bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the usefulness of a novel MRI-based breast density estimation algorithm in a cohort of women at high genetic risk of breast cancer: the UK MARIBS study
Authors: Thompson Deborah J , Leach Martin O , Kwan-Lim Gek , Gayther Simon A , Ramus Susan J , Warsi Iqbal , Lennard Fiona , Khazen Michael , Bryant Emilie , Reed Sadie , Boggis Caroline RM , Evans D Gareth , Eeles Rosalind A , Easton Douglas F , Warren Ruth ML ,   The UK study of MRI screening for breast cancer in women at high risk (MARIBS)
Published: November 2009

Abstract
Introduction
Mammographic breast density is one of the strongest known risk factors for breast cancer. We present a novel technique for estimating breast density based on 3D T1-weighted Magnetic Resonance Imaging (MRI) and evaluate its performance, including for breast cancer risk prediction, relative to two standard mammographic density-estimation methods.

Methods
The analyses were based on MRI (n = 655) and mammography (n = 607) images obtained in the course of the UK multicentre magnetic resonance imaging breast screening (MARIBS) study of asymptomatic women aged 31 to 49 years who were at high genetic risk of breast cancer. The MRI percent and absolute dense volumes were estimated using our novel algorithm (MRIBview) while mammographic percent and absolute dense area were estimated using the Cumulus thresholding algorithm and also using a 21-point Visual Assessment scale for one medio-lateral oblique image per woman. We assessed the relationships of the MRI and mammographic measures to one another, to standard anthropometric and hormonal factors, to BRCA1/2 genetic status, and to breast cancer risk (60 cases) using linear and Poisson regression.

Results
MRI percent dense volume is well correlated with mammographic percent dense area (R = 0.76) but overall gives estimates 8.1 percentage points lower (P < 0.0001). Both show strong associations with established anthropometric and hormonal factors. Mammographic percent dense area, and to a lesser extent MRI percent dense volume were lower in BRCA1 carriers (P = 0.001, P = 0.010 respectively) but there was no association with BRCA2 carrier status. The study was underpowered to detect expected associations between percent density and breast cancer, but women with absolute MRI dense volume in the upper half of the distribution had double the risk of those in the lower half (P = 0.009).

Conclusions
The MRIBview estimates of volumetric breast density are highly correlated with mammographic dense area but are not equivalent measures; the MRI absolute dense volume shows potential as a predictor of breast cancer risk that merits further investigation.
Variations in arterial blood pressure are associated with parallel changes in FlowTrac/Vigileo®-derived cardiac output measurements: a prospective comparison study
Authors: Eleftheriadis Savvas , Galatoudis Zisis , Didilis Vasilios , Bougioukas Ioannis , Schön Julika , Heinze Hermann , Berger Klaus-Ulrich , Heringlake Matthias 
Published: November 2009

Abstract
Introduction
The reliability of autocalibrated pressure waveform analysis by the FloTrac-Vigileo® (FTV) system for the determination of cardiac output in comparison with intermittent pulmonary arterial thermodilution (IPATD) is controversial. The present prospective comparison study was designed to determine the effects of variations in arterial blood pressure on the reliability of the FTV system in patients undergoing coronary artery bypass grafting (CABG).

Methods
Comparative measurements of cardiac output by FTV (derived from a femoral arterial line; software version 1.14) and IPATD were performed in 16 patients undergoing elective CABG in the period before institution of cardiopulmonary bypass. Measurements were performed after induction of anesthesia, after sternotomy, and during five time points during graft preparation. During graft preparation, arterial blood pressure was increased stepwise in intervals of 10 to 15 minutes by infusion of noradrenaline and lowered thereafter to baseline levels.

Results
Mean arterial blood pressure was varied between 85 mmHg and 115 mmHg. IPATD cardiac output did not show significant changes during periods with increased arterial pressure either during sternotomy or after pharmacological manipulation. In contrast, FTV cardiac output paralleled changes in arterial blood pressure; i.e. increased significantly if blood pressure was raised and decreased upon return to baseline levels. Mean arterial blood pressure (MAP) and FTV cardiac output were closely correlated (r = 0.63 (95% confidence interval [CI]: 0.49 - 0.74), P < 0.0001) while no correlation between MAP and IPATD cardiac output was observed. Bland-Altman analyses for FTV versus IPATD cardiac output measurements revealed a bias of 0.4 l/min (8.5%) and limits of agreement from 2.1 to -1.3 l/min (42.2 to -25.3%).

