gebhart/patrepeval huggingface dataset:
Capturing protein dynamics by time-resolved spectroscopy: Folding and electron tunneling in cytochromes (2013)

We have resolved the folding kinetics of two c-type cytochromes, one that exhibits twostate&#13;\nfolding and one that has an on-pathway folding intermediate. We resolve&#13;\nmillisecond-timescale folding by coupling time-resolved fluorescence energy transfer&#13;\n(FRET) with a continuous flow mixer. The efficiency of energy transfer between a dansyl&#13;\nlabel, attached to single-cysteine mutants, and the cytochrome heme during the folding&#13;\nprocess provides us with time-dependent distance distributions, which provide information&#13;\nabout the kinetics and mechanism of folding.We are also interested in characterizing the&#13;\npathway dependence of electron tunneling rates between metal sites in proteins. We have&#13;\nconverted a b-type cytochrome to a c-type cytochrome by covalently linking the porphyrin&#13;\nto cysteine residues. We investigate the effects of these changes to the protein structure,&#13;\ni.e., increased rigidity and potential new equatorial tunneling pathways, on the electron&#13;\ntransfer rates, measured via transient absorption, in a series of Ru-modified proteins.
414 Optimal Design of Softening-type Variable Stiffness Structure (2005)

The authors have proposed a concept of force dependent variable stiffness by introducing a certain internal gap in a continuum structure. This concept has been demonstrated to be valid for designing the structure of hardening-type bilinearity. This study discusses the design of continuum structure showing softening-type variable stiffness. Two different mean compliances are considered for a continuum structure at different ranges of external load divided by the stiffness switching level of working load. First, the compliant mechanism design problem is employed to obtain the initial design used for the following variable stiffness design. Second, the topology determination problem is formulated as the minimization of the structural volume under the constraints of prescribed mean compliances below and over the switching load level by using SIMP method. Third, the geometry determination problem is formulated based on the obtained topology, and is solved by the traction method. The effectiveness of the proposed design optimization problem is demonstrated through an example design problem.
Real-time imaging of Huntingtin aggregates diverting target search and gene transcription (2016)

The presumptive altered dynamics of transient molecular interactions in vivo contributing to neurodegenerative diseases have remained elusive. Here, using single-molecule localization microscopy, we show that disease-inducing Huntingtin (mHtt) protein fragments display three distinct dynamic states in living cells - 1) fast diffusion, 2) dynamic clustering and 3) stable aggregation. Large, stable aggregates of mHtt exclude chromatin and form 'sticky' decoy traps that impede target search processes of key regulators involved in neurological disorders. Functional domain mapping based on super-resolution imaging reveals an unexpected role of aromatic amino acids in promoting protein-mHtt aggregate interactions. Genome-wide expression analysis and numerical simulation experiments suggest mHtt aggregates reduce transcription factor target site sampling frequency and impair critical gene expression programs in striatal neurons. Together, our results provide insights into how mHtt dynamically forms aggregates and disrupts the finely-balanced gene control mechanisms in neuronal cells.
The cachexia associated with Trypanosoma cruzi acute infection in mice is attenuated by anti‐TNF‐a, but not by anti‐IL‐6 or anti‐IFN‐7 antibodies (1995)

SUMMARY BALB/c male mice acutely infected with Trypanosoma cruzi underwent a severe weight loss (around 20%, from day 18 to 31 post‐infection), when compared to age‐matched uninfected animals. Though mice regained weight later, when blood parasites were hardly detectable, wasting extended over the chronic phase of infection. The onset and the magnitude of weight loss were related to the mouse susceptibility to infection, since they were respectively earlier and higher in male mice which will die than in surviving ones, in males than in females, and in BALB/c than in B6D2 [(C57B1/6 × DBA/2)F1], a mouse strain more resistant to infection. Fat weight of infected mice (male BALB/c) was reduced by 60 to 80%, whereas lean mass was unaffected and water content rose by 6 to 10% in acute and chronic infection. Haematocrit was also decreased by 15–16% in acute infection. Animals failed to compensate their energetic loss since their food intake remained similar to that of uninfected animals. Injections of neutralizing anti‐TNF‐α monoclonal antibody into infected male mice, during the first two weeks but not later in infection, significantly attenuated the weight loss. Early administration of anti‐IL‐6 or anti‐IFN‐γ MoAbs did not improve the mouse wasting. Taken together, these data show that TNFis a key agent of cachexia occurring in the acute T. cruzi infection in mice.
A New Input-Parallel-Output-Series Three-Phase Hybrid Rectifier for Heavy-Duty Electric Vehicle Chargers (2022)

