gebhart/patrepeval huggingface dataset:
Developing Detection and Monitoring Strategies for <I>Planococcus minor</I> (Hemiptera: Pseudococcidae) (2012)

A pheromone-based system to locate and monitor Planococcus minor (Maskell), a pest of over 250 plants including citrus, grape, and cacao, was tested. The difficulty in distinguishing P. minor from the citrus mealybug, P. citri, makes finding and evaluating the impact of the pest challenging. Studies conducted in Puerto Rico determined that synthetic P. minor pheromone lures preaged 120 d in the field caught similar number of males as lures not aged (fresh). Molecular analysis of trapped mealybug males using mitochondrial cytochrome oxidase-1, the internal transcriber space two locus, and 28S-D2 gene showed the pheromone traps to be species specific. Traps baited with P. minor pheromone were used to monitor the pest in south Florida and to locate potential infestations. P. minor males were found at all locations studied in South Florida and were present in low numbers (1.03 +/- 0.69 mean +/- SE/trap/14 d). Over 14,000 terminals, fruit, and flowers were visually inspected over a 6 mo period of peak trap catches before the first adult P. minor female was found. The synthetic pheromone lures proved to be an effective tool to locate and monitor this pest new to the continental United States.
Parametric Study on CAI Combustion in a GDI Engine with an Air-Assisted Injector (2007)

&lt;div class="htmlview paragraph"&gt;Controlled auto-ignition (CAI) combustion and engine performance and emission characteristics have been intensively investigated in a single-cylinder gasoline direct injection (GDI) engine with an air-assisted injector. The CAI combustion was obtained by residual gas trapping. This was achieved by using low-lift short-duration cams and early closing the exhaust valves. Effects of EVC (exhaust valve closure) and IVO (intake valve opening) timings, spark timing, injection timing, coolant temperature, compression ratio, valve lift and duration, on CAI combustion and emissions were investigated experimentally. The results show that the EVC timing, injection timing, compression ratio, valve lift and duration had significant influences on CAI combustion and emissions. Early EVC and injection timing, higher compression ratio and higher valve lift could enhance CAI combustion. IVO timing had minor effect on CAI combustion. The spark timing had little effect on CAI combustion when the engine operated in the fully-developed CAI mode. Coolant temperature was revealed to have substantial impact on CAI combustion when the coolant temperature is below 65°C.&lt;/div&gt;
Estimation of Carbonate Elastic Properties from Nanoindentation Experiments to Reduce Uncertainties in Reservoir Modelling (2010)

SummaryPetrophysical properties of carbonate reservoirs, which are the majority of all hydrocarbon reservoirs worldwide, are much less predictable than the properties of siliciclastic reservoirs. This is mainly due to chemical interactions of carbonate rocks with percolating fluids that cause dissolution, ion exchange, and recrystallization in geological time. These processes result in dramatic changes in density, porosity, and permeability leading to inhomogeneity of carbonate rocks on micro-and meso-scales. Quantification of the elastic variability of carbonate grains on the microscale is the first step to constrain models and to obtain more realistic predictions of practically important rock properties of carbonate reservoirs. In this study, we present elastic moduli of an oolite sample from the Dampier Formation - Pleistocene of Southern Carnarvon Basin, Western Australia, obtained by nanoindentation. Young’s moduli of this highly heterogeneous sample are measured at 49 points regularly distributed in a 70x70micrometer rectangular grid on the sample’s surface. The frequency diagram shows bimodal distribution of the Young’s moduli oriented around values of 56 GPa and 144 GPa that correspond to low and high density components of the grain respectively. These two solid phases are apparent in the high resolution scanning electron microscope images. We used the obtained moduli of this composite grain for numerical modelling using finite element approach of elastic properties of the carbonate sample from micro-Computed Tomography images. The results compare favourably with the elastic moduli obtained from acoustic velocities measured by ultrasonic technique.
Single‐phase and binary phase nanogranular ferrites for magnetic hyperthermia application (2020)

