gebhart/patrepeval huggingface dataset:
Dual-color two-photon fluorescence correlation spectroscopy (2001)

Fluorescence correlation spectroscopy (FCS) is rapidly growing in popularity as a research tool in biological and biophysical research. Under favorable conditions, FCS measurements can produce an accurate characterization of the chemical, physical, and kinetic properties of a biological system. However, interpretation of FCS data quickly becomes complicated as the heterogeneity of a molecular system increases, as well as when there is significant non-stationery fluorescence background (e.g. intracellular autofluorescence). Use of multi-parameter correlation measurements is one promising approach that can improve the fidelity of FCS measurements in complex systems. In particular, the use of dual-color fluorescence assays, in which different interacting molecular species are labeled with unique fluorescent indicators, can tune the sensitivity of FCS measurements in favor of particular molecular species of interest, while simultaneously minimizing the contribution of other molecular species to the overall fluorescence correlation signal. Here we introduce the combined application of two-photon fluorescence excitation and dual-color cross-correlation analysis for detecting molecular interactions in solution. The use of two-photon excitation is particularly advantageous for dual-color FCS applications due to the uncomplicated optical alignment and the superior capabilities for intracellular applications. The theory of two-photon dual-color FCS is introduced, and initial results quantifying hybridization reactions between three independent single stranded DNA molecules are presented.
Solution-Gated Epitaxial Graphene as pH Sensor (2008)

A solution-gate field effect transistor (SGFET) has been fabricated on few-layer graphene (FLG). The ideally polarizable graphene/aqueous electrolyte interface allows the capacitive charging of the surface by hydroxyl (OH-) and hydroxonium ions (H3O+). The conductivity versus gate potential curve exhibits "V" shaped ambipolar transfer characteristics of graphene, with hole and electron mobilities of 3600 cm2/Vs and 2100 cm2/Vs, respectively. The shift of the negative gate potential with pH shows a supra-Nernstian response of 99 meV/pH. Our work points to the potential application of graphene in ultrafast and ultralow noise chemical or biological sensors.
Phosphine Gas Adsorption in a Series of Metal–Organic Frameworks (2015)

For the first time, phosphine adsorption has been evaluated in a series of metal–organic frameworks (MOFs). Open-metal coordination sites were found to significantly enhance the ability of MOFs to adsorb highly toxic phosphine gas, with the identity of the open-metal site also modulating the amount of gas adsorbed. The MOFs studied outperform activated carbon, a commonly used material to capture phosphine.
Supporting scenario-based requirements engineering (1998)

Scenarios have been advocated as a means of improving requirements engineering yet few methods or tools exist to support scenario based RE. The paper reports a method and software assistant tool for scenario based RE that integrates with use case approaches to object oriented development. The method and operation of the tool are illustrated with a financial system case study. Scenarios are used to represent paths of possible behavior through a use case, and these are investigated to elaborate requirements. The method commences by acquisition and modeling of a use case. The use case is then compared with a library of abstract models that represent different application classes. Each model is associated with a set of generic requirements for its class, hence, by identifying the class(es) to which the use case belongs, generic requirements can be reused. Scenario paths are automatically generated from use cases, then exception types are applied to normal event sequences to suggest possible abnormal events resulting from human error. Generic requirements are also attached to exceptions to suggest possible ways of dealing with human error and other types of system failure. Scenarios are validated by rule based frames which detect problematic event patterns. The tool suggests appropriate generic requirements to deal with the problems encountered. The paper concludes with a review of related work and a discussion of the prospects for scenario based RE methods and tools.
1.3 μm bidirectional optical transmission over 31 km of installed single-mode fibre using optical couplers (1984)

Results are reported of 1.3 μm bidirectional optical transmission over 31 km of installed cabled fibre at transmission rates of 34–650 Mbit/s using fused biconical tapered couplers manufactured at BTRL. With the introduction of 6 dB extra path loss it is possible to double the system capacity incurring only a small additional penalty at 34 and 140 Mbit/s and no other penalty at 320 and 650 Mbit/s.
An electric current tomograph (1988)

