gebhart/patrepeval huggingface dataset:
Embryonic Germ Cell Lines and Their Derivation from Mouse Primordial Germ Cells (2007)

When primordial germ cells of the mouse are cultured on feeder layers with the addition of the polypeptide signalling molecules leukaemia inhibitory factor, Steel factor and basic fibroblast growth factor they give rise to cells that resemble undifferentiated blastocyst-derived embryonic stem cells. These primordial germ cell-derived embryonic germ cells (EG cells) can be induced to differentiate extensively in culture and also form teratocarcinomas when injected into nude mice. Additionally, they contribute to chimeras when injected into host blastocysts. We have derived multiple EG cell lines from 8.5 days post coitum (dpc) embryos of C57BL/6 inbred mice. Four independent EG cell lines with normal male karyotypes have formed chimeras (up to 70% coat colour chimerism) when injected into BALB/c host blastocysts. Chimeric mice from all four cell lines are fertile, but only those from one line have transmitted coat colour markers through the germline. Studies have also been carried out to determine whether gonadal primordial germ cells can give rise to pluripotent EG cells. Germ cells from gonads of 15.5 dpc C57BL/6 embryos and newborn mice failed to produce EG cell lines. EG cell lines capable of forming teratocarcinomas and coat colour chimeras have been established from primordial germ cells of 12.5 dpc genital ridges. We are currently testing the genomic imprinting status of the insulin-like growth factor type 2 receptor gene (Igf2r) in our different EG cell lines.
Polymeric electro-optic materials: optimization of electro-optic activity, minimization of optical loss, and fine-tuning of device performance (2000)

Larry R. DaltonUniversity of WashingtonDepartment of ChemistrySeattle, Washington 98195-1700andUniversity of Southern CaliforniaLoker Hydrocarbon Research InstituteLos Angeles, California 90089-1661E-mail: dalton@chem.washington.eduE-mail: ldalton@methyl.usc.eduAbstract. Translation of the large molecular hyperpolarizability of chro-mophores into large macroscopic electro-optic activity by electric ﬁeldpoling of chromophore-containing polymers is opposed by molecular-shape-dependent intermolecular electrostatic interactions. Modiﬁcationof chromophore structure (shape) to minimize the deleterious effect ofsuch interactions leads to signiﬁcant improvement in electro-optic activ-ity. Drive voltage requirements for polymeric modulator devices are re-duced to values ranging from 0.7 to 5 V. Optical loss of electro-opticpolymer materials, at the communication wavelengths of 1.3 and 1.55mm, is deﬁned by C–H, O–H, and N–H vibrational absorptions and byscattering from index of refraction gradients in the material. The formerare signiﬁcantly reduced by partial deuteration and halogenation to val-ues slightly less than 1 dB/cm. A major source of optical loss encoun-tered in the utilization of polymeric electro-optic modulator devices iscoupling losses associated with the mode mismatch between silica ﬁberwaveguides and polymeric modulator waveguides. Recently, alternativecoupling strategies based on utilization of tapered transitions and verticaltransitions have dramatically reduced coupling losses. Total insertionlosses comparable to those for lithium niobate devices are realized. Fi-nally, a phototrimming technique is developed that enables ﬁne-tuning ofthe performance of circuit elements such as power splitters.
Chemical studies of the passivation of GaAs surface recombination using sulfides and thiols (1991)

