gebhart/patrepeval huggingface dataset:
Fabrication of Gold Nanoparticles by Pulsed Laser Ablation in Aqueous Media (2008)

The growth of Au nanoparticles by laser ablation processes has been systematically investigated. The morphology of Au metal nanoparticles was characterized with respect to laser wavelength, pulse duration, pulse energy, and surfactant concentrations in order to understand the nanoparticle formation process during laser ablation. Three different laser wavelengths including a nanosecond excimer laser operating at 248 nm, femto-second Ti:Sapphire laser operating at 776 nm and nanosecond diode-pumped Nd:YAG laser operating at its second harmonic wavelength of 532 nm were used for Au nanoparticles fabrication in surfactant-free and surfactant-containing aqueous solutions. Field emission SEM, XRD and UV-visible absorption spectrum were used for the characterization of Au nanoparticles. The parameters controlling the morphology of Au nanoparticles during laser ablation in surfactant-free and surfactant-containing aqueous media are discussed. It was found that particle size and size distribution of Au nanoparticles produced by nanosecond Nd:YAG and KrF excimer lasers are less affected by the laser fluence than that of femtosecond Ti:Sapphire laser.
Alpha-emitting bismuth cyclohexylbenzyl DTPA constructs of recombinant humanized anti-CD33 antibodies: pharmacokinetics, bioactivity, toxicity and chemistry. (1999)

Alpha-emitting antibodies are among the most potent cytotoxic agents known, yet are specific and appear safe in vivo. The physical and biochemical characteristics of the 213Bi isotope and its generation, as well as the biochemistry of the 213Bi-labeled CHX-A-DTPA-HuM195 construct, make it possible to use the constructs safely and feasibly in humans at therapeutic levels.
Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks (2015)

On both singled ended and paired-end synthetic next generation DNA sequence GCAT benchmarks Bowtie2GP runs up to 45% faster than Bowtie2. The lost in accuracy can be as little as 0.2-0.5% but up to 2.5% for longer sequences.
Inverted T channel FET (ITFET) - Fabrication and characteristics of vertical-horizontal, thin body, multi-gate, multi-orientation devices, ITFET SRAM bit-cell operation. A novel technology for 45nm and beyond CMOS. (2006)

In this paper we demonstrate for the first time a novel CMOS IT-FET (inverted T channel FET) architecture. We demonstrate well functional ITFET SRAM bit-cells. Vertical devices such as FinFET and planar ultra thin body devices have been shown to exhibit good short channel control and proposed for future device scaling. The ITFET is novel device architecture that takes advantage of both vertical and horizontal thin-body devices. A doped channel IT-FET process has been developed and is the focus of this paper. This technology can be scaled beyond 45nm technologies using undoped channels. An ITFET device comprises of an ultra thin body planar horizontal channels and vertical channels in a single device. The devices have multi-gate control around these channels to improve short channel control. A single device has multiple orientations and hence mobility enhancement of both (110) and (100) planes can be used optimally. The devices presented have 15nm planar horizontal thin body and 40nm vertical channels of 100nm height, 17Aring gate dielectric and 50nm gate length. These devices are especially useful in circuits that need ratioing such as in SRAM cells and a well functional SRAM cell is demonstrated
Multiwavelength performance of an apodized acousto-optic switch (1994)

The current surge of interest in wavelength-division-multiplexed (WDM) networks is fueled, in part, by the rapid evolution of integrated-optic WDM technology. One important component for wavelength-routed networks1 is the acoustooptic switch, which directs various nearby-spaced WDM channels, simultaneously and independently, to either of two ports. The classical acousto-optic filter response exhibits prominent sidelobes, which are the source of interchannel and interport cross talk among dense-packed WDM channels. Recently, several groups have successfully demonstrated significant sidelobe suppression by a range of techniques that apodize the acoustooptic interaction strength.2-5 The apodization scheme based on the surface-acoustic-wave (SAW) coupler2,3 places the active optical waveguide (which performs wavelength selection by a narrow-band polarization conversion) inside the remote arm of a SAW coupler, so that the SAW energy gradually builds up in the active region and then gradually departs, providing the smooth interaction profile required for apodization.
Next generation sequencing for TCR repertoire profiling: Platform‐specific features and correction algorithms (2012)

