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.

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.

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.

Characterization of AMA1-RON2L complex with native gel electrophoresis and capillary isoelectric focusing.

Rhoptry neck protein 2 (RON2) binds to the hydrophobic groove of apical membrane antigen 1 (AMA1), an interaction essential for invasion of red blood cells (RBCs) by Plasmodium falciparum (Pf) parasites. Vaccination with AMA1 alone has been shown to be immunogenic, but unprotective even against homologous challenge in human trials. However, the AMA1-RON2L (L is referred to as the loop region of RON2 peptide) complex is a promising candidate, as preclinical studies with Freund's adjuvant have indicated complete protection against lethal challenge in mice and superior protection against virulent infection in Aotus monkeys. To prepare for clinical trials of the AMA1-RON2L complex, identity and integrity of the candidate vaccine must be assessed, and characterization methods must be carefully designed to not dissociate the delicate complex during evaluation. In this study, we developed a native Tris-glycine gel method to separate and identify the AMA1-RON2L complex, which was further identified and confirmed by Western blotting using anti-AMA1 monoclonal antibodies (mAbs 4G2 and 2C2) and anti-RON2L polyclonal Ab coupled with mass spectrometry. The formation of complex was also confirmed by Capillary Isoelectric Focusing (cIEF). A short-term (48 h and 72 h at 4°C) stability study of AMA1-RON2L complex was also performed. The results indicate that the complex was stable for 72 h at 4°C. Our research demonstrates that the native Tris-glycine gel separation/Western blotting coupled with mass spectrometry and cIEF can fully characterize the identity and integrity of the AMA1-RON2L complex and provide useful quality control data for the subsequent clinical trials.

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.

Bandgap tuning of two-dimensional materials by sphere diameter engineering.

Developing a precise and reproducible bandgap tuning method that enables tailored design of materials is of crucial importance for optoelectronic devices. Towards this end, we report a sphere diameter engineering (SDE) technique to manipulate the bandgap of two-dimensional (2D) materials. A one-to-one correspondence with an ideal linear working curve is established between the bandgap of MoS2 and the sphere diameter in a continuous range as large as 360 meV. Fully uniform bandgap tuning of all the as-grown MoS2 crystals is realized due to the isotropic characteristic of the sphere. More intriguingly, both a decrease and an increase of the bandgap can be achieved by constructing a positive or negative curvature. By fusing individual spheres in the melted state, post-synthesis bandgap adjustment of the supported 2D materials can be realized. This SDE technique, showing good precision, uniformity and reproducibility with high efficiency, may further accelerate the potential applications of 2D materials.

In Situ Formation of Hierarchical Bismuth Nanodots/Graphene Nanoarchitectures for Ultrahigh-Rate and Durable Potassium-Ion Storage.

Metallic bismuth (Bi) has been widely explored as remarkable anode material in alkali-ion batteries due to its high gravimetric/volumetric capacity. However, the huge volume expansion up to ≈406% from Bi to full potassiation phase K3 Bi, inducing the slow kinetics and poor cycling stability, hinders its implementation in potassium-ion batteries (PIBs). Here, facile strategy is developed to synthesize hierarchical bismuth nanodots/graphene (BiND/G) composites with ultrahigh-rate and durable potassium ion storage derived from an in situ spontaneous reduction of sodium bismuthate/graphene composites. The in situ formed ultrafine BiND (≈3 nm) confined in graphene layers can not only effectively accommodate the volume change during the alloying/dealloying process but can also provide high-speed channels for ionic transport to the highly active BiND. The BiND/G electrode provides a superior rate capability of 200 mA h g-1 at 10 A g-1 and an impressive reversible capacity of 213 mA h g-1 at 5 A g-1 after 500 cycles with almost no capacity decay. An operando synchrotron radiation-based X-ray diffraction reveals distinctively sharp multiphase transitions, suggesting its underlying operation mechanisms and superiority in potassium ion storage application.

Experimental investigation of chirped amplitude modulation heterodyne ghost imaging.

We have constructed a chirped amplitude modulation heterodyne ghost imaging (CAM-HGI) experimental system that demonstrates a robust ability against background light in experiments. In the experiments, the background light is simulated by irradiating a spatiotemporal random modulated light field onto the target. The effects of background light, modulation depth and modulation duration of the signal light source on CAM-HGI are investigated experimentally. The results show that the quality of CAM-HGI can be improved by increasing the modulation depth and the modulation duration of the signal light source, and more importantly, an image with a good signal-to-noise ratio (SNR) can be achieved even when the irradiation SNR is lower than -30 dB. This technique of CAM-HGI has an important application prospect for laser imaging in strong background light environments.

