gebhart/patrepeval huggingface dataset:
Amyloid β-Induced Death in Neurons Involves Glial and Neuronal Hemichannels (2011)

The mechanisms involved in Alzheimer's disease are not completely understood and how glial cells contribute to this neurodegenerative disease remains to be elucidated. Because inflammatory treatments and products released from activated microglia increase glial hemichannel activity, we investigated whether amyloid-β peptide (Aβ) could regulate these channels in glial cells and affect neuronal viability. Microglia, astrocytes, or neuronal cultures as well as acute hippocampal slices made from GFAP-eGFP transgenic mice were treated with the active fragment of Aβ. Hemichannel activity was monitored by single-channel recordings and by time-lapse ethidium uptake, whereas neuronal death was assessed by Fluoro-Jade C staining. We report that low concentrations of Aβ(25-35) increased hemichannel activity in all three cell types and microglia initiate these effects triggered by Aβ. Finally, neuronal damage occurs by activation of neuronal hemichannels induced by ATP and glutamate released from Aβ(25-35)-activated glia. These responses were observed in the presence of external calcium and were differently inhibited by hemichannel blockers, whereas the Aβ(25-35)-induced neuronal damage was importantly reduced in acute slices made from Cx43 knock-out mice. Thus, Aβ leads to a cascade of hemichannel activation in which microglia promote the release of glutamate and ATP through glial (microglia and astrocytes) hemichannels that induces neuronal death by triggering hemichannels in neurons. Consequently, this work opens novel avenues for alternative treatments that target glial cells and neurons to maintain neuronal survival in the presence of Aβ.
Fast software image stabilization with color registration (2002)

We present the formulation and implementation of an image stabilization system capable of stabilizing video with very large displacements between frames. A coarse-to-fine technique is applied in resolution and in model spaces. The registration algorithm uses phase correlation to obtain an initial estimate for translation between images; then Levenberg-Marquardt method for nonlinear optimization is applied to refine the solution. Registration is performed in color space, using a subset of the pixels selected by a gradient-based sub-sampling criterion. This software implementation runs at 5 Hz on non-dedicated hardware (Silicon Graphics R10000 workstation).
Identification of cancer-testis genes expressed by melanoma and soft tissue sarcoma using bioinformatics. (2005)

Cancer-testis or germ cell antigens (GCAs) are a category of tumor antigens expressed by male germ cells and by cancers of diverse histological origin, but not usually by normal adult somatic tissue. These antigens include products encoded by the MAGE, BAGE, GAGE, SSX, and LAGE/NY-ESO-1 families that encode antigenic peptides recognized by T lymphocytes. In this study, we exploit oligonucleotide technology to identify genes in melanoma and soft tissue sarcoma (STS) that display a cancer-testis/GCA expression profile. We identified 59 such genes, including GCAs we knew to be recognized by T lymphocytes. Among our findings are the expression of PRAME in monophasic synovial sarcoma, PRAME and NY-ESO-1 in myxoid/round cell liposarcoma, and SSX2 and members of the GAGE family in malignant fibrous histiocytoma. Furthermore, the proto-oncogene DBL/MCF2 was identified as encoding a novel candidate GCA expressed by clear cell sarcoma/melanoma of soft parts (MSP). DBL/MCF2 peptides that are bound to HLA-A*0201 were identified and recognized by T lymphocytes. These results show the utility of high-throughput expression analysis in the efficient screening and identification of GCA candidates in cancer, and its application to the discovery of candidate targets for T cell immunity against GCAs expressed by cancer.
<i>Aspergillus oryzae laeA</i>Regulates Kojic Acid Synthesis Genes (2011)

Kojic acid synthesis genes regulation was investigated in Aspergillus oryzae. Our results indicate that kojic acid production was lost in the laeA disruption strain, but was recovered in the LaeA complement strain. Real-time PCR also confirmed that expression of kojic acid biosynthesis genes decreased in the laeA disruption strain, indicating that these genes are under the control of LaeA.
Human face recognition using neural networks (2002)

