gebhart/patrepeval huggingface dataset:
Amino Acid Residues That Define Both the Isoprenoid and CAAX Preferences of the Saccharomyces cerevisiae Protein Farnesyltransferase (1998)

Studies of the yeast protein farnesyltransferase (FTase) have shown that the enzyme preferentially farnesylates proteins ending in CAAX (C = cysteine, A = aliphatic residue, X = cysteine, serine, methionine, alanine) and to a lesser degree CAAL. Furthermore, like the type I protein geranylgeranyltransferase (GGTase-I), FTase can also geranylgeranylate methionine- and leucine-ending substrates both in vitro and in vivo. Substrate overlap of FTase and GGTase I has not been determined to be biologically significant. In this study, specific residues that influence the substrate preferences of FTase have been identified using site-directed mutagenesis. Three of the mutations altered the substrate preferences of the wild type enzyme significantly. The ram1p-74D FTase farnesylated only Ras-CIIS and not Ras-CII(M,L), and it geranylgeranylated all three substrates as well or better than wild type. The ram1p-206DDLF FTase farnesylated Ras-CII(S,M,L) at wild type levels but could no longer geranylgeranylate the Ras-CII(M,L) substrates. The ram1p-351FSKN FTase farnesylated Ras-CIIS and Ras-CIIM but not Ras-CIIL. The ram1p-351FSKN FTase was not capable of geranylgeranylating the Ras-CII(M,L) substrates, giving this mutant the attributes of the dogmatic FTase that only farnesylates non-leucine-ending CAAX substrates and does not geranylgeranylate any substrate. These results suggest that the isoprenoid and protein substrate specificities of FTase are interrelated. The availability of a mutant FTase that lacked substrate overlap with the protein GGTase-I made possible an analysis of the role of substrate overlap in normal cellular processes of yeast, such as mating and growth at elevated temperatures. Our findings suggest that neither farnesylation of leucine-ending CAAX substrates nor geranylgeranylation by the FTase is necessary for these cellular processes.
Decoupling control based on H/sub ∞/-mixed sensitivity problem (2002)

In this paper, decoupling control with state feedback and output feedback based on the H/sub /spl infin//-mixed sensitivity problem is presented. Decoupling performance in state feedback control is obtained by choosing the weighting functions properly. This is shown by clarifying the structure of the state feedback gain and the solution of the Riccati equation. Next, decoupling performance in output feedback control is shown by using the fact that the closed loop transfer matrices in state feedback and output feedback designed for the same weighting functions are same. Furthermore, an example of a ship motion control system is shown to demonstrate decoupling performance of the proposed design.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Effect of thermal fluctuations in topologicalp-wave superconductors (2013)

We study the effect of thermal fluctuations on the topological stability of chiral $p$-wave superconductors. We consider two models of superconductors: spinless and spinful with a focus on topological properties and Majorana zero-energy modes. We show that proliferation of vortex-antivortex pairs above the Kosterlitz-Thouless temperature ${T}_{\mathrm{KT}}$ drives the transition from a thermal quantum hall insulator to a thermal metal/insulator, and dramatically modifies the ground-state degeneracy splitting. Therefore, to utilize two-dimensional chiral $p$-wave superconductors for topological quantum computing, the temperature should be much smaller than ${T}_{\mathrm{KT}}$. Within the spinful chiral $p$-wave model, we also investigate the interplay between half-quantum vortices carrying Majorana zero-energy modes and full-quantum vortices having trivial topological charge, and discuss topological properties of half-quantum vortices in the background of proliferating full-quantum vortices.
Design of a Wide Output Voltage Dual Active Bridge Converter as Power Electronics Building Block for the Fast Charging of Electric Vehicles (2021)

