bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effects of digital image enhancement on the detection of vertical root fracture
Authors: Kamburoğlu Kıvanç , Murat Sema , Pehlivan Selcen Yüksel 
Published: January 2010

Abstract –  Aim:  To determine the effects of digital image enhancement on observer ability to detect experimentally induced vertical root fractures (VRF).Material and methods:  A total of 64 extracted human mandibular premolar teeth were used in this study. In 32 teeth, VRFs were created in the bucco‐lingual planes by gently tapping with screw‐type root‐canal pins. The remaining 32 intact teeth served as a control group. Digital images were obtained using a charge coupled device sensor. Three observers separately examined the original and four types of digitally enhanced images (enhanced using sharpness, zoom‐in, reverse‐contrast, and pseudo‐3D functions) at 1‐week intervals. All teeth were evaluated using a 5‐point scale for the presence/absence of VRF. Evaluations of each image set were repeated 1 month after the initial viewings. Kappa coefficients were calculated to investigate the degree of intra‐ and inter‐observer agreement. The areas under the receiver operating characteristic (ROC) curves (Az values) were calculated using the MedCalc statistical software. ROC values for each image type, observer and viewing were compared using t‐tests. A level of α = 0.05 was considered significant.Results:  Kappa coefficients for intra‐observer agreement ranged from 0.304 to 0.679. Inter‐observer agreement kappa values ranged from 0.109 to 0.399 for the first reading and from 0.106 to 0.380 for the second reading. Statistical comparisons between Az values for each observer showed no significant differences (P > 0.05) among image types.Conclusion:  There were no differences in diagnostic outcomes among differently enhanced images in the in vitro detection of VRF.
Humoral Immune Responses against theMycobacteriumtuberculosis38-Kilodalton, MTB48, and CFP-10/ESAT-6 Antigens in Tuberculosis
Authors: Wu Xueqiong , Yang Yourong , Zhang Junxian , Li Bangying , Liang Yan , Zhang Chuiying , Dong Mei , Cheng Hongbing , He Jufang 
Published: January 2010

ABSTRACTThe diagnosis of smear-negative and culture-negative patients with active tuberculosis (TB) is challenging. The detection ofMycobacteriumtuberculosis-specific antibodies in human sera has been an important diagnostic aid. However, detection of antibody responses to a single antigen usually has a low sensitivity for diagnosis of TB. In this study, humoral immune responses against recombinantM. tuberculosis38-kDa, MTB48, and CFP-10/ESAT-6 (culture filtrate protein 10/6-kDa early secreted antigen target ofM. tuberculosis) antigens in 250 Chinese TB patients and 260 healthy subjects were evaluated by an enzyme-linked immunosorbent assay (ELISA). The levels of antibodies against those antigens in TB patients, even in bacterium-negative ones, were significantly higher than those in healthy subjects (P< 0.001). The serodiagnostic sensitivities to detect antibodies against individual antigens, i.e., recombinantM. tuberculosis38-kDa, MTB48, and CFP-10/ESAT-6 antigens, in TB patients were 73.6%, 73.2%, and 60.4%, respectively, with specificities of 85.4%, 77.7%, and 73.8%, respectively. Importantly, the sensitivity to positively detect humoral responses to one of the antigens increased further. Our data suggest that the humoral immune responses toM. tuberculosisantigens in TB patients are heterogeneous. The 38-kDa, MTB48, and CFP-10/ESAT-6 antigens can be used as the cocktail antigens in the serodiagnosis of active TB, especially for smear- or culture-negative TB cases.
In Vitro
Synthesis of Sindbis Virus Genomic and Subgenomic RNAs: Influence of nsP4 Mutations and Nucleoside Triphosphate Concentrations
Authors: Li Mei-Ling , Wang Hongtao , Stollar Victor 
Published: January 2010

