bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene and stem cell therapy in peripheral arterial occlusive disease
Authors: Kalka C , Baumgartner Iris 
Published: July 2008

Abstract Peripheral arterial occlusive disease (PAOD) is a manifestation of systemic atherosclerosis strongly associated with a high risk of cardiovascular morbidity and mortality. In a considerable proportion of patients with PAOD, revascularization either by endovascular means or by open surgery combined with best possible risk factor modification does not achieve limb salvage or relief of ischaemic rest pain. As a consequence, novel therapeutic strategies have been developed over the last two decades aiming to promote neovascularization and remodelling of collaterals. Gene and stem cell therapy are the main directions for clinical investigation concepts. For both, preclinical studies have shown promising results using a wide variety of genes encoding for growth factors and populations of adult stem cells, respectively. As a consequence, clinical trials have been performed applying gene and stem cell-based concepts. However, it has become apparent that a straightforward translation into humans is not possible. While several trials reported relief of symptoms and functional improvement, other trials did not confirm this early promise of efficacy. Ongoing clinical trials with an improved study design are needed to conﬁrm the potential that gene and cell therapy may have and to prevent the gaps in our scientific knowledge that will jeopardize the establishment of angiogenic therapy as an additional medical treatment of PAOD. This review summarizes the experimental background and presents the current status of clinical applications and future perspectives of the therapeutic use of gene and cell therapy strategies for PAOD.
Which Presidents Are Most Memorable?
Authors: Devi Gayatri , Zhivotovskaya Emiliya , Schultz Sarah 
Published: July 2008

Background/rationale. Episodic memory loss is a hall-mark of Alzheimer’s disease (AD), with recall of recent events becoming progressively difficult. A commonly used tool, the recollection of US presidents, was assessed in evaluating episodic versus semantic memory loss among AD patients compared with spouse controls. Methods. A total of 36 patients (12 men, 24 women) with possible or probable AD were asked to “give the names of 5 US presidents” and concurrently administered the Mini-Mental State Examination (MMSE). Twenty-three spouses (12 men, 11 women) were controls. The year 1980 demarcated “remote” versus “recent” presidents. Results. Patients were older, had lower MMSE scores ( P < .001), and recalled fewer presidents than controls ( P < .005), after controlling for age. Among patients, men were more educated than women ( P < .05) and recalled more presidents ( P < .001). No gender differences were observed in controls. Conclusions. Patients with AD preferentially recalled remote presidents, supporting retention of semantic memory in this group. There were no gender differences between groups.
The BH3-only mimetic ABT-737 synergizes the antineoplastic activity of proteasome inhibitors in lymphoid malignancies
Authors: Paoluzzi Luca , Gonen Mithat , Bhagat Govind , Furman Richard R. , Gardner Jeffrey R. , Scotto Luigi , Gueorguiev Volodia D. , Heaney Mark L. , Manova Katia , O'Connor Owen A. 
Published: July 2008

AbstractOverexpression of antiapoptotic members of the Bcl-2 family is observed in approximately 80% of B-cell lymphomas, contributing to intrinsic and acquired drug resistance. Nullifying the antiapoptotic influence of these proteins can potentially overcome this resistance, and may complement conventional chemotherapy. ABT-737 is a BH3-only mimetic and potent inhibitor of the antiapoptotic Bcl-2 family members Bcl-2, Bcl-XL, and Bcl-w. In vitro, ABT-737 exhibited concentration-dependent cytotoxicity against a broad panel of lymphoma cell lines including mantle cell lymphoma (MCL) and diffuse large B-cell lymphoma (DLBCL). ABT-737 showed synergism when combined with the proteasome inhibitors bortezomib or carfilzomib in select lymphoma cell lines and induced potent mitochondrial membrane depolarization and apoptosis when combined with either. ABT-737 plus bortezomib also induced significant apoptosis in primary samples of MCL, DLBCL, and chronic lymphocytic leukemia (CLL) but no significant cytotoxic effect was observed in peripheral blood mononuclear cells from healthy donors. In severe combined immunodeficient beige mouse models of MCL, the addition of ABT-737 to bortezomib enhanced efficacy compared with either drug alone and with the control. Collectively, these data suggest that ABT-737 alone or in combination with a proteasome inhibitor represents a novel and potentially important platform for the treatment of B-cell malignancies.
Defective innate immunity predisposes murine neonates to poor sepsis outcome but is reversed by TLR agonists
Authors: Wynn James L. , Scumpia Philip O. , Winfield Robert D. , Delano Matthew J. , Kelly-Scumpia Kindra , Barker Tolga , Ungaro Ricardo , Levy Ofer , Moldawer Lyle L. 
Published: July 2008

