gebhart/patrepeval huggingface dataset:
Nitrate and Nitrite Control of Respiratory Nitrate Reduction in Denitrifying <i>Pseudomonas stutzeri</i> by a Two-Component Regulatory System Homologous to NarXL of <i>Escherichia coli</i> (1999)

Bacterial denitrification is expressed in response to the concurrent exogenous signals of low-oxygen tension and nitrate or one of its reduction products. The mechanism by which nitrate-dependent gene activation is effected was investigated in the denitrifying bacterium Pseudomonas stutzeri ATCC 14405. We have identified and isolated from this organism the chromosomal region encoding the two-component sensor-regulator pair NarXL and found that it is linked with the narG operon for respiratory nitrate reductase. The same region encodes two putative nitrate or nitrite translocases, NarK and NarC (the latter shows the highest similarity to yeast [Pichia] and plant [Nicotiana] nitrate transporters), and the nitrate-regulated transcription factor, DnrE, of the FNR family. The roles of NarX and NarL in nitrate respiration were studied with deletion mutants. NarL activated the transcription of narG, narK, and dnrE but did not affect the denitrification regulons for the respiratory substrates nitrite, nitric oxide, and nitrous oxide. The promoters of narG, narK, and dnrE carry sequence motifs, TACYYMT, which correspond to the NarL recognition sequence established for Escherichia coli. The cellular response toward nitrate and nitrite was mediated by the sensor protein NarX, which discriminated weakly between these oxyanions. Our data show that the NarXL two-component regulatory system has been incorporated into the bacterial denitrification process of P. stutzeri for selective regulation of nitrate respiration.
The angiotensin AT<sub>4</sub>receptor subtype as a target for the treatment of memory dysfunction associated with Alzheimer's disease (2008)

Over recent years antihypertensive drugs, particularly angiotensin-converting enzyme (ACE) inhibitors and angiotensin receptor blockers (ARBs), have been reported to have beneficial effects upon cognitive impairment. Such findings suggest that pharmacological manipulation of angiotensin ligands may be of clinical importance in slowing or halting the cognitive deterioration seen in vascular dementia and Alzheimer's disease. The mechanism(s) underlying these improvements in cognitive function remains unclear; however, important leads are emerging. The angiotensin AT4 receptor subtype, discovered by our laboratory in 1992, influences several important behaviours and physiologies, including learning and memory, and may play a role in this cognitive improvement. This review initially describes the therapeutic drugs approved by the Federal Drug Administration and new approaches presently being developed to treat Alzheimer's disease-induced cognitive impairment. Next, the biologically-active angiotensin ligands and their respective receptor subtypes are discussed, followed by the roles of angiotensin II, angiotensin IV, ACE inhibitors and ARBs in cognitive function. We conclude with a working hypothesis concerning the importance of the AT4 receptor subtype as a new potential drug target for the treatment of Alzheimer's disease-associated memory loss.
User Integrity Risk Calculation at the Alert Limit without Fixed Allocations (2004)

There are two major concepts to calculate the integrity for the user. Either it can be calculated which error magnitude has to be assumed to be compliant with a given integrity risk value (protection level concept), or the integrity risk can be directly calculated at the Alert Limit (AL). For the first concept fix allocations have to be established for each failure mechanism (e.g. 2% horizontal and 98% vertical like WAAS allocation) and HPL respectively VPL result. However, this has to be reconsidered if a the combined integrity risk value is specified (cf. Galileo SRD). Furthermore, user geometries which lead to high HPL are different from those which lead to high VPL values. In case of WAAS this does not have to be considered due to the fact that just 2% are allocated for the horizontal case and due to the fact that WAAS has compared to Galileo very relaxed availability requirements (cf. unavailability of 5% for SBAS vs. 0.5% for Galileo), so that the decrease in availability due to this fixed split can be tolerated. In case of Galileo four failure mechanisms need to be considered, horizontal, vertical and for each of them fault-free and one undetected error. Following the first concept, a fix allocation for each of the four failure mechanisms has to be specified, but the user geometries for which each mechanism might occur are totally different. Therefore, a WAAS similar concept would result in unrealistically high performance allocations with a huge impact on ground infrastructure and system cost due to the fact, that each of two mechanisms requires almost the same allocation. It seems more feasible to calculate the integrity risk for each failure mechanism at the AL and to compare the sum of all four contributions with the required integrity risk. This approach corresponds to the second concept. This paper outlines the described user integrity concept without fix allocations. Furthermore, detailed simulations are presented to verify the enhanced availability performance.
Stimulus Duration and Response Time Independently Influence the Kinetics of Lytic Cycle Reactivation of Epstein-Barr Virus (2009)

