bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of the disulfide bond configuration on the dynamics of the spin label attached to cytochrome c
Authors: Murzyn Krzysztof , Róg Tomasz , Blicharski Wojciech , Dutka Małgorzata , Pyka Janusz , Szytula Sebastian , Froncisz Wojciech 
Published: January 2006

AbstractA series of multi‐nanosecond molecular dynamics (MD) simulations of wild‐type cytochrome c and its spin‐labeled variants with the methanethiosulfonate moiety attached at position C102 were performed (1) to elucidate the effect of the spin probe presence on the protein structure and (2) to describe the structure and dynamics of the spin‐label moiety. Comparisons with the reference crystal structure of cytochrome c (PDB entry: 1YCC) indicate that the protein secondary structure is well preserved during simulations of the wild‐type cytochrome c but slightly changed in simulations of the cytochrome c labeled at position C102. At the time scale covered in our simulations, the spin label exhibits highly dynamical behavior. The number of observed distinct conformations of the spin label moiety is between 3 and 13. The spin probe was found to form short‐lived hydrogen bonds with the protein. Temporary hydrophobic interactions between the probe and the protein were also detected. The MD simulations directly show that the disulfide bond in the tether linking a spin probe with a protein strongly influence the behavior of the nitroxide group. The conformational flexibility and interaction with the protein are different for each of the two low energy conformations of the disulfide bond. Proteins 2006. © 2006 Wiley‐Liss, Inc.
SPINS: A laboratory information management system for organizing and archiving intermediate and final results from NMR protein structure determinations
Authors: Baran Michael C. , Moseley Hunter N. B. , Aramini James M. , Bayro Marvin J. , Monleon Daniel , Locke Jessica Y. , Montelione Gaetano T. 
Published: January 2006

AbstractRecent technological advances and experimental techniques have contributed to an increasing number and size of NMR datasets. In order to scale up productivity, laboratory information management systems for handling these extensive data need to be designed and implemented. The SPINS (Standardized ProteIn Nmr Storage) Laboratory Information Management System (LIMS) addresses these needs by providing an interface for archival of complete protein NMR structure determinations, together with functionality for depositing these data to the public BioMagResBank (BMRB). The software tracks intermediate files during each step of an NMR structure‐determination process, including: data collection, data processing, resonance assignments, resonance assignment validation, structure calculation, and structure validation. The underlying SPINS data dictionary allows for the integration of various third party NMR data processing and analysis software, enabling users to launch programs they are accustomed to using for each step of the structure determination process directly out of the SPINS user interface. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Crystallisation and optimisation of soft magnetic properties in amorphous FeCuXSi13B9 (X = Mn, Co, Zr)‐type alloys
Authors: Badura Grzegorz , Rasek Józef , Kwapuliński Piotr , Stokłosa Zbigniew , Pająk Lucjan 
Published: January 2006

AbstractIt has been shown that annealing of FeCu1XSi13B9 (X = Mn, Co, Zr) alloys at suitable temperatures T op and times τ p leads to an increase of the magnetic permeability and a decrease of the coercive force (optimisation effect of soft magnetic properties) determined at room temperature. The optimisation effect of soft magnetic properties in these alloys has been investigated by different experimental techniques. This effect has been attributed to the formation of a nanocrystalline phase, a change of the magnetostriction coefficient, stress, and a change of the concentration of microvoids. The diffusion parameters of the optimisation effect of soft magnetic properties, the Curie temperature and the temperatures of first and second stages of the crystallisation process have also been determined. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Phase transformation of Si upon epitaxial CVD growths of β‐SiC layer on Si substrates
Authors: Zhu W. L. , Zhu J. L. , Wan K. S. , Nishino S. , Pezzotti G. 
Published: January 2006

AbstractMicro‐Raman spectroscopy was applied to investigate the stress relaxation in the CVD growth of SiC on silicon substrates. We observed a double‐peak feature of the LO + 2TO silicon phonon in as‐grown SiC/Si samples, and tentatively ascribed it to phase transformation of silicon during the epitaxial growth. Stress analysis around the featured regions suggested that it might be related with incomplete relief of local stress, such as appearance of micropipes in suitable circumstances. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Kancheli and Knaifel
Authors: Quinn Peter 
Published: January 2006

