bluuebunny/crossref_metadata_2025_split huggingface dataset:
The NKG2D ligand ULBP4 binds to TCRγ9/δ2 and induces cytotoxicity to tumor cells through both TCRγδ and NKG2D
Authors: Kong Yan , Cao Wei , Xi Xueyan , Ma Chi , Cui Lianxian , He Wei 
Published: May 2009

AbstractUL16-binding proteins (ULBPs) belong to a family of ligands for NKG2D activating receptor of human natural killer (NK) cells. We previously reported that RAET1E2, a soluble isoform of the RAET1E (ULBP4), inhibits NKG2D-mediated NK cytotoxicity. In this study, we examined whether ULBP4 could be recognized by γδT cells via TCRγδ. Here we show that immobilized soluble ULBP4 (rULBP4) induces the proliferation of human ovarian epithelial carcinoma– or colonic carcinoma–derived Vδ2+ T cells in vitro. These Vδ2+ T cells secrete Th1 cytokines and display a strong cytolytic activity toward ULBP4-transfected targets. We also show that ULBP4 binds to a soluble chimeric protein containing TCRγ9/δ2 and activates TCR− Jurkat T cells transfected with TCRγ9/δ2. Moreover, both TCRγδ and NKG2D are involved in ULBP4-induced activation and cytotoxicity of γδT cells. We found that ULBP4 is expressed not only on human tumor cells, but also on Epstein-Barr virus (EBV)–infected peripheral blood cells. Taken together, our data suggest that ULBP4 functions as a ligand for both TCRγδ and NKG2D and may play a key role in immune surveillance of tumor development and clearance of viral infection.
Silencing CD36 gene expression results in the inhibition of latent-TGF-β1 activation and suppression of silica-induced lung fibrosis in the rat
Authors: Wang Xin , Chen Ying , Lv Lina , Chen Jie 
Published: May 2009

Abstract

Background
The biologically active form of transforming growth factor-β1 (TGF-β1) plays a key role in the development of lung fibrosis. CD36 is involved in the transformation of latent TGF-β1 (L-TGF-β1) to active TGF-β1. To clarify the role of CD36 in the development of silica-induced lung fibrosis, a rat silicosis model was used to observe both the inhibition of L-TGF-β1 activation and the antifibrotic effect obtained by lentiviral vector silencing of CD36 expression.

Methods
The rat silicosis model was induced by intratracheal injection of 10 mg silica per rat and CD36 expression was silenced by administration of a lentiviral vector (Lv-shCD36). The inhibition of L-TGF-β1 activation was examined using a CCL-64 mink lung epithelial growth inhibition assay, while determination of hydroxyproline content along with pathological and immunohistochemical examinations were used for observation of the inhibition of silica-induced lung fibrosis.

Results
The lentiviral vector (Lv-shCD36) silenced expression of CD36 in alveolar macrophages (AMs) obtained from bronchoalveolar lavage fluid (BALF) and the activation of L-TGF-β1 in the BALF was inhibited by Lv-shCD36. The hydroxyproline content of silica+Lv-shCD36 treated groups was significantly lower than in other experimental groups. The degree of fibrosis in the silica+Lv-shCD36-treated groups was less than observed in other experimental groups. The expression of collagen I and III in the silica+Lv-shCD36-treated group was significantly lower than in the other experimental groups.

Conclusion
These results indicate that silencing expression of CD36 can result in the inhibition of L-TGF-β1 activation in a rat silicosis model, thus further preventing the development of silica-induced lung fibrosis.
Impact of duplicate gene copies on phylogenetic analysis and divergence time estimates in butterflies
Authors: Pohl Nélida , Sison-Mangus Marilou P , Yee Emily N , Liswi Saif W , Briscoe Adriana D 
Published: May 2009

