gebhart/patrepeval huggingface dataset:
A New Physics-Based Approach for Estimating a Buried Object's Location, Orientation and Magnetic Polarization from EMI Data (2008)

Abstract A new physics-based expression is presented for determining a buried object's location, orientation and magnetic polarizibility. The approach assumes the target exhibits a dipolar response and requires only three global values: a magnetic field vector H, a vector potential A and a scalar magnetic potential ψ, all at a single location in space. Among these values, only the scattered magnetic field, H, is measurable with current electromagnetic induction sensors. Therefore, in order to estimate the scattered magnetic scalar and vector potentials from data, a numerical technique called the normalized surface magnetic source (NSMS) method is employed. Originally, in the NSMS model, the scattered magnetic field outside the object is reproduced mathematically by equivalent magnetic charges distributed on a three-dimensional (3-D) closed surface. Here, a two-dimensional (2-D) implementation of the NSMS that uses elementary magnetic dipoles, instead of magnetic charges distributed on a planar surface placed under the measurement grid, is utilized. These sources are used to estimate the scattered magnetic field's vector potential A and scalar magnetic potential ψ without a priori knowledge of the object's location and orientation. The amplitudes of the NSMS are determined by matching the measured magnetic field with the NSMS modeled field. Once the NSMS amplitudes are determined, H, A, and ψ are simulated on or above the measurement grid. The theoretical basis of the new approach, as well as the practical realization of the 2-D NSMS algorithm used to estimate H, A, and ψ above the measurement grid from actual data, is illustrated. Several numerical and experimental tests for actual EMI sensors are presented.
The Limited Influence of Unemployment on the Wage Bargain (2005)

When a job-seeker and an employer meet, find a prospective surplus, and bargain over the wage, conditions in the outside labor market, including especially unemployment, may be irrelevant. The job-seeker's threat point in the bargain is to delay bargaining, not to terminate bargaining and resume search at other employers. Similarly, the employer's threat point is to delay bargaining, not to terminate it. Consequently, the outcome of the bargain depends on the relative costs of delay to the parties, not on the results of irrational threats to disclaim any bargain. In a model of the labor market that otherwise adopts all of the features of the standard Mortensen-Pissarides model, unemployment is much more sensitive to changes in productivity than in the standard model, because feedback through the wage is absent. We also present models where the wage bargain is in partial contact with conditions in the labor market.
Correction: The effects of fermentation products of prebiotic fibres on gut barrier and immune functions in vitro (2018)

[This corrects the article DOI: 10.7717/peerj.5288.].
Interactions of Cyclins with Cyclin-Dependent Kinases:  A Common Interactive Mechanism (1997)

The formation of cdk-cyclin complexes has been investigated at the molecular level and quantified using spectroscopic approaches. In the absence of phosphorylation, cdk2, cdc2, and cdk7 form highly stable complexes with their "natural" cyclin partners with dissociation constants in the nanomolar range. In contrast, nonphosphorylated cdc2-cyclin H, cdk2-cyclin H, and cdk7-cyclin A complexes present a 25-fold lower stability. On the basis of both the structure of the cdk2-cyclin A complex and on our kinetic results, we suggest that interaction of any cyclin with any cdk involves the same hydrophobic contacts and induces a marked conformational change in the catalytic cleft of the cdks. Although cdks bind ATP strongly, they remain in a catalytically inactive conformation. In contrast, binding of the cyclin induces structural rearrangements which result in the selective reorientation of ATP, a concomitant 3-fold increase in its affinity, and a 5-fold decrease of its release from the active site of cdks.
Energy Efficient Spectrum Sensing and Handoff Strategies in Cognitive Radio Networks (2013)

