gebhart/patrepeval huggingface dataset:
In vivo antigen expression regulates CD4 T cell differentiation and vaccine efficacy against Mycobacterium tuberculosis infection (2021)

New vaccines are urgently needed against <i>Mycobacterium tuberculosis</i> (Mtb), which kills more than 1.4 million people each year. CD4 T cell differentiation is a key determinant of protective immunity against Mtb, but it is not fully understood how host-pathogen interactions shape individual antigen-specific T cell populations and their protective capacity. Here, we investigated the immunodominant Mtb antigen, MPT70, which is upregulated in response to IFN-γ or nutrient/oxygen deprivation of <i>in vitro</i> infected macrophages. Using a murine aerosol infection model, we compared the <i>in vivo</i> expression kinetics of MPT70 to a constitutively expressed antigen, ESAT-6, and analysed their corresponding CD4 T cell phenotype and vaccine-protection. For wild-type Mtb, we found that <i>in vivo</i> expression of MPT70 was delayed compared to ESAT-6. This delayed expression was associated with induction of less differentiated MPT70-specific CD4 T cells but, compared to ESAT-6, also reduced protection after vaccination. In contrast, infection with an MPT70-overexpressing Mtb strain promoted highly differentiated KLRG1<sup>+</sup>CX3CR1<sup>+</sup> CD4 T cells with limited lung-homing capacity. Importantly, this differentiated phenotype could be prevented by vaccination and, against the overexpressing strain, vaccination with MPT70 conferred similar protection as ESAT-6. Together our data indicate that high <i>in vivo</i> antigen expression drives T cells towards terminal differentiation and that targeted vaccination with adjuvanted protein can counteract this phenomenon by maintaining T cells in a protective less-differentiated state. These observations shed new light on host-pathogen interactions and provide guidance on how future Mtb vaccines can be designed to tip the immune-balance in favor of the host.
The arginine finger of bacteriophage T7 gene 4 helicase: Role in energy coupling (2004)

The DNA helicase encoded by gene 4 of bacteriophage T7 couples DNA unwinding to the hydrolysis of dTTP. The loss of coupling in the presence of orthovanadate (Vi) suggests that the gamma-phosphate of dTTP plays an important role in this mechanism. The crystal structure of the hexameric helicase shows Arg-522, located at the subunit interface, positioned to interact with the gamma-phosphate of bound nucleoside 5' triphosphate. In this respect, it is analogous to arginine fingers found in other nucleotide-hydrolyzing enzymes. When Arg-522 is replaced with alanine (gp4-R522A) or lysine (gp4-R522K), the rate of dTTP hydrolysis is significantly decreased. dTTPase activity of the altered proteins is not inhibited by Vi, suggesting the loss of an interaction between Vi and gene 4 protein. gp4-R522A cannot unwind DNA, whereas gp4-R522K does so, proportionate to its dTTPase activity. However, gp4-R522K cannot stimulate T7 polymerase activity on double-stranded DNA. These findings support the involvement of the Arg-522 residue in the energy coupling mechanism.
On Duobinary Turbo Codes for Block Fading Channels (2006)

Diversity coding for fading channels has been an area of active research for many years. In particular, performance hounds and code construction for several families of codes have been studied for block fading channels. In this work, we consider duobinary turbo codes for block fading channels. A simple decodability condition guaranteeing full diversity based on decodable subsets is introduced. The performance of systematic duobinary turbo codes is analyzed with regard to the channel interleaver and confirmed with simulations. An interesting relationship between the frame size and distance spectrum of these tailbiting codes is revealed
Leveraging Image‐based Localization for Infrastructure‐based Calibration of a Multi‐camera Rig (2014)

