gebhart/patrepeval huggingface dataset:
Concurrent multifunction transmit and receive applications with dynamic filtering (2010)

This paper demonstrates a concept for transmitting on one set of elements of a phased array while concurrently receiving on another set at a separate frequency. Cases are analyzed using measured data from an 8×8 microstrip stacked patch panel array operating at 33.8GHz, and relative coupling levels from interfering elements to receive elements are characterized over various scan angles for two array configurations - side-by-side contiguous blocks and for interleaved elements at separate frequencies. It is shown that an optimum transmit frequency exists that minimizes coupled power to receiving elements in the array for a given scan angle. Additional isolation between elements is achieved with a tunable bandpass-bandstop filter cascade that, when paired with a high-linearity low-noise amplifier, reduces interference from transmitting elements to within the receiver analog-to-digital converter's (ADC) dynamic range, such that receiving elements can operate concurrently next two 25W transmitting elements.
CD1d Degradation in Chlamydia trachomatis-infected Epithelial Cells Is the Result of Both Cellular and Chlamydial Proteasomal Activity (2007)

Chlamydia trachomatis is an obligate intracellular pathogen that can persist in the urogenital tract. Mechanisms by which C. trachomatis evades clearance by host innate immune responses are poorly described. CD1d is MHC-like, is expressed by epithelial cells, and can signal innate immune responses by NK and NKT cells. Here we demonstrate that C. trachomatis infection down-regulates surface-expressed CD1d in human penile urethral epithelial cells through proteasomal degradation. A chlamydial proteasome-like activity factor (CPAF) interacts with the CD1d heavy chain, and CPAF-associated CD1d heavy chain is then ubiquitinated and directed along two distinct proteolytic pathways. The degradation of immature glycosylated CD1d was blocked by the proteasome inhibitor lactacystin but not by MG132, indicating that degradation was not via the conventional proteasome. In contrast, the degradation of non-glycosylated CD1d was blocked by lactacystin and MG132, consistent with conventional cellular cytosolic degradation of N-linked glycoproteins. Immunofluorescent microscopy confirmed the interruption of CD1d trafficking to the cell surface, and the dislocation of CD1d heavy chains into both the cellular cytosol and the chlamydial inclusion along with cytosolic CPAF. C. trachomatis targeted CD1d toward two distinct proteolytic pathways. Decreased CD1d surface expression may help C. trachomatis evade detection by innate immune cells and may promote C. trachomatis persistence.
NMR spin diffusion measurements in disordered polymers: Insights and limitations (2019)

Nuclear magnetic resonance (NMR) spin diffusion measurements have been widely used to estimate domain sizes in a variety of polymer materials. In cases where the domains are well-described as regular, repeating structures (e.g., lamellar, cylindrical channels, monodispersed spherical domains), the domain sizes estimated from NMR spin diffusion experiments agree with the characteristic length scales obtained from small-angle x-ray scattering and microscopy. In our laboratory, recent NMR spin diffusion experiments for hydrated sulfonated Diels Alder poly(phenylene) (SDAPP) polymer membranes have revealed that assuming a simple structural model can often misrepresent or overestimate the domain size in situations where more complex and disordered morphologies exist. Molecular dynamics simulations of the SDAPP membranes predict a complex heterogeneous hydrophilic domain structure that varies with the degree of sulfonation and hydration and is not readily represented by a simple repeating domain structure. This heterogeneous morphology results in NMR-measured domain sizes that disagree with length scales estimated from the ionomer peak in scattering experiments. Here we present numerical NMR spin diffusion simulations that show how structural disorder in the form of domain size distributions or domain clustering can significantly impact the spin diffusion analysis and estimated domain sizes. Simulations of NMR spin diffusion with differing domain size distributions and domain clustering are used to identify the impact of the heterogeneous domain structure and highlight the limitations of using NMR spin diffusion techniques for irregular structures.
Adaptive laboratory evolution in S. cerevisiae highlights role of transcription factors in fungal xenobiotic resistance (2022)

