bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simplifying gene trees for easier comprehension
Authors: Lott Paul-Ludwig , Mundry Marvin , Sassenberg Christoph , Lorkowski Stefan , Fuellen Georg 
Published: April 2006

Abstract

Background
In the genomic age, gene trees may contain large amounts of data making them hard to read and understand. Therefore, an automated simplification is important.

Results
We present a simplification tool for gene trees called TreeSimplifier. Based on species tree information and HUGO gene names, it summarizes "monophyla". These monophyla correspond to subtrees of the gene tree where the evolution of a gene follows species phylogeny, and they are simplified to single leaves in the gene tree. Such a simplification may fail, for example, due to genes in the gene tree that are misplaced. In this way, misplaced genes can be identified. Optionally, our tool glosses over a limited degree of "paraphyly" in a further simplification step. In both simplification steps, species can be summarized into groups and treated as equivalent. In the present study we used our tool to derive a simplified tree of 397 leaves from a tree of 1138 leaves. Comparing the simplified tree to a "cartoon tree" created manually, we note that both agree to a high degree.

Conclusion
Our automatic simplification tool for gene trees is fast, accurate, and effective. It yields results of similar quality as manual simplification. It should be valuable in phylogenetic studies of large protein families. The software is available at http://www.uni-muenster.de/Bioinformatics/services/treesim/.
Design of microarray probes for virus identification and detection of emerging viruses at the genus level
Authors: Chou Cheng-Chung , Lee Te-Tsui , Chen Chun-Houh , Hsiao Hsiang-Yun , Lin Yi-Ling , Ho Mei-Shang , Yang Pan-Chyr , Peck Konan 
Published: April 2006

Abstract

Background
Most virus detection methods are geared towards the detection of specific single viruses or just a few known targets, and lack the capability to uncover the novel viruses that cause emerging viral infections. To address this issue, we developed a computational method that identifies the conserved viral sequences at the genus level for all viral genomes available in GenBank, and established a virus probe library. The virus probes are used not only to identify known viruses but also for discerning the genera of emerging or uncharacterized ones.

Results
Using the microarray approach, the identity of the virus in a test sample is determined by the signals of both genus and species-specific probes. The genera of emerging and uncharacterized viruses are determined based on hybridization of the viral sequences to the conserved probes for the existing viral genera. A detection and classification procedure to determine the identity of a virus directly from detection signals results in the rapid identification of the virus.

Conclusion
We have demonstrated the validity and feasibility of the above strategy with a small number of viral samples. The probe design algorithm can be applied to any publicly available viral sequence database. The strategy of using separate genus and species probe sets enables the use of a straightforward virus identity calculation directly based on the hybridization signals. Our virus identification strategy has great potential in the diagnosis of viral infections. The virus genus and specific probe database and the associated summary tables are available at http://genestamp.sinica.edu.tw/virus/index.htm
Flexible promoter architecture requirements for coactivator recruitment
Authors: Chiang Derek Y , Nix David A , Shultzaberger Ryan K , Gasch Audrey P , Eisen Michael B 
Published: April 2006

Abstract

Background
The spatial organization of transcription factor binding sites in regulatory DNA, and the composition of intersite sequences, influences the assembly of the multiprotein complexes that regulate RNA polymerase recruitment and thereby affects transcription. We have developed a genetic approach to investigate how reporter gene transcription is affected by varying the spacing between transcription factor binding sites. We characterized the components of promoter architecture that govern the yeast transcription factors Cbf1 and Met31/32, which bind independently, but collaboratively recruit the coactivator Met4.

Results
A Cbf1 binding site was required upstream of a Met31/32 binding site for full reporter gene expression. Distance constraints on coactivator recruitment were more flexible than those for cooperatively binding transcription factors. Distances from 18 to 50 bp between binding sites support efficient recruitment of Met4, with only slight modulation by helical phasing. Intriguingly, we found that certain sequences located between the binding sites abolished gene expression.

