PROSO Toolbox: a unified protein-constrained genome-scale modelling framework for strain designing and optimization

The genome-scale metabolic model with protein constraint (PC-model) has been increasingly popular for microbial metabolic simulations. We present PROSO Toolbox, a unified and simple-to-use PC-model toolbox that takes any high-quality genome-scale metabolic reconstruction as the input. The toolbox can construct a PC-model automatically, apply various algorithms for computational strain design and simulation, and help unveil metabolism from gene expression data through a state-of-the-art OVERLAY workflow. It also has detailed tutorials and documentation for maximum accessibility to researchers from diverse backgrounds. PROSO Toolbox, tutorials, and documentation are freely available online: https://github.com/QCSB/PROSO-Toolbox.Comment: 4 pages, 1 figur

Mining Implicit Relevance Feedback from User Behavior for Web Question Answering

Training and refreshing a web-scale Question Answering (QA) system for a multi-lingual commercial search engine often requires a huge amount of training examples. One principled idea is to mine implicit relevance feedback from user behavior recorded in search engine logs. All previous works on mining implicit relevance feedback target at relevance of web documents rather than passages. Due to several unique characteristics of QA tasks, the existing user behavior models for web documents cannot be applied to infer passage relevance. In this paper, we make the first study to explore the correlation between user behavior and passage relevance, and propose a novel approach for mining training data for Web QA. We conduct extensive experiments on four test datasets and the results show our approach significantly improves the accuracy of passage ranking without extra human labeled data. In practice, this work has proved effective to substantially reduce the human labeling cost for the QA service in a global commercial search engine, especially for languages with low resources. Our techniques have been deployed in multi-language services.Comment: Accepted by KDD 202

Understanding the Impact of Image Quality and Distance of Objects to Object Detection Performance

Deep learning has made great strides for object detection in images. The detection accuracy and computational cost of object detection depend on the spatial resolution of an image, which may be constrained by both the camera and storage considerations. Compression is often achieved by reducing either spatial or amplitude resolution or, at times, both, both of which have well-known effects on performance. Detection accuracy also depends on the distance of the object of interest from the camera. Our work examines the impact of spatial and amplitude resolution, as well as object distance, on object detection accuracy and computational cost. We develop a resolution-adaptive variant of YOLOv5 (RA-YOLO), which varies the number of scales in the feature pyramid and detection head based on the spatial resolution of the input image. To train and evaluate this new method, we created a dataset of images with diverse spatial and amplitude resolutions by combining images from the TJU and Eurocity datasets and generating different resolutions by applying spatial resizing and compression. We first show that RA-YOLO achieves a good trade-off between detection accuracy and inference time over a large range of spatial resolutions. We then evaluate the impact of spatial and amplitude resolutions on object detection accuracy using the proposed RA-YOLO model. We demonstrate that the optimal spatial resolution that leads to the highest detection accuracy depends on the 'tolerated' image size. We further assess the impact of the distance of an object to the camera on the detection accuracy and show that higher spatial resolution enables a greater detection range. These results provide important guidelines for choosing the image spatial resolution and compression settings predicated on available bandwidth, storage, desired inference time, and/or desired detection range, in practical applications

The contamination of Vibrio spp. of seashell products in 5 cities of Guangxi in 2017

Objective To determine the contamination of Vibrio parahaemolyticus, Vibrio vulnificus, Vibrio alginolyticus and Vibrio cholera in seashell products. Methods Seashell samples were collected from three coastal cities and two inland cities of Guangxi in 2017. Results There were 800 samples were collected. The total positive rate of Vibrio spp. was 76.5% (612/800). The positive rate of Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio cholera were 73.9% (591/800), 18.4% (147/800) and 0.1% (1/800), respectively. There was no Vibrio alginolyticus detected. For Vibrio parahaemolyticus, the positive rate was related to the samples source, samples status and the species of seashell. The positive rate in coastal areas was higher than inland areas, while the quantity was lower. Both the positive rate and quantity of Vibrio spp. in the live products were higher than fresh/chilled products. The positive rate of razor fish, mud clam, oyster and short necked clam were the highest and all above 75.0%. The positive rate of scallop and mussel was relatively low but the quantity was the highest. Around 1.0% (6/591) of the Vibrio parahaemolyticus positive samples was detected virulence genes. For the Vibrio vulnificus, the positive rate in rural areas was higher than urban areas, and coastal areas was higher than inland areas. The positive rate of razor fish and mud clam was the highest and both over 35.0%. Conclusion Vibrio parahaemolyticus and Vibrio vulnificus were highly contaminated in seashell products in Guangxi. It is necessary to strengthen the health education of food safety and the surveillance of Vibrio vulnificus in coastal rural areas

