Altered T cell development in an animal model of multiple sclerosis.

Multiple sclerosis (MS) is a chronic autoimmune disease that affects the central nervous system (CNS), leading to demyelination and axonal degeneration. Experimental autoimmune encephalomyelitis (EAE) is an animal model of MS that has significantly improved our understanding of MS. Studies have observed early thymic involution in MS patients, suggesting the potential involvement of the thymus in CNS autoimmunity. However, our knowledge of the thymus's role in autoimmune disorders affecting the CNS remains limited. In this study, we examined the effects of EAE induction on thymopoiesis and observed alterations in T cell development. These changes were characterized by increased apoptosis and decreased proliferation of thymocytes at the EAE peak stage. We also identified a blockade in the transition from CD4-CD8- double-negative thymocytes to CD4+CD8+ double-positive cells, as evidenced by the accumulation of double-negative stage 1 thymocytes at both the EAE onset and peak stages. Furthermore, positive selection was disrupted in the thymus of EAE mice at both stages, leading to an elevated proportion and number of CD4+CD8- and CD4-CD8+ single-positive cells. Meanwhile, we observed an augmented production of regulatory T cells in the thymus of EAE mice. Moreover, peripheral blood analysis of EAE mice at the onset stage showed expanded T cell subsets but not at the peak stage. We also observed altered expression patterns in thymus-derived CD4+CD8- and CD4-CD8+ single-positive cells between MS patients and healthy controls. Our findings demonstrate a modified T cell development in EAE/MS, providing valuable insights into the potential of modulating thymic function as a targeted therapeutic approach to MS/EAE.

Few-Shot Fault Diagnosis Based on an Attention-Weighted Relation Network.

As energy conversion systems continue to grow in complexity, pneumatic control valves may exhibit unexpected anomalies or trigger system shutdowns, leading to a decrease in system reliability. Consequently, the analysis of time-domain signals and the utilization of artificial intelligence, including deep learning methods, have emerged as pivotal approaches for addressing these challenges. Although deep learning is widely used for pneumatic valve fault diagnosis, the success of most deep learning methods depends on a large amount of labeled training data, which is often difficult to obtain. To address this problem, a novel fault diagnosis method based on the attention-weighted relation network (AWRN) is proposed to achieve fault detection and classification with small sample data. In the proposed method, fault diagnosis is performed through the relation network in few-shot learning, and in order to enhance the representativeness of feature extraction, the attention-weighted mechanism is introduced into the relation network. Finally, in order to verify the effectiveness of the method, a DA valve fault dataset is constructed, and experimental validation is performed on this dataset and another benchmark PU rolling bearing fault dataset. The results show that the accuracy of the network on DA is 99.15%, and the average accuracy on PU is 98.37%. Compared with the state-of-the-art diagnosis methods, the proposed method achieves higher accuracy while significantly reducing the amount of training data.

A flow-through chromatography purification process for Vero cell-derived influenza virus (H7N9).

Immunization is the most effective way to respond to an influenza epidemic. To produce Vero cell-derived influenza vaccines, a more efficient, stable and economical purification process is required. In this study, we purified the H7N9 influenza virus grown in Vero cells that were cultured in a serum-free medium by using a combination of anion exchange chromatography (AEC) and ligand-activated core chromatography (LCC), which avoids the virus capture step. After purification, 99.95 % host cell DNA (hcDNA) (final concentration: 28.69 pg/dose) and 98.87 % host cell protein (HCP) (final concentration: 28.28 ng/dose) were removed. The albumin content was 11.36 ng/dose. All these remnants met the current Chinese Pharmacopoeia and WHO requirements. The final virus recovery rate was 58.74 %, with the concentration of hemagglutinin recorded at 132.12 µg/mL. The flow-through chromatography purification process represents an alternative to the existing processes for cell-derived influenza viruses and might be suitable for the purification of other viruses as well.

Differential HbA1c response in the placebo arm of DPP-4 inhibitor clinical trials conducted in China compared to other countries: a systematic review and meta-analysis.

