bluuebunny/crossref_metadata_2025_split huggingface dataset:
GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed
Authors: Chen Rong , Mallelwar Rohan , Thosar Ajit , Venkatasubrahmanyam Shivkumar , Butte Atul J 
Published: December 2008

Abstract

Background
The amount of gene expression data in the public repositories, such as NCBI Gene Expression Omnibus (GEO) has grown exponentially, and provides a gold mine for bioinformaticians, but has not been easily accessible by biologists and clinicians.

Results
We developed an automated approach to annotate and analyze all GEO data sets, including 1,515 GEO data sets from 231 microarray types across 42 species, and performed 12,658 group versus group comparisons of 24 GEO-specified types. We then built GeneChaser, a web server that enables biologists and clinicians without bioinformatics skills to easily identify biological and clinical conditions in which a gene or set of genes was differentially expressed. GeneChaser displays these conditions in graphs, gives statistical comparisons, allows sort/filter functions and provides access to the original studies.
We performed a single gene search for Nanog and a multiple gene search for Nanog, Oct4, Sox2 and LIN28, confirmed their roles in embryonic stem cell development, identified several drugs that regulate their expression, and suggested their potential roles in sex determination, abnormal sperm morphology, malaria infection, and cancer.

Conclusion
We demonstrated that GeneChaser is a powerful tool to elucidate information on function, transcriptional regulation, drug-response and clinical implications for genes of interest.
nGASP – the nematode genome annotation assessment project
Authors: Coghlan Avril , Fiedler Tristan J , McKay Sheldon J , Flicek Paul , Harris Todd W , Blasiar Darin ,   the nGASP Consortium, Stein Lincoln D 
Published: December 2008

Abstract

Background
While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets across 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase.

Results
The most accurate gene-finders were 'combiner' algorithms, which made use of transcript- and protein-alignments and multi-genome alignments, as well as gene predictions from other gene-finders. Gene-finders that used alignments of ESTs, mRNAs and proteins came in second. There was a tie for third place between gene-finders that used multi-genome alignments and ab initio gene-finders. The median gene level sensitivity of combiners was 78% and their specificity was 42%, which is nearly the same accuracy reported for combiners in the human genome. C. elegans genes with exons of unusual hexamer content, as well as those with unusually many exons, short exons, long introns, a weak translation start signal, weak splice sites, or poorly conserved orthologs posed the greatest difficulty for gene-finders.

Conclusion
This experiment establishes a baseline of gene prediction accuracy in Caenorhabditis genomes, and has guided the choice of gene-finders for the annotation of newly sequenced genomes of Caenorhabditis and other nematode species. We have created new gene sets for C. briggsae, C. remanei, C. brenneri, C. japonica, and Brugia malayi using some of the best-performing gene-finders.
Genome wide association for substance dependence: convergent results from epidemiologic and research volunteer samples
Authors: Johnson Catherine , Drgon Tomas , Liu Qing-Rong , Zhang Ping-Wu , Walther Donna , Li Chuan-Yun , Anthony James C , Ding Yulan , Eaton William W , Uhl George R 
Published: December 2008

Abstract

Background
Dependences on addictive substances are substantially-heritable complex disorders whose molecular genetic bases have been partially elucidated by studies that have largely focused on research volunteers, including those recruited in Baltimore. Maryland. Subjects recruited from the Baltimore site of the Epidemiological Catchment Area (ECA) study provide a potentially-useful comparison group for possible confounding features that might arise from selecting research volunteer samples of substance dependent and control individuals. We now report novel SNP (single nucleotide polymorphism) genome wide association (GWA) results for vulnerability to substance dependence in ECA participants, who were initially ascertained as members of a probability sample from Baltimore, and compare the results to those from ethnically-matched Baltimore research volunteers.

Results
We identify substantial overlap between the home address zip codes reported by members of these two samples. We find overlapping clusters of SNPs whose allele frequencies differ with nominal significance between substance dependent vs control individuals in both samples. These overlapping clusters of nominally-positive SNPs identify 172 genes in ways that are never found by chance in Monte Carlo simulation studies. Comparison with data from human expressed sequence tags suggests that these genes are expressed in brain, especially in hippocampus and amygdala, to extents that are greater than chance.

