bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of AKAP‐4 as a new cancer/testis antigen for detection and immunotherapy of prostate cancer
Authors: Chiriva‐Internati Maurizio , Yu Yuefei , Mirandola Leonardo , D'Cunha Nicholas , Hardwicke Fred , Cannon Martin J. , Cobos Everardo , Kast W. Martin 
Published: April 2011

AbstractBACKGROUNDProstate cancer (PC) is the second most common cancer in older men, after skin cancer. PC is difficult to diagnose because the prostate‐specific antigen screening method is associated with many false positives. In addition there is a need to develop new and more effective treatments. Among presently available new treatments, immunotherapy is a promising approach. We investigated the expression of the cancer/testis antigen, AKAP‐4, in PC patients to evaluate the possibility of exploiting AKAP‐4 as a target for immunotherapy.METHODSWe analyzed normal prostate tissues, 15 patients with PC and the LnCAP PC cell line by immunohistochemistry. We tested AKAP‐4 immunogenicity through indirect ELISA on sera from patients and healthy subjects, and we generated in vitro AKAP‐4‐specific cytotoxic lymphocytes from peripheral blood mononuclear cells.RESULTSAKAP‐4 was shown both at the cytoplasmic and surface levels of the LnCAP PC cell line. AKAP‐4 was also highly expressed in PC cells from patients. We detected specific anti‐AKAP‐4 circulating immunoglobulins in AKAP‐4 positive subjects. Using recombinant AKAP‐4 loaded autologous dendritic cells, we generated AKAP‐4‐specific and HLA‐I‐restricted cytotoxic T lymphocytes able to kill PC cells in vitro. Further characterization indicated a Th‐1 skewing in the cytokine secretion profile of these cells.CONCLUSIONSWe demonstrate the aberrant expression of AKAP‐4 in PC, which will potentially be developed as a biomarker in PC. We provide evidence that AKAP‐4 is a potential target for PC adoptive immunotherapy or anti‐tumor vaccination. Prostate 72:12–23, 2012. © 2011 Wiley Periodicals, Inc.
The Association between pre‐operative PSA and prostate cancer‐specific mortality in patients with long‐term follow‐up after radical prostatectomy
Authors: Lewinshtein Dan , Teng Brandon , Valencia Ashley , Gibbons Robert , Porter Christopher R. 
Published: April 2011

AbstractBACKGROUNDThe clinical and pathologic predictors of prostate cancer‐specific mortality (PCSM) many years after radical prostatectomy (RP) remain to be fully elucidated. We explored the association between pre‐operative prostate‐specific antigen (PSA) and other pathologic predictors and PCSM in men who have undergone (RP).METHODSWe report on 459 patients with PCSM data after RP who were followed prospectively over a 23‐year period between 1987 and 1997. Cox regression and Kaplan–Meier analysis were used to evaluate pre‐operative PSA, pathologic Gleason sum, pathologic stage, and surgical margin status as predictors of PCSM.RESULTSThe median PSA was 6.6 ng/ml (±9.9) and the median follow‐up time was 9.4 (±4.9) years. Fourteen patients (3.1%) died of PC. On multivariate analysis, only PSA (HR: 1.050; P = 0.001) and binary Gleason sum (HR: 3.402; P = 0.043) remained significant predictors of PCSM. The predicted 10‐year PCSM was significantly worse in those patients in the highest PSA tertile compared to those in other tertiles [PSA > 9.9: 87% (82–92%) vs. PSA = 4–9.9: 95% (93.0–97.0%) vs. PSA = 0–3.9: 100.0% (100.0–100.0%)].CONCLUSIONSWe have highlighted the importance of pre‐operative PSA in predicting PCSM many years after RP. It is a more significant predictor than Gleason sum and pathologic stage. Thus, PSA may help identify patients with life‐threatening PC at a time when their disease is curable with definitive therapy. Prostate 72:24–29, 2012. © 2011 Wiley Periodicals, Inc.
Prostate cancer risk variants are not associated with disease progression
Authors: Szulkin Robert , Holmberg Erik , Stattin Pär , Xu Jianfeng , Zheng Sigun , Palmgren Juni , Grönberg Henrik , Wiklund Fredrik 
Published: April 2011

