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At least 109 records · Page 6

Utilizing Amino Acid Composition and Entropy of Potential Open Reading Frames to Identify Protein-Coding Genes

One of the main steps in gene-finding in prokaryotes is determining which open reading frames encode for a protein, and which occur by chance alone. There are many different methods to differentiate the two; the most prevalent approach is using shared homology with a database of known genes. This method presents many pitfalls, most notably the catch that you only find genes that you have seen before. The four most popular prokaryotic gene-prediction programs (GeneMark, Glimmer, Prodigal, Phanotate) all use a protein-coding training model to predict protein-coding genes, with the latter three allowing for the training model to be created ab initio from the input genome. Different methods are available for creating the training model, and to increase the accuracy of such tools, we present here GOODORFS, a method for identifying protein-coding genes within a set of all possible open reading frames (ORFS). Our workflow begins with taking the amino acid frequencies of each ORF, calculating an entropy density profile (EDP), using KMeans to cluster the EDPs, and then selecting the cluster with the lowest variation as the coding ORFs. To test the efficacy of our method, we ran GOODORFS on 14,179 annotated phage genomes, and compared our results to the initial training-set creation step of four other similar methods (Glimmer, MED2, PHANOTATE, Prodigal). We found that GOODORFS was the most accurate (0.94) and had the best F1-score (0.85), while Glimmer had the highest precision (0.92) and PHANOTATE had the highest recall (0.96).

59 BASIC BIOLOGICAL SCIENCES↗

Machine Reading at Scale: A Search Engine for Scientific and Academic Research

The Internet, much like our universe, is ever-expanding. Information, in the most varied formats, is continuously added to the point of information overload. Consequently, the ability to navigate this ocean of data is crucial in our day-to-day lives, with familiar tools such as search engines carving a path through this unknown. In the research world, articles on a myriad of topics with distinct complexity levels are published daily, requiring specialized tools to facilitate the access and assessment of the information within. Recent endeavors in artificial intelligence, and in natural language processing in particular, can be seen as potential solutions for breaking information overload and provide enhanced search mechanisms by means of advanced algorithms. As the advent of transformer-based language models contributed to a more comprehensive analysis of both text-encoded intents and true document semantic meaning, there is simultaneously a need for additional computational resources. Information retrieval methods can act as low-complexity, yet reliable, filters to feed heavier algorithms, thus reducing computational requirements substantially. In this work, a new search engine is proposed, addressing machine reading at scale in the context of scientific and academic research. It combines state-of-the-art algorithms for information retrieval and reading comprehension tasks to extract meaningful answers from a corpus of scientific documents. The solution is then tested on two current and relevant topics, cybersecurity and energy, proving that the system is able to perform under distinct knowledge domains while achieving competent performance.

Sousa, Norberto (ORCID:0000000329194817)↗

Direct reading of electrocardiograms and respiration rates

Technique for reading heart and respiration rates is more accurate and direct than the previous method. Index of a plastic calibrated card is aligned with a point on the electrocardiogram. Complexes are counted as indicated on the card and heart or respiration rate is read directly from the appropriate scale.

Wise, J. P.↗

Effect of photogrammetric reading error on slope-frequency distributions

The effect of reading error on two hypothetical slope frequency distributions and two slope frequency distributions from actual lunar data in order to ensure that these errors do not cause excessive overestimates of algebraic standard deviations for the slope frequency distributions. The errors introduced are insignificant when the reading error is small and the slope length is large. A method for correcting the errors in slope frequency distributions is presented and applied to 11 distributions obtained from Apollo 15, 16, and 17 panoramic camera photographs and Apollo 16 metric camera photographs.

Moore, H. J.↗

An efficient read-out system for multiwire proportional counter hodoscopes

An efficient scanning method for read-out of a multiwire proportional counter hodoscope is presented. This method which utilizes the grouping of wires in the hodoscope read-out system offers distinct advantages in speed and simplicity over systems employing long shift registers. Power consumption and cost can be minimized with this method because of slower clock speeds and a low parts count. This system has been constructed and used on a hodoscope for cosmic-ray trajectory measurements and a lower-power version has been designed for satellite applications.

Austin, R. W.↗

Inconsistencies in tape read and tape write programs on the I-100 image analysis system

The author has identified the following significant results. The tape read and write programs currently available on the 1-100 perform their intended functions of reading and writing tapes, but are difficult to use because they contain a number of inconsistencies. These inconsistencies can often be overcome by the use of work-around procedures and by trial and error, which is an inefficient use of expensive computer systems that should not be necessary.

Hocutt, W. T.↗

IRAC test report. Gallium doped silicon band 2: Read noise and dark current

A direct readout infrared detector array, a candidate for the Space Infrared Telescope Facility (SIRTF) Infrared Array Camera (IRAC), has been tested. The array has a detector surface of gallium doped silicon, bump bonded to a 58x62 pixel MOSFET multiplexer on a separate chip. Although this chip and system do not meet all the SIRTF requirements, the critically important read noise is within a factor of 3 of the requirement. Significant accomplishments of this study include: (1) development of a low noise correlated double sampling readout system with a readout noise of 127 to 164 electrons (based on the detector integrator capacitance of 0.1 pF); (2) measurement of the readout noise of the detector itself, ranging from 123 to 214 electrons with bias only (best to worst pixel), and 256 to 424 electrons with full clocking in normal operation at 5.4 K where dark current is small. Thirty percent smaller read noises are obtained at a temperature of 15K; (3) measurement of the detector response versus integration time, showing significant nonlinear behavior for large signals, well below the saturation level; and (4) development of a custom computer interface and suitable software for collection, analysis and display of data.

