gebhart/patrepeval huggingface dataset:
Out-of-plane high-Q inductors on low-resistance silicon (2003)

Integrated high-Q coils are much sought after because they enable high-quality radio-frequency circuits that do not rely on off-chip discretes. We present a novel surface micro-machined inductor with its coil axis parallel to the substrate plane. Coils fabricated on standard unaltered low-resistance silicon exhibit record-high-quality factors (Q) of over 70 at 1 GHz. The devices are made by three-dimensional (3-D) self-assembly of stress-engineered structures fabricated with standard semiconductor batch processing techniques. We also designed, fabricated, and characterized silicon Bi-CMOS L-C oscillators built around these coils. Compared side by side against state-of-the-art planar spirals, they produce a 12.3 dB lower phase noise at 100 kHz offset, and 14.6 dB after normalizing to frequency and power.
Mechanisms of Latent Image Formation in Photothermographic Silver Imaging Media (1996)

The purpose of this paper is to establish that significant differences exist between mechanisms of latent image formation in conventional silver halide emulsions and in dry processed, photothermographic silver media. We develop our analysis in two ways: (1) through a review of salient literature; and (2) by highlighting areas of research that clearly delineate between conventional silver halide and photothermographic media, involving mathematical modeling, laser spectroscopy, and photocharge studies. We conclude that catalytic juxtaposition of a silver carboxylate phase with a silver halide phase leads to profound changes in the photophysics of the silver halide. Thus characteristically different latent-image-forming mechanisms prevail in thermally developed media, compared with conventional, negative-working silver halide photographic films, and transfer of technology from one to the other is not obvious.
Cover Picture: Macromol. Rapid Commun. 1/2004 (2004)

Cover: A general workflow for combinatorial and high‐throughput polymer research, with examples, is shown. The cycle starts with the design of experiments (DoE), followed by automated polymer synthesis, high‐throughput screening, library preparation (thin films, dots and gradient libraries), property investigations and finally data mining. The background depicts polymer MALDI‐TOF MS data obtained during high‐throughput screening. Details can be found in the Review by M. A. R. Meier, R. Hoogenboom, and U. S. Schubert * on page 21.
Scalable photonic crystal chips for high sensitivity protein detection (2013)

Scalable microfabrication technology has enabled semiconductor and microelectronics industries, among other fields. Meanwhile, rapid and sensitive bio-molecule detection is increasingly important for drug discovery and biomedical diagnostics. In this work, we designed and demonstrated that photonic crystal sensor chips have high sensitivity for protein detection and can be mass-produced with scalable deep-UV lithography. We demonstrated label-free detection of carcinoembryonic antigen from pg/mL to μg/mL, with high quality factor photonic crystal nanobeam cavities.
A methionine aminopeptidase-2 inhibitor, PPI-2458, for the treatment of rheumatoid arthritis (2004)

The hallmark of rheumatoid arthritis (RA) is the progressive destruction of articular joints, characterized by invasive synovial hyperplasia and pathological neovascularization. Here we report that PPI-2458, a member of the fumagillin class of irreversible methionine aminopeptidase-2 (MetAP-2) inhibitors, potently inhibits the proliferation of human fibroblast-like synoviocytes (HFLS-RA), derived from RA patients, with a growth inhibitory concentration 50 (GI(50)) of 0.04 nM and a maximum inhibition of >95% at 1 nM. Human umbilical vein endothelial cells (HUVEC) are similarly inhibited in proliferation by PPI-2458 (GI(50), 0.2 nM). We developed a method to measure the level of MetAP-2 enzyme inhibition after exposure to PPI-2458 and demonstrate that growth inhibition of PPI-2458-sensitive HFLS-RA and HUVEC is linked to MetAP-2 enzyme inhibition, in a dose-dependent fashion. The secretion of several inflammatory mediators such as IL-6 and vascular endothelial growth factor from activated HFLS-RA was not inhibited by PPI-2458. The CNS toxicity profile of PPI-2458, determined by the incidence of seizures, is significantly improved over that of the parental compound TNP-470. In the rat model of peptidoglycan-polysaccharide-induced arthritis, PPI-2458 significantly attenuated paw swelling when therapeutically administered after the onset of chronic disease. We suggest that the mechanism of PPI-2458 action, highly selective and potent anti-proliferative activity on HFLS-RA and HUVEC in vitro, a significantly improved CNS toxicity profile, and marked attenuation of chronic disease in the rat peptidoglycan-polysaccharide arthritis model in vivo, positions this compound as a drug for the treatment of RA.
High-speed and Low-leakage Characteristics of 60-nm C-axis Aligned Crystalline Oxide Semiconductor FET with GHz-ordered Cutoff Frequency (2014)

