gebhart/patrepeval huggingface dataset:
AUTOMATED SOURCE PARAMETER AND LOW LEVEL WIND ESTIMATION FOR ATMOSPHERIC TRANSPORT AND DISPERSION APPLICATIONS (2011)

Accurate simulations of the atmospheric transport and dispersion rely heavily on the source term parameters necessary to characterize the initial release and meteorological conditions that drive the downwind dispersion. The source parameters are in many cases not known and consequently based on rudimentary assumptions. This is particularly true of accidental releases, and the intentional releases associated with terrorist incidents. Often the available meteorological observations are not representative of the conditions at the location of the release, which can result in significant errors in the hazard assessments downwind of the sensors even when the source parameters are accurately characterized. In this presentation we describe a computationally efficient algorithm that utilizes variational data assimilation techniques to produce a refined downwind hazard assessment by using all available observations to characterizing the release source parameters and the low-level winds. The underlying algorithm consists of a combination of modeling systems, including the Second order Closure Integrated PUFF model (SCIPUFF), its corresponding Source Term Estimation (STE) model, a hybrid Lagrangian-Eulerian Plume Model (LEPM), its formal adjoint, and the software infrastructure necessary to link them. SCIPUFF and its STE model are used to calculate a first guess source estimate based on the available chemical plume and meteorological observations. The LEPM and corresponding adjoint are then used to iteratively refine the SCIPUFF based STE estimate using variational data assimilation techniques. The entire process from beginning to end is completely automated and requires no human intervention. This algorithm has undergone testing using virtual single realization plume release data sets from the Virtual THreat Response Emulation and Analysis Testbed (VTHREAT) and data from the FUSION Field Trials 2007 (FFT07). An end-to-end prototype of this system has been developed to illustrate how it could potentially be deployed within the United States (US) Joint Effects Model (JEM). The STE prototype will be demonstrated in this presentation using VTHREAT generated chemical observations from point chemical detection systems. Preliminary results suggest that this concept provides an efficient means to better utilize CB and meteorological observations to provide a more accurate hazard assessment.
Rheology of poly (lactic acid)-based systems (2019)

Being commercialized in 1992, poly (lactic acid) (PLA) has been considered for biomedical applications and as a reliable substitute for a wide range of commodity and engineering applications where noncompostable petroleum-based polymers are currently being used. However, PLA suffers from series of drawbacks and it would not be applicable unless these shortcomings resolve somewhat. Besides the PLA’s brittleness and low toughness which originate from its higher glass transition temperature, the major shortcomings which negatively influence the other features of PLA are its low melt strength and slow crystallization kinetics. These weaknesses limit the processability, formability and foamability of PLA, and hence, the manufacturing of PLA based products. In this context, the improvement of rheological and viscoelastic properties of PLA is of a great importance as it enhances the melt strength. To control the PLA’s rheological and viscoelastic properties, various attempts such as varying the D-lactide content in PLA molecules, increasing the PLA’s molecular weight, the use of chain extender and branching, controlling the PLA’s crystallization, compounding with micro-/nano-sized fillers and blending with other polymers have been considered. This article critically reviews these studies that have been conducted so far on rheological investigations of various PLA-based systems.
Parallelism Exploitation of a Dimensionality Reduction Algorithm Applied to Hyperspectral Images (2016)

International audience
Requirements for Translation in Clinical Trials of Aromatherapy: The Case of theEssential Oil of Bergamot (BEO) for Management of Agitation in Severe Dementia (2022)

