gebhart/patrepeval huggingface dataset:
Systemic Overexpression of Angiopoietin-2 Promotes Tumor Microvessel Regression and Inhibits Angiogenesis and Tumor Growth (2007)

Angiopoietin-2 (Ang-2) is a conditional antagonist and agonist for the endothelium-specific Tie-2 receptor. Although endogenous Ang-2 cooperates with vascular endothelial growth factor (VEGF) to protect tumor endothelial cells, the effect on tumor vasculature of high levels of exogenous Ang-2 with different levels of VEGF has not been studied in detail. Here, we report that systemic overexpression of Ang-2 leads to unexpected massive tumor vessel regression within 24 h, even without concomitant inhibition of VEGF. By impairing pericyte coverage of the tumor vasculature, Ang-2 destabilizes the tumor vascular bed while improving perfusion in surviving tumor vessels. Ang-2 overexpression transiently exacerbates tumor hypoxia without affecting ATP levels. Although sustained systemic Ang-2 overexpression does not affect tumor hypoxia and proliferation, it significantly inhibits tumor angiogenesis, promotes tumor apoptosis, and suppresses tumor growth. The similar antitumoral, antiangiogenic efficacy of systemic overexpression of Ang-2, soluble VEGF receptor-1, and the combination of both suggests that concomitant VEGF inhibition is not required for Ang-2-induced tumor vessel regression and growth delay. This study shows the important roles of Ang-2-induced pericyte dropout during tumor vessel regression. It also reveals that elevated Ang-2 levels have profound pleiotropic effects on tumor vessel structure, perfusion, oxygenation, and apoptosis.
Using simulation to test the robustness of various existing production control policies (1991)

Compares four production control policies in terms of their robustness against random disturbances such as machine failures and demand fluctuations. A simulation model based on a VLSI wafer fabrication facility is used to test the performance of the policies. Several criteria, including average total WIP (work-in-progress), average backlog, and a cost function that is a combination of the first two criteria, are used to measure the performance. >
3D printing for microwave: Materials characterization and application in the field of absorbers (2015)

In this study, the microwave properties of a wide range of materials, formed by two types of additive technologies (stereolithography apparatus and fused deposition modeling) were extracted in the X-band (8-12 GHz). ABS filled with carbon was chosen to realize a demonstrator. This high loss material was shaped in the form of a pyramid by 3D printing technology. By introducing it into a short-circuited waveguide, a matched load covering the whole X-band was realized (return loss <; -30 dB). The flexibility of these techniques and the availability of low cost commercial materials suggest many potential applications in the microwave range.
An Enhanced Memetic Differential Evolution in Filter Design for Defect Detection in Paper Production (2008)

This article proposes an Enhanced Memetic Differential Evolution (EMDE) for designing digital filters which aim at detecting defects of the paper produced during an industrial process. Defect detection is handled by means of two Gabor filters and their design is performed by the EMDE. The EMDE is a novel adaptive evolutionary algorithm which combines the powerful explorative features of Differential Evolution with the exploitative features of three local search algorithms employing different pivot rules and neighborhood generating functions. These local search algorithms are the Hooke Jeeves Algorithm, a Stochastic Local Search, and Simulated Annealing. The local search algorithms are adaptively coordinated by means of a control parameter that measures fitness distribution among individuals of the population and a novel probabilistic scheme. Numerical results confirm that Differential Evolution is an efficient evolutionary framework for the image processing problem under investigation and show that the EMDE performs well. As a matter of fact, the application of the EMDE leads to a design of an efficiently tailored filter. A comparison with various popular metaheuristics proves the effectiveness of the EMDE in terms of convergence speed, stagnation prevention, and capability in detecting solutions having high performance.
Helping mobile software code reviewers (2016)

Mobile Developers commonly spend a significant amount of time and effort on conducting code reviews on newly introduced and domain-specific practices, such as platform-specific feature addition, quality of service anti-pattern refactorings, and battery-related bug fixes. To address these problems, we conducted a large empirical study over the software change history of 318 open source projects and investigated platform-dependent code changes from open source projects. Our analysis focuses on what types of changes mobile application developers typically make and how they perceive, recall, and communicate changed and affected code. Our study required the development of an automated strategy to examine open source repositories and categorize platform-related refactoring edits, bug repairs, and API updates, mining 1,961,990 commit changes. Our findings call for the need to develop a new recommendation system aimed at efficiently identifying required changes such as bug fixes and refactorings during mobile application code reviews.
A survey on software architecture analysis methods (2002)

