gebhart/patrepeval huggingface dataset:
An adaptive approach to mammographic image denoising and enhancement (2004)

This paper describes a new method for mammographic image noise suppression and enhancement based on the wavelet transform. At each resolution, coefficients associated with noise are modelled by Gaussian random variables; coefficients associated with edges are modelled by generalized Gaussian random variables, and a shrinkage function is assembled based on posterior probabilities. The shrinkage functions at consecutive scales are combined, and then applied to the wavelet coefficients. Given a resolution of analysis, the image denoising process is adaptive (i.e. does not require further parameter adjustments), and the selection of a gain factor provides the desired detail enhancement. The enhancement function was designed to avoid introducing artifacts in the enhancement process, which is essential in mammographic image analysis. Our preliminary results indicate that our method allows us to detect microcalcifications and other suspicious structures in situations where their detection would be difficult otherwise. Compared to other approaches, our method requires less parameter adjustments by the user.
Thermoplastic composite wind turbine blades: Vacuum infusion technology for anionic polyamide-6 composites (2007)

Due to the increasing costs of fossil fuels and the improved efficiency of wind turbines in the last decade, wind energy has become increasingly cost-efficient and is well on its way of becoming a mainstream source of energy. To maintain a continuous reduction in costs it is necessary to increase the size of the turbines. For the blades a structural redesign is inevitable and an aircraft-wing-like design consisting of ribs, spars and skins made of thermoplastic composite parts is proposed. Unfortunately, state-of-the-art melt processing of thermoplastic composites requires heavy presses, which makes it impossible to produce large and thick structures like wind turbine blades. As an alternative, this thesis describes the development of reactive processing of thermoplastic composites through vacuum infusion, which is a commonly used technique for manufacturing of thermoset composite wind turbine blades. An anionic polyamide-6 (APA-6) casting resin with water-like viscosity is used to impregnate a stack of "dry" glass fiber fabrics, after which in situ polymerization of the semi-crystalline APA-6 matrix takes place within 30 minutes at temperatures around 180°C. The developed technology was successfully applied to infuse 2 to 25 mm thick thermoplastic composites with a fiber volume content of 50%. These APA-6 composites possess outstanding static properties and a promising resistance against fatigue, which is one of the main requirements for wind turbine blade composites. Additional advantages for application in wind energy are the low costs of the resin, the short infusion and curing time, and the fact that APA-6 can be recycled in various ways in an economically sound manner. Increasing the moisture resistance of APA-6 composites is mentioned as most important recommendation for further development.
StackGuard: Simple Stack Smash Protection for GCC (2004)

Since 1998, StackGuard patches to GCC have been used to protect entire distributions from stack smashing buffer overflows. Performance overhead and software compatibility issues have been minimal. In its history, the parts of GCC that StackGuard has operated in have twice changed enough to require complete overhauls of the StackGuard patch. Since StackGuard is a mature technology, even see-ing re-implementations in other compilers, we propose that GCC adopt StackGuard as a stan-dard feature. This paper describes our recent work to bring StackGuard fully up to date with current GCC, introduce architecture indepen-dence, and extend the protection of stack data structures, while keeping the StackGuard patch as small, simple, and modular as possible. 1
miR-1207-5p suppresses lung cancer growth and metastasis by targeting CSF1 (2016)

We previously reported that miR-1207-5p can inhibit epithelial-mesenchymal transition (EMT) induced by growth factors such as EGF and TGF-β, but the exact mechanism is unclear. Here we identified that Colony stimulating factor 1 (CSF1) is a target gene of miR-1207-5p. CSF1 controls the production, differentiation and function of macrophage and promotes the release of proinflammatory chemokines. We showed that miR-1207-5p inhibited lung cancer cell A549 proliferation, migration and invasion in vitro, and suppressed the STAT3 and AKT signalings. miR-1207-5p overexpression can increase HUVEC angiogenesis, and can modulate the M2 phenotype of macrophage. miR-1207-5p also significantly inhibited A549 cells metastasis in a nude mouse xenograft model. miR-1207-5p and CSF1 expression levels and their relationship with lung cancer survival and metastasis status were assayed by means of a lung cancer tissue microarray. Macrophage is an essential part of the tumor microenvironment, thus the miR-1207-5p-CSF1 axis maybe a new regulator of lung cancer development through modulating the tumor microenvironment.
Improved Cell Survival in Infarcted Myocardium Using a Novel Combination Transmyocardial Laser and Cell Delivery System (2007)