A description is given of an instrument designed to acquire data for the construction of images of internal body structures based on measurements of electrical impedance made from a set of electrodes applied around the periphery of the body. The instrument applies currents at 15 kHz in any desired pattern to 32 electrodes and measures the resulting voltage at each electrode. The construction of a test phantom is also described and the results of initial studies showing the distinguishability of targets of differing sizes and conductivities placed in the phantom are reported. The system is able to distinguish the presence of 9-mm-diameter insulators or conductors placed in the center of a 30-cm-diameter circular tank of salt water. This system is capable of implementing an adaptive process of produce the best currents to distinguish the unknown conductivity from a homogeneous conductivity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Health, Wellness, and Safety Aspects of the Consumption of Kombucha (2015)

Functional foods have been identified as whole foods and fortified, enriched, or enhanced products which have a potentially beneficial effect on health when consumed as part of a varied diet on a regular basis, at effective levels. As consumer awareness on functional food escalates, the interest towards conducting scientific studies in this field has also proportionately increased. Many of the traditional food products are known to possess bioactive components, thus qualifying as functional food. Kombucha tea is produced by fermenting sugared black tea with a mixed culture of yeast and bacteria. Kombucha tea has gained immense popularity in recent times due to many associated health benefits. The therapeutic effects of this beverage are thought to be derived from the chemical composition of this beverage, mainly the polyphenols and secondary metabolites which are produced during fermentation. However, the safety aspects of the beverage also need to be taken into account when qualifying the beverage as a functional food. Nevertheless, Kombucha tea could be easily recognized as a beverage which is able to replace the consumption of carbonated beverages due to its possession of health benefits and therapeutic properties.
FP-Tree Based Algorithms Analysis: FP- Growth, COFI-Tree and CT-PRO (2011)

Mining frequent itemsets from the large transactional database is a very critical and important task. Many algorithms have been proposed from past many years, But FP-tree like algorithms are considered as very effective algorithms for efficiently mine frequent item sets. These algorithms considered as efficient because of their compact structure and also for less generation of candidates itemsets compare to Apriori and Apriori like algorithms. Therefore this paper aims to presents a basic Concepts of some of the algorithms (FP-Growth, COFI-Tree, CT-PRO) based upon the FP- Tree like structure for mining the frequent item sets along with their capabilities and comparisons.
Induction of Chalcone Synthase Expression in White Spruce by Wounding and Jasmonate (2000)

The phenylpropanoid pathway has important functions in angiospermous plants following exposure to environmental stresses, such as wounding and pathogen attack, that lead to production of compounds including lignin, flavonoids and phytoalexins. Chalcone synthase (CHS) is a key enzyme in this pathway, catalyzing the first step in flavonoid biosynthesis, whose expression can be induced in response to environmental stress. To explore the response of conifers to environmental stress, expression of spruce CHS and its inducibility were investigated. A partial spruce CHS cDNA clone was isolated using PCR. Examination of the expression patterns of the CHS gene family in white spruce revealed accumulation of CHS mRNA in needle tissue following mechanical wounding, or application of signal molecules like jasmonic acid or methyl jasmonate. Repeated mechanical wounding or jasmonate applications had an enhancing effect on transcript accumulation in needles. A systemic accumulation of CHS mRNAs following wounding was also observed. Conifers thus appear to possess a general wound response similar to that found for angiosperms, which includes CHS induction as well as its inducibility by jasmonic acid and airborne methyl jasmonate.
Performance Evaluation of Notched Biaxial Braided Composites (2004)

