gebhart/patrepeval huggingface dataset:
3D Multisource Full‐Waveform Inversion using Dynamic Random Phase Encoding (2010)

We have developed a multisource full‐waveform inversion algorithm using a dynamic phase encoding strategy with dual‐randomization—both the position and polarity of simultaneous sources are randomized and changed every iteration. The dynamic dual‐randomization is used to promote the destructive interference of crosstalk noise resulting from blending a large number of common shot gathers into a supergather. We compare our multisource algorithm with various algorithms in a numerical experiment using the 3D SEG/EAGE overthrust model and show that our algorithm provides a higher‐quality velocity tomogram than the other methods that use only monorandomization. This suggests that increasing the degree of randomness in phase encoding should improve the quality of the inversion result.
Peptide-induced anergy in allergen-specific human Th2 cells results in lack of cytokine production and B cell help for IgE synthesis. Reversal by IL-2, not by IL-4 or IL-13 (1995)

The induction of anergy in T cells is believed to be the result of triggering of the TCR in the absence of adequate costimulation mediated through the interaction of CD28 and its ligands, CD80 and CD86. Here, we demonstrate that stimulation of human group I allergen in Dermatophagoides pteronyssinus extract (Der p 1)-specific CD4+ Th2-like T cell clones with Der p 1-derived peptides in the absence of professional APC results in a state of nonresponsiveness. The induction of anergy occurred despite the expression of high levels of CD28, CD80, and CD86 on the surface of the T cell clones and was not prevented by the addition of anti-CD28 mAb. The anergic, Der p 1-specific, Th2 cells failed to mobilize calcium from intracellular stores, to proliferate, and to produce IL-2, IL-4, IL-13, GM-CSF, and TNF-alpha following optimal stimulation with Der p 1-derived peptide and autologous APC. However, they mobilized intracellular calcium following stimulation with Ca(2+)-ionophore and produced all of the above cytokines, including IFN-gamma, when stimulated with phorbol ester and Ca2+ ionophore. These results indicate that the anergic T cell clones are capable of responding to signals circumventing the TCR/CD3 complex activation pathway. In contrast to T cell clones optimally activated with peptide and APC, anergic T cells failed to induce IgG4 and IgE synthesis when cocultured with B cells, even in the presence of exogenous IL-4 or IL-13. Anergic T cells expressed normal levels of CD40L, suggesting that their inability to help in Ig production by B cells is due to conditions other than a lack of expression of this molecule. Finally, exogenous IL-2 restored the helper function of anergic Th2 T cells for IgE production by B cells, which was greatly enhanced by the addition of IL-4 or IL-13. These data suggest that induction of anergy in allergen-specific Th2 T cells by allergen-derived peptides may play an important role in the successful desensitization of allergic patients.
A New Type of Catalytic Tandem 1,4-Addition−Aldol Reaction Which Proceeds through an (Oxa-π-allyl)rhodium Intermediate (2002)

The reaction of 9-aryl-9-borabicyclo[3.3.1]nonanes (B-Ar-9BBN) with alpha,beta-unsaturated ketones and aldehydes in the presence of 3 mol % [Rh(OMe)(cod)](2) in toluene at 20 degrees C for 2 h gave high yields of the tandem 1,4-addition-aldol reaction products with high syn selectivity. The reaction proceeds through the catalytic cycle consisting of 1,4-addition of an organorhodium species to an alpha,beta-unsaturated ketone and the aldol addition of the resulting (oxa-pi-allyl)rhodium intermediate to an aldehyde.
Role of myokines in exercise and metabolism (2007)

