gebhart/patrepeval huggingface dataset:
Posttranscriptional regulation of p21WAF1/CIP1 expression in human breast carcinoma cells. (1996)

p21WAF1/CIP1 plays a major role in the induction of G1 arrest following DNA damage. Although p21WAF1/CIP1 expression is regulated by the tumor suppressor p53, induction of p21WAF1/CIP1 expression through p53-independent pathways has been described in numerous cell types. In this report, we describe the mechanism by which the retinoid 6-[3-(1-adamantyl)-4-hydroxyphenyl]-2-naphthalene carboxylic acid (CD437) induces p21WAF1/CIP1 in breast carcinoma cells possessing either a wild-type (MCF-7 cells) or mutated (MDA-MB-468 cells) p53. Exposure of MDA-MB-468 cells to this retinoid results in an approximately 10-fold increase in p21WAF1/CIP1 mRNA levels, whereas less than a 2-fold increase in p21WAF1/CIP1 gene transcription was observed as indicated by transient transfection experiments utilizing a p21WAF1/CIP1 promoter firefly luciferase reporter gene construct and nuclear run-off studies. We found similar results in the MCF-7 cells (Z-M. Shao et al., Oncogene, 11: 493-504, 1995). We have now found that while enhancing p21WAF1/CIP1 gene transcription minimally, this retinoid increases p21WAF1/CIP1 mRNA stability by 3-fold in both cell types. We also demonstrate that approximately 1.5 kb of the 3' untranslated region causes enhanced instability of p21WAF1/CIP1 mRNA. The retinoid-dependent increase in p21WAF1/CIP1 mRNA stability is accompanied by an increase in p21WAF1/CIP1 protein expression, as indicated by Western blot experiments utilizing anti-p21WAF1/CIP1 monoclonal antibody. This increase in p21WAF1/CIP1 is subsequently followed by the onset of programmed cell death in both cell types. Thus, CD437 is a novel retinoid which enhances p21WAF1/CIP1 mRNA levels through stabilization of the message regardless of the p53 status of the cell.
Mannose-Based Molecular Patterns on Stealth Microspheres for Receptor-Specific Targeting of Human Antigen-Presenting Cells (2008)

The targeting of antigen-presenting cells has recently gained strong attention for both targeted vaccine delivery and immunomodulation. We prepared surface-modified stealth microspheres that display various mannose-based ligands at graded ligand densities to target phagocytic C-type lectin receptors (CLRs) on human dendritic cells (DCs) and macrophages. Decoration of microspheres with carbohydrate ligands was achieved (i) by electrostatic surface assembly of mannan onto previously formed adlayers of poly( l-lysine) (PLL) or a mix of PLL and poly( l-lysine)- graft-poly(ethylene glycol) (PLL-PEG), or (ii) through assembly of PLL-PEG equipped with small substructure mannoside ligands, such as mono- and trimannose, as terminal substitution of the PEG chains. Microspheres carrying mannoside ligands were also studied in combination with an integrin-targeting RGD peptide ligand. Because of the presence of a mannan or PEG corona, such microspheres were protected against protein adsorption and opsonization, thus allowing the formation of specific ligand-receptor interactions. Mannoside density was the major factor for the phagocytosis of mannoside-decorated microspheres, although with limited efficiency. This strengthens the recent hypothesis by other authors that the mannose receptor (MR) only acts as a phagocytic receptor when in conjunction with yet unidentified partner receptor(s). Analysis of DC surface markers for maturation revealed that neither surface-assembled mannan nor mannoside-modified surfaces on the microspheres could stimulate DC maturation. Thus, phagocytosis upon recognition by CLRs alone cannot trigger DC activation toward a T helper response. The microparticulate platform established in this work represents a promising tool for systematic investigations of specific ligand-receptor interactions upon phagocytosis, including the screening for potential ligands and ligand combinations in the context of vaccine delivery and immunomodulation.
&#x03BB;-path fragmentation and De-fragmentation through dynamic grooming (2005)

