gebhart/patrepeval huggingface dataset:
Stress-Induced Changes of Hippocampal NMDA Receptors: Modulation by Duloxetine Treatment (2012)

It is now well established that the glutamatergic system contributes to the pathophysiology of depression. Exposure to stress, a major precipitating factor for depression, enhances glutamate release that can contribute to structural abnormalities observed in the brain of depressed subjects. On the other hand, it has been demonstrated that NMDA antagonists, like ketamine, exert an antidepressant effect at preclinical and clinical levels. On these bases, the purpose of our study was to investigate whether chronic mild stress is associated with specific alterations of the NMDA receptor complex, in adult rats, and to establish whether concomitant antidepressant treatment could normalize such deficits. We found that chronic stress increases the expression of the obligatory GluN1 subunit, as well as of the accessory subunits GluN2A and GluN2B at transcriptional and translational levels, particularly in the ventral hippocampus. Concomitant treatment with the antidepressant duloxetine was able to normalize the increase of glutamatergic receptor subunit expression, and correct the changes in receptor phosphorylation produced by stress exposure. Our data suggest that prolonged stress, a condition that has etiologic relevance for depression, may enhance glutamate activity through post-synaptic mechanisms, by regulating NMDA receptors, and that antidepressants may in part normalize such changes. Our results provide support to the notion that antidepressants may exert their activity in the long-term also via modulation of the glutamatergic synapse.
Control of the DNA Damage Checkpoint by Chk1 and Rad53 Protein Kinases Through Distinct Mechanisms (1999)

In response to DNA damage, cells activate checkpoint pathways that prevent cell cycle progression. In fission yeast and mammals, mitotic arrest in response to DNA damage requires inhibitory Cdk phosphorylation regulated by Chk1. This study indicates that Chk1 is required for function of the DNA damage checkpoint in Saccharomyces cerevisiae but acts through a distinct mechanism maintaining the abundance of Pds1, an anaphase inhibitor. Unlike other checkpoint mutants, chk1 mutants were only mildly sensitive to DNA damage, indicating that checkpoint functions besides cell cycle arrest influence damage sensitivity. Another kinase, Rad53, was required to both maintain active cyclin-dependent kinase 1, Cdk1(Cdc28), and prevent anaphase entry after checkpoint activation. Evidence suggests that Rad53 exerts its role in checkpoint control through regulation of the Polo kinase Cdc5. These results support a model in which Chk1 and Rad53 function in parallel through Pds1 and Cdc5, respectively, to prevent anaphase entry and mitotic exit after DNA damage. This model provides a possible explanation for the role of Cdc5 in DNA damage checkpoint adaptation.
A Data Stream Management System for Network Traffic Management (2001)

In this short position paper, we will describe the demands of network traffic management applications and we will discuss how a Data Stream Management System can provide a general and scalable platform for deploying these applications. 1 Network Traffic Management The problem of obtaining the best possible network performance in the growing Internet has given rise to the need for efficient network traffic management [2]. Broadly, traffic management can be divided into three tasks: (1) collecting data, e.g., network topology and utilization data, router configuration data; (2) processing the collected data, e.g., to detect problems such as link failure, to determine the best ways to optimize network performance; (3) deploying mechanisms for controlling network traffic. We focus on tasks (1) and (2) in the context of a large Internet Service Provider (ISP) such
Single-shot measurement of the full spatio-temporal field of ultrashort pulses with multi-spectral digital holography (2006)

We present a remarkably simple technique for measuring the full spatio-temporal electric field of a single ultrashort laser pulse. It involves capturing a large digital hologram containing multiple smaller holograms, each of which characterizes the spatial intensity and phase distributions of an individual frequency component of the pulse. From that single camera frame, we numerically reconstruct the complete electric field, E(x,y,t), using a direct algorithm. While holography requires a well-characterized reference pulse, this pulse can easily be generated from the pulse itself in most cases, so the technique is self-referencing. We experimentally demonstrate this technique using femtosecond pulses from a mode-locked Ti:Sapphire oscillator.
Pre‐B Cells and B Lymphocytes in Human Cord Blood and Adult Peripheral Blood (1987)

