gebhart/patrepeval huggingface dataset:
Improving Termination of MDG-Based Abstract State Enumeration via Term Schematization (2001)

The MDG approach for hardware verification was recently proposed to overcome some limitations of traditional ROBDD-based methods of automated verification. One of its weakness, however, is that it may suffer from the non termination of the state enumeration procedure. In this paper, we exploit an idea recently proposed of using term schematization to address this problem. We propose a strategy to direct the introduction of schematized terms in the state enumeration procedure. We show that for certain cases of non termination, it significantly improves over the previously known approaches.
Supplementary Methods and References from Adiponectin Receptor Signaling on Dendritic Cells Blunts Antitumor Immunity (2023)

&lt;p&gt;Description of additional methods and procedures used in the study. Also includes supplementary references.&lt;/p&gt;
Abstract LB-2: Open innovation drug discovery: A study in JQ1. (2013)

Abstract Collaborative research from our laboratory, in 2010, produced a first-in-class inhibitor of BET bromodomain proteins (JQ1). As an effort to promote a more open-innovation model of drug discovery, we endeavored to provide JQ1 without restriction of cost or delay to the scientific community. Toward this objective, we have optimized and completed a facile scaling synthesis capable of producing 100 g quantities of the active (+)-JQ1 stereoisomer. In the past 30 months, JQ1 has been provided to over 350 laboratories in more than a dozen countries. Through this research, BET bromodomain proteins have emerged as pharmacologically validated targets in multiple model systems of cancer including squamous carcinoma of the lung, head and neck, acute myeloid leukemia, multiple myeloma, Burkitt lymphoma, B-cell acute lymphoblastic leukemia, neuroblastoma and non-small cell lung cancer. More than 800 cancer cell lines and 25 murine models of cancer have been systematically screened with JQ1 for sensitivity to bromodomain inhibition, identifying additional therapeutic opportunities. Open availability of JQ1 has also lead to unexpected innovation outside of cancer research through studies identifying opportunities for BET bromodomain inhibition in such diverse fields as male contraception and HIV therapeutics. Since publication of the chemical structure and synthetic route to JQ1, seven new BET bromodomain inhibitors have appeared in the literature each derivatized from and/or benchmarked to the JQ1 molecule. Importantly, BET bromodomain inhibition has already accomplished clinical translation. To more objectively assess the consequence of open-innovation as a model of drug discovery, we have systematically analyzed metadata collected from published research and our ongoing efforts in compound distribution. Here, we present an interim analysis which relates the effect of open-innovation in drug discovery to the scope, productivity, reproducibility and importantly the pace of scientific research in epigenetic reader proteins. These results identify open-innovation in drug discovery as a catalyst for scientific discovery, bridging a gap between fields of research and the basic and clinical sciences. Citation Format: Daniel L. Shaw, Charles Y. Lin, Richard P. Oakley, Nicholas P. Semenkovich, Jun Qi, James E. Bradner. Open innovation drug discovery: A study in JQ1. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-2. doi:10.1158/1538-7445.AM2013-LB-2
The RND1 Small GTPase: Main Functions and Emerging Role in Oncogenesis (2019)

The Rho GTPase family can be classified into classic and atypical members. Classic members cycle between an inactive Guanosine DiPhosphate -bound state and an active Guanosine TriPhosphate-bound state. Atypical Rho GTPases, such as RND1, are predominantly in an active GTP-bound conformation. The role of classic members in oncogenesis has been the subject of numerous studies, while that of atypical members has been less explored. Besides the roles of RND1 in healthy tissues, recent data suggest that RND1 is involved in oncogenesis and response to cancer therapeutics. Here, we present the current knowledge on RND1 expression, subcellular localization, and functions in healthy tissues. Then, we review data showing that RND1 expression is dysregulated in tumors, the molecular mechanisms involved in this deregulation, and the role of RND1 in oncogenesis. For several aggressive tumors, RND1 presents the features of a tumor suppressor gene. In these tumors, low expression of <i>RND1</i> is associated with a bad prognosis for the patients. Finally, we highlight that <i>RND1</i> expression is induced by anticancer agents and modulates their response. Of note, <i>RND1</i> mRNA levels in tumors could be used as a predictive marker of both patient prognosis and response to anticancer agents.
Near‐Field Enhanced Plasmonic‐Magnetic Bifunctional Nanotubes for Single Cell Bioanalysis (2013)

