Search

Summary Small insertions and deletions (indels) in nucleotide sequence may be represented differently between mapping algorithms and variant callers, or in the flanking sequence context. Representational ambiguity is especially profound for complex indels, complicating comparisons between multiple mappings and call sets. Complex indels may additionally suffer from incomplete allele representation, potentially leading to critical misannotation of variant effect. We present indelPost, a Python library that harmonizes these ambiguities for simple and complex indels via realignment and read-based phasing. We demonstrate that indelPost enables accurate analysis of ambiguous data and can derive the correct complex indel alleles from the simple indel predictions provided by standard small variant detectors, with improved performance over a specialized tool for complex indel analysis. Availability and implementation indelPost is freely available at: https://github.com/stjude/indelPost. Supplementary information Supplementary data are available at Bioinformatics online.

The analysis of thermoacoustic engines and the equations that describe the internal physical phenomena are far from simple. Previous studies on energetic characterisation of thermoacoustic engines are based only on the determination of the active acoustic power flow distribution. In this paper, another variable, known as the reactive acoustic power, is additionally estimated and studied. This article proposes a simple method which is based on the combination of both active and reactive acoustic power flow for the evaluation and optimisation of thermoacoustic Stirling engines. In addition the paper illustrates the method using a thermoacoustic Stirling engine demonstrator design which is able to fit three different feedback branches. The results show that the amount of reactive acoustic power supplied towards the core branch differs depending on the specifications of the selected feedback branch. Besides, the amount of reactive acoustic power distributed towards the core branch is a good indicator of the grade of traveling-wave phasing. An improvement of 16.4% in the active acoustic power towards the extraction branch is achieved and besides, the amplification of the active acoustic power through the core branch has increased by 12%. The method can serve as an effective tool to study and optimise thermoacoustic devices.

The native SAD phasing method uses the anomalous scattering signals from the S atoms contained in most proteins, the P atoms in nucleic acids or other light atoms derived from the solution used for crystallization. These signals are very weak and careful data collection is required, which makes this method very difficult. One way to enhance the anomalous signal is to use long-wavelength X-rays; however, these wavelengths are more strongly absorbed by the materials in the pathway. Therefore, a crystal-mounting platform for native SAD data collection that removes solution around the crystals has been developed. This platform includes a novel solution-free mounting tool and an automatic robot, which extracts the surrounding solution, flash-cools the crystal and inserts the loop into a UniPuck cassette for use in the synchrotron. Eight protein structures (including two new structures) have been successfully solved by the native SAD method from crystals prepared using this platform.

Mesh stiffness variation is a phenomenon that occurs in a mechanical system when there is a change in number of teeth within the system. This phenomenon leads to parametric instabilities and can cause gear systems to experience severe vibration. This paper investigates the effect of mesh stiffness parameters like mesh phasing and contact ratios, in reducing vibrations, when applied to two-stage gear train. Each gear pair is replaced by two gear pairs, each having half the width as that of primary gear pair. The present study has adopted a systematic approach to develop theoretical expressions for evaluation of instability regions that are created by the connections formed between stiffness variations present at the two meshes and four meshes of the primary gear pairs and replaced gear pairs, respectively. The paper has also studied primary instability, secondary instability and combined instability. Required mesh phasing to eliminate instability regions for four gear meshes was found numerically using MATLAB. It is observed that replaced four gear pairs with proper mesh phasing eliminate the instability regions of original two gear pairs of two stage gear train.

Long-wavelength pulses from the Swiss X-ray free-electron laser (XFEL) have been used for de novo protein structure determination by native single-wavelength anomalous diffraction (native-SAD) phasing of serial femtosecond crystallography (SFX) data. In this work, sensitive anomalous data-quality indicators and model proteins were used to quantify improvements in native-SAD at XFELs such as utilization of longer wavelengths, careful experimental geometry optimization, and better post-refinement and partiality correction. Compared with studies using shorter wavelengths at other XFELs and older software versions, up to one order of magnitude reduction in the required number of indexed images for native-SAD was achieved, hence lowering sample consumption and beam-time requirements significantly. Improved data quality and higher anomalous signal facilitate so-far underutilized de novo structure determination of challenging proteins at XFELs. Improvements presented in this work can be used in other types of SFX experiments that require accurate measurements of weak signals, for example time-resolved studies., IUCrJ, 7 (6), ISSN:2052-2525

Structure determination of novel biological macromolecules by X-ray crystallo­graphy can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO, a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyalanine fragments from a set of distantly related sequence homologues. Alternatively, such templates were extracted in spherical volumes and given internal degrees of freedom to refine towards the target structure. Both modes relied on the rotation function in Phaser to identify or refine fragment models and its translation function to place them. Model completion from the placed fragments proceeded through phase combination of partial solutions and/or density modification and main-chain autotracing using SHELXE. The combined set of fragments was sufficient to arrive at a solution that resembled that determined by conventional molecular replacement using the known target structure as a search model. This approach obviates the need for a single, complete and highly accurate search model when phasing MicroED data, and permits the evaluation of large fragment libraries for this purpose., This work was performed as part of STROBE, an NSF Science and Technology Center, through grant DMR-1548924. This work was also supported by DOE grant DE-FC02-02ER63421 and NIH–NIGMS grants R35 GM128867 and P41GM136508. LSR is supported by USPHS National Research Service Award 5T32GM008496. RJB received a fellowship from FAPESP (16/24191-8 and 17/13485-3). CM is grateful to MICINN for her BES-2015-71397 scholarship associated with the Structural Biology Maria de Maeztu Unit of Excellence. This work was supported by grants BIO2015-64216-P, PGC2018-101370-B-100 and MDM2014-0435-01 (the Spanish Ministry of Economy and Competitiveness) and Generalitat de Catalunya (2017SGR-1192). JAR is supported as a Searle Scholar, a Pew Scholar and a Beckman Young Investigator. The Gonen laboratory is supported by the Howard Hughes Medical Institute; this work was also partially supported by the Janelia Research Campus Visitor Exchange Program.

