gebhart/patrepeval huggingface dataset:
The ER aminopeptidase, ERAP1, trims precursors to lengths of MHC class I peptides by a “molecular ruler” mechanism (2005)

Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an IFN-gamma-induced aminopeptidase in the endoplasmic reticulum that trims longer precursors to the antigenic peptides presented on MHC class I molecules. We recently reported that purified ERAP1 trimmed N-extended precursors but spared peptides of 8-9 residues, the length required for binding to MHC class I molecules. Here, we show another remarkable property of ERAP1: that it strongly prefers substrates 9-16 residues long, the lengths of peptides transported efficiently into the ER by the transporter associated with antigen processing (TAP) transporter. This aminopeptidase rapidly degraded a model 13-mer to a 9-mer and then stopped, even though the substrate and the product had identical N- and C-terminal sequences. No other aminopeptidase, including the closely related ER-aminopeptidase ERAP2, showed a similar length preference. Unlike other aminopeptidases, the activity of ERAP1 depended on the C-terminal residue of the substrate. ERAP1, like most MHC class I molecules, prefers peptides with hydrophobic C termini and shows low affinity for peptides with charged C termini. Thus, ERAP1 is specialized to process precursors transported by TAP to peptides that can serve as MHC class I epitopes. Its "molecular ruler" mechanism involves binding the hydrophobic C terminus of the substrate 9-16 residues away from the active site.
A Distributed Experimental Communications System (1983)

The packet experimental communications system (packet XCS) is a new experimental voice and data switch. It uses a local-area network (LAN) for digital voice transmission, with local intelligence for switching. The packet XCS also has highly distributed control. The individual sites cooperate to provide user services as well as internal data management. We have learned that several local networks, including CSMA/CD networks, can be made to work well for voice transmission and that highly distributed control is practical in such a system. A system has been constructed which is used as a testbed for distributed voice and data communications experiments. This system is purely for experimentation and does not indicate a direction for future Bell System product offerings.
Early cleavage of human embryos: an effective method for predicting successful IVF/ICSI outcome (2001)

Transfer of selected embryos that reached the 2-cell stage between 25 and 29 h post-insemination/ICSI is a reliable prognostic tool for patients undergoing assisted reproduction techniques.
Endothelium-dependent relaxation to aggregating platelets in isolated basilar arteries of control and hypercholesterolemic pigs. (1988)

The role of the endothelium was examined in the response to aggregating platelets in cerebral arteries from normal and hypercholesterolemic animals. Male Yorkshire pigs were fed either a normal diet or a 2% high-cholesterol diet for 10 weeks. Endothelium-dependent responses were examined in vitro. In rings of basilar arteries from control animals aggregating platelets caused endothelium-dependent relaxations, which were significantly inhibited by apyrase, an adenosine diphosphatase and triphosphatase, but were augmented by methiothepin, a combined S1- and S2-serotonergic blocker. In quiescent rings platelets induced contractions that were inhibited by the presence of the endothelium; these contractions were significantly inhibited by methiothepin, but not by ketanserin (an S2-serotonergic blocker) or dazoxiben (a thromboxane-synthetase blocker) in the presence or absence of SQ29548 (a thromboxane-receptor blocker). Adenosine diphosphate but not serotonin caused endothelium-dependent relaxations. In cholesterol-fed animals the endothelium-dependent relaxations in response to aggregating platelets and adenosine diphosphate were impaired. These experiments indicate that 1) the endothelium inhibits the vasoconstrictor effect of aggregating platelets in porcine cerebral arteries; 2) platelet-induced relaxations are achieved mainly by a purinergic mechanism, while platelet-induced contractions are mediated by activation of S1-serotonergic receptors with little contribution of thromboxanes; and 3) hypercholesterolemia impairs the endothelium-dependent relaxations in response to aggregating platelets due to the impaired responses to adenosine diphosphate.
The osmium-catalyzed asymmetric dihydroxylation: a new ligand class and a process improvement (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe osmium-catalyzed asymmetric dihydroxylation: a new ligand class and a process improvementK. Barry Sharpless, Willi Amberg, Youssef L. Bennani, Gerard A. Crispino, Jens Hartung, Kyu Sung Jeong, Hoi Lun Kwong, Kouhei Morikawa, Zhi Min Wang, and Cite this: J. Org. Chem. 1992, 57, 10, 2768–2771Publication Date (Print):May 1, 1992Publication History Published online1 May 2002Published inissue 1 May 1992https://pubs.acs.org/doi/10.1021/jo00036a003https://doi.org/10.1021/jo00036a003research-articleACS PublicationsRequest reuse permissionsArticle Views19709Altmetric-Citations1351LEARN 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
Interpretable Learning for Self-Driving Cars by Visualizing Causal Attention (2017)