The limited spectrum resources and dramatic growth of high data rate communications have motivated opportunistic spectrum access using the promising concept of cognitive radio networks. Although this concept has emerged primarily to enhance spectrum utilization, the importance of energy consumption poses new challenges, because energy efficiency and communication performance can be at odds. In this paper, the existing approaches to energy efficiency spectrum sensing and handoff are classified. The tradeoff between energy consumption and throughput is established as function of the numerous design parameters of cognitive radio networks, both in the case of local and of cooperative spectrum sensing. It is argued that a number of important aspects still needs to be researched, such as fairness, dynamic behavior, reactive and proactive schemes for energy efficiency.
Raytheon downhole information system. Electromagnetic borehole measurements while drilling system. Final report (1978)

A description is given of the Raytheon Downhole Information System (RDIS), a real time electromagnetic borehole measurements while drilling system, applicable to oil, gas, and geothermal drilling. It communicates in both directions through the earth in a single hop at a downlink data rate of 3 bps and uplink rates dependent on depth--typically 6 bits/second at 10,000 ft and 2 bits/second at 15,000 ft; electromagnetic signal transmission time of approximately .1 second. Downhole hardware for communications, sensors, and power are packaged in three 30 ft subs. Downhole hardware can be developed to permit operation in a 275/sup 0/C geothermal environment. A cost analysis is included that predicts RDIS service could be economically priced at approximately $1000/day. Commercial availability depends primarily on proof of capability by demonstration in a working drilling well. The most significant portions of needed hardware are available. A description of a geothermal drilling telemetry system is included in Appendix A.
Intelligent Intersections Reduce Crashes and Will Support the Safe Introduction of Autonomous Vehicles (2018)

Intersections are dangerous. In the U.S., approximately 40% of all crashes, 50% of serious collisions, and 20% of fatalities occur in intersections. Intersections are challenging due to complex interactions among pedestrians, bicycles and vehicles; absence of lane markings; difficulty in determining who has the right of way; blind spots; and illegal movements (e.g., vehicles running red lights). Many cities have developed Vision Zero plans seeking to eliminate traffic injuries and deaths through modifications to road infrastructure, such as adding bike lanes and pedestrian refuge islands. These modifications can be expensive (e.g., the cost of a protected intersection can range between $250,000 to more than a $1 million) and have mixed safety results. It is claimed autonomous vehicles (AVs) will prevent 94% of all crashes involving human error. However, the safety performance of AVs is far below that of human-driven cars. In California, the number of accidents and disengagements per AV mile traveled is 13 to 100 times worse than human-driven cars. The AV fatality rate is equally as bad. AVs find intersections especially challenging; 58 of 66 (88%) AV crashes reported to the California Department of Motor Vehicles (DMV) occurred in intersections.
Fluorescence imaging to study cancer burden on lymph nodes (2015)

Morbidity and complexity involved in lymph node staging via surgical resection and biopsy calls for staging techniques that are less invasive. While visible blue dyes are commonly used in locating sentinel lymph nodes, since they follow tumor-draining lymphatic vessels, they do not provide a metric to evaluate presence of cancer. An area of active research is to use fluorescent dyes to assess tumor burden of sentinel and secondary lymph nodes. The goal of this work was to successfully deploy and test an intra-nodal cancer-cell injection model to enable planar fluorescence imaging of a clinically relevant blue dye, specifically methylene blue along with a cancer targeting tracer, Affibody labeled with IRDYE800CW and subsequently segregate tumor-bearing from normal lymph nodes. This direct-injection based tumor model was employed in athymic rats (6 normal, 4 controls, 6 cancer-bearing), where luciferase-expressing breast cancer cells were injected into axillary lymph nodes. Tumor presence in nodes was confirmed by bioluminescence imaging before and after fluorescence imaging. Lymphatic uptake from the injection site (intradermal on forepaw) to lymph node was imaged at approximately 2 frames/minute. Large variability was observed within each cohort.
Compressive Sensing for over-the-air ultrasound (2011)

