gebhart/patrepeval huggingface dataset:
Fully persistent B+-trees (1991)

article Free Access Share on Fully persistent B+-trees Authors: Sitaram Lanka Computer Science Department, The Pennsylvania State University, University Park, PA Computer Science Department, The Pennsylvania State University, University Park, PAView Profile , Eric Mays IBM T.J. Watson Research Center, P.O. Box 218, Yorktown Heights, NY IBM T.J. Watson Research Center, P.O. Box 218, Yorktown Heights, NYView Profile Authors Info & Claims ACM SIGMOD RecordVolume 20Issue 2June 1991 pp 426–435https://doi.org/10.1145/119995.115861Online:01 April 1991Publication History 59citation978DownloadsMetricsTotal Citations59Total Downloads978Last 12 Months28Last 6 weeks5 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Naggen: A network attack graph generation tool — IEEE CNS 17 poster (2017)

Attack graphs constitute a powerful security tool aimed at modelling the many ways in which an attacker may compromise different assets in a network. Despite their usefulness in several security-related activities (e.g. hardening, monitoring, forensics), the complexity of these graphs can massively grow as the network becomes denser and larger, thus defying their practical usability. In this presentation, we first describe some of the problems that currently challenge the practical use of attack graphs. We then explain our approach based on core attack graphs, a novel perspective to address attack graph complexity. Finally, we present Naggen, a tool for generating, visualising and exploring core attack graphs. We use Naggen to show the advantages of our approach on different security applications.
Biodegradable polymers based on renewable resources. IV. Enzymatic degradation of polyesters composed of 1,4:3.6-dianhydro-D-glucitol and aliphatic dicarboxylic acid moieties (2000)

Enzymatic degradation of a series of polyesters prepared from 1,4:3.6-dianhydro-D-glucitol (1) and aliphatic dicarboxylic acids of the methylene chain length ranging from 2 to 10 were examined using seven different enzymes. Enzymatic degradability of these polyesters as estimated by water-soluble total organic carbon (TOC) measurement is dependent on the methylene chain length (m) of the dicarboxylic acid component for most of the enzymes examined. The most remarkable substrate specificity was observed for Rhizopus delemar lipase, which degraded polyester derived from 1 and suberic acid (m = 6) most readily. In contrast, degradation by Porcine liver esterase was nearly independent of the structure of the polyesters. Enzymatic degradability of the polyesters based on three isomeric 1,4:3.6-dianhydrohexitols and sebacic acid was found to decrease in the order of 1, 1,4:3.6-dianhydro-D-mannitol (2), and 1,4:3.6-dianhydro-L-iditol (3). Structural analysis of water-soluble degradation products formed during the enzymatic hydrolysis of polyester 5g derived from 1 and sebacic acid has shown that the preferential ester cleavage occurs at the O(5) position of 1,4:3.6-dianhydro-D-glucitol moiety in the polymer chain by enzymes including Porcine pancreas lipase, Rhizopus delemar lipase, and Pseudomonas sp. lipase. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 77: 338–346, 2000
Practical Byzantine fault tolerance (1999)

This paper describes a new replication algorithm that is able to tolerate Byzantine faults. We believe that Byzantinefault-tolerant algorithms will be increasingly important in the future because malicious attacks and software errors are increasingly common and can cause faulty nodes to exhibit arbitrary behavior. Whereas previous algorithms assumed a synchronous system or were too slow to be used in practice, the algorithm described in this paper is practical: it works in asynchronous environments like the Internet and incorporates several important optimizations that improve the response time of previous algorithms by more than an order of magnitude. We implemented a Byzantine-fault-tolerant NFS service using our algorithm and measured its performance. The results show that our service is only 3% slower than a standard unreplicated NFS.
Nearest-Neighbor Sample Compression: Efficiency, Consistency, Infinite Dimensions (2017)

