gebhart/patrepeval huggingface dataset:
In Situ Detection of Amino Acids from Bacterial Biofilms and Plant Root Exudates by Liquid Microjunction Surface-Sampling Probe Mass Spectrometry (2022)

The plant rhizosphere is a complex and dynamic chemical environment where the exchange of molecular signals between plants, microbes, and fungi drives the development of the entire biological system. Exogenous compounds in the rhizosphere are known to affect plant-microbe organization, interactions between organisms, and ultimately, growth and survivability. The function of exogenous compounds in the rhizosphere is still under much investigation, specifically with respect to their roles in plant growth and development, the assembly of the associated microbial community, and the spatiotemporal distribution of molecular components. A major challenge for spatiotemporal measurements is developing a nondisruptive and nondestructive technique capable of analyzing the exogenous compounds contained within the environment. A methodology using liquid microjunction-surface sampling probe-mass spectrometry (LMJ-SSP-MS) and microfluidic devices with attached microporous membranes was developed for <i>in situ</i>, spatiotemporal measurement of amino acids (AAs) from bacterial biofilms and plant roots. Exuded arginine was measured from a living <i>Pantoea</i> YR343 biofilm, which resulted in a chemical image indicative of biofilm growth within the device. Spot sampling along the roots of <i>Populus trichocarpa</i> with the LMJ-SSP-MS resulted in the detection of 15 AAs. Variation in AA concentrations across the root system was observed, indicating that exudation is not homogeneous and may be linked to local rhizosphere architecture and different biological processes along the root.
Human T-Cell Leukemia Virus Type I Tax Activation of NF-ΝB/Rel Involves Phosphorylation and Degradation of IΙBκ and RelA (p65)-Mediated Induction of the italic to c-rel Gene (1994)

The tax gene product of human T-cell leukemia virus type I (HTLV-I) is a potent transcriptional activator that both stimulates viral gene expression and activates an array of cellular genes involved in T-cell growth. Tax acts indirectly by inducing or modifying the action of various host transcription factors, including members of the NF-kappa B/Rel family of enhancer-binding proteins. In resting T cells, many of these NF-kappa B/Rel factors are sequestered in the cytoplasm by various ankyrin-rich inhibitory proteins, including I kappa B alpha. HTLV-I Tax expression leads to the constitutive nuclear expression of biologically active NF-kappa B and c-Rel complexes; however, the biochemical mechanism(s) underlying this response remains poorly understood. In this study, we demonstrate that Tax-stimulated nuclear expression of NF-kappa B in both HTLV-I-infected and Tax-transfected human T cells is associated with the phosphorylation and rapid proteolytic degradation of I kappa B alpha. In contrast to prior in vitro studies, at least a fraction of the phosphorylated form of I kappa B alpha remains physically associated with the NF-kappa B complex in vivo but is subject to rapid degradation, thereby promoting the nuclear translocation of the active NF-kappa B complex. We further demonstrate that Tax induction of nuclear c-Rel expression is activated by the RelA (p65) subunit of NF-kappa B, which activates transcription of the c-rel gene through an intrinsic kappa B enhancer element. In normal cells, the subsequent accumulation of nuclear c-Rel acts to inhibit its own continued production, indicating the presence of an autoregulatory loop. However, the pathologic action HTLV-I Tax leads to the deregulated and sustained nuclear expression of both NF-kappa B and c-Rel, a response that may contribute to HTLV-I-induced T-cell transformation.
Sobolev Sampling of Free Energy Landscapes (2022)

A family of fast sampling methods is introduced here for molecular simulations of systems having rugged free energy landscapes. The methods represent a generalization of a strategy consisting of adjusting a model for the free energy as a function of one- or more collective variables as a simulation proceeds. Such a model is gradually built as a system evolves through phase space from both the frequency of visits to distinct states and generalized force estimates corresponding to such states. A common feature of the methods is that the underlying functional models and their gradients are easily expressed in terms of the same parameters, thereby providing faster and more effective fitting of the model from simulation data than other available sampling techniques. They also eliminate the need to train simultaneously separate neural networks, while retaining the advantage of generating smooth and continuous functional estimates that enable biasing outside the support grid. Implementation of the methods is relatively simple and, more importantly, they are found to provide gains of up to several orders of magnitude in computational efficiency over existing approaches.
Chemogenetic stimulation of the Gi pathway in astrocytes suppresses neuroinflammation (2021)

