gebhart/patrepeval huggingface dataset:
A comparison of the decision tree approach and the neural-networks-based heuristic dynamic programming approach for subcircuit extraction problem (2003)

The applications of non-standard logic device are increasing fast in the industry. Many of these applications require high speed, low power, functionality and flexibility, which cannot be obtained by standard logic device. These special logic cells can be constructed by the topology design strategy automatically or manually. However, the need arises for the topology design verification. The layout versus schematic (LVS) analysis is an essential part of topology design verification, and subcircuit extraction is one of the operations in the LVS testing. In this paper, we first provided an efficient decision tree approach to the graph isomorphism problem, and then effectively applied it to the subcircuit extraction problem based on the solution to the graph isomorphism problem. To evaluate its performance, we compare it with the neural networks based heuristic dynamic programming algorithm (SubHDP) which is by far one of the fastest algorithms for subcircuit extraction problem.
An iron-regulated LysR-type element mediates antimicrobial peptide resistance and virulence in Yersinia pseudotuberculosis (2009)

During the course of its infection of the mammalian digestive tract, the entero-invasive, Gram-negative bacterium Yersinia pseudotuberculosis must overcome various hostile living conditions (notably, iron starvation and the presence of antimicrobial compounds produced in situ). We have previously reported that in vitro bacterial growth during iron deprivation raises resistance to the antimicrobial peptide polymyxin B; here, we show that this phenotype is mediated by a chromosomal gene (YPTB0333) encoding a transcriptional regulator from the LysR family. We determined that the product of YPTB0333 is a pleiotropic regulator which controls (in addition to its own expression) genes encoding the Yfe iron-uptake system and polymyxin B resistance. Lastly, by using a mouse model of oral infection, we demonstrated that YPTB0333 is required for colonization of Peyer's patches and mesenteric lymph nodes by Y. pseudotuberculosis.
PING: a Group-to-Individual Distributed Meeting System (2006)

Group-to-individual (G2I) distributed meeting is an important but understudied area. Because of the asymmetry between different parties in G2I meetings, it has two unique challenges: l)the remote participant tends to be ignored by the local participants; and 2) the remote participant has inferior audio, video, and data experience than the local participants. To address these issues, in this paper we present PING, a system explicitly designed for G2I distributed meetings that combines recent advances in both hardware, e.g., microphone arrays, remote person stand-in devices, and software, e.g., audio-video processing, to improve users' G2I meeting experience. We report how PING addresses the above two challenges and its system design and implementation
PoCUS in nephrology: a new tool to improve our diagnostic skills (2022)

Point-of-Care Ultrasonography (PoCUS) aims to include a fifth pillar (insonation) in the classical physical examination in order to obtain images to answer specific questions by the clinician at the patient's bedside, allowing rapid identification of structural or functional abnormalities, enabling more accurate volume assessment and supporting diagnosis, as well as guiding procedures. In recent years, PoCUS has started becoming a valuable tool in day-to-day clinical practice, adopted by healthcare professionals from various medical specialties, never replacing physical examination but improving patient and medical care and experience. Renal patients represent a wide range of diseases, which lends PoCUS a special role as a valuable tool in different scenarios, not only for volume-related information but also for the assessment of a wide range of acute and chronic conditions, enhancing the sensitivity of conventional physical examination in nephrology. PoCUS in the hands of a nephrologist is a precision medicine tool.
Abstract 1684: Preclinical anti-tumor efficacy of FGFR2-ADC BAY 1187982 in patient-derived gastric, breast and ovarian cancer models (2015)

