gebhart/patrepeval huggingface dataset:
A metagenomic analysis of soil bacteria extends the diversity of quorum‐quenching lactonases (2008)

A metagenomic library of 10,121 clones, generated from bacteria inhabiting a pasture soil from France, was screened for the presence of fosmids conferring either N-acylhomoserine lactone (NAHL) synthesis or NAHL degradation ability upon their Escherichia coli host. No clone producing NAHLs was identified whereas one, containing a 31 972 bp insert in fosmid p2H8, allowed NAHL degradation. This led to the cloning and identification of a gene, qlcA, encoding an NAHL-lactonase activity, as judged by lactone-ring closure and HPLC/MS analyses of NAHL degradation products. The qlcA gene efficiently quenched quorum-sensing regulated pathogenic functions when expressed in Pectobacterium carotovorum. The QlcA peptide belongs to the family of zinc-dependent metallohydrolases and appears to be distantly related to other NAHL-lactonases discovered in Agrobacterium, Bacillus, Photorhabdus and Rhizobium. In-silico analysis of the metagenomic insert revealed the occurrence of 20 orf, with a constant GC% and codon usage, suggesting a unique bacterial origin. Nine out of these 20 orf were homologous to genes encoding biosynthesis of arginine; they were clustered with an unusual succession argFJADBCRGH. The fosmid p2H8 is able to complement the argA, argB and argC mutants in E. coli. Phylogenetic analysis showed that 9 orf out of 20 were related to sequences from members of the Acidobacteria, supporting the hypothesis that the analysed insert might be originated from an organism related to this phylum.
An improved "charge pump" electronic ballast with low THD and low crest factor (2002)

The "charge pump" electronic ballast circuit, which employs a charging capacitor and a high frequency AC source to implement power factor correction (PFC), has become an attractive topology for ballasting fluorescent lamps because it eliminates the use of a bulky boost inductor. However, this circuit has the problems of high total harmonic distortion (THD) of the input current, and high crest factor (CF) of the lamp current. This paper analyzes the origin of the problems and proposes a novel solution. With the addition of two small clamping diodes, very good input current (PF>0.99, THD <5%) and lamp current (CF<1.6) can be obtained with open loop control. Experimental results are provided for verification.
High-Level Synthesis Blue Book (2010)

Are you an RTL or system designer that is currently using, moving, or planning to move to an HLS design environment?Finally, a comprehensive guide for designing hardware using C++ is here. Michael Fingeroffs High-Level Synthesis Blue Book presents the most effective C++ synthesis coding style for achieving high quality RTL. Master a totally new design methodology for coding increasingly complex designs! This book provides a step-by-step approach to using C++ as a hardware design language, including an introduction to the basics of HLS using concepts familiar to RTL designers. Each chapter provides easy-to-understand C++ examples, along with hardware and timing diagrams where appropriate. The book progresses from simple concepts such as sequential logic design to more complicated topics such as memory architecture and hierarchical sub-system design. Later chapters bring together many of the earlier HLS design concepts through their application in simplified design examples. These examples illustrate the fundamental principles behind C++ hardware design, which will translate to much larger designs. Although this book focuses primarily on C and C++ to present the basics of C++ synthesis, all of the concepts are equally applicable to SystemC when describing the core algorithmic part of a design.On completion of this book, readers should be well on their way to becoming experts in high-level synthesis.
Complex modes expansion with vector projection using power flow to simulate Lamb waves scattering from horizontal cracks and disbonds (2016)

This paper presents an inexpensive but accurate analytical method to calculate the scattering of straight-crested Lamb waves from cracks parallel to the plate surface. The same method is applicable for the disbond problem. In this method, the scatter field is expanded in terms of complex Lamb wave modes with unknown amplitudes. These unknown amplitudes are obtained from the boundary conditions using vector projection utilizing the power expression. The process works by projecting the stress conditions onto the displacement eigen-spaces of complex Lamb wave modes and vice versa. The authors call this technique "complex modes expansion with vector projection" (CMEP). The CMEP approach is versatile and can be readily applied to corrosion, cracks, or disbonds. In this paper, the CMEP method is applied to a horizontal crack in a plate. For verification of the results the authors compared them with the results obtained by using the finite element method (FEM) and literature. The FEM analysis was conducted in the frequency domain with non-reflecting boundaries. It was found that CMEP results correspond very well with FEM results over a wide frequency-thickness range up to 1.5 MHz mm with CMEP being orders of magnitude faster than FEM.
Iron-Catalyzed Hydrogenation of Amides to Alcohols and Amines (2016)

