gebhart/patrepeval huggingface dataset:
Meshfree and particle methods and their applications (2002)

Recent developments of meshfree and particle methods and their applications in applied mechanics are surveyed. Three major methodologies have been reviewed. First, smoothed particle hydrodynamics (SPH) is discussed as a representative of a non-local kernel, strong form collocation approach. Second, mesh-free Galerkin methods, which have been an active research area in recent years, are reviewed. Third, some applications of molecular dynamics (MD) in applied mechanics are discussed. The emphases of this survey are placed on simulations of finite deformations, fracture, strain localization of solids; incompressible as well as compressible flows; and applications of multiscale methods and nano-scale mechanics. This review article includes 397 references.
Enhanced Photocatalytic Hydrogen Evolution by Covalent Attachment of Plastocyanin to Photosystem I (2004)

A simple photocatalytic hydrogen-evolving system is reported based on intermolecular electron transfer using isolated Photosystem I (PSI) reaction centers as the photoactive element. The system is composed of platinized PSI covalently linked to plastocyanin (PC). Water-soluble sodium ascorbate is the electron donor. PC was attached to PSI by formation of peptide bonds with the cross-linking reagent 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride. Compared to the unlinked proteins, cross-linking of PC and PSI resulted in a substantial increase in light-driven reduction of hexachloroplatinate ions (PtCl62- + 4e- → Pt↓ + 6Cl-). Hydrogen photoevolution by cross-linked PC−platinized PSI was increased 3-fold both in initial rate and total yield. Analysis of the reaction indicates that covalent linkage of PC to PSI results in a greater rate of total electron throughput from sodium ascorbate to light-activated hydrogen evolution. In addition, although photocatalytic hydrogen-evolving activity was easily demonstrated in the cross-linked system, the native pathway of electron flow yielding enzymatic NADP+ reduction activity was not observed upon addition of the natural PSI electron-accepting system, ferredoxin plus ferredoxin:NADP+ oxidoreductase.
Near Optimal Solutions for Product Line Design and Selection: Beam Search Heuristics (1995)

Many practical product line design problems have large numbers of attributes and levels. In this case, if most attribute level combinations define feasible products, constructing product lines directly from part-worths data is necessary. For three typical formulations of this important problem, Kohli and Sukumar (Kohli, R., R. Sukumar. 1990. Heuristics for product-line design using conjoint analysis. Management Sci. 36 1464–1478.) present state-of-the-art heuristics to find good solutions. In this paper, we develop improved heuristics based on a beam search approach for solving these problems. In our computations for 435 simulated problems, significant improvements occur in five important performance measures used. Our heuristic solutions are closer to the optimal, have smaller standard deviation over replicates, take less computation time, obtain optimal solutions more often and identify a number of “good” product lines explicitly. Computation times for these problems are no more than 22 seconds on a PC, small enough for adequate sensitivity analysis. We also apply the heuristics to a real data set and clarify computational steps by giving a detailed example.
Management By Objectives Applied To the Business Communication Class (1971)

The objective of the experiment described here was to find an effective way of teaching communication without alienating students from the task of writing. Pre-test and post-test opinionnaires established that over sixty per cent of the students believed the course helped improve their writing.
Combining B-Mode and Color Flow Vessel Segmentation for Registration of Hepatic CT and Ultrasound Volumes (2012)

Multimodal registration of intraoperative ultrasound and preoperative computed tomography imaging is the basis for percutaneous hepatic interventions. Currently, a rigid registration is performed manually by the surgeon using vessel structures and other anatomical landmarks for visual guidance. In this work our approach for intraoperative vessel segmentation from two ultrasound imaging modes, namely B-Mode and color flow mode, is presented. This segmentation is an important step for automation of the intraoperative registration which relies on vessel structures visible in contrast enhanced CT and ultrasound volumes. This paper describes the problems that arise when using B-mode ultrasound for segmentation of vessels and how they can be solved by introducing additional vessel information from color flow imaging. On a total number of 21 patients, our system was applied successfully in 15 cases. For nine randomly chosen patients studied in this paper, our system achieves a 3.45 mm accuracy at points used for registration and 5.01 mm for other landmarks which were not used for the registration process.
Binding diversity of monoclonal antibodies to<i>α</i>(2 → 8) polysialic acid conjugated to outer membrane vesicle via adipic acid dihydrazide (1996)