AbstractBackgroundThe increase in availability of genomic sequences for a wide range of organisms has revealed gene duplication to be a relatively common event. Encounters with duplicate gene copies have consequently become almost inevitable in the context of collecting gene sequences for inferring species trees. Here we examine the effect of incorporating duplicate gene copies evolving at different rates on tree reconstruction and time estimation of recent and deep divergences in butterflies.ResultsSequences from ultraviolet-sensitive (UVRh), blue-sensitive (BRh), and long-wavelength sensitive (LWRh) opsins,EF-1αandCOIwere obtained from 27 taxa representing the five major butterfly families (5535 bp total). BothBRhandLWRhare present in multiple copies in some butterfly lineages and the different copies evolve at different rates. Regardless of the phylogenetic reconstruction method used, we found that analyses of combined data sets using either slower or faster evolving copies of duplicate genes resulted in a single topology in agreement with our current understanding of butterfly family relationships based on morphology and molecules. Interestingly, individual analyses ofBRhandLWRhsequences also recovered these family-level relationships. Two different relaxed clock methods resulted in similar divergence time estimates at the shallower nodes in the tree, regardless of whether faster or slower evolving copies were used, with larger discrepancies observed at deeper nodes in the phylogeny. The time of divergence between the monarch butterflyDanaus plexippusand the queenD. gilippus(15.3–35.6 Mya) was found to be much older than the time of divergence between monarch co-mimicLimenitis archippusand red-spotted purpleL. arthemis(4.7–13.6 Mya), and overlapping with the time of divergence of the co-mimetic passionflower butterfliesHeliconius eratoandH. melpomene(13.5–26.1 Mya). Our family-level results are congruent with recent estimates found in the literature and indicate an age of 84–113 million years for the divergence of all butterfly families.ConclusionThese results are consistent with diversification of the butterfly families following the radiation of angiosperms and suggest that some classes of opsin genes may be usefully employed for both phylogenetic reconstruction and divergence time estimation.
Chibby forms a homodimer through a heptad repeat of leucine residues in its C-terminal coiled-coil motif
Authors: Mofunanya Adaobi , Li Feng-Qian , Hsieh Jen-Chih , Takemaru Ken-Ichi 
Published: May 2009

AbstractBackgroundThe Wnt/β-catenin signaling pathway plays crucial roles in embryonic development and in maintenance of organs and tissues in adults. Chibby (Cby) is an evolutionarily conserved molecule that physically interacts with the key downstream coactivator β-catenin and represses its transcriptional activation potential. Although Cby harbors a predicted coiled-coil motif in the C-terminal region, its molecular nature and functional importance remain largely unexplored.ResultsHere we report that Cby forms a stable complex with itself. Alanine substitutions of two or more of four critical leucine residues within the C-terminal heptad repeats completely eliminate the Cby-Cby interaction. The Cby oligomer predominantly exists as a homodimer. Furthermore, we found that dimerization-deficient Cby mutants still retain the ability to bind to β-catenin and to repress β-catenin-dependent gene activation. More importantly, Cby homodimerization is required for its efficient interaction with the nuclear import receptor importin-α and subsequent nuclear translocation.ConclusionOur comprehensive mutational analysis of the Cby coiled-coil domain reveals that the four heptad leucine residues play an essential role in mediating Cby homodimerization. Although monomeric Cby is sufficient to bind to β-catenin and block β-catenin-mediated transcriptional activation, homodimer formation of Cby is indispensable for its efficient nuclear import.
Additive effect of LRP8/APOER2 R952Q variant to APOE ε2/ε3/ε4 genotype in modulating apolipoprotein E concentration and the risk of myocardial infarction: a case-control study
Authors: Martinelli Nicola , Olivieri Oliviero , Shen Gong-Qing , Trabetti Elisabetta , Pizzolo Francesca , Busti Fabiana , Friso Simonetta , Bassi Antonella , Li Lin , Hu Ying , Pignatti Pier Franco , Corrocher Roberto , Wang Qing Kenneth , Girelli Domenico 
Published: May 2009

Abstract

Background
The R952Q variant in the low density lipoprotein receptor-related protein 8 (LRP8)/apolipoprotein E receptor 2 (ApoER2) gene has been recently associated with familial and premature myocardial infarction (MI) by means of genome-wide linkage scan/association studies. We were interested in the possible interaction of the R952Q variant with another established cardiovascular genetic risk factor belonging to the same pathway, namely apolipoprotein E (APOE) ε2/ε3/ε4 genotype, in modulating apolipoprotein E (ApoE) plasma levels and risk of MI.

Methods
In the Italian cohort used to confirm the association of the R952Q variant with MI, we assessed lipid profile, apolipoprotein concentrations, and APOE ε2/ε3/ε4 genotype. Complete data were available for a total of 681 subjects in a case-control setting (287 controls and 394 patients with MI).

Results
Plasma ApoE levels decreased progressively across R952Q genotypes (mean levels ± SD = RR: 0.045 ± 0.020, RQ: 0.044 ± 0.014, QQ: 0.040 ± 0.008 g/l; P for trend = 0.047). Combination with APOE genotypes revealed an additive effect on ApoE levels, with the highest level observed in RR/non-carriers of the E4 allele (0.046 ± 0.021 g/l), and the lowest level in QQ/E4 carriers (0.035 ± 0.009 g/l; P for trend = 0.010). QQ/E4 was also the combined genotype with the most significant association with MI (OR 3.88 with 95%CI 1.08–13.9 as compared with RR/non-carriers E4).

