gebhart/patrepeval huggingface dataset:
Transfer of MicroRNAs by Embryonic Stem Cell Microvesicles (2009)

Microvesicles are plasma membrane-derived vesicles released into the extracellular environment by a variety of cell types. Originally characterized from platelets, microvesicles are a normal constituent of human plasma, where they play an important role in maintaining hematostasis. Microvesicles have been shown to transfer proteins and RNA from cell to cell and they are also believed to play a role in intercellular communication. We characterized the RNA and protein content of embryonic stem cell microvesicles and show that they can be engineered to carry exogenously expressed mRNA and protein such as green fluorescent protein (GFP). We demonstrate that these engineered microvesicles dock and fuse with other embryonic stem cells, transferring their GFP. Additionally, we show that embryonic stem cells microvesicles contain abundant microRNA and that they can transfer a subset of microRNAs to mouse embryonic fibroblasts in vitro. Since microRNAs are short (21-24 nt), naturally occurring RNAs that regulate protein translation, our findings open up the intriguing possibility that stem cells can alter the expression of genes in neighboring cells by transferring microRNAs contained in microvesicles. Embryonic stem cell microvesicles may be useful therapeutic tools for transferring mRNA, microRNAs, protein, and siRNA to cells and may be important mediators of signaling within stem cell niches.
Substrate sequence selectivity of APOBEC3A implicates intra-DNA interactions (2018)

The APOBEC3 (A3) family of human cytidine deaminases is renowned for providing a first line of defense against many exogenous and endogenous retroviruses. However, the ability of these proteins to deaminate deoxycytidines in ssDNA makes A3s a double-edged sword. When overexpressed, A3s can mutate endogenous genomic DNA resulting in a variety of cancers. Although the sequence context for mutating DNA varies among A3s, the mechanism for substrate sequence specificity is not well understood. To characterize substrate specificity of A3A, a systematic approach was used to quantify the affinity for substrate as a function of sequence context, length, secondary structure, and solution pH. We identified the A3A ssDNA binding motif as (T/C)TC(A/G), which correlated with enzymatic activity. We also validated that A3A binds RNA in a sequence specific manner. A3A bound tighter to substrate binding motif within a hairpin loop compared to linear oligonucleotide, suggesting A3A affinity is modulated by substrate structure. Based on these findings and previously published A3A-ssDNA co-crystal structures, we propose a new model with intra-DNA interactions for the molecular mechanism underlying A3A sequence preference. Overall, the sequence and structural preferences identified for A3A leads to a new paradigm for identifying A3A's involvement in mutation of endogenous or exogenous DNA.
A Virtual Screening Approach for Thymidine Monophosphate Kinase Inhibitors as Antitubercular Agents Based on Docking and Pharmacophore Models. (2005)

Docking and pharmacophore screening tools were used to examine the binding of ligands in the active site\nof thymidine monophosphate kinase of <i>Mycobacterium tuberculosis</i>. Docking analysis of deoxythymidine\nmonophosphate (dTMP) analogues suggests the role of hydrogen bonding and other weak interactions in\nenzyme selectivity. Water-mediated hydrogen-bond networks and a halogen-bond interaction seem to stabilize\nthe molecular recognition. A pharmacophore model was developed using 20 dTMP analogues. The\npharmacophoric features were complementary to the active site residues involved in the ligand recognition.\nOn the basis of these studies, a composite screening model that combines the features from both the docking\nanalysis and the pharmacophore model was developed. The composite model was validated by screening a\ndatabase spiked with 47 known inhibitors. The model picked up 42 of these, giving an enrichment factor of\n17. The validated model was used to successfully screen an in-house database of about 500 000 compounds.\nSubsequent screening with other filters gave 186 hit molecules.
Realistic force reflection in a spine biopsy simulator (2002)

