gebhart/patrepeval huggingface dataset:
Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions (2014)

The classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters are embedded in a complex network of looping interactions. Here we use a polymer model of chromatin fiber to investigate whether, and to what extent, looping interactions between elements in the vicinity of an enhancer-promoter pair can influence their contact frequency. Our equilibrium polymer simulations show that a chromatin loop, formed by elements flanking either an enhancer or a promoter, suppresses enhancer-promoter interactions, working as an insulator. A loop formed by elements located in the region between an enhancer and a promoter, on the contrary, facilitates their interactions. We find that different mechanisms underlie insulation and facilitation; insulation occurs due to steric exclusion by the loop, and is a global effect, while facilitation occurs due to an effective shortening of the enhancer-promoter genomic distance, and is a local effect. Consistently, we find that these effects manifest quite differently for in silico 3C and microscopy. Our results show that looping interactions that do not directly involve an enhancer-promoter pair can nevertheless significantly modulate their interactions. This phenomenon is analogous to allosteric regulation in proteins, where a conformational change triggered by binding of a regulatory molecule to one site affects the state of another site.
A self stabilizing underwater sub-surface inspection robot using hydrodynamic ground effect (2015)

In this paper we present a unique self stabilizing ellipsoidal robot for inspection of underwater structures using the principles of ground effect. Underwater metal structures - whether it is ship hulls or internals of a boiling water reactor - require subsurface inspection to detect internal cracks, hidden cavities and other structural damage. This is usually done with on-contact ultrasonic sensors, a slow process if the structure is not sufficiently smooth. However, ultrasound can also be used with a precisely controlled gap. Such precision is challenging relying solely on actuators for control. This paper exploits near surface hydrodynamics to self stabilize a body at a precise gap. Specifically we show how boundary layer and venturi effects combine to create a stable, zero force position at a very small distance from the surface - conceptually similar to air bearings sliders on hard disk drives. Below the stable point lift force dominates, while above it Venturi suction prevails, each bringing the body back to equilibrium. Limitations in the restoring force are considered in the stability analysis included in the paper. This self stabilization method opens a whole new door for non-contact subsurface inspection of underwater structures by autonomous vehicles as well as precision distance maintenance in underwater environment. Here we present our initial analysis and preliminary experimental results for the method when used with an ellipsoidal robot.
Computer-generated holograms with error compensation (1988)

We analyze computer-generated holograms (CGH) of Lohmann types I and III and discuss their overall errors employing the following modifications, listed in order of increasing importance: phase-only correction (Ptype), virtual increase of the cell number, optimized use of the available plotting area, expansion of the amplitude dynamic range (D-type), circular overflow correction (OFC), and iterative overall error compensation. We compare the computing and plotting times for the listed CGH variants and their accuracy. As an application, we show the reconstruction of very complicated fields which may excite multimode and singlemode optical fibers, and a line grating with an in-between phase shift of 180 degrees ; the latter structure is useful in producing lambda/4-shifted semiconductor DFB lasers. Finally, we comment on some advanced techniques employing a desk-top computer and laser printer for producing hologram masks.
Synchronized Oscillations in the Inferior Olive Are Controlled by the Hyperpolarization-Activated Cation Current <i>I</i> <sub>h</sub> (1997)

