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Computational deconvolution with single-cell RNA sequencing data as reference is pivotal to interpreting spatial transcriptomics data, but the current methods are limited to cell type resolution. Here we present Redeconve, an algorithm to deconvolute spatial transcriptomics data at single-cell resolution, enabling interpretation of spatial transcriptomics data with thousands of nuanced cell states. We benchmarked Redeconve with the state-of-the-art algorithms on diverse spatial transcriptomics datasets and platforms and demonstrated the superiority of Redeconve in terms of accuracy, resolution, robustness, and speed. Applications to a human pancreatic cancer dataset revealed cancer clone-specific T cell infiltration, and application to lymph node samples identified subtle cellular surroundings between IgA+ and IgG+ spots, providing novel insights into tumor immunology and the regulatory mechanisms underlying antibody class switch.

Background Current copy number variation (CNV) identification methods have rapidly become mature. However, the postdetection processes such as variant interpretation or reporting are inefficient. To overcome this situation, we developed REDBot as an automated software package for accurate and direct generation of clinical diagnostic reports for prenatal and products of conception (POC) samples. Methods We applied natural language process (NLP) methods for analyzing 30,235 in‐house historical clinical reports through active learning, and then, developed clinical knowledge bases, evidence‐based interpretation methods and reporting criteria to support the whole postdetection pipeline. Results Of the 30,235 reports, we obtained 37,175 CNV‐paragraph pairs. For these pairs, the active learning approaches achieved a 0.9466 average F1‐score in sentence classification. The overall accuracy for variant classification was 95.7%, 95.2%, and 100.0% in retrospective, prospective, and clinical utility experiments, respectively. Conclusion By integrating NLP methods in CNVs postdetection pipeline, REDBot is a robust and rapid tool with clinical utility for prenatal and POC diagnosis.

The estimation of 3D human body pose and shape from a single image has been extensively studied in recent years. However, the texture generation problem has not been fully discussed. In this paper, we propose an end-to-end learning strategy to generate textures of human bodies under the supervision of person re-identification. We render the synthetic images with textures extracted from the inputs and maximize the similarity between the rendered and input images by using the re-identification network as the perceptual metrics. Experiment results on pedestrian images show that our model can generate the texture from a single image and demonstrate that our textures are of higher quality than those generated by other available methods. Furthermore, we extend the application scope to other categories and explore the possible utilization of our generated textures., Comment: Accepted by CVPR2019

SummaryImprovements in shotgun proteomics approaches are hampered by increases in multiplexed (chimeric) spectra, as improvements in peak capacity, sensitivity or dynamic range all increase the number of co-eluting peptides. This results in diminishing returns using traditional search algorithms, as co-fragmented spectra are known to decrease identification rates. Here we describe MSCypher, a freely available software suite that enables an extensible workflow including a hybrid supervised machine learned strategy that dynamically adjusts to individual datasets. This results in improved identification rates and quantification of low-abundant peptides and proteins. In addition, the integration of peptide de novo sequencing and database searching enables an unbiased view of variants and high-intensity unassigned peptide spectral matches.HighlightsOpen-source end-to-end label-free proteomics workflowIntegrated database searching and machine learningCustomisable and extensible workflow including de novo sequencingOptimised for multiplexed spectra, challenging proteomics datasets and peptidomics applications

The water in Bohai Bay has become more and more eutrophic, causing a frequent red tide bloom. How to decrease eutrophication of this sea area is a pressing problem. The seawater often enters the estuary by flood tide, so the estuary may be a good place to remove eutrophic compounds from the seawater. This paper reported apocynum venetum seedlings growth status in water from Beitang estuary and its effects on nutrient removal. The results showed that apocynum venetum seedlings could grow both in flood tide water and in ebb tide water from Beitang estuarine, and the content of nitrogen and phosphorus in the water was significantly decreased by apocynum venetum seedlings, and the decrease level was largest for nitrite nitrogen in flood tide water. These results indicated that the eutrophic water in Bohai Bay was probably purified by apocynum venetum growing in ecological floating boat at estuarine.

Background Nitric oxide (NO) is a bioactive molecule that exerts a number of diverse actives in physiological processes in plants. In this paper we studied the effect of NO on photosynthesis rate of Phaeodactylum tricornumtum. Methods P. tricornutum was cultured in f/2 medium (Gulllard, 1962) which the salinity was 25‰, pH 8.0. The growth environment was set at day/night temperatures of 20/16 °C, 14 h photoperiod supplied by fluorescent lamps with tungsten supplement. The photosynthesis rate was represented by the release of oxygen which was determined by oxygenlab method (Shi, 1987). Exogenous NO was supplied by sodium nitroprusside (SNP). Membrance lipid superoxide level was represented by MDA content which was determined by TBA method (Wilbur, 1949). Results and discussion When P. tricornutum cultured in the environment of 100 μmol m−2 s−1 light intensity, the photosynthesis rate was increased by 14.4% by 150 nM NO. It is possible that NO increase photosynthesis rate by increase Chlorophyll content which plays an important role in photosynthesis. Therefore, the chlorophyll content was determined, and it was found that NO has no significant effect on chlorophyll content. Then NO probably affected photosynthesis rate by reducing photodamage. Therefore,the effect of NO on photosynthesis rate under different light intensity was studied. When light intensity was 150 μmol m−2 s−1, 200 μmol m−2 s−1, 250 μmol m−2 s−1 and 300 μmol m−2 s−1, the photosynthesis rate of P. tricornutum was increased by 150 nM NO by 15.0%, 15.6%, 88.3% and 66.5%, respectively. It was clear that the increase level of photosynthesis rate was larger under high light than that under low light. It had been shown that chloroplast easily produced superoxide oxygen under high light (Miskza, 1995), and NO could decrease superoxide oxygen content by increasing SOD and POD activity (Delledonne, 2001). Therefore,The increase of photosynthesis rate of P. tricornutum by NO probably ascribed to its protective role to cell structure. In order to prove this view, the membrance lipid superoxide test was conducted. And it was found when P. tricornutum cultured in medium contained 150 nM NO under 300 μmol m−2 s−1 light intensity, the MDA content was significant lower than that of control. Conclusion Exogenous NO increased photosynthesis rate of P. tricornutum, especially under high light environment. And one of the reason was NO protected cell structure from high light damage. Disclosure This work was supported by the Foundation (No. 201102) of Tianjin Key Laboratory of Marine Resources and Chemistry (Tianjin University of Science & Technology), PR China.

