bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis
Authors: Sun Chao , Li Ying , Wu Qiong , Luo Hongmei , Sun Yongzhen , Song Jingyuan , Lui Edmund MK , Chen Shilin 
Published: April 2010

Abstract

Background
American ginseng (Panax quinquefolius L.) is one of the most widely used herbal remedies in the world. Its major bioactive constituents are the triterpene saponins known as ginsenosides. However, little is known about ginsenoside biosynthesis in American ginseng, especially the late steps of the pathway.

Results
In this study, a one-quarter 454 sequencing run produced 209,747 high-quality reads with an average sequence length of 427 bases. De novo assembly generated 31,088 unique sequences containing 16,592 contigs and 14,496 singletons. About 93.1% of the high-quality reads were assembled into contigs with an average 8-fold coverage. A total of 21,684 (69.8%) unique sequences were annotated by a BLAST similarity search against four public sequence databases, and 4,097 of the unique sequences were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes. Based on the bioinformatic analysis described above, we found all of the known enzymes involved in ginsenoside backbone synthesis, starting from acetyl-CoA via the isoprenoid pathway. Additionally, a total of 150 cytochrome P450 (CYP450) and 235 glycosyltransferase unique sequences were found in the 454 cDNA library, some of which encode enzymes responsible for the conversion of the ginsenoside backbone into the various ginsenosides. Finally, one CYP450 and four UDP-glycosyltransferases were selected as the candidates most likely to be involved in ginsenoside biosynthesis through a methyl jasmonate (MeJA) inducibility experiment and tissue-specific expression pattern analysis based on a real-time PCR assay.

Conclusions
We demonstrated, with the assistance of the MeJA inducibility experiment and tissue-specific expression pattern analysis, that transcriptome analysis based on 454 pyrosequencing is a powerful tool for determining the genes encoding enzymes responsible for the biosynthesis of secondary metabolites in non-model plants. Additionally, the expressed sequence tags (ESTs) and unique sequences from this study provide an important resource for the scientific community that is interested in the molecular genetics and functional genomics of American ginseng.
Azithromycin effectiveness against intracellular infections of Francisella
Authors: Ahmad Saira , Hunter Lyman , Qin Aiping , Mann Barbara J , van Hoek Monique L 
Published: April 2010

Abstract

Background
Macrolide antibiotics are commonly administered for bacterial respiratory illnesses. Azithromycin (Az) is especially noted for extremely high intracellular concentrations achieved within macrophages which is far greater than the serum concentration. Clinical strains of Type B Francisella (F.) tularensis have been reported to be resistant to Az, however our laboratory Francisella strains were found to be sensitive. We hypothesized that different strains/species of Francisella (including Type A) may have different susceptibilities to Az, a widely used and well-tolerated antibiotic.

Results

In vitro susceptibility testing of Az confirmed that F. tularensis subsp. holarctica Live Vaccine Strain (LVS) (Type B) was not sensitive while F. philomiragia, F. novicida, and Type A F. tularensis (NIH B38 and Schu S4 strain) were susceptible. In J774A.1 mouse macrophage cells infected with F. philomiragia, F. novicida, and F. tularensis LVS, 5 μg/ml Az applied extracellularly eliminated intracellular Francisella infections. A concentration of 25 μg/ml Az was required for Francisella- infected A549 human lung epithelial cells, suggesting that macrophages are more effective at concentrating Az than epithelial cells. Mutants of RND efflux components (tolC and ftlC) in F. novicida demonstrated less sensitivity to Az by MIC than the parental strain, but the tolC disc-inhibition assay demonstrated increased sensitivity, indicating a complex role for the outer-membrane transporter. Mutants of acrA and acrB mutants were less sensitive to Az than the parental strain, suggesting that AcrAB is not critical for the efflux of Az in F. novicida. In contrast, F. tularensis Schu S4 mutants ΔacrB and ΔacrA were more sensitive than the parental strain, indicating that the AcrAB may be important for Az efflux in F. tularensis Schu S4. F. novicida LPS O-antigen mutants (wbtN, wbtE, wbtQ and wbtA) were found to be less sensitive in vitro to Az compared to the wild-type. Az treatment prolonged the survival of Galleria (G.) mellonella infected with Francisella.

