gebhart/patrepeval huggingface dataset:
Tailorable Exciton Transport in Doped Peptide–Amphiphile Assemblies (2017)

Light-harvesting biomaterials are an attractive target in photovoltaics, photocatalysis, and artificial photosynthesis. Through peptide self-assembly, complex nanostructures can be engineered to study the role of chromophore organization during light absorption and energy transport. To this end, we demonstrate the one-dimensional transport of excitons along naturally occurring, light-harvesting, Zn-protoporphyrin IX chromophores within self-assembled peptide-amphiphile nanofibers. The internal structure of the nanofibers induces packing of the porphyrins into linear chains. We find that this peptide assembly can enable long-range exciton diffusion, yet it also induces the formation of excimers between adjacent molecules, which serve as exciton traps. Electronic coupling between neighboring porphyrin molecules is confirmed by various spectroscopic methods. The exciton diffusion process is then probed through transient photoluminescence and absorption measurements and fit to a model for one-dimensional hopping. Because excimer formation impedes exciton hopping, increasing the interchromophore spacing allows for improved diffusivity, which we control through porphyrin doping levels. We show that diffusion lengths of over 60 nm are possible at low porphyrin doping, representing an order of magnitude improvement over the highest doping fractions.
Differential modulation of NMDA and AMPA receptors by cellular prion protein and copper ions (2018)

N-Methyl-D-aspartate receptors (NMDARs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) are two major types of ionotropic glutamate receptors involved in synaptic transmission. However, excessive activity of these receptors can be cytotoxic and thus their function must be precisely controlled. We have previously reported that NMDA receptor activity is dysregulated following genetic knockout of cellular prion protein (PrP<sup>C</sup>), and that PrP<sup>C</sup> regulation of NMDA receptors is copper-dependent. Here, we employed electrophysiological methods to study NMDAR and AMPAR currents of cultured hippocampal neurons from PrP<sup>C</sup> overexpresser mice. We show that NMDA receptor current amplitude and kinetics are differentially modulated by overexpression of human or mouse PrP<sup>C</sup>. By contrast, AMPA receptor activity was unaffected. Nonetheless, AMPA receptor activity was modulated by copper ions in a manner similar to what we previously reported for NMDA receptors. Taken together, our findings reveal that AMPA and NMDA receptors are differentially regulated by PrP<sup>C</sup>, but share common modulation by copper ions.
Numerical Fluid-Structure Interaction Model for the Connection of Outflow Cannula of LVAD to the Aorta (2011)

Purpose: Connecting outflow cannula of LVAD to the aorta is an underexplored issue but may have considerable impact. In fact the hemodynamic modifications due to implantation in this region can cause thromboembolic events. It is therefore important to understand the flow pattern in this region and the way device interacts with the cardiovascular system. We present here the mathematical settings and results of a numerical model of the anastomosis between the outflow cannula of LVAD and the aorta. Methods: The geometry of the aorta and that of nearby large arteries is obtained from MRI and CT-scan data. The geometry of the arterial wall and that of the cannula is obtained by extruding the fluid surface based on a relation between wall thickness and local radius. Simulations are run using the parallel Finite Element library LifeV, which can address 3D Fluid Structure Interaction (FSI). The interaction with the entire cardiovascular system is modeled by using a multiscale model. The latter allows the coupling between the 3D model and a 1D tree model of the rest of the cardiovascular system. Results: Our numerical model allows the understanding of the behavior of the blood flow near the anastomosis and the interaction between LVAD and the cardiovascular system. Besides, relevant parameters from the haemodynamical standpoint are identified in order to propose a general mathematical approach to identify an optimal configuration of the anastomosis between LVAD and aorta. Summary: Mathematical settings and results of a numerical model of the anastomosis between the outflow cannula of LVAD and the aorta.
Fibre-coupled handheld multiphoton microscope with active motion compensation for in vivo skin imaging (2015)

To address the challenge of sample motion during in vivo imaging, we present a handheld multiphoton microscope with active motion compensation. We demonstrate the system's ability to compensate motion in ex vivo mouse skin.
A Proposal for Evaluating Answer Distillation from Web Data (2016)

