gebhart/patrepeval huggingface dataset:
Phylogenetic Diversity of the Enteric Pathogen Salmonella enterica subsp. enterica Inferred from Genome-Wide Reference-Free SNP Characters (2013)

The enteric pathogen Salmonella enterica is one of the leading causes of foodborne illness in the world. The species is extremely diverse, containing more than 2,500 named serovars that are designated for their unique antigen characters and pathogenicity profiles-some are known to be virulent pathogens, while others are not. Questions regarding the evolution of pathogenicity, significance of antigen characters, diversity of clustered regularly interspaced short palindromic repeat (CRISPR) loci, among others, will remain elusive until a strong evolutionary framework is established. We present the first large-scale S. enterica subsp. enterica phylogeny inferred from a new reference-free k-mer approach of gathering single nucleotide polymorphisms (SNPs) from whole genomes. The phylogeny of 156 isolates representing 78 serovars (102 were newly sequenced) reveals two major lineages, each with many strongly supported sublineages. One of these lineages is the S. Typhi group; well nested within the phylogeny. Lineage-through-time analyses suggest there have been two instances of accelerated rates of diversification within the subspecies. We also found that antigen characters and CRISPR loci reveal different evolutionary patterns than that of the phylogeny, suggesting that a horizontal gene transfer or possibly a shared environmental acquisition might have influenced the present character distribution. Our study also shows the ability to extract reference-free SNPs from a large set of genomes and then to use these SNPs for phylogenetic reconstruction. This automated, annotation-free approach is an important step forward for bacterial disease tracking and in efficiently elucidating the evolutionary history of highly clonal organisms.
Structural Model of Lymphocyte Receptor NKR-P1C Revealed by Mass Spectrometry and Molecular Modeling (2012)

NKR-P1C is an activating immune receptor expressed on the surface of mouse natural killer cells. It has been widely used as a marker for NK cell identification in different mice strains. Recently we solved a crystal structure of the C-type lectin-like domain of a homologous protein, NKR-P1A, using X-ray crystallography and also described the strategy for rapid characterization of the protein conformation in solution. This procedure utilized chemical cross-linking, hydrogen/deuterium exchange, and molecular modeling. It was found that the solution structure differs from the crystal structure in the conformation of the loop region. The loop, detached from the protein compact core in the crystal structure, is closely attached to the core of the protein in solution. Here we present and interpret the solution structure of the C-type lectin-like domain of NKR-P1C using chemical cross-linking and molecular modeling. The validation of the model and conformation of the loop region in NKR-P1C were addressed using ion-mobility mass spectrometry.
Specific detection of Salmonella spp. by multiplex polymerase chain reaction (1993)

Three sets of oligonucleotide primers were used in the polymerase chain reaction (PCR) assay to detect Salmonella species. phoP primers specific to the phoP/phoQ loci of coliform pathogenic bacteria such as Salmonella, Shigella, Escherichia coli, and Citrobacter species served as presumptive indicators of enteric bacteria. In addition to the phoP primers, the Hin and the H-1i primers, which targeted a 236-bp region of hin/H2 and a 173-bp region of the H-1i flagellin gene, respectively, were used. Both Hin and H-1i primers are specific to motile Salmonella species and are not present in Shigella, E. coli, or Citrobacter species. Thus, by multiplex PCR amplification, Salmonella species including Salmonella typhi, Salmonella typhimurium, Salmonella paratyphi A, and Salmonella enteritidis can be specifically detected. Optimal reaction conditions have been described to demonstrate this specific, sensitive detection of Salmonella species. By using agarose gel electrophoresis for detection of the PCR-amplified products, the sensitivity of detection was 10(2) CFU after 25 cycles of PCR and 1 (10(0)) CFU after a 50-cycle double PCR. The efficacy of these primers was demonstrated on environmental isolates which had previously been confirmed as Salmonella species by the use of conventional cultural techniques. In addition, positive amplifications resulted from Salmonella species in environmental samples including soil and water.
A comparison of two obstacle avoidance path planners for autonomous underwater vehicles (2002)

