gebhart/patrepeval huggingface dataset:
Detecting and Preventing Drive-By Download Attack via Participative Monitoring of the Web (2013)

Drive-by Download Attack (DBD) is one of the major threats on the web infrastructure. DBD attacks are triggered by user access to a malicious website and force users to download malware by exploiting the vulnerabilities of web browsers or plugins. Malicious websites are ephemeral. Therefore, it is necessary to gather fresh information related to malicious activities to detect and prevent such attacks. In this paper, we propose a framework that combats with DBD attacks with users' voluntary monitoring of the web. This framework tackles the two issues: ways to obtain up-to-date information related malicious activities and ways to provide up-to-date information to the world. The framework aims to realize a security ecosystem: users actively offer information about their activities on the web (e.g. access URL, download contents), and security analysts inspect the information to detect new threats and devise countermeasures for any new threats and then provide the countermeasures to users as feedback. The framework consists of sensors located on the user side and a centralized center located on the network side. Sensors are deployed in the web browser, in web proxies, and DNS servers. Sensors monitors the access URLs download contents, the method of triggering the link events (e.g. mouse click, move, redirected by the server), then the sensors report the data to the center. The center analyzes the data, derives the statistical data and the web link structure, and detects new threats by facilitating the characteristics of malicious web pages. This paper also shows a real world example that demonstrates the potential of our framework. The example implies that our focus on the change of the web link structure can detect illegal falsification of web pages. Our framework can obtain long-term data on how many hosts users are forced to access by the access of a web page, so we believe that our framework can distinguish legitimate changes in web pages with compromised changes.
A Novel Platform for Detection of CK+ and CK− CTCs (2011)

Current assays for CTC capture likely miss populations of cells that have undergone EMT. Capture and study of CTCs that have undergone EMT would allow a better understanding of the mechanisms driving metastasis.
Identification of a transcriptional repressor related to the noncatalytic domain of histone deacetylases 4 and 5 (2000)

Histone deacetylases (HDACs) are involved in regulating transcription by modifying the core histones of the nucleosome. To date, six HDACs have been identified in mammalian cells: the yeast RPD3 homologs HDAC1, 2, and 3 and the yeast HDA1 homologs HDAC4, 5, and 6. HDAC4 and HDAC5 contain a noncatalytic N-terminal domain. Herein, we report the identification of a protein HDRP (HDAC-related protein) that shares 50% identity in deduced amino acid sequence to the noncatalytic N-terminal domain of HDAC4 and 5. The steady-state levels of HDRP mRNA are high in human brain, heart, and skeletal muscle and low in the several other tissues. HDRP has an apparent molecular mass of approximately 75 kDa. HDRP does not possess intrinsic HDAC activity but forms complexes with both HDAC1 and HDAC3. HDRP represses both basal and activated transcription in transient transfection assays when tethered to DNA as a Gal4-fusion protein. HDAC inhibitors do not reverse transcriptional repression mediated by Gal4-HDRP. Thus, HDRP is a transcriptional repressor and can repress transcription in the presence of HDAC inhibitors.
<title>Imaging genes, chromosomes, and nuclear structures using laser-scanning confocal microscopy</title> (1990)

For 350 years, the optical microscope has had a powerful symbiotic relationship with biology. Until this century, optical microscopy was the only means of examining cellular structure; in return, biologists have contributed greatly to the evolution of microscope design and technique. Recent advances in the detection and processing of optical images, together with methods for labelling specific biological molecules, have brought about a resurgence in the application of optical microscopy to the biological sciences. One of the areas in which optical microscopy is breaking new ground is in elucidating the large scale organization of chromatin in chromosomes and cell nuclei. Nevertheless, imaging the contents of the cell nucleus is a difficult challenge for light microscopy, for two principal reasons. First, the dimensions of all but the largest nuclear structures (nucleoli, vacuoles) are close to or below the resolving power of far field optics. Second, the native optical contrast properties of many important chromatin structures (eg. chromosome domains, centromere regions) are very weak, or essentially zero. As an extreme example, individual genes probably have nothing to distinguish them other than their sequence of DNA bases, which cannot be directly visualized with any current form of microscopy. Similarly, the interphase nucleus shows no direct visible evidence of focal chromatin domains. Thus, imaging of such entities depends heavily on contrast enhancement methods. The most promising of these is labelling DNA in situ using sequence-specific probes that may be visualized using fluorescent dyes. We have applied this method to detecting individual genes in metaphase chromosomes and interphase nuclei, and to imaging a number of DNA-containing structures including chromosome domains, metaphase chromosomes and centromere regions. We have also demonstrated the applicability of in situ fluorescent labelling to detecting numerical and structural abnormalities both in condensed metaphase chromosomes and in interphase nuclei. The ability to image the loci of fluorescent-labelled gene probes hybridized to chromosomes and to interphase nuclei will play a major role in the mapping of the human genome. This presentation is an overview of our laboratory's efforts to use confocal imaging to address fundamental questions about the structure and organization of genes, chromosomes and cell nuclei, and to develop applications useful in clinical diagnosis of inherited diseases.
High-performance liquid chromatography of proteins on stabilized polymer-diol-bonded silica-gel stationary phase (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHigh-performance liquid chromatography of proteins on stabilized polymer-diol-bonded silica-gel stationary phaseGyula. Szabo, Katalin. Offenmuller, and Edit. CsatoCite this: Anal. Chem. 1988, 60, 3, 213–216Publication Date (Print):February 1, 1988Publication History Published online1 May 2002Published inissue 1 February 1988https://pubs.acs.org/doi/10.1021/ac00154a005https://doi.org/10.1021/ac00154a005research-articleACS PublicationsRequest reuse permissionsArticle Views115Altmetric-Citations7LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Abnormalities in Monocyte Recruitment and Cytokine Expression in Monocyte Chemoattractant Protein 1–deficient Mice (1998)

