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At least 199 records · Page 11

Constructing high complexity synthetic libraries of long ORFs using in vitro selection

We present a method that can significantly increase the complexity of protein libraries used for in vitro or in vivo protein selection experiments. Protein libraries are often encoded by chemically synthesized DNA, in which part of the open reading frame is randomized. There are, however, major obstacles associated with the chemical synthesis of long open reading frames, especially those containing random segments. Insertions and deletions that occur during chemical synthesis cause frameshifts, and stop codons in the random region will cause premature termination. These problems can together greatly reduce the number of full-length synthetic genes in the library. We describe a strategy in which smaller segments of the synthetic open reading frame are selected in vitro using mRNA display for the absence of frameshifts and stop codons. These smaller segments are then ligated together to form combinatorial libraries of long uninterrupted open reading frames. This process can increase the number of full-length open reading frames in libraries by up to two orders of magnitude, resulting in protein libraries with complexities of greater than 10(13). We have used this methodology to generate three types of displayed protein library: a completely random sequence library, a library of concatemerized oligopeptide cassettes with a propensity for forming amphipathic alpha-helical or beta-strand structures, and a library based on one of the most common enzymatic scaffolds, the alpha/beta (TIM) barrel. Copyright 2000 Academic Press.

Non-NASA Center↗

Towards Scalable 3D Integration of 2T-nC FeRAM with Hundreds of Layer Stacking

In this article, we study the limits of the number of capacitors and read history dependence in a 2T-nC ferroelectric random-access memory (FeRAM) cell, paving the way for its high-density integration toward hundreds of stacked layers. Through a comprehensive experimental and simulation study on the scaling behavior of the 2T-nC FeRAM architecture, we demonstrate: (i) successful fabrication of 2T-64C cells with robust memory operation and clearly distinguishable ‘0’ and ‘1’ states, even in 64- capacitor configurations; (ii) that the parasitic capacitance of the floating node originates predominantly from the linear component of the ferroelectric capacitor, and its impact on n-scaling—due to degraded sense margin—can be mitigated by floating unselected capacitors with enough TΩ isolation; (iii) that sharing write and read transistors among n capacitors introduces a read history dependence issue due to fluctuating floating node voltage (VFN); and (iv) that a proposed FN discharge scheme can effectively eliminate read-sequence dependence, at the cost of reduced read endurance.

36 MATERIALS SCIENCE↗

Software approach to automatic patching of analog computer

The Automatic Patching Verification program (APV) is described which provides the hybrid computer programmer with a convenient method of performing a static check of the analog portion of his study. The static check insures that the program is patched as specified, and that the computing components being used are operating correctly. The APV language the programmer uses to specify his conditions and interconnections is similar to the FORTRAN language in syntax. The APV control program reads APV source program statements from an assigned input device. Each source program statement is processed immediately after it is read. A statement may select an analog console, set an analog mode, set a potentiometer or DAC, or read from the analog console and perform a test. Statements are read and processed sequentially. If an error condition is detected, an output occurs on an assigned output device. When an end statement is read, the test is terminated.

Source record↗

Development of an Automated Reader for Analysis and Storage of Personnel Dosimeter Badge Data

The collection and archiving of data from personnel dosimeters has become increasingly important in light of the lowered Threshold Limit Values (TLV) for HydraZine (HZ), MonoMethylHydrazine (MMH), and Unsymmetrical DiMethylHydrazine (UDMH). The American Conference of Government Industrial Hygienists (ACGIH) lowered the TLV from 100 parts per billion (ppb) to IO ppb and has caused increased concern over long term exposures of personnel to trace levels of these hypergols and other potentially harmful chemicals. An automated system of reading the exposure levels of personnel dosimeters and storing exposure data for subsequent evaluation has been developed. The reading of personnel dosimeter badges for exposure to potentially harmful vapor concentrations of hydrazines or other chemicals is performed visually by comparing the color developed by the badge with a calibrated color comparator. The result obtained using visual comparisons of the developed badge color with the comparator may vary widely from user to user. The automated badge reader takes the variability out of the dosimeter reading by accurately comparing the reflectance obtained from a colored spot on the badge with a reading on the same spot prior to any exposure to chemical vapors. The observed difference between the reflectance values is used as part of a calculation of the dose value for the badge based on a stored calibration curve. The badge reader also stores bar-code data unique to each badge, as well as bar-code information on the user, as part of the permanent badge record. The start and stop exposure times for each badge are recorded and can be used as part of the calculated concentration, in ppm, for each badge logged during a recording period. The badge reader is equipped with a number of badge holders, each of which is unique to a specific type of personnel dosimeter badge. This gives the reader maximum flexibility to allow for the reading of several different types of badges. Test results of the badge reader for several different types of personnel dosimeter badges are presented within the body of this paper.

