gebhart/patrepeval huggingface dataset:
Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast (2011)

A yeast strain lacking Met4p, the primary transcriptional regulator of the sulfur assimilation pathway, cannot synthesize methionine. This apparently simple auxotroph did not grow well in rich media containing excess methionine, forming small colonies on yeast extract/peptone/dextrose plates. Faster-growing large colonies were abundant when overnight cultures were plated, suggesting that spontaneous suppressors of the growth defect arise with high frequency. To identify the suppressor mutations, we used genome-wide single-nucleotide polymorphism and standard genetic analyses. The most common suppressors were loss-of-function mutations in OPI1, encoding a transcriptional repressor of phospholipid metabolism. Using a new system that allows rapid and specific degradation of Met4p, we could study the dynamic expression of all genes following loss of Met4p. Experiments using this system with and without Opi1p showed that Met4 activates and Opi1p represses genes that maintain levels of S-adenosylmethionine (SAM), the substrate for most methyltransferase reactions. Cells lacking Met4p grow normally when either SAM is added to the media or one of the SAM synthetase genes is overexpressed. SAM is used as a methyl donor in three Opi1p-regulated reactions to create the abundant membrane phospholipid, phosphatidylcholine. Our results show that rapidly growing cells require significant methylation, likely for the biosynthesis of phospholipids.
Arabinoxylo-Oligosaccharides and Inulin Impact Inter-Individual Variation on Microbial Metabolism and Composition, Which Immunomodulates Human Cells (2018)

Fecal batch fermentations coupled to cocultures of epithelial cells and macrophages were used to compare how arabinoxylo-oligosaccharides (AXOS) and inulin modulate gut microbial activity and composition of three different human donors and subsequently the epithelial permeability and immune response. Both inulin and AXOS decreased the pH during incubation (-1.5 pH units), leading to increased productions of acetate, propionate, and butyrate. Differences in terms of metabolites production could be linked to specific microbial alterations at genus level upon inulin/AXOS supplementation (i.e., Bifidobacterium, Bacteroides, Prevotella and unclassified Erysipelotrichaceae), as shown by 16S-targeted Illumina sequencing. Both products stimulated gut barrier and immune function with increases in TEER, NF-KB, IL-10, and IL-6. Ingredients with different structures selectively modulate the microbiota of a specific donor leading to differential changes at metabolic level. The extent of this effect is donor specific and is linked to a final specific modulation of the host's immune system.
Spin-Density Functionals from Current-Density Functional Theory and Vice Versa:A Road towards New Approximations (1997)

It is shown that the exchange-correlation functional of spin-density functional theory is identical, on a certain set of densities, with the exchange-correlation functional of current-density functional theory. This rigorous connection is used to construct new approximations of the exchange-correlation functionals. These include a conceptually new generalized-gradient spin-density functional and a nonlocal current-density functional.
Hepatitis C virus infection of human hepatoma cell line 7721 in vitro (2001)

The hepatoma line 7721 is not only susceptible to HCV but also supports its long-term replication in vitro.
Dynamic topological predicates and notifications in moving objects databases (2005)

This work addresses the problem of efficient reactive management of topological predicates in MOD (Moving Objects Databases) settings. Detecting the satisfiability of such predicates in mobile and dynamic environments requires management of continuous and persistent conditions. We introduce two dynamical topological predicates: moving-along and moving-towards and we present efficient algorithmic solutions for their processing. Based on this, we subsequently take a deeper insight in the behavioral aspects of a MOD which manages them and we argue that the traditional ECA (Event Condition Action) paradigm, while it may ensure correct behavior, is not well-suited for enabling the users to declaratively specify some of the parameters that may affect the efficiency aspect of the reactive behavior. Towards this end, we introduce the (ECA)2 (Evolving and Context-Aware Event-Condition-Action) paradigm as a tool for specification of the triggers used by a MOD that handles requests which span over a time-interval in dynamic environments.
Estimation of time and frequency selective channels in OFDM systems: a kalman filter structure (2005)

