bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Germ Cell Gene TDRD1 as an ERG Target Gene and a Novel Prostate Cancer Biomarker
Authors: Xiao Lijuan , Lanz Rainer B. , Frolov Anna , Castro Patricia D. , Zhang Zheng , Dong Baijun , Xue Wei , Jung Sung Yun , Lydon John P. , Edwards Dean P. , Mancini Michael A. , Feng Qin , Ittmann Michael M. , He Bin 
Published: June 2016

BACKGROUNDTMPRSS2‐ERG fusion occurs in about half of prostate cancers and results in over‐expression of the oncogenic ERG protein in the prostate. The mechanism by which ERG contributes to prostate cancer initiation and progression remains largely unknown. Because ERG is a transcriptional activator, we reasoned that the target genes regulated by ERG could contribute to prostate cancer development.METHODSIn a search for ERG target genes, we took advantage of published datasets from the MSKCC Prostate Oncogene Project, in which a comprehensive analysis was applied to define transcriptomes in 150 prostate tumors. We retrieved the mRNA expression dataset, split them based on ERG expression, and identified genes whose expression levels are associated with ERG mRNA levels.RESULTSmRNA expression levels of 21 genes were found to be significantly increased, while for one gene it was decreased in ERG‐positive prostate tumors. Among them, the expression of TDRD1 was the most significantly increased in ERG‐positive tumors. Among 131 primary prostate tumors which were primarily from European American patients, TDRD1 is over‐expressed in 68% of samples, while ERG is overexpressed in 48% of samples, suggesting an additional ERG‐independent mechanism of TDRD1 overexpression. In African American prostate tumors, TDRD1 mRNA is expressed in 44%, while ERG is expressed in 24% of samples. In normal tissues, TDRD1 mRNA is exclusively expressed in germ cells and its protein is also known as cancer/testis antigen 41.1 (CT41.1). We generated a mouse monoclonal antibody that recognizes human TDRD1 protein with high specificity and sensitivity. By Western blot analysis and immunohistochemistry (IHC) staining, we demonstrate that TDRD1 protein is expressed in the majority of human prostate tumors, but not in normal prostate tissue. Finally, TDRD1 is not induced in the prostate of ERG overexpression transgenic mice, suggesting that such model does not fully recapitulate the TMPRSS2/ERG fusion‐dependent human prostate cancer development.CONCLUSIONSOur results suggest TDRD1 as a novel prostate cancer biomarker. As an ERG target gene, TDRD1 might play an important role in human prostate cancer development, and as a cancer/testis antigen, TDRD1 might have long‐term potential to be a therapeutic target for prostate cancer immunotherapy. Prostate 76:1271–1284, 2016. © 2016 Wiley Periodicals, Inc.
A Novel System for Estimating Residual Disease and Pathologic Response to Neoadjuvant Treatment of Prostate Cancer
Authors: Murphy Claire , True Lawrence , Vakar‐Lopez Funda , Xia Jing , Gulati Roman , Montgomery Bruce , Tretiakova Maria 
Published: June 2016

BACKGROUNDPathologic variables that characterize response of prostate carcinoma to current neoadjuvant therapy have not been characterized in detail. This study reports (i) the histological features of prostate cancer treated with abiraterone and enzalutamide and inter‐pathologist variance in identifying these features, and (ii) the effect of the novel androgen deprivation agents on residual cancer volume.METHODSWe reviewed sections of prostatectomies from 37 patients treated with neoadjuvant agents and 22 untreated patients, tabulated the frequency of nine features of cancer (intact cancer glands, isolated cancer cells, poorly formed glands, cribriform architecture, clear spaces, intraductal carcinoma, solid sheets of cancer cells, prominent nucleoli, and previously described ABC grouping) and two features of benign glands (prominent basal cells and coalescent corpora amylacea). We used several methods, including a novel metric (visual grid system), to estimate residual tumor volume.RESULTSThe most highly reproducible features were ABC grouping (κ = 0.56–0.7), presence of intraductal carcinoma (κ = 0.34–0.72), cribriform architecture (κ = 0.42–0.68), solid sheets of tumor cells (κ = 0.44–0.56), and coalescent corpora amylacea (κ = 0.4–0.54). Among poorly reproducible features were prominent nucleoli (κ = 0.03–0.11), clear spaces (κ = 0.05–0.07), and poorly formed cancer glands (κ = 0.02–0.1). Determination of tumor mass was excellent regardless of the method used—maximum tumor size (κ = 0.9–0.94), tumor area (κ = 0.94–0.96), and grid‐based tumor cellularity (κ = 0.9).CONCLUSIONSWe propose using a set of parameters including maximum tumor size, tumor area/volume, cellularity, volume, and ABC grouping for evaluating radical prostatectomies post‐neoadjuvant therapy. Prostate 76:1285–1292, 2016. © 2016 Wiley Periodicals, Inc.
Extending the indication for robot‐assisted retroperitoneal partial nephrectomy to antero‐lateral renal tumors
Authors: Kim Hee Youn , Choe Hyun‐Sop , Lee Dong Sup , Yoo Jae Mo , Lee Seung‐Ju 
Published: June 2016