BACKGROUND: It has been observed that the efficacy of dipeptidyl peptidase-4 (DPP-4) inhibitors as compared to the placebo groups in some clinical trials conducted in China is weaker than that in trials conducted outside China, leading to the suspicion that this may be caused by differential Glycosylated Hemoglobin (HbA1c) response in the placebo arm of DPP-4 inhibitor clinical trials conducted in China compared to other countries. METHODS: We searched published articles and other documents related to phase III placebo-control trials of DPP-4 inhibitors in Type 2 diabetes mellitus (T2DM). We included studies from different countries and compared those conducted in China to those conducted in other countries. Meta-regression analysis was used to analyze the HbA1c response in the placebo arms. RESULTS: A total of 66 studies met the inclusion criteria and 10 were conducted within China. There were a total of 8303 participants (mean age 56, male 57 %) in placebo groups. The pooled change in HbA1c for the placebo groups of 10 trials conducted in patients with T2DM in China was 0.26 % (95 % CI [-0.36 %, -0.16 %], p-value < 0.001), compared to 0.015 % (95 % CI [-0.05 %, 0.08 %], p-value is 0.637) for 56 trials conducted outside of China. The difference of placebo effect between trials conducted in and outside China is -0.273 % (95 % CI [-0.42 %, -0.13 %], p-value is less than 0.001) while after excluding trials conducted in Japan, the difference is -0.203 % (95 % CI [-0.35 %, -0.06 %], p-value is 0.005). They are both statistically significant. CONCLUSIONS: The meta-analysis in the article demonstrates that there is statistically significant difference in the HbA1c response in the placebo arm of DPP-4 inhibitor clinical trials conducted in China compared to other countries. This differential HbA1c response in the placebo arm should be taken into consideration by both experimenters and medical decision makers when future DPP-4 studies are conducted in China.

Mechanistic relationships between hepatic genotoxicity and carcinogenicity in male B6C3F1 mice treated with polycyclic aromatic hydrocarbon mixtures.

The genotoxicity of a complex mixture [neutral fraction (NF)] from a wood preserving waste and reconstituted mixture (RM) mimicking the NF with seven major polycyclic aromatic hydrocarbons (PAHs) and benzo(a)pyrene (BaP) was investigated by determining DNA adducts and tumor incidence in male B6C3F1 mice exposed to three different doses of the chemical mixtures. The peak values of DNA adducts were observed after 24 h, and the highest levels of PAH-DNA adducts were exhibited in mice administered NF + BaP, and the highest tumor incidence and mortality were also observed in this group. DNA adduct levels after 1, 7, or 21 days were significantly correlated with animal mortality and incidence of total tumors including liver, lung, and forestomach. However, only hepatic DNA adducts after 7 days significantly correlated with liver tumor incidence. Most proteins involved in DNA repair including ATM, pATR, Chk1, pChk1, DNA PKcs, XRCC1, FANCD2, Ku80, Mre11, and Brca2 were significantly lower in liver tumor tissue compared to non-tumor tissue. Expressions of proteins involved in apoptosis and cell cycle regulation were also significantly different in tumor versus non-tumor tissues, and it is possible that PAH-induced changes in these gene products are important for tumor development and growth.

OTG-snpcaller: an optimized pipeline based on TMAP and GATK for SNP calling from ion torrent data.

Because the new Proton platform from Life Technologies produced markedly different data from those of the Illumina platform, the conventional Illumina data analysis pipeline could not be used directly. We developed an optimized SNP calling method using TMAP and GATK (OTG-snpcaller). This method combined our own optimized processes, Remove Duplicates According to AS Tag (RDAST) and Alignment Optimize Structure (AOS), together with TMAP and GATK, to call SNPs from Proton data. We sequenced four sets of exomes captured by Agilent SureSelect and NimbleGen SeqCap EZ Kit, using Life Technology's Ion Proton sequencer. Then we applied OTG-snpcaller and compared our results with the results from Torrent Variants Caller. The results indicated that OTG-snpcaller can reduce both false positive and false negative rates. Moreover, we compared our results with Illumina results generated by GATK best practices, and we found that the results of these two platforms were comparable. The good performance in variant calling using GATK best practices can be primarily attributed to the high quality of the Illumina sequences.

HTS-PEG: a method for high throughput sequencing of the paired-ends of genomic libraries.

