gebhart/patrepeval huggingface dataset:
Aminoglycoside Antibiotic-Derived Anion-Exchange Microbeads for Plasmid DNA Binding and in Situ DNA Capture (2014)

Plasmid DNA (pDNA) therapeutics are being investigated for gene therapy and DNA vaccines against diseases including cancer, cystic fibrosis and AIDS. In addition, several applications in modern biotechnology require pDNA for transient protein production. Here, we describe the synthesis, characterization, and evaluation of microbeads ("Amikabeads") derived from the aminoglycoside antibiotic amikacin for pDNA binding and in situ DNA capture from mammalian cells. The parental aminoglycoside-derived microbeads (Amikabeads-P) acted as anion-exchange materials, and demonstrated high capacities for binding pDNA. Binding of pDNA was significantly enhanced following quaternization of the amines on the microbeads (Amikabeads-Q). Amikabeads were further employed for the disruption and extraction of DNA from mammalian cells, indicating their utility for in situ DNA capture. Our results indicate that Amikabeads are a novel material, with multiple reactive groups for further conjugation, and can have several applications in plasmid DNA biotechnology.
Phytotoxicity of grey wastewater evaluated by toxicity tests (2006)

An algal growth inhibition test and a short-term acute assay for willows were used in order to evaluate the phytotoxicity of grey wastewater from different sources. Bathroom grey wastewaters were toxic towards algae (EC10 = 36 – 375 mL/L), whereas kitchen and laundry wastewaters were found to be toxic to both organisms (EC10 = 55 – 198 mL/L). The investigation showed that untreated grey wastewater could pose an environmental hazard if discharged into small-size receiving waters. Discharge to willow evaporation beds is problematic and toxic effects may be encountered, but, compared to direct discharge to surface water, the risks of toxic effects are much less pronounced.
Analysis of the EXAFS spectrum of hydroxyapatite (1986)

An analysis of the EXAFS spectrum of hydroxyapatite, Ca5(PO4)3OH, is described using a spherical-wave theory. Structural information on the local atomic environment surrounding the calcium ion is presented out to a distance of 0.6 nm. Phase shifts were calculated using the ab initio method described previously. Local atomic potentials were constructed using the muffin-tin approximation, choosing a local atomic arrangement consistent with the known crystal structure of hydroxyapatite. The accuracy of the phase shifts and the calculation procedure were checked using the EXAFS spectrum of calcium oxide. X-ray crystallography provided the initial EXAFS parameters used in simulating the spectrum of hydroxyapatite. The inter-atomic distance, rj, and the Debye-Waller terms, sigma j2, were refined to obtain the best agreement with experiment. To analyse the EXAFS fully, multiple scattering contributions needed to be included.
Reduction in the toxicity of a component of an artificial blood substitute by supercritical fluid fractionation (1988)

Artificial blood substitutes (ABS) containing the surfactant Pluronic F68 (F68) are reported to be cytotoxic to cell lines. Because of F68's reported impairment of granulocyte function, it was hypothesized that F68 was also responsible for the cytotoxicity of ABS, possibly as a result of a separable fraction of the F68, separation of which could be achieved using supercritical fluid fractionation (SFF). SFF employs gases, such as carbon dioxide, under high pressure to dissolve the parent compound, a process that is followed by step-by-step precipitation and recovery of the dissolved material. The toxicity of F68 to human and animal cells was investigated by culturing Hela and B16 cells in the presence or absence of F68. Cells were grown for 4 days, harvested, and counted. Hela and B16 growth were markedly inhibited by F68. Four lots of F68 at 20 mg per ml inhibited Hela growth by 54 +/- 10 percent (p less than 0.05). In four dose-response experiments, three lots of F68 caused 50 percent inhibition of cell growth at 25 +/- 17 mg per ml. Four lots of F68 were also processed by SFF. Hela cells were grown in the presence of control media, parent (unextracted) F68, the early fractions of SFF extraction (XT), and the residual (partially purified) (RES F68). All parent F68, XT, and RES F68 were at 20 mg per ml. In 11 studies, the XT were 77 +/- 25 percent more toxic than the parent F68 (p less than 0.02), and the RES F68 were 30 +/- 11 percent less toxic than parent F68 (p less than 0.02).(ABSTRACT TRUNCATED AT 250 WORDS)
Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction (2008)