Most existing calibration methods for multi‐camera rigs are computationally expensive, use installations of known fiducial markers, and require expert supervision. We propose an alternative approach called infrastructure‐based calibration that is efficient, requires no modification of the infrastructure (or calibration area), and is completely unsupervised. In infrastructure‐based calibration, we use a map of a chosen calibration area and leverage image‐based localization to calibrate an arbitrary multi‐camera rig in near real‐time. Due to the use of a map, before we can apply infrastructure‐based calibration, we have to run a survey phase once to generate a map of the calibration area. In this survey phase, we use a survey vehicle equipped with a multi‐camera rig and a calibrated odometry system, and self‐calibration based on simultaneous localization and mapping to build the map that is based on natural features. The use of the calibrated odometry system ensures that the metric scale of the map is accurate. Our infrastructure‐based calibration method does not assume an overlapping field of view between any two cameras, and it does not require an initial guess of any extrinsic parameter. Through extensive field tests on various ground vehicles in a variety of environments, we demonstrate the accuracy and repeatability of the infrastructure‐based calibration method for calibration of a multi‐camera rig. The code for our infrastructure‐based calibration method is publicly available as part of the CamOdoCal library at https://github.com/hengli/camodocal .
15N{31P} REDOR NMR Studies of the Binding of Phosphonate Reaction Intermediate Analogues to Saccharomyces cerevisiae Lumazine Synthase (2008)

Lumazine synthase catalyzes the reaction of 5-amino-6-D-ribitylamino-2,4(1H,3H)-pyrimidinedione(1) with (S)-3,4-dihydroxybutanone 4-phosphate (2) to afford 6,7-dimethyl-8-D-ribityllumazine(3), the immediate biosynthetic precursor of riboflavin. The overall reaction implies a series of intermediates that are incompletely understood. The 15N{31P} REDOR NMR spectra of three metabolically stable phosphonate reaction intermediate analogues complexed to Saccharomyces cereVisiae lumazine synthase have been obtained at 7 and 12 T. Distances from the phosphorus atoms of the ligands to the side chain nitrogens of Lys92, His97, Arg136, and His148 have been determined. These distances were used in combination with the X-ray crystal coordinates of one of the intermediate analogues complexed with the enzyme in a series of distance-restrained molecular dynamics simulations. The resulting models indicate mobility of the Lys92 side chain, which could facilitate the exchange of inorganic phosphate eliminated from the substrate in one reaction, with the organic phosphate-containing substrate necessary for the next reaction.
Voltage- and temperature-dependent activation of TRPV3 channels is potentiated by receptor-mediated PI(4,5)P2 hydrolysis (2011)

TRPV3 is a thermosensitive channel that is robustly expressed in skin keratinocytes and activated by innocuous thermal heating, membrane depolarization, and chemical agonists such as 2-aminoethyoxy diphenylborinate, carvacrol, and camphor. TRPV3 modulates sensory thermotransduction, hair growth, and susceptibility to dermatitis in rodents, but the molecular mechanisms responsible for controlling TRPV3 channel activity in keratinocytes remain elusive. We show here that receptor-mediated breakdown of the membrane lipid phosphatidylinositol (4,5) bisphosphate (PI(4,5)P(2)) regulates the activity of both native TRPV3 channels in primary human skin keratinocytes and expressed TRPV3 in a HEK-293-derived cell line stably expressing muscarinic M(1)-type acetylcholine receptors. Stimulation of PI(4,5)P(2) hydrolysis or pharmacological inhibition of PI 4 kinase to block PI(4,5)P(2) synthesis potentiates TRPV3 currents by causing a negative shift in the voltage dependence of channel opening, increasing the proportion of voltage-independent current and causing thermal activation to occur at cooler temperatures. The activity of single TRPV3 channels in excised patches is potentiated by PI(4,5)P(2) depletion and selectively decreased by PI(4,5)P(2) compared with related phosphatidylinositol phosphates. Neutralizing mutations of basic residues in the TRP domain abrogate the effect of PI(4,5)P(2) on channel function, suggesting that PI(4,5)P(2) directly interacts with a specific protein motif to reduce TRPV3 channel open probability. PI(4,5)P(2)-dependent modulation of TRPV3 activity represents an attractive mechanism for acute regulation of keratinocyte signaling cascades that control cell proliferation and the release of autocrine and paracrine factors.
Robotic go: Exploring a different perspective on human-computer interaction with the game of go (2009)

