gebhart/patrepeval huggingface dataset:
Microenvironmental Sensing by Fibroblasts Controls Macrophage Population Size (2022)

Abstract Animal tissues are comprised of diverse cell types. However, the mechanisms controlling the number of each cell type within tissue compartments remain poorly understood. Here, we report that different cell types utilize distinct strategies to control population numbers. Proliferation of fibroblasts, stromal cells important for tissue integrity, is limited by space availability. In contrast, proliferation of macrophages, innate immune cells involved in defense, repair, and homeostasis, is constrained by growth factor availability. Examination of density-dependent gene expression in fibroblasts revealed that Hippo and TGF- β target genes are both regulated by cell density. We found YAP1, the transcriptional co-activator of the Hippo signaling pathway, directly regulates expression of Csf1 , the lineage-specific growth factor for macrophages, through an enhancer of Csf1 that is specifically active in fibroblasts. Activation of YAP1 in fibroblasts elevates Csf1 expression and is sufficient to increase the number of macrophages at steady state. Our data also suggest that expression programs in fibroblasts that change with density may result from sensing of mechanical force through actin-dependent mechanisms. Altogether, we demonstrate that two different modes of population control are connected and coordinated to regulate cell numbers of distinct cell types. Sensing of the tissue environment may serve as a general strategy to control tissue composition. Significance Statement Collections of distinct cell types constitute animal tissues. To perform their unique functions, each cell type must exist in the correct number and proportion in a given tissue compartment. However, many of the mechanisms regulating and coordinating cell population sizes remain enigmatic. Our study characterizes two different modes of population size control, utilized by two ubiquitous cell types, macrophages and fibroblasts. Macrophage populations are more sensitive to the presence of growth factors in the environment and fibroblasts are more sensitive to space limitations. Intriguingly, space-sensing mechanisms in fibroblasts directly control the production of growth factor for macrophages and thus macrophage numbers. This link suggests a mechanism by which macrophage compartment size is controlled by stromal cells according to the microenvironment.
Viral Replication Rate Regulates Clinical Outcome and CD8 T Cell Responses during Highly Pathogenic H5N1 Influenza Virus Infection in Mice (2010)

Since the first recorded infection of humans with H5N1 viruses of avian origin in 1997, sporadic human infections continue to occur with a staggering mortality rate of >60%. Although sustained human-to-human transmission has not occurred yet, there is a growing concern that these H5N1 viruses might acquire this trait and raise the specter of a pandemic. Despite progress in deciphering viral determinants of pathogenicity, we still lack crucial information on virus/immune system interactions pertaining to severe disease and high mortality associated with human H5N1 influenza virus infections. Using two human isolates of H5N1 viruses that differ in their pathogenicity in mice, we have defined mechanistic links among the rate of viral replication, mortality, CD8 T cell responses, and immunopathology. The extreme pathogenicity of H5N1 viruses was directly linked to the ability of the virus to replicate rapidly, and swiftly attain high steady-state titers in the lungs within 48 hours after infection. The remarkably high replication rate of the highly pathogenic H5N1 virus did not prevent the induction of IFN-β or activation of CD8 T cells, but the CD8 T cell response was ineffective in controlling viral replication in the lungs and CD8 T cell deficiency did not affect viral titers or mortality. Additionally, BIM deficiency ameliorated lung pathology and inhibited T cell apoptosis without affecting survival of mice. Therefore, rapidly replicating, highly lethal H5N1 viruses could simply outpace and overwhelm the adaptive immune responses, and kill the host by direct cytopathic effects. However, therapeutic suppression of early viral replication and the associated enhancement of CD8 T cell responses improved the survival of mice following a lethal H5N1 infection. These findings suggest that suppression of early H5N1 virus replication is key to the programming of an effective host response, which has implications in treatment of this infection in humans.
Traversal recursion: a practical approach to supporting recursive applications (1986)

