gebhart/patrepeval huggingface dataset:
Phase I Study of Bryostatin 1: Assessment of Interleukin 6 and Tumor Necrosis Factor Induction In Vivo (1993)

The recommended dosage of bryostatin 1 for phase II studies is 25 micrograms/m2 by intravenous infusion for 1 hour once a week for 3 weeks, with no treatment in the 4th week. IL-6 and TNF-alpha plasma concentrations may be useful in monitoring biological activity of bryostatin 1. Future studies should explore use of this drug with other conventional immune modulators and conventional cytotoxic drugs.
Linear and Quadratic Subsets for Template-Based Tracking (2007)

We propose a method that dramatically improves the performance of template-based matching in terms of size of convergence region and computation time. This is done by selecting a subset of the template that verifies the assumption (made during optimization) of linearity or quadraticity with respect to the motion parameters. We call these subsets linear or quadratic subsets. While subset selection approaches have already been proposed, they generally do not attempt to provide linear or quadratic subsets and rely on heuristics such as textured-ness. Because a naive search for the optimal subset would result in a combinatorial explosion for large templates, we propose a simple algorithm that does not aim for the optimal subset but provides a very good linear or quadratic subset at low cost, even for large templates. Simulation results and experiments with real sequences show the superiority of the proposed method compared to existing subset selection approaches.
Enhancement of the photorefractive gain at 13–15 μm in CdTe using alternating electric fields (1992)

We report large enhancement of the two-beam-coupling gain in vanadium-doped cadmium telluride. We used the applied-alternating-field method with square and sinusoidal waveforms. With nominally square waveforms gain coefficients in excess of 10 cm−1 have been measured, which significantly exceed the absorption coefficient of 2 cm−1 for our sample. The results agree well with theory when the major effects of the ac waveform shape, internal field screening, and large-signal effects are taken into account.
Self-adjusting threshold-voltage scheme (SATS) for low-voltage high-speed operation (2002)

A circuit technique to reduce threshold voltage fluctuation by a use of self-substrate-bias is introduced. The substrate bias is controlled so that leakage current of a representative MOSFET is adjusted constant with a feedback loop. The threshold voltage can be controlled within /spl plusmn/0.05 V and the speed gains under 1.5 V and 1V V/sub DD/ are estimated to be a factor of 1.3 and 3, respectively. A test chip is fabricated and effectiveness of the scheme is investigated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
An active measurement system for shared environments (2007)

Testbeds composed of end hosts deployed across the Internet enable researchers to simultaneously conduct a wide variety of experiments. Active measurement studies of Internet path properties that require precisely crafted probe streams can be problematic in these environments. The reason is that load on the host systems from concurrently executing experiments (as is typical in PlanetLab) can significantly alter probe stream timings. In this paper we measure and characterize how packet streams from our local PlanetLab nodes are affected by experimental concurrency. We find that the effects can be extreme. We then set up a simple PlanetLab deployment in a laboratory testbed to evaluate these effects in a controlled fashion. We find that even relatively low load levels can cause serious problems in probe streams. Based on these results, we develop a novel system called <scp>MAD</scp> that can operate as a Linux kernel module or as a stand-alone daemon to support real-time scheduling of probe streams. <scp>MAD</scp> coordinates probe packet emission for all active measurement experiments on a node. We demonstrate the capabilities of <scp>MAD</scp>, showing that it performs effectively even under very high levels of multiplexing and host system load.
The Increase of Circulating Endothelial Progenitor Cells After Acute Ischemic Stroke Is Associated With Good Outcome (2007)

The increase of circulating EPC after acute ischemic stroke is associated with good functional outcome and reduced infarct growth. These findings suggest that EPC might participate in neurorepair after ischemic stroke.
Transforming growth factor-β and fibrosis (2007)

