gebhart/patrepeval huggingface dataset:
YAP orchestrates heterotypic endothelial cell communication via HGF/c-MET signaling in liver tumorigenesis (2020)

Abstract Next to cell autonomous mechanisms, the oncogene yes-associated protein (YAP) controls liver tumor initiation and progression via cell extrinsic functions creating a tumor-supporting environment. However, how YAP affects the microenvironment and in particular the vascular niche, which contributes to liver disease and hepatocarcinogenesis, is poorly understood. In this study, histo-morphological and molecular characterization of murine liver endothelial cells (ECs) populations and human single cell data revealed the presence of liver sinusoidal endothelial cells (LSECs) and capillary endothelial cells (CECs) in healthy liver tissue. In YAP S127A -induced tumorigenesis, a gradual replacement of LSECs by CECs was associated with dynamic changes in the expression of genes involved in EC subtype-specific paracrine communication. The formation of new potential communication hubs connecting CECs and LSECs included the hepatocyte growth factor (Hgf)/c-Met signaling pathway. In hepatocytes and tumor cells, YAP/ TEA domain transcription factor 4 (TEAD4)-dependent transcriptional induction of osteopontin (Opn) stimulated c-Met expression in ECs with CEC phenotype, which sensitized these cells to the pro-migratory effects of LSEC-derived Hgf. In human HCCs, the presence of a migration-associated tip-cell signature correlated with poor clinical outcome and the loss of LSEC marker gene expression. In addition, the replacement of LSECs by CECs with exclusive c-MET expression in a CEC subpopulation was confirmed at the single cell level. In summary, YAP-dependent changes of the liver vascular niche comprise the formation of heterologous communication hubs (e.g. the HGF/c-Met axis), in which tumor cell-derived factors modify the crosstalk between LSECs and CECs.
Figure S3 from LKB1-Dependent Regulation of TPI1 Creates a Divergent Metabolic Liability between Human and Mouse Lung Adenocarcinoma (2023)

&lt;p&gt;Figure S3. TPI1 phosphorylation regulates triose phosphate levels and metabolic flux.&lt;/p&gt;
Loss of surface and volume electrical conductivities in polymer compounds due to shear‐induced migration of conductive particles (2003)

Abstract The loss of surface and volume electrical conductivities of conductive polymer compounds as a result of shear‐induced migration of conductive filler particles is elucidated with the help of model equations by considering flow of uniformly mixed conductive polymer compounds through two‐dimensional channels, as in injection molding or extrusion of sheets and films. Matrix polymers of shear‐thinning nature and non‐colloidal conductive particles of spherical shape are considered. The effect of particle migration is found to be most severe in the case of compositions around the percolation threshold—an otherwise uniformly mixed conductive compound turns into an insulator because of migration of conductive particles from the surface to the bulk. In addition, the extent of migration of particles and consequently the loss of conductivity are found to be the greatest for Newtonian polymer matrices, where the gradients of shear stress are the highest. The extent of migration gradually reduces as the polymer becomes more shear‐thinning.
Respiratory Disorders Associated With Collagen Vascular Disease (2018)

This quick reference provides the latest information on the diagnosis and management of many common respiratory disorders seen in day-to-day practice, as well as a wide array of rarer pulmonary and sleep disorders. Content is presented in a concise, bulleted template featuring algorithms, tables, and figures that make it easy to find key information to aid in diagnosis and treatment.
Alkyne [3 + 2] Cycloadditions of Iodosydnones Toward Functionalized 1,3,5-Trisubstituted Pyrazoles (2009)

The cycloaddition of 4-iodosydnones with terminal alkynes proceeds with excellent regiocontrol to provide 5-iodo pyrazoles. These products participate smoothly in subsequent C-C and C-heteroatom bond forming processes.
Three-Dimensional Analysis of Thoracic Apical Sagittal Alignment in Adolescent Idiopathic Scoliosis (2009)

This 3D analysis of thoracic scoliosis demonstrated a consistent loss of kyphosis within the 5 thoracic apical vertebrae. The true apical sagittal profile was found to be overestimated by an average of 10 degrees as compared to the perceived alignment from standard lateral radiographs.
How sensitive is functional connectivity to electrode resampling on intracranial EEG? Implications for personalized network models in drug-resistant epilepsy (2019)

