bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bisphosphonates and pathologic complete response to taxane‐ and anthracycline‐based neoadjuvant chemotherapy in patients with breast cancer
Authors: Chavez‐MacGregor Mariana , Brown Erika , Lei Xiudong , Litton Jennifer , Meric‐Bernstram Funda , Mettendorf Elizabeth , Hernandez Leonel , Valero Vicente , Hortobagyi Gabriel N. , Gonzalez‐Angulo Ana Maria 
Published: May 2011

AbstractBACKGROUND:Several studies have suggested that bisphosphonates have an antitumor effect. In the current study, the authors sought to evaluate whether the use of bisphosphonates increased the rate of pathological complete response (pCR) in patients with breast cancer.METHODS:The authors identified 1449 patients with breast cancer who were receiving taxane‐ and anthracycline‐based neoadjuvant chemotherapy between 1995 and 2007 at The University of Texas MD Anderson Cancer Center. Patients who received bisphosphonates for osteopenia or osteoporosis while receiving chemotherapy were also identified. The primary outcome was the percentage of patients achieving a pCR. Groups were compared using the chi‐square test. A multivariable logistic regression model was fit to examine the relation between the use of bisphosphonates and pCR. An exploratory survival analysis using the Kaplan‐Meier method was performed; groups were compared using the log‐rank test.RESULTS:Of the 1449 patients included, 39 (2.7%) received bisphosphonates. Those receiving bisphosphonates were older (P < .001) and less likely to be obese (P = .04). The pCR rate was 25.4% in the bisphosphonate group and 16% in the nonbisphosphonate group (P = .11). In the multivariable model, patients treated with bisphosphonates tended to have higher rates of pCR (odds ratio, 2.18; 95% confidence interval, 0.90‐5.24); however, the difference was not found to be statistically significant. With a median follow‐up of 55 months (range, 3 months‐145 months), no differences in disease recurrence or survival were observed.CONCLUSIONS:The use of bisphosphonates at the time of neoadjuvant chemotherapy was not found to be associated with a statistically significant increase in the rates of pCR. The observed estimates suggest a positive effect; however, the small percentage of patients receiving bisphosphonates likely affected the power to detect a statistically significant difference. Cancer 2011;. © 2011 American Cancer Society.
Immersed boundary model of aortic heart valve dynamics with physiological driving and loading conditions
Authors: Griffith Boyce E. 
Published: May 2011

SUMMARYThe immersed boundary (IB) method is a mathematical and numerical framework for problems of fluid–structure interaction, treating the particular case in which an elastic structure is immersed in a viscous incompressible fluid. The IB approach to such problems is to describe the elasticity of the immersed structure in Lagrangian form, and to describe the momentum, viscosity, and incompressibility of the coupled fluid–structure system in Eulerian form. Interaction between Lagrangian and Eulerian variables is mediated by integral equations with Dirac delta function kernels. The IB method provides a unified formulation for fluid–structure interaction models involving both thin elastic boundaries and also thick viscoelastic bodies. In this work, we describe the application of an adaptive, staggered‐grid version of the IB method to the three‐dimensional simulation of the fluid dynamics of the aortic heart valve. Our model describes the thin leaflets of the aortic valve as immersed elastic boundaries, and describes the wall of the aortic root as a thick, semi‐rigid elastic structure. A physiological left‐ventricular pressure waveform is used to drive flow through the model valve, and dynamic pressure loading conditions are provided by a reduced (zero‐dimensional) circulation model that has been fit to clinical data. We use this model and method to simulate aortic valve dynamics over multiple cardiac cycles. The model is shown to approach rapidly a periodic steady state in which physiological cardiac output is obtained at physiological pressures. These realistic flow rates are not specified in the model, however. Instead, they emerge from the fluid–structure interaction simulation. Copyright © 2011 John Wiley & Sons, Ltd.
Cell adhesion molecule cadherin‐6 function in zebrafish cranial and lateral line ganglia development
Authors: Liu Q. , Dalman M.R. , Sarmah S. , Chen S. , Chen Y. , Hurlbut A.K. , Spencer M.A. , Pancoe L. , Marrs J.A. 
Published: May 2011

