gebhart/patrepeval huggingface dataset:
A-type lamins regulate retinoblastoma protein function by promoting subnuclear localization and preventing proteasomal degradation (2004)

The retinoblastoma protein (pRB) is a critical regulator of cell proliferation and differentiation and an important tumor suppressor. In the G(1) phase of the cell cycle, pRB localizes to perinucleolar sites associated with lamin A/C intranuclear foci. Here, we examine pRB function in cells lacking lamin A/C, finding that pRB levels are dramatically decreased and that the remaining pRB is mislocalized. We demonstrate that A-type lamins protect pRB from proteasomal degradation. Both pRB levels and localization are restored upon reintroduction of lamin A. Lmna(-/-) cells resemble Rb(-/-) cells, exhibiting altered cell-cycle properties and reduced capacity to undergo cell-cycle arrest in response to DNA damage. These findings establish a functional link between a core nuclear structural component and an important cell-cycle regulator. They further raise the possibility that altered pRB function may be a contributing factor in dystrophic syndromes arising from LMNA mutation.
Dedicated Short-Range Communications (DSRC) Standards in the United States (2011)

Wireless vehicular communication has the potential to enable a host of new applications, the most important of which are a class of safety applications that can prevent collisions and save thousands of lives. The automotive industry is working to develop the dedicated short-range communication (DSRC) technology, for use in vehicle-to-vehicle and vehicle-to-roadside communication. The effectiveness of this technology is highly dependent on cooperative standards for interoperability. This paper explains the content and status of the DSRC standards being developed for deployment in the United States. Included in the discussion are the IEEE 802.11p amendment for wireless access in vehicular environments (WAVE), the IEEE 1609.2, 1609.3, and 1609.4 standards for Security, Network Services and Multi-Channel Operation, the SAE J2735 Message Set Dictionary, and the emerging SAE J2945.1 Communication Minimum Performance Requirements standard. The paper shows how these standards fit together to provide a comprehensive solution for DSRC. Most of the key standards are either recently published or expected to be completed in the coming year. A reader will gain a thorough understanding of DSRC technology for vehicular communication, including insights into why specific technical solutions are being adopted, and key challenges remaining for successful DSRC deployment. The U.S. Department of Transportation is planning to decide in 2013 whether to require DSRC equipment in new vehicles.
Scaling Up Stochastic Dual Coordinate Ascent (2015)

Stochastic Dual Coordinate Ascent (SDCA) has recently emerged as a state-of-the-art method for solving large-scale supervised learning problems formulated as minimization of convex loss functions. It performs iterative, random-coordinate updates to maximize the dual objective. Due to the sequential nature of the iterations, it is typically implemented as a single-threaded algorithm limited to in-memory datasets. In this paper, we introduce an asynchronous parallel version of the algorithm, analyze its convergence properties, and propose a solution for primal-dual synchronization required to achieve convergence in practice. In addition, we describe a method for scaling the algorithm to out-of-memory datasets via multi-threaded deserialization of block-compressed data. This approach yields sufficient pseudo-randomness to provide the same convergence rate as random-order in-memory access. Empirical evaluation demonstrates the efficiency of the proposed methods and their ability to fully utilize computational resources and scale to out-of-memory datasets.
High-Mobility Bottom-Gate Thin-Film Transistors with Laser-Crystallized and Hydrogen-Radical-Annealed Polysilicon Films (1991)

High-performance bottom-gate thin-film transistors (TFTs) have been realized with excimer-laser-crystallized polysilicon films, for the first time. TFT characteristics were greatly dependent on the silicon film thickness as well as the pulsed-laser energy density. It was found also that posthydrogenation based on hydrogen-radical annealing improves the TFT characteristics drastically. The field-effect mobilities exceeded 220 cm 2 /Vs for electrons and 140 cm 2 /Vs for holes, respectively.
Versatile and Efficient Solid-Phase Syntheses of Pyrazoles and Isoxazoles (2000)

[reaction: see text] Condensation of aromatic or aliphatic esters with resin-supported acetyl carboxylic acids 2, followed by cyclization with hydrazines or hydroxylamine, activation of the linker, and cleavage using amines provides highly substituted, isomeric pyrazoles or isoxazoles 5. This general method gives products in excellent yields and purities in which the ratio of the two isomers can be easily controlled. A variation of this scheme generates 1,4,5- and 1,3, 4-trisubstituted pyrazoles and related isoxazoles. Post-cleavage reduction with borane converts pyrazole amides to amines such as 11.
Field and Laboratory Results of Carbon Dioxide and Nitrogen in Well Stimulation (1964)