Meneghelli, B. J.↗

Development of an Automated Reader for Analysis and Storage of Personnel Dosimeter Badge Data

The collection and archiving of data from personnel dosimeters has become increasingly important in light of the lowered threshold limit values (TLV) for hydrazine (HZ), monomethylhydrazine (MMH), and unsymmetrical dimethylhydrazine (UDMH). The American Conference of Government Industrial Hygienists (ACGIH) lowered the TLV from 100 parts per billion (ppb) to 10 ppb and has caused increased concern over long term exposures of personnel to trace levels of these hypergols and other potentially harmful chemicals. An automated system of reading the exposure levels of personnel dosimeters and storing exposure data for subsequent evaluation has been developed. The reading of personnel dosimeter badges for exposure lo potentially harmful vapor concentrations of hydrazines or other chemicals is performed visually by comparing the color developed by the badge with a calibrated color comparator. The result obtained using visual comparisons of the developed badge color with the comparator may vary widely from user to user. The automated badge reader takes the variability out of the dosimeter reading by accurately comparing the reflectance obtained from a colored spot on the badge with a reading on the same spot prior to any exposure to chemical vapors. The observed difference between the reflectance values is used as part of a calculation of the dose value for the badge based on a stored calibration curve. The badge reader also stores bar-code data unique to each badge, as well as bar-code information on the user, as part of the permanent badge record. The start and stop exposure times for each badge are recorded and can be used as part of the calculated concentration, in ppm, for each badge logged during a recording period. The badge reader is equipped with a number of badge holders, each of which is unique to a specific type of personnel dosimeter badge. This gives the reader maximum flexibility to allow for the reading of several different types of badges. Test results of the badge reader for several different types of personnel dosimeter badges are presented within the body of this paper.

Meneghelli, B. J.↗

Hiding the Disk and Network Latency of Out-of-Core Visualization

This paper describes an algorithm that improves the performance of application-controlled demand paging for out-of-core visualization by hiding the latency of reading data from both local disks or disks on remote servers. The performance improvements come from better overlapping the computation with the page reading process, and by performing multiple page reads in parallel. The paper includes measurements that show that the new multithreaded paging algorithm decreases the time needed to compute visualizations by one third when using one processor and reading data from local disk. The time needed when using one processor and reading data from remote disk decreased by two thirds. Visualization runs using data from remote disk actually ran faster than ones using data from local disk because the remote runs were able to make use of the remote server's high performance disk array.

Ellsworth, David↗

Algorithm for Detecting a Bright Spot in an Image

An algorithm processes the pixel intensities of a digitized image to detect and locate a circular bright spot, the approximate size of which is known in advance. The algorithm is used to find images of the Sun in cameras aboard the Mars Exploration Rovers. (The images are used in estimating orientations of the Rovers relative to the direction to the Sun.) The algorithm can also be adapted to tracking of circular shaped bright targets in other diverse applications. The first step in the algorithm is to calculate a dark-current ramp a correction necessitated by the scheme that governs the readout of pixel charges in the charge-coupled-device camera in the original Mars Exploration Rover application. In this scheme, the fraction of each frame period during which dark current is accumulated in a given pixel (and, hence, the dark-current contribution to the pixel image-intensity reading) is proportional to the pixel row number. For the purpose of the algorithm, the dark-current contribution to the intensity reading from each pixel is assumed to equal the average of intensity readings from all pixels in the same row, and the factor of proportionality is estimated on the basis of this assumption. Then the product of the row number and the factor of proportionality is subtracted from the reading from each pixel to obtain a dark-current-corrected intensity reading. The next step in the algorithm is to determine the best location, within the overall image, for a window of N N pixels (where N is an odd number) large enough to contain the bright spot of interest plus a small margin. (In the original application, the overall image contains 1,024 by 1,024 pixels, the image of the Sun is about 22 pixels in diameter, and N is chosen to be 29.)

