bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a radiosensitivity signature using integrative metaanalysis of published microarray data for NCI-60 cancer cells
Authors: Kim Han Sang , Kim Sang Cheol , Kim Sun Jeong , Park Chan Hee , Jeung Hei-Cheul , Kim Yong Bae , Ahn Joong Bae , Chung Hyun Cheol , Rha Sun Young 
Published: July 2012

AbstractBackgroundIn the postgenome era, a prediction of response to treatment could lead to better dose selection for patients in radiotherapy. To identify a radiosensitive gene signature and elucidate related signaling pathways, four different microarray experiments were reanalyzed before radiotherapy.ResultsRadiosensitivity profiling data using clonogenic assay and gene expression profiling data from four published microarray platforms applied to NCI-60 cancer cell panel were used. The survival fraction at 2 Gy (SF2, range from 0 to 1) was calculated as a measure of radiosensitivity and a linear regression model was applied to identify genes or a gene set with a correlation between expression and radiosensitivity (SF2). Radiosensitivity signature genes were identified using significant analysis of microarrays (SAM) and gene set analysis was performed using a global test using linear regression model. Using the radiation-related signaling pathway and identified genes, a genetic network was generated. According to SAM, 31 genes were identified as common to all the microarray platforms and therefore a common radiosensitivity signature. In gene set analysis, functions in the cell cycle, DNA replication, and cell junction, including adherence and gap junctions were related to radiosensitivity. The integrin, VEGF, MAPK, p53, JAK-STAT and Wnt signaling pathways were overrepresented in radiosensitivity. Significant genes includingACTN1,CCND1,HCLS1,ITGB5,PFN2,PTPRC,RAB13, andWAS, which are adhesion-related molecules that were identified by both SAM and gene set analysis, and showed interaction in the genetic network with the integrin signaling pathway.ConclusionsIntegration of four different microarray experiments and gene selection using gene set analysis discovered possible target genes and pathways relevant to radiosensitivity. Our results suggested that the identified genes are candidates for radiosensitivity biomarkers and that integrin signaling via adhesion molecules could be a target for radiosensitization.
Storage conditions of intestinal microbiota matter in metagenomic analysis
Authors: Cardona Silvia , Eck Anat , Cassellas Montserrat , Gallart Milagros , Alastrue Carmen , Dore Joel , Azpiroz Fernando , Roca Joaquim , Guarner Francisco , Manichanh Chaysavanh 
Published: July 2012

AbstractBackgroundThe structure and function of human gut microbiota is currently inferred from metagenomic and metatranscriptomic analyses. Recovery of intact DNA and RNA is therefore a critical step in these studies. Here, we evaluated how different storage conditions of fecal samples affect the quality of extracted nucleic acids and the stability of their microbial communities.ResultsWe assessed the quality of genomic DNA and total RNA by microcapillary electrophoresis and analyzed the bacterial community structure by pyrosequencing the 16S rRNA gene. DNA and RNA started to fragment when samples were kept at room temperature for more than 24 h. The use of RNAse inhibitors diminished RNA degradation but this protection was not consistent among individuals. DNA and RNA degradation also occurred when frozen samples were defrosted for a short period (1 h) before nucleic acid extraction. The same conditions that affected DNA and RNA integrity also altered the relative abundance of most taxa in the bacterial community analysis. In this case, intra-individual variability of microbial diversity was larger than inter-individual one.ConclusionsThough this preliminary work explored a very limited number of parameters, the results suggest that storage conditions of fecal samples affect the integrity of DNA and RNA and the composition of their microbial community. For optimal preservation, stool samples should be kept at room temperature and brought at the laboratory within 24 h after collection or be stored immediately at −20°C in a home freezer and transported afterwards in a freezer pack to ensure that they do not defrost at any time. Mixing the samples with RNAse inhibitors outside the laboratory is not recommended since proper homogenization of the stool is difficult to monitor.
Pathogenic Mycobacterium bovis strains differ in their ability to modulate the proinflammatory activation phenotype of macrophages
Authors: Andrade Marcelle RM , Amaral Eduardo P , Ribeiro Simone CM , Almeida Fabricio M , Peres Tanara V , Lanes Verônica , D’Império-Lima Maria Regina , Lasunskaia Elena B 
Published: August 2012

