gebhart/patrepeval huggingface dataset:
Signal-exon trap: a novel method for the identification of signal sequences from genomic DNA (2000)

We describe a genomic DNA-based signal sequence trap method, signal-exon trap (SET), for the identification of genes encoding secreted and membrane-bound proteins. SET is based on the coupling of an exon trap to the translation of captured exons, which allows screening of the exon-encoded polypeptides for signal peptide function. Since most signal sequences are expected to be located in the 5′-terminal exons of genes, we first demonstrate that trapping of these exons is feasible. To test the applicability of SET for the screening of complex genomic DNA, we evaluated two critical features of the method.Specificity was assessed by the analysis of random genomic DNA and efficiency was demonstrated by screening a 425 kb YAC known to contain the genes of four secretory or membrane-bound proteins. All trapped clones contained a translation initiation signal followed by a hydrophobic stretch of amino acids representing either a known signal peptide, transmembrane domain or novel sequence. Our results suggest that SET is a potentially useful method for the isolation of signal sequence-containing genes and may find application in the discovery of novel members of known secretory gene clusters, as well as in other positional cloning approaches.
Use of Modal Sensitivity to Operating Conditions for Damping Control in Power Systems (2011)

Small signal stability is an inherent characteristic of dynamic systems such as power systems. Pole positioning through power system stabilizers (PSS) is often used for improving damping in power systems. A well-designed PSS can be very effective in damping oscillations, especially local oscillations. However, designing PSSs for inter-area oscillations has been a very challenging task due to time-varying operating conditions affecting the oscillations. This paper explores the sensitivity relationship between oscillations and operating conditions, and employs the relationship to derive recommendations for operator's actions to adjust operating conditions for improving damping. Low damping is usually considered to be a result of heavy power transfer in long distance, while specific locations also have significant impact on damping of oscillations. Therefore, it is important to consider locations in deriving recommendations. This paper proposes the concept of relative modal sensitivity and presents its application in deriving recommendations for operator's action in damping control.
Simple, pulsed, electron beam gun (1977)

The construction of a simple, inexpensive electron beam gun is described. The pulsed power supply consists of a homemade spiral generator, constructed with aluminum and vinyl pressure-sensitive tapes, which is switched into the electron beam gun with a spark gap. The electron beam gun itself consists of a vacuum diode with a cold carbon cathode. From an inital charge voltage of 12 kV, the apparatus produces a 10-A beam of 100-keV electrons having a pulse duration of about 7 nsec and diameter of 6 mm.
Humor Recognition Using Deep Learning (2018)

Peng-Yu Chen, Von-Wun Soo. Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 2 (Short Papers). 2018.
Uniformity Masks Design Method Based on the Shadow Matrix for Coating Materials with Different Condensation Characteristics (2013)

An intuitionistic method is proposed to design shadow masks to achieve thickness profile control for evaporation coating processes. The proposed method is based on the concept of the shadow matrix, which is a matrix that contains coefficients that build quantitive relations between shape parameters of masks and shadow quantities of substrate directly. By using the shadow matrix, shape parameters of shadow masks could be derived simply by solving a matrix equation. Verification experiments were performed on a special case where coating materials have different condensation characteristics. By using the designed mask pair with complementary shapes, thickness uniformities of better than 98% are demonstrated for MgF₂ (m = 1) and LaF₃ (m = 0.5) simultaneously on a 280 mm diameter spherical substrate with the radius curvature of 200 mm.
Bioconversion of Beetle-Killed Lodgepole Pine Using SPORL: Process Scale-up Design, Lignin Coproduct, and High Solids Fermentation without Detoxification (2013)

