gebhart/patrepeval huggingface dataset:
Computational Design of Binding Proteins to EGFR Domain II (2014)

We developed a process to produce novel interactions between two previously unrelated proteins. This process selects protein scaffolds and designs protein interfaces that bind to a surface patch of interest on a target protein. Scaffolds with shapes complementary to the target surface patch were screened using an exhaustive computational search of the human proteome and optimized by directed evolution using phage display. This method was applied to successfully design scaffolds that bind to epidermal growth factor receptor (EGFR) domain II, the interface of EGFR dimerization, with high reactivity toward the target surface patch of EGFR domain II. One potential application of these tailor-made protein interactions is the development of therapeutic agents against specific protein targets.
Optical Magnetic Field Probe Sensor with High Accuracy Using Iron Garnet Films (1996)

Highly accurate optical magnetic field probe sensors using iron garnet films were developed. The sensors have high linearity and stable temperature characteristics because they adopt a new confocal optical system and a new garnet composition.
Altered Formation of Topotecan-Stabilized Topoisomerase I-DNA Adducts in Human Leukemia Cells (1997)

Topotecan (TPT) is a topoisomerase I (topo I) poison that has shown promising antineoplastic activity in solid tumors and acute leukemia. In the present study, a band depletion assay was used to evaluate the ability of TPT to stabilize topo I-DNA adducts in human leukemia cell lines and in clinical leukemia samples ex vivo. This assay showed that 50% of the cellular topo I in HL-60 human myelomonocytic leukemia cells became covalently bound to DNA at an extracellular TPT concentration of 4 micromol/L. In contrast, in 13 clinical specimens of human leukemia harvested before treatment of patients with TPT, the TPT concentration required to stabilize 50% of the cellular topo I in topo I-DNA complexes ranged from 3 to greater than 100 micromol/L (median, 30 micromol/ L). Flow microfluorimetry showed that cellular TPT accumulation varied over only a twofold range and failed to provide evidence for transport-mediated resistance in the clinical samples. These observations raise the possibility that formation of topo I-DNA adducts is diminished in many specimens of refractory/relapsed acute leukemia by a mechanism that might alter topo I sensitivity to TPT.
On the Apodization of Coherent Imaging Systems (1974)

A surprisingly large number of papers have been written on the effects of partially coherent light in image formation (for a recent review see Thompson 1969). Thus the major effects that can occur are well documented. With imaging systems that are used with transparent objects the characteristic edge ringing and edge shifting are familiar results. In reflective systems the speckle pattern is usually the most severe effect that often masks the ringing produced by coherent object illumination. Thus this paper will be primarily concerned with systems used in transmission. It is important to note that the majority of papers in this field assume diffraction limited performance of the imaging optics; this is, of course, laudable if the system is to be used with incoherent object illumination. If, however, the system is to be used with coherent or partially coherent object illumination then other considerations become important.
Ligand Binding Rapidly Induces Disulfide-dependent Dimerization of Glycoprotein VI on the Platelet Plasma Membrane (2007)

Thrombus formation in hemostasis or thrombotic disease is initiated by adhesion of circulating platelets to damaged blood vessel walls. Exposed subendothelial collagen interacting with platelet glycoprotein (GP) VI leads to platelet activation and integrin alpha(IIb)beta(3)-mediated aggregation. We previously showed that ligand binding to GPVI also induces metalloproteinase-dependent shedding, generating an approximately 55-kDa soluble ectodomain fragment and an approximately 10-kDa membrane-associated remnant. Here, treatment of platelets with collagen or the GPVI-targeting rattlesnake toxin convulxin also induces rapid (10-30 s) formation of a high molecular weight GPVI complex (GPVIc) under nonreducing conditions, as detected by immunoblotting with anti-GPVI antibodies. The appearance of an approximately 20-kDa remnant detectable using a polyclonal antibody against the GPVI cytoplasmic tail under nonreducing, but not reducing, conditions after ectodomain shedding and nonreduced/reduced two-dimensional SDS-polyacrylamide gel analysis of biotinylated platelets confirmed that that GPVIc was a homodimer. Formation of disulfide-linked GPVIc was prolonged in the presence of metalloproteinase inhibitor GM6001 and was independent of GPVI signaling because it was unaffected by inhibitors of Src kinases, Syk, or phosphoinositide 3-kinase. To identify the thiol involved in disulfide bond formation, wild-type or mutant GPVI, where two available sulfhydryls (Cys-274 and Cys-338) were individually mutated to serine, was expressed in rat basophilic leukemia cells. Dimerization of wild-type and C274S GPVI, but not the C338S mutant, was observed after treating cells with convulxin. We conclude that (i) a subpopulation of GPVI forms a constitutive dimer on the platelet surface, facilitating rapid disulfide cross-linking, (ii) convulxin or other GPVI agonists induce disulfide-linked GPVI dimerization independent of GPVI signaling, and (iii) the penultimate residue of the GPVI cytoplasmic tail, Cys-338, mediates disulfide-dependent dimer formation.
Diffusion and Reaction Studies in the System Al <sub>2</sub> O <sub>3</sub> ‐SiO <sub>2</sub> (1972)

