bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antigen Display, T-Cell Activation, and Immune Evasion during Acute and Chronic Ehrlichiosis
Authors: Nandi Bisweswar , Chatterjee Madhumouli , Hogle Kathryn , McLaughlin Maura , MacNamara Katherine , Racine Rachael , Winslow Gary M. 
Published: July 2009

ABSTRACTHow spatial and temporal changes in major histocompatibility complex/peptide antigen presentation to CD4 T cells regulate CD4 T-cell responses during intracellular bacterial infections is relatively unexplored. We have shown that immunization with an ehrlichial outer membrane protein, OMP-19, protects mice against fatal ehrlichial challenge infection, and we identified a CD4 T-cell epitope (IAb/OMP-19107-122) that elicited CD4 T cells following either immunization or infection. Here, we have used an IAb/OMP-19107-122-specific T-cell line to monitor antigen display ex vivo during acute and chronic infection withEhrlichia muris, a bacterium that establishes persistent infection in C57BL/6 mice. The display of IAb/OMP-19107-122by host antigen-presenting cells was detected by measuring intracellular gamma interferon (IFN-γ) production by the T-cell line. After intravenous infection, antigen presentation was detected in the spleen, peritoneal exudate cells, and lymph nodes, although the kinetics of antigen display differed among the tissues. Antigen presentation and bacterial colonization were closely linked in each anatomical location, and there was a direct relationship between antigen display and CD4 T-cell effector function. Spleen and lymph node dendritic cells (DCs) were efficient presenters of IAb/OMP-19107-122, demonstrating that DCs play an important role in ehrlichial infection and immunity. Chronic infection and antigen presentation occurred within the peritoneal cavity, even in the presence of highly activated CD4 T cells. These data indicated that the ehrlichiae maintain chronic infection not by inhibiting antigen presentation or T-cell activation but, in part, by avoiding signals mediated by activated T cells.
Physical activity, cardiorespiratory fitness and the incidence of type 2 diabetes in a prospective study of men
Authors: Sieverdes John C , Sui Xuemei , Lee Duck-chul , Church Timothy S , McClain Amanda , Hand Gregory A , Blair Steven N 
Published: July 2009

ObjectiveTo assess the independent and joint associations between self-reported physical activity (PA) and objectively measured cardiorespiratory fitness (CRF) from a maximal treadmill exercise test and the development of type 2 diabetes mellitus in a large cohort of men.MethodsParticipants for the current analysis were 23 444 men aged 20–85 years free of cardiovascular disease (CVD), cancer or diabetes at baseline. Incident diabetes were identified from mail-back surveys. Cox regression analysis was used to estimate hazard ratios (HRs), 95% confidence intervals (CIs) and diabetes incidence rates (per 10 000 man-years) according to exposure categories.ResultsDuring an average of 18 years of follow-up, 589 incident cases of diabetes were identified. After adjusting for age, examination year, survey response pattern, body mass index, smoking, drinking, fasting glucose, chronic diseases and family history of CVD or diabetes, the walking/jogging/running (WJR) and sport/fitness groups had a 40% and 28% lower risk of developing diabetes compared with the sedentary men, respectively (both p < 0.05). For CRF, diabetes incidence rates were 31.9, 14.5 and 6.5 for low-, moderate- and high-fitness groups, respectively. After adjustment for the above covariables, moderate and high CRF had a 38% and 63% lower risk of developing diabetes compared with the low CRF group (p trend<0.0001).ConclusionOur findings showed a lower risk of developing diabetes for men who participated in a WJR programme or sport/fitness activity, compared with those who were sedentary. Higher levels of fitness were associated with an inverse gradient of incident diabetes.
An improved method for constructing tissue microarrays from prostate needle biopsy specimens
Authors: McCarthy F , Fletcher A , Dennis N , Cummings C , O’Donnell H , Clark J , Flohr P , Vergis R , Jhavar S , Parker C , Cooper C S 
Published: July 2009