Due to the tight link between undertreated pain and agitation in dementia patients, aromatherapy can be a useful approach if an essential oil (EO) with powerful analgesic activity is used. The methodological difficulties of most aromatherapy trials have not allowed any definitive conclusion about the effectiveness of aromatherapy in dementia. The objective of the present perspective is to illustrate the long rigorous process leading from preclinical research to clinical translation of the EO of bergamot (BEO) for the management of agitation in dementia. A nanotechnology-based delivery system consisting of odorless alpha-tocopheryl stearate solid lipid nanoparticles (SLN) loaded with BEO (NanoBEO), has been proven active in acute and neuropathic pain models confirming the strong antinociceptive and anti-allodynic efficacy reported for BEO in preclinical studies. In particular, prolonged physicochemical stability of NanoBEO and titration in its main components are remarkable advantages allowing reproducible antinociceptive and anti-itch responses to be measured. Furthermore, the possibility to perform double-blind clinical trials made impossible so far because of the strong smell of essential oils used in aromatherapy. Demented patients receive limited treatment for chronic pain, particularly neuropathic. The BRAINAID (NCT04321889) trial will assess the effectiveness of NanoBEO on agitation and pain in severely demented patients to offer a safe tool able to provide relief to this fragile population. This double-blind clinical trial will be the first to assess the efficacy and safety of an engineered essential oil and will provide the rationale for the safer treatment of neuropsychiatric symptoms of dementia and pain in clinic.
Efficacy of immunotherapy with combination of cryotherapy and topical imiquimod for treatment of Kaposi sarcoma (2022)

Multiple treatment modalities for Kaposi sarcoma (KS) have been reported, including chemotherapy, radiation therapy, surgical excision, electrochemotherapy, and cryotherapy. Common topical treatments include timolol, imiquimod, and alitretinoin. We searched our institutional database for patients with ICD-9 or 10 codes for KS seen by a dermatologist with experience in KS management from July 1, 2004 to January 1, 2022. We screened patient charts to include patients who received combination therapy of cryotherapy followed by topical imiquimod three times a week for 2 months (n = 9). Patients were followed in the clinic every 3 months. Time to resolution was assessed by photographic evidence of resolution as determined by a dermatologist and corroborated with clinical documentation in patient charts. Median age (IQR) at KS diagnosis was 58 (27.5) years. All patients were male (n = 9, 100%). Majority were white (n = 7, 78%) and non-Hispanic (n = 8, 89%). Five (56%) had classic KS, one (11%) had HIV-associated KS, and three (33%) were HIV-negative men who have sex with men. Median time to resolution was 30.5 weeks, with a median of two treatments. In our study, 93% (n = 42/45) of lesions and 89% (n = 8/9) of patients experienced complete resolution during a median (range) duration of follow-up of 58 (13-209) weeks. Side effects were limited to pain during cryotherapy, occasional blister formation after cryotherapy, and mild inflammation due to imiquimod. No infections were observed. Combination therapy of cryotherapy and topical imiquimod may be an efficacious and comparatively low-risk treatment for limited, cutaneous KS.
Virtual Screening Studies to Design Potent CDK2-Cyclin A Inhibitors (2007)

The cell division cycle is controlled by cyclin-dependent kinases (CDK), which consist of a catalytic subunit (CDK1-CDK8) and a regulatory subunit (cyclin A-H). Pharmacophore analysis indicates that the best inhibitor model consists of (1) two hydrogen bond acceptors, (2) one hydrogen bond donor, and (3) one hydrophobic feature. The HypoRefine pharmacophore model gave an enrichment factor of 1.31 and goodness of fit score of 0.76. Docking studies were carried out to explore the structural requirements for the CDK2-cyclin A inhibitors and to construct highly predictive models for the design of new inhibitors. Docking studies demonstrate the important role of hydrogen bond and hydrophobic interactions in determining the inhibitor-receptor binding affinity. The validated pharmacophore model is further used for retrieving the most active hits/lead from a virtual library of molecules. Subsequently, docking studies were performed on the hits, and novel series of potent leads were suggested based on the interaction energy between CDK2-cyclin A and the putative inhibitors.
Routing and Logic Architecture (2003)

Reproductive compensation was studied in Russian (family planning) and Middle-Asian (with natural reproduction) urban and rural populations. Questionnaires were used describing postreproductive-age women having at least one pregnancy. The presence of reproductive compensation in a population was identified by comparison of two groups: "loaded" and "unloaded" by values of total and effective fertility. Families with excessive (compared with the mean population value) pregnancy outcome failure (spontaneous abortions, stillbirths, preproductive-age deaths of children) were ascribed to the loaded group. Reproductive compensation was discovered in all populations studied, which indicates that this phenomenon is wide-spread in human populations.
A Drosophila IκB kinase complex required for Relish cleavage and antibacterial immunity (2000)

