gebhart/patrepeval huggingface dataset:
Mutation and Phosphorylation Change the Oligomeric Structure of Phospholamban in Lipid Bilayers (1997)

Phospholamban (PLB), a 52-residue protein integral to the cardiac sarcoplasmic reticulum, is a key regulator of the Ca pump. PLB has been shown to form pentamers in the denaturing detergent sodium dodecyl sulfate (SDS), but its oligomeric state in the natural environment of the lipid membrane remains unknown. In order to address this issue, we performed electron paramagnetic resonance (EPR) experiments on two types of lipid-reconstituted, recombinant PLB: wild type (WT PLB) and a mutant substituted with alanine at leucine 37 (L37A PLB), whose propensity to oligomerize in SDS is greatly diminished. The lipid used in reconstitution was dioleoylphosphatidylcholine (DOPC) doped with a phospholipid spin-label that detects protein contact. EPR spectroscopy was used to determine the fraction of the total lipid molecules in contact with PLB. Our results show that, in phospholipid bilayers, WT PLB is oligomeric (effective oligomeric size of 3.52 +/- 0.71), while L37A PLB is monomeric (effective oligomeric size of 1.15 +/- 0.15). Thus, the oligomeric states of these proteins in the lipid membrane are remarkably similar to those in SDS solution. In particular, the point mutation in L37A PLB greatly destabilizes the PLB oligomer. Phosphorylation of PLB by protein kinase A, which has been shown to relieve inhibition of the cardiac Ca pump, changes the lipid-PLB interactions, decreasing the number of lipids restricted by contact with protein. The results are consistent with a phosphorylation-dependent increase of the effective oligomer size of WT PLB from 3.52 to 5.34 and of L37A PLB from 1.15 to 1.91. These phosphorylation effects were abolished in a medium with a high ionic strength. We conclude that the oligomeric states of PLB in lipid membranes are in a dynamic equilibrium that is perturbed by phosphorylation due to reduced electrostatic repulsion among PLB protomers.
Continuous-Time Delta-Sigma Modulators With Time-Interleaved FIR Feedback (2017)

The use of a single-bit quantizer in a wideband CTΔΣM is attractive, as the quantizer can be implemented in a power and area-efficient manner. Unfortunately, 1-bit CTΔΣMs are plagued by a host of difficulties. Clock jitter and quantizer metastability are particularly problematic, and the higher loop filter linearity needed to process the full-scale feedback waveform results in increased power dissipation. The use of a finite impulse response (FIR) feedback DAC is a power efficient way of addressing the challenges above. However, even this technique runs into difficulties at multi-GHz clock rates. This paper introduces the idea of time-interleaved (TI) FIR feedback to enhance the performance of a conventional FIR DAC. A single-bit CTΔΣM that uses a 2× TI-FIR DAC achieves 67.6/68.8/76 dB SNDR/SNR/DR in a 60 MHz bandwidth. Designed in a low leakage 65 nm CMOS process, the modulator operates at 6 GHz and occupies only 0.07 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . Its Walden Figure of Merit is 56.5 fJ/lvl.
Layout verification and optimization based on flexible design rules (2006)

A methodology for layout verification and optimization based on exible design rules is provided. This methodology is based on image parameter determined exible design rules (FDRs), in contrast with restrictive design rules (RDRs), and enables fine-grained optimization of designs in the yield-performance space. Conventional design rules are developed based on experimental data obtained from design, fabrication and measurements of a set of test structures. They are generated at early stage of a process development and used as guidelines for later IC layouts. These design rules (DRs) serve to guarantee a high functional yield of the fabricated design. Since small areas are preferred in integrated circuit designs due to their corresponding high speed and lower cost, most design rules focus on minimum resolvable dimensions.
In vitro and in vivo investigations of the wound healing effect of crude Spirulina extract and C-phycocyanin (2013)

