gebhart/patrepeval huggingface dataset:
Web graph similarity for anomaly detection (poster) (2008)

Web graphs are approximate snapshots of the web, created by search engines. Their creation is an error-prone procedure that relies on the availability of Internet nodes and the faultless operation of multiple software and hardware units. Checking the validity of a web graph requires a notion of graph similarity. Web graph similarity helps measure the amount and significance of changes in consecutive web graphs. These measurements validate how well search engines acquire content from the web. In this paper we study five similarity schemes: three of them adapted from existing graph similarity measures and two adapted from well-known document and vector similarity methods. We compare and evaluate all five schemes using a sequence of web graphs for Yahoo! and study if the schemes can identify anomalies that may occur due to hardware or other problems.
Recent Studies on Mechanisms of Bioactivation and Detoxification of 4-(Methylnitrosamino)-1-(3-Pyridyl)-1-Butanone (NNK), A Tobacco-Specific Lung Carcinogen (1996)

This article reviews recent advances in the biochemistry and molecular biology of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), a tobacco-specific pulmonary carcinogen believed to be involved in the induction of lung cancer in smokers. Several aspects of NNK bioactivation are addressed, including identification of its metabolites in laboratory animals and humans, cytochrome P450 enzyme involvement in its metabolic activation, DNA and protein adduct formation, biological significance of the major DNA adducts formed, and mutations in oncogenes from tumors induced by NNK. Collectively, the presently available data provide a reasonably clear picture of NNK bioactivation in rodents, although there are still important gaps in our mechanistic understanding of NNK-induced tumorigenesis. The studies in rodents and primates have facilitated development of methods to assess NNK bioactivation in humans, which will be applicable to studies of lung cancer susceptibility and prevention.
High-Throughput and Memory-Efficient Multimatch Packet Classification Based on Distributed and Pipelined Hash Tables (2013)

The emergence of new network applications, such as the network intrusion detection system and packet-level accounting, requires packet classification to report all matched rules instead of only the best matched rule. Although several schemes have been proposed recently to address the multimatch packet classification problem, most of them require either huge memory or expensive ternary content addressable memory (TCAM) to store the intermediate data structure, or they suffer from steep performance degradation under certain types of classifiers. In this paper, we decompose the operation of multimatch packet classification from the complicated multidimensional search to several single-dimensional searches, and present an asynchronous pipeline architecture based on a signature tree structure to combine the intermediate results returned from single-dimensional searches. By spreading edges of the signature tree across multiple hash tables at different stages, the pipeline can achieve a high throughput via the interstage parallel access to hash tables. To exploit further intrastage parallelism, two edge-grouping algorithms are designed to evenly divide the edges associated with each stage into multiple work-conserving hash tables. To avoid collisions involved in hash table lookup, a hybrid perfect hash table construction scheme is proposed. Extensive simulation using realistic classifiers and traffic traces shows that the proposed pipeline architecture outperforms HyperCuts and B2PC schemes in classification speed by at least one order of magnitude, while having a similar storage requirement. Particularly, with different types of classifiers of 4K rules, the proposed pipeline architecture is able to achieve a throughput between 26.8 and 93.1 Gb/s using perfect hash tables.
Propionibacterium acnes and Acne Vulgaris: New Insights from the Integration of Population Genetic, Multi-Omic, Biochemical and Host-Microbe Studies (2019)

The anaerobic bacterium <i>Propionibacterium acnes</i> is believed to play an important role in the pathophysiology of the common skin disease acne vulgaris. Over the last 10 years our understanding of the taxonomic and intraspecies diversity of this bacterium has increased tremendously, and with it the realisation that particular strains are associated with skin health while others appear related to disease. This extensive review will cover our current knowledge regarding the association of <i>P. acnes</i> phylogroups, clonal complexes and sequence types with acne vulgaris based on multilocus sequence typing of isolates, and direct ribotyping of the <i>P. acnes</i> strain population in skin microbiome samples based on 16S rDNA metagenomic data. We will also consider how multi-omic and biochemical studies have facilitated our understanding of <i>P. acnes</i> pathogenicity and interactions with the host, thus providing insights into why certain lineages appear to have a heightened capacity to contribute to acne vulgaris development, while others are positively associated with skin health. We conclude with a discussion of new therapeutic strategies that are currently under investigation for acne vulgaris, including vaccination, and consider the potential of these treatments to also perturb beneficial lineages of <i>P. acnes</i> on the skin.
Synthesis and In Vitro Screening of Novel Heterocyclic Compounds as Potential Breast Cancer Agents (2011)

