gebhart/patrepeval huggingface dataset:
A new disulfide‐linked dimer of a single‐chain antibody fragment against human CD47 induces apoptosis in lymphoid malignant cells via the hypoxia inducible factor‐1α pathway (2011)

CD47 belongs to the immunoglobulin superfamily and is associated with β-integrins. Recently it was reported that CD47 ligation rapidly induces apoptosis in B-chronic lymphocytic leukemia (CLL) cells. Chronic lymphocytic leukemia is still an incurable hematological malignancy even with the novel therapeutic agents; therefore, new and effective agents for the treatment of CLL in clinical settings are urgently needed. We generated a murine monoclonal antibody against an extracellular domain of human CD47 (designated MABL). Subsequently, we created a disulfide-stabilized dimer of a single-chain antibody fragment of MABL (S-S diabody) to get rid of the adverse effect of MABL such as hemagglutination. In this study, we analyzed the effects of this new antibody on cellular proliferation, and the molecular mechanism of CD47-mediated apoptosis in human lymphoid malignant cells. Treatment with S-S diabody alone induced apoptosis of CD47-positive primary B-CLL and leukemic cells (MOLT-4 and JOK-1). In addition, administration of S-S diabody significantly prolonged the survival of severe combined immunodeficiency (SCID) mice inoculated with JOK-1 cells. In gene expression profiling of the S-S diabody-treated MOLT-4 cells, hypoxia inducible factor (HIF)-1α downstream genes (RTP801 and BNIP3) were upregulated, and the mRNA expression levels of HIF-1α, RTP801 and BNIP3 were increased. Knockdown of HIF-1α by siRNA repressed S-S diabody-induced apoptosis in MOLT4 cells. In conclusion, CD47 will be a molecular target for the treatment of lymphoid malignancies, and S-S diabody might have potential as a novel therapeutic agent for B-CLL.
Characterization of Slag, Fly Ash and Portland Cement for Saltstone (2006)

Batch-to-batch variability in the chemical and physical properties of the fly ash, slag and portland cement (binders) will be an ongoing concern over the many years that salt waste from Tank 50 will be processed into grout at the Saltstone Processing Facility. This batch-to-batch variability in the properties of the binder materials translates to variability in the fresh and cured properties of Saltstone. Therefore, it is important to quantify the batch-to-batch variability of the binder materials and the resultant variation in grout properties. This report is the starting point for that process by providing the baseline (reference point) binder properties to which future batches of binder materials can be compared. For this characterization effort, properties of fly ash, slag and portland cement were obtained and documented in this report. These properties included particle size distribution by laser light scattering and dry sieving, particle size and morphology by scanning electron microscopy, true, aerated and tapped densities, chemical composition, rheological properties of the water based slurries made from individual binder material, and volatility through thermogravimetric analysis and differential thermal analysis. The properties presented in this report also provide a baseline data set to assist in problem solving efforts when or if unanticipated and/or unwanted processing events occur at the Saltstone Processing Facility.
I'm done simulating; now what? Verification coverage analysis and correctness checking of the DEC chip 21164 Alpha microprocessor (1996)

Digital's Alpha-based DECchip 21164 processor was verified extensively prior to fabrication of silicon. This simulation-based verification effort used implementation-directed, pseudorandom exercisers which were supplemented with implementationspecific, hand-generated tests. Special emphasis was placed on the tasks of checking for correct operation and functional coverage analysis. Coverage analysis shows where testing is incomplete, under the assumption that untested logic often contains bugs. Correctness checkers are various mechanisms (both during and after simulation) that monitor a test to determine if it was successful. This paper details the coverage analysis and correctness checking techniques that were used. We show how our methodology and its implementation was successful, and we discuss the reasons why this methodology allowed several minor bugs to escape detection until the first prototype systems were available. These bugs were corrected before any chips were shipped to customers.
Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits (2009)

