gebhart/patrepeval huggingface dataset:
Addition of C−H Bonds to the Catalytically Active Complex (PCP)Ir (PCP = η3-2,6-(tBu2PCH2)2C6H3) (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTAddition of C−H Bonds to the Catalytically Active Complex (PCP)Ir (PCP = η3-2,6-(tBu2PCH2)2C6H3)Mira Kanzelberger, Bharat Singh, Margaret Czerw, Karsten Krogh-Jespersen, and Alan S. GoldmanView Author Information Department of Chemistry, Rutgers University Piscataway, New Jersey 08854-8087 Cite this: J. Am. Chem. Soc. 2000, 122, 44, 11017–11018Publication Date (Web):October 21, 2000Publication History Received12 May 2000Published online21 October 2000Published inissue 1 November 2000https://doi.org/10.1021/ja001626sCopyright © 2000 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views2446Altmetric-Citations122LEARN 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 Read OnlinePDF (41 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Alkyls,Anions,Aromatic compounds,Hydrocarbons,Organic reactions Get e-Alerts
Evaluation of the toxicity and efficacy of paclitaxel nanoencapsulated with polyethyloxazoline polymers. (2013)

e13538 Background: Paclitaxel’s antineoplastic activity is limited by its solubility and toxicity. Encapsulation with polyethyloxazoline (PEOX) branched polymers can increase its solubility, decrease toxicity and enhance its antitumor efficacy. Methods: Paclitaxel was mixed with PEOX-based branched polymers at drug loading percentages of 11 - 17% to form nanoparticles (&lt; 90 nm in diameter). The product was purified and lyophilized as a white powder, designated FID-007. Its cytotoxicity was tested on normal human fibroblast cells and cell lines for human lung (A549), triple negative breast (MDA-MB-231) and ovarian (OV-90) cancers. Commercial paclitaxel drugs, Taxol and Abraxane, were similarly tested. Maximum tolerated dose (MTD) of the three drugs were determined in CD-1 mice. FID-007’s efficacy in controlling tumor growth was compared to the other drugs in vivo using xenograft tumor models in Scid mice with the three human cancer cell lines (20 mice per cancer). Saline and polymer were used as negative control treatments. Results: FID-007, Taxol and Abraxane showed similar cytotoxicity to all cancers.FID-007 was &gt; 10-fold less active in normal fibroblasts. The single dose MTD in CD-1 mice was &lt; 30 mg/kg for Taxol, 175 mg/kg for FID-007 and &gt;180 mg/kg for Abraxane. FID-007 exhibited the best efficacy in controlling tumor growth in mice compared to Taxol and Abraxane with the three human cancers. Results from the lung tumor study are presented in the Table. Conclusions: Encapsulation with PEOX-based polymers reduced the toxicity and significantly improved the efficacy of paclitaxel in controlling tumor growth in vitro and in vivo. [Table: see text]
Substrate-enhanced photothermal nano-imaging of surface polaritons in monolayer graphene (2021)

Surface polaritons comprise a wealth of light–matter interactions with deep sub-wavelength scale confinement of electromagnetic modes. However, their nanoscale localized dissipation and thermalization processes are not readily accessible experimentally. Here, we introduce photothermal force microscopy to image surface plasmon polaritons (SPPs) in monolayer graphene through their non-radiative SiO2 substrate dissipation. We demonstrate the real-space SPP imaging via photo-induced atomic force detection, and from comparison with scattering-type scanning near-field optical microscopy imaging attribute the force response to substrate dissipation-enhanced thermal expansion. This work illustrates that nano-optical tip–sample induced dissipative forces facilitate a direct mechanical detection of surface polariton interactions with monolayer sensitivity.
A CMOS 160 Mb/s phase modulation I/O interface circuit (2002)

This paper proposes an approach to data transfer that can potentially achieve high rates without requiring the ultra fast clocks of other approaches, or extra wide buses. The idea is to transfer multiple bits over each pin within each clock cycle using modulation techniques common in communication systems. Phase modulation is simple in implementation and demonstrates 160 Mb/s peak transfer rate per pin using a 20 MHz clock. This scheme may prove effective for chip-to-chip or system bus interface both on printed circuit boards (PCBs) and multi-chip modules (MCMs).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Tabular (2014)

We propose a new kind of probabilistic programming language for machine learning. We write programs simply by annotating existing relational schemas with probabilistic model expressions. We describe a detailed design of our language, Tabular, complete with formal semantics and type system. A rich series of examples illustrates the expressiveness of Tabular. We report an implementation, and show evidence of the succinctness of our notation relative to current best practice. Finally, we describe and verify a transformation of Tabular schemas so as to predict missing values in a concrete database. The ability to query for missing values provides a uniform interface to a wide variety of tasks, including classification, clustering, recommendation, and ranking.
Searching the Chlamydia Genomes for New Vaccine Candidates (2003)

