gebhart/patrepeval huggingface dataset:
11,12-Epoxyeicosatrienoic Acid-induced Inhibition of FOXO Factors Promotes Endothelial Proliferation by Down-Regulating p27 (2003)

Cytochrome P450-derived epoxyeicosatrienoic acids (EETs) stimulate endothelial cell proliferation and angiogenesis. In this study, we investigated the involvement of the forkhead box, class O (FOXO) family of transcription factors and their downstream target p27Kip1 in EET-induced endothelial cell proliferation. Incubation of human umbilical vein endothelial cells with 11,12-EET induced a time- and dose-dependent decrease in p27Kip1 protein expression, whereas p21Cip1 was not significantly affected. This effect on p27Kip1 protein was associated with decreased mRNA levels as well as p27Kip1 promoter activity. 11,12-EET also stimulated the time-dependent phosphorylation of Akt and of the forkhead factors FOXO1 and FOXO3a, effects prevented by the phosphatidylinositol 3-kinase inhibitor LY 294002. Transfection of endothelial cells with either a dominant-negative or an "Akt-resistant"/constitutively active FOXO3a mutant reversed the 11,12-EET-induced down-regulation of p27Kip1, whereas transfection of a constitutive active Akt decreased p27Kip1 expression independently of the presence or absence of 11,12-EET. To determine whether these effects are involved in EET-induced proliferation, endothelial cells were transfected with the 11,12-EET-generating epoxygenase CYP2C9. Transfection of CYP2C9 elicited endothelial cell proliferation and this effect was inhibited in cells co-transfected with CYP2C9 and either a dominant-negative Akt or constitutively active FOXO3a. Reducing FOXO expression using RNA interference, on the other hand, attenuated p27Kip1 expression and stimulated endothelial cell proliferation. These results indicate that EET-induced endothelial cell proliferation is associated with the phosphatidylinositol 3-kinase/Akt-dependent phosphorylation and inactivation of FOXO factors and the subsequent decrease in expression of the cyclin-dependent kinase inhibitor p27Kip1.
Substrate specificities of mouse heparan sulphate glucosaminyl 6-O-sulphotransferases (2003)

Glycosaminoglycan heparan sulphate interacts with a variety of proteins, such as growth factors, cytokines, enzymes and inhibitors and, thus, influences cellular functions, including adhesion, motility, differentiation and morphogenesis. The interactions generally involve saccharide domains in heparan sulphate chains, with precisely located O-sulphate groups. The 6-O-sulphate groups on glucosamine units, supposed to be involved in various interactions of functional importance, occur in different structural contexts. Three isoforms of the glucosaminyl 6-O-sulphotransferase (6-OST) have been cloned and characterized [H. Habuchi, M. Tanaka, O. Habuchi, K. Yoshida, H. Suzuki, K. Ban and K. Kimata (2000) J. Biol. Chem. 275, 2859-2868]. We have studied the substrate specificities of the recombinant enzymes using various O-desulphated poly- and oligo-saccharides as substrates, and using adenosine 3'-phosphate 5'-phospho[(35)S]sulphate as sulphate donor. All three enzymes catalyse 6-O-sulphation of both -GlcA-GlcNS- and -IdoA-GlcNS- (where GlcA represents D-glucuronic acid, NS the N-sulphate group and IdoA the L-iduronic acid) sequences, with preference for IdoA-containing targets, with or without 2-O-sulphate substituents. 6-OST1 showed relatively higher activity towards target sequences lacking 2-O-sulphate, e.g. the -GlcA-GlcNS- disaccharide unit. Sulphation of such non-O-sulphated acceptor sequences was generally favoured at low acceptor polysaccharide concentrations. Experiments using partially O-desulphated antithrombin-binding oligosaccharide as the acceptor revealed 6-O-sulphation of N-acetylated as well as 3-O-sulphated glucosamine residues with each of the three 6-OSTs. We conclude that the three 6-OSTs have qualitatively similar substrate specificities, with minor differences in target preference.
SoPhie: An Attentive GAN for Predicting Paths Compliant to Social and Physical Constraints (2019)