Abstract Near‐field enhanced bifunctional plasmonic‐magnetic (PM) nanostructures consisting of silica nanotubes with embedded solid nanomagnets and uniformly dual‐surface‐coated plasmonic Ag nanoparticles (NPs) are rationally synthesized. The solid embedded sections of nanotubes provide single‐molecule sensitivity with an enhancement factor up to 7.2 × 10 9 for surface‐enhanced Raman scattering (SERS). More than 2× SERS enhancement is observed from the hollow section compared to the solid section of the same nanotube. The substantial SERS enhancement on the hollow section is attributed to the dual‐sided coating of Ag NPs as well as the near‐field optical coupling of Ag NPs across the nanotube walls. Experimentation and modeling are carried out to understand the dependence of SERS enhancement on the NP sizes, junctions, and the near field effects. By tuning the aspect ratio of the embedded nanomagnets, the magnetic anisotropy of nanotubes can be readily controlled to be parallel or vertical to the long directions for nano‐manipulation. Leveraging the bifunctionality, a nanotube is magnetically maneuvered to a single living mammalian cell amidst many and its membrane composition is analyzed via SERS spectroscopy.
Phase variation in Mycobacterium tuberculosis glpK produces transiently heritable drug tolerance (2019)

Abstract The length and complexity of tuberculosis (TB) therapy, as well as the propensity of Mycobacterium tuberculosis to develop drug resistance, are major barriers to global TB control efforts. M. tuberculosis is known to have the ability to enter into a drug-tolerant state, which may explain many of these impediments to TB treatment. We have identified a novel mechanism of genetically encoded but rapidly reversible drug-tolerance in M. tuberculosis caused by transient frameshift mutations in a homopolymeric tract (HT) of seven cytosines (7C) in the glpK gene. Inactivating frameshift mutations associated with the 7C HT in glpK produce small colonies that exhibit heritable multi-drug increases in minimal inhibitory concentrations and decreases in drug-dependent killing; however, reversion back to a fully drug-susceptible large-colony phenotype occurs rapidly through the introduction of additional insertions or deletions in the same glpK HT region. These reversible frameshift mutations in the 7C HT of M. tuberculosis glpK occur in clinical isolates, accumulate in M. tuberculosis infected mice with further accumulation during drug treatment, and exhibit a reversible transcriptional profile including induction of dosR and sigH and repression of kstR regulons, similar to that observed in other in vitro models of M. tuberculosis tolerance. These results suggest that GlpK phase variation may contribute to drug-tolerance, treatment failure and relapse in human TB. Drugs effective against phase-variant M. tuberculosis may hasten TB treatment and improve cure rates. SIGNIFICANCE The ability of M. tuberculosis to survive during prolonged treatment has been attributed to either transient stress responses or fixed heritable drug-resistance producing mutations. We show that phase-variation in the M. tuberculosis glpK gene represents a third type of resistance mechanism. The ability of these glpK mutants to grow slowly and then rapidly revert suggests that these transiently-heritable changes may also explain how a hidden population of drug-tolerant bacteria develops during TB treatment. As a genetically trackable cause of drug-tolerance, M. tuberculosis glpK mutants provides a unique opportunity to study these phenomena at a cellular and mechanistic level. These mutants could also be used for developing drugs that target tolerant populations, leading to more rapid and effective TB treatments.
Physical Determinants of the Endocardial P Wave (1990)

