gebhart/patrepeval huggingface dataset:
Selecting for Functional Alternative Splices in ESTs (2002)

The expressed sequence tag (EST) collection in dbEST provides an extensive resource for detecting alternative splicing on a genomic scale. Using genomically aligned ESTs, a computational tool (TAP) was used to identify alternative splice patterns for 6400 known human genes from the RefSeq database. With sufficient EST coverage, one or more alternatively spliced forms could be detected for nearly all genes examined. To identify high (>95%) confidence observations of alternative splicing, splice variants were clustered on the basis of having mutually exclusive structures, and sample statistics were then applied. Through this selection, alternative splices expected at a frequency of >5% within their respective clusters were seen for only 17%-28% of genes. Although intron retention events (potentially unspliced messages) had been seen for 36% of the genes overall, the same statistical selection yielded reliable cases of intron retention for <5% of genes. For high-confidence alternative splices in the human ESTs, we also noted significantly higher rates both of cross-species conservation in mouse ESTs and of validation in the GenBank mRNA collection. We suggest quantitative analytical approaches such as these can aid in selecting useful targets for further experimental characterization and in so doing may help elucidate the mechanisms and biological implications of alternative splicing.
A Comprehensive Survey of Multiagent Reinforcement Learning (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Multiagent systems are rapidly finding applications in a variety of domains, including robotics, distributed control, telecommunications, and economics. The complexity of many tasks arising in these domains makes them difficult to solve with preprogrammed agent behaviors. The agents must, instead, discover a solution on their own, using learning. A significant part of the research on multiagent learning concerns reinforcement learning techniques. This paper provides a comprehensive survey of multiagent reinforcement learning (MARL). A central issue in the field is the formal statement of the multiagent learning goal. Different viewpoints on this issue have led to the proposal of many different goals, among which two focal points can be distinguished: stability of the agents' learning dynamics, and adaptation to the changing behavior of the other agents. The MARL algorithms described in the literature aim---either explicitly or implicitly---at one of these two goals or at a combination of both, in a fully cooperative, fully competitive, or more general setting. A representative selection of these algorithms is discussed in detail in this paper, together with the specific issues that arise in each category. Additionally, the benefits and challenges of MARL are described along with some of the problem domains where the MARL techniques have been applied. Finally, an outlook for the field is provided. </para>
Image motion estimation from motion smear-a new computational model (1996)

Motion smear is an important visual cue for motion perception by the human vision system (HVS). However, in image analysis research, exploiting motion smear has been largely ignored. Rather, motion smear is usually considered as a degradation of images that needs to be removed. In this paper, the authors establish a computational model that estimates image motion from motion smear information-"motion from smear". In many real situations, the shutter of the sensing camera must be kept open long enough to produce images of adequate signal-to-noise ratio (SNR), resulting in significant motion smear in images. The authors present a new motion blur model and an algorithm that enables unique estimation of image motion. A prototype sensor system that exploits the new motion blur model has been built to acquire data for "motion-from-smear". Experimental results on images with both simulated smear and real smear, using the authors' "motion-from-smear" algorithm as well as a conventional motion estimation technique, are provided. The authors also show that temporal aliasing does not affect "motion-from-smear" to the same degree as it does algorithms that use displacement as a cue. "Motion-from-smear" provides an additional tool for motion estimation and effectively complements the existing techniques when apparent motion smear is present.
Time domain measurement of the THz refractivity of water vapor (2012)

We report the measurement of the essentially frequency independent refractivity of water vapor from 0.1 to 1 THz, independent of the simultaneous strong THz pulse broadening and absorption. The humidity dependent transit time of THz pulses through a 170 m long round trip path was measured to a precision of 0.1 ps, using a mode-locked laser as an optical clock.
Summation of segmental velocities in the golf swing (1982)

The downswing phase in golf was represented as a double pendulum pivoted at the shoulder joint and hinged at the wrist. The motion of such a pendulum was used to derive a series of equations which were used to describe the instantaneous values of several of the component features of the downswing. Results of this analysis showed that an initial delay in the uncocking of the wrist would allow (a) acceleration of the arm to reach a greater value and (b) the acceleration of the club to be summed with the existing maximum angular acceleration of the proximal segment.
Electrostatic interactions in wild-type and mutant recombinant human myoglobins (1989)

