gebhart/patrepeval huggingface dataset:
Two‐dimensional NMR investigations of the interactions of antibodies with peptide antigens (1993)

To increase our understanding of the molecular basis for antibody specificity and for the cross-reactivity of anti-peptide antibodies with native proteins it is important to study the three-dimensional structure of antibody complexes with their peptide antigens. For this purpose it may not be necessary to solve the structure of the whole antibody complex but rather to concentrate on elucidating the combining site structure, the interactions of the antibody with its antigen and the bound peptide conformation. We have developed an NMR methodology based on two-dimensional difference spectrum measurements which extract the information concerning antibody-peptide interactions and intramolecular interactions in the bound ligand from the crowded and unresolved spectrum of the Fab complex. These measurements yield restraints on interproton distances in the complex which are used to dock the peptide into calculated models for the antibodies' combining sites. Comparison of the interactions of three antibodies against a cholera toxin peptide (CTP3), which differ in their cross-reactivity with the toxin, yields information about the size and conformation of antigenic determinants recognized by antibodies, the structure of their combining sites and relationships between antibodies' primary structure, and their interactions with peptide antigens.
Three-dimensional curve reconstruction from multiple images (2012)

In this study, the authors propose a new approach for reconstructing three-dimensional (3D) curves from multiple 2D images taken by uncalibrated cameras. The method is point based and does not require parameterisation of 2D or 3D curves. 2D curves are detected on multiple views as sequences of sampled points along the curves. A curve in 3D space is reconstructed as a sequence of 3D points sampled along the curve that minimise the geometric distances from their projections to the measured 2D curves on different images (i.e. 2D reprojection error). The minimisation problem is solved by an iterative algorithm which is guaranteed to converge to a (local) minimum of the 2D reprojection error. Without requiring calibrated cameras or additional point features, their method can reconstruct multiple 3D curves simultaneously from multiple images and it readily handles images with missing and/or partially occluded curves.
Clinical evaluation of a staphylococcal protein A immunoadsorption system in the treatment of myasthenia gravis patients (1999)

Patients with myasthenia gravis respond to treatment with plasma immunoadsorption. Further studies are required for a cost-benefit analysis.
Simple Enantioselective Syntheses of (2<i>R</i>,6<i>R</i>)-Hydroxynorketamine and Related Potential Rapid-Onset Antidepressants (2017)

A novel strategy for accessing cyclic α-amino ketones enantioselectively has opened a simple synthetic route to the antidepressant (2R,6R)-hydroxynorketamine and numerous analogues. Mechanistically guided catalyst selection was essential in an initial olefin epoxidation step. In a second crucial step, the epoxide was subjected to a novel O → N displacement that occurred with retention of configuration through the use of Al- or Ti-based azides, which promote epoxide activation and internal cis delivery of N<sub>3</sub> to carbon.
The effects of unsaturated fatty acids, oxidizing agents and Michael reaction acceptors on the induction of N-ethylmaleimide reductase in Escherichia coli: possible application for drug design of chemoprotectors. (1997)

Menadione and dimethyl maleate, Michael reaction acceptors, induced N-ethylmaleimide (NEM) reductase activity in Escherichia coli strain DH5a. Linoleic acid also induced NEM reductase activity, but oleic acid, which is less susceptible to lipid peroxidation than linoleic acid, did not induce NEM reductase activity. In addition, NEM reductase activity was induced by menadione and linoleic acid also in strain DH5, Y1088 and Y1090. Linoleic acid is not a Michael reaction acceptor, but is known to produce Michael reaction acceptors such as alkenals and 4-hydroxyalkenals as a result of free-radical-initiated lipid peroxidation. Thus, our findings suggested that lipid peroxidation was involved in the induction of NEM reductase by linoleic acid. The electrophilic property of Michael reaction acceptors provides the signal for induction of phase II enzymes such as glutathione S-transferase and quinone reductase in mammals. The inducer potency of phase II enzymes has been used to design chemoprotective drugs. Therefore, the inducible nature of this enzyme will serve not only for the elucidation of its physiological function, but also for the evaluation of chemoprotective drugs.
Adaptive algorithm selection method (AASM) for dynamic software tuning (2002)