AbstractNeonates exhibit an increased risk of sepsis mortality compared with adults. We show that in contrast to adults, survival from polymicrobial sepsis in murine neonates does not depend on an intact adaptive immune system and is not improved by T cell–directed adaptive immunotherapy. Furthermore, neonates manifest an attenuated inflammatory and innate response to sepsis, and have functional defects in their peritoneal CD11b+ cells. Activation of innate immunity with either a Toll-like receptor 4 (TLR4) or TLR7/8 agonist, but not a TLR3 agonist, increased the magnitude, but abbreviated the early systemic inflammatory response, reduced bacteremia, and improved survival to polymicrobial sepsis. TLR4 agonist pretreatment enhanced peritoneal neutrophil recruitment with increased oxidative burst production, whereas the TLR7/8 agonist also enhanced peritoneal neutrophil recruitment with increased phagocytic ability. These benefits were independent of the adaptive immune system and type I interferon signaling. Improving innate immune function with select TLR agonists may be a useful strategy to prevent neonatal sepsis mortality.
Toll-like receptors: lessons to learn from normal and malignant human B cells
Authors: Chiron David , Bekeredjian-Ding Isabelle , Pellat-Deceunynck Catherine , Bataille Régis , Jego Gaëtan 
Published: July 2008

AbstractThe humoral immune system senses microbes via recognition of specific microbial molecular motifs by Toll-like receptors (TLRs). These encounters promote plasma cell differentiation and antibody production. Recent studies have demonstrated the importance of the TLR system in enhancing antibody-mediated defense against infections and maintaining memory B cells. These results have led the way to the design of vaccines that target B cells by engaging TLRs. In hematologic malignancies, cells often retain B cell–specific receptors and associated functions. Among these, TLRs are currently exploited to target different subclasses of B-cell leukemia, and TLR agonists are currently being evaluated in clinical trials. However, accumulating evidence suggests that endogenous TLR ligands or chronic infections promote tumor growth, thus providing a need for further investigations to decipher the exact function of TLRs in the B-cell lineage and in neoplastic B cells. The aim of this review is to present and discuss the latest advances with regard to the expression and function of TLRs in both healthy and malignant B cells. Special attention will be focused on the growth-promoting effects of TLR ligands on leukemic B cells and their potential clinical impact.
HDAC6 inhibition enhances 17-AAG–mediated abrogation of hsp90 chaperone function in human leukemia cells
Authors: Rao Rekha , Fiskus Warren , Yang Yonghua , Lee Pearl , Joshi Rajeshree , Fernandez Pravina , Mandawat Aditya , Atadja Peter , Bradner James E. , Bhalla Kapil 
Published: July 2008

