gebhart/patrepeval huggingface dataset:
VIP-producing enteric neurons interact with innate lymphoid cells to regulate feeding-dependent intestinal epithelial barrier functions (2019)

ABSTRACT The intestinal mucosa serves as both a conduit for uptake of food-derived nutrients and microbiome-derived metabolites and as a barrier that prevents tissue invasion by microbes and tempers inflammatory responses to the myriad contents of the lumen. How the intestine coordinates physiological and immune responses to food consumption to optimize nutrient uptake while maintaining barrier functions remains unclear. Here, we describe how a gut neuronal signal triggered by food intake is integrated with intestinal antimicrobial and metabolic responses controlled by type 3 innate lymphoid cells (ILC3) 1-3 . Food consumption rapidly activates a population of enteric neurons that express vasoactive intestinal peptide (VIP) 4 . Projections of VIP-producing neurons (VIPergic neurons) in the lamina propria are in close proximity to clusters of ILC3 that selectively express VIP receptor type 2 (VIPR2 or VPAC2). ILC3 production of IL-22, which is up-regulated by commensal microbes such as segmented filamentous bacteria (SFB) 5-7 , is inhibited upon engagement of VIPR2. As a consequence, there is a reduction in epithelial cell-derived antimicrobial peptide, but enhanced expression of lipid-binding proteins and transporters 8 . During food consumption, activation of VIPergic neurons thus enhances growth of epithelial-associated SFB and increases lipid absorption. Our results reveal a feeding- and circadian-regulated dynamic intestinal neuro-immune circuit that promotes a trade-off between IL-22-mediated innate immune protection and efficiency of nutrient absorption. Modulation of this pathway may hence be effective for enhancing resistance to enteropathogen 2,3,9 and for treatment of metabolic diseases.
Simulation Model of Common-Mode Chokes for High-Power Applications (2010)

Linear and nonlinear Cauer-network models for nanocrystalline inductor cores are developed and used for circuit simulations of common-mode chokes for inverter-based drive systems of several hundred kW. Experimental measurements of the chokes' performance in a high-power test bed are compared to the model results. When the model is based on measured characteristics of the material used, the match to measured behavior is good. Damping inherent in the material characteristic is adequate, such that additional damping is not useful. The primary limitation to accurate prediction of loss in practice is the tolerance on specifications of core characteristics, particularly at high frequency where limits are not specified.
Techno-economic analysis on renewable energy via hydrogen, views from macro and micro scopes. (2019)

This paper addresses from both macro- and micro- areal coverage in introducing hydrogen system in terms of cost and performance, where the produced hydrogen from surplus photovoltaic (PV) power is stored. Feed-in tariff in Japan had successful achievement for great expansion of renewable energy systems (RES), causing problematic operation due to excess power by overcapacity of RES. One of the candidate approaches to overcome this surplus energy by RES is Power to gas (P2G) system, using electrolysis cells (ECs), fuel cells (FCs) or co-firing in gas turbines, both for energy conversion as well as power balancing. Numerous studies had been investigated on P2G however, within our knowledge no study had been addressed the system from both coverages with different capacity and scales. We investigate micro level (zero emission building in our university) and macro level (Kyushu, one of big regions in Japan). We describe for macro side preliminary result on economic analysis of using surplus power of RES via production and storage of hydrogen while for micro side research design.
A Research on Improving the Precision of Rotating-Wave Plate Polarization Measurement (2015)

The device errors of a rotating-wave-plate-based polarization measurement system can be mainly categorized as the angle error of the polarization prism, the fast axis angle error of wave-plate and the retardation error. By applying Fourier analysis to solve Stokes vectors, we obtain the formulas to calculate the three errors mentioned above, using linear 0° and 45° polarized light to illuminate the system for the error solving. We analyze the measurement errors of the degree of polariza ti on , the polarization purity and the intensity of polariz ati on state , under certain simulation conditions. The results show that after the calibration, the measurement accuracy is improved. Finally, we analyze the effects of the angle error of the linear polarized light used for calibration to the measurement of the three parameters.
A Phase 1, Dose-escalation, Double-blind, Block-randomized, Controlled Trial of Safety and Efficacy of Neosaxitoxin Alone and in Combination With 0.2% Bupivacaine, With and Without Epinephrine, for Cutaneous Anesthesia (2016)