Breast cancer is one of the most common non-cutaneous type of cancer in women in worldwide and a leading cause of cancer-related deaths, and is increasing year by year in almost every areas of the globe. Breast cancer is commonly classified into the following two major types: (1) non-invasive breast cancer (cancer cells are confined within the duct and lobules) and (2) invasive breast cancer (cancer cells invade through the walls of the duct or lobules and infiltrate the surrounding tissues). Various kinds of treatments are available for breast cancer, such as chemotherapy, radiotherapy and hormone therapy Many indole derivatives are reported as potent breast cancer agents, such as aplysinopsin analogs and indole-3-carbinols. Aplysinopsins are indole-derived marine natural products. The parent aplysinopsin was isolated for the first time (Kazlauskas, et al, 1977) as the major metabolite of eight Indo-Pacific sponge species, which are representatives of the genus Thorecta. The N-1-unsubstituted aplysinopsins have generated considerable interest due to their potentially useful medicinal properties (Dobroslawa, et al, 2009). Aplysinopsin has been reported as a potent cytotoxic agent against the K-cell line and methyl-aplysinopsins against L-1210 and K-cell lines has been reported as potent cytotoxic agents (Hollenbeak & Schmitz, 1977), and the anticancer activities of aplysinopsin and methyl-aplysinopsins against both 1210-and K-cells has also been reported Indole-3-carbinol, a phytochemical derived from cruciferous vegetables such as broccoli and Brussel sprouts, exhibits potent antiproliferative effects against human breast cancer cells and has been shown to decrease metastatic spread of tumors in experimental animals (Brew, et al., 2010). From the above observations and as part of a program for the development of small molecules as potential anticancer treatments Combretastins are plant products from the South African tree Combretum caffrum. This compound was found to inhibit tubulin polymerization, and competitively inhibit the www.intechopen.com
STAT1, NF-κB and ERKs play a role in the induction of lipocalin-2 expression in adipocytes (2013)

Lipocalin-2 (LCN2) is induced in conditions of obesity and Type 2 diabetes (T2DM). IFNγ and TNFα induce LCN2 expression in adipocytes in a manner that is dependent on transcription. The effects of these cytokines are additive. IFNγ induced STAT1 and TNFα induced NF-κB play a role in the induction of LCN2. In the LCN2 promoter, one NF-κB binding site and four STAT1 binding sites were identified by in silico and in vitro approaches. MAPK (ERKs 1 and 2) activation was required for the IFNγ and TNFα induction of LCN2 expression, but did not affect the nuclear translocation or DNA binding activity of STAT1 or NF-κB. The NF-κB binding site and the STAT1 binding sites we identified in vitro were confirmed by in vivo studies. Transfection of a LCN2 promoter/luciferase reporter construct confirmed acute activation by IFNγ and TNFα. Our studies identify mechanisms involved in the actions of cytokines secreted from immune cells in adipose tissue that induce LCN2 expression in conditions of obesity and T2DM.
Autoantibodies to neurofilaments (NF), glial fibrillary acidic protein (GFAP) and myelin basic protein (MBP) in workers exposed to lead. (1999)

An expanded follow-up assessment of the autoantibody response to neuronal and astroglial autoantigens (NF68; NF160; NF200; MBP; GFAP) as early markers of neurotoxicity was performed in male workers exposed to lead (Pb) of a battery factory (n=50) and a matched reference group (R) of workers at a food packing plant (n=39). Mean age, years of exposure and blood lead (PbB ug/dl) (+/-SD) for lead and R, respectively, were: Age:39 +/- 6; 41 +/- 7; Yrs. Exposed: 14 +/- 6:0; PbB: 32 +/- 11: 16 +/- 5 percent with detectable titers to nervous system proteins in the Pb and R populations, respectively, were: Anti-NF68: 59; 17; Anti-NF160: 28; 15; Anti-NF200: 25; 0; Anti-GFAP: 90; 20; Anti-MBP: 16; 4. Autoantibodies to nervous system proteins predominated in workers occupationally exposed to Pb compared to R. Anti-NF68 and GFAP titers were the most frequently encountered. Anti-NF68 titers were significantly correlated with years of exposure (r = 0.538, p < 0.0001) and with PbB (r=0.325, p < 0.05). Furthermore, the number of detectable autoantibody types correlated with clinical scores of sensorimotor deficits (r = 0.459, p < 0.0001). This study suggests that autoantibodies provide a promising biomarker of neurotoxicity while providing information on subcellular targets. It also raises concerns of toxicant-induced autoimmune neuropathy.
Wilson et al 2019_DBA data.xlsx (2019)

