gebhart/patrepeval huggingface dataset:
Bridging quantum and classical plasmonics with a quantum-corrected model (2012)

Electromagnetic coupling between plasmonic resonances in metallic nanoparticles allows for engineering of the optical response and generation of strong localized near-fields. Classical electrodynamics fails to describe this coupling across sub-nanometer gaps, where quantum effects become important owing to non-local screening and the spill-out of electrons. However, full quantum simulations are not presently feasible for realistically sized systems. Here we present a novel approach, the quantum-corrected model (QCM), that incorporates quantum-mechanical effects within a classical electrodynamic framework. The QCM approach models the junction between adjacent nanoparticles by means of a local dielectric response that includes electron tunnelling and tunnelling resistivity at the gap and can be integrated within a classical electrodynamical description of large and complex structures. The QCM predicts optical properties in excellent agreement with fully quantum mechanical calculations for small interacting systems, opening a new venue for addressing quantum effects in realistic plasmonic systems.
Calpain in Breast Cancer: Role in Disease Progression and Treatment Response (2015)

The calpains are a family of intracellular cysteine proteases that function in a wide array of cellular activities, including cytoskeletal remodelling, survival and apoptosis. The ubiquitously expressed micro (µ)-calpain and milli (m)-calpain are archetypal family members that require calcium for function and can be inhibited by their endogenous inhibitor calpastatin. This review describes the role of the calpain system in the prognosis of breast cancer and disease progression, in addition to the role of the calpain system in the response to breast cancer treatments, including chemotherapeutic, endocrine and targeted therapies.
Abstract 5263: An RNAi screen of the protein kinome identifies <i>CHEK1</i> as a therapeutic target in neuroblastoma (2010)

Abstract Background High-risk neuroblastoma is a pediatric cancer that is often fatal despite intense multimodality therapy associated with significant late effects for those who survive. Therefore, patients will benefit from treatment strategies that rationally exploit signaling pathways for which a tumor cell is selectively dependent. In an effort to identify novel therapeutic targets, we performed a comprehensive loss of function screen of the protein kinome in neuroblastoma cell models. Methods Using a validated siRNA library which targets the human protein kinome, we transiently transfected individual kinase siRNAs into four neuroblastoma cell lines and measured substrate adherent growth. We then ranked the top 100 most potent kinase siRNAs per cell line and integrated the lists to identify kinases with inhibition in multiple lines. Results Thirty targets emerged as potent in at least three of the four neuroblastoma cell lines. They were enriched for kinases involved in the cell cycle and mitosis. This select group was tested with an independent set of more specific siRNA pools in an expanded panel of eight neuroblastoma cell lines. The strikingly most potent to emerge from the secondary screen was the cell cycle checkpoint kinase CHEK1. CHEK1 knockdown appeared cytotoxic, often by 24 hours, coinciding with complete CHEK1 protein knockdown and an emergence of a substantial apoptotic fraction. As further validation of the siRNA results, pharmacologic inhibition with SB21807, a relatively specific CHEK1 inhibitor, showed cytotoxicity in 7 of 8 neuroblastoma cell lines with a median IC50 of 430 nM (range 62-677 nM), while the non-neuroblastoma lines RPE-1, DOAY and MCF7 cells were resistant with a median IC50 of 2609 nM (1066 - 2898 nM). The mechanism of selective inhibition in neuroblastoma is unclear as we did not identify mutations in the coding exons of CHEK1. Western blotting revealed, however, that CHEK1 is constitutively phosphorylated at the Ser 296 residue in 8/8 neuroblastoma cell lines and 10/16 primary tumors samples, but not in controls. Conclusion We have identified CHEK1 as a potential therapeutic target in neuroblastoma and are currently extending our work to understand the mechanism of this tumor's apparent selective sensitivity to CHEK1 inhibition. As CHEK1 inhibitors are currently in phase I/II clinical trials as chemosensitizers, we are also focused on determining the in vivo efficacy of combination CHEK1 inhibition with chemotherapy in neuroblastoma. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5263.
An Experimental Study of Vane Clocking Effects on Embedded Compressor Stage Performance (2009)