In vitro evolution and whole genome analysis were used to comprehensively identify the genetic determinants of chemical resistance in Saccharomyces cerevisiae. Sequence analysis identified many genes contributing to the resistance phenotype as well as numerous amino acids in potential targets that may play a role in compound binding. Our work shows that compound-target pairs can be conserved across multiple species. The set of 25 most frequently mutated genes was enriched for transcription factors, and for almost 25 percent of the compounds, resistance was mediated by one of 100 independently derived, gain-of-function SNVs found in a 170 amino acid domain in the two Zn<sub>2</sub>C<sub>6</sub> transcription factors YRR1 and YRM1 (p < 1 × 10<sup>-100</sup>). This remarkable enrichment for transcription factors as drug resistance genes highlights their important role in the evolution of antifungal xenobiotic resistance and underscores the challenge to develop antifungal treatments that maintain potency.
3D printing fluorescent material with tunable optical properties (2021)

The 3D printing of fluorescent materials could help develop, validate, and translate imaging technologies, including systems for fluorescence-guided surgery. Despite advances in 3D printing techniques for optical targets, no comprehensive method has been demonstrated for the simultaneous incorporation of fluorophores and fine-tuning of absorption and scattering properties. Here, we introduce a photopolymer-based 3D printing method for manufacturing fluorescent material with tunable optical properties. The results demonstrate the ability to 3D print various individual fluorophores at reasonably high fluorescence yields, including IR-125, quantum dots, methylene blue, and rhodamine 590. Furthermore, tuning of the absorption and reduced scattering coefficients is demonstrated within the relevant mamalian soft tissue coefficient ranges of 0.005-0.05 mm<sup>-1</sup> and 0.2-1.5 mm<sup>-1</sup>, respectively. Fabrication of fluorophore-doped biomimicking and complex geometric structures validated the ability to print feature sizes less than 200 μm. The presented methods and optical characterization techniques provide the foundation for the manufacturing of solid 3D printed fluorescent structures, with direct relevance to biomedical optics and the broad adoption of fast manufacturing methods in fluorescence imaging.
Geometric cues for directing the differentiation of mesenchymal stem cells (2010)

Significant efforts have been directed to understanding the factors that influence the lineage commitment of stem cells. This paper demonstrates that cell shape, independent of soluble factors, has a strong influence on the differentiation of human mesenchymal stem cells (MSCs) from bone marrow. When exposed to competing soluble differentiation signals, cells cultured in rectangles with increasing aspect ratio and in shapes with pentagonal symmetry but with different subcellular curvature-and with each occupying the same area-display different adipogenesis and osteogenesis profiles. The results reveal that geometric features that increase actomyosin contractility promote osteogenesis and are consistent with in vivo characteristics of the microenvironment of the differentiated cells. Cytoskeletal-disrupting pharmacological agents modulate shape-based trends in lineage commitment verifying the critical role of focal adhesion and myosin-generated contractility during differentiation. Microarray analysis and pathway inhibition studies suggest that contractile cells promote osteogenesis by enhancing c-Jun N-terminal kinase (JNK) and extracellular related kinase (ERK1/2) activation in conjunction with elevated wingless-type (Wnt) signaling. Taken together, this work points to the role that geometric shape cues can play in orchestrating the mechanochemical signals and paracrine/autocrine factors that can direct MSCs to appropriate fates.
Passive Intranasal Monoclonal Antibody Prophylaxis against MurinePneumocystis cariniiPneumonia (2002)