Conclusions
Acute variations in arterial blood pressure alter the reliability of the FlowTrac/Vigileo® device with the second-generation software. This finding may help to explain the variable results of studies comparing the FTV system with other cardiac output monitoring techniques, questions the usefulness of this device for hemodynamic monitoring of patients undergoing rapid changes in arterial blood pressure, and should be kept in mind when using vasopressors during FTV-guided hemodynamic optimization.
High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians
Authors: Matsuzaki Hajime , Wang Pei-Hua , Hu Jing , Rava Rich , Fu Glenn K 
Published: November 2009

AbstractBackgroundCopy number variants (CNVs) account for a large proportion of genetic variation in the genome. The initial discoveries of long (> 100 kb) CNVs in normal healthy individuals were made on BAC arrays and low resolution oligonucleotide arrays. Subsequent studies that used higher resolution microarrays and SNP genotyping arrays detected the presence of large numbers of CNVs that are < 100 kb, with median lengths of approximately 10 kb. More recently, whole genome sequencing of individuals has revealed an abundance of shorter CNVs with lengths < 1 kb.ResultsWe used custom high density oligonucleotide arrays in whole-genome scans at approximately 200-bp resolution, and followed up with a localized CNV typing array at resolutions as close as 10 bp, to confirm regions from the initial genome scans, and to detect the occurrence of sample-level events at shorter CNV regions identified in recent whole-genome sequencing studies. We surveyed 90 Yoruba Nigerians from the HapMap Project, and uncovered approximately 2,700 potentially novel CNVs not previously reported in the literature having a median length of approximately 3 kb. We generated sample-level event calls in the 90 Yoruba at nearly 9,000 regions, including approximately 2,500 regions having a median length of just approximately 200 bp that represent the union of CNVs independently discovered through whole-genome sequencing of two individuals of Western European descent. Event frequencies were noticeably higher at shorter regions < 1 kb compared to longer CNVs (> 1 kb).ConclusionsAs new shorter CNVs are discovered through whole-genome sequencing, high resolution microarrays offer a cost-effective means to detect the occurrence of events at these regions in large numbers of individuals in order to gain biological insights beyond the initial discovery.
Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora
Authors: Wang Shi , Zhang Lingling , Meyer Eli , Matz Mikhail V 
Published: November 2009

Abstract
Background
Worldwide, coral reefs are in decline due to a range of anthropogenic disturbances, and are now also under threat from global climate change. Virtually nothing is currently known about the genetic factors that might determine whether corals adapt to the changing climate or continue to decline. Quantitative genetics studies aiming to identify the adaptively important genomic loci will require a high-resolution genetic linkage map. The phylogenetic position of corals also suggests important applications for a coral genetic map in studies of ancestral metazoan genome architecture.

Results
We constructed a high-resolution genetic linkage map for the reef-building coral Acropora millepora, the first genetic map reported for any coral, or any non-Bilaterian animal. More than 500 single nucleotide polymorphism (SNP) markers were developed, most of which are transferable in populations from Orpheus Island and Great Keppel Island. The map contains 429 markers (393 gene-based SNPs and 36 microsatellites) distributed in 14 linkage groups, and spans 1,493 cM with an average marker interval of 3.4 cM. Sex differences in recombination were observed in a few linkage groups, which may be caused by haploid selection. Comparison of the coral map with other metazoan genomes (human, nematode, fly, anemone and placozoan) revealed synteny regions.