Conclusion
These results yield insight to the influence of both binding site architecture and local DNA flexibility on gene expression, and can be used to refine computational predictions of gene expression from promoter sequences. In addition, our approach can be applied to survey promoter architecture requirements for arbitrary combinations of transcription factor binding sites.
Bone erosions in rheumatoid arthritis can be repaired through reduction in disease activity with conventional disease-modifying antirheumatic drugs
Authors: Ideguchi Haruko , Ohno Shigeru , Hattori Hideaki , Senuma Akiko , Ishigatsubo Yoshiaki 
Published: April 2006

AbstractWe conducted the present study to determine whether repair of erosions occurs in patients with rheumatoid arthritis (RA) treated with conventional disease-modifying anti-rheumatic drugs (DMARDs) and to compare clinical characteristics between patients exhibiting and not exhibiting erosion repair. We included in the study a total of 122 RA patients who fulfilled the 1987 American College of Rheumatology criteria for RA; all patients had paired sequential radiographs of both hands and wrists showing erosive changes at baseline. Patients were classified into two groups according to the presence of repair of erosions at follow up, namely the 'repair observed' and 'repair not observed' groups. Clinical characteristics, disease activity, radiographic scores and treatment in the two groups were compared. Forty-four repairs were observed in 13 patients (10.7%). Compared with the repair not observed group, the functional class of the patients in the repair observed group was lower at baseline (P< 0.01) and the mean disease activity was lower at follow up (P< 0.005). The changes in radiographic scores per year (total radiographic score and erosion score) were lower (P< 0.05 andP< 0.01, respectively) in the repair observed group. No difference in treatment was observed. Repair of erosions was detected in 10.7% of RA patients treated with conventional DMARDs. Repairs were associated with low functional class at baseline and low disease activity at follow up. These observations support the importance of reduction in disease activity in RA patients. Because repair of erosions was detected in a substantial number of patients, assessment of erosion repair should be incorporated into the radiographic evaluation and scoring of RA.
The new IL-1 family member IL-1F8 stimulates production of inflammatory mediators by synovial fibroblasts and articular chondrocytes
Authors: Magne David , Palmer Gaby , Barton Jenny L , Mézin Francoise , Talabot-Ayer Dominique , Bas Sylvette , Duffy Trevor , Noger Marcus , Guerne Pierre-Andre , Nicklin Martin JH , Gabay Cem 
Published: April 2006

AbstractSix novel members of the IL-1 family of cytokines were recently identified, primarily through the use of DNA database searches for IL-1 homologues, and were named IL-1F5 to IL-1F10. In the present study, we investigated the effect of IL-1F8 on primary human joint cells, and examined the expression of the new IL-1 family members in human and mouse joints. Human synovial fibroblasts (hSFs) and human articular chondrocytes (hACs) expressed the IL-1F8 receptor (IL-1Rrp2) and produced pro-inflammatory mediators in response to recombinant IL-1F8. IL-1F8 mRNA expression was increased in hSFs upon stimulation with proinflammatory cytokines, whereas in hACs IL-1F8 mRNA expression was constitutive. However, IL-1F8 protein was undetectable in hSF and hAC culture supernatants. Furthermore, although IL-1β protein levels were increased in inflamed human and mouse joint tissue, IL-1F8 protein levels were not. IL-1F8 levels in synovial fluids were similar to or lower than those in matched serum samples, suggesting that the joint itself is not a major source of IL-1F8. Serum levels of IL-1F8 were similar in healthy donors, and patients with rheumatoid arthritis, osteoarthritis and septic shock, and did not correlate with inflammatory status. Interestingly however, we observed high IL-1F8 levels in several serum samples in all groups. In conclusion, IL-1F8 exerts proinflammatory effects in primary human joint cells. Joint and serum IL-1F8 protein levels did not correlate with inflammation, but they were high in some human serum samples tested, including samples from patients with rheumatoid arthritis. It remains to be determined whether circulating IL-1F8 can contribute to joint inflammation in rheumatoid arthritis.
Osteogenic protein 1 in synovial fluid from patients with rheumatoid arthritis or osteoarthritis: relationship with disease and levels of hyaluronan and antigenic keratan sulfate
Authors: Chubinskaya Susan , Frank Benjamin S , Michalska Margaret , Kumar Bhavna , Merrihew Charis A , Thonar Eugene J-MA , Lenz Mary Ellen , Otten Lori , Rueger David C , Block Joel A 
Published: April 2006