The TCR repertoire is a mirror of the human immune system that reflects processes caused by infections, cancer, autoimmunity, and aging. Next generation sequencing (NGS) is becoming a powerful tool for deep TCR profiling; yet, questions abound regarding the methodological approaches for sample preparation and correct data interpretation. Accumulated PCR and sequencing errors along with library preparation bottlenecks and uneven PCR efficiencies lead to information loss, biased quantification, and generation of huge artificial TCR diversity. Here, we compare Illumina, 454, and Ion Torrent platforms for individual TCR profiling, evaluate the rate and character of errors, and propose advanced platform-specific algorithms to correct massive sequencing data. These developments are applicable to a wide variety of next generation sequencing applications. We demonstrate that advanced correction allows the removal of the majority of artificial TCR diversity with concomitant rescue of most of the sequencing information. Thus, this correction enhances the accuracy of clonotype identification and quantification as well as overall TCR diversity measurements.
Hidden Conditional Random Fields (2007)

We present a discriminative latent variable model for classification problems in structured domains where inputs can be represented by a graph of local observations. A hidden-state Conditional Random Field framework learns a set of latent variables conditioned on local features. Observations need not be independent and may overlap in space and time.
Rationale-Based Engineering of a Potent Long-Acting FGF21 Analog for the Treatment of Type 2 Diabetes (2012)

Fibroblast growth factor 21 (FGF21) is a promising drug candidate for the treatment of type 2 diabetes. However, the use of wild type native FGF21 is challenging due to several limitations. Among these are its short half-life, its susceptibility to in vivo proteolytic degradation and its propensity to in vitro aggregation. We here describe a rationale-based protein engineering approach to generate a potent long-acting FGF21 analog with improved resistance to proteolysis and aggregation. A recombinant Fc-FGF21 fusion protein was constructed by fusing the Fc domain of human IgG1 to the N-terminus of human mature FGF21 via a linker peptide. The Fc positioned at the N-terminus was determined to be superior to the C-terminus as the N-terminal Fc fusion retained the βKlotho binding affinity and the in vitro and in vivo potency similar to native FGF21. Two specific point mutations were introduced into FGF21. The leucine to arginine substitution at position 98 (L98R) suppressed FGF21 aggregation at high concentrations and elevated temperatures. The proline to glycine replacement at position 171 (P171G) eliminated a site-specific proteolytic cleavage of FGF21 identified in mice and cynomolgus monkeys. The derived Fc-FGF21(RG) molecule demonstrated a significantly improved circulating half-life while maintaining the in vitro activity similar to that of wild type protein. The half-life of Fc-FGF21(RG) was 11 h in mice and 30 h in monkeys as compared to 1-2 h for native FGF21 or Fc-FGF21 wild type. A single administration of Fc-FGF21(RG) in diabetic mice resulted in a sustained reduction in blood glucose levels and body weight gains up to 5-7 days, whereas the efficacy of FGF21 or Fc-FGF21 lasted only for 1 day. In summary, we engineered a potent and efficacious long-acting FGF21 analog with a favorable pharmaceutical property for potential clinical development.
Paternal age effect of YY aneuploidy in human sperm, as assessed by fluorescence in situ hybridization (1997)

Sperm samples were collected from 18 healthy men of various ages. Multicolor FISH was performed on each sample, using probes for the sex chromosomes and chromosome 1. A minimum of 10,000 sperm per donor was analyzed. The Pearson correlation coefficient was used to determine if there was an association between donor age and disomy frequency for the sex chromosomes.
Isolation of DNA from biological specimens without extraction with phenol. (1985)

Journal Article Isolation of DNA from biological specimens without extraction with phenol. Get access G J Buffone, G J Buffone Search for other works by this author on: Oxford Academic Google Scholar G J Darlington G J Darlington Search for other works by this author on: Oxford Academic Google Scholar Clinical Chemistry, Volume 31, Issue 1, 1 January 1985, Pages 164–165, https://doi.org/10.1093/clinchem/31.1.164 Published: 01 January 1985
Expression cloning and characterization of the canine parietal cell gastrin receptor. (1992)

