pmcid string | abstract string | text string | metadata dict |
|---|---|---|---|
PMC509407 | How growth regulators provoke context-specific signals is a fundamental question in developmental biology. In plants, both auxin and brassinosteroids (BRs) promote cell expansion, and it was thought that they activated this process through independent mechanisms. In this work, we describe a shared auxin:BR pathway requ... | # Introduction
The continuous shaping of plant form is a marvel of signal integration. In early seedling development this is particularly clear, as environmental cues, such as light, profoundly alter the innate morphogenetic program. How diverse pathways merge to determine a discrete cellular growth response is largel... | {
"pmid": "15328536",
"doi": "10.1371/journal.pbio.0020258",
"article_title": "Interdependency of Brassinosteroid and Auxin Signaling in Arabidopsis",
"journal_title": "PLoS Biology",
"epub": "2004-08-24 00:00:00",
"authors": [
"Jennifer L Nemhauser",
"Todd C Mockler",
"Joanne Chory"
],
"art... |
PMC509408 | The visual cortex responds to repeated presentations of the same stimulus with high variability. Because the firing mechanism is remarkably noiseless, the source of this variability is thought to lie in the membrane potential fluctuations that result from summated synaptic input. Here this hypothesis is tested through ... | # Introduction
In the primary visual cortex (V1), different trials of presentation of an identical stimulus yield highly variable firing rates [CIT_REF]. This trial-to-trial variability is not inherited from subcortical inputs, as these respond in a much more consistent fashion [CIT_REF]. Instead, variability has been... | {
"pmid": "15328535",
"doi": "10.1371/journal.pbio.0020264",
"article_title": "Amplification of Trial-to-Trial Response Variability by Neurons in Visual Cortex",
"journal_title": "PLoS Biology",
"epub": "2004-08-24 00:00:00",
"authors": [
"Matteo Carandini"
],
"article_type": "research-article",
"... |
PMC509409 | Prostate cancer is a leading killer of men in the industrialized world. Underlying this disease is the aberrant action of the androgen receptor (AR). AR is distinguished from other nuclear receptors in that after hormone binding, it preferentially responds to a specialized set of coactivators bearing aromatic-rich moti... | # Introduction
The androgen receptor (AR) is the cellular mediator of the actions of the hormone 5-α dihydrotestosterone (DHT). Androgen binding to AR leads to activation of genes involved in the development and maintenance of the male reproductive system and other tissues such as bone and muscle. However, it is the p... | {
"pmid": "15328534",
"doi": "10.1371/journal.pbio.0020274",
"article_title": "Recognition and Accommodation at the Androgen Receptor Coactivator Binding Interface",
"journal_title": "PLoS Biology",
"epub": "2004-08-24 00:00:00",
"authors": [
"Eugene Hur",
"Samuel J Pfaff",
"E. Sturgis Payne",
... |
PMC509418 | # Background
Establishing genomic resources for closely related species will provide comparative insights that are crucial for understanding diversity and variability at multiple levels of biological organization. We developed ESTs for Mexican axolotl (Ambystoma mexicanum) and Eastern tiger salamander (A. tigrinum tig... | # Background
Establishing genomic resources for closely related species will provide comparative insights that are crucial for understanding diversity and variability at multiple levels of biological organization. Expressed sequence tags (EST) are particularly useful genomic resources because they enable multiple line... | {
"pmid": "15310388",
"doi": "10.1186/1471-2164-5-54",
"article_title": "From biomedicine to natural history research: EST resources for ambystomatid salamanders",
"journal_title": "",
"epub": "2004-08-13 00:00:00",
"authors": [
"Srikrishna Putta",
"Jeramiah J Smith",
"John A Walker",
"Mathi... |
PMC509421 | # Background
It has been suggested that lithium increases choline concentrations, although previous human studies examining this possibility using^{1}H magnetic resonance spectroscopy (^{1}H MRS) have had mixed results: some found increases while most found no differences.
# Methods
The present study utilized^{1}H M... | # Background
Bipolar disorder is a chronic severe mental illness affecting approximately 1% of the adult population. The most widely used mood stabilizer for this condition is lithium [CIT_REF], although the exact mechanism by which it is clinically effective remains undetermined. One suggestion is that it acts via ef... | {
"pmid": "15283867",
"doi": "10.1186/1475-2832-3-13",
"article_title": "Brain choline concentrations may not be altered in euthymic bipolar disorder patients chronically treated with either lithium or sodium valproate",
"journal_title": "",
"epub": "2004-07-30 00:00:00",
"authors": [
"Ren H Wu",
"T... |
PMC509425 | # Background
Dendritic Cell (DC) vaccination is a very promising therapeutic strategy in cancer patients. The immunizing ability of DC is critically influenced by their migration activity to lymphatic tissues, where they have the task of priming naïve T-cells. In the present study in vivo DC migration was investigated... | # Background
Dendritic Cell (DC) vaccination is one of the most promising tools of immunological therapy for cancer. Administration of DC, generated and loaded with tumor antigens ex vivo, can be used to circumvent tumor immunotolerance [CIT_REF]. A large number of immature DC (iDC) can be produced by culturing periph... | {
"pmid": "15285807",
"doi": "10.1186/1479-5876-2-27",
"article_title": "Evaluation of in vivo labelled dendritic cell migration in cancer patients",
"journal_title": "",
"epub": "2004-07-30 00:00:00",
"authors": [
"Ruggero Ridolfi",
"Angela Riccobon",
"Riccardo Galassi",
"Gianluigi Giorgett... |
PMC509426 | # Background
While the basic ethical issues regarding consent may be universal to all countries, the consent procedures required by international review boards which include detailed scientific and legal information, may not be optimal when administered within certain populations. The time and the technicalities of th... | # Background
It is estimated that nearly 7.2 million people in Asia and the Pacific region are now living with HIV/AIDS, one million of whom acquired the virus in 2002 [CIT_REF]. Of these, more than 2.4 million are women (ages 15–45) [CIT_REF]. India's national HIV prevalence rate of less than 1% offers little indicat... | {
"pmid": "15287983",
"doi": "10.1186/1741-7015-2-28",
"article_title": "Optimizing the HIV/AIDS informed consent process in India",
"journal_title": "",
"epub": "2004-08-02 00:00:00",
"authors": [
"J Sastry",
"H Pisal",
"S Sutar",
"N Kapadia-Kundu",
"A Joshi",
"N Suryavanshi",
"... |
PMC509428 | # Background
In the microarray experiment, many undesirable systematic variations are commonly observed. Normalization is the process of removing such variation that affects the measured gene expression levels. Normalization plays an important role in the earlier stage of microarray data analysis. The subsequent analy... | # Background
cDNA microarrays consist of thousands of individual DNA sequences printed in a high density array on a glass slide. After being reverse-transcribed into cDNA and labeled using red (Cy5) and green (Cy3) fluorescent dyes, two target mRNA samples are hybridized with the arrayed DNA sequences or probes. Then,... | {
"pmid": "15268767",
"doi": "10.1186/1471-2105-5-97",
"article_title": "Two-stage normalization using background intensities in cDNA microarray data",
"journal_title": "",
"epub": "2004-07-21 00:00:00",
"authors": [
"Dankyu Yoon",
"Sung-Gon Yi",
"Ju-Han Kim",
"Taesung Park"
],
"article_... |
PMC512282 | # Background
The mammalian retina is a valuable model system to study neuronal biology in health and disease. To obtain insight into intrinsic processes of the retina, great efforts are directed towards the identification and characterization of transcripts with functional relevance to this tissue.
# Results
With th... | # Background
The mammalian retina is a highly structured tissue developmentally originating from neuroectodermal evagination of the diencephalon and subsequent invagination processes resulting in the formation of two cellular layers which ultimately give rise to the inner neural retina and the outer retinal pigment ep... | {
"pmid": "15283859",
"doi": "10.1186/1471-2164-5-50",
"article_title": "The Retinome – Defining a reference transcriptome of the adult mammalian retina/retinal pigment epithelium",
"journal_title": "",
"epub": "2004-07-29 00:00:00",
"authors": [
"Heidi L Schulz",
"Thomas Goetz",
"Juergen Kaschk... |
PMC512283 | # Background
Global gene expression studies with microarrays can offer biological insights never before possible. However, the technology possesses many sources of technical variability that are an obstacle to obtaining high quality data sets. Since spotted microarrays offer design/content flexibility and potential co... | # Background
The generation of reliable gene expression data with cDNA microarrays requires fabrication of quality arrays. This task encompasses the amplification of adequate amounts of concentrated PCR product for use as probe from the cDNA clone, followed by ordered arraying of the probes onto coated glass slides. T... | {
"pmid": "15294027",
"doi": "10.1186/1471-2164-5-53",
"article_title": "Immobilized probe and glass surface chemistry as variables in microarray fabrication",
"journal_title": "",
"epub": "2004-08-04 00:00:00",
"authors": [
"Martin J Hessner",
"Lisa Meyer",
"Jennifer Tackes",
"Sanaa Muheise... |
PMC512284 | # Background
Going from a gene sequence to its function in the context of a whole organism requires a strategy for targeting mutations, referred to as reverse genetics. Reverse genetics is highly desirable in the modern genomics era; however, the most powerful methods are generally restricted to a few model organisms.... | # Background
Rapid progress being made in genome sequencing projects provides raw material for the potential understanding of gene function, so effective reverse genetic strategies are increasingly in demand [CIT_REF]. Sequence information alone may be sufficient to consider a gene to be of interest, because sequence ... | {
"pmid": "15282033",
"doi": "10.1186/1471-2229-4-12",
"article_title": "Discovery of induced point mutations in maize genes by TILLING",
"journal_title": "",
"epub": "2004-07-28 00:00:00",
"authors": [
"Bradley J Till",
"Steven H Reynolds",
"Clifford Weil",
"Nathan Springer",
"Chris Bur... |
PMC512285 | # Background