Engineered G protein-coupled receptors (GPCRs) are commonly used in chemogenetics as designer receptors exclusively activated by designer drugs (DREADDs). Although several GPCRs have been studied in astrocytes using a chemogenetic approach, the functional role of the astrocytic G<sub>i</sub> pathway is not clear, as the literature is conflicting depending on the brain regions or behaviors investigated. In this study, we evaluated the role of the astrocytic G<sub>i</sub> pathway in neuroinflammation using a G<sub>i</sub> -coupled DREADD (hM4Di). G<sub>i</sub> -DREADD was expressed in hippocampal astrocytes of a lipopolysaccharide (LPS)-induced neuroinflammation mouse model using adeno-associated viruses. We found that astrocyte G<sub>i</sub> -DREADD stimulation using clozapine N-oxide (CNO) inhibits neuroinflammation, as characterized by decreased levels of proinflammatory cytokines, glial activation, and cognitive impairment in mice. Subsequent experiments using primary astrocyte cultures revealed that G<sub>i</sub> -DREADD stimulation significantly downregulated LPS-induced expression of Nos2 mRNA and nitric oxide production. Similarly, in vitro calcium imaging showed that activation of the astrocytic G<sub>i</sub> pathway attenuated intracellular calcium transients triggered by LPS treatment, suggesting a positive correlation between enhanced calcium transients and the inflammatory phenotype of astrocytes observed in the inflamed brain. Taken together, our results indicate that the astrocytic G<sub>i</sub> pathway plays an inhibitory role in neuroinflammation, providing an opportunity to identify potential cellular and molecular targets to control neuroinflammation.
Search for W′ → tb decays in the lepton + jets final state in pp collisions at $ \sqrt{s} $ = 8 TeV (2014)

Results are presented from a search for the production of a heavy gauge boson W decaying into a top and a bottom quark, using a data set collected by the CMS experiment at s = 8 TeV and corresponding to an integrated luminosity of 19.5 fb -1 . Various models of W -boson production are studied by allowing for an arbitrary combination of left-and right-handed couplings. The analysis is based on the detection of events with a lepton (e, ), jets, and missing transverse energy in the final state. No evidence for Wboson production is found and 95% confidence level upper limits on the production cross section times branching fraction are obtained. For W bosons with purely right-handed couplings, and for those with left-handed couplings assuming no interference effects, the observed 95% confidence level limit is M (W ) > 2.05 TeV. For W bosons with purely lefthanded couplings, including interference effects, the observed 95% confidence level limit is M (W ) > 1.84 TeV. The results presented in this paper are the most stringent limits published to date.
A solution processed nanostructured p-type NiO electrode for efficient inverted perovskite solar cells (2016)

Here we report a solution processed nanostructured NiO as a hole transport layer (HTL) for efficient inverted MAPb(I<sub>1-x</sub>Br<sub>x</sub>)<sub>3</sub> (x = 0.3) perovskite solar cells (PSCs). The best performing p-i-n PSC exhibits 15.35% power conversion efficiency with a current density (J<sub>SC</sub>) of 19.85 mA cm<sup>-2</sup>, an open circuit voltage (V<sub>OC</sub>) of 1.056 V and a fill factor (FF) of 0.73. The developed method is simple and cost effective.
Whetstone: A Method for Training Deep Artificial Neural Networks for Binary Communication (2018)

This paper presents a new technique for training networks for low-precision communication. Targeting minimal communication between nodes not only enables the use of emerging spiking neuromorphic platforms, but may additionally streamline processing conventionally. Low-power and embedded neuromorphic processors potentially offer dramatic performance-per-Watt improvements over traditional von Neumann processors, however programming these brain-inspired platforms generally requires platform-specific expertise which limits their applicability. To date, the majority of artificial neural networks have not operated using discrete spike-like communication. We present a method for training deep spiking neural networks using an iterative modification of the backpropagation optimization algorithm. This method, which we call Whetstone, effectively and reliably configures a network for a spiking hardware target with little, if any, loss in performance. Whetstone networks use single time step binary communication and do not require a rate code or other spike-based coding scheme, thus producing networks comparable in timing and size to conventional ANNs, albeit with binarized communication. We demonstrate Whetstone on a number of image classification networks, describing how the sharpening process interacts with different training optimizers and changes the distribution of activity within the network. We further note that Whetstone is compatible with several non-classification neural network applications, such as autoencoders and semantic segmentation. Whetstone is widely extendable and currently implemented using custom activation functions within the Keras wrapper to the popular TensorFlow machine learning framework.
Contribution à la modélisation des circulateurs ultra miniatures : étude des limitations en fréquence (1995)

