bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural and thermodynamic analysis of the GFP:GFP‐nanobody complex
Authors: Kubala Marta H. , Kovtun Oleksiy , Alexandrov Kirill , Collins Brett M. 
Published: October 2010

AbstractThe green fluorescent protein (GFP)‐nanobody is a single‐chain VHH antibody domain developed with specific binding activity against GFP and is emerging as a powerful tool for isolation and cellular engineering of fluorescent protein fusions in many different fields of biological research. Using X‐ray crystallography and isothermal titration calorimetry, we determine the molecular details of GFP:GFP‐nanobody complex formation and explain the basis of high affinity and at the same time high specificity of protein binding. Although the GFP‐nanobody can also bind YFP, it cannot bind the closely related CFP or other fluorescent proteins from the mFruit series. CFP differs from GFP only within the central chromophore and at one surface amino acid position, which lies in the binding interface. Using this information, we have engineered a CFP variant (I146N) that is also able to bind the GFP‐nanobody with high affinity, thus extending the toolbox of genetically encoded fluorescent probes that can be isolated using the GFP‐nanobody.
Androgen hypersensitivity in prostate cancer: Molecular perspectives on androgen deprivation therapy strategies
Authors: Foley Ruth , Marignol Laure , Keane John P. , Lynch Thomas H. , Hollywood Donal 
Published: October 2010

AbstractAndrogen deprivation therapy is initially successful in treating advanced prostate cancer. However, after a period of time tumors inevitably recur. Improved understanding of the various biochemical causes of resistance to hormonal therapy is of crucial importance for developing more effective therapeutic strategies in this cohort of patients. This review discusses the preclinical evidence for androgen hypersensitivity (AH), as a mechanism by which tumors become hormone‐refractory (HR). We propose that the growth of some such tumors may be not only stimulated by, but also dependent on low hormone levels, and furthermore, that normal hormone concentrations can have an inhibitory effect on growth. The incidence and importance of AH merits further investigation both in preclinical studies and during clinical trials of intermittent androgen withdrawal or testosterone replacement. We suggest that a subset of HR prostate cancer patients who have androgen‐hypersensitive tumors could be particularly amenable to these treatments. Finally, potential approaches for developing biomarkers to identify such patients are explored. Prostate 77:550–557, 2011. © 2010 Wiley‐Liss, Inc.
Effective targeting of prostate cancer by lymphocytes redirected by a PSMA × CD3 bispecific single‐chain diabody
Authors: Fortmüller Kerstin , Alt Karen , Gierschner Dorothee , Wolf Philipp , Baum Volker , Freudenberg Nikolaus , Wetterauer Ulrich , Elsässer‐Beile Ursula , Bühler Patrick 
Published: October 2010

AbstractBACKGROUNDFor redirecting T‐lymphocytes to induce prostate cancer cell lysis, we constructed a novel bispecific single‐chain (bsc) diabody directed to the prostate specific membrane antigen (PSMA) and the T‐cell receptor (TCR)‐associated CD3 molecule on T‐cells.METHODSThe PSMA × CD3 bsc diabody was generated from an anti‐CD3 single chain Fv fragment (scFv) and the anti‐PSMA scFv D7. It was expressed in E. coli and purified from the periplasmic extract and culture supernatant by immobilized metal affinity chromatography (IMAC). The binding properties were tested on PSMA‐expressing prostate cancer cells and PSMA‐negative cell lines as well as on Jurkat cells by flow cytometry. For in vitro functional analysis, a cell viability test (WST‐1) was used and activation of T‐cells was determined by measuring the surface marker expression of CD25 and CD69. For in vivo evaluation, the diabody was administered in combination with human peripheral blood lymphocytes (Ly) in a C4‐2 xenograft‐SCID mouse model.RESULTSSpecific binding of the PSMA × CD3 bsc diabody both to CD3‐positive Jurkat cells and PSMA‐expressing C4‐2 cells was shown by flow cytometry. In vitro, the PSMA × CD3 bsc diabody proved to be a potent agent for retargeting CD4+ and CD8+ human lymphocytes to lyse C4‐2 prostate cancer cells. Treatment of SCID mice bearing C4‐2 tumor xenografts with the diabody and human lymphocytes efficiently inhibited tumor growth.CONCLUSIONSThe PSMA × CD3 bsc diabody bears a high potential for the immunotherapy of prostate cancer. Prostate 71:588–596, 2011. © 2010 Wiley‐Liss, Inc.
Internal prostatic architecture on transrectal ultrasonography predicts future prostatic growth: Natural history of prostatic hyperplasia in a 15‐year longitudinal community‐based study
Authors: Fukuta Fumimasa , Masumori Naoya , Mori Mitsuru , Tsukamoto Taiji 
Published: October 2010

