yeon 
Published: June 2010

Abstract

Background
Use of acupuncture has widely increased in patients with chronic low back pain. However, the evidence supporting its efficacy remains unclear. In this article, we report the design and the protocol of a multi-center randomized sham-controlled trial to treat chronic low back pain. Our goal is to verify the effect of acupuncture on chronic low back pain.

Methods/Design
This study is a multi-center randomized sham-controlled trial with 2 parallel arms. Participants included in the study met the following criteria: 1) low back pain lasting for at least the last 3 months, 2) a documented ≥ 5 points on a 10 cm visual analog scale for bothersomeness of low back pain at the time of screening and 3) between 18 and 65 years of age. Participants were blinded to the real and sham acupuncture treatments. The real acupuncture treatment group received real acupuncture 2 times a week, during a total of 12 sessions over 6 weeks. The control group received sham acupuncture during the same period. In order to assess the primary and secondary outcome measures, the participants were asked to fill out a questionnaire at the baseline and 6, 8, 12 and 24 weeks after starting the treatments. The primary outcome was measured using the visual analog scale for bothersomeness of low back pain at 8 weeks after the initiation of treatments.

Discussion
The result of this trial (which will be available in 2010) will demonstrate the efficacy of using acupuncture to treat chronic low back pain.

Trial registration
This study is registered with the U.S. National Institutes of Health Clinical Trials registry: NCT00815529
A prospective cohort study to investigate cost-minimisation, of Traditional open, open fAst track recovery and laParoscopic fASt track multimodal management, for surgical patients with colon carcinomas (TAPAS study)
Authors: Reurings Jurrian C , Spanjersberg Willem R , Oostvogel Henk JM , Buskens Erik , Maring John , Kruijt Flip , Rosman Camiel , van Duivendijk Peter , Dejong Cees HC , van Laarhoven Cees JHM 
Published: June 2010

Abstract

Background
The present developments in colon surgery are characterized by two innovations: the introduction of the laparoscopic operation technique and fast recovery programs such as the Enhanced Recovery After Surgery (ERAS) recovery program. The Tapas-study was conceived to determine which of the three treatment programs: open conventional surgery, open 'ERAS' surgery or laparoscopic 'ERAS' surgery for patients with colon carcinomas is most cost minimizing?

Method/design
The Tapas-study is a three-arm multicenter prospective cohort study.
All patients with colon carcinoma, eligible for surgical treatment within the study period in four general teaching hospitals and one university hospital will be included. This design produces three cohorts: Conventional open surgery is the control exposure (cohort 1). Open surgery with ERAS recovery (cohort 2) and laparoscopic surgery with ERAS recovery (cohort 3) are the alternative exposures. Three separate time periods are used in order to prevent attrition bias.
Primary outcome parameters are the two main cost factors: direct medical costs (real cost price calculation) and the indirect non medical costs (friction method). Secondary outcome parameters are mortality, complications, surgical-oncological resection margins, hospital stay, readmission rates, time back to work/recovery, health status and quality of life.
Based on an estimated difference in direct medical costs (highest cost factor) of 38% between open and laparoscopic surgery (alfa = 0.01, beta = 0.05), a group size of 3×40 = 120 patients is calculated.

Discussion
The Tapas-study is three-arm multicenter cohort study that will provide a cost evaluation of three treatment programs for patients with colon carcinoma, which may serve as a guideline for choice of treatment and investment strategies in hospitals.

Trial registration
ISRCTN44649165.
Simultaneously performed off-pump coronary artery bypass grafting and colectomy: a case report
Authors: Dedeilias Panagiotis , Nenekidis Ioannis , Koletsis Efstratios , Baikoussis Nikolaos G , Hountis Panagiotis , Exarhos Dimitrios , Klimopoulos Serafim 
Published: June 2010

Abstract
This is written so as to report the case of a 71-year-old male with a diagnosis of sigmoid adenocarcinoma accompanied by severe coronary artery disease and unstable angina, which was subject to simultaneous surgical treatment. The patient initially underwent an off-pump coronary artery revascularization in order to avoid the complications of cardiopulmonary bypass, providing the opportunity of a colectomy at the same time with the use of safe surgical means. Our case suggests that performing an off-pump bypass procedure prior to cancer surgery can be an appropriate course of action in carefully selected cases.
A novel method for purifying bluetongue virus with high purity by co-immunoprecipitation with agarose protein A
Authors: Zhen Song , Changyuan Dong , Lulu Wang , Dong-E Chen , Guoming Bi , Ming Dai , Jun Liu 
Published: June 2010

Abstract

Background
Bluetongue virus (BTV) is an icosahedral non-enveloped virus within the genus Orbivirus of Reoviridae and exists as 24 distinct serotypes. BTV can infect all ruminant species and causes severe sickness in sheep. Recently, it was reported that BTV can infect some human cancer cells selectively. Because of the important oncolysis of this virus, we developed a novel purifying method for large-scale production. The purifying logic is simple, which is picking out all the components unwanted and the left is what we want. The process can be summarized in 4 steps: centrifugation, pulling down cell debrises and soluble proteins by co-immunoprecipitation with agarose Protein A, dialysis and filtration sterilization after concentration.

Results
The result of transmission electron microscope (TEM) observation showed that the sample of purified virus has a very clear background and the virions still kept intact. The result of 50% tissue culture infective dose (TCID50) assay showed that the bioactivity of purified virus is relatively high.

