gebhart/patrepeval huggingface dataset:
Neuroprotective Effect of WEB 1881 FU (Nebracetam) on an Ischemia-Induced Deficit of Glucose Uptake in Rat Hippocampal and Cerebral Cortical Slices and CA1 Field Potential in Hippocampal Slices. (1992)

Effect of WEB 1881 FU (nebracetam) on hypoxia and ischemia-induced impairment of 2-deoxyglucose (2DG) uptake and CA1 field potentials induced by hypoxia and hypoxia/hypoglycemia (ischemia) in rat brain slices was evaluated and compared to the findings obtained with pentobarbital and idebenone. Hippocampal and cortical slices were exposed to 15-20 min of ischemia, and then these slices were returned to oxygenated and glucose-containing buffer for 6 hr. Ischemia reduced both 30 mM KCl-induced 2DG uptake and CA1 field potentials elicited by the stimulation of Schaffer collaterals in the hippocampus. Pretreatment of nebracetam at 1 mM or pentobarbital at 0.1 mM attenuated a decline of 2DG uptake and CA1 field potentials under the condition of ischemia. In addition, nebracetam and pentobarbital relatively recovered the increase of 2DG uptake in the hippocampus under hypoxia for 45 min. Furthermore, these drugs also attenuated the decline of 2DG uptake induced by 10 mM glutamate for 20 min. However, treatment with idebenone did not recover the deficit of 2DG uptake and CA1 field potential. The present result suggests that nebracetam and pentobarbital exert neuroprotective actions against not only ischemia but also glutamate toxicity.
Effects of interactions between HfO<sub>2</sub> and poly-Si on MOSCAP and MOSFET electrical behavior (2003)

In this paper, we report on the interactions between HfO/sub 2/ and poly-Si with varying HfO/sub 2/ films. The impact HfO/sub 2/ interaction on important parameters such as gate leakage, yield, flatband voltage and mobility were discussed.
Exogenous exposure to dihydroxyacetone mimics high fructose induced oxidative stress and mitochondrial dysfunction (2021)

Dihydroxyacetone (DHA) is a three-carbon sugar that is the active ingredient in sunless tanning products and a by-product of electronic cigarette (e-cigarette) combustion. Increased use of sunless tanning products and e-cigarettes has elevated exposures to DHA through inhalation and absorption. Studies have confirmed that DHA is rapidly absorbed into cells and can enter into metabolic pathways following phosphorylation to dihydroxyacetone phosphate (DHAP), a product of fructose metabolism. Recent reports have suggested metabolic imbalance and cellular stress results from DHA exposures. However, the impact of elevated exposure to DHA on human health is currently under-investigated. We propose that exogenous exposures to DHA increase DHAP levels in cells and mimic fructose exposures to produce oxidative stress, mitochondrial dysfunction, and gene and protein expression changes. Here, we review cell line and animal model exposures to fructose to highlight similarities in the effects produced by exogenous exposures to DHA. Given the long-term health consequences of fructose exposure, this review emphasizes the pressing need to further examine DHA exposures from sunless tanning products and e-cigarettes.
Biomarkers of Neurodegenerative Diseases: Biology, Taxonomy, Clinical Relevance, and Current Research Status (2022)

The understanding of neurodegenerative diseases, traditionally considered to be well-defined entities with distinguishable clinical phenotypes, has undergone a major shift over the last 20 years. The diagnosis of neurodegenerative diseases primarily requires functional brain imaging techniques or invasive tests such as lumbar puncture to assess cerebrospinal fluid. A new biological approach and research efforts, especially in vivo, have focused on biomarkers indicating underlying proteinopathy in cerebrospinal fluid and blood serum. However, due to the complexity and heterogeneity of neurodegenerative processes within the central nervous system and the large number of overlapping clinical diagnoses, identifying individual proteinopathies is relatively difficult and often not entirely accurate. For this reason, there is an urgent need to develop laboratory methods for identifying specific biomarkers, understand the molecular basis of neurodegenerative disorders and classify the quantifiable and readily available tools that can accelerate efforts to translate the knowledge into disease-modifying therapies that can improve and simplify the areas of differential diagnosis, as well as monitor the disease course with the aim of estimating the prognosis or evaluating the effects of treatment. The aim of this review is to summarize the current knowledge about clinically relevant biomarkers in different neurodegenerative diseases.
Performance of flexible polymeric light-emitting diodes under bending conditions (2003)