The management of acute myocardial infarction (AMI) has improved over the last 50 years with the more frequent use of effective medicines and procedures. The clinical benefit of the speciality of the attending physician is less clear. The United Kingdom National Service Framework for coronary heart diseas... | # Background
The management of acute myocardial infarction (AMI) has improved over the last 50 years with the more frequent use of effective medicines and procedures. The clinical benefit of the speciality of the attending physician is less clear. The effect of the speciality of the attending physician on mortality in... | {
"pmid": "15298699",
"doi": "10.1186/1471-2261-4-14",
"article_title": "Outcome after acute myocardial infarction: a comparison of patients seen by cardiologists and general physicians",
"journal_title": "",
"epub": "2004-08-06 00:00:00",
"authors": [
"Ibrahim Abubakar",
"David Kanka",
"Barbara... |
PMC512286 | # Background
The 6 minutes walk test (6MWT) is a useful assessment instrument for the exercise capacity of elderly persons. The impact of the health status on the 6MWT-distance in elderly, however, remains unclear, reducing its value in clinical settings. The objective of this study was to investigate to what extent t... | # Background
Aging results in an important decrease of muscle power and exercise capacity[CIT_REF]. Therefore, elderly often function at the limit of their capacity in order to fulfill the activities of daily living [CIT_REF]. Determination of the remaining physical capacity can be important in clinical decision-makin... | {
"pmid": "15272934",
"doi": "10.1186/1471-2318-4-6",
"article_title": "The six-minute walk test in community dwelling elderly: influence of health status.",
"journal_title": "",
"epub": "2004-07-23 00:00:00",
"authors": [
"Ivan Bautmans",
"Margareta Lambert",
"Tony Mets"
],
"article_type": ... |
PMC512288 | # Background
To determine whether previously reported loci predisposing to nonsyndromic high myopia show linkage to common myopia in pedigrees from two ethnic groups: Ashkenazi Jewish and Amish. We hypothesized that these high myopia loci might exhibit allelic heterogeneity and be responsible for moderate /mild or com... | # Background
Myopia is one of the leading causes of vision loss around the world[CIT_REF]. In the United States, myopia affects approximately 25% of adult Americans[CIT_REF]. Ethnic diversity appears to distinguish different groups with regard to prevalence. Caucasians have a higher prevalence than African Americans[C... | {
"pmid": "15291966",
"doi": "10.1186/1471-2350-5-20",
"article_title": "Candidate high myopia loci on chromosomes 18p and 12q do not play a major role in susceptibility to common myopia",
"journal_title": "",
"epub": "2004-08-03 00:00:00",
"authors": [
"Grace Ibay",
"Betty Doan",
"Lauren Reider... |
PMC512290 | # Background
Matrix metalloproteinases [MMPs], which degrade the extracellular matrix, play an important role in the invasion and metastasis of squamous cell carcinomas. One MMP, MMP-13, is thought to play a central role in MMP activation. The purpose of this study was to investigate MMP-13 and TIMP-1 expression in sq... | # Background
The invasion of surrounding tissues by neoplastic cells is one of the most important steps in tumor progression. Proteolytic enzymes such as matrix metalloproteinases [MMPs] contribute to tumor expansion by degrading components of the extracellular matrix [ECM]. MMPs are a 21-member family of zinc-depende... | {
"pmid": "15291964",
"doi": "10.1186/1471-2407-4-42",
"article_title": "Elevated expression of MMP-13 and TIMP-1 in head and neck squamous cell carcinomas may reflect increased tumor invasiveness",
"journal_title": "",
"epub": "2004-08-03 00:00:00",
"authors": [
"Nil Culhaci",
"Kubilay Metin",
... |
PMC512291 | # Background
The Hedgehog (Hh) signaling pathway regulates a variety of developmental processes, including vasculogenesis, and can also induce the expression of pro-angiogenic factors in fibroblasts postnatally. Misregulation of the Hh pathway has been implicated in a variety of different types of cancer, including pa... | # Background
The Hedgehog family of genes encodes secreted signaling molecules that regulate cell proliferation and cell fate determination. In mammals, there are three such genes: Sonic hedgehog (Shh), Indian hedgehog (Ihh), and Desert hedgehog (Dhh). All three Hedgehog (Hh) proteins function by binding to the transm... | {
"pmid": "15294024",
"doi": "10.1186/1471-2407-4-43",
"article_title": "Hedgehog-interacting protein is highly expressed in endothelial cells but down-regulated during angiogenesis and in several human tumors",
"journal_title": "",
"epub": "2004-08-04 00:00:00",
"authors": [
"Catherine L Olsen",
"P... |
PMC512292 | # Background
The fusion protein RUNX1-CBFA2T1 associated with t(8;21)-positive acute myeloid leukaemia is a potent inhibitor of haematopoetic differentiation. The role of RUNX1-CBFA2T1 in leukaemic cell proliferation is less clear. We examined the consequences of siRNA-mediated RUNX1-CBFA2T1 depletion regarding prolif... | # Background
The chromosomal translocation t(8;21) (q22;q22), which is associated with 10–15% of all cases of acute myeloid leukaemia, fuses the DNA binding domain of the transcription factor RUNX1 (also called AML1 or CBFα) to the almost complete open reading frame of CBFA2T1 (also named MTG8 or ETO) [CIT_REF]. The r... | {
"pmid": "15298716",
"doi": "10.1186/1471-2407-4-44",
"article_title": "The oncogenic fusion protein RUNX1-CBFA2T1 supports proliferation and inhibits senescence in t(8;21)-positive leukaemic cells",
"journal_title": "",
"epub": "2004-08-06 00:00:00",
"authors": [
"Natalia Martinez",
"Bettina Dresc... |
PMC512293 | # Background
Cognitive traits derived from neuropsychological test data are considered to be potential endophenotypes of schizophrenia. Previously, these traits have been found to form a valid basis for clustering samples of schizophrenia patients into homogeneous subgroups. We set out to identify such clusters, but a... | # Background
Schizophrenia is a severe mental illness which tends to run in families. Moreover, schizophrenia is a complex disorder with multiple environmental as well as genetic predisposing effects. Previous studies have shown that many neuropsychological functions are impaired in schizophrenia patients, and, to a l... | {
"pmid": "15271222",
"doi": "10.1186/1471-244X-4-20",
"article_title": "Family-based clusters of cognitive test performance in familial schizophrenia",
"journal_title": "",
"epub": "2004-07-22 00:00:00",
"authors": [
"Fabian Hoti",
"Annamari Tuulio-Henriksson",
"Jari Haukka",
"Timo Partonen... |
PMC512294 | # Background
Numerous malaria epidemics have occurred in western Kenya, with increasing frequency over the past 20 years. A variety of hypotheses on the etiology of these epidemics have been put forth, with different implications for surveillance and control. We investigated the ecological and socioeconomic factors pr... | # Background
The World Health Organization estimates that 300 to 500 million people are diagnosed with malaria annually, causing 1.1 to 2.7 million deaths. Approximately 1 million of these deaths are among children in sub-Saharan Africa, where 90% of all malaria cases occur [CIT_REF]. During the 1950's and 1960's, a c... | {
"pmid": "15296512",
"doi": "10.1186/1471-2458-4-33",
"article_title": "Field assessments in western Kenya link malaria vectors to environmentally disturbed habitats during the dry season",
"journal_title": "",
"epub": "2004-08-05 00:00:00",
"authors": [
"John C Carlson",
"Brian D Byrd",
"Franc... |
PMC512295 | # Background
The time required for radiographic union following femoral fracture increases with age in both humans and rats for unknown reasons. Since abnormalities in fracture innervation will slow skeletal healing, we explored whether abnormal mRNA expression of genes related to nerve cell activity in the older rats... | # Background
Bone formation to bridge the fracture gap following skeletal fracture slows with age in both humans [CIT_REF] and rats [CIT_REF]. While young, 6-week-old rats reach radiographic union by 4 weeks after femoral fracture, adult, 26-week-old rats require 10 weeks, and older, 52-week-old rats need in excess of... | {
"pmid": "15291962",
"doi": "10.1186/1471-2474-5-24",
"article_title": "Altered mRNA expression of genes related to nerve cell activity in the fracture callus of older rats: A randomized, controlled, microarray study",
"journal_title": "",
"epub": "2004-08-03 00:00:00",
"authors": [
"Martha H Meyer",
... |
PMC512296 | # Background
Mixed evergreen forests form the smallest, most widely distributed and fragmented biome in southern Africa. Within South Africa, 44% of this vegetation type has been transformed. Afromontane forest only covers 0.56% of South Africa, yet it contains 5.35% of South Africa's plant species. Prior to this inve... | # Background
Mixed evergreen forests form the smallest, most widely distributed and fragmented biome in southern Africa [CIT_REF]. Originally classified as Undifferentiated Afromontane forest [CIT_REF], 44% of this vegetation type within South Africa has been transformed [CIT_REF]. The forest biome only covers 0.56% o... | {
"pmid": "15287991",
"doi": "10.1186/1472-6785-4-9",
"article_title": "Preliminary inventory and classification of indigenous afromontane forests on the Blyde River Canyon Nature Reserve, Mpumalanga, South Africa",
"journal_title": "",
"epub": "2004-08-02 00:00:00",
"authors": [
"Mervyn C Lötter",
... |
PMC514489 | Mutual policing is an important mechanism that maintains social harmony in group-living organisms by suppressing the selfish behavior of individuals. In social insects, workers police one another (worker-policing) by preventing individual workers from laying eggs that would otherwise develop into males. Within the fram... | # Introduction
Major evolutionary transitions [CIT_REF] require the evolution of mechanisms that moderate within-group conflict [CIT_REF]. One such mechanism is mutual policing, where members of a group collectively prevent individuals from acting in their own selfish interests [CIT_REF]. The best example of mutual po... | {
"pmid": "15328531",
"doi": "10.1371/journal.pbio.0020248",
"article_title": "Conflict over Male Parentage in Social Insects",
"journal_title": "PLoS Biology",
"epub": "2004-08-24 00:00:00",
"authors": [
"Robert L Hammond",
"Laurent Keller"
],
"article_type": "research-article",
"license_kind... |
PMC514496 | # Background
The relationship between the burden of uncomplicated malaria and transmission intensity is unclear and a better understanding of this relationship is important for the implementation of intervention programmes.
