Assembly Alignment Research Articles

Vision-based trajectory monitoring for assembly alignment of precast concrete bridge components

The prefabricated structures are popularly used because of their high efficiency and it is important to ensure their installation quality. The current installation is guided by visual observation and total station, which is inaccurate and time-consuming. This study presents a stereo-vision-based pose measurement technique for guiding the installation to address the problems. The contributions are as follows: 1) A framework of a vision-based 6-DOF pose monitoring system is designed to track the precast member continuously; 2) A two-level adjustment strategy is suggested by transferring the relative pose measurement between the precast member and existing structure to the process to determine the relative relations of two coordinate systems; 3) A robust deep-learning-based ellipse detection method is proposed to identify and classify the artificial targets accurately. The proposed technique is evaluated in both indoor experiments and the construction of an expressway viaduct to demonstrate its accuracy and effectiveness.

Vision-Aided Brush Alignment Assembly System for Precision Conductive Slip Rings

The alignment precision of manual brush assembly for a precision conductive slip ring is critical to its performance of reliability and service lifetime. Currently, the alignment precision cannot be guaranteed since it largely depends on the operator’s experiences and skill level. In this paper, a machine vision-aided method is proposed to measure the ring groove positions as the brush alignment objective, and track the relative brush position deviation during the manual brush alignment assembly. A vision-aided brush alignment assembly system is also developed to provide quantitative position deviation for the precise alignment of the brush and the ring groove, ensuring higher alignment accuracy and efficiency. The experimental results indicate that, with the developed system, the brush alignment assembly accuracy can be controlled within ±0.02 mm.

A two-step metagenomics approach for the identification and mitochondrial DNA contig assembly of vertebrate prey from the blood meals of common vampire bats (Desmodus rotundus)

The feeding behaviour of the sanguivorous common vampire bat (Desmodus rotundus) facilitates the transmission of pathogens that can impact both human and animal health. To formulate effective strategies in controlling the spread of diseases, there is a need to obtain information on which animals they feed on. One DNA-based approach, shotgun sequencing, can be used to obtain such information. Even though it is costly, shotgun sequencing can be used to simultaneously retrieve prey and vampire bat mitochondrial DNA for population studies within one round of sequencing. However, due to the challenges of analysing shotgun sequenced metagenomic data such as false negatives/positives and typically low proportion of reads mapped to diet items, shotgun sequencing has not been used for the identification of prey from common vampire bat blood meals. To overcome these challenges and generate longer mitochondrial contigs which could be useful for prey population studies, we shotgun sequenced common vampire bat blood meal samples (n = 8) and utilised a two-step metagenomic approach based on combining existing bioinformatic workflows (alignment and mtDNA contig assembly) to identify prey. After validating our results from detections made through metabarcoding, we accurately identified the common vampire bats’ prey in six out of eight samples without any false positives. We also generated prey mitochondrial contig lengths between 138 bp to 3231 bp (median = 770 bp, Q1 = 262 bp, Q3 = 1766 bp). This opens the potential to conduct phylogenetic and phylogeographic monitoring of elusive prey species in future studies, through the analyses of blood meal metagenomic data.

AAPFE: Aligned Assembly Pre-Training Function Embedding for Malware Analysis

The use of natural language processing to analyze binary data is a popular research topic in malware analysis. Embedding binary code into a vector is an important basis for building a binary analysis neural network model. Current solutions focus on embedding instructions or basic block sequences into vectors with recurrent neural network models or utilizing a graph algorithm on control flow graphs or annotated control flow graphs to generate binary representation vectors. In malware analysis, most of these studies only focus on the single structural information of the binary and rely on one corpus. It is difficult for vectors to effectively represent the semantics and functionality of binary code. Therefore, this study proposes aligned assembly pre-training function embedding, a function embedding scheme based on a pre-training aligned assembly. The scheme creatively applies data augmentation and a triplet network structure to the embedding model training. Each sub-network extracts instruction sequence information using the self-attention mechanism and basic block graph structure information with the graph convolution network model. An embedding model is pre-trained with the produced aligned assembly triplet function dataset and is subsequently evaluated against a series of comparative experiments and application evaluations. The results show that the model is superior to the state-of-the-art methods in terms of precision, precision ranking at top N (p@N), and the area under the curve, verifying the effectiveness of the aligned assembly pre-training and multi-level information extraction methods.

