gebhart/patrepeval huggingface dataset:
Axonal degeneration in the <i>Trembler‐j</i> mouse demonstrated by stimulated single‐fiber electromyography (2007)

The Trembler-j (Tr-j) mouse is a naturally occurring mutant with a point mutation in the peripheral myelin protein-22 gene causing severe peripheral nerve demyelination. It is a genetically homologous murine model for Charcot-Marie-Tooth disease type 1A (CMT 1A). Our prior pilot studies using stimulated single-fiber needle electromyograpy (SSFEMG) showed increased jitter in 60-day-old Tr-j mice compared to age-matched, wildtype animals. The aim of this study was to better elucidate the etiology of increased jitter in Tr-j mice and test the following hypotheses: (1) the increased jitter in Tr-j mice is due to turnover of endplates secondary to axonal degeneration with reinnervation and not to conduction block secondary to demyelination of motor nerve axons; and (2) aging Tr-j mice demonstrate increased jitter and fiber density compared with younger mutant mice due to progressive motor axon loss. SSFEMG studies performed on 60- and 140-day-old mice indicated that average mean consecutive difference (MCD) and fiber density estimates (FDE) were significantly increased in Tr-j mice at both ages compared to age-matched wildtypes. FDE also increased substantially in older mutant mice. Intraperitoneal neostigmine injections produced significant reductions in average MCD in Tr-j mice, suggesting that impaired neuromuscular transmission is an early pathologic feature in these mice and likely reflects distal axonal degeneration. Our findings corroborate our prior pilot study, although in a much larger number of animals across a wider age span. Our study also indicates that SSFEMG, performed in a serial fashion, is a useful, noninvasive method of detecting progressive axon loss in this murine model of CMT 1A. This technique may be a valuable tool to study the affects of genetic or pharmaceutical interventions in murine models of peripheral neuropathy. Muscle Nerve, 2007.
The relationship between transplacental O<sub>2</sub> diffusion and placental expression of PlGF, VEGF and their receptors in a placental insufficiency model of fetal growth restriction (2003)

Placental growth factor (PlGF) and vascular endothelial growth factor (VEGF) are involved in placental angiogenesis through interactions with the VEGFR-1 and VEGFR-2 receptors. The placenta of pregnancies whose outcome is fetal growth restriction (FGR) are characterized by abnormal angiogenic development, classically associated with hypoxia. The present study evaluated the near-term expression of this growth factor family in an ovine model of placental insufficiency-FGR, in relationship to uteroplacental oxygenation. Compared to controls, FGR pregnancies demonstrated a 37% increase in uterine blood flow (FGR vs. control, 610.86+/-48.48 vs. 443.17+/-37.39 ml min(-1) (kg fetus)(-1); P<0.04), which was associated with an increased maternal uterine venous PO2 (58.13+/-1.00 vs. 52.89+/-1.26 mmHg; P<0.02), increased umbilical artery systolic/diastolic ratio (3.90+/-0.33 vs. 2.12+/-0.26, P<0.05), and fetal hypoxia (arterial PO2; 12.79+/-0.97 vs. 18.65+/-1.6 mmHg, P<0.005). Maternal caruncle PlGF mRNA was increased in FGR (P<0.02), while fetal cotyledon VEGF mRNA was reduced (P<0.02). VEGFR-1 mRNA was also reduced in FGR fetal cotyledon (P<0.001) but was not altered in caruncle tissue. Immunoblot analysis of PlGF and VEGF demonstrated single bands at 19,000 and 18,600 Mr, respectively. Caruncle PlGF concentration was increased (P<0.04), while cotyledon VEGF was decreased (P<0.05) in FGR placentae. The data establish that uterine blood flow is not reduced in relationship to metabolic demands in this FGR model and that the transplacental PO2 gradient is increased, maintaining umbilical oxygen uptake per unit of tissue. Furthermore, these data suggest that an increased transplacental gradient of oxygen generates changes in angiogenic growth factors, which may underline the pathophysiology of the post-placental hypoxic FGR.
Dialogue Act Classification in Group Chats with DAG-LSTMs (2019)

