gebhart/patrepeval huggingface dataset:
Protease activated receptor 2: a new target for IBS treatment. (2008)

Proteinase-activated receptors (PARs) are G-protein-coupled receptors that are activated by the proteolytic cleavage of their N-terminal domain. The new N-terminal sequence that is exposed by proteolysis acts as a tethered ligand, which binds to and activates the receptor. PAR-2 is highly expressed in the gastrointestinal tract, where it is found in endothelial cells, colonic myocytes, enterocytes (both on basolateral and apical membranes), enteric neurons, terminals of mesenteric afferent nerves and immune cells. In the gastrointestinal tract, PAR-2 may be activated by tryptase from mast cells but also by luminal proteases such as trypsin and possibly bacterial proteases. In addition to effects on motility, ion and mucus secretion, activation of PAR-2 receptors from luminal affects visceral pain. In rats, the intracolonic infusion of PAR-2 agonists (SLIGRL, trypsin) initiates a delayed hypersensitivity to colonic distension. These effects are locally mediated since they are not observed for systemic administration. Interestingly, such pronociceptive effect of local activation of PAR-2 is associated with increased colonic paracellular permeability. Blockade of such increase in permeability, prevents the occurrence of hypersensitivity to rectal distension suggesting that activation of the local immune system by luminal toxins and antigens is responsible for the sensitization of primary afferent terminals to mechanical stimuli. Consequently, blockade of PAR-2 receptors at the periphery and/or inhibition of colonic luminal protease activity may be new interesting targets for the treatment of gut hypersensitivity and IBS. A recent study has evidenced that stool supernatants from diarrhea predominant IBS patients have a high level of serine-protease activity that increases permeability and colonic hypersensitivity when infused intra-colonically in mice, and these effects are linked to activation of PAR-2 receptors. These data support a possible role of luminal proteases in the pathogenesis of IBS and give a rationale to target PARs and more specifically PAR-2 as future treatment of IBS.
NDE applications of SQUID magnetometry to electrochemical systems (1991)

A technique utilizing state-of-the-art SQUID magnetometers for noninvasive evaluation of the electrochemical reactivity of materials has been extended to practical systems. For example, sensitization of type-304 stainless steel has been identified. Magnetic signals produced by sensitized and unsensitized samples in acid demonstrate clear differences between the two types of samples. As a second example, electrodeposition of zinc, simulating recharging of Zn/Ni and Zn/Ag batteries, has been noninvasively monitored via magnetic signals. Disturbances in the current distribution over time, caused by nonuniform deposition, have been detected and compared to simulations of dendritic growth. Further investigations will be enhanced by increased flexibility, sensitivity, and spatial resolution available in a prototype SQUID instrument being developed.
Compensation of Quadrature Imbalance in an Optical QPSK Coherent Receiver (2008)

This letter explores the Gram-Schmidt orthogonalization procedure (GSOP) for compensation of quadrature imbalance in an optical 90 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">deg</sup> hybrid. We present computer simulations for an optical QPSK communication system using a digital coherent receiver and investigate the impact of quadrature imbalance on the required optical signal-to-noise ratio for the receiver and the frequency estimation algorithm. We then demonstrate the improvement which can be achieved using the GSOP, including the impact of quantization in the digital coherent receiver. Finally, we show that the GSOP can equally be applied to polarization-division multiplexed systems, applying the GSOP in conjunction with the constant modulus algorithm to demultiplex a PDM-QPSK signal.
Scripting COM components in Haskell (2002)

The expressiveness of higher-order typed languages such as Haskell or ML makes them an attractive medium in which to write software components. Hitherto, however, their use has been limited by the all-or-nothing problem: it is hard to write just part of an application in these languages. Component-based programming using a binary standard such as Microsoft's Component Object Model (COM) offers a solution to this dilemma, by specifying a language-independent interface between components. This paper reports about our experience with exploiting this opportunity in the purely functional language Haskell. We describe a design for integrating COM components into Haskell programs, and we demonstrate why someone might want to script their COM components in this way.
Identification of Hemolytic Activity in Saliva of the Lone Star Tick (Acari: Ixodidae) (1997)