ABSTRACT

Two positive-strand mRNAs are made in Sindbis virus-infected cells, the genomic (G) RNA and the subgenomic (SG) RNA. In mosquito cells infected with wild-type (wt) Sindbis virus, the latter is made in excess over the former; however, in cells infected with SVpzf or SVcpc more G RNA is made than SG RNA. Use was made of
in vitro
systems to investigate the effects of the SVpzf and SVcpc mutations on the synthesis of SG and G RNAs. Our findings indicate that under standard reaction conditions, the SG/G RNA ratio
in vitro
reflects the ratio of SG to G RNA made in infected mosquito cells. We observed further that the RNA patterns seen
in vitro
are affected not only by the SVpzf and SVcpc mutations but also by the nucleoside triphosphate concentrations in the reaction mixtures and that introduction of these mutations into nsP4 and the promoter/template change the relative amounts of SG and G RNAs that are made, likely through the choice of promoter. We conclude that with respect to the SVpzf and SVcpc mutations, it is mainly the nucleotide changes in the SG promoter, not the amino acid changes in nsP4, that determine the SG/G RNA ratio that results. Further, it was observed that the SVpzf mutations enhance the
in vitro
synthesis of SG RNA at the lowest concentrations of UTP/CTP and that the single SVcpc mutation enhances the synthesis of G RNA at the lowest concentrations of CTP tested. We also identified three Arg residues in nsP4, R545, R546, and R547, that are needed for the synthesis of G RNA but not SG RNA.
The DR1 and DR6 First Exons of Human Herpesvirus 6A Are Not Required for Virus Replication in Culture and Are Deleted in Virus Stocks That Replicate Well in T-Cell Lines
Authors: Borenstein Ronen , Zeigerman Haim , Frenkel Niza 
Published: January 2010

ABSTRACT

Human herpesvirus 6A (HHV-6A) and HHV-6B are lymphotropic viruses which replicate in cultured activated cord blood mononuclear cells (CBMCs) and in T-cell lines. Viral genomes are composed of 143-kb unique (U) sequences flanked by ∼8- to 10-kb left and right direct repeats, DR
L
and DR
R
. We have recently cloned HHV-6A (U1102) into bacterial artificial chromosome (BAC) vectors, employing DNA replicative intermediates. Surprisingly, HHV-6A BACs and their parental DNAs were found to contain short ∼2.7-kb DRs. To test whether DR shortening occurred during passaging in CBMCs or in the SupT1 T-cell line, we compared packaged DNAs from various passages. Restriction enzymes, PCR, and sequencing analyses have shown the following. (i) Early (1992) viral preparations from CBMCs contained ∼8-kb DRs. (ii) Viruses currently propagated in SupT1 cells contained ∼2.7-kb DRs. (iii) The deletion spans positions 60 to 5545 in DR
L
, including genes encoded by DR1 through the first exon of DR6. The pac-2-pac-1 packaging signals, the DR7 open reading frame (ORF), and the DR6 second exon were not deleted. (iv) The DR
R
sequence was similarly shortened by 5.4 kb. (v) The DR1 through DR6 first exon sequences were deleted from the entire HHV-6A BACs, revealing that they were not translocated into other genome locations. (vi) When virus initially cultured in CBMCs was passaged in SupT1 cells no DR shortening occurred. (vii) Viral stocks possessing short DRs replicated efficiently, revealing the plasticity of herpesvirus genomes. We conclude that the DR deletion occurred once, producing virus with advantageous growth “conquering” the population. The DR1 gene and the first DR6 exon are not required for propagation in culture.
Functional Analysis of RNA Structures Present at the 3′ Extremity of the Murine Norovirus Genome: the Variable Polypyrimidine Tract Plays a Role in Viral Virulence
Authors: Bailey Dalan , Karakasiliotis Ioannis , Vashist Surender , Chung Liliane Man Wah , Reese Jivan , McFadden Nora , Benson Alicia , Yarovinsky Felix , Simmonds Peter , Goodfellow Ian 
Published: January 2010

ABSTRACT

Interactions of host cell factors with RNA sequences and structures in the genomes of positive-strand RNA viruses play various roles in the life cycles of these viruses. Our understanding of the functional RNA elements present in norovirus genomes to date has been limited largely to
in vitro
analysis. However, we recently used reverse genetics to identify evolutionarily conserved RNA structures and sequences required for norovirus replication. We have now undertaken a more detailed analysis of RNA structures present at the 3′ extremity of the murine norovirus (MNV) genome. Biochemical data indicate the presence of three stable stem-loops, including two in the untranslated region, and a single-stranded polypyrimidine tract [p(Y)] of variable length between MNV isolates, within the terminal stem-loop structure. The well-characterized host cell pyrimidine binding proteins PTB and PCBP bound the 3′-untranslated region via an interaction with this variable sequence. Viruses lacking the p(Y) tract were viable both in cell culture and upon mouse infection, demonstrating that this interaction was not essential for virus replication. However, competition analysis with wild-type MNV in cell culture indicated that the loss of the p(Y) tract was associated with a fitness cost. Furthermore, a p(Y)-deleted mutant showed a reduction in virulence in the STAT1
−/−
mouse model, highlighting the role of RNA structures in norovirus pathogenesis. This work highlights how, like with other positive-strand RNA viruses, RNA structures present at the termini of the norovirus genome play important roles in virus replication and virulence.
A Single Amino Acid Substitution in the Capsid of Foot-and-Mouth Disease Virus Can Increase Acid Lability and Confer Resistance to Acid-Dependent Uncoating Inhibition
Authors: Martín-Acebes Miguel A. , Rincón Verónica , Armas-Portela Rosario , Mateu Mauricio G. , Sobrino Francisco 
Published: January 2010

