gebhart/patrepeval huggingface dataset:
Structural approaches to protein sequence analysis (1993)

Various protein sequence analysis techniques are described, aimed at improving the prediction of protein structure by means of pattern matching. To investigate the possibility that improvements in amino acid comparison matrices could result in improvements in the sensitivity and accuracy of protein sequence alignments, a method for rapidly calculating amino acid mutation data matrices from large sequence data sets is presented. The method is then applied to the membrane-spanning segments of integral membrane proteins in order to investigate the nature of amino acid mutability in a lipid environment. Whilst purely sequence analytic techniques work well for cases where some residual sequence similarity remains between a newly characterized protein and a protein of known 3-D structure, in the harder cases, there is little or no sequence similarity with which to recognize proteins with similar folding patterns. In the light of these limitations, a new approach to protein fold recognition is described, which uses a statistically derived pairwise potential to evaluate the compatibility between a test sequence and a library of structural templates, derived from solved crystal structures. The method, which is called optimal sequence threading, proves to be highly successful, and is able to detect the common TIM barrel fold between a number of enzyme sequences, which has not been achieved by any previous sequence analysis technique. Finally, a new method for the prediction of the secondary structure and topology of membrane proteins is described. The method employs a set of statistical tables compiled from well-characterized membrane protein data, and a novel dynamic programming algorithm to recognize membrane topology models by expectation maximization. The statistical tables show definite biases towards certain amino acid species on the inside, middle and outside of a cellular membrane.
Inheritance of Labdanoid Producing Ability in<i>Nicotiana tabacum</i> (1980)

Journal Article Inheritance of Labdanoid Producing Ability in Nicotiana tabacum Get access Hideyuki Tomita, Hideyuki Tomita Utsunomiya Tobacco Experiment Station, The Japan Tobacco and Salt Public Corporation, 1900 Idei, Oyama, Tochigi 323, Japan Search for other works by this author on: Oxford Academic Google Scholar Masayoshi Sato, Masayoshi Sato Utsunomiya Tobacco Experiment Station, The Japan Tobacco and Salt Public Corporation, 1900 Idei, Oyama, Tochigi 323, Japan Search for other works by this author on: Oxford Academic Google Scholar Nobumaro Kawashima Nobumaro Kawashima Utsunomiya Tobacco Experiment Station, The Japan Tobacco and Salt Public Corporation, 1900 Idei, Oyama, Tochigi 323, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 44, Issue 10, 1 October 1980, Pages 2517–2518, https://doi.org/10.1080/00021369.1980.10864358 Published: 01 October 1980 Article history Received: 09 June 1980 Published: 01 October 1980
Morphine augmentation increases gallbladder visualization in patients pretreated with cholecystokinin. (1997)

Hepatobiliary imaging with CCK pretreatment and imaging for 90 min was insufficient to identify all patent cystic ducts. Morphine augmentation significantly increased the frequency of gallbladder visualization in patients pretreated with CCK.
Characterizing and Evaluating Fraud in Electronic Transactions (2012)

The volume of electronic transactions has raised a lot in last years, mainly due to the popularization of ecommerce, such as online retailers. We also observe a significant increase in the number of fraud cases, resulting in billions of dollars losses each year worldwide. Therefore it is important and necessary to developed and apply techniques that can assist in fraud detection, which motivates our research. This work aims to apply and evaluate computational intelligence techniques to identify fraud in electronic transactions, more specifically in credit card operations. In order to evaluate the techniques, we define a concept of economic efficiency and apply them in a actual dataset of the most popular Brazilian electronic payment service. Our results show good performance in fraud detection, presenting gains up to 43 percent compared to the actual scenario of the company.
Soil Moisture Estimation Using Thermal Inertia: Potential and Sensitivity to Data Conditions (2011)

Abstract Thermal inertia retrieval using a thermal infrared remote sensing technique has been examined as a possible method for estimating soil moisture. This method is an application of the theory that thermal inertia highly correlates with soil water content. This study shows a method for retrieving thermal inertia from a heat budget model of the earth’s surface using radiative surface temperatures, insolation, and meteorological data observed in field experiments. In bare to sparsely vegetated areas, this method has the potential to estimate subsurface soil moisture with a precision of ±3%–4% of the daily volumetric soil moisture content at a significance level of 5%, which is enough to roughly classify thermal inertia estimates into a few levels of soil moisture (e.g., wet, middle, and dry). The analysis also includes an examination of the practical performance of the thermal inertia estimation according to the temporal resolution of the data, assuming the use of satellite and routine meteorological data. It is found that the following combination of data can achieve the precision given above: radiative surface temperature from geostationary/multiple polar orbiting satellites, insolation retrieved from geostationary satellite data, and routine meteorological data.
Nature-Inspired Metaheuristic Algorithms (2008)