During the past 20 yr, it has been well documented that exercise has a profound effect on the immune system. With the discovery that exercise provokes an increase in a number of cytokines, a possible link between skeletal muscle contractile activity and immune changes was established. For most of the last century, researchers sought a link between muscle contraction and humoral changes in the form of an “exercise factor,” which could mediate some of the exercise-induced metabolic changes in other organs such as the liver and the adipose tissue. We suggest that cytokines and other peptides that are produced, expressed, and released by muscle fibers and exert either paracrine or endocrine effects should be classified as “myokines.” Since the discovery of interleukin (IL)-6 release from contracting skeletal muscle, evidence has accumulated that supports an effect of IL-6 on metabolism. We suggested that muscle-derived IL-6 fulfils the criteria of an exercise factor and that such classes of cytokines should be named “myokines.” Interestingly, recent research demonstrates that skeletal muscles can produce and express cytokines belonging to distinctly different families. Thus skeletal muscle has the capacity to express several myokines. To date the list includes IL-6, IL-8, and IL-15, and contractile activity plays a role in regulating the expression of these cytokines in skeletal muscle. The present review focuses on muscle-derived cytokines, their regulation by exercise, and their possible roles in metabolism and skeletal muscle function and it discusses which cytokines should be classified as true myokines.
A Yolk-Shell Design for Stabilized and Scalable Li-Ion Battery Alloy Anodes (2012)

Silicon is regarded as one of the most promising anode materials for next generation lithium-ion batteries. For use in practical applications, a Si electrode must have high capacity, long cycle life, high efficiency, and the fabrication must be industrially scalable. Here, we design and fabricate a yolk-shell structure to meet all these needs. The fabrication is carried out without special equipment and mostly at room temperature. Commercially available Si nanoparticles are completely sealed inside conformal, thin, self-supporting carbon shells, with rationally designed void space in between the particles and the shell. The well-defined void space allows the Si particles to expand freely without breaking the outer carbon shell, therefore stabilizing the solid-electrolyte interphase on the shell surface. High capacity (∼2800 mAh/g at C/10), long cycle life (1000 cycles with 74% capacity retention), and high Coulombic efficiency (99.84%) have been realized in this yolk-shell structured Si electrode.
Association of chromosome 10 losses and negative prognosis in oligoastrocytomas (2002)

Oligoastrocytomas are mixed gliomas harboring different genetic alterations and with heterogeneous clinical evolution. We have looked for correlations between genetic losses and clinical evolution in 34 oligoastrocytomas. Loss of heterozygosity (LOH) with different microsatellite markers was studied on chromosomes 1p, 10q, 17p, and 19q. LOH on 1p was found in 44% of the tumors, on 10q in 24%, on 17p in 18%, and on 19q in 38%. LOH on 1p and 19q was combined in 29% of the patients. LOH on 1p was associated with significantly longer overall survival (p = 0.0092) and LOH on 10q with shorter overall survival (p = 0.0206). The observation that LOH on 10q predicts a short survival in oligoastrocytomas is novel and provides further evidence that genetic analysis may help to predict the clinical evolution of different gliomas, giving a more rationale basis to therapeutic options.
Submicrometer Dimple Array Based Interference Color Field Displays and Sensors (2006)

We report a technique for producing bright color fields over extended surfaces, via optical interference, with the capability of producing arbitrary visible colors in areas as small as 100 microm2. Periodic arrays of submicrometer dimples are fabricated on reflective silicon surfaces, and diffraction-induced mutual interference of light reflected from the upper and lower levels of the dimpled surfaces generates color depending on wavelength scaled dimple depth and periodicity. Colors of the entire visible spectrum can be generated by dimple arrays with different dimple depths. The topological permeability of such an open surface readily allows infusion of liquids, with different refractive indices, for color switching and detection. These easy to fabricate, scalable, robust devices, on solid as well as flexible supports, could find a wide range of applications such as cheap high-resolution printable dye/pigment-free displays, reliable index-of-refraction sensors with color readout for liquids, and lab-on-chip liquid flow monitors.
Predicting Optimal Resolving Power for Ambient Pressure Ion Mobility Spectrometry (2008)

