bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of rice glycosyl hydrolase family 1 and expression of Os4bglu12 β-glucosidase
Authors: Opassiri Rodjana , Pomthong Busarakum , Onkoksoong Tassanee , Akiyama Takashi , Esen Asim , Ketudat Cairns James R 
Published: December 2006

Abstract

Background
Glycosyl hydrolase family 1 (GH1) β-glucosidases have been implicated in physiologically important processes in plants, such as response to biotic and abiotic stresses, defense against herbivores, activation of phytohormones, lignification, and cell wall remodeling. Plant GH1 β-glucosidases are encoded by a multigene family, so we predicted the structures of the genes and the properties of their protein products, and characterized their phylogenetic relationship to other plant GH1 members, their expression and the activity of one of them, to begin to decipher their roles in rice.

Results
Forty GH1 genes could be identified in rice databases, including 2 possible endophyte genes, 2 likely pseudogenes, 2 gene fragments, and 34 apparently competent rice glycosidase genes. Phylogenetic analysis revealed that GH1 members with closely related sequences have similar gene structures and are often clustered together on the same chromosome. Most of the genes appear to have been derived from duplications that occurred after the divergence of rice and Arabidopsis thaliana lineages from their common ancestor, and the two plants share only 8 common gene lineages. At least 31 GH1 genes are expressed in a range of organs and stages of rice, based on the cDNA and EST sequences in public databases. The cDNA of the Os4bglu12 gene, which encodes a protein identical at 40 of 44 amino acid residues with the N-terminal sequence of a cell wall-bound enzyme previously purified from germinating rice, was isolated by RT-PCR from rice seedlings. A thioredoxin-Os4bglu12 fusion protein expressed in Escherichia coli efficiently hydrolyzed β-(1,4)-linked oligosaccharides of 3–6 glucose residues and laminaribiose.

Conclusion
Careful analysis of the database sequences produced more reliable rice GH1 gene structure and protein product predictions. Since most of these genes diverged after the divergence of the ancestors of rice and Arabidopsis thaliana, only a few of their functions could be implied from those of GH1 enzymes from Arabidopsis and other dicots. This implies that analysis of GH1 enzymes in monocots is necessary to understand their function in the major grain crops. To begin this analysis, Os4bglu12 β-glucosidase was characterized and found to have high exoglucanase activity, consistent with a role in cell wall metabolism.
Case report: Infective endocarditis caused by Brevundimonas vesicularis
Authors: Yang Mei-Li , Chen Yen-Hsu , Chen Tun-Chieh , Lin Wei-Ru , Lin Chun-Yu , Lu Po-Liang 
Published: December 2006

Abstract

Background
There are few reports in the literature of invasive infection caused by Brevundimonas vesicularis in patients without immunosuppression or other predisposing factors. The choice of antimicrobial therapy for bacteremia caused by the pathogen requires more case experience to be determined.

Case presentation
The case of a 40-year-old previously healthy man with subacute endocarditis proposed to be contributed from an occult dental abscess is described. The infection was found to be caused by B. vesicularis on blood culture results. The patient recovered without sequelae after treatment with ceftriaxone followed by subsequent ciprofloxacin therapy owing to an allergic reaction to ceftriaxone and treatment failure with ampicillin/sulbactam.

Conclusion
To our knowledge, this is the first report of B. vesicularis as a cause of infective endocarditis. According to an overview of the literature and our experience, we suggest that third-generation cephalosporins, piperacillin/tazobactam, and ciprofloxacin are effective in treating invasive B. vesicularis infections, while the efficacy of ampicillin-sulbactam needs further evaluation.
Pain during ice water test distinguishes clinical bladder hypersensitivity from overactivity disorders
Authors: Mukerji Gaurav , Waters Janet , Chessell Iain P , Bountra Chas , Agarwal Sanjiv K , Anand Praveen 
Published: December 2006

Abstract

Background
The Bladder cooling reflex (BCR) i.e. uninhibited detrusor contractions evoked by intravesical instillation of cold saline, is a segmental reflex believed to be triggered by menthol sensitive cold receptors in the bladder wall, with the afferent signals transmitted by C fibres. The BCR is a neonatal reflex that becomes suppressed by descending signals from higher centres at approximately the time when the child gains full voluntary control of voiding. It re-emerges in adults with neurogenic detrusor overactivity as a consequence of loss of central descending inhibition, resulting from conditions such as spinal cord injury or multiple sclerosis. We have recently shown an increase of nerve fibres expressing the cool and menthol receptor TRPM8 in both overactive (IDO) and painful bladder syndrome (PBS), but its functional significance is unknown. We have therefore studied the bladder cooling reflex and associated sensory symptoms in patients with PBS and overactivity disorders.

