bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atlases of Minnesota Water Sustainability: Creation from Models, Analytical Methods, and Database of Watershed Characteristics
Authors: Nieber John , Kanivetsky Roman , Peterson Heidi , Lahoud Francisco , Mulla David , Shmagin Boris 
Published: October 2008

AbstractConfident assessment of the numbers of regional water balance and water resources for Atlases of MN Water Sustainability (AMNWS) has to be based on the best science, advanced knowledge and modern technology. Creating a watershed characteristic database is the first and most significant step in the analysis of time spatial distributions of Minnesota’s water balance components. The database spatially associates hydrologic data (annual discharge, monthly proportion, and yield) with topographical, soil and vadoze zone, ecological and hydrogeological conditions and properties. USGS stream flow data for 129 gauging stations surrounding MN was manipulated within ArcGIS. Characteristics of the 129 watersheds (drainage areas 100-10000 square miles) were summarized to create a matrix database (1947-1971 (79 watersheds), 1955-1979 (93), and 1976-2006 (74). Model as formal integrator of knowledge plays a central role for hydrological process in the landscape environment study. The use of cyber model of landscape (Krcho, 1978) and watershed as part of it (Shmagin, 1997) provides research tasks for data analyses. Six research tasks implied 17 initial matrixes incorporated the existing longtime hydrological data (from 25 to 109 years). Special part of database includes temperatures and precipitation (from 56 to 106 years) for 90 meteorological stations for MN and surrounding states (from US Historical Climatology Network: http://cdiac.ornl.gov/epubs/ndp/ushcn/usa_monthly.html). The data analysis (multivariate exploratory techniques) operates with two kinds of data: time series and maps that are integrated with use of GIS. Statistic was used with this database to transform initial matrixes of watershed characteristics into linear components and residual matrixes, establishing characteristics interconnections. To combine the results of data analysis of layered quantities and qualitative information onto a map of water resources with defined unit boundaries requires the fuzzy logic approach for regionalization (Shmagin and Chen, 2006). For AMNWS future developments, the watershed characteristics database can be upgraded to include monitoring of the surface and ground water regimes.
Position-dependent motif characterization using non-negative matrix factorization
Authors: Hutchins Lucie N. , Murphy Sean M. , Singh Priyam , Graber Joel H. 
Published: October 2008

Abstract
Motivation: Cis-acting regulatory elements are frequently constrained by both sequence content and positioning relative to a functional site, such as a splice or polyadenylation site. We describe an approach to regulatory motif analysis based on non-negative matrix factorization (NMF). Whereas existing pattern recognition algorithms commonly focus primarily on sequence content, our method simultaneously characterizes both positioning and sequence content of putative motifs.
Results: Tests on artificially generated sequences show that NMF can faithfully reproduce both positioning and content of test motifs. We show how the variation of the residual sum of squares can be used to give a robust estimate of the number of motifs or patterns in a sequence set. Our analysis distinguishes multiple motifs with significant overlap in sequence content and/or positioning. Finally, we demonstrate the use of the NMF approach through characterization of biologically interesting datasets. Specifically, an analysis of mRNA 3′-processing (cleavage and polyadenylation) sites from a broad range of higher eukaryotes reveals a conserved core pattern of three elements.
Contact: joel.graber@jax.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Regulatory T cells in human immunodeficiency virus-infected patients are elevated and independent of immunological and virological status, as well as initiation of highly active anti-retroviral therapy
Authors: Gaardbo J C , Nielsen S D , Vedel S J , Ersbøll A K , Harritshøj L , Ryder L P , Nielsen J O , Kolte L 
Published: October 2008

Summary
Infection with human immunodeficiency virus (HIV) causes a dysregulation of the immune system. This is caused by HIV-specific as well as non-specific mechanisms and has not been explained fully. In particular, knowledge is lacking about the potential role of host-mediated immunosuppressive mechanisms. During recent years it has become evident that a subpopulation of T cells [T regulatory (Tregs)] play a major role in sustaining tolerance to self-antigens. To investigate the influence of initiation of highly active anti-retroviral therapy (HAART) on the Treg level in HIV-infected patients we have conducted a prospective study enrolling treatment-naive HIV-infected patients just prior to starting treatment with HAART, measuring levels of Tregs by flow cytometry and mRNA expression of forkhead box P3 (FoxP3) at weeks 0, 4, 12 and 24 of treatment. In this prospective study neither the percentage of CD4+CD25high+ nor the expression of FoxP3 changed significantly during 24 weeks of HAART. Furthermore, HIV patients have higher Tregs measured as percentages of CD4+CD25high+ cells paralleled by higher levels of FoxP3 compared with healthy controls. The elevated level of Tregs was found to be independent of both immunological and virological status, indicating that initiation of HAART has minor effects on the Treg level in HIV-infected patients.
Do cytokines have any role in Wilson's disease?
Authors: Goyal M K , Sinha S , Patil S A , Jayalekshmy V , Taly A B 
Published: October 2008

