gebhart/patrepeval huggingface dataset:
Structural Protein Relationships Among Eastern Equine Encephalitis Viruses (1994)

We have re-evaluated the relationships among the polypeptides of eastern equine encephalitis (EEE) viruses using SDS-PAGE and peptide mapping of individual virion proteins. Four to five distinct polypeptide bands were detected upon SDS-PAGE analysis of viruses: the E1, E2 and C proteins normally associated with alphavirus virions, as well as an additional more rapidly-migrating E2-associated protein and a high M(r) (HMW) protein. In contrast with previous findings by others, the electrophoretic profiles of the virion proteins of EEE viruses displayed a marked correlation with serotype. The protein profiles of the 33 North American (NA)-serotype viruses examined were remarkably homogeneous, with variation detected only in the E1 protein of two isolates. In contrast, considerable heterogeneity was observed in the migration profiles of both the E1 and E2 glycoproteins of the 13 South American (SA)-type viruses examined. Peptide mapping of individual virion proteins using limited proteolysis with Staphylococcus aureus V8 protease confirmed that, in addition to the homogeneity evident among NA-type viruses and relative heterogeneity among SA-type viruses, the E1 and E2 proteins of NA- and SA-serotype viruses exhibited serotype-specific structural variation. The C protein was highly conserved among isolates of both virus serotypes. Endoglycosidase analyses of intact virions did not reveal substantial glycosylation differences between the glycoproteins of NA- and SA-serotype viruses. Both the HMW protein and the E2 protein (doublet) of EEE virus appeared to contain, at least in part, high-mannose type N-linked oligosaccharides. No evidence of O-linked glycans was found on either the E1 or the E2 glycoprotein. Despite the observed structural differences between proteins of NA- and SA-type viruses, Western blot analyses utilizing polyclonal antibodies indicated that immunoreactive epitopes appeared to be conserved.
Detection and identification of volatile compounds evolved from human hair and scalp using headscape gas chromatography (1988)

Headspace sampling methods, both static and dynamic in conjunction with gas chromatography or GC/MS, were developed to collect volatile species from human hair and scalp. A number of compounds were detected and almost all subsequently identified. The latter belong to various chemical classes such as alkanes, alkenes, alcohols, aldehydes, ketones, acids, and 3'-lactones. A chiral chromatographic system was developed, capable of resolving the enantiomeric pairs of 3'-lactones. The samples collected from human hair and scalp were found to contain racemic mixtures of 3'-lactones. Basically, the same volatile species were encountered in all subjects over an experimental population, but large differences were observed in their amount and distribution from one subject to another. These species are believed to derive from skin surface lipids through oxidative processes which may be purely physicochemical in nature but could also involve some microbiological activity of the resident flora.
Transient isotachophoresis for sensitivity enhancement in capillary electrophoresis-mass spectrometry for peptide analysis (2000)

Transient isotachophoresic (ITP) focusing was used for the on-line analysis of peptides by capillary zone electrophoresis-mass spectrometry (CZE-MS), allowing injection volumes of up to 0.9 microL. A sheath liquid electrospray interface was used with a single quadrupole mass analyzer. First, the technique was applied to the qualitative analysis of a tryptic digest of cytochrome c, resulting in low-background, high-quality spectra. Second, the linear range was investigated by selected ion monitoring (SIM) for a peptidomimetic direct thrombin inhibitor melagatran (Mr 429.5) and two endogenous peptides, substance P (Mr 1348) and calcitonin gene-related peptide (alpha-CGRP; Mr 3806).
Kinetic equivalence of stable-isotope-labeled and unlabeled phenytoin (1981)