This paper presents a new approach to dynamic software tuning called the adaptive algorithm selection method (AASM). The AASM is built into the calling sequence of a library. When the library is called, the AASM is activated. The AASM selects and executes the optimum algorithm from registered algorithms in a library, based on data and machine type. As a result, the software is automatically tuned and the execution time is shortened. The relation between the data and the best algorithm for a given machine is learned by a neural network from the results of performance tests of the registered algorithms. We experimented on a multi-strings search problem with the AASM on the following machines: the CRAY X-MP/216, FACOM M 1800/30, and SUN Sparc Station 2. From these experiments we demonstrated that the AASM is able to minimize the execution time.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Tissue deformation spatially modulates VEGF signaling and angiogenesis (2012)

Physical forces play a major role in the organization of developing tissues. During vascular development, physical forces originating from a fluid phase or from cells pulling on their environment can alter cellular signaling and the behavior of cells. Here, we observe how tissue deformation spatially modulates angiogenic signals and angiogenesis. Using soft lithographic templates, we assemble three-dimensional, geometric tissues. The tissues contract autonomously, change shape stereotypically and form patterns of vascular structures in regions of high deformations. We show that this emergence correlates with the formation of a long-range gradient of Vascular Endothelial Growth Factor (VEGF) in interstitial cells, the local overexpression of the corresponding receptor VEGF receptor 2 (VEGFR-2) and local differences in endothelial cells proliferation. We suggest that tissue contractility and deformation can induce the formation of gradients of angiogenic microenvironments which could contribute to the long-range patterning of the vascular system.
Fractionation of High‐Amylose Maize Starches by Differential Alcohol Precipitation and Chromatography of the Fractions (1998)

ABSTRACT Three high‐amylose maize starches (HAS) and a common corn starch (CCS) were subjected to differential alcohol precipitation using isoamyl alcohol and 1‐butanol to obtain fractions designated as amylose (AM), amylopectin (AP), and intermediate material (IM). For each starch, IM had a blue value and an iodine binding wavelength maximum (λ max ) between the λ max of the respective AM and AP. Size‐exclusion chromatography (SEC) showed similarities in the AM from CCS and HAS. HAS AP had higher blue values and iodine binding λ max values than CCS AP. SEC of the intact HAS AP and IM both showed large proportions of material eluting after the void volume (45–85%) when compared to CCS AP and IM. Chain length (CL) distributions of debranched AP and IM indicated that these fractions from each starch were highly branched, and that AP had a shorter average chain length than IM. Consequently, the differential precipitation behavior of the HAS AP and IM appears dependent on general branching structure rather than size. We conclude that in both CCS and HAS, AP and IM are subsets of the branched molecules with AP as the predominant fraction. For HAS, AP and IM include molecules of a size typical for AM and contain a higher proportion of chains that are longer than those of CCS AP. Differential alcohol precipitation is a useful method of separating amylose, amylopectin, and intermediate material from HAS.
Transcriptional control of herpesvirus gene expression: gene functions required for positive and negative regulation. (1986)

We have used an in vitro nuclear run-off assay to measure the levels of transcription of specific herpes simplex virus genes at different times during a lytic infection. We analyzed the effects of inhibition of DNA replication and of defects in two herpes simplex virus regulatory proteins on the transcription of these genes. We present evidence that the transcription of the alpha ICP4 gene is negatively regulated during a lytic infection. The regulation of ICP4 gene transcription requires the beta protein ICP8 (where ICP = infected cell polypeptide). Transcription of the beta ICP8, gamma 1 ICP5, and gamma 2 glycoprotein C (gC) genes was dependent on ICP4, and transcription of the gamma 2gC gene was strongly inhibited when DNA replication was blocked. Defects in ICP8 also resulted in increased levels of transcription of the ICP4, ICP8, ICP5, and gC genes from parental viral genomes. Our results suggest that ICP8 may be important in maintaining the highly ordered cascade of viral gene expression.
Outer Membrane Protein A of <i>Escherichia coli</i> O157:H7 Stimulates Dendritic Cell Activation (2006)