Conclusion
The convergent results from these probability sample and research volunteer sample datasets support prior genome wide association results. They fail to support the idea that large portions of the molecular genetic results for vulnerability to substance dependence derive from factors that are limited to research volunteers.
Class I histone deacetylases 1, 2 and 3 are highly expressed in renal cell cancer
Authors: Fritzsche Florian R , Weichert Wilko , Röske Annika , Gekeler Volker , Beckers Thomas , Stephan Carsten , Jung Klaus , Scholman Katharina , Denkert Carsten , Dietel Manfred , Kristiansen Glen 
Published: December 2008

Abstract

Background
Enhanced activity of histone deacetylases (HDAC) is associated with more aggressive tumour behaviour and tumour progression in various solid tumours. The over-expression of these proteins and their known functions in malignant neoplasms has led to the development of HDAC inhibitors (HDI) as new anti-neoplastic drugs. However, little is known about HDAC expression in renal cell cancer.

Methods
We investigated the expression of HDAC 1, 2 and 3 in 106 renal cell carcinomas and corresponding normal renal tissue by immunohistochemistry on tissue micro arrays and correlated expression data with clinico-pathological parameters including patient survival.

Results
Almost 60% of renal cell carcinomas expressed the HDAC isoforms 1 and 2. In contrast, HDAC 3 was only detected in 13% of all renal tumours, with particular low expression rates in the clear cell subtype. HDAC 3 was significantly higher expressed in pT1/2 tumours in comparison to pT3/4 tumours. Expression of class I HDAC isoforms correlated with each other and with the proliferative activity of the tumours. We found no prognostic value of the expression of any of the HDAC isoforms in this tumour entity.

Conclusion
Class I HDAC isoforms 1 and 2 are highly expressed in renal cell cancer, while HDAC 3 shows low, histology dependent expression rates. These unexpected differences in the expression patterns suggests alternative regulatory mechanisms of class I HDACs in renal cell cancer and should be taken into account when trials with isoform selective HDI are being planned. Whether HDAC expression in renal cancers is predictive of responsiveness for HDI will have to be tested in further studies.
Provincial prenatal record revision: a multiple case study of evidence-based decision-making at the population-policy level
Authors: Edwards Nancy , Semenic Sonia , Premji Shahirose , Montgomery Phyllis , Williams Beverly , Olson Joanne , Mansi Omaima 
Published: December 2008

Abstract

Background
There is a significant gap in the knowledge translation literature related to how research evidence actually contributes to health care decision-making. Decisions around what care to provide at the population (rather than individual) level are particularly complex, involving considerations such as feasibility, cost, and population needs in addition to scientific evidence. One example of decision-making at this "population-policy" level involves what screening questions and intervention guides to include on standardized provincial prenatal records. As mandatory medical reporting forms, prenatal records are potentially powerful vehicles for promoting population-wide evidence-based care. However, the extent to which Canadian prenatal records reflect best-practice recommendations for the assessment of well-known risk factors such as maternal smoking and alcohol consumption varies markedly across Canadian provinces and territories. The goal of this study is to better understand the interaction of contextual factors and research evidence on decision-making at the population-policy level, by examining the processes by which provincial prenatal records are reviewed and revised.

Methods
Guided by Dobrow et al.'s (2004) conceptual model for context-based evidence-based decision-making, this study will use a multiple case study design with embedded units of analysis to examine contextual factors influencing the prenatal record revision process in different Canadian provinces and territories. Data will be collected using multiple methods to construct detailed case descriptions for each province/territory. Using qualitative data analysis techniques, decision-making processes involving prenatal record content specifically related to maternal smoking and alcohol use will be compared both within and across each case, to identify key contextual factors influencing the uptake and application of research evidence by prenatal record review committees. All study participants will be required to give written informed consent prior to participating in data collection.

