gebhart/patrepeval huggingface dataset:
A practical technique for verification of three‐dimensional conformal dose distributions in stereotactic radiosurgery (2000)

The trend toward conformal techniques in stereotactic radiosurgery necessitates an accurate and practical method for verification of irregular three-dimensional dose distributions. This work presents the design and evaluation of a phantom system facilitating the measurement of conformal dose distributions using one or more arrays of up to 20 radiographic films separated by 3.2 mm-thick tissue-equivalent spacers. Using Electron Gamma Shower version 4 (EGS4) Monte Carlo simulation, we show that for 6 MV radiosurgical photon beams this arrangement preserves tissue-equivalence to within 1%. The phantom provides 0.25 mm in-plane spatial resolution and multiple sets of films may be used to resample the dose volume in orthogonal planes. Dedicated software has been developed to automate the process of ordering and orienting of scanned film images, conversion of scanned pixel value to dose, resampling of one or more sets of film images and subsequent export of images in DICOM format for coregistration of planned and measured dose volumes. Calculated and measured isodose surfaces for a simple, circular-beam treatment agree to within 1.5 mm throughout the dose volume. For conformal radiosurgical applications, the measured and planned dose distributions agree to within the uncertainty of the manufacture of irregularly shaped collimators. The sensitivity of this technique to minor spatial inaccuracies in beam shaping is also demonstrated.
Genomic-assisted phylogenetic analysis and marker development for next generation soybean cyst nematode resistance breeding (2016)

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is a serious soybean pest. The use of resistant cultivars is an effective approach for preventing yield loss. In this study, 19,652 publicly available soybean accessions that were previously genotyped with the SoySNP50K iSelect BeadChip were used to evaluate the phylogenetic diversity of SCN resistance genes Rhg1 and Rhg4 in an attempt to identify novel sources of resistance. The sequence information of soybean lines was utilized to develop KASPar (KBioscience Competitive Allele-Specific PCR) assays from single nucleotide polymorphisms (SNPs) of Rhg1, Rhg4, and other novel quantitative trait loci (QTL). These markers were used to genotype a diverse set of 95 soybean germplasm lines and three recombinant inbred line (RIL) populations. SNP markers from the Rhg1 gene were able to differentiate copy number variation (CNV), such as resistant-high copy (PI 88788-type), low copy (Peking-type), and susceptible-single copy (Williams 82) numbers. Similarly, markers for the Rhg4 gene were able to detect Peking-type (resistance) genotypes. The phylogenetic information of SCN resistance loci from a large set of soybean accessions and the gene/QTL specific markers that were developed in this study will accelerate SCN resistance breeding programs.
Transcriptional Gene Silencing Using Small RNAs (2009)

RNA interference is a potent gene silencing pathway initiated by short molecules of double-stranded RNA. Small interfering RNAs (siRNAs) with full sequence complementarity to mRNAs induce cleavage of their target transcripts in the cytoplasm. Recent evidence has shown, however, that siRNAs can also function in the nucleus of mammalian cells to affect changes in chromatin structure. When targeted to promoter regions, siRNAs load into the effector protein Argonaute-1 (AGO1) and direct the formation of silent chromatin domains. This mechanism is known as transcriptional gene silencing (TGS), and the development of TGS as a novel therapeutic modality would be applicable to chronic diseases where long-term, heritable silencing of target genes is warranted. Here we discuss how small RNAs can be used to direct TGS in mammalian cells.
Effect of insulating layer material on RF-induced heating for external fixation system in 1.5 T MRI system (2013)

The radio frequency (RF)-induced heating is a major concern when patients with medical devices are placed inside a magnetic resonance imaging (MRI) system. In this article, numerical studies are applied to investigate the potentials of using insulated materials to reduce the RF heating for external fixation devices. It is found that by changing the dielectric constant of the insulation material, the RF-induced heating at the tips of devices can be altered. This study indicates a potential technique of developing external fixation device with low MRI RF heating.
Compression-tuned single-frequency Bragg-grating fiber laser (1995)

