Accuracy Assessment of Geometric-Distortion Identification Methods for Sentinel-1 Synthetic Aperture Radar Imagery in Highland Mountainous Regions.

SAR imagery plays a crucial role in geological and environmental monitoring, particularly in highland mountainous regions. However, inherent geometric distortions in SAR images often undermine the precision of remote sensing analyses. Accurately identifying and classifying these distortions is key to analyzing their origins and enhancing the quality and accuracy of monitoring efforts. While the layover and shadow map (LSM) approach is commonly utilized to identify distortions, it falls short in classifying subtle ones. This study introduces a novel LSM ground-range slope (LG) method, tailored for the refined identification of minor distortions to augment the LSM approach. We implemented the LG method on Sentinel-1 SAR imagery from the tri-junction area where the Xiaojiang, Pudu, and Jinsha rivers converge at the Yunnan-Sichuan border. By comparing effective monitoring-point densities, we evaluated and validated traditional methods-LSM, R-Index, and P-NG-against the LG method. The LG method demonstrates superior performance in discriminating subtle distortions within complex terrains through its secondary classification process, which allows for precise and comprehensive recognition of geometric distortions. Furthermore, our research examines the impact of varying slope parameters during the classification process on the accuracy of distortion identification. This study addresses significant gaps in recognizing geometric distortions and lays a foundation for more precise SAR imagery analysis in complex geographic settings.

The LiV3O8 Superlattice Cathode with Optimized Zinc Ion Insertion Chemistry for High Mass-Loading Aqueous Zinc-Ion Batteries.

Resolving the sluggish transport kinetics of divalent Zn2+ in the cathode lattice and improving mass-loading performance are crucial for advancing the zinc-ion batteries (AZIBs) application. Herein, PEO-LiV3O8 superlattice nanosheets (PEO-LVO) with expanded interlayer spacing (1.16 nm) are fabricated to provide a high-rate, stable lifetime, and large mass-loading cathode. The steady in-plane expansion without shrinkage after the first cycle, but reversible H+/Zn2+ co-insertion in PEO-LVO are demonstrated by operando synchrotron X-ray diffraction and ex situ characterizations. Moreover, the large capacity of PEO-LVO is traced back to the optimized Zn2+ insertion chemistry with increased Zn2+ storage ratio, which is facilitated by the interlayer PEO in lowering the Zn2+ diffusion barrier and increased number of active sites from additional interfaces, as anticipated by density functional theory. Due to the optimized ion insertion resulting in stalled interfacial byproducts and rapid kinetics, PEO-LVO achieves excellent high mass-loading performance (areal capacity up to 6.18 mAh cm-2 for freestanding electrode with 24 mg cm-2 mass-loading and 2.8 mAh cm-2 at 130 mA cm-2 for conventional electrode with 27 mg cm-2 mass-loading). As a proof-of-concept, the flexible all-solid-state fiber-shaped AZIBs with high mass-loading woven into a fabric can power an electronic watch, highlighting the application potential of PEO-LVO cathode.

Flanked Block-Interchange Distance on Strings.

Rearrangement sorting problems impact profoundly in measuring genome similarities and tracing historic scenarios of species. However, recent studies on genome rearrangement mechanisms disclosed a statistically significant evidence, repeats are situated at the ends of rearrangement relevant segments and stay unchanged before and after rearrangements.To reflect the principle behind this evidence, we propose flanked block-interchange, an operation on strings that exchanges two substrings flanked by identical left and right symbols in a string. The flanked block-interchange distance problem is formulated as finding a shortest sequence of flanked block-interchanges to transform a string into the other. We propose a sufficient and necessary condition for deciding whether two strings can be transformed into each other by flanked block-interchanges. This condition is linear time verifiable. Under this condition for two strings, we present a [Formula: see text]-approximation algorithm for the flanked block-interchange distance problem where each symbol occurs at most k times in a string and a polynomial algorithm for this problem where each symbol occurs at most twice in a string. We show that the problem of flanked block-interchange distance is NP-hard at last.