Correlation of 3'-phosphoadenosine-5'-phosphosulfate synthase 1 (PAPSS1) expression with clinical parameters and prognosis in esophageal squamous cell carcinoma

Background. In recent years, 3'- phosphoadenosine-5'-phosphosulfate synthase 1 (PAPSS1) has been found to be highly expressed in some cancers and significantly associated with prognosis. Nevertheless, the role of PAPSS1 in esophageal squamous cell carcinoma (ESCC) is poorly understood. Methods. In this study, PAPSS1 expression in ESCC samples was researched through real-time quantitative polymerase chain reaction (qPCR), immunohistochemistry (IHC), and western blot (WB) techniques. siRNA technology was then used to inhibit PAPSS1 expression in ESCC cells, and cytologic tests were conducted to research gene affection on cell apoptosis, proliferation, and migration. Then, the expression of Bcl2, Ki67, and Snail was detected using qPCR and WB tests. These experimental data were analyzed by GraphPad software, where the P-value <0.05 was statistically significant. Results. The results showed that PAPSS1 expression level in ESCC tissues was higher than in the adjacent tissues. The data also showed that PAPSS1 was significantly correlated with N stage, and that the patients with high expressions had longer survival time. After transfection for 48 hours, the cell apoptosis rate of siRNA-PAPSS1 transfected groups decreased significantly, whereas the cell proliferation rate and migration ability increased relative to the control. At the same time, the expression levels of Bcl2, Ki67 and Snail were all upregulated by siRNA-PAPSS1. PAPSS1, however, was suppressed. Conclusions. PAPSS1 may be an ESCC suppressor gene, and its specific molecular mechanism in ESCC needs to be further studied

Genotype-phenotype correlation in patients with 21-hydroxylase deficiency.

INTRODUCTION: 21-hydroxylase deficiency (21OHD) is the most common cause of congenital adrenal hyperplasia (CAH). However, patients with 21OHD manifest various phenotypes due to a wide-spectrum residual enzyme activity of different CYP21A2 mutations. METHODS: A total of 15 individuals from three unrelated families were included in this study. Target Capture-Based Deep Sequencing and Restriction Fragment Length Polymorphism was conducted on peripheral blood DNA of the three probands to identify potential mutations/deletions in CYP21A2; Sanger sequencing was conducted with the DNA from the family members of the probands. RESULTS: Dramatically different phenotypes were seen in the three probands of CAH with different compound heterozygous mutations in CYP21A2. Proband 1 manifested simple virilizing with mutations of 30-kb deletion/c.[188A\u3eT;518T\u3eA], the latter is a novel double mutants classified as SV associated mutation. Although both probands carry the same compound mutations [293-13C\u3eG]:[518T\u3eA], gonadal dysfunction and giant bilateral adrenal myelolipoma were diagnosed for proband 2 and proband 3, respectively. CONCLUSION: Both gender and mutations contribute to the phenotypes, and patients with the same compound mutations and gender could present with different phenotypes. Genetic analysis could help the etiologic diagnosis, especially for atypical 21OHD patients

CRAFTS for Fast Radio Bursts : extending the dispersion-fluence relation with new FRBs detected by FAST

We report three new FRBs discovered by the Five-hundred-meter Aperture Spherical radio Telescope (FAST), namely FRB 181017.J0036+11, FRB 181118, and FRB 181130, through the Commensal Radio Astronomy FAST Survey (CRAFTS). Together with FRB 181123, which was reported earlier, all four FAST-discovered FRBs share the same characteristics of low fluence (1000 pc cm(-3)), consistent with the anticorrelation between DM and fluence of the entire FRB population. FRB 181118 and FRB 181130 exhibit band-limited features. FRB 181130 is prominently scattered (tau(s) 8 ms) at 1.25 GHz. FRB 181017.J0036+11 has full-bandwidth emission with a fluence of 0.042 Jy ms, which is one of the faintest FRB sources detected so far. CRAFTS has started to build a new sample of FRBs that fills the region for more distant and fainter FRBs in the fluence-DME diagram, previously out of reach of other surveys. The implied all-sky event rate of FRBs is 1.24(-0.90)(+1.94) x 5 sky(-1) day(-1) at the 95% confidence interval above 0.0146 Jy ms. We also demonstrate here that the probability density function of CRAFTS FRB detections is sensitive to the assumed intrinsic FRB luminosity function and cosmological evolution, which may be further constrained with more discoveries