Wideband continuously tunable single-frequency lasers are required in a wide range of spectroscopic, communications, and sensor applications. To date, tensile stress has been used to achieve continuous tuning in Bragg-grating fiber lasers.1 Strain tuning yields a Bragg-wavelength change of approximately 1.2 nm/millistrain in the 1.55-µm regime and is limited by the fiber strength. Young's modulus for SiO2 is 1.02×107 psi (5.27×108 Torr). For fiber proof tested at 100 kpsi (5.17 M Torr), a maximum strain of roughly 1% can be applied without degrading the fiber strength and eventually breaking the fiber. This limits tensile strain tuning to the 10-nm regime. Fiber strength limitations associated with tensile stress are relieved with compressive stress is implemented because silica is 23 times as strong under compression as it is under tension.2 A single-frequency erbium-doped, Bragg-grating fiber laser that uses uniform compression to continuously tune over a 32-nm range while maintaining uniform power is described.
TRPV2 Is Activated by Cannabidiol and Mediates CGRP Release in Cultured Rat Dorsal Root Ganglion Neurons (2008)

Transient receptor potential V2 (TRPV2) has been proposed to be a high-threshold thermosensor. However, further elucidation of the channel properties and physiological role of TRPV2 have been hindered by the lack of selective pharmacological tools as well as by the species-dependent differences in the activation of this channel. In the present study, we have used cell-based calcium mobilization and electrophysiological assays to identify and characterize several novel cannabinoid TRPV2 agonists. Among these, cannabidiol was found to be the most robust and potent (EC(50) = 3.7 microM), followed by Delta(9)-tetrahydrocannabinol (EC(50) = 14 microM) and cannabinol (EC(50) = 77.7 microM). We also demonstrated that cannabidiol evoked a concentration-dependent release of calcitonin gene-related peptide (CGRP) from cultured rat dorsal root ganglion neurons in a cannabinoid receptor- and TRPV1-independent manner. Moreover, the cannabidiol-evoked CGRP release depended on extracellular calcium and was blocked by the nonselective TRP channel blocker, ruthenium red. We further provide evidence through the use of small interfering RNA knockdown and repetitive stimulation studies, to show that cannabidiol-evoked CGRP release is mediated, at least in part, by TRPV2. Together, these data suggest not only that TRPV2 may comprise a mechanism whereby cannabidiol exerts its clinically beneficial effects in vivo, but also that TRPV2 may constitute a viable, new drug target.
Robust non-reciprocal lasing in topological cavities of arbitrary geometries (2018)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text B. Bahari, A. Ndao, F. Valini, A. E. Amili, Y. Fainman, and B. Kante, "Robust non-reciprocal lasing in topological cavities of arbitrary geometries," in Conference on Lasers and Electro-Optics, OSA Terchnical Digest (online) (Optica Publishing Group, 2018), paper FM4Q.8. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Stereospecific metallocene catalysts: Scope and limits of rational catalyst design (1995)

Abstract Structure‐performance relationships in the propene polymerization behaviour of a number of silicon bridged bisindenyl zirconocenes show a rational pattern. Prognosis of the polymerization behaviour of different type structures, however, often fails, which is demonstrated by three examples of new zirconocenes. These include two bisindenyl complexes with two‐membered silicon bridges and one isospecific bridged fluorenyl cyclopentadienyl species. It is thus demonstrated that the scope of a “rational catalyst design” in the field of metallocene catalysts is still limited.
High Dynamic Range Infrared Sensors for Remote Sensing Applications (2018)

In this presentation, we will report our recent efforts in achieving high performance in Antimonides type-II superlattice (T2SL) based infrared photodetectors using the barrier infrared detector (BIRD) architecture. The recent emergence of barrier infrared detectors such as the nBn [1] and the XBn [2] have resulted in mid-wave infrared (MWIR) and long-wave infrared (LWIR) detectors with substantially higher operating temperatures than previously available in III-V semiconductor based MWIR and LWIR detectors. The initial nBn devices used either InAs absorber grown on InAs substrate, or lattice-matched InAsSb alloy grown on GaSb substrate, with cutoff wavelengths of ~ 3.2 μm and ~ 4 μm, respectively. While these detectors could operate at much higher temperatures than existing MWIR detectors based on InSb, their spectral responses do not cover the full ( 3 - 5.5 μm) Mwir atmospheric transmission window. There also have been nBn detectors based on the InAs/GaSb T2SL absorber [3], [4].
NB4, a maturation inducible cell line with t(15;17) marker isolated from a human acute promyelocytic leukemia (M3) (1991)