Abstract Focal epilepsy is a clinical condition arising from disordered brain networks. Network models hold promise to map these networks, localize seizure generators, and inform targeted interventions to control seizures. However, incomplete sampling of epileptic brain due to sparse placement of intracranial electrodes may profoundly affect model results. In this study, we evaluate the robustness of several published network measures applied to intracranial electrode recordings and propose an algorithm, using network resampling, to determine confidence in model results. We retrospectively subsampled intracranial EEG data from 28 patients who were implanted with grid, strip, and depth electrodes during evaluation for epilepsy surgery. We recalculated global and local network metrics after both randomly and systematically resampling subsets of intracranial EEG electrode contacts. We found that sensitivity to incomplete sampling varied significantly across network metrics, and that this sensitivity was independent of the distance of removed contacts from the seizure onset zone. We present an algorithm, using random resampling, to compute patient-specific confidence intervals for network localizations on both global and nodal network statistics. Our findings highlight the difference in robustness between commonly used network metrics and provide tools to assess confidence in intracranial network localization. We present these techniques as an important step toward assessing the accuracy of intracranial electrode implants and translating personalized network models of seizures into rigorous, quantitative approaches to invasive therapy.
Enhancing Dexterity in Robotic Manipulation via Hierarchical Contact Exploration (2023)

Planning robot dexterity is challenging due to the non-smoothness introduced by contacts, intricate fine motions, and ever-changing scenarios. We present a hierarchical planning framework for dexterous robotic manipulation (HiDex). This framework explores in-hand and extrinsic dexterity by leveraging contacts. It generates rigid-body motions and complex contact sequences. Our framework is based on Monte-Carlo Tree Search and has three levels: 1) planning object motions and environment contact modes; 2) planning robot contacts; 3) path evaluation and control optimization. This framework offers two main advantages. First, it allows efficient global reasoning over high-dimensional complex space created by contacts. It solves a diverse set of manipulation tasks that require dexterity, both intrinsic (using the fingers) and extrinsic (also using the environment), mostly in seconds. Second, our framework allows the incorporation of expert knowledge and customizable setups in task mechanics and models. It requires minor modifications to accommodate different scenarios and robots. Hence, it provides a flexible and generalizable solution for various manipulation tasks. As examples, we analyze the results on 7 hand configurations and 15 scenarios. We demonstrate 8 tasks on two robot platforms.
Stereoselectivity in Reactions of Metal Complexes. Part X. Kinetics and stereoselectivity of the inner‐sphere electron‐transfer reaction between [Co(bamap)H2O]+ (bamap = 2,6‐bis(3‐carboxy‐1,2‐dimethyl‐2‐azapropyl)pyridine) and optically active iron(II) complexes (1988)

Abstract The kinetics of the electron‐transfer reaction between racemic or optically active [Co(bamap)H 2 O] + and optically active Fe 2+ complexes of the three new pentadentate ligands bamap, alamp, and valmp has been investigated. All the reacting species show C 2 symmetry. With respect to aquo‐Fe 2+ , the reaction rate for the Fe 2+ complexes is enhanced by a factor of 10 4 to 10 5 , and the observed k ΔΛ / k ΛΛ ratio is 1.0, 1,9, and 1.2, respectively. In all cases where stereoselectivity is observed, the reaction is faster between the complexes of opposite absolute configuration ( ΔΛ or ΛΔ ) than between species with the same configuration ( ΛΛ or ΔΔ ). The stereoselectivity effects are discussed of the basis of the structure of the transition state and the interatomic distances between the two metal centers at the moment of electron transfer.
A machine-learning based bio-psycho-social model for the prediction of non-obstructive and obstructive coronary artery disease (2023)

NCT02737982.
Coastal Atlas Interoperability (2012)

This chapter defines the coastal web atlases interoperability problem, introduces interoperability standards, and describes the development of a semantic mediator prototype to provide a common access point to coastal data, maps and information from distributed coastal web atlases. The prototype showcases how ontologies and ontology mappings can be used to integrate different heterogeneous and autonomous atlases (or information systems), using international standards such as ISO-19139 for metadata encoding and the Open Geospatial Consortium’s Catalogue Service for the Web specification. Lessons learned from this prototype will help build regional atlases and improve decision support systems as part of a new International Coastal Atlas Network (ICAN).
Cuff electrodes for very small diameter nerves — Prototyping and first recordings in vivo (2014)

