gebhart/patrepeval huggingface dataset:
Substrate residues N‐terminal to the cleavage site of botulinum type B neurotoxin play a role in determining the specificity of its endopeptidase activity (1996)

Clostridium botulinum type B neurotoxin is a highly specific zinc-endopeptidase which cleaves vesicle-associated membrane protein (VAMP/synaptobrevin), a critical component of the vesicle docking/fusion mechanism. In this study, substrate residues flanking the N-terminal side of the cleavage site are shown to play a key role in enzyme substrate recognition. Two aspartate residues in this region are identified as critical determinants of the neurotoxin's specificity. These findings are discussed in relation to the mechanism by which botulinum type B neurotoxin cleaves its substrate.
Pharmacogenomics of β-Adrenergic Receptor Physiology and Response to β-Blockade (2011)

Myocardial β-adrenergic receptors (βARs) are important in altering heart rate, inotropic state, and myocardial relaxation (lusitropy). The β1AR and β2AR stimulation increases cyclic adenosine monophosphate concentration with the net result of myocyte contraction, whereas β3AR stimulation results in decreased inotropy. Downregulation of β1ARs in heart failure, as well as an increased β3AR activity and density, lead to decreased cyclic adenosine monophosphate production and reduced inotropy. The βAR antagonists are commonly used in patients with coronary artery disease and heart failure; however, perioperative use of βAR antagonists is controversial. Individual patient's response to beta-blocker therapy is an area of intensive research, and apart from pharmacokinetics, pharmacodynamics, and ethnic differences, genetic alterations have become more important in the last 20 years. The most common genetic variants in humans are single nucleotide polymorphisms (SNPs). There are 2 clinically relevant SNPs for the β1AR (Ser49Gly, Arg389Gly), 3 for the β2AR (Arg16Gly, Gln27Glu, Thr164Ile), and 1 for the β3AR (Trp64Arg). Although results are somewhat controversial, generally large datasets have the potential to show a relationship between βAR SNPs and outcomes such as development and progression of heart failure, coronary artery disease, vascular reactivity, hypertension, asthma, obesity, and diabetes. Although βAR SNPs may not directly cause disease, they appear to be risk factors for, and modifiers of, disease and the response to stress and drugs. In the perioperative setting, this has specifically been demonstrated for the Arg389Gly β1AR polymorphism with which patients with the Gly variant had a higher incidence of adverse perioperative events. Knowing that genetic variants play an important role, perioperative medicine will likely change from simple therapeutic intervention to a more personalized way of adrenergic receptor modulation.
Neutron and Gamma Ray Dosimetry in Spent-Fuel Radiation Environments Using Silicon Carbide Semiconductor Radiation Detectors (2001)

Silicon carbide semiconductor radiation detectors are resistant to radiation induced damage and can be operated at elevated and changing temperatures., Silicon carbide radiation detectors have been shown to have linear responses to both neutrons and gamma rays. Furthermore, these responses are separable on the basis of pulse height, making simultaneous monitoring of both neutrons and gamma rays possible. The neutron and gamma ray sensitivities of silicon carbide radiation detectors are well-matched to the radiation environments characteristic of spent nuclear fuel. Measurements have been carried out in mixed gamma/neutron fields in a hot cell and at a reactor facility under conditions chosen to approximate the radiation fields typically encountered in the vicinity of spent nuclear fuel assemblies. The results of these measurements and the application of silicon carbide radiation detectors to spent fuel dosimetry are discussed.
Effectiveness of reactive case detection for malaria elimination in three archetypical transmission settings: a modelling study (2017)

Reactive case detection is recommended only for settings where transmission has recently been reduced rather than all low-transmission settings. This is demonstrated in a modelling framework with strong out-of-sample accuracy across a range of transmission settings while including methodologies for understanding the most resource-effective allocations of health workers. This approach generalizes to providing a platform for planning rational scale-up of health systems based on locally-optimized impact according to simplified stratification.
Policondrite recidivante: estudo retrospectivo de seis casos. (2006)