Source record↗

Analog Nonvolatile Computer Memory Circuits

In nonvolatile random-access memory (RAM) circuits of a proposed type, digital data would be stored in analog form in ferroelectric field-effect transistors (FFETs). This type of memory circuit would offer advantages over prior volatile and nonvolatile types: In a conventional complementary metal oxide/semiconductor static RAM, six transistors must be used to store one bit, and storage is volatile in that data are lost when power is turned off. In a conventional dynamic RAM, three transistors must be used to store one bit, and the stored bit must be refreshed every few milliseconds. In contrast, in a RAM according to the proposal, data would be retained when power was turned off, each memory cell would contain only two FFETs, and the cell could store multiple bits (the exact number of bits depending on the specific design). Conventional flash memory circuits afford nonvolatile storage, but they operate at reading and writing times of the order of thousands of conventional computer memory reading and writing times and, hence, are suitable for use only as off-line storage devices. In addition, flash memories cease to function after limited numbers of writing cycles. The proposed memory circuits would not be subject to either of these limitations. Prior developmental nonvolatile ferroelectric memories are limited to one bit per cell, whereas, as stated above, the proposed memories would not be so limited. The design of a memory circuit according to the proposal must reflect the fact that FFET storage is only partly nonvolatile, in that the signal stored in an FFET decays gradually over time. (Retention times of some advanced FFETs exceed ten years.) Instead of storing a single bit of data as either a positively or negatively saturated state in a ferroelectric device, each memory cell according to the proposal would store two values. The two FFETs in each cell would be denoted the storage FFET and the control FFET. The storage FFET would store an analog signal value, between the positive and negative FFET saturation values. This signal value would represent a numerical value of interest corresponding to multiple bits: for example, if the memory circuit were designed to distinguish among 16 different analog values, then each cell could store 4 bits. Simultaneously with writing the signal value in the storage FFET, a negative saturation signal value would be stored in the control FFET. The decay of this control-FFET signal from the saturation value would serve as a model of the decay, for use in regenerating the numerical value of interest from its decaying analog signal value. The memory circuit would include addressing, reading, and writing circuitry that would have features in common with the corresponding parts of other memory circuits, but would also have several distinctive features. The writing circuitry would include a digital-to-analog converter (DAC); the reading circuitry would include an analog-to-digital converter (ADC). For writing a numerical value of interest in a given cell, that cell would be addressed, the saturation value would be written in the control FFET in that cell, and the non-saturation analog value representing the numerical value of interest would be generated by use of the DAC and stored in the storage FFET in that cell. For reading the numerical value of interest stored in a given cell, the cell would be addressed, the ADC would convert the decaying control and storage analog signal values to digital values, and an associated fast digital processing circuit would regenerate the numerical value from digital values.

MacLeod, Todd↗

Gigabit Ethernet Asynchronous Clock Compensation FIFO

Clock compensation for Gigabit Ethernet is necessary because the clock recovered from the 1.25 Gb/s serial data stream has the potential to be 200 ppm slower or faster than the system clock. The serial data is converted to 10-bit parallel data at a 125 MHz rate on a clock recovered from the serial data stream. This recovered data needs to be processed by a system clock that is also running at a nominal rate of 125 MHz, but not synchronous to the recovered clock. To cross clock domains, an asynchronous FIFO (first-in-first-out) is used, with the write pointer (wprt) in the recovered clock domain and the read pointer (rptr) in the system clock domain. Because the clocks are generated from separate sources, there is potential for FIFO overflow or underflow. Clock compensation in Gigabit Ethernet is possible by taking advantage of the protocol data stream features. There are two distinct data streams that occur in Gigabit Ethernet where identical data is transmitted for a period of time. The first is configuration, which happens during auto-negotiation. The second is idle, which occurs at the end of auto-negotiation and between every packet. The identical data in the FIFO can be repeated by decrementing the read pointer, thus compensating for a FIFO that is draining too fast. The identical data in the FIFO can also be skipped by incrementing the read pointer, which compensates for a FIFO draining too slowly. The unique and novel features of this FIFO are that it works in both the idle stream and the configuration streams. The increment or decrement of the read pointer is different in the idle and compensation streams to preserve disparity. Another unique feature is that the read pointer to write pointer difference range changes between compensation and idle to minimize FIFO latency during packet transmission.