( Anesthesiology. 2015;123(4):873–885) Prolonged local anesthesia has been successfully achieved in both animals and humans using a site-1 sodium channel blocker called Neosaxitoxin (NeoSTX). The purpose of this study was to assess the safety of NeoSTX when administered through injection by itself, combined with bupivacaine, and combined with bupivacaine and epinephrine. The authors hypothesized that the drug would prove safe from a cardiovascular, neuromuscular, and respiratory standpoint. A secondary aim for this study was to evaluate the association between plasma concentrations of NeoSTX and any possible negative symptoms or bodily changes.
Probing the Quantum Interference between Singly and Doubly Resonant Top-Quark Production in <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>p</mml:mi><mml:mi>p</mml:mi></mml:math> Collisions at <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msqrt><mml:mi>s</mml:mi></mml:msqrt><mml:mo>=</mml:mo><mml:mn>13</mml:mn><mml:mtext> </mml:mtext><mml:mtext> </mml:mtext><mml:mi>TeV</mml:mi></mml:math> with the ATLAS Detector (2018)

This Letter presents a normalized differential cross-section measurement in a fiducial phase-space region where interference effects between top-quark pair production and associated production of a single top quark with a W boson and a b-quark are significant. Events with exactly two leptons (ee, μμ, or eμ) and two b-tagged jets that satisfy a multiparticle invariant mass requirement are selected from 36.1 fb^{-1} of proton-proton collision data taken at sqrt[s]=13 TeV with the ATLAS detector at the LHC in 2015 and 2016. The results are compared with predictions from simulations using various strategies for the interference. The standard prescriptions for interference modeling are significantly different from each other but are within 2σ of the data. State-of-the-art predictions that naturally incorporate interference effects provide the best description of the data in the measured region of phase space most sensitive to these effects. These results provide an important constraint on interference models and will guide future model development and tuning.
Clustering of Human Endogenous Retrovirus Sequences with Median Self-Organizing Map (2003)

Mutual relationships of human endogenous retroviruses (HERVs) and their similarities to other DNA elements are studied in this paper. We demonstrate that a completely data-driven grouping is able to reflect same kinds of relationships as more traditional biological classifications and phylogenetic taxonomies. The clusters and their visualization were computed with the Median Self-Organizing Map algorithm of pairwise FASTA-based distances. The wholesequence distances are able to distinguish between the different known types of endogenous elements, and exogenous retroviruses. The HERVs become grouped meaningfully.
An example of energy straggling in an ion accelerator (1985)

We solve the Poisson–Vlasov equations for volume-produced ions, fast neutrals, and backstreaming electrons in a Mirror Fusion Test Facility 80-keV preprototype neutral beam source. Neutral pressure distributions are estimated from known gas feed rates and calculated accelerator column conductance, and are calibrated by comparing measured and calculated electron backstreaming power (computed by solving another Vlasov equation). The depletion of atomic yield from these volume processes is computed for sources in which the atomic yield is 100% in the extraction region. The energy distribution of neutrals and ions is also established.
Shooting Down the Server Front-End Bottleneck (2020)