# Methods
A 6-month longitudinal study monitoring risk factors for anaemia and febrile malari... | # Background
Plasmodium falciparum malaria remains an important public health problem in sub-Saharan Africa. To develop and assess the efficacy of control measures, it is important to obtain a better understanding of how the malaria disease burden is distributed among population groups and how this burden is affected ... | {
"pmid": "15282030",
"doi": "10.1186/1475-2875-3-26",
"article_title": "Malaria morbidity and immunity among residents of villages with different Plasmodium falciparum transmission intensity in North-Eastern Tanzania",
"journal_title": "",
"epub": "2004-07-28 00:00:00",
"authors": [
"John PA Lusingu",
... |
PMC514497 | # Background
Once malaria occurs, deaths can be prevented by prompt treatment with relatively affordable and efficacious drugs. Yet this goal is elusive in Africa. The paradox of a continuing but easily preventable cause of high mortality raises important questions for policy makers concerning care-seeking and access ... | # Background
Malaria continues to be the largest single component of the burden of disease in sub-Saharan Africa, even though simple, effective and affordable treatments exist. Malaria's pervasive morbidity and high mortality persist because of failed transactions between those at risk of malaria transmission and avai... | {
"pmid": "15282029",
"doi": "10.1186/1475-2875-3-27",
"article_title": "Care-seeking patterns for fatal malaria in Tanzania",
"journal_title": "",
"epub": "2004-07-28 00:00:00",
"authors": [
"Don de Savigny",
"Charles Mayombana",
"Eleuther Mwageni",
"Honorati Masanja",
"Abdulatif Minhaj... |
PMC514498 | # Background
Loa loa has recently emerged as a filarial worm of significant public health importance as a consequence of its impact on the African Programme for Onchocerciasis Control (APOC). Severe, sometimes fatal, encephalopathic reactions to ivermectin (the drug of choice for onchocerciasis control) have occurred ... | # Background
Knowledge of the spatial distribution of Loa loa is important in countries involved in the African Programme for Onchocerciasis Control (APOC) and is also now a significant issue for the Global Programme to Eliminate Lymphatic Filariasis (GPELF). Both programmes rely on the wide-scale distribution of anti... | {
"pmid": "15298709",
"doi": "10.1186/1475-2883-3-7",
"article_title": "Mapping the distribution of Loa loa in Cameroon in support of the African Programme for Onchocerciasis Control",
"journal_title": "",
"epub": "2004-08-06 00:00:00",
"authors": [
"Madeleine C Thomson",
"Valérie Obsomer",
"Jos... |
PMC514531 | # Background
Currently there is a lot of interest in the flexible framework offered by item banks for measuring patient relevant outcomes, including functional status. However, there are few item banks, which have been developed to quantify functional status, as expressed by the ability to perform activities of daily ... | # Background
It is now widely accepted that examining quality of life is an important aspect in the treatment and evaluation of many conditions. Functional status is seen as an important determinant of quality of life. A wide variety of instruments have been developed to quantify functional status [CIT_REF]. These ins... | {
"pmid": "15291958",
"doi": "10.1186/1477-7525-2-42",
"article_title": "The AMC Linear Disability Score project in a population requiring residential care: psychometric properties",
"journal_title": "",
"epub": "2004-08-03 00:00:00",
"authors": [
"Rebecca Holman",
"Robert Lindeboom",
"Marinus V... |
PMC514532 | The need for public-private partnerships arose against the backdrop of inadequacies on the part of the public sector to provide public good on their own, in an efficient and effective manner, owing to lack of resources and management issues. These considerations led to the evolution of a range of interface arrangements... | # Public-private partnerships in health – a global call to action
Public-private partnerships are being increasingly encouraged as part of the comprehensive development framework. The need to foster such arrangements is supported by a clear understanding of the public sectors inability to provide public goods entirely... | {
"pmid": "15282025",
"doi": "10.1186/1478-4505-2-5",
"article_title": "Public – private 'partnerships' in health – a global call to action",
"journal_title": "",
"epub": "2004-07-28 00:00:00",
"authors": [
"Sania Nishtar"
],
"article_type": "research-article",
"license_kind": "CC BY"
} |
PMC514537 | The physiological flux of oxygen is extreme in exercising skeletal muscle. Hypoxia is thus a critical parameter in muscle function, influencing production of ATP, utilization of energy-producing substrates, and manufacture of exhaustion-inducing metabolites. Glycolysis is the central source of anaerobic energy in anima... | # Introduction
During exercise in normoxia, the partial pressure of oxygen in muscle tissue has been shown to dip to as low as 3.1 mm Hg, whereas in the capillary, it remains at 38 mm Hg [CIT_REF]. In order to maintain effort, skeletal muscle exertion must be able to rely on pathways designed to help the tissue cope w... | {
"pmid": "15328538",
"doi": "10.1371/journal.pbio.0020288",
"article_title": "Loss of Skeletal Muscle HIF-1α Results in Altered Exercise Endurance",
"journal_title": "PLoS Biology",
"epub": "2004-08-24 00:00:00",
"authors": [
"Steven D Mason",
"Richard A Howlett",
"Matthew J Kim",
"I. Mark ... |
PMC514539 | # Background
Microarray studies in cancer compare expression levels between two or more sample groups on thousands of genes. Data analysis follows a population-level approach (e.g., comparison of sample means) to identify differentially expressed genes. This leads to the discovery of 'population-level' markers, i.e., ... | # Background
Studies of differential expression of individual genes often find genes that are up-regulated in some tumors, and down-regulated in others. Microarray studies typically seek to identify differentially expressed genes using use fold-change [CIT_REF], t-tests [CIT_REF], and models [CIT_REF]. Studies of glob... | {
"pmid": "15307894",
"doi": "10.1186/1471-2105-5-110",
"article_title": "Tests for finding complex patterns of differential expression in cancers: towards individualized medicine",
"journal_title": "",
"epub": "2004-08-12 00:00:00",
"authors": [
"James Lyons-Weiler",
"Satish Patel",
"Michael J ... |
PMC514540 | # Background
In eukaryotes, RNA polymerase III (RNAP III) transcribes the genes for small RNAs like tRNAs, 5S rRNA, and several viral RNAs, and short interspersed repetitive elements (SINEs). The genes for these RNAs and SINEs have internal promoters that consist of two regions. These two regions are called the A and ... | # Background
Phylogenetic relationships among animals, fungi, and plants have been a controversial issue. Although fungi traditionally had been considered more closely related to plants than to animals, Whittaker and Margulis [CIT_REF] classified the fungi as a separate kingdom in their five-kingdom classification: th... | {
"pmid": "15298704",
"doi": "10.1186/1471-2148-4-26",
"article_title": "Similarities in transcription factor IIIC subunits that bind to the posterior regions of internal promoters for RNA polymerase III",
"journal_title": "",
"epub": "2004-08-09 00:00:00",
"authors": [
"Sachiko Matsutani"
],
"artic... |
PMC514541 | # Background
Annotating genomes remains an hazardous task. Mistakes or gaps in such a complex process may occur when relevant knowledge is ignored, whether lost, forgotten or overlooked. This paper exemplifies an approach which could help to ressucitate such meaningful data.
# Results
We show that a set of closely r... | # Background
As a consequence of the deluge of completely sequenced genomes belonging to a large array of species, one can expect to identify many homologues of enzymes which have been previously well studied at the experimental level. This seems to be the general rule and the public sequence databanks (DDBJ/EMBL/GenB... | {
"pmid": "15287962",
"doi": "10.1186/1471-2164-5-52",
"article_title": "Retrieving sequences of enzymes experimentally characterized but erroneously annotated: the case of the putrescine carbamoyltransferase",
"journal_title": "",
"epub": "2004-08-02 00:00:00",
"authors": [
"Daniil G Naumoff",
"Yin... |
PMC514542 | # Background
p68 (Ddx5) and p72 (Ddx17) are highly related members of the DEAD box family and are established RNA helicases. They have been implicated in growth regulation and have been shown to be involved in both pre-mRNA and pre-rRNA processing. More recently, however, these proteins have been reported to act as tr... | # Background
The DEAD/H box family of RNA helicases has been demonstrated to be involved in virtually all processes that require manipulation of RNA including transcription, pre-mRNA and pre-rRNA processing, RNA export, ribosome assembly and translation [CIT_REF]. Although, in vitro, several members of this family hav... | {
"pmid": "15298701",
"doi": "10.1186/1471-2199-5-11",
"article_title": "The p68 and p72 DEAD box RNA helicases interact with HDAC1 and repress transcription in a promoter-specific manner",
"journal_title": "",
"epub": "2004-08-06 00:00:00",
"authors": [
"Brian J Wilson",
"Gaynor J Bates",
"Sama... |
PMC514545 | # Background
Publication bias, as typically defined, refers to the decreased likelihood of studies' results being published when they are near the null, not statistically significant, or otherwise "less interesting." But choices about how to analyze the data and which results to report create a publication bias within... | # Background
A study is more likely to appear in the literature, and thus be indexed and publicly available, if it shows a strong, statistically significant, or otherwise "better" result. A study that does not show such results has a greater chance of remaining hidden in a file drawer, either because the author (or fu... | {
"pmid": "15296515",
"doi": "10.1186/1471-2288-4-20",
"article_title": "Publication bias in situ",
"journal_title": "",
"epub": "2004-08-05 00:00:00",
"authors": [
"Carl V Phillips"
],
"article_type": "research-article",
"license_kind": "CC BY"
} |
PMC514546 | # Background
Endothelial nitric oxide synthase (eNOS) has previously been detected in the glandular part of the human gastric mucosa. Furthermore, nitric oxide (NO) has been shown to influence gastric secretion in various animal models. The present study was conducted to investigate the influence of exogenously and en... | # Background
Nitric oxide (NO) is produced from L-arginine in a reaction catalyzed by the enzyme nitric oxide synthase (NOS)[CIT_REF]. NO is an important biological signalling molecule that influences circulation by regulating vascular smooth muscle tone and modulating systemic blood pressure. Furthermore, NO is invol... | {
"pmid": "15298720",
"doi": "10.1186/1471-230X-4-16",
"article_title": "Nitric oxide-an endogenous inhibitor of gastric acid secretion in isolated human gastric glands",
"journal_title": "",
"epub": "2004-08-06 00:00:00",
"authors": [
"Anna Berg",
"Stefan Redeen",
"Ann-Charlott Ericson",
"S... |
PMC514551 | # Background
We studied the expression of DMBT1 (deleted in malignant brain tumor 1), a putative tumor suppressor gene, in normal, proliferative, and malignant breast epithelium and its possible relation to cell cycle.
# Methods
Sections from 17 benign lesions and 55 carcinomas were immunostained with anti DMBT1 ant... | # Background
DMBT1 (Deleted in Malignant Brain Tumor) at chromosome 10q25.3–26.1, was considered a tumour suppressor gene because frequent deletions and/or lack of expression had been found in malignant tumours of the brain [CIT_REF], the gastrointestinal tract [CIT_REF], and the lung [CIT_REF].
However, recent evide... | {
"pmid": "15301691",
"doi": "10.1186/1471-2407-4-46",
"article_title": "DMBT1 expression is down-regulated in breast cancer",
"journal_title": "",
"epub": "2004-08-09 00:00:00",
"authors": [
"P Braidotti",
"PG Nuciforo",
"J Mollenhauer",
"A Poustka",
"C Pellegrini",
"A Moro",
"G... |
PMC514552 | # Background
Combining bright light exposure and physical exercise may be an effective way of relieving depressive symptoms. However, relatively little is known about individual factors predicting either a good response or treatment failure. We explored background variables possibly explaining the individual variation... | # Background
At northern latitudes reduced vitality, increased appetite and sleep complaints are common symptoms during wintertime, even among people considered healthy [CIT_REF]. Atypical depressive symptoms, which are often seen in seasonal depression, appear to correlate with decreased illumination [CIT_REF]. Expos... | {
"pmid": "15306031",
"doi": "10.1186/1471-244X-4-22",
"article_title": "Drop-out and mood improvement: a randomised controlled trial with light exposure and physical exercise [ISRCTN36478292]",
"journal_title": "",
"epub": "2004-08-11 00:00:00",
"authors": [
"Sami Leppämäki",
"Jari Haukka",
"Jo... |
PMC514553 | # Background
The Mental Health First Aid training course was favorably evaluated in an uncontrolled trial in 2002 showing improvements in participants' mental health literacy, including knowledge, stigmatizing attitudes, confidence and help provided to others. This article reports the first randomized controlled trial... | # Background
In 2000 we developed a Mental Health First Aid course in response to the findings of two large national mental health surveys in Australia [CIT_REF]. These findings included a high prevalence rate of mental health problems (approximately 20% of adults in any one year), the poor mental health literacy of m... | {
"pmid": "15310395",
"doi": "10.1186/1471-244X-4-23",
"article_title": "Mental health first aid training in a workplace setting: A randomized controlled trial [ISRCTN13249129]",
"journal_title": "",
"epub": "2004-08-15 00:00:00",
"authors": [
"Betty A Kitchener",
"Anthony F Jorm"
],
"article_ty... |
PMC514555 | # Background
Miscarriage is a common event but is remarkably difficult to measure in epidemiological studies. Few large-scale population-based studies have been conducted in the UK.
