bluuebunny/crossref_metadata_2025_split huggingface dataset:
Autoantigens signal through chemokine receptors: uveitis antigens induce CXCR3- and CXCR5-expressing lymphocytes and immature dendritic cells to migrate
Authors: Howard O. M. Zack , Dong Hui Fang , Su Shao Bo , Caspi Rachel R. , Chen Xin , Plotz Paul , Oppenheim Joost J. 
Published: February 2005

AbstractWe tested the hypothesis that interaction between autoantigens and chemoattractant receptors may be an important step in the development of autoimmunity. The retinal autoantigens S-antigen (S-Ag) and interphotoreceptor retinoid binding protein (IRBP) can induce autoimmune uveitis in rodent models. We evaluated the chemotactic activity of S-Ag and IRBP and found that both induced migration of human and mouse immature dendritic cells (iDCs) and lymphocytes, but not neutrophils, monocytes, or mature DCs. Cross-desensitization studies and single-receptor transfected cells revealed that subfamily of alpha chemokine receptors CXCR5 and CXCR3 mediated the chemotactic effect of IRBP, while only CXCR3 was required for the chemotactic response to S-Ag. Examination of the relationships between chemoattraction and the ability to elicit pathology at the protein or peptide levels in the mouse uveitis model revealed dissociation of the capacity to induce uveitis, lymphocyte proliferation, and chemoattraction. These studies suggest that IRBP and S-Ag can initiate innate and, in sensitive individuals, adaptive immune response by attracting iDCs and T and B cells expressing CXCR3 and CXCR5.
Molecular basis for positive and negative signaling by the natural killer cell receptor 2B4 (CD244)
Authors: Eissmann Philipp , Beauchamp Lisa , Wooters Joe , Tilton John C. , Long Eric O. , Watzl Carsten 
Published: February 2005

AbstractTriggering of 2B4 (CD244) can induce natural killer (NK)-cell activation, costimulation, or even inhibition of NK-cell activity. Here, we investigate the molecular basis for the different signals generated by 2B4. We show that the first immunoreceptor tyrosine-based switch motif (ITSM) within the cytoplasmic tail of 2B4 is sufficient for 2B4-mediated NK-cell activation, whereas the third ITSM can negatively influence 2B4 signaling. We further identify signaling molecules that associate with 2B4. Signaling lymphocyte activation molecule-associated protein (SAP) can bind to all 4 ITSMs of 2B4 in a phosphorylation-dependent manner. The phosphorylated third ITSM can additionally recruit the phosphatases SHP-1, SHP-2, SHIP, and the inhibitory kinase Csk. SAP acts as an inhibitor of interactions between 2B4 and these negative regulatory molecules, explaining how 2B4 inhibits NK-cell activation in the absence of functional SAP, as occurs in cells from patients with X-linked lymphoproliferative syndrome (XLP). Recently, another function for SAP was proposed: SAP can recruit the kinase Fyn to the SLAM (CD150) immune receptor. We now show that Fyn can also associate with phosphorylated 2B4. Finally, we demonstrate that Fyn and Csk can both phosphorylate 2B4, suggesting a possible mechanism of 2B4 phosphorylation. (Blood. 2005;105:4722-4729)
Automated generation of heuristics for biological sequence comparison
Authors: Slater Guy St C , Birney Ewan 
Published: February 2005

Abstract
Background
Exhaustive methods of sequence alignment are accurate but slow, whereas heuristic approaches run quickly, but their complexity makes them more difficult to implement. We introduce bounded sparse dynamic programming (BSDP) to allow rapid approximation to exhaustive alignment. This is used within a framework whereby the alignment algorithms are described in terms of their underlying model, to allow automated development of efficient heuristic implementations which may be applied to a general set of sequence comparison problems.

Results
The speed and accuracy of this approach compares favourably with existing methods. Examples of its use in the context of genome annotation are given.

Conclusions
This system allows rapid implementation of heuristics approximating to many complex alignment models, and has been incorporated into the freely available sequence alignment program, exonerate.
Leisure-time versus full-day energy expenditure: a cross-sectional study of sedentarism in a Portuguese urban population
Authors: Gal Diane L , Santos Ana-Cristina , Barros Henrique 
Published: February 2005

Abstract
Background
Low physical activity is known to be a potential risk factor for cardiovascular disease. With high prevalence of cardiovascular diseases in the Portuguese urban population, little is known about how sedentary this population is and what factors are associated to sedentary lifestyles. This study's objective was to examine sedentary lifestyles and their determinants through a cross-sectional study.