The advent of computers and the World Wide Web diversified the way in which the game of Go is played. While traditional human-to-human play still remains an important form of game play, amateur players, along with some professional players, have shifted the play domain from “off-line” club houses to “on-line” Go servers. Computer Go is an important field of study to develop a software to play Go or a Go engine. In addition to human-to-human play, a Go engine or computer intelligence to play Go adds another axis to play configuration: human-to-computer play and computer-to-computer play. These revolutions in the game of Go happened in an extremely short period of time compared to the history of the game, which is more than 4,000 years. We summarize this unavoidable change for the first time in the literature, to our knowledge, and propose a novel way to interact with the current technological advances. We present the new Human-Machine-Computer-Network Interface concept and our implementation of the machine interface with a robot arm. This Lynxmotion robotic arm named Cheonsoo-I successfully places stones on a board under the proposed architecture.
Measurement of Line Tension from Cell Coalescence Events in a Langmuir Film (1997)

Epifluorescence microscopy was used to examine Langmuir films of an alkoxy-substituted (phenylene acetylene−pyridine acetylene) polymer. The polymer was observed to form microscopic two-dimensional emulsion-like cellular network morphologies after treatment by a simple processing procedure. Cell coalescence was found to be an important process in the evolution of the cellular network. As observed under the microscope, cell coalescence is similar to the bursting of a soap bubble. An estimate of the line tension was made using an analogue of an equation developed by Culick and others to describe the rim velocity of a bursting soap bubble.
Randomized rule selection in transformation-based learning: a comparative study (2001)

Transformation-Based Learning (TBL) is a relatively new machine learning method that has achieved notable success on language problems. This paper presents a variant of TBL, called Randomized TBL, that overcomes the training time problems of standard TBL without sacrificing accuracy. It includes a set of experiments on part-of-speech tagging in which the size of the corpus and template set are varied. The results show that Randomized TBL can address problems that are intractable in terms of training time for standard TBL. In addition, for language problems such as dialogue act tagging where the most effective features have not been identified through linguistic studies, Randomized TBL allows the researcher to experiment with a large set of templates capturing many potentially useful features and feature interactions.
Optimization of optical nonlinearity of semiconductor-doped glasses (1986)

Semiconductor-doped glasses consisting of 100–1000-Å microcrystallites of CdSxSe1−x, embedded in borosilicate glass available commercially as color filters exhibit very interesting nonlinear effects. Degenerate four-wave mixing and phase conjugation arising from electronic processes have been reported in these glasses.1-3 Evidence for quantum size effects at low temperatures for electrons confined to microcrystallites has also been presented.4 These glasses provide potentially useful media for room-temperature nonlinear signal processing based on guided-wave or etalon devices due to their relatively large nonlinear index of refraction. Here we report on the measurement of the nonlinear index in these materials using an interferometric technique. The nonlinear index is measured for samples prepared in different growth conditions to examine the role of crystallite formation on optimization of the nonlinearity. An enhancement of the nonlinear index is obtained with some specific growth parameters.
Semi‐Batch Precipitation of Calcium Oxalate Monohydrate (1992)

Abstract Calcium oxalate monohydrate (COM) formation on the semi‐batch precipitation of CaCl 2 and Na 2 C 2 O 4 solutions in the stoichiometric ratio carried out at pH = 6 and 37 or 70°C, respectively, was studied. When a certain level of supersaturation in the system is reached, individual COM crystals of a rather uniform size are formed. These crystals then grown and form ‘loose’ agglomerates that later develop into compact and spherical particles. The particle size distribution (PSD) rapidly shifts during early stages of precipitation towards larger sizes as a result of crystal growth and agglomeration. Later the PSD reaches a shape and position on the size axis that remain virtually constant with progressing precipitation. COM agglomerates consisting of mainly intergrown crystals are formed by mechanism of primary and secondary agglomeration. The primary agglomeration can constitute an important factor in urolithiasis.
ChemInform Abstract: A New Method for the Preparation of 3,5‐Disubstituted Butenolides. (1988)

