gebhart/patrepeval huggingface dataset:
AN IMAGE DENOISING METHOD BASED ON WAVELET TRANSFORM (2002)

In this paper, a new image denoising method based on wavelet transform is proposed. It includes horizontal, vertical and diagonal-directions of 1D and 2D wavelet transform denoising process. It can reserve the directional edge of 1D wavelet transform denoising, and eliminate the blurred edge of 2D wavelet transform denoising. The results show that this method is effective both in reserving the edge and in removing noise.
Spontaneous emission enhancement of colloidal perovskite nanocrystals by a photonic crystal cavity (2017)

We demonstrate coupling of lead halide perovskite nanocrystals to a nanophotonic cavity. From photoluminescence measurements, we observe a factor of 10 enhancement in brightness from the cavity mode emission. We perform room temperature time-resolved lifetime measurements that demonstrate an average spontaneous emission rate enhancement of 2.9 for perovskite nanocrystals within the cavity as compared to those located on the unpatterned surfaces. Our method provides a way towards realizing efficient light emitters and low-threshold lasers, as well as fast nonlinear optical devices, using solution processable materials.
Bone induction by porous glass ceramic made from Bioglass® (45S5) (2001)

Porous glass ceramic, which was prepared from Bioglass® powder (45S5, U.S. Biomaterials) by foaming with diluted H2O2 solution and sintering at 1000 °C for 2 h, was implanted as cylinders (5 mm in diameter and 6 mm in length) in thigh muscles of dogs for 3 months. Histological observation was made on thin un-decalcified sections. Bone formation was histologically found in pores of all implants (X16) retrieved from 16 dogs. The bone tissue was also identified with backscattered scanning electron microscopy observation (BSE) and energy dispersive X-ray microanalysis (EDX). This is the first report of bone induction in soft tissues of animals by glass ceramic that has long been recognized as a bioactive (osteoconductive) biomaterial. The present results justify the impetus to investigate the osteoinductivity of calcium phosphate-based biomaterials, to study the mechanism of bone induction (osteoinduction) by calcium phosphate-based biomaterials, to develop osteoinductive calcium phosphate-based biomaterials, and to examine the relation between osteoinduction and osteoconduction. © 2001 John Wiley & Sons, Inc. J Biomed Mater Res (Appl Biomater) 58: 270–276, 2001
Molecular Origin of Electric Double-Layer Capacitance at Multilayer Graphene Edges (2016)

Multilayer graphenes have been widely used as active materials for electric double-layer capacitors (EDLCs), where their numerous edges are demonstrated to play a crucial role in charge storage. In this work, the interfacial structure and capacitive behaviors of multilayer graphene edges with representative interlayer spacing are studied via molecular dynamics (MD) simulations. Compared with planar graphite surfaces, edges can achieve a 2-fold increase in the specific capacitance at a wider interlayer spacing of ∼5.0 Å. Unusually, the molecular origins for achieved charge storage are predominantly attributed to the structural evolutions of solvents occurring in the double layer, going beyond the traditional views of regulating the capacitance by ion adsorption/separation. Specifically, diverse ionic distributions exhibit similar screening ability and EDLC thickness, while water molecules can counterbalance the interfacial electric fields more effectively at edge site. The as-obtained findings will be instructive in designing graphene-based EDLCs for advanced capacitive performances.
FePd, FePt, and CoPt alloy epitaxial thin films with flat surface grown on MgO(111) substrate (2014)

FePd, FePt, and CoPt alloy epitaxial films of 40 nm thickness are prepared on MgO(111) singlecrystal substrates by employing two different methods. One is a one-step method consisting of hightemperature deposition at 600 °C and the other is a two-step method consisting of low-temperature deposition at 200 °C followed by annealing at 600 °C. Although the preparation method is different, similar final crystal structures are realized for all the film materials. FePd and FePt alloy films grow on the substrates with six L10(111) variants, whose c-axes are about 35° canted from the substrate surface and rotated around the film normal by 60° each other. The order degrees of FePd and FePt films prepared by one- and two-step methods, (Sone-step, Stwo-step), are estimated to be (0.25, 0.33) and (0.08, 0.15), respectively. On the contrary, L10 ordered phase formation is not recognized for CoPt alloy films. The films prepared by one-step method have rough surfaces surrounded by side facets, whereas the films prepared by two-step method have very flat surfaces with the arithmetical mean roughness of 0.3 nm. The two-step method is useful for preparation of L10 ordered films with flat surface.
Deep Neural Network based Secured Control of Flying Vehicle in Urban Environment (2022)

