gebhart/patrepeval huggingface dataset:
Magnetic-resonance-based electrical property mapping using Global Maxwell Tomography with an 8-channel head coil at 7 Tesla: a simulation study (2020)

Objective: Global Maxwell Tomography (GMT) is a recently introduced volumetric technique for noninvasive estimation of electrical properties (EP) from magnetic resonance measurements. Previous work evaluated GMT using ideal radiofrequency (RF) excitations. The aim of this simulation study was to assess GMT performance with a realistic RF coil. Methods: We designed a transmit-receive RF coil with 8 decoupled channels for 7T head imaging. We calculated the RF transmit field (B[superscript 1][subscript 1) inside heterogeneous head models for different RF shimming approaches, and used them as input for GMT to reconstruct EP for all voxels. Results: Coil tuning/decoupling remained relatively stable when the coil was loaded with different head models. Mean error in EP estimation changed from 7.5% to 9.5% and from 4.8% to $7.2% for relative permittivity and conductivity, respectively, when changing head model without re-tuning the coil. Results slightly improved when an SVD-based RF shimming algorithm was applied, in place of excitation with one coil at a time. Despite errors in EP, RF transmit field (B<formula><tex>$+1$</tex></formula><formula><tex>$_1$</tex></formula>) and absorbed power could be predicted with less than 0.5% error over the entire head. GMT could accurately detect a numerically inserted tumor. Conclusion: This work demonstrates that GMT can reliably reconstruct EP in realistic simulated scenarios using a tailored 8-channel RF coil design at 7T. Future work will focus on construction of the coil and optimization of GMT&#x0027;s robustness to noise, to enable in vivo GMT experiments. Significance: GMT could provide accurate estimations of tissue EP, which could be used as biomarkers and could enable patient-specific estimation of RF power deposition, which is an unsolved problem for ultra-high-field magnetic resonance imaging.
Learning Physical Activities in Immersive Virtual Environments (2006)

This paper describes a framework for constructing a three-dimensional immersive environment that can be used for training physical activities. In the proposed system, an immersive environment is constructed through realistic reconstruction of a scene by applying a stereo algorithm on a set of images that is captured from multiple viewpoints. Specifically, twelve camera clusters that consist of four camera quadruples are used to capture full body human motions, where each camera cluster is processed by a pc independently and synchronously so that they can compute 3d information of the scene in real-time fashion. This paper discusses in detail system architectures that enable synchronous operations across multiple computers while achieving parallel computations within each multi-processor system. A set of experiments are performed to learn taichi lessons in this environment where students are instructed to follow pre-recorded teacher's movements while observing both their own motions and the teacher in real-time from arbitrary viewpoints.
High-level resistance to oxidative stress in Lactococcus lactis conferred by Bacillus subtilis catalase KatE (2005)

Lactococcus lactis, a lactic acid bacterium widely used for food fermentations, is often exposed to damaging stress conditions. In particular, oxidative stress leads to DNA, protein and membrane damages that can be lethal. As L. lactis has no catalase, the impact of production of the Bacillus subtilis haem catalase KatE on its oxidative stress resistance was tested. This cytoplasmic catalase was engineered for extracellular expression in L. lactis with an optimization strategy based on fusion to the nisin-inducible promoter and a lactococcal signal peptide (SP(Usp45)). The production of KatE by L. lactis conferred an 800-fold increase in survival after 1 h exposure to 4 mM hydrogen peroxide, and a 160-fold greater survival in long-term (3 days) survival of aerated cultures in a cydA mutant, which is unable to respire. The presence of KatE protected DNA from oxidative damage and limited its degradation after long-term aeration in a cydA/recA mutant, defective in DNA repair. L. lactis is thus able to produce active catalase that can provide efficient antioxidant activity.
A Machine Learning Approach for Power Allocation in HetNets Considering QoS (2018)

