gebhart/patrepeval huggingface dataset:
Rotational dynamics in motor cortex are consistent with a feedback controller (2020)

Summary Recent studies hypothesize that motor cortical (MC) dynamics are generated largely through its recurrent connections based on observations that MC activity exhibits rotational structure. However, behavioural and neurophysiological studies suggest that MC behaves like a feedback controller where continuous sensory feedback and interactions with other brain areas contribute substantially to MC processing. We investigated these apparently conflicting theories by building recurrent neural networks that controlled a model arm and received sensory feedback about the limb. Networks were trained to counteract perturbations to the limb and to reach towards spatial targets. Network activities and sensory feedback signals to the network exhibited rotational structure even when the recurrent connections were removed. Furthermore, neural recordings in monkeys performing similar tasks also exhibited rotational structure not only in MC but also in somatosensory cortex. Our results argue that rotational structure may reflect dynamics throughout voluntary motor circuits involved in online control of motor actions. Highlights Neural networks with sensory feedback generate rotational dynamics during simulated posture and reaching tasks Rotational dynamics are observed even without recurrent connections in the network Similar dynamics are observed not only in motor cortex, but also in somatosensory cortex of non-huma n primates as well as sensory feedback signals Results highlight rotational dynamics may reflect internal dynamics, external inputs or any combination of the two.
Development of Gendine-Coated Cannula for Continuous Subcutaneous Insulin Infusion for Extended Use (2015)

Continuous subcutaneous insulin infusion (CSII) using pumps is a widely used method for insulin therapy in patients with diabetes mellitus. Among the major factors that usually lead to the discontinuation of CSII are CSII set-related issues, including infection at the infusion site. The American Diabetic Association currently recommends rotating sites every 2 to 3 days. This recommendation adds cost and creates inconvenience. Therefore, in order to prevent infections and extend the duration between insertion site changes, we developed a Teflon cannula coated with a combination of gentian violet and chlorhexidine (gendine) and tested its antimicrobial efficacy against different pathogens. The cannulas were coated with gendine on the exterior surface and dried. The efficacy and durability of gendine-coated cannulas were determined against methicillin-resistant Staphylococcus aureus, Staphylococcus epidermidis, methicillin-susceptible S. aureus, Streptococcus pyogenes, vancomycin-resistant enterococci, Escherichia coli, Pseudomonas aeruginosa, Candida albicans, and Candida glabrata using a biofilm colonization method. The cytotoxicity of gendine was assessed against mouse fibroblast cell lines. The gendine-coated cannulas showed complete prevention of biofilm colonization of all organisms tested for up to 2 weeks (P < 0.0001) compared to that with the uncoated control. A gendine-coated catheter against mouse fibroblast cells was shown to be noncytotoxic. Our in vitro results show that a novel gendine cannula is highly effective in completely inhibiting the biofilm of multidrug-resistant pathogens for up to 2 weeks and may have potential clinical applications, such as prolonged use, cost reduction, and lower infection rate.
Comparison of Formulations for Representing the Fluid-Solid Coupling Using the Spectral Element Method (2020)

International audience
Alteromonas stellipolaris sp. nov., a novel, budding, prosthecate bacterium from Antarctic seas, and emended description of the genus Alteromonas (2004)

Seven novel, cold-adapted, strictly aerobic, facultatively oligotrophic strains, isolated from Antarctic sea water, were investigated by using a polyphasic taxonomic approach. The isolates were Gram-negative, chemoheterotrophic, motile, rod-shaped cells that were psychrotolerant and moderately halophilic. Buds were produced on mother and daughter cells and on prosthecae. Prostheca formation was peritrichous and prosthecae could be branched. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains belong to the γ - Proteobacteria and are related to the genus Alteromonas , with 98·3 % sequence similarity to Alteromonas macleodii and 98·0 % to Alteromonas marina , their nearest phylogenetic neighbours. Whole-cell fatty acid profiles of the isolates were very similar and included C 16 : 0 , C 16 : 1 ω 7 c , C 17 : 1 ω 8 c and C 18 : 1 ω 8 c as the major fatty acid components. These results support the affiliation of these isolates to the genus Alteromonas . DNA–DNA hybridization results and differences in phenotypic characteristics show that the strains represent a novel species with a DNA G+C content of 43–45 mol%. The name Alteromonas stellipolaris sp. nov. is proposed for this novel species; the type strain is ANT 69a T (=LMG 21861 T =DSM 15691 T ). An emended description of the genus Alteromonas is given.
The Role of Dickkopf-1 in Thyroid Hormone–Induced Changes of Bone Remodeling in Male Mice (2019)