This paper proposes a scheme to produce realistic force reflection in a needle insertion problem. The target system is a spine needle biopsy simulator for tumor inspection by needle insertion. Simulated force is calculated using a 3D human tissue model and the orientation and position of the needle, and is produced through the PHANToM/sup TM/ device. To generate realistic force reflection, the directional force of the needle has been generated by a related tissue model, and the rotational force is generated using a pivot to keep the needle in the initial inserted direction after puncturing the skin. Since the haptic device has limitations in generating high stiffness and large damping, a scale-down model and digital filter are used to stabilize the system.
Allylic Oxidation of Alkenes Catalyzed by a Copper–Aluminum Mixed Oxide (2014)

A strategy for the allylic oxidation of cyclic alkenes with a copper-aluminum mixed oxide as catalyst is presented. The reaction involves the treatment of an alkene with a carboxylic acid employing tert-butyl hydroperoxide as the oxidant. In all cases, the corresponding allylic esters are obtained. When L-proline is employed, the allylic alcohol or ketone is obtained. The oxidation of cyclohexene and valencene has been optimized by design of experiments (DoE) statistical methodology.
Eye movement behavior identification for Alzheimer’s disease diagnosis (2018)

We develop a deep-learning approach to differentiate between the eye movement behavior of people with neurodegenerative diseases during reading compared to healthy control subjects. The subjects with and without Alzheimer’s disease read well-defined and previously validated sentences including high- and low-predictable sentences, and proverbs. From these eye-tracking data trial-wise information is derived consisting of descriptors that capture the reading behavior of the subjects. With this information a set of denoising sparse-autoencoders are trained and a deep neural network is built using the trained autoencoders and a softmax classifier that identifies subjects with Alzheimer’s disease with 89.78% accuracy. The results are very encouraging and show that such models promise to be helpful for understanding the dynamics of eye movement behavior and its relation with underlying neuropsychological processes.
Variable time delay of microwave signals using high dispersion fibre (1993)

A programmable time delay of 0–5 ns has been demonstrated for a 3 GHz signal using a tunable semiconductor diode laser and 1 km of a new high-dispersion fibre.
Tenellin and bassianin, metabolites of Beauveria species. Structure elucidation with 15N- and doubly 13C-enriched compounds using 13C nuclear magnetic resonance spectroscopy (1974)

13 C n.m.r. spectroscopy and biosynthetic labelling with [15N]nitrate and [1,2-13C]acetate proved to be valuable adjuncts to established chemical and spectroscopic methods in elucidating the structures of tenellin and bassianin as 3-acyl derivatives of 1,4-dihydroxy-5-p-hydroxyphenyl-2(1H)-pyridone.
Pulsed-Laser Atom-Probe FIM Study of Solid Surfaces (1983)

A linear type pulsed-laser time of flight atom-probe field ion microscope has been developed which uses laser pulses of 300 ps from a nitrogen laser for field desorbing surface atoms. It is a time of flight mass spectrometer and an ion energy analyzer of single atom detecting sensitivity with good mass and energy resolution. The new system is used to study the energy distribution of field desorbed inert gas atoms such as Ne+ and Ar+, and field evaporated metal ions. The formation of metal helide ions such as RhHe++, PtHe++ and PtHe2++, and metal hydride ions such as AuH+, AuH2+, and AuH3+ has been studied by observing both the mass spectra and the energy distributions. The formation of H+, H2+, and H3+ from atomically well defined metal surfaces under the influence of an applied field is also studied.
Stepwise synthesis of cellodextrins assisted by a mutant cellulase (2000)

Abstract A 4 II ‐protected α‐cellobiosyl fluoride is an efficient donor for the enzymatic stepwise condensations onto methyl ß‐D‐glycoside acceptors. These reactions, catalyzed by the Cel7B E197A glycosynthase from Humicola insolens , gave cellodextrins from degree of polymerization 3 to 6 in high yields.
Identification and Characterization of a Gene with Base Substitutions Associated with the Absorptive Hypercalciuria Phenotype and Low Spinal Bone Density (2002)