&lt;p&gt;This paper proposes a solution to the circuit topology of heavy-duty electric vehicle (HDEV) chargers. In light of the original hybrid rectifier, a new unidirectional Input-Parallel-Output-Series (IPOS) three-phase hybrid rectifier is proposed and analyzed. The IPOS topology is advantageous at ultra-high power rating to interface the next-generation HDEV batteries which require a high and wide output voltage range of 800~1500 V with available 600/1200V commercial semiconductors. Moreover, the proposed topology is efficient, cost-effective, and scalable with the grid input current harmonic components in compliance with the IEEE-519 standard. The benefits of the IPOS topology are supported by circuit derivation, control strategy, analytical modelling, simulation, and experimental verification.&lt;/p&gt;
Synthesis of a Room Temperature Stable 12CaO·7Al2O3 Electride from the Melt and Its Application as an Electron Field Emitter (2006)

A room temperature (RT) stable electride was realized by thermally annealing an insulating 12CaO·7Al2O3 (C12A7) single crystal in a calcium metal vapor. Here we report a simple and direct method for synthesizing polycrystalline C12A7 electride (C12A7:e-); the solidification of a “melt” in a reducing atmosphere and the crystallization of a “glass” with an oxygen-deficient composition in a vacuum. The carbon-related anion (C22-) presumably serves as the template for the formation of the C12A7 phase in the solidification process and may be spontaneously released from the lattice during the cooling process, leaving mobile electrons in the lattice. Also the C22- ions accommodated in the glass may play a significant role in the formation of C12A7:e- during the crystallization. The polycrystalline C12A7:e- exhibits an electrical conductivity up to 5 S·cm-1 at 300 K, which corresponds to an electron concentration of ∼3 × 1019 cm-3 and a nearly equal mobility of ∼0.1 cm2·V-1·s-1 to that of the single crystalline C12A7:e-. A large current density of ∼12 μA·cm-2 is obtained in the electron field emission from a flat surface of the polycrystalline C12A7:e- with a work function of ∼0.6 eV for an applied electric field of 2.4 × 105 V·cm-1. These simple synthetic methods make it possible to produce efficiently the electride in large volume, which will facilitate the C12A7:e- research, paving a way for various applications including cold electron emission.
A Unified Approach to Wearable Ballistocardiogram Gating and Wave Localization (2020)

Prior work using the BCG itself or the ECG to gate the BCG beats and localize the waves to compute PTT are not ideally suited to the wearable BCG. Our approach may foster the development of cuff-less BP monitoring technologies based on the wearable BCG.
Carbon Nano-Onions Reinforced Multilayered Thin Film System for Stimuli-Responsive Drug Release (2020)

Herein, poly (<i>N</i>-(4-aminophenyl) methacrylamide))-carbon nano-onions (PAPMA-CNOs = f-CNOs) and anilinated-poly (ether ether ketone) (AN-PEEK) have synthesized, and AN-PEEK/f-CNOs composite thin films were primed via layer-by-layer (LbL) self-assembly for stimuli-responsive drug release. The obtained thin films exhibited pH-responsive drug release in a controlled manner; pH 4.5 = 99.2% and pH 6.5 = 59.3% of doxorubicin (DOX) release was observed over 15 days. Supramolecular π-π stacking interactions between f-CNOs and DOX played a critical role in controlling drug release from thin films. Cell viability was studied with human osteoblast cells and augmented viability was perceived. Moreover, the thin films presented 891.4 ± 8.2 MPa of the tensile strength (σult), 43.2 ± 1.1 GPa of Young's modulus (E), and 164.5 ± 1.7 Jg<sup>-1</sup> of toughness (K). Quantitative scrutiny revealed that the well-ordered aligned nanofibers provide critical interphase, and this could be responsible for augmented tensile properties. Nonetheless, a pH-responsive and mechanically robust biocompatible thin-film system may show potential applications in the biomedical field.
From Ziplock Snakes to Velcro™ Surfaces (1995)

