gebhart/patrepeval huggingface dataset:
A comprehensive library of fluorescent constructs of SARS-CoV-2 proteins and their initial characterization in different cell types (2020)

Comprehensive libraries of plasmids for SARS-CoV-2 proteins with various tags (e.g. Strep, HA, Turbo) are now available. They enable the identification of numerous potential protein-protein interactions between the SARS-CoV-2 virus and host proteins. To facilitate further cellular investigations, notably by imaging techniques, we present here a large library of SARS CoV-2 protein constructs fused with green and red fluorescent proteins and their initial characterization in various human cell lines including lung epithelial cell models (A549, BEAS-2B), as well as in budding yeast. The localization of a few SARS-CoV-2 proteins matches their proposed interactions with host proteins. These include the localization of Nsp13 to the centrosome, Orf3a to late endosomes, and Orf9b to mitochondria.
Isolation and structure of a novel charged member of the red–pigment-concentrating hormone-adipokinetic hormone family of peptides isolated from the corpora cardiaca of the blowfly <i>Phormia terraenovae</i> (Diptera) (1990)

A hypertrehalosaemic neuropeptide from the corpora cardiaca of the blowfly Phormia terraenovae has been isolated by reversed-phase h.p.l.c., and its primary structure was determined by pulsed-liquid phase sequencing employing Edman chemistry after enzymically deblocking the N-terminal pyroglutamate residue. The C-terminus was also blocked, as indicated by the lack of digestion when the peptide was incubated with carboxypeptidase A. The octapeptide has the sequence pGlu-Leu-Thr-Phe-Ser-Pro-Asp-Trp-NH2 and is clearly defined as a novel member of the RPCH/AKH (red-pigment-concentrating hormone/adipokinetic hormone) family of peptides. It is the first charged member of this family to be found. The synthetic peptide causes an increase in the haemolymph carbohydrate concentration in a dose-dependent fashion in blowflies and therefore is named 'Phormia terraenovae hypertrehalosaemic hormone' (Pht-HrTH). In addition, receptors in the fat-body of the American cockroach (Periplaneta americana) recognize the peptide, resulting in carbohydrate elevation in the blood. However, fat-body receptors of the migratory locust (Locusta migratoria) do not recognize this charged molecule, and thus no lipid mobilization is observed in this species.
Efficient parametric frequency conversion in lithium niobate nanophotonic chips (2019)

Chip-integrated nonlinear photonics holds the key for advanced optical information processing with superior performance and novel functionalities. Here, we present an optimally mode-matched, periodically poled lithium niobate nanowaveguide for efficient parametric frequency conversions on chip. Using a 4-mm nanowaveguide with subwavelength mode confinement, we demonstrate second harmonic generation with efficiency over 2200% W
−1
c
m
−2, and broadband difference frequency generation over a 4.3-THz spectral span. These allow us to generate correlated photon pairs over multiple frequency channels via spontaneous parametric down conversion, all in their fundamental spatial modes, with a coincidence to accidental ratio as high as 600. The high efficiency and dense integrability of the present chip devices may pave a viable route to scalable nonlinear applications in both classical and quantum domains.
A Simple Linear Technique for Measuring the Spectral Phase of Complicated Pulses with High Resolution (2006)

We present a simplified, alignment-free spectral interferometer using optical fibers. Using spatial fringes the spectral resolution is improved and time-domain filtering is unnecessary. To demonstrate this technique, we measure temporal chirp and a 14-ps double-pulse.
Mechanism of the Covalent Inhibition of Human Transmembrane Protease Serine 2 as an Original Antiviral Strategy (2023)

Abstract The Transmembrane Protease Serine 2 (TMPRSS2) is a human enzyme which is involved in the maturation and post-translation of different proteins. In addition of being overexpressed in cancer cells, TMPRSS2 plays a further fundamental role in favoring viral infections by allowing the fusion of the virus envelope and the cellular membrane, notably in SARS-CoV-2. In this contribution we resort to multiscale molecular modeling to unravel the structural and dynamical features of TMPRSS2 and its interaction with a model lipid bilayer. Furthermore, we shed light into the mechanism of action of a potential inhibitor (Nafamostat), determining the free-energy profile associated with the inhibition reaction, and showing the facile poisoning of the enzyme. Our study, while providing the first atomistically resolved mechanism of TMPRSS2 inhibition, is also fundamental in furnishing a solid framework for further rational design targeting transmembrane proteases in a host-directed antiviral strategy. TOC GRAPHICS
Modeling of High-Performance p-Type III–V Heterojunction Tunnel FETs (2010)

