gebhart/patrepeval huggingface dataset:
Probing the Catalytic Triad of an Archaeal RNA Splicing Endonuclease (2008)

Among the four known mechanisms of intron removal, three are reputedly catalyzed by RNA molecules. In the fourth mechanism, a protein endonuclease removes introns from nuclear tRNA and all archaeal RNAs. Three strictly conserved residues of the splicing endonuclease, a histidine, a lysine, and a tyrosine, were predicted to catalyze the intron cleavage reaction in a manner similar to that of the catalytic triad of ribonuclease A. Single-turnover kinetic parameters were obtained for the wild-type enzyme and two triad mutants. Mutation of histidine to alanine produced an at least approximately 28-fold reduction; mutation of tyrosine to phenylalanine produced an at least approximately 7-fold reduction in activity, while a histidine and tyrosine double mutation abolished cleavage. The single mutation of lysine to glutamic acid abolished RNA cleavage activity in the absence of a divalent metal but maintained a substantial level of activity in the presence of specific divalent metals. These data support important functional roles already proposed for the catalytic triad and suggest an intriguing hypothesis in which the splicing endonuclease is an intermediate in the transition from the RNA to the RNP world.
Secondary school students' illusion of linearity: the role of direct versus indirect perimeter and area measures (2003)

sponsorship: Afdeling Didactiek.
Easy Variational Inference for Categorical Models via an Independent Binary Approximation (2022)

We pursue tractable Bayesian analysis of generalized linear models (GLMs) for categorical data. Thus far, GLMs are difficult to scale to more than a few dozen categories due to non-conjugacy or strong posterior dependencies when using conjugate auxiliary variable methods. We define a new class of GLMs for categorical data called categorical-from-binary (CB) models. Each CB model has a likelihood that is bounded by the product of binary likelihoods, suggesting a natural posterior approximation. This approximation makes inference straightforward and fast; using well-known auxiliary variables for probit or logistic regression, the product of binary models admits conjugate closed-form variational inference that is embarrassingly parallel across categories and invariant to category ordering. Moreover, an independent binary model simultaneously approximates multiple CB models. Bayesian model averaging over these can improve the quality of the approximation for any given dataset. We show that our approach scales to thousands of categories, outperforming posterior estimation competitors like Automatic Differentiation Variational Inference (ADVI) and No U-Turn Sampling (NUTS) in the time required to achieve fixed prediction quality.
Improving Transferability of Adversarial Patches on Face Recognition with Generative Models (2021)

Face recognition is greatly improved by deep convolutional neural networks (CNNs). Recently, these face recognition models have been used for identity authentication in security sensitive applications. However, deep CNNs are vulnerable to adversarial patches, which are physically realizable and stealthy, raising new security concerns on the real-world applications of these models. In this paper, we evaluate the robustness of face recognition models using adversarial patches based on transferability, where the attacker has limited accessibility to the target models. First, we extend the existing transfer-based attack techniques to generate transferable adversarial patches. However, we observe that the transferability is sensitive to initialization and degrades when the perturbation magnitude is large, indicating the overfitting to the substitute models. Second, we propose to regularize the adversarial patches on the low dimensional data manifold. The manifold is represented by generative models pre-trained on legitimate human face images. Using face-like features as adversarial perturbations through optimization on the manifold, we show that the gaps between the responses of substitute models and the target models dramatically decrease, exhibiting a better transferability. Extensive digital world experiments are conducted to demonstrate the superiority of the proposed method in the black-box setting. We apply the proposed method in the physical world as well.
Serum angiotensin-1 converting enzyme activity processes a human immunodeficiency virus 1 gp160 peptide for presentation by major histocompatibility complex class I molecules. (1992)