The aim of this study was to evaluate the influence of crude Spirulina extract and C-phycocyanin (C-PC) isolated from crude Spirulina extract on cultured human keratinocyte, using in vitro and in vivo models of wound healing. Spirulina has been used as a nutraceutical and source of potential pharmaceuticals, however it is not known which component of the cyanobacteria is effective for wound healing. In in vitro model, cultured human keratinocyte were used to investigate the effects of crude Spirulina extract (PSE) and C-phycocyanin (C-PC) extracts on processes involved in keratinocyte proliferation, regeneration and migration. Keratinocyte proliferation and regeneration were monitored by the colorimetric (MTT) assay and migration was monitored in relation to the closure of a denuded area scratched in a confluent monolayer. On the other hand, in in vivo model using Sprague-Dawley male rats, effects of PSE and C-PC on tissue regeneration were investigated. Results of in vivo wound healing study were monitored by means of histological examinations. PSE extract showed the best growth stimulation at 33.5 µg/mL dose of treatment, which revealed a cell viability ranging from 100 to 270% after 72 h. Cell viability was also good for C-PC and was measured as high as 213%. Cell viability and proliferation difference between PSE and C-PC were observed not to be significant (p > 0.05) at the range of doses (33.5 to 0.0335 µg/mL) studied. In in vivo efficiency of the PSE and C–PC, it was observed that 1.25% C-PC has a better effect on the 7th day compared to other preparations.
Carrier detection of unbalanced QPSK direct sequence signals (2003)

This paper reports on detecting the presence of direct sequence spread spectrum signals through detection of the 2f and 4f carrier components of the signals produced by nonlinear techniques. The modulation studied is a generic unbalanced quadrature phase-shift-keyed (UQPSK) modulation, i.e. a QPSK signal with unequal power in the two channels. The complete range of channel power ratio is covered, with equal emphasis on the generic unbalanced case and the two limiting cases of BPSK and (balanced) QPSK. Analytic expressions are presented for the detected signal-to-noise ratio of carrier harmonics 2f and 4f as a function of SNR, channel power ratio, and normalized input bandwidth. The interest is in detecting covert direct sequence spread spectrum signals, i.e. those with SNR <0 dB. Measurements confirm every aspect of the theory. The least detectable signal type is balanced QPSK, which is detectable (at 4f) at a threshold SNR ranging from -2 to -13 dB as the detection process gain (chip rate/detection bandwidth) is varied from 40 to 80 dB.
Fine Grained Citation Span for References in Wikipedia (2017)

Verifiability is one of the core editing principles in Wikipedia, editors being encouraged to provide citations for the added content. For a Wikipedia article, determining the citation span of a citation, i.e. what content is covered by a citation, is important as it helps decide for which content citations are still missing.
Simulation on nanoimprint of grating structures (2010)

Nanoimprint lithography (NIL) is an important nanolithography process with low cost, high throughput and high resolution. It creates patterns by mechanical deformation of imprint resist. Fabricating gratings by NIL can manufacture lots of replica in a fast way. Simulation on the NIL process has a vital role on choosing optimized parameters. One finite element analysis software DEFORM was used to analyze different imprint factors. Through simulation optimization, it was found that imprint temperature, pressure and time strongly affected the replication fidelity. The simulation result will guide the NIL experiment.
Nitroxyl (HNO) Release from New Functionalized N‐Hydroxyurea‐Derived Acyl Nitroso‐9,10‐dimethylanthracene Cycloadducts. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Optical amplification and optical filter based signal processing for cost and energy efficient spatial multiplexing (2011)

Spatial division multiplexing has been proposed as an option for further capacity increase of transmission fibers. Application of this concept is attractive only, if cost and energy efficient implementations can be found. In this work, optical amplification and optical filter based signal processing concepts are investigated. Deployment of multi mode fibers as the waveguide type for erbium doped fiber amplifiers potentially offers cost and energy efficiency advantages compared to using multi core fibers in preamplifier as well as booster stages. Additional advantages can be gained from optimization of the amplifier module design. Together with transponder design optimizations, they can increase the attractiveness of inverse spatial multiplexing, which is proposed as an intermediate step. Signal processing based on adaptive passive optical filters offers an alternative approach for the separation of channels at the receiver which have experienced mode coupling along the link. With this optical filter based approach, fiber capacity can potentially be increased faster and more energy efficiently than with solutions relying solely on electronic signal processing.
Sorting cells alters their redox state and cellular metabolome (2018)

