gebhart/patrepeval huggingface dataset:
Fast Ray Sorting and Breadth‐First Packet Traversal for GPU Ray Tracing (2010)

Abstract We present a novel approach to ray tracing execution on commodity graphics hardware using CUDA. We decompose a standard ray tracing algorithm into several data‐parallel stages that are mapped efficiently to the massively parallel architecture of modern GPUs. These stages include: ray sorting into coherent packets, creation of frustums for packets, breadth‐first frustum traversal through a bounding volume hierarchy for the scene, and localized ray‐primitive intersections. We utilize the well known parallel primitives scan and segmented scan in order to process irregular data structures, to remove the need for a stack, and to minimize branch divergence in all stages. Our ray sorting stage is based on applying hash values to individual rays, ray stream compression, sorting and decompression. Our breadth‐first BVH traversal is based on parallel frustum‐bounding box intersection tests and parallel scan per each BVH level. We demonstrate our algorithm with area light sources to get a soft shadow effect and show that our concept is reasonable for GPU implementation. For the same data sets and ray‐primitive intersection routines our pipeline is ∼3x faster than an optimized standard depth first ray tracing implemented in one kernel.
CRISPR-Cas9 mediated mutagenesis of a DMR6 ortholog in tomato confers broad-spectrum disease resistance (2016)

Abstract Pathogenic microbes are responsible for severe production losses in crops worldwide. The use of disease resistant crop varieties can be a sustainable approach to meet the food demand of the world’s growing population. However, classical plant breeding is usually laborious and time-consuming, thus hampering efficient improvement of many crops. With the advent of genome editing technologies, in particular the CRISPR-Cas9 ( c lustered r egularly i nterspaced s hort p alindromic r epeats-Cas9) system, we are now able to introduce improved crop traits in a rapid and efficient manner. In this work, we genome edited durable disease resistance in tomato by modifying a specific gene associated with disease resistance. Recently, it was demonstrated that inactivation of a single gene called DMR6 ( downy mildew resistance 6 ) confers resistance to several pathogens in Arabidopsis thaliana . This gene is specifically up-regulated during pathogen infection, and mutations in the dmr6 gene results in increased salicylic acid levels. The tomato SlDMR6-1 orthologue Solyc03g080190 is also up-regulated during infection by Pseudomonas syringae pv. tomato and Phytophthora capsici . Using the CRISPR-Cas9 system, we generated tomato plants with small deletions in the SlDMR6-1 gene that result in frameshift and premature truncation of the protein. Remarkably, these mutants do not have significant detrimental effects in terms of growth and development under greenhouse conditions and show disease resistance against different pathogens, including P. syringae , P. capsici and Xanthomonas spp.
Angiogenesis: a Dynamic Balance of Stimulators and Inhibitors (1997)