AbstractCadherins regulate the vertebrate nervous system development. We previously showed that cadherin‐6 message (cdh6) was strongly expressed in the majority of the embryonic zebrafish cranial and lateral line ganglia during their development. Here, we present evidence that cdh6 has specific functions during cranial and lateral line ganglia and nerve development. We analyzed the consequences of cdh6 loss‐of‐function on cranial ganglion and nerve differentiation in zebrafish embryos. Embryos injected with zebrafish cdh6 specific antisense morpholino oligonucleotides (MOs, which suppress gene expression during development; cdh6 morphant embryos) displayed a specific phenotype, including (i) altered shape and reduced development of a subset of the cranial and lateral line ganglia (e.g., the statoacoustic ganglion and vagal ganglion) and (ii) cranial nerves were abnormally formed. These data illustrate an important role for cdh6 in the formation of cranial ganglia and their nerves. Developmental Dynamics 240:1716–1726, 2011. © 2011 Wiley‐Liss, Inc.
Effects of n‐3 PUFA on insulin resistance after an oral fat load
Authors: Derosa Giuseppe , Cicero Arrigo F.G. , Fogari Elena , D'Angelo Angela , Bonaventura Aldo , Maffioli Pamela 
Published: May 2011

AbstractThe aim of this study was to evaluate the effects of ω‐3 PUFA (n‐3 PUFA) on lipid profile and insulin resistance biomarkers. Patients were assigned to receive placebo or n‐3 PUFA 1 g three times a day, during the meals, for 6 months. We evaluated: body mass index (BMI), body weight, fasting plasma glucose (FPG), fasting plasma insulin (FPI), homeostasis model assessment insulin resistance index (HOMA‐IR), blood pressure, lipid profile, resistin (r), retinol binding protein‐4 (RBP‐4), adiponectin (ADN), visfatin, and vaspin. Furthermore patients underwent an oral fat load (OFL) and an euglycemic hyperinsulinemic clamp to evaluate M value, and total glucose requirement (TGR). Triglycerides value obtained with n‐3 PUFA was lower, while HDL‐C, and ADN values were higher compared to placebo. After the OFL, and comparing the OFL performed at the baseline and at the end of the study, there was a decrease of triglycerides (Tg), resistin (r), and RBP‐4 values, and an increase of ADN value with n‐3 PUFA, but not with placebo. We conclude that the treatment with n‐3 PUFA resulted in a greater improvement of lipid profile and ADN compared to placebo in a baseline condition, and an improvement of all insulin resistance parameters after an OFL.Practical applications: The inverse association between dietary intake of n‐3 PUFA and cardiovascular disease morbidity/mortality was primarily established following the observation that the Greenland Inuits had low mortality from coronary heart disease despite a fat‐rich diet. Our group has already shown that n‐3 PUFA improved the lipid profile and the coagulation, fibrinolytic, and inflammatory parameters compared to placebo. We also observed that highly purified n‐3 PUFA supplementation significantly reduced the blood pressure, pulse pressure, and basal heart rate in hypertriglyceridemic patients with normal‐high blood pressure. The current study showed that treatment with n‐3 PUFA not only improved lipid profile in a baseline situation, but it also improved all insulin resistance parameters in a post‐prandial situation simulated with an OFL. This is another important action of the n‐3 PUFA which can increase their utility in the clinical practice.
Aqueous enzymatic process for oil and protein extraction from Moringa oleifera seed
Authors: Latif Sajid , Anwar Farooq , Hussain Abdullah I. , Shahid Muhammad 
Published: May 2011

AbstractFive commercial enzyme mixtures were evaluated for simultaneous oil and protein extraction from Moringa seed through enzyme‐assisted aqueous extraction (EAE). Protex 7L was found to be the best enzyme for highest oil (69.4%) extraction and protein (75.4%) recovery in the aqueous phase. The quality parameters of enzyme‐assisted aqueous extracted oil (EAEO), aqueous extracted oil (AEO), and hexane extracted oil (HEO) were compared. Among oils produced by these methods, fatty acids (FAs) profiles, density, refractive index, iodine value, saponification value, and unsaponifiable matter were found to be analogous, whereas significantly (p < 0.05) lower color and free FA contents in the EAEO and AEO than that of HEO were observed. The specific extinctions at 232 and 270 nm, p‐anisidine, and peroxide values of the EAEO and AEO were improved in comparison to HEO. An increase in tocopherol content and antioxidant activity measured by total phenolic content, DPPH radical scavenging capacity, and inhibition of linoleic acid oxidation in the EEO was observed as compared to the AEO and HEO. In general, the quality of the EAEO was improved and a significant amount of protein was simultaneously extracted which can be employed in food/feed applications.
Effect of acyl migration in Lipozyme TL IM‐catalyzed interesterification using a triacylglycerol model system
Authors: Svensson Julia , Adlercreutz Patrick 
Published: May 2011