Here we report the identification of a Drosophila IkappaB kinase complex containing DmIKKbeta and DmIKKgamma, homologs of the human IKKbeta and IKKgamma proteins. We show that this complex is required for the signal-dependent cleavage of Relish, a member of the Rel family of transcriptional activator proteins, and for the activation of antibacterial immune response genes. In addition, we find that the activated DmIKK complex, as well as recombinant DmIKKbeta, can phosphorylate Relish in vitro. Thus, we propose that the Drosophila IkappaB kinase complex functions, at least in part, by inducing the proteolytic cleavage of Relish. The N terminus of Relish then translocates to the nucleus and activates the transcription of antibacterial immune response genes. Remarkably, this Drosophila IkappaB kinase complex is not required for the activation of the Rel proteins Dif and Dorsal through the Toll signaling pathway, which is essential for antifungal immunity and dorsoventral patterning during early development. Thus, a yet to be identified IkappaB kinase complex must be required for Rel protein activation via the Toll signaling pathway.
Superconductivity in Niobium Containing Ferromagnetic Gadolinium or Paramagnetic Yttrium Dispersions (1969)

Gadolinium and yttrium dispersions were prepared in pure niobium by solidification from the melt; the size, shape, and distribution of the particles were determined metallographically. The superconducting critical temperature and critical field of niobium were unaltered by the presence of the dispersions indicating that neither gadolinium nor yttrium have measurable solubility in solid niobium. Both gadolinium and yttrium dispersions produced large hysteresis in magnetization and large critical current densities. The degree of magnetic hysteresis produced in niobium by these dispersions has only been exceeded in niobium by fast neutron irradiation. Ferromagnetic gadolinium and weakly paramagnetic yttrium appear equally effective as flux pins. It is suggested that the nature of the particle superconducting matrix interface is more important for flux pinning than the bulk magnetic properties of the dispersed phases.
Protease inhibitors as a model for NCL disease, with special emphasis on the infantile and adult forms (1992)

An animal model of NCL disease has been developed with the use of protease inhibitors. Young rats received a continuous infusion of various specific protease inhibitors or of physiological saline into the lateral ventricle of the brain using osmotic mini-pumps. Treatment lasted for 2 weeks, at which time animals were sacrificed and the brains were removed and processed for light or electron microscopic analysis. The thiol protease inhibitors leupeptin and E64C, but not saline or the serine protease inhibitor aprotinin, caused a massive accumulation of ceroid-lipofuscin (CL) in brain cells that bore a strong morphological resemblance to the CL in the infantile and adult forms of NCL disease, and bore similarity to the CL of the late infantile and juvenile forms. Leupeptin also caused the death of cerebellar Purkinje cells, as is seen in the infantile and adult forms of NCL. Further evidence is presented in support of the hypothesis (Ivy et al.: Science 226:985-987, 1984) that decreased or defective lysosomal thiol proteases or their substrates may underly the pathogenesis of at least the infantile and adult forms of NCL disease. Administration of protease inhibitors to the brains of young rats provides an important model for studying the cellular mechanisms of ceroid-lipofuscino-genesis.
A PRELIMINARY STUDY OF RELATIONSHIPS BETWEEN ELEMENTAL ACCUMULATION AND RADIOACTIVE CESIUM CONTAMINATION IN LENTINULA EDODES (SHIITAKE) BASED ON PIXE ANALYSIS (2011)

