bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the pathogenesis of renal cell carcinoma: pathway and bioinformatics analysis of dysregulated genes and proteins
Authors: Romaschin Alexander D. , Youssef Youssef , Chow Tsz-fung F. , Siu K.W. Michael , DeSouza Leroi V. , Honey R. John , Stewart Robert , Pace Kenneth T. , Yousef George M. 
Published: December 2008

Abstract
We recently identified a group of proteins which are dysregulated in renal cell carcinoma (RCC). In this study, we performed bioinformatics and pathway analysis of these proteins. Proteins were mapped to gene ontology biological processes. The upregulated proteins tend to cluster in processes, such as cancer initiation and progression. In addition, we identified a number of pathways that are significantly enriched in RCC. Some of these are ‘common’ pathways which are dysregulated in many cancers, but we also identified a number of pathways which were not previously linked to RCC. In addition to their potential prognostic values, many of these pathways have a potential as therapeutic targets for RCC. To verify our findings, we compared our proteins to a pool of datasets from published reports. Although there were only a minimal number of common proteins, there was a significant overlap between the identified pathways in the two groups. Moreover, out of 16 individually discovered genes identified by a literature search, 10 were found to be related to our dysregulated pathways. We also verified the upregulation of the mammalian target of rapamycin signaling pathway in RCC by immunohistochemistry. Finally, we highlight the potential clinical applications of pathway analysis in kidney cancer.
Role of catalytic and non-catalytic subsite residues in ribonuclease activity of human eosinophil-derived neurotoxin
Authors: Sikriwal Deepa , Seth Divya , Batra Janendra K. 
Published: December 2008

AbstractHuman eosinophil-derived neurotoxin (EDN), a secretory protein from eosinophils, is a member of the RNase A superfamily. The ribonucleolytic activity of EDN is central to its biological activities. EDN binds RNA in a cationic cleft, and the interaction between EDN and RNA substrate extends beyond the scissile bond. Based on its homology with RNase A, putative substrate binding subsites have been identified in EDN. The B1and B2subsites interact specifically with bases, whereas P0, P1, and P2subsites interact with phosphoryl groups. In this study, we evaluated the role of putative residues of these subsites in the ribonucleolytic activity of EDN. We demonstrate that of the two base binding subsites, B1is critical for the catalytic activity of EDN, as the substrate cleavage was dramatically reduced upon substitution of B1subsite residues. Among the phosphate-binding subsites, P1is the most crucial as mutations of its constituting residues totally abolished the catalytic activity of EDN. Mutation of P0and P2subsite residues only affected the catalytic activity on the homopolymer Poly(U). Our study demonstrates that P1and B1subsites of EDN are critical for its catalytic activity and that the other phosphate-binding subsites are involved in the activity on long homopolymeric substrates.
A completed KLK activome profile: investigation of activation profiles of KLK9, 10, and 15
Authors: Yoon Hyesook , Blaber Sachiko I. , Debela Mekdes , Goettig Peter , Scarisbrick Isobel A. , Blaber Michael 
Published: December 2008

AbstractWe previously reported the activation profiles of the human kallikrein-related peptidases (KLKs) as determined from a KLK pro-peptide fusion-protein system. That report described the activity profiles of 12 of the 15 mature KLKs versus the 15 different pro-KLK sequences. The missing profiles in the prior report, involving KLK9, 10, and 15, are now described. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis, mass spectrometry, and N-terminal sequence analyses show that KLK9 and 10 exhibit low hydrolytic activities towards all of the 15 pro-KLK sequences, while KLK15 exhibits significant activity towards both Arg- and Lys-containing KLK pro-sequences. The ability of KLK15 to activate pro-KLK8, 12, and 14 is confirmed using recombinant pro-KLK proteins, and shown to be significant for activation of pro-KLK8 and 14, but not 12. These additional data for KLK9, 10, and 15 now permit a completed KLK activome profile, using a KLK pro-peptide fusion-protein system, to be described. The results suggest that KLK15, once activated, can potentially feed back into additional pro-KLK activation pathways. Conversely, KLK9 and 10, once activated, are unlikely to participate in further pro-KLK activation pathways, although similar to KLK1 they may activate other bioactive peptides.
Determination of three amino acids causing alteration of proteolytic activities of staphylococcal glutamyl endopeptidases
Authors: Nemoto Takayuki K. , Ono Toshio , Shimoyama Yu , Kimura Shigenobu , Ohara-Nemoto Yuko 
Published: December 2008

