gebhart/patrepeval huggingface dataset:
Use of an Imperfect Neutral Diluent and Outer Vesicle Layer Scooting Mode Hydrolysis To Analyze the Interfacial Kinetics, Inhibition, and Substrate Preferences of Bee Venom Phospholipase A2 (1997)

Interfacial catalytic constants for bee venom phospholipase A2 (bvPLA2) have been obtained for its action on vesicles of the anionic phospholipid 1,2-dimyristoylphosphatidylmethanol (DMPM) in the highly processive scooting mode. Spectroscopic measurements which directly measure transbilayer movement of membrane components show that this exchange does not occur in anionic vesicles that have undergone complete bvPLA2-catalyzed hydrolysis of all phospholipids in the outer vesicle monolayer. 3-Hexadecyl-sn-glycero-1-phosphocholine (D-LPC) is an adequate neutral diluent for bvPLA2, which is defined as an amphiphile that forms an aggregate to which enzyme binds but neutral diluent molecules bind weakly in the enzyme's active site. D-LPC has weak affinity for the active site of bvPLA2, and theory and protocols are developed that allow its use to determine equilibrium dissociation constants for competing active site ligands. Some of the properties of bvPLA2 are shared by other 14 kDa PLA2s. (1) Ca2+ is required for binding of ligands to the active site but not for the binding of enzyme to the interface. (2) bvPLA2 does not significantly discriminate between phospholipids with different polar head groups or acyl chains. (3) bvPLA2 does not bind to phosphatidylcholine vesicles, and binding occurs if anionic amphiphiles are present in the vesicle. Novel features of bvPLA2 include the following: (1) Neutral diluents for other 14 kDa phospholipases A2 are not neutral diluents for bvPLA2. (2) Saturation of the active site with a variety of different ligands does not completely prevent histidine alkylation by 2-bromo-4'-nitroacetophenone, and Ca2+ binding does not change the rate of histidine alkylation. Finally, the carbohydrate portion of bvPLA2 does not alter the interfacial catalytic properties of the enzyme. Kinetic analysis of bvPLA2 in the scooting mode together with previous studies with other 14 kDa PLA2s provides a paradigm for the quantitative analysis of interfacial catalysis.
Designing a norepinephrine optical tracer for imaging individual noradrenergic synapses and their activity in vivo (2018)

Norepinephrine is a monoamine neurotransmitter with a wide repertoire of physiological roles in the peripheral and central nervous systems. There are, however, no experimental means to study functional properties of individual noradrenergic synapses in the brain. Development of new approaches for imaging synaptic neurotransmission is of fundamental importance to study specific synaptic changes that occur during learning, behavior, and pathological processes. Here, we introduce fluorescent false neurotransmitter 270 (FFN270), a fluorescent tracer of norepinephrine. As a fluorescent substrate of the norepinephrine and vesicular monoamine transporters, FFN270 labels noradrenergic neurons and their synaptic vesicles, and enables imaging synaptic vesicle content release from specific axonal sites in living rodents. Combining FFN270 imaging and optogenetic stimulation, we find heterogeneous release properties of noradrenergic synapses in the somatosensory cortex, including low and high releasing populations. Through systemic amphetamine administration, we observe rapid release of cortical noradrenergic vesicular content, providing insight into the drug's effect.
Monitoring Volatile Organic Compounds in Flue Gas Using Direct Sampling Ion Trap Mass Spectrometry (1996)

Quantitative measurement of volatile organic compound concentrations in flue gas that has a high percentage of water vapor at low part-per-billion (ppb) to part-per-trillion levels represents a demanding analytical challenge. Direct sampling ion trap mass spectrometers developed at Oak Ridge National Laboratory are promising candidates to be developed into monitors of continuous emissions for these and other compounds at very low levels. Two direct sampling interfaces, a sorbent trap/thermal desorption interface and a continuous air monitor, have been tested in field studies of effluent from hazardous-waste incinerators. These interfaces demonstrate both an integrated, time-averaged and a raw gas, real-time approach to flue gas monitoring with detection limits in the ppb to sub-ppb range. The use of these interfaces for flue-gas monitoring with examples drawn from field tests are discussed.
On optimal input distribution and capacity limit of Bernoulli-Gaussian impulsive noise channels (2012)

