gebhart/patrepeval huggingface dataset:
Quantitative aspects of reversible osmotic opening of the blood-brain barrier (1980)

Retrograde infusion of a hypertonic arabinose solution into the right external carotid artery of rats reversibly increases cerebrovascular permeability to [14C]sucrose in the right cerebral hemisphere. PA ([14C]sucrose permeability x capillary surface area) rises from a control mean of 11 x 10(-6) S-1 to above 200 x 10(-6) S-1. The rise correlates with an increased staining of the brain by intravascular Evans blue, and is followed by a transient, 1-1.5% increase in brain water content. At least 20 s of infusion is required for 1.6 M arabinose solution to effectively open the blood-brain barrier. The increase in cerebrovascular permeability is temporary, however, because PA remains slightly elevated 1-2 h after infusion and is normal 6 h after infusion. It is suggested that osmotic barrier opening is mediated by cerebrovascular dilatation as well as by shrinkage of the vascular endothelium. By quantitatively defining thresholds of infusate concentration and infusion time for osmotic barrier opening, and by characterizing the time course of increased PA, the experiments establish criteria for applying the osmotic method to experimental pharmacology of the central nervous system.
Enhancing semantic and geographic annotation of web images via logistic canonical correlation regression (2009)

Photo community sites such as Flickr and Picasa Web Album host a massive amount of personal photos with millions of new photos uploaded every month. These photos constitute an overwhelming source of images that require effective management. There is an increasingly imperative need for semantic annotation of these web images. This paper addresses the problem by considering two kinds of annotation: semantic annotation and geographic annotation. Both are useful for image search and retrieval and for facilitating communities and social networks. This paper proposes a novel method of Logistic Canonical Correlation Regression (LCCR) for the annotation task. This model exploits the canonical correlation between heterogeneous features and an annotation lexicon of interest, and builds a generalized annotation engine based on canonical correlations in order to produce enhanced annotation for web images. We validate the effectiveness of our algorithm using a dataset of over 380,000 images tagged with GPS coordinates.
Flow Requirements of Spawning Atlantic Salmon in an Upland Stream: Implications for Water‐Resource Management (2001)

Abstract The spawning sites selected by female Atlantic salmon (Salmo salar) were surveyed over three consecutive years in the Girnock Burn, Aberdeenshire, Scotland. Discharge was calculated for each spawning site to assess within‐catchment variation in spawning discharge selection. In total, 428 incidents of female spawning activity were logged at 48 sites. Fish selected relatively high flows in which to spawn, with the lowest utilised discharge being equivalent to the burn's 50 percentile flow. The results emphasise the importance of relatively high flows during the spawning season and, more specifically, a range of flows which ensures that sites are distributed as widely as possible and are accessible and suitable.
Arginine residues are critical for the heparin-cofactor activity of antithrombin III (1985)

A dilution/quench technique was used to monitor the time course of chemical modification on the heparin-cofactor (a) and progressive thrombin-inhibitory (b) activities of human antithrombin III. Treatment of antithrombin III (AT III) with 2,4,6-trinitrobenzenesulphonate at pH 8.3 and 25 degrees C leads to the loss of (a) at 60-fold more rapid rate than the loss of (b). This is consistent with previous reports [Rosenberg & Damus (1973) J. Biol. Chem. 248, 6490-6505; Pecon & Blackburn (1984) J. Biol. Chem. 259, 935-938] that lysine residues are involved in the binding of heparin to AT III, but not in thrombin binding. Treatment of AT III with phenylglyoxal at pH 8.3 and 25 degrees C again leads to a more rapid loss of (a) than of (b), with the loss of the former proceeding at a 4-fold faster rate. The presence of heparin during modification with phenylglyoxal significantly decreases the rate of loss of (a). Full loss of (a) correlates with the modification of seven arginine residues per inhibitor molecule, whereas loss of (b) does not commence until approximately four arginine residues are modified and is complete upon the modification of approximately eleven arginine residues per inhibitor molecule. This suggests that (the) arginine residue(s) in AT III are involved in the binding of heparin in addition to the known role of Arg-393 at the thrombin-recognition site [Rosenberg & Damus (1973) J. Biol. Chem. 248, 6490-6505; Jörnvall, Fish & Björk (1979) FEBS Lett. 106, 358-362].
Adsorption behavior of Rhodamine B on nanoporous polymers (2015)

This study demonstrates that nanoporous materials possess good adsorption capacities for Rhodamine B in water.
Uncertainty associated with form assessment in coordinate metrology (2013)

In this paper, we describe techniques for evaluating the uncertainties associated with the assessment of form error, i.e., the departure from ideal geometry of a manufactured part, in coordinate metrology. The techniques take into account measurement uncertainty, sampling effects due to the fact that the form error is determined from a finite set of coordinate data points, and the spatial correlation of the form errors. The techniques are designed to be practical, without the need for complex computation.
Inflammation of the Atherosclerotic Cap and Shoulder of the Plaque Is a Common and Locally Observed Feature in Unruptured Plaques of Femoral and Coronary Arteries (1999)

