bluuebunny/crossref_metadata_2025_split huggingface dataset:
OCT2, SSX and SAGE1 reveal the phenotypic heterogeneity of spermatocytic seminoma reflecting distinct subpopulations of spermatogonia
Authors: Lim Jasmine , Goriely Anne , Turner Gareth DH , Ewen Katherine A , Jacobsen Grete Krag , Graem Niels , Wilkie Andrew OM , Rajpert‐De Meyts Ewa 
Published: April 2011

AbstractSpermatocytic seminoma (SS) is a rare testicular neoplasm that occurs predominantly in older men. In this study, we aimed to shed light on the histogenesis of SS by investigating the developmental expression of protein markers that identify distinct subpopulations of human spermatogonia in the normal adult testis. We analysed the expression pattern of OCT2, SSX2‐4, and SAGE1 in 36 SS cases and four intratubular SS (ISS) as well as a series of normal testis samples throughout development. We describe for the first time two different types of SS characterized by OCT2 or SSX2‐4 immunoexpression. These findings are consistent with the mutually exclusive antigenic profile of these markers during different stages of testicular development and in the normal adult testis. OCT2 was expressed predominantly in Adark spermatogonia, SSX2‐4 was present in Apale and B spermatogonia and leptotene spermatocytes, whilst SAGE1 was exclusively present in a subset of post‐pubertal germ cells, most likely B spermatogonia. The presence of OCT2 and SSX2‐4 in distinct subsets of germ cells implies that these markers represent germ cells at different maturation stages. Analysis of SAGE1 and SSX2‐4 in ISS showed spatial differences suggesting ongoing maturation of germ cells during progression of SS tumourigenesis. We conclude that the expression pattern of OCT2, SSX2‐4, and SAGE1 supports the origin of SS from spermatogonia and provides new evidence for heterogeneity of this tumour, potentially linked either to the cellular origin of SS or to partial differentiation during tumour progression, including a hitherto unknown OCT2‐positive variant of the tumour likely derived from Adark spermatogonia. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
MicroRNAs in colorectal cancer metastasis
Authors: de Krijger Inge , Mekenkamp Leonie JM , Punt Cornelis JA , Nagtegaal Iris D 
Published: April 2011

AbstractMetastatic disease is the major cause of death in colorectal cancer (CRC) patients. The metastatic process is highly inefficient and comprises multiple sequential steps. While many genetic factors relevant in this process have already been identified, the epigenetic factors underlying each step still remain obscure. MicroRNAs (miRNAs) are key regulators in tumourigenesis, but their role in the development of cancer metastasis is poorly investigated. The majority of miRNAs involved in the metastatic process have been identified in breast cancer cell lines, and in CRC less data are available. We review the role of miRNAs in the metastatic pathway of CRC, including escape of apoptosis, epithelial–mesenchymal transition (EMT), angiogenesis, and invasion. Better understanding of the complex role of miRNAs in the development of CRC metastases may provide new insights that could be of therapeutic consequence. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Proteomic analysis of microvesicles derived from human colorectal cancer ascites
Authors: Choi Dong‐Sic , Park Jung Ok , Jang Su Chul , Yoon Yae Jin , Jung Jin Woo , Choi Do‐Young , Kim Jung‐Wook , Kang Ji Seon , Park Jaesung , Hwang Daehee , Lee Kyung‐Hee , Park Sang‐Hyun , Kim Yoon‐Keun , Desiderio Dominic M. , Kim Kwang Pyo , Gho Yong Song 
Published: April 2011

AbstractThe presence of malignant ascites in the peritoneal cavity is a poor prognostic indicator of low survival rate. Various cancer cells, including those of colorectal cancer (CRC), release microvesicles (exosomes) into surrounding tissues and peripheral circulation including malignant ascites. Although recent progress has revealed that microvesicles play multiple roles in tumor progression, the protein composition and the pathological function of malignant ascites‐derived microvesicles are still unknown. Here, we report the first global proteomic analyses of highly purified microvesicles derived from human CRC ascites. With 1‐D SDS‐PAGE and nano‐LC‐MS/MS analyses, we identified a total of 846 microvesicular proteins from ascites of three CRC patients with high confidence; 384 proteins were identified in at least two patients. We identified proteins that might function in tumor progression via disruption of epithelial polarity, migration, invasion, tumor growth, immune modulation, and angiogenesis. Furthermore, we identified several potential diagnostic markers of CRC including colon‐specific surface antigens. Our proteomic analyses will help to elucidate diverse functions of microvesicles in cancer progression and will aid in the development of novel diagnostic tools for CRC.
Damp‐heat degradation and repair of oxide‐passivated silicon
Authors: McIntosh Keith R. , Dai Xi 
Published: April 2011