Many capabilities that are needed for recursive applications in engineering and project management are not well supported by the usual formulations of recursion. We identify a class of recursions called “traversal recursions” (which model traversals of a directed graph) that have two important properties they can supply the necessary capabilities and efficient processing algorithms have been defined for them. First we present a taxonomy of traversal recursions based on properties of the recursion on graph structure and on unusual types of metadata. This taxonomy is exploited to identify solvable recursions and to select an execution algorithm. We show how graph traversal can sometimes outperform the more general iteration algorithm. Finally we show how a conventional query optimizer architecture can be extended to handle recursive queries and views.
Current rectification by nanoparticles in bipolar nanopores (2022)

Bipolar nanochannels comprising two domains of positively and negatively charged walls along the pore axis are known to rectify current when exposed to an electric potential bias. We find that addition of charged nanoparticles can increase rectification considerably, by approximately one order of magnitude. Two bipolar channel geometries are considered here; their behavior is examined at rest and under the influence of a negative bias and a positive bias, respectively. We do so by relying on a molecular-level model of the electrolyte solution in the channels. The large increase in current rectification can be explained by the inherent electric field that charged nanoparticles generate within the channel. This effect is found to be largely dependent on the pore's geometry, its charge distribution, and the sign of the nanoparticles' charge, thereby offering new opportunities for design of engineered nanopore membrane-nanoparticle systems for energy storage.
Supplementary Figure 7 from Sangivamycin-like Molecule 6 Exhibits Potent Anti-Multiple Myeloma Activity through Inhibition of Cyclin-Dependent Kinase-9 (2023)

&lt;p&gt;PDF file, 124K, Comparison of MM oncoprotein and housekeeper protein half-lives.&lt;/p&gt;
A High‐Throughput Approach to Repurposing Olefin Polymerization Catalysts for Polymer Upcycling (2022)

Efficient and economical plastic waste upcycling relies on the development of catalysts capable of polymer degradation. A systematic high-throughput screening of twenty-eight polymerization catalyst precursors, belonging to the catalyst families of metallocenes, ansa-metallocenes, and hemi- and post-metallocenes, in cis-1,4-polybutadiene (PB) degradation reveals, for the first time, important structure-activity correlations. The upcycling conditions involve activation of the catalysts (at 0.18 % catalyst loading) with tri-iso-butyl aluminum at 50 °C in toluene. The data indicate the ability to degrade PB is a general reactivity profile of neutral group 4 metal hydrides. A simple quantitative-structure activity relationship (QSAR) model utilizing two descriptors for the distribution of steric bulk in the active pocket and one measuring the metal ion electrophilicity reveals the degradation ability improves with increased but not overbearing steric congestion and lower electrophilicity.
Radiogenomic-Based Survival Risk Stratification of Tumor Habitat on Gd-T1w MRI Is Associated with Biological Processes in Glioblastoma (2020)

Our findings suggest that prognostic radiomic features from routine Gd-T1w MRI may also be significantly associated with key biological processes that affect response to chemotherapy in GBM.
Laboratory Experiments on Bentonite Samples: FY16 Progress (2016)

The primary goal of this study is to improve the understanding of U(VI) sorption and diffusion behavior in sodium-montmorillonite in order to support the development of realistic conceptual models describing these processes in performance assessment models while (1) accounting for potential changes in system conditions over time and space, (2) avoiding overly conservative transport predictions, and (3) using a minimum number of fitting parameters.
A vector mapping scheme for efficient implementation of beamforming MIMO systems (2008)

Quantized feedback in multiple antenna systems has the potential to increase throughput and/or reduce probability of outage. However, current beamforming codebook designs lead to large implementation complexity of the channel quantizer. We propose a vector mapping scheme to construct beamforming codebooks from existing codebooks. We show that beamforming codebooks constructed via the proposed vector mapping have a structure that allows an efficient implementation of the channel quantizer. We show that the proposed vector mapping can also be used to simplify the implementation of the channel quantizer in a WiMAX compliant system, where the codebooks have already been defined. Simulation results validate the proposed codebook construction method.
N-terminal Domain of Yeast Telomerase Reverse Transcriptase: Recruitment of Est3p to the Telomerase Complex (2003)