Monocyte chemoattractant protein 1 (MCP-1) is a CC chemokine that attracts monocytes, memory T lymphocytes, and natural killer cells. Because other chemokines have similar target cell specificities and because CCR2, a cloned MCP-1 receptor, binds other ligands, it has been uncertain whether MCP-1 plays a unique role in recruiting mononuclear cells in vivo. To address this question, we disrupted SCYA2 (the gene encoding MCP-1) and tested MCP-1-deficient mice in models of inflammation. Despite normal numbers of circulating leukocytes and resident macrophages, MCP-1(-/-) mice were specifically unable to recruit monocytes 72 h after intraperitoneal thioglycollate administration. Similarly, accumulation of F4/80+ monocytes in delayed-type hypersensitivity lesions was impaired, although the swelling response was normal. Development of secondary pulmonary granulomata in response to Schistosoma mansoni eggs was blunted in MCP-1(-/-) mice, as was expression of IL-4, IL-5, and interferon gamma in splenocytes. In contrast, MCP-1(-/-) mice were indistinguishable from wild-type mice in their ability to clear Mycobacterium tuberculosis. Our data indicate that MCP-1 is uniquely essential for monocyte recruitment in several inflammatory models in vivo and influences expression of cytokines related to T helper responses.
Implementing a University Paradigm for Effective Community Engagement (2007)

Community engagement is emerging as a core function of Australian universities and their faculties. The collaboration and development of effective and sustainable partnerships can strengthen the role of the university within the community and influence those who formulate policy. This paper reports on the development and implementation of key principles and processes that are foundational to community engagement: relationship formation; sustainability; forming mutually beneficial goals; mentoring; social justice frameworks; communication; awareness-raising; identifying social injustice issues and inequalities that need to be investigated and addressed; and supportive university structures. These principles and processes are illuminated through two key community engagement projects involving the Faculty of Education. The first is the development of a teacher education program in Bachau, East Timor, and the second is a community based tertiary education program, Clemente, for the poor and marginalised within Australia’s society. Through these programs, Australian Catholic University has evolved an understanding of the critical relevance of community engagement in making a difference in peoples’ lives. Further, the programs have provided additional insights into the organisational structures required for effective community engagement. These include recognition of the time involved in forming, developing and maintaining relationships, and negotiating and implementing community engagement activities.
Extremely Flexible Nanoscale Ultrathin Body Silicon Integrated Circuits on Plastic (2012)

In recent years, flexible devices based on nanoscale materials and structures have begun to emerge, exploiting semiconductor nanowires, graphene, and carbon nanotubes. This is primarily to circumvent the existing shortcomings of the conventional flexible electronics based on organic and amorphous semiconductors. The aim of this new class of flexible nanoelectronics is to attain high-performance devices with increased packing density. However, highly integrated flexible circuits with nanoscale transistors have not yet been demonstrated. Here, we show nanoscale flexible circuits on 60 Å thick silicon, including functional ring oscillators and memory cells. The 100-stage ring oscillators exhibit the stage delay of ~16 ps at a power supply voltage of 0.9 V, the best reported for any flexible circuits to date. The mechanical flexibility is achieved by employing the controlled spalling technology, enabling the large-area transfer of the ultrathin body silicon devices to a plastic substrate at room temperature. These results provide a simple and cost-effective pathway to enable ultralight flexible nanoelectronics with unprecedented level of system complexity based on mainstream silicon technology.
Synthesis of Conformationally Constrained DTPA Analogs. Incorporation of the Ethylenediamine Units as Aminopyrrolidines (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of Conformationally Constrained DTPA Analogs. Incorporation of the Ethylenediamine Units as AminopyrrolidinesMatthew A. Williams and Henry RapoportCite this: J. Org. Chem. 1994, 59, 13, 3616–3625Publication Date (Print):July 1, 1994Publication History Published online1 May 2002Published inissue 1 July 1994https://doi.org/10.1021/jo00092a022RIGHTS & PERMISSIONSArticle Views681Altmetric-Citations31LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (1 MB) Get e-Alerts Get e-Alerts
Nuclear protein profiling of Jurkat cells during heat stress‐induced apoptosis by 2‐DE and MS/MS (2007)

