gebhart/patrepeval huggingface dataset:
Rapid TCR:Epitope Ranker (RAPTER): A primary human T cell reactivity screening assay pairing epitope and TCR at single cell resolution (2022)

Abstract Identifying epitopes that T cells respond to is critical to understanding T cell-mediated immunity. Traditional multimer and other single cell assays often require large blood volumes and/or expensive HLA-specific reagents and provide limited phenotypic and functional information. Here, we present the Rapid TCR:Epitope Ranker (RAPTER) assay, a single cell RNA sequencing (scRNA-SEQ) method that uses primary human T cells and antigen presenting cells (APCs) to assess functional T cell reactivity at single cell resolution. Using hash-tag oligonucleotide (HTO) coding and T cell activation-induced markers (AIM), RAPTER defines paired epitope specificity and TCR sequence and can include RNA- and protein-level T cell phenotype information. We demonstrate that RAPTER identified specific reactivities to viral and tumor antigens at sensitivities as low as 0.15% of total CD8+ T cells, and deconvoluted low-frequency circulating HPV16-specific T cell clones from a cervical cancer patient. The specificities of TCRs identified by RAPTER for MART1, EBV, and influenza epitopes were functionally confirmed in vitro. In summary, RAPTER identifies low-frequency T cell reactivities using primary cells from low blood volumes, and the resulting paired TCR: ligand information can directly enable immunogenic antigen selection for vaccine epitope inclusion, antigen-specific TCR tracking, and TCR cloning for further therapeutic development.
ChemInform Abstract: THE HIGH SPEED ELECTRODEPOSITION OF TIN/LEAD ALLOYS (1982)

Abstract Für die in der Elektronik‐Industrie wichtigen Sn/Pb‐Legierungen wurde der Einfluß von Oberflächen‐Agenzien auf die Elektroabscheidung aus HBF 4 ‐Lösungen untersucht.
1327: Current Status of Clinical Trials in Urothelial Cancers: A Summary from the ACOSOG Gu Working Group (2005)

You have accessJournal of UrologyPodium, Tuesday, May 24, 2005, 1:00 - 3:00pm1 Apr 20051327: Current Status of Clinical Trials in Urothelial Cancers: A Summary from the ACOSOG Gu Working Group Bernard H. Bochner, Robert G. Uzzo, Mitchell Sokoloff, Louis L. Pisters, Surena F. Matin, Martin G. Sanda, John Colberg, Christopher G. Wood, Badrinath R. Konety, David F. Penson, and ACOSOG GU Working Group Bernard H. BochnerBernard H. Bochner More articles by this author , Robert G. UzzoRobert G. Uzzo More articles by this author , Mitchell SokoloffMitchell Sokoloff More articles by this author , Louis L. PistersLouis L. Pisters More articles by this author , Surena F. MatinSurena F. Matin More articles by this author , Martin G. SandaMartin G. Sanda More articles by this author , John ColbergJohn Colberg More articles by this author , Christopher G. WoodChristopher G. Wood More articles by this author , Badrinath R. KonetyBadrinath R. Konety More articles by this author , David F. PensonDavid F. Penson More articles by this author , and ACOSOG GU Working Group More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)35472-7AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "1327: Current Status of Clinical Trials in Urothelial Cancers: A Summary from the ACOSOG Gu Working Group." The Journal of Urology, 173(4S), p. 360 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 173Issue 4SApril 2005Page: 360 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Bernard H. Bochner More articles by this author Robert G. Uzzo More articles by this author Mitchell Sokoloff More articles by this author Louis L. Pisters More articles by this author Surena F. Matin More articles by this author Martin G. Sanda More articles by this author John Colberg More articles by this author Christopher G. Wood More articles by this author Badrinath R. Konety More articles by this author David F. Penson More articles by this author ACOSOG GU Working Group More articles by this author Expand All Advertisement PDF downloadLoading ...
Inverse Salt Sensitivity of Blood Pressure Is Associated with an Increased Renin-Angiotensin System Activity (2022)

