gebhart/patrepeval huggingface dataset:
Genome Editing with CompoZr Custom Zinc Finger Nucleases (ZFNs) (2012)

Genome editing is a powerful technique that can be used to elucidate gene function and the genetic basis of disease. Traditional gene editing methods such as chemical-based mutagenesis or random integration of DNA sequences confer indiscriminate genetic changes in an overall inefficient manner and require incorporation of undesirable synthetic sequences or use of aberrant culture conditions, potentially confusing biological study. By contrast, transient ZFN expression in a cell can facilitate precise, heritable gene editing in a highly efficient manner without the need for administration of chemicals or integration of synthetic transgenes. Zinc finger nucleases (ZFNs) are enzymes which bind and cut distinct sequences of double-stranded DNA (dsDNA). A functional CompoZr ZFN unit consists of two individual monomeric proteins that bind a DNA "half-site" of approximately 15-18 nucleotides (see Figure 1). When two ZFN monomers "home" to their adjacent target sites the DNA-cleavage domains dimerize and create a double-strand break (DSB) in the DNA. Introduction of ZFN-mediated DSBs in the genome lays a foundation for highly efficient genome editing. Imperfect repair of DSBs in a cell via the non-homologous end-joining (NHEJ) DNA repair pathway can result in small insertions and deletions (indels). Creation of indels within the gene coding sequence of a cell can result in frameshift and subsequent functional knockout of a gene locus at high efficiency. While this protocol describes the use of ZFNs to create a gene knockout, integration of transgenes may also be conducted via homology-directed repair at the ZFN cut site. The CompoZr Custom ZFN Service represents a systematic, comprehensive, and well-characterized approach to targeted gene editing for the scientific community with ZFN technology. Sigma scientists work closely with investigators to 1) perform due diligence analysis including analysis of relevant gene structure, biology, and model system pursuant to the project goals, 2) apply this knowledge to develop a sound targeting strategy, 3) then design, build, and functionally validate ZFNs for activity in a relevant cell line. The investigator receives positive control genomic DNA and primers, and ready-to-use ZFN reagents supplied in both plasmid DNA and in-vitro transcribed mRNA format. These reagents may then be delivered for transient expression in the investigator's cell line or cell type of choice. Samples are then tested for gene editing at the locus of interest by standard molecular biology techniques including PCR amplification, enzymatic digest, and electrophoresis. After positive signal for gene editing is detected in the initial population, cells are single-cell cloned and genotyped for identification of mutant clones/alleles.
A Cloud-Agnostic Container Orchestrator for Improving Interoperability (2018)

The last several years have seen a rapid increase in the use of containers and containerizing services, such as Docker, Kubernetes, and LXC. With such a rise comes a vast increase in opportunities for improved portability, security, and automation. While many of these opportunities are being taken advantage of in containers today, there remains many more possibilities that have not been explored. In this paper, we present a novel approach to container management that enables the rapid live migration of stateful containers between any hosts within private, public, or hybrid clouds, through a simple interface that provides a high-level view of the network of computing nodes and the containers running on them. Finally, we provide a vision for container management that allows greatly improved security and resiliency through autonomous and self-migrating containers existing across the scope of the Internet.
Integration of Three‐Dimensional Left Atrial Magnetic Resonance Images into a Real‐Time Electroanatomic Mapping System: Validation of a Registration Method (2008)

Our registration method, which is mainly based on the surface registration of the posterior wall of the left atrium, enables almost 90% of PVs to be isolated by means of an anatomically based catheter ablation approach.
Texture mapping for cel animation (1998)

We present a method for applying complex textures to hand-drawn characters in cel animation. The method correlates features in a simple, textured, 3-D model with features on a hand-drawn figure, and then distorts the model to conform to the hand-drawn artwork. The process uses two new algorithms: a silhouette detection scheme and a depth-preserving warp. The silhouette detection algorithm is simple and efficient, and it produces continuous, smooth, visible contours on a 3-D model. The warp distorts the model in only two dimensions to match the artwork from a given camera perspective, yet preserves 3-D effects such as self-occlusion and foreshortening. The entire process allows animators to combine complex textures with hand-drawn artwork, leveraging the strengths of 3-D computer graphics while retaining the expressiveness of traditional handdrawn cel animation. CR Categories: I.3.3 and I.3.7 [Computer Graphics].
Cross-reactivities in memory cytotoxic T lymphocyte recognition of heterologous viruses. (1994)

