gebhart/patrepeval huggingface dataset:
Plant-based expression of SARS-CoV-2 antigen for use in an oral vaccine (2021)

Abstract Oral and intra-nasal vaccines represent a key means of inducing mucosal-based immunity against infection with SARS-CoV-2, yet such vaccines represent only a minority of candidates currently in development. In this brief communication, we assessed the expression of the SARS-CoV-2 Receptor Binding Domain (RBD) subunit of the surface-exposed Spike glycoprotein in the leaves of nine edible plant species (lettuce, spinach, collard greens, tomato, cucumber, radish, arugula, pepper, and Coho greens), with a goal of identifying a suitable candidate for the development of an oral vaccine against COVID-19. We report lettuce ( Lactuca sativa L. cv. Hilde II Improved) to be a preferred host to support in planta expression of SARS-CoV-2 RBD, representing an important first step towards development of a plant-based oral vaccine.
Revamping JavaScript static analysis via localization and remediation of root causes of imprecision (2016)

Static analysis is challenged by the dynamic language constructs of JavaScript which often lead to unacceptable performance and/or precision results. We describe an approach that focuses on improving the practicality and accuracy of points-to analysis and call graph construction for JavaScript programs. The approach first identifies program constructs which are sources of imprecision (i.e., root causes) through monitoring the static analysis process. We then examine and suggest specific context-sensitive analyses to apply. Our technique is able to to find that the root causes comprise less than 2% of the functions in JavaScript library applications. Moreover, the specialized analysis derived by our approach finishes within a few seconds, even on programs which can not complete within 10 minutes with the original analysis.
Quantifying cryptic Symbiodinium diversity within Orbicella faveolata and Orbicella franksi at the Flower Garden Banks, Gulf of Mexico (2014)

The genetic composition of the resident Symbiodinium endosymbionts can strongly modulate the physiological performance of reef-building corals. Here, we used quantitative metabarcoding to investigate Symbiodinium genetic diversity in two species of mountainous star corals, Orbicella franksi and Orbicella faveolata, from two reefs separated by 19 km of deep water. We aimed to determine if the frequency of different symbiont genotypes varied with respect to coral host species or geographic location. Our results demonstrate that across the two reefs both coral species contained seven haplotypes of Symbiodinium, all identifiable as clade B and most closely related to type B1. Five of these haplotypes have not been previously described and may be endemic to the Flower Garden Banks. No significant differences in symbiont composition were detected between the two coral species. However, significant quantitative differences were detected between the east and west banks for three background haplotypes comprising 0.1%-10% of the total. The quantitative metabarcoding approach described here can help to sensitively characterize cryptic genetic diversity of Symbiodinium and potentially contribute to the understanding of physiological variations among coral populations.
Chronic hyperammonemia induces tonic activation of NMDA receptors in cerebellum (2009)

Reduced function of the glutamate--nitric oxide (NO)--cGMP pathway is responsible for some cognitive alterations in rats with hyperammonemia and hepatic encephalopathy. Hyperammonemia impairs the pathway in cerebellum by increasing neuronal nitric oxide synthase (nNOS) phosphorylation in Ser847 by calcium-calmodulin-dependent protein kinase II (CaMKII), reducing nNOS activity, and by reducing nNOS amount in synaptic membranes, which reduces its activation following NMDA receptors activation. The reason for increased CaMKII activity in hyperammonemia remains unknown. We hypothesized that it would be as a result of increased tonic activation of NMDA receptors. The aims of this work were to assess: (i) whether tonic NMDA activation receptors is increased in cerebellum in chronic hyperammonemia in vivo; and (ii) whether this tonic activation is responsible for increased CaMKII activity and reduced activity of nNOS and of the glutamate--NO--cGMP pathway. Blocking NMDA receptors with MK-801 increases cGMP and NO metabolites in cerebellum in vivo and in slices from hyperammonemic rats. This is because of reduced phosphorylation and activity of CaMKII, leading to normalization of nNOS phosphorylation and activity. MK-801 also increases nNOS in synaptic membranes and reduces it in cytosol. This indicates that hyperammonemia increases tonic activation of NMDA receptors leading to reduced activity of nNOS and of the glutamate--NO--cGMP pathway.
Mining Large-Scale Music Data Sets (2012)