Conclusion
These studies demonstrate that Type A Francisella strains, as well as F. novicida and F. philomiragia, are sensitive to Az in vitro. Francisella LPS and the RND efflux pump may play a role in Az sensitivity. Az also has antimicrobial activity against intracellular Francisella, suggesting that the intracellular concentration of Az is high enough to be effective against multiple strains/species of Francisella, especially in macrophages. Az treatment prolonged survival an in vivo model of Francisella- infection.
Cell-associated hemolysis activity in the clinical strain of Pseudomonas fluorescens MFN1032
Authors: Sperandio Daniel , Rossignol Gaelle , Guerillon Josette , Connil Nathalie , Orange Nicole , Feuilloley Marc GJ , Merieau Annabelle 
Published: April 2010

Abstract

Background
MFN1032 is a clinical Pseudomonas fluorescens strain able to grow at 37°C. MFN1032 cells induce necrosis and apoptosis in rat glial cells at this temperature. This strain displays secretion-mediated hemolytic activity involving phospholipase C and cyclolipopeptides. Under laboratory conditions, this activity is not expressed at 37°C. This activity is tightly regulated and is subject to phase variation.

Results
We found that MFN1032 displays a cell-associated hemolytic activity distinct from the secreted hemolytic activity. Cell-associated hemolysis was expressed at 37°C and was only detected in vitro in mid log growth phase in the presence of erythrocytes. We studied the regulation of this activity in the wild-type strain and in a mutant defective in the Gac two-component pathway. GacS/GacA is a negative regulator of this activity. In contrast to the Pseudomonas fluorescens strains PfO-1 and Pf5, whose genomes have been sequenced, the MFN1032 strain has the type III secretion-like genes hrc RST belonging to the hrpU operon. We showed that disruption of this operon abolished cell-associated hemolytic activity. This activity was not detected in P.fluorescens strains carrying similar hrc genes, as for the P. fluorescens psychrotrophic strain MF37.

Conclusions
To our knowledge this the first demonstration of cell-associated hemolytic activity of a clinical strain of Pseudomonas fluorescens. Moreover, this activity seems to be related to a functional hrpU operon and is independent of biosurfactant production. Precise link between a functional hrpU operon and cell-associated hemolytic activity remains to be elucidated.
Genetic structure of Plasmodium vivax and Plasmodium falciparum in the Bannu district of Pakistan
Authors: Khatoon Lubna , Baliraine Frederick N , Bonizzoni Mariangela , Malik Salman A , Yan Guiyun 
Published: April 2010

Abstract

Background

Plasmodium vivax and Plasmodium falciparum are the major causative agents of malaria. While knowledge of the genetic structure of malaria parasites is useful for understanding the evolution of parasite virulence, designing anti-malarial vaccines and assessing the impact of malaria control measures, there is a paucity of information on genetic diversity of these two malaria parasites in Pakistan. This study sought to shed some light on the genetic structure of P. vivax and P. falciparum in this understudied region.

Methods
The genetic diversities of P. vivax and P. falciparum populations from the densely populated, malaria-endemic Bannu district of Pakistan were evaluated by analysis of their merozoite surface protein (msp) genes by PCR-RFLP. Specifically, the Pvmsp-3α and Pvmsp-3β genes of P. vivax and the Pfmsp-1 and Pfmsp-2 genes of P. falciparum were analysed.

Results
In P. vivax, genotyping of Pvmsp-3α and Pvmsp-3β genes showed a high level of diversity at these loci. Four distinct allele groups: A (1.9 kb), B (1.5 kb), C (1.2 kb), and D (0.3 kb) were detected for Pvmsp-3α, type A being the most prevalent (82%). Conversely, amplification of the P. vivax msp-3β locus produced two allele groups: A (1.7-2.2 kb, 62%) and B (1.4-1.5 kb, 33%), with 5% mixed-strain infections. Restriction analysis of Pvmsp-3α and Pvmsp-3β yielded 12 and 8 distinct alleles, respectively, with a combined mixed genotype prevalence of 20%. In P. falciparum, all three known genotypes of Pfmsp-1 and two of Pfmsp-2 were observed, with MAD20 occurring in 67% and 3D7/IC in 65% of the isolates, respectively. Overall, 24% P. falciparum samples exhibited mixed-strain infections.