In Situ Formed Amorphous Bismuth Sulfide Cathodes with a Self-Controlled Conversion Storage Mechanism for High Performance Hybrid Ion Batteries.

Conversion-type electrodes offer a promising multielectron transfer alternative to intercalation hosts with potentially high-capacity release in batteries. However, the poor cycle stability severely hinders their application, especially in aqueous multivalence-ion systems, which can fundamentally impute to anisotropic ion diffusion channel collapse in pristine crystals and irreversible bond fracture during repeated conversion. Here, an amorphous bismuth sulfide (a-BS) formed in situ with unprecedentedly self-controlled moderate conversion Cu2+ storage is proposed to comprehensively regulate the isotropic ion diffusion channels and highly reversible bond evolution. Operando synchrotron X-ray diffraction and substantive verification tests reveal that the total destruction of the Bi─S bond and unsustainable deep alloying are fully restrained. The amorphous structure with robust ion diffusion channels, unique self-controlled moderate conversion, and high electrical conductivity discharge products synergistically boosts the capacity (326.7 mAh g-1 at 1 A g-1 ), rate performance (194.5 mAh g-1 at 10 A g-1 ), and long-lifespan stability (over 8000 cycles with a decay rate of only 0.02 ‰ per cycle). Moreover, the a-BS Cu2+ ‖Zn2+ hybrid ion battery can well supply a stable energy density of 238.6 Wh kg-1 at 9760 W kg-1 . The intrinsically high-stability conversion mechanism explored on amorphous electrodes provides a new opportunity for advanced aqueous storage.

Cation Defect-Engineered Boost Fast Kinetics of Two-Dimensional Topological Bi2 Se3 Cathode for High-Performance Aqueous Zn-Ion Batteries.

The challenge with aqueous zinc-ion batteries (ZIBs) lies in finding suitable cathode materials that can provide high capacity and fast kinetics. Herein, two-dimensional topological Bi2 Se3 with acceptable Bi-vacancies for ZIBs cathode (Cu-Bi2-x Se3 ) is constructed through one-step hydrothermal process accompanied by Cu heteroatom introduction. The cation-deficient Cu-Bi2-x Se3 nanosheets (≈4 nm) bring improved conductivity from large surface topological metal states contribution and enhanced bulk conductivity. Besides, the increased adsorption energy and reduced Zn2+ migration barrier demonstrated by density-functional theory (DFT) calculations illustrate the decreased Coulombic ion-lattice repulsion of Cu-Bi2-x Se3 . Therefore, Cu-Bi2-x Se3 exhibits both enhanced ion and electron transport capability, leading to more carrier reversible insertion proved by in situ synchrotron X-ray diffraction (SXRD). These features endow Cu-Bi2-x Se3 with sufficient specific capacity (320 mA h g-1 at 0.1 A g-1 ), high-rate performance (97 mA h g-1 at 10 A g-1 ), and reliable cycling stability (70 mA h g-1 at 10 A g-1 after 4000 cycles). Furthermore, quasi-solid-state fiber-shaped ZIBs employing the Cu-Bi2-x Se3 cathode demonstrate respectable performance and superior flexibility even under high mass loading. This work implements a conceptually innovative strategy represented by cation defect design in topological insulator cathode for achieving high-performance battery electrochemistry.

Unravelling Twin Topotactic/Nontopotactic Reactive TiSe2 Cathodes for Aqueous Batteries.