Deep neural perception and control networks are likely to be a key component of self-driving vehicles. These models need to be explainable - they should provide easy-to-interpret rationales for their behavior - so that passengers, insurance companies, law enforcement, developers etc., can understand what triggered a particular behavior. Here we explore the use of visual explanations. These explanations take the form of real-time highlighted regions of an image that causally influence the network's output (steering control). Our approach is two-stage. In the first stage, we use a visual attention model to train a convolution network end-to-end from images to steering angle. The attention model highlights image regions that potentially influence the network's output. Some of these are true influences, but some are spurious. We then apply a causal filtering step to determine which input regions actually influence the output. This produces more succinct visual explanations and more accurately exposes the network's behavior. We demonstrate the effectiveness of our model on three datasets totaling 16 hours of driving. We first show that training with attention does not degrade the performance of the end-to-end network. Then we show that the network causally cues on a variety of features that are used by humans while driving.
Heterocyclic Peptide Backbone Modifications in an α-Helical Coiled Coil (2004)

In this paper, we present 1,2,3-triazole epsilon2-amino acids incorporated as a dipeptide surrogate at three positions in the sequence of a known alpha-helical coiled coil. Biophysical characterization indicates that the modified peptides retain much of the helical structure of the parent sequence, and that the thermodynamic stability of the coiled coil depends on the position of the incorporation of the epsilon-residue. Crystal structures obtained for each peptide give insight into the chemical behavior and conformational preferences of the non-natural amino acid and show that the triazole ring can participate in the backbone hydrogen bonding of the alpha-helix as well as template an interhelical crossing between chains in the bundle.
A simple method for determining the modulation transfer function in digital radiography (1992)

The authors developed a simple method for determining the presampling modulation transfer function (MTF). which includes the unsharpness of the detector and the effect of the sampling aperture, in digital radiographic (DR) systems. With this method, the presampling MTF is determined by the Fourier transform of a ;finely sampled' line spread function (LSF) obtained with a slightly angulated slit in a single exposure. Since the effective sampling distance becomes much smaller than the original sampling distance of the DR system, the effect of aliasing on the MTF calculations can be eliminated. The authors applied this method to the measurement of the presampling MTF of a compound radiographic system and examined the directional dependence, the effect of exponential extrapolation, and the effect of different sampling distances. It is shown that the technique of multiple slit exposure and exponential extrapolation of the LSF tail, which has been commonly used in analog seven-film systems, can be employed in DR systems. The authors determined the glare fraction in order to estimate the component of low-frequency drop mainly due to ;glare'
Bayes Optimal Multilabel Classification via Probabilistic Classifier Chains (2010)

In the realm of multilabel classification (MLC), it has become an opinio communis that optimal predictive performance can only be achieved by learners that explicitly take label dependence into account. The goal of this paper is to elaborate on this postulate in a critical way. To this end, we formalize and analyze MLC within a probabilistic setting. Thus, it becomes possible to look at the problem from the point of view of risk minimization and Bayes optimal prediction. Moreover, inspired by our probabilistic setting, we propose a new method for MLC that generalizes and outperforms another approach, called classifier chains, that was recently introduced in the literature.
Anterograde Spread of Herpes Simplex Virus Type 1 Requires Glycoprotein E and Glycoprotein I but Not Us9 (2009)