Abstract

Staphylococcus aureus, Staphylococcus epidermidis, and Staphylococcus warneri secrete glutamyl endopeptidases, designated GluV8, GluSE, and GluSW, respectively. The order of their protease activities is GluSE<GluSW<<GluV8. In the present study, we investigated the mechanism that causes these differences. Expression of chimeric proteins between GluV8 and GluSE revealed that the difference is primarily attributed to amino acid residues 170–195, which define the intrinsic protease activity, and additionally to residues 119–169, which affect the proteolytic sensitivity. Among nine substitutions present in residues 170–195 of the three proteases, the substitutions at positions 185, 188, and 189 were responsible for the changes in their activities, and the combination of W185, V188, and P189, which naturally occurs in GluV8, exerts the highest protease activity. W185 and P189 were indispensable for full activity, but V188 could be replaced by hydrophobic amino acids. These three amino acid residues appear to create a substrate-binding pocket together with the catalytic triad and the N-terminal V1, and therefore define the K
m values of the proteases. We also describe a method to produce a chimeric form of GluSE and GluV8 that is resistant to proteolysis, and therefore possesses 4-fold higher activity than the wild-type recombinant GluV8.
The assembly and activation of kinin-forming systems on the surface of human U-937 macrophage-like cells
Authors: Barbasz Anna , Kozik Andrzej 
Published: December 2008

AbstractA complex of three plasma proteins, including the high molecular mass kininogen (HK), prekallikrein (PK), and factor XII (FXII), is known to assemble on cell surfaces to release bradykinin-related proinflammatory peptides (kinins). Only recently, the binding of HK to human macrophages was described in the U-937 cell line model. In the present study, the adsorption of the other components of plasma kinin-generating system to these cells was characterized. FXII was found to tightly bind to U-937 cells and was also shown to partially compete with HK for the same binding sites on the macrophage surface. The Mac-1 and gC1qR proteins were found to be receptors for FXII on the cell surface. PK indirectly docked to the macrophages via the cell-bound HK and FXII. Within the complex of these proteins assembled on the macrophage, PK could be activated by FXII/FXIIa or independently of this factor, and the active PK effectively released kinins from HK. The cell surface-bound HK could also be the substrate for tissue kallikrein approaching the cell from the bulk fluid. The kinins released at the surface are suggested to induce secondary responses in the macrophages, leading to further propagation of the inflammatory state.
Study of smoking behavior and smoking-related attitudes among preclinical medical students
Authors: Pikó Bettina 
Published: December 2008

