gebhart/patrepeval huggingface dataset:
Role of ARF6, Rab11 and External Hsp90 in the Trafficking and Recycling of Recombinant-Soluble Neisseria meningitidis Adhesin A (rNadA) in Human Epithelial Cells (2014)

Neisseria meningitidis adhesin A (NadA) is a meningococcus surface protein thought to assist in the adhesion of the bacterium to host cells. We have previously shown that NadA also promotes bacterial internalization in a heterologous expression system. Here we have used the soluble recombinant NadA (rNadA) lacking the membrane anchor region to characterize its internalization route in Chang epithelial cells. Added to the culture medium, rNadA internalizes through a PI3K-dependent endocytosis process not mediated by the canonical clathrin or caveolin scaffolds, but instead follows an ARF6-regulated recycling pathway previously described for MHC-I. The intracellular pool of rNadA reaches a steady state level within one hour of incubation and colocalizes in endocytic vesicles with MHC-I and with the extracellularly labeled chaperone Hsp90. Treatment with membrane permeated and impermeable Hsp90 inhibitors 17-AAG and FITC-GA respectively, lead to intracellular accumulation of rNadA, strongly suggesting that the extracellular secreted pool of the chaperone is involved in rNadA intracellular trafficking. A significant number of intracellular vesicles containing rNadA recruit Rab11, a small GTPase associated to recycling endosomes, but do not contain transferrin receptor (TfR). Interestingly, cell treatment with Hsp90 inhibitors, including the membrane-impermeable FITC-GA, abolished Rab11-rNadA colocalization but do not interfere with Rab11-TfR colocalization. Collectively, these results are consistent with a model whereby rNadA internalizes into human epithelial cells hijacking the recycling endosome pathway and recycle back to the surface of the cell via an ARF6-dependent, Rab11 associated and Hsp90-regulated mechanism. The present study addresses for the first time a meningoccoccal adhesin mechanism of endocytosis and suggests a possible entry pathway engaged by N. meningitidis in primary infection of human epithelial cells.
Hamiltonian formulation of Maxwell's equations for waveguides (propagation-constant consideration) (2008)

In Chapter 4 we have derived perturbation theory for Maxwell's equations to find corrections to the electromagnetic state eigenfrequency ω due to small changes in the material dielectric constant. Applied to the case of systems incorporating absorbing materials, we have concluded that absorption introduces an imaginary part to the modal frequency, thus resulting in decay of the modal power in time. While this result is intuitive for resonator states localized in all spatial directions, it is somewhat not straightforward to interpret for the case of waveguides in which energy travels freely along the waveguide direction. In the case of waveguides, a more natural description of the phenomenon of energy dissipation would be in terms of a characteristic modal decay length, or, in other words, in terms of the imaginary contribution to the modal propagation constant. The Hamiltonian formulation of Maxwell's equations in the form (2.70) is an eigenvalue problem with respect to ω2, thus perturbation theory formalism based on this Hamiltonian form is most naturally applicable for finding frequency corrections. In the following sections we develop the Hamiltonian formulation of Maxwell's equations in terms of the modal propagation constant, which allows, naturally, perturbative formulation with respect to the modal propagation constant.
Effects of different doses of nitrogen treatments on isoprene emission from Ficus glomerata (2010)

In the present investigation on the effect of nitrogen treatments on emission of isoprene from Ficus glomerata has been evaluated. Four sets of plants were treated with following four doses of nitrogen in the form of ammonium nitrate solution (i) 10 mM (ii) 50 mM (iii) 100 mM (iv) 200 (mM) and control set was designed without any treatment. Nitrogen treated as well as control plants were sampled for isoprene emission using a dynamic flow through enclosure chamber technique and samples were analysed with the help of GC-FID. Isoprene emissions from control, 10 mM, 50 mM, 100 mM, and 200 mM nitrogen treated plants were found to be 27.5 ± 4 ?gg-1h-1, 56 ± 6 ?gg-1h-1, 91 ± 11 ?gg-1h-1, 101 ± 10 ?gg-1h-1, and 15 ± 4 ?gg-1h-1 respectively. Lowest isoprene emission (15 ± 4 ?gg-1h-1) was noticed in plants treated with 200 mM nitrogen. Isoprene emissions were found to increase exponentially in plants treated with nitrogen up to 100 mM. Nevertheless, plants treated with 200 mM nitrogen exhibited decrease in emission by 46 per cent, probably on account of nitrite toxicity and reduction in soil pH at high nitrogen dose.
Fast and effective text mining using linear-time document clustering (1999)