Angiogenesis, the formation of new blood vessels from a pre-existing vasculature, is tightly regulated in normal adults. Under physiological circumstances, angiogenesis occurs in only a few instances; e.g., the female reproductive system in response to ovulation or gestation, the normal hair cycle, etc. In these examples, growth of new capillaries is tightly controlled by an interplay of growth regulatory proteins which act either to stimulate or to inhibit blood vessel growth. Normally, the balance between these forces is tipped in favor of inhibition and consequently capillary growth is restrained. Under certain pathological circumstances, however, local inhibitory controls are unable to restrain the increased activity of angiogenic inducers. Thus, in wound healing, inflammation and tumors, to name just a few examples, angiogenesis is integral to the pathology, engendering the hope that these pathological entities could be regulated by pharmacological and/or genetic suppression (or enhancement) of blood vessel growth. This hope, in turn, has fostered interest in the molecular mechanisms that regulate angiogenesis. In this chapter, we have reviewed the current literature regarding some angiogenic stimulators and inhibitors, emphasizing vascular permeability factor (VPF, also known as vascular endothelial growth factor or VEGF), as a major angiogenic inducer, and thrombospondin (TSP) as the best known example of a natural inhibitor of vessel growth.
Design, synthesis, and kinetic evaluation of high-affinity FKBP ligands and the X-ray crystal structures of their complexes with FKBP12 (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDesign, synthesis, and kinetic evaluation of high-affinity FKBP ligands and the X-ray crystal structures of their complexes with FKBP12Dennis A. HoltDennis A. HoltMore by Dennis A. Holt, Juan I. LuengoJuan I. LuengoMore by Juan I. Luengo, Dennis S. YamashitaDennis S. YamashitaMore by Dennis S. Yamashita, Hye Ja OhHye Ja OhMore by Hye Ja Oh, Arda L. KonialianArda L. KonialianMore by Arda L. Konialian, Hwa Kwo YenHwa Kwo YenMore by Hwa Kwo Yen, Leonard W. RozamusLeonard W. RozamusMore by Leonard W. Rozamus, Martin BrandtMartin BrandtMore by Martin Brandt, Mary J. BossardMary J. BossardMore by Mary J. Bossard, Mark A. LevyMark A. LevyMore by Mark A. Levy, Drake S. EgglestonDrake S. EgglestonMore by Drake S. Eggleston, Jun LiangJun LiangMore by Jun Liang, L. Wayne SchultzL. Wayne SchultzMore by L. Wayne Schultz, Thomas J. StoutThomas J. StoutMore by Thomas J. Stout, and Jon ClardyJon ClardyMore by Jon ClardyCite this: J. Am. Chem. Soc. 1993, 115, 22, 9925–9938Publication Date (Print):November 1, 1993Publication History Published online1 May 2002Published inissue 1 November 1993https://pubs.acs.org/doi/10.1021/ja00075a008https://doi.org/10.1021/ja00075a008research-articleACS PublicationsRequest reuse permissionsArticle Views2412Altmetric-Citations204LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Clinical utility of quantitative RT‐PCR targeted to α1,4‐N‐acetylglucosaminyltransferase mRNA for detection of pancreatic cancer (2006)

alpha1,4-N-Acetylglucosaminyltransferase (alpha4GnT) is a glycosyltransferase responsible for the biosynthesis of alpha1,4-GlcNAc-capped O-glycans, and is frequently expressed in pancreatic cancer cells but not peripheral blood cells. In the present study, we tested the clinical utility of alpha4GnT mRNA expressed in the mononuclear cell fraction of peripheral blood as a biomarker of pancreatic cancer. Total RNA isolated from the peripheral blood mononuclear cells from 55 pancreatic cancer patients, 10 chronic pancreatitis patients, and 70 cancer-free volunteers was analyzed quantitatively by reverse transcription-polymerase chain reaction with primers specific for alpha4GnT, and the expression level of alpha4GnT mRNA relative to that of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was measured. When the ratio of alpha4GnT to GAPDH transcripts exceeded a defined cut-off value, patients were considered to have pancreatic cancer. By these standards, 76.4% of the pancreatic cancer patients were detected by this assay. A strong correlation was obtained between positivity in this assay and the expression of alpha4GnT protein detected immunohistochemically in pancreatic cancer tissues resected subsequently, suggesting that alpha4GnT mRNA detected in the peripheral blood is derived from circulating pancreatic cancer cells. Although increased levels of alpha4GnT mRNA was detected in 40.0% of chronic pancreatitis patients and 17.1% of cancer-free volunteers, the expression levels were significantly lower than those seen in pancreatic cancer patients. These results suggest that quantitative analysis of alpha4GnT mRNA expressed in the mononuclear cell fraction of peripheral blood will contribute to the detection of pancreatic cancer.
Proteolytic Processing of the Astrovirus Capsid (2000)

To further characterize the nature of proteolytic processing of the astrovirus capsid, we infected Caco-2 cells with a high multiplicity of astrovirus without trypsin in the presence of 5 to 10% fetal calf serum. These infections were characterized by pulse-chase labeling with [35S]Smethionine, electron microscopy, gel electrophoresis of purified viral particles, and analysis of infectivity of such particles with and without added trypsin. Pulse-chase experiments showed that the astrovirus capsid protein was initially translated as an approximately 87-kDa protein. The 87-kDa capsid protein was rapidly converted intracellularly to a 79-kDa form which was found in smaller amounts in the cell supernatant. Purification by differential centrifugation yielded particles that appeared quite similar to trypsin-grown astrovirus particles by negatively stained electron microscopy. These particles were antigenically distinct from trypsin-treated virions as demonstrated by their various reactions with monoclonal antibodies in a solid-phase immunoassay. The purified trypsin-free particles were mainly composed of the 79-kDa capsid protein which was found to have an amino terminus at residue 71 of the entire open reading frame 2 (ORF2) product. The cleavage site was identified in a highly conserved region of the astrovirus ORF2 product. These trypsin-free particles were minimally infectious in cultured Caco-2 cells but became highly infectious (10(5)-fold increase) after trypsin but not chymotrypsin treatment. This trypsin-enhanced infectivity correlated with conversion of the 79-kDa capsid protein to three smaller peptides of approximately 34, 29, and 26 kDa.
Cellular and molecular changes in 3T3 cells transformed spontaneously or by DNA transfection. (1985)