This paper addresses the problem of path prediction for multiple interacting agents in a scene, which is a crucial step for many autonomous platforms such as self-driving cars and social robots. We present SoPhie; an interpretable framework based on Generative Adversarial Network (GAN), which leverages two sources of information, the path history of all the agents in a scene, and the scene context information, using images of the scene. To predict a future path for an agent, both physical and social information must be leveraged. Previous work has not been successful to jointly model physical and social interactions. Our approach blends a social attention mechanism with physical attention that helps the model to learn where to look in a large scene and extract the most salient parts of the image relevant to the path. Whereas, the social attention component aggregates information across the different agent interactions and extracts the most important trajectory information from the surrounding neighbors. SoPhie also takes advantage of GAN to generates more realistic samples and to capture the uncertain nature of the future paths by modeling its distribution. All these mechanisms enable our approach to predict socially and physically plausible paths for the agents and to achieve state-of-the-art performance on several different trajectory forecasting benchmarks.
Memory design using a one-transistor gain cell on SOI (2002)

A 512-kb memory has been developed featuring a one-transistor gain cell of size 7F/sup 2/ (F = 0.18 /spl mu/m) on SOI. The cell named the floating body transistor cell (FBC) has the ability to achieve a 4F/sup 2/ cell using self-aligned contact technologies and is proved to be scalable with respect to a cell signal. A basic operation was verified by device simulation and hardware measurement. An array driving method is disclosed which makes selective write possible. A cell signal sensing system consisting of a pair of reference cells written opposite data and comparing the combined current with the doubled cell current is shown to be robust against cell parameter variations in process and temperature. A random access time of 40 ns was simulated. Nondestructive readout and C/sub b//C/sub s/. free signal development drastically improve cell efficiency.
Modeling Web application architectures with UML (1999)

When put to the test, the term Web application has slightly different meanings to different people. Some believe a Web application is anything that uses Java, others consider a Web application anything that uses a Web server. The general consensus is somewhere in between. In this article, a Web application will be loosely defined as a Web system (Web server, network, HTTP, browser) in which user input (navigation and data input) effects the state of the business. This definition attempts to establish that a Web application is a software system with business state, and that its front end is in large part delivered via a Web system.
Definitive Hematopoiesis in the Yolk Sac Emerges from Wnt-Responsive Hemogenic Endothelium Independently of Circulation and Arterial Identity (2015)

Adult-repopulating hematopoietic stem cells (HSCs) emerge in low numbers in the midgestation mouse embryo from a subset of arterial endothelium, through an endothelial-to-hematopoietic transition. HSC-producing arterial hemogenic endothelium relies on the establishment of embryonic blood flow and arterial identity, and requires β-catenin signaling. Specified prior to and during the formation of these initial HSCs are thousands of yolk sac-derived erythro-myeloid progenitors (EMPs). EMPs ensure embryonic survival prior to the establishment of a permanent hematopoietic system, and provide subsets of long-lived tissue macrophages. While an endothelial origin for these HSC-independent definitive progenitors is also accepted, the spatial location and temporal output of yolk sac hemogenic endothelium over developmental time remain undefined. We performed a spatiotemporal analysis of EMP emergence, and document the morphological steps of the endothelial-to-hematopoietic transition. Emergence of rounded EMPs from polygonal clusters of Kit(+) cells initiates prior to the establishment of arborized arterial and venous vasculature in the yolk sac. Interestingly, Kit(+) polygonal clusters are detected in both arterial and venous vessels after remodeling. To determine whether there are similar mechanisms regulating the specification of EMPs with other angiogenic signals regulating adult-repopulating HSCs, we investigated the role of embryonic blood flow and Wnt/β-catenin signaling during EMP emergence. In embryos lacking a functional circulation, rounded Kit(+) EMPs still fully emerge from unremodeled yolk sac vasculature. In contrast, canonical Wnt signaling appears to be a common mechanism regulating hematopoietic emergence from hemogenic endothelium. These data illustrate the heterogeneity in hematopoietic output and spatiotemporal regulation of primary embryonic hemogenic endothelium.
Platinum-catalyzed cyclizations viacarbene intermediates: syntheses of complementary positional isomers of isoxazoles (2012)