The impact of band lineup and source doping concentration on the performance of heterojunction tunnel FETs (H-TFETs) with type-II heterointerface is investigated by simulations. Exemplarily, H-TFETs based on InAs/Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> Ga <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-x</sub> Sb heterostructures are studied. Varying the Al content x, the band lineup can be adjusted from staggered to broken. We find that a staggered band lineup and a medium source doping concentration yield the best ON/OFF-state performance in terms of an inverse subthreshold slope that is smaller than 60 mV/dec and f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> values in the terahertz range.
Prognostic Factors for Survival in Patients with High-Grade Meningioma and Recurrence-Risk Stratification for Application of Radiotherapy (2014)

We propose recurrence-risk stratification for postoperative HGM patients using clinically available factors. Our results suggest that the prognosis for patients with high-risk HGMs is dismal, whereas HGM patients belonging to the low-risk group could have favorable prognoses. This stratification provides us with the criteria necessary to determine whether to apply adjuvant radiotherapy to postoperative HGM patients, and to also help identify potentially curable HGMs without adjuvant radiotherapy.
LSD-based 3D printing of alumina ceramics (2017)

An improved method of powder 3D printing leading to dense ceramic parts is presented. The application of powder-based binder jetting 3D printing technologies to technical ceramics is generally limited by the low packing density of the powder and by the need to use a flowable powder. With layer-wise slurry deposition, it is, however, possible to deposit powder beds with high particle packing and furthermore using submicron powders. This method was combined with the binder jetting technology to develop a novel process, named LSD-print. By means of LSD-print, a submicron Al2O3 powder could be processed to produce samples with a density comparable with that of standard pressed samples, both in the green state and after sintering.
The biochemistry of the metabolic poison propionate 3‐nitronate and its conjugate acid, 3‐nitropropionate (2013)

3-Nitropropionate (3-NPA) is a nitro aliphatic compound found in numerous plants and fungi. The nitro compound exists in equilibrium with its conjugate base, propionate 3-nitronate (P3N) and has a pKa approaching the physiological range of 9.1. Since 1920, more than 30 species of plant and fungi have been identified as producing 3-NPA as a means of defense from herbivores. Glycoside products containing moieties of 3-NPA found in parts of the plants most accessible to herbivores can be easily hydrolyzed to free 3-NPA by bacterial enzymes in the gut of animals. In addition to providing a defense mechanism, the nitro compound is an intermediate in the nitrification process of leguminous plants. The synthesis of 3-NPA in these plants and fungi is poorly understood. P3N, which readily forms from 3-NPA at physiological pH, is a potent inhibitor of the key enzyme succinate dehydrogenase in the Krebs cycle and electron transport chain. Inhibition of succinate dehydrogenase in humans and livestock causes neurotoxicity and in some cases death. Several enzymes catalyze the oxidation of 3-NPA or P3N; all contain a noncovalently bound flavin cofactor and are found in the organisms that produce 3-NPA. With k(cat)/K(m) values of >10(6) M(-1) s(-1), nitronate monooxygenases can quickly and efficiently oxidize P3N to malonic semialdehyde as a means of protecting the organism from killing itself. Although it was discovered almost a century ago, the biochemistry and physiological role of 3-NPA/P3N are just emerging.
Design and implementation of a WirelessHART simulator for process control (2010)

The WirelessHART protocol is one of the most promising standards for wireless communication in industrial automation plant systems. Control processes and the communication between them must be scheduled appropriately, such that the I/O data is correlated. In large networks, selecting a suitable schedule is a long and error prone exercise. This research report illustrates the design and realization of a WirelessHART system development tool, meant to support the design decisions in communication and processing scheduling. A simulator of such a system is built, to preview the resulting system performance. The purpose of designing the simulator is to support a more efficient usage of the timing specifications, and to offer collision free communication between network devices. The tool allows the development of the system starting from control loop levels, and provides information of possible errors in dataflow dependencies and network access conflicts.
Single step UV-photolithography fabrication of SU-8 honeycombs with microchannels for cells positioning on silicon oxide-based nanopillars (2014)