Hemolytic activity was identified in the saliva of Amblyomma americanum (L.) when red blood cells from sheep were incubated with tick saliva in the presence of phosphatidylcholine and sodium deoxycholate. The hemolytic activity was destroyed by boiling or treating with trypsin. The hemolytic activity in tick saliva was calcium-dependent, and inhibited by a phospholipase A2 inhibitor oleyloxyethyl phosphorylcholine. Phosphatidylserine could replace phosphatidylcholine in the hemolytic assays but phosphatidylethanolamine and phosphatidylinositol were ineffective. Size exclusion chromatography of tick saliva revealed one peak of hemolytic activity, which correlated with the activity of tick salivary phospholipase A2, both having a molecular weight approximately 55,000 daltons. These results suggest that the hemolytic activity in tick saliva results from salivary phospholipase A2. The hemolytic activity in tick saliva may play a role in lysing host red blood cells, thus facilitating the tick digestive process.
Effects of VDT monitor placement and single versus bifocal glasses on somatic discomfort and postural profiles in data entry tasks. (2004)

A study was conducted to determine the effects of VDT monitor positions and the use of single vision versus bifocal glasses on somatic elements in the data entry task. Eight male subjects performed data entry using a word processor in eight half-hour sessions with the four different monitor placements, i.e. "eye-level", "shoulder-level-front", "shoulder-level-side", and "sunken-level", wearing the two types of glasses. A subjective discomfort rating questionnaire covering 12 somatic elements was completed by the subject after each session. The head inclination and angle of gaze to the monitor were measured with a goniometer. The results revealed that the somatic elements which were affected significantly by the placement of the VDT monitor and the type of glasses were discomfort in the neck and back regions and eyestrain, respectively. The neck-back discomfort scores were highest at the "eye-level", lowest at the "sunken-level", and intermediate at the "shoulder-level-side" position. The "shoulder-level-front" position was not significantly different in the discomfort from other three positions. The eyestrain was significantly greater with the bifocal than with the single vision glasses. The lower the monitor was placed, the more forward was the head and gaze inclined. The head was inclined less forward, or even more backward, and the gaze was inclined more forward, with the bifocal than with the single vision glasses. As a conclusion, the VDT operators were advised to avoid the "eye-level" and "shoulder-level-side" positions and to prefer the "sunken-level" and "shoulder-level-front" positions as the first and second best choices, respectively. The preference becomes more critical for the wearers of bifocal glasses that suffer from postural constraints in viewing.
Probe of specific interaction between a simplified synthetic glycopolymer and erythrocytes as mediated by a glucose transporter (GLUT) on a cell membrane (2001)

In order to develop a biomimetic polymer for cell recognition, we synthesized poly [3-O-(4'-vinylbenzyl)-D-glucose] (PVG), a polystyrene derivative with reduced glucose moiety, and studied the specific interaction of this PVG with erythrocytes, carried by a glucose transporter (GLUT-1), on a cell membrane. To clarify the specific interaction between the PVG and the erythrocytes, fluorescein isothiocyanate- (FITC) labeled polymer was used to prove and visualize the specific interaction. We found that labeled polymer strongly binds to erythrocytes, probably due to the specific interaction mediated by the presence of GLUT-1 on the cell membrane. The fluorescence intensity of PVG on erythrocytes was time and dose dependent. To verify the specific interaction between the PVG and the erythrocytes, cells were pretreated with phloretin, an inhibitor of GLUT-1, before adding the FITC-labeled PVG polymer to the cell-culture medium. This treatment suppressed the interaction of PVG with erythrocytes. A confocal laser microscopic study further confirmed this interaction. The results from this study provide evidence that a biomimetic polymer of PVG interacts with erythrocytes mediated by GLUT-1 on cell membranes.
Qantas bans pensioner: An abuse of process (2017)

Has Qantas gone too far by imposing a lifetime flying ban on a pensioner for an incident unrelated to the safety of passengers and crew? It is considered that it has, and that the ban is unwarranted and unlawful.
Molecular Phenotyping of the <i>pal1</i> and <i>pal2</i> Mutants of <i>Arabidopsis thaliana</i> Reveals Far-Reaching Consequences on Phenylpropanoid, Amino Acid, and Carbohydrate Metabolism (2004)