Stem cell therapy has been used to treat ischemic cardiac disease with promising early results. However, there has been limited success using cell therapy in infarcted tissue. The cells have an inadequate microvascular environment in order to survive once implanted into scar tissue. The goal of this study was to create a microvascular environment into infarcted myocardial tissue using transmyocardial laser revascularization (TMR) as a pretreatment before cell implantation and evaluate cell survival afterwards. Balloon occlusion catheter-based myocardial infarct of the circumflex artery was created in a porcine model. The infarct was allowed to mature for 2 weeks. Three groups consisting of TMR alone (TMR), TMR + fluorescent-labeled allogeneic mesenchymal stem cells (MSCs) (TMR + Cells), and MSCs alone (Cells) were injected into the infarcted tissue using a combination TMR and cell delivery system (Phoenix, Cardiogenesis). The hearts were explanted at 1 week after treatment for cell and tissue evaluation. The myocardial infarcts were verified in all animals using both ultrasound and direct visual imaging. All arms of the study were successful with a mean of 2.0 +/- 10(6) MSCs injected per site into the scar tissue. All animals survived to explant at 1 week. On histological examination, 300 high-power fields were evaluated demonstrating that the TMR + Cells group had 25 +/- 5 cells and the Cells group 5 +/- 2 cells compared to baseline TMR alone by fluorescence. The use of TMR as a pretreatment for MSC injection increases early cell survival in infarcted tissue without increased adverse events. Further long-term functional and differentiation analysis will be required to evaluate the efficacy for future clinical translation.
Rapid Effects of a Protective O-Polysaccharide-Specific Monoclonal IgA on Vibrio cholerae Agglutination, Motility, and Surface Morphology (2015)

2D6 is a dimeric monoclonal immunoglobulin A (IgA) specific for the nonreducing terminal residue of Ogawa O-polysaccharide (OPS) of Vibrio cholerae. It was previously demonstrated that 2D6 IgA is sufficient to passively protect suckling mice from oral challenge with virulent V. cholerae O395. In this study, we sought to define the mechanism by which 2D6 IgA antibody protects the intestinal epithelium from V. cholerae infection. In a mouse ligated-ileal-loop assay, 2D6 IgA promoted V. cholerae agglutination in the intestinal lumen and limited the ability of the bacteria to associate with the epithelium, particularly within the crypt regions. In vitro fluorescence digital video microscopy analysis of antibody-treated V. cholerae in liquid medium revealed that 2D6 IgA not only induced the rapid (5- to 10-min) onset of agglutination but was an equally potent inhibitor of bacterial motility. Scanning electron microscopy showed that 2D6 IgA promoted flagellum-flagellum cross-linking, as well as flagellar entanglement with bacterial bodies, suggesting that motility arrest may be a consequence of flagellar tethering. However, monovalent 2D6 Fab fragments also inhibited V. cholerae motility, demonstrating that antibody-mediated agglutination and motility arrest are separate phenomena. While 2D6 IgA is neither bactericidal nor bacteriostatic, exposure of V. cholerae to 2D6 IgA (or Fab fragments) resulted in a 5-fold increase in surface-associated blebs, as well an onset of a wrinkled surface morphotype. We propose that the protective immunity conferred by 2D6 IgA is the result of multifactorial effects on V. cholerae, including agglutination, motility arrest, and possibly outer membrane stress.
Effects of Nitrogen Addition to Fluorinated Silicon Dioxide Films (1998)