Organic light-emitting diodes were fabricated on a 125-μm-thick polyethylene terephthalate substrate covered with 100 nm indium tin oxide. The luminance–current–voltage performance and the emission spectrum of the devices are investigated in the bent state under mechanical stress at different bending radii. Down to a curvature of 15 mm, no significant decrease in the device performance is found compared to the relaxed state, as well as to conventional devices on glass substrates.
Probing the Structure and Mechanism of Ras Protein with an Expanded Genetic Code (1993)

Mutations in Ras protein at positions Gly12 and Gly13 (phosphate-binding loop L1) and at positions Ala59, Gly60, and Gln61 (loop L4) are commonly associated with oncogenic activation. The structural and catalytic roles of these residues were probed with a series of unnatural amino acids that have unusual main chain conformations, hydrogen bonding abilities, and steric features. The properties of wild-type and transforming Ras proteins previously thought to be uniquely associated with the structure of a single amino acid at these positions were retained by mutants that contained a variety of unnatural amino acids. This expanded set of functional mutants provides new insight into the role of loop L4 residues in switch function and suggests that loop L1 may participate in the activation of Ras protein by effector molecules.
Characterization of Symptoms after Radical Prostatectomy and Their Relation to Postoperative Complications (2021)

While symptoms are common after RP, substantial improvements occur over the first 10 days. Severe or very severe symptoms conferred at most a small absolute increase in complication risk, which should be reassuring to patients and clinicians.
Odd skipped-related 1 controls the pro-regenerative response of Fibro-Adipogenic Progenitors (2022)

Abstract Skeletal muscle regeneration requires the coordinated interplay of diverse tissue-resident- and infiltrating cells. Fibro-adipogenic progenitors (FAPs) are an interstitial cell population that provides a beneficial microenvironment for muscle stem cells (MuSCs) during muscle regeneration. Here we show that the transcription factor Osr1 is essential for FAPs to communicate with MuSCs and infiltrating macrophages, thus coordinating muscle regeneration. Conditional inactivation of Osr1 impaired muscle regeneration with reduced myofiber growth and formation of excessive fibrotic tissue with reduced stiffness. Osr1-deficient FAPs acquired a fibrogenic identity with altered matrix secretion and cytokine expression resulting in impaired MuSC viability, expansion and differentiation. Immune cell profiling suggested a novel role for Osr1-FAPs in macrophage polarization. In vitro analysis suggested that increased TGFβ signaling and altered matrix deposition by Osr1-deficient FAPs actively suppressed regenerative myogenesis. In conclusion, we show that Osr1 is central to FAP function orchestrating key regenerative events such as inflammation, matrix secretion and myogenesis.
Photonic 640-Gb/s Reconfigurable OTDM Add–Drop Multiplexer Based on Pump Depletion in a Single PPLN Waveguide (2011)

All-optical time-domain channel extraction and clearing operations based on nonlinear effects in a periodically poled lithium niobate (PPLN) waveguide is investigated at 640 Gb/s. The suitability of this device for 640-Gb/s signal processing has been confirmed exploiting only pump depletion. Moreover, a 640-Gb/s reconfigurable optical time-division multiplexing (OTDM) add-drop multiplexer is demonstrated, using a single PPLN waveguide based on a counterpropagating configuration. Error-free operation confirms the effectiveness of a single device for simultaneous add-drop functions. Reconfigurable operations have been verified through bit error rate measurements, including the case of simultaneous add-drop of multiple channels in the OTDM frame.
Bipolar transistors in silicon-on-sapphire (SOS): effects of nanosecond thermal processing (2002)

Nanosecond thermal processing (NTP) using a XeCl excimer laser was employed in the fabrication of npn bipolar transistors in silicon-on-sapphire (SOS). Functional devices, with current gain approach 100, were obtained. The deleterious effects of diffusion pipes in SOS material were minimized using rapid laser activation of ion implanted dopant. Devices were fabricated using n-type epitaxially deposited silicon on double-solid-phase-epitaxy (DSPE) improved SOS. The total thickness of the first and second silicon epi-layers was nominally 2.0 mu m. Devices were fabricated using three different laser fluences for the emitter anneal. This corresponds to a variation in melt duration and corresponding metallurgical junction depth.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Poly(vinylidene fluoride) with Grafted Zwitterionic Polymer Side Chains for Electrolyte-Responsive Microfiltration Membranes (2003)