GIYA KANCHELI: Time…and again; V & V; Piano Quartet. Gidon Kremer (vln), Oleg Maisenberg (pno), Kremerata Baltica, The Bridge Ensemble. ECM New Series 461 8182.ALEXANDER KNAIFEL: Psalm 51 (50); Amicta Sole. Mstislav Rostropovich (vlc), Tatiana Melentieva (sop), Glinka Choral College, State Hermitage Orchestra c. Arkady Shteinlukht. ECM New Series 472 0832.
Tissue Bioenergetics and Microvascular Perfusion Are Impaired in Rat Ileal Mucosa in Normotensive Sepsis
Authors: ROSE JIM , MARTIN CLAUDIO 
Published: January 2006

ABSTRACTObjective: Sepsis is a systemic inflammatory response to a bacterial infection. Inflammation may result in injury to the small bowel and an increase in translocation of bacteria and toxins across the mucosal barrier, which may contribute to the progression of sepsis. Microcirculatory perfusion or cytopathic hypoxia may cause impairment of tissue bioenergetics and injury in sepsis. The objective of this study was to determine if sepsis is associated with microcirculatory hypoperfusion and impaired tissue bioenergetics in the ileal mucosa.Materials and Methods: Sprague‐Dawley rats were randomized to cecal ligation and perforation (sepsis group, n = 12) or control group (n = 14) and received arterial and venous catheters and fluid resuscitation. Following 24 h, rats were anesthetized with isoflurane and the ileum was prepared for intravital microscopy. Images of NADH fluorescence, which is an index of tissue bioenergetics, central arterial diameter, red cell velocity, red cell flux, and average intercapillary area, were recorded in 6–9 villi in each rat.Results: Central arterial red cell flux (control 277 ± 30 cell/s, sepsis 108 ± 13 cells/s, p < .05), diameter (control 10.4 ± 0.4 μ m, sepsis 8.2 ± 0.3 μ m, p < .05) and red cell velocity (control 590 ± 47 μ m/s, sepsis 449 ± 63 μ m/s, p < .05) were decreased while average intercapillary area (control 815 ± 171 μ m2, sepsis 1412 ± 364 μ m2, p < .05) and NADH fluorescence (control 116 ± 6 AIU, sepsis 154 ± 9 AIU, p < .05) were increased at the villus tip in the sepsis group.Conclusion: Sepsis is associated with bioenergetic impairment and capillary hypoperfusion at the villus tip and a decrease in red cell flux in the central arteriole.
Predicting Nursing Facility Residents' Quality of Life Using External Indicators
Authors: Degenholtz Howard B. , Kane Rosalie A. , Kane Robert L. , Bershadsky Boris , Kling Kristen C. 
Published: January 2006

Purpose. A newly developed brief measure of nursing facility (NF) resident self‐reported quality of life (QOL) has been proposed for inclusion in a modified version of the minimum data set (MDS). There is considerable interest in determining whether it is possible to develop indicators of QOL that are more convenient and less expensive than direct, in‐person interviews with residents.Design and Methods. QOL interview data from 2,829 residents living in 101 NFs using a 14‐item version of a longer instrument were merged with data from the MDS and the Online Survey and Certification Automated Record (OSCAR). Bivariate and multivariate hierarchical linear modeling were used to assess the association of QOL with potential resident and facility level indicators.Results. Resident and facility level indicators were associated with self‐reported QOL in the expected direction. At the individual resident level, QOL is negatively associated with physical function, visual acuity, continence, being bedfast, depression, conflict in relationships, and positively associated with social engagement. At the facility level, QOL is negatively associated with citations for failing to accommodate resident needs or providing a clean, safe environment. The ratio of activities staff to residents is positively associated with QOL. This study did not find an association between QOL and either use of restraints or nurse staff levels. Approximately 9 percent of the total variance in self‐reported QOL can be attributed to differences among facilities; 91 percent can be attributed to differences among residents. Resident level indicators explained about 4 percent of the variance attributable to differences among residents, and facility factors explained 49 percent of the variance attributable to differences among NFs. However, the different variables explained only 10 percent of the variance in self‐reported QOL.Implications. A brief self‐report measure of NF resident QOL is consistently associated with measures that can be constructed from extant data sources. However, the level of prediction possible from these data sources does not justify reliance on external indicators of resident QOL for policy purposes.
Should Episode‐Based Economic Profiles Be Risk Adjusted to Account for Differences in Patients' Health Risks?
Authors: Thomas J. William 
Published: January 2006

