gebhart/patrepeval huggingface dataset:
RAGE Ligation Affects T Cell Activation and Controls T Cell Differentiation (2008)

The pattern recognition receptor, RAGE, has been shown to be involved in adaptive immune responses but its role on the components of these responses is not well understood. We have studied the effects of a small molecule inhibitor of RAGE and the deletion of the receptor (RAGE-/- mice) on T cell responses involved in autoimmunity and allograft rejection. Syngeneic islet graft and islet allograft rejection was reduced in NOD and B6 mice treated with TTP488, a small molecule RAGE inhibitor (p < 0.001). RAGE-/- mice with streptozotocin-induced diabetes showed delayed rejection of islet allografts compared with wild type (WT) mice (p < 0.02). This response in vivo correlated with reduced proliferative responses of RAGE-/- T cells in MLRs and in WT T cells cultured with TTP488. Overall T cell proliferation following activation with anti-CD3 and anti-CD28 mAbs were similar in RAGE-/- and WT cells, but RAGE-/- T cells did not respond to costimulation with anti-CD28 mAb. Furthermore, culture supernatants from cultures with anti-CD3 and anti-CD28 mAbs showed higher levels of IL-10, IL-5, and TNF-alpha with RAGE-/- compared with WT T cells, and WT T cells showed reduced production of IFN-gamma in the presence of TTP488, suggesting that RAGE may be important in the differentiation of T cell subjects. Indeed, by real-time PCR, we found higher levels of RAGE mRNA expression on clonal T cells activated under Th1 differentiating conditions. We conclude that activation of RAGE on T cells is involved in early events that lead to differentiation of Th1(+) T cells.
The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitidis (1999)

The extent to which recombination disrupts the bifurcating treelike phylogeny and clonal structure imposed by binary fission on bacterial populations remains contentious. Here, we address this question with a study of nucleotide sequence data from 107 isolates of the human pathogen Neisseria meningitidis. Gene fragments from 12 house-keeping loci distributed around the meningococcal chromosome were analyzed, showing that (1) identical alleles are disseminated among genetically diverse isolates, with no evidence for linkage disequilibrium; (2) different loci give distinct and incongruent phylogenetic trees; and (3) allele sequences are incompatible with a bifurcating treelike phylogeny at all loci. These observations are consistent with the hypothesis that meningococcal populations comprise organisms assembled from a common gene pool, with alleles and allele fragments spreading independently, together with the occasional importation of genetic material from other species. Further, they support the view that recombination is an important genetic mechanism in the generation new meningococcal clones and alleles. Consequently, for anything other than the short-term evolution of this species, a bifurcating treelike phylogeny is not an appropriate model.
A Graph Autoencoder Approach to Causal Structure Learning (2019)

Causal structure learning has been a challenging task in the past decades and several mainstream approaches such as constraint- and score-based methods have been studied with theoretical guarantees. Recently, a new approach has transformed the combinatorial structure learning problem into a continuous one and then solved it using gradient-based optimization methods. Following the recent state-of-the-arts, we propose a new gradient-based method to learn causal structures from observational data. The proposed method generalizes the recent gradient-based methods to a graph autoencoder framework that allows nonlinear structural equation models and is easily applicable to vector-valued variables. We demonstrate that on synthetic datasets, our proposed method outperforms other gradient-based methods significantly, especially on large causal graphs. We further investigate the scalability and efficiency of our method, and observe a near linear training time when scaling up the graph size.
Highly conductive and stretchable poly(dimethylsiloxane):poly(3,4-ethylenedioxythiophene):poly(styrene sulfonic acid) blends for organic interconnects (2013)

Naturally immiscible PEDOT:PSS and PDMS, which are a typical conducting polymer and an transparent elastomer, respectively, were blended by the support of PDMS-b-PEO. A block copolymer, PDMS-b-PEO, consisting of hydrophobic PDMS backbones and hydrophilic PEO side chains, significantly improved the miscibility of PEDOT:PSS and PDMS. At an optimal PDMS-b-PEO concentration of 30%, a cured PEDOT:PSS:PDMS film was found to be comprised of three-dimensional PDMS networks and a PEDOT:PSS phase filling in between the networks. The optimal blend film exhibited a conductivity comparable to a pure PEDOT:PSS film and a maximum strain to rupture of about 75%. It was also demonstrated that interconnects made of this blend film functioned well irrespective of the substrate and the pattern size, and could reproducibly operate under strains up to 50%. These results indicate that the PEDOT:PSS:PDMS blends could be a practical choice for organic interconnects for future stretchable electronics.
Phase Locking, Period-Doubling Bifurcations, and Irregular Dynamics in Periodically Stimulated Cardiac Cells (1981)