Transforming growth factor-beta (TGF-beta), a prototype of multifunctional cytokine, is a key regulator of extracellular matrix (ECM) assembly and remodeling. Specifically, TGF-beta isoforms have the ability to induce the expression of ECM proteins in mesenchymal cells, and to stimulate the production of protease inhibitors that prevent enzymatic breakdown of the ECM. Elevated TGF-beta expression in affected organs, and subsequent deregulation of TGF-beta functions, correlates with the abnormal connective tissue deposition observed during the onset of fibrotic diseases. During the last few years, tremendous progress has been made in the understanding of the molecular aspects of intracellular signaling downstream of the TGF-beta receptors. In particular, Smad proteins, TGF-beta receptor kinase substrates that translocate into the cell nucleus to act as transcription factors, have been studied extensively. The role of Smad3 in the transcriptional regulation of type I collagen gene expression and in the development of fibrosis, demonstrated both in vitro and in animal models with a targeted deletion of Smad3, is of critical importance because it may lead to novel therapeutic strategies against these diseases. This review focuses on the mechanisms underlying Smad modulation of fibrillar collagen expression and how it relates to fibrotic processes.
Altered Histone Mark Deposition and DNA Methylation at Homeobox Genes in Human Oral Squamous Cell Carcinoma (2014)

We recently reported a role of polycomb repressive complex 2 (PRC2) and PRC2 trimethylation of histone 3 lysine 27 (H3K27me3) in the regulation of homeobox (HOX) (Marcinkiewicz and Gudas, 2013, Exp Cell Res) gene transcript levels in human oral keratinocytes (OKF6-TERT1R) and tongue squamous cell carcinoma (SCC) cells. Here, we assessed both the levels of various histone modifications at a subset of homeobox genes and genome wide DNA methylation patterns in OKF6-TERT1R and SCC-9 cells by using ERRBS (enhanced reduced representation bisulfite sequencing). We detected the H3K9me3 mark at HOXB7, HOXC10, HOXC13, and HOXD8 at levels higher in OKF6-TERT1R than in SCC-9 cells; at IRX1 and SIX2 the H3K9me3 levels were conversely higher in SCC-9 than in OKF6-TERT1R. The H3K79me3 mark was detectable only at IRX1 in OKF6-TERT1R and at IRX4 in SCC-9 cells. The levels of H3K4me3 and H3K36me3 marks correlate with the transcript levels of the assessed homeobox genes in both OKF6-TERT1R and SCC-9. We detected generally lower CpG methylation levels on DNA in SCC-9 cells at annotated genomic regions which were differentially methylated between OKF6-TERT1R and SCC-9 cells; however, some genomic regions, including the HOX gene clusters, showed DNA methylation at higher levels in SCC-9 than OKF6-TERT1R. Thus, both altered histone modification patterns and changes in DNA methylation are associated with dysregulation of homeobox gene expression in human oral cavity SCC cells, and this dysregulation potentially plays a role in the neoplastic phenotype of oral keratinocytes.
RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome (2010)

This RNA-Seq atlas extends the analyses of previous gene expression atlases performed using Affymetrix GeneChip technology and provides an example of new methods to accommodate the increase in transcriptome data obtained from next generation sequencing. Data contained within this RNA-Seq atlas of Glycine max can be explored at http://www.soybase.org/soyseq.
Multithreaded Asynchronous Graph Traversal for In-Memory and Semi-External Memory (2010)

Processing large graphs is becoming increasingly important for many domains such as social networks, bioinformatics, etc. Unfortunately, many algorithms and implementations do not scale with increasing graph sizes. As a result, researchers have attempted to meet the growing data demands using parallel and external memory techniques. We present a novel asynchronous approach to compute Breadth-First-Search (BFS), Single-Source-Shortest-Paths, and Connected Components for large graphs in shared memory. Our highly parallel asynchronous approach hides data latency due to both poor locality and delays in the underlying graph data storage. We present an experimental study applying our technique to both In-Memory and Semi-External Memory graphs utilizing multi-core processors and solid-state memory devices. Our experiments using synthetic and real-world datasets show that our asynchronous approach is able to overcome data latencies and provide significant speedup over alternative approaches. For example, on billion vertex graphs our asynchronous BFS scales up to 14 x on 16-cores.
Is cancer dangerous to the immune system? (1996)