2014 International Conference on Solid State Devices and Materials,High-speed and Low-leakage Characteristics of 60-nm C-axis Aligned Crystalline Oxide Semiconductor FET with GHz-ordered Cutoff Frequency
Danish Bacille Calmette-Guerin Vaccine-Induced Disease in Human Immunodeficiency Virus-Infected Children (2003)

An analysis of isolates of Mycobacterium tuberculosis complex was performed to determine the prevalence of bacille Calmette-Guérin (BCG) disease among human immunodeficiency virus (HIV)-infected children. Speciation was done with polymerase chain reaction; 183 isolates from mycobacterial cultures for 49 HIV-infected patients were analyzed. The Danish Mycobacterium bovis BCG strain was isolated from 5 patients. No cases of Tokyo M. bovis BCG strain disease were detected. All patients were asymptomatic at birth, <12 months of age, and severely immunodeficient at presentation. Four patients had regional axillary adenitis ipsilateral to the vaccination site, and 2 had pulmonary BCG disease. Two patients with regional BCG disease had simultaneous pulmonary M. tuberculosis infection. Although chest radiographic features were similar to those seen in patients with tuberculosis, BCG disease should be considered in HIV-infected infants with right axillary adenitis ipsilateral to the vaccination site. Young, symptomatic, HIV-infected infants are at risk for BCG-related complications. Controlled, population-based studies are needed to assess the risk of BCG in HIV-infected children.
Proteins of rat serum: I. Establishing a reference two‐dimensional electrophoresis map by immunodetection and microbore high performance liquid chromatography‐electrospray mass spectrometry (1998)

In the present investigation, we have identified 56 major spots, or spot rows, corresponding to 22 proteins, in the 2-DE pattern of adult male rats. This was done mainly by applying two complementary techniques, namely immunoblotting and high performance liquid chromatography-mass spectrometry (HPLC-MS) peptide mapping. Glycoproteins were characterized by affinity blotting with six lectins. We have also detailed how rat serum differs from human serum in two main respects: (i) relative abundance of individual proteins, which amounts in some cases to a complete absence in either sample, and (ii) varying molecular parameters for homologous proteins. It was thus possible to establish a first-generation reference map of rat serum proteins, which can be accessed through http://weber.u.washington.edu/ruedilab/aebersold++ +.html. We hope the present database will be a useful reference for the evaluation of changes in serum protein distribution in the course of pharmacological and toxicological studies. The recognition of species-specific proteins appears of special relevance in this respect.
Cloning and disruption of a gene required for growth on acetate but not on ethanol: The acetyl‐coenzyme a synthetase gene of Saccharmoyces cerevisiae (1992)

Abstract A DNA fragment of Saccharomyces cerevisiae with high homology to the acetyl‐coenzyme A (acetyl‐CoA) synthetase genes of Aspergillus nidulans and Neurospora crassa has been cloned, sequenced and mapped to chromsome I. It contains an open reading frame of 2139 nucleotides, encoding a predicted gene product of 79·2 kDa. In contrast to its ascomycete homologs, there are no introns in the coding sequence. The first ATG codon of the open reading frame is in an unusual context for a translational start site, while the next ATG, 24 codons dowunstream, is in a more conventional context. Possible implications of two alternative traslational start sites for the celular lacalization of the enzyme are disussed. A stable mutant of this gene, obtained by the gene disruptiona technique, had the same low basal acitivity of acetyl‐CoA synthetase as wild‐type cells when grown on glucose but completely lacked the strong increase in activity upon entering the stationary phase, providing direct proof that the gene encodes an inducible acetlyl‐CoA synthetase ( ACSI ) of yeast. As expected, the mutant was unable to grow on acetate as sole carbon source. Nevertheless, it showed normal induction os isocitrate lyase on acetate media, indicating that activity of acetyl‐CoA sytheatase is dispensable for incuctionof the glyoxylate cycle in S. cerevisiae . Surprisingly, disruption of the ACSI gene did not affect growth on media containing ethanol as the sole crbon source. Demonstrating that threre are alternative pathways pathways leading to acetyl‐CoA under these condintions.
Deterministic Absolute Negative Mobility for Micro- and Submicrometer Particles Induced in a Microfluidic Device (2016)