Passive antibody immunoprophylaxis is one method used to protect patients against infection if they are unable to mount an adequate active immune response. Topical application of antibody may be effective against infections at mucosal sites. Using a SCID mouse model of Pneumocystis carinii pneumonia, we were able to demonstrate protection against an airborne challenge with P. carinii by intranasal administration of antibody. Immunoglobulin M (IgM) monoclonal antibodies to an epitope shared by mouse and human P. carinii organisms reduced organism numbers by more than 99% under the conditions described. An IgG1 switch variant of one of the IgM monoclonal antibodies was also protective. These experiments provide a model for exploring the utility of this approach in protecting at-risk patients from infection with P. carinii.
LGG-51. METABOLIC PROFILING IN PEDIATRIC LOW GRADE GLIOMA IDENTIFIES GLUTATHIONE DEPLETION AFTER MTORC1 INHIBITION AND VALIDATES EVEROLIMUS AND CARBOPLATIN AS A POTENTIAL COMBINATION THERAPY (2018)

The mTOR pathway contributes to the tumorigenicity of aggressive pediatric low grade glioma (pLGG) and TORC1 inhibitors have demonstrated efficacy in treating pLGG cell lines. The FDA-approved TORC1 inhibitor, everolimus, is currently in clinical trials for patients with recurrent/refractory pLGG. We hypothesized that metabolic alterations downstream of TORC1 inhibition could be targeted to synergize with everolimus and reduce pLGG tumorigenicity. We identified through unbiased metabolic screens and stable isotope tracing that glutathione was downregulated (p<0.001) after everolimus treatment in both in vitro and in vivo models of pLGGs. Based on this finding, we combined everolimus with carboplatin, a DNA damaging agent that is detoxified by glutathione conjugation. We treated 5 pLGG models (4 cell lines and one patient-derived xenograft) representing a range of mutations commonly found in pLGG including, BRAF-KIAA1549 fusion, BRAFV600E, and NF1 loss. To our knowledge, this study is the first to use a pLGG NF1 null cell line, JHH-NF1-PA1. Carboplatin synergized with everolimus to slow cell growth in most cell lines (CI<1 at Fa 0.5). The combination increased expression of apoptotic markers, (cleaved-PARP, cleaved caspase-3) and markers of DNA damage (phosphorylation of gamma-H2AX, 154%-1800% increase compared to carboplatin alone). The combination of carboplatin and everolimus reduced BRAFV600E-driven BT40 pLGG xenograft tumor growth better than either agent alone, (p<0.001 by ANOVA). Exogenous glutathione rescued the effects of everolimus, further supporting the mechanism of synergy between these agents. In summary, this study provides the pre-clinical justification for combining everolimus with carboplatin in pLGG clinical trials.
A Security Layer for Smartphone-to-Vehicle Communication Over Bluetooth (2013)

Modern vehicles are increasingly being interconnected with computer systems, which collect information both from vehicular sources and Internet services. Unfortunately, this creates a nonnegligible attack surface, which extends when vehicles are partly operated via smartphones. In this letter, a hierarchically distributed control system architecture which integrates a smartphone with classical embedded systems is presented, and an ad-hoc, end-to-end security layer is designed to demonstrate how a smartphone can interact securely with a modern vehicle without requiring modifications to the existing in-vehicle network. Experimental results demonstrate the effectiveness of the approach.
New ball grid array module test sockets (2002)

New sockets have been-designed and fabricated for testing advanced BGA modules. The socket can easily be custom designed to match any BGA footprint, size and pitch. The socket materials, including the contact metallurgy, frame and the elastomeric materials, are capable of performing burn-in test at temperatures higher than 150/spl deg/C for a prolonged time in air. The compliance of the sockets are tailored to bring just enough contact force to penetrate the thin oxide layer on the solder without severely deforming the solder ball. As a result, low and stable contact resistance has been achieved with low contact force in repeated touch-down cycles. The contact force to solder balls ranges from 12 to 50 grams per contact at 10 mils displacement. The contact structure and geometry have been enhanced to allow for multiple module test cycles (>50000 life cycles) with negligible damage to the contact pads.
Mask topography effects of hole patterns on hyper-NA lithography (2007)

