gebhart/patrepeval huggingface dataset:
SEDA (2001)

We propose a new design for highly concurrent Internet services, which we call the staged event-driven architecture (SEDA). SEDA is intended to support massive concurrency demands and simplify the construction of well-conditioned services. In SEDA, applications consist of a network of event-driven stages connected by explicit queues . This architecture allows services to be well-conditioned to load, preventing resources from being overcommitted when demand exceeds service capacity. SEDA makes use of a set of dynamic resource controllers to keep stages within their operating regime despite large fluctuations in load. We describe several control mechanisms for automatic tuning and load conditioning, including thread pool sizing, event batching, and adaptive load shedding. We present the SEDA design and an implementation of an Internet services platform based on this architecture. We evaluate the use of SEDA through two applications: a high-performance HTTP server and a packet router for the Gnutella peer-to-peer file sharing network. These results show that SEDA applications exhibit higher performance than traditional service designs, and are robust to huge variations in load.
Formation of a glutathione conjugate and a semistable transportable glucuronide conjugate of N2-oxidized species of 2-amino-1-methyl-6phenylimidazo[4,5-b]pyridine (PHIP) in rat liver (1991)

We have previously shown that 2-hydroxamino-1-methyl-6-phenylimidazo[4,5-b]pyridine(2-h ydroxamino-PhIP) is the principal metabolite leading to mutations in Salmonella typhimurium TA98 and DNA damage in mammalian cells. In rat hepatocytes this metabolite can be further conjugated to 2-(N-beta-D-glucuronopyranosyl (hydroxamino)-1-methyl-6-phenylimidazo[4, 5-b]pyridine[N(OH)-gluc-PhIP]. Its rate of formation was increased in hepatocytes from polychlorinated biphenyl (PCB)-pretreated animals. This metabolite is the main metabolite of PhIP in bile and it is hydrolyzed both by human and rat intestinal bacteria. Smaller amounts are excreted into urine. The evidence for the proposed structure is based on 1H- and 13C-NMR, beta-glucuronidase-lability giving 2-hydroxamino-PhIP upon hydrolysis and on the results obtained by using biochemical enzyme inhibitors. N(OH)-gluc-PhIP may be important for genotoxic lesions and tumors of 2-amino-1methyl-6-phenylimidazo [4,5-b]pyridine (PhIP) in extrahepatic tissue. In hepatocytes and bile from PCB-pretreated rats a PhIP-glutathione conjugate, 2-glutathionyl-1-methyl-6-phenylimidazo[4,5-b]pyridine (GSH-PhIP) was also found. The evidence for the proposed structure is based on 1H-NMR and high-resolution mass spectrometry. The metabolite can also be produced by a direct nucleophilic substitution of the nitro group in 2-nitro-PhIP by glutathione (GSH) in vitro. The metabolite did not form from 2-hydroxamino-PhIP and GSH either directly or in the presence of glutathione S-transferase. The formation of GSH-PhIP in rat liver and isolated cells only at a high rate of 2-hydroxamino-PhIP formation (PCB-treated animals) indicates that 2-nitro-PhIP may be formed in the liver during such N-oxidation of PhIP.
β Sheet Structure in Amyloid β Fibrils and Vibrational Dipolar Coupling (2005)

Fibrils formed by amyloid beta proteins were labeled with 13C at various positions and examined by infrared spectroscopy to detect vibrational dipolar coupling, implying close physical proximity. The results support key features of several recently proposed models for amyloid fibril structure, but they also add some important caveats. For instance, they support the conclusion that the beta structure is parallel; however, the coupling is not as strong as expected when residues are in register. This may be explained by out-of-register alignment of adjacent strands, or nonstandard parallel sheet structure that yields suboptimal alignment of labeled dipole moments. The data also point to a significant structural difference between fibrils formed by the 40-residue amyloid beta protein and fibrils formed by residues 10-35.
A combined analysis of immunogenicity, antibody kinetics and vaccine efficacy from phase 2 trials of the RTS,S malaria vaccine (2014)