Abstract The study demonstrates the performance of heating efficiency in single‐phase and binary phase spinel ferrite nanosystems. Ferrimagnetic cobalt ferrite (CoFe 2 O 4 ) (CFO) and superparamagnetic copper ferrite/copper oxide (CuFe 2 O 4 /CuO) (CuF) nanosystems of different particle sizes were synthesized through a microwave‐assisted coprecipitation method. The heating behavior was observed in range of both field amplitudes (8‐24 kA/m at 516 kHz) and frequencies (325‐973 kHz at 12 kA/m). The heating efficiency was analyzed and compared by means of particle size, magnetization, effective anisotropy constant, and Néel relaxation mechanism. Indeed, the heating rate was maximized in larger ferrite particles with low effective anisotropy constant. Moreover, though the magnetization and effective anisotropy constant of single‐phase CoFe 2 O 4 nanoparticles were higher, the binary phase CuFe 2 O 4 /CuO nanosystems of similar crystallite size (28 nm) exhibited superior heating efficiency (4.21°C/s). For a field amplitude and frequency of 24 kA/m and 516 kHz, the heating rate of CuF and CFO ferrites with different crystallite sizes decreased in the order of 4.21 &gt; 2.14 &gt; 0.58 &gt; 0.52 °C/s for 29 nm &gt; 25 nm &gt; 12 nm &gt; 15 nm , respectively. The results emphasize that binary phase ferrite nanoparticles are better thermoseeds than the single‐phase ferrites for the magnetic hyperthermia application.
Interferometer for phase measurements in phase-shift masks (1993)

The etch depth of phase shift masks is typically measured by means of profilometry and the expected phase shift is calculated from a knowledge of the refractive index at the lithographic wavelength of interest. In the case of masks utilizing deposited films the index may differ from values for bulk materials and commonly varies to some degree with method of deposition. The interferometer offers a method for the measurement of phase directly and, hence, for a means to obtain refractive index values for phase shift films on quartz blank substrates. Arrangements are described for direct phase measurements using visible, 632.8 nm, and UV, 257 nm, radiation.
Efficient Subtractive Cloning of Genes Activated by Lipopolysaccharide and Interferon γ in Primary-Cultured Cortical Cells of Newborn Mice (2013)

Innate immune responses play a central role in neuroprotection and neurotoxicity during inflammatory processes that are triggered by pathogen-associated molecular pattern-exhibiting agents such as bacterial lipopolysaccharide (LPS) and that are modulated by inflammatory cytokines such as interferon γ (IFNγ). Recent findings describing the unexpected complexity of mammalian genomes and transcriptomes have stimulated further identification of novel transcripts involved in specific physiological and pathological processes, such as the neural innate immune response that alters the expression of many genes. We developed a system for efficient subtractive cloning that employs both sense and antisense cRNA drivers, and coupled it with in-house cDNA microarray analysis. This system enabled effective direct cloning of differentially expressed transcripts, from a small amount (0.5 µg) of total RNA. We applied this system to isolation of genes activated by LPS and IFNγ in primary-cultured cortical cells that were derived from newborn mice, to investigate the mechanisms involved in neuroprotection and neurotoxicity in maternal/perinatal infections that cause various brain injuries including periventricular leukomalacia. A number of genes involved in the immune and inflammatory response were identified, showing that neonatal neuronal/glial cells are highly responsive to LPS and IFNγ. Subsequent RNA blot analysis revealed that the identified genes were activated by LPS and IFNγ in a cooperative or distinctive manner, thereby supporting the notion that these bacterial and cellular inflammatory mediators can affect the brain through direct but complicated pathways. We also identified several novel clones of apparently non-coding RNAs that potentially harbor various regulatory functions. Characterization of the presently identified genes will give insights into mechanisms and interventions not only for perinatal infection-induced brain damage, but also for many other innate immunity-related brain disorders.
Basic Concepts in Systems Biology (2006)

