bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clustering methods applied in the detection of Ki67 hot‐spots in whole tumor slide images: An efficient way to characterize heterogeneous tissue‐based biomarkers
Authors: Lopez Xavier Moles , Debeir Olivier , Maris Calliope , Rorive Sandrine , Roland Isabelle , Saerens Marco , Salmon Isabelle , Decaestecker Christine 
Published: June 2012

AbstractWhole‐slide scanners allow the digitization of an entire histological slide at very high resolution. This new acquisition technique opens a wide range of possibilities for addressing challenging image analysis problems, including the identification of tissue‐based biomarkers. In this study, we use whole‐slide scanner technology for imaging the proliferating activity patterns in tumor slides based on Ki67 immunohistochemistry. Faced with large images, pathologists require tools that can help them identify tumor regions that exhibit high proliferating activity, called “hot‐spots” (HSs). Pathologists need tools that can quantitatively characterize these HS patterns. To respond to this clinical need, the present study investigates various clustering methods with the aim of identifying Ki67 HSs in whole tumor slide images. This task requires a method capable of identifying an unknown number of clusters, which may be highly variable in terms of shape, size, and density. We developed a hybrid clustering method, referred to as Seedlink. Compared to manual HS selections by three pathologists, we show that Seedlink provides an efficient way of detecting Ki67 HSs and improves the agreement among pathologists when identifying HSs. © 2012 International Society for Advancement of Cytometry
Temporally controlled targeted somatic mutagenesis in mouse eye pigment epithelium
Authors: Mori Mikiro , Gargowitsch Laetitia , Bornert Jean‐Marc , Garnier Jean‐Marie , Mark Manuel , Chambon Pierre , Metzger Daniel 
Published: June 2012

AbstractTo generate temporally controlled site‐specific somatic mutations in the mouse eye pigment epithelium, we generated a TRP1‐Cre‐ERT2 transgenic mouse line that expresses the tamoxifen‐dependent Cre‐ERT2 recombinase under the control of the tyrosinase‐related protein 1 (TRP1) promoter. Cre‐ERT2 transcripts were readily detected in the retinal pigment epithelium (RPE), and tamoxifen treatment of adult TRP1‐Cre‐ERT2 transgenic mice induced efficient excision of floxed DNA in patches of RPE cells, in numerous epithelial cells of the iris and ciliary body, and in very few cells of the neural retina. Importantly, no excision was detected in any cells in the absence of tamoxifen treatment. Thus, the TRP1‐Cre‐ERT2 mouse line provides a powerful tool to study in vivo gene functions in the mouse eye pigment epithelium. genesis 1–18 2012. © 2012 Wiley Periodicals, Inc.
Longitudinal differentiation among pelagic populations in a planktic foraminifer
Authors: Ujiié Yurika , Asami Takahiro , de Garidel‐Thoron Thibault , Liu Hui , Ishitani Yoshiyuki , de Vargas Colomban 
Published: June 2012

AbstractEvolutionary processes in marine plankton have been assumed to be dependent on the oceanic circulation system, which transports plankton between populations in marine surface waters. Gene flow facilitated by oceanic currents along longitudinal gradients may efficiently impede genetic differentiation of pelagic populations in the absence of confounding marine environmental effects. However, how responsible oceanic currents are for the geographic distribution and dispersal of plankton is poorly understood. We examined the phylogeography of the planktic foraminifer Pulleniatina obliquiloculata in the Indo‐Pacific Warm Pool (IPWP) by using partial small subunit ribosomal DNA (SSU rDNA) sequences. We found longitudinal clines in the frequencies of three distinct genetic types in the IPWP area. These frequencies were correlated with environmental factors that are characteristic of three water masses in the IPWP. Noteworthy, populations inhabiting longitudinally distant water masses at the Pacific and Indian sides of the IPWP were genetically different, despite transportation of individuals via oceanic currents. These results demonstrate that populations of pelagic plankton have diverged genetically among different water masses within a single climate zone. Changes of the oceanic circulation system could have impacted the geographic patterns of dispersal and divergence of pelagic plankton.
On stochastic modelling of groundwater uptake in semi‐arid water‐limited systems: root density and seasonality effects
Authors: Vervoort R. W. , van der Zee S. E. A. T. M. 
Published: June 2012

