gebhart/patrepeval huggingface dataset:
Electrical Performances of Tellurium-Rich GexTe1-x Phase Change Memories (2011)

This paper investigates the electrical performance of Tellurium-rich Ge <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> Te <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-x</sub> (with x = 0.3, 0.4, 0.5) Phase Change Memory (PCM) devices. Analysis performed on lance-type PCM cells showed an increase in threshold voltage and crystallization temperature as the Te content is increased. Furthermore, the current required to program the memory in the high resistive state decreased. The improved stability of amorphous phase in Te-rich materials gives rise to higher data retention in our devices.
Analogs of growth hormone-releasing factor (1-29) amide containing the reduced peptide bond isostere in the N-terminal region (1990)

Previous peptide structure-activity investigations employing the psi[CH2NH] peptide bond isostere have produced antagonists when inserted into various sequences. These include bombesin, in which the incorporation of Leu13 psi[CH2NH]Leu14 produced a potent antagonist, and tetragastrin, with which Boc-Trp-Leu psi[CH2NH]Asp-Phe-NH2 is an antagonist. In this study, we chose to investigate the effect of this isostere on growth hormone-releasing factor (1-29) amide. Analogues were prepared by solid-phase synthesis and the isosteres incorporated by racemization-free reductive alkylation with a preformed protected amino acid aldehyde in the presence of NaBH3CN. The aldehydes were prepared by the reduction of the protected N,O-dimethyl hydroxamates with LiAlH4 at 0 degrees C. The purified analogues were assayed in a 4-day primary culture of male rat anterior pituitary cells for growth hormone (GH) release. Potential antagonists were retested in the presence of GRF(1-29)NH2. The following results were obtained: At position 5-6, a very weak agonist was produced with much less than 0.01% activity. Incorporation of the isostere in positions 1-2, 2-3, and 6-7 gave weak agonists with approximately 0.1% activity. Agonists with 0.39% and 1.6% activity were produced by incorporation at 10-11 and 3-4, respectively. The analogue [Ser9 psi[CH2NH]Tyr10]GRF(1-29)NH2 was found to be an antagonist in the 10 microM range vs 1 nM GRF and had no agonist activity at doses as high as 0.1 mM.
Supplementary Figure 2 from STAT3 Mediates Resistance to MEK Inhibitor through MicroRNA miR-17 (2023)

Supplementary Figure 2 from STAT3 Mediates Resistance to MEK Inhibitor through MicroRNA miR-17
Macromol. Chem. Phys. 8/2018 (2018)

Back Cover: In article number 1700417 by Daniel T. Hallinan Jr. and co-workers, gold nanoparticles are grafted with poly(ethylene oxide). The polymer-grafted nanoparticles are self-assembled into monolayers from solvents of different quality, and the distance between particles is dictated by the polymer chain length and solvent quality. This provides a direct means to examine grafted polymer scaling.
DNA Computation in Mammalian Cells: MicroRNA Logic Operations (2013)

DNA computation can utilize logic gates as modules to create molecular computers with biological inputs. Modular circuits that recognize nucleic acid inputs through strand hybridization activate computation cascades to produce controlled outputs. This allows for the construction of synthetic circuits that can be interfaced with cellular environments. We have engineered oligonucleotide AND gates to respond to specific microRNA (miRNA) inputs in live mammalian cells. Both single and dual-sensing miRNA-based computation devices were synthesized for the cell-specific identification of endogenous miR-21 and miR-122. A logic gate response was observed with miRNA expression regulators, exhibiting molecular recognition of miRNA profile changes. Nucleic acid logic gates that are functional in a cellular environment and recognize endogenous inputs significantly expand the potential of DNA computation to monitor, image, and respond to cell-specific markers.
Selectivity of Kinase Inhibitor Fragments (2011)

A kinase-focused screening set of fragments has been assembled and has proved successful for the discovery of ligand-efficient hits against many targets. Here we present some of our general conclusions from this exercise. Notably, we present the first profiling results for literature fragments that have previously been used as starting points for optimization against individual kinases. We consider the importance of screening format and the extent to which selectivity is helpful in selecting fragments for progression. Results are also outlined for fragments targeting the DFG-out conformation and for atypical kinases such as PIM1 and lipid kinases.
Oligodb—interactive design of oligo DNA for transcription profiling of human genes (2002)

