gebhart/patrepeval huggingface dataset:
The oxidative demethylase ALKBH3 marks hyperactive gene promoters in human cancer cells (2015)

The genomic binding pattern of ALKBH3 revealed a putative novel hyperactive promoter type. Further, we propose that ALKBH3 is an intrinsic DNA repair protein that suppresses transcription associated DNA damage at highly expressed genes and thereby plays a role to maintain genomic integrity in ALKBH3-overexpressing cancer cells. These results raise the possibility that ALKBH3 may be a potential target for inhibiting cancer progression.
Thyroid hormone-dependent pituitary tumor cell growth in serum-free chemically defined culture. A new regulatory role for apotransferrin (1991)

Thyroid hormone dependent GH1 rat pituitary tumor cell growth in serum-free chemically defined medium required a serum-derived mediator (i.e., thyromedin) which was identified as transferrin [Sirbasku, D.A., Stewart, B.H., Pakala, R., Eby, J.E., Sato, H., & Roscoe, J.M. (1990) Biochemistry 30, 295-304]. The transferrin isolated was consistent with the equine R or D variants and was biologically active only as apotransferrin (apoTf). To determine if other variants of horse transferrin also were thyromedins, a purification was developed which yielded seven separate forms. Initially, only four of these had activity when assayed in standard "iron salts containing" medium (ED50 values of 290-1160 nM). To further assess activity, the iron contents of all seven were altered either by saturation with ferric ammonium citrate or by citrate/acid depletion of the metal ion. Thereafter, potencies were compared in "iron salts containing" and "iron salts reduced" media. All seven variants proved to be active as apoTf. Bioassays in which apoTf was maximized showed ED50 values of 2.1-3.8 nM. Conversely, assays in which thyromedins were converted to Tf.2Fe showed no activity. Previously, the only known physiological function of apoTf was that of a carrier/detoxifier of iron; this study indicates a new role in hormone-dependent pituitary cell growth.
p38 Mitogen‐Activated Protein Kinase Activity Commits Embryonic Stem Cells to Either Neurogenesis or Cardiomyogenesis (2006)

Mouse embryonic stem (ES) cells can be differentiated, in vitro into a variety of cell types including cardiac cells and neurons. This process is strictly controlled by the potent morphogen retinoic acid (RA). At a concentration of 10(-7) M, RA induces ES cell differentiation into neurons and, conversely, inhibits cardiomyogenesis. We found that p38 mitogen-activated protein kinase (p38MAPK) activity peaked spontaneously, between day 3 and day 5, during ES cell differentiation and that RA completely inhibited this peak of activity. In contrast to wild-type cells, which required RA treatment, p38alpha(-/-) ES cells differentiated spontaneously into neurons and did not form cardiomyocytes. Moreover, inhibition of the peak of p38MAPK activity by a specific inhibitor, PD169316, committed ES cells into the neuronal lineage and blocked cardiomyogenesis. By genetic and biochemical approaches, we demonstrate that, in two different ES cell lines, the control of p38MAPK activity constitutes an early switch, committing ES cells into either neurogenesis (p38 off) or cardiomyogenesis (p38 on).
Permeability of Nitric Oxide through Lipid Bilayer Membranes (1996)

Profiles of the local nitric oxide (.NO) diffusion-concentration product across the egg yolk phosphatidylcholine membrane in the absence and presence of 30 mol% cholesterol were obtained using line-broadening electron paramagnetic resonance (EPR) and lipid-soluble nitroxide spin labels. Membrane .NO permeability coefficients were calculated from these profiles. At 20 degrees C, values of 93 and 77 cm/s for membranes in the absence and presence of cholesterol were obtained, compared with 73 and 66 cm/s for water layers of the same thickness as the membranes. Fluid-phase membranes are not barriers to .NO transport. Cholesterol significantly increases .NO transport in the center of the lipid bilayer.
Modulated Chemical Doping of Individual Carbon Nanotubes (2000)