Background:Prostate cancer diagnosis is routinely made by the histopathological examination of formalin fixed needle biopsy specimens. Frequently this is the only cancer tissue available from the patient for the analysis of diagnostic and prognostic biomarkers. There is, therefore, an urgent need for methods that allow the high-throughput analysis of these biopsy samples using immunohistochemical (IHC) markers and fluorescence in situ hybridisation (FISH) analysis based markers.Methods:A method that allows the construction of tissue microarrays (TMAs) from diagnostic prostate needle biopsy cores has previously been reported. However, the technique only allows the production of low-density biopsy TMAs with a maximum of 20 cores per TMA. Here two methods are presented that allow the rapid and uniform production of biopsy TMAs containing between 54 and 72 biopsy cores. IHC and FISH techniques were used to detect biomarker status.Results:Biopsy TMAs were constructed from prostate needle biopsy specimens taken from 102 patients entered into an active surveillance trial and 201 patients in a radiotherapy trial. The detection rate for cancer in slices of these biopsy TMAs was 66% and 79% respectively. Slices of a biopsy TMA prepared from biopsies from active surveillance patients were used to detect multiple IHC markers and to scoreTMPRSS2-ERGfusion status in a FISH-based assay.Conclusions:The construction of biopsy TMAs provides an effective method for the multiplex analysis of IHC and FISH markers and for their assessment as prognostic biomarkers in the context of clinical trials.
Prognostic significance of neuron-associated protein expression in non-muscle-invasive urothelial bladder cancer
Authors: Mhawech-Fauceglia P , Ali L , Cheney R T , Groth J , Herrmann F R 
Published: July 2009

Background:Numerous novel genes have been identified in urothelial bladder cancer (UBC); genes including ninjurin, synuclein and neuropilin seem to be associated with invasive tumours and aggressive behaviour.Aims:To define the protein expression of these biomarkers and to reveal their prognostic value in a large series of superficial (pTa) and minimally invasive (pT1) cases of UBC with a long and adequate follow-up.Methods:Tissue microarray was done on 183 paraffin-embedded tumour tissues (pTa 81, pT1 102). Statistical analysis was performed to define the association between each of these biomarkers, clinical data and tumour outcomes.Results:There was a statistically significant association between synuclein expression and tumour stage (p = 0.029). Ninjurin expression was significantly associated with tumour progression in univariate analysis. Tumour grade seemed to have an independent value in predicting tumour recurrence and progression.Conclusion:Tumours with strong synuclein expressions are more likely to be more advanced tumours (pT1). Tumours expressing ninjurin tend to progress slower than those with no ninjurin expressions. Synuclein and neuropilin failed to show any value in predicting tumour behaviour.
Direct trimming of NURBS surfaces on the GPU
Authors: Schollmeyer Andre , Fröhlich Bernd 
Published: July 2009

This paper presents a highly efficient direct trimming technique for NURBS surfaces, which is applicable to tessellation-based rendering as well as ray tracing systems. The central idea is to split the trim curves into monotonic segments with respect to the two parameter dimensions of the surface patches. We use an optimized bisection method to classify a point with respect to each monotonic trim curve segment without performing an actual intersection test. Our hierarchical acceleration structure allows the use of a large number of such curve segments and performs the bisection method only for points contained in the bounding boxes of the curve segments.
We have integrated our novel point classification scheme into a GPU-based NURBS ray casting system and implemented the entire trimmed NURBS rendering algorithm in a single OpenGL GLSL shader. The shader can handle surfaces and trim curves of arbitrary degrees, which allows the use of original CAD data without incorporating any approximations. Performance data confirms that our trimming approach can deal with hundreds of thousands of trim curves at interactive rates. Our point classification scheme can be applied to other application domains dealing with complex curved regions including flood fills, font rendering and vector graphics mapped on arbitrary surfaces.
Minimizing CPU energy in real-time systems with discrete speed management
Authors: Bini Enrico , Buttazzo Giorgio , Lipari Giuseppe 
Published: July 2009