-Retrospectively, plaque rupture is often colocalized with inflammation of the cap and shoulder of the atherosclerotic plaque. Local inflammation is therefore considered a potential marker for plaque vulnerability. However, high specificity of inflammation for plaque rupture is a requisite for application of inflammation markers to detect rupture-prone lesions. The objective of the present study was to investigate the prevalence and distribution (local versus general) of inflammatory cells in nonruptured atherosclerotic plaques. The cap and shoulder of the plaque were stained for the presence of macrophages and T lymphocytes in 282 and 262 cross sections obtained from 74 coronary and 50 femoral arteries, respectively. From most cases, 2 atherosclerotic arteries were studied to gain insight into the local and systemic distribution of the inflammatory process. In 45% and 41% of all cross sections, staining for macrophages was observed in the femoral and coronary arteries, respectively. Rupture of the fibrous cap was observed in 2 femoral and 3 coronary artery segments and was always colocalized with inflammatory cells. At least 1 cross section stained positively for CD68 or acid phosphatase in 84% and 71% of all femoral and coronary arteries, respectively. Only 1 femoral and 6 coronary arteries revealed a positive stain for CD68 in all investigated segments. Inflammation of the cap and shoulder of the plaque is a common feature, locally observed, in atherosclerotic femoral and coronary arteries. The high prevalence of local inflammatory responses should be considered if they are used as a diagnostic target to detect vulnerable, rupture-prone lesions.
Activation-independent Parathyroid Hormone Receptor Internalization Is Regulated by NHERF1 (EBP50) (2003)

Parathyroid hormone (PTH) regulates extracellular calcium homeostasis through the type 1 PTH receptor (PTH1R) expressed in kidney and bone. The PTH1R undergoes beta-arrestin/dynamin-mediated endocytosis in response to the biologically active forms of PTH, PTH-(1-34), and PTH-(1-84). We now show that amino-truncated forms of PTH that do not activate the PTH1R nonetheless induce PTH1R internalization in a cell-specific pattern. Activation-independent PTH1R endocytosis proceeds through a distinct arrestin-independent mechanism that is operative in cells lacking the adaptor protein Na/H exchange regulatory factor 1 (NHERF1) (ezrin-binding protein 50). Using a combination of radioligand binding experiments and quantitative, live cell confocal microscopy of fluorescently tagged PTH1Rs, we show that in kidney distal tubule cells and rat osteosarcoma cells, which lack NHERF1, the synthetic antagonist PTH-(7-34) and naturally circulating PTH-(7-84) induce internalization of PTH1R in a beta-arrestin-independent but dynamin-dependent manner. Expression of NHERF1 in these cells inhibited antagonist-induced endocytosis. Conversely, expression of dominant-negative forms of NHERF1 conferred internalization sensitivity to PTH-(7-34) in cells expressing NHERF1. Mutation of the PTH1R PDZ-binding motif abrogated interaction of the receptor with NHERF1. These mutated receptors were fully functional but were now internalized in response to PTH-(7-34) even in NHERF1-expressing cells. Removing the NHERF1 ERM domain or inhibiting actin polymerization allowed otherwise inactive ligands to internalize the PTH1R. These results demonstrate that NHERF1 acts as a molecular switch that legislates the conditional efficacy of PTH fragments. Distinct endocytic pathways are determined by NHERF1 that are operative for the PTH1R in kidney and bone cells.
Vacuum arc cathode spot grouping and motion in magnetic fields (2002)

Two of the important vacuum arc phenomena observed when the arc runs in a transverse magnetic field are cathode spot grouping and the cathode spot retrograde motion, i.e., in the anti-Amperian direction. This paper summarizes the main experimental observations and proposes a physical model for spot grouping and spot retrograde motion. The proposed spot motion model take in account the previous theoretical model of the cathode thermal regime and the plasma flow near the cathode surface that is based on two conditions: i) the heat loss in the cathode bulk is relatively small to the heat influx, and ii) the plasma flow in the Knudsen layer is impeded. In the present model, the current per group spot is calculated by assuming that the plasma kinetic pressure is comparable to the self-magnetic pressure in the acceleration region of cathode plasma jet. The model includes equations for the current per spot group, spot velocity dependence on the magnetic field and on the arc current in vacuum, as well as in gas filled arc gap. The calculated currents per spot group and spot velocity increase linearly with the magnetic field and arc current, and this dependencies well agree with previous observations. The cathode spot retrograde motion in short electrode gaps and at atmospheric pressure arcs, and the reversal motion in strong magnetic fields (>1 T) observed by Robson and Engel are discussed. The details of the retrograde motion observed in the last decades including the spot velocity dependence on the electrode gap, roughness, temperature, and material could be understood in the frame of the proposed model.
Response of blood leukocytes to thrombin receptor peptides (1993)