This article describes the iron-catalyzed hydrogenation of unactivated amides. Under the optimal conditions, a PNP-ligated Fe catalyst affords 25–300 turnovers of products derived from C–N bond cleavage. This reaction displays a broad substrate scope, including a variety of 2° and 3° amide substrates. The reaction progress of N,N-dimethylformamide hydrogenation has been monitored in situ using Raman spectroscopy. This technique enables direct comparison of the relative activity of the Fe-PNP catalyst to that of its Ru analogue. Under otherwise identical conditions, the Fe and Ru catalysts exhibit rates within a factor of 2.
A genomics approach to the early stages of triterpene saponin biosynthesis in <i>Medicago truncatula</i> (2002)

The saponins of the model legume Medicago truncatula are glycosides of at least five different triterpene aglycones: soyasapogenol B, soyasapogenol E, medicagenic acid, hederagenin and bayogenin. These aglycones are most likely derived from beta-amyrin, a product of the cyclization of 2,3-oxidosqualene. Mining M. truncatula EST data sets led to the identification of sequences putatively encoding three early enzymes of triterpene aglycone formation: squalene synthase (SS), squalene epoxidase (SE), and beta-amyrin synthase (beta-AS). SS was functionally characterized by expression in Escherichia coli, two forms of SE by complementation of the yeast erg1 mutant, and beta-AS by expression in yeast. Beta-amyrin was the sole product of the cyclization of squalene epoxide by the recombinant M. truncatulabeta-AS, as judged by GC-MS and NMR. Transcripts encoding beta-AS, SS and one form of SE were strongly and co-ordinately induced, associated with accumulation of triterpenes, upon exposure of M. truncatula cell suspension cultures to methyl jasmonate. Sterol composition remained unaffected by jasmonate treatment. Molecular verification of induction of the triterpene pathway in a cell culture system provides a new tool for saponin pathway gene discovery by DNA array-based approaches.
A bipolar, two component laser-Doppler velocimeter (1975)

A fringe mode laser-Doppler velocimeter is described that instantaneously measures two orthogonal velocity components that have fluctuating signs. The optical system utilizes an equiangular configuration of three intersecting beams which allows measurements of the normal velocity component to be taken in close proximity to a wall. Acousto-optic frequency shifting of two beams is used to eliminate cross channel interference and to provide detection of the velocity polarity. The instrument is applicable to flows having velocities in the range of +or-1 mm s-1 to +or-10 m s-1.
Clinical Correlates and Prognostic Significance of Six-minute Walk Test in Patients with Primary Pulmonary Hypertension: Comparison with Cardiopulmonary Exercise Testing (2000)