The advent of Compressive Sensing has provided significant mathematical tools to enhance the sensing capabilities of hardware devices. In this paper we apply Compressive Sensing to improve over-the-air ultrasonic sensing capabilities. We demonstrate that using an appropriate scene model it is possible to pose three-dimensional surface reconstruction of a scene as a sparse recovery problem. By transmitting incoherent wideband ultrasonic pulses and receiving their reflections a sensor array can sense the scene and reconstruct it using standard CS reconstruction algorithms. We further demonstrate that it possible to construct virtual arrays that exploit the sensors' motion. Thus we can obtain three-dimensional scene reconstruction using a linear mobile array.
TheBravyi–Kitaev transformation: Properties and applications (2015)

Quantum chemistry is an important area of application for quantum computation. In particular, quantum algorithms applied to the electronic structure problem promise exact, efficient methods for determination of the electronic energy of atoms and molecules. The Bravyi–Kitaev transformation is a method of mapping the occupation state of a fermionic system onto qubits. This transformation maps the Hamiltonian of n interacting fermions to an ‐local Hamiltonian of n qubits. This is an improvement in locality over the Jordan–Wigner transformation, which results in an O ( n )‐local qubit Hamiltonian. We present the Bravyi–Kitaev transformation in detail, introducing the sets of qubits which must be acted on to change occupancy and parity of states in the occupation number basis. We give recursive definitions of these sets and of the transformation and inverse transformation matrices, which relate the occupation number basis and the Bravyi–Kitaev basis. We then compare the use of the Jordan–Wigner and Bravyi–Kitaev Hamiltonians for the quantum simulation of methane using the STO‐6G basis. © 2015 Wiley Periodicals, Inc.
Gas-Phase Ion Mobilities and Structures of Benzene Cluster Cations (C6H6)n+, n = 2−6 (2003)

Benzene clusters are generated by pulsed supersonic beam expansion, ionized by electron impact, mass-selected and then injected into a drift cell for ion mobility measurements in a helium buffer gas. The measured collision cross sections and theoretical calculations are used to determine the structures of the cluster cations (C(6)H(6))(n)(+) with n = 2-6. Density functional theory calculation, at an all-electron level and without any symmetry constraint, predicts that the dimer cation has two nearly degenerate ground state structures with the sandwich configuration more stable than the T-configuration by only 0.07 eV. The ion mobility experiment indicates that only one structure is observed for the mass-selected dimer cation at room temperature. The calculated cross section for the sandwich structure agrees very well (within 2.4%) with the experimental value. For the n = 3-6 clusters, the experiments suggest the presence of at least two structural isomers for each cluster. A Monte Carlo minimum-energy search technique using the 12-site OPLS potential for benzene is used to determine the structures of the lowest-energy isomers. The calculated cross sections for the two lowest-energy isomers of the n = 3-6 clusters agree well with the experimental results. The clusters' structures reveal two different growth patterns involving a sandwich dimer core or a pancake trimer stack core. The lowest-energy isomers of the n = 3-6 clusters incorporate the pancake trimer stack as the cluster's core. The trimer stack allows the charge to hop between two dimers, thus maximizing charge resonance interaction in the clusters. For larger clusters, the appearance of magic numbers at n = 14, 20, 24, 27, and 30 is consistent with the incorporation of a sandwich dimer cation within icosahedral, double icosahedral, and interpenetrating icosahedral structures. On the basis of the ion mobility results and the structural calculations, the parallel-stacked motif among charged aromatic-aromatic interactions is expected to play a major role in determining the structures of multi aromatic components. This conclusion may provide new insights for experimental and theoretical studies of molecular design and recognition involving aromatic systems.
Responding to the challenge of untreatable gonorrhea: ETX0914, a first-in-class agent with a distinct mechanism-of-action against bacterial Type II topoisomerases (2015)