Aerial transport for daily inter- and intra-urban passenger mobility has been a human dream for decades ago. Now, the dream is near to be realized after the great technological advances achieved recently. As urban populations' size increases, traffic congestion and air pollution remain major threats to economic growth. However, questions concerning safe and secure autonomous flying vehicles remain to be answered, especially in a highly dynamic environment. This research paper presents a Deep Neural Network (DNN) algorithm as an additional component that avoids obstacles and increases the tracking efficiency of Cascaded Proportional Integral Derivative with Feed Forward (PID+FF) controller for flying vehicles. In the current paper, we introduce KaNET: a convolution neural network designed to safely drive and improve tracking performance. Simultaneously, cascaded PID+FF algorithms are applied to regulate the atti-tude/altitude of a flying vehicle. To ensure a safe and secure flight in a dynamic environment, the proposed KaNET generates two outputs for each input image. The first output is the probability of a collision allowing the flying vehicle to recognize and react quickly to hazardous situations. The second output represents a steering angle that helps the vehicle to keep flying and avoiding obstacles. The cascaded PID+ FF is used to control and maintain the desired position and orientation of the flying vehicle. Results have shown that the proposed approach improves tracking accuracy and avoids obstacles in highly dynamic environments.
Behaviors Of Plasma-induced Pre-tunneling Leakage Current In MOS Capacitor (1997)

A new technique to evaluate the plasma-induced gate oxide damage is proposed. The pre-tunneling leakage current in a MOS capacitor appears after the plasma process, and the magnitude has a close relation with the degree of oxide damage. By measuring this leakage current, a continuous change of plasma damage can be detected.
Automatic Delineation of the Myocardial Wall From CT Images Via Shape Segmentation and Variational Region Growing (2013)

Prognosis and diagnosis of cardiac diseases frequently require quantitative evaluation of the ventricle volume, mass, and ejection fraction. The delineation of the myocardial wall is involved in all of these evaluations, which is a challenging task due to large variations in myocardial shapes and image quality. In this paper, we present an automatic method for extracting the myocardial wall of the left and right ventricles from cardiac CT images. In the method, the left and right ventricles are located sequentially, in which each ventricle is detected by first identifying the endocardium and then segmenting the epicardium. To this end, the endocardium is localized by utilizing its geometric features obtained on-line from a CT image. After that, a variational region-growing model is employed to extract the epicardium of the ventricles. In particular, the location of the endocardium of the left ventricle is determined via using an active contour model on the blood-pool surface. To localize the right ventricle, the active contour model is applied on a heart surface extracted based on the left ventricle segmentation result. The robustness and accuracy of the proposed approach is demonstrated by experimental results from 33 human and 12 pig CT images.
Mutation of cysteine 111 in Dopa decarboxylase leads to active site perturbation (1997)

Cysteine 111 in Dopa decarboxylase (DDC) has been replaced by alanine or serine by site-directed mutagenesis. Compared to the wild-type enzyme, the resultant C111A and C111S mutant enzymes exhibit Kcat values of about 50% and 15%, respectively, at pH 6.8, while the K(m) values remain relatively unaltered for L-3,4-dihydroxyphenylalanine (L-Dopa) and L-5-hydroxytryptophan (L-5-HTP). While a significant decrease of the 280 nm optically active band present in the wild type is observed in mutant DDCs, their visible co-enzyme absorption and CD spectra are similar to those of the wild type. With respect to the wild type, the Cys-111-->Ala mutant displays a reduced affinity for pyridoxal 5'-phosphate (PLP), slower kinetics of reconstitution to holoenzyme, a decreased ability to anchor the external aldimine formed between D-Dopa and the bound co-enzyme, and a decreased efficiency of energy transfer between tryptophan residue(s) and reduced PLP. Values of pKa and pKb for the groups involved in catalysis were determined for the wild-type and the C111A mutant enzymes. The mutant showed a decrease in both pK values by about 1 pH unit, resulting in a shift of the pH of the maximum velocity from 7.2 (wild-type) to 6.2 (mutant). This change in maximum velocity is mirrored by a similar shift in the spectrophotometrically determined pK value of the 420-->390 nm transition of the external aldimine. These results demonstrate that the sulfhydryl group of Cys-111 is catalytically nonessential and provide strong support for previous suggestion that this residue is located at or near the PLP binding site (Dominici P, Maras B, Mei G, Borri Voltattorni C. 1991. Eur J Biochem 201:393-397). Moreover, our findings provide evidence that Cys-111 has a structural role in PLP binding and suggest that this residue is required for maintenance of proper active-site conformation.
Light-based 3D printing of functional polydimethylsiloxane- based microfluidic chips (2021)