The purpose of the architecture evaluation of a software system is to analyze the architecture to identify potential risks and to verify that the quality requirements have been addressed in the design. This survey shows the state of the research at this moment, in this domain, by presenting and discussing eight of the most representative architecture analysis methods. The selection of the studied methods tries to cover as many particular views of objective reflections as possible to be derived from the general goal. The role of the discussion is to offer guidelines related to the use of the most suitable method for an architecture assessment process. We will concentrate on discovering similarities and differences between these eight available methods by making classifications, comparisons and appropriateness studies.
A complete digital optics applied to digital holographic microscopy: application to chromatic aberration compensation (2007)

In optics, optical elements are used to transform, to filter or to process physical wavefronts in order to magnify images, compensate for aberration or to suppress unwanted diffracted order for example. Because digital holography provides numerical wavefronts, we developed a digital optics, involving numerical elements such as numerical lenses and pinholes, to mimic numerically what is usually done physically, with the advantage to be able to define any shape for these elements and to place them everywhere without obstruction problems. We demonstrate that automatic and non-automatic procedures allow diffracted order or parasitic interferences filtering, compensation for aberration and image distortion, and control of position and magnification of reconstructed wavefront. We apply this digital optics to compensate for chromatic aberration in multi-wavelength holography in order to have perfect superposition between wavefronts reconstructed from digital hologram recorded with different wavelengths. This has a great importance for synthetic wavelength digital holography or tomographic digital holography that use multiple wavelengths.
E7090, a Novel Selective Inhibitor of Fibroblast Growth Factor Receptors, Displays Potent Antitumor Activity and Prolongs Survival in Preclinical Models (2016)

The FGFR signaling pathway has a crucial role in proliferation, survival, and migration of cancer cells, tumor angiogenesis, and drug resistance. FGFR genetic abnormalities, such as gene fusion, mutation, and amplification, have been implicated in several types of cancer. Therefore, FGFRs are considered potential targets for cancer therapy. E7090 is an orally available and selective inhibitor of the tyrosine kinase activities of FGFR1, -2, and -3. In kinetic analyses of the interaction between E7090 and FGFR1 tyrosine kinase, E7090 associated more rapidly with FGFR1 than did the type II FGFR1 inhibitor ponatinib, and E7090 dissociated more slowly from FGFR1, with a relatively longer residence time, than did the type I FGFR1 inhibitor AZD4547, suggesting that its kinetics are more similar to the type V inhibitors, such as lenvatinib. E7090 showed selective antiproliferative activity against cancer cell lines harboring FGFR genetic abnormalities and decreased tumor size in a mouse xenograft model using cell lines with dysregulated FGFR Furthermore, E7090 administration significantly prolonged the survival of mice with metastasized tumors in the lung. Our results suggest that E7090 is a promising candidate as a therapeutic agent for the treatment of tumors harboring FGFR genetic abnormalities. It is currently being investigated in a phase I clinical trial. Mol Cancer Ther; 15(11); 2630-9. ©2016 AACR.
An ultra-large deformation bidirectional actuator based on a carbon nanotube/PDMS composite and a chitosan film (2019)

Actuating materials can convert external stimuli (humidity, light, electricity, etc.) into mechanical energy and realize multiple forms of movements. However, a majority of current actuating materials are driven by a single stimulus with a small degree of actuation and rough control which is unfavorable for practical applications. Here, a new type of bidirectional actuating material based on carbon nanotube/PDMS composites and chitosan films is proposed. Thanks to the robust mechanical support by PDMS, due to the ultra-large water capacity in between chitosan chains and strong near-infrared light absorption by carbon nanotube layers, the actuator can be driven by humidity and light for an ultra-large actuation curvature (3.91 cm<sup>-1</sup> in humidity actuation, 3.84 cm<sup>-1</sup> in light actuation). The well-established light power-curvature, relative humidity-curvature profiles and a fine mechanic modelling of the actuator show the possibility of controlling the actuator's bending. A lab application as a cargo-moving device preliminarily demonstrates a robust mechanical functionality of this actuator with a low body weight.
Development of layered Zn-Fe coatings for better corrosion protection (2010)

