bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fatal Bioprosthetic Aortic Valve Endocarditis Due to
Cardiobacterium valvarum
Authors: Geißdörfer Walter , Tandler René , Schlundt Christian , Weyand Michael , Daniel Werner G. , Schoerner Christoph 
Published: May 2007

ABSTRACT

Cardiobacterium valvarum
was isolated from the blood of a 71-year-old man with fatal aortic valve endocarditis. The API NH system was used for phenotypic characterization of the
C. valvarum
strain. This is the first case of infective endocarditis caused by
C. valvarum
in Germany and the first case worldwide affecting a prosthetic valve and lacking an obvious dental focus.
Isolation and Propagation of the Ap-Variant 1 Strain of
Anaplasma phagocytophilum
in a Tick Cell Line
Authors: Massung Robert F. , Levin Michael L. , Munderloh Ulrike G. , Silverman David J. , Lynch Meghan J. , Gaywee Jariyanart K. , Kurtti Timothy J. 
Published: May 2007

ABSTRACT

The first tissue culture isolates of the unique
Anaplasma phagocytophilum
strain, Ap-Variant 1, were obtained in the
Ixodes scapularis
tick-derived cell line ISE6. Two isolates were from goat blood samples: one from a goat infected with
I. scapularis
ticks from Rhode Island and a second from a goat infected by serial passage of blood from the first infected goat. Eight isolates were made directly from
I. scapularis
ticks collected from white-tailed deer in Minnesota and represent the first isolations of an
Anaplasma
species directly from ticks. Each of the 10 isolates had a 16S rRNA gene sequence identical to that previously described for Ap-Variant 1, but differences within the
ank
gene were found that suggest natural variation. Prevalence of
Anaplasma
in the Minnesota ticks was 63.9%; 23 of 36 ticks tested by PCR were positive. Six of the tick-derived isolates were obtained from a set of 18 PCR-positive ticks, for a 33.3% isolation success rate. The conservation of host tropism among the Rhode Island and Minnesota isolates of Ap-Variant 1 was examined by use of experimental infections of mice and a goat. A Minnesota tick-derived isolate (MN-61-2) was used to inoculate naïve animals, and this isolate was able to infect a goat but unable to infect each of five mice, confirming that the Minnesota isolates have the same host tropism as Ap-Variant 1 from the northeastern United States. Light and electron microscopy of the Ap-Variant 1 isolate MN-61-2 in ISE6 cells showed cytoplasmic inclusions characteristic of
A. phagocytophilum
with pleomorphic bacteria in membrane-bound vacuoles and both electron-dense and electron-lucent forms.
Temporal Analysis of Andes Virus and Sin Nombre Virus Infections of Syrian Hamsters
Authors: Wahl-Jensen Victoria , Chapman Jennifer , Asher Ludmila , Fisher Robert , Zimmerman Michael , Larsen Tom , Hooper Jay W. 
Published: May 2007

ABSTRACTAndes virus (ANDV) and Sin Nombre virus (SNV) are rodent-borne hantaviruses that cause a highly lethal hemorrhagic fever in humans known as hantavirus pulmonary syndrome (HPS). There are no vaccines or specific drugs to prevent or treat HPS, and the pathogenesis is not understood. Syrian hamsters infected with ANDV, but not SNV, develop a highly lethal disease that closely resembles HPS in humans. Here, we performed a temporal pathogenesis study comparing ANDV and SNV infections in hamsters. SNV was nonpathogenic and viremia was not detected despite the fact that all animals were infected. ANDV was uniformly lethal with a mean time to death of 11 days. The first pathology detected was lymphocyte apoptosis starting on day 4. Animals were viremic and viral antigen was first observed in multiple organs by days 6 and 8, respectively. Levels of infectious virus in the blood increased 4 to 5 logs between days 6 and 8. Pulmonary edema was first detected ultrastructurally on day 6. Ultrastructural analysis of lung tissues revealed the presence of large inclusion bodies and substantial numbers of vacuoles within infected endothelial cells. Paraendothelial gaps were not observed, suggesting that fluid leakage was transcellular and directly attributable to infecting virus. Taken together, these data imply that HPS treatment strategies aimed at preventing virus replication and dissemination will have the greatest probability of success if administered before the viremic phase; however, because vascular leakage is associated with infected endothelial cells, a therapeutic strategy targeting viral replication might be effective even at later times (e.g., after disease onset).
Influenza Virus Hemagglutinin and Neuraminidase, but Not the Matrix Protein, Are Required for Assembly and Budding of Plasmid-Derived Virus-Like Particles
Authors: Chen Benjamin J. , Leser George P. , Morita Eiji , Lamb Robert A. 
Published: May 2007

