gebhart/patrepeval huggingface dataset:
In vitro simultaneous measurement of refractive index and thickness of biological tissue by the low coherence interferometry (2000)

We proposed and demonstrated in vitro simultaneous measurement of refractive index and thickness of biological tissue. The technique is based on the low coherence interferometry combined with precise translation stages. Refractive indices were determined with the accuracy of less than 1% for tissue samples of a few hundred micron thickness, including chicken tissue, human tooth and nail. Simultaneous measurement of refractive index and thickness of multilayer tissue are also demonstrated.
Human monoclonal anti-T cell antibody from a patient with juvenile rheumatoid arthritis. (1987)

Antibody JRAI is a human monoclonal IgM antibody derived from a patient with juvenile rheumatoid arthritis that is cytotoxic to a subpopulation of normal T lymphocytes. JRAI recognizes approximately 80% of normal peripheral blood T cells, 90% of CD4+ cells, and 75% of CD8+ cells, as determined by complement-mediated cytotoxicity. Within the CD8+ population, JRAI preferentially spares OKM1+ and Leu-11+ cells. These CD8+ cells retain suppressor-effector potential and show enriched natural killer cell activity. Within the CD4+ population, JRAI preferentially kills cells within the Leu-8+ subset, which contains suppressor-inducer cells, and spares the Leu-8- subset, which contains the helpers for immunoglobulin synthesis. JRAI appears to recognize a previously undefined human lymphocyte surface molecule expressed differentially on phenotypically and functionally distinct subsets of human T cells.
Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets (2011)

High-throughput sequencing technologies have strongly impacted microbiology, providing a rapid and cost-effective way of generating draft genomes and exploring microbial diversity. However, sequences obtained from impure nucleic acid preparations may contain DNA from sources other than the sample. Those sequence contaminations are a serious concern to the quality of the data used for downstream analysis, causing misassembly of sequence contigs and erroneous conclusions. Therefore, the removal of sequence contaminants is a necessary and required step for all sequencing projects. We developed DeconSeq, a robust framework for the rapid, automated identification and removal of sequence contamination in longer-read datasets (150 bp mean read length). DeconSeq is publicly available as standalone and web-based versions. The results can be exported for subsequent analysis, and the databases used for the web-based version are automatically updated on a regular basis. DeconSeq categorizes possible contamination sequences, eliminates redundant hits with higher similarity to non-contaminant genomes, and provides graphical visualizations of the alignment results and classifications. Using DeconSeq, we conducted an analysis of possible human DNA contamination in 202 previously published microbial and viral metagenomes and found possible contamination in 145 (72%) metagenomes with as high as 64% contaminating sequences. This new framework allows scientists to automatically detect and efficiently remove unwanted sequence contamination from their datasets while eliminating critical limitations of current methods. DeconSeq's web interface is simple and user-friendly. The standalone version allows offline analysis and integration into existing data processing pipelines. DeconSeq's results reveal whether the sequencing experiment has succeeded, whether the correct sample was sequenced, and whether the sample contains any sequence contamination from DNA preparation or host. In addition, the analysis of 202 metagenomes demonstrated significant contamination of the non-human associated metagenomes, suggesting that this method is appropriate for screening all metagenomes. DeconSeq is available at http://deconseq.sourceforge.net/.
Polymethylated DOTA Ligands. 1. Synthesis of Rigidified Ligands and Studies on the Effects of Alkyl Substitution on Acid−Base Properties and Conformational Mobility (2002)

This work describes the synthesis and the conformational properties of new polymethylated macrocyclic ligands of potential interest for magnetic resonance imaging. M4cyclen, (2S,5S,8S,11S)-2,5,8,11-tetramethyl-1,4,7,10-tetraazacyclododecane, was obtained by cyclotetramerization of (2S)-1-benzyl-2-methylaziridine followed by catalytic hydrogenation. The ligands M4DOTA, [(2S,5S,8S,11S)-4,7,10-tris-carboxymethyl-2,5,8,11-tetramethyl- 1,4,7,10-tetraazacyclododecan-1-yl]acetic acid, and M4DOTMA, (R)-2-[(2S,5S,8S,11S)-4,7,10-tris-((R)-1-carboxyethyl)-2,5,8,11-tetramethyl-1,4,7,10-tetraazacyclododecan-1-yl]propionic acid, were prepared by carboxyalkylation of M4cyclen in the presence of Na(2)CO(3). The triacetic ligand M4DO3A, [(2S,5S,8S,11S)-4,7-bis-carboxymethyl-2,5,8,11-tetramethyl-1,4,7,10-tetraazacyclododecan-1-yl]acetic acid, was obtained in good yields without traces of M4DOTA if NaHCO(3) was the acid scavenger when adding the carboxylic arms. In the same conditions, cyclen yielded M4DOTA in 82% yield. The difference between the reactivity of cyclen and M4cyclen is assigned to the high basicity of the substituted tetraamine as estimated by NMR titration. The one- and two-dimensional (1)H and (13)C NMR spectra of M4DOTA and M4DOTMA in the H(4)L or H(6)L(2+) forms are interpreted as arising from a slow exchange between two elongated geometries in which the methyl substituents are in one of the two possible equatorial-like positions, either close to or away from the carboxylic arms. The axial-like positions are sterically too crowded and cannot be occupied by the methyl groups. An elongated conformation is also adopted by DOTMA, (R)-2-[4,7,10-tris-((R)-carboxyethyl)-1,4,7,10-tetraazacyclododecan-1-yl]propionic acid, in the H(6)L(2+) form. The rigidification of the polymethylated ligands allows a detailed NMR analysis that cannot be carried out on the parent unsubstituted ligand DOTA.
Intraoperative photodynamic therapy for retroperitoneal sarcomas (1988)