Modulation doping of a semiconducting single-walled carbon nanotube along its length leads to an intramolecular wire electronic device. The nanotube is doped n-type for half of its length and p-type for the other half. Electrostatic gating can tune the system into p-n junctions, causing it to exhibit rectifying characteristics or negative differential conductance. The system can also be tuned into n-type, exhibiting single-electron charging and negative differential conductance at low temperatures. The low-temperature behavior is manifested by a quantum dot formed by chemical inhomogeneity along the tube.
Just how mad are you? finding strong and weak opinion clauses (2004)

There has been a recent swell of interest in the automatic identification and extraction of opinions and emotions in text. In this paper, we present the first experimental results classi-fying the strength of opinions and other types of subjectivity and classifying the subjectivity of deeply nested clauses. We use a wide range of features, including new syntactic fea-tures developed for opinion recognition. In 10-fold cross-validation experiments using support vector regression, we achieve improvements in mean-squared error over baseline ranging from 57 % to 64%.
WaldBoost — Learning for Time Constrained Sequential Detection (2005)

In many computer vision classification problems, both the error and time characterizes the quality of a decision. We show that such problems can be formalized in the framework of sequential decision-making. If the false positive and false negative error rates are given, the optimal strategy in terms of the shortest average time to decision (number of measurements used) is the Wald's sequential probability ratio test (SPRT). We built on the optimal SPRT test and enlarge its capabilities to problems with dependent measurements. We show how to overcome the requirements of SPRT - (i) a priori ordered measurements and (ii) known joint probability density functions. We propose an algorithm with near optimal time and error rate trade-off, called WaldBoost, which integrates the AdaBoost algorithm for measurement selection and ordering and the joint probability density estimation with the optimal SPRT decision strategy. The WaldBoost algorithm is tested on the face detection problem. The results are superior to the state-of-the-art methods in the average evaluation time and comparable in detection rates.
Nucleotide binding and cofactor activities of purified bovine brain and bacterially expressed ADP-ribosylation factor (1989)

The ADP-ribosylation factor (ARF) is a member of the small molecular weight GTP-binding protein family and serves as the cofactor in the cholera toxin-catalyzed activation of the stimulatory regulatory subunit (Gs) of adenylate cyclase. Bovine Arf1 has been expressed at high levels and purified from bacteria. The recombinant Arf1 was compared with purified bovine brain Arf and shown to be nearly identical with respect to immunoblotting, guanine nucleotide binding, GTP hydrolysis, and cholera toxin cofactor activities. The only known chemical difference between the recombinant and brain proteins is the lack of myristic acid at the amino terminus of the expressed protein. The preparation of nucleotide-free Arf1 has allowed a more accurate determination of the binding constants for guanine nucleotides and revealed a significantly higher affinity for GDP than was previously determined. The effect of magnesium ions on nucleotide affinities was also determined and found to be quite different for the different guanine nucleotides. We have shown that GDP binds to the protein in the absence of magnesium, while GTP or guanosine 5'-O-(thiotriphosphate) can only bind to Arf1 in the presence of nanomolar (or higher) levels of the free metal. This characterization of the nucleotide binding and the ability to produce large amounts of a single species of ARF with full retention of a range of activities should greatly facilitate subsequent studies on the structure and function of ARF.
Object-oriented modeling of hybrid systems (1993)

A new methodology for the object--oriented description of models consisting of a mixture of continuous and discrete components is presented. The object--oriented paradigm enables the user to describe such models in a modular fashion that permits the reuse of these models independently of the environment in which they are to be embedded. The paper explains the basic mechanisms needed for object--oriented modeling of hybrid systems by means of language constructs available in the object--oriented modeling language Dymola. It then addresses more advanced concepts such as variable structure models containing e.g. ideal electrical switches, ideal diodes and dry friction. INTRODUCTION Hybrid models contain both continuous and discrete parts. In simulation programs, the continuous parts are described by sets of differential equations and algebraic equations in either explicit form (ODE) or implicit form (DAE). Traditionally, the discrete parts are expressed with event descriptions. A numeric...
The Staphylococcal Ferritins Are Differentially Regulated in Response to Iron and Manganese and via PerR and Fur (2004)

