gebhart/patrepeval huggingface dataset:
Redox modifications of spinach chloroplast fructose‐1,6‐bisphosphatase (1996)

Complete activation of chloroplast fructose-1, 6-bisphosphatase by dithiothreitol involves the reduction of its four disulfide bonds as revealed by thiol titration and activity measurement. Both before and after reduction, the enzyme is inhibited by the thiol-specific reagent 5,5'-dithiobis(2-nitro-benzoic acid) with complete inactivation upon modifications of the four accessible thiols. However, oxidative modification of the enzyme facillitates the reduction of the four mentioned disulfide bonds as the process of activation by DTT is accelerated.
High-mobility polymer gate dielectric pentacene thin film transistors (2002)

We have fabricated pentacene organic thin film transistors with spin-coated polymer gate dielectric layers, including cross-linked polyvinylphenol and a polyvinylphenol-based copolymer, and obtained devices with excellent electrical characteristics, including carrier mobility as large as 3 cm2/V s, subthreshold swing as low as 1.2 V/decade, and on/off current ratio of 105. For comparison, we have also fabricated pentacene transistors using thermally grown silicon dioxide as the gate dielectric and obtained carrier mobilities as large as 1 cm2/V s and subthreshold swing as low as 0.5 V/decade.
Distributed wide-area traffic management for cloud services (2012)

The performance of interactive cloud services depends heavily on which data centers handle client requests, and which wide-area paths carry traffic. While making these decisions, cloud service providers also need to weigh operational considerations like electricity and bandwidth costs, and balancing server loads across replicas. We argue that selecting data centers and network routes independently, as is common in today's services, can lead to much lower performance or higher costs than a coordinated decision. However, fine-grained joint control of two large distributed systems---e.g., DNS-based replica-mapping and data center multi-homed routing---can be administratively challenging. In this paper, we introduce the design of a system that jointly optimizes replica-mapping and multi-homed routing, while retaining the functional separation that exists between them today. We show how to construct a provably optimal distributed solution implemented through local computations and message exchanges between the mapping and routing systems.
Structures of N‐termini of helices in proteins (1997)

We have surveyed 393 N-termini of alpha-helices and 156 N-termini of 3(10)-helices in 85 high resolution, non-homologous protein crystal structures for N-cap side-chain rotamer preferences, hydrogen bonding patterns, and solvent accessibilities. We find very strong rotamer preferences that are unique to N-cap sites. The following rules are generally observed for N-capping in alpha-helices: Thr and Ser N-cap side chains adopt the gauche - rotamer, hydrogen bond to the N3 NH and have psi restricted to 164 +/- 8 degrees. Asp and Asn N-cap side chains either adopt the gauche - rotamer and hydrogen bond to the N3 NH with psi = 172 +/- 10 degrees, or adopt the trans rotamer and hydrogen bond to both the N2 and N3 NH groups with psi = 1-7 +/- 19 degrees. With all other N-caps, the side chain is found in the gauche + rotamer so that the side chain does not interact unfavorably with the N-terminus by blocking solvation and psi is unrestricted. An i, i + 3 hydrogen bond from N3 NH to the N-cap backbone C = O in more likely to form at the N-terminus when an unfavorable N-cap is present. In the 3(10)-helix Asn and Asp remain favorable N-caps as they can hydrogen bond to the N2 NH while in the trans rotamer; in contrast, Ser and Thr are disfavored as their preferred hydrogen bonding partner (N3 NH) is inaccessible. This suggests that Ser is the optimum choice of N-cap when alpha-helix formation is to be encouraged while 3(10)-helix formation discouraged. The strong energetic and structural preferences found for N-caps, which differ greatly from positions within helix interiors, suggest that N-caps should be treated explicitly in any consideration of helical structure in peptides or proteins.
Stretchable Energy‐Harvesting Tactile Electronic Skin Capable of Differentiating Multiple Mechanical Stimuli Modes (2014)