We have demonstrated an experimental setup for the coherent phasing of a seven-channel fibre laser system ( λ = 1064 nm) in a scheme comprising a master oscillator and a set of parallel amplifiers with lithium niobate-based fibre-optic phase modulators. Using a stochastic parallel gradient algorithm, an instrumental phase modulator control unit ensures a bandwidth of the system up to 450 kHz. The effectiveness of phasing of light transmitted through a turbulent medium with a characteristic time scale τ turb has been studied experimentally as a function of phasing time τ ph. The results demonstrate that the average Strehl ratio begins to rise at τ turb/τ ph ⩾ 2 and that the effectiveness of compensation for dynamic phase distortions in the beam propagation path rises sharply at τ turb/τ ph ≈ 20. For τ turb/τ ph ⩾ 30 – 40, the average Strehl ratio remains constant at the level reached.

Low spectral resolution and extensive peak overlap are the common challenges that preclude quantitative analysis of nuclear magnetic resonance (NMR) data with the established peak integration method. While numerous model-based approaches overcome these obstacles and enable quantification, they intrinsically rely on rigid assumptions about functional forms for peaks, which are often insufficient to account for all unforeseen imperfections in experimental data. Indeed, even in spectra with well-separated peaks whose integration is possible, model-based methods often achieve suboptimal results, which in turn raises the question of their validity for more challenging datasets. We address this problem with a simple model adjustment procedure, which draws its inspiration directly from the peak integration approach that is almost invariant to lineshape deviations. Specifically, we assume that the number of mixture components along with their ideal spectral responses are known; we then aim to recover all useful signals left in the residual after model fitting and use it to adjust the intensity estimates of modelled peaks. We propose an alternative objective function, which we found particularly effective for correcting imperfect phasing of the data – a critical step in the processing pipeline. Application of our method to the analysis of experimental data shows the accuracy improvement of 20 %–40 % compared to the simple least-squares model fitting.

This letter presents a single-layer dual-circular-polarization reflectarray antenna with independent beam control for each polarization. First, a novel phasing approach, combining the variable-size approach and the element rotation approach together, is theoretically devised to achieve independent phase shifts for left hand circular polarized antenna (LHCP) and right hand circular polarized antenna (RHCP) waves. Then, a single-layer nested split-ring element has been designed as an example, and independent 360° phase shift for each circular polarization has been achieved. Finally, a Ka-band (20 GHz) reflectarray prototype with a circular aperture of 390 mm in diameter is designed, fabricated, and tested. Independent pencil beams radiating to the predesigned directions for each polarization were achieved. The measured gain is 35.5 dBi at –30° with the aperture efficiency of 52.7% for the LHCP excitation, and the measured gain is 35.4 dBi at 30° with the aperture efficiency of 51.6% for the RHCP excitation. The measured 1 dB gain bandwidths are 10.5% (19.4–21.5 GHz) and 10.0% (19.5–21.5 GHz) for the LHCP and RHCP excitations, respectively.

This article describes the development of a simplified verification model (SVM) for an early-warning radar system, which is the first step to building a digital twin for such a system. An SVM is useful for the understanding of the operating principles of a device, thus enabling the determination of its control parameters. It is demonstrated that an SVM can be used for the development of calibration and phasing algorithms for the transmitting and receiving paths with respect to an external source and a reference signal. In addition, an SVM can simulate the processing of signals from various targets, such as aircrafts or satellites. This article presents the architecture of the developed SVM and its control interface. SVMs can be used to generate source data for the development of more complex models.

The development of experimental techniques, in particular the emergence of the X-ray free-electron lasers, allows one to register the scattering from an isolated particle and, thereby, opens a door to the study of a fine three-dimensional structure of non-crystalline biological objects by X-ray diffraction methods. The possibility to measure non-Bragg reflections makes experimental data mutually dependent and essentially simplifies the structure solution. The sampling of experimental scattering data to a sufficiently fine grid makes the structure determination equivalent to phasing of structure factor magnitudes for a 'virtual' crystal with extremely large solvent content. This makes density modification phasing methods especially powerful supposing the object envelope is known. At the same time, such methods may be sensitive to the accuracy of the predefined envelope and completeness of experimental data and may suffer from non-uniqueness of the solution of the phase problem. The mask-based approach is a preliminary phasing method that performs random search for connected object envelopes possessing of the structure factor magnitudes close to the values observed in X-ray experiment. The alignment and averaging of the phase sets corresponding to selected putative envelopes produce an approximate solution of the phase problem. Beside the estimation of unknown phase values this approach allows one to estimate the values of structure factor magnitudes lost in the experiment, e.g. those corresponding to beam-stop shade zone or to oversaturated reflections.