AbstractBackgroundTuberculosis, caused byMycobacterium tuberculosisorMycobacterium bovis,remains one of the leading infectious diseases worldwide. The ability of mycobacteria to rapidly grow in host macrophages is a factor contributing to enhanced virulence of the bacteria and disease progression. Bactericidal functions of phagocytes are strictly dependent on activation status of these cells, regulated by the infecting agent and cytokines. Pathogenic mycobacteria can survive the hostile environment of the phagosome through interference with activation of bactericidal responses. To study the mechanisms employed by highly virulent mycobacteria to promote their intracellular survival, we investigated modulating effects of two pathogenicM. bovisisolates and a referenceM. tuberculosisH37Rv strain, differing in their ability to multiply in macrophages, on activation phenotypes of the cells primed with major cytokines regulating proinflammatory macrophage activity.ResultsBone marrow- derived macrophages obtained from C57BL/6 mice were infected by mycobacteria after a period of cell incubation with or without treatment with IFN-γ, inducing proinflammatory type-1 macrophages (M1), or IL-10, inducing anti-inflammatory type-2 cells (M2). Phenotypic profiling of M1 and M2 was then evaluated. TheM. bovisstrain MP287/03 was able to grow more efficiently in the untreated macrophages, compared with the strains B2 or H37Rv. This strain induced weaker secretion of proinflammatory cytokines, coinciding with higher expression of M2 cell markers, mannose receptor (MR) and arginase-1 (Arg-1). Treatment of macrophages with IFN-γ and infection by the strains B2 and H37Rv synergistically induced M1 polarization, leading to high levels of inducible nitric oxide synthase (iNOS) expression, and reduced expression of the Arg-1. In contrast, the cells infected with the strain MP287/03 expressed high levels of Arg-1 which competed with iNOS for the common substrate arginine, leading to lower levels of NO production.ConclusionsThe data obtained demonstrated that the strain, characterized by increased growth in macrophages, down- modulated classical macrophage activation, through induction of an atypical mixed M1/M2 phenotype.
Comparison of freezing tolerance, compatible solutes and polyamines in geographically diverse collections of Thellungiella sp. and Arabidopsis thaliana accessions
Authors: Lee Yang Ping , Babakov Alexei , de Boer Bert , Zuther Ellen , Hincha Dirk K 
Published: August 2012

AbstractBackgroundThellungiellahas been proposed as an extremophile alternative toArabidopsisto investigate environmental stress tolerance. However,Arabidopsisaccessions show large natural variation in their freezing tolerance and here the tolerance ranges of collections of accessions in the two species were compared.ResultsLeaf freezing tolerance of 16Thellungiellaaccessions was assessed with an electrolyte leakage assay before and after 14 days of cold acclimation at 4°C. Soluble sugars (glucose, fructose, sucrose, raffinose) and free polyamines (putrescine, spermidine, spermine) were quantified by HPLC, proline photometrically. The ranges in nonacclimated freezing tolerance completely overlapped betweenArabidopsisandThellungiella. After cold acclimation, someThellungiellaaccessions were more freezing tolerant than anyArabidopsisaccessions. Acclimated freezing tolerance was correlated with sucrose levels in both species, but raffinose accumulation was lower inThellungiellaand only correlated with freezing tolerance inArabidopsis. The reverse was true for leaf proline contents. Polyamine levels were generally similar between the species. Only spermine content was higher in nonacclimatedThellungiellaplants, but decreased during acclimation and was negatively correlated with freezing tolerance.ConclusionThellungiellais not an extremophile with regard to freezing tolerance, but some accessions significantly expand the range present inArabidopsis. The metabolite data indicate different metabolic adaptation strategies between the species.
Ganglion cysts of the cruciate ligaments: a series of 31 cases and review of the literature
Authors: Mao Yongtao , Dong Qirong , Wang Yi 
Published: August 2012

Abstract

Background
A case series for ganglion cyst of the cruciate ligament with MRI findings, clinical presentation, and management options along with review of literature is presented.