In this paper, we rigorously analyze the optimal input distribution and capacity of an additive Bernoulli-Gaussian (BG) impulsive noise (IN) channel in high and low input power regimes. First, we obtain an input distribution for which the channel output is Gaussian distributed. This distribution, if valid, shall result in the capacity of the channel. At an asymptotically high input power level, we then show that the derived input is always valid and in fact, it resembles a Gaussian distribution. As such, the Gaussian channel input is considered approximately optimal. Using the monotonicity property of the characteristic function (CF), we then develop a necessary condition for the existence of the derived optimal input for a finite level of input power. The condition indicates that a sufficiently high input power is usually required. Then focusing on the low power region, we first derive an upper bound on the channel capacity assuming full knowledge of noise state. A closed-form expression of the mutual information (MI) achieved by Gaussian inputs, which is considered as a lower bound on the channel capacity, is then developed. By comparing these two bounds, it is shown that a Gaussian input asymptotically results in the capacity. Interestingly, it is also demonstrated that such a capacity is the same as the capacity of an erasure channel in low power regimes.
A Novel Biodegradable Septal Defect Occluder the “Chinese Lantern” Design, Proof of Concept (2011)

This work proves the feasibility of interventional closure of ASD or PFO with an innovative biodegradable device, which we call the "Chinese Lantern" for its symbolic design.
Reactive Caching for Composed Services (2018)

Sometimes, service clients repeat requests in a polling loop in order to refresh their view. However, such polling may be slow to pick up changes, or may increase the load unacceptably, in particular for composed services that disperse over many components. We present an alternative reactive polling API and reactive caching algorithm that combines the conceptual simplicity of polling with the efficiency of push-based change propagation. A reactive cache contains a summary of a distributed read-only operation and maintains a connection to its dependencies so changes can be propagated automatically. We first formalize the setting using an abstract calculus for composed services. Then we present a fault-tolerant distributed algorithm for reactive caching that guarantees eventual consistency. Finally, we implement and evaluate our solution by extending the Orleans actor framework, and perform experiments on two benchmarks in a distributed cloud deployment. The results show that our solution provides superior performance compared to polling, at a latency that comes close to hand-written change notifications. Conference slides are available here.
Intelligent Trip Modeling for the Prediction of an Origin–Destination Traveling Speed Profile (2014)

Accurate prediction of the traffic information in real time such as flow, density, speed, and travel time has important applications in many areas, including intelligent traffic control systems, optimizing vehicle operations, and the routing selection for individual drivers on the road. This is also a challenging problem due to dynamic changes of traffic states by many uncertain factors along a traveling route. In this paper, we present an Intelligent Trip Modeling System (ITMS) that was developed using machine learning to predict the traveling speed profile for a selected route based on the traffic information available at the trip starting time. The ITMS contains neural networks to predict short-term traffic speed based on the traveling day of the week, the traffic congestion levels at the sensor locations along the route, and the traveling time and distances to reach individual sensor locations. The ITMS was trained and evaluated by using ten months of traffic data provided by the California Freeway Performance Measurement System along a California Interstate I-405 route that is 26 mi long and contains 52 traffic sensors. The ITMS was also evaluated by the traffic data acquired from a 32-mi-long freeway section in the state of Michigan. Experimental results show that the proposed system, i.e., ITMS, has the capability of providing accurate predictions of dynamic traffic changes and traveling speed at the beginning of a trip and can generalize well to prediction of speed profiles on the freeway routes other than the routes the system was trained on.
DNA Microarray Transcriptional Profiling of Bacteriophage Bfk20 (2010)