The first enzyme of the phenylpropanoid pathway, Phe ammonia-lyase (PAL), is encoded by four genes in Arabidopsis thaliana. Whereas PAL function is well established in various plants, an insight into the functional significance of individual gene family members is lacking. We show that in the absence of clear phenotypic alterations in the Arabidopsis pal1 and pal2 single mutants and with limited phenotypic alterations in the pal1 pal2 double mutant, significant modifications occur in the transcriptome and metabolome of the pal mutants. The disruption of PAL led to transcriptomic adaptation of components of the phenylpropanoid biosynthesis, carbohydrate metabolism, and amino acid metabolism, revealing complex interactions at the level of gene expression between these pathways. Corresponding biochemical changes included a decrease in the three major flavonol glycosides, glycosylated vanillic acid, scopolin, and two novel feruloyl malates coupled to coniferyl alcohol. Moreover, Phe overaccumulated in the double mutant, and the levels of many other amino acids were significantly imbalanced. The lignin content was significantly reduced, and the syringyl/guaiacyl ratio of lignin monomers had increased. Together, from the molecular phenotype, common and specific functions of PAL1 and PAL2 are delineated, and PAL1 is qualified as being more important for the generation of phenylpropanoids.
All‐Vacuum‐Deposited Stoichiometrically Balanced Inorganic Cesium Lead Halide Perovskite Solar Cells with Stabilized Efficiency Exceeding 11% (2017)

Vacuum-sublimed inorganic cesium lead halide perovskite thin films are prepared and integrated in all-vacuum-deposited solar cells. Special care is taken to determine the stoichiometric balance of the sublimation precursors, which has great influence on the device performance. The mixed halide devices exhibit exceptional stabilized power conversion efficiency (11.8%) and promising thermal and long-term stabilities.
Ejecución autonómica de las normas comunitarias: (comentario a la STC/1992, de 28 de mayo) (1993)

Human p.V37I mutation of <i>GJB2</i> gene was strongly correlated with late-onset progressive hearing loss, especially among East Asia populations. We generated a knock-in mouse model based on human p.V37I variant (c.109G>A) that recapitulated the human phenotype. Cochlear pathology revealed no significant hair cell loss, stria vascularis atrophy or spiral ganglion neuron loss, but a significant change in the length of gap junction plaques, which may have contributed to the observed mild endocochlear potential (EP) drop in homozygous mice lasting lifetime. The cochlear amplification in homozygous mice was compromised, but outer hair cells' function remained unchanged, indicating that the reduced amplification was EP- rather than prestin-generated. In addition to ABR threshold elevation, ABR wave I latencies were also prolonged in aged homozygous animals. We found in homozygous IHCs a significant increase in I<sub>Ca</sub> but no change in Ca<sup>2+</sup> efficiency in triggering exocytosis. Environmental insults such as noise exposure, middle ear injection of KCl solution and systemic application of furosemide all exacerbated the pathological phenotype in homozygous mice. We conclude that this <i>Gjb2</i> mutation-induced hearing loss results from 1) reduced cochlear amplifier caused by lowered EP, 2) IHCs excitotoxicity associated with potassium accumulation around hair cells, and 3) progression induced by environmental insults.
Mass Fingerprinting of the Venom and Transcriptome of Venom Gland of Scorpion Centruroides tecomanus (2013)

