gebhart/patrepeval huggingface dataset:
An NMR study on the interaction of Escherichia coli DinI with RecA-ssDNA complexes (2003)

The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity. Using nuclear magnetic resonance (NMR) spectroscopy, we show that DinI tightly binds to the central region of RecA (between the N- and C-terminal domains) and that this interaction is enhanced upon the oligomerisation of RecA. On the other hand, DinI did not inhibit the interaction between 4mer single-stranded (ss)DNA and RecA- ATPgammaS, but had a slight effect on the structure of ssDNA-RecA-ATPgammaS complexes involving 8mer and 12mer ssDNA. We hypothesise that prevention of repressor binding to the intermolecular cleft region of RecA protomers by DinI, with the possibility of a slight conformational change induced in the DinI-bound ssDNA-RecA-ATPgammaS complex, together function to inhibit the co-protease activity of RecA.
Reaction of Glyoxal with 2‘-Deoxyguanosine, 2‘-Deoxyadenosine, 2‘-Deoxycytidine, Cytidine, Thymidine, and Calf Thymus DNA:  Identification of DNA Adducts (2005)

Glyoxal (ethanedial) is an increasingly used industrial chemical that has been found to be mutagenic in bacteria and mammalian cells. In this study, the reactions of glyoxal with 2'-deoxyguanosine, 2'-deoxyadenosine, 2'-deoxycytidine, cytidine, thymidine, and calf thymus DNA have been studied in aqueous buffered solutions. The nucleoside adducts were isolated by reversed-phase liquid chromatography and characterized by their UV absorbance and 1H and 13C NMR spectroscopic and mass spectrometric features. The reaction with 2'-deoxyguanosine gave one adduct, the previously known 3-(2'-deoxy-beta-D-erythro-pentofuranosyl)-5,6,7-trihydro-6,7-dihydroxyimidazo[1,2-a]purine-9-one adduct. The reaction of 2'-deoxyadenosine with glyoxal resulted in the formation of a previously not reported N6-(hydroxyacetyl)-2'-deoxyadenosine adduct. In the reaction of glyoxal with 2'-deoxycytidine and cytidine at neutral conditions and 37 degrees C, 5-hydroxyacetyl pyrimidine derivatives were obtained. When the cytidine reaction was performed at pH 4.5 and 50 degrees C, the 5-hydroxyacetyl derivative of uridine was formed through deamination of cytidine-glyoxal. Adducts in the thymidine reaction could not be detected. In the reaction of glyoxal with calf thymus DNA, the 2'-deoxyguanosine-glyoxal and 2'-deoxyadenosine-glyoxal adducts were obtained, the former being the major adduct.
Improvement of secure access control agent for distributed files (2003)

In 1998, we proposed an access control agent system for distributed files. This agent works as a proxy for authors of the files and enables the authors to control their files. The agent restricts the software access of the user who does not obey the condition for the usage of distributed files. However, in this agent system there is an assumption on the role of system participants. Without this assumption the agent system actually faces a problem called role problem and can be abused by the system participants. In this paper, we propose a solution for the role problem in which the rights of authors are protected more securely in the use of distributed files.
Characterization and Distribution of a Cloned Rat μ‐Opioid Receptor (1995)

We have cloned and expressed a rat brain cDNA, TS11, that encodes a mu-opioid receptor based on pharmacological, physiological, and anatomical criteria. Membranes were prepared from COS-7 cells transiently expressing TS11 bound [3H]diprenorphine with high affinity (KD = 0.23 +/- 0.04 nM). The rank order potency of drugs competing with [3H]diprenorphine was as follows: levorphanol (Ki = 0.6 +/- 0.2 nM) approximately beta-endorphin (Ki = 0.7 +/- 0.05 nM) approximately morphine (Ki = 0.8 +/- 0.5 nM) approximately [D-Ala2, N-Me-Phe4,Gly-ol5]-enkephalin (DAMGO; Ki = 1.6 +/- 0.5 nM) uch much greater than U50,488 (Ki = 910 +/- 0.78 nM) > [D-Pen2,5]- enkephalin (Ki = 3,170 +/- 98 nM) > dextrorphan (Ki = 4,100 +/- 68 nM). The rank order potencies of these ligands, the stereospecificity of levorphanol, and morphine's subnanomolar Ki are consistent with a mu-opioid binding site. Two additional experiments provided evidence that this opioid-binding site is functionally coupled to G proteins: (a) in COS-7 cells 50 microM 5'-guanylylimidodiphosphate shifted a fraction of receptors with high affinity for DAMGO (IC50 = 3.4 +/- 0.5 nM) to a lower-affinity state (IC50 = 89.0 +/- 19.0 nM), and (b) exposure of Chinese hamster ovary cells stably expressing the cloned mu-opioid receptor to DAMGO resulted in a dose-dependent, naloxone-sensitive inhibition of forskolin-stimulated cyclic AMP production. The distribution of mRNA corresponding to the mu-opioid receptor encoded by TS11 was determined by in situ hybridization to brain sections prepared from adult female rats. The highest levels of mu-receptor mRNA were detected in the thalamus, medial habenula, and the caudate putamen; however, significant hybridization was also observed in many other brain regions, including the hypothalamus.
In Vitro Characterization of a Novel Consensus Bacterial 6-Phytase and One of its Variants (2020)