ABSTRACT

The acid-dependent disassembly of foot-and-mouth disease virus (FMDV) is required for viral RNA release from endosomes to initiate replication. Although the FMDV capsid disassembles at acid pH, mutants escaping inhibition by NH
4
Cl of endosomal acidification were found to constitute about 10% of the viruses recovered from BHK-21 cells infected with FMDV C-S8c1. For three of these mutants, the degree of NH
4
Cl resistance correlated with the sensitivity of the virion to acid-induced inactivation of its infectivity. Capsid sequencing revealed the presence in each of these mutants of a different amino acid substitution (VP3 A123T, VP3 A118V, and VP2 D106G) that affected a highly conserved residue among FMDVs located close to the capsid interpentameric interfaces. These residues may be involved in the modulation of the acid-induced dissociation of the FMDV capsid. The substitution VP3 A118V present in mutant c2 was sufficient to confer full resistance to NH
4
Cl and concanamycin A (a V-ATPase inhibitor that blocks endosomal acidification) as well as to increase the acid sensitivity of the virion to an extent similar to that exhibited by mutant c2 relative to the sensitivity of the parental virus C-S8c1. In addition, the increased propensity to dissociation into pentameric subunits of virions bearing substitution VP3 A118V indicates that this replacement also facilitates the dissociation of the FMDV capsid.
Dynamics of uncertainty in geological interpretation
Authors: Polson Debbie , Curtis Andrew 
Published: January 2010

Abstract:
Interpretation of geological data is based on both personal judgement and previous experience of related scenarios. In combining such information geologists employ heuristics (rules of thumb), and are therefore subject to biases that are well known in cognitive psychology and are common to all expert judgements. Here we analyse dynamic uncertainty in an evolving geological interpretation. Through a well-designed elicitation process we show how the inclusion of multiple experts influences interpretational bias. In particular, group convergence of opinion is observed, and we show how this can be differentiated from ‘herding' behaviour similar to that observed in economic bubbles by forcing a consensus to be reached. Thus we can identify when and why the judgement of a single geological expert should be treated with caution. This process can be applied to any geological interpretational scenario.
Cratonic basins and the long-term subsidence history of continental interiors
Authors: Armitage John J. , Allen Philip A. 
Published: January 2010

Abstract:Cratonic basins form within stable regions of the continental interior and initiate during periods of break-up and dispersal of supercontinental assemblies, when the continental lithosphere may experience tensional stress. We investigate the subsidence of cratonic basins using a 1D forward model of protracted stretching at low strain rates of thick continental lithosphere. At low strain rates, subsidence history departs from the uniform instantaneous model, as supported by calculations of the thermal Péclet number. Cooling as a result of upward advection is matched by thermal diffusion, producing a subsidence trajectory with a near-constant slope and a slight elbow when stretching ceases. The model is used to evaluate the subsidence history of boreholes in cratonic basin-fills. Marked accelerations and decelerations of subsidence, attributed to secondary mechanisms such as the dynamic response to mantle convection, are removed from the backstripped, water-loaded subsidence curves to obtain the ‘reduced' subsidence. Fits to the reduced curves indicate strain rates ofc. 10−16s−1, stretching durations of 50 Ma, and stretch factors of as little as 1.1–1.3, despite the extreme longevity of subsidence. Cratonic basins are therefore part of the rift–drift suite, occupying a portion of the existence field at low stretch factors and low extensional strain rate.
Vitamins B2 and B6 and Genetic Polymorphisms Related to One-Carbon Metabolism as Risk Factors for Gastric Adenocarcinoma in the European Prospective Investigation into Cancer and Nutrition
Authors: Eussen Simone J.P.M. , Vollset Stein Emil , Hustad Steinar , Midttun Øivind , Meyer Klaus , Fredriksen Åse , Ueland Per Magne , Jenab Mazda , Slimani Nadia , Ferrari Pietro , Agudo Antonio , Sala Núria , Capellá Gabriel , Del Giudice Giuseppe , Palli Domenico , Boeing Heiner , Weikert Cornelia , Bueno-de-Mesquita H. Bas , Büchner Frederike L. , Carneiro Fátima , Berrino Franco , Vineis Paolo , Tumino Rosario , Panico Salvatore , Berglund Göran , Manjer Jonas , Stenling Roger , Hallmans Göran , Martínez Carmen , Arrizola Larraitz , Barricarte Aurelio , Navarro Carmen , Rodriguez Laudina , Bingham Sheila , Linseisen Jakob , Kaaks Rudolf , Overvad Kim , Tjønneland Anne , Peeters Petra H.M. , Numans Mattijs E. , Clavel-Chapelon Françoise , Boutron-Ruault Marie-Christine , Morois Sophie , Trichopoulou Antonia , Lund Eiliv , Plebani Mario , Riboli Elio , González Carlos A. 
Published: January 2010