The use of energy minimizing deformable models in various applications has become very popular. The issue of initializing such models, however, has not received much attention although the model’s performance depends critically on its initial state. We aim at obtaining good convergence and segmentation properties from a minimum of a priori information.We present a new approach to segmentation of 2- and 3-Dimensional shapes that initializes and then optimizes a deformable model given only the data and a very small number of 2-D or 3-D seed points respectively. This is a valuable capability for medical, robotic and cartographic applications where such seed points can be naturally supplied. In effect, the 2-D “snake” and the 3-D surface model are clamped onto the object boundary in manner reminiscent of a ziplock or velcro being closed.We develop the method’s mathematic framework and show results using 2-D cartographic data. Preliminary results in 3-D using volumetric medical data are shown as well.
Intermolecular electronic coupling in organic molecular thin films measured by temperature modulation spectroscopy (2010)

Temperature modulation spectroscopy is used to obtain the temperature dependences of oscillator strength, exciton transition energy, and linewidth for a copper phthalocyanine thin film. With increasing temperature, the oscillator strength exhibits a pronounced decrease for charge transfer (CT) excitons, making this technique suitable for differentiating exciton types. From the measured magnitude and temperature dependence of the CT oscillator strength, we obtain estimates for the intermolecular electronic coupling and its exponential decay coefficient.
Fixed gap source model for MoM analysis of linear antennas using sinusoidal reaction matching (2002)

The method of moment (MoM) using sinusoidal reaction matching has been used extensively in analyzing the thin wire antennas, because of its high accuracy and stability. In this article, the fixed gap source model is applied to the MoM analysis using sinusoidal reaction matching. The elements of the voltage vector corresponding to the feed are derived. This source model is applied to both the thin wire approximation (reduced kernel approximation) and the full kernel formulation. The results of the analysis are compared with the results of the conventional methods and measurement to show the accuracy of the proposed method.
Detection rate and outcome of colonic serrated epithelial changes in patients with ulcerative colitis or Crohn's colitis (2014)

Serrated epithelial changes and sessile serrated polyps are uncommonly detected by colonoscopy in chronic ulcerative colitis and Crohn's disease patients. Histology with changes of serrated epithelium may be associated with risk of subsequent colorectal neoplasia, however further studies are needed to explore this relationship.
Abstract 43: Detection of bladder cancer-associated gene methylation using next-gen bisulfite sequencing. (2013)

Abstract DNA methylation profiling of bladder cancer specific gene promoters has been shown to be a sensitive and specific diagnostic tool for early- and late-stage bladder cancer. We have recently shown that a urine-based assay that combines DNA and protein biomarkers can accurately triage patients undergoing evaluation for bladder cancer. As part of this assay, hypermethylation of Twist1 and Nid2 is performed by conventional methylation-specific PCR (cMSP). To increase throughput and lower cost, we have now developed an approach to determine the methylation at single-base resolution of CpG sites using next generation bisulfite sequencing. In addition to Twist1 and Nid2, methylation of the Vimentin promoter, which has been shown to be associated with epithelial to mesenchymal transition (EMT) in bladder cancer, was also evaluated using this technique. To determine the sensitivity of this approach, amplification was performed on control bisulfite converted genomic DNA that was either enzymatically methylated or chemically unmethylated at CpG sites using non-methylation specific PCR. Twist1, Nid2 and Vimentin PCR products were subsequently used as template for emulsion PCR and sequenced using the Ion Torrent PGM. Methylation status was determined by aligning sequencing reads to unmethylated reference sequences. In this assay, 0.4% methylated DNA could be reliably detected in 10 ng of bisulfite converted DNA, more than doubling the sensitivity of the current assay as well as potentially generating a single-base resolution mapping of additional CpG sites not yet quantified for Twist1, Nid2 and Vimentin. The clinical performance of the Next-Gen bisulfite sequencing assays for Twist1, Nid2 and Vimentin is currently being tested using urine samples from patients with bladder cancer as well as from age matched individuals who present with hematuria but who are found to be cancer-free. The technique we have developed could be used to detect other hypermethylated genes in a variety of bodily fluids where percent methylation may be much lower than in tumor tissue samples. Citation Format: Andrew R. Dunn, Shuqiang Li, Cecilia A. Fernandez, Anthony P. Shuber. Detection of bladder cancer-associated gene methylation using next-gen bisulfite sequencing. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 43. doi:10.1158/1538-7445.AM2013-43
Consistency Analysis of Data-Usage Purposes in Mobile Apps (2021)