Titanium selenide (TiSe2 ), a model transition metal chalcogenide material, typically relies on topotactic ion intercalation/deintercalation to achieve stable ion storage with minimal disruption of the transport pathways but has restricted capacity (<130 mAh g-1 ). Developing novel energy storage mechanisms beyond conventional intercalation to break capacity limits in TiSe2 cathodes is essential yet challenging. Herein, the ion storage properties of TiSe2 are revisited and an unusual thermodynamically stable twin topotactic/nontopotactic Cu2+ accommodation mechanism for aqueous batteries is unraveled. In situ synchrotron X-ray diffraction and ex situ microscopy jointly demonstrated that topotactic intercalation sustained the ion transport framework, nontopotactic conversion involved localized multielectron reactions, and these two parallel reactions are miraculously intertwined in nanoscale space. Comprehensive experimental and theoretical results suggested that the twin-reaction mechanism significantly improved the electron transfer ability, and the reserved intercalated TiSe2 structure anchored the reduced titanium monomers with high affinity and promoted efficient charge transfer to synergistically enhance the capacity and reversibility. Consequently, TiSe2 nanoflake cathodes delivered a never-before-achieved capacity of 275.9 mAh g-1 at 0.1 A g-1 , 93.5% capacity retention over 1000 cycles, and endow hybrid batteries (TiSe2 -Cu||Zn) with a stable energy supply of 181.34 Wh kg-1 at 2339.81 W kg-1 , offering a promising model for aqueous ion storage.

Accumulative Delocalized Mo 4d Electrons to Bound the Volume Expansion and Accelerate Kinetics in Mo6S8 Cathode for High-Performance Aqueous Cu2+ Storage.

Electronic structure defines the conductivity and ion absorption characteristics of a functional electrode, significantly affecting the charge transfer capability in batteries, while it is rarely thought to be involved in mesoscopic volume and diffusion kinetics of the host lattice for promoting ion storage. Here, we first correlate the evolution in electronic structure of the Mo6S8 cathode with the ability to bound volume expansion and accelerate diffusion kinetics for high-performance aqueous Cu2+ storage. Operando synchrotron energy-dispersive X-ray absorption spectroscopy reveals that accumulative delocalized Mo 4d electrons enhance the Mo-Mo interaction with distinctly contracting and uniformizing Mo6 clusters during the reduction of Mo6S8, which potently restrain lattice expansion and release space to promote Cu2+ diffusion kinetics. Operando synchrotron X-ray diffraction and comprehensive characterizations further validate the structural and electrochemical properties induced by the Cu2+ intercalation electronic structure, endowing the Mo6S8 cathode a high specific capacity with small volume expansion, fast ions diffusion, and long-term cycling stability.

Ultrahigh-Speed Aqueous Copper Electrodes Stabilized by Phosphorylated Interphase.

High-energy metal anodes for large-scale reversible batteries with inexpensive and nonflammable aqueous electrolytes promise the capability of supporting higher current density, satisfactory lifetime, nontoxicity, and low-cost commercial manufacturing, yet remain out of reach due to the lack of reliable electrode-electrolyte interphase engineering. Herein, in situ formed robust interphase on copper metal electrodes (CMEs) induced by a trace amount of potassium dihydrogen phosphate (0.05 m in 1 m CuSO4 -H2 O electrolyte) to fulfill all aforementioned requirements is demonstrated. Impressively, an unprecedented ultrahigh-speed copper plating/stripping capability is achieved at 100 mA cm-2  for over 12 000 cycles, corresponding to an accumulative areal capacity up to tens of times higher than previously reported CMEs. The use of solid-electrolyte interface-protection strategy brings at least an order of magnitude improvement in cycling stability for symmetric cells (Cu||Cu, 2800 h) and full batteries with CMEs using either sulfur cathodes (S||Cu, 1000 cycles without capacity decay) or zinc anodes (Cu||Zn with all-metal electrodes, discharge voltage ≈1.02 V). The comprehensive analysis reveals that the hydrophilic phosphate-rich interphase nanostructures homogenize copper-ion deposition and suppress nucleation overpotential, enabling dendrite-free CMEs with sustainability and ability to tolerate unusual-high power densities. The findings represent an elegant forerunner toward the promising goal of metal electrode applications.

Malaria transmission-blocking vaccines Pfs230D1-EPA and Pfs25-EPA in Alhydrogel in healthy Malian adults; a phase 1, randomised, controlled trial.