In multi-layer networks, where more than one layer is dynamic, i.e., connections are set up using not only the upper, e.g., IP layer but the underlying wavelength layer as well leads often to suboptimal performance. In this paper we discuss the lightpath fragmentation and de-fragmentation problem, where the lightpath system cannot follow the traffic changes fast enough. We show what it depends on, when is it critical and how much does it deteriorate the performance of the network.
Simplex Optimization Applied To Electrofusion Biotechnology (2005)

Electrofusion is a rapidly expanding field. The primary focus of our electrofusion work has been in the development of cell-tissue applications. Utilization of this technology will be enhanced by the optimization of fusion parameters. Therefore, this study was initiated to develop a method that could be used to optimize electrofusion parameters. Our main interest is the optimization of cell-tissue electrofusion. However, we first applied the simplex optimization scheme to a cell-cell electrofusion system. A cell-cell system was chosen to focus on procedure development without the additional variables associated with biological tissue.
Figure S5 from LAMC2 Regulates Key Transcriptional and Targetable Effectors to Support Pancreatic Cancer Growth (2023)

&lt;p&gt;Suppl. Figure 5. A. RNA expression of KRAS, AREG, DUSP6 and FOSL1 in PATU8902 and HPAFII cells expressing a TET-inducible KRAS shRNA or a control shRNA. B. Box and whiskers plot showing Mean Fluorescence Intensity (MFI) of Areg, Dusp6, Fosl1 upon KRas inactivation in iKRAS GEM. Error bars correspond to s.d. C. Heat map of downregulated genes in HPAFII cells expressing a tet-inducible LAMC2 shRNA compared to control group (shRNA GFP). D. LAMC2 and FOSL1 mRNA expression in PATU8902 and HPAFII cells expressing a tet-inducible LAMC2 shRNA or a control shRNA. Error bars correspond to s.d. E. mRNA expression of overlapping LAMC2 and FOSL1 downregulated genes (LAMC2 -ctrl-, FGFBP1, HMGA1, AURKA, HMMR, PLK1, SNAI2 and PITPNC1) in PATU8902 and HPAFII cells expressing a TET-inducible LAMC2 shRNA or a control shRNA. F. Protein expression of phospho-ERK, ERK. Phospho-EGFR, EGFR in PATU8902 and HPAFII cells expressing a TETinducible LAMC2 shRNAs or a control shRNA. Quantification: pEGFR levels normalized to total EGFR levels and housekeeping protein levels. G. Fosl1 and AXL protein expression in PATU8902 and HPAFII cells treated with AKTi (10μM) and vehicle control. Quantification: AXL and FOSL1 levels normalized to housekeeping protein levels.&lt;/p&gt;
Bcl-2 blocks degranulation but not fas-based cell-mediated cytotoxicity. (1995)

The ability of bcl-2 in target cells to block cell-mediated cytotoxicity by allospecific CTL was tested. The blocking effect was variable. Because killing by CTL involves two different pathways, degranulation (perforin plus granzymes) and fas, we examined the effect of bcl-2 on these pathways independently. Bcl-2 in target cells blocked apoptotic cell death induced either by cytotoxic granule extracts or by CTL killing under conditions in which the fas pathway is blocked. On the other hand, bcl-2 had no effect on target cell-killing either by Fas-specific mAb or by CTL capable of killing only via the fas pathway. These data suggest bcl-2 may block apoptotic lysis induced by perforin plus granzymes, but not apoptotic lysis induced via the fas pathway. Thus, any analysis of the effect of bcl-2 on apoptotic cell death in target cells killed by CTL must take into account the relative contributions of the degranulation vs fas pathways.
Performance evaluation of adaptive beamforming in 5G-V2X networks (2017)

Vehicles are the third fastest growing connected device type after smart phones and tablets. Also, automotive industry is interested to get more vehicles connected to the internet to improve traffic safety and efficiency. This creates a need for Vehicle-to-Everything (V2X) communications. In this work, the possibility of exploiting beamforming in LTE-V2X is considered. Singular value decomposition (SVD) receiver and precoder is implemented in an LTE-A system level simulator and the performance on multi-lane highway scenario is simulated and analyzed in downlink Vehicle-to-Infrastructure (V2I) scenario. The performance is compared to the conventional maximum-ratio combining (MRC) and LTE codebook precoded minimum mean square error (MMSE) receivers. In addition, the switched-beam beamforming is imitated by modified antenna patterns with 7 and 15 narrow beams. The results show that the SVD receiver provides gain compared to the conventional MRC and MMSE receivers in ideal scenario. Furthermore, with modified antenna patterns, the performance was enhanced when compared to the default antenna pattern.
A Framework for Thermal Spray Shape Deposition: The MD* System (2018)

