bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteome data set of human gingival crevicular fluid from healthy periodontium sites by multidimensional protein separation and mass spectrometry
Authors: Carneiro L. G. , Venuleo C. , Oppenheim F. G. , Salih E. 
Published: October 2011

Carneiro LG, Venuleo C, Oppenheim FG, Salih E. Proteome data set of human gingival crevicular fluid from healthy periodontium sites by multidimensional protein separation and mass spectrometry. J Periodont Res 2012; 47: 248–262. © 2011 John Wiley & Sons A/SBackground and Objective:  Gingival crevicular fluid has been of major interest for many decades as a valuable body fluid that may serve as a source of biomarkers for both periodontal and systemic diseases. Owing to its very small sample size, submicroliter volumes, identification of its protein composition by classical biochemical methods has been limited. The advent of highly sensitive mass spectrometric technology has permitted large‐scale identification of protein components of many biological samples. This technology has been employed to identify the protein composition of gingival crevicular fluid from inflamed and periodontal sites. In this report, we present a proteome data set of gingival crevicular fluid from healthy periodontium sites.Material and Methods:  A combination of a periopaper collection method with application of multidimensional protein separation and mass spectrometric technology led to a large‐scale documentation of the proteome of gingival crevicular fluid from healthy periodontium sites.Results:  The approaches used have culminated in identification of 199 proteins in gingival crevicular fluid of periodontally healthy sites. The present gingival crevicular fluid proteome from healthy sites was compared and contrasted with those proteomes of gingival crevicular fluid from inflamed and periodontal sites, as well as serum. The cross‐correlation of the gingival crevicular fluid and plasma proteomes permitted dissociation of the 199 identified gingival crevicular fluid proteins into 105 proteins (57%) that can be identified in plasma and 94 proteins (43%) that are distinct and unique to the gingival crevicular fluid microenvironment. Such analysis also revealed distinctions in protein functional categories between serum proteins and those specific to the gingival crevicular fluid microenvironment.Conclusion:  Firstly, the data presented herein provide the proteome of gingival crevicular fluid from periodontally healthy sites through establishment of innovative analytical approaches for effective analysis of gingival crevicular fluid from periopapers both at the level of complete elusion and with removal of abundant albumin, which restricts identification of low‐abundant proteins. Secondly, it adds significantly to the knowledge of gingival crevicular fluid composition and highlights new groups of proteins specific to the gingival crevicular fluid microenvironment.
Prophaenognatha, a New Aclopinae Genus from the Yixian Formation, China and Its Phylogenetic Position Based on Morphological Characters (Coleoptera: Scarabaeidae)
Authors: BAI Ming , REN Dong , YANG Xingke 
Published: October 2011

Abstract:Prophaenognatha robusta gen. et sp. nov. (Scarabaeoidea: Scarabaeidae: Aclopinae), the best‐preserved aclopine fossil so far, is described and illustrated from the Upper Jurassic‐Lower Cretaceous Yixian Formation of the Jehol Biota, western Liaoning Province, NE China. The key to extinct and extant genera of Aclopinae is given and the monophyly of extant and fossil Aclopinae lineages is supported by five character states. The new taxon provides evidence about the evolution of Scarabaeoidea with its phylogenetic position inferred based on 68 morphological characters.
A New Three‐Dimensional Superstructure in Bafertisite
Authors: LI Guowu , XIONG Ming , SHI Nicheng , MA Zhesheng 
Published: October 2011