The solution of coiled-coil crystal structures may be achieved by AMPLE through the use of ensembled ab initio models in molecular replacement. Improvements in ab initio modelling of elongated helices and oligomeric coiled-coils allow AMPLE to solve a greater number of coiled-coil structures and at lower resolution than previously achieved., The phase problem remains a major barrier to overcome in protein structure solution by X-ray crystallography. In recent years, new molecular-replacement approaches using ab initio models and ideal secondary-structure components have greatly contributed to the solution of novel structures in the absence of clear homologues in the PDB or experimental phasing information. This has been particularly successful for highly α-helical structures, and especially coiled-coils, in which the relatively rigid α-helices provide very useful molecular-replacement fragments. This has been seen within the program AMPLE, which uses clustered and truncated ensembles of numerous ab initio models in structure solution, and is already accomplished for α-helical and coiled-coil structures. Here, an expansion in the scope of coiled-coil structure solution by AMPLE is reported, which has been achieved through general improvements in the pipeline, the removal of tNCS correction in molecular replacement and two improved methods for ab initio modelling. Of the latter improvements, enforcing the modelling of elongated helices overcame the bias towards globular folds and provided a rapid method (equivalent to the time requirements of the existing modelling procedures in AMPLE) for enhanced solution. Further, the modelling of two-, three- and four-helical oligomeric coiled-coils, and the use of full/partial oligomers in molecular replacement, provided additional success in difficult and lower resolution cases. Together, these approaches have enabled the solution of a number of parallel/antiparallel dimeric, trimeric and tetrameric coiled-coils at resolutions as low as 3.3 Å, and have thus overcome previous limitations in AMPLE and provided a new functionality in coiled-coil structure solution at lower resolutions. These new approaches have been incorporated into a new release of AMPLE in which automated elongated monomer and oligomer modelling may be activated by selecting ‘coiled-coil’ mode.

A new version (2.0) of the pipeline IPCAS (Iterative Protein Crystal structure Automatic Solution) has been released, in which the program OASIS performs direct-method single-wavelength anomalous diffraction/single isomorphous replacement phasing and direct-method-aided partial-structure extension. IPCAS incorporates the widely used packages CCP4 and PHENIX for locating heavy atoms, density modification, molecular replacement, model building and refinement. Important extensions to the previous version of IPCAS include a resolution screening method for non-crystallographic symmetry searching, an alternate model-building protocol for avoiding premature convergence and direct-method image processing for electron microscopy maps, including single-particle cryo-EM maps. Moreover, a new graphical user interface is provided for controlling and real-time monitoring of the whole dual-space iterative process, which works as a plugin to CCP4i. Applications of the new IPCAS to difficult cases have yielded promising results, including `direct-method phasing and fragment extension' from weak anomalous diffraction signal data and `direct-method-aided partial-structure extension' from low-homology models.

Combining data-analysis statistics from crystallographic software with machine learning can predict the chances of experimental phasing success., This study describes a method to estimate the likelihood of success in determining a macromolecular structure by X-ray crystallography and experimental single-wavelength anomalous dispersion (SAD) or multiple-wavelength anomalous dispersion (MAD) phasing based on initial data-processing statistics and sample crystal properties. Such a predictive tool can rapidly assess the usefulness of data and guide the collection of an optimal data set. The increase in data rates from modern macromolecular crystallography beamlines, together with a demand from users for real-time feedback, has led to pressure on computational resources and a need for smarter data handling. Statistical and machine-learning methods have been applied to construct a classifier that displays 95% accuracy for training and testing data sets compiled from 440 solved structures. Applying this classifier to new data achieved 79% accuracy. These scores already provide clear guidance as to the effective use of computing resources and offer a starting point for a personalized data-collection assistant.

A noncrystallographic symmetry-constrained map obtained by direct density optimization is efficient and equivalent to a noncrystallographic symmetry-averaging map. Using the noncrystallographic symmetry-constrained map, the structure of a T = 1 Penaeus vannamei nodavirus shell-domain subviral particle was newly determined by including twinned data., Noncrystallographic symmetry (NCS) averaging following molecular-replacement phasing is generally the major technique used to solve a structure with several molecules in one asymmetric unit, such as a spherical icosahedral viral particle. As an alternative method to NCS averaging, a new approach to optimize or to refine the electron density directly under NCS constraints is proposed. This method has the same effect as the conventional NCS-averaging method but does not include the process of Fourier synthesis to generate the electron density from amplitudes and the corresponding phases. It has great merit for the solution of structures with limited data that are either twinned or incomplete at low resolution. This method was applied to the case of the T = 1 shell-domain subviral particle of Penaeus vannamei nodavirus with data affected by twinning using the REFMAC5 refinement software.

Motivation Full-length transcript reconstruction is very important and quite challenging for the widely used RNA-seq data analysis. Currently, available RNA-seq assemblers generally suffered from serious limitations in practical applications, such as low assembly accuracy and incompatibility with latest alignment tools. Results We introduce iPAC, a new genome-guided assembler for reconstruction of isoforms, which revolutionizes the usage of paired-end and sequencing depth information via phasing and combing paths over a newly designed phasing graph. Tested on both simulated and real datasets, it is to some extent superior to all the salient assemblers of the same kind. Especially, iPAC is significantly powerful in recovery of lowly expressed transcripts while others are not. Availability and implementation iPAC is freely available at http://sourceforge.net/projects/transassembly/files. Supplementary information Supplementary data are available at Bioinformatics online.