This paper reports a novel technique to realize honeycomb arrangements of cell containers interconnected by microchannels using SU-8, a commonly used epoxy-based negative photoresist. These structures are fabricated using a single UV-photolithography exposure. With optimized process parameters, microchannels of various aspect ratios are produced. The cell containers and microchannels are used for the organization of axonal growth between neurons. Each container is centered on a nanopillar array promoting cell positioning. The proof of concept is given by the successful growth of interconnected PC12 cells. About 2-µm-high and 500-nm-wide silicon oxide-based nanopillars are produced by deep reactive ion etching using a photoresist mask. They are passivated by a 10-nm-thick silicon nitride layer. The resulting surface is biocompatible. The nanopillar arrays define areas for neurite and cell adhesion, while appropriately enhanced individual nanopillars can later be used for the recording of intracellular potentials. Next, the honeycomb structures are fabricated by a technique making use of a single photolithographic mask, a single SU-8 layer and standard equipment for stepper-based, optical projection lithography. Tuning the focus depth to negative values allows us to focus the reticle in the upper part of the SU-8 film, leading to an UV exposure imbalance between its upper and lower parts. As a consequence, pairs of neighboring SU-8 columns are connected in their upper parts by arches and separated in their lower parts by microchannels with aspect ratios depending on the column design parameters. Achieved microchannels widths range from 3 to 10 µm, while lengths extend from 5 to 30 µm for an SU-8 resist film thickness of 50 µm. After oxygen plasma treatment, PC12 cells in solution were cultured on the chip during one week. Cells settled on the whole chip and grew neurites through the SU-8 microchannels, thus setting up interconnections between all cell containers.
THE $A^{1} \Sigma^{+} - X^{1} \Sigma^{+}$ AND $A^{\prime 1}\Pi - X^{1} \Sigma^{+}$ CHEMILUMINESCENCE SPECTRA OF SrO FROM A FOURIER TRANSFORM FROM SPECTROMETER (2000)

The $A^{1} \\Sigma^{+} - X^{1} \\Sigma^{+}$ and $A^{\\prime 1}\\Pi - X^{1} \\Sigma^{+}$ spectra of SrO were observed in the range of 3,900 to $13,600 cm^{-1}$ at a resolution of about $0.03 cm^{-1}$. The SrO chemiluminescence was produced in a Broida-type oven from the $Sr + N_{2}O$ reaction and detected with a Fourier transform, spectrometer. A total of 75 bands from $^{88}SrO, \\;^{87}SrO$ and $^{86}SrO$ were measured for the A-X transition, and vibrational levels of the ground state were analyzed up to $v^{\\prime\\prime} = 12$. Over 10.000 rovibrational lines from the A-X transition were fitted to obtain significantly improved spectral constants of the ground state. Strong perturbations were observed in the A state. The $A^{\\prime}-X$ infrared emission spectrum was also analyzed. A set of Dunham parameters for the $A^{\\prime}$ state was obtained through the fitting of the data.
Caspase-independent cell death in AML: caspase inhibition in vitro with pan-caspase inhibitors or in vivo by XIAP or Survivin does not affect cell survival or prognosis (2003)

