bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analysis of expression of histone H2a genes in mouse
Authors: Nishida Hiromi , Suzuki Takahiro , Ookawa Hiroki , Tomaru Yasuhiro , Hayashizaki Yoshihide 
Published: August 2005

Abstract

Background
At least 18 replication-dependent histone H2a genes are distributed in 3 Hist gene clusters on different chromosomes of the mouse genome. In this analysis we designed specific PCR primers for each histone H2a transcript and studied the expression levels and patterns using quantitative RT-PCR (qRT-PCR). In addition, we compared histone H3 K9 acetylation levels in the promoter regions of H2a genes by ChIP (chromatin immunoprecipitation) – quantitative PCR (qPCR) analysis.

Results
RT-PCR analysis indicated that all 20 histone H2a genes assessed in this study are expressed. The replication-dependent histone H2a genes have different expression levels but similar expression patterns. Among the 20 histone H2a genes, the expression-level of H2afz, a replication-independent gene, was highest, and that of Hist1h2aa, a replication-dependent gene, was lowest. Among 18 replication-dependent H2a genes, the expression level of Hist3h2a was highest. The ChIP-qPCR analysis showed that histone H3 K9 acetylation levels in promoter regions of both H2afz and Hist3h2a are clearly higher than that in the promoter region of Hist1h2aa. The H3 K9 acetylation level in the promoter of Hist1h2aa is similar to that in the γ-satellite region.

Conclusion
These results strongly suggest that histone H3 K9 acetylation plays a role in the expression of histone genes.
Dual activation of pathways regulated by steroid receptors and peptide growth factors in primary prostate cancer revealed by Factor Analysis of microarray data
Authors: Lozano Juan Jose , Soler Marta , Bermudo Raquel , Abia David , Fernandez Pedro L , Thomson Timothy M , Ortiz Angel R 
Published: August 2005

AbstractBackgroundWe use an approach based on Factor Analysis to analyze datasets generated for transcriptional profiling. The method groups samples into biologically relevant categories, and enables the identification of genes and pathways most significantly associated to each phenotypic group, while allowing for the participation of a given gene in more than one cluster. Genes assigned to each cluster are used for the detection of pathways predominantly activated in that cluster by finding statistically significant associated GO terms. We tested the approach with a published dataset of microarray experiments in yeast. Upon validation with the yeast dataset, we applied the technique to a prostate cancer dataset.ResultsTwo major pathways are shown to be activated in organ-confined, non-metastatic prostate cancer: those regulated by the androgen receptor and by receptor tyrosine kinases. A number of gene markers (HER3, IQGAP2 and POR1) highlighted by the software and related to the later pathway have been validated experimentallya posteriorion independent samples.ConclusionUsing a new microarray analysis tool followed bya posterioriexperimental validation of the results, we have confirmed several putative markers of malignancy associated with peptide growth factor signalling in prostate cancer and revealed others, most notably ERRB3 (HER3). Our study suggest that, in primary prostate cancer, HER3, together or not with HER4, rather than in receptor complexes involving HER2, could play an important role in the biology of these tumors. These results provide new evidence for the role of receptor tyrosine kinases in the establishment and progression of prostate cancer.
Spatiotemporal receptive field properties of epiretinally recorded spikes and local electroretinograms in cats
Authors: Wilms Marcus , Eckhorn Reinhard 
Published: August 2005

Abstract

Background
Receptive fields of retinal neural signals of different origin can be determined from extracellular microelectrode recordings at the inner retinal surface. However, locations and types of neural processes generating the different signal components are difficult to separate and identify. We here report epiretinal receptive fields (RFs) from simultaneously recorded spikes and local electroretinograms (LERGs) using a semi-chronic multi-electrode in vivo recording technique in cats. Broadband recordings were filtered to yield LERG and multi unit as well as single unit spike signals. RFs were calculated from responses to multifocal pseudo-random spatiotemporal visual stimuli registered at the retinal surface by a 7-electrode array.