Murine monoclonal antibodies (mAbs) were generated using group B Neisseria meningitidis and Escherichia coli K1 polysaccharides (PSs) conjugated to outer membrane vesicle (OMV) via adipic acid dihydrazide, and were used to identify the immunodeterminants expressed on these capsular PSs. Ten mAbs representative of IgM and all subclasses of IgG were obtained which recognized diverse immunodeterminants on alpha(2-->8) polysialic acid (PSA). The specificity of mAbs to different antigenic determinants was assessed by their differential binding to PSA attached to a solid phase by different methods and confirmed by absorption studies. Two mAbs from the E. coli K1 fusion were directed to the O-acetyl epitope and the rest reacted with both the PSs only when attached to a solid phase by certain means. The methods by which PSA was coated on the solid phase had an impact on the epitope expression and binding pattern. At the concentrations used, the O-acetyl-specific mAbs, IgG1 and IgG3 mAbs were not bactericidal against group B N. meningitidis, whereas other mAbs were. The conjugates B and K1 PSs present to the murine immune system different antigenic determinants, some of which elicit bactericidal antibodies.
RF loss mechanisms in GaN‐based high‐electron‐mobility‐transistor on silicon: Role of an inversion channel at the AlN/Si interface (2017)

One of the epitaxial issues pertaining to the growth of AlGaN/GaN HEMTs on Si is the decrease of parasitic losses that can adversely impact the RF device performances. We characterized the microwave losses in coplanar waveguides (CPWs) on GaN‐based high‐electron‐mobility‐transistors (HEMTs) and their buffer layers on Silicon substrate, up to 40 GHz. The RF losses depend not only on the crystalline quality but also on the residual tensile stress in AlN buffer, as well as its thickness. The mechanism of interfacial lossy channel induced by the piezoelectric field is discussed. Adopting a thin high‐low‐high temperature (HLH) AlN buffer can help to reduce the tensile stress leading to a reduction of RF losses. We suggest that a thinner p‐type AlN and/or p‐AlGaN‐on‐thin AlN near the interface can suppress the electron interfacial lossy channel, which helps the GaN‐HEMT‐on‐HR Si to remain in a high frequency range and at high‐temperature operation.
‘DURVIT’: a phase-I trial of single low-dose durvalumab (Medi4736) IntraTumourally injected in cervical cancer: safety, toxicity and effect on the primary tumour- and lymph node microenvironment (2018)

NTR6119 , 1-nov-2016.
Growing Artificial Societies: Social Science from the Bottom Up (1998)

Part I Introduction: Artificial Society models life and death on the sugarscape sex, culture and conflict - the emergence of history sugar and spice - trade comes to the sugarscape disease agents a society is born artificial societies versus traditional models artificial societies versus a life toward generative social science - can you grow it?. Part II Life and death on the sugarscape: in the beginning - there was sugar the agents artificial society on the sugarscape wealth and its distribution in the agent population social networks of neighbours migration summary. Part III Sex, culture and conflict - the emergence of history: sexual reproduction cultural processes combat the proto-history. Part IV Sugar and spice - trade comes to the sugarscape: spice - a second commodity trade rules markets of bilateral traders emergent economic networks social computation, emergent computation summary and conclusions. Part V Disease processes: models of disease transmission and immune response immune system response disease transmission digital diseases on the sugarscape disease transmission networks. Part VI Conclusions: summary some extensions of the current model other artificial societies formal analysis of artificial societies generative social science looking ahead. Appendices: software engineering aspects of artificial societies summary of rule notation state-dependence on the welfare function.
Dopamine receptor sequences. Therapeutic levels of neuroleptics occupy D2 receptors, clozapine occupies D4. (1992)