Staphylococcus aureus and Staphylococcus epidermidis ferritin (FtnA and SefA, respectively) homologues are antigenic and highly conserved. A previous study showed that ftnA is a component of the S. aureus PerR regulon with its transcription induced by elevated iron and repressed by PerR, which functions as a manganese-dependent transcriptional repressor. We have further investigated the role of iron and Fur in the regulation of PerR regulon genes ftnA (ferritin), ahpC (alkyl-hydroperoxidase), and mrgA (Dps homologue) and shown that iron has a major role in the regulation of the PerR regulon and hence the oxidative stress response, since in the presence of both iron and manganese, transcription of PerR regulon genes is induced above the repressed levels observed with manganese alone. Furthermore the PerR regulon genes are differentially regulated by metal availability and Fur. First, there is an additional level of PerR-independent regulation of ftnA under low-iron conditions which is not observed with ahpC and mrgA. Second, there is a differential response of these genes to Fur as ftnA expression is constitutive in a fur mutant, while ahpC expression is constitutive under low-Fe/Mn conditions but some repression of ahpC still occurs in the presence of manganese, whereas mrgA expression is still repressed in the fur mutant as in wild-type S. aureus, although there is a decrease in the overall level of mrgA transcription. These studies have also shown that FtnA expression is regulated by growth phase, but maximal transcription of ftnA differs dependent on the growth medium. Moreover, there are significant regulatory differences between the S. aureus and S. epidermidis ferritins, as sefA expression in contrast to that of ftnA is derepressed under low-Fe/Mn ion conditions.
Microcurrent electrical neuromuscular stimulation facilitates regeneration of injured skeletal muscle in mice. (2015)

Conservative therapies, mainly resting care for the damaged muscle, are generally used as a treatment for skeletal muscle injuries (such as muscle fragmentation). Several past studies reported that microcurrent electrical neuromuscular stimulation (MENS) facilitates a repair of injured soft tissues and shortens the recovery period. However, the effects of MENS on the regeneration in injured skeletal muscle are still unclear. The purpose of this study was to investigate the effect of MENS on the regenerative process of injured skeletal muscle and to elucidate whether satellite cells in injured skeletal muscle are activated by MENS by using animal models. Male C57BL/6J mice, aged 7 weeks old, were used (n = 30). Mice were randomly divided into two groups: (1) cardiotoxin (CTX)-injected (CX, n = 15) and (2) CTX-injected with MENS treatment (MX, n=15) groups. CTX was injected into tibialis anterior muscle (TA) of mice in CX and MX groups to initiate the necrosis-regeneration cycle of the muscle. TA was dissected 1, 2, and 3 weeks after the injection. Muscle weight, muscle protein content, the mean cross-sectional areas of muscle fibers, the relative percentage of fibers having central nuclei, and the number of muscle satellite cells were evaluated. MENS facilitated the recovery of the muscle dry weight and protein content relative to body weight, and the mean cross-sectional areas of muscle fibers in CTX-induced injured TA muscle. The number of Pax7-positive muscle satellite cells was increased by MENS during the regenerating period. Decrease in the percentages of fibers with central nuclei after CTX-injection was facilitated by MENS. MENS may facilitate the regeneration of injured skeletal muscles by activating the regenerative potential of skeletal muscles. Key pointsMicrocurrent electrical neuromuscular stimulation (MENS) facilitated the recovery of the relative muscle dry weight, the relative muscle protein content, and the mean cross-sectional areas of muscle fibers of injured TA muscle in mice.The number of satellite cells was increased by MENS during the regenerating phase of injured skeletal muscle.Decrease in the percentages of fibers with central nuclei was facilitated by MENS.MENS may facilitate the regeneration of injured skeletal muscles.
Formation of derivatives of cyclopentane-1,3-dione from oxazolones (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFormation of derivatives of cyclopentane-1,3-dione from oxazolonesHans Muxfeldt and Richard Stephen SchneiderCite this: J. Org. Chem. 1968, 33, 4, 1645–1647Publication Date (Print):April 1, 1968Publication History Published online1 May 2002Published inissue 1 April 1968https://pubs.acs.org/doi/10.1021/jo01268a074https://doi.org/10.1021/jo01268a074research-articleACS PublicationsRequest reuse permissionsArticle Views111Altmetric-Citations2LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
4.3: Transparent ZnO Thin Film Transistor Array for the Application of Transparent AM‐OLED Display (2006)

