gebhart/patrepeval huggingface dataset:
Effects of changing the interaction between subdomains on the thermostability of <i>Bacillus</i> neutral proteases (1992)

Variants of the thermolabile neutral protease (Npr) of B. subtilis (Npr-sub) and the thermostable neutral protease of B. stearothermophilus (Npr-ste) were produced by means of site-directed mutagenesis and the effects of the mutations on thermostability were determined. Mutations were designed to alter the interaction between the middle and C-terminal subdomain of these enzymes. In all Nprs a cluster of hydrophobic contacts centered around residue 315 contributes to this interaction. In thermostable Nprs (like Npr-ste) a 10 residue beta-hairpin, covering the domain interface, makes an additional contribution. The hydrophobic residue at position 315 was replaced by smaller amino acids. In addition, the beta-hairpin was deleted from Npr-ste and inserted into Npr-sub. The changes in thermostability observed after these mutations confirmed the importance of the hydrophobic cluster and of the beta-hairpin for the structural integrity of Nprs. Combined mutants showed that the effects of individual mutations affecting the interaction between the subdomains were not additive. The effects on thermostability decreased as the strength of the subdomain interaction increased. The results show that once the subdomain interface is sufficiently stabilized, additional stabilizing mutations at the same interface do not further increase thermostability. The results are interpreted on the basis of a model for the thermal inactivation of neutral proteases, in which it is assumed that inactivation results from the occurrence of local unfolding processes that render these enzymes susceptible to autolysis.
Impact of Cellular miRNAs on Circulating miRNA Biomarker Signatures (2011)

Effective diagnosis and surveillance of complex multi-factorial disorders such as cancer can be improved by screening of easily accessible biomarkers. Highly stable cell free Circulating Nucleic Acids (CNA) present as both RNA and DNA species have been discovered in the blood and plasma of humans. Correlations between tumor-associated genomic/epigenetic/transcriptional changes and alterations in CNA levels are strong predictors of the utility of this biomarker class as promising clinical indicators. Towards this goal microRNAs (miRNAs) representing a class of naturally occurring small non-coding RNAs of 19-25 nt in length have emerged as an important set of markers that can associate their specific expression profiles with cancer development. In this study we investigate some of the pre-analytic considerations for isolating plasma fractions for the study of miRNA biomarkers. We find that measurement of circulating miRNA levels are frequently confounded by varying levels of cellular miRNAs of different hematopoietic origins. In order to assess the relative proportions of this cell-derived class, we have fractionated whole blood into plasma and its ensuing sub-fractions. Cellular miRNA signatures in cohorts of normal individuals are catalogued and the abundance and gender specific expression of bona fide circulating markers explored after calibrating the signal for this interfering class. A map of differentially expressed profiles is presented and the intrinsic variability of circulating miRNA species investigated in subsets of healthy males and females.
Development and <i>in vitro</i> characterization of chitosan-coated polymeric nanoparticles for oral delivery and sustained release of the immunosuppressant drug mycophenolate mofetil (2018)

Two chitosan-coated nanoparticles formulations of MMF had high EE and a desirable sustained drug release profile in the effort to design a once-daily dosage form for MMF.
Protecting Social Network Users from Impersonation (2018)

Malicious actors on social networks often create fake accounts that impersonate legitimate users in order to carry out scams, send spam and phishing messages, or engage in other abusive behavior. The act of assuming a real person»s identity gives the bad actor an additional level of trust that can make the attack more likely to succeed. In addition to the direct damage caused by the fraudulent activity, impersonation erodes users» trust in the platform and damages the brand of the legitimate user being impersonated. In this paper, we present a large-scale system that identifies and takes action on impersonation profiles on a social network. The system is composed of three tiers of protection: (1) an offline system that protects all users by searching for profile data duplicity combined with suspicious signals; (2) an offline system with stricter logic that proactively protects high-profile users in population segments that have historically been targeted for impersonation; and (3) an online system that provides low-latency protection to a manually curated list of individuals that have been actively targeted by impersonation. The tiers build on one another with decreasing detection latency and more targeted user coverage. We have deployed our system on the professional social network LinkedIn and drastically reduced the extent of impersonation abuse on LinkedIn. Specifically, we observed a reduction in the impersonator median time-to-detect of more than $98%$, a more than fourfold improvement in recall (as measured on a monthly basis) and reduction over $95%$ in the number of impersonation reports by the most targeted company on LinkedIn.
An Immunoradiometric Assay for Thymosin α 1 (1996)