Stable isotope labeling (SIL) of a drug results in a higher molecular weight than that of the unlabeled drug. SIL tracer doses can be quantitated separately from unlabeled drug by gas chromatography-mass spectrometry (GC-MS) without exposing the patient to radiation. The higher molecular weight of SIL drug could cause a higher energy of activation for (and slowing of) metabolic reactions ("isotope effect"). To evaluate possible isotope effect, three dogs and three men were infused with a mixture containing equal amounts of SIL (2-13C-1,3-15N2) and unlabeled phenytoin (PHT). Plasma and urine were collected at regular intervals. Concentrations of SIL and unlabeled PHT and HPPH (the major metabolite of PHT) were determined by GC-MS. Within each subject there was no trend for concentrations of SIL PHT or HPPH to be higher or lower than concentrations of their unlabeled analogs (greater than 0.20 to 0.90). There was no difference in the distribution and elimination half-lifes (t 1/2s), volume of distribution, volume of central compartment, or clearance of the two forms of PHT. Thus, no isotope effect was found.
Attention-based Deep Multiple Instance Learning (2018)

Multiple instance learning (MIL) is a variation of supervised learning where a single class label is assigned to a bag of instances. In this paper, we state the MIL problem as learning the Bernoulli distribution of the bag label where the bag label probability is fully parameterized by neural networks. Furthermore, we propose a neural network-based permutation-invariant aggregation operator that corresponds to the attention mechanism. Notably, an application of the proposed attention-based operator provides insight into the contribution of each instance to the bag label. We show empirically that our approach achieves comparable performance to the best MIL methods on benchmark MIL datasets and it outperforms other methods on a MNIST-based MIL dataset and two real-life histopathology datasets without sacrificing interpretability.
Giant tunneling magnetoresistance with electron beam evaporated MgO barrier and CoFeB electrodes (2010)

Electron-beam (EB) evaporated MgO grows with (001) texture on amorphous CoFeB when the deposition rate is kept below 5 pm/s. Magnetic tunnel junctions (MTJs) fabricated using this method exhibit ∼240% magnetoresistance at room temperature for a 2.5 nm thick EB-MgO barrier, which is similar to the value for a radio frequency (rf) sputtered barrier with the same junction geometry. The average barrier height of the EB-MgO is 0.48 eV, which is higher than previously reported values for rf-MgO barriers and it increases with increasing annealing temperature. Our results show that EB-MgO could be a simpler alternative to rf-MgO in MTJs without any compromise in the tunnelling magnetoresistance.
Microarray Analysis of Changes in mRNA Levels in the Rat Retina after Experimental Elevation of Intraocular Pressure (2004)

The activation of glia and the complement system after IOP elevation, which is similar to that described in several neurodegenerative diseases and after optic nerve transection, suggests that this rat glaucoma model could be used to evaluate the neuroprotective potential of therapeutic agents that target these processes.
Secure in-band wireless pairing (2011)

This paper presents the first wireless pairing protocol that works in-band, with no pre-shared keys, and protects against MITM attacks. The main innovation is a new key exchange message constructed in a manner that ensures an adversary can neither hide the fact that a message was transmitted, nor alter its payload without being detected. Thus, any attempt by an adversary to interfere with the key exchange translates into the pairing devices detecting either invalid pairing messages or an unacceptable increase in the number of such messages. We analytically prove that our design is secure against MITM attacks, and show that our protocol is practical by implementing a prototype using off-the-shelf 802.11 cards. An evaluation of our protocol on two busy wireless networks (MIT’s campus network and a reproduction of the SIGCOMM 2010 network using traces) shows that it can effectively implement key exchange in a real-world environment. 1
Development of a New Lewis Acid-Catalyzed Claisen Rearrangement (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTDevelopment of a New Lewis Acid-Catalyzed Claisen RearrangementTehshik P. Yoon, Vy M. Dong, and David W. C. MacMillanView Author Information Department of Chemistry, University of California, Berkeley, California 94720 Cite this: J. Am. Chem. Soc. 1999, 121, 41, 9726–9727Publication Date (Web):October 4, 1999Publication History Received14 June 1999Published online4 October 1999Published inissue 1 October 1999https://pubs.acs.org/doi/10.1021/ja9919884https://doi.org/10.1021/ja9919884rapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views6036Altmetric-Citations84LEARN 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 (2)»Supporting Information Supporting Information SUBJECTS:Adducts,Allyl group,Anions,Metals,Rearrangement Get e-Alerts
Towards Fully Optimized BICM Transceivers (2011)