Old Problems and New Perspectives for Chlamydial Vaccines Post-genomic Approaches Genomic Screening Results Concluding Considerations Reference
IRIS: Big data-informed discovery of cancer immunotherapy targets arising from pre-mRNA alternative splicing (2019)

Abstract Aberrant alternative splicing (AS) is widespread in cancer, leading to an extensive but largely unexploited repertoire of potential immunotherapy targets. Here we describe IRIS, a computational platform leveraging large-scale cancer and normal transcriptomics data to discover AS-derived tumor antigens for T-cell receptor (TCR) and chimeric antigen receptor T-cell (CAR-T) therapies. Applying IRIS to RNA-Seq data from 22 glioblastomas resected from patients, we identified candidate epitopes and validated their recognition by patient T cells, demonstrating IRIS’s utility for expanding targeted cancer immunotherapy.
Ginsenosides for therapeutically targeting inflammation through modulation of oxidative stress (2023)

Ginsenosides are steroid glycosides derived from ginseng plants such as Panax ginseng, Panax quinquefolium, and Panax notoginseng. Advances in recent studies have identified numerous physiological functions of each type of ginsenoside, i.e., immunomodulatory, antioxidative, and anti-inflammatory functions, in the context of inflammatory diseases. Accumulating evidence has revealed the molecular mechanisms by which the single or combined ginsenoside(s) exhibit anti-inflammatory effects, although it remains largely unclear. It is well known that excessive production of reactive oxygen species (ROS) is associated with pathological inflammation and cell death in a variety of cells, and that inhibition of ROS generation ameliorates the local and systemic inflammatory responses. The mechanisms by which ginsenosides attenuate inflammation are largely unknown; however, targeting ROS is suggested as one of the crucial mechanisms for the ginsenosides to control the pathological inflammation in the immune and non-immune cells. This review will summarize the latest progress in ginsenoside studies, particularly in the context of antioxidant mechanisms for its anti-inflammatory effects. A better understanding of the distinct types and the combined action of ginsenosides will pave the way for developing potential preventive and therapeutic modalities in treating various inflammation-related diseases.
Narrow-band light emission in a semiconductor-fiber asymmetric waveguide coupler (2002)

We have demonstrated a narrow-band, fiber-coupled light emitter based on evanescent coupling between a semiconductor waveguide and a polished single mode fiber. The semiconductor waveguide uses distributed Bragg reflector mirror layers to phase-match to the low index fiber at certain resonant wavelengths. The wavelength selectivity of the emission spectrum is caused by the very different dispersion characteristics of the two waveguides. A minimum linewidth of 1.5 nm is obtained.
Accurate segmentation of head and neck radiotherapy CT scans with 3D CNNs: consistency is key (2023)

<i>Objective.</i>Automatic segmentation of organs-at-risk in radiotherapy planning computed tomography (CT) scans using convolutional neural networks (CNNs) is an active research area. Very large datasets are usually required to train such CNN models. In radiotherapy, large, high-quality datasets are scarce and combining data from several sources can reduce the consistency of training segmentations. It is therefore important to understand the impact of training data quality on the performance of auto-segmentation models for radiotherapy.<i>Approach.</i>In this study, we took an existing 3D CNN architecture for head and neck CT auto-segmentation and compare the performance of models trained with a small, well-curated dataset (<i>n</i>= 34) and then a far larger dataset (<i>n</i>= 185) containing less consistent training segmentations. We performed 5-fold cross-validations in each dataset and tested segmentation performance using the 95th percentile Hausdorff distance and mean distance-to-agreement metrics. Finally, we validated the generalisability of our models with an external cohort of patient data (<i>n</i>= 12) with five expert annotators.<i>Main results.</i>The models trained with a large dataset were greatly outperformed by models (of identical architecture) trained with a smaller, but higher consistency set of training samples. Our models trained with a small dataset produce segmentations of similar accuracy as expert human observers and generalised well to new data, performing within inter-observer variation.<i>Significance.</i>We empirically demonstrate the importance of highly consistent training samples when training a 3D auto-segmentation model for use in radiotherapy. Crucially, it is the consistency of the training segmentations which had a greater impact on model performance rather than the size of the dataset used.
Mobilization as a Preparative Regimen for Hematopoietic Stem Cell (HSC) Transplantation in Rhesus Macaques. (2005)