In the early 1960s, there was a bifurcation of emphasis in biology. Molecular biology had arrived, providing a growing understanding of DNA, protein, and other chemical components of cells. A science was emerging that had rigor in terms of analytical chemistry and controlled experimentation, and relevance to biochemical and genetic functions of cells and occasionally to their phenotypes. Holistic emphasis in biology, which had primarily been practiced through physiology, faded into the background as it is much more difficult to state hypotheses, do controlled experiments, or execute the scientific process for the behavior of systems and networks in biology. However, as outlined in the introductory chapter, this situation has now changed. We now have technology that allows for the detailed enumeration of biological components, enabling us to study cells and complex biological processes as systems. As a consequence, systems biology has arisen as a new field. This new field does not yet have a well-defined and articulated conceptual basis. In this chapter, we will attempt to collect some of the key issues that represent to the conceptual foundations of systems biology. Its content is not intended to be, and cannot be, complete but rather represents an attempt to initiate this process.
Extrahepatic Replication of Duck Hepatitis B Virus: More Than Expected (1990)

Replication of duck hepatitis B virus in extrahepatic tissue such as pancreas, kidney and spleen has been well documented. To assess whether there is more widespread extrahepatic virus replication, we assayed brain, heart, lung, thymus, pancreas, kidney, spleen and intestine of 1- to 16-wk-old ducklings for the presence of duck hepatitis B virus DNA and mRNA by blotting and in situ methods. Replicative intermediates and single-stranded duck hepatitis B virus DNA and RNA transcripts were detected in the brain, lung, heart, intestine, kidney, pancreas and spleen. In situ hybridization showed evidence of viral replication in the lung epithelium, germinal center of spleen, acinar cell of pancreas and tubular epithelium of kidney. These data suggest that extrahepatic duck hepatitis B virus replication is more widespread than previously thought. It is yet to be determined whether widespread extrahepatic replication is unique to duck hepatitis B virus infection or is a common feature of other mammalian hepatitis B-like viruses.
Human trans -editing enzyme displays tRNA acceptor stem specificity and relaxed amino acid selectivity (2020)

Abstract Accurate translation of genetic information into proteins is vital for cell sustainability. ProXp-ala prevents proteome-wide Pro-to-Ala mutations by hydrolyzing misacylated Ala-tRNA Pro , which is synthesized by prolyl-tRNA synthetase (ProRS). Bacterial ProXp-ala was previously shown to combine a size-based exclusion mechanism with conformational and chemical selection for the recognition of the alanyl moiety, while tRNA Pro is selected via recognition of tRNA acceptor stem elements G72 and A73. The identity of these critical bases changed during evolution with eukaryotic cytosolic tRNA Pro possessing a cytosine at the corresponding positions. The mechanism by which eukaryotic ProXp-ala adapted to these changes remains unknown. In this work, recognition of the aminoacyl moiety and tRNA acceptor stem by human ( Hs ) ProXp-ala was examined. Enzymatic assays revealed that Hs ProXp-ala requires C72 and C73 in the context of Hs cytosolic tRNA Pro for efficient deacylation of mischarged Ala-tRNA Pro . The strong dependence on these bases prevents cross-species deacylation of bacterial Ala-tRNA Pro or of Hs mitochondrial Ala-tRNA Pro by the human enzyme. Similar to the bacterial enzyme, Hs ProXp-ala showed strong tRNA acceptor-stem recognition but differed in its amino acid specificity profile relative to bacterial ProXp-ala. Changes at conserved residues in both the Hs and bacterial ProXp-ala substrate binding pockets modulated this specificity. These results illustrate how the mechanism of substrate selection diverged during the evolution of the ProXp-ala family and provides the first example of a trans -editing domain whose specificity evolved to adapt to changes in its tRNA substrate.
The effects of phytochemical pesticides on the growth of cultured invertebrate and vertebrate cells (2002)