ABSTRACTIn recent ecohydrological modelling, a common basis has been found in methodology and axiomas, such as the minimalist, systems analysis approach and a piecewise linear root zone water loss function. In this paper, we consider the loss function for root zones in contact with ground water through capillary upflow and including deep root systems. The basic assumption of a piecewise linear behaviour is not well supported, and we highlight how this generates a series of new research questions, related to important knowledge gaps at the interface of physics, plant physiology and ecology. We develop analytical solutions for the probability density functions for soil saturation and evapotranspiration for simple ecohydrological box models that are based on different vegetation groundwater feedbacks, for which numerical results have been presented earlier. In the case of intermediate groundwater levels and wetter climates, a feedback model that regulates groundwater uptake in response to root zone wetness regulates the transpiration most realistically. In semi‐arid regions, root zone salinization may occur as a result of groundwater quality and ineffective root zone leaching. How to combine the adverse effects of drought and osmotic stress in models is subject to debate, and several alternatives are presented. Seasonality is another unexplored area, and we highlight how this affects root zone salinization. Finally, a further feedback between upper root zone density and transpiration regulation in the loss function highlights dependence of deep rooted vegetation on groundwater. Experimental data are needed as the availability at this time is limiting further development of models. Copyright © 2012 John Wiley & Sons, Ltd.
On the Possibility of Uphill Intramolecular Electron Transfer in Multicopper Oxidases: Electrochemical and Quantum Chemical Study of Bilirubin Oxidase
Authors: Shleev Sergey , Andoralov Viktor , Falk Magnus , Reimann Curt T. , Ruzgas Tautgirdas , Srnec Martin , Ryde Ulf , Rulíšek Lubomír 
Published: June 2012

AbstractThe catalytic cycle of multicopper oxidases (MCOs) involves intramolecular electron transfer (IET) from the Cu‐T1 copper ion, which is the primary site of the one‐electron oxidations of the substrate, to the trinuclear copper cluster (TNC), which is the site of the four‐electron reduction of dioxygen to water. In this study we report a detailed characterization of the kinetic and electrochemical properties of bilirubin oxidase (BOx) – a member of the MCO family. The experimental results strongly indicate that under certain conditions, e.g. in alkaline solutions, the IET can be the rate‐limiting step in the BOx catalytic cycle. The data also suggest that one of the catalytically relevant intermediates (most likely characterized by an intermediate oxidation state of the TNC) formed during the catalytic cycle of BOx has a redox potential close to 0.4 V, indicating an uphill IET process from the T1 copper site (0.7 V) to the Cu‐T23. These suggestions are supported by calculations of the IET rate, based on the experimentally observed Gibbs free energy change and theoretical estimates of reorganization energy obtained by combined quantum and molecular mechanical (QM/MM) calculations.
Accelerating Effect of Tetramethylthiourea on the Kinetics of Zn2+ Electroreduction
Authors: Nieszporek Jolanta 
Published: June 2012

AbstractThe results of kinetic measurements of Zn2+ electroreduction on mercury electrode in the presence of tetramethylthiourea showed the two‐step character of the electrode process. The acquisition of nonlinear wide potential range Tafel plots was found to offer a good opportunity to examine the Zn2+ electroreduction mechanism. Three mechanisms including the ion transfer step followed by the electron exchange step (IE mechanism), the adsorption step (IA mechanism) and the chemical step followed by electron transfer (CE) were applied. The accelerating influence of tetramethylthiourea on Zn2+ electroreduction was found to result from possible complexes formation in the diffuse layer. The ion transport step is probably combined with the loss or exchange of a ligand. The second step probably consists in the electron transfer or adsorption process connected with partial charge transfer.
A Simple Route of Modifying Copper Electrodes for the Determination of Methanol and Ethylene Glycol
Authors: Hu Xuefeng , Wang Jichang 
Published: June 2012