Background:: Microbial phytases are added to animal feed to hydrolyze phytic acid (myoinositol hexakisphosphate, IP6) and phytate (salt of phytic acid) increasing phosphorus bioavailability. Novel phytases with enhanced bio-efficacy are being developed. Objective:: To characterize the biochemical and enzymatic properties of a novel consensus bacterial 6- phytase and its variant (PhyG), produced in Trichoderma reesei. Methods:: The in vitro specific activity, kinetic parameters, pH-activity profiles (relative to pH5.5), IP6 degradation, hydrolysis products and phosphate release of the phytases were determined using sodium phytate substrate. Melting point (Tm) was determined by differential scanning calorimetry and thermostability assessed by measuring residual activity at different temperatures. In vivo effects of PhyG supplementation at 0 to 1,000 FTU/kg on ileal IP6 digestibility and IP ester concentrations were determined in piglets. Results:: Both phytases exhibited pH optima of 3.5-4.5, high relative activity over a wide pH range (pH2.0-5.0), and substantial relative activity at pH1.5. At pH3.0, the specific activity of the PhyG variant was 1487 U/mg protein and at pH3.5 the kinetic constants were 240 μM (Km) and 1873 s-1 (Kcat). The hydrolysis of IP6 by both phytases was rapid. The major initial hydrolysis product was DLI( 1,2,3,4,5)P5, designating the phytases as bacterial 6-phytases (EC 3.1.3.26). Hydrolysis occurred at the D-3 (L-1) position in ~30% of instances, indicating a dual-specificity. Conclusion: Both phytases showed high thermostability compared to wild type and existing commercial bacterial 6-phytases; PhyG exhibited 95% residual activity after 20 min incubation at 85.4ºC (pH5.5), Tm50 of ~93.2ºC and Tm of 98.8ºC. In vivo, PhyG at 1,000 FTU/kg achieved an ileal digestibility of IP6 of 89.3%.
Young and Elderly Users' Emotion Recognition of Dynamically Formed Expressions Made by a Non-Human Virtual Agent (2019)

The development of non-human robots and virtual agents is focused on encouraging affective communication between humans and agents while supporting the daily life of individuals. For an agent to achieve affective communication with a wide range of users, understanding emotion recognition of an agent's expression is important. In previous studies, age has had an obvious effect on emotion recognition. However, the effect of age on emotion recognition in the context of non-human agents is not yet well understood. In this study, we investigated emotion recognition of young and elderly users when confronted with a non-human agent's expressions. A questionnaire with a seven-emotion alternative forced choice task was used to analyze emotion recognition in 62 young and 39 elderly users. Dynamically formed virtual agent expressions were used to analyze the effect of non-human expressions on emotion recognition. The elderly users had a higher variability of emotion recognition compared with the young users. Studying the individual characteristics of emotion recognition should be prioritized would allow for more affective communication between elderly users and non-human agents.
Preparation and condensations of 3-lithiomethylquinoline (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation and condensations of 3-lithiomethylquinolineEdwin M. Kaiser and Jimmie D. PettyCite this: J. Org. Chem. 1976, 41, 4, 716–717Publication Date (Print):February 20, 1976Publication History Published online1 May 2002Published inissue 20 February 1976https://pubs.acs.org/doi/10.1021/jo00866a034https://doi.org/10.1021/jo00866a034research-articleACS PublicationsRequest reuse permissionsArticle Views62Altmetric-Citations14LEARN 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
Abstract 4597: Characterization and targeting of radiation-inducible neoantigens in multiple cancer types (2014)