High and low sodium diets are associated with increased blood pressure and cardiovascular morbidity and mortality. The paradoxical response of elevated BP in low salt diets, aka inverse salt sensitivity (ISS), is an understudied vulnerable 11% of the adult population with yet undiscovered etiology. A linear relationship between the number of single nucleotide polymorphisms (SNPs) in the dopamine D<sub>2</sub> receptor (<i>DRD2,</i> rs6276 and 6277), and the sodium myo-inositol cotransporter 2 (<i>SLC5A11</i>, rs11074656), as well as decreased expression of these two genes in urine-derived renal proximal tubule cells (uRPTCs) isolated from clinical study participants suggest involvement of these cells in ISS. Insight into this newly discovered paradoxical response to sodium is found by incubating cells in low sodium (LS) conditions that unveil cell physiologic differences that are then reversed by mir-485-5p miRNA blocker transfection and bypassing the genetic defect by <i>DRD2</i> re-expression. The renin-angiotensin system (RAS) is an important counter-regulatory mechanism to prevent hyponatremia under LS conditions. Oversensitive RAS under LS conditions could partially explain the increased mortality in ISS. Angiotensin-II (AngII, 10 nmol/L) increased sodium transport in uRPTCs to a greater extent in individuals with ISS than SR. Downstream signaling of AngII is verified by identifying lowered expression of nuclear factor erythroid 2-related factor 2 (NRF2), CCCTC-binding factor (CTCF), and manganese-dependent mitochondrial superoxide dismutase (SOD2) only in ISS-derived uRPTCs and not SR-derived uRPTCs when incubated in LS conditions. We conclude that <i>DRD2</i> and <i>SLC5A11</i> variants in ISS may cause an increased low sodium sensitivity to AngII and renal sodium reabsorption which can contribute to inverse salt-sensitive hypertension.
Instructional Course Lectures, The American Academy of Orthopaedic Surgeons - Fixation with a Modular Stem in Revision Total Hip Arthroplasty*† (1999)

BONO, JAMES V. M.D.‡; MCCARTHY, JOSEPH C. M.D.‡; LEE, JO-ANN R.N.‡, BOSTON; CARANGELO, ROBERT J. M.D.§, NEW BRITAIN, CONNECTICUT; TURNER, RODERICK H. M.D.‡, BOSTON, MASSACHUSETTS Author Information
A membrane-spanning macrocyclic bolaamphiphile lipid mimic of archaeal lipids (2016)

The synthesis of a 72-membered macrocyclic tetraester bolaamphiphile is accomplished in six chemical steps from commercially available starting materials using copper-accelerated azide–alkyne coupling to close the macrocycle in high yield. Related diester amphiphiles and an acyclic tetraester bolaamphiphile were also prepared. The set of lipids bearing nitrophenyl phosphate head groups were incorporated into phospholipid vesicles but failed to undergo phosphate hydrolysis in basic conditions, undergoing efficient elimination in competition. The same lipid cores bearing phosphate-linked nitrobenzoxadiazole (NBD) head groups also incorporated into phospholipid vesicles and the NBD fluorescence was quenched with cobalt ions. The proportion of membrane-spanning bolaamphiphiles was determined from the ratio of cobalt quenching in the presence and in the absence of a detergent. The macrocyclic bolaamphiphile is incorporated into phospholipid vesicles such that 48 ± 4% of the NBD head groups are in the outer leaflet, consistent with a membrane-spanning orientation. The acyclic bolaamphiphile is incorporated with 75 ± 3% of the NBD head groups accessible to quencher in the absence of a detergent suggesting U-shaped incorporation in the outer leaflet of the bilayer membrane. In ring size and spanning ability, the macrocyclic bolaamphiphile mimics naturally occurring macrocyclic archaeal lipids.
Fatigue Behavior in an Fe-N Binary Ferritic Steel: Similarity and Difference between Carbon and Nitrogen (2020)