Efficient separations of particles with micron and submicron dimensions are extremely useful in preparation and analysis of materials for nanotechnological and biological applications. Here, we demonstrate a nonintuitive, yet efficient, separation mechanism for μm and subμm colloidal particles and organelles, taking advantage of particle transport in a nonlinear post array in a microfluidic device under the periodic action of electrokinetic and dielectrophoretic forces. We reveal regimes in which deterministic particle migration opposite to the average applied force occurs for a larger particle, a typical signature of deterministic absolute negative mobility (dANM), whereas normal response is obtained for smaller particles. The coexistence of dANM and normal migration was characterized and optimized in numerical modeling and subsequently implemented in a microfluidic device demonstrating at least 2 orders of magnitude higher migration speeds as compared to previous ANM systems. We also induce dANM for mouse liver mitochondria and envision that the separation mechanisms described here provide size selectivity required in future separations of organelles, nanoparticles, and protein nanocrystals.
A simple technique for surface area determination (1979)

An inexpensive apparatus for BET (Brunauer, Emmett and Teller) surface area measurement using krypton with a lower limit of 0.001 m2 has been developed. Operation is made simple by the use of an MKS Baratron pressure gauge and a constant-volume system.
Presence of 2',5'-oligo(A) and of enzymes that synthesize, bind, and degrade 2',5'-oligo(A) in HeLa cell nuclei. (1982)

Nuclei prepared from HeLa cells by lysis with nonionic detergents or by a nonaqueous fractionation procedure were assayed for enzymatic activities which synthesize, bind, and degrade 2',5'-oligo(A). Isolated nuclei synthesized micromolar concentrations of 2',5'-oligo(A) when incubated with poly(inosinic) . poly(cytidylic) acid. The products of nuclear synthesis were identified with authentic 2',5'-oligo(A) by several criteria. The nuclei synthesized nanomolar amounts of 2',5'-oligo(A) even when incubated without added double-stranded RNA. These oligonucleotides were identified by their pattern of degradation with different nucleases and by a specific competition-binding assay. This assay revealed the presence in nuclei of an activity which binds 2',5'-oligo(A) with an affinity constant similar to that of the cytoplasmic binding activity previously identified with the 2',5'-oligo(A)-dependent endoribonuclease (Nilsen, T. W., Wood, D. L., and Baglioni, C. (1981) J. Biol. Chem. 256, 10751-10754). The nuclei had also an activity which degraded 2',5'-oligo(A). Finally, unincubated nuclei isolated by the nonaqueous fractionation procedure contained detectable concentrations of 2',5'-oligo(A). These results show that an activator of the enzyme which synthesize 2',5'-oligo(A) is present in nuclei and that these oligonucleotides are normally formed in HeLa cells, and suggest a possible role for the 2',5'-oligo(A)-activated endoribonuclease in nuclear RNA metabolism.
Hydrolysis of Bimatoprost (Lumigan) to its Free Acid by Ocular Tissue In Vitro (2003)

We determined whether bimatoprost, which has been reported to act via putative prostamide receptors, could be hydrolyzed to its free acid (17-phenyl-PGF(2 alpha)), a potent FP receptor agonist, by human ocular tissue in vitro. We developed a gas chromatography/mass spectrometric method to measure 17-phenyl-PGF(2 alpha) levels at sub-picomolar levels. We then analyzed the amount of 17-phenyl-PGF(2 alpha) present after incubation of 50 microl Lumigan (0.03% bimatoprost) with eye tissue using this assay. We found that cornea, sclera, iris, and ciliary body, all rapidly hydrolyzed bimatoprost to 17-phenyl-PGF(2 alpha) with linear kinetics at a rate of 6.3, 2.0, 2.8, and 1.5 pmol mg tissue(-1) hr(-1), respectively. For cornea, sclera, and ciliary body, this linear rate of hydrolysis continued over a period of at least three hours, while iris-induced hydrolysis did not continue beyond one hour. Our findings suggest that bimatoprost can act as prodrug for FP receptor activation and questions the concept of a "prostamide receptor" agonist.
Cas9-mediated targeting of viral RNA in eukaryotic cells (2015)

Clustered, regularly interspaced, short palindromic repeats-CRISPR associated (CRISPR-Cas) systems are prokaryotic RNA-directed endonuclease machineries that act as an adaptive immune system against foreign genetic elements. Using small CRISPR RNAs that provide specificity, Cas proteins recognize and degrade nucleic acids. Our previous work demonstrated that the Cas9 endonuclease from Francisella novicida (FnCas9) is capable of targeting endogenous bacterial RNA. Here, we show that FnCas9 can be directed by an engineered RNA-targeting guide RNA to target and inhibit a human +ssRNA virus, hepatitis C virus, within eukaryotic cells. This work reveals a versatile and portable RNA-targeting system that can effectively function in eukaryotic cells and be programmed as an antiviral defense.
Comparison of the effects of gamma radiation and low temperature hydrogen peroxide gas plasma sterilization on the molecular structure, fatigue resistance, and wear behavior of UHMWPE (1998)