Dopamine (DA) D2, D3, and D4 receptors are targets for antipsychotic drugs. The recent cloning, deoxyribonucleic acid sequencing, and brain location of these receptors provide new insight on the DA hypothesis of schizophrenia, particularly for the basis of antipsychotic therapy of schizophrenia. In schizophrenia brain tissue, D2 receptors are elevated and have lost the link to D1 receptors. Brain positron-emission tomography studies of patients may also reveal elevated D2, depending on the method used. Hallucinations and positive symptoms are blocked when about 70% of the D2 receptors are occupied by neuroleptic drugs. An analysis of the literature indicates that therapeutic concentrations of antipsychotic drugs (in the patient's cerebrospinal fluid or plasma water) act primarily at D2 receptors, with the exception of clozapine, which acts at D4 receptors.
Extracellular matrix in spinal cord regeneration: getting beyond attraction and inhibition (2002)

Department of Neurobiology and Anatomy, University of Utah, School of Medicine, 50 N. Medical Drive, Salt Lake City, UT 84132, USA CACorresponding Author
A Novel Pharmacologic Inhibitor of the NLRP3 Inflammasome Limits Myocardial Injury After Ischemia–Reperfusion in the Mouse (2013)

The small molecule 16673-34-0, an intermediate substrate in the glyburide synthesis free of the cyclohexylurea moiety, inhibits the formation of the NLRP3 inflammasome in cardiomyocytes and limits the infarct size after myocardial ischemia-reperfusion in the mouse, without affecting glucose metabolism.
Development of a Standard Swine Hemorrhage Model for Efficacy Assessment of Topical Hemostatic Agents (2011)

A rigorous hemorrhage model was developed for future evaluation of new hemostatic agents and comparison with CG, the current standard of care. This model may not be suitable for testing every agent and some modifications may be necessary for specific applications. Furthermore, laboratory studies using this or similar models must be accompanied by operational testing in the field to confirm the efficacy and practical utility of selected agents when used on the battlefield.
Gallium arsenide nanoparticles: synthesis and characterisation (2003)

Gallium arsenide nanoparticles have been prepared from GaCl3 and As(NMe2)3 in 4-ethylpyridine. UV spectra and emission luminescence show strong peaks for samples isolated after short reaction times. Time resolved photoluminescence (TRPL) was carried out using time-correlated single photon counting (TCSPC). The emission observed was confirmed as mainly arising from GaAs dots. Powder XRD data confirm the formation of the cubic GaAs phase. TEM imaging showed monodispersed nanoparticles with sizes ranging from 2 nm (for early aliquots) to 6 nm for later samples after the injection of additional precursor.
Protein-Fragment Complementation Assays for Large-Scale Analysis, Functional Dissection and Dynamic Studies of Protein–Protein Interactions in Living Cells (2011)

Protein-fragment Complementation Assays (PCAs) are a family of assays for detecting protein-protein interactions (PPIs) that have been developed to provide simple and direct ways to study PPIs in any living cell, multicellular organism, or in vitro. PCAs can be used to detect PPI between proteins of any molecular weight and expressed at their endogenous levels. Proteins are expressed in their appropriate cellular compartments and can undergo any posttranslational modification or degradation that, barring effects of the PCA fragment fusion, they would normally undergo. Assays can be performed in any cell type or model organism that can be transformed or transfected with gene expression DNA constructs. Here we focus on recent applications of PCA in the budding yeast, Saccharomyces cerevisiae, that cover the gamut of applications one could envision for studying any aspect of PPIs. We present detailed protocols for large-scale analysis of PPIs with the survival-selection dihydrofolate reductase (DHFR), reporter PCA, and a new PCA based on a yeast cytosine deaminase reporter that allows for both survival and death selection. This PCA should prove a powerful way to dissect PPIs. We then present methods to study spatial localization and dynamics of PPIs based on fluorescent protein reporter PCAs.
The CVT test design on a tester (2011)

Based on the CVT test method in the vehicle which is provided by the automaker, the CVT test items on a tester are designed. The CVT tester is made and then the oil pressure test, the transmission ratio test, the slip rate test and the system efficiency test are carried out on it. The test result can not only evaluate the CVT performance, but also analyze the slip rate and the CVT's system efficiency. Therefore, it can be used for the performance evaluation and the optimal control.
Oxidation mechanisms of soybean biodiesel based on spectroscopic analysis (2013)