Analyses of the relationships between different viruses and viral proteins have focused on homologies between linear amino acid sequences, but cross-reactivities at the level of T cell recognition may not be dependent on a conserved linear sequence of several amino acids. The CTL response to Pichinde virus (PV) and vaccinia virus (VV) in C57BL/6 mice previously immunized with lymphocytic choriomeningitis virus (LCMV) included the reactivation of memory cytotoxic T lymphocyte (CTL) specific to LCMV. Limiting dilution assays (LDA) demonstrated that at least part of this reactivation of memory cells in LCMV-immune mice related to cross-reactivity at the clonal level, even though acute infections with these viruses in nonimmune mice elicited CTL responses that did not cross-react in conventional bulk CTL assays. Precursor CTL (pCTL) to LCMV were generated in splenic leukocytes from LCMV-immune mice acutely infected with PV or VV when stimulated in vitro with only the second virus but not with uninfected peritoneal exudate cells (PECs). Cytotoxicity mediated by LCMV-specific CTL clones activated by PV infection was greatly inhibited by anti-CD8 antibody, suggesting that these memory CTL clones recognizing LCMV-infected targets were of low affinity. LCMV-immune splenocytes stimulated in vitro with PV or VV demonstrated a low but significant precursor frequency (p/f) to the heterologous viruses, and splenocytes from PV- or VV-immune mice when stimulated in vitro against LCMV generated a low but significant p/f to LCMV. Short-term CTL clones cross-reactive between LCMV and PV were derived from splenic leukocytes from LCMV-immune mice acutely infected with PV. To distinguish whether the cross-reactivity was directed against a viral peptide or a virus-induced endogenous cellular neoantigen, we demonstrated that a pCTL frequency to PV about 1/4-1/7 that of the frequency to LCMV could be generated from LCMV-immune splenic leukocytes stimulated with the immunodominant LCMV NP peptide. A partially homologous PV peptide generated from the equivalent site to the LCMV NP peptide did not sensitize targets to lysis by either LCMV- or PV-specific CTLs, suggesting that the cross-reactivity in killing was not due to evolutionarily conserved equivalent sequences. Experiments also indicated that prior immunity to one virus could modulate future primary immune responses to a second virus. Elevated pCTL frequencies to PV were seen after acute PV infection of LCMV-immune mice, and elevated pCTL frequencies to LCMV were seen after acute LCMV infection of PV- and VV-immune mice.(ABSTRACT TRUNCATED AT 400 WORDS)
A Device for Plotting Rays in a Stratified Medium (1947)

A device is described which was developed for the rapid computation of rays in a medium in which the index of refraction or speed is a function of only one rectangular coordinate. It was used during the war for the computation of sound fields in water in the ray approximation, and hence is called the sonic ray plotter. It could also be applied to the ray approximation solution of the problem of the propagation of radar signals in a stratified atmosphere, since it is possible to transform the curvature of the earth into an additional refractive index that depends only on the height above a plane earth.
A filtration and vacuum distillation unit for the purification of alkali metals (1958)

Abstract A combined filtration and vacuum distillation apparatus for producing high‐purity alkali metals is described. Operating data for the preparation of distilled lithium, sodium and potassium are given.
Gene expression drives local adaptation in humans (2013)

The molecular basis of adaptation--and, in particular, the relative roles of protein-coding versus gene expression changes--has long been the subject of speculation and debate. Recently, the genotyping of diverse human populations has led to the identification of many putative "local adaptations" that differ between populations. Here I show that these local adaptations are over 10-fold more likely to affect gene expression than amino acid sequence. In addition, a novel framework for identifying polygenic local adaptations detects recent positive selection on the expression levels of genes involved in UV radiation response, immune cell proliferation, and diabetes-related pathways. These results provide the first examples of polygenic gene expression adaptation in humans, as well as the first genome-scale support for the hypothesis that changes in gene expression have driven human adaptation.
Convolutional neural network for video fire and smoke detection (2016)

