Effects of nitrate- and ammonium- nitrogen on anatomical and physiological responses of Catalpa bungei under full and partial root-zone drought.

Catalpa bungei is a precious timber species distributed in North China where drought often occurs. To clarify adaptive responses of C. bungei to partial- and full- root-zone drought under the influence of nitrogen forms, a two-factor experiment was conducted in which well-watered (WW), partial root-zone drought in horizontal direction (H-PRD) and in vertical direction (V-PRD), and full root-zone drought (FRD) were combined with nitrate-nitrogen (NN) and ammonium-nitrogen (AN) treatments. C. bungei responded to FRD by sharply closing stomata, decreasing gas exchange rate and increasing leaf instantaneous water use efficiency (WUEi). Under FRD condition, the growth of seedlings was severely inhibited and the effect of N forms was covered up by the drastic drought effect. In comparison, stomata conductance and gas exchanges were moderately inhibited by PRDs. WUEi in V-PRD treatment was superior to H-PRD due to the active stomata regulation resulting from a higher ABA level and active transcription of genes in abscisic acid (ABA) signaling pathway under V-PRD. Under both PRDs and FRD, nitrate benefited antioxidant defense, stomata regulation and leaf WUEi. Under V-PRD, WUEi in nitrate treatment was superior to that in ammonium treatment due to active stomata regulation by signaling network of nitric oxide (NO), Ca2+ and ABA. Under FRD, WUEi was higher in nitrate treatment due to the favoring photosynthetic efficiency resulting from active NO signal and antioxidant defense. The interactive effect of water and N forms was significant on wood xylem development. Superoxide dismutase (SOD) and catalase (CAT) largely contributes to stress tolerance and xylem development.

Prognostic factors in patients with secondary hemophagocytic lymphohistioc ytosis in a Chinese cohort.

Hemophagocytic lymphohistiocytosis (HLH) is a rare hyperinflammatory syndrome with high mortality mediated by an unbridled and persistent activation of cytotoxic T lymphocytes and natural killer cells. However, the influence factors of early death in adult sHLH patients are still not fully elucidated, which need further investigating. We have conducted an observational study of adult HLH patients between January 2016 and December 2022. All patients are enrolled according to HLH-2004 criteria. Clinical manifestations, laboratory data, treatments, and outcomes have been recorded. Influence factors associated with prognosis are calculated by using logistic regression models. Overall, 220 patients enrolled in this study. The etiologies of HLH were divided into five groups including autoimmune-associated hemophagocytic syndrome (AAHS) (n = 90, 40.9%), malignancies (n = 73, 33.2%), EBV-HLH (n = 18, 8.2%), infection excluded EBV (n = 24, 10.9%), and other triggers (n = 15, 6.8%). Among them, EBV-HLH had the highest mortality (77.8%), and AAHS had the lowest mortality (14.4%). Multivariate analysis indicated that age (≥ 38 years old), cytopenia ≥ 2 lines, platelets (≤ 50 × 109/L), aspartate aminotransferase (≥ 135U/L), prothrombin time (≥ 14.9 s) and activated partial thromboplastin time (≥ 38.5s), EBV, and fungal infection are independent risk factors for poor prognosis of HLH. Adult HLH patients with elder age, cytopenia ≥ 2 lines, levels of decreased platelets, increased AST, prolonged PT and APTT, EBV, and fungal infection tend to have a poor prognosis.

Glycine-Modified Co-MOF Pervaporation Membrane to Enhance Water Transporting.

Cobalt-based metal-organic frameworks (Co-MOFs) with a two-dimensional layered morphology have received increasing attention for pervaporation due to their stability and hydrophilic properties. Using amino glycine (Gly) as a cross-linking agent, the Co-MOF ultrathin two-dimensional membrane doped with organic filler sodium alginate (SA) with the "brick-mixed-sand" structure was proposed. Polyacrylonitrile (PAN) was selected as the support layer of the hybrid membrane. The introduction of Gly efficiently solved the nanomaterial stacking problem and controllably adjusted the interlayer spacing between the nanosheets, which demonstrated good performance for ethanol dehydration. The results of this experimental research showed that the total flux of alcohol/water (9:1) separation by Gly-Co-MOF-SA/PAN hybrid membranes reached 1902 g m-2 h-1, which was 67% higher than that of the pure SA membranes. The "brick-mixed-sand" lamellar dense morphology of Gly-Co-MOF not only enhances membrane hydrophilicity but also provides effective channels for the rapid transport of water, which is expected to be used for the dehydration of organic solvents.