CRAFTS for Fast Radio Bursts Extending the dispersion-fluence relation with new FRBs detected by FAST

We report three new FRBs discovered by the Five-hundred-meter Aperture Spherical radio Telescope (FAST), namely FRB 181017.J0036+11, FRB 181118 and FRB 181130, through the Commensal Radio Astronomy FAST Survey (CRAFTS). Together with FRB 181123 that was reported earlier, all four FAST-discovered FRBs share the same characteristics of low fluence ($\leq$0.2 Jy ms) and high dispersion measure (DM, $>1000$ \dmu), consistent with the anti-correlation between DM and fluence of the entire FRB population. FRB 181118 and FRB 181130 exhibit band-limited features. FRB 181130 is prominently scattered ($\tau_s\simeq8$ ms) at 1.25 GHz. FRB 181017.J0036+11 has full-bandwidth emission with a fluence of 0.042 Jy ms, which is one of the faintest FRB sources detected so far. CRAFTS starts to built a new sample of FRBs that fills the region for more distant and fainter FRBs in the fluence-$\rm DM_E$ diagram, previously out of reach of other surveys. The implied all sky event rate of FRBs is $1.24^{+1.94}_{-0.90} \times 10^5$ sky$^{-1}$ day$^{-1}$ at the $95\%$ confidence interval above 0.0146 Jy ms. We also demonstrate here that the probability density function of CRAFTS FRB detections is sensitive to the assumed intrinsic FRB luminosity function and cosmological evolution, which may be further constrained with more discoveries.Comment: 9 Pages, 4 Plots and 1 Table. The Astrophysical Journal Letter Accepte

Novel context-specific genome-scale modelling explores the potential of triacylglycerol production by Chlamydomonas reinhardtii

Abstract Gene expression data of cell cultures is commonly measured in biological and medical studies to understand cellular decision-making in various conditions. Metabolism, affected but not solely determined by the expression, is much more difficult to measure experimentally. Finding a reliable method to predict cell metabolism for expression data will greatly benefit metabolic engineering. We have developed a novel pipeline, OVERLAY, that can explore cellular fluxomics from expression data using only a high-quality genome-scale metabolic model. This is done through two main steps: first, construct a protein-constrained metabolic model (PC-model) by integrating protein and enzyme information into the metabolic model (M-model). Secondly, overlay the expression data onto the PC-model using a novel two-step nonconvex and convex optimization formulation, resulting in a context-specific PC-model with optionally calibrated rate constants. The resulting model computes proteomes and intracellular flux states that are consistent with the measured transcriptomes. Therefore, it provides detailed cellular insights that are difficult to glean individually from the omic data or M-model alone. We apply the OVERLAY to interpret triacylglycerol (TAG) overproduction by Chlamydomonas reinhardtii, using time-course RNA-Seq data. We show that OVERLAY can compute C. reinhardtii metabolism under nitrogen deprivation and metabolic shifts after an acetate boost. OVERLAY can also suggest possible ‘bottleneck’ proteins that need to be overexpressed to increase the TAG accumulation rate, as well as discuss other TAG-overproduction strategies

Effect of mole weight ratio of reaction on propagation of cellular detonations

The propagation of two-dimensional cellular detonations is investigated numerically using a one-step reversible reaction model. The effect of the average mole weight ratio W-B/W-A of the product and reactant on the one-dimensional Zeldovich-von Neumann-Doring (ZND) detonation and cellular detonation behavior is analyzed in detail. Several interesting cellular detonation phenomena are observed in the numerical simulations. These can be divided into five categories according to the cell patterns of detonation, i.e., regular, relatively regular, irregular, half-cell propagating, and decoupled detonation. The results indicate that differences in cell size under different values of W-B/W-A modify the cellular detonation behavior. The ZND detonation parameters under various W-B/W-A values are studied and related to the cell size. The results show that the reaction zone length and maximum heat release rate are clearly influenced by W-B/W-A. Furthermore, for both ZND detonation and cellular detonation, the reaction zone length decreases as W-B/W-A increases, which effectively reduces the cell size. To elucidate the effects of the reaction zone length on cell size, thermoacoustic instability theory is introduced to investigate the acoustic perturbations in the reaction zone. This allows the correlation between the propagation frequency and cell number along the width of the duct to be determined. Correlation analysis indicates that the cell number has a strong linear dependence on the perturbation frequency. (C) 2022 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license(http://creativecommons.org/licenses/by/4.0/)