Methods
The BCR, elicited by ice water test (IWT) was performed in patients with painful bladder syndrome (PBS, n = 17), idiopathic detrusor overactivity (IDO, n = 22), neurogenic detrusor overactivity (NDO, n = 4) and stress urinary incontinence (as controls, n = 21). The IWT was performed by intravesical instillation of cold saline (0 – 4°C). A positive IWT was defined as presence of uninhibited detrusor contraction evoked by cold saline, associated with urgency or with fluid expulsion. Patients were asked to report and rate any pain and cold sensation during the test.

Results
A positive IWT was observed in IDO (6/22, 27.3%) and NDO (4/4, 100%) patients, but was negative in all control and PBS patients. Thirteen (76.5%) PBS patients reported pain during the IWT, with significantly higher pain scores during ice water instillation compared to the baseline (P = 0.0002), or equivalent amount of bladder filling (100 mls) with saline at room temperature (P = 0.015). None of the control or overactive (NDO/IDO) patients reported any pain during the IWT.

Conclusion
The BCR in DO may reflect loss of central inhibition, which appears necessary to elicit this reflex; the pain elicited in PBS suggests afferent sensitisation, hence sensory symptoms are evoked but not reflex detrusor contractions. The ice water test may be a useful and simple marker for clinical trials in PBS, particularly for novel selective TRPM8 antagonists.
Apigenin inhibits pancreatic cancer cell proliferation through G2/M cell cycle arrest
Authors: Ujiki Michael B , Ding Xian-Zhong , Salabat M Reza , Bentrem David J , Golkar Laleh , Milam Ben , Talamonti Mark S , Bell Richard H , Iwamura Takeshi , Adrian Thomas E 
Published: December 2006

Abstract

Background
Many chemotherapeutic agents have been used to treat pancreatic cancer without success. Apigenin, a naturally occurring flavonoid, has been shown to inhibit growth in some cancer cell lines but has not been studied in pancreatic cancer. We hypothesized that apigenin would inhibit pancreatic cancer cell growth in vitro.

Results
Apigenin caused both time- and concentration-dependent inhibition of DNA synthesis and cell proliferation in four pancreatic cancer cell lines. Apigenin induced G2/M phase cell cycle arrest. Apigenin reduced levels of cyclin A, cyclin B, phosphorylated forms of cdc2 and cdc25, which are all proteins required for G2/M transition.

Conclusion
Apigenin inhibits growth of pancreatic cancer cells through suppression of cyclin B-associated cdc2 activity and G2/M arrest, and may be a valuable drug for the treatment or prevention of pancreatic cancer.
Nectin-2-mediated entry of a syncytial strain of herpes simplex virus via pH-independent fusion with the plasma membrane of Chinese hamster ovary cells
Authors: Delboy Mark G , Patterson Jennifer L , Hollander Aimee M , Nicola Anthony V 
Published: December 2006

Abstract

Background
Herpes simplex virus (HSV) can utilize multiple pathways to enter host cells. The factors that determine which route is taken are not clear. Chinese hamster ovary (CHO) cells that express glycoprotein D (gD)-binding receptors are model cells that support a pH-dependent, endocytic entry pathway for all HSV strains tested to date. Fusion-from-without (FFWO) is the induction of target cell fusion by addition of intact virions to cell monolayers in the absence of viral protein expression. The receptor requirements for HSV-induced FFWO are not known. We used the syncytial HSV-1 strain ANG path as a tool to evaluate the complex interplay between receptor usage, membrane fusion, and selection of entry pathway.

Results
Inhibitors of endocytosis and endosome acidification blocked ANG path entry into CHO cells expressing nectin-1 receptors, but not CHO-nectin-2 cells. Thus, under these conditions, nectin-2 mediates pH-independent entry at the plasma membrane. In addition, CHO-nectin-2 cells supported pH-dependent, endocytic entry of different strains of HSV-1, including rid1 and HFEM. The kinetics of ANG path entry was rapid (t1/2 of 5–10 min) regardless of entry route. However, HSV-1 ANG path entry by fusion with the CHO-nectin-2 cell plasma membrane was more efficient and resulted in larger syncytia. ANG path virions added to the surface of CHO-nectin-2 cells, but not receptor-negative CHO cells or CHO-nectin-1 cells, induced rapid FFWO.