Methods
2134 adults (18 years and older) were interviewed using a standard questionnaire, comprising of social, behavioural and clinical information. Time spent in a variety of activities per day, including: work, household chores, sports, sedentary leisure time and sleep, were self-reported. Energy expenditure was estimated based on the related metabolic equivalent (MET) and time spent in each activity (min/day). Those with less than 10% of energy expenditure at a moderate intensity of 4 METs or higher were categorised as sedentary. The proportion of sedentary people and 95% Confidence Intervals (CI) were calculated, and the magnitude of associations, between sedentary lifestyles and the population characteristics, were computed as age-adjusted odds ratios using logistic regression.

Results
Sedentarism in both genders during leisure time is high at 84%, however in full day energy expenditure, which includes physical activity at work, sleeping hours and household chores, 79% of males and 86% of females are found to be sedentary. In leisure-time only, increased age is associated with higher odds of being sedentary in both genders, as well as in women with increased BMI. In comparison, in full-day energy expenditure, sedentarism is more likely to occur in those with higher levels of education and in white-collar workers.

Conclusions
A high prevalence of sedentarism is found in the study participants when measuring leisure-time and full-day energy expenditure. The Portuguese population may therefore benefit from additional promotion of physical activity.
Low density DNA microarray for detection of most frequent TP53 missense point mutations
Authors: Rangel-López Angélica , Maldonado-Rodríguez Rogelio , Salcedo-Vargas Mauricio , Espinosa-Lara Juana Mercedes , Méndez-Tenorio Alfonso , Beattie Kenneth L 
Published: February 2005

Abstract
Background
We have developed an oligonucleotide microarray (genosensor) utilizing a double tandem hybridization technique to search for 9 point mutations located in the most frequently altered codons of the TP53 gene. Isolated and multiplexed PCR products, 108 and 92 bp long, from exons 7 and 8, respectively, were obtained from 24 different samples. Single-stranded target DNA was then prepared from isolated or multiplexed PCR products, through cyclic DNA synthesis. Independent ssDNA's were annealed with the corresponding pairs of labeled stacking oligonucleotides to create partially duplex DNA having a 7-nt gap, which contains the sequence that will be interrogated by the capture probes forming double tandem hybridization. In the case of multiplexed ssPCR products, only two stacking oligonucleotides were added per target, therefore the gap for the PCR products having two consecutive codons to be interrogated in exon 7 was 12 nt long, so only single tandem hybridization was produced with these respective probes.

Results
18 codon substitutions were found by DNA sequencing. In 13 of them a perfect correlation with the pattern of hybridization was seen (In 5 no signal was seen with the wt probe while a new signal was seen with the appropriate mutant probe, and in 8 more, as expected, no signal was seen with any probe due to the absence of the corresponding probe in the array). In 3 other cases a mutation was falsely suggested by the combination of the absence of the wild type signal along with a false signal in the other probe. In the other 2 cases the presence of the mutation was not detected due to the production of a false hybridization signal with the wild type probe. In both cases (false mutation or no mutation detected) relatively stable mismatched target/probe duplexes should be formed. These problems could be avoided by the addition of probes to improve the performance of the array.

Conclusion
Our results demonstrate that a simple TP53 microarray employing short (7-mer) probes, used in combination with single or double tandem hybridization approach and a simple or multiplex target preparation method, can identify common TP53 missense mutations from a variety of DNA sources with good specificity.
Initiation to heroin injecting among heroin users in Sydney, Australia: cross sectional survey
Authors: Day Carolyn A , Ross Joanne , Dietze Paul , Dolan Kate 
Published: February 2005

Abstract
Background
Heroin injection is associated with health and social problems including hepatitis C virus (HCV) transmission. Few studies have examined the circumstances surrounding initiation to heroin injecting, especially current users initiating others. The current study aimed to examine the age of first heroin use and injection; administration route of first heroin use; relationship to initiator; the initiation of others among a group of heroin users; and to examine these factors in relation to HCV status and risk.