AbstractBACKGROUNDFrom 1992 to 1993, we conducted a cross‐sectional community‐based study to clarify the prevalence of benign prostatic hyperplasia in Japanese men aged 40–79. Based on the results, we hypothesized that the internal prostatic architecture (IPA) on transrectal ultrasonography (TRUS) would predict future prostatic growth. We investigated the changes in prostate volume (PV) over time and validated our hypothesis on predictors for future prostatic growth.METHODSOf 319 participants in the initial study, the PV of 104 men was evaluated by TRUS with approximately a 15‐year follow‐up in the current study. We categorized prostates into three groups based on the IPA: group 1, invisible transition zone (TZ); group 2, visible TZ with an unclear border; and group 3, visible TZ with a clear border.RESULTSOverall PV significantly increased from 17.4 ml to 23.9 ml (P < 0.001). The median PV changes by age decade (40s, 50s, 60s, and 70s) were 5.5, 5.6, 8.6, and 11.1 ml, respectively. Those by baseline PV <20 ml, 20–25 ml, and ≥25 ml were 5.3, 9.8, and 14.7 ml, respectively. Those by baseline IPA for group 1, group 2, and group 3 were 4.7, 6.5, and 17.3 ml, respectively. Multiple linear regression analysis indicated that PV (P = 0.027) and the IPA (P < 0.001) at baseline were independent predictors for future prostatic growth.CONCLUSIONSThis was the first study by longitudinal community‐based study that the PV in Japanese men increased during 15 years. The IPA on TRUS is useful for predicting future prostatic growth. Prostate 71:597–603, 2011. © 2010 Wiley‐Liss, Inc.
Androgen regulation of micro‐RNAs in prostate cancer
Authors: Waltering Kati K. , Porkka Kati P. , Jalava Sanni E. , Urbanucci Alfonso , Kohonen Pekka J. , Latonen Leena M. , Kallioniemi Olli P. , Jenster Guido , Visakorpi Tapio 
Published: October 2010

AbstractBACKGROUNDAndrogens play a critical role in the growth of both androgen dependent and castration‐resistant prostate cancer (CRPC). Only a few micro‐RNAs (miRNAs) have been suggested to be androgen regulated. We aim to identify androgen regulated miRNAs.METHODSWe utilized LNCaP derived model, we have established, and which overexpresses the androgen receptor (AR), the VCaP cell line, and 13 intact‐castrated prostate cancer (PC) xenograft pairs, as well as clinical specimens of untreated (PC) and CRPC. The expression of miRNAs was analyzed by microarrays and quantitative RT‐PCR (Q‐RT‐PCR). Transfection of pre‐miR‐141 and anti‐miR‐141 was also used.RESULTSSeventeen miRNAs were >1.5‐fold up‐ or downregulated upon dihydrotestosterone (DHT) treatment in the cell lines, and 42 after castration in the AR‐positive xenografts. Only four miRNAs (miR‐10a, miR‐141, miR‐150*, and miR‐1225‐5p) showed similar androgen regulation in both cell lines and xenografts. Of those, miR‐141 was found to be expressed more in PC and CRPC compared to benign prostate hyperplasia. Additionally, the overexpression of miR‐141 enhanced growth of parental LNCaP cells while inhibition of miR‐141 by anti‐miR‐141 suppressed the growth of the LNCaP subline overexpressing AR.CONCLUSIONSOnly a few miRNAs were found to be androgen‐regulated in both cell lines and xenografts models. Of those, the expression of miR‐141 was upregulated in cancer. The ectopic overexpression of miR‐141 increased growth of LNCaP cell suggesting it may contribute to the progression of PC. Prostate 71:604–614, 2011. © 2010 Wiley‐Liss, Inc.
A role for class 3 semaphorins in prostate cancer
Authors: Blanc V. , Nariculam J. , Munson P. , Freeman A. , Klocker H. , Masters J. , Williamson M. 
Published: October 2010