All-Atom Simulation Method for Zeeman Alignment and Dipolar Assembly of Magnetic Nanoparticles.

Magnetic nanoparticles (MNPs) can organize into novel structures in solutions with excellent order and unique geometries. However, studies of the self-assembly of smaller MNPs are challenging due to a complicated interplay between external magnetic fields and van der Waals, electrostatic, dipolar, steric, and hydrodynamic interactions. Here, we present a novel all-atom molecular dynamics simulation method to enable detailed studies of the dynamics, self-assembly, structure, and properties of MNPs as a function of core sizes and shapes, ligand chemistry, solvent properties, and external field. We demonstrate the use and effectiveness of the model by simulating the self-assembly of oleic acid ligand-functionalized magnetite (Fe3O4) nanoparticles, with spherical and cubic shapes, into rings, lines, chains, and clusters under a uniform external magnetic field. We found that the long-range electrostatic interactions can favor the formation of a chain over a ring, the ligands promote MNP cluster growth, and the solvent can reduce the rotational diffusion of the MNPs. The algorithm has been parallelized to take advantage of multiple processors of a modern computer and can be used as a plugin for the popular simulation software LAMMPS to study the behavior of small MNPs and gain insights into the physics and chemistry of different magnetic assembly processes with atomistic details.

Limitations of Phylogenomic Data Can Drive Inferred Speciation Rate Shifts.

Biodiversity analyses of phylogenomic timetrees have produced many high-profile examples of shifts in the rate of speciation across the tree of life. Temporally correlated events in ecology, climate, and biogeography are frequently invoked to explain these rate shifts. In a re-examination of 15 genomic timetrees and 25 major published studies of the pattern of speciation through time, we observed an unexpected correlation between the timing of reported rate shifts and the information content of sequence alignments. Here, we show that the paucity of sequence variation and insufficient species sampling in phylogenomic data sets are the likely drivers of many inferred speciation rate shifts, rather than the proposed biological explanations. Therefore, data limitations can produce predictable but spurious signals of rate shifts even when speciation rates may be similar across taxa and time. Our results suggest that the reliable detection of speciation rate shifts requires the acquisition and assembly of long phylogenomic alignments with near-complete species sampling and accurate estimates of species richness for the clades of study.

Discordant Genome Assemblies Drastically Alter the Interpretation of Single-Cell RNA Sequencing Data Which Can Be Mitigated by a Novel Integration Method.

Advances in sequencing and assembly technology have led to the creation of genome assemblies for a wide variety of non-model organisms. The rapid production and proliferation of updated, novel assembly versions can create vexing problems for researchers when multiple-genome assembly versions are available at once, requiring researchers to work with more than one reference genome. Multiple-genome assemblies are especially problematic for researchers studying the genetic makeup of individual cells, as single-cell RNA sequencing (scRNAseq) requires sequenced reads to be mapped and aligned to a single reference genome. Using the Astyanax mexicanus, this study highlights how the interpretation of a single-cell dataset from the same sample changes when aligned to its two different available genome assemblies. We found that the number of cells and expressed genes detected were drastically different when aligning to the different assemblies. When the genome assemblies were used in isolation with their respective annotations, cell-type identification was confounded, as some classic cell-type markers were assembly-specific, whilst other genes showed differential patterns of expression between the two assemblies. To overcome the problems posed by multiple-genome assemblies, we propose that researchers align to each available assembly and then integrate the resultant datasets to produce a final dataset in which all genome alignments can be used simultaneously. We found that this approach increased the accuracy of cell-type identification and maximised the amount of data that could be extracted from our single-cell sample by capturing all possible cells and transcripts. As scRNAseq becomes more widely available, it is imperative that the single-cell community is aware of how genome assembly alignment can alter single-cell data and their interpretation, especially when reviewing studies on non-model organisms.