Large collections of music audio are now common and present an interesting research opportunity: what statistical patterns and structure can be discovered across thousands or millions of examples? Unfortunately, copyright restrictions can interfere with access to such collections, so we have developed the Million Song Dataset, including derived features but not the original audio, to support commercial-scale music analysis on a common, research database. The audio features are augmented by a wide range of metadata including lyrics, tags, and listener playcounts. Now the database is ready, we have begun analyzing the content, including tasks such as identifying cover songs -- significantly harder for such a large collection.
Temperature sensitivity of carbon decomposition in soil aggregates along a climatic gradient (2016)

Global warming affects the carbon (C) pools in terrestrial ecosystems, accelerating biological processes that feed back into the phenomenon of climate change. Globally, grassland ecosystems accumulate large quantities of organic C into soils and are considered a corner stone for global warming mitigation. The aim of this study was to evaluate the temperature sensitivity of C decomposition in different soil aggregate fractions in grassland ecosystems across a north-south latitudinal gradient in Chile. Soil samples were collected from Mediterranean semi-arid (MSA; 3231' to 3419' south latitude), temperate semi-oceanic (TSO; 3536' to 3627' south latitude), temperate oceanic (TO; 4036' to 4303' south latitude) and subpolar semi-oceanic (SPSO; 4357' to 4740' south latitude) climate zones, and water-stable macroaggregates (250-2,000 m) and free microaggregates (50-250 m) were isolated. Two experiments were performed using short-term incubations (14 days). First, absolute soil respiration and specific soil respiration from isolated aggregates were assessed at 20 C, and second, the isolated aggregates were incubated at different temperature levels (20-30 C for MSA and TSO; 10-20 C for TO and SPSO) to quantify the energy of activation (E a ) and temperature sensitivity (Q 10 ) . In general, the results do not provide evidence of differences between soil aggregate fractions in any of the evaluated parameters, but the soils differed across the latitudinal gradient. High absolute respiration rates and specific respiration, which were related to high grassland productivity, were observed in soils from TO and SPSO zones. The Q 10 values demonstrated a strong positive correlation with annual precipitation, so C decomposition in soils from zones with high precipitation exhibits increased temperature sensitivity.
Ultrastructure of cryopreserved horse embryos. (1987)

Embryos were recovered non-surgically at about Day 6 after ovulation from 15 Quarter horse-type mares and were evaluated for morphological changes which may occur because of exposure to the cryoprotectant and/or cryopreservation. Electron microscopy was used to elucidate the fine structure of intracellular organelles which, if damaged, could cause cellular death. The horse embryo does not totally re-expand in the 10% glycerol freezing medium, nor will it completely re-expand in the isotonic holding medium following glycerol removal whether or not the embryo has been frozen. Embryos in this study were frozen by the same protocol which had resulted in a 30% pregnancy rate for similarly frozen embryos. Junctional complexes between trophoblast cells, as well as the plasma and nuclear membranes of trophoblast and inner cell mass (ICM) cells, were intact after treatment in all embryos. Changes in lipid droplets and some mitochondrial degeneration were observed in the ICM cells of the glycerol-treated embryos. The change in the lipid was not observed in the frozen-thawed embryos, but mitochondrial changes were evident in the trophoblast and ICM cells, with the most extensive mitochondrial damage in the ICM cells.
Implementing, Connecting, and Evaluating a Standard-Based Integrated Operating Room within a German University Hospital (2018)