Abstract We have fabricated 2.15 inch AM‐OLED panel composed of 176 × 144 (106 dpi) transparent pixels driven by ZnO‐TFT. Transparent ZnO thin film deposited by means of atomic layer deposition at 100°C was used for the active channel. The ZnO TFT had a mobility of 1.13cm 2 /V.s, a threshold voltage of 0.8V, and an on/off ratio of 10 6 . The fabrication of the ZnO TFT array for AM‐OLED display has been carried out with four‐mask process. and the integration of the ZnO TFT array and the transparent OLED consisted of a transparent anode and cathode and organic layers led to really transparent display.
Cutting Edge: WIP, a Binding Partner for Wiskott-Aldrich Syndrome Protein, Cooperates with Vav in the Regulation of T Cell Activation (2000)

Wiskott-Aldrich syndrome protein (WASP)-interacting protein (WIP), specifically binds to a region of WASp that is frequently mutated in Wiskott-Aldrich syndrome. Due to the similar phenotypes of WASp- and Vav-deficient T cells, and the putative importance of the WIP/WASp complex in mediating normal signals from the TCR, we investigated the role of WIP in regulating NF-AT/AP-1-mediated gene transcription. We show that WIP has the ability to enhance Vav-mediated activation of NF-AT/AP-1 gene transcription. In addition, we provide evidence that the interaction of WIP with WASp is necessary, but not sufficient for the ability of WIP to regulate NF-AT/AP-1 activity. Finally, we have identified a region in WIP required for its regulation of NF-AT/AP-1 activity. Our data suggests that the WIP-WASp interaction is important for NF-AT/AP-1-mediated gene transcription, and that defects seen in the activation of T cells from WAS patients may be due to the inability of these cells to form a functional WIP/WASp-signaling complex.
Lysyl oxidase-like protein localizes to sites of de novo fibrinogenesis in fibrosis and in the early stromal reaction of ductal breast carcinomas. (1998)

Lysyl oxidase (LO) initiates the first step in the crosslinking of collagens and elastin and has also been shown to function as a tumor suppressor. The purpose of the present work was to determine whether the products of a newly described LO-like gene (LOXL) that encodes a close homolog of LO, the LO-like (LOL) protein, is associated with extracellular matrix remodeling during fibrotic disorders. Specific antibody against LOL identified proteins of approximately 30, 42, 52 and 68 kd in various cells and in bovine aorta. These proteins were immunochemically distinct from the recombinant LO expressed by fibroblasts and from the bovine aorta LO. The LO gene (LOX) and LOXL were transiently up-regulated at early stages of liver granuloma development in Schistosoma mansoni-infected mice, although the peak of LOL mRNA synthesis preceded that of LO. LOL protein and LO were colocalized at sites of fibrogenesis in human lung fibrosis and in the stromal reaction of bronchiolo-alveolar carcinomas and of in situ ductal breast tumors. In conclusion, the LOL protein was identified as a secreted protein and localized in the extracellular matrix in active fibrotic diseases and in the early stromal reaction of breast cancer.
Real-Time Reservoir Model Updating Using Ensemble Kalman Filter (2005)

