gebhart/patrepeval huggingface dataset:
Autonomic Wireless Sensor Networks: A Systematic Literature Review (2014)

Autonomic computing (AC) is a promising approach to meet basic requirements in the design of wireless sensor networks (WSNs), and its principles can be applied to efficiently manage nodes operation and optimize network resources. Middleware for WSNs supports the implementation and basic operation of such networks. In this systematic literature review (SLR) we aim to provide an overview of existing WSN middleware systems that address autonomic properties. The main goal is to identify which development approaches of AC are used for designing WSN middleware system, which allow the self-management of WSN. Another goal is finding out which interactions and behavior can be automated in WSN components. We drew the following main conclusions from the SLR results: (i) the selected studies address WSN concerns according to the self-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mrow><mml:mrow><mml:mi>*</mml:mi></mml:mrow></mml:mrow></mml:math>properties of AC, namely, self-configuration, self-healing, self-optimization, and self-protection; (ii) the selected studies use different approaches for managing the dynamic behavior of middleware systems for WSN, such as policy-based reasoning, context-based reasoning, feedback control loops, mobile agents, model transformations, and code generation. Finally, we identified a lack of comprehensive system architecture designs that support the autonomy of sensor networking.
Design and Analysis of an In-Plane Resonant Nano-Electro-Mechanical Sensor for Sub-Attogram-Level Molecular Mass-Detection (2009)

This paper presents the In-Plane Resonant NEM (IP R-NEM) sensor based on the mass-detection principle. The proposed sensor features a mass-detection limit of sub atto gram and the sensitivity of the order of zepto gram/Hz, more than eight orders smaller than that of recent QCM-based sensors. The sensor is designed and analyzed using the three-dimensional FEM simulation. Self-assembled linker molecules and adsorbed target molecules on the beam surface are modelled by adding an extra surface coating layer. We study two different surface detection schemes, top-and-bottom and all-around surface detection. The IP R-NEM sensor is integrated with a MOSFET for electrical detection, and the transient response is studied on the system-level using a hybrid electro-mechanical circuit simulation.
Heterogeneously integrated microdisk lasers for optical interconnects and optical logic (2011)

Optical interconnect and optical packet switching systems could take advantage of small footprint, low power lasers and optical logic elements. Microdisk lasers, with a diameter below 10&#956;m and fabricated in InP membranes with a high index contrast, offer this possibility at the telecom wavelengths. The lasers are fabricated using heterogeneous integration of InP membranes on silicon-on-insulator (SOI) passive waveguide circuits, which allows to combine the active elements with compact, high-index contrast passive elements. The lasing mode in such microdisk lasers is a whispering gallery mode, which can be either in the clockwise (CW) or counter clockwise direction (CCW) or in both. The coupling to the SOI wire waveguides is through evanescent coupling. Predefined, unidirectional operation can be achieved by terminating the SOI wires at one end with Bragg gratings. For all-optical flip-flops, the laser operation must be switchable between CW and CCW, using short optical pulses. Unidirectional operation in either direction is only possible if the coupling between CW and CCW direction is very small, requiring small sidewall surface roughness, and if the gain suppression is sufficiently large, requiring large internal power levels. All-optical flip-flops based on microdisk lasers with diameter of 7.5&mu;m have been demonstrated. They operate with a CW power consumption of a few mW and switch in 60ps with switching energies as low as 1.8fJ. Operation as all-optical gate has also been demonstrated. The surface roughness is limited through optimized etching of the disks and the large internal power is obtained through good heat sink.
Segmentation gene product Fushi tarazu is an LXXLL motif-dependent coactivator for orphan receptor FTZ-F1 (2001)