The first stretchable energy-harvesting electronic-skin device capable of differentiating and generating energy from various mechanical stimuli, such as normal pressure, lateral strain, bending, and vibration, is presented. A pressure sensitivity of 0.7 kPa(-1) is achieved in the pressure region <1 kPa with power generation of tens of μW cm(-2) from a gentle finger touch.
Dedicated bifurcation analysis: basic principles (2011)

Over the last several years significant interest has arisen in bifurcation stenting, in particular stimulated by the European Bifurcation Club. Traditional straight vessel analysis by QCA does not satisfy the requirements for such complex morphologies anymore. To come up with practical solutions, we have developed two models, a Y-shape and a T-shape model, suitable for bifurcation QCA analysis depending on the specific anatomy of the coronary bifurcation. The principles of these models are described in this paper, as well as the results of validation studies carried out on clinical materials. It can be concluded that the accuracy, precision and applicability of these new bifurcation analyses are conform the general guidelines that have been set many years ago for conventional QCA-analyses.
Integrin Signaling (1999)

Cells reside in a protein network, the extracellular matrix (ECM), which they secrete and mold into the intercellular space. The ECM exerts profound control over cells. The effects of the matrix are primarily mediated by integrins, a family of cell surface receptors that attach cells to the matrix and mediate mechanical and chemical signals from it. These signals regulate the activities of cytoplasmic kinases, growth factor receptors, and ion channels and control the organization of the intracellular actin cytoskeleton. Many integrin signals converge on cell cycle regulation, directing cells to live or die, to proliferate, or to exit the cell cycle and differentiate.
Quad‐Mesh Generation and Processing: A Survey (2013)

Abstract Triangle meshes have been nearly ubiquitous in computer graphics, and a large body of data structures and geometry processing algorithms based on them has been developed in the literature. At the same time, quadrilateral meshes, especially semi‐regular ones, have advantages for many applications, and significant progress was made in quadrilateral mesh generation and processing during the last several years. In this survey we discuss the advantages and problems of techniques operating on quadrilateral meshes, including surface analysis and mesh quality, simplification, adaptive refinement, alignment with features, parametrisation and remeshing.
Tyre Models for the Study of In-Plane Dynamics (1994)

SUMMARYA flexible ring model of the tyre is presented in this paper. The natural frequencies and mode shapes of the tyre are obtained from this ring model. The vibration transmission properties of the tyre between the tyre-road contact point and the wheel axle are analysed. Based on the results of this flexible ring model, a simplified tyre model is developed, which is able to describe the zeroth and first order vibration modes of the tyre. Residual stiffnesses are introduced to take into account the contribution of higher order modes on the total deformation of the tyre. A tyre-road interface model based on the well-known brush model is also developed and integrated into the simplified tyre model. The parameters of both models are established for two different tyres. Finally some numerical results are presented.
Adaptive beamforming methods for dynamically steered microphone array systems (2008)

This paper introduces two methods for the integration of a dynamically steered beamforming filter with acoustic echo cancellation (AEC) and adaptive generalized sidelobe canceler (GSC) based beamforming methods. We evaluate the performance of a beamforming system with moving and changing source positions. Individual contributions of adaptive beamforming and steering independent AEC processing methods are evaluated for high level echo cancellation in a typical office environment. The results show that the proposed adaptive beamforming method increases the overall AEC performance even if GSC adaptation would be disturbed by dynamic beam steering.
Two-dimensional transmit/receive ceramic piezoelectric arrays: Construction and performance (1978)

Two-dimensional (2D) ceramic piezoelectric arrays, in which each cell may both transmit and receive (T/R) ultrasonic information, are described. Their fabrication is based upon integrated circuit and hybrid construction techniques. High-voltage custom DMOS integrated circuits are used to provide the T/R capability. Detailed acoustic and electrical performance results on 16 x 16 prototype arrays operating at 2.4 MHz are presented. These measwements show the arrays to be adequate for many medical imaging and NOT applications and superior in performance to other reported 2D arrays, although not as high performance as commercially available single element transducers because of compromises in construction techniques required to achieve the 2D capability.
On saying “Enough already!” in SQL (1997)