Amorphous fluorinated silicon dioxide ( a -SiO 2 :F) films doped with nitrogen were deposited by changing the ammonia flow rate using plasma-enhanced chemical vapor deposition from SiH 4 –O 2 –CF 4 –NH 3 mixtures. The effects of nitrogen addition to the films on both the dielectric constant ( ε s ) determined from the capacitance vs. voltage characteristics and the bonding properties examined by infrared absorption measurements, were investigated. These results were also discussed in terms of a change in the partial charge on the constituent Si, O, F and N atoms caused by adding F and N atoms to SiO 2 films. When a -SiO 2 films are doped by 2-3 at.% with both fluorine and nitrogen under high rf power and high deposition temperature ( T d ) conditions, films with low ε s (≈3.2) and high water resistivity were obtained. It was suggested that Si–F bonds, which act to decrease ε s value, are stabilized by forming Si–N bonds near the Si–F bonds and by removing weaker Si–F bonds under high rf power and high T d .
Zur Synthese heterocyclischer Phosphonsäureester (1973)

Abstract Methylenaktive Phosphonsäureester des Typs 1 und 10 reagieren unter basischen Bedingungen mit den Arylaziden 2 unter Bildung der heterocyclischen Phosphonsäureester 4 und 12 . Die Verbindungen 4 und 8 unterliegen einer Dimroth‐Umlagerung. Die Ester 1 liefern mit den Nitriloxiden 3 die Phosphonsäureester 5 . Aus 7 und 2 entstehen die Diazoester 9 .
<i>Ink4a</i> / <i>Arf</i> tumor suppressor does not modulate the degenerative conditions or tumor spectrum of the telomerase-deficient mouse (2007)

The Rb/p16(Ink4a) and p53/p19Arf tumor suppressor pathways have been linked to diverse cancer-relevant processes, including those governing the cellular responses to telomere dysfunction. In this study, we sought to provide direct genetic evidence of a role for the Ink4a/Arf tumor suppressor gene, encoding both p16(Ink4a) and p19(Arf), in modulating the cellular and tissue phenotypes associated with telomere dysfunction by using the mTerc Ink4a/Arf mouse model. In contrast to the rescue associated with p53 deficiency, Ink4a/Arf deficiency did not attenuate the degenerative phenotypes elicited by telomere dysfunction in the late-generation mTerc-/- mice. Furthermore, in contrast to accelerated cancer onset and increased epithelial cancers of late-generation mTerc-/- p53 mutant mice, late-generation mTerc-/- Ink4a/Arf mutant mice experienced a delayed tumor onset and maintained the lymphoma and sarcoma spectrum. Consistent with the negligible role of Ink4a/Arf in the telomere checkpoint response in vivo, late-generation mTerc-/- Ink4a/Arf-/- tissues show activated p53, and derivative tumor cell lines sustain frequent loss of p53 function, whereas all early generation mTerc Ink4a/Arf-/- tumor cell lines remain intact for p53. In addition, the late-generation mTerc-/- Ink4a/Arf-/- tumors showed activation of the alternative lengthening of telomere mechanism, underscoring the need for adaptation to the presence of telomere dysfunction in the absence of p16(Ink4a) and p19(Arf). These observations highlight the importance of genetic context in dictating whether telomere dysfunction promotes or suppresses age-related degenerative conditions as well as the rate of initiation and type of spontaneous cancers.
An Enterprise Intelligent System Development and Solution Framework (2007)

The recent trend has been using hybrid approach rather than using a single intelligent technique to solve the problems. In this paper, we describe and discuss a framework to develop enterprise solutions that are backed by intelligent techniques. The framework not only uses intelligent techniques themselves but it is a complete environment that includes various interfaces and components to develop the intelligent solutions. The framework is completely Web-based and uses XML extensively. It can work like shared plat-form to be accessed by multiple developers, users and decision makers.
Designer Dendrimers:  Branched Oligosulfonimides with Controllable Molecular Architectures (2006)