Objective. To determine whether additional risk adjustment is necessary in economic profiling of physicians when claims data are already grouped into episodes of care, and to measure effects of risk adjustment on cost efficiency rankings of physicians.Data Sources. Four years of inpatient, outpatient, professional, and pharmacy claims data from a mixed model HMO.Study Design. Claims data were processed through Symmetry Health Data Systems' episode treatment group (ETG) grouper to define episodes of care and Symmetry's episode risk group (ERG) software to define measures of patients' health risk scores. For each episode type (ETG), ETG‐mean expected costs were calculated as the mean costs of all episodes of that type, and risk‐adjusted expected costs were calculated using three alternative risk model formulations.Data Collection. Within specialties, physicians were ranked from most cost efficient to least cost efficient, based on standardized difference between actual and expected costs. ETG‐mean based rankings were compared with risk‐adjusted rankings. Analyses were performed for cardiologists, family practitioners, general surgeons, and neurologists.Principal Findings. With all three risk models, risk scores were essentially unrelated to episode costs in approximately three‐fourths of episode categories (ETGs). In a sample of ETGs for which risks–costs relationships appeared to exist, split sample validation showed the relationships to be unstable or spurious in all except one ETG. Within specialties, risk‐adjusted cost efficiency rankings differ little from ETG‐mean adjusted rankings.Conclusions. Depending upon the purpose for which economic profiling is performed, additional risk adjustment, beyond that already provided by episode grouping, may be unnecessary. Additional research may be needed to identify and validate ETG‐level relationships between patient risks and episode costs.
The ECM proteoglycan decorin links desmoplasia and inflammation in chronic pancreatitis
Authors: Köninger J , Giese N A , Bartel M , di Mola F F , Berberat P O , di Sebastiano P , Giese T , Büchler M W , Friess H 
Published: January 2006

Background:Recurrent inflammation in chronic pancreatitis (CP) is not well understood.Aims:To investigate whether decorin, an extracellular matrix (ECM) proteoglycan with macrophage modulating activity, is a pathogenic factor allowing diseased pancreatic stroma to sustain inflammation by affecting the cytokine profile of accumulating inflammatory cells.Methods:Decorin was examined in 18 donors and 32 patients with CP by quantitative reverse transcription polymerase chain reaction (QRT-PCR), western blotting, and immunohistochemistry of pancreatic specimens. QRT-PCR was used to assess cytokine expression in donor peripheral blood mononuclear cells (PBMC), exposed or not to decorin in vitro, and to compare it with the cytokine profile of circulating and resident mononuclear cells (MNC) of patients with CP.Results:In CP, desmoplasia is associated with overexpression of decorin in the growing ECM and enlarged pancreatic nerves. In culture, exposure of MNC to decorin stimulated expression of the MNC recruiting chemokine MCP-1. In biopsies, MNC infiltrates in decorin rich CP tissue showed a 300-fold upregulation of MCP-1 compared with decorin free peripheral blood, whereas no difference was found in basal MCP-1 expression in PBMC of patients versus donors. This effect was specific for MCP1—other inflammatory cytokines, such as interleukin 1β and tumour necrosis factor α, were not affected.Conclusion:Decorin is a molecular marker of desmoplasia in CP, and excessive decorin may allow fibrotic masses to nourish and protract inflammation by deregulating the process of MNC accumulation and activation. These data provide a molecular basis for surgical resection of diseased tissue as a treatment option in CP.
Morules and morule-like features associated with carcinomas in various organs: report with immunohistochemical and molecular studies
Authors: Makishi S , Kinjo T , Sawada S , Chinen K , Hirayasu T , Hamada T , Saito K , Iwamasa T 
Published: January 2006