With the diminishing effectiveness of current antibacterial therapies, it is critically important to discover agents that operate by a mechanism that circumvents existing resistance. ETX0914, the first of a new class of antibacterial agent targeted for the treatment of gonorrhea, operates by a novel mode-of-inhibition against bacterial type II topoisomerases. Incorporating an oxazolidinone on the scaffold mitigated toxicological issues often seen with topoisomerase inhibitors. Organisms resistant to other topoisomerase inhibitors were not cross-resistant with ETX0914 nor were spontaneous resistant mutants to ETX0914 cross-resistant with other topoisomerase inhibitor classes, including the widely used fluoroquinolone class. Preclinical evaluation of ETX0914 pharmacokinetics and pharmacodynamics showed distribution into vascular tissues and efficacy in a murine Staphylococcus aureus infection model that served as a surrogate for predicting efficacious exposures for the treatment of Neisseria gonorrhoeae infections. A wide safety margin to the efficacious exposure in toxicological evaluations supported progression to Phase 1. Dosing ETX0914 in human volunteers showed sufficient exposure and minimal adverse effects to expect a highly efficacious anti-gonorrhea therapy.
Validated computational models predict vagus nerve stimulation thresholds in preclinical animals and humans (2023)

<i>Objective.</i>We demonstrated how automated simulations to characterize electrical nerve thresholds, a recently published open-source software for modeling stimulation of peripheral nerves, can be applied to simulate accurately nerve responses to electrical stimulation.<i>Approach.</i>We simulated vagus nerve stimulation (VNS) for humans, pigs, and rats. We informed our models using histology from sample-specific or representative nerves, device design features (i.e. cuff, waveform), published material and tissue conductivities, and realistic fiber models.<i>Main results.</i>Despite large differences in nerve size, cuff geometry, and stimulation waveform, the models predicted accurate activation thresholds across species and myelinated fiber types. However, our C fiber model thresholds overestimated thresholds across pulse widths, suggesting that improved models of unmyelinated nerve fibers are needed. Our models of human VNS yielded accurate thresholds to activate laryngeal motor fibers and captured the inter-individual variability for both acute and chronic implants. For B fibers, our small-diameter fiber model underestimated threshold and saturation for pulse widths >0.25 ms. Our models of pig VNS consistently captured the range of<i>in vivo</i>thresholds across all measured nerve and physiological responses (i.e. heart rate, A<i>δ</i>/B fibers, A<i>γ</i>fibers, electromyography, and A<i>α</i>fibers). In rats, our smallest diameter myelinated fibers accurately predicted fast fiber thresholds across short and intermediate pulse widths; slow unmyelinated fiber thresholds overestimated thresholds across shorter pulse widths, but there was overlap for pulse widths >0.3 ms.<i>Significance.</i>We elevated standards for models of peripheral nerve stimulation in populations of models across species, which enabled us to model accurately nerve responses, demonstrate that individual-specific differences in nerve morphology produce variability in neural and physiological responses, and predict mechanisms of VNS therapeutic and side effects.
Substrate Profile Analysis and ACP‐Mediated Acyl Transfer in Streptomyces coelicolor Type III Polyketide Synthases (2007)

Protein partners. We report the biochemical characterization of two type III polyketide synthases (PKS) from Streptomyces coelicolor. Remarkably, germicidin synthase (Gcs)/SCO7221 was able to utilize both acyl-CoA and acyl-ACP as starter units for the production of pyrone containing compounds. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2268/2007/z700026_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Steganalysis for Markov Cover Data With Applications to Images (2006)

The difficult task of steganalysis, or the detection of the presence of hidden data, can be greatly aided by exploiting the correlations inherent in typical host or cover signals. In particular, several effective image steganalysis techniques are based on the strong interpixel dependencies exhibited by natural images. Thus, existing theoretical benchmarks based on independent and identically distributed (i.i.d.) models for the cover data underestimate attainable steganalysis performance and, hence, overestimate the security of the steganography technique used for hiding the data. In this paper, we investigate detection-theoretic performance benchmarks for steganalysis when the cover data are modeled as a Markov chain. The main application explored here is steganalysis of data hidden in images. While the Markov chain model does not completely capture the spatial dependencies, it provides an analytically tractable framework whose predictions are consistent with the performance of practical steganalysis algorithms that account for spatial dependencies. Numerical results are provided for image steganalysis of spread-spectrum and perturbed quantization data hiding.
Thyroid Hormone-Regulated Actin Polymerization in Brain (1997)