Epstein-Barr virus (EBV) can be reactivated from latency into the lytic cycle by many stimuli believed to operate by different mechanisms. Cell lines containing EBV differ in their responses to inducing stimuli, yet all stimuli require de novo protein synthesis (44). A crucial step preliminary to identifying these proteins and determining when they are required is to measure the duration of stimulus and response time needed for activation of expression of EBV BRLF1 and BZLF1, the earliest viral indicators of reactivation. Here we show, with four EBV-containing cell lines that respond to different inducing agents, that stimuli that are effective at reactivating EBV can be divided into two main groups. The histone deacetylase inhibitors sodium butyrate and trichostatin A require a relatively long period of exposure, from 2 to 4 h or longer. Phorbol esters, anti-immunoglobulin G (anti-IgG), and, surprisingly, 5-aza-2'-deoxycytidine require short exposures of 15 min or less. The cell/virus background influences the response time. Expression of the EBV BZLF1 and BRLF1 genes can be detected before 2 h in Akata cells treated with anti-IgG, but both long- and short-duration stimuli required 4 or more hr to activate BZLF1 and BRLF1 expression in HH514-16, Raji, or B95-8 cells. Thus, stimulus duration and response time are independent variables. Neither stimulus duration nor response time can be predicted by the number of cells activated into the lytic cycle. These experiments shed new light on the earliest events leading to lytic cycle reactivation of EBV.
A rule-based inference engine which is optimal and VLSI implementable (2003)

An inference engine for rule-based expert systems which forms part of the EXPRES system is developed and presented. It is shown to be universal, correct, and optimal with respect to time. Its correctness is due to the following facts: the engine is invoked when attributes change, conditions are checked when their attributes take values, rules are examined whenever their conditions change, and actions are executed when their rules are fired. Optimality of execution time is primarily due to the fact that nothing is done which does not need doing. In particular, nothing happens until attributes change value, conditions are evaluated only if their attributes are defined, and rules are examined only when their conditions are true. Another reason for the efficiency of the inference engine is that it is a finite-state machine which operates on a graph rather than a tree. A VLSI implementation of the system that allows automatic design of universal as well as special-purpose expert systems on a chip is proposed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Internal routing protocol in gigabit CARNet network - selection and transition (2004)

The internal routing protocol in an autonomous system (AS) describes how the routers, devices of the third level of the OSI network model, establish mutual communication by sending notices on available network segments. The selection framework of IP routing protocols is determined by different parameters of theoretical and practical nature. A theoretical overview is given using the comparison of possibilities described in corresponding IETF RFC standards. Practical considerations relating to specifically determined conditions in a particular network, including the topology and interdependencies with other implemented technologies, additionally define the selection framework of a corresponding internal routing protocol. The selection of the internal protocol for the CARNet network (TCP/IP private WAN network), which was a component of the first stage in constructing the gigabit CARNet network, is dealt in this paper
Estimation of inspiratory pressure drop in neonatal and pediatric endotracheal tubes (1999)