Concentration-resistance relationship and PK/PD evaluation of danofloxacin against emergence of resistant Pasteurella multocida in an in vitro dynamic model.

AIMS: This study aimed to assess the pharmacokinetic/pharmacodynamic (PK/PD) targets of danofloxacin to minimize the risk of selecting resistant P. multocida mutants and to identify the mechanisms underlying their resistance in an in vitro dynamic model, attaining the optimum dosing regimen of danofloxacin to improve its clinical efficacy based on the mutant selection window (MSW) hypothesis. METHODS AND RESULTS: Danofloxacin at seven dosing regimens and five days of treatment were simulated to quantify the bactericidal kinetics and enrichment of resistant mutants upon continuous antibiotic exposure. The magnitudes of PK/PD targets associated with different efficacies were determined in the model. The 24 h danofloxacin area under the concentration-time curve to MIC ratios (AUC24h/MIC) associated with bacteriostatic, bactericidal and eradication effects against P. multocida were 34, 52, and 64 h. This translates to average danofloxacin concentrations (Cav) over 24 h being 1.42, 2.17, and 2.67 times the MIC, respectively. An AUC/MIC-dependent antibacterial efficacy and AUC/MPC (mutant prevention concentration)-dependent enrichment of P. multocida mutants in which maximum losses in danofloxacin susceptibility occurred at a simulated AUC24h/MIC ratio of 72 h (i.e. Cav of 3 times the MIC). The overexpression of efflux pumps (acrAB-tolC) and their regulatory genes (marA, soxS, and ramA) was associated with reduced susceptibility in danofloxacin-exposed P. multocida. The AUC24h/MPC ratio of 19 h (i.e. Cav of 0.8 times the MPC) was determined to be the minimum mutant prevention target value for the selection of resistant P. multocida mutants. CONCLUSIONS: The emergence of P. multocida resistance to danofloxacin exhibited a concentration-dependent pattern and was consistent with the MSW hypothesis. The current clinical dosing regimen of danofloxacin (2.5 mg kg-1) may have a risk of treatment failure due to inducible fluoroquinolone resistance.

LONGITUDINAL CHANGES OF POSTERIOR VORTEX VEINS IN HIGHLY MYOPIC EYES DETERMINED BY RETROSPECTIVE ANALYSES OF INDOCYANINE GREEN ANGIOGRAMS.

PURPOSE: To assess the longitudinal changes of the posterior vortex veins (VVs) in highly myopic (HM) eyes. METHODS: The medical records of 1,730 consecutive HM eyes that had undergone indocyanine green angiography were studied. Eyes that had posterior VVs and had undergone at least two indocyanine green angiography examinations with a minimum interval of 3 years were selected from this group. RESULTS: Ninety-one eyes of 78 patients met the inclusion criteria. A total of 124 posterior VVs were identified. Over an average interval of 7.8 ± 5.0 years, 41 (33.1%) of the 124 posterior VVs had marked changes consisting mainly of an attenuation of vessels in 36 posterior VVs (87.8%) and alterations in the drainage course in 16 posterior VVs (39.0%). Fifteen posterior VVs had both types of changes. Most of the attenuations of the vessels occurred for smaller branches, but a complete loss of the entire trunk was seen in three eyes. Additionally, four eyes had posterior VV changes in association with changes of peripheral VVs. CONCLUSION: Posterior VV in highly myopic eyes can undergo changes with increasing time. The associated factors included the development and progression of myopic maculopathy lesions. In some cases, the blood drainage shifted from posterior VV to peripheral VV by forming anastomotic channels.

Influence of Social Distance on Foreign Language Effect in Moral Judgment.