Abstract Antibody-drug conjugates (ADC) represent a promising therapeutic approach for treatment of cancer. We have developed a novel ADC directed against fibroblast growth factor receptor 2 (FGFR2). FGFR2 is overexpressed in several cancer indications, such as gastric, breast, and ovarian cancer and thus represents a potential therapeutic target for treatment of FGFR2-positive cancer patients with ADC-based therapy. FGFR2-ADC consists of a fully human anti-FGFR2-Ab (BAY 1179470) conjugated via a stable linker to a novel auristatin cytotoxic agent licensed from Seattle Genetics. FGFR2-ADC exhibits low nM to sub-nM potency in vitro in a panel of FGFR2-positive cancer cells lines (SNU-16, MFM-223, NCI-H716) while being inactive against FGFR2-low or -negative cell lines (MDA-MB-231, HEK-293, BaF/3) and highly selective versus a control ADC. FGFR2-ADC is highly efficacious in monotherapy and results in tumor growth inhibition in the gastric cancer xenograft model SNU-16 and tumor regression in the breast cancer xenograft model MFM-223. FGFR2-ADC induces tumor stasis in the colorectal cancer xenograft model NCI-H716 and regrown tumors are sensitive to a second treatment cycle of FGFR2-ADC. FGFR2-ADC shows high efficacy in vivo in monotherapy in patient-derived (PDX) FGFR2-positive murine xenograft models, e.g. in the ovarian cancer model OV30-0511A. FGFR2-ADC is also efficacious in the gastric cancer PDX model GC10-0608 and the breast cancer model MAXF857. The toxophore metabolite of FGFR2-ADC was more than 30-fold enriched in tumors versus other organs (liver, spleen, kidneys) in NCI-H716 tumor-bearing mice. Based on the preclinical efficacy, PK and tolerability data, evaluation of FGFR2-ADC in cancer patients appears warranted. A Phase I study is planned. Citation Format: Anette Sommer, Charlotte Kopitz, Christoph Schatz, Ruprecht Zierz, Joachim Schuhmacher, Sabine Wittemer-Rump, Klaas Prins, Manuela Braun, Frank Reetz, Bertolt Kreft, Hung T. Huynh, Karl Ziegelbauer. Preclinical anti-tumor efficacy of FGFR2-ADC BAY 1187982 in patient-derived gastric, breast and ovarian cancer models. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1684. doi:10.1158/1538-7445.AM2015-1684
APOE epsilon variation in multiple sclerosis susceptibility and disease severity (2006)

Overall, these findings do not support a role for APOE in multiple sclerosis, and underscore the importance of using large sample sizes to detect modest genetic effects, particularly in studies of genotype-phenotype relationships.
The Deadly Quartet (Covid-19, Old Age, Lung Disease, and Heart Failure) Explains Why Coronavirus-Related Mortality in Northern Italy Was So High (2020)

Since its outbreak in China at the end of 2019, the new coronavirus disease (COVID-19) was characterized by both easy spreading and high mortality. The latter proved to be way more elevated in the North of Italy -with a peak of 18.4% in region Lombardia and even 31% in the city of Bergamo and surrounding county- than in the rest of the world. In an attempt to conceptualize the reasons for such a dramatic situation, four key elements have been identified: COVID-19 itself, old age, lung disease, and heart failure. Their harmful combination has been named "The deadly quartet". The underlying risk factors, among which a lot of them are distinctive features of the population in northern Italy, have been summarized as "unmodifiable", "partially modifiable", and "modifiable", for the sake of clarity. Up-to-date scientific evidence in this field has been described in the form of a narrative and easy-to-read review.
Carnitine-Acyltransferase System Inhibition, Cancer Cell Death, and Prevention of Myc-Induced Lymphomagenesis (2013)

Our data indicate that it is possible to tackle c-myc-driven tumorigenesis by altering lipid metabolism and exploiting the neoplastic cell addiction to FA oxidation.
Probing the Azaaurone Scaffold against the Hepatic and Erythrocytic Stages of Malaria Parasites (2016)

The potential of azaaurones as dual-stage antimalarial agents was investigated by assessing the effect of a small library of azaaurones on the inhibition of liver and intraerythrocytic lifecycle stages of the malaria parasite. The whole series was screened against the blood stage of a chloroquine-resistant Plasmodium falciparum strain and the liver stage of P. berghei, yielding compounds with dual-stage activity and sub-micromolar potency against erythrocytic parasites. Studies with genetically modified parasites, using a phenotypic assay based on the P. falciparum Dd2-ScDHODH line, which expresses yeast dihydroorotate dehydrogenase (DHODH), showed that one of the azaaurone derivatives has the potential to inhibit the parasite mitochondrial electron-transport chain. The global urgency in finding new therapies for malaria, especially against the underexplored liver stage, associated with chemical tractability of azaaurones, warrants further development of this chemotype. Overall, these results emphasize the azaaurone chemotype as a promising scaffold for dual-stage antimalarials.
Inhibition of TFG function causes hereditary axon degeneration by impairing endoplasmic reticulum structure (2013)