Lerna: transformer architectures for configuring error correction tools for short- and long-read genome sequencing

BackgroundSequencing technologies are prone to errors, making error correction (EC) necessary for downstream applications. EC tools need to be manually configured for optimal performance. We find that the optimal parameters (e.g., k-mer size) are both tool- and dataset-dependent. Moreover, evaluating the performance (i.e., Alignment-rate or Gain) of a given tool usually relies on a reference genome, but quality reference genomes are not always available. We introduce Lerna for the automated configuration of k-mer-based EC tools. Lerna first creates a language model (LM) of the uncorrected genomic reads, and then, based on this LM, calculates a metric called the perplexity metric to evaluate the corrected reads for different parameter choices. Next, it finds the one that produces the highest alignment rate without using a reference genome. The fundamental intuition of our approach is that the perplexity metric is inversely correlated with the quality of the assembly after error correction. Therefore, Lerna leverages the perplexity metric for automated tuning of k-mer sizes without needing a reference genome.ResultsFirst, we show that the best k-mer value can vary for different datasets, even for the same EC tool. This motivates our design that automates k-mer size selection without using a reference genome. Second, we show the gains of our LM using its component attention-based transformers. We show the model’s estimation of the perplexity metric before and after error correction. The lower the perplexity after correction, the better the k-mer size. We also show that the alignment rate and assembly quality computed for the corrected reads are strongly negatively correlated with the perplexity, enabling the automated selection of k-mer values for better error correction, and hence, improved assembly quality. We validate our approach on both short and long reads. Additionally, we show that our attention-based models have significant runtime improvement for the entire pipeline—18times faster than previous works, due to parallelizing the attention mechanism and the use of JIT compilation for GPU inferencing.ConclusionLerna improves de novo genome assembly by optimizing EC tools. Our code is made available in a public repository at: https://github.com/icanforce/lerna-genomics.

UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs).

BackgroundThe use of Ultraconserved Elements (UCEs) as genetic markers in phylogenomics has become popular and has provided promising results. Although UCE data can be easily obtained from targeted enriched sequencing, the protocol for in silico analysis of UCEs consist of the execution of heterogeneous and complex tools, a challenge for scientists without training in bioinformatics. Developing tools with the adoption of best practices in research software can lessen this problem by improving the execution of computational experiments, thus promoting better reproducibility.New informationWe present UCEasy, an easy-to-install and easy-to-use software package with a simple command line interface that facilitates the computational analysis of UCEs from sequencing samples, following the best practices of research software. UCEasy is a wrapper that standardises, automates and simplifies the quality control of raw reads, assembly and extraction and alignment of UCEs, generating at the end a data matrix with different levels of completeness that can be used to infer phylogenetic trees. We demonstrate the functionalities of UCEasy by reproducing the published results of phylogenomic studies of the bird genus Turdus (Aves) and of Adephaga families (Coleoptera) containing genomic datasets to efficiently extract UCEs.

Deformation control during the welding of AP1000 main pump casing and steam generator

• The AP1000 main pump casing and SG outlet nozzle have strict requirements on alignment precision. • A special RCP bracket is needed for precise assembling. • The joint between pump casing and SG should be TIG welded with different alloy materials. • The first few layers of welding have great influences on the pitch angle and the angle change. The welding of the AP1000 Reactor Coolant Pump (RCP) casing and Steam Generator (SG) is an important issue to maintain the integrity of pressure boundary. The position tolerance of pump casing nozzles after welding will directly affect the internal components of the main pump, as well as the on-site assembling processes. This article investigated the method of controlling deformations during welding (such as assembly alignment, groove design, welding process control, etc), in order to prevent excessive welding deformation and therefore extra discrepancies during pump casing positioning. In this paper, we have developed a welding process, which can allow the installations of AP1000 pump casings to meet all nuclear grade requirements.