AbstractCopper foil electrodes were modified in a stirred NaOH solution at room temperature. Measurements with scanning electron microscopy, energy‐dispersive X‐ray spectroscopy and X‐ray photoelectron spectroscopy confirmed the simultaneous structural transformation and chemical modification of the foil surface. The as‐prepared electrodes produced isolated anodic peaks in the cyclic voltammogram of methanol or ethylene glycol in alkaline solution. The highest anodic peak current was achieved at the electrode that was modified for 5 hours. Amperometric study illustrates that the modified electrode can detect lower than 100 µM methanol with a sensitivity of 15.8 µA/mM or 10 µM ethylene glycol with a sensitivity of 193 µA/mM. Importantly, the method is robust and the prepared electrodes show great reproducibility.
Direct and delayed X‐ray‐induced DNA damage in male mouse germ cells
Authors: Cordelli Eugenia , Eleuteri Patrizia , Grollino Maria Giuseppa , Benassi Barbara , Blandino Giovanni , Bartoleschi Cecilia , Pardini Maria Chiara , Di Caprio Edoardo Vittorio , Spanò Marcello , Pacchierotti Francesca , Villani Paola 
Published: June 2012

AbstractSperm DNA integrity is essential for the accurate transmission of paternal genetic information. Various stages of spermatogenesis are characterized by large differences in radiosensitivity. Differentiating spermatogonia are susceptible to radiation‐induced cell killing, but some of them can repair DNA damage and progress through differentiation. In this study, we applied the neutral comet assay, immunodetection of phosphorylated H2AX (γ‐H2AX) and the Sperm Chromatin Structure Assay (SCSA) to detect DNA strand breaks in testicular cells and spermatozoa at different times following in vivo X‐ray irradiation. Radiation produced DNA strand breaks in testicular cells that were repaired within the first few hours after exposure. Spermatozoa were resistant to the induction of DNA damage, but non‐targeted DNA lesions were detected in spermatozoa derived from surviving irradiated spermatogonia. These lesions formed while round spermatids started to elongate within the testicular seminiferous tubules. The transcription of pro‐apoptotic genes at this time was also enhanced, suggesting that an apoptotic‐like process was involved in DNA break production. Our results suggest that proliferating spermatogonia retain a memory of the radiation insult that is recognized at a later developmental stage and activates a process leading to DNA fragmentation. Environ. Mol. Mutagen. 2012. © 2012 Wiley Periodicals, Inc.
The frequency of Pig‐a mutant red blood cells in rats exposed in utero to N‐ethyl‐N‐nitrosourea
Authors: Dobrovolsky Vasily N. , Heflich Robert H. , Ferguson Sherry A. 
Published: June 2012

AbstractThe Pig‐a assay has been developed as a rapid sensitive measure of gene mutation in adult rats; however, no data exist on its ability to detect mutation following in utero exposures or in neonatal animals. Pregnant Sprague‐Dawley rats were treated daily on gestational days 12–18 with oral doses of 0, 6, or 12 mg/kg/day N‐ethyl‐N‐nitrosourea (ENU); following parturition, the offspring and dams were monitored over a period of 5 months for the frequency of CD59‐deficient erythrocytes as a marker of Pig‐a mutation. Significant dose‐related increases in Pig‐a mutant red blood cells (RBCs) were observed in ENU‐treated dams. However, only very weak increases in RBC Pig‐a mutant frequency (MF) were noted in offspring treated in utero with the lower ENU dose. The higher ENU dose produced extremely variable responses in the offspring as a function of age, even among littermates, ranging from a steady low or moderately high Pig‐a MF to a rapidly increasing or decreasing Pig‐a MF. The manifestation kinetics of Pig‐a mutant RBCs in the offspring suggest that the change from predominantly hepatic to predominantly bone marrow erythropoiesis that occurs during early development may have contributed to this variability. Our results indicate that using the RBC Pig‐a model for mutation detection in animals treated in utero may require analysis of multiple offspring from the same litter to account for potential “jack pot” effects, and that detection of the earliest treatment effect (i.e., in neonates using the hepatic RBC fraction) may require optimization of blood processing. Environ. Mol. Mutagen. 2012. Published 2012 Wiley Periodicals, Inc.
A projection method for the spectral solution of non‐homogeneous and incompressible Navier–Stokes equations
Authors: Pierro Bastien Di , Abid Malek 
Published: June 2012