The synthesis of “designer” dendrimers and dendrons with sulfonimide units at every branching point is reported. The synthesis is based on a series of (regio)selective functionalization reactions of amines and sulfonamides allowing precise control of the dendrimers' shape, the number of branches in each generation, and their peripheral decoration with functional groups. In principle, structurally different branches can be incorporated at any position within the dendrimer structure at will. Structurally perfect symmetrical and two-faced “Janus”-type dendrimers, as well as dendrimers and dendrons with intended interstices were synthesized on a preparative scale and fully characterized. Oligosulfonimide dendrons of various generations bearing an aryl bromide functional group at their focal points were attached to a p-phenylene core with the aid of Suzuki cross-coupling reactions resulting in dendrimers with photoactive terphenyl cores. The structure and the high purity of all dendritic sulfonimides were confirmed by means of 1H and 13C NMR, electrospray ionization mass spectrometry (ESI-MS), and elemental analysis. The utility of MALDI-TOF mass spectrometry for the analytical characterization of these dendrimers was evaluated in comparison to electrospray ionization. Two model branched oligosulfonimides were characterized in the solid state by single-crystal X-ray analysis. Reaction selectivities and conformation of sulfonimide branching points were rationalized by DFT calculations.
Interleukin 2 and lymphokine-activated killer cell therapy: analysis of a bolus interleukin 2 and a continuous infusion interleukin 2 regimen. (1990)

Several groups have described the efficacy of interleukin 2 (IL-2) plus lymphokine-activated killer (LAK) cells in the treatment of cancer patients with significant response rates noted in patients with renal cell cancer and malignant melanoma; however, the optimum regimen remains undefined. The Biological Response Modifiers Program of the National Cancer Institute conducted two consecutive Phase I/II studies evaluating the toxicity and clinical efficacy of different methods of IL-2 and LAK cell therapy. In the first trial, we modified the standard Rosenberg regimen by decreasing the duration of priming in an attempt to reduce the toxicity related to this phase of the therapy and thereby administer more IL-2 doses with the LAK cells. In the second trial, we used a continuous i.v. infusion IL-2 regimen and altered both the leukapheresis procedure and the LAK cell culture techniques based on our in vitro and preclinical studies suggesting that 2-day LAK cells were superior. Thirty cancer patients received i.v. bolus IL-2 at 100,000 units/kg every 8 h for 3 days during priming and for 5 days during LAK cell administration. A second group of 22 cancer patients received IL-2 by continuous i.v. infusion at 3 x 10(6) units/m2 for 5 days during priming and an additional 5 days of IL-2 with the LAK cell phase of the treatment. The timing of the start of the leukapheresis procedures, their duration and number, and the LAK cell culture techniques differed in the two trials. Overall, 52 patients with various cancers were treated. The toxicities associated with each regimen were similar to those seen in other IL-2 plus LAK cell trials. Four patients (one each with melanoma and diffuse large cell lymphoma and two with renal cell cancer) exhibited partial responses lasting 2, 4, 10, and 15+ mo. Serial tumor biopsies from treated patients demonstrated that therapy can produce a marked mononuclear cell infiltrate and an increase in HLA-DR expression on tumor cells. There was no difference in the overall response rate between the two regimens, but toxicity was less with continuous i.v. infusion IL-2. The 5-day continuous i.v. infusion regimen resulted in significantly higher rebound lymphocytosis, cell yield from leukapheresis, and number of LAK cells harvested from culture.
Load Forecasting via Deep Neural Networks (2017)

Nowadays, electricity plays a vital role in national economic and social development. Accurate load forecasting can help power companies to secure electricity supply and scheduling and reduce wastes since electricity is difficult to store. In this paper, we propose a novel Deep Neural Network architecture for short term load forecasting. We integrate multiple types of input features by using appropriate neural network components to process each of them. We use Convolutional Neural Network components to extract rich features from historical load sequence and use Recurrent Components to model the implicit dynamics. In addition, we use Dense layers to transform other types of features. Experimental results on a large data set containing hourly loads of a North China city show the superiority of our method. Moreover, the proposed method is quite flexible and can be applied to other time series prediction tasks.
Comparing Graph Representations of Protein Structure for Mining Family-Specific Residue-Based Packing Motifs (2005)

We find recurring amino-acid residue packing patterns, or spatial motifs, that are characteristic of protein structural families, by applying a novel frequent subgraph mining algorithm to graph representations of protein three-dimensional structure. Graph nodes represent amino acids, and edges are chosen in one of three ways: first, using a threshold for contact distance between residues; second, using Delaunay tessellation; and third, using the recently developed almost-Delaunay edges. For a set of graphs representing a protein family from the Structural Classification of Proteins (SCOP) database, subgraph mining typically identi- fies several hundred common subgraphs corresponding to spatial motifs that are frequently found in proteins in the family but rarely found outside of it. We find that some of the large motifs map onto known functional regions in two protein families explored in this study, i.e., serine proteases and kinases. We find that graphs based on almost-Delaunay edges significantly reduce the number of edges in the graph representation and hence present computational advantage, yet the patterns extracted from such graphs have a biological interpretation approximately equivalent to that of those extracted from distance based graphs.
Comparative Genomic Analysis of N2-Fixing and Non-N2-Fixing Paenibacillus spp.: Organization, Evolution and Expression of the Nitrogen Fixation Genes (2014)