Clustering is a powerful technique for large-scale topic discovery from text. It involves two phases: first, feature extraction maps each document or record to a point in high-dimensional space, then clustering algorithms automatically group the points into a hierarchy of clusters. We describe an unsupervised, near-linear time text clustering system that offers a number of algorithm choices for each phase. We introduce a methodology for measuring the quality of a cluster hierarchy in terms of F-Measure, and present the results of experiments comparing different algorithms. The evaluation considers some feature selection parameters (tfidfand feature vector length) but focuses on the clustering algorithms, namely techniques from Scatter/Gather (buckshot, fractionation, and split/join) and kmeans. Our experiments suggest that continuous center adjustment contributes more to cluster quality than seed selection does. It follows that using a simpler seed selection algorithm gives a better time/quality tradeoff. We describe a refinement to center adjustment, "vector average damping," that further improves cluster quality. We also compare the near-linear time algorithms to a group average greedy agglomerative clustering algorithm to demonstrate the time/quality tradeoff quantitatively.
Modular Functionalization of Electrodes by Cross‐Coupling Reactions at Their Surfaces (2011)

Abstract Due to the increasing importance of modified electrodes for many applications in nanotechnology, including molecular electronics, bioelectronics, and sensors, there is a need to find ways to chemically attach suitable molecular films onto the electrodes. Combining the electroreduction of aryl diazonium salts with the Sonogashira cross‐coupling reaction, a new modular technique to modify electrodes is presented. The new technique allows a wide range of functional groups to be introduced onto electrode surfaces with high surface coverage by the functional subunit. Various organic subunits, including redox chromophores, are successfully attached to platinum electrodes. The corresponding films are characterized using cyclic voltammetry, X‐ray photoelectron spectroscopy, atomic force microscopy, and contact‐angle measurements. The electroreduction of diazonium salts is successfully achieved on a broad variety of conducting and semiconducting surfaces, which shows that the technique is applicable to a broad variety of substrates.
On Antiscience and Antisemitism (2023)

Recent surges in antivaccine activism and other antiscience trends now converge with rising antisemitism. During the COVID-19 pandemic, authoritarian elements from the far right in North America and Europe often invoked Nazi imagery to describe vaccinations or at times even blame the Jewish people for COVID-19 origins and vaccine profiteering. Such tropes represent throwbacks to the 14th century, when European Jews were persecuted during the time of the bubonic plague. This article provides both historical and recent perspectives on the links between antiscience and antisemitism, together with the author's personal experience as a Jewish vaccine scientist targeted by both dark forces. New approaches to uncoupling antisemitism from antiscience, while combating both, are essential for saving lives and preserving democratic values.
Heat Losses From the Human Head (1957)

A simple gradient calorimeter was developed for measurements of nonevaporative heat loss of the head, and used on three subjects, with heads unprotected but the body adequately clothed, at temperatures between 32°C and − 21°C. Heat loss was linearly related to external temperature by the regression equation (correlation coefficient 0.97 ± 0.01), H = (284.8 – 7.55 x t°C) in K Cal/m2 of head per hour. This means that at −4°C the heat loss from the head may amount to half the total resting heat production of the man. The insulation of the tissues of the head was calculated as about 0.4 clo units, and did not change with the external temperature. To see if it would change if there was general vasoconstriction or vasodilation, a second series of experiments was carried out: a) at 10°C with the subjects unclothed; b) at 20°C with the subjects clothed; and c) at 29°C with subjects clothed and with a heating pad on the chest. While the tissue insulation of the finger increased by a factor of six times in (a) compared with (b), that of the head was constant. In (c) the tissue insulation of the head decreased slightly, indicating slight vasodilation. The importance of insulation of the head in the cold to extend the tolerance time is pointed out by practical examples. Submitted on October 17, 1956
The Professional Dilettante: Ludovic Vitet and Le Globe (2001)