Thrombin has receptor-mediated effects on a variety of cell types. A recently cloned platelet thrombin receptor exerts its effects by a tethered-ligand mechanism. A similar receptor was shown in at least two nonplatelet cell types, fibroblasts and endothelial cells. Thrombin has biologically important effects on leukocytes, but the type of receptor mediating the effects is not known. Therefore, we examined the responses of monocytes, neutrophils, and lymphocytes to thrombin and to an agonist specific for the platelet-type thrombin receptor. We compared the effects of a peptide (SFLLRNPNDKYEPF) corresponding to residues 42-55 of the cloned platelet thrombin receptor on calcium flux in platelets and leukocytes. The thrombin receptor peptide induced increases in intracellular calcium in platelets and monocytes that reached a maximum at 5 microM peptide. The maximal increase was similar in magnitude to the response to thrombin. Lymphocytes showed a small and variable increase in intracellular calcium in response to thrombin or the thrombin receptor agonist. The thrombin receptor peptide had no effect on neutrophil calcium concentrations. When the amino acid corresponding to Arg 46 was replaced with Ala in the synthetic peptide, the ability to increase intracellular calcium was abolished for both platelets and monocytes. The peptide instead had thrombin antagonist activity. Thus, monocytes respond to thrombin receptor peptides similarly to platelets. We conclude that human monocytes possess a thrombin receptor similar to that present on platelets. Furthermore, the residue corresponding to Arg 46 of the thrombin receptor is critical for receptor agonist activity.
Scheduling dependent real-time activities (1990)

A real-time application is typically composed of a number of cooperating activities that must execute within specific time intervals. Since there are usually more activities to be executed than there are processors on which to execute them, several activities must share a single processor. Necessarily, satisfying the activities timing constraints is a prime concern in making the scheduling decisions for that processor. Unfortunately, the activities are not independent. Rather, they share data and devices, observe concurrency constraints on code execution and send signals to one another. These interactions can be modeled as contention for shared resources that must be used by one activity at a time. An activity awaiting access to a resource currently held by another activity is said to depend on that activity, and a dependency relationship is said to exist between them. Dependency relationships may encompass both precedence constraints and resource conflicts. No algorithm solves the problem of scheduling activities with dynamic dependency relationships in a way that is suitable for all real-time systems. This thesis provides an algorithm, called DASA, that is effective for scheduling the class of real-time systems known as supervisory control systems. Simulation experiments that account for the time required to make scheduling decisions demonstrate that DASA provides equivalent or superior performance to other scheduling algorithms of interest under a wide range of conditions for parameterized. synthetic workloads. DASA performs particularly well during overloads. when it is impossible to complete all of the activities. This research makes a number of contributions to the field of computer science, including: a formal model for analyzing scheduling algorithms; the DASA scheduling algorithm, which integrates resource management with standard scheduling functions; results that demonstrate the efficacy of DASA in a variety of situations, and simulator.
Enzyme–microbe synergy during cellulose hydrolysis by <i>Clostridium thermocellum</i> (2006)

Specific cellulose hydrolysis rates (g of cellulose/g of cellulase per h) were shown to be substantially higher (2.7- to 4.7-fold) for growing cultures of Clostridium thermocellum as compared with purified cellulase preparations from this organism in controlled experiments involving both batch and continuous cultures. This "enzyme-microbe synergy" requires the presence of metabolically active cellulolytic microbes, is not explained by removal of hydrolysis products from the bulk fermentation broth, and appears due to surface phenomena involving adherent cellulolytic microorganisms. Results support the desirability of biotechnological processes featuring microbial conversion of cellulosic biomass to ethanol (or other products) in the absence of added saccharolytic enzymes.
Characterization of Thiol-conjugated Metabolites of 2-Propylpent-4-enoic Acid (4-eneVPA), a Toxic Metabolite of Valproic Acid, by Electrospray Tandem Mass Spectrometry (1996)