Mountain pine beetle killed Lodgepole pine (Pinus contorta Douglas ex Loudon) wood chips were pretreated using an acidic sulfite solution of approximately pH = 2.0 at a liquor to wood ratio of 3 and sodium bisulfite loading of 8 wt % on wood. The combined hydrolysis factor (CHF), formulated from reaction kinetics, was used to design a scale-up pretreatment on 2000 g wood chips at a relatively low temperature of 165 C that reduced furan formation and facilitated high solids saccharification and fermentation. The pretreated solids and liquor were disk milled together to result in a biomass whole slurry of 25% total solids. The whole biomass slurry was directly used to conduct simultaneous enzymatic saccharification and combined fermentation (SSCombF) using a commercial cellulase and Saccharomyces cerevisiae YRH400 without detoxification. A terminal ethanol titer of 47.1 g L-1 with a yield of 306 L (tonne wood)-1, or 72.0% theoretical, was achieved when SSCombF was conducted at an unwashed solids loading of 18%. The lignosulfonate (LS) from SPORL was highly sulfonated and showed better dispersibility than a high purity commercial softwood LS, and therefore has potential as a directly marketable coproduct.
Using signals scattered from diffuse inhomogeneities to correct for phase aberrations caused by a phase-screen far from the transducer (2002)

The phase and the amplitude of an acoustical wave will be disturbed if the wave propagates through human tissue. These distortions reduce the quality of medical ultrasound images. Several scientists have suggested methods to do corrections. So far, all presented methods have at least one important weakness. The methods based on time delay focusing do not correct well for distortions caused by phase aberrations introduced far from the transducer. The time reversal mirror (TRM) method does not have this limitation, but it needs a point scatterer to reflect the emitted wave. In this paper, a way to combine the best of the two methods are presented. The suggested method is based on delay and amplitude focusing (DAF).
Fast Binding Kinetics and Conserved 3D Structure Underlie the Antagonistic Activity of Mutant TNF: Useful Information for Designing Artificial Proteo-Antagonists (2009)

Tumour necrosis factor (TNF) is an important cytokine that induces an inflammatory response predominantly through the TNF receptor-1 (TNFR1). A crucial strategy for the treatment of many autoimmune diseases, therefore, is to block the binding of TNF to TNFR1. We previously identified a TNFR1-selective antagonistic mutant TNF (R1antTNF) from a phage library containing six randomized amino acid residues at the receptor-binding site (amino acids 84-89). Two R1antTNFs, R1antTNF-T2 (A84S, V85T, S86T, Y87H, Q88N and T89Q) and R1antTNF-T8 (A84T, V85P, S86A, Y87I, Q88N and T89R), were successfully isolated from this library. Here, we analysed R1antTNF-T8 using surface plasmon resonance spectroscopy and X-ray crystallography to determine the mechanism underlying the antagonistic activity of R1antTNF. The kinetic association/dissociation parameters of R1antTNF-T8 were higher than those of wild-type TNF, indicating more rapid bond dissociation. X-ray crystallographic analysis suggested that the binding mode of the T89R mutation changed from a hydrophobic to an electrostatic interaction, which may be responsible for the antagonistic behaviour of R1antTNF. Knowledge of these structure-function relationships will facilitate the design of novel TNF inhibitors based on the cytokine structure.
The Ravenscar Group: A coeval analogue for the Middle Jurassic reservoirs of the North Sea and offshore Mid-Norway (2005)

In recent years the application of biostratigraphy to hydrocarbon exploration and development has become increasingly important both scientifically and economically. The demand for higher stratigraphical resolution in field development studies has resulted in the utilization of new approaches. However, in under-explored areas with little reliable primary biostratigraphical data, conventional methods using relatively coarse biozonations still have relevance. The aim of this volume is to encourage an exchange of ideas and to seed new research initiatives particularly within integrated multidisciplinary teams. The papers are divided into four main themes which cover a broad range of modern applications of biostratigraphy. The first three themes are: UK North Sea field development; outcrop analogues; and international exploration and development. The final section discusses new methodologies, such as the application of correspondence analysis and multivariate correlation of wells, and palynological processing techniques applicable to the wellsite.
Center driven winder basics for the rubber industry (2002)

This paper presents the basic considerations for the design of center driven winders used in the rubber industry. The subject is presented in a step by step thought process to try to help a person understand the basics and how to modify the controls to meet specific requirements. The paper was designed as a teaching tool to help new engineers who have never worked on winders.
Wireless Medium-Access Control Protocols (2008)