The objective of the work is to fabricate and functionalize 3D printed PDMS-based microfluidic chips through digital light processing DLP-3D printing.
Ku Binds Telomeric DNA in Vitro (1999)

Ku is a heterodimeric protein with high binding affinity for ends, nicks, and gaps in double-stranded DNA. Both in mammalian cells and in budding yeast, Ku plays a role in nonhomologous end joining in the double strand break repair pathway. However, Ku has a more significant role in DNA repair in mammalian cells compared with yeast, in which a homology-dependent pathway is the predominant one. Recently Ku has been shown to be a likely component of the telomeric complex in yeast, suggesting the possibility of a similar role for Ku at mammalian telomeres. However, long single-stranded G-rich overhangs are continuously present at mammalian but not at yeast telomeres. These overhangs have the potential to fold in vitro into G-G base-paired conformations, such as G-quartets, that might prevent Ku from recognizing telomeric ends and thus offer a mechanism to sequester the telomere from the prevalent double strand break repair pathway in mammals. We show here that Ku binds to mammalian telomeric DNA ends in vitro and that G-quartet conformations are unable to prevent Ku from binding with high affinity to the DNA. Our results indicate that the DNA binding characteristics of Ku are consistent with its direct interaction with telomeric DNA in mammalian cells and its proposed role as a telomere end factor.
Comparative Analysis of Flow Cytometric Techniques in Assessment of ZAP-70 Expression in Relation to lgV H Mutational Status in Chronic Lymphocytic Leukemia (2007)

We compared 1 subjective and 5 objective flow cytometric methods to evaluate ζ-associated protein (ZAP-70) expression in relation to immunoglobulin heavy-chain variable-region (IgVH) gene mutational status in 154 samples from 125 patients with chronic lymphocytic leukemia (CLL). ZAP-70 expression determined by all methods used correlated with IgVH gene mutational status, but none of them demonstrated high concordance rates. Of the objective methods, ZAP-70 staining determined as a ratio of molecules of equivalent soluble fluorochrome intensity in CLL cells to that in normal B cells (ZAP-70+ staining in IgVH germline cases, 59%; ZAP-70– in IgVH mutated cases, 75%) or T cells (ZAP-70+ in IgVH germline cases, 66%; ZAP-70– in IgVH mutated cases, 57%) provides the best combination for assigning ZAP-70+ status to IgVH germline and ZAP-70– status to IgVH mutated cases. The subjective method based on ZAP-70 expression in natural killer/T cells gave a similar result, but reproducibility between laboratories may be difficult. Further studies on ZAP-70 expression in relation to clinical parameters may address whether ZAP-70 is an independent prognostic marker for CLL.
Targeting Neuroinflammation to Treat Alzheimer’s Disease (2017)

Over the past few decades, research on Alzheimer's disease (AD) has focused on pathomechanisms linked to two of the major pathological hallmarks of extracellular deposition of beta-amyloid peptides and intra-neuronal formation of neurofibrils. Recently, a third disease component, the neuroinflammatory reaction mediated by cerebral innate immune cells, has entered the spotlight, prompted by findings from genetic, pre-clinical, and clinical studies. Various proteins that arise during neurodegeneration, including beta-amyloid, tau, heat shock proteins, and chromogranin, among others, act as danger-associated molecular patterns, that-upon engagement of pattern recognition receptors-induce inflammatory signaling pathways and ultimately lead to the production and release of immune mediators. These may have beneficial effects but ultimately compromise neuronal function and cause cell death. The current review, assembled by participants of the Chiclana Summer School on Neuroinflammation 2016, provides an overview of our current understanding of AD-related immune processes. We describe the principal cellular and molecular players in inflammation as they pertain to AD, examine modifying factors, and discuss potential future therapeutic targets.
‘Setting down experiments of the sciences’ (2021)

