gebhart/patrepeval huggingface dataset:
A Linguistic Perspective on the Drake Equation (2023)

Frank Drake set a research agenda for the search for extraterrestrial intelligence (SETI) with an equation designed to estimate the number of planets in our galaxy hosting intelligent life. This chapter proposes a similar equation regarding the likelihood of being able to communicate with extraterrestrials. In line with Drake’s original motivation, the purpose of this chapter is to map out important areas of study regarding the structure of possible alien languages, rather than to provide a specific answer. However, the results of this discussion suggest that although there would be a variety of practical challenges, it seems likely that humans and intelligent extraterrestrials would have at least overlapping cognitive capacities for communication and might be able to communicate with each other. This chapter focuses on perception and understanding as the critical properties of successful communication and specifically how they may be determined by grammatical and other factors. By studying these questions, we may also be able to frame our understanding of human languages from an objective perspective, for example by considering which properties are coincidental and possibly uniquely human, and which would be typical of the communicative abilities of any highly intelligent species.
LISP ITR Graceful Restart (2013)

The Locator/ID Separation Protocol (LISP) is a map-and-encap mechanism
to enable communications between hosts identified with their Endpoint
IDentifier (EID) over the Internet where EIDs are not routable. To do
so, packets toward EIDs are encapsulated in packets with routing
locators (RLOCs) to form dynamic tunnels. An Ingress Tunnel Router
(ITR) that encapsulates EID packets determines tunnel endpoints via
mappings that associate EIDs to RLOCs. Before encapsulating a packet,
the ITR queries the mapping system to obtain the mapping associated to
the EID of the packet it must encapsulate. Such mapping is cached by
the ITR in its local EID-to-RLOC cache for any subsequent
encapsulation for the same EID. LISP is scalable because EID-to-RLOC
mappings are cached on ITRs. Initially, the cache is empty and is
populated progressively according to the traffic traversing the ITR.
However, after an ITR is restarted, e.g., for maintenance reason, its
cache is empty which means that all packets that are re-routed to the
freshly restarted ITR will cause cache misses and a potentially high
loss rate. In this draft, we present mechanisms to reduce the negative
impact on traffic caused by the restart of an ITR in a LISP network.
Selective optical trapping using optical beams with fractional helical phase (2004)

The Laguerre-Gaussian beams or higher-order Bessel beams, which possess a full-doughnut shaped intensity pattern at the center, repel the low index particles away from the dark central spot due to radiation pressure. Optical beams with fractional helical phase are possible solutions to this problem, as they possess a clear opening slit. By using a spatial light modulator, we demonstrate the control of an opening slit by embedding different fractional helical phase into Bessel beams and Gaussian beams. This dynamic opening and closing of the slit will allow a possible selective process of the micro-particles. This is also a new way to control the guiding of particles in the transverse plane instead of the propagation direction.
Microporous metal–organic framework containing cages with adjustable portal dimensions for adsorptive CO2 separation (2012)

The excellent breakthrough separation performance of a new microporous MOF for CO2/N2 and CO2/CH4 gas mixtures results from the combination of different equilibrium uptake amounts depending on the adsorption enthalpies of the adsorbates and different uptake kinetics depending on their kinetic diameters.
Multivalent Protein Binding and Precipitation by Self-Assembling Molecules on a DNA Pentaplex Scaffold (2009)

A supramolecular assembly containing an isoguanosine pentaplex with both a "protein-binding" face and a "reporter" face has been generated. When phosphocholine is appended to the protein-binding face this supramolecular assembly binds multivalently to the pentameric human C-reactive protein, a biomolecule implicated in inflammation and heart disease.
A likelihood approach to analysis of network data (2006)

Biological, sociological, and technological network data are often analyzed by using simple summary statistics, such as the observed degree distribution, and nonparametric bootstrap procedures to provide an adequate null distribution for testing hypotheses about the network. In this article we present a full-likelihood approach that allows us to estimate parameters for general models of network growth that can be expressed in terms of recursion relations. To handle larger networks we have developed an importance sampling scheme that allows us to approximate the likelihood and draw inference about the network and how it has been generated, estimate the parameters in the model, and perform parametric bootstrap analysis of network data. We illustrate the power of this approach by estimating growth parameters for the Caenorhabditis elegans protein interaction network.
Grasp compliance achieved with a planar hand composed of multiple 3-joint fingers (2022)