Centruroides tecomanus is a Mexican scorpion endemic of the State of Colima, that causes human fatalities. This communication describes a proteome analysis obtained from milked venom and a transcriptome analysis from a cDNA library constructed from two pairs of venom glands of this scorpion. High perfomance liquid chromatography separation of soluble venom produced 80 fractions, from which at least 104 individual components were identified by mass spectrometry analysis, showing to contain molecular masses from 259 to 44,392 Da. Most of these components are within the expected molecular masses for Na(+)- and K(+)-channel specific toxic peptides, supporting the clinical findings of intoxication, when humans are stung by this scorpion. From the cDNA library 162 clones were randomly chosen, from which 130 sequences of good quality were identified and were clustered in 28 contigs containing, each, two or more expressed sequence tags (EST) and 49 singlets with only one EST. Deduced amino acid sequence analysis from 53% of the total ESTs showed that 81% (24 sequences) are similar to known toxic peptides that affect Na(+)-channel activity, and 19% (7 unique sequences) are similar to K(+)-channel especific toxins. Out of the 31 sequences, at least 8 peptides were confirmed by direct Edman degradation, using components isolated directly from the venom. The remaining 19%, 4%, 4%, 15% and 5% of the ESTs correspond respectively to proteins involved in cellular processes, antimicrobial peptides, venom components, proteins without defined function and sequences without similarity in databases. Among the cloned genes are those similar to metalloproteinases.
Compressed text indexes (2009)

A compressed full-text self-index represents a text in a compressed form and still answers queries efficiently. This represents a significant advancement over the (full-)text indexing techniques of the previous decade, whose indexes required several times the size of the text. Although it is relatively new, this algorithmic technology has matured up to a point where theoretical research is giving way to practical developments. Nonetheless this requires significant programming skills, a deep engineering effort, and a strong algorithmic background to dig into the research results. To date only isolated implementations and focused comparisons of compressed indexes have been reported, and they missed a common API, which prevented their re-use or deployment within other applications. The goal of this article is to fill this gap. First, we present the existing implementations of compressed indexes from a practitioner's point of view. Second, we introduce the Pizza&Chili site, which offers tuned implementations and a standardized API for the most successful compressed full-text self-indexes, together with effective test-beds and scripts for their automatic validation and test. Third, we show the results of our extensive experiments on these codes with the aim of demonstrating the practical relevance of this novel algorithmic technology.
Fundamental Properties of Local Anesthetics. II. Measured Octanol (1990)

Because local anesthetic molecules interact with ion channel proteins embedded in membranes to effect impulse blockade, and because their clinical potency often depends on both vascular absorption and distribution into the tissue surrounding the site of deposition, the ability to partition into these various compartments is an important determinant of local anesthetic action. Therefore, the hydrophobic nature of local anesthetics used clinically was characterized by the octanol:buffer partition coefficients of their charged (P+) and neutral (Po) species. This was accomplished by previously described optical methods in which direct spectrophotometric measurement of both the pH-dependent distribution coefficient (Q) and of the ionization permit calculation of the pKa and partition coefficients. The rates of alkaline hydrolysis of ester-linked molecules also were measured to assess potential interference of such hydrolysis with the physicochemical assays. Results indicate that the hydrophobicity of a local anesthetic is increased by manipulation of the molecular structure at three sites: (a) the aromatic ring; (b) the intermediate linking group; and (c) the tertiary amine. Po for the agents studied was 10(3)-10(5) times greater than P+. Although there is no systematic relationship between hydrophobicity and pKa, the latter is greater with ester-linked (pKa = 8.59-9.30) than with amide-linked (pKa = 7.92-8.21) local anesthetics. All of the charged species, with the exception of bupivacaine, selectively partition into the aqueous environment (P+ less than 1.0). The temperature dependence of partitioning of the local anesthetics, measured at 25 and 36 degrees C, indicates an entropy-driven hydrophobic uptake. Solutions buffered with bicarbonate and including 5% CO2 showed the same local anesthetic partitioning as that of CO2-free solutions, suggesting that potentiation of impulse blockade by CO2 is not due to increased membrane uptake. Correlations of physicochemical properties of local anesthetics with potencies on isolated nerve confirm that the more potent local anesthetics have greater octanol:buffer partition coefficients, and that the ester-linked local anesthetics are more potent than their amide-linked counterparts having the same hydrophobicities. The correlations of structure with potency also suggest that the extracellular protonated species may contribute to impulse blockade.
Rayleigh-Scattering-Induced RIN and Amplitude-to-Phase Conversion as a Source of Length-Dependent Phase Noise in OEOs (2013)