Summary
The aim of this study was to determine the serum cytokine levels in patients with Wilson's disease (WD) and correlate with phenotype, therapeutic status and laboratory data. In this cross-sectional study, the serum levels of cytokines were estimated in 34 patients (M : F, 23 : 11; drug-naive, 11) with WD (mean age: 13·8 ± 8·6 and 19·6 ± 9·03 years) and compared with 30 controls. The following serum cytokines were analysed using enzyme-linked immunosorbent assay: (i) tumour necrosis factor (TNF)-α, (ii) interferon (IFN)-γ, (iii) interleukin (IL)-2, (iv) IL-6 and (v) IL-4. Serum TNF-α (P &lt; 0·001), IFN-γ (P = 0·005) and IL-6 (P &lt; 0·001) were detectable in WD compared with controls. However, serum level elevation of IL-4 (P = 0·49) and IL-2 (P = 0·11), although detectable compared with controls, was statistically insignificant. The disease severity and therapeutic status did not affect the cytokines. Presence of anaemia, leucopenia, thrombocytopenia, pancytopenia and hepatic dysfunction did not influence cytokine levels. There was a significant negative correlation between IL-6 and ceruloplasmin (P = 0·04) and anti-inflammatory cytokines (IL-4) and copper level (P = 0·01). Serum cytokines, both proinflammatory and anti-inflammatory subtypes, were elevated significantly in patients with WD. Further studies would establish their role in its pathogenesis.
Calcium ion release from calcium hydroxide stimulated fibronectin gene expression in dental pulp cells and the differentiation of dental pulp cells to mineralized tissue forming cells by fibronectin
Authors: Mizuno M. , Banzai Y. 
Published: October 2008

AbstractAim  The effect of calcium ions on dental pulp cells was examined and the mechanism of dentine bridge formation by calcium hydroxide was investigated.Methodology  Human dental pulp cells were treated with high concentration of calcium or magnesium ions for 24 h and fibronectin gene expression was measured by the quantitative PCR method. Human dental pulp cells were then cultured on fibronecin‐coated dishes for 24 h, and osteocalcin and osteopontin gene expression, which are typical phenotypes of mineralized tissue forming cells, were measured by the quantitative PCR method.Results  Fibronectin gene expression was stimulated by calcium ions dose‐dependently. On the other hand, magnesium ions did not influence fibronectin gene expression. Furthermore, pulp cells cultured on fibronectin‐coated dishes enhanced the expression of phenotypes of mineralized tissue forming cells.Conclusions  Calcium ions released from calcium hydroxide stimulates fibronectin synthesis in dental pulp cells. Fibronectin might induce the differentiation of dental pulp cells to mineralized tissue forming cells that are the main cells to form dentine bridges, via contact with cells.
Mechanical behaviour of nickel‐titanium rotary endodontic instruments in simulated clinical conditions: a computational study
Authors: Necchi S. , Taschieri S. , Petrini L. , Migliavacca F. 
Published: October 2008

AbstractAim  To develop an accurate finite element (FE) model for studying rotary endodontic instruments and to demonstrate the usefulness of the FE method in improving the knowledge of the mechanical behaviour of these instruments during root canal preparation.Methodology  An accurate geometrical model of a Ni‐Ti ProTaper F1 instrument was created. The interaction between the rotating instrument and differently shaped root canals during the insertion and removal procedure was studied using FE analyses. The complex thermo‐mechanical behaviour of the Ni‐Ti alloy was reproduced using an ad hoc computational subroutine. With the aim of demonstrating the enhanced performance of the shape memory alloy employment, the same analysis was performed on a ‘virtual’ ProTaper F1 made of stainless steel.Results  The Ni‐Ti instrument operated in its pseudo‐elastic range and was able to recover its original shape and to follow the canal curvature without deviation. The radius and the position of the canal curvature are the most critical parameters that determined the stress in the instrument with higher stress levels being produced by decreasing the radius and moving from the apical to the mid root position.Conclusions  The most demanding working conditions were observed in canals with sharp curves, especially in areas where the instruments had larger diameters. To prevent possible damage to instruments and fracture, it is advised that the instruments should be discarded following their use in such canals.
Ex vivo evaluation of dye penetration associated with various dentine bonding agents in conjunction with different irrigation solutions used within the pulp chamber
Authors: Bansal S. , Tewari S. 
Published: October 2008