The front-end bottleneck is a well-established problem in server workloads owing to their deep software stacks and large instruction footprints. Despite years of research into effective L1-I and BTB prefetching, state-of-the-art techniques force a trade-off between metadata storage cost and performance. Temporal Stream prefetchers deliver high performance but require a prohibitive amount of metadata to accommodate the temporal history. Meanwhile, BTB-directed prefetchers incur low cost by using the existing in-core branch prediction structures but fall short on performance due to BTB’s inability to capture the massive control flow working set of server applications. This work overcomes the fundamental limitation of BTB-directed prefetchers, which is capturing a large control flow working set within an affordable BTB storage budget. We re-envision the BTB organization to maximize its control flow coverage by observing that an application’s instruction footprint can be mapped as a combination of its unconditional branch working set and, for each unconditional branch, a spatial encoding of the cache blocks around the branch target. Effectively capturing a map of the application’s instruction footprint in the BTB enables highly effective BTB-directed prefetching that outperforms the state-of-the-art prefetchers by up to 10% for equivalent storage budget.
Effectively Partitioned Implementation for Successive-Cancellation Polar Decoder (2019)

This paper proposes an effective field-programmable gate array (FPGA) implementation of a successive-cancellation (SC) decoder for polar codes that have recently attracted attention as error-correcting codes adopted for 5G wireless systems. We focus on effective ways of partitioning the SC decoding procedure into combinational and sequential logic parts. It can be shown that the SC decoder of length N(= N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) can be divided into two parts: N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> SC decoders of length N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> and a single SC decoder of length N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> . While the N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> decoders in the first part can perform in parallel, the decoding procedure in the second part is performed sequentially, which causes a bottleneck due to a long latency. We present an SC decoder architecture in which the first part is implemented using sequential logic circuits, and the second part is implemented using only combinational logic circuits. The overall latency and clock frequency of the decoder are balanced by the divisor N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> of N, and we show that an appropriate choice of N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> yields an efficient implementation with a high throughput. We demonstrate an FPGA implementation of the decoder architecture for a 1024-bit-length polar code and show that our FPGA decoder can achieve three times higher throughput than the conventional sequential semi-parallel decoder without significantly increasing the hardware resources.
Ageing and early-stage Parkinson's disease affect separable neural mechanisms of mesolimbic reward processing (2007)

The ability to learn stimulus-reward associations on the basis of reward prediction errors critically depends on the mesolimbic dopaminergic system including the dopaminergic midbrain and the ventral striatum. It is known that healthy elderly and patients with Parkinson's disease are less proficient than healthy young adults in learning stimulus-reward contingencies, but it is unclear whether this is due to dysfunctional mesolimbic reward prediction or due to deficiency in processing the rewards per se. We used a well-established event-related fMRI reward-prediction paradigm to address this question. Young adults showed the well-replicated pattern of midbrain and ventral striatal activation for stimuli that predicted monetary reward when compared with stimuli that predicted neutral feedback. Also, as expected, the predicted reward feedback itself did not elicit a mesolimbic response. Healthy elderly subjects and unmedicated early-stage idiopathic Parkinson's disease patients showed the opposite pattern with an absent mesolimbic reward prediction response, but mesolimbic activation to the reward feedback itself. This suggests that the healthy elderly and Parkinson's disease patients were less proficient in learning the predictive value of the reward cues despite preserved mesolimbic processing of reward prediction errors. Parkinson's disease patients additionally displayed a relatively increased response of the anterior cingulate during reward feedback processing and diminished functional connectivity of the midbrain and ventral striatum. Our results are compatible with existing behavioural evidence that both groups exhibit a particularly pronounced deficit in learning from positive feedback and support the view that a tendency to underestimate expected values of reward cues might underlie this deficit. Furthermore, alterations in reward processing in Parkinson's disease extend beyond accelerated ageing effects and include altered connectivity within the mesolimbic system.
P-doped diamond grown on (110)-textured microcrystalline diamond: growth, characterization and devices (2009)