Conclusion
Our data suggest that LRP8 R952Q variant may have an additive effect to APOE ε2/ε3/ε4 genotype in determining ApoE concentrations and risk of MI in an Italian population.
Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks
Authors: Andrabi Munazah , Mizuguchi Kenji , Sarai Akinori , Ahmad Shandar 
Published: May 2009

Abstract

Background
DNA recognition by proteins is one of the most important processes in living systems. Therefore, understanding the recognition process in general, and identifying mutual recognition sites in proteins and DNA in particular, carries great significance. The sequence and structural dependence of DNA-binding sites in proteins has led to the development of successful machine learning methods for their prediction. However, all existing machine learning methods predict DNA-binding sites, irrespective of their target sequence and hence, none of them is helpful in identifying specific protein-DNA contacts. In this work, we formulate the problem of predicting specific DNA-binding sites in terms of contacts between the residue environments of proteins and the identity of a mononucleotide or a dinucleotide step in DNA. The aim of this work is to take a protein sequence or structural features as inputs and predict for each amino acid residue if it binds to DNA at locations identified by one of the four possible mononucleotides or one of the 10 unique dinucleotide steps. Contact predictions are made at various levels of resolution viz. in terms of side chain, backbone and major or minor groove atoms of DNA.

Results
Significant differences in residue preferences for specific contacts are observed, which combined with other features, lead to promising levels of prediction. In general, PSSM-based predictions, supported by secondary structure and solvent accessibility, achieve a good predictability of ~70–80%, measured by the area under the curve (AUC) of ROC graphs. The major and minor groove contact predictions stood out in terms of their poor predictability from sequences or PSSM, which was very strongly (>20 percentage points) compensated by the addition of secondary structure and solvent accessibility information, revealing a predominant role of local protein structure in the major/minor groove DNA-recognition. Following a detailed analysis of results, a web server to predict mononucleotide and dinucleotide-step contacts using PSSM was developed and made available at http://sdcpred.netasa.org/ or http://tardis.nibio.go.jp/netasa/sdcpred/.

Conclusion
Most residue-nucleotide contacts can be predicted with high accuracy using only sequence and evolutionary information. Major and minor groove contacts, however, depend profoundly on the local structure. Overall, this study takes us a step closer to the ultimate goal of predicting mutual recognition sites in protein and DNA sequences.
The study on the outsourcing of Taiwan's hospitals: a questionnaire survey research
Authors: Hsiao Chih-Tung , Pai Jar-Yuan , Chiu Hero 
Published: May 2009

Abstract

Background
The aim of this study was to assess the outsourcing situation in Taiwanese hospitals and compares the differences in hospital ownership and in accreditation levels.

Methods
This research combined two kinds of methods: a questionnaire survey and the in-depth interview to two CEOs of the sample hospitals. One hospital is not-for-profit, while the other is a public hospital and the research samples are from the hospital data from Taiwan's 2005 to 2007 Department of Health qualifying lists of hospital accreditation. The returned questionnaires were analyzed with STATISTICA® 7.1 version software.

Results
The results for non-medical items showed medical waste and common trash both have the highest rate (94.6 percent) of being outsourced. The gift store (75 percent) and linen (73 percent) follow close behind, while the lowest rate of outsourcing is in utility maintenance (13.5 percent). For medical items, the highest rate of outsourcing is in the ambulance units (51.4 percent), while the hemodialysis center follows close behind with a rate of 50 percent. For departments of nutrition, pharmacy, and nursing however, the outsourcing rate is lower than 3 percent. This shows that Taiwan's hospitals are still conservative in their willingness to outsource for medical items. The results of the satisfaction paired t-test show that the non-medical items have a higher score than the medical items. The factor analysis showed the three significant factors in of non medical items' outsourcing are "performance", "finance", and "human resource". For medical items, the two factors are "operation" and satisfaction". To further exam the factor validity and reliability of the satisfaction model, a confirmative factor analysis (CFA) was conducted using structure equation modeling (SEM) method and found the model fitting well.