AbstractAim  To compare the effect of sodium hypochlorite (NaOCl), chlorhexidine, povidone iodine and sodium ascorbate on dye penetration associated with various dentine adhesives used within the pulp chamber.Methodology  One hundred and sixteen mandibular molar teeth were divided into eight groups of 12 teeth each by irrigation regimen and adhesive system. The roof of pulp chambers and roots were removed under water cooling. The pulp chambers in the experimental groups were irrigated with 5.25% NaOCl, 0.2% chlorhexidine, 5% w/v povidone iodine or 5.25% NaOCl followed by sodium ascorbate and restored with Surefil using either Prime & Bond NT or Xeno III with each irrigation regimen. Twenty teeth were used as control specimens in which no disinfectant was used before bonding. Ten teeth from each group were immersed in 2% methylene blue dye and assessed for dye penetration. The data were statistically analysed by Kruskal–Wallis and Mann–Whitney U‐tests. Two samples in each group were observed under scanning electron microscopy for interfacial gap evaluation.Results  No significant difference was found in dye leakage between control and groups with 5.25% NaOCl pretreatment with both adhesive systems. Chlorhexidine and povidone iodine pretreatment resulted in significantly less dye penetration with Xeno III as compared with Prime & Bond NT. Sodium ascorbate treatment following NaOCl application significantly reduced microleakage and improved the marginal adaptation with both adhesive systems.Conclusions  The type of irrigant affected the sealing ability of bonding agents inside the pulp chamber and was material specific. Xeno III had less dye penetration with CHX and povidone iodine whilst sodium ascorbate pretreatment after NaOCl reduced dye penetration with both PBNT and Xeno III.
Microscopic appearance and apical seal of root canals filled with gutta‐percha and ProRoot Endo Sealer after immersion in a phosphate‐containing fluid
Authors: Weller R. N. , Tay K. C. Y. , Garrett L. V. , Mai S. , Primus C. M. , Gutmann J. L. , Pashley D. H. , Tay F. R. 
Published: October 2008

AbstractAim  To investigate the sealing quality of ProRoot Endo Sealer, a calcium silicate‐based sealer and its morphologic characteristics after immersion in a phosphate‐containing fluid (PCF).Methodology  Single‐rooted canals were filled with gutta‐percha and either ProRoot Endo Sealer or two commercially available zinc oxide eugenol (ZOE)‐based and epoxy resin‐based sealers. The sealers were allowed to set for 6 days and the filled teeth were immersed in PCF for 24 h before fluid leakage evaluation. After initial leakage evaluation at the 7th day, each filled root was restored and reimmersed in PCF for 28 days before the second phase of leakage evaluation at 35 days. Cryofractured specimens of additional teeth filled with the three sealers were examined using scanning electron microscopy after immersion in PCF for the two periods.Results  One‐way repeated measures anova and Tukey test revealed significant differences between the ZOE‐based sealer at 35 days and the calcium silicate‐based sealer at 35 days (P < 0.001), and between the ZOE‐based sealer at 7 days and the calcium silicate‐based sealer at 35 days (P = 0.001). No difference was found between the epoxy resin‐based sealer and the calcium silicate‐based sealer after both storage periods. Cryofractured calcium silicate‐based sealer specimens demonstrated apatite‐like crystalline deposits along the apical and middle thirds of the canal walls via transformation from amorphous calcium phosphate‐like precursors.Conclusions  ProRoot Endo Sealer is comparable in sealing quality to the epoxy resin‐based sealer and seals better than the ZOE‐based sealer after immersion in PCF. The calcium silicate‐based sealer also demonstrates ex vivo bioactivity when it comes into contact with phosphate ions.
Assessment of vascularity as an index of angiogenesis in periradicular granulomas. Comparison with oral carcinomas and normal tissue counterparts
Authors: Davey K. J. , Perrier S. , Ohe G. , Gilbert A. D. , Bankfalvi A. , Saunders W. P. , Schor S. L. , Schor A. M. 
Published: October 2008

