gebhart/patrepeval huggingface dataset:
NetBouncer: client-legitimacy-based high-performance DDoS filtering (2004)

We describe "NetBouncer", an approach and set of technologies for providing practical and high-performance defenses against distributed denial-of-service (DDoS) attacks. The central innovation in the NetBouncer approach to filtering and mitigating DDoS attacks is the ability to distinguish legitimate traffic from illegitimate ones so as to enable the discarding of only illegitimate traffic. In particular, this allows a NetBouncer-enabled network to distinguish DDoS congestion from flash crowd congestion situations. This provides a unique advantage over other DDoS mitigation techniques such as those based on filtering and congestion control where some loss of legitimate traffic is inevitable. The NetBouncer approach is characterized as an end-point-based solution to DDoS protection. It provides localized protection at potential choke points or bottlenecks that may exist in front of hosts and servers. NetBouncer attempts to block traffic as close to the victim as possible, while upstream of the nearest bottleneck. The immediate manifestation of NetBouncer technology is as a high-speed packet processing in-line appliance based on network processor technology. However, the long-term evolution, adoption and integration of NetBouncer technology may be in the back-plane/fast path of commercial high-speed routers.
The Effect of Resveratrol on a Cell Model of Human Aging (2007)

The natural polyphenol resveratrol stimulates sirtuins and extends lifespan. Here resveratrol inhibited expression of replicative senescence marker INK4a in human dermal fibroblasts, and 47 of 19,000 genes from microarray experiments were differentially expressed. These included genes for growth, cell division, cell signaling, apoptosis, and transcription. Genes involved in Ras and ubiquitin pathways, Ras-GRF1, RAC3, and UBE2D3, were downregulated. The changes suggest resveratrol might alter sirtuin-regulated downstream pathways, rather than sirtuin activity. Serum deprivation and high confluency caused nuclear translocation of the SIRT1-regulated transcription factor FOXO3a. Our data indicate resveratrol's actions might cause FOXO recruitment to the nucleus.
Crystallization and preliminary X-ray analysis of a native human tRNA synthetase whose allelic variants are associated with Charcot–Marie–Tooth disease (2006)

Glycyl-tRNA synthetase (GlyRS) is one of a group of enzymes that catalyze the synthesis of aminoacyl-tRNAs for translation. Mutations of human and mouse GlyRSs are causally associated with Charcot-Marie-Tooth disease, the most common genetic disorder of the peripheral nervous system. As the first step towards a structure-function analysis of this disease, native human GlyRS was expressed, purified and crystallized. The crystal belonged to space group P4(3)2(1)2 or its enantiomorphic space group P4(1)2(1)2, with unit-cell parameters a = b = 91.74, c = 247.18 A, and diffracted X-rays to 3.0 A resolution. The asymmetric unit contained one GlyRS molecule and had a solvent content of 69%.
Polymerase Chain Reaction with Single-Sided Specificity: Analysis of T Cell Receptor δ Chain (1989)

In the polymerase chain reaction (PCR), two specific oligonucleotide primers are used to amplify the sequences between them. However, this technique is not suitable for amplifying genes that encode molecules where the 5' portion of the sequences of interest is not known, such as the T cell receptor (TCR) or immunoglobulins. Because of this limitation, a novel technique, anchored polymerase chain reaction (A-PCR), was devised that requires sequence specificity only on the 3' end of the target fragment. It was used to analyze TCR delta chain mRNA's from human peripheral blood gamma delta T cells. Most of these cells had a V delta gene segment not previously described (V delta 3), and the delta chain junctional sequences formed a discrete subpopulation compared with those previously reported.
Correlation of in vitro and in vivo growth suppression of MCF-7 human breast cancer by 2,3,7,8-tetrachlorodibenzo-p-dioxin. (1993)