Survivin and XIAP, members of the protein family known as the inhibitors of apoptosis, interfere with the activation of caspases, called the "cell death executioners." We examined Survivin (n = 116) and XIAP (n = 172) expression in primary acute myeloid leukemia (AML) blasts and assessed the impact of their expression on prognosis. They were detected in all samples analyzed. However, no correlation was observed with cytogenetics, remission attainment, or overall survival of patients with AML. To investigate the importance of caspases in chemotherapy-induced apoptosis in AML, we treated OCI-AML3 cells with Ara-C, doxorubicin, vincristine, and paclitaxel, which induced caspase cleavage and apoptosis. Blocking of caspase activation by pan-caspase inhibitor abolished poly(adenosine diphosphate [ADP]-ribose) polymerase cleavage and DNA fragmentation but did not prevent chemotherapy-induced cell death and did not inhibit, or only partially inhibited, mitochondrial release of cytochrome c, Smac, apoptosis-inducing factor (AIF), or loss of mitochondrial membrane potential. Caspase inhibition also did not protect AML blasts from chemotherapy-induced cell death in vitro. These results suggest that expression levels of Survivin or XIAP have no prognostic impact in AML patients. Although anticancer drugs induced caspase cleavage and apoptosis, cell killing was caspase independent. This may partially explain the lack of prognostic impact of XIAP and Survivin and may suggest caspase-independent mechanisms of cell death in AML.
A Feeding Network With Collinearly Centered Longitudinal Coupling Slots for a Rectangular Parallel-Plate Slot Array Antenna (2023)

This article proposes a novel feeding network with collinearly centered longitudinal coupling slots for uniform excitation of rectangular parallel-plate slot array antennas. Compared to conventional coupling slots arrangement solutions, longitudinal slots along the centerline of the waveguide on the broad wall are employed for minimizing the vibration of field distribution in the parallel plates. Coupling walls are inserted in the waveguide to produce asymmetry for an appropriate excitation of each slot. The arrayed coupling slots are designed in HFSS, manufactured, and tested experimentally. The measured results show a directivity of 37.1 dBi and 87.2% aperture efficiency at 9.65 GHz with a reflection level of less than −16 dB. The novel feeding waveguide realizes a significant 1.2 dB directivity and 21% aperture efficiency enhancement compared to the traditional feed with inclined coupling slots.
A new design of cemented stem using functionally graded materials (FGM) (2014)

One of the most frequent complications of total hip replacement (THR) is aseptic loosening of femoral component which is primarily due to changes of post-operative stress distribution pattern with respect to intact femur. Stress shielding of the femur is known to be a principal factor in aseptic loosening of hip replacements. Many designers show that a stiff stem shields the surrounding bone from mechanical loading causing stress shielding. Others show that reducing stem stiffness promotes higher proximal interface shear stress which increases the risk of proximal interface failure. Therefore, the task of this investigation is to solve these conflicting problems appeared in the cemented total hip replacement. The finite element method and optimization technique are used in order to find the optimal stem material which gives the optimal available stress distribution between the proximal medial femoral bone and the cement mantle interfaces. The stem is designed using the concept of functionally graded material (FGM) instead of using the conventional most common used stem material. The results showed that there are four feasible solutions from the optimization runs. The best of these designs is to use a cemented stem graded from titanium at the upper stem layer to collagen at the lower stem layer. This new cemented stem design completely eliminates the stress shielding problem at the proximal medial femoral region. The stress shielding using the cemented functionally graded stem is reduced by 98% compared to titanium stem.
Distinct contextual roles for Notch signalling in skeletal muscle stem cells (2014)

Notch signalling acts in virtually every tissue during the lifetime of metazoans. Recent studies have pointed to multiple roles for Notch in stem cells during quiescence, proliferation, temporal specification, and maintenance of the niche architecture. Skeletal muscle has served as an excellent paradigm to examine these diverse roles as embryonic, foetal, and adult skeletal muscle stem cells have different molecular signatures and functional properties, reflecting their developmental specification during ontology. Notably, Notch signalling has emerged as a major regulator of all muscle stem cells. This review will provide an overview of Notch signalling during myogenic development and postnatally, and underscore the seemingly opposing contextual activities of Notch that have lead to a reassessment of its role in myogenesis.
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mi>g</mml:mi></mml:mrow></mml:math>-factors and discrete energy level velocities in nanoparticles (2006)

We establish relations between the statistics of $g$ factors and the fluctuations of energy in metallic nanoparticles where spin-orbit coupling is present. These relations assume that the electron dynamics in the grain is chaotic. The expressions we provide connect the second moment of the $g$ factor to the root-mean square ``level velocity'' (the derivative of the energy with respect to magnetic field) calculated at magnetic fields larger than a characteristic correlation field. Our predictions relate readily observable quantities and allow for a parameter-free comparison with experiments.
Introduction to Fundamental Medical Mycology (2011)