In this paper, we study a simple SQL extension that enables query writers to explicitly limit the cardinality of a query result. We examine its impact on the query optimization and run-time execution components of a relational DBMS, presenting two approaches—a Conservative approach and an Aggressive approach—to exploiting cardinality limits in relational query plans. Results obtained from an empirical study conducted using DB2 demonstrate the benefits of the SQL extension and illustrate the tradeoffs between our two approaches to implementing it.
Peroxisome proliferator‐activated receptor δ agonists inhibit T helper type 1 (Th1) and Th17 responses in experimental allergic encephalomyelitis (2010)

Multiple sclerosis (MS) is a neurological disorder that affects more than a million people world-wide. The aetiology of MS is not known and there is no medical treatment available that can cure MS. Experimental autoimmune encephalomyelitis (EAE) is a T-cell-mediated autoimmune disease model of MS. The pathogenesis of EAE/MS is a complex process involving activation of immune cells, secretion of inflammatory cytokines and destruction of myelin sheath in the central nervous system (CNS). Peroxisome proliferator-activated receptors (PPARs) are nuclear hormone receptor transcription factors that regulate cell growth, differentiation and homeostasis. PPAR agonists have been used in the treatment of obesity, diabetes, cancer and inflammation. We and others have shown that PPARgamma, alpha and delta agonists inhibit CNS inflammation and demyelination in the EAE model of MS. In this study we show that the PPARdelta agonists GW501516 and L165041 ameliorate MOGp35-55-induced EAE in C57BL/6 mice by blocking interferon (IFN)-gamma and interleukin (IL)-17 production by T helper type 1 (Th1) and Th17 cells. The inhibition of EAE by PPARdelta agonists was also associated with a decrease in IL-12 and IL-23 and an increase in IL-4 and IL-10 expression in the CNS and lymphoid organs. These findings indicate that PPARdelta agonists modulate Th1 and Th17 responses in EAE and suggest their use in the treatment of MS and other autoimmune diseases.
Neuroprotection by a novel NMDAR functional glycine site partial agonist, GLYX-13 (2009)

GLYX-13 (threonine-proline-proline-threonine-amide) is an amidated di-pyrrolidine that acts as a functional partial agonist at the glycine site on N-methyl-D-aspartate glutamate receptors (NMDARs). GLYX-13 can both increase NMDAR conductance at NR2B-containing receptors, and reduce conductance of non-NR2B-containing receptors. Here, we report that GLYX-13 potently reduces delayed (24 h) death of CA1 pyramidal neurons produced by bilateral carotid occlusion in Mongolian gerbils, when administered up to 5 h post-ischemia. GLYX-13 also reduced delayed (24 h) neuronal death of CA1, CA3, and dentate gyrus principal neurons elicited by oxygen/glucose deprivation in in-vitro hippocampal organotypic slice cultures, when applied up to 2 h post-oxygen/glucose deprivation. The glycine site full agonist D-serine completely occluded neuroprotection, indicating that GLYX-13 acts by modulating activation of this site.
Prior Infection and Passive Transfer of Neutralizing Antibody Prevent Replication of Severe Acute Respiratory Syndrome Coronavirus in the Respiratory Tract of Mice (2004)

Following intranasal administration, the severe acute respiratory syndrome (SARS) coronavirus replicated to high titers in the respiratory tracts of BALB/c mice. Peak replication was seen in the absence of disease on day 1 or 2, depending on the dose administered, and the virus was cleared within a week. Viral antigen and nucleic acid were detected in bronchiolar epithelial cells during peak viral replication. Mice developed a neutralizing antibody response and were protected from reinfection 28 days following primary infection. Passive transfer of immune serum to naïve mice prevented virus replication in the lower respiratory tract following intranasal challenge. Thus, antibodies, acting alone, can prevent replication of the SARS coronavirus in the lung, a promising observation for the development of vaccines, immunotherapy, and immunoprophylaxis regimens.
A New Method to Measure Cellular Toxicity of Non-Fibrillar and Fibrillar Alzheimer's Aβ Using Yeast (2008)