The purpose of this study was to compare the effect of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on the in vitro and in vivo 17 beta-estradiol (E2)-dependent growth of MCF-7 human breast cancer cells. In culture, a major component of postconfluent growth of MCF-7 cells is E2 dependent. In vivo, MCF-7 cells fail to grow as xenografts without exogenous E2 support. Thus the effect of TCDD on postconfluent MCF-7 growth in culture was compared with its effect on MCF-7 xenograft growth in immunosuppressed mice. A concentration of 10(-9) M E2 was optimal for supporting postconfluent growth of MCF-7 cells in culture into multicellular aggregates (foci) on a monolayer background. The 50% inhibitory dose of TCDD under these conditions was 3 x 10(-10) M, while E2-dependent focus development was completely inhibited by 10(-8) M TCDD. Weekly i.p. administration of TCDD (5 micrograms/kg) to mice bearing MCF-7 tumor xenografts resulted in inhibition of the tumor growth rate for the first 2 weeks, followed by recovery to the control growth rate during the third week. These recovered tumors were found to retain estrogen-dependent growth as shown by second generation transplantation studies. The p.o. route of TCDD administration yielded a similar 2-week transient suppression of growth with a concentration of 8 micrograms TCDD/kg body weight but only a 1-week growth rate latency with a 2-microgram/kg body weight dose. A single 5-micrograms/kg dose given 1 day after implantation was virtually noninhibitory. These results indicate that TCDD suppression of estrogen-dependent MCF-7 human breast cancer cell growth in vitro was predicative of a similar growth suppression of MCF-7 solid tumor xenografts in vivo. However, additional host-related factors must be involved in vivo, since suppression of tumor growth is transient. These studies provide a basis for future in vivo investigations of TCDD endocrine toxicity by using the MCF-7 tumor as a surrogate estrogen-responsive human organ and to examine the efficacy of TCDD and related Ah receptor-mediated compounds in the management of human estrogen-dependent breast cancer.
Genetic analysis of cystic fibrosis using linked DNA markers. (1986)

Genetic linkage has been analyzed between cystic fibrosis (CF) and a number of markers on the long arm of chromosome 7, including D7S15, COL1A2, PON, MET, D7S8, and TCRB, using a cohort of 47 Canadian and 13 Danish CF families. The analysis confirms the previous observations that both MET and D7S8 are closely linked to CF. Based on the result from one family, MET appears to be more proximal to the centromere than CF. Our analysis also suggests that genetic heterogeneity may account for the high recombination fraction between CF and D7S8 observed in another family. In addition, a strong linkage disequilibrium has been observed between CF and the two closely flanking markers.
Treatment of bicalutamide-induced breast events (2007)

Bicalutamide is a competitive nonsteroidal androgen receptor antagonist. In the European Union and a number of other countries, bicalutamide 150 mg per day is approved as an adjuvant to primary treatments (radical prostatectomy or radiotherapy) or as monotherapy as an alternative to surgical or medical castration in men with locally advanced, nonmetastatic prostate cancer. The ongoing bicalutamide Early Prostate Cancer (EPC) program has shown that breast events, defined as gynecomastia, breast pain or both, are a significant limitation of bicalutamide. Nearly 90% of patients experienced one or both symptoms and nearly 16% of patients withdrew from the EPC program as a consequence of bicalutamide-induced breast events. Tamoxifen, anastrozole and radiotherapy have all been studied as options for the treatment of breast events. To date, tamoxifen appears to be the superior agent in terms of outcomes; however, further studies are still required to determine the optimal dose and timing of tamoxifen administration for both prophylaxis and treatment. In addition, the impact on prostate cancer control remains uncertain. An ongoing clinical trial using toremifene to prevent morphometric vertebral fractures in men undergoing medical and/or surgical castration will provide some additional data on the effects of selective estrogen receptor modulators in men with prostate cancer.
Orthogonal Connectivity Factorization: Interpretable Decomposition of Variability in Correlation Matrices (2016)

In many multivariate time series, the correlation structure is nonstationary, that is, it changes over time. The correlation structure may also change as a function of other cofactors, for example, the identity of the subject in biomedical data. A fundamental approach for the analysis of such data is to estimate the correlation structure (connectivities) separately in short time windows or for different subjects and use existing machine learning methods, such as principal component analysis (PCA), to summarize or visualize the changes in connectivity. However, the visualization of such a straightforward PCA is problematic because the ensuing connectivity patterns are much more complex objects than, say, spatial patterns. Here, we develop a new framework for analyzing variability in connectivities using the PCA approach as the starting point. First, we show how to analyze and visualize the principal components of connectivity matrices by a tailor-made rank-two matrix approximation in which we use the outer product of two orthogonal vectors. This leads to a new kind of transformation of eigenvectors that is particularly suited for this purpose and often enables interpretation of the principal component as connectivity between two groups of variables. Second, we show how to incorporate the orthogonality and the rank-two constraint in the estimation of PCA itself to improve the results. We further provide an interpretation of these methods in terms of estimation of a probabilistic generative model related to blind separation of dependent sources. Experiments on brain imaging data give very promising results.
Phase-selective entrainment of nonlinear oscillator ensembles (2016)