We have devised a web-based system for interactive design of suitable oligos for transcription profiling experiments with user-defined parameters. Oligodb is based on predicted human gene transcripts from the ENSEMBL project. The web interface allows the user to retrieve oligos for human transcripts in a flexible manner. Criteria for selecting the oligos are low similarity to all other known human genes, the absence of stable secondary structures, the length of the oligo, and the absence of low complexity regions. Furthermore, the user may select oligos corresponding to the desired position in the 5'-3' direction of the transcript, and based on the melting temperature. All data and results are tightly web-linked to the corresponding data entries of ENSEMBL project.
Multiplexed detection of bacterial nucleic acids using Cas13 in droplet microarrays (2022)

Rapid and accurate diagnosis of infections is fundamental to individual patient care and public health management. Nucleic acid detection methods are critical to this effort, but are limited either in the breadth of pathogens targeted or by the expertise and infrastructure required. We present here a high-throughput system that enables rapid identification of bacterial pathogens, bCARMEN, which utilizes: (1) modular CRISPR-Cas13-based nucleic acid detection with enhanced sensitivity and specificity; and (2) a droplet microfluidic system that enables thousands of simultaneous, spatially multiplexed detection reactions at nanoliter volumes; and (3) a novel preamplification strategy that further enhances sensitivity and specificity. We demonstrate bCARMEN is capable of detecting and discriminating 52 clinically relevant bacterial species and several key antibiotic resistance genes. We further develop a simple proof of principle workflow using stabilized reagents and cell phone camera optical readout, opening up the possibility of a rapid point-of-care multiplexed bacterial pathogen identification and antibiotic susceptibility testing.
Cell adhesion molecules and ischemic stroke (2008)

Several experiments using cell surface adhesion molecules as targets of stroke therapy are promising yet inadequate. Clinical trials using immune blockade of adhesion molecules by antibodies have failed due to immune reactions of the host. Further clinical trials are needed to test the efficacy of humanized antibodies or non-immunogenic agents that interfere with cell adhesion mechanisms. Adhesion blocking strategies seem to be effective particularly at reperfusion and use of these strategies with thrombolytic therapies justifies a continued effort to define the role of adhesion molecules in the pathophysiology of cerebral ischemia-reperfusion.
Different sequence patterns in signal peptides from mycoplasmas, other gram-positive bacteria, andEscherichia coli: A multivariate data analysis (1999)

Signal peptides are essential N-terminal extensions in export proteins, and have a positively charged N-terminus, a hydrophobic central core, and a C-terminal cleavage region. They interact in a consecutive manner with different accessory proteins during the secretion process. Potential patterns or periodicity in the amino acid (aa) sequence were searched, using multivariate techniques, for a large number of signal peptides from mollicutes (mycoplasmas), other Gram-positive bacteria, and Escherichia coli. Mollicutes signal peptides were significantly different from the E. coli and Gram-positive ones by their N-terminal charge, peptide length, and especially, unique periodicities of side chain hydrophobicity and volumes. Their lipoprotein signal peptides were longer than for any other bacteria. Significant differences were also recorded between the other bacterial peptide groups. Specific aa patterns were more related within the signal peptides from several groups of secreted bacillus enzymes, than for all signal peptides from one bacillus species. In E. coli, signal peptides from proteins routed for the various destinations revealed significant and compartment-specific sequence patterns not evident by other methods. This was substantiated from a large number of signal peptide secretion mutants for the E. coli periplasmic space. It is proposed that the differences in aa patterns and side-chain properties are related to the secondary structure sidedness and topology of the signal peptides, and important for specific interactions during the secretion process.
Orientation Zernike polynomials: a useful way to describe the polarization effects of optical imaging systems (2009)