Conclusions
Our study develops a framework that will be essential for future studies of adaptation in coral and it also provides an important resource for future genome sequence assembly and for comparative genomics studies on the evolution of metazoan genome structure.
Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis
Authors: Pankla Rungnapa , Buddhisa Surachat , Berry Matthew , Blankenship Derek M , Bancroft Gregory J , Banchereau Jacques , Lertmemongkolchai Ganjana , Chaussabel Damien 
Published: November 2009

Abstract
Background
Melioidosis is a severe infectious disease caused by Burkholderia pseudomallei, a Gram-negative bacillus classified by the National Institute of Allergy and Infectious Diseases (NIAID) as a category B priority agent. Septicemia is the most common presentation of the disease with a 40% mortality rate even with appropriate treatments. Better diagnostic tests are therefore needed to improve therapeutic efficacy and survival rates.

Results
We have used microarray technology to generate genome-wide transcriptional profiles (>48,000 transcripts) from the whole blood of patients with septicemic melioidosis (n = 32), patients with sepsis caused by other pathogens (n = 31), and uninfected controls (n = 29). Unsupervised analyses demonstrated the existence of a whole blood transcriptional signature distinguishing patients with sepsis from control subjects. The majority of changes observed were common to both septicemic melioidosis and sepsis caused by other infections, including genes related to inflammation, interferon-related genes, neutrophils, cytotoxic cells, and T-cells. Finally, class prediction analysis identified a 37 transcript candidate diagnostic signature that distinguished melioidosis from sepsis caused by other organisms with 100% accuracy in a training set. This finding was confirmed in 2 independent validation sets, which gave high prediction accuracies of 78% and 80%, respectively. This signature was significantly enriched in genes coding for products involved in the MHC class II antigen processing and presentation pathway.

Conclusions
Blood transcriptional patterns distinguish patients with septicemic melioidosis from patients with sepsis caused by other pathogens. Once confirmed in a large scale trial this diagnostic signature might constitute the basis of a differential diagnostic assay.
Conjugated Equine Estrogen Influence on Mammographic Density in Postmenopausal Women in a Substudy of the Women's Health Initiative Randomized Trial
Authors: McTiernan Anne , Chlebowski Rowan T. , Martin Christopher , Peck Jennifer David , Aragaki Aaron , Pisano Etta D. , Wang C.Y. , Johnson Karen C. , Manson JoAnn E. , Wallace Robert B. , Vitolins Mara Z. , Heiss Gerardo 
Published: November 2009

PurposeIncreased mammographic density is associated with increased breast cancer risk and reduced sensitivity of screening mammography and is related to hormone exposure. However, the effects of conjugated equine estrogens (CEEs) alone on mammographic density in diverse racial/ethnic populations are not established. We examined the effect of CEE alone on mammographic density in a subsample of the Women's Health Initiative (WHI) clinical trial participants.Patients and MethodsIn the WHI trial, women were randomly assigned to daily CEE 0.625 mg or placebo. The effect of CEE on mammographic percent density was determined over 1 and 2 years in a stratified random sample of 435 racially and ethnically diverse participants from 15 of 40 WHI clinics.ResultsUse of CEE resulted in mean increase in mammographic percent density of 1.6 percentage points (95% CI, 0.8 to 2.4) at year 1 compared with a mean decrease of 1.0 percentage point (95% CI, −1.7 to −0.4) in the placebo group (P < .001). The effect persisted for 2 years, with a mean increase of 1.7 percentage points (95% CI, 0.7 to 2.7) versus a mean decrease of 1.2 percentage points (95% CI, −1.8 to −0.5; P < .001) in the hormone and placebo groups, respectively. These effects were greater in women age 60 to 79 years (P = .03 for interaction across age).ConclusionUse of CEE results in a modest but statistically significant increase in mammographic density that is sustained over at least a 2-year period. The clinical significance of the CEE effect on mammographic density remains to be determined.
Effective Strategies for Management of Hypertension After Vascular Endothelial Growth Factor Signaling Inhibition Therapy: Results From a Phase II Randomized, Factorial, Double-Blind Study of Cediranib in Patients With Advanced Solid Tumors
Authors: Langenberg Marlies H.G. , van Herpen Carla M.L. , De Bono Johann , Schellens Jan H.M. , Unger Clemens , Hoekman Klaas , Blum Hubert E. , Fiedler Walter , Drevs Joachim , Le Maulf Florence , Fielding Anitra , Robertson Jane , Voest Emile E. 
Published: November 2009

