gebhart/patrepeval huggingface dataset:
Frequency of microsatellite sequences in rice (Oryza sativaL.) (1995)

This study was undertaken to estimate the relative frequencies of 13 microsatellite motifs in the rice genome as a basis for efficient development of a microsatellite map. Two dinucleotide, seven trinucleotide, and four tetranucleotide repeat motifs were end labelled and used as hybridization probes to screen genomic and cDNA libraries of rice, cv. IR36. Optimal washing temperatures for identification of clones containing specific microsatellite motifs were estimated based on washing temperatures near Td (dissociation temperature; Td = Tm - 7.6 degrees C). Sequencing of 20 putatively positive clones corresponding to each of 4 microsatellite motifs suggested that while Td provides a useful predictor of washing stringency for most of the repeats studied, those with a very high GC or AT content were most prone to error. The results from screening the rice genomic library suggest that there are an estimated 1360 poly(GA)n and 1230 poly(GT)n microsatellites in the rice genome, and that the relative frequency of different repeats decreased with increasing size of the motif. The most frequently observed microsatellites in the cDNA library were the same as for genomic library, but no poly(CGG)n, poly(ATC)n, or tetranucleotide motifs were observed among cDNA in this study.
Total synthesis of rapamycin via a novel titanium-mediated aldol macrocyclization reaction (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTotal synthesis of rapamycin via a novel titanium-mediated aldol macrocyclization reactionCheryl M. Hayward, Daniel Yohannes, and Samuel J. DanishefskyCite this: J. Am. Chem. Soc. 1993, 115, 20, 9345–9346Publication Date (Print):October 1, 1993Publication History Published online1 May 2002Published inissue 1 October 1993https://pubs.acs.org/doi/10.1021/ja00073a083https://doi.org/10.1021/ja00073a083research-articleACS PublicationsRequest reuse permissionsArticle Views1928Altmetric-Citations96LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Function of the Niemann–Pick type C proteins and their bypass by cyclodextrin (2011)

Experimental data are consistent with a model for the sequential action of the NPC1 and NPC2 proteins in moving cholesterol out of the late endosomes/lysosomes. Recent data demonstrate that treatment of NPC-deficient mice with cyclodextrin extends their life span, thereby suggesting a potential therapy for NPC patients.
Method of Individual Identification Based on Electroencephalogram Analysis (2009)

Biometric based on Electroencephalogram have proved to be unique enough between subjects for applications. A new method on identifying the individuality of persons by using parametric was used for identification of motor imagery. In this paper, autoregressive mode, phase synchronization, Energy Spectral Density and linear complexity value were used as EEG features. Neural network was employed for identification of individual differences. Then, identification rate was analyzed by different data length and wave band. The result shows that high identification ratio was tongue movement and that perfect accuracy depends on the Paradigm of motor imagery and wave band.
Fibromodulin as a novel tumor-associated antigen (TAA) in chronic lymphocytic leukemia (CLL), which allows expansion of specific CD8+ autologous T lymphocytes (2004)

Fibromodulin (FMOD) was shown to be highly overexpressed in chronic lymphocytic leukemia (CLL) cells compared with normal B lymphocytes by gene expression profiling. Therefore FMOD might serve as potential tumor-associated antigen (TAA) in CLL, enabling expansion of FMOD-specific T cells. In CLL samples derived from 16 different patients, high expression of FMOD by real-time reverse transcriptase-polymerase chain reaction (RT-PCR) was detectable in contrast to normal B lymphocytes. We used unpulsed native CLL cells and CD40 ligand (CD40L)-stimulated CLL cells as antigen-presenting cells (APCs) to expand autologous T cells from 13 patients. The number of T cells during 4 weeks of in vitro culture increased 2- to 3.5-fold and the number of T cells recognizing FMOD peptides bound to HLA-A2 dimers increased 10-fold. The expanded T cells also were able to secrete interferon-gamma (IFN-gamma) upon recognition of the antigen demonstrated by IFN-gamma ELISPOT assays. T cells not only recognized HLA-A2-binding FMOD peptides presented by transporter-associated with antigen-processing (TAP)-deficient T2 cells, but also FMOD overexpressing autologous CLL cells in an HLA-A2-restricted manner. In summary, FMOD was shown for the first time to be naturally processed and presented as TAA in primary CLL cells, enabling the expansion of autologous tumor-specific T cells.
The blood–brain barrier in health and disease (2012)