Previous research has shown that moral choice depends on language, a phenomenon known as the moral foreign language effect (mFLE). The current study examines the influence of social distance on the mFLE. In Experiment 1, 200 participants were randomly assigned to either close or distant social distance in English or Chinese. In Experiment 2, 188 participants were randomly assigned to either English or Chinese and were presented with eight moral dilemmas, each with five different levels of social distance. After reading the dilemma, participants made a choice on a binary scale (Yes/No) in both Experiments 1 and 2 or on a more sensitive 100-point scale in Experiment 2. The results showed that the mFLE was present in distant social distance but absent in close social distance. Finally, a meta-analysis of the results from both studies confirmed the effect of social distance on the mFLE. These findings demonstrate that social distance might play an important role in moderating the mFLE in moral judgment.

Tyro3 receptor tyrosine kinase contributes to pathogenic phenotypes of fibroblast-like synoviocytes in rheumatoid arthritis and disturbs immune cell balance in experimental arthritis.

Rheumatoid arthritis (RA) is a systemic autoimmune disorder characterized by synovitis and joint damage, the underlying causes of which remain unclear. Our prior investigations revealed a notable correlation between the expression of Tyro3 Protein Tyrosine Kinase (Tyro3TK) and the progression of RA. To further elucidate the pathogenic role of Tyro3TK in RA, we analyzed the influence of Tyro3TK on pathogenic phenotypes of RA fibroblast like synoviocyte (FLS) in vitro and compared disease severity, joint damages and immunological parameters of K/BxN serum transfer arthritis (STA) in Tyro3TK-/- deficient mice and wild type controls. Our findings underscored the remarkable effectiveness of Tyro3TK blockade, as evidenced by diminished secretion of inflammatory cytokines and matrix metalloproteinases (MMPs), curtailed migration and invasiveness of RAFLS, and attenuated differentiation of pathogenic helper T cell subsets mediated by RAFLS. Correspondingly, our in vivo investigations illuminated the more favorable outcomes in Tyro3TK-deficient mice, characterized by reduced joint pathology, tempered synovial inflammation, and restored immune cell equilibrium. These data suggested that Tyro3TK might contribute to aggravated autoimmune arthritis and immunological pathology and act as a potential therapeutic target for RA.

Environmental DNA unveiling the fish community structure and diversity features in the Yangtze River basin.

Fish, as top predators in aquatic ecosystems, play an important role in maintaining the structure and functioning of these ecosystems, making their diversity a topic of great interest. This study focused on the Yangtze River Basin to investigate the fish community structure and diversity using environmental DNA (eDNA) technology. The results showed that a total of 71616 fish operational taxonomic units (OTUs) and 90 fish belonging to 23 families were detected, with the Cyprinidae family being the dominant group, followed by the Cobitidae, Amblycipitidae, etc. Compared to historical traditional morphological fish surveys, the quantity of fish detected using eDNA was relatively low, but the overall distribution pattern of fish communities was generally consistent. The highest fish Shannon-Wiener diversity index in the Yangtze River Basin sites reaches 2.60 with an average value of 1.25. The fish diversity index was higher in the downstream compared to the middle and upstream regions, and there were significant differences among different sampling sites. Significant environmental factors influencing α-diversity included chlorophyll-a, chemical oxygen demand, dissolved oxygen, total nitrogen, and elevation. Non-metric multidimensional scaling (NMDS) analysis revealed significant differences in fish community composition between the upstream and middle/lower reaches of the Yangtze River, while the composition of fish communities in the middle and lower reaches was more similar. Redundancy analysis (RDA) indicated that total organic carbon (TOC) was positively correlated with fish community distribution in the upstream, while water temperature and NO3-N were negatively correlated with fish distribution in the upstream. NH3-N and CODMn were negatively correlated with fish distribution in the middle and downstream regions, indicating a relatively severe water pollution in these areas. Additionally, fish communities in the Yangtze River displayed a typical distance decay pattern.

Distribution of heavy metals influenced by pumped storage hydropower in abandoned mines: Leaching test and modelling simulation.

