gebhart/patrepeval huggingface dataset:
Host Gene Induction and Transcriptional Reprogramming in Kaposi’s Sarcoma-Associated Herpesvirus (KSHV/HHV-8)-Infected Endothelial, Fibroblast, and B Cells (2004)

Kaposi's sarcoma-associated herpesvirus (KSHV/HHV-8) is etiologically linked to the endothelial tumor Kaposi's sarcoma and with two lymphoproliferatve disorders, primary effusion lymphoma and multicentric Castleman's disease. HHV-8 infects a variety of target cells both in vivo and in vitro, binds to the in vitro target cells via cell surface heparan sulfate, and uses the alpha(3)beta(1) integrin as one of the entry receptors. Within minutes of infection, HHV-8 induced the integrin-mediated signaling pathways and morphological changes in the target cells (S. M. Akula et al., Cell, 108: 407-419, 2002; P. P. Naranatt et al., J. Virol., 77: 1524-1539, 2003). As an initial step toward understanding the role of host genes in HHV-8 infection and pathogenesis, modulation of host cell gene expression immediately after infection was examined. To reflect HHV-8's broad cellular tropism, mRNAs collected at 2 and 4 h after infection of primary human endothelial [human adult dermal microvascular endothelial cells (HMVECd)] and foreskin fibroblast [human foreskin fibroblast (HFF)] cells and human B cell line (BJAB) were analyzed by oligonucleotide array with approximately 22,000 human transcripts. With a criteria of >2-fold gene induction as significant, approximately 1.72% of the genes were differentially expressed, of which, 154 genes were shared by at least two cells and 33 genes shared by all three cells. HHV-8-induced transcriptional profiles in the endothelial and fibroblast cells were closely similar, with substantial differences in the B cells. In contrast to the antiapoptotic regulators induced in HMVECd and HFF cells, proapoptotic regulators were induced in the B cells. A robust increase in the expression of IFN-induced genes suggestive of innate immune response induction was observed in HMVECd and HFF cells, whereas there was a total lack of immunity related protein inductions in B cells. These striking cell type-specific behaviors suggest that HHV-8-induced host cell gene modulation events in B cells may be different compared with the adherent endothelial and fibroblast target cells. Functional clustering of modulated genes identified several host molecules hitherto unknown to HHV-8 infection. These results indicate that early during infection, HHV-8 reprograms the host transcriptional machinery regulating a variety of cellular processes including apoptosis, transcription, cell cycle regulation, signaling, inflammatory response, and angiogenesis, all of which may play important roles in the biology and pathogenesis of HHV-8.
The Galileo fault tree analysis tool (2003)

We present Galileo, a dynamic fault tree modeling and analysis tool that combines the innovative DIF-Tree analysis methodology with a rich user interface built using package-oriented programming. DIFTree integrates binary decision diagram and Markov methods under the common notation of dynamic fault trees, allowing the user to exploit the benefits of both techniques while avoiding the need to learn additional notations and methodologies. Package-oriented programming (POP) is a software architectural style in which large-scale software packages are used as components, exploiting their rich functionality and familiarity to users. Galileo can be obtained for free under license for evaluation, and can be downloaded from the World-Wide Web.
Ethylene is a positive regulator of root hair development in <i>Arabidopsis thaliana</i> (1995)

Evidence is provided that ethylene is a positive regulator of hair cell development in the root epidermis of Arabidopsis thaliana. Treatment of seedlings with increasing concentrations of the ethylene precursor, 1-aminocyclopropane-1-carboxylic acid (ACC) results in progressively more root hair cells developing in positions normally occupied by non-hair cells. Consistent with these findings are observations that treatments that block either ethylene synthesis or its perception reduce the number of root hairs. A model is proposed in which either ethylene or ACC is a signal involved in specifying the pattern of cell differentiation in the Arabidopsis root epidermis.
DRG-cache: a data retention gated-ground cache for low power (2002)

In this paper we propose a novel integrated circuit and architectural level technique to reduce leakage power consumption in high performance cache memories using a single Vt (transistor threshold voltage) process. We utilize the concept of gated-ground (an NMOS transistor inserted between the ground line and SRAM cell) to achieve a reduction in leakage energy without significantly affecting performance. Experimental results on gated-ground caches show that data are retained (DRG-cache) even in stand-by mode of operation. Data are restored when the gated-ground transistor is turned on. Turning off the gated-ground transistor in turn gives a large reduction in leakage power. This technique requires no extra circuitry; the row decoder itself can be used to control the gated-ground transistor. The technique is applicable to data and instruction caches as well as different levels of cache hierarchy such as the L1, L2, or L3 caches. We fabricated a test chip in TSMC 0.25 /spl mu/ technology to show the data retention capability and the cell stability of DRG-cache. Our simulation results on 100 nm and 70 nm processes (Berkeley Predictive Technology Model) show 16.5% and 27% reduction in consumed energy in L1 cache and 50% and 47% reduction in L2 cache with less than 5% impact on execution time and within 4% increase in area overhead.
Room2Room (2016)