Conclusion
HSV-1 ANG path can enter CHO cells by either endocytic or non-endocytic pathways depending on whether nectin-1 or nectin-2 is present. In addition to these cellular receptors, one or more viral determinants is important for the selection of entry pathway. HSV-induced FFWO depends on the presence of an appropriate gD-receptor in the target membrane. Nectin-1 and nectin-2 target ANG path to divergent cellular pathways, and these receptors may have different roles in triggering viral membrane fusion.
Human coronavirus 229E encodes a single ORF4 protein between the spike and the envelope genes
Authors: Dijkman Ronald , Jebbink Maarten F , Wilbrink Berry , Pyrc Krzysztof , Zaaijer Hans L , Minor Philip D , Franklin Sally , Berkhout Ben , Thiel Volker , van der Hoek Lia 
Published: December 2006

Abstract

Background
The genome of coronaviruses contains structural and non-structural genes, including several so-called accessory genes. All group 1b coronaviruses encode a single accessory protein between the spike and envelope genes, except for human coronavirus (HCoV) 229E. The prototype virus has a split gene, encoding the putative ORF4a and ORF4b proteins. To determine whether primary HCoV-229E isolates exhibit this unusual genome organization, we analyzed the ORF4a/b region of five current clinical isolates from The Netherlands and three early isolates collected at the Common Cold Unit (CCU) in Salisbury, UK.

Results
All Dutch isolates were identical in the ORF4a/b region at amino acid level. All CCU isolates are only 98% identical to the Dutch isolates at the nucleotide level, but more closely related to the prototype HCoV-229E (>98%). Remarkably, our analyses revealed that the laboratory adapted, prototype HCoV-229E has a 2-nucleotide deletion in the ORF4a/b region, whereas all clinical isolates carry a single ORF, 660 nt in size, encoding a single protein of 219 amino acids, which is a homologue of the ORF3 proteins encoded by HCoV-NL63 and PEDV.

Conclusion
Thus, the genome organization of the group 1b coronaviruses HCoV-NL63, PEDV and HCoV-229E is identical. It is possible that extensive culturing of the HCoV-229E laboratory strain resulted in truncation of ORF4. This may indicate that the protein is not essential in cell culture, but the highly conserved amino acid sequence of the ORF4 protein among clinical isolates suggests that the protein plays an important role in vivo.
Hindcasting of nutrient loadings from its catchment on a highly valuable coastal lagoon: the example of the Fleet, Dorset, UK, 1866–2004
Authors: Weber Geraint J , O'Sullivan Patrick E , Brassley Paul 
Published: December 2006

Abstract

Background
Nutrient loadings from its catchment upon The Fleet, a highly valuable coastal lagoon in Southern England, were hindcast for the period AD 1866–2004, using a catchment model, export coefficients, and historical data on land use changes, livestock numbers, and human population. Agriculture was the main nutrient source throughout, other inputs representing minor contributions. Permanent pasture was historically the main land use, with temporary grassland and cereals increasing during the mid-20th century. Sheep, the main 19th century livestock, were replaced by cattle during the 1930s.

Results
Total nitrogen loadings rose from ca 41 t yr-1 during the late 19th century to 49–54 t yr-1 for the mid-20th, increasing to 98 t yr-1 by 1986. Current values are ca 77 t yr-1. Total phosphorus loads increased from ca 0.75 t yr-1 for the late 19th century to ca 1.6 t yr-1 for the mid-20th, reached ca 2.2 t yr-1 in 1986, and are now ca 1.5 t yr-1. Loadings rose most rapidly between 1946 and 1988, owing to increased use of inorganic fertilisers, and rising sheep and cattle numbers. Livestock were the main nutrient source throughout, but inputs from inorganic fertilisers increased after 1946, peaking in 1986. Sewage treatment works and other sources contribute little nitrogen, but ca 35% of total phosphorus. Abbotsbury Swannery, an ancient Mute Swan community, provides ca 0.5% of total nitrogen, and ca 5% of total phosphorus inputs.