# Methods
This was a population-based two-stage postal survey of reproductive histories of adult women living in the United Kingdom in ... | # Background
Despite improvements in obstetric care in the UK over the past fifty years, it is estimated that around one in five pregnancies will end in miscarriage (fetal death before 24 weeks) [CIT_REF]. The personal and public health impact of pregnancy loss is a neglected area in medical research and strategies of... | {
"pmid": "15298712",
"doi": "10.1186/1471-2458-4-35",
"article_title": "The National Women's Health Study: assembly and description of a population-based reproductive cohort",
"journal_title": "",
"epub": "2004-08-07 00:00:00",
"authors": [
"Noreen Maconochie",
"Pat Doyle",
"Susan Prior"
],
... |
PMC514556 | # Background
One estimate suggests that by 2010 more than 30% of a physician's time will be spent using information technology tools. The aim of this study is to assess the information and communication technologies (ICT) skills of medical students in Tanzania. We also report a pilot intervention of peer mentoring tra... | # Background
Developments in information and communication technology occur at an astonishing rate. The World Wide Web (WWW) doubled in size during the first 6 months of 2000 and by 2005 the number of Internet users is likely to pass the one billion mark [CIT_REF]. This has had huge implications for medical practice t... | {
"pmid": "15306029",
"doi": "10.1186/1471-2458-4-37",
"article_title": "Assessing computer skills in Tanzanian medical students: an elective experience",
"journal_title": "",
"epub": "2004-08-12 00:00:00",
"authors": [
"Miriam Samuel",
"John C Coombes",
"J Jaime Miranda",
"Rob Melvin",
... |
PMC514562 | # Background
Intrathecal baclofen pump has been used effectively with increasing frequency in patients with severe spasticity, particularly for those patients who are unresponsive to conservative pharmacotherapy or develop intolerable side effects at therapeutic doses of oral baclofen. Drowsiness, nausea, headache, mu... | # Background
Baclofen is a gamma-aminobutyric acid (GABA) analog that has inhibitory effects on spinal cord reflexes and brain. Intrathecal baclofen (ITB) therapy consists of long-term delivery of baclofen to the intrathecal space. Intrathecal baclofen has been used to treat spasticity due to cerebral palsy, brain or ... | {
"pmid": "15301690",
"doi": "10.1186/1472-6904-4-6",
"article_title": "Intrathecal baclofen withdrawal syndrome-a life-threatening complication of baclofen pump: A case report",
"journal_title": "",
"epub": "2004-08-09 00:00:00",
"authors": [
"Imran Mohammed",
"Asif Hussain"
],
"article_type": ... |
PMC514565 | # Background
Malaria is one of the oldest and deadliest infectious diseases in humans. Many mathematical models of malaria have been developed during the past century, and applied to potential interventions. However, malaria remains uncontrolled and is increasing in many areas, as are vector and parasite resistance to... | # Background
Not so long ago, in 1998, Sherman declared: "Of all the human afflictions, the greatest toll has been exacted by malaria. Even today, malaria, which is caused by protozoan parasites of the genus Plasmodium, disables and kills more people than any other infectious disease." [CIT_REF]
In line with the pion... | {
"pmid": "15285781",
"doi": "10.1186/1475-2875-3-29",
"article_title": "A simulation model of African Anopheles ecology and population dynamics for the analysis of malaria transmission",
"journal_title": "",
"epub": "2004-07-30 00:00:00",
"authors": [
"Jean-Marc O Depinay",
"Charles M Mbogo",
"... |
PMC514566 | # Background
Both host and pathogen factors contribute to disease outcome in Plasmodium falciparum infection. The feasibility of studying the P. falciparum in vivo transcriptome to understand parasite transcriptional response while it resides in the human host is presented.
# Methods
A custom made oligonucleotide ar... | # Background
Plasmodium falciparum infection remains a major health problem worldwide. Its complex life cycle has hampered standard methods for the study of pathogenesis. New approaches to elucidate parasite biology using whole genomic methods have provided insight into gene function, transcriptional regulation and st... | {
"pmid": "15296511",
"doi": "10.1186/1475-2875-3-30",
"article_title": "In vivo transcriptional profiling of Plasmodium falciparum",
"journal_title": "",
"epub": "2004-08-05 00:00:00",
"authors": [
"Johanna P Daily",
"Karine G Le Roch",
"Ousmane Sarr",
"Xuemin Fang",
"Yingyao Zhou",
... |
PMC514567 | # Background
Temperature is a frequently used parameter to describe the predicted size of lesions computed by computational models. In many cases, however, temperature correlates poorly with lesion size. Although many studies have been conducted to characterize the relationship between time-temperature exposure of tis... | # Introduction
The mitigation of primary and metastatic tumors by radiofrequency ablation is a developing research area. The goal of ablation is to necrose treatment volumes by raising the temperature of targeted tissues. Ablation probes are inserted percutaneously, laparoscopically, or during surgery into cancerous t... | {
"pmid": "15298708",
"doi": "10.1186/1475-925X-3-27",
"article_title": "Thermal modeling of lesion growth with radiofrequency ablation devices",
"journal_title": "",
"epub": "2004-08-06 00:00:00",
"authors": [
"Isaac A Chang",
"Uyen D Nguyen"
],
"article_type": "research-article",
"license_ki... |
PMC514568 | # Background
The developments in echocardiography or ultrasound cardiography (UCG) have improved our clinical capabilities. However, advanced hardware and software capabilities have resulted in UCG facilities of dubious clinical benefits. Is tissue Doppler echocardiography (TDE) is one such example?
# Presentation of... | # Background
Echocardiography or Ultrasound Cardiography (UCG) is a key investigation in cardiology. Its non-invasive nature makes it a widely acceptable and safe form of investigation. In many cases it has surpassed cardiac catheterisation in diagnostic yield and has become the investigation of choice.
The rapid dev... | {
"pmid": "15307890",
"doi": "10.1186/1476-7120-2-12",
"article_title": "Tissue Doppler echocardiography – A case of right tool, wrong use",
"journal_title": "",
"epub": "2004-08-12 00:00:00",
"authors": [
"George Thomas"
],
"article_type": "research-article",
"license_kind": "CC BY"
} |
PMC514570 | # Background
Lipopolysaccharide (LPS) treatment of animals down-regulates the expression of hepatic genes involved in a broad variety of physiological processes, collectively known as the negative hepatic acute phase response (APR). Retinoid X receptor α (RXRα), the most highly expressed RXR isoform in liver, plays a ... | # Background
LPS, a major constituent of the outer membrane of gram-negative bacteria, potently stimulates host innate immune response [CIT_REF]. LPS-induced activation of monocytes/macrophages leads to the release of proinflammatory cytokines such as interleukin-1β (IL-1β), interleukin-6 (IL-6), and tumor necrosis fa... | {
"pmid": "15312234",
"doi": "10.1186/1478-1336-2-4",
"article_title": "Endotoxin leads to rapid subcellular re-localization of hepatic RXRα: A novel mechanism for reduced hepatic gene expression in inflammation",
"journal_title": "",
"epub": "2004-08-16 00:00:00",
"authors": [
"Romi Ghose",
"Tracy ... |
PMC514571 | # Background
Suicide gene therapy employing the prodrug activating system Herpes simplex virus type 1 thymidine kinase (HSV-TK)/ ganciclovir (GCV) has proven to be effective in killing experimental brain tumors. In contrast, glioma patients treated with HSV-TK/ GCV did not show significant treatment benefit, most like... | # Background
Treatment with the suicide gene/ prodrug activating system herpes simplex virus type I thymidine kinase/ ganciclovir (HSV-TK/ GCV) is highly efficient in animal models of malignant glioma [CIT_REF]. In contrast, clinical trials employing the HSV-TK/ GCV system and a retroviral vector have demonstrated onl... | {
"pmid": "15294018",
"doi": "10.1186/1479-0556-2-7",
"article_title": "A dual function fusion protein of Herpes simplex virus type 1 thymidine kinase and firefly luciferase for noninvasive in vivo imaging of gene therapy in malignant glioma",
"journal_title": "",
"epub": "2004-08-04 00:00:00",
"authors": [... |
PMC514572 | # Background
The need for safe and effective treatment of dengue virus (DEN), a class A agent that causes dengue hemorrhagic fever/dengue shock syndrome, has been a critical global priority. An effective vaccine for DEN is not yet available. In this study the possibility of attenuating DEN infection using adeno-associ... | # Introduction
The need for a safe and effective prophylaxis or treatment for dengue virus (DEN) infection, a category A mosquito-borne human pathogen, is a critical global priority. DEN causes dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS), which is associated with heterologous secondary DEN infection and a... | {
"pmid": "15301687",
"doi": "10.1186/1479-0556-2-8",
"article_title": "Attenuation of dengue virus infection by adeno-associated virus-mediated siRNA delivery",
"journal_title": "",
"epub": "2004-08-09 00:00:00",
"authors": [
"Weidong Zhang",
"Rajeswari Singam",
"Gary Hellermann",
"Xiaoyuan... |
PMC514608 | # Background
The strikingly young age of new variant Creutzfeldt-Jacob disease (vCJD) cases remains unexplained. Age dependent susceptibility to infection has been put forward, but differential dietary exposure to contaminated food products in the UK population according to age and sex during the bovine spongiform enc... | # Background
Owing to the lack of data concerning age dependent dietary exposure to bovine material in food in the UK, mathematical models used in the study of new variant Creutzfeldt-Jacob disease (vCJD) have postulated an age risk function for contamination where the influence of age dependent dietary exposure to co... | {
"pmid": "15304199",
"doi": "10.1186/1471-2334-4-26",
"article_title": "Epidemiological evidence of higher susceptibility to vCJD in the young",
"journal_title": "",
"epub": "2004-08-10 00:00:00",
"authors": [
"Pierre-Yves Boëlle",
"Jean-Yves Cesbron",
"Alain-Jacques Valleron"
],
"article_t... |
PMC514609 | # Background
We sought to evaluate the hypothesis that the high incidence of cutaneous melanoma in white persons in central Alabama is associated with a predominance of Irish and Scots descent.