High‐temperature diffusion kinetics and phase relations between couples of fused SiO 2 or cristobalite and sapphire or mullite were investigated in air and in helium. Subsolidus liquid formation between sapphire and cristobalite indicates the existence of a metastable system without mullite. A liquid phase is considered to be essential for the nucleation of mullite. The growth rate of mullite exceeded its dissolution rate in semi‐infinite fused‐SiO 2 ‐sapphire couples above 1634°C. The inter‐facial liquid compositions provided data for a minor revision of the mullite liquidus curve. Diffusion coefficients calculated from the Al profiles vary greatly with concentration and temperature, resulting in a large range of values for apparent activation energy, which decreases with increasing Al 2 O 3 content (∼310 to ∼60 kcal/mol for ∼4 to ∼22 wt% Al 2 O 3 ). The diffusion process in the liquid is considered to be cooperative movement of oxygen‐containing Al and Si complexes whose nature changes with composition and temperature; this change in the diffusing species contributes to the range in the values of experimental apparent activation energies.
Prediction of the Effective Radioprotective Dose of WR-2721 in Humans through an Interspecies Tissue Distribution Study (1976)

L. C. Washburn, J. J. Rafter, R. L. Hayes, Prediction of the Effective Radioprotective Dose of WR-2721 in Humans through an Interspecies Tissue Distribution Study, Radiation Research, Vol. 66, No. 1 (Apr., 1976), pp. 100-105
Heterogeneity within Animal Thioredoxin Reductases (2001)

Animal thioredoxin reductases (TRs) are selenocysteine-containing flavoenzymes that utilize NADPH for reduction of thioredoxins and other protein and nonprotein substrates. Three types of mammalian TRs are known, with TR1 being a cytosolic enzyme, and TR3, a mitochondrial enzyme. Previously characterized TR1 and TR3 occurred as homodimers of 55-57-kDa subunits. We report here that TR1 isolated from mouse liver, mouse liver tumor, and a human T-cell line exhibited extensive heterogeneity as detected by electrophoretic, immunoblot, and mass spectrometry analyses. In particular, a 67-kDa band of TR1 was detected. Furthermore, a novel form of mouse TR1 cDNA encoding a 67-kDa selenoprotein subunit with an additional N-terminal sequence was identified. Subsequent homology analyses revealed three distinct isoforms of mouse and rat TR1 mRNA. These forms differed in 5' sequences that resulted from the alternative use of the first three exons but had common downstream sequences. Similarly, expression of multiple mRNA forms was observed for human TR3 and Drosophila TR. In these genes, alternative first exon splicing resulted in the formation of predicted mitochondrial and cytosolic proteins. In addition, a human TR3 gene overlapped with the gene for catechol-O-methyltransferase (COMT) on a complementary DNA strand, such that mitochondrial TR3 and membrane-bound COMT mRNAs had common first exon sequences; however, transcription start sites for predicted cytosolic TR3 and soluble COMT forms were separated by approximately 30 kilobases. Thus, this study demonstrates a remarkable heterogeneity within TRs, which, at least in part, results from evolutionary conserved genetic mechanisms employing alternative first exon splicing. Multiple transcription start sites within TR genes may be relevant to complex regulation of expression and/or organelle- and cell type-specific location of animal thioredoxin reductases.
Pseudomembranous Colitis in a Patient with Cystic Fibrosis (1994)

Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, U.S.A.
Error-correction technique for random-access memories (1982)

On-chip error correction for random-access memories is not very popular because of the high overhead necessary. This paper presents a technique that performs a single-bit correction and a double-bit detection on clocked memories where all column data is internally available, with an area penalty of less than 20 percent. The timing overhead for on-chip implementation is less than the time required to generate a parity bit. The detection and correction operation is transparent to the user and does not require different cycle times for the detection and the correction.
Isotopically selective photochemistry in molecular crystals (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIsotopically selective photochemistry in molecular crystalsRobin M. Hochstrasser and David S. KingCite this: J. Am. Chem. Soc. 1975, 97, 16, 4760–4762Publication Date (Print):August 1, 1975Publication History Published online1 May 2002Published inissue 1 August 1975https://pubs.acs.org/doi/10.1021/ja00849a051https://doi.org/10.1021/ja00849a051research-articleACS PublicationsRequest reuse permissionsArticle Views181Altmetric-Citations67LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A Mechanically Tunable Artificial Magnetic Conductor Using 3-D Printing Technology (2018)