The blood-brain barrier (BBB) is a term used to describe a series of properties possessed by the vasculature of the central nervous system (CNS) that tightly regulate the movement of ions, molecules, and cells between the blood and the CNS. This barrier is crucial to provide the appropriate environment to allow for proper neural function, as well as protect the CNS from injury and disease. In this review, I discuss the cellular and molecular composition of the BBB and how the development and function of the BBB is regulated by interactions with the CNS microenvironment. I further discuss what is known about BBB dysfunction during CNS injury and disease, as well as methodology used to deliver drugs across the BBB to the CNS.
cing: measuring network-internal delays using only existing infrastructure (2004)

Several techniques have been proposed for measuring network-internal delays. However, those that rely on router responses have questionable performance, and all proposed alternatives require either new functionality in routers or the existence of a measurement infrastructure. In this paper we revisit the feasibility of measuring network-internal delays using only existing infrastructure, focusing on the use of ICMP timestamp probes to routers. We present network measurements showing that ICMP timestamp is widely supported and that TTL-responses often perform poorly, and we analyze the effect of path instability and routing irregularities on the performance and applicability of using ICMP timestamp. We also confirm that router responses rarely introduce errors in our measurements. Finally, we present a practical algorithm for clock artifact removal that addresses problems with previous methods and has been found to perform well in our setting.
Effect of geometry of planar antenna arrays on Cramer-Rao Bounds for DOA estimation (2010)

In this paper, the effect of the geometry of planar antenna arrays on the accuracy of Direction of Arrival (DOA) estimation of impinging signals is studied. The expressions of Cramer-Rao Bounds (CRB) for the two-dimensional (2-D) DOA estimation are derived. Based on the hexagonal, square, L, cross and Y shaped antenna arrays, the CRBs of the elevation and azimuth angles of estimated DOA are investigated according to the received power ratio of signal to noise (SNR) and the fixed and the changing direction of impinging signal.
CC chemokine receptor 5 and interleukin-1 receptor antagonist gene polymorphisms in patients with primary Sjögren's syndrome. (2003)

In this population of patients with Sjögren's syndrome, the frequency of CCR5 delta 32/CCR5 genotype is significantly decreased. The data suggests that carrier status for the CCR5 delta 32 allele may contribute to protection from the development of primary Sjögren's syndrome. In contrast, IL-1Ra VNTR polymorphism does not confer susceptibility to primary Sjögren's syndrome in Slovak Caucasians.
Knowledge Selection for Laser Drilling in the Oil and Gas Industry (2006)

To maximize oil and gas production profitability, it is paramount to reach the whole reservoir and extract the oil and gas in it efficiently. Therefore the well should be drilled as quickly as possible to start production as soon as possible. The laser drilling literature reviews, lab experiments, and numerical models have proven so far that this novel technique performs better and faster than the conventional rotary drilling technique. In addition, this eliminates the problem of contaminated water, soil, and rocks due to the use of toxic muds while rotary drilling. As a result, the drilling and production operations costs are minimized. This paper introduces the knowledge elements for laser drilling system that will be optimized by an expert system. This system comprises oil and gas well parameters, rock properties, and laser properties and parameters. Based on these data, the corresponding rate of penetration and drilling time are evaluated
An Efficient SS/TDMA Time Slot Assignment Algorithm (1979)

