gebhart/patrepeval huggingface dataset:
Opposing FGF and retinoid pathways: a signalling switch that controls differentiation and patterning onset in the extending vertebrate body axis (2004)

Construction of the trunk/caudal region of the vertebrate embryo involves a set of distinct molecules and processes whose relationships are just coming into focus. In addition to the subdivision of the embryo into head and trunk domains, this "caudalisation" process requires the establishment and maintenance of a stem zone. This sequentially generates caudal tissues over a long period which then undergo differentiation and patterning in the extending body axis. Here we review recent studies that show that changes in the signalling properties of the paraxial mesoderm act as a switch that controls onset of differentiation and pattern in the spinal cord. These findings identify distinct roles for different caudalising factors; in particular, Fibroblast Growth Factor (FGF) inhibits differentiation in the caudal stem zone, while Retinoic acid (RA) provided rostrally by somitic mesoderm is required for neuronal differentiation and establishment of ventral neural pattern. Furthermore, the mutual opposition of FGF and RA pathways controls not only neural differentiation but also mesoderm segmentation and might also underlie the progressive assignment of rostrocaudal identity by regulating Hox gene availability and activation.
Multiobjective control with frictional contacts (2007)

Standing is a fundamental skill mastered by humans and animals alike. Although easy for adults, it requires careful and deliberate manipulation of contact forces. The variation in contact configuration (e.g., standing on one foot, on uneven ground, or while holding on for support) presents a difficult challenge for interactive simulation of humans and animals, especially while performing tasks in the presence of external disturbances. We describe an analytic approach for control of standing in three-dimensional simulations based upon local optimization. At any point in time, the control system solves a quadratic program to compute actuation by maximizing the performance of multiple motion objectives subject to constraints imposed by actuation limits and contact configuration. This formulation is suitable for interactive animation and it adapts to the proportions of any character model in any non-planar, frictional contact configuration.
The Adaptive Biased Coin Design for Sequential Experiments (1978)

In comparing two treatments, eligible subjects come to the experiment sequentially and must be treated at once. To reduce experimental bias and to increase the precision of inference about treatment effects, the adaptive biased coin design, which offers a compromise between perfect balance and complete randomization, is proposed and analyzed. This new design has the property that it forces a small-sized experiment to be balanced, but tends toward the complete randomization scheme as the size of the experiment increases.
Design and Implementation of a Middleware for Data Storage in Opportunistic Grids (2007)

Shared machines in opportunistic grids typically have large quantities of unused disk space. These resources could be used to store application and checkpointing data when the machines are idle, allowing those machines to share not only computational cycles, but also disk space. In this paper, we present the design and implementation of OppStore, a middleware that provides reliable distributed data storage using the free disk space from shared grid machines. The system utilizes a two-level peer-to-peer organization to connect grid machines in a scalable and fault- tolerant way. Finally, we use the concept of virtual ids to deal with resource heterogeneity, enabling heterogeneity- aware load-balancing selection of storage sites.
Joint Learning of Distributed Representations for Images and Texts (2015)

This technical report provides extra details of the deep multimodal similarity model (DMSM) which was proposed in (Fang et al. 2015, arXiv:1411.4952). The model is trained via maximizing global semantic similarity between images and their captions in natural language using the public Microsoft COCO database, which consists of a large set of images and their corresponding captions. The learned representations attempt to capture the combination of various visual concepts and cues.
TGF-beta-3 Promotes Scarless Repair of Cleft Lip in Mouse Fetuses (2002)

TGF-beta3 mediates epithelial-mesenchymal transformation during normal fusion of lip and palate, but how TGF-beta3 functions during cleft lip repair remains unexplored. We hypothesize that TGF-beta3 promotes fetal cleft lip repair and fusion by increasing the availability of mesenchymal cells. In this investigation, we demonstrated that cleft lips in mouse fetuses were repaired by fetal surgery, producing scarless fusion. At the site of the operation, we first observed an infusion of platelets expressing TGF-beta3, followed by increased expression of cyclin D1 and tenascin-C, and coupled with increased mesenchymal cell proliferation. In an ex vivo serumless culture system, cleft lip explants fused in the presence of exogenous TGF-beta3. Cultured lips also showed up-regulation in cyclin D1 and tenascin-C expression. These findings suggest that microsurgical repair of cleft lip in the fetus that produced scarless fusion is mediated by TGF-beta3 regulation of mesenchymal cell proliferation and migration at the site of repair.
Long‐lived polymer radicals, 2. An ESR study on the reactions of the propagating polymer radicals of <i>N</i>‐methylacrylamide and <i>N</i>‐methylmethacrylamide with vinyl monomers at room temperature (1980)

