Integrated System for On-Site Rapid and Safe Screening of COVID-19.

Since the outbreak of coronavirus disease 2019 (COVID-19), the epidemic has been spreading around the world for more than 2 years. Rapid, safe, and on-site detection methods of COVID-19 are in urgent demand for the control of the epidemic. Here, we established an integrated system, which incorporates a machine-learning-based Fourier transform infrared spectroscopy technique for rapid COVID-19 screening and air-plasma-based disinfection modules to prevent potential secondary infections. A partial least-squares discrimination analysis and a convolutional neural network model were built using the collected infrared spectral dataset containing 857 training serum samples. Furthermore, the sensitivity, specificity, and prediction accuracy could all reach over 94% from the results of the field test regarding 968 blind testing samples. Additionally, the disinfection modules achieved an inactivation efficiency of 99.9% for surface and airborne tested bacteria. The proposed system is conducive and promising for point-of-care and on-site COVID-19 screening in the mass population.

Web-based computational chemistry education with CHARMMing I: Lessons and tutorial.

This article describes the development, implementation, and use of web-based "lessons" to introduce students and other newcomers to computer simulations of biological macromolecules. These lessons, i.e., interactive step-by-step instructions for performing common molecular simulation tasks, are integrated into the collaboratively developed CHARMM INterface and Graphics (CHARMMing) web user interface (http://www.charmming.org). Several lessons have already been developed with new ones easily added via a provided Python script. In addition to CHARMMing's new lessons functionality, web-based graphical capabilities have been overhauled and are fully compatible with modern mobile web browsers (e.g., phones and tablets), allowing easy integration of these advanced simulation techniques into coursework. Finally, one of the primary objections to web-based systems like CHARMMing has been that "point and click" simulation set-up does little to teach the user about the underlying physics, biology, and computational methods being applied. In response to this criticism, we have developed a freely available tutorial to bridge the gap between graphical simulation setup and the technical knowledge necessary to perform simulations without user interface assistance.

[Experimental study about the impact of the regeneration of interstitial cell of Cajal on gastric emptying in rats undergoing Roux-en-Y gastrojejunostomy].

OBJECTIVE: To investigate the impact of the regeneration of interstitial cell of Cajal (ICC) on the conduction of slow wave and gastric emptying in rats undergoing Roux-en-Y gastrojejunostomy. METHODS: Twenty male SD rats were randomly divided into experimental group and control group. The experimental group consisted of ten rats undergoing Roux-en-Y gastrojejunostomy. The control group only underwent pyloric transection and anastomosis. Gastric scintigraphy was performed in the two groups respectively to measure the half time of gastric emptying (t1/2) at sixteen weeks after the surgical manipulations, and then the myoelectrical activities near the gastrojejunal anastomosis were recorded. The study also observed the regeneration of ICC by the electron microscopy. The data of the 2 groups was compared by t test. RESULTS: In the sixteenth postoperative week, the t1/2 was (23.5 ± 4.5) minutes for rats in the Roux-en-Y group and (10.2 ± 2.3) minutes for those in the control group, indicating delayed gastric emptying in the Roux-en-Y group (t=7.978, P=0.000), accompanied with the abnormal myoelectrical activities near the gastrojejunal anastomosis. The morphological detection showed that ICC near the gastrojejunal anastomosis regenerated and reconstructed their network in the rats of the experimental group. CONCLUSION: The abnormal myoelectrical activities near the gastrojejunal anastomosis, basing on the regeneration and reconstruction of ICC, may make a significant delay on the gastric emptying.

A 26-week repeated-dose toxicity study of allisartan isoproxil in Sprague-Dawley rats.

Allisartan isoproxil (ALS-3) is a selective, nonpeptide blocker of the angiotensin II type 1 receptor. It is a new antihypertensive drug under development with a novel chemical structure. The aim of this study was to evaluate the potential toxicity of ALS-3 in Sprague-Dawley rats. Animals were orally administered either vehicle or ALS-3 at doses of 20, 80 and 320 mg/kg once-daily for 26 weeks, followed by a 6-week recovery period. Toxicity was assessed by mortality, clinical signs, body weight, food consumption, hematology, coagulation, serum chemistry, gross necropsy, organ weights and microscopic examination. Decreased body-weight gain was noted at 320 mg/kg/day in both sexes as well as at the 80-mg/kg/day dose in females. Food consumption was decreased at all doses in males and at 80- and 320-mg/kg/day doses in females. Decreased erythrocyte parameters (erythrocyte count, hemoglobin and hematocrit) were observed in males receiving 320 mg/kg/day. Elevated urea nitrogen (BUN), increased kidney weight, decreased heart weight and exacerbation of chronic progressive nephropathy (CPN) severity were all observed in males at 80 and 320 mg/kg/day. However, only an exacerbated incidence of CPN was observed in females at 320 mg/kg/day. All changes were reversed after the 6-week recovery period, except BUN and CPN. Based on these results, we concluded that a dose of 20 mg/kg/day was the no observed adverse effect level. The toxicity target organ was the kidney. Males were more affected than females.