Modern metaheuristic algorithms such as bee algorithms and harmony search start to demonstrate their power in dealing with tough optimization problems and even NP-hard problems. This book reviews and introduces the state-of-the-art nature-inspired metaheuristic algorithms in optimization, including genetic algorithms, bee algorithms, particle swarm optimization, simulated annealing, ant colony optimization, harmony search, and firefly algorithms. We also briefly introduce the photosynthetic algorithm, the enzyme algorithm, and Tabu search. Worked examples with implementation have been used to show how each algorithm works. This book is thus an ideal textbook for an undergraduate and/or graduate course. As some of the algorithms such as the harmony search and firefly algorithms are at the forefront of current research, this book can also serve as a reference book for researchers.
<i>Atoh1</i> null mice show directed afferent fiber growth to undifferentiated ear sensory epithelia followed by incomplete fiber retention (2005)

Inner ear hair cells have been suggested as attractors for growing afferent fibers, possibly through the release of the neurotrophin brain-derived neurotrophic factor (BDNF). Atoh1 null mice never fully differentiate hair cells and supporting cells and, therefore, may show aberrations in the growth and/or retention of their innervation. We investigated the distribution of cells positive for Atoh1- or Bdnf-mediated beta-galactosidase expression in Atoh1 null and Atoh1 heterozygotic mice and correlated the distribution of these cells with their innervation. Embryonic day (E) 18.5 Atoh1 null and heterozygotic littermates show Atoh1- and BDNF-beta-galactosidase-positive cells in comparable distributions in the canal cristae and the cochlea apex. Atoh1-beta-galactosidase-positive but only occasional Bdnf-beta-galactosidase-positive cells are found in the utricle, saccule, and cochlea base of Atoh1 null mutant mice. Absence of Bdnf-beta-galactosidase expression in the utricle and saccule of Atoh1 null mice is first noted at E12.5, a time when Atoh1-beta-galactosidase expression is also first detected in these epithelia. These data suggest that expression of Bdnf is dependent on ATOH1 protein in some but does not require ATOH1 protein in other inner ear cells. Overall, the undifferentiated Atoh1- and Bdnf-beta-galactosidase-positive cells show a distribution reminiscent of that in the six sensory epithelia in control mice, suggesting that ear patterning processes can form discrete patches of Atoh1 and Bdnf expression in the absence of ATOH1 protein. The almost normal growth of afferent and efferent fibers in younger embryos suggests that neither fully differentiated hair cells nor BDNF are necessary for the initial targeted growth of fibers. E18.5 Atoh1 null mice have many afferent fibers to the apex of the cochlea, the anterior and the posterior crista, all areas with numerous Bdnf-beta-galactosidase-positive cells. Few fibers remain to the saccule, utricle, and the base of the cochlea, all areas with few or no Bdnf-beta-galactosidase-positive cells. Thus, retention of fibers is possible with BDNF, even in the absence of differentiated hair cells.
Interpretation of scattering phenomenology in dielectric-coated wire via joint time-frequency processing (2002)

We carry out a phenomenological study of scattering from dielectric-coated wires. The scattering data are collected by both numerical simulation and by chamber measurement. The short-time Fourier transform (STFT) technique is used to extract the pertinent scattering physics of the structure. The surface wave, or the so-called the Goubau mode, is excited due to the dielectric coating around the wire. The features of this mode are studied and an interpretation of the dispersive behavior is given in the joint time-frequency plane with the help of the STFT technique. One way to gain better resolution in the joint time-frequency plane is with the Wigner-Ville distribution (WVD). However, it is well known that cross-term interference occurs between any pair of auto-terms in the joint-time frequency plane. To suppress the cross terms in the WVD, the time-frequency distribution series (TFDS) which takes the WVD of the Gabor expansion of the original signal is implemented. By keeping only the lower order terms in the series, a good compromise between resolution and cross term interference can be achieved.
Nucleotide sequence of cDNA for mouse osteopontin-like protein (1989)

Journal Article Nucleotide sequence of cDNA for mouse osteopontin-like protein Get access Yoshitaka Miyazaki, Yoshitaka Miyazaki Department of Pathology, Medical College of OitaOita, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Mihoko Setoguchi, Mihoko Setoguchi Department of Pathology, Medical College of OitaOita, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Seiji Yoshida, Seiji Yoshida Department of Pathology, Medical College of OitaOita, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Yasunori Higuchi, Yasunori Higuchi Department of Pathology, Medical College of OitaOita, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Shin'ichiro Akizuki, Shin'ichiro Akizuki Department of Pathology, Medical College of OitaOita, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Shunsuke Yamamoto Shunsuke Yamamoto Department of Pathology, Medical College of OitaOita, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 8, 25 April 1989, Page 3298, https://doi.org/10.1093/nar/17.8.3298 Published: 25 April 1989 Article history Received: 13 March 1989 Published: 25 April 1989
A New Despeckling Method in Ultrasonography: Anisotropic Diffusion Filtering Followed by Total Variation Denoising (2013)