While privacy laws and regulations require apps and services to disclose the purposes of their data collection to the users (i.e., why do they collect my data?), the data usage in an app's actual behavior does not always comply with the purposes stated in its privacy policy. Automated techniques have been proposed to analyze apps' privacy policies and their execution behavior, but they often overlooked the purposes of the apps' data collection, use and sharing. To mitigate this oversight, we propose PurPliance, an automated system that detects the inconsistencies between the data-usage purposes stated in a natural language privacy policy and those of the actual execution behavior of an Android app. PurPliance analyzes the predicate-argument structure of policy sentences and classifies the extracted purpose clauses into a taxonomy of data purposes. Purposes of actual data usage are inferred from network data traffic. We propose a formal model to represent and verify the data usage purposes in the extracted privacy statements and data flows to detect policy contradictions in a privacy policy and flow-to-policy inconsistencies between network data flows and privacy statements. Our evaluation results of end-to-end contradiction detection have shown PurPliance to improve detection precision from 19% to 95% and recall from 10% to 50% compared to a state-of-the-art method. Our analysis of 23.1k Android apps has also shown PurPliance to detect contradictions in 18.14% of privacy policies and flow-to-policy inconsistencies in 69.66% of apps, indicating the prevalence of inconsistencies of data practices in mobile apps.
Impaired Host Immunity Contributes to Helicobacter pylori Eradication Failure (2002)

These results support the hypothesis that impaired mucosal immunity, particularly involving the secretion of IL-4, may contribute to H. pylori eradication failure. Measurement of whole blood secretion of IL-4 may predict which patients are more likely to fail standard antibiotic therapy.
Homological product codes (2014)

Quantum codes with low-weight stabilizers known as LDPC codes have been actively studied recently due to their potential applications in fault-tolerant quantum computing. However, all families of quantum LDPC codes known to this date suffer from a poor distance scaling limited by the square-root of the code length. This is in a sharp contrast with the classical case where good families of LDPC codes are known that combine constant encoding rate and linear distance. Here we propose the first family of good quantum codes with low-weight stabilizers. The new codes have a constant encoding rate, linear distance, and stabilizers acting on at most O(√n) qubits, where n is the code length. For comparison, all previously known families of good quantum codes have stabilizers of linear weight. Our proof combines two techniques: randomized constructions of good quantum codes and the homological product operation from algebraic topology. We conjecture that similar methods can produce good stabilizer codes with stabilizer weight O(nα) for any α > 0.
Nanometer-scale vibrational dynamics in biological membranes (2009)

We report on dynamic properties of supported phospholipid membranes, using a spectroscopy technique based on terahertz surface guided waves. The transmitted spectra clearly show not only signal decrease of about 10% due to water absorption, but also transmission dips caused by the vibrational motions of membrane molecules.
Population Balance Model of Lithium Ion Batteries (2016)

We develop a physical-statistical model of particle-based battery electrodes in Li ion batteries. Graphite particles and metal oxide crystallites are the active components in the battery electrodes. During charging/discharging cycles, electrodes experience reversible changes and they go through irreversible structural transformations. Our hierarchical approach employs a particle population balance model based on Fokker-Planck theory. It relates structure-transforming processes at the particle level to macroscopic changes in physicochemical properties and performance. At the particle level, the model accounts for particle activation or deactivation during charging or discharging. Moreover, at the negative electrode, it incorporates formation and growth of the solid electrolyte interphase (SEI), as well as the formation of cracks in the SEI and growth of the SEI area. At the positive electrode, it accounts for the kinetics of crystallite dissolution and isolation. These processes determine changes in the statistical particle density distribution function. So far, we have incorporated an SEI growth model into the population balance model. Our initial results show that the SEI thickness increases from 30 nm to 80 nm after 500 cycles. In a future step, we will include formation of cracks in the SEI and crack-initiated growth of the SEI surface and we will link these changes to the battery performance parameters e.g. capacity fade and power fade.
Time-gated detection of protein-protein interactions with transcriptional readout (2017)