Renewable energy generation varies frequently, making it difficult to match electricity demand. Pumped storage hydropower plants can alleviate this problem by reducing the unevenness of renewable energy generation. It is a new exploration of energy storage methods to construct pumped storage hydropower plants by using underground goaf of abandoned mines and mining subsidence water area. However, the construction of lower reservoirs using underground goaf areas of abandoned mines can lead to potential heavy metal pollution. To assess the impact of using abandoned mines for pumped storage hydropower on the downstream surface water environment, this work first analyzed the release characteristics of heavy metals from underground goaf and surface dump through field sampling and leaching tests, then constructed a water-environment model of the downstream surface water based on the experimental results and water environment theory, and finally simulated and analyzed the impact of underground pollutants pumped to the surface on downstream surface water-quality in typical hydrological years. The maximum error between the simulated values and measured values of the hydrodynamic model was 0.1, and the overall error was within a reasonable range (±0.2 m). The comparison between simulated values and measured values of heavy metal concentration in water quality model showed RMSE values ranged from 0.003 to 0.81, with an average of 0.4; the SI ranged from 0.84 to 0.95, with an average of 0.89. During the simulation of low, normal, and high flow years, pollution downstream was concentrated near the drainage outlet, and the underground pollutants pumped to the surface influenced the concentration of heavy metals there. After a period of drainage, the concentration of heavy metals decreased. Drainage volume was an important factor affecting the concentration of heavy metals downstream surface water. These results prove that the water environment model established based on MIKE21 is reliable and can provide guidance for the simulation and control of heavy metal pollution in the utilization of abandoned mines for pumped storage hydropower. This work provides a reproducible idea and method to assess the impact of using abandoned mines and mining subsidence water area for pumped storage hydropower on downstream surface water and ensure the safety of the ecological environment.

Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences.

In metagenomic studies of microbial communities, the short reads come from mixtures of genomes. Read assembly is usually an essential first step for the follow-up studies in metagenomic research. Understanding the power and limitations of various read assembly programs in practice is important for researchers to choose which programs to use in their investigations. Many studies evaluating different assembly programs used either simulated metagenomes or real metagenomes with unknown genome compositions. However, the simulated datasets may not reflect the real complexities of metagenomic samples and the estimated assembly accuracy could be misleading due to the unknown genomes in real metagenomes. Therefore, hybrid strategies are required to evaluate the various read assemblers for metagenomic studies. In this paper, we benchmark the metagenomic read assemblers by mixing reads from real metagenomic datasets with reads from known genomes and evaluating the integrity, contiguity and accuracy of the assembly using the reads from the known genomes. We selected four advanced metagenome assemblers, MEGAHIT, MetaSPAdes, IDBA-UD and Faucet, for evaluation. We showed the strengths and weaknesses of these assemblers in terms of integrity, contiguity and accuracy for different variables, including the genetic difference of the real genomes with the genome sequences in the real metagenomic datasets and the sequencing depth of the simulated datasets. Overall, MetaSPAdes performs best in terms of integrity and continuity at the species-level, followed by MEGAHIT. Faucet performs best in terms of accuracy at the cost of worst integrity and continuity, especially at low sequencing depth. MEGAHIT has the highest genome fractions at the strain-level and MetaSPAdes has the overall best performance at the strain-level. MEGAHIT is the most efficient in our experiments. Availability: The source code is available at https://github.com/ziyewang/MetaAssemblyEval.

Utility of autoantibody against an UCH-L1 epitope as a serum diagnostic marker for neuropsychiatric systemic lupus erythematosus.