There is an increase in usage of smaller cells or femtocells to improve performance and coverage of next-generation heterogeneous wireless networks (HetNets). However, the interference caused by femtocells to neighboring cells is a limiting performance factor in dense HetNets. This interference is being managed via distributed resource allocation methods. However, as the density of the network increases so does the complexity of such resource allocation methods. Yet, unplanned deployment of femtocells requires an adaptable and self-organizing algorithm to make HetNets viable. As such, we propose to use a machine learning approach based on Q-learning to solve the resource allocation problem in such complex networks. By defining each base station as an agent, a cellular network is modeled as a multi-agent network. Subsequently, cooperative Q-learning can be applied as an efficient approach to manage the resources of a multi-agent network. Furthermore, the proposed approach considers the quality of service (QoS) for each user and fairness in the network. In comparison with prior work, the proposed approach can bring more than a four-fold increase in the number of supported femtocells while using cooperative Q-learning to reduce resource allocation overhead.
Intrusion Detection for Encrypted Web Accesses (2007)

As various services are provided as web applications, attacks against web applications constitute a serious problem. Intrusion detection systems (IDSes) are one solution, however, these systems do not work effectively when the accesses are encrypted by protocols. Because the IDSes inspect the contents of a packet, it is difficult to find attacks by the current IDS. This paper presents a novel approach to anomaly detection for encrypted web accesses. This approach applies encrypted traffic analysis to intrusion detection, which analyzes contents of encrypted traffic using only data size and timing without decryption. First, the system extracts information from encrypted traffic, which is a set comprising data size and timing for each web client. Second, the accesses are distinguished based on similarity of the information and access frequencies are calculated. Finally, malicious activities are detected according to rules generated from the frequency of accesses and characteristics of HTTP traffic. The system does not extract private information or require enormous pre-operation beforehand, which are needed in conventional encrypted traffic analysis. We show that the system detects various attacks with a high degree of accuracy, adopting an actual dataset gathered at a gateway of a network and the DARPA dataset.
Distributed Full-duplex via Wireless Side Channels: Bounds and Protocols (2012)

In this paper, we study a three-node full-duplex network, where a base station is engaged in simultaneous up- and downlink communication in the same frequency band with two half-duplex mobile nodes. To reduce the impact of inter- node interference between the two mobile nodes on the system capacity, we study how an orthogonal side-channel between the two mobile nodes can be leveraged to achieve full-duplex-like multiplexing gains. We propose and characterize the achievable rates of four distributed full-duplex schemes, labeled bin-and- cancel, compress-and-cancel, estimate-and-cancel and decode- and-cancel. Of the four, bin-and-cancel is shown to achieve within 1 bit/s/Hz of the capacity region for all values of channel parameters. In contrast, the other three schemes achieve the near-optimal performance only in certain regimes of channel values. Asymptotic multiplexing gains of all proposed schemes are derived to show that the side-channel is extremely effective in regimes where inter-node interference has the highest impact.
Highly Selective H2O2‐Based Oxidation of Alkylphenols to p‐Benzoquinones Over MIL‐125 Metal–Organic Frameworks (2013)

Abstract The titanium‐based metal–organic framework MIL‐125 and its amine‐functionalized analog, MIL‐125_NH 2 , have been synthesized and characterized by elemental analysis, XRD, SEM, TEM, N 2 adsorption measurements, and spectroscopic techniques, including FTIR, Raman, and DR UV/Vis spectroscopy. Catalytic properties of MIL‐125 and MIL‐125_NH 2 were evaluated in the selective oxidation of two representative alkyl‐substituted phenols, 2,3,6‐trimethylphenol and 2,6‐di‐ tert ‐butylphenol, with the clean oxidant H 2 O 2 . With both MIL‐125 and MIL‐125_NH 2 , the selectivity toward the corresponding p ‐benzoquinones was 100 %. Samples of MIL‐125 with different sizes of crystallites (0.5, 1.5, and 5 μm) demonstrated similar reaction rates, thus indicating the absence of diffusion limitations. The efficiency of the oxidant utilization and stability of the MIL‐125 structure increased upon decreasing the amount of water in the reaction mixture. Even if the structural integrity of MIL‐125 was destroyed by the reaction medium, the metal–organic framework acted as a precursor for the highly active, selective, and recyclable catalyst. The MIL‐125‐derived materials were stable toward titanium leaching, behaved as true heterogeneous catalysts, and could easily be recovered by filtration and reused several times without the loss of the catalytic properties.
Protease-activated receptors and glycoprotein VI cooperatively drive the platelet component in thromboelastography (2023)