Steady-state photoluminescence, time-resolved photoluminescence, and x-ray photoelectron spectroscopy have been used to study the electrical and chemical properties of GaAs surfaces exposed to inorganic and organic sulfur donors. Despite a wide variation in S2−(aq) concentration, variation of the pH of aqueous HS−solutions had a small effect on the steady-state n-type GaAs photoluminescence intensity, with surfaces exposed to pH=8, 0.1-M HS−(aq) solutions displaying comparable luminescence intensity relative to those treated with pH=14, 1.0-M Na2S⋅9H2O(aq). Organic thiols (R-SH, where R=−CH2CH2SH or −C6H4Cl) dissolved in nonaqueous solvents were found to effect increases in steady-state luminescence yields and in time-resolved luminescence decay lifetimes of (100)-oriented GaAs. X-ray photoelectron spectroscopy showed that exposure of GaAs surfaces to these organic systems yielded thiols bound to the GaAs surface, but such exposure did not remove excess elemental As and did not form a detectable As2S3 overlayer on the GaAs. These results imply that complete removal of As0 or formation of monolayers of As2S3 is not necessary to effect a reduction in the recombination rate at etched GaAs surfaces. Other compounds that do not contain sulfur but that are strong Lewis bases, such as methoxide ion, also improved the GaAs steady-state photoluminescence intensity. These results demonstrate that a general class of electron-donating reagents can be used to reduce nonradiative recombination at GaAs surfaces, and also imply that prior models focusing on the formation of monolayer coverages of As2S3 and Ga2S3 are not adequate to describe the passivating behavior of this class of reagents. The time-resolved, high level injection experiments clearly demonstrate that a shift in the equilibrium surface Fermi-level energy is not sufficient to explain the luminescence intensity changes, and confirm that HS− and thiol-based reagents induce substantial reductions in the surface recombination velocity through a change in the GaAs surface state recombination rate.
Expression, biotinylation and purification of a biotin-domain peptide from the biotin carboxy carrier protein of Escherichia coli acetyl-CoA carboxylase (1994)

A protein segment consisting of the C-terminal 87 residues of the biotin carboxy carrier protein from Escherichia coli acetyl-CoA carboxylase was overexpressed in E. coli. The expressed biotin-domain peptide can be fully biotinylated by coexpression with a plasmid that overproduces E. coli biotin ligase. The extent of biotinylation was limited in vivo, but could be taken to completion in cell lysates on addition of ATP and biotin. We used the coexpression of biotin ligase and acceptor protein to label the biotin-domain peptide in vitro with [3H]biotin, which greatly facilitated development of a purification procedure. The apo (unbiotinylated) form of the protein was prepared by induction of biotin-domain expression in a strain lacking the biotin-ligase-overproduction plasmid. The apo domain could be separated from the biotinylated protein by ion-exchange chromatography or non-denaturing PAGE, and was converted into the biotinylated form of the peptide on addition of purified biotin ligase. The identify of the purified biotin-domain peptide was confirmed by N-terminal sequence analysis, amino acid analysis and m.s. The domain was readily produced and purified in sufficient quantities for n.m.r. structural analysis.
The dataflow model (2015)

Unbounded, unordered, global-scale datasets are increasingly common in day-to-day business (e.g. Web logs, mobile usage statistics, and sensor networks). At the same time, consumers of these datasets have evolved sophisticated requirements, such as event-time ordering and windowing by features of the data themselves, in addition to an insatiable hunger for faster answers. Meanwhile, practicality dictates that one can never fully optimize along all dimensions of correctness, latency, and cost for these types of input. As a result, data processing practitioners are left with the quandary of how to reconcile the tensions between these seemingly competing propositions, often resulting in disparate implementations and systems. We propose that a fundamental shift of approach is necessary to deal with these evolved requirements in modern data processing. We as a field must stop trying to groom unbounded datasets into finite pools of information that eventually become complete, and instead live and breathe under the assumption that we will never know if or when we have seen all of our data, only that new data will arrive, old data may be retracted, and the only way to make this problem tractable is via principled abstractions that allow the practitioner the choice of appropriate tradeoffs along the axes of interest: correctness, latency, and cost. In this paper, we present one such approach, the Dataflow Model, along with a detailed examination of the semantics it enables, an overview of the core principles that guided its design, and a validation of the model itself via the real-world experiences that led to its development.
Preparation and characterization of immunoconjugates for antibody-targeted photolysis (1990)