A growing appreciation of the metabolic artifacts of cell culture has generated heightened enthusiasm for performing metabolomics on populations of cells purified from tissues and biofluids. Fluorescence activated cell sorting, or FACS, is a widely used experimental approach to purify specific cell types from complex heterogeneous samples. Here we show that FACS introduces oxidative stress and alters the metabolic state of cells. Compared to unsorted controls, astrocytes subjected to FACS prior to metabolomic analysis showed altered ratios of GSSG to GSH, NADPH to NADP<sup>+</sup>, and NAD<sup>+</sup> to NADH. Additionally, a 50% increase in reactive oxygen species was observed in astrocytes subjected to FACS relative to unsorted controls. At a more comprehensive scale, nearly half of the metabolomic features that we profiled by liquid chromatography/mass spectrometry were changed by at least 1.5-fold in intensity due to cell sorting. Some specific metabolites identified to have significantly altered levels as a result of cell sorting included glycogen, nucleosides, amino acids, central carbon metabolites, and acylcarnitines. Although the addition of fetal bovine serum to the cell-sorting buffer decreased oxidative stress and attenuated changes in metabolite concentrations, fetal bovine serum did not preserve the metabolic state of the cells during FACS. We conclude that, irrespective of buffer components and data-normalization strategies we examined, metabolomic results from sorted cells do not accurately reflect physiological conditions prior to sorting.
User-Guided Level Set Segmentation of Anatomical Structures with ITK-SNAP (2005)

Active contour segmentation and its robust implementation using level sets have been studied thoroughly in the medical image analysis literature. Despite the availability of these powerful methods, clinical research still largely relies on manual slice-by-slice outlining for anatomical structure segmentation. To bridge the gap between methodological advances and clinical routine, we developed ITK-SNAP: an open source application intended to make level set segmentation easily accessible to a wide range of users with various levels of mathematical expertise. We briefly describe this new tool and report the results of a validation study in which ITK-SNAP was compared to manual segmentation of the caudate in the context of an ongoing child neuroimaging autism study.
<scp>HER2 RNA</scp> Aptamer‐ and Cell Penetrating Peptide‐Mediated Delivery of Multimeric Antisense Strands of <scp>siRNAs</scp> for Gene Silencing (2016)

In this study, we describe the development of a new siRNA delivery method for enhanced gene silencing, which is based on HER2 RNA aptamer‐ and cell penetrating peptide (CPP)‐mediated intracellular delivery of multimeric antisense strands of siRNAs . By making use of HER2 RNA aptamer or peptide nucleic acid‐linked CPP as delivery moiety for multimeric antisense strands of siRNAs , the multimeric siRNAs were observed to show significant gene silencing effects even without any delivery vehicles, in comparison with the conventional duplexed monomeric siRNAs mixed with lipofectamine. Our observations suggest that the introduction of RNA aptamer or CPP to multimeric siRNA as delivery moiety of siRNA delivery system can allow efficient target gene suppression with slow and steady but persistent intracellular uptake capacity.
Graft copolymerization of<i>N</i>‐isopropylacrylamide on styrene‐butadiene‐styrene block copolymer (2001)

Abstract Graft polymerization of N ‐isopropylacrylamide (NIPAAm) onto styrene‐butadiene‐styrene (SBS) block copolymer using benzoyl peroxide was studied to improve the water absorptivity and thermosensitivity of SBS. The influence of various grafting reaction factors on the conversion of NIPAAm and the grafting percentage of SBS‐ g ‐NIPAAm were also investigated in the study. The experimental results showed that the conversion of SBS‐ g ‐NIPAAm was enhanced as the monomers of NIPAAm were increased. The maximum conversion of SBS‐ g ‐NIPAAm was observed when the molar ratio of NIPAAm to butadiene was 1.25. In addition, increasing the reaction time enhanced the conversion of SBS‐ g ‐NIPAAm; the maximum grafting percentage was obtained with a 4‐h reaction. The optimal concentration of the initiator was 3 × 10 −4 mol/20 mL of toluene, and the grafting reaction occurred at over 65°C. The test results of the hydrophilicity of the grafted membranes showed that the hydrophilicity and thermosensitivity were significantly enhanced by grafting NIPAAm onto SBS. © 2001 John Wiley & Sons, Inc. J Appl Polym Sci 82: 2641–2650, 2001
Phosphoryl Oxime Inhibition of Acetylcholinesterase during Oxime Reactivation Is Prevented by Edrophonium (1999)