A pilot study was done to determine the feasibility of adjuvant photodynamic therapy (PDT) in recurrent retroperitoneal sarcomas. Ten patients, who had recurrences after conventional methods of treatment, had repeated resections of the tumor and intraoperative photodynamic treatment to the tumor bed. The methods and equipment used are detailed. In eight of ten patients, a complete resection was possible, and two patients are alive without recurrence at 28 and 24 months. There were no complications from the therapy. Tumors elicited red fluorescence, which helped in identifying residual tumor areas. Adjuvant PDT is a feasible alternative although its effectiveness should be evaluated further.
Arrestin Interactions with G Protein-coupled Receptors (1995)

Arrestins play an important role in quenching signal transduction initiated by G protein-coupled receptors. To explore the specificity of arrestin-receptor interaction, we have characterized the ability of various wild-type arrestins to bind to rhodopsin, the beta 2-adrenergic receptor (beta 2AR), and the m2 muscarinic cholinergic receptor (m2 mAChR). Visual arrestin was found to be the most selective arrestin since it discriminated best between the three different receptors tested (highest binding to rhodopsin) as well as between the phosphorylation and activation state of the receptor (> 10-fold higher binding to the phosphorylated light-activated form of rhodopsin compared to any other form of rhodopsin). While beta-arrestin and arrestin 3 were also found to preferentially bind to the phosphorylated activated form of a given receptor, they only modestly discriminated among the three receptors tested. To explore the structural characteristics important in arrestin function, we constructed a series of truncated and chimeric arrestins. Analysis of the binding characteristics of the various mutant arrestins suggests a common molecular mechanism involved in determining receptor binding selectivity. Structural elements that contribute to arrestin binding include: 1) a C-terminal acidic region that serves a regulatory role in controlling arrestin binding selectivity toward the phosphorylated and activated form of a receptor, without directly participating in receptor interaction; 2) a basic N-terminal domain that directly participates in receptor interaction and appears to serve a regulatory role via intramolecular interaction with the C-terminal acidic region; and 3) two centrally localized domains that are directly involved in determining receptor binding specificity and selectivity. A comparative structure-function model of all arrestins and a kinetic model of beta-arrestin and arrestin 3 interaction with receptors are proposed.
Injectable iron as a preventative for nutritional anemia in the young pig. (1966)

THAN FOUR DECADES have passed since anemia was associated with iron deficiency in the young pig (26) . 1 Shortly thereafter, it was demonstrated that feeding iron salts to the sow did not delay the onset of anemia in baby pigs (9, 14, 15, and 16).A greater incidence of anemia was reported in pigs reared indoors than in those raised out of doors ( 9).An outside factor was associated with the prevention of anemia in young pigs reared out of doors and on concrete (9 and 14).However, it was soon demonstrated that pigs reared out of doors and on concrete developed anemia as rapidly as those reared indoors ( 13 and 3 5) .Daily doses of 25 mg.iron sulfate and 5 mg.copper sulfate prevented anemia from birth to weaning in young pigs ( 15 and 16), as did larger doses administered weekly (17).Swabbing the sow's udder with solutions containing iron and copper salts also prevented anemia in young pigs ( 14, 17, and 3 5).The role of soil in providing iron to protect pigs against anemia was also demonstrated (7, 8, 12, and 19).From the early 1930's to the 1950's, swine producers and others concerned with nutritional anemia in young pigs sought a method that would greatly reduce the work required to prevent anemia by daily swabbing of the sow's udder with a Sf[turated ferrous sulfate (copperas) solution, daily or weekly administration of iron salts or tablets to individual pigs, or provision of fresh uncontaminated sod.
Blockade of VEGFR1 and 2 Suppresses Pathological Angiogenesis and Vascular Leakage in the Eye (2011)