Conclusion
Hospitals, especially for public hospitals, can get benefits from outsourcing to revive the full-time-equivalent and human resource limitation.
Pharmacological Blockade of TRPA1 Inhibits Mechanical Firing in Nociceptors
Authors: Kerstein Patrick C , del Camino Donato , Moran Magdalene M , Stucky Cheryl L 
Published: May 2009

Background TRPA1 has been implicated in both chemo- and mechanosensation. Recent work demonstrates that inhibiting TRPA1 function reduces mechanical hypersensitivity produced by inflammation. Furthermore, a broad range of chemical irritants require functional TRPA1 to exert their effects. In this study we use the ex-vivo skin-nerve preparation to directly determine the contribution of TRPA1 to mechanical- and chemical-evoked responses at the level of the primary afferent terminal. Results Acute application of HC-030031, a selective TRPA1 antagonist, inhibited all formalin responses in rat C fibers but had no effect on TRPV1 function, assessed by capsaicin responsiveness. Genetic ablation experiments corroborated the pharmacological findings as C fibers from wild type mice responded to both formalin and capsaicin, but fibers from their TRPA1-deficient littermates responded only to capsaicin. HC-030031 markedly reduced the mechanically-evoked action potential firing in rat and wild type mouse C fibers, particularly at high-intensity forces, but had no effect on the mechanical responsiveness of Aδ fiber nociceptors. Furthermore, HC-030031 had no effect on mechanically-evoked firing in C fibers from TRPA1-deficient mice, indicating that HC-030031 inhibits mechanically-evoked firing via a TRPA1-dependent mechanism. Conclusion Our data show that acute pharmacological blockade of TRPA1 at the cutaneous receptive field inhibits formalin-evoked activation and markedly reduces mechanically-evoked action potential firing in C fibers. Thus, functional TRPA1 at sensory afferent terminals in skin is required for their responsiveness to both noxious chemical and mechanical stimuli.
The expression profile of microRNAs in a model of 7,12-dimethyl-benz[a]anthrance-induced oral carcinogenesis in Syrian hamster
Authors: Yu Tao , Wang Xiao-yi , Gong Ren-guo , Li An , Yang Sen , Cao Yu-tang , Wen Yu-ming , Wang Chang-mei , Yi Xin-zhu 
Published: May 2009

Abstract

Background
Non-coding RNA molecules, such as microRNAs, may play an important role in carcinogenesis. Recent studies have indicated that microRNAs are involved in initiation and progression of various malignancies. However, little work has been done to compare the microRNA expression patterns in oral cancer. In this study, we constructed an animal model of oral squamous cell carcinoma to investigate expression profiles of microRNAs in oral carcinogenesis.

Methods
The animal model of oral squamous cell carcinoma was conducted by tri-weekly (Monday, Wednesday, and Friday) painting with 5% DMBA in acetone. Six Syrian hamsters, including three from the treated group and three from the control group, were used as a training group for microRNA microarray analysis. All microarray data were analyzed by Significance Analysis of Microarrays (SAM) and CLUSTER 3.0 software, and this result was further confirmed by qRT-PCR assay.

Results
Seventeen microRNAs were differentially expressed in oral squamous cell carcinoma. Five microRNAs (hsa-miR-21, hsa-miR-200b, hsa-miR-221, hsa-miR-338, and mmu-miR-762) were significantly upregulated and twelve microRNAs (hsa-miR-16, hsa-miR-26a, hsa-miR-29a, hsa-miR-124a, hsa-miR-125b, mmu-miR-126-5p, hsa-miR-143, hsa-miR-145, hsa-miR-148b, hsa-miR-155, hsa-miR-199a, and hsa-miR-203) were down-regulated in cancer tissues. The expression levels of hsa-miR-21 and hsa-miR-16 seen with Stem-loop qRT-PCR were also seen in microarray analysis in all samples.

Conclusion
Our findings identified specific microRNA expression in oral squamous cell carcinoma and suggested that microRNAs have a role in oral carcinogenesis.
Impact of Resistance to Thyroid Hormone on the Cardiovascular System in Adults
Authors: Pulcrano Melania , Palmieri Emiliano Antonio , Ciulla Deborah Mannavola Michele , Campi Irene , Covelli Danila , Lombardi Gaetano , Biondi Bernadette , Beck-Peccoz Paolo 
Published: May 2009