Dialogue act (DA) classification has been studied for the past two decades and has several key applications such as workflow automation and conversation analytics. Researchers have used, to address this problem, various traditional machine learning models, and more recently deep neural network models such as hierarchical convolutional neural networks (CNNs) and long short-term memory (LSTM) networks. In this paper, we introduce a new model architecture, directed-acyclic-graph LSTM (DAG-LSTM) for DA classification. A DAG-LSTM exploits the turn-taking structure naturally present in a multi-party conversation, and encodes this relation in its model structure. Using the STAC corpus, we show that the proposed method performs roughly 0.8% better in accuracy and 1.2% better in macro-F1 score when compared to existing methods. The proposed method is generic and not limited to conversation applications.
ChemInform Abstract: O‐Alkyl‐5′,5′‐dinucleoside Phosphates as Prodrugs of 3′‐Azidothymidine and Cordycepin. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Thermally actuated tapping mode atomic force microscopy with polymer microcantilevers (2009)

This paper demonstrates a thermally actuated tapping mode atomic force microscopy (AFM) with a polymer cantilever. The cantilever (350x250x3 microm(3)) is made from polyimide and includes an embedded resistive heater for thermal actuation. The oscillation of the cantilever is due to the stress gradient caused by alternating heating and cooling from the periodic ac excitation of the heater. The tip oscillation amplitude is 5-10 nm in air. The oscillation occurs at 2omega and is a linear function of the applied voltage. The maximum oscillation amplitude is seen at 0.8 Hz with a 3dB frequency of 26 Hz. The damping of the oscillation due to tip-sample interaction is used to image the sample without any optomechanical feedback. Scans with a 200 nm tall grating indicate a resolution comparable to deflection signal from the AFM in contact mode.
Probability Analysis of Successful Cyber Attacks in SDN-based Networks (2018)

Risk assessment plays a key role in the information security management of organizations to protect their assets against cyber threats and reduce the risk of attacks to their infrastructures. One key element in the risk assessment process is the determination of the probability of occurrence of elementary attack actions. For that, this paper suggests a novel model which considers vulnerability severities, attack scenarios and various potential actors and their motivations. Based on the results obtained from the new model we further infer the most likely attack scenarios. An SDN-based network infrastructure is taken as an example scenario to demonstrate our new approach.
Halogen radicals contribute to photooxidation in coastal and estuarine waters (2016)

Although halogen radicals are recognized to form as products of hydroxyl radical ((•)OH) scavenging by halides, their contribution to the phototransformation of marine organic compounds has received little attention. We demonstrate that, relative to freshwater conditions, seawater halides can increase photodegradation rates of domoic acid, a marine algal toxin, and dimethyl sulfide, a volatile precursor to cloud condensation nuclei, up to fivefold. Using synthetic seawater solutions, we show that the increased photodegradation is specific to dissolved organic matter (DOM) and halides, rather than other seawater salt constituents (e.g., carbonates) or photoactive species (e.g., iron and nitrate). Experiments in synthetic and natural coastal and estuarine water samples demonstrate that the halide-specific increase in photodegradation could be attributed to photochemically generated halogen radicals rather than other photoproduced reactive intermediates [e.g., excited-state triplet DOM ((3)DOM*), reactive oxygen species]. Computational kinetic modeling indicates that seawater halogen radical concentrations are two to three orders of magnitude greater than freshwater (•)OH concentrations and sufficient to account for the observed halide-specific increase in photodegradation. Dark (•)OH generation by gamma radiolysis demonstrates that halogen radical production via (•)OH scavenging by halides is insufficient to explain the observed effect. Using sensitizer models for DOM chromophores, we show that halogen radicals are formed predominantly by direct oxidation of Cl(-) and Br(-) by (3)DOM*, an (•)OH-independent pathway. Our results indicate that halogen radicals significantly contribute to the phototransformation of algal products in coastal or estuarine surface waters.
The plasma cell membrane glycoprotein, PC-1, is a threonine-specific protein kinase stimulated by acidic fibroblast growth factor. (1991)