# Methods
Frequencies of country of ancestry reports were tabulated. The reports were also converted to scores that reflect... | # Background
The incidence of cutaneous melanoma in Alabama is high (16.9 and 8.6 per 100,000 men and women, respectively, in 1998) [CIT_REF]. The average annual incidence rate in Alabama during 1996 was 15.5 per 100,000 for men and 8.8 per 100,000 for women, indicating that the incidence in men is increasing. This is... | {
"pmid": "15310399",
"doi": "10.1186/1471-2407-4-47",
"article_title": "Ancestry reported by white adults with cutaneous melanoma and control subjects in central Alabama",
"journal_title": "",
"epub": "2004-08-13 00:00:00",
"authors": [
"Ronald T Acton",
"Ellen H Barton",
"William W Hollowell",... |
PMC514611 | # Background
Physical exercise has become a cornerstone of management of chronic obstructive pulmonary disease (COPD) because it leads to clinically relevant improvements of exercise capacity and health-related quality of life (HRQL). Despite the scarcity of randomised trials directly comparing exercise protocols, cur... | # Background
Impaired exercise capacity, dyspnoea and reduced health-related quality of life (HRQL) are common complaints of patients with chronic obstructive pulmonary disease (COPD). A major exercise-limiting factor in COPD is peripheral muscle dysfunction characterised by atrophic muscles and reduced fatigue resist... | {
"pmid": "15310394",
"doi": "10.1186/1471-2466-4-5",
"article_title": "Interval exercise versus continuous exercise in patients with moderate to severe chronic obstructive pulmonary disease – study protocol for a randomised controlled trial [ISRCTN11611768]",
"journal_title": "",
"epub": "2004-08-13 00:00:00... |
PMC514612 | # Background
Sustainable DNA resources and reliable high-throughput genotyping methods are required for large-scale, long-term genetic association studies. In the genetic dissection of common disease it is now recognised that thousands of samples and hundreds of thousands of markers, mostly single nucleotide polymorph... | # Background
In order to locate the disease variants involved in complex common disease it is now generally accepted that very large sample numbers will be required [CIT_REF]. Not only do the sample collections need to provide high quality gDNA, for the purpose of accurate genotyping, they also need to be sustainable.... | {
"pmid": "15279678",
"doi": "10.1186/1472-6750-4-15",
"article_title": "Investigating the utility of combining Φ29 whole genome amplification and highly multiplexed single nucleotide polymorphism BeadArray™ genotyping",
"journal_title": "",
"epub": "2004-07-27 00:00:00",
"authors": [
"Rebecca Pask",
... |
PMC514616 | Although much is known about the reproductive biology of pond-breeding frogs, there is comparatively little information about terrestrial-breeding anurans, a highly successful and diverse group. This study investigates the activation and in vitro fertilization of eggs of the Puerto Rican coqui frog obtained by hormonal... | # Background
The study of reproduction and its artificial manipulation is important in many fields. For example, in sea urchins, an animal's testes can be dissected and sperm is activated by exposure to seawater. Eggs can be released by injecting KCl into the perivisceral cavity, and mixing eggs and sperm in vitro pro... | {
"pmid": "15296510",
"doi": "10.1186/1477-7827-2-60",
"article_title": "In vitro fertilization and artificial activation of eggs of the direct-developing anuran Eleutherodactylus coqui",
"journal_title": "",
"epub": "2004-08-05 00:00:00",
"authors": [
"Esteban Toro",
"Scott F Michael"
],
"artic... |
PMC514697 | # Background
The general problem of RNA secondary structure prediction under the widely used thermodynamic model is known to be NP-complete when the structures considered include arbitrary pseudoknots. For restricted classes of pseudoknots, several polynomial time algorithms have been designed, where the O (n^{6})time... | # Background
## Biological relevance
Pseudoknots have been shown to be functionally relevant in many RNA mediated processes. Examples are the self-splicing group I introns [CIT_REF], ribosomal RNAs, or RNaseP. Recently, pseudoknots were located in prion proteins of humans, and confirmed for many other species [CIT_RE... | {
"pmid": "15294028",
"doi": "10.1186/1471-2105-5-104",
"article_title": "Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics",
"journal_title": "",
"epub": "2004-08-04 00:00:00",
"authors": [
"Jens Reeder",
"Robert Giegerich"
],
"article_typ... |
PMC514698 | # Background
Recent technological advances in high-throughput data collection allow for experimental study of increasingly complex systems on the scale of the whole cellular genome and proteome. Gene network models are needed to interpret the resulting large and complex data sets. Rationally designed perturbations (e.... | # Background
While similarity (homology) of DNA sequence between organisms can be used to propose potential gene functions, transcriptional regulation, and protein pathways (e.g., [CIT_REF], there are often major differences in the protein products, functions, and pathway involvement of genes with nearly identical seq... | {
"pmid": "15304201",
"doi": "10.1186/1471-2105-5-108",
"article_title": "Linear fuzzy gene network models obtained from microarray data by exhaustive search",
"journal_title": "",
"epub": "2004-08-10 00:00:00",
"authors": [
"Bahrad A Sokhansanj",
"J Patrick Fitch",
"Judy N Quong",
"Andrew A... |
PMC514699 | # Background
Short oligonucleotide arrays have several probes measuring the expression level of each target transcript. Therefore the selection of probes is a key component for the quality of measurements. However, once probes have been selected and synthesized on an array, it is still possible to re-evaluate the resu... | # Background
In a relatively short time microarrays have become a well established technique, widely used by researchers. Microarrays offer nothing less than to be able to monitor simultaneously the expression levels for thousands of genes.
The RNA molecules from the biological sample are called targets, and the poly... | {
"pmid": "15310390",
"doi": "10.1186/1471-2105-5-111",
"article_title": "Alternative mapping of probes to genes for Affymetrix chips",
"journal_title": "",
"epub": "2004-08-14 00:00:00",
"authors": [
"Laurent Gautier",
"Morten Møller",
"Lennart Friis-Hansen",
"Steen Knudsen"
],
"article... |
PMC514701 | # Background
Microarray technologies produced large amount of data. The hierarchical clustering is commonly used to identify clusters of co-expressed genes. However, microarray datasets often contain missing values (MVs) representing a major drawback for the use of the clustering methods. Usually the MVs are not treat... | # Background
The genome projects have increased our knowledge of genomic sequences for several organisms. Taking advantage of this knowledge, the microarrays technologies allow the characterization of a whole-genome expression by showing the relative transcript levels of thousand of genes in one experiment [CIT_REF]. ... | {
"pmid": "15324460",
"doi": "10.1186/1471-2105-5-114",
"article_title": "Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering",
"journal_title": "",
"epub": "2004-08-23 00:00:00",
"authors": [
"Alexandre G de Brevern",
"Serge Hazout",
"A... |
PMC514702 | # Background
Pooled human embryonic stem cells (hESC) cell lines were profiled to obtain a comprehensive list of genes common to undifferentiated human embryonic stem cells.
# Results
Pooled hESC lines were profiled to obtain a comprehensive list of genes common to human ES cells. Massively parallel signature sequen... | # Background
Multiple large-scale analytical techniques to assess gene expression in defined cell populations have been developed. These include microarray analysis, EST enumeration, SAGE and MPSS. Each of these techniques offers unique advantages and disadvantages. Technique selection largely depends on the expertise... | {
"pmid": "15304200",
"doi": "10.1186/1471-213X-4-10",
"article_title": "MPSS profiling of human embryonic stem cells",
"journal_title": "",
"epub": "2004-08-10 00:00:00",
"authors": [
"Ralph Brandenberger",
"Irina Khrebtukova",
"R Scott Thies",
"Takumi Miura",
"Cai Jingli",
"Raj Pur... |
PMC514708 | # Background
The glutamatergic dysfunction hypothesis of schizophrenia suggests that genes involved in glutametergic transmission are candidates for schizophrenic susceptibility genes. We have been performing systematic association studies of schizophrenia with the glutamate receptor and transporter genes. In this stu... | # Background
Schizophrenia is a severe mental disorder characterized by hallucinations, delusions, disorganized thoughts, and various cognitive impairments. The life-time prevalence is about 1%, and genetic factors were known to play a critical role in its pathogenesis [CIT_REF]. Based on the fact that phencyclidine (... | {
"pmid": "15296513",
"doi": "10.1186/1471-244X-4-21",
"article_title": "Association study of polymorphisms in the excitatory amino acid transporter 2 gene (SLC1A2) with schizophrenia",
"journal_title": "",
"epub": "2004-08-06 00:00:00",
"authors": [
"Xiangdong Deng",
"Hiroki Shibata",
"Hideaki ... |
PMC514710 | # Background
Polycistronic retroviral vectors that contain several therapeutic genes linked via internal ribosome entry sites (IRES), provide new and effective tools for the co-expression of exogenous cDNAs in clinical gene therapy protocols. For example, tricistronic retroviral vectors could be used to genetically mo... | # Background
Gene therapy protocols would strongly benefit from the development of a one step technique that would allow cells to be genetically modified through the introduction of several therapeutic genes. In order to induce the translation and expression of exogenous cDNAs, carried by a single vector, researchers ... | {
"pmid": "15279677",
"doi": "10.1186/1472-6750-4-16",
"article_title": "Use and comparison of different internal ribosomal entry sites (IRES) in tricistronic retroviral vectors",
"journal_title": "",
"epub": "2004-07-27 00:00:00",
"authors": [
"Victorine Douin",
"Stephanie Bornes",
"Laurent Cre... |
PMC514711 | # Background
There are now several ways to generate fluorescent fusion proteins by randomly inserting DNA encoding the Green Fluorescent Protein (GFP) into another protein's coding sequence. These approaches can be used to map regions in a protein that are permissive for GFP insertion or to create novel biosensors. Wh... | # Background
Biosensors based on GFP-fusion proteins are powerful tools for observing real-time events within living cells. Insertion of GFP within another protein has produced biosensors capable of signaling intracellular events through intrinsic fluorescence changes [CIT_REF], fluorescence resonance energy transfer ... | {
"pmid": "15317651",
"doi": "10.1186/1472-6750-4-17",
"article_title": "A faster way to make GFP-based biosensors: Two new transposons for creating multicolored libraries of fluorescent fusion proteins",
"journal_title": "",
"epub": "2004-08-18 00:00:00",
"authors": [
"Douglas L Sheridan",
"Thomas ... |
PMC514716 | # Background
The aims of this study were to determine whether observed geographic variations in breast cancer incidence are random or statistically significant, whether statistically significant excesses are temporary or time-persistent, and whether they can be explained by covariates such as socioeconomic status (SES... | # Background
This study is an observational epidemiological investigation of breast cancer incidence in Massachusetts. It examines geographic variations over a ten year period using both purely spatial and space-time models to determine whether observed fluctuations in incidence rates are random or whether fluctuation... | {
"pmid": "15291960",
"doi": "10.1186/1476-072X-3-17",
"article_title": "The geographic distribution of breast cancer incidence in Massachusetts 1988 to 1997, adjusted for covariates",
"journal_title": "",
"epub": "2004-08-03 00:00:00",
"authors": [
"T Joseph Sheehan",
"Laurie M DeChello",
"Mart... |
PMC514720 | Dendritic cells (DC) are known to present exogenous protein Ag effectively to T cells. In this study we sought to identify the proteases that DC employ during antigen processing. The murine epidermal-derived DC line Xs52, when pulsed with PPD, optimally activated the PPD-reactive Th1 clone LNC.2F1 as well as the Th2 cl... | # Review
Dendritic cells (DC) are professional antigen presenting cells that induce primary antigen specific T cell responses [CIT_REF] and exhibit all functional properties required to present exogenous antigen (Ag) to immunologically naïve T cells. These properties include: a) uptake of exogenous Ag via receptor-med... | {
"pmid": "15287985",
"doi": "10.1186/1476-8518-2-8",
"article_title": "Identification of proteases employed by dendritic cells in the processing of protein purified derivative (PPD)",
"journal_title": "",
"epub": "2004-08-02 00:00:00",
"authors": [
"Mansour Mohamadzadeh",
"Hamid Mohamadzadeh",
... |
PMC514884 | Because deleterious alleles arising from mutation are filtered by natural selection, mutations that create such alleles will be underrepresented in the set of common genetic variation existing in a population at any given time. Here, we describe an approach based on this idea called VERIFY (variant elimination reinforc... | # Introduction
Exonic splicing enhancers (ESEs) were identified about a decade ago as short oligonucleotide sequences that enhance exon recognition by the splicing machinery (reviewed in [CIT_REF]). Sequences with ESE activity have been identified in both plants and animals and have been found to occur frequently in c... | {
"pmid": "15340491",
"doi": "10.1371/journal.pbio.0020268",
"article_title": "Single Nucleotide Polymorphism–Based Validation of Exonic Splicing Enhancers",
"journal_title": "PLoS Biology",
"epub": "2004-08-31 00:00:00",
"authors": [
"William G Fairbrother",
"Dirk Holste",
"Christopher B Burge"... |
PMC514893 | # Background
Chemokines are involved in many biological activities ranging from leukocyte differentiation to neuronal morphogenesis. Despite numerous reports describing chemokine function, little is known about the molecular changes induced by cytokines.