AbstractSiO2‐passivated Si degrades when exposed to a ‘damp‐heat’ atmosphere of 85% relative humidity and 85 °C. We find the effective surface recombination velocity at the SiO2/Si interface of phosphorus‐diffused (111) Si to increase from 2200 to 11 000 cm/s after 7 days of damp‐heat exposure. This degradation is of concern to many high‐efficiency solar cells, which are manufactured from SiO2‐passivated Si with phosphorus‐diffused (111) facets at the front surface, and which must withstand 1000 h of damp‐heat exposure during reliability testing. Our experiments indicate that the damp‐heat exposure causes (i) absorption of H2O into the SiO2, (ii) an increase in the concentration of H at the SiO2/Si interface, (iii) a latent source of degradation that continues after samples are returned to room conditions, and (iv) SiO2/Si interface damage that can be repaired by a short anneal at 300 °C in N2. The results of these experiments are discussed in relation to the various mechanisms that might underlie damp‐heat degradation of SiO2/Si interfaces.
X‐ray diffraction of cubic Gd2O3/Er under high pressure
Authors: Zou Xu , Gong Chen , Liu Bingbing , Li Quanjun , Li Zepeng , Liu Bo , Liu Ran , Liu Jing , Chen Zhiqiang , Zou Bo , Cui Tian , Bai Xue , Song Hongwei 
Published: April 2011

AbstractIn this paper, we report the in situ high pressure X‐ray diffraction studies on Er3+ doped Gd2O3 in a diamond anvil cell up to 39.8 GPa at room temperature. Several phase transitions have been identified in our studies. The structural transformation from a starting cubic phase to a hexagonal phase occurred during the sample compression process, at 8.57 GPa. And the hexagonal phase was stable from 12.5 GPa up to the highest pressure in this study but was not quenchable and transformed to a monoclinic phase after pressure release. An anomalous high pressure behavior in the hexagonal type Gd2O3 phase was observed, which might be caused by an electron transition influenced by Er3+ ions doping. By fitting the compression data to the Birch–Murnaghan equation of state, the bulk moduli of the cubic and two hexagonal (at p < 19.9 GPa and p > 27.0 GPa) Gd2O3 phases were determined to be 164 ± 3, 185 ± 7, and 150 ± 10 GPa with $B'_{0} = 4$, respectively.
A perspective on the CASPT2 method
Authors: Pulay Peter 
Published: April 2011

AbstractThe CASPT2 method, developed by Roos and coworkers, is reviewed. The rationale for a method that can deal with arbitrary strongly correlated systems at affordable computational cost is presented, and the main milestones in the 20‐year history of CASPT2 are listed. The basic features of the method are summarized. The strengths and weaknesses of CASPT2 are assessed. Its main strength is its ability to deal with arbitrary electronic states at a reasonable computational cost, and giving exact spin states. Its main limitation is that, it is not a black box method, and requires considerable experience to use. Another limitation is that, for accurate results, the active space must be generally larger than the minimum required to describe only the strong (static) correlation. Including dynamical correlation at an earlier stage may resolve some of these issues. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem 111:3273–3279, 2011
Kinetic parameters for the reaction of hydroxyl radical with CH3OCH2F (HFE‐161) in the temperature range of 200–400 K: Transition state theory and Ab initio calculations
Authors: Kaliginedi Veerabhadrarao , Ali Mohamad Akbar , Rajakumar B. 
Published: April 2011