The paper describes the development of a human face recognition system (HFRS) using multilayer perceptron artificial neural networks (MLP). The MLP network is trained with a set of face images until it is in a "learned" state. The network is capable of classifying the face input into its class. In the case of the subject face is not one of those trained, the network will register it as unknown. The system, which takes the face image input from video camera, is also developed to detect the presence of an object in front of the camera and to search for the human facial area automatically. The detected facial area is then used as the inputs to the neural network to perform recognition.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
An Approach for Nanolithography Using Electron Holography (1993)

A technique of electron holography was applied to nanofabrication. Electron interference fringes whose spacing was 108 nm were successfully recorded on polymethylmethacrylate (PMMA) resist using a W<100> thermal field emission (TFE) gun and an electron biprism both set on a conventional transmission electron microscope (TEM). Furthermore, we have attempted the fabrication of a free-standing multi-biprism by electron beam lithography and dry etching, leading to a new fabrication method of a nanoscale grating with a short exposure.
Porous Structures of Polymer Films Prepared by Spin Coating with Mixed Solvents under Humid Condition (2006)

We investigate the effects of interfacial energy between water and solvent as well as polymer concentration on the formation of porous structures of polymer films prepared by spin coating of cellulose acetate butyrate (CAB) in mixed solvent of tetrahydrofuran (THF) and chloroform under humid condition. The interfacial energy between water and the solvent was gradually changed by the addition of chloroform to the solvent. At a high polymer concentration (0.15 g/cm3 in THF), porous structures were limited only at the top surfaces of CAB films, regardless of interfacial energies, due to the high viscosity of the solution. At a medium concentration (approximately 0.08 g/cm3 in THF), CAB film had relatively uniform pores at the top surface and very small pores inside the film because of the mixing of the water droplets with THF solution. When chloroform was added to THF, pores at the inner CAB film had a comparable size with those at the top surface because of the reduced degree of the mixing between the water droplets and the mixed solvent. A further decrease in polymer concentration (0.05 g/cm3 in THF) caused the final films to have a two-layer porous structure, and the size of pores at each layer was almost the same.
Improving the performance of JVM startup using the shared class cache (2017)

The Java Virtual Machine (JVM) is responsible for executing all Java programs, so performance improvements in the JVM, especially pertaining to the startup of an application, have wide-ranging impact. This paper presents a solution that reduces the bottleneck by analyzing and optimizing various data structures inside the JVM before a Java application starts executing. The shared class cache, which was added to IBM's J9 VM to share classes and other immutable data across multiple runs of a JVM, is expanded to include additional data. Runtime improvements of between 15% and 20% were achieved in standard benchmark programs.
Regulation of cardiac contractile function by troponin I phosphorylation (2005)

Cardiac troponin I (cTnI) is a key regulatory protein in cardiac muscle contraction and relaxation, linking Ca(2+)-troponin C binding with activation of crossbridge reactions with the thin filament. In recent years, it has become increasingly apparent that myofilament properties as well as changes in intracellular Ca(2+) have a major role in the dynamic modulation of contractile function. The phosphorylation of specific serine and threonine residues on cTnI by several different kinases represents a major physiological mechanism for alteration of myofilament properties. Furthermore, altered thin filament function plays an important role in the contractile dysfunction associated with heart failure. Modification of cTnI by protein kinases A and C has been extensively studied with especially useful information deriving from (a) in vitro studies in reconstituted detergent-skinned fibre bundles in which endogenous cTnI was replaced with various targeted cTnI mutants and (b) transgenic animals in which endogenous cTnI was similarly manipulated through overexpression of cardiomyocyte-targeted cTnI mutants. cTnI may also be specifically modified by protein kinase G, p21-activated kinases and by dephosphorylation. This review focuses on recent advances in understanding the mechanisms of cTnI modification by these kinases and the consequent functional effects both under physiological conditions and in pathophysiological settings.
Effect of Land Application of Phosphorus-Saturated Gypsum on Soil Phosphorus in a Laboratory Incubation (2012)

