Different Bacterial Communities Involved in Peptide Decomposition between Normoxic and Hypoxic Coastal Waters

RGD peptides has been used to detect cell surface integrin and direct clinical effective therapeutic drug selection. Herein we report that a quick one step detection of cell surface marker that was realized by a specially designed NiFe-based magnetic biosensing cell chip combined with functionalized magnetic nanoparti- cles. Magnetic nanoparticles with 20-30 nm in diameter were prepared by coprecipitation and modified with RGD-4C, and the resultant RGD-functionalized magnetic nanoparticles were used for targeting cancer cells cul- tured on the NiFe-based magnetic biosensing chip and distinguish the amount of cell surface receptor-integrin. Cell lines such as Calu3, Hela, A549, CaFbr, HEK293 and HUVEC exhibiting different integrin expression were chosen as test samples. Calu3, Hela, HEK293 and HUVEC cells were successfully identified. This approach has advantages in the qualitative screening test. Compared with traditional method, it is fast, sensitive, low cost, easy-operative, and needs very little human intervention. The novel method has great potential in applications such as fast clinical cell surface marker detection, and diagnosis of early cancer, and can be easily extended to other biomedical applications based on molecular recognition

One Step Quick Detection of Cancer Cell Surface Marker by Integrated NiFe-based Magnetic Biosensing Cell Cultural Chip

RGD peptides has been used to detect cell surface integrin and direct clinical effective therapeutic drug selection. Herein we report that a quick one step detection of cell surface marker that was realized by a specially designed NiFe-based magnetic biosensing cell chip combined with functionalized magnetic nanoparticles. Magnetic nanoparticles with 20-30 nm in diameter were prepared by coprecipitation and modified with RGD-4C, and the resultant RGD-functionalized magnetic nanoparticles were used for targeting cancer cells cultured on the NiFe-based magnetic biosensing chip and distinguish the amount of cell surface receptor-integrin. Cell lines such as Calu3, Hela, A549, CaFbr, HEK293 and HUVEC exhibiting different integrin expression were chosen as test samples. Calu3, Hela, HEK293 and HUVEC cells were successfully identified. This approach has advantages in the qualitative screening test. Compared with traditional method, it is fast, sensitive, low cost, easy-operative, and needs very little human intervention. The novel method has great potential in applications such as fast clinical cell surface marker detection, and diagnosis of early cancer, and can be easily extended to other biomedical applications based on molecular recognition

Adversarial Auto-Augment with Label Preservation: A Representation Learning Principle Guided Approach

Data augmentation is a critical contributing factor to the success of deep learning but heavily relies on prior domain knowledge which is not always available. Recent works on automatic data augmentation learn a policy to form a sequence of augmentation operations, which are still pre-defined and restricted to limited options. In this paper, we show that a prior-free autonomous data augmentation's objective can be derived from a representation learning principle that aims to preserve the minimum sufficient information of the labels. Given an example, the objective aims at creating a distant "hard positive example" as the augmentation, while still preserving the original label. We then propose a practical surrogate to the objective that can be optimized efficiently and integrated seamlessly into existing methods for a broad class of machine learning tasks, e.g., supervised, semi-supervised, and noisy-label learning. Unlike previous works, our method does not require training an extra generative model but instead leverages the intermediate layer representations of the end-task model for generating data augmentations. In experiments, we show that our method consistently brings non-trivial improvements to the three aforementioned learning tasks from both efficiency and final performance, either or not combined with strong pre-defined augmentations, e.g., on medical images when domain knowledge is unavailable and the existing augmentation techniques perform poorly. Code is available at: https://github.com/kai-wen-yang/LPA3}{https://github.com/kai-wen-yang/LPA3.Comment: 36th Conference on Neural Information Processing Systems (NeurIPS 2022

Radioactive iodine therapy strategies for distinct types of differentiated thyroid cancer: a propensity score–matched analysis

BackgroundThe management guidelines of radioactive Iodine (RAI) therapy for distinct types of differentiated thyroid carcinoma (DTC) were the same in clinical practice. However, in distinct types DTC, differences in RAI avidity and response existed and the effect of RAI therapy could not be equated.MethodsDTC patients’ data in SEER database were extracted to perform retrospective analysis. The differences between case group and control group were compared by chi-square tests. We used Kaplan-Meier statistics and Cox regression analyses to investigate cancer-specific survival (CSS). Propensity score–matched was performed to make 1:1 case-control matching.Results105195 patients who receiving total thyroidectomy were identified in SEER database. Compared to papillary thyroid carcinoma (PTC) (52.3%), follicular thyroid carcinoma (FTC) (63.8%) and oncocytic carcinoma of thyroid (OCA) (64.4%) had higher rates of RAI therapy. In the multivariable Cox regression model, RAI therapy was independent prognosis factor in PTC but not in OCA and FTC. In subgroup analysis, RAI therapy could improve prognosis in PTC when gross extrathyroidal extension or lymph node metastases or early survival when distant metastases (DM) were presented. However, OCA and FTC patients with DM rather than regional lesions only could benefit from RAI therapy. High-risk patients receiving RAI therapy showed a better prognosis in PTC but not in OCA and FTC.ConclusionRAI therapy was an effective treatment for DTC and should be considered individually in PTC, OCA and FTC patients. Our results provided further guideline for treatment selection in DTC

Specific, simple and rapid detection of porcine circovirus type 2 using the loop-mediated isothermal amplification method