Abstract In this paper, the realization of any specified planar Cartesian compliance for an object grasped by a compliant hand is addressed. The hands considered have 2 or more fingers for which each has 3 modulated elastic joints and predetermined link lengths. Geometric construction-based compliance synthesis procedures are developed. Using these procedures, a large set of compliant behaviors can be realized by a single hand simply by adjusting the configuration of each finger and by adjusting the joint stiffness (using variable stiffness actuation) of each finger joint.
A novel approach for electrical tuning of nano-textured zinc oxide surfaces for ultra-sensitive troponin-T detection (2015)

We have developed a novel and ultrasensitive biosensor by functionalizing surface terminations of zinc oxide using two specific linker chemistries, which has enabled fg mL<sup>−1</sup> level detection of a cardiac stress biomarker, troponin-T.
Solid-Phase Synthesis of 2,4-Diaminopyrimidines via Lewis Acid-Mediated Aromatic Nucleophilic Substitution (2004)

Primary amines were immobilized on (4-formyl-3,5-dimethoxyphenoxy)methylpolystyrene resin via reductive amination. Attachment of two different 4-chloro-2-methylthiopyrimidines, followed by sulfide oxidation, led to their corresponding sulfone intermediates. Aromatic nucleophilic substitution with various anilines or heteroaromatic amines in the presence of trimethyl aluminum afforded the desired 2,4-diaminopyrimidines after acidic cleavage from the resin. The synthetic methodology described herein was validated with the synthesis of a small 162-member library.
4-Anilino-7,8-dialkoxybenzo[g]quinoline-3-carbonitriles as Potent Src Kinase Inhibitors (2005)

It has been previously reported that appropriately substituted 4-anilinoquinoline-3-carbonitriles are potent inhibitors of Src kinase, with biological activity in vitro and in vivo. Structural modifications to these compounds have been explored, providing the 4-anilinobenzo[g]quinoline-3-carbonitriles as a series with enhanced Src inhibitory properties. The synthesis and structure-activity relationships of these 4-anilino-7,8-dialkoxybenzo[g]quinoline-3-carbonitriles are presented here. Analogues with cyclic basic amine groups attached via ethoxy linkages at the C-8 position were the most active in vitro, with subnanomolar IC50 values against Src kinase observed for a majority of the compounds synthesized. Compound 17d was more potent in vitro than the analogously substituted 4-anilinoquinoline-3-carbonitrile SKI-606, which is undergoing evaluation in clinical trials. The most potent analogue synthesized was 17a, with an IC50 of 0.15 nM against Src kinase and with an IC50 of 10 nM against Src-transformed fibroblasts. Molecular modeling studies provided a rationale for the exceptional activity observed for these compounds, with favorable van der Waals interactions playing the major role. Compound 17c was found to be highly selective for Src kinase when tested against a panel of other kinases, with modest selectivity versus the Src family kinases Lyn and Fyn. Following ip dosing at 50 mg/kg, analogues 17c and 17d were shown to have plasma levels that significantly exceeded the cellular IC50 values against Src-transformed fibroblasts. In an Src-transformed fibroblast xenograft model, both compounds exhibited a significant inhibition of tumor growth.
Experimental Study for the Effect of Vaned Diffuser Leading Edge on the Noise Generated From a Centrifugal Fan (2009)

This paper studies a novel vaned diffuser with inclined leading edge to reduce the fan noise. The aerodynamic performances and sound pressure level (SPL) of the centrifugal fan with five different diffusers were measured in an anechoic chamber, and the inclined angles of the five diffusers are 45°, 60°, 120°, 135° and 150°, respectively. The flow coefficient of the fan varies from 0.037 to 0.14, the rotational speed ranges from 20000rpm to 35000rpm. The test results show that, by using diffuser vanes with inclined leading edge, the overall noise of the fan is reduced in the experimental conditions, and it has the minimum value at the flow rate coefficient of 0.084. The overall noise reduction of 5.3dB was made with the diffuser leading edge inclined angle of 150°.
COVID-19 Classification of X-ray Images Using Deep Neural Networks (2020)