Although diffusion theory predicts that IMS resolving power increases with the square root of the voltage applied across the drift tube, in practice, there exists an optimum voltage above which resolving power decreases. This optimum voltage was determined to be both compound and initial ion pulse width dependent. A "conditional" resolving power equation is introduced that can be used to quickly approximate realistic resolving powers for specific instrumental operating parameters and compounds. Using four common environmental contaminants (trichloroethylene, tetrachloroethylene, methyl tert-butyl ether, methyl isobutyl ketone), diffusion-limited (theoretical), R d, conditional, R c, and actual (or measured), R m, IMS resolving powers were determined and compared for a small IMS instrument designed for subsurface measurements. Detection limits determined at the optimal resolving power for the environmental contaminants ranged from 18 parts per trillion volume-to-volume (ppt v) to 80 parts per billion volume-to-volume (ppb v). The maximal measured resolving power for our small, ambient-pressure stand-alone IMS ranged from 42 to 54, yielding an IMS resolving power efficiency, defined as R m/ R c x 100%, of 56-74% of the maximal conditional resolving power possible.
Heuristic approach to deriving models for gene finding (1999)

Computer methods of accurate gene finding in DNA sequences require models of protein coding and non-coding regions derived either from experimentally validated training sets or from large amounts of anonymous DNA sequence. Here we propose a new, heuristic method producing fairly accurate inhomogeneous Markov models of protein coding regions. The new method needs such a small amount of DNA sequence data that the model can be built 'on the fly' by a web server for any DNA sequence >400 nt. Tests on 10 complete bacterial genomes performed with the GeneMark.hmm program demonstrated the ability of the new models to detect 93.1% of annotated genes on average, while models built by traditional training predict an average of 93.9% of genes. Models built by the heuristic approach could be used to find genes in small fragments of anonymous prokaryotic genomes and in genomes of organelles, viruses, phages and plasmids, as well as in highly inhomogeneous genomes where adjustment of models to local DNA composition is needed. The heuristic method also gives an insight into the mechanism of codon usage pattern evolution.
147. Effective Gene Transfer to Human Glioma Cells Using High Capacity Adenoviral Vectors: Human Glioma Cells Express Substantial Levels of CAR and Integrin Adenoviral Co-Receptors (2006)

Glioblastoma Multiforme (GBM) is the most common subtype of primary brain tumor and, to date, it has no cure. Although adenoviral vectors have been used for gene delivery to glioma tumors in clinical trials, the infectivity of adenoviral vectors in human glioma cells as well as their expression of adenoviral receptors remains controversial. In the present work we report on the expression of two adenoviral receptors, i.e., Coxsackie adenoviral receptor (CAR) and Integrin αV (INT) in murine and human glioma cells. Further, we also report that novel, gutless high-capacity adenoviral (HC- Ad) vectors efficiently infect and express their respective therapeutic transgenes in glioma cell lines derived from murine and human GBM. We constructed and purified HC-Ad vectors expressing b- Galactosidase, HSV1-thymidine kinase (TK) or human soluble Flt3L (hsFlt3L). These were used to infect mouse GL26 cells, rat CNS-1 cells, and the established human glioma cell lines, U251 and U87, and the primary glioma cell lines, derived from surgical biopsies, i.e., IN859 and IN 2045. All cells tested expressed variable amounts of both, CAR and INT, as detected by immunocytochemistry and Western blots. The infectivity and expression of HC-Ad vectors encoding b-Gal was determined by immunocytochemistry and enzymatic activity. High transgene expression was achieved in all the human glioma cells, and in rat CNS-1 cells, while the expression in GL26 cells was lower. The HC-Ad vector encoding TK was successfully expressed in all the cell lines under study, as detected by immunocytochemistry. In the presence of the prodrug ganciclovir, this vector induced cell death in all the murine and human glioma cells, as measured by flow cytometric analysis of cell death. The HC-Ad vector expressing Flt3L also infected efficiently the different cell lines tested as assessed by immunocytochemistry. Finally, high levels of Flt3L were detected, by ELISA, in the supernatant of infected cultures. Our data show that adenoviral receptors are expressed not only in murine glioma cell lines used in preclinical GBM models, but also in human glioma cell lines and primary GBM cell cultures. Importantly, adenoviral vectors successfully infected human glioma cells and elicited high expression levels of the therapeutic transgenes. Taken together, our data strongly support the use of adenoviral vectors in gene therapy approaches for the treatment of human GBM.
Radio propagation characteristics for line-of-sight microcellular and personal communications (1993)

