gebhart/patrepeval huggingface dataset:
P2‐436: Dose‐dependent effects of dietary folate, vitamin B‐12 and vitamin B‐6 on plasma lipid profile in rats (2012)

Folate, vitamins B-12 and B-6 are essential nutritional components in one-carbon metabolism in different ways and typically increase methylation capacity. This could support methylation of phosphatidylethanolamine (PE) to phosphatidylcholine (PC) by PE- N -methyltransferase (PEMT) in the liver. It has been suggested that PC synthesis by PEMT influence circulating levels of polyunsaturated fatty acids, like docosahexaenoic acid (DHA) (Watkins et al., J Nutr 2003; Pynn et al., J Lipid Res 2011). The aim of the present experiment was to investigate whether dietary enrichment with the three B-vitamins could affect plasma lipid composition and particularly plasma DHA levels in rats. After feeding rats one of four diets with increasing levels of folate, vitamins B-12 and B-6 (0%, 100%, 400%, or 1600% of the recommended daily intake) for 4 weeks, plasma fatty acid composition was analyzed using GC and the polar lipid profile was analyzed at the Kansas Lipidomics Research Center using triple quadrupole MS. In addition, plasma homocysteine concentration was measured as an indicator of methylation capacity. The results of the GC analysis indicate that dietary folate, vitamins B-12 and B-6 dose-dependently increased plasma DHA concentration. Plasma DHA and homocysteine showed a significant negative correlation. Data analysis of the polar lipid profile is ongoing. The first results demonstrate the interdependence between folate, vitamins B-12 and B-6 intake and plasma DHA. In this way, intake of supplemental B-vitamins may increase the availability of DHA for processes like neuronal membrane phospholipid synthesis. The increase in plasma DHA may be explained by the effects of B-vitamins on methylation capacity and subsequent enhancement of PC synthesis by the PEMT pathway. Details on this mechanism, implications for Alzheimer's disease, and pending additional results of the MS analysis will be presented.
“It/I”: A Theater Play Featuring an Autonomous Computer Character (2002)

“It/I” is a two-character theater play in which the human character I (played by a real actor) is taunted and played with by an autonomous computer character It on a computer-controlled, camera-monitored stage. The play, performed before live audiences in November 1997, brought an automatic computer character to a theatrical stage for the first time ever. This paper reports the experience and examines important technical developments needed for the successful production of “It/I”. In particular we describe the interval script paradigm used to program the computer character and the ACTSCRIPT language for communication of actions and goals. Although our experiments have been restricted to physical interactive spaces, we believe that interval scripts and ACTSCRIPT can successfully address the control and management of any virtual environment with a complex temporal structure or a strong underlying narrative.
PlantGDB: a resource for comparative plant genomics (2007)

PlantGDB (http://www.plantgdb.org/) is a genomics database encompassing sequence data for green plants (Viridiplantae). PlantGDB provides annotated transcript assemblies for >100 plant species, with transcripts mapped to their cognate genomic context where available, integrated with a variety of sequence analysis tools and web services. For 14 plant species with emerging or complete genome sequence, PlantGDB's genome browsers (xGDB) serve as a graphical interface for viewing, evaluating and annotating transcript and protein alignments to chromosome or bacterial artificial chromosome (BAC)-based genome assemblies. Annotation is facilitated by the integrated yrGATE module for community curation of gene models. Novel web services at PlantGDB include Tracembler, an iterative alignment tool that generates contigs from GenBank trace file data and BioExtract Server, a web-based server for executing custom sequence analysis workflows. PlantGDB also hosts a plant genomics research outreach portal (PGROP) that facilitates access to a large number of resources for research and training.
Applied AI matters: AI4Code (2021)

