gebhart/patrepeval huggingface dataset:
Abstract 259: Novel peptide directed targeting of EWS-FLI1 impairs tumor cell growth (2011)

Abstract Introduction: Patients with Ewing's Sarcoma require improved therapy. EWS-FLI1 fusion protein provides a unique targeting opportunity. In the quest for protein partners, we identified a novel peptide sequence that binds to EWS-FLI1 using phage display. We hypothesize that by identifying peptides, and their cognate proteins, we can modulate the function of EWS-FLI1 to improve therapies for ESFT patients. Methods: Secreted peptide-alkaline phosphatase conjugates were used in ELISA for resolving binding regions. Cytotoxicity experiments were analyzed with MTT or WST reduction. Cell cycle analysis were performed using flow cytometry. Results: A phage display experiment to identify EWS-FLI1 peptides resulted in 96 phage clones that demonstrated binding to EWS-FLI1 by ELISA. Those 96 phage clones resulted in sequences that yielded twenty-seven unique peptides. Peptide A1 is one of 27 unique peptides that was commercially synthesized fused to penetratin (16aa) to facilitate intracellular transport. The cytotoxicity of A1 peptide was evaluated in TC32 and TC71 (EWS-FLI1, type I), A4573 (EWS-FLI1, type III), JN-DSRCT (desmoplastic small round blue cell tumor containing EWS-WT1), and SKNAS (a neuroblastoma cell line lacking EWS-FLI1 rearrangement). The IC50 level for A1 is between 5 -15 μM in cell lines bearing EWS fusion proteins. However, it is more than 50 μM in cells without the rearrangement. A1-alkaline phosphatase (A1-AP) conjugates were prepared with alanine substitutions throughout the peptide. Wild-type non-conjugated A1 competed away the interaction between the EWS-FLI1 and A1-AP, confirming its ability to bind to EWS-FLI1. Mutations in A1 demonstrated that the lysine residues are critical for binding to EWS-FLI1. The minimal interacting amino acids were validated using shortened and mutated versions of A1 in both ELISA and cell growth assays, including soft agar. A1 peptide blocked cell cycle progression of synchronized ESFT cells and caused accumulation at S phase. A1 peptide also inhibited EWS-FLI1 dependent transcription. Discussion: The A1 peptide directly binds to the EWS-FLI1 oncoprotein and leads to cell death in cells with either the EWS-FLI1 or EWS-WT1 fusion proteins. While A1 was discovered based on binding to EWS-FLI1; toxicity in JN-DSRCT studies suggest that the A1 peptide may have potency to EWS bearing fusion proteins. These findings present a novel method of targeting EWS rearranged oncoproteins and could lead to novel therapies Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 259. doi:10.1158/1538-7445.AM2011-259
Cationic Tungsten Imido Alkylidene N-Heterocyclic Carbene Complexes That Contain Bulky Ligands (2021)

Neutral and cationic tungsten imido alkylidene complexes of the general formulas W(NtBu)(CHR1)(OR2)Cl(NHC), W(N-2,6-bis(2,4,6-tri-iPr-C6H4)phenyl)(CHR1)Cl2(NHC), [W(NtBu)(CHR1)(OR2)(NHC)][B(ArF)4] and [W(N-2,6-bis(2,4,6-tri-iPr-C6H4)phenyl)(CHR1)Cl(NHC)][B(ArF)4] (R1 = CMe3, CMe2Ph; R2 = sterically demanding alkoxide; B(ArF)4 = tetrakis(3,5-(CF3)2-C6H3)borate; NHC = N-heterocyclic carbene) were prepared. Two electronically different NHCs, namely 1,3-dimethylimidazol-2-ylidene (IMe) and 1,3-dimethyl-4,5-dichloroimidazol-2-ylidene (IMeCl), as well as a variety of terphenolates and a chiral biphenolate were employed. Z-selective homometathesis (HM) of unfunctionalized olefins was achieved with a selectivity of up to 90% and decent turnover numbers (TON) of up to 480 in the HM of 1-dodecene. Additionally, the reactivity of the cationic tungsten tert-butylimido complexes in the reaction with vinyltrimethylsilane and ethylene was investigated, which yielded the corresponding silyl-alkylidene complex and, for the first time, a fully characterized cationic tungsten(IV) NHC ethylene complex.
Rapid Evolution of a Fragment-like Molecule to Pan-Metallo-Beta-Lactamase Inhibitors: Initial Leads toward Clinical Candidates (2022)

