MCPNET: Development of an interpretable deep learning model based on multiple conformations of the compound for predicting developmental toxicity.

The development of deep learning models for predicting toxicological endpoints has shown great promise, but one of the challenges in the field is the accuracy and interpretability of these models. The bioactive conformation of a compound plays a critical role for it to bind in the target. It is a big issue to figure out the bioactive conformation in deep learning without the co-crystal structure or highly precise molecular simulations. In this study, we developed a deep learning framework of Multi-Conformation Point Network (MCPNET) to construct classification and regression models, respectively, based on electrostatic potential distributions on vdW surfaces around multiple conformations of the compound using a dataset of compounds with developmental toxicity in zebrafish embryo. MCPNET applied 3D multi-conformational surface point cloud to extract the molecular features for model training, which may be critical for capturing the structural diversity of compounds. The models achieved an accuracy of 85 % on the classification task and R2 of 0.66 on the regression task, outperforming traditional machine learning models and other deep learning models. The key feature of our model is its interpretability with the component visualization to identify the factors contributing to the prediction and to understand the compound action mechanism. MCPNET may predict the conformation quietly close to the bioactive conformation of a compound by attention-based multi-conformation pooling mechanism. Our results demonstrated the potential of deep learning based on 3D molecular representations in accurately predicting developmental toxicity. The source code is publicly available at https://github.com/Superlit-CC/MCPNET.

Synthesis of 2,3-Fused Quinazolinones via the Radical Cascade Pathway and Reaction Mechanistic Studies by DFT Calculations.

An efficient radical cascade cyclization of unactivated alkenes toward the synthesis of a series of ring-fused quinazolinones has been developed in moderate to excellent yields using commercially available ethers, alkanes, and alcohols, respectively, under a base-free condition in a short time without a transition metal as catalyst. Notably, the transformations can be carried out with the advantages of a broad substrate scope and high atomic economy. Density functional theory calculations and wavefunction analyses were performed to elucidate the radical reaction mechanism.

Whole transcriptome analysis reveals that immune infiltration- lncRNAs are related to cellular apoptosis in liver transplantation.

Introduction: In most instances, liver transplantation (LT) is the only available treatment for end-stage liver diseases. However, LT could also induce serious liver diseases or injury, and the underlying mechanisms of LT-induced complications remain largely unknown, especially the mechanisms of the dysfunction of the immune system mediated by long noncoding RNAs (lncRNAs). Methods: In this study, we globally analyzed the proportion of immune cells by using the transcriptome sequencing data (RNA-seq) of needle-core liver biopsies from pre- and post-transplantation recipients. Dysregulated lncRNAs were found to be correlated with the altered fractions of immune cells. We finally explored the potential targets of dysregulated lncRNAs and analyzed their functions in LT. Results: We found that in the samples, some immune cells changed significantly after LT, including CD4 T cells, NK cells and mast cells. The proportion of macrophages in different polarization states also changed significantly, with M0 macrophages increasing and M2 macrophages decreasing. Through weighted gene co-expression network analysis (WGCNA), 7 gene expression modules related to LT were identified. These modules were related to changes in the proportion of different immune cells. The functions of these modules represent the response modes of different functional genes after LT. Among these modules, MEtan and MEyellow modules were primarily enriched in apoptosis and inflammatory pathways. Twelve immunity-related lncRNAs were identified for the first time, and the regulatory network co-changing with immune cells was also identified. The co-expressed genes of these lncRNAs were highly enriched in apoptosis-related pathways. Many apoptosis-related genes were found to be up-regulated after LT. Discussion: In summary, we speculated that the expression and regulation of these apoptotic genes may be related to the changes in the proportion of immune cells. Some of these lncRNAs and apoptosis-related genes have been reported to be related to cell proliferation and apoptosis. They are also potential biomarkers or therapeutic targets.

Reliable CA-(Q)SAR generation based on entropy weight optimized by grid search and correction factors.