Data associated with the paper "Estimates for energy expenditure in free-living animals using acceleration proxies; a reappraisal", accepted for publication in the Journal of Animal Ecology in 2019.
The Perils of Healthcare Workforce Forecasting: A Case Study of the Philadelphia Metropolitan Area (2003)

In 1996, a widely circulated and influential forecast for the Philadelphia Metropolitan Area stated that a decline in hospital and healthcare employment in the region would occur over the next five years. It also suggested that this decline would exacerbate the problem of an oversupply of nurses seeking hospital employment. The forecast reflected a regional leadership and expert consensus on the impact of the managed care transformation on workforce needs and was supported by short-term statistical trends in regional utilization and employment. Confounding these predictions was the fact that hospital and healthcare employment actually grew. By the end of 2001, hospitals in the region were experiencing problems in recruiting sufficient numbers of nurses, pharmacists, and technicians. The forecast failed to anticipate the impact of a strong regional economy on supply and underestimated the resilience of underlying forces that have driven the long-term growth in healthcare workforce demand. More effective ongoing monitoring can help moderate the fluctuation of workforce shortages and surpluses.
Error-correcting Codes for Fibre-optic Communication Systems (2012)

Electronic signal processing techniques have assumed a prominent role in the design of\nfibre-optic communication systems. However, state-of-the-art systems operate at per-channel data rates of 100 Gb/s, which constrains the class of communication algorithms that can be practically implemented. Relative to LDPC-like codes, product-like codes with syndrome-based decoding have decoder dataflow requirements that are smaller by more than two orders of magnitude, which strongly motivates the search for powerful product-like codes. This thesis presents a new class of high-rate binary error-correcting codes, staircase codes, whose construction combines ideas from convolutional and block coding. A G.709-compliant staircase code is proposed, and FPGA-based simulation results show that performance within 0.5 dB of the Shannon Limit is attained for bit-error-rates below 1E-15. An error-floor analysis technique is presented, and the G.709-compliant staircase code is shown to have an error floor below 1E-20. Using staircase codes, a pragmatic approach for coded modulation in fibre-optic communication systems is presented that provides reliable communications to within 1 bit/s/Hz of the capacity of a QAM-modulated system modeled via the generalized non-linear Schrodinger equation. A system model for a real-world DQPSK receiver with correlated bit-errors is presented, along with an analysis technique to estimate the resulting error floor for the G.709-\ncompliant staircase code. By applying a time-varying pseudorandom interleaver of size\n2040 to the output of the encoder, the error \nfloor of the resulting system is shown to be\nless than 1E-20.
Amperometric Detection of Glucose Using a Conjugated Polyelectrolyte Complex with Single-Walled Carbon Nanotubes (2010)

The conjugated polymer, poly[3-(3-N,N-diethylaminopropoxy)thiophene] (PDAOT), was synthesized and employed in the supramolecular functionalization of single-walled carbon nanotubes (SWNTs). Highly stable aqueous solutions of PDAOT−SWNT complexes were obtained after sonication under mildly acidic conditions. UV−vis absorption and Raman spectroscopy studies showed that the noncovalent functionalization did not change the nanotube structure and retained its inherent properties. The reactions of [Fe(CN6)]3−/4− redox couple on Au electrodes modified with PDAOT and the PDAOT−SWNT films were studied using electrochemical impedance spectroscopy and cyclic voltammetry. A lower electron-transfer resistance and higher current response were observed on the Au/PDAOT−SWNT electrode compared with the Au/PDAOT electrode. We prepared glucose biosensors by entrapping glucose oxidase (GOx) within the PDAOT and PDAOT−SWNT films. Under optimized conditions, the Au/PDAOT−SWNT/GOx biosensor exhibited fast current response to glucose with a detection limit of 5 μM and a sensitivity of 700 ± 26 μA/mM·cm2. The responsiveness of the Au/PDAOT−SWNT/GOx biosensor can be attributed to the synergistic effect of the high conductivity and nondenaturing microenvironment of the PDAOT and the large active surface area and electrical conductivity provided by the SWNTs.
Extracting Infrared Spectra of Protein Secondary Structures Using a Library of Protein Spectra and the Ramachandran Plot (2015)