Reactivation of organophosphate (OP)-inhibited acetylcholinesterase (AChE) is a key objective in the treatment of OP poisoning. This study with native, wild-type, and mutant recombinant DNA-expressed AChEs, each inhibited by representative OP compounds, establishes a relationship between edrophonium acceleration of oxime-induced reactivation of OP-AChE conjugates and phosphoryl oxime inhibition of the reactivated enzyme that occurs during reactivation by pyridinium oximes LüH6 and TMB4. No such recurring inhibition could be observed with HI-6 as the reactivator due to the extreme lability of the phosphoryl oximes formed by this oxime. Phosphoryl oximes formed during reactivation of the ethoxy methylphosphonyl-AChE conjugate by LüH6 and TMB4 were isolated for the first time and their structures confirmed by (31)P NMR. However, phosphoryl oximes formed during the reactivation of the diethylphosphoryl-AChE conjugate were not sufficiently stable to be detected by (31)P NMR. The purified ethoxy methylphosphonyl oximes formed during the reactivation of ethoxy methylphosphonyl-AChE conjugate with LüH6 and TMB4 are 10- to 22-fold more potent than MEPQ as inhibitors of AChE and stable for several hours at pH 7.2 in HEPES buffer. Reactivation of both ethoxy methylphosphonyl- and diethylphosphoryl-AChE by these two oximes was accelerated in the presence of rabbit serum paraoxonase, suggesting that organophosphorus hydrolase can hydrolyze phosphoryl oxime formed during the reactivation. Our results emphasize that certain oximes, such as LüH6 and TMB4, if used in the treatment of OP pesticide poisoning may cause prolonged inhibition of AChE due to formation of phosphoryl oximes.
Epithelial differentiation in <i>Drosophila</i> (1997)

Our understanding of epithelial development in Drosophila has been greatly improved in recent years. Two key regulators of epithelial polarity, Crumbs and DE-cadherin, have been studied at the genetic and molecular levels and a number of additional genes are being analyzed that contribute to the differentiation of epithelial cell structure. Epithelial architecture has a profound influence on morphogenetic movements, patterning and cell-type determination. The combination of embryological and genetic/molecular tools in Drosophila will help us to elucidate the complex events that determine epithelial cell structure and how they relate to morphogenesis and other developmental processes.
Dislocation propagation in GaN films formed by epitaxial lateral overgrowth (2000)

We have investigated by scanning electron microscopy (SEM) and transmission electron microscopy (TEM) the relationship between surface morphological evolution and dislocation propagation in GaN films formed by epitaxial lateral overgrowth (ELO) in hydride vapour phase epitaxy. The SEM observations revealed that step and terrace structures were formed on (0001) surfaces of the films both in the earlier and the later stages of growth, suggesting the occurrence of step-flow growth during ELO. Bending dislocations with laterally propagated segments were frequently observed in the ELO films and their morphology led to a reduction in threading dislocation density in the film surface regions. Systematic TEM observations were performed to reveal the detailed structure of the bending dislocations. Comparison between the SEM and the TEM results showed that the lateral propagation of the dislocation was closely related to the appearance of the [1101) facets. A mechanism for dislocation propagation is discussed that explains the observed dislocation structure and surface step morphology.
Protein Structure Modeling with MODELLER (2008)

Genome sequencing projects have resulted in a rapid increase in the number of known protein sequences. In contrast, only about one-hundredth of these sequences have been characterized using experimental structure determination methods. Computational protein structure modeling techniques have the potential to bridge this sequence-structure gap. This chapter presents an example that illustrates the use of MODELLER to construct a comparative model for a protein with unknown structure. Automation of similar protocols (correction of protcols) has resulted in models of useful accuracy for domains in more than half of all known protein sequences.
Non-halogenated solvents for environmentally friendly processing of high-performance bulk-heterojunction polymer solar cells (2013)