Ma már köztudott, hogy a megelőzhető halálozás legfontosabb oka a dohányzás, ennek ellenére a fiatal populáció dohányzásának megelőzése ma sem megoldott népegészségügyi probléma. Az orvostanhallgatók dohányzása azért is érdemel kiemelt figyelmet, mert az egészségügyi szakemberek dohányzáshoz való viszonyulása szerepmodellként érvényesül a betegek körében.
Célkitűzés:
A jelen kutatás célja a szegedi preklinikai (első- és másodéves) orvostanhallgatók dohányzói státusának, dohányzási gyakoriságának és a dohányzással kapcsolatos attitűdjeinek megismerése volt.
Módszer:
Összesen 212 hallgatót vontak be az elemzésbe, az évfolyamok mintegy 50%-a adott információt a dohányzásról, illetve a dohányzással kapcsolatos vélekedéseikről. Az attitűdök megismeréséhez a The Students’ Health and Lifestyle Study, The University of Western Ontario (Kanada) skálájának 20 állítását alkalmazták, amelyek adaptálása már korábban megtörtént.
Eredmények:
Kimutatták, hogy az 1990-es évek kutatási eredményeihez viszonyítva a dohányosok száma nem csökkent, sőt némi emelkedést figyelhettek meg. Sem az első, sem a második évfolyamon nem volt különbség a férfi és női hallgatók között a dohányzói státus szerint. Több nem dohányzó hallgató fogadja el saját modellszerepét.
Következtetések:
Az addikciókat érintő interdiszciplináris kurzusok mellett szükség van olyan gyakorlatorientált, betegcentrikus kurzusokra is, ahol a dohányzásról való leszoktatás módszereinek alapjait is elsajátíthatják a hallgatók. Emellett szükség van a dohányzó orvostanhallgatók számára olyan programra, amely segíti a leszokást.
The role of osteocalcin in the connection of bone and glucose metabolism in humans
Authors: Buday Barbara , Kulcsár Enikő , Literáti Nagy Botond , Horváth Tünde , Vitai Márta , Vecsei Istvánné , Bezzegh Katalin , Kiss József , Péterfai Éva , Koltay László , Korányi László 
Published: December 2008

Egerekben az osteocalcin hiányakor csökken a pancreas β-sejtjeinek proliferációja, és bennük azinzulin, a zsírsejtekben pedig azadiponektingénexpressziója.Módszer:Az inzulinérzékenység, a csontállapot, illetve az osteocalcin kapcsolatát 45 egészséges (nő: 20, férfi: 25) és 92 glükózintoleráns (nő: 51, férfi: 41) egyén esetében vizsgálták. Nemenként elkülönítve mérték a testösszetételt, a csontok denzitását, a csontbontás és a csontépítés markereit és hyperinsulinaemiás-normoglykaemiás teszttel az inzulinérzékenységet tükröző cukorfelhasználást.Eredmények:Az osteocalcinszintek a két nemben hasonlóak voltak, de a glükózintoleráns férfi betegek osteocalcinszintje alacsonyabb volt, mint az egészségeseké (24,5±11 vs. 18,1±9 ng/ml,p< 0,05). Az egészséges csoportban, mindkét nemben pozitív volt a korreláció az osteocalcin és az izomszövet cukorfelhasználása között (M-érték: nők:r= +0,319,p< 0,05, férfiak:r= 0,481,p< 0,01), de a glükózintoleráns csoportokban ez a kapcsolat eltűnt. Az osteocalcin egyik nemben sem mutatott korrelációt az adiponektinszinttel. Többváltozós lineáris regresszió alapján az osteocalcin szignifikáns független prediktoraaz összes nőesetében az éhomi vércukor, a teljes test és az izomtömeg cukorfelhasználása, a cukorfelhasználás sebessége, az ösztradiol és az LDL-koleszterin-vérszint (92%-os determináció), míg azösszes férfiesetében a szérumkalcium, az OGTT során mért glükózszintek görbe alatti területe, a szabadzsírsav-szint, az inzulogenikus index, a HOMA-IR és a has/csípő körfogat (95%-os determináció) volt. A csontbontást-csontépítést jellemző BMU-index csak nők esetében korrelált szignifikánsan az M-értékekkel.Következtetés:Vizsgálatunk egészségesek esetében megerősítette az inzulinérzékenység–osteocalcin kapcsolatot emberi vonatkozásban is, de a csontanyagcsere–energia-háztartás közötti kapcsolatban jelentős nemi különbséget talált, amely nem az osteocalcin szintjén alakult ki.
History Matching Using the Ensemble Kalman Filter on a North Sea Field Case
Authors: Haugen Vibeke , Nævdal Geir , Natvik Lars-Jøergen , Evensen Geir , Berg Aina M. , Flornes Kristin M. 
Published: December 2008