Orphan receptors for whom cognate ligands have not yet been identified form a large subclass within the nuclear receptor superfamily. To address one aspect of how they might regulate transcription, we analyzed the mode of interaction between the Drosophila orphan receptor FTZ-F1 (NR5A3) and a segmentation gene product Fushi tarazu (FTZ). Strong interaction between these two factors was detected by use of the mammalian one- and two-hybrid interaction assays without addition of ligand. This interaction required the AF-2 core and putative ligand-binding domain of FTZ-F1 and the LXXLL motif of FTZ. The requirement of these elements was further confirmed by examination of their target gene expression in Drosophila embryos and observation of a cuticle phenotype in transgenic fly lines that express mutated factors. In Drosophila cultured cells, FTZ is required for FTZ-F1 activation of a FTZ-F1 reporter gene. These results reveal a resemblance in the mode of interaction between FTZ-F1 and FTZ and that of nuclear receptor-coactivator and indicate that direct interaction is required for regulation of gene expression by FTZ-F1. Thus, we propose that FTZ may represent a category of LXXLL motif-dependent coactivators for nuclear receptors.
Combining regression and classification methods for improving automatic speaker age recognition (2010)

We present a novel approach to automatic speaker age classification, which combines regression and classification to achieve competitive classification accuracy on telephone speech. Support vector machine regression is used to generate finer age estimates, which are combined with the posterior probabilities of well-trained discriminative gender classifiers to predict both the age and gender of a speaker. We show that this combination performs better than direct 7-class classifiers. The regressors and classifiers are trained using longterm features such as pitch and formants, as well as short-term (frame-based) features derived from MAP adaptation of GMMs that were trained on MFCCs.
On Projection Matrices and their Applications in Computer Vision. (2001)

Projection matrices from projective spaces # # to # # have long been used in multiple-view geometry to model the perspective projection created by the pin-hole camera. In this work we introduce higher-dimensional mappings # # ## # # , # ### ## ## # for the representation of various applications in which the world we view is no longer rigid. We also describe the multi-view constraints from these new projection matrices (where ###) and methods for extracting the (non-rigid) structure and motion for each application. 1
Chemical vapor detection using a passive infrared bioinspired sensor (2022)

Standoff detection of chemicals remains a crucial need for a variety of applications of importance for defense, homeland security, environmental, and industrial applications. The goal of standoff chemical sensing is to enable the identification and classification of an unknown hazardous or toxic chemical, without any operator or instrument having to come in direct contact with the chemical itself. Currently, standoff detection of chemical vapors is carried out using optical sensing techniques. Passive infrared (IR) sensors have identified chemical vapor clouds at ranges exceeding one kilometer by detecting, spectrally resolving, and analyzing scene radiance. Currently available passive IR sensors have substantial size, weight, power, and cost (SWaP-C) limitations, which reduce the number of sensors capable of being deployed in a given area, or precludes their use altogether in certain circumstances. To address these limitations, we are developing a unique passive low SWaP-C IR sensor capable of detecting chemical vapors when viewed against a cold-sky or terrestrial background. This sensor, inspired by human color vision, will use only the response through three broadband infrared optical filters to discriminate between target chemicals and background interferents. The key technology of the PBS is a commercially available pyroelectric quadrant chip sensor which contains four channels with unique bandpass IR filters installed. We demonstrate results collected using a variable temperature blackbody in the laboratory, which represents passive IR sensing against various background conditions. These results demonstrate the first step in the development of a passive bioinspired IR sensor which will use only low-cost commercially available components, and be capable of rapidly providing actionable detection of chemical vapor clouds
Tuberculin Skin Testing Compared with T-Cell Responses to Mycobacterium tuberculosis -Specific and Nonspecific Antigens for Detection of Latent Infection in Persons with Recent Tuberculosis Contact (2001)