Chromosome aberration (CA) is a serious genotoxicity of a compound, leading to carcinogenicity and developmental side effects. In the present manuscript, we developed a QSAR model for CA prediction using artificial intelligence methodologies. The reliable QSAR model was constructed based on an enlarged data set of 3208 compounds by optimizing machine learning and deep learning algorithms based on hyperparametric iterations and using multiple descriptors of molecular fingerprint in combination with drug-like molecular properties (MP) screened by entropy weight methodology on the open-source Python platform. Furthermore, molecular similarity for returning search and molecular connection index for additional descriptor were additionally introduced to differentiate the compounds with high similarity for correct CA prediction for QSAR model generation. The final generated CA-(Q)SAR model exhibited good prediction accuracy of 80.6%. The bias of the final model is about 0.9793. On the basis of generated QSAR model, data analyses were further performed to analyze the typical structure features in numerical intervals (MPI) of molecular properties MW, XlogP, and TPSA, respectively, for potential CA or non-CA toxicity with a normalized occurrence probability (NOP) more than 70%, which may provide useful clues for drug design of leads or candidate devoid of CA genotoxicity.

Hypothalamic regulation of energy homoeostasis when consuming diets of different energy concentrations: comparison between Tibetan and Small-tailed Han sheep.

Seasonal energy intake of Tibetan sheep on the harsh Qinghai-Tibetan Plateau (QTP) fluctuates greatly and is often well below maintenance requirements. The aim of this study was to gain insight into how the hypothalamus regulates energy homoeostasis in Tibetan sheep. We compared Tibetan and Small-tailed Han sheep (n 24 of each breed), which were each allocated randomly into four groups and offered one of four diets that differed in digestible energy densities: 8·21, 9·33, 10·45 and 11·57 MJ/kg DM. Sheep were weighed every 2 weeks, and it was assumed that the change in body weight (BW) reflected the change in energy balance. The arcuate nucleus of the hypothalamus in Tibetan sheep had greater protein expressions of neuropeptide Y (NPY) and agouti-related peptide (AgRP) when in negative energy balance, but lesser protein expressions of proopiomelanocortin (POMC) and cocaine and amphetamine-regulated transcript (CART) when in positive energy balance than Small-tailed Han sheep. As a result, Tibetan sheep had a lesser BW loss when in negative energy balance and stored more energy and gained more BW when in positive energy balance than Small-tailed Han sheep with the same dietary intake. Moreover, in the hypothalamic adenosine monophosphate-activated protein kinase (AMPK) regulation pathway, Tibetan sheep had greater adenosine monophosphate-activated protein kinase-α 2 protein expression than Small-tailed Han sheep, which supported the premise of a better ability to regulate energy homoeostasis and better growth performance. These differences in the hypothalamic NPY/AgRP, POMC/CART and AMPK pathways between breeds conferred an advantage to the Tibetan over Small-tailed Han sheep to cope with low energy intake on the harsh QTP.

Identification of candidate biomarkers of liver hydatid disease via microarray profiling, bioinformatics analysis, and machine learning.

OBJECTIVES: Liver echinococcosis is a severe zoonotic disease caused by Echinococcus (tapeworm) infection, which is epidemic in the Qinghai region of China. Here, we aimed to explore biomarkers and establish a predictive model for the diagnosis of liver echinococcosis. METHODS: Microarray profiling followed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis was performed in liver tissue from patients with liver hydatid disease and from healthy controls from the Qinghai region of China. A protein-protein interaction (PPI) network and random forest model were established to identify potential biomarkers and predict the occurrence of liver echinococcosis, respectively. RESULTS: Microarray profiling identified 1152 differentially expressed genes (DEGs), including 936 upregulated genes and 216 downregulated genes. Several previously unreported biological processes and signaling pathways were identified. The FCGR2B and CTLA4 proteins were identified by the PPI networks and random forest model. The random forest model based on FCGR2B and CTLA4 reliably predicted the occurrence of liver hydatid disease, with an area under the receiver operator characteristic curve of 0.921. CONCLUSION: Our findings give new insight into gene expression in patients with liver echinococcosis from the Qinghai region of China, improving our understanding of hepatic hydatid disease.