BACKGROUND: Malaria transmission-blocking vaccines target mosquito-stage parasites and will support elimination programmes. Gamete vaccine Pfs230D1-EPA/Alhydrogel induced superior activity to zygote vaccine Pfs25-EPA/Alhydrogel in malaria-naive US adults. Here, we compared these vaccines in malaria-experienced Malians. METHODS: We did a pilot safety study then double-blind, block-randomised, comparator-controlled main-phase trial in malaria-intense Bancoumana, Mali. 18-50-year-old healthy non-pregnant, non-breastfeeding consenting adult residents were randomly assigned (1:1:1:1) to receive four doses at months 0, 1, 4·5, and 16·5 of either 47 µg Pfs25, 40 µg Pfs230D1 or comparator (Twinrix or Menactra)-all co-administered with normal saline for blinding-or 47 µg Pfs25 plus 40 µg Pfs230D1 co-administered. We documented safety and tolerability (primary endpoint in the as-treated populations) and immunogenicity (secondary endpoint in the as-treated populations: ELISA, standard-membrane-feeding assay, and mosquito direct skin feed assay). This trial is registered at ClinicalTrials.gov, NCT02334462. FINDINGS: Between March 19, and June 2, 2015, we screened 471 individuals. Of 225 enrolled for the pilot and main cohorts, we randomly assigned 25 participants to pilot safety cohort groups of five (20%) to receive a two-dose series of Pfs25-EPA/Alhydrogel (16 µg), Pfs230D1-EPA/Alhydrogel (15 µg) or comparator, followed by Pfs25-EPA/Alhydrogel (16 µg) plus Pfs230D1-EPA/Alhydrogel (15 µg) or comparator plus saline. For the main cohort, we enrolled 200 participants between May 11 and June 2, 2015, to receive a four-dose series of 47 µg Pfs25-EPA/Alhydrogel plus saline (n=50 [25%]; Pfs25), 40 µg Pfs230D1-EPA/Alhydrogel plus saline (n=49 [25%]; Pfs230D1), 47 µg Pfs25-EPA/Alhydrogel plus 40 µg Pfs230D1-EPA/Alhydrogel (n=50 [25%]; Pfs25 plus Pfs230D1), or comparator (Twinrix or Menactra) plus saline (n=51 [25%]). Vaccinations were well tolerated in the pilot safety and main phases. Most vaccinees became seropositive after two Pfs230D1 or three Pfs25 doses; peak titres increased with each dose thereafter (Pfs230D1 geometric mean: 77·8 [95% CI 56·9-106·3], 146·4 [108·3-198·0], and 410·2 [301·6-558·0]; Pfs25 geometric mean 177·7 [130·3-242·4] and 315·7 [209·9-474·6]). Functional activity (mean peak transmission-reducing activity) appeared for Pfs230D1 (74·5% [66·6-82·5]) and Pfs25 plus Pfs230D1 (68·6% [57·3-79·8]), after the third dose and after the fourth dose (88·9% [81·7-96·2] for Pfs230D1 and 85·0% [78·4-91·5] Pfs25 plus Pfs230D1) but not for Pfs25 (58·2% [49·1-67·3] after the third dose and 58·2% [48·5-67·9] after the fourth dose). Pfs230D1 transmission-reducing activity (73·7% [64·1-83·3]) persisted 10 weeks after the fourth dose. Transmission-reducing activity of 80% was estimated at 1659 ELISA units for Pfs25, 218 for Pfs230D1, and 223 for Pfs230D1 plus Pfs25. After 3850 direct skin feed assays, 35 participants (12 Pfs25, eight Pfs230D1, five Pfs25 plus Pfs230D1, and ten comparator) had transmitted parasites at least once. The proportion of positive assays in vaccine groups (Pfs25 33 [3%] of 982 [-0·013 to 0·014], Pfs230D1 22 [2%] of 954 [-0·005 to 0·027], and combination 11 [1%] of 940 [-0·024 to 0·002]) did not differ from that of the comparator (22 [2%] of 974), nor did Pfs230D1 and combination groups differ (-0·024 to 0·001). INTERPRETATION: Pfs230D1 but not Pfs25 vaccine induces durable serum functional activity in Malian adults. Direct skin feed assays detect parasite transmission to mosquitoes but increased event rates are needed to assess vaccine effectiveness. FUNDING: Intramural Research Program of the National Institute of Allergy and Infectious Diseases and US National Institutes of Health.