Results
LERGs exhibit spatially unimodal RFs always centered at the location of the electrode tip. Spike-RFs are either congruent with LERG-RFs (N = 26/61) or shifted distally (N = 35/61) but never proximally with respect to the optic disk. LERG-RFs appear at shorter latencies (11.9 ms ± 0.5 ms, N = 18) than those of spikes (18.6 ms ± 0.4 ms, N = 53). Furthermore, OFF-center spike-RFs precede and have shorter response rise times than ON-center spike-RFs. Our results indicate that displaced spike-RFs result from action potentials of ganglion cell axons passing the recording electrode en route to the optic disk while LERG-RFs are related to superimposed postsynaptic potentials of cells near the electrode tip.

Conclusion
Besides contributing to the understanding of retinal function we demonstrate the caveats that come with recordings from the retinal surface, i.e., the likelihood of recordings from mixed sets of retinal neurons. Implications for the design of an epiretinal visual implant are discussed.
Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana
Authors: Mudge Joann , Cannon Steven B , Kalo Peter , Oldroyd Giles ED , Roe Bruce A , Town Christopher D , Young Nevin D 
Published: August 2005

Abstract

Background
Recent genome sequencing enables mega-base scale comparisons between related genomes. Comparisons between animals, plants, fungi, and bacteria demonstrate extensive synteny tempered by rearrangements. Within the legume plant family, glimpses of synteny have also been observed. Characterizing syntenic relationships in legumes is important in transferring knowledge from model legumes to crops that are important sources of protein, fixed nitrogen, and health-promoting compounds.

Results
We have uncovered two large soybean regions exhibiting synteny with M. truncatula and with a network of segmentally duplicated regions in Arabidopsis. In all, syntenic regions comprise over 500 predicted genes spanning 3 Mb. Up to 75% of soybean genes are colinear with M. truncatula, including one region in which 33 of 35 soybean predicted genes with database support are colinear to M. truncatula. In some regions, 60% of soybean genes share colinearity with a network of A. thaliana duplications. One region is especially interesting because this 500 kbp segment of soybean is syntenic to two paralogous regions in M. truncatula on different chromosomes. Phylogenetic analysis of individual genes within these regions demonstrates that one is orthologous to the soybean region, with which it also shows substantially denser synteny and significantly lower levels of synonymous nucleotide substitutions. The other M. truncatula region is inferred to be paralogous, presumably resulting from a duplication event preceding speciation.

Conclusion
The presence of well-defined M. truncatula segments showing orthologous and paralogous relationships with soybean allows us to explore the evolution of contiguous genomic regions in the context of ancient genome duplication and speciation events.
Development of ESTs from chickpea roots and their use in diversity analysis of the Cicergenus
Authors: Buhariwalla Hutokshi K , B Jayashree , Eshwar K , Crouch Jonathan H 
Published: August 2005

Abstract
Background
Chickpea is a major crop in many drier regions of the world where it is an important protein-rich food and an increasingly valuable traded commodity. The wild annual Cicer species are known to possess unique sources of resistance to pests and diseases, and tolerance to environmental stresses. However, there has been limited utilization of these wild species by chickpea breeding programs due to interspecific crossing barriers and deleterious linkage drag. Molecular genetic diversity analysis may help predict which accessions are most likely to produce fertile progeny when crossed with chickpea cultivars. While, trait-markers may provide an effective tool for breaking linkage drag. Although SSR markers are the assay of choice for marker-assisted selection of specific traits in conventional breeding populations, they may not provide reliable estimates of interspecific diversity, and may lose selective power in backcross programs based on interspecific introgressions. Thus, we have pursued the development of gene-based markers to resolve these problems and to provide candidate gene markers for QTL mapping of important agronomic traits.