Microarray-hybridization specificity is one of the main effectors of microarray result quality. In the present review, we suggest a definition for specificity that spans four hybridization levels, from the single probe to the microarray platform. For increased hybridization specificity, it is important to quantify the extent of the specificity at each of these levels, and correct the data accordingly. We outline possible effects of low hybridization specificity on the obtained results and list possible effectors of hybridization specificity. In addition, we discuss several studies in which theoretical approaches, empirical means or data filtration were used to identify specificity effectors, and increase the specificity of the hybridization results. However, these various approaches may not yet provide an ultimate solution; rather, further tool development is needed to enhance microarray-hybridization specificity.
Optimization of InGaAs/InAlAs Avalanche Photodiodes (2017)

In this paper, we report a two-dimensional (2D) simulation for InGaAs/InAlAs separate absorption, grading, charge, and multiplication avalanche photodiodes (SAGCM APDs) and study the effect of the charge layer and multiplication layer on the operating voltage ranges of APD. We find that with the increase of the thicknesses as well as the doping concentrations of the charge layer and the multiplication layer, the punchthrough voltage increases; with the increase of the doping concentrations of two layers and the thickness of the charge layer, the breakdown voltage decreases; with the increase of the thickness of the multiplication layer, the breakdown voltage first rapidly declines and then slightly rises.
Cell cycle expression of RNA duplex unwindase activity in mammalian cells. (1988)

An RNA duplex unwindase activity has been found by using an in vitro assay with various types of mammalian, somatic cells, including HeLa, mouse plasmacytoma, and Burkitt lymphoma. The unwindase activity is very low in mouse fibroblast 3T3 cells arrested into quiescence, but increases when the cells are released into renewed growth by serum. In addition, a gel retardation assay proved to be specific and sensitive for detection of RNA duplex-unwindase complexes.
Foam for fracturing and acid stimulation. Part. 1 (1982)

Foam was first successfully used as a fracturing fluid in the late 1960's and early 1970's in the Ohio and w. Texas areas. Since that time, much has been learned about the dynamics of foam and the fluid has been improved greatly and refined. Today, ca. 3600 foam fracs are performed each year, representing 10% of the total fracs undertaken. Foamed acid stimulation is employed in ca. 1000 wells annually. Foam has proven to be an effective stimulation fluid when used correctly, possible of engendering 10-fold and higher production increases. The full potential and benefit of foam has yet to be realized, because foam stimulation does present sometimes difficult problems in planning and execution. A better understanding of this technology will mitigate or eliminate unfounded fears as to the use of foam and provide added benefit and more productive wells for all concerned.
Return of the JRAD (2015)

Ignacio Diaz Aguilar’s felony conviction for document forgery made him a priority for deportation and disqualified him from the possibility of discretionary relief from removal, despite apparently significant equities and mitigating factors. And yet, when Federal District Court Judge Jack B. Weinstein sentenced Mr. Aguilar, he recommended that the government not deport him, even though no legal rules provided him with a route to that result. This essay places Judge Weinstein’s recommendation in a broader context, explaining its importance within the modern deportation regime. Statutory reforms and new agency practices have made criminal history the primary marker of noncitizen undesirability. Even longtime lawful permanent residents with only minor convictions often cannot escape removal or make a case for discretionary relief. As a result, the immigration system is in tension with the principle that under a humane system of justice the penalty should fit the crime.Judge Weinstein’s sentencing order in Aguilar points the way to an administrative reform that would decrease the likelihood of disproportionate removals in cases that involve noncitizens with a criminal history. This essay argues that a sentencing judge’s recommendation against deportation could serve as a disproportionality rule of thumb, tempering and refining the role that criminal history plays in deportation decisions. Immigration authorities could rely on such recommendations -- as well as other forms of relief from all-out criminal punishment (e.g., pardons, expungements, and deferred adjudications) -- as signals that a noncitizen’s encounter with the criminal system presumptively should not lead to deportation. While this presumption can and should be overcome in some situations, deportation should be the exception in cases where the end result of the criminal process involves elimination or mitigation of the underlying criminal conviction. So long as Congress fails to restore adjudicative discretion to immigration judges or to rollback over-inclusive deportation grounds through legislative means, the system must rely on second-best solutions to achieve proportionality.
Divalent cobalt as a label to study lymphocyte distribution using PET and SPECT. (1998)