We introduce the new concept of orientation Zernike polynomials, a base function representation of retardation and diattenuation in close analogy to the wavefront description by scalar Zernike polynomials. We show that the orientation Zernike polynomials provide a complete and systematic description of vector imaging using high numerical aperture lithography lenses and, hence, a basis for an in depth understanding of both polarized and unpolarized imaging, and its modeling.
Supplementary Materials and Methods from Antitumor Activity of the Glutaminase Inhibitor CB-839 in Triple-Negative Breast Cancer (2023)

&lt;p&gt;PDF - 246K, Supplementary Materials and Methods.&lt;/p&gt;
Kitty (2014)

We present Kitty, a sketch-based tool for authoring dynamic and interactive illustrations. Artists can sketch animated drawings and textures to convey the living phenomena, and specify the functional relationship between its entities to characterize the dynamic behavior of systems and environments. An underlying graph model, customizable through sketching, captures the functional relationships between the visual, spatial, temporal or quantitative parameters of its entities. As the viewer interacts with the resulting dynamic interactive illustration, the parameters of the drawing change accordingly, depicting the dynamics and chain of causal effects within a scene. The generality of this framework makes our tool applicable for a variety of purposes, including technical illustrations, scientific explanation, infographics, medical illustrations, children's e-books, cartoon strips and beyond. A user study demonstrates the ease of usage, variety of applications, artistic expressiveness and creative possibilities of our tool.
Design of the adaptive optics systems for GMT (2006)

The Giant Magellan Telescope (GMT) includes adaptive optics (AO) as an integral component of its design. Planned scientific applications of AO span an enormous parameter space: wavelengths from 1 to 25 &#956;m, fields of view from 1 arcsec to 8 arcmin, and contrast ratio as high as 10<sup>9</sup>. The integrated systems are designed about common core elements. The telescope's Gregorian adaptive secondary mirror, with seven segments matched to the primary mirror segments, will be used for wavefront correction in all AO modes, providing for high throughput and very low background in the thermal infrared. First light with AO will use wavefront reconstruction from a constellation of six continuous-wave sodium laser guide stars to provide ground-layer correction over 8 arcmin and diffraction-limited correction of small fields. Natural guide stars will be used for classical AO and high contrast imaging. The AO system is configured to feed both the initial instrument suite and ports for future expansion.
Synthesis of aza and carbocyclic β-carbolines for the treatment of alcohol abuse. Regiospecific solution to the problem of 3,6-disubstituted β- and aza-β-carboline specificity (2015)

A novel two step protocol was developed to gain regiospecific access to 3-substituted β- and aza-β-carbolines, 3-PBC (1), 3-ISOPBC (2), βCCt (3), 6-aza-3-PBC (4) and 6-aza-3-ISOPBC (5). These β-carbolines (1-3) are potential clinical agents to reduce alcohol self-administration, especially 3-ISOPBC·HCl (2·HCl) which appears to be a potent anti-alcohol agent active against binge drinking in a rat model of maternally deprived (MD) rats. The method consists of two consecutive palladium-catalyzed reactions: a Buchwald-Hartwig amination followed by an intramolecular Heck-type cyclization in high yield.
Micro-optical coherence tomography for high-resolution morphologic imaging of cellular and nerval corneal micro-structures (2020)

We demonstrate the highest resolution (1.5×1.5×1 µm) micrometer optical coherence tomography (µOCT) imaging of the morphologic micro-structure of excised swine and non-human primate corneas. Besides epithelial, stromal, and endothelial cell morphology, this report focuses on investigating the most peripheral corneal nerve fibers, the nerve fibers of the subbasal plexus (SBP). Alterations of SBP nerve density and composition are reportedly linked to major neurologic disorders, such as diabetic neuropathy, potentially indicating earliest onsets of denervation. Here, the fine, hyperreflective, epithelial nerve structures located just above Bowman's membrane, are i) visualized using our µOCT prototype, ii) validated by comparison to fluorescence confocal microscopy (including selective immunohistochemical staining), and iii) segmented using state-of-the-art image processing. Here, we also introduce polarization sensitive (PS) µOCT imaging, demonstrating, to the best of our knowledge, the highest resolution corneal PS-OCT scans reported to date.
Abstract A29: Hypoxia regulated long noncoding RNAs and antisense transcripts in breast cancer: Novel insights of noncoding transcriptional regulation in hypoxic microenvironment (2016)