Abstract The third edition of Grove’s Dictionary passes the following judgement on Baron Henri Blaze de Bury, son of Castil-Blaze: ‘in literary skill he surpassed his father; in musical knowledge he was decidedly his inferior’. As sentence length summaries go, this may be fair enough. But the way the judgement is presented is significant, the two halves causally balanced as though any increase of literary ability will occasion a decrease in musical expertise. The assessment thereby hints at an academic bias that has only become more familiar since: suspicion of the musical amateur.
Assessment of Microsoft Kinect technology (Kinect for Xbox and Kinect for windows) for patient monitoring during external beam radiotherapy (2013)

In external beam radiotherapy, patient misalignment during set-up and motion during treatment may result in lost dose to target tissue and increased dose to normal tissues, reducing therapeutic benefit. The most common method for initial patient setup uses room mounted lasers and surface marks on the skin. We propose to use the Microsoft Kinect which can capture a complete patient skin surface representing a multiplicity of 3D points in a fast reproducible, marker-less manner. Our first experiments quantitatively assess the technical performance of Kinect technology using a planar test object and a precision motion platform to compare the performance of Kinect for Xbox and Kinect for Windows. Further experiments were undertaken to investigate the likely performance of using the Kinect during treatment to detect respiratory motion, both in supine and prone positions. The Windows version of the Kinect produces superior performance of less than 2mm mean error at 80-100 cm distance.
Relative Rates of Bromine–Magnesium Exchange Reactions in Substituted Bromobenzene Derivatives (2007)

Against expectation: How can the site of Br–Mg exchange in multiply brominated compounds be predicted? Competition experiments with different substituents X and Y (see scheme; X, Y=H, F, Cl, Br, CF3, CO2tBu, CN) reveal a counterintuitive order of substituent effects. The aim of the study is to enable the selectivity of halogen–magnesium exchange reactions of polyfunctional compounds to be predicted. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2008/z704100_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Synthetic Polymeric Biomaterials (1984)

A review is presented of the applications of synthetic polymers in medicine. The major uses of these biomaterials are in devices and implants for diagnosis or therapy. The composition and properties, characterization, and biologic interactions of a wide variety of synthetic polymers are reviewed. Biologic testing and clearance of biomaterials for clinical use are also covered.
Defense From the Group A Streptococcus by Active and Passive Vaccination With the Streptococcal Hemoprotein Receptor (2011)

Shr is a promising vaccine candidate that is capable of eliciting bactericidal antibody response and conferring immunity against systemic GAS infection in both passive and active vaccination models.
A role in vacuolar arginine transport for yeast Btn1p and for human CLN3, the protein defective in Batten disease (2003)

In Saccharomyces cerevisiae, transport of arginine into the vacuole has previously been shown to be facilitated by a putative H+/arginine antiport. We confirm that transport of arginine into isolated yeast vacuoles requires ATP and we demonstrate a requirement for a functional vacuolar H+-ATPase. We previously reported that deletion of BTN1 (btn1-delta), an ortholog of the human Batten disease gene CLN3, resulted in a decrease in vacuolar pH during early growth. We report that this altered vacuolar pH in btn1-delta strains underlies a lack of arginine transport into the vacuole, which results in a depletion of endogenous vacuolar arginine levels. This arginine transport defect in btn1-delta is complemented by expression of either BTN1 or the human CLN3 gene and strongly suggests a function for transport of, or regulation of the transport of, basic amino acids into the vacuole or lysosome for yeast Btn1p, and human CLN3 protein, respectively. We propose that defective transport at the lysosomal membrane caused by an absence of functional CLN3 is the primary biochemical defect that results in Batten disease.
PPPS-2013: Optimal control of laser-plasma instabilities using spike trains of uneven duration and delay (STUD pulses) (2013)