Relapsing Polycondritis is a rare connective tissue disease of unknown aetiology that is manifested by inflammatory changes in cartilaginous tissues but the immune damage can spread and involve other tissues.Six patients with relapsing poycondritis treated in our service, between 1990 and 2003, were reviewed. The clinical features, age of onset, time from onset to diagnosis, disease associations and treatment were focused.The female-to-male ratio in our series was 2:4, The median age onset of symptoms was 52 years. A diagnosis delay varied from 8 months to 4 years, with a median time of 18 months. All the five patients had auricular and nasal condritis, laringotracheal involvement was detected in four patients, arthralgia and arthritis also in four patients, cardiac involvement was present in two patients, myelodysplastic syndrome in one patient and ocular disease in four patients.This is small sample study that differs from other studies in sex distribution. This disease is more frequent in females and in our sample men were more affected. The clinical manifestations and disease associations were similar to other populations. Calling attention is the best way to diminish time to diagnosis of this rare pathology.
Investigating the Plasma Surface Modification of Polystyrene at Low Ion Power Densities (2004)

A new grid-separated, two-chamber low-pressure plasma reactor [Dhayal, M.; Forder, D.; R. Short, D.; Bradley, J. W. Vacuum 2003, 70, 67]1 has been developed to study the surface modification of polymeric materials under low ion power density bombardment. Through external biasing of the grids, the ion flux Γ and energy E of the bombarding plasma ions at the substrate can be controlled independently (within certain experimental limits). Importantly, this can be achieved without changing the VUV component of the plasma. In the present arrangement, ion power densities (qΓE) in the range 0.7−15.5 W m-2 can be achieved. This allows a low power density regime to be explored, not possible in typical glass barrel RF reactors often used for surface modification of polymeric materials, in which ion power densities are typically 10−160 W m-2. The effect of ion energy and flux on the surface modification of polystyrene (PS) was quantified by the ratio of atomic oxygen to carbon in the post-treated samples exposed to air (measured by X-ray photoelectron spectroscopy, XPS). It was found that, over the whole available range in ion fluxes, (1.7−5 × 1018 m-2 s-1) and energies (1.5−23 eV), the O/C ratios did not change with O/C about 0.1 to 0.12 for plasma exposure times of 90 s. With elimination of the ion species from the processing region of the discharge through grid biasing, the O/C ratios were also found not to change, indication that below a certain threshold of ion power (at least 15.5 W m-2) ions play little role in the surface modification. By replacing the grids with a LiF window (cutoff wavelength λc 104 nm) having a transparency in the VUV region (<200 nm) at least as good as the geometric transmission area of the two grid system we observe again little change in O/C, indicating that the dominant species in production of free radical sites is the VUV, with any excited neutral species and radicals in the plasma playing a minor role.
Tracking the Frenet-Serret frame associated to a highly maneuvering target in 3D (2017)

In this paper we consider the problem of tracking a maneuvering aircraft. The dynamical model used is based on assumptions of nearly constant tangential velocity, curvature, and torsion, of the target trajectory. Using the Frenet-Serret frame, that is, an element of the special orthogonal group SO(3) we cast the tracking problem into a filtering on Lie groups framework. We then use an invariant extended Kalman filter to estimate the various quantities involved. The resulting filter is simple to implement, and gracefully accomodates some realistic target trajectories.
A Receding-Horizon Framework for Co-Optimizing the Velocity and Power-Split of Automated Plug-In Hybrid Electric Vehicles (2021)

Abstract This paper presents a control framework to co-optimize the velocity and power-split operation of a plug-in hybrid vehicle (PHEV) online in the presence of traffic constraints. The principal challenge in its online implementation lies in the conflict between the long control horizon required for global optimality and limits in available computational power. To resolve the conflict between the length of horizon and its computation complexity, we propose a receding-horizon strategy where co-states are used to approximate the future cost, helping to shorten the prediction horizon. In particular, we update the co-state using a nominal trajectory and the temporal-difference (TD) error based on co-state dynamics. Our simulation results demonstrate a 12% fuel economy improvement over the sequential/layered control strategy for a given driving scenario. Moreover, its real-time practicality is evidenced by a computation time per model predictive controller (MPC) step on average of around 80 ms within a 10 s prediction horizon.
Abstract 4713: BET bromodomain inhibition synergizes with PD-1 blockade to facilitate anti-tumor response in Kras-mutant non-small cell lung cancer (2018)