Thermally induced molecular graft copolymerization of the zwitterionic monomer, N,N‘-dimethyl(methylmethacryloyl ethyl)ammonium propanesulfonate (DMAPS), with the ozone-preactivated poly(vinylene fluoride) (PVDF) was carried out in a mixed solvent of N-methyl-2-pyrrolidone (NMP) and dimethyl sulfoxide (DMSO). The chemical composition of the resulting PVDF with grafted DMAPS polymer (PDMAPS) side chains, or the PDMAPS-g-PVDF copolymers, was analyzed by elemental analysis. An increase in the [DMAPS]/[-CH2CF2-] molar feed ratio used for graft polymerization gave rise to an increase in the graft concentration of the DMAPS polymer in the copolymer. Microfiltration (MF) membranes were prepared from the DMSO solutions of the copolymers by phase inversion in aqueous media of different ionic strength and temperature. The surface composition and morphology of the MF membranes were investigated by X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM), respectively. The mean pore size of the membrane decreased with the increase in graft concentration of the PDMAPS-g-PVDF copolymer. However, it increased with an increase in the ionic strength of the casting bath. Due to the anti-polyelectrolyte effect, the permeability of aqueous solutions through the PDMAPS-g-PVDF MF membranes exhibited a dependence on electrolyte concentration. The flow rate was observed to decrease as the electrolyte concentration of the permeate was increased.
<title>Fiber lasers in ultrafast optics</title> (1999)

The current status of ultrafast fiber lasers is discussed. Recent advances in optical fiber designs as well as improved saturable absorbers have greatly improved the performance and the reliability of ultrafast fiber oscillators. Equally significant have been improvements in ultrafast fiber amplifier designs and compact chirped pulse amplification systems in conjunction with chirped periodically-poled LiNbO<SUB>3</SUB>, which now allow the manufacture of compact ultrafast fiber laser systems that can exceed the performance of conventional ultrafast lasers based on bulk optics. The unique size advantage of fiber lasers opens up the field of ultrafast optics to novel OEM-type applications. For example ultrafast fiber lasers have been successfully employed as subsystems in all-optical time delay scanning, for two-photon microscopy as well as for THz pulse generation.
Characterization and Electrochemical Behaviour of AV4S8 (A=Ga,Ge) Materials as Negative Electrodes of Sodium-Ion Batteries (2014)

Lithium-ion batteries have become essential in recent years. Due to both the difficult access and the cost of the alkaline element, a new field of research concerning sodium-ion batteries has recently emerged. Many compounds have been proposed as positive electrodes for Na-ion batteries. However, since sodium does not intercalate into graphite as much as lithium (1), there is a clear need for high capacity materials for negative electrode materials. Intercalation compounds such as Na 2 Ti 3 O 7 (2) or NaTi 2 (PO 4 ) 3 (3) or Sb-based compounds (4) come usually with a somehow limited capacity (~ 200-400 mAh.g -1 ). Here, we present the possible use of a class of chalcogenide materials, AV4S8 (A=Ga,Ge), as a negative electrode in sodium-ion batteries. The reactivity of AV 4 S 8 with Na leads to a remarkable specific capacity of 800 mAh/g for the first discharge at a C/20 rate (1 complete charge in 20 hours), followed by a reversible reaction associated with a 500 mAh/g capacity retained after 30 cycles. Many experiments were performed in order to understand the reaction mechanism of sodium with the AV 4 S 8 materials. Electrochemical, in situ X-ray diffraction (Figure 1) and transmission electron microscopy experiments suggest that a smooth conversion mechanism is occurring and that the capacity fade is largely due to reactions with the electrolyte at low potential. EDX and TEM observations, as well as EELS experiments performed at the vanadium L-edge, indicate that a reduction of the vanadium oxidation state occurs during the discharge process. XAS experiments performed at the Vanadium and Germanium K edges also clearly demonstrate that all the elements are involved during the electrochemical processes. Synthesis, structural characterization and electrochemical behaviour of AV 4 S 8 will be discussed in details in the presentation. Results obtained on the AV 4 S 8 phases are very promising and demonstrate that this new class of materials is a good candidate as a negative electrode for Na-ion batteries. References (1). M. M. Doeff, Y. Ma, S. J. Visco,L. C. De Jonghe, J. Electrochem.Soc. 140 , L169 (1993). (2). P. Senguttuvan, G.l. Rousse, V. Seznec, J.-M. Tarascon, M.R. Palacin, Chemistry of Materials, 23 , 4109-4111 (2011). (3). S.I. Park, I. Gocheva, S. Okada, J.-i. Yamaki, J. Electrochem. Soc. 158 , A1067-A1070 (2011). (4). A. Darwiche, C. Marino, M.T. Sougrati, B. Fraisse, L. Stievano, L. Monconduit, Journal of the American Chemical Society, 134 , 20805-20811 (2012).
Potential Therapeutic Use of the Rosemary Diterpene Carnosic Acid for Alzheimer’s Disease, Parkinson’s Disease, and Long-COVID through NRF2 Activation to Counteract the NLRP3 Inflammasome (2022)