Previous research has shown that vane clocking, the circumferential indexing of adjacent vane rows with similar vane counts, can be an effective means to increase stage performance, reduce discrete frequency noise, and/or reduce the unsteady blade forces that can lead to high cycle fatigue. The objective of this research was to experimentally investigate the effects of vane clocking in an embedded compressor stage, focusing on stage performance. Experiments were performed in the intermediate-speed Purdue three-stage compressor, which consists of an IGV followed by three stages. The IGV, Stator 1, and Stator 2 vane rows have identical vane counts, and the effects of vane clocking were studied on Stage 2. Much effort went into refining performance measurements to enable the detection of small changes in stage efficiency associated with vane clocking. At design loading, the change in stage efficiency between the maximum and minimum efficiency clocking configurations was 0.27 points. The maximum efficiency clocking configuration positioned the Stator 1 wake at the Stator 2 leading edge. This condition produced a shallower and thinner Stator 2 wake compared with the clocking configuration that located the wake in the middle of the Stator 2 passage. At high loading, the change in Stage 2 efficiency associated with vane clocking effects increased to 1.07 points; however, the maximum efficiency clocking configuration was the case where the Stator 1 wake passed through the middle of the downstream vane passage. Thus, impingement of the upstream vane wake on the downstream vane leading edge resulted in the best performance at design point but provided the lowest efficiency at an off-design condition.
A surface plate calorimeter (1973)

A small surface plate calorimeter, about 8 mm*12 mm*0.2 mm thick, is described for measuring the steady state convection and radiation heat transfer from the surface of a heated body in air. The calorimeter, which may be attached to the surface of the body with double-sided adhesive tape, has been tested on heated cylinders in free and forced convection.
Phase I Study of Lapatinib in Combination With Chemoradiation in Patients With Locally Advanced Squamous Cell Carcinoma of the Head and Neck (2009)

The recommended phase II dose is lapatinib 1,500 mg/d with chemoradiotherapy in patients with LA SCCHN; this regimen is associated with an acceptable tolerability profile. Given these findings, randomized phase II and III studies of lapatinib plus chemoradiotherapy have been initiated.
Energy Efficient IoT Sensor With RF Wake-Up and Addressing Capability (2017)

In this article, we present a complete design for an optimized energy-efficient sensor for use in Internet of Things networks based on the concept of radio wake-up, with embedded addressing capability. Experimental and analytical results demonstrate the validity of the proposed design in terms of low power consumption and efficient functionality compared to existing solutions that are based on periodic wake-up patterns.
Effects of Renin-Angiotensin Inhibition on ACE2 and TMPRSS2 Expression: Insights into COVID-19 (2020)

Angiotensin-converting enzyme 2 (ACE2), a component of the renin-angiotensin system, is a receptor for SARS-CoV-2, the virus that causes COVID-19. To determine whether the renin-angiotensin inhibition regulates ACE2 expression, either enalapril (an angiotensin-converting enzyme inhibitor) or losartan (an AT1 receptor blocker) was infused subcutaneously to male C57BL/6J mice for two weeks. Neither enalapril nor losartan changed abundance of ACE2 mRNA in lung, ileum, kidney, and heart. Viral entry also depends on transmembrane protease serine 2 (TMPRSS2) to prime the S protein. TMPRSS2 mRNA was abundant in lungs and ileum, modest in kidney, but barely detectable in heart. TMPRSS2 mRNA abundance was not altered by either enalapril or losartan in any of the 4 tissues. Next, we determined whether depletion of angiotensinogen (AGT), the unique substrate of the renin-angiotensin system, changes ACE2 and TMPRSS2 mRNA abundance. AGT antisense oligonucleotides (ASO) were injected subcutaneously to male C57BL/6J mice for 3 weeks. Abundance of ACE2 mRNA was unchanged in any of the 4 tissues, but TMPRSS2 mRNA was significantly decreased in lungs. Our data support that the renin-angiotensin inhibition does not regulate ACE2 and hence are not likely to increase risk for COVID-19.
Air polishing: a review of current literature. (2013)