Information retrieval systems can attempt to answer the user’s query directly, by extracting an appropriate passage of text from a corpus and presenting it on the results page. However, sometimes the passage of text contains extraneous information, or multiple passages are needed to form an answer. In cases like these, some sort of answer distillation system could be useful, taking as input the query and the answer-containing passage, and producing a succinct answer for presentation to the user. We formulate the problem of answer distillation as a sub-problem of machine comprehension and natural language generation, drawing techniques from neural machine learning, information retrieval, and natural language processing. To do well in answer distillation, we could benefit from a dataset consisting of many examples of query-passage pairs with their corresponding “ground-truth” or distilled answers. We also need to have a metric to measure the quality of the distilled answers. In this paper we share our early ideas on building such a dataset and solicit feedback from the community. Our goal is to align our needs for an answer distillation dataset and the needs of future academic research in this space. In particular, we propose that having a large number of reference answers available per query would be beneficial, and consequently suggest extensions to metrics like BLEU and METEOR for the scenario where this is true.
The ρ1 GABA receptor cloned from rat retina is down-modulated by protons (1996)

We have cloned and sequenced the full-length cDNA of the rat GABA (gamma-aminobutyric acid) rho 1 receptor subunit. The deduced amino acid sequence (474 amino acids) of the rat rho 1 receptor is 95% homologous to the previously cloned human rho 1 receptor. The rho 1 cDNA includes a 5' 129 bp and a 3' 2.6 kb untranslated region, which contains a sequence homologous to the human medium reiteration frequency repetitive sequence, MER18. The rat rho 1 receptor shows 45-50% similarity to the GABAA receptor beta subunits. This similarity is among the highest between all GABAA receptor subunit classes, giving no support at the molecular level to the classification of the rho subunits to a novel GABAC receptor class. The rat rho 1 cDNA formed functional GABA receptors insensitive to bicuculline, but sensitive to blockade by picrotoxin, when transiently expressed in the human embryonic kidney cell line HEK 293. We studied the sensitivity of the rho 1-mediated GABA current to variations in extracellular pH (pH0), and found that these receptors are strongly down-modulated by H+ ions. A decrease in pH0 from 7.4 to 6.4 decreased the GABA current by 51 +/- 8%, whereas an increase in pH0 from 7.4 to 8.4 increased the current by 77 +/- 8%. In view of the up-regulatory effect of protons on the GABA current observed in a number of preparations, the rho 1 receptors may contain a novel down-regulatory binding site for protons characteristic to these receptors.
Using PredictiveModeling for Cross-Program Design Space Exploration in Multicore Systems (2007)

The vast number of transistors available through modern fabrication technology gives architects an unprecedented amount of freedom in chip-multiprocessor (CMP) designs. However, such freedom translates into a design space that is impossible to fully, or even partially to any significant fraction, explore through detailed simulation. In this paper we propose to address this problem using predictive modeling, a well-known machine learning technique. More specifically we build models that, given only a minute fraction of the design space, are able to accurately predict the behavior of the remaining designs orders of magnitude faster than simulating them. In contrast to previous work, our models can predict performance metrics not only for unseen CMP configurations for a given application, but also for unseen configurations of a new application that was not in the set of applications used to build the model, given only a very small number of results for this new application. We perform extensive experiments to show the efficacy of the technique for exploring the design space of CMP's running parallel applications. The technique is used to predict both energy-delay and execution time. Choosing both explicitly parallel applications and applications that are parallelized using the thread-level speculation (TLS) approach, we evaluate performance on a CMP design space with about 95 million points using 18 benchmarks with up to 1000 training points each. For predicting the energy-delay metric, prediction errors for unseen configurations of the same application range from 2.4% to 4.6% and for configurations of new applications from 3.1% to 4.9%.
The evolution of RET inhibitor resistance in RET-driven lung and thyroid cancers (2022)