Absorptive hypercalciuria (AH) is a kidney stone-forming condition frequently complicated by bone loss. Previously, we mapped the locus for an inherited form of AH to chromosome 1q23.3-q24. We have sequenced a putative gene (subsequently shown by others to be homologous with the rat soluble adenylate cyclase gene) in this region in 12 unrelated Caucasian AH patients. Eighteen base substitutions were identified in the soluble adenylate cyclase human homolog gene. All sequence variations were further evaluated in 3-68 additional unrelated AH patients and 19-132 normal subjects, and 1 additional base substitution was identified. Six of the identified sequence variations occurred with increased frequency in the AH population and tracked with the AH phenotype in AH families. Calculated odds ratios showed that the occurrence of any 4 of these individual base substitutions was associated with a 2.2- to 3.5-fold increase in estimated risk for AH (P < 0.02). In addition, 1 or more base changes was associated with a lower L2-L4 vertebral bone density. Sequence analysis of 3 other genes within the AH linkage interval showed no difference in the distribution of sequence variations between AH and normal populations. This is the first description of a specific gene defect associated with AH.
ELISA for Guinea-pig IgG1: An Alternative to the PCA Test for Relative Allergenicity (1991)

An ELISA method to replace the PCA (passive cutaneous anaphylaxis) test has been developed for use in the evaluation of relative allergenicity in guinea-pigs (Dunkin-Hartley). The method detects antigen-specific IgG1 antibodies formed in the guinea-pig during sensitisation, and correlates well with the corresponding PCA test. The relative importance of IgG1 and IgE for relative allergenicity in the Dunkin-Hartley guinea-pig strain is discussed.
Host‐guest interactions in gas phase chemical sensing of permethyl‐6<sup>I</sup>‐alkenoylamino‐6<sup>I</sup>‐deoxy‐β‐cyclodextrin derivatized porous silicon (2007)

Abstract Porous silicon surface was modified by photochemically activated hydrosilylation reaction with permethyl‐6 I ‐alkenoylamino‐6 I ‐deoxy‐β‐cyclodextrins. In the presence of controlled amounts of various organic molecules in gas phase photoluminescence response from this derivatized porous silicon revealed formation of host‐guest complexes between β‐cyclodextrin and detected molecules. The strongest modification of photoluminescence response was observed for aromatic compounds that have optimal molecular size for strong interaction with β‐cyclodextrin cavity. For low concentrations of aromatic molecules we observed PL enhancement most probably due to electron transfer from β‐cyclodextrin‐analyte complex to porous silicon. For higher concentrations – after saturation of the β‐cyclodextrin sites – a combined response with dominant PL quenching was observed. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
What is the most reliable ultrasound parameter for assessment of fetal head descent? (2010)

Digital pelvic examination for determining the fetal head position during labor is not accurate. The most reproducible of the 3D measurements for progression of the fetal head in labor is the progression angle.
Differential expression of LKB1, PD-L1, and PD-L2 in KRAS-mutant non-small cell lung cancer in never-smokers. (2014)