Abstract The frequencies of pre‐B cells and B lymphocytes subpopulations were studied in 43 cord blood and 21 adult peripheral blood samples using a direct immunofluorescence double staining method. We found pre‐B cells in 40 out of 43 cord blood samples studied, a rate of 93%, and in 16 of 21 adult blood samples, a rate of 76%. The mean frequency of pre‐B cells in cord blood lymphocytes was 0.7%, while that in adult blood lymphocytes was 0.2%. The pre‐B cells in both groups were all small pre‐B cells. The mean frequency of B lymphocytes in cord blood was 11.4%, higher than that in adult blood (5.4%). The difference in B lymphocyte frequency between cord blood and adult blood was exclusively due to high frequency of surface IgM‐positive and IgD‐positive B lymphocytes in the cord blood.
Identification of a Novel Adhesion Molecule Involved in the Virulence ofLegionella pneumophila (2005)

Legionella pneumophila is an intracellular bacterium, and its successful parasitism in host cells involves two reciprocal phases: transmission and intracellular replication. In this study, we sought genes that are involved in virulence by screening a genomic DNA library of an L. pneumophila strain, 80-045, with convalescent-phase sera of Legionnaires' disease patients. Three antigens that reacted exclusively with the convalescent-phase sera were isolated. One of them, which shared homology with an integrin analogue of Saccharomyces cerevisiae, was named L. pneumophila adhesion molecule homologous with integrin analogue of S. cerevisiae (LaiA). The laiA gene product was involved in L. pneumophila adhesion to and invasion of the human lung alveolar epithelial cell line A549 during in vitro coculture. However, its presence did not affect multiplication of L. pneumophila within a U937 human macrophage cell line. Furthermore, after intranasal infection of A/J mice, the laiA mutant was eliminated from lungs and caused reduced mortality compared to the wild isolate. Thus, we conclude that the laiA gene encodes a virulence factor that is involved in transmission of L. pneumophila 80-045 and may play a role in Legionnaires' disease in humans.
CMOS Active Pixel Sensors for Low Power, Highly Miniaturized Imaging Systems (1996)

The complementary metal-oxide-semiconductor (CMOS) active pixel sensor (APS) technology has been developed over the past three years by NASA at the Jet Propulsion Laboratory, and has reached a level of performance comparable to CCDs with greatly increased functionality but at a very reduced power level.
Allelotype of human breast carcinoma: a second major site for loss of heterozygosity is on chromosome 6q. (1991)

Loss of heterozygosity (LOH), which is detected with polymorphic DNA markers by comparing constitutional and tumor genotypes, has been observed at a number of different chromosome arms in primary breast tumors. These include 1p, 1q, 3p, 11p, 13q, 17p and 18q. We present here the results of a screening of all non-acrocentric chromosome arms, including those of the X chromosome, with at least one polymorphic marker per arm, in a total of 86 breast carcinomas. This dataset, termed an allelotype, indicates that in addition to the chromosome regions listed above, allelic loss may be observed in more than 30% of informative cases on 6q, 8q, 9q, 15q, and 16q. Multiple LOH involving at least two different chromosomes in a single tumor was observed in approximately 75% of the investigated tumors, and revealed complex chromosome involvement. Six different combinations of concurrent LOH at two different chromosome arms were found to be significantly correlated (r greater than 0.45; P less than 0.01). Tumors showing LOH at 3p or 17p were preferentially aneuploid, while LOH at 6q and 17q was inversely correlated with the number of positive lymph nodes and age respectively.
An improved chemical approach toward the C‐terminal sequence analysis of proteins containing all natural amino acids (1998)