The six-minute walk test is a submaximal exercise test that can be performed even by a patient with heart failure not tolerating maximal exercise testing. To elucidate the clinical significance and prognostic value of the six-minute walk test in patients with primary pulmonary hypertension (PPH), we sought (1) to assess the relation between distance walked during the six-minute walk test and exercise capacity determined by maximal cardiopulmonary exercise testing, and (2) to investigate the prognostic value of the six-minute walk test in comparison with other noninvasive parameters. The six-minute walk test was performed in 43 patients with PPH, together with echocardiography, right heart catheterization, and measurement of plasma epinephrine and norepinephrine. Symptom-limited cardiopulmonary exercise testing was performed in a subsample of patients (n = 27). Distance walked in 6 min was significantly shorter in patients with PPH than in age- and sex-matched healthy subjects (297 +/- 188 versus 655 +/- 91 m, p < 0. 001). The distance significantly decreased in proportion to the severity of New York Heart Association functional class. The distance walked correlated modestly with baseline cardiac output (r = 0.48, p < 0.05) and total pulmonary resistance (r = -0.49, p < 0. 05), but not significantly with mean pulmonary arterial pressure. In contrast, the distance walked correlated strongly with peak V O(2) (r = 0.70, p < 0.001), oxygen pulse (r = 0.57, p < 0.01), and V E-VCO(2) slope (r = -0.66, p < 0.001) determined by cardiopulmonary exercise testing. During a mean follow-up period of 21 +/- 16 mo, 12 patients died of cardiopulmonary causes. Among noninvasive parameters including clinical, echocardiographic, and neurohumoral parameters, only the distance walked in 6 min was independently related to mortality in PPH by multivariate analysis. Patients walking < 332 m had a significantly lower survival rate than those walking farther, assessed by Kaplan-Meier survival curves (log-rank test, p < 0.01). These results suggest that the six-minute walk test, a submaximal exercise test, reflects exercise capacity determined by maximal cardiopulmonary exercise testing in patients with PPH, and it is the distance walked in 6 min that has a strong, independent association with mortality.
Acquired ADAMTS-13 deficiency in pediatric patients with severe sepsis (2007)

We studied the state of ultra-large von Willebrand factor (ULVWF) proteolysis in 21 pediatric patients with severe sepsis and found that the overall group of patients had moderately reduced ADAMTS-13 activity, but 31% had severe enzymatic deficiency. The severe deficiency correlated with greater adhesion activity of von Willebrand factor, severity of thrombocytopenia and plasma levels of interleukin-6. It also correlated clinically with severity of illness and organ dysfunction. These results suggest that ULVWF proteolysis is insufficient in septic patients and severely deficient in a subgroup of patients. The deficiency may contribute to the development of thrombocytopenia and ischemic organ failure associated with sepsis.
Section 156 of the Insolvency Act : a third party's forgotten remedy? : practice note (2015)

The principle of subrogation is well established in South African law and allows an insurance company to litigate under the name of the insured for the recovery of damages incurred. Any judgment obtained for, or against, the insured is thereafter settled by the insurance company, subject to the terms and conditions of the agreement of insurance entered into between the parties.
Optical properties of metallo-dielectric microspheres in opal structures (2003)

We report the fabrication of opal structure using metallo-dielectric silica microspheres. Mono-dispersed silica microspheres were coated with silver using an electrode-less wet-plating technique. Thin slabs of opal were obtained by assembling the silver-coated microspheres between two glass plates using a forced-packing method. The optical properties of the resulting opal structure were studied in the infrared range. Good agreement is obtained with the predictions of a multiple scattering approach, provided that the silver layer is modelled as a silver composite.
Unified nomenclature for chromatography (1993)

Abstract The background of the new Unified Nomenclature for Chromatography just accepted by the International Union of Pure and Applied Chemistry (IUPAC) is explained and selected highlights of the new rules are elaborated.
Learning From Demonstration in the Wild (2019)

Learning from demonstration (LfD) is useful in settings where hand-coding behaviour or a reward function is impractical. It has succeeded in a wide range of problems but typically relies on manually generated demonstrations or specially deployed sensors and has not generally been able to leverage the copious demonstrations available in the wild: those that capture behaviours that were occurring anyway using sensors that were already deployed for another purpose, e.g., traffic camera footage capturing demonstrations of natural behaviour of vehicles, cyclists, and pedestrians. We propose video to behaviour (ViBe), a new approach to learn models of behaviour from unlabelled raw video data of a traffic scene collected from a single, monocular, initially uncalibrated camera with ordinary resolution. Our approach calibrates the camera, detects relevant objects, tracks them through time, and uses the resulting trajectories to perform LfD, yielding models of naturalistic behaviour. We apply ViBe to raw videos of a traffic intersection and show that it can learn purely from videos, without additional expert knowledge.
Improving Strategies in the Development of Protein‐Downregulation‐Based Antiandrogens (2021)