Background: The clinical manifestations of resistance to thyroid hormone (RTH) are highly variable, and the impact of RTH on the cardiovascular system has been poorly investigated.
Aim: The objective of the study was to evaluate the cardiovascular characteristics of 16 untreated and asymptomatic patients with RTH compared with 16 euthyroid healthy controls to define the cardiovascular involvement in RTH syndrome.
Patients and Methods: Sixteen untreated and asymptomatic RTH patients (eight males; aged 33 ± 12 yr, range 21–45 yr) and 16 controls (nine males; aged 33 ± 5 yr, range 24–42 yr) were enrolled. Clinical data, thyroid status, and echocardiographic results were recorded.
Results: Heart rate was comparable with that of controls, whereas arterial pressure was higher than controls. Mean interventricular septum diastolic thickness and mean left ventricular (LV) posterior wall diastolic thickness were significantly lower in RTH patients than controls with a consequent significant decrease of the mean LV mass and LV mass indexed by body surface area. Patients also had abnormalities of myocardial relaxation as indicated by a significant increase of peak A and consequent reduction of the early to late ratio. Finally, systemic vascular resistance was significantly higher in RTH patients than controls.
Conclusions: Our results suggest the presence of cardiovascular alterations in asymptomatic and untreated RTH patients similar to those reported in hypothyroid patients. Our strict selection likely created a bias in the inclusion of a particular type of RTH patients, who could represent a minority of patients with RTH. However, no correlation was found between the type of mutation and cardiovascular characteristics of RTH patients.
Electrophilic Substitution of Thiophenes with Arylpalladium(II) and Platinum(II) Complexes: Mechanistic Studies on Palladium-Catalyzed CH Arylation of Thiophenes
Authors: Sugie Atsushi , Furukawa Hirotoshi , Suzaki Yuji , Osakada Kohtaro , Akita Munetaka , Monguchi Daiki , Mori Atsunori 
Published: May 2009

Abstract
Mechanistic studies on palladium-catalyzed CH arylation of thiophenes which has been shown by our group are carried out by a stoichiometric reaction of organometallic complexes. The reaction of arylpalladium(II) halide with 2,3-dibromothiophene in the presence of AgNO3/KF as an activator induces electrophilic substitution at the CH bond of the thiophene to give CH arylated product. The similar reaction of arylplatinum(II) halide with thiophene derivatives affords the aryl(thienyl)platinum(II) complex which is an analog of a precursor of the product of the CH arylation reaction. These results suggest that the palladium-catalyzed CH arylation reaction of thiophenes proceeds through electrophilic substitution.
Variation of the Uncoupled OD Stretching Frequency with Electrolyte Concentration in Aqueous Electrolyte Solutions
Authors: Yonehama Kazue , Yoshimura Yukihiro , Takekiyo Takahiro , Kanno Hitoshi 
Published: May 2009

Abstract
Uncoupled OD stretching Raman spectra were measured for many aqueous electrolyte solutions as a function of electrolyte concentration. There are three types of variations of frequencies of uncoupled OD stretching Raman spectra with electrolyte concentration. The first type shows monotonous increase in frequency with increasing salt concentration, the second shows curved variation with a maximum higher than the frequency of pure liquid water, and the third exhibits a constant decrease in frequency with salt concentration. It is confirmed that the cationic effect on the OH (or OD) stretching frequency is very small so far as the charge of the cations is the same. Structure-making anions strengthen the average strength of hydrogen bonds and structure-breaking ones weaken the hydrogen bonds as compared with those in pure liquid water.
Computational Study of Excited-State Intramolecular-Proton-Transfer of o-Hydroxybenzaldehyde and Its Derivatives
Authors: Nagaoka Shin-ichi , Teramae Hiroyuki , Nagashima Umpei 
Published: May 2009

Abstract
The excited-state intramolecular-proton-transfer of o-hydroxybenzaldehyde and its derivatives (o-formyl-substituted phenols) was studied by means of an ab initio molecular-orbital method. The computational results are consistent with the experimental fluorescence quantum yield and support the nodal-plane model. The energy difference between the ground state and the lowest excited 1(π,π*) state decreases as the electron-withdrawing property of a substituent bonded to the carbonyl carbon of o-hydroxybenzaldehyde becomes stronger. However, the substituent effect does not largely distort the potential energy surface of o-formyl-substituted phenols.
In Situ Self-Assembly of 1D Copper(II) Coordination Polymer Containing EO Azide and Phenolate Bridges: Crystal Structure and Magnetic Properties
Authors: Liu Zhiliang , Han Weihua , Liu Caiming , Di Xiaowei , Zhang Jun , Zhang Deqing 
Published: May 2009

Abstract
A novel one-dimensional copper(II) coordination polymer with formula [CuII(L1)(N3)]n (1), has been prepared via in situ self-assembly. Compound 1 consists of 1D uniform chains in which the copper(II) ions are bridged by end-on azide and an oxygen of salicylideneamine (L1). Magnetic susceptibility measurement reveals the existence of relatively strong ferromagnetic interactions in the 1D chain.