bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sustained inhibition of tumor growth and prolonged survival following sequential administration of doxorubicin and zoledronic acid in a breast cancer model
Authors: Ottewell Penelope D. , Lefley Diane V. , Cross Simon S. , Evans C. Alyson , Coleman Robert E. , Holen Ingunn 
Published: July 2009

AbstractCombination therapy, using agents that target the microenvironment as well as the cancer cells, is common in the treatment of advanced breast cancer. Here, we show that a 6‐week course of weekly sequential administration of the cytotoxic drug doxorubicin (2 mg/kg), followed 24 hr later by the antiresorptive agent zoledronic acid (100 μg/kg), causes substantial inhibition of subcutaneous MDA‐MB‐436 breast tumor growth in immunocompromised mice, leading to significantly increased survival. Tumor growth did not resume following withdrawal of treatment after 6 weeks, with 60% of the animals in this group surviving for more than 160 days. In comparison, animals receiving single‐agent therapy all died within 50 days. Molecular analysis of the tumors showed no effect on cell cycle or apoptosis following administration of 100 μg/kg zoledronic acid or 2 mg/kg doxorubicin alone. When doxorubicin was administered 24 hr before zoledronic acid, tumors displayed decreased expression of CYCLINS E1, B, D1 and D3 as well as CDK2, CDC2, CDK4 and CDK7, indicative of cell‐cycle inhibition. Tumors from animals receiving sequential treatment also showed induction of both intrinsic‐ and extrinsic‐apoptotic pathways, with increased expression of BAX, decreased expression of BCL‐2 and activation of CASPASE 3, 8 and 9. Accumulation of the unprenylated form of RAP1a, a surrogate marker for uptake of zoledronic acid, was only detected in tumors from animals treated with doxorubicin 24 hr before zoledronic acid. Our data are the first to show a sustained antitumor effectin vivofollowing a limited course of sequential administration of doxorubicin followed by zoledronic acid.
Synergistic antitumor effects of FGFR2 inhibitor with 5‐fluorouracil on scirrhous gastric carcinoma
Authors: Yashiro Masakazu , Shinto Osamu , Nakamura Kazunori , Tendo Masashige , Matsuoka Tasuku , Matsuzaki Taro , Kaizaki Ryoji , Miwa Atsushi , Hirakawa Kosei 
Published: July 2009

AbstractScirrhous gastric carcinoma (SGC) carries the highest mortality because of a frequent metastasis to lymph node (LN). S1, a 5‐fluorouracil (5‐FU) analog, is clinically available for gastric cancer at an advanced stage. Fibroblast growth factor receptor 2 (FGFR2) is required for the proliferation of SGC. The objective of this study is to clarify the benefit of a combination of S1 and kinase inhibitors including FGFR2 inhibitor Ki23057 in gastric cancer. OCUM‐2MLN and KATO‐III were derived from SGC. MKN‐7 and MKN‐74 were derived from non‐SGC. MTT assay was used to examine the growth‐inhibitory activity of 5 small‐synthetic molecules including Ki23057, Sunitinib, Glivec, Lapatinib or SU11274, in cells cultured with 5‐FU. Combination effects of 5‐FU with Ki23057 on proliferation, apoptosis and mRNA expression were examined. S1 and/or Ki23057 were administered to murine models of SGC created by the orthotopic inoculation of OCUM‐2MLN cells. Ki23057 at 100 nM significantly (p < 0.01) inhibited the proliferation and decreased the phosphorylation of FGFR2 in SGC cells, but not in non‐SGC. Ki23057 showed synergistic antitumor effects for SGC cells in combination with 5‐FU using CalcuSyn analysis, but Sunitinib, Glivec, Lapatinib and SU11274 did not. The combination of Ki23057 and 5‐FU decreased DPD expression and increased apoptosis rates and p21 expression level of SGC cells. The combined administration of S1 and Ki23057 significantly (p < 0.05) decreased orthotopic tumors as well as LN metastasis more effectively than S1 alone. These findings suggested that the combined treatment with 5‐FU and Ki23057 produced synergistic antitumor effects and is therapeutically promising for SGC treatment.
Methods and limitations of ‘clumped’ CO2 isotope (Δ47) analysis by gas‐source isotope ratio mass spectrometry
Authors: Huntington K. W. , Eiler J. M. , Affek H. P. , Guo W. , Bonifacie M. , Yeung L. Y. , Thiagarajan N. , Passey B. , Tripati A. , Daëron M. , Came R. 
Published: July 2009