Endotracheal tubes (ETTs) constitute a resistive extra load for intubated patients. The ETT pressure drop (DeltaP(ETT)) is usually described by empirical equations that are specific to one ETT only. Our laboratory previously showed that, in adult ETTs, DeltaP(ETT) is given by the Blasius formula (F. Lofaso, B. Louis, L. Brochard, A. Harf, and D. Isabey. Am. Rev. Respir. Dis. 146: 974-979, 1992). Here, we also propose a general formulation for neonatal and pediatric ETTs on the basis of adimensional analysis of the pressure-flow relationship. Pressure and flow were directly measured in seven ETTs (internal diameter: 2.5-7.0 mm). The measured pressure drop was compared with the predicted drop given by general laws for a curved tube. In neonatal ETTs (2.5-3.5 mm) the flow regime is laminar. The DeltaP(ETT) can be estimated by the Ito formula, which replaces Poiseuille's law for curved tubes. For pediatric ETTs (4.0-7.0 mm), DeltaP(ETT) depends on the following flow regime: for laminar flow, it must be calculated by the Ito formula, and for turbulent flow, by the Blasius formula. Both formulas allow for ETT geometry and gas properties.
Endoscopic Hemostasis of Esophageal and Gastric Variceal Bleeding with Histoacryl (1990)

Endoscopic injection of the tissue adhesive n-butyl-2-cyano-acrylate (Histoacryl) has been tried for esophageal or fundic variceal bleeding in 23 patients. Definitive hemostasis was achieved in 22 with a single injection of Histoacryl. Throughout the entire hospitalization period, which was completed with at least two weekly sessions of conventional sclerotherapy, only one recurrent bleeding was recorded. Four patients died of hepatic decompensation. It is suggested that Cyanoacrylate could overcome some of the shortcomings of conventional sclerotherapy such as early recurrent hemorrhage and bleeding from fundic varices.
The Level of γ-Glutamyltransferase in Serum, Effect of Carbohydrate Heterogeneity on Clearance Rate (1993)

The measurement of serum gamma-glutamyltransferase (GT) is a frequently used parameter of liver diseases. The serum enzyme originates from liver and is cleared from the circulation by the galactose receptor in liver. The rate of uptake will thus vary with the amount of terminal galactose residues on the enzymes' carbohydrate moiety. Using an experimental rat model we have studied the relative clearance rates of variant forms of GT with different carbohydrate composition. GT purified from pancreas and kidney contains less sialic acid and showed considerably higher clearance rates than the enzyme from liver. The rapid uptake of the kidney and pancreas enzymes indicates that these enzymes may not reach detectable levels if released from these organs to the circulation. On the other hand, GT in serum of alcoholics contains increased amount of sialic acid and this enzyme variant showed a slightly decreased clearance rate compared to the normal liver enzyme. Increased sialylation of GT may thus contribute to the increased level of the enzyme in serum after alcohol abuse.
Pedestrian Notification Methods in Autonomous Vehicles for Multi-Class Mobility-on-Demand Service (2016)

In this paper, we describe methods of conveying perception information and motion intention from self driving vehicles to the surrounding environment. One method is by equipping autonomous vehicles with Light-Emitting Diode (LED) strips to convey perception information; typical pedestrian-driver acknowledgement is replaced by visual feedback via lights which change color to signal the presence of obstacles in the surrounding environment. Another method is by broadcasting audio cues of the vehicle's motion intention to the environment. The performance of the autonomous vehicles as social robots is improved by building trust and engagement with interacting pedestrians. The software and hardware systems are detailed, and a video demonstrates the working system in real application. Further extension of the work for multi-class mobility in human environments is discussed.
Signal interception: a unifying theoretical framework for feature detection (1988)

The unifying framework of the spectral-correlation theory of cyclostationary signals is used to present a broad treatment of weak, random signal detection for interception purposes. The relationships among a variety of previously proposed ad hoc detectors, optimum detectors, and newly proposed detectors are established. The spectral-correlation-plane approach to the interception problem is put forth as especially promising for detection, classification, and estimation in particularly difficult environments involving unknown and changing noise levels and interference activity. A fundamental drawback of the popular radiometric methods in such environments is explained.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Digital Instantaneous Frequency Meter (1979)

A basic instrument is described which produces a parallel digital output proportional to frequency once per cycle, i.e., instantaneously. This is achieved by means of a reciprocal time generator which continuously generates digitally the reciprocal of the time elapsed between successive incoming pulses and the output of which is sampled and held at the end of each cycle. The meter is a 12-bit instrument having an accuracy of ±1 count plus clock stability. An analog output and a digital readout can be readily obtained. The range of the instrument is from zero to fc × 2-12 Hz, where fc is the clock frequency in hertz. Thus the range can be varied by appropriate adjustment of fc. An additional circuit to provide an analog output proportional to rate of change of frequency, also on a cycle-to-cycle basis, is suggested.
Globule: a collaborative content delivery network (2006)