Hereditary spastic paraplegias are a clinically and genetically heterogeneous group of gait disorders. Their pathological hallmark is a length-dependent distal axonopathy of nerve fibers in the corticospinal tract. Involvement of other neurons can cause additional neurological symptoms, which define a diverse set of complex hereditary spastic paraplegias. We present two siblings who have the unusual combination of early-onset spastic paraplegia, optic atrophy, and neuropathy. Genome-wide SNP-typing, linkage analysis, and exome sequencing revealed a homozygous c.316C>T (p.R106C) variant in the Trk-fused gene (TFG) as the only plausible mutation. Biochemical characterization of the mutant protein demonstrated a defect in its ability to self-assemble into an oligomeric complex, which is critical for normal TFG function. In cell lines, TFG inhibition slows protein secretion from the endoplasmic reticulum (ER) and alters ER morphology, disrupting organization of peripheral ER tubules and causing collapse of the ER network onto the underlying microtubule cytoskeleton. The present study provides a unique link between altered ER architecture and neurodegeneration.
Vibration analysis of coupled flexural torsional mode tuning fork type quartz crystals resonator (2003)

The frequency-temperature characteristics of a tuning-fork-type quartz crystal resonator which couples the torsional mode vibration to the flexural mode vibration are analyzed, and the estimated values of the various constants for a resonator manufactured for trial experiments are presented. A secular equation coupling the torsional mode vibration to the flexural mode vibration is first derived and used for a theoretical analysis of the frequency-temperature characteristics of the resonator. The calculated values are shown to agree well with experimental values obtained for the manufactured resonator. The results indicate that resonators with excellent frequency-temperature characteristics, low crystal impedance, and a high quality factor are realized.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Small Molecule SOS1 Agonists Modulate MAPK and PI3K Signaling via Independent Cellular Responses (2019)

Activating mutations in RAS can lead to oncogenesis by enhancing downstream signaling, such as through the MAPK and PI3K pathways. Therefore, therapeutically targeting RAS may perturb multiple signaling pathways simultaneously. One method for modulating RAS signaling is to target the activity of the guanine nucleotide exchange factor SOS1. Our laboratory has discovered compounds that bind to SOS1 and activate RAS. Interestingly, these SOS1 agonist compounds elicit biphasic modulation of ERK phosphorylation and simultaneous inhibition of AKT phosphorylation levels. Here, we utilized multiple chemically distinct compounds to elucidate whether these effects on MAPK and PI3K signaling by SOS1 agonists were mechanistically linked. In addition, we used CRISPR/Cas9 gene-editing to generate clonally derived SOS1 knockout cells and identified a potent SOS1 agonist that rapidly elicited on-target molecular effects at substantially lower concentrations than those causing off-target effects. Our findings will allow us to further define the on-target utility of SOS1 agonists.
Very active CeO2-zeolite catalysts for NOx reduction with NH3 (2002)

Selective catalytic reduction of NO with NH3 over high weight percentage CeO2-zeolites showed excellent NOx conversions at very high space velocities under simulated exhaust gas conditions in the presence of H2O.
Improved Fischer Indole Reaction for the Preparation of N,N-Dimethyltryptamines: Synthesis of L-695,894, a Potent 5-HT1D Receptor Agonist (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTImproved Fischer Indole Reaction for the Preparation of N,N-Dimethyltryptamines: Synthesis of L-695,894, a Potent 5-HT1D Receptor AgonistCheng-yi Chen, Chris H. Senanayake, Timothy J. Bill, Robert D. Larsen, Thomas R. Verhoeven, and Paul J. ReiderCite this: J. Org. Chem. 1994, 59, 13, 3738–3741Publication Date (Print):July 1, 1994Publication History Published online1 May 2002Published inissue 1 July 1994https://pubs.acs.org/doi/10.1021/jo00092a046https://doi.org/10.1021/jo00092a046research-articleACS PublicationsRequest reuse permissionsArticle Views2422Altmetric-Citations135LEARN 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
A METHOD TO ACHIEVE HIGH FIDELITY IN INTERNET-DISTRIBUTED HARDWARE-IN-THE-LOOP SIMULATION (2012)