Abstract:A new superstructure was found in bafertisite [(Ba0.98Na0.02)1.00(Fe1.71Mn0.26Mg0.01)1.98 TiO [(Si1.82Ti0.04Al0.03Cr0.01)1.90O7](OH1.40F0.53Cl0.03)1.96] from Donghai County, Jiangsu Province, China. The occurrence of the superstructure reflections were observed by single crystal diffraction using a SMAR APEX CCD. The a*, b* and c* axis directions revealed extra weak reflection spots of the superstructure. The apparent 2a, 2b and 2c superstructure is monoclinic with unit cell a= 10.6502(15) Å, b= 13.7233(19)Å, c= 21.6897(3)Å, α= 90°, β= 94.698(3)°, γ=90°, space group Cm, Z= 16. If c* extra weak reflections are ignored, the secondary supercell gave a cell a= 10.6548(15)Å, b=13.7284(19)Å, c= 11.6900(17)Å, α= 90°, β= 112.322(28)°, γ= 90°, space group Cm, Z= 8. The basic subcell was obtained by ignoring all extra weak reflection spots and gave: a= 5.3249(17)Å, b=6.8669(22)Å, c= 10.8709(36) Å, α= 90°, β= 94.740(62)°, γ= 90°, space P21/m, Z= 2. The superstructure has been refined to R= 0.063 for 7805 [R(int)= 0.0266] unique reflections I>2δ(I). The structure consists of an octahedra (O) sheet sandwiched between two heteropolyhedral (H) sheets. These sheets consist of Ti‐octahedra and twin tetrahedral disilicate groups [Si2O7]. The O sheet comprises (Fe,Mg)O4 octahedra. The large Ba cation is located in the interlayer area. The refined structure shows Fe, Mg are partly ordered. The shifting of the TiO6 octahedron and SiO4 tetrahedron sites in the sheet may be a consequence of the superstructure.
Petrology and Geochemistry of Post‐Collisional Early Miocene Volcanism in the Karacadaǧ Area (Central Anatolia, Turkey)
Authors: ASAN Kürşad , KURT Hüseyin 
Published: October 2011

Abstract:Early Miocene (ca. 21–18 Ma) volcanism in the Karacadaǧ area comprises three groups of volcanic rocks: (1) calcalkaline suite (andesitic to rhyolitic lavas and their pyroclastics), (2) mildly‐alkaline suite (alkali basalt, hawaiite, mugearite, benmoreite and trachydacite), and (3) a single trachyandesitic flow unit. Field observations, 40Ar/39Ar ages and geochemical data show that there was a progressive temporal transition from group 1 to 3 in a post‐collisional tectonic setting. The calcalkaline suite rocks with medium‐K in composition resemble those of subduction‐related lavas, whereas the mildly‐alkaline suite rocks having a sodic tendency (Na2O/K2O=1.5–3.2) resemble those of within‐plate lavas. Incompatible element and Sr‐Nd isotopic characteristics of the suites suggest that the lithospheric mantle beneath the Karacadaǧ area was heterogeneously enriched by two processes before collision: (1) enrichment by subduction‐related processes, which is important in the genesis of the calcalkaline volcanism, (2) enrichment by small degree melts from the astenosphere, which dominates the mildly alkaline volcanism. Perturbation of the enriched lithosphere by either delamination following collision and uplift or removal of the subducted slab following subduction and collision (i.e., slab breakoff) is the likely mechanism for the initiation of the post‐collision volcanism.
Grains Containing Oil Inclusions in Different Hydrocarbon Production and Show Types of Sandstone Reservoirs from the Central Junggar Basin, Northwest China
Authors: CAO Jian , WANG Xulong , SUN Ping'an , SHI Xinpu , HU Wenxuan , YAO Suping , ZHANG Yueqian , TANG Yong , XIE Xiaomin 
Published: October 2011

