gebhart/patrepeval huggingface dataset:
An Indicator Response Surface-Based Monte Carlo Method for Efficient Component and System Reliability Analysis (2003)

Reliability analysis methods are commonly used in engineering design, in order to meet reliability and quality measures. An accurate and efficient computational method is presented for reliability analysis of engineering systems at both the component and system levels. The method can easily handle implicit, highly nonlinear limit-state functions, with correlated or non-correlated random variables, which are described by any probabilistic distribution. It is based on a constructed response surface of an indicator function, which determines the “failure” and “safe” regions, according to the performance function. A Monte Carlo simulation (MCS) calculates the probability of failure based on a response surface of the indicator function, instead of the computationally expensive limit-state function. The Cross-Validated Moving Least Squares (CVMLS) method is used to construct the response surface of the indicator function, based on an Optimum Symmetric Latin Hypercube (OSLH) sampling technique. A number of numerical examples highlight the superior accuracy and efficiency of the proposed method over commonly used reliability methods.
Carotid Intraplaque Hemorrhage Imaging at 3.0-T MR Imaging: Comparison of the Diagnostic Performance of Three T1-weighted Sequences (2010)

Purpose To compare the diagnostic performances of three T1-weighted 3.0-T magnetic resonance (MR) sequences at carotid intraplaque hemorrhage (IPH) imaging, with histo logic analysis as the reference standard. Materials and Methods Institutional review board approval and informed consent were obtained for this HIPAA-compliant study. Twenty patients scheduled for carotid endarterectomy underwent 3.0-T carotid MR imaging, including two-dimensional fast spin-echo, three-dimensional time-of-flight (TOF), and three-dimensional magnetization-prepared rapid acquisition gradient-echo (RAGE) sequences. Two reviewers blinded to the histologic findings assessed the presence, area, and signal intensity of IPH with each sequence. Detection statistics (sensitivity, specificity, and Cohen κ values) and agreement between area measurements (Pearson correlation coefficient [r] values) were calculated for each sequence. Results When all 231 available MR sections were included for analysis, the magnetization-prepared RAGE (κ = 0.53) and fast spin-echo (κ = 0.42) sequences yielded moderate agreement between MR and histologic measurements, while the TOF sequence yielded fair agreement (k = 0.33). However, when 47 sections with either small IPHs or heavily calcified IPHs were excluded, sensitivity, specificity, and κ values, respectively, were 80%, 97%, and 0.80 for magnetization-prepared RAGE imaging; 70%, 92%, and 0.63 for fast spin-echo imaging; and 56%, 96%, and 0.57 for TOF imaging. MR imaging–histologic analysis correlation for IPH area was highest with magnetization-prepared RAGE imaging (r = 0.813), followed by TOF (r = 0.745) and fast spin-echo (r = 0.497) imaging. The capability of these three sequences for IPH detection appeared to be in good agreement with the quantitative contrast of IPH versus background plaque tissue. Conclusion The magnetization-prepared RAGE sequence, as compared with the fast spin-echo and TOF sequences, demonstrated higher diagnostic capability for the detection and quantification of IPH. Potential limitations of 3.0-T IPH MR imaging are related to hemorrhage size and coexisting calcification. © RSNA, 2010
PtenDeletion in Adult Neural Stem/Progenitor Cells Enhances Constitutive Neurogenesis (2009)

Here we show that conditional deletion of Pten in a subpopulation of adult neural stem cells in the subependymal zone (SEZ) leads to persistently enhanced neural stem cell self-renewal without sign of exhaustion. These Pten null SEZ-born neural stem cells and progenies can follow the endogenous migration, differentiation, and integration pathways and contribute to constitutive neurogenesis in the olfactory bulb. As a result, Pten deleted animals have increased olfactory bulb mass and enhanced olfactory function. Pten null cells in the olfactory bulb can establish normal connections with peripheral olfactory epithelium and help olfactory bulb recovery from acute damage. Following a focal stroke, Pten null progenitors give rise to greater numbers of neuroblasts that migrate to peri-infarct cortex. However, in contrast to the olfactory bulb, no significant long-term survival and integration can be observed, indicating that additional factors are necessary for long-term survival of newly born neurons after stroke. These data suggest that manipulating PTEN-controlled signaling pathways may be a useful step in facilitating endogenous neural stem/progenitor expansion for the treatment of disorders or lesions in regions associated with constitutive neurogenesis.
Isolation and Characterization of cLV25, a Bacteroides fragilis Chromosomal Transfer Factor Resembling Multiple Bacteroides sp. Mobilizable Transposons (2002)