In this research, the Zn-Fe coating having successive layers of alloys of two different compositions were developed alternatively on mild steel for better corrosion protection. The multilayer coatings, or alternatively, composition modulated alloy (CMA) coatings of different configurations have been developed, and their corrosion behaviors were evaluated by electrochemical DC and AC methods. The cyclic cathode current densities and numbers of layers have been optimised for peak corrosion stability of the coatings. Under optimal condition, the CMA coating having 300 layers, having about 67 nm average thickness was found to be approximately six times higher corrosion resistant than monolayer coating of same thickness. The better corrosion resistance was attributed to the changed dielectric property, consequent to difference in phase structure of alloys in alternate layers, evidenced by dielectric spectroscopy and X-ray diffraction (XRD) study, respectively. Layers formation and corrosion mechanisms were examined using Scanning Electron Microscopy (SEM).
N-acetylcysteine inhibits germination of conidia and growth of Aspergillus spp. and Fusarium spp (1996)

N-Acetylcysteine inhibited hyphal growth and germination of conidia of Aspergillus spp. and Fusarium spp. N-Acetylcysteine inhibited conidial germination as well as or better than L-cysteine. Cysteine-related compounds may provide a potential therapeutic strategy against agriculturally and medically important fungal pathogens.
Imaging Induction of Cytoprotective Enzymes in Intact Human Cells: Coumberone, a Metabolic Reporter for Human AKR1C Enzymes Reveals Activation by Panaxytriol, an Active Component of Red Ginseng (2008)

We here present an optical method for monitoring the activity of the inducible aldo-keto reductases AKR1C2 and AKR1C3 in living human cells. The induction of these enzymes is regulated by the antioxidant response element (ARE), as demonstrated in recent literature, which in turn is dependent on the transcription factor Nrf2. The activation of ARE leads to the transcription of a coalition of cytoprotective enzymes and thus represents an important target for the development of new therapies in the area of neurodegenerative diseases and cancer. Through the use of Coumberone, a metabolic fluorogenic probe, and isoform-selective inhibitors, the upregulation of cellular stress markers AKR1C2 and AKR1C3 can be quantitatively measured in the presence of ARE activator compounds, via either a fluorimetric assay or fluorescence microscopy imaging of intact cells. The method has both high sensitivity and broad dynamic range, as demonstrated by induction studies in three cell lines with dramatically different metabolic capabilities (transfected monkey kidney COS-1 cells, human neuroblastoma IMR-32 cells, and human liver HepG2 cells). We applied the new method to examine a number of neurotrophic natural products (spirotenuipesine A, spirotenuipesine B, scabronine G-methylester, and panaxytriol), and discovered that panaxytriol, an active component of red ginseng extracts, is a potent ARE inducer. The upregulation of AKR1C enzymes, induced by chemically homogeneous panaxytriol, was partially dependent on PKC and PI3K kinases as demonstrated by the application of selective inhibitors. This cellular mechanism may account for panaxytriol's neurotrophic, neuroprotective, and anticancer properties. The protective effects of ARE inducers against tumorgenesis and neurodegeneration fuel the growing interest in this area of research and the method described here will greatly enable these endeavors.
Growth of InSb and InAs1−<i>x</i>Sb<i>x</i> on GaAs by molecular beam epitaxy (1988)

InSb and InAs1−xSbx epitaxial layers have been successfully grown on (100)GaAs substrates by molecular beam epitaxy. Remarkably good morphologies were obtained despite the large lattice mismatch (14%) between InSb and GaAs. Room-temperature electron mobilities as high as 57 000 cm2/V s were measured in InSb layers of about 5 μm thick with ND−NA∼1.6×1016 cm−3. The substrate temperature and Sb/In flux ratio were found to critically influence the quality of InSb epilayers. By employing dimeric instead of tetrameric sources, the composition of the InAs1−xSbx films was observed to be relatively independent of substrate temperature. Electron mobilities of 20 000 and 8800 cm2/V s, at 300 and 77 K, respectively, were obtained for a 1.6-μm-thick InAs1−xSbx (x=0.67) layer.
A Binary-Activation, Multi-Level Weight RNN and Training Algorithm for ADC-/DAC-Free and Noise-Resilient Processing-in-Memory Inference With eNVM (2023)