# Methods
We have isolated and identified by differential disp... | # Background
CXC and CC chemokines are small soluble proteins expressed and secreted by a number of cell types during the initial host response to injury, allergens, antigens, or invading microorganisms [CIT_REF]. These ligands selectively attract leukocytes to inflammatory foci via facilitation of cellular adhesion, ... | {
"pmid": "15296517",
"doi": "10.1186/1471-2172-5-17",
"article_title": "Identification of genes differentially expressed in T cells following stimulation with the chemokines CXCL12 and CXCL10",
"journal_title": "BMC Immunology",
"epub": "2004-08-05 00:00:00",
"authors": [
"JE Nagel",
"RJ Smith",
... |
PMC514894 | # Background
The fliC and fljB genes in Salmonella code for the phase 1 (H1) and phase 2 (H2) flagellin respectively, the rfb cluster encodes the majority of enzymes for polysaccharide (O) antigen biosynthesis, together they determine the antigenic profile by which Salmonella are identified. Sequencing and characteris... | # Background
Salmonella express flagellar (H), polysaccharide (O) and capsular (Vi) antigens which determine strain pathogenicity and therefore variation of these antigens has formed the basis for Salmonella serotyping. The Kauffmann-White scheme, first published in 1929, divides Salmonella into more than 2500 serotyp... | {
"pmid": "15298703",
"doi": "10.1186/1471-2180-4-31",
"article_title": "Towards the development of a DNA-sequence based approach to serotyping of Salmonella enterica",
"journal_title": "",
"epub": "2004-08-06 00:00:00",
"authors": [
"Chloe KB Mortimer",
"Tansy M Peters",
"Saheer E Gharbia",
... |
PMC514895 | # Background
Most of the existing RNA structure prediction programs fold a completely synthesized RNA molecule. However, within the cell, RNA molecules emerge sequentially during the directed process of transcription. Dedicated experiments with individual RNA molecules have shown that RNA folds while it is being trans... | # Background
Most of the existing computational methods for RNA secondary structure prediction fold an already completely synthesized RNA molecule. This is done either by minimizing its free energy (e.g. done by MFOLD [CIT_REF] and by the programs of the VIENNA package [CIT_REF]) or by maximizing the probability under... | {
"pmid": "15298702",
"doi": "10.1186/1471-2199-5-10",
"article_title": "Co-transcriptional folding is encoded within RNA genes",
"journal_title": "",
"epub": "2004-08-06 00:00:00",
"authors": [
"Irmtraud M Meyer",
"István Miklós"
],
"article_type": "research-article",
"license_kind": "CC BY"
... |
PMC514896 | # Background
The visit to the emergency department (ED) constitutes a brief, yet an important point in the continuum of medical care. The aim of our study was to evaluate the continuity of care of adult ED visitors.
# Methods
We retrospectively reviewed all ED discharge summaries for over a month 's period. The ED c... | # Background
The emergency department (ED) is intended to treat medical urgencies or emergencies, but a large proportion of visits are due to problems that could be treated in the primary care setting [CIT_REF]. ED services are available 24 hours a day while primary care facilities have limited service hours. In the I... | {
"pmid": "15298721",
"doi": "10.1186/1471-2296-5-16",
"article_title": "Primary care follow up of patients discharged from the emergency department: a retrospective study",
"journal_title": "",
"epub": "2004-08-07 00:00:00",
"authors": [
"Shlomo Vinker",
"Eliezer Kitai",
"Yaacov Or",
"Sasso... |
PMC514897 | # Background
In the many descriptive studies on prescribed psychotropic drug use by community-dwelling older persons, several sociodemographic and other factors associated with drug use receive inconsistent support.
# Method
Empirical reports with data on at least benzodiazepine or antidepressant drug use in samples... | # Background
The use of prescribed psychotropic drugs by older persons has been a subject of interest for several decades [CIT_REF]. Psychotropic drugs are defined as substances that act directly on the central nervous system, affecting mood, cognition, and behavior, and usually include anxiolytics, sedatives and hypn... | {
"pmid": "15310409",
"doi": "10.1186/1472-6955-3-3",
"article_title": "Factors associated with psychotropic drug use among community-dwelling older persons: A review of empirical studies",
"journal_title": "",
"epub": "2004-08-13 00:00:00",
"authors": [
"Philippe Voyer",
"David Cohen",
"Sylvie ... |
PMC515177 | # Background
Cryptic structural abnormalities within the subtelomeric regions of chromosomes have been the focus of much recent research because of their discovery in a percentage of people with mental retardation (UK terminology: learning disability). These studies focused on subjects (largely children) with various ... | # Background
The isolation of unique DNA probes from the sub-telomeric regions of all chromosomes has opened up a field of cytogenetics research that was previously inaccessible to conventional karyotyping protocols [CIT_REF]. Since then a number of studies have shown that cryptic structural abnormalities (deletions, ... | {
"pmid": "15310400",
"doi": "10.1186/1471-2350-5-21",
"article_title": "A 4q35.2 subtelomeric deletion identified in a screen of patients with co-morbid psychiatric illness and mental retardation",
"journal_title": "",
"epub": "2004-08-13 00:00:00",
"authors": [
"Ben S Pickard",
"Edward J Hollox",
... |
PMC515284 | # Background
We and others have shown four distinct and presumably related effects of mammalian proliferating cell nuclear antigen (PCNA) on DNA synthesis catalyzed by mammalian DNA polymerase δ(pol δ). In the presence of homologous PCNA, pol δ exhibits 1) increased absolute activity; 2) increased processivity of DNA ... | # Background
Many Drosophila melanogaster homologs of the proteins required for both DNA replication and repair have been identified and in several cases purified to apparent homogeneity. These include DNA polymerase α holoenzyme [CIT_REF], DNA polymerase δ(pol δ) [CIT_REF], replication protein A (RP-A; [CIT_REF], rep... | {
"pmid": "15310391",
"doi": "10.1186/1471-2091-5-13",
"article_title": "Site-specific mutagenesis of Drosophila proliferating cell nuclear antigen enhances its effects on calf thymus DNA polymerase δ",
"journal_title": "",
"epub": "2004-08-13 00:00:00",
"authors": [
"Dmitry Ju Mozzherin",
"Maeve Mc... |
PMC515296 | # Background
Order Charadriiformes (shorebirds) is an ideal model group in which to study a wide range of behavioural, ecological and macroevolutionary processes across species. However, comparative studies depend on phylogeny to control for the effects of shared evolutionary history. Although numerous hypotheses have... | # Background
The shorebirds and allies (Aves: Charadriiformes; [CIT_REF] present an exceptional group for studying numerous evolutionary hypotheses. Their remarkable diversity of social mating system, parental care, sexual dimorphism, ecology and life-history make them an ideal group for unravelling the mechanisms of,... | {
"pmid": "15329156",
"doi": "10.1186/1471-2148-4-28",
"article_title": "A supertree approach to shorebird phylogeny",
"journal_title": "",
"epub": "2004-08-24 00:00:00",
"authors": [
"Gavin H Thomas",
"Matthew A Wills",
"Tamás Székely"
],
"article_type": "research-article",
"license_kind"... |
PMC515299 | # Background
Defensins comprise a large family of cationic antimicrobial peptides that are characterized by the presence of a conserved cysteine-rich defensin motif. Based on the spacing pattern of cysteines, these defensins are broadly divided into five groups, namely plant, invertebrate, α-, β-, and θ-defensins, wit... | # Background
Defensins constitute a large family of small, cysteine-rich, cationic peptides that are capable of killing a broad spectrum of pathogens, including various bacteria, fungi, and certain enveloped viruses [CIT_REF]. These peptides play a critical role in host defense and disease resistance by protecting the... | {
"pmid": "15310403",
"doi": "10.1186/1471-2164-5-56",
"article_title": "A genome-wide screen identifies a single β-defensin gene cluster in the chicken: implications for the origin and evolution of mammalian defensins",
"journal_title": "",
"epub": "2004-08-13 00:00:00",
"authors": [
"Yanjing Xiao",
... |
PMC515300 | # Background
Gram-negative bacteria cause most nosocomial respiratory infections. At the University of Cumhuriyet, we examined 328 respiratory isolates of Enterobacteriaceae and Acinetobacter baumanii organisms in Sivas, Turkey over 3 years. We used disk diffusion or standardized microdilution to test the isolates aga... | # Background
Nosocomial bacterial pneumonia is frequently polymicrobial, with gram-negative bacilli predominating [CIT_REF]. Because delays in antimicrobial treatment can lead to adverse outcomes, the choice of empirical therapy is vital. Many effective antimicrobial agents are available, but the treatment of nosocomi... | {
"pmid": "15320954",
"doi": "10.1186/1471-2180-4-32",
"article_title": "Antibiotic susceptibility patterns among respiratory isolates of Gram-negative bacilli in a Turkish university hospital",
"journal_title": "",
"epub": "2004-08-22 00:00:00",
"authors": [
"Ugur Gonlugur",
"Mustafa Zahir Bakici",... |
PMC515301 | # Background
Real-time reverse transcription PCR (RT-PCR) has greatly improved the ease and sensitivity of quantitative gene expression studies. However, accurate measurement of gene expression with this method relies on the choice of a valid reference for data normalization. Studies rarely verify that gene expression... | # Background
For many years the vast majority of gene expression studies have employed non-quantitative or semi-quantitative RNA gel blots and RT-PCR analysis. Real-time PCR technology has removed many of the difficulties associated with quantitative gene expression studies [CIT_REF], and real-time quantitative RT-PCR... | {
"pmid": "15317655",
"doi": "10.1186/1471-2229-4-14",
"article_title": "Validating internal controls for quantitative plant gene expression studies",
"journal_title": "",
"epub": "2004-08-18 00:00:00",
"authors": [
"Amy M Brunner",
"Igor A Yakovlev",
"Steven H Strauss"
],
"article_type": "r... |
PMC515302 | # Background
Several reviews of published cluster randomised trials have reported that about half did not take clustering into account in the analysis, which was thus incorrect and potentially misleading. In this paper I ask whether cluster randomised trials are increasing in both number and quality of reporting.
# M... | # Background
Cluster randomised trials are those where research subjects are not allocated to treatments independently, but as a group. For example, in a study of counselling patients on physical activity in general practice, practices were allocated to counselling or control and patients aged 40–79 years who attended... | {
"pmid": "15310402",
"doi": "10.1186/1471-2288-4-21",
"article_title": "Cluster randomised trials in the medical literature: two bibliometric surveys",
"journal_title": "",
"epub": "2004-08-13 00:00:00",
"authors": [
"J Martin Bland"
],
"article_type": "research-article",
"license_kind": "CC BY"
... |
PMC515304 | # Background
S100A4 is a small Ca^{2+} -binding protein of the S100 family with metastasis-promoting properties. Recently, secreted S100A4 protein has been shown to possess a number of functions, including induction of angiogenesis, stimulation of cell motility and neurite extension.
