gebhart/patrepeval huggingface dataset:
Oral sensitization with shrimp tropomyosin induces in mice allergen-specific IgE, T cell response and systemic anaphylactic reactions (2008)

Appropriate murine models of shrimp tropomyosin (ST) allergy would be useful in investigating the mechanisms underlying food allergy in human subjects, as well as for the pre-clinical evaluation of efficacy and safety of novel therapeutic approaches. These models should mimic immune and clinical features of human disease, including anaphylactic response. We sensitized C3H/HeJ mice by the oral route with purified ST using cholera toxin (CT) as adjuvant. ST-specific IgE, IgG1, IgG2a and IgA responses were evaluated by ELISA. Spleen cell proliferation and cytokine production by allergen-specific activation were assessed. Jejunum and colon fragments were collected to evaluate the local expression of cytokine genes by PCR. Local and systemic anaphylactic reactions induced by oral ST challenge were scored according to symptoms observed. Faecal samples were collected to assess local IgA production and histamine levels. Oral sensitization with ST plus CT induced in mice significant levels of serum IgE and IgG1 and faecal IgA. ST-specific cell proliferation and IL-4, IL-13 and IFN-gamma cytokine production were induced in the spleen. After oral challenge, 100% of mice had anaphylactic symptoms while no symptoms were observed in challenged naive mice. Faecal histamine content after ST challenge appeared significantly increased in sensitized mice when compared with that observed in pre-immune mice. Jejunum mRNA expression of T(h)2 cytokines was up-regulated by ST sensitization. These results support the importance of the oral way of sensitization and of the in-depth characterization of the anaphylactic response for the development of a suitable in vivo model of food allergy.
Characterizing Bitcoin donations to open source software on GitHub (2019)

Web-based hosting services for version control, such as GitHub, have made it easier for people to develop, share, and donate money to software repositories. In this paper, we study the use of Bitcoin to make donations to open source repositories on GitHub. In particular, we analyze the amount and volume of donations over time, in addition to its relationship to the age and popularity of a repository. We scanned over three million repositories looking for donation addresses. We then extracted and analyzed their transactions from Bitcoin's public blockchain. Overall, we found a limited adoption of Bitcoin as a payment method for receiving donations, with nearly 44 thousand deposits adding up to only 8.3 million dollars in the last 10 years. We also found weak positive correlation between the amount of donations in dollars and the popularity of a repository, with highest correlation (r=0.013) associated with number of forks.
A High Temperature Specimen Stage Heated by Electron Bombardment (1960)

A new specimen holder which is heated by the electron bombardment has been developed. The temperature of the holder and the image brightness can be controlled independently on each other. The power required to raise the temperature of the holder at l,000°C is less than 10W. Owing to the very low power consumption, the high resolution better than 60 is easily obtained even at a high temperature such as 850°C.
HPLC analysis of Phenolic Substances and Anti-Alzheimer's Activity of Korean<i>Quercus</i>Species (2016)

This study aimed to establish the quantitative method to analyze the content of peroxynitrite-scavengers belonging to polyphenols in six Korean Quercus species (Quercus mongolica, Q. dentata, Q. acutissima, Q. alienta, Q. serrata, and Q. variabilis) by HPLC. The twelve peroxynitrite-scavengers, flavanols (catechins: (+)-catechin, (−)-epicatechin, and (−)-epigallocatechin), flavonols (kaempferol and quercetin), flavonol glycosides (astragalin, quercitrin, and isoquercitrin), flavonol acylated glycosides (astragalin 6''-gallate and isoquercitrin 6''-gallate), gallic acid and its dimer (ellagic acid) were analyzed by HPLC. Further, anti-Alzheimer's activity was assayed in a passive avoidance testusing mice by measuring the retention latency (sec), the concentration of acetylcholine (ACh), and acetylcholinesterase (AChE) activity. Simultaneous analysis of the extracts of the six Quercus leaves was achieved on a Capcell C18 column (5 µm, 250 mm × 4.6 mm i.d.) with a gradient elution of 0.05% HAc and 0.05% HAc in CH3CN. In the extract of Q. mongolica leaves, the content of gallic acid (32.53 mg/g), (+)-catechin (28.78 mg/g), (−)-epicatehin (22.03 mg/g), astragalin 6''-gallate (20.94 mg/g), and isoquercitrin 6''-gallate (44.11 mg/g) and peroxynitrite-scavenging activity (IC50, 0.831 µg/ml) were high. This extract delayed the retention latency and inhibited acetylcholinesterase activity in scopolamine-induced memory impairment of mice, suggesting that it has anti-Alzheimer's activity.
Epidemiology of Hepatitis C Virus in Bangladeshi General Population (2009)