AbstractBACKGROUNDClass 3 semaphorins are secreted proteins that act as guidance cues for migrating cells via their transmembrane receptors plexins and neuropilins. Semaphorins have a role in cancer affecting tumor progression both directly, and indirectly by affecting angiogenesis.METHODSThe expression of semaphorins and their receptors in prostate cancer cell lines and tissue was determined by RT‐PCR, Western blotting and immunohistochemistry. The effect of Sema3E on prostate cancer cell lines was determined by adhesion assays and transwell migration assays.RESULTSSemaphorins and their receptors, plexins and neuropilins, are widely co‐expressed in prostate cancer cell lines and tissue with a significant overexpression of Sema3E in tumor tissue. Sema3E affected integrin‐mediated adhesion to fibronectin of prostate cancer cells, and inhibited their motility. Expression of Sema3C was upregulated and Sema3A and Sema3E were down regulated in prostate cells by hypoxia, consistent with an additional role for Sema3A and 3E as anti‐angiogenic factors in prostate cancer.CONCLUSIONSSemaphorin 3E is aberrantly expressed in prostate cancer and affects adhesion and motility of prostate cancer cells, indicating a role for the Sema3E/PlexinD1 signaling pathway in prostate cancer and identifying a new possible target for therapy. Prostate 71:649–658, 2011. © 2010 Wiley‐Liss, Inc.
Use of irinotecan for treatment of small cell carcinoma of the prostate
Authors: Tung Wei‐Lin , Wang Yuwei , Gout Peter W. , Liu Dean‐Mo , Gleave Martin , Wang Yuzhuo 
Published: October 2010

AbstractBACKGROUNDProstatic small cell carcinoma (SCC) is a rare variant of prostate cancer. It is extremely aggressive and resistant to available therapies with a median survival range of 5–17 months. No standard chemotherapeutic regimen has been established for its treatment. In search of a new therapeutic approach, we examined the response of patient‐derived prostatic SCC tissue xenografts to irinotecan, a topoisomerase I inhibitor.METHODSA tumor tissue line was established from a patient's prostatic SCC by subrenal capsule grafting using NOD‐SCID mice. Mice carrying subcutaneous transplants of the tumor line were then treated for 2 weeks with irinotecan alone and in combination with cisplatin. The effect on tumor volume, histopathology, and apoptosis were determined.RESULTSThe prostatic SCC tissue line resembled the donor tissue in morphologic and immunohistochemical features. Irinotecan (20 mg/kg/day; days 1–3, 8–10) completely arrested xenograft growth with a small reduction in tumor volume and only minor weight loss of the hosts (7%); irinotecan (12 mg/kg; same schedule) + cisplatin (2.5 mg/kg/day; days 1 and 8) had a similar effect, but with lower weight loss. While the growth inhibition involved apoptosis, it was also associated with a marked increase in autophagy.CONCLUSIONSTumor tissue lines established via subrenal capsule xenografting provide models with clinical relevance and the present study suggests that irinotecan could be useful for therapy of refractory prostatic SCC, in particular in combination with cisplatin. Prostate 71:675–681, 2011. © 2010 Wiley‐Liss, Inc.
Kondo‐like resonance in ZnO:Eu
Authors: Blanca‐Romero A. , Berrondo M. , Rivas‐Silva J. F. 
Published: October 2010

AbstractDoping ZnO with Eu results in the hybridization of the f atomic orbitals of the Eu with the bands of the host material. The strongest interaction turns out to be with the oxygen s‐p band. This hybridization manifests itself as a Kondo‐like resonance, namely, the appearance of a narrow resonant f band close to the Fermi level. Our aim in the present work is to calculate the electronic structure of ZnO:Eu in which the lanthanide ion replaces one of the Zn ions inducing a geometric relaxation on the system. We have used two reliable crystal electronic structure codes for our calculation. The program WIEN2k [Blaha, P., et al. WIEN2k, An Augmented Plane Wave + Local Orbitals Program for Calculating Crystal Properties, 2001] allows us to include the effects of the f the GGA + U model (generalized gradient approximation plus U) for the relaxed configuration. On the other hand, the program CRYSTAL06 [http://www.crystal.unito.it/] allows us to monitor the charge of the Eu ion using a judicious mix of the Hartree‐Fock nonlocal exchange term with the density functional exchange‐correlation potential. Results are presented for the density of states (both the total and the partial contribution from the f electrons), as well as maps of the spin density around the Eu ion, both clearly showing the presence of the resonant f bands. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Intrinsic minimal atomic basis representation of molecular electronic wavefunctions
Authors: Laikov Dimitri N. 
Published: October 2010