This article presents a general framework to analyze and design embedded systems minimizing the energy consumption without violating timing requirements. A set of realistic assumptions is considered in the model in order to apply the results in practical real-time applications. The processor is assumed to have as a set of discrete operating modes, each characterized by speed and power consumption. The energy overhead and the transition delay incurred during mode switches are considered. Task computation times are modeled with a part that scales with the speed and a part having a fixed duration, to take I/O operations into account.
The proposed method allows to compute the optimal sequence of voltage/speed changes that approximates the minimum continuous speed, which guarantees the feasibility of a given set of real-time tasks, without violating the deadline constraints. The analysis is performed both under fixed and dynamic priority assignments.
Stream data clustering based on grid density and attraction
Authors: Tu Li , Chen Yixin 
Published: July 2009

Clustering real-time stream data is an important and challenging problem. Existing algorithms such as CluStream are based on the
k
-means algorithm. These clustering algorithms have difficulties finding clusters of arbitrary shapes and handling outliers. Further, they require the knowledge of
k
and user-specified time window. To address these issues, this article proposes
D-Stream
, a framework for clustering stream data using a density-based approach.

Our algorithm uses an online component that maps each input data record into a grid and an offline component that computes the grid density and clusters the grids based on the density. The algorithm adopts a density decaying technique to capture the dynamic changes of a data stream and a attraction-based mechanism to accurately generate cluster boundaries.
Exploiting the intricate relationships among the decay factor, attraction, data density, and cluster structure, our algorithm can efficiently and effectively generate and adjust the clusters in real time. Further, a theoretically sound technique is developed to detect and remove sporadic grids mapped by outliers in order to dramatically improve the space and time efficiency of the system. The technique makes high-speed data stream clustering feasible without degrading the clustering quality. The experimental results show that our algorithm has superior quality and efficiency, can find clusters of arbitrary shapes, and can accurately recognize the evolving behaviors of real-time data streams.
Fixed Point Theorems for a Weaker Meir-Keeler Type "Equation missing" -Set Contraction in Metric Spaces
Authors: Chen Chi-Ming , Chang Tong-Huei 
Published: July 2009

AbstractWe define a weaker Meir-Keeler type function and establish the fixed point theorems for a weaker Meir-Keeler type "Equation missing"-set contraction in metric spaces.
Religious Disputations and Imperial Ideology
Authors: Rezavi Syed Ali Nadeem 
Published: July 2009

The concept of religious debate is encountered even in the pre-Mughal period in India: we hear of special assemblies ( mahzar) that held religious discussions but were confined to controversial themes within predominantly the Hanafi school of thought. But such debates were the instruments of the orthodoxy to consolidate their sway over the dissenters. The evidence of these religious assemblies (majlis) under the reign of Akbar is as early as 1570. However, from the testimonies of a critique of Akbar (Badauni), a theologian (Shaikh Nurul Haq) and a known sycophant and courtier (Abul Fazl), it appears that the constitution of the Ibadatkhana and the discussions being held therein were not an extension of the type of religious debates that were held or organized before. It is the argument of this essay that the Ibadatkhana was an instrument of ‘tolerance’ for the imposition of ‘Reason’. Throughout his reign there was a stress on reason (‘aql’), which was to be given precedence over traditionalism (taqlid). This article, on the basis of contemporary sources, further goes on to fix the location of the Ibadatkhana at Fathpur Sikri. The author proposes that the so-called daftarkhana was in fact the place where this important edifice was located.
Role of leukemia cell invadosome in extramedullary infiltration
Authors: Stefanidakis Michael , Karjalainen Katja , Jaalouk Diana E. , Gahmberg Carl G. , O'Brien Susan , Pasqualini Renata , Arap Wadih , Koivunen Erkki 
Published: July 2009