Method
Heroin users in Sydney were recruited through needle and syringe programs, a methadone clinic and snowballing. Participants were interviewed about their own initiation to heroin use, blood-borne virus risk and knowledge, and whether they had initiated others to heroin injecting. Information on HCV status was collected via self-report. Data was analysed using univariate and multivariate statistical techniques for Normally distributed continuous and categorical data.

Results
The study recruited 399 heroin users, with a mean age of 31 years, 63% were male, 77% reported heroin as their primary drug and 59% were HCV positive (self-report). Mean age at first heroin use and injection was 19 and 21 years, respectively. The majority of heroin users commenced heroin use via injecting (65%), younger users (<25 years, 25–30 years) were less likely than older users (>30 years) to commence heroin use parenterally. Participants were initiated to injection mainly by friends (63%). Thirty-seven percent reported initiating others to heroin injection, but few factors were related to this behaviour. Those with longer heroin using careers were more likely to report initiating others to heroin injection, but were no more likely to have done so in the preceding 12 months. Participants who had initiated others were more likely to have shared injecting equipment (12 vs 23%), but were no more likely to be HCV positive (self-report) than those who did not.

Conclusion
Interventions to prevent heroin users initiating others to injecting are necessary. Peer groups may be well positioned to implement such interventions.
Spontaneous rupture of giant gastric stromal tumor into gastric lumen
Authors: Mehta Rajiv M , Sudheer Vayoth O , John Anil K , Nandakumar Raghavan R , Dhar Puneet S , Sudhindran Surendran , Balakrishnan Vallath 
Published: February 2005

Abstract
Background
Gastrointestinal stromal tumors (GIST) constitute a large majority of mesenchymal tumors of the gastrointestinal (GI) tract, which express the c-kit proto-oncogene protein, a cell membrane receptor with tyrosine kinase activity. GI stromal tumors of the stomach are usually associated with bleeding, abdominal pain or a palpable mass.

Case presentation
A 75-year-old male presented with upper abdominal pain and palpable mass. Computed tomographic (CT) scan of the abdomen showed a large mass arising in the posterior aspect of fundus, body, and greater curvature of the stomach. Second day after the admission, there was significant reduction in the size of the tumor, clinically as well as radiologically. Endoscopic biopsy showed large bulge in fundus and corpus of the stomach posteriorly with an opening in the posterior part of the corpus, and biopsy from the edge of the opening reveled GIST. Patient underwent curative resection.

Conclusion
Spontaneous ruptured of giant gastric stromal tumor is very rare presentation of stomach GIST. Thorough clinical examination and timely investigation can diagnose rare complication.
Kaposi's sarcoma associated herpes virus-encoded viral FLICE inhibitory protein activates transcription from HIV-1 Long Terminal Repeat via the classical NF-κB pathway and functionally cooperates with Tat
Authors: Sun Qinmiao , Matta Hittu , Chaudhary Preet M 
Published: February 2005

Abstract
Background
The nuclear transcription factor NF-κB binds to the HIV-1 long terminal repeat (LTR) and is a key regulator of HIV-1 gene expression in cells latently infected with this virus. In this report, we have analyzed the ability of Kaposi's sarcoma associate herpes virus (KSHV, also known as Human Herpes virus 8)-encoded viral FLIP (Fas-associated death domain-like IL-1 beta-converting enzyme inhibitory protein) K13 to activate the HIV-1 LTR.

Results
We present evidence that vFLIP K13 activates HIV-1 LTR via the activation of the classical NF-κB pathway involving c-Rel, p65 and p50 subunits. K13-induced HIV-1 LTR transcriptional activation requires the cooperative interaction of all three components of the IKK complex and can be effectively blocked by inhibitors of the classical NF-κB pathway. K13 mutants that lacked the ability to activate the NF-κB pathway also failed to activate the HIV-1 LTR. K13 could effectively activate a HIV-1 LTR reporter construct lacking the Tat binding site but failed to activate a construct lacking the NF-κB binding sites. However, coexpression of HIV-1 Tat with K13 led to synergistic activation of HIV-1 LTR. Finally, K13 differentially activated HIV-1 LTRs derived from different strains of HIV-1, which correlated with their responsiveness to NF-κB pathway.