Second generation sequencing has been widely used to sequence whole genomes. Though various paired-end sequencing methods have been developed to construct the long scaffold from contigs derived from shotgun sequencing, the classical paired-end sequencing of the Bacteria Artificial Chromosome (BAC) or fosmid libraries by the Sanger method still plays an important role in genome assembly. However, sequencing libraries with the Sanger method is expensive and time-consuming. Here we report a new strategy to sequence the paired-ends of genomic libraries with parallel pyrosequencing, using a Chinese amphioxus (Branchiostoma belcheri) BAC library as an example. In total, approximately 12,670 non-redundant paired-end sequences were generated. Mapping them to the primary scaffolds of Chinese amphioxus, we obtained 413 ultra-scaffolds from 1,182 primary scaffolds, and the N50 scaffold length was increased approximately 55 kb, which is about a 10% improvement. We provide a universal and cost-effective method for sequencing the ultra-long paired-ends of genomic libraries. This method can be very easily implemented in other second generation sequencing platforms.

Biodegradation of simple chemical mixtures in soil.

Exogenous microorganisms often are used to enhance bioremediation. This study compared the capabilities of two exogenous microbial cultures and an indigenous population to detoxify a Weswood silt loam soil amended with a simple chemical mixture. The first three treatments were unamended soils inoculated with either indigenous microorganisms, Pseudomonas aeruginosa, or Phanerochaete sordida. Three additional treatments consisted of soil amended with benzo[a]pyrene, pentachlorophenol, and 2,4,6-trinitrotoluene, which were inoculated with either indigenous microorganisms, P. aeruginosa, or P. sordida. Samples were collected from the soils at several time points from 0 through 540 or 720 d, sequentially extracted with methylene chloride and methanol, and analyzed for genotoxicity (using the Salmonella/microsome assay) and chemical degradation. Although the indigenous microorganisms were effective for removal of benzo[a]pyrene, the Pseudomonas bacteria exhibited slightly greater removal rates for 2,4,6,-trinitrotoluene. The fungal cultures were significantly more effective at degrading pentachlorophenol. The day 540 extracts from all model chemical-amended treatments were genotoxic. In most cases, the day 540 extracts were more genotoxic than the day 0 extracts. The results suggest that, under appropriate conditions, enriched cultures of microorganisms may have an increased capacity to degrade individual chemicals. However, the products of degradation in some cases might be more genotoxic than the parent compounds.

A comparison of two methods for fractionating complex mixtures in preparation for toxicity analysis.

Chemical fractionation is a widely used tool for the chemical and toxicological characterization of complex mixtures. The objective of this research was to compare two frequently employed methods for fractionating a wood preserving waste (WPW) containing polycyclic aromatic hydrocarbons (PAHs) and pentachlorophenol (PCP). The first method involved fractionation of the WPW into acid, base, and neutral fractions using a liquid-liquid acid/base/neutral (A/B/N) technique. The second method utilized alumina column chromatography to produce two fractions, A1 and A2. Gas chromatography and mass spectrometry were used to quantify the chemical components in all fractions. The alumina method recovered 473,338 mg of total PAHs (tPAHs) per kilogram crude, while the A/B/N method yielded only 193,379 mg tPAHs/kg crude. In contrast, the A/B/N method recovered 13.7 mg PCP/kg crude while the alumina method yielded only 0.5 mg PCP/kg crude. Three bioassays were used to determine the toxicity of the crude extract and fractions. The neutral and A1 fractions contained the highest levels of tPAHs and benzo[a]pyrene (BaP) but failed to induce a positive response in the Salmonella/microsome assay with concentrations containing as much as 1800 and 2500 ng BaP/plate, respectively. In the Escherichia coli prophage induction assay, the acid fraction, which contained 472 mg PCP/kg fraction, induced a positive response, as did the base fraction, which did not contain detectable PCP. Significant reduction of gap junctional intercellular communication in hepatic cells occurred with the crude extract and acid, base, and neutral fractions. Overall, the results of these bioassays suggest that PCP genotoxicity was expressed in the acid fraction, whereas the cumulative genotoxicity of genotoxic PAHs appeared to be masked in the isolates from either fractionation method. The optimal fractionation method for a mixture of chlorophenols and PAHs may involve a refined hybrid method.