A fabrication method for cuff electrodes to interface small nerves was developed. Medical grade silicone rubber conforms the body of the cuff and insulation of the wires, platinum was used as metal for the embedded wiring and contacts. Planar electrode arrays where fabricated using a picosecond laser and then positioned into a carrying tube to provide the third dimension with the desired inner diameter (Ø 0.3-0.5 mm). The post preparation of the cuffs after structuring allows the fabrication of a stable self-closing flap that insulates the opening slit of the cuff without the need of extra sutures. Basic for the success of the cuff is the laser-based local thinning of both the silicone rubber and the metal at defined sections. This is critical to permit the PDMS' body to dominate the mechanical properties. Finite element modeling was applied to optimize the displacement ability of the cuff, leading to design capable of withstanding multiple implantation procedures without wire damage. Furthermore, the contact's surface was roughened by laser patterning to increase the charge injection capacity of Pt to 285 μC/cm(2) measured by voltage transient detection during pulse testing. The cuff electrodes were placed on a small sympathetic nerve of an adult female Sprague-Dawley rat for recording of spontaneous and evoked neural activity in vivo.
Modeling pathological intracranial pressure waveforms in idiopathic intracranial hypertension (2007)

Idiopathic intracranial hypertension (IIH) is a syndrome of unknown cause characterized by elevated intracranial pressure (ICP). By representing an abnormally collapsible sinus with a downstream Starling-like resistor, our previous modeling efforts have produced explanations for various phenomenon associated with IIH.
OMNI-DIRECTIONAL REFLECTOR USING A LOW REFRACTIVE INDEX MATERIAL (2004)

Triple-layer omni-directional reflectors (ODRs) consisting of a semiconductor, a transparent quarter-wavelength dielectric layer and metal layer have high reflectivities at all angles of incidence. In this paper, triple-layer ODRs are demonstrated that incorporate nanoporous SiO 2 , a novel low-refractive-index (low-n) material with refractive indices n ≪ 1.46 as well as dense SiO 2 (n = 1.46). GaP and Ag serve as the semiconductor and metal layer materials, respectively. An angle-integrated transverse electric (TE) mode reflectivity of R avg | TE = 99.9 % and transverse magnetic (TM) mode reflectivity R avg | TM = 98.9 % are calculated for the triple-layer ODRs employing nanoporous SiO 2 . Reflectivity measurements, including the angular dependence of R, are presented. Novel hybrid ODRs consisting of semiconductor, a several micron thick low-n dielectric material layer, a distributed Bragg reflector (DBR) and metal layer have outstanding reflectivities for all incident angles. GaP and Ag serve as the semiconductor and metal layer, respectively. Nanoporous SiO 2 is used as the low-n material. TiO 2 and dense SiO 2 serve as the DBR materials. The angle-intergrated reflectivities of the TE and TM modes are calculated to be larger than 99.9 % for the hybrid ODRs. The results indicate the great potential of the ODRs for light-emitting diodes with high light extraction efficiency.
Does bendamustine impact the mobilization of peripheral blood stem cells? A multicenter retrospective study of 23 cases (2016)

Bendamustine is used in the treatment of different relapsing or refractory subtypes of lymphoma. Its impact on the yield of peripheral blood stem cells is not well known. Twenty three patients who received bendamustine followed immediately or after another chemotherapy by stem cell mobilization (SCM) were included. The patients were divided into two groups: group 1 (n=17), in whom SCM was performed immediately after bendamustine chemotherapy, and group 2 (n=6), in whom SCM was performed after another cycle of chemotherapy. The success rate of mobilization after Bendamustine+/-plerixafor was 36% (eight cytapheresis succeeded for a total number of 22 cytapheresis); and 75% after other approaches (chemotherapy based or steady state) used for patients who received bendamustine previously. Although bendamustine used alone was not an effective drug to mobilize stem cells, this agent does not seem to have detrimental effects on subsequent SCM.
Effect of strain-compensation in stacked 1.3μm InAs∕GaAs quantum dot active regions grown by metalorganic chemical vapor deposition (2004)