SUMMARYThis paper is devoted to the development of a parallel, spectral and second‐order time‐accurate method for solving the incompressible and variable density Navier–Stokes equations. The method is well suited for finite thickness density layers and is very efficient, especially for three‐dimensional computations. It is based on an exact projection technique. To enforce incompressibility, for a non‐homogeneous fluid, the pressure is computed using an iterative algorithm. A complete study of the convergence properties of this algorithm is done for different density variations. Numerical simulations showing, qualitatively, the capabilities of the developed Navier–Stokes solver for many realistic problems are presented. The numerical procedure is also validated quantitatively by reproducing growth rates from the linear instability theory in a three‐dimensional direct numerical simulation of an unstable, non‐homogeneous, flow configuration. It is also shown that, even in a turbulent flow, the spectral accuracy is recovered. Copyright © 2012 John Wiley & Sons, Ltd.
Association study of GRIK1 gene polymorphisms in schizophrenia: case–control and family‐based studies
Authors: Hirata Yuko , Zai Clement C. , Souza Renan P. , Lieberman Jeffrey A. , Meltzer Herbert Y , Kennedy James L. 
Published: June 2012

Glutamatergic function is one of the major hypotheses for schizophrenia. Within the glutamate system, the glutamate receptor ionotropic kainate‐1 (GRIK1) gene is thought to be particularly involved in schizophrenia because of the reported reduction of GRIK1 in the dorsolateral prefrontal cortex of patients.ObjectiveWe examined single‐nucleotide polymorphisms (SNPs) in the GRIK1 gene for possible association with schizophrenia.MethodsWe analyzed eight SNPs across the GRIK1 gene in 202 case–control pairs and 108 small nuclear families.ResultsFor the case–control study, we found nominal significant associations in the analysis of rs469472 (p = 0.028) and its haplotypes. In the family‐based study, nominal significant association was also observed for rs469472 (p = 0.046), as well as rs455892 (p = 0.024). The marker rs469472 was associated with schizophrenia when we combined the case–control and family samples (p = 0.027). The association findings did not survive correction for multiple testing.ConclusionsBecause we observed similar association findings with marker rs469472 in two independent samples, further analyses in larger samples are warranted. Copyright © 2012 John Wiley & Sons, Ltd.
An armed oncolytic herpes simplex virus expressing thrombospondin‐1 has an enhanced in vivo antitumor effect against human gastric cancer
Authors: Tsuji Toshiaki , Nakamori Mikihito , Iwahashi Makoto , Nakamura Masaki , Ojima Toshiyasu , Iida Takeshi , Katsuda Masahiro , Hayata Keiji , Ino Yasushi , Todo Tomoki , Yamaue Hiroki 
Published: June 2012

AbstractAdvanced gastric cancer is a common disease, but the conventional treatments are unsatisfactory because of the high recurrence rate. One of the promising new therapies is oncolytic virotherapy, using oncolytic herpes simplex viruses (HSVs). Thrombospondin‐1 (TSP‐1) suppresses tumor progression via multiple mechanisms including antiangiogenesis. Our approach to enhance the effects of oncolytic HSVs is to generate an armed oncolytic HSV that combines the direct viral oncolysis with TSP‐1‐mediated function for gastric cancer treatment. Using the bacterial artificial chromosome (BAC) system, a 3rd generation oncolytic HSV (T‐TSP‐1) expressing human TSP‐1 was constructed for human gastric cancer treatment. The enhanced efficacy of T‐TSP‐1 was determined in both human gastric cancer cell lines in vitro and subcutaneous tumor xenografts of human gastric cancer cells in vivo. In addition, we examined the apoptotic effect of T‐TSP‐1 in vitro, and the antiangiogenic effect of T‐TSP‐1 in vivo compared with a non‐armed 3rd generation oncolytic HSV, T‐01. No apparent apoptotic induction by T‐TSP‐1 was observed for human gastric cancer cell lines TMK‐1 cells but for MKN1 cells in vitro. Arming the viruses with TSP‐1 slightly inhibited their replication in some gastric cancer cell lines, but the viral cytotoxicity was not attenuated. In addition, T‐TSP‐1 exhibited enhanced therapeutic efficacy and inhibition of angiogenesis compared with T‐01 in vivo. In this study, we established a novel armed oncolytic HSV, T‐TSP‐1, which enhanced the antitumor efficacy by providing a combination of direct viral oncolysis with antiangiogenesis. Arming oncolytic HSVs may be a useful therapeutic strategy for gastric cancer therapy.
Induction of CD8 T‐cell responses restricted to multiple HLA class I alleles in a cancer patient by immunization with a 20‐mer NY‐ESO‐1f (NY‐ESO‐1 91‐110) peptide
Authors: Eikawa Shingo , Kakimi Kazuhiro , Isobe Midori , Kuzushima Kiyotaka , Luescher Immanuel , Ohue Yoshihiro , Ikeuchi Kazuhiro , Uenaka Akiko , Nishikawa Hiroyoshi , Udono Heiichiro , Oka Mikio , Nakayama Eiichi 
Published: June 2012