Improvements to the sensitivity of the search for suitable molecular-replacement search models in SIMBAD through the use of Phaser and an ensemble-based model database are reported., The conventional approach to search-model identification in molecular replacement (MR) is to screen a database of known structures using the target sequence. However, this strategy is not always effective, for example when the relationship between sequence and structural similarity fails or when the crystal contents are not those expected. An alternative approach is to identify suitable search models directly from the experimental data. SIMBAD is a sequence-independent MR pipeline that uses either a crystal lattice search or MR functions to directly locate suitable search models from databases. The previous version of SIMBAD used the fast AMoRe rotation-function search. Here, a new version of SIMBAD which makes use of Phaser and its likelihood scoring to improve the sensitivity of the pipeline is presented. It is shown that the additional compute time potentially required by the more sophisticated scoring is counterbalanced by the greater sensitivity, allowing more cases to trigger early-termination criteria, rather than running to completion. Using Phaser solved 17 out of 25 test cases in comparison to the ten solved with AMoRe, and it is shown that use of ensemble search models produces additional performance benefits.

Eisenia hydrolysis-enhancing protein (EHEP), which is a novel protein that has been identified in Aplysia kurodai, protects β-glucosidases from phlorotannin inhibition to facilitate the production of glucose from the laminarin abundant in brown algae. Hence, EHEP has attracted attention for its potential applications in producing biofuel from brown algae. In this study, EHEP was purified from the natural digestive fluid of A. kurodai and was crystallized using the sitting-drop vapor-diffusion method. Native and SAD (single-wavelength anomalous diffraction) data sets were successfully collected at resolutions of 1.20 and 2.48 Å using wavelengths of 1.0 and 2.1 Å, respectively, from crystals obtained in initial screening. The crystals belonged to space group P212121 and contained one EHEP molecule in the asymmetric unit. All 20 S-atom sites in EHEP were located and the phases were determined by the SAD method using the S atoms in the natural protein as anomalous scatterers (native-SAD). After phase improvement, interpretable electron densities were obtained and 58% of the model was automatically built.

Software Product Lines (SPLs) are rarely developed from scratch. Commonly, they emerge from one product when there is a need to create tailored variants, or from existing variants created in an ad-hoc way once their separated maintenance and evolution become challenging. Despite the vast literature about re-engineering systems into SPLs and related technical approaches, there is a lack of detailed analysis of the process itself and the effort involved. In this paper, we provide and analyze empirical data of the extraction processes of two open-source case studies, namely ArgoUML and Phaser. Both cases emerged from the transition of a monolithic system into an SPL. The analysis relies on information mined from the version control history of their respective source-code repositories and the discussion with developers that took part in the process. Unlike previous works that focused mostly on the structural results of the final SPL, the contribution of this study is an in-depth characterization of the processes. With this work, we aimed at providing a deeper understanding of the strategies for SPL extraction and their implications. Our results indicate that the source code changes can range from almost a fourth to over half of the total lines of code. Developers may or may not use branching strategies for feature extraction. Additionally, the problems faced during the extraction process may be due to lack of tool support, complexity on managing feature dependencies and issues with feature constraints. We made publicly available the datasets and the analysis scripts of both case studies to be used as a baseline for extractive SPL adoption research and practice. Version of record

A novel dual-polarization, single-layer reflectarray has been designed and manufactured to operate at receive (20 GHz) and transmit (30 GHz) frequencies for Ka-band terminal antennas. The reflectarray unit cell is composed of several types of resonant elements printed on the upper side of a conductor-backed substrate, which are designed to produce a collimated beam at 20 and 30 GHz in dual polarization. Cross-shaped loops are used to provide the required phases at 20 GHz, while crossed dipoles and modified truncated rings are used to control the phasing at 30 GHz. The resonant lengths of the proposed elements have been adjusted cell by cell by means of a two-dimensional interpolation method to achieve the required phase shift at each frequency. Two different feeds have been used to illuminate the reflectarray at 20 and 30 GHz. The measured gain is 28.02 dBi at 20 GHz and 32.14 dBi at 30 GHz. The measurement results show that the radiation patterns of the designed single-layer reflectarray antenna are in good agreement with those achieved from the simulations.

Funder: CCP4, Funder: Max‐Planck‐Gesellschaft; Id: http://dx.doi.org/10.13039/501100004189, The assessment of CASP models for utility in molecular replacement is a measure of their use in a valuable real‐world application. In CASP7, the metric for molecular replacement assessment involved full likelihood‐based molecular replacement searches; however, this restricted the assessable targets to crystal structures with only one copy of the target in the asymmetric unit, and to those where the search found the correct pose. In CASP10, full molecular replacement searches were replaced by likelihood‐based rigid‐body refinement of models superimposed on the target using the LGA algorithm, with the metric being the refined log‐likelihood‐gain (LLG) score. This enabled multi‐copy targets and very poor models to be evaluated, but a significant further issue remained: the requirement of diffraction data for assessment. We introduce here the relative‐expected‐LLG (reLLG), which is independent of diffraction data. This reLLG is also independent of any crystal form, and can be calculated regardless of the source of the target, be it X‐ray, NMR or cryo‐EM. We calibrate the reLLG against the LLG for targets in CASP14, showing that it is a robust measure of both model and group ranking. Like the LLG, the reLLG shows that accurate coordinate error estimates add substantial value to predicted models. We find that refinement by CASP groups can often convert an inadequate initial model into a successful MR search model. Consistent with findings from others, we show that the AlphaFold2 models are sufficiently good, and reliably so, to surpass other current model generation strategies for attempting molecular replacement phasing.

Herein we present the newest version of the HKL-3000 system that integrates data collection, data reduction, phasing, model building, refinement, and validation. The system significantly accelerates the process of structure determination and has proven its high value for the determination of very high-quality structures. The heuristic for choosing the best approach for every step of structure determination for various quality samples and diffraction data has been optimized. The latest modifications increase the likelihood of a successful structure determination with challenging data. The HKL-3000 is a successor of HKL and HKL-2000 programs. The use of the HKL family of programs has been reported for over 73,000 PDB deposits, that is, almost 50% of macromolecular structures determined with X-ray diffraction.

