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Motivation Long-read phasing has been used for reconstructing diploid genomes, improving variant calling and resolving microbial strains in metagenomics. However, the phasing blocks of existing methods are broken by large Structural Variations (SVs), and the efficiency is unsatisfactory for population-scale phasing. Results This article presents a novel algorithm, LongPhase, which can simultaneously phase single nucleotide polymorphisms (SNPs) and SVs of a human genome in 10–20 min, 10× faster than the state-of-the-art WhatsHap, HapCUT2 and Margin. In particular, co-phasing SNPs and SVs produces much larger haplotype blocks (N50 = 25 Mbp) than those of existing methods (N50 = 10–15 Mbp). We show that LongPhase combined with Nanopore ultra-long reads is a cost-effective and highly contiguous solution, which can produce between one and 26 blocks per chromosome arm without the need for additional trios, chromosome-conformation and strand-seq data. Availabilityand implementation LongPhase is freely available at https://github.com/twolinin/LongPhase/. Supplementary information Supplementary data are available at Bioinformatics online.

NMR spectra acquired with experiments using frequency-sweeps such as the wide-band uniform-rate smooth truncation (WURST) spin-echo and Carr-Purcell-Meiboom-Gill (CPMG) sequences cannot be absorptively phased by using only conventional zeroth- and first-order phase correction. Implementation of phase correction up to the second-order is described for obtaining absorptive spectra, which have more desirable line shapes and noise properties than magnitude spectra. The relationship of the second-order phase to the parameters of frequency sweeps is derived. The second-order phasing in the frequency-domain is equivalent to a point spread in the time-domain signal. The application of second-order phase correction is demonstrated with a wideline 35Cl CPMG spikelet spectrum.

IUCrJ 8(6), 905 - 920 (2021). doi:10.1107/S2052252521008046, Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables essentially radiation-damage-free macromolecular structure determination using microcrystals that are too small for synchrotron studies. However, SFX experiments often require large amounts of sample in order to collect highly redundant data where some of the many stochastic errors can be averaged out to determine accurate structure-factor amplitudes. In this work, the capability of the Swiss X-ray free-electron laser (SwissFEL) was used to generate large-bandwidth X-ray pulses [$����/��$ = 2.2% full width at half-maximum (FWHM)], which were applied in SFX with the aim of improving the partiality of Bragg spots and thus decreasing sample consumption while maintaining the data quality. Sensitive data-quality indicators such as anomalous signal from native thaumatin micro-crystals and de novo phasing results were used to quantify the benefits of using pink X-ray pulses to obtain accurate structure-factor amplitudes. Compared with data measured using the same setup but using X-ray pulses with typical quasi-monochromatic XFEL bandwidth (����/�� = 0.17% FWHM), up to fourfold reduction in the number of indexed diffraction patterns required to obtain similar data quality was achieved. This novel approach, pink-beam SFX, facilitates the yet underutilized de novo structure determination of challenging proteins at XFELs, thereby opening the door to more scientific breakthroughs., Published by Chester

Many in-band full-duplex (IBFD) applications require omnidirectional radiation coverage in addition to multilayered self-interference cancellation (SIC). While system-level SIC approaches often require high-isolation antennas before implementing analog and/or digital methods, maintaining the desired omnidirectional transmit/receive patterns is difficult for compact designs that utilize the same polarization. This article discusses the concept development and design progression of the circular mode phasing technique applied to omnidirectional IBFD antenna arrays. The theoretical fundamentals are presented along with simulation results and then validated through the discussion of two prototype antennas, which were measured to provide up to 60 dB of isolation over 2.4–2.5 GHz, which is the highest reported for this SIC method. Additionally, the evolution of this concept for a collection of measured prototypes is summarized and characterized with a unique figure of merit, which should help advance the application of this technique within future IBFD systems.

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. This research was partially funded by CNPq, grant no. 408356/2018-9; FAPPR, grant no. 51435; and FAPERJ PDR-10 Fellowship 202073/2020. Open access funding provided by Johannes Kepler University Linz

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

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.

Multi-aperture imaging systems can be used to decrease the size, weight, and cost of an imaging system while retaining a resolution related to the diameter of the aperture gain. One solution for phasing apertures in an array uses anamorphic pupil remapping and a computational phase correction algorithm. It is shown that using blazed gratings to remap the aperture fields reduces field dependent contrast and leads to piston corrections for partially coherent illumination. Additionally, rotational aperture synthesis is used to combine two piston corrected images and create an image with resolution increases in more than just the axis of aperture gain.

In this paper, co-phasing errors of a segmented primary mirror tiled by hexagonal segments are successfully calculated for the 12-meter Large aperture Optical/infrared Telescope (LOT). Co-phasing errors including out-of-plane errors are simulated separately and comprehensively based on several software simulation platforms. PAOLA simulation results show that the Strehl Ratio (SR) of LOT is larger than 0.8 when the RMS value of tip-tilt obeying a normal distribution is less than 0.018 arcsec, and the SR of LOT is larger than 0.8 when the RMS value of piston obeying a normal distribution is less than 40 nm. Besides, simulation results of Zemax show that the SR of LOT is larger than 0.8 when the RMS value of tip-tilt obeying a normal distribution is less than 0.02 arcsec, and the SR of LOT is larger than 0.8 when the RMS value of piston obeying a normal distribution is less than 40 nm. These simulation results successfully lay a solid foundation for LOT (especially the segmented primary mirror with active optics).