Conclusion
These results indicate that both P. vivax and P. falciparum populations in Pakistan are highly diverse.
Organ-, inflammation- and cancer specific transcriptional fingerprints of pancreatic and hepatic stellate cells
Authors: Erkan Mert , Weis Nadine , Pan Zheng , Schwager Christian , Samkharadze Tamar , Jiang Xiaohua , Wirkner Ute , Giese Nathalia A. , Ansorge Wilhelm , Debus Jürgen , Huber Peter E. , Friess Helmut , Abdollahi Amir , Kleeff Jörg 
Published: April 2010

Abstract

Background
Tissue fibrosis is an integral component of chronic inflammatory (liver and pancreas) diseases and pancreatic cancer. Activated pancreatic- (PSC) and hepatic- (HSC) stellate cells play a key role in fibrogenesis. To identify organ- and disease-specific stellate cell transcriptional fingerprints, we employed genome-wide transcriptional analysis of primary human PSC and HSC isolated from patients with chronic inflammation or cancer.

Methods
Stellate cells were isolated from patients with pancreatic ductal adenocarcinoma (n = 5), chronic pancreatitis (n = 6), liver cirrhosis (n = 5) and liver metastasis of pancreatic ductal adenocarcinoma (n = 6). Genome-wide transcriptional profiles of stellate cells were generated using our 51K human cDNA microarray platform. The identified organ- and disease specific genes were validated by quantitative RT-PCR, immunoblot, ELISA, immunocytochemistry and immunohistochemistry.

Results
Expression profiling identified 160 organ- and 89 disease- specific stellate cell transcripts. Collagen type 11a1 (COL11A1) was discovered as a novel PSC specific marker with up to 65-fold higher expression levels in PSC compared to HSC (p < 0.0001). Likewise, the expression of the cytokine CCL2 and the cell adhesion molecule VCAM1 were confined to HSC. PBX1 expression levels tend to be increased in inflammatory- vs. tumor- stellate cells. Intriguingly, tyrosine kinase JAK2 and a member of cell contact-mediated communication CELSR3 were found to be selectively up-regulated in tumor stellate cells.

Conclusions
We identified and validated HSC and PSC specific markers. Moreover, novel target genes of tumor- and inflammation associated stellate cells were discovered. Our data may be instrumental in developing new tailored organ- or disease-specific targeted therapies and stellate cell biomarkers.
Diagnosis and phylogenetic analysis of Orf virus from goats in China: a case report
Authors: Zhang Keshan , Lu Zhongxin , Shang Youjun , Zheng Haixue , Jin Ye , He Jijun , Liu Xiangtao 
Published: April 2010

Abstract

Background
Orf virus (ORFV) is the etiological agent of contagious pustular dermatitis and is the prototype of the genus Parapoxvirus (PPV). It causes a severe exanthematous dermatitis that afflicts domestic and wild small ruminants.

Case presentation
In the present study, an outbreak of proliferative dermatitis in farmed goats. The presence of ORFV in tissue scrapings from the lips was confirmed by B2L gene polymerase chain reaction (PCR) amplification. The molecular characterization of the ORFV was performed using PCR amplification, DNA sequencing and phylogenetic analysis of the B2L gene.

Conclusion
The results of this investigation indicated that the outbreak was caused by infection with an ORFV that was closely related genetically to Nantou (DQ934351), which was isolated from the Tai wan province of China and Hoping (EU935106), which originated from South Korea in 2008. This is the first report of the phylogenetic analysis of ORFV from goats in China.
Clonal status and clinicopathological observation of cervical minimal deviation adenocarcinoma
Authors: Gong Li , Zhang Wen-Dong , Liu Xiao-Yan , Han Xiu-Juan , Yao Li , Zhu Shao-Jun , Lan Miao , Li Yan-Hong , Zhang Wei 
Published: April 2010

Abstract

Background
Minimal deviation adenocarcinoma (MDA) of the uterine cervix is defined as an extremely well differentiated variant of cervical adenocarcinoma, with well-formed glands that resemble benign glands but show distinct nuclear anaplasia or evidence of stromal invasion. Thus, MDA is difficult to differentiate from other cervical hyperplastic lesions. Monoclonality is a major characteristic of most tumors, whereas normal tissue and reactive hyperplasia are polyclonal.

Methods
The clinicopathological features and clonality of MDA were investigated using laser microdissection and a clonality assay based on the polymorphism of androgen receptor (AR) and X-chromosomal inactivation mosaicism in female somatic tissues.