BackgroundWhen analyzing DNA sequence data of an individual, knowing which nucleotide was inherited from each parent can be beneficial when trying to identify certain types of DNA variants. Mendelian inheritance logic can be used to accurately phase (haplotype) the majority (67–83%) of an individual's heterozygous nucleotide positions when genotypes are available for both parents (trio). However, when all members of a trio are heterozygous at a position, Mendelian inheritance logic cannot be used to phase. For such positions, a computational phasing algorithm can be used. Existing phasing algorithms use a haplotype reference panel, sequencing reads, and/or parental genotypes to phase an individual; however, they are limited in that they can only phase certain types of variants, require a specific genotype build, require large amounts of storage capacity, and/or require long run times. We created trioPhaser to address these challenges.ResultstrioPhaser uses gVCF files from an individual and their parents as initial input, and then outputs a phased VCF file. Input trio data are first phased using Mendelian inheritance logic. Then, the positions that cannot be phased using inheritance information alone are phased by theSHAPEIT4 phasing algorithm. Using whole-genome sequencing data of 52 trios, we show that trioPhaser, on average, increases the total number of phased positions by 21.0% and 10.5%, respectively, when compared to the number of positions thatSHAPEIT4or Mendelian inheritance logic can phase when either is used alone. In addition, we show that the accuracy of the phased calls output by trioPhaser are similar to linked-read and read-backed phasing.ConclusiontrioPhaser is a containerized software tool that uses both Mendelian inheritance logic andSHAPEIT4to phase trios when gVCF files are available. By implementing both phasing methods, more variant positions are phased compared to what either method is able to phase alone.

Whole-genome data has become significantly more accessible over the last two decades. This can largely be attributed to both reduced sequencing costs and imputation models which make it possible to obtain nearly whole-genome data from less expensive genotyping methods, such as microarray chips. Although there are many different approaches to imputation, the Hidden Markov Model remains the most widely used. In this study, we compared the latest versions of the most popular Hidden Markov Model based tools for phasing and imputation: Beagle 5.2, Eagle 2.4.1, Shapeit 4, Impute 5 and Minimac 4. We benchmarked them on three input datasets with three levels of chip density. We assessed each imputation software on the basis of accuracy, speed and memory usage, and showed how the choice of imputation accuracy metric can result in different interpretations. The highest average concordance rate was achieved by Beagle 5.2, followed by Impute 5 and Minimac 4, using a reference-based approach during phasing and the highest density chip. IQS and R2 metrics revealed that IMPUTE5 obtained better results for low frequency markers, while Beagle 5.2 remained more accurate for common markers (MAF>5%). Computational load as measured by run time was lower for Beagle 5.2 than Impute 5 and Minimac 4, while Minimac utilized the least memory of the imputation tools we compared. ShapeIT 4, used the least memory of the phasing tools examined, even with the highest density chip. Finally, we determined the combination of phasing software, imputation software, and reference panel, best suited for different situations and analysis needs and created an automated pipeline that provides a way for users to create customized chips designed to optimize their imputation results.

Diesel engines equipped with ignition assist devices such as glow plugs may improve combustion behavior at low temperatures and with low cetane fuels found in remote fields. The coordination of injection timing and the energy input of the ignition assist needs to continuously adjust to maintain the best combustion phasing at all conditions. However, most diesel engines do not use closed-loop combustion control and operate in a sub-optimal manner because the dispersion of combustion phasing, also known as cycle-to-cycle variability, requires careful feedback controller design. This work presents an initial investigation of a control-oriented model that captures the average and statistical influence of commercial glow plugs used for ignition assist beyond the start-up phase. Experiments were conducted at a single speed and load operating point as a proof of concept to obtain a model that quantifies the combustion phasing statistics and thus can guide feedback control design. The developed phenomenological model includes the engine’s thermal state because it impacts combustion behavior over the course of repeated experiments. The 3-term mean phasing model and 2-term standard deviation model estimate start of combustion within 0.6 and 0.2 crank angle degrees, respectively, and can be readily expanded to more operating conditions.

Segmented primary mirror provides many crucial important advantages for the construction of extra-large space telescopes. The imaging quality of this class of telescope is susceptible to phasing error between primary mirror segments. Deep learning has been widely applied in the field of optical imaging and wavefront sensing, including phasing segmented mirrors. Compared to other image-based phasing techniques, such as phase retrieval and phase diversity, deep learning has the advantage of high efficiency and free of stagnation problem. However, at present deep learning methods are mainly applied to coarse phasing and used to estimate piston error between segments. In this paper, deep Bi-GRU neural work is introduced to fine phasing of segmented mirrors, which not only has a much simpler structure than CNN or LSTM network, but also can effectively solve the gradient vanishing problem in training due to long term dependencies. By incorporating phasing errors (piston and tip-tilt errors), some low-order aberrations as well as other practical considerations, Bi-GRU neural work can effectively be used for fine phasing of segmented mirrors. Simulations and real experiments are used to demonstrate the accuracy and effectiveness of the proposed methods.