Le choix de la technologie mmic pour la realisation de l'etage hyperfrequence des systemes embarques (radar ou satellite) se justifie par les nombreux avantages que cette technologie confere. En depit des etudes faites en ce sens, l'isolation entre emetteur et recepteur a partir des modules mmic reste un probleme non encore resolu. De nombreux efforts ont ete consentis pour realiser la fonction de duplexage a l'aide des commutateurs ou de circulateurs a base d'elements actifs. Ces derniers sont peu utilises, compte tenu notamment de leur consommation de puissance. Aux tres basses frequences, on a pu reduire la taille des circulateurs a ferrite par emploi d'elements localises a couplage non reciproque. La montee en frequence de tels circulateurs est associee d'une part a la possibilite de reduire les dimensions du cur du circulateur en utilisant des technologies d'integration particulieres et, d'autre part, pour ces technologies, a la maitrise du comportement en frequence des differents elements constitutifs du circulateur et les effets parasites associes. Par rapport aux analyses basse frequence decrivant le fonctionnement de tels circulateurs, deux types d'etudes sont effectues pour obtenir des avancees significatives dans la maitrise de la modelisation de ces dispositifs en tres haute frequence: l'etude du cur et de son eventuelle delocalisation consecutive aux limites de realisations actuelles au regard de la geometrie particuliere de celui-ci, notamment l'entrelacement. La modelisation fine des elements qui, associes au cur du circulateur permettent de fixer la frequence de travail ainsi que la maitrise de l'ensemble des elements parasites associes aux choix technologiques et dont l'importance croit avec la frequence. Cette modelisation fait appel a une etude electromagnetique des discontinuites que l'on retrouve dans le dispositif et dont les effets influent sur les performances, et qui sont source de limitations en frequence. Ce travail est donc oriente dans les deux voies citees ci-dessus. Nous prenons en compte la necessaire gradation des difficultes en relation avec les bandes de frequences choisies pour tester la maitrise des modeles developpes et l'adequation des technologies retenues. La faisabilite de ce type de circulateur est prouvee a plus de 9 ghz avec de tres bonnes performances. Le choix de la technologie de realisation prend en compte le meilleur compromis entre les difficultes de realisation, les performances et le cout. Les resultats obtenus, non encore publies a ce jour, n'occultent pas la necessite de developper une approche numerique d'etude globale, si l'on desire aller au dela de la bande x
Speech comprehension is correlated with temporal response patterns recorded from auditory cortex (2001)

Speech comprehension depends on the integrity of both the spectral content and temporal envelope of the speech signal. Although neural processing underlying spectral analysis has been intensively studied, less is known about the processing of temporal information. Most of speech information conveyed by the temporal envelope is confined to frequencies below 16 Hz, frequencies that roughly match spontaneous and evoked modulation rates of primary auditory cortex neurons. To test the importance of cortical modulation rates for speech processing, we manipulated the frequency of the temporal envelope of speech sentences and tested the effect on both speech comprehension and cortical activity. Magnetoencephalographic signals from the auditory cortices of human subjects were recorded while they were performing a speech comprehension task. The test sentences used in this task were compressed in time. Speech comprehension was degraded when sentence stimuli were presented in more rapid (more compressed) forms. We found that the average comprehension level, at each compression, correlated with (i) the similarity between the frequencies of the temporal envelopes of the stimulus and the subject's cortical activity ("stimulus-cortex frequency-matching") and (ii) the phase-locking (PL) between the two temporal envelopes ("stimulus-cortex PL"). Of these two correlates, PL was significantly more indicative for single-trial success. Our results suggest that the match between the speech rate and the a priori modulation capacities of the auditory cortex is a prerequisite for comprehension. However, this is not sufficient: stimulus-cortex PL should be achieved during actual sentence presentation.
Dynamic coherent beam combining based on a setup of microlens arrays (2020)