AbstractImmunogenicity of a long 20‐mer NY‐ESO‐1f peptide vaccine was evaluated in a lung cancer patient TK‐f01, immunized with the peptide with Picibanil OK‐432 and Montanide ISA‐51. We showed that internalization of the peptide was necessary to present CD8 T‐cell epitopes on APC, contrasting with the direct presentation of the short epitope. CD8 T‐cell responses restricted to all five HLA class I alleles were induced in the patient after the peptide vaccination. Clonal analysis showed that B*35:01 and B*52:01‐restricted CD8 T‐cell responses were the two dominant responses. The minimal epitopes recognized by A*24:02, B*35:01, B*52:01 and C*12:02‐restricted CD8 T‐cell clones were defined and peptide/HLA tetramers were produced. NY‐ESO‐1 91‐101 on A*24:02, NY‐ESO‐1 92‐102 on B*35:01, NY‐ESO‐1 96‐104 on B*52:01 and NY‐ESO‐1 96‐104 on C*12:02 were new epitopes first defined in this study. Identification of the A*24:02 epitope is highly relevant for studying the Japanese population because of its high expression frequency (60%). High affinity CD8 T‐cells recognizing tumor cells naturally expressing the epitopes and matched HLA were induced at a significant level. The findings suggest the usefulness of a long 20‐mer NY‐ESO‐1f peptide harboring multiple CD8 T‐cell epitopes as an NY‐ESO‐1 vaccine. Characterization of CD8 T‐cell responses in immunomonitoring using peptide/HLA tetramers revealed that multiple CD8 T‐cell responses comprised the dominant response.
Oxidative inhibition of Hsp90 disrupts the super‐chaperone complex and attenuates pancreatic adenocarcinoma in vitro and in vivo
Authors: Sarkar Sayantani , Dutta Devawati , Samanta Suman Kumar , Bhattacharya Kaushik , Pal Bikas Chandra , Li Jinping , Datta Kaustubh , Mandal Chhabinath , Mandal Chitra 
Published: June 2012

AbstractPancreatic cancer is almost always fatal, in part because of its delayed diagnosis, poor prognosis, rapid progression and chemoresistance. Oncogenic proteins are stabilized by the Hsp90, making it a potential therapeutic target. We investigated the oxidative stress‐mediated dysfunction of Hsp90 and the hindrance of its chaperonic activity by a carbazole alkaloid, mahanine, as a strategic therapeutic in pancreatic cancer. Mahanine exhibited antiproliferative activity against several pancreatic cancer cell lines through apoptosis. It induced early accumulation of reactive oxygen species (ROS) leading to thiol oxidation, aggregation and dysfunction of Hsp90 in MIAPaCa‐2. N‐acetyl‐L‐cysteine prevented mahanine‐induced ROS accumulation, aggregation of Hsp90, degradation of client proteins and cell death. Mahanine disrupted Hsp90‐Cdc37 complex in MIAPaCa‐2 as a consequence of ROS generation. Client proteins were restored by MG132, suggesting a possible role of ubiquitinylated protein degradation pathway. Surface plasmon resonance study demonstrated that the rate of interaction of mahanine with recombinant Hsp90 is in the range of seconds. Molecular dynamics simulation showed its weak interactions with Hsp90. However, no disruption of the Hsp90‐Cdc37 complex was observed at an early time point, thus ruling out that mahanine directly disrupts the complex. It did not impede the ATP binding pocket of Hsp90. Mahanine also reduced in vitro migration and tube formation in cancer cells. Further, it inhibited orthotopic pancreatic tumor growth in nude mice. Taken together, these results provide evidence for mahanine‐induced ROS‐mediated destabilization of Hsp90 chaperone activity resulting in Hsp90‐Cdc37 disruption leading to apoptosis, suggesting its potential as a specific target in pancreatic cancer.