We examine the Bayes-consistency of a recently proposed 1-nearest-neighbor-based multiclass learning algorithm. This algorithm is derived from sample compression bounds and enjoys the statistical advantages of tight, fully empirical generalization bounds, as well as the algorithmic advantages of a faster runtime and memory savings. We prove that this algorithm is strongly Bayes-consistent in metric spaces with finite doubling dimension --- the first consistency result for an efficient nearest-neighbor sample compression scheme. Rather surprisingly, we discover that this algorithm continues to be Bayes-consistent even in a certain infinite-dimensional setting, in which the basic measure-theoretic conditions on which classic consistency proofs hinge are violated. This is all the more surprising, since it is known that $k$-NN is not Bayes-consistent in this setting. We pose several challenging open problems for future research.
Binding interactions of kistrin with platelet glycoprotein IIb‐IIIa: Analysis by site‐directed mutagenesis (1993)

The binding interactions between platelet fibrinogen receptor, glycoprotein (GP) IIb-IIIa, and kistrin, a snake venom disintegrin protein that contains the adhesion site recognition sequence Arg-Gly-Asp (RGD) and potently inhibits platelet aggregation, have been investigated by site-directed mutagenesis of a synthetic kistrin gene. Kistrin was expressed as a fusion protein in Escherichia coli under control of the alkaline phosphatase promoter. This construction included the stII signal sequence to direct secretion to the periplasmic space and one synthetic (Z) domain of Staphylococcal protein A to allow affinity purification using IgG Sepharose. Kistrin was cleaved from the Z-domain by site-specific proteolysis using a mutant subtilisin BPN' and purified by reverse-phase HPLC. This approach facilitated the rapid purification of a set of 43 alanine replacement mutants whose relative affinity for GP IIb-IIIa was measured by competition with immobilized kistrin and by inhibition of platelet aggregation in human platelet-rich plasma. Alanine replacements at R49, G50, and D51 led to weaker inhibitors of platelet aggregation by 90-fold, 2-fold, and > 200-fold, respectively. The conservative D51E mutant was still > 100-fold less potent whereas R49K had a minor effect (1.8-fold), implying the critical nature of the aspartate for high affinity binding. However, mutations outside of the RGD region led to proteins indistinguishable from kistrin, suggesting no substantial secondary binding interactions. Furthermore, reduced kistrin is not active. We therefore propose that a favorable conformation of the RGD region alone is responsible for the high affinity binding of kistrin to GP IIb-IIIa.
Nucleotide sequence and expression of the cloned gene of bacteriphage SP6 RNA polymerase (1987)

The coding region of the gene for bacteriophage SP6 RNA polymerase was cloned into pBR322, and its entire nucleotide sequence was deduced. The predicted amino acid sequence for the polymerase consists of 874 amino acid residues with a total molecular weight of 98,561 daltons. Comparison of the amino acid sequence with that of T7 RNA polymerase reveals that regions with partial homology are present along the sequence. The coding region of SP6 RNA polymerase was inserted into an E. coli expression vector. The polymerase gene was efficiently expressed in E. coli cells, and the enzymatic properties of the expressed polymerase were very similar to those of the enzyme synthesized in SP6 phage-infected Salmonella typhimurium cells.
Extraction and Analysis of the Single Motor Unit F-Wave of the Median Nerve (2012)

The matrix type multielectrodes have been proved to be useful for getting the information of motor unit (MU) properties (Monster et al., 1980; Reucher et al., 1987; Yamada et al., 1987; Masuda and Sadoyama, 1988; Kleine et al., 2000; Gazzoni et al., 2004). By this electromyography (EMG) technique, we can obtain many essential properties of MU that could not be obtained by conventional surface EMG and/or needle EMG. One of them is the waveform property of motor unit action potential (MUAP) which is enabled by extracting the single propagating MUAP. Another is the two-dimensional location of motor end-plates. There have been many applications of multichannel surface EMG for measuring voluntary muscle activities, but few for evoked EMG responses. However, recent studies have demonstrated the applications of the multichannel surface EMG for the measurement of muscle fiber conduction velocities (MFCVs) (Metani et al., 2005) , for the estimation of firing thresholds (Yamada, 2004), and for the motor unit number estimate (MUNE) (Blok et al., 2005; van Dijk et al., 2008). The F-wave represents a long latency response detected from a muscle following stimulation of a peripheral nerve at supramaximal intensity. The F-waves are produced by antidromic activation of motor neurons. The latency and the waveform of the F-wave change with each stimulus. The F-wave studies are widely used in clinical neurophysiology as a quantitative estimation method of the objective pathological changes. The F-waves that consist of a single MUAP occur also with submaximal stimulation. Low intensity stimulation could increase the probability of the single MU F-wave (Komori et al., 1991; Doherty et al., 1994; Stashuk et al., 1994; Yamada, 2004), and reduce the discomfort of the subjects. Therefore, different MUAPs can be readily analyzed by classifying F-waves. Many studies concerned with the single MU F-wave were performed for the estimation of the conduction velocity of nerve fibers (Doherty et al., 1994; Felice, 1998; Wang et al., 1999) and the MUNE (Stashuk et al., 1994; Hara et al., 2000). The conventional surface EMG technique was used in these studies, and there were few applications of multichannel surface EMG for F-wave studies. In a previous study, we investigated the classification and analysis of multichannel bipolar F-waves (Yamada et al., 2007). It is difficult to detect deep MUs from the bipolar EMG. So, in the present study, the thenar MUs F-waves were investigated by extracting single MU Fwaves from monopolar multichannel surface EMG signals. By increasing the number of
Single treatment with RNAi against prion protein rescues early neuronal dysfunction and prolongs survival in mice with prion disease (2008)