A Kalman-filter based channel estimator of OFDM systems in a time-frequency-selective fading environment is studied. Based on an AR model of the dynamic channel, a vector Kalman filter of dimension equal to the number of subcarriers can be used to track the channel. It is proposed that a scalar Kalman filter be employed for each subcarrier to estimate the channel gain. The channel estimate is further refined with an MMSE combiner. This two-step structure, with the per-subchannel Kalman estimator explores the time-domain correlation of each subchannel, and with the MMSE combiner explores the frequency-domain correlations between the subchannels, offering a performance comparable to the much more complicated vector Kalman estimator.
Chemical constituents of the volatile oil from leaves of Annona coriacea and in vitro antiprotozoal activity (2011)

The essential oil of the leaves from Annona coriacea Mart., Annonaceae, was extracted by hydrodistillation in a Clevenger apparatus and analyzed by GC/MS and GC/FID. The oil yield was 0.05% m/m. Sixty compounds were identified, in a complex mixture of sesquiterpenes (76.7%), monoterpenes (20.0%) and other constituents (3.3%). Bicyclogermacrene was its major compound (39.8%) followed by other sesquiterpenes. Most of the monoterpenes were in low concentration (<1%). Only β-pinene and pseudolimonene presented the highest level of 1.6%. The volatile oil presented anti-leishmanial and trypanocidal activity against promastigotes of four species of Leishmania and trypomastigotes of Trypanosoma cruzi, showing to be more active against Leishmania (L.) chagasi (IC50 39.93 µ g/mL) (95% CI 28.00-56.95 µ g/mL).
Myocardial protection by the novel vasodilating beta-blocker, carvedilol: potential relevance of anti-oxidant activity. (1993)

Taken together, these data indicate that carvedilol is a potent cardioprotective drug, which presumably acts by multiple mechanisms, possibly including a novel anti-oxidant effect that is not shared by other beta-blockers.
Regulation of the Intracellular Free Iron Pool by Dpr Provides Oxygen Tolerance to <i>Streptococcus mutans</i> (2004)

Dpr is an iron-binding protein required for oxygen tolerance in Streptococcus mutans. We previously proposed that Dpr could confer oxygen tolerance to the bacterium by sequestering intracellular free iron ions that catalyze generation of highly toxic radicals (Y. Yamamoto, M. Higuchi, L. B. Poole, and Y. Kamio, J. Bacteriol. 182:3740-3747, 2000; Y. Yamamoto, L. B. Poole, R. R. Hantgan, and Y. Kamio, J. Bacteriol. 184:2931-2939, 2002). Here, we examined the intracellular free iron status of wild-type (WT) and dpr mutant strains of S. mutans, before and after exposure to air, by using electron spin resonance spectrometry. Under anaerobic conditions, free iron ion concentrations of WT and dpr strains were 225.9 +/- 2.6 and 333.0 +/- 61.3 microM, respectively. Exposure of WT cells to air for 1 h induced Dpr expression and reduced intracellular free iron ion concentrations to 22.5 +/- 5.3 microM; under these conditions, dpr mutant cells maintained intracellular iron concentration at 230.3 +/- 28.8 microM. A decrease in cell viability and genomic DNA degradation was observed in the dpr mutant exposed to air. These data indicate that regulation of the intracellular free iron pool by Dpr is required for oxygen tolerance in S. mutans.
Robust Multiview 3D Pose Estimation Using Time of Flight Cameras (2021)

In this work, we introduce a robust multi-view 3D pose estimation method which leverages infra-red intensity image and the depth information from the ToF camera. We use the intensity image as an input to a CNN based 2D key point detector from multiple view ports and forward project them to calculate the 3D joint position. If a keypoint is missing in one of the views we benefit from the depth information from the ToF camera. This results in a robust system which is robust against material reflectivity and occlusion. Our experiments show that the system is able to deliver 3D joint positions with a maximum positional error of only 4 cm independent of the material reflectivity. We also compare our technique with different 3D key point estimation techniques. We compare our system to a state-of-the-art CNN based multi-view depth based pose estimation technique to lift 2D key points from a single image to 3D pose. The maximum euclidean distance from the ground truth and its deviation for each system are evaluated against VICON, a marker based motion capture system.
Loss of Neural Cell Adhesion Molecule Induces Tumor Metastasis by Up-regulating Lymphangiogenesis (2004)