Acute promyelocytic leukemia (APL) is a well-defined entity among acute leukemia, cytogenetically characterized by a t(15;17) (q22;q11–12) translocation. In vitro and in vivo studies suggest that all-trans retinoic acid (RA) treatment restores cell maturation. We have isolated the first permanent cell line with t(15;17), derived from the marrow of a patient with APL in relapse. The establishment of the cell line, its morphologic, karyotypic, and immunohistochemical features are reported. RA induced cell line maturation. Cells strongly expressed myeloid markers, but also some T-cell markers. Additional karyotypic abnormalities, a 12p rearrangement and the possible presence of a homogeneous staining region (HSR) on 19q+ are discussed both in relation to T-cell (CD2, CD4) and monocyte (CD9) markers, and to the acquired cell growth autonomy. The cell line represents a remarkable tool for biomolecular studies.
Fermentation of <scp>D</scp>-xylose, xylitol, and <scp>D</scp>-xylulose by yeasts (1982)

Fifteen yeasts which can assimilate D-xylose were examined for the ability to convert this pentose to ethanol. In six of the seven genera investigated the conversion was enhanced when air had access to the medium. Therefore, the ability to convert D-xylose to ethanol under these conditions is probably common among yeasts. Growth under the same conditions on xylitol, a putative catabolite of D-xylose, led to only traces of ethanol. The effects of growth on another putative catabolite, D-xylose, were complex, but some of the strains which were among the better producers of ethanol from D-xylose produced less from D-xylulose.
Immunoreactivity of Five Monoclonal Antibodies against the 37-Kilodalton Common Cell Wall Protein (PsaA) of<i>Streptococcus pneumoniae</i> (1998)

Five monoclonal antibodies (MAbs) were produced against the Streptococcus pneumoniae pneumococcal surface adhesin A (PsaA) 37-kDa common cell wall protein. These antibodies were used in a dot immunoblot and Western blot study of clinical isolates of S. pneumoniae to detect the presence of the protein. By both assays, the MAbs reacted with clinical isolates representing the 23 type-specific serotypes present in the licensed pneumococcal polysaccharide vaccine. Western blot analysis confirmed the presence of a protein migrating in the gel with a molecular mass of 37 kDa. An extension of the study by using dot immunoblot analysis that included an analysis of the 90 serotypes of S. pneumoniae showed that all five MAbs reacted with 89 of the 90 serotypes tested. MAb 1B6, the exception, did not react with S. pneumoniae serotype 16F. Dot immunoblot analysis of the MAbs with Enterococcus faecalis and viridans streptococci showed varied reactivity patterns, depending on the species. The MAbs against the 37-kDa antigen did not react with Escherichia coli, respiratory pathogens, or nonpathogens representing 22 genera and 29 species of bacteria. All five MAbs also reacted with five multidrug-resistant strains of S. pneumoniae. In summary, these MAbs may be useful for detection of pneumococcal antigen and may lead to the development of diagnostic assays for pneumococcal disease.
A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins (2000)

Approximately 12 X-Y homologous gene pairs have been identified in the non-recombining portions of human sex chromosomes. These X-Y gene pairs fall into two categories. In the first category, both X and Y homologs are ubiquitously expressed. In the second category, the X homolog is ubiquitously expressed, whereas the Y homolog is expressed exclusively in the testis. Here we describe a family of human X-Y genes that cannot be assigned to either category. Designated VCX / Y ( Variable Charge X / Y; VCY previously known as BPY1 ), this gene family has multiple members on both X and Y, and all appear to be expressed exclusively in male germ cells. Members of the VCX / Y family share a high degree of sequence identity, with the exception that a 30 nucleotide unit is tandemly repeated in X-linked members but is present only once in Y-linked members. These atypical features suggest that the VCX / Y family has evolved in a manner previously unrecognized for mammalian X-Y genes. We also found that a copy of VCX is present in CRI-S232, a previously described genomic fragment derived from the X chromosome. Studies have shown that aberrant recombination between arrays of CRI-S232-homologous repeats flanking the steroid sulfatase ( STS ) gene results in STS deletion, which is manifested clinically as X-linked ichthyosis. The revelation that CRI-S232 contains VCX offers a more precise description of the genetic etiology of X-linked ichthyosis: it results from aberrant recombination between VCX gene arrays that flank the STS locus.
A principled approach to nondeferred reference-counting garbage collection (2008)