An asymmetric electrolyte to simultaneously meet contradictory requirements of anode and cathode.

One of the major obstacles hindering the application of zinc metal batteries is the contradictory demands from the Zn metal anode and cathodes. At the anode side, water induces serious corrosion and dendrite growth, remarkably suppressing the reversibility of Zn plating/stripping. At the cathode side, water is essential because many cathode materials require both H+ and Zn2+ insertion/extraction to achieve a high capacity and long lifespan. Herein, an asymmetric design of inorganic solid-state electrolyte combined with hydrogel electrolyte is presented to simultaneously meet the as-mentioned contrary requirements. The inorganic solid-state electrolyte is toward the Zn anode to realize a dendrite-free and corrosion-free highly reversible Zn plating/stripping, and the hydrogel electrolyte enables consequent H+ and Zn2+ insertion/extraction at the cathode side for high performance. Therefore, there is no hydrogen and dendrite growth detected in cells with a super high-areal-capacity up to 10 mAh·cm-2 (Zn//Zn), ~5.5 mAh·cm-2 (Zn//MnO2) and ~7.2 mAh·cm-2 (Zn//V2O5). These Zn//MnO2 and Zn//V2O5 batteries show remarkable cycling stability over 1000 cycles with 92.4% and over 400 cycles with 90.5% initial capacity retained, respectively.

Elucidating the Reaction Mechanism of Mn2+ Electrolyte Additives in Aqueous Zinc Batteries.

Aqueous zinc batteries (ZIBs) have attracted considerable attention in recent years because of their high safety and eco-friendly features. Numerous studies have shown that adding Mn2+ salts to ZnSO4 electrolytes enhanced overall energy densities and extended the cycling life of Zn/MnO2 batteries. It is commonly believed that Mn2+ additives in the electrolyte inhibit the dissolution of MnO2 cathode. To better understand the role of Mn2+ electrolyte additives, the ZIB using a Co3 O4 cathode instead of MnO2 in 0.3 m MnSO4 + 3 m ZnSO4 electrolyte is built to avoid interference from MnO2 cathode. As expected, the Zn/Co3 O4 battery exhibits electrochemical characteristics nearly identical to those of Zn/MnO2 batteries. Operando synchrotron X-ray diffraction (XRD), ex situ X-ray absorption spectroscopy (XAS), and electrochemical analyses are carried out to determine the reaction mechanism and pathway. This work demonstrates that the electrochemical reaction occurring at cathode involves a reversible Mn2+ /MnO2 deposition/dissolution process, while a chemical reaction of Zn2+ /Zn4 SO4 (OH)6 ∙5H2 O deposition/dissolution is involved during part of the charge/discharge cycle due to the change in the electrolyte environment. The reversible Zn2+ /Zn4 SO4 (OH)6 ∙5H2 O reaction contributes no capacity and lowers the diffusion kinetics of the Mn2+ /MnO2 reaction, which prevents the operation of ZIBs at high current densities.

Ultrastable Cu2+ Intercalation Chemistry Based on a Niobium Sulfide Nanosheet Cathode for Advanced Aqueous Storage Devices.

Exploring stable and durable cathodes for cost-effective reversible aqueous batteries is highly desirable for grid-scale energy storage applications, but significant challenges remain. Herein, we disclosed an ultrastable Cu2+ intercalation chemistry in mass-produced exfoliated NbS2 nanosheets to build ultralong lifespan aqueous batteries with cost advantages. Anisotropic interplanar expansion of NbS2 lattices balanced dynamic Cu2+ incorporation and the highly reversible redox reaction of Nb4+/Nb(4-δ)+ couple were illuminated by operando synchrotron X-ray diffraction and energy dispersive X-ray absorption spectroscopy, affording an extraordinary capacity of approximately 317 mAh g-1 at 1 A g-1 and a good stability of 92.2% capacity retention after 40000 cycles at 10 A g-1. Impressively, a budget NbS2||Fe hybrid ion cell involving an aqueous electrolyte/Fe-metal anode is established and provides a reliable energy supply of 225.4 Wh kg-1 at 750 W kg-1, providing insights for building advanced aqueous battery systems for large-scale applications.