In this paper, a novel rotationally tunable artificial magnetic conductor (AMC) is proposed for antenna enhancements. The designed AMC unit cell consists of two rotational elements which are designed by using 3-D printing technology. The operating frequency range of the multiband AMC shifts as the rotational elements move in different angles. Simulations are carried out in CST Microwave Studio (MWS) in order to demonstrate the phase reflection change by using the proposed mechanical structure. Results show that the proposed AMC provides a stable narrow-band-pass operation bandwidth of 0.2 GHz at low-frequency range and a wide band-pass operation bandwidth of 1.4 GHz at higher frequency ranges. The results also show a stable frequency shift response as rotation angles of incidence go up to 90°. The proposed AMC structure can also provide a band-stop frequency response.
Unified Mobile Protocol Stack with Network Sub-Protocol Component Framework. (2005)

The presence of facial nerve palsy associated with an ipsilateral parotid tumor is virtually pathognomonic for a malignant parotid tumor. However, several case reports have documented the occurrence of facial nerve palsy caused by benign parotid lesions. A case of Warthin's tumor causing facial nerve palsy is presented and discussed histologically. To our knowledge, histological examination of the nerve bundles has never before been reported. The histological findings suggest that ischemia of the nerve caused by external compression resulted in facial nerve palsy.
Voice services concepts for intelligent networks (2002)

The author describes the types of functionalities anticipated for intelligent networks (IN), including the call states involved, the extending and customizing of existing services, user vs. subscriber interface issues, and services interactions. It is suggested that initial services offered using IN will probably be very simple and have few interactions either within IN or with switch-based services. However, as skill in using the IN functionalities grows, so will the number, complexity, and interactions of IN services. Services interactions and user vs. subscriber issues will also be more elegantly handled as experience teaches how and when to use points in call and the assist functionality. Perhaps most encouraging of all is that this learning process is also applicable in defining the types of control structures needed for the other networks and services evolving into the future, such as data, broadband, multimedia, etc.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
MapCHECK used for rotational IMRT measurements: Step‐and‐shoot, Tomotherapy, RapidArc (2010)

When properly modified, the MapCHECK response becomes isotropic. It can then be used for patient-specific QA measurements for IMRT treatments delivered with step-and-shoot and rotational techniques such as helical Tomotherapy and RapidArc.
A Primer on the Signature Method in Machine Learning (2016)

We provide an introduction to the signature method, focusing on its theoretical properties and machine learning applications. Our presentation is divided into two parts. In the first part, we present the definition and fundamental properties of the signature of a path. The signature is a sequence of numbers associated with a path that captures many of its important analytic and geometric properties. As a sequence of numbers, the signature serves as a compact description (dimension reduction) of a path. In presenting its theoretical properties, we assume only familiarity with classical real analysis and integration, and supplement theory with straightforward examples. We also mention several advanced topics, including the role of the signature in rough path theory. In the second part, we present practical applications of the signature to the area of machine learning. The signature method is a non-parametric way of transforming data into a set of features that can be used in machine learning tasks. In this method, data are converted into multi-dimensional paths, by means of embedding algorithms, of which the signature is then computed. We describe this pipeline in detail, making a link with the properties of the signature presented in the first part. We furthermore review some of the developments of the signature method in machine learning and, as an illustrative example, present a detailed application of the method to handwritten digit classification.
A Chemical Genetics Approach for the Discovery of Apoptosis Inducers:From Phenotypic Cell Based HTS Assay and Structure-Activity Relationship Studies, to Identification of Potential Anticancer Agents and Molecular Targets. (2006)

The approach of chemical genetics has been widely used to study biological systems and to discover new drugs, signaling pathways and targets. The current review focuses on the development and utilization of a cell- and caspase-based apoptosis induction assay for the discovery of apoptosis inducers. We began with the development of a cell based phenotypic assay, which was used for the identification of small molecules that exhibit apoptosis inducing activities, including N-phenyl nicotinamides, gambogic acid, indole-2-carboxylic acid benzylidene-hydrazides, 4-aryl-4H-chromenes and 3-aryl-5-aryl-1,2,4-oxadiazoles. Through medicinal chemistry and biological studies, in vivo active compounds were identified, such as MX116407 as a tumor vascular disrupting agent with potent in vivo anticancer activity. The molecular targets of in vivo active compounds were identified using reagents designed and synthesized based on the SAR, including the identification of tail-interacting protein 47 (TIP47), an insulin-like growth factor II (IGF II) receptor binding protein, as the molecular target of 3-aryl-5-aryl-1,2,4-oxadiazoles; and Transferrin receptor I (TfR), a transmembrane protein that interacts with transferrin (Tf) for the transport of iron into cells, as the molecular target of gambogic acid. We demonstrated that chemical genetics is a very useful approach for anticancer drug research, from the discovery of potential drugs, to the understanding of signaling pathways and identification of druggable targets.
FDA Perspective on Companion Diagnostics: An Evolving Paradigm (2014)