The breadth-first path planner is compared to the optimal A* path planner in terms of distance traveled and computation time. Certain modifications are added to the obstacle avoidance algorithm to increase its robustness to vehicle position uncertainties arising from the Doppler/INS system. Simulation results show that the A* path planner generates paths that are between 0.8 and 1.1 times the length of the paths generated by the breadth-first approach. Computationally, however, the A* solution takes anywhere from 1.5 to 19.8 times longer to calculate. Repeated trials in simulated, dense obstacle fields have verified that despite position uncertainties, the obstacle avoidance algorithm safely guides an autonomous underwater vehicle along a planned path to the desired end point.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Surface-Enhanced Counter Electrode Materials for the Fabrication of Ultradurable Electrochromic Devices (2022)

Electrochromic devices (ECDs) and especially electrochromic supercapacitors, where the real-time state of charge is indicated by the color, have a wide range of applications. However, to meet modern challenges, these devices should demonstrate exceptional charge–discharge durability. In this work, we demonstrate that electrochemical cycling stability of ECDs based on a monolayer of 4′-(4-pyridyl)-2,2′:6′,2″-terpyridine–iron(II) complex that was covalently linked to the working electrode (WE) can be drastically enhanced by a proper design of the counter electrode (CE). Enhancing the surface area of the flat indium tin oxide (ITO) CE by a layer of screen-printed ITO nanoparticles results in an ECD that upon continuous spectro-electrochemical switching for 600 cycles demonstrates negligible deterioration of the change in optical density. The enhanced surface area of the CE significantly diminishes the electrode and gel electrolyte degradation and allows us to gain fundamental insight into the pathway of degradation of the electrochromic molecules at the WE. During prolonged cycling (20,000 and 50,000 cycles), the overall total resistance of ECDs remains fairly unchanged, while the capacitance decreases due to a loss of the pseudocapacitive component associated with electrochromic molecules. X-ray photoelectron spectroscopy (XPS) suggests that this loss is likely due to the cleavage of the linkage C–N+ bond followed by the dissolution of the entire metal complex molecule into the electrolyte.
Photoswitching of Ligand Association with a Photoresponsive Polymer−Protein Conjugate (2002)

Light-regulated molecular switches that reversibly control biomolecular function could provide new opportunities for controlling activity in diagnostics, affinity separations, bioprocessing, therapeutics, and bioelectronics applications. Here we show that site-specific conjugation of light-responsive polymers near the biotin-binding pocket of streptavidin provides control of ligand binding affinity in response to UV and visible light irradiation. Two different light-responsive polymers were utilized that display opposite photoresponsive solubility changes under UV or visible (vis) light irradiation in aqueous solutions. At 40 degrees C, the N,N-dimethylacrylamide (DMA)-co-4-phenylazophenyl acrylate (AZAA) copolymer (DMAA) was soluble under UV irradiation and precipitated under visible light, while the DMA-co-N-4-phenylazophenyl acrylamide (AZAAm) copolymer (DMAAm) was soluble under visible irradiation and precipitated under UV light. Both polymers were synthesized with a vinyl sulfone terminus and conjugated to the Glu116Cys (E116C) streptavidin mutant via thiol coupling. The DMAA-streptavidin conjugate bound biotin efficiently when the polymer was in the soluble state under UV irradiation, but under visible irradiation, the polymer collapsed and blocked free biotin association. Furthermore, if biotin was allowed to bind when the polymer was in the soluble state under UV irradiation, then when the polymer was collapsed by visible light, the streptavidin released the bound biotin. The DMAAm-streptavidin conjugate showed the opposite response, with association of biotin allowed under visible light irradiation and blocked under UV irradiation. The photoresponses of the streptavidin conjugates thus correspond to the original photoresponsive phase transition properties of the polymer switches triggered by the cis-trans isomerization of the diazo chromophores.
Social signaling in decision making (2005)