Bit-interleaved coded modulation (BICM) transceivers often use equally spaced constellations and a random interleaver. In this paper, we propose a new BICM design, which considers hierarchical (nonequally spaced) constellations, a bit-level multiplexer, and multiple interleavers. It is shown that this new scheme increases the degrees of freedom that can be exploited in order to improve its performance. Analytical bounds on the bit error rate (BER) of the system in terms of the constellation parameters and the multiplexing rules are developed for the additive white Gaussian Noise (AWGN) and Nakagami-m fading channels. These bounds are then used to design the BICM transceiver. Numerical results show that, compared to conventional BICM designs, and for a target BER of 10^{-6}, gains up to 3 dB in the AWGN channel are obtained. For fading channels, the gains depend on the fading parameter, and reach 2 dB for a target BER of 10^{-7} and m=5.
Healthcare II: multi-objective simulation optimization for a cancer treatment center (2001)

This paper presents a case study application of a cancer treatment center facility. A simulation model was created and integrated to a multi-objective optimization heuristic developed by the authors with the purpose of finding the best combination of control variables that optimize the performance of four different objectives related to the system. The results obtained show that the implementation of the proposed solution could improve the four objectives in comparison to the existing solution.
Determination of Absolute Counts of Circulating Regulatory T Cells in Cynomolgus Macaques Using an Optimized Flow Cytometric Method (2011)

Regulatory T cells (Tregs) are a rare subset of lymphocytes that inhibit the activation and effector functions of T cells and are important regulators of immune responses. Although Tregs are well characterized in humans and rodents, little is known about their immunophenotyping (IP) profile in cynomolgus macaques (Macaca fascicularis), which is an important species for pharmacological and toxicological evaluation of potential immune modulators because of their similar physiologic, genetic, and metabolic response patterns to humans. The authors have developed an immunophenotyping panel using a high-throughput 96-well microtiter plate-based assay to detect circulating Tregs (CD3(+)CD4(+)CD25(hi)FoxP3(+)) and have determined the normal range for the number of Tregs in naive healthy cynomolgus macaques to be 56.4 to 179.7 cells/µL (mean ± SEM = 113.6 ± 5.1 cells/µL; n = 25). Furthermore, the authors compared the resulting FoxP3(+) Treg profiles with a CD127(lo) cell-surface panel (CD3(+)CD4(+)CD25(hi) CD127(lo)) and found a close correlation between the absolute numbers of CD3(+)CD4(+)CD25(hi)FoxP3(+) and CD3(+)CD4(+)CD25(hi)CD127(lo) cells (mean ± SD = 120 ± 8.0 cells/µL). Quantification of circulating Tregs in cynomolgus macaques in this high-throughput assay may help to identify drug candidates that affect this rare, but critical, immunoregulatory cell population.
Regulation of Helminth-Induced Th2 Responses by Thymic Stromal Lymphopoietin (2009)

Thymic stromal lymphopoietin was recently identified as a master switch for the development of allergen-driven Th2 responses. However, the role of thymic stromal lymphopoietin (TSLP) in the development of helminth-induced Th2 responses is unclear. Here, using TSLPR(-/-) mice, we show that while TSLPR signaling participates in the development of Schistosoma mansoni egg-induced CD4(+) Th2 responses, it plays only a transient role in the development of Th2-dependent pathology in the lung, liver, and intestine. Studies conducted in a pulmonary granuloma model showed that while a reduction in IL-4/IL-13-dependent granulomatous inflammation and tissue eosinophilia was observed in TSLPR(-/-) mice undergoing a primary response, lesion formation was not affected during a secondary granulomatous response, even though IL-5 and IL-13 were modestly reduced in the knockout mice. To evaluate the importance of TSLPR signaling in the development of a chronic Th2-dependent response, TSLPR(-/-) mice were also infected with S. mansoni cercariae. Here, the only significant difference noted in TSLPR(-/-) mice was a modest decrease in liver fibrosis in acutely infected animals. The transient decrease in fibrosis was associated with increased production of the antifibrotic cytokine IFN-gamma and decreased production of the profibrotic cytokine IL-13. Although the altered cytokine response persisted in chronically infected TSLPR(-/-) mice, it failed to reduce granuloma formation or fibrosis, confirming that TSLPR signaling plays a limited role in the development of chronic Th2-dependent pathology. Collectively, these findings suggest that while TSLPR signaling serves a key role in allergen-driven Th2 responses, it exerts minor regulatory activity during this chronic helminth infection.
Formalising key distribution in the presence of trust using object-Z (2003)