Oxyberberine suppressed the carbon tetrachloride-induced liver fibrosis by inhibiting liver inflammation in a sirtuin 3-dependent manner in mice.

Previous studies have shown that oxyberberine (OBB), a novel gut microbiota metabolite of berberine, exhibited prominent protective property against acute liver injury and non-alcoholic fatty liver diseases, however, the effect of OBB on liver fibrosis and its potential mechanisms remain largely unknown. This study was aimed to study the effects of OBB on carbon tetrachloride (CCl4)-induced liver fibrosis and tried to clarify the potential mechanisms by focusing on regulating of sirtuin 3 (SIRT3)-mediated liver inflammation. OBB significantly alleviated the liver injury and fibrosis in CCl4-treated C57/BL6 mouse livers. OBB evidently down-regulated the expression of inflammatory factors and reduced the levels of inflammatory factors in CCl4-treated mouse livers. Noteworthy, CCl4-treated decreased the mRNA and protein expression of SIRT3, and treatment with OBB notably increased the expression of SIRT3 both in transcriptional and translational levels in CCl4-treated mice livers. OBB also suppressed the cell viability of TGF-ß1-stimulated JS-1 cells and inhibited the protein expression of α-SMA but increased the expression of SIRT3 in stimulated JS-1 cells. Moreover, depletion of SIRT3 weakened the anti-inflammatory effects of OBB in stimulated JS-1 cells. Interestingly, the anti-liver injury and anti-fibrotic effects of OBB could be available in CCl4-treated WT (129S1/SvImJ) mice but were unavailable in CCl4-treated SIRT3 knockout (KO) mice. In addition, the anti-inflammatory effect of OBB was only found in CCl4-treated WT mice but was not in SIRT3 KO mice. Collectively, these findings suggested that OBB suppressed the liver injury and fibrosis through inhibition of liver inflammation in a SIRT3-dependent manner in CCl4-treated mice.

Recent advances in photothermal therapy-based multifunctional nanoplatforms for breast cancer.

Breast cancer (BC) is one of the most common cancers in women worldwide; however, the successful treatment of BC, especially triple-negative breast cancer (TNBC), remains a significant clinical challenge. Recently, photothermal therapy (PTT), which involves the generation of heat under irradiation to achieve photothermal ablation of BC with minimal invasiveness and outstanding spatial-temporal selectivity, has been demonstrated as a novel therapy that can overcome the drawbacks of chemotherapy or surgery. Significantly, when combining PTT with chemotherapy and/or photodynamic therapy, an enhanced synergistic therapeutic effect can be achieved in both primary and metastatic BC tumors. Thus, this review discusses the recent developments in nanotechnology-based photothermal therapy for the treatment of BC and its metastasis to provide potential strategies for future BC treatment.

Redox-responsive hyaluronan-conjugated polypyrrole nanoparticles targeting chemo-photothermal therapy for breast cancer.

The combination of chemo-photothermal therapy has a wide application prospect in the intensive treatment of cancer. In this study, we developed a complex nanoparticle consist of polypyrrole, cystine dihydrochloride and hyaluronan. The polypyrrole nanoparticles loaded with paclitaxel exhibited good photothermal effects, and the drug release can be triggered by combined response of temperature and redox. In vitro biological studies indicated the nanoparticles could effectively induced apoptosis of MDA-MB-231 breast cancer cells involved in the potential mechanism of inhibition of biological expression of heat shock proteins and JAK-STAT signaling pathway. In addition, the nanoparticles have a significant inhibitory effect on cancer growth in breast tumor-bearing mice model, indicating that they have great potential for synergistic chemo-photothermal therapy.

CTCF-Induced lncRNA C5orf66-AS1 Facilitates the Progression of Triple-Negative Breast Cancer via Sponging miR-149-5p to Up-Regulate CTCF and CTNNB1 to Activate Wnt/ß-Catenin Pathway.