Abstract Ensemble Kalman Filter (EnKF) has been reported to be very efficient for real-time updating of reservoir model to match the most current production data. Using EnKF, an ensemble of reservoir models assimilating the most current observations of production data are always available. Thus the estimations of reservoir model parameters, and their associated uncertainty, as well as the forecasts are always up-to-date. In this paper, we apply the EnKF for continuously updating an ensemble of permeability models to match real-time multiphase production data. We improve the previously EnKF by resolving the flow equations after Kalman filter updating so that the updated static and dynamic parameters are always consistent. By doing so, we show that the production data are also better matched for some cases. We investigate the sensitivity of using different number of realizations in the EnKF. Our results show that a relatively large number of realizations are needed to obtain stable results, particularly for the reliable assessment of uncertainty. The sensitivity of using different covariance functions is also investigated. The efficiency and robustness of EnKF is clearly demonstrated using an example. By assimilating more production data, new features of heterogeneity in reservoir model can be revealed with reduced uncertainty, resulting in more accurate predictions.
Anisotropic hopping conduction in spin-coated PEDOT:PSS thin films (2007)

The charge transport in spin-coated poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) has been investigated as a function of temperature and electric field. Both the magnitude and the transport mechanism are found to be strongly anisotropic. This striking behavior is quantitatively explained in terms of a morphological model in which flattened, quasimetallic PEDOT-rich grains are organized in horizontal layers that are separated by continuous insulating PSS lamellas. In this model, the in-plane conductivity is described by three-dimensional variable range hopping between $\ensuremath{\sim}25\phantom{\rule{0.3em}{0ex}}\mathrm{nm}$ sized PEDOT-rich particles separated by subnanometer PSS barriers, while the out-of-plane conductivity is described by nearest-neighbor hopping between more widely spaced molecular sites. These length scales are supported by previously reported scanning probe measurements.
Acoustic trauma: Single neuron basis for the ’’half-octave shift’’ (1981)

Exposure to an intense pure tone can induce a loss of hearing sensitivity. If this loss recovers, then the desensitization is regarded as a temporary threshold shift (TTS). At the single auditory neuron level this TTS was monitored as a loss of sensitivity at the neuron's most sensitive or characteristic frequency (CF). When pure-tone exposures were presented at frequency intervals measured from the neuron CF, then a frequency half an octave below the CF was the most effective for inducing a CF TTS. All exposure frequencies higher than half an octave below the CF produce a marked reduction in TTS growth with intensity, when compared to lower exposure frequencies. This behavior is such that, with increasing exposure frequency higher than the -1/2-octave point, the intensity needed to produce a given TTS grew faster than the neuron sensitivity. However, below the -1/2-octave point all exposure frequencies were similarly behaved. Strong similarities exist between the frequency-specific requirements for TTS and the mechanical and neural nonlinearities found in other studies. This suggests that the half-octave shift may well be a direct result of basilar membrane nonlinearities.
Induced pluripotent stem cells from CINCA syndrome patients as a model for dissecting somatic mosaicism and drug discovery (2012)

Chronic infantile neurologic cutaneous and articular (CINCA) syndrome is an IL-1-driven autoinflammatory disorder caused mainly by NLRP3 mutations. The pathogenesis of CINCA syndrome patients who carry NLRP3 mutations as somatic mosaicism has not been precisely described because of the difficulty in separating individual cells based on the presence or absence of the mutation. Here we report the generation of NLRP3-mutant and nonmutant-induced pluripotent stem cell (iPSC) lines from 2 CINCA syndrome patients with somatic mosaicism, and describe their differentiation into macrophages (iPS-MPs). We found that mutant cells are predominantly responsible for the pathogenesis in these mosaic patients because only mutant iPS-MPs showed the disease relevant phenotype of abnormal IL-1β secretion. We also confirmed that the existing anti-inflammatory compounds inhibited the abnormal IL-1β secretion, indicating that mutant iPS-MPs are applicable for drug screening for CINCA syndrome and other NLRP3-related inflammatory conditions. Our results illustrate that patient-derived iPSCs are useful for dissecting somatic mosaicism and that NLRP3-mutant iPSCs can provide a valuable platform for drug discovery for multiple NLRP3-related disorders.