Results
The results demonstrated that the glands were positive for CEA, Ki-67, and p53 and negative for estrogen receptor (ER), progesterone receptor (PR), and high-risk human papilloma virus (HPV) DNA. The index of proliferation for Ki-67 was more than 50%. However, the stromal cells were positive for ER, PR, vimentin, and SM-actin. The clonal assay showed that MDA was monoclonal. Thus, our findings indicate that MDA is a true neoplasm but is not associated with high-risk HPV.

Conclusions
Diagnosis of MDA depends mainly on its clinical manifestations, the pathological feature that MDA glands are located deeper than the lower level of normal endocervical glands, and immunostaining.
The proteasome inhibitor bortezomib inhibits T cell-dependent inflammatory responses
Authors: Yanaba Koichi , Yoshizaki Ayumi , Muroi Eiji , Hara Toshihide , Ogawa Fumihide , Shimizu Kazuhiro , Sato Shinichi 
Published: April 2010

Abstract
Bortezomib enhances T cell apoptosis by inhibiting NF-κB activation, thereby suppressing cutaneous T cell-dependent inflammatory responses by reducing interferon-γ production.
CHS is a cutaneous, T cell-dependent, inflammatory reaction mediated mainly by antigen-specific effector T cells. Bortezomib is a proteasome inhibitor that has shown impressive efficacy for the treatment of multiple myeloma. In the current study, we have assessed the effect of bortezomib treatment of CHS in mice and found that bortezomib potently inhibited CHS responses. The attenuation of CHS responses was associated with decreased inflammatory cell infiltration in the challenged skin. Specifically, bortezomib-treated mice showed significantly decreased numbers of CD4+ and CD8+ T cells in the challenged skin and draining lymph nodes. Cytoplasmic IFN-γ production by CD4+ and CD8+ T cells in the draining lymph nodes was decreased substantially by bortezomib treatment. Notably, bortezomib enhanced T cell apoptosis by inhibiting NF-κB activation during CHS responses. Thus, bortezomib treatment is likely to induce T cell death, thereby suppressing CHS responses by reducing IFN-γ production. These findings suggest that bortezomib treatment could be a promising strategy for treating autoimmune and inflammatory disease.
Phase II Evaluation of Paclitaxel and Carboplatin in the Treatment of Carcinosarcoma of the Uterus: A Gynecologic Oncology Group Study
Authors: Powell Matthew A. , Filiaci Virginia L. , Rose Peter G. , Mannel Robert S. , Hanjani Parviz , DeGeest Koen , Miller Brigitte E. , Susumu Nobuyuki , Ueland Frederick R. 
Published: April 2010

Purpose Platinum and taxane compounds have demonstrated activity in uterine carcinosarcoma (malignant mixed Mullerian tumor). Ifosfamide plus paclitaxel is the regimen with established superiority based on a randomized phase III trial conducted through the Gynecologic Oncology Group. However, the toxicity, multiday schedule, and limited activity of this regimen support further development of novel regimens. Our primary objective was to estimate the antitumor activity and toxicity of paclitaxel plus carboplatin in patients with uterine carcinosarcomas. Patients and Methods Eligible patients had advanced stage (III or IV), persistent or recurrent measurable disease, and no prior chemotherapy. Patients received paclitaxel at 175 mg/m2 intravenously (IV) over 3 hours plus carboplatin (area under the serum concentration-time curve = 6) IV over 30 minutes every 3 weeks until disease progression or until adverse effects occurred. Common Terminology Criteria for Adverse Events v3.0 was used to grade adverse events. Results Fifty-five patients were entered onto the study with nine being excluded from analysis, leaving 46 evaluable for analysis. Treatment was well tolerated with expected hematologic toxicity and minimal nonhematologic grade 4 toxicity (one cardiovascular and two pain) with 59% of patients completing six or more cycles of chemotherapy. The proportions of patients with confirmed complete and partial responses were 13% and 41%, respectively, resulting in a total overall response rate of 54% (95% CI, 37% to 67%). Conclusion Paclitaxel plus carboplatin demonstrates antitumor activity against uterine carcinosarcoma with acceptable toxicity and warrants further evaluation in phase III randomized trials.
Neurosurgery and the Anatomy of Reading
Authors: Greenblatt Samuel H. 
Published: April 2010