DTA-SiST: de novo transcriptome assembly by using simplified suffix trees.

BACKGROUND: Alternative splicing allows the pre-mRNAs of a gene to be spliced into various mRNAs, which greatly increases the diversity of proteins. High-throughput sequencing of mRNAs has revolutionized our ability for transcripts reconstruction. However, the massive size of short reads makes de novo transcripts assembly an algorithmic challenge. RESULTS: We develop a novel radical framework, called DTA-SiST, for de novo transcriptome assembly based on suffix trees. DTA-SiST first extends contigs by reads that have the longest overlaps with the contigs' terminuses. These reads can be found in linear time of the lengths of the reads through a well-designed suffix tree structure. Then, DTA-SiST constructs splicing graphs based on contigs for each gene locus. Finally, DTA-SiST proposes two strategies to extract transcript-representing paths: a depth-first enumeration strategy and a hybrid strategy based on length and coverage. We implemented the above two strategies and compared them with the state-of-the-art de novo assemblers on both simulated and real datasets. Experimental results showed that the depth-first enumeration strategy performs always better with recall and also better with precision for smaller datasets while the hybrid strategy leads with precision for big datasets. CONCLUSIONS: DTA-SiST performs more competitive than the other compared de novo assemblers especially with precision measure, due to the read-based contig extension strategy and the elegant transcripts extraction rules.

A graph-based filtering method for top-down mass spectral identification.

BACKGROUND: Database search has been the main approach for proteoform identification by top-down tandem mass spectrometry. However, when the target proteoform that produced the spectrum contains post-translational modifications (PTMs) and/or mutations, it is quite time consuming to align a query spectrum against all protein sequences without any PTMs and mutations in a large database. Consequently, it is essential to develop efficient and sensitive filtering algorithms for speeding up database search. RESULTS: In this paper, we propose a spectrum graph matching (SGM) based protein sequence filtering method for top-down mass spectral identification. It uses the subspectra of a query spectrum to generate spectrum graphs and searches them against a protein database to report the best candidates. As the sequence tag and gaped tag approaches need the preprocessing step to extract and select tags, the SGM filtering method circumvents this preprocessing step, thus simplifying data processing. We evaluated the filtration efficiency of the SGM filtering method with various parameter settings on an Escherichia coli top-down mass spectrometry data set and compared the performances of the SGM filtering method and two tag-based filtering methods on a data set of MCF-7 cells. CONCLUSIONS: Experimental results on the data sets show that the SGM filtering method achieves high sensitivity in protein sequence filtration. When coupled with a spectral alignment algorithm, the SGM filtering method significantly increases the number of identified proteoform spectrum-matches compared with the tag-based methods in top-down mass spectrometry data analysis.

Modified Sauerbrey equation: a facile method to quantitatively probe the conformation of isolated molecules at solid-liquid interfaces.

Despite the increasingly popular application of the quartz crystal microbalance (QCM) technique in monitoring phenomena taking place at solid-liquid interfaces, ranging from changes in mass to changes in conformation, a simple, direct relationship between QCM signal and surface mass remains elusive. In this paper, we report that the proportional relationship between the QCM signal and the surface mass arises from the linear relationship between the viscosity of the layer adsorbed at the solid-liquid interface and the surface coverage, as well as a small viscosity shift. The proportionality coefficient depends on the intrinsic viscosity of adsorbates, solvent density, and quartz crystal thickness. The intrinsic viscosity is dominated by the conformation of the entire molecular chain and the adsorption blob for end-grafted and physisorbed molecules, respectively. Using this modified Sauerbrey equation, the phenomena relating to the conformation of discrete chains at the solid-liquid interfaces can be semi-quantitatively described.

Fourier-Transform Ghost Imaging with Hard X Rays.