A novel optical concept is introduced with standard components for highly efficient coherent beam combining a system of (<i>N x N</i>) beams. In a proof-of-principle experiment a well-defined setup with microlens arrays (MLAs) is used to create a beam matrix of 5 x 5 beams. For the combination step the same setup is employed, and the created 25 beams are combined. A combination efficiency above 90% is achieved. Furthermore, the concept allows for dynamic beam combination, i.e., the resulting number of beams and corresponding positions can be controlled by the absolute phases of the array of input beams. A proof-of-principle experiment shows excellent agreement with the model.
RTA 1701 is an orally-bioavailable, potent, and selective RORγt inhibitor that suppresses Th17 differentiation in vitro and is efficacious in mouse models of autoimmune disease. (2018)

Abstract Retinoic acid-related orphan receptor γt (RORγt) is a transcription factor that directs the differentiation of Th17 cells, a subset of CD4+ helper T cells involved in autoimmune disorders. Once differentiated, Th17 cells secrete interleukin-17A (IL-17A) and other key cytokines implicated in autoimmune and inflammatory disease. Antibodies that target Th17 cells are approved for several autoimmune disorders, validating the important role of Th17 cells in disease. RTA 1701 is a potent and selective RORγt inhibitor in preclinical development for autoimmune disorders. It inhibits the activity of RORγt, as assessed using ligand binding domain and full-length RORγt reporters. Moreover, RTA 1701 is selective for RORγt and does not inhibit the activity of two closely-related receptors, RORα and RORβ. By inhibiting RORγt, RTA 1701 blocks Th17 differentiation of naïve CD4+ T cells and IL-17A production by both Th17 polarized CD4+ T cells and activated peripheral blood mononuclear cells (PBMCs). The expression of other RORγt target genes and Th17 signature genes (eg, IL-17F, IL-21, CCL20) is also reduced following RTA 1701 treatment of Th17-polarized naïve CD4+ T cells, as assessed by qPCR. RTA 1701 is orally bioavailable with excellent pharmacokinetic properties in rodents and monkey. Furthermore, this compound is efficacious in animal models of autoimmune disease, including the collagen-induced arthritis (CIA) mouse model of rheumatoid arthritis and the experimental autoimmune encephalomyelitis (EAE) mouse model of multiple sclerosis. Together, these results suggest that RORγt inhibition by RTA 1701 may have therapeutic potential in Th17-associated autoimmune disorders.
Computerized electrocardiogram data transformation enables effective algorithmic differentiation of wideQRScomplex tachycardias (2022)

Accurate WCT differentiation may be accomplished using computerized data of (i) the WCT ECG alone and (ii) paired WCT and baseline ECGs.
The Methemoglobin Reduction Test for Primaquine-Type Sensitivity of Erythrocytes (1962)

THE INCREASING IMPORTANCE in medicine of the inherited susceptibility to hemolysis, known as primaquine-type sensitivity or erythrocytic glucose-6-phosphate dehydrogenase (G-6-PD) deficiency, has been summarized by Kellermeyer et al., in this issue ofTHE JOURNAL. Several laboratory methods have been devised for the identification of this primaquine-type sensitivity of red blood cells. The Methemoglobin Reduction Test developed by Brewer et al. has several advantages over previous tests. It is simple and inexpensive to perform; it clearly separates individuals with normal erythrocytes from those with full susceptibility to hemolysis; and it allows semiquantitative evaluation of intermediate susceptibility. The following simplification of the Methemoglobin Reduction Test increases its value and practicability for use in diagnosis. Certain steps used in the original method have been omitted or modified in order to increase the versatility of the procedure, e.g., the preparation of the incubation tubes in advance. The end-point is determined visually by gross inspection.
4D Printing of a Bioinspired Microneedle Array with Backward‐Facing Barbs for Enhanced Tissue Adhesion (2020)