Rosemary (<i>Rosmarinus officinalis</i> [family Lamiaceae]), an herb of economic and gustatory repute, is employed in traditional medicines in many countries. Rosemary contains carnosic acid (CA) and carnosol (CS), abietane-type phenolic diterpenes, which account for most of its biological and pharmacological actions, although claims have also been made for contributions of another constituent, rosmarinic acid. This review focuses on the potential applications of CA and CS for Alzheimer's disease (AD), Parkinson's disease (PD), and coronavirus disease 2019 (COVID-19), in part via inhibition of the NLRP3 inflammasome. CA exerts antioxidant, anti-inflammatory, and neuroprotective effects via phase 2 enzyme induction initiated by activation of the KEAP1/NRF2 transcriptional pathway, which in turn attenuates NLRP3 activation. In addition, we propose that CA-related compounds may serve as therapeutics against the brain-related after-effects of SARS-CoV-2 infection, termed "long-COVID." One factor that contributes to COVID-19 is cytokine storm emanating from macrophages as a result of unregulated inflammation in and around lung epithelial and endovascular cells. Additionally, neurological aftereffects such as anxiety and "brain fog" are becoming a major issue for both the pandemic and post-pandemic period. Many reports hold that unregulated NLRP3 inflammasome activation may potentially contribute to the severity of COVID-19 and its aftermath. It is therefore possible that suppression of NLRP3 inflammasome activity may prove efficacious against both acute lung disease and chronic neurological after-effects. Because CA has been shown to not only act systemically but also to penetrate the blood-brain barrier and reach the brain parenchyma to exert neuroprotective effects, we discuss the evidence that CA or rosemary extracts containing CA may represent an effective countermeasure against both acute and chronic pathological events initiated by SARS-CoV-2 infection as well as other chronic neurodegenerative diseases including AD and PD.
Optimizing Radiolabeled Engineered Anti-p185HER2 Antibody Fragments for In vivo Imaging (2005)

We have recently described the in vivo properties of an iodinated anti-p185HER2 engineered antibody fragment [minibody (scFv-C(H)3)2; 80 kDa], made from the internalizing 10H8 monoclonal antibody. Although the 10H8 minibody showed excellent binding to the target in vitro, only modest tumor uptake [5.6 +/- 1.7% injected dose per gram (ID/g) of tissue] was achieved in nude mice bearing MCF7/HER2 breast cancer tumors. Here, in an attempt to improve targeting, the 10H8 minibody was conjugated to 1,4,7,10-tetraazacyclododecane-N, N', N'', N'''-tetraacetic acid (DOTA), radiometal labeled, and evaluated in vivo. The tumor uptake of 111In-DOTA 10H8 minibody was 5.7 +/- 0.1% ID/g, similar to the radioiodinated 10H8 minibody. However, in addition to the expected liver clearance, the kidneys had unexpectedly high activity (34.0 +/- 4.0% ID/g). A minibody derived from a second anti-p185(HER2) antibody (trastuzumab; hu4D5v8) was also made. Tumor uptakes, evaluated by quantitative microPET using 64Cu-DOTA hu4D5v8 minibody, were 4.2 +/- 0.5% ID/g. Furthermore, in non-tumor-bearing mice, 111In-DOTA hu4D5v8 minibody exhibited similar elevated uptake in the kidneys (28.4 +/- 6.5% ID/g). Immunohistochemical staining of kidneys from non-tumor-bearing mice showed strong specific staining of the proximal tubules, and Western blot analysis of kidney lysate confirmed the presence of cross-reactive antigen. To further improve tumor uptake and normal tissue distribution, a larger hu4D5v8 fragment [(scFv-C(H)2-C(H)3)2; 105 kDa] was made, engineered to exhibit rapid clearance kinetics. This fragment, when evaluated by microPET, exhibited improved tumor targeting (12.2 +/- 2.4% ID/g) and reduced kidney uptake (13.1 +/- 1.5% ID/g). Thus, by manipulating the size and format of anti-p185(HER2) antibody fragments, the kidney activity was reduced and high or low expression of p185HER2 in xenografts could be distinguished by microPET imaging.
PolyDoc: Surveying PDF Files from the PolySwarm network (2023)