Infrared (IR) spectra from 1200 to 1800 cm(-1) of the pure α-helix and β-sheet secondary structures have been extracted using a covariant least-squares procedure which relates a library of 40 infrared (IR) solution protein spectra from the work of Dong, Carpenter, and Caughey and amino acid fractions of the proteins based on assignments by STRIDE (secondary structure identification) of Eisenhaber and Argos. The excitonic splitting of the β-sheet structures is determined for this library of solution proteins. The method is extended to find a set of spectral basis functions that analyze IR spectra of protein samples for α-helix and β-sheet content. A rigorous error analysis including covariance, the correlations between the input library spectra, was used to justify the results and avoid less meaningful results. The utility of the results on α-helix and β-sheet regions is demonstrated by detecting protein changes due to cancer in imaging Fourier transform IR (FTIR) spectra of liver tissue slices. This work ends with a method to extract IR spectra of less prominent torsional angle distributions.
Ischemic acute kidney injury induces a distant organ functional and genomic response distinguishable from bilateral nephrectomy (2007)

Acute kidney injury (AKI) is associated with significant mortality, which increases further when combined with acute lung injury. Experiments in rodents have shown that kidney ischemia-reperfusion injury (IRI) facilitates lung injury and inflammation. To identify potential ischemia-specific lung molecular pathways involved, we conducted global gene expression profiling of lung 6 or 36 h following 1) bilateral kidney IRI, 2) bilateral nephrectomy (BNx), and 3) sham laparotomy in C57BL/6J mice. Bronchoalveolar lavage fluid analysis revealed increased total protein, and lung histology revealed increased cellular inflammation following IRI, but not BNx, compared with sham controls. Total RNA from whole lung was isolated and hybridized to 430MOEA (22,626 genes) GeneChips (n = 3/group), which were analyzed by robust multichip average and significance analysis of microarrays and linked to gene ontology (GO) terms using MAPPFinder. The microarray power analysis predicted that the false discovery rate (q < 1%) and > or =50%-fold change compared with sham would represent significant changes in gene expression. Analysis identified 266 and 455 ischemia-specific, AKI-associated lung genes with increased expression and 615 and 204 with decreased expression at 6 and 36 h, respectively, compared with sham controls. Real-time PCR analysis validated select array changes in lung serum amyloid A3 and endothelin-1. GO analysis revealed significant activation (Z > 1.95) of several proinflammatory and proapoptotic biological processes. Ischemic AKI induces functional and transcriptional changes in the lung distinct from those induced by uremia alone. Further investigation using this lung molecular signature induced by kidney IRI will provide mechanistic insights and new therapies for critically ill patients with AKI.
A 25 kDa α<sub>2</sub>‐microglobulin‐related protein is a component of the 125 kDa form of human gelatinase (1992)

Besides the monomeric mammalian 95 kDa progelatinase, two additional forms, a disulfide-bridged 220 kDa dimer and a 125 kDa form were isolated from human PMN leukocytes. The 125 kDa progelatinase was identified as a covalently linked, disulfide-bridged heterodimer formed of the monomer with a 25 kDa protein. This 25 kDa protein was isolated from gelatinase bound to the affinity support of gelatin-Sepharose and eluted by DTE-containing buffer. The amino acid sequence of tryptic peptides of this protein revealed homology with an alpha 2-microglobulin-related protein from rats, a protein so far unknown in humans.
Receding horizon control for temporal logic specifications (2010)