Conclusion
The Fleet has been grossly overloaded with nitrogen since 1866, climaxing during the 1980s. Total phosphorus inputs lay below 'permissible' limits until the 1980s, exceeding them in inner, less tidal parts of the lagoon, during the 1940s. Loadings on Abbotsbury Bay exceeded 'permissible' limits by the 1860s, becoming 'dangerous' during the mid-20th century. Phosphorus stripping at point sources will not significantly reduce loadings to all parts of the lagoon. Installation of 5 m buffer strips throughout the catchment and shoreline will marginally affect nitrogen loadings, but will reduce phosphorus inputs to the West Fleet below 'permissible' limits. Only a combination of measures will significantly affect Abbotsbury Bay, where, without effluent diversion, loadings will remain beyond 'permissible'.
A proteomics study of the response of North Ronaldsay sheep to copper challenge
Authors: Simpson Deborah M , Mobasheri Ali , Haywood Susan , Beynon Robert J 
Published: December 2006

Abstract

Background
The objective of this proteomics study was to identify proteins that changed expression as a result of copper challenge in the uniquely copper sensitive North Ronaldsay sheep and further, to compare those changes in expression with the more copper tolerant Cambridge breed. Such data gives us a proteome-centered perspective of the pathogenesis of copper-induced oxidative stress in this breed.

Results
Many proteins respond to copper challenge, but this study focuses on those exhibiting a differential response between the two breeds, related to liver copper content. As copper accumulated in the tissue, the pattern of expression of several proteins was markedly different, in North Ronaldsay sheep as compared to the Cambridge breed.

Conclusion
The pattern of changes was consistent with the greatly enhanced susceptibility of North Ronaldsay sheep to copper-induced oxidative stress, focused on mitochondrial disturbance with consequent activation of hepatic stellate cells. The expression profiles were sufficiently complex that the response could not simply be explained as a hypersensitivity to copper in North Ronaldsay sheep.
p66 Shc and tyrosine-phosphorylated Shc in primary breast tumors identify patients likely to relapse despite tamoxifen therapy
Authors: Frackelton A Raymond , Lu Li , Davol Pamela A , Bagdasaryan Robert , Hafer Laurie J , Sgroi Dennis C 
Published: December 2006

Abstract
Introduction
Shc adapter proteins are secondary messenger proteins involved in various cellular pathways, including those mediating receptor tyrosine kinase signaling and apoptosis in response to stress. We have previously reported that high levels of tyrosine-phosphorylated Shc (PY-Shc) and low levels of its inhibitory p66 Shc isoform are strongly prognostic for identifying both early node-negative and more advanced, node-positive, primary breast cancers with high risk for recurrence. Because aberrant activation of tyrosine kinases upstream of Shc signaling proteins has been implicated in resistance to tamoxifen – the most widely prescribed drug for treatment of estrogen receptor-positive breast cancer – we hypothesized that Shc isoforms may identify patients at increased risk of relapsing despite tamoxifen treatment.

Methods
Immunohistochemical analyses of PY-Shc and p66 Shc were performed on archival primary breast cancer tumors from a population-based cohort (60 patients, 9 relapses) and, for validation, an independent external cohort (31 patients, 13 relapses) in which all patients received tamoxifen as a sole systemic adjuvant prior to relapse.

Results
By univariate and multivariate analyses, the Shc proteins were very strong and independent predictors of treatment failure in both the population-based cohort (interquartile hazard ratio = 8.3, 95% confidence interval [CI] 1.8 to 38, P = 0.007) and the validating cohort (interquartile relative risk = 12.1, 95% CI 1.7 to 86, P = 0.013).

Conclusion
These results suggest that the levels of PY-Shc and p66 Shc proteins in primary tumors identify patients at high risk for relapsing despite treatment with tamoxifen and therefore with further validation may be useful in guiding clinicians to select alternative adjuvant treatment strategies.
A modified McCabe score for stratification of patients after intensive care unit discharge: the Sabadell score
Authors: Fernandez Rafael , Baigorri Francisco , Navarro Gema , Artigas Antonio 
Published: December 2006

Abstract
Introduction
Mortality in the ward after an intensive care unit (ICU) stay is considered a quality parameter, and is described as a source of avoidable mortality. Additionally, the attending intensivist frequently anticipates fatal outcome after ICU discharge. Our objective was to test the ability of a new score to stratify patients according to ward mortality after ICU discharge.