We propose a new algorithm for training neural networks with binary activations and multi-level weights, which enables efficient processing-in-memory circuits with embedded nonvolatile memories (eNVM). Binary activations obviate costly DACs and ADCs. Multi-level weights leverage multi-level eNVM cells. Compared to existing algorithms, our method not only works for feed-forward networks (e.g., fully-connected and convolutional), but also achieves higher accuracy and noise resilience for recurrent networks. In particular, we present an RNN-based trigger-word detection PIM accelerator, with detailed hardware noise models and circuit co-design techniques, and validate our algorithm's high inference accuracy and robustness against a variety of real hardware non-idealities.
CD47 Receptor Globally Regulates Metabolic Pathways That Control Resistance to Ionizing Radiation (2015)

Modulating tissue responses to stress is an important therapeutic objective. Oxidative and genotoxic stresses caused by ionizing radiation are detrimental to healthy tissues but beneficial for treatment of cancer. CD47 is a signaling receptor for thrombospondin-1 and an attractive therapeutic target because blocking CD47 signaling protects normal tissues while sensitizing tumors to ionizing radiation. Here we utilized a metabolomic approach to define molecular mechanisms underlying this radioprotective activity. CD47-deficient cells and cd47-null mice exhibited global advantages in preserving metabolite levels after irradiation. Metabolic pathways required for controlling oxidative stress and mediating DNA repair were enhanced. Some cellular energetics pathways differed basally in CD47-deficient cells, and the global declines in the glycolytic and tricarboxylic acid cycle metabolites characteristic of normal cell and tissue responses to irradiation were prevented in the absence of CD47. Thus, CD47 mediates signaling from the extracellular matrix that coordinately regulates basal metabolism and cytoprotective responses to radiation injury.
Dual role of the Smad4/DPC4 tumor suppressor in TGFβ-inducible transcriptional complexes (1997)

Upon ligand binding, the receptors of the TGFbeta family phosphorylate Smad proteins, which then move into the nucleus where they activate transcription. To carry out this function, the receptor-activated Smads 1 and 2 require association with the product of deleted in pancreatic carcinoma, locus 4 (DPC4), Smad4. We investigated the step at which Smad4 is required for transcriptional activation. Smad4 is not required for nuclear translocation of Smads 1 or 2, or for association of Smad2 with a DNA binding partner, the winged helix protein FAST-1. Receptor-activated Smad2 takes Smad4 into the nucleus where they form a complex with FAST-1 that requires these three components to activate transcription. Smad4 contributes two functions: Through its amino-terminal domain, Smad4 promotes binding of the Smad2/Smad4/FAST-1 complex to DNA; through its carboxy-terminal domain, Smad4 provides an activation function required for Smad1 or Smad2 to stimulate transcription. The dual function of Smad4 in transcriptional activation underscores its central role in TGFbeta signaling.
Entropy gives rise to topologically associating domains (2020)

We investigate chromosome organization within the nucleus using polymer models whose formulation is closely guided by experiments in live yeast cells. We employ bead-spring chromosome models together with loop formation within the chains and the presence of nuclear bodies to quantify the extent to which these mechanisms shape the topological landscape in the interphase nucleus. By investigating the genome as a dynamical system, we show that domains of high chromosomal interactions can arise solely from the polymeric nature of the chromosome arms due to entropic interactions and nuclear confinement. In this view, the role of bio-chemical related processes is to modulate and extend the duration of the interacting domains.
Oncogenesis Following Delivery of a Nonprimate Lentiviral Gene Therapy Vector to Fetal and Neonatal Mice (2005)