An Immunoradiometric assay for thymosin alpha 1(1-28) was developed using a monoclonal and a polyclonal antiserum which were raised against synthetic thymosin alpha 1(1-28) and thymosin alpha 1(16-28), respectively. A monoclonal antibody, specific for the (acetylated ser1) 1-5 sequence of thymosin alpha 1, was immobilized on polystyrene beads for the solid phase, and a polyclonal antiserum specific for the 16-28 sequence was employed. This method relies on the formation of an immune complex consisting of a 125I-labelled anti-rabbit IgG goat antibody, polyclonal antiserum, thymosin alpha 1, and the solid phase monoclonal antibody. Radioactivity on the solid phase is directly proportional to the amount of thymosin alpha 1 present in the specimen. The minimal detection limit of this assay system was approximately 1.9 pg/ml. The mean values of thymosin alpha 1 in plasma of healthy subject, ranging in age from 0 to 3 years was approximately five fold higher than that of higher ages. HPLC analysis of plasma of a healthy subjects revealed a single immunoreactive form which eluted with the same retention time as that of synthetic thymosin alpha 1. This assay will be extremely useful for the measurement of thymosin alpha 1 in biologic fluids and tissues.
Simple (Imidazol‐2‐ylidene)‐Pd‐acetate Complexes as Effective Precatalysts for Sterically Hindered Suzuki—Miyaura Couplings. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Input-output system identification of a thermoacoustic oscillator near a Hopf bifurcation using only fixed-point data (2020)

We present a framework for performing input-output system identification near a Hopf bifurcation using data from only the fixed-point branch, prior to the Hopf point itself. The framework models the system with a van der Pol-type equation perturbed by additive noise, and identifies the system parameters via the corresponding Fokker-Planck equation. We demonstrate the framework on a prototypical thermoacoustic oscillator (a flame-driven Rijke tube) undergoing a supercritical Hopf bifurcation. We find that the framework can accurately predict the properties of the Hopf bifurcation and the limit cycle beyond it. This study constitutes an experimental demonstration of system identification on a reacting flow using only prebifurcation data, opening up pathways to the development of early warning indicators for nonlinear dynamical systems near a Hopf bifurcation.
Positive-Tone, Aqueous-Developable, Polynorbornene Dielectric (2012)

Abstract not Available.
Enhancing transport networks with Internet protocols (1998)

Transport networks are facing new challenges and opportunities because of the explosive growth of data traffic. Besides having to meet the ever-increasing bandwidth demand, transport networks need to provide new functionalities for the support of data applications. For example, they should provide elastic data pipes which guarantee minimum bandwidths but also allow expansion when extra bandwidth is available. They should support instant and automatic discovery and configuration of layer 3 nodes which, traditionally, is possible only for LANs. Enhanced transport systems with inherent packet multiplexing can meet these challenges. It will be natural to use Internet protocols and technologies to implement these packet transport systems, and thereby reuse much of the existing Internet infrastructure already widely deployed.
Glucoamylase produced by Rhizopus and by a recombinant yeast containing the Rhizopus glucoamylase gene. (1986)

Recombinant Rhizopus glucoamylase produced by a yeast containing the Rhizopus glucoamylase gene was purified, characterized, and compared with native Rhizopus glucoamylase. The recombinant glucoamylase was similar to Glue 1, one of three forms of Rhizopus native glucoamylase, but it degraded raw starch more efficiently than the native glucoamylase. Recombinant glucoamylase and Glue 1 adsorbed to gelatinized soluble starch as well as raw starch. These findings suggested that Rhizopus glucoamylase consists of two domains; one for causing adsorption to the starch and the other for catalyzing degradation of the starch molecule.
Chaos in MEMS, parameter estimation and its potential application (1998)