Aln2tbl: building a mitochondrial features table from a assembly alignment in fasta format

The sequencing, annotation and analysis of complete mitochondrial genomes is an important research tool in phylogeny and evolution. Starting with the primary sequence, genes/features are generally annotated automatically to obtain preliminary annotations in the form of a feature table. Further manual curation in a graphic alignment editor is nevertheless necessary to revise annotations. As such, the automatically generated feature table is invalidated and has to be modified manually before submission to data banks. We developed aln2tbl.py, a python script that recreates a feature table from a manually refined alignment of genes mapped on the mitochondrial genome in fasta format. The feature table is populated with notes and annotations specific to mitochondrial genomes. The table can be used to create a sqn file to be submitted directly to data banks. In summary, our scripts fills one gap in the available toolbox and, combined with other software, allows the automation of the entire process, from primary sequence to annotated genome submission, even if a manual curation step is conducted in a visual sequence editor.

Engineered whole cut meat-like tissue by the assembly of cell fibers using tendon-gel integrated bioprinting

With the current interest in cultured meat, mammalian cell-based meat has mostly been unstructured. There is thus still a high demand for artificial steak-like meat. We demonstrate in vitro construction of engineered steak-like tissue assembled of three types of bovine cell fibers (muscle, fat, and vessel). Because actual meat is an aligned assembly of the fibers connected to the tendon for the actions of contraction and relaxation, tendon-gel integrated bioprinting was developed to construct tendon-like gels. In this study, a total of 72 fibers comprising 42 muscles, 28 adipose tissues, and 2 blood capillaries were constructed by tendon-gel integrated bioprinting and manually assembled to fabricate steak-like meat with a diameter of 5 mm and a length of 10 mm inspired by a meat cut. The developed tendon-gel integrated bioprinting here could be a promising technology for the fabrication of the desired types of steak-like cultured meats.

Psi-Caller: A Lightweight Short Read-Based Variant Caller With High Speed and Accuracy.

With the rapid development of short-read sequencing technologies, many population-scale resequencing studies have been carried out to study the associations between human genome variants and various phenotypes in recent years. Variant calling is one of the core bioinformatics tasks in such studies to comprehensively discover genomic variants in sequenced samples. Many efforts have been made to develop short read-based variant calling approaches; however, state-of-the-art tools are still computationally expensive. Meanwhile, cutting-edge genomics studies also have higher requirements on the yields of variant calling. Herein, we propose Partial-Order Alignment-based single nucleotide polymorphism (SNV) and Indel caller (Psi-caller), a lightweight variant calling algorithm that simultaneously achieves high performance and yield. Mainly, Psi-caller recognizes and divides the candidate variant site into three categories according to the complexity and location of the signatures and employs various methods including binomial model, partial-order alignment, and de Bruijn graph-based local assembly to handle various categories of candidate variant sites to call and genotype SNVs/Indels, respectively. Benchmarks on simulated and real short-read sequencing data sets demonstrate that Psi-caller is times faster than state-of-the-art tools with higher or equal sensitivity and accuracy. It has the potential to well handle large-scale data sets in cutting-edge genomics studies.

P–230 The NAD+ precursor nicotinamide riboside protects against postovulatary aging in vitro