An improved chemical method, capable of derivatizing all natural amino acids to their corresponding thiohydantoins, is described. This involves activation by acetyl chloride in TFA followed by derivatization with ammonium thiocyanate. Possible interference of reactive side chains was investigated by reacting N-acetylamino acids as well as several peptides with propionyl chloride instead of acetyl chloride. The products were characterized by PDMS mass spectrometry and 1H-NMR. This chemical method allows, for the first time, complete derivatization of N-acetylproline to proline thiohydantoin. Applying this chemistry to peptides with a C-terminal proline, the yields for formation of proline thiohydantoin were found to be up to 60%, depending on the peptide sequence. The previous inability to derivatize C-terminal proline to thiohydantoin was thought to stem from the fact that proline cannot form the oxazolonium ion required for efficient reaction with the thiocyanate ion. However, we have found mass spectrometric evidence for the existence of a proline oxazolonium ion, under basic as well as under acidic conditions. This improvement in derivatization of C-terminal amino acids including proline is a major step forward in the development of a general chemical C-terminal sequencing method that permits the C-terminal sequence analysis of proteins of any amino acid composition.
An integrated genomic analysis of Tudor domain–containing proteins identifies PHD finger protein 20‐like 1 (PHF20L1) as a candidate oncogene in breast cancer (2015)

Tudor domain-containing proteins (TDRDs), which recognize and bind to methyl-lysine/arginine residues on histones and non-histone proteins, play critical roles in regulating chromatin architecture, transcription, genomic stability, and RNA metabolism. Dysregulation of several TDRDs have been observed in various types of cancer. However, neither the genomic landscape nor clinical significance of TDRDs in breast cancer has been explored comprehensively. Here, we performed an integrated genomic and transcriptomic analysis of 41 TDRD genes in breast cancer (TCGA and METABRIC datasets) and identified associations among recurrent copy number alterations, gene expressions, clinicopathological features, and survival of patients. Among seven TDRDs that had the highest frequency (>10%) of gene amplification, the plant homeodomain finger protein 20-like 1 (PHF20L1) was the most commonly amplified (17.62%) TDRD gene in TCGA breast cancers. Different subtypes of breast cancer had different patterns of copy number and expression for each TDRD. Notably, amplification and overexpression of PHF20L1 were more prevalent in aggressive basal-like and Luminal B subtypes and were significantly associated with shorter survival of breast cancer patients. Furthermore, knockdown of PHF20L1 inhibited cell proliferation in PHF20L1-amplified breast cancer cell lines. PHF20L1 protein contains N-terminal Tudor and C-terminal plant homeodomain domains. Detailed characterization of PHF20L1 in breast cancer revealed that the Tudor domain likely plays a critical role in promoting cancer. Mechanistically, PHF20L1 might participate in regulating DNA methylation by stabilizing DNA methyltransferase 1 (DNMT1) protein in breast cancer. Thus, our results demonstrated the oncogenic potential of PHF20L1 and its association with poor prognostic parameters in breast cancer.
Capacitive Resistivity Imaging with Towed Arrays (2007)

Abstract The capacitive resistivity (CR) technique is a generalization of the conventional DC resistivity method that facilitates measurements of electrical resistivity on engineered surfaces and highly resistive ground. The CR methodology allows the use of towed sensor arrays, thus enabling the rapid collection of high-resolution resistivity data. Under quasi-static conditions, CR data are equivalent to galvanic DC measurements so that CR datasets can be interpreted with conventional DC inversion algorithms. In this study, we demonstrate that the methodology and fundamental parameters of the CR technique facilitate spatial sampling at the centimeter scale for towing speeds of the order of 2.5 km/h. We argue that the dipole-dipole array is the most suitable geometry for dynamic CR measurements and present example data acquired with a prototype instrument using plate-wire combinations arranged in an equatorial geometry. The information content of raw CR data is found to be dominant over towing-induced noise and a direct comparison with DC profile data shows good agreement between both techniques. Based on these findings, we show that tomographic imaging is possible using datasets acquired with moving arrays. Closer investigation of the practical aspects of towed-array capacitive resistivity imaging (CRI) highlights the similarities with galvanic multi-electrode surveys, but the different geometric constraints and sampling regime of CRI give rise to advantages (high lateral resolution) as well as disadvantages (limitations in vertical resolution). We conclude our study with recommendations for practical CRI survey procedures and present a field example where we have successfully imaged a subsurface target in 3D. Towed-array CRI is found to provide equivalent (and in some ways superior) information about the shallow subsurface when compared to DC ERT (electrical resistivity tomography); it therefore widens the scope of electrical imaging surveys to environments where the conventional methodology would be impractical.
[Noninvasive monitoring of the hepatocellular carcinoma growth by the method of 1H and 23Na nuclear magnetic resonance]. (2009)