In this paper we present theoretical analysis and experimental results on the dynamic behavior of a bistable microelectromechanical systems (MEMS) oscillator, demonstrate the existence of a strange attractor in the MEMS device, and perform model verification using the experimental data. Secure communication schemes based on synchronized chaos are also applied to the device and successfully performed in the simulation.
Abstract 3763: UCART22: allogenic adoptive immunotherapy of leukemia by targeting CD22 with CAR T-cells (2017)

Abstract Adoptive immunotherapy using autologous T-cells endowed with chimeric antigen receptors (CARs) has given rise to long-term durable remissions and remarkable objective response rates in patients with refractory leukemia, raising hopes that a wider application of CAR technology may lead to a new paradigm in cancer treatment. However, a limitation of the current autologous approach is that CAR T-cells must be manufactured on a "per patient basis". To overcome this limitation, we have developed a standardized platform for manufacturing T-cells from third-party healthy donors to generate allogeneic "off-the-shelf" engineered CAR+ T-cell-based frozen products. Our allogenic platform utilizes the Transcription Activator-Like Effector Nuclease (TALEN) gene editing technology to inactivate the TCRα constant (TRAC) gene, significantly reducing the potential for T-cells bearing alloreactive TCR’s to mediate Graft-versus-Host Disease (GvHD). We have previously demonstrated the precise and efficient disruption of the the TRAC gene by gene editing, yielding up to 85% of TCRαβ-negative cells. This allows the production of TCRαβ-deficient T-cells that no longer mediate alloreactivity in a xeno-GvHD mouse model. In the clinic, the proof of concept of the applicability of our allogeneic platform was achieved with early compassionate use for patients treated with UCART19, an allogeneic engineered CAR T-cell product directed against CD19. UCART19 clinical trials are currently ongoing. Here, we have developed T-cells targeting CD22 which is expressed on tumor cells from the majority of patients with B-cells leukemia. In a first step, we have screened multiple antigen recognition domains in the context of different CAR architectures to identify effective CAR candidates displaying activity against cells expressing variable levels of the CD22 antigen. As a safety feature, T-cells are engineered to co-express a depletion gene, rendering them sensitive to the monoclonal antibody rituximab. Several constructs of depletion genes have been evaluated in the context of the CD22 CAR. In addition, experiments in an orthotopic ALL mouse model using UCART22 cells demonstrated important anti-tumor activity in vivo. The ability to carry out large scale manufacturing of allogeneic, non-alloreactive CD22 specific T-cells from a single healthy donor can offer the possibility of an off-the-shelf treatment that would be immediately available for administration to a large number of leukemic patients. UCART22 could also offer an alternative to patients who may relapse with CD19-negative tumors after CD19 CAR T-cell treatment. Citation Format: Agnès Gouble, Cécile Schiffer-Mannioui, Severine Thomas, Anne-Sophie Gautron, Laurent Poirot, Julianne Smith. UCART22: allogenic adoptive immunotherapy of leukemia by targeting CD22 with CAR T-cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3763. doi:10.1158/1538-7445.AM2017-3763
Short-circuit fault-tolerant control for five-phase fault-tolerant permanent magnet motors with trapezoidal back-EMF (2021)

When a short-circuit fault occurs in a phase, the faulty phase needs to be removed artificially from the system because of the loss of the capability to generate torque. In this case, both the short-circuit current and phase-loss fault would generate additional torque ripples. In this study, a novel fault-tolerant control strategy is introduced to achieve low torque ripple operation of five-phase fault-tolerant permanent magnet synchronous motors with trapezoidal back electromotive force (FTPMSM-TEMF) in the event of a short-circuit fault. The key concept of this method is to compensate for the torque ripples caused by the short-circuit current and the adverse effect of the phase-loss. Based on the torque expression under fault conditions, the torque ripple caused by the short-circuit current can be offset by injecting a certain pulsating component into the torque expression in the phase-loss condition. This would result in smooth operation under fault conditions. Moreover, to track the fault-tolerant alternating currents, the model of the deadbeat current predictive control is extended and restructured for the fault condition. The effectiveness and feasibility of the proposed fault-tolerant strategy are verified by experimental results.
Replica consistency of CORBA objects in partitionable distributed systems (1997)