Research on video analysis for fire detection has become a hot topic in computer vision. However, the conventional algorithms use exclusively rule-based models and features vector to classify whether a frame is fire or not. These features are difficult to define and depend largely on the kind of fire observed. The outcome leads to low detection rate and high false-alarm rate. A different approach for this problem is to use a learning algorithm to extract the useful features instead of using an expert to build them. In this paper, we propose a convolutional neural network (CNN) for identifying fire in videos. Convolutional neural network are shown to perform very well in the area of object classification. This network has the ability to perform feature extraction and classification within the same architecture. Tested on real video sequences, the proposed approach achieves better classification performance as some of relevant conventional video fire detection methods and indicates that using CNN to detect fire in videos is very promising.
Mononuclear Leukocytes Preferentially Bind via CD44 to Hyaluronan on Human Intestinal Mucosal Smooth Muscle Cells after Virus Infection or Treatment with Poly(I·C) (1999)

Pathological changes in inflammatory bowel disease include an increase in intestinal mucosal mononuclear leukocytes and hyperplasia of the muscularis mucosae smooth muscle cells (M-SMCs). Because virus infections have correlated with disease flare, we tested the response of cultured M-SMCs to respiratory syncytial virus, measles virus, and the viral analogue, poly(I.C). Adhesion of U937 cells and peripheral blood mononuclear cells was used to measure the leukocyte-interactive potential of M-SMCs. Untreated M-SMCs, only minimally adhesive for leukocytes, bound U937 cells after treatment with respiratory syncytial virus or measles virus. Mononuclear leukocytes also bound to poly(I.C)-treated M-SMCs. Although both vascular cell adhesion molecule-1 mRNA and protein increased 3-4-fold in poly(I.C)-treated M-SMC cultures, U937 cell adhesion was not blocked by an anti-vascular cell adhesion molecule-1 monoclonal antibody. However, hyaluronidase digestion of poly(I.C)- or virus-treated M-SMCs dramatically reduced leukocyte adhesion ( approximately 75%). Fluorophore-assisted carbohydrate electrophoresis demonstrated a approximately 3-fold increase in surface-bound hyaluronan on poly(I.C)-treated M-SMCs compared with untreated controls. In addition, pretreatment of mononuclear cells with a blocking anti-CD44 antibody, greatly decreased adhesion to poly(I.C)-treated M-SMCs. Recognition of this virus-induced hyaluronan/CD44 mechanism of mesenchymal cell/leukocyte interaction introduces a new avenue in the research of gut inflammation.
Lewis Acidity Enhancement of Triarylboranes via Peripheral Decoration with Cationic Groups (2008)

The cationic boranes [Ar(N+)BMes(2)](+), [Ar(N+)(2)BMes](2+), and [Ar(N+)(3)B](3+) (Ar(N+) = [4-(Me(3)N)-2,6-Me(2)-C(6)H(2)](+); Mes = mesityl) have been synthesized and studied by cyclic voltammetry. The results obtained in this study show that the reduction potential of these derivatives in THF is increased by 0.36 V upon each substitution of a mesityl by a cationic Ar(N+) anilium group. Remarkably, the trication [3](3+), whose triflate salt is water soluble, complexes cyanide anions in pure water at pH 7. These properties underscore the dramatic effects caused by the increased number of cationic groups.
Brain Mapping in Sedated Infants and Young Children with Passive-Functional Magnetic Resonance Imaging (1999)

Functional magnetic resonance imaging (fMRI) in pediatric patients presents a unique set of problems due to the need for patient compliance, the frequent need for sedation and an early developmental status. A new method for using fMRI in sedated infants and young children is presented using passive stimuli focused on visual, sensorimotor and language functions. All of these stimuli are presented such that no patient interaction is required. Eight sedated children undergoing diagnostic MRI scans of the brain participated in these passive fMRI procedures. Cortical regions were identified using standard techniques applied to the blood-oxygen-level-dependent signal which is the basis for fMRI. The results support the feasibility of brain mapping in sedated children with passive fMRI techniques.
Thrombosis: tangled up in NETs (2013)