Abstract KRAS mutation is present in about 30% of human lung adenocarcinomas. While recent advances in targeted therapy have shown great promise, KRAS remains undruggable and concurrent alterations in tumor suppressors render KRAS mutant tumors even more resistant to existing therapies. Contributing to the refractoriness of KRAS mutant tumors harboring these co-mutations are immunosuppressive mechanisms such as increased presence of suppressive Tregs in tumors and elevated expression of the inhibitory receptor PD-1 on tumor-infiltrating T cells. BET bromodomain inhibitors demonstrate clinical benefit in hematologic malignancies, and prior reports demonstrate their Treg-disruptive effects in a NSCLC model. Targeting PD-1 inhibitory signals through anti-PD-1 antibody blockade has also shown substantial therapeutic impact in lung cancer although these outcomes are still limited to a minor pool of patients. We therefore hypothesized that the BET bromodomain inhibitor JQ1 would synergize with PD-1 blockade to promote robust anti-tumor response in lung cancer. In the present study, using Kras+/LSL-G12D; Trp53L/L (KP) mouse models of non-small cell lung cancer, we identified cooperative effects among JQ1 and anti-PD-1 that included reduced numbers of tumor-infiltrated Tregs and enhanced activation of tumor-infiltrating T cells, which exhibited a Th1 cytokine profile that favored their demonstrated improved effector function. Furthermore, lung-tumor-bearing mice under this combinatorial treatment regimen showed robust and long-lasting anti-tumor responses compared to either agent alone, culminating in substantial improvement in the survival of treated mice. Thus, combining BET bromodomain inhibition with immune checkpoint blockade offers a promising therapeutic approach for solid malignancies such as lung adenocarcinoma. Citation Format: Dennis O. Adeegbe, Shengwu Liu, Michaela Bowden, Peter S. Hammerman, James E. Bradner, Anil K. Rustgi, Adam J. Bass, Gordon J. Freeman, Huawei Chen, kwok-Kin Wong. BET bromodomain inhibition synergizes with PD-1 blockade to facilitate anti-tumor response in Kras-mutant non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4713.
In-Situ Structural Characterization of Ultra-Thin Epitaxial Metal Films and Multilayers Observed with Grazing Incidence X-Ray Scattering (1994)

The flexibility of physical vapor deposition allows fabrication of near ideal structures which can be used to investigate fundamental aspects of the mechanics of materials. One important phenomena which can be addressed is the deformation which occurs during relaxation of epitaxial strains. We have developed a unique sputter deposition system capable of performing in-situ structural characterization using grazing incidence x-ray scattering (GIXS). This gives us the ability to accurately measure lattice parameters of films in the monolayer thickness regime. Using this capability, we have investigated epitaxial orientation relations and coherency stress relaxation in several epitaxial film systems, including Cu on Fe (001), and Co on Pt (111).
Responses of polymers to laser plasma EUV light beyond ablation threshold and micromachining (2011)