Fatigue crack initiation and propagation behavior of a water-quenched fully ferritic nitrogen steel were investigated by means of tension-compression fatigue tests. The Fe-0.011 mass% N steel showed no serrated flow associated with dynamic strain aging, and showed a fatigue limit of 150 MPa alongside a non-propagating fatigue crack. The major mode of crack initiation was at the grain boundaries, and the cracks propagated along the grain boundaries and interiors at and above the fatigue limit. The Fe-N steel did not exhibit a significant level of coaxing effect. The results were compared with our previous findings in Fe-0.006 and 0.017C steels, and the similarity and difference were discussed.
Conformational Isomerism in 1-Substituted Derivatives of 3,3-Dimethylbutane (1967)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConformational Isomerism in 1-Substituted Derivatives of 3,3-DimethylbutaneGeorge M. Whitesides, John P. Sevenair, and Rudolph W. GoetzCite this: J. Am. Chem. Soc. 1967, 89, 5, 1135–1144Publication Date (Print):March 1, 1967Publication History Published online1 May 2002Published inissue 1 March 1967https://doi.org/10.1021/ja00981a019RIGHTS & PERMISSIONSArticle Views171Altmetric-Citations57LEARN 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 (1 MB) Get e-Alerts Get e-Alerts
Low NOx Combustion by a Cyclone-Jet Combustor (2001)

For achieving a stable premixed combustion, there is a device termed the cyclone combustor, which consists of a cylindrical chamber and fuel nozzles installed tangentially on the sidewall. In this combustor an extremely stable flame can be obtained in the swirl flow, formed along the inner wall of the combustor. The authors utilized this combustor as a flame holder, to burn a high velocity jet flowing axially in the central part, and termed this new combustor a cyclone-jet combustor. In the present study, an excellent flame stability is shown for the cyclone-jet combustor and, by comparing premixed, non-premixed and partially premixed flames, the low NOx combustion characteristics were experimentally examined for this combustor.
Dissecting genealogy and cell cycle as sources of cell-to-cell variability in MAPK signaling using high-throughput lineage tracking (2013)

Cells, even those having identical genotype, exhibit variability in their response to external stimuli. This variability arises from differences in the abundance, localization, and state of cellular components. Such nongenetic differences are likely heritable between successive generations and can also be influenced by processes such as cell cycle, age, or interplay between different pathways. To address the contribution of nongenetic heritability and cell cycle in cell-to-cell variability we developed a high-throughput and fully automated microfluidic platform that allows for concurrent measurement of gene expression, cell-cycle periods, age, and lineage information under a large number of temporally changing medium conditions and using multiple strains. We apply this technology to examine the role of nongenetic inheritance in cell heterogeneity of yeast pheromone signaling. Our data demonstrate that the capacity to respond to pheromone is passed across generations and that the strength of the response correlations between related cells is affected by perturbations in the signaling pathway. We observe that a ste50Δ mutant strain exhibits highly heterogeneous response to pheromone originating from a unique asymmetry between mother and daughter response. On the other hand, fus3Δ cells were found to exhibit an unusually high correlation between mother and daughter cells that arose from a combination of extended cell-cycle periods of fus3Δ mothers, and decreased cell-cycle modulation of the pheromone pathway. Our results contribute to the understanding of the origins of cell heterogeneity and demonstrate the importance of automated platforms that generate single-cell data on several parameters.
Petroleomics via Orbitrap mass spectrometry with resolving power above 1 000 000 at m/z 200 (2018)

