gebhart/patrepeval huggingface dataset:
Abstract 5481: Therapy of human LN229 glioblastoma growing in the brain of nude mice by Macitentan, a dual endothelin receptor A and B antagonist, combined with Temozolomide. (2013)

Abstract Purpose: We determined whether the blockade of endothelin receptor pathways can reverse the chemoprotection mediated by astrocytes and produce therapy of Human LN 229 Glioblastoma cells growing in the brain of nude mice treated with the dual endothelin receptor antagonist, Macitentan and Temozolomide (TMZ). Materials and Methods: In the first set of experiments, murine astrocytes were cultured with tumor cells in the presence or absence of Macitentan and TMZ. For therapy studies the leuciferas labeled LN229 cells were implanted (stereotactically) into the brains of nude mice. The mice were ear tagged and imaged by IVIS spectrometer at multiple times. On day 24 the mice were randomized to receive vehicle, TMZ (p.o., 7.5mg/kg, one week on and two weeks off), Macitentan (p.o., 10mg/kg, daily) and Macitentan plus TMZ. Survival of mice was compared by Kaplan-Meyer curve (log-rank test) and immunohistochemical analyses were carried out for multiple markers. Results: Simultaneous blocking of endothelin receptor A and B pathways reversed the in culture protection induced by astrocytes against TMZ (p&lt;0.05). Therapy with Macitentan and TMZ significantly prolonged the survival of mice (p&lt;0.0001) .The blockade of endothelin receptor A and B significantly decreased the level of expression of phosphorylated AKT and MAPK, and down-regulated the expression of BCL2L1, TWIST1 and GSTA5 in LN 229 cells growing in the brain. Proliferation of tumor cells and tumor-associated endothelial cells was significantly decreased. Moreover the apoptosis of LN229 cells was significantly increased in the brain of the combination treatment group. Conclusion: Blockade of endothelin receptor A and B pathways by Macitentan combined with TMZ provides a new approach for the treatment of patients with Glioblastoma. Citation Format: Sun Jin Kim, Seung Wook Kim, Hyun Jin Choi, Ho Jeong Lee, Francois Lehembre, Junqin He, Urs Regenass, Charles A Conrad, W.K. Yung, Isaiah J. Fidler. Therapy of human LN229 glioblastoma growing in the brain of nude mice by Macitentan, a dual endothelin receptor A and B antagonist, combined with Temozolomide. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5481. doi:10.1158/1538-7445.AM2013-5481
Optimization of trans-splicing ribozyme efficiency and specificity by in vivo genetic selection (2002)

Trans-splicing ribozymes are RNA-based catalysts capable of splicing RNA sequences from one transcript specifically into a separate target transcript. In doing so, a chimeric mRNA can be produced, and new gene activities triggered in living cells dependent on the presence of the target mRNA. Based on this ability of trans-splicing ribozymes to deliver new gene activities, a simple and versatile plating assay was developed in Saccharomyces cerevisiae for assessing and optimizing constructs in vivo. Trans-splicing ribozymes were used to splice sequences encoding a GAL4-derived transcription activator into a target transcript from a prevalent viral pathogen. The transcription activator translated from this new mRNA in turn triggered the expression of genes under the regulatory control of GAL4 upstream-activating sequences. Two of the activated genes complemented metabolic deficiencies in the host strain, and allowed growth on selective media. A simple genetic assay based on phenotypic conversion from auxotrophy to prototrophy was established to select efficient and specific trans-splicing ribozymes from a ribozyme library. This simple assay may prove valuable for selecting optimal target sites for therapeutic agents such as ribozymes, antisense RNA and antisense oligodeoxyribonucleotides, and for optimizing the design of the therapeutic agents themselves, in higher eukaryotes.
Erratum: Counting graphene layers on glass via optical reflection microscopy [Appl. Phys. Lett. 94, 143101 (2009)] (2009)

First Page
Early‐phase cerebral arteriogenesis: Evidence of endothelial activation, vascular proliferation and local inflammation (2008)