ABSTRACT
For influenza virus, we developed an efficient, noncytotoxic, plasmid-based virus-like particle (VLP) system to reflect authentic virus particles. This system was characterized biochemically by analysis of VLP protein composition, morphologically by electron microscopy, and functionally with a VLP infectivity assay. The VLP system was used to address the identity of the minimal set of viral proteins required for budding. Combinations of viral proteins were expressed in cells, and the polypeptide composition of the particles released into the culture media was analyzed. Contrary to previous findings in which matrix (M1) protein was considered to be the driving force of budding because M1 was found to be released copiously into the culture medium when M1 was expressed by using the vaccinia virus T7 RNA polymerase-driven overexpression system, in our noncytotoxic VLP system M1 was not released efficiently into the culture medium. Additionally, hemagglutinin (HA), when treated with exogenous neuraminidase (NA) or coexpressed with viral NA, could be released from cells independently of M1. Incorporation of M1 into VLPs required HA expression, although when M1 was omitted from VLPs, particles with morphologies similar to those of wild-type VLPs or viruses were observed. Furthermore, when HA and NA cytoplasmic tail mutants were included in the VLPs, M1 failed to be efficiently incorporated into VLPs, consistent with a model in which the glycoproteins control virus budding by sorting to lipid raft microdomains and recruiting the internal viral core components. VLP formation also occurred independently of the function of Vps4 in the multivesicular body pathway, as dominant-negative Vps4 proteins failed to inhibit influenza VLP budding.
Adeno-Associated Virus Type 2 (AAV2) Capsid-Specific Cytotoxic T Lymphocytes Eliminate Only Vector-Transduced Cells Coexpressing the AAV2 Capsid In Vivo
Authors: Li Chengwen , Hirsch Matthew , Asokan Aravind , Zeithaml Brian , Ma Hong , Kafri Tal , Samulski R. Jude 
Published: May 2007

ABSTRACT
A recent clinical trial has suggested that recombinant adeno-associated virus (rAAV) vector transduction in humans induces a cytotoxic T-lymphocyte (CTL) response against the AAV2 capsid. To directly address the ability of AAV capsid-specific CTLs to eliminate rAAV-transduced cells in vitro and in vivo in mice, we first demonstrated that AAV2 capsid-specific CTLs could be induced by dendritic cells with endogenous AAV2 capsid expression or pulsed with AAV2 vectors. These CTLs were able to kill a cell line stable for capsid expression in vitro and also in a mouse tumor xenograft model in vivo. Parent colon carcinoma (CT26) cells transduced with a large amount of AAV2 vectors in vitro were also destroyed by these CTLs. To determine the effect of CTLs on the elimination of target cells transduced by AAV2 vectors in vivo, we carried out adoptive transfer experiments. CTLs eliminated liver cells with endogenous AAV2 capsid expression but not liver cells transduced by AAV2 vectors, regardless of the reporter genes. Similar results were obtained for rAAV2 transduction in muscle. Our data strongly suggest that AAV vector-transduced cells are rarely eliminated by AAV2 capsid-specific CTLs in vivo, even though the AAV capsid can induce a CTL response. In conclusion, AAV capsid-specific CTLs do not appear to play a role in elimination of rAAV-transduced cells in a mouse model. In addition, our data suggest that the mouse model may not mimic the immune response noted in humans and additional modification to AAV vectors may be required for further study in order to elicit a similar cellular immune response.
Sphagnum establishment and expansion in black spruce (Picea mariana) boreal forests
Authors: Fenton Nicole J. , Béland Catherine , De Blois Sylvie , Bergeron Yves 
Published: April 2007