The tuberculin skin test (TST) is used for the identification of latent tuberculosis (TB) infection (LTBI) but lacks specificity in Mycobacterium bovis BCG-vaccinated individuals, who constitute an increasing proportion of TB patients and their contacts from regions where TB is endemic. In previous studies, T-cell responses to ESAT-6 and CFP-10, M. tuberculosis-specific antigens that are absent from BCG, were sensitive and specific for detection of active TB. We studied 44 close contacts of a patient with smear-positive pulmonary TB and compared the standard screening procedure for LTBI by TST or chest radiographs with T-cell responses to M. tuberculosis-specific and nonspecific antigens. Peripheral blood mononuclear cells were cocultured with ESAT-6, CFP-10, TB10.4 (each as recombinant antigen and as a mixture of overlapping synthetic peptides), M. tuberculosis sonicate, purified protein derivative (PPD), and short-term culture filtrate, using gamma interferon production as the response measure. LTBI screening was by TST in 36 participants and by chest radiographs in 8 persons. Nineteen contacts were categorized as TST negative, 12 were categorized as TST positive, and 5 had indeterminate TST results. Recombinant antigens and peptide mixtures gave similar results. Responses to TB10.4 were neither sensitive nor specific for LTBI. T-cell responses to ESAT-6 and CFP-10 were less sensitive for detection of LTBI than those to PPD (67 versus 100%) but considerably more specific (100 versus 72%). The specificity of the TST or in vitro responses to PPD will be even less when the proportion of BCG-vaccinated persons among TB contacts evaluated for LTBI increases.
Melting-Induced Evolution of Morphology, Entanglement Density, and Ultradrawability of Solution-Crystallized Ultrahigh-Molecular-Weight Polyethylene (2021)

The melting-induced change in the density of physical network junctions, which are formed by chain entanglements and network junctions due to anchoring of chain segments to crystals, is studied by 1H NMR T2 relaxometry for solution- and melt-crystallized ultrahigh-molecular-weight polyethylene (UHMWPE), sc-UH, and mc-UH, respectively. The NMR results are complemented by real-time synchrotron wide- and small-angle X-ray scattering (WAXS and SAXS) analyses to extract the sizes of the crystalline lamellae and intercrystalline domains. Below the melting temperature, the network of physical junctions is denser in the amorphous phase of mc-UH than the one in sc-UH owing to a lower entanglement density and a smaller number of physical junctions from polymer crystals in sc-UH. However, the difference in the total density of physical junctions between mc-UH and sc-UH films decreases with decreasing crystallinity during melting. At the end of the melting trajectory, at vanishing crystallinity, the volume-average entanglement density, as characterized by the NMR method, is approximately the same in sc- and mc-UH. This indicates that the entanglement density in sc-UH films increases during melting owing to the fast buildup of local chain entanglements. These entanglements are formed by segments of the same chain, neighboring chains, or both due to a displacement of chain fragments upon lamellar thickening and due to the so-called “chain explosion” that occurs locally in the amorphous domains. The increase in the entanglement density in sc-UH is additionally confirmed by the solid-state drawability of sc-UH films that were annealed in the melting region but below the end of melting. The maximum draw ratio decreases and the drawing stress increases with the increasing annealing temperature.
The CNN-Corpus in Spanish (2019)

This paper details the development and features of the CNN-corpus in Spanish, possibly the largest test corpus for single document extractive text summarization in the Spanish language. Its current version encompasses 1,117 well-written texts in Spanish, each of them has an abstractive and an extractive summary. The development methodology adopted allows good-quality qualitative and quantitative assessments of summarization strategies for tools developed in the Spanish language.
Bayesian Inference of Atomic Diffusivity in a Binary Ni/Al System Based on Molecular Dynamics (2011)