Braided composites have good properties in mutually orthogonal directions, more balanced properties than traditional tape laminates, and have potentially better fatigue and impact resistance due to the interlacing. Another benefit is reduced manufacturing cost by reducing part count. Because of these potential benefits braided composites are being considered for various applications ranging from primary/secondary structures for aerospace structures [1]. These material systems are gaining popularity, in particular for the small business jets, where FAA requires take off weights of 12,500 lb. or less. The new process, Vacuum Assisted Resin Transfer Molding (VARTM), is low cost, affordable and suitable for high volume manufacturing environment. Recently the aircraft industry has been successful in manufacturing wing flaps, using carbon fiber braids and epoxy resin and the VARTM process. To utilize these VARTM manufactured braided materials to the fullest advantage (and hence to avoid underutilization), it is necessary to understand their behavior under different loading and environmental conditions. This will reduce uncertainty and hence reduce the factor of safety in the design. It is well known fact that the strength of the composite structure reduces because of discontinuities and abrupt change in the cross-section. Accurate knowledge of strength and failure mechanism of notched and unnotched composites is very important for design of composite structures. This research addresses the behavior of notched braided composites under static tensile loading.
Stem cell factor induces outgrowth of c-<i>kit</i>-positive neurites and supports the survival of c-<i>kit</i>-positive neurons in dorsal root ganglia of mouse embryos (1993)

The c-kit receptor tyrosine kinase is highly expressed by about 10% of the neurons in the dorsal root ganglia (DRGs) of mouse embryos. We investigated the in vitro effect of stem cell factor (SCF), the ligand for c-kit receptor, on DRGs. Recombinant murine SCF (rmSCF) induced the outgrowth of c-kit-positive neurites from DRGs of normal (+/+) embryos. The effect of SCF was dose dependent and completely abolished by anti-c-kit ACK2 monoclonal antibody (mAb). Some neurites whose outgrowth was induced by nerve growth factor (NGF) were c-kit-positive, but anti-NGF mAb did not inhibit the rmSCF-induced neurite outgrowth. rmSCF did not induce neurite outgrowth from DRGs of W/W embryos that did not express c-kit receptors on the cell surface and of W42/W42 mutant embryos that expressed c-kit receptors without tyrosine kinase activity. rmSCF also had a trophic effect on c-kit-positive neurons in the culture of dissociated DRG cells. Most c-kit-positive neurons appeared to respond to NGF as well, and the SCF-responsive subpopulation represented about 10% of NGF-responsive neurons. rmSCF did not support the survival of DRG neurons from embryos of W/W and W42/W42 genotypes. These results suggest that the stimulus through the c-kit receptor tyrosine kinase has an important role in development of the peripheral nervous system.
Effect of Grapefruit Juice, Naringin, Naringenin, and Bergamottin on the Intestinal Carrier-Mediated Transport of Talinolol in Rats (2008)

The effect of two varieties of grapefruit juice (white and ruby red) and its selected components (naringin, naringenin, and bergamottin) was investigated on the activity of the P-glycoprotein (P-gp) in male Sprague-Dawley rats. Talinolol, a nonmetabolized P-gp substrate, was used as a marker compound. The white grapefruit juice (GFJ) had a minor effect on talinolol pharmacokinetics, but the ruby red GFJ reduced the C max and the AUC (0-infinity) by 60% and 50% of the control, respectively. However, among the GFJ constituents tested, bergamottin (0.22 mg/kg) was the most potent component augmenting the C max and the AUC (0-infinity) of talinolol by 2.4- and 1.8-fold, respectively, if compared to the control group. The flavonoids naringenin (0.7 mg/kg) and naringin (2.4 and 9.4 mg/kg) had a similar effect increasing the talinolol C max and AUC (0-infinity) by 1.5- to 1.8-fold, respectively. In conclusion, the effect of GFJ on P-gp activity seems to depend on the variety, the concentration of compounds in the juice, and the composition of different ingredients.
Implementing loudness models in Matlab (2004)

In the field of psychoacoustic analysis the goal is to construct a transformation that will map a time domain waveform into a domain that will best capture the response of a human perceiving sound. A key element of such transformations is the mapping between the sound intensity in decibels and its actual perceived loudness. A number of difdferent loudness models exist to achieve this mapping. This paper examines implementation strategies for some of the more well-known models in the Matlab software environment.
Heterologous Expression of Epothilone Biosynthetic Genes in <i>Myxococcus xanthus</i> (2002)

