bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Pathology of Spontaneously Occurring Malignant Lymphoma in Sheep
Authors: Johnstone A. C. , Manktelow B. W. 
Published: January 2010

The most common locations of tumours in 22 sheep with malignant lymphoma were the lymph nodes (19 sheep), spleen (14), liver (13), kidney (10), small intestine (9) and heart (9). The distribution of the lesions could be classified as multicentric (14 sheep), alimentary (6), skin (1) and thymic (1). Histological examination of malignant lymphomas from 40 sheep showed there were three reticulum cell sarcomas, and 37 lymphosarcomas. The lymphosarcomas were further classified on the basis of cytological features as lymphoblastoid, lymphocytic/prolymphocytic, prolymphocytic and lymphocytic in 14, 6, 11 and six cases, respectively. Viruses were not detected by electron microscopy in tumourous tissue from 10 sheep with malignant lymphoma.
Correlation of Microbiological and Histological Findings in Bovine Fibrinous Pneumonia
Authors: Schiefer B. , Ward G. E. , Moffatt R. E. 
Published: January 2010

In a retrospective morphological and microbiological study, 39 of 55 cases of bovine fibrinous pneumonia were diagnosed as fibrinous pleuropneumonia. Twenty-nine of these 39 (74%) were associated with Pasteurella hemolytica, but only two cases (5%) with P. multocida. In contrast, of the 16 cases classified as fibrinous bronchopneumonia, one (6%) was associated with P. hemolytica, and nine (56%) with P. multocida. In eight cases Mycoplasma and Hemophilus somnus were found in association with either P. hemolytica or P. multocida but were never isolated alone. We concluded that the use of the term pasteurellosis, implying Pasteurella as the cause, is imprecise because lesions associated with P. hemolytica fulfill the criteria of a fibrinous pleuropneumonia, whereas P. multocida is more likely to cause a bronchopneumonia with moderate amounts of fibrin.
Morphology of the “Sulphur Granules” (Drusen) in Some Actinomycotic Infections. A Light and Electron Microscopic Study
Authors: Bestetti G. 
Published: January 2010

The granules (Drusen) within the inflammatory lesions in three cases of infection by Actinomyeetales were studied with light and electron microscopy. The material consisted of subcutaneous granulomas caused by Actinomyces bovis in a cow, epidural granulomas caused by A. viscosus in the spinal canal of a cat and cerebral granulomas caused by Nocardia in a dog. The granules of A. bovis were 2000 to 3000 micrometers in diameter. Their centers consisted of a slightly basophilic, gram- and grocott-negative material with branching, gram-and grocott-positive filaments. The periphery was slightly basophilic or eosinophilic, but gram- and grocott-positive. Its surface was made of clubs (15 × 3.5 micrometers); they were acidophilic, gram- and grocott-negative. In the center of the granule there are numerous type a cells (coccobacillary cells with a trilaminar cell wall of 12 nanometers) and rarely type b cells (filaments with bilaminar cell wall of 30 nanometers). The periphery was made of germinative centers of type a cells. The clubs were lytic type b cells, embedded in an amorphous material. The granules (Drusen) of A. viscosus were 200 to 600 micrometers in diameter. Their center was slightly eosinophilic, gram- and grocott-negative and contained gram- and grocott-positive filaments. Their periphery was basophilic and contained alternating gram-and grocott-negative areas and radial gram- and grocott-positive filaments. There were no clubs. In the center there were type b cells (filaments with a trilaminar cellular wall of 30 nanometers). The periphery was made of germinative centers of type a cells (coccobacillary with a trilaminar cell wall of 10 to 11 nanometers). The germinative centers were separated from each other by radial bundles of type b cells. The granules (Drusen) of Nocardia were acidophilic, gram- and grocott-positive and surrounded by 1.8 × 0.5-micrometer clubs that were acidophilic, gram- and grocott-negative. There were type a cells (filamentous to bacillary with monolaminar cell wall of 19 nanometers and cross wall) and type b cells (filamentous to bacillary with monolaminar cell wall of 65 nanometers and without cross wall). The remarkable morphological differences of the three species of Actinomycetales are specific, independent from host and type of tissue, and therefore reliable for diagnostic purposes.
Canine Gastric Adenocarcinoma
Authors: Patnaik A. K. , Hurvitz A. I. , Johnson G. F. 
Published: January 2010