ABSTRACT Horizontal DNA transfer contributes significantly to the dissemination of antibiotic resistance genes in Bacteroides fragilis . To further our understanding of DNA transfer in B. fragilis , we isolated and characterized a new transfer factor, cLV25. cLV25 was isolated from B. fragilis LV25 by its capture on the nonmobilizable Escherichia coli-Bacteroides shuttle vector pGAT400ΔBglII. Similar to other Bacteroides sp. transfer factors, cLV25 was mobilized in E. coli by the conjugative plasmid R751. Using Tn 1000 mutagenesis and deletion analysis of cLV25, two mobilization genes, bmgA and bmgB , were identified, whose predicted proteins have similarity to DNA relaxases and mobilization proteins, respectively. In particular, BmgA and BmgB were homologous to MocA and MocB, respectively, the two mobilization proteins of the B. fragilis mobilizable transposon Tn 4399 . A cis -acting origin of transfer ( oriT ) was localized to a 353-bp region that included nearly all of the intergenic region between bmgB and orf22 and overlapped with the 3′ end of orf22 . This oriT contained a putative nic site sequence but showed no significant similarity to the oriT regions of other transfer factors, including Tn 4399 . Despite the lack of sequence similarity between the oriT s of cLV25 and Tn 4399 , a mutation in the cLV25 putative DNA relaxase, bmgA , was partially complemented by Tn 4399 . In addition to the functional cross-reaction with Tn 4399 , a second distinguishing feature of cLV25 is that predicted proteins have similarity to proteins encoded not only by Tn 4399 but by several Bacteroides sp. transfer factors, including NBU1, NBU2, CTnDOT, Tn 4555 , and Tn 5520 .
Degradation of Basement‐Membrane Collagen by Neutral Proteases from Human Leukocytes (1980)

A neutral extract from human leukocytes was shown to have proteolytic activity which could degrade triple-helical basement membrane collagen from bovine lens capsules into specific triple-helical sub-fragments. The enzymes responsible is not identical to the leukocyte collagenase active against interstitial collagen types I, II and III. After denaturation, the neutral protease reaction products showed three major peptides with molecular weights of 70,000, 50,000 and 30,000, by dodecylsulphate gel electrophoresis analysis. Electron microscopic observation and viscosity measurements showed the initial twice-pepsinized collagen to be comprised of intact rod-like molecules about 300 nm long. The fragments produced by the protease were also triple-helical and were resistant to the action of trypsin at 20 degrees C. The fragments were completely degraded by purified bacterial collagenase or by raising the reaction temperature above the melting temperature of the basement membrane collagen during incubation with leukocyte extract. Enzyme activity has its pH optimum between 7 and 9, EDTA, EGTA and 1,10-phenanthroline (metal-chelating agents) completely inhibited enzyme activity, as did serum. Partial inhibition of the activity was obtained with phenylmethylsulfonyl fluoride and soybean trypsin inhibitor.
Kinetics of recombinant immunoglobulin production by mammalian cells in continuous culture (1991)

A clonal derivative of a transfectant of the SP2/O myeloma cell line producing a chimeric monoclonal antibody was maintained in steady-state, continuous culture at dilution rates ranging from 0.21 to 1.04 day(-1). The steady-state values for nonviable and total cell concentrations increased as the dilution rate decreased, while the viable cell concentration was roughly independent of the dilution rate. At steady state, the specific growth rate increased and the specific death rate decreased as the dilution rate increased. The maximum specific growth rate was 1.15 day(-1). Antibody production was growth associated and the specific rate of antibody production increased linearly as the specific growth rate increased.
Stochastic explanation of speckle contrast detection in ultrasound-modulated optical tomography (2006)