Abstract The propargylic ethers (I) react with the zirconocene hydride (II) to form the alkenylzirconium compounds (III) which are carbonylated to form the intermediate acylzirconium complexes (V).
Chorioallantoic membrane grafting of the embryonic murine kidney. An improved in vitro technique for studying kidney morphogenesis. (1981)

Previous experimental investigations of embryonic kidney development with in vitro organ culture techniques have been limited by the short duration of explant viability. Utilization of chick chorioallantoic membranes for transplanting undifferentiated murine kidney rudiments has allowed vascularization of the grafts with advanced maturation and the appearance of early nephron units.
A Flow Cytometry-based Assay to Identify Compounds That Disrupt Binding of Fluorescently-labeled CXC Chemokine Ligand 12 to CXC Chemokine Receptor 4 (2018)

Pharmacological targeting of G protein-coupled receptors (GPCRs) is of great importance to human health, as dysfunctional GPCR-mediated signaling contributes to the progression of many diseases. The ligand/receptor pair CXC chemokine ligand 12 (CXCL12)/CXC chemokine receptor 4 (CXCR4) has raised significant clinical interest, for instance as a potential target for the treatment of cancer and inflammatory diseases. Small molecules as well as therapeutic antibodies that specifically target CXCR4 and inhibit the receptor's function are therefore considered to be valuable pharmacological tools. Here, a flow cytometry-based cellular assay that allows identification of compounds (e.g., small molecules) that abrogate CXCL12 binding to CXCR4, is described. Essentially, the assay relies on the competition for receptor binding between a fixed amount of fluorescently labeled CXCL12, the natural chemokine agonist for CXCR4, and unlabeled compounds. Hence, the undesirable use of radioactively labeled probes is avoided in this assay. In addition, living cells are used as the source of receptor (CXCR4) instead of cell membrane preparations. This allows easy adaptation of the assay to a plate format, which increases the throughput. This assay has been shown to be a valuable generic drug discovery assay to identify CXCR4-targeting compounds. The protocol can likely be adapted to other GPCRs, at least if fluorescently labeled ligands are available or can be generated. Prior knowledge concerning the intracellular signaling pathways that are induced upon activation of these GPCRs, is not required.
Diffusion and Solubility of Simple Gases through a Copolymer of Hexafluoropropylene and Tetrafluoroethylene (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiffusion and Solubility of Simple Gases through a Copolymer of Hexafluoropropylene and TetrafluoroethyleneR. A. Pasternak, G. L. Burns, and J. HellerCite this: Macromolecules 1971, 4, 4, 470–475Publication Date (Print):July 1, 1971Publication History Published online1 May 2002Published inissue 1 July 1971https://pubs.acs.org/doi/10.1021/ma60022a022https://doi.org/10.1021/ma60022a022research-articleACS PublicationsRequest reuse permissionsArticle Views211Altmetric-Citations31LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Iron Catalyzed Synthesis and Chemical Recycling of Telechelic, 1,3-Enchained Oligocyclobutanes (2020)

Closed-loop recycling offers the opportunity to help mitigate plastic waste through reversible polymer construction and deconstruction. While examples of the chemical recycling polymers are known, few have been applied to materials derived from abundant commodity olefinic monomers that are the building blocks of ubiquitous plastic resins. Here we describe a [2+2] cycloaddition oligomerization of 1,3-butadiene to yield a previously unrealized telechelic microstructure of (1,n’-divinyl)oligocyclobutane. This material is thermally stable, has stereoregular segments arising from chain-end control, and exhibits high crystallinity even at low molecular weight. Exposure of the oligocyclobutane to vacuum in the presence of the pyridine(diimine) iron precatalyst used to synthesize it resulted in deoligomerization to generate pristine butadiene, demonstrating a rare example of closed-loop chemical recycling of an oligomeric material derived from a commodity hydrocarbon feedstock.
Quadruple Functionalization of a Tetraphenylethylene Aromatic Scaffold with Ynamides or Tetracyanobutadienes: Synthesis and Optical Properties (2022)