Room2Room is a telepresence system that leverages projected augmented reality to enable life-size, co-present interaction between two remote participants. Our solution recreates the experience of a face-to-face conversation by performing 3D capture of the local user with color + depth cameras and projecting their life-size virtual copy into the remote space. This creates an illusion of the remote person's physical presence in the local space, as well as a shared understanding of verbal and non-verbal cues (e.g., gaze, pointing.) In addition to the technical details of two prototype implementations, we contribute strategies for projecting remote participants onto physically plausible locations, such that they form a natural and consistent conversational formation with the local participant. We also present observations and feedback from an evaluation with 7 pairs of participants on the usability of our solution for solving a collaborative, physical task.
High performance preconditioning on supercomputers for the 3D device simulator MINIMOS (1990)

Discretization and iterative solution of the semiconductor equations in a three-dimensional rectangular region lead to very large sparse linear systems. Nevertheless, design engineers and scientists of device physics need reliable results in short time in order to draw the best advantage out of computer simulation when designing new technologies and advanced devices. This goal can be achieved by use of pre-conditioned iterative methods for the solution of the linear equations on powerful computers as vector and concurrent supercomputers. To achieve optimum performance of such methods special algorithms and coding techniques have to be used in order to allow vectorization and parallelization of the inherent recurrence relations. We have investigated Jacobi and incomplete LU-factorization methods along with various hand tuning options with special emphasis on application on a SIEMENS/Fujitsu VP200. Results are compared with those obtained on a Cray-2 and an ALLIANT/FX40 minisupercomputer.
Consistency conditions upon 3D CT data and the wave equation (2002)

Source trajectories and reconstruction algorithms for clinical volumetric computerized tomography (VCT) will require optimization for efficiency and image quality. VCT data is highly overdetermined, satisfying an ultrahyperbolic partial differential equation. Characteristic boundary value problems for the hyperbolic wave equation and ultrahyperbolic equation are compared, focusing in this paper on a mathematically instructive open-gantry VCT geometry. This example provides physical insight into consistency conditions upon VCT data, clearly showing which information about the object can and cannot be recovered from a set of measured projections. Furthermore, this example demonstrates that efficient numerical solvers for the ultrahyperbolic equation can provide tremendous flexibility in the choice of reconstruction algorithm.
Precision waveguide cells for the measurement of complex permittivity of lossy liquids and biological tissue at 35 GHz (1987)

A waveguide system is described which enables the complex permittivity of high loss, high permittivity liquids and solid tissues to be measured accurately at 35 GHz. The design and constructional details of an experimental cell are given. Some test data are presented and the experimental errors are considered.
A Special-Function Unit for Sorting and Sort-Based Database Operations (1986)

Achieving efficiency in database management functions is a fundamental problem underlying many computer applications. Efficiency is difficult to achieve using the traditional general-purpose von Neumann processors. Recent advances in microelectronic technologies have prompted many new research activities in the design, implementation, and application of database machines which are tailored for processing database management functions. To build an efficient system, the software algorithms designed for this type of system need to be tailored to take advantage of the hardware characteristics of these machines. Furthermore, special hardware units should be used, if they are cost- effective, to execute or to assist the execution of these software algorithms.
ColorPalette: A Knowledge-based system to select colors for a palette (1988)

This paper describes ColorPalette, a knowledge-based system to advise users in selecting colors for a palette used for computer screen design applications. Color selections and advice are based on principles of human computer interface design and color theory, gathered through both research and knowledge acquisition from a human expert. The user may put together various color combinations to form acceptable and successful palettes. The system consists of a color data-base of facts formulated from an HSV color model, a knowledge base that can reason about these colors and their relations to each other, and a set of rules based on the interface design and color theory research. Colors may be added to and removed from the palette as desired, as long as they meet the criteria of the knowledge-based system. The system may be called on to propose a sample palette with desired characteristics, or may be asked to suggest a color that is recommended to go with the current palette. An explanation facility is available to explain the system's decisions to allow or restrict the adding of colors, and to explain why a certain color has been suggested.\nColorPalette is written in Prolog, taking advantage of Prolog's structural foundations, logic programming support, database management capabilities, and natural format for rule-based systems. ColorPalette has a simple command-line interface, with potential extensions to be able to support graphical selection of colors. It is implemented on an Apple Macintosh, and with such extensions would be able to take advantage of Color Quickdraw calls for interactive color selection and display.
Scattering of Electromagnetic Plane Waves from Inhomogeneous Spherically Symmetric Objects (1962)