Abstract Heat stress causes severe constraints on numerous physiological functions of cells, such as the repression of splicing of mRNA precursors. In this study, we performed proteomic profiling of a nuclear fraction of Jurkat cells during heat stress using 2‐DE and LC‐MS/MS. We found 10 protein spots whose expression had changed after heat stress at 43°C for 30 min. Seven of those protein spots, periodic tryptophan protein 1 homolog (PWP1), importin β‐1 subunit, sumoylated protein, splicing factor 3a subunit 3 (SF3a3), TAR DNA‐binding protein 43, U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit (U2AF35) and small ubiquitin‐related modifier‐1 (SUMO‐1) were downregulated, while three other protein spots, Protein SET, 40S ribosomal protein SA and 60S acidic ribosomal protein P0 were upregulated by the heat stress. We focused on the downregulation of two splicing factors, which might participate in the repression of pre‐mRNA processing by heat stress, leading to cell apoptosis.
Structural features of ribonucleotide reductase (1986)

Herpes simplex virus type 1 (HSV-1) encodes a ribonucleotide reductase which comprises two polypeptides with sizes of 136,000 (RR1) and 38,000 mol. wt. (RR2). We have determined the entire DNA sequence specifying HSV-1 RR1 and have identified two adjacent open reading frames in varicella-zoster virus (VZV) which have homology to HSV RR1 and RR2; the predicted sizes for the VZV RR1 and RR2 polypeptides are 87,000 and 35,000 mol. wt. respectively. Amino acid comparisons with RR1 and RR2 polypeptides from other organisms indicate that HSV-1 RR1 contains a unique N-terminal domain which is absent from other RR1 polypeptides apart from HSV-2 RR1. These N-terminal amino acid sequences are poorly conserved between HSV-1 and HSV-2 in contrast to the remainder of the protein which shows greater than 90% homology. Polypeptide structural predictions suggest that the HSV-1 N-terminal domain may be separated into two regions, namely, a beta-sheet structure followed by a nonstructured area. Across the remainder of RR1 and RR2, comparisons also reveal blocks of amino acids conserved between the different ribonucleotide reductases, and these may be important for enzyme activity. From predictions on the structure of these conserved blocks, we have proposed that the location of a substrate binding site within RR1 is centered on three conserved glycine residues in a region which is predicted to adopt a beta-sheet/turn/alpha-helical structure; this approximates to the structure for ADP nucleotide binding folds. Finally, we propose that the promoters for the HSV and Epstein-Barr virus (EBV) RR2 transcripts have evolved by separate evolutionary routes.
Defects in secretion, aggregation, and thrombus formation in platelets from mice lacking Akt2 (2004)

Prior studies have shown that PI3Ks play a necessary but incompletely defined role in platelet activation. One potential effector for PI3K is the serine/threonine kinase, Akt, whose contribution to platelet activation was explored here. Two isoforms of Akt were detected in mouse platelets, with expression of Akt2 being greater than Akt1. Deletion of the gene encoding Akt2 impaired platelet aggregation, fibrinogen binding, and granule secretion, especially in response to low concentrations of agonists that activate the G(q)-coupled receptors for thrombin and thromboxane A(2). Loss of Akt2 also impaired arterial thrombus formation and stability in vivo, despite having little effect on platelet responses to collagen and ADP. In contrast, reducing Akt1 expression had no effect except when Akt2 was also deleted. Activation of Akt by thrombin was abolished by deletion of Galpha(q) but was relatively unaffected by deletion of Galpha(i2), which abolished Akt activation by ADP. From these results we conclude that Akt2 is a necessary component of PI3K-dependent signaling downstream of G(q)-coupled receptors, promoting thrombus growth and stability in part by supporting secretion. The contribution of Akt1 is less evident except in the setting in which Akt2 is absent.
Adipose tissue stearoyl-CoA desaturase mRNA is increased by obesity and decreased by polyunsaturated fatty acids (1996)

