A Local Concentration-based Descriptor Predicting the Stacking Fault Energy of Refractory High Entropy Alloys

Stacking fault energy (SFE) is an essential parameter for characterizing mechanical properties. However, in high entropy alloys (HEAs), the local chemical environment varies significantly across different stacking fault planes, resulting in a substantial fluctuation of SFE values rather than a unique value, which prohibits the prediction of the local SFE. Herein, we proposed an effective descriptor based on the local concentration ratio near stacking fault to quantitatively predict the local SFE of refractory HEAs. We find that the role of a given element in determining SFE strongly depends on its valence-electron number relative to other components and the contribution of its s- and d-electrons to its cohesive properties, which can be understood in the framework of the tight-binding model. Notably, the descriptor not only unifies the local nature of SFE from simple alloys to HEAs but also helps to quickly design HEAs as the involved parameters are easily accessible.Comment: 20 pages,10 figure

Controlling Class Layout for Deep Ordinal Classification via Constrained Proxies Learning

For deep ordinal classification, learning a well-structured feature space specific to ordinal classification is helpful to properly capture the ordinal nature among classes. Intuitively, when Euclidean distance metric is used, an ideal ordinal layout in feature space would be that the sample clusters are arranged in class order along a straight line in space. However, enforcing samples to conform to a specific layout in the feature space is a challenging problem. To address this problem, in this paper, we propose a novel Constrained Proxies Learning (CPL) method, which can learn a proxy for each ordinal class and then adjusts the global layout of classes by constraining these proxies. Specifically, we propose two kinds of strategies: hard layout constraint and soft layout constraint. The hard layout constraint is realized by directly controlling the generation of proxies to force them to be placed in a strict linear layout or semicircular layout (i.e., two instantiations of strict ordinal layout). The soft layout constraint is realized by constraining that the proxy layout should always produce unimodal proxy-to-proxies similarity distribution for each proxy (i.e., to be a relaxed ordinal layout). Experiments show that the proposed CPL method outperforms previous deep ordinal classification methods under the same setting of feature extractor.Comment: Accepted by AAAI 202

Development of a Blocking Primer to Inhibit the PCR Amplification of the 18S rDNA Sequences of Litopenaeus vannamei and Its Efficacy in Crassostrea hongkongensis

Diversity analyses of the eukaryotic microorganisms in the gut of marine animals is hampered by the presence of host DNA in the samples. PCR amplification of rRNA genes of eukaryotic microorganisms is inefficient with universal primers targeting 18S rRNA gene when the host DNA is dominant. In this study, we designed several blocking primers to inhibit PCR amplification of rRNA genes of the shrimp Litopenaeus vannamei, and tested their efficacy on the oyster Crassostrea hongkongensis. We first compared the intensity of PCR product bands obtained with and without the blocking primers. Then, one primer was selected for further verification using high-throughput sequencing. Our results showed that X-BP2-DPO was the most effective blocking primer in suppressing the host 18S amplification compared to nine other candidates. The inhibition rate was 99% for the amplification of shrimp rDNA, and 17% for the amplification of oyster rDNA. The concentration of the blocking primer in the PCR mixture was an important factor to be considered in the experimental design. The development of blocking primers provided a valid method to study the composition and characteristics of eukaryotic microorganisms in shrimp gut for a better understanding of its diets

A case of malonyl coenzyme A decarboxylase deficiency with novel mutations and literature review

IntroductionMalonyl coenzyme A decarboxylase deficiency is caused by an abnormality in the MLYCD gene. The clinical manifestations of the disease involve multisystem and multiorgan.MethodsWe collected and analyzed a patient's clinical characteristics, genetic chain of evidence and RNA-seq. We use the search term “Malonyl-CoA Decarboxylase Deficiency” on Pubmed to collect cases reported.ResultsWe report a 3-year-old girl who is presented with developmental retardation, myocardial damage and elevated C3DC. High-throughput sequencing identified heterozygous mutation (c.798G>A, p.Q266?) in the patient inherited from her father. The other heterozygous mutation (c.641+5G>C) was found in the patient inherited from her mother. RNA-seq showed that there were 254 differential genes in this child, among which 153 genes were up-regulated and 101 genes were down-regulated. Exon jumping events occurred in exons encoding PRMT2 on the positive chain of chromosome 21, which led to abnormal splicing of PRMT2. (P<0.05, FDR<0.05). The result of SNP showed that there were multiple mutation sites on chromosome 1, which may affect the downstream gene variation at the DNA level. The literature review identified 54 cases described since 1984.DiscussionIt is the first report about the locus, adding a new item to the MLYCD mutation library. Developmental retardation and cardiomyopathy are the most common clinical manifestations, with commonly elevated malonate and malonyl carnitine levels in children