AbstractAim  To quantify vascularity in periradicular granulomas using different endothelial markers, and assess its value as an index of angiogenesis by comparing granulomas with healthy periodontal ligament (PDL). To use oral tumours, compared with adjacent normal mucosa, as positive controls.Methodology  Paraffin‐embedded sections were stained with antibodies to von Willebrand factor (vWF), a pan‐endothelial marker, and CD105, a putative marker for angiogenic vessels. Vascularity was quantified by different methods reflecting vessel volume and density.Results  Irrespective of the marker or method used, vascularity values were similar in periradicular granuloma and PDL. Both tissues were highly vascularized, with levels similar to those found in oral squamous cell carcinoma. Vascularity was significantly higher in the latter than in normal mucosa. Fewer vessels were positive for CD105 than for vWF in the normal mucosa, whereas similar numbers were found in the other tissues examined.Conclusions  A comparison of vascularity in oral tumours and normal oral mucosa provided evidence of angiogenesis in the former. Staining with CD105 added limited value to staining with vWF in these tissues. In contrast, a comparison of periradicular granuloma and PDL failed to demonstrate evidence of angiogenesis in the granuloma. As all vessels were similarly stained with vWF and CD105 in granuloma and PDL, a possible hypothesis is that all vessels are newly formed in these tissues. A more plausible alternative is that CD105 expression may reflect the metabolic activity or intrinsic characteristics of the tissues, rather than the presence of angiogenic vessels.
Significant contribution of the pgdA gene to the virulence of Streptococcus suis
Authors: Fittipaldi Nahuel , Sekizaki Tsutomu , Takamatsu Daisuke , De La Cruz Domínguez‐Punaro María , Harel Josée , Bui Nhat Khai , Vollmer Waldemar , Gottschalk Marcelo 
Published: October 2008

Summary Streptococcus suis is a major swine pathogen and emerging zoonotic agent. In this study we have determined the muropeptide composition of S. suis peptidoglycan (PG) and found, among other modifications, N‐deacetylated compounds. Comparison with an isogenic mutant showed that the product of the pgdA gene is responsible for this specific modification which occurred in very low amounts. Low level of PG N‐deacetylation correlated with absence of significant lysozyme resistance when wild‐type S. suis was grown in vitro. On the other hand, expression of the pgdA gene was increased upon interaction of the bacterium with neutrophils in vitro as well as in vivo in experimentally inoculated mice, suggesting that S. suis may enhance PG N‐deacetylation under these conditions. Evaluation of the ΔpgdA mutant in both the CD1 murine and the porcine models of infection revealed a significant contribution of the pgdA gene to the virulence traits of S. suis. Reflecting a severe impairment in its ability to persist in blood and decreased ability to escape immune clearance mechanisms mediated by neutrophils, the ΔpgdA mutant was highly attenuated in both models. The results of this study suggest that modification of PG by N‐deacetylation is an important factor in S. suis virulence.
The hmuUV genes of Sinorhizobium meliloti 2011 encode the permease and ATPase components of an ABC transport system for the utilization of both haem and the hydroxamate siderophores, ferrichrome and ferrioxamine B
Authors: Cuív Páraic Ó , Keogh Damien , Clarke Paul , O'Connell Michael 
Published: October 2008