Agricultural drainage ditches can deliver high loads of phosphorus (P) to surface water. Installation of filter structures containing P sorbing materials (PSMs), including gypsum, is an emerging practice that has shown promise to reduce these P loads. The objective of this study was to evaluate what effect soil amendment with gypsum would have on soil P concentrations and forms in a laboratory incubation experiment. Gypsum was saturated at two levels with P, and applied to a silt loam and a sandy loam at two rates. The treated soils were incubated in the laboratory at 25°C, and samples were collected on eight dates between 0 and 183 days after amendment. Spent gypsum application did not significantly increase soil water-extractable or Mehlich 3 P when applied at typical agronomic rates. This appears to be a viable strategy to remove P from agricultural drainage waters but does not appear to provide any additional P fertilizer value.
Contact angles and wetting velocity measured electrically (1999)

We describe two new measurement techniques for studying the wetting behavior of a liquid on a surface. First, we measure the contact angle of a droplet, by measuring the capacitance between a conducting droplet and a subsurface counter electrode. The estimated error in the measured contact angle is 2% for contact angles in the range between 60° and 120°. In the second measurement technique, we detect the current as a function of time, which provides information about the dynamics of a droplet wetting the substrate. The time-integrated current is related to the base area of the droplet. Consequently, we can derive the radial velocity of the three-phase line of the droplet. The time resolution of the measurement technique is limited by the charging time of the initial capacitance, in our case approximately 0.5 ms.
C5a impairs phagosomal maturation in the neutrophil through phosphoproteomic remodeling (2020)

Critical illness is accompanied by the release of large amounts of the anaphylotoxin, C5a. C5a suppresses antimicrobial functions of neutrophils which is associated with adverse outcomes. The signaling pathways that mediate C5a-induced neutrophil dysfunction are incompletely understood. Healthy donor neutrophils exposed to purified C5a demonstrated a prolonged defect (7 hours) in phagocytosis of Staphylococcus aureus. Phosphoproteomic profiling of 2712 phosphoproteins identified persistent C5a signaling and selective impairment of phagosomal protein phosphorylation on exposure to S. aureus. Notable proteins included early endosomal marker ZFYVE16 and V-ATPase proton channel component ATPV1G1. An assay of phagosomal acidification demonstrated C5a-induced impairment of phagosomal acidification, which was recapitulated in neutrophils from critically ill patients. Examination of the C5a-impaired protein phosphorylation indicated a role for the PI3K VPS34 in phagosomal maturation. Inhibition of VPS34 impaired neutrophil phagosomal acidification and killing of S. aureus. This study provides a phosphoproteomic assessment of human neutrophil signaling in response to S. aureus and its disruption by C5a, identifying a defect in phagosomal maturation and mechanisms of immune failure in critical illness.
Targeting Chemophotothermal Therapy of Hepatoma by Gold Nanorods/Graphene Oxide Core/Shell Nanocomposites (2013)

Nanographene oxide (NGO) are highly suitable to be the shells of inorganic nanomaterials to enhance their biocompatibility and hydrophilicity for biomedical applications while retaining their useful photonic, magnetic, or radiological functions. In this study, a novel nanostructure with gold nanorods (AuNRs) encapsulated in NGO shells is developed to be an ultraefficient chemophotothermal cancer therapy agent. The NGO shells decrease the toxicity of surfactant-coated AuNRs and provide anchor points for the conjugation of hyaluronic acid (HA). The HA-conjugated NGO-enwrapped AuNR nanocomposites (NGOHA-AuNRs) perform higher photothermal efficiency than AuNRs and have the capability of targeting hepatoma Huh-7 cells. NGOHA-AuNR is applied to load doxorubicin (DOX), and it exhibits pH-responsive and near-infrared light-triggered drug-release properties. Chemophotothermal combined therapy by NGOHA-AuNRs-DOX performs 1.5-fold and 4-fold higher targeting cell death rates than single chemotherapy and photothermal therapy, respectively, with biosafety to nontargeting cells simultaneously. Furthermore, our strategy could be extended to constructing other NGO-encapsulated functional nanomaterial-based carrier systems.
Simulation of 1.3-μm AlGaInAs/InP strained MQW lasers (2005)