Loss or gain of DNA methylation can affect gene expression and is sometimes transmitted across generations. Such epigenetic alterations are thus a possible source of heritable phenotypic variation in the absence of DNA sequence change. However, attempts to assess the prevalence of stable epigenetic variation in natural and experimental populations and to quantify its impact on complex traits have been hampered by the confounding effects of DNA sequence polymorphisms. To overcome this problem as much as possible, two parents with little DNA sequence differences, but contrasting DNA methylation profiles, were used to derive a panel of epigenetic Recombinant Inbred Lines (epiRILs) in the reference plant Arabidopsis thaliana. The epiRILs showed variation and high heritability for flowering time and plant height ( approximately 30%), as well as stable inheritance of multiple parental DNA methylation variants (epialleles) over at least eight generations. These findings provide a first rationale to identify epiallelic variants that contribute to heritable variation in complex traits using linkage or association studies. More generally, the demonstration that numerous epialleles across the genome can be stable over many generations in the absence of selection or extensive DNA sequence variation highlights the need to integrate epigenetic information into population genetics studies.
Effects of adrenoceptor agonists and antagonists on smooth muscle cells and neuromuscular transmission in the guinea‐pig renal artery and vein (1983)

In the guinea-pig renal artery and vein, the membrane potential was -66.8 mV and -46.8 mV, the length constant 0.54 mm and 0.43 mm, and the time constant 240 ms and 98 ms, respectively. The maximum slope of the depolarization produced by a 10 fold increase [K]o was 46 mV in the renal artery and 39 mV in the renal vein. Noradrenaline (NA over 5 X 10(-7)M in the artery and over 10(-7)M in the vein) depolarized the membrane and slightly reduced the membrane resistance, assessed from relative changes in the amplitude of electrotonic potential. The action of NA was suppressed by prazosin in the artery but by yohimbine in the vein, i.e. the alpha 1-adrenoceptor is present in the extrajunctional muscle membrane in the renal artery while the alpha 2-adrenoceptor is present in the renal vein. Dopamine and isoprenaline did not modify the membrane properties. In the renal artery, repetitive perivascular nerve stimulation (0.1 ms, 50 Hz, 5 shocks) evoked excitatory junction potential (e.j.p.). Applications of guanethidine (10(-6) M) or tetrodotoxin (3 X 10(-7) M) abolished the generation of the e.j.p.. Low concentrations of phentolamine (5 X 10(-7) M), prazosin (10(-7) M) and yohimbine (5 X 10(-7) M) enhanced the e.j.p. amplitude, while high concentrations of phentolamine (10(-5) M) and prazosin (greater than 10(-5) M) reduced the amplitude of e.j.p.s. NA, dopamine and clonidine consistently suppressed the amplitude of e.j.ps, at any given concentration over 10(-7) M. Spontaneous generated miniature e.j.ps (m.e.j.ps) were recorded on rare occasions. Phentolamine and yohimbine both at 5 x 10(-7) M and prazosin 10(-7) M increased the appearance of m.e.j.ps. 5 In the renal vein, repetitive nerve stimulation failed to generate the e.j.p. Sympathetic innervation to this tissue seems to be sparse. 6 Specificity of innervation and adrenoceptors present on smooth muscle cells in both the renal artery and vein are discussed, and the presynaptic regulation ofNA release is compared with findings in other vascular tissues.
Adaptive trellis-coded modulation for bandlimited meteor burst channels (1992)

The throughput performances of three adaptive information rate techniques on the bandlimited meteor burst channel are investigated. Closed-form expressions for throughput are derived based on the channel model commonly used in the literature. The throughput performance is compared to the conventional fixed information rate modem and upper bounds on throughput improvement over the fixed rate modem are derived. It is shown that an adaptive technique that uses trellis-coded modulation (TCM) with three phase-shift keyed (PSK) signal sets can increase throughput over the conventional fixed rate modem by more than a factor of 3. Data from the US Air Force High Latitude Meteor-Scatter Test Bed confirm the superiority of the adaptive TCM technique. A practical implementation is suggested that uses a single rate 1/2 convolutional code for all three PSK signal sets. The use of this single code, versus the three best Ungerboeck codes, results in a throughput loss of less than 2%. An expression for the theoretical information capacity of the bandlimited meteor burst channel is derived. >
Dipicolinic acid (DPA) assay revisited and appraised for spore detection (1999)