Abstract Study question Can nicotinamide riboside, one of the NAD+ precursor, protect against postovulatary aging in vitro? Summary answer The NAD+ precursor nicotinamide riboside can protect against postovulatary aging in vitro. What is known already Postovulatory aging(POA) has been considered one of the most intractable challenges that limit the successful rate of ART. Multiple cellular and molecular changes have been involved during the process of POA. The NAD+ is a prominent redox cofactor which is indispensable to DNA repair, energy metabolism, autophagy, genomic stability as well as epigenetic homeostasis. Over the last several decades, increasingly studies have eported that NAD+ contents decline with age across multiple tissues and loss of it are implicated in various diseases associated to aging. As one of a precursor of NAD+, nicotinamide riboside play important role in regulating oxidative stress. Study design, size, duration In this study, we take advantage of in vitro aging model to explore the influences of NR administration on the postovulatory aged oocytes in mice. We analyzed the association of NR supplementation with the aging-related deterioration of oocyte quality, such as mitochondrial dysfunction, mislocalization of cortical granules, followed by embryonic development potential and the NAD+/SIRT1 signaling. We used 3582 oocytes totally. Participants/materials, setting, methods CD–1 mice oocytes/ in vitro culture/ UPLC-MS/MS for NAD+ contents measurement ,DCFH-DA staining for ROS detecting, γH2AX staining for DNA damage measurement, BODIPY FL ATP staining for ATP detecting, LCA-FITC staining to assess the distribution and dynamics of cortical granules (CGs), In vitro fertilization, Quantitative real time PCR Main results and the role of chance NR supplementation exerted protective effects on morphological defects of oocytes, and that these protective effects were concentration dependent. We detected a significantly decline in NAD+ levels in aging oocytes, however, NAD+ accumulation was present in aging oocytes after 200μM NR treatment, indicating that NR administration might be a feasible strategy to enhance the quality of aging oocytes. Furthermore, NR indeed elevated the embryonic development potential of POA oocytes after fertilization. Our findings revealed that NR administration effectively ameliorated ROS accumulation in POA oocytes.Then we tried to uncover the effects of NR on the meiotic apparatus in aging oocytes. NR supplementation can partially restores normal spindle assembly and chromosome alignment in postovulatory aging oocytes. Furthermore, we investigated the protective effects of NR on mitochondrial function through following expects: mitochondrial distribution, ATP production and mitochondrial membrane potential. NR treatment could promote mitochondrial function in oocytes during postovulatory aging in vitro. In addition, DNA damage and mislocalized CGs during postovulatory aging might be rescued by the supplementation of NR. Based on these evidences, we identified that NR improved the quality of aging oocytes by NAD+/SIRT1 axis. Limitations, reasons for caution Only in vitro, shown only in mice. Wider implications of the findings: Our work represents a clinically effective pharmacological chemical to improve infertility caused by POA process. Further studies are needed to define the related mechanisms of NR supplementation on oocyte quality as well as reproductive outcomes clinically. Trial registration number N

Towards Cable-to-Cable Connectors for Flexible Thin-Film Superconducting Transmission Lines

We describe our initial approach and progress towards a reliable and useful technique to connect multiple flexible superconducting cables using a cable-to-cable connector. The test structure comprises multiple components, including flexible thin-film superconducting cables, a bridging connector, a silicon well chip, and a polyimide membranes with Cu pillars. The thin-film superconducting cables used in this work contain 12 parallel Nb lines. A bridging connector which was used to connect two superconducting cables had a stripline structure with 12 parallel superconducting Nb transmission lines with 300 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\mu$</tex-math></inline-formula> m pitch among them. A silicon well chip and a polyimide membrane with Cu pillars have been used in the assembly for high-precision micro-mechanical alignment and to apply uniform pressure on the contact points of cables and the bridging connector. DC resistances of signal traces of connected flexible cables were measured at temperature ranging from 293 K to 4.2 K in an evacuated cryogenic environment. We present the details of the design, fabrication, assembly, and test results, which show that this is a promising cable-to-cable connection approach.

Global and Targeted RNA-Sequencing Assessment of Cancer Testis Antigen Re-Expression Following Azacitidine in Myelodysplastic Syndromes