Abstract Acrylamide (AAm), methacrylamide (MAm), N ‐methylacrylamide (NMAAm) and N ‐methylmethacrylamide (NMMAm) were found to yield long‐lived propagating polymer radicals in the photo‐sensitized polymerizations in 1,4‐dioxane or benzene. The concentration of poly(NMAAm) radicals reached 1.10 −3 mol/l. Some post‐effect was observed at room temperature in the photo‐sensitized polymerization of AAm with di‐ tert ‐butyl peroxide in 1,4‐dioxane, while no post‐polymerization proceeded at room temperature in the polymerization of NMMAm in benzene. The reactions of poly(NMAAm) and poly(NMMAm) radicals with various vinyl monomers were found to produce long‐lived propagating polymer radicals of the second monomers at room temperature. Polymer radicals of non‐homopolymerizable monomers such as α‐methylstyrene and 1,1‐diphenylethylene were easily formed in such a block‐copolymerization matrix. The formation of the propagating polymer radicals of the vinyl monomers was investigated by means of ESR spectroscopy.
Reevaluation of pediatric sepsis definition (2016)

Sepsis is one of leading cause of death in children.Consistent high mortality is associated with unclear understanding of pathophysiology of sepsis.Low sensitivity and specificity have been encountered in definition of sepsis.Therefore, new definition will be developed which defines sepsis as infection plus organ dysfunction.


Key words: 
Sepsis; Definition; Children
Murine IgA binding factors produced by Fc alpha R(+) T cells: role of Fc gamma R(+) cells for the induction of Fc alpha R and formation of IgA-binding factor in Con A-activated cells. (1984)

The relationship between the production of a T cell factor having affinity for IgA (IgA-binding factor(s); IgA BF) and the expression of Fc receptors specific for IgA (Fc alpha R) was studied by using murine spleen cells activated with concanavalin A (Con A blasts). Fc alpha R was detected by the cytophilic binding of anti-TNP murine IgA myeloma protein (MOPC 315 IgA) to Con A blasts as determined by an indirect rosette method with trinitrophenylated sheep red blood cells (TNP-SRBC). After 18 hr preculture with IgA, Fc alpha R was expressed on 15 to 20% of Con A blasts, which released IgA BF suppressing the in vitro IgA synthesis of the spleen cells stimulated with pokeweed mitogen (PWM). Without preculture with IgA, there was neither induction of Fc alpha R nor the production of IgA BF from Con A blasts. Fc alpha R was not induced on Con A blasts by IgA if Fc gamma R(+) cells were depleted from the blasts by rosetting with SRBC sensitized with rabbit IgG antibody (EA gamma). Even after preculture with IgA, the suppressive IgA BF was undetectable in the culture supernatant of Con A blasts depleted of the Fc gamma R(+) cell population. By using a double rosette method with EA gamma and trinitrophenylated quail red blood cells, Fc alpha R proved to be co-expressed on Fc gamma R(+) precursor T cells in the Con A blasts. The results suggested that both Fc gamma R and Fc alpha R could be co-expressed on Con A blasts, as is the case with T2D4 Fc gamma R(+), Fc alpha R(+) T hybridoma cells, which are known to produce IgG-binding factor(s) (IgG BF) and IgA BF. The relationship between Fc gamma R and Fc alpha R on a single cell was studied by using monoclonal anti-Fc gamma R antibody (2. 4G2 ). The reactivity of 2. 4G2 antibody with T cell Fc gamma R was proved by the inhibition of EA gamma rosette formation by Con A blasts or T2D4 cells. The addition of 2. 4G2 monoclonal antibody, however, did not affect the induction of Fc alpha R on Con A blasts by IgA. Furthermore, the binding of IgA to Fc alpha R already expressed on L5178Y T lymphoma cell line cells was not inhibited by the monoclonal antibody. The results confirmed that Fc alpha R are distinct from Fc gamma R co-expressed on the same Con A blasts, and that the expression of Fc alpha R on Fc gamma R(+) T cells and their production of suppressive IgA BF may be induced by the binding of IgA to Fc alpha R.
Distinct Methylation of <i>IFNG</i> in the Gut (2009)