AbstractThe geochemistry of multiply substituted isotopologues (‘clumped‐isotope’ geochemistry) examines the abundances in natural materials of molecules, formula units or moieties that contain more than one rare isotope (e.g. 13C18O16O, 18O18O, 15N2, 13C18O16O22−). Such species form the basis of carbonate clumped‐isotope thermometry and undergo distinctive fractionations during a variety of natural processes, but initial reports have provided few details of their analysis. In this study, we present detailed data and arguments regarding the theoretical and practical limits of precision, methods of standardization, instrument linearity and related issues for clumped‐isotope analysis by dual‐inlet gas‐source isotope ratio mass spectrometry (IRMS). We demonstrate long‐term stability and subtenth per mil precision in 47/44 ratios for counting systems consisting of a Faraday cup registered through a 1012 Ω resistor on three Thermo‐Finnigan 253 IRMS systems. Based on the analyses of heated CO2 gases, which have a stochastic distribution of isotopes among possible isotopologues, we document and correct for (1) isotopic exchange among analyte CO2 molecules and (2) subtle nonlinearity in the relationship between actual and measured 47/44 ratios. External precisions of ∼0.01‰ are routinely achieved for measurements of the mass‐47 anomaly (a measure mostly of the abundance anomaly of 13C‐18O bonds) and follow counting statistics. The present technical limit to precision intrinsic to our methods and instrumentation is ∼5 parts per million (ppm), whereas precisions of measurements of heterogeneous natural materials are more typically ∼10 ppm (both 1 s.e.). These correspond to errors in carbonate clumped‐isotope thermometry of ±1.2 °C and ±2.4 °C, respectively. Copyright © 2009 John Wiley & Sons, Ltd.
Surface‐enhanced Raman scattering studies of carbon nanotubes using Ag‐core Au‐shell nanoparticles
Authors: Kumar G. V. Pavan 
Published: July 2009

AbstractSurface‐enhanced Raman scattering from carbon nanotube bundles adsorbed with plasmon‐tunable Ag‐core Au‐shell nanoparticles (Ag@Au nps) was carried out for the first time. By utilizing nanoparticles whose plasmon resonance peak (541, 642 nm) closely matches the commonly used Raman excitation sources (532, 632.81 nm), we can observe a large enhancement in the Raman signatures of carbon nanotubes. We obtain greater enhancement in the Raman signal for the above case when compared to nanotubes adsorbed with conventional Ag, Au or other ‘off resonant’ Ag@Au nps. The power‐dependent SERS experiment on single‐walled nanotubes (SWNTs) with resonant Ag@Au nps reveals a linear behavior between the G‐band intensity and the photon flux density, which is in agreement with the vibrational pumping model of SERS. The observed enhancement by resonance matching is pronounced for carbon nanotubes and may lead to insights into understanding nanotube–nanoparticle interaction. Copyright © 2009 John Wiley & Sons, Ltd.
Thrombotic events in neonates receiving recombinant factor VIIa or fresh frozen plasma
Authors: Puetz John , Darling Ginger , Brabec Petr , Blatny Jan , Mathew Prasad 
Published: July 2009

AbstractBackgroundNumerous recent reports have described the use of recombinant factor VIIa (rFVIIa) in non‐hemophilia bleeding situations for achievement of hemostasis. However, its use in clinical situations other than hemophilia patients with inhibitors has been complicated by some reports of thrombotic events. rFVIIa has been used successfully to treat coagulopathic and/or bleeding neonates. The prevalence of thrombotic events in these neonates is completely unknown. This study was initiated to determine the risk of thrombotic events associated with rFVIIa use in neonates.ProcedureAll published literature in non‐hemophilic, non‐congenital factor VII deficient neonates receiving rFVIIa was reviewed. In addition, all data submitted to the SeveN Bleep Registry, a web‐based registry of rFVIIa uses in non‐hemophilic children was analyzed. As the baseline risk of thrombotic events in bleeding and/or coagulopathic neonates is not known, we also reviewed the records of 100 consecutive neonates from a single institution who received fresh frozen plasma (FFP) alone to treat their coagulopathy and/or bleeding episode.ResultsA total of 134 neonates received rFVIIa. Of these, 10 (7.5%) had a thrombotic event. The baseline risk of thrombotic events in neonates receiving FFP was 7%.ConclusionsOverall the prevalence of thrombotic events in bleeding and/or coagulopathic neonates appears to be around 7%, whether or not they receive rFVIIa. Pediatr Blood Cancer 2009;53:1074–1078. © 2009 Wiley‐Liss, Inc.
A general strategy for the bacterial expression of amyloidogenic peptides using BCL‐XL‐1/2 fusions
Authors: Yonemoto Isaac T. , Wood Malcolm R. , Balch William E. , Kelly Jeffery W. 
Published: July 2009