Thyroid hormones regulate bone homeostasis, and exogenously induced hyperthyroidism and hypothyroidism in mice was recently found to be associated with an altered expression of the Wnt inhibitor Dickkopf-1 (Dkk1), a determinant of bone mass. Here, we assessed the role of Dkk1 in thyroid hormone-induced changes in bone using conditional Dkk1 knockout mice. Male mice with a global (Dkk1fl/fl;Rosa26-CreERT2) or osteocyte-specific (Dkk1fl/fl;Dmp1:Cre) deletion of Dkk1 were pharmacologically rendered hypothyroid or hyperthyroid. The bone phenotype was analyzed using micro-CT analysis, dynamic histomorphometry, and serum concentrations of bone turnover markers. Hypothyroid and hyperthyroid Cre-negative mice of either Cre line revealed the expected changes in bone volume with hypothyroid mice displaying a 40% to 60% increase in vertebral trabecular bone volume, while hyperthyroid mice lost 45% to 60% of bone volume. Similar changes were observed at the spine. Interestingly, Cre-positive mice of both lines did not gain or lose as much bone at the femur when rendered hypothyroid or hyperthyroid. While Cre-negative hypothyroid mice gained 80% to 100% bone volume, Cre-positive hypothyroid mice only increased their bone volume by 55% to 90%. Similarly, Cre-negative hyperthyroid mice lost 74% to 79% bone, while Cre-positive hyperthyroid mice merely lost 40% to 54%. Despite these site-specific differences, both global and osteocyte-specific Dkk1 knockout mice displayed similar changes in bone turnover as their Cre-negative controls in the hypothyroid and hyperthyroid states. While osteoblast and osteoclast parameters were increased in hyperthyroidism, hypothyroidism potently suppressed bone cell activities. Loss of Dkk1 is not sufficient to fully reverse thyroid hormone-induced changes in bone mass and bone turnover.
SELEN-IX TM : SELENIUM REMOVAL FROM MINING AFFECTED RUNOFF USING ION EXCHANGE BASED TECHNOLOGY (2014)

Growing awareness of selenium bioaccumulation has resulted in selenium management becoming an important environmental issue for mining operations. Selen-IX™ is a novel ion exchange based technology developed by BioteQ to provide an effective solution for removing selenium oxyanions from mine impacted water to single-digit µg/L levels. The technology offers significant potential benefits when compared to incumbent biological treatment processes, including substantially reduced capital and operating costs and significantly reduced production of a selenium-containing sludge for final disposal. This paper reviews the key features of the Selen-IX™ process and presents the results of recent pilot testing on selenium impacted water.
Adam-based Augmented Random Search for Control Policies for Distributed Energy Resource Cyber Attack Mitigation (2022)

Volt-VAR and Volt-Watt control functions are mechanisms that are included in distributed energy resource (DER) power electronic inverters to mitigate excessively high or low voltages in distribution systems. In the event that a subset of DER have had their Volt-VAR and Volt-Watt settings compromised as part of a cyber-attack, we propose a mechanism to control the remaining set of non-compromised DER to ameliorate large oscillations in system voltages and large voltage imbalances in real time. To do so, we construct control policies for individual non-compromised DER, directly searching the policy space using an Adam-based augmented random search (ARS). In this paper we show that, compared to previous efforts aimed at training policies for DER cybersecurity using deep reinforcement learning (DRL), the proposed approach is able to learn optimal (and sometimes linear) policies an order of magnitude faster than conventional DRL techniques (e.g., Proximal Policy Optimization).
Solution processed nanostructures towards efficient and low-cost water splitting (2017)