AbstractHistone deacetylase 6 (HDAC6) is a heat shock protein 90 (hsp90) deacetylase. Treatment with pan-HDAC inhibitors or depletion of HDAC6 by siRNA induces hyperacetylation and inhibits ATP binding and chaperone function of hsp90. Treatment with 17-allylamino-demothoxy geldanamycin (17-AAG) also inhibits ATP binding and chaperone function of hsp90, resulting in polyubiquitylation and proteasomal degradation of hsp90 client proteins. In this study, we determined the effect of hsp90 hyperacetylation on the anti-hsp90 and antileukemia activity of 17-AAG. Hyperacetylation of hsp90 increased its binding to 17-AAG, as well as enhanced 17-AAG–mediated attenuation of ATP and the cochaperone p23 binding to hsp90. Notably, treatment with 17-AAG alone also reduced HDAC6 binding to hsp90 and induced hyperacetylation of hsp90. This promoted the proteasomal degradation of HDAC6. Cotreatment with 17-AAG and siRNA to HDAC6 induced more inhibition of hsp90 chaperone function and depletion of BCR-ABL and c-Raf than treatment with either agent alone. In addition, cotreatment with 17-AAG and tubacin augmented the loss of survival of K562 cells and viability of primary acute myeloid leukemia (AML) and chronic myeloid leukemia (CML) samples. These findings demonstrate that HDAC6 is an hsp90 client protein and hyperacetylation of hsp90 augments the anti-hsp90 and antileukemia effects of 17-AAG.
Cytotoxic T lymphocytes directed to the preferentially expressed antigen of melanoma (PRAME) target chronic myeloid leukemia
Authors: Quintarelli Concetta , Dotti Gianpietro , De Angelis Biagio , Hoyos Valentina , Mims Martha , Luciano Luigia , Heslop Helen E. , Rooney Cliona M. , Pane Fabrizio , Savoldo Barbara 
Published: July 2008

Abstract
The cancer testis antigen (CTA) preferentially expressed antigen of melanoma (PRAME) is overexpressed in many hematologic malignancies, including chronic myeloid leukemia (CML). The sensitivity of CML to donor lymphocyte infusion after allogeneic stem cell transplantation suggests this tumor can be highly susceptible to cellular immunotherapy targeted to tumor associated antigens. We therefore tested whether functional PRAME-specific cytotoxic T lymphocytes (PRAME CTLs) could be generated and expanded from healthy donors and CML patients, or whether the limited immunogenicity of this CTA coupled with tumor-associated anergy would preclude this approach. Using optimized culture conditions and HLA-A*02–restricted PRAME-peptides, we have consistently generated PRAME CTLs from 8/9 healthy donors and 5/6 CML patients. These CTLs released IFNγ in response to PRAME peptides (between 113 ± 8 and 795 ± 23 spot forming cells/105 T cells) and lysed PRAME peptide–loaded cells (45 ± 19% at an effector:target [E:T] ratio of 20:1) in a MHC-restricted fashion. Importantly, these CTLs recognized and had cytotoxic activity against HLA-A*02+/PRAME+ tumor cell lines, and could recognize and respond to primary CML cells. PRAME CTLs were generated almost exclusively from the naive T-cell compartment, and clonal analysis showed these cells could have high αβTCR-peptide avidity. PRAME CTLs or vaccines may thus be of value for patients with CML.
Microarray data mining: A novel optimization-based approach to uncover biologically coherent structures
Authors: Tan Meng P , Smith Erin N , Broach James R , Floudas Christodoulos A 
Published: July 2008

Abstract

Background
DNA microarray technology allows for the measurement of genome-wide expression patterns. Within the resultant mass of data lies the problem of analyzing and presenting information on this genomic scale, and a first step towards the rapid and comprehensive interpretation of this data is gene clustering with respect to the expression patterns. Classifying genes into clusters can lead to interesting biological insights. In this study, we describe an iterative clustering approach to uncover biologically coherent structures from DNA microarray data based on a novel clustering algorithm EP_GOS_Clust.

Results
We apply our proposed iterative algorithm to three sets of experimental DNA microarray data from experiments with the yeast Saccharomyces cerevisiae and show that the proposed iterative approach improves biological coherence. Comparison with other clustering techniques suggests that our iterative algorithm provides superior performance with regard to biological coherence. An important consequence of our approach is that an increasing proportion of genes find membership in clusters of high biological coherence and that the average cluster specificity improves.