Lamb, Gerald↗

Feedforward, high density, programmable read only neural network based memory system

Neural network-inspired, nonvolatile, programmable associative memory using thin-film technology is demonstrated. The details of the architecture, which uses programmable resistive connection matrices in synaptic arrays and current summing and thresholding amplifiers as neurons, are described. Several synapse configurations for a high-density array of a binary connection matrix are also described. Test circuits are evaluated for operational feasibility and to demonstrate the speed of the read operation. The results are discussed to highlight the potential for a read data rate exceeding 10 megabits/sec.

Daud, Taher↗

Image enhancement filters significantly improve reading performance for low vision observers

As people age, so do their photoreceptors; many photoreceptors in central vision stop functioning when a person reaches their late sixties or early seventies. Low vision observers with losses in central vision, those with age-related maculopathies, were studied. Low vision observers no longer see high spatial frequencies, being unable to resolve fine edge detail. We developed image enhancement filters to compensate for the low vision observer's losses in contrast sensitivity to intermediate and high spatial frequencies. The filters work by boosting the amplitude of the less visible intermediate spatial frequencies. The lower spatial frequencies. These image enhancement filters not only reduce the magnification needed for reading by up to 70 percent, but they also increase the observer's reading speed by 2-4 times. A summary of this research is presented.

Lawton, T. B.↗

The Effect of Compressibility on the Pressure Reading of a Prandtl Pitot Tube at Subsonic Flow Velocity

Errors arising from yawed flow were also determined up to 20 degrees angle of attack. In axial flow, the Prandtl pitot tube begins at w/a approx. = 0.8 to give an incorrect static pressure reading, while it records the tank pressure correctly, as anticipated, up to sonic velocity. Owing to the compressibility of the air, the Prandtl pitot tube manifests compression shocks when the air speed approaches velocity of sound. This affects the pressure reading of the instrument. Because of the increasing importance of high speed in aviation, this compressibility effect is investigated in detail.

Walchner, O↗

Passive, Direct-Read Monitoring System for Selective Detection and Quantification of Hydrogen Chloride

Monitoring the exposure of an employee to hydrogen chloride or hydrochloric acid in the presence of other acids has been a challenge to the industrial hygiene community. The capability of a device to differentiate the levels of acid vapors would allow for more accurate determinations of exposure and therefore improved occupational health. In this work, a selective direct-read colorimetric badge system was validated for Short Term Exposure Limit (STEL) monitoring of hydrogen chloride. The passive colorimetric badge system consists of a direct reading badge and a color scale. The badge has a coated indicator layer with a diffusive resistance in the shape of an exclamation mark. An exclamation mark will appear if hydrogen chloride is present in the atmosphere at concentrations at or above 2.0 ppm. By using the color scale, the intensity of the color formed on the badge can be further quantified up to 25 ppm. The system was validated according to a protocol based on the NIOSH Protocol for the Evaluation of Passive Monitors. The badge was exposed to relative humidities ranging from 11% to 92%, temperatures ranging from 7 C to 400 C and air velocities ranging from 5 cm/sec to 170 cm/sec. All experiments were conducted in a laboratory vapor generation system. Hydrofluoric acid, nitric acid, sulfuric acid, chlorine, hydrogen sulfide and organic acids showed no effect on the performance of the hydrogen chloride monitoring system. The passive badge and color scale system exceeded the accuracy requirements as defined by NIOSH. At ambient conditions, the mean coefficient of variation was 10.86 and the mean bias was 1.3%. This data was presented previously at the American Industrial Hygiene Conference and Exposition in Toronto, Canada in June 1999.

Chapman, K. B.↗

Electronic Thermometer Readings

NASA Stennis' adaptive predictive algorithm for electronic thermometers uses sample readings during the initial rise in temperature and applies an algorithm that accurately and rapidly predicts the steady state temperature. The final steady state temperature of an object can be calculated based on the second-order logarithm of the temperature signals acquired by the sensor and predetermined variables from the sensor characteristics. These variables are calculated during tests of the sensor. Once the variables are determined, relatively little data acquisition and data processing time by the algorithm is required to provide a near-accurate approximation of the final temperature. This reduces the delay in the steady state response time of a temperature sensor. This advanced algorithm can be implemented in existing software or hardware with an erasable programmable read-only memory (EPROM). The capability for easy integration eliminates the expense of developing a whole new system that offers the benefits provided by NASA Stennis' technology.