Telomerase is a reverse transcriptase that maintains chromosome ends. The N-terminal half of the catalytic protein subunit (TERT) contains three functional domains (I, II, and III) that are conserved among TERTs but not found in other reverse transcriptases. Guided by an amino acid sequence alignment of nine TERT proteins, mutations were introduced into yeast TERT (Est2p). In support of the proposed alignment, mutation of virtually all conserved residues resulted in loss-of-function or temperature sensitivity, accompanied by telomere shortening. Overexpression of telomerase component Est3p led to allele-specific suppression of the temperature-sensitive mutations in region I, suggesting that Est3p interacts with this protein domain. As predicted by the genetic results, a lethal mutation in region I resulted in loss of Est3p from the telomerase complex. We conclude that Est2p region I is required for the recruitment of Est3p to yeast telomerase. Given the phylogenetic conservation of region I of TERT, this protein domain may provide the equivalent function in all telomerases.
ChemInform Abstract: Phosphates as New Catalysts of Organic Synthesis in Heterogeneous Media (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Few-Cycle Driven Relativistically Oscillating Plasma Mirrors: A Source of Intense Isolated Attosecond Pulses (2012)

The conditions required for the production of isolated attosecond pulses from relativistically oscillating mirrors (ROM) are investigated numerically and experimentally. In simulations, carrier-envelope-phase-stabilized three-cycle pulses are found to be sufficient to produce isolated attosecond pulses, while two-cycle pulses will predominantly lead to isolated attosecond pulses even in the absence of carrier-envelope stabilization. Using a state-of-the-art laser system delivering three-cycle pulses at multiple-terawatt level, we have generated higher harmonics up to 70 eV photon energy via the ROM mechanism. The observed spectra are in agreement with theoretical expectations and highlight the potential of few-cycle-driven ROM harmonics for intense isolated attosecond pulse generation for performing extreme ultraviolet-pump extreme ultraviolet-probe experiments.
Supplementary document for Reduced Optical Losses in Refractory Plasmonic Titanium Nitride Thin Films Deposited With Molecular Beam Epitaxy - 4844551.pdf (2020)

Supplemental Document contains information related to growth and optical characterization.
Performance Characteristics of a Novel Radioactive Isotope Detection and Notification System Designed for Use in Hospitals (2011)

Recently, University of Pittsburgh Medical Center (UPMC) Cancer Centers has installed an Emergency Department Notification System (EDNS) in one of its hospitals. This system, manufactured by Thermo Fisher Scientific (Thermo Fisher Scientific, Inc., 81 Wyman Street, Waltham, MA 02454), was designed to discriminate non-medical radioactive isotopes from medical radioactive isotopes routinely used in nuclear medicine and radiation treatments. It is modular in nature and consists of four NaI(Tl) scintillation detectors, a 512 channels multi-channel analyzer, a system controller, and a database-monitoring server. A series of tests were carried out to evaluate the performance characteristics of this system using a variety of radioactive sources of varying activities. These included measurements of minimum detectable activity, detector response distance to various source activities, detector response to different speeds of a moving radioisotope, and single and multiple radioisotope identification and classification. Measured results show that the system is capable of identifying radioactive sources of nominal activity 0.13 MBq (3.5 μCi) and higher in a relatively short period of time (<11.1 s). The database-monitoring server could send an alarm signal to appropriate personnel when the analysis of the results indicated the presence of a non-medical or threat radioisotope. The present paper reports these results.
Decoupling synchronization and data transfer in message passing systems of parallel computers (1995)