AbstractLipase‐ (Lipozyme TL IM) catalyzed interesterification of triacylglycerols was studied at water activities (aw) from 0.22 to 0.8. The substrates trilaurin (LLL) and 1,3‐palmitin‐2‐olein (POP) were used in equimolar amounts to facilitate separate measurements of the interesterification in the sn‐1,3 positions and changes in the fatty acid (FA) composition in the sn‐2 position. The reaction at aw = 0.35 was the fastest, and that at aw = 0.84 the slowest, due to increased hydrolysis. The interesterification in the sn‐1,3 positions was above 90% after 2 h reaction at aw = 0.22, 0.35, and 0.54, and the main triacylglycerols were LLP, POL, LOL, and PLP. The FA composition in the sn‐2 position was conserved during the first 1–2 h, and the randomization due to acyl migration was complete after 24 h. During the entire reaction, FA present in the sn‐1,3 positions were removed from the triacylglycerols by the enzyme, and a fraction of them was released by hydrolysis. The gradual change in the composition of the free FA thus reflected the randomization of FA within the triacylglycerol molecules. Improved knowledge on the factors affecting the rates of interesterification, hydrolysis, and randomization is required to develop tailor‐made lipid products.Practical applications: In an ideal 1,3‐specific lipase‐catalyzed interesterification reaction, the FA composition in the sn‐2 position remains constant. In practice, small changes are seen in the FA composition in this position, and under certain conditions a completely randomized FA distribution can be obtained. Randomization is slower than interesterification. Uncontrolled hydrolysis should be avoided because it lowers the TAG yield. By varying the reaction time, different triacylglycerol mixtures can be produced: i.e. products originating from 1,3‐specific interesterification, as well as partially or completely randomized products.
Performance evaluation of a distributed hybrid test framework to reproduce the collapse behavior of a structure
Authors: Wang Tao , Mosqueda Gilberto , Jacobsen Andres , Cortes‐Delgado Maria 
Published: May 2011

SUMMARYA hybrid numerical and experimental simulation to collapse was conducted on a one‐half scale moment‐resisting frame building with two experimental substructures at different locations. An extensible hybrid test framework was used that adopts a generalized interface to encapsulate each numerical or tested substructure, through which only boundary displacements and forces are exchanged. Equilibrium and compatibility between substructures are enforced by an iterative quasi‐Newton procedure, while adopting a predictor‐and‐corrector method to avoid loading reversals on physically tested substructures. To overcome difficulties in controlling stiff axial and rotational deformations at the boundaries, the flexible test scheme employs either open‐loop or closed‐loop control at the boundaries: enforcing either compatibility or equilibrium, or both requirements at critical boundaries. The effectiveness of the extensible framework and its capability to simulate structural behavior through collapse is demonstrated by a geographically distributed test that reproduced the collapse behavior of a four‐story, two‐bay, steel moment frame previously tested on an earthquake simulator. A comparison of both experiments highlights the viability of the hybrid test as an effective tool for the performance evaluation of structural systems from the onset of damage through collapse. Copyright © 2011 John Wiley & Sons, Ltd.
Large eddy simulation in generalized curvilinear coordinates using conventional approach: Theory and validation
Authors: Panjwani Balram , Ertesvåg Ivar S. , Gruber Andrea , Rian Kjell Erik 
Published: May 2011