Monoclonal antibody (MAb)-dextran-tin(IV) chlorin e6 (SnCe6) immunoconjugates were prepared by a new technique involving the use of reducing, terminal-modified dextran carriers and site-specific modification of the Fc oligosaccharide moiety on the antibodies. Dextran carriers were synthesized to increase the number of SnCe6 molecules attached to a MAb. The dextran carriers were coupled to the MAb via a single, chain-terminal hydrazide group to prevent aggregation of MAbs. Conjugates were prepared with antimelanoma MAb 2.1 containing up to 18.9 SnCe6 molecules per MAb. Under neutral conditions, no hydrolysis of the hydrazone bond between the MAb and the dextran carrier could be detected, and the hydrazone was not stabilized by reduction with NaCNBH3 or NaBH4. Analysis of the purified immunoconjugates showed that approximately two dextran carrier chains were attached to a MAb regardless of the number of SnCe6 molecules linked to a dextran carrier. Site-specific covalent attachment of the SnCe6-dextran chains to the MAb was confirmed by SDS-PAGE. HPLC analysis of the conjugates gave a single species eluting in the range of 200-240 kDa. As determined by a competitive inhibition radioimmunoassay using viable SK-MEL-2 human malignant melanoma cells, the conjugates showed excellent retention of antigen-binding activity relative to unconjugated MAb.
Single-patch broadband circularly polarized microstrip antennas (2002)

The authors present a new design of a single-patch broadband circularly polarized microstrip antenna with dual capacitively-coupled feeds connected to a Wilkinson power divider having a 90/spl deg/-phase shift between its two outputs. A thick air substrate is used in the present proposed design, and impedance matching is obtained through capacitive coupling between the two feeds and the radiating patch. A design example of the proposed antenna with a circular radiating patch has been implemented, and experimental results show that, with the distance between the radiating patch and the ground plane being less than 10% times the center operating wavelength, the proposed antenna can have an impedance bandwidth greater than 50% and a 3-dB axial-ratio bandwidth about 34%. The antenna gain bandwidth, defined to be within 1-dB gain variation in the axial-ratio bandwidth, is 29%, with the antenna gain level about 7.0 dBi. Details of the proposed antenna design and experimental results are presented and discussed.
Fetuin/α2-HS Glycoprotein Is a Transforming Growth Factor-β Type II Receptor Mimic and Cytokine Antagonist (1996)

The serum glycoprotein fetuin is expressed during embryogenesis in multiple tissues including limb buds and has been shown to promote bone remodeling and stimulate cell proliferation in vitro. In this report, we demonstrate that fetuin antagonizes the antiproliferative action of transforming growth factor-beta1 (TGF-beta1) in cell cultures. Surface plasmon resonance measurements show that fetuin binds directly to TGF-beta1 and TGF-beta2 and with greater affinity to the TGF-beta-related bone morphogenetic proteins (BMP-2, BMP-4, and BMP-6). In a competitive enzyme-linked immunosorbent assay, fetuin blocked binding of TGF-beta1 to the extracellular domain of TGF-beta receptor type II (TbetaRII), one of the primary TGF-beta-binding receptors. A comparison of fetuin and TbetaRII shows homology in an 18-19-amino acid sequence, which we have designated TGF-beta receptor II homology 1 domain (TRH1). Since the TRH1 sequence is known to form a disulfide loop in fetuin, cyclized TRH1 peptides from both fetuin and TbetaRII were chemically synthesized and tested for cytokine binding activity. Cyclized TRH1 peptide from TbetaRII bound to TGF-beta1 with greater affinity than to BMP-2, while the cyclized TRH1 peptide from fetuin bound preferentially to BMP-2. Finally, fetuin or neutralizing anti-TGF-beta antibodies blocked osteogenesis and deposition of calcium-containing matrix in cultures of dexamethasone-treated rat bone marrow cells. In summary, these experiments define the TRH1 peptide loop as a cytokine-binding domain in both TbetaRII and fetuin and suggest that fetuin is a natural antagonist of TGF-beta and BMP activities.
Septin collar formation in budding yeast requires GTP binding and direct phosphorylation by the PAK, Cla4 (2004)