We provide here a comparative genome analysis of 31 strains within the genus Paenibacillus including 11 new genomic sequences of N2-fixing strains. The heterogeneity of the 31 genomes (15 N2-fixing and 16 non-N2-fixing Paenibacillus strains) was reflected in the large size of the shell genome, which makes up approximately 65.2% of the genes in pan genome. Large numbers of transposable elements might be related to the heterogeneity. We discovered that a minimal and compact nif cluster comprising nine genes nifB, nifH, nifD, nifK, nifE, nifN, nifX, hesA and nifV encoding Mo-nitrogenase is conserved in the 15 N2-fixing strains. The nif cluster is under control of a σ(70)-depedent promoter and possesses a GlnR/TnrA-binding site in the promoter. Suf system encoding [Fe-S] cluster is highly conserved in N2-fixing and non-N2-fixing strains. Furthermore, we demonstrate that the nif cluster enabled Escherichia coli JM109 to fix nitrogen. Phylogeny of the concatenated NifHDK sequences indicates that Paenibacillus and Frankia are sister groups. Phylogeny of the concatenated 275 single-copy core genes suggests that the ancestral Paenibacillus did not fix nitrogen. The N2-fixing Paenibacillus strains were generated by acquiring the nif cluster via horizontal gene transfer (HGT) from a source related to Frankia. During the history of evolution, the nif cluster was lost, producing some non-N2-fixing strains, and vnf encoding V-nitrogenase or anf encoding Fe-nitrogenase was acquired, causing further diversification of some strains. In addition, some N2-fixing strains have additional nif and nif-like genes which may result from gene duplications. The evolution of nitrogen fixation in Paenibacillus involves a mix of gain, loss, HGT and duplication of nif/anf/vnf genes. This study not only reveals the organization and distribution of nitrogen fixation genes in Paenibacillus, but also provides insight into the complex evolutionary history of nitrogen fixation.
Transforming Growth Factor β (TGF-β)-Smad Target Gene Protein Tyrosine Phosphatase Receptor Type Kappa Is Required for TGF-β Function (2005)

Transforming growth factor beta (TGF-beta) inhibits proliferation and promotes cell migration. In TGF-beta-treated MCF10A mammary epithelial cells overexpressing HER2 and by chromatin immunoprecipitation, we identified novel Smad targets including protein tyrosine phosphatase receptor type kappa (PTPRK). TGF-beta up-regulated PTPRK mRNA and RPTPkappa (receptor type protein tyrosine phosphatase kappa, the protein product encoded by the PTPRK gene) protein in tumor and nontumor mammary cells; HER2 overexpression down-regulated its expression. RNA interference (RNAi) of PTPRK accelerated cell cycle progression, enhanced response to epidermal growth factor (EGF), and abrogated TGF-beta-mediated antimitogenesis. Endogenous RPTPkappa associated with EGF receptor and HER2, resulting in suppression of basal and ErbB ligand-induced proliferation and receptor phosphorylation. In MCF10A/HER2 cells, TGF-beta enhanced cell motility, FAK phosphorylation, F-actin assembly, and focal adhesion formation and inhibited RhoA activity. These responses were abolished when RPTPkappa was eliminated by RNA interference (RNAi). In cells expressing RPTPkappa RNAi, phosphorylation of Src at Tyr527 was increased and (activating) phosphorylation of Src at Tyr416 was reduced. These data suggest that (i) RPTPkappa positively regulates Src; (ii) HER2 signaling and TGF-beta-induced RPTPkappa converge at Src, providing an adequate input for activation of FAK and increased cell motility and adhesion; and (iii) RPTPkappa is required for both the antiproliferative and the promigratory effects of TGF-beta.