Abstract Objectives In the midst of the coronavirus disease 2019 (COVID-19) outbreak, chest X-ray (CXR) imaging is playing an important role in diagnosis and monitoring of patients with COVID-19. Machine learning solutions have been shown to be useful for X-ray analysis and classification in a range of medical contexts. In this study, we propose a machine learning model for detection of patients tested positive for COVID-19 from CXRs that were collected from inpatients hospitalized in four different hospitals. We additionally present a tool for retrieving similar patients according to the model’s results on their CXRs. Methods In this retrospective study, 1384 frontal CXRs, of COVID-19 confirmed patients imaged between March-August 2020, and 1024 matching CXRs of non-COVID patients imaged before the pandemic, were collected and used to build a deep learning classifier for detecting patients positive for COVID-19. The classifier consists of an ensemble of pre-trained deep neural networks (DNNS), specifically, ReNet34, ReNet50, ReNet152, vgg16, and is enhanced by data augmentation and lung segmentation. We further implemented a nearest-neighbors algorithm that uses DNN-based image embeddings to retrieve the images most similar to a given image. Results Our model achieved accuracy of 90.3%, (95%CI: 86.3%-93.7%) specificity of 90% (95%CI: 84.3%-94%), and sensitivity of 90.5% (95%CI: 85%-94%) on a test dataset comprising 15% (350/2326) of the original images. The AUC of the ROC curve is 0.96 (95%CI: 0.93-0.97). Conclusion We provide deep learning models, trained and evaluated on CXRs that can assist medical efforts and reduce medical staff workload in handling COVID-19. Key Points A machine learning model was able to detect chest X-ray (CXR) images of patients tested positive for COVID-19 with accuracy and detection rate above 90%. A tool was created for finding existing CXR images with imaging characteristics most similar to a given CXR, according to the model’s image embeddings.
Borrelia burgdorferiGene Expression In Vivo and Spirochete Pathogenicity (2000)

Borrelia burgdorferi spirochetes that do not cause arthritis or carditis were developed and used to investigate Lyme disease pathogenesis. A clonal isolate of B. burgdorferi N40 (cN40), which induces disease in C3H/HeN (C3H) mice, was repeatedly passaged in vitro to generate nonpathogenic spirochetes. The passage 75 isolate (N40-75) was infectious for C3H mice but did not cause arthritis or carditis, and spirochetes were at low levels or absent in the joints or hearts, respectively. N40-75 could, however, cause disease in severe combined immunodeficient (SCID) mice, suggesting that the response in immunocompetent mice prevented effective spirochete dissemination and the subsequent development of arthritis and carditis. Administration of immune sera at 4 days after spirochete challenge aborted N40-75, but not cN40, infection in SCID mice. A B. burgdorferi genomic expression library was differentially probed with sera from cN40- and N40-75-infected mice, to identify genes that may not be effectively expressed by N40-75 in vivo. N40-75 was defective in the up-regulation of several genes that are preferentially expressed during mammalian infection, including dbpAB, bba64, and genes that map to the cp32 family of plasmids. These data suggest that adaptation and gene expression may be required for B. burgdorferi to effectively colonize the host, evade humoral responses, and cause disease.
Visualizing Mitochondrial FoF1-ATP Synthase as the Target of the Immunomodulatory Drug Bz-423. (2018)

Targeting the mitochondrial enzyme F<sub>o</sub>F<sub>1</sub>-ATP synthase and modulating its catalytic activities with small molecules is a promising new approach for treatment of autoimmune diseases. The immunomodulatory compound Bz-423 is such a drug that binds to subunit OSCP of the mitochondrial F<sub>o</sub>F<sub>1</sub>-ATP synthase and induces apoptosis <i>via</i> increased reactive oxygen production in coupled, actively respiring mitochondria. Here, we review the experimental progress to reveal the binding of Bz-423 to the mitochondrial target and discuss how subunit rotation of F<sub>o</sub>F<sub>1</sub>-ATP synthase is affected by Bz-423. Briefly, we report how Förster resonance energy transfer can be employed to colocalize the enzyme and the fluorescently tagged Bz-423 within the mitochondria of living cells with nanometer resolution.
Using in-process testing metrics to estimate post-release field quality of Java programs (2006)