AbstractBackgroundRobot‐assisted retroperitoneal partial nephrectomy (RARPN) is typically employed for posterior renal tumors. This work aimed to extend the indication of RARPN to patients with selected antero‐lateral renal tumor.MethodsPatients who underwent RARPN between December 2013 and September 2015 at the authors' institution were enrolled. Two intersecting lines were drawn on an axial CT image to define the medial/lateral nature of anterior renal tumors. Patients with antero‐lateral tumor and posterior tumor were compared.ResultsAntero‐lateral tumors constituted 56.1% (32/57) of the total cases. The perioperative outcomes between the two groups were comparable. Although the operation time was longer for the antero‐lateral tumor group, it did not show statistical significance. No cases had positive margins. There was one case of Clavien‐Dindo grade IIIa complication in the antero‐lateral tumor group.ConclusionsRARPN is a safe and effective procedure not only for posterior renal tumors but also for carefully selected antero‐lateral renal tumors. Copyright © 2016 John Wiley & Sons, Ltd.
The Wnt pathway: a key network in cell signalling dysregulated by viruses
Authors: van Zuylen Wendy J. , Rawlinson William D. , Ford Caroline E. 
Published: June 2016

SummaryViruses are obligate parasites dependent on host cells for survival. Viral infection of a cell activates a panel of pattern recognition receptors that mediate antiviral host responses to inhibit viral replication and dissemination. Viruses have evolved mechanisms to evade and subvert this antiviral host response, including encoding proteins that hijack, mimic and/or manipulate cellular processes such as the cell cycle, DNA damage repair, cellular metabolism and the host immune response. Currently, there is an increasing interest whether viral modulation of these cellular processes, including the cell cycle, contributes to cancer development. One cellular pathway related to cell cycle signalling is the Wnt pathway. This review focuses on the modulation of this pathway by human viruses, known to cause (or associated with) cancer development. The main mechanisms where viruses interact with the Wnt pathway appear to be through (i) epigenetic modification of Wnt genes; (ii) cellular or viral miRNAs targeting Wnt genes; (iii) altering specific Wnt pathway members, often leading to (iv) nuclear translocation of β‐catenin and activation of Wnt signalling. Given that diverse viruses affect this signalling pathway, modulating Wnt signalling could be a generalised critical process for the initiation or maintenance of viral pathogenesis, with resultant dysregulation contributing to virus‐induced cancers. Further study of this virus–host interaction may identify options for targeted therapy against Wnt signalling molecules as a means to reduce virus‐induced pathogenesis and the downstream consequences of infection. Copyright © 2016 John Wiley & Sons, Ltd.
Multifunctional, Biocompatible, Non‐peptidic Hydrogels: from Water Purification to Drug Delivery
Authors: Baker Benjamin C. , Higgins Clare L. , Ravishankar Divyashree , Colquhoun Howard M. , Stevens Gary C. , Greco Francesca , Greenland Barnaby W. , Hayes Wayne 
Published: June 2016

AbstractA novel series of low molecular weight non‐peptidic, biocompatible super‐hydrogelators with both water purification and drug delivery properties have been developed. Linking the bis aromatic urea groups responsible for gelation together to form bi‐ and tri‐armed gelators, affords good control over gelation and water purification properties. The use of the gels as effective drug scavengers and delivery systems has been demonstrated with dye substrates, via pH inversion, as monitored by UV‐vis spectroscopy. Finally, the systems′ abilities as both drug scavenging and delivery systems have been demonstrated with the clinically‐approved drugs chlorpromazine and doxorubicin, respectively.
Theoretical Investigations on Naphthodithiophene Diimide‐Based Copolymers as Acceptor for All‐Polymer Solar Cell Applications
Authors: Liu Xiaorui , Huang Chengzhi , Wang Lei , Shen Wei , He Rongxing , Li Ming 
Published: June 2016