Abstract Targeted therapy remains one of the biggest challenges in the effective treatment of cancer. Due to their heterogeneity, not all tumors respond to a particular treatment regimen with similar efficacy. Thus, there is an urgent need to develop targeted therapies that are not only highly specific to cancer subtypes but also have minimal toxicity towards normal tissue. Currently, development of anti-cancer antibodies is limited to antigens that are either overexpressed or antigens that are only expressed in a few patients. This limits both the number of available targets and their selectivity for tumors. Using phage display technology, we have identified proteins that are induced by clinical doses of ionizing radiation (IR): tax-interacting protein 1 (TIP-1) and TATA box-associated factor 15 (TAF-15). Following IR treatment, cell surface expression of both TIP-1 and TAF-15 is enhanced in a number of human cancers, including brain, lung, breast and pancreatic cancer. The underlying premise is that IR induces a stress response resulting from DNA strand breaks and activation of ATM repair pathways. After IR stress, these antigens translocate to the surface where they can be targeted for therapeutic purposes. These radiation-inducible neoantigens present a new synergistic model for the treatment of cancer using IR. In this study, we characterized both radiation-inducible targets in vitro and in vivo. Western blotting, immunohistochemistry and flow cytometry data all demonstrated increased cell surface expression of both TIP-1 and TAF-15 after irradiation. We also developed a monoclonal antibody and a single chain antibody against TIP-1 and are currently in the process of developing antibodies against TAF-15. ELISA and near infra-red whole mouse imaging results demonstrate high affinity and high specificity of our lead anti-TIP-1 antibody and anti-TAF15 peptide in lung, brain, breast and pancreatic cancer. Dosimetry studies using immunofluorescence and Western blot analysis show a dose-dependent increase in expression of TIP-1 and TAF15, suggesting that these proteins may play a key role in the cancer cell's response to radiation stress. We are currently in the process of characterizing the mechanisms of how these proteins contribute to radioresistance and cancer survival processes such as proliferation, apoptosis and metastasis. Citation Format: Lincoln Muhoro, Heping Yan, Jeremy Hunn, Dinesh Thotala, Daniel Ferraro, Dennis Hallahan. Characterization and targeting of radiation-inducible neoantigens in multiple cancer types. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4597. doi:10.1158/1538-7445.AM2014-4597
Hermaphroditic Chirality of a D2‐Symmetric Saddle‐Shaped Porphyrin in Multicomponent Spontaneous Optical Resolution: Inclusion Cocrystals with Double‐Helical Porphyrin Arrays (2006)

The dynamic dual chirality of D2-symmetric saddle-shaped porphyrin 1 decreases the stereochemical complexity of cocrystallization with racemic mandelic acid derivatives, such as BrMA, and allows spontaneous optical resolution (see picture). Each resulting cocrystal is porous and consists of one-handed double-helical porphyrin arrays in which chiral guests are enantioselectively included. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z503054_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Dysregulation of Mdm2 and Mdm4 alternative splicing underlies motor neuron death in spinal muscular atrophy (2018)

Ubiquitous deficiency in the survival motor neuron (SMN) protein causes death of motor neurons-a hallmark of the neurodegenerative disease spinal muscular atrophy (SMA)-through poorly understood mechanisms. Here, we show that the function of SMN in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs) regulates alternative splicing of Mdm2 and Mdm4, two nonredundant repressors of p53. Decreased inclusion of critical Mdm2 and Mdm4 exons is most prominent in SMA motor neurons and correlates with both snRNP reduction and p53 activation in vivo. Importantly, increased skipping of Mdm2 and Mdm4 exons regulated by SMN is necessary and sufficient to synergistically elicit robust p53 activation in wild-type mice. Conversely, restoration of full-length Mdm2 and Mdm4 suppresses p53 induction and motor neuron degeneration in SMA mice. These findings reveal that loss of SMN-dependent regulation of Mdm2 and Mdm4 alternative splicing underlies p53-mediated death of motor neurons in SMA, establishing a causal link between snRNP dysfunction and neurodegeneration.
Tracking Salmonella Enteritidis in the Genomics Era: Clade Definition Using a SNP-PCR Assay and Implications for Population Structure (2021)

Salmonella enterica serovar Enteritidis (or Salmonella Enteritidis, SE) is one of the oldest members of the genus Salmonella, based on the date of first description and has only gained prominence as a significant bacterial contaminant of food over the last three or four decades. Currently, SE is the most common Salmonella serovar causing foodborne illnesses. Control measures to alleviate human infections require that food isolates be characterized and this was until recently carried out using Pulsed-Field Gel Electrophoresis (PFGE) and phage typing as the main laboratory subtyping tools for use in demonstrating relatedness of isolates recovered from infected humans and the food source. The results provided by these analytical tools were presented with easy-to-understand and comprehensible nomenclature, however, the techniques were inherently poorly discriminatory, which is attributable to the clonality of SE. The tools have now given way to whole genome sequencing which provides a full and comprehensive genetic attributes of an organism and a very attractive and superior tool for defining an isolate and for inferring genetic relatedness among isolates. A comparative phylogenomic analysis of isolates of choice provides both a visual appreciation of relatedness as well as quantifiable estimates of genetic distance. Despite the considerable information provided by whole genome analysis and development of a phylogenetic tree, the approach does not lend itself to generating a useful nomenclature-based description of SE subtypes. To this end, a highly discriminatory, cost-effective, high throughput, validated single nucleotide based genotypic polymerase chain reaction assay (SNP-PCR) was developed focussing on 60 polymorphic loci. The procedure was used to identify 25 circulating clades of SE, the largest number so far described for this organism. The new subtyping test, which exploited whole genome sequencing data, displays the attributes of an ideal subtyping test: high discrimination, low cost, rapid, highly reproducible and epidemiological concordance. The procedure is useful for identifying the subtype designation of an isolate, for defining the population structure of the organism as well as for surveillance and outbreak detection.
Supported N-alkylimidazole-decorated dendrons as heterogeneous catalysts for the Baylis–Hillman reaction (2010)