Abstract:The values of grains containing oil inclusions (GOI) in 120 reservoir sandstone samples from the central Junggar Basin of Northwest China were investigated. The sandstones are characterized by different types of hydrocarbon production and shows. The values range from 0.015% to 19.9%, and show a fairly good correlation with the hydrocarbon production/shows, which are qualitatively suggestive of reservoir hydrocarbon abundance and petroleum migration. Thus, it may be implied that the values can reflect hydrocarbon migration, being not controlled mainly by the other influencing factors. Further correlation between the values and the reservoir hydrocarbon production and show types indicates that the GOI method can be used in hydrocarbon migration study when the petroleum type of a reservoir is normal oil or gas alone, but it should be used with caution when light oil charges the reservoirs or a complex hydrocarbon migration event takes place. The case study in the central Junggar Basin using the method presents some new understanding on hydrocarbon migration. Thus, the method may help to solve specific petroleum geological problems, and can be treated as a routine tool in hydrocarbon migration study.
Oral application of 1,7‐dimethylxanthine (paraxanthine) attenuates the formation of experimental cholestatic liver fibrosis
Authors: Klemmer Ildikó , Yagi Shintaro , Gressner Olav A. 
Published: October 2011

Aim:  Several epidemiological studies suggest a beneficial effect of coffee consumption on the formation and progression of fibrogenic diseases, particularly of the liver. Recent data now point to a modulation of transforming growth factor‐β (TGF‐β) signaling by paraxanthine (1,7‐dimethylxanthine [1,7‐DMX]), the demethylated primary metabolite of caffeineMethods:  Twenty adult Sprague–Dawley rats were bile duct ligated (BDL) or sham operated with or without concomitant oral 1,7‐DMX (1 mM) application. Serum was investigated by standard biochemical analysis, in‐house connective tissue growth factor (CTGF), enzyme linked immunosorbent assay (ELISA) or liquid chromatography‐mass spectrometry analysis. Liver tissue was stained using hematoxylin‐eosin (HE) and Sirius‐red staining. Whole liver lysates, primary rat hepatocytes (PC) and hepatic stellate cells (HSC) were investigated by CTGF, and total Smad2/3 Western blot analysis, CTGF reporter gene assay or an in‐house malondialdehyde ELISA.Results:  The in vitro 50% inhibitory dose (ID50) of 1,7‐DMX was 0.95 mM by for CTGF promoter activity and protein expression in PC and 1.25 mM for protein expression in HSC. Oral 1,7‐DMX application (1 mM) attenuated cholestatic hepatocellular injury in vivo as determined by biochemical serum analysis and reduced intercellular collagen deposition in the cholestatic rat liver (HE‐ and Sirius‐red staining). Western Blot analysis of whole liver lysates revealed a reduction of intrahepatic concentrations of Smad2/3 and CTGF following oral 1,7‐DMX intake. However, serum CTGF concentrations were not reduced in 1,7‐DMX treated BDL rats. Oral 1,7‐DMX furthermore led to a reduction of intrahepatic lipid peroxidation (malondialdehyde concentrations) as markers of oxidative stress in BDL rats.Conclusion:  Our pilot study warrants further studies of 1,7‐DMX as a potential new drug to fight fibrotic processes, not just of the liver.
Aspergillus versicolor, a New Causative Agent of Canine Disseminated Aspergillosis
Authors: Zhang Shuping , Corapi Wayne , Quist Erin , Griffin Sarah , Zhang Michael 
Published: October 2011

ABSTRACTDisseminated aspergillosis in dogs has been associated withAspergillus terreusorA. deflectusinfection. We report a case of disseminatedA. versicolorinfection presenting as diskospondylitis, osteomyelitis, and pyelonephritis. The diagnosis was made based on clinical, radiographic, and pathological findings. The etiologic agent was identified by fungal culture and internal transcribed spacer (ITS) ribosomal DNA (rDNA) sequencing. This is the first description of canine aspergillosis caused byA. versicolor.
Characterization of Human Endogenous Retroviral Elements in the Blood of HIV-1-Infected Individuals
Authors: Contreras-Galindo Rafael , Kaplan Mark H. , Contreras-Galindo Angie C. , Gonzalez-Hernandez Marta J. , Ferlenghi Ilaria , Giusti Fabiola , Lorenzo Eric , Gitlin Scott D. , Dosik Michael H. , Yamamura Yasuhiro , Markovitz David M. 
Published: October 2011