ABSTRACT Outer membrane protein A (OmpA) is located in the membrane of Escherichia coli and other gram-negative bacteria and plays a multifunctional role in bacterial physiology and pathogenesis. In enterohemorrhagic E. coli (EHEC), especially serotype O157:H7, OmpA interacts with cultured human intestinal cells and likely acts as an important component to stimulate the immune response during infection. To test this hypothesis, we analyzed the effect of EHEC OmpA on cytokine production by dendritic cells (DCs) and on DC migration across polarized intestinal epithelial cells. OmpA induced murine DCs to secrete interleukin-1 (IL-1), IL-10, and IL-12 in a dose-dependent manner, and this effect was independent of Toll-like receptor 4. Although DCs displayed differential responses to EHEC OmpA and OmpA-specific antibodies enhanced DC cytokine secretion, we cannot discard that other EHEC surface elements were likely to be involved. While OmpA was required for bacterial binding to polarized Caco-2 cells, it was not needed for the induction of cytokine production by Caco-2 cells or for human DC migration across polarized cells.
Modulation of Chondrocyte Activity in vitro in Response to Ascorbic Acid (1981)

The aim of this study was to examine the response of secondary cartilage to ascorbic acid in vitro. Cells which had not attained the prechondroblast stage when cultured, did not chondrify in vitro, even when exposed to high levels (400 microgram/ml) of ascorbic acid. On the other hand, prechondroblasts cultured in the presence of low levels (100 microgram/ml) of ascorbic acid did chondrify. Once cytodifferentiation commenced, chondrogenesis was independent of the presence of ascorbic acid in the medium. Cartilage which differentiated in the presence of continuous high levels ( greater than 200 microgram/ml) of ascorbic acid modulated to a tissue which consisted of hypertropic chondrocytes in a highly collagenous extracellular matrix. At the light-microscopic level, this tissue was classified as chondroid bone. At the ultrastructural level, the collagen was seen to be in the form of cross-banded fibres more typical of bone than cartilage. Prelabelling of cultures with either [3H]-thymidine or [3H]-proline showed that neither dedifferentiation of chondrocytes nor the resumption of mitotic activity was responsible for the alterations in the extracellular matrix. The differentiated chondrocytes can secrete an altered extracellular matrix without undergoing cytological dedifferentiation. The role of ascorbic acid in the attainment and maintenance of the differentiated state is briefly discussed.
Clinical Data-Mining (2009)

Abstract Clinical data-mining (CDM) involves the conceptualization, extraction, analysis, and interpretation of available clinical data for practice knowledge-building, clinical decision-making, and practitioner reflection. Depending upon the type of data mined, CDM can be qualitative or quantitative; it is generally retrospective, but may be meaningfully combined with original data collection. Any research method that relies on the contents of case records or information systems data inevitably has limitations, but with proper safeguards these can be minimized. Among CDM's strengths however, are that it is unobtrusive, inexpensive, presents little risk to research subjects, and is ethically compatible with practitioner value commitments. When conducted by practitioners, CDM yields conceptual as well as data-driven insight into their own practice- and program-generated questions. This book covers all the basics of conducting practitioner-initiated CDM studies or CDM doctoral dissertations, drawing extensively on published CDM studies and completed CDM dissertations from multiple social work settings in the United States, Australia, Israel, Hong Kong, and the United Kingdom. In addition, it describes consulting principles to help with forging collaborative university-agency CDM partnerships.
Image compression using an efficient edge cartoon + texture model (2003)

Wavelet-based image coders optimally represent smooth regions and isolated point singularities. However, wavelet coders are less adept at representing perceptually important edge singularities, and coding performance suffers significantly as a result. We propose a novel two-stage image coder framework based on modeling images as edge cartoons + textures. In stage 1, we infer and efficiently code the edge information from the image using a multiscale wedgelet decomposition. In stage 2, we code the residual, "edgeless" texture image using a standard wavelet coder. Our preliminary coder improves significantly over standard wavelet coding techniques in terms of visual quality.
Change of Formation Yield and Characterization of PCC Particle Synthesized with Impurity Ions Contents by Carbonation Process (2006)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Evolving the architecture of SQL Server for modern hardware trends (2015)