Background Digital operating rooms (ORs), when optimally designed and integrated, can reduce the complexity of the surgery suite. However, many integrated ORs are effectively isolated from other IT systems in the hospital because there is little or no connectivity with them. Within the German flagship project OR.NET, concepts and components were developed for a standard-based connection of the OR with hospital IT systems. Objectives The aim of this work was to implement and evaluate OR.NET concepts and components within the existing IT landscape of a German university hospital. This article describes and evaluates the implemented architecture and processes for connecting a demo OR to existing hospital IT systems at Heidelberg University Hospital. Methods For the design, establishment, and evaluation of standard-based connections of the demo OR with hospital IT systems, the iterative method “Design and Creation” with four iterations was applied. Results A generic and a concrete architecture for several standard-based connection concepts of the demo OR were developed. Furthermore, the concrete architecture was implemented and evaluated for its technical and clinical relevance. The main benefits of the project were the establishment of basic requisites for improving the efficiency within the OR, easier operation of medical devices as a result of harmonized human–machine interfaces, and providing additional data for improving healthcare. Conclusion OR.NET concepts for a standard-based connection of the OR with hospital IT systems have proven to be promising. They can serve as a reference for further integration scenarios in other hospitals.
Joint Decision Making and Motion Planning for Road Vehicles Using Particle Filtering (2016)

This paper describes a probabilistic framework for real-time, joint decision making and trajectory generation of road vehicles. The selection of desired lane and state profile is posed as a stochastic nonlinear estimation problem. The nonlinear estimator is integrated with a sampling-based motion planner that computes candidate paths and corresponding state trajectories, while accounting for obstacle motion. The motion planner is implemented in receding horizon and repeatedly replans, based on stored candidate trajectories. A simulated autonomous highway-driving example illustrates how vehicle dynamics is naturally handled in the framework. The results show that the framework is capable of making effective online decisions and computing safe trajectories.
Acoustic Radiation Force Impulse Imaging (ARFI) on an IVUS Circular Array (2014)

Our long-term goal is the detection and characterization of vulnerable plaque in the coronary arteries of the heart using intravascular ultrasound (IVUS) catheters. Vulnerable plaque, characterized by a thin fibrous cap and a soft, lipid-rich necrotic core is a precursor to heart attack and stroke. Early detection of such plaques may potentially alter the course of treatment of the patient to prevent ischemic events. We have previously described the characterization of carotid plaques using external linear arrays operating at 9 MHz. In addition, we previously modified circular array IVUS catheters by short-circuiting several neighboring elements to produce fixed beamwidths for intravascular hyperthermia applications. In this paper, we modified Volcano Visions 8.2 French, 9 MHz catheters and Volcano Platinum 3.5 French, 20 MHz catheters by short-circuiting portions of the array for acoustic radiation force impulse imaging (ARFI) applications. The catheters had an effective transmit aperture size of 2 mm and 1.5 mm, respectively. The catheters were connected to a Verasonics scanner and driven with pushing pulses of 180 V p-p to acquire ARFI data from a soft gel phantom with a Young's modulus of 2.9 kPa. The dynamic response of the tissue-mimicking material demonstrates a typical ARFI motion of 1 to 2 microns as the gel phantom displaces away and recovers back to its normal position. The hardware modifications applied to our IVUS catheters mimic potential beamforming modifications that could be implemented on IVUS scanners. Our results demonstrate that the generation of radiation force from IVUS catheters and the development of intravascular ARFI may be feasible.
Scattering Effectiveness of Monoenergetic Neutrons in the Various Shielding Materials (1972)