AbstractThe measurement of body fluid levels of biochemical markers in joint tissues has begun to provide clinically useful information. Synovial fluid (SF) plays an important role in articular joint lubrication, nutrition, and metabolism of cartilage and other connective tissues within the joint. The purpose of our study was to identify and characterize osteogenic protein 1 (OP-1) in SF from patients with rheumatoid arthritis (RA) or with osteoarthritis (OA) and to correlate levels of OP-1 with those of hyaluronan (HA) and antigenic keratan sulfate (AgKS). SF was aspirated from the knees of patients with either RA or OA and from the knees of asymptomatic organ donors with no documented history of joint disease. The presence of detectable OP-1 in SF was demonstrated by western blots with specific anti-pro-OP-1 and anti-mature OP-1 antibodies. Measurement of levels of OP-1, HA and AgKS was performed using ELISAs. OP-1 was identified in human SF in two forms, pro-OP-1 and active (mature) OP-1 – mature OP-1 being detected only in SF from OA patients and RA patients. Levels of OP-1 and HA were higher in RA patients than in OA patients and asymptomatic donors, while the level of AgKS was highest in SF from asymptomatic donors. Statistically significant differences were found between SF levels of OP-1 in RA and OA patients and between SF levels of AgKS among the three groups tested. The SF content of OP-1 tended to correlate positively with HA levels, but negatively with AgKS concentrations. In conclusion, the results of this study suggest that measurement of OP-1 in joint fluid may have value in the clinical evaluation of joint disease processes.
Euthanasia: the role of the psychiatrist
Authors: Naudts Kris , Ducatelle Caroline , Kovacs Jozsef , Laurens Kristin , Van Den Eynde Frederique , Van Heeringen Cornelis 
Published: April 2006

SummaryBelgium has become one of the few countries in the world where euthanasia is legally allowed within a specific juridical framework. Even more unique is the inclusion of grounds for requesting euthanasia on the basis of mental suffering. Further refinement of the legal, medical and psychiatric approach to the issue is required in order to clear up essential practical and ethical matters. Psychiatrists and their professional organisations need to play a greater role in this ongoing debate and contribute from a clinical, scientific and ethical point of view.
Quantifying the contributions of three types of information to the prediction of criminal conviction using the receiver operating characteristic
Authors: Buchanan Alec , Leese Morven 
Published: April 2006

BackgroundQuantifying the contributions that different types of information make to the accurate prediction of offending offers the prospects of improved practice and better use of resources.AimsTo quantify the contributions made by three types of information – demographic data alone, demographic and criminal record and demographic, criminal record and legal class of disorder – to the prediction of criminal conviction in patients.MethodAll 425 patients discharged from the three special (high secure) hospitals in England and Wales over 2 years were followed for 10.5 years. The contribution of each type of information was described in terms of the area under the receiver operating characteristic curve (AUC) and the number needed to detain (NND).ResultsThe AUC values using the three types of information were 0.66, 0.72 and 0.73 respectively. Prediction based on the full model using an optimal probability cut-off implies an NND of 2. The AUCs for serious offences were 0.67, 0.69 and 0.75 respectively.ConclusionsFor long-term prediction of conviction on any charge, information on legal class adds little to the accuracy of predictions made using only a patient's age, gender and criminal record. In the prediction of serious offences alone the contribution of legal class is significant.
Impact ofIGF-IandCYP19Gene Polymorphisms on the Survival of Patients With Metastatic Prostate Cancer
Authors: Tsuchiya Norihiko , Wang Lizhong , Suzuki Hiroyoshi , Segawa Takehiko , Fukuda Hisami , Narita Shintaro , Shimbo Masaki , Kamoto Toshiyuki , Mitsumori Kenji , Ichikawa Tomohiko , Ogawa Osamu , Nakamura Akira , Habuchi Tomonori 
Published: April 2006