The basic architecture of SQL Server, as well as other major database systems, goes back to a time when main memories were (very) small, data lived on disk, machines had a single (slow) processor, and OLTP was the only workload that mattered. This is not an optimal design for today's environment with large main memories, plenty of cores, and where transactional and analytical processing are equally important. To adapt to these trends and take advantage of the opportunities they offer SQL Server has added support for column store indexes and in-memory tables over the last two releases. The two features are aimed at dramatically improving performance on analytical and transactional workloads, respectively. This paper gives an overview of the design of the two features and the performance improvements they provide.
In Situ One-Pot Synthesis of 1-Dimensional Transition Metal Oxide Nanocrystals (2005)

One-dimensional colloidal metal oxide nanocrystals are of great importance in materials chemistry, but reports on these materials are rare due to lack of well-defined synthetic protocols. In this paper, we present a general and highly effective one-pot synthetic protocol to produce 1-dimensional nanostructures of transition metal oxide (e.g., W(18)O(49), TiO(2), Mn(3)O(4), and V(2)O(5)) through thermally induced crystal growth processes from a mixture of metal chloride and surfactants.
Public sector roles in strengthening corporate social responsibility: a baseline study (2002)

This report categorizes and discusses the range of roles that public sector agencies have played in providing an enabling environment for corporate social responsibility (CSR). The starting point is a broad definition of CSR that goes well beyond a more limited understanding of CSR as being about business activities that go beyond compliance. A broader definition that considers the overall potential commitment of business to sustainable development is better suited to understanding public sector roles in CSR. The report assesses some important overall drivers for public sector engagement in pro-CSR activities in developing countries, as well as constraints to engagement.
Ultrafast recovery time in a strained InGaAs-AlAs p-i-n modulator (1995)

We have performed sub-picosecond resolution measurements of the optical recovery of InGaAs-AlAs multiple quantum well p-i-n structures that exhibit strong excitonic features, a clear quantum confined Stark effect and low photocurrent. The recovery times, measured as a function of applied electrical bias and optical excitation density, are much shorter than that predicted by carrier thermionic emission rates from the quantum wells. An observed ultrafast recovery time of 28 ps makes this material system promising as a fast modulator with low thermal dissipation or as a saturable absorber for semiconductor and fiber laser mode locking.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The Analysis of Importance and Satisfaction of Outdoor Sportswear Selection Attribute Factors of Consumers in their 20s using the IPA Method in the Corona Era (2022)

본 연구는 IPA기법을 활용하여 코로나 시대에 20대 소비자들이 인식하는 아웃도어스포츠웨어 선택속성에 대한 중요도와 만족도를 분석하는 데 목적이 있다. 본 연구의 대상자는 경기, 부산 지역에 위치한 20대 남녀를 대상으로 모집단을 선정하였다. 편의표본추출법을 이용하여 표본을 추출하였다. 총 350부의 설문지 중 응답이 불성실하다고 판단되거나 무응답한 설문지 41부를 제외한 총 309부의 설문자료를 실제분석에 이용하였다. 자료처리는 SPSS 23.0 version for Window를 이용하여 탐색적 요인분석, 신뢰도 분석, 빈도분석, t-test 그리고 IPA분석을 실시하였다. 이러한 결과, 다음과 같은 결론이 나타났다. Ⅰ사분면은 색상, 디자인, 체온 유지, 내구성, 땀 흡수, 신축성 있는 편안함, 착용감의 편안함, 옷 무게, 일상생활 착용, 외출복 겸용으로 착용이 나타났다. Ⅱ사분면은 아름다움의 표현, 방수의 기능, 원활한 A/S으로 나타났다. Ⅲ사분면은 타인이 잘 아는 브랜드, 유행하는 브랜드, 고가더라도 유명 브랜드, 유명 연예인 착용브랜드, 개성의 표현, 모임 시 착용, 사은품 증정, 할부, 매장직원의 친절로 나타났다. Ⅳ사분면은 브랜드명으로 나타났다.
Electrodeposition of Composite Coatings of Cu/AlO(OH) Using Allyl Alcohol as an Additive (2017)