Background:Morules have been reported in pulmonary blastoma (PB), well differentiated fetal adenocarcinoma of the lung (WDFA), and uterine endometrioid carcinoma (EC), and rarely in other carcinomas. β Catenin gene mutation has been associated with morule formation.Aims:To compare and clarify the cellular characteristics of morules in carcinomas in various organs and show that morules are distinct from epithelial cellular nodules.Methods:Twenty tumours were studied: two PBs, three WDFAs, three papillary lung adenocarcinomas, 11 ECs, and one papillary thyroid carcinoma. Numerous epithelial cell, oncofetal, and neuropeptide antibodies were used for immunohistochemistry. β Catenin gene mutation was investigated.Results:Morules in PBs and ECs were uniform cell clusters distinct from squamous differentiation. All were immunonegative for epithelial cell and oncofetal antigens, but those in ECs were positive for neurone specific enolase γ (NSEγ). Synaptophysin, encephalin, and somatostatin were sporadically immunopositive in PB morules. Morules were not seen in the other carcinomas and WDFAs, although morule-like features closely resembling morules histopathologically were seen. These were positive for epithelial cell and oncofetal antigens, and showed squamous differentiation. Their nuclei were more atypical and slightly larger than those in morules. Morule-like features were seen in WDFAs. β Catenin gene mutation was demonstrated in one EC and PB, and in two WDFAs.Conclusion:Morules were non-epithelial cell clusters showing neuronal differentiation. There were two types: endometrioid type, expressing NSEγ, and blastoma type, expressing neuropeptides. In contrast, similar morule-like features were epithelial nodules. Although the number of cases was small, the presence of morules showed no clear prognostic correlations.
Epidemiology of non-Hodgkin lymphomas in Tyrol/Austria from 1991 to 2000
Authors: Mitterlechner T , Fiegl M , Mühlböck H , Oberaigner W , Dirnhofer S , Tzankov A 
Published: January 2006

Aims:To analyse the entity specific incidence and disease specific survival (DSS) of non-Hodgkin lymphomas (NHLs) in Tyrol/Austria, 1991–2000.Methods:Data from 1307 NHLs (excluding primary cutaneous lymphomas and monoclonal gammopathies of undetermined significance) were obtained. Current status was available for all patients. Except for 29 cases of small lymphocytic (CLL/SLL), lymphoblastic leukaemia (ALL), and myeloma (MM), which were diagnosed cytologically, diagnoses were reclassified on paraffin wax embedded archival material according to new World Health Organisation criteria. Sex specific age adjusted standardised incidence rates were computed using Segi’s population weighting. Annual incidence changes were calculated by weighted least square regression analysis. Survival was estimated by the Kaplan–Meier method and compared by log rank test.Results:NHL more frequently affected men (male/female ratio, 1.52). Mean age of occurrence was 61 and 66 years for men and women, respectively. The incidence rate of 14.3 remained constant. There was a significant increase in diffuse large B cell lymphoma (DLBCL) and decrease in CLL/SLL in men, and a decrease in MM in women. Overall DSS was 64% during the mean follow up (43 months). Age, T-NHL, λ light chain restriction in MM, and male sex in CLL/SLL were associated with poor prognosis. In B-NHL, DSS decreased in the following order: hairy cell leukaemia, marginal zone lymphoma, follicular lymphoma, Burkitt lymphoma, ALL, DLBCL, CLL, MM, and mantle cell lymphoma.Conclusions:The incidence of NHL in Tyrol has changed in the past decade, with a significant increase in DLBCL, decrease in CLL/SLL in men, and decrease in MM in women.
Aberrant expression of VEGF-C is related to grade of cervical intraepithelial neoplasia (CIN) and high risk HPV, but does not predict virus clearance after treatment of CIN or prognosis of cervical cancer
Authors: Branca M , Giorgi C , Santini D , Di Bonito L , Ciotti M , Benedetto A , Paba P , Costa S , Bonifacio D , Di Bonito P , Accardi L , Favalli C , Syrjänen K 
Published: January 2006

Aims:Increased angiogenesis leads to invasion in cervical cancer. Vascular endothelial growth factors (VEGFs) are involved in angiogenesis, but molecular links to the most important aetiological agent, human papillomavirus (HPV), need clarifying.Material/Methods:Archival samples—150 squamous cell carcinomas (SCCs) and 152 cervical intraepithelial neoplasia (CIN) lesions—were examined immunohistochemically for anti-VEGF-C antibody and for HPV by polymerase chain reaction (PCR). Follow up data were available for all SCC cases, and 67 CIN lesions were monitored with serial PCR to assess HPV clearance/persistence after treatment.Results:High risk (HR) HPV types were closely associated with CIN (odds ratio, 19.12; 95% confidence interval, 2.31 to 157.81) and SCC (27.25; 3.28 to 226.09). There was a linear increase of VEGF-C expression—weak in CIN1 and intense in CIN3 and SCC (20.49; 8.69 to 48.26). VEGF-C upregulation was a sensitive (93.5%; 95% CI, 90.1% to 96.9%) marker of HR-HPV type (4.70; 2.17 to 10.21), but lost its significance in multivariate regression—p16INK4aand survivin were equally strong independent predictors of HR-HPV. Aberrant expression of VEGF-C did not predict clearance/persistence of HR-HPV after treatment of CIN. In cervical cancer, VEGF-C had no prognostic value in univariate or multivariate survival analysis. After adjustment for HR-HPV, FIGO stage, age, and tumour grade, only FIGO stage and age remained independent prognostic predictors.Conclusions:VEGF-C is an early marker of cervical carcinogenesis, with linearly increasing expression starting from low grade CIN. VEGF-C expression is closely related to HR-HPV in cervical lesions, probably because of its p53 independent upregulation by the E6 oncoprotein of HR-HPV.
Importance of lymph vessels in gastric cancer: a prognostic indicator in general and a predictor for lymph node metastasis in early stage cancer
Authors: Nakamura Y , Yasuoka H , Tsujimoto M , Kurozumi K , Nakahara M , Nakao K , Kakudo K 
Published: January 2006