High-performance bulk-heterojunction (BHJ) polymer solar cells (PSCs) processed from non-halogenated solvents with power conversion efficiency values over 7% are demonstrated for the first time. The effects of these solvents on the morphology, charge mobility, and PSC device performance have been systematically studied. The general applicability of these non-halogenated solvents to diverse polymer/fullerene systems has also been demonstrated.
Benchmarking VQE with the LMG model (2021)

The Variational Quantum Eigensolver (VQE) is a promising algorithm for Noisy Intermediate-Scale Quantum (NISQ) computation. Verification and validation of NISQ algorithms is an important task. We consider the exactly-diagonalizable Lipkin-Meshkov-Glick (LMG) model as a candidate for benchmarking. We can use the Bethe ansatz to construct eigenstates of the trigonometric LMG model using quantum circuits inspired by the LMG's underlying algebraic structure. We construct circuits with depth $O(N)$ and $O(\log_2 N)$ that can prepare any trigonometric LMG eigenstate of $N$ particles. The number of gates required for both circuits is $O(N)$.
Accelerating the Evolution of Evolvable Hardware-based Packet Classifiers (2007)

In modern networks, the requirements towards network equipment rise together with the bandwidth. Customers and Internet service providers ask for more and more services like Voice-over-IP, IP-TV, and data services with a dependable quality. To satisfy these demands, the requirements towards packet classification as key functionality in network equipment, e.g., routers become overwhelming. We developed a packet classifier based on an evolvable hardware hash function and investigated its performance with real world data. The performance did show a reasonable degradation compared to random numbers. The computation time, which is required for evolving one generation in the genetic algorithm, corresponds to the actual fitness. We did find possibilities to maximize the speed of fitness evaluation by taking advantage of the fact, that the whole packet classifier including the fitness evaluation module is a pure hardware implementation based on FPGA technology. We were thus able to increase the performance of the evolvable packet classifier significantly while limiting the additional required hardware resources
Strategies for the Generation of Molecularly Imprinted Polymeric Nitroxide Catalysts (2005)

[reaction: see text] Two strategies for preparing catalytically active molecularly imprinted nitroxide-containing polymers are outlined. Both strategies rely upon the thermal rearrangement chemistry of tertiary amine N-oxides. To this end, several polymers were prepared and the polymeric nitroxides were revealed by oxidation with m-CPBA. All of the resulting polymeric catalysts proved to be competent mediators of the oxidation of alcohols.
Chronic postsurgical pain after nitrous oxide anesthesia (2011)

Nitrous oxide is an antagonist at the N-methyl-D-aspartate receptor and may prevent the development of chronic postsurgical pain. We conducted a follow-up study in the Evaluation of Nitrous Oxide in the Gas Mixture for Anaesthesia (ENIGMA) trial patients to evaluate the preventive analgesic efficacy of nitrous oxide after major surgery. The ENIGMA trial was a randomized controlled trial of nitrous oxide-based or nitrous oxide-free general anesthesia in patients presenting for noncardiac surgery lasting more than 2 hours. Using a structured telephone interview, we contacted all ENIGMA trial patients recruited in Hong Kong (n=640). We recorded the severity of postsurgical pain of at least 3 months' duration that was not due to disease recurrence or a pre-existing pain syndrome, using the modified Brief Pain Inventory. The impact of postsurgical pain on quality of life was also measured. Pain intensity, opioid and other analgesic requirements during the first week of surgery, were retrieved from the trial case report form and medical records. A total of 46 (10.9%) patients reported pain that persisted from the index surgery, and 39 (9.2%) patients had severe pain. In addition, patients with chronic pain rated poorly in all attributes of the quality-of-life measures compared with those who were pain free. In a multivariate analysis, nitrous oxide decreased the risk of chronic postsurgical pain. In addition, severe pain in the first postoperative week, wound complication, and abdominal incision increased the risk of chronic pain. In conclusion, chronic postsurgical pain was common after major surgery in the ENIGMA trial. Intraoperative nitrous oxide administration was associated with a reduced risk of chronic postsurgical pain.