Complex data formats implicitly demand complex logic to parse and apprehend them. The Portable Document Format (PDF) is among the most demanding formats because it is used as both a data exchange and presentation format, and it has a particularly stringent tradition of supporting in-teroperability and consistent presentation. These requirements create complexity that presents an opportunity for adversaries to encode a variety of exploits and attacks. To investigate whether there is an association between structural malforms and malice (using PDF files as the example challenge format), we built PolyDoc, a tool that conducts format-aware tracing of files pulled from the PolySwarm network. The PolySwarm network crowdsources threat intelligence by running files through several industry-scale threat-detection engines. The PolySwarm network provides a PolyScore, which indicates whether a file is safe or malicious, as judged by threat-detection engines. We ran PolyDoc in a live hunt mode to gather PDF files submitted to PolySwarm and then trace the execution of these PDF files through popular PDF tools such as Mutool, Poppler, and Caradoc. We collected and analyzed 58,906 files from PolySwarm. Further, we used the PDF Error Ontology to assign error categories based on tracer output and compared them to the PolyScore. Our work demonstrates three core insights. First, PDF files classified as malicious contain syntactic malformations. Second, “uncategorized” error ontology classes were common across our different PDF tools—demonstrating that the PDF Error Ontology may be underspecified for files that real-world threat engines receive. Finally, attackers leverage specific syntactic malformations in attacks: malformations that current PDF tools can detect.
Supplementary Table 3 from A Preclinical Trial and Molecularly Annotated Patient Cohort Identify Predictive Biomarkers in Homologous Recombination–deficient Pancreatic Cancer (2023)

&lt;p&gt;Supplementary Table 3 shows the establishment of primary cell cultures from HRD PDAC xenografts&lt;/p&gt;
Clinical significance of the bronchodilator response in children with severe asthma (2019)

Lung function, that is FEV<sub>1</sub> % predicted, is a predictor of BD response in children with asthma. Additionally, smoke exposure, higher FeNO or IgE level, and low peripheral blood neutrophils are associated with a greater likelihood of BD reversibility. BD response can identify a phenotype of pediatric asthma associated with low lung function and poor asthma control.
A Novel Low-overhead Delay Testing Technique for Arbitrary Two-Pattern Test Application (2005)

With increasing process fluctuations in nano-scale technology, testing for delay faults is becoming essential in manufacturing test to complement stuck-at-fault testing. Design-for-testability techniques, such as enhanced scan are typically associated with considerable overhead in die-area, circuit performance, and power during normal mode of operation. This paper presents a novel test technique, which can be used as an alternative to the enhanced scan based delay fault testing method, with significantly less design overhead. Instead of using an extra latch as in the enhanced scan method, we propose using supply gating at the first level of logic gates to hold the state of a combinational circuit. Experimental results on a set of ISCAS89 benchmarks show an average reduction of 33% in area overhead with an average improvement of 71% in delay overhead and 90% in power overhead during normal mode of operation, compared to the enhanced scan implementation.
SRNL Laboratory Directed Research & Development (2015)

The Laboratory Directed Research and Development Program at Savannah River National Laboratory supports high quality research and development to further the mission of the Department of Energy.
DOM-Q-NET: Grounded RL on Structured Language (2019)

Building agents to interact with the web would allow for significant improvements in knowledge understanding and representation learning. However, web navigation tasks are difficult for current deep reinforcement learning (RL) models due to the large discrete action space and the varying number of actions between the states. In this work, we introduce DOM-Q-NET, a novel architecture for RL-based web navigation to address both of these problems. It parametrizes Q functions with separate networks for different action categories: clicking a DOM element and typing a string input. Our model utilizes a graph neural network to represent the tree-structured HTML of a standard web page. We demonstrate the capabilities of our model on the MiniWoB environment where we can match or outperform existing work without the use of expert demonstrations. Furthermore, we show 2x improvements in sample efficiency when training in the multi-task setting, allowing our model to transfer learned behaviours across tasks.