Since its introduction in 1995, DNA microarray technology proved itself as an irreplaceable high- throughput technique providing valuable insights into the gene expression patterns and/or the genome identification of whole living organism. Unlike the traditional comparison of expression patterns from cells exposed to two different conditions, the transcriptional profiling of viral expression during time course study of host infection represent a unique technical challenge to a conventional approach. This book describes a global gene expression profiling of bacteriophage BFK20 infecting an industrial L-lysine producer Brevibacterium flavum CCM 251 determined by using the custom DNA microarrays in a loop design. New functions were assigned and/or proposed to several gene products of so far unknown function considering their co-expression pattern by utilizing “guilt-by- association” algorithm. The study provided further insight into phage lifecycle and can be particularly useful to professionals in Virology, Molecular Biology & Biotechnology fields considering performing a viral whole genome time-course expression analysis.
Selective Production of Fungal Beauveriolide I or III by Fermentation in Amino Acid-supplemented Media. (2002)

Beauveriolides I and III, cyclic depsipeptides composed of L-Phe, L-Ala, D-Leu and (3S,4S)-3-hydroxy-4-methyloctanoic acid, and L-Phe, L-Ala, L-allo-Ile and (3S,4S)-3-hydroxy-4-methyloctanoic acid, respectively, were previously isolated from the culture broth of fungal Beauveria sp. FO-6979 as inhibitors of macrophage foam cell formation. To improve the production of these compounds by fermentation, the culture conditions were studied. The production of both beauveriolides was increased five to ten folds by fermentation in the culture media containing tryptone. Further study revealed that addition of L-Leu/L-Ile, but not D-Leu/D-allo-Ile, to the culture medium yielded a high and selective production of beauveriolide I or III. As a result, regardless of their separation difficulty due to the similar physico-chemical properties, a large amount of beauveriolide I or III was prepared from the culture broth obtained from L-Leu- or L-Ile-supplemented fermentation, respectively, by one step purification using silica gel column chromatography.
P1894Serum light-chain neurofilament is associated with brain atrophy in patients with atrial fibrillation (2019)

Abstract Background and aims There is emerging evidence that atrial fibrillation (AF) is associated with cognitive dysfunction, increased risk for dementia and reduced brain volume independent of stroke, but the underlying mechanisms of these associations remain unclear. Here, we investigated the association of serum light-chain neurofilament (sNfL), a neuroaxonal injury biomarker, with brain atrophy in AF patients. Methods Explorative analysis from the Swiss-AF cohort study, a multicenter prospective observationalstudy which recruited patients aged ≥45 years with documented AF (NCT02105844). In baseline blood samples, sNfL concentrations were measured in duplicates using a single-molecule array assay. Brain MRI was obtained at baseline and at two years using a standardized protocol including a 3D T1-weighted MPRAGE sequence, on which Structural Image Evaluation using Normalization of Atrophy (SIENA) with optimized parameters for brain extraction was applied to calculate the two-year percentage whole brain volume change (PBVC). Results We included 245 Swiss-AF patients (median age 73, 73% male). Two-year PBVC was significantly associated with baseline sNfL in linear regression, with a 0.09% whole brain volume decrease per 10 pg/ml sNfL increase (95% CI [0.05–0.13], p&lt;0.001). This association remained significant after adjustment for age, history of stroke and other vascular risk factors. Neurofilament and brain atrophy Conclusion Increasing baseline sNfL was predictive of higher two-year brain atrophy rates independent of stroke history in AF patients. This association might reflect a chronic neurodegenerative process in AF. Acknowledgement/Funding Swiss National Science Foundation
Huygens’ Metasurfaces Enabled by Magnetic Dipole Resonance Tuning in Split Dielectric Nanoresonators (2017)