Abstract Carbon dioxide and nitrogen have both proven to be useful aids in will stimulation. Laboratory data are presented showing the effect of carbon dioxide on foaming agents, corrosion, reaction rate of hydrochloric acid, fluid-loss additives and clay swelling. Carbon dioxide is generally beneficial for all of these except the fluid-loss additives. The corrosion rate of carbonated water is very low compared to inhibited hydrochloric acid. A chart of the viscosity of carbon dioxide is presented. If is estimated that carbon dioxide can reduce friction loss of oil-base fluids by 29 to 60 per cent. Individual field results and conclusions from other summaries are presented. Both nitrogen and carbon dioxide are effective in removal of stimulation fluids. Carbon dioxide has proven useful in removing water or emulsion blocks. Introduction The use of nitrogen and carbon dioxide in well stimulations has grown rapidly in the past two years. The uses and advantages of these gases have been described previously for well stimulation, testing and cementing programs. Because of the differences in physical and chemical properties between nitrogen and carbon dioxide, one gas is usually better suited than the other for a specific application. Generally speaking, nitrogen is superior in low injection rate applications and when precise volume control is critical. Carbon dioxide, on the other hand, is better adaptable to high rate fracturing and acid treatments. Gases were introduced to the oil and gas industry primarily as an aid to recovery of stimulation fluids. This application still accounts for the major usage of nitrogen and carbon dioxide. Special applications, however, which utilize specific properties of the gases, are being discovered continually. The development of these methods is opening the door to better controls over well performance. Effect of a Foaming Additive with Nitrogen and Carbon Dioxide By the nature of the solubility-pressure relationship of carbon dioxide, an induced solution-gas-drive mechanism is created when the pressure is lowered and the gas comes out of solution. To demonstrate this effect the apparatus shown in Fig. 1 was constructed. The 160-cc cell was filled to 100 cc with the fluid to be tested, a gas pressure (nitrogen or CO2) of about 800 psi was applied and allowed to come to equilibrium. The valve was then opened and the amount of liquid carried over was measured in a graduated cylinder. These tests were also conducted using various amounts of foaming additive to see if the additive would enhance the recovery. The results of these tests are given in Table 1. As expected, the recovery of fluids was substantially greater when using CO2 than when using nitrogen. For example, at 80F the recovery with CO2, and no foaming additive was 40 per cent, while with nitrogen it was essentially zero. The addition of the foaming agent increased the recovery substantially. With CO2 the recovery increased from 40 per cent to 70 per cent when 0.2 per cent foaming additive was used.
Language support for Morton-order matrices (2001)

The uniform representation of 2-dimensional arrays serially in Morton order (or {\eee} order) supports both their iterative scan with cartesian indices and their divide-and-conquer manipulation as quaternary trees. This data structure is important because it relaxes serious problems of locality and latency, and the tree helps to schedule multi-processing. Results here show how it facilitates algorithms that avoid cache misses and page faults at all levels in hierarchical memory, independently of a specific runtime environment. We have built a rudimentary C-to-C translator that implements matrices in Morton-order from source that presumes a row-major implementation. Early performance from LAPACK's reference implementation of \texttt{dgesv} (linear solver), and all its supporting routines (including \texttt{dgemm} matrix-multiplication) form a successful research demonstration. Its performance predicts improvements from new algebra in back-end optimizers. We also present results from a more stylish \texttt{dgemm} algorithm that takes better advantage of this representation. With only routine back-end optimizations inserted by hand (unfolding the base case and passing arguments in registers), we achieve machine performance exceeding that of the manufacturer-crafted {\tt dgemm} running at 67% of peak flops. And the same code performs similarly on several machines. Together, these results show how existing codes and future block-recursive algorithms can work well together on this matrix representation. Locality is key to future performance, and the new representation has a remarkable impact.
Rapamycin reduces intrahepatic alpha-1-antitrypsin mutant Z protein polymers and liver injury in a mouse model (2010)

