bluuebunny/crossref_metadata_2025_split huggingface dataset:
The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci
Authors: Polineni Pavana , Aragonda Prathyusha , Xavier Suresh R , Furuta Richard , Adelson David L 
Published: June 2006

Abstract

Background
Many important agricultural traits such as weight gain, milk fat content and intramuscular fat (marbling) in cattle are quantitative traits. Most of the information on these traits has not previously been integrated into a genomic context. Without such integration application of these data to agricultural enterprises will remain slow and inefficient. Our goal was to populate a genomic database with data mined from the bovine quantitative trait literature and to make these data available in a genomic context to researchers via a user friendly query interface.

Description
The QTL (Quantitative Trait Locus) data and related information for bovine QTL are gathered from published work and from existing databases. An integrated database schema was designed and the database (MySQL) populated with the gathered data. The bovine QTL Viewer was developed for the integration of QTL data available for cattle. The tool consists of an integrated database of bovine QTL and the QTL viewer to display QTL and their chromosomal position.

Conclusion
We present a web accessible, integrated database of bovine (dairy and beef cattle) QTL for use by animal geneticists. The viewer and database are of general applicability to any livestock species for which there are public QTL data. The viewer can be accessed at http://bovineqtl.tamu.edu.
MATER protein expression and intracellular localization throughout folliculogenesis and preimplantation embryo development in the bovine
Authors: Pennetier Sophie , Perreau Christine , Uzbekova Svetlana , Thélie Aurore , Delaleu Bernadette , Mermillod Pascal , Dalbiès-Tran Rozenn 
Published: June 2006

Abstract

Background

Mater (Maternal Antigen that Embryos Require), also known as Nalp5 (NACHT, leucine rich repeat and PYD containing 5), is an oocyte-specific maternal effect gene required for early embryonic development beyond the two-cell stage in mouse. We previously characterized the bovine orthologue MATER as an oocyte marker gene in cattle, and this gene was recently assigned to a QTL region for reproductive traits.

Results
Here we have analyzed gene expression during folliculogenesis and preimplantation embryo development. In situ hybridization and immunohistochemistry on bovine ovarian section revealed that both the transcript and protein are restricted to the oocyte from primary follicles onwards, and accumulate in the oocyte cytoplasm during follicle growth. In immature oocytes, cytoplasmic, and more precisely cytosolic localization of MATER was confirmed by immunohistochemistry coupled with confocal microscopy and immunogold electron microscopy. By real-time PCR, MATER messenger RNA was observed to decrease strongly during maturation, and progressively during the embryo cleavage stages; it was hardly detected in morulae and blastocysts. The protein persisted after fertilization up until the blastocyst stage, and was mostly degraded after hatching. A similar predominantly cytoplasmic localization was observed in blastomeres from embryos up to 8-cells, with an apparent concentration near the nuclear membrane.

Conclusion
Altogether, these expression patterns are consistent with bovine MATER protein being an oocyte specific maternal effect factor as in mouse.
Comparative genomics of regulation of heavy metal resistance in Eubacteria
Authors: Permina EA , Kazakov AE , Kalinina OV , Gelfand MS 
Published: June 2006

Abstract

Background
Heavy metal resistance (HMR) in Eubacteria is regulated by a variety of systems including transcription factors from the MerR family (COG0789). The HMR systems are characterized by the complex signal structure (strong palindrome within a 19 or 20 bp promoter spacer), and usually consist of transporter and regulator genes. Some HMR regulons also include detoxification systems. The number of sequenced bacterial genomes is constantly increasing and even though HMR resistance regulons of the COG0789 type usually consist of few genes per genome, the computational analysis may contribute to the understanding of the cellular systems of metal detoxification.

Results
We studied the mercury (MerR), copper (CueR and HmrR), cadmium (CadR), lead (PbrR), and zinc (ZntR) resistance systems and demonstrated that combining protein sequence analysis and analysis of DNA regulatory signals it was possible to distinguish metal-dependent members of COG0789, assign specificity towards particular metals to uncharacterized loci, and find new genes involved in the metal resistance, in particular, multicopper oxidase and copper chaperones, candidate cytochromes from the copper regulon, new cadmium transporters and, possibly, glutathione-S-transferases.