SHANDLING, A.H., ET AL.: Physical Determinants of the Endocardial P Wave. Reliable atrial sensing of intrinsic P wave activity is important to ensure optimal atrial or dual chamber pacemaker function. Various physical factors (e.g., posture, respiration, exercise) may influence P wave characteristics and impair adequate sensing. To investigate this phenomenon, we measured the average of three P wave amplitudes (PWA) and calculated slew rates from telemetered printouts acquired from Pacesetter pacemakers in 32 patients. These measurements were performed in various body positions, with upright exercise and in varying stages of respiration. Results: the mean supine PWA increased on full inspiration (3.56 ± 1.3 mV versus 3.25 ± 1.2 mV during quiet respiration, p &lt; 0.001), and also increased significantly with full expiration. The mean PWA increased on assuming the erect position (3.25 ± 1.2 mV increasing to 3.49 ± 2.3 mV, p &lt; 0.001); in the upright position, the mean erect PWA during quiet respiration was not significantly influenced by the stage of respiration. The mean upright exercise PWA did not differ significantly from the preexercise erect PWA (3.50 f 1.2 with exercise, and 3.47 ± 1.5 before exercise; P = NS). Calculated slew rates were not different lying versus standing. Conclusions: the mean supine PWA increases significantly at the extremes of respiration and on assuming the erect body position; upright exercise results in no appreciable change in the erect PWA. Atrial sensitivity adjustments based on standard supine testing should be adequate for all body positions. (PACE, Vol. 13, December, Part I 1990)
Tailored light-matter interaction through epsilon-near-zero modes. (2016)

Abstract not provided.
Draft Genome Sequence of Robinsoniella peoriensis 6600698, a Confounder of Clostridium difficile Diagnosis (2016)

Robinsoniella peoriensis is a Gram-positive, strictly anaerobic, spore-forming, rod-shaped organism. Here, we report the draft genome of R. peoriensis 6600698, initially classified as Clostridium difficile due to growth on selective agar, a fecal gdh PCR-positive result, and clinical symptoms. R. peoriensis is a potential confounder of C. difficile diagnosis.
mRNA Levels in Control Rat Liver Display Strain-Specific, Hereditary, and AHR-Dependent Components (2011)

Rat is a major model organism in toxicogenomics and pharmacogenomics. Hepatic mRNA profiles after treatment with xenobiotic chemicals are used to predict and understand drug toxicity and mechanisms. Surprisingly, neither inter- and intra-strain variability of mRNA abundances in control rats nor the heritability of rat mRNA abundances yet been established. We address these issues by studying five populations: the popular Sprague-Dawley strain, sub-strains of Long-Evans and Wistar rats, and two lines derived from crosses between the Long-Evans and Wistar sub-strains. Using three independent techniques--variance analysis, linear modelling, and unsupervised pattern recognition--we characterize extensive intra- and inter-strain variability in mRNA levels. We find that both sources of variability are non-random and are enriched for specific functional groups. Specific transcription-factor binding-sites are enriched in their promoter regions and these genes occur in "islands" scattered throughout the rat genome. Using the two lines generated by crossbreeding we tested heritability of hepatic mRNA levels: the majority of rat genes appear to exhibit directional genetics, with only a few interacting loci. Finally, a comparison of inter-strain heterogeneity between mouse and rat orthologs shows more heterogeneity in rats than mice; thus rat and mouse heterogeneity are uncorrelated. Our results establish that control hepatic mRNA levels are relatively homogeneous within rat strains but highly variable between strains. This variability may be related to increased activity of specific transcription-factors and has clear functional consequences. Future studies may take advantage of this phenomenon by surveying panels of rat strains.
Enzymatic degradation of somatostatin by rat plasma and hypothalamus (1978)

A highly sensitive and specific radioimmunoassay for somatostatin has been used to study inactivation of the neurohormone by plasma and hypothalamic peptidase(s). Specificity of the inactivation process was indicated by the absence of interference by addition of luteinizing hormone releasing hormone, thyrotropin-releasing hormone, oxytocin, or substance P. The inactivating ability of hypothalamic tissue and plasma was destroyed by heating and the protease inhibitor benzamidine prevented plasma activity, thus suggesting the enzymatic nature of the processes involved. The present data suggest that the inactivation of somatostatin by hypothalamus and plasma could be an important factor in the regulation of circulating somatostatin levels.
On the use of a seismic sensor as a seismic source (2013)