This paper verifies the potential of utilizing the Dual Active Bridge (DAB) converter as a 10 kW Power Electronics Building Block (PEBB) for the charging of Electric Vehicles (EVs) where a wide output voltage range is required. Following the tendency of the new EV charging standards from CCS and CHAdeMO, the commonly employed isolated DC-DC converter should be able to supply the rated power for different vehicles which employ battery technologies which could range from 300 V up to 1000 V. Rectangular (or phase-shift), triangular and trapezoidal modulation strategies are investigated, of which the last two techniques are used for designing the PEBB. Suitable SiC-based semiconductors are chosen, the passive components are designed and the power losses are derived for the whole operating range. It is found that a high power efficiency can be achieved using the designed system.
Phosphorylation‐Dependent Regulation of Apical Membrane Chloride Channels in Normal and Cystic Fibrosis Airway Epitheliuma (1989)

The observations described herein allow us to make several inferences about PKC and regulation of normal and CF Cl- channels. FIGURE 5 shows a model that summarizes these observations. In this model, for the sake of clarity, we refer to the channel as a single entity, but note that it may consist of multiple subunits and associated proteins. FIGURE 5A shows the channel in an inactivated state following excision from the cell. The channel can be activated by strong membrane depolarization, via an unknown mechanism, or by phosphorylation with PKA or PKC at a low [Ca2+] We speculate that PKA and PKC may phosphorylate and activate the channel at the same site, or region of the channel, because phosphorylation-dependent activation by both is defective in CF. This result suggests that the CF defect might lie in a defective phosphorylation site on the channel, or associated protein, or in the mechanism that converts phosphorylation into a change in channel conformation, such as activation. Activated channels can be inactivated by PKC at a high [Ca2+]. At high [Ca2+], PKC maintains the channel in an inactivated state and it inactivates channels that have been activated by PKC at low [Ca2+], by depolarization, or by PKA. Both activation and inactivation appear to result from phosphorylation; neither can be explained by down-regulation of the channel. There are several possible ways to explain the two opposite effects of PKC on the Cl- channel: different responses may be due to an effect of Ca2+ on the channel, on PKC, or on the interaction between the two.(ABSTRACT TRUNCATED AT 250 WORDS)
Multi-pulse, plane-wave acoustic contrast agent imaging with a 16 MHz linear array (2019)

Plane-wave imaging allows high-frame rates, and with high-frequency (HF) ultrasound, fine-spatial and temporal resolution. HF, plane-wave multi-pulse (MP) imaging methods of acoustic contrast agents (UCAs) are still an unexplored area for small-animal and small-parts imaging. The MP methods of pulse inversion (PI, + 1 and -1 pair) and amplitude modulation (AM, + 1 and + ½ pair) were compared to standard plane-wave compound imaging for a flow of the UCA Definity in a linear-channel, wall-less flow phantom using a 16-MHz linear array. Transmissions were made at -10, 1 and 10 deg. Definity was diluted in water to 2000:1 and a flow was established through the phantom. Beamformed data were processed to find RMS values in a flow and background region in order to calculate contrast-to-noise ratio (CTR). The MP methods resulted in an 8 dB improvement in CTR relative to standard plane-wave imaging. The absolute intensity of the flow and background regions dropped for PI and AM relative to standard plane-wave imaging. At all acoustic drive pressures, PI and AM CTRs were statistically different than with standard imaging (p &amp;lt; 10-4). PI and AM CTRs were statistically different above 1 MPa (p &amp;lt; 10-4) where PI had a 3 dB higher CTR.
Nanoparticles Based on PLGA:Poloxamer Blends for the Delivery of Proangiogenic Growth Factors (2010)