Conclusion
Our data indicate that the specificity of the COG0789 systems can be determined combining phylogenetic analysis and identification of DNA regulatory sites. Taking into account signal structure, we can adequately identify genes that are activated using the DNA bending-unbending mechanism. In the case of regulon members that do not reside in single loci, analysis of potential regulatory sites could be crucial for the correct annotation and prediction of the specificity.
Inhaled ciclesonide versus inhaled budesonide or inhaled beclomethasone or inhaled fluticasone for chronic asthma in adults: a systematic review
Authors: Dyer Matthew J , Halpin David MG , Stein Ken 
Published: June 2006

Abstract

Background
Ciclesonide is a new inhaled corticosteroids licensed for the prophylactic treatment of persistent asthma in adults. Currently beclomethasone dipropionate, budesonide and fluticasone propionate are the most commonly prescribed inhaled corticosteroids for the treatment of asthma but there has been no systematic review comparing the effectiveness and safety ciclesonide to these agents. We therefore aimed to systematically review published randomised controlled trials of the effectiveness and safety of ciclesonide compared to alternative inhaled corticosteroids in people with asthma.

Methods
We performed literature searches on MEDLINE, EMBASE, PUBMED, the COCHRANE LIBRARY and various Internet evidence sources for randomised controlled trials or systematic reviews comparing ciclesonide to beclomethasone or budesonide or fluticasone in adult humans with persistent asthma. Data was extracted by one reviewer.

Results
Five studies met the inclusion criteria. Methodological quality was variable. There were no trials comparing ciclesonide to beclomethasone. There was no significant difference between ciclesonide and budesonide or fluticasone on the following outcomes: lung function, symptoms, quality of life, airway responsiveness to a provoking agent or inflammatory markers. However, the trials were very small in size, increasing the possibility of a type II error. One trial demonstrated that the combined deposition of ciclesonide (and its active metabolite) in the oropharynx was 47% of that of budesonide while another trial demonstrated that the combined deposition of ciclesonide (and its active metabolite) in the oropharynx was 53% of that of fluticasone. One trial demonstrated less suppression of cortisol in overnight urine collection after ciclesonide compared to fluticasone (geometric mean fold difference = 1.5, P < 0.05) but no significant difference in plasma cortisol response.

Conclusion
There is very little evidence comparing CIC to other ICS, restricted to very small, phase II studies of low power. These demonstrate CIC has similar effectiveness and efficacy to FP and BUD (though equivalence is not certain) and findings regarding oral deposition and HPA suppression are inconclusive. There is no direct comparative evidence that CIC causes fewer side effects since none of the studies reported patient-based outcomes.
Fecopneumothorax and colopleural fistula – uncommon complications of Crohn's disease
Authors: Barišiæ G , Krivokapiæ Z , Adžiæ T , Pavloviæ A , Popoviæ M , Gojniæ M 
Published: June 2006

Abstract

Background
Colopleural fistula and fecopneumothorax are very rare complications of Crohn's disease. Fistula formation is frequent in Crohn's disease and occurs in approximately 33% of patients. On the other hand, fistulous communication between the pleural cavity and adjacent organs below the diaphragm is extremely rare.

Case presentation
We describe the case of 27 year-old female with colopleural fistula as a complication of Crohn's disease. The diagnosis was established with clinical exam, barium enema, chest X-ray, abdominal and chest CT exam. The treatment was surgical.

Conclusion
Colopleural fistula and fecopneumothorax are rare but life treating complications of Crohn's disease. Surgical treatment is mandatory as soon as the diagnosis is established.
Phosphatidylcholine-specific phospholipase C (PC-PLC) is required for LPS-mediated macrophage activation through CD14
Authors: Cuschieri Joseph , Billgren Jens , Maier Ronald V 
Published: June 2006