Nondeferred reference-counting (RC) garbage collection is among the oldest memory-management methods. Despite offering unique advantages, little attention has been paid on how to correctly implement it for modern programming languages. This paper revisits this collection method and describes how to implement it for a modern object-oriented language in an optimizing compiler.
<title>Novel flight instrument display to minimize the risk of spatial disorientation</title> (1997)

This novel flight instrument display presents information to the pilot in a simple and easily comprehensible format by integrating the five orientational flight parameters. It allows the pilot to select specific orientation parameters and then follow a simple tracking task which ensures that these parameters are maintained or, if necessary, recovered. The pilot can at any time check any parameter he wishes, but is free from the requirement to continually sample and combine information from the traditional instruments to maintain stable flight. Cognitive workload to maintain orientation is thus reduced. Our assessment of the display in a UH-60 helicopter simulator showed that the novel display makes recovery from unusual aircraft attitudes and instrument flying easier than when using the standard instrument panel.
Full space-time simulation for high-brightness semiconductor lasers (1997)

A semiconductor laser model is presented, which resolves the full time, longitudinal and lateral space dependences. The model is applied to an investigation of the dynamical stability of an integrated master-oscillator power-amplifier (MOPA) device. The model captures the full gain and refractive index bandwidth as a function of total carrier density. Our simulation confirms, for the first time, some recent experimental observations of high frequency whole beam oscillations and experimental reports that complex transverse filamentation occurs at high power amplifier currents.
Effective Fractionation of Lignocellulose Using a Mild Acetone-based Organosolv Process (2017)

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Polarization-multiplexed, dual-beam swept source optical coherence\n tomography angiography (2017)

A polarization-multiplexed, dual-beam setup is proposed to expand the field\nof view for a swept source optical coherence tomography angiography (OCTA)\nsystem. This method used a Wollaston prism to split sample path light into two\northogonal-polarized beams. This allowed two beams to shine on the cornea at an\nangle separation of ~ 14 degrees, which led to a separation of ~ 4.2 mm on the\nretina. A 3-mm glass plate was inserted into one of the beam paths to set a\nconstant path length difference between the two polarized beams so the\ninterferogram from the two beams are coded at different frequency bands. The\nresulting OCTA images from the two beams were coded with a depth separation of\n~ 2 mm. 5x5 mm2 angiograms from the two beams were obtained simultaneously in 4\nseconds. The two angiograms then were montaged to get a wider field of view\n(FOV) of ~ 5x9.2 mm2.\n
Generalized field-splitting algorithms for optimal IMRT delivery efficiency (2007)

Intensity-modulated radiation therapy (IMRT) uses radiation beams of varying intensities to deliver varying doses of radiation to different areas of the tissue. The use of IMRT has allowed the delivery of higher doses of radiation to the tumor and lower doses to the surrounding healthy tissue. It is not uncommon for head and neck tumors, for example, to have large treatment widths that are not deliverable using a single field. In such cases, the intensity matrix generated by the optimizer needs to be split into two or three matrices, each of which may be delivered using a single field. Existing field-splitting algorithms used the pre-specified arbitrary split line or region where the intensity matrix is split along a column, i.e., all rows of the matrix are split along the same column (with or without the overlapping of split fields, i.e., feathering). If three fields result, then the two splits are along the same two columns for all rows. In this paper we study the problem of splitting a large field into two or three subfields with the field width as the only constraint, allowing for an arbitrary overlap of the split fields, so that the total MU efficiency of delivering the split fields is maximized. Proof of optimality is provided for the proposed algorithm. An average decrease of 18.8% is found in the total MUs when compared to the split generated by a commercial treatment planning system and that of 10% is found in the total MUs when compared to the split generated by our previously published algorithm.
Lipopolysaccharide (LPS) from Brucella abortus is less toxic than that from Escherichia coli, suggesting the possible use of B. abortus or LPS from B. abortus as a carrier in vaccines (1992)