The Eternal system enhances the CORBA standard to provide fault tolerance within distributed systems that are susceptible to network partitioning. Fault tolerance is achieved through consistent replication of both client and server objects. Objects may be actively or passively replicated, and replicated objects of both types may coexist. Nested operations involving both active and passive objects are accommodated. Suppression of duplicate operations is ensured by unique message and operation identifiers. Continued operation is allowed in all components of a partitioned network. State transfer mechanisms and fulfilment operations restore the consistency of the states of the replicas when communication is re-established and the components remerge.
Ultra-open acoustic metamaterial silencer (2019)

Recently, with advances in acoustic metamaterial science, the possibility of sound attenuation using subwavelength structures, while maintaining permeability to air, has been demonstrated. However, the ongoing challenge addressed herein is the fact that among such air-permeable structures to date, the open areas represents only small fraction of the overall area of the material. In the presented work, in order to address this challenge, we firstly demonstrate that a transversely-placed bilayer medium with large degrees of contrast in the layers' acoustic properties exhibits an asymmetric transmission, similar to the Fano-like interference phenomenon. Next, we utilize this design methodology and propose a deep-subwavelength acoustic metasurface unit cell comprising nearly 60% open area for air passage, while serving as a high-performance selective sound silencer. Finally, the proposed unit cell performance is validated experimentally, demonstrating a reduction in the transmitted acoustic energy of up to 94%. This ultra-open metamaterial (UOM) design, leveraging a Fano-like interference, enables high-performance sound silencing in a design featuring a large degree of open area, which may find utility in applications in which highly efficient, air-permeable sound silencers are required, such as smart sound barriers, fan or engine noise reduction, among others.
Tailoring of arteriovenous graft-to-vein anastomosis angle to attenuate pathological flow fields (2021)

Arteriovenous grafts are routinely placed to facilitate hemodialysis in patients with end stage renal disease. These grafts are conduits between higher pressure arteries and lower pressure veins. The connection on the vein end of the graft, known as the graft-to-vein anastomosis, fails frequently and chronically due to high rates of stenosis and thrombosis. These failures are widely believed to be associated with pathologically high and low flow shear strain rates at the graft-to-vein anastomosis. We hypothesized that consistent with pipe flow dynamics and prior work exploring vein-to-artery anastomosis angles in arteriovenous fistulas, altering the graft-to-vein anastomosis angle can reduce the incidence of pathological shear rate fields. We tested this via computational fluid dynamic simulations of idealized arteriovenous grafts, using the Bird-Carreau constitutive law for blood. We observed that low graft-to-vein anastomosis angles ([Formula: see text]) led to increased incidence of pathologically low shear rates, and that high graft-to-vein anastomosis angles ([Formula: see text]) led to increased incidence of pathologically high shear rates. Optimizations predicted that an intermediate ([Formula: see text]) graft-to-anastomosis angle was optimal. Our study demonstrates that graft-to-vein anastomosis angles can significantly impact pathological flow fields, and can be optimized to substantially improve arteriovenous graft patency rates.
Decreasing distortion using low delay codes for bursty packet loss channels (2003)

The strict delay constraints of real-time communication applications in packet networks limit the use of automatic repeat request (ARQ) (retransmission systems) and error correction codes with extensive interleaving and decoding over long intervals. Since packet losses can introduce significant impairments, we study the effectiveness of low delay channel coding techniques to increase transmission quality across links with bursty losses. Specifically, we consider the benefits of the newly discovered class of low delay convolutional codes known as maximally short codes. By analyzing a Gaussian source transmitted over a Gilbert-Elliott channel, we demonstrate that these codes can achieve significant gains in comparison to uncoded transmission schemes or traditional coded schemes employing Reed-Solomon block codes. To complement and validate the theoretical analysis we also present results from informal listening tests with a voice-over-IP application.
Potential column chromatography generators for ionic Ga-68. I. Inorganic substrates. (1979)