Our study provides further evidence that both VEGFR1 and 2 mediate pathological angiogenesis and vascular leakage in these models of ocular disease and suggests that antagonist antibodies to these receptor tyrosine kinases (RTKs) are potential therapeutic agents.
Maintaining the Confidentiality of Medical Records Shared over the Internet and the World Wide Web (1997)

The Boston Electronic Medical Record Collaborative is working to develop a system that will use the World Wide Web to transfer computer-based patient information to clinicians in emergency departments. Maintaining adequate confidentiality of these records while still facilitating patient care is paramount to this effort. This paper describes an explicit protocol that would make it possible to electronically identify patients and providers, secure permission for release of records, and track information that is transmitted. It is hoped that other, similar efforts now underway will be able to use and build on this model. Comment on this proposal is invited from all parties with an interest in confidentiality. The system will be used only with "scrubbed" data-data from which all identifiers have been removed-until it is generally agreed that the confidentiality methods proposed here are appropriate and sufficient.
Preventive Effect of Monoclonal Anti-L3T4 Antibody on Development of Diabetes in NOD Mice (1987)

We analyzed the surface phenotypes of infiltrated cells in pancreases of nonobese diabetic (NOD) mice with monoclonal antibodies to mouse lymphocytes. Most of the infiltrated cells were Thy1+ and Ly1+ T-lymphocytes, and most of them were L3T4+ helper T-lymphocyte subsets. To elucidate the role of L3T4+ T-lymphocytes in the development of insulitis and diabetes in NOD mice, we treated the animals with injections of monoclonal anti-L3T4 antibody. Administration of this antibody prevented the insulitis and diabetes in NOD mice. These results lead to conclusions that the L3T4+ helper T-lymphocytes may play an essential role in the pathogenesis of type I diabetes and that the manipulation of the OKT4+ (Leu3+) T-lymphocyte subset, the human homology of L3T4, with monoclonal antibodies may provide effective therapy for human type I diabetes.
Recognition of DNA by Synthetic Antibodies (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRecognition of DNA by Synthetic AntibodiesShana M. Barbas, Peter Ghazal, Carlos F. Barbas III, and Dennis R. BurtonCite this: J. Am. Chem. Soc. 1994, 116, 5, 2161–2162Publication Date (Print):March 1, 1994Publication History Published online1 May 2002Published inissue 1 March 1994https://doi.org/10.1021/ja00084a073RIGHTS & PERMISSIONSArticle Views116Altmetric-Citations19LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (902 KB) Get e-Alerts Get e-Alerts
Classification Accuracy Score for Conditional Generative Models (2019)

Deep generative models (DGMs) of images are now sufficiently mature that they produce nearly photorealistic samples and obtain scores similar to the data distribution on heuristics such as Frechet Inception Distance (FID). These results, especially on large-scale datasets such as ImageNet, suggest that DGMs are learning the data distribution in a perceptually meaningful space and can be used in downstream tasks. To test this latter hypothesis, we use class-conditional generative models from a number of model classes—variational autoencoders, autoregressive models, and generative adversarial networks (GANs)—to infer the class labels of real data. We perform this inference by training an image classifier using only synthetic data and using the classifier to predict labels on real data. The performance on this task, which we call Classification Accuracy Score (CAS), reveals some surprising results not identified by traditional metrics and constitute our contributions. First, when using a state-of-the-art GAN (BigGAN-deep), Top-1 and Top-5 accuracy decrease by 27.9% and 41.6%, respectively, compared to the original data; and conditional generative models from other model classes, such as Vector-Quantized Variational Autoencoder-2 (VQ-VAE-2) and Hierarchical Autoregressive Models (HAMs), substantially outperform GANs on this benchmark. Second, CAS automatically surfaces particular classes for which generative models failed to capture the data distribution, and were previously unknown in the literature. Third, we find traditional GAN metrics such as Inception Score (IS) and FID neither predictive of CAS nor useful when evaluating non-GAN models. Furthermore, in order to facilitate better diagnoses of generative models, we open-source the proposed metric.
Immobilized oxidoreductase as an additive for refolding inclusion bodies: application to antibody fragments (2003)