Gene therapy by use of integrating vectors carrying therapeutic transgene sequences offers the potential for a permanent cure of genetic diseases by stable vector insertion into the patients' chromosomes. However, three cases of T cell lymphoproliferative disease have been identified almost 3 years after retrovirus gene therapy for X-linked severe combined immune deficiency. In two of these cases vector insertion into the LMO2 locus was implicated in leukemogenesis, demonstrating that a more profound understanding is required of the genetic and molecular effects imposed on the host by vector integration or transgene expression. In vivo models to test for retro- and lentiviral vector safety prior to clinical application are therefore needed. Here we present a high incidence of lentiviral vector-associated tumorigenesis following in utero and neonatal gene transfer in mice. This system may provide a highly sensitive model to investigate integrating vector safety prior to clinical application.
Zebrafish endoderm formation is regulated by combinatorial Nodal, FGF and BMP signalling (2006)

In the zebrafish embryo, the mesoderm and endoderm originate from common precursors and segregate during gastrulation by mechanisms that are largely unknown. Understanding how the signalling pathways that regulate endoderm and mesoderm formation interact is crucial to understanding how the germ layers are established. Here, we have analysed how the FGF and BMP pathways interact with Nodal signalling during the process of endoderm formation. We found that activation of the FGF/ERK pathway disrupts endoderm formation in the embryo and antagonizes the ability of an activated form of Tar/Acvr1b to induce endoderm at the animal pole. By contrast, inhibition of FGF signalling increases the number of endodermal precursors and potentiates the ability of Tar*/Acvr1b to induce endoderm at the animal pole. Using a pharmacological inhibitor of the FGF receptor, we show that reducing FGF signalling partially rescues the deficit of endoderm precursors in bon mutant embryos. Furthermore, we found that overexpression of BMPs compromises endoderm formation, suggesting that formation of endoderm precursors is negatively regulated by BMPs on the ventral side. We show that simultaneous inhibition of the FGF/Ras and BMP pathways results in a dramatic increase in the number of endoderm precursors. Taken together, these data strongly suggest that BMP and FGF-ERK pathways cooperate to restrict the number of endodermal progenitors induced in response to Nodal signalling. Finally, we investigated the molecular basis for the FGF-MAPK-dependent repression of endoderm formation. We found that FGF/ERK signalling causes phosphorylation of Casanova/Sox32, an important regulator of endoderm determination, and provide evidence that this phosphorylation attenuates its ability to induce sox17. These results identify a molecular mechanism whereby FGF attenuates Nodal-induced endodermal transcription factors and highlight a potential mechanism whereby mesoderm and endoderm fates could segregate from each other.
Reaction of vinyl sulphone with α-metallated nitriles (1981)

Vinyl sulphones (1) were subjected to nucleophilic addition by α-lithionitriles (2) and gave cyclized products, 3-oxothian 1,1-dioxides (3) or cyclopropane derivatives (4), in satisfactory yields according to the substituents on the reagents. The cyclopropanation reactions could be extended to the formation of cyclopropyl sulphides (12)–(16) in good yields.
Digital System, Evidence &#x00026; Forensics Issues in Correctional Environments (2010)

The correctional environment is one of the most controlled in the United States. Despite the regimented system that epitomizes correctional facilities, digital systems have entered that environment as contraband and data back channels subject to compromise that threaten control of institution and the effectiveness of incarceration for the incapacitation of offenders. We examined data on this issue and possible solutions.
Evidence that Ecotropic Murine Leukemia Virus Contamination in TZM-bl Cells Does Not Affect the Outcome of Neutralizing Antibody Assays with Human Immunodeficiency Virus Type 1 (2009)

The TZM-bl cell line that is commonly used to assess neutralizing antibodies against human immunodeficiency virus type 1 (HIV-1) was recently reported to be contaminated with an ecotropic murine leukemia virus (MLV) (Y. Takeuchi, M. O. McClure, and M. Pizzato, J. Virol. 82:12585-12588, 2008), raising questions about the validity of results obtained with this cell line. Here we confirm this observation and show that HIV-1 neutralization assays performed with a variety of serologic reagents in a similar cell line that does not harbor MLV yield results that are equivalent to those obtained in TZM-bl cells. We conclude that MLV contamination has no measurable effect on HIV-1 neutralization when TZM-bl cells are used as targets for infection.