Source record↗

Clustering and Recurring Anomaly Identification: Recurring Anomaly Detection System (ReADS)

This viewgraph presentation reviews the Recurring Anomaly Detection System (ReADS). The Recurring Anomaly Detection System is a tool to analyze text reports, such as aviation reports and maintenance records: (1) Text clustering algorithms group large quantities of reports and documents; Reduces human error and fatigue (2) Identifies interconnected reports; Automates the discovery of possible recurring anomalies; (3) Provides a visualization of the clusters and recurring anomalies We have illustrated our techniques on data from Shuttle and ISS discrepancy reports, as well as ASRS data. ReADS has been integrated with a secure online search

McIntosh, Dawn↗

Techniques for writing and reading data on an optical disk which include formation of holographic optical gratings in plural locations on the optical disk

An optical memory for storing and/or reading data on an optical disk. The optical disk incorporates a material in which holographic gratings can be created, and subsequently detected, at plural locations within the disk by an electro-optical head. Creation and detection of holographic gratings with variable diffraction efficiency is possible with the electro-optical head. Multiple holographic gratings can also be created at each one of the plural locations via a beam of light which has a different wavelength or point of focus. These data elements can be read by the electro-optical head using a beam of light sequentially varied in wavelength or point of focus to correspond to the multiple holographic gratings to be recorded.

Liu, Tsuen-Hsi↗

Algorithm for Identifying Erroneous Rain-Gauge Readings

An algorithm analyzes rain-gauge data to identify statistical outliers that could be deemed to be erroneous readings. Heretofore, analyses of this type have been performed in burdensome manual procedures that have involved subjective judgements. Sometimes, the analyses have included computational assistance for detecting values falling outside of arbitrary limits. The analyses have been performed without statistically valid knowledge of the spatial and temporal variations of precipitation within rain events. In contrast, the present algorithm makes it possible to automate such an analysis, makes the analysis objective, takes account of the spatial distribution of rain gauges in conjunction with the statistical nature of spatial variations in rainfall readings, and minimizes the use of arbitrary criteria. The algorithm implements an iterative process that involves nonparametric statistics.

Rickman, Doug↗

Using Redundancy To Reduce Errors in Magnetometer Readings

A method of reducing errors in noisy magnetic-field measurements involves exploitation of redundancy in the readings of multiple magnetometers in a cluster. By "redundancy"is meant that the readings are not entirely independent of each other because the relationships among the magnetic-field components that one seeks to measure are governed by the fundamental laws of electromagnetism as expressed by Maxwell's equations. Assuming that the magnetometers are located outside a magnetic material, that the magnetic field is steady or quasi-steady, and that there are no electric currents flowing in or near the magnetometers, the applicable Maxwell 's equations are delta x B = 0 and delta(raised dot) B = 0, where B is the magnetic-flux-density vector. By suitable algebraic manipulation, these equations can be shown to impose three independent constraints on the values of the components of B at the various magnetometer positions. In general, the problem of reducing the errors in noisy measurements is one of finding a set of corrected values that minimize an error function. In the present method, the error function is formulated as (1) the sum of squares of the differences between the corrected and noisy measurement values plus (2) a sum of three terms, each comprising the product of a Lagrange multiplier and one of the three constraints. The partial derivatives of the error function with respect to the corrected magnetic-field component values and the Lagrange multipliers are set equal to zero, leading to a set of equations that can be put into matrix.vector form. The matrix can be inverted to solve for a vector that comprises the corrected magnetic-field component values and the Lagrange multipliers.

Kulikov, Igor↗

Reducing the Read Noise of HAWAII-2RG Detector Systems with Improved Reference Sampling and Subtraction (IRS2)

IRS2 is a Wiener-optimal approach to using all of the reference information that Teledyne's HAWAII-2RG detector arrays provide. Using a new readout pattern, IRS2 regularly interleaves reference pixels with the normal pixels during readout. This differs from conventional clocking, in which the reference pixels are read out infrequently, and only in a few rows and columns around the outside edges of the detector array. During calibration, the data are processed in Fourier space, which is <;:lose to the noise's eigenspace. Using IRS2, we have reduced the read noise of the James Webb Space Telescope Near Infrared Spectrograph by 15% compared to conventional readout. We are attempting to achieve further gains by calibrating out recently recognized non-stationary noise that appears at the frame rate.

Rauscher, Bernard J.↗

A Fluorescence‐Based Transient Expression Assay for the Analysis of Upstream Open Reading Frames in Plants

Upstream open reading frames (uORFs) are regulatory elements present in the 5′ leaders of mRNA that can significantly impact downstream gene expression in eukaryotes. In crop engineering, editing of uORFs can provide an avenue to upregulate expression of native genes without the need to add persistent transgenic copies. Even with genome-wide methods to identify translated uORFs such as ribosome profiling, their functional characterization depends on validation through reporter gene assays and mutagenesis studies. Current screening methods for plants use luciferases or protoplasts to measure differential gene expression between wild-type and mutated transcript leaders, which requires tissue processing and/or substrate addition. Here, we present a time- and cost-efficient alternative to investigate transcript leaders by co-expression of two fluorescent proteins in Nicotiana benthamiana leaf tissue and test our assay on genes involved in photoprotection, editing of which could provide a pathway to increase CO 2 assimilation during sun–shade transitions.

Nicotiana benthamiana↗