Knowledge gained through x-ray crystallography fostered structural determination of materials and greatly facilitated the development of modern science and technology in the past century. However, it is only applied to crystalline structures and cannot resolve noncrystalline materials. Here we demonstrate a novel lensless Fourier-transform ghost imaging method with pseudothermal hard x rays that extends x-ray crystallography to noncrystalline samples. By measuring the second-order intensity correlation function of the light, Fourier-transform diffraction pattern of a complex amplitude sample is achieved at the Fresnel region in our experiment and the amplitude and phase distributions of the sample in the spatial domain are retrieved successfully. For the first time, ghost imaging is experimentally realized with x rays. Since a highly coherent x-ray source is not required, the method can be implemented with laboratory x-ray sources and it also provides a potential solution for lensless diffraction imaging with fermions, such as neutrons and electrons where intensive coherent sources usually are not available.

Electrical and optoelectrical modification of cadmium sulfide nanobelts by low-energy electron beam irradiation.

In this report, we describe a method for modifying electrical and optoelectrical properties of CdS nanobelts using low-energy (lower than 10 keV) e-beam irradiation in a scanning electron microscope. The electrical conductivity of the nanobelts was dramatically improved via the irradiation of e-beams. The modified conductivity of the nanobelts depends on the energy of the e-beam; it exhibits a larger photocurrent and higher external quantum efficiency but slower time-response than that before the modification. A possible mechanism about the modification is the increase of electron accumulation (injected electrons) in the nanobelts due to e-beam irradiation. In addition, the optoelectrical modification could be caused by the trapped electrons in the nanobelts and the decrease of contact resistance between the nanobelts and metal electrodes induced by e-beam irradiation. The results of this work are significant for the in situ study of semiconductor nanostructures in the electron microscope. Besides, the method of electrical and optoelectrical modification presented here has potential application in electronics and optoelectronics.

Isomorphism and similarity for 2-generation pedigrees.

We consider the emerging problem of comparing the similarity between (unlabeled) pedigrees. More specifically, we focus on the simplest pedigrees, namely, the 2-generation pedigrees. We show that the isomorphism testing for two 2-generation pedigrees is GI-hard. If the 2-generation pedigrees are monogamous (i.e., each individual at level-1 can mate with exactly one partner) then the isomorphism testing problem can be solved in polynomial time. We then consider the problem by relaxing it into an NP-complete decomposition problem which can be formulated as the Minimum Common Integer Pair Partition (MCIPP) problem, which we show to be FPT by exploiting a property of the optimal solution. While there is still some difficulty to overcome, this lays down a solid foundation for this research.

Combining viral vectored and protein-in-adjuvant vaccines against the blood-stage malaria antigen AMA1: report on a phase 1a clinical trial.

The development of effective vaccines against difficult disease targets will require the identification of new subunit vaccination strategies that can induce and maintain effective immune responses in humans. Here we report on a phase 1a clinical trial using the AMA1 antigen from the blood-stage Plasmodium falciparum malaria parasite delivered either as recombinant protein formulated with Alhydrogel adjuvant with and without CPG 7909, or using recombinant vectored vaccines--chimpanzee adenovirus ChAd63 and the orthopoxvirus MVA. A variety of promising "mixed-modality" regimens were tested. All volunteers were primed with ChAd63, and then subsequently boosted with MVA and/or protein-in-adjuvant using either an 8- or 16-week prime-boost interval. We report on the safety of these regimens, as well as the T cell, B cell, and serum antibody responses. Notably, IgG antibody responses primed by ChAd63 were comparably boosted by AMA1 protein vaccine, irrespective of whether CPG 7909 was included in the Alhydrogel adjuvant. The ability to improve the potency of a relatively weak aluminium-based adjuvant in humans, by previously priming with an adenoviral vaccine vector encoding the same antigen, thus offers a novel vaccination strategy for difficult or neglected disease targets when access to more potent adjuvants is not possible.

Dynamic matching algorithm for viral structure prediction.

Most viruses have RNA genomes, their biological functions are expressed more by folded architecture than by sequence. Among the various RNA structures, pseudoknots are the most typical. In general, RNA secondary structures prediction doesn't contain pseudoknots because of its difficulty in modeling. Here we present an algorithm of dynamic matching to predict RNA secondary structures with pseudoknots by combining the merits of comparative and thermodynamic approaches. We have tested and verified our algorithm on some viral RNA. Comparisons show that our algorithm and loop matching method has similar accuracy and time complexity, and are more sensitive than the maximum weighted matching method and Rivas algorithm. Among the four methods, our algorithm has the best prediction specificity. The results show that our algorithm is more reliable and efficient than the other methods.

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.

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.

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.