With the emergence and rapid spreading of NDM-1 and existence of clinically relevant VIM-1 and IMP-1, discovery of pan inhibitors targeting metallo-beta-lactamases (MBLs) became critical in our battle against bacterial infection. Concurrent with our fragment and high-throughput screenings, we performed a knowledge-based search of known metallo-beta-lactamase inhibitors (MBLIs) to identify starting points for early engagement of medicinal chemistry. A class of compounds exemplified by <b>11</b>, discovered earlier as <i>B. fragilis</i> metallo-beta-lactamase inhibitors, was selected for <i>in silico</i> virtual screening. From these efforts, compound <b>12</b> was identified with activity against NDM-1 only. Initial exploration on metal binding design followed by structure-guided optimization led to the discovery of a series of compounds represented by <b>23</b> with a pan MBL inhibition profile. In <i>in vivo</i> studies, compound <b>23</b> in combination with imipenem (IPM) robustly lowered the bacterial burden in a murine infection model and became the lead for the invention of MBLI clinical candidates.
A novel method for surface modification to promote cell attachment to hydrophobic substrates (1998)

The ability to study and regulate cell behavior at a biomaterial interface requires strict control over material surface chemistry. Perhaps the greatest challenge to researchers working in this area is preventing the fouling of a given surface due to uncontrolled protein adsorption. This work describes a method for coupling peptides to hydrophobic materials for the purpose of simultaneously preventing nonspecific protein adsorption and controlling cell adhesion. A hexapeptide containing the ubiquitous RGD cell-adhesion motif was coupled to polystyrene (PS) via a polyethylene oxide (PEO) tether in the form of a modified PEO/PPO/PEO triblock copolymer. Triblocks were adsorbed onto PS at a density of 3.3 +/- (5.14 x 10(-4)) mg/m2 (1.4 x 10(5) +/- 2.12 x 10(1) molecules/microm2), which was determined by isotope 125I labeling. The peptide, GRGDSY, was activated at the N terminus with N-Succinimidyl 3-(2-pyridyldithio) propionate and coupled to immobilized triblocks where the terminal hydroxyls had been converted to sulfhydryl groups. Surface peptide density was measured by amino acid analysis and found to be 1.4 x 10(4) +/- 0.47 x 10(4) molecules/microm2. PS modified with PEO/PPO/PEO copolymers alone was found to be inert to cell adhesion both in the presence of serum proteins and when exposed to activated RGD peptide. In contrast, PS conjugated with RGD via endgroup-activated PEO/PPO/PEO copolymers supported cell adhesion and spreading. The surface coupling scheme reported here should prove valuable for studying cell-ligand interactions under simplified and highly controlled conditions.
A Min-Variance Iterative Method for Fast Smart Dummy Feature Density Assignment in Chemical-Mechanical Polishing (2005)

Dummy feature filling is an efficient approach for reducing wafer-topography variation in chemical-mechanical polishing (CMP), which is the key planarization process in modern VLSI fabrication. In this paper, we present a new min-variance iterative method for fast smart dummy feature density assignment and post-CMP topography variation reduction. This method iteratively selects target areas using an efficient CMP low-pass filter model and a variance-minimizing heuristic, and assigns/removes dummy features accordingly. Because of the efficient usage of the 2D fast Fourier transform (FFT), the computational cost of this new method is close to O(nlog(n)), making it much faster than the existing linear programming method that costs O(n/sup 3/). Numerical experiments show the computational cost of our new method is almost negligible when compared with the LP method and its solution is very close to the optimal solution.
Rational Design of Engineered Cationic Antimicrobial Peptides Consisting Exclusively of Arginine and Tryptophan, and Their Activity against Multidrug-Resistant Pathogens (2013)