&lt;title&gt;ABSTRACT&lt;/title&gt; &lt;p&gt;One of the main challenges of co-simulating hardware-in-the-loop systems in real-time over the Internet is the fidelity of the simulation. The stochastic delay of the Internet may significantly distort the dynamics of the network-integrated system. This paper presents the development of an iterative learning control based approach to improve fidelity in such network-integrated systems. Towards this end, a new metric for characterizing fidelity is proposed first, which, unlike some existing metrics, does not require knowledge about the reference dynamics (i.e., dynamics that would be observed, if the system was physically connected). #ext, using this metric, the problem of improving fidelity is formulated as an iterative learning control problem. Finally, the proposed approach is utilized in a case study, which shows that the proposed approach can significantly improve the fidelity in Internet-distributed hardware-in-the-loop simulation.&lt;/p&gt;
The Effect of Fluorinated Solvents on the Physicochemical Properties, Ionic Association, and Free Volume of a Prototypical Solvate Ionic Liquid (2022)

Solvate ionic liquid (SIL) synthesis and properties depend on a delicate balancing of cation-solvent and cation-anion interactions to produce materials containing only cation-solvent complexes and solvent-separated anions. Most SILs meeting these characteristics fall within the paradigm of oligomeric ethylene oxides (e.g. glymes and glycols) and lithium salts. Targeted functionalization of solvent molecules to achieve desired properties is a relatively unexplored avenue of research. Fluorinated solvents have significantly different electric charge distributions compared to their nonfluorinated analogs. We test the impact of solvent fluorination for a SIL created from equimolar mixtures of lithium bis(trifluoromethylsulfonyl)imide (LiNTf<sub>2</sub> ) and triethylene glycol (TEG), hereafter [(TEG)<sub>1</sub> Li]NTf<sub>2</sub> . In the first experiment, TEG is partially substituted with 2,2,4,4,5,5,7,7-octafluoro-3,6-dioxaoctane-1,8-diol (FTEG). This leads to a precipitous decrease in ionic conductivity and larger quantities of ionically-associated Li(NTf<sub>2</sub> )<sub>2</sub> <sup>-</sup> species, as detected with vibrational spectroscopy. These observations suggest FTEG does not readily coordinate Li<sup>+</sup> ions in a manner analogous to TEG. Computational studies reinforce this conclusion. Relative complex cation stabilities are ranked as [(FTEG)<sub>1</sub> Li]<sup>+</sup> >[(TEG)<sub>1</sub> Li]<sup>+</sup> . A second experiment adds FTEG as a diluent to [(TEG)<sub>1</sub> Li]NTf<sub>2</sub> . This places FTEG and TEG in competition to coordinate a limited number of Li<sup>+</sup> ions. The resulting mixtures exhibit conductivity enhancement over the parent SIL and minimal changes in ion speciation due to the poor Li<sup>+</sup> binding by FTEG compared to TEG. Positron annihilation lifetime spectroscopic studies point to increased amounts of free volume upon dilution of FTEG. This likely explains the origin of the conductivity and viscosity enhancements.
Cyclic analogs of luteinizing hormone-releasing hormone with significant biological activities (1978)

There is evidence that, in its receptor-binding conformation, the N and C terminus of LH-RH may be in close proximity and two cyclic analogues of the hormone were synthesized to test the hypothesis. Cyclic [beta-Ala1,D-Ala6,Gly10]- and [6-aminohexanoic acid1,D-Ala6,Gly10]-LH-RH were prepared by treatment of their linear precursor peptides with dicyclohexylcarbodiimide in the presence of 1-hydroxybenzotriazole in dilute dimethylformamide solution. Although the linear peptides possessed no detectable LH-releasing activity in ovariectomized rats, the cyclic beta-Ala analogue had 1.2% the activity of LH-RH, whereas the longer chain cyclic 6-aminohexanoic acid analogue had 0.65% activity. These results support the concept of an important interaction between the ends of the LH-RH molecule possibly involving hydrogen-bond formation between the pyrrolidone carbonyl group of pyroglutamic acid and the glycinamide group.
Power Grid Verification (2010)