Nonverbal communication is an important and often underestimated instrument in social interactions. The paralinguistic elements of speech, which are described in common speech as ”tone of voice”, are one channel of the nonverbal communication. They, together with conversational dynamics, are a very powerful measurement for interactions, without looking at the content of the conversation. A subset of these features, the social signaling measurements, are very useful when analyzing and quantifying conversation. The goal of this thesis is to better understand the framework of social signaling. We applied the social signaling measurements to negotiations as well as to small group interactions. For negotiation we were able to predict up to 30 % of the variance in individual outcome. The use of automated algorithms enables to build real-time feedback mechanisms that can then
TINJAUAN HUBUNGAN HUKUM PERJANJIAN LEASING KENDARAAN BERMOTOR (2020)

Abstrak Artikel ini bertujuan untuk mengetahui konstruksi hukum para pihak dalam perjanjian leasing kendaraan  bermotor. Penelitian hukum ini termasuk jenis penelitian hukum normatif yang bersifat preskriptif dan  terapan. Pendekatan yang digunakan adalah pendekatan perundang-undangan ( statute approach ) dengan  sumber data sekunder yang ditunjang dengan data primer sebagai data pendukungnya. Teknik pengumpulan  data menggunakan studi kepustakaan dan studi lapangan. Selanjutnya teknik analisis data menggunakan  metode deduksi. Hasil penelitian yang penulis lakukan didapatkan kesimpulan bahwa konstruksi hukum  perjanjian leasing tidak memenuhi syarat sahnya perjanjian yang keempat berdasarkan Pasal 1320  KUHPerdata. Perjanjian leasing bertentangan dengan Pasal 65 ayat (2) Undang-undang No. 22 Tahun  2009 tentang Lalu Lintas dan Angkutan Jalan dalam hal hak milik objek leasing secara yuridis berdasarkan  BPKB. Meskipun perjanjian leasing didasarkan pada asas kebebasan berkontrak, namun keberadaannya  tidak boleh bertentangan dengan undang-undang, kesusilaaan, maupun ketertiban umum seperti yang diatur  dalam Pasal 1337 KUHPerdata. Sehingga akibat hukumnya perjanjian tersebut seharusnya batal demi  hukum. Khusus untuk leasing kendaraan bermotor dalam perjanjian leasing , para pihak seharusnya sepakat  untuk mengesampingkan Pasal 65 ayat (2) tersebut sebagaimana para pihak mengesampingkan Pasal 1266  KUHPerdata bagi debitur dalam perjanjian. Kata Kunci: Perjanjian Leasing ; Hubungan Hukum; Akibat Hukum.
The Dominant Role of Chalcogen Bonding in the Crystal Packing of 2D/3D Aromatics (2014)

Abstract The chalcogen bond is a nonclassical σ‐hole‐based noncovalent interaction with emerging applications in medicinal chemistry and material science. It is found in organic compounds, including 2D aromatics, but has so far never been observed in 3D aromatic inorganic boron hydrides. Thiaboranes, harboring a sulfur heteroatom in the icosahedral cage, are candidates for the formation of chalcogen bonds. The phenyl‐substituted thiaborane, synthesized and crystalized in this study, forms sulfur⋅⋅⋅π type chalcogen bonds. Quantum chemical analysis revealed that these interactions are considerably stronger than both in their organic counterparts and in the known halogen bond. The reason is the existence of a highly positive σ‐hole on the positively charged sulfur atom. This discovery expands the possibilities of applying substituted boron clusters in crystal engineering and drug design.
Applications Of Time And Wavelength Division Multiplexing To Digital Optical Code Plates (1988)

This paper discusses the application of pulse time division multiplexing and wavelength division multiplexing to reflective digital optical code plates for sensing position on aircraft. Particular attention is given to temperature drifts and component tolerances in the optical power budgets. Both wavelength and time division multiplexing have been proposed for referencing analog ratiometric sensors and for multiplexing digital optical signals such as from a reflective code plate or an array of discrete sensors. The use of either technique in these applications is limited by the aircraft environment, particularly by the temperature induced drift of the source and optical component properties. The paper concludes that each approach is constrained by environmental effects and small power budget. In addition, the performance of the reflective WDM system is strongly dependent on the number of connectors used in the interconnect fiber. Development of either of these sensor concepts requires careful design and evaluation to resolve these problems.
Feature Loss After Denoising of SPECT Projection Data using a U-Net (2020)