ABSTRACT

We previously reported finding the RNA of a type K human endogenous retrovirus, HERV-K (HML-2), at high titers in the plasma of HIV-1-infected and cancer patients (R. Contreras-Galindo et al., J. Virol. 82:9329–9236, 2008.). The extent to which the HERV-K (HML-2) proviruses become activated and the nature of their activated viral RNAs remain important questions. Therefore, we amplified and sequenced the full-length RNA of the
env
gene of the type 1 and 2 HERV-K (HML-2) viruses collected from the plasma of seven HIV-1-infected patients over a period of 1 to 3 years and from five breast cancer patients in order to reconstruct the genetic evolution of these viruses. HERV-K (HML-2) RNA was found in plasma fractions of HIV-1 patients at a density of ∼1.16 g/ml that contained both immature and correctly processed HERV-K (HML-2) proteins and virus-like particles that were recognized by anti-HERV-K (HML-2) antibodies. RNA sequences from novel HERV-K (HML-2) proviruses were discovered, including K111, which is specifically active during HIV-1 infection. Viral RNA arose from complete proviruses and proviruses devoid of a 5′ long terminal repeat, suggesting that the expression of HERV-K (HML-2) RNA in these patients may involve sense and antisense transcription. In HIV-1-infected individuals, the HERV-K (HML-2) viral RNA showed evidence of frequent recombination, accumulation of synonymous rather than nonsynonymous mutations, and conserved N-glycosylation sites, suggesting that some of the HERV-K (HML-2) viral RNAs have undergone reverse transcription and are under purifying selection. In contrast, HERV-K (HML-2) RNA sequences found in the blood of breast cancer patients showed no evidence of recombination and exhibited only sporadic viral mutations. This study suggests that HERV-K (HML-2) is active in HIV-1-infected patients, and the resulting RNA message reveals previously undiscovered HERV-K (HML-2) genomic sequences.
Viral Expression Directs the Fate of B Cells in Bovine Leukemia Virus-Infected Sheep
Authors: Florins Arnaud , de Brogniez Alix , Elemans Marjet , Bouzar Amel-Baya , François Carole , Reichert Michal , Asquith Becca , Willems Luc 
Published: October 2011

ABSTRACT

The host immune response is believed to tightly control viral replication of deltaretroviruses such as human T-lymphotropic virus type 1 (HTLV-1) and bovine leukemia virus (BLV). However, this assumption has not been definitely proven
in vivo
. In order to further evaluate the importance of the immune response in the BLV model, we studied the fate of cells in which viral expression was transiently induced. Using a dual fluorochrome labeling approach, we showed that
ex vivo
induction of viral expression induces higher death rates of B cells
in vivo
. Furthermore, cyclosporine treatment of these animals indicated that an efficient immune response is required to control virus-expressing cells.
Structural Basis for Norovirus Inhibition and Fucose Mimicry by Citrate
Authors: Hansman Grant S. , Shahzad-ul-Hussan Syed , McLellan Jason S. , Chuang Gwo-Yu , Georgiev Ivelin , Shimoike Takashi , Katayama Kazuhiko , Bewley Carole A. , Kwong Peter D. 
Published: October 2011

ABSTRACT
Human noroviruses bind with their capsid-protruding domains to histo-blood-group antigens (HBGAs), an interaction thought to direct their entry into cells. Although human noroviruses are the major cause of gastroenteritis outbreaks, development of antivirals has been lacking, mainly because human noroviruses cannot be cultivated. Here we use X-ray crystallography and saturation transfer difference nuclear magnetic resonance (STD NMR) to analyze the interaction of citrate with genogroup II (GII) noroviruses. Crystals of citrate in complex with the protruding domain from norovirus GII.10 Vietnam026 diffracted to 1.4 Å and showed a single citrate bound at the site of HBGA interaction. The citrate interaction was coordinated with a set of capsid interactions almost identical to that involved in recognizing the terminal HBGA fucose, the saccharide which forms the primary conserved interaction between HBGAs and GII noroviruses. Citrate and a water molecule formed a ring-like structure that mimicked the pyranoside ring of fucose. STD NMR showed the protruding domain to have weak affinity for citrate (460 μM). This affinity, however, was similar to the affinities of the protruding domain for fucose (460 μM) and H type 2 trisaccharide (390 μM), an HBGA shown previously to be specifically recognized by human noroviruses. Importantly, competition STD NMR showed that citrate could compete with HBGA for norovirus binding. Together, the results suggest that citrate and other glycomimetics have the potential to block human noroviruses from binding to HBGAs.
Microtubule- and Dynein-Dependent Nuclear Trafficking of Rhesus Rhadinovirus in Rhesus Fibroblasts
Authors: Zhang Wei , Greene Whitney , Gao Shou-Jiang 
Published: October 2011