Results
An EST library was constructed after subtractive suppressive hybridization (SSH) of root tissue from two very closely related chickpea genotypes (Cicer arietinum). A total of 106 EST-based markers were designed from 477 sequences with functional annotations and these were tested on C. arietinum. Forty-four EST markers were polymorphic when screened across nine Cicer species (including the cultigen). Parsimony and PCoA analysis of the resultant EST-marker dataset indicated that most accessions cluster in accordance with the previously defined classification of primary (C. arietinum, C. echinospermum and C. reticulatum), secondary (C. pinnatifidum, C. bijugum and C. judaicum), and tertiary (C. yamashitae, C. chrossanicum and C. cuneatum) gene-pools. A large proportion of EST alleles (45%) were only present in one or two of the accessions tested whilst the others were represented in up to twelve of the accessions tested.

Conclusion
Gene-based markers have proven to be effective tools for diversity analysis in Cicer and EST diversity analysis may be useful in identifying promising candidates for interspecific hybridization programs. The EST markers generated in this study have detected high levels of polymorphism amongst both common and rare alleles. This suggests that they would be useful for allele-mining of germplasm collections for identification of candidate accessions in the search for new sources of resistance to pests / diseases, and tolerance to abiotic stresses.
Autoimmune hepatitis in India: profile of an uncommon disease
Authors: Choudhuri Gourdas , Somani Sanjay K , Baba Chalamalasetty S , Alexander George 
Published: August 2005

Abstract
Background
Autoimmune hepatitis (AIH) has been reported to show considerable geographical variation in frequency and clinical manifestations. It is considered a rare cause of liver disease in India. The present study was undertaken to determine the incidence, clinical, biochemical and histological profile of AIH in this part of the world.

Methods
Patients presenting with acute or chronic liver disease between January 1999 and June 2002 were evaluated prospectively. AIH was diagnosed using the international autoimmune hepatitis group criteria. Workup included clinical, biochemical, USG, viral markers, UGI endoscopy, AI markers (ANA, SMA, Anti-LKM, AMA, RF, p-ANCA) using indirect immunofluorescence and liver biopsy if possible.

Results
Forty-one of 2401 (1.70%) patients were diagnosed to have autoimmune liver disease. Out of these, 38 had autoimmune hepatitis and the rest 3 had primary biliary cirrhosis. The mean age of the patients of autoimmune hepatitis was 36.2 (15.9) years, 34 (89.4%) were females, and the duration of symptoms was 20.3 (20.5) months. Nineteen (50%) of them presented with chronic hepatitis, 13 (34.2%) as cirrhosis, 5 (13.1%) with acute hepatitis and 1 (2.6%) with cholestatic hepatitis. The presentations were jaundice in 21 (55.2%), pedal edema and hepatomegaly in 17 (44.7%), splenomegaly in 13 (34.2%), encephalopathy, abdominal pain in 9 (23.6%) and fever in 8 (21%). Twelve had esophageal varices and 3 had bled. Biochemical parameters were ALT 187 (360) U/L, AST 157 (193) U/L, ALP 246 (254) U/L, globulin 4.1 (1.6) g/dL, albumin 2.8 (0.9) g/dL, bilirubin 5.2 (7.4) mg/dL, prothrombin time 17 (7) sec and ESR 47 (17) sec. The autoimmune markers were SMA (24), ANA (15), both SMA and ANA (4), AMA (1), rheumatoid factor (2), pANCA (1), and Anti-LKM in none. Thirty (79%) patients had definite AIH and eight (21%) had probable AI hepatitis. Associated autoimmune diseases was seen in 15/38 (39.4%), diabetes 4, hypothyroidism 3, vitiligo 2, thrombocytopenia 2, rheumatoid arthritis 2, Sjogren's syndrome 1 and autoimmune polyglandular syndrome III in 1. Viral markers were positive in two patients, one presenting as acute hepatitis and HEV-IgM positive and another anti-HCV positive.