The participation of a hyperpolarization-activated cationic current in the generation of oscillations in single inferior olive neurons and in the generation of ensemble oscillations in the inferior olive nucleus (IO) of the guinea pig and ferret was investigated in slices maintained in vitro. Intracellular recordings in guinea pig or ferret 10 neurons revealed that these cells could generate sustained endogenous oscillations (4-10 Hz) at hyperpolarized membrane potentials (-60 to -67 mV) after the intracellular injection of a brief hyperpolarizing current pulse. These oscillations appeared as the rhythmic generation of a low-threshold Ca2+ spike that typically initiated one or two fast Na+-dependent action potentials. Between low-threshold Ca2+ spikes was an afterhyperpolarization that formed a "pacemaker" potential. Local application of apamin resulted in a large reduction in the amplitude of the afterhyperpolarization, indicating that a Ca2+-activated K+ current makes a strong contribution to its generation. However, even in the presence of apamin, hyperpolarization of IO neurons results in a "depolarizing sag" of the membrane potential that was blocked by local application of Cs+ or partial replacement of extracellular Na+ with choline+ or N-methyl-D-glucamine+, suggesting that I(h) also contributes to the generation of the afterhyperpolarization. Extracellular application of low concentrations of cesium resulted in hyperpolarization of the membrane potential of IO neurons and spontaneous 5- to 6-Hz oscillations in single, as well as networks, of IO neurons. Application of larger concentrations of cesium reduced the frequency of oscillation to 2-3 Hz or blocked the oscillation entirely. On the basis of these results, we propose that I(h) contributes to single and ensemble oscillations in the IO in two ways: 1) I(h) contributes to the determination of the resting membrane potential such that reduction of I(h) results in hyperpolarization of the membrane potential and an increased propensity of oscillation through removal of inactivation of the low-threshold Ca2+ current; and 2) I(h) contributes to the generation of the afterhyperpolarization and the pacemaker potential between low-threshold Ca2+ spikes.
Recovering the spectrum of a narrow-band process from syncopated samples (1979)

A nonuniform sampling strategy, phase quadrature sampling, in which a process of bandwith B is sampled at rate B in each of two channels where the two channels are pi/2 out of phase at frequency B is described. Phase quadrature sampling is a special case of sampling, where the phase between channels is fixed but arbitrary. A simple method for recovering the spectrum of the input process from syncopated samples is derived. The derivation indicates what values of phase between channels result in lossless sampling.
Isocorannulenofuran:  A Versatile Building Block for the Synthesis of Large Buckybowls (2006)

Isocorannulenofuran, synthesized in two steps from accessible bromocorannulene, gives Diels-Alder adducts with benzynes which can be deoxygenated to produce large polycyclic aromatic hydrocarbons (PAHs) combining the bowl-shaped corannulene subunit with planar fragments. [reaction: see text]
Preferential Removal of a Methylenedioxy Group from Optically Active Isoquinolines (1976)

the a.prphine
Structure of human glycolate oxidase in complex with the inhibitor 4-carboxy-5-[(4-chlorophenyl)sulfanyl]-1,2,3-thiadiazole (2009)

Glycolate oxidase, a peroxisomal flavoenzyme, generates glyoxylate at the expense of oxygen. When the normal metabolism of glyoxylate is impaired by the mutations that are responsible for the genetic diseases hyperoxaluria types 1 and 2, glyoxylate yields oxalate, which forms insoluble calcium deposits, particularly in the kidneys. Glycolate oxidase could thus be an interesting therapeutic target. The crystal structure of human glycolate oxidase (hGOX) in complex with 4-carboxy-5-[(4-chlorophenyl)sulfanyl]-1,2,3-thiadiazole (CCPST) has been determined at 2.8 A resolution. The inhibitor heteroatoms interact with five active-site residues that have been implicated in catalysis in homologous flavodehydrogenases of L-2-hydroxy acids. In addition, the chlorophenyl substituent is surrounded by nonconserved hydrophobic residues. The present study highlights the role of mobility in ligand binding by glycolate oxidase. In addition, it pinpoints several structural differences between members of the highly conserved family of flavodehydrogenases of L-2-hydroxy acids.
A low-profile Archimedean spiral antenna using an EBG ground plane (2004)

This letter presents the implementation of electromagnetic band-gap (EBG) structures with an inherently wide-band Archimedean spiral antenna. The EBG structure is designed to emulate a perfect magnetic conductor. The combination of technologies produces a low-profile and wide-band antenna. Utilization of an EBG structure offers an antenna height reduction of more than 69%, including the thickness of the EBG structure, compared to the traditional /spl lambda//4 cavity backed implementation of spiral antennas. Specifically, this approach allows the spiral antenna to maintain a considerable fraction (71 %) of its designed inherent broad-band behavior with no loss to its directive gain. In addition, the presented design offers full scalability.
[Dexrazoxane (ICRF-187)--a cardioprotectant and modulator of action of some anticancer drugs]. (2006)