In a retrospective study of 26 gastric adenocarcinomas of the dog, 17 were found to have histologic features of the diffuse type and nine of the intestinal type similar to those of the same tumor in man. The intestinal type was characterized by distinct glandular structures lined with well polarized cells at the primary and metastatic sites and mild desmoplastic reaction. Three subtypes with distinct histologic features (papillary, five; acinar, three; solid, one) were recognized in this group. Fourteen of the diffuse adenocarcinomas were characterized by random infiltration by neoplastic cells, singly or in clusters, often with signet ring cells and severe desmoplastic reaction. The remaining three diffuse adenocarcinomas also had recognizable acinar structures and were considered to be glandular subtypes of the diffuse type. In eight dogs there was a 7:1 male to female ratio for dogs with the intestinal type and in 16 dogs a 2:1 male to female ratio for dogs with the diffuse type. Two of the nine intestinal type of adenocarcinomas, but none of the diffuse tumors, had intraluminal growths. Metaplasia of gastric epithelium was seen in nearly half the tumors; this was more common in the intestinal type (six of nine). Different degrees of carcinomatosis were seen in 24 of 26 dogs. Regional lymph nodes were involved in the 20 dogs whose nodes were available for examination. Distant metastases were seen in 19 of 26 dogs; liver, lungs and adrenal glands were the most common sites. Various degrees of lymphoid cell infiltration, suggesting the antigenic quality of the neoplasms, were seen in 15 dogs. Additional neoplasms were seen in eight dogs.
Beiträge zum Lebenszyklus der Frenkelien. IV. Pathomorphologische Befunde an den Organen experimentell infizierter Rötelmäuse
Authors: Geisel O. , Kaiser E. , Krampitz H. E. , Rommel M. 
Published: January 2010

In 1975 the buzzard ( Buteo buteo) was found to be the final host of Frenkelia clethrionomyobuteonis. After this discovery it became possible to investigate systematically the pathomorphology of the infection in the intermediate host, the bank vole ( Clethrionomys glareolus). Fifty bank voles were infected orally with a suspension of sporocysts recovered from the faeces of experimentally infected buzzards. Each rodent received 7000 sporocysts. Six controls each were given a faecal suspension from a non-infected buzzard. The voles were killed between 1 and 140 days after infection and examined histologically. Between the 5th and 8th day of the infection during the schizogonic multiplication of the parasite a focal necrosis of liver cells and of the liver parenchyma is observed followed by a reversible resorptive inflammation associated with siderophagia and the occurrence of giant cells. The spleen was spodogenously enlarged up to twice its normal size. There also was haemosiderosis of the bone marrow, the liver and the spleen up to 25 days after infection. At the same time the erythropoiesis in the bone marrow, the spleen and in the lymph nodes increased; there also was a lymphoid hyperplasia in spleen and lymph nodes. About 10 days after infection a reversible infiltration with lymphocytes and plasma cells developed in the liver, heart and brain. This infiltration was again detectable as perivascular and meningeal reactions in the brain after the 49th day after infection. The second asexual multiplication of the parasite was seen histologically in the grey and white matter of the central nervous system after the 18th day of infection. The developing cysts increased in size continuously thereby compressing the surrounding nervous tissue. Disseminated focal necrosis with resorptive inflammatory components was prominent in the parenchyma of the brain after the 49th day of infection. It was possible to differentiate between damage in single organs and systemic pathological lesions. The lesions in single organs were directly connected with the development of parasitic stages in the liver (schizonts) and in the brain (cysts). The generalized lesions occurred in the haemopoietic system after an impairment of the blood during the first asexual multiplication. They also occurred in the immunocytic systems after the first and during the second asexual multiplication and during the relatively late cystic phase of the parasite in the brain. The pathogenesis of the disintegration of blood cells is not clear. The immunocytic reaction can be considered an immunological response of the host against the parasite. The effect of the development of the cysts on the function and structure of the central nervous system is expected to lead to an increasing impairment of the motility of the intermediate host.
Frequency of Canine and Feline Tumors in a Defined Population
Authors: MacVean D. W. , Monlux A. W. , Anderson P. S. , Silberg S. L. , Roszel J. F. 
Published: January 2010

