gebhart/patrepeval huggingface dataset:
104 Distinct spatial profile of inflammatory gene expression in the brain of a mouse model of neuropsychiatric lupus (2021)

<h3>Background</h3> SLE is an incurable autoimmune disease that results in central nervous system (CNS) involvement with clinical manifestations including anxiety and depression. However, the mechanism/s underlying these neuropsychiatric symptoms (NPSLE) remain unknown. An elevated type 1 interferon (IFNa) signature has been commonly observed in SLE patients, particularly within the CNS of NPSLE patients (Crow et al., 2014, Shiozawa et al., 1992). Given the diversity of clinical CNS manifestations, we hypothesized that type 1 interferon-mediated inflammation occurs in spatially distinct regions within the CNS, resulting in differential behavioral outcomes depending on the impacted brain region. <h3>Methods</h3> Spatial distribution of inflammatory gene expression in the brain was performed using MERFISH, a multiplexed spatial transcriptomics platform employing a custom set of RNA probes. Cell source and <i>in situ</i> results were validated by RT-PCR, RNA scope and single nucleus sequencing of RNA (sNuc-Seq). <h3>Results</h3> Characterization of <i>Sle 1, yaa</i> mice in behavior assays, identified anxiety-like, and fatigue-like behaviors consistent with NPSLE. Notably, the behavior changes correlate with distinct patches of interferon stimulated gene (ISG) expression within the subcortical regions of mouse brains. Preliminary single nucleus sequencing (sNuc-Seq) and <i>in situ</i> hybridization results implicate astrocytes and oligodendrocytes as the major cell classes enriched in these ISG patches. <h3>Conclusions</h3> In summary, our results validate a mouse behavioral model of NPSLE, and show spatially distinct regions of ISG expression within the CNS, opening up a new avenue of investigation into the fundamental mechanisms of NPSLE. <h3>Acknowledgements</h3> The work was supported by a grant from the NIH R01AR072965.
Multicamera vision-based approach to flexible feature measurement for inspection and reverse engineering (1993)

The vision-based coordinate measurement system, developed at the National Research Council Canada, is a multicamera passive system that combines the principles of stereo vision, photogrammetry, knowledge-based techniques, and an object-oriented design methodology to provide precise coordinate and dimension measurements of parts for applications such as dimensional inspection, positioning and tracking of objects, and reverse engineering. For a vision system to be considered for such applications, its performance and design parameters must be well understood. A description of the system, the techniques employed for calibration, a performance evaluation procedure, an accuracy analysis, and test results are presented.
[RE: Proposals for Getty Match, September 28, 1989] (1989)

Photocopy of a memorandum from Bruce Burton to Jack Davis, in regards to their proposals and applications sent to various foundations in order to match the Getty Center for Education in the Arts grant for North Texas Institute for Educators on the Visual Arts and their education reform program. Attached to the memo is a newsletter clipping from Dallas Times Herald about the CEO of Burlington Northern, a foundation that Davis and his associate William McCarter plan to submit a grant application to.
Fractal Dimension of Dielectric Breakdown (1984)

It is shown that the simplest nontrivial stochastic model for dielectric breakdown naturally leads to fractal structures for the discharge pattern. Planar discharges are studied in detail and the results are compared with properly designed experiments.
The Structure of Nanoparticulate Aggregates of Titania as a Function of Shear (2009)

This chapter contains sections titled: Introduction Experimental Results and Discussion Conclusions Acknowledgements
The soluble isoform of CTLA‐4 as a regulator of T‐cell responses (2013)

CTLA-4 is a crucial immune regulator that mediates both negative costimulation signals to T cells, and regulatory T (Treg)-cell extrinsic control of effector responses. Here we present evidence supporting a novel mechanism for this extrinsic suppression, executed by the alternatively spliced soluble CTLA-4 isoform (sCTLA-4). Analyses of human T cells in vitro show that sCTLA-4 secretion can be increased during responses, and has potent inhibitory properties, since isoform-specific blockade of its activity significantly increased Ag-driven proliferation and cytokine (IFN-γ, IL-17) secretion. Treg cells were demonstrated to be a prominent source of sCTLA-4, which contributed to suppression in vitro when their numbers were limiting. The soluble isoform was also produced by, and inhibited, murine T cells responding to Ag in vitro, and blockade of its activity in vivo protected against metastatic spread of melanoma in mice. We conclude that sCTLA-4 is an important immune regulator, responsible for at least some of the inhibitory effects previously ascribed to the membrane-bound isoform. These results suggest that the immune system exploits the different CTLA-4 isoforms for either intrinsic or extrinsic regulation of T-cell activity.
Extent and Duration of Small Intestinal Mucosal Injury in Intractable Diarrhea of Infancy (1980)