Conclusions
Our results suggest that concomitant infection with KSHV/HHV8 may stimulate HIV-1 LTR via vFLIP K13-induced classical NF-κB pathway which cooperates with HIV-1 Tat protein.
Comparative context analysis of codon pairs on an ORFeome scale
Authors: Moura Gabriela , Pinheiro Miguel , Silva Raquel , Miranda Isabel , Afreixo Vera , Dias Gaspar , Freitas Adelaide , Oliveira José L , Santos Manuel AS 
Published: February 2005

AbstractCodon context is an important feature of gene primary structure that modulates mRNA decoding accuracy. We have developed an analytical software package and a graphical interface for comparative codon context analysis of all the open reading frames in a genome (the ORFeome). Using the complete ORFeome sequences of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans and Escherichia coli, we show that this methodology permits large-scale codon context comparisons and provides new insight on the rules that govern the evolution of codon-pair context.
Nuclear localization is required for Dishevelled function in Wnt/β-catenin signaling
Authors: Itoh Keiji , Brott Barbara K , Bae Gyu-Un , Ratcliffe Marianne J , Sokol Sergei Y 
Published: February 2005

Abstract
Background
Dishevelled (Dsh) is a key component of multiple signaling pathways that are initiated by Wnt secreted ligands and Frizzled receptors during embryonic development. Although Dsh has been detected in a number of cellular compartments, the importance of its subcellular distribution for signaling remains to be determined.

Results
We report that Dsh protein accumulates in cell nuclei when Xenopus embryonic explants or mammalian cells are incubated with inhibitors of nuclear export or when a specific nuclear-export signal (NES) in Dsh is disrupted by mutagenesis. Dsh protein with a mutated NES, while predominantly nuclear, remains fully active in its ability to stimulate canonical Wnt signaling. Conversely, point mutations in conserved amino-acid residues that are essential for the nuclear localization of Dsh impair the ability of Dsh to activate downstream targets of Wnt signaling. When these conserved residues of Dsh are replaced with an unrelated SV40 nuclear localization signal, full Dsh activity is restored. Consistent with a signaling function for Dsh in the nucleus, treatment of cultured mammalian cells with medium containing Wnt3a results in nuclear accumulation of endogenous Dsh protein.

Conclusions
These findings suggest that nuclear localization of Dsh is required for its function in the canonical Wnt/β-catenin signaling pathway. We discuss the relevance of these findings to existing models of Wnt signal transduction to the nucleus.
Infant‐Directed Speech Facilitates Word Segmentation
Authors: Thiessen Erik D. , Hill Emily A. , Saffran Jenny R. 
Published: February 2005

AbstractThere are reasons to believe that infant‐directed (ID) speech may make language acquisition easier for infants. However, the effects of ID speech on infants' learning remain poorly understood. The experiments reported here assess whether ID speech facilitates word segmentation from fluent speech. One group of infants heard a set of nonsense sentences spoken with intonation contours characteristic of adult‐directed (AD) speech, and the other group heard the same sentences spoken with intonation contours characteristic of ID speech. In both cases, the only cue to word boundaries was the statistical structure of the speech. Infants were able to distinguish words from syllable sequences spanning word boundaries after exposure to ID speech but not after hearing AD speech. These results suggest that ID speech facilitates word segmentation and may be useful for other aspects of language acquisition as well. Issues of direction of preference in preferential listening paradigms are also considered.
Improved Thermal Stability of Europium Complex Nanoclusters Embedded in Silica Colloidal Spheres
Authors: Zhao Dan , Qin Weiping , Zhang Jisen , De Gejihu , Zhang Jishuang 
Published: February 2005

Abstract
Europium complex nanoclusters are introduced into monodisperse colloidal silica spheres by a modified Stöber method. Transmission electron microscopy measurements confirm that the hybrid spheres possess smooth surface and core-shell structure. The hybrid spheres display strong characteristic luminescence of the Eu3+ ions. Furthermore they exhibit an improved thermal stability compared with the pure rare earth (RE) complex.
Vanadium-catalyzed Isomerization of Cyclopropanemethanols to Homoallylic Alcohols Involving C–C Bond Cleavage
Authors: Maeda Yasunari , Nishimura Takahiro , Uemura Sakae 
Published: February 2005

Abstract
Some vanadium compounds work as effective catalysts for isomerization of cyclopropanemethanols to the corresponding homoallylic alcohols. This reaction may proceed via [3,3]sigmatropic rearrangement involving an oxovanadium cyclopropane-methanolate accompanied by the C–C bond cleavage.
Fabrication of MgO Hierarchical Nanostructures by a Thermal Evaporation Method
Authors: Yan Peng , Ye Changhui , Fang Xiaosheng , Zhao Jianwei , Wang Zhenyang , Zhang Lide 
Published: February 2005