This paper proposes a novel hybrid method to reduce speckle noise in ultrasonography. This method applies the total variation denoising algorithm to the output image of a recently reported anisotropic diffusion filter. Performance of the proposed method is illustrated using simulated and clinical images. Experimental results indicate the proposed method outperforms the existing despeckling schemes in terms of both speckle reduction and edge preservation.
Metallic nanocluster gratings generated by near-field coupling of localized surface plasmons (2006)

Metallic nanocluster gratings composed of a 3-dimensionally periodic distribution of silver nanoparticles are successfully formed in a dielectric. A periodic arrangement of silver nanoclusters are created by holographic interference of two continuous-wave laser beams in a glass medium with embedded ~10 nm silver nanoparticles. The diffraction efficiency is much higher for the nanocluster gratings formed by TE-polarized (parallel to grating fringes) beams than those formed by TM-polarized beams. This strong polarization dependence in the formation of nanocluster gratings reveals that strong near-field coupling between localized surface plasmons excited at the metallic nanoparticles is one of the dominant mechanisms governing the rearrangement of the silver nanoparticles. The nonlinear response of metallic nanoparticles is greatly enhanced when the incident light is polarized along the lines of the silver nanoparticles.
Retrofit of flat panel color displays in the F-16A/B (2003)

Replacement of the Radar Electro-Optical (REO) Display Set, including its monochrome cathode ray tubes in the F-16A/B, with color active matrix liquid crystal displays presents many opportunities to improve the information presentation to the pilot and the pilot's interaction with the avionics system. The author presents the process followed by Battelle under the US Air Force Material Command's Design Engineering Program to develop the display formats and pilot-computer interface with the improved REO Display Set. While the general guideline for computer-generated images is no more than five to seven colored elements at a time, the system being designed for the F-16A/B provides many more colors for reasons of realism in future images to be displayed in combat and transport aircraft. The system provides for technology insertion and growth due to its use of an open system architecture implementation of a multiprocessing capability. While the initial software will implement the F-16A/B REO systems' symbology, the capability is provided to generate realistic images that will aid pilots in performance of their missions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Conditional Neural Processes (2018)

Deep neural networks excel at function approximation, yet they are typically trained from scratch for each new function. On the other hand, Bayesian methods, such as Gaussian Processes (GPs), exploit prior knowledge to quickly infer the shape of a new function at test time. Yet GPs are computationally expensive, and it can be hard to design appropriate priors. In this paper we propose a family of neural models, Conditional Neural Processes (CNPs), that combine the benefits of both. CNPs are inspired by the flexibility of stochastic processes such as GPs, but are structured as neural networks and trained via gradient descent. CNPs make accurate predictions after observing only a handful of training data points, yet scale to complex functions and large datasets. We demonstrate the performance and versatility of the approach on a range of canonical machine learning tasks, including regression, classification and image completion.
An LDPC Decoder with Time Domain Analog and Digital Mixed Signal Processing (2013)

Time-domain analog and digital mixed-signal processing (TD-AMS) is presented. Analog computation is more energy- and area-efficient at the cost of its limited accuracy, whereas digital computation is more versatile and derives greater benefits from technology scaling. Besides, design automation tools for digital circuits are much more sophisticated than those for analog circuits. TD-AMS exploits both advantages, and is a solution better suited to implementing a system on chip including functions for which high computational accuracy is not required, such as error correction, image processing, and machine learning. As an example, a low-density parity-check (LDPC) code decoder with the technique is implemented in 65 nm CMOS and achieves the best reported efficiencies of 10.4 pJ/bit and 6.1 Gbps/mm2.
Structural studies of proteins by high-flux X-ray and neutron solution scattering (1988)

Research Article| September 01 1988 Structural studies of proteins by high-flux X-ray and neutron solution scattering S J Perkins S J Perkins Department of Biochemistry and Chemistry, Royal Free Hospital School of Medicine, Rowland Hill Street, London NW3 2PF, U.K. Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1988) 254 (2): 313–327. https://doi.org/10.1042/bj2540313 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation S J Perkins; Structural studies of proteins by high-flux X-ray and neutron solution scattering. Biochem J 1 September 1988; 254 (2): 313–327. doi: https://doi.org/10.1042/bj2540313 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1988 London: The Biochemical Society1988 Article PDF first page preview Close Modal You do not currently have access to this content.
Joint blind and semi-blind detection and channel estimation for space-time trellis coded systems (2004)