AbstractWe present an effective approach to modulate the electron‐withdrawing ability and the molecular planarity in donor‐acceptor (D−A) copolymer in order to develop the design strategy of acceptor polymers for improvement of the organic solar cell (OSC) performances. To confirm this strategy, based on a series of the D−A polymers (PNDIT (P1), PNDIS (P2) and PNDIBz (P3)), by modification of the electron‐withdrawing capability on those polymer backbones, a series of new D−A polymers (Pa1‐Pa3) were designed. The polymers Pa1‐Pa3 exhibit better planarity than that of corresponding P1‐P3, respectively. Compared with the properties of P1‐P3, Pa1‐Pa3 as acceptor materials not only yield a redshift and stronger absorption spectrum which results in a wider absorption within the solar spectrum, but also show much better electron acceptor properties, smaller exciton binding energy for charge dissociation and larger electron mobility. The results confirmed that the design strategy on adjustment of the electron‐withdrawing ability and the molecular planarity in D−A copolymer is a reliable approach to obtain the promising polymers as acceptors in OSC applications.
A novel amidase from Brevibacterium epidermidis ZJB-07021: gene cloning, refolding and application in butyrylhydroxamic acid synthesis
Authors: Ruan Li-Tao , Zheng Ren-Chao , Zheng Yu-Guo 
Published: June 2016

Abstract
A novel amidase gene (bami) was cloned from Brevibacterium epidermidis ZJB-07021 by combination of degenerate PCR and high-efficiency thermal asymmetric interlaced PCR (hiTAIL-PCR). The deduced amino acid sequence showed low identity (≤55 %) with other reported amidases. The bami gene was overexpressed in Escherichia coli, and the resultant inclusion bodies were refolded and purified to homogeneity with a recovery of 22.6 %. Bami exhibited a broad substrate spectrum towards aliphatic, aromatic and heterocyclic amides, and showed the highest acyl transfer activity towards butyramide with specific activity of 1331.0 ± 24.0 U mg−1. Kinetic analysis demonstrated that purified Bami exhibited high catalytic efficiency (414.9 mM−1 s−1) for acyl transfer of butyramide, with turnover number (K cat) of 3569.0 s−1. Key parameters including pH, substrate/co-substrate concentration, reaction temperature and catalyst loading were investigated and the Bami showed maximum acyl transfer activity at 50 °C, pH 7.5. Enzymatic catalysis of 200 mM butyramide with 15 μg mL−1 purified Bami was completed in 15 min with a BHA yield of 88.1 % under optimized conditions. The results demonstrated the great potential of Bami for the production of a variety of hydroxamic acids.
Continuous harvesting of a dominant bracken alters a cool‐temperate montane grassland community and increases plant diversity in Nagano, Japan
Authors: Suzuki Ryo O. , Kenta Tanaka , Sato Miyuki , Masaki Daisuke , Kanai Ryuji 
Published: June 2016

AbstractDeclines in biodiversity can be caused by intense land‐use or by land abandonment. Traditional plant‐gathering in Japan has declined or has often been abandoned in recent decades. However, little is known about how traditional plant‐gathering affects the diversity, productivity, and composition of plant communities. Traditionally, bracken (Pteridium aquilinum subsp. japonicum) served as a natural resource in Japan, and people continue to harvest it in some places. We conducted a 4‐year field experiment in a cool‐temperate grassland on the Sugadaira Plateau, Nagano Prefecture, comparing a continuous harvesting treatment of the dominant Pteridium with a non‐harvested control. We wanted to determine whether Pteridium harvesting would alter plant species richness, total productivity, and plant community composition. Local people harvested Pteridium shoots in a 1800 m2 treatment area each year from 2011 to 2014. By 2014, species richness and diversity (Shannon index) had significantly increased while Pteridium abundance (number of shoots and biomass) had decreased in the harvest treatment when compared with the control. Total productivity, measured as combined aboveground biomass of all vascular plant species, was similar between the treatment and control; however, community composition differed. Harvested plots had a higher biomass of erect‐formed, invasive and native species, but lower biomass of small‐formed species when compared with the control. Our results suggest that traditional plant‐gathering, such as periodic Pteridium harvesting can result in increases in plant diversity while total productivity is maintained. However, long‐term monitoring is recommended to detect any subsequent undesirable changes in the community, such as increases in invasive species populations.
Garnet-Staurolite-Mica Schist from Rangli Rangliot, Eastern Himalaya: Constraints from Phase Equilibria and Thermobarometry
Authors: Prakash Divya , Tewari Suparna 
Published: June 2016

