gebhart/patrepeval huggingface dataset:
The effect of economic factors on the welfare of livestock and poultry. (2020)

This chapter describes how standards implemented by major meat buyers can be used to improve welfare, how different marketing systems can either improve welfare or make it worse, how to use incentive payments to improve welfare, the negative effects of biological overload of an animal on its welfare and how short-term economic gains obtained by converting pastureland to crops may be detrimental to both welfare and sustainability. Economic factors can serve as either incentives to improve animal welfare or disincentives that may worsen animal welfare. High standards set by large meat buyers can be powerful motivators to improve animal treatment. An animal-based objective scoring system that was developed for slaughter plants has been used successfully by major retail buyers to enforce better standards. Animal-based measures such as lameness, body condition, and injury scoring are now being used to assess animal welfare on farms. The financial penalty is removal from the approved supplier list. Holding transporters and producers financially accountable for bruises, death losses, and dark cutters will reduce them greatly. Animal welfare will suffer in segmented markets where producers are not held financially accountable for bruises or sickness. The loss gets passed on to the next segment in the marketing chain. Selling animals through many dealers is usually detrimental to welfare. People handling animals should receive extra payments for low bruising and death losses. Economic factors may decrease welfare by encouraging producers to overcrowd animals or convert pastureland to crops.
Divergence and Convergence in Enzyme Evolution: Parallel Evolution of Paraoxonases from Quorum-quenching Lactonases (2011)

We discuss the basic features of divergent versus convergent evolution and of the common scenario of parallel evolution. The example of quorum-quenching lactonases is subsequently described. Three different quorum-quenching lactonase families are known, and they belong to three different superfamilies. Their key active-site architectures have converged and are strikingly similar. Curiously, a promiscuous organophosphate hydrolase activity is observed in all three families. We describe the structural and mechanistic features that underline this converged promiscuity and how this promiscuity drove the parallel divergence of organophosphate hydrolases within these lactonase families by either natural or laboratory evolution.
Homelink: a unique service (1986)

Abstract Homelink brings a comprehensive range of Nottingham Building Society services to customers at home, on their own TV sets, by means of Prestei which creates a link between the customer, anywhere in the country, and the Society’s computers. In 1983 when Homelink was launched, John Webster, the Society’s Managing Director, was nominated ‘Financial Innovator of the Year’ by the Daily Telegraph, and in 1985 the Society was the proud recipient of a Rita (Recognition of Information Technology Award). Yet only a few years earlier, whilst many building societies were spending vast sums on developments to allow real time passbook updating in branches, which was the then latest phase in society computer development, the Nottingham was consciously conserving its data processing resources.
A Description of the Technique for Nuclear Transplantation inXenopus laevis (1960)

ABSTRACT Technical details are given of a method of transplanting embryonic nuclei in X. laevis. This technique is based on Briggs &amp; King’s method for R. pipiens. Owing to certain differences between the eggs of Rana and Xenopus, their technique has been modified for Xenopus. The main modification for Xenopus concerns the use of ultra-violet irradiation instead of enucleation by a needle. Differences between transplantation techniques for Rana and Xenopus are unlikely to account for the differences in experimental results obtained with these species.
Stealthy Information Leakage Through Peripheral Exploitation in Modern Embedded Systems (2020)

Embedded systems are being aggressively integrated in every aspect of modern life, with uses ranging from personal devices to devices deployed in critical systems, such as autonomous vehicles, aircrafts, and industrial control systems. Embedded systems handle sensitive information, which can be potentially exposed leveraging their poor security posture. In this paper, we present a novel attack vector that automates stealthy information leakage from modern embedded systems. Specifically, we leverage the Device Tree, a data structure that describes the hardware profile of a system, to extract detailed information about the target system. Utilizing this information, we introduce a stealthy attack that attempts to bridge the air-gap by transferring data from memory directly to analog peripherals. The attack resides solely in the peripherals, completely transparent to the main CPU, by judiciously short-circuiting specific components. We implement this attack on a commercial Programmable Logic Controller (PLC), leaking information over the available LEDs. We evaluate the presented attack vector in terms of stealthiness, and we demonstrate no observable overhead on both CPU performance and DMA transfer speed. Furthermore, we propose a generalized defense scheme for peripheral exploitation attacks by establishing a hardware root of trust through JTAG debugging. Our methodology keeps track of peripheral traffic through JTAG-enabled monitoring, alerts the system for possible malicious behavior and handles the threat removal. We test our defense in terms of imposed performance overhead and overall potency, achieving solid detection of the underlying attack at a low performance cost.
Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations (2016)

