Running ahead of evolution - AI based simulation for predicting future high-risk SARS-CoV-2 variants

The never-ending emergence of SARS-CoV-2 variations of concern (VOCs) has challenged the whole world for pandemic control. In order to develop effective drugs and vaccines, one needs to efficiently simulate SARS-CoV-2 spike receptor binding domain (RBD) mutations and identify high-risk variants. We pretrain a large protein language model on approximately 408 million protein sequences and construct a high-throughput screening for the prediction of binding affinity and antibody escape. As the first work on SARS-CoV-2 RBD mutation simulation, we successfully identify mutations in the RBD regions of 5 VOCs and can screen millions of potential variants in seconds. Our workflow scales to 4096 NPUs with 96.5% scalability and 493.9x speedup in mixed precision computing, while achieving a peak performance of 366.8 PFLOPS (reaching 34.9% theoretical peak) on Pengcheng Cloudbrain-II. Our method paves the way for simulating coronavirus evolution in order to prepare for a future pandemic that will inevitably take place. Our models are released at https://github.com/ZhiweiNiepku/SARS-CoV-2_mutation_simulation to facilitate future related work.

Diagnostic staging laparoscopy in gallbladder carcinoma and hilar cholangiocarcinoma: a meta-analysis / 中华肝胆外科杂志

Objective To analyze the impact of diagnostic staging laparoscopy in gallbladder carcinoma and hilar cholangiocarcinoma.Methods The Medline,Embase,Web of Science,Cochrane library and Google Scholar were searched for literature on staging laparoscopy (SL) in gallbladder carcinoma and hilar cholangiocarcinoma.The sensitivity,specificity and diagnostic accuracy of SL were evaluated.Results Eight studies were included in the meta-analysis.During laparoscopy,unresectable disease was found in 316 of 1 062 patients (29.8％),of whom 32.4％ were patients with suspected hilar cholangiocarcinoma (HC) and 27.6％ were patients with suspected gall-bladder cancer (GBC).The sensitivities were 0.556 (95％ CI:0.495-0.616) for patients with HC and 0.642 (95％ CI:0.579-0.701) for patients with GBC.The pooled specificity for SL was 100％ (95％ CI:0.993-1.000) for all the studies.Conclusion For patients with gallbladder cancer or hilar cholangiocarcinoma,SL combined with intraoperative ultrasound improved the accuracy of diagnosis and avoided unnecessary laparotomy.

Rate-Performance-Loss Optimization for Inter-Frame Deep Feature Coding From Videos.

With the explosion in the use of cameras in mobile phones or video surveillance systems, it is impossible to transmit a large amount of videos captured from a wide area into a cloud for big data analysis and retrieval. Instead, a feasible solution is to extract and compress features from videos and then transmit the compact features to the cloud. Meanwhile, many recent studies also indicate that the features extracted from the deep convolutional neural networks will lead to high performance for various analysis and recognition tasks. However, how to compress video deep features meanwhile maintaining the analysis or retrieval performance still remains open. To address this problem, we propose a high-efficiency deep feature coding (DFC) framework in this paper. In the DFC framework, we define three types of features in a group-of-features (GOFs) according to their coding modes (i.e., I-feature, P-feature, and S-feature). We then design two prediction structures for these features in a GOF, including a sequential prediction structure and an adaptive prediction structure. Similar to video coding, it is important for P-feature residual coding optimization to make a tradeoff between feature bitrate and analysis/retrieval performance when encoding residuals. To do so, we propose a rate-performance-loss optimization model. To evaluate various feature coding methods for large-scale video retrieval, we construct a video feature coding data set, called VFC-1M, which consists of uncompressed videos from different scenarios captured from real-world surveillance cameras, with totally 1M visual objects. Extensive experiments show that the proposed DFC can significantly reduce the bitrate of deep features in the videos while maintaining the retrieval accuracy.

Iodine nutritional status of vulnerable people in Inner Mongolia after adjustment of iodized salt standard / 中华地方病学杂志

Objective To investigate the iodine nutrition level of vulnerable people in Inner Mongolia after adjustment of iodized salt standard and to provide theoretical bases for scientific iodine supplementation. Methods In 2013, 3 cities were selected from eastern, central and western parts of Inner Mongolia in accordance with the random number table, 3 or 4 counties were selected from each target city, 5 units according to their sub-area position of east, south, west, north and center were selected from each county, and then 1 township was selected from each unit, 5 groups of target population including school children aged 8- 10, women of childbearing age, pregnant and lactating women and infants each at least 10 people were investigated in each township. Edible salt samples from their homes and urine samples were collected. The direct titration method among the generic methods of iodide testing for salt production industry (GB/T 13025.7-2012) was used to determine the salt iodine level, and As3+-Ce4+catalytic spectrophotometry using ammonium per sulfate digestion (WS/T 107-2009) was used to test the urinary iodine level. Results Totally 3 300 samples of edible salt from local residents had been examined and median iodine was 26.20 mg/kg. The median of urinary iodine was 190.6μg/L of 1 289 school-age children;was 183.6μg/L of 621 women of childbearing age; was 178.2 μg/L o f 876 pregnant women; was 178.6 μg/L of 664 lactating women and was 167.7μg/L of 599 infants. Conclusion After adjustment of iodized salt standard, iodine nutrition level is suitable in all vulnerable people.