The performance of the high-field MegaOrbitrap Fourier transform mass spectrometer (FT-MS) with electrospray ionization (ESI) was evaluated to perform petroleum sample characterization <i>via</i> classical petroleomics approaches. Pertinent parameters that underpin the main figures of merit, that is, signal to noise ratios, dynamic range, spectral error, scan speed, mass accuracy and mass resolving power = <i>R</i> <sub>p</sub>, and provide subsidies to develop these analyzers were tested. Comparisons are made with data obtained using the most common petroleomics instrument, which is a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS), that has been used in the last decade in our laboratory for crude oil analysis providing <i>R</i> <sub>p</sub> of 340 000 at <i>m</i>/<i>z</i> 400 with transients of 3 s duration, and has been extensively demonstrated to fulfill all major requirements for precise petroleomics investigations. The high-field compact MegaOrbitrap mass analyzer, when operated at an <i>R</i> <sub>p</sub> = 840 000 at <i>m</i>/<i>z</i> 400 (<i>R</i> <sub>p</sub> > 1 000 000 at <i>m</i>/<i>z</i> 200) with a detection time of 3 s, was found to be well suited for adequate characterization of crude oil. Accurate class classification and mass accuracy below 1 ppm was obtained leading to proper, comprehensive petroleomics characterization.
MYC-driven increases in mitochondrial DNA copy number occur early and persist throughout prostatic cancer progression (2023)

Increased mitochondrial function may render some cancers vulnerable to mitochondrial inhibitors. Since mitochondrial function is regulated partly by mitochondrial DNA copy number (mtDNAcn), accurate measurements of mtDNAcn could help reveal which cancers are driven by increased mitochondrial function and may be candidates for mitochondrial inhibition. However, prior studies have employed bulk macrodissections that fail to account for cell type-specific or tumor cell heterogeneity in mtDNAcn. These studies have often produced unclear results, particularly in prostate cancer. Herein, we developed a multiplex <i>in situ</i> method to spatially quantify cell type specific mtDNAcn. We show that mtDNAcn is increased in luminal cells of high-grade prostatic intraepithelial neoplasia (HGPIN), is increased in prostatic adenocarcinomas (PCa), and is further elevated in metastatic castration-resistant prostate cancer. Increased PCa mtDNAcn was validated by two orthogonal methods and is accompanied by increases in mtRNAs and enzymatic activity. Mechanistically, MYC inhibition in prostate cancer cells decreases mtDNA replication and expression of several mtDNA replication genes, and MYC activation in the mouse prostate leads to increased mtDNA levels in the neoplastic prostate cells. Our <i>in situ</i> approach also revealed elevated mtDNAcn in precancerous lesions of the pancreas and colon/rectum, demonstrating generalization across cancer types using clinical tissue samples.
Time Reversal Focusing Applied to Lithotripsy (1996)

Time reversal of ultrasonic field allows a very efficient approach to focusing pulsed ultrasonic waves through lossless inhomogeneous media. Time reversal mirrors (TRM) are made of large transducer arrays, allowing the incident acoustic field to be sampled, time reversed and re-emitted. Time reversal processing permits a choice of any temporal window to be time reversed, allowing operation in an iterative mode. In multitarget media, this process converges on the most reflective target, i.e., the dominant scatterer. In this paper, the time reversal process is applied to track, in real time, a moving gall bladder or kidney stone embedded in its surrounding medium. We investigate the feasibility of a piezoelectric shock wave generator in which the focal zone is moved electronically to track the stone during a lithotripsy treatment. We show that TRM allows us to obtain sharp focusing on one bright point of the stone. The time of flight profile is then determined and used in a least-mean-square method to calculate the spatial coordinates of the stone.
Shadowing in urban environments with microcellular or peer-to-peer links (2012)

This paper revisits the modeling of shadowing in urban microcells, putting particular emphasis on the impact of street canyons. We argue that a categoriztion of links according to dominant propagation effects (line-of-sight, single diffraction, multiple diffraction) more accurately reproduces not only shadowing variance, but also the autocorrelation behaviour. This hypothesis is supported and quantified by ray launching simulations from downtown Los Angeles. A generic model and simulation methodology are also provided.
Integrated microHall magnetometer to measure the magnetic properties of nanoparticles (2017)