The emergence of multidrug-resistant (MDR) pathogens underscores the need for new antimicrobial agents to overcome the resistance mechanisms of these organisms. Cationic antimicrobial peptides (CAPs) provide a potential source of new antimicrobial therapeutics. We previously characterized a lytic base unit (LBU) series of engineered CAPs (eCAPs) of 12 to 48 residues demonstrating maximum antibacterial selectivity at 24 residues. Further, Trp substitution in LBU sequences increased activity against both P. aeruginosa and S. aureus under challenging conditions (e.g., saline, divalent cations, and serum). Based on these findings, we hypothesized that the optimal length and, therefore, the cost for maximum eCAP activity under physiologically relevant conditions could be significantly reduced using only Arg and Trp arranged to form idealized amphipathic helices. Hence, we developed a novel peptide series, composed only of Arg and Trp, in a sequence predicted and verified by circular dichroism to fold into optimized amphipathic helices. The most effective antimicrobial activity was achieved at 12 residues in length (WR12) against a panel of both Gram-negative and Gram-positive clinical isolates, including extensively drug-resistant strains, in saline and broth culture and at various pH values. The results demonstrate that the rational design of CAPs can lead to a significant reduction in the length and the number of amino acids used in peptide design to achieve optimal potency and selectivity against specific pathogens.
Device-to-device proximity discovery for LTE systems (2015)

Device-to-device (D2D) proximity discovery enables spectral reuse via D2D communications as well as a range of innovative proximity services, such as enhanced social networking and location services. To develop a scalable discovery mechanism, signals transmitted by geographically disparate devices should not differ drastically in their received power at each monitoring device. Discovery schemes are proposed to deal with this near-far issue. Analysis and simulation results are provided to characterize the performance of discovery schemes.
Quasi-Walsh PN sequences and their applications in robust CDMA communication systems (2002)

Systems of quasi-Walsh functions are developed which simultaneously enable multiple access as well as secure communication and jamming resistance. In this system, a pseudo random sequence of diagonal isometries post multiplies a Hadamard matrix, thereby generating the orthogonal direct spreading sequences. Minimal mutual interference is a consequence of the resulting orthogonal spreading. Utilizing bit-by-bit distinct orthogonal codes gives the added benefit of high signal hiding capability and jamming resistance. An encoding scheme is presented which uniquely determines the actual quasi-Walsh system in use.
Progress Towards Arrays of Microcalorimeter X-Ray Detectors (2001)

Abstract The high performance of single-pixel microcalorimeter EDS (μ,cal EDS) has been shown to be very useful for a variety of microanalysis cases. The primary advantage of jxcal EDS over conventional EDS is the factor of 25 improvement in energy resolution (∽3 eV in real-time). This level of energy resolution is particularly important for applications such as nanoscale contaminant analysis where it is necessary to resolve peak overlaps at low x-ray energies. Because μcal EDS offers practical solutions to many microanalysis problems, several companies are proceeding with commercialization of single-pixel μal EDS technology. Two drawbacks limiting the application of uxal EDS are its low count rate (∽500 s−1) and small area (∽0.04 mm for a bare single pixel, ∽5 mm2 with a polycapillary optic). We are developing a 32x32 pixel array with a total area of 40 mm2 and with a total count rate between 105 s−1 and 106 s−1.
Exact Interior Reconstruction from Truncated Limited‐Angle Projection Data (2008)

Using filtered backprojection (FBP) and an analytic continuation approach, we prove that exact interior reconstruction is possible and unique from truncated limited-angle projection data, if we assume a prior knowledge on a subregion or subvolume within an object to be reconstructed. Our results show that (i) the interior region-of-interest (ROI) problem and interior volume-of-interest (VOI) problem can be exactly reconstructed from a limited-angle scan of the ROI/VOI and a 180 degree PI-scan of the subregion or subvolume and (ii) the whole object function can be exactly reconstructed from nontruncated projections from a limited-angle scan. These results improve the classical theory of Hamaker et al. (1980).
Change Bursts as Defect Predictors (2010)