Abstract:
Rangli Rangliot is an integral part of lesser Himalaya. The area around Rangli Rangliot consists of garnet-staurolite-mica schist and it is characterized by mineral assemblage garnet-biotite-muscovite-staurolite-quartz± plagioclase. Different reaction textures are of particular interest as they reflect discontinuous or continuous reactions under changing physical conditions. The relative XMg in the minerals varies in the order: muscovite&gt; biotite&gt; staurolite&gt; garnet, and the XMn decreases in the order: garnet&gt;staurolite&gt;biotite&gt;muscovite. The P-T evolution of the garnet-staurolite-mica schist has been constrained through the use of internally consistent TWEEQU programme and Perple_X software in the KFMASH model system. The combination of these two approaches demonstrates that the garnet-staurolite-mica schist experienced peak pressure and temperature at 5.8 kbar and 590 °C. The proposed clockwise P-T path implies that rocks from the study area could have resulted from thickened continental crust undergoing decompression.
Magnitud de las diferencias: reanálisis de efectos de un tratamiento
Authors: Merino-Soto César , Angulo-Ramos Marisol 
Published: June 2016

En una reciente evaluación del aprendizaje en entornos de simulación, mediante un diseño pretest-postest, sus resultados respaldan el efecto adaptativo de la exposición a escenarios de simulación clínica. Sin embargo, su diseño analítico únicamente enfatizó la significación estadística como evidencia de sus conclusiones, y esta puede ponerse en cuestionamiento.
DATING A PRE-IMPERIAL TEXT: THE CASE STUDY OF THEBOOK OF LORD SHANG
Authors: Pines Yuri 
Published: June 2016

AbstractThis article explores the dating of theBook of Lord Shang(Shangjunshu商君書). Despite the importance of this text as one of major ideological products of the Warring States period (453–221b.c.e.), it remained largely ignored in mainstream Western Sinology, in part because of the confusion about the dates of its composition. The article analyzes different criteria employed by earlier scholars to ascertain the dates of individual chapters of theBook of Lord Shangand investigates the relative weight of each of these criteria. This results in a methodologically transparent discussion, which not only advances our understanding of the complex textual history of theBook of LordShang but also makes a step toward establishment of a commonly acceptable set of dating determinants which may be employed in investigating the dates of other pre-imperial (i.e. pre-221b.c.e.) texts.
Selenium status in neonates with connatal infection
Authors: Wiehe Lennart , Cremer Malte , Wisniewska Monika , Becker Niels-Peter , Rijntjes Eddy , Martitz Janine , Hybsier Sandra , Renko Kostja , Bührer Christoph , Schomburg Lutz 
Published: June 2016

AbstractInfectious diseases impair Se metabolism, and low Se status is associated with mortality risk in adults with critical disease. The Se status of neonates is poorly characterised, and a potential impact of connatal infection is unknown. We hypothesised that an infection negatively affects the Se status of neonates. We conducted an observational case–control study at three intensive care units at the Charité-Universitätsmedizin Berlin, Germany. Plasma samples were collected from forty-four neonates. On the basis of clinical signs for bacterial infection and concentrations of IL-6 or C-reactive protein, neonates were classified into control (n23) and infected (n21) groups. Plasma Se and selenoprotein P (SePP) concentrations were determined by X-ray fluorescence and ELISA, respectively, at day of birth (day 1) and 48 h later (day 3). Se and SePP showed a positive correlation in both groups of neonates. Se concentrations indicative of Se deficit in adults (<20 µg/l) were observed in four infected neonates and one control subject, and three infected neonates had very low SePP concentrations (<0·5 mg/l). The univariate analysis revealed a significant difference in Se and SePP concentrations between the groups. Both parameters correlated inversely to IL-6 in neonates with severe inflammation (IL-6>500 ng/l). During antibiotic therapy, SePP increased significantly from day 1 (1·03 (sd0·10) mg/l) to day 3 (1·34 (sd0·10) mg/l), indicative of improved hepatic Se metabolism. We conclude that both Se and SePP are suitable biomarkers for assessing Se status in neonates and for identifying subjects at risk of deficiency.
Microenvironment of macula flava in the human vocal fold as a stem cell niche
Authors: Sato K , Chitose S , Kurita T , Umeno H 
Published: June 2016