Optoelectronic oscillators (OEOs) are hybrid RF-photonic oscillators that promise to be environmentally robust frequency sources with very low phase noise. Recent experiments have shown that the excess flicker phase noise in these systems grows with the length of the optical fiber loop. In this paper, we detail a mechanism for this length-dependent flicker noise in which Rayleigh-scattering-induced amplitude noise in the optical fiber combines with amplitude-to-phase noise conversion in the nonlinear electronic components. We derive an analytic model of the loop noise that includes these effects and verify this model by comparing it to numerical calculations and experimental results.
SUMO targeting of a stress-tolerant Ulp1 SUMO protease (2018)

SUMO proteases of the SENP/Ulp family are master regulators of both sumoylation and desumoylation and regulate SUMO homeostasis in eukaryotic cells. SUMO conjugates rapidly increase in response to cellular stress, including nutrient starvation, hypoxia, osmotic stress, DNA damage, heat shock, and other proteotoxic stressors. Nevertheless, little is known about the regulation and targeting of SUMO proteases during stress. To this end we have undertaken a detailed comparison of the SUMO-binding activity of the budding yeast protein Ulp1 (ScUlp1) and its ortholog in the thermotolerant yeast Kluyveromyces marxianus, KmUlp1. We find that the catalytic UD domains of both ScUlp1 and KmUlp1 show a high degree of sequence conservation, complement a ulp1Δ mutant in vivo, and process a SUMO precursor in vitro. Next, to compare the SUMO-trapping features of both SUMO proteases we produced catalytically inactive recombinant fragments of the UD domains of ScUlp1 and KmUlp1, termed ScUTAG and KmUTAG respectively. Both ScUTAG and KmUTAG were able to efficiently bind a variety of purified SUMO isoforms and bound immobilized SUMO1 with nanomolar affinity. However, KmUTAG showed a greatly enhanced ability to bind SUMO and SUMO-modified proteins in the presence of oxidative, temperature and other stressors that induce protein misfolding. We also investigated whether a SUMO-interacting motif (SIM) in the UD domain of KmULP1 that is not conserved in ScUlp1 may contribute to the SUMO-binding properties of KmUTAG. In summary, our data reveal important details about how SUMO proteases target and bind their sumoylated substrates, especially under stress conditions. We also show that the robust pan-SUMO binding features of KmUTAG can be exploited to detect and study SUMO-modified proteins in cell culture systems.
Real-time digital holographic microscopy using the graphic processing unit (2008)

Digital holographic microscopy (DHM) is a well-known powerful method allowing both the amplitude and phase of a specimen to be simultaneously observed. In order to obtain a reconstructed image from a hologram, numerous calculations for the Fresnel diffraction are required. The Fresnel diffraction can be accelerated by the FFT (Fast Fourier Transform) algorithm. However, real-time reconstruction from a hologram is difficult even if we use a recent central processing unit (CPU) to calculate the Fresnel diffraction by the FFT algorithm. In this paper, we describe a real-time DHM system using a graphic processing unit (GPU) with many stream processors, which allows use as a highly parallel processor. The computational speed of the Fresnel diffraction using the GPU is faster than that of recent CPUs. The real-time DHM system can obtain reconstructed images from holograms whose size is 512 x 512 grids in 24 frames per second.
Finding Frequent Itemsets using Apriori Algorihm to Detect Intrusions in Large Dataset (2014)

With the growth of hacking and exploiting tools and invention of new ways of intrusion, Intrusion detection and prevention is becoming the major challenge in the world of network security. The increasing network traffic and data on Internet is making this task more demanding. There are various approaches being utilized in intrusion detections, but unfortunately any of the systems so far is not completely flawless. The flase positive rates makes it extremely hard for to analyze and react to attacks. Intrusion detection systems using data mining approaches make it possible to search patterns and rules in large amount of audit data. In this paper, we represent an model to integrate association rules to intrusion detection to design and implement an network intrusion detection system. Our technnique is used to generate attack rules that will detect the attacks in network audit data using anomaly detection. This shows that the association rules mining algorithm is capable of detecting network intrusions. The KDD dataset which is freely available online is used for our experimentation and results are discussed. Our aim is to experiment with dfiiferent parameters of apriori algorithm to build a string intrusion detection system using association rule mining.