Routine tooth polishing continues to be an integral part of clinical practice even though the concept of selective polishing was introduced in the 1980s. This procedure assists in the removal of stains and plaque biofilm and provides a method for applying various medicaments to the teeth, such as desensitizing agents. Use of traditional polishing methods, i.e. a rubber-cup with prophylaxis paste, has been shown to remove the fluoride-rich outer layer of the enamel and cause significant loss of cementum and dentin over time. With the growing body of evidence to support alternative tooth polishing methods, dental hygiene practitioners should familiarize themselves with contemporary methods including air polishing. The purpose of this review is to provide a comprehensive overview of recent advancements in air polishing. The effect of air-powder polishing on hard and soft tissues, restorative materials, sealants, orthodontic appliances and implants, as well as health risks and contraindications to air polishing are discussed. A comprehensive computer based search made use of the following databases: CINAHL, Ovid Medline and PubMed. Articles that were not available on these sites were requested from Wilson Interlibrary.
Efficient haplotype matching between a query and a panel for genealogical search (2019)

Supplementary data are available at Bioinformatics online.
System-on-Chip Design Methodology for a Statistical Coder (2006)

In this paper, we propose a system-on-chip software hardware co-design methodology for a statistical coder. We use the context adaptive binary arithmetic coder (CABAC) used in the main profile of the H.264/AVC video coding standard as a design example. The design methodology first involves performance and complexity analyses of the existing CABAC reference software, and thus the top-level CABAC software hardware architecture can be conceptualized. The design is aimed to strike a balance between software modules and hardware modules based on design constraints. Verification is performed by comparing the compressed bit stream generated by the reference CABAC SW (without any HW assisted circuitries), with that output by the top-level CABAC architecture (with HW assisted circuitries). Standard video test sequences have been used for verification purpose. The CABAC architecture is then put within the system-on-chip frame work where system bus and its signals, input/output FIFO buffers, debug structures, reset circuit, etc. are designed into. Compared to existing statistical coders, this design is aimed for significant coding time saving by balancing timing between software modules and hardware modules, is well verified with standard video test sequences, and is reusable as an IP in a SoC environment
Expression of <i>Veratrum</i> alkaloid teratogenicity in the mouse (1990)

Jervine, a steroidal alkaloid found as a minor constituent in the teratogenic range plant Veratrum californicum, has produced similar terata in sheep, rabbit, hamster, and chick, although the sensitivity to the alkaloid varies in the different species. Sprague Dawley rats and Swiss Webster mice are relatively insensitive. The aim of this study was to determine the teratogenic potential of jervine in three strains of mice and to ascertain if the response is strain dependent. One strain, Swiss N:GP(S), was retested since a Swiss Webster strain had been found previously to be jervine-resistant. In addition, we tested C57BL/6J and A/J, which are known to differ in their response to the teratogenic action of steroids and vitamin A. Mice were treated by gavage with single doses of jervine (70, 150, or 300 mg/kg body weight) on either day 8, 9, or 10 of gestation. Jervine was teratogenic to C57BL/6J and A/J mice but not to N:GP(S). The induced terata included cleft lip with or without cleft palate, isolated cleft palate, mandibular micrognathia or agnathia, and limb malformations. Fetal teratogenicity and maternal and fetal toxicity were highly correlated. The prevalence of each defect and fetal death was a function of strain, dose, and time of treatment. Maternal death was higher in C57BL/6J than in A/J mice. Although some of the terata were similar, the response pattern between strains was different from corticosteroids and vitamin A for both sensitive period and the strain dose response. An effect on differentiation of chondrocyte precursors may account for many of the defects, but an earlier lethal effect on differentiation of neural crest cells or precordal mesenchyme may also occur.
Reducing false positives in intrusion detection systems using data-mining techniques utilizing support vector machines, decision trees, and naive Bayes for off-line analysis (2016)