Article Decoupling synchronization and data transfer in message passing systems of parallel computers Share on Authors: T. Stricker School of Computer Science, Carnegie Mellon University, Pittsburgh, PA School of Computer Science, Carnegie Mellon University, Pittsburgh, PAView Profile , J. Stichnoth School of Computer Science, Carnegie Mellon University, Pittsburgh, PA School of Computer Science, Carnegie Mellon University, Pittsburgh, PAView Profile , D. O'Hallaron School of Computer Science, Carnegie Mellon University, Pittsburgh, PA School of Computer Science, Carnegie Mellon University, Pittsburgh, PAView Profile , S. Hinrichs School of Computer Science, Carnegie Mellon University, Pittsburgh, PA School of Computer Science, Carnegie Mellon University, Pittsburgh, PAView Profile , T. Gross School of Computer Science, Carnegie Mellon University, Pittsburgh, PA and Institut für Computer Systeme, ETH Zürich, CH 8092 Zürich School of Computer Science, Carnegie Mellon University, Pittsburgh, PA and Institut für Computer Systeme, ETH Zürich, CH 8092 ZürichView Profile Authors Info & Claims ICS '95: Proceedings of the 9th international conference on SupercomputingJuly 1995 Pages 1–10https://doi.org/10.1145/224538.224539Online:03 July 1995Publication History 25citation370DownloadsMetricsTotal Citations25Total Downloads370Last 12 Months2Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
High sensitivity cardiac troponin T in patients not having an acute coronary syndrome: results from the TRAPID-AMI study (2017)

Hs-cTnT may help predict whether non-ACS ED patients have a final non-ACS cardiac or non-cardiac/unknown origin diagnoses.
Signaling cascades implicated in muscarinic regulation of proliferation of neural stem and progenitor cells (2004)

Muscarinic acetylcholine receptors (mAChRs) belong to the G-protein-coupled receptor superfamily that transduces signals through multiple intracellular signaling cascades to regulate a wide variety of physiological responses. Recently, it has been discovered that subtypes of mAChRs are expressed in proliferative neuroepithelial cells of the ventricular zone and in basic fibroblast growth factor-expanded neural stem and progenitor cell cultures. Activation of the mAChRs by ACh or its analogue carbachol leads to increased DNA synthesis and neurogenesis. The mitogenic effects of muscarinic agonists are likely mediated via mAChR-activated multisignaling pathways. The exact intracellular mechanisms underlying mAChR-modulated DNA synthesis and neurogenesis are not fully understood. However, several pathways through Ras-mitogen-activated protein kinase, phosphatidylinositol 3-kinase-Akt, protein kinase C, c-Src and Ca(2+) signaling have been shown to play roles in this dynamic process. These novel signaling cascades may improve our understanding of the intracellular mechanisms underlying mAChR-stimulated neural progenitor proliferation and provide insights for therapeutic drug development.
Data from Pan-HER, an Antibody Mixture Simultaneously Targeting EGFR, HER2, and HER3, Effectively Overcomes Tumor Heterogeneity and Plasticity (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Accumulating evidence indicates a high degree of plasticity and compensatory signaling within the human epidermal growth factor receptor (HER) family, leading to resistance upon therapeutic intervention with HER family members.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design/Results:&lt;/b&gt; We have generated Pan-HER, a mixture of six antibodies targeting each of the HER family members EGFR, HER2, and HER3 with synergistic pairs of antibodies, which simultaneously remove all three targets, thereby preventing compensatory tumor promoting mechanisms within the HER family. Pan-HER induces potent growth inhibition in a range of cancer cell lines and xenograft models, including cell lines with acquired resistance to therapeutic antibodies. Pan-HER is also highly efficacious in the presence of HER family ligands, indicating that it is capable of overcoming acquired resistance due to increased ligand production. All three target specificities contribute to the enhanced efficacy, demonstrating a distinct benefit of combined HER family targeting when compared with single-receptor targeting.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Our data show that simultaneous targeting of three receptors provides broader efficacy than targeting a single receptor or any combination of two receptors in the HER family, especially in the presence of HER family ligands. Pan-HER represents a novel strategy to deal with primary and acquired resistance due to tumor heterogeneity and plasticity in terms of HER family dependency and as such may be a viable alternative in the clinic. &lt;i&gt;Clin Cancer Res; 21(18); 4110–22. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;i&gt;See related commentary by Yarden and Sela, p. 4030&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Selective Classifiers for Part-of-Speech Tagging (2014)