We have introduced tensile layers embedded in a GaAs matrix to compensate compressive strain in stacked 1.3μm InAs quantum dot (QD) active regions. The effects of the strain compensation are systematically investigated in five-stack and ten-stack QD structures where we have inserted InxGa1−xP (x=0.30 or 0.36) layers. High-resolution x-ray diffraction spectra quantify the overall strain in each sample and indicate &amp;gt;35% strain reduction can be accomplished. Both atomic force and transmission electron microscope images confirm that strain compensation improves material crystallinity and QD uniformity. With aggressive strain compensation, room temperature QD photoluminescence intensity is significantly increased demonstrating a reduced defect density.
CybergeoNet - Scientific translations (2022)

Created in 1996, Cybergeo, European Journal of Geography is native digital journal which was conceived from the start for publication in all European languages. In order to better promote its authors’ articles internationally, it is undertaking actions to improve and translate its metadata into English, Spanish and Chinese. CybergeoNet is a laureate of the AAP "Scientific Translations" launched in 2019 by the Ministry of Higher Education, Research and Innovation (MESRI) in France. It has developed an efficient, and quality, collaborative translation method that is transferable to other scientific journals published and managed by research laboratories. The aim is to ensure that authors and editorial teams become more competent in translation. A guide of good practices is proposed to the community. CybergeoNet is carried by Cybergeo : European Journal of Geography in partnership with two international journals Brussels Studies and ViaTourism and the digital encyclopedia of geography Hypergeo.
Surface Topography and Surface Elemental Composition Analysis of Helixone®, a New High-Flux Polysulfone Dialysis Membrane (2001)

Modern dialysis membranes need to fulfil two basic requirements. Firstly, the membrane structure, defined in terms of the size, structure and distribution of the pores at the inner separating layer of the membrane must be such that uraemic solutes of a defined molecular-weight range are selectively removed. Secondly, the physical and chemical properties of the blood-contacting surface must be such that minimal blood-material interactions take place that could either affect the functioning of the membrane, or, cause adverse reactions for the patient. A new polysulfone dialysis membrane, Helixone, has been developed specifically for the elimination of larger uraemic toxins using convective therapy modalities such as haemodiafiltration. The membrane is characterised by the nanoscale modulation of the innermost surface structures that lead to significantly increased sieving coefficients for molecules such as beta2-microglobulin, while maintaining the extremely low albumin removal property of the high-flux Fresenius Polysulfone membrane. A recent publication (Ronco C, Bowry SK. Nanoscale modulation of the pore dimensions, size distribution and structure of a new polysulfone-based high-flux dialysis membrane. Int J Artif Organs 2001; 24: 726-35) described the characterisation of the membrane of Helixone in terms of the membrane wall structure- and permeation-related parameters. In this paper, we describe the analysis of membrane surface parameters that influence the biocompatibility as well as the functioning of a membrane. The degree of roughness and the type of chemical groups of a blood-contacting surface are two of the main determinants of the biocompatibility characteristics of a membrane. The surface elemental composition of Helixone was determined using electron spectroscopy for elemental analysis (ESCA) while the surface topography of the membrane was evaluated using atomic force microscopy (AFM). The analysis showed that Helixone has an improved, smoother blood-contacting surface and retains the essential surface chemistry, and therefore the acknowledged biocompatibility profile, of the Fresenius Polysulfone membrane.
Very high efficiency SiGe and GaN High Power Amplifiers for tile modules (2014)

International audience
Human papillomavirus oncogenes reprogram the cervical cancer microenvironment independently of and synergistically with estrogen (2017)