SUMMARYLarge eddy simulation (LES) methodology in curvilinear coordinates is presented in this study, where filtering is performed prior to the transformation in contrast to the alternate approach proposed by Jordan [J. Comput. Phys. 1999; 148:322–340], where filtering is done after the transformation. The main objective of the present study is to elaborate on the problems mentioned by Jordan with the conventional approach, and its consequences for the overall accuracy. The paper also provides remedies to the problems associated with the conventional approach. The present method treats the Leonard term in physical space rather than in computational space. Some practical difficulties associated with the alternate approach are also considered. Main advantages with the present conventional approach are: first an existing Reynolds averaged Navier–Stokes code can easily be extended for LES and second a wide range of existing advanced subgrid stress model can be used without any modifications. Filtering in physical space introduces a commutation error between filtering and differentiation due to non‐uniform meshes. The commutation filters in generalized coordinates are presented. LESs of four standard test cases are carried out to validate the present methodology. The four standard test cases are: (i) a lid‐driven cavity at Reynolds number (Re) of 12 000, (ii) a pipe flow at a friction Reynolds number Reτ of 360, (iii) a backward facing step at Re = 5100, and (iv) an axisymmetric confined dump combustor at Re = 11000. The results are validated against the reference data (direct numerical simulation or experiments). The mean velocity profiles and the turbulence intensities compared satisfactorily with the reference data. Copyright © 2011 John Wiley & Sons, Ltd.
A novel WWTR1‐CAMTA1 gene fusion is a consistent abnormality in epithelioid hemangioendothelioma of different anatomic sites
Authors: Errani Costantino , Zhang Lei , Sung Yun Shao , Hajdu Mihai , Singer Samuel , Maki Robert G. , Healey John H. , Antonescu Cristina R. 
Published: May 2011

AbstractThe classification of epithelioid vascular tumors remains challenging, as there is considerable morphological overlap between tumor subtypes, across the spectrum from benign to malignant categories. A t(1;3)(p36.3;q25) translocation was reported in two cases of epithelioid hemangioendothelioma (EHE), however, no follow‐up studies have been performed to identify the gene fusion or to assess its prevalence in a larger cohort of patients. We undertook a systematic molecular analysis of 17 EHE, characterized by classic morphological and immunophenotypic features, from various anatomical locations and with different malignant potential. For comparison, we analyzed 13 epithelioid hemangiomas, five epithelioid angiosarcomas, and four epithelioid sarcoma‐like EHE. A fluorescence in situ hybridization (FISH) positional cloning strategy, spanning the cytogenetically defined regions on chromosomes 1p36.3 and 3q25, confirmed rearrangements in two candidate genes from these loci in all EHE cases tested. None of the other benign or malignant epithelioid vascular tumors examined demonstrated these abnormalities. Subsequent reverse transcription‐polymerase chain reaction (RT‐PCR) confirmed in three EHE the WWTR1‐CAMTA1 fusion product. CAMTA1 and WWTR1 have been previously shown to play important roles in oncogenesis. Our results demonstrate the presence of a WWTR1‐CAMTA1 fusion in all EHE tested from bone, soft tissue, and visceral location (liver, lung) in keeping with a unique and specific pathological entity. Thus, FISH or RT‐PCR analysis for the presence of WWTR1‐CAMTA1 fusion may serve as a useful molecular diagnostic tool in challenging diagnoses. © 2011 Wiley‐Liss, Inc.
Relative 8q gain predicts disease‐specific survival irrespective of the TMPRSS2‐ERG fusion status in diagnostic biopsies of prostate cancer
Authors: Barros‐Silva João D. , Ribeiro Franclim R. , Rodrigues Ângelo , Cruz Ricardo , Martins Ana T. , Jerónimo Carmen , Henrique Rui , Teixeira Manuel R. 
Published: May 2011