The androgen receptor (AR) plays a crucial role in the occurrence and development of prostate cancer (PCa), and its signaling pathway remains active in castration-resistant prostate cancer (CRPC) patients. The resistance against antiandrogen drugs in current clinical use is a major challenge for the treatment of PCa, and thus the development of new generations of antiandrogens is under high demand. Recently, strategies for downregulating the AR have attracted significant attention, given its potential in the discovery and development of new antiandrogens, including G-quadruplex stabilizers, ROR-γ inhibitors, AR-targeting proteolysis targeting chimeras (PROTACs), and other selective AR degraders (SARDs), which are able to overcome current resistance mechanisms such as acquired AR mutations, the expression of AR variable splices, or overexpression of AR. This review summarizes the various strategies for downregulating the AR protein, at either the mRNA or protein level, thus providing new ideas for the development of promising antiandrogen drugs.
Scaling cloud-native Apache Spark on Kubernetes for workloads in external storages (2018)

CERN Scalable Analytics Section currently offers shared YARN clusters to its users as monitoring, security and experiment operations. YARN clusters with data in HDFS are difficult to provision, complex to manage and resize. This imposes new data and operational challenges to satisfy future physics data processing requirements. As of 2018, there were over 250 PB of physics data stored in CERN’s mass storage called EOS. Hadoop-XRootD Connector allows to read over network data stored in CERN EOS. CERN’s on-premise private cloud based on OpenStack allows to provision on-demand compute resources. Emergence of technologies as Containers-as-a-Service in Openstack Magnum and support for Kubernetes as native resource scheduler for Apache Spark, give opportunity to increase workflow reproducability on different compute infrastructures with use of containers, reduce operational effort of maintaining computing cluster and increase resource utilization via cloud elastic resource provisioning. This trades-off the operational features with datalocality known from traditional systems as Spark/YARN with data in HDFS.In the proposed architecture of cloud-managed Spark/Kubernetes with data stored in external storage systems as EOS, Ceph S3 or Kafka, physicists and other CERN communities can on-demand spawn and resize Spark/Kubernetes cluster, having fine-grained control of Spark Applications. This work focuses on Kubernetes CRD Operator for idiomatically defining and running Apache Spark applications on Kubernetes, with automated scheduling and on-failure resubmission of long-running applications. Spark Operator was introduced with design principle to allow Spark on Kubernetes to be easy to deploy, scale and maintain with similar usability of Spark/YARN.The analysis of concerns related to non-cluster local persistent storage and memory handling has been performed. The architecture scalability has been evaluated on the use case of sustained workload as physics data reduction, with files in ROOT format being stored in CERN mass-storage called EOS. The series of microbenchmarks has been performed to evaluate the architecture properties compared to state-of-the-art Spark/YARN cluster at CERN. Finally, Spark on Kubernetes workload use-cases have been classified, and possible bottlenecks and requirements identified.
FUSED QUINOLINE HETEROCYCLES. II. FIRST SYNTHESIS OF 1,2,3,4,5,6-HEXAAZAACEANTHRYLENES AND 5,7,8,10a,11-PENTAAZABENZO[a]-FLUORENES (2001)

The new tetracyclic ring systems 5-alkyl-1,5-dihydro-1,2,3,4,5,6-hexaazaaceanthrylenes 5a–d were synthesized by diazotization of 4-alkylamino-3-amino-1H-pyrazolo[4,3-c]quinolines 4a–d. The 4-arylamino-3-diazo-1H-pyrazolo-[4,3-c]- quinolines 6e–h, which were prepared by diazotisation of the corresponding amines 4e–h, readily formed the novel tetracyclic ring system ethyl 6-arylamino-10-methyl-5,7,8,10a,11-pentaazabenzo[a]fluorene-9-carboxylates 8e–h, when treated with ethyl acetoacetate.
Galactose-induced retinal microangiopathy in rats. (1995)

Two years of galactosemia in rats seems to reproduce only a portion of the lesions characteristic of diabetic retinopathy in patients or dogs. Nevertheless, lesions characteristic of at least the early stages of retinopathy clearly do develop in this galactosemic rat model, and are not restrained by inhibition of retinal polyol accumulation by 62%.
Robust detection and classification of longitudinal changes in color retinal fundus images for monitoring diabetic retinopathy (2006)