A 32P-labeled protein that co-purified with acidic fibroblast growth factor (aFGF) receptor from bovine liver proved to be a distinct membrane protein, which itself has kinase activity that is stimulated by aFGF. The protein was designated MAFP for major aFGF-stimulated phosphoprotein. MAFP was purified from bovine liver using immunoaffinity chromatography with monoclonal antibody to MAFP following Triton X-100 extraction of plasma membranes and wheat germ lectin-Sepharose 4B column chromatography. The purified MAFP showed molecular masses of 130 kDa and 260 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis under reducing and nonreducing conditions, respectively. Purified MAFP elicited aFGF-stimulated Thr-specific autophosphorylation activity and phosphorylation activity toward protein substrates (myelin basic protein and histone). Amino acid sequence analyses of 16 peptide fragments of MAFP, produced by endoproteinase Lys-C digestion followed by reduction and S-pyridylethylation, showed approximately 80-100% homology with the cDNA-deduced amino acid sequences of human and mouse plasma cell membrane glycoprotein, PC-1 (Buckley, M. F., Loveland, K. A., McKinstry, W. J., Garson, O. M., and Goding, J. W. (1990) J. Biol. Chem. 265, 17506-17511), suggesting that MAFP is the bovine version of PC-1. The amino acid sequences of bovine MAFP, human and mouse PC-1 reveal a putative ATP binding site in their extracellular domains. These results suggest that MAFP(PC-1) is an ectoprotein kinase. In addition to the kinase activity, MAFP(PC-1) was also found to possess alkaline nucleotide phosphodiesterase activity. It is now clear that several of the unique properties previously attributed to the aFGF receptor kinase are actually properties of this novel Thr-specific ectoprotein kinase, which co-purifies with the aFGF receptor and is responsive to stimulation by aFGF.
Genetic Synthesis of Periodic Protein Materials (1991)

Genetic engineering offers a novel approach to the development of\nadvanced polymeric materials, in particular protein-based materials.\nBiological synthesis provides levels of control of polymer chain architecture\nthat cannot yet be attained by current methods of chemical synthesis. In\naddition to employing naturally occurring genetic templates artificial genes\ncan be designed to encode completely new materials with customized properties.\nIn the present paper we: 1) review the concepts and technology of creating\nprotein-based materials by genetic engineering, 2) discuss the merits of\nproducing crystalline lamellar proteins by this approach, and 3) review\nprogress made by our group in generating such materials by genetic strategies.\nFull descriptions appear elsewhere about the parameters to be considered in\ndesigning artificial protein genes of this type, the effectiveness of\ndifferent gene construction and expression strategies utilized by us thus far\nand, the specific properties of the various materials derived from these\nefforts (1,2).\nProgress made by other groups involved in developing periodic proteins by\nmolecular biological strategies are described in refs. 3-8. The latter\nstudies include genetic engineering of artificial silk-like proteins (3,4),\npoly-aspartylphenylalanine (5), an α/β barrel domain (octarellin; 6), the\ncollagen tripeptide GlyProPro (7) and human tropoelastin (8). Advances with\nthe silk-like proteins (SLP) have been particularly impressive. In addition\nto producing multi-gram quantities of pure SLP homopolymers, this group has successfully generated block copolymers of SLP interspersed with core peptides of mammalian elastin and the human fibronectin cell attachment element. While publications are still lacking it appears that a numiber of groups are striving to create genetically engineered variants of the repetitive bioadhesive proteins produced by mussels and barnacles (9).
Probing the specific ion effects of biocompatible hydrated choline ionic liquids on lactate oxidase biofunctionality in sensor applications (2013)

This paper presents an extended study on the ion effects of a series of biocompatible hydrated choline based ionic liquids (ILs) on lactate oxidase (LOx), an important enzyme in biosensing technology for the in vitro detection of lactic acid. Secondary structural analysis revealed changes in the protein conformation in hydrated ILs, while thermal unfolding/aggregation dynamics showed different profiles in the presence or absence of ILs. Moreover, LOx thermally denaturised at 90 °C showed residual activity in the presence of chloride and dihydrogen phosphate anions. Kinetic and lifetime studies were also performed, providing a better understanding of the ion effects of ILs on the biocatalytic activity of the enzyme.
Characterization of Ocular Surface Symptoms From Optometric Practices in North America (2001)

Our results show that symptoms of ocular irritation and visual disturbances were relatively common in this unselected clinical population. The intensity of many ocular symptoms increased late in the day, which suggested that environmental factors played a role in the etiology of the symptoms.
Chemical approaches to therapeutically target the metabolism and signaling of the endocannabinoid 2-AG and eicosanoids (2014)