Triple-negative breast cancer (TNBC) represents one of the subtypes of breast cancer with high aggressiveness. Long noncoding RNAs (lncRNAs) are well-known to function as crucial regulators in human cancers which include TNBC. Nevertheless, the specific role of the lncRNA C5orf66-AS1 in TNBC is unclear. In this study, we tested C5orf66-AS1 expression in TNBC cells using quantitative real-time PCR (qRT-PCR) and used functional assays to detect cell behaviors, which showed that C5orf66-AS1 was highly expressed in TNBC cells and that C5orf66-AS1 knockdown attenuated cell proliferation, migration, and invasion while promoting cell apoptosis. Through a luciferase reporter assay, RNA immunoprecipitation (RIP) assay, and chromatin immunoprecipitation (ChIP) assay, we identified the binding capacity of C5orf66-AS1 to RNAs. Furthermore, miR-149-5p was proven to be sponged by C5orf66-AS1. CCCTC-binding factor (CTCF) was confirmed as the target of miR-149-5p and could transcriptionally activate C5orf66-AS1 expression in TNBC cells. We also discovered that C5orf66-AS1 activated the Wnt/ß-catenin signaling pathway by upregulating catenin beta 1 (CTNNB1). Importantly, CTNNB1 could be targeted by miR-149-5p. In rescue assays, it was proven that overexpressing CTCF and CTNNB1 or inhibiting miR-149-5p could totally reverse the inhibitory effect of silencing C5orf66-AS1 on TNBC progression. In short, the lncRNA C5orf66-AS1 acted as an oncogene to facilitate TNBC malignancy.

Pyloric resection and delayed gastric liquid emptying in rats.

BACKGROUND: Surgical resection of the distal stomach impairs gastric emptying. Generally, pylorus and the antrum are removed in the distal gastrectomy, however, the pylorus is removed individually under specific circumstances. We focus on the relation between the pyloric resection and the gastric liquid emptying. AIMS: The present investigation aimed to explore the pylorectomy how to influence gastric liquid emptying in rats. METHODS: Pylorectomy and end-to-end gastroduodenal anastomosis were conducted in rats. Electrodes were implanted in the gastrointestinal serosal surface near the stoma. Total stomach, proximal stomach, distal stomach and duodenal liquid emptying, myoelectricities in the gastrointestinal tract near the stoma, and structures were examined with scintigraphy, electrode recording in vivo, and electron microscopy, respectively. RESULTS: Delayed total stomach and distal stomach emptying were found in pylorectomy rats (p<0.001). However, there was no difference in the proximal stomach and the duodenal liquid emptying compared to the controls (p>0.05). The myoelectricity of 3-5 cpm (cycles/min) in antrum and 10-12 cpm in duodenum were found in the controls and no retrograde or antegrade myoelectricities were recorded in the duodenum and antrum. High-frequency myoelectricities (tachygastria) were recorded in the antrum near the stoma (p<0.01), the retrograde and antegrade myoelectricities propagating through the stoma were recorded, and the regenerated interstitial cells of Cajal were found in stoma under electron microscope observation in pylorectomy rat. CONCLUSIONS: The gastroduodenal incoordination and abnormal myoelectricity related to impaired contraction in the antrum caused the delayed liquid gastric emptying in pylorectomy rats.

Alpinetin exerts anti-inflammatory, anti-oxidative and anti-angiogenic effects through activating the Nrf2 pathway and inhibiting NLRP3 pathway in carbon tetrachloride-induced liver fibrosis.

Alpinetin is the major active ingredient of Alpiniakatsumadai Hayata. As a kind of novel plant-derived flavonoid, alpinetin has shown potent hepatoprotective effect against many liver diseases such as non-alcoholic fatty liver and lipopolysaccharide/d-Galactosamine-induced liver injury. However, its roles in liver fibrosis remain to be determined. The aim of the current study was to investigate the effect of alpinetin in mice with carbon tetrachloride (CCl4)-induced liver fibrosis, and to elucidate the underlying mechanisms of action. Alpinetin ameliorated the CCl4-induced liver injury and fibrosis in mice, as shown by decreased collagen deposition and the decreased expression of liver fibrosis marker proteins. Alpinetin suppressed the inflammation and oxidative stress in fibrotic livers of mice, as evidenced by decreased levels of proinflammatory factors, the decreased reactive oxygen species (ROS) and malondialdehyde (MDA) levels, and the increased activities of antioxidant enzymes. In addition, alpinetin attenuated the angiogenesis in fibrotic livers of the test animals. Mechanistically, alpinetin inhibited the CCl4-induced expression of NLRP3, ASC, cleaved caspase-1, mature (cleaved-) IL-1ß, and IL-18 in livers of mice. Furthermore, alpinetin resulted in an increased in the nuclear expression and a decrease in the cytoplasmic expression of Nrf2, as well as increased protein expression of downstream target enzymes, GCLC, HO-1, NQO1, and GCLM, thus exerting the antioxidant effect. Overall, these findings suggested that the anti-fibrotic effect of alpinetin can be attributed to the inhibition of NLRP3-mediated anti-inflammatory activities and Nrf2-mediated anti-oxidative activities, in addition to the decrement of hepatic angiogenesis.