Magnetic nanoparticles (MNPs) are widely used in biomedical and clinical applications, including medical imaging, therapeutics, and biological sample processing. Rapid characterization of MNPs, notably their magnetic moments, should facilitate optimization of particle synthesis and accelerate assay development. Here, we report a compact and low-cost magnetometer for fast, on-site MNP characterization. Termed integrated microHall magnetometer (iHM), our device was fabricated using standard semiconductor processes: an array of Hall sensors, transistor switches, and amplifiers were integrated into a single chip, thus improving the detection sensitivity and facilitating chip operation. By applying the iHM, we demonstrate versatile magnetic assays. We measured the magnetic susceptibility and moments of MNPs using small sample amounts (∼10 pL), identified different MNP compositions in mixtures, and detected MNP-labeled single cells.
60 GHz Frequency Sharing Study between Fixed Service Systems and Small-Cell Systems with Modular Antenna Arrays (2015)

This paper presents numerical simulation results in order to identify how much interference can be generated to a fixed service (FS) receiver from nearby small cell networks when the FS systems and small-cell systems are sharing a 60 GHz mmWave frequency band. For this 60 GHz frequency sharing study, two different scenarios are considered, i.e., the aggregation of interference into an FS receiver occurred by every transmission (i) from base stations (BSs) to their associated user elements (UEs); (ii) from UEs and their associated BSs. Moreover, 60 GHz mmWave specific propagation characteristics and attenuation factors are considered for more precise simulation study. The simulation results determine how much interference rejection is required to protect the operation of FS.
Photonic quantum simulation of ground state configurations of Heisenberg square and checkerboard lattice spin systems (2012)

Photonic quantum simulators are promising candidates for providing insight into other small- to medium-sized quantum systems. The available photonic quantum technology is reaching the state where significant advantages arise for the quantum simulation of interesting questions in Heisenberg spin systems. Here we experimentally simulate such spin systems with single photons and linear optics. The effective Heisenberg-type interactions among individual single photons are realized by quantum interference at the tunable direction coupler followed by the measurement process. The effective interactions are characterized by comparing the entanglement dynamics using pairwise concurrence of a four-photon quantum system. We further show that photonic quantum simulations of generalized Heisenberg interactions on a four-site square lattice and a six-site checkerboard lattice are in reach of current technology.
Chemical encoding of amphiphilic copolymers for a dual controlled release from their assemblies (2014)

Amphiphilic random copolymers are designed to bear a corrosion inhibitor as cleavable side group, which can be released upon activation by chemical reduction.
Supplementary Figure 3A from Aberrant Silencing of Cancer-Related Genes by CpG Hypermethylation Occurs Independently of Their Spatial Organization in the Nucleus (2023)

Supplementary Figure 3A from Aberrant Silencing of Cancer-Related Genes by CpG Hypermethylation Occurs Independently of Their Spatial Organization in the Nucleus
Fast rigorous modeling of photoresist in lithography (2021)

The fast rigorous model (FRM) is a first principles solver based on sequential simulations of photochemical reactions in photoresists. We report the evaluation of FRM relative to compact models (CM1) for NTD OPC model accuracy. We demonstrate equivalent or better accuracy to CM1 when FRM is combined with a CM1 model of the same composition. In the case of CTR to FRM comparison, FRM is 34% more accurate in calibration and prediction on average across 20 testcases. FRM is 5% more predictive than the most complex CM1 modelform tested with similar calibration accuracy. FRM supplemented with limited CM1 terms provides better verification accuracy for SRAF printing and hotspot detection. Further, the input data needed to train the FRM model in order to achieve high predictive accuracy is a fraction (1-5%) of that needed by more complex CM1 modelforms. Finally, we show through the Akaike Information Criteria method that FRM is more predictive than an equivalent CM1 model based on the degrees of freedom in the modelform and quantity of data available.
Operating a Manufacturing Plant in an Asian Culture (1992)

With many US companies owning production plants in foreign countries and others planning to do so, what does it take to run a metal fabricating plant overseas, especially in a developing country and in an Asian culture? Consider ABB Combustion Engineering Systems (ABB/CE), which in a joint venture with two Indonesian firms has set up a boiler components plant on the country's main island of Java.
DPSSLs: status and prospects for materials processing (1999)

The pricing of high power diode arrays and the status and prospects for high power, high brightness Nd:YAG and Yb:YAG DPSSLs are reviewed.