Abstract
Lipid rafts, composed of sphingolipids, are critical to Toll-like receptor 4 (TLR4) assembly during lipopolysaccharide (LPS) exposure, as a result of protein kinase C (PKC)-ζ activation. However, the mechanism responsible for this remains unknown. The purpose of this study is to determine if LPS-induced TLR4 assembly and activation are dependent on the sphingolipid metabolite ceramide produced by phosphatidylcholine-specific phospholipase C (PC-PLC) or CD14. To study this, THP-1 cells were stimulated with LPS. Selected cells were pretreated with the PC-PLC inhibitor D609, exogenous C2 ceramide, CD14 neutralizing antibody, or TLR4 neutralizing antibody. LPS led to production of ceramide, phosphorylation of PKC-ζ, and assembly of the TLR4 within lipid rafts. This was followed by activation of the mitogen-activated protein kinase family and the liberation of cytokines. Pretreatment with D609 or CD14 blockade was associated with attenuated LPS-induced ceramide production, TLR4 assembly on lipid rafts, and cytokine production. Pretreatment with TLR4 blockade did not affect LPS-induced ceramide production but was associated with significant attenuation in cytokine production. Treatment with C2 ceramide prior to LPS reversed the inhibitory effects induced by D609 but not of CD14 or TLR4 blockade. C2 ceramide alone induced the activation of PKC-ζ and the assembly of TLR4 but was not associated with cytokine liberation. This study demonstrates that TLR4 assembly and activation following LPS exposure require the production of ceramide by PC-PLC, which appears to be CD14-dependent.
Proline-Directed Protein Kinase FA Is a Powerful and Independent Prognostic Predictor for Progression and Patient Survival of Hepatocellular Carcinoma
Authors: Hsu Yu-Chen , Fu Hsiao-Hui , Jeng Yung-Ming , Lee Po-Huang , Yang Shiaw-Der 
Published: June 2006

Purpose Molecular, cellular, and animal studies have established that overexpressed proline-directed protein kinase FA (PDPK FA) is essential for the development of tumorigenesis, invasion, and metastasis of human cancer cells. However, the prognostic role of PDPK FA in cancer patients remains largely unknown. In this study, association of PDPK FA expression with poor prognosis of hepatocellular carcinoma (HCC) patients was examined. Patients and Methods PDPK FA expression in the resected tumors of 134 HCC patients (112 men and 22 women) with ages ranging from 33 to 83 years (mean, 55 years) was analyzed by immunohistochemistry. Highly condensed cytoplasmic and nuclear PDPK FA associated with tumor cells was used as the major scoring parameter for positive PDPK FA expression. Results Approximately 68% of the patients (91 of 134) exhibited positive PDPK FA expression. Patients with positive PDPK FA showed poorer disease-free survival and overall survival (P < .001). Cox multivariate regression analysis further established PDPK FA as the strongest independent prognosticator for progression and patient survival of HCC (hazard ratio [HR], 2.878; 95% CI, 1.634 to 5.067 for disease-free survival; and HR, 5.035; 95% CI, 2.137 to 11.866 for overall survival; P < .001). Conclusion Consistent with PDPK FA’s essential role in the development of highly malignant phenotypes, the present study establishes the potential prognostic role of PDPK FA in progression and patient survival of surgically resected primary HCC. Taken together, PDPK FA represents a new modifiable signal-transducing target for prognostic prediction and adjuvant treatment of patients with aggressive HCC after hepatic resection.
Estrogen-Independent Proliferation Is Present in Estrogen-ReceptorHER2-Positive Primary Breast Cancer After Neoadjuvant Letrozole
Authors: Ellis Matthew J. , Tao Yu , Young Oliver , White Sharon , Proia Alan D. , Murray Julliette , Renshaw Lorna , Faratian Dana , Thomas Jeremy , Dowsett Mitch , Krause Andreas , Evans Dean B. , Miller William R. , Dixon J. Michael 
Published: June 2006