Pharmacophore modeling is a widely used technique in computer-aided drug discovery. Structure-based pharmacophore models of a ligand in complex with a protein have proven to be useful for supporting in silico hit discovery, hit to lead expansion, and lead optimization. As a structure-based approach it depends on the correct interpretation of ligand–protein interactions. There are legitimate concerns about the fidelity of the bound ligand and about non-physiological contacts with parts of the crystal and the solvent effects that influence the protein structure. A possible way to refine the structure of a protein–ligand system is to use the final structure of a given MD simulation. In this study we compare pharmacophore models built using the initial protein–ligand structure obtained from the protein data bank (PDB) with pharmacophore models built with the final structure of a molecular dynamics simulation. We show that the pharmacophore models differ in feature number and feature type and that the pharmacophore models built from the last structure of a MD simulation shows in some cases better ability to distinguish between active and decoy ligand structures.
Sulong - execution of LLVM-based languages on the JVM (2016)

For the last decade, the Java Virtual Machine (JVM) has been a popular platform to host languages other than Java. Language implementation frameworks like Truffle allow the implementation of dynamic languages such as JavaScript or Ruby with competitive performance and completeness. However, statically typed languages are still rare under Truffle. We present Sulong, an LLVM IR interpreter that brings all LLVM-based languages including C, C++, and Fortran in one stroke to the JVM. Executing these languages on the JVM enables a wide area of future research, including high-performance interoperability between high-level and low-level languages, combination of static and dynamic optimizations, and a memory-safe execution of otherwise unsafe and unmanaged languages.
Circadian Rhythms of Sense and Antisense Transcription in Sugarcane, a Highly Polyploid Crop (2013)

Commercial sugarcane (Saccharum hybrid) is a highly polyploid and aneuploid grass that stores large amounts of sucrose in its stem. We have measured circadian rhythms of sense and antisense transcription in a commercial cultivar (RB855453) using a custom oligoarray with 14,521 probes that hybridize to sense transcripts (SS) and 7,380 probes that hybridize to antisense transcripts (AS).We estimated that 32% of SS probes and 22% AS probes were rhythmic. This is a higher proportion of rhythmic probes than the usually found in similar experiments in other plant species. Orthologs and inparalogs of Arabidopsis thaliana, sugarcane, rice, maize and sorghum were grouped in ortholog clusters. When ortholog clusters were used to compare probes among different datasets, sugarcane also showed a higher proportion of rhythmic elements than the other species. Thus, it is possible that a higher proportion of transcripts are regulated by the sugarcane circadian clock. Thirty-six percent of the identified AS/SS pairs had significant correlated time courses and 64% had uncorrelated expression patterns. The clustering of transcripts with similar function, the anticipation of daily environmental changes and the temporal compartmentation of metabolic processes were some properties identified in the circadian sugarcane transcriptome. During the day, there was a dominance of transcripts associated with photosynthesis and carbohydrate metabolism, including sucrose and starch synthesis. During the night, there was dominance of transcripts associated with genetic processing, such as histone regulation and RNA polymerase, ribosome and protein synthesis. Finally, the circadian clock also regulated hormone signalling pathways: a large proportion of auxin and ABA signalling components were regulated by the circadian clock in an unusual biphasic distribution.
Modelling Degradation and Replication Kinetics of the Zika Virus In Vitro Infection (2020)

Mathematical models of in vitro viral kinetics help us understand and quantify the main determinants underlying the virus-host cell interactions. We aimed to provide a numerical characterization of the Zika virus (ZIKV) in vitro infection kinetics, an arthropod-borne emerging virus that has gained public recognition due to its association with microcephaly in newborns. The mathematical model of in vitro viral infection typically assumes that degradation of extracellular infectious virus proceeds in an exponential manner, that is, each viral particle has the same probability of losing infectivity at any given time. We incubated ZIKV stock in the cell culture media and sampled with high frequency for quantification over the course of 96 h. The data showed a delay in the virus degradation in the first 24 h followed by a decline, which could not be captured by the model with exponentially distributed decay time of infectious virus. Thus, we proposed a model, in which inactivation of infectious ZIKV is gamma distributed and fit the model to the temporal measurements of infectious virus remaining in the media. The model was able to reproduce the data well and yielded the decay time of infectious ZIKV to be 40 h. We studied the in vitro ZIKV infection kinetics by conducting cell infection at two distinct multiplicity of infection and measuring viral loads over time. We fit the mathematical model of in vitro viral infection with gamma distributed degradation time of infectious virus to the viral growth data and identified the timespans and rates involved within the ZIKV-host cell interplay. Our mathematical analysis combined with the data provides a well-described example of non-exponential viral decay dynamics and presents numerical characterization of in vitro infection with ZIKV.
An application of entity-relationship data modeling techniques to the automated manufacturing process (2003)