Background: Hepatitis C virus is encountered sporadically in Bangladesh. It results in a wide range liver diseases, with asymptomatic acute hepatitis rarely at one end to HCC at the other end of the spectrum. Methods: 1018 individuals of different age groups and sex with varied religious, educational and social backgrounds were tested for anti-HCV by ELISA. Before testing, blood samples were preserved at -20C. The study was conducted in a semi-urban location on the outskirts of Dhaka. Results: 0.88% tested positive for anti HCV. None of them tested positive for HBsAg. There was a male predominance and those who tested positive were mostly between 17 and 50 years of age. Major risk factors for exposure to HBV appeared to be injudicious use of injectable medications, treatment by unqualified, traditional practitioners, mass-vaccination against cholera and smallpox, barbers and body piercing. Conclusion: HCV remains an important cause of morbidity and mortality in Bangladesh.
Anionic Clay Modified Electrode for Detection of Alcohols. An Electrocatalytic Amperometric Sensor (2000)

The mechanism of the electrocatalytic oxidation towards a wide series of alcohols, by an electrode covered with the [Ni/Al–Cl] hydrotalcyte-like clay, has been analyzed in the different steps it consists of. Such a clay has been reported to be electrically conductive via a mechanism that shows similarities with that of the redox polymers. The overall process occurs in quite a complicated physical system that is completely different both from a classical electrode-solution one and from an electrode covered with a film of heterogeneous catalyst. By varying the characteristics of the substrate, in terms of steric hindrance and dipole moment of the molecule, the factors affecting the redox mediator-substrate reaction have been studied. The concentration ranges where the amperometric response varies linearly have been determined for the different substrates considered.
Inhibitory effects of various derivatives of azidothymidine triphosphate on reverse transcriptase and DNA polymerases (1988)

status: Published
Probes for the Conformational Transitions of Phosphorylase <i>b</i> (1971)

1 The effects of temperature and ligands (AMP, IMP and glucose 1-phosphate) on the properties of rabbit muscle phosphorylase b have been examined by several methods. 2 The non-covalently bound fluorescent probe 2-methylanilino naphthalene 6-sulphonate is shown to detect the dimer to tetramer transition induced by AMP. The aggregation is slow and has a second order rate constant of 3.1×105 M−1 min−1. 3 The interaction of Mn2+ with phosphorylase b is studied by proton relaxation enhancement and electron spin resonance. The limitations of graphical procedures for analysing proton relaxation enhancement data are discussed and better iterative procedures are presented. 4 There are two equivalent and independent binding sites for Mn2+ per phosphorylase b dimer. These sites (Kd= 0.17 mM) have a 30-fold higher affinity for Mn2+ than those involved in tetramer formation as measured by methylanilino naphthalene sulphonate fluorescence. 5 The reaction of a specific sulphydryl reagent, 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole with phosphorylase b can be separated into sets of one fast and two slowly reacting groups per protomer. Modification of one of the slow groups results in inactivation. 6 The temperature dependences of the proton relaxation rates and of the pattern of – SH reactivity discontinuities at around 13 °C. This has been interpreted as a change in the enzyme conformation. 7 AMP increases the limiting proton relaxation enhancement from 10.9 to 14 and decreases the reactivity with 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole of the slow – SH groups. The increase in the limiting proton relaxation enhancement is not due to aggregation but is likely to be a result of a ligand induced conformational chnage. 8 Glucose 1-phosphate decreases the limiting proton relaxation enhancement from 10.9 to 5.8 and increases the reactivity of one of the slow thiols. On this basis it is argued that the glucose 1-phosphate induced change is different from that caused by AMP. 9 The limiting proton relaxation enhancement in the presence of both AMP and glucose 1-phosphate is about 9 suggesting that this represents a fourth conformation. 10 Phosphorylase b modified with 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole in the presence of AMP is fully active and the fluorescence of the nitrobenzo-oxa-diazole lable is partially quenched when AMP binds. The fluorescence changes show the same AMP concentration dependence as the increase in the proton relaxation enhancement, suggesting that the two probes detect the same transition in the enzyme. 11 A scheme is presented for the activation of phosphorylase b by AMP and involves transitions between four conformations of the enzyme at room temperature. These transitions still occur at low temperature but are superimposed on a different basic form of the enzyme.
<i>In situ</i>calibration of an interferometric velocity sensor for measuring small scale flow structures using a Talbot-pattern (2017)