Mucosal expression of proinflammatory cytokines plays a pivotal role in inflammatory bowel disease (IBD) pathogenesis. Epigenetic remodeling of chromatin via DNA methylation regulates gene expression. In this study, IFNG DNA methylation was analyzed within the mucosal compartment in both normal and IBD populations and compared to its peripheral counterparts. Overall IFNG methylation (across eight CpG sites) was significantly lower in lamina propria (LP) T cells compared to peripheral blood (PB) T cells. No methylation differences were detected when comparing PB T derived from normal to IBD patients. However, LP T-cell DNA derived from IBD patients displayed different levels of IFNG methylation of the upstream regulatory regions compared to DNA from normal controls. In fact, IFNG DNA promoter methylation levels functionally correlate with IFNG mRNA expression in unstimulated T cells, using quantitative real-time PCR. A 5% decrease in promoter methylation status is associated with nearly a 3-fold increase in IFNG expression. Likewise, methylation of the single -54 bp IFNG SnaB1 site strongly inhibited IFNG promoter expression. These results suggest that the epigenetic methylation status of IFNG may play a mechanistic role in the modulation of cytokine secretion in the mucosa.
Hydrodynamics from dissipative particle dynamics (1995)

Starting from the stochastic differential equations corresponding to the updating algorithm of dissipative particle dynamics we derive, with a standard technique of projection operators, the hydrodynamic equations for the mass and momentum density fields. The connection of the original parameters of the model with the viscosity and speed of sound of the fluid is clarified.
Chromatographic Separation of Strontium and Cesium with Mixed Zeolite, Column (1995)

Chromatographic separation of heat-generating nuclides and 90Sr and 137C from high-level liquid wastes has been studied by means of column packed with inorganic ion-exchangers. The distribution coefficients (K d) of Sr2+ and Cs+ onto zeolites decreased with increasing concentrations of monovalent cations. The retention volumes (V R) with a 2M (=mol/dm3) NH4Cl solution decreased in the order, natural mordenite (NM)≫ chabazite>clinoptilolite for Cs+, and titanic acid≫zeolite Y for Sr2+. The column containing mixtures of Y and NM was effective for selective adsorption of Sr2+ and Cs+ from a simulated waste solution, and chromatographic separation of these adsorbed nuclides was accomplished by passing a 2M NH4CL solution through the column of mixing ratio of Y: NM=3:2.
Chemical imaging with a confocal scanning Fourier-transform–Raman microscope (1994)

Traditional approaches in confocal microscopy have focused on techniques to generate volumetric intensity or phase images of an object. In these different imaging modes the scattered optical-field properties depend on local refractive index and absorption, properties not unique to a given material. We report here on a confocal microscope that uses Raman scattered light to generate volumetric chemical images of a material. We designed and built a prototype instrument, called a confocal scanning laser Raman microscope, that combines a confocal scanning laser microscope with a Fourier-transform-Raman spectrometer. The high depth and lateral spatial resolution of the confocal optics design define a volume element from which the Raman scattered light is collected, and the spectrometer analyzes its spectral content. The sample is scanned through the microscope probe volume, and a chemical image isgenerated based on the content of the Raman spectrum extracted from each scan position in the sample. The results inclu e instrument characterization measurements and examples of confocal chemical imaging.
Magnetic imaging reference sample (1996)

We propose a reference sample for magnetic imaging. We have chosen a thin-film magnetic hard disk as a representative sample because the domains are very stable magnetically and thermally. This type of sample is also of fundamental interest to the disk drive industry, currently the largest user of magnetic force microscopy. Disk samples are prepared by writing a special magnetic pattern consisting of various transition spacings designed to explore certain aspects of magnetic imaging. Disks are then cut into coupons, cleaned and patterned with a reference grid of numbered 20 /spl mu//spl times/20 /spl mu/m Au frames. These frames allow easy navigation around the sample. We believe a sample of this type can help define limits, expectations and claims of resolution, as well as instrument sensitivity and ease of operation.
Replication of Influenza A Viruses in an Avian Macrophage Cell Line (1991)