These results warrant further exploration of cobalt as a PET or SPECT label of human lymphocytes.
Proliferative and cytotoxic T cells to AIDS virus glycoproteins in chimpanzees immunized with a recombinant vaccinia virus expressing AIDS virus envelope glycoproteins. (1987)

PBL from chimpanzees immunized with a recombinant vaccinia virus that expresses HIV envelope glycoproteins ("env"), were found to proliferate after stimulation with HIV or with "env". Furthermore, CTL clones lytic for autologous target cells expressing HIV envelope glycoproteins were generated after stimulation of the chimpanzees' PBL with "env", indicating that immunization of these primates with a recombinant vaccinia virus primes HIV-specific CTL and also that HIV envelope glycoproteins serve as target antigens for CTL.
Quantitative Measurement of Shear-Stress Effects on Endothelial Cells (2003)

Over the past 20 yr, great strides have been made toward understanding the role of fluid hemodynamic forces in the vascular wall homeostasis at the molecular level. In vivo studies have demonstrated that blood vessels are adaptive to physiological changes in blood flow, with vessels tending to enlarge in areas of high flow and tending to reduce their lumen diameter in low-flow regimes (1,2). Furthermore, altered hemodynamics have been implicated in the pathogenesis of many cardiovascular disorders, such as thrombosis, atherosclerosis, and vessel wall injury. Vascular endothelial cells serve as a barrier between perfused tissues and flowing blood, and they are believed to act as a sensor of the local biomechanical environment. The hemodynamic forces generated in the vasculature include frictional wall shear-stress, cyclic strain, and hydrostatic pressure (3). For the purpose of this chapter, we will focus on methods for examining the link between fluid wall shear-stress and endothelial cell function. Advances in our understanding of the effects of shear-stress on endothelial cell function require that cell populations be exposed to controlled, well-defined, flow-induced shear-stress environments. Since in vivo studies have the inherent problem that they cannot quantitatively define the shearing forces or separate their effects from the other components of the hemodynamic system, in vitro flow studies using cultured cells are extensively used.
Imaging in High Resolution HAADF-STEM (2005)

By improving coherence and brightness, HAADF-STEM enables us to obtain incoherent images with comparable resolution to HRTEM. This paper reviews imaging in the high resolution HAADF-STEM and the dynamical simulations on the basis of Bloch theory. Its capability for performing quantitative structural and compositional analysis is discussed as well. Finally the advantages and disadvantages of HAADF-STEM are presented.
Isolation and characterization of Chinese hamster ovary cell mutants defective in intracellular low density lipoprotein-cholesterol trafficking. (1990)