ABSTRACT
We investigated the role of microtubules in rhesus rhadinovirus (RRV) nuclear trafficking in rhesus fibroblasts. Intact microtubules and microtubule dynamics are required for RRV trafficking to perinuclear regions. RRV trafficking was reduced by an inhibitor of the dynein motor and overexpression of dynamitin. Furthermore, RRV particles are colocalized with microtubules and dynein proteins. These results highlight the important roles of microtubules and dynein-dynactin complexes in the transport of RRV particles to nuclei during primary infection.
Whole slide images for primary diagnostics in dermatopathology: a feasibility study
Authors: Al-Janabi Shaimaa , Huisman André , Vink Aryan , Leguit Roos J , Offerhaus G Johan A , ten Kate Fiebo J W , van Dijk Marijke R , van Diest Paul J 
Published: October 2011

BackgroundDuring the last decade, whole slide images (WSI) have been used in many areas of pathology such as teaching, research, digital archiving, teleconsultation and quality assurance testing. However, WSI have not regularly been used for routine diagnosis, because of the lack of validation studies.AimTo test the validity of using WSI for primary diagnosis of skin diseases.Materials and methods100 skin biopsies and resections which had been diagnosed light microscopically one year previously were scanned at 20× magnification, and rediagnosed by six pathologists (every pathologist assessed his own cases), having the original clinical information available, but blinded to the original diagnoses. The WSI diagnoses were compared to the initial light microscopy diagnosis and classified as concordant, slightly discordant (without clinical consequences) or discordant.ResultsThe light microscopy and the WSI based diagnosis were concordant in 94% of the cases. The light microscopy and WSI diagnosis were slightly discordant in 6% of the cases. For one of the slightly discrepant cases the WSI diagnosis was considered better, while the original diagnosis was preferred for the other five cases. There were no discordant cases with clinical or prognostic implications.ConclusionPrimary histopathological diagnosis of skin biopsies and resections can be done digitally using WSI.
Dual-level direct dynamics study on the hydrogen abstraction reaction of fluorine atom with 1,1-difluoro-1-chloroethane
Authors: Wang Li , Liu Song , He Hongqing , Zhang Jinglai 
Published: October 2011

The kinetic properties of the reaction of F atoms with CH2H′CF2Cl are investigated by a dual-level direct dynamics method. Optimized geometries and frequencies of all the stationary points and extra points along the minimum-energy path (MEP) are obtained at the MPW1K/6–311+G(d,p) level of theory. Two complexes with energy less than that of the reactants are located in the two reactant paths, respectively. The energy profiles of two reactions are refined with the interpolated single-point energies (ISPE) method at the G3(MP2)/MPW1K level. The rate constants are evaluated using the canonical variational transition state theory (CVT) with a small-curvature tunneling correction (SCT) over a wide range of temperature 200–2000 K. Agreement between the calculated CVT/SCT rate constant and the experimental value is good at 295 K. Our calculations show that the reaction path CH2H′CF2Cl + F → CH2CF2Cl + H′F (Ra) is the major reaction path below 400 K. Moreover, the contribution of CH2H′CF2Cl + F → CHH′CF2Cl + HF (Rb) to the whole reaction increases with the temperature increasing and exceeds path Ra to be the major reaction path.
Significance of Dysregulated Metadherin and MicroRNA-375 in Head and Neck Cancer
Authors: Hui Angela B.Y. , Bruce Jeff P. , Alajez Nehad M. , Shi Wei , Yue Shijun , Perez-Ordonez Bayardo , Xu Wei , O'Sullivan Brian , Waldron John , Cummings Bernard , Gullane Patrick , Siu Lillian , Liu Fei-Fei 
Published: October 2011