Three foldases--the apical domain of GroEL (mini-chaperone) and two oxidoreductases (DsbA and DsbC) from Escherichia coli--were studied in refolding a protein with immunoglobulin fold (immunoglobulin-folded protein) that had been produced as inclusion bodies in E.coli. The foldases promoted the refolding of single-chain antibody fragments from denaturant-solubilized and reduced inclusion bodies in vitro, and also effectively functioned as alternatives for labilizing agent and oxidizing reagent in the stepwise dialysis system. Immobilization of the oxidoreductases enhanced refolding and recovery of functional single-chain antibody in the dialysis system, suggesting that immobilized oxidoreductases can be used as an effective additive for refolding immunoglobulin-folded proteins in vitro.
X-ray Structure of the ZnII β-Lactamase from Bacteroides fragilis in an Orthorhombic Crystal Form (1998)

beta-Lactamases are extracellular or periplasmic bacterial enzymes which confer resistance to beta-lactam antibiotics. On the basis of their catalytic mechanisms, they can be divided into two major groups: active-site serine enzymes (classes A, C and D) and the ZnII enzymes (class B). The first crystal structure of a class B enzyme, the metallo-beta-lactamase from Bacillus cereus, has been solved at 2.5 A resolution [Carfi, Pares, Duée, Galleni, Duez, Frère & Dideberg (1995). EMBO J. 14, 4914-4921]. Recently, the crystal structure of the metallo-beta-lactamase from Bacteroides fragilis has been determined in a tetragonal space group [Concha, Rasmussen, Bush & Herzberg (1996). Structure, 4, 823-836]. The structure of the metallo-beta-lactamase from B. fragilis in an orthorhombic crystal form at 2.0 A resolution is reported here. The final crystallographic R is 0.196 for all the 32501 observed reflections in the range 10-2.0 A. The refined model includes 458 residues, 437 water molecules, four zinc and two sodium ions. These structures are discussed with reference to Zn binding and activity. A catalytic mechanism is proposed which is coherent with metallo-beta-lactamases being active with either one Zn ion (as in Aeromonas hydrophila) or two Zn ions (as in B. fragilis) bound to the protein.
Atopic Dermatitis and Atopy (1998)

Atopic dermatitis (AD) is a chronic inflammatory skin disease frequently seen in patients with a personal or family history of asthma and allergic rhinitis. The term atopic dermatitis was first introduced in 1933 by Hill and Sulzberger in recognition of this close association between AD and respiratory allergy. During the past 10 years, there have been extraordinary strides made in our understanding of the immunopathogenesis of allergic diseases. In particular, this constellation of inherited illnesses have now been demonstrated to be associated with activation of a specific group of cytokine genes encompassing interleukin (IL)-3, IL-4, IL-5, IL-13, and granulocyte-macrophage colony-stimulating factor (GM-CSF). The molecular basis for selective activation of this cytokine gene cluster and their immunologic consequences are now actively being pursued by many laboratories. However, it is clear that allergic diseases result from a polygenic inheritance pattern that not only involves cytokine-gene activation but other less-well-defined gene products as well. In addition, the clinical expression of allergic diseases is highly dependent on a complex interaction between the host and its environment, e.g., allergen exposure. This chapter will review some of these recent developments and their clinical implications.KeywordsAtopic DermatitisAllergic RhinitisAllergic DiseaseAllergy Clin ImmunolAtopic DiseaseThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Control and understanding: Owning your home network (2012)

Wireless home networks are increasingly deployed in people's homes worldwide. Unfortunately, home networks have evolved using protocols designed for backbone and enterprise networks, which are quite different in scale and character to home networks. We believe this evolution is at the heart of widely observed problems experienced by users managing and using their home networks. In this paper we investigate redesign of the home router to exploit the distinct social and physical characteristics of the home. We extract two key requirements from a range of ethnographic studies: users desire greater understanding of and control over their networks' behaviour. We present our design for a home router that focuses on monitoring and controlling network traffic flows, and so provides a platform for building user interfaces that satisfy these two user requirements. We describe and evaluate our prototype which uses NOX and OpenFlow to provide per-flow control, and a custom DHCP implementation to enable traffic isolation and accurate measurement from the IP layer. It also provides finer-grained per-flow control through interception of wireless association and DNS resolution. We evaluate the impact of these modifications, and thus the applicability of flow-based network management in the home.
GELDANAMYCIN, A NEW ANTIBIOTIC (1970)

A new crystalline antimicrobial compound, geldanamycin, has been discovered in the culture nitrates of Streptomyces hygroscopicus var. geldanus var. nova. Geldanamycin is moderately active in vitro against protozoa, bacteria and fungi. It is also active against L-1210 and KB cells growing in culture and against the parasite Syphacia ohlevata, in vivo. The fermentation, assay, chromatography and isolation as well as its biological and chemical properties were investigated. On the basis of its physical and chemical properties, geldanamycin is a complex molecule consisting of an unsaturated moiety attached to a quinone.