The spontaneous rhythmic activity of aggregates of embryonic chick heart cells was perturbed by the injection of single current pulses and periodic trains of current pulses. The regular and irregular dynamics produced by periodic stimulation were predicted theoretically from a mathematical analysis of the response to single pulses. Period-doubling bifurcations, in which the period of a regular oscillation doubles, were predicted theoretically and observed experimentally.
Compile-time partitioning of iterative parallel loops to reduce cache coherency traffic (1991)

Adaptive data partitioning (ADP) which reduces the execution time of parallel programs by reducing interprocessor communication for iterative parallel loops is discussed. It is shown that ADP can be integrated into a communication-reducing back end for existing parallelizing compilers or as part of a machine-specific partitioner for parallel programs. A multiprocessor model to analyze program execution factors that lead to interprocessor communication and a model for the iterative parallel loop to quantify communication patterns within a program are defined. A vector notation is chosen to quantify communication across a global data set. Communication parameters are computed by examining the indexes of array accesses and are adjusted to reflect the underlying system architecture by compensating for cache line sizes. These values are used to generate rectangular and hexagonal partitions that reduce interprocessor communication.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Dehydrooligopeptides. XV. Useful Syntheses of Dehydrodipeptides by the Enzymatic Coupling of <i>α</i>-Dehydroglutamate with Various <i>α</i>-Amino Acid Amides Using Proteases (1993)

Abstract Novel enzymatic syntheses of various dehydrodipeptides by the coupling of α,γ-dimethyl N-benzyloxycarbonyl(Z)-α-dehydroglutamate [Cbz–ΔGlu(OMe)–OMe; 1] with α-amino acid amides (H–AA–NHR) using proteases, such as papain and α-chymotrypsin A (CT), are described. It was found that there was conspicuous difference between the catalytic actions of papain and CT toward 1. In the case of papain, the selective coupling of α-ester of 1 with H–AA–NHR took place to give Cbz–ΔGlu(OMe)–AA–NHR, while in the case of CT the coupling of γ-ester of 1 proceeded predominantly to give Cbz–ΔGlu(AA–NHR)–OMe. The present study suggests that both papain and CT may become a versatile tool for the organic synthesis by the coupling of not only ΔGlu derivatives but also the other α-dehydroamino acids with α-amino acids or peptides.
Highly Piezoelectric Shear-Horizontal-Type Boundary Waves (1997)

This paper describes theoretical studies on piezoelectric shear-horizontal (SH) type boundary waves propagating along the surface of a separation between piezoelectric and non-piezoelectric materials. According to the guiding mechanism for this type of waves, it is expected that the application of highly piezoelectric materials results in a wide range of existence of combinations for various materials. Numerical analysis shows that SH-type leaky boundary waves exist for combinations of Si/LiNbO 3 , Si/LiTaO 3 and YAG/LiNbO 3 . The electromechanical coupling factor K 2 of 10.0% is obtainable for SH-type leaky boundary waves in [001]-Si<110 >/175°YX-LiNbO 3 , in which the velocity is about 4,465 m/s and the attenuation due to leaky nature is substantially zero.
Finite Reynolds number effects in the Bretherton problem (2001)

In this paper we investigate the effect of fluid inertia in the classical Bretherton problem in which a semi-infinite air finger displaces viscous fluid in a two-dimensional channel. The governing free-surface Navier–Stokes equations are discretized by a finite element method and the system’s behavior is studied for capillary and Reynolds numbers in the ranges 0.05&lt;Ca&lt;5 and 0&lt;Re&lt;280, respectively. It is shown that at a finite Reynolds number, a sequence of closed vortices develops in the recirculating flow region ahead of the bubble tip. The largest of these vortices is located near the bubble tip where it significantly affects the pressure distribution and leads to a noticeable increase in the overall pressure rise across the bubble tip. The underlying physical mechanisms are discussed in detail.
Metal-triggered Structural Transformations, Aggregation, and Fibrillation of Human α-Synuclein (2001)

Parkinson's disease involves the aggregation of alpha-synuclein to form fibrils, which are the major constituent of intracellular protein inclusions (Lewy bodies and Lewy neurites) in dopaminergic neurons of the substantia nigra. Occupational exposure to specific metals, especially manganese, copper, lead, iron, mercury, zinc, aluminum, appears to be a risk factor for Parkinson's disease based on epidemiological studies. Elevated levels of several of these metals have also been reported in the substantia nigra of Parkinson's disease subjects. We examined the effect of various metals on the kinetics of fibrillation of recombinant alpha-synuclein and in inducing conformational changes, as monitored by biophysical techniques. Several di- and trivalent metal ions caused significant accelerations in the rate of alpha-synuclein fibril formation. Aluminum was the most effective, along with copper(II), iron(III), cobalt(III), and manganese(II). The effectiveness correlated with increasing ion charge density. A correlation was noted between efficiency in stimulating fibrillation and inducing a conformational change, ascribed to formation of a partially folded intermediate. The potential for ligand bridging by polyvalent metal ions is proposed to be an important factor in the metal-induced conformational changes of alpha-synuclein. The results indicate that low concentrations of some metals can directly induce alpha-synuclein fibril formation.
View relevance driven materialized view selection in data warehousing environment (2002)