Summary form only given. We show new results on the effectiveness of STUD pulses to control, in an adaptive manner, fast or slow parametric instabilities in laser-plasma interactions <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> . Fluid simulations <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and statistical optical theory are used to show how Stimulated Brillouin Scattering (SBS) can be suppressed in inhomogeneous flowing plasmas in the strong ion-wave damping regime with structured laser beams. When STUD pulses are being tailored to the evolution of the instability to be controlled, a number of key pulse shaping ingredients must be varied to optimize the fit. Chief among these is the modulation period, the duty cycle and the spatial scrambling rate of the pump laser's space-time evolution profile. We will show that for a probe beam, which is also composed of fast STUD pulse modulations, steady state behavior of drastically reduced instability levels is possible with the proper adaptive targetting of the pump STUD pulse profile. Nothing need be known about the plasma conditions a priori in order to execute this plan. It is believed that future lasers for high intensity laser-matter interactions and laser-fusion where instabilities are expected to be controlled and steered, STUD pulses offer a very attractive path forward. Current ambiguities and disasters in such high intensity inertial confinement fusion (ICF) settings could be a thing of the past with the implementation of these ultra-fast optics inspired pulse shaping techniques. Statistical, nonlinear and ultrafast optics are the three major ingredients necessary to execute this plan. These will be amply demonstrated.
Predicting postoperative intraocular lens position and refraction (2004)

Calculation errors from formulas and confusing adjusting parameters can be avoided if calculations and measurements are performed on a clear and simple physical basis. Nevertheless, an individual prediction error, typically 0.5 to 1.0 diopter, seems to be unavoidable.
Research in natural language (1973)

One of the most active areas of Artificial Intelligence research today is the understanding of natural language. From the earliest days of computing, people have been intrigued by the idea of communicating easily with computers. In the past few years, new techniques and larger systems have combined to open new possibilities for expressing ideas to computers in natural language. Question answering systems are approaching a level useful in real applications areas. Advanced computing applications like automatic programming will base their interaction with the user on natural language capabilities. In almost every area of computing, it is easy to imagine ways in which language understanding could make computers more accessible, not only for those who use them now, but for a much wider range of people without special training.
Coverage probability analysis of three uplink power control schemes: Stochastic geometry approach (2018)

In cellular networks, each mobile station adjusts its power level under control of its base station, i.e., through uplink transmit power control, which is essential to reach desired signal-to-interference-plus-noise ratio (SINR) at the base station and to limit inter-cell interference. The optimal levels of transmit power in a network depend on path loss, shadowing, and multipath fading, as well as the network configuration. However, since path loss is distance dependent and the cell association distances are correlated due to the cell association policies, the performance analysis of the uplink transmit power control is very complicated. Consequently, the impact of a specific power control algorithm on network performance is hard to quantify. In this paper, we analyze three uplink transmit power control schemes. We assume the standard power-law path loss and composite Rayleigh-lognormal fading. Using stochastic geometry tools, we derive the cumulative distribution function and the probability density function of the uplink transmit power and the resulting network coverage probability. It is shown that the coverage is highly dependent on the severity of shadowing, the power control scheme, and its parameters, but invariant of the density of deployment of base stations when the shadowing is mild and power control is fractional. At low SINRs, compensation of both path loss and shadowing improves the coverage. However, at high SINRs, compensating for path loss only improves coverage. Increase in the severity of shadowing significantly reduces the coverage.
Differential effects of microenvironmentally presented interleukin 3 versus soluble growth factor on primitive human hematopoietic cells. (1991)