Methods
Of 8663 consecutive patients referred for knee MR imaging, 31 were diagnosed with ganglion cysts of the cruciate ligaments, including 21 men and 10 women of ages 12 to 73 years (mean: 37). A review of charts revealed that knee pain was the chief complaint in all cases. Arthroscopic debridement of ganglion cyst was performed in 11 patients.

Results
MRI proved to be a valuable tool in diagnosing and deciding management of these cases. All 11 patients who underwent arthroscopic treatment were symptom-free on a minimum follow-of one year.

Conclusion
Cyst formation associated with cruciate ligament of the knee is an infrequent cause of knee pain. MR imaging was important in confirming the cyst lesions and provided useful information prior to arthroscopy. Arthroscopic debridement of ganglion cyst produced excellent outcome without recurrence. This study describes the pertinent MRI and intraoperative findings of ganglion cyst.
Adsorption of β-galactosidase of Alicyclobacillus acidocaldarius on wild type and mutants spores of Bacillus subtilis
Authors: Sirec Teja , Strazzulli Andrea , Isticato Rachele , De Felice Maurilio , Moracci Marco , Ricca Ezio 
Published: August 2012

Abstract

Background
The Bacillus subtilis spore has long been used as a surface display system with potential applications in a variety of fields ranging from mucosal vaccine delivery, bioremediation and biocatalyst development. More recently, a non-recombinant approach of spore display has been proposed and heterologous proteins adsorbed on the spore surface. We used the well-characterized β-galactosidase from the thermoacidophilic bacterium Alicyclobacillus acidocaldarius as a model to study enzyme adsorption, to analyze whether and how spore-adsorption affects the properties of the enzyme and to improve the efficiency of the process.

Results
We report that purified β- galactosidase molecules were adsorbed to purified spores of a wild type strain of B. subtilis retaining ca. 50% of their enzymatic activity. Optimal pH and temperature of the enzyme were not altered by the presence of the spore, that protected the adsorbed β- galactosidase from exposure to acidic pH conditions. A collection of mutant strains of B. subtilis lacking a single or several spore coat proteins was compared to the isogenic parental strain for the adsorption efficiency. Mutants with an altered outermost spore layer (crust) were able to adsorb 60-80% of the enzyme, while mutants with a severely altered or totally lacking outer coat adsorbed 100% of the β- galactosidase molecules present in the adsorption reaction.

Conclusion
Our results indicate that the spore surface structures, the crust and the outer coat layer, have an negative effect on the adhesion of the β- galactosidase. Electrostatic forces, previously suggested as main determinants of spore adsorption, do not seem to play an essential role in the spore-β- galactosidase interaction. The analysis of mutants with altered spore surface has shown that the process of spore adsorption can be improved and has suggested that such improvement has to be based on a better understanding of the spore surface structure. Although the molecular details of spore adsorption have not been fully elucidated, the efficiency of the process and the pH-stability of the adsorbed molecules, together with the well documented robustness and safety of spores of B. subtilis, propose the spore as a novel, non-recombinant system for enzyme display.
Antibacterial activity of plasma from crocodile (Crocodylus siamensis) against pathogenic bacteria
Authors: Kommanee Jintana , Preecharram Sutthidech , Daduang Sakda , Temsiripong Yosapong , Dhiravisit Apisak , Yamada Yuzo , Thammasirirak Sompong 
Published: July 2012

Abstract

Background
The Siamese crocodile (Crocodylus siamensis) is a critically endangered species of freshwater crocodiles. Crocodilians live with opportunistic bacterial infection but normally suffer no adverse effects. They are not totally immune to microbial infection, but their resistance thereto is remarkably effective. In this study, crude and purified plasma extracted from the Siamese crocodile were examined for antibacterial activity against clinically isolated, human pathogenic bacterial strains and the related reference strains.