High-risk human papillomaviruses (HPVs) infect epithelial cells and are causally associated with cervical cancer, but HPV infection is not sufficient for carcinogenesis. Previously, we reported that estrogen signaling in the stromal tumor microenvironment is associated with cervical cancer maintenance and progression. We have now determined how HPV oncogenes and estrogen treatment affect genome-wide host gene expression in laser-captured regions of the cervical epithelium and stroma of untreated or estrogen-treated nontransgenic and HPV-transgenic mice. HPV oncogene expression in the cervical epithelium elicited significant gene-expression changes in the proximal stromal compartment, and estrogen treatment uniquely affected gene expression in the cervical microenvironment of HPV-transgenic mice compared with nontransgenic mice. Several potential estrogen-induced paracrine-acting factors were identified in the expression profile of the cervical tumor microenvironment. The microenvironment of estrogen-treated HPV-transgenic mice was significantly enriched for chemokine/cytokine activity and inflammatory and immune functions associated with carcinogenesis. This inflammatory signature included several proangiogenic CXCR2 receptor ligands. A subset of the same CXCR2 ligands was likewise increased in cocultures of early-passage cells from human cervical samples, with levels highest in cocultures of cervical fibroblasts and cancer-derived epithelial cells. Our studies demonstrate that high-risk HPV oncogenes profoundly reprogram the tumor microenvironment independently of and synergistically with estrogen. These observations illuminate important means by which HPVs can cause cancer through alterations in the tumor microenvironment.
The Drosophila Neurally Altered Carbohydrate Mutant Has a Defective Golgi GDP-fucose Transporter (2012)

The defect underlying reduced HRP epitope expression in Drosophila nac 1 mutants has not been identified. Results: nac 1 flies have a defective GDP-fucose transporter.
Abstract B229: TBKI kinase inhibition blocks RANTES secretion and exhibits minimal tumor growth inhibition in oncogenic Ras-driven tumor models. (2013)

Abstract TANK-binding kinase 1 (TBK1) is a non-canonical IKK family member and plays a critical role in innate immunity by modulating cytokine production, interferon, and NF-kB signaling. It is recently reported that TBK1 directly engages Akt survival signaling to support oncogenic Ras-driven transformation. TBK1 is also identified as a synthetic lethal partner in KRas mutant NSCLC through systematic RNA interference. In this study, we have characterized LSN3090729, a 4-aryl-2-aminopyrimidine derivative as a selective TBK1 kinase inhibitor. Biochemical and cellular analyses demonstrate that LSN3090729 is a potent TBK1 kinase inhibitor, and selectively inhibits TBK1 based on in vitro activities in biochemical assays developed with a panel of protein kinases. In Panc-1, a pancreatic tumor cell line with KRas mutation, LSN3090729 inhibits EGF-induced phosphorylation of AKT at both Thr308 and Ser473 sites. Pharmacokinetic analysis shows that LSN3090729 has an over 70% of oral bioavailability with an acceptable half life in rodents. In a mouse pharmacology model, LSN3090729 blocks LPS-induced RANTES secretion in a dose-dependent manner with 67%, 79%, and 90% inhibition at 10, 30, and 100 mg/kg, respectively. LSN3090729 is assessed for its anti-proliferation activities in vitro in a panel of tumor cells with KRas mutation or other genetic background. The sensitivity of these tumor cells to LSN3090729 in two dimensional proliferation or three dimensional soft agar growth assays appears not correlated with status of KRas mutation. In xenograft models of HCT116 and Panc-1, both with a KRas mutation, treatment of LSN3090729 exhibits minimal anti-tumor growth activities, suggesting that a combination approach might be required for TBK1 kinase inhibition to be effective in cancer settings. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B229. Citation Format: Robert Van Horn, Tinggui Yin, Xiaoyi Zhang, Chunping Yu, Youyan Zhang, Xue-Qian Gong, Sean Buchanan, Xiang S. Ye, William McMillen, David Barda, Sheng-Bin Peng. TBKI kinase inhibition blocks RANTES secretion and exhibits minimal tumor growth inhibition in oncogenic Ras-driven tumor models. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B229.
Author Identification with Chicken Swarm Optimization Algorithm and Adaboost Approaches (2020)

Author identification takes an important place in Natural Language Processing (NLP). Each written document carries the trail of its author. In this study, we aim to realize the author identification via the traces belonging to author be retrieved from the text. A raw dataset was created with 25 columnists and randomly selected 2024 texts from different newspapers in the Turkish language. A dataset with character and lexical features with natural language processing methods were prepared over the raw dataset. The feature selection process was realized with the combination of the Chicken swarm optimization and the ensemble learning algorithms on the prepared dataset. The results were evaluated before and after the feature selection method was applied. The highest success rate with 93.99% was achieved when Adaboost with J48 algorithm was applied after the feature selection process carried out.