A novel synthesis of regioisomeric isoxazoles is described. Using catalytic platinum, both propargylic N-hydroxycarbamates and N-alkoxycarbonyl amino ethers can be cyclized to form differentially substituted isoxazoles. Reaction conditions are developed that address specific aspects of the catalytic manifold. A unique mechanism involving a Pt-carbene intermediate is proposed, and deuterium labeling studies corroborate this hypothesis. This regiocomplementary approach to isoxazoles is highlighted in the syntheses of antirhinovirus analogues, illustrating the relevance of this science to medicinal chemistry.
Synergistic Activity of Colistin and Ceftazidime against Multiantibiotic-Resistant Pseudomonas aeruginosa in an In Vitro Pharmacodynamic Model (2003)

Despite the marketing of a series of new antibiotics for antibiotic-resistant gram-positive bacteria, no new agents for multiple-antibiotic-resistant gram-negative infections will be available for quite some time. Clinicians will need to find more effective ways to utilize available agents. Colistin is an older but novel antibiotic that fell into disfavor with clinicians some time ago yet still retains a very favorable antibacterial spectrum, especially for Pseudomonas and Acinetobacter spp. Time-kill curves for two strains of multiantibiotic-resistant Pseudomonas aeruginosa were generated after exposure to colistin alone or in combination with ceftazidime or ciprofloxacin in an in vitro pharmacodynamic model. MICs of colistin, ceftazidime, ciprofloxacin, piperacillin-tazobactam, imipenem, and tobramycin were 0.125, > or =32, >4, >128/4, 16, and >16 mg/liter, respectively. Colistin showed rapid, apparently concentration-dependent bactericidal activity at concentrations between 3 and 200 mg/liter. We were unable to detect increased colistin activity at concentrations above 18 mg/liter due to extremely rapid killing. The combination of colistin and ceftazidime was synergistic (defined as at least a 2-log(10) drop in CFU per milliliter from the count obtained with the more active agent) at 24 h. Adding ciprofloxacin to colistin did not enhance antibiotic activity. These data suggest that the antibacterial effect of colistin combined with ceftazidime can be maximized at a peak concentration of < or =18 mg/liter.
Identification and properties of two extracellular proteases from Brevundimonas diminuta (2000)

Extracellular proteases from Brevundimonas diminuta (syn. Pseudomonas diminuta) were studied in sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) containing a copolymerized substrate. Two proteases were detected migrating at 67 kDa and 50 kDa: both of them hydrolysed preferentially gelatin, but casein was also degraded and a slight hydrolysis was observed with hemoglobin. No detectable extracellular proteolytic activity was found in bovine serum albumin-containing gels. The optima temperature and pH for proteolytic activity were between 40ºC and 50ºC in a pH ranging from 7.0 to 11.0, respectively. These enzymes were isolated by analytical high performance liquid chromatography (HPLC). Protease assays with the synthetic substrate Z-Phe-Arg-MCA and the inhibitors EGTA, EDTA and 1, 10 phenanthroline point out that these enzymes are metalloproteases.
Microprocessor implementation of a parallel processor (1977)

A wide variety of uses have been proposed for the spectrum of currently available microprocessor systems. Included in this set of applications is the use of microprocessors for implementing larger systems; here, the possibility of employing bit slice microprocessors for various parts of a multiple control unit SIMD processor is discussed. A brief summary of bit slice microprocessor architecture is given, followed by an outline of individual applications to various components such as control units and arithmetic/logic units of the SIMD processor.
Type, Density, and Location of Immune Cells Within Human Colorectal Tumors Predict Clinical Outcome (2006)

The role of the adaptive immune response in controlling the growth and recurrence of human tumors has been controversial. We characterized the tumor-infiltrating immune cells in large cohorts of human colorectal cancers by gene expression profiling and in situ immunohistochemical staining. Collectively, the immunological data (the type, density, and location of immune cells within the tumor samples) were found to be a better predictor of patient survival than the histopathological methods currently used to stage colorectal cancer. The results were validated in two additional patient populations. These data support the hypothesis that the adaptive immune response influences the behavior of human tumors. In situ analysis of tumor-infiltrating immune cells may therefore be a valuable prognostic tool in the treatment of colorectal cancer and possibly other malignancies.
Phosphoenolpyruvate-dependent phosphotransferase system enzyme III and plasmid-encoded sucrose transport in Escherichia coli K-12 (1982)