Effects of Murine Cytomegalovirus Infection on Sperm Viability in Mice / 华中科技大学学报（医学）（英德文版）

In order to explore the effects of testicular infection of murine cytomegalovirus (MCMV) on mature sperm viability at different periods following MCMV inoculation in mice, 91 BALB/c mice without MCMV infection were randomly divided into two groups: an experimental group (n=56) and a control group (n= 35). The mice in the experimental group were treated by inoculating MCMV intratesticularly, while those in the controlled group were directly inoculated with DMEM without MCMV. The mice in both groups were sacrificed separately on the day 1,1.5, 2, 4, 6, 9 and 14 post-inoculation (D1, 1.5,2, 4, 6, 9 and 14 PI). The MCMV M83 mRNA gene was detected in the testis by in situ hybridization (ISH) with MCMV late-mRNA probe labeled with digoxin.Sperm viability of mature sperm in the epididymis cauda was measured. The results demonstrated the positive signal of ISH of MCMV was found mainly in the cytoplasm of the testicular interstitial cells and spermatogenic cells in the experimental group. Compared with that in the controlled group, the sperm viability in the experimental group was decreased significantly on D1 PI and D1.5PI (P＜ 0.05). No statistically significant difference in the sperm viability was found after D2 PI between two groups (P＞0.05). This suggested that sperm viability in mice might be descended significantly shortly after MCMV infection and might return to normal with time, indicating that MCMV acute infection might temporarily degrade sperm quality and influence procreation transiently.

Effects of murine cytomegalovirus infection on sperm viability in mice / 华中科技大学学报（医学）（英德文版）

In order to explore the effects of testicular infection of murine cytomegalovirus (MCMV) on mature sperm viability at different periods following MCMV inoculation in mice, 91 BALB/c mice without MCMV infection were randomly divided into two groups: an experimental group (n = 56) and a control group (n = 35). The mice in the experimental group were treated by inoculating MCMV intratesticularly, while those in the controlled group were directly inoculated with DMEM without MCMV. The mice in both groups were sacrificed separately on the day 1, 1. 5, 2, 4, 6, 9 and 14 post-inoculation (D1) 1. 5, 2, 4, 6, 9 and 14 PI). The MCMV M83 mRNA gene was detected in the testis by in situ hybridization (ISH) with MCMV late-mRNA probe labeled with digoxin. Sperm viability of mature sperm in the epididymis cauda was measured. The results demonstrated the positive signal of ISH of MCMV was found mainly in the cytoplasm of the testicular interstitial cells and spermatogenic cells in the experimental group. Compared with that in the controlled group, the sperm viability in the experimental group was decreased significantly on D1 PI and D1.5 PI (P 0.05). This suggested that sperm viability in mice might be descended significantly shortly after MCMV infection and might return to normal with time, indicating that MCMV acute infection might temporarily degrade sperm quality and influence procreation transiently.

Experimental study of the effect of rhTNF-alpha on human sperm mitochondrial function and motility in vitro / 中华男科学杂志

<p><b>OBJECTIVE</b>To study the effect of rhTNF-alpha on human sperm mitochondrial function and motility in vitro.</p><p><b>METHODS</b>Fifty-six semen samples collected by masturbation were analyzed according to WHO protocols. Semen samples from 40 healthy men were prepared using Percoll centrifugation. Sperm suspension was diluted to a concentration of 10 x 10(6)/ml in Ham's F10 medium. Sperm samples were incubated with rhTNF-alpha solution (final concentration 0.03 microg/L, 0.06 microg/L, 0.09 microg/L and 0.27 microg/L, respectively) for 0.5 h, 1 h, 2 h, 3 h and 4 h at 37 degrees C in 5% CO2, and comparative studies were made with a control group. Ten microl sperm samples were examined with CASA technique, 250 microl stained in the presence of 10 microg/ml Rh123 and PI, and mitochondrial function analyzed by flow cytometry.</p><p><b>RESULTS</b>Significant differences were found between the experimental groups (final concentration 0.06 microg/L, 0.09 microg/L and 0.27 microg/L) and the control group in viability, straight line velocity, curvilinear velocity, average path velocity, progressive motility of human sperm and the number of spermatozoa with normal mitochondrial function (P < 0.01) except the final concentration 0.03 microg/L group (P > 0.05). Motility of human sperm lowered with the increase of rhTNF-alpha concentration and incubation time, and r values were 0.675, 0.691, 0.762, 0.693, 0.724 and 0.571, 0.594, 0.752, 0.791, 0.816, respectively (P < 0.01). The number of spermatozoa with normal mitochondrial function decreased with the increased rhTNF-alpha concentration and incubation time, and r values were 0.615, 0.643, 0.752, 0.691, 0.754 and 0.532, 0.567, 0.782, 0.692, 0.854, respectively (P < 0.01).</p><p><b>CONCLUSION</b>rhTNF-alpha can reduce human sperm motility function in vitro, possibly by interfering with human sperm mitochondrial function.</p>