Alpha-1-antitrypsin (a1AT) deficiency is caused by homozygosity for the a1AT mutant Z gene and occurs in one in 2000 Americans. The Z mutation confers an abnormal conformation on the a1AT mutant Z protein, resulting in accumulation within the endoplasmic reticulum of hepatocytes and chronic liver injury. Autophagy is one of several proteolytic mechanisms activated to cope with this hepatocellular protein burden, and is likely important in disposal of the unique polymerized conformation of the a1AT mutant Z protein, which is thought to be especially injurious to the cell. Recent data indicate that rapamycin may more efficiently upregulate autophagy when given in weekly dose pulses, as compared with a daily regimen. Therefore, we evaluated the effect of rapamycin on PiZ mice, a well-characterized model which recapitulates human a1AT liver disease. Daily dosing had no effect on autophagy, on accumulation of a1AT mutant Z protein or on liver injury. Weekly dosing of rapamycin did increase autophagic activity, as shown by increased numbers of autophagic vacuoles. This was associated with reduction in the intrahepatic accumulation of a1AT mutant Z protein in the polymerized conformation. Markers of hepatocellular injury, including cleavage of caspase 12 and hepatic fibrosis, were also decreased. In conclusion, this is the first report of a successful in vivo method for reduction of intrahepatic a1AT mutant Z polymerized protein. Application of this finding may be therapeutic in patients with a1AT deficiency by reducing the intracellular burden of the polymerized, mutant Z protein and by reducing the progression of liver injury.
Involvement of Phosphoinositide 3-Kinase γ in Angiogenesis and Healing of Experimental Myocardial Infarction in Mice (2010)

PI3Kgamma expression and catalytic activity are involved at different levels in reparative neovascularization and healing of MI.
fos/jun repression of cardiac-specific transcription in quiescent and growth-stimulated myocytes is targeted at a tissue-specific cis element. (1993)

Unlike that of skeletal muscle cells in which growth and differentiation appear mutually exclusive, growth stimulation of cardiac cells is characterized by transient expression of early response nuclear proto-oncogenes as well as induction of several cardiac-specific markers. This observation led to the speculation that these proto-oncogenes, particularly c-fos and c-jun, might act as positive regulators of cardiac transcription. We have examined the role of c-jun and c-fos in basal and growth-stimulated cardiac transcription, using the cardiac-specific atrial natriuretic factor (ANF) gene as a marker. The results indicate that c-jun and c-fos are negative regulators of ANF transcription. Inducers of jun and fos activity, such as mitogens and growth factors, inhibited endogenous ANF transcripts. In transient cotransfection assays, jun and fos were able to trans-repress the ANF promoter in both quiescent and alpha 1-adrenergic stimulated myocytes. This repression was specific to myocyte cultures and was not observed in nonmuscle cells. Deletion analysis indicated that repression does not require typical AP-1-binding sites (tetradecanoyl phorbol acetate response elements) or serum response elements but is targeted at a cardiac-specific element within the ANF promoter. Various Fos-related proteins, including Fra-1, Fos B, and v-Fos, were able to trans-repress ANF transcription. In addition, C-terminal c-fos mutants which no longer repress transcription of such early growth response genes as c-fos and EGR-1 retained the ability to repress ANF transcription. Repression by c-jun occurs via the N-terminal activation domain and does not require the DNA-binding domain, suggesting that proto-oncogene repression involves interaction with one or more limiting cardiac-specific coactivators.
Neuroprotective Effects of Nonfeminizing Estrogens in Retinal Photoreceptor Neurons (2012)

Retinal diseases such as macular degeneration and glaucoma are disorders that target specific retinal neurons that can ultimately lead to vision loss. Under these conditions and pathologies, retinal neurons can die via apoptosis that may be due to increased oxidative stress. The neuroprotective effects of 17b-estradiol (E2) and three synthetic nonfeminizing estrogen analogs (ZYC-26, ZYC-23, and ZYC-3) were investigated to examine their abilities to protect retinal neurons against glutamate toxicity.
Nucleation, Growth, and Repair of a Cobalt-Based Oxygen Evolving Catalyst (2012)