It has been long known that denoising of Single Photon Emission Computed Tomography (SPECT) projection data from multi channel collimators harbors the danger that features are filtered away as distinction between noise and signal in the 2D projection image does not consider the tomographic information (see Vija, Yahil et al.). We investigate if an approach using Neural Networks can overcome the past issues, by training a U-Net on Monte Carlo Simulations of the XCAT phantom. Although error metrics indicate improvement of signal statistics, we observe a loss of image features after the reconstruction. We show that when using OSEM reconstruction without denoising in projection domain, these features can be preserved.
Enhancing Monte Carlo proxy applications on GPUs (2020)

In Monte Carlo neutron transport simulations, a computational routine commonly known as the ”cross-section lookup” has been identified as being the most computationally expensive part of these applications. A tool which is commonly used as a proxy application for these routines, named ”XSBench”, was created to simulate popular algorithms used in these routines on CPUs. Currently, however, as GPU-based HPC resources have become more widely available, there has been significant interest and efforts invested in moving these traditionally CPU-based simulations to GPUs. Unfortunately, the algorithms commonly used in the cross-section lookup routine were originally devised and developed for CPU-based platforms, and have seen limited study on GPUs to date. Additionally, platforms such as XSBench implement approximations which may have a negligible effect on CPUs, but may be quite impactful to performance on GPUs given the more resource-limited nature of the latter. As a result, we have created VEXS, a new tool for modeling the cross-section lookup routine which removes or at least reduces the approximations made by XSBench in order to provide a more realistic prediction of algorithm performance on GPUs. In this paper, we detail our efforts to remove and reduce these approximations, show the resulting improvement in performance prediction in comparison to a reference production code, Shift, and provide some basic profiling analysis of the resulting application.
Electromechanical Properties of Robocasted Barium Titanate Ceramics (2020)

This work presents the fabrication of dense polycrystalline barium titanate (BaTiO 3 , BT) for electromechanical transduction using robocasting and cold isostatic pressing (CIP). The use of CIP as post‐treatment is proposed to eliminate defects and increase the density of robocasted parts to improve the piezoelectric performance. For robocasting, pastes containing 50 and 52 vol% are developed; the resulting green robocasted parts are CIPed at 100 and 150 MPa. Using this proposed technique, samples robocasted with BT52 and CIPed at 150 MPa display a relative density of ≈98%, comparable with reference polycrystalline samples. In addition, an increase in both the piezoelectric charge and voltage coefficient is observed in robocasted parts, with the values up to 195 pC/N and 12 × 10 −3 Vm N −1 , respectively. These values, which are comparable with previous studies of polycrystalline BT, indicate that the combined robocasting and CIP technique is a possible method for producing 3D printed piezoelectric sensors.
Optimum sparse array beamforming for general rank signal models (2018)

Sparse array design professes several advantages over their uniform array counterparts, including high resolution and ability to deal with large number of sources in the field of view (FOV). In this paper, we examine sparse arrays achieving maximum signal-to-interference plus noise ratio (MaxSINR) for three different cases, namely, single point source, multiple point sources and Gaussianly spread source, operating in an interference active environment. Our approach does not require any apriori knowledge of the source directions of arrival and their respective power. We formulate the problem as quadratically constraint quadratic program (QCQP), where the cost function is penalized with weighted l <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> -norm squared of the beamformer weight vector, and propose an iterative technique to control the desired sparsity. It is shown that the optimum sparse array utilizes the array aperture effectively and provides considerable performance improvement over a compact uniform linear array (ULA). Simulation results are presented to show the effectiveness of proposed algorithm for array configurability in the case of both single and general rank signal correlation matrices.
BENZENE METHOD MEASURES TRITIUM IN RAIN WITHOUT ISOTOPE ENRICHMENT (1963)