Conclusion
This study will advance knowledge in the field of evidence-based decision-making by illustrating the complex interaction of contextual factors and evidence on health policy decision-making by provincial-level committees. By increasing the transparency of decision-making within provincial prenatal record committees, this study will help inform more effective strategies for enhancing the integration of best-practice evidence into prenatal records.
Monocytes are essential for inhibition of synovial T-cell glucocorticoid-mediated apoptosis in rheumatoid arthritis
Authors: Makrygiannakis Dimitrios , Revu Shankar , Neregård Petra , af Klint Erik , Snir Omri , Grundtman Cecilia , Catrina Anca Irinel 
Published: December 2008

Abstract
Introduction
Rheumatoid arthritis (RA) is characterized by synovial inflammation with local accumulation of mononuclear cells such as macrophages and lymphocytes. We previously demonstrated that intra-articular glucocorticoids decrease the synovial tissue (ST) T-cell population and therefore aimed to investigate whether this is mediated through modulation of apoptosis.

Methods
Apoptosis and cell phenotype were evaluated by immunohistochemistry and dual-immunofluorescence in synovial biopsy sections from 12 RA patients before and after a mean of 11 days of an intra-articular triamcinolone knee injection. In vitro, RA synovial fluid (SF)-derived T cells were evaluated for Annexin V expression by multicolor flow cytometry after 24-hour exposure to dexamethasone, methylprednisolone, or triamcinolone. We also tested induction of apoptosis by dexamethasone on psoriatic arthritis SF-derived T cells using the same method.

Results
Intra-articular glucocorticoids reduced ST T cells but not macrophage number. ST apoptosis levels were unchanged following treatment, virtually absent from lymphoid aggregates, and minimal in CD3+ cells both before and after treatment. RA SF T cells were resistant to glucocorticoid-induced apoptosis when cultured in the presence of monocytes but were rendered sensitive to all three tested compounds upon SF isolation. Furthermore, transwell coculture of monocytes and T cells demonstrated that soluble factor(s) and not cellular contact are essential for T-cell resistance to glucocorticoid-mediated apoptosis. This feature is RA-specific as far as dexamethasone-induced apoptosis in nonisolated SF T cells obtained from psoriatic arthritis patients is concerned.

Conclusions
We demonstrate that monocytes rescue synovial T cells from glucocorticoid-induced apoptosis, a feature that is specific for RA. To overcome this, we propose the use of monocyte-targeted therapies rather than T-cell apoptosis-inducing therapies.
Singular value decomposition-based regression identifies activation of endogenous signaling pathways in vivo
Authors: Liu Zhandong , Wang Min , Alvarez James V , Bonney Megan E , Chen Chien-chung , D'Cruz Celina , Pan Tien-chi , Tadesse Mahlet G , Chodosh Lewis A 
Published: December 2008

AbstractThe ability to detect activation of signaling pathways based solely on gene expression data represents an important goal in biological research. We tested the sensitivity of singular value decomposition-based regression by focusing on functional interactions between the Ras and transforming growth factor beta signaling pathways. Our findings demonstrate that this approach is sufficiently sensitive to detect the secondary activation of endogenous signaling pathways as it occurs through crosstalk following ectopic activation of a primary pathway.
Male reproductive development: gene expression profiling of maize anther and pollen ontogeny
Authors: Ma Jiong , Skibbe David S , Fernandes John , Walbot Virginia 
Published: December 2008

Abstract
Background
During flowering, central anther cells switch from mitosis to meiosis, ultimately forming pollen containing haploid sperm. Four rings of surrounding somatic cells differentiate to support first meiosis and later pollen dispersal. Synchronous development of many anthers per tassel and within each anther facilitates dissection of carefully staged maize anthers for transcriptome profiling.

Results
Global gene expression profiles of 7 stages representing 29 days of anther development are analyzed using a 44 K oligonucleotide array querying approximately 80% of maize protein-coding genes. Mature haploid pollen containing just two cell types expresses 10,000 transcripts. Anthers contain 5 major cell types and express >24,000 transcript types: each anther stage expresses approximately 10,000 constitutive and approximately 10,000 or more transcripts restricted to one or a few stages. The lowest complexity is present during meiosis. Large suites of stage-specific and co-expressed genes are identified through Gene Ontology and clustering analyses as functional classes for pre-meiotic, meiotic, and post-meiotic anther development. MADS box and zinc finger transcription factors with constitutive and stage-limited expression are identified.

