bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Cytochrome P450 Engineering Database: integration of biochemical properties
Authors: Sirim Demet , Wagner Florian , Lisitsa Andrey , Pleiss Jürgen 
Published: November 2009

Abstract

Background
Cytochrome P450 monooxygenases (CYPs) form a vast and diverse enzyme class of particular interest in drug development and a high biotechnological potential. Although very diverse in sequence, they share a common structural fold. For the comprehensive and systematic comparison of protein sequences and structures the Cytochrome P450 Engineering Database (CYPED) was established. It was built up based on an extensible data model that enables its functions readily enhanced.

Description
The new version of the CYPED contains information on sequences and structures of 8613 and 47 proteins, respectively, which strictly follow Nelson's classification rules for homologous families and superfamilies. To gain biochemical information on substrates and inhibitors, the CYPED was linked to the Cytochrome P450 Knowledgebase (CPK). To overcome differences in the data model and inconsistencies in the content of CYPED and CPK, a metric was established based on sequence similarity to link protein sequences as primary keys. In addition, the annotation of structurally and functionally relevant residues was extended by a reliable prediction of conserved secondary structure elements and by information on the effect of single nucleotide polymorphisms.

Conclusion
The online accessible version of the CYPED at http://www.cyped.uni-stuttgart.de provides a valuable tool for the analysis of sequences, structures and their relationships to biochemical properties.
An expression database for roots of the model legume Medicago truncatula under salt stress
Authors: Li Daofeng , Su Zhen , Dong Jiangli , Wang Tao 
Published: November 2009

Abstract

Background

Medicago truncatula is a model legume whose genome is currently being sequenced by an international consortium. Abiotic stresses such as salt stress limit plant growth and crop productivity, including those of legumes. We anticipate that studies on M. truncatula will shed light on other economically important legumes across the world. Here, we report the development of a database called MtED that contains gene expression profiles of the roots of M. truncatula based on time-course salt stress experiments using the Affymetrix Medicago GeneChip. Our hope is that MtED will provide information to assist in improving abiotic stress resistance in legumes.

Description
The results of our microarray experiment with roots of M. truncatula under 180 mM sodium chloride were deposited in the MtED database. Additionally, sequence and annotation information regarding microarray probe sets were included. MtED provides functional category analysis based on Gene and GeneBins Ontology, and other Web-based tools for querying and retrieving query results, browsing pathways and transcription factor families, showing metabolic maps, and comparing and visualizing expression profiles. Utilities like mapping probe sets to genome of M. truncatula and In-Silico PCR were implemented by BLAT software suite, which were also available through MtED database.

Conclusion
MtED was built in the PHP script language and as a MySQL relational database system on a Linux server. It has an integrated Web interface, which facilitates ready examination and interpretation of the results of microarray experiments. It is intended to help in selecting gene markers to improve abiotic stress resistance in legumes. MtED is available at http://bioinformatics.cau.edu.cn/MtED/.
Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site
Authors: Wang Pingzhang , Yu Peng , Gao Peng , Shi Taiping , Ma Dalong 
Published: November 2009

AbstractBackgroundAlternative polyadenylation sites within a gene can lead to alternative transcript variants. Although bioinformatic analysis has been conducted to detect polyadenylation sites using nucleic acid sequences (EST/mRNA) in the public databases, one special type, single-block EST is much less emphasized. This bias leaves a large space to discover novel transcript variants.ResultsIn the present study, we identified novel transcript variants in the human genome by detecting intronic polyadenylation sites. Poly(A/T)-tailed ESTs were obtained from single-block ESTs and clustered into 10,844 groups standing for 5,670 genes. Most sites were not found in other alternative splicing databases. To verify that these sites are from expressed transcripts, we analyzed the supporting EST number of each site, blasted representative ESTs against known mRNA sequences, traced terminal sequences from cDNA clones, and compared with the data of Affymetrix tiling array. These analyses confirmed about 84% (9,118/10,844) of the novel alternative transcripts, especially, 33% (3,575/10,844) of the transcripts from 2,704 genes were taken as high-reliability. Additionally, RT-PCR confirmed 38% (10/26) of predicted novel transcript variants.ConclusionOur results provide evidence for novel transcript variants with intronic poly(A) sites. The expression of these novel variants was confirmed with computational and experimental tools. Our data provide a genome-wide resource for identification of novel human transcript variants with intronic polyadenylation sites, and offer a new view into the mystery of the human transcriptome.
Correlation of microsynteny conservation and disease gene distribution in mammalian genomes
Authors: Lovell Simon C , Li Xiting , Weerasinghe Nimmi R , Hentges Kathryn E 
Published: November 2009