MicroRNA-29a-3p Downregulation Causes Gab1 Upregulation to Promote Glioma Cell Proliferation

Background/Aims: Glioma causes significant human mortalities annually. Molecularly-targeted therapy is a focus of glioma research. Methods: Grb2-associated binding 1 (Gab1) expression and microRNA-29a-3p (“miR-29a-3p”) expression in human glioma cells and tissues were tested by Western blotting assay and qRT-PCR assay. shRNA/siRNA strategy was applied to silence Gab1 in human glioma cells. miR-29a or anti-sense miR-29a construct was transfected to human glioma cells. Cell proliferation was tested by BrdU ELISA assay and cell counting assay. Results: We show that expression of Gab1 was significantly elevated in human glioma tissues and cells, which correlated with downregulation of its putative microRNA: miR-29a-3p. In A172 glioma cells and primary human glioma cells, Gab1 shRNA/siRNA inhibited Akt-Erk activation and cell proliferation. Forced-expression of miR-29a-3p downregulated Gab1, inhibiting glioma cell proliferation, whereas miR-29a-3p was in-effective on cell proliferation in Gab1-silenced A172 cells. Furthermore, introduction of a 3’-untranslated region (3’-UTR) mutant Gab1 (UTR-G160A) blocked miR-29a-3p-induced inhibition on Akt signaling and A172 cell proliferation. Conclusions: miR-29a-3p downregulation leads to Gab1 upregulation to promote glioma cell proliferation

Human cytomegalovirus immediate early 1 protein causes loss of SOX2 from neural progenitor cells by trapping unphosphorylated STAT3 in the nucleus

MHL was supported by the Ministry of Science and Technology of China (National Program on Key Basic Research Project 2015CB755600), the National Natural Science Foundation of China (81620108021, 31170155, and 81427801), the Sino-Africa Joint Research Centre (SAJC201605) and a seed grant from the University of Idaho (YDP-764). MN and CP were supported by the Wellcome Trust Institutional Strategic Support Fund, MN was supported by the Medical Research Council (MR/P022146/1) and Tenovus Scotland (T15/38), and CP was supported by the Deutsche Forschungsgemeinschaft (PA 815/2-1).The mechanisms underlying neurodevelopmental damage caused by virus infections remain poorly defined. Congenital human cytomegalovirus (HCMV) infection is the leading cause of fetal brain development disorders. Previous work has linked HCMV infection to perturbations of neural cell fate, including premature differentiation of neural progenitor cells (NPCs). Here, we show that HCMV infection of NPCs results in loss of the SOX2 protein, a key pluripotency-associated transcription factor. SOX2 depletion maps to the HCMV major immediate early (IE) transcription unit and is individually mediated by the IE1 and IE2 proteins. IE1 causes SOX2 downregulation by promoting the nuclear accumulation and inhibiting the phosphorylation of STAT3, a transcriptional activator of SOX2 expression. Deranged signaling resulting in depletion of a critical stem cell protein is an unanticipated mechanism by which the viral major IE proteins may contribute to brain development disorders caused by congenital HCMV infection.PostprintPeer reviewe

Sentinel lymph node biopsy as guidance for radical trachelectomy in young patients with early stage cervical cancer

<p>Abstract</p> <p>Background</p> <p>The purpose of this study was to assess the feasibility and accuracy of sentinel lymph nodes (SLNs) detection using 99mTc phytate in predicting pelvic lymph nodes status for radical abdominal trachelectomy (RAT) in patients with early stage cervical cancer.</p> <p>Methods</p> <p>Sixty-eight women with stage IA2-IB1 cervical cancer and scheduled to undergo fertility-sparing surgery enrolled in this study. 99mTc-labeled phytate was injected before surgery. Intraoperatively, SLNs were identified, excised, and submitted to fast frozen section. Systematic bilateral pelvic lymphadenectomy and/or para-aortic lymph node dissection was performed. Then RAT was performed in patients with negative SLNs. All nodes were sent for routine pathological examination and immunostained with anti-cytokeratin antibody to detect micrometastases. Outcomes of follow up and fertility were observed.</p> <p>Results</p> <p>SLNs were identified in 64 of 68 patients (94.1%). Of these, SLNs of 8 patients (11.8%) were positive on frozen sections and proved to be metastasis by final pathologic examination. The sensitivity, accuracy, and false negative rates were 100%, 100%, and 0%, respectively. All 60 patients with negative SLN underwent RAT successfully. Two relapses occurred and no one died of tumor progression during follow-up. Five of the 15 patients with procreative desire conceived 8 pregnancies (3 term delivery, 2 premature birth, 1 spontaneous abortion, and 2 were still in the duration of pregnancy) after surgery.</p> <p>Conclusions</p> <p>The identification of SLN using 99mTc-labeled phytate is accurate and safe to assess pelvic nodes status in patients with early cervical cancer. SLNs biopsy guided RAT is feasible for patients who desire to have fertility preservation.</p

