gebhart/patrepeval huggingface dataset:
Scaling theory of polymer adsorption (1976)

We discuss the equilibrium properties of flexible chains adsorbed on a flat surface, assuming that a) adsorption is weak, resulting in large thicknesses D for the adsorption layer, b) the chains are very long, c) the solvent is good, so that excluded volume effects become important (contrary to an early opinion of Hoeve). The repulsion between monomers are incorporated through a scaling theory which goes beyond the usual mean field (Flory-Huggins) approximations. The central assumption is that polymer concentrations in the first layer and in the next layers scale in the same way, (although they do differ by a constant factor). We can then predict the surface exponents of interest in terms of standard exponents for self avoiding walks; for the latter we use the Flory values. One then finds three regimes of adsorption : (i) In the dilute limit (separate coils) D is independent of the polymerization index N, and varies with the strength of the effective monomer surface attraction (measured by a small parameter δ) according to D ∼ δ -3/2 instead of D ∼ δ-1 in mean field. (ii) There is a semi dilute regime where the coils begin to overlap, but where D remains essentially the same. (iii) The most important case corresponds to the plateau in the adsorption isotherm : here we show that the correlations inside the layer are similar to those in a three dimensional system. Then D ∼ Nδ(ln cB) -1 where cB is the bulk concentration. The dependence on N is stronger than in mean field (D ∼ N1/2) but not incompatible with existant data.
Electron diffraction and Raman studies of the effect of substrate misorientation on ordering in the AlGaInP system (1999)

We report a systematic study of the effect of substrate orientation on the ordering in the AlGaInP system, including the Al0.52In0.48P lattice-matched ternary case. Four AlGaInP/GaAs/AlInP samples were grown by metalorganic vapor phase epitaxy under identical growth conditions on [100] substrates orientated 0°, 2°, 10° and 15° either towards the [110] or the [111] axis. The ordering in both the AlInP and the AlGaInP layers was studied by electron diffraction and the Raman scattering technique. The tendency for ordering decreased with increasing misorientation and is less for (AlxGa1−x)0.52In0.48P than for AlInP. The AlInP was found to spontaneously order even when grown after a completely disordered AlGaInP layer. The Raman results show features correlated to the electron diffraction results and hence we conclude that this technique constitutes a reliable nondestructive means of characterizing this system.
POST: A secure, resilient, cooperative messaging system (2003)

POST is a decentralized messaging infrastructure that supports a wide range of collaborative applications, including electronic mail, instant messaging, chat, news, shared calendars and whiteboards. POST is highly resilient, secure, scalable and does not rely on dedicated servers. Instead, POST is built upon a peer-to-peer (p2p) overlay network, consisting of participants&amp;apos; desktop computers. POST offers three simple and general services, namely (i) secure, single-copy message storage, (ii) metadata based on single-writer logs, and (iii) event notification. We sketch POST&amp;apos;s basic messaging infrastructure and show how POST can be used to construct a cooperative, secure email service called ePOST.
Mass spectrometry in metabolome analysis (2004)

In the post-genomic era, increasing efforts have been made to describe the relationship between the genome and the phenotype in cells and organisms. It has become clear that even a complete understanding of the state of the genes, messages, and proteins in a living system does not reveal its phenotype. Therefore, researchers have started to study the metabolome (or the metabolic complement of functional genomics). Within this context, mass spectrometry (MS) has increasingly occupied a central position in the methodologies developed for determination of the metabolic state. This review is mainly focused on the status of MS in the metabolome field, trying to direct the reader to the main approaches for analysis of metabolites, reviewing basic methodologies in sample preparation, and the most recent MS techniques introduced. Apart from the description of the different methods, this review will try to state a general comparison between the several different techniques that involve MS and metabolite analysis, and will highlight their limitations and preferred applicability.
How to use expert advice (1993)