Arteriogenesis holds potential as a novel treatment for ischemic vascular disease. Our study aimed at an identification of key processes of early‐phase cerebral arteriogenesis in vivo. In a rat model of nonischemic cerebral hypoperfusion the posterior cerebral artery (PCA) constitutes a main collateral to the contralateral hemisphere. Following reversed flow, endothelial cell (EC) activation was assessed by electron microscopy. Gene expression during biomechanical EC activation was analyzed by cDNA microarray. Proarteriogenic vascular proliferation and local inflammation were evaluated. PCA diameters increase significantly(+30%). Ultrastructural EC activation occurs at 3d postoperatively, followed by CD68+ cellular transmigration and sustained vessel wall proliferation. Of 164 genes deregulated, 48 contain shear stress response elements (SSREs) or NFkB binding sites in their promoter regions. Arteriogenesis leads to NFkB activation as shown by local NFkB p65 expression. Cerebral arteriogenesis is initiated by EC activation through changed blood flow, facilitating monocyte influx and collateral proliferation. Gene expression is modified by biomechanical activation via SSREs and the pro‐inflammatory environment (NFkB activation, monocyte influx). Therapeutic arteriogenesis may aim at 1) biomechanical EC activation 2)vascular proliferation or 3)local monocyte function.
Accuracy vs. precision in general purpose neural digital VLSI architectures (2002)

The paper provides a sensitivity analysis to measure the loss in accuracy induced by perturbations affecting multilayered perceptrons. Differing from that suggested in the related literature, we do not assume a large number of weights or independence among inputs for the neurons nor again strict requirements on the nonlinear function. Results are then tailored to digital VLSI implementations where perturbations, caused by quantisation, affect the device inputs, weights, internal values and outputs.
ABSORPTION CHANGES IN BACTERIAL CHROMATOPHORES‐II. A NEW CHLOROPHYLL‐LIKE PIGMENT FROM THE OXIDATION OF CHROMATQPHORES FROM <i>RHODOSPIRILLUM RUBRUM</i> (1965)

Abstract— Evidence is presented which points to (at least) two bound forms of bacteriochlor‐ophyll present in chromatophores of Rhodospirillum rubrum , both of them readily converted to unbound bacteriochlorophyll (abs. max 770 mμ) when the chromatophores are extracted with acetone or ethanol. Controlled oxidation of the chromatophores with Ir(IV) or with Zn (II) and ferricyanide preferentially destroys the more strongly absorbing pigment (abs. max 880 mμ) but brings about only a slight decrease in the magnitude of the photoinduced absorption changes at 810 and 792 mμ. Such oxidations yield a new pigment, absorbing at 715 mμ in the aqueous preparation and, more strongly, at 680–684 mu when the pigment is extracted into organic solvents. This pigment is formed irreversibly and is therefore different from the material formed by photooxidation of chromatophores. Its visible spectrum and the spectrum of the material formed from it by acidification suggest that it is a chlorophyll‐like substance, possibly derived from bacteriochlorophyll by (two‐electron) oxidation of one of the dihydropyrrole rings to a pyrrole ring. Directions are given for separation of this pigment from other colored compounds present in the oxidation mixtures.
Abstract P6-10-28: Therapeutic stratification of triple negative breast cancer by integrating chemosensitivity & phospho-proteome profiles (2020)

Abstract Triple negative breast cancer (TNBC) is a highly aggressive type of breast cancer with poor prognosis that accounts approximately for 15% of breast cancer cases. The lack of targetable hormonal receptors or HER2/ErbB2 makes TNBC therapeutically challenging and existing drug treatments are often ineffective. TNBC is also a highly heterogeneous class of breast cancer, and different genetic approaches have not been so far successful in identifying clinically useful patient stratification strategies to date. In previous studies, we have discovered a correlation between targeted phospho-proteomics and mitotic inhibitor sensitivities in TNBC cells, suggesting the potential of using phospho-proteome profiles to identifying markers predictive of actionable therapeutic strategies. In the current study, we further explored the potential of phospho-proteomics for TNBC stratification and drug chemo-sensitivity prediction. We screened 25 TNBC cell lines against 517 oncology compounds, and in parallel ran mass spectrometry-based global phospho-proteome profiling of the same cell lines, resulting in 4283 confident phospho-peptide quantifications. Using multitask multiple kernel learning, we integrated the phospho-peptide data with other publicly available omics data for the 25 TNBC cell lines (genomics, transcriptomics, metabolomics, and methylomics), and developed a multi-omics machine learning model to quantify the predictive contribution of each omics profile to drug response prediction. When considering all the 517 compounds, we found that the phospho-proteomic and gene expression data were most informative for the prediction of compound’s chemo-sensitivity. This integrated approach has the potential to both identify panels of multi-omics markers for individual drug classes, as well as to stratify the heterogeneous TNBC cells based on their genomic, molecular and functional profiles. Citation Format: Prson Gautam, Xiangju Qin, Julia Vainonen, Srikar Nagelli, Johanna Lampe, Juha Klefström, Jukka Westermarck, Krister Wennerberg, Tero Aittokallio. Therapeutic stratification of triple negative breast cancer by integrating chemosensitivity & phospho-proteome profiles [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-10-28.
Mechanism of Activation of Human Plasma Prekallikrein (1979)