The paper considers a multiple-input multiple-output (MIMO) communication system, which uses space-time trellis coding (STTC). A novel method of decoding STTC without a need to transmit training sequences is developed. The technique uses only a single channel estimate to acquire a complete set of the channels' estimates while performing STTC detection. The method is akin to blind trellis search techniques (per-survivor processing - PSP) and adaptive Viterbi. Our solution consists of the deployment of a bank of Kalman filters. The bank of Kalman filters is coupled with Viterbi type decoders, which produce tentative decisions based on Kalman channel predictions. In return, the Kalman filters use the tentative decisions to update and track the MIMO channels corresponding to a number of tracked hypotheses. The proposed technique is particularly applicable to space-time systems operating in rapidly fading environments, where STTC can be decoded and MIMO channels efficiently tracked without relying on periodic pilot sequences.
Interlayer coupling and magnetic reversal of antiferromagnetically coupled media (2002)

We characterize the interlayer coupling and magnetic reversal of antiferromagnetically coupled recording layers. We show that the granular structure and reduced thickness values of the lower layer result in its reversal being strongly thermally activated at room temperature. We also find that the granular structure of the layers produces large dipolar fields which favor antiparallel alignment of the layer magnetizations. These dipolar fields overcome the ferromagnetic regions in the oscillatory coupling as a function of Ru thickness tRu, causing the interlayer coupling to be only antiferromagnetic for tRu&gt;5 Å.
Candida albicans proteinases: resolving the mystery of a gene family (2001)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
A comparison of the insulin- and epidermal growth factor-stimulated protein kinases from human placenta. (1984)

The characteristics of the insulin- and epidermal growth factor (EGF)-stimulated tyrosine-specific protein kinases in a wheat germ lectin-Sepharose-purified preparation of solubilized placenta membranes were compared. The specific activity of the insulin-stimulated kinase in this preparation was 72 nmol/min/mg whereas the specific activity of the EGF-stimulated kinase was 312 nmol/min/mg using a synthetic peptide as the phosphorylatable substrate. The two enzymes showed similar divalent metal ion requirements and nucleotide specificities. In addition, both kinases were inhibited by treatment with N-ethylmaleimide. However, the EGF-stimulated enzyme was more sensitive to modification by this reagent than was the insulin-stimulated kinase. When examined for their ability to utilize a number of different proteins as substrates, the insulin- and EGF-stimulated kinases exhibited similar but not identical substrate specificities. These similarities at the molecular level may be the basis of the similarity between the actions of insulin and EGF at the cellular level.
An Introduction to Robust Codes over Finite Fields (2013)

We consider the problem of securing data using linear and nonlinear codes over the binary numbers. We start by developing a conservation law for codes. Then we explain why linear codes, which are easy to understand and implement, are useful when protecting data from rarely occurring random errors. By a simple argument, we demonstrate that linear codes are not a good way to secure data against an attacker. Having ruled out linear codes for this purpose, we take up nonlinear codes. We explain what a finite field is and how data can be represented by elements of a finite field. We then consider codes that are nonlinear functions of the data---the elements of the finite field. We show that binary quadratic codes suffer from the same deficiencies as linear codes. Next we consider cubic codes. First, we show that cubic codes do a good job of detecting changes made by an attacker. Then we demonstrate that certain cubic codes provide a large measure of protection against attackers and some protection against certain relatively common random errors. We show that cubic codes are also reasonably efficient in a well-defined sense. Finally, we briefly consider other interesting nonlinear codes.
Resident Assessments: A New Tool for Measuring and Improving Nursing Home Quality (1992)

The United States is adopting a resident assessment instrument nationwide that holds great potential for the measurement and improvement of nursing home quality. The steps necessary to ultimately use the assessment instrument to evaluate institutional quality at the facility level are discussed. Drawing from experience with a standardized resident assessment system used in Virginia since 1983, Anne Glass describes how assessments were employed in an exploratory project to examine the relative performance of 135 facilities. A model of nursing home quality is included to explain how indicators drawn from assessments relate to quality. Advantages of using a resident-assessment-based system to evaluate institutional quality are outlined. When computerized, this wealth of data will help clarify facility norms and support continuous quality improvement.
The Effect of Low-Level Laser Irradiation on Sperm Motility, and Integrity of the Plasma Membrane and Acrosome in Cryopreserved Bovine Sperm (2015)

We conclude that LLLI may exert beneficial effects in the preservation of live sperm. A dose of 4 joules prior to cryopreservation was more effective than a dose of 6 joules in preserving sperm motility.