Gastrin is an important stimulant of acid secretion by gastric parietal cells and is structurally related to the peptide hormone cholecystokinin (CCK). The pharmacologic properties of the parietal cell gastrin receptor are very similar to the predominant CCK receptor in the brain, CCK-B. Neither the gastrin nor the CCK-B receptor have been cloned thus far, making it difficult to resolve whether these two receptors are distinct. We have isolated a clone encoding the canine gastrin receptor by screening a parietal cell cDNA expression library using a radioligand-binding strategy. Nucleotide sequence analysis revealed an open reading frame encoding a 453-amino acid protein with seven putative hydrophobic transmembrane domains and significant homology with members of the beta-adrenergic family of G protein-coupled receptors. The expressed recombinant receptor shows the same binding specificity for gastrin/CCK agonists and antagonists as the canine parietal cell receptor. Gastrin-stimulated phosphatidylinositol hydrolysis and intracellular Ca2+ mobilization in COS-7 cells expressing the cloned receptor suggest second-messenger signaling through phospholipase C. Affinity labeling of the expressed receptor in COS-7 cells revealed a protein identical in size to the native parietal cell receptor. Gastrin receptor transcripts were identified by high-stringency RNA blot analysis in both parietal cells and cerebral cortex, suggesting that the gastrin and CCK-B receptors are either highly homologous or identical.
In Vivo Formation of 8-Epi-Prostaglandin F2αIs Increased in Hypercholesterolemia (1997)

F2-isoprostanes are bioactive prostaglandin (PG)-like compounds that are produced from arachidonic acid through a nonenzymatic process of lipid peroxidation catalyzed by oxygen free-radicals. 8-Epi-PGF2 alpha may amplify the platelet response to agonists, circulates in plasma, and is excreted in urine. We examined the hypothesis that the formation of 8-epi-PGF2 alpha is altered in patients with hypercholesterolemia and contributes to platelet activation in this setting. Urine samples were obtained from 40 hypercholesterolemic patients and 40 age- and sex-matched control subjects for measurement of immunoreactive 8-epi-PGF2 alpha. Urinary excretion of 11-dehydro-thromboxane (TX) B2, a major metabolite of TXA2, was measured as an in vivo index of platelet activation. Low-dose aspirin, indobufen, and vitamin E were used to investigate the mechanism of formation and effects of 8-epi-PGF2 alpha on platelet activation. Urinary 8-epi-PGF2 alpha was significantly (P = .0001) higher in hypercholesterolemic patients than in control subjects: 473 +/- 305 versus 205 +/- 95 pg/mg creatinine. Its rate of excretion was inversely related to the vitamin E content of LDL and showed a positive correlation with urinary 11-dehydro-TXB2. Urinary 8-epi-PGF2 alpha was unchanged after 2-week dosing with aspirin and indobufen despite complete suppression of TX metabolite excretion. Vitamin E supplementation was associated with dose-dependent reductions in both urinary 8-epi-PGF2 alpha and 11-dehydro-TXB2 by 34% to 36% and 47% to 58% at 100 and 600 mg daily, respectively. We conclude that the in vivo formation of the F2-isoprostane 8-epi-PGF2 alpha is enhanced in the vast majority of patients with hypercholesterolemia. This provides an aspirin-insensitive mechanism possibly linking lipid peroxidation to amplification of platelet activation in the setting of hypercholesterolemia. Dose-dependent suppression of enhanced 8-epi-PGF2 alpha formation by vitamin E supplementation may contribute to the beneficial effects of antioxidant treatment.
Spatial dependence of the optical collection efficiency in flow cytometry (1995)

The sensitive flow cytometric detection of fluorescent species in liquid sample streams requires efficient collection of light from small [approximately 1 picoliter (pl)] sample volumes. This is often accomplished with high numerical aperture (NA) imaging collection optics used in combination with a spatial filter. A method to measure the spatial variation of the optical collection efficiency within the sample volume, using a submicrometer light source, is described. Measurements of the relative optical collection efficiency are presented for two optical collection systems used in our laboratory for single molecule detection. The measurement are in qualitative agreement with relative optical collection efficiency calculations using a simple geometrical optics model. Absolute measurements of the peak collection efficiencies for the two collection systems are also presented. These absolute collection efficiency measurements are in good quantitative agreement with ideal collection efficiencies calculated using measured transmissions and rated NAs of the collection optics. The utility of this information for the characterization and optimization of sensitive fluorescence detection apparatus is discussed.
Isolation and characterization of expressible cDNA clones for mouse Thy-1: a model system for cDNA expression of cell surface proteins. (1986)