Abstract
B vitamins and polymorphisms in genes coding for enzymes involved in one-carbon metabolism may affect DNA synthesis and methylation and thereby be implicated in carcinogenesis. Previous data on vitamins B2 and B6 and genetic polymorphisms other than those involving MTHFR as risk factors for gastric cancer (GC) are sparse and inconsistent. In this case-control study nested within the European Prospective Investigation into Cancer and Nutrition cohort, cases (n = 235) and controls (n = 601) were matched for study center, age, sex, and time of blood sampling. B2 and B6 species were measured in plasma, and the sum of riboflavin and flavin mononucleotide was used as the main exposure variable for vitamin B2 status, whereas the sum of pyridoxal 5′-phosphate, pyridoxal, and 4-pyridoxic acid was used to define vitamin B6 status. In addition, we determined eight polymorphisms related to one-carbon metabolism. Relative risks for GC risk were calculated with conditional logistic regression, adjusted for Helicobacter pylori infection status and smoking status. Adjusted relative risks per quartile (95% confidence interval, Ptrend) were 0.85 (0.72-1.01, 0.06) for vitamin B2 and 0.78 (0.65-0.93, &lt;0.01) for vitamin B6. Both relations were stronger in individuals with severe chronic atrophic gastritis. The polymorphisms were not associated with GC risk and did not modify the observed vitamin-cancer associations. In summary, results from this large European cohort study showed an inverse association between vitamin B2 and GC risk, which is borderline significant, and a significant inverse association between vitamin B6 and GC risk. Cancer Epidemiol Biomarkers Prev; 19(1); 28–38
Comparison of Liquid Chromatography-Tandem Mass Spectrometry, RIA, and ELISA Methods for Measurement of Urinary Estrogens
Authors: Faupel-Badger Jessica M. , Fuhrman Barbara J. , Xu Xia , Falk Roni T. , Keefer Larry K. , Veenstra Timothy D. , Hoover Robert N. , Ziegler Regina G. 
Published: January 2010

AbstractAbsolute and relative concentrations of estrogens and estrogen metabolites are important for clinical decisions as well as for epidemiologic, experimental, and clinical research on hormonal carcinogenesis. RIA and ELISA are routinely used for measuring estrogen metabolites in blood and urine due to efficiency and low cost. Here, we compare absolute and ranked concentrations of estrone, estradiol, and estriol measured by indirect RIA and of 2-hydroxyestrone and 16α-hydroxyestrone measured by ELISA to the concentrations obtained using a novel liquid chromatography-tandem mass spectrometry (LC-MS/MS) method, which measures 15 estrogen metabolites concurrently. We used overnight urine samples collected from control women (362 premenopausal and 168 postmenopausal) participating in a population-based case-control study of breast cancer among Asian American women ages 20 to 55 years. When comparing RIA or ELISA levels to LC-MS/MS, absolute concentrations for the five estrogen metabolites ranged from 1.6 to 2.9 and 1.4 to 11.8 times higher in premenopausal and postmenopausal women, respectively (all P &lt; 0.0001). However, LC-MS/MS measurements were highly correlated [Spearman r (rs) = 0.8-0.9] with RIA and ELISA measurements in premenopausal women and moderately correlated (rs = 0.4-0.8) in postmenopausal women. Measurements of the 2-hydroxyestrone:16α-hydroxyestrone ratio, a putative biomarker of breast cancer risk, were moderately correlated in premenopausal women (rs = 0.6-0.7) but only weakly correlated in postmenopausal women (rs = 0.2). LC-MS/MS had higher intraclass correlation coefficients (≥99.6%) and lower coefficients of variation (≤9.4%) than ELISA (≥97.2% and ≤14.2%) and RIA (≥95.2% and ≤17.8%). Comparison with the LC-MS/MS method suggests that the widely used RIA and ELISA estrogen metabolite measures may be problematic, especially at low estrogen metabolite levels characteristic of postmenopausal women. Cancer Epidemiol Biomarkers Prev; 19(1); 292–300
Familial Melanoma: A Meta-analysis and Estimates of Attributable Fraction
Authors: Olsen Catherine M. , Carroll Heidi J. , Whiteman David C. 
Published: January 2010