Boreal forest bryophyte communities are made up of distinct colonies of feathermosses that cover the forest floor. In some black spruce ( Picea mariana (Mill.) BSP) boreal forests, Sphagnum spp. establish colonies on the forest floor 30–40 years after the feathermosses, and ultimately expand to dominate the community. The mechanisms that permit the Sphagnum spp. to establish and expand are unknown. The objectives of this study were to examine the establishment and expansion substrates of Sphagnum spp., and the conditions correlated with colony expansion. Forty colonies, in six stands, of Sphagnum capillifolium (Ehrh.) Hedw. were dissected to determine their substrates, and the environmental conditions in which all colonies present were growing were measured. Coarse woody debris was the dominant establishment and early expansion substrate for Sphagnum capillifolium colonies. With age as the control factor, large colonies showed a significant partial correlation with canopy openness, and there were fewer individuals per cm3 in large colonies than there were in small colonies. These results suggest that Sphagnum establishment in these communities is dependent on the presence of coarse woody debris, and expansion is linked to the stand break-up, which would allow an increase in light intensity, and rainfall to reach the colony. Consequently the community change represented by Sphagnum establishment and expansion is initially governed by a stochastic process and ultimately by habitat availability and species competition.
Male Diagnosis of the Female Pen in Late Victorian Britain: Private Assessments ofSupernatural Religion
Authors: Cadwallader Alan H. 
Published: May 2007

ABSTRACTAnonymity is a feature of the explosion of publications in nineteenthcentury England. Its motivations were variegated just as efforts to expose an anonymous author were also driven by a variety of agendas. One of the longest retentions of anonymity attached to a work that profoundly disturbed Victorian religiosity was the threevolume book titledSupernatural Religion. The Dublin Divinity Professor, George Salmon's private correspondence with Bishop J.B. Lightfoot near the end of Lightfoot's life posited the author as a woman, Mrs Humphry Ward. An analysis of Salmon's letters is set into the context of the private and public writings of key protagonists in the debates, and reveals deep-seated attitudes about gender, learning, writing, national identity, morality and anonymity in some elite intellectual circles of the society and church of the time.
Novel c-CBL and CBL-b ubiquitin ligase mutations in human acute myeloid leukemia
Authors: Caligiuri Michael A. , Briesewitz Roger , Yu Jianhua , Wang Lisheng , Wei Min , Arnoczky Kristy J. , Marburger Trent B. , Wen Jing , Perrotti Danilo , Bloomfield Clara D. , Whitman Susan P. 
Published: May 2007

Abstract
The CBL ubiquitin ligase targets a variety of activated tyrosine kinases (TKs) for degradation. Many TKs are mutationally or autocrine activated and/or often overexpressed at the mRNA and protein levels in acute leukemias. We hypothesized that CBL is mutated in patients with acute myeloid leukemia (AML). Four of 12 patients and the MOLM-13 cell line harbored c-CBL mutations, either RNA splicing mutations, missense mutations, or a nucleotide insertion. Additionally, 1 of the 12 patients harbored a missense mutation in the related CBL-b gene. Each c-CBL mutation involves the structurally important α-helix within the linker region, while the mutation in CBL-b was located in the Ub-E2 protein-binding RING finger. Short-interfering RNA knockdown of mutant c-CBL present in MOLM-13 cells was growth inhibitory. In summary, novel mutations in c-CBL and CBL-b have been identified in human AML and may represent potential targets for novel therapeutics.
Concordant but not discordant bone marrow involvement in diffuse large B-cell lymphoma predicts a poor clinical outcome independent of the International Prognostic Index
Authors: Chung Randy , Lai Raymond , Wei Peter , Lee Jason , Hanson John , Belch Andrew R. , Turner A. Robert , Reiman Tony 
Published: May 2007