We investigate the use of seismic sensors as small seismic sources. A voltage signal is applied to a geophone that forces the mass within the geophone to move. The movement of the mass generates a seismic wavefield that is recorded with an array of geophones operating in the conventional sense. We observe higher-frequency (25 Hz and above) surface and body waves propagating from the geophone source at offsets of 10s of meters. We further demonstrate the use of a more powerful geophone-like source allowing seismic waves to be observed at longer offsets. Potential developments and future applications are discussed, including the integration of small sources into an acquisition system, near-surface characterization using small sources, and the determination of receiver locations through inversion of small source recordings.
Influence of collagen and some proteins on gel properties of jellyfish gelatin (2021)

Marine gelatin is one of the food proteins used in food and non-food products, offering desirable functionalities such as gelling, thickening, and binding. Jellyfish has been chosen for this gelatin research, in view of the benefits of its main collagen protein and lower fat content, which may reduce the amounts of chemicals used in the preparative steps of gelatin production. To date, the lack of identified proteins in gelatin has limited the understanding of differentiating intrinsic factors quantitatively and qualitatively affecting gel properties. No comparison has been made between marine gelatin of fish and that of jellyfish, regarding protein type and distribution differences. Therefore, the study aimed at characterizing jellyfish gelatin extracted from by-products, that are i.e., pieces that have broken off during the grading and cleaning step of salted jellyfish processing. Different pretreatment by hydrochloric acid (HCl) concentrations (0.1 and 0.2 M) and hot water extraction time (12 and 24 h) were studied as factors in jellyfish gelatin extraction. The resultant jellyfish gelatin with the highest gel strength (JFG1), as well as two commercial gelatins of fish gelatin (FG) and bovine gelatin (BG), were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The results show that the jellyfish gelatin (JFG1) extracted with 0.1 M HCl at 60°C for 12 h delivered a maximum gel strength of 323.74 g, which is lower than for FG and BG, exhibiting 640.65 and 540.06 g, respectively. The gelling and melting temperatures of JFG1 were 7.1°C and 20.5°C, displaying a cold set gel and unstable gel at room temperature, whereas the gelling and melting temperatures of FG and BG were 17.4°C, 21.3°C, and 27.5°C, 32.7°C, respectively. Proteomic analysis shows that 29 proteins, of which 10 are types of collagen proteins and 19 are non-collagen proteins, are common to all BG, FG, and JFG1, and that JFG1 is missing 3 other collagen proteins (collagen alpha-2 (XI chain), collagen alpha-2 (I chain), and collagen alpha-2 (IV chain), that are important to gel networks. Thus, the lack of these 3 collagen types influences the inferior gel properties of jellyfish gelatin.
Missing transverse energy performance of the CMS detector (2011)

Americanae nace como un proyecto conjunto que surge dentro de la Red Europea de Información y Documentación sobre América Latina (REDIAL), y que ha afrontado la Biblioteca de la Agencia Española de Cooperación Internacional para el Desarrollo (AECID). Esta nueva biblioteca virtual hace más accesibles los libros digitales de tema americanista a los investigadores y usuarios interesados de cualquier parte del mundo.
ACTIVE DETECTION EXPERIMENTS ON THE 16 MV HERMES-III FACILITY USING PULSED BREMSSTRAHLUNG EXCITATION. (2016)

Abstract not provided.
Increase in Mutual Information During Interaction of the Brain with Environment Contributes to Perception (2019)

Perception and motor interaction with physical surroundings can be analyzed by the changes in probability laws governing two possible outcomes of neuronal activity, namely the presence or absence of spikes (binary states). Perception and motor interaction with physical environment are accounted partly by the reduction in entropy within the probability distributions of binary states of neurons in distributed neural circuits, given the knowledge about the characteristics of stimuli in physical surroundings. This reduction in the total entropy of multiple pairs of circuits in networks, by an amount equal to the increase of mutual information among them, occurs as sensory information is processed successively from lower to higher cortical areas or between different areas at the same hierarchical level but belonging to different networks. The increase in mutual information is partly accounted by temporal coupling as well as synaptic connections as proposed by Bahmer and Gupta [1]. We propose that robust increases in mutual information, measuring the association between the characteristics of sensory inputs and neural circuits connectivity patterns, are partly responsible for perception and successful motor interactions with physical surroundings. It is also argued that perception from a sensory input is the result of networking of many circuits to a common circuit that primarily processes the given sensory input.
Overexpression of miR-9 in mast cells is associated with invasive behavior and spontaneous metastasis (2014)