Abstract
Tumors and vascular malformations in the posterior parts of the dominant hemisphere are frequently associated with preoperative alexias, and surgical maneuvers in these areas may cause the appearance of this neurobehavioral deficit as an operative complication. Lesions of the dominant (left) angular gyrus are associated with the syndromes of alexia with agraphia. Alexia without agraphia results from lesions of the pathways which conduct visual information from the calcarine areas to the left angular gyrus (splenium of the corpus callosum, left lingual and fusiform gyri, left transverse and vertical occipital fasciculi). A brief bedside examination (outlined in the text) provides useful pre-and postoperative localizing information. Fresh cadaver studies of the brain in situ have shown that the approximate center of the left angular gyrus area is found by first locating a point 9 cm forward along the midline from the inion and then moving 4/14; cm laterally. These measurements define a point which is a few centimeters medial and posterior to the center of the parietal eminence.
Mechanical Engineering Aspects of the Space Shuttle Orbiter–Design, Manufacture and Operation
Authors: Griffin G D 
Published: April 2010

The designers of the Space Shuttle were faced with engineering challenges for which little or no precedent existed, and which required unique and innovative mechanical engineering approaches for their solution. Before the Shuttle Program, all manned space vehicles were designed for high reliability single mission capability. In contrast, the Shuttle Orbiter has the requirements of reusability for 100 missions, in order to minimize operational costs, and has to be highly weight efficient to meet vehicle performance requirements. The Space Shuttle is a versatile aerospace vehicle in that it takes off like a rocket, manoeuvres in Earth orbit like a spacecraft, and lands like an airplane. In performing these functions, the Shuttle undergoes a wide spectrum of aerodynamic, acoustic, and inertial loadings, along with exposure to the temperature extremes of space, plus a severe aerothermodynamic heating environment during entry. These environments, along with unique mission requirements, resulted in design challenges of unprecedented complexity. The space vehicle that evolved has provided a flexibility never before achieved in space operations, and allows space to be treated as a resource, rather than as a hostile, uninviting environment. This paper provides an overview of the Space Shuttle Program, details of some typical mechanical engineering challenges that evolved during the development phase of the Program, and some operational performance observations. In particular, the paper focuses on activities associated with the Orbiter's structure, mechanical systems and thermal protection systems. The innovative design solutions that were developed for the Shuttle, and their outstanding performance during the flight test program, lend confidence in man's engineering ability to achieve a permanent presence in space.
Simulations To Assess the Influence of Car Lateral Impact Characteristics on Occupant Kinematics
Authors: Hardy R N , Suthurst G D 
Published: April 2010

Car occupants are particularly prone to injuries during side impact accidents. The major reason for this is the considerably inferior impact characteristic of the side of the car when compared to that of the front. Means of reducing the vulnerability of the occupant can be assessed most efficiently by computer simulations where there are no problems of repeatability. Provided the simulation techniques used are validated their predictions can be relied upon to provide accurate design guidance. This paper describes the use of previously developed techniques whereby components of the side of a car were tested to assess their properties and so enable a baseline model to be set up for structural simulations using the CRASH-D finite element program Simulations to determine the kinematics of the car occupant were also set up using the Calspan CVS program and an APROD dummy model. The effects of changing component properties or adding further components to the structural model were then assessed not only by their influence on the overall intrusion resistance of the car but also by their influence on the kinematics of the occupant and the likely level of his injuries.
The Ford 2.5 Litre Direct Injection Naturally Aspirated Diesel Engine
Authors: Bird G L 
Published: April 2010

The advantages of a high-speed direct injection diesel over an indirect injection engine are well established. In the last decade many studies have been presented which suggest that most of the technical issues preventing operation at high speed have been overcome. The new Ford 2.5 litre engine introduces a first generation of production high-speed direct injection engines. Based on controlled high swirl air management, combined with high rates of fuel injection, the engine produces 52 kW at 4000 r/min. Initial installation of the 2.5 litre high-speed direct injection engine is in the Ford Transit range of vehicles where 25 per cent fuel economy improvements over its predecessor, the York 2.36 litre indirect injection engine, have been achieved. Designed to meet the demands of modern vehicle application, the engine includes many features to improve reliability and durability. This paper describes the engine systems and components of the engine, together with the key aspects of the performance development with specific reference to the actions employed to control noise.