Article How to use expert advice Share on Authors: Nicolò Cesa-Bianchi View Profile , Yoav Freund View Profile , David P. Helmbold View Profile , David Haussler View Profile , Robert E. Schapire View Profile , Manfred K. Warmuth View Profile Authors Info & Claims STOC '93: Proceedings of the twenty-fifth annual ACM symposium on Theory of ComputingJune 1993 Pages 382–391https://doi.org/10.1145/167088.167198Online:01 June 1993Publication History 71citation406DownloadsMetricsTotal Citations71Total Downloads406Last 12 Months8Last 6 weeks3 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Discriminative persistent homology of brain networks (2011)

It is known that the brain network has small-world and scale-free topology, but the network structures drastically change depending on how to threshold a connectivity matrix. The exact threshold criterion is difficult to determine. In this paper, instead of trying to determine one fixed optimal threshold, we propose to look at the topological changes of brain network while increasing the threshold continuously. This process of continuously changing threshold level and looking at the resulting topological feature is related to the Rips filtration in persistent homology. The sequence of topological features obtained during the Rips filtration can be visualized and interpreted using barcode. As an illustration, we apply the Rips filtration to construct the FDG-PET based functional brain networks out of 24 attention deficit hyperactivity disorder (ADHD) children, 26 autism spectrum disorder (ASD) children and 11 pediatric control subjects. We visually show the topological evolution of the brain networks using the barcode and perform statistical inference on the group differences. This is the first paper that deals with the persistence homology of the brain networks.
Heterocyclic Sulfur Compounds-Cv 1,2-Dihmtdro-3,1,2,γ5-Benzothiazaphosphinine-2,4-Dithiones—A New Synthetic Route to 2-Arylamino-Thiobenzamides and To 2-(2-Arylaminophenyl)-4,5-Dihydrothiazoles (Or Oxazoles) (1986)

Abstract 2-Alkoxy-1-aryl-1,2-dihydro-3,1,2γ-benzothiazaphosphinint-2,4-dithiones react with a primary or secondary alkylamine and an alcohol giving a 2-arylaminc-thiobenzamide and an O,O-dialkyl alkylammonium dithiophosphate. Ethane-1,2-diamine and propanc-1,3-diamine, with the same reagents, give a 2,2′-bis-(arylamino)-N,N'-di(or tri)methylenebis(thiobenzamide) accompanied, respectively, by a 242-arylaminophenyl)-4,5-dihydrc-1H-imidazole or by a 2-(2-arylaminophenyl)-1,4,5,6-tetrahydropyrimidine. In similar conditions, 2-amincethanol leads to the expected thiobenzamide. often accompanied by a 2-(2-arylaminophenyl)4,5-dihydrooxazole. With 2-amino-ethanethiol, a 2-(2-arylaminophenyl)-4.5-dihydrothazole is obtained.
Oncogenic Isocitrate Dehydrogenase Mutations: Mechanisms, Models, and Clinical Opportunities (2013)

Heterozygous mutations in catalytic arginine residues of isocitrate dehydrogenases 1 and 2 (IDH1 and IDH2) are common in glioma, acute myeloid leukemia, chondrosarcoma, cholangiocarcinoma, and angioimmunoblastic T-cell lymphoma. The mutant enzymes acquire a neomorphic activity that converts α-ketoglutarate (α-KG) to D-2-hydroxyglutarate (D2HG), a rare metabolite. In cells and tissues expressing mutant IDH, D2HG concentrations are highly elevated. D2HG may act as an "oncometabolite" by inhibiting a class of α-KG-dependent enzymes involved in epigenetic regulation, collagen synthesis, and cell signaling. Knock-in mouse models of IDH1 mutations have shed light on these mechanisms and will provide valuable animal models for further investigation.
Probing the combining site of an anti-carbohydrate antibody by saturation-mutagenesis: Role of the heavy-chain CDR3 residues (1993)