Summary Sinorhizobium meliloti, the endosymbiont of Medicago sativa, can use haem compounds, including haemoglobin and leghaemoglobin, when growing in the free‐living state. The components of the system involved in haem acquisition were confirmed to be ShmR, an outer membrane receptor, and HmuTUV, predicted to be an ABC transport system comprising a periplasmic protein, a permease and an ATPase respectively. The roles of HmuTUV in haem transport were confirmed in a heterologous expression system in Escherichia coli in conjunction with HasR, the outer membrane haem receptor of Serratia marcescens. hmuTUV mutants of S. meliloti showed a reduced capacity to acquire haem, suggesting the presence of a second haem acquisition system in the organism. S. meliloti can also acquire iron from xenosiderophores and the genes encoding the outer membrane receptors for ferrichrome and ferrioxamine B, fhuA1 and fhuA2, respectively, were identified. In light of this it is proposed that fhuA2 should be renamed foxA in the S. meliloti 1021 genome sequence. A siderophore reductase, FhuF, with the capacity to complement an E. coli ferrioxamine B reductase mutant, was identified encoded by a gene next to fhuA2. In the same transcriptional unit as fhuF the gene fhuP was identified and shown to encode a protein necessary for transport of ferrichrome and ferrioxamine B and predicted to be periplasmic. Interestingly, the remaining components of the transport system for the siderophores are HmuU and HmuV. Ferrichrome, ferrioxamine B and haem compounds therefore share components of the same transport system in S. meliloti.
Alteration in glycerol and metalloid permeability by a single mutation in the extracellular C‐loop of Leishmania major aquaglyceroporin LmAQP1
Authors: Uzcategui Nestor L. , Zhou Yao , Figarella Katherine , Ye Jun , Mukhopadhyay Rita , Bhattacharjee Hiranmoy 
Published: October 2008

SummaryThe Leishmania major aquaglyceroporin, LmAQP1, is responsible for the transport of antimonite [Sb(III)], an activated form of Pentostam or Glucantime. Downregulation of LmAQP1 provides resistance to trivalent antimony compounds and increased expression of LmAQP1 in drug‐resistant parasites can reverse the resistance. Besides metalloid transport, LmAQP1 is also permeable to water, glycerol, methylglyoxal, dihydroxyacetone and sugar alcohols. LmAQP1 also plays a physiological role in volume regulation and osmotaxis. In this study, we examined the role of extracellular C‐loop glutamates (Glu143, Glu145 and Glu152) in LmAQP1 activity. Alteration of both Glu143 and Glu145 to alanines did not affect either the biochemical or physiological properties of the protein, suggesting that neither residue is critical for LmAQP1 activity. Alteration of Glu152 to alanine, aspartate and glutamine affected metalloid transport in the order, wild‐type > E152Q > E152D > E152A. In fact, axenic amastigotes expressing E152A LmAQP1 accumulated negligible levels of either arsenite [As(III)] or Sb(III). Alteration of Glu152 significantly affected volume regulation and osmotaxis, suggesting that Glu152 is critical for the physiological activity of the parasite. More importantly, alteration of Glu152 to alanine did not affect glycerol permeability. Although the metalloids, As(III) and Sb(III), are believed to be transported through aquaglyceroporin channels as they behave as inorganic molecular mimic of glycerol, this is the first report where metalloid and glycerol transport can be dissected by a single mutation at the extracellular pore entry of LmAQP1 channel.
Detection of raised intracranial pressure by ultrasound measurement of optic nerve sheath diameter in African children
Authors: Beare Nicholas A. V. , Kampondeni Sam , Glover Simon J. , Molyneux Elizabeth , Taylor Terrie E. , Harding Simon P. , Molyneux Malcolm E. 
Published: October 2008

SummaryObjective  To evaluate optic nerve sheath (ONS) ultrasound as a non‐invasive method of detecting raised intracranial pressure (ICP) and to establish normal ONS diameter data for African children.Method  Children with acute neurological disease admitted to the Paediatric Department of Queen Elizabeth Central Hospital, Malawi had ultrasound measurements of ONS diameter. Controls were children admitted to the same department with non‐neurological disease. The mean of three measurements of the ONS diameter was used for analysis. Children were assessed for clinical signs of raised ICP. Patients had CT brain scans if required for their normal clinical care.Results  In 14 children with neurological disease and clinical signs suggestive of raised ICP, the mean ONS diameter was 5.4 mm (range 4.3–6.2 mm). Radiological signs on CT scans substantiated the presence of raised ICP in eight (all those scanned). In seven children with neurological disease but no specific signs of raised ICP the mean ONS diameter was 3.6 mm (range 2.8–4.4 mm). None of four of these patients examined by CT scan had signs of elevated ICP. The mean ONS diameter in 30 controls without neurological disease was 3.5 mm (range 2.5–4.1 mm). If 4.2 mm is taken as the upper limit of normal the sensitivity and specificity of this test for elevated ICP is 100% and 86%, respectively.Conclusion  ONS ultrasound is an accurate method for detecting raised ICP that can be applied in a broad range of settings. It has the advantages of being a non‐invasive, bedside test, which can be repeated multiple times for re‐evaluation.