Summary
This paper applies the ensemble Kalman filter (EnKF) to history match a North Sea field model. This is, as far as we know, one of the first published studies in which the EnKF is applied in a realistic setting using real production data. The reservoir-simulation model has approximately 45,000 active grid cells, and 5 years of production data are assimilated. The estimated parameters consist of the permeability and porosity fields, and the results are compared with a model previously established using a manual history-matching procedure. It was found that the EnKF estimate improved the match to the production data. This study, therefore, supported previous findings when using synthetic models that the EnKF may provide a useful tool for history matching reservoir parameters such as the permeability and porosity fields.
Sweep Efficiency of Miscible Floods in a High-Pressure Quarter-Five-Spot Model
Authors: Lewis E. , Dao E. K. , Mohanty K. K. 
Published: December 2008

Summary
Evaluation and improvement of sweep efficiency are important for miscible displacement of medium-viscosity oils. A high-pressure quarter-five-spot cell was used to conduct multicontact miscible (MCM) water-alternating-gas (WAG) displacements at reservoir conditions. A dead reservoir oil (78 cp) was displaced by ethane. The minimum miscibility pressure (MMP) for ethane with the reservoir oil is approximately 4.14 MPa (600 psi). Gasflood followed by waterflood improves the oil recovery over waterflood alone in the quarter five-spot. As the pressure decreases, the gasflood oil recovery increases slightly in the pressure range of 4.550–9.514 MPa (660–1,380 psi) for this undersaturated viscous oil. WAG improves the sweep efficiency and oil recovery in the quarter five-spot over the continuous gas injection. WAG injection slows down gas breakthrough. A decrease in the solvent amount lowers the oil recovery in WAG floods, but significantly more oil can be recovered with just 0.1 pore volume (PV) solvent (and water) injection than with waterflood alone. Use of a horizontal production well lowers the sweep efficiency over the vertical production well during WAG injection. Sweep efficiency is higher for the nine-spot pattern than for the five-spot pattern during gas injection. Sweep efficiency during WAG injection increases with the WAG ratio in the five-spot model.
Capillary Pressure and Wettability Behavior of CO2 Sequestration in Coal at Elevated Pressures
Authors: Plug Willem-Jan , Mazumder Saikat , Bruining Johannes 
Published: December 2008

SummaryEnhanced coalbed-methane (ECBM) recovery combines recovery of methane (CH4) from coal seams with storage of carbon dioxide (CO2). The efficiency of ECBM recovery depends on the CO2 transfer rate between the macrocleats, via the microcleats to the coal matrix. Diffusive transport of CO2 in the small cleats is enhanced when the coal is CO2-wet. Indeed, for water-wet conditions, the small fracture system is filled with water and the rate of CO2 sorption and CH4 desorption is affected by slow diffusion of CO2. This work investigates the wetting behavior of coal using capillary pressures between CO2 and water, measured continuously as a function of water saturation at in-situ conditions. To facilitate the interpretation of the coal measurements, we also obtain capillary pressure curves for unconsolidated-sand samples. For medium-and high-rank coal, the primary drainage capillary pressure curves show a water-wet behavior. Secondary forced-imbibition experiments show that the medium-rank coal becomes CO2-wet as the CO2 pressure increases. High-rank coal is CO2-wet during primary imbibition. The imbibition behavior is in agreement with contact-angle measurements. Hence, we conclude that imbibition tests provide the practically relevant data to evaluate the wetting properties of coal.
SURFACE PLASMON RESONANCE ABSORPTION OF ALBUMIN/WATER ON Ni THIN FILM DEPOSITED ON Si AT 230°C
Authors: Yang Y.-L. , Young T.-F. , Kuo W.-C. , Fang S.-H. , Chao Y.-K. 
Published: December 2008