The nthracycline antibiotics are among the most widely used and effective anticancer drugs. The therapeutic efficacy of this class of drugs is limited by cumulative cardiac toxicity. Dexrazoxane is the only clinically approved cardioprotective agent used in anthracycline-containing anticancer therapy. Its cardioprotective action allows the use of a much higher cumulative dose of anthracyclines and improvement in the effectiveness of treatment. Anthracyclines form complexes with iron ions, which are very active in the production of reactive oxygen species responsible for the lipid peroxidation of mitochondrial and endoplasmatic reticulum membranes. This process seems to be the major cause of anthracycline-induced cardiotoxicity. Dexrazoxane exerts its protective effects by rapid and complete binding of ferric and ferrous ions, even by displacing the metal ions from complexes with anthracyclines. Besides its cardioprotective effect, dexrazoxane also exhibits anticancer properties. Like other derivatives of bisdioxopiperazine, dexrazoxane is a catalytic inhibitor of eukaryotic DNA topoisomerase II, the key enzyme controlling DNA topology and contributing to the replication and transcription processes. Dexrazoxane is able to lock topoisomerase II at the stage of the enzyme reaction cycle where the enzyme forms a closed clamp around the DNA. This phenomenon seems to be the main reason for the generation of DNA double-strand breaks by dexrazoxane as well as its cytotoxicity against quickly proliferating cancer cells. Other effects of its topoisomerase II catalytic inhibition is the induction of cell differentiation and apoptosis. Dexrazoxane may be used not only as a cardioprotective agent, but also as a modulator of action of some anticancer drugs by enhancing their selectivity or by delaying the development of multidrug resistance.
Defending against a Denial-of-Service Attack on TCP. (1999)

In this paper we propose a real-time anomaly detection method for detecting TCP SYN-flooding attacks. This method is based on the intensities of SYN segments which are measured on a network monitoring machine, in realtime. In the currently available solutions we note several important flaws such as the possibility of denying access to legitimate clients and/or causing service degradation at the potential target machines, therefore we aim to minimize such unwanted effects by acting only when it is necessary to do so: during an attack.
Performance Evaluation of Phase Estimation Algorithms in Equalized Coherent Optical Systems (2009)

We assess the performance of a coherent optical system employing a phase estimation algorithm combined with a least mean square decision-directed equalizer in a feedback configuration and compare it to the constant modulus algorithm with an independent carrier phase estimation approach for 16-quadratic-amplitude-modulation transmission. Both series and parallel implementations are discussed. Hardware issues regarding a recursive implementation of the estimation filter are also reported.
Combining Continuous Fluid Typing, Wireline Formation Testers, and Geochemical Measurements for an Improved Understanding of Reservoir Architecture (2008)

Summary Identifying compartmentalization and understanding reservoir structure are of critical importance to reservoir development. Traditional methods of identifying reservoir compartmentalization, such as drillstem tests and extended well tests, often become impractical in deepwater settings, with costs approaching the costs of new wells and emissions becoming increasingly undesirable. Thus, compartments often have to be identified by some other means. Individual formation-pressure measurements, downhole fluid analysis (DFA), and geochemistry are known to provide important information about reservoir architecture. When these powerful methods are combined systematically and applied to data sets, the resulting synergy delivers a much more accurate and robust picture of the reservoir. In this paper, we review a number of case studies in which we have successfully combined continuous fluid/facies mapping, pressure-gradient measurements, DFA, and geochemistry for a reservoir-continuity assessment in a diverse range of geological settings, including a wide range of field sizes, structural environments, reservoir lithologies, and oil types. Particular emphasis is placed on comparing the strengths and limitations of the different techniques in revealing reservoir architecture, especially vertical-permeability barriers. We present a number of unambiguous cases, for which multiple data streams might be viewed as being somewhat redundant. More-ambiguous cases, in which the multiple data streams are required to make a robust assessment of key reservoir properties, are also presented.
Synthesis and Characterization of Dibenzo[<i>a</i>,<i>d</i>]cyclohepten‐5‐one Derivatives for Light‐Emitting Diodes (2015)