The ability to organize and finely manipulate the hierarchy and timing of dynamic processes is important for understanding and influencing brain functions, sleep and metabolic cycles, and many other natural phenomena. However, establishing spatiotemporal structures in biological oscillator ensembles is a challenging task that requires controlling large collections of complex nonlinear dynamical units. In this report, we present a method to design entrainment signals that create stable phase patterns in ensembles of heterogeneous nonlinear oscillators without using state feedback information. We demonstrate the approach using experiments with electrochemical reactions on multielectrode arrays, in which we selectively assign ensemble subgroups into spatiotemporal patterns with multiple phase clusters. The experimentally confirmed mechanism elucidates the connection between the phases and natural frequencies of a collection of dynamical elements, the spatial and temporal information that is encoded within this ensemble, and how external signals can be used to retrieve this information.
Somatic Mutations Lead to an Oncogenic Deletion of Met in Lung Cancer (2006)

Activating mutations in receptor tyrosine kinases play a critical role in oncogenesis. Despite evidence that Met kinase is deregulated in human cancer, the role of activating mutations in cancers other than renal papillary carcinoma has not been well defined. Here we report the identification of somatic intronic mutations of Met kinase that lead to an alternatively spliced transcript in lung cancer, which encodes a deletion of the juxtamembrane domain resulting in the loss of Cbl E3-ligase binding. The mutant receptor exhibits decreased ubiquitination and delayed down-regulation correlating with elevated, distinct Met expression in primary tumors harboring the deleted receptor. As a consequence, phospho-Met and downstream mitogen-activated protein kinase activation is sustained on ligand stimulation. Cells expressing the Met deletion reveal enhanced ligand-mediated proliferation and significant in vivo tumor growth. A hepatocyte growth factor competitive Met antagonist inhibits receptor activation and proliferation in tumor cells harboring the Met deletion, suggesting the important role played by ligand-dependent Met activation and the potential for anticancer therapy. These results support a critical role for Met in lung cancer and somatic mutation-driven splicing of an oncogene that leads to a different mechanism for tyrosine kinase activation through altered receptor down-regulation in human cancer.
RADIUS and IPv6 (2001)

This document specifies the operation of RADIUS (Remote Authentication Dial In User Service) when run over IPv6 as well as the RADIUS attributes used to support IPv6 network access.
Candida albicans ALS1: domains related to a Saccharomyces cerevisiae sexual agglutinin separated by a repeating motif (1995)

Transfer of budding Candida albicans yeast cells from the rich, complex medium YEPD to the defined tissue culture medium RPMI 1640 (RPMI) at 37 degrees C and 5% CO2 causes rapid onset of hyphal induction. Among the genes induced under these conditions are hyphal-specific genes as well as genes expressed in response to changes in temperature, CO2 and specific media components. A cDNA library constructed from cells incubated for 20 min in RPMI was differentially screened with yeast (YEPD)- and hyphal (RPMI)-specific probes resulting in identification of a gene expressed in response to culture conditions but not regulated by the yeast-hyphal transition. The deduced gene product displays significant identity to Saccharomyces cerevisiae alpha-agglutinin, encoded by AG alpha 1, an adhesion glycoprotein that mediates mating of haploid cells. The presence of this gene in C. albicans is curious since the organism has not been observed to undergo meiosis. We designate the C. albicans gene ALS1 (for agglutinin-like sequence). While the N- and C-termini of the predicted 1260-amino-acid ALS1 protein resemble those of the 650-amino-acid AG alpha 1, ALS1 contains a central domain of tandem repeats consisting of a highly conserved 36-amino-acid sequence not present in AG alpha 1. These repeats are also present on the nucleotide level as a highly conserved 108 bp motif. Southern and Northern blot analyses indicate a family of C. albicans genes that contain the tandem repeat motif; at least one gene in addition to ALS1 is expressed under conditions similar to those for ALS1 expression. Genomic Southern blots from several C. albicans isolates indicate that the number of copies of the tandem repeat element in ALS1 differs across strains and, in some cases, between ALS1 alleles in the same strain, suggesting a strain-dependent variability in ALS1 protein size. Potential roles for the ALS1 protein are discussed.
Synthesis of Some New 4,5-Substituted-4H-1,2,4-triazole-3-thiol Derivatives (2004)