Abstract
In diffuse large B-cell lymphoma (DLBCL), previous studies have suggested that, while concordant bone marrow (BM) involvement confers a poor prognosis, discordant BM involvement does not. Whether this correlation is independent of the non-Hodgkin lymphoma International Prognostic Index (IPI) was previously unknown. We reviewed all DLBCL case histories from 1986 to 1997 at our center with complete staging, IPI data, and follow-up. A total of 55 (11.2%) of 489 patients had BM involvement, including 29 with concordant involvement and 26 with discordant involvement. The 55 patients with BM involvement had a poor prognosis compared with the uninvolved BM group (5-year overall survival [OS], 34.5% versus 46.9%; log-rank P = .019). However, concordant involvement portended a very poor prognosis (5-year OS, 10.3%; P < .001), whereas discordant involvement did not (5-year OS, 61.5%, P value nonsignificant). Compared with the discordant subset, the concordant subset patients were older, had a higher serum lactate dehydrogenase level, and a significantly higher IPI. However, the poor survival associated with concordant BM involvement was independent of the IPI score (P = .002, Cox regression). We conclude that in patients with DLBCL, concordant but not discordant BM involvement confers a very poor clinical outcome. Furthermore, concordant BM involvement is an independent adverse prognostic factor.
Worse outcome and more chronic GVHD with peripheral blood progenitor cells than bone marrow in HLA-matched sibling donor transplants for young patients with severe acquired aplastic anemia
Authors: Schrezenmeier Hubert , Passweg Jakob R. , Marsh Judith C. W. , Bacigalupo Andrea , Bredeson Christopher N. , Bullorsky Eduardo , Camitta Bruce M. , Champlin Richard E. , Gale Robert Peter , Fuhrer Monika , Klein John P. , Locasciulli Anna , Oneto Rosi , Schattenberg Antonius V. M. B. , Socie Gerard , Eapen Mary 
Published: May 2007

AbstractWe analyzed the outcome of 692 patients with severe aplastic anemia (SAA) receiving transplants from HLA-matched siblings. A total of 134 grafts were peripheral blood progenitor cell (PBPC) grafts, and 558 were bone marrow (BM) grafts. Rates of hematopoietic recovery and grades 2 to 4 chronic graft-versus-host disease (GVHD) were similar after PBPC and BM transplantations regardless of age at transplantation. In patients older than 20 years, chronic GVHD and overall mortality rates were similar after PBPC and BM transplantations. In patients younger than 20 years, rates of chronic GVHD (relative risk [RR] 2.82; P = .002) and overall mortality (RR 2.04; P = .024) were higher after transplantation of PBPCs than after transplantation of BM. In younger patients, the 5-year probabilities of overall survival were 73% and 85% after PBPC and BM transplantations, respectively. Corresponding probabilities for older patients were 52% and 64%. These data indicate that BM grafts are preferred to PBPC grafts in young patients undergoing HLA-matched sibling donor transplantation for SAA.
Recursive Cluster Elimination (RCE) for classification and feature selection from gene expression data
Authors: Yousef Malik , Jung Segun , Showe Louise C , Showe Michael K 
Published: May 2007

Abstract

Background
Classification studies using gene expression datasets are usually based on small numbers of samples and tens of thousands of genes. The selection of those genes that are important for distinguishing the different sample classes being compared, poses a challenging problem in high dimensional data analysis. We describe a new procedure for selecting significant genes as recursive cluster elimination (RCE) rather than recursive feature elimination (RFE). We have tested this algorithm on six datasets and compared its performance with that of two related classification procedures with RFE.

Results
We have developed a novel method for selecting significant genes in comparative gene expression studies. This method, which we refer to as SVM-RCE, combines K-means, a clustering method, to identify correlated gene clusters, and Support Vector Machines (SVMs), a supervised machine learning classification method, to identify and score (rank) those gene clusters for the purpose of classification. K-means is used initially to group genes into clusters. Recursive cluster elimination (RCE) is then applied to iteratively remove those clusters of genes that contribute the least to the classification performance. SVM-RCE identifies the clusters of correlated genes that are most significantly differentially expressed between the sample classes. Utilization of gene clusters, rather than individual genes, enhances the supervised classification accuracy of the same data as compared to the accuracy when either SVM or Penalized Discriminant Analysis (PDA) with recursive feature elimination (SVM-RFE and PDA-RFE) are used to remove genes based on their individual discriminant weights.