Prion diseases are fatal neurodegenerative conditions for which there is no effective treatment. Prion propagation involves the conversion of cellular prion protein, PrP(C), to its conformational isomer, PrP(Sc), which accumulates in disease. Here, we show effective therapeutic knockdown of PrP(C) expression using RNAi in mice with established prion disease. A single administration of lentivirus expressing a shRNA targeting PrP into each hippocampus of mice with established prion disease significantly prolonged survival time. Treated animals lived 19% and 24% longer than mice given an "empty" lentivirus, or not treated, respectively. Lentivirally mediated RNAi of PrP also prevented the onset of behavioral deficits associated with early prion disease, reduced spongiform degeneration, and protected against neuronal loss. In contrast, mice receiving empty virus or no treatment developed early cognitive impairment and showed severe spongiosis and neuronal loss. The focal use of RNAi therapeutically in prion disease further supports strategies depleting PrP(C), which we previously established to be a valid target for prion-based treatments. This approach can now be used to define the temporal, quantitative, and regional requirements for PrP knockdown for effective treatment of prion disease and to explore mechanisms involved in predegenerative neuronal dysfunction and its rescue.
Piecing Together the Mosaic of Early Mammalian Development through MicroRNAs (2008)

The microRNA (miRNA) pathway represents an integral component of the gene regulation circuitry that controls development. In recent years, the role of miRNAs in embryonic stem (ES) cells and mammalian embryogenesis has begun to be explored. A few dozens of miRNAs expressed in mammalian ES cells, either exclusively or nonexclusively, have been cloned. The overall role of miRNAs in ES cells and embryonic development has been assessed by examining the effect of knocking out Dicer, an RNase III enzyme required for miRNA and small interfering RNA biogenesis, as well as DGCR8, a nuclear protein specifically involved in miRNA biogenesis. In addition, the role of a cluster of miRNAs specifically expressed in ES cells, the miR-290-295 group, has been investigated by the knock-out approach. These analyses have revealed the crucial role of miRNAs in ES cell differentiation, lineage specification, and organogenesis, especially neurogenesis and cardiogenesis. Systematic investigation of the role of miRNAs in ES cells and embryos will allow us to find missing pieces of the mosaic of early development.
Low Latency Video Streaming Over Peer-To-Peer Networks (2006)

We study peer-to-peer multicast streaming, where a source distributes real-time video to a large population of hosts by making use of their forwarding capacity rather than relying on dedicated media servers. We present a distributed streaming protocol which builds and maintains multiple multicast trees. The protocol is combined with an adaptive scheduling algorithm which ensures packets destined to a large number of peers, or particularly important to decode the video, are sent in priority. Experiments carried out over a simulated network of up to 3000 peers illustrate the performance of the protocol. For low latency video streaming, the prioritization algorithm offers performance gains, especially for large audiences and low latencies
Transfection of HepG2 cells with infectious hepatitis C virus genome. (1997)