AbstractBACKGROUNDCurrently used prognostic markers are limited in their ability to accurately predict disease progression among patients with localized prostate cancer. We examined 23 reported prostate cancer susceptibility variants for association with disease progression.METHODSDisease progression was explored among 4,673 Swedish patients treated for clinically localized prostate cancer between 1997 and 2002. Prostate cancer progression was defined according to primary treatment as a composed event reflecting termination of deferred treatment, biochemical recurrence, local progression, or presence of distant metastasis. Association between single variants, and all variants combined, were performed in Cox regression analysis assuming both log‐additive and co‐dominant genetic models.RESULTSThree of the 23 genetic variants explored were nominally associated with prostate cancer progression; rs9364554 (P = 0.041) on chromosome 6q25 and rs10896449 (P = 0.029) on chromosome 11q13 among patients treated with curative intent; and rs4054823 (P = 0.008) on chromosome 17p12 among patients on surveillance. However, none of these associations remained statistically significant after correction for multiple testing. The combined effect of all susceptibility variants was not associated with prostate cancer progression neither among patients receiving treatment with curative intent (P = 0.14) nor among patients on surveillance (P = 0.92).CONCLUSIONSWe observed no evidence for an association between any of 23 established prostate cancer genetic risk variants and disease progression. Accumulating evidence suggests separate genetic components for initiation and progression of prostate cancer. Future studies systematically searching for genetic risk variants associated with prostate cancer progression and prognosis are warranted. Prostate 72:30–39, 2012. © 2011 Wiley Periodicals, Inc.
Expression of NF‐κB‐related proteins and their modulation during TNF‐α‐provoked apoptosis in prostate cancer cells
Authors: Rodríguez‐Berriguete Gonzalo , Fraile Benito , Paniagua Ricardo , Aller Patricio , Royuela Mar 
Published: April 2011

AbstractBACKGROUNDThe involvement of TNF‐α in cancer development is controversial, since this cytokine was reported to act either as tumor promoter or suppressor. TNF‐α may activate signaling pathways critical for life/death decisions, such as mitogen‐activated protein kinases (MAPKs) and the anti‐apoptotic NF‐κB pathway. In this work, we investigate the activation status of NF‐κB‐related proteins in human prostate cancerous versus normal epithelium, and the alterations in the NF‐κB pathway in relation to cell death in TNF‐α‐treated LNCaP (androgen‐independent cells) and PC3 (androgen‐independent) prostate cancer cell lines.METHODSThe expression of phospho‐p38‐MAPK, phospho‐IKK‐α/β and phospho‐IκB‐α, total IκB‐α, and p65‐ and p50‐NF‐κB, were analyzed by immunohistochemistry in cancerous and normal prostate samples. The toxicity of TNF‐α in LNCaP and PC3 cells, with or without kinase and NF‐κB inhibitors, was assessed by changes on viability (MTT assay) and apoptosis (loss of DNA, annexin‐V binding, and caspase cleavage/activation). Expression of NF‐κB‐related proteins in these cell lines was measured by Western blot.RESULTSPhospho‐IκB‐α, phospho‐IKK‐α/β and phospho‐p38 levels, cytoplasmic p50 to IκB‐α ratio, and nuclear p50 and p65, levels, were increased in cancerous epithelium, suggesting activation of the NF‐κB pathway in prostatic malignance. TNF‐α caused apoptosis with higher efficacy in LNCaP cells, and this response was potentiated by p38‐MAPK inhibitor (LNCaP cells) and IKK‐β inhibitor (both cell lines). However, the protective action of IKK‐β was mediated by NF‐κB only in LNCaP cells.CONCLUSIONSIKK‐β mediates both NF‐κB‐dependent and ‐independent anti‐apoptotic functions in prostate cancerous epithelium. IKK‐β and p38‐MAPK may represent useful therapeutic targets against prostate cancer. Prostate 72:40–50, 2012. © 2011 Wiley Periodicals, Inc.
Treatment decision‐making for localized prostate cancer: What younger men choose and why
Authors: Sidana Abhinav , Hernandez David J. , Feng Zhaoyong , Partin Alan W. , Trock Bruce J. , Saha Surajit , Epstein Jonathan I. 
Published: April 2011