Background and Aim: Azanucleoside DNA-hypomethylating agents have remarkable clinical activity in myelodysplastic sindromes (MDS) and acute myeloid leukemia (AML), particularly at low, non-cytotoxic doses favoring hypomethylation over cytotoxicity. Cancer/testis antigens (CTAs) encoding immunogenic proteins are normally expressed in the testicles and trophoblastic cells of the ovary and in some malignant tissues: these antigens are expressed to variable degrees particularly in melanoma, multiple myeloma, lung and breast cancer, but expression is quite infrequent in myeloid malignancies. However, they have been shown to undergo derepression after the use of demethylating agents in cell line models. Due to their tumor-restricted expression and their potential immunogenicity, we aimed to comprehensively study CTAs re-expression following azacitidine (AZA) treatment in MDS patients.Methods and Patients: We enrolled 32 patients with MDS (n =22) and chronic myelomonocytic leukemia (n = 10). Deep RNA-sequencing (RNA-Seq) was performed on RNA extracted from blood at day 0 and at day +28 of the first AZA cycle, from 12 patients and compared with 9 healthy donors. RNA-Seq (mean 106 million reads per sample) was sequenced on a HiSeq4000. After TopHat alignment and Cufflinks assembly, expression profile was calculated as FPKM. Targeted RNA-Seq (tRNA-Seq) designed to capture 214 CTA genes was performed on a validation cohort of 20 patients (40 samples). Coverage analysis as well as mapping the reads and alignment was done using the Ion Torrent Browser Suite. We used LIMMA package or empirical analysis of digital gene expression data in R (edgeR) to identify differential expressed genes between day 0 and d+28 samples, and between responder and non-responder groups. A log2 fold change (FC) > 10 and a p<0.1 were considered as significant.Results: The median age of the cohort was 69 (range 48-81 years). The cohort consisted of MDS (75%) and MDS/MPN (25%) patients. MDS Patients were stratified based on IPSS as low (8%), intermediate-1 (23%), intermediate-2 (46%), and high (23%) risk groups and MDS/MPN patients based on CPSS as low (20%), intermediate-1 (20%) and intermediate-2 (60%) . A homogeneous treatment schedule with AZA (75 mg/m2/day x 7 days every 4 weeks) was received by each patient. Seventeen patients were classified as responders (achieving complete remission (CR), marrow CR, partial remission, or stable disease with haematological improvement according to the 2006 International Working Group (IWG) criteria for evaluating MDS. Five patients progressed within the 6 first cycles; otherwise response evaluation was performed after the sixth cycle.In the screening RNA-Seq experiment, MAGEB3, AKAP4, POTEB2 and TMPRSS12 were non-expressed in control or MDS pretreatment, but re-expressed after 1 cycle of Aza; ADAM29, and XAGE1E were non expressed in controls, but expressed in MDS samples: an upregulation which increased after the first cycle.Regarding the tRNA-Seq cohort, on average, we achieved 3.888.308 mapped reads per sample (p25-p75, 1.2x106 - 5.9x106) which represents a sufficient depth for digital gene expression profiling of 214 genes. CTAs re-expressed after one AZA cycle in tRNA-Seq validation cohort: CT45A5, BRDT, TFDP3, TSPY3, TSPY2 showed an FC >10 and a p<0.05 and ADAM29. SLCO6A1, PAGE5 and RQCD1 showed a p<0.05 but a FC<10. CTAs with an increased expression in MDS after Aza: FMR1NB, ADAM29, and XAGE1E were not expressed in controls, re-expressed in MDS before treatment and showed an upregulation after AZA. Responders vs non responders: strikingly CT45A4, and SPAG17 were markedly overexpressed in non-responders than in responders (FC >10, = 0.006; p=0.01), and viceversa for PRM1 and TFDP3 (FC>10; p=0.01, p 0.006).Conclusions: This is the first study to assess, in a global and sentitive design, the targetable re-expression of CTAs following therapeutical demethylation in MDS. Strikingly, in addition to finding attractive targets for cancer immunotherapy, some CTAs were exclusively and markedly re-expressed in non-responders. We also show that targeted RNA-Seq can overcome the test posed by the wide range of the RNA population by sequencing targeted genes providing a vast enrichment of weakly expressed transcripts. DisclosuresNo relevant conflicts of interest to declare.

Combination Treatment of OSI-906 with Aurora B Inhibitor Reduces Cell Viability via Cyclin B1 Degradation-Induced Mitotic Slippage.

Insulin-like growth factor 1 receptor (IGF1R), a receptor-type tyrosine kinase, transduces signals related to cell proliferation, survival, and differentiation. We recently reported that OSI-906, an IGF1R inhibitor, in combination with the Aurora B inhibitor ZM447439 suppresses cell proliferation. However, the mechanism underlying this suppressive effect is yet to be elucidated. In this study, we examined the effects of combination treatment with OSI-906 and ZM447439 on cell division, so as to understand how cell proliferation was suppressed. Morphological analysis showed that the combination treatment generated enlarged cells with aberrant nuclei, whereas neither OSI-906 nor ZM447439 treatment alone caused this morphological change. Flow cytometry analysis indicated that over-replicated cells were generated by the combination treatment, but not by the lone treatment with either inhibitors. Time-lapse imaging showed mitotic slippage following a severe delay in chromosome alignment and cytokinesis failure with furrow regression. Furthermore, in S-trityl-l-cysteine–treated cells, cyclin B1 was precociously degraded. These results suggest that the combination treatment caused severe defect in the chromosome alignment and spindle assembly checkpoint, which resulted in the generation of over-replicated cells. The generation of over-replicated cells with massive aneuploidy may be the cause of reduction of cell viability and cell death. This study provides new possibilities of cancer chemotherapy.

