gebhart/patrepeval huggingface dataset:
Kinase requirements in human cells: I. Comparing kinase requirements across various cell types (2008)

shRNA loss-of-function screens were used to identify kinases that were rate-limiting for promoting cell proliferation and survival. Here, we study the differences in kinase requirements among various human cells, including freshly prepared primary cells, isogenic cells, immortalized cells, and cancer cell lines. Closely related patterns of kinase requirements among the various cell types were observed in three cases: (i) in repeat experiments using the same cells, (ii) with multiple populations of freshly prepared primary epithelial cells isolated from the same tissue source, and (iii) between nearly isogenic cells that differ from each other by the expression of a single gene. Other commonly used cancer cell lines were distinct from one another, even when they were isolated from similar tumor types. Even primary cells of different lineages isolated from the same tissue source showed many differences. The differences in kinase requirements among cell lines observed in this study suggest that the control of proliferation and survival may be significantly different between cell lines and that simple comparisons from any one cell to another may be misleading. Although the regulation of cell proliferation and survival are heavily studied areas, we did not see a bias in these screens toward the identification of previously known and well studied kinases, suggesting that our knowledge of molecular events in these areas is still meager.
Editorial (2016)

Are the Prudential principle (barring shareholder claims for reflective loss) and the Bartlett duty happy bed fellows? Thirteen years on from Privy Council’s seminal decision the implications of &lt;it&gt;Schmidt v Rosewood&lt;/it&gt; are still being worked through.
Separation of Diffraction Objects in Post-Stack Reverse Time Depth Migration (2014)

This paper proposes a new method for imaging small- scale diffraction objects. Its basis is separation of specular reflection and diffraction components of the total wavefield in the migrated domain. Reverse-time migration has been utilized to produce surface dip-angle common image gathers. One uses continuity of diffractions in the dip-angle CIGs as a criterion for separating reflections from diffractions. Synthetic and data examples illustrate efficient application of the method.
Intracellular oxidative stress induced by nitric oxide synthesis inhibition increases endothelial cell adhesion to neutrophils. (1994)

The objective of the present study was to determine whether prolonged inhibition of nitric oxide synthesis in endothelial cells increased the surface adhesion of these cells for neutrophils. Human umbilical vein endothelial cells (HUVECs) were grown to confluence in 48-well microtiter plates. Exposure of HUVECs to the nitric oxide synthesis inhibitor NG-nitro-L-arginine methyl ester (L-NAME) did not cause neutrophil adhesion at 1 hour but increased adhesion at 4 hours in a dose-dependent manner. The increased adhesion was prevented with L-arginine or nitric oxide donors but not an analogue of cGMP. The increased adhesion was inhibited by monoclonal antibodies directed against the beta 2-integrin CD18 and endothelial cell adhesion molecule ICAM-1. Platelet-activating factor (PAF) receptor antagonist WEB 2086 also prevented the L-NAME-induced neutrophil adhesion. Intracellular oxygen radical scavengers (dimethyl sulfoxide, butylated hydroxytoluene, and alpha, alpha'-dipyridyl), the iron chelator desferrioxamine, and the mitochondrial inhibitor azide inhibited the L-NAME-induced neutrophil adhesion, whereas extracellular oxygen radical scavengers (superoxide dismutase and catalase) had no effect. HUVECs were loaded with 2',7'-dichlorodihydrofluorescein diacetate, and oxidation to the fluorescent dichlorodihydrofluorescein (DCHF) was monitored. Fluorescence was enhanced in the L-NAME-treated HUVECs throughout the 4-hour incubation, an event inhibitable by an antioxidant and azide. The magnitude of the intracellular oxidation of DCHF was equivalent to approximately 0.8 mumol/L H2O2. These data suggest that prolonged nitric oxide synthesis inhibition in HUVECs causes an oxidant- and PAF-associated rise in adhesion on the surface of these endothelial cells for neutrophils.
Low-Molecular-Weight Heparin in Thrombosis and Cancer (2004)