The hypothesis of immunologic surveillance of neoplasia is predicated on the theory that the immune system is capable of discriminating self from foreign antigens, and that tumor-specific antigens are regarded by the immune system as nonself. We propose here an alternate view, that the immune system has evolved to detect danger by employing 'professional' antigen-presenting cells as sentinels of tissue distress. In this model, cancers do not appear dangerous to the immune system, so that the default response of T cells to tumors is to be turned off. We discuss the implications for immunotherapy of malignancy.
Detecting copy number variation with mated short reads (2010)

The development of high-throughput sequencing (HTS) technologies has opened the door to novel methods for detecting copy number variants (CNVs) in the human genome. While in the past CNVs have been detected based on array CGH data, recent studies have shown that depth-of-coverage information from HTS technologies can also be used for the reliable identification of large copy-variable regions. Such methods, however, are hindered by sequencing biases that lead certain regions of the genome to be over- or undersampled, lowering their resolution and ability to accurately identify the exact breakpoints of the variants. In this work, we develop a method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where mate pairs mapping discordantly to the reference serve to indicate the presence of variation. Our algorithm, called CNVer, combines this information within a unified computational framework called the donor graph, allowing us to better mitigate the sequencing biases that cause uneven local coverage and accurately predict CNVs. We use CNVer to detect 4879 CNVs in the recently described genome of a Yoruban individual. Most of the calls (77%) coincide with previously known variants within the Database of Genomic Variants, while 81% of deletion copy number variants previously known for this individual coincide with one of our loss calls. Furthermore, we demonstrate that CNVer can reconstruct the absolute copy counts of segments of the donor genome and evaluate the feasibility of using CNVer with low coverage datasets.
Use of real-time reverse transcriptase polymerase chain reaction assay and cell culture methods for detection of swine influenza A viruses (2005)

Results indicate that real-time RT-PCR assay is a fast and accurate test for screening numerous nasal swab specimens for swine influenza virus. Some viruses were isolated in only MDCK or Mv1Lu cells, indicating that use of >1 cell line may be required to isolate a broad range of influenza A viruses.
Li-alloy based anode materials for Li secondary batteries (2010)

Research to develop alternative electrode materials with high energy densities in Li-ion batteries has been actively pursued to satisfy the power demands for electronic devices and hybrid electric vehicles. This critical review focuses on anode materials composed of Group IV and V elements with their composites including Ag and Mg metals as well as transition metal oxides which have been intensively investigated. This critical review is devoted mainly to their electrochemical performances and reaction mechanisms (313 references).
Differentiation of Human Embryonic Stem Cells and Induced Pluripotent Stem Cells to Cardiomyocytes (2012)

Since human embryonic stem cells were first differentiated to beating cardiomyocytes a decade ago, interest in their potential applications has increased exponentially. This has been further enhanced over recent years by the discovery of methods to induce pluripotency in somatic cells, including those derived from patients with hereditary cardiac diseases. Human pluripotent stem cells have been among the most challenging cell types to grow stably in culture, but advances in reagent development now mean that most laboratories can expand both embryonic and induced pluripotent stem cells robustly using commercially available products. However, differentiation protocols have lagged behind and in many cases only produce the cell types required with low efficiency. Cardiomyocyte differentiation techniques were also initially inefficient and not readily transferable across cell lines, but there are now a number of more robust protocols available. Here, we review the basic biology underlying the differentiation of pluripotent cells to cardiac lineages and describe current state-of-the-art protocols, as well as ongoing refinements. This should provide a useful entry for laboratories new to this area to start their research. Ultimately, efficient and reliable differentiation methodologies are essential to generate desired cardiac lineages to realize the full promise of human pluripotent stem cells for biomedical research, drug development, and clinical applications.
Combination of 5-Fluorouracil and N1,N11-Diethylnorspermine Markedly Activates Spermidine/Spermine N1-Acetyltransferase Expression, Depletes Polyamines, and Synergistically Induces Apoptosis in Colon Carcinoma Cells (2004)