To acquire a knowledge of radio propagation characteristics in the microcellular environments for personal communications services (PCS), a comprehensive measurement program was conducted by Telesis Technologies Laboratory (TTL) in the San Francisco Bay area using three base station antenna heights of 3.2 m, 8.7 m, and 13.4 m and two frequencies at 900 MHz and 1900 MHz. Five test settings were chosen in urban, suburban, and rural areas in order to study propagation in a variety of environments. This paper reports the LOS measurements in different environments, all of which show variations of signal strength with distance that have distinct near and far regions separated by a break point. It was also found that the location of the break point for different frequencies and antenna heights can be calculated based on first Fresnel zone clearance. The regression analysis reveals a slope that is less than two before the break point, while it is greater than two after the break point. This break distance can be used to define the size of microcell and to design for fast hand-off. Beyond the first Fresnel zone break distance the base station antenna height gain was observed to approximately follow the square power law of antenna height.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Immunotoxin resistance in multidrug resistant cells. (2003)

Multidrug resistance (MDR) can be mediated, in part, by overexpression of P-glycoprotein (P-gp) and is characterized by broad resistance to several structurally, chemically, and pharmacologically distinct chemotherapeutic compounds. It has been hypothesized that immunological approaches to cytolysis may be used to overcome drug resistance. RV+ is a P-gp-expressing variant of the human myeloid leukemic cell line HL60 that displays a typical MDR phenotype. MDR RV+ cells displayed relative resistance to the immunotoxin (IT) HuM195-gelonin and to free rGelonin. K562 leukemia cells retrovirally infected to overexpress P-gp are also resistant to HuM195-gelonin. In addition, a monoclonal antibody capable of inhibiting the function of P-gp was able to partially reverse resistance to the IT. These data indicated that the expression of P-gp may contribute to IT resistance in RV+. Resistance to the IT was not mediated through decreased binding to cells, nor reduced internalization into the cell because the IT displayed similar kinetics of binding and internalization for both the parental HL60 and MDR RV+ cell lines. Comparison of the cytotoxicity of other ribosome-inactivating toxins indicated that RV+ cells were not universally resistant to toxins: RV+ cells were sensitive to the actions of ricin A chain, which acts on precisely the same RNase target as gelonin. Sensitivity of the MDR RV+ cells to the protein synthesis inhibitor cycloheximide, saponin, and Pseudomonas exotoxin A additionally confirmed that the resistance was not mediated through the ribosome and that pathways downstream from the inactivation of protein synthesis leading to cell death were not substantially perturbed in the MDR cells. Resistance could be partially abrogated by bafilomycin A, which inhibits lysosomal function. Moreover, direct visualization by confocal microscopy of the intracellular trafficking route of the IT showed that the IT accumulated preferentially in the lysosome in MDR RV+ cells but not in sensitive cells. These observations implicated the process of increased lysosomal degradation as the most likely basis for resistance. Such pathways of resistance may be important in the therapeutic applications of ITs, now becoming available for human use.
Gauging the performance of an in-situ interferometer (2000)

Recently, an in-situ technique for measuring exposure tool projection lens aberrations was introduced by Litel Instruments. In this study we attempt to gauge the performance of the interferometer through comparison of simulated lithographic patterns using the wavefronts measured by the interferometer, with experimental data collected from printed wafers. Our results compare simulation and experiment for cases of field curvature, lithographic astigmatism, linewidth abnormality, and dense- iso bias. As an additional gauge, we show that the change in the measured focus and 3rd order spherical aberration terms followed the theoretical trend for changing position along the optical axis.
Development of a Tunable Wide-Range Gene Induction System Useful for the Study of Streptococcal Toxin-Antitoxin Systems (2013)