Anterograde neuronal spread (i.e., spread from the neuron cell body toward the axon terminus) is a critical component of the alphaherpesvirus life cycle. Three viral proteins, gE, gI, and Us9, have been implicated in alphaherpesvirus anterograde spread in several animal models and neuron culture systems. We sought to better define the roles of gE, gI, and Us9 in herpes simplex virus type 1 (HSV-1) anterograde spread using a compartmentalized primary neuron culture system. We found that no anterograde spread occurred in the absence of gE or gI, indicating that these proteins are essential for HSV-1 anterograde spread. However, we did detect anterograde spread in the absence of Us9 using two independent Us9-deleted viruses. We confirmed the Us9 finding in different murine models of neuronal spread. We examined viral transport into the optic nerve and spread to the brain after retinal infection; the production of zosteriform disease after flank inoculation; and viral spread to the spinal cord after flank inoculation. In all models, anterograde spread occurred in the absence of Us9, although in some cases at reduced levels. This finding contrasts with gE- and gI-deleted viruses, which displayed no anterograde spread in any animal model. Thus, gE and gI are essential for HSV-1 anterograde spread, while Us9 is dispensable.
Antigenic Drift in Visna: Virus Variation During Long-term Infection of Icelandic Sheep (1983)

A group of 20 Icelandic sheep were infected intracerebrally with visna virus strain 1514, and 209 virus isolates were obtained from the blood, cerebrospinal fluid, and central nervous system (CNS) over a period of 7 years, during which eight animals developed clinical signs of visna necessitating sacrifice. (i) Using type-specific antisera, it was found that 12 (16%) of 76 isolates tested escaped neutralization. These 12 variant viruses were distributed randomly among animals and over time, and did not replace the infecting strain even though all sheep developed homotypic antibody within 3 months of infection. The one exception was sheep no. 1557 (an animal without clinical visna), where the last six isolates were variants. (ii) A total of 35 blood and CNS isolates from seven of these sheep (including five with clinical visna) were tested against serial samples of their own sera. Autologous antisera neutralized all isolates tested with the exception of isolates from sheep 1557. None of the isolates obtained at sacrifice from the five sheep with clinical visna escaped neutralization with autologous antisera. These data suggest that although variant viruses are encountered at considerable frequency during long-term infection of Icelandic sheep, the variants usually do not replace the infecting strain. Antigenic drift does not appear to be essential for virus persistence or for the development of clinically evident CNS lesions.
Surface-mediated release of a synthetic small-molecule modulator of bacterial quorum sensing: Gradual release enhances activity (2010)

We demonstrate an approach to the surface-mediated release of a synthetic N-acylated L-homoserine lactone (AHL) modulator of bacterial quorum sensing (QS). AHL released gradually from thin films of poly(lactide-co-glycolide) (PLG) is shown to activate QS in the model symbiont Vibrio fischeri at levels that exceed those promoted by direct solution-based administration.
Una formulación de mínimo peso con restricciones en tensión en optimización topológica de estructuras (2012)