Our findings demonstrate that unique miRNA expression profiles correlate with the biological behavior of canine MCTs. Furthermore, dysregulation of miR-9 is associated with MCT metastasis potentially through the induction of an invasive phenotype, identifying a potentially novel pathway for therapeutic intervention.
Step-down impedance control network resonant DC-DC converter utilizing an enhanced phase-shift control for wide-input-range operation (2016)

This paper introduces an isolated step-down impedance control network (ICN) resonant dc-dc converter that utilizes enhanced inverter and rectifier phase-shifts to achieve both soft-switching and output voltage regulation. Compared to previously presented ICN converters, which utilize burst-mode control to achieve output voltage regulation, this ICN converter with the proposed enhanced phase-shift control has dramatically reduced output capacitance requirement. The avoidance of burst-mode control also simplifies the design of the converter's input EMI filter, reduces switch stresses due to overshoots during repeated startup transitions, and improves converter efficiency by eliminating startup and shutdown losses as well as by reducing conduction losses when backing off in power. A prototype 1-MHz, 120-W step-down ICN resonant converter designed for an input voltage range of 18 V to 75 V, an output voltage of 12 V, and a 10:1 output power range has been designed, built and tested with both burst-mode control and the proposed enhanced phase-shift control. When operated with the enhanced phase-shift control, the prototype ICN converter achieves a peak efficiency of 95.7% and maintains full-power efficiency above 91.7% across its 4:1 input voltage range. Compared to when operated under burst-mode control, the ICN converter with enhanced phase-shift control reduces converter losses by up to 30% and reduces the output capacitance requirement by two orders of magnitude.
A model for calculating impact ionization transition rate in wurtzite GaN for use in breakdown voltage simulation (2013)

A model for calculating impact ionization transition rate (IITR) in wurtzite GaN has been developed for use in breakdown voltage simulations. The characteristic feature of the model is to calculate energy-dependent IITR by taking a conduction band index into account. Depending on the band index, the IITR values calculated by the proposed model show spreading by three orders of magnitude in the electron energy range from 6.5 to 8 eV, while this spreading is totally disregarded in the conventional model. An impact ionization coefficient is calculated based on a full band Monte Carlo simulation which incorporates IITRs by the proposed model. The calculated impact ionization coefficients by the proposed model exhibit better agreements with those by the rigorous model. The proposed model is applied to the calculation of breakdown characteristics for AlGaN/GaN HEMTs and demonstrates a higher breakdown voltage by about 30% than that by the conventional model.
Dye Sensitization Mechanisms in Photopolymer Layer for Laser-Printing Plate. (1999)

To reveal bulky-substituent effect of pyrromethene dye in sensitization mechanisms in photopolymer layer for laser-printing plate, the sensitization mechanisms of a pyrromethene dye, which has a bulky t-butylmethyl group at 5 atom, with a radical generating reagent, 1, 3, 7, 9-tetramethyl-5-t butylmethylpyrromethene-BF2 (BHB) and with 3, 3′, 4, 4′-tetrakis(t-butyldioxycarbonyl)benzophenone (BP), in a poly(methylmethacylate) (PMMA) film were investigated by means of both laser flash photolysis using total reflection cell and a single photon counting as well as in dilute solution, and compared to the sensitization mechanisms for a pyrromethene dye, which has a non-bulky methyl group at atom 5, 1, 3, 7, 9-tetramethyl-5-methylpyrromethene-BF2 (BHM) [l-i].
Evaluation of Tissue Doppler Tei index for global left ventricular function in mice after myocardial infarction: Comparison with Pulsed Doppler Tei index (2005)

Tissue Doppler Tei index is appropriate to characterize global left ventricular function in mice after MI.