The 42 amino acid amyloid-beta (Abeta) can exist in multiple physical states including oligomers and fibrils. This study shows that fibril formation is hastened by the biological buffers required to support the growth of mammalian cells, but is prevented if Abeta is maintained in water. Here we describe a method to produce Abeta in oligomeric form and the comparison of stable fibrillar and non-fibrillar forms in cell toxicity studies in water, achieved through the use of yeast. We show that extracellular, non-fibrillar Abeta causes a dose dependent loss of cell viability while fibrillar Abeta has low toxicity.
The function of the milk-clotting enzymes bovine and camel chymosin studied by a fluorescence resonance energy transfer assay (2015)

Enzymatic coagulation of bovine milk can be divided in 2 steps: an enzymatic step, in which the Phe105-Met106 bond of the milk protein bovine κ-casein is cleaved, and an aggregation step. The aspartic peptidases bovine and camel chymosin (EC 3.4.23.4) are typically used to catalyze the enzymatic step. The most commonly used method to study chymosin activity is the relative milk-clotting activity test that measures the end point of the enzymatic and aggregation step. This method showed that camel chymosin has a 2-fold higher milk-clotting activity toward bovine milk than bovine chymosin. To enable a study of the enzymatic step independent of the aggregation step, a fluorescence resonance energy transfer assay has been developed using a peptide substrate derived from the 98-108 sequence of bovine κ-casein. This assay and Michaelis-Menten kinetics were employed to determine the enzymatic activity of camel and bovine chymosin under milk clotting-like conditions (pH 6.65, ionic strength 80 mM). The results obtained show that the catalytic efficiency of camel chymosin is 3-fold higher than bovine chymosin. The substrate affinity and catalytic activity of bovine and camel chymosin increase at lower pH (6.00 and 5.50). The glycosylation of bovine and camel chymosin did not affect binding of the fluorescence resonance energy transfer substrate, but doubly glycosylated camel chymosin seems to have slightly higher catalytic efficiency. In the characterization of the enzymes, the developed assay is easier and faster to use than the traditionally used relative milk-clotting activity test method.
Thermal–electrical co-optimisation of floorplanning of three-dimensional integrated circuits under manufacturing and physical design constraints (2011)

Although the stacking of multiple strata to produce three-dimensional (3D) integrated circuits (ICs) improves interconnect length and hence reduces power and latency, it also results in the exacerbation of the thermal management challenge owing to the increased power density. There is a need for design tools to understand and optimise the trade-off between electrical and thermal design at the device and block levels. This study presents results from thermal–electrical co-optimisation for block-level floorplanning in a multi-die 3D IC under various manufacturing and physical design constraints. A method for temperature computation based on linearity of the governing energy equation is presented. This method is combined with previously reported electrical delay models for 3D ICs to simultaneously optimise both the maximum temperature and the interconnect length. It is shown that co-optimisation of thermal and electrical objectives results in a floorplan that is attractive from both perspectives. Physical design constraints because of cost-effective 3D manufacturing such as using fully or partly identical dies using reciprocal design symmetry (RDS), differentiated technology in each die and thinned die/wafer are discussed and their impact on the thermal–electrical co-optimisation is investigated. In some cases, the cheapest manufacturing choice, such as using identical die, for each layer may not result in optimal thermal and electrical design. Results presented in this work highlight the need for thermal and electrical co-design in multi-strata microelectronics, and for reconciling manufacturing and design considerations in order to develop practical design tools for 3D ICs.
Self Assembly of Amphiphilic (PEG)3-PLA Copolymer as Polymersomes: Preparation, Characterization, and Their Evaluation As Drug Carrier (2010)