This work focuses on characterizing the integral features of atomic diffusion in Ni/Al nanolaminates based on molecular dynamics (MD) computations. Attention is focused on the simplified problem of extracting the diffusivity, D, in an isothermal system at high temperature. To this end, a mixing measure theory is developed that relies on analyzing the moments of the cumulative distribution functions (CDFs) of the constituents. The mixing measures obtained from replica simulations are exploited in a Bayesian inference framework, based on contrasting these measures with corresponding moments of a dimensionless concentration evolving according to a Fickian process. The noise inherent in the MD simulations is described as a Gaussian process, and this hypothesis is verified both a priori and using a posterior predictive check. Computed values of D for an initially unmixed system rapidly heated to 1500 K are found to be consistent with experimental correlation for diffusion of Ni into molten Al. On the contrary, large discrepancies with experimental predictions are observed when D is estimated based on large-time mean-square displacement (MSD) analysis, and when it is evaluated using the Arrhenius correlation calibrated against experimental measurements of self-propagating front velocities. Implications are finally drawn regarding extension of the present work and potential refinement of continuum modeling approaches.
Ensemble Modeling for Aromatic Production in Escherichia coli (2009)

Ensemble Modeling (EM) is a recently developed method for metabolic modeling, particularly for utilizing the effect of enzyme tuning data on the production of a specific compound to refine the model. This approach is used here to investigate the production of aromatic products in Escherichia coli. Instead of using dynamic metabolite data to fit a model, the EM approach uses phenotypic data (effects of enzyme overexpression or knockouts on the steady state production rate) to screen possible models. These data are routinely generated during strain design. An ensemble of models is constructed that all reach the same steady state and are based on the same mechanistic framework at the elementary reaction level. The behavior of the models spans the kinetics allowable by thermodynamics. Then by using existing data from the literature for the overexpression of genes coding for transketolase (Tkt), transaldolase (Tal), and phosphoenolpyruvate synthase (Pps) to screen the ensemble, we arrive at a set of models that properly describes the known enzyme overexpression phenotypes. This subset of models becomes more predictive as additional data are used to refine the models. The final ensemble of models demonstrates the characteristic of the cell that Tkt is the first rate controlling step, and correctly predicts that only after Tkt is overexpressed does an increase in Pps increase the production rate of aromatics. This work demonstrates that EM is able to capture the result of enzyme overexpression on aromatic producing bacteria by successfully utilizing routinely generated enzyme tuning data to guide model learning.
Genetic literacy series: clinical application of pharmacogenetics for adverse reactions to antiepileptic drugs (2019)

Adverse drug reactions are a leading cause of treatment failure with antiepileptic drugs. Adverse drug reactions are also a major source of morbidity and mortality, and a substantial burden on the use and costs of health care. Recent pharmacogenetic studies have shown that some adverse drug reactions are associated with genetic variants, which has changed how we select antiepileptic drugs for individual patients. This article, beginning with a case of an adverse drug reaction induced by carbamazepine, will answer four key questions about pharmacogenetics of adverse drug reactions: (1) What types of adverse drug reactions can be caused by antiepileptic drugs? (2) What is pharmacogenetics? (3) How does pharmacogenetics play a role in the adverse drug reactions of antiepileptic drugs? and (4) How do we apply pharmacogenetic testing in clinical practice? Our goal is to increase awareness of the contributions of genetic variation to adverse drug reactions of antiepileptic drugs.
Path Finding under Uncertainty through Probabilistic Inference (2015)

We introduce a new approach to solving path-finding problems under uncertainty by representing them as probabilistic models and applying domain-independent inference algorithms to the models. This approach separates problem representation from the inference algorithm and provides a framework for efficient learning of path-finding policies. We evaluate the new approach on the Canadian Traveler Problem, which we formulate as a probabilistic model, and show how probabilistic inference allows high performance stochastic policies to be obtained for this problem.
The Effect of Magnetic Field on Magnetotactic Bacteria Behaviors (2008)

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How to make a correct multiprocess program execute correctly on a multiprocessor (1997)

A multiprocess program executing on a modern multiprocessor must issue explicit commands to synchronize memory accesses. A method is proposed for deriving the necessary commands from a correctness proof of the underlying algorithm in a formalism based on temporal relations among operation executions.
Characterisation of metal mirrors on GaAs (1996)