<p>Abstract</p> <p>Background</p> <p>Porcine circovirus type 2 (PCV2) is the causative agent of postweaning multisystemic wasting syndrome (PMWS), and porcine dermatitis and nephropathy syndrome (PDNS). It has caused heavy losses in global agriculture in recent decades. Rapid detection of PCV2 is very important for the effective prophylaxis and treatment of PMWS.</p> <p>Results</p> <p>A loop-mediated isothermal amplification (LAMP) assay was used to detect PCV2 in this study. Three pairs of primers were specially designed for recognizing eight distinct sequences of the ORF2 gene. This gene lies in the PCV2 virus genome sequence, and encodes the Rep protein that is involved in virus replication. Time and temperature conditions for amplification of PCV2 genes were optimized to be 55 min at 59°C. The analysis of clinical samples indicated that the LAMP method was highly sensitive. The detection limit for PCV2 by the LAMP assay was 10 copies, whereas the limit by conventional PCR was 1000 copies. The assay did not cross-react with PCV1, porcine reproductive and respiratory syndrome virus, porcine epidemic diarrhea virus, transmissible gastroenteritis of pigs virus or rotavirus. When 110 samples were tested using the established LAMP system, 95 were detected as positive.</p> <p>Conclusion</p> <p>The newly developed LAMP detection method for PCV2 was more specific, sensitive, rapid and simple than before. It complements and extends previous methods for PCV2 detection and provides an alternative approach for detection of PCV2.</p

Rapid detection of porcine circovirus type 2 using a TaqMan-based real-time PCR

Porcine circovirus type 2 (PCV2) and the associated disease postweaning multisystemic wasting syndrome (PMWS) have caused heavy losses in global agriculture in recent decades. Rapid detection of PCV2 is very important for the effective prophylaxis and treatment of PMWS. To establish a sensitive, specific assay for the detection and quantitation of PCV2, we designed and synthesized specific primers and a probe in the open reading frame 2. The assay had a wide dynamic range with excellent linearity and reliable reproducibility, and detected between 102 and 1010 copies of the genomic DNA per reaction. The coefficient of variation for Ct values varied from 0.59% to 1.05% in the same assay and from 1.9% to 4.2% in 10 different assays. The assay did not cross-react with porcine circovirus type 1, porcine reproductive and respiratory, porcine epidemic diarrhea, transmissible gastroenteritis of pigs and rotavirus. The limits of detection and quantitation were 10 and 100 copies, respectively. Using the established real-time PCR system, 39 of the 40 samples we tested were detected as positive

Analysis of HCV Isolates Among the Li Ethnic in Hainan Island of South China Reveals Their HCV-6 Unique Evolution and a New Subtype

Background/Aims: Hainan Island has been inhabited by the “Li” aboriginal minority for centuries where the HCV genotype distribution patterns maybe remarkably different from other parts of China. We aimed to provide a better understanding of the infection with HCV genotype 6 among “Li” aboriginals on Hainan Island. Methods: Firstly, using RT-PCR and DNA sequencing to determined 517 partial HCV Core-E1(115 from Li Ethnic, 402 from Han Ethnic) and 8 full-length genomes from Li ethnic in Hainan Island successfully, and then using the phylogenetic tree to determine the HCV genotype distribution and analyze the evolution of them. Results: Phylogenetic tree analysis showed that the distribution pattern of HCV genotypes among the Han and Li ethnic population exhibits significant diferences: 6a was the most prevalent subtype in Han ethnic of Hainan Island followed by 1b, 3b, 2a, 3a, and 1a. All genomes from Li ethnic were classified into genotype 6, while 84 out of 115 (73%) could not be classified. Nine sequences (HN1350 et al.) from Li ethnic might be assigned to a new subtype 6xh as their p-distances ranged from 5.9∼9.7%. Furthermore, we sequenced and characterized full-length genomes for eight HCV-6 isolates which were all from Li ethnic in Hainan Island. Among these isolates, the HN1350 was classified as a new subtype: 6xh. Conclusion: Overall, we firstly defined a new subtype of genotype 6xh through partial and new full length genome. And we found a unique distribution pattern of HCV 6 in the Li tribe, which might provide a better way to understand the genetic diversity of HCV-6 and to investigate the phylogeny of HCV strains from Li tribe

Involvement of histone deacetylation in MORC2-mediated down-regulation of carbonic anhydrase IX

Carbonic anhydrase IX (CAIX) plays an important role in the growth and survival of tumor cells. MORC2 is a member of the MORC protein family. The MORC proteins contain a CW-type zinc finger domain and are predicted to have the function of regulating transcription, but no MORC2 target genes have been identified. Here we performed a DNA microarray hybridization and found CAIX mRNA to be down-regulated 8-fold when MORC2 was overexpressed. This result was further confirmed by northern and western blot analysis. Our results also showed that the protected region 4 (PR4) was important for the repression function of MORC2. Moreover, MORC2 decreased the acetylation level of histone H3 at the CAIX promoter. Meanwhile, trichostatin A (TSA) had an increasing effect on CAIX promoter activity. Among the six HDACs tested, histone deacetylase 4 (HDAC4) had a much more prominent effect on CAIX repression. ChIP and ChIP Re-IP assays showed that MORC2 and HDAC4 were assembled on the same region of the CAIX promoter. Importantly, we further confirmed that both proteins are simultaneously present in the PR4-binding complex. These results may contribute to understanding the molecular mechanisms of CAIX regulation