T cell stimulation by the human immunodeficiency virus 1 gp160-derived peptide p18 presented by H-2Dd class I major histocompatibility complex molecules in a cell-free system was found to require proteolytic cleavage. This extracellular processing was mediated by peptidases present in fetal calf serum. In vitro processing of p18 resulted in a distinct reverse phase high performance liquid chromatography profile, from which a biologically active product was isolated and sequenced. This peptide processing can be specifically blocked by the angiotensin-1 converting enzyme (ACE) inhibitor captopril, and can occur by exposing p18 to purified ACE. The ability of naturally occurring extracellular proteases to convert inactive peptides to T cell antigens has important implications for understanding cytotoxic T lymphocyte responses in vivo, and for rational peptide vaccine design.
Graft-derived cell-free DNA, a noninvasive early rejection and graft damage marker in liver transplantation: A prospective, observational, multicenter cohort study (2017)

In this study, determination of GcfDNA in plasma by ddPCR allowed for earlier and more sensitive discrimination of acute rejection in LTx patients as compared with conventional LFTs. Potential blood microchimerism was quantitatively low and had no significant influence on GcfDNA value. Further research, which should ideally include protocol biopsies, will be needed to establish the practical value of GcfDNA measurements in the management of LTx patients.
Critical state models for flux-pinning-induced magnetostriction in type-II superconductors (1994)

Models and calculated results are presented for the flux-pinning-induced magnetostriction in type-II superconductors. Three models are considered for the critical state; the original Bean model, the Kim model, and the exponential model in which the critical current density is assumed to depend exponentially on the flux density. The analytic expressions of the length change under the magnetic field are derived for specimens having infinite slab geometry and under the assumption that the reversible part of the total magnetization is negligibly small. The results are used for computer simulations and the hysteresis loops are calculated over a wide range of the relevant parameters. Since the pinning-induced magnetostriction reveals the pinning force directly, the hysteresis loops for each model have different features which are discussed in detail. It is also shown that the pinning force of the sample can be directly inferred from the width of the magnetostriction hysteresis loop. Finally, the experimental results on high-temperature superconductors are discussed in comparison with the calculated results.
PCB pad design for board to board SMP connector (2014)

The design of printed circuit board (PCB) pad for SMP connector is presented. A detailed design and parameterization study are performed using HFSS, a commercial finite element tool. The PCB pad for the vertical SMP connector and surface mounted SMP connector are optimized. According to the simulation result, the return loss and insertion loss for SMP-to-microstrip transitions are better than 26 dB and 0.12 dB respectively from DC to 6 GHz, and the return loss and insertion loss for SMP-to-coplanar waveguide (CPW) transitions are better than 10 dB and 0.7 dB respectively up to 26.5 GHz.
Efficient Energy Transfer to Achieve Narrow Bandwidth Red Emission from Eu3+-Grafting Conjugated Polymers (2002)

A convenient approach to novel Eu3+-grafting conjugated polymers to achieve sharp red emission for polymeric light emitting diodes (PLEDs) has been developed in this contribution. The structure of polymer 1 is verified by FT-IR, 1H, 13C NMR and elemental analysis. The results indicate that efficient intramolecular Föster energy transfer depends on the overlap between the fluorescent spectrum of polymer 1 and absorption spectrum of Eu3+ chelates. Eu(DBM)3 is obviously the best one for accepting energy from polymer 1 among three Eu3+ chelates to exhibit the sharp red emission. The investigation also shows that the efficiency of energy transfer relies on the content of Eu3+ in the complexes. The investigations on the photophysical and electrochemical properties also show that the HOMO and LUMO energy levels and the band gap of complexes have no alteration with the attachment of the Eu3+ chelate in comparison with those of polymer 1 due to the Eu3+ chelate at the side chain of the whole molecule. The pure red electroluminescence is achieved from the fabrication of PLEDs using complex 5 as the active layer with the configuration of ITO/PVK/complex 5/Ba/Al.
Towards a discretely actuated steerable cannula (2012)