In this work we have studied the surface plasmon resonance (SPR) absorption of Albumin on NiSi nanoparticle thin film deposited on Si. The thin films were deposited by means of RF sputtering on Si at various temperatures and times for different thicknesses, and characterized by grazing angle XRD and SEM. From these experimental conditions, we only observed a formation of NiSi nanoparticles deposited on Si at 230°C for 15 min to 30 min. The silicon atoms seem to emerge out of the surface and react with Nickel's. Due to the high activation energy, this mechanism would not take place at lower temperatures, such as RT and 122°C. Mixture of Albumin and water with varied concentrations has been prepared for the measurement of SPR absorption on the NiSi nanoparticle thin film. We found the spectra of SPR absorption of Albumin on the sample, which NiSi nanoparticle thin film was deposited on Si at 230°C, exhibits a specific shift due to the formation of NiSi nanoparticle.
Theoretical analysis and experimental study on SO2 adsorption onto pistachio‐nut‐shell activated carbon
Authors: Lua Aik Chong , Yang Ting 
Published: December 2008

AbstractThe adsorption study of SO2 onto the activated carbon prepared from pistachio‐nut shell was studied theoretically and experimentally. A single‐particle sorption model known as concentration‐dependent surface diffusivity micropore, surface and macropore diffusion control model incorporating micropore, macropore and surface diffusions, together with a nonlinear isotherm at the micropore mouth, has been derived and solved by a finite difference method. The effects of different types of nonlinear isotherms and concentration dependent surface diffusivities have been thoroughly studied. The effects of adsorbate concentration and temperature on adsorption were studied experimentally. Good agreement was found between the model predictions and the experimental results. The value of the tortuosity factor and the extracted diffusion coefficients obtained are consistent with their corresponding values reported. © 2008 American Institute of Chemical Engineers AIChE J 2009
Update on the therapy for myelodysplastic syndrome
Authors: Kasner Margaret T. , Luger Selina M. 
Published: December 2008

AbstractThe myelodysplastic syndromes (MDS) are a diverse group of clonal hematopoietic stem cell disorders characterized by cytopenias. Patients have a risk of developing acute leukemia though most subcome to complications of low blood counts. Over the past decade many novel treatments have been developed and investigation of new agents is ongoing. In this article, we discuss the classification and prognostic systems that are used in MDS, the agents available for treatment of MDS as well as review supportive and palliative care options for patients who are not candidates for, or opt against, newer treatment strategies. Am. J. Hematol. 2009. © 2008 Wiley‐Liss, Inc.
Primary breast non‐Hodgkin's lymphoma: A large single center study of initial characteristics, natural history, and prognostic factors
Authors: Validire Patricia , Capovilla Mathieu , Asselain Bernard , Kirova Youlia , Goudefroye Rémi , Plancher Corine , Fourquet Alain , Zanni Manuela , Gaulard Philippe , Vincent‐Salomon Anne , Decaudin Didier 
Published: December 2008

AbstractThe aims of this study were to define the initial pathological and clinical characteristics, and prognostic factors of patients with primary breast malignant lymphoma (PBL). All patients treated at the Institut Curie for lymphoma with breast involvement were reviewed. A pathological review of all cases was performed. Forty‐five cases were selected in whom 38 cases were of diffuse large B‐cell lymphoma. A complete analysis was then performed on these 38 patients. Twenty out of 28 cases (71%) of cases were Bcl‐2 positive and four out of 28 (14%) had a CD10 positive staining. Peculiar initial characteristics showed nodal involvement in 58% of the cases and two or more extra‐nodal sites in 31% of the cases. Among the 37 patients for whom all data were available, and according to the International Prognostic Index, 19 patients (51%) were classified in the low‐risk group, 5 cases (14%) in the low‐ to intermediate‐risk group, 6 patients (16%) in the intermediate‐ to high‐risk group, and 7 (19%) case in the high‐risk group. At the end of initial therapy, 34 patients (89%) achieved CR. With a median follow‐up of 96 months, 18 patients (47%) relapsed of whom 3 had a relapse in central nervous system site. The 5‐year disease‐free (DFS) and overall survivals (OS) were 54% and 61%, respectively. In multivariate analysis, the presence of 2 or more extranodal sites was prognostic for lower DFS (P= 0.0008) and OS (P= 0.09), and a performance status ≥1 was prognostic for lower OS (P= 0.005). Finally, when our series was compared with a historical series of 111 patients with aggressive nodal lymphomas, we observed significant lower survival rates in localized PBL (P< 0.03). Initial breast localization has a pejorative impact on the outcome of patients with Non‐Hodgkin's Lymphoma (NHL), with an impressive adverse influence of additional extranodal sites. These results suggest a specific management of NHL with breast involvement. Am. J. Hematol., 2009. © 2008 Wiley‐Liss, Inc.
High frequency and proliferation of CD4+FOXP3+ Treg in HIV‐1‐infected patients with low CD4 counts
Authors: Bi Xiuqiong , Suzuki Yasuhiro , Gatanaga Hiroyuki , Oka Shinichi 
Published: December 2008