Thirty infants with intractable diarrhea of infancy (IDI) underwent small bowel biopsies in order to determine the extent and duration of small intestinal mucosal injury. The onset of the persistent diarrhea occurred prior to 3 months of age and continued for an average of 48 days prior to investigation. In 18 cases, no associated entities were found. Mucosal injury was invariably found in all 30 infants: grade IV injury in 11, grade III in eight, grade II in nine, and grade I atrophy in one. Disaccharidase activities were diminished and corresponded to the degree of atrophy. Lactase activity was diminished to a greater extent than sucrase and maltase. Significant, persistent mucosal injury existed for an average of six months in 16 of the 23 (70%) repeat biopsies. All infants were given an elemental diet (ED). Twelve of the 30 infants required parenteral nutrition (PN). These infants were gradually advanced to an oral elemental diet and maintained on this diet until histologic findings and disaccharidase levels were normal. Eighteen infants were fed and maintained on an elemental diet by mouth from time of admission until normal histologic findings and disaccharidases were found. No mortality occurred during management and follow-up. Twenty-two of the 28 infants in whom follow-up growth data were available excelled in weight and height velocity. The data suggest that prolonged injury to the small intestinal mucosa is a common finding in many cases of intractable diarrhea of infancy. Elemental diets should be started early in the course of protracted diarrhea in young infants, and may need to be continued for several months since histologic and enzymatic changes of the small intestine may persist for extended periods.
Morphological and biomechanical analyses of the human healthy and glaucomatous aqueous outflow pathway: Imaging-to-modeling (2023)

Characterizing the accurate morphology of the outflow tissues may significantly contribute to constructing more accurate, robust, and reliable models, that can eventually help to better understand the dynamic IOP regulation, hydrodynamics of the aqueous humor, and outflow resistance dynamic in the human eyes. This model demonstrates proof of concept for determining changes to outflow resistance in healthy and glaucomatous tissues and thus may be utilized in larger cohorts of donor tissues where disease specificity, race, age, and gender of the eye donors may be accounted for.
Myrothecium roridum Tri4 encodes a multifunctional oxygenase required for three oxygenation steps (2007)

The biosyntheses of both macrocyclic trichothecenes in Myrothecium roridum and simple trichothecenes in Fusarium species begin with the cyclization of farnesyl pyrophosphate to form the sesquiterpene hydrocarbon trichodiene. A previous study showed that Myrothecium has a cluster of 3 genes that are homologous with Fusarium trichothecene genes: Tri4, a P450 oxygenase; Tri5, the sesquiterpene cyclase; and Tri6, a zinc-finger regulatory gene. Fusarium graminearum Tri4 (FgTri4) and M. roridum MrTri4 (MrTri4) have 66.9% identity. In this study, MrTri4 was expressed in Fusarium verticillioides. Liquid cultures of transformant strains expressing MrTri4 converted exogenous trichodiene to isotrichodiol, indicating that MrTri4 controls 3 oxygenation steps and that the product of MrTRI4 is isotrichodiol.
Isolation and Characterization of Chicken Interleukin-17 cDNA (2002)

Interleukin-17 (IL-17) is a proinflammatory cytokine produced by activated T cells. A 917-bp cDNA encoding the IL-17 gene was isolated from our EST cDNA library prepared from intestinal intraepithelial lymphocytes (IELs) of Eimeria-infected chickens. It contained a 507-bp open reading frame (ORF) predicted to encode a protein of 169 amino acids (aa) with a molecular mass of 18.9 kDa, a 27-residue NH(2)-terminal signal peptide, a single potential N-linked glycosylation site, and 6 cysteine residues conserved with mammalian IL-17. Chicken IL-17 (chIL-17) shared 37%-46% amino acid sequence identity to the previously described mammalian homologs and also was homologous to the ORF 13 of Herpesvirus saimiri (HVS 13). By Northern blot analysis, IL-17 transcripts were identified in a reticuloendotheliosis virus (REV)-transformed chicken lymphoblast cell line (CU205) and conconavalin A (ConA)-stimulated splenic lymphocytes but not other chicken cell lines or normal tissues. Conditioned medium from COS-7 cells transfected with ChIL-17 cDNA induced IL-6 production by chicken embryonic fibroblasts, suggesting a functional role for the cytokine in avian immunity.
Modification of growth kinetics in surfactant-mediated epitaxy (1995)