This paper reports the isolation and characterization of Chinese hamster ovary cell mutants defective in low density lipoprotein (LDL)-cholesterol trafficking. The parental cell line was 25-RA, which possesses LDL receptors and various cholesterogenic enzyme activities that are partially resistant to down regulation by exogenous sterols (Chang, T. Y., and J. S. Limanek. 1980. J. Biol. Chem. 255:7787-7795). Because these cells accumulate a large amount of intracellular cholesteryl ester when grown in medium containing 10% fetal calf serum, mutagenized populations of 25-RA cells were grown in the presence of a specific inhibitor of acyl-coenzyme A: cholesterol acyltransferase (ACAT), which depleted their cholesteryl ester stores. Without this cholesterol ester storage, 99% of 25-RA cells die after 5-d growth in cholesterol starvation medium, while the mutant cells, which accumulate free cholesterol intracellularly, survived. In two mutant clones chosen for characterization, activation of cholesteryl ester synthesis by LDL was markedly reduced in the mutant cells compared with 25-RA cells. This lack of activation of cholesterol ester synthesis in the mutant cells could not be explained by defective uptake and/or processing of LDL or by a decreased amount of ACAT, as determined by in vitro enzyme activity. Mutant cells grown in the presence of LDL contain numerous cytosolic particles that stain intensely with the fluorescent compound acridine orange, suggesting that they are acidic. The particles are also stained with filipin, a cholesterol-specific fluorescent dye. Indirect immunofluorescence with a monoclonal antibody specific for a lysosomal/endosomal fraction revealed a staining pattern that colocalized with the filipin signal. The mutant phenotype was recessive. The available evidence indicates that the mutant cells can take up and process LDL normally, but the hydrolyzed cholesterol accumulates in an acidic compartment, probably the lysosomes, where it can not be transported to its normal intracellular destinations.
Nitridation of Silicon and Oxidized‐Silicon (1982)

The nitridation of silicon and oxidized‐silicon has been studied. The nitrided films were prepared at 900°–1150°C under ammonia partial pressures of 10−3 to 5 kg/cm2 in nitrogen and were analyzed by ellipsometry and Auger electron spectroscopy. For films formed by nitridation of silicon, we found that the growth kinetics and properties such as chemical composition, etching rate, and oxidation resistance were independent of the ammonia partial pressure. The nitridation of silicon can be explained by a modified Ritchie‐Hunt theory, which assumes that a very slow surface reaction at the ammonia‐nitride interface is the rate‐determining factor, using the logarithmic rate law. According to this modified Ritchie‐Hunt theory, the nitridation of silicon proceeds mainly by cation migration under a constant electric field. On the other hand, it was found that the nitridation of oxidized‐silicon depended strongly on the ammonia parital pressure. This dependence may be caused by diffusion of ammonia or its derivatives through the oxide. The conversion of silicon dioxide to silicon oxynitride occurred throughout the oxide.
Automatic 3D cloning and real-time animation of a human face (2002)

We describe our techniques for the automatic cloning of a human face which can be animated in real time using both video and audio inputs. Our system can be used for video conferencing and telecooperative work at various sites with shared virtual environment inhabited by virtual clones. This work is part of a European project VIDAS (AC057). A generic face model is used which is modified to fit to the real face. Primarily, two aspects are considered: (1) modeling involving the construction of a 3D texture mapped face model fitting to the real face; (2) animation of the new constructed face. Automatic texture fitting is employed to produce the virtual face with texture mapping from the real face image. A model independent facial animation module provides real time animation. The system allows integration of audio and video inputs and produces a synchronized visual and acoustic output.
A robust scene-change detection method for video segmentation (2001)

This paper proposes a new method that combines the intensity and motion information to detect scene changes such as abrupt scene changes and gradual scene changes. Two major features are chosen as the basic dissimilarity measures, and self- and cross-validation mechanisms are employed via a static scene test. We also develop a novel intensity statistics model for detecting gradual scene changes. Experimental results show that the proposed algorithms are effective and outperform the previous approaches.
ACE1, a copper-dependent transcription factor, activates expression of the yeast copper, zinc superoxide dismutase gene. (1991)

Copper, zinc superoxide dismutase (SOD1 gene product) (superoxide:superoxide oxidoreductase, EC 1.15.1.1) is a copper-containing enzyme that functions to prevent oxygen toxicity. In the yeast Saccharomyces cerevisiae, copper levels exert some control over the level of SOD1 expression. We show that the ACE1 transcriptional activator protein, which is responsible for the induction of yeast metallothionein (CUP1) in response to copper, also controls the SOD1 response to copper. A single binding site for ACE1 is present in the SOD1 promoter region, as demonstrated by DNase I protection and methylation interference experiments, and is highly homologous to a high-affinity ACE1 binding site in the CUP1 promoter. The functional importance of this DNA-protein interaction is demonstrated by the facts that (i) copper induction of SOD1 mRNA does not occur in a strain lacking ACE1 and (ii) it does not occur in a strain containing a genetically engineered SOD1 promoter that lacks a functional ACE1 binding site.
Stronger Baselines for Trustable Results in Neural Machine Translation (2017)