# Methods
Cell cultures from two... | # Background
The S100 protein family consists of at least 21 small, acidic, Ca^{2+} -binding proteins with different expression patterns and apparently diverse functional and biological properties [CIT_REF]. The S100A4 protein has been associated with increased metastatic capacity of cancer cells [CIT_REF], but how S1... | {
"pmid": "15318945",
"doi": "10.1186/1471-2407-4-52",
"article_title": "Sensitization of interferon-γ induced apoptosis in human osteosarcoma cells by extracellular S100A4",
"journal_title": "",
"epub": "2004-08-19 00:00:00",
"authors": [
"Kjetil Boye Pedersen",
"Kristin Andersen",
"Øystein Fod... |
PMC515305 | # Background
The relative role of anti apoptotic (i.e. Bcl-2) or pro-apoptotic (e.g. Bax) proteins in tumor progression is still not completely understood.
# Methods
The rat glioma cell line A15A5 was stably transfected with human Bcl-2 and Bax transgenes and the viability of theses cell lines was analyzed in vitro ... | # Background
Glioblastoma Multiforme (GBM) are the most common and aggressive tumors of the central nervous system (CNS) [CIT_REF]. Current treatments (e.g. chemo-and radiotherapy) have been relatively unsuccessful and no significant improvement in the prognosis has been recorded over the last 20 years [CIT_REF]. Canc... | {
"pmid": "15331018",
"doi": "10.1186/1471-2407-4-54",
"article_title": "Opposite role of Bax and BCL-2 in the anti-tumoral responses of the immune system",
"journal_title": "",
"epub": "2004-08-24 00:00:00",
"authors": [
"Gwenola Bougras",
"Pierre-François Cartron",
"Fabien Gautier",
"Stéph... |
PMC515306 | # Background
Although a rare disease, uveal melanoma is the most common primary intraocular malignancy in adults, with an incidence rate of up to 1.0 per 100,000 persons per year in Europe. Only a few consistent risk factors have been identified for this disease. We present the study design of an ongoing incident case... | # Background
Although a rare disease, uveal melanoma of the eye is the most common primary intraocular malignancy in adults, with an incidence rate of up to 1.0 per 100,000 person years (age-standardized, world standard) in Europe [CIT_REF]. Only a few consistent risk factors have been identified for this disease. One... | {
"pmid": "15318944",
"doi": "10.1186/1471-2415-4-11",
"article_title": "Case-control study on uveal melanoma (RIFA): rational and design",
"journal_title": "",
"epub": "2004-08-19 00:00:00",
"authors": [
"Andrea Schmidt-Pokrzywniak",
"Karl-Heinz Jöckel",
"Norbert Bornfeld",
"Andreas Stang"
... |
PMC515309 | # Background
Joining a model for the molecular evolution of a protein family to the paleontological and geological records (geobiology), and then to the chemical structures of substrates, products, and protein folds, is emerging as a broad strategy for generating hypotheses concerning function in a post-genomic world.... | # Background
The emergence of complete genomes for many organisms, including humans, has created the need for hypotheses concerning the "function" of specific genes that encode specific proteins. While "function" is interpreted by different workers in different ways [CIT_REF], Darwinian theory (by axiom) requires that... | {
"pmid": "15315709",
"doi": "10.1186/1741-7007-2-19",
"article_title": "The planetary biology of cytochrome P450 aromatases",
"journal_title": "",
"epub": "2004-08-17 00:00:00",
"authors": [
"Eric A Gaucher",
"Logan G Graddy",
"Tang Li",
"Rosalia CM Simmen",
"Frank A Simmen",
"David... |
PMC515310 | # Background
Focal clusters of slow wave activity in the delta frequency range (1–4 Hz), as measured by magnetencephalography (MEG), are usually located in the vicinity of structural damage in the brain. Such oscillations are usually considered pathological and indicative of areas incapable of normal functioning owing... | # Background
Cerebrovascular stroke is a highly prevalent condition and the major cause of language impairment in adults. Immediately following a stroke about 38% of the affected population experience aphasia [CIT_REF]. Spontaneous recovery is reported within the first six months after the event, while only minimal sp... | {
"pmid": "15331014",
"doi": "10.1186/1741-7007-2-20",
"article_title": "Intensive language training enhances brain plasticity in chronic aphasia",
"journal_title": "",
"epub": "2004-08-25 00:00:00",
"authors": [
"Marcus Meinzer",
"Thomas Elbert",
"Christian Wienbruch",
"Daniela Djundja",
... |
PMC515311 | # Background
The coronary artery calcium (CAC) score is an independent predictor of coronary heart disease. We sought to combine information from the CAC score with information from conventional cardiac risk factors to produce post-test risk estimates, and to determine whether the score may add clinically useful infor... | # Background
Aggressive primary prevention of coronary heart disease (CHD) is most appropriate in patients at relatively high risk of CHD events [CIT_REF]. The coronary artery calcium (CAC) score is an independent predictor of coronary heart disease risk [CIT_REF], and therefore may help in deciding how aggressively t... | {
"pmid": "15327691",
"doi": "10.1186/1741-7015-2-31",
"article_title": "What does my patient's coronary artery calcium score mean? Combining information from the coronary artery calcium score with information from conventional risk factors to estimate coronary heart disease risk",
"journal_title": "",
"epub"... |
PMC515365 | Integration of mitochondrial DNA fragments into nuclear chromosomes (giving rise to nuclear DNA sequences of mitochondrial origin, or NUMTs) is an ongoing process that shapes nuclear genomes. In yeast this process depends on double-strand-break repair. Since NUMTs lack amplification and specific integration mechanisms,... | # Introduction
Insertion of new sequences into nuclear DNA has a major impact on its architecture and is an important mechanism for the evolution of eukaryotic genomes. Moreover, when targeted to gene loci, these insertions can be mutagenic, and in humans this process contributes to a number of diseases [CIT_REF]. The... | {
"pmid": "15361937",
"doi": "10.1371/journal.pbio.0020273",
"article_title": "Continued Colonization of the Human Genome by Mitochondrial DNA",
"journal_title": "PLoS Biology",
"epub": "2004-09-07 00:00:00",
"authors": [
"Miria Ricchetti",
"Fredj Tekaia",
"Bernard Dujon"
],
"article_type": ... |
PMC515366 | The Drosophila peptidoglycan recognition protein SA (PGRP-SA) is critically involved in sensing bacterial infection and activating the Toll signaling pathway, which induces the expression of specific antimicrobial peptide genes. We have determined the crystal structure of PGRP-SA to 2.2-Å resolution and analyzed its pe... | # Introduction
Activation of innate immunity in response to bacterial pathogens requires a group of molecules, known as the pattern recognition receptors, that recognize conserved motifs, present in bacteria but absent in higher eukaryotes, and trigger downstream signaling events. In Drosophila, two distinct signal tr... | {
"pmid": "15361936",
"doi": "10.1371/journal.pbio.0020277",
"article_title": "A Drosophila Pattern Recognition Receptor Contains a Peptidoglycan Docking Groove and Unusual L,D-Carboxypeptidase Activity",
"journal_title": "PLoS Biology",
"epub": "2004-09-07 00:00:00",
"authors": [
"Chung-I Chang",
"... |
PMC515367 | Identifying regions of the human genome that have been targets of natural selection will provide important insights into human evolutionary history and may facilitate the identification of complex disease genes. Although the signature that natural selection imparts on DNA sequence variation is difficult to disentangle ... | # Introduction
Despite intense study and interest, a detailed understanding of the evolutionary and demographic forces that have shaped extant patterns of human genomic variation remains elusive. An important goal in studies of DNA sequence variation is to identify loci that have been targets of natural selection and ... | {
"pmid": "15361935",
"doi": "10.1371/journal.pbio.0020286",
"article_title": "Population History and Natural Selection Shape Patterns of Genetic Variation in 132 Genes",
"journal_title": "PLoS Biology",
"epub": "2004-09-07 00:00:00",
"authors": [
"Joshua M Akey",
"Michael A Eberle",
"Mark J Rie... |
PMC515368 | The von Hippel-Lindau (VHL) tumor suppressor functions as a ubiquitin ligase that mediates proteolytic inactivation of hydroxylated α subunits of hypoxia-inducible factor (HIF). Although studies of VHL-defective renal carcinoma cells suggest the existence of other VHL tumor suppressor pathways, dysregulation of the HIF... | # Introduction
The von Hippel-Lindau (VHL) gene is a tumor suppressor that is mutated in the majority of both hereditary and sporadic, clear-cell renal carcinomas [CIT_REF]. In hereditary VHL disease affected individuals are also predisposed to pheochromocytomas and retinal/central nervous system hemangioblastomas and... | {
"pmid": "15361934",
"doi": "10.1371/journal.pbio.0020289",
"article_title": "Genetic Analysis of Pathways Regulated by the von Hippel-Lindau Tumor Suppressor in Caenorhabditis elegans",
"journal_title": "PLoS Biology",
"epub": "2004-09-07 00:00:00",
"authors": [
"Tammie Bishop",
"Kah Weng Lau",
... |
PMC516016 | # Background
The Hotdog fold was initially identified in the structure of Escherichia coli FabA and subsequently in 4-hydroxybenzoyl-CoA thioesterase from Pseudomonas sp. strain CBS. Since that time structural determinations have shown a number of other apparently unrelated proteins also share the Hotdog fold.
# Resu... | # Background
We have found the HotDog domain, as we suggest calling the Hotdog fold, to be widespread in eukaryotes, bacteria, and archaea and to be involved in a range of cellular processes, from thioester hydrolysis, to phenylacetic acid degradation and transcriptional regulation of fatty acid biosynthesis. We prese... | {
"pmid": "15307895",
"doi": "10.1186/1471-2105-5-109",
"article_title": "The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases",
"journal_title": "",
"epub": "2004-08-12 00:00:00",
"authors": [
"Shane C Dillon",
"Alex Bateman"
],
"article_type": "research-article",
"lic... |
PMC516017 | # Background
The CBFA2T3 locus located on the human chromosome region 16q24.3 is frequently deleted in breast tumors. CBFA2T3 gene expression levels are aberrant in breast tumor cell lines and the CBFA2T3B isoform is a potential tumor suppressor gene. In the absence of identified mutations to further support a role fo... | # Background
Allelic loss of heterozygosity (LOH) of the human chromosome 16q in several sporadic cancer types, including breast, prostate and ovary cancers, suggests this chromosome arm harbors tumor suppressive loci [CIT_REF]. The most frequent region of allelic loss occurs within 3-megabases (Mb) at 16q24.3 between... | {
"pmid": "15301688",
"doi": "10.1186/1476-4598-3-22",
"article_title": "Aberrant CBFA2T3B gene promoter methylation in breast tumors",
"journal_title": "",
"epub": "2004-08-10 00:00:00",
"authors": [
"Anthony J Bais",
"Alison E Gardner",
"Olivia LD McKenzie",
"David F Callen",
"Grant R ... |
PMC516019 | # Background
Benzo(a)pyrene (BaP), anthracene (ANTH) and chrysene (CHRY) are polynuclear aromatic hydrocarbons (PAHs) implicated in renal toxicity and carcinogenesis. These PAHs elicit cell type-specific effects that help predict toxicity outcomes in vitro and in vivo. While BaP and ANTH selectively injure glomerular ... | # Background
The biological effects of PAHs are often mediated by oxidative metabolism of the parent hydrocarbon to reactive intermediates that adduct DNA and induce oxidative stress [CIT_REF]. In the kidney, PAHs elicit cell type-specific effects that differentially influence glomerular versus tubular epithelial cell... | {
"pmid": "15315710",
"doi": "10.1186/1477-3163-3-12",
"article_title": "Inducible cytochrome P450 activities in renal glomerular mesangial cells: biochemical basis for antagonistic interactions among nephrocarcinogenic polycyclic aromatic hydrocarbons",
"journal_title": "",
"epub": "2004-08-17 00:00:00",
"... |
PMC516020 | # Background
Viral promoters are used in mammalian expression vectors because they generally have strong activity in a wide variety of cells of differing tissues and species.