AbstractThe problem of finding an effective minimal atomic basis that spans the exact occupied wavefunctions of a mean‐field theory at a given molecular geometry, which has a number of special properties, is studied and a new general procedure is developed that (1) solves for a raw minimal set of strongly atom‐centered functions—products of spherical harmonics and molecule‐optimized radial parts—that approximately span the occupied molecular wavefunctions and minimize the sum of their energies, (2) uses projection operators to get a new set of deformed atom‐centered functions that exactly span the occupied space and fall into core and valence subsets, (3) applies a new zero‐bond‐dipole orthogonalization scheme to the core‐orthogonalized valence subset so that for each two‐center product of these functions the projection of its dipole moment along the line going through the two centers is zero. The resulting effective minimal atomic basis is intrinsic to the molecular problem and does not need a free‐atoms input. Some interesting features of the zero‐bond‐dipole orthogonalization are showing up in the atomic population analysis of a diverse set of molecules. The new procedure may be useful for the interpretation of electronic structure, for the construction of model Hamiltonians in terms of transferable molecular integrals, and for the definition of active valence space in the treatment of electron correlation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
The quantum theory of atoms in positronic molecules: A case study on diatomic species
Authors: Goli Mohammad , Shahbazian Shant 
Published: October 2010

AbstractThis article presents the first systematic study of a series of diatomic positronic species using the recently proposed regional approach: the quantum theory of atoms in positronic molecules (QTAIPM). This survey includes the LiH,e+, NaH,e+, LiF,e+, NaF,e+, BeO,e+, MgO,e+, CN−,e+, and OH−,e+species as typical examples. The computational algorithm of the whole analysis is communicated and reviewed in detail. The topological analysis of the joint density distribution reveals topological structures similar to those observed for the purely electronic systems; that is, each system decomposes into two quantum atoms. By considering some of the regional properties of these quantum atoms, it is demonstrated that the positron affects them seriously through two different mechanisms: direct and indirect contributions, the latter refers to electronic and geometric relaxations. The computational results clearly reveal the fact that the regional properties of the quantum atoms of positronic molecules are not deducible from their purely electronic counterparts; thus, an independent analysis is required for each positronic molecule. The positronic population is considered as a typical regional property showing that the attachment of a positron to a purely electronic system enhances the polarization of the electronic distribution. The concept of regional positron affinities is also introduced and discussed as a nonroutine application of the QTAIPM. The results of this article set the stage for further study on the quantum atoms of polyatomic positronic species. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Possibility of proton passage through all metal aromatic Al42− ring in HAl4−
Authors: Satpati Priyadarshi 
Published: October 2010

AbstractWe report theoretical investigations on HAl in which the proton can move through the Al ring similar to umbrella inversion. The potential energy for the motion is a double well, with an activation barrier of 4.45 kcal/mol. We find that excitation to v = 6 vibrational levels should lead to easy passage of H+ through the ring. After considering the tunnelling effect, inversion rate at 298 K is calculated using transition state theory and is found to be 1.3 × 1010/s−1. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Reference ranges for Doppler assessment of uterine artery resistance and pulsatility indices in dichorionic twin pregnancies
Authors: Geipel A. , Hennemann F. , Fimmers R. , Willruth A. , Lato K. , Gembruch U. , Berg C. 
Published: October 2010

AbstractObjectivesTo construct reference ranges of uterine artery Doppler parameters against gestation in twin pregnancies and to present charts of the pulsatility index (PI) and resistance index (RI) for clinical use.MethodsThis was an observational study of the uterine circulation in 557 women with dichorionic twin pregnancies at 17–38 weeks' gestation. Uterine artery measurements were performed by color and pulsed Doppler imaging. The uterine artery PI and RI were calculated as a mean of both sides. Reference ranges were constructed by regression of each index on gestational age. For this purpose, a regression model with fractional polynomials was fitted to the data. Furthermore, the presence of uterine artery notching was recorded.ResultsNew reference curves and tables of percentiles of the uterine artery PI and RI are presented. The calculated indices both showed a significant decrease with gestational age. Compared with singleton values, mean twin PI values were lower during the whole course of pregnancy. The prevalence of bilateral notching was 4.6% at 17–19 weeks' gestation and 3.1% at 20–24 weeks.ConclusionsUterine artery Doppler indices in twin pregnancies are lower than in singleton pregnancies. Therefore, the use of uterine artery reference ranges adapted to twin gestations seems more appropriate for identifying low‐ and high‐risk groups. Copyright © 2011 ISUOG. Published by John Wiley & Sons, Ltd.
Linking energy and climate (before 1974)
Authors: Shulman Peter A. 
Published: October 2010