Epothilones are potential anticancer drugs that stabilize microtubules in a manner similar to paclitaxel (Taxol). Epothilones are produced from the myxobacterium Sorangium cellulosum, which has a 16-h doubling time and produces only milligram-per-liter amounts of epothilone A and epothilone B. Furthermore, genetic manipulation of S. cellulosum is difficult. To produce epothilones in a more genetically amenable and rapidly growing host, we chose the closely related and best-characterized myxobacteria Myxococcus xanthus. We inserted 65.4 kb of S. cellulosum DNA that encompassed the entire epothilone gene cluster into the chromosome of M. xanthus by a series of homologous recombination events. The resulting strain produced epothilones A and B. Construction of a strain that contained a mutation in epoK, the P450 epoxidase, resulted in production of epothilones C and D.
Maximum power point tracking using neural networks for grid-connected photovoltaic system (2005)

This paper proposes a method of maximum power point tracking (MPPT) using neural networks for grid-connected photovoltaic systems. The system is composed of a boost converter and a single-phase inverter connected to a utility grid. The maximum power point tracking control is based on output from neural networks to control a switch of a boost converter. Back-propagation neural networks is utilized as pattern classifier. Back-propagation neural networks is an example of nonlinear layered feed-forward networks. The single phase inverter uses hysteresis current control which provides current with sinusoidal waveform. Therefore, the system is able to deliver energy with low harmonics and high power factor. MPPT using neural networks are simulated and implemented to evaluate performance. Simulation and experimental results are provided for neural networks and fixed duty ratio under the same atmospheric condition. From the simulation and experimental results, neural networks can deliver more power than the conventional controller
Mosquito Cellular Factors and Functions in Mediating the Infectious entry of Chikungunya Virus (2013)

Chikungunya virus (CHIKV) is an arthropod-borne virus responsible for recent epidemics in the Asia Pacific regions. A customized gene expression microarray of 18,760 transcripts known to target Aedes mosquito genome was used to identify host genes that are differentially regulated during the infectious entry process of CHIKV infection on C6/36 mosquito cells. Several genes such as epsin I (EPN1), epidermal growth factor receptor pathway substrate 15 (EPS15) and Huntingtin interacting protein I (HIP1) were identified to be differentially expressed during CHIKV infection and known to be involved in clathrin-mediated endocytosis (CME). Transmission electron microscopy analyses further revealed the presence of CHIKV particles within invaginations of the plasma membrane, resembling clathrin-coated pits. Characterization of vesicles involved in the endocytic trafficking processes of CHIKV revealed the translocation of the virus particles to the early endosomes and subsequently to the late endosomes and lysosomes. Treatment with receptor-mediated endocytosis inhibitor, monodansylcadaverine and clathrin-associated drug inhibitors, chlorpromazine and dynasore inhibited CHIKV entry, whereas no inhibition was observed with caveolin-related drug inhibitors. Inhibition of CHIKV entry upon treatment with low-endosomal pH inhibitors indicated that low pH is essential for viral entry processes. CHIKV entry by clathrin-mediated endocytosis was validated via overexpression of a dominant-negative mutant of Eps15, in which infectious entry was reduced, while siRNA-based knockdown of genes associated with CME, low endosomal pH and RAB trafficking proteins exhibited significant levels of CHIKV inhibition. This study revealed, for the first time, that the infectious entry of CHIKV into mosquito cells is mediated by the clathrin-dependent endocytic pathway.
Reduction of the size of infarction by allopurinol in the ischemic-reperfused canine heart. (1986)