The Tulsa Registry of Canine and Feline Neoplasms was the second animal tumor registry in the United States concerned with a defined population in a delimited geographic area. Only tumors histologically confirmed by registry pathologists were included in frequency statistics based on the annual dog and cat population presented to veterinarians. During the first registry year, about 1% of the 63,504 dogs and 0.5% of the 11,909 cats had one or more primary tumors. While the incidence rate for malignant tumors in dogs was similar to that in cats, the incidence of benign tumors of dogs was over 10 times that of cats. The most common tumors were sebaceous adenoma in dogs and lymphosarcoma in cats. Mammary cancer was the most common malignant tumor in dogs. Mammary tumors of female dogs were significantly more frequent in Pointers, Poodles and Boston Terriers, in that order, than in other breeds. A greater incidence of mammary tumors among intact compared to spayed female dogs was seen for virtually every age group except in the Pointer breed.
Peliosis Hepatis-like Lesion in Aging Rats
Authors: Lee K. P. 
Published: January 2010

The incidence of peliosis hepais-like lesions in two-year-old Charles River-CD Sprague-Dawley rats (Charles River Breeding laboratories, Wilmington, MA) was almost twice as high in males as females. Blood lakes developed from progressive expansion of sinusoids with destruction of the hepatic cell cords. The endothelial processes of the blood lakes had edematous swelling, vesiculation, and denudation. The microvilli of hepatocytes became swollen, blunted, and sloughed where the endothelial processes were disrupted. Subsequently, the hepatocytes were exposed directly to circulating blood cells and had degenerative changes with accumulation of red blood cells in the cytoplasm. The membrane-bound cysts were observed with the blood lakes and were bounded with atrophic hepatocytes or membranous wall extending to the Disse's space of adjacent hepatocytes. The cysts were filled with proteinaccous fluid, fibrin, and a few red blood cells. The wall of membrane-bound cysts consisted of endothelial processes extending from the endothelial cells of adjacent hepatocytes. The wall appeared to develop from adhesion of endothelial processes surrounding sinusoidal spaces of the hepatocytes following lysis of atrophic hepatocytes.
Effective and long-term control of EBV PTLD after transfer of peptide-selected T cells
Authors: Moosmann Andreas , Bigalke Iris , Tischer Johanna , Schirrmann Leah , Kasten Julitta , Tippmer Stefanie , Leeping Marina , Prevalšek Dušan , Jaeger Gundula , Ledderose Georg , Mautner Josef , Hammerschmidt Wolfgang , Schendel Dolores J. , Kolb Hans-Jochem 
Published: January 2010

AbstractPosttransplantation lymphoproliferative disease (PTLD) associated with Epstein-Barr virus (EBV) is a life-threatening complication after allogeneic hematopoietic stem cell transplantation. PTLD is efficiently prevented by adoptive transfer of EBV-specific T cells from the donor. To make EBV-specific T cells available in urgent clinical situations, we developed a rapid protocol for their isolation by overnight stimulation of donor blood cells with peptides derived from 11 EBV antigens, interferon-γ surface capture, and immunomagnetic separation. Six patients with PTLD received 1 transfusion of EBV-specific T cells. No response was seen in 3 patients who had late-stage disease with multiorgan dysfunction at the time of T-cell transfer. In 3 patients who received T cells at an earlier stage of disease, we observed complete and stable remission of PTLD. Two patients have remained free from EBV-associated disease for more than 2 years. CD8+ T cells specific for EBV early antigens rapidly expanded after T-cell transfer, temporarily constituted greater than 20% of all peripheral blood lymphocytes, and were maintained throughout the observation period. Thus, a rapid and sustained reconstitution of a protective EBV-specific T-cell memory occurred after the infusion of small numbers of directly isolated EBV-specific T cells.
Biana: a software framework for compiling biological interactions and analyzing networks
Authors: Garcia-Garcia Javier , Guney Emre , Aragues Ramon , Planas-Iglesias Joan , Oliva Baldo 
Published: January 2010

Abstract

Background
The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties.

