Underwater dynamic polarization imaging without dependence on the background region.

Active-polarization imaging holds significant promise for achieving clear underwater vision. However, only static targets were considered in previous studies, and a background region was required for image restoration. To address these issues, this study proposes an underwater dynamic polarization imaging method based on image pyramid decomposition and reconstruction. During the decomposition process, the polarized image is downsampled to generate an image pyramid. Subsequently, the spatial distribution of the polarization characteristics of the backscattered light is reconstructed by upsampling, which recovered the clear scene. The proposed method avoids dependence on the background region and is suitable for moving targets with varying polarization properties. The experimental results demonstrate effective elimination of backscattered light while sufficiently preserving the target details. In particular, for dynamic targets, processing times that fulfill practical requirements and yield superior recovery effects are simultaneously obtained.

Highly Stable HfO2 Memristors through van der Waals Electrode Lamination and Delamination.

Memristors have attracted considerable attention in the past decade, holding great promise for future neuromorphic computing. However, the intrinsic poor stability and large device variability remain key limitations for practical application. Here, we report a simple method to directly visualize the origin of poor stability. By mechanically removing the top electrodes of memristors operated at different states (such as SET or RESET), the memristive layer could be exposed and directly characterized through conductive atomic force microscopy, providing two-dimensional area information within memristors. Based on this technique, we observed the existence of multiple conducting filaments during the formation process and built up a physical model between filament numbers and the cycle-to-cycle variation. Furthermore, by improving the interface quality through the van der Waals top electrode, we could reduce the filament number down to a single filament during all switching cycles, leading to much controlled switching behavior and reliable device operation.

Exact optical path difference and complete performance analysis of a spectral zooming imaging spectrometer.

The optical path difference (OPD) equations of the dual Wollaston prisms (DWP) with an adjustable air gap (AG) are derived by the wave normal tracing method, which is suitable for arbitrary incidence plane and angle. The spatial distribution of the OPD for various AG is presented. The validity of the OPD equation is verified by comparing the calculated interferograms with experimentally observed one. The performance of a novel static birefringent Fourier transform imaging spectrometer (SBFTIS) based on the DWP is investigated. The spectral resolution can be adjusted by changing the AG and the field of view can reach 10.0°, which is much larger than that predicted by our previous work. The results obtained in this article provide a theoretical basis for completely describing the optical transmission characteristic of the DWP and developing the high-performance birefringent spectral zooming imaging spectrometer.

Low-cost and simple fabrication of hierarchical Al nanopit arrays for deep ultraviolet refractive index sensing.

Herein, we proposed a simple non-lithographic way to fabricate hierarchical Al nanopit arrays performed as deep ultraviolet (DUV, 200-300 nm) refractive index sensing. Only by adjusting the Al deposition thickness on the Al nanopit array, the hierarchical Al nanopit arrays with tunable plasmonic properties in the DUV region were obtained. The prepared hierarchical Al nanopit arrays are of very good time stability and its RI sensitivity and concentration detection limit of adenine ethanol solution reach 311 nm/RIU and5×10-6M,respectively, as the Al deposition thickness is 60 nm. Furthermore, the electric field distribution simulation results show that high RI sensing characteristic are mainly attributed to the local surface plasmon resonance. This investigation provides a facile way to develop low cost, high efficient and easily fabricated Al-based RI sensor in the DUV region.

Selection signature reveals genes associated with susceptibility loci affecting respiratory disease due to pleiotropic and hitchhiking effect in Chinese indigenous pigs.