The effect of IL-3 on hematopoiesis in long-term culture (LTC) was studied by cocultivating normal human marrow cells with human marrow fibroblast feeders engineered to constitutively produce IL-3 and by adding soluble IL-3 to LTC according to a variety of dose-time schedules. Feeders stably producing 7 ng/ml IL-3, or LTC to which 10 ng/ml IL-3 was added daily for 5 wk, but not once or twice weekly for the same time period, increased the output of mature nonadherent cells and progenitors from LTC as compared to control cultures. At the time of the weekly half-medium change, when primitive clonogenic progenitors in the adherent layer of standard LTC are quiescent, such cells were actively cycling in cultures containing a continuous source of an adequate dose of IL-3. In LTC, where the proportion of IL-3-producing cells in the feeder layer was diluted to 10% and no IL-3 was detectable in culture medium, primitive adherent layer progenitors were, nevertheless, maintained as a population of continuously proliferating cells. Thus, the presence of IL-3 in LTC can enhance the proliferation and differentiation of very early human hematopoietic cells, but the concentration, duration of exposure, and method of IL-3 presentation are important determinants of the ultimate effects observed.
Activation of specific T cell lines by the antigens avidin and myelin basic protein in the absence of antigen‐presenting cells (1987)

We have investigated the specific activation by soluble antigen of rat or mouse long-term T helper cell lines using antigen-presenting cell (APC)-free culture conditions. Some T cell lines specific for avidin or myelin basic protein responded to native antigen in the absence of added APC. Responses in the absence of APC were substantial and specific although, as would be expected, lower than in the presence of APC. Proliferation could not be inhibited by culture with anti-Ia antibodies and the ability of lines to respond to antigen in the absence of APC did not correlate with the endogeneous surface Ia expression of the lines. Furthermore, irradiated T cells were unable to act as presenting cells for lines cells of the same or a different specificity. This suggests that the T cells did not present antigen to each other, and demonstrates, along with other data shown, that activation cannot be attributed to undetected APC remaining in the cultures. Anti-avidin T cell lines differed markedly in their ability to respond to avidin in the absence of added APC.S2, an anti-avidin line of H-2s genotype consistently responded well to avidin seen in the absence of added APC; K2, an H-2k anti-avidin line, responded moderately and B3, and H-2b anti-avidin line, although the most prolific responder in the presence of APC, never responded to antigen in their absence. Z1a, a Lewis rat-derived T cell line specific for myelin basic protein, proliferated well in response to the antigen in the absence of added APC. The present findings demonstrate that some T cells can recognize and respond to native antigens without the mediation of specialized APC.
Detection of blinding attack in quantum key distribution (2016)

Security of an ideal system for quantum key distribution can be formally proved. However, technological imperfections of real systems can be misused by an eavesdropper to get information about the key without causing a detectable change in the error rate. An example of this is the blinding attack where the eavesdropper manipulates detectors of the receiving party. To avoid such an attack, technical modifications of the device are usually required. In this paper we show that an extended measurement, similar to the Bell test measurement, can reveal the blinding attack without any modification of the device.
The Slow‐Release Strategy in Suzuki–Miyaura Coupling (2010)

Abstract Despite great advances in metal‐catalyzed cross‐coupling reactions, their efficacy is often compromised by side reactions, reducing the yield, or requiring a large excess of one component. Suzuki–Miyaura cross‐coupling is no exception, as the boronic acid functionality can be susceptible to a range of undesired processes. A number of methods have been developed to mitigate these side reactions, and herein we focus on the “slow‐release” strategy. These conditions involve deployment of a “masking” reagent that protects the vulnerable boronic acid functionality from degradation, particularly protodeboronation, whilst simultaneously facilitating controlled liberation of the active reagent into the catalytic milieu. Under suitably tailored conditions, this dual‐action approach ensures that the concentration of the free boronic acid is minimized, thus attenuating its degradation but still facilitating transmetallation of the organoboron species with the key organopalladium intermediate.