In neutron shielding, the scattering effect is equally important as the attenuations in shielding materials. In the present study, the scattered dose equivalent was measured using a Rem counter for water, paraffin, borated paraffin, ordinary and heavy concrete, lead, iron, and tissue equivalent material in three different angles: 45, 90, and 135, respectively. The measurements were performed for the neutron, having the energies of 0.5, 1, 2, 5, and 18 MeV, which are produced from the Van do Graaff accelerator. The scattered dose equivalent ratios were increased with increasing the thickness of scattering materials and saturated at a certain thickness although they were different from one to other materials under study. The ratios were large for lead and iron while they were small for the hydrogen containing materials such as water and paraffin etc.
A novel iron loss calculation method on power converters based on dynamic minor loop (2005)

The authors have reported a novel iron loss calculation method based on a loss-map of the magnetic materials. A distinctive feature of this method is that the iron loss on the inductors can easily be calculated in many kinds of converters dynamically. The dynamic measuring method of the dynamic minor-magnetic loop by using the buck-chopper circuit is presented. Next, some typical characteristics of the loss map derived from the dynamic minor loop measurement is discussed. Also, a novel iron loss calculation method of the ac filter inductor on the PWM inverter by using the loss-map method is described. Some experimental results shows that the iron loss obtained from this calculation method coincides well with the actual one
Computer generated holographic optics used in laser powder fusion (2004)

Conventional laser cladding systems use a focussing nozzle to direct the beam to the work piece, and by using either blown or pre placed powder, they are able to fuse the powder to the substrate. The shortfall of this process is that, once sectioned, a parabolic transverse profile is seen. This is due to the Gaussian irradiance distribution of the beam and no conventional optics can remedy the problem. Diffractive optical elements, however, can be designed for each process. Models of thermal conduction in the powder and the substrate can be utilised to produce a diffractive optical element specific to this operation. This enables a rectangular spot with a semi-idealised intensity cross section to be delivered to the work piece, reorganising 90% of the 1.2kW CO2 laser beam. When the diffractive optical element is applied to the laser cladding process, the resultant transverse clad profile is uniformly rectangular with a lack of ‘shoulder rounding’. The laser cladding operation produced complex microstructures, which could not be satisfactorily categorised with optical microscopy. This lead to the simplification of the process by removing the powder. Autogenous bead on plate laser welds have therefore been manufactured, using both conventional optics and diffractive optical elements, in order to determine the solidification microstructure of 316L stainless steel. Optical microscopy, electron back-scatter diffraction (EBSD), energy dispersive spectroscopy (EDS), have been employed to assist in the characterisation of the complex microstructures produced.
$\boldsymbol{\sim 8.5\mu \mathrm{m}}$ InP-based quantum cascade lasers grown on GaAs by MOCVD (2022)

InP-based quantum cascade lasers on (001) GaAs with watt-level output power and low pulsed threshold-current density at RT. A 35-stage <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$\ln 0.53\text{GaAs}/\text{In}0.52\text{AlAs}$</tex> lattice-matched active-region QCL is grown by MOCVD, on an InP metamorphic buffer with strained InAs or InGaAs quantum wells as dislocation filters.
Robust Multi-Agent Bandits Over Undirected Graphs (2022)

We consider a multi-agent multi-armed bandit setting in which $n$ honest agents collaborate over a network to minimize regret but $m$ malicious agents can disrupt learning arbitrarily. Assuming the network is the complete graph, existing algorithms incur $O( (m + K/n) \log (T) / Δ)$ regret in this setting, where $K$ is the number of arms and $Δ$ is the arm gap. For $m \ll K$, this improves over the single-agent baseline regret of $O(K\log(T)/Δ)$. In this work, we show the situation is murkier beyond the case of a complete graph. In particular, we prove that if the state-of-the-art algorithm is used on the undirected line graph, honest agents can suffer (nearly) linear regret until time is doubly exponential in $K$ and $n$. In light of this negative result, we propose a new algorithm for which the $i$-th agent has regret $O( ( d_{\text{mal}}(i) + K/n) \log(T)/Δ)$ on any connected and undirected graph, where $d_{\text{mal}}(i)$ is the number of $i$'s neighbors who are malicious. Thus, we generalize existing regret bounds beyond the complete graph (where $d_{\text{mal}}(i) = m$), and show the effect of malicious agents is entirely local (in the sense that only the $d_{\text{mal}}(i)$ malicious agents directly connected to $i$ affect its long-term regret).
ChemInform Abstract: Polymer Supported Reagents: An Efficient and Simple Method for the Synthesis of Triaryl Phosphates. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Supplementary Table S2 from Androgen Receptor Signaling Regulates DNA Repair in Prostate Cancers (2023)