Human prekallikrein (PK) is in plasma complexed to High Moleculair Weight Kininogen (HMWK). The formation of a complex of PK with HMWK was demonstrated by cross-immunoelectrophoresis. Purified PK alone did not migrate upon electrophoresis, however when mixed with HMWK or Fletcher plasma, PK migrated with the same mobility as PK present in normal plasma. Also addition of PK to HMWK resulted in a reduction of the electrophoretic mobility of HMWK on cross-immunoelectrophoresis using anti-HMWK. Fitzgerald plasma which is deficient in HMWK has a PK clotting activity of 26% but no detectable PK-antigen level. Reconstitution with HMWK yielded PK-antigen levels corresponding to the PK-clotting activity. Addition of HMWK to normal plasma did not increase the PK-antigen levels. PK was activated by purified human (β-XIIa (28, 000 mol.wt) and by bovine α-XIIa (80, 000 mol.wt). Activation by αXIIa but not by by β-XII was enhanced by the presence of HMWK and dextran sulphate. After complete activation by α-XIIa in the presence of HMWK kallikrein remained complexed to HMWK. The generation of kallikrein activity paralelled the extent of proteolytic cleavage. SDS-polyacrylamide gel electrophoresis in the presence of reducing agents showed that both α-XIIa and β-XIIa generated fragments with apparent mol.wt’s of 52,000, 42,000 and 37,000. These fragments are initially held together by disulfide bonds, a second relatively slow cleavage generates fragments with similar mol. wt’s but observed on non reduced SDS-gels. This cleavage is not accompanied by a decrease in kallikrein activity.
Early establishment of epithelial apoptosis in the developing human small intestine (2000)

In the adult small intestine, the dynamic renewal of the epithelium is characterized by a sequence of cell production in the crypts, cell maturation and cell migration to the tip of villi, where apoptosis is undertaken. Little is known about enterocytic apoptosis during development. In man, intestinal architectural features and functions are acquired largely by mid-gestation (18-20 wks); the question whether the establishment of enterocytic apoptotic processes parallels or not the acquisition of other intestinal functional features remains open. In the present study, we approached this question by examining enterocytic apoptosis during development of the human jejunum (9-20 wks gestation), using the ISEL (in situ terminal uridine deoxynucleotidyl nick-end labelling) method. Between 9 and 17 wks, apoptotic enterocytes were not evidenced. However, beginning at the 18 wks stage, ISEL-positive enterocytes were regularly observed at the tip of villi. Since the Bcl-2 family of proteins constitutes a critical checkpoint in apoptosis, acting upstream of the apoptotic machinery, we investigated the expression of six Bcl-2 homologs (Bcl-2, Bcl-X(L), Mcl-1, Bax, Bak, Bad) and one non-homologous associated molecule (Bag-1). By immunofluorescence, we found that all homologs analyzed were expressed by enterocytes between 9 and 20 wks. However, Bcl-2 homologs underwent a gradual compartmentalization of epithelial expression along the maturing crypt-villus axis, to establish gradients of expression by 18-20 wks. Western blot analyses indicated that the expression levels of Bcl-2 homologs were modulated during morphogenesis of the crypt-villus axis, in parallel to their gradual compartmentalization of expression. Altogether, these data suggest that regulatory mechanisms of human enterocytic apoptosis become established by mid-gestation (18-20 wks) and coincide with the maturation of the crypt-villus axis of cell proliferation, differentiation and renewal.
Study of nanostructure of highly purified water by measuring scattering matrix elements of laser radiation (2008)