Venous thromboembolism (VTE) is a recognized complication of malignant disease and multiple risk factors contribute to the hypercoagulability that commonly accompanies malignancy. Thromboprophylaxis with antithrombotic drugs such as the low-molecular-weight heparins (LMWHs) can be used to control the hypercoagulable state and to reduce the incidence of VTE in patients with cancer. Clinical and biochemical data suggest that LMWHs may also inhibit tumor growth, leading to a survival benefit in these patients. Many cancer patients reportedly have a hypercoaguable state, with recurrent thrombosis due to the impact of cancer cells and chemotherapy or radiotherapy on the coagulation cascade. Studies have demonstrated that unfractionated heparin (UFH) or its low-molecular-weight fractions interfere with various processes involved in tumor growth and metastasis. Clinical trials in cancer patients with thromboembolic disorders have suggested a clinically relevant effect of LMWHs (as compared with UFH) on the survival of cancer patients with deep vein thrombosis. Similarly, the impact of warfarin on the survival of cancer patients with thromboembolic disorders was demonstrated in certain tumor types. Studies from our laboratory demonstrated a significant role for LMWH, warfarin, anti-VIIa, and LMWH releasable tissue factor pathway inhibitor on the regulation of angiogenesis, tumor growth, and tumor metastasis. However, a direct anticancer effect for heparin in cancer patients without thrombosis still remains to be clinically documented.
A Case for Thalamic Mechanisms of Schizophrenia: Perspective From Modeling 22q11.2 Deletion Syndrome (2021)

Schizophrenia is a severe, chronic psychiatric disorder that devastates the lives of millions of people worldwide. The disease is characterized by a constellation of symptoms, ranging from cognitive deficits, to social withdrawal, to hallucinations. Despite decades of research, our understanding of the neurobiology of the disease, specifically the neural circuits underlying schizophrenia symptoms, is still in the early stages. Consequently, the development of therapies continues to be stagnant, and overall prognosis is poor. The main obstacle to improving the treatment of schizophrenia is its multicausal, polygenic etiology, which is difficult to model. Clinical observations and the emergence of preclinical models of rare but well-defined genomic lesions that confer substantial risk of schizophrenia (e.g., 22q11.2 microdeletion) have highlighted the role of the thalamus in the disease. Here we review the literature on the molecular, cellular, and circuitry findings in schizophrenia and discuss the leading theories in the field, which point to abnormalities within the thalamus as potential pathogenic mechanisms of schizophrenia. We posit that synaptic dysfunction and oscillatory abnormalities in neural circuits involving projections from and within the thalamus, with a focus on the thalamocortical circuits, may underlie the psychotic (and possibly other) symptoms of schizophrenia.
Using Graphics and Animation to Visulize Instruction Pipelining and its Hazards (1993)

The breakthrough of pipelined microprocessors has brought about a need to teach instruction pipelining in electrical and computer engineering curricula at the undergraduate level to a considerable depth. Although the idea of pipelining is conceptually simple, students often find pipelining difficult to visualize. Only the most talented students assimilate the ideas of how hazard issues are eliminated. Based on the pedagogical approach used in the landmark book “Computer Architecture—A Quantitative Approach” by John Hennessy and David Patterson, we have developed a graphical tool that uses animation and other graphical techniques to visualize how a pipelined datapath and control unit work. In this paper, we describe the graphical tool and outline a laboratory that makes use of it.
Nanosecond mid-infrared pulse generation via modulated thermal emissivity (2019)

We demonstrate the generation of nanosecond mid-infrared pulses via fast modulation of thermal emissivity enabled by the absorption of visible pump pulses in unpatterned silicon and gallium arsenide. The free-carrier dynamics in these materials result in nanosecond-scale modulation of thermal emissivity, which leads to nanosecond pulsed thermal emission. To our knowledge, the nanosecond thermal-emissivity modulation in this work is three orders of magnitude faster than what has been previously demonstrated. We also indirectly observed subnanosecond thermal pulses from hot carriers in semiconductors. The experiments are well described by our multiphysics model. Our method of converting visible pulses into the mid infrared using modulated emissivity obeys different scaling laws and can have significant wavelength tunability compared to approaches based on conventional nonlinearities.
Quantum-Dot Devices and Quantum-Dot Cellular Automata (1997)

We discuss novel nanoelectronic architecture paradigms based on cells composed of coupled quantum-dots. Boolean logic functions may be implemented in specific arrays of cells representing binary information, the so-called Quantum-Dot Cellular Automata (QCA). Cells may also be viewed as carrying analog information and we outline a network-theoretic description of such Quantum-Dot Nonlinear Networks (Q-CNN). In addition, we discuss possible realizations of these structures in a variety of semiconductor systems (including GaAs/AlGaAs, Si/SiGe, and Si/SiO 2 ), rings of metallic tunnel junctions, and candidates for molecular implementations.
Unraveling Deterministic Mesoscopic Polarization Switching Mechanisms: Spatially Resolved Studies of a Tilt Grain Boundary in Bismuth Ferrite (2009)