Transformed cell lines have been selected following exposure of NIH 3T3 cells to a calcium phosphate precipitate containing DNA from: the human colon carcinoma cell line, SW 480; the cloned Harvey sarcoma virus ras gene; the parental NIH 3T3 cell line; or no DNA (a spontaneous transformant). Unlike the parental 3T3 cells, each of these lines readily formed malignant spindle cell tumors in Swiss nu/mu mice. Southern blots confirmed the presence of the human homologue of the Kirsten ras gene in the cells transformed by SW480 DNA, and the Harvey ras gene in the cells transformed with that cloned sequence. The morphology of each of the lines was different, the cells transformed with the human and viral ras genes being the most aberrant (but not identical) and forming the most extensive foci in culture. These ras transformed lines also exhibited anchorage-independent growth, while the two other transformed lines did not. Both of the ras transformed lines, as well as the spontaneously transformed line, exhibited a pronounced disruption of actin microfilament structure. Two-dimensional gel electrophoresis of 35S-methionine-labeled peptides revealed that these three lines also had a marked decrease in an acidic peptide of 32K daltons.
BMPs Promote Proliferation and Migration of Endothelial Cells via Stimulation of VEGF-A/VEGFR2 and Angiopoietin-1/Tie2 Signalling (2007)

The differentiation, growth, and survival of endothelial cells (ECs) are regulated by multiple signalling pathways, such as vascular endothelial growth factors (VEGFs) and angiopoietins through their receptor tyrosine kinases, VEGF receptor (VEGFR) 2 and Tie2, respectively. Bone morphogenetic proteins (BMPs), members of the transforming growth factor (TGF)-beta family, have been implicated in the development and maintenance of vascular systems. However, their effects on EC proliferation remain to be elucidated. In the present study, we show that BMPs induce the proliferation and migration of mouse embryonic stem cell (ESC)-derived endothelial cells (MESECs) and human microvascular endothelial cells (HMECs). Addition of BMP-4 to culture induced significant proliferation and migration of both types of ECs. BMP-4 also increased the expression and phosphorylation of VEGFR2 and Tie2. These findings suggest that BMP signalling activates endothelium via activation of VEGF/VEGFR2 and Angiopoietin/Tie2 signalling.
Facile Syntheses of Symmetrical Diaryliodonium Salts from Various Arenes, with Sodium Metaperiodate as the Coupling Reagent in Acidic Media¹ (2008)

An easy, inexpensive, safe, and effective preparative procedure to obtain symmetrical diaryliodonium bromides (in 17-88% crude yields) from various arenes is presented in this paper. A novel method for the in situ preparation of iodosyl sulfate (Chrétien’s reagent) is given. Eleven exemplary crude diaryliodonium bromides were readily oxidatively metathesized with 40% aqueous tetrafluoroboric acid and 30% aqueous hydrogen peroxide (in boiling acetone, used both as a solvent and ‘halogen scavenger’) to give pure diaryliodonium tetrafluoroborates in 15-85% yields.
Wireless passive sensor for pH monitoring inside a small bioreactor (2013)

A wireless passive pH sensor for continuous remote bioprocess monitoring is presented. The sensor is small enough to fit inside a small bioreactor or test tube. It consists of a planar spiral inductor connected in parallel to a varactor forming a LC resonant circuit. A pH combination electrode made of an iridium/iridium oxide sensing electrode and a silver/silver chloride reference electrode, is connected in parallel to the varactor. As the medium pH changes, the voltage across the electrodes varies, shifting the resonant frequency of the sensor. For in-fluid monitoring the sensor is hermetically sealed to encapsulate, and reduce parasitic capacitive coupling and eddy current loss. The resonant frequency of the sensor is tracked remotely by an interrogator inductor inductively coupled to the sensor. The sterilizable sensor was used for remote pH monitoring of Yarrowia lipolytica fermentation in a shake flask over 67 hours. Experiment shows that the medium pH can be monitored with 2.46 MHz/pH sensitivity and maximum deviation of 0.07 pH from a commercial pH probe measurement over a 6.55.26 pH range.
Processing and Pretreatment Effects on Vanadium Transport in Nafion Membranes (2015)