BACKGROUND: Porcine respiratory disease is one of the most important health problems which causes significant economic losses. OBJECTIVE: To understand the genetic basis for susceptibility to swine enzootic pneumonia (EP) in pigs, we detected 102,809 SNPs in a total of 249 individuals based on genome-wide sequencing data. METHODS: Genome comparison of three susceptibility to swine EP pig breeds (Jinhua, Erhualian and Meishan) with two western lines that are considered more resistant (Duroc and Landrace) using XP-EHH and FST statistical approaches identified 691 positively selected genes. Based on QTLs, GO terms and literature search, we selected 14 candidate genes that have convincible biological functions associated with swine EP or human asthma. RESULTS: Most of these genes were tested by several methods including transcription analysis and candidated genes association study. Among these genes: CYP1A1 and CTNNB1 are involved in fertility; TGFBR3 plays a role in meat quality traits; WNT2, CTNNB1 and TCF7 take part in adipogenesis and fat deposition simultaneously; PLAUR (completely linked to AXL, r2=1) plays an essential role in the successful ovulation of matured oocytes in pigs; CLPSL2 (strongly linked to SPDEF, r2=0.848) is involved in male fertility. CONCLUSION: These adverse genes susceptible to swine EP may be selected while selecting for economic traits (especially reproduction traits) due to pleiotropic and hitchhiking effect of linked genes. Our study provided a completely new point of view to understand the genetic basis for susceptibility or resistance to swine EP in pigs thereby, provide insight for designing sustainable breed selection programs. Finally, the candidate genes are crucial due to their potential roles in respiratory diseases in a large number of species, including human.

Bolometric Effect in Bi2 O2 Se Photodetectors.

Bi2 O2 Se is emerging as a photosensitive functional material for optoelectronics, and its photodetection mechanism is mostly considered to be a photoconductive regime in previous reports. Here, the bolometric effect is discovered in Bi2 O2 Se photodetectors. The coexistence of photoconductive effect and bolometric effect is generally observed in multiwavelength photoresponse measurements and then confirmed with microscale local heating experiments. The unique photoresponse of Bi2 O2 Se photodetectors may arise from a change of hot electrons during temperature rises instead of photoexcited holes and electrons. Direct proof of the bolometric effect is achieved by real-time temperature tracking of Bi2 O2 Se photodetectors under time evolution after light excitation. Moreover, the Bi2 O2 Se bolometer shows a high temperature coefficient of resistance (-1.6% K-1 ), high bolometric coefficient (-31 nA K-1 ), and high bolometric responsivity (>320 A W-1 ). These findings offer a new approach to develop bolometric photodetectors based on Bi2 O2 Se layered materials.

In-plane anisotropy in twisted bilayer graphene probed by Raman spectroscopy.

Monolayer graphene has high symmetrical crystal structure and exhibits in-plane isotropic physical properties. However, twisted bilayer graphene (tBLG) is expected to differ physically, due to the broken symmetry introduced by the interlayer coupling between adjacent graphene layers. This symmetry breaking is usually accompanied by in-plane anisotropy in their electrical, optical and thermal properties. However, the existence of in-plane anisotropy in tBLG has remained evasive until now. Here, an unambiguous identification of the in-plane anisotropy in tBLG is established by angle-resolved polarized Raman spectroscopy. It was found that the double-resonant two-dimensional band is anisotropic. The degree of in-plane anisotropy is found to be dependent on the misorientation angles, which is two- and four-fold for tBLG with misorientation angles of 15° and 20°, respectively. This finding adds a new dimension to the properties of graphene, which opens a possibility to the development of graphene-based angle-resolved photonics and electronics.

A genome-wide scan for selection signatures in Yorkshire and Landrace pigs based on sequencing data.