The authors describe a Fabry-Perot technique for determining the reflectivity and the phase of the interface between a semiconductor and a multilayer metal structure as it will be realised in actual device fabrication. The reflection coefficients of GaAs to Ti/Au, Pd/Au, Au and Ag interfaces are measured at 1.55 µm.
Histochemical evidence for lipid A (endotoxin) in eukaryote chloroplasts (2006)

Lipopolysaccharide (LPS) (a.k.a., endotoxin) is an essential component of the outer leaflet of the outer membrane of gram-negative bacteria and is a potent activator of the innate immune system of animals. Lipid A, the glycolipid core of LPS, is the agent responsible for disease and death from gram-negative sepsis, an important cause of human mortality and morbidity. Although it is generally accepted that lipid A is restricted to the prokaryotes, recent efforts to purify molecules from green algae with structural features unique to lipid A have met with success. Furthermore, the vascular plant Arabidopsis thaliana has been found to contain genes that encode all of the enzymes of the biosynthetic pathway for lipid A. It is not known whether vascular plants synthesize lipid A or where lipid A might be located in the tissues. For the present study, we used affinity reagents for lipid A to probe green alga and tissues of the garden pea for a light microscopic localization of lipid A in these eukaryote cells. We find staining for lipid A in free-living and endosymbiotic green algae and in the chloroplasts of vascular plants, indicating that this molecule is not restricted to prokaryotes, but is found also in select eukaryotes.
The soluble epoxide hydrolase gene harbors sequence variation associated with susceptibility to and protection from incident ischemic stroke (2005)

Stroke is the leading cause of severe disability and the third leading cause of death, accounting for one of every 15 deaths in the USA. We investigated the association of polymorphisms in the soluble epoxide hydrolase gene (EPHX2) with incident ischemic stroke in African-Americans and Whites. Twelve single nucleotide polymorphisms (SNPs) spanning EPHX2 were genotyped in a case-cohort sample of 1336 participants from the Atherosclerosis Risk in Communities (ARIC) study. In each racial group, Cox proportional hazard models were constructed to assess the relationship between incident ischemic stroke and EPHX2 polymorphisms. A score test method was used to investigate the association of common haplotypes of the gene with risk of ischemic stroke. In African-Americans, two common EPHX2 haplotypes with significant and opposing relationships to ischemic stroke risk were identified. In Whites, two common haplotypes showed suggestive indication of an association with ischemic stroke risk but, as in African-Americans, these relationships were in opposite direction. These findings suggest that multiple variants exist within or near the EPHX2 gene, with greatly contrasting relationships to ischemic stroke incidence; some associated with a higher incidence and others with a lower incidence.
Cover Picture: The Chemistry and Biology of Soluble Guanylate Cyclase Stimulators and Activators / Nicotinic Acetylcholine Receptor Agonists: A Milestone for Modern Crop Protection / Polyurethanes: Versatile Materials and Sustainable Problem Solvers for Today’s Challenges (Angew. Chem. Int. Ed. 36/2013) (2013)

Excellence in research and innovation …︁ …︁ in the fields of healthcare, crop science, and material science formed the basis of the 150 years of sustained growth at Bayer and will guarantee its future success. Recent examples such as Riociguat, a soluble guanylate cyclase (sGC) stimulator for the treatment of pulmonary hypertension, novel selective insecticidally active nicotinic acetyl choline receptor (nAChR) ligands as current and future effective agents for invertebrate pest control, as well as innovative, diverse, and versatile polyurethane-based materials, and their broad and valuable applications demonstrate Bayer′s high innovation potential. The three Reviews covering these topics by M. Follmann et al. on page 9442 ff., P. Jeschke et al. on page 9464 ff., and H.-W. Engels et al. on page 9422 ff., as well as four Minireviews on carbon nanotubes, herbicides, sulfoximine pharmacophores, and electroactive polymers, written by Bayer researchers, can be found in this issue. Many other contributions in this “150 years Bayer” issue are an indication of the worldwide collaboration between Bayer researchers and academic laboratories.