Small scale flow phenomena play an important role across engineering, biological and chemical sciences. To gain deeper understanding of the influence of those flow phenomena involved, measurement techniques with high spatial resolution are often required, presuming a calibration of very low uncertainty. To enable such measurements, a method for the in situ calibration of an interferometric flow velocity profile sensor is presented. This sensor, with demonstrated spatial resolution better than 1 μm, allows for spatially-resolving measurements with low velocity uncertainty in flows with high velocity gradients, on condition that the spatial behavior of the interference fringe systems is well-known by calibration with low uncertainty, especially challenging to obtain at applications with geometries difficult to access. The calibration method described herein uses three interfering beams to form the interference fringe systems of the sensor, yielding Doppler burst signals exhibiting two peaks in the frequency domain whose amplitude ratio varies periodically along the measurement volume major z-axis, giving a further independent value of the axial tracer particle position that can be used to determine the calibration functions of the sensor during the flow measurement. A flow measurement in a microchannel experimentally validates that the presented approach allows for simultaneously estimating the calibration functions and the velocity profile, providing flow measurements with very low systematic measurement errors of the particle position of less than 400 nm (confidence interval 95%). In that way, the interferometric flow velocity profile sensor utilizing the in situ self-calibration method promises valuable insights on small scale flow phenomena, such as those given in shear and boundary layer flows, by featuring reliable flow measurements due to minimum systematic and statistical measurement errors.
High‐rate, power‐efficient coding for optical communication: Design and performance evaluation (1992)

Abstract In the direct detection optical communication system which detects the optical pulse by counting the photons, it is known that the information transmitted by each photon has an important role in the performance evaluation of the error‐correcting code, in addition to the code rate and the decoding error rate. Especially, for the code which can achieve arbitrarily small error rate by increasing the code length, the performance of the code can be evaluated based on the code rate and the information efficiency. However, these two evaluation measures are in a trade‐off relation; and there is a limit if one attempts to improve both. From such a viewpoint, this paper determines the bounds for the code rate and the information efficiency and determines the limit of performance when the ideal error‐correcting code is applied to the direct detection optical communication. Then, as a code which can arbitrarily achieve a small error rate, a new code based on the iterated code is proposed. It is shown that if the code rate is less than 0.75, the proposed code can achieve a better information efficiency than the conventional code with the same code rate.
Emerging device solutions for the post-classical CMOS era (2003)

In pushing the scaling limits down to sub 50 nm devices it is well known that classical CMOS will reach its limits. Innovative processes, materials and/or device architectures will be required to overcome the major bottlenecks. In this paper a short overview of the challenges of scaling will first be presented and the major bottlenecks will be identified. These are related to both physical and technological limitations. The most likely solutions as perceived in the recent international roadmaps will be discussed in more detail.
Exact Theory of Tracking of Moving Underwater Object by Short-Base Navigation System Attached to an Imperfectly Stabilized Moving Ship (1970)

The theory of locating a deep submersible by measurement of time delays in arrival of an acoustic pulse from the deep submersible to three hydrophones of a short-base navigational system has been developed in detail. The theory incorporates all the relevant variables such as the translational and rotational positions and velocities of the tracking ship and the variation of acoustic speed with depth. No restrictions have been placed on the relative values of the horizontal and vertical coordinates of the submersible relative to the tracking ship. A numerical example is given to demonstrate the use of the theory and to show the effects of ignoring the motion of the tracking ship and the variation of acoustic speed with oceanic depth.
Nonequilibrium thermodynamics and Fisher information: Sound wave propagation in a dilute gas (2003)

As recently shown, a constrained Fisher-information extremizing (CFIE) process is able to deal with both equilibrium and nonequilibrium thermodynamic processes, thus being able to reproduce results deduced by a recourse to Boltzmann's transport equation (BTE). Here, we discuss the propagation of sound waves in a dilute gas and compare the ensuing CFIE solutions with those obtained by a recourse to Grad's approach to the BTE. The final molecular distribution function arrived at is the same following two alternative routes, either (i) the BTE via the Grad approach or (ii) the constrained Fisher treatment that does not require the use of the BTE. The way the necessary a priori information is used in these two instances, is however, quite different.
The Lung Microbiome of Ugandan HIV-Infected Pneumonia Patients Is Compositionally and Functionally Distinct from That of San Franciscan Patients (2014)

Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome was significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population.
Phase transformations under dynamic loading (2019)

Dynamic loading of materials on the micro-scale has become of prime importance. For phase transformations in various materials that exhibit the brittle-to-ductile transition, there is an ongoing debate as to what precise mechanisms are responsible for the transition but many theories have converged over the years. Silicon nitride was shown to undergo a phase transformation from hexagonal to the cubic phase under pressure. However, no phase transformations have been observed for silicon carbide under pressures that can be achieved during contact loading. For the case of silicon, work has been done to understand the phase transformations that take place during machining using molecular dynamics simulations. For Gallium arsenide (GaAs), the pressure-induced phase transformation during ultra-precision cutting was inferred from the high values of residual strains in the finished surface, as measured by Raman microspectroscopy. However, the pressure-induced transformation in GaAs under contact loading is not likely to occur at room temperature.
Antibody effector function is regulated by a combination of adaptive and innate signals (2012)