The hepatotoxicity of the anticonvulsant drug valproic acid (VPA) is most likely associated with the bioactivation of its metabolite 2-propylpent-4-enoic acid (4-ene VPA), which is known to induce hepatic microvesicular steatosis in rats. This paper presents an on-line liquid chromatographic/tandem mass spectrometric (LC/MS/MS) identification of new glutathione (GSH)-related conjugates of the reactive metabolites of 4-ene VPA. Bile samples collected from male Sprague-Dawley rats dosed intraperitoneally with 4-ene VPA or its [2H7]-analogue (100 mg kg-1) were injected on to an ODS column interfaced to a LC/MS/MS instrument using electrospray ionization. LC was developed such that no overlapping of peaks occurred among those metabolites which may potentially produce common fragment ions of interest. Subsequent comparison of LC retention times and MS/MS full fragment ion spectra generated for putative metabolites with that of authentic reference compounds made available by chemical synthesis confirmed the presence of the GSH, cysteinylglycine, cysteine and N-acetylcysteine (NAC) conjugates of 2-(2'-carboxypentanyl)oxirane (4,5-epoxy VPA) and (E)-2-propylpenta-2,4-dienoic acid ((E)-2,4-diene VPA), respectively. Quantitatively, the biliary thiol conjugates accounted for 5% of the dose. This observation is novel for 4-ene VPA metabolism in terms of the degradation of GSH conjugates to the corresponding mercapturic acids possibly occurring within the liver as opposed to an inter-organ process which involves the kidney. In addition, the GSH- and NAC-glucuronide di-conjugates of (E)-2,4-diene VPA were also identified as the biliary metabolites with the GSH-glucuronide di-conjugate being 10% of the corresponding mono-GSH conjugate. Taken together, these data clearly indicate that reactive metabolites of VPA can react with hepatic GSH via several different metabolic pathways and may subsequently produce depletion of GSH that leads to toxic consequences.
The effect of an InP cap layer on the photoluminescence of an In<i>x</i>Ga1–<i>x</i>As1–<i>y</i>P<i>y</i>/In<i>z</i>Al1– <i>z</i>As quantum well heterostructure (2017)

The effect of an InP cap on the photoluminescence (PL) spectrum of an InGaAsP/InAlAs quantum well (QW) is investigated using excitation power and temperature dependent PL. An as-grown sample with the InP cap layer shows an inverted interface created between InP and InAlAs that has a transition energy very close to the transition energy of the QW; consequently, there is an overlap between them. On the other hand, the QW sample with the cap layer etched away does not have a feature due to the inverted interface; even at very low power, the only observed feature is due to the QW transition.
Perplexity—a measure of the difficulty of speech recognition tasks (1977)

Using counterexamples, we show that vocabulary size and static and dynamic branching factors are all inadequate as measures of speech recognition complexity of finite state grammars. Information theoretic arguments show that perplexity (the logarithm of which is the familiar entropy) is a more appropriate measure of equivalent choice. It too has certain weaknesses which we discuss. We show that perplexity can also be applied to languages having no obvious statistical description, since an entropy-maximizing probability assignment can be found for any finite-state grammar. Table I shows perplexity values for some well-known speech recognition tasks. Perplexity Vocabulary Dynamic Phone Word size branching factor IBM-Lasers 2.14 21.11 1000 1000 IBM-Raleigh 1.69 7.74 250 7.32 CMU-AIX05 1.52 6.41 1011 35
Niche of harmful alga <i>Aureococcus anophagefferens</i> revealed through ecogenomics (2011)

Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking, because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements showed that the harmful alga Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the genome of A. anophagefferens and compared its gene complement with those of six competing phytoplankton species identified through metaproteomics. Using an ecogenomic approach, we specifically focused on gene sets that may facilitate dominance within the environmental conditions present during blooms. A. anophagefferens possesses a larger genome (56 Mbp) and has more genes involved in light harvesting, organic carbon and nitrogen use, and encoding selenium- and metal-requiring enzymes than competing phytoplankton. Genes for the synthesis of microbial deterrents likely permit the proliferation of this species, with reduced mortality losses during blooms. Collectively, these findings suggest that anthropogenic activities resulting in elevated levels of turbidity, organic matter, and metals have opened a niche within coastal ecosystems that ideally suits the unique genetic capacity of A. anophagefferens and thus, has facilitated the proliferation of this and potentially other HABs.
Objective Assessment of a Speech Enhancement Scheme with an Automatic Speech Recognition-Based System. (2018)

A single-ended method for the prediction of perceived listening effort based on an automatic speech recognition system was adopted from the literature and modified to evaluate a near-end listening enhancement (NELE) scheme. The listening effort prediction method employs a deep time delay neural network (TDNN) that was trained as part of an automatic speech recognizer. The TDNN computes phoneme posterior probabilities (or âposteriorgramsâ), which degrade in the presence of noise or other distortions. The degree of posteriorgram degradation is quantified by a performance measure and serves as a predictor for mean subjective listening effort ratings of normal-hearing listeners. The modification of the original method consists of the usage of a TDNN (in contrast to a regular feed-forward DNN used before), which was trained on a much bigger speech corpus. Without any task-specific training or optimization, the modified method achieves a very high correlation with subject ive listening effort ratings from the used test data set of unprocessed and NELE-processed speech in two types of background noise (r = 0.98), generalizes to unseen noise conditions, and produces consistent predictions across these conditions that can be directly compared.