Pigs have experienced dramatic selection due to domestication, which has led to many different phenotypes when compared to their wild counterparts, especially in the last several decades. Currently, genome-wide scans in both cattle and humans showing positive selection footprints have been investigated. However, few studies have focused on porcine selection footprints, particularly on a genome-wide scale. Surveying for selection footprints across porcine genomes can be quite valuable for revealing the genetic mechanisms of phenotypic diversity. Here, we employed a medium sequencing depth (5-20x/site per individual, on average) approach called genotyping by genome reducing and sequencing (GGRS) to detect genome-wide selection signatures of two domestic pig breeds (Yorkshire and Landrace) that have been under intensive selection for traits of muscle development, growth and behavior. The relative extended haplotype homozygosity test, which identifies selection signatures by measuring the characteristics of haplotypes' frequency distribution within a single population, was also applied to identify potential positively selected regions. As a result, signatures of positive selection were found in each breed. However, most selection signatures were population specific and related to genomic regions containing genes for biological categories including brain development, metabolism, growth and olfaction. Furthermore, the result of the gene set enrichment analysis indicated that selected regions of the two breeds presented a different over-representation of genes in the Gene Ontology annotations and Kyoto Encyclopedia of Genes and Genomes pathways. Our results revealed a genome-wide map of selection footprints in pigs and may help us better understand the mechanisms of selection in pig breeding.

Photodegradation and van der Waals Passivation of Violet Phosphorus.

Violet phosphorus (VP), a novel two-dimensional (2D) nanomaterial, boasts structural anisotropy, a tunable optical bandgap, and superior thermal stability compared with its allotropes. Its multifunctionality has sparked widespread interest in the community. Yet, the VP's air susceptibility impedes both probing its intrinsic features and device integration, thus making it of urgent significance to unveil the degradation mechanism. Herein, we conduct a comprehensive study of photoactivated degradation effects on VP. A nitrogen annealing method is presented for the effective elimination of surface adsorbates from VP, as evidenced by a giant surface-roughness improvement from 65.639 nm to 7.09 nm, enabling direct observation of the intrinsic morphology changes induced by photodegradation. Laser illumination demonstrates a significant thickness-thinning effect on VP, manifested in the remarkable morphological changes and the 73% quenching of PL intensity within 160 s, implying its great potential for the efficient selected-area etching of VP at high resolution. Furthermore, van der Waals passivation of VP using 2D hexagonal boron nitride (hBN) was achieved. The hBN-passivated channel exhibited improved surface roughness (0.512 nm), reduced photocurrent hysteresis, and lower responsivity (0.11 A/W @ 450 nm; 2 µW), effectively excluding adsorbate-induced electrical and optoelectrical effects while disabling photodegradation. Based on our experimental results, we conclude that three possible factors contribute to the photodegradation of VP: illumination with photon energy higher than the bandgap, adsorbed H2O, and adsorbed O2.

Uncovering the transcriptional circuitry in skeletal muscle regeneration.

Skeletal muscle has a remarkable ability to regenerate after repeated and complete destruction of the tissue. The healing phases for an injured muscle undergo an activation program controlled by a dynamically inducible transcriptional regulatory network. Mapping a complex mammalian transcriptional network is confronted by significant challenges and requires the integration of multiple experimental data types. In this work we present a system approach to describe the transcriptional circuitry during skeletal muscle regeneration using time-course expression data and motif scanning information. Time-lagged correlation analysis was utilized to evaluate the transcription factor (TF) → target associations. Our analysis identified six TFs that potentially play a central role throughout the regeneration process. Four of them have previously been described to be important for muscle regeneration and differentiation. The remaining two TFs are identified as novel regulators that may have a role in the regeneration process. We hope that our work may provide useful clues to help accelerate the recovery process in injured skeletal muscle.

WRKY gene family evolution in Arabidopsis thaliana.

The Arabidopsis thaliana WRKY proteins are characterized by a sequence of 60 amino acids including WRKY domain. It is well established that these proteins are involved in the regulation of various physiological programs unique to plants including pathogen defense, senescence and response to environmental stresses, which attracts attention of the scientific community as to how this family might have evolved. We tried to satisfy this curiosity and analyze reasons for duplications of these gene sequences leading to their diversified gene actions. The WRKY sequences available in Arabidopsis thaliana were used to evaluate selection pressure following duplication events. A phylogenetic tree was constructed and the WRKY family was divided into five sub-families. After that, tests were conducted to decide whether positive or purified selection played key role in these events. Our results suggest that purifying selection played major role during the evolution of this family. Some amino acid changes were also detected in specific branches of phylogeny suggesting that relaxed constraints might also have contributed to functional divergence among sub-families. Sites relaxed from purifying selection were identified and mapped onto the structural and functional regions of the WRKY1 protein. These analyses will enhance our understanding of the precise role played by natural selection to create functional diversity in WRKY family.