Our results demonstrate that standard TEG is not sensitive to platelet signaling pathways critical for integrin inside-out activation and platelet hemostatic function. Furthermore, we provide the first evidence that PARs and glycoprotein VI play redundant roles in platelet-mediated clot contraction in TEG.
Molecular cloning and nucleotide sequence of cDNA encoding the entire precursor of rat liver medium chain acyl coenzyme A dehydrogenase. (1987)

cDNA encoding the precursor of rat liver medium chain acyl-CoA dehydrogenase (EC 1.3.99.3) was cloned and sequenced. The longest cDNA insert isolated was 1866 bases in length. This cDNA encodes the entire protein of 421-amino acids including a 25-amino acid leader peptide and a 396-amino acid mature polypeptide. The identity of the medium chain acyl-CoA dehydrogenase clone was confirmed by matching the amino acid sequence predicted from the cDNA to the NH2-terminal and nine internal tryptic peptide sequences derived from pure rat liver medium chain acyl-CoA dehydrogenase. The calculated molecular masses of the precursor medium chain acyl-CoA dehydrogenase, the mature medium chain acyl-CoA dehydrogenase, and the leader peptide are 46,600, 43,700, and 2,900 daltons, respectively. The leader peptide contains five basic amino acids and only one acidic amino acid; thus, it is positively charged, overall. Cysteine residues are unevenly distributed in the mature portion of the protein; five of six are found within the NH2-terminal half of the polypeptide. Comparison of medium chain acyl-CoA dehydrogenase sequence to other flavoproteins and enzymes which act on coenzyme A ester substrates did not lead to unambiguous identification of a possible FAD-binding site nor a coenzyme A-binding domain. The sequencing of other homologous acyl-CoA dehydrogenases will be informative in this regard.
eTransform: Transforming Enterprise Data Centers by Automated Consolidation (2012)

Modern day enterprises have a large IT infrastructure comprising thousands of applications running on servers housed in tens of data centers geographically spread out. These enterprises periodically perform a transformation of their entire IT infrastructure to simplify, decrease operational costs and enable easier management. However, the large number of different kinds of applications and data centers involved and the variety of constraints make the task of data center transformation challenging. The state-of-the-art technique for performing this transformation is simplistic, often unable to account for all but the simplest of constraints. We present eTransform, a system for generating a transformation and consolidation plan for the IT infrastructure of large scale enterprises. We devise a linear programming based approach that simultaneously optimizes all the costs involved in enterprise data centers taking into account the constraints of applications groups. Our algorithm handles the various idiosyncrasies of enterprise data centers like volume discounts in pricing, wide-area network costs, traffic matrices, latency constraints, distribution of users accessing the data etc. We include a disaster recovery (DR) plan, so that eTransform, thus provides an integrated disaster recovery and consolidation plan to transform the enterprise IT infrastructure. We use eTransform to perform case studies based on real data from three different large scale enterprises. In our experiments, eTransform is able to suggest a plan to reduce the operational costs by more than 50% from the "as-is" state of these enterprise to the consolidated enterprise IT environment. Even including the DR capability, eTransform is still able to reduce the operational costs by more than 25% from the simple "as-is" state. In our experiments, eTransform is able to simultaneously optimize multiple parameters and constraints and discover solutions that are 7x cheaper than other solutions.
Stability of spiral wave reentry on curved surfaces (2002)