El diseño óptimo de estructuras ha estado tradicionalmente orientado a la resolución de problemas de optimización de formas y dimensiones. Sin embargo, más recientemente ha surgido otra rama de investigación que propone modelos que proporcionan soluciones estructurales óptimas y que no requieren la definición previa de la tipología estructural: la optimización topológica de estructuras. Estas formulaciones proporcionan tanto la tipología estructural como la forma y dimensiones óptimas. Las formulaciones más habituales de estos planteamientos pretenden obtener una solución que maximice la rigidez de la estructura dadas unas limitaciones en la cantidad de material a utilizar. Estas formulaciones han sido ampliamente analizadas y utilizadas en la práctica pero presentan inconvenientes muy importantes tanto desde un punto de vista numérico como práctico. En este artículo se propone una formulación diferente a la de máxima rigidez para el problema de optimización topológica de estructuras que minimiza el peso e incorpora restricciones en tensión. Las ventajas de este tipo de planteamientos son muy importantes dado que se minimiza el coste de la solución, que es la situación más habitual en ingeniería, y además se garantiza la validez estructural de la misma. Además esta formulación permite evitar algunos de los problemas e inestabilidades numéricas que presentan las formulaciones de máxima rigidez. Finalmente, se resuelven algunos ejemplos prácticos para comprobar la validez de los resultados y las ventajas que ofrece la formulación propuesta.
Recombinant L-Asparaginase from Zymomonas mobilis: A Potential New Antileukemic Agent Produced in Escherichia coli (2016)

L-asparaginase is an enzyme used as a chemotherapeutic agent, mainly for treating acute lymphoblastic leukemia. In this study, the gene of L-asparaginase from Zymomonas mobilis was cloned in pET vectors, fused to a histidine tag, and had its codons optimized. The L-asparaginase was expressed extracellularly and intracellularly (cytoplasmically) in Escherichia coli in far larger quantities than obtained from the microorganism of origin, and sufficient for initial cytotoxicity tests on leukemic cells. The in silico analysis of the protein from Z. mobilis indicated the presence of a signal peptide in the sequence, as well as high identity to other sequences of L-asparaginases with antileukemic activity. The protein was expressed in a bioreactor with a complex culture medium, yielding 0.13 IU/mL extracellular L-asparaginase and 3.6 IU/mL intracellular L-asparaginase after 4 h of induction with IPTG. The cytotoxicity results suggest that recombinant L-asparaginase from Z. mobilis expressed extracellularly in E.coli has a cytotoxic and cytostatic effect on leukemic cells.
Simple device for the direct visualization of oral-cavity tissue fluorescence (2006)

Early identification of high-risk disease could greatly reduce both mortality and morbidity due to oral cancer. We describe a simple handheld device that facilitates the direct visualization of oral-cavity fluorescence for the detection of high-risk precancerous and early cancerous lesions. Blue excitation light (400 to 460 nm) is employed to excite green-red fluorescence from fluorophores in the oral tissues. Tissue fluorescence is viewed directly along an optical axis collinear with the axis of excitation to reduce inter- and intraoperator variability. This robust, field-of-view device enables the direct visualization of fluorescence in the context of surrounding normal tissue. Results from a pilot study of 44 patients are presented. Using histology as the gold standard, the device achieves a sensitivity of 98% and specificity of 100% when discriminating normal mucosa from severe dysplasia/carcinoma in situ (CIS) or invasive carcinoma. We envisage this device as a suitable adjunct for oral cancer screening, biopsy guidance, and margin delineation.
Measuring Statistical Geometric Properties of Tomographic Images of Soils (2008)

Porous media modeling is relevant in several applications, such as agricultural engineering, where soil compaction analysis requires the estimation of soil transport properties. For example, the prediction of root growing patterns and their environmental impact is usually measured by analyzing soil fluid infiltration capacity and water retention. Recently, tomographic images have been used in nondestructive tests of soil. However, using such images is challenging for two reasons: (1) Tomographic images are usually noisy, which complicates their segmentation, and (2) modeling the soil structure requires establishing adjacency relations among neighboring tomographic slices, which has a significant computational cost due to the combinatorial nature of this problem. In this paper, we propose a solution for both problems. The experimental results show that soil samples can be analyzed and classified with significant accuracy using our proposed approach.
Dopamine Quinones Activate Microglia and Induce a Neurotoxic Gene Expression Profile (2006)