Abstract
Melanoma commonly clusters in families, and the recent identification of numerous genotypes predicting higher risks of melanoma has led to the widespread perception that this cancer is predominantly a genetic disease. We conducted a systematic review of the literature and meta-analysis to quantify the contribution of familial factors to melanoma, estimated by the population attributable fraction (PAF). Eligible studies were those that permitted quantitative assessment of the association between histologically confirmed melanoma and family history of the disease; we identified 22 such studies using citation databases, followed by manual review of retrieved references. We calculated summary RRs using weighted averages of the log RR, taking into account random effects, and used these to estimate the PAF. Overall, family history was associated with a significant 2-fold increased risk of melanoma (odds ratio, 2.06; 95% confidence interval, 1.72-2.45); however, there was significant heterogeneity (P = 0.01). The pooled estimate for population-based studies (n = 11) was 2.03 (1.70-2.43), and 2.51 (1.55-4.07) for clinic/hospital-based studies (n = 11), both with significant heterogeneity (P = 0.049 and P = 0.013, respectively). Two studies used record linkage to verify family history in relatives; the pooled risk estimate from these two studies was 2.52 (2.11-3.00) with no evidence of heterogeneity (P = 0.258). Estimates of PAF associated with a positive family history ranged from 0.007 for Northern Europe to 0.064 for Australia (0.040 for all regions combined). Our findings suggest that only a small percentage of melanoma cases (always &lt;7%) are attributable to familial risk; the majority of melanomas are presumably attributable to other factors. Cancer Epidemiol Biomarkers Prev; 19(1); 65–73
Multifactorial Regulation of E-Cadherin Expression: An Integrative Study
Authors: Reinhold William C. , Reimers Mark A. , Lorenzi Philip , Ho Jennifer , Shankavaram Uma T. , Ziegler Micah S. , Bussey Kimberly J. , Nishizuka Satoshi , Ikediobi Ogechi , Pommier Yves G. , Weinstein John N. 
Published: January 2010

Abstract
E-cadherin (E-cad) is an adhesion molecule associated with tumor invasion and metastasis. Its down-regulation is associated with poor prognosis for many epithelial tumor types. We have profiled E-cad in the NCI-60 cancer cell lines at the DNA, RNA, and protein levels using six different microarray platforms plus bisulfite sequencing. Here we consider the effects on E-cad expression of eight potential regulatory factors: E-cad promoter DNA methylation, the transcript levels of six transcriptional repressors (SNAI1, SNAI2, TCF3, TCF8, TWIST1, and ZFHX1B), and E-cad DNA copy number. Combined bioinformatic and pharmacological analyses indicate the following ranking of influence on E-cad expression: (1) E-cad promoter methylation appears predominant, is strongly correlated with E-cad expression, and shows a 20% to 30% threshold above which E-cad expression is silenced; (2) TCF8 expression levels correlate with (−0.62) and predict (P &lt; 0.00001) E-cad expression; (3) SNAI2 and ZFHX1B expression levels correlate positively with each other (+0.83) and also correlate with (−0.32 and −0.30, respectively) and predict (P = 0.03 and 0.01, respectively) E-cad expression; (4) TWIST1 correlates with (−0.34) but does not predict E-cad expression; and (5) SNAI1 expression, TCF3 expression, and E-cad DNA copy number do not correlate with or predict E-cad expression. Predictions of E-cad regulation based on the above factors were tested and verified by demethylation studies using 5-aza-2′-deoxycytidine treatment; siRNA knock-down of TCF8, SNAI2, or ZFHX1B expression; and combined treatment with 5-aza-2′-deoxycytidine and TCF8 siRNA. Finally, levels of cellular E-cad expression are associated with levels of cell-cell adhesion and response to drug treatment. Mol Cancer Ther; 9(1); 1–16