The carbohydrate-binding site in Fab fragments of an antibody specific for Salmonella serogroup B O-polysaccharide has been probed by site-directed mutagenesis using an Escherichia coli expression system. Of the six hypervariable loops, the CDR3 of the heavy chain was selected for exhaustive study because of its significant contribution to binding-site topography. A total of 90 mutants were produced and screened by an affinity electrophoresis/Western blotting method. Those of particular interest were further characterized by enzyme immunoassay, and on this basis seven of the mutant Fabs were selected for thermodynamic characterization by titration microcalorimetry. With regard to residues that hydrogen bond to ligand through backbone interactions, Gly102H could not be substituted, while several side chains could be introduced at Gly100H and Tyr103H with relatively little effect on antigen binding. There was, however, a preference for nonpolar side chains at position 103H. Substitution of His101H with carboxylate and amide side chains gave mutants with binding affinities approaching that of the wild type; complete side-chain removal by mutation to Gly was tolerated with a 10-fold reduction in binding constant. Analysis of binding by titration microcalorimetry revealed some dramatic thermodynamic changes hidden by the similarity of the binding constants. Similar effects were observed with residue changes in an Arg-Asp salt-bridge at the base of the loop. These results indicate that alterations to higher affinity anti-carbohydrate antibodies are characterized by an enthalpy-entropy compensation factor which allows for fundamental changes in the nature of the binding interactions but impedes engineering for increases in affinity.
Pathophysiologic and Transcriptomic Analyses of Viscerotropic Yellow Fever in a Rhesus Macaque Model (2014)

Infection with yellow fever virus (YFV), an explosively replicating flavivirus, results in viral hemorrhagic disease characterized by cardiovascular shock and multi-organ failure. Unvaccinated populations experience 20 to 50% fatality. Few studies have examined the pathophysiological changes that occur in humans during YFV infection due to the sporadic nature and remote locations of outbreaks. Rhesus macaques are highly susceptible to YFV infection, providing a robust animal model to investigate host-pathogen interactions. In this study, we characterized disease progression as well as alterations in immune system homeostasis, cytokine production and gene expression in rhesus macaques infected with the virulent YFV strain DakH1279 (YFV-DakH1279). Following infection, YFV-DakH1279 replicated to high titers resulting in viscerotropic disease with ∼72% mortality. Data presented in this manuscript demonstrate for the first time that lethal YFV infection results in profound lymphopenia that precedes the hallmark changes in liver enzymes and that although tissue damage was noted in liver, kidneys, and lymphoid tissues, viral antigen was only detected in the liver. These observations suggest that additional tissue damage could be due to indirect effects of viral replication. Indeed, circulating levels of several cytokines peaked shortly before euthanasia. Our study also includes the first description of YFV-DakH1279-induced changes in gene expression within peripheral blood mononuclear cells 3 days post-infection prior to any clinical signs. These data show that infection with wild type YFV-DakH1279 or live-attenuated vaccine strain YFV-17D, resulted in 765 and 46 differentially expressed genes (DEGs), respectively. DEGs detected after YFV-17D infection were mostly associated with innate immunity, whereas YFV-DakH1279 infection resulted in dysregulation of genes associated with the development of immune response, ion metabolism, and apoptosis. Therefore, WT-YFV infection is associated with significant changes in gene expression that are detectable before the onset of clinical symptoms and may influence disease progression and outcome of infection.
Preimplantation genetic testing for Marfan syndrome (1996)