Therapeutic products are now being developed that target particular molecular lesions found in various types of cancers. The ability to correctly identify patients whose cancers have targetable lesions generally depends on a well-validated diagnostic test. Development and use of diagnostic tests together with therapies in clinical trials yields the information necessary to make a regulatory determination that both products are safe and effective, likely have clinical utility when used together, and reach the market for patient benefit. This model, called co-development, has been developed relatively recently, and is being put to use in numerous cancer therapeutic development programs. The U.S. Food and Drug Administration (FDA) has articulated a policy that requires the coapproval of a diagnostic with a therapeutic product when the diagnostic is essential to the safe and effective use of the therapeutic product. At the same time, FDA has implemented a number of processes to manage the model without slowing the approval of the co-developed products. New diagnostic technologies, together with a rapid uptick in interest in targeted drugs, will challenge the still-evolving regulatory paradigm, but will likely result in some simplified approaches presenting new challenges in determining safety and effectiveness, but all with the promise of greater benefit to patients with cancer. See all articles in this CCR Focus section, "The Precision Medicine Conundrum: Approaches to Companion Diagnostic Co-development."
Analysis of fluid light valve control layers for high-definition television large picture projection (1985)

Here, proceeding from a previous study, the deformation problem of a viscose fluid is analyzed under simplified conditions as regards the physical model. This viscose fluid is used as the light control organ in the light valve method of large-screen television projection. By using simple approximate relationship, the important properties, such as dynamic behavior, frequency response, stability behavior, and resolution limit of the control layer and their dependence on material and system parameter are discussed in detail. The theoretical knowledge obtained from this analysis agrees to a large extent with the experimental results.
Ghrelin Cells in the Gastrointestinal Tract (2010)

Ghrelin is 28-amino-acid peptide that was discovered from the rat and human stomach in 1999. Since the discovery of ghrelin, various functions of ghrelin, including growth hormone release, feeding behavior, glucose metabolism, memory, and also antidepressant effects, have been studied. It has also been reported that ghrelin in the gastrointestinal tract has an important physiological effect on gastric acid secretion and gastrointestinal motility. Ghrelin has a unique structure that is modified by O-acylation with n-octanoic acid at third serine residues, and this modification enzyme has recently been identified and named ghrelin O-acyl transferase (GOAT). Ghrelin is considered to be a gut-brain peptide and is abundantly produced from endocrine cells in the gastrointestinal mucosa. In the gastrointestinal tract, ghrelin cells are most abundant in the stomach and are localized in gastric mucosal layers. Ghrelin cells are also widely distributed throughout the gastrointestinal tract. In addition, abundance of ghrelin cells in the gastric mucosa is evolutionally conserved from mammals to lower vertebrates, indicating that gastric ghrelin plays important roles for fundamental physiological functions. Ghrelin cells in the gastrointestinal tract are a major source of circulating plasma ghrelin, and thus understanding the physiology of these cells would reveal the biological significance of ghrelin.
Electrolytic model system for reductive dehalogenation in aqueous environments (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectrolytic model system for reductive dehalogenation in aqueous environmentsCraig S. Criddle and Perry L. McCartyCite this: Environ. Sci. Technol. 1991, 25, 5, 973–978Publication Date (Print):May 1, 1991Publication History Published online1 May 2002Published inissue 1 May 1991https://pubs.acs.org/doi/10.1021/es00017a022https://doi.org/10.1021/es00017a022research-articleACS PublicationsRequest reuse permissionsArticle Views322Altmetric-Citations103LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
FPGA Vernier Digital-to-Time Converter With 1.58 ps Resolution and 59.3 Minutes Operation Range (2010)

The first FPGA multiple channel digital-to-time converter, or digital pulse generator, is proposed to further extend FPGA applications into analog domain. Based on vernier principle, the effective resolution is made equivalent to the period difference of two phase-locked loop (PLL) outputs. The finer than ever DTC resolution of 1.58 ps is achieved with an Altera Stratix III FPGA chip. The DNL and INL are verified to be -0.086 ~ +0.12 LSB and -0.93 ~ +0.75 LSB respectively for input value varied from 1 to 1026. The widest operation range of 59.3 minutes is accomplished with 51 functioning input bits. Except for 2 shared PLLs, there are only 422 combinational ALUTs and 84 dedicated logic registers utilized per channel for 224-channel circuit implementation. The power consumption per channel is simulated to be 3.04 mW only. With a simple but powerful structure, the design cost is substantially reduced from those of its predecessors.