By using the mouse Thy-1 gene as a model, we have developed a procedure to distinguish functional vs nonfunctional cDNA of lymphocyte surface antigens by transfecting COS-7 monkey cells and testing for expression of cell surface products encoded by the cDNA inserts. By cross-hybridization with a mouse Thy-1 probe, we isolated cDNA clones from a pcD-expression library prepared from mRNA of C5 cells. Two functional clones were distinguished from the remainder by detection of Thy-1.2 on the surface of 0.5% of COS-7 cells transiently transfected by the DEAE-Dextran method. Inclusion of chloroquine in the transfection procedure greatly facilitated the detection of functional cDNA by raising the percentage of expressing cells to 30%. Nucleotide sequencing of one functional cDNA, about 1700 bp long, confirmed that the gene encodes a protein whose sequence agrees with the published Thy-1.2 protein sequence with the additional 31 amino acids attached at the COOH-terminus. A 75 bp 5' untranslated region preceding the coding region contains 50 bp not found in the genomic clones. Comparison indicates that one or more introns are present in the 5' untranslated region, but are not found in the mature mRNA. The first exon may be separated by at least 1 kb intron from the initiation codon. Because the expressible clones are approximately the size of the mRNA seen on Northern blots, we believe that these clones are nearly full-length cDNA. Dilution experiments indicate that this strategy should also be useful for identifying functional cDNA clones for cell surface proteins solely on the basis of their expression in mammalian cells.
In vivo CD40-gp39 interactions are essential for thymus-dependent humoral immunity. II. Prolonged suppression of the humoral immune response by an antibody to the ligand for CD40, gp39. (1993)

The ligand for CD40 has been recently identified as a 39-kd protein, gp39, expressed on the surface of activated CD4+ T helper cells (Th). In vitro, soluble CD40 and anti-gp39 have been shown to block the ability of Th to activate B cells, suggesting that gp39-CD40 interactions are important to T cell-dependent B cell activation. Here it is shown that in vivo administration of anti-gp39 dramatically reduced both primary and secondary humoral immune responses to erythrocytes and soluble protein antigens without altering responses to the T-independent type II antigen, trinitrophenyl-Ficoll. Treatment of mice for 4 d with anti-gp39 inhibited the anti-sheep red blood cell (SRBC) response for at least 3 wk and inhibited the expression of all immunoglobulin isotypes in secondary responses to the protein antigen, keyhole limpet hemocyanin. To examine the direct effect of anti-gp39 on Th function, SRBC-immune Th cells from anti-gp39-treated mice were adoptively transferred and shown to be fully capable of providing help. These results suggest that anti-gp39 treatment does not cause Th deletion or anergy. Anti-gp39 may mediate its profound immunosuppressive effects on humoral immunity by blocking gp39-CD40 interactions. Moreover, these studies establish gp39-CD40 as an important receptor-ligand pair for the targeting of therapeutic antibodies to control thymus-dependent humoral responses.
Cytoplasmic TRADD Confers a Worse Prognosis in Glioblastoma (2013)

Tumor necrosis factor receptor 1 (TNFR1)-associated death domain protein (TRADD) is an important adaptor in TNFR1 signaling and has an essential role in nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation and survival signaling. Increased expression of TRADD is sufficient to activate NF-κB. Recent studies have highlighted the importance of NF-κB activation as a key pathogenic mechanism in glioblastoma multiforme (GBM), the most common primary malignant brain tumor in adults.We examined the expression of TRADD by immunohistochemistry (IHC) and find that TRADD is commonly expressed at high levels in GBM and is detected in both cytoplasmic and nuclear distribution. Cytoplasmic IHC TRADD scoring is significantly associated with worse progression-free survival (PFS) both in univariate and multivariate analysis but is not associated with overall survival (n = 43 GBMs). PFS is a marker for responsiveness to treatment. We propose that TRADD-mediated NF-κB activation confers chemoresistance and thus a worse PFS in GBM. Consistent with the effect on PFS, silencing TRADD in glioma cells results in decreased NF-κB activity, decreased proliferation of cells, and increased sensitivity to temozolomide. TRADD expression is common in glioma-initiating cells. Importantly, silencing TRADD in GBM-initiating stem cell cultures results in decreased viability of stem cells, suggesting that TRADD may be required for maintenance of GBM stem cell populations. Thus, our study suggests that increased expression of cytoplasmic TRADD is both an important biomarker and a key driver of NF-κB activation in GBM and supports an oncogenic role for TRADD in GBM.
Isoleucine Accumulation by Regulatory Mutants of Serratia marcescens : Lack of Both Feedback Inhibition and Repression (1972)