Chemical separations for Ga-68 from Ge-68 using adsorption chromatography on inorganic materials are described. The adsorbents used were TiO2, ZrO2, and SiO2. Distribution coefficients for Ge and Ga on these absorbents were determined as a function of reagent concentration and duration of equilibration. The distribution coefficient (w/w) for Ge on SiO2 reached 250 in 6 N HNO3, whereas Ga was no significantly adsorbed. Therefore, Ga-68 can be collected with a mall volume of 6 N HNO3 eluent. By contrast, large volumes of 1 N HNO3 were necessary to collect Ga-68 from ZrO2, since the KD of Ga under these circumstances was about 50. The Ga-68 eluted from TiO2 was chemically contaminated with titanates and would require additional chemical manipulation in order to make it injectable. All the adsorbents could lead to chromatographic systems that would allow acceptable chemical separations. However, the specific requirements for a radionuclide generator, usable in a hospital environment, make the SiO2-based system the most attractive.
Double-clad photonic-crystal-fiber based scanning microscopy (2005)

We report the development of a novel double-clad photonic-crystal-fiber based multiphoton scanning microscope, which has a number of advantages over conventional scanning microscopes.
Gene transfer of CFTR to airway epithelia: low levels of expression are sufficient to correct Cl <sup>−</sup> transport and overexpression can generate basolateral CFTR (2005)

Gene transfer of CFTR cDNA to airway epithelia is a promising approach to treat cystic fibrosis (CF). Most gene transfer vectors use strong viral promoters even though the endogenous CFTR promoter is very weak. To learn whether expressing CFTR at a low level in a fraction of cells would correct Cl(-) transport, we mixed freshly isolated wild-type and CF airway epithelial cells in varying proportions and generated differentiated epithelia. Epithelia with approximately 20% wild-type cells generated approximately 70% the transepithelial Cl(-) current of epithelia containing 100% wild-type cells. These data were nearly identical to those previously obtained with CFTR expressed under control of a strong promoter in a CF epithelial cell line. We also tested high level CFTR expression using the very strong cytomegalovirus (CMV) promoter as well as the cytokeratin-18 (K18) promoter. In differentiated airway epithelia, the CMV promoter generated 50-fold more transgene expression than the K18 promoter, but the K18 promoter generated more transepithelial Cl(-) current at high vector doses. Using functional studies, we found that with marked overexpression, some CFTR channels were present in the basolateral membrane where they shunted Cl(-) flow, thereby reducing net transepithelial Cl(-) transport. These results suggest that very little CFTR is required in a fraction of CF epithelial cells to complement Cl(-) transport because transepithelial Cl(-) flow is limited at the basolateral membrane. Thus they suggest a broad leeway in promoter strength for correcting the CF gene transfer, although at very high expression levels CFTR may be mislocalized to the basolateral membrane.
Thin films of novel ferroelectric composites (1996)

Abstract Composites of BSTO combined with other non electrically active oxides have demonstrated adjustable electronic properteis which can be tailored for use in various electronic devices.[1,2] These novel composites of barium strontium titanate (BSTO) and oxide III compounds have already exhibited promising results in their ceramic form.[3] The additive oxides modify the dielectric constant, tunability (change in the dielectric constant with applied voltage), and dielectric loss of the material. One application has been for use in phased array antennas and insertion has been accomplished into several working antenna systems.[4] To further accommodate the frequencies required by these phased array antennas, thin films of the composites have been fabricated. Preliminary studies have indicated that thin films of such composites exhibit similar behavior as their bulk ceramic counterparts.[5] The purpose of this study is to investigate the properties of the BSTO/oxide III based compounds in thin film form.