AbstractBackground:There is growing evidence that the cells in the maculae flavae are tissue stem cells of the human vocal fold mucosa, and that the maculae flavae are a candidate for a stem cell niche. The role of microenvironment in the maculae flavae of the human vocal fold mucosa was investigated.Method:Anterior maculae flavae from six surgical specimens were cultured in a mesenchymal stem cell growth medium or a Dulbecco's modified Eagle's medium.Results:Using mesenchymal stem cell growth medium, the subcultured cells formed a colony-forming unit, and cell division reflected asymmetric self-renewal. This indicates that these cells are mesenchymal stem cells or stromal stem cells in the bone marrow. Using Dulbecco's modified Eagle's medium, the subcultured cells showed symmetric cell division without a colony-forming unit.Conclusion:A proper microenvironment in the maculae flavae of the human vocal fold mucosa is necessary to be effective as a stem cell niche that maintains the stemness of the contained tissue stem cells.
Roman Sacrifice, Inside and Out
Authors: Schultz Celia E. 
Published: June 2016

ABSTRACTThe ‘insider-outsider problem’ has had little impact on the study of religion in pre-Christian Rome. Classicists generally assume that the modern idea of sacrifice as the ritual killing of an animal applies to the Roman context. This study argues, however, that the apparent continuity is illusory in some important ways and that we have lost sight of some fine distinctions that the Romans made among the rituals they performed.Sacrificiumincluded vegetal and inedible offerings, and it was not the only Roman ritual that had living victims. Romansacrificiumis both less and more than the typical etic notion of sacrifice.
HPV genotypes detected in the oropharyngeal mucosa of HIV-infected men who have sex with men in Northern Italy
Authors: MARTINELLI M. , MAZZA F. , FRATI E. R. , FASOLO M. M. , COLZANI D. , BIANCHI S. , FASOLI E. , AMENDOLA A. , ORLANDO G. , TANZI E. 
Published: June 2016

SUMMARYThe aim of this study was to investigate the epidemiological profile of HPV oropharyngeal infections in HIV-infected men who have sex with men. A total of 135 subjects were enrolled at the L. Sacco University Hospital (Milan, Italy) to evaluate their HPV oropharyngeal infection status at baseline and at a follow-up visit at least 12 months later. HPV DNA was detected from oropharyngeal swabs using an in-house nested PCR that amplifies a segment of the L1 gene. The PCR products were then sequenced and genotyped. A greater percentage of high-risk genotypes was identified compared to low-risk genotypes (13·7% vs. 6·9%, P < 0·05), and two uncommon alpha-HPV genotypes were detected, i.e. HPV-102 and HPV-114. HPV infection prevalence was 24·4% and the cumulative incidence was 24·1%. During the follow-up period, one case of HPV infection (HPV-33) persisted, while the overall rate of infection clearance was 58·3%. HPV oropharyngeal infection was widespread in the cohort examined, and most of the infections were transient and cleared within 12 months. These results may help to clarify the role of HPV in the oropharynx and may also improve our understanding of the need to implement preventive strategies in at-risk populations.
A second note on the feasibility of generalized universal composability
Authors: GONZÁLEZ ALONSO , HEVIA ALEJANDRO 
Published: June 2016

Yao et al. (A note on the feasibility of generalized universal composability.Theory and Applications of Models of Computationpp. 474–485, 2007; A note on the feasibility of generalised universal composability.Mathematical Structures in Computer Science,19(1), pp. 193–205) claimed a potential limitation on the class of protocols that could be securely implemented in the generalized universal composability (GUC) framework proposed by Canetti et al. (Universally composable security with global setup.Lecture Notes in Computer Science, pp. 61–85, 2007). Specifically, Yao et al. presented a concrete attack on a GUC Zero Knowledge (GUCZK) protocol, a natural adaptation Blum's ZK proof for Directed Hamiltonicity using the general GUC feasibility of Canetti et al. (Universally composable security with global setup.Lecture Notes in Computer Science, pp. 61–85, 2007). Interestingly, the attack was not analysed in the GUC model in Yao et al. (A note on the feasibility of generalised universal composability.Mathematical Structures in Computer Science19(1), pp. 193–205, 2009) but in theFUC model, a new UC-like framework proposed in the same work. Nonetheless, Yao et al. (A note on the feasibility of generalised universal composability.Mathematical Structures in Computer Science19(1), pp. 193–205, 2009) argued that, in light of this attack, GUC would lose its concurrent general composability and proof of knowledge properties. Concretely, they argue that GUC composability would now be with respect to some adversaries with limited access to external arbitrary protocols.In this work, we show that the claimed attack from Yao et al. is indeed harmless and does not contradict the security of the mentioned GUCZK protocol, thus restoring the general feasibility for GUC.