Abstract Tumour hypoxia is a common feature of tumour microenvironment and contributes to an aggressive phenotype across multiple types of cancers. Hypoxia-inducible factor (HIF) is a key element regulating expression of hundreds of coding and non-coding RNAs, which act to both improve oxygen delivery and to reduce cellular demand of oxygen. We performed a comprehensive analysis on hypoxic transcription landscape and epigenetic markers of transcriptional activation in MCF-7 breast cancer cells under hypoxia using next generation sequencing. Analyses revealed that all classes of non-coding RNA are profoundly regulated by hypoxia including piwiRNA, miRNA, tRNA, and sn/snoRNA. Analysis revealed downregulation of snRNAs and tRNAs in hypoxia, whereas miRNAs, antisense transcripts and lncRNAs are globally upregulated in hypoxia. Many novel natural antisense transcripts are induced under hypoxia and their expression is dependent on HIF. Hypoxia-induced natural antisense transcripts are associated with both induction and repression in cis. Moreover, large numbers of lncRNAs are found overexpressed under hypoxia and are associated with HIF binding and elevated level of RNApol2 and H3K4me3, suggesting direct transcriptional regulation of lncRNAs by HIF. Among the most hypoxia induced lncRNA was NEAT1, which is a direct transcriptional target of HIF-2α. We confirmed the hypoxic NEAT1 upregulation in a number of breast cancer cell lines and in tumour xenografts models treated with bevacizumab. Hypoxia induced NEAT1 directly increase the formation of nuclear paraspeckles bodies. Moreover, hypoxic induction of NEAT1 contributes to increase cell proliferation, cell survival, and inhibit apoptosis. Furthermore, we found that NEAT1 is required to retain hypoxia induced hyper edited Junctional Adhesion Molecule A (JAM-A) mRNA in nucleus to inhibit its translation. Finally, in a large breast cancers cohort, high expression of NEAT1 is linked with poor prognosis and with different clinicopathological features. Our results extend knowledge of the hypoxic transcriptional response into the spectrum of non-coding transcripts. These findings provide novel mechanisms of transcriptional regulation in hypoxic tumours through non-coding RNAs and open new avenues to find novel pathways and targets to develop therapies for breast cancer. Citation Format: Hani Choudhry, Ashwag Albukhari, Matteo Morotti, Syed Haider, Daniela Moralli, Johannes Schödel, Catherine Green, Carme Camps, Francesca Buffa, Peter Ratcliffe, Ioannis Ragoussis, David Mole, Adrian Harris. Hypoxia regulated long noncoding RNAs and antisense transcripts in breast cancer: Novel insights of noncoding transcriptional regulation in hypoxic microenvironment. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A29.
PRDX1 Counteracts Catastrophic Telomeric Cleavage Events That Are Triggered by DNA Repair Activities Post Oxidative Damage (2020)

Telomeres are prone to damage inflicted by reactive oxygen species (ROS). Oxidized telomeric DNA and nucleotide substrates inhibit telomerase, causing telomere shortening. In addition, ROS can induce telomeric single-strand DNA breaks (SSBs). The peroxiredoxin-PRDX1 is enriched in telomeric chromatin and this counteracts ROS-induced telomere damage. Here, we identify DNA processing after oxidative stress as a main source of telomeric DNA cleavage events in the absence of PRDX1. In PRDX1-depleted cells, poly(ADP-ribose) polymerase (PARP)-dependent telomeric repair is often incomplete, giving persistent SSBs that are converted into telomeric double-strand breaks during replication, leading to rapid telomere shortening. Interestingly, PARP1 inhibition dampens telomere shortening, triggering stabilization of the homologous recombination (HR) factor BRCA1 and RAD51-mediated repair of telomeres. Overall, our results reveal that, in the absence PRDX1, incomplete PARP1-dependent DNA repair and competition between PARP1 and HR cause ROS-induced telomeric catastrophe.
DSP for High-Speed Fiber-Wireless Convergence (2018)