Conclusions
We propose that the extensive gene expression of anther cells and pollen represents the key test of maize genome fitness, permitting strong selection against deleterious alleles in diploid anthers and haploid pollen. Because flowering plants show a substantial bias for male-sterile compared to female-sterile mutations, we propose that this fitness test is general. Because both somatic and germinal cells are transcriptionally quiescent during meiosis, we hypothesize that successful completion of meiosis is required to trigger maturation of anther somatic cells.
Adenosine and IFN-α synergistically increase IFN-γ production of human NK cells
Authors: Jeffe Florian , Stegmann Kerstin A , Broelsch Felix , Manns Michael P , Cornberg Markus , Wedemeyer Heiner 
Published: December 2008

AbstractPrevention of overwhelming immune reactions is essential for an organism to survive. Adenosine, a ribonucleoside produced by various cell types during inflammatory processes, has been shown to inhibit effector functions of different immune cells. Here, we show that the adenosine A3 receptor agonist iodobenzyl methylcarboxamidoadenosine potently inhibited proliferation, IFN-γ production, and cytotoxicity of activated human lymphoid cells. Stimulation of the A3 receptor also caused apoptosis of activated PBMC. However, when PBMC were stimulated with IFN-α, adenosine did not decrease, but synergistically increased, the IFN-γ production of NK cells. This effect was also mediated mainly via the A3 receptor. Thus, our data suggest that adenosine differentially contributes to the regulation of immune responses during inflammatory processes: It may increase effector functions of NK cells in combination with IFN-α but also prevents overwhelming immune responses by inhibiting proliferation and induction of apoptosis of activated lymphoid cells. Future studies need to define the role of the different adenosine receptors in more detail.
Human eosinophils constitutively express multiple Th1, Th2, and immunoregulatory cytokines that are secreted rapidly and differentially
Authors: Spencer Lisa A , Szela Craig T , Perez Sandra A C , Kirchhoffer Casey L , Neves Josiane S , Radke Amy L , Weller Peter F 
Published: December 2008

AbstractEosinophils are innate immune leukocytes implicated in the initiation and maintenance of type 2 immune responses, including asthma and allergy. The ability to store and rapidly secrete preformed cytokines distinguishes eosinophils from most lymphocytes, which must synthesize cytokine proteins prior to secretion and may be a factor in the apparent Th2 bias of eosinophils. Multiple studies confirm that human eosinophils from atopic or hypereosinophilic donors can secrete over 30 cytokines with a varying and often opposing immune-polarizing potential. However, it remains unclear whether all of these cytokines are constitutively preformed and available for rapid secretion from eosinophils in the circulation of healthy individuals or are restricted to eosinophils from atopic donors. Likewise, the relative concentrations of cytokines stored within eosinophils have not been studied. Here, we demonstrate that human blood eosinophils are not singularly outfitted with Th2-associated cytokines but rather, constitutively store a cache of cytokines with nominal Th1, Th2, and regulatory capacities, including IL-4, IL-13, IL-6, IL-10, IL-12, IFN-γ, and TNF-α. We demonstrate further rapid and differential release of each cytokine in response to specific stimuli. As agonists, strong Th1 and inflammatory cytokines elicited release of Th2-promoting IL-4 but not Th1-inducing IL-12. Moreover, a large quantity of IFN-γ was secreted in response to Th1, Th2, and inflammatory stimuli. Delineations of the multifarious nature of preformed eosinophil cytokines and the varied stimulus-dependent profiles of rapid cytokine secretion provide insights into the functions of human eosinophils in mediating inflammation and initiation of specific immunity.
Statins alter neutrophil migration by modulating cellular Rho activity—a potential mechanism for statins-mediated pleotropic effects?
Authors: Maher B M , Dhonnchu T Ni , Burke J P , Soo A , Wood A E , Watson R W G 
Published: December 2008