Comparative analysis of MTF-1 binding sites between human and mouse.

MTF-1 is a crucial transcription factor involved in the cellular response to heavy-metal load and other stresses by specifically binding to metal response elements (MREs). Thus far only a handful of direct target genes are known for this transcription factor, limiting our understanding of the biological network it governs. In this article we try to employ a computational strategy based on the generation of literature-based positional weight matrices (PWM) and log-likelihood scoring of the candidate binding sites (BSs) for identification of direct targets of the transcription factor MTF-1 in human and mouse. Through comparisons, we explore the conservation and unique characteristics between two species. Our results show that the numbers of MREs differ dramatically between species and their positions relative to their cognate promoter is also flexible. Importantly, we identify a set of target genes generally well conserved between human and mouse. Finally, by combining expression analysis we provide two putative targets (HMGCR and CYP51A), which regulate lipid metabolism conserved in human and mouse. Overall, interspecies comparison from our study may provide some valuable information for further studying human Wilson disease (WD) using mouse model systems.

ReCGiP, a database of reproduction candidate genes in pigs based on bibliomics.

BACKGROUND: Reproduction in pigs is one of the most economically important traits. To improve the reproductive performances, numerous studies have focused on the identification of candidate genes. However, it is hard for one to read all literatures thoroughly to get information. So we have developed a database providing candidate genes for reproductive researches in pig by mining and processing existing biological literatures in human and pigs, named as ReCGiP. DESCRIPTION: Based on text-mining and comparative genomics, ReCGiP presents diverse information of reproduction-relevant genes in human and pig. The genes were sorted by the degree of relevance with the reproduction topics and were visualized in a gene's co-occurrence network where two genes were connected if they were co-cited in a PubMed abstract. The 'hub' genes which had more 'neighbors' were thought to be have more important functions and could be identified by the user in their web browser. In addition, ReCGiP provided integrated GO annotation, OMIM and biological pathway information collected from the Internet. Both pig and human gene information can be found in the database, which is now available. CONCLUSIONS: ReCGiP is a unique database providing information on reproduction related genes for pig. It can be used in the area of the molecular genetics, the genetic linkage map, and the breeding of the pig and other livestock. Moreover, it can be used as a reference for human reproduction research.

Comparative analysis of vertebrate PEPT1 and PEPT2 genes.

The plasma membrane transport proteins belong to SoLute Carrier 15 (SLC15) family and two members of this family have been characterized extensively in higher vertebrates, namely PEPT1 and PEPT2. Despite many efforts have made to define a pharmacophore model for efficient binding and transporting of substrates, there is not a comprehensive study performed to elucidate the evolutionary mechanisms among the SLC15 family members and to statistically evaluate sequence conservation and functional divergence between members. In this study, we compared and contrasted the rates and patterns of molecular evolution of 2 PEPT genes. Phylogenetic tree assembly with all available vertebrate PEPTs suggests that the PEPTs originated by duplications and diverged from a common protein at the base of the eukaryotic tree. Topological structure demonstrates both members share the similar hydrophobic domains (TMDs), which have been constrained by purifying selection. Although both genes show qualitatively similar patterns, their rates of evolution differ significantly due to an increased rate of synonymous substitutions in the structural domains in one copy, suggesting substantial differences in functional constraint on each gene. Site-specific profiles were established by posterior probability analysis revealing significantly divergent regions mainly locate at the hydrophobic region between predicted transmembrane domains 9 and 10 of the proteins. Thus, these results provide the evidence that several amino acid residues with reduced selective constraints are largely responsible for functional divergence between the paralogous PEPTs. These findings may provide a starting point for further experimental verifications.