Intrusion detection systems monitor network or host packets in an attempt to detect malicious activities on a system. Anomaly detection systems have success in exposing new attacks, commonly referred to as `zero' day attacks, yet have high false positive rates. False positive events occur when an activity is flagged for investigation yet it was determined to be benign upon analysis. Computational power and valuable resources are wasted when the irrelevant data is processed, data flagged, analyst alerted, and the irrelevant data is finally disregarded. In an effort to make intrusion detection systems more efficient the false positive rate must be reduced. This paper proposes a model for reducing false positives using data mining techniques by combining support vector machines (SVM), decision trees, and Naïve Bayes.
Sex Steroid Hormones and Cell Dynamics in the Periodontium (1994)

The biological changes that occur in tissues of the periodontium during puberty, the menstrual cycle, pregnancy, menopause, and oral contraceptive use have heightened interest in the relationship between sex steroid hormones and periodontal health. These clinical observations coupled with tissue specificity of hormone localization, identification of hormone receptors, as well as the metabolism of hormones have strongly suggested that periodontal tissues are targets for androgens, estrogens, and progestins. The etiologies of periodontal endocrinopathies are diverse; nonetheless, periodontal pathologies may be a consequence of the actions and interactions of sex steroid hormones on specific cells found in the periodontium.
FiberID: molecular-level secret for identification of things (2014)

This paper describes a new physical unclonable function for identification, FiberID, which uses the molecular level Rayleigh backscatter pattern within a small section of telecommunication-grade optical fiber as a means of verification and identification. The verification process via FiberID is experimentally studied, and an equal error rate (EER) of 0.06% is achieved. Systematic evaluation of FiberID is conducted in term of physical length and ambient temperature. Due to its inherent irreproducibility, FiberID holds the promise to significantly enhance current identification, security, and anti-counterfeiting technologies.
Fibre laser welding of aluminium alloy (2009)

The objectives of this research are to investigate the effects of various welding conditions on penetration and defect formation, to clarify their welding phenomena and to develop the procedure of reduction of the defect. Fibre laser bead-on-plate welding was performed on several aluminium alloys, in particular A5083, at the power of 6 or 10 kW and several power densities from 0.4 kW/mm2. It was found that the weld beads were narrower and deeper with an increase in the laser power density. For example, fully penetrated weld beads in 10 mm thick plates were produced at the laser power density of 640 kW/mm2 and the welding speed of 10 m/min. However, convex–concave bead surfaces were formed. Moreover, in the case of the high power density, no porosity and many pores were present at high and low welding speeds, respectively. On the other hand, in the case of the ultra-high power density, few pores were generated in high speed welding. These reasons were interpreted by observing keyhole behaviour, bubble formation and the molten pool geometry during high power fibre laser welding with a high-speed video camera and microfocused X-ray transmission in situ observation method. Moreover, the porosity in the weld bead was reduced and prevented by the utilization of nitrogen gas instead of Ar gas, or the forward inclination angle of 40° (50° from the right angle) in Ar shielding gas.
Chemical Composition and Larvicidal Activity against Aedes aegypti Larvae of Essential Oils from Four Guarea Species (2010)

The essential oils of four Guarea species collected at Manaus (Amazonas, Brazil) were obtained by hydrodistillation and analyzed by GC-MS. Except for one diterpene detected, the compounds identified in the essential oils were hydrocarbons and oxygenated sesquiterpenes. The major sesquiterpenes were alpha-santalene (26.26%) and alpha-copaene (14.61%) from G. convergens branches; caryophyllene epoxide (40.91%) and humulene epoxide II (14.43%) from G. humaitensis branches; cis-caryophyllene (33.37%) and alpha-trans-bergamotene (11.88%) from G. scabra leaves; caryophyllene epoxide (36.54%) in leaves and spathulenol (14.34%) in branches from G. silvatica. The diterpene kaurene (15.61%) was found in G. silvatica leaves. Larvicidal activity assay of essential oils against third-instar Aedes aegypti larvae revealed that at higher concentrations (500 and 250 microg/mL), all the essential oils caused 100% mortality after 24 h of exposure. The most active essential oils were those of G. humaitensis branches (LC(50) 48.6 microg/mL), G. scabra leaves (LC(50) 98.6 microg/mL) and G. silvatica (LC(50) 117.9 microg/mL). The differences in the toxicity of essential oils of Guarea species on A. aegypti are due to qualitative and quantitative variations of the components, therefore the larvicidal effect may be due to higher amount of the sesquiterpenes with caryophyllane skeleton.
Determination of Microbial Diversity of Aeromonas Strains on the Basis of Multilocus Sequence Typing, Phenotype, and Presence of Putative Virulence Genes (2011)