Optimization of a 1300-nm AlGaInAs/InP strained multiple quantum-well structure with an electron stop layer, which is located between the active region and the p-type GRIN-SCH layer, is studied numerically with a LASTIP simulation program. Specifically, the effect of the electron stop layer on the characteristic temperature and the temperature dependence of the slope efficiency are investigated. Various physical parameters at different operating temperatures are adjusted so that the threshold currents of the simulated laser structure can be matched to the results measured experimentally by Selmic et al. Our simulated results suggest that the AlInAs is a better material for the electron stop layer than the GaAsP. With the use of a p-type Al<sub>0.5</sub>In<sub>0.5</sub>As electron stop layer and an active region consisting of Al<sub>0.175</sub>Ga<sub>0.095</sub>In<sub>0.73</sub>As(6 nm)/Al<sub>0.27</sub>Ga<sub>0.21</sub>In<sub>0.52</sub>As(10 nm), a characteristic temperature of as high as 94.7 K is achieved for the 250-µm-long AlGaInAs/InP strained quantum-well laser under study.
Synthesizing program input grammars (2017)

We present an algorithm for synthesizing a context-free grammar encoding the language of valid program inputs from a set of input examples and blackbox access to the program. Our algorithm addresses shortcomings of existing grammar inference algorithms, which both severely overgeneralize and are prohibitively slow. Our implementation, GLADE, leverages the grammar synthesized by our algorithm to fuzz test programs with structured inputs. We show that GLADE substantially increases the incremental coverage on valid inputs compared to two baseline fuzzers.
New aspects in the pathophysiology of cutaneous melanoma: a review of the role of thioproteins and the effect of nitrosoureas. (1992)

The importance of thioproteins, essential to the ribonucleotide reduction pathway, has been demonstrated in human primary and metastatic melanoma tissues. The thioredoxin reductase/thioredoxin and the glutathione reductase/glutathione/glutaredoxin electron transfer pathways represent alternative electron donors for ribonucleotide reductase and regulate the synthesis of deoxyribonucleotides, the substrates for DNA synthesis, in the S phase of the cell cycle. In addition to their important role in DNA synthesis and cell division, these thioproteins provide effective antioxidant defence against oxygen radicals and hydrogen peroxide. In human metastatic melanoma cells and tissues the thioredoxin reductase/thioredoxin system is located both in the cell cytosol and on plasma membranes and is under allosteric regulation by calcium. As a consequence, calcium plays an important role in determining the intracellular redox status, cell division and differentiation. Recently, the intracellular redox conditions have been shown to be important in the reaction of alkylating anti-tumour drugs such as the chloroethylnitrosoureas. In addition to previously established mechanisms, these highly reactive drugs inhibit thioredoxin reductase, glutathione reductase and ribonucleotide reductase by chloroethylation of their respective thiolate active sites. Incorporation of the 14C chloroethyl group in drug sensitive and resistant human metastatic melanoma cell lines depends on the redox status, with resistant cells being more oxic than sensitive cells. Thioredoxin reductase is 500-fold more sensitive than glutathione reductase to the newly developed nitrosourea, Fotemustine (diethyl-1-[3,2 chloroethyl]-3-nitrosoureido ethyl phosphonate). It has been shown that melanomas which respond to Fotemustine therapy contain more thioredoxin reductase whereas resistant metastases yielded the opposite result.(ABSTRACT TRUNCATED AT 250 WORDS)
Micro Processing a Path to Aggressive Instrument Miniaturization for Micro and Picosats (2005)

Advanced micro-fabrication and packaging techniques provided through microelectromechanical systems (MEMS) technology enable fabrication and system integration of a miniature flat plasma spectrometer (FlaPS) capable of making fine resolution measurements of the kinetic energy spectra and angular distributions of ions in a space environment. This instrument demonstration flies on USAFA Falconsat-3 and represents a demonstration of how advanced fabrication techniques for the microprocessing world can be utilized to derive aggressive miniaturization. High performance metrics in terms of sensitivity and resolution are achievable with significant reductions in mass and power compared to conventional spectrometers. A FlaPS instrument, including sensor-head array, printed circuit board with amplifier array electronics, power supply, and chassis has been designed and built to occupy a volume of approximately 200 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> in a 0.5kg, 300mW package. This technique could easily be migrated to other instruments and in the future potentially to subsystems
High-performance Bias-drift-free Modulators Based on Heterogeneous Silicon and Lithium Niobate Platform (2021)

we demonstrate high-speed and bias-drift-free Mach-Zehnder modulators based on the heterogeneous silicon and lithium niobate platform and exhibit a low half-wave voltage of 3 V, and electro-optic modulation bandwidth of at least 70 GHz.
The arc-transversal median algorithm: a geometric approach to increasing ultrasonic sensor azimuth accuracy (2003)