This chapter contains sections titled: Topics not Covered, or Receiving Secondary Emphasis Biosafety Considerations: Before You Begin Work with Pathogenic Fungi… Fungi Defined: Their Ecologic Niche Medical Mycology A Brief History of Medical Mycology Rationale for Fungal Identification Sporulation Dimorphism Sex in Fungi Classification of Mycoses Based on the Primary Site of Pathology Taxonomy/Classification: Kingdom Fungi General Composition of the Fungal Cell Primary Pathogens Endemic Versus Worldwide Presence Opportunistic Fungal Pathogens Determinants of Pathogenicity General References in Medical Mycology Selected References for Introduction to Fundamental Medical Mycology Websites Cited Questions
Comparison of nonparametric and parametric methods for time-frequency heart rate variability analysis in a rodent model of cardiovascular disease (2020)

The aim of time-varying heart rate variability spectral analysis is to detect and quantify changes in the heart rate variability spectrum components during nonstationary events. Of the methods available, the nonparametric short-time Fourier Transform and parametric time-varying autoregressive modeling are the most commonly employed. The current study (1) compares short-time Fourier Transform and autoregressive modeling methods influence on heart rate variability spectral characteristics over time and during an experimental ozone exposure in mature adult spontaneously hypertensive rats, (2) evaluates the agreement between short-time Fourier Transform and autoregressive modeling method results, and (3) describes the advantages and disadvantages of each method. Although similar trends were detected during ozone exposure, statistical comparisons identified significant differences between short-time Fourier Transform and autoregressive modeling analysis results. Significant differences were observed between methods for LF power (p ≤ 0.014); HF power (p ≤ 0.011); total power (p ≤ 0.027); and normalized HF power (p = 0.05). Furthermore, inconsistencies between exposure-related observations accentuated the lack of agreement between short-time Fourier Transform and autoregressive modeling overall. Thus, the short-time Fourier Transform and autoregressive modeling methods for time-varying heart rate variability analysis could not be considered interchangeable for evaluations with or without interventions that are known to affect cardio-autonomic activity.
Multifocal Dural Enhancement Associated With Temporal Arteritis (2000)

It is proposed that the temporal arteritis caused the multifocal dural enhancement and temporalis muscle enhancement on magnetic resonance imaging.
Performance analysis of dual-pump nonlinear amplifying loop mirror mode-locked all-fibre laser (2019)

Abstract We numerically characterise, in the three-dimensional space of adjustable cavity parameters, the performance of a recently reported layout of a flexible figure-8 laser having two independently pumped segments of active fibre in its bidirectional ring (Smirnov et al 2017 Opt. Lett . 42 1732–5). We show that this optimisation problem can be efficiently addressed by applying a regression model based on a neural-network algorithm.
Optimization of UWB applicator for hyperthermia treatment of human head (2013)

An Ultra-Wideband (UWB) applicator for hyperthermia treatment of human head is developed. The system depends on the design of an array of small foot-print horn elements to allow the construction of large sized-array to surround the human-head. A waveform optimization tool is developed based on genetic algorithms to localize the energy into the tumor location. Computational analysis is performed using CST and experimental measurements are obtained using DASY5 system. Results of the field and SAR image distributions within the human head phantom illustrate the promising performance of this applicator design.
Initial human subject results for breast bi-plane correlation imaging technique (2007)

Computer aided detection (CADe) systems often present multiple false-positives per image in projection mammography due to overlapping anatomy. To reduce the number of such false-positives, we propose performing CADe on image pairs acquired using a bi-plane correlation imaging (BCI) technique. In this technique, images are acquired of each breast at two different projection angles. A traditional CADe algorithm operates on each image to identify suspected lesions. The suspicious areas from both projections are then geometrically correlated, eliminating any lesion that is not identified on both views. Proof of concept studies showed that that the BCI technique reduced the numbers of false-positives per case up to 70%.
Control of self-pumped phase-conjugate reflectivity using incoherent erasure (1990)

We use an incoherent erase beam to control optical chaos and to increase the phase-conjugate reflectivity in a self-pumped phase-conjugate mirror. Focused and large-area incoherent illumination was used to modify or eliminate selected gratings in the crystal.