We present Globule, a collaborative content delivery network developed by our research group. Globule is composed of Web servers that cooperate across a wide area network to provide performance and availability guarantees to the sites they host. We discuss the issues involved in developing and setting up a large-scale collaborative CDN and provide solutions for many of its unique problems
Msx1 Cooperates with Histone H1b for Inhibition of Transcription and Myogenesis (2004)

During embryogenesis, differentiation of skeletal muscle is regulated by transcription factors that include members of the Msx homeoprotein family. By investigating Msx1 function in repression of myogenic gene expression, we identified a physical interaction between Msx1 and H1b, a specific isoform of mouse histone H1. We found that Msx1 and H1b bind to a key regulatory element of MyoD, a central regulator of skeletal muscle differentiation, where they induce repressed chromatin. Moreover, Msx1 and H1b cooperate to inhibit muscle differentiation in cell culture and in Xenopus animal caps. Our findings define a previously unknown function for "linker" histones in gene-specific transcriptional regulation.
Wilhelm Ostwald (1853–1932): A Note on the History of Culturology (1951)

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Feature-preserving non-local denoising of static and time-varying range data (2007)

We present a new method for noise removal on static and time-varying range data. Our approach predicts the restored position of a perturbed vertex using similar vertices in its neighborhood. It defines the required similarity measure in a new non-local fashion which compares regions of the surface instead of point pairs. This allows our algorithm to obtain a more accurate denoising result than previous state-of-the-art approaches and, at the same time, to better preserve fine features of the surface. Furthermore, our approach is easy to implement, effective, and flexibly applicable to different types of scanned data. We demonstrate this on several static and interesting new time-varying datasets obtained using laser and structured light scanners.
Increase in levels of polyubiquitin and proteasome mRNA in skeletal muscle during starvation and denervation atrophy (1995)

Most of the increased protein degradation in muscle atrophy caused by starvation and denervation is due to activation of a non-lysosomal ATP-dependent proteolytic process. To determine whether expression of the ubiquitin-proteasome-dependent pathway is activated in atrophying muscles, we measured the levels of mRNA for ubiquitin (Ub) and proteasome subunits, and Ub content. After rats had been deprived of food for 1 or 2 days, the concentration of the two polyubiquitin (polyUb) transcripts increased 2-4-fold in the pale extensor digitorum longus muscle and 1-2.5-fold in the red soleus, whereas total muscle RNA and total mRNA content fell by 50%. After denervation of the soleus, there was a progressive 2-3-fold increase in polyUb mRNA for 1-3 days, whereas total RNA content fell. On starvation or denervation, Ub concentration in the muscles also rose by 60-90%. During starvation, polyUb mRNA levels also increased in heart, but not in liver, kidney, spleen, fat, brain or testes. Although the polyUb gene is a heat-shock gene that is induced in muscles under certain stressful conditions, the muscles of starving rats or after denervation did not express other heat-shock genes. On starvation or denervation, mRNA for several proteasome subunits (C-1, C-3, C-5, C-8 and C-9) also increased 2-4-fold in the atrophying muscles. When the food-deprived animals were re-fed, levels of Ub and proteasome mRNA in their muscles returned to control values within 1 day. In contrast, no change occurred in the levels of muscle mRNAs encoding cathepsin L, cathepsin D and calpain 1 on denervation or food deprivation. Thus polyUb and proteasome mRNAs increased in atrophying muscles in co-ordination with activation of the ATP-dependent proteolytic process.
Allosteric interpretation of haemoglobin properties (1975)

It is our purpose to review recent experiments on haemoglobin in order to discuss them in terms of the two state model of cooperativity. Excellent previous reviews are available of the chemistry of haemoglobin (Antonini & Brunori, 1971; Gibson, 1959 b ) which are referred to when possible. The plethora of data necessitates that a selection must be made in a review. An intentionally wide range of experiments is selected to exhibit
Fabrication and Characteristics of High Brightness White Emission Electroluminescent Device (1999)