OBJECTIVES: Neuropsychiatric systemic lupus erythematosus (NPSLE) is one of the most serious complications of systemic lupus erythematosus (SLE), lacking efficient diagnostic biomarkers. Previous studies have shown that anti-ubiquitin carboxyl hydrolase L1(UCH-L1) autoantibody is a promising cerebrospinal fluid (CSF) biomarker for NPSLE diagnosis. The purpose of this study is to explore the serum autoantibodies against different UCH-L1 epitopes and investigate the potential diagnostic value of serum autoantibodies against different UCH-L1 epitopes in NPSLE. METHODS: The epitopes of UCH-L1 protein were predicted in DNAStar software. The serum levels of different UCH-L1 epitope autoantibodies in 40 NPSLE patients, 32 SLE patients without neuropsychiatric symptoms and 21 healthy controls were determined by enzyme-linked immunosorbent assay (ELISA). Data were analysed using Pearson correlation analysis, ROC curve analysis, nonparametric Mann-Whitney test, t-test and χ2 test. RESULTS: We screened three candidate epitopes of UCH-L1 protein. The autoantibody against amino acid 58 to 69 of UCH-L1 (UCH58-69) showed highest diagnostic power in distinguishing NPSLE patients from SLE patients without neuro-psychiatric symptoms (p=0.0038). The ROC analysis showed that the specificity and sensitivity of anti-UCH58-69 were 92.3% and 37.5%, respectively. In addition, increased serum anti-UCH58-69 levels were associated with increased SLEDAI, CSF microprotein, CSF leukocyte count, ESR, AnuA, anti-dsDNA, IgG and IgM but with decrease of C3 in SLE patients. CONCLUSIONS: The serum levels of anti-UCH58-69 significantly increased in NPSLE patients compared with SLE patients without neuropsychiatric symptoms and were correlated with disease severity. Anti-UCH58-69 autoantibody may become a novel serum biomarker for NPSLE non-invasive diagnosis, which might be applicable for NPSLE early screening and diagnosis.

The genetics of specific cognitive abilities.

Most research on individual differences in performance on tests of cognitive ability focuses on general cognitive ability (g), the highest level in the three-level Cattell-Horn-Carroll (CHC) hierarchical model of intelligence. About 50% of the variance of g is due to inherited DNA differences (heritability) which increases across development. Much less is known about the genetics of the middle level of the CHC model, which includes 16 broad factors such as fluid reasoning, processing speed, and quantitative knowledge. We provide a meta-analytic review of 747,567 monozygotic-dizygotic twin comparisons from 77 publications for these middle-level factors, which we refer to as specific cognitive abilities (SCA), even though these factors are not independent of g. Twin comparisons were available for 11 of the 16 CHC domains. The average heritability across all SCA is 56%, similar to that of g. However, there is substantial differential heritability across SCA and SCA do not show the developmental increase in heritability seen for g. We also investigated SCA independent of g (SCA.g). A surprising finding is that SCA.g remain substantially heritable (53% on average), even though 25% of the variance of SCA that covaries with g has been removed. Our review highlights the need for more research on SCA and especially on SCA.g. Despite limitations of SCA research, our review frames expectations for genomic research that will use polygenic scores to predict SCA and SCA.g. Genome-wide association studies of SCA.g are needed to create polygenic scores that can predict SCA profiles of cognitive abilities and disabilities independent of g.

Risk of neurodegeneration among residents of electronic waste recycling areas.

The abnormal disposal process of electronic waste (e-waste) always emits a variety of toxic substances that enter the human body through various environmental media and can have many adverse health effects. Metals are thought to be inextricably linked to neurodegeneration. In the present study, we tried to explore the neurodegenerative status of subjects exposed to e-waste and the association between metal intake and neurodegeneration. We recruited the residents near the e-waste recycling area (the exposed group) and the residents without any e-waste contact history (the reference group) for a comparative study with detection and analysis of metals, biomarkers associated with neurodegeneration or oxidative stress (OS). The results showed that the metals between the reference and exposed group were significantly different. The concentrations of Brain-derived neurotrophic factor (BDNF) and ß-amyloid protein 42 (Aß42) in the exposed groups were significantly lower, while the levels of Euchromatic Histone lysine Methyltransferase 1 (EHMT1), Bromodomain Adjacent to Zinc finger domain 2B (BAZ2B) and Malondialdehyde (MDA) were significantly higher than in the reference groups. Although the ratio of Aß42/Aß40 had no statistical significance in the two groups, the medians of the ratio in the exposed group was lower than in the reference group. The linear regression and mediating effect analysis showed that MDA (OS) might mediate the effects of metals on EHMT1(pAg-MDA <0.001, pMDA-EHMT1 <0.05, pAg-EHMT1 <0.001). It could be inferred from the results of the present investigation that e-waste exposure had a high risk of neurodegeneration, especially Sliver (Ag) and Nickel (Ni).