Conclusion
The results from these clustering experiments provide a robust basis for extracting motifs and trans-acting factors that determine particular patterns of expression. In addition, the biological coherence of the clusters is iteratively assessed independently of the clustering. Thus, this method will not be severely impacted by functional annotations that are missing, inaccurate, or sparse.
Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species
Authors: Keller Oliver , Odronitz Florian , Stanke Mario , Kollmar Martin , Waack Stephan 
Published: July 2008

Abstract

Background
For many types of analyses, data about gene structure and locations of non-coding regions of genes are required. Although a vast amount of genomic sequence data is available, precise annotation of genes is lacking behind. Finding the corresponding gene of a given protein sequence by means of conventional tools is error prone, and cannot be completed without manual inspection, which is time consuming and requires considerable experience.

Results
Scipio is a tool based on the alignment program BLAT to determine the precise gene structure given a protein sequence and a genome sequence. It identifies intron-exon borders and splice sites and is able to cope with sequencing errors and genes spanning several contigs in genomes that have not yet been assembled to supercontigs or chromosomes. Instead of producing a set of hits with varying confidence, Scipio gives the user a coherent summary of locations on the genome that code for the query protein. The output contains information about discrepancies that may result from sequencing errors. Scipio has also successfully been used to find homologous genes in closely related species. Scipio was tested with 979 protein queries against 16 arthropod genomes (intra species search). For cross-species annotation, Scipio was used to annotate 40 genes from Homo sapiens in the primates Pongo pygmaeus abelii and Callithrix jacchus. The prediction quality of Scipio was tested in a comparative study against that of BLAT and the well established program Exonerate.

Conclusion
Scipio is able to precisely map a protein query onto a genome. Even in cases when there are many sequencing errors, or when incomplete genome assemblies lead to hits that stretch across multiple target sequences, it very often provides the user with the correct determination of intron-exon borders and splice sites, showing an improved prediction accuracy compared to BLAT and Exonerate. Apart from being able to find genes in the genome that encode the query protein, Scipio can also be used to annotate genes in closely related species.
Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection
Authors: Jung Inkyung , Lee Jaehyung , Lee Soo-Young , Kim Dongsup 
Published: July 2008

Abstract

Background
Nonnegative matrix factorization (NMF) is a feature extraction method that has the property of intuitive part-based representation of the original features. This unique ability makes NMF a potentially promising method for biological sequence analysis. Here, we apply NMF to fold recognition and remote homolog detection problems. Recent studies have shown that combining support vector machines (SVM) with profile-profile alignments improves performance of fold recognition and remote homolog detection remarkably. However, it is not clear which parts of sequences are essential for the performance improvement.

Results
The performance of fold recognition and remote homolog detection using NMF features is compared to that of the unmodified profile-profile alignment (PPA) features by estimating Receiver Operating Characteristic (ROC) scores. The overall performance is noticeably improved. For fold recognition at the fold level, SVM with NMF features recognize 30% of homolog proteins at > 0.99 ROC scores, while original PPA feature, HHsearch, and PSI-BLAST recognize almost none. For detecting remote homologs that are related at the superfamily level, NMF features also achieve higher performance than the original PPA features. At > 0.90 ROC50 scores, 25% of proteins with NMF features correctly detects remotely related proteins, whereas using original PPA features only 1% of proteins detect remote homologs. In addition, we investigate the effect of number of positive training examples and the number of basis vectors on performance improvement. We also analyze the ability of NMF to extract essential features by comparing NMF basis vectors with functionally important sites and structurally conserved regions of proteins. The results show that NMF basis vectors have significant overlap with functional sites from PROSITE and with structurally conserved regions from the multiple structural alignments generated by MUSTANG. The correlation between NMF basis vectors and biologically essential parts of proteins supports our conjecture that NMF basis vectors can explicitly represent important sites of proteins.