Residue Val68 in human myoglobin has been replaced by Asn, Asp, and Glu with site-directed mutagenesis. Purified proteins were characterized by isoelectric focusing and by absorption, CD, and NMR spectroscopy. These studies demonstrated that Mb is able to tolerate substitution of the buried hydrophobic residue Val68 by Asn, Asp, and Glu. In the metaquo derivatives of the Glu and Asp mutants, the negative charge at residue 68 is stabilized by a favorable Coulombic interaction with the heme iron. In the absence of this interaction, as in the metcyano and ferrous deoxy derivatives, the relatively nonpolar protein interior cannot stabilize an isolated buried negative charge, and the carboxylate is either protonated or stabilized via a salt bridge with the nearby distal histidine. Hence in the Asp and Glu mutant proteins, both reduction and cyanide binding are accompanied by proton uptake by the protein. The apoproteins were prepared and reconstituted with the chlorophyll derivative zinc pyrochlorophyllide a. Absorption and fluorescence spectra were quite similar for wild-type and all mutant proteins reconstituted with this derivative. These results do not support the point charge model for the red shifts observed in the spectra of chlorophylls associated with photosynthetic proteins. From the pH dependence of the absorption spectrum of zinc pyrochlorophyllide a in the Glu mutant, the apparent pKa of the buried glutamate residue was estimated to be 8.9. This increase of 4.4 pH units, over the value for Glu in aqueous solution, provides a measure of the polarity of the protein interior.
ULTRASOUND AND VISUAL EXAMINATION OF WOOD BASED PRODUCTS (2005)

Many pathogenic antibodies in myasthenia gravis (MG) and its animal model, experimental autoimmune MG (EAMG), are directed against the main immunogenic region (MIR) of the acetylcholine receptor (AcChoR). These antibodies are highly conformation dependent; hence, linear peptides derived from native receptor sequences are poor candidates for their immunoneutralization. We employed a phage-epitope library to identify peptide-mimotopes capable of preventing the pathogenicity of the anti-MIR mAb 198. We identified a 15-mer peptide (PMTLPENYFSERPYH) that binds specifically to mAb 198 and inhibits its binding to AcChoR. A 10-fold increase in the affinity of this peptide was achieved by incorporating flanking amino acid residues from the coat protein as present in the original phage library. This extended peptide (AEPMTLPENYFSERPYHPPPP) was constrained by the addition of cysteine residues on both ends of the peptide, thus generating a cyclic peptide that inhibited the binding of mAb 198 to AcChoR with a potency that is three orders of magnitude higher when compared with the parent library peptide. This cyclic peptide inhibited the in vitro binding of mAb 198 to AcChoR and prevented the antigenic modulation of AcChoR caused by mAb 198 in human muscle cell cultures. The cyclic peptide also reacted with several other anti-MIR mAbs and the sera of EAMG rats. In addition, this peptide blocked the ability of mAb 198 to passively transfer EAMG in rats. Further derivatization of the cyclic peptide may aid in the design of suitable synthetic mimotopes for modulation of MG.
Progress in cybernetics and systems research. Vol. XI. Data base design. International Information Systems. Semiotic Systems. Artificial Intelligence. Cybernetics and Philosophy. Special aspects (1982)

This book covers current research topics in six areas. These are data base design, international information systems, semiotic systems, artificial intelligence, cybernetics and philosophy, and special aspects of systems research. 1326 references.
Classes, Databases, and Prediction Methods of Pharmaceutically and Commercially Important Cystine-Stabilized Peptides (2018)