The RTS,S malaria vaccine is currently undergoing phase 3 trials. High vaccine-induced antibody titres to the circumsporozoite protein (CSP) antigen have been associated with protection from infection and episodes of clinical malaria. Using data from 5,144 participants in nine phase 2 trials, we explore predictors of vaccine immunogenicity (anti-CSP antibody titres), decay in antibody titres, and the association between antibody titres and clinical outcomes. We use empirically-observed relationships between these factors to predict vaccine efficacy in a range of scenarios. Vaccine-induced anti-CSP antibody titres were significantly associated with age (P = 0.04), adjuvant (P <0.001), pre-vaccination anti-hepatitis B surface antigen titres (P = 0.005) and pre-vaccination anti-CSP titres (P <0.001). Co-administration with other vaccines reduced anti-CSP antibody titres although not significantly (P = 0.095). Antibody titres showed a bi-phasic decay over time with an initial rapid decay in the first three months and a second slower decay over the next three to four years. Antibody titres were significantly associated with protection, with a titre of 51 (95% Credible Interval (CrI): 29 to 85) ELISA units/ml (EU/mL) predicted to prevent 50% of infections in children. Vaccine efficacy was predicted to decline to zero over four years in a setting with entomological inoculation rate (EIR) = 20 infectious bites per year (ibpy). Over a five-year follow-up period at an EIR = 20 ibpy, we predict RTS,S will avert 1,782 cases per 1,000 vaccinated children, 1,452 cases per 1,000 vaccinated infants, and 887 cases per 1,000 infants when co-administered with expanded programme on immunisation (EPI) vaccines. Our main study limitations include an absence of vaccine-induced cellular immune responses and short duration of follow-up in some individuals. Vaccine-induced anti-CSP antibody titres and transmission intensity can explain variations in observed vaccine efficacy.
Radiation Thermometry Using a Wide Spectral Band (1989)

Effects of profile of spectral emissivity are analyzed on temperature estimation in the wide band radiation thermometry. These effects are based on the fact that average emissivity used for temperature estimation is a weighted mean of the spectral emissivity through the observation band of a radiometer, and that the weight is described by spectral radiance of a blackbody. The results of the analysis are as follows:(1) If an object is not a graybody, the mean emissivity depends on the temperature of the object, (2) Emissivity measured by changing the temperature does not correspond to the mean emissivity, because the weight of the measured emissivity is the differential of the spectral radiance of the blackbody with respect to the temperature, and(3) The difference between the mean emissivity and the measured one causes the biased error in the temperature estimation, where, amplitude and sign of the error depend on the shape of the spectral emissivity in the observation band.These effects are quantitatively evaluated by numerical simulation, and qualitatively confirmed by actual measurement of temperature of water vapor and of a silicon plate.
From Aggregation to Inhibition: N-Amination Converts Amyloidogenic Tau Peptides into Soluble Antagonists of Cellular Seeding (2021)

The spread of neurofibrillary tangles resulting from tau protein aggregation is a hallmark of Alzheimer’s and related neurodegenerative diseases. Early oligomerization of tau involves conformational reorganization into parallel b-sheet structures and supramolecular assembly into toxic fibrils. Despite the need for selective inhibitors of tau propagation, b-rich protein assemblies are inherently difficult to target with small molecules. Here, we describe a minimalist approach to mimic the aggregation-prone modules within tau. We carried out a backbone residue scan and show that amide N-amination completely abolishes the tendency of these peptides to self-aggregate, rendering them soluble mimics of ordered b-strands from the tau R2 and R3 domains. Several N-amino peptides (NAPs) inhibit disease-associated tau aggregation and prevent fibril formation in vitro. We further demonstrate that NAPs 12 and 13 are effective at blocking the cellular seeding of endogenous tau by interacting with both monomeric or fibrillar forms of extracellular tau. Peptidomimetic 12 is serum stable, non-toxic to neuronal cells, and selectivity inhibits the aggregation of tau over Ab­42. Structural analysis of our lead NAPs shows considerable conformational constraint imposed by the N-amino groups. The enhanced rigidity and full complement of sidechains thus enables NAPs to recognize tau fibrils. The described backbone N-amination approach provides a rational basis for the mimicry of other aggregation-prone peptides that drive pathogenic protein assembly.
Addressing the petascale data challenge using in-situ analytics (2011)