entitlted 'Photoelectrochemical Performance of NiO-coated ZnO-CdS Core-Shell Photoanode' [1].In the last few years, photoelectrochemistry has emerged as a realistic technology for energy storage [2,3].In a photoelectrochemical cell (PEC), light is absorbed in a semiconductor, the electron-hole pairs separate and are used for a separate oxidation and reduction reactions at each the junction with the electrolyte.As a result, chemical fuels such as hydrogen, methanol and even more caloric fuels could be generated [4,5].In the race for efficiency, the design of each electrode in the PEC device has turned out to be key [6].Optimal design involves optimizing band alignment with the electrolyte, effective protection against corrosion and photonic design to enhance light absorption.In addition, a catalyst at the surface of the electrodes is needed so that the reactions do not become kinetically limited.In their paper, Iyengar et al provide a smart and low-cost design of the photoanode of a PEC.They start by optimizing the conditions for the fabrication of a sparse array of ZnO nanorods that they then cover with CdS.This layer provides the photonic design for high light absorption and at the same time ensures an effective electron-hole pair separation.On top of this structure, they then deposit a mesoporous layer of co-catalyst NiO, formed by an intricate mesh of vertical nanosheets.Overall, this work exploits all advantages of nanostructures for photoelectrochemistry, ranging from the photonics to enhancing the kinetics of reactions and optimizing carrier collection.It is a beautiful work that sets the path towards higher efficiency in the hydrogen evolution reaction.This design scheme is universal, and could certainly be applied to other materials and photoelectrochemistry reactions.Last but not least, all materials are obtained by solution-processing methods and could therefore be easily scalable to larger device sizes and high mass volume production at a low cost.This paper should inspire other groups to go over this initial efficiency of 4% towards 10% or higher.The technological impact will then be major.
The gut microbiota of insects – diversity in structure and function (2013)

Insect guts present distinctive environments for microbial colonization, and bacteria in the gut potentially provide many beneficial services to their hosts. Insects display a wide range in degree of dependence on gut bacteria for basic functions. Most insect guts contain relatively few microbial species as compared to mammalian guts, but some insects harbor large gut communities of specialized bacteria. Others are colonized only opportunistically and sparsely by bacteria common in other environments. Insect digestive tracts vary extensively in morphology and physicochemical properties, factors that greatly influence microbial community structure. One obstacle to the evolution of intimate associations with gut microorganisms is the lack of dependable transmission routes between host individuals. Here, social insects, such as termites, ants, and bees, are exceptions: social interactions provide opportunities for transfer of gut bacteria, and some of the most distinctive and consistent gut communities, with specialized beneficial functions in nutrition and protection, have been found in social insect species. Still, gut bacteria of other insects have also been shown to contribute to nutrition, protection from parasites and pathogens, modulation of immune responses, and communication. The extent of these roles is still unclear and awaits further studies.
Metallic Transfer Films Studied In Situ and Ex Situ: The Case of Cold-Sprayed Al-Al2O3 (2013)

International audience
Developing imidazoles as CEST MRI pH sensors (2016)

A series of intra-molecular hydrogen bonded imidazoles and related heterocyclic compounds were screened for their N-H chemical exchange saturation transfer (CEST) magnetic resonance imaging (MRI) contrast properties. Of the compounds, imidazole-4,5-dicarboxamides (I45DCs) were found to provide the strongest contrast, with the contrast produced at a large chemical shift from water (7.8 ppm) and strongly dependent on pH. We have tested several probes based on this scaffold, and demonstrated that these probes could be applied for in vivo detection of kidney pH after intravenous administration. Copyright © 2016 John Wiley & Sons, Ltd.
HIV Type 1 Subtypes, Coreceptor Usage, and CCR5 Polymorphism (1997)