In this work, composite coatings of Cu/AlO(OH) were produced by electrodeposition on steel substrates using a pyrophosphate-based bath containing allyl alcohol as an additive. The electrodeposition of the composite coatings was carried out using a 23 central composite design (CCD), aiming to verify the effects of the deposition parameters (previous stirring time (t), the stirring speed (S) and the current density (j)), considered the entry variables, on the electrochemical behavior of Cu/AlO(OH) coating, the response variables of the CCD. The results indicated that a decrease of the parameters j and S directly influenced the values ​​of Rp and Rct, leading to the production of protective coatings. The best result (Rp = 211 Ω and Rct = 221 Ω) was obtained under conditions where t = 120 min, S = 1300 rpm and j = 7 A m-2. Dispersed bohemite particles could be noted on the surface of the composite coating.
Three cytosolic glutamine synthetase isoforms localized in different-order veins act together for N remobilization and seed filling in Arabidopsis (2018)

Glutamine synthetase (GS) is central for ammonium assimilation and consists of cytosolic (GS1) and chloroplastic (GS2) isoenzymes. During plant ageing, GS2 protein decreases due to chloroplast degradation, and GS1 activity increases to support glutamine biosynthesis and N remobilization from senescing leaves. The role of the different Arabidopsis GS1 isoforms in nitrogen remobilization was examined using 15N tracing experiments. Only the gln1;1-gln1;2-gln1;3 triple-mutation affecting the three GLN1;1, GLN1;2, and GLN1;3 genes significantly reduced N remobilization, total seed yield, individual seed weight, harvest index, and vegetative biomass. The triple-mutant accumulated a large amount of ammonium that could not be assimilated by GS1. Alternative ammonium assimilation through asparagine biosynthesis was increased and was related to higher ASN2 asparagine synthetase transcript levels. The GS2 transcript, protein, and activity levels were also increased to compensate for the lack of GS1-related glutamine biosynthesis. Localization of the different GLN1 genes showed that they were all expressed in the phloem companion cells but in veins of different order. Our results demonstrate that glutamine biosynthesis for N-remobilization occurs in veins of all orders (major and minor) in leaves, it is mainly catalysed by the three major GS1 isoforms (GLN1;1, GLN1;2, and GLN1;3), and it is alternatively supported by AS2 in the veins and GS2 in the mesophyll cells.
Advances in Carbonate Stimulation Methodology – From Wormholes to Long-Term Productivity (2010)

Abstract Effective acid stimulation can be critical to achieving the desired long-term production rates from targeted reservoir layers. ExxonMobil has developed an integrated, multi-disciplinary methodology for carbonate matrix stimulation of long completion intervals.1 The methodology is a continuous process which includes geological characterization, reservoir objectives, completion strategy, stimulation design with the necessary experimental testing, implementation, and evaluation. The methodology has recently been customized in collaboration with RasGas to achieve objectives for K1-K32 and K1-K43 completions in the North Field, the world’s largest, non-associated gas field. Building upon this success, ExxonMobil continues to study the fundamentals of carbonate stimulation and its impact on long-term productivity to enhance the process and apply it to a wider range of reservoirs and well types. This paper presents preliminary results from three areas of ongoing research: (a) improved understanding of 3-D wormhole growth through large-scale experiments and visualization techniques, (b) integrated wormhole modeling and complex fluid flow during stimulation of long horizontal wells, and (c) enhanced post-stimulation evaluation method that integrates stimulation physics, well test analyses, and long-term reservoir performance predictions. Integration of these technological advancements with existing knowledge provides an enhanced methodology for the stimulation of carbonate reservoirs with an increased focus on long-term productivity.
Bioluminescence: a versatile technique for imaging cellular and molecular features (2013)

Bioluminescence is a ubiquitous imaging modality for visualizing biological processes in vivo. This technique employs visible light and interfaces readily with most cell and tissue types, making it a versatile technology for preclinical studies. Here we review basic bioluminescence imaging principles, along with applications of the technology that are relevant to the medicinal chemistry community. These include noninvasive cell tracking experiments, analyses of protein function, and methods to visualize small molecule metabolites. In each section, we also discuss how bioluminescent tools have revealed insights into experimental therapies and aided drug discovery. Last, we highlight the development of new bioluminescent tools that will enable more sensitive and multi-component imaging experiments and, thus, expand our broader understanding of living systems.