A method for measuring the tritium activity in rain by converting the water samples to benzene and counting in a liquid-scintillation counter is described. This method gives results in good agreement with results of other methods and exhibits good reproducibility. (D.C.W.)
Human brain weight is correlated with expression of the ‘housekeeping genes’ beta-2-microglobulin (β2M) and TATA-binding protein (TBP) (2010)

The findings were not anticipated; they need replication in another brain series, and a more systematic survey is indicated. In the interim, we suggest that quantitative gene expression studies in human brain should inspect for a potential influence of brain weight, especially as the affected transcripts are commonly used as reference genes for normalization purposes in studies of neurological and psychiatric disorders. The relationship of brain weight with β2-microglobulin mRNA may reflect the roles of major histocompatibility complex class I genes in synapse formation and plasticity.
Header Height Control of a Combine Harvester System (2010)

There are appreciable losses in crop output at all the stages in grain production like harvesting, transportation, storage, etc. To reduce grain loss during the harvesting process, it is desirable to effectively control the header height of the combine harvester. The desired header height control is able to follow the shape of the terrain and reject disturbances from the ground. This paper presents an optimal state feedback LQR controller to achieve the control objectives. By properly defining the states and choosing the cost function, the full state feedback controller is shown to accomplish the control goals. Then a reduced states feedback controller, which uses a skyhook damper in the controller, is used to simplify the full state feedback controller. Simulation results show that with less feedback information, the reduced order state feedback controller preserves the ability to achieve good reference tracking and disturbance rejection.
A Real-time Video Fire Flame and Smoke Detection Algorithm (2013)

Real-time video fire flame and smoke detection method based on foreground image accumulation and optical flow technique is presented. Accumulation images are calculated of the foreground images which are extracted using frame differential method. Two parameters are used for the foreground image accumulation to differentiate flame candidate areas from that of smoke. The flame regions are recognized by a statistical model build by foreground accumulation image, while the optical flow is calculated and a motion feature discriminating model to recognize smoke regions is used. The algorithm could realize the real-time fire detection of the following three detection cases: fire with flame and none smoke, fire with smoke and none flame, and fire with both flame and smoke.
Volumetry of the Pituitary Gland: An Initial in vitro and in vivo MR Study (2004)

Purpose: We have attempted to evaluate the reliability of a new volumetric technique for MR imaging applied on measurements of phantoms with defined volumes and the normal pituitary gland (PG) of healthy individuals. Methods: In nine males without a clinical history of pituitary abnormalities and in a phantom study we performed triplicate MRI measurements before and after repositioning for volumetry of the PG or the phantoms, respectively. Using a standard head coil on a 1.5 T scanner, a tilted sagittal T1w 3D magnetization-prepared rapid gradient-echo sequence was applied with TR/TE/alpha=15/5ms/30, 256×256 matrix, 192 slices, 1mm thickness and an isovoxel size of 1×1×1mm3. For interactive segmentation, a semi-automated 3D-watershed transform was applied to the gradient image. Each segmentation took approx. 4 minutes. Volume was assessed by voxel counting. Results: Mean volume of the nine pituitary glands was 0.62ml (SD:0.02ml) with variation coefficients (VC) between 2.68% and 6.32%, respectively. Furthermore, the intraobserver variability with four repeated volume analyses of an identical MRI measurement ranged from 1.44% to 3.67%. After intravenous administration of contrast medium, the volume calculation showed an overestimation because of reduced demarcation of PG. Reliable and precise results could be ensured up to a slice thickness of 1.8mm, preferably by coronal scanning. The VC from the phantom volume measurements (0.3, 0.5, 0.9, 1.0 and 1.6ml) only ranged from 0.49% (SD:0.006ml) to 1.98% (0.005ml). Conclusion: Our initial results demonstrate a high reliability without a significant difference of volumetric measurement for our in vitro and in vivo studies. This method provides a precise volume estimation of PG up to a slice thickness of 1.8mm and can improve the monitoring of PG volume in follow-up-studies after surgical or conservative treatment.