In this paper, we describe a receding horizon framework that satisfies a class of linear temporal logic specifications sufficient to describe a wide range of properties including safety, stability, progress, obligation, response and guarantee. The resulting embedded control software consists of a goal generator, a trajectory planner, and a continuous controller. The goal generator essentially reduces the trajectory generation problem to a sequence of smaller problems of short horizon while preserving the desired system-level temporal properties. Subsequently, in each iteration, the trajectory planner solves the corresponding short-horizon problem with the currently observed state as the initial state and generates a feasible trajectory to be implemented by the continuous controller. Based on the simulation property, we show that the composition of the goal generator, trajectory planner and continuous controller and the corresponding receding horizon framework guarantee the correctness of the system. To handle failures that may occur due to a mismatch between the actual system and its model, we propose a response mechanism and illustrate, through an example, how the system is capable of responding to certain failures and continues to exhibit a correct behavior.
Purification and characterization of the heat-labile toxin of Bordetella pertussis (1991)

A procedure is described for purification of pertussis heat-labile toxin (PEHLT) from cells of Bordetella pertussis. The purification procedure, performed in the cold and in the presence of protease inhibitors, gives 1,350-fold purification with yields of about 60%. The toxin was shown to be a single-chain polypeptide of 140 kDa, pI 6.02. It was completely inactivated by heating at 56 degrees C for 60 min. Rabbit antiserum prepared against PEHLT neutralized the toxin and gave a single precipitin line on immunodiffusion. In immunodiffusion assays, this anti-PEHLT serum did not react with pertussis toxin, filamentous hemagglutinin, or preparations of pertussis adenylate cyclase. Purified PEHLT elicited dermonecrosis and atrophy of the spleen. PEHLT is extraordinarily active; 0.4 X 10(-12) g caused necrotic lesions in newborn mice, and with 18- to 20-g mice the 50% lethal dose was about 11 X 10(-9) g.
On the efficacy of separating control and data into different frequency bands (2005)

Radio spectrum allocated for use in unlicensed wireless networks is distributed across non-contiguous frequency bands. Existing MAC protocols, like IEEE 802.11, operate only in contiguous bands. Several small slices of frequency are available in lower frequency bands that are not utilized. We propose utilizing a sliver of unused spectrum in the lower frequency band as a low rate control channel to improve the capacity of infrastructure and multi-hop wireless networks. The proposed control channel-based MAC Protocol (C/sup 2/M) increases the throughput by moving the contention resolution overheads to the separate low rate channel. We allow simultaneous channel contention and data transmission by incorporating advance reservation on the control channel, and data aggregation on the data channel. Simulation results show that compared to IEEE 802.11, C/sup 2/M significantly improves network performance.
Secure random number generation using chaotic circuits (2003)

The authors show how to use a chaotic circuit as a secure random number generator and given an example using a first-order, nonuniformly sampling, digital phase-locked loop (DPLL) operating in a chaotic regime. The security of the proposed generators is estimated from the information loss property of chaotic systems. For a generator implemented using a chaotic DPLL, two important cases are considered. First, given no prior information concerning the initial conditions of a continuously running circuit, the authors establish how long one should wait after taking a bit before one can securely take another bit. Secondly, given knowledge of the initial conditions at startup (up to measurement and noise uncertainty), they show how long one should wait before starting the bit sampling.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
CD4-CD8- T cells from mice with collagen arthritis display aberrant expression of type <i>l</i> K+ channels. (1990)

Expression of voltage-gated K+ channels in mAb-defined T cell subsets from normal mice and mice with experimental autoimmune arthritis was studied with the patch-clamp whole-cell recording technique in combination with fluorescence microscopy. CD4+CD8- Th cells from DBA/1 LacJ mice with type II collagen arthritis expressed low levels of type n K+ channels, and CD4-CD8+ T cells (cytotoxic) showed small numbers of type l or n' K+ channels, like their phenotypic counterparts in normal mice. CD4-CD8-Thy-1.2+ (double negative or DN) T cells from the diseased mice, however, displayed an abundance of type l K+ channels compared to DN T cells in normal mice, or mice immunized with CFA. Furthermore, the aberrant expression of type l K+ channels correlated with the presence of active disease. DN T cells from mice with SLE, type-1 diabetes mellitus, and experimental allergic encephalomyelitis, also exhibited a high number of type l K+ channels. These results suggest that expression of numerous type l K+ channels may be a useful marker for DN T cells associated with these autoimmune disorders.