AbstractAcute myelogenous leukemias (AMLs) are characterized by medullary and extramedullary invasion. We hypothesized that a supramolecular complex, the leukemia-cell invadosome, which contains certain integrins, matrix metalloproteinases (MMPs), and other as-yet unidentified proteins, is essential for tissue invasion and may be central to the phenotypic diversity observed in the clinic. Here we show that the specific binding of MMP-9 to leukocyte surface β2 integrin is required for pericellular proteolysis and migration of AML-derived cells. An efficient antileukemia effect was obtained by the hexapeptide HFDDDE, a motif of the MMP-9 catalytic domain that mediates integrin binding: HFDDDE prevented proMMP-9 binding, transmigration through a human endothelial cell layer, and extracellular matrix degradation. Notably, the functional protein anchorage between β2 integrin and proMMP-9 described in this study does not involve the enzymatic active sites targeted by known MMP inhibitors. Taken together, our results provide a biochemical working definition for the human leukemia invadosome. Disruption of specific protein complexes within this supramolecular target complex may yield a new class of anti-AML drugs with anti-invasion (rather than or in addition to cytotoxic) attributes.
Nucleologenesis and embryonic genome activation are defective in interspecies cloned embryos between bovine ooplasm and rhesus monkey somatic cells
Authors: Song Bong-Seok , Lee Sang-Hee , Kim Sun-Uk , Kim Ji-Su , Park Jung Sun , Kim Cheol-Hee , Chang Kyu-Tae , Han Yong-Mahn , Lee Kyung-Kwang , Lee Dong-Seok , Koo Deog-Bon 
Published: July 2009

Abstract

Background
Interspecies somatic cell nuclear transfer (iSCNT) has been proposed as a tool to address basic developmental questions and to improve the feasibility of cell therapy. However, the low efficiency of iSCNT embryonic development is a crucial problem when compared to in vitro fertilization (IVF) and intraspecies SCNT. Thus, we examined the effect of donor cell species on the early development of SCNT embryos after reconstruction with bovine ooplasm.

Results
No apparent difference in cleavage rate was found among IVF, monkey-bovine (MB)-iSCNT, and bovine-bovine (BB)-SCNT embryos. However, MB-iSCNT embryos failed to develop beyond the 8- or 16-cell stages and lacked expression of the genes involved in embryonic genome activation (EGA) at the 8-cell stage. From ultrastructural observations made during the peri-EGA period using transmission electron microscopy (TEM), we found that the nucleoli of MB-iSCNT embryos were morphologically abnormal or arrested at the primary stage of nucleologenesis. Consistent with the TEM analysis, nucleolar component proteins, such as upstream binding transcription factor, fibrillarin, nucleolin, and nucleophosmin, showed decreased expression and were structurally disorganized in MB-iSCNT embryos compared to IVF and BB-SCNT embryos, as revealed by real-time PCR and immunofluorescence confocal laser scanning microscopy, respectively.

Conclusion
The down-regulation of housekeeping and imprinting genes, abnormal nucleolar morphology, and aberrant patterns of nucleolar proteins during EGA resulted in developmental failure in MB-iSCNT embryos. These results provide insight into the unresolved problems of early embryonic development in iSCNT embryos.
Detection of differentially expressed genes between Erhualian and Large White placentas on day 75 and 90 of gestation
Authors: Zhou Quan-Yong , Fang Ming-Di , Huang Ting-Hua , Li Chang-Chun , Yu Mei , Zhao Shu-Hong 
Published: July 2009

Abstract

Background
Placental efficiency is strongly associated with litter size, fetal weight and prenatal mortality. Together with its rapid growth during late gestation, the Large White pig breed shows a significant increase in placental size and weight, but this does not occur in the highly prolific Chinese pig breeds. To understand the molecular basis of placental development during late gestation in Chinese indigenous and Western breeds with different placental efficiency, female placental samples were collected from six pregnant Erhualian gilts at gestation day 75 (E75) and day 90 (E90) and from six pregnant Large White gilts at gestation day 75 (L75) and day 90 (L90). Two female placentas from one sow were used to extract RNA and then pooled in equal volumes. Twelve pooled samples were hybridized to the porcine Affymetrix GeneChip.

Results
A total of 226 and 577 transcripts were detected that were differentially expressed between E75 and L75 and between E90 and L90 (p < 0.01, q < 0.2), respectively. Gene Ontology (GO) analysis revealed that these genes belong to the class of genes that participate in angiogenesis and development. Real-time RT-PCR confirmed the differential expression of eight selected genes. Significant differential expression of five genes in the VEGF pathway was also detected between the breeds. A search of chromosomal location revealed that 44 differentially expressed genes located to QTL regions related to reproduction. Differential expression of six candidate imprinted genes was also confirmed. Three of the six genes (PLAGL1, DIRAS3, and SLC38A4) showed monoallelic expression in the porcine placenta.