A MAC protocol is used to address resolving potential contention and collision when the communication medium is used. Many MAC protocols have been proposed for wireless networks (e.g., Bharghavan et al., 1994; Fullmer, 1998; Fullmer and Garcia-Luna-Aceves, 1995; Garcia-Luna-Aceves and Tzamaloukas, 1999; Garcias and Garcia-Luna-Aceves, 1996; Lin and Gerla, 1997b; Lu et al., 1999; Vaidya et al., 2000), which often assume a common channel shared by mobile hosts.
ChemInform Abstract: ORGANIC SULFUR MECHANISMS. 18. THE SULFO‐COPE REARRANGEMENT AND OTHER THERMAL L REACTIONS OF UNSATURATED SULFONYL SPECIES (1976)

Abstract Die Sulfone (I) lagern sich beim Erhitzen in Pyridin‐Äthanol im geschlossenen Rohr in die Sulfonate (II) um.
Thermal management using "dry" phase change material (2003)

The thermal response characteristic of a hybrid cooler that is charged with a "dry" solid-solid phase change compound is evaluated. A mathematical model that simulates the performance of a cooler/heat storage unit is formulated. A prototype heat sink that incorporates heat storage using a "dry" PCM is tested, and used to benchmark the simulation model. Different heating and cooling strategies are evaluated and a figure of merit characteristic of the cooler/PCM under development is introduced.
<i>P</i> -wave reflection coefficients for transversely isotropic models with vertical and horizontal axis of symmetry (1997)

Abstract The study of P-wave reflection coefficients in anisotropic media is important for amplitude variation with offset (AVO) analysis. While numerical evaluation of the reflection coefficient is straightforward, numerical solutions do not provide analytic insight into the influence of anisotropy on the AVO signature. To overcome this difficulty, I present an improved approximation for P-wave reflection coefficients at a horizontal boundary in transversely isotropic media with vertical axis of symmetry (VTI media). This solution has the same AVO-gradient term describing the low-order angular variation of the reflection coefficient as the equations published previously, but is more accurate for large incidence angles. The refined approximation is then extended to transverse isotropy with a horizontal axis of symmetry (HTI), which is caused typically by a system of vertical cracks. Comparison of the approximate reflection coefficients for P-waves incident in the two vertical symmetry planes of HTI media indicates that the azimuthal variation of the AVO gradient is a function of the shear-wave splitting parameter γ, and the anisotropy parameter describing P-wave anisotropy for nearvertical propagation in the vertical plane containing the symmetry axis.
Optical vortices evolving from helicoidal integer and fractional phase steps (2004)

The evolution of a wave starting at z = 0a s exp(iαφ) (0 φ 0as trength n optical vortex, whose neighbourhood is described in detail. Far from the axis, the wave is the sum of exp{i(αφ + kz)} and a diffracted wave from r = 0. The paraxial wave and the wave far from the vortex are incorporated into a uniform approximation that describes the wave with high accuracy, even well into the evanescent zone. For fractional α ,n o fractional-strength vortices can propagate; instead, the interferenc eb etween an additional diffracted wave, from the phase step discontinuity, with exp{i(αφ + kz)} and the wave scattered from r = 0, generates a pattern of strength-1 vortex lines, whose total (signed) strength Sα is the nearest integer to α .F or small|α − n| ,t heselines are close t ot hez axis. As α passes n +1 /2, Sα jumps by unity, so a vortex is born. The mechanism involves an infinite chain of alternating-strength vortices close to the positive x axis for α = n +1 /2, which annihilate in pairs differently when α> n +1 / 2a nd when α< n +1 /2. There is a partial analogy between α and the quantum flux in the Aharonov–Bohm effect.
Ranking music data by relevance and importance (2008)

Due to the rapidly increasing availability of audio files on the Web, it is relevant to augment search engines with advanced audio search functionality. In this context, the ranking of the retrieved music is an important issue. This paper proposes a music ranking method capable of flexibly fusing the music based on its relevance and importance. The fusion is controlled by a single parameter, which can be intuitively tuned by the user. The notion of authoritative music among relevant music is introduced, and social media mined from the Web is used in an innovative manner to determine both the relevance and importance of music. The proposed method may support users with diverse needs when searching for music.
A comparison of headache and non-headache sufferers on measures of social support and mental health problems. (2008)