Abstract

Background
With the completion of the whole genome sequence for many organisms, investigations into genomic structure have revealed that gene distribution is variable, and that genes with similar function or expression are located within clusters. This clustering suggests that there are evolutionary constraints that determine genome architecture. However, as most of the evidence for constraints on genome evolution comes from studies on yeast, it is unclear how much of this prior work can be extrapolated to mammalian genomes. Therefore, in this work we wished to examine the constraints on regions of the mammalian genome containing conserved gene clusters.

Results
We first identified regions of the mouse genome with microsynteny conservation by comparing gene arrangement in the mouse genome to the human, rat, and dog genomes. We then asked if any particular gene types were found preferentially in conserved regions. We found a significant correlation between conserved microsynteny and the density of mouse orthologs of human disease genes, suggesting that disease genes are clustered in genomic regions of increased microsynteny conservation.

Conclusion
The correlation between microsynteny conservation and disease gene locations indicates that regions of the mouse genome with microsynteny conservation may contain undiscovered human disease genes. This study not only demonstrates that gene function constrains mammalian genome organization, but also identifies regions of the mouse genome that can be experimentally examined to produce mouse models of human disease.
Comparison of a new transcutaneous bilirubinometer (Bilimed®) with serum bilirubin measurements in preterm and full-term infants
Authors: Karen Tanja , Bucher Hans Ulrich , Fauchère Jean-Claude 
Published: November 2009

Abstract

Background
The gold standard to assess hyperbilirubinemia in neonates remains the serum bilirubin measurement. Unfortunately, this is invasive, painful, and costly. Bilimed®, a new transcutaneous bilirubinometer, suggests more accuracy compared to the existing non-invasive bilirubinometers because of its new technology. It furthermore takes into account different skin colours. No contact with the skin is needed during measurement, no additional material costs occur. Our aim was to assess the agreement between the Bilimed® and serum bilirubin in preterm and term infants of different skin colours.

Methods
The transcutaneous bilirubin measurements were performed on the infant's sternum and serum bilirubin was determined simultaneously. The agreement between both methods was assessed by Pearson's correlation and by Bland-Altman analysis.

Results
A total of 117 measurement cycles were performed in 99 term infants (group1), further 47 measurements in 38 preterm infants born between 34 - 36 6/7 gestational weeks (group 2), and finally 21 measurements in 13 preterm infants born between 28 - 33 6/7 gestational weeks (group 3). The mean deviation and variability (+/- 2SD) of the transcutaneous from serum bilirubin were: -14 (+/- 144) μmol/l; -0.82 (+/- 8.4) mg/dl in group 1, +16 (+/- 91) μmol/l;+0.93(+/- 5.3) mg/dl in group 2 and -8 (+/- 76) μmol/l; -0.47 (+/- 4.4) mg/dl in group 3. These limits of agreement are too wide to be acceptable in a clinical setting. Moreover, there was to be a trend towards less good agreement with increasing bilirubin values.

Conclusion
Despite its new technology the Bilimed® has no advantages, and more specifically no better agreement not only in term and near-term Caucasian infants, but also in non-Caucasian and more premature infants.
Self-medication with over-the-counter drugs and complementary medications in South Australia's elderly population
Authors: Goh Lynn Yeen , Vitry Agnes I , Semple Susan J , Esterman Adrian , Luszcz Mary A 
Published: November 2009