The efficacy of the highly selective RET inhibitor selpercatinib is now established in RET-driven cancers, and we sought to characterize the molecular determinants of response and resistance. We find that the pre-treatment genomic landscape does not shape the variability of treatment response except for rare instances of RAS-mediated primary resistance. By contrast, acquired selpercatinib resistance is driven by MAPK pathway reactivation by one of two distinct routes. In some patients, on- and off-target pathway reactivation via secondary RET solvent front mutations or MET amplifications are evident. In other patients, rare RET-wildtype tumor cell populations driven by an alternative mitogenic driver are selected for by treatment. Multiple distinct mechanisms are often observed in the same patient, suggesting polyclonal resistance may be common. Consequently, sequential RET-directed therapy may require combination treatment with inhibitors targeting alternative MAPK effectors, emphasizing the need for prospective characterization of selpercatinib-treated tumors at the time of monotherapy progression.
Peripheral Nerve Injury in Developing Rats Reorganizes Motor Cortex. (1986)

We investigated the effect of neonatal nerve leisons on cerebral motor cortex organization by comparing the cortical motor representation of normal adult rats with adult rats that had one forelimb removed on the day of birth. Mapping of cerebral neocortex with electrical simulation revealed an altered relationship between the motor cortex and the remaining muscles. While distal forelimb movements are normally elicited at the lowest threshold in the motor cortex forelimb area, the same stimuli activated shoulder and trunk muscles in experimental animals. In addition an expanded cortical representation of intact body parts was present and there was an absence of a distinct portion of motor cortex. These data demonstrate that representation patterns in motor cortex are subject to environmental events that occur during development. Keywords: Neuroplasticity.
Insulin action in pancreatic acini from streptozotocin-treated rats. III. Electron microscope autoradiography of 125I-insulin (1981)

Electron microscope autoradiographs were prepared from diabetic rat pancreatic acini that had been incubated with 125I-insulin. Distribution histograms of the distance of the 125I-insulin silver grains from the nearest plasma membrane were prepared and compared with a histogram of an 125I line source. After 3 min of incubation, insulin was located predominately on the plasma membrane, but even at this early time 15% of the grains had an intracellular location. After 30 min of incubation, there was a decrease in grains on the plasma membrane and an increase (to 45%) in grains localized in the cell. At both times of incubation, a comparison of the distribution of the insulin grains overlying subcellular organelles to a theoretical random grain distribution pattern indicated that the intracellular distribution of insulin grains was nonrandom. At 3 min, there was a relative concentration of grains over the plasma membrane and vesicles with an average diameter of 100 nm. At 30 min, there was a concentration of grains over the plasma membrane, 100-nm vesicle, and Golgi. These studies suggest that 125I-insulin is internalized into pancreatic acinar cells in a time-dependent manner and then is nonrandomly distributed inside the cell.
Magnetic Resonance Elastography of Liver (2013)

Magnetic resonance elastography (MRE) has been successfully implemented in the assessment of diffuse liver diseases. Currently, MRE is the most accurate noninvasive technique for detection and staging of liver fibrosis with a potential to replace liver biopsy. Magnetic resonance elastography is able to differentiate isolated fatty liver disease from steatohepatitis with or without fibrosis. Potential clinical applications include the differentiation of benign and malignant focal liver masses and the assessment of treatment response in diffuse liver diseases.
<title>Ray-following model of sonar range sensing</title> (1991)

We present a simulation-based model of sonar range sensing for robot navigation that accounts for multiple reflections of the sonar signal between transmission and reception. This gives more realistic results than previous models. The approach is to follow sample signal rays from the transmitter through reflections off walls and diffraction at corners to their possible return to the receiver. Parameters of the model are frequency minimum and maximum range and signal detection threshold (relative to emitted signal strength after linear gain compensation) . The results of Kuc and Siegel'' are employed to determine transducer impulse response and the strength of corner signals due to diffraction relative to reflected signals.
A new polymorphic probe on chromosome 3p: LIB35-53(D3S731) (1991)