AbstractBACKGROUND AND OBJECTIVEThe literature lacks knowledge about information preferences and decision‐making in young prostate cancer patients. This study provides insight into information sources consulted and factors dictating treatment decision‐making in young prostate cancer patients.METHODSSubjects were identified from pathology consult service of a National Center of Excellence. Questionnaires were mailed to 986 men, under 50 years of age, diagnosed with Gleason score 6 prostate cancer between 2001 and 2005.RESULTSFour hundred ninety‐three men responded. The most common primary therapies were surgery 397 (81.4%), radiation 52 (10.7%), and active surveillance (AS) 26 (5.3%). Participants with at least some college education (P = 0.003) or annual income >$100,000 (P = 0.003) were more likely to consult three or more doctors. Amongst all treatments, “doctor's recommendation” was the most influential information source, although relatively less important in the AS group. Internet was the second most frequent information source. Participants with higher education (P = 0.0003) and higher income (P = 0.002) considered sexual function more important while making a treatment choice. Only 2% of the men preferred a passive role in the decision‐making. Informed decision‐making was preferred more by patients who chose radiation and AS while shared decision‐making was preferred more by surgery patients (P < 0.05). The majority (89%) of the respondents did not regret their decision. No difference in satisfaction levels was found between different treatment modalities.CONCLUSIONSThis study provides insight into information sources consulted, such as the greater internet use, and various factors dictating treatment decision‐making in young prostate cancer patients. There was an overall very high satisfaction rate regardless of the therapy chosen. Prostate 72:58–64, 2012. © 2011 Wiley Periodicals, Inc.
The association between inflammation‐related genes and serum androgen levels in men: The prostate, lung, colorectal, and ovarian study
Authors: Meyer Tamra E. , Chu Lisa W. , Li Qizhai , Yu Kai , Rosenberg Philip S. , Menashe Idan , Chokkalingam Anand P. , Quraishi Sabah M. , Huang Wen‐Yi , Weiss Jocelyn M. , Kaaks Rudolf , Hayes Richard B. , Chanock Stephen J. , Hsing Ann W. 
Published: April 2011

AbstractBACKGROUNDAndrogens and inflammation have been implicated in the etiology of several cancers, including prostate cancer. Serum androgens have been shown to correlate with markers of inflammation and expression of inflammation‐related genes.METHODSIn this report, we evaluated associations between 9,932 single nucleotide polymorphisms (SNPs) marking common genetic variants in 774 inflammation‐related genes and four serum androgen levels (total testosterone [T], bioavailable T [BioT]; 5α‐androstane‐3α, 17β‐diol glucuronide [3αdiol G], and 4‐androstene‐3,17‐dione [androstenedione]), in 560 healthy men (median age 64 years) drawn from the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial. Baseline serum androgens were measured by radioimmunoassay. Genotypes were determined as part of the Cancer Genetic Markers of Susceptibility Study genome‐wide scan. SNP‐hormone associations were evaluated using linear regression of hormones adjusted for age. Gene‐based P values were generated using an adaptive rank truncated product (ARTP) method.RESULTSSuggestive associations were observed for two inflammation‐related genes and circulating androgen levels (false discovery rate [FDR] q‐value <0.1) in both SNP and gene‐based tests. Specifically, T was associated with common variants in MMP2 and CD14, with the most significant SNPs being rs893226G > T in MMP2 and rs3822356T > C in CD14 (FDR q‐value = 0.09 for both SNPs). Other genes implicated in either SNP or gene‐based tests were IK with T and BioT, PRG2 with T, and TNFSF9 with androstenedione.CONCLUSIONThese results suggest possible cross‐talk between androgen levels and inflammation pathways, but larger studies are needed to confirm these findings and to further clarify the interrelationship between inflammation and androgens and their effects on cancer risk. Prostate 72:65–71, 2012. © 2011 Wiley Periodicals, Inc.
Preoperative insulin‐like growth factor‐binding protein‐3 (IGFBP‐3) blood level predicts gleason sum upgrading
Authors: Terracciano Daniela , Bruzzese Dario , Ferro Matteo , Mazzarella Claudia , Di Lorenzo Giuseppe , Altieri Vincenzo , Mariano Angela , Macchia Vincenzo , Di Carlo Angelina 
Published: April 2011