Experiments on modulation interference microscopy and measurement of light scattering matrix elements showed that double distilled water purified from solid impurities contains macroscopic scatterers of optical radiation. It follows from numerical calculation that these scatterers can be micrometer-scale clusters formed by polydisperse air bubbles with effective radii of 70 to 90 nm. The fractal dimension of such clusters is within 2.4–2.8 and their concentration is ∼ 106 cm−3.
Thermodynamics of molten iron alloys containing oxygen, aluminium, silicon and chromium (1963)

A study has been made of the aluminium-oxygen equilibrium in liquid iron by studying the reaction. Electrolytic iron in pure alumina crucibles was maintained at a constant temperature under a controlled water-vapour/hydrogen gas mixture until equilibrium was established between solid, liquid and gas phases. The melts were then quenched in a stream of hydrogen and subsequently analysed for aluminium and oxygen. The value of this type of work is largely dependent upon accurate analytical techniques and in the present case analytical uncertainties have been reduced by carrying out experiments at 1723
Violences et pouvoirs politiques (1996)

La politique est un champ de bataille où les hommes s’affrontent pour la conquête, l’exercice, la conservation ou la contestation du pouvoir.Que la violence soit au cœur du politique, l’histoire l’atteste surabondamment. Omniprésente dans l’histoire et dans l’espace, elle est également multiforme, imposant d’emblée le recours au pluriel et à la pluridisciplinarité.Tel est l’objectif de ce livre, qui envisage l’étude des rapports entre violences et pouvoirs politiques à partir de plusieurs orientations de réflexion complémentaires.Cette étude montre que la violence politique est un révélateur particulièrement efficace des dysfonctionnements sociaux et qu’elle constitue un des prismes privilégiés au travers desquels l’observateur des sociétés humaines peut prétendre mieux cerner leurs réalités.
SRP--Where the RNA and Membrane Worlds Meet (2000)

Working out how the signal recognition particle (SRP) of cells directs newly synthesized proteins destined for secretion to the endoplasmic reticulum (ER) has proved a gargantuan task. That task has just been made easier, as explained in a Perspective by
 Peter Walter and colleagues, by the solving of the crystal structure of the RNA-protein core of the SRP (
 Batey
 et al .)
ARRAYED CAPTURE, ASSAYING AND BINARY COUNTING OF CELLS IN A STOPPED-FLOW SEDIMENTATION MODE (2011)

In this work we present a centrifugal microfluidic platform for highly efficient trapping, staining and identification of biological cells. V-shaped geometric traps are used to captured mixed populations of cells under stagnant flow conditions. We demonstrate the capability to discriminate cells based on surface markers (EpCAM) as well as on intracellular markers (ESR1). Captured cells are arrayed in single cell ordered pattern and align in a well-defined focal plane which greatly facilitates the readout of cell-based assays.
Nondestructive monitoring of metal surfaces corrosion by radiofrequency methods [using EM slow wave structure propagation] (2002)

This paper introduces a radiofrequency (RF) method for sensing the corrosion processes on metal surfaces. A sensor, based on the propagation characteristics of electromagnetic slow wave structures (SWS), has been designed and constructed. The method is based on the use of RF slow-wave structures, which have suitable propagation and skin-effect characteristics on metal surfaces. The details of the design parameters of the sensor are given and the signal processing to extract the useful information from the sensor has been discussed. The propagation characteristics of the SWS electromagnetic waves in the corroding metals have been investigated in detail and compared with the microwave techniques. Mathematical analysis is introduced to explain the behavour of the electromagnetic waves on corroding metal surfaces. The proposed sensor can also be applied to pipelines, tanks, and other industrial installations that have protective coats on their surfaces to monitor the thickness and effectiveness of these coats.
A practical controller design of distributed energy resources for stabilization of interconnected power system based on synchronized phasor measurements (2009)