Conclusions
This method can purify BTV-10 with high quality and high biological activity on large-scale production. It also can be used for purifying other BTV serotypes.
Therapeutic approach to Gradenigo's syndrome: a case report
Authors: Kantas Ilias , Papadopoulou Anna , Balatsouras Dimitrios G , Aspris Andreas , Marangos Nikolaos 
Published: June 2010

Abstract

Introduction
Traditional management of Gradenigo's syndrome requires aggressive and radical surgery without any attempt to preserve hearing. Recent reports, however, describe a successful outcome after conservative surgical intervention without labyrinthectomy. A similar outcome has also been reported in patients who were only prescribed with antibiotics and did not undergo myringotomy.

Case presentation
We report the case of a 24-year-old Caucasian Greek woman with Gradenigo's syndrome who was treated by draining her petrous apex via an infralabyrithine approach between her posterior semicircular canal and the jugular bulb. Her inner ear was not sacrificed during the procedure. She presented pre-operatively with ipsilateral conductive hearing loss, which recovered completely four weeks after the surgery.

Conclusions
Patients with Gradenigo's syndrome may be successfully treated with a combination of long-term permanent drainage and ventilation of the apical cells with corresponding hearing preservation. This can be achieved via a combination of transmastoid, infralabyrinthine and suprajugular approaches, if such would be allowed by the anatomy of the region or if there is enough space between the posterior semicircular canal and the jugular bulb.
Time to achieve remission determines time to be in remission
Authors: Schipper Lydia G , Fransen Jaap , den Broeder Alfons A , Van Riel Piet LCM 
Published: June 2010

Abstract
Introduction
Though remission is currently a treatment goal in patients with rheumatoid arthritis (RA), the number of patients who achieve and sustain remission in daily practice is still small. It is suggested that early remission will be associated with sustainability of remission. The aim was to study the association between time-to-remission and sustainability of remission in a cohort of early RA patients treated according to daily practice.

Methods
For this study, three-year follow-up data were used from the Nijmegen RA Inception Cohort of patients included between 1985 and 2005 (N = 753). Patients were included upon diagnosis (ACR criteria), were systematically evaluated at three-monthly visits and treated according to daily practice. Remission was defined according to the Disease Activity Score (DAS) <1.6 and the ACR remission criteria. Remission of at least 6 months duration was regarded as sustained remission. Predictors for time-to-remission were identified by Cox-regression analyses. The relation between time-to-remission and sustained remission was analyzed using longitudinal binary regression.

Results
N = 398 (52%) patients achieved remission with a median time-to-remission of 12 months. Male gender, younger age and low DAS at baseline were predictive to reach remission rapidly. There were n = 142 (36%) patients experiencing sustained remission, which was determined by a shorter time-to-remission only. The relationship between time-to-remission and sustained remission was described by a significant odds ratio (1.11) (1.10 to 1.12-95% CI) that was constant over the whole period 1985 to 2005. Results obtained with the ACR remission criteria were similar.

Conclusions
A shorter time-to-remission is related to sustainability of remission, supporting striving for early remission in patients with RA.
Primary Disseminated Multifocal Ewing Sarcoma: Results of the Euro-EWING 99 Trial
Authors: Ladenstein Ruth , Pötschger Ulrike , Le Deley Marie Cécile , Whelan Jeremy , Paulussen Michael , Oberlin Odile , van den Berg Henk , Dirksen Uta , Hjorth Lars , Michon Jean , Lewis Ian , Craft Alan , Jürgens Heribert 
Published: June 2010

Purpose To improve the poor prognosis of patients with primary disseminated multifocal Ewing sarcomas (PDMES) with a dose-intense treatment concept. Patients and Methods From 1999 to 2005, 281 patients with PDMES were enrolled onto the Euro-EWING 99 R3 study. Median age was 16.2 years (range, 0.4 to 49 years). Recommended treatment consisted of six cycles of vincristine, ifosfamide, doxorubicin, and etoposide (VIDE), one cycle of vincristine, dactinomycin, and ifosfamide (VAI), local treatment (surgery and/or radiotherapy), and high-dose busulfan-melphalan followed by autologous stem-cell transplantation (HDT/SCT). Results After a median follow-up of 3.8 years, event-free survival (EFS) and overall survival (OS) at 3 years for all 281 patients were 27% ± 3% and 34% ± 4% respectively. Six VIDE cycles were completed by 250 patients (89%); 169 patients (60%) received HDT/SCT. The estimated 3-year EFS from the start of HDT/SCT was 45% for 46 children younger than 14 years. Cox regression analyses demonstrated increased risk at diagnosis for patients older than 14 years (hazard ratio [HR] = 1.6), a primary tumor volume more than 200 mL (HR = 1.8), more than one bone metastatic site (HR = 2.0), bone marrow metastases (HR = 1.6), and additional lung metastases (HR = 1.5). An up-front risk score based on these HR factors identified three groups with EFS rates of 50% for score ≤ 3 (82 patients), 25% for score more than 3 to less than 5 (102 patients), and 10% for score ≥ 5 (70 patients; P < .0001). Conclusion PDMES patients may survive with intensive multimodal therapy. Age, tumor volume, and extent of metastatic spread are relevant risk factors. A score based on these factors may facilitate risk-adapted treatment approaches.