The marriage of Artificial Intelligence (AI) techniques to problems surrounding the generation, maintenance, and use of source code has come to the fore in recent years as an important AI application area1. A large chunk of this recent attention can be attributed to contemporaneous advancements in Natural Language Processing (NLP) techniques and sub-fields. The naturalness hypothesis, which states that "software is a form of human communication" and that code exhibits patterns that are similar to (human) natural languages (Devanbu, 2015; Hindle, Barr, Gabel, Su, &amp; Devanbu, 2016), has allowed for the application of many of these NLP advances to code-centric usecases. This development has contributed to a spate of work in the community --- much of it captured in a survey by Allamanis, Barr, Devanbu, and Sutton (2018) that focuses on classifying these approaches by the type of probabilistic model applied to source code. This increase in the variety of AI techniques applied to source code has found various manifestations in the industry at large. Code and software form the backbone that underpins almost all modern technical advancements: it is thus natural that breakthroughs in this area should reflect in the emergence of real world deployments.
ALS/FTD mutations in UBQLN2 impede autophagy by reducing autophagosome acidification through loss of function (2020)

Mutations in <i>UBQLN2</i> cause amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and other neurodegenerations. However, the mechanism by which the UBQLN2 mutations cause disease remains unclear. Alterations in proteins involved in autophagy are prominent in neuronal tissue of human ALS <i>UBQLN2</i> patients and in a transgenic P497S UBQLN2 mouse model of ALS/FTD, suggesting a pathogenic link. Here, we show UBQLN2 functions in autophagy and that ALS/FTD mutant proteins compromise this function. Inactivation of UBQLN2 expression in HeLa cells reduced autophagic flux and autophagosome acidification. The defect in acidification was rescued by reexpression of wild type (WT) UBQLN2 but not by any of the five different UBQLN2 ALS/FTD mutants tested. Proteomic analysis and immunoblot studies revealed P497S mutant mice and UBQLN2 knockout HeLa and NSC34 cells have reduced expression of ATP6v1g1, a critical subunit of the vacuolar ATPase (V-ATPase) pump. Knockout of UBQLN2 expression in HeLa cells decreased turnover of ATP6v1g1, while overexpression of WT UBQLN2 increased biogenesis of ATP6v1g1 compared with P497S mutant UBQLN2 protein. In vitro interaction studies showed that ATP6v1g1 binds more strongly to WT UBQLN2 than to ALS/FTD mutant UBQLN2 proteins. Intriguingly, overexpression of ATP6v1g1 in UBQLN2 knockout HeLa cells increased autophagosome acidification, suggesting a therapeutic approach to overcome the acidification defect. Taken together, our findings suggest that UBQLN2 mutations drive pathogenesis through a dominant-negative loss-of-function mechanism in autophagy and that UBQLN2 functions as an important regulator of the expression and stability of ATP6v1g1. These findings may have important implications for devising therapies to treat <i>UBQLN2</i>-linked ALS/FTD.
Personalization of ventricular cardiac conduction system models to reproduce patient electrocardiogram (2021)

Cardiac electrical activation is a fundamental mechanism that controls cardiac function. It is key for a computational model to be able to reproduce the patient ECG and the underlying sequence of activation of the ventricles. In this study, we propose to personalize the activation sequence by estimating a compatible cardiac conduction system (CCS) for a given patient from his electroanatom-ical map. We perform the study on five subjects in sinus rhythm from which we estimated the CCS and performed forward simulations to obtain the virtual ECG. Errors at the endocardium were in average 5.72ms, and correlation between clinical and simulated ECG ranged between 0.75 and 0.90. We concluded that the methodology is feasible to personalize the sequence of activation with the advantage of providing an underlying structure for the CCS.
Highly Asymmetric Chiral Domain-Wall Velocities in Y-Shaped Junctions (2018)

Recent developments in spin-orbit torques allow for highly efficient current-driven domain wall (DW) motion in nanowires with perpendicular magnetic anisotropy. Here, we show that chiral DWs can be driven into nonequilibrium states that can persist over tens of nanoseconds in Y-shaped magnetic nanowire junctions that have an input and two symmetric outputs. A single DW that is injected into the input splits and travels at very different velocities in the two output branches until it reaches its steady-state velocity. We find that this is due to the disparity between the fast temporal evolution of the spin current derived spin-orbit torque and a much-slower temporal evolution of the DMI-derived torque. Changing the DW polarity inverts the velocity asymmetry in the two output branches, a property that we use to demonstrate the sorting of domains.
Enhanced Static and Dynamic Properties of Highly Miscible Fullerene-Free Green-Selective Organic Photodetectors (2021)