Reentrant spiral waves propagating on curved surfaces lying in 3D space were modeled using a finite element solution of a modified FitzHugh-Nagumo system. Under some conditions, surface topology could induce drift of nominally stationary spirals, even in the absence of heterogeneity or anisotropy. These dynamics may be important in the maintenance of reentrant arrhythmias.
High‐luminance and luminous‐efficacy mercury‐free flat fluorescent lamp (MFFL) with local‐dimming functionality (2011)

Abstract— In order to realize high‐luminance and luminous‐efficacy mercury‐free flat fluorescent lamps (MFFLs) for LCD backlighting, the phosphor profile was optimized to enlarge the surface area. The proposed uneven profile of the rear phosphor increases the effective surface area of the phosphor, resulting in a wide luminance range from 3000 to 16,788 cd/m 2 with a corresponding high luminous efficacy from 66 to 34.7 lm/W, respectively. Also, a dynamic operation method for an adaptive local‐dimming and scanning operation is proposed which can be used in a 32‐in. multi‐structured configuration having one inverter system. With the deployment of the bipolar drive scheme and dual auxiliary electrodes, a stable and selective diffuse glow discharge with high luminance is possible.
Anodic Electrodeposition of Several Metal Organic Framework Thin Films on Indium Tin Oxide Glass (2019)

We present the rapid synthesis of a series of metal–organic framework (MOF) thin films on indium tin oxide (ITO) glass. ITO was first electrodeposited with either copper or zinc microcrystalline films (Cu-ITO and Zn-ITO, respectively) from simple aqueous/ethanol salt solutions. These metallic deposits served as the metal cation source during their partial anodic dissolution and the initial nucleation sites during electrochemical MOF (EMOF) film growth. Four different EMOF films were prepared by this method. HKUST-1 and the two-dimensional (2D) cationic framework [Cu(C10H8N2)2+]Br2 (CBBr) were each grown on Cu-ITO. Zn6(OH)3(BTC)3(H20)3·7H2O (Zn-BTC, BTC = benzene tricarboxylate) and the 2D framework [Zn(BPDC)(H2O)]·H2O (Zn-BPDC, BPDC = 2,2′-bipyridine-5,5′-dicarboxylate) were each grown on Zn-ITO. Physical characterization was carried out using grazing incidence X-ray diffraction, scanning electron microscopy, and energy-dispersive X-ray spectroscopy. Our results show these films were well adhered, homogeneous, self-closing, and of relatively low surface roughness in each case. The ability to vary the dimensionality, metal node, linker, and charge of the EMOF on a conductive transparent substrate opens up a wide range of possible compositions, properties, and applications.
ACCELERATION OF THE EMERGENCE OF BACTERIAL ANTIBIOTIC RESISTANCE (2011)

We designed and fabricated a two-dimensional microfluidic device to mimic the heterogeneous environment in naturally occurring bacteria culture. We demonstrated that it is possible to fix resistance to the powerful antibiotic ciprofloxacin (Cipro) in E. coli within 10 hours through a combination of antibiotic gradients and bacterial metapopulation. Simulation based on a deterministic model shows the evolution is accelerated in a slanted fitness landscape, compared to uniformly high and uniformly low fitness landscape.
Design of Directivity Patterns with a Unique Null of Maximum Multiplicity (2015)

Differential beamforming is one of the most popular beamforming approaches, which has the great potential to form frequency-invariant directivity patterns. In this paper, we study the design of beampatterns with multiple nulls in the same direction, which is clearly different from the design of beampatterns with distinct nulls. Our contributions are as follows. First, we show how to constrain multiple nulls to the same direction and design the desired beampattern with both the traditional and robust approaches. Second, we derive an explicit form of the white noise gain (WNG) of the traditional approach as a function of the frequency, interelement spacing, and null direction, which shows that the cardioid is the optimal beampattern as far as the WNG is concerned. Third, we prove that the WNG improvement of the robust approach rarely depends on the null direction at low frequencies. Finally, considering the fact that the robust differential beamforming approach may produce a frequency-dependent beampattern while improving the WNG, we develop a weighted-norm approach that can make a good compromise between the robustness of differential beamforming with respect to white noise and the frequency-invariant beampattern. The performance of the developed approach is verified by simulations.
Soft-tissue imaging with C-arm cone-beam CT using statistical reconstruction (2014)