AbstractRate coefficients for the reaction of the hydroxyl radical with CH3OCH2F (HFE‐161) were computed using transition state theory coupled with ab initio methods, viz., MP2, G3MP2, and G3B3 theories in the temperature range of 200–400 K. Structures of the reactants and transition states (TSs) were optimized at MP2(FULL) and B3LYP level of theories with 6‐31G* and 6‐311++G** basis sets. The potential energy surface was scanned at both the level of theories. Five different TSs were identified for each rotamer. Calculations of Intrinsic reaction coordinates were performed to confirm the existence of all the TSs. The kinetic parameters due to all different TSs are reported in this article. The rate coefficients for the title reaction were computed to be k = (9 ± 1.08) × 10−13 exp [−(1,713 ± 33)/T] cm3 molecule−1 s−1 at MP2, k = (7.36 ± 0.42) × 10−13 exp [−(198 ± 16)/T] cm3 molecule−1 s−1 at G3MP2 and k = (5.36 ± 1.57) × 10−13 exp [−(412 ± 81)/T] cm3 molecule−1 s−1 at G3B3 theories. The atmospheric lifetimes of CH3OCH2F at MP2, G3MP2, and G3B3 level of theories were estimated to be 20, 0.1, and 0.3 years, respectively. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
On the role of the triplet state in the cis/trans isomerization of rhodopsin: A CASPT2//CASSCF study of a model chromophore
Authors: González‐Luque Remedios , Olaso‐González Gloria , Merchán Manuela , Coto Pedro B. , Serrano‐Andrés Luis , Garavelli Marco 
Published: April 2011

AbstractThe possibility of population of the lowest‐lying triplet state (T1) in the early events of the photochemical isomerization process of a model chromophore of Rhodopsin (Rh) has been analyzed using multireference perturbation theory (CASPT2//CASSCF) methods. It is shown that the characteristics of the isomerization process namely small S1−T1 gap, presence of hydrogen out of plane active vibrational modes, and existence of a dense manifold of vibrational states, render possible the fulfilment of the conditions needed for the population of T1. The possible consequences for the photochemistry and photophysics of Rh are also discussed. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem 111:3431–3437, 2011
π‐electron currents in polycyclic conjugated hydrocarbons: Coronene and its isomers having five and seven member rings
Authors: Randić Milan , Novič Marjana , Vračko Marjan , Vukičević Damir , Plavšić Dejan 
Published: April 2011

AbstractWe have outlined novel graph theoretical model for computing π‐electron currents in π‐electron polycyclic conjugated hydrocarbons. We start with Kekulé valence structures of a polycyclic conjugated hydrocarbon and their conjugated circuits. To each 4n+2 conjugated circuits we assign counter clockwise current i and to each 4n conjugated circuit we assign clockwise current i. By adding the contributions from all conjugated circuits in a single Kekulé valence structure one obtains π‐electron current pattern for the particular Kekulé valence structure. By adding the conjugated circuit currents in all Kekulé valence structure one obtains the pattern of π‐electron currents for considered molecule. We report here π‐electron current patters for coronene and 17 its isomers, which have been recently considered by Balaban et al., obtained by replacing one or more pairs of peripheral benzene rings with five and seven member rings. Our results are compared with their reported π‐electron current density patters computed by ab initio molecular orbital (MO) computations and satisfactory parallelism is found between two so disparate approaches. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
DFT and MP2 study of isomery scheme in Formazan and intermolecular and intramolecular proton transfer between its tautomers
Authors: Tavakol Hossein 
Published: April 2011

AbstractDFT and Moller Plesset (MP2) calculations were applied to study of isomery scheme in formazan. Formazan that can be presented by three tautomers and eight isomers has various applications in dyes, complexes, and biochemistry. The structures of its isomers and related transition states were optimized, and important molecular parameters, IR frequencies, and energetic results were extracted. The relative stabilities of formazan isomers in the gas phase were found to be as 1EZ >1ZZ >1EE >1ZE >2EE > 3 >2EZ >2ZZ >TS1 >TS3 >TS2. Thermodynamic data confirms that tautomer 1 is major tautomer, and all possible tautomerism interconversions have small rates at room temperature. Then, relative stabilities were calculated in different solvents (chloroform, tetrahydrofuran, acetone, and water). The relative stabilities and thermodynamic data in solvents are nearly similar to those in the gas phase, but the rate constants are slightly more than that in the gas phase. Moreover, relative stabilities of formazan isomers and intermolecular proton transfer in presence of one to three molecules of water have been studied. The results showed that activation barriers in water‐assisted tautomerisms are in general lower than those in the gas phase, but the relative energies of isomers do not change importantly by water clusters. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
24 IPR isomers of fullerene C84: Cage deformation as geometrical characteristic of local strains
Authors: Khamatgalimov Ayrat R. , Kovalenko Valeri I. 
Published: April 2011