Purpose Hypertension is a commonly reported adverse effect after administration of vascular endothelial growth factor (VEGF) inhibitors. Cediranib is a highly potent and selective VEGF signaling inhibitor of all three VEGFRs. This study prospectively investigated hypertension management to help minimize dose interruptions/reductions to maximize cediranib dose intensity. Patients and Methods Patients (n = 126) with advanced solid tumors were randomly assigned to one of four groups: cediranib 30 or 45 mg/d with or without antihypertensive prophylaxis. All patients developing hypertension on cediranib treatment were treated with a standardized, predefined hypertension management protocol. Results Cediranib was generally well tolerated, and all groups achieved high-dose intensities in the first 12 weeks (> 74% in all groups). Antihypertensive prophylaxis did not result in fewer dose reductions or interruptions. Increases in blood pressure, including moderate and severe readings of hypertension, were seen early in treatment in all groups and successfully managed. Severe hypertension occurred in one patient receiving prophylaxis versus 18 in the nonprophylaxis groups. Overall, there were nine partial responses, and 38 patients experienced stable disease ≥ 8 weeks. Conclusion To our knowledge, this is the first prospective investigation of hypertension management during administration of a VEGF signaling inhibitor. All four regimens were well tolerated with high-dose intensities and no strategy was clearly superior. The current cediranib hypertension management protocol appears to be effective in managing hypertension compared with previous cediranib studies where no plan was in place, and early recognition and treatment of hypertension is likely to reduce the number of severe hypertension events. This protocol is included in all ongoing cediranib clinical studies.
Nodal Staging Score: A Tool to Assess Adequate Staging of Node-Negative Colon Cancer
Authors: Gönen Mithat , Schrag Deborah , Weiser Martin R. 
Published: November 2009

Purpose Adequate nodal staging of colon cancer has been defined as pathologic examination of at least 12 lymph nodes. We sought to refine this definition by quantifying the likelihood that a pathologically node-negative patient has, indeed, no positive nodes. Patients and Methods Patients with stage I-III adenocarcinoma of the colon between 1994 and 2005 and had at least one lymph node pathologically examined were identified from the Surveillance, Epidemiology and End Results (SEER) database (n = 131,953). We estimated the sensitivity of the pathologic staging of locoregional spread using a beta-binomial model and developed the nodal staging score (NSS), which is the probability that a patient is correctly staged as node negative. NSS is a function of T stage and the number of examined nodes. Results The probability of missing a positive node that is in fact truly present is 29.7% if five nodes are examined, 20.0% if eight are examined, and drops to 13.6% for 12 nodes are examined. An NSS of 90% can be achieved by examining a single node for T1 and four nodes for T2 tumors. To maintain similar levels of NSS for T3, 13 nodes need to be examined and for T4 lesions, 21 nodes need to be examined. Graphical and tabular tools are provided to facilitate calculation of NSS and treatment decision making in practice. Conclusion The minimum number of examined nodes for adequate staging depends on the T stage. The score we developed indicates the adequacy of nodal staging for patients with no positive nodes and can assist clinical decision making in the patient without nodal metastasis.
Molecular Theory Including Quantum Effects and Thermal Fluctuations
Authors: Shigeta Yasuteru 
Published: November 2009