The endocannabinoid system, most popularly known as the target of the psychoactive component of marijuana, Δ(9)-tetrahydrocannabinol (THC), is a signaling network that modulates a diverse range of physiological processes including nociception, behavior, cognitive function, appetite, metabolism, motor control, memory formation, and inflammation. While THC and its derivatives have garnered notoriety in the eyes of the public, the endocannabinoid system consists of two endogenous signaling lipids, 2-arachidonoylglycerol (2-AG) and N-arachidonoylethanolamine (anandamide), which activate cannabinoid receptors CB1 and CB2 in the nervous system and peripheral tissues. This review will focus on the recent efforts to chemically manipulate 2-AG signaling through the development of inhibitors of the 2-AG-synthesizing enzyme diacylglycerol lipase (DAGL) or the 2-AG-degrading enzyme monoacylglycerol lipase (MAGL), and assessing the therapeutic potential of DAGL and MAGL inhibitors in pain, inflammation, degenerative diseases, tissue injury, and cancer.
The interaction of 2-phenylbenzimidazole compounds with DNA: The influence of terminal substituents (2002)

We have studied the influence of terminal substituents, amidinium group and N-methylpiperazine ring, of 2-phenylbenzimidazole compounds (1-6; Figure 1) on their DNA-binding modes. Experimental results reveal that 1-3 are accepted in intercalation pockets owing to structural flexibility of the N-methylpiperazine ring, while 4-6 bind to the groove of DNA because of steric hindrance between the amidinium group and the DNA phosphate-sugar backbone.
Densification mechanism of TiB2-1%CoB and TiB2-5%TaB2-1%CoB systems. (1986)

Sintered TiB2-1%CoB and TiB2-5%TaB2-1%CoB materials have high density and high trasverse rupture strength. In the present study, the densification mechanism of the above materials has been investigated. It has been found that even a small amount (1 wt% or less) of CoB added to TiB2 or to TiB2-5%TaB2 has a remarkable effect on densification, and that the mixture of TiB2-1%CoB shows remarkable shrinkage during sintering under the die pressure of 200 kg/cm2 even at 1400°C which is lower than the melting point of CoB. These results suggest that the densification of these materials is caused mainly by an activated sintering process under die pressure. In this process, atoms on the surface of TiB2 (or TaB2) grains dissolve into the CoB phase so that a carrier phase may be formed in the contact area between the TiB2 (or TaB2) grain and the CoB phase. Then, the surface atoms on any TiB2 (or TaB2) grain can diffuse rapidly to other grains through the carrier phase.
A resource-shared VLIW processor architecture for area-efficient on-chip multiprocessing (2005)

We propose an area-efficient resource-shared VLIW processor (RSVP) for future leaky nm process technologies. It consists of several single-way independent processor units (IPUs) that share parallel processor resources. Each IPU works as a variable-way VLIW processor sharing the parallel resources according to priorities of given tasks. RSVP allocates shared parallel resources to the IPUs cycle by cycle. It can minimize the number of NOPs that waste power. The performance per power (P3) of a 4-parallel 4-way RSVP that corresponds to four 4way VLIWs is 3.7% better than a conventional 4-parallel 4-way VLIW multiprocessor in the current 90nm process. We estimate that the RSVP achieves 36% less leakage power and 28% better P3 in the future 25nm process. We have fabricated an RSVP test chip that contains two IPU and a shared resource equivalent to two 2way VLIWs in a 180nm process. It is functional at 100MHz clock speed and its power is 130mW.
Membrane invaginations facilitate reversible water flux driving tunable iridescence in a dynamic biophotonic system (2013)