A fully automated approach is presented for robust detection and classification of changes in longitudinal time-series of color retinal fundus images of diabetic retinopathy. The method is robust to: 1) spatial variations in illumination resulting from instrument limitations and changes both within, and between patient visits; 2) imaging artifacts such as dust particles; 3) outliers in the training data; 4) segmentation and alignment errors. Robustness to illumination variation is achieved by a novel iterative algorithm to estimate the reflectance of the retina exploiting automatically extracted segmentations of the retinal vasculature, optic disk, fovea, and pathologies. Robustness to dust artifacts is achieved by exploiting their spectral characteristics, enabling application to film-based, as well as digital imaging systems. False changes from alignment errors are minimized by subpixel accuracy registration using a 12-parameter transformation that accounts for unknown retinal curvature and camera parameters. Bayesian detection and classification algorithms are used to generate a color-coded output that is readily inspected. A multiobserver validation on 43 image pairs from 22 eyes involving nonproliferative and proliferative diabetic retinopathies, showed a 97% change detection rate, a 3% miss rate, and a 10% false alarm rate. The performance in correctly classifying the changes was 99.3%. A self-consistency metric, and an error factor were developed to measure performance over more than two periods. The average self consistency was 94% and the error factor was 0.06%. Although this study focuses on diabetic changes, the proposed techniques have broader applicability in ophthalmology.
The design of an IEEE standard math accelerator unit (1985)

The design of the WE32106 Math Accelerator Unit, which provides the WE32100 microprocessor with IEEE standard (Draft 10) floating-point capabilities, is described. The chip implements a host of floating-point operations in single, double, and double-extended precision, as well as the complete set of IEEE standard requirements for fault and exception handling. The chip provides a high-speed co-processor interface to the WE32100 microprocessor, as well as a general-purpose memory-mapped peripheral-mode interface to other microprocessors. The chip is implemented in 1.5 /spl mu/m twin-tub CMOS III technology.
An introduction to access security in UMTS (2004)

The first generation of cellular mobile communications systems contained few if any security measures to protect the system operator and users. The second generation generally did a lot better, and contained entity authentication and confidentiality protection. Although this was a major improvement, security protection in the second generation left a lot to be desired. With the advent of 3G mobile systems a serious effort has been made to create a consistent security architecture based on the threats and risks a 3G system faces.
A Kernel Theory of Modern Data Augmentation (2018)

Data augmentation, a technique in which a training set is expanded with class-preserving transformations, is ubiquitous in modern machine learning pipelines. In this paper, we seek to establish a theoretical framework for understanding data augmentation. We approach this from two directions: First, we provide a general model of augmentation as a Markov process, and show that kernels appear naturally with respect to this model, even when we do not employ kernel classification. Next, we analyze more directly the effect of augmentation on kernel classifiers, showing that data augmentation can be approximated by first-order feature averaging and second-order variance regularization components. These frameworks both serve to illustrate the ways in which data augmentation affects the downstream learning model, and the resulting analyses provide novel connections between prior work in invariant kernels, tangent propagation, and robust optimization. Finally, we provide several proof-of-concept applications showing that our theory can be useful for accelerating machine learning workflows, such as reducing the amount of computation needed to train using augmented data, and predicting the utility of a transformation prior to training.
Cytokine-Dependent Blimp-1 Expression in Activated T Cells Inhibits IL-2 Production (2007)

After Ag activation of naive T cells in vitro, extensive growth and differentiation into effector cells depend upon IL-2. DNA microarray analysis was used to identify IL-2-dependent molecules regulating this process. In this study, we show that the transcriptional repressor B lymphocyte-induced maturation protein 1 (Blimp-1) is expressed by a cytokine-dependent pathway in activated T lymphocytes. IL-2 production by activated CD4(+) and CD8(+) T cells inversely correlated with Blimp-1 levels as higher IL-2 production was associated with lower Blimp-1 expression. Furthermore, ectopic expression of Blimp-1 by activated T cells inhibited IL-2 production but enhanced granzyme B and CD25 expression. Collectively, these findings indicate that there is a negative feedback regulatory loop in activated T cells such that IL-2 inhibits its own production through induction of Blimp-1 while promoting an effector cell phenotype.