Identification of the chemokine receptors CCR5 and CXCR4 as the major coreceptors for HIV-1 entry has greatly assisted our understanding of HIV-1 pathogenesis, transmission, and tropism. However, most of our current knowledge on coreceptor usage comes from studies using HIV-1 strains or env genes derived from the genetic subtype B predominant in North America and western Europe. In this report, the coreceptor usage of 20 primary viral isolates representative of genetic subtypes A, B, C, D, E, and group O was examined. Thirty-nine full-length CCR5 sequences from individuals of diverse geographic origins were also obtained to examine the possible effect of CCR5 polymorphism on HIV-1 subtype distribution. Our results indicate that (1) CCR5 and CXCR4 serve as the two major coreceptors for viruses belonging to HIV-1 subtypes A, B, C, D, E, and group O, whereas other chemokine receptors such as CCR2b and CCR3 play only a minor role in facilitating viral entry into stimulated PBMCs; (2) the coreceptor usage is determined by the viral phenotype rather than its genotype because all NSI strains, irrespective of their subtype classification, utilize CCR5, whereas all SI strains are able to use CXCR4; and (3) there is no geographic clustering of CCR5 polymorphism in different ethnic populations, suggesting that CCR5 diversity is not the underlying explanation for differences in the spread of different HIV-1 subtypes. Therefore, the uneven worldwide distribution of HIV-1 subtypes is more likely the result of stochastic dissemination.
A Generalized Simulation Model of Chillers and Heat Pumps to Be Calibrated on Published Manufacturer's Data (2010)

This paper shows how semi-empirical models of chillers and heat pumps can be calibrated on the basis of manufacturer’s published data, which is most of the time the only available source of information. A calibration methodology is proposed and illustrated for different technologies of vapor-compression machines, pointing out tips and tricks. Whatever the size and technology (e.g. scroll, screw or reciprocating compressors), the semi-empirical model is found to predict both full load and part load performance with a very good accuracy. This is partially due to the tailor-made formalism of the model, which allows describing the main features of the machine.
Photonics as a means to implement intra-rack resource disaggregation (2022)

Future HPC and datacenter systems are expected to contain an increasingly heterogeneous set of compute and memory resources as a strategy to preserve performance scaling in the long term. This heterogeneity, combined with the low average resource usage of today’s systems, motivate resource disaggregation to allow applications to pool and compose no more than the fine-grain resources they require. In this paper, we start by motivating resource disaggregation by observing average utilization and rate of change of memory bandwidth and latency in NERSC’s Cori. We then perform an analytical analysis that quantifies if today’s photonic links and switches would meet key metrics to minimize overhead, and what that overhead will be. Finally, we perform preliminary experiments to demonstrate that even this minimal overhead penalizes application performance in some cases. Our study motivates future work on more aggressive photonic links and switches in order to make resource disaggregation more attractive in future systems.
Plug & Play Generative Networks: Conditional Iterative Generation of Images in Latent Space (2016)

Generating high-resolution, photo-realistic images has been a long-standing goal in machine learning. Recently, Nguyen et al. (2016) showed one interesting way to synthesize novel images by performing gradient ascent in the latent space of a generator network to maximize the activations of one or multiple neurons in a separate classifier network. In this paper we extend this method by introducing an additional prior on the latent code, improving both sample quality and sample diversity, leading to a state-of-the-art generative model that produces high quality images at higher resolutions (227x227) than previous generative models, and does so for all 1000 ImageNet categories. In addition, we provide a unified probabilistic interpretation of related activation maximization methods and call the general class of models "Plug and Play Generative Networks". PPGNs are composed of 1) a generator network G that is capable of drawing a wide range of image types and 2) a replaceable "condition" network C that tells the generator what to draw. We demonstrate the generation of images conditioned on a class (when C is an ImageNet or MIT Places classification network) and also conditioned on a caption (when C is an image captioning network). Our method also improves the state of the art of Multifaceted Feature Visualization, which generates the set of synthetic inputs that activate a neuron in order to better understand how deep neural networks operate. Finally, we show that our model performs reasonably well at the task of image inpainting. While image models are used in this paper, the approach is modality-agnostic and can be applied to many types of data.
Increased Oxidative and Nitrative Stress Accelerates Aging of the Retinal Vasculature in the Diabetic Retina (2015)