The mechanism of nucleation, steady-state growth, and repair is investigated for an oxygen evolving catalyst prepared by electrodeposition from Co(2+) solutions in weakly basic electrolytes (Co-OEC). Potential step chronoamperometry and atomic force microscopy reveal that nucleation of Co-OEC is progressive and reaches a saturation surface coverage of ca. 70% on highly oriented pyrolytic graphite substrates. Steady-state electrodeposition of Co-OEC exhibits a Tafel slope approximately equal to 2.3 × RT/F. The electrochemical rate law exhibits a first order dependence on Co(2+) and inverse orders on proton (third order) and proton acceptor, methylphosphonate (first order for 1.8 mM ≤ [MeP(i)] ≤ 18 mM and second order dependence for 32 mM ≤ [MeP(i)] ≤ 180 mM). These electrokinetic studies, combined with recent XAS studies of catalyst structure, suggest a mechanism for steady state growth at intermediate MeP(i) concentration (1.8-18 mM) involving a rapid solution equilibrium between aquo Co(II) and Co(III) hydroxo species accompanied with a rapid surface equilibrium involving electrolyte dissociation and deprotonation of surface bound water. These equilibria are followed by a chemical rate-limiting step for incorporation of Co(III) into the growing cobaltate clusters comprising Co-OEC. At higher concentrations of MeP(i) ([MeP(i)] ≥ 32 mM), MePO(3)(2-) equilibrium binding to Co(II) in solution is suggested by the kinetic data. Consistent with the disparate pH profiles for oxygen evolution electrocatalysis and catalyst formation, NMR-based quantification of catalyst dissolution as a function of pH demonstrates functional stability and repair at pH values >6 whereas catalyst corrosion prevails at lower pH values. These kinetic insights provide a basis for developing and operating functional water oxidation (photo)anodes under benign pH conditions.
Lipoic and Dihydrolipoic Acids as Antioxidants. a Critical Evaluation (1994)

A detailed evaluation of the antioxidant and pro-oxidant properties of lipoic acid (LA) and dihydrolipoic acid (DHLA) was performed. Both compounds are powerful scavengers of hypochlorous acid, able to protect alpha 1-antiproteinase against inactivation by HOCl. LA was a powerful scavenger of hydroxyl radicals (OH.) and could inhibit both iron-dependent OH. generation and peroxidation of ox-brain phospholipid liposomes in the presence of FeCl3-ascorbate, presumably by binding iron ions and rendering them redox-inactive. By contrast, DHLA accelerated iron-dependent OH. generation and lipid peroxidation, probably by reducing Fe3+ to Fe2+. LA inhibited this pro-oxidant action of DHLA. However, DHLA did not accelerate DNA degradation by a ferric bleomycin complex and slightly inhibited peroxidation of arachidonic acid by the myoglobin-H2O2 system. Under certain circumstances, DHLA accelerated the loss of activity of alpha-antiproteinase exposed to ionizing radiation under a N2O/O2 atmosphere and also the loss of creatine kinase activity in human plasma exposed to gas-phase cigarette smoke. Neither LA nor DHLA reacted with superoxide radical (O.2-) or H2O2 at significant rates, but both were good scavengers of trichloromethylperoxyl radical (CCl3O2.). We conclude that LA and DHLA have powerful antioxidant properties. However, DHLA can also exert pro-oxidant properties, both by its iron ion-reducing ability and probably by its ability to generate reactive sulphur-containing radicals that can damage certain proteins, such as alpha 1-antiproteinase and creatine kinase.
Carbon Nanotubes as Active Components for Gas Sensors (2009)

The unique structure of carbon nanotubes endows them with fantastic physical and chemical characteristics. Carbon nanotubes have been widely studied due to their potential applications in many fields including conductive and high‐strength composites, energy storage and energy conversion devices, sensors, field emission displays and radiation sources, hydrogen storage media, and nanometer‐sized semiconductor devices, probes, and quantum wires. Some of these applications have been realized in products, while others show great potentials. The development of carbon nanotubes‐based sensors has attracted intensive interest in the last several years because of their excellent sensing properties such as high selectivity and prompt response. Carbon nanotube‐based gas sensors are summarized in this paper. Sensors based on single‐walled, multiwalled, and well‐aligned carbon nanotubes arrays are introduced. Modification of carbon nanotubes with functional groups, metals, oxides, polymers, or doping carbon nanotubes with other elements to enhance the response and selectivity of the sensors is also discussed.
Generation of Species Cross-reactive Aptamers Using “Toggle” SELEX (2001)