The formation and properties of (110)-textured P-doped microcrystalline CVD diamond were studied. Based on several microscopy techniques, with a special emphasis on electron backscattered diffraction, a detailed determination of the grain orientations with respect to the exact [110] axis is given. The different orientations present in the film, in combination with low phosphine concentrations in the gas phase, lead to a variation in P incorporation that can vary over three orders of magnitude, as determined with cathodoluminescence mapping. The role of the surface morphology in the observation of these large incorporation differences is explained. Hall measurements confirm that the films are n-type conductive with a thermal activation energy of 0.56 eV. Based on B-doped substrates, pn junctions were created, showing a rectification ratio of nearly 10(4) at ± 25 V.
OPERAnet: A Multimodal Activity Recognition Dataset Acquired from Radio Frequency and Vision-based Sensors (2021)

This paper presents a comprehensive dataset intended to evaluate passive Human Activity Recognition (HAR) and localization techniques with measurements obtained from synchronized Radio-Frequency (RF) devices and vision-based sensors. The dataset consists of RF data including Channel State Information (CSI) extracted from a WiFi Network Interface Card (NIC), Passive WiFi Radar (PWR) built upon a Software Defined Radio (SDR) platform, and Ultra-Wideband (UWB) signals acquired via commercial off-the-shelf hardware. It also consists of vision/Infra-red based data acquired from Kinect sensors. Approximately 8 hours of annotated measurements are provided, which are collected across two rooms from 6 participants performing 6 daily activities. This dataset can be exploited to advance WiFi and vision-based HAR, for example, using pattern recognition, skeletal representation, deep learning algorithms or other novel approaches to accurately recognize human activities. Furthermore, it can potentially be used to passively track a human in an indoor environment. Such datasets are key tools required for the development of new algorithms and methods in the context of smart homes, elderly care, and surveillance applications.
Genistein inhibits both constitutive and EGF-stimulated invasion in ER-negative human breast carcinoma cell lines. (1998)

Genistein, a natural flavone compound, has been proposed to be responsible for the lower rate of breast cancer in Asian women. The cellular mechanisms of genistein's inhibition of breast cancer progression are largely unknown. In a previous study our laboratory has presented evidence that genistein inhibits cell proliferation of breast carcinoma cells, an inhibition which is associated with a specific G2/M arrest, induction of p21WAF/CIP1 expression and apoptosis. In the present study, we present experimental evidence that illustrates that the actions of genistein are not limited to anti-proliferation: we show that genistein can inhibit both constitutive as well as epidermal growth factor (EGF)-stimulated invasion in estrogen receptor (ER)-negative human breast carcinoma lines, MDA-MB-231 and MDA-MB-468. This inhibition is characterized by the down regulation of MMP-9 (92 kDa type IV collagenase) and up regulation of TIMP-1 (tissue inhibitor of metalloproteinases) and the trypsin inhibitors: protease nexin-II (PN-II) and alpha 1-antitrypsin (alpha 1-AT). The in vivo actions of genistein may therefore extend beyond those traditionally implicated in chemoprevention, e.g., antiproliferation; genistein may act in vivo by blocking additional stages of breast cancer progression such as those stages resulting in invasion and metastasis.
Homogeneity versus diversity: inhibition of plasma PAI-1 in murine sepsis proved lethal in homogeneous cohorts but not in all-inclusive populations (2012)