Abstract The myeloablative conditioning regimens currently used for hematopoietic stem cell (HSC) transplantation are associated with significant morbidity and mortality. Alternative strategies to promote engraftment of infused HSCs with increased safety warrant investigation. In a murine model, we previously demonstrated that, in absence of irradiation, mobilization with AMD3100 (a CXCR4 antagonist) before marrow transplantation vacated microenvironmental niches and resulted in higher levels of engraftment of transplanted HSCs compared to controls (no AMD3100 treatment before transplantation) (Abkowitz JL et al., Blood (ASH Annual Meeting Abstracts)104 (11): 1187, 2004). In this study, we hypothesized that AMD3100 mobilization before transplantation could also promote HSC engraftment in a large animal model, eliminating the need for toxic myeloablative conditioning. Peripheral blood cells from two rhesus macaques were collected by apheresis 3 hours after administration of a single dose of AMD3100 1mg/Kg. CD34+ cells were enriched and transduced for four days in the presence of cytokines and fibronectin with non-expression Moloney murine leukemia virus-derived retroviral vectors (G1PLI) that carry a bacterial neomycin phosphotransferase resistance gene (neoR). The neoR-marked CD34+ cells were reinfused in the non-myeloablated animals, immediately after AMD3100 mobilization and apheresis repeated on the day of transplantation. NeoR-marking levels of approximately 0.1% were detected in both peripheral blood MNC and granulocytes at two months (animal 2RC102) and four months (animal RQ4791) after transplantation. Previous transplantation studies performed without prior myeloablative conditioning or mobilization preparative regimen resulted in no long-term in vivo gene marking. We mathematically confirmed that this observed level of gene marking is what can be expected when AMD3100 mobilization is used as a conditioning regimen. Previous studies have estimated the number of long-term repopulating HSCs at 6 per 105 CD34+ cells (Abkowitz JL et al, Blood96: 3399, 2000). In animal RQ4791, approximately 4.5X107 CD34+ cells, and therefore 2700 HSCs, were mobilized after AMD3100 administration. The total number of HSCs per animal is thought to be conserved in mammals and has been estimated at 11,000 to 22,000 (Abkowitz JL et al, Blood100: 2665, 2002). Hence, 12–24% of HSCs were mobilized after a single dose of AMD3100, consequently opening 12–24% of microenvironmental niches for engraftment. If 1% of engrafted HSCs are marked, 0.12–0.24% long-term marking levels are expected, correlating well with the observed marking level of 0.1%. These results imply that the number of available niches in large animals, as in murine models, regulates the number of HSCs that engraft. As importantly, mobilization with AMD3100 could provide a non-toxic preparative approach in large mammals, including humans, to improve HSC engraftment in transplantation for genetic and other nonmalignant disorders.
Dendritic cells fused with mastocytoma cells elicit therapeutic antitumor immunity (1998)

Characterization of the spontaneous immune response that frequently occurs in tumor-bearing animals, as well as immunization using dendritic cells pulsed with tumor antigens, suggests that a limiting factor of the tumor-specific immune response may be a defect in the co-stimulatory signal that is required for optimal activation of T cells. In this work, we describe a new approach to improve the antigen-presenting capacity of tumor cells, which does not require a source of purified tumor-associated antigen. We fused P815 mastocytoma cells with bone marrow-derived dendritic cells. We obtained one hybrid that displayed the phenotypic and functional properties of dendritic cells and expressed mRNA coding for the tumor-associated antigen P815 A/B. Injections of irradiated hybrid cells prevented the growth of preimplanted mastocytoma and induced long-lasting tumor resistance.
Authenticity Control of Food Flavorings - Merits and Limitations of Chiral Analysis (2015)

Chirality plays an important role in nature. In bio-recognition and transformation processes chirality acts as a basic selector for enzymes, microorganisms, plants and human beings. In 1848, Louis Pasteur was the first to report on the two stereoisomers of ammonium tartrate, and the famous British physicist Lord Kelvin concluded in 1883: "I call any geometrical figure or any groups of points chiral and say it has chirality if its image in a plane mirror, ideally realized cannot be brought to coincide with itself." Nowadays the principles of chirality are important for the investigation of natural products and xenobiotics as well. Multiple fields of research like pharma, plant physiology, feed, food and flavor chemistry are using enantioselective methods. Since chiral flavoring substances are sometimes characterized by different aroma and/or taste profiles as well as flavor intensities, enantiospecific evaluation of aroma compounds is key.
Simulation Trajectories For The Article "Molecular Conformation And Bilayer Pores In A Nonionic Surfactant Lamellar Phase Studies With 13C-1H Solid-State Nmr And Molecular Dynamics Simulations" (2015)

Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r System: 80 wt% C12E5, T=298K Other files available: http://dx.doi.org/10.6084/m9.figshare.861071
Pseudomonas aeruginosaExoY, a cyclic GMP- and cyclic UMP-generating nucleotidyl cyclase (2013)