Data management, processing and analysis costs are quickly dominating computational and data-enabled sciences, and are limiting the potential impacts of advanced simulations running at extreme scales on the high-end computing systems. This presentation explores how in-situ data analytics and in-transit data transformation and data manipulation can be used to address these data challenges at petascale and beyond. Specifically, this presentations describes solutions developed as part of the Rutgers Spaces Project and deployed within the ADIOS framework.
Capacity estimation and waveform assignment in military networks (2012)

Military networks are required to provide continued connectivity and capacity thus providing a means to transport a diverse set of applications ranging from short mission critical messages to constant video surveillance. However, the environments that military networks have to function are often not benign and are generally fraught with bandwidth/capacity limitations. It is however imperative for military networks to be able to continue transporting key applications despite severe capacity fluctuations. The above in turn underscores the necessity for efficient capacity estimation techniques that can be used by network planners & designers when they deploy networks. While wireless network capacity estimation is a challenging problem in itself, the heterogeneous, multi-tier networks envisioned for use by the military, combined with the unpredictable changes (caused by both natural fluctuations, and/or by malicious jamming) to the underlying network, make the problem of capacity estimation for military networks extremely hard. In this paper we present a systematic approach to estimating capacity for Military mobile ad hoc networks, and also present the power of using capacity estimation techniques to assist with the problem of waveform assignment to subnets in a Military network.
Proper sizing of the sampling inlet line for a continuous air monitoring station (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProper sizing of the sampling inlet line for a continuous air monitoring stationV. M. Yamada and R. J. CharlsonCite this: Environ. Sci. Technol. 1969, 3, 5, 483–484Publication Date (Print):May 1, 1969Publication History Published online1 May 2002Published inissue 1 May 1969https://pubs.acs.org/doi/10.1021/es60028a010https://doi.org/10.1021/es60028a010research-articleACS PublicationsRequest reuse permissionsArticle Views49Altmetric-Citations9LEARN 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
Chip-level anti-reverse engineering using transformable interconnects (2015)

Cloning of integrated circuit (IC) chips have emerged as a significant threat to the semiconductor industry. Unauthorized extraction of design information from IC chips can be carried out in numerous ways. Invasive methods physically disassemble chip package and gain access to the different layers of a die through the low-cost delaying processing. This paper presents a new countermeasure exploiting transformable IC technologies. Transformable ICs are fabricated using materials that not only are electronically active but also change their electrical properties and physical compositions when experiencing invasive attacks. Simulation results demonstrate the proposed approach in improving the complexity of chip reverse engineering without introducing large performance overhead.
Activation and Stabilization of Aldimines by an ortho‐Trifluoromethyl Substituent in Direct Vinylogous Mannich‐Type Reactions. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Food-signal theory: population regulation and the functional response (1991)

Journal Article Food-signal theory: population regulation and the functional response Get access B.J Rothschild B.J Rothschild University of Maryland Centre for Environment and Estuarine Studies, Chesapeake Biological LaboratoryPO Box 38, Solomons, MD 20688, USA Search for other works by this author on: Oxford Academic Google Scholar Journal of Plankton Research, Volume 13, Issue 5, 1991, Pages 1123–1135, https://doi.org/10.1093/plankt/13.5.1123 Published: 01 September 1991 Article history Received: 22 September 1990 Accepted: 03 June 1991 Published: 01 September 1991
Plasma genetic and genomic abnormalities predict treatment response and clinical outcome in advanced prostate cancer (2015)