Key distribution and trust management are two areas of interest in the world of internet security and are often merged to provide key distribution in the presence of trust relationships. We present two generic models using the Object-Z formalism, one for key distribution and another for trust management, and we show how the models can be combined via inheritance to produce concise models of key distribution in the presence of trust. We use Pretty Good Privacy as a specific example.
Sepsis and Postanesthetic Hepatitis (1972)

LOMANTO, CHARLES M.D.; HUVOS, ANDREW G. M.D.; FIOCCO, GUY P.; HOWLAND, WILLIAM S. M.D. Author Information
meso Epoxides in Asymmetric Synthesis: Enantioselective Opening by Nucleophiles in the Presence of Chiral Lewis Acids (1992)

The metal center coordinates to the epoxide oxygen atom, and the chiral ligand environment enables a nucleophile to discriminate between the formally enantiotopic carbon–oxygen bonds. The method developed by W. A. Nugent functions along this principle: the reaction of a range of meso epoxides with tri-alkylsilyl azides can be catalyzed by a new chiral Lewis acid derived from zirconium and gives β-azido alcohols in very good enantiomeric excesses. Nu = N3, R1R2 = CH3, (CH2)4, etc.
Beta-Cell Defence and Repair Mechanisms in Human Pancreatic Islets (1996)

In vivo and in vitro data obtained in rodents indicate that beta-cells can trigger efficient repair mechanisms following non-lethal injury. Recent observations suggest that human pancreatic islets are more resistant than rodent islets to damage by alkylating agents, free oxygen radicals, nitric oxide and cytokines. This increased resistance to injury is associated with higher expression of heat shock protein 70, catalase and superoxide dismutase. These findings emphasise the potential relevance of beta-cell repair and/or defence mechanisms in the development of human IDDM.
Human-Restricted Bacterial Pathogens Block Shedding of Epithelial Cells by Stimulating Integrin Activation (2010)

Colonization of mucosal surfaces is the key initial step in most bacterial infections. One mechanism protecting the mucosa is the rapid shedding of epithelial cells, also termed exfoliation, but it is unclear how pathogens counteract this process. We found that carcinoembryonic antigen (CEA)-binding bacteria colonized the urogenital tract of CEA transgenic mice, but not of wild-type mice, by suppressing exfoliation of mucosal cells. CEA binding triggered de novo expression of the transforming growth factor receptor CD105, changing focal adhesion composition and activating beta1 integrins. This manipulation of integrin inside-out signaling promotes efficient mucosal colonization and represents a potential target to prevent or cure bacterial infections.
Binding of acylated peptides and fatty acids to phospholipid vesicles: Pertinence to myristoylated proteins (1993)