Duhachek, Jeff↗

Demonstration of Time Domain Multiplexed Readout for Magnetically Coupled Calorimeters

Magnetically coupled calorimeters (MCC) have extremely high potential for x-ray applications due to the inherent high energy resolution capability and being non-dissipative. Although very high energy-resolution has been demonstrated, until now there has been no demonstration of multiplexed read-out. We report on the first realization of a time domain multiplexed (TDM) read-out. While this has many similarities with TDM of transition-edge-sensors (TES), for MGGs the energy resolution is limited by the SQUID read-out noise and requires the well established scheme to be altered in order to minimize degradation due to noise aliasing effects. In cur approach, each pixel is read out by a single first stage SQUID (SQ1) that is operated in open loop. The outputs of the SQ1 s are low-pass filtered with an array of low cross-talk inductors, then fed into a single-stage SQUID TD multiplexer. The multiplexer is addressed from room temperature and read out through a single amplifier channel. We present results achieved with a new detector platform. Noise performance is presented and compared to expectations. We have demonstrated multiplexed X-ray spectroscopy at 5.9keV with delta_FWHM=10eV. In an optimized setup, we show it is possible to multiplex 32 detectors without significantly degrading the Intrinsic detector resolution.

Porst, J.-P.↗

Leveraging Radiofrequency Identification Success Beyond Hazardous Material Inventory Management at a National Laboratory

Effective inventory management can be overshadowed by conflicting priorities in organizational procedures, particularly in research-focused institutions such as national laboratories that handle expensive, delicate, and hazardous materials. Here, this study investigated the potential of radiofrequency identification (RFID) technology, currently used for hazardous chemical inventory, in applications with higher metal interference and absorption, specifically pressure release device (PRD) compliance and nuclear container management, at Lawrence Livermore National Laboratory (LLNL). This study was done to document best practices to enhance inventory identification speeds for inventory reconciliation and inventory recall and to explore optimal configurations for RFID implementation compared to traditional manual methods of equipment management. Tests were conducted to determine the ideal RFID tag orientation (read at angles of 0°, 90°, and 270°), various container layouts (linear, separated, curved, operational), and ID methods such as manual, barcode, and RFID performing three trials per method per orientation. Results indicated that 0° was the optimal read angle for minimizing metallic interference, and the operational and curved arrangements significantly outperformed the linear and separated configurations in read speed. 3D printed mounts were developed and tested, increasing the read range of the RFID reader by up to 235% in cases of high metallic interference. The RFID technology demonstrated an average speed increase of 65% over a simplified manual identification, which supports the conclusion that RFID is a more efficient method for large hazardous inventory management and equipment reconciliation. Additionally, capturing meta-data, such as location and date, can be used to query for inventory recall and automated updating of record information.

42 ENGINEERING↗

ZrH2 as measured on ARCS for NXS2021

This data is for ZrH2 in an Al can it is measured at room temperature. This data was used for the Neutron and Xray scattering school in 2021. It was measured on the ARCS direct geometry spectrometer at the spallation neutron source. The .nxs files are event files that can be read and processed with Mantid. The nxspe files are auto reduced files that can be read with Mantid, Dave, or Mslice. Both types of files are hdf5 and can be read with any tool that reads hdf5.

MATERIALS SCIENCE↗

Modularization of EDGE Workflows Using Nextflow: Improving the Efficiency and Maintainability of Bioinformatics Software

EDGE is a bioinformatics platform developed in 2016 by researchers at Los Alamos National Laboratory (LANL) to facilitate the analysis of next-generation sequencing data by researchers with varying levels of experience in bioinformatics (Li et al., 2017). Users with single-end, paired-end or long-read sequencing data can provide their reads as input to EDGE and select the combination of workflows to run that are most useful for their research (e.g., quality control of reads, genome assembly, or the taxonomic classification of input reads). Table 1 summarizes the modules available in EDGE. EDGE is available as a web platform at https://edgebioinformatics.org, as installable source code maintained on GitHub under a GPLv3 license, and as a publicly hosted Docker image.