AbstractScreening tools have greatly improved prostate cancer (PCa) detection, but the disease course is heterogeneous, and standard clinicopathological parameters do not fully discriminate aggressive from indolent tumors. To evaluate the prognostic value of the TMPRSS2‐ERG fusion gene combined with chromosome arm 8q relative gain in diagnostic biopsies of PCa, we studied a consecutive series of 200 diagnostic needle biopsies from patients with 10‐year disease‐specific survival data. TMPRSS2‐ERG fusion gene status and relative 8q gain were assessed by fluorescent in situ hybridization in whole formalin fixed paraffin‐embedded biopsies. The TMPRSS2‐ERG fusion gene was detected in 43.5% of PCa and was associated with lower Gleason score (P = 0.045), whereas relative 8q gain was present in 48% of PCa and was associated in high‐Gleason score (P < 0.001). ERG rearrangement alone was not associated with clinical outcome, whereas relative 8q gain predicted worse disease‐specific survival in PCa patients both with and without the TMPRSS2‐ERG fusion gene (P < 0.001), independently of Gleason score, clinical stage, and treatment modality. We conclude that relative 8q gain in diagnostic needle biopsies is a poor prognostic factor independent of the TMPRSS2‐ERG fusion gene status and of standard clinicopathological parameters. © 2011 Wiley‐Liss, Inc.
Identification of genetic disparity between primary and metastatic melanoma in human patients
Authors: Swoboda Alexander , Rasin‐Streden Doris , Schanab Oliver , Okamoto Ichiro , Pehamberger Hubert , Petzelbauer Peter , Mikula Mario 
Published: May 2011

AbstractIt is commonly accepted that cancer cell progression is accompanied by accumulation of genetic changes. Here we searched for copy number variations in melanoma and asked whether homozygous losses always cumulate during tumor cell progression. Therefore we investigated either melanoma cell lines or tissue derived from the primary lesion and from the lymph node metastasis of the same individual patient. In vitro studies of melanoma cell lines revealed high migratory and anchorage independent growth of metastasis‐derived cells. Surprisingly, whole genome DNA analysis of a primum‐derived cell line revealed a total of 10 homozygous losses, whereas the matched metastasis‐derived cell line only shared five of those losses. We further tested these cells in a mouse model for intradermal melanoma growth and detected fast growth of the metastasis‐derived cell line and no growth of primum‐derived cells. Additionally, we screened matched pairs of patient‐derived melanoma primum and metastasis samples and we could also identify a case with homozygous deletions exclusively present in the primary lesion. Therefore, we suggest that tumor cell progression at the metastatic niche can occur parallel and independently from the primary tumor. We propose that for mutation‐targeted therapy genotyping should be performed not only from primary, but also from metastatic melanoma. © 2011 Wiley‐Liss, Inc.
Chromosomal copy number alterations are associated with tumor response to chemoradiation in locally advanced rectal cancer
Authors: Chen Zhenbin , Liu Zheng , Li Wenyan , Qu Kun , Deng Xutao , Varma Madhulika G. , Fichera Alessandro , Pigazzi Alessio , Garcia‐Aguilar Julio 
Published: May 2011

AbstractRectal cancer response to chemoradiation (CRT) varies from no response to a pathologic complete response (pCR). Identifying predictive biomarkers of response would therefore be useful. We assessed whether chromosomal copy number alterations (CNAs) can assist in predicting pCR. Pretreatment tumor biopsies and paired normal surgical tissues from the proximal resection margin were collected from 95 rectal cancer patients treated with preoperative CRT and total mesorectal excision in a prospective Phase II study. Tumor and control DNA were extracted, and oligonucleotide array‐based comparative genomic hybridization (aCGH) was used to identify CNAs, which were correlated with pCR. Ingenuity pathway analysis (IPA) was then used to identify functionally relevant genes in aberrant regions. Finally, a predictive model for pCR was built using support vector machine (SVM), and leave‐one‐out cross validation assessed the accuracy of aCGH. Chromosomal regions most commonly affected by gains were 20q11.21‐q13.33, 13q11.32‐23, 7p22.3‐p22.2, and 8q23.3‐q24.3, and losses were present at 18q11.32‐q23, 17p13.3‐q11.1, 10q23.1, and 4q32.1‐q32.3. The 25 (26%) patients who achieved a pCR had significantly fewer high copy gains overall than non‐pCR patients (P = 0.01). Loss of chromosomal region 15q11.1‐q26.3 was significantly associated with non‐pCR (P < 0.00002; Q‐bound < 0.0391), while loss of 12p13.31 was significantly associated with pCR (P < 0.0003; Q‐bound < 0.097). IPA identified eight genes in the imbalanced chromosomal regions that associated with tumor response. SVM identified 58 probes that predict pCR with 76% sensitivity, 97% specificity, and positive and negative predictive values of 91% and 92%. Our data indicate that chromosomal CNAs can help identify rectal cancer patients more likely to develop a pCR to CRT. © 2011 Wiley‐Liss,Inc.