Methods
Crude plasma was prepared from whole blood of the Siamese crocodile by differential sedimentation. The crude plasma was examined for antibacterial activity by the liquid growth inhibition assay. The scanning electron microscopy was performed to confirm the effect of crude crocodile plasma on the cells of Salmonella typhi ATCC 11778. Effect of crude crocodile plasma on cell viability was tested by MTT assay. In addition, the plasma was purified by anion exchange column chromatography with DEAE-Toyopearl 650 M and the purified plasma was tested for antibacterial activity.

Results
Crude plasma was prepared from whole blood of the Siamese crocodile and exhibited substantial antibacterial activities of more than 40% growth inhibition against the six reference strains of Staphylococcus aureus, Salmonella typhi, Escherichia coli, Vibrio cholerae, Pseudomonas aeruginosa, and Staphylococcus epidermidis, and the four clinical isolates of Staphylococcus epidermidis, Pseudomonas aeruginosa, Salmonella typhi, and Vibrio cholerae. Especially, more than 80% growth inhibition was found in the reference strains of Salmonella typhi, Vibrio cholerae, and Staphylococcus epidermidis and in the clinical isolates of Salmonella typhi and Vibrio cholerae. The effect of the crude plasma on bacterial cells of Salmonella typhi, a certain antibacterial material probably penetrates progressively into the cytoplasmic space, perturbing and damaging bacterial membranes. The effect of the crude plasma was not toxic by the yellow tetrazolium bromide (MTT) assay using a macrophage-like cell, RAW 264.7. The pooled four fractions, designated as fractions D1-D4, were obtained by column chromatography, and only fraction D1 showed growth inhibition in the reference strains and the clinical, human pathogenic isolates.

Conclusions
The crude and purified plasma from the Siamese crocodile significantly showed antibacterial activity against pathogenic bacteria and reference strains by damage cell membrane of target bacterial cells. From the MTT assay, the Siamese crocodile plasma was not cytotoxic to the cells.
First-in-man application of a novel therapeutic cancer vaccine formulation with the capacity to induce multi-functional T cell responses in ovarian, breast and prostate cancer patients
Authors: Berinstein Neil L , Karkada Mohan , Morse Michael A , Nemunaitis John J , Chatta Gurkamal , Kaufman Howard , Odunsi Kunle , Nigam Rita , Sammatur Leeladhar , MacDonald Lisa D , Weir Genevieve M , Stanford Marianne M , Mansour Marc 
Published: August 2012

Abstract

Background
DepoVaxTM is a novel non-emulsion depot-forming vaccine platform with the capacity to significantly enhance the immunogenicity of peptide cancer antigens. Naturally processed HLA-A2 restricted peptides presented by breast, ovarian and prostate cancer cells were used as antigens to create a therapeutic cancer vaccine, DPX-0907.

Methods
A phase I clinical study was designed to examine the safety and immune activating potential of DPX-0907 in advanced stage breast, ovarian and prostate cancer patients. A total of 23 late stage cancer patients were recruited and were divided into two dose/volume cohorts in a three immunization protocol.

Results
DPX-0907 was shown to be safe with injection site reactions being the most commonly reported adverse event. All breast cancer patients (3/3), most of ovarian (5/6) and one third of prostate (3/9) cancer patients exhibited detectable immune responses, resulting in a 61% immunological response rate. Immune responses were generally observed in patients with better disease control after their last prior treatment. Antigen-specific responses were detected in 73% of immune responders (44% of evaluable patients) after the first vaccination. In 83% of immune responders (50% of evaluable patients), peptide-specific T cell responses were detected at ≥2 time points post vaccination with 64% of the responders (39% of evaluable patients) showing evidence of immune persistence. Immune monitoring also demonstrated the generation of antigen-specific T cell memory with the ability to secrete multiple Type 1 cytokines.

Conclusions
The novel DepoVax formulation promotes multifunctional effector memory responses to peptide-based tumor associated antigens. The data supports the capacity of DPX-0907 to elicit Type-1 biased immune responses, warranting further clinical development of the vaccine. This study underscores the importance of applying vaccines in clinical settings in which patients are more likely to be immune competent.