The purpose of this work was to find the specific effects of hole patterns in 32nm node logic by analyzing in the Fourier domain and to clarify the mechanism of mask topography effects. Our focus patterns extend from the lines and spaces (LS) to the contact hole (CH). We also attempt to perform factor analyses of mask topography effects. Intensities of LS and CH patterns are simulated using three mask models. For each of the three models, the method of approximating the mask topography effect is different. As a result, a serious difference among the three mask models has been found with respect to the intensity profile for 32nm node and beyond, though the mask sizes for all models are the same. As the accuracy of mask model improved, it was found that the image contrast tends to decrease on LS patterns while increasing on CH patterns. The qualitative interpretation of the trend of contrast variations can be described by analyzing in the Fourier domain. The mask topography effects can be separated into waveguide and shadowing effects using scatter graphs. It is concluded from the result that one of the major differences between LS and CH is attributable to phase differences between 0th order and 1st order diffractions, because the size of effects for CH have been larger than that for LS.
Transcription-controlled gene therapy against tumor angiogenesis (2004)

A major drawback of current approaches to antiangiogenic gene therapy is the lack of tissue-specific targeting. The aim of this work was to trigger endothelial cell-specific apoptosis, using adenoviral vector-mediated delivery of a chimeric death receptor derived from the modified endothelium-specific pre-proendothelin-1 (PPE-1) promoter. In the present study, we constructed an adenovirus-based vector that targets tumor angiogenesis. Transcriptional control was achieved by use of a modified endothelium-specific promoter. Expression of a chimeric death receptor, composed of Fas and TNF receptor 1, resulted in specific apoptosis of endothelial cells in vitro and sensitization of cells to the proapoptotic effect of TNF- . The antitumoral activity of the vectors was assayed in two mouse models. In the model of B16 melanoma, a single systemic injection of virus to the tail vein caused growth retardation of tumor and reduction of tumor mass with central tumor necrosis. When the Lewis lung carcinoma lung-metastasis model was applied, i.v. injection of vector resulted in reduction of lungmetastasis mass, via an antiangiogenic mechanism. Moreover, by application of the PPE-1-based transcriptional control, a humoral immune response against the transgene was avoided. Collectively, these data provide evidence that transcriptionally controlled, angiogenesis-targeted gene therapy is feasible.
Synthesis and characterization of a selenabenzene (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and characterization of a selenabenzeneJoseph Stackhouse, G. H. Senkler Jr., Bruce E. Maryanoff, and Kurt MislowCite this: J. Am. Chem. Soc. 1974, 96, 25, 7835–7836Publication Date (Print):December 1, 1974Publication History Published online1 May 2002Published inissue 1 December 1974https://pubs.acs.org/doi/10.1021/ja00832a050https://doi.org/10.1021/ja00832a050research-articleACS PublicationsRequest reuse permissionsArticle Views52Altmetric-Citations13LEARN 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
Sensitivity of primary hematopoietic tumors and tumor lines to the novel HDAC inhibitor PCI-24781 (2007)

14062 PCI-24781 (formerly CRA-024781) is a novel HDAC inhibitor that is in phase I clinical trials in patients with solid and hematopoietic malignancies. PCI-24781 has favorable pharmacokinetic and pharmacodynamic profiles in animal models and in humans. In the present study we show that PCI-24781 potently induces cell death in a variety of hematopoietic cell lines derived from B-cell, T-cell and myeloid malignancies, and in primary acute leukemic blasts from bone marrow aspirates. In tumor cell lines, growth inhibition and apoptosis were noted at drug concentrations ≡ 0.125 μM and were accompanied by known biochemical markers of HDAC inhibition including histone and tubulin hyperacetylation. To demonstrate the potential clinical utility of PCI-24781 in hematologic tumors, primary leukemia samples were isolated from patients and screened for resistance to PCI-24781-induced growth arrest in vitro. Of these 25 primary samples (10 acute myelogenous leukemia (AML), 6 multiple myeloma (MM) and 9 acute lymphocytic leukemia (ALL)), some of which were derived from patients who had failed standard therapy, none was resistant to PCI-24781 at 0.5 μM and only 4 (1 AML, 2 MM, and 1 ALL) were considered resistant at 50 nM. Gene expression analysis using DNA microarrays on these primary tumor samples revealed alterations of gene expression consistent with HDAC inhibition and defined potential pathways of activity for this compound in these tumors. These results demonstrate that hematopoietic tumors and tumor-derived cell lines are highly sensitive in vitro to the novel HDAC inhibitor PCI-24781. The high sensitivity of primary tumor cells to treatment with PCI-24781 in vitro coupled with the favorable pharmacokinetics of this compound in humans suggests that patients with hematopoietic malignancies would be responsive to treatment with PCI-24781 in clinical trials. No significant financial relationships to disclose.
Pressure dependence of optical transitions in semiconducting single‐walled carbon nanotubes (2004)