Hepatitis C virus (HCV) represents one of the major causes of acute and chronic hepatitis, cirrhosis, and hepatocellular carcinoma (HCC) around the world. Our knowledge of the life cycle of HCV, however, is limited. Current studies are hampered by the lack of a reproducible, high-level in vitro replication system of HCV. We sought to establish HCV replication in HepG2 cells by gene transfer of in vitro transcribed HCV RNA. In preliminary experiments, diethylaminoethyl-dextran led to more efficient gene transfer than cationic liposomes (lipofectin, lipofectamine, and DOTAP). Therefore, in subsequent experiments, HepG2 cells were transfected with full-length (9.6-kb) and near-full-length (9.4-kb) HCV RNA using diethylaminoethyl-dextran. Transfection with subgenomic HCV RNA and mock transfection were used as controls. Positive- and negative-strand HCV RNA sequences were detected by reverse transcription polymerase chain reaction (KT-PCR) for 60 days in the infectious HCV RNA transfected HepG2 cells. The presence of negative-strand HCV RNA, presumably representing replicative intermediates, was confirmed by ribonuclease protection assay. The intracellular levels of HCV RNA were measured by quantitative competitive RT-PCR from 10 to 50 days after transfection and were stable over this time period at moderately high levels (10(8) to 10(10) genomes per mg of total RNA). Expression of viral core and nonstructural proteins was detected in the cytoplasm of transfected cells by immunostaining. Virus-like particles measuring 50 to 60 nm in diameter were found by electron microscopy in cytoplasmic vesicles and conditioned media of the cells transfected with infectious HCV RNA but not in cells transfected with truncated HCV RNA. Culture supernatants of infectious HCV RNA transfected HepG2 cells were infectious for Daudi cells for three passages tested. The truncated HCV RNA lacking NS5 and 3' untranslated region (3' UTR) of HCV was replication incompetent. This is the first demonstration of HCV particles in HepG2 cells after transfection with infectious HCV RNA. We conclude that we have established a reproducible HCV replication system in HepG2 cells that can be used to study the life cycle of HCV and to test anti-HCV agents.
Antigenic and functional organization of human parainfluenza virus type 3 fusion glycoprotein (1989)

Twenty-six monoclonal antibodies (MAbs) (14 neutralizing and 12 nonneutralizing) were used to examine the antigenic structure, biological properties, and natural variation of the fusion (F) glycoprotein of human type 3 parainfluenza virus (PIV3). Analysis of laboratory-selected antigenic variants and of PIV3 clinical isolates indicated that the panel of MAbs recognizes at least 20 epitopes, 14 of which participate in neutralization. Competitive binding assays indicated that the 14 neutralization epitopes are organized into three nonoverlapping antigenic sites (A, B, and C) and one bridge site (AB) and that the 6 nonneutralization epitopes form four sites (D, E, F, and G). Most of the neutralizing MAbs were involved in nonreciprocal competitive binding reactions, suggesting that they induce conformational changes in other neutralization epitopes. Fusion-inhibition and complemented-enhanced neutralization assays indicated that antigenic sites AB, B, and C may correspond to functional domains of the F molecule. Our results indicated that antibody binding alone is not sufficient for virus neutralization and that many anti-F MAbs neutralize by mechanisms not involving fusion-inhibition. The degree of antigenic variation in the F epitopes of clinical strains was examined by binding and neutralization tests. It appears that PIV3 frequently develops mutations that produce F epitopes which efficiently bind antibodies, but are completely resistant to neutralization by these antibodies.
Regulation of olfactory neurogenesis by amidated neuropeptides (2001)

The existence of stem cells in the CNS raises issues concerning the ability of nervous tissues to regenerate in the adult mammal and provides new perspectives on the treatment of degenerative disease and traumatic injury of the nervous system. These cells have a relatively limited range of locations within the nervous system and include cells of the rostral migratory stream, hippocampus, retina, and olfactory epithelium. The olfactory epithelium has been studied as a model of adult neuronal regeneration, with neuronal precursor/basal cells serving as the olfactory "stem cells." The identification of factors that promote neuronal proliferation or regeneration within the olfactory epithelium can provide clues to the process of adult mammalian nervous system repair and treatment. Multiple factors have been examined that appear to influence the proliferation and subsequent maturation of basal cells. These factors include nerve growth factor, fibroblast growth factor-2, epidermal growth factor, and insulin/insulin-like growth factor-1. Recently, two amidated neuropeptides, neuropeptide Y (NPY) and pituitary adenylate cyclase-activating polypeptide (PACAP38), identified in the olfactory epithelium have been shown to promote dramatically neuronal proliferation. The effects of NPY and PACAP suggest that amidated neuropeptides may serve a broad developmental and regenerative role in the mammalian olfactory epithelium.
APPLICATION OF CHARGE‐COUPLED DEVICE TECHNOLOGY FOR MEASUREMENT OF LASER LIGHT AND FLUORESCENCE DISTRIBUTION IN TUMORS FOR PHOTODYNAMIC THERAPY (1991)