Reduced expression of neural cell adhesion molecule (NCAM) has been implicated in the progression to tumor malignancy in cancer patients. Previously, we have shown that the loss of NCAM function causes the formation of lymph node metastasis in a transgenic mouse model of pancreatic beta cell carcinogenesis (Rip1Tag2). Here we show that tumors of NCAM-deficient Rip1Tag2 transgenic mice exhibit up-regulated expression of the lymphangiogenic factors vascular endothelial growth factor (VEGF)-C and -D (17% in wild-type versus 60% in NCAM-deficient Rip1Tag2 mice) and, with it, increased lymphangiogenesis (0% in wild-type versus 19% in NCAM-deficient Rip1Tag2 mice). Repression of VEGF-C and -D function by adenoviral expression of a soluble form of their cognate receptor, VEGF receptor-3, results in reduced tumor lymphangiogenesis (56% versus 28% in control versus treated mice) and lymph node metastasis (36% versus 8% in control versus treated mice). The results indicate that the loss of NCAM function causes lymph node metastasis via VEGF-C- and VEGF-D-mediated lymphangiogenesis. These results also establish Rip1Tag2;NCAM-deficient mice as a unique model for stochastic, endogenous tumor lymphangiogenesis and lymph node metastasis in immunocompetent mice.
Evidence of functional lymphocytes in some (leaky) scid mice. (1988)

Although the majority of severe combined immune deficiency (scid) mice lack functional lymphocytes, some (2-23%) appear to develop a limited number of B and T cells between 3 and 9 mo old. Most of these leaky scid mice were shown to contain very few clones (less than or equal to 3) of Ig-producing plasmacytes. Clonal progeny were distributed unevenly in the lymphatic tissues and appeared as discrete plasmacytic foci. In many cases, individual clones persisted for several months and produced abnormally high concentrations of Ig that included multiple isotypes. Functional T cells were inferred from the ability of leaky mice to reject allogeneic skin grafts, a T cell-dependent reaction. Interestingly, approximately 40% of leaky mice developed thymic lymphomas. In other respects, leaky mice resembled regular scid mice; e.g., their splenic cells failed to express common lymphocyte antigens (Ly-5[B220], Ly-1) and to proliferate in response to lymphocyte mitogens. Histologically, their lymphoid tissues retained the same general pattern of severe lymphocytic deficiency as scid mice.
Mobility of lysozyme inside oxidized starch polymer microgels (2011)

The aim of this paper is to determine the mobility of protein molecules inside oxidized potato starch polymer (OPSP) microgel particles (spherical, 10–20 µm in diameter). This provides relevant information for controlled uptake and release applications of such systems. The mobility of Alexa-488 labelled lysozyme inside the microgel is measured by fluorescence recovery after photobleaching (FRAP) in combination with confocal laser scanning microscopy (CLSM). CLSM images show that the protein molecules distribute quite homogeneously over the microgel particles. By fitting the FRAP data with a model based on exchange between bleached and unbleached protein molecules inside the gel, we identified several protein fractions of different mobility. Increasing the salt concentration (NaCl) or the pH causes a shift in the distribution towards the more mobile fractions. This is consistent with earlier uptake and release measurements, which showed that the binding affinity decreases with increasing salt concentration and pH. At low protein concentrations, at which the microgel is not saturated with protein, the mobility of the bound protein molecules is more restricted than at protein concentrations where the uptake is complete. This is attributed to binding of the protein molecules to multiple binding sites. The model explains reasonably the mechanism of protein mobility inside the microgel, indicating that embedded ingredients with charge properties comparable to those of lysozyme can be protected at low salt concentration and low pH. Increasing the salt concentration or the pH triggers the release.
ScalableBody (2016)

Most telepresence robots have a fixed-size body, and are unable to change the camera or display position. Therefore, although making eye contact is important in human expression, current fixed-size telepresence robots fail to achieve this.
Mobility of Asphaltene Samples Studied by <sup>13</sup>C NMR Spectroscopy (1998)