XLEB11-95(D3S730) is a 1.0 kb EcoRI fragment isolated from a Charon 21A human chromosome 3 library (1).Polymorphism: EcoRI digestion of genomic DNA and hybridization with the probe detects a two-allele polymorphism:2.1 kb (El) and 1.0 kb (E2).Frequency: Estimated from 30 unrelated Caucasians.E1:0.47 E2:0.53 Frequency of heterozygosity: 0.50 Not Polymorphic For: BamHI, BgIll, Dral, HindU, Hinfl, MspI, Pvul, RsaI and TaqI.Chromosomal Localization: Using a somatic cell hybrid panel (2) which was based on linkage groups anchored to physically localized markers, the probe was assigned to the short arm of chromosome 3 between 3p24-3p26.Mendelian Inheritance: Mendelian inheritance has been demonstrated in a two generation von Hippel-Lindau disease (VHL) family.Probe
Future Network Scaling And The Need For Massive Opto-Electronic Array Integration (2017)

A close look at the evolution of network traffic across multiple market segments and of associated data processing, storage, and communication technologies over the past 10+ years reveals some very clear long-term trends, independent of short-term application hypes. These consistent trends inform our projections of network traffic and of information and communication technologies into the coming 10+ years. Most importantly, increasingly pronounced scaling disparities between demand and supply in wide-area data communications leaves our industry no other option than introducing massively integrated parallelism to implement the 10+ Terabit/s transponders working over Petabit/s systems that will be required well within 10 years. This major next step in the evolution of optical communication systems is likely to ultimately yield opto-electronic processing engines that combine large arrays of client and line interfaces with sophisticated coherent digital signal processing in a common package (fiber-in/fiber-out), taking full advantage of new holistic co-designs.
An unusual case of pseudo-merohedral twinning in orthorhombic crystals of Dicer (2007)

The crystal structure of the enzyme Dicer from Giardia intestinalis was solved to 3.3 A resolution by MAD using crystals belonging to space group P2(1)2(1)2 [Macrae et al. (2006), Science, 311, 195-198]. These crystals were derived from crystals that diffracted X-rays to 3.0 A resolution but were refractory to structure determination because they were twinned. It is shown here that the original Dicer crystals represent an unusual case of perfect pseudo-merohedral twinning of orthorhombic crystals. Before the twinning problem was overcome, it was possible to calculate a low-resolution electron-density map in space group P4(1) that was used to build a partial molecular model. Experimental phases were sufficient to identify heavy-atom sites that indicated space-group inconsistency, leading to identification of the true space group. This information guided the search for different crystallization conditions that yielded untwinned crystals and ultimately a fully interpretable electron-density map.
Biocatalytic Synthesis of Poly(L‐Lactide) by Native and Recombinant Forms of the Silicatein Enzymes (2005)

Enzymatic polymer synthesis is of considerable interest because of the synthetic advantages afforded by biological catalysts. Silicatein enzymes have shown broad synthetic utility for inorganic materials, and recombinant and native silicateins have been applied in the preparation of poly(L-lactide) (PLA). The picture shows native silicatein filaments coated with PLA (scale bar=4 μm).
A Polynomial Algorithm for Computing the Optimal Repair Strategy in a\n System with Independent Component Failures (2013)

The goal of diagnosis is to compute good repair strategies in response to\nanomalous system behavior. In a decision theoretic framework, a good repair\nstrategy has low expected cost. In a general formulation of the problem, the\ncomputation of the optimal (lowest expected cost) repair strategy for a system\nwith multiple faults is intractable. In this paper, we consider an interesting\nand natural restriction on the behavior of the system being diagnosed: (a) the\nsystem exhibits faulty behavior if and only if one or more components is\nmalfunctioning. (b) The failures of the system components are independent.\nGiven this restriction on system behavior, we develop a polynomial time\nalgorithm for computing the optimal repair strategy. We then go on to introduce\na system hierarchy and the notion of inspecting (testing) components before\nrepair. We develop a linear time algorithm for computing an optimal repair\nstrategy for the hierarchical system which includes both repair and inspection.\n
Triple, Mutually Orthogonal Cycloadditions Through the Design of Electronically Activated SNO-OCTs (2020)