Cystine-stabilized peptides represent a large family of peptides characterized by high structural stability and bactericidal, fungicidal, or insecticidal properties. Found throughout a wide range of taxa, this broad and functionally important family can be subclassified into distinct groups dependent upon their number and type of cystine bonding patters, tertiary structures, and/or their species of origin. Furthermore, the annotation of proteins related to the cystine-stabilized family are under-represented in the literature due to their difficulty of isolation and identification. As a result, there are several recent attempts to collate them into data resources and build analytic tools for their dynamic prediction. Ultimately, the identification and delivery of new members of this family will lead to their growing inclusion into the repertoire of commercial viable alternatives to antibiotics and environmentally safe insecticides. This review of the literature and current state of cystine-stabilized peptide biology is aimed to better describe peptide subfamilies, identify databases and analytics resources associated with specific cystine-stabilized peptides, and highlight their current commercial success.
Difference in Receptor Usage between Severe Acute Respiratory Syndrome (SARS) Coronavirus and SARS-Like Coronavirus of Bat Origin (2007)

Severe acute respiratory syndrome (SARS) is caused by the SARS-associated coronavirus (SARS-CoV), which uses angiotensin-converting enzyme 2 (ACE2) as its receptor for cell entry. A group of SARS-like CoVs (SL-CoVs) has been identified in horseshoe bats. SL-CoVs and SARS-CoVs share identical genome organizations and high sequence identities, with the main exception of the N terminus of the spike protein (S), known to be responsible for receptor binding in CoVs. In this study, we investigated the receptor usage of the SL-CoV S by combining a human immunodeficiency virus-based pseudovirus system with cell lines expressing the ACE2 molecules of human, civet, or horseshoe bat. In addition to full-length S of SL-CoV and SARS-CoV, a series of S chimeras was constructed by inserting different sequences of the SARS-CoV S into the SL-CoV S backbone. Several important observations were made from this study. First, the SL-CoV S was unable to use any of the three ACE2 molecules as its receptor. Second, the SARS-CoV S failed to enter cells expressing the bat ACE2. Third, the chimeric S covering the previously defined receptor-binding domain gained its ability to enter cells via human ACE2, albeit with different efficiencies for different constructs. Fourth, a minimal insert region (amino acids 310 to 518) was found to be sufficient to convert the SL-CoV S from non-ACE2 binding to human ACE2 binding, indicating that the SL-CoV S is largely compatible with SARS-CoV S protein both in structure and in function. The significance of these findings in relation to virus origin, virus recombination, and host switching is discussed.
Transforming Students' Inquiry Skills with Computer-Based Simulations (2008)

The application of web-based learning environment “Young Scientist” (http://bio.edu.ee/noor) in developing the 6th grade students’ inquiry skills (aged 10-12) was studied. The main objectives have been to evaluate the development of students’ inquiry skills and how the development of these skills depends on their pre-skills. 302 students all over Estonia solved three problems in the following topics: “The Production of Plants”, “The Fertilization of Plants”, and “The Biological Control of Plant-hazardous Insects”. According to the results of the pre- and post-test their skills of formulating problems, research questions, and hypotheses, planning and conducting investigations, analyzing data, and skills of making inferences developed statistically significantly. Spearman correlation demonstrated that the highest development occurred among the students with initial low level of inquiry skills. The only exception was found in the case of formulating research questions since more advanced pre-skills led to higher development.
Handwritten Character Recognition by Alternately Trained Relaxation Convolutional Neural Network (2014)

Deep learning methods have recently achieved impressive performance in the area of visual recognition and speech recognition. In this paper, we propose a hand- writing recognition method based on relaxation convolutional neural network (R-CNN) and alternately trained relaxation convolutional neural network (ATR-CNN). Previous methods regularize CNN at full-connected layer or spatial-pooling layer, however, we focus on convolutional layer. The relaxation convolution layer adopted in our R-CNN, unlike traditional convolutional layer, does not require neurons within a feature map to share the same convolutional kernel, endowing the neural network with more expressive power. As relaxation convolution sharply increase the total number of parameters, we adopt alternate training in ATR-CNN to regularize the neural network during training procedure. Our previous C- NN took the 1st place in ICDAR'13 Chinese Handwriting Character Recognition Competition, while our latest ATR-CNN outperforms our previous one and achieves the state-of-the-art accuracy with an error rate of 3.94%, further narrowing the gap between machine and human observers (3.87%).
Expression of the gene encoding protein A in Staphylococcus aureus and coagulase-negative staphylococci (1984)