New blood vessel formation is a critical requirement for treating many vascular and ischemia related diseases, as well as for many tissue engineering applications. Angiogenesis and vasculogenesis, in fact, represent crucial processes for the functional regeneration of complex tissues through tissue engineering strategies. Several growth factors (GFs) and signaling molecules involved in blood vessels formation have been identified, but their application to the clinical setting is still strongly limited by their extremely short half-life in the body. To overcome these limitations, we have developed a new injectable controlled release device based on polymeric nanoparticles for the delivery of two natural proangiogenic GFs: platelet derived growth factor (PDGF-BB) and fibroblast growth factor (FGF-2). The nanoparticle system was prepared by a modified solvent diffusion technique, encapsulating the GF both in presence and in the absence of two stabilizing agents: bovine serum albumin (BSA) and heparin sodium salt (Hp). The developed nanocarriers were characterized for morphology, size, encapsulation efficiency, release kinetics in vitro and GF activity in cell cultures. The results have indicated that the coencapsulation of stabilizing agents can preserve the GF active structure and, in addition, increase their encapsulation efficiency into nanoparticles. Through this optimization process, we were able to raise the encapsulation efficiency of FGF-2 to 63%, and that of PDGF-BB to 87%. These PLGA:poloxamer blend nanoparticles loaded with GFs were able to release PDGF-BB and FGF-2 in a sustained fashion for more than a month. This work also confirms other positive features of PLGA:poloxamer nanoparticles. Namely, they are able to maintain their stability in simulated biological medium, and they are also nontoxic to cell culture models. Incubation of nanoparticles loaded with FGF-2 or PDGF-BB with endothelial cell culture models has confirmed that GFs are released in a bioactive form. Altogether, these results underline the interest of PLGA:poloxamer nanoparticles for the controlled delivery of GFs and substantiate their potential for the treatment of ischemic diseases and for tissue engineering applications.
REMIX (2017)

Outlier detection is the identification of points in a dataset that do not conform to the norm. Outlier detection is highly sensitive to the choice of the detection algorithm and the feature subspace used by the algorithm. Extracting domain-relevant insights from outliers needs systematic exploration of these choices since diverse outlier sets could lead to complementary insights. This challenge is especially acute in an interactive setting, where the choices must be explored in a time-constrained manner. In this work, we present REMIX, the first system to address the problem of outlier detection in an interactive setting. REMIX uses a novel mixed integer programming (MIP) formulation for automatically selecting and executing a diverse set of outlier detectors within a time limit. This formulation incorporates multiple aspects such as (i) an upper limit on the total execution time of detectors (ii) diversity in the space of algorithms and features, and (iii) meta-learning for evaluating the cost and utility of detectors. REMIX provides two distinct ways for the analyst to consume its results: (i) a partitioning of the detectors explored by REMIX into perspectives through low-rank non-negative matrix factorization; each perspective can be easily visualized as an intuitive heatmap of experiments versus outliers, and (ii) an ensembled set of outliers which combines outlier scores from all detectors. We demonstrate the benefits of REMIX through extensive empirical validation on real-world data.
Effect of carbaprostacyclin (PGI2-analogue), prostaglandin E1 and latanoprost (PGF2a-analogue) on collagen gel compaction in vitro and interstitial fluid pressure in vivo (1998)

Effect of carbaprostacyclin (PGI2-analogue), prostaglandin E1 and latanoprost (PGF2a-analogue) on collagen gel compaction in vitro and interstitial fluid pressure in vivo
ChemInform Abstract: Conformationally Constrained Dipeptides: Synthesis of 7,5‐ and 6,5‐ Fused Bicyclic Lactams by Stereoselective Radical Cyclizations. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Synthesis of Dihydro‐1,4‐oxathiins by Action of Chlorine on 1,3‐Oxathiolanes. (1988)

Abstract Treatment of the 1,3‐oxathiolanes (I) with chlorine yields the dihydrooxathiines (II) as the main products.
LONG-TERM ELECTRICAL CAPSULAR STIMULATION IN PATIENTS WITH OBSESSIVE-COMPULSIVE DISORDER (2008)

Nuttin, Bart J. M.D., Ph.D.; Gabriëls, Loes A. M.D., M.Sc.Eng.; Cosyns, Paul R. M.D., Ph.D.; Meyerson, Björn A. M.D., Ph.D.; Andréewitch, Sergej M.D.; Sunaert, Stefan G. M.D.; Maes, Alex F. M.D., Ph.D.; Dupont, Patrick J. Ph.D.; Gybels, Jan M. M.D., Ph.D.; Gielen, Frans Ph.D.; Demeulemeester, Hilde G. Ph.D.
Multi-Tier Cooperative Broadcasting With Hierarchical Modulations (2006)