Abstract The deterministic mesoscopic mechanism of ferroelectric domain nucleation is probed at a single atomically‐defined model defect: an artificially fabricated bicrystal grain boundary (GB) in an epitaxial bismuth ferrite film. Switching spectroscopy piezoresponse force microscopy (SS‐PFM) is used to map the variation of local hysteresis loops at the GB and in its immediate vicinity. It is found that the the influence of the GB on nucleation results in a slight shift of the negative nucleation bias to larger voltages. The mesoscopic mechanisms of domain nucleation in the bulk and at the GB are studied in detail using phase‐field modeling, elucidating the complex mechanisms governed by the interplay between ferroelectric and ferroelastic wall energies, depolarization fields, and interface charge. The combination of phase‐field modeling and SS‐PFM allows quantitative analysis of the mesoscopic mechanisms for polarization switching, and hence suggests a route for unraveling the mechanisms of polarization switching at a single defect level and ultimately optimizing materials properties through microstructure engineering.
Mediated interactions beyond the nearest neighbor in an array of superconducting qubits (2021)

We consider mediated interactions in an array of floating transmons, where each qubit capacitor consists of two superconducting pads galvanically isolated from ground. Each such pair contributes two quantum degrees of freedom, one of which is used as a qubit, while the other remains fixed. However, these extraneous modes can generate coupling between the qubit modes that extends beyond the nearest neighbor. We present a general formalism describing the formation of this coupling and calculate it for a one-dimensional chain of transmons. We show that the strength of coupling and its range (that is, the exponential falloff) can be tuned independently via circuit design to realize a continuum from nearest-neighbor-only interactions to interactions that extend across the length of the chain. We present designs with capacitance and microwave simulations showing that various interaction configurations can be achieved in realistic circuits. Such coupling could be used in analog simulation of different quantum regimes or to increase connectivity in digital quantum systems. Thus mechanism must also be taken into account in other types of qubits with extraneous modes.
Erhöhte Serumkonzentrationen von löslichem TREM-1 (Triggering Receptor Expressed on Myeloid cells-1) bei Patienten mit COPD (2007)

Die COPD wird zunehmend als eine systemische Erkrankung erkannt, die mit erhöhten Markern systemischer Entzündung assoziiert ist. TREM-1 ist ein kürzlich identifizierter Rezeptor auf neutrophilen Granulozyten, Monozyten und Makrophagen. TREM-1 Expression wird hochreguliert durch mikrobielle Produkte wie bestimmte Toll-like-Rezeptor-Liganden. Wir untersuchten die Spiegel von löslichem TREM-1 (sTREM-1) im Serum von 12 Patienten mit COPD (GOLD Stadium I-IV, FEV1: 51±6%) und 10 Gesunden retrospektiv mit einem neu entwickelten ELISA. In der Kontrollgruppe waren die sTREM-1 Spiegel niedrig (Mittelwert±SEM: 0,78±0,57 pg/ml). Im Gegensatz dazu waren die Spiegel bei Patienten mit COPD signifikant erhöht (14,79±2,82 pg/ml, p<0,05). Zusätzlich zeigten die sTREM-1 Spiegel eine negative Korrelation mit dem COPD-Schweregrad, ausgedrückt als FEV1 % vom Sollwert (r2=–0,69). Zusammenfassend zeigen diese Daten erhöhte Serumkonzentrationen von sTREM bei Patienten mit COPD. Dieser Anstieg scheint mit dem Schweregrad der Erkrankung zu korrelieren. Die Relevanz von sTREM-1 als ein potentieller Marker bei COPD sollte in prospektiven Studien evaluiert werden.
Optimizing the positioning of transceivers and technological choices for RFID tags in aircrafts (2010)