The genus Aeromonas has been described as comprising several species associated with the aquatic environment, which represents their principal reservoir. Aeromonas spp. are commonly isolated from diseased and healthy fish, but the involvement of such bacteria in human infection and gastroenteritis has frequently been reported. The primary challenge in establishing an unequivocal link between the Aeromonas genus and pathogenesis in humans is the extremely complicated taxonomy. With the aim of clarifying taxonomic relationships among the strains and phenotypes, a multilocus sequencing approach was developed and applied to characterize 23 type and reference strains of Aeromonas spp. and a collection of 77 field strains isolated from fish, crustaceans, and mollusks. All strains were also screened for putative determinants of virulence by PCR (ast, ahh1, act, asa1, eno, ascV, and aexT) and the production of acylated homoserine lactones (AHLs). In addition, the phenotypic fingerprinting obtained from 29 biochemical tests was submitted to the nonparametric combination (NPC) test methodology to define the statistical differences among the identified genetic clusters. Multilocus sequence typing (MLST) achieved precise strain genotyping, and the phylogenetic analysis of concatenated sequences delineated the relationship among the taxa belonging to the genus Aeromonas, providing a powerful tool for outbreak traceability, host range diffusion, and ecological studies. The NPC test showed the feasibility of phenotypic differentiation among the majority of the MLST clusters by using a selection of tests or the entire biochemical fingerprinting. A Web-based MLST sequence database (http://pubmlst.org/aeromonas) specific for the Aeromonas genus was developed and implemented with all the results.
Dendritic BC1 RNA: Functional Role in Regulation of Translation Initiation (2002)

In neurons, local protein synthesis in synaptodendritic microdomains has been implicated in the growth and plasticity of synapses. Prerequisites for local translation are the targeted transport of RNAs to distal sites of synthesis in dendrites and translational control mechanisms to limit synthesis to times of demand. Here we identify dendritic BC1 RNA as a specific repressor of translation. Experimental use of internal ribosome entry mechanisms and sucrose density gradient centrifugation showed that BC1-mediated repression targets translation at the level of initiation. Specifically, BC1 RNA inhibited formation of the 48S preinitiation complex, i.e., recruitment of the small ribosomal subunit to the messenger RNA (mRNA). However, 48S complex formation that is independent of the eukaryotic initiation factor 4 (eIF4) family of initiation factors was found to be refractory to inhibition by BC1 RNA, a result that implicates at least one of these factors in the BC1 repression pathway. Biochemical experiments indicated a specific interaction of BC1 RNA with eIF4A, an RNA unwinding factor, and with poly(A)-binding protein. Both proteins were found enriched in synaptodendritic microdomains. Significantly, BC1-mediated repression was shown to be effective not only in cap-dependent translation initiation but also in eIF4-dependent internal initiation. The results suggest a functional role of BC1 RNA as a mediator of translational control in local protein synthesis in nerve cells.
Strict Liability for Abnormally Dangerous Activity: The Negligence Barrier (1999)

My main thesis is that the doctrine of strict liability for abnormally dangerous activity (which I sometimes refer to by the acronym SLADA), memorialized in sections 519 and 520 of the Restatement (Second) of Torts,' has evolved to the point of near extinction because courts have concluded that the negligence system functions effectively to deter the serious risks posed by the activities involved. The Restatement (Second) provides that strict liability is inapplicable when the high degree of risk can be eliminated by the exercise of reasonable care.2 The evidence demonstrates that courts are increasingly making precisely that finding, usually without any reliance on record evidence, but instead on a judicial sense that very few risks are incapable of being rendered safe by reasonable precautions. This movement away from strict liability and toward negligence I refer to as "the negligence barrier."