Brucella abortus may be useful as a component of vaccines. This is because it possesses several unique properties as a carrier that enable it to stimulate human B cells even in the relative absence of T cells. Human immunodeficiency virus type 1 proteins conjugated to B. abortus could induce neutralizing antibodies against human immunodeficiency virus type 1. Recently we showed that the characteristics of lipopolysaccharide (LPS) derived from B. abortus are similar to those of the whole bacterium in that the LPS acts as a T-independent type 1 carrier in mice. In this study we wanted to determine whether LPS derived from B. abortus is associated with the adverse effects seen with other bacterial endotoxins. LPS purified from B. abortus by butanol extraction was shown to have less than 2% (wt/wt) contamination by protein and less than 1% (wt/wt) contamination by nucleic acids and to contain 1% (wt/wt) ketodeoxyoctanic acid. Compared with LPS derived from Escherichia coli, B. abortus LPS was 10,000-fold less potent in eliciting fever in rabbits, 268-fold less potent in killing D-galactosamine-sensitized mice, and 1,400-fold and 400-fold less potent in inducing interleukin-1 beta and tumor necrosis factor alpha production, respectively. These results suggest that B. abortus LPS is much less likely than the LPS from E. coli to evoke endotoxic shock; therefore, it may be feasible to incorporate B. abortus as a component of vaccines.
Analysis of extended partial least squares for monitoring large-scale processes (2005)

This brief analyzes the recently proposed extended partial least squares (EPLS) algorithm and reveals that it does not: 1) allow the generalized score variables to be geometrically interpreted, 2) reconstruct the recorded process variables, and 3) produce statistically independent variables for process monitoring. To overcome these deficiencies, an improved EPLS algorithm is introduced, which utilizes generalized scores to identify statistical monitoring models. The brief finally presents an industrial application study of a chemical reaction process to show that improved EPLS offers enhanced diagnosis of abnormal process behavior.
Convolutional Polar Codes (2017)

Arikan's Polar codes attracted much attention as the first efficiently decodable and capacity achieving codes. Furthermore, Polar codes exhibit an exponentially decreasing block error probability with an asymptotic error exponent upper bounded by 1/2. Since their discovery, many attempts have been made to improve the error exponent and the finite block-length performance, while keeping the bloc-structured kernel. Recently, two of us introduced a new family of efficiently decodable error-correction codes based on a recently discovered efficiently-contractible tensor network family in quantum many-body physics, called branching MERA. These codes, called branching MERA codes, include Polar codes and also extend them in a non-trivial way by substituting the bloc-structured kernel by a convolutional structure. Here, we perform an in-depth study of a particular example that can be thought of as a direct extension to Arikan's Polar code, which we therefore name Convolutional Polar codes. We prove that these codes polarize and exponentially suppress the channel's error probability, with an asymptotic error exponent log_2(3)/2 which is provably better than for Polar codes under successive cancellation decoding. We also perform finite block-size numerical simulations which display improved error-correcting capability with only a minor impact on decoding complexity.
Reciprocal Regulation between SIRT6 and miR-122 Controls Liver Metabolism and Predicts Hepatocarcinoma Prognosis (2015)

Mice overexpressing the longevity protein SIRT6 or deficient for the liver's most prevalent microRNA miR-122 display a similar set of phenotypes, including improved lipid profile and protection against damage linked to obesity. Here, we show that miR-122 and SIRT6 negatively regulate each other's expression. SIRT6 downregulates miR-122 by deacetylating H3K56 in the promoter region. MiR-122 binds to three sites on the SIRT6 3' UTR and reduces its levels. The interplay between SIRT6 and miR-122 is manifested in two physiologically relevant ways in the liver. First, they oppositely regulate a similar set of metabolic genes and fatty acid β-oxidation. Second, in hepatocellular carcinoma patients, loss of a negative correlation between SIRT6 and miR-122 expression is significantly associated with better prognosis. These findings show that SIRT6 and miR-122 negatively regulate each other to control various aspects of liver physiology and SIRT6-miR-122 correlation may serve as a biomarker for hepatocarcinoma prognosis.