AbstractBACKGROUNDAbout 43% of men with low Gleason grade prostate cancer (PCa) at biopsy will be finally diagnosed with high‐grade PCa at radical prostatectomy (RP). Gleason sum at RP is a good indicator of biochemical recurrence and poor clinical outcome. Therefore, there is a need to improve clinical evaluation of PCa aggressiveness in order to choice appropriate treatment. To this aim an easy‐available tool is represented by circulating biomarkers. Among these, the best candidates are some molecules involved in PCa pathogenesis such as IGFBP‐2 and IGFBP‐3, IL‐6, and its soluble receptor (SIL‐6R).METHODSIn this study, we evaluated the ability of preoperative IGFBP‐2, IGFBP‐3, IL‐6, and SIL‐6R serum levels to predict Gleason score upgrade in 52 PCa patients.RESULTSWe found that IGFBP‐3 median levels were significantly lower in patients who showed Gleason upgrading from biopsy to RP (P = 0.024). We also found an association between biopsy T‐stage and Gleason Upgrade (P = 0.011). Using multivariate logistic regression model, we demonstrated that the association of IGFBP‐3 serum levels together with biopsy T‐stage and biopsy Gleason score was useful to calculate a prognostic risk score. ROC curve analysis of risk score showed a good ability to predict GSU (AUC = 0.81; 95% CI 0.69–0.93).CONCLUSIONSOur results suggest that preoperative IGFBP‐3 circulating levels determination may be useful to predict Gleason score upgrading alone and/or in combination with biopsy T‐stage and biopsy Gleason score. Prostate 72:100–107, 2012. © 2011 Wiley Periodicals, Inc.
Full‐configuration‐interaction study of the metal‐insulator transition in a model system: Hn linear chains n=4, 6,…, 16
Authors: Bendazzoli Gian Luigi , Evangelisti Stefano , Monari Antonio 
Published: April 2011

AbstractThe metal‐insulator transition induced by electron correlation (Mott transition) is studied with ab initio full CI methods in model systems. These are linear chains of equally spaced hydrogen atoms. Different indicators of the metal‐insulator transition (maximum of the localization tensor or of the polarizability) areused and discussed. It is shown that the different indicators give concordant results, and that the transition is associated to a change in electron correlation, measured by the “particle‐hole” symmetric correlation entropy. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem 111:3416–3423, 2011
Unique QM/MM potential energy surface exploration using microiterations
Authors: Melaccio Federico , Olivucci Massimo , Lindh Roland , Ferré Nicolas 
Published: April 2011

AbstractThe determination and the characterization of important points of a potential energy surface can be carried out routinely using any molecular modelling software based on either a quantum mechanical (QM) or a classical (molecular mechanics, MM) description of the particle interactions. However the coupling of the QM and MM descriptions (QM/MM) gives rise to severe efficiency limitations during a geometry optimization of the whole system, especially when both subsystems are coupled electrostatically. This work introduces two simple improvements, mainly developed in the framework of the electrostatic potential fitted method to ensure the uniqueness of the QM/MM potential energy surface. The first one aims to improve the approximate Hessian matrix used in the QM optimization step. The second one tries to recouple electrostatically the QM and MM subsystems when microiterations are used. These methods are tested on a very simple system (a QM water molecule in a MM water box) before to be applied to the investigation of the light absorption in the rhodopsin protein at the multireference second‐order perturbation level of theory (CASPT2). This work is dedicated to the memory of Prof. B. O. Roos. He was a great support for the implementation of the QM/MM method in the Molcas package. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem 111:3339–3346, 2011
How to select active space for multiconfigurational quantum chemistry?
Authors: Veryazov Valera , Malmqvist Per Åke , Roos Björn O. 
Published: April 2011

AbstractBjörn Roos is one of the pioneers in the development and usage of multiconfigurational methods, in particular, the complete active space self‐consistent field method and the perturbational complete active space perturbation theory through second order. To perform multiconfigurational calculations using these methods, a set of active orbitals must be selected, and the success of the methods depends on the choice of this set. This is not only sometimes easy but also sometimes difficult, especially for use of the more recent RASSCF and RASPT2 methods (which use a “restricted active space” rather than the complete one). Although an automated procedure for selecting the active orbitals would be a preferable solution, this does not seem feasible yet. An account of the problem is given, with examples and some approaches that usually work. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem 111:3329–3338, 2011
Electronic spectra of nitroethylene
Authors: Borges Itamar , Barbatti Mario , Aquino Adélia J.A. , Lischka Hans 
Published: April 2011