In industrial practice, information on the software field quality of a product is available too late in the software lifecycle to guide affordable corrective action. An important step towards remediation of this problem lies in the ability to provide an early estimation of post-release field quality. This paper presents a suite of nine static in-process unit test metrics, the Software Testing and Reliability Early Warning for Java (STREW-J) metric suite. The STREW-J metrics can be used to leverage the software testing effort to predict post-release field quality early and throughout the software development phases. The metric suite is applicable for software products implemented in Java for which an extensive suite of automated unit test cases are incrementally created as development proceeds. We built and validated a prediction model using the STREW-J metrics via a three-phase case study approach which progressively involved 22 small-scale academic projects, 27 medium-sized open source projects, and five industrial projects. The ability of the STREW-J metric suite to estimate post-release field quality via a statistical regression model was evaluated in the three different environments. The error in estimation and the sensitivity of the predictions indicate the STREW-J metric suite can be used effectively to predict postrelease software field quality.
Cyclosporin A blocks calcium-dependent pathways of gene activation. (1991)

We have used an interleukin-2 (IL-2) promoter-CAT fusion gene to study activation of IL-2 gene expression by IL-1, phytohemagglutinin (PHA), phorbol myristate acetate (PMA), and calcium ionophore in the murine thymoma line EL4 and the human lymphoma line Jurkat. The two cell lines respond differently to combinations of these stimuli. IL-1 in combination with suboptimal concentration of PMA induced chloramphenicol acetyltransferase (CAT) activity in EL4. In Jurkat cells, IL-1 failed to synergize with PMA or PHA. Cotransfection with the IL-2/CAT gene and a construct capable of expressing murine T-cell type IL-1 receptors converted Jurkat cells to IL-1 responsiveness. IL-1 in combination with PHA but not with PMA resulted in induction of CAT activity in these cells. Induction of IL-2/CAT activity by all stimuli in both cell lines was blocked by the presence of EGTA in the culture medium. EGTA did not inhibit IL-1/PMA activation of an SV40 early promoter-CAT fusion gene in either EL4 or Jurkat cells; therefore, calcium was not required for IL-1 or PMA signal transduction. Jurkat cells were shown to differ from EL4 in their requirement for calcium mobilization. Two different calcium-dependent pathways of gene activation were distinguished, both of which were blocked by the immunosuppressive drug cyclosporin A.
Effects of an Experiential Learning Activities-Focused Smoking Prevention Program in Elementary School Students: On the Basis of the Attitude-Social Influence-Efficacy Model (2019)

We aimed to examine the effects of an experiential learning activities-focused smoking prevention (ELSP) program on the basis of the Attitude-Social Influence-Efficacy (ASE) model in elementary school students. Methods: A non-equivalent control group pre-test and post-test design was conducted with 84 participants who were in the fifth grade of two elementary schools in Seongnam city, South Korea. The two schools were allocated into either the ELSP (n=42) or control (n=42) group. The ELSP group completed five ELSP classes, while the control group completed five traditional lecture-based classes during the 5 weeks. Both groups were examined before and after 5 weeks, using ASE measures of smoking attitude, social influence, self-efficacy for the refusal of smoking temptation, and intention not to smoke. Data were collected from August to September 2017.
Listeria monocytogenes: review of pathogenesis and virulence determinants-targeted immunological assays (2021)

<i>Listeria monocytogenes</i> is one of the most invasive foodborne pathogens and is responsible for numerous outbreaks worldwide. Most of the methods to detect this bacterium in food require selective enrichment using traditional bacterial culture techniques that can be time-consuming and labour-intensive. Moreover, molecular methods are expensive and need specific technical knowledge. In contrast, immunological approaches are faster, simpler, and user-friendly alternatives and have been developed for the detection of <i>L. monocytogenes</i> in food, environmental, and clinical samples. These techniques are dependent on the constitutive expression of <i>L. monocytogenes</i> antigens and the specificity of the antibodies used. Here, updated knowledge on pathogenesis and the key immunogenic virulence determinants of <i>L. monocytogenes</i> that are used for the generation of monoclonal and polyclonal antibodies for the serological assay development are summarised. In addition, immunological approaches based on enzyme-linked immunosorbent assay, immunofluorescence, lateral flow immunochromatographic assays, and immunosensors with relevant improvements are highlighted. Though the sensitivity and specificity of the assays were improved significantly, methods still face many challenges that require further validation before use.
Human pharmacokinetic (PK) characterization of the novel dual-action anti-HER3/EGFR antibody MEHD7945A (MEHD) in patients with refractory/recurrent epithelial tumors. (2012)