We have investigated responses of PDMS, PMMA and acrylic block copolymers (BCP) to EUV light from laserproduced plasma beyond ablation thresholds and micromachining. We generated wide band EUV light around 100 eV by irradiation of Ta targets with Nd:YAG laser light. In addition, narrow band EUV light at 11 and 13 nm were generated by irradiation of solid Xe and Sn targets, respectively, with pulsed CO<sub>2</sub> laser light. The generated EUV light was condensed onto samples, using an ellipsoidal mirror. The EUV light was incident through windows of contact masks on the samples. We found that through-holes with a diameter of 1 &mu;m can be fabricated in PDMS sheets with thicknesses of 10 &mu;m. PDMS sheets are ablated if they are irradiated with EUV light beyond a threshold power density, while PDMS surfaces were modified by irradiation with the narrow band EUV light at lower power densities. Effective ablation of PMMA sheets can be applied to a LIGA-like process for fabricating micro-structures of metals using the practical apparatus. Furthermore, BCP sheets were ablated to have micro-structures. Thus, we have developed a practical technique for microma chining of PMMA, PDMS and BCP sheets in a micrometer scale.
Botanical inhibitors of SARS-CoV-2 viral entry: a phylogenetic perspective (2023)

Throughout the SARS-CoV-2 pandemic, the use of botanical dietary supplements in the United States has increased, yet their safety and efficacy against COVID-19 remains underexplored. The Quave Natural Product Library is a phylogenetically diverse collection of botanical and fungal natural product extracts including popular supplement ingredients. Evaluation of 1867 extracts and 18 compounds for virus spike protein binding to host cell ACE2 receptors in a SARS-CoV-2 pseudotyped virus system identified 310 extracts derived from 188 species across 76 families (3 fungi, 73 plants) that exhibited ≥ 50% viral entry inhibition activity at 20 µg/mL. Extracts exhibiting mammalian cytotoxicity > 15% and those containing cardiotoxic cardiac glycosides were eliminated. Three extracts were selected for further testing against four pseudotyped variants and infectious SARS-CoV-2 and were then further chemically characterized, revealing the potent (EC<sub>50</sub> < 5 µg/mL) antiviral activity of Solidago altissima L. (Asteraceae) flowers and Pteridium aquilinum (L.) Kuhn (Dennstaedtiaceae) rhizomes.
Impact of ASR Performance on Spoken Grammatical Error Detection (2019)

Computer assisted language learning (CALL) systems aidlearners to monitor their progress by providing scoring andfeedback on language assessment tasks. Free speaking tests al-low assessment of what a learner has said, as well as how theysaid it. For these tasks, Automatic Speech Recognition (ASR)is required to generate transcriptions of a candidate’s responses,the quality of these transcriptions is crucial to provide reliablefeedback in downstream processes. This paper considers theimpact of ASR performance on Grammatical Error Detection(GED) for free speaking tasks, as an example of providing feed-back on a learner’s use of English. The performance of an ad-vanced deep-learning based GED system, initially trained onwritten corpora, is used to evaluate the influence of ASR errors.One consequence of these errors is that grammatical errors canresult from incorrect transcriptions as well as learner errors, thismay yield confusing feedback. To mitigate the effect of theseerrors, and reduce erroneous feedback, ASR confidence scoresare incorporated into the GED system. By additionally adaptingthe written text GED system to the speech domain, using ASRtranscriptions, significant gains in performance can be achieved.Analysis of the GED performance for different grammatical er-ror types and across grade is also presented.
Viscosity of silicate solutions (1993)

High precision viscosity measurements of electrolyte solns. were used to obtain information about interionic interactions. In solns. of Me4N+ (TMA) silicates values for the A and D coeff. in the Jones-Dole equation are significantly higher than for Na and K silicate solns. Ion assocn. between cations and anions in the silicate solns. studied is excluded by EMF measurements. The A and D coeffs. of solns. which contain both alkali metal and TMA silicate were in the range of the values of alkali metal silicate solns. As an explanation for this behavior probably hydrophilic and hydrophobic structured solvent regions are present around resp. the silicate and the TMA which cannot overlap. This causes a repulsion between these ions superimposed on the electrostatic attraction. [on SciFinder (R)]
Simulating Business Processes – A Review of Tools and Techniques (2012)