Trial Registration
ClinicalTrials.gov NCT01095848
Influence of the ratio of gate length to drain-to-source distance on the electron mobility in AlGaN/AlN/GaN heterostructure field-effect transistors
Authors: Lv Yuanjie , Lin Zhaojun , Meng Lingguo , Luan Chongbiao , Cao Zhifang , Yu Yingxia , Feng Zhihong , Wang Zhanguo 
Published: August 2012

Abstract
Using measured capacitance-voltage curves with different gate lengths and current–voltage characteristics at low drain-to-source voltage for the AlGaN/AlN/GaN heterostructure field-effect transistors (HFETs) of different drain-to-source distances, we found that the dominant scattering mechanism in AlGaN/AlN/GaN HFETs is determined by the ratio of gate length to drain-to-source distance. For devices with small ratio (here, less than 1/2), polarization Coulomb field scattering dominates electron mobility. However, for devices with large ratio (here, more than 1/2), longitudinal optical (LO) phonon scattering and interface roughness scattering are dominant. The reason is closely related to polarization Coulomb field scattering.
Risk factors of brain metastases in completely resected pathological stage IIIA-N2 non-small cell lung cancer
Authors: Ding Xiao , Dai Honghai , Hui Zhouguang , Ji Wei , Liang Jun , Lv Jima , Zhou Zongmei , Yin Weibo , He Jie , Wang Luhua 
Published: July 2012

Abstract

Background
Brain metastases (BM) is one of the most common failures of locally advanced non-small cell lung cancer (LA-NSCLC) after combined-modality therapy. The outcome of trials on prophylactic cranial irradiation (PCI) has prompted us to identify the highest-risk subset most likely to benefit from PCI. Focusing on patients with completely resected pathological stage IIIA-N2 (pIIIA-N2) NSCLC, we aimed to assess risk factors of BM and to define the highest-risk subset.

Methods
Between 2003 and 2005, the records of 217 consecutive patients with pIIIA-N2 NSCLC in our institution were reviewed. The cumulative incidence of BM was estimated using the Kaplan–Meier method, and differences between the groups were analyzed using log-rank test. Multivariate Cox regression analysis was applied to assess risk factors of BM.

Results
Fifty-three (24.4 %) patients developed BM at some point during their clinical course. On multivariate analysis, non-squamous cell cancer (relative risk [RR]: 4.13, 95 % CI: 1.86–9.19; P = 0.001) and the ratio of metastatic to examined nodes or lymph node ratio (LNR) ≥ 30 % (RR: 3.33, 95 % CI: 1.79–6.18; P = 0.000) were found to be associated with an increased risk of BM. In patients with non-squamous cell cancer and LNR ≥ 30 %, the 5-year actuarial risk of BM was 57.3 %.

Conclusions
In NSCLC, patients with completely resected pIIIA-N2 non-squamous cell cancer and LNR ≥ 30 % are at the highest risk for BM, and are most likely to benefit from PCI. Further studies are warranted to investigate the effect of PCI on this subset of patients.
Sex differences in human adipose tissues – the biology of pear shape
Authors: Karastergiou Kalypso , Smith Steven R , Greenberg Andrew S , Fried Susan K 
Published: August 2012

Abstract
Women have more body fat than men, but in contrast to the deleterious metabolic consequences of the central obesity typical of men, the pear-shaped body fat distribution of many women is associated with lower cardiometabolic risk. To understand the mechanisms regulating adiposity and adipose tissue distribution in men and women, significant research attention has focused on comparing adipocyte morphological and metabolic properties, as well as the capacity of preadipocytes derived from different depots for proliferation and differentiation. Available evidence points to possible intrinsic, cell autonomous differences in preadipocytes and adipocytes, as well as modulatory roles for sex steroids, the microenvironment within each adipose tissue, and developmental factors. Gluteal-femoral adipose tissues of women may simply provide a safe lipid reservoir for excess energy, or they may directly regulate systemic metabolism via release of metabolic products or adipokines. We provide a brief overview of the relationship of fat distribution to metabolic health in men and women, and then focus on mechanisms underlying sex differences in adipose tissue biology.