This paper presents an efficient time slot assignment algorithm for an SS/TDMA system. The technique utilized in the algorithm is a systematic method of finding distinct representatives from the row sets of a traffic matrix. The assignment efficiency resulting from the algorithm is 100% for any traffic matrix. The number of switching modes generated by the algorithm is bounded by <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n^{2} - 2n + 2</tex> for an <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n \times n</tex> traffic matrix. The computational procedures are illustrated by an example for the Advanced WESTAR system. Also included in the paper are the computer simulation results on the numbers of required switching modes for various simulated traffic matrices.
The Role of Small Leucine-rich Proteoglycan (SLRP) Family in Pathological Lesions and Cancer Cell Growth (2005)

The roles of lumican, a member of the small-leucine-rich-proteoglycan (SLRP) family, in pathological fibrosis, cancer tissues and tumor cell growth were reviewed. Lumican is predominantly localized in the areas of pathological fibrosis including the thickened intima of human coronary arteries, ischemic and reperfused hearts, and acute pancreatitis and chronic pancreatitis (CP)-like lesions adjacent to pancreatic cancer nests. In these lesions, lumican mRNA and protein were transiently and ectopically overexpressed in most of the vascular smooth muscle cells (VSMCs) that migrated into the thickened intima, myocardial cells adjacent to an ischemic lesion, acinar cells, islet cells and fibroblasts of pathological pancreatic tissues. The low expression level of lumican in breast cancer is associated with rapid progression and poor survival. Lumican mRNA in breast cancer is overexpressed in fibroblasts adjacent to cancer cells but not in cancer cells. Furthermore, the high expression level of lumican is associated with a high pathological tumor grade, a low estrogen receptor level in the cancer tissues, and young age of patients. The suppression of lumican expression in culture cells induces their cell growth. Lumican-transfected tumor cells are characterized by a strong suppression of their anchorage-independent growth and capacity of invasion. Lumican significantly suppressed subcutaneous tumor formation in syngenic mice, with a concomitant decrease in cyclin D1 expression level, and induced and/or enhanced the apoptosis of these cells. The autocrine mechanism in cancer cells and the paracrine mechanism in cancer cells and fibroblasts via transforming growth factor (TGF)-beta and Smad signals may play important roles in the regulation of tumor growth by SLRPs.
Programmable Pulsed Magnetic Field System for Biological Applications (2014)

In this paper, a pulsed magnetic field system developed for biological applications is presented. The proposed pulsed power setup generates repetitive controlled frequency and width square wave 0-4 kV electrical pulses and supports currents up to 1000 A. As a load, a solenoid-type inductor is used with integrated plastic cuvette for biological cells. Homogeneous repetitive microsecond range pulsed magnetic field up to 15 T inside the effective volume of the cuvette can be generated. The development process, the structure of the pulsed magnetic field setup, and the solutions implemented to achieve biomedical applicability are overviewed in this paper. The presented experimental results showing contactless permeabilization of biological cells in pulsed magnetic field have an excellent potential for the development of a new biomedical treatment technique and applicability of the setup.
In Vivo Flow Cytometry (2004)

The fate of circulating tumor cells is an important determinant of their ability to form distant metastasis. Here, we demonstrate the use of in vivo flow cytometry as a powerful new method for detecting quantitatively circulating cancer cells. We specifically examine the circulation kinetics of two prostate cancer cell lines with different metastatic potential in mice and rats. We find that the cell line and the host environment affect the circulation kinetics of prostate cancer cells, with the intrinsic cell line properties determining the initial rate of cell depletion from the circulation and the host affecting cell circulation at later time points.
One-bit massive MIMO: Channel estimation and high-order modulations (2015)