In this study appropriate hydrazide compounds, furan-2-carboxylic acid hydrazide (1) and phenylacetic acid hydrazide (2) were converted into 1,4-substituted thiosemicarbazides 4a-e and 5a-e and 4-amino-5-(furan-2-yl or benzyl)-4H-1,2,4-triazole-3-thiols 7 and 10. The 1,4-substituted thiosemicarbazides were then converted into 5-(furan-2-yl or benzyl)-4-(aryl)-4H-1,2,4-triazole-3-thiols 8a-e and 9a-e. In addition, the azomethines 11a-d and 12a-d were prepared from the corresponding arylaldehydes and the 4-amino-5-(furan-2-yl or benzyl)-4H-1,2,4-triazole-3-thiols 7 and 10. The structures of all the synthesized compounds were confirmed by elemental analyses, IR, (1)H-NMR and(13) C-NMR spectra.
Transplant arterial vasculopathy: evidence for a dual pattern of endothelial injury and the source of smooth muscle cells in lesions of intimal hyperplasia. (1996)

With use of this straight artery model of transplantation for studying TGVD, we have shown the following: 1. Intimal thickening occurs in a time-dependent predictable manner only in allografts. 2. Endothelial injury as a result of procurement, preservation, and reperfusion by itself does not result in the development of intimal thickening. Additional endothelial injury associated with the presence of an early mononuclear infiltrate is necessary for the development of TGVD. 3. The development of intimal hyperplasia is initially cellular, consisting mainly of macrophages and a smaller proportion of lymphocytes. The macrophages are later replaced by SMCs. These findings are summarized in Figure 16. 4. The source of the SMCs in intimal lesions is most likely the recipient media.
Long Distance Video Camera Measurements of Structures (2015)

Tall buildings, long-span bridges, and other structures that have physical access issues can be difficult or costly to instrument to measure structural vibrations. Videos cameras offer a potential method for noncontact measurement of structures. Measurements have previously been made over long distances with targets placed on the structure of interest, however this addition removes much of the flexibility of using a camera in the first place. This paper will present a method for measuring displacements of structures from long range with a video camera in an uncontrolled and natural environment. The technique relies on optical flow processing of the video to determine the displacements of structures in the frame. A pilot study of a long range video camera measurement of a structure from a distance of over 500 feet will be shown as an example of the current possibilities of long range measurements. The issues of atmospheric turbulence and camera motion will be discussed and potential efforts in solving these issues will be described along with a discussion of camera requirements. doi: 10.12783/SHM2015/385
Identification of a 5‐nucleotide sequence that controls expression of the ica locus in Staphylococcus aureus and characterization of the DNA‐binding properties of IcaR (2003)

Biofilm formation is an important aspect of the pathogenesis of staphylococcal infections. A beta-1,6-linked N-acetyl glucosamine polysaccharide is critical to biofilm elaboration and is synthesized by proteins encoded by the intercellular adhesion (ica) locus. These studies were undertaken to characterize the mechanism by which transcription of the ica locus in S. aureus is regulated using isogenic S. aureus MN8 and MN8 mucoid (MN8m) strains, the latter of which constitutively overproduces biofilm. Transformation of the ica locus from MN8m to the ica knock-out mutants of two strains, MN8 and NCTC 10833, conferred a strong biofilm-producing phenotype. Sequence analysis revealed a 5-nucleotide deletion within the promoter region of the ica locus in MN8m compared with the sequence in the wild-type locus. Deletion or substitution of these 5 nucleotides within the wild-type ica locus augmented transcription of the ica locus and induced the strong biofilm-producing phenotype. Gel shift analysis demonstrated that a protein(s) within cell-free lysates from strain MN8 bind(s) specifically to oligonucleotides representative of the wild-type ica promoter sequence and that this binding is greatly diminished by the deletion or substitution of the 5 nucleotides. DNase I footprint analysis revealed that purified IcaR, thought to be a regulator of ica transcription, also binds to the ica promoter sequence just upstream of the ica start codon, but its affinity for the ica promoter is unaffected by deletion of the 5-nucleotide motif. These findings identify a 5-nucleotide motif within the ica promoter region that has a functional role in transcriptional regulation of the ica locus that is independent of IcaR, and also show that IcaR binds to the promoter region of the S. aureus ica locus.
Application of a multilevel Redfield theory to electron transfer in condensed phases (1992)