In software development, every change induces a risk. What happens if code changes again and again in some period of time? In an empirical study on Windows Vista, we found that the features of such change bursts have the highest predictive power for defect-prone components. With precision and recall values well above 90%, change bursts significantly improve upon earlier predictors such as complexity metrics, code churn, or organizational structure. As they only rely on version history and a controlled change process, change bursts are straight-forward to detect and deploy.
Using perceptual distance to improve the selection of dirty paper trellis codes for watermarking (2005)

Previous watermarking research based on dirty paper trellis coding [G.L. Miller et al., 2002] proposed a method for informed coding by which the best code from the set of codewords representing the message was selected based on maximizing the linear correlation between the codewords and the original cover Work. However, this does not guarantee that the linear correlation is maximized in the watermarked cover Work. This is because the chosen codeword must be attenuated due to fidelity constraints. Since there is no clear relationship between linear correlation and fidelity, a codeword that is chosen to maximize linear correlation may be very difficult to embed if it is perceptually very different from the underlying cover Work. We show that this is in fact the case and suggest a solution to this problem that involves a cost function that is a linear combination of perceptual distance and linear correlation. Experimental results demonstrate 50% and 25% improvements in bit and message error rates respectively.
Extreme visualisation of query optimizer search space (2009)

This demonstration showcases a system for visualizing and analyzing search spaces generated by the SQL Anywhere optimizer during the optimization process of a SQL statement. SQL Anywhere dynamically optimizes each statement every time it is executed. The decisions made by the optimizer during the optimization process are both cost-based and heuristics adapted to the current state of the server and the database instance. Many performance issues can be understood and resolved by analyzing the search space generated when optimizing a certain request. In our experience, there are two main classes of performance issues related to the decisions made by a query optimizer:(1) a request is very slow due to a suboptimal access plan; and (2) a request has a different, less optimal access plan than a previous execution. We have enhanced SQL Anywhere to log, in a very compact format, its search space during the optimization process when tracing mode is on. These search space logs can be used for performance analysis in the absence of the database instances or of extra information about the SQL Anywhere server state at the time the logs were generated. This demonstration introduces the SearchSpaceAnalyzer System, a research prototype used to analyze the search spaces of the SQL Anywhere optimizer. The system visualizes and analyzes (1) a single search space and (2) the differences between two search spaces generated for the same query by two different optimization processes. The SearchSpaceAnalyze System can be used for the analysis of any query optimizer search spaces as long as the logged data is recorded using the syntax understood by the system.
Milk-protein-based edible films and coatings (1994)

The article reviews important protein characteristics, then relates these to the properties of milk-protein-based edible films and coatings
Mining generalised disjunctive association rules (2001)

This paper introduces generalised disjunctive association rules such as "People who buy bread also buy butter jam", and "People who buy either raincoats or umbrellas also buy flashlights". A generalised disjunctive association rule allows the disjunction of conjuncts, "People who buy jackets also buy bow ties or neckties and tiepins". Such rules capture contextual inter-relationships among items.Given a context (antecedent), there may be a large number of generalised disjunctive association rules that satisfy the minsupp and minconf constraints. It is computationally expensive to find all such rules. We present algorithm thrifty traverse which borrows concepts such as subsumption from propositional logic to mine a subset of such rules in a computationally feasible way. We experimented with our algorithm on US census data as well as transaction data from a grocery superstore to demonstrate its computational feasibility, utility and scalability.
Chemical Structures of Hetero-oligosaccharides Produced by<i>Arthrobacter</i>sp. K-1<i>β</i>-Fructofuranosidase (1994)

The structures of hetero-oligosaccharides obtained by the action of transglycosylation of Arthrobacter sp. K-1 beta-fructofuranosidase, using sucrose as the fructosyl donor, and several mono- and di-sacchrides as the acceptors were investigated. The main transfer products to most reducing mono- and di-sacchrides were non-reducing oligosaccharides with a fructosyl residue linked to a hemiacetal hydroxyl group. In the presence of L-sorbose, the enzyme produced 2-O-beta-D-fructofuranosyl-alpha-L-sorbopyranoside as the major product. With D-galactose or L-arabinose, the enzyme produced not only non-reducing oligosaccharides, but also reducing oligosaccharides, which were identified as 3-O-beta-D-fructofuranosyl-D-galactopyranose and 4-O-beta-D-fructofuranosyl-L-arabinopyranose, respectively. When a non-reducing sugar such as methyl alpha-glucoside was used as an acceptor, the product formed had a fructosyl residue linked at the C6 hydroxyl group.
Multifunctional and compact spectrometers based on cylindrical beam volume holograms (2007)