138 headaches sufferers and 138 subjects without headaches were studied to investigate if there were differences between headache and non-headache sufferers in terms of their mental health and social support levels. The overall results of this study indicated that headache sufferers, as compared with non-headache sufferers had slightly more mental health problems, and more social support from their family members. When the results were scrutinised in more detail, it was observed that headache sufferers reported that they felt less capable of making decisions about things, were not always able to face up to their problems, and sometimes thought about themselves as a worthless. Given that the study was based on a community, rather than clinic sample, further research would be required to examine the differing the types of headaches that people are suffering from, and the intensity of the headaches, in relation to mental health problems.
Zidovudine‐induced mitochondrial myopathy is associated with muscle carnitine deficiency and lipid storage (1994)

The use of zidovudine (AZT) for the treatment of acquired immunodeficiency syndrome (AIDS) induces a DNA-depleting mitochondrial myopathy, which is histologically characterized by the presence of muscle fibers with "ragged-red"-like features, red-rimmed or empty cracks, granular degeneration, and rods (AZT fibers). Because dysfunctioning muscle mitochondria may lead to defects of beta-oxidation of fatty acids, we examined the degree of neutral fat accumulation and muscle carnitine levels in the muscle biopsy specimens from 21 patients with AZT-induced myopathic symptoms of varying severity. Six patients with no AZT fibers had normal endomyofibrillar lipid deposits and muscle carnitine levels; 7 patients with fewer than 5 AZT fibers per field had a mild (+) to moderate (++) increase in lipid droplets, and reduced muscle carnitine levels (3 patients); and 8 patients with more than 5 AZT fibers had severe muscle changes, a ++ to marked ( ) increase in lipid droplets, and reduced muscle carnitine levels (6 patients). Serial sections showed lipid globules often within "cracks" or vacuoles of the abnormal muscle fibers. We conclude that the muscle mitochondrial impairment caused by AZT results in (1) accumulation of lipid within the muscle fibers owing to poor utilization of long-chain fatty acids, (2) reduction of muscle carnitine levels probably due to decreased carnitine uptake by the muscle, and (3) depletion of energy stores within the muscle fibers. The findings may have potential therapeutic implications in the treatment of AZT-induced myopathic symptoms using oral carnitine supplementation.
Electronic states of the pristine and alkali-metal-intercalated monolayer graphite/Ni(111) systems (1994)

The electronic states of the pristine and alkali-metal-intercalated monolayer graphite (MG)/Ni(111) systems are investigated by using angle-resolved ultraviolet photoelectron spectroscopy and x-ray-photoelectron spectroscopy (XPS). The electronic structure of the MG is modified largely by hybridization of the \ensuremath{\pi} orbitals of the graphite layer with the d orbitals of the substrate. The deposition of alkali-metal atoms onto the graphite overlayer at room temperature results in the penetration of the adsorbates into the interface between the MG and the Ni(111) surface. This intercalation causes the change in the band structure of the system because of the dilation of the MG-Ni interlayer distance. The intercalation of the alkali-metal atoms also shows the broadening of the XPS peak of the C 1s core level of the MG.
Selection of Column Dimensions and Gradient Conditions to Maximize the Peak-Production Rate in Comprehensive Off-Line Two-Dimensional Liquid Chromatography Using Monolithic Columns (2010)

The peak-production rate (peak capacity per unit time) in comprehensive off-line two-dimensional liquid chromatography (LC/x/LC) was optimized for the separation of peptides using poly(styrene-co-divinylbenzene) monolithic columns in the reversed-phase (RP) mode. A first-dimension ((1)D) separation was performed on a monolithic column operating at a pH of 8, followed by sequential analysis of all the (1)D fractions on a monolithic column operating at a pH of 2. To obtain the highest peak-production rate, effects of column length, gradient duration, and sampling time were examined. RP/x/RP was performed at undersampling conditions using a short 10 min (1)D gradient. The peak-production rate was highest using a 50 mm long (2)D column applying an 8-10 min (2)D gradient time and was almost a factor of two higher than when a 250 mm monolithic column was used. The best way to obtain a higher peak-production rate in off-line LC/x/LC proved to be an increase in the number of (1)D fractions collected. Increasing the (2)D gradient time was less effective. The potential of the optimized RP/x/RP method is demonstrated by analyzing proteomics samples of various complexities. Finally, the trade-off between peak capacity and analysis time is discussed in quantitative terms for both one-dimensional RP gradient-elution chromatography and the off-line two-dimensional (RP/x/RP) approach. At the conditions applied, the RP/x/RP approach provided a higher peak-production rate than the (1)D-LC approach when collecting three (1)D fractions, which corresponds to a total analysis time of 60 min.
Study of Bone Marrow and Embryonic Stem Cell-Derived Human Mesenchymal Stem Cells for Treatment of<i>Escherichia coli</i>Endotoxin-Induced Acute Lung Injury in Mice (2015)