A range of cultured cells of invertebrate and vertebrate origin was grown in the presence of a number of phytochemical pesticides to test the effect of the latter on cell proliferation. The main observation was that azadirachtin was a potent inhibitor of insect cell replication, with an EC50 of 1.5 x 10(10) M against Spodoptera cells and of 6.3 x 10(9) M against Aedes albopictus cells, whilst affecting mammalian cells only at high concentrations (> 10(-4) M). As expected, the other phytochemical pesticides, except for rotenone, had little effect on the growth of the cultured cells. Rotenone was highly effective in inhibiting the growth of insect cells (EC50:10(-8) M) but slightly less toxic towards mammalian cells (EC50:2 x 10(-7) M). Neem terpenoids other than azadirachtin and those very similar in structure significantly inhibited growth of the cell cultures, but to a lesser degree. The major neem seed terpenoids, nimbin and salannin, for example, inhibited insect cell growth by 23% and 15%, respectively.
Reconstructions of phase contrast, phased array multicoil data (1994)

We present a reconstruction method for phased array multicoil data that is compatible with phase contrast MR angiography. The proposed algorithm can produce either complex difference or phase difference angiograms. Directional flow and quantitative information are preserved with the phase difference reconstruction. The proposed method is computationally efficient and avoids intercoil cancellation errors near the velocity aliasing boundary. Feasibility of the method is demonstrated on human scans.
Analysis of Histone Deacetylase Inhibitor, FK228, Effect on Chronic Myelogenous Leukemia Cell Line. (2004)

Abstract Chronic myelogenous leukemia (CML) results from transformation of hematopoietic cells by the BCR/ABL gene. Although high rates of hematologic responses to imatinib therapy, the acquired resistance to imatinib has been recognized as a major problem in the treatment of CML Histone deacetylases (HDACs) and histone acetyltransferases (HATs) regulate gene expression and cell growth. Recently, HDAC inhibitors have known as a new class of anti-cancer drugs. One of the HDAC inhibitor, FK228 (FR901228, depsipeptide) is now doing the clinical trial for the treatment of patients, such as peripheral T-cell lymphoma, but there was not known to the CML. In this study, we used the TF-1 BCR-ABL cell line, which were transfected BCR/ABL gene to the leukemia cell line, TF-1. We show here that FK228 potently induced apoptosis of TF-1 BCR-ABL cells, compare to the parental cell line, TF-1, in a dose and time depend fashion. BCR-ABL, intracellular molecular chaperone, heat shock protein 90 (HSP90), and p53 which regulate cell cycle, were acetylated after FK228 treatment, but not glycogen synthase kinase-3 β(GSK-3β) and signal-transducing activators of transcription 5 (STAT5). Histone H4 is also acetylated after FK228 treatment. In a cell cycle analysis, TF-1 BCR-ABL cells were stopped at G2-M phase after FK228 treatment. The activity of MAPK and Src kinases were blocked after FK228 treatment in a time and dose depend fashion, but p38 was activated. Inhibitor of apoptosis proteins (c-IAPs) have prevented cell death by inhibiting effectors caspases. IAPs were inhibited by FK228 and caspase3, caspase9 and poly (ADP-ribose) polymerase (PARP) were activated in a time and dose depend manner. Histone acetylation and caspase activitation were not blocked by treatment of p38 inhibitor, SB203580. Our study supports the future clinical trial of FK228 in the management of CML patients.
Evaluation of the subcutaneous route for glucose monitoring in patients undergoing deep hypothermia (2007)

Blaha, J.1; Kremen, M.1; Grus, T.1; Ellmerer, M.2; Lindner, J.1; Lips, M.1; Kotulak, T.1; Rubes, D.1; Matias, M.1; Haluzik, M.1Author Information
Uncertainty evaluation in power measurements with commercial data acquisition boards (2011)

The paper deals with the metrological characterization of a digital wattmeter developed by using a personal computer, a shunt, two commercial data acquisition boards and commercial software. The uncertainty of the active power measurements is assessed individually characterizing the voltage channel, the current channel and the phase displacement measurement between the two channels. In particular, the uncertainty on the voltage and current rms measurements is evaluated by using an already proposed approach based on the Monte Carlo method and on the usage of five parameters, while the uncertainty on the phase angle is experimentally estimated. In order to validate the proposed approach for the uncertainty evaluation, various experiments were carried out and a comparison with the Italian National Standard wattmeter was made. The results show that the proposed PC-based solution can be suitable for the development of standard instrumentation, since its accuracy is comparable to the accuracy of much more expensive and sophisticated instrumentation
Testing Computer Software, Second Edition (1993)