Liquid biopsies, examinations of tumor components in body fluids, have shown promise for predicting clinical outcomes. To evaluate tumor-associated genomic and genetic variations in plasma cell-free DNA (cfDNA) and their associations with treatment response and overall survival, we applied whole genome and targeted sequencing to examine the plasma cfDNAs derived from 20 patients with advanced prostate cancer. Sequencing-based genomic abnormality analysis revealed locus-specific gains or losses that were common in prostate cancer, such as 8q gains, AR amplifications, PTEN losses and TMPRSS2-ERG fusions. To estimate tumor burden in cfDNA, we developed a Plasma Genomic Abnormality (PGA) score by summing the most significant copy number variations. Cox regression analysis showed that PGA scores were significantly associated with overall survival (p < 0.04). After androgen deprivation therapy or chemotherapy, targeted sequencing showed significant mutational profile changes in genes involved in androgen biosynthesis, AR activation, DNA repair, and chemotherapy resistance. These changes may reflect the dynamic evolution of heterozygous tumor populations in response to these treatments. These results strongly support the feasibility of using non-invasive liquid biopsies as potential tools to study biological mechanisms underlying therapy-specific resistance and to predict disease progression in advanced prostate cancer.
Efficient 12-mutation testing in the CFTR gene: a general model for complex mutation analysis (1993)

The identification of the cystic fibrosis transmembrane conductance regulator (CFTR) gene has led to the identification of more than 225 presumed disease-causing mutations at the locus. The diagnosis of cystic fibrosis or the carrier state by direct DNA analysis is hindered by this large number. A practical assay must be able to detect enough mutations to achieve clinically significant sensitivity. The use of allele-specific oligonucleotide probes is the most promising of the available methods. However, to date this has generally involved tedious probe-by-probe hybridizations, due to variations in the oligonucleotides' denaturation temperatures caused by differences in their G-C base-pair content. We have developed a rapid, cost-effective assay that simultaneously detects 12 CFTR mutations after multiplex polymerase-chain-reaction amplification of genomic DNA. The test may be readily extended to detect additional mutations at minimal increase in the cost per test or the turnaround time. We improve specificity and avoid the need for individual hybridizations by the use of tetramethylammonium chloride to virtually eliminate the effects of G-C differences. Coupled with non-invasive sample-collection methods, this is an immediately practical assay for cystic fibrosis. More generally, it will serve as a model for the development of diagnostic tests in other genetic disorders involving complex mutation analysis.
COPEPTIN, A PREDICTOR OF CARDIOMETABOLIC RISK FACTORS AND ORGAN DAMAGE (2011)

Enhörning, S.; Bankir, L.; Bouby, N.; Struck, J.; Hedblad, B.; Nilsson, P.; Morgenthaler, N.; Melander, O. Author Information
Oral N-acetylcysteine decreases IFN-γ production and ameliorates ischemia-reperfusion injury in steatotic livers (2022)