We studied the binding of fatty acids and acylated peptides to phospholipid vesicles by making electrophoretic mobility and equilibrium dialysis measurements. The binding energies of the anionic form of the fatty acids and the corresponding acylated glycines were identical; the energies increased by 0.8 kcal/mol per number of carbons in the acyl chain (Ncarbon = 10, 12, 14, 16), a value identical to that for the classical entropy-driven hydrophobic effect discussed by Tanford [The Hydrophobic Effect (1980) Wiley, New York]. The unitary Gibbs free binding energy, delta Gou, of myristoylated glycine, 8 kcal/mol, is independent of the nature of the electrically neutral lipids used to form the vesicles. Similar binding energies were obtained with other myristoylated peptides (e.g., Gly-Ala, Gly-Ala-Ala). The 8 kcal/mol, which corresponds to an effective dissociation constant of 10(-4) M for myristoylated peptides with lipids, provides barely enough energy to attach a myristoylated protein in the cytoplasm to the plasma membrane. Thus, other factors that reduce (e.g., hydrophobic interaction of myristate with the covalently attached protein) or enhance (e.g., electrostatic interactions of basic residues with acidic lipids; protein-protein interactions with intrinsic receptor proteins) the interaction of myristoylated proteins with membranes are likely to be important and may cause reversible translocation of these proteins to the membrane.(ABSTRACT TRUNCATED AT 250 WORDS)
Members of the Arabidopsis Dynamin-Like Gene Family, ADL1, Are Essential for Plant Cytokinesis and Polarized Cell Growth[W] (2003)

Polarized membrane trafficking during plant cytokinesis and cell expansion are critical for plant morphogenesis, yet very little is known about the molecular mechanisms that guide this process. Dynamin and dynamin-related proteins are large GTP binding proteins that are involved in membrane trafficking. Here, we show that two functionally redundant members of the Arabidopsis dynamin-related protein family, ADL1A and ADL1E, are essential for polar cell expansion and cell plate biogenesis. adl1A-2 adl1E-1 double mutants show defects in cell plate assembly, cell wall formation, and plasma membrane recycling. Using a functional green fluorescent protein fusion protein, we show that the distribution of ADL1A is dynamic and that the protein is localized asymmetrically to the plasma membrane of newly formed and mature root cells. We propose that ADL1-mediated membrane recycling is essential for plasma membrane formation and maintenance in plants.
Dynacortin, a Genetic Link between Equatorial Contractility and Global Shape Control Discovered by Library Complementation of a Dictyostelium discoideum Cytokinesis Mutant (2000)

We have developed a system for performing interaction genetics in Dictyostelium discoideum that uses a cDNA library complementation/multicopy suppression strategy. Chemically mutagenized cells were screened for cytokinesis-deficient mutants and one mutant was subjected to library complementation. Isolates of four different genes were recovered as modifiers of this strain's cytokinesis defect. These include the cleavage furrow protein cortexillin I, a novel protein we named dynacortin, an ezrin-radixin-moesin-family protein, and coronin. The cortexillin I locus and transcript were found to be disrupted in the strain, identifying it as the affected gene. Dynacortin is localized partly to the cell cortex and becomes enriched in protrusive regions, a localization pattern that is similar to coronin and partly dependent on RacE. During cytokinesis, dynacortin is found in the cortex and is somewhat enriched at the poles. Furthermore, it appears to be reduced in the cleavage furrow. The genetic interactions and the cellular distributions of the proteins suggest a hypothesis for cytokinesis in which the contraction of the medial ring is a function of spatially restricted cortexillin I and myosin II and globally distributed dynacortin, coronin, and RacE.
The inverse protein folding problem: self consistent mean field optimisation of a structure specific mutation matrix. (1997)

The goal of the inverse folding problem is to supply a list of sequences compatible with a known protein structure. If two-body interactions are taken into account in energy calculations, an exhaustive exploration of the energy landscape in sequence space cannot be achieved because of the huge number of possible combinations. To circumvent this problem, we propose a method in which multiple copies corresponding to every possible side-chain type are attached to each C alpha position in the protein. The weights of each copy (stored in the sequence matrix SM) are refined using mean field theory: each side-chain copy interacts with the mean field generated by all possible side-chain copies at neighbouring positions, weighted by their respective probabilities. The potential energy is simply taken to be amino acid pair potentials of mean force. The method converges in a few cycles to a self-consistent solution. The refined matrix does not depend on the starting point; therefore the method succeeds in removing memory effects. Starting solely from the backbone of the known structure, and without information from the initial sequence, the final sequence matrix SM is shown to be able to retrieve significant sequence information, as observed through a series of structure-recognizes-sequence(s) computer experiments. The issue of specificity is discussed in detail.