Here, this work describes how manufacturing processes and pretreatments affect the proton conductivity and vanadyl permeability of Nafion® and how these properties are altered by running in a cell. Five Nafion membranes were examined: reinforced XL100, dispersion cast NR211 and NR212, and extruded N115 and N117. The membranes were subjected to pretreatments that included annealing at 120°C and immersing in ambient temperature and boiling water and sulfuric acid. Vanadyl permeability varied by ~15X with pretreatment and ~3X with manufacturing process. Variations in ionic conductivity were comparatively modest: ~1.5X with pretreatment and ~1.2X with processing. Differences in permeability can be eliminated by annealing the extruded membranes above their glass-transition temperature or by immersing in boiling sulfuric acid. The differences induced by processing and pretreatments were largely absent from membranes removed from vanadium redox cells subjected to repeated charge/discharge cycles.
Isolation and Identification of Sea Buckthorn (Hippophae rhamnoides) Phenolics with Antioxidant Activity and α-Glucosidase Inhibitory Effect (2010)

This study was performed to evaluate the antioxidant and α-glucosidase inhibitory effects from the extract, fractions, and isolated compounds of sea buckthorn leaves. Six compounds, kaempferol-3-O-β-D-(6''-O-coumaryl) glycoside, 1-feruloyl-β-D-glucopyranoside, isorhamnetin-3-O-glucoside, quercetin 3-O-β-D-glucopyranoside, quercetin 3-O-β-D-glucopyranosyl-7-O-α-L-rhamnopyranoside, and isorhamnetin-3-O-rutinoside, were isolated from sea buckthorn leaf extracts. The butanol fraction (EC(50) = 1.81 μg/mL) along with quercetin 3-O-β-D-glucopyranoside (EC(50) = 1.86 μg/mL) had a higher DPPH radical-scavenging activity and showed stronger reducing power (OD(700) = 1.83 and 1.78, respectively). The butanol fraction (477 mg GAE/g) contained the highest amount of phenolic compounds and also the most powerful α-glucosidase inhibitory effect (86%) at 5 μg/mL. The results indicate that sea buckthorn leaf extracts could potentially be used for food additives and the development of useful natural compounds.
Structured Silicon Anodes for Lithium Battery Applications (2003)

TEST 02 - Elsevier's Scopus, the largest abstract and citation database of peer-reviewed literature. Search and access research from the science, technology, medicine, social sciences and arts and humanities fields.
Computation of channel capacity and rate-distortion functions (1972)

By defining mutual information as a maximum over an appropriate space, channel capacities can be defined as double maxima and rate-distortion functions as double minima. This approach yields valuable new insights regarding the computation of channel capacities and rate-distortion functions. In particular, it suggests a simple algorithm for computing channel capacity that consists of a mapping from the set of channel input probability vectors into itself such that the sequence of probability vectors generated by successive applications of the mapping converges to the vector that achieves the capacity of the given channel. Analogous algorithms then are provided for computing rate-distortion functions and constrained channel capacities. The algorithms apply both to discrete and to continuous alphabet channels or sources. In addition, a formalization of the theory of channel capacity in the presence of constraints is included. Among the examples is the calculation of close upper and lower bounds to the rate-distortion function of a binary symmetric Markov source.
Novel SOI p-channel MOSFETs with higher strain in si channel using double SiGe heterostructures (2002)

We have studied p-channel advanced SOI MOSFETs using double SiGe heterostructures fabricated by the combination of SIMOX and high-quality strained-Si/SiGe regrowth technologies, in order to introduce higher strain in Si channel. It was revealed that this double SiGe structure of second Si/sub 0.82/Ge/sub 0.18/Si/sub 0.93/Ge/sub 0.07/allows the second SiGe layer to relax by about 70%, because of the elastic energy balance between the second and the first-SiGe layers. As a result, the strain of Si layer on this double SiGe structure becomes higher than that of the single SiGe structure. Strained SOI p-MOSFETs using the double layer SiGe structure exhibited higher hole mobility than that of strained-SOI MOSFETs with single Si/sub 0.9/Ge/sub 0.1/ structure. The hole mobility enhancement of 30% and 45% was achieved in the strained-SOI MOSFETs with double SiGe structures, compared to that of the universal curve and the control-SOI MOSFETs, respectively.
Enhanced hematopoiesis in vivo and in vitro by splenic stromal cells derived from the mouse with recombinant granulocyte colony-stimulating factor (1992)