Methamphetamine (METH) intoxication leads to persistent damage of dopamine (DA) nerve endings of the striatum. Recently, we and others have suggested that the neurotoxicity associated with METH is mediated by extensive microglial activation. DA itself has been shown to play an obligatory role in METH neurotoxicity, possibly through the formation of quinone species. We show presently that DA-quinones (DAQ) cause a time-dependent activation of cultured microglial cells. Microarray analysis of the effects of DAQ on microglial gene expression revealed that 101 genes were significantly changed in expression, with 73 genes increasing and 28 genes decreasing in expression. Among those genes differentially regulated by DAQ were those often associated with neurotoxic conditions including inflammation, cytokines, chemokines, and prostaglandins. In addition, microglial genes associated with a neuronally protective phenotype were among those that were downregulated by DAQ. These results implicate DAQ as one species that could cause early activation of microglial cells in METH intoxication, manifested as an alteration in the expression of a broad biomarker panel of genes. These results also link oxidative stress, chemical alterations in DA to its quinone, and microglial activation as part of a cascade of glial-neuronal crosstalk that can amplify METH-induced neurotoxicity.
Conformational Nature of the Borrelia burgdorferi B31 Outer Surface Protein C Protective Epitope (1999)

Active immunization with Escherichia coli-expressed recombinant outer surface protein C (OspC) of Borrelia burgdorferi has been demonstrated to confer protection against a tick-transmitted infection on laboratory animals. A previous study in this laboratory showed that OspC antibody raised against a denatured immunogen isolated from B. burgdorferi cells failed to provide protective immunity. Therefore, to determine whether the protective epitope of the recombinant antigen was sensitive to denaturation, recombinant OspC preparations were subjected to heat and chemical treatments prior to animal immunization. Following seroconversion to OspC, the animals were challenged with an infectious dose of B. burgdorferi B31 by tick bite. Whereas mice immunized with a soluble, nondenatured form continued to show protection rates close to 100%, mice that had been immunized with denatured antigen were not protected. Furthermore, mice that were immunized with an insoluble (rather than a soluble), nondenatured form of the recombinant OspC showed a protection rate of only 40%. Protective epitope localization experiments showed that either the amino or the carboxy end of the recombinant protein was required to react with a protective OspC-specific monoclonal antibody. The data from these experiments demonstrate that a conformational organization of the protein is essential for the protective capability of the strain B31 OspC immunogen.
Characterization of estolides produced from the acid‐catalyzed condensation of oleic acid (1994)

Abstract Estolides produced from an acid‐catalyzed condensation of oleic acid were characterized by high‐performance liquid chromatography (HPLC), gas chromatography (GC), GC‐mass spectrometry (MS) and nuclear magnetic resonance (NMR). C‐8 reverse‐phase HPLC provided a clean resolution of the estolide oligomers present in the reaction mixtures, allowing an average oligomier distribution to be calculated. Corroboration of HPLC results were obtained either through hydrolysis of the estolide mixture and quantitation of the hydroxy fatty acid content by GC, through the integration of the α‐methylene protons adjacent to the carbonyl of the acids vs. the esterns in the 1 H NMR spectrum, or by titration of the carboxylic acid with standardized base. GC and GC‐MS analysis of the hydrolyzed estolide mixture indicated that the ester position were centered around the original double‐bond position, with linkages ranging from positions 5–13. Likewise, the unsaturation was distributed along the fatty acid backbone.
The insect-trapping rim of Nepenthes pitchers (2009)

Carnivorous pitcher plants of the genus Nepenthes capture prey with a pitfall trap that relies on a micro-structured, slippery surface. The upper pitcher rim (peristome) is fully wettable and causes insects to slip by aquaplaning on a thin water film. The high wettability of the peristome is probably achieved by a combination of hydrophilic surface chemistry, surface roughness and the presence of hygroscopic nectar. Insect foot attachment could be prevented by the delayed drainage of the thin water film between the adhesive pad and the surface. Drainage should be faster for insects with a hairy adhesive system; however, they slip equally on the wet peristome. Therefore the stability of the water film against dewetting appears to be the key factor for aquaplaning. New experimental techniques may help to clarify the detailed function of the pitcher plant peristome and to explore its potential for biomimetic applications.