The influence of Sb, As, Ga, and In as surfactants on the Si/Si(111) homoepitaxy is studied using scanning tunneling microscopy. The nucleation of two-dimensional (2D) Si islands on the surfactant-terminated surface was studied as a function of temperature. The island densities and depleted zones show Arrhenius behavior. Surfactants modify the Si epitaxy in quite a different way. Indium as surfactant increases the diffusivity of the Si atoms, whereas Sb and As drastically decrease the diffusion length of Si. When we apply these results to Ge epitaxy on Si the reduction of the diffusion length is shown to be essential for the suppression of 3D islanding in surfactant-mediated Ge/Si heteroepitaxy. Generally, elements of group III and IV as surfactants that enhance the diffusivity in Si homoepitaxy lead to 3D islanding in Ge/Si heteroepitaxy. Elements of group V and VI reduce the diffusion length in Si homoepitaxy and give rise to a suppression of 3D islanding in Ge/Si heteroepitaxy. The temperature dependence and rate dependence of the nucleation of 2D islands in Si/Si(111) homoepitaxy can be described in the framework of classical nucleation theories yielding a critical nucleus size of 6 and an activation energy of diffusion of 0.75 eV. Experimentally no indication for a reflective potential barrier for step-down motion of diffusing Si atoms (Ehrlich-Schwoebel barrier) was found.
RATE OF PROGRESSION OF SCOLIOSIS AFTER INTRATHECAL BACLOFEN PUMP IMPLANTATION (2005)

AAP Annual Meeting Abstracts: Abstracts of the Scientific Papers and Posters Presented at the Annual Meeting of the Association of Academic Physiatrists: Tucson, Arizona February 22–26, 2005: Scientific Paper Presentations
Transparent network security policy enforcement (2000)

Permission is granted for noncommercial reproduction of the work for educational or research purposes.
Block Copolymer Micellization as a Protection Strategy for DNA Origami (2017)

Abstract DNA nanotechnology enables the synthesis of nanometer‐sized objects that can be site‐specifically functionalized with a large variety of materials. For these reasons, DNA‐based devices such as DNA origami are being considered for applications in molecular biology and nanomedicine. However, many DNA structures need a higher ionic strength than that of common cell culture buffers or bodily fluids to maintain their integrity and can be degraded quickly by nucleases. To overcome these deficiencies, we coated several different DNA origami structures with a cationic poly(ethylene glycol)–polylysine block copolymer, which electrostatically covered the DNA nanostructures to form DNA origami polyplex micelles (DOPMs). This straightforward, cost‐effective, and robust route to protect DNA‐based structures could therefore enable applications in biology and nanomedicine where unprotected DNA origami would be degraded.
Using polymorphism to improve expert system maintainability (1991)

The problems encountered in applying object-oriented programming to expert systems are described. A production system called Clasp, which addresses these difficulties, is presented. Clasp integrates methods, production rules, and terminological definitions for classes. The approach is a further generalization of Common Loops and the Common Lisp Operating System, which have all extended notion of methods in which all argument types can describe the applicability of methods. The system was designed to improve the modularity and reusability of the rule base, to support the development of a more consistent and homogeneous knowledge base, and to enhance the predictability of rules.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Adaptive simulated annealing for maximum temperature (2004)

It is difficult to determine the appropriate temperature parameters which control the acceptance probability in Simulated Annealing, which is a typical meta-heuristic method in the optimization methods. In this paper, we propose a new simulated annealing method that determines the maximum temperature adaptively. The proposed method is base on an important temperature by finding an upper limit of the important temperature in a heating process from the lowest temperature. Using this method, the total annealing steps can be decreased to half without making the accuracy of solution worse. We apply this method to some of the travelling salesman problems and confirmed its effectiveness.
An efficient design and implementation of LSM-tree based key-value store on open-channel SSD (2014)