Splenic stromal cells (CF-1 cells) were established from a mouse administered recombinant human granulocyte colony-stimulating factor (rG-CSF) to clarify the mechanism of splenic extramedullary hematopoiesis induced by the factor. The cells were negative for alkaline phosphatase, factor VIII-related antigen, mac I, and phagocytosis. They were positive for acid phosphatase, collagen type I, collagen type III, and fibronectin. CF-1 cells were not converted to adipocytes in a confluent culture with 10(-6) mol/L hydrocortisone. [35S]rG-CSF bound to CF-1 cells specifically in the growth phase but not in the resting phase. The CF-1 cells had greater colony-stimulating activities than the normal splenic stromal cells. When CF-1 cells were added to bone marrow cells in the spleen colony-forming cells (CFU-S) assay, the number of colonies in the spleen increased between 1.4 and 1.8 times the control without these stromal cells. On the other hand, the normal splenic stromal cells had no effect on increasing the number of CFU-S colonies. Therefore, these data suggest that a factor- dependent hematopoietic microenvironment is generated in the spleen by rG-CSF, and the stromal cells that have the hematopoietic potency become dominant in splenic extramedullary hematopoiesis induced by rG- CSF.
Periductal interleukin-17 production in association with biliary innate immunity contributes to the pathogenesis of cholangiopathy in primary biliary cirrhosis (2009)

An innate immune response to bacterial components is speculated to be involved in the pathogenesis of primary biliary cirrhosis (PBC). Recently, CD4-positive T helper type 17 (Th17) cells, characterized by the secretion of interleukin (IL)-17, have been implicated in the pathogenesis of autoimmune diseases. Human Th17 cells are generated from Th0 cells by IL-6 and IL-1 beta and maintained by IL-23. In this study, the role of IL-17 in PBC and its association with biliary innate immunity were examined. Using cultured human biliary epithelial cells (BECs), the expression of Th17-related cytokines and chemokines and changes therein on treatment with pathogen-associated molecular patterns (PAMPs) and IL-17 were examined. Immunohistochemistry for IL-17 and Th17-related cytokines was performed using tissue samples of human liver. Consequently, the expression of IL-6, IL-1 beta, IL-23p19 and IL-23/IL-12p40 mRNAs, and their up-regulation by PAMPs, were found in BECs. Moreover, BECs possessed IL-17-receptors and stimulation with IL-17 induced production of IL-6, IL-1 beta, IL-23p19 and chemokines. Several IL-17-positive cells had infiltrated damaged bile ducts and the expression of IL-6 and IL-1 beta was enhanced in the bile ducts of PBC patients. In conclusion, IL-17-positive cells are associated with the chronic inflammation of bile ducts in PBC which is associated causally with the biliary innate immune responses to PAMPs.
Inertial and vision head tracker sensor fusion using a particle filter for augmented reality systems (2004)

A basic problem with augmented reality systems using head-mounted displays (HMDs) is the perceived latency or lag. This delay corresponds to the elapsed time between the moment when the user's head moves and the moment of displaying the corresponding virtual objects in the HMD. One way to eliminate or reduce the effects of system delays is to predict the future head locations. Actually, the most used filter to predict head motion is the extended Kalman filter (EKF). However, when dealing with nonlinear models (like head motion) in state equation and measurement relation and a non Gaussian noise assumption, the EKF method may lead to a non optimal solution. In this paper, we propose to use sequential Monte Carlo methods, also known as particle filters to predict head motion. These methods provide general solutions to many problems with any nonlinearities or distributions. Our purpose is to compare, both in simulation and in real task, the results obtained by particle filter with those given by EKF.
Why Do Children With ADHD Discontinue Their Medication? (2012)

Many children discontinue ADHD medication within the first year, often because of psychological side effects or perceived inadequate medication effectiveness. Improved methods for psychological side effect management, setting realistic medication goals, and assessing therapeutic success are needed.