Cerro Negro (CN) and Furrial asphaltenes have been analyzed using both liquid and solid-state 13C NMR spectroscopy. The spin−lattice relaxation times exhibited by the carbons in the resin containing CN asphaltene samples indicate that these carbons relax more slowly than the equivalent carbons in the resin-free samples. This fact suggests a higher mobility of the molecules in the sample in the presence of resins. CP/MAS experiments showed that, in general, all asphaltene samples have rigid alicyclic structures. This fact is consistent with the presence of condensed aliphatic rings. The results of the measurements of the cross-polarization relaxation times obtained from the variable contact-time CP/MAS experiments indicate that Cerro Negro samples are more “mobile” than Furrial. These findings point toward the presence of a larger number of CH2 chains bonding different ring clusters in the Cerro Negro samples.
Control of light polarization in InGaAsP/InP lasers by injection of light pulses (1997)

Light emission from a ridge waveguide 1.3 μm InGaAsP/InP semiconductor laser pumped both electrically and optically was analyzed by polarization- and time-resolved measurements. The electric and the optical excitation was realized with a dc-bias current and with 150 ps pulses from a Q-switched Nd-YAG laser at 1.064 μm wavelength, respectively. The pump light was introduced into the InGaAsP/InP laser through a window opened in the substrate gold contact. The steady-state P–I characteristics of the semiconductor laser exhibited a transition from TM- to TE-polarized light emission if the injection current surpasses a certain value that depends on the heatsink temperature. Depending on the dc-bias current and the optical pulse power, a variety of different emission characteristics of the semiconductor laser were observed: pure TE or TM pulsations, in combination with a background cw emission in some cases; simultaneous emission of TE and TM pulses and switching between TM and TE emission states with switching times as short as 30 ps.
Quorum sensing between bacterial species on the skin protects against epidermal injury in atopic dermatitis (2019)

Colonization of the skin by <i>Staphylococcus aureus</i> is associated with exacerbation of atopic dermatitis (AD), but any direct mechanism through which dysbiosis of the skin microbiome may influence the development of AD is unknown. Here, we show that proteases and phenol-soluble modulin α (PSMα) secreted by <i>S. aureus</i> lead to endogenous epidermal proteolysis and skin barrier damage that promoted inflammation in mice. We further show that clinical isolates of different coagulase-negative staphylococci (CoNS) species residing on normal skin produced autoinducing peptides that inhibited the <i>S. aureus agr</i> system, in turn decreasing PSMα expression. These autoinducing peptides from skin microbiome CoNS species potently suppressed PSMα expression in <i>S. aureus</i> isolates from subjects with AD without inhibiting <i>S. aureus</i> growth. Metagenomic analysis of the AD skin microbiome revealed that the increase in the relative abundance of <i>S. aureus</i> in patients with active AD correlated with a lower CoNS autoinducing peptides to <i>S. aureus</i> ratio, thus overcoming the peptides' capacity to inhibit the <i>S. aureus agr</i> system. Characterization of a <i>S. hominis</i> clinical isolate identified an autoinducing peptide (SYNVCGGYF) as a highly potent inhibitor of <i>S. aureus agr</i> activity, capable of preventing <i>S. aureus</i>-mediated epithelial damage and inflammation on murine skin. Together, these findings show how members of the normal human skin microbiome can contribute to epithelial barrier homeostasis by using quorum sensing to inhibit <i>S. aureus</i> toxin production.
Study of long term structural and functional changes in medically controlled glaucoma (2014)