Abstract
Purpose: Despite recent improvements in local control of head and neck cancers (HNC), distant metastasis remains a major cause of death. Hence, further understanding of HNC biology, and in particular, the genes/pathways driving metastasis is essential to improve outcome.
Experimental Design: Quantitative reverse transcriptase PCR (qRT-PCR) was used to measure the expression of miR-375 and metadherin (MTDH) in HNC patient samples. Targets of miR-375 were confirmed using qRT-PCR, Western blot analysis, and luciferase assays. Phenotypic effects of miR-375 reexpression and MTDH knockdown were assessed using viability (MTS), clonogenic survival, cell migration/invasion, as well as in vivo tumor formation assays. The prognostic significance of miR-375 or MTDH in nasopharyngeal carcinoma (NPC) was determined by comparing low versus high expression groups.
Results: MiR-375 expression was significantly reduced (P = 0.01), and conversely, MTDH was significantly increased (P = 0.0001) in NPC samples. qRT-PCR, Western blots, and luciferase assays corroborated MTDH as a target of miR-375. Reexpression of miR-375 and siRNA knockdown of MTDH both decreased cell viability and clonogenic survival, cell migration/invasion, as well as in vivo tumor formation. NPC patients whose tumors expressed high levels of MTDH experienced significantly lower survival and, in particular, higher distant relapse rates (5-year distant relapse rates: 26% vs. 5%; P = 0.005).
Conclusions: Dysregulation of miR-375 and MTDH may represent an important oncogenic pathway driving human HNC progression, particularly distant metastases, which is now emerging as a major cause of death for HNC patients. Hence, targeting this pathway could potentially be a novel therapeutic strategy by which HNC patient outcome could be improved. Clin Cancer Res; 17(24); 7539–50. ©2011 AACR.
Effects of collagen-induced rheumatoid arthritis on amyloidosis and microvascular pathology in APP/PS1 mice
Authors: Park Sun Mi , Shin Jin Hee , Moon Gyeong Joon , Cho Sung Ig , Lee Yong Beom , Gwag Byoung Joo 
Published: October 2011

Abstract

Background
Evidence suggests that rheumatoid arthritis (RA) may enhance or reduce the progression of Alzheimer's disease (AD). The present study was performed to directly explore the effects of collagen-induced rheumatoid arthritis (CIA) on amyloid plaque formation, microglial activation, and microvascular pathology in the cortex and hippocampus of the double transgenic APP/PS1 mouse model for AD. Wild-type or APP/PS1 mice that received type II collagen (CII) in complete Freund's adjuvant (CFA) at 2 months of age revealed characteristics of RA, such as joint swelling, synovitis, and cartilage and bone degradation 4 months later. Joint pathology was accompanied by sustained induction of IL-1β and TNF-α in plasma over 4 weeks after administration of CII in CFA.

Results
CIA reduced levels of soluble and insoluble amyloid beta (Aβ) peptides and amyloid plaque formation in the cortex and hippocampus of APP/PS1 mice, which correlated with increased blood brain barrier disruption, Iba-1-positive microglia, and CD45-positive microglia/macrophages. In contrast, CIA reduced vessel density and length with features of microvascular pathology, including vascular segments, thinner vessels, and atrophic string vessels.

Conclusions
The present findings suggest that RA may exert beneficial effects against Aβ burden and harmful effects on microvascular pathology in AD.