Background: Most clinical trials of sepsis treatment modalities fail at their primary objective of establishing superiority over placebo when added to background standard of care. While there is no definitive explanation for the high failure rate, it might be stated that our attempts to insert a new therapeutic agent into standard of care encounters severe problems with definition of exactly what stage is ongoing, and what are the criteria for progression or resolution from that time point onwards. Clearly there is need for a means of defining steps in the septic process that would apply to individuals, and to better define the course of sepsis in each patient after they are enrolled in a trial. Methods: For core model development, 30 septic patients were studied for time-related progression in relation to biomarkers, employing a Load Model in a neural net algorithm in MatLab. Causative bacterial infections were linked to primary infection sites. In order to minimize overparameterization, the model was allowed to estimate outputs using the best three input parameters. Bacterial load was tracked from origin using clinical and microbiologic data to provide an estimate at the start of sepsis. The bacterial load as well as clinical and laboratory parameters were model inputs with the output parameter being organ failures and/ or mortality. Results: At onset of sepsis, human bacterial load estimates ranged from between 10 8 and 10 11 CFU, which is consistent with inocula in animal models of sepsis. Sepsis proceeds to organ failures and mortality in a series of steps that are initially linked to bacterial load and inflammatory response, followed by coagulopathy, ischemia, oxygen deprivation in organs and tissues, and culminating in organ failures. The later stages of sepsis are all driven by metabolic parameters, and there seems to be little benefit to blocking inflammation at later stages. Substrate and oxygen deficiencies must be addressed first. Conclusion: Neural net progression models based on biomarkers and physiological markers are able to describe the evolution of sepsis to septic shock, organ failures, and provide some evidence that mortality may be a consequence of the stages of sepsis. Overall, these models appear useful to the task of sorting out organ failure endpoints and mechanisms in individual patients with sepsis progression across sepsis to septic shock.
The role of molecular oxygen in clavulanic acid biosynthesis: evidence for a bacterial oxidative deamination (1988)

Growth of cultures of Streptomyces clavuligerus(ATCC 27064) in an 18O2-containing atmosphere resulted in efficient and equal incorporations of molecular oxygen into the oxazolidine ring and the allylic hydroxy group of clavulanic acid.
SynapsEM: computer-assisted synapse morphometry (2020)

Abstract The structural features of a synapse, in part, determine its output. Synapses are extremely small and tightly packed with vesicles and other organelles. Visualizing synaptic structure requires imaging by electron microscopy, and the features in micrographs must be quantified using morphometry. Three parameters are typically assessed from each specimen: 1) the sizes of individual vesicles and organelles, 2) the absolute number and densities of organelles, and 3) distances between organelles and key features at synapses such as active zone membranes and dense projections. For data to be valid, the analysis must be repeated from hundreds or thousands of images from several biological replicates, a daunting task. Here we report a custom computer program to analyze these features: SynapsEM. In short, we developed macros for ImageJ/Fiji to record x,y-coordinates of segmented structures; the coordinates are then exported as text files. Independent investigators can reload the images and text files to confirm or re-evaluate the segmentation using ImageJ. The Matlab program calculates and reports key synaptic parameters from the coordinates. Since the values are calculated, rather than measured from each micrograph, other parameters can be extracted in Matlab by additional scripting. Thus, this program can accelerate morphometry of synapses and promote a more comprehensive analysis of synaptic ultrastructure.
Two prognostic groups of inflammatory breast cancer have distinct genotypes. (2003)

Patients with IBC can be separated into two major prognostic groups on the basis of initial clinical signs, which appear to be subtended by different molecular alterations.
Supplementary Tables 1-5 from Considerations for the Clinical Application of Chimeric Antigen Receptor T Cells: Observations from a &lt;i&gt;Recombinant DNA Advisory Committee Symposium&lt;/i&gt; Held June 15, 2010 (2023)

Supplementary Tables 1-5 from Considerations for the Clinical Application of Chimeric Antigen Receptor T Cells: Observations from a &lt;i&gt;Recombinant DNA Advisory Committee Symposium&lt;/i&gt; Held June 15, 2010
Elasticity of mixed silver-halide polycrystalline optical fibers (1993)

The elastic strain limit of polycrystalline mixed AgClxBr1−x fibers was studied. These fibers are useful as flexible infrared optical fibers, and the elastic bending regime is preferred for applications which require many bending cycles. The experimental method was based on the spring-back upon releasing a stressed material, and used specifically calculated expressions. Elastic strain limit values are in the range of 0.15%–0.4%. They depend on composition going through a maximum at around the AgCl0.5Br0.5 composition. The dependence on composition is explained by a theoretical model, which is based on a solid-solution internal stress field, and uses material constants.