The virulent avian influenza virus A/Ty/Ont/7732/66 (H5N9) (Ty/Ont) causes severe destruction of the lymphoid cells in infected birds. Previous studies have suggested that viral infection of macrophages may be involved. However, Ty/Ont failed to replicate productively in primary cultures of chicken macrophages. Therefore, in an effort to develop an in vitro system for our studies, we examined the susceptibility of an avian macrophage cell line, HD11, to Ty/Ont. We found that Ty/Ont replicated in the HD11 cells to high titres, as measured by haemagglutination (HA) assays and infectivity yields. To determine whether this property was unique to Ty/Ont, we also examined the replication of influenza viruses representative of all 13 HA subtypes and an attenuated variant of Ty/Ont. All of the tested viruses replicated in HD11 cells; the avirulent strains required the presence of trypsin in the culture medium whereas virulent viruses and the attenuated variant of Ty/Ont did not. These results suggest that the HD11 cells can support the replication of a wide variety of influenza viruses and that this continuous avian cell line may prove useful for in vitro studies on these viruses.
Concentrations of antisecretory factor in eggs and in chicken blood plasma (1994)

1. In the present study, the concentration of antisecretory factor (ASF), a lectin with hormone-like properties, and with the capacity to regulate water and electrolyte transport in the small intestine, was higher in hen's egg yolk than in egg white (1.20 v. 0.46 units/ml). 2. The blood plasma concentrations of ASF activity were higher in d-old chicks (1.03 units/ml) than in 7-d-old (0.42 units/ml) or 21-d-old birds (0.18 units/ml); the contents were found to be high again in 35-d-old chickens, but to have decreased by 60 to 90% after transport to slaughter 1 day later. 3. The amount of ASF activity was lower in two groups of chickens manifesting patent loose droppings at slaughter (0.15 units/ml in one group, and 0.08 units/ml in the other), than in two groups with normal faecal consistency (0.65 units/ml in one group, and 0.72 units/ml in the other). 4. The results demonstrate the presence of ASF in eggs, and a variation of ASF activity in chickens blood plasma in relation to age, stress and faecal consistency. The interpretation of these data suggests a regulatory influence of ASF on chicken intestinal transport of water.
On-chip Vector Coprocessor Sharing for Multicores (2011)

For most of the applications that make use of a vector coprocessor, the resources are not highly utilized due to the lack of sustained data parallelism, which sometimes occurs due to vector-length changes in dynamic environments. The motivation of our work stems from (a) the mandate for multicore designs to make efficient use of the on-chip resources, (b) the frequent presence of vector operations in high-performance scientific and embedded applications, (c) the increased probability that different cores may deal with different vector lengths at various times, and (d) different vector kernels in the same or different application suites may have diverse computation needs. Our objective is to provide a versatile design framework that can facilitate vector coprocessor sharing among multiple cores in a manner that maximizes resource utilization while also yielding very high performance at reduced cost. We propose three basic shared vector coprocessor architectures for multicores based on coarse-grain, fine-grain and vector lane sharing. We benchmark these distinct vector architectures for a dual-core system using the floating-point performance and resource utilization metrics. Our analysis shows that vector lane sharing, where the number of vector lanes assigned to a core can be controlled dynamically, provides the greatest flexibility and generally yields very good results. Since, however, each of the three design choices has its own performance advantages under certain vector-load conditions, we ultimately suggest a hybrid vector coprocessor design that can support all three architectural choices as per the core and application collective needs.
A novel cryptosystem based on abstract automata and Latin cubes (2015)

In this paper we introduce a novel block cipher based on the composition of abstract finite automata and Latin cubes. For information encryption and decryption the apparatus uses the same secret keys, which consist of key-automata based on composition of abstract finite automata such that the transition matrices of the component automata form Latin cubes. The aim of the paper is to show the essence of our algorithms not only for specialists working in compositions of abstract automata but also for all researchers interested in cryptosystems. Therefore, automata theoretical background of our results is not emphasized. The introduced cryptosystem is important also from a theoretical point of view, because it is the first fully functioning block cipher based on automata network.
Effects of <i>Antrodia camphorata</i> on viability, apoptosis, [Ca<sup>2+</sup>]<sub>i</sub>, and MAPKs phosphorylation in MG63 human osteosarcoma cells (2007)