Marfan syndrome (MFS) is an autosomal dominant disease that affects the skeletal, ocular and cardiovascular systems. Defects in the gene that codes for fibrillin (FBN-1) are responsible for MFS. Here we report the world's first use of preimplantation genetic testing (PGT) to achieve a clinical pregnancy and live birth of a baby free of a Marfan mutation. One or two blastomeres from each embryo were tested for a CA repeat within the FBN-1 gene. The prospective mother is homozygous for the CA repeat (2/2) and has two normal copies of the FBN-1 gene, while the prospective father is heterozygous for the CA repeat (1/2), and is affected with the Marfan syndrome. In the father's family, allele 2 segregates with the mutated FBN-1 gene. For PGT, any embryo diagnosed as heterozygous for the CA repeat (1/2) would be presumed to have inherited normal FBN-1 genes from the father and the mother and be unaffected. One in-vitro fertilization (IVF) cycle yielded 12 embryos for preimplantation testing; six of the embryos were heterozygous for the CA repeat (1/2) and presumed to be free of the Marfan mutation. Five of the six embryos were subsequently transferred into the uterus. The fetus was tested by chorionic villus sampling and found to be free of the Marfan mutation by the same linkage analysis, had a normal fetal echocardiogram, and was normal at birth.
Models for asymmetric [2+2] cycloadditions (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTModels for asymmetric [2+2] cycloadditionsC. Houge, A. M. Frisque-Hesbain, A. Mockel, L. Ghosez, J. P. Declercq, G. Germain, and M. Van MeersscheCite this: J. Am. Chem. Soc. 1982, 104, 10, 2920–2921Publication Date (Print):May 1, 1982Publication History Published online1 May 2002Published inissue 1 May 1982https://pubs.acs.org/doi/10.1021/ja00374a036https://doi.org/10.1021/ja00374a036research-articleACS PublicationsRequest reuse permissionsArticle Views716Altmetric-Citations76LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Double-graphene-layer terahertz laser: concept, characteristics, and comparison (2013)

We propose and analyze the concept of injection terahertz (THz) lasers based on double-graphene-layer (double-GL) structures utilizing the resonant radiative transitions between GLs. We calculate main characteristics of such double-GL lasers and compare them with the characteristics of the GL lasers with intra-GL interband transitions. We demonstrate that the double-GL THz lasers under consideration can operate in a wide range of THz frequencies and might exhibit advantages associated with the reduced Drude absorption, weaker temperature dependence, voltage tuning of the spectrum, and favorable injection conditions.
Activated T–cell-mediated Immunotherapy With a Chimeric Receptor Against CD38 in B-cell Non-Hodgkin Lymphoma (2009)

T-cell-mediated immunotherapy with a chimeric antigen receptor (CAR) is expected to become a powerful treatment for cancer. CD38, highly expressed in B-cell non-Hodgkin lymphoma (B-NHL) cells, is an attractive target in immunotherapy for B-NHL. We retrovirally transduced a T-cell line, Hut78, expressing little CD38, with an anti-CD38-CAR. Hut78 cells with the anti-CD38-CAR were cocultured with B-NHL cell lines bearing CD38 and also B-NHL cells from patients. Four days later most of the lymphoma cells were killed (the level of cytotoxicity was >95%). By contrast, there was undetectable cytotoxicity against CD38-negative cell lines. Then, we introduced the anti-CD38-CAR into human peripheral T cells. However, the recovery of viable cells was very low, presumably because of an autolytic reaction caused by the association of the anti-CD38-CAR with CD38 on the cell surface. The addition of an anti-CD38 antibody increased the yield of viable transduced T cell probably by blocking the autolytic reaction. We cocultured human peripheral T cells bearing anti-CD38-CAR with B-NHL cells. The median specific cytotoxicity was greater than 90%. These cells were injected 4 times into NOD/SCID mice, which were inoculated with B-NHL cells luciferase. Luciferase activity was not detectable even 30 days after the inoculation in 5 of 6 mice injected. By contrast, it increased in all of the mice injected with the mock vector-transduced T cell. In conclusion, T cell with the anti-CD38-CAR showed powerful cytotoxicity against B-NHL cells in vitro and in vivo. These findings may provide an important clue for improving the methodology of T-cell-mediated immunotherapy.
History-less checking of dynamic integrity constraints (2003)

An efficient implementation method is described for dynamic integrity constraints formulated in past temporal logic. Although the constraints can refer to past states of the database, their checking does not require that the entire database history be stored. Instead, every database state is extended with auxiliary relations that contain the historical information necessary for checking constraints. Auxiliary relations can be implemented as materialized relational views. The author analyzes the computational cost of the method and outlines how it can be implemented by using existing database technology. Related work on dynamic integrity constraints is surveyed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Electrophoretic transfer of DNA, RNA and protein onto diazobenzyloxymethyl (DBM) - paper (1980)