Initiating Reversible Aqueous Copper-Tellurium Conversion Reaction with High Volumetric Capacity through Electrolyte Engineering.

Pursuing conversion-type cathodes with high volumetric capacity that can be used in aqueous environments remains rewarding and challenging. Tellurium (Te) is a promising alternative electrode due to its intrinsic attractive electronic conductivity and high theoretical volumetric capacity yet still to be explored. Herein, the kinetically/thermodynamically co-dominat copper-tellurium (Cu-Te) alloying phase-conversion process and corresponding oxidation failure mechanism of tellurium are investigated using in situ synchrotron X-ray diffraction and comprehensive ex situ characterization techniques. By virtue of the fundamental insights into the tellurium electrode, facile and precise electrolyte engineering (solvated structure modulation or reductive antioxidant addition) is implemented to essentially tackle the dramatic capacity loss in tellurium, affording reversible aqueous Cu-Te conversion reaction with an unprecedented ultrahigh volumetric capacity of up to 3927 mAh cm-3 , a flat long discharge plateau (capacity proportion of ≈81%), and an extraordinary level of capacity retention of 80.4% over 2000 cycles at 20 A g-1 of which lifespan thousand-fold longer than Cu-Te conversion using CuSO4 -H2 O electrolyte. This work paves a significant avenue for expanding high-performance conversion-type cathodes toward energetic aqueous multivalent-ion batteries.

Automatic accurate longitudinal location of structural defects in sewer pipes via monocular ranging.

Rough manual interpretation distance cannot keep up with the intelligent detection and interpretation of sewer pipe defects. We present an automatic location method for the accurate longitudinal distance of the structural defects in sewer pipes via a pinhole-based defect monocular ranging model via image processing of pipe diameters. Then the model verification experiment is undertaken through a comparison with the actual data of the pipe size and the camera parameters. The results of the experiment demonstrate an improved accuracy of this method of defect spatial location and the robustness and stability of the model of the accurate acquisition of the longitudinal distance based on the monocular ranging between the inspection robot and the pipe defect.

A Volume Self-Regulation MoS2 Superstructure Cathode for Stable and High Mass-Loaded Zn-Ion Storage.

Engineering multifunctional superstructure cathodes to conquer the critical issue of sluggish kinetics and large volume changes associated with divalent Zn-ion intercalation reactions is highly desirable for boosting practical Zn-ion battery applications. Herein, it is demonstrated that a MoS2/C19H42N+ (CTAB) superstructure can be rationally designed as a stable and high-rate cathode. Incorporation of soft organic CTAB into a rigid MoS2 host forming the superlattice structure not only effectively initiates and smooths Zn2+ transport paths by significantly expanding the MoS2 interlayer spacing (1.0 nm) but also endows structural stability to accommodate Zn2+ storage with expansion along the MoS2 in-plane, while synchronous shrinkage along the superlattice interlayer achieves volume self-regulation of the whole cathode, as evidenced by in situ synchrotron X-ray diffraction and substantial ex situ characterizations. Consequently, the optimized superlattice cathode delivers high-rate performance, long-term cycling stability (∼92.8% capacity retention at 10 A g-1 after 2100 cycles), and favorable flexibility in a pouch cell. Moreover, a decent areal capacity (0.87 mAh cm-2) is achieved even after a 10-fold increase of loading mass (∼11.5 mg cm-2), which is of great significance for practical applications. This work highlights the design of multifunctional superlattice electrodes for high-performance aqueous batteries.

ContactLib-ATT: a structure-based search engine for homologous proteins.