Interest in mutually exclusive pairs of bioorthogonal labeling reagents continues to drive the design of new compounds capable of fast and predictable reactions. The ability to easily modify heterocyclic strained cyclooctynes containing sulfamate backbones (SNO-OCTs) enables electronic tuning of the relative rates of reactions of SNO-OCTs in cycloadditions with Type I–III dipoles. As opposed to optimizations based on just one specific dipole class, the electrophilicity of the alkynes in SNO-OCTs can be manipulated to achieve divergent reactivities and furnish mutually orthogonal dual ligation systems. Significant rate enhancements for reactions of a difluorinated SNO-OCT derivative compared to the parent scaffold were noted, with the second-order rate constant in cycloadditions with diazoacetamides exceeding 1 M−1 s −1 . Computational and experimental studies were employed to inform the design of triple ligation systems that encompass three orthogonal reactivities. Finally, polar SNO-OCTs are rapidly internalized by mammalian cells and remain functional in the cytosol for live-cell labeling, highlighting their potential for diverse in vitro and in vivo applications.
Transient stability with grid connection and wind turbine drive-train effects (2009)

This paper assesses transient stability of grid-connected wind turbines, combining grid-connection, wind turbine flexibility, and induction generator stability features. Through a grid-connected 2 MW wind turbine cage-generator, the investigation is conducted to identify the critical clearing time (CCT) and critical speed (CS), using in detail modelling. These steady-state concepts for transient stability, are time-domain extended to identify a set of possible critical couples instead of a rigid one, as is the case of the steady-state approach. In this way, more flexible control and protection strategies may be designed, for low voltage fault ride-through requirements and compliance.
Oxygen interacts with priming, moisture content and temperature to affect the longevity of lettuce and onion seeds (2011)

Abstract Lettuce ( Lactuca sativa L.) and onion ( Allium cepa L.) seeds have relatively short longevity during storage and their germination is sensitive to environmental stress. Seed priming (controlled hydration followed by drying) can improve seed germination under stressful conditions, inducing faster and more uniform germination over broader temperature ranges, but it can also reduce seed longevity in storage. Controlled deterioration (CD) tests are often employed to study longevity by ageing seeds rapidly at elevated temperature and moisture content, and primed seeds are particularly sensitive to CD conditions. As reactive oxygen (O 2 ) species are thought to be involved in seed deterioration, we tested whether storage under reduced O 2 atmospheres (0 and 2% O 2 ) would extend the longevity of primed and non-primed seeds under low relative humidity (RH) (33% RH+37°C) and CD (75% RH+50°C) storage conditions. The longevity of both non-primed and primed lettuce seeds in low RH storage was extended by anaerobic environments, but the effect of O 2 was much less under CD conditions. In onion, only primed seeds exhibited a beneficial effect of low O 2 atmospheres under both types of ageing conditions. In both species, storage under anaerobic conditions was beneficial for extending the longevity of primed seeds, but was not able to ameliorate fully the negative effect of priming on storage life.
Anti-Fab Aptamers for Shielding Virus from Neutralizing Antibodies (2012)

Oncolytic viruses are promising therapeutics that can selectively replicate in and kill tumor cells. However, repetitive administration of viruses provokes the generation of neutralizing antibodies (nAbs) that can diminish their anticancer effect. In this work, we selected DNA aptamers against the antigen binding fragment (Fab) of antivesicular stomatitis virus polyclonal antibodies to shield the virus from nAbs and enhance its in vivo survival. For the first time, we used flow cytometry and electrochemical immunosensing to identify aptamers targeting the Fab region of antibodies. We evaluated the aptamers in a cell-based infection assay and found that several aptamer clones provide more than 50% shielding of VSV from nAbs and thus have the potential to enhance the delivery of VSV without compromising the patient's immune system. In addition, we developed a bifunctional label-free electrochemical immunosensor for the quantitation of aptamer-mediated degree of shielding and the amount of vesicular stomatitis virus (VSV) particles. Electrochemical impedance spectroscopy was employed to interrogate the level of VSV in a linear range from 5 × 10(4) to 5 × 10(6) PFU mL(-1) with a detection limit of 10(4) PFU mL(-1).