AbstractA systematic study of the electronic excited states of nitroethylene (C2H3NO2) was carried out using the approximate coupled‐cluster singles‐and‐doubles approach with the resolution of the identity (RI‐CC2), the time dependent density functional theory with the CAMB3LYP functional (TDDFT/CAMB3LYP) and the DFT multireference configuration interaction (DFT/MRCI) method. Vertical transition energies and optical oscillator strengths were computed for a maximum of 20 singlet transitions. Semiclassical simulations of the ultraviolet (UV) spectra were performed at the RI‐CC2 and DFT/MRCI levels. The main features in the UV spectrum were assigned to a weak n‐π* transition, and two higher energy πCC+O‐π* bands. These characteristics are common to molecules containing NO2 groups. Simulated spectra are in good agreement with the experimental spectrum. The energy of the bands in the DFT/MRCI simulation agrees quite well with the experiment, although it overestimates the band intensities. RI‐CC2 produced intensities comparable to the experiment, but the bands were blue shifted. A strong πCC+O‐π* band, not previously measured, was found in the 8–9 eV range. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Interesting periodic variations in physical and chemical properties of homonuclear diatomic molecules
Authors: Kamal C. , Banerjee Arup , Ghanty Tapan K. , Chakrabarti Aparna 
Published: April 2011

AbstractWe carry out a systematic study of various ground state and response properties of homonuclear diatomic molecules (from hydrogen to rubidium, including transition metals) as a function of atomic number of constituent atoms. We perform the ground state and response property calculations by using state of the art density functional theory/time dependent density functional theory. We observe that several properties of homonuclear diatomic molecules show periodic variations along rows and columns of the periodic table. The periodic variations in the ground state properties of diatomic molecules may be explained by the nature and type of the bond that exists between the constituent atoms. Similarly, the periodic variations in the response properties such as static dipole polarizability and strength of the van der Waals interaction between diatomic molecules have been correlated with the variations in metallic/nonmetallic character of the elements along the periodic table. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
General solution of the coulomb–dirac problem: calculation of a divergence‐free lamb shift
Authors: Ritchie Burke 
Published: April 2011

AbstractPaul Dirac's time‐dependent equation is inferred from the scalar product of an electron's four‐momentum and an electromagnetic four‐potential on identifying an electromagnetic carrier‐wave energy with the electron's rest‐mass energy (Maxwell–Dirac equivalency). Dirac's Schroedinger‐like temporally harmonic solution is not the general solution to his time‐dependent equation, because it constrains all four components of his vector wave function to oscillate in time at a single frequency. In fact, it is equivalent to an approximation method known as adiabatic elimination, which is widely used in the optical‐physics literature to solve temporally coupled equations. The general time‐dependent solution for the Coulomb problem includes coupled positive‐ and negative‐energy states whose wave function is a mixture of bound and unbound components. The Maxwell–Dirac equivalency permits the unbound component, which is known as Zitterbewegung in the free‐elecron problem, to be interpreted as a photonic component, which conserves energy for a ground state in which the electron simultaneously occupies two states whose separation is of order 2mc2. Equations of motion for a photon, which are formed from the scalar product of a photon's four‐momentum and an electromagnetic four‐potential, are also presented and used to calculate a divergence‐free Lamb shift. Finally, Dirac's general time‐dependent solution is shown to contain subatomic bound states for the Coulomb problem, even though such states are forbidden in Dirac's standard solution. These states exist for an electron, whose positive‐ (negative‐) energy motion is attractive (repulsive), or for a positron, whose positive‐ (negative‐) energy motion is repulsive (attractive), respectively. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
EVALUATING DAM RE‐OPERATION FOR FRESHWATER CONSERVATION IN THE SUSTAINABLE RIVERS PROJECT
Authors: Konrad C. P. , Warner A. , Higgins J. V. 
Published: April 2011

ABSTRACTSustainable management of global water resources requires changing of dam operations to maintain river, floodplain and estuary ecosystems. Re‐operating dams for ecological objectives must be evaluated rigorously because of the complexity of ecological responses to streamflow, uncertainty in the long‐term and large‐scale conservation impacts on freshwater ecosystems and the foregone environmental or social benefits from other uses of water. Prescribed releases at five demonstration sites in the Sustainable Rivers Project, a partnership between the US Army Corps of Engineers (Corps) and The Nature Conservancy to plan and implement environmental flow prescriptions at Corps dams nationwide, have been evaluated in terms of their immediate and direct ecological outcomes. Advancing dam re‐operation as a freshwater conservation strategy at these and other sites will require additional evidence about longer‐term and broader impacts on biodiversity and ecosystems. A pragmatic framework for monitoring and evaluating dam re‐operation as a conservation strategy includes a balanced assessment of direct responses and long‐term effects, institutional partnerships that can implement monitoring and evaluation at an ecosystem scale and improved reporting of scientific investigations to facilitate long‐term monitoring and cross‐site learning. Copyright © 2011 John Wiley & Sons, Ltd.