AbstractBiophysical studies on amyloidogenic and aggregation‐prone peptides often require large quantities of material. However, solid‐phase synthesis, handling, and purification of peptides often present challenges on these scales. Recombinant expression is an attractive alternative because of its low cost, the ability to isotopically label the peptides, and access to sequences exceeding ∼50 residues. However, expression systems that seek to solubilize amyloidogenic peptides suffer from low yields, difficult optimizations, and isolation challenges. We present a general strategy for expressing and isolating amyloidogenic peptides in Escherichia coli by fusion to a polypeptide that drives the expression of attached peptides into bacterial inclusion bodies. This scheme minimizes toxicity during bacterial growth and enables the processing and handling of the peptides in denaturing solutions. Immobilized metal affinity chromatography, reverse phase HPLC, and cyanogen bromide cleavage are used to isolate the peptide, followed by further reverse phase HPLC, which yields milligram quantities of the purified peptide. We demonstrate that driving the peptides into inclusion bodies using fusion to BCL‐XL‐1/2 is a general strategy for their expression and isolation, as exemplified by the production of 11 peptides species.
Flux compactifications of string theory on twisted tori
Authors: Hull C.M. , Reid‐Edwards R.A. 
Published: July 2009

AbstractGlobal aspects of Scherk‐Schwarz dimensional reduction are discussed and it is shown that it can usually be viewed as arising from a compactification on the compact space obtained by identifying a (possibly non‐compact) group manifold 𝒢 under a discrete subgroup Γ, followed by a truncation. This allows a generalisation of Scherk‐Schwarz reductions to string theory or M‐theory as compactifications on 𝒢/Γ, but only in those cases in which there is a suitable discrete subgroup of 𝒢. We analyse such compactifications with flux and investigate the gauge symmetry and its spontaneous breaking. We discuss the covariance under O(d,d), where d is the dimension of the group 𝒢, and the relation to reductions with duality twists. The compactified theories promote a subgroup of the O(d,d) that would arise from a toroidal reduction to a gauge symmetry, and we discuss the interplay between the gauge symmetry and the O(d,d,ℤ T‐duality group, suggesting the role that T‐duality should play in such compactifications.
On the modelling of over‐ocean hurricane surface winds and their uncertainty
Authors: Khare S. P. , Bonazzi A. , West N. , Bellone E. , Jewson S. 
Published: July 2009

AbstractThis paper investigates the modelling of over‐ocean hurricane surface wind fields and their associated uncertainty. The wind models tested include parameterized balance models, a two‐dimensional numerical planetary boundary‐layer model and a three‐dimensional (3D) linear analytical boundary‐layer model. Using a set of archived over‐ocean surface wind field reconstructions for validation, a series of cross‐validation experiments has been performed for a range of norms. For norms that quantify predictability of vector fields, a particular configuration of the 3D analytical model was found to be superior to the other models tested. Using residual fields derived from fitting the wind models to the validation data, the issue of how to model the uncertainty (in the form of a covariance) in the speed field has also been examined. Covariance models based on truncated empirical orthogonal function representations were found to be optimal. Copyright © 2009 Royal Meteorological Society
An Influence of the Aromatic Side Chains Conformations in Positions 2 and 3 of Vasopressin Analogs on Interactions with Vasopressin and Oxytocin Receptors
Authors: Ślusarz Rafał , Ślusarz Magdalena J. 
Published: July 2009