2567 Background: MEHD is a novel dual-action human IgG1 antibody that blocks ligand binding to HER3 and EGFR, and elicits antibody-dependent cell-mediated cytotoxicity (ADCC). MEHD demonstrates single-agent activity in a broad panel of tumor models, including models resistant to anti-HER3 or anti-EGFR treatment alone. The objective of this analysis was to characterize the PK of MEHD associated with body weight (BW)-based dosing used in a phase I study in patients with epithelial tumors and to evaluate the potential for using fixed dosing in future studies. Methods: Preliminary non-compartmental and population PK analyses were performed using patient data from the dose-escalation stage [1, 4, 10, 15, 22, and 30 mg/kg every two weeks (q2w)] and expansion stage (14 mg/kg q2w) of the phase I study. Patient demographic data and other relevant clinical covariates were evaluated in the population analysis. PK simulation of 1000 subjects with a log-normal BW distribution was performed to compare the inter-individual variability of MEHD exposure following fixed or BW-based dosing. Results: As expected,MEHD exhibited nonlinear PK. In the noncompartmenal analysis, the apparent clearance (CL) decreased in a dose-dependent fashion (about 40 to 9.9 mL/day/kg from 1 to 30 mg/kg) and approached linearity at doses &gt;10 mg/kg (q2w). In the population analysis, the PK profile of MEHD was well described by a two compartment model with linear and nonlinear clearance. The target-mediated clearance was consistent with that of anti-EGFR antibodies. The nonspecific CL and central volume of distribution (V1) values were approximately 6 mL/day/kg and 52.4 mL/kg, respectively. BW had a moderate effect on V1, but not on CL. PK simulations suggest that, compared with BW-based dosing, fixed dosing would result in less inter-individual variability in MEHD exposure. Both 1100 mg q2w or 1650 mg q3w of MEHD achieve the targeted therapeutic exposure. Conclusions: The dual-action antibody MEHD demonstrated PK consistent with anti-EGFR antibodies. Fixed dosing of MEHD on an every 2 or 3 week schedule is supported.
Transesterification of Dimethyl Carbonate with Ethanol To Form Ethyl Methyl Carbonate and Diethyl Carbonate: A Comprehensive Study on Chemical Equilibrium and Reaction Kinetics (2011)

This article studies the consecutive transesterification of dimethyl carbonate with ethanol to form ethyl methyl carbonate and diethyl carbonate. The chemical equilibrium and reaction kinetics of this system are investigated experimentally and theoretically. To enhance the reaction rate, the homogeneous catalyst sodium ethoxide was applied. Molar-based and activity-based chemical equilibrium constants were calculated from experimental results, and their temperature dependence was described using the van’t Hoff equation. An activity-based kinetic model that considers the temperature dependence of the reaction rate constants with the Arrhenius equation was derived.
EUV assist layers for use in multilayer processes (2012)

Extreme ultraviolet (EUV) exposure is among the front-runners for single-exposure lithography for the 16-nm node and below. Previous work has shown that assist layers are critical for performing EUV lithography. Assist layers enhance the adhesion of EUV photoresists, block substrate contamination, and improve the resolution, line width roughness, and sensitivity (RLS) trade-off. As we progress from development to manufacturing, materials must mature to align with industry needs. To bring devices produced using EUV lithography to reality, a trilayer process is the best and most flexible option. The requirements for a trilayer process include utilizing assist layers with a good etch selectivity to the carbon-rich etch transfer layer (ETL) and to the photoresist coupled with good RLS performance. In this paper, we report the study of new assist layers made with novel resins that have shown superior lithography performance, as well as high etch selectivity to both the ETL and the photoresist. We have demonstrated how to significantly improve the lithography with the benefits of the pattern transfer requirements for trilayer processing.