Conclusion
The present work demonstrates that applying NMF to profile-profile alignments can reveal essential features of proteins and that these features significantly improve the performance of fold recognition and remote homolog detection.
Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits
Authors: Mo Delin , Zhu Zhengmao , te Pas Marinus FW , Li Xinyun , Yang Shulin , Wang Heng , Wang Huanling , Li Kui 
Published: July 2008

Abstract

Background
In a previous screen to identify differentially expressed genes associated with embryonic development, the porcine PNAS-4 gene had been found. Considering differentially expressed genes in early stages of muscle development are potential candidate genes to improve meat quality and production efficiency, we determined how porcine PNAS-4 gene regulates meat production. Therefore, this gene has been sequenced, expression analyzed and associated with meat production traits.

Results
We cloned the full-length cDNA of porcine PNAS-4 gene encoding a protein of 194 amino acids which was expressed in the Golgi complex. This gene was mapped to chromosome 10, q11–16, in a region of conserved synteny with human chromosome 1 where the human homologous gene was localized. Real-time PCR revealed that PNAS-4 mRNA was widely expressed with highest expression levels in skeletal muscle followed by lymph, liver and other tissues, and showed a down-regulated expression pattern during prenatal development while a up-regulated expression pattern after weaning. Association analysis revealed that allele C of SNP A1813C was prevalent in Chinese indigenous breeds whereas A was dominant allele in Landrace and Large White, and the pigs with homozygous CC had a higher fat content than those of the pigs with other genotypes (P < 0.05).

Conclusion
Porcine PNAS-4 protein tagged with green fluorescent protein accumulated in the Golgi complex, and its mRNA showed a widespread expression across many tissues and organs in pigs. It may be an important factor affecting the meat production efficiency, because its down-regulated expression pattern during early embryogenesis suggests involvement in increase of muscle fiber number. In addition, the SNP A1813C associated with fat traits might be a genetic marker for molecular-assisted selection in animal breeding.
High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome
Authors: Novaes Evandro , Drost Derek R , Farmerie William G , Pappas Georgios J , Grattapaglia Dario , Sederoff Ronald R , Kirst Matias 
Published: July 2008

Abstract

Background
Benefits from high-throughput sequencing using 454 pyrosequencing technology may be most apparent for species with high societal or economic value but few genomic resources. Rapid means of gene sequence and SNP discovery using this novel sequencing technology provide a set of baseline tools for genome-level research. However, it is questionable how effective the sequencing of large numbers of short reads for species with essentially no prior gene sequence information will support contig assemblies and sequence annotation.

Results
With the purpose of generating the first broad survey of gene sequences in Eucalyptus grandis, the most widely planted hardwood tree species, we used 454 technology to sequence and assemble 148 Mbp of expressed sequences (EST). EST sequences were generated from a normalized cDNA pool comprised of multiple tissues and genotypes, promoting discovery of homologues to almost half of Arabidopsis genes, and a comprehensive survey of allelic variation in the transcriptome. By aligning the sequencing reads from multiple genotypes we detected 23,742 SNPs, 83% of which were validated in a sample. Genome-wide nucleotide diversity was estimated for 2,392 contigs using a modified theta (θ) parameter, adapted for measuring genetic diversity from polymorphisms detected by randomly sequencing a multi-genotype cDNA pool. Diversity estimates in non-synonymous nucleotides were on average 4x smaller than in synonymous, suggesting purifying selection. Non-synonymous to synonymous substitutions (Ka/Ks) among 2,001 contigs averaged 0.30 and was skewed to the right, further supporting that most genes are under purifying selection. Comparison of these estimates among contigs identified major functional classes of genes under purifying and diversifying selection in agreement with previous researches.

Conclusion
In providing an abundance of foundational transcript sequences where limited prior genomic information existed, this work created part of the foundation for the annotation of the E. grandis genome that is being sequenced by the US Department of Energy. In addition we demonstrated that SNPs sampled in large-scale with 454 pyrosequencing can be used to detect evolutionary signatures among genes, providing one of the first genome-wide assessments of nucleotide diversity and Ka/Ks for a non-model plant species.