AbstractBackgroundA number of surveys have examined use of complementary and alternative medicines (CAM) in Australia. However, there are limited Australian data on use of CAM and over-the-counter (OTC) medicines in the elderly population. The main aims of this study were to examine self-medication practices with CAM and OTC medicines among older Australians and variables associated with their use.MethodsThe Australian Longitudinal Study of Ageing (ALSA) is an ongoing multidisciplinary prospective study of the older population which commenced in 1992 in South Australia. Data collected in 4 waves of ALSA between 1992 and 2004 were used in this study with a baseline sample of 2087 adults aged 65 years and over, living in the community or residential aged care. OTC medicines were classified according to the World Health Organization Anatomical Therapeutic Chemical (ATC) classification. CAM were classified according a modified version of the classification adopted by the Therapeutics Goods Administration (TGA) in Australia.ResultsThe prevalence of CAM or OTC use ranged from 17.7% in 2000-2001 to 35.5% in 2003-2004. The top classes of CAM and OTC medicines used remained relatively constant over the study period. The most frequent classes of CAM used were vitamins and minerals, herbal medicines and nutritional supplements while the most commonly used OTC were analgesics, laxatives and low dose aspirin. Females and those of younger age were more likely to be CAM users but no variable was associated with OTC use.ConclusionParticipants seemed to self-medicate in accordance with approved indications, suggesting they were informed consumers, actively looking after their own health. However, use of analgesics and aspirin are associated with an increased risk of adverse drug events in the elderly. Future work should examine how self-medication contributes to polypharmacy and increases the risk of adverse drug reactions.
Tsukamurella tyrosinosolvens - An unusual case report of bacteremic pneumonia after lung transplantation
Authors: Ménard Armelle , Degrange Sébastien , Peuchant Olivia , Nguyen Thi Diem Tien , Dromer Claire , Maugein Jeanne 
Published: November 2009

Abstract

Background
Lung transplant recipients have an increased risk for actinomycetales infection secondary to immunosuppressive regimen.

Case presentation
A case of pulmonary infection with bacteremia due to Tsukamurella tyrosinosolvens in a 54-year old man who underwent a double lung transplantation four years previously is presented.

Conclusion
The identification by conventional biochemical assays was unsuccessful and hsp gene sequencing was used to identify Tsukamurella tyrosinosolvens.
Frontal skull craniotomy combined with moderate-dose radiotherapy effectively ameliorate a rare case of non-secretory, multiple myeloma with orbital involvement
Authors: Ko Hui-Ling , Chen Ching-Lin , Chi Kwan-Hwa 
Published: November 2009

Abstract

Background
Orbital infiltration in patients with multiple myeloma is a rare condition, with less than 50 cases reported in the medical literature. Most patients undergo conservative treatment because multiple myeloma is a disseminated systemic disease.

Case presentation
A 43-year-old male subject with multiple myeloma and long-term survival presented with orbital involvement. The subject lacked the typical features and poor prognostic factors associated with multiple myeloma, such as renal failure, hypercalcemia, and paraprotein in the serum and urine. The orbital computed tomographic scan revealed the tumor encasing the optic nerve, but without prominent bony destruction. Therefore, a frontal skull craniotomy with an epidural entrance to the orbital space was performed, to completely extirpate the orbital mass. The surgical procedure was followed by moderate-dose radiation therapy. After 32 months of follow-up care, the subject is doing well with excellent local control.

Conclusion
Although the effectiveness and applicability of this approach remains to be determined, this case report demonstrates that accurate and early detection combined with local surgical treatment and appropriate radio/chemotherapy, can be applied to effectively extend an orbital multiple myeloma patient's life.
Antinociceptive Action of Oxytocin Involves Inhibition of Potassium Channel Currents in Lamina Ii Neurons of the Rat Spinal Cord
Authors: Breton Jean Didier , Poisbeau Pierrick , Darbon Pascal 
Published: November 2009

Background Growing evidence in the literature shows that oxytocin (OT) has a strong spinal anti-nociceptive action. Oxytocinergic axons originating from a subpopulation of paraventricular hypothalamic neurons establish synaptic contacts with lamina II interneurons but little is known about the functional role of OT with respect to neuronal firing and excitability. Results Using the patch-clamp technique, we have recorded lamina II interneurons in acute transverse lumbar spinal cord slices of rats (15 to 30 days old) and analyzed the OT effects on action potential firing ability. In the current clamp mode, we found that bath application of a selective OT-receptor agonist (TGOT) reduced firing in the majority of lamina II interneurons exhibiting a bursting firing profile, but never in those exhibiting a single spike discharge upon depolarization. Interestingly, OT-induced reduction in spike frequency and increase of firing threshold were often observed, leading to a conversion of the firing profile from repetitive and delayed profiles into phasic ones and sometimes further into single spike profile. The observed effects following OT-receptor activation were completely abolished when the OT-receptor agonist was co-applied with a selective OT-receptor antagonist. In current and voltage clamp modes, we show that these changes in firing are strongly controlled by voltage-gated potassium currents. More precisely, transient IA currents and delayed-rectifier currents were reduced in amplitude and transient IA current was predominantly inactivated after OT bath application. Conclusion This effect of OT on the firing profile of lamina II neurons is in good agreement with the antinociceptive and analgesic properties of OT described in vivo.
Mixed hepatoblastoma and teratoma of the liver in a 3-year-old child: a unique combination and clinical challenge
Authors: Moll Alexander , Krenauer Alexander , Bierbach Uta , Till Holger , Hirsch Wolfgang , Leuschner Ivo , Schmitz Nicole , Wittekind Christian , Aigner Thomas 
Published: November 2009