Results
We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php.

Conclusions
BIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules.
A variational Bayes algorithm for fast and accurate multiple locus genome-wide association analysis
Authors: Logsdon Benjamin A , Hoffman Gabriel E , Mezey Jason G 
Published: January 2010

Abstract

Background
The success achieved by genome-wide association (GWA) studies in the identification of candidate loci for complex diseases has been accompanied by an inability to explain the bulk of heritability. Here, we describe the algorithm V-Bay, a variational Bayes algorithm for multiple locus GWA analysis, which is designed to identify weaker associations that may contribute to this missing heritability.

Results
V-Bay provides a novel solution to the computational scaling constraints of most multiple locus methods and can complete a simultaneous analysis of a million genetic markers in a few hours, when using a desktop. Using a range of simulated genetic and GWA experimental scenarios, we demonstrate that V-Bay is highly accurate, and reliably identifies associations that are too weak to be discovered by single-marker testing approaches. V-Bay can also outperform a multiple locus analysis method based on the lasso, which has similar scaling properties for large numbers of genetic markers. For demonstration purposes, we also use V-Bay to confirm associations with gene expression in cell lines derived from the Phase II individuals of HapMap.

Conclusions
V-Bay is a versatile, fast, and accurate multiple locus GWA analysis tool for the practitioner interested in identifying weaker associations without high false positive rates.
Lineage-specific co-evolution of the Egf receptor/ligand signaling system
Authors: Laisney Juliette AGC , Braasch Ingo , Walter Ronald B , Meierjohann Svenja , Schartl Manfred 
Published: January 2010

Abstract

Background
The epidermal growth factor receptor (Egfr) with its numerous ligands has fundamental roles in development, cell differentiation and physiology. Dysfunction of the receptor-ligand system contributes to many human malignancies. Consistent with such various tasks, the Egfr gene family has expanded during vertebrate evolution as a consequence of several rounds of whole genome duplication. Of particular interest is the effect of the fish-specific whole genome duplication (FSGD) on the ligand-receptor system, as it has supplied this largest group of vertebrates with additional opportunities for sub- and/or neofunctionalization in this signaling system.

Results
We identified the predicted components of the Egf receptor-ligand signaling system in teleost fishes (medaka, platyfish, stickleback, pufferfishes and zebrafish). We found two duplicated egfr genes, egfra and egfrb, in all available teleost genomes. Surprisingly only one copy for each of the seven Egfr ligands could be identified in most fishes, with zebrafish hbegf being the only exception. Special focus was put on medaka, for which we more closely investigated all Egf receptors and Egfr ligands. The different expression patterns of egfra, egfrb and their ligands in medaka tissues and embryo stages suggest differences in role and function. Preferential co-expression of different subsets of Egfr ligands corroborates the possible subfunctionalization and specialization of the two receptors in adult tissues. Bioinformatic analyses of the ligand-receptor interface between Egfr and its ligands show a very weak evolutionary conservation within this region. Using in vitro analyses of medaka Egfra, we could show that this receptor is only activated by medaka ligands, but not by human EGF. Altogether, our data suggest a lineage-specific Egfr/Egfr ligand co-evolution.