Publication in the conference proceedings of EUSIPCO, Florence, Italy, 2006
Titanium Coating of the Boston Keratoprosthesis (2016)

Purpose We tested the feasibility of using titanium to enhance adhesion of the Boston Keratoprosthesis (B-KPro), ultimately to decrease the risk of implant-associated complications. Methods Cylindrical rods were made of poly(methyl methacrylate) (PMMA), PMMA coated with titanium dioxide (TiO2) over a layer of polydopamine (PMMATiO2), smooth (Ti) and sandblasted (TiSB) titanium, and titanium treated with oxygen plasma (Tiox and TiSBox). Topography and surface chemistry were analyzed by scanning electron microscopy (SEM), atomic force microscopy (AFM), and X-ray photoelectron spectroscopy (XPS). Adhesion force between rods and porcine corneas was measured ex vivo. Titanium sleeves, smooth and sandblasted, were inserted around the stem of the B-KPro and implanted in rabbits. Tissue adhesion to the stem was assessed and compared to an unmodified B-Kpro after 1 month. Results X-ray photoelectron spectroscopy demonstrated successful deposition of TiO2 on polydopamine-coated PMMA. Oxygen plasma treatment did not change the XPS spectra of titanium rods (Ti and TiSB), although it increased their hydrophilicity. The materials did not show cell toxicity. After 14 days of incubation, PMMATiO2, smooth titanium treated with oxygen plasma (Tiox), and sandblasted titanium rods (TiSB, TiSBox) showed significantly higher adhesion forces than PMMA ex vivo. In vivo, the use of a TiSB sleeve around the stem of the B-KPro induced a significant increase in tissue adhesion compared to a Ti sleeve or bare PMMA. Conclusions Sandblasted titanium sleeves greatly enhanced adherence of the B-KPro to the rabbit cornea. This approach may improve adhesion with the donor cornea in humans as well. Translational relevance This approach may improve adhesion with donor corneas in humans.
SS18-SSX, the Oncogenic Fusion Protein in Synovial Sarcoma, Is a Cellular Context-Dependent Epigenetic Modifier (2015)

The prevalence and specificity of unique fusion oncogenes are high in a number of soft tissue sarcomas (STSs). The close relationship between fusion genes and clinicopathological features suggests that a correlation may exist between the function of fusion proteins and cellular context of the cell-of-origin of each tumor. However, most STSs are origin-unknown tumors and this issue has not yet been investigated in detail. In the present study, we examined the effects of the cellular context on the function of the synovial sarcoma (SS)-specific fusion protein, SS18-SSX, using human pluripotent stem cells (hPSCs) containing the drug-inducible SS18-SSX gene. We selected the neural crest cell (NCC) lineage for the first trial of this system, induced SS18-SSX at various differentiation stages from PSCs to NCC-derived mesenchymal stromal cells (MSCs), and compared its biological effects on each cell type. We found that the expression of FZD10, identified as an SS-specific gene, was induced by SS18-SSX at the PSC and NCC stages, but not at the MSC stage. This stage-specific induction of FZD10 correlated with stage-specific changes in histone marks associated with the FZD10 locus and also with the loss of the BAF47 protein, a member of the SWI/SNF chromatin-remodeling complex. Furthermore, the global gene expression profile of hPSC-derived NCCs was the closest to that of SS cell lines after the induction of SS18-SSX. These results clearly demonstrated that the cellular context is an important factor in the function of SS18-SSX as an epigenetic modifier.
Study of silica-based intrinsically emitting nanoparticles produced by an excimer laser (2019)