An entity-relationship (E-R) model has been developed to generically represent aspects of process information flow in a hierarchical automated manufacturing facility. The facility is expected to be networked and to consist of a global controller, local controllers, etc. and IC processing equipment, organized in a hierarchical fashion. The development of the model is presented through a case study of an automated semiconductor manufacturing facility. In developing the model, subschemas are first developed for the various component modules in the facility. The modules are then incorporated using a form of E-R model clustering and integration techniques into a schema for the entire facility. The generic structural properties of the schema are clearly evident. The development and application of E-R constructs to model time sequencing and ordering aspects of process information flow in the facility are potential areas of future research.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Integrating Technology Into Standard Weight Loss Treatment (2013)

Weconducteda2-arm,12-monthstudy(Oc-tober1,2007,throughSeptember31,2010).Seventyadults(body mass index 25 and 40 [calculated as weight inkilogramsdividedbyheightinmeterssquared])wereran-domly assigned either to standard-of-care group treat-ment alone (standard group) or to the standardand con-nective mobile technology system ( mobile group).ParticipantsattendedbiweeklyweightlossgroupsheldbytheVeteransAffairsoutpatientclinic.The mobilegroupwasprovidedpersonaldigitalassistantstoself-monitordietand physical activity; they also received biweekly coach-ing calls for 6 months. Weight was measured at baselineand at 3-, 6-, 9-, and 12-month follow-up.
Stress Dependence of Sapphire Cathodoluminescence from Optically Active Oxygen Defects as a Function of Crystallographic Orientation (2007)

The cathodoluminescence (CL) spectrum of the synthetic sapphire single crystal has been studied with respect to the different crystallographic planes of the crystal in order to describe the tensorial stress dependence of the band related to oxygen defects. Experiments provide the link between CL spectral shift and stress, which is referred to as the piezo-spectroscopic (PS) relationship. Using the biaxial stress field developed at the tip of cracks generated from the corners of a Vickers indentation, we clearly detected stress dependence for the cumulative band arising from the F+-center transition of optically active oxygen vacancies. The matrix of PS coefficients along different crystallographic axes of single-crystal sapphire could be precisely determined. The shallow nature of the electron probe may enable the characterization of surface stress fields with a spatial resolution that may not be easily available by conventional laser probes. The PS calibration results collected on oxygen-defect bands allow the direct determination of unknown surface residual stress fields stored in sapphire substrates for electronics applications.
Describing first-order spatio-temporal distortions in ultrashort pulses using normalized parameters (2007)

We develop a first-order description of spatio-temporal distortions in ultrashort pulses using normalized parameters that allow for a direct assessment of their severity, and we give intuitive pictures of pulses with different amounts of the various distortions. Also, we provide an experimental example of the use of these parameters in the case of spatial chirp monitored in real-time during the alignment of an amplified laser system.
A channel assignment and power setting scheme by fuzzy logics for OFDMA-based macro-femto systems (2012)

In this paper, we propose a fuzzy-based channel assignment and power setting (FCAP) scheme for OFDMA-based macro-femto systems to effectively mitigate the interference caused by the deployment of femto base stations (FBSs). The FCAP scheme is a distributed solution for the spectrum allocation and interference mitigation problems in the macro-femto systems. By using the fuzzy logics, it dynamically determines the total number of available subchannels for the considering FBS. According to this determination, the FBS selects its preference subchannels to avoid using the same subchannels as its neighboring FBSs. Also, the FCAP scheme sets the transmission power by using the fuzzy logics to achieve a balance between the throughput maximization and the interference mitigation. Simulation results show that, the FCAP scheme can enhance the average SINR of femto users by 8.5 % and 29.4 % compared to the optimal downlink spectrum sharing scheme and the flexible spectrum usage and power control scheme, respectively.
Sonic Hedgehog as a mediator of long‐range signaling* (2002)

The ability of Hedgehog (Hh) proteins to exert their biological effects is regulated by a series of post-translational processes. These processes include an intramolecular cleavage, covalent addition of cholesterol and/or palmitate, and conversion into a multimeric freely diffusible form. The processing of Hh proteins affects their trafficking, potency, and ability to signal over many cell diameters. Accordingly, the loss of gene products required for these processes abrogates the Hh proteins' abilities to exert their effects, which can be long range, short range, or both. We review here recent evidence demonstrating that Hh proteins are directly responsible for their long-range biological effects. Additionally, we integrate both genetic and biochemical data to delineate a model illustrating how the unusual biochemistry of Hh family members may allow them to act as morphogens, signaling over both short and long distances.
The myrosinase‐glucosinolate interaction mechanism studied using some synthetic competitive inhibitors (1996)