8032 Background: KRAS mutation is the most common oncogenic alteration in lung adenocarcinoma and is detected in smokers and up to 15% of never smokers. The tumor suppressor LKB1 is commonly mutated in NSCLC and LKB1 mutations occur concurrently in 30% of KRAS mutant NSCLC. In murine models, KRAS mutant tumors with concurrent LKB1 loss did not respond to docetaxel/selumetinib treatment. Immune checkpoint blockade by anti-PD-1/PD-L1 monoclonal antibodies (MoAb) is being clinically evaluated. Clinical responses to these agents correlate with PD-L1 expression and smoking status. We aimed to determine the expression of LKB1, PD-L1 and PD-L2 in KRAS mutant NSCLC from smokers (KS) and never smokers (KNS). Methods: We evaluated the clinical and molecular characteristics of KRAS mutant NSCLC patients (pts) using an institutional database. We examined LKB1, PD-L1, PD-L2 tumor expression by immunohistochemistry (IHC). IHC was performed using the murine MoAbs Ley37D/G6 (LKB1), 9A11 (PD-L1) and 9E5 (PD-L2). LKB1 staining was scored as intact or lost, with any degree of expression qualifying as intact, PD-L1 positive if >5% of cells were stained and PD-L2 positive if >10%. Results: Between 8/09 and 1/14 we identified 514 KRAS mutant NSCLC pts (stage I 22%/II 10%/III 19%/IV 49%) of which 39 were never smokers (incidence 7.6%) We analyzed 114 pts with available tissue using IHC (30 KNS and 84 KS). LKB1 loss was detected in 29% of cases (95%CI, 21-38%) and was significantly less frequent in KNS pts (KS 34% vs KNS 13%; P= 0.035). KRAS transversion mutations were more frequent in KS vs KNS pts (78% vs 37%; P= 0.0001). LKB1 staining was intact in 95% of KNS pts with transition mutations. Pts with LKB1 loss had more metastatic sites and brain involvement (47% vs 24%, P= 0.0472). PD-L1 was expressed in 19% of KRAS mutant cases and PD-L2 in 45% and were inversely correlated (r=-0.86, P <0.0001). PD-L1/PD-L2 expression was not related to either LKB1 status or type of KRAS mutation. PD-L1/PD-L2 IHC 3+ vs 1+/2+ staining was more frequent in KS vs KNS pts (50% vs 20%; 40% vs 13% respectively). Conclusions: KRAS mutant NSCLC is a heterogeneous disease. Our findings may have implications for choosing KRAS mutant pts for ongoing trials of MEK and PD-1/PD-L1 inhibitors.
Likelihood Models for Clustered Binary and Continuous Out comes: Application to Developmental Toxicology (1999)

In developmental toxicology, methods based on dose response modeling and quantitative risk assessment are being actively pursued. Among live fetuses, the presence of malformations and reduction in fetal weight are of primary interest, but ordinarily, the dose-response relationships are characterized in each of the outcomes separately while appropriately accounting for clustering within litters. Jointly modeling the outcomes, allowing different relationships with dose while incorporating the correlation between the fetuses and the outcomes, may be more appropriate. We propose a likelihood-based model that is an extension of a correlated probit model to incorporate continuous outcomes. Our model maintains a marginal dose-response interpretation for the individual outcomes while taking into account both the correlations between outcomes on an individual fetus and those due to clustering. The joint risk of malformation and low birth weight can then be estimated directly. This approach is particularly well suited to estimating safe dose levels as part of quantitative risk assessment.
Triply resonant coupled-cavity electro-optic modulators for RF to optical signal conversion (2019)