We report an experimental study demonstrating the feasibility to produce both pure and Ge-doped silica nanoparticles (size ranging from tens up to hundreds of nanometers) using nanosecond pulsed KrF laser ablation of bulk glass. In particular, pure silica nanoparticles were produced using a laser pulse energy of 400 mJ on pure silica, whereas Ge-doped nanoparticles were obtained using 33 and 165 mJ per pulse on germanosilicate glass. The difference in the required energy is attributed to the Ge doping, which modifies the optical properties of the silica by facilitating energy absorption processes such as multiphoton absorption or by introducing absorbing point defects. Defect generation in bulk pure silica before nanoparticle production starts is also suggested by our results. Regarding the Ge-doped samples, scanning electron microscopy (SEM) and cathodoluminescence (CL) investigations revealed a good correspondence between the morphology of the generated particles and their emission signal due to the germanium lone pair center (GLPC), regardless of the energy per pulse used for their production. This suggests a reasonable homogeneity of the emission features of the samples. Similarly, energy dispersive X-ray spectroscopy (EDX) data showed that the O, Ge and Si signals qualitatively correspond to the particle morphology, suggesting a generally uniform chemical composition of the Ge-doped samples. No significant CL signal could be detected in pure silica nanoparticles, evidencing the positive impact of Ge for the development of intrinsically emitting nanoparticles. Transmission electron microscope (TEM) data suggested that the Ge-doped silica nanoparticles are amorphous. SEM and TEM data evidenced that the produced nanoparticles tend to be slightly more spherical in shape for a higher energy per pulse. Scanning transmission electron microscope (STEM) data have shown that, regardless of size and applied energy per pulse, in each nanoparticle, some inhomogeneity is present in the form of brighter (i.e., more dense) features of a few nanometers.
A neuromorphic system for object detection and classification (2013)

Unattended object detection, recognition and tracking on unmanned reconnaissance platforms in battlefields and urban spaces are topics of emerging importance. In this paper, we present an unattended object recognition system that automatically detects objects of interest in videos and classifies them into various categories (e.g., person, car, truck, etc.). Our system is inspired by recent findings in visual neuroscience on feed-forward object detection and recognition pipeline and mirrors that via two main neuromorphic modules (1) A front-end detection module that combines form and motion based visual attention to search for and detect “integrated” object percepts as is hypothesized to occur in the human visual pathways; (2) A back-end recognition module that processes only the detected object percepts through a neuromorphic object classification algorithm based on multi-scale convolutional neural networks, which can be efficiently implemented in COTS hardware. Our neuromorphic system was evaluated using a variety of urban area video data collected from both stationary and moving platforms. The data are quite challenging as it includes targets at long ranges, occurring under variable conditions of illuminations and occlusion with high clutter. The experimental results of our system showed excellent detection and classification performance. In addition, the proposed bio-inspired approach is good for hardware implementation due to its low complexity and mapping to off-the-shelf conventional hardware.
Comparison between time reversal focusing in absorbing medium and inverse filtering (2002)

To focus ultrasonic waves in inhomogeneous media using a phased array, one has to calculate the optimal set of signals (for monochromatic waves, amplitude and phase (D.R. Jackson and D.R. Dowling, 1991)) to be applied on the transducers of the array. The solution obtained by Time Reversal Processing (TRP) corresponds to the spatial and temporal filter matched to an initial source available in the medium. However, this process doesn't ensure that the field amplitude at other locations is as small as possible. The authors have illustrated this problem previously using the example of focusing through the human skull, which is an absorbing medium. The authors found that in order to obtain good focusing, it is necessary to add to the time reversal process an amplitude compensation that takes into account absorption. Another approach consists in using an entire array of transducers on both sides of the skull. The authors measure and compare the focal quality obtained in the different cases: matched filter, inverse filter and amplitude compensation combined with time reversal.
Vehicle–Vehicle Channel Models for the 5-GHz Band (2008)

In this paper, we describe the results of a channel measurement and modeling campaign for the vehicle-to-vehicle (V2V) channel in the 5-GHz band. We describe measurements and results for delay spread, amplitude statistics, and correlations for multiple V2V environments. We also discuss considerations used in developing statistical channel models for these environments and provide some sample results. Several statistical channel models are presented, and using simulation results, we elucidate tradeoffs between model implementation complexity and fidelity. The channel models presented should be useful for system designers in future V2V communication systems.