Full-chip verification requires one to check if the power grid voltage drop does not exceed a certain threshold. The traditional simulation-based solution to this problem is computationally expensive, because of the large variety of possible circuit behaviors that would need to be simulated; it also has the disadvantage that it requires full knowledge of the details of the circuit attached to the grid, thereby precluding early verification of the grid. We propose a power grid verification technique that can be applied before the complete circuit has been designed and without exact knowledge of the circuit currents. We use current constraints; which are upper bound constraints on the currents that can be drawn from the grid, as a way to capture the uncertainty about the circuit details and activity. We propose one technique where we verify the worst case voltage as an optimization problem. Using this voltage verification and the constraints we also check the worst case delay of critical paths within the design. Lastly we implement a method of partitioning that allows us to verify grids of an industrial size within reasonable simulation times.
ChemInform Abstract: Quaternary Salts of 2‐((Hydroxyimino)methyl)imidazole. Part 3. Synthesis and Evaluation of (Alkenyloxy)‐, (Alkynyloxy)‐, and (Aralkyloxy)methyl Quaternized 2‐((Hydroxyimino)methyl)‐1‐alkylimidazolium Halides as Reactivators and Therapy for Soman Intoxication. (1989)

Abstract Forty‐six imidazolium halides such as (V) are prepared by reaction of the imidazole (IV) with chloromethyl ethers such as (III) which are obtained from the corresponding alcohols (I) and trioxane (II) in the presence of HCl.
Lithium Enolates Derived from Pyroglutaminol: Mechanism and Stereoselectivity of an Azaaldol Addition (2016)

A lithium enolate derived from an acetonide-protected pyroglutaminol undergoes a highly selective azaaldol addition with (E)-N-phenyl-1-[2-(trifluoromethyl)phenyl]methanimine. The selectivity is sensitive to tetrahydrofuran (THF) concentration, temperature, and the presence of excess lithium diisopropylamide base. Rate studies show that the observable tetrasolvated dimeric enolate undergoes reversible deaggregation, with the reaction proceeding via a disolvated-monomer-based transition structure. Limited stereochemical erosion stems from the intervention of a trisolvated-monomer-based pathway, which is suppressed at low THF concentrations and elevated temperature. Endofacial selectivity observed with excess lithium diisopropylamide (LDA) is traced to an intermediate dianion formed by subsequent lithiation of the monomeric azaaldol adduct, which is characterized as both a dilithio form and a trilithio dianion-LDA mixed aggregate.
Data from A <i>Survivin</i> Gene Signature Predicts Aggressive Tumor Behavior (2023)

&lt;div&gt;Abstract&lt;p&gt;Gene signatures that predict aggressive tumor behavior at the earliest stages of disease, ideally before overt tissue abnormalities, are urgently needed. To search for such genes, we generated a transgenic model of survivin, an essential regulator of cell division and apoptosis overexpressed in cancer. Transgenic expression of survivin in the urinary bladder did not cause histologic abnormalities of the urothelium. However, microarray analysis revealed that survivin-expressing bladders exhibited profound changes in gene expression profile affecting extracellular matrix and inflammatory genes. Following exposure to a bladder carcinogen, &lt;i&gt;N&lt;/i&gt;-butyl-&lt;i&gt;N&lt;/i&gt;-(4-hydroxybutyl) nitrosamine (OH-BBN), survivin transgenic animals exhibited accelerated tumor progression, preferential incidence of tumors as compared with premalignant lesions, and dramatically abbreviated survival. Conversely, transgenic expression of a survivin Thr&lt;sup&gt;34&lt;/sup&gt;→Ala dominant-negative mutant did not cause changes in gene expression or accelerated tumor progression after OH-BBN treatment. Therefore, survivin expression induces global transcriptional changes in the tissue microenvironment that may promote tumorigenesis. Detection of survivin or its associated gene signature may provide an early biomarker of aggressive tumor behavior before the appearance of tissue abnormalities.&lt;/p&gt;&lt;/div&gt;