Background:Metastasis to regional lymph nodes (LNs) through lymphatic vessels is common in cancer progression and is an important prognostic factor in many cancers. Recent evidence suggests that tumour lymphangiogenesis promotes lymphatic metastasis.Aims:To study the role of lymph vessel density (LVD) in gastric cancer and investigate whether LVD is associated with LN metastasis/prognosis.Methods:Lymphatics of 117 primary human gastric cancer cases were investigated by quantitative immunohistochemical staining for podoplanin. The relation between LVD and LN metastasis and other established clinicopathological parameters was analysed. The relation between LVD and prognosis was also studied.Results:Mean LVD of “hot spots” was 11.6/case. LVD significantly correlated with LN and podoplanin positive lymphatic invasion. High LVD was associated with worse overall survival. In multivariate analysis, positive LVD was a significant independent predictor of overall survival, depth of invasion, and TNM stage. LVD significantly correlated with LN metastasis at surgery and podoplanin positive lymphatic invasion. In multivariate analysis, positive LVD was an independent significant predictor of LN metastasis.Conclusions:Increased podoplanin expression is significantly associated with LN metastasis, and may play an important role in detecting LN metastasis in gastric cancer. Furthermore, LVD may be a significant prognostic factor in gastric cancer at any stage. In addition, LVD and lymph vessel invasion detected by podoplanin immunohistochemistry are associated with LN metastasis in T1 early gastric cancer. LVD assessment by podoplanin immunohistochemistry may become a useful predictor of LN metastasis in T1 early gastric cancer and may influence the decision making process for additional surgery.
KAZHDAN CONSTANTS FOR SLn(ℤ)
Authors: KASSABOV MARTIN 
Published: January 2006

In this article we improve the known Kazhdan constant for SL n(ℤ) with respect to the generating set of the elementary matrices. We prove that the Kazhdan constant is bounded from below by [Formula: see text], which gives the exact asymptotic behavior of the Kazhdan constant, as n goes to infinity, since [Formula: see text] is an upper bound. We can use this bound to improve the bounds for the spectral gap of the Cayley graph of SL n(𝔽p) and for the working time of the product replacement algorithm for abelian groups.
Direct evidence for ex vivo expansion of human hematopoietic stem cells
Authors: Ando Kiyoshi , Yahata Takashi , Sato Tadayuki , Miyatake Hiroko , Matsuzawa Hideyuki , Oki Masayuki , Miyoshi Hiroyuki , Tsuji Takashi , Kato Shunichi , Hotta Tomomitsu 
Published: January 2006

AbstractTo characterize human hematopoietic stem cells (HSCs), xenotransplantation techniques such as the severe combined immunodeficiency (SCID) mouse repopulating cell (SRC) assay have proven the most reliable methods thus far. While SRC quantification by limiting dilution analysis (LDA) is the gold standard for measuring in vitro expansion of human HSCs, LDA is a statistical method and does not directly establish that a single HSC has self-renewed in vitro. This would require a direct clonal method and has not been done. By using lentiviral gene marking and direct intra-bone marrow injection of cultured CD34+ CB cells, we demonstrate here the first direct evidence for self-renewal of individual SRC clones in vitro. Of 74 clones analyzed, 20 clones (27%) divided and repopulated in more than 2 mice after serum-free and stroma-dependent culture. Some of the clones were secondary transplantable. This indicates symmetric self-renewal divisions in vitro. On the other hand, 54 clones (73%) present in only 1 mouse may result from asymmetric divisions in vitro. Our data demonstrate that current ex vivo expansion conditions result in reliable stem cell expansion and the clonal tracking we have employed is the only reliable method that can be used in the development of clinically appropriate expansion methods.