Using diffusion weighted 1H, single-quantum 23Na and triple-quantum-filtered 23Na magnetic resonance imaging water apparent diffusion coefficient (ADC), total tissue Na+ and intracellular Na+ were monitored in hepatocellular carcinoma (HCC) in rats and in the surrounding liver tissue. The tumor water ADC was approximately 50% higher compared to the nearby healthy liver tissue but did not increase during 28 days of tumor growth (double time 3.9 days). The HCC growth was associated with an increase in both total tissue and intracellular 23Na signal intensity especially after 21 days post-cell inoculation reflecting possible changes in extracellular space and in intracellular ionic metabolism.
Meta-analysis of gene expression data: a predictor-based approach (2007)

Abstract Motivation: With the increasing availability of cancer microarray data sets there is a growing need for integrative computational methods that evaluate multiple independent microarray data sets investigating a common theme or disorder. Meta-analysis techniques are designed to overcome the low sample size typical to microarray experiments and yield more valid and informative results than each experiment separately. Results: We propose a new meta-analysis technique that aims at finding a set of classifying genes, whose expression level may be used to answering the classification question in hand. Specifically, we apply our method to two independent lung cancer microarray data sets and identify a joint core subset of genes which putatively play an important role in tumor genesis of the lung. The robustness of the identified joint core set is demonstrated on a third unseen lung cancer data set, where it leads to successful classification using very few top-ranked genes. Identifying such a set of genes is of significant importance when searching for biologically meaningful biomarkers. Contact: ruppin@post.tau.ac.il Supplementary information: Supplementary data are available at Bioinformatics online.
An Attack Surface Metric (2010)

Measurement of software security is a long-standing challenge to the research community. At the same time, practical security metrics and measurements are essential for secure software development. Hence, the need for metrics is more pressing now due to a growing demand for secure software. In this paper, we propose using a software system's attack surface measurement as an indicator of the system's security. We formalize the notion of a system's attack surface and introduce an attack surface metric to measure the attack surface in a systematic manner. Our measurement method is agnostic to a software system's implementation language and is applicable to systems of all sizes; we demonstrate our method by measuring the attack surfaces of small desktop applications and large enterprise systems implemented in C and Java. We conducted three exploratory empirical studies to validate our method. Software developers can mitigate their software's security risk by measuring and reducing their software's attack surfaces. Our attack surface reduction approach complements the software industry's traditional code quality improvement approach for security risk mitigation and is useful in multiple phases of the software development lifecycle. Our collaboration with SAP demonstrates the use of our metric in the software development process.
Inhibition of NF-KB-Rel A expression by antisense oligodeoxynucleotides suppresses synthesis of urokinase-type plasminogen activator (uPA) but not its inhibitor PAl-1 (1995)