Unlike its nuclear optical model counterpart, the problem of the scattering of light from spherically symmetric inhomogeneous absorbing particles cannot in general be predicted directly from solutions of the usual wave equation. An exact theory is derived from Maxwell's equations and the resultant scattering coefficients are found to depend upon the solutions of two differential equations, one of which is of the familiar Schr\"odinger form. Specific calculations based on the Green-Wyatt form factor illustrate the dependence of the polarization and scattered intensities on surface diffuseness. The results are compared with similar nuclear calculations.
Umap and Bismap: quantifying genome and methylome mappability (2018)

Short-read sequencing enables assessment of genetic and biochemical traits of individual genomic regions, such as the location of genetic variation, protein binding and chemical modifications. Every region in a genome assembly has a property called 'mappability', which measures the extent to which it can be uniquely mapped by sequence reads. In regions of lower mappability, estimates of genomic and epigenomic characteristics from sequencing assays are less reliable. These regions have increased susceptibility to spurious mapping from reads from other regions of the genome with sequencing errors or unexpected genetic variation. Bisulfite sequencing approaches used to identify DNA methylation exacerbate these problems by introducing large numbers of reads that map to multiple regions. Both to correct assumptions of uniformity in downstream analysis and to identify regions where the analysis is less reliable, it is necessary to know the mappability of both ordinary and bisulfite-converted genomes. We introduce the Umap software for identifying uniquely mappable regions of any genome. Its Bismap extension identifies mappability of the bisulfite-converted genome. A Umap and Bismap track hub for human genome assemblies GRCh37/hg19 and GRCh38/hg38, and mouse assemblies GRCm37/mm9 and GRCm38/mm10 is available at https://bismap.hoffmanlab.org for use with genome browsers.
Biosynthesis of cellulose‐enriched tension wood in <i>Populus</i>: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis (2005)

Stems and branches of angiosperm trees form tension wood (TW) when exposed to a gravitational stimulus. One of the main characteristics of TW, which distinguishes it from normal wood, is the formation of fibers with a thick inner gelatinous cell wall layer mainly composed of crystalline cellulose. Hence TW is enriched in cellulose, and deficient in lignin and hemicelluloses. An expressed sequence tag library made from TW-forming tissues in Populus tremula (L.) x tremuloides (Michx.) and data from transcript profiling using microarray and metabolite analysis were obtained during TW formation in Populus tremula (L.) in two growing seasons. The data were examined with the aim of identifying the genes responsible for the change in carbon (C) flow into various cell wall components, and the mechanisms important for the formation of the gelatinous cell wall layer (G-layer). A specific effort was made to identify carbohydrate-active enzymes with a putative function in cell wall biosynthesis. An increased C flux to cellulose was suggested by a higher abundance of sucrose synthase transcripts. However, genes related to the cellulose biosynthetic machinery were not generally affected, although the expression of secondary wall-specific CesA genes was modified in both directions. Other pathways for which the data suggested increased activity included lipid and glucosamine biosynthesis and the pectin degradation machinery. In addition, transcripts encoding fasciclin-like arabinogalactan proteins were particularly increased and found to lack true Arabidopsis orthologs. Major pathways for which the transcriptome and metabolome analysis suggested decreased activity were the pathway for C flux through guanosine 5'-diphosphate (GDP) sugars to mannans, the pentose phosphate pathway, lignin biosynthesis, and biosynthesis of cell wall matrix carbohydrates. Several differentially expressed auxin- and ethylene-related genes and transcription factors were also identified.
A slot-line MSW signal-to-noise enhancer (1985)

A broadband MSW signal-to-noise enhancer is described which is based on a slot-line transducer that can efficiently launch MSW onto a metallized surface of a YIG film. The effect of metallizing the YIG surface is to increase the bandwidth, from the approximately 1 GHz previously demonstrated with a microstrip device, to approximately 3.5 GHz in the slotline device. Ideally the spacing between the YIG film and the metal layer should be zero, however, in practice a residual non-uniform spacing of approximately 7 μm resulted in a decreased bandwidth. Enhancement of greater than 5 dB was measured, at a power level of +20 dBm, over a 2.2 GHz bandwidth with a threshold power level of 0 dBm.
Nanoparticle Drug Release (2012)

With the development of nanotechnologies and nanosciences,nanoparticles that fascinates more and more biomedical researchers are intensively used as drug carriers.Currently,many nanoparticles have been used in clinical.It has great significance to make further studies on nanoparticles.In this article we introduced several often used drug release carriers and their applications and progresses.The challenge and applications of nanoparti cles as carriers were previewed.
A decade of rabbit fertility data: Study of historical control animals (1992)