Background The Fc region of IgG contains a single N-glycosylation site, which is known to be important for effecting immune activation through interaction with Fc receptors and complement molecules. Changes to the structure of these sugars can thus be very influential in determining the specific effector function of individual antibodies. Whereas therapeutic antibodies can be produced with particular effector functions in vitro, little is known regarding how glycosylation is regulated in primary B cells.
8 Hydrogen in metals (2000)

Abstract This chapter focuses on special classes of materials. For QENS studies metal/hydrogen systems are particularly suited due to the huge incoherent scattering cross section of H, low concentrated systems and thus single particle behaviour can be studied, the mobility is large and thus well-pronounced line broadening are obtained, and if H is replaced by D, additionally coherent QENS can be performed. Long range diffusion studies are presented for intermetallic hydrides which allow statements about the rate limiting step in the hydrogen absorption kinetics. For NbDx, an extensive study of the collective diffusion is presented; the separation of coherent and incoherent scattering is done both by software (skillful data evaluation) and by hardware (polarization analysis). Then the diffusion mechanisms in metal/hydrogen systems of increasing complexity are discussed, where QENS exhibits its full power because of single-crystalline samples: H in fcc metals, H in bcc metals, hexagonal closed packed α-phase hydrides, β-V2H as an example of an ordered metal hydride, and LaNi5Hα as an example of an intermetallic hydride. Another scientific problem is the nature of the single diffusion step: hydrogen tunnelling in Nb doped with O, N, C, and in α-ScHx. Tunnelling is even more pronounced for the positive muon, an exotic isotope of the proton; muon diffusion studies in Al and Cu are presented for comparison. Finally, examples of hydrogen diffusion in disordered systems (crystalline metals with trapping impurities or even amorphous metals) are discussed.
Single-molecule imaging of the H-ras membrane-anchor reveals domains in the cytoplasmic leaflet of the cell membrane (2007)

In the last decade evidence has accumulated that small domains of 50-700 nm in diameter are located in the exoplasmic leaflet of the plasma membrane. Most of these domains supposedly consist of specific sets of lipids and proteins, and are believed to coordinate signal transduction cascades. Whether similar domains are also present in the cytoplasmic leaflet of the plasma membrane is unclear so far. To investigate the presence of cytoplasmic leaflet domains, the H-Ras membrane-targeting sequence was fused to the C-terminus of the enhanced yellow fluorescent protein. Using single-molecule fluorescence microscopy, trajectories of individual molecules diffusing in the cytoplasmic leaflet of the plasma membrane were recorded. From these trajectories, the diffusion of individual membrane-anchored enhanced yellow fluorescent protein molecules was studied in live cells on timescales from 5 to 200 ms. The results show that the diffusion of 30-40% of the molecules is constrained in domains with a typical size of 200 nm. Neither breakdown of actin nor cholesterol extraction changed the domain characteristics significantly, indicating that the observed domains may not be related to the membrane domains identified so far.
Immune Modulation of the T Cell Response in Asthma through Wnt10b (2015)

Asthma is a chronic inflammatory disease, which is characterized by activation of CD4(+) T helper 2 cells orchestrating an allergic airway response. Whereas the role of Wnt family members in regulating T cell maintenance and maturation is established, their contribution to T cell activation in allergic asthma is not known. We hypothesized that Wnt10b plays a role in the modulation of the allergic airway response and affects T cell activation and polarization. Using an in vivo house dust mite asthma model, Wnt10b-deficient (Wnt10b(-/-)) mice were allergen-sensitized and inflammation, as well as T cell activation, was studied in vivo and in vitro. Wnt10b(-/-) mice exhibited an augmented inflammatory phenotype with an increase in eosinophils in the bronchoalveolar lavage and IL-4 and IL-13 in the lungs when compared with wild-type mice. In vitro studies confirmed an increased T helper type 2 polarization and increased T cell activation of Wnt10b(-/-) cells. Accordingly, the percentage of naive T cells was elevated by the addition of recombinant Wnt10b protein. Finally, Wnt10b(-/-) mice exhibited an increase in the percentage of effector T cells in the lungs after house dust mite sensitization, which indicated a heightened activation state, measured by an increased percentage of CD69(hi)CD11a(hi) cells. These findings suggest that Wnt10b plays an important role in regulating asthmatic airway inflammation through modification of the T cell response and is a prospective target in the disease process.
Ventilatory Capacity and Risk for Dementia (2000)

Ventilatory capacity, measured by spirometry in a representative sample of very elderly people, is cross-sectionally related to dementia. Taking evidence from longitudinal studies into account, this result suggests that decreased respiratory function may increase the risk for dementia, independent from already known risk factors.