Abstract Three novel dibenzo[ a , d ]cyclohepten‐5‐one derivatives containing hole‐transporting groups were synthesized and characterized. These compounds exhibit good thermal stabilities. Single crystals of DBHO‐TPA and DBHO‐DPA were successfully grown from dichloromethane and their crystal structures were determined from X‐ray diffraction data. Two molecules, DBHO‐TPA and DBHO‐DPA , have a nonplanar structure while seven‐membered ring comprised in dibenzo[ a , d ]cyclohepten‐5‐one is not planar. Electrochemical properties of three compounds indicate that the different substituents on 3,7‐positions of the dibenzo[ a , d ]cyclohepten‐5‐one derivatives have a small effect on the energy levels of the highest occupied molecular orbitals. The blue‐green light‐emitting diodes based on dibenzo[ a , d ]cyclohepten‐5‐one derivatives were fabricated.
Anti-CD9 monoclonal antibodies induce homotypic adhesion of pre-B cell lines by a novel mechanism. (1990)

Anti-CD9 mAb are known agonists of platelet aggregation, but have not been implicated in cell-cell adhesion. We show here in an experimental system that the anti-CD9 mAb 50H.19, ALB6, and BA-2 can induce rapid, and irreversible, homotypic aggregation of the CD9-positive pre-B lymphoblastoid cell lines NALM-6 and HOON, but not of the CD9-negative B cell line Raji. The specificity of the response is indicated by the failure to effect aggregation with mAb directed to CD24, or to HLA class I Ag. The initiation of strong homotypic aggregates of lymphoid cells is a property ascribed to lymphocyte function-associated Ag-1 (LFA-1), a member of the beta 2 subfamily of leukocyte integrins. We show that CD9-induced aggregation is an active process which proceeds at 37 degrees C, but not at 4 degrees C, requires the expenditure of metabolic energy, and a functioning cytoskeleton, and is not inhibited by Arg-Gly-Asp-Ser peptide. These are properties described for LFA-1-mediated aggregation. However, because beta 2-integrins are not expressed on NALM-6 or HOON cells, they are not the mediators of CD9-induced aggregation. In contrast to LFA-1-mediated adhesion which is Mg2+ dependent, CD9-induced adhesion has an absolute requirement for Ca2+, but not Mg2+, indicating that a Ca2(+)-dependent event is sufficient for adhesion. However, Mg2+ enhances adhesion even at optimal concentrations of Ca2+, implicating an additional Mg2(+)-dependent event which requires Ca2+ to be effective. These findings suggest that CD9 Ag regulates a novel mechanism for promoting tight cell-cell adhesion which requires both Ca2+ and Mg2+ for optimal expression.
Fluorine Compounds of Xenon and Radon (1962)

Xenon and fluorine combine readily. Xenon tetrafluoride is a colorless crystalline material, stable at room remperature. The existence of at least one other fluoride and two oxyfluorides has been demonstrated. The heaviest "inert gas," radon, also reacts with fluorine, yielding a compound less volatile than xenon tetrafluoride.
Development of Chemo-Mechanical Grinding (CMG) Process : Surface and Sub-surface Analysis of Si Wafer Produced by CMG(M^4 processes and micro-manufacturing for science) (2005)

For the final finishing of single crystal Si wafers, unlike the conventional polishing, we have developed a dry fixed-abrasive process by effective use of solid-state reaction between the CeO_2 abrasives and Si. Si is removed in a form of complex cerium-oxygen-silicon when two materials are subject to the conditions of about 0.8 MPa pressure and 15 m/s relative velocity. The fabricated φ300mm Si wafers are examined on both surface and subsurface. The results show no defect or mechanical imperfection being introduced during fabrication, and far better quality than the achievables by CMP.
The Effect of Minnelide against SARS-CoV-2 in a Murine Model (2021)