Delayed gate fluorescence detection of dipicolinic acid (DPA), a universal and specific component of bacterial spores, has been appraised for use in a rapid analytical method for the detection of low concentrations of bacterial spores. DPA was assayed by fluorimetric detection of its chelates with lanthanide metals. The influence of the choice and concentration of lanthanide and buffer ions on the fluorescence assay was studied as well as the effects of pH and temperature. The optimal system quantified the fluorescence of terbium monodipicolinate in a solution of 10 microM terbium chloride buffered with 1 M sodium acetate, pH 5.6 and had a detection limit of 2 nM DPA. This assay allowed the first real-time monitoring of the germination of bacterial spores by continuously quantifying exuded DPA. A detection limit of 10(4) Bacillus subtilis spores ml-1 was reached, representing a substantial improvement over previous rapid tests.
15.3: Invited Paper : Volume Holographic Components for Display Applications (2000)

Abstract Volume holographic components are being used to enhance the performance of a variety of liquid crystal and projection display systems. Holographic components address the ever‐present need within display systems for more efficient light management. With proper design, holographic components address this need with higher light throughput, reduced thickness and weight, reduced energy consumption, and additional opportunities for unique system functions. This paper describes design parameters and examples of improved devices by introducing the unique features of diffractive holographic components. These features include angular and spectral selectivity, high efficiency, and multiple optical functions designed into single components. Holographic reflectors, front diffusers, and compensations films have been developed and used in direct view liquid crystal displays. Holographic color filters and projection screens have also been developed based on this technology. For these applications the holographic component and system will be discussed. Finally, design considerations will be discussed that relate to the development of new display systems and components.
Realization of the Quantum Toffoli Gate with Trapped Ions (2009)

Gates acting on more than two qubits are appealing as they can substitute complex sequences of two-qubit gates, thus promising faster execution and higher fidelity. One important multiqubit operation is the quantum Toffoli gate that performs a controlled NOT operation on a target qubit depending on the state of two control qubits. Here we present the first experimental realization of the quantum Toffoli gate in an ion trap quantum computer, achieving a mean gate fidelity of 71(3)%. Our implementation is particularly efficient as the relevant logic information is directly encoded in the motion of the ion string.
Orientation and three-dimensional organization of actin filaments in dividing cultured cells. (1993)

The current hypothesis of cytokinesis suggests that contractile forces in the cleavage furrow are generated by a circumferential band of actin filaments. However, relatively little is known about the global organization of actin filaments in dividing cells. To approach this problem we have used fluorescence-detected linear dichroism (FDLD) microscopy to measure filament orientation, and digital optical sectioning microscopy to perform three-dimensional reconstructions of dividing NRK cells stained with rhodamine-phalloidin. During metaphase, actin filaments in the equatorial region show a slight orientation along the spindle axis, while those in adjacent regions appear to be randomly distributed. Upon anaphase onset and through cytokinesis, the filaments become oriented along the equator in the furrow region, and along the spindle axis in adjacent regions. The degree of orientation appears to be dependent on cell-cell and cell-substrate adhesions. By performing digital optical sectioning microscopy on a highly spread NRK subclone, we show that actin filaments organize as a largely isotropic cortical meshwork in metaphase cells and convert into an anisotropic network shortly after anaphase onset, becoming more organized as cytokinesis proceeds. The conversion is most dramatic on the adhering ventral surface which shows little or no cleavage activity, and results in the formation of large bundles along the equator. On the dorsal surface, where cleavage occurs actively, actin filaments remain isotropic, showing only subtle alignment late in cytokinesis. In addition, stereo imaging has led to the discovery of a novel set of filaments that are associated with the cortex and traverse through the cytoplasm. Together, these studies provide important insights into the process of actin remodeling during cell division and point to possible additional mechanisms for force generation.
Clustering of time-course gene expression datausing a mixed-effects model with B-splines (2003)

Matlab programs are available on request from the authors.
Fabrication of surface micro- and nanostructures for superhydrophobic surfaces in electric and electronic applications (2008)