A quantum mechanical theory of photoinduced electron transfer, based on the Redfield theory of relaxation, is developed and applied to the standard two state–one mode system interacting with a thermal bath. Quantum mechanical treatment of the reaction coordinate allows incorporation of both finite vibrational dephasing and energy flow rates into the description of electron transfer dynamics. The field–matter interaction is treated explicitly to properly incorporate the total energy and magnitude of the vibrational coherence present in the initially prepared state. Calculation of the reduced density matrix of the system is carried out in a vibronic basis that diagonalizes the electron exchange coupling so that the method is valid for arbitrarily large coupling strength. For weak electronic coupling, we demonstrate the equivalence between the results from Redfield theory and those obtained from the standard perturbative expression (golden rule) for nonadiabatic electron transfer. We then discuss quantitatively the breakdown of the Fermi golden rule with increasing electronic coupling strength. The failure of the golden rule is seen to result from either slow energy equilibration in the reactant or product well or from quantum interference effects resulting from finite dephasing rates. For cases where the reorganization energy is large compared to the frequency of reactive motion, such that we may ignore nuclear tunneling, results from the theory show good agreement with those from the semiclassical Landau–Zener theory when motion of the reaction coordinate through the surface crossing region can be considered to be ballistic. Finally results are shown in the weak damping (coherent) limit that demonstrate interference effects between phase coherences involving states in both wells.
Candida infections in patients with acute leukemia: Ineffectiveness of nystatin prophylaxis and relationship between oropharyngeal and systemic candidiasis (1982)

Ninety-three hospitalizations of 70 patients, who underwent induction chemotherapy for acute leukemia to determine the effectiveness of oral nystatin in preventing oropharyngeal and systemic candidiasis were reviewed. Sixty-two percent of patients who received prophylactic nystatin and 58% of patients who did not receive nystatin developed oropharyngeal candidiasis; 11% of patients who received prophylaxis and 21% of those who did not receive prophylaxis developed systemic candidiasis. The use of oral nystatin did not significantly diminish the risk of developing either type of Candida infection. Oropharyngeal candidiasis occurred more commonly in patients who had severe and prolonged leukopenia, had received more parenteral antibiotics, and had developed chemotherapy-induced mucositis. Systemic candidiasis developed almost exclusively in patients who had prior oropharyngeal candidiasis. Guidelines for the empiric use of amphotericin B in these patients are provided.
Inhibitory Effect of Macrolides on Interleukin‐8 Secretion From Cultured Human Nasal Epithelial Cells (1997)

The mechanism of macrolide therapy in chronic sinusitis patients is unclear. The authors studied the effect of macrolides on interleukin (IL)-8 secretion from cultured human nasal epithelial cells. Epithelial cells harvested from the nasal polyps of patients with chronic sinusitis were primary-cultured, and secreted IL-8 in culture media was measured by enzyme immunoassay. The cells secreted considerable amounts of IL-8 constitutively and in response to lipopolysaccharide. The secretion was significantly inhibited by 10(-5) M of erythromycin, clarithromycin, roxithromycin, and josamycin. 10(-6) M erythromycin still showed the inhibitory effect, whereas the same concentration of josamycin did not. These results indicate that macrolide antibiotics may act as an immunomodulator to reduce IL-8 in inflammatory sites and, at least partially, account for the clinically discrepant effects between 14- and 16-membered ring macrolides in long-term low-dose therapy for chronic sinusitis.