Abstract Ynamides are useful and versatile building blocks in organic synthesis, from which 1,1,4,4‐tetracyanobutadienes (TCBD) can be prepared for application in molecular electronics. However, their insertion onto multi‐functional molecular scaffold remains a synthetic challenge. In this work, we report the two‐steps synthesis in good isolated yield (64 % overall, 89 % stepwise) of a tetraphenylethylene (TPE) bearing four ynamides, and its further one‐step conversion into the tetra‐TCBD derivative through a [2+2] cycloaddition‐retroelectrocyclization sequence. The concomitant formation of the four ynamides required a specific optimisation of the reaction conditions. Although a poor fluorescent emitter in solution, the tetra‐TCBD compound displayed near‐infrared luminescence in the solid state, which is an attractive optoelectronic feature when considering future applications in molecular electronic devices.
PHYSIOLOGY, PHARMACOLOGY AND CONTACT LENSES* (1971)

ABSTRACT: The materials likely to be present as contamination on the surface of a contact lens, from the patient's environment, and from the glandular secretion discharging into the precorneal tear film are mentioned. Cationic, anionic and nonionic surface active agents used in cleaning lenses, their mode of action and the concentration considered necessary in the maintenance of clean lenses, as well as antimicrobial substances used as preservatives, chelating agents and wetting agents included in contact lens wetting and soaking solutions, are described and commented upon.
Zoom-and-pick (2005)

Designing interfaces for interactive handheld projectors is an exiting new area of research that is currently limited by two problems: hand jitter resulting in poor input control, and possible reduction of image resolution due to the needs of image stabilization and warping algorithms. We present the design and evaluation of a new interaction technique, called zoom-and-pick, that addresses both problems by allowing the user to fluidly zoom in on areas of interest and make accurate target selections. Subtle design features of zoom-and-pick enable pixel-accurate pointing, which is not possible in most freehand interaction techniques. Our evaluation results indicate that zoom-and-pick is significantly more accurate than the standard pointing technique described in our previous work.
Regions of conformational flexibility in the proprotein convertase PCSK9 and design of antagonists for LDL cholesterol lowering (2020)

The proprotein convertase subtilisin/kexin type 9 (PCSK9) regulates plasma LDL cholesterol levels by binding to the liver LDL receptor (LDLR) and promoting its degradation. Therefore, PCSK9 has become a compelling new therapeutic target for lipid lowering and the prevention of cardiovascular disease. PCSK9 contains two regions of conformational flexibility, the N-terminal regions of the prodomain and of the catalytic domain. The recognition that the latter region, the so-called P' helix, is able to transition from an α-helical to a disordered state gave rise to new strategies to develop small molecule inhibitors of PCSK9 for lipid lowering. In the ordered state the P' helix is buried in a groove of the PCSK9 catalytic domain located next to the main LDLR binding site. The transition to a disordered state leaves the groove site vacated and accessible for compounds to antagonize LDLR binding. By use of a groove-directed phage display strategy we were able to identify several groove-binding peptides. Based on structural information of PCSK9-peptide complexes, a minimized groove-binding peptide was generated and utilized as an anchor to extend towards the adjacent main LDLR binding site, either by use of a phage-displayed peptide extension library, or by appending organic moieties to yield organo-peptides. Both strategies led to antagonists with pharmacologic activities in cell-based assays. The intricate bipartite mechanism of the potent organo-peptide inhibitors was revealed by structural studies, showing that the core peptide occupies the N-terminal groove, while the organic moiety interacts with the LDLR binding site to create antagonism. These findings validate the PCSK9 groove as an attractive target site and should inspire the development of a new class of small molecule antagonists of PCSK9.
A PHOTOLUMINESCENCE STUDY OF $C_{60}$ AND $C_{70}$ (1992)

Author Institution: Department of Chemistry, The University of Michigan
Efficient 355-nm generation in high-quality CsB/sub 3/O/sub 5/ fabricated by post-growth heat treatments (2005)

Post-growth heat treatments of CsB/sub 3/O/sub 5/ enable to produce high-quality optical devices free from scattering centers. It has generated 14-W UV radiation at 355 nm, which is three times higher than that obtained by LiB/sub 3/O/sub 5/.