Double mutants of Serratia marcescens resistant to isoleucine hydroxamate and alpha-aminobutyric acid accumulated large amounts of isoleucine in a salts-sugar medium and lacked both feedback inhibition and repression of the isoleucine biosynthesis.
Accuracy assessment and interpretation for optical tracking systems (2004)

Highly accurate spatial measurement systems are among the enabling technologies that have made image-guided surgery possible in modern operating theaters. Assessing the accuracies of such systems is subject to much ambiguity, though. The underlying mathematical models that convert raw sensor data into position and orientation measurements of sufficient accuracy complicate matters by providing measurements having non-uniform error distributions throughout their measurement volumes. Users are typically unaware of these issues, as they are usually presented with only a few specifications based on some "representative" statistics that were themselves derived using various data reduction methods. As a result, much of the important underlying information is lost. Further, manufacturers of spatial measurement systems often choose protocols and statistical measures that emphasize the strengths of their systems and diminish their limitations. Such protocols often do not reflect the end users' intended applications very well. Users and integrators thus need to understand many aspects of spatial metrology in choosing spatial measurement systems that are appropriate for their intended applications. We examine the issues by discussing some of the protocols and their statistical measures typically used by manufacturers. The statistical measures for a given protocol can be affected by many factors, including the volume size, region of interest, and the amount and type of data collected. We also discuss how different system configurations can affect the accuracy. Single-marker and rigid body calibration results are presented, along with a discussion of some of the various factors that affect their accuracy. Although the findings presented here were obtained using the NDI Polaris optical tracking systems, many are applicable to spatial measurement systems in general.
Neural net robot controller with guaranteed tracking performance (1995)

A neural net (NN) controller for a general serial-link robot arm is developed. The NN has two layers so that linearity in the parameters holds, but the "net functional reconstruction error" and robot disturbance input are taken as nonzero. The structure of the NN controller is derived using a filtered error/passivity approach, leading to new NN passivity properties. Online weight tuning algorithms including a correction term to backpropagation, plus an added robustifying signal, guarantee tracking as well as bounded NN weights. The NN controller structure has an outer tracking loop so that the NN weights are conveniently initialized at zero, with learning occurring online in real-time. It is shown that standard backpropagation, when used for real-time closed-loop control, can yield unbounded NN weights if (1) the net cannot exactly reconstruct a certain required control function or (2) there are bounded unknown disturbances in the robot dynamics. The role of persistency of excitation is explored.
Computational Algorithm-Driven Evaluation of Monocytic Myeloid-Derived Suppressor Cell Frequency for Prediction of Clinical Outcomes (2014)

Evaluation of myeloid-derived suppressor cells (MDSC), a cell type implicated in T-cell suppression, may inform immune status. However, a uniform methodology is necessary for prospective testing as a biomarker. We report the use of a computational algorithm-driven analysis of whole blood and cryopreserved samples for monocytic MDSC (m-MDSC) quantity that removes variables related to blood processing and user definitions. Applying these methods to samples from patients with melanoma identifies differing frequency distribution of m-MDSC relative to that in healthy donors. Patients with a pretreatment m-MDSC frequency outside a preliminary definition of healthy donor range (<14.9%) were significantly more likely to achieve prolonged overall survival following treatment with ipilimumab, an antibody that promotes T-cell activation and proliferation. m-MDSC frequencies were inversely correlated with peripheral CD8(+) T-cell expansion following ipilimumab. Algorithm-driven analysis may enable not only development of a novel pretreatment biomarker for ipilimumab therapy, but also prospective validation of peripheral blood m-MDSCs as a biomarker in multiple disease settings.