PurposeThe prognosis of metastatic prostate cancer significantly differs among individuals. While various clinical and biochemical prognostic factors for survival have been suggested, the progression and response to treatment of those patients may also be defined by host genetic factors. In this study, we evaluated genetic polymorphisms as prognostic predictors of metastatic prostate cancer.Patients and MethodsOne hundred eleven prostate cancer patients with bone metastasis at the diagnosis were enrolled in this study. Thirteen genetic polymorphisms were genotyped using polymerase chain reaction-restriction fragment length polymorphism or an automated sequencer with a genotyping software.ResultsAmong the polymorphisms, the long allele (over 18 [CA] repeats) of insulin-like growth factor-I (IGF-I) and the long allele (over seven [TTTA] repeats) of cytochrome P450 (CYP) 19 were significantly associated with a worse cancer-specific survival (P = .016 and .025 by logrank test, respectively). The presence of the long allele of either the IGF-I or CYP19 polymorphisms was an independent risk factor for death (P = .019 or .026, respectively). Furthermore, the presence of the long allele of both the IGF-I and CYP19 polymorphisms was a stronger predictor for survival (P = .001).ConclusionThe prognosis of metastatic prostate cancer patients is suggested to be influenced by intrinsic genetic factors. The IGF-I (CA) repeat and CYP19 (TTTA) repeat polymorphisms may be novel predictors in prostate cancer patients with bone metastasis at the diagnosis.
Phase I, Pharmacokinetic, and Pharmacodynamic Study of Intravenously Administered Ad5CMV-p53, an Adenoviral Vector Containing the Wild-Type p53 Gene, in Patients With Advanced Cancer
Authors: Tolcher Anthony W. , Hao Desiree , de Bono Johann , Miller Alex , Patnaik Amita , Hammond Lisa A. , Smetzer Leslie , Van Wart Hood Jill , Merritt James , Rowinsky Eric K. , Takimoto Chris , Von Hoff Dan , Eckhardt S. Gail 
Published: April 2006

Purpose The purpose of this study was to assess the feasibility of administering Ad5CMV-p53, an adenoviral vector containing the wild-type p53 gene to patients with advanced malignancies, characterize the pertinent pharmacokinetic parameters, identify evidence of viral uptake in both normal and tumor tissue, and seek evidence of antitumor activity. Methods Patients were treated with escalating doses of Ad5CMV-p53 intravenously over 30 minutes on days 1, 2, and 3, every 28 days. The clearance of circulating Ad5CMV-p53 (INGN 201) DNA was characterized in the plasma and paired tumor and skin biopsies were performed in patients treated at the two highest dose levels to assess vector uptake into tissues. Results Seventeen patients received 36 courses of Ad5CMV-p53 at doses ranging from 3 × 1010 to 3 × 1012 virus particles (vp). Fatigue, nausea, vomiting, and fever were common, but rarely severe. Abnormalities of coagulation parameters, including decreases in fibrinogen and increases in fibrin degradation products at 3 × 1012vp, precluded additional dose escalation. Ad5CMV-p53 DNA could be detected in the plasma by polymerase chain reaction assay in the majority of patients at 14 days and 28 days at doses of 3 × 1010 and higher. Six patients treated at 1 × 1012vp and 3 × 1012vp dose levels had Ad5CMV-p53 DNA detected within paired tumor tissue collected day 4. Conclusion Ad5CMV-p53 can be safely and repetitively administered up to 1 × 1012vp intravenously daily for 3 consecutive days. The absence of severe toxicities, the presence of circulating adenovirus 24 hours after administration, and detectable p53 transgene within tumor tissue distant from the site of administration demonstrates that systemic therapy with this adenoviral vector containing p53 is feasible.
Facile and Selective Conversion of Ethylenediaminetetraacetate to Ethylenediamine-N,N,N′-triacetate on a Cobalt Complex
Authors: Yashiro Morio , Mori Tomonori , Yoshikawa Sadao , Shiraishi Shinsaku 
Published: April 2006