AbstractThe structures of 24 IPR‐isomers of C84 fullerene with distributed single, double and delocalized bonds are presented. Obtained results are fully supported by DFT quantum‐chemical calculations of electronic and geometrical structures of these isomers. Two reasons of instability of fullerene molecules are their radical origin and/or high local strain. Distortion of pentagons as well as hexagons with alternating single and double bonds is the most significant geometrical parameter reflecting local strain of a molecule. These distortions are measured as maximal dihedral angles of those cycles and reach 20 degrees in mostly deformed hexagons and pentagons. In contrast high values of dihedral angles in hexagons with delocalized π‐bonds are typical for stable isomers. Other geometric parameters such as valence angles, sums of valence angles and dihedral angles between approximate planes of fused rings have no marked influence on stability. The development of strain‐related criteria for fullerene stability will be helpful in the prediction which isomers might potentially be observable in experiment. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
ABIOTIC & BIOTIC RESPONSES OF THE COLORADO RIVER TO CONTROLLED FLOODS AT GLEN CANYON DAM, ARIZONA, USA
Authors: Melis T.S. , Korman J. , Kennedy T.A. 
Published: April 2011

ABSTRACTClosure of Glen Canyon Dam reduced sand supply to the Colorado River in Grand Canyon National Park by about 94% while its operation has also eroded the park's sandbar habitats. Three controlled floods released from the dam since 1995 suggest that sandbars might be rebuilt and maintained, but only if repeated floods are timed to follow tributary sand deliveries below the dam. Monitoring data show that sandbars are dynamic and that their erosion after bar building is positively related with mean daily discharge and negatively related with tributary sand production after controlled floods. The March 2008 flood affected non‐native rainbow trout abundance in the Lees Ferry tailwater, which supports a blue ribbon fishery. Downstream trout dispersal from the tailwater results in negative competitive interactions and predation on endangered humpback chub. Early survival rates of age‐0 trout increased more than fourfold following the 2008 flood, and twofold in 2009, relative to prior years (2006–2007). Hatch‐date analysis indicated that early survival rates were much higher for cohorts that emerged about 2 months after the 2008 flood relative to cohorts that emerged earlier that year. The 2009 survival data suggest that tailwater habitat improvements persisted for at least a year, but apparently decreased in 2010. Increased early survival rates for trout coincided with the increased availability of higher quality drifting food items after the 2008 flood owing to an increase in midges and black flies, preferred food items of rainbow trout. Repeated floods from the dam might sustainably rebuild and maintain sandbars if released when new tributary sand is available below the tailwater. Spring flooding might also sustain increased trout abundance and benefit the tailwater fishery, but also be a potential risk to humpback chub in Grand Canyon. Copyright © 2011 John Wiley & Sons, Ltd.
EMERGENT SANDBAR CONSTRUCTION FOR LEAST TERNS ON THE MISSOURI RIVER: EFFECTS ON FORAGE FISHES IN SHALLOW‐WATER HABITATS
Authors: Stucker J. H. , Buhl D. A. , Sherfy M. H. 
Published: April 2011

ABSTRACTEmergent sandbars on the Missouri River are actively managed for two listed bird species, piping plovers and interior least terns. As a plunge‐diving piscivore, endangered least terns rely on ready access to appropriately sized slender‐bodied fish: <52 mm total length for adults and <34 mm total length for young chicks. As part of a multi‐agency recovery programme, aimed at enhancing nesting habitat for plovers and terns, the U.S. Army Corps of Engineers mechanically created several emergent sandbars on the Missouri River. However, it was unknown whether sandbar construction is a benefit or a detriment to forage abundance for least terns. Therefore, we studied the shallow‐water (<1.5 m) fish community near river and mechanically created emergent sandbars during three nesting seasons (2006–2008). We sampled every 2 weeks each year from late May to July within 15–16 areas to document the relative abundance, species richness and size classes of fish. Fish relative abundance was negatively related to depth. Catches were dominated by schooling species, including emerald shiner, sand shiner, spotfin shiner and bigmouth buffalo. Significant inter‐annual differences in relative abundance were observed, with generally increasing trends in intra‐seasonal relative abundance of shiners and the smallest size classes of fish (<34 mm). Significant differences in the fish communities between the sandbar types were not detected in this study. Results suggest that mechanical sandbar habitats host comparable fish communities at similar levels of relative abundance. Further analyses are required to evaluate if the levels of fish relative abundance are adequate to support least tern foraging and reproduction. Published in 2011 by John Wiley & Sons, Ltd.
Application of the continual reassessment method to a phase I dose‐finding trial in Japanese patients: East meets West
Authors: Morita Satoshi 
Published: April 2011