Abstract The effects of applied hydrostatic pressure on the optical transitions in semiconducting single‐walled carbon nanotubes with different diameters and chiralities have been studied using optical absorption and photoluminescence spectroscopy. The excitonic transitions associated with the band‐gap (the first van Hove transition) energies in the carbon nanotubes are found to shift to lower energy at a rate depending on nanotube structure. The excitonic transitions between the first excited confinement states (the second van Hove transitions) are found to be much less sensitive to the applied hydrostatic pressure. All nanotubes show a dependence on their chirality in terms of pressure coefficient of the band‐gap energy, with the larger‐diameter nanotubes exhibiting a higher sensitivity of the band‐gap energy to hydrostatic pressure. (© 2004 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Coordination Compounds Based on 1,2,3,4-Tetrahydro-isoquinoline-3-carboxylic Acid (2007)

Syntheses of 2,6-bis[((3S)-3-(methoxycarbonyl)-1,2,3,4-tetrahydroisoquinolin-2-yl)carbonyl]pyridine and its coordination compounds with Cu2+, Co2+, Co3+, or Fe3+ are described. By means of 1H- and 13C-NMR spectra it was proved that 2,6-bis[((3S)-3-(methoxycarbonyl)-1,2,3,4-tetrahydroisoquinolin-2-yl)carbonyl]pyridine as well as its coordination compound with Co3+ exist in the form of a mixture of three conformers, differing in the conformations at the two amide groups present. The prepared coordination compounds were tested in the enantioselective catalysis of the nitroaldol addition of nitromethane with 2-nitrobenzaldehyde or 4-nitrobenzaldehyde, and in the Michael addition of ethyl 2-oxocyclohexanecarboxylate to but-3-en-2-one.
Transcriptional and posttranscriptional modulation of calcitonin gene expression by sodium n-butyrate in cultured human medullary thyroid carcinoma. (1988)

The TT cell line of human medullary thyroid carcinoma produces large quantities of calcitonin (CT) and calcitonin gene-related peptide (CGRP) mRNAs by alternative splicing of a primary CT gene transcript. We have previously shown that the relative levels of these mRNAs depend on the growth stages of the TT cells in culture and that these mRNAs can be increased acutely at the transcriptional level by phorbol esters (12-O-tetradecanoylphorbol-13-acetate) and the cyclic nucleotide, cyclic AMP. We show here that the naturally occurring fatty acid butyrate, unlike 12-O-tetradecanoylphorbol-13-acetate or cyclic AMP, has a delayed stimulatory effect on CT gene transcription, and also can modulate the posttranscriptional processing of RNA from this gene. Treatment of the TT cells with butyrate leads to a 5-fold increase in CT gene transcription after a lag period of 48 h and to a sustained decrease in the calcitonin gene-related peptide to CT mRNA ratio throughout the growth curve of these cells. In addition to its effects on CT gene expression, butyrate also decreases cellular proliferation and c-myc expression in the TT cells. These changes suggest that butyrate induces cultured human medullary thyroid carcinoma cells to acquire in vitro properties more consistent with the differentiated phenotype of the mature thyroid C-cell which is characterized by a low calcitonin gene-related peptide to CT ratio.