Hyperglycemia-induced retinal oxidative and nitrative stress can accelerate vascular cell aging, which may lead to vascular dysfunction as seen in diabetes. There is no information on whether this may contribute to the progression of diabetic retinopathy (DR). In this study, we have assessed the occurrence of senescence-associated markers in retinas of streptozotocin-induced diabetic rats at 8 and 12 weeks of hyperglycemia as compared to normoglycemic aging (12 and 14 months) and adult (4.5 months) rat retinas. We have found that in the diabetic retinas there was an up-regulation of senescence-associated markers SA-β-Gal, p16INK4a and miR34a, which correlated with decreased expression of SIRT1, a target of miR34a. Expression of senescence-associated factors primarily found in retinal microvasculature of diabetic rats exceeded levels measured in adult and aging rat retinas. In aging rats, retinal expression of senescence associated-factors was mainly localized at the level of the retinal pigmented epithelium and only minimally in the retinal microvasculature. The expression of oxidative/nitrative stress markers such as 4-hydroxynonenal and nitrotyrosine was more pronounced in the retinal vasculature of diabetic rats as compared to normoglycemic aging and adult rat retinas. Treatments of STZ-rats with the anti-nitrating drug FeTPPS (10mg/Kg/day) significantly reduced the appearance of senescence markers in the retinal microvasculature. Our results demonstrate that hyperglycemia accelerates retinal microvascular cell aging whereas physiological aging affects primarily cells of the retinal pigmented epithelium. In conclusion, hyperglycemia-induced retinal vessel dysfunction and DR progression involve vascular cell senescence due to increased oxidative/nitrative stress.
Emission of greenhouse gases from controlled incineration of cattle manure (2012)

Greenhouse gas emission is a potential limiting factor in livestock farming development. While incineration is one approach to minimize livestock manure, there are concerns about significant levels of nitrogen and organic compounds in manure as potential sources of greenhouse gas emissions (N2O and CH4). In this study, the effects of various incineration conditions, such as the furnace temperature and air ratio on N2O and CH4 formation behaviour, of cattle manure (as a representative livestock manure) were investigated in a pilot rotary kiln furnace. The results revealed that N2O emissions decreased with increasing temperature and decreasing air ratio. In addition, CH4 emissions tended to be high above 800 degrees C at a low air ratio. The emission factors for N2O and CH4 under the general conditions (combustion temperature of 800-850 degrees C and air ratio of 1.4) were determined to be 1.9-6.0% g-N2O-N/g-N and 0.0046-0.26% g-CH4/g-burning object, respectively. The emission factor for CH4 differed slightly from the published values between 0.16 and 0.38% g-CH4/g-burning object. However, the emission factor for N2O was much higher than the currently accepted value of 0.7% g-N2O-N/g-N and, therefore, it is necessary to revise the N2O emission factor for the incineration of livestock manure.
Integrating genetic variants into clinical models for hepatocellular carcinoma risk stratification in cirrhosis (2022)

The identification of patients at higher risk of developing liver cancer is pivotal to improve the performance of surveillance. Risk assessment can be achieved by combining several clinical and biological parameters used in routine practice. The addition of patients' genetic characteristics can modestly improve this prediction and will ultimately pave the way for precision medicine in patients eligible for HCC surveillance, allowing physicians to trigger personalised screening strategies.
Nearly 3-6µm Spectral Comb Derived from Tm Mode-locked Laser using GaAs-based Degenerate OPO (2012)

We use a degenerate OPO pumped by an ultrafast 2050-nm Tm-fiber laser to generate a broadband mid-infrared comb. A GaAs gain element and dispersion management access an ~octave-wide output spectrum extending from 3.1 to 5.9µm
Low-power single- and double-edge-triggered flip-flops for high-speed applications (2005)

The paper presents new low-power flip-flops which are faster compared to previously proposed structures. The single-edge-triggered flip-flop, called the MHLFF (modified hybrid latch flip-flop), reduces the power dissipation of the HLFF (hybrid latch flip-flop) by avoiding unnecessary node transitions. To reduce the power consumption of the flip-flop further, the double-edge-triggered modified hybrid latch flip-flop (DMHLFF) is also proposed. The power consumption in the clock tree is reduced by halving the clock frequency of the MHLFF for the same throughput. In addition to the low power, the speed is higher while the area is not larger. The increase in the speed is achieved by lowering the number of the stack transistors in the discharge path.