Molecular selection and functional divergence of HIF-α proteins in vertebrates.

HIF-α transcription factors, as key master regulators of oxygen homeostasis, constitute a subgroup of the large bHLH-PAS transcription factor family and have been identified in many vertebrates. Although the amino acid sequences of bHLH-PAS domain are conserved, the physiological and pathological roles of this family are variable. They also have different patterns of expression. It is possible that the HIF-α copies have been retained as a consequence of adaptive amino acid replacements or relaxed selective constraint which have conferred subtle changes in function after duplications. Phylogenetic analysis indicated that at least two major duplications had occurred early in the vertebrate lineages. Analyses of the ratios of nonsynonymous/synonymous substitution rates revealed that relaxation of selective constraints might play important roles over evolutionary time and shape variation in some members of the family. The coefficients of functional divergence (θ) estimated between pairwise comparisons of gene groups from HIF-1α, HIF-2α, and HIF-3α indicated statistically significant site-specific shift of evolutionary rates between them, suggesting that altered functional constraints may have taken place at some amino acid residues after their duplications. Moreover, we also mapped sites identified to have been relaxed from purifying selection onto the three-dimensional structure of human HIF-2α. Overall, our study demonstrated that the functional diversity of HIF-αs members may be caused by relaxed negative selection on the N-terminal transactivation domains after HIF-αs duplications, which recruited new partners leading to functional specificity.

FoxO gene family evolution in vertebrates.

BACKGROUND: Forkhead box, class O (FoxO) belongs to the large family of forkhead transcription factors that are characterized by a conserved forkhead box DNA-binding domain. To date, the FoxO group has four mammalian members: FoxO1, FoxO3a, FoxO4 and FoxO6, which are orthologs of DAF16, an insulin-responsive transcription factor involved in regulating longevity of worms and flies. The degree of homology between these four members is high, especially in the forkhead domain, which contains the DNA-binding interface. Yet, mouse FoxO knockouts have revealed that each FoxO gene has its unique role in the physiological process. Whether the functional divergences are primarily due to adaptive selection pressure or relaxed selective constraint remains an open question. As such, this study aims to address the evolutionary mode of FoxO, which may lead to the functional divergence. RESULTS: Sequence similarity searches have performed in genome and scaffold data to identify homologues of FoxO in vertebrates. Phylogenetic analysis was used to characterize the family evolutionary history by identifying two duplications early in vertebrate evolution. To determine the mode of evolution in vertebrates, we performed a rigorous statistical analysis with FoxO gene sequences, including relative rate ratio tests, branch-specific dN/dS ratio tests, site-specific dN/dS ratio tests, branch-site dN/dS ratio tests and clade level amino acid conservation/variation patterns analysis. Our results suggest that FoxO is constrained by strong purifying selection except four sites in FoxO6, which have undergone positive Darwinian selection. The functional divergence in this family is best explained by either relaxed purifying selection or positive selection. CONCLUSION: We present a phylogeny describing the evolutionary history of the FoxO gene family and show that the genes have evolved through duplications followed by purifying selection except for four sites in FoxO6 fixed by positive selection lie mostly within the non-conserved optimal PKB motif in the C-terminal part. Relaxed selection may play important roles in the process of functional differentiation evolved through gene duplications as well.

Regression-based approach for testing the association between multi-region haplotype configuration and complex trait.