The phasing parameter F determines the relative phasing between satellites in different orbital planes and thereby affects the relative position of the satellites in a constellation. The collisions between satellites within the constellation can be avoided if the minimum distance among them is large. From among the possible values of F in a constellation, a value of F is desired that leads to the maximum value of the minimum distance between satellites. We investigate F for two biggest upcoming satellite constellations including Starlink Phase 1 Version 3 and Kuiper Shell 2. No existing work or FCC filing provides a value of F that is suitable for these two constellations. We look for the best value of F in these constellations that provides the maximum value of the minimum distance to ensure intra-constellation avoidance of collisions between satellites. To this end, we simulate each constellation for each value of F to find its best value based on ranking. Out of the 22 and 36 possible values of F for Starlink Phase 1 Version 3 and Kuiper Shell 2, respectively, it is observed that the best value of F with highest ranking is 17 and 11 that leads to the largest minimum distance between satellites of 61.83 km and 55.89 km in these constellations, respectively., Comment: Accepted for publication in proceedings of 2021 5G World Forum Workshop on Satellite and Non-Terrestrial Networks

Trapping ions, performing qubit operations and quantum multi-qubit gates require complex pulse spectra on several frequency bands. The Smart Arbitrary Waveform Generators (SAWG) Sayma and Phaser are designed to trap control and generate the Short-time Fourier transform (STFT) pulses. They have quad channels of over 1.2 GS/s (Giga Samples per second) 16-bit DACs and a few MS/s (Mega Samples per second) ADCs. These modules are dedicated to implementing qubit operations, both optically and electronically. The Sayma and Phaser modules are part of the Sinara family - a modular, open-source measurement and control hardware ecosystem dedicated to quantum applications that require deterministic high-resolution timing. The hardware is controlled and managed by the ARTIQ open-source software platform, which provides nanosecond timing resolution and sub-microsecond latency via a high-level programming language. We present the Sayma and the Phaser construction and obtained characteristics.

After admixture, recombination breaks down genomic blocks of contiguous ancestry. The breakdown of these blocks forms a new "molecular clock" that ticks at a much faster rate than the mutation clock, enabling accurate dating of admixture events in the recent past. However, existing theory on the breakdown of these blocks, or the accumulation of delineations between blocks, so-called "junctions", has mostly been limited to using regularly spaced markers on phased data. Here, we present an extension to the theory of junctions using the ancestral recombination graph that describes the expected number of junctions for any distribution of markers along the genome. Furthermore, we provide a new framework to infer the time since admixture using unphased data. We demonstrate both the phased and unphased methods on simulated data and show that our new extensions have improved accuracy with respect to previous methods, especially for smaller population sizes and more ancient admixture times. Lastly, we demonstrate the applicability of our method on three empirical data sets, including labcrosses of yeast (Saccharomyces cerevisae) and two case studies of hybridization in swordtail fish and Populus trees. Funding information: Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México, Grant/Award Number: 2018

There are three types of left-turn traffic signal phasing: protected, permitted, and protected-permitted. Using protected-permitted, the traffic signal displays a sequence of a static green arrow followed by a flashing yellow arrow. With protected phasing, only a static green arrow is shown. Traditionally, crash data, traffic volumes, and engineering judgement are used to select the type of left-turn operation. This approach often takes several years to accumulate statistically significant crash data, and engineering judgement can vary considerably. This study utilizes connected vehicle data to analyze the change on vehicle delay, progression, and hard-acceleration at a location where a protected-permitted left-turn was changed to a protected-only. Over 7,000 vehicle trajectories (172,000 GPS points) were analyzed. The analysis found that hard-accelerations after the stop bar decreased by 14% following the change on the left-turn phasing. However, control delay increased by 28 seconds, corresponding to a decrease in level of service from C to E for the left-turning vehicles. This paper contributes a methodology that can assess efficiency and safety surrogate measures that can be scaled in a systematic manner. This scalable technique is particularly valuable for agencies that want to assess operations and/or prioritize improvements across hundreds or thousands of signals. In this study, the effects on vehicle behavior and signal performance after changing the eastbound (EB) left-turn fixed-time phasing at the intersection of US-40 and German Church Rd., located east of Indianapolis (Fig. 1, callout ii), are analyzed.

Microcrystal electron diffraction (MicroED) is transforming the visualization of molecules from nanocrystals, rendering their three-dimensional atomic structures from previously unamenable samples. Peptidic structures determined by MicroED include naturally occurring peptides, synthetic protein fragments and peptide-based natural products. However, as a diffraction method, MicroED is beholden to the phase problem, and its de novo determination of structures remains a challenge. ARCIMBOLDO, an automated, fragment-based approach to structure determination. It eliminates the need for atomic resolution, instead enforcing stereochemical constraints through libraries of small model fragments, and discerning congruent motifs in solution space to ensure validation. This approach expands the reach of MicroED to presently inaccessible peptidic structures including segments of human amyloids, and yeast and mammalian prions, and portends a more general phasing solution while limiting model bias for a wider set of chemical structures.

Transcript assembly (i.e., to reconstruct the full-length expressed transcripts from RNA-seq data) has been a critical but yet unsolved step in RNA-seq analysis. Modern RNA-seq protocols can produce paired-/multiple-end RNA-seq reads, where information is available that two or more reads originate from the same transcript. The long-range constraints implied in these paired-/multiple-end reads can be much beneficial in correctly phasing the complicated spliced isoforms. However, there often exist gaps among individual ends, which may even contain junctions, making the efficient use of such constraints algorithmically challenging. Here we introduce Scallop2, a new reference-based transcript assembler optimized for multiple-end (including paired-end) RNA-seq data. Scallop2 uses an algorithmic frame-work that first represents reads from the same molecule as the so-called multiple-end phasing paths in the context of a splice graph, then “bridges” each multiple-end phasing path into a long, single-end phasing path, and finally decomposes the splice graph into paths (i.e., transcripts) guided by the bridged phasing paths. An efficient bridging algorithm is designed to infer the true path connecting two consecutive ends following a novel formulation that is robust to sequencing errors and transcript noises. By observing that failing to bridge two ends is mainly due to incomplete splice graphs, we propose a new method to determine false starting/ending vertices of the splice graphs which has been showed efficient in reducing false positive rate. Evaluations on both (multiple-end) single-cell RNA-seq datasets from Smart-seq3 protocol and Illumina paired-end RNA-seq samples demonstrate that Scallop2 vastly outperforms recent assemblers including StringTie2, Scallop, and CLASS2 in assembly accuracy.