Background Modern society has made a lot of demands for long hours of visual task performance, such as reading novels in mobile phone, viewing motion images on TV, editing documents on computer, etc. These demands easily lead to visual fatigue. How to assess visual fatigue? There is no, to our knowledge, an effective method. In this paper we studied the variation of nitrite content in human tear under visual fatigue, in order to find a method to assess visual fatigue. Methods 20 Healthy non myopia volunteers (aged 20–25 years, 10 males and 10 females) took part in the study. The tear of volunteers suffered visual fatigue by reading in inadequate lighting or editing documents on computer was collected by cotton. And then the nitrite content in tear was measured by spectrophotometer assay based on Greiss reaction (Green et al., 1982). Results and discussion When the volunteers read newspaper in the environment of 30 lux, 200 lux and 40,000 lux light intensity for 2 h, the nitrite content in tear were 78.2 μmol/L, 61.3 μmol/L and 112.1 μmol/L respectively,and the order of eye ache and eye bulge was 40,000 lux >30 lux >200 lux. However, when the volunteers just sat in this environment, the nitrite content were 43.5 μmol/L, 40.1 μmol/L and 50.3 μmol/L respectively, and there is no significant subjective symptoms of eye ache and eye bulge except 40,000 lux in which the participants feel a little eye bulge. It was clear that reading increased the content of nitrite in tear which was positive correlation with the subjective symptom of visual fatigue. When the volunteers editing documents on computer for 2 h, they also feel eye ache and eye bulge. And the nitrite content in tear was 75.6 μmol/L which was 189 % of that in tear before editing. Conclusion Long hours reading or editing documents on computer increased nitrite content in tear which was positive correlation with the subjective symptom of visual fatigue. Therefore the nitrite content in tear can be taken as a marker of assessing visual fatigue. Disclosure This work was supported by the Foundation of Tianjin developing marine economy by science and technology (KJXH2012-14).

Background Hydrogen sulfide ( H 2 S) is now considered the third gaseous signal molecule along with nitric oxide and carbon monoxide. It has been shown that at appropriate concentrations it plays important physiological functions. The marine diatom Phaeodactylum tricornutum is a potential source of the pharmaceutically valuable ω -3 polyunsaturated fatty acid eicosapentaenoic acid (EPA). This paper studied the effect of exogenous H 2 S on P. tricornutum growth rate and EPA content. Materials and methods The P. tricornutum were grown in f/2 medium with or without sodium hydrosulfide at 25 °C and illuminated with cool-white fluorescent light at a level of 60 μmol/m s (12L:12D). The cultures were routinely shaken (2–3 times per day) and while at exponential growth the cells were harvested at the end of dark period and used for the experimentations. The growth rate was determined by cell number variation. The EPA was extracted by chloroform–methanol (2:1) and the content was determined by gas chromatography (GC-17A). Results The cell number variation of P. tricornutum cultured in the medium contained respectively 0.0 mmol/L, 0.3 mmol/L, 0.6 mmol/L, 0.9 mmol/L and 1.2 mmol/L sodium hydrosulfide were 6.2 × 10 5 cells/mL, 6.1 × 10 5 cells/mL, 9.6 × 10 5 cells/mL, 4.9 × 10 5 cells/mL and 2.8 × 10 5 cells/mL. It indicated that exogenous H 2 S had no significant impact on P. tricornutum growth at low concentration (0.3 mmol/L). And it inhibited P. tricornutum growth at high concentration (above 0.9 mmol/L). And it promoted P. tricornutum growth at 0.6 mmol/L concentration. Under the same culture condition, the EPA content variation were 384 mg/g dry weight, 402 mg/g dry weight, 399 mg/g dry weight, 498 mg/g dry weight and 524 mg/g dry weight. It was clear that high concentration H 2 S promoted EPA accumulation and low concentration H 2 S had no significant effect on EPA accumulation. Conclusion Both growth and EPA accumulation in P. tricornutum were effected by gaseous signal molecule H 2 S. And the role of H 2 S on them depended on its concentration. High concentration H 2 S inhibited P. tricornutum growth but promoted EPA accumulation.