In our study, the superhydrophobic surface based on biomimetic lotus leave is explored to maintain the desired properties for self-cleaning. In controlling bead-up and roll-off characteristics of water droplets the contact angle and contact angle hysteresis were very important and we investigated the determining conditions on different model surfaces with micro- and nanostructures. Two governing equations were proposed, one for contact angle based on Laplace pressure and one for contact angle hysteresis based on Young-Dupré equation. Based on these understanding on superhydrophobicity, possible applications of the superhydrophobicity for self-cleaning and water repellency were explored and application related technical issues were addressed.&#13;\nBased on our understanding of the roughness effect on superhydrophobicity (both contact angle and hysteresis), structured surfaces from polybutadiene, polyurethane, silica, and Si etc were successfully prepared. For engineering applications of superhydrophobic surfaces, stability issues regarding UV, mechanical robustness and humid environment need to be investigated. Among these factors, UV stability is the first one to be studied. Silica surfaces with excellent UV stability were prepared. UV stability on the surface currently is 5,500 h according the standard test method of ASTM D 4329. No degradation on surface superhydrophobicity was observed. New methods for preparing superhydrophobic and transparent silica surfaces were investigated using urea-choline chloride eutectic liquid to generate fine roughness and reduce the cost for preparation of surface structures. &#13;\nAnother possible application for self-cleaning in photovoltaic panels was investigated on Si surfaces by construction of the two-scale rough structures followed by fluoroalkyl silane treatment. &#13;\nRegarding the mechanical robustness, epoxy-silica superhydrophobic surfaces were prepared by O2 plasma etching to generate enough surface roughness of silica spheres followed by fluoroalkyl silane treatment. A robustness test method was proposed and the test results showed that the surface is among the most robust surfaces for the superhydrophobic surfaces we prepared and currently reported in literature.
Role of intracellular calcium handling in force-interval relationships of human ventricular myocardium. (1990)

Experiments were performed in human working myocardium to investigate the relationship of intracellular calcium handling and availability to alterations in the strength of contraction produced by changes in stimulation rate and pattern. Both control and myopathic muscles exhibited potentiation of peak isometric force during the postextrasystolic contraction which was associated with an increase in the peak intracellular calcium transient. Frequency-related force potentiation was attenuated in myopathic muscles compared to controls. This occurred despite an increase in resting intracellular calcium and in the peak amplitude of the calcium transient as detected with aequorin. Therefore, abnormalities in contractile function of myopathic muscles during frequency-related force potentiation are not due to decreased availability of intracellular calcium, but more likely reflect differences in myofibrillar calcium responsiveness. Sarcolemmal calcium influx may also contribute to frequency-related changes in contractile force in myopathic muscles as suggested by a decrease in action potential duration with increasing stimulation frequency which is associated with fluctuations in peak calcium transient amplitude.
Scattering of Surface Plasmon Polaritons by a Circularly Symmetric Surface Defect (1997)

By the use of the method of reduced Rayleigh equations, we develop a theory of the scattering of a surface plasmon polariton from a cirularly symmetric defect on a metal surface. We derive and solve one-dimensional integral equations for the scattering amplitudes corresponding to different rotational numbers $m$. We calculate the differential cross sections for scattering into the vacuum and into other surface waves, and the field intensity near the surface. The results show agreement with recent experimental data. We also consider resonant scattering due to surface shape resonances.
Viral hepatitis comparative epidemiology (1990)

The epidemiology of HAV, HBV, HCV, HDV and HEV is compared. Spread of HAV and HEV is by the faecal/oral route whereas HBV, HCV and HDV are spread by blood or blood products. HEV is more likely to produce large epidemics than HAV but sporadic cases also occur. HBV, HCV and HDV all occur after blood transfusion, in haemophiliacs and intravenous drug abusers but they differ in their geographical distribution and in the frequency of perinatal transmission which is only common with HBV. Superinfection and interaction between these viruses is discussed.
Synthesis and enzymic and ionotropic activity of some new 8-substituted and 6,8-disubstituted derivatives of adenosine cyclic 3',5'-monophosphate (1980)