Dielectric metasurfaces that exploit the different Mie resonances of nanoscale dielectric resonators are a powerful platform for manipulating electromagnetic fields and can provide novel optical behavior. In this work, we experimentally demonstrate independent tuning of the magnetic dipole resonances relative to the electric dipole resonances of split dielectric resonators (SDRs). By increasing the split dimension, we observe a blue shift of the magnetic dipole resonance toward the electric dipole resonance. Therefore, SDRs provide the ability to directly control the interaction between the two dipole resonances within the same resonator. For example, we achieve the first Kerker condition by spectrally overlapping the electric and magnetic dipole resonances and observe significantly suppressed backward scattering. Moreover, we show that a single SDR can be used as an optical nanoantenna that provides strong unidirectional emission from an electric dipole source.
Methyl to trifluoromethyl substitution as a strategy to increase the membrane permeability of short peptides (2021)

Here, we investigated the effect of CH<sub>3</sub> to CF<sub>3</sub> substitution on the membrane permeability of peptides. We synthesized a series of peptides with CF<sub>3</sub> groups and corresponding nonfluorinated peptides and measured the membrane permeability of the peptides. As a result, we demonstrated that CH<sub>3</sub> to CF<sub>3</sub> substitution is useful for increasing the membrane permeability of di-/tri-peptides.
Induced pluripotent stem cell-derived hepatocytes as an alternative to human adult hepatocytes. (2012)

Recent advances in induced pluripotent stem (iPS) cell research have attracted much attention. The ability to generate such cells from somatic cells has implications for overcoming both immunological rejection and the ethical issues associated with embryonic stem (ES) cells. Hepatocytes derived from patient-specific iPS cells offer a possible solution to the shortage of cell sources in cell replacement therapy, drug screening, and disease model. Despite such great promise, however, recent articles have questioned the viability of the therapeutic applications of iPS cells. These cells must, therefore, satisfy stringent criteria prior to practical use. The main focus of this review is a description of the current status of hepatic differentiation technology of iPS cells and a discussion of the concerns regarding the practical use of these techniques in cell replacement therapy, drug screening, and disease model. The current status of strategies for generating iPS cells and the accumulated knowledge on strategies for differentiating ES cells into hepatocytes will be summarized. We also refer to the possibility of direct conversion of adult somatic cells into functional hepatocytes.
A User Study of Perceived Carbon Footprint (2019)

We propose a statistical model to understand people's perception of their carbon footprint. Driven by the observation that few people think of CO2 impact in absolute terms, we design a system to probe people's perception from simple pairwise comparisons of the relative carbon footprint of their actions. The formulation of the model enables us to take an active-learning approach to selecting the pairs of actions that are maximally informative about the model parameters. We define a set of 18 actions and collect a dataset of 2183 comparisons from 176 users on a university campus. The early results reveal promising directions to improve climate communication and enhance climate mitigation.
Microvalve thickness and topography measurements in microfluidic devices by white-light confocal microscopy (2009)

A microvalve is a key part in a multilayer microfluidic device to control the fluid flow, and its thickness directly determines its performance. In this paper, a three-dimensional measurement technology using a white-light confocal microscope is developed for measuring both the topography and thickness of microvalves. The impact of system parameters and sample parameters on measurement accuracy is discussed in detail, particularly for measurement with a dry objective. With this technique, the microvalve thicknesses before and after bonding were characterized with submicrometer measurement sensitivity and about 1 microm measurement accuracy.
Production of antibodies and antibody fragments in Escherichia coli and a comparison of their functions, uses and modification. (2003)

Antibody-based drugs are now used in the clinic, and their importance as therapeutics is expected to increase in the coming decade, both in terms of diseases treated and market value. However, the proportion of patients that can be treated is to some extent affected by the availability and cost of the therapeutic. Therefore, the means of production and purification of the therapeutic entity, as well as the type of therapeutic entity, are of great concern. Escherichia coli represents a good production host in terms of scale and speed of production, but it also has technical and biological limitations. The aim of this review is to describe and discuss the relative benefits and limitations of E coli as a host for the production of antibodies and engineered antibody fragments.
<title>Baseline redundancy in the MIRAS radiometer</title> (1997)