The effects of gamma radiation and low temperature hydrogen peroxide gas plasma (HPGP) sterilization on structure and cyclic mechanical properties were examined for orthopedic grade ultra-high-molecular-weight polyethylene (UHMWPE) and compared to each other as well as to no sterilization (control). Density was monitored with a density gradient column and was found to be directly influenced by the sterilization method employed: Gamma radiation led to an increase, while plasma did not. Oxidation of the polymer was studied by observing changes in the carbonyl peak with Fourier transform infrared spectrometry and was found to be strongly affected by both gamma radiation and subsequent aging, while plasma sterilization had little effect. Gamma radiation resulted in embrittlement of the polymer and a decreased resistance to fatigue crack propagation. This mechanical degradation was a direct consequence of postradiation oxidation and molecular evolution of the polymer and was not observed in the plasma-sterilized polymer. Both gamma radiation and plasma sterilization led to improved wear performance of the UHMWPE compared to the nonsterile control material.
Antitumor effect of the histone deacetylase inhibitor LAQ824 in combination with 13-cis-retinoic acid in human malignant melanoma (2007)

Resistance to chemotherapy is a major hurdle in the treatment of malignant melanoma. Histone deacetylase (HDAC) inhibitors have been shown to have antitumor activity in different tumor types, including melanoma, and to reverse epigenetic repression of tumor suppressor genes, such as retinoic acid receptor beta (RARbeta). In this study, we tested the antitumor effect of the HDAC inhibitor LAQ824 in combination with 13-cis-retinoic acid (CRA) on two human melanoma cell lines both in vitro and in vivo. Treatment of LAQ824 showed a dose-dependent inhibitory effect on A2058 and HMV-I cell lines in a clonogenic assay. These cell lines were relatively resistance to CRA. On treatment with combination of LAQ824 and CRA, a greater inhibitory effect (up to 98%) was achieved compared with single agents. Lack of RARbeta2 gene expression was associated with histone acetylation and gene methylation at the promoter level. Treatment with LAQ824 restored retinoid sensitivity by reverting RARbeta2 epigenetic silencing. The biological effect of LAQ824 was associated with p21 induction in both cell lines but G(2) cell cycle arrest in A2058 and apoptosis in HMV-I cell line. The induction of apoptosis by LAQ824 was associated with increased reactive oxygen species and induction of SM22 gene expression in HMV-I but not in A2058 cell line. Administration of the free radical scavenger l-N-acetylcysteine blocked LAQ824 + CRA-mediated apoptosis in HMV-I cells, suggesting a primary role for reactive oxygen species generation in LAQ824 + CRA-associated lethality. Combination treatment showed 61% and 82% growth inhibition in A2058 and HMV-I tumors, respectively. Greater induction of in vivo apoptosis was observed in the HMV-I but not in the A2058 tumors treated with combination therapy compared with single agents. These results suggest that the HDAC inhibitor LAQ824 has a greater antitumor activity in combination with CRA in melanoma tumors but the degree of induced apoptosis may vary. Combination of HDAC inhibitors and retinoids represents a novel therapeutic approach for malignant melanoma that warrants clinical testing.
Long-term stability of endogenous B-type natriuretic peptide (BNP) and amino terminal proBNP (NT-proBNP) in frozen plasma samples (2004)