Background In previous studies we showed that in addition to the cyclic nucleotides (cNMPs) cAMP and cGMP, mammalian cells also contain cCMP and cUMP [for review see [1], [2]]. cCMP and cUMP are generated by the bacterial exotoxins CyaA from Bordetella pertussis and edema factor (EF) from Bacillus anthracis as well as nitric oxide (NO)stimulated soluble guanylyl cyclase (sGC). cCMP and cUMP activate cAMP-dependent protein kinase (PKA), cGMP-dependent protein kinase (PKG) and cyclic nucleotide-regulated ion channels (HCN channels). cUMP, but not cCMP, is degraded by several known phosphodiesterases (PDEs). cCMP and cUMP are also exported from cells via multidrug resistance proteins (MRPs 4 and 5). These findings suggest that cCMP and cUMP constitute second messenger molecules with distinct signalling properties. Pseudomonas aeruginosa is an important pathogenic bacterium, specifically in patients with cystic fibrosis. P. aeruginosa injects effector proteins into host cells via the type III secretion system and, thereby, manipulates their functions. One of the effector proteins of P. aeruginosa is ExoY. ExoY possesses structural similarity with CyaA and EF in the catalytic domain and was assumed to constitute an adenylyl cyclase (AC) [3]. However, the cAMP-forming capacity of ExoY is rather low. More recently, it has been shown that ExoY is capable of producing large quantities of cGMP [4]. On this background, we examined the question whether ExoY also exhibits cytidylyland uridylyl cyclase activity. Methods We transfected mammalian cells with a plasmid encoding ExoY or a catalytically inactive ExoY mutant (ExoY-M). We also infected cells with P. aeruginosa encoding ExoY or ExoY-M. In addition, we infected mice intratracheally with P. aeruginosa. We determined cNMP concentrations with highly sensitive and specific HPLC-MS/MS and HPLC-MS/TOF methods. We assessed cell morphology, apoptosis and label-free dynamic mass distribution, constituting a holistic and unbiased assay for cell activation.
Localization of a non-cooperative target with distributedbinary observations (2017)

Thesis (Ph. D.)--University of Rochester. Department of Electrical and Computer Engineering, 2017
NMR Hydrogen Exchange and Relaxation Reveal Positions Stabilized by p53 Rescue Mutants N239Y and N235K (2021)

Abstract Inactivation of p53 is found in over 50% of all cancers; p53 disfunction is often caused by a single missense mutation localized in the DNA binding domain (DBD). Rescue mutants N235K and N239Y stabilize and restore function to multiple p53 cancer mutants. Here, we use NMR to compare protein dynamics between WT and rescue mutants to understand the mechanism of stabilization. We measured and compared folding dynamics by calculating protection factors (PFs) from NMR hydrogen exchange rates of backbone amides. We find that both rescue mutants impose a global stabilizing effect that dampens their motions compared to WT DBD, predominantly in the β-sandwich. However, a few regions become more flexible in rescue mutants. Notably, positions that have increased PFs map to cancer mutants rescued by each mutant. We also compared relaxation results to obtain flexibility information in the ps to ns timescale regime. Protein sequence analysis was used to determine the occurrence of these rescue mutants in nature and showed that 235K is found in mice and rats, but there is no evidence of 239Y occurring naturally in any species. Understanding the mechanism by which stabilizing mutants rescue p53 may reveal novel avenues for the development of cancer therapeutics. Our findings suggest that cancer therapeutics aimed at restoring p53 function could consider protein dynamics as a metric of drug efficacy. Statement of Significance Two mutations (N235K and N239Y) within the DNA binding domain of p53 are known to reverse the effects of multiple cancer mutants. However, the mechanism of rescue is not clear since the crystal structures of these mutants are virtually identical to that of the WT. Here we use NMR methods to show that the protein dynamics of the rescue mutants are significantly different compared to WT, allowing us to describe the stability on a per-residue basis. Although these mutations are only four residues apart, they stabilize the structure distinctly in different regions, consistent with the specific cancer mutations they to which they restore function.
Supplementary Figure 1 from Construction and Characterization of Novel, Recombinant Immunotoxins Targeting the <i>Her2/neu</i> Oncogene Product: <i>In vitro</i> and <i>In vivo</i> Studies (2023)

Supplementary Figure 1 from Construction and Characterization of Novel, Recombinant Immunotoxins Targeting the &lt;i&gt;Her2/neu&lt;/i&gt; Oncogene Product: &lt;i&gt;In vitro&lt;/i&gt; and &lt;i&gt;In vivo&lt;/i&gt; Studies