AbstractIn this work, the receptor‐bound conformation of nine vasopressin (CYFQNCPRG‐NH2, AVP) analogs substituted in positions 2 or 3 with 2‐aminoindane‐2‐carboxylic acid have been investigated using molecular modeling methods. The synthesis and functional assays of the analogs have been recently described. For comparison, the molecular dynamics of the selected analogs has been conducted. We have observed the relationship between the value of valence angle between the aromatic rings in positions 2 and 3 and the biological activity of the analogs. Both, in restricted space of the receptor cavities and unlimited continuous water environment, the same valence angles prevail, thus seem to be energetically more favorable for the particular peptides. Moreover, the residues responsible for analogs binding to the receptors have been identified.
OpenIGTLink: an open network protocol for image‐guided therapy environment
Authors: Tokuda Junichi , Fischer Gregory S. , Papademetris Xenophon , Yaniv Ziv , Ibanez Luis , Cheng Patrick , Liu Haiying , Blevins Jack , Arata Jumpei , Golby Alexandra J. , Kapur Tina , Pieper Steve , Burdette Everette C. , Fichtinger Gabor , Tempany Clare M. , Hata Nobuhiko 
Published: July 2009

AbstractBackgroundWith increasing research on system integration for image‐guided therapy (IGT), there has been a strong demand for standardized communication among devices and software to share data such as target positions, images and device status.MethodWe propose a new, open, simple and extensible network communication protocol for IGT, named OpenIGTLink, to transfer transform, image and status messages. We conducted performance tests and use‐case evaluations in five clinical and engineering scenarios.ResultsThe protocol was able to transfer position data with submillisecond latency up to 1024 fps and images with latency of <10 ms at 32 fps. The use‐case tests demonstrated that the protocol is feasible for integrating devices and software.ConclusionThe protocol proved capable of handling data required in the IGT setting with sufficient time resolution and latency. The protocol not only improves the interoperability of devices and software but also promotes transitions of research prototypes to clinical applications. Copyright © 2009 John Wiley & Sons, Ltd.
Bactericidal performance of photocatalytic titanium dioxide particle mixture under ultraviolet and fluorescent light: an in vitro study
Authors: Koseki Hironobu , Shiraishi Koutaro , Tsurumoto Toshiyuki , Asahara Tomohiko , Baba Koumei , Taoda Hiroshi , Terasaki Nao , Shindo Hiroyuki 
Published: July 2009

AbstractWhen ultraviolet (UV) light comes into contact with titanium dioxide (TiO2), a variety of free radicals are released to provide a potent oxidizing power. Few reports are available, however, evaluating the bactericidal effects of TiO2 particle under UV light and fluorescent light (FL) in the same line of research for clinical applications. In the present study, we set out to evaluate the in vitro photocatalytic bactericidal effects on Staphylococcus aureus, which is one of the most common pathogens of infectious disease, in an aqueous system of TiO2 particles irradiated by UV and FL. A TiO2 particle mixture containing 0.019 mg/ml of TiO2 was prepared. A bacterial solution was added dropwise to the mixture, and the resulting product was irradiated by UV or FL light. The colony‐forming units were counted and the bacterial survival rate was calculated. Control samples maintained a relatively high bacterial survival rate. In the TiO2 mixture group, however, the bacterial survival rate decreased steadily, reaching 9.4% after 60 min of exposure to UV light and 10.9% after 60 min of FL irradiation. Distributing the TiO2 particles in a water mixture produces highly efficient light absorption and enables greater and more frequent adhesion with bacteria, allowing a high degree of photocatalytic antibacterial action. Although the quantity was inferior to UV, our TiO2 particles were able to show effective bactericidal activity even under FL. The TiO2 particle mixture is expected to prove effective in preventing postoperative infection. Copyright © 2009 John Wiley & Sons, Ltd.
Formaldehyde‐assisted isolation of regulatory elements
Authors: Nagy Peter L. , Price David H. 
Published: July 2009

AbstractFormaldehyde‐Assisted Isolation of Regulatory Elements (FAIRE) is based on locus‐specific variations in the ability of protein components of chromatin to trap genomic DNA following formaldehyde treatment. This variation is mostly due to uneven nucleosome distribution since histones are the most abundant and highly crosslinkable components of chromatin. The method can identify and enrich for physically accessible DNA segments of the eukaryotic genome corresponding to known regulatory regions and regions that might have thus far unidentified structural role in the nuclear organization of chromatin. The enrichment patterns are cell type specific and thus might provide information about how transcriptional systems are organized and regulated in various tissues and how they might be disrupted in disease states. Analysis of a 268 kb region of chromosome 19 in human fibroblasts shown here demonstrates that while most DNA fragments detected by FAIRE correspond to sites of DNaseI hypersensitivity in active regions of chromatin, some are found in otherwise repressed chromatin domains and at other sites that are not found with other methods used to probe chromatin structure. Further exploration of FAIRE is warrented due to the simplicity of the protocol and recent advancements in massively parallel sequencing. Copyright © 2009 John Wiley & Sons, Inc.This article is categorized under:

Laboratory Methods and Technologies > Genetic/Genomic Methods
The mammalian phenotype ontology: enabling robust annotation and comparative analysis
Authors: Smith Cynthia L. , Eppig Janan T. 
Published: July 2009

AbstractThe mouse has long been an important model for the study of human genetic disease. Through the application of genetic engineering and mutagenesis techniques, the number of unique mutant mouse models and the amount of phenotypic data describing them are growing exponentially. Describing phenotypes of mutant mice in a computationally useful manner that will facilitate data mining is a major challenge for bioinformatics. Here we describe a tool, the Mammalian Phenotype (MP) ontology, for classifying and organizing phenotypic information related to the mouse and other mammalian species. The MP ontology has been applied to mouse phenotype descriptions in the Mouse Genome Informatics (MGI) Database (http://www.informatics.jax.org/), the Rat Genome Database (RGD, http://rgd.mcw.edu), the Online Mendelian Inheritance in Animals (OMIA, http://omia.angis.org.au/), and elsewhere. Use of this ontology allows comparisons of data from diverse sources, facilitates comparisons across mammalian species, assists in identifying appropriate experimental disease models, and aids in the discovery of candidate disease genes and molecular signaling pathways. Copyright © 2009 John Wiley & Sons, Inc.This article is categorized under:

Analytical and Computational Methods > Computational Methods
Comparison of prenatal care coverage in early adolescents, late adolescents, and adult pregnant women in the Peruvian Amazon
Authors: Ryan Julia A. , Casapía Martín , Aguilar Eder , Silva Hermánn , Joseph Serene A. , Gyorkos Theresa W. 
Published: July 2009

AbstractObjectiveTo compare prenatal care coverage between adolescent (early and late) and adult pregnant women in Iquitos, Peru.MethodsA random sample of 4467 birth records was collected. Multivariate analyses were performed to compare prenatal care coverage in all adolescent (10–14 years, 15–19 years) and adult (≥ 20 years) age groups and then for primiparous women only.ResultsThe mean number of visits was 5.0 for adolescents aged 10–14 years, 6.1 for adolescents aged 15–19 years, and 6.2 for women aged 20 years or older. For primiparous women, the means were 5.1, 6.2, and 6.8, for the respective age groups. Both the proportion attending and the number of prenatal visits were significantly lower in primiparous adolescents aged 10–14 years than in primiparous women aged 20 years or older (aOR 0.25; 95% CI, 0.10–0.62 and aRR 0.83; 95% CI, 0.74–0.94, respectively).ConclusionAll women attended prenatal care more frequently than the WHO's recommended 4 visits; however, early adolescents attended significantly less often than late adolescents or adult women. Further study of this inequality is warranted to adequately inform local health services.
Thymopericardial Augmented Encasement for Coronary Artery Bypass Graft Surgery
Authors: Ohtsuka Toshiya , Ninomiya Mikio , Nonaka Takahiro 
Published: July 2009

Objective A pedicled prepericardial fat flap was created to augment the pericardial cavity and applied for patients undergoing coronary artery bypass grafting. The efficacy and durability of this method were investigated. Methods Between July 2005 and November 2008, the present technique was applied for consecutive 245 patients (165 men and 80 women, aged 67 ± 8.3 years) undergoing isolated coronary artery bypass grafting in which 240 (98.0%) were off-pump cases. The left and/or right internal thoracic artery and the gastroepiploic artery were used in 244 and 160 patients, respectively, and the saphenous vein and the radial artery were used in 51 and 10 patients, respectively. Ninety-seven (40.0%) patients had been diabetic, 18 (7.3%) had had chronic renal failure, and three were redo cases. The prepericardial soft tissue, involving the pedicled thymic gland, was dissected en bloc and sewn with pericardiotomies to wrap the heart and the grafts. Angiography or three-dimensional computed tomography was used to assess the intrapericardial pathways of each graft and a long-term durability of the fat pad. Results Early angiography or three-dimensional computed tomography proved that the graft pathways were unaffected by the encasements. Resternotomies in two patients and sternal treatments for infectious dehiscence in two patients were safely achievable. Five-year postoperative computed tomography showed the intact fat pad in the retrosternal space. Conclusions The present technique can encase the heart not the least jeopardizing each pathway of the grafts, and the durable fat pad functions protectively when the sternotomy is either reopened or infected.