Guest Editorial Special Issue: “From Deletion-Correction to Graph Reconstruction: In Memory of Vladimir I. Levenshtein”

There are few mathematicians whose contributions go beyond named conjectures and theorems: Vladimir Iosifovich Levenshtein ( , 1935–2017) is one such true exception. During the five decades of his active research career, he enriched combinatorics, coding, and information theory with elegant problem formulations, ingenious algorithmic solutions, and highly original proof techniques. However, his work accomplished much more—it paved the way for the creation and advancement of new scientific disciplines, such as natural language processing, metagenomics, sequence alignment, and reference-based genome assembly, as well as DNA-based data storage, to name a few. A crucial concept behind sequence alignment algorithms used in phylogeny, comparative, and cancer genomics, as well as in natural language processing is the Levenshtein (edit) distance and its extension, termed the Damerau–Levenshtein distance between strings. The Levenshtein distance equals the smallest number of insertions, deletions, or substitutions required to convert one string into another. Levenshtein introduced this metric in 1965 [item 1) in the Appendix], followed by the notion of deletion and insertion error-correcting codes that have since been used in a myriad of systems presented with synchronization errors [items 1) and 2) in the Appendix]. Levenshtein’s work also inspired the introduction of the trace reconstruction problem [items 3) and 4) in the Appendix] which has since sparked substantial interest in the field of DNA-based data storage.

WAPL orchestrates porcine oocyte meiotic progression via control of spindle assembly checkpoint activity

BackgroundIn mitotic cells, WAPL acts as a cohesin release factor to remove cohesin complexes from chromosome arms during prophase to allow the accurate chromosome segregation in anaphase. However, we have recently documented that Wapl exerts a unique meiotic function in the spindle assembly checkpoint (SAC) control through maintaining Bub3 stability during mouse oocyte meiosis I. Whether this noncanonical function is conserved among species is still unknown.MethodsWe applied RNAi-based gene silencing approach to deplete WAPL in porcine oocytes, validating the conserved roles of WAPL in the regulation of SAC activity during mammalian oocyte maturation. We also employed immunostaining, immunoblotting and image quantification analyses to test the WAPL depletion on the meiotic progression, spindle assembly, chromosome alignment and dynamics of SAC protein in porcine oocytes.ResultsWe showed that depletion of WAPL resulted in the accelerated meiotic progression by displaying the precocious polar body extrusion and compromised spindle assembly and chromosome alignment. Notably, we observed that the protein level of BUB3 was substantially reduced in WAPL-depleted oocytes, especially at kinetochores.ConclusionsCollectively, our data demonstrate that WAPL participates in the porcine oocyte meiotic progression through maintenance of BUB3 protein levels and SAC activity. This meiotic function of WAPL in oocytes is highly conserved between pigs and mice.

Fast calibration method of alignment prism based on image transformation relation

The alignment assembly based on the principle of coaxial imaging has high accuracy, and the accuracy of coaxial imaging is the key to it. Manually calibrating the pose of the prism to ensure the accuracy of coaxial imaging, which has disadvantages such as difficult operation and long time consuming. This paper analyzes the image relation between the upper and lower parts of the prism based on the optical imaging theory, and solves the image transformation relation between the target part and the assembly part with an experimental method, and proposes a rapid calibration method for the alignment prism based on the image transformation relation. The tedious steps of manually adjusting the prism are eliminated. The experimental results show that this method realizes the high-precision assembly of parts by the micro-assembly system.