We review recent advances in the common public radio interfaces (CPRI/eCPRI) between remote radio units and baseband units via optical fiber, and discuss how DSP may be used to support both CPRI and eCPRI to achieve high bandwidth efficiency and low processing latency.
Size-Dependent Extinction Coefficients of PbS Quantum Dots (2006)

We report here on a detailed study on PbS colloidal quantum dots. A characterization via X-ray diffraction (XRD) and high-resolution transmission electron microscopy (HRTEM) allowed us to reliably determine the diameter and the shape of the nanocrystals. These data, together with second-derivative analysis of the absorption spectra, allowed us to determine the size dependence of seven transitions in the absorption spectrum; some of these transitions were identified on the basis of their normalized confinement energy. The size dependence of the first excitonic transition was best modeled by a four-band envelope approach which considers the anisotropy of the band edges (Andreev, A. D.; Lipovskii, A. A. Phys. Rev. B: Condens. Matter Mater. Phys. 1999, 59, 15402-15404). The extinction coefficients were calculated using concentrations obtained from inductively coupled plasma atomic emission spectrometry (ICP-AES), and their size dependence was found to follow a power law with exponent equal to approximately 2.5. In contrast with what was expected from the effective mass approximation, the per particle absorption cross section of the lowest transition was found to be strongly dependent on the particle size.
Upper bound on the periodic autocorrelation of unified complex Hadamard transforms sequences (2002)

The periodic autocorrelation (PAC) properties of a family of orthogonal sequences, the unified complex Hadamard transforms (UCHTs), are analyzed in this paper. The family is divided into a few groups in accordance to different characteristics of the sequences. Different upper bounds on the out-of-phase PAC are found for each group. The performance of the UCHTs sequences is compared with the Walsh-Hadamard sequences. It is shown that some UCHTs sequences provide better upper bound on the out-of-phase PAC.
<title>New results concerning Gaussian beam wave propagation</title> (1993)

Recent studies of beam wave propagation have led to a new and useful method of analysis for describing the diffractive geometry of a Gaussian beam and to a number of new results involving optical turbulence effects. This paper is primarily a review of these studies.
ChemInform Abstract: Thiazolo[4,5‐d]pyrimidine Thiones and ‐ones as Corticotropin‐Releasing Hormone (CRH‐R1) Receptor Antagonists. (1999)

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.
Synthesis of aza-crown ethers (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleSynthesis of aza-crown ethersKrzysztof E. Krakowiak, Jerald S. Bradshaw, and Daria J. Zamecka-KrakowiakCite this: Chem. Rev. 1989, 89, 4, 929–972Publication Date (Print):June 1, 1989Publication History Published online1 May 2002Published inissue 1 June 1989https://pubs.acs.org/doi/10.1021/cr00094a008https://doi.org/10.1021/cr00094a008research-articleACS PublicationsRequest reuse permissionsArticle Views4064Altmetric-Citations282LEARN 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
60 Years Young: The Evolving Role of Allogeneic Hematopoietic Stem Cell Transplantation in Cancer Immunotherapy (2021)

The year 2020 marked the 30th anniversary of the Nobel Prize in Medicine awarded to E. Donnall Thomas for the development of allogeneic hematopoietic stem cell transplantation (allo-HSCT) to treat hematologic malignancies and other blood disorders. Dr. Thomas, "father of bone marrow transplantation," first developed and reported this technique in 1957, and in the ensuing decades, this seminal study has impacted fundamental work in hematology and cancer research, including advances in hematopoiesis, stem cell biology, tumor immunology, and T-cell biology. As the first example of cancer immunotherapy, understanding the mechanisms of antitumor biology associated with allo-HSCT has given rise to many of the principles used today in the development and implementation of novel transformative immunotherapies. Here we review the historical basis underpinning the development of allo-HSCT as well as advances in knowledge obtained by defining mechanisms of allo-HSCT activity. We review how these principles have been translated to novel immunotherapies currently utilized in clinical practice and describe potential future applications for allo-HSCT in cancer research and development of novel therapeutic strategies.