Laser and fluorescence light distributions with applications for photodynamic therapy were measured in mouse tumors using a non-invasive electronic optical imaging system. The system consists of a liquid-nitrogen-cooled, charge-coupled-device (CCD) array camera under computer control with 576 x 384 detection elements having dimensions of 23 microns x 23 microns. The available dynamic range of the array is approx. 10(3), and the effective wavelength range is 400-1000 nm. An interstitially placed cylindrical diffusing optical fiber was used to provide tumor illumination. The light distribution pattern from the fiber was determined by immersing the cylindrical diffusing tip in a fluorescing solution and recording the emission image. Fluorescence imaging facilitates an accurate measurement of light intensity distribution while avoiding problems associated with the directional nature of other detection methods used with diffusing fibers. Radiation-induced fibrosarcoma tumors on C3H mice were grown to about 1 cm diameter for in vivo recording of light distribution from the tumor volume and for determination of effective light penetration distance at 18 wavelengths in the range 458-995 nm. Endogenous tumor fluorescence and Photofrin II fluorescence intensity were measured over the wavelength range 585-725 nm to investigate the possible application of CCD imaging technology for drug distribution measurements. Model experiments were begun to evaluate the relative importance of potential distortions of light distribution measurements using this approach.
Cytokine regulation of ezrin expression in the human colon cancer cell line HT29. (1996)

Ezrin is a membrane-cytoskeleton linker protein and belongs to the TERM family. It has been implicated in the membrane ruffling, motility, and metastatic process of tumour cells. This study examined the effects of a range of cytokines on the expression of ezrin in the human colon cancer cell line, HT29. Levels of ezrin were determined by Northern and Western blotting and indirect immunofluorescence. We report that IL-2, IL-8, IL-10 and IGF-I had an inhibitory effect on the expression, whereas EGF and IL-11 enhanced cellular ezrin levels. Immunofluorescence confirmed that these changes were seen both in cytosol and generalised membrane. It is concluded that ezrin expression in tumour cells can be regulated by cytokines and this bears importance in the understanding of its role in tumour biology.
Frame-theoretic Designs for Future Wireless Communications (2019)

Motivated by the historically proven depletion of communication resources, and respectively, by the lack of inherent redundancy necessary for robust and accurate signal processing and identification under orthogonal wireless communications systems, we use in this work over-complete redundant representations, i.e., Frame Theory. To this point, such non-orthogonal signal decompositions provide alternative, yet robust representations, and respectively, aid signal processing of modern and future wireless communications systems beyond the limitations of their traditional orthogonal counterparts.

For instance, the millimeter wave (mmWave) initial access (IA) sparse channel estimation
and training beamforming optimization problems are reduced to the generic frame design of the measurement matrix for compressed sensing (CS). Similarly, for non-orthogonal multiple access (NOMA) systems, the code-domain NOMA (CD-NOMA) transmission is abstracted as a generic linear model based on the synthesis linear operator of a frame. Under this abstraction, valuable information-theoretic insights regarding the optimum design of CD-NOMA multiplexing schemes are extracted. Albeit different, both problems lead interestingly to common frame design principles based on incoherence, representational tightness and unit-normality frame-theoretic attributes.

To provide a full system description, we complement these designs with newly proposed modern signal processing for the sparse recovery of the mmWave channel, or respectively, for the joint multi-user detection (MUD) on the receiving side of a MC-NOMA transceiver. Numerical experiments and software simulations confirm the general theoretic results and highlight, once more, the superiority of the proposed frame-theoretic designs against the existent art.