Abstract Chapter 2: ‘Setting down experiments of the sciences: printing and the works of Thomas Willis’ starts with a brief account of Willis as a reader, identifying c.100 authors, ancient and contemporary, whom he cites in the treatises. Within a general account of the book trade in the mid-seventeenth century, the tensions relating to censorship and licensing for potential authors are described. Willis’s first books were produced by individuals closely associated with publications of the Royal Society. It is explained that after the fire of London, publication moved to Oxford under the influence of his brother-in-law, Samuel Fell. The chapter provides brief biographies of thirty-four members of the book trade involved in publishing Willis’s books in England. This is followed by a similar approach to description of the book trade in continental Europe where editions of Thomas Willis’s books were published by twenty-three individuals working in the Netherlands, France, Switzerland, and Italy. {149 words}
Facile Synthesis of Model Indazolo[2,1-c][1,3,4]benzotriazepine-5,13-diones (2008)

In basic media, 2-aminobenzoic acids (5) react with 2-[N-(1-carboxyphenyl)]hydrazonoyl chlorides (6, 7) (precursors of the reactive nitrile imine 1,3-dipolar species) to afford good yields of the corresponding 2-[N'-(1-carboxyphenyl-2-amino)hydrazino]benzoic acids (8a-d, 9a).The latter acyclic adducts, in the presence of 1,1'-carbonyldiimidazole (CDI), undergo two consecutive lactamizations involving both activated carboxyl groups and the suitably located hydrazino-NH partners, to deliver the respective indazolo[2,1-c]-[1,3,4]benzotriazepin-5,13-diones (10a-d, 11a).Structural assignments for these novel tetracyclic products are based on analytical and spectral (IR, MS, NMR) data, and confirmed by single crystal X-ray structure determination for 10a.
Human Powered Submarine 2013 (2013)

The design cycle began with a very new team with only few senior members with some experience from the year prior. It was decided early that our goals as a team were to apply our knowledge gained from the classroom into design exercises with a heavy focus on research. Much of the effort was spent early on developing a web site, www.uw-hps.com, and a sales brochure for use with fundraising and public awareness. At the same time other members were busy developing designs and formulating the research to be conducted.
Ultrafast Magnetism Dynamics Measure Using Tabletop Ultrafast EUV Sources (2013)

In our work to date, we made two significant advances. First we demonstrated element-selective demagnetization dynamics for the first time, with a record time resolution for x-ray probing of 55 fs. Second, in new work, we were able to probe the timescale of the exchange interaction in magnetic materials, also for the first time. Our measurements were made using the transverse magneto-optic Kerr effect (T-MOKE) geometry, since the reflectivity of a magnetic material changes with the direction of the magnetization vector of a surface. In our experiment, we periodically reversed the magnetization direction of a grating structure made of Permalloy (Ni80Fe20) using an external magnetic field. To achieve maximum contrast, we used HHG light spanning the M-shell (3p) absorption edges of Fe and Ni. Our characterization of the static magnetization of a Permalloy sample shows high magnetic asymmetry at photon energies just above and below the absorption edges at 55 eV and 65 eV, respectively. This result is in excellent agreement with measurements done on the same using a synchrotron source.
One-Pot Synthesis of VOHPO<sub>4</sub>·0.5H<sub>2</sub>O with High Growth of the (001) Plane:  An Important Catalyst Precursor of (VO)<sub>2</sub>P<sub>2</sub>O<sub>7</sub> (1997)

VOHPO4·0.5H2O, an important catalyst precursor of (VO)2P2O7, was synthesized at 473 K by using V metal not only for a reducing agent of V2O5 but also for a V source. The resulting VOHPO4·0.5H2O showed a high growth of (001) plane, and calcination in a N2 atmosphere resulted in the formation of (VO)2P2O7.
Dynorphin Promotes Abnormal Pain and Spinal Opioid Antinociceptive Tolerance (2000)