The aim of the present study was to assess the long-term stability of endogenous B-type natriuretic peptide (BNP) and amino terminal proBNP (NT-proBNP) in plasma samples stored at -20 degrees C without addition of protease inhibitors (e.g., aprotinin). Stability of BNP and NT-proBNP was tested in 60 EDTA plasma samples with BNP values between 30 and 420 pg/ml. Initial BNP and NT-proBNP plasma concentrations were determined within four hours after blood collection using the AxSYM BNP and the Elecsys NT-proBNP assays. Subsequently, all samples were stored at -20 degrees C and were thawed for the second BNP and NT-proBNP determination on the two instruments after one day, 30 days, 60 days, 90 days and 120 days, respectively. Mean recovery (i.e., residual immunoreactivity) of BNP and NT-proBNP expressed in percent of the initial value for the given time interval of storage was calculated. Mean recovery of BNP was less than 70% after one day of storage at -20 degrees C and decreased to less than 50% after two to four months of storage (e.g., recovery of endogenous BNP after three months of storage at -20 degrees C ranging from 0% to 71%). In contrast, mean recovery of NT-proBNP was generally greater than 90%, irrespective of the duration of storage at -20 degrees C (e.g., recovery of endogenous NT-proBNP after three months of storage at -20 degrees C ranging from 91% to 112%). In conclusion, the determination of endogenous BNP with the AxSYM assay using frozen plasma samples may not be valid under the conditions tested. In contrast, NT-proBNP as measured by the Elecsys assay may be stored at -20 degrees C for at least four months without a relevant loss of the immunoreactive analyte.
Sequence dependence of paclitaxel (Taxol) combined with cisplatin or alkylators in human cancer cells. (1994)

Clinical trials combining paclitaxel with other active chemotherapy agents are currently underway. In vitro preclinical studies may assist in the selection of appropriate drug combinations or sequences for clinical investigation. We have used clonogenic cell survival assays and DNA flow cytometry to examine the effect of paclitaxel combined with melphalan, thiotepa, or cisplatin on the survival and cell-cycle parameters of human lung A549 and breast MCF-7 adenocarcinoma cells. A549 and MCF-7 cells were incubated with paclitaxel for 24 h, followed by a 1 h exposure to cisplatin, melphalan, or thiotepa. Both cell types were also incubated with cisplatin or an alkylator for 1 h followed by a 24 h paclitaxel exposure. When the paclitaxel exposure preceded either melphalan, thiotepa, or cisplatin, the cytotoxicity was additive for both cell lines tested. When cisplatin or alkylator exposure was given prior to the paclitaxel, cytotoxicity was also additive in MCF-7 cells. However, cisplatin or alkylators were antagonistic to paclitaxel cytotoxicity when they preceded the paclitaxel exposure in A549 cells (e.g., 2% survival with 100 nM paclitaxel vs. 7% survival with cisplatin and paclitaxel). Cell-cycle analysis revealed that exposure to 100 nM paclitaxel for 24 h blocked a majority of the cells into the G2/M phase (> or = 80% for A549 cells, 60-65% for MCF-7 cells). However, exposure to alkylators before incubation in paclitaxel reduced the proportion of A549 but not MCF-7 cells in G2/M--e.g., exposure to 30 micrograms/ml cisplatin prior to paclitaxel exposure caused only 25% of A549 and 55% of MCF-7 cells to block in G2/M.(ABSTRACT TRUNCATED AT 250 WORDS)
DiFS: Distributed Flow Scheduling for Data Center Networks (2013)

Data center networks leverage multiple parallel paths connecting end host pairs to offer high bisection bandwidth for cluster computing applications. However, state of the art distributed multi-pathing protocols such as Equal Cost Multipath (ECMP) use static flow-to-link assignment, which is load-oblivious. They may cause bandwidth loss due to \emph{flow collisions} on a same link. Recently proposed centralized scheduling algorithm or host-based multi-pathing may suffer from scalability problems. In this paper, we present Distributed Flow Scheduling (DiFS) for data center networks, which is a switch-only distributed solution. DiFS allows switches cooperate to avoid over-utilized links and find available paths without centralized control. DiFS is scalable and can react quickly to dynamic traffic, because it is independently executed on switches and requires no synchronization. Extensive experiments show that the aggregate bisection bandwidth of DiFS using various traffic patterns is much better than that of ECMP, and is similar to or higher than that of a recent proposed centralized scheduling algorithm.
Interference Effects in the Multiphoton Ionization of Sodium (1995)

Sodium atoms are ionized by 777 nm, 150 fs laser pulses. Modulations are observed in the multiphoton ionization yield as a function of laser intensity. The oscillations are attributed to Ramsey interference caused by coherent population transfer between bound states at two different times during a single laser pulse.
Phase 0 Clinical Studies in Oncology (2008)

In the design of first-in-human (FIH) studies in oncology, some changes are incremental; others are major shifts in goals and approaches. The contemporary emphasis on molecularly targeted agents has accelerated the trend toward biomarker studies, but these investigations remain as secondary findings in phase I behind the classic end points of toxicity and occasional tumor shrinkage. In contrast, evaluation of target modulation is the primary goal of phase 0 and is intended to inform decision making regarding further development of the relevant compound. Clinical Pharmacology & Therapeutics (2009); 85, 2, 204–207 doi:10.1038/clpt.2008.246