Loss of expression of protein tyrosine kinase 7 in invasive ductal breast cancers.

Protein tyrosine kinase 7 (PTK7) is a catalytically inactive receptor tyrosine kinase that is involved in development and tumorigenesis. PTK7 expression and its functional roles have been investigated in several human cancers, although controversial results have been obtained. In this study, we investigated the expression of PTK7 protein in invasive ductal breast cancer tissues, and analyzed its relationship with clinicopathologic parameters. Seventy-nine consecutive invasive breast cancer tissues were included in the study, and PTK7 protein was detected in invasive ductal breast cancers and normal breast epithelial cells by immunohistochemistry. Positive staining was noted in all normal breast epithelial cells and differential expression was observed in breast carcinomas. Thirty-eight of 79 samples (48.1%) were negative or stained weakly for PTK7 (-), 19 (24.1%) showed moderate staining (+), and 22 (27.8%) were strongly stained (++). PTK7 expression was negatively associated with tumor grade (P=0.025, r=-0.251), tumor-node-metastasis stage (P=0.004, r=-0.317), lymph node metastasis (P=0.002, r=-0.351), human epidermal growth factor receptor 2 expression (P=0.029, r=-0.245), and Ki67 expression (P=0.004, r=-0.317), and positively associated with estrogen receptor (ER) expression (P=0.037, r=0.235). No significant relationship was found between PTK7 expression and patient age or progesterone receptor (PR) expression. Our data indicated that PTK7 protein was down-regulated in breast cancer cells compared with healthy epithelial cells, and that PTK7 may be a tumor suppressor gene in breast cancer. Future studies should explore the molecular mechanisms underlying the down-regulation and functional roles of PTK7 in breast cancer.

[Impact of abnormal myoelectricity at gastroduodenal anastomosis on gastric emptying in rats].

OBJECTIVE: To explore the impact of abnormal myoelectricity at gastroduodenal anastomosis on gastric emptying in rats. METHODS: Rats were randomly divided into experimental group (n=16) and control group (n=16). Pylorectomy and end-to-end gastroduodenal anastomosis were performed in the experimental group and electrodes were implanted in the serosal surface adjacent to the anastomosis. Slow waves were recorded by the implanted electrode in vivo. Gastric emptying was examined by scintigraphy. RESULTS: At the first week after surgery, antral slow-wave frequency was significantly lower in the experimental group (0.8±1.4 vs. 3.3±1.2, P<0.01), as was the duodenal slow-wave frequency (2.1±0.6 vs. 11.1±0.7, P<0.01). There was no consecutive slow-waves transduction across the pylorus or the anastomosis. Within 12-16 weeks after operation, antral slow-wave frequency in the experimental group and the control group were (8.7±0.6) cpm and (4.0±0.4) cpm, respectively (P<0.01), and duodenal slow-wave frequency were (11.1±0.8) cpm and (10.8±0.7) cpm, respectively (P>0.05). Retrograde and antegrade myoelectricity transduction through the anastomosis were detected. The mean semi-emptying time in the proximal stomach was 14.7 min in the experimental group and 13.6 min in the control group (P>0.05). Radionuclide retention rate was 25.4% in the experimental group and 39.4% in the control group (P>0.05). The mean semi-emptying time in the distal stomach was 25.3 min in the experimental group and 10.5 min in the control group (P<0.01). Radionuclide retention rate was 46.4% in the experimental group and 18.7% in the control group (P<0.01). CONCLUSION: The abnormal myoelectricity in the region of gastroduodenal stoma may delay liquid gastric emptying in pylorectomy rats.