SARS-CoV-2-Specific Adaptive Immunity in COVID-19 Survivors With Asthma

BackgroundAsthma patients potentially have impaired adaptive immunity to virus infection. The levels of SARS-CoV-2-specific adaptive immunity between COVID-19 survivors with and without asthma are presently unclear.MethodsCOVID-19 survivors (patients with asthma n=11, with allergies n=8, and COVID-19 only n=17) and non-COVID-19 individuals (asthmatic patients n=10 and healthy controls n=9) were included. The COVID-19 patients were followed up at about 8 months and 16 months after discharge. The clinical characteristics, lymphocyte subsets, memory T cells, and humoral immunity including SARS-CoV-2 specific antibodies, SARS-CoV-2 pseudotyped virus neutralization assay, and memory B cells were analyzed in these subjects.ResultsThe strength of virus-specific T cell response in COVID-19 survivors was positively correlated with the percentage of blood eosinophils and Treg cells (r=0.4007, p=0.0188; and r=0.4435, p=0.0086 respectively) at 8-month follow-up. There were no statistical differences in the levels of SARS-CoV-2-specific T cell response between the COVID-19 survivors with, and without, asthma. Compared to those without asthma, the COVID-19 with asthma survivors had higher levels of SARS-CoV-2-specific neutralizing antibodies (NAbs) at the 8-month follow-up (p&lt;0.05). Moreover, the level of NAbs in COVID-19 survivors was positively correlated with the percentage of Treg and cTfh2 cells (r=0.5037, p=0.002; and r=0.4846, p=0.0141), and negatively correlated with the percentage of Th1 and Th17 cells (r=-0.5701, p=0.0003; and r=-0.3656, p=0.0308), the ratio of Th1/Th2, Th17/Treg, and cTfh1/cTfh2 cell (r=-0.5356, r=-0.5947, r=-0.4485; all p&lt;0.05). The decay rate of NAbs in the COVID-19 survivors with asthma was not significantly different from that of those without asthma at 16-month follow-up.ConclusionThe level of SARS-CoV-2-specific NAbs in COVID-19 survivors with asthma was higher than that of those without asthma at 8-month follow-up. The SARS-CoV-2-specific T cell immunity was associated with blood eosinophils and Treg percentages. The SARS-CoV-2-specific humoral immunity was closely associated with cTfh2/cTfh1 imbalance and Treg/Th17 ratio. According to the findings, asthmatic patients in COVID-19 convalescent period may benefit from an enhanced specific humoral immunity, which associates with skewed Th2/Th1 and Treg/Th17 immune

CodeFuse-13B: A Pretrained Multi-lingual Code Large Language Model

Code Large Language Models (Code LLMs) have gained significant attention in the industry due to their wide applications in the full lifecycle of software engineering. However, the effectiveness of existing models in understanding non-English inputs for multi-lingual code-related tasks is still far from well studied. This paper introduces CodeFuse-13B, an open-sourced pre-trained code LLM. It is specifically designed for code-related tasks with both English and Chinese prompts and supports over 40 programming languages. CodeFuse achieves its effectiveness by utilizing a high quality pre-training dataset that is carefully filtered by program analyzers and optimized during the training process. Extensive experiments are conducted using real-world usage scenarios, the industry-standard benchmark HumanEval-x, and the specially designed CodeFuseEval for Chinese prompts. To assess the effectiveness of CodeFuse, we actively collected valuable human feedback from the AntGroup's software development process where CodeFuse has been successfully deployed. The results demonstrate that CodeFuse-13B achieves a HumanEval pass@1 score of 37.10%, positioning it as one of the top multi-lingual code LLMs with similar parameter sizes. In practical scenarios, such as code generation, code translation, code comments, and testcase generation, CodeFuse performs better than other models when confronted with Chinese prompts.Comment: 10 pages with 2 pages for reference