Abstract
Primary liver tumors in children are rare with malignant hepatoblastoma being the most common neoplasm. In this report, we describe the diagnosis and clinical management of a large liver tumor in a 3-year-old child that displayed the features of both, conventional hepatoblastoma and malignant teratoma. Pathological assessment on a pre-operative bioptical specimen showed an immature teratoid tumor with no area of hepatoblastic differentiation present. Histological and immunhistological examination of the resected tumor specimen additionally showed tumor areas of very different differentiation pattern intermixed with each other, namely areas of hepatoblastoma-typical and neuroblastoma-like morphology as well as areas of rhadomyosarcomatous differentiation.
After chemotherapy the tumor size increased and an extended right hemihepatectomy was performed. Post-operatively, the general condition of the child improved and adjuvant chemotherapy was started two weeks later. 36 months after initial diagnosis the patient is healthy, in good general condition, and without any sign of residual tumor disease.
Overall, we describe the diagnosis and clinical management of a large liver tumor in a 3-year-old child that displayed the features of both, conventional hepatoblastoma and malignant teratoma and was designated as mixed hepatoblastoma and teratoma. Though mesenchymal tumor portions can occur within hepatoblastomas, most commonly osteoid or chondroid, our case is different as it presents a large spectrum of mesenchymal and epithelial differentiation pattern in most of the lesion.
In vitro proliferation of human osteogenic cells in presence of different commercial bone substitute materials combined with enamel matrix derivatives
Authors: Reichert Christoph , Al-Nawas Bilal , Smeets Ralf , Kasaj Adrian , Götz Werner , Klein Marcus O 
Published: November 2009

Abstract

Background
Cellular reactions to alloplastic bone substitute materials (BSM) are a subject of interest in basic research. In regenerative dentistry, these bone grafting materials are routinely combined with enamel matrix derivatives (EMD) in order to additionally enhance tissue regeneration.

Materials and methods
The aim of this study was to evaluate the proliferative activity of human osteogenic cells after incubation over a period of seven days with commercial BSM of various origin and chemical composition. Special focus was placed on the potential additional benefit of EMD on cellular proliferation.

Results
Except for PerioGlas®, osteogenic cell proliferation was significantly promoted by the investigated BSM. The application of EMD alone also resulted in significantly increased cellular proliferation. However, a combination of BSM and EMD resulted in only a moderate additional enhancement of osteogenic cell proliferation.

Conclusion
The application of most BSM, as well as the exclusive application of EMD demonstrated a positive impact on the proliferation of human osteogenic cells in vitro. In order to increase the benefit from substrate combination (BSM + EMD), further studies on the interactions between BSM and EMD are needed.
Clinical-dosimetric analysis of measures of dysphagia including gastrostomy-tube dependence among head and neck cancer patients treated definitively by intensity-modulated radiotherapy with concurrent chemotherapy
Authors: Li Baoqing , Li Dan , Lau Derick H , Farwell D Gregory , Luu Quang , Rocke David M , Newman Kathleen , Courquin Jean , Purdy James A , Chen Allen M 
Published: November 2009

Abstract

Purpose
To investigate the association between dose to various anatomical structures and dysphagia among patients with head and neck cancer treated by definitive intensity-modulated radiotherapy (IMRT) and concurrent chemotherapy.