Various key-value (KV) stores are widely employed for data management to support Internet services as they offer higher efficiency, scalability, and availability than relational database systems. The log-structured merge tree (LSM-tree) based KV stores have attracted growing attention because they can eliminate random writes and maintain acceptable read performance. Recently, as the price per unit capacity of NAND flash decreases, solid state disks (SSDs) have been extensively adopted in enterprise-scale data centers to provide high I/O bandwidth and low access latency. However, it is inefficient to naively combine LSM-tree-based KV stores with SSDs, as the high parallelism enabled within the SSD cannot be fully exploited. Current LSM-tree-based KV stores are designed without assuming SSD's multi-channel architecture.
Design of Direct-driven Permanent-magnet Generators for Wind Turbines (1996)

This thesis presents an investigation of how a direct-driven wind turbine generator should be designed and how small and efficient such a generator will be. Advantages and disadvantages of various types of direct-driven wind turbine generators are discussed, and a radial-flux permanent-magnet generator connected to a forced-commutated rectifier is chosen for a detailed theoretical investigation. Further, a design method is developed for the electromagnetic part of the chosen generator type. The generator is optimized with a simplified cost function which, besides including the cost of the active generator parts and the cost of the structure, also includes the cost of the average losses. Therefore, a method to calculate the average losses is derived. The design method is used to investigate the optimization of a 500 kW generator, and the size, efficiency and active weight of optimized generators from 30 kW to 3 MW are presented. A result of the investigation is that the outer diameters of the direct-driven generators are only slightly larger than the width of conventional wind energy converter nacelles. A comparison of average efficiency shows that direct-driven generators, including the losses in the frequency converters, are more efficient than conventional wind energy converter drive trains. Compared with other direct-driven generators, the proposed generator type is small, mainly because of the forced-commutated rectifier and because the generator is not required to produce a pull-out torque higher than the rated torque.
Depth-camera-based rebar detection and digital reconstruction for robotic concrete spraying (2021)

Abstract In this paper, we tackle the challenge of detection and accurate digital reconstruction of steel rebar meshes using a set of industrial depth cameras. A construction example under investigation in this paper is robotic concrete spraying, where material is sprayed onto double-curved single layered rebar meshes. Before the spraying process can start, the location and geometry of the rebar mesh needs to be accurately know. We present an automatic image-based processing approach of depth images for grid point extraction at an accuracy of a few mm. Furthermore, we propose a sequence of execution steps in a robotic setup, including the hand–eye calibration, which enables the direct georeferencing of multiple data sets acquired from various poses into a common coordinate system. With the proposed approach we are able to digitally reconstruct a mesh of an unknown geometry in under 10 min with an accuracy better than 5 mm. The digitally reconstructed mesh allows for computation of material needed for its construction, enabling sustainable use of concrete in digital fabrication. The accurately reconstructed digital mesh, generated based on the proposed approach in this paper, is the input for the following spraying step, allowing for generation of accurate spray trajectories.
Increased expression of histone deacetylase 7 during hepatic stellate cell activation promotes pro-fibrogenic gene expression (2015)

Recent evidence has highlighted a pathological imbalance in hepatic fibrosis between the acetylation and deacetylation of histone proteins regulated by histone deacetylases (HDACs). However, the role of individual HDACs in liver fibrosis is almost completely unknown. Recently, we identified that HDAC7 can bind to the promotor of the hepatocyte growth factor (HGF) gene, and herewith, suppresses the expression of this anti-fibrogenic factor in activated hepatic stellate cells (Hepatology. 2014 Sep;60(3):1066 – 81).
ChemInform Abstract: Secondary Metabolites Isolated from the Fungus Monascus pilosus (2010)

Abstract isolation and structure of a new pyran‐2‐one derivative, monascuspyrone (I) along with nine known compounds
Unsupervised Lateral Chromatic Aberration (LCA) detection and correction for improved image fidelity (2023)