Despite the plethora of genetic tools that have been developed for use in Streptococcus mutans, the S. mutans genetic system still lacks an effective gene induction system exhibiting low basal expression and strong inducibility. Consequently, we created two hybrid gene induction cassettes referred to as Xyl-S1 and Xyl-S2. Both Xyl-S cassettes are xylose inducible and controlled by the Bacillus megaterium xylose repressor. The Xyl-S cassettes each demonstrated >600-fold-increased reporter activity in the presence of 1.2% (wt/vol) xylose. However, the Xyl-S1 cassette yielded a much higher maximum level of gene expression, whereas the Xyl-S2 cassette exhibited much lower uninduced basal expression. The cassettes also performed similarly in Streptococcus sanguinis and Streptococcus gordonii, which suggests that they are likely to be useful in a variety of streptococci. We demonstrate how both Xyl-S cassettes are particularly useful for the study of toxin-antitoxin (TA) modules using both the previously characterized S. mutans mazEF TA module and a previously uncharacterized HicAB TA module in S. mutans. HicAB TA modules are widely distributed among bacteria and archaea, but little is known about their function. We show that HicA serves as the toxin component of the module, while HicB serves as the antitoxin. Our results suggest that, in contrast to that of typical TA modules, HicA toxicity in S. mutans is modest at best. The implications of these results for HicAB function are discussed.
Orthogonal intercellular signaling for programmed spatial behavior (2016)

Bidirectional intercellular signaling is an essential feature of multicellular organisms, and the engineering of complex biological systems will require multiple pathways for intercellular signaling with minimal crosstalk. Natural quorum-sensing systems provide components for cell communication, but their use is often constrained by signal crosstalk. We have established new orthogonal systems for cell-cell communication using acyl homoserine lactone signaling systems. Quantitative measurements in contexts of differing receiver protein expression allowed us to separate different types of crosstalk between 3-oxo-C6- and 3-oxo-C12-homoserine lactones, cognate receiver proteins, and DNA promoters. Mutating promoter sequences minimized interactions with heterologous receiver proteins. We used experimental data to parameterize a computational model for signal crosstalk and to estimate the effect of receiver protein levels on signal crosstalk. We used this model to predict optimal expression levels for receiver proteins, to create an effective two-channel cell communication device. Establishment of a novel spatial assay allowed measurement of interactions between geometrically constrained cell populations via these diffusible signals. We built relay devices capable of long-range signal propagation mediated by cycles of signal induction, communication and response by discrete cell populations. This work demonstrates the ability to systematically reduce crosstalk within intercellular signaling systems and to use these systems to engineer complex spatiotemporal patterning in cell populations.
The role of Kupffer cell activation and viral gene expression in early liver toxicity after infusion of recombinant adenovirus vectors (1997)

Systemic application of first-generation adenovirus induces pathogenic effects in the liver. To begin unraveling the mechanisms underlying early liver toxicity after adenovirus infusion, particularly the role of macrophage activation and expression of viral genes in transduced target cells, first-generation adenovirus or adenovirus vectors that lacked most early and late gene expression were administered to C3H/HeJ mice after transient depletion of Kupffer cells by gadolinium chloride treatment. Activation of NF-kappaB, and the serum levels of the proinflammatory cytokines tumor necrosis factor (TNF) and interleukin-6 (IL-6) were studied in correlation with liver damage, apoptosis, and hepatocellular DNA synthesis. While Kupffer cell depletion nearly eliminated adenovirus-induced TNF release, it resulted in a more robust IL-6 release. These responses were greatly reduced in animals receiving the deleted adenovirus. Although there were quantitative differences, NF-kappaB activation was observed within minutes of first-generation or deleted adenovirus vector administration regardless of the status of the Kupffer cells, suggesting that the induction is related to a direct effect of the virus particle on the hepatocyte. Early liver toxicity as determined by serum glutamic-pyruvic transaminase elevation and inflammatory cell infiltrates appeared to be dependent on adenovirus-mediated early gene expression and intact Kupffer cell function. Kupffer cell depletion had little effect on adenovirus-mediated hepatocyte apoptosis but did increase hepatocellular DNA synthesis. Finally, Kupffer cell depletion decreased the persistence of transgene (human alpha1-antitrypsin [hAAT]) expression that was associated with a more pronounced humoral immune response against hAAT. The elucidation of these events occurring after intravenous adenovirus injection will be important in developing new vectors and transfer techniques with reduced toxicity.