The nonopioid actions of spinal dynorphin may promote aspects of abnormal pain after nerve injury. Mechanistic similarities have been suggested between opioid tolerance and neuropathic pain. Here, the hypothesis that spinal dynorphin might mediate effects of sustained spinal opioids was explored. Possible abnormal pain and spinal antinociceptive tolerance were evaluated after intrathecal administration of [D-Ala(2), N-Me-Phe(4), Gly-ol(5)]enkephalin (DAMGO), an opioid mu agonist. Rats infused with DAMGO, but not saline, demonstrated tactile allodynia and thermal hyperalgesia of the hindpaws (during the DAMGO infusion) and a decrease in antinociceptive potency and efficacy of spinal opioids (tolerance), signs also characteristic of nerve injury. Spinal DAMGO elicited an increase in lumbar dynorphin content and a decrease in the mu receptor immunoreactivity in the spinal dorsal horn, signs also seen in the postnerve-injury state. Intrathecal administration of dynorphin A(1-17) antiserum blocked tactile allodynia and reversed thermal hyperalgesia to above baseline levels (i.e., antinociception). Spinal dynorphin antiserum, but not control serum, also reestablished the antinociceptive potency and efficacy of spinal morphine. Neither dynorphin antiserum nor control serum administration altered baseline non-noxious or noxious thresholds or affected the intrathecal morphine antinociceptive response in saline-infused rats. These data suggest that spinal dynorphin promotes abnormal pain and acts to reduce the antinociceptive efficacy of spinal opioids (i.e., tolerance). The data also identify a possible mechanism for previously unexplained clinical observations and offer a novel approach for the development of strategies that could improve the long-term use of opioids for pain.
Research highlights: cell separation at the bench and beyond (2014)

We highlight recent progress in applying micro- and nanotechnology enabled cell separations to life sciences and clinical use. Microfluidic systems operate on a scale that matches that of cells (10-100 μm) and therefore allow interfacing and separations that are sensitive at this scale. Given the corresponding dimensions, it is not surprising that a wide array of microfluidic cell separation technologies have been developed using hydrodynamic, electrical, magnetic and optical forces, and have been applied to a range of biological and clinical problems in sample preparation. Passive separation approaches have distinct advantages for point of care applications or when downstream cell-based therapies are envisioned. We highlight a recent approach that allows for passive hydrodynamic filtering of cells over almost two orders of magnitude in flow conditions, which allowed the researchers to interface with a standard manual pipettor, creating a "microfluidic pipette tip". In a second work, passive separation by size yields distinct populations of mesenchymal stem cells that can be used therapeutically. The researchers report on other biophysical separations that would be expected to refine these cell populations further for the most efficacious cell-based therapies. In an intriguing twist, we highlight a creative idea in which stem cell populations could potentially also be extracted from a patient with less invasive surgeries, performing the separation using magnetic nanoparticles in vivo without bulk tissue disruption. New cell separation technologies will continue to be demonstrated, however, a major research thrust appears to be now developing these technologies to address unique application niches in point-of-care sample preparation for research and diagnostics or cell-based therapies.
Nano-granular texture of cement hydrates (2017)

Mechanical behavior of concrete crucially depends on cement hydrates, the “glue” of cement. The design of high performance and more environmentally friendly cements demands a deeper understanding of the formation of the multiscale structure of cement hydrates, when they precipitate and densify. We investigate the precipitation and setting of nano-grains of cement hydrates using a combination of Monte Carlo and Molecular Dynamics numerical simulations and study their texture from nano up to the micron scale. We characterize the texture of cement hydrates using the local volume fraction distribution, the pore size distribution, the scattering intensity and the chord length distribution and we compare them with experiments. Our nano-granular model provides cement structure with realistic texture and mechanics and can be further used to investigate degradation mechanisms.
Draft Genome Sequence of the Biofuel-Relevant Microalga Desmodesmus armatus (2020)

A draft genome of 906 scaffolds of 115.8 Mb was assembled for <i>Desmodesmus armatus</i>, a diploid, lipid- and storage carbohydrate-accumulating microalga proven relevant for large-scale, outdoor cultivation, and serves as a model alga platform for improving photosynthetic efficiency and carbon assimilation for next-generation bioenergy production.
Hybrid Silicon Evanescent Photonic Integrated Circuit Technology (2007)

The hybrid silicon evanescent device platform utilizes III -V gain materials bonded to passive silicon waveguides. In this paper, we discuss this device platform, and present hybrid silicon evanescent laser and amplifier device results.