Assembly at the mother-bud neck of a filamentous collar containing five septins (Cdc3, Cdc10, Cdc11, Cdc12, and Shs1) is necessary for proper morphogenesis and cytokinesis. We show that Cdc10 and Cdc12 possess GTPase activity and appropriate mutations in conserved nucleotide-binding residues abrogate GTP binding and/or hydrolysis in vitro. In vivo, mutants unable to bind GTP prevent septin collar formation, whereas mutants that block GTP hydrolysis do not. GTP binding-defective Cdc10 and Cdc12 form soluble heteromeric complexes with other septins both in yeast and in bacteria; yet, unlike wild-type, mutant complexes do not bind GTP and do not assemble into filaments in vitro. Absence of a p21-activated protein kinase (Cla4) perturbs septin collar formation. This defect is greatly exacerbated when combined with GTP binding-defective septins; conversely, the septin collar assembly defect of such mutants is suppressed efficiently by CLA4 overexpression. Cla4 interacts directly with and phosphorylates certain septins in vitro and in vivo. Thus, septin collar formation may correspond to septin filament assembly, and requires both GTP binding and Cla4-mediated phosphorylation of septins.
Precise measurement of the self-diffusion coefficient for poly(ethylene glycol) in aqueous solution using uniform oligomers (2005)

Uniform poly(ethylene glycol) (PEG) oligomers, with a degree of polymerization n=1-40, were separated by preparative supercritical fluid chromatography from commercial monodispersed samples. Diffusion coefficients, D, for separated uniform PEG oligomers were measured in dilute solutions of deuterium oxide (D(2)O) at 30 degrees C, using pulsed-field gradient nuclear magnetic resonance. The measured D for each molecular weight was extrapolated to infinite dilution. Diffusion coefficients obtained at infinite dilution follow the scaling behavior of Zimm-type diffusion, even in the lower molecular weight range. Molecular-dynamics simulations for PEG in H(2)O also showed this scaling behavior, and reproduced close hydrodynamic interactions between PEG and water. These findings suggest that diffusion of PEG in water is dominated by hydrodynamic interaction over a wide molecular weight range, including at low molecular weights around 1000.
RIP-2 MD5 Authentication (1997)

Growth in the Internet has made us aware of the need for improved
authentication of routing information. RIP-2 provides for
unauthenticated service (as in classical RIP), or password
authentication. [STANDARDS-TRACK]
Defining the Inside and Outside of a Catalytic RNA Molecule (1989)

Ribozymes are RNA molecules that catalyze biochemical reactions. Fe(II)-EDTA, a solvent-based reagent which cleaves both double- and single-stranded RNA, was used to investigate the structure of the Tetrahymena ribozyme. Regions of cleavage alternate with regions of substantial protection along the entire RNA molecule. In particular, most of the catalytic core shows greatly reduced cleavage. These data constitute experimental evidence that an RNA enzyme, like a protein enzyme, has an interior and an exterior. Determination of positions where the phosphodiester backbone of the RNA is on the inside or on the outside of the molecule provides major constraints for modeling the three-dimensional structure of the Tetrahymena ribozyme. This approach should be generally informative for structured RNA molecules.
ATAD2 overexpression links to enrichment of B-MYB-translational signatures and development of aggressive endometrial carcinoma (2015)

We have explored the potential for clinical implementation of ATAD2 as a biomarker for aggressive endometrial cancer by investigating to what extent immunohistochemical (IHC) staining for ATAD2 is feasible, reflects clinical phenotype and molecular subgroups of endometrial carcinomas. Increased expression of the ATAD2 gene has been implicated in cancer development and progression in a number of tissues, but few studies have investigated ATAD2 expression using IHC. Here we show that high ATAD2 protein expression is significantly associated with established clinical-pathological variables for aggressive endometrial cancer, also in the subset of estrogen receptor α (ERα) positive tumors. Protein and mRNA expression of ATAD2 were highly correlated (P < 0.001), suggesting that IHC staining may represent a more clinically applicable measure of ATAD2 level in routinely collected formalin fixed paraffin embedded specimens. Gene expression alterations in samples with high ATAD2 expression revealed upregulation of several cancer-related genes (B-MYB, CDCs, E2Fs) and gene sets that previously have been linked to aggressive disease and potential for new targeting therapies. Our results support that IHC staining for ATAD2 may be a clinically applicable biomarker reflecting clinical phenotype and targetable alterations in endometrial carcinomas to be further explored in controlled clinical trials.
Targeted Liposomes: Convenient Coupling of Ligands to Preformed Vesicles Using “Click Chemistry” (2006)