 Abstract—There is a great need for simulation of dynamic/temporal aspects of business processes. The current standard for modeling business processes is BPMN and in this review, the various techniques and tools that use BPMN for simulation are studied. The review also points to shortcomings in BPMN support for simulation and in the BPM tools claim to support simulation of business processes. We also present a case for general purpose DES tools to widen their scope and create components/plugins to convert BPMN output to DES input. Index Terms—BPM, BPMN; BPD; BPC; simulation; business process; discrete event; operations research; DES; DEVS.
Supplementary Figures 1 - 5 from Multifactorial T-cell Hypofunction That Is Reversible Can Limit the Efficacy of Chimeric Antigen Receptor–Transduced Human T cells in Solid Tumors (2023)

&lt;p&gt;PDF file - 756K, Supplemental Fig 1. EMP and EMMESO mesothelin expression. Supplemental Fig 2. EMMESO flank tumors retain antigen expression in vivo. Supplemental Fig 3. MesoCAR TILs are unable to secrete IL-2 in response to antigen. Supplemental Fig 4. Supplemental IL-2 helps but is not necessary for CAR TIL recovery. Supplemental Fig 5. IFNγ and TNFα secretion by CAR TILs recovers after resting away from tumor.&lt;/p&gt;
Ionizing radiation sensors utilizing optically stimulated luminescence in SnO-doped SrO-B<inf>2</inf>O<inf>3</inf> and ZnO-P<inf>2</inf>O<inf>5</inf> glass (2014)

Optically stimulated luminescence (OSL) phenomenon is based on the presence of electron and/or hole traps and luminescence centers in storage phosphor materials. During exposure to ionizing radiation such as x-ray, γ-ray and β-ray, the traps are occupied with charged carriers such as electrons and holes that are created by irradiation with ionizing radiation. De-trapping of these carriers requires energy. The energy is provided by stimulating of the phosphor materials with visible or infrared light. During a de-trapping transition, free carriers created by the absorption of photons from the stimulating radiation field, recombine with the luminescence centers, whereby visible photons (OSL) are emitted. Since the OSL intensity is in the most cases proportional to absorbed dose of ionizing radiation, the phosphor materials which exhibit the OSL phenomenon adapt to two-dimensional imaging sensor for ionizing radiation. In this paper, we investigated the OSL characteristics of SnO-doped SrO-B <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> O <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> glass and SnO-doped ZnO-P <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> O <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</inf> glass. Consequently, these glasses are useful as photostimulable phosphor materials of passive type sensor for ionizing radiation.
Vectorial Diffusion for Facile Solution‐Processed Self‐Assembly of Insoluble Semiconductors: A Case Study on Metal Phthalocyanines (2014)

Solution processibility is one of the most intriguing properties of organic semiconductors. However, it is difficult to find a suitable solvent and solution process for most semiconductors. For example, metal phthalocyanines (MPcs) are only soluble in non-volatile solvents, which prevent their applications from solution process. For the first time, vectorial diffusion is utilized for solution processing of MPcs. The obtained large F16CuPc and α-phase CuPc crystals and the efficient phase separation of them suggest the vectorial diffusion process is as slow as a self-assembly process, which is helpful to yield large crystals and purify the semiconductors. This method, which only uses common commercial solvents without any complex and expensive instruments and high-temperature operation, provides a facile approach for purification of organic semiconductors and growth of their crystals in large quantities.
Measurement and Analysis of Traffic Exchange Services (2015)

Traffic exchange services enable members to bring traffic to their websites from a diverse pool of IP addresses, in return for visiting sites of other members. We examine the world of traffic exchanges to characterize their makeup, usage, and monetization. We find that the ecosystem includes a range of services, from manual exchanges where participants must solve CAPTCHAs between successive page views, to exchanges that provide tools that automatically surf without requiring any user action. By "milking" a sample of these exchanges, we analyze month-long datasets to examine the nature of URLs that members submit to them. We find a wide prevalence of URLs for services that pay users in return for views to their content, and at least 30% of the requested impressions are for pages that clearly participate in a class of impression fraud called referrer spoofing. We also analyze the size and composition of a sample of these exchange networks by making purchases, finding that the exchanges delivered visits from roughly 200K unique IP~addresses, and that in some exchange networks, the majority of visits came from cloud hosting services.