From the Publisher:
This book will teach you how to test computer software under real-world conditions. The authors have all been test managers and software development managers at well-known Silicon Valley software companies. Successful consumer software companies have learned how to produce high-quality products under tight time and budget constraints. The book explains the testing side of that success.
Who this book is for:*Testers and Test Managers*Project Managers-Understand the timeline, depth of investigation, and quality of communication to hold testers accountable for.*Programmers-Gain insight into the sources of errors in your code, understand what tests your work will have to pass, and why testers do the things they do.*Students-Train for an entry-level position in software development.
What you will learn:*How to find important bugs quickly*How to describe software errors clearly*How to create a testing plan with a minimum of paperwork*How to design and use a bug-tracking system*Where testing fits in the product development process*How to test products that will be translated into other languages*How to test for compatibility with devices, such as printers*What laws apply to software quality
JACK FALK consults on software quality management and software engineering management. Jack is certified in Software Quality Engineering by the American Society of Quality. He is Vice Chair of the Santa Clara Valley Software Quality Association and an active participant in the Los Altos Workshops on Software Testing. 
HUNG Q. NGUYEN is Founder, President, and CEO of softGear technology. He has worked in the computer software and hardware industries, holding management positionsinengineering, quality assurance, testing, product development, and information technology, as well as making significant contributions as a tester and programmer. He is an ASQ-Certified Quality Engineer, and a senior member and San Francisco Section Certification Chairman of the American Society for Quality.
Identification of a naturally processed HLA A0201‐restricted viral peptide from cells expressing human papillomavirus type 16 E6 oncoprotein (1994)

Human papillomavirus (HPV) DNA encoding the oncogenic proteins E6 and E7 is usually retained in cervical carcinomas, implicating these proteins as potential target antigens for immune recognition in this virally associated tumor. We have characterized endogenously processed peptides eluted from major histocompatibility complex class I molecules in cells infected with a recombinant vaccinia expressing the HPV-16 E6 oncoprotein. The reverse-phase chromatography profile of peptides eluted from isolated HLA-A0201 molecules in cells expressing the E6 oncoprotein differs from that of cells not expressing E6. Sequential Edman degradation of novel peaks found in the peptide profiles from cells expressing HPV-16 E6 led to the identification of a naturally processed HLA-A0201-restricted E6 peptide of sequence KLPQLCTEL. This approach has allowed the identification of a viral peptide which is processed and presented by cells expressing the E6 oncoprotein and is a likely target for cytotoxic T lymphocyte recognition in HLA-A0201-positive patients.
Angiotensin Blockade Inhibits Osteopontin Expression in Non-infarcted Myocardium After Myocardial Infarction (2005)

Osteopontin has been reported to have an important role in cardiac fibrosis. However, little is known about the effects of angiotensin-converting enzyme inhibitor (ACEI) and angiotensin type 1 receptor blockers (ARB) on osteopontin expression in infarcted myocardium. The purpose of this study was to elucidate the effects of an ACEI (perindpril) and an ARB (candesartan cilexitil) on cardiac function as assessed by Doppler echocardiography and cardiac osteopontin expression associated with cardiac remodeling in myocardial infarcted rats. ACEI or ARB was administered after myocardial infarction (MI). At 4 weeks after MI, cardiac function, and mRNAs in non-infarcted myocardium were analyzed. ACEI and ARB equally prevented left ventricular dilatation, reduction of ejection fraction, and the increase in E/A wave velocity ratio and the rate of E wave deceleration by MI. ACEI and ARB significantly suppressed increased mRNA expression of atrial natriuretic peptide, brain natriuretic peptide, osteopontin, and collagen I and III in the non-infarcted ventricle at 4 weeks. Immunohistochemically stained osteopontin was increased in interstitial fibrosis of non-infarcted myocardium. Both ACEI and ARB significantly prevented cardiac fibrosis and osteopontin expression. In conclusion, angiotensin blockade inhibits osteopontin expression in non-infarcted myocardium and prevents cardiac remodeling after MI.