The configurational changes and the oxidation mechanisms of unsaturated fatty acid methyl ester molecules in the oxidation process was analyzed, according to the principles of free radical reactions and the results of both infra red spectras and UV spectra. An idea was put forward that, during oxidation, cis-trans isomerization might occur in unsaturated fatty acid methyl ester molecules and conjugated double-bond might produce due to transfer of double-bond.
Immune response activation by a Toll-like receptor 7 agonist: Results of a phase 1 study (2005)

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Function of the ste signal transduction pathway for mating pheromones sustains MAT alpha 1 transcription in Saccharomyces cerevisiae. (1993)

Sterile mutants of Saccharomyces cerevisiae were isolated from alpha * cells having the a/alpha aar1-6 genotype (exhibiting alpha mating ability and weak a mating ability as a result of a defect in a1-alpha 2 repression). Among these sterile mutants, we found two ste5 mutants together with putative ste7, ste11, and ste12 mutants of the signal transduction pathway of mating pheromones. The amino acid sequence of the Ste5p protein predicted from the nucleotide sequence of a cloned STE5 DNA has a domain rich in acidic amino acids close to its C terminus, a cysteine-rich sequence, resembling part of a zinc finger structure, in its N-terminal half, and a possible target site of cyclic AMP-dependent protein kinase at its C terminus. Northern (RNA) blot analysis revealed that STE5 transcription is under a1-alpha 2-Aar1p repression. The MAT alpha 1 cistron has a single copy of the pheromone response element in its 5' upstream region, and its basal level of transcription was reduced in these ste mutant cells. However, expression of the MAT alpha 1 cistron was not enhanced appreciably by pheromone signals. One of the ste5 mutant alleles conferred a sterile phenotype to a/alpha aar1-6 cells but a mating ability to MATa cells.
An adaptive transform approach for image compression (2002)

A new transform/subband coding algorithm is proposed. Its original characteristic is that the transform operator is continuously updated during the encoding process on the base of previously decoded samples. Unlike other content based algorithms, no data overhead is implied and the method can be easily incorporated into most image compression schemes. Simulation results demonstrate that a substantial benefit can be derived from the method in the context of still image and video compression. We describe and justify an adaptation algorithm for fixed size orthogonal transforms suitable for video compression, showing how it can be applied to a particular class of time-varying filter banks, thereby eliminating the specific drawbacks of transform coding, while retaining the advantages of continuous adaptation.
Characterization of Recombinant Human Lactoferrin Secreted in Milk of Transgenic Mice (1997)

Human lactoferrin (hLF) is an iron-binding protein involved in host defense against infection and severe inflammation. Transgenic mice were produced harboring either hLF cDNA or genomic hLF sequences fused to regulatory elements of the bovine alphaS1 casein gene. Recombinant hLF expressed in the milk of transgenic mice (transgenic hLF) was compared with natural (human milk-derived) hLF. Immunological identity of the two forms was shown by double antibody immunoassays and the absence of an anti-hLF antibody response in transgenic mice on hyperimmunization with natural hLF. Mono S cation-exchange chromatography and N-terminal protein sequencing of transgenic and natural hLF revealed identical cationicity and N-terminal sequences. SDS-polyacrylamide gel electrophoresis and absorbance measurements of purified transgenic hLF showed this protein was 90% saturated with iron, whereas natural hLF is only 3% saturated. The pH-mediated release of iron from transgenic hLF was not different from that of iron-saturated natural hLF. Unsaturated transgenic hLF could be completely resaturated upon addition of iron. Slight differences in mobility between transgenic and natural hLF on SDS-polyacrylamide gel electrophoresis were abolished by enzymatic deglycosylation. Binding of transgenic and natural hLF to a range of ligands, including bacterial lipopolysaccharide, heparin, single-stranded DNA, Cibacron blue FG 3A, and lectins, was not different. Based on these observations, we anticipate that (unsaturated) rhLF and natural hLF will exert similar, if not identical, antibacterial and anti-inflammatory activity in vivo.
Mycotoxin production by Fusarium oxysporum and Fusarium sporotrichioides isolated from Baccharis spp. from Brazil (1989)