AbstractThe frequency of Treg is reported to be higher in patients with chronic HIV type 1 (HIV‐1) infection and CD45RA+ Treg exist in normal adults. In this study, we found a lower absolute number (15 cells/μL) but a higher proportion (16.2%) of FOXP3+ cells (Treg) in the CD4+ population in treatment‐naïve HIV‐1 patients with low CD4 (<200 cells/μL) counts than in those with high CD4 counts (34 cells/μL and 9.3%) or healthy adults (48 cells/μL and 7.5%). In HIV‐1 patients, CD45RA+CCR7+, CD45RA−CCR7+, and CD45RA−CCR7− subsets were identified in the Treg population, and the proportion of CD45RA−CCR7− Treg was higher (57.9%) in patients with low CD4 than high CD4 counts (38.3%). Treg were in a high proliferation state especially in patients with low CD4 counts. HIV viral load correlated positively with the Treg proliferation rate and the proportion of CD45RA−CCR7− Treg. Furthermore, the proliferation of Treg correlated positively with the CD45RA−CCR7− Treg proportion but negatively with Treg numbers. Successful antiretroviral therapy resulted in a limited increase in Treg numbers, but their frequency was reduced in 1–2 months due to a rapid rebound of FOXP3− CD4+cells. Our results suggest that HIV‐activating Treg may be a reason for the high frequencies of Treg and CD45RA−CCR7− Treg in the peripheral blood of late‐stage HIV‐1‐infected patients.
Lipid‐mediated presentation of MHC class II molecules guides thymocytes to the CD4 lineage
Authors: Komaniwa Satoshi , Hayashi Hiroshi , Kawamoto Hiroshi , Sato Satoshi B. , Ikawa Tomokatsu , Katsura Yoshimoto , Udaka Keiko 
Published: December 2008

AbstractPrevious studies on the MHC class‐specific differentiation of CD4+CD8+ thymocytes into CD4+ and CD8+ T cells have focused on the role of coreceptor molecules. However, CD4 and CD8 T cells develop according to their MHC class specificities even in these mice lacking coreceptors. This study investigated the possibility that lineage is determined not only by coreceptors, but is also guided by the way how MHC molecules are presented. MHC class II molecules possess a highly conserved Cys in their transmembrane domain, which is palmitoylated and thereby associates with lipid rafts, whereas neither palmitoylation nor raft association was observed with MHC class I molecules. The generation of CD4 T cells was impaired and that of CD8 T cells was augmented when the rafts on the thymic epithelial cells were disrupted. This was due to the conversion of MHC class II‐specific thymocytes from the CD4 lineage to CD8. The ability of I‐Ad molecule to associate with rafts was lost when its transmembrane Cys was replaced. The development of DO11.10 thymocytes recognizing this mutant I‐Adm was converted from CD4 to CD8. These results suggest that the CD4 lineage commitment is directed by the raft‐associated presentation of MHC class II molecules.