The potential for statistical image reconstruction methods such as penalized-likelihood (PL) to improve C-arm cone-beam CT (CBCT) soft-tissue visualization for intraoperative imaging over conventional filtered backprojection (FBP) is assessed in this work by making a fair comparison in relation to soft-tissue performance. A prototype mobile C-arm was used to scan anthropomorphic head and abdomen phantoms as well as a cadaveric torso at doses substantially lower than typical values in diagnostic CT, and the effects of dose reduction via tube current reduction and sparse sampling were also compared. Matched spatial resolution between PL and FBP was determined by the edge spread function of low-contrast (∼ 40-80 HU) spheres in the phantoms, which were representative of soft-tissue imaging tasks. PL using the non-quadratic Huber penalty was found to substantially reduce noise relative to FBP, especially at lower spatial resolution where PL provides a contrast-to-noise ratio increase up to 1.4-2.2 × over FBP at 50% dose reduction across all objects. Comparison of sampling strategies indicates that soft-tissue imaging benefits from fully sampled acquisitions at dose above ∼ 1.7 mGy and benefits from 50% sparsity at dose below ∼ 1.0 mGy. Therefore, an appropriate sampling strategy along with the improved low-contrast visualization offered by statistical reconstruction demonstrates the potential for extending intraoperative C-arm CBCT to applications in soft-tissue interventions in neurosurgery as well as thoracic and abdominal surgeries by overcoming conventional tradeoffs in noise, spatial resolution, and dose.
Supplementary Table 1 from Temporal Dissection of Tumorigenesis in Primary Cancers (2023)

Supplementary Table 1 from Temporal Dissection of Tumorigenesis in Primary Cancers
Millimeter-Wave Dielectric Properties of Highly Refractive Single Crystals Characterized by Waveguide Cavity Resonance (2019)

This paper reports precision measurements of the electromagnetic permittivity of five highly refractive, single-crystal materials, SrTiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , KTaO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , rutile TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , LiTaO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , and LiNbO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , using a single, well-controlled, frequency-scalable procedure over the frequency ranges 25-110 and 140-220 GHz. Real permittivity values were highly consistent for different samples measured across multiple frequency bands. For SrTiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , KTaO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , and TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , real permittivities were more consistent with lower frequency values than typically reported in the millimeter-wave region of the spectrum. Real permittivities of LiTaO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> and LiNbO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> agreed with most reported data. The intrinsic dielectric loss of SrTiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , KTaO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , and the extraordinary axis of rutile TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> was also characterized over the ranges 25-110 and 140-220 GHz, and intrinsic loss per unit frequency was found to be consistent with values measured at other frequencies by dielectric resonators and quasi-optical techniques.
Synthesis and Antiviral Evaluation of 2′,3′-β-C-Disubstituted Nucleoside Analogue ProTides to Test a Conformational Model of Potency Against Hepatitis C (2022)

Abstract An analysis of nucleoside active metabolite potencies against Hepatitis C virus (HCV) versus their parent ground-state energetic conformational bias as calculated by density functional theory suggested that nucleotides with a small difference between their antipodal energies are more likely to have potent antiviral activity compared to those with larger energetic differences. This energetic conformational bias was thought to be manipulated with substitutions along the ­ribofuranose ring. From 2′-C-methyluridine, a representative nucleoside with fair anti-HCV activity, two C3′ modifications in particular (ethyne and methyl) showed contrasting antipodal biases relative to each other while originating from a common synthetic intermediate, allowing a test of reasonable extremes of the computational model with a divergent nine-step synthesis. Antiviral activity of the compounds contradicted that suggested by the model, indicating a need for further refinement with additional biostructural considerations.