Thyroid hormones play an important role in the growth and development of the brain. Central to the proper integration of neuronal circuitry is the ability of the growing neurite to interpret guidance cues during its migration. The action cytoskeleton is especially rich in the growth cone, and is a likely target for thyroid hormone regulation. This brief review summarizes work showing that thyroxine, but not T3, dynamically regulates the polymerization of the actin cytoskeleton in astrocytes. The ability of T4 to enhance actin polymerization, without directly affecting gene expression, has a profound effect on the ability of the cell to interact with laminin, the major extracellular matrix protein in the developing brain. T4 also regulates the formation of key cell contacts with extracellular matrix guidance cues. These processes are likely to participate in thyroid hormone's regulation of brain development.
Supplementary Figures 1 - 7 from Re-engineering Vesicular Stomatitis Virus to Abrogate Neurotoxicity, Circumvent Humoral Immunity, and Enhance Oncolytic Potency (2023)

&lt;p&gt;PDF file - 6330KB, Schematic representation of the recombinant vesicular stomatitis virus (VSV) genomes and its replication potential (S1). rVSV(GP) administration i.c. is associated with marginal inflammation (S2). rVSV(GP) tissue distribution after systemic application is almost consistent with rVSV (S3). rVSV(GP) is comparable to rVSV with regard to its in vitro antitumour efficacy (S4). Replication fitness of rVSV(GP) vs. rVSV in glioma cells (S5). Intratumoural virus administration in s.c. G62 human glioblastoma xenografts leads to productive infection and massive viral burst (S6). U87rfp tumour relapse was not due to OV therapy resistance (S7).&lt;/p&gt;
DNA Polymerase Selectivity: Sugar Interactions Monitored with High-Fidelity Nucleotides This work was supported by a grant from the Deutsche Forschungsgemeinschaft. We thank Professor Dr. Michael Famulok for his continuing support. (2001)

Do enzyme–sugar interactions contribute to DNA-polymerase fidelity? With the novel chemical probes 1 (R=CH3, CH2CH3, CH(CH3)2, CH2CH(CH3)2), which are used by a DNA polymerase more selectively than the natural counterpart (R=H), insights are obtained into the influence of enzyme–sugar interactions on the selectivity of the enzyme.
Synthesis, Reactivity, and Ring-Opening Polymerization (ROP) of Tin-Bridged [1]Ferrocenophanes (1998)

Novel tin-bridged [1]ferrocenophanes (1) undergo ring-opening polymerization to yield unusual bimetallic high-molecular-weight poly(ferrocenylstannane)s (2). They also undergo insertion of platinum to afford a 1-stanna-2-platina[2]ferrocenophane (3).
Measurement of the MTF and MRTD for focal plane arrays (1993)

The use of focal plane arrays (FPAs) in infrared imaging systems is becoming increasingly important. There are problems, however, in measuring their modulation transfer function (MTF) and their minimum resolvable temperature difference (MRTD) since these performance measures vary with the exposition of the image on the FPA. This limitation has been overcome through the introduction of a discrete MTF for these imaging systems using discrete Fourier transform techniques. This discrete MTF is a unique function of spatial frequency and has been measured using a microscanned discrete line spread function. It has also formed the basis of an objective MRTD, the results of which have been compared with subjective measurements.
Table S2 from Expression of Adipocyte/Macrophage Fatty Acid–Binding Protein in Tumor-Associated Macrophages Promotes Breast Cancer Progression (2023)

&lt;p&gt;Table S2 analyzes the association of A-FABP levels with breast cancer survival using TCGA dataset.&lt;/p&gt;