The phosphoenolpyruvate-dependent carbohydrate:phosphotransferase system enzyme IISCR, specific for and regulated by sucrose, was analyzed in derivatives of Escherichia coli K-12 carrying the sucrose plasmid pUR404. Enzyme IIScr, coded for by gene scrA of the plasmid, depended for its transport and phosphorylation activity directly on the phosphotransferase system enzyme IIIGlc, Scr, coded for by the chromosomal gene crr.
A 1H‐NMR study of human interleukin‐1β (1986)

Complete identification of spin systems in the aromatic region of recombinant human interleukin-1 beta has been achieved using two-dimensional homonuclear Hartmann-Hahn spectroscopy. In addition, sequence-specific assignments for the four tyrosine residues have been carried out with the help of a series of mutant proteins, obtained by site-directed mutagenesis of the cloned gene. It is shown that, for the mutant proteins investigated, either none or only local structural changes occur. The use of NMR spectroscopy to determine the structural identity of site-directed mutant proteins with respect to the wild-type protein is discussed.
Floating-Potential Dielectrophoresis-Controlled Fabrication of Single-Carbon-Nanotube Transistors and Their Electrical Properties (2005)

We present a floating-potential dielectrophoresis method used for the first time to achieve controlled alignment of an individual semiconducting or metallic single-walled carbon nanotube (SWCNT) between two electrical contacts with high repeatability. This result is significantly different from previous reports, in which bundles of SWCNTs were aligned between electrode arrays by a conventional dielectrophoresis process where the results were only collected from the control electrode regions. In this study, our alignment focus is not only on the regions of the control electrodes but also on those of the floating electrodes. Our results indicate that bundles of carbon nanotubes along with impurities were first moved into the region between two control electrodes while individual nanotubes without impurities were straightened and aligned between two floating electrodes. The measurements for the back-gated nanotube transistors made by this method displayed an on-off ratio and transconductance of 10(5) and 0.3 microS, respectively. These output and transport properties are comparable with those of nanotube transistors made by other methods. Most importantly, the findings in this study show an effective way to separate individual nanotubes from bundles and impurities and advance the processes for site-selective fabrication of single-SWCNT transistors and related electrical devices.
A New Blood Diluent for Counting the Erythrocytes and Leucocytes of the Chicken (1952)

INTRODUCTION HEMATOLOGICAL studies on chickens have long been hampered by the lack of a quick, readily applicable, and quantitative method for the enumeration of the leucocytes. This problem stems from the fact that the nuclei of bird erythrocytes are not destroyed in the usual procedure for mammalian blood cell enumeration and therefore cannot be distinguished from the leucocytes. LITERATURE The first method for counting leucocytes in avian blood was proposed by Warthin (1906) who suggested an indirect method for counting these cells. This method entails the use of a diluent which preserves all the blood cells. The total leucocyte count can be calculated by determining the total number of cells in a cu. mm. of blood (leucocyte and erythrocyte) and subsequently ascertaining the ratio between these cells in a stained smear. In using the indirect method, one must assume that the blood cells are equally distributed throughout the smear. This . . .
The myosin power stroke (2002)

Optical trapping technology now allows investigators in the motility field to measure the forces generated by single motor molecules. A handful of research groups have exploited this approach to further develop our understanding of the actin-based motor, myosin, an ATPase that is capable of converting chemical energy into mechanical work during a cyclical interaction with filamentous actin. In this regard, myosin-II from muscle is the most well-characterized myosin superfamily member. By combining the data obtained from optical trap assays with that from ensemble biochemical and mechanical assays, this review discusses the fundamental properties of the myosin-II power stroke and, perhaps more significantly, how these properties are governed by this molecule's atomic structure and the biochemical transitions that define its catalytic cycle.
Construction of repeat-free fluorescence in situ hybridization probes (2011)