We developed p-n junction organic photodetectors (OPDs) composed of a polymer donor and a nonfullerene acceptor (NFA) to increase both the responsivity (<i>R</i>) and detectivity (<i>D*</i>) while maintaining a narrow wavelength selectivity. The selection of the polymer donor and NFA with similar green (G) absorption is important for achieving G-wavelength selectivity in these OPDs, which differentiates them from current fullerene-based OPDs and NFA-based panchromatic absorption OPDs. In addition, mixing the polymer donor and asymmetric NFA was efficient toward increasing the miscibility and decreasing the interfacial energy difference of the blended films, resulting in the formation of a uniform and well-mixed nanomorphology in the photoconductive layer. Two-dimensional (2D) grazing incidence X-ray diffraction and Fourier-transform infrared spectroscopy revealed that the lamellar ordering of the polymer donor was enhanced in the blend film prepared with an asymmetric NFA, whereas the aggregation of a symmetric NFA in the blend films did not increase the lamellar ordering of the polymer donor. Consequently, we achieved an <i>R</i> value of 0.31 A/W and <i>D*</i> value of 2.0 × 10<sup>13</sup> Jones with a full width at half-maximum value of 230 nm at -2 V and fast response time of 27 μs without any external bias in the asymmetric NFA-based OPDs. The enhancement in the lamellar ordering and miscibility of the blended films are crucial toward increasing the static and dynamic properties of OPDs.
Ultrasonically induced microtransport (2002)

Fluid motion induced by traveling flexural waves in 4 mu m thick membranes was observed using 2.5 mu m diameter polystyrene spheres in water to make the fluid motion visible. Visual observation of the spheres indicates that they move in the direction of wave propagation with a speed proportional to the square of the acoustic amplitude. The maximum speed is 130 mu m/s for an RF drive voltage of 7.1 Vrms at 3.5 MHz; the wavelength is 100 mu m. Standing Lamb waves, which can be seen visually with a phase-contrast microscope, are found to trap particles, including bacteria located in a drop of water that contacts the membrane. A first order model of Lamb-wave micropumping is presented, based on acoustic streaming theory. Important parameters for device design and operation are discussed, along with options for integrating the device into microflow systems. Possible applications include temperature redistribution in ICs and miniature chemical processing systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Thienopyrimidine Bisphosphonate (ThPBP) Inhibitors of the Human Farnesyl Pyrophosphate Synthase: Optimization and Characterization of the Mode of Inhibition (2013)

Human farnesyl pyrophosphate synthase (hFPPS) controls the post-translational prenylation of small GTPase proteins that are essential for cell signaling, cell proliferation, and osteoclast-mediated bone resorption. Inhibition of hFPPS is a clinically validated mechanism for the treatment of lytic bone diseases, including osteoporosis and cancer related bone metastases. A new series of thienopyrimidine-based bisphosphonates (ThP-BPs) were identified that inhibit hFPPS with low nanomolar potency. Crystallographic evidence revealed binding of ThP-BP inhibitors in the allylic subpocket of hFPPS. Simultaneous binding of inorganic pyrophosphate in the IPP subpocket leads to conformational closing of the active site cavity. The ThP-BP analogues are significantly less hydrophilic yet exhibit higher affinity for the bone mineral hydroxyapatite than the current N-BP drug risedronic acid. The antiproliferation properties of a potent ThB-BP analogue was assessed in a multiple myeloma cell line and found to be equipotent to the best current N-BP drugs. Consequently, these compounds represent a new structural class of hFPPS inhibitors and a novel scaffold for the development of human therapeutics.
ChemInform Abstract: Fluorous Techniques for the Synthesis and Separation of Organic Molecules (2001)

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.
MnO 2 Thin Film Electrodes for Enhanced Reliability of Thin Glass Capacitors (2015)