&lt;p&gt;Supplementary Table S2 - PDF file 250K, Defining AR-regulated DNA repair genes in LNCaP&lt;/p&gt;
Dioxygen activation in the photochemistry of some oxo-metalloporphyrin complexes (1986)

Ultraviolet irradiation of the peroxo-complexes [Ti(O2)(tpp)] and [Mo(O2)(tpp)](tpp = 5,10,15,20-tetraphenylporphyrinate) induces elimination of O2 and generation of the corresponding oxometalloporphyrins [TiO(tpp)] and [MoO(tpp)]. Reductive elimination of O2 from [{Fe(tpp)}2O] also occurs upon irradiation of argon-purged solutions. Studies using spin traps in e.s.r. experiments, together with quenching experiments, indicate that photolysis of the peroxocomplexes produces O2 in the 1Δg excited state. For [{Fe(tpp)}2O] the results differ with the conditions used. In aerated CH2Cl2 solutions, 1O2 is produced in the quenching process of the excited states by O2. In degassed CH2Cl2 solutions apparently 1O2 is not formed in the photoinduced deoxygenation reaction, but rather, studies using spin traps for e.s.r. investigations have indicated the formation of the superoxide ion O2–. The attack on solvent by 1O2 and of photogenerated O2– involving radical formation, is also discussed.
A Novel Assay Platform for the Detection of Translation Modulators of Spermidine/ Spermine Acetyltransferase (2014)

Spermidine/spermine-N1-acetyltransferase (SSAT) is a mitochondrial-localized enzyme that is highly inducible and tightly controlled and is the rate-limiting enzyme in polyamine catabolism. It is known that SSAT is induced when polyamine level increases. Although multiple mechanisms have been implicated, translational control is thought to be paramount. Previous studies with transgenic and knockout mice suggested that for certain human conditions, the modulation of SSAT levels could offer therapeutic benefits. Besides polyamines and their analogs, certain stimuli can increase SSAT levels, suggesting that the development of reporters for high throughput screening can lead to the identification of novel pharmacophores that can modulate SSAT translation. Here we report the development and validation of a luciferase-based biosensor system for the identification of compounds that are able to either promote or prevent the translation of SSAT. The system uses HEK293T cells transfected with a construct composed of SSAT mRNA modified to lack upstream open reading frame (uORF) function, is mutated to reduce translational repression and is linked with luciferase. As a proof of principle of the utility of the SSAT translation sensor, we screened the Prestwick drug library (1,200 FDA Approved compounds). The library contained 15 compounds that activated SSAT translation by at least 40% more than the basal expression, but none exceeded the positive control N1, N11-diethylnorspermine. On the other hand, 38 compounds were found to strongly inhibit SSAT translation. We conclude that this biosensor can lead to the identification of novel pharmacophores that are able to modulate the translation of SSAT.
Inverse design of engineered materials for extreme optical devices (2018)

Optical devices based on engineered materials can achieve performances not possible with conventional design methodologies. However, these performances come at the cost of relatively unconstrained design spaces which necessitates the development of efficient optimization algorithms. Furthermore, engineered optical devices, as opposed to classical designs, may possess multifunctional behaviors which places additional demands on the optimization algorithms in order to maximize the performance. To this end, two custom state-of-the-art multi-objective optimization algorithms are presented and their application towards the inverse design of engineered materials for the realization of extreme optical devices is discussed.