Reproductive data for 1795 artificially inseminated Hra: (NZW)SPF control rabbits in 93 developmental toxicity studies conducted from 1980 through 1989 were summarized. Data were obtained during terminal Caesarean-sectioning procedures performed on animals which survived to day 29 of gestation and during postmortem evaluation of does which aborted, delivered prematurely, or were found dead. Significant seasonal variation was not observed. Average pregnancy rate, percentage of rabbits that aborted, and percentage of rabbits that delivered prematurely throughout the decade were 86, 2.0, and 1.6%, respectively. Average numbers of corpora lutea, implantations, live fetuses, dead fetuses, early resorptions, and late resorptions for each doe that survived to scheduled termination were 10.8, 7.8, 7.1, 0.02, 0.49, and 0.15, respectively. The various vehicles used, routes of administration, and a variety of maternal and paternal factors were compared with the fertility data, and no correlations were observed. Rabbits that aborted earlier in gestation had fewer implantations than does which aborted late or delivered prematurely. Does which resorbed 100% of their conceptuses had fewer corpora lutea and implantations when compared with rabbits in the remainder of the population. Rabbits pregnant at scheduled termination which had a low number of corpora lutea or implantation sites had higher than expected pre- and postimplantation losses relative to the population as a whole. Does with a high number of corpora lutea had significantly higher preimplantation loss relative to the general population. This may indicate the presence of a "ceiling value" for the number of ova that can become fertilized and/or implant when the ovulation rate is high and which probably varies according to strain as well as a number of factors related to the individual rabbit. Based upon the results of this study and the work of a previous author, a minimum of four corpora lutea may be necessary for the successful maintenance of pregnancy in the New Zealand white rabbit. The minimum number of corpora lutea required may be strain dependent and may bear a relationship to the normal litter size of the strain.
Evaluation of floating point image compression (2009)

Recently, compression of High Dynamic Range (HDR) photography gained attention in the standardization of the Microsoft HDPhoto compression scheme as JPEG-XR. While integer data of 16 bits/pixel (bpp) in scRGB color-space can represent images up to a dynamic range of about 3.5 magnitudes in luminance, even higher ranges are more efficiently represented by floating-point number formats. In this work, the author presents the approach taken by JPEG-XR for compressing such data, and shows that this method when applied to JPEG 2000 generates equally good results. Furthermore, it is shown that the method performs nearly optimal under a mathematical quality index that is closely related to SSIM, and to the mean square error of the HDR images when rendered to the LDR regime.
GTE Sintered Silicon Nitride (1984)

A status of GTE sintered silicon nitride for advanced heat engines will be presented. This will include an update of: sintering and final properties for a number of GTE silicon nitride compositions, microstructure, density, surface finish, strength, Weibull modulus, oxidation resistance, fracture toughness etc. The status of heat engine components fabricated by injection molding or isopressed/green machining and their performance will be reviewed along with correlations between the shape fabrication technique, strength, and Weibull modulus. Costs and availability will be included where possible. Future directions for increased reliability in silicon nitride structural ceramics will be summarized.
Mechanism of Protection by Diethyldithiocarbamate against Cisplatin Ototoxicity: Antioxidant System (1995)

This investigation was undertaken to explain the possible mechanism(s) of protection by diethyldithiocarbamate (DDTC) against cisplatin ototoxicity. Male Wistar rats (250–275 g) underwent pretreatment auditory brain stem-evoked responses (ABRs). The different groups of rats were injected as follows: (1) cisplatin (16 mg/kg ip), (2) cisplatin plus DDTC (16 mg/kg ip + 600 mg/kg, sc), and (3) control rats. Post-treatment ABRs were performed after 3 days and the rats were euthanized and cochleae were harvested. The cochleae were analyzed for glutathione (GSH) and oxidized glutathione, by HPLC, and for the activities of the antioxidant enzymes, and malondialdehyde levels, by spectrophotometry. The cisplatin-injected rats showed a threshold elevation of 36 ± 3.05 dB above the pretreatment thresholds using click stimulus. Rats treated with cisplatin and then DDTC did not show a significant elevation of hearing threshold. DDTC-mediated protection was associated with higher levels of GSH (0.81 ± 0.11 nmol/mg tissue), compared to 0.45 ± 0.02 nmol/mg tissue following administration of cisplatin alone. Administration of cisplatin + DDTC restored the cochlear GSH-Px activity to control level. Cisplatin-treated rats were found to have decreased GSH-Px activity (75% of control). Cochlear SOD and CAT activities and MDA levels showed a decreasing trend in the animals injected with cisplatin + DDTC, compared to cisplatin-alone-treated rats. These data suggest that the protection conferred by DDTC against cisplatin ototoxicity is associated with sparing of the cochlear GSH/GSH-Px.