Lateral Chromatic Aberration is a defect of optical lenses in connection with focusing different wavelengths of light (red, blue, green) at different locations in the focal plane, which leads to resolution loss and color artifacts (fringes). To preserve image fidelity, we have developed a robust multi-phase unsupervised method (not using a reference image for calibration and without prior knowledge of the lens), that is based on edge matching in different color planes. We are able to estimate parameters of a lateral chromatic aberration correction model, which is then used to avoid these artefacts by correct resampling of red and blue color planes with sub-pixel accuracy. This method is suitable for real-time implementation in consumer-grade image/video systems and shows very promising results.
Placental Vesicles Carry Active Endothelial Nitric Oxide Synthase and Their Activity is Reduced in Preeclampsia (2017)

Preeclampsia, a multisystem hypertensive disorder of pregnancy, is associated with increased systemic vascular resistance. Placentae from patients with preeclampsia have reduced levels of endothelial nitric oxide synthase (eNOS) and, thus, less nitric oxide (NO). Syncytiotrophoblast extracellular vesicles (STBEV), comprising microvesicles (STBMV) and exosomes, carry signals from the syncytiotrophoblast to the mother. We hypothesized that STBEV-bound eNOS (STBEV-eNOS), capable of producing NO, are released into the maternal circulation. Dual-lobe ex vivo placental perfusion and differential centrifugation was used to isolate STBEV from preeclampsia (n=8) and normal pregnancies (NP; n=11). Plasma samples of gestational age-matched preeclampsia and NP (n=6) were used to isolate circulating STBMV. STBEV expressed placental alkaline phosphatase, confirming placental origin. STBEV coexpressed eNOS, but not inducible nitric oxide synthase, confirmed using Western blot, flow cytometry, and immunodepletion. STBEV-eNOS produced NO, which was significantly inhibited by <i>N</i> <sup>G</sup>-nitro-l-arginine methyl ester (eNOS inhibitor; <i>P</i><0.05) but not by <i>N</i>-(3-(aminomethyl) bezyl) acetamidine) (inducible nitric oxide synthase inhibitor). STBEV-eNOS catalytic activity was confirmed by visualizing eNOS dimerization. STBEV-eNOS was more abundant in uterine vein compared with peripheral blood, indicating placental origin. STBEV isolated from preeclampsia-perfused placentae had lower levels of STBEV-eNOS (STBMV; <i>P</i><0.05) and overall lower NO activity (STBMV, not significant; syncytiotrophoblast extracellular exosomes, <i>P</i><0.05) compared with those from NP. Circulating plasma STBMV from preeclampsia women had lower STBEV-eNOS expression compared with that from NP women (<i>P</i><0.01). This is the first observation of functional eNOS expressed on STBEV from NP and preeclampsia placentae, as well as in plasma. The lower STBEV-eNOS NO production seen in preeclampsia may contribute to the decreased NO bioavailability in this disease.
Case of Resuscitative Endovascular Balloon Occlusion of the Aorta (REBOA) Use in Penetrating Abdominal Aortic Injury (2017)

We present the successful utilization of resuscitative endovascular balloon occlusion of the aorta (REBOA) in a case of penetrating abdominal aortic injury. This allowed for hemorrhagic control and exposure of a large aortic defect at the level of the celiac access, which otherwise would have been diffi cult to control in an open fashion. Although use in this specifi c injury pattern in the literature is limited, REBOA can be a life-saving maneuver.
Nicotinamide cofactor ratios in engineered strains ofClostridium thermocellumandThermoanaerobacterium saccharolyticum (2016)

Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are bacteria under investigation for production of biofuels from plant biomass. Thermoanaerobacterium saccharolyticum has been engineered to produce ethanol at high yield (>90% of theoretical) and titer (>70 g/l). Efforts to engineer C. thermocellum have not, to date, been as successful, and efforts are underway to transfer the ethanol production pathway from T. saccharolyticum to C. thermocellum One potential challenge in transferring metabolic pathways is the possibility of incompatible levels of nicotinamide cofactors. These cofactors (NAD(+), NADH, NADP(+) and NADPH) and their oxidation state are important in the context of microbial redox metabolism. In this study we directly measured the concentrations and reduced oxidized ratios of these cofactors in a number of strains of C. thermocellum and T. saccharolyticum by using acid/base extraction and enzymatic assays. We found that cofactor ratios are maintained in a fairly narrow range, regardless of the metabolic network modifications considered. We have found that the ratios are similar in both organisms, which is a relevant observation in the context of transferring the T. saccharolyticum ethanol production pathway to C. thermocellum.