Integrating RFID (Radio Frequency Identification) technologies on helicopter parts is a major challenge. Our technology concerns the implantation of RFID tags in an aircraft with a complex system of transceivers. Technologies have to be developed and adapted to the aeronautic requirements that are very constraining for on-board items. The objective is to read and update each tag in the aircraft according to harsh environment (metal parts, temperature, vibration, etc.). Tags will support and improve many processes and industrial operations in the aeronautical industry. It spreads from supply to maintenance through production and operation conditions. This paper intends to present the optimization problem related to implementing a global RFID system into an aircraft. In fact, the parameters and decision variables are really close and connected to each other. A model which is taking into account and optimizing the results has a really big place and importance for us. It represents a huge matter for the global system weight and price. For us, the important thing is the possible generalization of the modelling. It has to be applicable whatever the kind or model of aircraft it is. If we go further, it can be developed on every similar system (cars, etc.). The property of generalization is important for the repeatability and credibility of the optimization model.
Walking the Path: A New Journey to Explore and Discover Through Visual Analytics (2006)

Under the leadership of the US Department of Homeland Security (DHS), researchers at the Pacific Northwest National Laboratory (PNNL) established a research center focusing on the discipline of visual analytics in 2004. A year later, the center led a multidisciplinary panel representing academia, industry, and government to formally define directions and priorities for future research and development (R&amp;D) for visual analytics tools. The R&amp;D agenda, Illuminating the Path, defines the term visual analytics as ‘the science of analytical reasoning facilitated by interactive visual interfaces’. This article describes our progress to date in walking that path. We briefly describe the background of the subject, present major professional activities and accomplishments of its community, and highlight some of the ongoing R&amp;D efforts being carried out by researchers at PNNL to fulfill the requirements and missions of a new discipline that promises to change the way we deal with today's information.
Droplet Retention Time and Pressure Drop in SiSiC Open-Cell Foams Used as Droplet Separation Devices: A Numerical Approach (2019)

Open-cell foams are a promising alternative for the separation of liquid droplets suspended in gas flows at comparably low pressure drops. Separation in such ceramic foams is investigated using the residence time distribution of droplets derived from pore-scale CFD simulations. Silicon-infiltrated silicon carbide (SiSiC) open-cell foam samples (20 and 45 pores per inch, ppi) are considered. The foam structure was reconstructed from microcomputed tomography (μCT) images. To track the droplets, a Lagrangian discrete-phase model was used. The effects of pore size and pore density on the droplet retention time were studied. The flow pressure drop showed remarkable agreement with the in-house experimental measurements. The droplet separation efficiency within the foam structure was found to generally increase with the inlet gas velocity and the droplet inertia.
Modulating the External Facets of Functional Nanocrystals Enabled by Two-Dimensional Oxide Crystal Templates (2017)

The nature of the external crystal facets is critical to control the (photo)catalytic properties. Two-dimensional materials can expose only one type of crystal facet among zero-dimensional (0D), one-dimensional (1D), and two-dimensional (2D) materials. Controllable tuning of the nature of the external crystal facets of 2D materials is highly desirable but very challenging. Here, we show that 2D particles with the desirable crystal facet for high-performance photocatalytic H<sub>2</sub> generation can be obtained by using 2D metal oxide materials (i.e., nanosheets of Ca<sub>2</sub>Nb<sub>3</sub>O<sub>10</sub> and Ti<sub>0.87</sub>O<sub>2</sub>) as templates taking consideration of the crystal configuration of 2D oxide and target compounds. We demonstrate that anatase TiO<sub>2</sub> crystals grown on different nanosheet templates exhibit variations in photocatalytic hydrogen production rates from aqueous phase methanol solutions (6.7%), which can be attributed to the nature of the main crystal facet exposed. In view of the large number of 2D materials that have already been synthesized, this work offers a key to design and synthesize nanoparticles with the desirable specific external crystal facet for (photo)catalysis application.
Characterization of Bile Salt/Cyclodextrin Interactions Using Isothermal Titration Calorimetry (2001)