MotivationHaplotype phasing approaches have been shown to improve accuracy of the search space of neoantigen prediction by determining if adjacent variants are located on the same chromosomal copy. However, the aneuploid nature of cancer cells as well as the admixture of different clones in tumor bulk sequencing data are challenging the current diploid based phasing algorithms. We present microphaser, a small-scale phasing approach to improve haplotyping variants in cancer samples. Microphaser aims to create a more accurate neopeptidome for downstream neoantigen prediction.ResultsMicrophaser achieves large concordance with state-of-the-art phasing-aware neoantigen prediction pipeline neoepiscope, with differences in edge cases and an improved filtering step.AvailabilityMicrophaser is written in the Rust programming language. It is made available via Github (https://github.com/koesterlab/microphaser)and Bioconda. The corresponding prediction pipeline (https://github.com/snakemake-workflows/dna-seq-neoantigen-prediction) has been written within the Snakemake workflow management system and can be deployed as part of the snakemake-workflows project.

Velocity of a deeply non-relativistic particle can change during its acceleration inside an RF cavity significantly enough to cause a deviation of the energy gain from a linear model. This paper derives formulae for corrections to the energy gain in a two-gap RF cavity calculated by taking into account this velocity change in the next approximation. Then, the results are compared with direct particle tracking of an HWR cavity used at the PIP2IT test accelerator. The formulae significantly extend the range of parameters where analytical calculations work with a good accuracy. The approach is applied to two aspects of cavity phasing.

This article further explores a previously proposed gray-box neural network approach to modeling LFO (low-frequency oscillator) modulated time-varying audio effects. The network inputs are both the unprocessed audio and LFO signal. This allows the LFO to be freely controlled after model training. This paper introduces an improved process for accurately measuring the frequency response of a time-varying system over time, which is used to annotate the neural network training data with the LFO of the effect being modeled. Accuracy is improved by using a frequency domain synthesized chirp signal and using shorter and more closely spaced chirps. A digital flanger effect is used to test the accuracy of the method and neural network models of two guitar effects pedals, a phaser and flanger, were created. The improvement in the system measurement method is reflected in the accuracy of the resulting models, which significantly outperform previously reported results. When modeling a phaser and flanger pedal, error-to-signal ratios of 0.2% and 0.3% were achieved, respectively. Previous work suggests errors of this size are often inaudible. The model architecture can run in real time on a modern computer while using relatively little processing power.

This study investigates the effect of applying scenario-based phase designs for isolation valve installation by developing an optimal multiphase valve design model while previous research f...

Traffic accidents cause a huge loss to the society. According to statistics, 50% of all accidents occur at urban intersections and 47% of these are due to left-turn collisions. Countermeasure Implementation at these locations therefore can play a vital role in the improvement of traffic safety. This study illustrates a methodology for evaluation of urban 4-legged signalized intersections treated with left-turn priority phasing. The methodology is applied to three important collisions types: those due to left-turn collisions; those due to left-turn side impact collisions; and all impact types combined collisions. Data used in this analysis were obtained from the City of Toronto. Safety Performance Functions for left-turn and all impact types combined collisions which were developed by the City of Toronto, were calibrated and used in an empirical Bayesian methodology that was employed to estimate the expected frequency of accidents occurring at each intersection in order to evaluate the effectiveness of left-turn priority phasing in reducing this frequency. The results revealed that left-turn priority phasing can be an effective treatment for addressing and reducing the number of collision at signalized intersections. Flashing advance green phasing is more effective in improving safety for two of three types; all left-turn and all impact types combined collisions. Left-turn green arrow (protected/permissive) phasing is more effective for left-turn side impact collisions. By implementing this type of treatment, the number of crashes and the associated monetary loss to society could be significantly reduced.

SAD phasing of XFEL data is shown to require accurate error estimates from the merged reflection intensities. Various methods of treating the errors are presented, including a best-practice approach that refines error-correction terms using a nonlinear least-squares method., A nonlinear least-squares method for refining a parametric expression describing the estimated errors of reflection intensities in serial crystallographic (SX) data is presented. This approach, which is similar to that used in the rotation method of crystallographic data collection at synchrotrons, propagates error estimates from photon-counting statistics to the merged data. Here, it is demonstrated that the application of this approach to SX data provides better SAD phasing ability, enabling the autobuilding of a protein structure that had previously failed to be built. Estimating the error in the merged reflection intensities requires the understanding and propagation of all of the sources of error arising from the measurements. One type of error, which is well understood, is the counting error introduced when the detector counts X-ray photons. Thus, if other types of random errors (such as readout noise) as well as uncertainties in systematic corrections (such as from X-ray attenuation) are completely understood, they can be propagated along with the counting error, as appropriate. In practice, most software packages propagate as much error as they know how to model and then include error-adjustment terms that scale the error estimates until they explain the variance among the measurements. If this is performed carefully, then during SAD phasing likelihood-based approaches can make optimal use of these error estimates, increasing the chance of a successful structure solution. In serial crystallography, SAD phasing has remained challenging, with the few examples of de novo protein structure solution each requiring many thousands of diffraction patterns. Here, the effects of different methods of treating the error estimates are estimated and it is shown that using a parametric approach that includes terms proportional to the known experimental uncertainty, the reflection intensity and the squared reflection intensity to improve the error estimates can allow SAD phasing even from weak zinc anomalous signal.