Squids have used their tunable iridescence for camouflage and communication for millions of years; materials scientists have more recently looked to them for inspiration to develop new "biologically inspired" adaptive optics. Iridocyte cells produce iridescence through constructive interference of light with intracellular Bragg reflectors. The cell's dynamic control over the apparent lattice constant and dielectric contrast of these multilayer stacks yields the corresponding optical control of brightness and color across the visible spectrum. Here, we resolve remaining uncertainties in iridocyte cell structure and determine how this unusual morphology enables the cell's tunable reflectance. We show that the plasma membrane periodically invaginates deep into the iridocyte to form a potential Bragg reflector consisting of an array of narrow, parallel channels that segregate the resulting high refractive index, cytoplasmic protein-containing lamellae from the low-index channels that are continuous with the extracellular space. In response to control by a neurotransmitter, the iridocytes reversibly imbibe or expel water commensurate with changes in reflection intensity and wavelength. These results allow us to propose a comprehensive mechanism of adaptive iridescence in these cells from stimulation to color production. Applications of these findings may contribute to the development of unique classes of tunable photonic materials.
Comparison of etching processes of silicon and germanium in SF6–O2 radio-frequency plasma (1995)

Reactive ion etching of Si and Ge in SF6–O2 is investigated. Etch rate shows that Si etching is selective with respect to Ge in SF6–O2 (O2&lt;50%); the reverse is observed in SF6–O2 (O2≳50%). In agreement with the compared evolution of the F and O concentration in the plasma and of the etch product formation rate obtained respectively, by optical emission spectroscopy and mass spectrometry, the x-ray photon spectroscopy surface analysis reveals that the growth of a SiOxFy layer quenches the Si etching whereas the formation of GeOxFy does not inhibit Ge etching. Using a simple model, an experimental surface reactivity is defined and expressed in function of the experimental data. Results suggest a different behavior for sulfur and oxygen on both materials.
Up-regulation of biosynthetic processes associated with growth by trehalose 6-phosphate (2010)

Trehalose 6-phosphate (T6P), the precursor of trehalose, is a signaling molecule in plants with strong effects on metabolism, growth and development. We recently showed that in growing tissues T6P is an inhibitor of SnRK1 of the SNF1-related group of protein kinases. SnRK1 acts as transcriptional integrator in response to carbon and energy supply. In microarray experiments on seedlings of transgenic Arabidopsis with elevated T6P content we found that expression of SnRK1 marker genes was affected in a manner to be predicted by inhibition of SnRK1 by T6P in vivo. A large number of genes involved in reactions that utilize carbon, e.g., UDP-glucose dehydrogenase genes involved in cell wall synthesis, were upregulated. T6P was also found to affect developmental signaling pathways, probably in a SnRK1-independent manner. This includes upregulation of genes encoding UDP-glycosyltransferases that are involved in the glycosylation of hormones. In addition, genes involved in auxin response and light signaling were affected. Many of these genes belong to pathways that link the circadian clock to plant growth and development. The overall pattern of changes in gene expression supports a role for T6P in coordinating carbon supply with biosynthetic process involved in growth and development.
Device-correlated metrology for overlay measurements (2014)

One of the main issues with accuracy is the bias between the overlay (OVL) target and actual device OVL. In this study, we introduce the concept of device-correlated metrology (DCM), which is a systematic approach to quantify and overcome the bias between target-based OVL results and device OVL values. In order to systematically quantify the bias components between target and device, we introduce a new hybrid target integrating an optical OVL target with a device mimicking critical dimension scanning electron microscope (CD-SEM) target. The hybrid OVL target is designed to accurately represent the process influence on the actual device. In the general case, the CD-SEM can measure the bias between the target and device on the same layer after etch inspection (AEI) for all layers, the OVL between layers at AEI for most cases and after develop inspection for limited cases such as double-patterning layers. The results have shown that for the innovative process compatible hybrid targets the bias between the target and device is small, within the order of CD-SEM noise. Direct OVL measurements by CD-SEM show excellent correlation between CD-SEM and optical OVL measurements at certain conditions. This correlation helps verify the accuracy of the optical measurement results and is applicable for the imaging base OVL method using several target types advance imaging metrology, advance imaging metrology in die OVL, and the scatterometrybase OVL method. Future plans include broadening the hybrid target design to better mimic each layer process conditions such as pattern density. Additionally, for memory devices we are developing hybrid targets which enable other methods of accuracy verification.
A physicist's view on current questions in atomic spectrometry (1987)

Simple considerations and elementary physics are used to address four questions raised in connection with current developments in analytical atomic spectrometry. How can we increase the speed of ETA-AAS? What are the limitations to sample introduction in ICP-AES, also with respect to solid samples? What are the merits of high-resolution ICP-AES? How can non-metals be determined directly?