Many dielectric thin films for energy storage capacitors fail by thermal breakdown events under high‐field drive conditions. The lifetime of the device can be improved under conditions where the current path within the defect regions in dielectrics is eliminated. Self‐healing electrodes were developed by depositing a manganese dioxide (MnO 2 ) thin film between the glass substrate and an aluminum film. For this purpose, thin films of MnO 2 on boroaluminosilicate glass were fabricated via chemical solution deposition and heat‐treated at temperatures in the range 500°C–900°C. The α‐MnO 2 structure was stabilized by Ba 2+ insertion to form the hollandite structure. The phase transition temperature of α‐MnO 2 to Mn 2 O 3 is strongly dependent on the Ba concentration, with transition temperatures of 600°C and 675°C with Ba concentrations of [Ba]/[Mn] = 0.04 and 0.1, respectively. The electrical resistivity increased from 4.5 Ω·cm for MnO 2 to 10 5 Ω·cm for Mn 2 O 3 . Both dielectric breakdown strength and the associated cleared aluminum electrode area increased with an MnO 2 interlayer between Al electrodes and the borosilicate glass. The enhancement in dielectric strength was related with self‐healing. The associated redox reaction between MnO 2 and Mn 2 O 3 was also proved by RAMAN spectroscopy following dielectric breakdown.
Nogo-A-targeting antibody promotes visual recovery and inhibits neuroinflammation after retinal injury (2020)

Abstract N-Methyl-D-aspartate (NMDA)-induced neuronal cell death is involved in a large spectrum of diseases affecting the brain and the retina such as Alzheimer’s disease and diabetic retinopathy. Associated neurological impairments may result from the inhibition of neuronal plasticity by Nogo-A. The objective of the current study was to determine the contribution of Nogo-A to NMDA excitotoxicity in the mouse retina. We observed that Nogo-A is upregulated in the mouse vitreous during NMDA-induced inflammation. Intraocular injection of a function-blocking antibody specific to Nogo-A (11C7) was carried out 2 days after NMDA-induced injury. This treatment significantly enhanced visual function recovery in injured animals. Strikingly, the expression of potent pro-inflammatory molecules was downregulated by 11C7, among which TNFα was the most durably decreased cytokine in microglia/macrophages. Additional analyses suggest that TNFα downregulation may stem from cofilin inactivation in microglia/macrophages. 11C7 also limited gliosis presumably via P.Stat3 downregulation. Diabetic retinopathy was associated with increased levels of Nogo-A in the eyes of donors. In summary, our results reveal that Nogo-A-targeting antibody can stimulate visual recovery after retinal injury and that Nogo-A is a potent modulator of excitotoxicity-induced neuroinflammation. These data may be used to design treatments against inflammatory eye diseases.
Long life lithium batteries with stabilized electrodes (2023)

The present invention relates to non-aqueous electrolytes having electrode stabilizing additives, stabilized electrodes, and electrochemical devices containing the same. Thus the present invention provides electrolytes containing an alkali metal salt, a polar aprotic solvent, and an electrode stabilizing additive. In certain electrolytes, the alkali metal salt is a bis(chelato)borate and the additives include substituted or unsubstituted linear, branched or cyclic hydrocarbons comprising at least one oxygen atom and at least one aryl, alkenyl or alkynyl group. In other electrolytes, the additives include a substituted aryl compound or a substituted or unsubstituted heteroaryl compound wherein the additive comprises at least one oxygen atom. There are also provided methods of making the electrolytes and batteries employing the electrolytes. The invention also provides for electrode materials. Cathodes of the present invention may be further stabilized by surface coating the particles of the spinel or olivine with a material that can neutralize acid or otherwise lessen or prevent leaching of the manganese or iron ions. In some embodiments the coating is polymeric and in other embodiments the coating is a metal oxide such as ZrO.sub.2, TiO.sub.2, ZnO, WO.sub.3, Al.sub.2O.sub.3, MgO, SiO.sub.2, SnO.sub.2 AlPO.sub.4, Al(OH).sub.3, a mixture of any two or more thereof.
Magneto-transport in transition metal multilayered structures (1997)