# Methods
The utility of the BLV LTR/promoter (BLVp) for use in mammalian expression vectors was investigated through direct comparison to the... | # Background
Viral promoters are commonly used as regulatory elements in gene therapy vectors due to their strong activity in various cell lines in vitro. Probably the most widely used promoter in mammalian expression systems is the human cytomegalovirus immediate-early gene (CMV) promoter. The CMV promoter induces hi... | {
"pmid": "15327692",
"doi": "10.1186/1479-0556-2-11",
"article_title": "Comparison of bovine leukemia virus (BLV) and CMV promoter-driven reporter gene expression in BLV-infected and non-infected cells",
"journal_title": "",
"epub": "2004-08-24 00:00:00",
"authors": [
"Jerome S Harms",
"Kurt A Eakl... |
PMC516021 | Modulation of the immune system by genetically modified immunological effector cells is of potential therapeutic value in the treatment of malignancies. Interleukin-2 (IL-2) is a crucial cytokine which induces potent antitumor response. Cytokine-induced killer cells (CIK) have been described as highly efficient cytotox... | # Introduction
Advances in the characterization of cytokines and tumor antigens, coupled with our increasing ability to manipulate gene expression, have fostered a new era of tumor immunotherapy [CIT_REF]. Interleukin-2 (IL-2) affects a variety of components of the cellular immune system, including B cells and macroph... | {
"pmid": "15329148",
"doi": "10.1186/1479-0556-2-12",
"article_title": "Human cytokine-induced killer cells have enhanced in vitro cytolytic activity via non-viral interleukin-2 gene transfer",
"journal_title": "",
"epub": "2004-08-25 00:00:00",
"authors": [
"Srinivas Nagaraj",
"Carsten Ziske",
... |
PMC516024 | # Background
Profile-based analysis of multiple sequence alignments (MSA) allows for accurate comparison of protein families. Here, we address the problems of detecting statistically confident dissimilarities between (1) MSA position and a set of predicted residue frequencies, and (2) between two MSA positions. These ... | # Background
Profile-based methods of sequence analysis use multiple sequence alignments (MSA) to extract information about conserved features of a protein family, which are impossible to decipher from a single sequence. Such methods increase both the sensitivity of homology detection and the quality of produced align... | {
"pmid": "15296518",
"doi": "10.1186/1471-2105-5-106",
"article_title": "Estimates of statistical significance for comparison of individual positions in multiple sequence alignments",
"journal_title": "",
"epub": "2004-08-05 00:00:00",
"authors": [
"Ruslan I Sadreyev",
"Nick V Grishin"
],
"arti... |
PMC516025 | # Background
During granulopoiesis in the bone marrow, the nucleus differentiates from ovoid to lobulated shape. Addition of retinoic acid (RA) to leukemic HL-60 cells induces development of lobulated nuclei, furnishing a convenient model system for nuclear differentiation during granulopoiesis. Previous studies from ... | # Background
Granulopoiesis, the differentiation of peripheral blood granulocytes, involves dramatic nuclear and cytoplasmic structural changes [CIT_REF]. Committed bone marrow progenitor cells possess ovoid-shaped nuclei with prominent nucleoli and a paucity of heterochromatin. The mature terminally differentiated hu... | {
"pmid": "15317658",
"doi": "10.1186/1471-2121-5-30",
"article_title": "Cytoskeletal influences on nuclear shape in granulocytic HL-60 cells",
"journal_title": "",
"epub": "2004-08-19 00:00:00",
"authors": [
"Ada L Olins",
"Donald E Olins"
],
"article_type": "research-article",
"license_kind"... |
PMC516027 | # Background
Endogenous reference genes are commonly used to normalize expression levels of other genes with the assumption that the expression of the former is constant in different tissues and in different physiopathological conditions. Whether this assumption is correct it is, however, still matter of debate. In th... | # Background
Endogenous reference alse referred to as house keeping genes defines in biology the theoretical assumption that certain genes are ubiquitously expressed in nucleated cells possibly because their stable expression is essential for cell survival and welfare in all physio-pathological circumstances. In pract... | {
"pmid": "15310404",
"doi": "10.1186/1471-2164-5-55",
"article_title": "Selection and validation of endogenous reference genes using a high throughput approach",
"journal_title": "",
"epub": "2004-08-13 00:00:00",
"authors": [
"Ping Jin",
"Yingdong Zhao",
"Yvonne Ngalame",
"Monica C Panelli... |
PMC516028 | # Background
Gene expression technologies have the ability to generate vast amounts of data, yet there often resides only limited resources for subsequent validation studies. This necessitates the ability to perform sorting and prioritization of the output data. Previously described methodologies have used functional ... | # Background
Gene expression profiling, along with other methods to evaluate the global changes in genomes, provides the opportunity to understand whole scale changes present in human biology. Yet the sheer mass of data presented by these techniques often makes subsequent analysis difficult. Techniques such as gene ex... | {
"pmid": "15318950",
"doi": "10.1186/1471-2164-5-58",
"article_title": "Cross-species global and subset gene expression profiling identifies genes involved in prostate cancer response to selenium",
"journal_title": "",
"epub": "2004-08-20 00:00:00",
"authors": [
"Michael Schlicht",
"Brian Matysiak"... |
PMC516029 | # Background
The thymus is the primary site for T-cell development and induction of self-tolerance. Previous approaches towards manipulation of T-cell differentiation have used intrathymic injection of antigens, as proteins, cells or adenoviruses, leading to transient expression of the foreign protein. Lentiviral vect... | # Background
The thymus is a bilobate organ derived from embryonic endoderm and mesoderm differentiation and is located just above the heart (reviewed in [CIT_REF]. It is the primary organ for maturation of T cells. This process involves the interaction between developing thymocytes and thymic stromal cells. Thymic st... | {
"pmid": "15318949",
"doi": "10.1186/1471-2172-5-18",
"article_title": "In situ transduction of stromal cells and thymocytes upon intrathymic injection of lentiviral vectors",
"journal_title": "",
"epub": "2004-08-19 00:00:00",
"authors": [
"Gilles Marodon",
"David Klatzmann"
],
"article_type":... |
PMC516030 | # Background
The periodic pattern of DNA in exons is a known phenomenon. It was suggested that one of the initial causes of periodicity could be the universal (RNY) _{n} pattern (R=A or G, Y=C or U, N=any base) of ancient RNA. Two major questions were addressed in this paper. Firstly, the cause of DNA periodicity, whi... | # Background
Periodicity of DNA in exons, with the period being equal to 3 nucleotides, has been well known for some time [CIT_REF]. This periodicity reflects correlations between nucleotide positions along coding sequences [CIT_REF], which is caused by the asymmetry in base composition at the three coding positions [... | {
"pmid": "15315715",
"doi": "10.1186/1471-2199-5-12",
"article_title": "Periodicity of DNA in exons",
"journal_title": "",
"epub": "2004-08-18 00:00:00",
"authors": [
"Stephen T Eskesen",
"Frank N Eskesen",
"Brian Kinghorn",
"Anatoly Ruvinsky"
],
"article_type": "research-article",
"l... |
PMC516031 | # Background
Serum Response Factor (SRF) is a transcription factor that is required for the expression of many genes including immediate early genes, cytoskeletal genes, and muscle-specific genes. SRF is activated in response to extra-cellular signals by its association with a diverse set of co-activators in different... | # Background
Quiescent cells exposed to growth factors respond by expressing a variety of immediate early genes (IEG) that do not need new protein synthesis for their expression [CIT_REF]. Serum or growth factor induced expression of many of these immediate early genes, such as c-fos, egr1, cyr61 and pip92, is depende... | {
"pmid": "15329155",
"doi": "10.1186/1471-2199-5-13",
"article_title": "Expression profiling of serum inducible genes identifies a subset of SRF target genes that are MKL dependent",
"journal_title": "",
"epub": "2004-08-25 00:00:00",
"authors": [
"Ahalya Selvaraj",
"Ron Prywes"
],
"article_typ... |
PMC516032 | # Background
Understanding the factors that affect patients' utilisation of health services is important for health service provision and effective patient management. This study aimed to investigate the specific morbidity and demographic factors related to the frequency with which general practice patients visit a ge... | # Background
The frequency of patient visits to general/family practice is affected by a range of factors including patient characteristics, physician/practice factors and broader issues such as access to services. A major contributor to the variance in visit rates to general/family practitioners is the complexity of ... | {
"pmid": "15318948",
"doi": "10.1186/1471-2296-5-17",
"article_title": "The contribution of demographic and morbidity factors to self-reported visit frequency of patients: a cross-sectional study of general practice patients in Australia",
"journal_title": "",
"epub": "2004-08-20 00:00:00",
"authors": [
... |
PMC516033 | # Background
Esophagectomy is considered the gold standard for the treatment of high-grade dysplasia in Barrett's esophagus (BE) and for noninvasive adenocarcinoma (ACA) of the distal esophagus. If all of the metaplastic epithelium is removed, the patient is considered "cured". Despite this, BE has been reported in pa... | # Background
The incidence of esophageal adenocarcinoma has increased more rapidly than any other form of cancer since the 1970s and now represents the majority of esophageal neoplasms in the West [CIT_REF]. Barrett's esophagus is the replacement of native squamous mucosa by specialized intestinal metaplasia and is kn... | {
"pmid": "15327696",
"doi": "10.1186/1471-230X-4-18",
"article_title": "Recurrent Barrett's esophagus and adenocarcinoma after esophagectomy",
"journal_title": "",
"epub": "2004-08-25 00:00:00",
"authors": [
"Herbert C Wolfsen",
"Lois L Hemminger",
"Kenneth R DeVault"
],
"article_type": "re... |
PMC516035 | # Background
The aim of this experimental study was to determine the effect of mild hyperthermia on tumor response and angioneogenesis in an isolated limb perfusion model with a human melanoma xenograft.
# Methods
A human melanoma xenograft was implanted into the hindlimbs of 30 athymic nude rats. The animals were r... | # Background
Hyperthermic isolated limb perfusion is an established treatment for multiple, locoregional intransit metastases of malignant melanoma and soft tissue sarcomas of the extremities. It was introduced 1957 by Creech and Krementz [CIT_REF]. The procedure allows a high locoregional concentration of cytostatics... | {
"pmid": "15324457",
"doi": "10.1186/1471-2407-4-53",
"article_title": "The impact of surgery and mild hyperthermia on tumor response and angioneogenesis of malignant melanoma in a rat perfusion model",
"journal_title": "",
"epub": "2004-08-23 00:00:00",
"authors": [
"Joerg Pelz",
"Marco Mollwitz",... |
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