An efficient and convenient chemoselective conjugation method based on "click chemistry" was developed for coupling ligands to the surface of preformed liposomes. It can be performed under mild conditions in aqueous buffers; the use of a water soluble Cu(I) chelator, such as bathophenanthrolinedisulfonate, was essential to obtain good yields in reasonable reaction times. A model reaction was achieved in which, in a single step, an unprotected alpha-D-mannosyl derivative carrying a spacer arm functionalized with an azide group was conjugated to the surface of vesicles presenting a synthetic lipid carrying a terminal alkyne function. When liposomes composed of saturated phospholipids were used, the reaction conditions developed in the present work did not damage the membranes as measured by the absence of leakage of entrapped 5,6-carboxyfluorescein. Moreover, as assessed by agglutination experiments using concanavalin A, the mannose residues were perfectly accessible on the surface of the targeted vesicles.
Time-frequency transforms: a new approach to first heart sound frequency dynamics (1992)

The binomial joint time-frequency transform is used to test the hypothesis that first heart sound frequency rises during the isovolumic contraction period. Cardiac vibrations were recorded from eight open-chest dogs using an ultralight accelerometer cemented directly to the epicardium of the anterior left ventricle. Three characteristic time-frequency spectral patterns were evident in the animals investigated: (1) a frequency component that rose from approximately 40-140 Hz in a 30-50-ms interval immediately following the ECG R-wave, (2) a slowly varying or static frequency of 60-100 Hz beginning midway through the isovolumic contraction period, and (3) broadband peaks occurring at the time of the Ia and Ib high frequency components. The binomial transform provided much better resolution than the spectrograph or spectrogram. By revealing the onset and dynamics of first heart sound frequencies, time-frequency transforms may allow mechanical assessment of individual cardiac structures.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Imaging of Aortic Atherosclerotic Lesions by <sup>125</sup>I-LDL, <sup>125</sup>I-Oxidized-LDL, <sup>125</sup>I-HDL and <sup>125</sup>I-BSA (2001)

Our findings demonstrate that both (125)I-HDL and (125)I-BSA as well as (125)I-LDL are accumulated in atherosclerotic plaques and that they can be used for the detection of atherosclerotic lesions.
Inflammation-Induced IL-6 Functions as a Natural Brake on Macrophages and Limits GN (2015)

IL-6 can mediate proinflammatory effects, and IL-6 receptor (IL-6R) blockade as a treatment for inflammatory diseases has entered clinical practice. However, opposing effects of IL-6 have been observed in models of GN. Although IL-6 is proinflammatory in murine lupus nephritis, protective effects have been observed for IL-6 in the nephrotoxic nephritis (NTN) model of acute crescentic GN. In light of the potential dangers of IL-6-directed treatment, we studied the mechanisms underlying the contradictory findings in GN. IL-6 can signal through the membrane-bound IL-6R, which is expressed only on hepatocytes and certain leukocytes (classic), or through the soluble IL-6R, which binds the ubiquitously expressed gp130 (alternative). Preemptive treatment of mice with anti-IL-6R or anti-IL-6 worsened NTN, whereas selective blockade of alternative IL-6 signaling by the fusion protein sgp130Fc did not. FACS analysis of mouse spleen cells revealed proinflammatory macrophages express the highest levels of IL-6Rα, and in vitro treatment with IL-6 blocked macrophage proliferation. Furthermore, proinflammatory macrophages were expanded during inflammation in IL-6(-/-) mice. Late application of anti-IL-6 after establishment of adaptive nephritogenic immunity was sufficient to aggravate NTN within 2.5 days, a period when macrophages are active. Finally, NTN was aggravated in mice with macrophage-specific impairment of IL-6 classic signaling, coincident with enhanced macrophage proliferation and accumulation in the kidney. Our data thus reveal a novel mechanism in which IL-6-mediated dampening of macrophage activation protects tissues from overshooting immune responses. This finding has important implications for potential IL-6-directed therapies and supports the careful choice of recipient patients and timing.