Several percutaneous needle-based and intravascular procedures require guidance of the diagnostic or therapeutic tool to the target location by maneuvering the needle or catheter to correct for the error in reaching the target location. Hence, in this paper we present our work towards developing a discretely actuated steerable needle/cannula with multiple degrees-of-freedom to `steer' the cannula by discrete actuation along the cannula length. We are interested in using the cannula to introduce both diagnostic and therapeutic tools, which may otherwise be difficult to deliver to the appropriate location. We use two antagonistic SMA wires as actuators to generate the required bending forces at each joint. SMA wires were annealed through a customized training process to an arc shape and mounted in the machined grooves on the outer surface of the cannula to generate local bending upon thermal actuation. We propose to use temperature feedback to control the position of the SMA actuators. To use temperature feedback as the feedback signal for enabling individual joint actuation, we had to fully characterize the SMA actuator. Classical uniaxial testing devices and experimental setup used in characterizing straight annealed SMA wires are not applicable in this work since the SMA wire is annealed in an arbitrary shape. Hence, we also present an experimental setup and a procedure for characterizing an SMA actuator that transforms into an arc shape upon thermal actuation.
Diagnosis and Treatment of Bladder Cancer: How Can We Improve? (2012)

The majority of patients with bladder cancer will be diagnosed following an episode of hematuria. With few exceptions, these patients should be referred for a complete urologic evaluation, including a history and physical examination, flexible cystoscopy, imaging of the upper urinary tract, and optional urine cytology. Those found to have a bladder tumor should undergo transurethral resection for the combined purposes of initial staging and treatment. Delays in diagnosing invasive bladder cancer are associated with adverse outcomes. In this review, we cover the diagnosis and management of bladder cancer. In addition, we discuss ways to improve outcomes through increased public awareness, improvements in tumor detection, accurate staging, and regimented patient surveillance.
In Vitro and In Vivo Antistaphylococcal Activity of Human Stratum Corneum Lipids (1988)

Despite the assumption that sebum-derived fatty acids are responsible for cutaneous antimicrobial defense, no studies have assessed the contribution of epidermis-derived lipids. Herein, we tested the antistaphylococcal effects of human stratum corneum lipids, enriched in endogenous, keratinocyte-derived species obtained by lipid extraction and thin-layer chromatography, for antimicrobial activity in both in vitro and in vivo systems. Whereas the most potent species in vitro were the free fatty acids, polar lipids and glycosphingolipids also demonstrated antistaphylococcal activity in vitro, while other neutral lipids displayed virtually none, results that were confirmed with authentic standards in vitro. In a pilot study on delipidized forearm test sites in human volunteers, naturally occurring free fatty acids, polar lipids, and glycosphingolipids exhibited significantly more antistaphylococcal activity than other stratum corneum lipids or vehicle controls. Finally, biopsy specimens of incubated skin sites demonstrated penetration of staphylococci through lipid-enriched intercellular domains. These results provide the first evidence that endogenous, epidermis-derived skin lipids may contribute to cutaneous antimicrobial resistance.
A New Physical Method To Crosslink The Gelatin Microspheres. (2000)

New Physical Method To Crosslink The Gelatin Microspheres.
ChemInform Abstract: Mechanistic Studies of Phosphorus‐Oxygen Bond Cleavages in Group 7 Dinuclear Complexes of 2‐Pyridyl Dimethylphosphinite. (1986)

Abstract The dinuclear chelates (I) rearrange in benzene a! 80°C with P‐Obond cleavage to provide the corresponding derivatives (II) containing bridging PMez and 2‐pyridyloxo.
Magnetoelastic Effects Associated with Elastic Surface Wave Propagation in Epitaxial Garnet Films (1976)