Conclusion
Our study detected many genes that showed differential expression between placentas of two divergent breed of pigs, and confirmed the imprinting of three genes. These findings help to elucidate the genetic control of placental efficiency and improve the understanding of placental development.
A new cold-adapted β-D-galactosidase from the Antarctic Arthrobacter sp. 32c – gene cloning, overexpression, purification and properties
Authors: Hildebrandt Piotr , Wanarska Marta , Kur Józef 
Published: July 2009

Abstract

Background
The development of a new cold-active β-D-galactosidases and microorganisms that efficiently ferment lactose is of high biotechnological interest, particularly for lactose removal in milk and dairy products at low temperatures and for cheese whey bioremediation processes with simultaneous bio-ethanol production.

Results
In this article, we present a new β-D-galactosidase as a candidate to be applied in the above mentioned biotechnological processes. The gene encoding this β-D-galactosidase has been isolated from the genomic DNA library of Antarctic bacterium Arthrobacter sp. 32c, sequenced, cloned, expressed in Escherichia coli and Pichia pastoris, purified and characterized. 27 mg of β-D-galactosidase was purified from 1 L of culture with the use of an intracellular E. coli expression system. The protein was also produced extracellularly by P. pastoris in high amounts giving approximately 137 mg and 97 mg of purified enzyme from 1 L of P. pastoris culture for the AOX1 and a constitutive system, respectively. The enzyme was purified to electrophoretic homogeneity by using either one step- or a fast two step- procedure including protein precipitation and affinity chromatography. The enzyme was found to be active as a homotrimeric protein consisting of 695 amino acid residues in each monomer. Although, the maximum activity of the enzyme was determined at pH 6.5 and 50°C, 60% of the maximum activity of the enzyme was determined at 25°C and 15% of the maximum activity was detected at 0°C.

Conclusion
The properties of Arthrobacter sp. 32cβ-D-galactosidase suggest that this enzyme could be useful for low-cost, industrial conversion of lactose into galactose and glucose in milk products and could be an interesting alternative for the production of ethanol from lactose-based feedstock.
No evidence for an association between the -36A>C phospholamban gene polymorphism and a worse prognosis in heart failure
Authors: Santos Diogo GB , Medeiros Alessandra , Brum Patrícia C , Mill José G , Mansur Alfredo J , Krieger José E , Pereira Alexandre C 
Published: July 2009

Abstract

Background
In Brazil, heart failure leads to approximately 25,000 deaths per year. Abnormal calcium handling is a hallmark of heart failure and changes in genes encoding for proteins involved in the re-uptake of calcium might harbor mutations leading to inherited cardiomyopathies. Phospholamban (PLN) plays a prime role in cardiac contractility and relaxation and mutations in the gene encoding PLN have been associated with dilated cardiomyopathy. In this study, our objective was to determine the presence of the -36A>C alteration in PLN gene in a Brazilian population of individuals with HF and to test whether this alteration is associated with heart failure or with a worse prognosis of patients with HF.

Methods
We genotyped a cohort of 881 patients with HF and 1259 individuals from a cohort of individuals from the general population for the alteration -36A>C in the PLN gene. Allele and genotype frequencies were compared between groups (patients and control). In addition, frequencies or mean values of different phenotypes associated with cardiovascular disease were compared between genotypic groups. Finally, patients were prospectively followed-up for death incidence and genotypes for the -36A>C were compared regarding mortality incidence in HF patients.

Results
No significant association was found between the study polymorphism and HF in our population. In addition, no association between PLN -36A>C polymorphism and demographic, clinical and functional characteristics and mortality incidence in this sample of HF patients was observed.

Conclusion
Our data do not support a role for the PLN -36A>C alteration in modulating the heart failure phenotype, including its clinical course, in humans.