Abstract Microneedle (MN), a miniaturized needle with a length‐scale of hundreds of micrometers, has received a great deal of attention because of its minimally invasive, pain‐free, and easy‐to‐use nature. However, a major challenge for controlled long‐term drug delivery or biosensing using MN is its low tissue adhesion. Although microscopic structures with high tissue adhesion are found from living creatures in nature (e.g., microhooks of parasites, barbed stingers of honeybees, quills of porcupines), creating MNs with such complex microscopic features is still challenging with traditional fabrication methods. Here, a MN with bioinspired backward‐facing curved barbs for enhanced tissue adhesion, manufactured by a digital light processing 3D printing technique, is presented. Backward‐facing barbs on a MN are created by desolvation‐induced deformation utilizing cross‐linking density gradient in a photocurable polymer. Barb thickness and bending curvature are controlled by printing parameters and material composition. It is demonstrated that tissue adhesion of a backward‐facing barbed MN is 18 times stronger than that of barbless MN. Also demonstrated is sustained drug release with barbed MNs in tissue. Improved tissue adhesion of the bioinspired MN allows for more stable and robust performance for drug delivery, biofluid collection, and biosensing.
Convolutional Autoencoding of Small Targets in the Littoral Sonar Acoustic Backscattering Domain (2022)

Automated target recognition is an important task in the littoral warfare domain, as distinguishing mundane objects from mines can be a matter of life and death. This is initial work towards the application of convolutional autoencoding to the littoral sonar space, with goals of disentangling the reflection noise prevalent in underwater acoustics and allowing recognition of the shape and material of targets. The autoencoders were trained on magnitude Fourier transforms of the TREX13 dataset. Clusters in the encoding space representing the known variable of measurement distance between the target and the sensor were found. An encoding vector space of around 16 dimensions appeared sufficient, and the space was shown to generalize well to unseen data.
MR-compatible electrode and navigation system for MR-guided microwave endometrial ablation (2007)

To accomplish MR-guided microwave endometrial ablation, a sounding applicator type MR-compatible microwave electrode has been constructed. The visibility of the electrode in MR images was appropriate and temperature changes during microwave ablation were clearly shown with MR temperature maps. Optical and electromagnetic tracking systems for this electrode have also been developed. Both of them were able to control MR image planes with its curved electrode tip, successfully. With the optical tracking system, however, the configuration needs to be changed depending on the direction of the electrode because of the visibility of diodes. Meanwhile, electromagnetic tracking system could be used in any directions of the electrode without taking care of the line of sights and was found to be quite useful for such curved surgical instruments.
Caveolin-1 and Dopamine-Mediated Internalization of NaKATPase in Human Renal Proximal Tubule Cells (2009)

In moderate sodium-replete states, dopamine 1-like receptors (D1R/D5R) are responsible for regulating >50% of renal sodium excretion. This is partly mediated by internalization and inactivation of NaKATPase, when associated with adapter protein 2. We used dopaminergic stimulation via fenoldopam (D1-like receptor agonist) to study the interaction among D1-like receptors, caveolin-1 (CAV1), and the G protein-coupled receptor kinase type 4 in cultured human renal proximal tubule cells (RPTCs). We compared 2 groups of RPTCs, 1 of cell lines that were isolated from normal subjects (nRPTCs) and a second group of cell lines that have D1-like receptors that are uncoupled (uncoupled RPTCs) from adenylyl cyclase second messengers. In nRPTCs, fenoldopam increased the plasma membrane expression of D1R (10.0-fold) and CAV1 (1.3-fold) and markedly decreased G protein-coupled receptor kinase type 4 by 94+/-8%; no effects were seen in uncoupled RPTCs. Fenoldopam also increased the association of adapter protein 2 and NaKATPase by 53+/-9% in nRPTCs but not in uncoupled RPTCs. When CAV1 expression was reduced by 86.0+/-8.5% using small interfering RNA, restimulation of the D1-like receptors with fenoldopam in nRPTCs resulted in only a 7+/-9% increase in association between adapter protein 2 and NaKATPase. Basal CAV1 expression and association with G protein-coupled receptor kinase type 4 was decreased in uncoupled RPTCs (58+/-5% decrease in association) relative to nRPTCs. We conclude that the scaffolding protein CAV1 is necessary for the association of D1-like receptors with G protein-coupled receptor kinase type 4 and the adapter protein 2-associated reduction in plasma membrane NaKATPase.