AbstractThe ability of neutrophils to sense and migrate toward damaged tissue is a vital component of the innate immune response. Paradoxically, this same migration serves as the hallmark of a number of inflammatory conditions, including ischemic reperfusion injury, atherosclerosis, arthritis, and Crohn’s disease. More recent evidence suggests that neutrophil infiltration into the cardiac allograft following transplantation is a contributing factor in allograft rejection. We have demonstrated previously a positive correlation between the degree of neutrophil migration and subsequent rejection grades in a cohort of cardiac transplant recipients. Intracellular signaling pathways that are intimately involved in neutrophil migration thus offer potential targets of manipulation in the treatment of such conditions. 3-Hydroxy-3-methylyglutaryl-coenzyme A reductase inhibitors or statins are emerging as potential anti-inflammatory agents and have a proven survival benefit in the transplant population. Yet, little is known about their ability to modulate neutrophil function and their subsequent mechanism of action. We demonstrate here that pravastatin, simvastatin, and atorvastatin significantly reduce neutrophil transendothelial migration toward the chemoattractant fMLP. This effect is independent of any change in neutrophil adhesion or adhesion molecule expression but is related to the ability of statins to reduce fMLP-induced Rho activity in neutrophils. This was confirmed by the ability of the Rho precursor geranylgeranyl pyrophosphate to rescue the statin-mediated reduction in neutrophil transendothelial migration. Understanding the mechanisms of action of statins in the neutrophil allows for their use in targeting excessive migration in inappropriate inflammatory conditions.
Inhibition of spontaneous neutrophil apoptosis by parabutoporin acts independently of NADPH oxidase inhibition but by lipid raft-dependent stimulation of Akt
Authors: Remijsen Quinten , Vanden Berghe Tom , Parthoens Eef , Asselbergh Bob , Vandenabeele Peter , Willems Jean 
Published: December 2008

AbstractNeutrophil cell death plays a crucial role in neutrophil homeostasis and the resolution of inflammation. The superoxide-producing NADPH oxidase is involved in pathogen degradation and subsequent activation of cell death programs. Neutrophils from patients with chronic granulomatous disease, who have a deficient NADPH oxidase activity, have been demonstrated previously to have a prolonged lifespan, suggesting that a basal NADPH oxidase activity also regulates spontaneous neutrophil turnover. The NADPH oxidase inhibitor parabutoporin (PP) does delay spontaneous apoptosis, but this effect is completely independent of NADPH oxidase inhibition. Instead, the prosurvival effect of PP depends on activation of protein kinase B/Akt via lipid raft signaling. Disruption of lipid rafts abrogates the prosurvival effect without interfering with NADPH oxidase activity. Furthermore, we cannot detect a different rate of spontaneous apoptosis between normal and NADPH oxidase-deficient neutrophils, arguing against a role of NADPH oxidase in spontaneous neutrophil apoptosis.
Molecular Mechanism of Action of Pharmacoperone Rescue of Misrouted GPCR Mutants: The GnRH Receptor
Authors: Janovick Jo Ann , Patny Akshay , Mosley Ralph , Goulet Mark T. , Altman Michael D. , Rush Thomas S. , Cornea Anda , Conn P. Michael 
Published: December 2008

Abstract
The human GnRH receptor (hGnRHR), a G protein-coupled receptor, is a useful model for studying pharmacological chaperones (pharmacoperones), drugs that rescue misfolded and misrouted protein mutants and restore them to function. This technique forms the basis of a therapeutic approach of rescuing mutants associated with human disease and restoring them to function. The present study relies on computational modeling, followed by site-directed mutagenesis, assessment of ligand binding, effector activation, and confocal microscopy. Our results show that two different chemical classes of pharmacoperones act to stabilize hGnRHR mutants by bridging residues D98 and K121. This ligand-mediated bridge serves as a surrogate for a naturally occurring and highly conserved salt bridge (E90–K121) that stabilizes the relation between transmembranes 2 and 3, which is required for passage of the receptor through the cellular quality control system and to the plasma membrane. Our model was used to reveal important pharmacophoric features, and then identify a novel chemical ligand, which was able to rescue a D98 mutant of the hGnRHR that could not be rescued as effectively by previously known pharmacoperones.