Methods and materials
Thirty-nine patients with squamous cancer of the head and neck were treated by definitive concurrent chemotherapy and IMRT to a median dose of 70 Gy (range, 68 to 72). In each patient, a gastrostomy tube (GT) was prophylacticly placed prior to starting treatment. Prolonged GT dependence was defined as exceeding the median GT duration of 192 days. Dysphagia was scored using standardized quality-of-life instruments. Dose-volume histogram (DVH) data incorporating the superior/middle pharyngeal constrictors (SMPC), inferior pharyngeal constrictor (IPC), cricoid pharyngeal inlet (CPI), and cervical esophagus (CE) were analyzed in relation to prolonged GT dependence, dysphagia, and weight loss.

Results
At 3 months and 6 months after treatment, 87% and 44% of patients, respectively, were GT dependent. Spearman's ρ analysis identified statistical correlations (p < 0.05) between prolonged GT dependence or high grade dysphagia with IPC V65, IPC V60, IPC Dmean, and CPI Dmax. Logistic regression model showed that IPC V65 > 30%, IPC V60 > 60%, IPC Dmean > 60 Gy, and CPI Dmax > 62 Gy predicted for greater than 50% probability of prolonged GT dependence.

Conclusion
Our analysis suggests that adhering to the following parameters may decrease the risk of prolonged GT dependence and dysphagia: IPC V65 < 15%, IPC V60 < 40%, IPC Dmean < 55 Gy, and CPI Dmax < 60 Gy.
A small supernumerary marker chromosome present in a Turner syndrome patient not derived from X- or Y-chromosome: a case report
Authors: Sheth Frenny , Ewers Elisabeth , Kosyakova Nadezda , Weise Anja , Sheth Jayesh , Desai Manisha , Andrieux Joris , Vermeesch Joris , Hamid Ahmed B , Ziegler Monika , Liehr Thomas 
Published: November 2009

Abstract

Background
Small supernumerary marker chromosomes (sSMC) can be present in numerically abnormal karyotypes like in a 'Turner-syndrome karyotype' mos 45,X/46,X,+mar.

Results
Here we report the first case of an sSMC found in Turner syndrome karyotypes (sSMCT) derived from chromosome 14 in a Turner syndrome patient. According to cytogenetic and molecular cytogenetic characterization the karyotype was 46,X,+del(14)(q11.1). The present case is the third Turner syndrome case with an sSMCT not derived from the X- or the Y-chromosome.

Conclusion
More comprehensive characterization of such sSMCT might identify them to be more frequent than only ~0.6% in Turner syndrome cases according to available data.
Regulation of Steroidogenic Acute Regulatory Protein Transcription in Largemouth Bass by Orphan Nuclear Receptor Signaling Pathways
Authors: Kocerha Jannet , Prucha Melinda S. , Kroll Kevin J. , Steinhilber Dieter , Denslow Nancy 
Published: November 2009

AbstractThe steroidogenic acute regulatory (StAR) protein mediates the rate-limiting step of mitochondrial transport of cholesterol for steroid biosynthesis. To investigate the regulation of this protein in lower vertebrates, we cloned the StAR coding region from large-mouth bass for analysis. Induction of the mRNA corresponded with increasing levels of plasma sex steroids in vivo. Cultures of largemouth bass ovarian follicles were exposed to dibutyryl cAMP (dbcAMP), a potent signaling molecule for steroidogenesis. StAR mRNA expression was significantly up-regulated by dbcAMP signaling, suggesting that the 5′ regulatory region of the gene is functionally conserved. To further analyze its transcriptional regulation, a 2.9-kb portion of the promoter was cloned and transfected into Y-1 cells, a steroidogenic mouse adrenocortical cell line. The promoter activity was induced in a dose-responsive manner upon stimulation with dbcAMP; however, deletion of 1 kb from the 5′ end of the promoter segment significantly diminished the transcriptional activation. A putative retinoic acid-related receptor-α/rev-erbα element was identified between the −1.86- and −2.9-kb region and mutated to assess its potential role in dbcAMP regulation of the promoter. Mutation of the rev-erbα element significantly impeded dbcAMP-induced activation. Chromatin immunoprecipitation and EMSA results revealed rev-erbα and retinoic acid-related receptor-α enrichment at the site under basal and dbcAMP-induced conditions, respectively. These results implicate important roles for these proteins previously uncharacterized for the StAR promoter. Altogether these data suggest novel regulatory mechanisms for dbcAMP up-regulation of StAR transcription in the distal part of the largemouth bass promoter.