The synthesis of certain new 8-(arythio)- and 8-(alkylthio)-cAMP derivatives and N6-alkyl- and N6-dialkyl-8-(arylthio) and -8-(alkylthio) derivatives of cAMP is reported. On the basis of activation of protein kinase, several N6-alkyl-8-(benzylthio)-cAMP derivatives were selected for evaluation as inotropic agents using cat papillary muscle in vitro. Activity in these studies resulted in the selection of several analogues for in vivo studies in the anesthetized dogs. The best inotropic agent selected on the basis of in vivo studies was N6-butyl-8-(benzylthio)-cAMP (26), which exhibited an increase in blood-flow rate of 85% with no increase in heart rate. A large-scale synthesis of 26 from cAMP is reported via N1-alkylation, followed by a Dimroth rearrangement, reduction, bromination, and nucleophilic displacement via benzyl mercaptan. The N6-alkyl-8-substituted-cAMP derivatives represent a new class of potent inotropic agents. The direct mechanism of action of 26 suggests the possible utility of this cyclic nucleotide to treat clinical myocardial infarction by rapid intravenous infusion.
Alterations in bovine lymphocyte function during the periparturient period (1989)

Lymphocytes from 8 Holstein heifers were evaluated during the periparturient period for mitogen-induced lymphocyte blastogenic responses. Phytohemagglutinin P- and concanavalin A-induced lymphocyte blastogenesis increased 2 and 3 weeks before parturition, respectively. However, by the first week after parturition, lymphocyte blastogenesis was markedly impaired.
First-principles studies of GaN(0001) heteroepitaxy onZrB2(0001) (2005)

We conduct first-principles total-energy density functional calculations to study the heteroepitaxial growth behavior of GaN(0001) on $\mathrm{Zr}{\mathrm{B}}_{2}(0001)$ substrates. Using repeated free-surface terminated slabs, our calculated surface energies suggest that the $\mathrm{Zr}{\mathrm{B}}_{2}(0001)$ surface is Zr terminated. The relative stability of six different models of the $\mathrm{Ga}\mathrm{N}(0001)∕\mathrm{Zr}{\mathrm{B}}_{2}(0001)$ interface is examined as a function of the chemical potentials of Ga and Zr, and the most favorable interface consists of tetrahedrally coordinated N with one Ga-N bond and three N-Zr bonds. This interface structure gives rise to N-polarity in the GaN epitaxial film. Both of these findings agree with previously reported experimental results.
Human Cathepsin F (1998)

A cDNA for a novel human papain-like cysteine protease, designated cathepsin F, has been cloned from a lambdagt10-skeletal muscle cDNA library. The nucleotide sequence encoded a polypeptide of 302 amino acids composed of an 88-residue propeptide and a 214-residue mature protein. Protein sequence comparisons revealed 58% homology with cathepsin W; about 42-43% with cathepsins L, K, S, H, and O; and 38% with cathepsin B. Sequence comparisons of the propeptides indicated that cathepsin F and cathepsin W may form a new cathepsin subgroup. Northern blot analysis showed high expression levels in heart, skeletal muscle, brain, testis, and ovary; moderate levels in prostate, placenta, liver, and colon; and no detectable expression in peripheral leukocytes and thymus. The precursor polypeptide of human recombinant cathepsin F, produced in Pichia pastoris, was processed to its active mature form autocatalytically or by incubation with pepsin. Mature cathepsin F was highly active with comparable specific activities toward synthetic substrates as reported for cathepsin L. The protease had a broad pH optimum between 5.2 and 6.8. Similar to cathepsin L, its pH stability at cytosolic pH (7.2) was short, with a half-life of approximately 2 min. This may suggest a function in an acidic cellular compartment. Transient expression of T7-tagged cathepsin F in COS-7 cells revealed a vesicular distribution of the gene product in the juxtanuclear region of the cells. However, contrary to all known cathepsins, the open reading frame of the cathepsin F cDNA did not encode a signal sequence, thus suggesting that the protease is targeted to the lysosomal compartment via an N-terminal signal peptide-independent lysosomal targeting pathway.
Normally-On SiC JFETs in power converters: Gate driver and safe operation (2010)

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