Pluridirectional high-energy agile scanning electronic radiotherapy (PHASER) is next-generation medical linac technology for ultra-rapid highly conformal image-guided radiation, fast enough to "freeze" physiological motion, affording improved accuracy, precision, and potentially superior FLASH radiobiological therapeutic index. Designed for compactness, economy, and clinical efficiency, it is also intended to address barriers to global access to curative radiotherapy.

The features of the multimode steady-state generation of superradiant heterolasers, in which quantum dots with a long incoherent relaxation time serve as an active medium, while low-Q combined Fabry–Perot cavities with a distributed feedback of counter-propagating waves serve as cavities, are studied. It is shown that due to the quantum-coherent dynamics of optical dipole oscillations and population inversion of the working levels in a quantum-dot ensemble with strong inhomogeneous broadening of the spectral line, the simultaneous lasing of modes with various degrees of phasing and/or correlation and with qualitatively different dynamic behavior, notably, quasi-stationary, metastable, self-modulation, pulse-periodic, and quasi-chaotic is possible.

The effects of the phase difference between fore- and hindwings are experimentally investigated on the aerodynamic force, aerodynamic efficiency, and longitudinal control forces for tandem flapping...

When using remote radiophysical methods in problems of monitoring the environment, the central place belongs to solving problems of determining its electrophysical characteristics, i.e. dielectric permittivity e, conductivity c (complex permittivity ek). The complex dielectric permittivity e, determined in one way or another, serves as the basis for determining the physical characteristics of the medium under study: temperature, humidity, salinity, hardness, etc. The method for remote determination of complex dielectric permittivity is proposed based on relative amplitude-phase relations in the radar receiver channels (orthogonal in polarization) (we call it determination of the polarization phasor). Knowledge of the polarization phasor makes it possible to determine uniquely both the permittivity and the conductivity of the surface under investigation. The latter is presented in the form of a series of universal graphs which allow one to directly interpret the physical characteristics of surfaces. It shows how the polarization phasor is placed on the KLL-sphere. In addition, the trajectory of the phaser on this sphere is investigated in the case when the physical characteristics of the investigated surface change. The random nature of local changes in the electrophysical properties of the surface under study leads to random fluctuations of the polarization phasor. The paper contains a two-dimensional density distribution of the permittivity and conductivity, as well as the corresponding one-dimensional densities. A graphic illustration of the relations obtained is given.

This paper presents a quadrature injection-locked frequency tripler (ILFT) adopting third-harmonic phase shifters for quadrature signal injection at the third-harmonic band. Two capacitively degenerated differential transconductor pairs inject quadrature currents to the main I/Q $LC$ tanks. The degeneration networks are optimally designed to create quadrature injection signals at the third harmonic of injection signal. The presented third-harmonically quadrature phasing technique increases an injection-locking range effectively with the minimizing injection signal loss compared with prior conventional injection techniques employing phase shifters at the fundamental frequency. The proposed ILFT is implemented in 130-nm CMOS technology. The measured injection-locking range is 3.3% (~800 MHz) at the 23.6-GHz center frequency with 0-dBm input injection power. The locking range of the proposed ILFT is twice wider than that of prior state-of-the-art ILFTs adopting single differential signal injections or polyphase filter-based quadrature signal injections. The proposed ILFT consumes 10.4 mW, and the chip size is $0.5\times0.25$ mm2 without pads.

Protected–permissive left turn (PPLT) phasing has been popular and widely used in many urban intersections in North America because of its operational benefits. A significant number of intersections have recently been upgraded with four-section signal heads with flashing yellow arrow (FYA) indication for an effective protected–permissive left turn operation. The present study seeks to find appropriate length of two red intervals whose roles are important, but different during the transition period of FYA-PPLT phasing. One is a red interval for delayed-start of permissive left turn movements; the other is additional red interval for delayed-start of opposing through movements. Micro-traffic simulation and conflict analysis are explored to assess the effects of the red intervals on intersection efficiency and safety. A useful reference, which describes the balanced length of the two red intervals under varying traffic levels, is developed as a result.

Planetary gearboxes have a wide range of applications, but due to their complex layout, the diagnostics of planetary gearboxes is more challenging than that of fixed-axis gearboxes. This is especially so for planet gears, as multiple planets mesh simultaneously, share the same rotating speed and are in mesh with both the sun and ring gears. To enable the development of reliable diagnostic and, even more critically, prognostic algorithms, the detection of a fault needs to be complemented with information about its location and the dominant failure mode. In this study, we present a comprehensive procedure to diagnose localised planet gear faults, adding to fault detection the differential diagnosis of cracks and spalls and the identification of the faulty planet. To do this, first the transmission error (TE) of planet cracks and spalls is investigated using a finite element model. This is aimed at providing a thorough understanding of how these two types of faults result in different excitations of the system. A lumped parameter model (LPM) is then used to link the changes in TE to specific vibration patterns, which are identified as characteristic of either tooth cracks or spalls. These observations are then combined with a recently proposed concept that uses mesh phasing to identify which planet gear carries a fault, resulting in a comprehensive framework that can both diagnose the type of fault and determine which planet gear it is on. The methodology is verified using experimental data obtained from a planetary gearbox test rig.