Ultrasound-modulated optical tomography is an imaging technique that detects ultrasonically tagged light in optically turbid media to obtain images with optical contrast and ultrasonic spatial resolution. A CCD-camera-based speckle contrast detection scheme has been introduced previously to detect modulated light emerging from the ultrasonic sample volume. Differences in speckle contrast were experimentally observed when ultrasound was applied compared to when it was not. In this paper we provide an analytic explanation for this phenomenon and connect speckle statistics with ultrasonic field parameters. The theory predicts that speckle contrast changes linearly with applied acoustic intensity. This prediction is experimentally validated for both 1 and ultrasound. Signal dependence on ultrasound frequency is discussed.
Does the Environment Influence the Employment Growth of SMEs? (2009)

Abstract A great deal of empirical research has been devoted to the study of the impact of a firm's environmental characteristics on its growth. However, most of this work focused on one or a few predictors. Furthermore, no research has provided an exhaustive list of all variables previously studied. We have tried to fill this gap and have tested on a sample of Belgian SMEs the potential influence of 15 variables on employment growth. On the basis of Mintzberg's classification, we have grouped our variables into three sub-categories of determinants relating to the generosity or hostility of the environment, to its stability or dynamism and to its simplicity or complexity. Our results show that employment growth within SMEs is only influenced by two variables linked to the generosity sub-group. These also show that the environment, at least if it is studied independently, has only an extremely limited influence on the growth of SMEs. This leads us to question the validity of purely external approaches to firms’ employment growth, such as the theory of population ecology of organizations.
Safety and immunogenicity of Shigella sonnei-CRM9 and Shigella flexneri type 2a-r EPAsucc conjugate vaccines in one- to four-year-old children (2003)

These experimental Shigella conjugate vaccines were safe and immunogenic in 1- to 4-year-old children.
Parametric coding of spatial audio (2004)

A wide range of techniques for coding a single speech or audio signal channel have been developed over the last few decades. In addition to pure redundancy reduction, sophisticated source and receiver models have been considered for reducing the bitrate. Only a few techniques address joint-coding of the channels of stereo1 and multi-channel audio signals. Stereo and multi-channel audio signals evoke an auditory spatial image in a listener. Thus the receiver model may consider properties of spatial hearing of the auditory system for reducing the bitrate. This has been done in previous techniques by considering the importance of interaural level difference cues at high frequencies and by considering the binaural masking level difference for computing the masked threshold for multiple audio channels. The coding scheme proposed in this thesis aims at being more systematic and parameterized. A stereo or multi-channel audio signal is represented as a single downmixed audio channel plus side information. The side information contains the inter-channel cues inherent in the original audio signal that are relevant for the perception of the properties of the auditory spatial image. At the decoder the stereo or multi-channel audio signal is reconstructed such that its inter-channel cues approximate the corresponding cues of the original audio signal. This enables coding of stereo or multi-channel audio signals at a bitrate nearly as low as a mono audio coding bitrate because the side information contains about two orders of magnitude less information than the original audio channel waveforms. This corresponds to a significant bitrate reduction compared to conventional state-of-the-art coders. Several subjective tests were conducted, indicating that good audio quality can be achieved by the proposed scheme. A number of variations of the coding scheme are proposed. These include different combinations of conventional multi-channel audio coders and the proposed coding scheme, and a scheme which provides flexibility at the decoder to manipulate the auditory spatial image. A model for source localization in the presence of concurrent sound (other sources and reflections) is proposed. The results from a number of previous psychophysical studies are predicted successfully by the model. The model is also applied for comparing audio signals to corresponding signals coded with the proposed scheme. 1In this thesis, the term "stereo audio signal" always refers to two-channel stereo audio signals.
Venous Leg Ulcers in a Patient with Klinefelter's Syndrome and Increased Activity of Plasminogen Activator Inhibitor-1 (2003)

Sir, Klinefelter’s syndrome, originally described by Klinefelter et al. in 1942 (1), is the most frequent major abnormality of sexual differentiation in men with two or more X-chromosomes. Its prevalence has been estimated at one male birth in 500. The prevalence of leg ulcers as a result of a venous insufficiency in patients with Klinefelter’s syndrome is about 13% (2). The pathogenesis of this venous insufficiency is still unknown.
Experimental elimination of tumor necrosis factor in low-dose endotoxin models has variable effects on survival (1991)