Species cross-reactivity facilitates the preclinical evaluation of potentially therapeutic molecules in animal models. Here we describe an in vitro selection strategy in which RNA ligands (aptamers) that bind both human and porcine thrombin were selected by "toggling" the protein target between human and porcine thrombin during alternating rounds of selection. The "toggle" selection process yielded a family of aptamers, all of which bound both human and porcine thrombin with high affinity. Toggle-25, a characteristic member, inhibited two of thrombin's most important functions: plasma clot formation and platelet activation. If appropriate targets are available, the toggle strategy is a simple measure that promotes cross-reactivity and may be generalizable to related proteins of the same species as well as to other combinatorial library screening strategies. This strategy should facilitate the isolation of ligands with needed properties for gene therapy and other therapeutic and diagnostic applications.
Control of rotary heart assist devices (2000)

Rotary assist devices are state of the art blood pumps that are used in therapies to treat weak hearts, usually associated with myocardial diseases. We develop three indices to detect the occurrence of suction in these pumps: pulsatility index, diminishing returns index and harmonic index. Experimental studies in calves show that these indices can detect suction at approximately the same speed. Control of ventricular assist devices based only on suction detection may not satisfy other requirements for some hemodynamic variables. A multi-objective optimization scheme has been developed to consider other hemodynamic variables. We demonstrate the feasibility of this approach using a Physbe simulation of AOP and LAP. A non-inferior set of pump speeds was found that includes speeds that optimize performance with respect to these two variables.
Growth hormone-releasing hormone promotes survival of cardiac myocytes in vitro and protects against ischaemia–reperfusion injury in rat heart (2009)

Our findings suggest that GHRH promotes cardiac myocyte survival through multiple signalling mechanisms and protects against I/R injury in isolated rat heart, indicating a novel cardioprotective role of this hormone.
Chemometric evaluation of the solvent properties of liquid organic salts (1995)

Abraham's solvation parameter model was used to characterize the solvent properties of 38 liquid organic salts at a reference temperature of 121.4 °C. These salts are strong hydrogen-bond bases with a significant capacity for dipole–dipole and dipole-induced dipole interactions. The primary characteristics that dominate their solvent properties are the extent of charge localization on the anion and the extent of association between solvent molecules resulting from intermolecular hydrogen bonding. Their solvent properties cannot be duplicated by common non-ionic solvents used as stationary phases in gas chromatography.
Cytosine Arabinoside Promotes Cytotoxic Effect of T Cells on Leukemia Cells Mediated by Bispecific Antibody (2013)

Chemotherapeutic drugs can enhance an immune response of the host against the tumor in addition to killing cancer cells by direct cytotoxicity. Therefore, the combination of chemotherapy and immunotherapy is a promising approach for eliminating tumors, particularly in advanced stages. A strategic medication is to use a bispecific antibody format that is capable of recruiting polyclonal T cells around antibody-target-expressing tumor cells. Recently, we have constructed a bispecific antibody, anti-CD3×anti-CD19, in a diabody configuration. In this study, we measured B7 family members B7.1 (CD80) and B7.2 (CD86) expressed on a CD19(+) human leukemia cell line, Nalm-6, stimulated by cytosine arabinoside (Ara-C). We found that a low concentration of Ara-C could upregulate CD80 expressed on CD19(+) Nalm-6 cells. The cytotoxicity of T lymphocytes against Nalm-6 cells in vitro and in vivo mediated by the anti-CD3×anti-CD19 diabody with or without a low dose of Ara-C was compared. The combination of the anti-CD3×anti-CD19 diabody and Ara-C showed the greatest effectiveness in enhancing the cytotoxicity of T cells against the tumor cells in vitro and in vivo. Activated T cells expressed higher levels of CD25 and CD69 and released more interleukin 2. Both perforin/granzyme B system and Fas/FasL pathway were involved in the diabody-induced T-cell cytotoxicity. Moreover, the activated T cells could upregulate ICAM-3 expression on Nalm-6 cells, and inhibition of LFA-1-ICAM-3 interaction impaired cytotoxicity of T cells. It was noted that Ara-C could upregulate CD80 expressed on two of five specimens of acute B lymphoblastic leukemia patient-derived cells. Cytotoxicity of T cells against these two patient-derived cells was enhanced in the presence of the anti-CD3×anti-CD19 diabody. These findings indicate that treatment strategy using both cytotoxic lymphocyte-based immunotherapy and chemotherapy may have synergistic effects.