Abstract The present study explored the effect of Antrodia camphorata (AC) on viability, apoptosis, mitogen‐activated protein kinases (MAPKs) phosphorylation, and Ca 2+ regulation in MG63 human osteosarcoma cells. AC (25–50 µg/ml) did not affect cell viability, but at 100–200 µg/ml decreased viability and induced apoptosis in a concentration‐dependent manner. AC at concentrations of 25–200 µg/ml did not alter basal [Ca 2+ ] i , but at 25 µg/ml decreased [Ca 2+ ] i increases induced by ATP, bradykinin, histamine, and thapsigargin. ATP, bradykinin, and histamine increased cell viability while thapsigargin decreased it. AC (25 µg/ml) pretreatment failed to alter bradykinin‐ and thapsigargin‐induced effects on viability, but potentiated ATP‐ and histamine‐induced increases in viability. Immunoblotting showed that MG63 cells did not have background phospho‐JNK and phospho‐p38 mitogen‐activated protein kinases (MAPKs); and AC did not induce the phosphorylation of these two MAPKs. Conversely, the cells had significant background phospho‐ERK MAPK that was inhibited by 200 µg/ml AC. The ERK‐specific inhibitor PD98059 also induced cell death. Collectively, in MG63 cells, AC exerted multiple effects on viability and [Ca 2+ ] i , caused apoptosis probably via inhibition of ERK MAPK phosphorylation. Drug Dev Res 68:71–78, 2007. © 2007 Wiley‐Liss, Inc.
Identification of Androgen-Regulated Genes in Mouse Kidney by Representational Difference Analysis and Random Arbitrarily Primed Polymerase Chain Reaction (1998)

The molecular nature of tissue-specific gene regulation by androgens has not been well defined, partly as a result of the variable expression and incomplete regulation of currently available gene models. We have therefore aimed to establish more informative models by identifying alternative genes whose expression is tightly and coordinately regulated by androgens. Female C57BL/6 mice were dosed with dihydrotestosterone- or sham-treated for 8 days, after which kidneys were removed and complementary DNA (cDNA) prepared. We then applied the subtractive hybridization techniques of random arbitrarily primed-PCR and PCR-coupled subtractive hybridization method of cDNA representational difference analysis to the isolated cDNA. In addition to well characterized androgen-regulated genes [e.g. KAP (kidney androgen-regulated protein)], we demonstrate the differential expression of six genes previously not known to be under androgen control. RNA levels of SA, Cytochrome P450 4B1, IL-6ST (interleukin-6 signal transducer), OATP (organic anion transporter), and a newly identified gene, MJAM, were up-regulated by androgen, while 16-α-hydroxylase was decreased. Expression of these transcripts was inhibited in dihydrotestosterone-treated females by flutamide and in males by castration, confirming their dependence on androgens. Although all the genes demonstrate tissue-specific regulation by androgen, SA showed both kidney specificity and absolute requirement for androgen for its expression. These newly identified androgen-regulated genes will constitute very useful models for studying the nature of tissue-specific gene regulation by androgens.
9C1 - Single transverse and longitudinal mode Q-switched ruby laser (1966)

Single transverse and longitudinal modes have been observed in the output of a passive <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</tex> -switched ruby laser when two spherical mirrors are used for the resonator. This result has been consistently obtained with several rods, with two sets of mirrors of different radius of curvature, and with a few values of reflectivity of the mirrors which proves that it is typical of a spherical resonator. The saturable absorber is a solution of vanadium phtalocyanine in nitrobenzene. To have a single transverse mode, the mirror alignment and the position of the rod within the cavity is critical. When the laser oscillates in a single mode, the output pulse is very reproducible and the fluctuations of peak amplitude and width of the pulse are less than ∼3 percent. Furthermore, as expected, the output beam has a very good spatial coherence and its divergence approaches the limits set by diffraction. As far as peak output power and width of the pulse, the best results have been obtained with one concave and one convex mirror of ∼ 5-m radius of curvature, one mirror being 99 percent and the other 50 percent reflecting. A pulse of 1 MW peak power and 30 ns half-width has been obtained.