PurposeTo investigate the impact of human epidermal growth factor receptor (HER) 1 and HER2 gene amplification on endocrine therapy responsiveness, a fluorescence in situ hybridization (FISH) study was conducted on tumor samples from 305 postmenopausal patients with stage II and III estrogen receptor (ER) –positive (ER ≥ 10%) breast cancers treated on two independent neoadjuvant endocrine therapy trials.Patients and MethodsFISH analysis focused on HER1 and/or HER2 immunohistochemistry (IHC) -positive patients and a random selection of HER1/2 IHC-negative patients. HER2 FISH status was correlated with response and changes in the proliferation marker Ki67.ResultsHER1 was rarely amplified (< 1%), and HER2 amplification was observed in 9.2% of patients. Letrozole response by clinical measurement (71% HER2 FISH positive v 71% HER2 FISH negative), mammogram (44% HER2 FISH positive v 47% HER2 FISH negative), or ultrasound (47% HER2 FISH positive v 54% HER2 FISH negative) was not impaired by HER2 FISH-positive status. In contrast, HER2 FISH-positive tumors showed higher histologic grade (P = .009), higher pretreatment Ki67 (P = .005), and less Ki67 suppression after letrozole when compared with HER2 FISH-negative tumors (P = .0001). Similar observations regarding Ki67 were made in a smaller cohort of tamoxifen-treated tumors.ConclusionNeoadjuvant letrozole is clinically effective in ER-positive HER2 FISH-positive tumors, indicating sensitivity to short-term estrogen deprivation. However, continued proliferation despite ongoing letrozole or tamoxifen treatment in the majority of ER-positive HER2 FISH-positive samples (88%) could imply therapeutic resistance that may manifest later in the clinical course of the disease. Discordance between clinical and biomarker findings in this study serves to emphasize the need for surrogate end point validation in neoadjuvant endocrine trials through correlation with information on long-term outcomes.
Rituximab-CHOP Versus CHOP Alone or With Maintenance Rituximab in Older Patients With Diffuse Large B-Cell Lymphoma
Authors: Habermann Thomas M. , Weller Edie A. , Morrison Vicki A. , Gascoyne Randy D. , Cassileth Peter A. , Cohn Jeffrey B. , Dakhil Shaker R. , Woda Bruce , Fisher Richard I. , Peterson Bruce A. , Horning Sandra J. 
Published: June 2006

Purpose To address early and late treatment failures in older patients with diffuse large B-cell lymphoma (DLBCL), we designed a two-stage randomized trial of cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP) versus rituximab plus CHOP (R-CHOP), with a second random assignment to maintenance rituximab (MR) or observation in responding patients. Patients and Methods Untreated DLBCL patients who were 60 years or older were randomly assigned to R-CHOP (n = 318) or CHOP (n = 314); 415 responders were randomly assigned to MR (n = 207) or observation (n = 208). The primary end point was failure-free survival (FFS). All P values were two sided. Results Three-year FFS rate was 53% for R-CHOP patients and 46% for CHOP patients (P = .04) at a median follow-up time of 3.5 years. Two-year FFS rate from second random assignment was 76% for MR compared with 61% for observation (P = .009). No significant differences in survival were seen according to induction or maintenance therapy. FFS was prolonged with MR after CHOP (P = .0004) but not after R-CHOP (P = .81) with 2-year FFS rates from second random assignment of 77%, 79%, 74%, and 45% for R-CHOP, R-CHOP + MR, CHOP + MR, and CHOP, respectively. In a secondary analysis excluding MR patients, R-CHOP alone reduced the risks of treatment failure (P = .003) and death (P = .05) compared with CHOP alone. Conclusion Rituximab administered as induction or maintenance with CHOP chemotherapy significantly prolonged FFS in older DLBCL patients. After R-CHOP, no benefit was provided by MR. These results, which are consistent with an additive effect of rituximab, suggest that future studies could focus on maintenance strategies with novel agents as well as new induction therapies.
The Chemistry of Disilyne with a Genuine Si–Si Triple Bond: Synthesis, Structure, and Reactivity
Authors: Sekiguchi Akira , Ichinohe Masaaki , Kinjo Rei 
Published: June 2006

Abstract
In this account, our recent results on the chemistry of a stable silicon–silicon triply-bonded compound, disilyne, including recent advances in the chemistry of stable alkyne analogues of heavier group 14 elements, are described. Our original extremely bulky trialkylsilyl substituent, Dis2iPrSi [Dis = CH(SiMe3)2], has enabled the isolation of disilyne as a stable compound, which has been completely characterized by various spectroscopic techniques, as well as X-ray crystallography. Some reactivity of our isolable disilyne will be discussed.
Selective Recognition of Trp- and Tyr-Rich Oligopeptides by Self-Assembled Coordination Hosts
Authors: Tashiro Shohei , Fujita Makoto 
Published: June 2006