This paper present.s t.he framework for a solid-freeform-fabrication syst.em based on thermal spray&#13;\nshape deposition t.o build mult.i-mat.erial st.ruct.ures by incremen tal build-up of t.hin cross-sect.ional layers.&#13;\nThe basis of theMD* System (recursively, Mask and Deposit.) is to spray each layer using disposable&#13;\nmasks to shape each layer. A thermal spray approach has the potential to build dense parts with&#13;\ndesirable mechanical properties. Metal. ceramic, plastic, laminate, and composite structures can be&#13;\ndeposited. Since l11asking enables selective deposition wit.hin a layer, complet.e assemblies composed of&#13;\ndifferent mat.erials can be creat.ed in a single process. For example, int.egrated electronic/mechanical&#13;\nstructures are feasible.
Asymmetries in the Control of Saccadic Eye Movements to Bifurcating Targets (1987)

Abstract : The task of responding to one of two simultaneously presented targets often reveals unexpected yet profound preferences in the direction of saccadic eye movements. In the present investigation, a simple experimental paradigm was used in which a single point of light bifurcates symmetrically to the left and right of the fixation point. Under these conditions, most subjects show an eye movement response preference to either the left or right. The present data show that this preference can be eliminated by delaying the onset of the target, presented in the preferred direction, by about 40 milliseconds. This indicates that in the sequence of events occurring prior to the execution of a saccade, a window of time of this duration is allocated for decisions concerning direction, of response even when targets are presented to both visual hemifields. It was also found that the bifurcating targets interact to significantly increase response latencies in both the preferred and nonpreferred directions. Further, the interaction is asymmetrical, in that a target presented in the preferred direction has a greater effect that a target in the nonpreferred direction on responses in the counter direction. The results suggest an asymmetry in hemispheric interaction that has not previously been demonstrated in the visual-oculomotor system. Keywords: Target detection; target discrimination.
Human Inter-Individual DNA Sequence Variation in Candidate Genes, Drug Targets, the Importance of Haplotypes and Pharmacogenomics (2003)

The identification of genes predisposing to human diseases is of paramount importance for understanding the molecular basis of the disease and individually different drug response, and will establish new routes to diagnosis and therapeutic advances of immense medical benefit. A key step common to all strategies for disease gene identification is the systematic analysis of candidate gene sequences to identify specific sequence variations associated with disease or any other phenotype of pharmaceutical relevance. In this article, current concepts and approaches to haplotype-based candidate gene analysis are reviewed. Moreover, a comprehensive summary of recent studies and data on the amount, nature, pattern and structure of genetic variation in candidate genes is given. These data demonstrate altogether remarkable gene sequence and haplotype diversity. Numerous individually different forms of a gene may exist. This presents challenges to the traditional views of the concept of "a" gene with far-reaching implications on the functional analysis of candidate gene variation, on the establishment of "sequence"-"structure"-"function" and complex haplotype/genotype-phenotype relationships, on the identification, evaluation and prioritization of drug targets and the concept of a "personalized medicine" in general. Moreover, present and future approaches to the identification of candidate and disease genes will be addressed. These include whole genome-based approaches such as integrative genomics as well as functional genomics-based approaches to analyze and model complex biological and medical processes. The analysis of whole complex systems in particular will provide the basis to make "maximally informed" guesses on candidate genes and address complex variability patterns in genes as well as complex genotype-phenotype relationships comprehensively at an advanced level.
Seeking the Ultimate Nanolaser (2006)

Deep reinforcement learning empowers automated inverse design and optimization of photonic crystals for nanoscale laser cavities,
Temporal and spatial oversampling in direct sequence CDMA systems: A linear algebra approach (2003)

In this work we present a unified analysis of the capacity and performance gains attainable by oversampling at the receiver in the temporal and spatial domains under multiple transmit antennas through a linear algebra approach. We quantify the increase in dimensionality gain beyond the spreading factor and illustrate the increase in system performance.
Role of myocyte enhancing factor 2B in epithelial myofibroblast transition of human gingival keratinocytes (2012)