Using synthetic deoxy-glucotropaeolins (6d-GTL, 4d- GTL, 3d-GTL, 2d-GTL) as substrates, myrosinase activity was studied in comparison to that determined on native glucotropaeolin (GTL) isolated from ripe Lepidium sativum seeds. When the deoxy substrates were used, in addition to an overall strong reaction rate decline, a significant decrease in the reaction rate was observed in going from 6d- to 2d-GTL. This finding allows us to propose a mechanism of catalysis which appears to be similar in many respects to that established for beta-glucosidases. Finally, 2d-GTL was shown to be the first strong competitive inhibitor of myrosinase ever reported.
Mechanical Interferometry of Nanoscale Motion and Local Mechanical Properties of Living Zebrafish Embryos (2009)

We present an interferometric imaging technique that permits local measurement of mechanical properties and nanomechanical motion in small living animals. Measurements of nanomechanical properties and spatially resolved pulsations of <60 nm were recorded for the developing eye of a living zebrafish (Danio rerio) embryo, an important model organism. We also used magnetic microreflectors to conduct contact nanomechanical indentation measurements of the stiffness of the embryonic eye.
Expectation Consistent Approximate Inference: Generalizations and\n Convergence (2016)

Approximations of loopy belief propagation, including expectation propagation\nand approximate message passing, have attracted considerable attention for\nprobabilistic inference problems. This paper proposes and analyzes a\ngeneralization of Opper and Winther's expectation consistent (EC) approximate\ninference method. The proposed method, called Generalized Expectation\nConsistency (GEC), can be applied to both maximum a posteriori (MAP) and\nminimum mean squared error (MMSE) estimation. Here we characterize its fixed\npoints, convergence, and performance relative to the replica prediction of\noptimality.\n
Keratinocytes cultured from patients with Hailey-Hailey disease and Darier disease display distinct patterns of calcium regulation (2005)

The results demonstrate that the defects in SPCA1 and SERCA2 calcium ATPases result in distinct patterns of calcium metabolism. This is also supported by the different clinical features of the diseases.
VCA-Net: Visual Creativity Analysis using Deep Neural Network✱ (2022)

Electrical signals generated in the brain, known as Electroencephalographic signals (EEG) are used to measure electrical activities in the brain. EEG methods being non-invasive, affordable, and portable, are used in this work. Analysis of Visual Creativity has clinical application in monitoring the progress of patients suffering from neurodegenerative diseases. In this work, EEG is used to analyze Visual Creativity by classifying the two brain states (1) Creative and (2) Non-creative using the in-house collected data. Data is collected from the participants performing the following tasks: (1) Planning to draw, (2) Drawing, and (3) Monotonous Tasks. Drawing and Monotonous Tasks are considered for the classification in the proposed work. Two types of analysis are carried out (1) converting EEG time-series data into a sequence of topology preserving feature maps and (2) feature maps generated using Spectral Entropy. The EEG data is first pre-processed to down-sample and band-limit the signals followed by ICA to remove the artifact. The artifact-removed EEG data is decomposed into three sub-bands. The decomposed time-series data is converted to a sequence of feature maps that preserves spatial, spectral, and temporal information. Another set of feature maps is also generated using Spectral Entropy from artifact-removed EEG data. Two types of Deep Learning frameworks are proposed (1) VCA-Net video - a deep learning framework consisting of temporal convolution that extracts spatial information and preserves temporal information which is extracted by a combination of LSTM and 1D convolution and (2) VCA-Net image - a deep learning framework which extracts the spatial information using Feature Pyramid Network (FPN) and Atrous Spatial Pyramid Pooling (ASPP). Drawing and Monotonous tasks are classified with a mean accuracy of 70.87% and 65.62% using VCA-Net image and VCA-Net video respectively.
Immunosuppression in Sepsis (2011)

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Converting gem-Dimethyl Groups into Cyclopropanes via Pd-Catalyzed Sequential C−H Activation and Radical Cyclization (2006)

A novel route to the synthesis of cyclopropane derivatives is described. 1,1-Dimethyls in 2-(1,1-dimethylalkyl)dimethyloxazolines are first converted into 1,3-diiodide derivatives via Pd-catalyzed sequential C-H activation and then radically cyclized to provide 2-(1-alkylcylclopropyl)dimethyloxazolines. The use of EtOAc as a solvent is crucial for the diiodination of the functionalized substrates. [reaction: see text]
Tomographic Imaging Ultra-Thick Specimens with Nanometer Resolution (2008)

Extended abstract of a paper presented at Microscopy and Microanalysis 2008 in Albuquerque, New Mexico, USA, August 3 – August 7, 2008