Interest in neural machine translation has grown rapidly as its effectiveness has been demonstrated across language and data scenarios.
Tunable threshold voltage and flatband voltage in pentacene field effect transistors (2006)

Charged interface states are introduced by UV-ozone treatment of a polymer gate dielectric, parylene, prior to deposition of the organic semiconductor, pentacene, thereby modifying the organic field effect transistor (OFET) operation from enhancement to depletion mode. Quasistatic capacitance-voltage measurements and the corresponding current-voltage characteristics show that the threshold voltage VT and flatband voltage VFB can be shifted by over +50V, depending on the ozone exposure time. This work demonstrates that careful control of the semiconductor-insulator interface state densities is essential to VT and VFB control and the fabrication of reliable OFET integrated circuits.
Apparatus for the growth of crystals from small volumes of solution (1972)

An apparatus has been developed for the growth of large single crystals from minimum quantities of solvent. The technique has been used to grow crystals of potassium dihydrogen orthophosphate and potassium dideuterium orthophosphate, the latter from D2O.
New algorithms for fast discovery of association rules (1997)

Association rule discovery has emerged as an important problem in knowledge discovery and data mining. The association mining task consists of identify-ing the frequent itemsets, and then forming conditional implication rules among them. In this paper we present ecient algorithms for the discovery of frequent itemsets, which forms the compute intensive phase of the task. The algorithms utilize the structural properties of frequent itemsets to facilitate fast discovery. The related database items are grouped together into clusters representing the potential maximal frequent itemsets in the database. Each cluster induces a sub-lattice of the itemset lattice. Ecient lattice traversal techniques are pre-sented, which quickly identify all the true maximal frequent itemsets, and all their subsets if desired. We also present the eect of using dierent database layout schemes combined with the proposed clustering and traversal techniques. The proposed algorithms scan a (pre-processed) database only once, addressing the open question in association mining, whether all the rules can be eciently extracted in a single database pass. We experimentally compare the new algo-rithms against the previous approaches, obtaining improvements of more than an order of magnitude for our test databases.
The allegiance and experience of student literacy teachers in the post‐compulsory education context: competing communities of practice (2010)

This article contributes to a body of work that addresses the process of ‘becoming a teacher’ and focuses on the relationship of the higher education (HE) (theoretical) component of the teaching qualification to the (practical) placement experience that student teachers undertake. This study approaches the data through the concept of ‘community of practice’ aiming to interrogate its usefulness as a theoretical idea that can illuminate the experience of student teachers studying on a Post Graduate Certificate in Education, Post‐Compulsory Education (PGCE PCE) for teachers of adult literacy course in the UK. The ‘community of practice’ concept has been widely used to describe the process whereby student teachers gain entry into a professional identity via ‘situated learning’. The idea is attractive, suggesting as it does that there is a strongly communicative dimension to learning how to teach and that an apprenticeship‐type relationship – in which culture and values are shared – is possible. This article originates from a small‐scale research project that used a collaborative methodological approach. It considers some broad applications of the communities of practice concept from the literature as applied to post‐compulsory education teacher education. Then, drawing on ethnographic data from a cohort of pre‐service literacy student teachers, the article goes on to suggest an alternative model of such a community. The central perspective it posits is that it is possible to achieve shared understandings about what it means to be a literacy teacher in further education (FE) settings in a localised community of practice (the tutor group itself), but that one of the cohesive forces that helps sustain such a community is that it defines itself against many of the cultural norms that have taken root in the current culture of FE colleges in England, not least among Skills for Life teachers.