Two shuttle vectors containing the gene for protein A (spa) from Staphylococcus aureus have been constructed to study expression of the gene in various strains of S. aureus and in the coagulase-negative species Staphylococcus epidermidis, Staphylococcus capitis, and Staphylococcus xylosus. One plasmid, pSPA15, contains the complete structural gene for protein A, which binds to the cell wall in various Staphylococcus species. The other plasmid, pSPA16, codes for a truncated protein A lacking the C-terminal part called region X. The latter is exclusively extracellular in all Staphylococcus species tested, which confirms the importance of region X for cell wall binding. The expression of the plasmid-coded protein A in various strains of S. aureus is strongly correlated to the expression of the chromosomal spa gene. The coagulase-negative species expressing plasmid-encoded protein A produce 12 to 30% of the amount coded by the chromosomal spa gene in S. aureus strains Cowan I and A676.
Evaluation of visual fatigue during VDT tasks (2002)

This study was designed to evaluate visual fatigue induced during VDT tasks using newly developed equipment that can simultaneously measure pupillary change, focal accommodation and eye movement. The changes in these three physiological measures, taken during a VDT task, were used to propose an index for evaluating visual fatigue. Through multiple regression analysis, an index to describe the psychological sense of visual fatigue was obtained. In this index, the minimum pupil diameter, velocity of focal accommodation for constriction, and width of focal accommodation were included. The results showed that visual fatigue resulting from a VDT task includes not one factor but multiple factors. The index shows that visual fatigue in VDT tasks can be evaluated effectively using both pupil diameter and focal accommodation. This index enables us to assess visual fatigue induced during a VDT task.
Neue Lokalanästhetika (1959)

Abstract The mixed anhydride method has been used successfully in the synthesis of a series of pyridinecarboxamides. Hydrogenation of some of these products furnished piperidinecarboxarnides which were found to possess excellent local anesthetic properties and low toxicities.
Scavenging of Hydroxyl Radicals by Ceria Nanoparticles: Effect of Particle Size and Concentration (2016)

The most commonly used proton exchange membranes (PEMs) for hydrogen and direct methanol fuel cells are the perfluorosulfonic acid ionomers (PFSA) such as Nafion, which are based on a Teflon-like backbone with side chains containing sulfonic groups. These materials exhibit good mechanical, chemical, and thermal stability in both oxidative and reductive media; however, the fuel cell is a reactor with strong oxidizing power, capable of reducing the durability of the PEMs. The centrality of hydroxyl radicals, HO·, in the degradation mechanism of PFSA is well documented in numerous papers, including our work. Therefore, membrane durability remains a critical issue for further development of fuel cell applications. We present the use of ceria nanoparticles (NPs) for mitigating the chemical degradation process and describe their effectiveness for scavenging hydroxyl radicals as a function of their size and concentrations. The hydroxyl radicals were generated by UV-irradiation of hydrogen peroxide, and the radicals were detected by spin trapping electron spin resonance (ESR) with 5,5-dimethyl-1-pyrroline-N-oxide (DMPO) as the spin trap. The size of the ceria NPs was in the range 7.1–14.7 nm, as determined by X-ray diffraction (XRD), and the molar concentration of ceria was varied between 0 and 200 μM. The ESR results indicated that larger NPs are more effective scavengers of the HO· radicals. Transmission electron microscopy (TEM) data measured in the scanning TEM (STEM) mode showed pronounced agglomeration of the smaller NPs. Consideration of both TEM and ESR results suggests that the agglomerated particles do not contribute fully to radical scavenging. This conclusion is due to the short diffusion distances of short-lived species such as hydroxyl radicals, typically 4–6 nm, compared to 10–20 nm for stable species. The results of this study indicated that scavenging of hydroxyl radicals is more effective for larger NPs.
The CU Airborne MAX-DOAS instrument: vertical profiling of aerosol extinction and trace gases (2013)