The thymidylate synthase inhibitor 5-fluorouracil (5-FU) is used widely for chemotherapy of colorectal carcinoma. Recent studies showed that 5-FU affects polyamine metabolism in colon carcinoma cells. We therefore examined whether combinations of 5-FU with drugs that specifically target polyamine metabolism, i.e. N1,N11-diethylnorspermine (DENSPM) or alpha-difluoromethylornithine (DFMO), have synergistic effects in killing HCT116 colon carcinoma cells with wild-type or absent p53. Our results showed that simultaneous 5-FU and DENSPM, a spermine analogue, synergistically increased transcript levels of the polyamine catabolism enzyme spermidine/spermine N1-acetyltransferase, depleted spermine and spermidine, increased acetylated spermidine, and produced synergistic tumor cell apoptosis in both p53 wild-type and p53-null variants. By contrast, simultaneous combination of 5-FU with DFMO, an inhibitor of the polyamine biosynthetic enzyme ornithine decarboxylase, depleted putrescine but did not produce synergistic cell killing. Some pre-treatment and post-treatment regimens of DENSPM and DFMO were antagonistic to 5-FU depending on cellular p53 status. Protein and transcriptome expression analysis showed that combined 5-FU and DENSPM treatment activated caspase 9, but not caspase 3, and significantly suppressed NADH dehydrogenases and cytochrome c oxidases, consistent with the observed increase in hydrogen peroxide, loss of mitochondrial membrane potential, and release of cytochrome c. Our findings demonstrate the importance of the polyamine pathway in 5-FU effects and suggest that the combination of 5-FU with DENSPM has potential for development as therapy for colorectal carcinoma.
Coupled Resonant Coil Sensors for Remote Passive Monitoring Applications (2010)

The thesis describes development and application of coupled resonant coil sensors, which is of growing interest for remote monitoring applications. An interrogation technique, which improves the accuracy and interrogation range of coupled resonant coil sensors, is introduced. The method uses time-domain gating to produce measurements that are dominated by the response of the sensor coil and are immune to surrounding object interference. For application in structural health monitoring a low cost embeddable coupled coil sensor, which is able to monitor the corrosion potential of reinforcement steel is presented. Results of an accelerated corrosion test using the sensor indicate that corrosion potential can be monitored with a resolution less than 10 mV and a sensitivity of 0.76 kHz/mV. The last part describes a coupled-coil pH sensor based on pH electrode potential measurement. A linear response over a 4 to 10 pH dynamic range and 50 kHz/pH sensitivity are achieved with a 0.1 pH resolution and 30 s response time.
Sequence Features Surrounding the Translation Initiation Sites Assigned on the Genome Sequence of Synechocystis sp. Strain PCC6803 by Amino-terminal Protein Sequencing (1996)

To characterize the sequence features surrounding the translation initiation sites on the genome of Synechocystis sp. strain 6803, the total proteins extracted from the cell were resolved by two-dimensional electrophoresis, and the amino-terminal sequences of the relatively abundant protein spots were determined. By comparison of the determined amino-terminal sequences with the nucleotide sequence of the entire genome, the translation initiation sites of a total of 72 proteins were successfully assigned on the genome. The sequence features emerged from the nucleotide sequences at and surrounding the translation initiation sites were as follows: (1) In addition to the three initiation codons, ATG, GTG, and TTG, evidence was obtained that ATT was also used as a rare initiation codon; (2) the core sequences (GAGG, GGAG and AGGA) of the Shine-Dalgarno sequence were identified in the appropriate position preceding the 35 initiation sites (48.6%); and (3) the preferential sequence surrounding the initiation codons was formulated as 5'-YY[...]R-3' where Y and R denote pyrimidine and purine nucleotides, respectively, and three dots represent the initiation codons. The result obtained would provide valuable information for improvement of the gene-finding software, and the approach used in this study should be applicable for comprehensive analysis of the expression profiles of cellular proteins.
Evaluation of the Stability of Nonfouling Ultrathin Poly(ethylene glycol) Films for Silicon-Based Microdevices (2003)