The essential role of urokinase-type plasminogen activator (uPA) in tumor invasion and metastasis stresses the necessity of a fine-tuned cellular control over its expression. It has been shown that changes in uPA directly correlate with changes in cell invasiveness. We examined the role of Rel-related proteins in uPA synthesis by human ovarian cancer cells by inhibiting their expression using the antisense (AS) oligodeoxynucleotide (ODN) technology. Exposure of OV-MZ-6 cells to 10 microM phosphorothioate (PS)-derivatized AS-ODN directed to Rel A led to a maximal 50% decrease of uPA antigen in cell lysates and a 70% reduction in cell cultures supernatants accompanied by a significant transient decline in uPA mRNA levels. Antisense-PS-ODN directed to NF-kappa B1 (p50) or c-rel had no effect on uPA protein expression. AS-PS-ODN directed to Rel A also affected the proteolytic capacity of OV-MZ-6 cells reflected by an approximately 70% decrease in the fibrinolytic capacity of the cells within 24 h compared to untreated controls. AS-PS-ODN directed to I kappa B alpha expression increased uPA in cell culture supernatants up to 50%. uPA receptor (uPAR) production and synthesis of plasminogen activator inhibitor type-1 (PAI-1) were not altered by either AS-PS-ODN applied. Western blot and gel retardation analyses revealed constitutive expression of Rel-related proteins in nuclear protein extracts of OV-MZ-6 cells. Thus these proteins seem to be implicated in uPA regulation and may thereby contribute to tumor spread and metastasis.
Optimum quantizer performance for a class of non-Gaussian memoryless sources (1984)

The performance of optimum quantizers subject to an entropy constraint is studied for a wide class of memoryless sources. For a general distortion criterion, necessary conditions are developed for optimality and a recursive algorithm is described for obtaining the optimum quantizer. Under a mean-square error criterion, the performance of entropy encoded uniform quantization of memoryless Gaussian sources is well-known to be within <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.255</tex> bits/sample of the rate-distortion bound at relatively high rates. Despite claims to the contrary, it is demonstrated that similar performance can be expected for a wide range of memoryless sources. Indeed, for the cases considered, the worst case performance is observed to be less than <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.3</tex> bits/sample from the rate-distortion bound, and in most cases this disparity is less at Iow rates.
Is inclusivism possible? (1997)

ABSTRACT This paper begins by analysing the notion of inclusion, the experiences which give rise to it and the set of ideas, termed ‘Inclusivism’, which animate it. It illustrates how the notion might operate in practice by reference to the situation of visually impaired children in schools, and examines the scope for an inclusive approach in a variety of other contexts, such as the built environment and the dissemination of information. It distinguishes between different types of inclusivism ‐ hard, soft and stupid ‐ and suggests that the quest for full inclusion may be illusory, on the ground that the notion, in its most thoroughgoing form, is both Utopian and elitist
On a Generalized Framework for Modeling the Effects of Process Variations on Circuit Delay Performance Using Response Surface Methodology (2007)

A generalized methodology for modeling the effects of process variations on circuit delay performance is proposed by directly relating the variations in process parameters to variations in delay metric of a digital circuit. The 2-input nand gate is used as a library element for 65 nm gate length technology, whose delay is extensively characterized by mixed-mode simulations. This information is then used in a general-purpose circuit simulator SEQUEL, by incorporating appropriate templates for the nand gate library. A 4-bit times 4-bit Wallace tree multiplier circuit, consisting of about 300 2-input nand gates, is used as a representative combinational circuit to demonstrate the proposed methodology. The variation in the multiplier delay is characterized by an extensive Monte Carlo analysis. To extend this methodology for a generic technology library with a variety of library elements, modeling of nand gate delays by response surface methodology (RSM), in terms of process parameters, is carried out using design of experiments (DOE). A simple piecewise quadratic model, based on the least squares method (LSM), is proposed for one-parameter variation to address significant cubic effects observed in the delay response function. Then, a hybrid model for gate delays is generated by superimposing the interaction terms of DOE-RSM model upon the quadratic model of one-parameter variation to address the generalized case of simultaneous variations in multiple process parameters. The proposed methodology has been demonstrated for nand gate library with 266 gates, and the simplicity and generality of the approach make it equally applicable to a large library of cells for both statistical timing analysis and statistical circuit simulation at the gate level