We propose a new class of slitless spectrometers using cylindrical beam volume holograms. These holograms disperse an input beam in one direction in an output plane while they do not affect the beam in the perpendicular direction. We show that the spectral mapping of the input beam can be obtained in one direction and the beam can be independently modified in the perpendicular direction. Using this unique property, we demonstrate a spectral wrapping technique to considerably increase the operation spectral range of the slitless spectrometers, without sacrificing their resolution.
Assessment of the influence of losses on the performance of the electromagnetic time reversal fault location method (2017)

Electromagnetic time reversal (EMTR) has been shown to be an efficient method for locating faults in AC and DC power grids. In the available literature, the back-propagation medium has been considered to have identical losses as the direct-time medium. However, the telegrapher's equations describing the travelling wave propagation are time-reversal invariant if and only if inverted losses are considered in the back propagation phase. This paper presents an analysis of the impact of losses on the performance of the EMTR-based fault location method for power networks. In this respect, three back-propagation models are proposed, analyzed and compared. It is shown that a lossy back-propagation model, for which the wave equations are not rigorously time-reversal invariant, results in accurate fault locations. Finally, an EMTR fault location system based on the lossy back-propagation model and a fast electromagnetic transient simulation platform is developed and its performances validated.
Etching depth dependence of the effective refractive index in two-dimensional photonic-crystal-patterned vertical-cavity surface-emitting laser structures (2003)

A vertical-cavity surface-emitting laser (VCSEL) having a two-dimensional (2-D) photonic crystal structure on its surface has been investigated for single-lateral-mode operation. We evaluated the effective index change of a VCSEL cavity introduced by a 2-D pattern. Our experimental results showed good agreement with a theoretical model in which the influence of a finite etching depth was taken into consideration. The etching-depth dependence parameter γ, which can be explained by the optical power distribution inside a VCSEL structure, will be helpful for controlling the lateral mode of VCSEL devices.
Determination of cations and anions by capillary electrophoresis combined with suppressed conductivity detection (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of cations and anions by capillary electrophoresis combined with suppressed conductivity detectionNebojsa. Avdalovic, Christopher A. Pohl, Roy D. Rocklin, and John R. StillianCite this: Anal. Chem. 1993, 65, 10, 1470–1475Publication Date (Print):May 15, 1993Publication History Published online1 May 2002Published inissue 15 May 1993https://pubs.acs.org/doi/10.1021/ac00058a027https://doi.org/10.1021/ac00058a027research-articleACS PublicationsRequest reuse permissionsArticle Views543Altmetric-Citations106LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Shape-Aware Organ Segmentation by Predicting Signed Distance Maps (2019)

In this work, we propose to resolve the issue existing in current deep learning based organ segmentation systems that they often produce results that do not capture the overall shape of the target organ and often lack smoothness. Since there is a rigorous mapping between the Signed Distance Map (SDM) calculated from object boundary contours and the binary segmentation map, we exploit the feasibility of learning the SDM directly from medical scans. By converting the segmentation task into predicting an SDM, we show that our proposed method retains superior segmentation performance and has better smoothness and continuity in shape. To leverage the complementary information in traditional segmentation training, we introduce an approximated Heaviside function to train the model by predicting SDMs and segmentation maps simultaneously. We validate our proposed models by conducting extensive experiments on a hippocampus segmentation dataset and the public MICCAI 2015 Head and Neck Auto Segmentation Challenge dataset with multiple organs. While our carefully designed backbone 3D segmentation network improves the Dice coefficient by more than 5% compared to current state-of-the-arts, the proposed model with SDM learning produces smoother segmentation results with smaller Hausdorff distance and average surface distance, thus proving the effectiveness of our method.