The creation of nonfouling surfaces is one of the major prerequisites for microdevices for biomedical and analytical applications. Poly(ethylene glycol) (PEG), a water soluble, nontoxic, and nonimmunogenic polymer has the unique ability of reducing nonspecific protein adsorption and cell adhesion and, therefore, is generally coupled with a wide variety of surfaces to improve their biocompatibility. The performance of these modified surfaces for long-term biomedical applications largely depends on the stability of these PEG films. To this end, we have investigated the stability of covalently coupled ultrathin PEG films on silicon in aqueous in vivo like conditions for a period of 4 weeks. The PEG-modified silicon substrates were incubated in PBS (37 degrees C, pH 7.4, 5% CO2) for different periods of time and then characterized using the techniques of ellipsometry, contact angle measurement, X-ray photoelectron spectroscopy, and atomic force microscopy. The ability of the PEG-modified surfaces to control protein fouling was examined by protein adsorption studies using fluorescein isothiocyanate labeled bovine serum albumin and ellipsometry. Furthermore, the ability of these films to control fibroblast adhesion was examined. Studies suggest that the PEG-modified surfaces retain their protein and cell repulsive nature even though the PEG film thickness decreases for the period of investigation.
Statistical tests for presence of cyclostationarity (1994)

The presence of kth-order cyclostationarity is defined in terms of nonvanishing cyclic-cumulants or polyspectra. Relying upon the asymptotic normality and consistency of kth-order cyclic statistics, asymptotically optimal /spl chi//sup 2/ tests are developed to detect the presence of cycles in the kth-order cyclic cumulants or polyspectra, without assuming any specific distribution on the data. Constant false alarm rate tests are derived in both time- and frequency-domain and yield consistent estimates of possible cycles present in the kth-order cyclic statistics. Explicit algorithms for k/spl les/4 are discussed. Existing approaches are rather empirical and deal only with k/spl les/2 case. Simulation results are presented to confirm the performance of the given tests.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
4-Substituted nicotinic acids and nicotinamides. Part III. Preparation of 4-methylnicotinic acid riboside (1969)

A method for the synthesis of nicotinic acid ribosides is described. The stepwise reaction between the tetra-n-butylammonium salt of nicotinic acid and 3,5-di-O-benzoyl-β-D-ribofuranosyl chloride gives 1-O-nicotinoyl-3,5-di-O-benzoyl-D-ribofuranose and 1-(3,5-di-O-benzoyl-D-ribofuranosyl)-3-(3,5-di-O-benzoyl-D-ribofuranosyloxycarbonyl)pyridinium chloride. The riboside obtained by stepwise hydrolysis of the quaternary derivative was essentially the β-anomer. 4-Methylnicotinic acid derivatives were similarly obtained.
Molecular Beacons: A New Approach to Plant Virus Detection (2000)

ABSTRACT Molecular beacons are single-stranded nucleic acid molecules with a stem-loop conformation. The stem portion consists of complementary sequences at the 5' and 3' terminals of the molecule, while the loop portion consists of probe sequences that are complementary to the target sequences of choice. A fluorescent moiety is attached to one end, while a quenching moiety is attached to the opposite end. Reverse transcription-polymerase chain reactions are carried out with primers that amplify specific genome sequences of interest, yielding targets complementary to their respective molecular beacons for subsequent detection. Here, we have designed four molecular beacons specific to the RNA-dependent RNA polymerase and coat protein genes of two orchid viruses, namely Cymbidium mosaic virus (CymMV) and Odontoglossum ringspot virus (ORSV). This technology is successfully applied to detect as little as 0.5 ng of viral RNA of both orchid viruses simultaneously in 100 mg of coinfected Oncidium orchid leaves. This rapid and specific technique is applicable to the orchid industry, which routinely carries out virus indexing and screening for virus-resistant cultivars. We belief that use of this molecular beacon approach can be extended to the detection of multiple plant viruses in various crops.