Abstract
Ethylenediaminetetraacetatocobaltate(III) is converted to aqua(ethylenediamine-N,N,N′-triacetate)cobalt(III) selectively in a 1 mol dm−3 K2CO3 aqueous solution at room temperature in the presence of PbO2. This reaction could be a simple and versatile procedure to obtain ed3a-type ligands.
Evaluation of Association between Cyclodextrins and Various Inorganic Anions in Aqueous Solutions by 81Br NMR Spectroscopy
Authors: Yamashoji Yuko , Fujiwara Manabu , Matsushita Takayuki , Tanaka Minoru 
Published: April 2006

Abstract
The line-broadening of 81Br NMR signals observed in the presence of CyDs was applied to evaluate their binding abilities toward inorganic anions in aqueous solutions. The apparent association constants of α -CyD with anions have been found to decrease in the order SCN− &gt; ClO4− &gt; I− &gt; NO3− &gt; Br− F− &gt; Cl−.
Synthesis and Spectral Characterization of a Rotaxane of β-Cyclodextrin Threaded by a 4,4′-Diaminostilbene
Authors: Kunitake Masashi , Kotoo Kengo , Manabe Osamu , Muramatsu Tsuyoshi , Nakashima Naotoshi 
Published: April 2006

Abstract
A rotaxane, in which a stilbene moiety threads the cavity of β-cyclodextrin (β-CyD), has been synthesized. The rotaxane structure has been proved by uv-visible and induced circular dichlorism (CD) spectra.
The Catalytic Activities of IgG and IgM Monoclonal Antibodies for the Hydrolysis of p-Nitrophenyl Acetate
Authors: Ohkubo Katsutoshi , Urata Yasuo , Seri Kei-ichi , Ishida Hitoshi , Sagawa Takashi , Nakashima Toshihiro , Imagawa Yoshitaka 
Published: April 2006

Abstract
The catalytic activities of IgG and IgM monoclonal antibodies (Antibody KD2-1–KD2-260) derived from a hapten of p-nitrophenyl hydrogen 4-(hydroxycarbonyl)butylphosphonate were examined in the hydrolysis of p-nitrophenyl acetate in 2.4–4.0% (v/v) MeCN-H2O in Tris-HCl buffer (pH 5.0–8.0) at 293–308 K. The most efficient Antibody KD2-260 resulted in kcat/kuncat = 2.1 × 103 (308 K) – 3.1 × 103 (293 K), Km = 4.9 × 10−6 (293 K) – 1.5 × 10−5 mol dm−3 (308 K, and Km/Ki = 80 (303 K) at pH 6.0.
Methanol Synthesis from CO2 and H2 over Cu/ZnO/Ga2O3 Catalyst
Authors: Fujitani Tadahiro , Saito Masahiro , Kanai Yuki , Takeuchi Masami , Moriya Keiko , Watanabe Taiki , Kawai Motomitsu , Kakumoto Terumitu 
Published: April 2006

Abstract
The methanol synthesis activity per unit copper surface area of Cu/ZnO catalyst combined with Ga2O3 was higher than those of Cu/ZnO and Cu/ZnO/Al2O3 catalyst in the hydrogenation of carbon dioxide.
Photoinduced Electron Transfer Reactions of Di(4-methoxyphenyl)ethanal in Solution. Sensitizer-dependent Decay Pathways of the Aldehyde Cation Radical
Authors: Akaba Ryoichi , Kamata Masaki , Kuriyama Yasunao , Sakuragi Hirochika , Tokumaru Katsumi 
Published: April 2006