A method has been developed for the electrophoretic transfer of DNA, RNA, protein and ribonucleoprotein particles from a variety of gels onto diazobenzyloxymethyl (DBM) - paper. Conditions for the electrophoretic transfer of these macromolecules have been optimized to allow for nearly quantitative transfer and covalent coupling. DNA and RNA electrophoretically transferred to DBM-paper retain their ability to hybridize with specific probes. The high efficiency of transfer and the high capacity of DBM-paper for nucleic acids makes possible the sensitive detection of specific nucleotide sequences. Similar efficiency is achieved in electrophoretic transfer and covalent coupling of proteins to DBM-paper. Macromolecules can also be electrophoretically transferred and bound to DBM-paper incapable of covalent bond formation. Their elution from the paper in high salt provides a new and useful preparative method for isolation of DNA, RNA and protein.
Development of complement therapeutics for inhibition of immune‐mediated red cell destruction (2005)

A major objective of my National Blood Foundation (NBF)-funded proposal was to produce recombinant soluble forms of a complement regulatory protein called complement receptor 1 (CR1) that carries the Knops blood group system antigens to perform antibody neutralization studies. By generating these recombinant proteins, we were able to inhibit several Knops antibodies in patient serum samples, thereby demonstrating their usefulness for clinical use. Interestingly, the recombinant CR1 proteins generated through NBF funding were also found to strongly reduce complement-mediated red cell destruction in a mouse hemolytic transfusion model. In this review, I will outline our NBF-funded studies, give an overview of recent advances from our group and others in the development of complement therapeutics, and highlight their potential use in the transfusion medicine setting.
The Crystal Structure Analysis of d(CGCGAASSCGCG)2, a Synthetic DNA Dodecamer Duplex Containing Four 4'-Thio-2'-Deoxythymidine Nucleotides (1996)

The crystal structure refinement of the synthetic dodecamer d(CGCGAASSCGCG), where S = 4'-thio-2'-deoxythymidine, has converged at R=0.201 for 2605 reflections with F > 2sigma(F) in the resolution range 8.0-2.4 A for a model consisting of the dodecamer duplex and 66 water molecules. A comparison of its structure with that of the native dodecamer d(CGCGAATTCGCG) has revealed that the major differences between the two structures is a change in the conformation of the sugar-phosphate backbone in the regions at and adjacent to the positions of the modified nucleosides. Examination of the fine structural parameters for each of the structures reveals that the thiosugars adopt a C3'-exo conformation in d(CGCGAASSCGCG), rather than the approximate C1'-exo conformation found for the analogous sugars in the structure of d(CGCGAATTCGCG). The observed differences in structure between the two duplexes may help to explain the enhanced resistance to nuclease digestion of synthetic oligonucleotides containing 4'-thio-2'-deoxynucleotides.
Coherent ray tracing via stream filtering (2008)

We introduce an approach to coherent ray tracing based on a new stream filtering algorithm. This algorithm, which is motivated by breadth-first ray traversal and elimination of inactive ray elements, exploits the coherence exhibited by processing arbitrarily-sized groups of rays in SIMD fashion. These groups are processed by a series of filters that partition rays into active and inactive subsets throughout the various stages of the rendering process. We present results obtained with a detailed cycle-accurate simulation of a hardware architecture that supports wider-than-four SIMD processing and efficient scatter/gather memory and stream partitioning operations. In this context, stream filtering achieves frame rates of 15-25 fps for scenes of high geometric complexity rendered with path tracing and a variety of advanced visual effects.
A Survey of Data Mining and Machine Learning Methods for Cyber Security Intrusion Detection (2015)

This survey paper describes a focused literature survey of machine learning (ML) and data mining (DM) methods for cyber analytics in support of intrusion detection. Short tutorial descriptions of each ML/DM method are provided. Based on the number of citations or the relevance of an emerging method, papers representing each method were identified, read, and summarized. Because data are so important in ML/DM approaches, some well-known cyber data sets used in ML/DM are described. The complexity of ML/DM algorithms is addressed, discussion of challenges for using ML/DM for cyber security is presented, and some recommendations on when to use a given method are provided.