59 BASIC BIOLOGICAL SCIENCES↗

Bacteroides expand the functional versatility of a universal transcription factor and transcribed DNA to program capsule diversity

This record contains a list of Snakemake rules (Snakefile) to process a raw *.fastq.gz (from GEO record: GSE281607) using Cutadapt, map a processed *.fastq file using Bowtie, convert mapped reads to *.bed files using Samtools and Bedtools, and count the occurance of each Bacteriodes fragilis str NCTC 9343 genome position anywhere in a mapped read and as the 3' end of a mapped read using Bedtools. It further contains *ebwt files to assist with Bowtie mapping, *genome file to be used with Bedtools, a *.fasta file (useful to regenerate *ebwt files), and the completely processed *bed and *txt read files (generated by Snakemake and R) as references. In addition, a *.pdb file is included and represents the predicted interaction between UpeY and UpaZ.

Landick, Robert↗

Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes

Genomic DNA from each sample was prepared using the Wizard Genomic DNA Purification Kit (Promega) and after, DNA was quantified using the QuantiFluor ONE dsDNA System (Promega). Genomic DNA underwent shearing to ~200 bp fragments via sonication and the gDNA fragments were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Bead-based size selection was used to select ~200 bp fragments and the fragments then underwent a splinkerette PCR using a Tn5-enriching forward primer and custom reverse primers for multiplexing. A final bead-based size selection was used to select for the correct length DNA. DNA was sequenced at the University of Michigan Advanced Genomics Core using Illumina sequencing with a custom read primer reading the last 10 nt of the transposon. PhiX174 DNA spike was added to the run to ensure sufficient sequence diversity on the flow cell. Then, a custom index read primer and standard Illumina primer were used to sequence the index reads and PhiX174, respectively.

Keck, James L.↗

Survey of reader preferences concerning the format of NASA technical reports

A survey was conducted to determine the opinions of readers concerning the format (organization) of NASA technical reports and usage of technical report components. A survey questionnaire was sent to 513 LaRC engineers and scientists and 600 engineers and scientists from three (3) professional/technical societies. The response rates were 74 and 85 percent, respectively. The questionnaire included the order in which users read report components, the components reviewed or read to determine whether to read a report, report components which could be deleted, the desirability of a table of contents, the desirability of both a summary and abstract, the location of the symbols list and glossary, the integration of illustrative material, the preferred format for reference citations, column layout and right margin treatment, and person/voice. The results of the reader preference survey indicated that the conclusion was the component most often ready by survey respondents. The summary, conclusion, abstract, title page, and introduction were the components used most frequently to determine if a report would actually be read. Respondents indicated that a summary as well as an abstract should be included, that the definition of symbols and glossary of terms should be located in the front of the report, and that illustrative material should be integrated with the text rather than grouped at the end of the report. Citation by number was the preferred format for references. A one-column, ragged right margin was preferred. Third person, passive voice was the style of writing preferred by the respondents.

Pinelli, T. E.↗

Pseudolog Digital-to-Analog Converter

Sensitivity decreases by 10 at beginning of each input decade. Method conceived to convert binary-coded data to suitable linear form for stripchart recording. Strip-chart recordings obtained from typical pressure readings in a vacuum system during pumpdown. In reading curve, BCD digital vacuum-gage output processed by analog-to-digital converter in such way that only reading digits (but not range) appear in output. In range and reading, range also converted to analog and placed as most significant digit.

Gooder, S. T.↗

Comparing the effectiveness of software testing strategies

This study compares the results of code reading, functional testing, and structural testing in three aspects of software testing: fault detection effectiveness, fault detection cost, and classes of faults detected. Thirty two professional programmers and 42 advanced students applied the three techniques to four unit-sized programs in a fractional experimental design. The major results of this study are the following: (1) With the professional programmers, code reading detected more software faults and had a higher detection rate than did functional or structural testing, while functional testing detected more faults than did structural testing, but functional and structural testing were not different in fault detection rate. (2) In one advanced student subject group, code reading and functional testing were not different in faults found, but were superior to structural testing, while in the other advanced student subject group there was no difference among the techniques. (3) With the advanced student subjects, the three techniques were not different in fault deteciton rate. (4) Number of faults observed, fault detection rate, and total effort in detection depended on the type of software tested. (5) Code reading detected more interface faults than did the other methods. (6) Functional testing detected more control faults than did the other methods. (7) When asked to estimate the percentage of faults detected, code readers gave the most accurate estimates while functional testers gave the least accurate estimates. Appendix B includes the source code for the word.

Basili, Victor R.↗