This study was performed to assess the effect of allopurinol in a canine preparation of myocardial infarction. Dogs underwent occlusion of the left circumflex coronary artery for 90 min, followed by reperfusion for 6 hr. Three groups were studied: (1) control, (2) dogs receiving 25 mg/kg allopurinol 18 hr before occlusion and 50 mg/kg 5 min before occlusion, and (3) dogs receiving allopurinol as above plus 5 mg/kg superoxide dismutase over 1 hr beginning 15 min before reperfusion. Infarct size expressed as a percentage of the area at risk was 40 +/- 4 in the control group, 22 +/- 5 in the allopurinol group (p less than .05 vs control), and 17 +/- 4 in the allopurinol plus superoxide dismutase group (p less than .05 vs control). The differences in infarct size were not due to differences in myocardial oxygen supply or demand. Neutrophil superoxide anion production was not altered by allopurinol treatment. The results suggest that myocardial xanthine oxidase may generate oxygen radicals that play a role in myocardial injury due to ischemia and reperfusion.
Optimized Crew Scheduling at Air New Zealand (2001)

The aircrew-scheduling problem consists of two important subproblems: the tours-of-duty planning problem to generate minimum-cost tours of duty (sequences of duty periods and rest periods) to cover all scheduled flights, and the rostering problem to assign tours of duty to individual crew members. Between 1986 and 1999, Air New Zealand staff and consultants in collaboration with the University of Auckland have developed eight application-specific optimization-based computer systems to solve all aspects of the tours-of-duty planning and rostering processes for Air New Zealand's national and international operations. These systems have saved NZ$15,655,000 per year while providing crew rosters that better respect crew members' preferences.
An Experiment-Based Algorithm for Predicting the Partitioning of Unfolded Peptides into Phosphatidylcholine Bilayer Interfaces (2005)

Knowing the partitioning free energy of unfolded polypeptides into membrane interfaces is necessary for understanding membrane protein stability and for designing antimicrobial and other peptides. Experiment-based whole-residue free-energy (hydropathy) scales for amino acids in unfolded peptides, derived from the partitioning of host-guest pentapeptides (Ac-WLXLL) into the interfaces of phosphatidylcholine bilayers and into n-octanol, have been determined by W. C. Wimley, S. H. White, and colleagues [(1996) Nat. Struc. Biol. 3, 842; Wimley, W. C. et al. (1996) Biochemistry 35, 5109]. These scales offer the possibility of computing absolute partitioning free energies of unfolded peptides given only their amino acid sequences. However, the scales are incomplete, because partitioning free energies of N- and C-terminal groups are missing. To complete the scales, we have measured the pH-dependent partitioning of the host-guest pentapeptide variants AcWL-X-LL-NH(2) and WL-X-LL-NH(2) (X = G or W) into palmitoyloleoylphosphatidylcholine (POPC) bilayer interfaces and n-octanol. These measurements, in combination with the earlier ones, lead to hydrophobicity scale values for protonation, deprotonation, or acetylation of the N terminus and protonation, deprotonation, or amidation of the C terminus. A surprising finding is that a charged N terminus has a much smaller effect on bilayer partitioning than a charged C terminus. We present a simple algorithm for computing the absolute partitioning free energies of unfolded peptides into the phosphatidylcholine bilayer interface.
Geodesic Active Contour Based Fusion of Visible and Infrared Video for Persistent Object Tracking (2007)

Persistent object tracking in complex and adverse environments can be improved by fusing information from multiple sensors and sources. We present a new moving object detection and tracking system that robustly fuses infrared and visible video within a level set framework. We also introduce the concept of the flux tensor as a generalization of the 3D structure tensor for fast and reliable motion detection without eigen-decomposition. The infrared flux tensor provides a coarse segmentation that is less sensitive to illumination variations and shadows. The Beltrami color metric tensor is used to define a color edge stopping function that is fused with the infrared edge stopping function based on the grayscale structure tensor. The min fusion operator combines salient contours in either the visible or infrared video and drives the evolution of the multispectral geodesic active contour to refine the coarse initial flux tensor motion blobs. Multiple objects are tracked using correspondence graphs and a cluster trajectory analysis module that resolves incorrect merge events caused by under-segmentation of neighboring objects or partial and full occlusions. Long-term trajectories for object clusters are estimated using Kalman filtering and watershed segmentation. We have tested the persistent object tracking system for surveillance applications and demonstrate that fusion of visible and infrared video leads to significant improvements for occlusion handling and disambiguating clustered groups of objects