FISH probes are generally made out of BAC clones with genomic DNA containing a variable amount of repetitive DNA that will need to be removed or blocked for FISH analysis. To generate repeat free (RF) Probes without loss in genomic coverage, a random library is made from BAC clones by whole-genome amplification (WGA). Libraries are denatured in the presence of excess C(0)t-1 DNA and allowed to re-anneal followed by digestion of all double-stranded elements by duplex-specific nuclease (DSN). Selective amplification of all elements not containing repetitive sequences is realized by a sequential amplification. The final RF products can be re-amplified and used as a stock for future probe production. The RF probes have a lower background, the signal intensity build up is faster and there is no need for blocking DNA. The signal to background ratio of the RF was higher as compared to repeat containing probes.
An Advisory System for Customers’ Objective Needs Elicitation in Mass Customization (2003)

To better understand customer requirements in mass customization, we introduce here a model distinguishing between the objective and the subjective customers’ needs. The model points out that the explicitly expressed customer requirements do not necessarily correspond to what customers really want. This model enables the explanation of the main shortcomings of the existing customer interaction systems. We conclude that customers should be better assisted during the elicitation process. Then, we briefly examine recommender systems within E-commerce. However, they are not able to provide customer assistance based on objective needs. Therefore, we introduce the notion of advisory systems for mass customization and we outline its basic structure. To better elicit the objective customers needs, we identify main extension fields of the system. Furthermore, to ensure the implementation of the extended advisory system, we describe the required technical infrastructure.
Specific biochemical inactivation of oncogenic Ras proteins by nucleoside diphosphate kinase. (2003)

Activating mutations of Ras have been implicated in approximately 30% of human cancers. In every case, the biochemical consequence of such mutations is to disrupt the GTPase activity of Ras and to render Ras resistant to the actions of GTPase activating proteins. Consequently, oncogenic Ras mutants are "locked" in a GTP-bound active state. We detected a potent activity in Escherichia coli extract that can efficiently convert mutationally activated GTP-bound Ras to the inactive GDP-bound form. Purification of the protein responsible for this activity led to the identification of the enzyme nucleoside diphosphate kinase (Ndk). The human orthologue of Ndk is the NM23 metastasis suppressor, which we found to exhibit a similar activity. Purified Ndk effectively inactivates several of the oncogenic forms of Ras that are seen frequently in human cancers, including RasD12, the most commonly detected Ras mutation. Significantly, Ndk does not detectably affect wild-type Ras or an activated form of the Ras-related Rho GTPase. These results demonstrate that it is possible, through biochemical means, to specifically inactivate oncogenic Ras as a potential therapeutic approach to tumors that harbor Ras mutations. Moreover, the results suggest that the loss of NM23 expression that is commonly observed during tumor progression could lead to increased potency of oncogenic Ras proteins.
Pain in preterm infants: Effects of sex, gestational age, and neonatal illness severity. (2012)

Made available in DSpace on 2013-11-04T13:08:07Z (GMT). No. of bitstreams: 1\nS1983-32882012000100003.pdf: 348647 bytes, checksum: c8b6eac9bdf03d84ef5fc8f4d1bae71b (MD5)\n Previous issue date: 2012
Repressor of P elements in Drosophila melanogaster : Cytotype determination by a defective P element carrying only open reading frames 0 through 2 (1987)

The P element is a type of transposable element in Drosophila melanogaster. Characteristics of the syndrome of "hybrid dysgenesis" are due to transposition of P elements, and the molecular mechanism for regulation of this transposition has been unknown. In this study a Q strain (which carries only defective P elements in its genome but still is able to repress the transposition of complete P elements although defective in transposase activity) was used to determine the structure of the P element with this repressor (or P cytotype-determining) domain. Examination of the cytotype and structure of the P elements of particular strains with reduced copy number of P elements showed that the P element with a repressor domain was defective, being deleted between bases 1991 and 2448. This region corresponds to most of the third intron [between open reading frame (ORF) 2 and ORF 3] as well as half the ORF 3 of an intact P element. Therefore ORF 3 was deemed to be unnecessary for repressor production.