White emission thin film electroluminescent device was fabricated using ZnS for phosphor layer and BST ferroelectric thin film for insulating layer. For fabrication conditions of BST thin film, stoichiometry of target was , substrate temperature was , working pressure was 30 mTorr, and A: ratio was 9:1. At this time, dielectric constant was 209 at 1kHz frequency. For phosphor layer ZnS:Mn, ZnS:Tb, and ZnS:Ag were used. Mixing rates of activators were respectively 0.8, 0.8, and 1 wt%. Total thickness of phosphor tapers was 500 nm, thickness of lower insulating layer was 200 nm, and thickness of upper insulating layer was 400 nm. In this conditions, luminescence threshold voltage of thin film electroluminescent device was , maximum brightness was at . Luminescence spectrum peak was observed at region of blue(450 nm), green(550 nm), and red(600 nm).
Curli Fibers Are Highly Conserved between <i>Salmonella typhimurium</i> and <i>Escherichia coli</i> with Respect to Operon Structure and Regulation (1998)

Mouse-virulent Salmonella typhimurium strains SR-11 and ATCC 14028-1s express curli fibers, thin aggregative fibers, at ambient temperature on plates as judged by Western blot analysis and electron microscopy. Concomitantly with curli expression, cells develop a rough and dry colony morphology and bind the dye Congo red (called the rdar morphotype). Cloning and characterization of the two divergently transcribed operons required for curli biogenesis, csgBA(C) and csgDEFG, from S. typhimurium SR-11 revealed the same gene order and flanking genes as in Escherichia coli. The divergence of the curli region between S. typhimurium and E. coli at the nucleotide level is above average (22.4%). However, a high level of conservation at the protein level, which ranged from 86% amino acid homology for the fiber subunit CsgA to 99% homology for the lipoprotein CsgG, implies functional constraints on the gene products. Consequently, S. typhimurium genes on low-copy-number plasmids were able to complement respective E. coli mutants, although not always to wild-type levels. rpoS and ompR are required for transcriptional activation of (at least) the csgD promoter. The high degree of conservation at the protein level and the identical regulation patterns in E. coli and S. typhimurium suggest similar roles of curli fibers in the same ecological niche in the two species.
Prospects of vaccines for medically important fungi Is a vaccine needed against<i>Candida</i><i>albicans</i>? (2005)

The development of a useful Candida vaccine is a distinct possibility despite the fact that individuals with a lifetime of commensal sensitization do not develop sterile immunity to the organism. An effective Candida vaccine would be invaluable in preventing hematogenously disseminated candidiasis, as well as mucocutaneous disease. This review is a discussion of our current understanding of the interplay between commensal and pathogenic forms of Candida albicans and approaches toward active and passive immunoprevention against candidiasis.
Dosage of amyloid precursor protein affects axonal contact guidance in Down syndrome (2013)

Amyloid precursor protein (APP), encoded on Hsa21, functions as a cell adhesion molecule (CAM) in axonal growth cones (GCs) of the developing brain. We show here that axonal GCs of human fetal Down syndrome (DS) neurons (and of a DS mouse model) overexpress APP protein relative to euploid controls. We investigated whether DS neurons generate an abnormal, APP-dependent GC phenotype in vitro. On laminin, which binds APP and β1 integrins (Itgb1), DS neurons formed enlarged and faster-advancing GCs compared to controls. On peptide matrices that bind APP only, but not on those binding exclusively Itgb1 or L1CAM, DS GCs were significantly enlarged (2.0-fold), formed increased close adhesions (1.8-fold), and advanced faster (1.4-fold). In assays involving alternating stripes of monospecific matrices, human control GCs exhibited no preference for any of the substrates, whereas DS GCs preferred the APP-binding matrix (cross-over decreased significantly from 48.2 to 27.2%). Reducing APP expression in DS GCs with siRNA normalized most measures of the phenotype, including substrate choice. These experiments show that human DS neurons exhibit an APP-dependent, abnormal GC phenotype characterized by increased adhesion and altered contact guidance. The results suggest that APP overexpression may perturb axonal pathfinding and circuit formation in developing DS brain.