General-purpose protein structure embedding can be used for many important protein biology tasks, such as protein design, drug design and binding affinity prediction. Recent researches have shown that attention-based encoder layers are more suitable to learn high-level features. Based on this key observation, we propose a two-level general-purpose protein structure embedding neural network, called ContactLib-ATT. On local embedding level, a biologically more meaningful contact context is introduced. On global embedding level, attention-based encoder layers are employed for better global representation learning. Our general-purpose protein structure embedding framework is trained and tested on the SCOP40 2.07 dataset. As a result, ContactLib-ATT achieves a SCOP superfamily classification accuracy of 82.4% (i.e., 6.7% higher than state-of-the-art method). On the same dataset, ContactLib-ATT is used to simulate a structure-based search engine for remote homologous proteins, and our top-10 candidate list contains at least one remote homolog with a probability of 91.9%.

mzMD: visualization-oriented MS data storage and retrieval.

MOTIVATION: Drawing peaks in a data window of an MS dataset happens at all time in MS data visualization applications. This asks to retrieve from an MS dataset some selected peaks in a data window whose image in a display window reflects the visual feature of all peaks in the data window. If an algorithm for this purpose is asked to output high-quality solutions in real time, then the most fundamental dependence of it is on the storage format of the MS dataset. RESULTS: We present mzMD, a new storage format of MS datasets and an algorithm to query this format of a storage system for a summary (a set of selected representative peaks) of a given data window. We propose a criterion Q-score to examine the quality of data window summaries. Experimental statistics on real MS datasets verified the high speed of mzMD in retrieving high-quality data window summaries. mzMD reported summaries of data windows whose Q-score outperforms those mzTree reported. The query speed of mzMD is the same as that of mzTree whereas its query speed stability is better than that of mzTree. AVAILABILITY AND IMPLEMENTATION: The source code is freely available at https://github.com/yrm9837/mzMD-java. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MultiTrans: An Algorithm for Path Extraction Through Mixed Integer Linear Programming for Transcriptome Assembly.

Recent advances in RNA-seq technology have made identification of expressed genes affordable, and thus boosting repaid development of transcriptomic studies. Transcriptome assembly, reconstructing all expressed transcripts from RNA-seq reads, is an essential step to understand genes, proteins, and cell functions. Transcriptome assembly remains a challenging problem due to complications in splicing variants, expression levels, uneven coverage and sequencing errors. Here, we formulate the transcriptome assembly problem as path extraction on splicing graphs (or assembly graphs), and propose a novel algorithm MultiTrans for path extraction using mixed integer linear programming. MultiTrans is able to take into consideration coverage constraints on vertices and edges, the number of paths and the paired-end information simultaneously. We benchmarked MultiTrans against two state-of-the-art transcriptome assemblers, TransLiG and rnaSPAdes. Experimental results show that MultiTrans generates more accurate transcripts compared to TransLiG (using the same splicing graphs) and rnaSPAdes (using the same assembly graphs). MultiTrans is freely available at https://github.com/jzbio/MultiTrans.

Algorithms and Hardness for Scaffold Filling to Maximize Increased Duo-Preservations.

Scaffold filling is a critical step in DNA assembly. Its basic task is to fill the missing genes (fragments) into an incomplete genome (scaffold) to make it similar to the reference genome. There have been a lot of work under distinct measurements in the literature of genome comparison. For genomes with gene duplications, common string partition reveals the similarity more precisely, since it constructs a one-to-one correspondence between the same segments in the two genomes. In this paper, we adopt duo-preservation as the measurement, which is the complement of common string partition, i.e., the number of duo-preservations added to the number of common strings is exactly the length of a genome. Towards a proper scaffold filling, we just focus on the increased duo-preservations. This problem is called scaffold filling to maximize increased duo-preservations (abbr. SF-MIDP). We show that SF-MIDP is solvable in linear time for a simple version where all the genes of the scaffold are matched in a block-matching, but MAX SNP-complete for the general version, and cannot be approximated within [Formula: see text]. Moreover, we present a basic approximation algorithm of factor 2, by which the optimal solution can be described in a new way, and then, improve the approximation factor to [Formula: see text] via a greedy method.