The microwave imaging radiometer with aperture synthesis (MIRAS) is an L-band two-dimensional interferometer which the European Space Agency is studying for the global mapping of soil moisture and ocean salinity. The antenna of this instrument has been optimized to reduce the number of receivers and correlators required for the interferometric processing. The antenna is an array of 3 coplanar arms spaced 120 degrees each one with 43 small antenna elements. In addition there is one element at the center of the array and, for calibration purposes, other three in between the arms. The in-phase and quadrature components of the voltage received by each small antenna in the array are correlated with those of any other antenna element. Every cross correlation is a sample of the so called visibility function at the spatial frequency defined by the relative coordinates of the corresponding pair of antenna elements. The brightness temperature distribution is then obtained basically by an inverse Fourier transform of the visibility function. Since more than one antenna pair may have the same baseline coordinates some spatial frequencies of the visibility function are measured more than once. These points of the visibility function are said to be redundant. This paper deals with the redundancy in MIRAS radiometer. The number of redundant points, its distribution in the spatial frequency domain and there the degree of redundancy is first analyzed. Then the correlation between redundant measurements is studied aiming at estimating the improvement in radiometric resolution when redundancies are combined. A trade-off between radiometric resolution gain and increased number of correlators is performed and some conclusions are finally drawn to be applied to the current design of MIRAS digital correlator unit. Passed preliminary results (Ref. 1) show that about 30% of all possible cross correlations correspond to redundancies while the estimated improvement in the radiometric resolution when using them is only of 1%.
Fc Receptor-Mediated Immunity Against Bordetella pertussis (2001)

The relevance of specific Abs for the induction of cellular effector functions against Bordetella pertussis was studied. IgG-opsonized B. pertussis was efficiently phagocytosed by human polymorphonuclear leukocytes (PMN). This process was mediated by the PMN IgG receptors, FcgammaRIIa (CD32) and FcgammaRIIIb (CD16), working synergistically. Furthermore, these FcgammaR triggered efficient PMN respiratory burst activity and mediated transfer of B. pertussis to lysosomal compartments, ultimately resulting in reduced bacterial viability. Bacteria opsonized with IgA triggered similar PMN activation via FcalphaR (CD89). Simultaneous engagement of FcalphaRI and FcgammaR by B. pertussis resulted in increased phagocytosis rates, compared with responses induced by either isotype alone. These data provide new insights into host immune mechanisms against B. pertussis and document a crucial role for Ig-FcR interactions in immunity to this human pathogen.
Brillouin spectroscopy is insensitive to stiffness after correcting for the influence of water content in hydrogels (Conference Presentation) (2019)

Brillouin spectroscopy provides a non-invasive, label-free method to evaluate the mechanical properties of biological materials. Prior studies have shown that the longitudinal elastic modulus, M, measured by Brillouin spectroscopy correlates with the Young’s modulus, E, of cells and tissues. However, M and E for hydrated materials are both influenced by water content. Using hydrogels as a simple model for hydrated biological materials, we designed experiments to separate the effects of E and water content on M. Polyethylene oxide (PEO) hydrogels were prepared with an average molecular weight of 1, 4 or 8 MDa and water content of 92, 95 or 98.5% (v/v). Polyacrylamide (PA) hydrogels were prepared with 10% acrylamide and 0.03-0.30% N-methylene-bis-acrylamide (w/v). E was measured by rheometry for PEO hydrogels and by unconfined compression for PA hydrogels. M was measured using a custom-built Brillouin spectrometer. For PEO hydrogels, E increased with molecular weight, whilst M was unaffected by molecular weight and decreased with increasing water content. For PA hydrogels, both M and E decreased over time due to swelling, but no single relationship could describe how M changed in terms of E. Regardless of swelling, all values of collapsed onto a single relationship that depended only on water content. After correcting for water content, measurements from Brillouin spectroscopy no longer correlate with Young’s modulus for hydrated materials. This work cautions against the straightforward application of Brillouin spectroscopy for optical elastography, but suggests that Brillouin spectroscopy and microscopy may be useful for investigating mechanisms involving changes in local water content.