AIM: Prospectively analyze the long term structural and functional changes in patients of primary open angle glaucoma(POAG) receiving medical therapy(beta blockers and non beta blockers). In this study an attempt has been made to evaluate whether medical reduction of IOP prevents or delays the progression of glaucomatous visual field loss and/or optic nerve damage in patients with open angle glaucoma. · METHODS: Study conducted over a period of 27 months,at a tertiary eye care hospital including both eyes of 40 patients with POAG. Group 1(20 patients,40 eyes) received beta-blockers,and Group 2(20 patients,40 eyes) received non-beta-blockers. Each patient underwent intraocular pressure measurement,best corrected visual acuity,slit-lamp,fundus examination,gonioscopy,central corneal thickness,visual field assessment by Humphrey automated perimetry and retinal nerve fibre layer thickness by Stratus optical coherence tomography at baseline and at two subsequent visits. The average time interval between each visit was 10-11 months. The statistical analysis was done using one-way analysis of variance(ANOVA). Post-hoc test,using tukey' method were adopted. Probablity(P) value of 0.05 or less was considered to be statistically significant. ·RESULTS: A total of 80 eyes of 40 patients of POAG were enrolled,24 males,16 females,age group 50-80 years. In both beta and non beta blocker group,reduction(improvement) in mean IOP from initial levels to the levels achieved at the 2nd and 3rd visits was statistically significant. One way ANOVA(df=2),fisher f value =11.64,P =0.000,one way ANOVA(df =3),fisher f value =35.61,P =0.000. Both mean deviation(MD) and pattern standard deviation(PSD) in both beta and nonbeta blockers at different visits were not statistically significant. Retinal nerve fibre layer thickness(RNFL)-only mean inferior retinal nerve fibre layer,the difference between the mean value in beta and non beta blocker groupwere statistically significant. [unpaired t test value(df =78) =2.27,P =0.03]. Side effects with beta blocker were conjunctival hyperemia(10%),burning(5%),and conjunctival hyperemia(5%) in non beta blockers. ·CONCLUSION: Non-beta-blockers are as effective as beta-blockers in bringing about a significant lowering of intraocular pressure to the normal range,and in preventing progressive damage to the visual fields and retinal nerve fibre layer. The absence of systemic side effects and superior IOP lowering efficacy has made non beta-blockers attractive for first line therapy for the treatment of glaucoma worldwide.
Institutions and entrepreneurship (2010)

How do institutions affect entrepreneurship? Conversely, how do entrepreneurs impact institutions? Institutional theory has long struggled to explain the action and agency inherent in entrepreneurship (DiMaggio, 1988; Barley & Tolbert, 1997). Contemporary institutionalist research in organization studies began with the question of how the institutional environment shapes the structures and behaviors of existing organizations. This research largely focused on how normative, regulative, and cognitive dimensions of the environment (Scott, 2008) constrain large, mature organizations and the circumstances that increase the adoption of new structures by such organizations (Meyer & Rowan, 1977; DiMaggio & Powell, 1983; Tolbert & Zucker, 1983). A subsequent wave of research in the institutional tradition focused on institutional change within mature organizational fields (see Dacin, Goodstein, & Scott, 2002). Some recent research has studied the actors – “institutional entrepreneurs” – that create new or transform existing institutions (e.g., Greenwood, Suddaby, & Hinings, 2002; Maguire, Hardy, & Lawrence, 2004). Much less attention, however, has been paid within the institutional-theory literature to entrepreneurship: the processes of founding and managing new organizations.
The Characterization of High Temperature Electronics for Future Aircraft Engine Digital Electronic Control Systems (1988)

The characterization of high temperature electronics is presented including high temperature effects, semiconductors and barrier metallizations. Design solutions and material selections for mitigation of high temperature effects are indicated. The following semiconductor materials are considered as future high temperature candidates: - Silicon (Si) - Gallium arsenide (GaAs) - Gallium phosphide (GaP) - Silicon carbide (SiC) - Diamond like carbon (C) This characterization was originally prepared in accordance with the USAF Future Advance Controls Technology Study (FACTS).
Capability of etched multilayer EUV mask fabrication (2014)

Recently, development of next generation extremely ultraviolet lithography (EUVL) equipment with high-NA (Numerical Aperture) optics for less than hp10nm node is accelerated. Increasing magnification of projection optics or mask size using conventional mask structure has been studied, but these methods make lithography cost high because of low through put and preparing new large mask infrastructures. To avoid these issues, etched multilayer EUV mask has been proposed. As a result of improvement of binary etched multilayer mask process, hp40nm line and space pattern on mask (hp10nm on wafer using 4x optics) has been demonstrated. However, mask patterns are easily collapsed by wet cleaning process due to their low durability caused by high aspect ratio. We propose reducing the number of multilayer pairs from 40 to 20 in order to increase durability against multilayer pattern collapse. With 20pair multilayer blank, durable minimum feature size of isolated line is extended from 80nm to 56nm. CD uniformity and linearity of 20pair etched multilayer pattern are catching up EUV mask requirement of 2014.