Abstract
MgO hierarchical nanostructures were prepared through a simple thermal evaporation method. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images reveal the 4-fold symmetric MgO hierarchical morphologies. These structures may be helpful in studies of nanostructure growth mechanisms and find applications in numerous fields.
Effect of Ag Nanoparticles for Electrochemical Sensing of Brilliant Cresyl Blue
Authors: Li Mao-Guo , Gao Ying-Chun , Kan Xian-Wen , Wang Guang-Feng , Fang Bin 
Published: February 2005

Abstract
The modification of gold electrode by 1,4-benzenedimethanethiol (BDT) self-assembled monolayer and Ag nanoparticles was prepared and its electrochemical sensing of brilliant cresyl blue (BCB) was observed. The results suggested that the methods of electrochemical determination on the modified electrode could be applied in many fields.
Impact of Adherence, Knowledge, and Quality of Life on Anticoagulation Control
Authors: Davis Nichola J , Billett Henny H , Cohen Hillel W , Arnsten Julia H 
Published: February 2005

BACKGROUND: Patients receiving chronic warfarin therapy who have poor anticoagulation control are at increased risk for adverse events. However, it is unknown how adherence to warfarin, patient demographics, patient knowledge about therapy, and perceived impact of warfarin therapy on quality of life are associated with anticoagulation control. OBJECTIVE: To determine the association between these patient factors and anticoagulation control in patients attending 2 anticoagulation clinics in the Bronx, New York City. METHODS: A cross-sectional survey of 52 patients was conducted. The 4-item Morisky survey was used to assess self-reported adherence. Patient knowledge about warfarin therapy and the perceived impact of warfarin therapy on quality of life were determined by self-administered questionnaires. Associations between adherence, patient knowledge, impact of warfarin therapy on quality of life, and anticoagulation control were determined with t-tests, χ2 analysis, and logistic regression. RESULTS: Only 14% of patients had good anticoagulation control. Adequate adherence was reported by 50% of patients and was significantly associated with good anticoagulation control (p = 0.01). Thirty-seven percent of participants had good knowledge of anticoagulation, and 19% of participants reported that warfarin negatively impacted their quality of life. Knowledge about warfarin therapy and impact of warfarin on quality of life were not significantly associated with anticoagulation control. CONCLUSIONS: Adherence is one of many factors that contribute to anticoagulation control. Adequate adherence, as determined by the Morisky survey, was significantly associated with anticoagulation control. Patient demographic characteristics, knowledge about warfarin therapy, and perceived impact of warfarin on quality of life were not associated with anticoagulation control.
Optimization and evaluation of surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) with reversed-phase protein arrays for protein profiling
Authors: Aivado Manuel , Spentzos Dimitrios , Alterovitz Gil , Otu Hasan H. , Grall Franck , Giagounidis Aristoteles A. N. , Wells Meghan , Cho Je-Yoel , Germing Ulrich , Czibere Akos , Prall Wolf C. , Porter Chris , Ramoni Marco F. , Libermann Towia A. 
Published: February 2005

AbstractSurface-enhanced laser desorption/ionization (SELDI) time-of-flight mass spectrometry with protein arrays has facilitated the discovery of disease-specific protein profiles in serum. Such results raise hopes that protein profiles may become a powerful diagnostic tool. To this end, reliable and reproducible protein profiles need to be generated from many samples, accurate mass peak heights are necessary, and the experimental variation of the profiles must be known. We adapted the entire processing of protein arrays to a robotics system, thus improving the intra-assay coefficients of variation (CVs) from 45.1% to 27.8% (p<0.001). In addition, we assessed up to 16 technical replicates, and demonstrated that analysis of 2–4 replicates significantly increases the reliability of the protein profiles. A recent report on limited long-term reproducibility seemed to concord with our initial inter-assay CVs, which varied widely and reached up to 56.7%. However, we discovered that the inter-assay CV is strongly dependent on the drying time before application of the matrix molecule. Therefore, we devised a standardized drying process and demonstrated that our optimized SELDI procedure generates reliable and long-term reproducible protein profiles with CVs ranging from 25.7% to 32.6%, depending on the signal-to-noise ratio threshold used.