Tumor necrosis factor alpha (TNF) is thought to play a major role in the pathogenesis of septic shock. Anti-TNF antibody was preadministered in low-dose endotoxin lethality models in which BALB/c mice were challenged with small amounts of lipopolysaccharide following their sensitization with either carrageenan (CAR) or D-galactosamine (D-GalN). Although the antibody virtually eliminated circulating TNF in both the CAR and the D-GalN models, only the D-GalN model mice were afforded survival, adding to a growing body of evidence that substances other than TNF play a key role in endotoxin-induced lethality. Further examination of sera from these mice showed a much greater elevation of interleukin-6 levels in the CAR-sensitized group than in the D-GalN-sensitized group.
Development of electrical activity in cardiac myocyte aggregates derived from mouse embryonic stem cells (2003)

Embryonic stem cells differentiate into cardiac myocytes, repeating in vitro the structural and molecular changes associated with cardiac development. Currently, it is not clear whether the electrophysiological properties of the multicellular cardiac structure follow cardiac maturation as well. In long-term recordings of extracellular field potentials with microelectrode arrays consisting of 60 substrate-integrated electrodes, we examined the electrophysiological properties during the ongoing differentiation process. The beating frequency of the growing preparations increased from 1 to 5 Hz concomitant to a decrease of the action potential duration and action potential rise time. A developmental increase of the conduction velocity could be attributed to an increased expression of connexin43 gap junction channels. Whereas isoprenalin elicited a positive chronotropic response from the first day of spontaneous beating onward, a concentration-dependent negative chronotropic effect of carbachol only developed after approximately 4 days. The in vitro development of the three-dimensional cardiac preparation thus closely follows the development described for the mouse embryonic heart, making it an ideal model to monitor the differentiation of electrical activity in embryonic cardiomyocytes.
Role of Surface Termination in Atomic Layer Deposition of Silicon Nitride (2015)

There is an urgent need to deposit uniform, high-quality, conformal SiN(x) thin films at a low-temperature. Conforming to these constraints, we recently developed a plasma enhanced atomic layer deposition (ALD) process with bis(tertiary-butyl-amino)silane (BTBAS) as the silicon precursor. However, deposition of high quality SiNx thin films at reasonable growth rates occurs only when N2 plasma is used as the coreactant; strongly reduced growth rates are observed when other coreactants like NH3 plasma, or N2-H2 plasma are used. Experiments reported in this Letter reveal that NH(x)- or H- containing plasmas suppress film deposition by terminating reactive surface sites with H and NH(x) groups and inhibiting precursor adsorption. To understand the role of these surface groups on precursor adsorption, we carried out first-principles calculations of precursor adsorption on the β-Si3N4(0001) surface with different surface terminations. They show that adsorption of the precursor is strong on surfaces with undercoordinated surface sites. In contrast, on surfaces with H, NH2 groups, or both, steric hindrance leads to weak precursor adsorption. Experimental and first-principles results together show that using an N2 plasma to generate reactive undercoordinated surface sites allows strong adsorption of the silicon precursor and, hence, is key to successful deposition of silicon nitride by ALD.
Lesions of Acute Inhaled Lethal Ricin Intoxication in Rhesus Monkeys (1996)

Five unimmunized adult rhesus monkeys weighing 5.9-6.3 kg were challenged with a precalculated, inhaled dose of 20.95-41.8 micrograms/kg of aerosolized ricin. Two males and three females either died or were killed at the onset of respiratory distress between 36 and 48 hours post-ricin inhalation and were necropsied. Consistent gross and microscopic lesions were confined to the thoracic cavity. All monkeys had multifocal to coalescing fibrinopurulent pneumonia, diffuse necrosis, and acute inflammation of airways, and nearly diffuse alveolar flooding, with peribronchovascular edema. All monkeys also had purulent tracheitis, fibrinopurulent pleuritis, and purulent mediastinal lymphadenitis. One male monkey and one female monkey had bilateral adrenocortical necrosis. We attributed the cause of death to asphyxiation following massive pulmonary alveolar flooding. The lesions of acute inhaled ricin intoxication in rhesus monkeys closely resembled those lesions reported in rats with acute inhaled ricin intoxication.
Efficient Gene Delivery and Expression in Pancreas and Pancreatic Tumors by Capsid-Optimized AAV8 Vectors (2017)