Analysis of the suppression of spurious frequencies by the blocking effect in an injection-locked optoelectronic oscillator.

The blocking effect causing the suppression of spurious frequencies in an injection-locked optoelectronic oscillator (IL-OEO) is studied in this paper. The blocking effect analysis in nonlinear systems is carried out using the Volterra series and is experimentally measured in a microwave amplifier. The blocking effect in the nonlinear system helps in analyzing the suppression of spurious frequencies in an IL-OEO. Under injection locking, the spurious frequencies in the IL-OEO are significantly suppressed, and the spurs are further suppressed when the power of the reference signal is increased.

Ray tracing method for removing sidelobe laser interference in AOTF-based hyperspectral imaging.

The sidelobe phenomenon of acousto-optic tunable filter (AOTF)-based hyperspectral imaging is the result of the phase mismatching condition, which will reduce the quality of hyperspectral imaging data. This phenomenon can be observed in two specified scenes, namely, high brightness panchromatic target imaging and high brightness monochromatic target imaging. In this paper, the acousto-optic interaction in these two scenes is discussed using the phase matching condition. As a follow-up work of the previous related research, this paper studies laser interference in AOTF imaging, which is a typical example of the second case. A method to remove laser sidelobes in AOTF-based hyperspectral imaging is proposed, which combines a series of procedures including laser point extraction, reverse imaging before AOTF, ray tracing in AOTF, forward imaging process after AOTF, and laser elimination. Experimental results have verified the effectiveness of the proposed method.

Cobalt exposure increases the risk of fibrosis of people living near E­waste recycling area.

The toxicity of heavy metals is one of the major public health issues leading to hazardous effects on humans. Many studies focus on the adverse effects on people who were working in or living near E-waste recycling. However, little is known to the sustaining effects of E-waste exposure on human health after the recycling factories were shut down. In the present study, we collected the blood of people living near E­waste recycling facilities after the recycling factories were closed for 2 years. Eight heavy metals were examined in all blood samples. The results revealed that the blood levels of lead (Pb), nickel (Ni), cobalt (Co), mercury (Hg) were significantly higher in the exposed group than in the reference group, and no difference was observed for copper (Cu), zinc (Zn), stannum (Sn), cadmium (Cd). Transforming growth factor-ß (TGF-ß) and alpha-smooth muscle actin (α-SMA) were analyzed as the important indicators of fibrosis, which were statistically significantly higher in the exposed group than in the reference group. 8-isoprostane (8-I) and malondialdehyde (MDA) as the biomarkers of oxidative stress (OS) were elevated in the exposed group. Furthermore, both Spearman correlation and multiple linear regression showed that Co was positively correlated with TGF-ß, α-SMA and 8-I in the exposed group. Accordingly, we speculate that high concentrations of Co dissolved in the blood may increase the risk of tissue fibrosis through stimulating myofibroblast activation and OS involve in the process, which may provide some potential new hints for the intervention for tissue fibrosis in the future.

The changes of essential trace elements in residents from an e-waste site and the relationships between elements and hormones of the hypothalamic-pituitary-thyroid (HPT) axis.

The heavy metals pollution and related health issues were widely reported in e-waste sites, while the impacts of e-waste exposure on the essential trace elements have been neglected. The aim of this study was focused on the internal Cu, Fe, Mn and Zn levels in the residents from an e-waste site and the potential endocrine disrupting effects of these essential trace elements on the hypothalamic-pituitary-thyroid (HPT) axis. This was a cross-sectional study that 87 subjects were recruited from the e-waste site and 81 from the reference site. The results indicated that the e-waste exposed group had significantly lower Fe, Mn level when compared with the reference group (p < 0.05). Cu and Zn were also lower in the exposed group but the differences were not statistically significant. The exposed group had significantly higher TSH level and Fe was significantly associated with TSH in the females (ß (95% CI): - 1.892 (-3.309, -0.475), p = 0.009), rather than in males or all subjects. The exposed group also showed oxidative stress which was indicated by the increased concentrations of MDA and 8-iso-PG. It was further indicated the elevated MDA was mediated by the increase of TSH in the females but not directly related to Fe. In conclusion, the e-waste exposed group showed a decrease of essential trace elements, an increase of TSH and oxidative stress. The decreased Fe was related to the elevated TSH in the females, which further indirectly mediated the increase of oxidative stress. The results suggested that the internal exposure levels and the potential health effects of the essential trace elements in populations from e-waste sites should be of more concern. And the women might be more vulnerable and they need more protection to against the adverse health effects from e-waste.