Conclusions
Our data indicate that medaka Egfr signaling occurs via its two copies, Egfra and Egfrb, each of them being preferentially coexpressed with different subsets of Egfr ligands. This fish-specific occurrence of Egf receptor specialization offers unique opportunities to study the functions of different Egf receptor-ligand combinations and their biological outputs in vertebrates. Furthermore, our results strongly support the use of homologous ligands in future studies, as sufficient cross-specificity is very unlikely for this ligand/receptor system.
The chitobiose transporter, chbC, is required for chitin utilization in Borrelia burgdorferi
Authors: Rhodes Ryan G , Atoyan Janet A , Nelson David R 
Published: January 2010

Abstract

Background
The bacterium Borrelia burgdorferi, the causative agent of Lyme disease, is a limited-genome organism that must obtain many of its biochemical building blocks, including N-acetylglucosamine (GlcNAc), from its tick or vertebrate host. GlcNAc can be imported into the cell as a monomer or dimer (chitobiose), and the annotation for several B. burgdorferi genes suggests that this organism may be able to degrade and utilize chitin, a polymer of GlcNAc. We investigated the ability of B. burgdorferi to utilize chitin in the absence of free GlcNAc, and we attempted to identify genes involved in the process. We also examined the role of RpoS, one of two alternative sigma factors present in B. burgdorferi, in the regulation of chitin utilization.

Results
Using fluorescent chitinase substrates, we demonstrated an inherent chitinase activity in rabbit serum, a component of the B. burgdorferi growth medium (BSK-II). After inactivating this activity by boiling, we showed that wild-type cells can utilize chitotriose, chitohexose or coarse chitin flakes in the presence of boiled serum and in the absence of free GlcNAc. Further, we replaced the serum component of BSK-II with a lipid extract and still observed growth on chitin substrates without free GlcNAc. In an attempt to knockout B. burgdorferi chitinase activity, we generated mutations in two genes (bb0002 and bb0620) predicted to encode enzymes that could potentially cleave the β-(1,4)-glycosidic linkages found in chitin. While these mutations had no effect on the ability to utilize chitin, a mutation in the gene encoding the chitobiose transporter (bbb04, chbC) did block utilization of chitin substrates by B. burgdorferi. Finally, we provide evidence that chitin utilization in an rpoS mutant is delayed compared to wild-type cells, indicating that RpoS may be involved in the regulation of chitin degradation by this organism.

Conclusions
The data collected in this study demonstrate that B. burgdorferi can utilize chitin as a source of GlcNAc in the absence of free GlcNAc, and suggest that chitin is cleaved into dimers before being imported across the cytoplasmic membrane via the chitobiose transporter. In addition, our data suggest that the enzyme(s) involved in chitin degradation are at least partially regulated by the alternative sigma factor RpoS.
CXCR4/SDF1 mediate hypoxia induced chondrosarcoma cell invasion through ERK signaling and increased MMP1 expression
Authors: Sun Xiaojuan , Wei Lei , Chen Qian , Terek Richard M 
Published: January 2010

AbstractBackgroundChondrosarcoma is a disease that does not respond to conventional cytotoxic chemotherapy and expression of MMP1 is a marker for a poor prognosis. The mechanism of increased MMP1 expression in chondrosarcoma is not completely known. Our goal is to identify molecular pathways that could serve as therapeutic targets. Chondrosarcoma become hypoxic as they grow, are capable of eliciting an angiogenic response, and typically metastasize to the lungs. The present study determined the effect of hypoxia and specifically HIF-1a on expression of CXCR4 and MMP1 and their role in chondrosarcoma cell invasion.ResultsCXCR4 and its ligand, SDF1, are upregulated in primary chondrosarcoma tumors compared to normal articular cartilage, and CXCR4 was upregulated in chondrosarcoma cell line JJ compared to normal chondrocytes. Hypoxia and specifically HIF-1a increased CXCR4 and MMP1 expression in JJ cell line and chondrosarcoma invasionin vitro. The hypoxia mediated increase in MMP1 expression and chondrosarcoma invasion could be inhibited by siRNA directed at HIF-1a or CXCR4, the CXCR4 inhibitor AMD3100, as well as with ERK inhibitor U0126 and ERK siRNA.ConclusionsChondrosarcoma cell invasion is increased by hypoxia induced expression of CXCR4 and MMP1 and is mediated by HIF-1a and ERK. Both invasion and MMP1 can be inhibited with CXCR4 blockade, suggesting that CXCR4/SDF1 signaling may be a therapeutic target for chondrosarcoma.