Abstract
Recent progress in our theoretical developments and applications where thermal fluctuations and quantum effects are important are reviewed. We first show that motions of a confined atom coupled with a fullerene cage cause large thermal fluctuation of the effective charge on the confined atom and that the fluctuation is sensitive to applied temperature and the number of confined species. Second, two different approaches to treat nuclear quantum effects are discussed. One is non-Born–Oppenheimer (NBO) molecular theory, which is one of an extension of molecular orbital theory for electrons to nuclear motions. This method is suitable to describe static and stationary nuclear (vibrational) states so we apply this method to obtain vibrationally coupled electron density of a protonatable amino acid. We compare the obtained electron density through NBO treatment with conventional calculations. The other approach is referred as to quantum cumulant dynamics (QCD), which is a generalization of quantized Hamiltonian dynamics initially proposed by Prezhdo. This method is applied to vibrational analyses. The ordinary normal mode analysis (NMA) is extended to include quantum degrees of freedom based on QCD formalism, which gives a better description of the vibrational state, where ordinary NMA gives incorrect results. Vibrational frequencies of small molecules by the QCD simulation are compared with those by classical molecular dynamics (MD). It is found that QCD is superior to classical MD in that the results obtained by QCD are in good agreement with those by full quantum treatment. Finally the theoretical background of a real-space grid-based time-dependent density functional theory (RSTDDFT) is explained. This method is applied to solve a NBO problem by using an imaginary time propagator and electron dynamics driven by an off-resonant circularly polarized laser plus in addition to using a real time propagator. For the latter case, we investigate atom-centered dipole moment and induced current and detect the electronic fluctuation in a SiH4 molecule after irradiation.
Theoretical Investigations on How to Reproduce d–π Bonds: Transition-Metal Cation–Benzene Complex Calculations
Authors: Tsuneda Takao , Hirosawa Tsuyoshi , Nakatsuka Yutaka , Hirao Kimihiko 
Published: November 2009

Abstract
Reproducibilities of d–π bonds were investigated on calculating complexes of first-row transition-metal cation (M+) and benzene (Bz). Calculations were carried out for half-sandwich MBz+ and sandwich MBz2+ complexes with several types of density functional theories (DFTs) and single-configurational wave function theories (WFTs). As a result, it was concluded that electron correlations are required to give the binding energies of d–π bonds even qualitatively, and DFTs would reproduce d–π bonds with quantitative accuracies only if electron correlations and long-range exchange interactions were both taken into consideration in exchange-correlation functionals used. In MBz+ calculations, WFTs fairly underestimated the binding energies for early transition metals (M = Sc–Cr) because of multiconfigurational effects. In contrast, DFTs overestimated them for late transition metals (M = Fe–Cu) due to insufficient long-range interactions in exchange functionals. For MBz2+, DFTs and WFTs gave similar binding energies for MBz2+, although WFTs slightly overestimated them for late transition metals. Furthermore, it was suggested that the experimental binding energies of CrBz2+ and MnBz2+ are probably misestimated.
The Single- and Double-Strand Cleavage of DNA by a Cationic Dicobalt Complex by Visible Light
Authors: Shimakoshi Hisashi , Kaieda Takeshi , Hisaeda Yoshio 
Published: November 2009

Abstract
A one-pot synthesis of a new polycationic organo–dicobalt complex having dual cationic alkyl groups as radical sources is reported. The complex was characterized by elemental analysis, UV–vis, 1H NMR, IR, and CSI-mass spectroscopies. CSI-MS afforded intact parent ion peak with labile cobalt–carbon bonds in the complex. The complex was photosensitive, and photocleavage of the cobalt–carbon bonds upon irradiation with visible light produced dual cationic carbon-centered radicals that were detected by EPR spin-trapping. Strong binding of the dicobalt complex with six cationic moieties toward DNA was confirmed by ethidium bromide displacement assays with Kapp = 3.2 × 107 M−1 at 298 K, the value was 100 times that of corresponding monocobalt complex with Kapp = 3.3 × 105 M−1. The dicobalt complex exhibited high ability for single- and double-strand DNA cleavage in comparison with that for the corresponding monocobalt complex under irradiation with visible light.
Structural Relationships among Methyl-, Dimethyl-, and Trimethylammonium Phosphododecatungstates
Authors: Busbongthong Suntharee , Ozeki Tomoji 
Published: November 2009

Abstract
Crystals of (CH3NH3)3[PW12O40]·2H2O (1), [(CH3)2NH2]3[PW12O40] (2), and [(CH3)3NH]3[PW12O40] (3) exhibit a similar packing of cations and anions, although they crystallize into different space group types, namely, and , respectively. Their structures were interpreted in terms of supergroup–subgroup relationships, revealing that the basic arrangements of cations and anions are primarily dominated by electrostatic interactions on which hydrogen bonds exert influences.