SolidBin: improving metagenome binning with semi-supervised normalized cut.

MOTIVATION: Metagenomic contig binning is an important computational problem in metagenomic research, which aims to cluster contigs from the same genome into the same group. Unlike classical clustering problem, contig binning can utilize known relationships among some of the contigs or the taxonomic identity of some contigs. However, the current state-of-the-art contig binning methods do not make full use of the additional biological information except the coverage and sequence composition of the contigs. RESULTS: We developed a novel contig binning method, Semi-supervised Spectral Normalized Cut for Binning (SolidBin), based on semi-supervised spectral clustering. Using sequence feature similarity and/or additional biological information, such as the reliable taxonomy assignments of some contigs, SolidBin constructs two types of prior information: must-link and cannot-link constraints. Must-link constraints mean that the pair of contigs should be clustered into the same group, while cannot-link constraints mean that the pair of contigs should be clustered in different groups. These constraints are then integrated into a classical spectral clustering approach, normalized cut, for improved contig binning. The performance of SolidBin is compared with five state-of-the-art genome binners, CONCOCT, COCACOLA, MaxBin, MetaBAT and BMC3C on five next-generation sequencing benchmark datasets including simulated multi- and single-sample datasets and real multi-sample datasets. The experimental results show that, SolidBin has achieved the best performance in terms of F-score, Adjusted Rand Index and Normalized Mutual Information, especially while using the real datasets and the single-sample dataset. AVAILABILITY AND IMPLEMENTATION: https://github.com/sufforest/SolidBin. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Complete mitochodrial genome of the crab spider Ebrechtella tricuspidata (Araneae: Thomisidae): A novel tRNA rearrangement and phylogenetic implications for Araneae.

Mitochondrial genomes are widely used for phylogenetic and phylogeographic analyses among arthropods, but there is a lack of sufficient mitochondrial genome sequence data for spiders. Herein, we sequenced and characterized the complete mitochondrial genome of a crab spider Ebrechtella tricuspidata (Araneae: Thomisidae). The circular mitochondrial genome is 14,352 bp long, including a standard set of 37 genes and an A + T-rich region. Nucleotide composition is highly biased toward A + T nucleotides (77.3%). A novel gene order rearrangement is detected by a tRNA (trnL1) translocation. Tandem repeats are not identified in the A + T-rich region. Most of the tRNAs are greatly reduced in size and cannot be folded into typical cloverleaf-shaped secondary structures. The phylogenetic analysis confirms that the mitochondrial genome sequences are useful in resolving higher-level relationship of Araneae. Overall, our data present in this study will elevate our knowledge on the architecture and evolution of spider mitochondrial genome.

Surface-roughness measurement based on scalar field correlation with active millimeter-wave imaging system.

Active millimeter-wave (MMW) imaging is of interest because it has played an important role in the area of personnel surveillance over the past decades. Through reconstructing reflectivity, potential threats can be recognized based on shape. Besides reflectivity, diverse physical characteristics should be explored so that supplementary information can be used to assist recognition. This paper presents a surface-roughness measurement method using holographic data that has already been acquired during security checks. Based on scalar diffraction theory and speckle metrology, a simple mathematical relation between the correlation of holographic fields and surface roughness has been derived. Consequently, another kind of information, that is, the surface-roughness estimate, can be used to help differentiate similarly shaped articles. Results of simulations and laboratory experiments have shown its validation and potential in application to MMW imaging systems.