This paper describes a new method for improving the azimuth accuracy of range information using conventional (Polaroid) low-resolution ultrasonic sensors mounted in a circular array on a mobile robot. Although ultrasonic sensors are fairly accurate in measuring distance in depth, they commonly have significant uncertainty in azimuth. We model this uncertainty with a uniform distribution along an arc. This means that the echo has an equal likelihood of originating from any point along the arc. We then introduce a new method to fuse sonar data to better approximate the actual obstacle location. This new method is termed the arc transversal median method because the robot determines the location of an object 1) by intersecting one arc with other arcs, 2) then by considering only "transversal" intersections, those which exceed a threshold in angle, and 3) by taking the median of the intersections. The median is a robust estimator that is insensitive to noise; a few stray readings will not affect its value. We show, via some simple geometric relationships, that this method can improve the azimuth accuracy of the sonar sensor by a specified amount under well-defined conditions. Experimental results on an ultrasonic sensor array situated on a mobile robot verify this approach.
SMART – a program to measure SEM resolution and imaging performance (2002)

It is important to be able to measure the parameters, such as spatial resolution, astigmastism, signal-to-noise ratio, and drift and instability, that characterize the performance of a scanning electron microscope. These quantities can be determined most reliably by a Fourier analysis of digital micrographs from the instrument, recorded under conditions of interest. A program designed to implement all of the necessary steps in an automated manner has been developed as a 'macro' for the popular, and freely available, NIH Image and SCION Image programs.
Generic Dispensing And Substitution In Mail And Retail Pharmacies (2004)

Mail-order pharmacies have lower aggregate generic-dispensing rates than their retail counterparts. This fact has been used as evidence of self-dealing that could arise when a pharmacy benefit manager (PBM) is both a plan administrator and a pharmacy owner. Using the aggregate generic-dispensing rate, however, is problematic because it confounds variation in performance with differences in demand. Controlling for therapeutic mix alone explains 87 percent of the apparent difference in aggregate dispensing rates. An alternative measure--one that fully controls for differences in price and indications across molecules within a category--eliminates the discrepancy in dispensing rates.
Assessing the influence of sample tagging and library preparation on DNA metabarcoding (2019)

Metabarcoding is increasingly used to assess species diversity by high-throughput sequencing where millions of sequences can be generated in parallel and multiple samples can be analysed in one sequencing run. Generating amplified fragments with a unique sequence identifier ('tag') for each sample is crucial, as it allows assigning sequences to the original samples. The tagging through so-called fusion primers is a fast and cheap alternative to commercially produced ligation-based kits. However, little is known about potential bias and inconsistencies introduced by the long nucleotide tail attached to those primers, which could lead to deficient reports of community composition in metabarcoding studies. We therefore tested the consistency and taxa detection efficiency of fusion primers in (1) a one-step and (2) two-step PCR protocol as well as (3) a commercially manufactured Illumina kit using mock communities of known composition. The Illumina kit delivered the most consistent results and detected the highest number of taxa. However, success of the two-step PCR approach was only marginally lower compared to the kit with the additional advantage of a much more competitive price per library. While most taxa were also detected with the one-step PCR approach, the consistency between replicates including read abundance was substantially lower. Our results highlight that method choice depends on the precision needed for analysis as well as on economic considerations and recommend the Illumina kit to obtain most accurate results and the two-step PCR approach as a much cheaper yet very robust alternative.
MAGNETIC PROPERTIES OF GLASSY (Fe- Ni)<sub>86</sub>B<sub>14</sub> ALLOYS (1980)

Thermomagnetization, crystallization behaviour, mass density and magnetostriction data obtained for glassy (Fe-Ni)86 B14 alloys suggest that the local atomic structures resemble those of the corresponding crystalline Fe-Ni alloys.