The contributions by blood cells to pathological venous thrombosis were only recently appreciated. Both platelets and neutrophils are now recognized as crucial for thrombus initiation and progression. Here we review the most recent findings regarding the role of neutrophil extracellular traps (NETs) in thrombosis. We describe the biological process of NET formation (NETosis) and how the extracellular release of DNA and protein components of NETs, such as histones and serine proteases, contributes to coagulation and platelet aggregation. Animal models have unveiled conditions in which NETs form and their relation to thrombogenesis. Genetically engineered mice enable further elucidation of the pathways contributing to NETosis at the molecular level. Peptidylarginine deiminase 4, an enzyme that mediates chromatin decondensation, was identified to regulate both NETosis and pathological thrombosis. A growing body of evidence reveals that NETs also form in human thrombosis and that NET biomarkers in plasma reflect disease activity. The cell biology of NETosis is still being actively characterized and may provide novel insights for the design of specific inhibitory therapeutics. After a review of the relevant literature, we propose new ways to approach thrombolysis and suggest potential prophylactic and therapeutic agents for thrombosis.
Tumor Necrosis Factor Alpha‐Stimulated Endothelium: An Inducer of Dendritic Cell Development from Hematopoietic Progenitors and Myeloid Leukemic Cells (2004)

Especially when exposed to inflammatory stimuli, endothelial cells (EC) have been shown to promote the maturation of monocytes into dendritic cells (DC) and the long-term proliferation of CD34+ cells by constitutive cytokine production and direct cellular contact. We therefore hypothesized that cytokine-stimulated EC would induce hematopoietic progenitor cells to develop into mature dendritic cells. To test this theory, human CD34+ cells derived from cord blood or leukapheresis products were cultured with a monolayer of either interleukin (IL)-1beta, IL-4, or tumor necrosis factor (TNF)-alpha-stimulated human umbilical cord EC. The cells in suspension were analyzed weekly over a period of 6 weeks. IL-1beta supported cell expansion, whereas IL-4 had no effect on cell expansion or DC differentiation. Only TNF-alpha-stimulated EC induced the development of mature, allostimulatory DC with a high expression of CD83, HLA-DR, CD1a, and costimulatory molecules like CD80 and CD86. Acute myeloid leukemia cells from the cell line Kasumi-1 also developed DC-like features when cocultured with TNF-alpha-stimulated EC. Direct contact between endothelial and progenitor cells increased the number of developing DC. Cell cycle analysis and apoptosis studies demonstrated a reduced G2M fraction, an increased S fraction, and a decrease in TNF-alpha-dependent apoptosis of DC developing in the presence of endothelial cells. As shown by electron and confocal microscopic studies, intimate interactions between EC and DC occurred, resulting in the internalization of the developing DC within the EC monolayer and a bidirectional exchange of proteins. We conclude that, via the action of TNF-alpha, inflamed human endothelium can induce CD34+ and leukemic cells to differentiate into dendritic cells.
An f:10 Camera for Astronomical Spectroscopy (1951)

An f:1.0 spectrograph camera with a nearly flat field was designed by splitting the symmetrical ball lens of Sutton and adding correcting components. The resulting 7-element objective has longitudinal spherical aberration not exceeding 0.001 mm between 7000A and 9000A.The camera is constructed so that all adjustments of tilt and focus are made from behind the plateholder. The plate emulsion is kept within 0.025 mm of the focal plane even when the camera is operated upside down.In astronomical use the camera photographs several hundred angstroms of spectrum at one time on flat plates, with good definition through the range 4000A to 9000A. As compared to modified Schmidt cameras, it has the disadvantage of a field limited to 7 degrees by vignetting, but is comparable in light efficiency, and has the greater convenience of allowing the use of glass plates large enough to carry multiple exposures.
Control of hearing-aid saturated sound pressure level by frequency-shaped output compression limiting (1999)