Abstract Severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, is the causative agent of coronavirus disease 2019, COVID-19, and the current COVID-19 pandemic. Even as more vaccine candidates are released, more treatment options are critically needed. Here, we investigated the use of Minnelide, a water soluble pro-drug with anti-inflammatory properties, for the treatment of COVID-19. To do this, k18-hACE2 mice were infected with SARS-CoV-2 or given PBS control intranasally. The next day mice were either treated daily with low dose (0.0025mg/day) or high dose Minnelide (0.005mg/day), or given vehicle control intraperitoneal. Mice were weighed daily, and sacrificed at day 6 and 10 post-infection to analyze viral burden, cytokine response, and pathology. We observed a reduction in viral load in the lungs of Minnelide-treated mice infected with SARS-CoV-2 at day 10 post-infection compared to day 6 post-infection. All SARS-CoV-2 infected non-treated mice were moribund six days post-infection while treatment with Minnelide extended survival for both low (60% survival) and high (100% survival) dose treated mice ten days post-infection. Interestingly, cytokine analysis demonstrated a significant reduction in IL-6 (lung and heart) and D-dimer (serum) in high dose treated SARS-CoV-2 infected mice compared to mice infected with SARS-CoV-2 alone at day 6 post-infection. Additionally, histology analysis revealed that Minnelide treatment significantly improved lung pathology ten days post-infection with SARS-CoV-2 with all the mice exhibiting normal lung tissue with thin alveolar septa and no inflammatory cells. Overall, our study exhibits potential for the use of Minnelide to improve survival in COVID-19 patients.
Mechanisms and Kinetics of Noncatalytic Ether Reaction in Supercritical Water. 2. Proton-Transferred Fragmentation of Dimethyl Ether to Formaldehyde in Competition with Hydrolysis (2005)

Noncatalytic reaction pathways and rates of dimethyl ether (DME) in supercritical water are determined in a tube reactor made of quartz according to liquid- and gas-phase 1H and 13C NMR observations. The reaction is studied at two concentrations (0.1 and 0.5 M) in supercritical water at 400 °C and over a water-density range of 0.1−0.6 g/cm3. The supercritical water reaction is compared with the neat one (in the absence of solvent) at 0.1 M and 400 °C. DME is found to decompose through (i) the proton-transferred fragmentation to methane and formaldehyde and (ii) the hydrolysis to methanol. Formaldehyde from reaction (i) is consecutively subjected to four types of redox reactions. Two of them proceed even without solvent: (iii) the unimolecular proton-transferred decarbonylation forming hydrogen and carbon monoxide and (iv) the bimolecular self-disproportionation generating methanol and carbon monoxide. When the solvent water is present, two additional paths are open: (v) the bimolecular self-disproportionation of formaldehyde with reactant water, producing methanol and formic acid, and (vi) the bimolecular cross-disproportionation between formaldehyde and formic acid, yielding methanol and carbonic acid. Methanol is produced through the three types of disproportionations (iv)−(vi) as well as the hydrolysis (ii). The presence of solvent water decelerates the proton-transferred fragmentation of DME; the rate constant is reduced by 40% at 0.5 g/cm3. This is caused by the suppression of low-frequency concerted motion corresponding to the reaction coordinate for the simultaneous C−O bond scission and proton transfer from one methyl carbon to the other. In contrast to the proton-transferred fragmentation, the hydrolysis of DME is markedly accelerated by increasing the water density. The latter becomes more important than the former in supercritical water at densities greater than 0.5 g/cm3.
Optimize the flight path for airlines using real-time information (2015)

As the reserve of crude oil is becoming fewer, we can expect higher oil prices in the long run Among the various operating costs in the Airlines, the fuel cost takes the biggest portion. Additionally the en-route fuel consumption is influenced by the weather such as wind speed and direction. This study is aimed at saving an airline's fuel costs by using real-time weather information en-route. It employs an integer programming model to search for an optimum flight path that minimizes the flight operating costs of an aircraft (including fuel costs, airway expenses, crew salaries, as well as maintenance and depreciation costs) for a specific flight. In the model, both airway choice and flight level selection are taken into account to search for the optimum path. For the first stage, the airline of interest chooses a suitable airway before departure according to her calculation based on some pre-set conditions in order to save fuel consumption. Since different airways depart a lot in oceanic flights, it is assumed that the airway decision is not changeable after the aircraft entering a specific gate fix. On the other hand, flight levels can be changed during the cruise phase. Pilots are able to change their flight level to optimize their fuel efficiency, on the basis of weather information provided by their airline or other third parties. Mathematically, there is an objective function that minimizes fuel consumption. Additionally, there are several constraints that take care o some techniques such as the maximum levels of each descend operation. Two set of empirical data (Transpacific and Asia-Pacific to Europe) from a Taiwanese airline are used to validate the mathematical formulation that has the potential to efficiently solve the defined problem with an exact solution. The research indicates that it is possible for airlines to use real-time weather information to save their fuel costs.