The interactions of cholate, deoxycholate, glycocholate, and taurocholate with methyl-β-cyclodextrin and 2-hydroxypropyl-β-cyclodextrin were studied by means of isothermal titration calorimetry and molecular modeling. The binding constants, standard molar enthalpy, Gibbs free energy, and entropy changes were determined for the formation of bile salt/cyclodextrin inclusion complexes. We observed a 1:1 stoichiometry for all inclusion complexes and could demonstrate marked differences in binding affinity between the different bile salt and cyclodextrin molecules. The dihydroxy bile salt deoxycholate showed significantly higher affinity toward methyl-β-cyclodextrin (K = 6276 ± 164 M-1) and 2-hydroxypropyl-β-cyclodextrin (K = 4429 ± 34 M-1) compared to the trihydroxy bile salt cholate (K = 2693 ± 25 M-1 and K = 2510 ± 98 M-1, respectively). The conjugation of cholate with glycine or taurine lowered its affinity markedly toward methyl-β-cyclodextrin (K = 1958 ± 178 M-1 and K = 2148 ± 33 M-1, respectively). Our molecular modeling and docking data suggest that the most probable mode of binding would be by insertion of the bile salt A-ring into the rim of the cyclodextrin containing the secondary alcohol moieties. Our results show that bile salt binding to cyclodextrin is influenced both by the degree of bile salt hydroxylation and by bile salt conjugation.
Bioensaios de alelopatia com extratos hidroalcoólico de Senna alata. (2007)

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Is Tau the Initial Pathology in Dopaminergic Nigrostriatal Degeneration? Studies in Parkinsonism and Parkinson’s Disease (2022)

Abstract While Parkinson’s disease (PD) remains clinically defined by cardinal motor symptoms resulting from nigrostriatal degeneration, it is now appreciated that PD consists of multiple pathologies, but it is unclear which occurs first and which are responsible for the nigrostriatal degeneration. For the past number of years, we have been studying a well-characterized cohort of subjects with motor impairment that we have termed mild motor deficits (MMD). Motor deficits were determined on a modified and validated Unified Parkinson’s Disease Rating Scale III (UPDRS III), but they occur to a degree insufficient to diagnose PD. We consider this population to have prodromal PD. However, in past studies, cases in this cohort had a selection bias as both a clinical syndrome in between no motor deficits and PD, plus nigral Lewy pathology as defined post-mortem, were required for inclusion. Therefore, in this study, we only based inclusion on a clinical phenotype intermediate between no motor impairment and PD. Then, we divided this group further based upon whether or not they had a synucleinopathy. Here we demonstrate that loss of nigral dopaminergic neurons, loss of putamenal dopaminergic innervation, loss of TH-phenotype in the substantia nigra and putamen, and changes in axonal transport occur equally in groups with and without nigral alpha-synuclein aggregates. Indeed, the common feature of these two groups is that both have similar degrees of AT8-expressing phospho-tau, a pathology not seen in the nigrostriatal system of aged-matched controls. These finding were confirmed with early (CP13) and late (PHF1) tau markers. This suggests that the initiation of nigrostriatal dopaminergic neurodegeneration occurs independently of alpha-synuclein aggregation and is likely tau mediated.
&lt;title&gt;Present and future of 3.5-in. magneto-optical disk&lt;/title&gt; (1998)

The current 3.5' MO disk has a capacity of 640 MB. To increase capacity/recording density, we investigated magnetically induced super resolution. Double mask rear aperture detection is described, resulting in two to four times increase in capacity. In future we want to achieve 15 GB or 20 Gb/in<SUP>2</SUP> five years later from now and 150 GB ten years later. Various technologies to achieve them are surveyed. To increase performance we proposed multi-beam optical head. Laser-assisted magnetic recording will be a breakthrough to the density limitation of magnetic recording caused by thermal fluctuation.
Tellurium compound provides pro-apoptotic signaling in drug resistant multiple myeloma (2020)

Multiple Myeloma, effectively treated by chemotherapeutic drugs, relapses due to drug resistance. We tested here the capacity of mesenchymal stromal cells, from the bone marrow of patients or from adipose tissue of healthy individuals, to induce drug resistance in Myeloma cell lines. We show that drug resistance can be achieved by factors secreted by the various MSC's. Mass spectrometry analysis of MSC's conditioned media revealed that fibronectin, was particularly instrumental in providing anti-apoptotic signals to MM cells. Moreover, we demonstrate that SAS ([octa-O-bis-(R,R)tartarate ditellurane]), an immunomodulator Tellurium compound, is not only able of blocking the physical interaction between MM cells and fibronectin but is also capable of re-sensitizing the cells to the chemotherapeutic drugs. Finally, we show that this re-sensitization is coupled with the blocking of pAKT induction, in MM cells, by the MSC's. These results indicate that SAS may be useful in the treatment of drug resistant MM.