It has recently emerged that the myogenic contribution of the epithelial mesenchymal transition plays a role in neoplastic invasion and metastasis. Myocyte enhancing factor 2B (MEF2B) is the only MEF2 isoform expressed during early embryonic development, and is herein proposed to transactivate the downstream target proteins of the epithelial myofibroblast transition (EMyT). We have previously generated eight preneoplastic cell lines with spindle and cobblestone morphology from human gingival mucosal keratinocytes immortalized by E6/E7 of human papillomavirus type 16. Spindle cells formed tubulogenic morphogenesis on Matrigel and exhibited contractility, anchorage-independent growth and invasiveness to a greater extent than cobblestone cells. Expression of MEF2B mRNA and myofibroblast proteins was higher in spindle cells compared with cobblestone cells. Epidermal growth factor (EGF) treatment of cobblestone cells also induced expression of these genes. Knockdown of MEF2B in a cobblestone cell line abolished EGF-induced upregulation of MEF2, vimentin and non-muscle caldesmon proteins, but enhanced basal expression of mesenchymal vimentin and fibronectin. Differential regulation of intermediate filaments revealed an unrecognized role of MEF2B in myogenic transformation of the epithelial to a myofibroblast phenotype, which occurs as epithelioid variants in some soft tissue sarcomas.
A micro-rover navigation and control system for autonomous planetary exploration (2004)

This paper describes an end-to-end control system for autonomous navigation of a small vehicle at a remote place, e.g. in space for planetary exploration. Due to a realistic background of this study the proposed method has to deal with limited knowledge about the environment as well as limited system resources and operational boundary conditions, especially a very large time delay in the communication between the ground control station and the space segment. To overcome these constraints the remote system has to act in a very autonomous way. Ground support minimizes the computational load of the remote system. High-level information interchange reduces the communication bandwidth requirements.
English Pig Farmers’ Knowledge and Behaviour towards African Swine Fever Suspicion and Reporting (2016)

African swine fever (ASF) is a notifiable, virulent swine disease, and is a major threat to animal health and trade for many European Union (EU) countries. Early detection of the introduction of ASF virus is of paramount importance to be able to limit the potential extent of outbreaks. However, the timely and accurate reporting of ASF primary cases strongly depends on how familiar pig farmers are with the clinical signs, and their motivation to report the disease. Here, an online questionnaire survey was conducted between December 2014 and April 2015 to investigate English pig farmers' knowledge and behaviour towards ASF in terms of clinical suspicion and reporting. Multivariable logistic regression analysis was used to identify factors influencing the two variables of interest: 1) farmers who "would immediately suspect ASF" if they observed clinical signs of fever, lethargy, reduced eating and high mortality on their farm and 2) farmers who "would immediately report ASF" if they suspected ASF on their farm. The questionnaire was completed by 109 pig farmers. Results indicate that pig farmers having poor knowledge about ASF clinical signs and limited concern about ASF compared with other pig diseases are less likely to consider the possibility of an outbreak of ASF on their farm. In addition, pig farmers lacking awareness of outbreaks in other countries, having a perception of the negative impact on them resulting from false positive reporting and the perceived complexity of reporting procedures are less likely to report an ASF suspicion. These findings indicate important areas for educational campaigns targeted at English pig farmers to focus on in an attempt to increase the likelihood of a rapid response in the event of an ASF outbreak.
Profibrotic properties of C1q+ interstitial macrophages in silica-induced pulmonary fibrosis in mice (2022)