We investigate the information-theoretic throughout achievable on a fading communication link when the receiver is equipped with one-bit analog-to-digital converters (ADCs). The analysis is conducted for the setting where neither the transmitter nor the receiver have a priori information on the realization of the fading channels. This means that channel-state information needs to be acquired at the receiver on the basis of the one-bit quantized channel outputs. We show that least-squares (LS) channel estimation combined with joint pilot and data processing is capacity achieving in the single-user, single-receive-antenna case. We also investigate the achievable uplink throughput in a massive multiple-input multiple-output system where each element of the antenna array at the receiver base-station feeds a one-bit ADC. We show that LS channel estimation and maximum-ratio combining are sufficient to support both multiuser operation and the use of high-order constellations. This holds in spite of the severe non-linearity introduced by the one-bit ADCs.
Design and global optimization of high-efficiency thermophotovoltaic systems (2010)

Despite their great promise, small experimental thermophotovoltaic (TPV) systems at 1000 K generally exhibit extremely low power conversion efficiencies (approximately 1%), due to heat losses such as thermal emission of undesirable mid-wavelength infrared radiation. Photonic crystals (PhC) have the potential to strongly suppress such losses. However, PhC-based designs present a set of non-convex optimization problems requiring efficient objective function evaluation and global optimization algorithms. Both are applied to two example systems: improved micro-TPV generators and solar thermal TPV systems. Micro-TPV reactors experience up to a 27-fold increase in their efficiency and power output; solar thermal TPV systems see an even greater 45-fold increase in their efficiency (exceeding the Shockley-Quiesser limit for a single-junction photovoltaic cell).
Etched facet technology for GaN and blue lasers (2006)

In the late 1980's, etched facet lasers were demonstrated at Cornell University using a process based on chemically assisted ion beam etching (CAIBE). These etched facets allowed, for the first time, mirror reflectivities to be obtained that were equal to those of cleaved facets. Over the past few years, BinOptics Corporation has used this proprietary Etched Facet Technology (EFT) in fabricating InP based lasers with a quality equal to those of cleaved facets. Etched facets allow mirrors to be placed on the epitaxial substrate with very high precision. EFT eliminates losses that result from mechanical facet cleaving, allows wafer-scale testing and coating, and enables monolithic integration. BinOptics Corporation has now developed a modified version of its EFT for GaN materials and blue lasers where mechanical cleaving losses can be even more problematic. The relatively high defect density of currently available GaN materials creates an additional yield advantage for EFT: it allows the formation of shorter cavity devices with fewer defects per device. The first etched facet GaN devices are Fabry-Perot type ridge waveguide lasers emitting at 405nm for optical storage applications. However, as demonstrated in InP, it is planned to extend the technology to horizontal-cavity surface-emitting lasers (HCSELs) with integrated monitoring photodetectors (MPDs). A surface-emitting blue laser will allow two-dimensional arrays for high power applications and monolithic integration of additional functions. For example, the integration of a blue HCSEL with a receive detector will enable the creation of a compact optical head.
Separation of Toxin and Hemagglutinin from Crystalline Toxin of Clostridium botulinum Type A by Anion Exchange Chromatography and Determination of Their Dimensions by Gel Filtration (1968)

Abstract Crystalline preparations of Clostridium botulinum type A toxin were fractionated on DEAE-cellulose columns with Tris-HCl buffers at pH 8.0. The isolated toxic fraction was free of hemagglutinating activity and contained 5 times the specific activity of the crystalline toxin. The second fraction was a powerful hemagglutinin but was only feebly toxic; it emerged from the column as one or more peaks, under different elution conditions. By rechromatography and immunological tests, the toxicity of the second fraction was shown to be due to contamination with traces of the toxic fraction. By several criteria, the toxic and hemagglutinating components appeared to be at least two different proteins. Most of the information obtainable from the ultracentrifugal analysis of these substances was also obtained by gel filtration on a Sephadex G-200 column and with much smaller protein concentrations. At physiological pH, the toxic fraction had a molecular weight of 150,000 and a Stokes radius of 48 A; these dimensions were in agreement with those established in vivo by other investigators. The hemagglutinin appeared to exist in three forms of aggregation with molecular weights of 290,000, 500,000, and 900,000.
AIM/CD5L: a key protein in the control of immune homeostasis and inflammatory disease (2015)