Particle-induced X-ray emission (PIXE) analysis of Lentinula edodes (Shiitake) mushrooms contaminated with radioactive cesium was performed to study relationships between concentrations of principal elements of shiitake mushrooms and their radioactive cesium levels. After the Fukushima nuclear disaster caused by the huge tsunami on March 11, 2011, we collected five shiitake samples in Marumori town, Miyagi Prefecture, on April 21, 2011. The mean radioactive level of the samples was 228 Bq/kg (the sum of 134 Cs and 137 Cs ). The preliminary result of PIXE analysis using an internal standard method has demonstrated that shiitake mushrooms significantly collect rubidium as well as potassium. It is suggested that radioactive cesium is accumulated in shiitake just like rubidium during the course of potassium uptake.
Alpha coincidence detection for the assay of actinides (2013)

Interferences in both decay counting and mass counting techniques limit their application for some environmental monitoring applications. For example, <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">238</sup> U interferes with <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">238</sup> Pu in mass spectrometry measurements, while in conventional alpha spectroscopy measurements it is nearly impossible to separate <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">238</sup> Pu from <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">241</sup> Am and <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">239</sup> Pu from <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">240</sup> Pu. These interferences are typically resolved by using chemical separation and/or different measurement techniques for different isotopes. We are investigating radiation detector concepts to simultaneously assay these four isotopes with minimal sample preparation by exploiting radiation signatures measured in coincidence with the predominate alpha decays of these isotopes. Particles in coincidence with the alpha decay include conversion electrons, gamma rays, x-rays, and Auger electrons. Each decay has a unique energy distribution enabling the separation of the isotopes. We are exploring two basic detector concepts to achieve these goals: a silicon-based design and a gas-detector design. The silicon system provides the potential for higher energy resolution at the cost of lower efficiency compared to a gas detector. In this paper, we will describe our evaluation of the different detector concepts, which will include estimations of potential detection efficiency, ability to resolve the isotopes, sample preparation and equipment requirements.
Manganese Transport in the Cyanobacterium Synechocystis sp. PCC 6803 (1996)

We have inactivated the genes encoding components of MntABC, an ABC (ATP binding cassette) transporter system for manganese in the cyanobacterium Synechocystis sp. PCC 6803. The growth rates of these mutant strains were significantly lower in a manganese-deficient medium and were restored to near normal levels upon addition of micromolar concentrations of Mn2+, indicating the presence of a second transport system for manganese in this organism. 54Mn2+ uptake experiments indicated that the MntABC transporter was induced under manganese starvation conditions, whereas the second transporter system was induced in the presence of micromolar levels of manganese. Both of these systems were nonfunctional at low temperatures and could transport trace levels of 54Mn2+, reflecting high affinity active transport. The initial rates of Mn2+ uptake for cells grown with or without manganese exhibited biphasic saturation kinetics, suggesting that Mn2+ can also be accumulated by a low affinity system in these bacteria. The kinetic parameters for the MntABC transporter system are Km = 1-3 microM and Vmax = 3-8 pmol/min.10(8) cells. Accumulation of manganese by this system was competitively inhibited by Cd2+ (Ki = 4-8 microM), Co2+ and Zn2+ (Ki = 8-15 microM). In contrast, the second high affinity system was highly specific for manganese and was not inhibited by any tested metal ion. We have also demonstrated that in this organism, photosynthetic electron transport is necessary for optimal rates of manganese uptake.
Ontogeny of DA1 receptor-adenylate cyclase coupling in proximal convoluted tubules (1990)

The natriuretic effect of dopamine (DA) is less in younger than in older animals. The natriuretic (DA) is less in younger than in older animals. The natriuretic effect of DA is due in part to occupation of renal tubular DA1 receptors, which are most abundant in the proximal convoluted tubule (PCT). However, it has not been determined whether ontogenic differences in DA1-receptor density, affinity, or coupling to intracellular second messengers are involved in the reduced natriuretic effect of DA in the young animal. We therefore studied the DA1 receptor by radioligand binding with the DA1 antagonist 125I-SCH 23982 and the effect of DA1 agonists and guanine nucleotides on adenylate cyclase (AC) activity in microdissected PCT during development in Wistar-Kyoto rats (WKY). The dissociation constant (Kd) and maximum receptor density (Bmax) were similar in all groups (Kd, in nM: 11.9 +/- 0.7 at 3 wk, 10.6 +/- 0.4 at 8 wk, and 12.2 +/- 1.2 at 20 wk; Bmax, in fmol/mm PCT: 0.24 +/- 0.02 at 3 wk, 0.23 +/- 0.01 at 8 wk, and 0.24 +/- 0.01 at 20 wk). Basal AC activities were similar, and forskolin (10(-5) M), which directly stimulates AC, increased AC activity to a similar extent in all age groups. However, the DA1 agonists, fenoldopam (10(-5) M) and SND-919-CL2 (10(-6) M), increased AC activity in PCT to a greater extent in 20-wk-old (55 +/- 7%) than in 3-wk-old rats (27 +/- 1%).(ABSTRACT TRUNCATED AT 250 WORDS)
Real-time adaptive encoding for 3D optical memories (2002)