AbstractEstablishing a link between the consumption of fossil fuels and global climate change has depended both on scientific research as well as assumptions about the pace of social change, technological innovation, and economic growth. Late 19th century research into the role of carbon dioxide and climate focused on explaining the historical cooling of the ice ages; consideration of future warming as a result of energy use remained theoretical and focused on benefits centuries away. After declining scientific interest in the carbon dioxide theory in the early 20th century, it was revived again in the late 1930s, gradually stimulating further research that led to a more sophisticated understanding of the global carbon cycle and prospects for future warming. This research began incorporating more realistic expectations of future energy growth. In the early 1970s, scientists, politicians, and the general public began paying more attention to research into anthropogenic climate change, in part due to a renewed attention to the social costs of energy systems alongside a growing focus on global environmental issues. Future historical research into energy and climate change should examine the role of predictions and expectations of social change in shaping the agenda of scientific research.WIREs Clim Change2010 1 773–780 DOI: 10.1002/wcc.78This article is categorized under:Climate, History, Society, Culture > Technological Aspects and Ideas
Addressing sustainable development and climate change together using sustainomics
Authors: Munasinghe Mohan 
Published: October 2010

AbstractThis paper seeks to practically address two major global challenges—sustainable development and climate change. Developmental problems such as poverty are already formidable. Climate change is the ultimate risk multiplier, exacerbating the other crises too. Its worst impacts fall on the poor who are least responsible for the problem. The world currently faces multiple economic, social, and environmental threats. The economic collapse is the most urgent. The social crisis arises from global poverty, inequity, and inappropriate governance. Finally, mankind has caused severe environmental damage, including climate change. Present trends could destabilize global society. The way forward requires better use of economic stimulus packages to support green investments, social safety nets, and better price policies. A long‐term vision goes beyond our current focus on surface level indicators. Instead, deeper issues need to be addressed systematically by focusing on both the immediate drivers and underlying pressures. The most effective approach is to integrate climate change policies into national sustainable development strategy, using the sustainomics framework. First is the practical, step‐by‐step approach of ‘making development more sustainable’ (MDMS). Second, we need a balanced and integrated analysis from three main perspectives: social, economic, and environmental. Third, the analysis must transcend conventional boundaries imposed by values, discipline, space, time, stakeholder viewpoints, and operationality. Finally, sustainomics provides many practical tools. This approach is applied globally to reconcile climate change risk management and development aspirations. Some practical national level applications are also described involving integration of adaptation and mitigation policies into sustainable development strategy. Specific cases include macroeconomic policy adjustment, sustainable pricing policies, renewable energy projects, and climate impacts on food security, agriculture, and water. Although the issues are complex and serious, both the climate change and sustainable development problems could be solved together, provided we begin immediately. WIREs Clim Change 2011 2 7–18 DOI: 10.1002/wcc.86This article is categorized under:

Climate and Development > Social Justice and the Politics of Development
Pseudogrand tour
Authors: Moustafa Rida E. 
Published: October 2010

AbstractThe pseudogrand tour (PGT) is an approximate version of the grand tour (GT), and an example of the dynamic data visualization methods that assist in exploring hyperdimensional data through a continuous sequence of lower dimensional projections. The PGT adds the time dimensionality to the visualization process which in turn increases the human interaction with the data and reveals comprehensive views of the data. The PGT has some clear advantage suitable for the dynamic data visualization—such as the fast and easy computation, can be constructed using many orthogonal bases (interpolation functions), and the flexibility to visualize the projections as a sequence of scatterplot frames changing over time or a static profile plots of interpolated projections. This article focuses on the implementations of the PGT, the use of interpolation functions, the extensions to higher dimensions, and the scalability to large data points. WIREs Comp Stat 2010 2 711–718 DOI: 10.1002/wics.133This article is categorized under:

Statistical Learning and Exploratory Methods of the Data Sciences > Exploratory Data Analysis
Statistical and Graphical Methods of Data Analysis > Statistical Graphics and Visualization