With today's advanced technologies, various types of distributed energy resources (DERs) with relatively fast controllability option have been brought into practical applications. This paper presents a metaheuristic-based controller design of controllable DER for stability enhancement based on synchronized phasor measurements. With the most recent data, a simplified oscillation model (SOM) is evaluated and referred to as an estimated power system model for detection and assessment of an estimated inter-area oscillation mode. Subsequently, an extended SOM is formulated by including dynamic effects of DER control system. The designed controller can be achieved via a metaheuristic method with less effort towards the design specification. Moreover, performance of the designed controller can be evaluated during design to avoid its adverse effects. Some simulation results demonstrate and confirm the applicability and effectiveness of the proposed controller design method.
5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation (2013)

2-Oxoglutarate and iron dependent oxygenases are therapeutic targets for human diseases. Using a representative 2OG oxygenase panel, we compare the inhibitory activities of 5-carboxy-8-hydroxyquinoline (IOX1) and 4-carboxy-8-hydroxyquinoline (4C8HQ) with that of two other commonly used 2OG oxygenase inhibitors, <i>N</i>-oxalylglycine (NOG) and 2,4-pyridinedicarboxylic acid (2,4-PDCA). The results reveal that IOX1 has a broad spectrum of activity, as demonstrated by the inhibition of transcription factor hydroxylases, representatives of all 2OG dependent histone demethylase subfamilies, nucleic acid demethylases and γ-butyrobetaine hydroxylase. Cellular assays show that, unlike NOG and 2,4-PDCA, IOX1 is active against both cytosolic and nuclear 2OG oxygenases without ester derivatisation. Unexpectedly, crystallographic studies on these oxygenases demonstrate that IOX1, but not 4C8HQ, can cause translocation of the active site metal, revealing a rare example of protein ligand-induced metal movement.
[Isolation and characterization of dipeptidylpeptidase IV from human seminal plasma]. (1986)

Two forms of dipeptidylpeptidase IV with molecular weights (gel distribution chromatography) of 270 kD and about 1450 kD were isolated from human seminal plasma. The enzymes migrating differently in electrophoresis possess identical catalytic properties in regard to pH optimum, kinetic constants and the influence of effectors. The high-molecular form loses at 65 degrees C its enzymatic activity significantly more slowly. After 60 min of incubation at 68 degrees C, human seminal plasma has still about 12-32% (N = 50) dipeptidylpeptidase activity. Through the action of Triton X-100 or chymotrypsin the high-molecular form can be transferred into the low-molecular one without loss of activity. In 80 healthy human sperm donors the average proportion of the low-molecular form of peptidase was determined to be 9-22%.
Drude Weight, Cyclotron Resonance, and the Dicke Model of Graphene Cavity QED (2012)

The unique optoelectronic properties of graphene make this two-dimensional material an ideal platform for fundamental studies of cavity quantum electrodynamics in the strong-coupling regime. The celebrated Dicke model of cavity quantum electrodynamics can be approximately realized in this material when the cyclotron transition of its 2D massless Dirac fermion carriers is nearly resonant with a cavity photon mode. We develop the theory of strong matter-photon coupling in this circumstance, emphasizing the essential role of a dynamically generated matter energy term that is quadratic in the photon field and absent in graphene's low-energy Dirac model.
A time-dependent topic model for multiple text streams (2011)

In recent years social media have become indispensable tools for information dissemination, operating in tandem with traditional media outlets such as newspapers, and it has become critical to understand the interaction between the new and old sources of news. Although social media as well as traditional media have attracted attention from several research communities, most of the prior work has been limited to a single medium. In addition temporal analysis of these sources can provide an understanding of how information spreads and evolves. Modeling temporal dynamics while considering multiple sources is a challenging research problem. In this paper we address the problem of modeling text streams from two news sources - Twitter and Yahoo! News. Our analysis addresses both their individual properties (including temporal dynamics) and their inter-relationships. This work extends standard topic models by allowing each text stream to have both local topics and shared topics. For temporal modeling we associate each topic with a time-dependent function that characterizes its popularity over time. By integrating the two models, we effectively model the temporal dynamics of multiple correlated text streams in a unified framework. We evaluate our model on a large-scale dataset, consisting of text streams from both Twitter and news feeds from Yahoo! News. Besides overcoming the limitations of existing models, we show that our work achieves better perplexity on unseen data and identifies more coherent topics. We also provide analysis of finding real-world events from the topics obtained by our model.