Conclusion
In India, autoimmune hepatitis is uncommon and usually presents with chronic hepatitis or cirrhosis, acute hepatitis being less common. Age at presentation was earlier but clinical parameters and associated autoimmune diseases were similar to that reported from the west. Primary biliary cirrhosis is rare. Type II AIH was not observed.
Absence of pathogenic mitochondrial DNA mutations in mouse brain tumors
Authors: Kiebish Michael A , Seyfried Thomas N 
Published: August 2005

AbstractBackgroundSomatic mutations in the mitochondrial genome occur in numerous tumor types including brain tumors. These mutations are generally found in the hypervariable regions I and II of the displacement loop and unlikely alter mitochondrial function. Two hypervariable regions of mononucleotide repeats occur in the mouse mitochondrial genome, i.e., the origin of replication of the light strand (OL) and the Arg tRNA.MethodsIn this study we examined the entire mitochondrial genome in a series of chemically induced brain tumors in the C57BL/6J strain and spontaneous brain tumors in the VM mouse strain. The tumor mtDNA was compared to that of mtDNA in brain mitochondrial populations from the corresponding syngeneic mouse host strain.ResultsDirect sequencing revealed a few homoplasmic base pair insertions, deletions, and substitutions in the tumor cells mainly in regions of mononucleotide repeats. A heteroplasmic mutation in the 16srRNA gene was detected in a spontaneous metastatic VM brain tumor.ConclusionNone of the mutations were considered pathogenic, indicating that mtDNA somatic mutations do not likely contribute to the initiation or progression of these diverse mouse brain tumors.
Is Microsporidial keratitis an emerging cause of stromal keratitis? – a case series study
Authors: Vemuganti Geeta K , Garg Prashant , Sharma Savitri , Joseph Joveeta , Gopinathan Usha , Singh Shashi 
Published: August 2005

Abstract

Background
Microsporidial keratitis is a rare cause of stromal keratitis. We present a series of five cases of microsporidial keratitis from a single centre in southern India with microbiologic and histopathologic features.

Case presentation
Patient charts of five cases of microsporidial stromal keratitis diagnosed between January 2002 and June 2004 were reviewed retrospectively for clinical data, microbiologic and histopathologic data. The presence of microsporidia was confirmed by special stains on corneal scrapings and/or corneal tissues, and electron microscopy. All patients were immunocompetent with a preceding history of trauma in three. Four patients presented with unilateral, small, persisting deep stromal infiltrates, of uncertain etiology, in the cornea, which were not responding to conventional antimicrobial treatment and required penetrating keratoplasty in three. Fifth case was unsuspected and underwent keratoplasty for post-traumatic scar. Three of five cases were diagnosed on corneal scrapings, prior to keratoplasty, while two were diagnosed only on histology. The microsporidia appeared as oval well defined bodies with dense staining at one pole. None of the patients showed recurrence following keratoplasty.

Conclusion
Microsporidia, though rare, should be suspected in chronic culture-negative stromal keratitis. Organisms could lie dormant without associated inflammation.
Bilateral neuro-retinitis following chick embryo cell anti-rabies vaccination – a case report
Authors: Saxena Rohit , Sethi Harinder Singh , Rai Harminder Kumar , Menon Vimla 
Published: August 2005

Abstract

Background
The Optic nerve is rarely involved after sheep brain anti-rabies vaccination in the form of retrobulbar neuritis or papillitis. Bilateral neuroretinitis after chick embryo cell antirabies vaccination has not been reported.

Case presentation
We report the case of a 56 year old male who developed bilateral neuro-retinitis following three injections of antirabies vaccine prepared from the chick embryo.

Conclusion
The chick embryo cell antirabies vaccine can cause bilateral neuroretinits which has not been reported previously.
The impact of changes to heroin supply on blood-borne virus notifications and injecting related harms in New South Wales, Australia
Authors: Day Carolyn , Degenhardt Louisa , Gilmour Stuart , Hall Wayne 
Published: August 2005

Abstract

Background
In early 2001 Australia experienced a sudden and unexpected disruption to heroin availability, know as the 'heroin shortage'. This 'shortage has been linked to a decrease in needle and syringe output and therefore possibly a reduction in injecting drug use. We aimed to examine changes, if any, in blood-borne viral infections and presentations for injecting related problems related to injecting drug use following the reduction heroin availability in Australia, in the context of widespread harm reduction measures.