Conclusion
SVM-RCE provides improved classification accuracy with complex microarray data sets when it is compared to the classification accuracy of the same datasets using either SVM-RFE or PDA-RFE. SVM-RCE identifies clusters of correlated genes that when considered together provide greater insight into the structure of the microarray data. Clustering genes for classification appears to result in some concomitant clustering of samples into subgroups.
Our present implementation of SVM-RCE groups genes using the correlation metric. The success of the SVM-RCE method in classification suggests that gene interaction networks or other biologically relevant metrics that group genes based on functional parameters might also be useful.
Robust imputation method for missing values in microarray data
Authors: Yoon Dankyu , Lee Eun-Kyung , Park Taesung 
Published: May 2007

Abstract

Background
When analyzing microarray gene expression data, missing values are often encountered. Most multivariate statistical methods proposed for microarray data analysis cannot be applied when the data have missing values. Numerous imputation algorithms have been proposed to estimate the missing values. In this study, we develop a robust least squares estimation with principal components (RLSP) method by extending the local least square imputation (LLSimpute) method. The basic idea of our method is to employ quantile regression to estimate the missing values, using the estimated principal components of a selected set of similar genes.

Results
Using the normalized root mean squares error, the performance of the proposed method was evaluated and compared with other previously proposed imputation methods. The proposed RLSP method clearly outperformed the weighted k-nearest neighbors imputation (kNNimpute) method and LLSimpute method, and showed competitive results with Bayesian principal component analysis (BPCA) method.

Conclusion
Adapting the principal components of the selected genes and employing the quantile regression model improved the robustness and accuracy of missing value imputation. Thus, the proposed RLSP method is, according to our empirical studies, more robust and accurate than the widely used kNNimpute and LLSimpute methods.
Immunomodulation by maternal autoantibodies of the fetal serotoninergic 5-HT4receptor and its consequences in early BALB/c mouse embryonic development
Authors: Kamel Rehab , Garcia Simone , Lezoualc'h Frank , Fischmeister Rodolphe , Muller Sylviane , Hoebeke Johan , Eftekhari Pierre 
Published: April 2007

AbstractBackgroundThe presence of functional 5-HT4receptors in human and its involvement in neonatal lupus erythematosus (NLE) have prompted us to study the receptor expression and role during embryogenesis. Earlier we managed to demonstrate that female BALB/c mice immunized against the second extracellular loop (SEL) of the 5-HT4receptor gave birth to pups with heart block. To explain this phenomenon we investigated the expression of 5-HT4receptors during mouse embryogenesis. At the same time we looked whether the consequence of 5-HT4receptor immunomodulation observed earlier is in relation to receptor expression.We studied the expression of 5-HT4receptor at the mRNA level and its two isoforms 5-HT4(a)and 5-HT4(d)at the protein level in embryos from BALB/c mice, at 8th, 12th, 18thgestation days (GD) and 1 day post natal (DPN). Simultaneously the receptor activity was inhibited by rising antibodies, in female mice against SEL of the receptor. The mice were mated and embryos were collected at 8th, 12th, 18thGD and 1 DPN.Results5-HT4receptor mRNA increased in brain from 12thGD to 1 DPN. Its expression gradually decreased in heart and disappeared at birth. This was consistent with expression of the receptor isoforms 5-HT4(a) and (d). Abnormalities like decreased number of embryos, growth delay, spina bifida and sinus arrhythmia from 12thGD were documented in pups of mice showing anti-5-HT4receptor antibodies.Conclusionserotoninergic 5-HT4receptor plays an important role in mouse foetal development. In BALB/c mice there is a direct relation between the expression of receptor and the deleterious effect of maternal anti-5-HT4receptor autoantibodies in early embryogenesis.