Surface wave delay lines have been fabricated on epitaxial garnet films, using a ZnO coating and interdigital transducers for elastic wave excitation. Amplitude and phase delay variations of the delayed signal have been measured as a function of an in‐plane magnetic field, at frequencies of 210 MHz and 335 MHz. For pure YIG films, the strongest effects are observed when the films are not magnetically saturated, exhibiting stripe domain patterns. The observed absorptions are explained by the gyromagnetic resonances driven by the effective field associated with the elastic strains. This effective field was determined from the relevant terms of the magnetoelastic energy; the stripe domain resonances were computed only for a (1, 0, 0) oriented film. An “easy‐plane” film of GdGa doped YIG was also used and good agreement was found between gyromagnetic resonances and acoustic absorptions. Also the motion of stripe domains induced by an elastic wave has been observed. The drift velocity has been measured as a function of incident power. A discussion of this new effect is given.
Occurrence of Fusarium species and mycotoxins in Swiss oats—Impact of cropping factors (2017)

Between 2013 and 2015, 325 samples of commercially grown oats were collected in Switzerland along with data on respective cropping factors. The incidence of different Fusarium species was determined using a seed health test and quantitative PCR was used to measure the amount of F. poae and F. langsethiae DNA. Mycotoxins were quantified by LC–MS/MS. Among all Fusarium species, F. poae was found to be dominant whereas T-2/HT-2 toxins were the major mycotoxins. Samples from fields with the previous crop cereal showed the highest concentrations of T-2/HT-2. Higher amounts of nivalenol (NIV) and T-2/HT-2 were detected in samples from fields with reduced tillage compared with samples from ploughed fields. Furthermore, we observed a higher contamination with NIV and T-2/HT-2 in winter sown varieties compared with spring sown varieties. Results from the current study are highly valuable to develop recommendations for optimised cropping systems that reduce the risk of mycotoxin contamination of oat grains.
First‐YearWilkinson Microwave Anisotropy Probe(WMAP) Observations: Foreground Emission (2003)

Full sky maps are made in five microwave frequency bands to separate the temperature anisotropy of the CMB from foreground emission. We define masks that excise regions of high foreground emission. The effectiveness of template fits to remove foreground emission from the WMAP data is examined. These efforts result in a CMB map with minimal contamination and a demonstration that the WMAP CMB power spectrum is insensitive to residual foreground emission. We construct a model of the Galactic emission components. We find that the Milky Way resembles other normal spiral galaxies between 408 MHz and 23 GHz, with a synchrotron spectral index that is flattest (beta ~ -2.5) near star-forming regions, especially in the plane, and steepest (beta ~ -3) in the halo. The significant synchrotron index steepening out of the plane suggests a diffusion process in which the halo electrons are trapped in the Galactic potential long enough to suffer synchrotron and inverse Compton energy losses and hence a spectral steepening. The synchrotron index is steeper in the WMAP bands than in lower frequency radio surveys, with a spectral break near 20 GHz to beta < -3. The modeled thermal dust spectral index is also steep in the WMAP bands, with beta ~ 2.2. Microwave and H alpha measurements of the ionized gas agree. Spinning dust emission is limited to < ~5% of the Ka-band foreground emission. A catalog of 208 point sources is presented. Derived source counts suggest a contribution to the anisotropy power from unresolved sources of (15.0 +- 1.4) 10^{-3} microK^2 sr at Q-band and negligible levels at V-band and W-band.
Representations of Blacks and Blackness in the Renaissance (2012)

In Playing in the Dark, Toni Morrison argues that figurations of blackness have a central role in the work of twentieth-century white writers.1 The present essay asks whether, and how, this perception might be applied to the study of Renaissance culture. The inquiry proceeds in three steps. The first is to assess the question of historical methodology. What follows is a survey of images of blacks in visual art of the Renaissance period, which provides a context for the last step, the examination of Shakespeare's comedies as a specific test
Modeling the effect of bubble plumes on high frequency acoustic propagation in shallow water (2013)