We investigate the use of selective classi-fiers for part-of-speech tagging (POS). The idea is to allow classifiers to abstain on hard instances, passing them to down-stream classifiers that may have more context available. In this report we focus on just the first stage of such a cascade, and ask whether selective classifiers attain the accuracies needed on those instances they accept, given that such instances will not be revisited by downstream pro-cessing. We show that a selective classi-fier that is constructed as an abstaining committee of two off-the-shelf POS tag-gers can indeed achieve very high accura-cies with modest drops in coverage. We also compute the overall accuracy when all instances are voted on by applying ma-jority vote to the abstentions, and we find that this results in state of the art accura-cies, robustly.
A randomized, controlled, split‐face study of topical timolol maleate 0.5% eye drops for the treatment of erythematotelangiectatic rosacea (2021)

In this small study, the application of topical timolol maleate was safe and effective for the treatment of ETR.
ChemInform Abstract: POTENTIAL ANTITUMOR AGENTS. 22. LATENTIATED CONGENERS OF THE 4′‐(9‐ACRIDINYLAMINO)METHANESULFONANILIDES (1977)

Abstract Aus den Sulfonamiden (I) werden mit Säurechlori‐ den (II) die Substitutionsprodukte (III) hergestellt, die zu den Aminen (IV) reduziert und dann mit dem Chloracridin (V) zu (VI) kondensiert werden.
Supplementary Table 6 from TYK2–STAT1–BCL2 Pathway Dependence in T-cell Acute Lymphoblastic Leukemia (2023)

&lt;p&gt;XLSX file - 23K, Clinical, biologic and molecular characteristics of the T-ALL patient samples analyzed. See separate file.&lt;/p&gt;
Direct polymerization of surface‐tethered polyelectrolyte layers in aqueous solution via surface‐confined atom transfer radical polymerization (2007)

Abstract The direct polymerization of deprotonated acidic monomers in aqueous solutions was achieved via surface‐confined atom transfer radical polymerization (SC‐ATRP) to produce surface‐tethered polyelectrolyte brushes. Layers of poly(itaconic acid), poly(methacrylic acid), and sodium poly(styrene sulfonate) were grown by SC‐ATRP from self‐assembled initiator monolayers of [BrC(CH 3 ) 2 COO(CH 2 ) 11 S] 2 on gold substrates. The polymer layers were characterized with variable‐angle ellipsometry and external‐reflection Fourier transform infrared spectroscopy. Without intervention, atom transfer radical polymerization catalysts were deactivated by complexation with the deprotonated acidic monomers, disproportionation, and dissociation during the polymerization of these monomers in water; the result was the cessation of polymer growth. The addition of an alkali salt to the reaction media suppressed catalyst deactivation, allowing polymer layers to increase in thickness linearly for longer periods of time with respect to salt‐free conditions. This result suggested an improved degree of polymerization control. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 566–575, 2007
Design of a Switched Broad-Band Communications Network for Interactive Services (1975)

The congestion in broad-band communications networks resulting from the increased demand for interactive services is considered. It is shown that services such as a video library could not be provided to the majority of subscribers in a conventional CATV network. A design is developed for a space division multiplex broad-band network which can be expanded at minimum cost to meet an increasing demand for interactive services. The network contains two signal distribution networks: a cablecast system similar to the Rediffusion system, and a switched communication network providing point-to-point circuits for both one-way and two-way services. All broad-band signals are transmitted to the subscribers in the 1- to 10-MHz spectrum, permitting the use of twisted pair video cables and a minimum number of cable amplifiers. The broad-band cable network (BCN) is organized around 15 local switching exchanges and one central exchange. Multipoint switches in local exchanges under wired-logic circuit control connect individual subscriber communication lines to any channel. Crosspoint matrix switching groups in the local and central exchanges connect communication circuits in the broad-band communication network under programmed computer control. This network is accessed via links terminating on one channel of the multiposition switches. Per-subscriber costs are estimated to be 190 dollars for a cablecast system serving 3800 subscribers. Additional expenditures per subscriber of 40 dollars for fixed costs and 40 dollars for variable costs would provide interactive services. The range of interactive services provided would be extremely flexible, including both one-way video library service and point-to-point two-way communications.