Metallic multilayered structures comprising alternating ferromagnetic and non-ferromagnetic lay-ers exhibit enhanced magnetoresistance values compared with the magnetoresistance of the in-dividual magnetic layers. The largest changes in resistance are found in sputter-deposited 110 oriented crystalline Co/Cu multilayers in which the Co layers are doped with small amounts of Fe. Values of giant magnetoresistance (GMR) of ∼110 % at room temperature and ∼220 % at 4.2 K are found. The origin of the magnetoresistance relates to spin-dependent scattering at the interfaces between the Co and Cu layers. These very large MR values make GMR materi-als attractive for a variety of applications for which magnetic field sensors are required. Simple exchange-biased sandwich structures (spin-valve sandwiches) are described which exhibit large changes in resistance in very small fields. 1
High light extraction efficiency in bulk-GaN based volumetric violet light-emitting diodes (2014)

We report on the light extraction efficiency of III-Nitride violet light-emitting diodes with a volumetric flip-chip architecture. We introduce an accurate optical model to account for light extraction. We fabricate a series of devices with varying optical configurations and fit their measured performance with our model. We show the importance of second-order optical effects like photon recycling and residual surface roughness to account for data. We conclude that our devices reach an extraction efficiency of 89%.
Suppression of temperature-dependent gain variation of conventional EDFA by hybrid connection of antimony-doped silica EDF (2003)

A new technique to suppress temperature dependence of EDFA gain is proposed and experimentally demonstrated. A specially designed EDF, the glass host of which is Sb-doped silica, showed an opposite sign of temperature dependent gain coefficients in C-band compared to Al-doped silica EDFs. Concatenation of those two EDFs showed an improved gain variation less than ±0.37 dB for the saturated gain over 15 dB, within −40 to +80°C.
Bacterial droplet-based single-cell RNA-seq reveals heterogeneity in bacterial populations and in response to antibiotic perturbation (2022)

Abstract We introduce BacDrop, a highly scalable technology for bacterial single-cell RNA sequencing that has overcome many challenges hindering the development of scRNA-seq in bacteria. BacDrop can be applied to thousands or millions of cells from both gram-negative and gram-positive species. It features universal ribosomal RNA depletion and combinatorial barcodes that enable multiplexing and massively parallel sequencing. We applied BacDrop to study Klebsiella pneumoniae clinical isolates and to elucidate their heterogeneous responses to antibiotic stress. In an unperturbed population presumed to be homogenous, we find within- population heterogeneity largely driven by the expression of mobile genetic elements that promote the evolution of antibiotic resistance. Under antibiotic perturbation, BacDrop revealed transcriptionally distinct subpopulations associated with different phenotypic outcomes including antibiotic persistence. BacDrop thus can capture cellular states that cannot be detected by bulk RNA-seq, which will unlock new microbiological insights into bacterial responses to perturbations and larger bacterial communities such as the microbiome.
Self-Induced Vibration Mechanism with Artificial Muscle Actuator Driven by Pressure (2022)

This paper describes a self-induced vibration mechanism with an artificial muscle driven by pressure. We proposed a mechanism to generate a vibration using the shrinkage force of an inside muscle and the elastic deformation force of exoskeleton, inspired by the skeletal structure of flapping insects. This mechanism generates a vibration at a constant inflow rate by controlling the opening and closing of the outlet. In order to produce the self-induced vibration mechanism, we produced an artificial muscle and an exoskeleton, and assembled them. The self-induced vibration mechanism generated at a frequency of approximately 0.5~6.5 Hz by setting the inflow rate to 0.3~1.5 L/min.
Computerized Automation Controls in Dairy Processing (2018)

The purpose of automation is to increase process efficiency, safety, productivity, and product quality. This is generally achieved by means of a control system that has been &quot;programmed&quot; with a set of instructions. Process parameters such as temperature and pressure were originally controlled by human operators. In the 1940s pneumatic instrumentation was developed to sense process parameters and provide feedback control. Heating and cooling are essential steps in all dairy processing operations. Selective control of microbial growth or lethality is achieved by appropriately heating and/or cooling the product. The objective of pasteurization is to inactivate spoilage microorganisms so that the milk will be safe and will have a longer shelf life than its unpasteurized counterpart. Homogenization is the process by which the stability of milk fat emulsion is improved by decreasing the average diameter of milk fat globules.