Despite efforts to use adeno-associated viral (AAV) vector-mediated gene therapy for treatment of pancreatic ductal adenocarcinoma (PDAC), transduction efficiency remains a limiting factor and thus improvement of AAV delivery would significantly facilitate the treatment of this malignancy. Site-directed mutagenesis of specific tyrosine (Y) residues to phenylalanine (F) on the surface of various AAV serotype capsids has been reported as a method for enhancing gene transfer efficiencies. In the present studies, we determine whether Y-to-F mutations could also enhance AAV8 gene transfer in the pancreas to facilitate gene therapy for PDAC. Three different Y-to-F mutant vectors (a single-mutant, Y733F; a double-mutant, Y447F+Y733F; and a triple-mutant, Y275F+Y447F+Y733F) and wild-type AAV8 (WT-AAV8) were administered by intraperitoneal or tail-vein routes to Kras<sup>G12D+/-</sup>, Kras<sup>G12D+/-</sup>/Pten<sup>+/-</sup>, and wild-type mice. The transduction efficiency of these vectors expressing the mCherry reporter gene was evaluated 2 weeks post administration in pancreas or PDAC and correlated with viral genome copy numbers. Our comparative and quantitative analyses of the transduction profiles demonstrated that the Y-to-F double-mutant exhibited the highest mCherry expression in pancreatic tissues (range 45-70%) compared with WT-AAV8 (7%; p < 0.01). We also detected a 7-fold higher level of vector genome copy numbers in normal pancreas following transduction with the double-mutant AAV8 compared with WT-AAV8 (10,285 vs. 1,500 vector copies/μg DNA respectively, p < 0.05). In addition, we observed that intraperitoneal injection of the double-mutant AAV8 led to a 15-fold enhanced transduction efficiency as compared to WT-AAV8 in mouse PDAC, with a corresponding ∼14-fold increase in vector genome copy numbers (26,575 vs. 2,165 copies/μg DNA respectively, p < 0.05). These findings indicate that the Y447+Y733F-AAV8 leads to a significant enhancement of transduction efficiency in both normal and malignant pancreatic tissues, suggesting the potential use of this vector in targeting pancreatic diseases in general, and PDAC in particular.
Acyclic Diene Metathesis with a Monomer from Renewable Resources: Control of Molecular Weight and One‐Step Preparation of Block Copolymers (2008)

The preparation of a long-chain aliphatic alpha,omega-diene from plant oil derivatives and its subsequent polymerization through acyclic diene metathesis (ADMET) is described. The ADMET bulk polymerization of the thus-obtained monomer, undecyl undecenoate, was investigated and optimized by applying ruthenium-based metathesis catalysts from Grubbs and Hoveyda-Grubbs, leading to high-molecular-weight polyesters. Moreover, by applying different amounts of methyl 10-undecenoate as a chain stopper in this ADMET step growth polymerization, the molecular weight of the resulting polyester could be tuned in a range from approximately 10 to 45 kDa. Finally, the application of a poly(ethylene glycol) methyl ether acrylate as the chain stopper led to the preparation of ABA triblock copolymers in a one-step, one-pot procedure.
Utilizing a personalization-enabled access node in support of converged cross-domain scoring and advertising (2010)

Personalization of Internet Protocol (IP) and Internet services is a topic that is attracting significant interest. This paper suggests a novel network-centric method of extracting demographic and psychographic individual profiles from Internet Protocol television (IPTV) activities and correlating these profiles with unauthenticated behavioral profiles mined from Internet traffic in order to create converged cross-domain (IPTV, Internet, and IP Multimedia Subsystem [IMS]) scoring. The method is based on extending the access network with behavioral mining engines and utilizes a novel approach to mapping between authenticated and unauthenticated profiles extracted from different domains. The advantage of the suggested method is that it can offer superior accuracy in targeting individual users, adapts quickly to temporal changes in interests, can work with or without user authentication (addressing security concerns on the Internet), and expands traditional Internet advertising beyond the Internet context. A full end-to-end architecture and call flows are introduced and use cases analyzed, showing the benefits that the new method can offer in terms of improved service personalization and minimization of time required for the system to adapt to new user interests and behaviors.