Fusarium oxysporum isolated from roots of and soil around Baccharis species from Brazil produced the trichothecenes T-2 toxin, HT-2 toxin, diacetoxyscirpenol, and 3'-OH T-2 (TC-1), whereas Fusarium sporotrichioides from the same source produced T-2 toxin, HT-2 toxin, acetyl T-2, neosolaniol, TC-1, 3'-OH HT-2 (TC-3), iso-T-2, T-2 triol, T-2 tetraol, and the nontrichothecenes moniliformin and fusarin C. Several unknown toxins were found but not identified. Not found were macrocyclic trichothecenes, zearalenone, wortmannin, and fusarochromanone (TDP-1).
Solid-phase oligonucleotide synthesis: a renaissance (1978)

A practical solid-phase method is described using a polar polyamide support for the synthesis of medium-length oligodeoxyribonucleotides. Chain assembly can be facilitated with the aid of a modified solid-phase peptide synthesiser. Hplc on both analytical and preparative scale allows rapid monitoring of syntheses as well as efficient final purification of the desired oligonucleotide.
Nature of ≡SiOCrO<sub>2</sub>Cl and (≡SiO)<sub>2</sub>CrO<sub>2</sub>Sites Prepared by Grafting CrO<sub>2</sub>Cl<sub>2</sub>onto Silica (2008)

The room-temperature reaction between chromyl chloride and Sylopol 952 silicas pretreated at 200, 450, and 800 °C was investigated using IR, XANES, and EXAFS spectroscopy, as well as by DFT modeling. On the silicas pretreated at 200 and 450 °C, the structurally uniform sites formed by the reaction with one surface hydroxyl group are described as ≡SiOCrO2Cl. Unreacted silanols persist on these silicas even in the presence of excess CrO2Cl2, and on the silica pretreated at 200 °C some participate in hydrogen bonding with the grafted monochlorochromate sites. On the silica pretreated at 800 °C, both ≡SiOCrO2Cl and (≡SiO)2CrO2 sites are formed. The latter are produced despite the absence of hydrogen-bonded hydroxyl pairs on the support. The origin of the chromate sites is proposed to be the reaction between CrO2Cl2 and hydroxyl-substituted siloxane 2-rings. These rings are likely formed at 800 °C by condensation between a pair of vicinal silanols in which one of the silanols is also a member of a geminal pair.
Probing the Time Scale of FPOP (Fast Photochemical Oxidation of Proteins): Radical Reactions Extend Over Tens of Milliseconds (2016)

Hydroxyl radical (⋅OH) labeling with mass spectrometry detection reports on protein conformations and interactions. Fast photochemical oxidation of proteins (FPOP) involves ⋅OH production via H2O2 photolysis by UV laser pulses inside a flow tube. The experiments are conducted in the presence of a scavenger (usually glutamine) that shortens the ⋅OH lifetime. The literature claims that FPOP takes place within 1 μs. This ultrafast time scale implies that FPOP should be immune to labeling-induced artifacts that may be encountered with other techniques. Surprisingly, the FPOP time scale has never been validated in direct kinetic measurements. Here we employ flash photolysis for probing oxidation processes under typical FPOP conditions. Bleaching of the reporter dye cyanine-5 (Cy5) served as readout of the time-dependent radical milieu. Surprisingly, Cy5 oxidation extends over tens of milliseconds. This time range is four orders of magnitude longer than expected from the FPOP literature. We demonstrate that the glutamine scavenger generates metastable secondary radicals in the FPOP solution, and that these radicals lengthen the time frame of Cy5 oxidation. Cy5 and similar dyes are widely used for monitoring the radical dose experienced by proteins in solution. The measured Cy5 kinetics thus strongly suggest that protein oxidation in FPOP extends over a much longer time window than previously thought (i.e., many milliseconds instead of one microsecond). The optical approach developed here should be suitable for assessing the performance of future FPOP-like techniques with improved temporal labeling characteristics. Graphical Abstract ᅟ.