Effects of P2Y1 receptor on glial fibrillary acidic protein and glial cell line-derived neurotrophic factor production of astrocytes under ischemic condition and the related signaling pathways.

OBJECTIVE: The present study aimed to explore the role of P2Y(1) receptor in glial fibrillary acidic protein (GFAP) production and glial cell line-derived neurotrophic factor (GDNF) secretion of astrocytes under ischemic insult and the related signaling pathways. METHODS: Using transient right middle cerebral artery occlusion (tMCAO) and oxygen-glucose-serum deprivation for 2 h as the model of ischemic injury in vivo and in vitro, immunofluorescence, quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR), Western blotting, enzyme linked immunosorbent assay (ELISA) were used to investigate location of P2Y(1) receptor and GDNF, the expression of GFAP and GDNF, and the changes of signaling molecules. RESULTS: Blockage of P2Y(1) receptor with the selective antagonist N(6)-methyl-2'-deoxyadenosine 3',5'-bisphosphate diammonium (MRS2179) reduced GFAP production and increased GDNF production in the antagonist group as compared with simple ischemic group both in vivo and in vitro. Oxygen-glucose-serum deprivation and blockage of P2Y(1) receptor caused elevation of phosphorylated Akt and cAMP response element binding protein (CREB), and reduction of phosphorylated Janus kinase2 (JAK2) and signal transducer and activator of transcription3 (STAT3, Ser727). After blockage of P2Y(1) receptor and deprivation of oxygen-glucose-serum, AG490 (inhibitor of JAK2) reduced phosphorylation of STAT3 (Ser727) as well as expression of GFAP; LY294002, an inhibitor of phosphatidylinositol 3-kinase (PI3-K), decreased phosphorylation of Akt and CREB; the inhibitor of mitogen-activated protein kinase kinase1/2 (MEK1/2) U0126, an important molecule of Ras/extracellular signal-regulated kinase (ERK) signaling pathway, decreased the phosphorylation of JAK2, STAT3 (Ser727), Akt and CREB. CONCLUSION: These results suggest that P2Y(1) receptor plays a role in the production of GFAP and GDNF in astrocytes under transient ischemic condition and the related signaling pathways may be JAK2/STAT3 and PI3-K/Akt/CREB, respectively, and that crosstalk probably exists between them.

Transcriptional regulatory network discovery via multiple method integration: application to e. coli K12.

Transcriptional regulatory network (TRN) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete TRNs. We develop a methodology, TRND, that integrates a preliminary TRN, microarray data, gene ontology and phylogenic similarity to accurately discover TRNs and apply the method to E. coli K12. The approach can easily be extended to include other methodologies. Although gene ontology and phylogenic similarity have been used in the context of gene-gene networks, we show that more information can be extracted when gene-gene scores are transformed to gene-transcription factor (TF) scores using a preliminary TRN. This seems to be preferable over the construction of gene-gene interaction networks in light of the observed fact that gene expression and activity of a TF made of a component encoded by that gene is often out of phase. TRND multi-method integration is found to be facilitated by the use of a Bayesian framework for each method derived from its individual scoring measure and a training set of gene/TF regulatory interactions. The TRNs we construct are in better agreement with microarray data. The number of gene/TF interactions we discover is actually double that of existing networks.

Transcriptional regulatory networks via gene ontology and expression data.

Transcriptional regulatory network (TRN) discovery using information from a single source does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete TRNs. A methodology, TRND, that integrates a preliminary TRN, gene expression data and gene ontology is developed to discover TRNs. The method is applied to a comprehensive set of expression data on B cell and a preliminary TRN that included 1,335 genes, 443 transcription factors (TFs) and 4032 gene/TF interactions. Predictions were obtained for 443 TFs and 9,589 genes. 14,616 of 4,247,927 possible gene/TF interactions scored higher than the imposed threshold. Results for three TFs, E2F-4, p130 and c-Myc, were examined in more detail to assess the accuracy of the integrated methodology. Although the training sets for E2F-4 and p130 were rather limited, the activities of these two TFs were found to be highly correlated and a large set of coregulated genes is predicted. These predictions were confirmed with published experimental results not used in the training set. A similar test was run for the c-Myc TF using the comprehensive resource www.myccancergene.org. In addition, correlations between expression of genes that encode TFs and TF activities were calculated and showed that the assumption of TF activity correlates with encoding gene expression might be misleading. The constructed B cell TRN, and scores for individual methodologies and the integrated approach are available at systemsbiology.indiana.edu/trndresults.