Pulmonary fibrosis (PF) is a progressive fibrotic disease with poor prognosis and suboptimal therapeutic options. Although macrophages have been implicated in PF, the role of macrophage subsets, particularly interstitial macrophages (IMs), remains unknown. We performed a time-series single-cell RNA sequencing analysis of the silica-induced mouse PF model. Among the macrophage subsets in fibrotic lungs, Lyve1<sup>lo</sup> MHC II<sup>hi</sup> IMs increased with fibrosis, and highly expressed profibrotic genes. Additionally, we identified C1q as an IM-specific marker. Experiments with C1q-diphtheria toxin receptor-GFP knock-in (C1qKI) mice revealed that IMs are distributed around fibrotic nodules. Depletion of C1q<sup>+</sup> IMs in C1qKI mice decreased activated fibroblasts and epithelial cells; however, bodyweight loss and neutrophil infiltration were exacerbated in silica-induced PF. Collectively, these results suggest that IMs have profibrotic and anti-inflammatory properties and that the selective inhibition of the profibrotic function of IMs without compromising their anti-inflammatory effects is a potential novel therapeutic strategy for PF.
Correlation Between the Frequency of Painful Crises in Sickle Cell Anemia and the Biomarkers of Inflammation, Endothelial Dysfunction, Coagulation Activation and Bone Metabolism (2017)

Objective: Sickle cell anemia is a widespread inherited hemolytic anemia, characterized by chronic hemolysis, infections, recurrent occlusion of the microcirculation and painful crises. In this cross-sectional study, we investigated the correlation between biomarkers of inflammation, endothelial dysfunction, coagulation activation and bone metabolism, with the frequency of painful crisis in sickle cell anemia adult patients, to understand the potential role of these biomarkers in the management of sickle cell anemia.&#x0D; Methods: Sixty-three sickle cell anemia patients were enrolled in this study. They were divided into three groups based on the frequency of pain crises to mildly, moderately, and severely affected. Twenty-five healthy volunteers were enrolled as controls. Plasma levels of different biomarkers were tested, including tumor necrosis factor alpha, soluble intercellular adhesion molecule-1, D-dimer, sclerostin, and nitric oxide.&#x0D; Results: Tumor necrosis factor alpha, soluble intercellular adhesion molecule-1, and D-Dimer plasma levels were significantly higher in sickle cell anemia patients when compared to the controls, while nitric oxide levels were notably lower in the patients' group. Sickle cell anemia patients with severe pain showed higher tumor necrosis factor alpha, soluble intercellular adhesion molecule-1 and D-dimer levels than those mildly and moderately affected with painful crisis. Positive correlations were observed between all measured biomarkers and the frequency of the painful crisis, except for nitric oxide, which showed a negative correlation.&#x0D; Conclusion: Tumor necrosis factor alpha, soluble intercellular adhesion molecule-1, nitric oxide, and D-dimer can be used to assess sickle cell anemia severity and prognosis, and thus may affect determining appropriate management strategies.
Further characterization of a protein kinase from foot-and-mouth disease virus (1982)

Acid disruption of foot-and-mouth disease virus released a protein kinase activity that sedimented at less than 7S. This enzyme was separated into three peaks of activity by ion-exchange and hydroxylapatite chromatography. Analysis of the various enzyme fractions by polyacrylamide gel electrophoresis and silver staining revealed that one of the fractions lacked the major virion structural proteins, but still contained two or three other polypeptides. This enzyme phosphorylated mainly one protein (P17) in an in vitro assay.
Interface magnetism and superparamagnetism of Co/Cu multilayers (1993)

The magnetic properties of Co/Cu multilayers were investigated from 5 to 380 K and analyzed in terms of the interface magnetism and mean-field model. The interface, which is about 1.2 Å thick, is nonmagnetic at room temperature and becomes magnetic at 5 K with the average magnetization of 40% of the pure Co magnetization. The samples of X Å Co/10 Å Cu behaved superparamagnetically as X ranged from 4 to 6.5 Å and did not show superparamagnetic behavior for thinner or thicker Co layer thickness.
Multi-scale description of the electronic transport within the hierarchical architecture of a composite electrode for lithium battery (2009)

ID = 421
Inhibition of adenosine deaminase by deaza derivatives of adenosine and purine riboside. (1983)

Deaza analogs of adenosine, where carbon substitutes for nitrogen, are not substrates for adenosine deaminase (adenosine aminohydrolase EC 3.5.4.4); little is reported on their ability to be inhibitors. Among the deaza analogs of adenosine and purine riboside that we have been testing, 1-deazaadenosine proved to be the best inhibitor (Ki = 6.6 X 10(-7)M). 1-deazapurine riboside, 1,3-dedeazadenosine, 3-deazaadenosine have affinity by about two and three order of magnitude lower.