AbstractAfter cancer‐related phase I dose‐finding trials are completed in Western countries, further phase I trials are often conducted to determine recommended doses (RDS) for Japanese patients. This may be due to concerns about possible differences in treatment tolerability between Caucasians and Japanese. In most of these, a conventional ‘3 +3’ cohort study design is used in making dose escalation decisions, possibly due to its relatively easy implementation. Since its proposal by O'Quigleybiet al. (1990; Biometrics, 46:33–48), the continual reassessment method (CRM) has been used increasingly in cancer‐related phase I dose‐finding studies as an alternative to ‘3 +3’ designs. One of the principal advantages of applying a Bayesian CRM may be the utilization of all available prior information to estimate RDS through prior distributions that are assumed for model parameters representing the dose–toxicity relationship. In this paper, we present an application of the Bayesian CRM to a phase I dose‐finding study in Japanese patients with advanced breast cancer using an informative prior elicited from clinical investigators. In some settings, it may be appropriate to use an informative prior that reflects the accurate and comprehensive previous knowledge of clinical investigators. On the other hand, for a model‐based Bayesian outcome‐adaptive clinical trial, it is necessary to establish sufficiently vague priors so that accumulating data dominate decisions as the amount of observed data increases. Thus, we retrospectively investigated the relative strength of the prior using a recently proposed method to compute a prior effective sample size. Copyright © 2011 John Wiley & Sons, Ltd.
Evaluating regional vulnerability to climate change: purposes and methods
Authors: Malone Elizabeth L. , Engle Nathan L. 
Published: April 2011

AbstractAs the emphasis in climate change research, international negotiations, and developing‐country activities has shifted from mitigation to adaptation, vulnerability has emerged as a bridge between impacts on one side and the need for adaptive changes on the other. Still, the term vulnerability remains , its meaning changing with the scale, focus, and purpose of each assessment. Understanding regional vulnerability has advanced over the past several decades, with studies using a combination of indicators, case studies and analogs, stakeholder‐driven processes, and scenario‐building methodologies. As regions become increasingly relevant scales of inquiry for bridging the aggregate and local, for every analysis, it is perhaps most appropriate to ask three ‘what’ questions: ‘What/who is vulnerable?’, ‘What is vulnerability?’, and ‘Vulnerable to what?’ The answers to these questions will yield different definitions of vulnerability as well as different methods for assessing it. Vulnerability research that is primarily quantitative has been dominated by the use of indicators. Regional vulnerability research can also focus on or include stakeholder involvement processes, especially helpful in generating agreement on issues and understanding context‐specific aspects of vulnerability and prospective adaptations. Creating scenarios is another increasingly useful method that helps researchers, policymakers, and other stakeholders think about the future and plan options for alternative futures. Current research efforts are emphasizing stakeholder involvement, with a dual focus on vulnerability assessment and social learning in the process; and scenario analyses, which may be expert‐defined or stakeholder‐driven. Both tend to span impacts, vulnerability, and adaptation decision making for a particular place and conditions. WIREs Clim Change 2011 2 462–474 DOI: 10.1002/wcc.116This article is categorized under:

Assessing Impacts of Climate Change > Evaluating Future Impacts of Climate Change
Evaluation of the elastic properties of a functionally‐graded coating from the indentation measurements
Authors: Aizikovich S. , Krenev L. , Sevostianov I. , Trubchik I. , Evich L. 
Published: April 2011

AbstractThe paper focuses on the development of a mathematical model connecting penetration profile of a rigid circular indenter with elastic properties of a functionally graded coating (FGC). We introduce the concept of stiffness function dependent on the radius of the contact zone for FGC coupled with a homogeneous half‐space. This approach allows one to determine the properties variation across the coating. Several most typical numerical examples are discussed in detail to illustrate effect of the Young's modulus variation on the stiffness function. These examples also show that the proposed methodology allows one to identify and experimentally distinguish between different types of variation of FGC elastic properties.