In this paper we model the effect of bubbles on high frequency acoustic propagation in shallow water under strong winds. Underwater bubble clouds provide locally significant modifications of the sound speed field. The modified sound speed field contributes to a major transmission loss to sound propagation and scattering of the signals. We adopt the bubble field model developed by Norton, et al., generate range dependent discrete bubble plumes and compute the sound speed profile of each bubble plume. We expand our previous work on modeling the effect of rough sea surface and bubble plumes, to include both β- and γ-plumes in the model. We particularly compare cases where the random distribution of β- and γ-plumes are generated differently. With a bubble perturbed sound speed field, we model the communication channel using a rough surface parabolic equation model to generate a complex pressure field at a selected set of ranges and depths. These pressure fields form the basic frequency response of the channel. Our results show that under strong winds, bubbles contribute to large transmission loss and cannot be neglected. The dominant contribution to attenuation is due to β plumes rather than γ plumes. However γ plumes cannot be ignored because their existence affects the spacing between β plumes. And the spacing between β plumes is a significant factor, which results in less attenuation compared to closely spaced β plumes.
A Rapid Cell Expansion Process for Production of Engineered Autologous CAR-T Cell Therapies (2016)

The treatment of B-cell malignancies by adoptive cell transfer (ACT) of anti-CD19 chimeric antigen receptor T cells (CD19 CAR-T) has proven to be a highly successful therapeutic modality in several clinical trials.<sup>1-6</sup> The anti-CD19 CAR-T cell production method used to support initial trials relied on numerous manual, open process steps, human serum, and 10 days of cell culture to achieve a clinical dose.<sup>7</sup> This approach limited the ability to support large multicenter clinical trials, as well as scale up for commercial cell production. Therefore, studies were completed to streamline and optimize the original National Cancer Institute production process by removing human serum from the process in order to minimize the risk of viral contamination, moving process steps from an open system to functionally closed system operations in order to minimize the risk of microbial contamination, and standardizing additional process steps in order to maximize process consistency. This study reports a procedure for generating CD19 CAR-T cells in 6 days, using a functionally closed manufacturing process and defined, serum-free medium. This method is able to produce CD19 CAR-T cells that are phenotypically and functionally indistinguishable from cells produced for clinical trials by the previously described production process.
Comparison of Particulate Matter and Number Emissions from a Floating and a Fixed Caliper Brake System of the Same Lining Formulation (2020)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;The particulate emissions of two brake systems were characterized in a dilution tunnel optimized for PM10 measurements. The larger of them employed a fixed caliper (FXC) and the smaller one a floating caliper (FLC). Both used ECE brake pads of the same lining formulation. Measured properties included gravimetric PM2.5 and PM10, Particle Number (PN) concentrations of both untreated and thermally treated (according to exhaust PN regulation) particles using Condensation Particle Counters (CPCs) having 23 and 10 nm cut-off sizes, and an Optical Particle Sizer (OPS). The brakes were tested over a section (trip-10) novel test cycle developed from the database of the Worldwide harmonized Light-Duty vehicles Test Procedure (WLTP). A series of trip-10 tests were performed starting from unconditioned pads, to characterize the evolution of emissions until their stabilization. Selected tests were also performed over a short version of the Los Angeles City Cycle. PM2.5 emissions of burnished pads averaged at 2.6 mg/km/brake and 4.1 mg/km/brake for the FLC and the FXC system, respectively. A large fraction of the airborne PM was found to be larger than 2.5 μm, leading to 2.7 times higher PM10 emissions. Therefore, proper PM10 measurements will require careful considerations on the operating tunnel parameters to minimize particle losses. The FXC system yielded ~50% higher PM and two times higher PN emissions despite the 22% lower disc temperatures measured with an embedded thermocouple. No indication of volatile particle formation was observed, with more than 80% of total PN having an optical diameter larger than 300 nm. The results illustrate the challenges associated with the use of disc temperature measurements for the control of a representative braking procedure.&lt;/div&gt;&lt;/div&gt;