CD5L, a soluble protein belonging to the SRCR superfamily, is expressed mostly by macrophages in lymphoid and inflamed tissues. The expression of this protein is transcriptionally controlled by LXRs, members of the nuclear receptor family that play major roles in lipid homeostasis. Research undertaken over the last decade has uncovered critical roles of CD5L as a PRR of bacterial and fungal components and in the control of key mechanisms in inflammatory responses, with involvement in processes, such as infection, atherosclerosis, and cancer. In this review, we summarize the current knowledge of CD5L, its roles at the intersection between lipid homeostasis and immune response, and its potential use as a diagnostic biomarker in a variety of diseases, such as TB and liver cirrhosis.
SERUM YKL-40 LEVELS IN HEALTHY CHILDREN AND ADULTS. COMPARISON WITH SERUM AND SYNOVIAL FLUID LEVELS OF YKL-40 IN PATIENTS WITH OSTEOARTHRITIS OR TRAUMA OF THE KNEE JOINT (1996)

YKL-40 is a recently discovered human glycoprotein which is related in amino acid sequence to the chitinase protein family. YKL-40 is a major secretory protein of human chondrocytes and synoviocytes, and could play a role in tissue remodelling. The aim of the study was to establish the serum YKL-40 level in normal subjects and to evaluate serum YKL-40 as a marker for osteoarthritis. Serum YKL-40 was 80 micrograms/l in healthy children (n = 476) and 102 micrograms/l in healthy adults (n = 260). No age or sex differences were found in serum YKL-40 in subjects younger than 70 yr, but thereafter serum YKL-40 increased significantly. Patients with late-stage osteoarthritis of the knee (n = 37) had significantly higher serum YKL-40 (1.5-fold; P < 0.01) compared to healthy age-matched subjects, whereas patients with early-stage osteoarthritis of the knee or recent torn cruciate ligaments or menisci did not have elevated serum YKL-40. The level of YKL-40 in serum and synovial fluid correlated significantly, and 10-fold higher values were found in synovial fluid. YKL-40 levels in serum and synovial fluid of patients with acute severe synovial inflammation were significantly higher (P < 0.05-P < 0.001) than those in patients with no, light or moderate synovitis of the knee joint. Furthermore, YKL-40 correlated significantly (P < 0.01) with the amino-terminal propeptide of type III procollagen, but not with serum C-reactive protein. Our data indicate that YKL-40 in synovial fluid and serum may reflect human articular cartilage degradation and the degree of synovial inflammation in the knee joint.
Identification of proteins from two-dimensional polyacrylamide gels using a novel acid-labile surfactant (2002)

Protein identification by peptide mass mapping usually involves digestion of gel-separated proteins with trypsin, followed by mass measurement of the resulting peptides by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Positive identification requires measurement of enough peptide masses to obtain a definitive match with sequence information recorded in protein or DNA sequence databases. However, competitive binding and ionization of residual surfactant introduced during polyacrylamide gel electrophoresis (PAGE) can inhibit solid-phase extraction and MS analysis of tryptic peptides. We have evaluated a novel, acid-labile surfactant (ALS) as an alternative to sodium dodecylsulfate (SDS) for two-dimensional (2-D) PAGE separation and MALDI-MS mapping of proteins. ALS was substituted for SDS at the same concentration in buffers and gels used for 2-D PAGE. Manual and automated procedures for spot cutting and in-gel digestion were used to process Coomassie stained proteins for MS analysis. Results indicate that substituting ALS for SDS during PAGE can significantly increase the number of peptides detected by MALDI-MS, especially for proteins of relatively low abundance. This effect is attributed to decomposition of ALS under acidic conditions during gel staining, destaining, peptide extraction and MS sample preparation. Automated excision and digestion procedures reduce contamination by keratin and other impurities, further enhancing MS identification of gel separated proteins.