We propose an on-chip triply resonant electro-optic modulator architecture for RF-to-optical signal conversion and provide a detailed theoretical analysis of the optimal "circuit-level" device geometries and their performance limits. The designs maximize the RF-optical conversion efficiency through simultaneous resonant enhancement of the RF drive signal, a continuous-wave (CW) optical pump, and the generated optical sideband. The optical pump and sideband are resonantly enhanced in respective supermodes of a two-coupled-cavity optical resonator system, while the RF signal can be enhanced in addition by an LC circuit formed by capacitances of the optical resonator active regions and (integrated) matching inductors. We show that such designs can offer 15-50 dB improvement in conversion efficiency over conventional microring modulators. In the proposed configurations, the photon lifetime (resonance linewidth) limits the instantaneous RF bandwidth of the electro-optic response but does not limit its central RF frequency. The latter is set by the coupling strength between the two coupled cavities and is not subject to the photon lifetime constraint inherent to conventional singly resonant microring modulators. This feature enables efficient operation at high RF carrier frequencies without a reduction in efficiency commonly associated with the photon lifetime limit and accounts for 10-30 dB of the total improvement. Two optical configurations of the modulator are proposed: a "basic" configuration with equal Q-factors in both supermodes, most suitable for narrowband RF signals, and a "generalized" configuration with independently tailored supermode Q-factors that supports a wider instantaneous bandwidth. A second significant 5-20 dB gain in modulation efficiency is expected from RF drive signal enhancement by integrated LC resonant matching, leading to the total expected improvement of 15-50 dB. Previously studied triply-resonant modulators, with coupled longitudinal [across the free spectral range (FSR)] modes, have large resonant mode volume for typical RF frequencies, which limits the interaction between the optical and RF fields. In contrast, the proposed modulators support maximally tightly confined resonant modes, with strong coupling between the mode fields, which increases and maintains high device efficiency across a range of RF frequencies. The proposed modulator architecture is compact, efficient, capable of modulation at high RF carrier frequencies and can be applied to any cavity design or modulation mechanism. It is also well suited to moderate Q, including silicon, implementations, and may be enabling for future CMOS RF-electronic-photonic systems on chip.
Diagnostic parameters for monitoring peri-implant conditions. (2004)

Systematic and continuous monitoring of peri-implant tissues during maintenance care is recommended for the early diagnosis of peri-implant disease.
Evaluation of gene expression measurements from commercial microarray platforms (2003)

Multiple commercial microarrays for measuring genome-wide gene expression levels are currently available, including oligonucleotide and cDNA, single- and two-channel formats. This study reports on the results of gene expression measurements generated from identical RNA preparations that were obtained using three commercially available microarray platforms. RNA was collected from PANC-1 cells grown in serum-rich medium and at 24 h following the removal of serum. Three biological replicates were prepared for each condition, and three experimental replicates were produced for the first biological replicate. RNA was labeled and hybridized to microarrays from three major suppliers according to manufacturers' protocols, and gene expression measurements were obtained using each platform's standard software. For each platform, gene targets from a subset of 2009 common genes were compared. Correlations in gene expression levels and comparisons for significant gene expression changes in this subset were calculated, and showed considerable divergence across the different platforms, suggesting the need for establishing industrial manufacturing standards, and further independent and thorough validation of the technology.
A digital interferometer for wavelength measurement (1980)

A simple fringe-counting interferometer for laser wavelength measurement is described. Measured values of the wavelengths of several helium-neon, argon and krypton laser lines, stabilised by saturated absorption in iodine vapour, are presented, with uncertainties of two parts in 108 (99% confidence).
Oscillations in chemical systems. V. Quantitative explanation of band migration in the Belousov-Zhabotinskii reaction (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOscillations in chemical systems. V. Quantitative explanation of band migration in the Belousov-Zhabotinskii reactionRichard J. Field and Richard M. NoyesCite this: J. Am. Chem. Soc. 1974, 96, 7, 2001–2006Publication Date (Print):April 1, 1974Publication History Published online1 May 2002Published inissue 1 April 1974https://pubs.acs.org/doi/10.1021/ja00814a003https://doi.org/10.1021/ja00814a003research-articleACS PublicationsRequest reuse permissionsArticle Views745Altmetric-Citations163LEARN 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
Single Metal/Dual High-k Gate Stack with Low V<inf>th</inf> and Precise Gate Profile Control for Highly Manufacturable Aggressively Scaled CMISFETs (2007)

We have proposed a single metal/dual high-k (SMDH), low-Vth gate stack for aggressively scaled CMISFETs. The Vth is controlled by MgO- and Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> -containing high-k for n and pMISFETs, respectively. The gate profile can be more easily controlled by taking advantage of a common W/TiN gate stack on both high-k's. We have successfully obtained 0.21 and -0.33 V of V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> for a 1-mum long n and pMISFET by the proposed SMDH gate stacks. We also found that MgO suppresses PBTI and that it enhances electron mobility.