Stearoyl-CoA desaturase (SCD) is a key regulatory enzyme in the synthesis of unsaturated fatty acids. Although regulation of hepatic SCD by obesity and polyunsaturated fatty acids (PUFA) has been well investigated, no studies have addressed whether similar regulation occurs in adipose tissue. We addressed these questions by feeding control (12% corn oil) and high-PUFA (48% corn oil) diets to lean and obese Zucker rats and analyzing SCD mRNA levels in adipose tissue and liver. We report that SCD mRNA content was dramatically elevated in adipose tissue of obese vs. lean rats on both diets and was significantly decreased by PUFA in both genotypes. Interestingly, we demonstrate that SCD expression was directly downregulated in a dose dependent manner by PUFA in 3T3-L1 adipocytes. We conclude that 1) obese Zucker rats overexpress the SCD gene in both liver and adipose tissue and 2) PUFA directly suppress SCD expression in adipocytes. Further studies will elucidate the mechanisms responsible for obesity- and PUFA-mediated regulation of SCD in adipose cells.
Configuration Tree Solver: A Technology for Automated Design and Configuration (1992)

Configuration is a process of generating a definitive description of a product that satisfies a set of specified requirements and known constraints. Knowledge-based technology is an important factor in automation of configuration tasks found in mechanical design. In this paper, we describe a configuration technique that is well suited for configuring “decomposable” artifacts with reasonably well defined structure and constraints. This technique may be classified as a member of a general class of decompositional approaches to configuration. The domain knowledge is structured as a general model of the artifact, an and-or hierarchy of the artifact’s elements, features, and characteristics. The model includes constraints and local specialists which are attached to the elements of the and-or tree. Given the specific configuration requirements, the problem solving engine searches for a solution, a subtree, that satisfies the requirements and the applicable constraints. We describe an application of this approach that performs configuration and design of an automotive component.
Inhibition of AKT survival pathway by a small molecule inhibitor in human endometrial cancer cells (2004)

The PTEN (phosphatase and tensin homolog deleted on chromosome 10) tumour suppressor is mutated in 40-50% of human endometrial cancers. PTEN exerts its effects in part via inhibition of the antiapoptotic protein AKT. We demonstrate that two endometrial cancer cell lines that harbour PTEN mutations, Ishikawa and RL95-2, have high levels of phosphorylated AKT and high AKT kinase activity. Two additional endometrial cancer cell lines that express wild-type PTEN, Hec1A and KLE, have little phosphorylated AKT and minimal demonstrable AKT kinase activity. We tested a potential inhibitor of the AKT pathway, API-59CJ-OMe, in these four cell lines. We found that API-59CJ-OMe inhibits AKT kinase activity and induces apoptosis in the Ishikawa and RL95-2 cell lines with high AKT activity, but has little effect on Hec1A and KLE cells without AKT activity. API-59CJ-OMe may therefore have therapeutic potential for those endometrial cancers that harbour PTEN mutations and AKT activation.
Engineering of high-precision base editors for site-specific single nucleotide replacement (2019)

RNA-guided nucleases of the CRISPR/Cas type can be repurposed as programmable nucleotide deaminases to mediate targeted nucleotide substitutions. Such base editors have enormous potential in genome editing, gene therapy and precision breeding. However, current editors suffer from limited specificity in that they edit different and/or multiple bases within a larger sequence window. Using cytidine deaminase base editors that elicit C-to-T mutations, we show here that high editing precision can be achieved by engineering the connection between the deaminase domain and the Cas domain of the editor. By systematically testing different linker sequences and removing non-essential sequences from the deaminase, we obtain high-precision base editors with narrow activity windows that can selectively edit a single cytidine at a specific position with high accuracy and efficiency. These base editors will enable the use of genome editing in applications where single-nucleotide changes are required and off-target editing of adjacent nucleotides is not tolerable.
Control of Feshbach resonances by quantum interference (2002)

We describe how a quasibound state that is in Feshbach resonance with an incoming atom wave and is coupled to a nondecaying bound state by an electromagnetic field will exhibit a quantum interference that controls the collision dynamics. By varying the frequency of a coupling field, the elastic cross section may be modulated. By varying the amplitude of a coupling field, the bound diatomic population may be increased by several orders of magnitude.
Nephrogenic Systemic Fibrosis and Class Labeling of Gadolinium-based Contrast Agents by the Food and Drug Administration (2012)

In 2007, the Food and Drug Administration requested that manufacturers of all approved gadolinium-based contrast agents (GBCAs), drugs widely used in magnetic resonance imaging, use nearly identical text in their product labeling to describe the risk of nephrogenic systemic fibrosis (NSF). Accumulating information about NSF risks led to revision of the labeling text for all of these drugs in 2010. The present report summarizes the basis and purpose of this class-labeling approach and describes some of the related challenges, given the evolutionary nature of the NSF risk evidence. The class-labeling approach for presentation of product risk is designed to decrease the occurrence of NSF and to enhance the safe use of GBCAs in radiologic practice.
Protein Microarray for Disease Analysis (2011)

Protein microarrays have been used for a wide variety of important tasks, such as identifying protein-protein interactions, discovering disease biomarkers, identifying DNA-binding specificity by prote