The Baylis-Hillman reaction between methyl vinyl ketone and aromatic aldehydes, catalyzed by N-alkylated imidazoles immobilized on polystyrene via dipolar cycloaddition, esterification or nucleophilic substitution, exhibits a remarkable positive dendritic effect.
EMFORCED: EM-based Fingerprinting Framework for Counterfeit Detection with Demonstration on Remarked and Cloned ICs (2018)

Today’s globalized electronics supply chain is prone to counterfeit chip proliferation. Existing techniques to detect counterfeit integrated circuits (ICs) are limited by relatively high cost, lengthy inspection time, destructive nature, and restriction to a pre-packaging environment. We propose a novel method of counterfeit IC detection which takes advantage of design-specific electromagnetic (EM) fingerprints generated by simulating on-chip clock distribution networks. Through exploitation of the chip’s physical characteristics, our technique can help detect foundry of origin. We validate our approach on 8051 microcontrollers from three different vendors and utilize principal component analysis to distinguish the acquisitions by vendor. Our results show that near-field EM measurements combined with unsupervised machine learning provide ≈ 99% accuracy in counterfeit detection through design-specific fingerprint classification.
File Classification Based on Spiking Neural Networks (2020)

In this paper, we propose a system for file classification in large data sets based on spiking neural networks (SNNs). File information contained in key-value metadata pairs is mapped by a novel correlative temporal encoding scheme to spike patterns that are input to an SNN. The correlation between input spike patterns is determined by a file similarity measure. Unsupervised training of such networks using spike-timing-dependent plasticity (STDP) is addressed first. Then, supervised SNN training is considered by backpropagation of an error signal that is obtained by comparing the spike pattern at the output neurons with a target pattern representing the desired class. The classification accuracy is measured for various publicly available data sets with tens of thousands of elements, and compared with other learning algorithms, including logistic regression and support vector machines. Simulation results indicate that the proposed SNN-based system using memristive synapses may represent a valid alternative to classical machine learning algorithms for inference tasks, especially in environments with asynchronous ingest of input data and limited resources.
Vertex-based inter-frame boundary encoding scheme (1998)

The boundary is approximated by a polygon which can be encoded with the smallest number of bits for maximum distortion. The temporal redundancy between two successive frames is efficiently removed with the proposed scheme, resulting in a lower bit rate than the conventional algorithms.
Republished: Left atrial appendage occlusion (2015)

Left atrial appendage (LAA) occlusion for stroke and thromboembolism prevention in patients with atrial fibrillation (AF) represents a significant advancement in the field of cardiovascular disease. Prevention and avoidance of the devastating consequences of thromboembolic complications from AF continues to be central in the management of these patients. The role of LAA as a nidus for thrombus formation is well documented. Multiple approaches to exclude the LAA from the circulation either percutaneously or surgically have been described and are undergoing testing. Although pharmacological therapy for stroke prevention remains the cornerstone of treatment, device and surgical exclusion of the LAA have proven to be viable alternatives in carefully selected patients. Even though current evidence show that LAA occlusion is safe and effective, approval and adoption of this strategy has been quite difficult due to paucity of randomised clinical trial data on the risk and benefit ratio, cost effectiveness and the issues of procedural risk as well as longer-term outcome. This review aims to provide an update on the current status of LAA occlusion, specifically looking at interpretation of current clinical data, available techniques and devices, issues with current devices and future direction.
Experimental Demonstration of Electromagnetic Tunneling Through an Epsilon-Near-Zero Metamaterial at Microwave Frequencies (2008)

Silveirinha and Engheta have recently proposed that electromagnetic waves can tunnel through a material with an electric permittivity (epsilon) near zero (ENZ). An ENZ material of arbitrary geometry can thus serve as a perfect coupler between incoming and outgoing waveguides with identical cross-sectional area, so long as one dimension of the ENZ is electrically small. In this Letter we present an experimental demonstration of microwave tunneling between two planar waveguides separated by a thin ENZ channel. The ENZ channel consists of a planar waveguide in which complementary split ring resonators are patterned on the lower surface. A tunneling passband is found in transmission measurements, while a two-dimensional spatial map of the electric field distribution reveals a uniform phase variation across the channel--both measurements in agreement with theory and numerical simulations.