A data warehouse uses multiple materialized views to efficiently process a given set of queries. These views are accessed by read-only queries and need to be maintained after updates to base tables. Due to the space constraint and maintenance cost constraint, the materialization of all views is not possible. Therefore, a subset of views needs to be selected to be materialized. The problem is NP-hard, therefore, exhaustive search is infeasible. In this paper, we design a View Relevance Driven Selection (VRDS) algorithm based on view relevance to select views. We take into consideration the query processing cost and the view maintenance cost. Our experimental results show that our heuristic aims to minimize the total processing cost, which is the sum of query processing cost and view maintenance cost. Finally, we compare our results against a popular greedy algorithm.
Molecular Dipole Chains:  Excitations and Dissipation (1998)

As a model for orientational excitation of molecular arrays, we examine the excitation behavior and energy flow patterns in a model system. The model is simply a chain of classical point dipoles with fixed mass center, rotating in a plane containing the intermolecular axis, and interacting by the classical dipole potential. At low energies, the dispersion relation is quite different from that for a phonon system, showing a flat frequency maximum at k = 0. Correlation function analysis shows a significant transition from the low-energy regime in which the local dipole motion is predominantly oscillatory (with periodic correlation functions and Fourier components that maximize at a well-defined oscillation frequency), to a high-energy situation in which a Rayleigh peak occurs in the k = 0 Fourier component, and finite frequency response occurs only for higher wave vector. Physically, this transition occurs for thermal energy roughly equal to the typical magnitude of the local dipolar interaction. Thus for energies above this transition, the kinetic energies are high enough that the local motion is predominantly rotatory rather than oscillatory. These changes are also seen in the frequency moments and Kirkwood g-factors. The simulations show that initial energy deposited in one rotating dipole passes down the chain almost like a solitary wave, reflecting off of the free chain end and then traversing the chain again.
The crystal structure of an antiparallel chair-type G-quadruplex formed by Bromo-substituted human telomeric DNA (2019)

Human telomeric guanine-rich DNA, which could adopt different G-quadruplex structures, plays important roles in protecting the cell from recombination and degradation. Although many of these structures were determined, the chair-type G-quadruplex structure remains elusive. Here, we present a crystal structure of the G-quadruplex composed of the human telomeric sequence d[GGGTTAGG8GTTAGGGTTAGG20G] with two dG to 8Br-dG substitutions at positions 8 and 20 with syn conformation in the K+ solution. It forms a novel three-layer chair-type G-quadruplex with two linking trinucleotide loops. Particularly, T5 and T17 are coplanar with two water molecules stacking on the G-tetrad layer in a sandwich-like mode through a coordinating K+ ion and an A6•A18 base pair. While a twisted Hoogsteen A12•T10 base pair caps on the top of G-tetrad core. The three linking TTA loops are edgewise and each DNA strand has two antiparallel adjacent strands. Our findings contribute to a deeper understanding and highlight the unique roles of loop and water molecule in the folding of the G-quadruplex.
Biodistribution and Clearance of Contrast-Carrying MREV Liposomes (1990)

Contrast-carrying liposomes (CCLs) have been shown to increase the attenuation coefficient of the liver and spleen during computed tomographic (CT) imaging. A modification of the reverse-phase evaporation preparative technique ("MREV") led to production of CCLs that entrap contrast media efficiently. After intravenous injection, MREVs are phagocytized by the Kupffer cells of the liver and the macrophages of the spleen. The biodistribution and clearance of MREVs were studied to evaluate their potential for clinical use, MREVs carrying iodine-125-iotrolan were administered intravenously to 12 rats at doses of 400 mg lipid (containing 400 mg iodine) per kilogram body weight. Pairs of rats were anesthetized and scanned at 3 hours, and 1, 7, 14, 27 and 48 days; CT attenuation values of liver, spleen, blood, kidneys and bladder were measured. Immediately following CT, the rats were killed and tissue specimens were radioassayed. Maximum iodine content in liver and spleen was reached at one day and sustained at high levels for seven days. Biologic removal half-time of the agent in both the liver and spleen was six days. Maximum CT enhancements over baseline were observed at 24 hours and reached 210 delta HU in the liver and 880 delta HU in the spleen per gram iodine injected per kilogram body weight. It is concluded that MREVs have appropriate imaging characteristics, biodistribution, and clearance to be effective CT contrast agents.
Numerical Modeling of Topographic Influences on Shallow Front Formation and Evolution: Quasi-Stationary Coastal Front (1993)