To determine the optimal source of mesenchymal stem cells (MSCs) for cell-based therapy for acute lung injury, bone marrow (BM)- and embryonic stem cell-derived human MSC (ES-MSCs) were compared as therapeutic agents for Escherichia coli endotoxin-induced lung injury in mice. ES-MSCs behaved similarly to BM-MSCs by markedly decreasing the inflammatory response induced by endotoxin. However, unlike BM-MSCs, ES-MSCs provided no protective effects against increasing lung water and protein permeability, in part because of an increase in expression of matrix metallopeptidase 9 by ES-MSCs. In patients with acute respiratory distress syndrome, impaired alveolar fluid clearance (i.e., no resolution of pulmonary edema fluid) has been associated with higher mortality rates. Although ES-MSCs might ultimately be found to have properties superior to those of BM-MSCs, such as for immunomodulation, these results highlight the need for a disease-specific potency assay for stem cell-based therapy.
Ion-channel assembly. (1995)

Transmembrane ion channels regulate the movement of ions (particularly Na+, K+, Ca2+ and Cl-) across cellular membranes, and are critical to numerous aspects of neurobiology. Cells express a diverse array of ion-channel proteins that vary widely in their ion selectivity and in their modulation by ligands (such as neurotransmitters) or by membrane voltage. Most ion channels are multisubunit proteins and, as such, undergo an intricate series of post-translational folding, modification and oligomerization events to achieve their correct functional quaternary structure. The means by which the cell is able to accomplish this complex process of ion-channel assembly is a topic that is beginning to be addressed experimentally.
Control over Catenation in Metal−Organic Frameworks via Rational Design of the Organic Building Block (2009)

Metal-organic frameworks (MOFs), a hybrid class of materials comprising inorganic nodes and organic struts, have potential application in many areas due to their high surface areas and uniform pores and channels. One of the key challenges to be overcome in MOF synthesis is the strong propensity for catenation (growth of multiple independent networks within a given crystal), as catenation reduces cavity sizes and diminishes porosity. Here we demonstrate that rational design of organic building blocks, which act as strut-impervious scaffolds, can be exploited to generate highly desired noncatenated materials in a controlled fashion.
A Neural Network Method for Detection of Obstructive Sleep Apnea and Narcolepsy Based on Pupil Size and EEG (2008)

Electroencephalogram (EEG) is able to indicate states of mental activity ranging from concentrated cognitive efforts to sleepiness. Such mental activity can be reflected by EEG energy. In particular, intrusion of EEG theta wave activity into the beta activity of active wakefulness has been interpreted as ensuing sleepiness. Pupil behavior can also provide information regarding alertness. This paper develops an innovative signal classification method that is capable of differentiating subjects with sleep disorders which cause excessive daytime sleepiness (EDS) from normal control subjects who do not have a sleep disorder based on EEG and pupil size. Subjects with sleep disorders include persons with untreated obstructive sleep apnea (OSA) and narcolepsy. The Yoss pupil staging rule is used to scale levels of wakefulness and at the same time theta energy ratios are calculated from the same 2-s sliding windows by Fourier or wavelet transforms. Then, an artificial neural network (NN) of modified adaptive resonance theory (ART2) is utilized to identify the two groups within a combined group of subjects including those with OSA and healthy controls. This grouping from the NN is then compared with the actual diagnostic classification of subjects as OSA or controls and is found to be 91% accurate in differentiating between the two groups. The same algorithm results in 90% correct differentiation between narcoleptic and control subjects.