Abstract. The University of Colorado Airborne Multi-Axis Differential Optical Absorption Spectroscopy (CU AMAX-DOAS) instrument uses solar stray light to detect and quantify multiple trace gases, including nitrogen dioxide (NO2), glyoxal (CHOCHO), formaldehyde (HCHO), water vapor (H2O), nitrous acid (HONO), iodine monoxide (IO), bromine monoxide (BrO), and oxygen dimers (O4) at multiple wavelengths (absorption bands at 360, 477, 577, 632 nm) simultaneously in the open atmosphere. The instrument is unique as it (1) features a motion compensation system that decouples the telescope field of view from aircraft movements in real time (<0.35° accuracy), and (2) includes measurements of solar stray light photons from nadir, zenith, and multiple elevation angles forward and below the plane by the same spectrometer/detector system. Sets of solar stray light spectra collected from nadir to zenith scans provide some vertical profile information within 2 km above and below the aircraft altitude, and the vertical column density (VCD) below the aircraft is measured in nadir view. Maximum information about vertical profiles is derived simultaneously for trace gas concentrations and aerosol extinction coefficients over similar spatial scales and with a vertical resolution of typically 250 m during aircraft ascent/descent. The instrument is described, and data from flights over California during the CalNex (California Research at the Nexus of Air Quality and Climate Change) and CARES (Carbonaceous Aerosols and Radiative Effects Study) air quality field campaigns is presented. Horizontal distributions of NO2 VCD (below the aircraft) maps are sampled with typically 1 km resolution, and show good agreement with two ground-based MAX-DOAS instruments (slope = 0.95 ± 0.09, R2 = 0.86). As a case study vertical profiles of NO2, CHOCHO, HCHO, and H2O concentrations and aerosol extinction coefficients, ε, at 477 nm calculated from O4 measurements from a low approach at Brackett airfield inside the South Coast Air Basin (SCAB) are presented. These profiles contain ~12 degrees of freedom (DOF) over a 3.5 km altitude range, an independent information approximately every 250 m. The boundary layer NO2 concentration, and the integral aerosol extinction over height (aerosol optical depth, AOD) agrees well with nearby ground-based in situ NO2 measurement, and AERONET station. The detection limits of NO2, CHOCHO, HCHO, H2O442, &amp;varepsilon;360, &amp;varepsilon;477 for 30 s integration time spectra recorded forward of the plane are 5 ppt, 3 ppt, 100 ppt, 42 ppm, 0.004 km−1, 0.002 km−1 in the free troposphere (FT), and 30 ppt, 16 ppt, 540 ppt, 252 ppm, 0.012 km−1, 0.006 km−1 inside the boundary layer (BL), respectively. Mobile column observations of trace gases and aerosols are complimentary to in situ observations, and help bridge the spatial scales that are probed by satellites and ground-based observations, and predicted by atmospheric models.
Droplet and particle manipulation in emulsions and suspensions using 3D electro-osmotic micropumps (2008)

This paper presents investigations on droplet and particle manipulation in microfiuidic channels realized in SU-8/glass technology, which is based on a competitive interplay of viscous drag, gravitational, buoyancy and dielectrophoretic forces. The latter are induced by alternating current (AC) driven three-dimensional (3D) stepped electrode arrays in the channel, enabling so called 3D AC electro-osmotic pumping, as it has been proposed recently. Due to size- and density-dependent differences in polarizability, targeted particles resp. droplets in the fluid stream can be slowed down or even pinned above the electrode structures by adjusting the operation parameters of the pump. Hence the presented device can be utilized for simultaneous pumping and manipulation of droplets and particles in emulsions and suspensions.
High-T/sub c/ superconducting magnets based on thick film arrangements (1993)

High-T/sub c/ superconducting magnets built with Y-Ba-Cu-O or Bi(Pb)-Sr-Ca-Cu-O thick films are discussed. Critical current densities of the samples prepared by an oxalate route are between 7000 and 23000 A/cm/sup 2/ at helium temperatures depending on the details of the preparation. The self-magnetic field of the individual layer rings are 0.5-1.7 mT which can produce field strength of the magnets of 55-178 mT, corresponding to the experimental critical currents. If the specimens of oxide-nitrate reactions can provide critical current densities of 5000-15000 A/cm/sup 2/ at nitrogen temperatures they lead to the number of ampere-turns of 550-22500 A/cm and magnetic field intensity of 69 mT -2.82 T. Since the applicable techniques of the film preparation are very flexible concerning the shape and size of the products, magnetic field profiles of different character can be obtained for various purposes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>