A two-dimensional mesoscale numerical model is used to investigate to pographic influences on shallow front formation and evolution. The shallow front is idealized as a coastal front near the southeastern China coast, with the downstream topographic features including the Taiwan Strait, the Taiwan Is land and the Central Mountain Range (CMR). Shallow frontogenesis near the coast occurs as a direct result of differential heating in the boundary layer for near-surface onshore ambient flow. The idealized shallow coastal front shows similar thermal structures with the lower part of Mei-Yu fronts stagnating over the southeastern China coast, indicating that differential heating for the former similarly plays the. role of geostrophic deformation in frontogenesis for the latter. Although the packed frontal isentropes tend to reside over the China coast, the frontal leading updraft may advect offshore as the shear of the upper-level offshore ambient flow is present. The associated cloud band hence is not necessarily confined near the China coast. Based on the numer ical control experiments, cloud development in response to the interaction processes among the moving frontal updraft, the developed land breeze over the island and the CMR discussed.
Generate Identity-Preserving Faces by Generative Adversarial Networks (2017)

Generating identity-preserving faces aims to generate various face images keeping the same identity given a target face image. Although considerable generative models have been developed in recent years, it is still challenging to simultaneously acquire high quality of facial images and preserve the identity. Here we propose a compelling method using generative adversarial networks (GAN). Concretely, we leverage the generator of trained GAN to generate plausible faces and FaceNet as an identity-similarity discriminator to ensure the identity. Experimental results show that our method is qualified to generate both plausible and identity-preserving faces with high quality. In addition, our method provides a universal framework which can be realized in various ways by combining different face generators and identity-similarity discriminator.
Beyond a single pathway: combination therapy in pulmonary arterial hypertension (2016)

There is a strong rationale for combining therapies to simultaneously target three of the key pathways implicated in the pathogenesis of pulmonary arterial hypertension (PAH). Evidence to support this strategy is growing, and a number of studies have demonstrated that combination therapy, administered as either a sequential or an initial regimen, can improve long-term outcomes in PAH. Dual combination therapy with a phosphodiesterase-5 inhibitor and an endothelin receptor antagonist is the most widely utilised combination regimen. However, some patients fail to achieve their treatment goals on dual therapy and may benefit from the addition of a third drug. The use of triple therapy in clinical practice was previously reserved for patients with severe disease due to the need for parenteral administration of prostanoids. Although triple therapy with parenteral prostanoids plays a key role in the management of severe PAH, the approval of oral therapies that target the prostacyclin pathway means that all three pathways can now be targeted with oral drugs at an earlier disease stage. Furthermore, there is evidence demonstrating that this approach can delay disease progression. Based on the evidence available, it is becoming increasingly clear that all PAH patients should be offered the benefits of combination therapy.
VLSI implementation of a 2-D DCT in a compiler (1991)

A 100 MHz realization of a 2D DCT (discrete cosine transform) in a compiler is presented. An optimal nibble-serial distributed arithmetic architecture is used for an efficient direct implementation of the DCT. The compiler, which is based on BiCMOS gate array technology and functional module generation technology, is used to support a rapid prototyping environment. An 8*8 inverse 2D DCT example in a 0.8 mu m BiCMOS gate array is given to illustrate the performance and flexibility of this approach. The design flow and a proposed development system, the Signal Analysis Workstation (SAW), are shown for customized system integrations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
On Cyclic Intermediates in Substitution Reactions. I. The Alkaline Hydrolysis of Some Aliphatic Bromoacids (1951)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOn Cyclic Intermediates in Substitution Reactions. I. The Alkaline Hydrolysis of Some Aliphatic BromoacidsJohn F. Lane and Harold W. HeineCite this: J. Am. Chem. Soc. 1951, 73, 3, 1348–1350Publication Date (Print):March 1, 1951Publication History Published online1 May 2002Published inissue 1 March 1951https://doi.org/10.1021/ja01147a148RIGHTS & PERMISSIONSArticle Views128Altmetric-Citations16LEARN 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 InReddit PDF (371 KB) Get e-Alerts Get e-Alerts
High-performance thin-film polarizing beam splitter operating at angles greater than the critical angle (2000)

A new type of thin-film polarizing beam splitter (PBS) is proposed that is based on the effects of light interference and frustrated total internal reflection. This PBS has a significantly better performance than conventional thin-film PBS's. It is nonabsorbing, broadband, and wide angle and has high extinction ratios in both the transmitted and the reflected beams. The principles and theory of this PBS are described in detail. Several PBS's designed for the visible and the infrared spectral regions are described. The measured results for a prototype visible PBS of this type are presented as well.