BACKGROUND: It is quite common that the genetic architecture of complex traits involves many genes and their interactions. Therefore, dealing with multiple unlinked genomic regions simultaneously is desirable. RESULTS: In this paper we develop a regression-based approach to assess the interactions of haplotypes that belong to different unlinked regions, and we use score statistics to test the null hypothesis of non-genetic association. Additionally, multiple marker combinations at each unlinked region are considered. The multiple tests are settled via the minP approach. The P value of the "best" multi-region multi-marker configuration is corrected via Monte-Carlo simulations. Through simulation studies, we assess the performance of the proposed approach and demonstrate its validity and power in testing for haplotype interaction association. CONCLUSION: Our simulations showed that, for binary trait without covariates, our proposed methods prove to be equal and even more powerful than htr and hapcc which are part of the FAMHAP program. Additionally, our model can be applied to a wider variety of traits and allow adjustment for other covariates. To test the validity, our methods are applied to analyze the association between four unlinked candidate genes and pig meat quality.

Interlayer Difference of Bilayer-Stacked MoS2 Structure: Probing by Photoluminescence and Raman Spectroscopy.

This work reports the interlayer difference of exciton and phonon performance between the top and bottom layer of a bilayer-stacked two-dimensional materials structure (BSS). Through photoluminescence (PL) and Raman spectroscopy, we find that, compared to that of the bottom layer, the top layer of BSS demonstrates PL redshift, Raman E 2 g 1 mode redshift, and lower PL intensity. Spatial inhomogeneity of PL and Raman are also observed in the BSS. Based on theoretical analysis, these exotic effects can be attributed to substrate-coupling-induced strain and doping. Our findings provide pertinent insight into film-substrate interaction, and are of great significance to researches on bilayer-stacked structures including twisted bilayer structure, Van der Waals hetero- and homo-structure.

Assessment of Autozygosity Derived From Runs of Homozygosity in Jinhua Pigs Disclosed by Sequencing Data.

Jinhua pig, a well-known Chinese indigenous breed, has evolved as a pig breed with excellent meat quality, greater disease resistance, and higher prolificacy. The reduction in the number of Jinhua pigs over the past years has raised concerns about inbreeding. Runs of homozygosity (ROH) along the genome have been applied to quantify individual autozygosity to improve the understanding of inbreeding depression and identify genes associated with traits of interest. Here, we investigated the occurrence and distribution of ROH using next-generation sequencing data to characterize autozygosity in 202 Jinhua pigs, as well as to identify the genomic regions with high ROH frequencies within individuals. The average inbreeding coefficient, based on ROH longer than 1 Mb, was 0.168 ± 0.052. In total, 18,690 ROH were identified in all individuals, among which shorter segments (1-5 Mb) predominated. Individual ROH autosome coverage ranged from 5.32 to 29.14% in the Jinhua population. On average, approximately 16.8% of the whole genome was covered by ROH segments, with the lowest coverage on SSC11 and the highest coverage on SSC17. A total of 824 SNPs (about 0.5%) and 11 ROH island regions were identified (occurring in over 45% of the samples). Genes associated with reproduction (HOXA3, HOXA7, HOXA10, and HOXA11), meat quality (MYOD1, LPIN3, and CTNNBL1), appetite (NUCB2) and disease resistance traits (MUC4, MUC13, MUC20, LMLN, ITGB5, HEG1, SLC12A8, and MYLK) were identified in ROH islands. Moreover, several quantitative trait loci for ham weight and ham fat thickness were detected. Genes in ROH islands suggested, at least partially, a selection for economic traits and environmental adaptation, and should be subject of future investigation. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the pig genome.

Near-Infrared Photoelectric Properties of Multilayer Bi2O2Se Nanofilms.

The near-infrared (NIR) photoelectric properties of multilayer Bi2O2Se nanofilms were systematically studied in this paper. Multilayer Bi2O2Se nanofilms demonstrate a sensitive photo response to NIR, including a high photoresponsivity (~ 101 A/W), a quick response time (~ 30 ms), a high external quantum efficiency (~ 20,300%), and a high detection rate (1.9 × 1010 Jones). These results show that the device based on multilayer Bi2O2Se nanofilms might have great potentials for future applications in ultrafast, highly sensitive NIR optoelectronic devices.