To fit a hearing aid successfully, it is important to set the Saturated Sound Pressure Level (SSPL) or Maximum Power Output (MPO) appropriately. The SSPL should be low enough to prevent sounds from being amplified to uncomfortable loudness, and yet high enough to maximize speech intelligibility and signal quality. To help attain an optimum SSPL setting, a novel output compression limiting scheme, with shapable MPO (ShaMPO), has been devised. In ShaMPO, the SSPL is shaped across frequencies in accordance with the individual user's loudness discomfort levels (LDLs). The contributions of different frequency regions to loudness are controlled by summing the amplified signal power relative to the LDLs across frequencies, and using this signal to control a wideband compressor. This scheme and a conventional output compression limiting (AGCo) scheme have been implemented in a digital hearing aid. Ten subjects, with moderately-severe to profound sensorineural hearing losses, participated in a study comparing speech intelligibility and listening comfort for the two schemes. Results showed that there were no significant differences in the speech perception scores between AGCo and ShaMPO, even when the speech was presented at 80 dBA, at which level both schemes were in compression much of the time. However, an examination of how subjects selected the SSPL for the two schemes revealed that, in many instances, AGCo would permit some sounds with compact spectra to be amplified above LDL, whereas ShaMPO would not. Thus the ShaMPO scheme can improve listening comfort for some intense sounds without a loss of speech intelligibility. In contrast, half the subjects found speech at 80 dBA to be uncomfortably loud when listening through their own aids.
Myelin-Associated Inhibitors Regulate Cofilin Phosphorylation and Neuronal Inhibition through LIM Kinase and Slingshot Phosphatase (2006)

Myelin-associated inhibitors (MAIs) signal through a tripartate receptor complex on neurons to limit axon regeneration in the CNS. Inhibitory influences ultimately converge on the cytoskeleton to mediate growth cone collapse and neurite outgrowth inhibition. Rho GTPase and its downstream effector Rho kinase are key signaling intermediates in response to MAIs; however, the links between Rho and the actin cytoskeleton have not been fully defined. We found that Nogo-66, a potent inhibitory fragment of Nogo-A, signals through LIM (LIM is an acronym of the three gene products Lin-11, Isl-1, and Mec-3) kinase and Slingshot (SSH) phosphatase to regulate the phosphorylation profile of the actin depolymerization factor cofilin. Blockade of LIMK1 activation and subsequent cofilin phosphorylation circumvents myelin-dependent inhibition in chick dorsal root ganglion neurons, suggesting that phosphorylation and inactivation of cofilin is critical for neuronal inhibitory responses. Subsequent activation of SSH1 phosphatase mediates cofilin dephosphorylation and reactivation. Overexpression of SSH1 does not mimic the neurite outgrowth inhibitory effects of myelin, suggesting an alternative role in MAI inhibition. We speculate that SSH-mediated persistent cofilin activation may be responsible for maintaining an inhibited neuronal phenotype in response to myelin inhibitors.
Blockchain Based Distributed Control System for Edge Computing (2017)

Edge computing proposes a novel model for providing computational resources close to end devices that are connected to the network. It has numerous applications in Internet of Things, as well as smart grids, healthcare, smart home, etc. This paper presents ongoing research regarding the use of blockchain technology as a platform hierarchical and distributed control systems based on IEC 61499 standard. Hyperledger Fabric was selected as the blockchain solution, where function blocks are to be implemented as smart contracts on a supervisor level. The integration with the edge nodes that perform on the executive level responsible for actual process control is based on a micro-services architecture where Docker containers implement function blocks, and Kubernetes platform is used for orchestrating the execution of containers across the edge resources.
Locating facial features with color information (2002)

In the present paper we suggest a new method for inferring the face location and scale from the color information. At first facial region segmentation is performed with the vertical projection of the gray level pixel value. Second a horizontal projection can be used to localize the vertical edges of the eyes. Within the borders of the eyes we use a gradient decomposed Hough transform to find eye centres in the low brightness region. Once the eyes are reliably detected, we can easily find the position of the mouth depending on a natural constant biometric relation. We calculating two projection curves with the color information. Computer simulation shows that this algorithm is robust.
Common Open Policy Service (COPS) Over Transport Layer Security (TLS) (2005)

to secure Common Open Policy Service (COPS) connections over the Internet.