There are a variety of factors that can limit the set of allowable code words that are useable on an optical memory block. In this paper, we will primarily consider inter- symbol interference (ISI) and the noise margins required to represent an individual bit. Fo example, code words must maintain a specific topological separation of '1' bits so that ISI does not raise the intensity of neighboring '0's' above a pre-set threshold. Typically this is accomplished by a static encoding that uses a pre-selected set of code words based on these properties of the storage media and the optical system. Alternatively, our approach provides for a dynamic analysis of all data currently stored in the region surrounding a particular block and defines the allowable code words uniquely for each block. We assume the existence of a 'smart' read head that is capable of analyzing a page of data and calculating the allowable codes in real-time based on the actual data in the surrounding region. We use point-spread function based mathematical model for optical readout system to evaluate and carry out data encoding. Our experiments show 81% spatial utilization while recent publications present only 45% utilization.
Abstract 18982: Right Atrial Dysfunction From Speckle Tracking Strain Echocardiography Associated With Mortality in Patients With Pulmonary Hypertension. (2016)

Introduction: Right atrial (RA) size is an established marker for adverse outcomes in pulmonary arterial hypertension (PAH). Independent of RA size, RA function is impaired in PAH. However, the pro...
Methylene blue inhibits Caspase-6 activity, and reverses Caspase-6-induced cognitive impairment and neuroinflammation in aged mice (2019)

Activated Caspase-6 (Casp6) is associated with age-dependent cognitive impairment and Alzheimer disease (AD). Mice expressing human Caspase-6 in hippocampal CA1 neurons develop age-dependent cognitive deficits, neurodegeneration and neuroinflammation. This study assessed if methylene blue (MB), a phenothiazine that inhibits caspases, alters Caspase-6-induced neurodegeneration and cognitive impairment in mice. Aged cognitively impaired Casp6-overexpressing mice were treated with methylene blue in drinking water for 1 month. Methylene blue treatment did not alter Caspase-6 levels, assessed by RT-PCR, western blot and immunohistochemistry, but inhibited fluorescently-labelled Caspase-6 activity in acute brain slice intact neurons. Methylene blue treatment rescued Caspase-6-induced episodic and spatial memory deficits measured by novel object recognition and Barnes maze, respectively. Methylene blue improved synaptic function of hippocampal CA1 neurons since theta-burst long-term potentiation (LTP), measured by field excitatory postsynaptic potentials (fEPSPs) in acute brain slices, was successfully induced in the Schaffer collateral-CA1 pathway in methylene blue-treated, but not in vehicle-treated, Caspase-6 mice. Increased neuroinflammation, measured by ionized calcium binding adaptor molecule 1 (Iba1)-positive microglia numbers and subtypes, and glial fibrillary acidic protein (GFAP)-positive astrocytes, were decreased by methylene blue treatment. Therefore, methylene blue reverses Caspase-6-induced cognitive deficits by inhibiting Caspase-6, and Caspase-6-mediated neurodegeneration and neuroinflammation. Our results indicate that Caspase-6-mediated damage is reversible months after the onset of cognitive deficits and suggest that methylene blue could benefit Alzheimer disease patients by reversing Caspase-6-mediated cognitive decline.