Methods
A prospective cohort study was performed in the general ICU of a university-affiliated hospital. In 2003 and 2004 we prospectively recorded the attending intensivist's subjective prognosis at ICU discharge about the hospital outcome for each patient admitted to the ICU (the Sabadell score), which was later compared with the real hospital outcome.

Results
We studied 1,521 patients with a mean age of 60.2 ± 17.8 years. The median (25–75% percentile) ICU stay was five (three to nine) days. The ICU mortality was 23.8%, with 1,156 patients being discharged to the ward. Post-ICU ward mortality was 9.6%, mainly observed in patients with a Sabadell score of 3 (81.3%) or a score of 2 (41.1%), whereas lower mortality was observed in patients scoring 1 (17.2%) and scoring 0 (1.7%). Multivariate analysis selected age and the Sabadell score as the only variables associated with ward mortality, with an area under the receiver operating curve of 0.88 (95% CI 0.84–0.93) for the Sabadell score.

Conclusion
The Sabadell score at ICU discharge works effectively to stratify patients according to hospital outcome.
An eye’s view of T regulatory cells
Authors: Stein-Streilein Joan , Taylor Andrew W 
Published: December 2006

AbstractT regulatory (Treg) cells have been studied for more than 30 years. Recently, changing technology and attitudes have led to new interest in T cell regulation of the immune responses. The eye is an immune-privileged site with unique mechanisms for the prevention of damaging immune inflammation. The eye fashions its Treg cells in novel ways to prevent immune inflammation locally and systemically. The purpose of this mini-review is to condense and summarize reports of Treg cells dependent on the eye in the context of the Treg literature in general.
Critical role for adaptive T cell immunity in experimental eosinophilic esophagitis in mice
Authors: Mishra Anil , Schlotman James , Wang Meiqin , Rothenberg Marc E 
Published: December 2006

AbstractWe have previously developed a murine model of allergen-induced eosinophilic esophagitis (EE), characterized by intraepithelial eosinophils, extracellular granule deposition, and epithelial cell hyperplasia, features that mimic the pathophysiological changes observed in individuals with various forms of EE. We now test the hypothesis that adaptive T cell immunity is critical in initiating experimental EE. We first demonstrate that EE induction is associated with an increase in lymphocyte subpopulations (B+, CD4+, and CD8+ cells) in the esophagus. We induced experimental EE in wild-type and various lymphocyte subpopulation-deficient mice by intranasal allergen sensitization. Eosinophil levels and epithelial cell proliferation were determined by performing antimajor basic protein and antiproliferation cell nuclear antigen immunohistochemical analysis. Eosinophil accumulation in the esophagus was ablated completely in RAG1 gene-deficient mice, but no role for B cells or antigen-specific antibodies was found, as B cell-deficient (IgH6) mice developed unabated, experimental EE. In addition, T cell-deficient (forkhead box N1−/−) mice were protected from the induction of experimental EE. CD8α-deficient mice developed unaltered, experimental EE, and CD4-deficient mice were only protected moderately from disease induction. Taken together, these studies indicate a role for CD4+ and CD4− cell populations in EE pathogenesis and demonstrate that experimental allergen-induced EE is dependent on adaptive T cell immunity.
Adolescent-onset psychosis: prevalence, needs and service
provision
Authors: Boeing Leonie , Murray Val , Pelosi Anthony , McCabe Robert , Blackwood Douglas , Wrate Robert 
Published: December 2006

BackgroundLittle is known of the epidemiology and care needs of people with
adolescent-onset psychosis.AimsTo examine prevalence and the cross-sectional disability, needs and
service provision for adolescent-onset psychosis in areas of central
Scotland with a total population of 1.75 million.MethodWe identified and contacted 103 young people using an opt-out research
design. Fifty-three participants and their carers and keyworkers were
interviewed using a modified version of the Cardinal Needs Schedule.ResultsThe 3-year prevalence was 5.9 per 100 000 general population. Twenty-one
(20%) adolescents were not in contact with mental health services; 80% of
first admissions were to adult acute psychiatric wards. Those interviewed
had high levels of morbidity: 29 (55%) had serious to pervasive
impairment of functioning; there were relatively high levels of
side-effects, negative symptoms, anxiety, occupational, friendship and
family difficulties. Care provision was better for ‘clinical' than for
‘social' domains; 20% had five or more unmet needs; 17% had at least one
intractable problem.ConclusionsThis low-prevalence disorder requires an assertive multi-agency approach
in the context of a national planning framework.