Abstract
A coordination host recognized various aromatic peptides containing Trp and Tyr residues in a highly sequence-selective fashion. For example, two similar hexa-peptides, Ac-Ser-Gly-Ala-Trp-Trp-Ala-NH2 and Ac-Ala-Trp-Trp-Ala-Gly-Ser-NH2, were selectively discriminated by the restricted inner space of coordination cages. We also demonstrated that the charged peptides were efficiently discriminated by the cage owing to the highly cationic property of the cage (12+). Furthermore, the cages selectively discriminated two similar peptides, Ac-Ala-Trp-Trp-NH2 and Ac-Ala-Tyr-Tyr-NH2, because of differences in the strength of charge-transfer interaction between the cage and the electron-rich aromatic residues. This selectivity was controlled by modulating the solution pH. The colorization of the aromatic peptide solutions by charge-transfer interaction could also be applicable to the naked-eye recognition of three aromatic residues, Trp, Tyr, and Phe.
Synthesis and Properties of Trispiro[truxenetris(cycloalkane)]s
Authors: Satoh Hiroyasu , Yamamoto Gaku , Mazaki Yasuhiro 
Published: June 2006

Abstract
Four of the title compounds, where cyclopropane, cyclobutane, cyclopentane, and cyclohexane rings are spiro-annelated at the 5-, 10-, and 15-positions of truxene, were synthesized and their spectral properties were studied. X-ray molecular structures were elucidated for the cyclopropane compound.
Reversible On–Off Photoswitching of Hydrogen Bonding for Self-Assembled Fibers Comprising Physical Gels
Authors: Moriyama Masaya , Mizoshita Norihiro , Kato Takashi 
Published: June 2006

Abstract
We report on photo-stimulated reversible association and dissociation of hydrogen bonding for self-assembled fibers comprising physical gels. The gels are formed by a hydrogen-bonded gelator containing photochromic azobenzene moieties. The photoswitching of hydrogen bonding is caused by the changes of molecular polarity for the azobenzene moieties.
Age at menopause, and knowledge of and attitudes to menopause, of women in Karachi, Pakistan
Authors: Baig L A , Karim S A 
Published: June 2006

Objectives. The objectives of the study were to identify the average age at menopause in Karachi and to assess knowledge of and attitudes to the menopause among Pakistani women in different social strata. Study design. A population-based cross-sectional study of 960 women aged over 35 years was conducted. Results. As insufficient data were available for 35 women, 925 interviews were analysed. There were 287 menopausal women, whose mean (SD) age at menopause was 47.1 (4.7) years (95% CI 46.8 to 47.6). Of these 287 women, 135 (47%) wanted their menses to continue and 235 (82%) had consulted a physician after the menopause. Of all 925 women, 58% knew the correct definition of the menopause, all had consulted a physician for various symptoms related to the menopause and 53% said that women should consult a physician premenopausally. Symptoms experienced by premenopausal women included lack of sleep (25%), fear of infertility (13%) and urinary incontinence (18%). The majority of the overall sample (52%) were sexually active. Of the sexually active women, 16% had marital problems, compared with 44% of sexually inactive women, and this difference was statistically significant ( P < 0.0001). Source of knowledge about the menopause included relatives (35%), television (18%), neighbours (17%), friends (17%) and health-care providers (14%). Conclusions. Evidence-based information about the menopause should be provided for Pakistani women.
Cognitive behaviour therapy for schizophrenia: Relationship between anxiety symptoms and therapy
Authors: Naeem Farooq , Kingdon David , Turkington Douglas 
Published: June 2006

Aims. To explore the relationship between symptoms of anxiety and cognitive behaviour therapy (CBT) in patients with schizophreniaDesign. Separate subanalyses of two randomized controlled trials comparing CBT for schizophrenia against befriending in the London Newcastle (LN) study, and against treatment as usual in the insight into schizophrenia (IS) study.Main outcome measures. Assessment of anxiety symptoms using the Brief Scale for Anxiety (BSA) derived from the Comprehensive Psychopathological Rating Scale (CPRS), at baseline, end of therapy and follow‐up.Results. In both studies, anxiety symptoms positively correlated with overall psychopathology, hallucinations and depression. In the LN study, patients with persecutory delusions and with distress due to akathisia and incapacity due to abnormal movements scored significantly higher on the BSA. In the IS study, anxiety scores were also positively correlated with; delusions, negative symptoms, relationship problems and problems with activities of daily living, living conditions, occupation and activities. Both subanalyses showed CBT had beneficial effects on anxiety symptoms compared with the control groups. Overall prognosis was found to be better in those with low anxiety in the LN study.Conclusions. CBT improves anxiety symptoms in psychosis. We did not find an association between anxiety symptoms at baseline and outcome of cognitive therapy in this group of patients with schizophrenia.