Abstract Transcriptional assays such as yeast two hybrid, split ubiquitin, and Tango that convert transient protein-protein interactions (PPIs) in cells into stable expression of transgenes are powerful tools for PPI discovery, high-throughput screens, and analysis of large cell populations. However, these assays frequently suffer from high background and they lose all information about PPI dynamics. To address these limitations, we developed a light-gated transcriptional assay for PPI detection called PPI-FLARE (PPI-Fast Light- and Activity-Regulated Expression). PPI-FLARE requires both a PPI to deliver TEV protease proximal to its cleavage peptide, and externally-applied blue light to uncage the cleavage peptide, in order to release a membrane-tethered transcription factor (TF) for translocation to the nucleus. We used PPI-FLARE to detect the ligand-induced association of 12 different PPIs in living mammalian cells, with a temporal resolution of 5 minutes and a ±ligand signal ratio up to 37. By systematically shifting the light irradiation window, we could reconstruct PPI time-courses, distinguishing between GPCRs that engage in transient versus sustained interactions with the cytosolic effector arrestin. When combined with FACS, PPI-FLARE enabled &gt;100-fold enrichment of cells experiencing a specific GPCR-arrestin PPI during a short 10-minute light window over cells missing that PPI during the same time window. Due to its high specificity, sensitivity, and generality, PPI-FLARE should be a broadly useful tool for PPI analysis and discovery.
CVD Growth of 3C‐SiC on 4H/6H Mesas (2006)

Abstract This article describes growth and characterization of the highest quality reproducible 3C‐SiC heteroepitaxial films ever reported. By properly nucleating 3C‐SiC growth on top of perfectly on‐axis (0001) 4H‐SiC mesa surfaces completely free of atomic scale steps and extended defects, growth of 3C‐SiC mesa heterofilms completely free of extended crystal defects can be achieved. In contrast, nucleation and growth of 3C‐SiC mesa heterofilms on top of 4H‐SiC mesas with atomic‐scale steps always results in numerous observable dislocations threading through the 3C‐SiC epilayer. High‐resolution X‐ray diffraction (HRXRD) and high resolution cross‐sectional transmission electron microscopy (HRXTEM) measurements indicate non‐trivial, in‐plane, lattice mismatch between the 3C and 4H layers. This mismatch is somewhat relieved in the step‐free mesa case via misfit dislocations confined to the 3C/4H interfacial region without dislocations threading into the overlying 3C‐SiC layer. These results indicate that the presence or absence of steps at the 3C/4H heteroepitaxial interface critically impacts the quality, defect structure, and relaxation mechanisms of single‐crystal heteroepitaxial 3C‐SiC films.
Erratum: “Magnetoresistance due to domain walls in an epitaxial microfabricated Fe wire” [Appl. Phys. Lett. 73, 1298 (1998)] (1998)

First Page
Clock construction in fully asynchronous parallel systems and PRAM simulation (1992)

The authors discuss the question of simulating synchronous computations on asynchronous systems. They consider an asynchronous system with very weak, or altogether lacking any, atomicity assumptions. The first contribution of this paper is a novel clock for asynchronous systems. The clock is a basic tool for synchronization in the asynchronous environment. It is a very robust construction and can operate in a system with no atomicity assumptions, and in the presence of a dynamic scheduler. The behavior of the clock is obtained with overwhelming probability (1-2/sup - alpha n/, alpha >0). The authors show how to harness this clock to drive a PRAM simulation on an asynchronous system. The resulting simulation scheme is more efficient than existing ones, while actually relaxing the assumptions on the underlying asynchronous system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>