Methods
Time series analysis of State level databases on HIV, hepatitis B, hepatitis C notifications and hospital and emergency department data. Examination of changes in HIV, hepatitis B, hepatitis C notifications and hospital and emergency department admissions for injection-related problems following the onset of the heroin shortage; non-parametric curve-fitting of number of hepatitis C notifications among those aged 15–19 years.

Results
There were no changes observed in hospital visits for injection-related problems. There was no change related to the onset heroin shortage in the number of hepatitis C notifications among persons aged 15–19 years, but HCV notifications have subsequently decreased in this group. No change occurred in HIV and hepatitis B notifications.

Conclusion
A marked reduction in heroin supply resulted in no increase in injection-related harm at the community level. However, a delayed decrease in HCV notifications among young people may be related. These changes occurred in a setting with widespread, publicly funded harm reduction initiatives.
Health disparities and advertising content of women's magazines: a cross-sectional study
Authors: Duerksen Susan C , Mikail Amy , Tom Laura , Patton Annie , Lopez Janina , Amador Xavier , Vargas Reynaldo , Victorio Maria , Kustin Brenda , Sadler Georgia Robins 
Published: August 2005

Abstract
Background
Disparities in health status among ethnic groups favor the Caucasian population in the United States on almost all major indicators. Disparities in exposure to health-related mass media messages may be among the environmental factors contributing to the racial and ethnic imbalance in health outcomes. This study evaluated whether variations exist in health-related advertisements and health promotion cues among lay magazines catering to Hispanic, African American and Caucasian women.

Methods
Relative and absolute assessments of all health-related advertising in 12 women's magazines over a three-month period were compared. The four highest circulating, general interest magazines oriented to Black women and to Hispanic women were compared to the four highest-circulating magazines aimed at a mainstream, predominantly White readership. Data were collected and analyzed in 2002 and 2003.

Results
Compared to readers of mainstream magazines, readers of African American and Hispanic magazines were exposed to proportionally fewer health-promoting advertisements and more health-diminishing advertisements. Photographs of African American role models were more often used to advertise products with negative health impact than positive health impact, while the reverse was true of Caucasian role models in the mainstream magazines.

Conclusion
To the extent that individual levels of health education and awareness can be influenced by advertising, variations in the quantity and content of health-related information among magazines read by different ethnic groups may contribute to racial disparities in health behaviors and health status.
HEGPOL: Randomized, placebo controlled, multicenter, double-blind clinical trial to investigate hepatoprotective effects of glycine in the postoperative phase of liver transplantation [ISRCTN69350312]
Authors: Luntz Steffen P , Unnebrink Kristina , Seibert-Grafe Monika , Bunzendahl Hartwig , Kraus Thomas W , Büchler Markus W , Klar Ernst , Schemmer Peter 
Published: August 2005

Abstract

Background
Kupffer cell-dependent ischemia / reperfusion (I/R) injury after liver transplantation is still of high clinical relevance, as it is strongly associated with primary dysfunction and primary nonfunction of the graft. Glycine, a non-toxic, non-essential amino acid has been conclusively shown in various experiments to prevent both activation of Kupffer cells and reperfusion injury. Based on both experimental and preliminary clinical data this study protocol was designed to further evaluate the early effect of glycine after liver transplantation.

Methods / design
A prospective double-blinded randomized placebo-controlled multicenter study with two parallel groups in a total of 130 liver transplant recipients was designed to assess the effect of multiple intravenous doses of glycine after transplantation. Primary endpoints in hierarchical order are: peak levels of both aspartat-amino-transaminase (AST) and alanine-amino-transaminase (ALT) as surrogates for the progression of liver related injury, as well as both graft and patient survival up to 2 years after transplantation. Furthermore, the effect of glycine on cyclosporine A-induced nephrotoxicity is evaluated.

Discussion
The ongoing clinical trial represents an advanced element of the research chain, along which a scientific hypothesis has to go by, in order to reach the highest level of evidence; a randomized, prospective, controlled double-blinded clinical trial. If the data of this ongoing research project confirm prior findings, glycine would improve the general outcome after liver transplantation.