Type 1 Natural Killer T-cells (NKT1 cells) play a critical role in mediating hepatic ischemia-reperfusion injury (IRI). Although hepatic steatosis is a major risk factor for preservation type injury, how NKT cells impact this is understudied. Given NKT1 cell activation by phospholipid ligands recognized presented by CD1d, we hypothesized that NKT1 cells are key modulators of hepatic IRI because of the increased frequency of activating ligands in the setting of hepatic steatosis. We first demonstrate that IRI is exacerbated by a high-fat diet (HFD) in experimental murine models of warm partial ischemia. This is evident in the evaluation of ALT levels and Phasor-Fluorescence Lifetime (Phasor-FLIM) Imaging for glycolytic stress. Polychromatic flow cytometry identified pronounced increases in CD45+CD3+NK1.1+NKT1 cells in HFD fed mice when compared to mice fed a normal diet (ND). This observation is further extended to IRI, measuring <i>ex vivo</i> cytokine expression in the HFD and ND. Much higher interferon-gamma (IFN-γ) expression is noted in the HFD mice after IRI. We further tested our hypothesis by performing a lipidomic analysis of hepatic tissue and compared this to Phasor-FLIM imaging using "long lifetime species", a byproduct of lipid oxidation. There are higher levels of triacylglycerols and phospholipids in HFD mice. Since N-acetylcysteine (NAC) is able to limit hepatic steatosis, we tested how oral NAC supplementation in HFD mice impacted IRI. Interestingly, oral NAC supplementation in HFD mice results in improved hepatic enhancement using contrast-enhanced magnetic resonance imaging (MRI) compared to HFD control mice and normalization of glycolysis demonstrated by Phasor-FLIM imaging. This correlated with improved biochemical serum levels and a decrease in IFN-γ expression at a tissue level and from CD45+CD3+CD1d+ cells. Lipidomic evaluation of tissue in the HFD+NAC mice demonstrated a drastic decrease in triacylglycerol, suggesting downregulation of the PPAR-γ pathway.
INFLUENCE OF SURFACE MICROTOPOGRAPHY ON FORMATION OF CAPSULES; AN IN VIVO STUDY OF STAINLESS STEEL IMPLANTS IN RABBITS (2002)

Movement between an implant surface and overlying soft tissue gives rise to fibrous capsule formation with a liquid filled void. Clinically, this situation is more prevalent with electropolished stainless steel (EPSS) implants compared to commercially pure titanium (CpTi) implants. We hypothesise this is mainly due to lack of microtopography on the EPSS. Four experimental EPSS surfaces with varying microtopographies were selected by a combination of morphological analysis using the scanning electron microscope and quantitative roughness analysis using laser profilometry. Standard treated EPSS (ISO 5832/1) and CpTi (ISO 5832/2) surfaces were also used. The plates had only one screw hole at either end so that the interaction of the tissue with an intact surface could be evaluated. Six plates of each type were implanted on both the left and right tibia, randomly, of 18 white New Zealand rabbits under the muscle for 12 weeks. After sacrifice samples underwent standard histological processing. Briefly, fixation, dehydration, embedding in methyl methacrylate, sectioning at 250μm slices (with implant), grinding to 50μm and staining with Giemsa. Digital images were taken with a light microscope and the size of thickening of connective tissue on the implant surface and the presence or absence of a liquid filled void was observed. Results showed no voids present on the CpTi samples. The standard EPSS had 3/6 plates with a void. The experimental EPSS surfaces were in-between these results. There was no relationship between quantitative measurements of average roughness (Ra) and the presence or absence of a void. There was a relationship between lack of fine microroughness of a surface (as seen with the SEM) and the presence of a void. The size of capsular thickening was not related to the Ra of the surface. These results support that void formation is mainly due to lack of microtopography on the plates.
Efficient expression of tetracycline-responsive gene after transfection of dentate gyrus neurons in vitro (2000)

Gene transfer into neurons both in vivo and in vitro may aid in understanding of gene regulation and function in nerve cells. Especially desirable is ability to control the gene expression. In this study we developed conditions for transfection of hippocampal dentate gyrus neurons in dissociated cultures in vitro by calcium-phosphate method. Furthermore, we describe an effective use of tetracycline responsive gene promoter (Tet-On) system for the controlled and very efficient expression of transfected genes. Under optimal conditions as established in this study, efficiency of transfection of neurons with green fluorescent protein (GFP) driven by constitutive cytomegalovirus (CMV) early promoter reached 2.7%. With tetracycline responsive promoter percentage of GFP-positive neurons raised in the presence of tetracycline analog, doxycycline up to 20%. Application of the Tet-On system resulted in almost 10-fold induction of GFP expression.