(PEG)(3)-PLA copolymer has been explored for the formation of polymersomes. For this, three chains of methoxy-PEG(1100) were directly attached to citric acid by esterification. (Methoxy-PEG(1100))(3)-citrate was then reacted at its hydroxyl terminal with different moles of d,l-lactide by ring-opening polymerization to obtain polymers with five different PEG-to-PLA ratios ranging from 10:90 to 90:10. Polymers were characterized by GPC, FTIR, (1)H NMR, and DSC, films were characterized for hydrophilicity by contact angle, and surface topography was observed by SEM and AFM. All five polymers were evaluated for the formation of polymersomes. Among these, polymers with PEG content of 10-30% were able to self-assemble into polymersomes. To affirm their self-arrangement and drug carrier properties, hydrophilic and hydrophobic dyes were simultaneously encapsulated in these structures. SEM and TEM analysis of the blank polymersomes confirmed the vesicular nature of the polymersomes, whereas CLSM analysis of dye-loaded polymersomes demonstrated the presence of two separate regions viz. hydrophilic core and hydrophobic wall. Hydrophobic dye, fluorescein was released relatively faster from the wall of polymersomes, whereas hydrophilic dye, propidium iodide, was released in controlled fashion up to 18 days. It is expected that these systems may serve as a suitable carrier for simultaneous or separate delivery of drug molecules with varying physicochemical properties.
Fatty acid biosynthesis as a target for novel antibacterials. (2004)

The bacterial fatty acid synthesis pathway has significant potential as a target for the development of novel antibacterials. The pathway has been extensively studied in Escherichia coli, the crystal structures of the compounds involved are known and homologous genes are readily identified in the genomes of important pathogens. The currently used drugs triclosan and isoniazid are known to target one step in the pathway. Other experimental compounds such as thiolactomycin and cerulenin effectively inhibit other steps. These known pathway inhibitors are reviewed and the areas for potential future developments are explored.
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods (2011)

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.
HLA class I haplotype diversity is consistent with selection for frequent existing haplotypes (2017)

The major histocompatibility complex (MHC) contains the most polymorphic genetic system in humans, the human leukocyte antigen (HLA) genes of the adaptive immune system. High allelic diversity in HLA is argued to be maintained by balancing selection, such as negative frequency-dependent selection or heterozygote advantage. Selective pressure against immune escape by pathogens can maintain appreciable frequencies of many different HLA alleles. The selection pressures operating on combinations of HLA alleles across loci, or haplotypes, have not been extensively evaluated since the high HLA polymorphism necessitates very large sample sizes, which have not been available until recently. We aimed to evaluate the effect of selection operating at the HLA haplotype level by analyzing HLA A~C~B~DRB1~DQB1 haplotype frequencies derived from over six million individuals genotyped by the National Marrow Donor Program registry. In contrast with alleles, HLA haplotype diversity patterns suggest purifying selection, as certain HLA allele combinations co-occur in high linkage disequilibrium. Linkage disequilibrium is positive (Dij'>0) among frequent haplotypes and negative (Dij'<0) among rare haplotypes. Fitting the haplotype frequency distribution to several population dynamics models, we found that the best fit was obtained when significant positive frequency-dependent selection (FDS) was incorporated. Finally, the Ewens-Watterson test of homozygosity showed excess homozygosity for 5-locus haplotypes within 23 US populations studied, with an average Fnd of 28.43. Haplotype diversity is most consistent with purifying selection for HLA Class I haplotypes (HLA-A, -B, -C), and was not inferred for HLA Class II haplotypes (-DRB1 and-DQB1). We discuss our empirical results in the context of evolutionary theory, exploring potential mechanisms of selection that maintain high linkage disequilibrium in MHC haplotype blocks.