Abstract
Laser flash photolyses of di(4-methoxyphenyl)ethanal in the presence of electron-accepting sensitizers such as 2,4,6-triphenylpyrylium tetrafluoroborate and 9,10-dicyanoanthracene have been carried out. Chemical properties of the sensitizers or their one-electron reduced species and an added electrolyte greatly influenced the reaction course of the photogenerated aldehyde cation radical in solution.
35Cl NQR Spectra of 1,3-Dichloro-5,5-diphenylhydantoin and Related Compounds
Authors: Nagao Yoshitaka , Katagiri Shigeyoshi 
Published: April 2006

Abstract
The 35Cl NQR spectra were measured for 1,3-dichloro-5,5-diphenylhydantoin, 1, N-chloro-4,4-diphenyl-2-oxazolidone, 2, N-chloro-α,α-diphenylsuccinimide, 3, and 1-chloro-5,5-diphenyl-3-methylhydantoin, 4, at liquid nitrogen temperature. The resonance frequencies for these compounds were as follows: 1, 55.019, 56.460 MHz; 2, 52.914 MHz; 3, 53.492, 53.717 MHz; 4, 54.097 MHz.
Enhanced Catalytic Activity of Silica-Deposited Alumina for Selective Reduction of Nitrogen Monoxide by Ethene in Oxidizing Atmosphere
Authors: Okazaki Noriyasu , Kohno Takuya , Inoue Ryo , Imizu Yuzo , Tada Akio 
Published: April 2006

Abstract
The effect of silica deposition by CVD method onto alumina catalyst on its catalytic activity for the titled reaction was examined. The deposition of a small amount of silica resulted in the enhancement of the activity, whereas the activity was greatly affected by the variation of alkoxy silane as a source of silica.
In Turn or in Reverse Palladium-Catalyzed Carbonyl Allylation and Diels-Alder Reaction by 2-Methylene-3-buten-1-ol
Authors: Masuyama Yoshiro , Fuse Manabu , Kurusu Yasuhiko 
Published: April 2006

Abstract
Using PdCl2(PhCN)2-SnCl2, 2-methylene-3-buten-2-ol causes carbonyl allylation of various aldehydes to afford 1-substituted-3-methylene-4-penten-1-ols; the Diels-Alder reaction of those with dienophiles produces 1-(2-hydroxyethyl)cyclohexenes. Diels-Alder reaction of 2-methylene-3-buten-1-ol with dienophiles followed by carbonyl allylation produces structurally isomeric 1-methylene-2-(hydroxymethyl)cyclohexanes.
A Conformationally Controlled Regioselective Rearrangement of 2-Substituted 1-Alkynylcyclopropanols to 2-Cyclopenten-1-ones via Hexacarbonyldicobalt Complex
Authors: Iwasawa Nobuharu , Iwamoto Mari 
Published: April 2006

Abstract
The rearrangement of hexacarbonyldicobalt-complexed 2-substituted 1-alkynylcyclopropanol derivatives is conformationally controlled to give 4- or 5-substituted 2-cyclopentenones regioselectively. In the cases of the reactions of 2-monosubstituted 1-alkynylcyclopropanol derivatives, either regioisomer can be selectively obtained by the appropriate choice of the substrates.
Effect of Dimethylsulfoxide as a Masking Agent for Chlorine in the Selective Determination of Aqueous Chlorine Dioxide
Authors: Imaizumi Noriko , Nakahara Yumiko , Suzuki Kayoko , Oikawa Kikuo 
Published: April 2006

Abstract
For the selective determination of aqueous chlorine dioxide(ClO2) in the mixed solution with chlorine, dimethylsulfoxide(DMSO) was used as a masking agent for chlorine. In spectrophotometric and iodometric determination of ClO2, a large excess of DMSO did not affect on ClO2, but it completely depressed the interference from chlorine.