Co-Occurrence of Cystic and Alveolar Echinococcosis in the Liver: A Case Report.

Morbidity of mixed cystic and alveolar echinococcosis (CE and AE) is exceptionally rare. Less literature retrieved from a database on the internet detailed the content, including radiography, pathology, and therapeutics data. Such a case of co-occurrence of the different Echinococcus species was diagnosed and treated at our hospital center from Nov 2019 to Feb 2020. A 30 yr old female from the pastoral area in Qinghai Province, China, was diagnosed with a case of echinococcosis and diagnosis was confirmed after image studies, immunoassaying of hydatid enzymes, life history and pathology result. The patient underwent hepatectomy along with excision of the internal capsule. Post-operative pathology was done, and it confirmed a mixed infection of both CE and AE. The patient recovered well without complications after liver-protecting and tissue repair treatment for 15 days. Knowing about infective mode and immune method of the case might be vital for research on variation for Echinococcus infection.

Comparison between Tibetan and Small-tailed Han sheep in adipocyte phenotype, lipid metabolism and energy homoeostasis regulation of adipose tissues when consuming diets of different energy levels.

This study aimed to gain insight into how adipose tissue of Tibetan sheep regulates energy homoeostasis to cope with low energy intake under the harsh environment of the Qinghai-Tibetan Plateau (QTP). We compared Tibetan and Small-tailed Han sheep (n 24 of each breed), all wethers and 1·5 years of age, which were each divided randomly into four groups and offered diets of different digestible energy (DE) densities: 8·21, 9·33, 10·45 and 11·57 MJ DE/kg DM. When the sheep lost body mass and were assumed to be in negative energy balance: (1) adipocyte diameter in subcutaneous adipose tissue was smaller and decreased to a greater extent in Tibetan than in Small-tailed Han sheep, but the opposite occurred in the visceral adipose tissue; (2) Tibetan sheep showed higher insulin receptor mRNA expression and lower concentrations of catabolic hormones than Small-tailed Han sheep and (3) Tibetan sheep had lower capacity for glucose and fatty acid uptake than Small-tailed Han sheep. Moreover, Tibetan sheep had lower AMPKα mRNA expression but higher mammalian target of rapamycin mRNA expression in the adipocytes than Small-tailed Han sheep. We concluded that Tibetan sheep had lower catabolism but higher anabolism in adipose tissue and reduced the capacity for glucose and fatty acid uptake to a greater extent than Small-tailed Han sheep to maintain energy homoeostasis when in negative energy balance. These responses provide Tibetan sheep with a high ability to cope with low energy intake and with the harsh environment of the QTP.

Tibetan sheep have a high capacity to absorb and to regulate metabolism of SCFA in the rumen epithelium to adapt to low energy intake.

The nutritional intake of Tibetan sheep on the harsh Qinghai-Tibetan Plateau is often under maintenance requirements, especially during the long, cold winter. However, they have adapted well and even thrive under these conditions. The aim of the present study was to gain insight into how the rumen epithelium of Tibetan sheep has adapted to the consumption of low-energy-level diets. For this purpose, we compared Tibetan and small-tailed Han sheep (n 24 of each breed, all wethers and 1·5 years of age), which were divided randomly into one of four groups and offered ad libitum diets of different digestible energy (DE) densities: 8·21, 9·33, 10·45 and 11·57 MJ DE/kg DM. The Tibetan sheep had higher rumen concentrations of total SCFA, acetate, butyrate and iso-acids but lower concentrations of propionate than small-tailed Han sheep. The Tibetan sheep had higher absorption capability of SCFA due to the greater absorption surface area and higher mRNA expression of the SCFA absorption relative genes than small-tailed Han sheep. For the metabolism of SCFA in the rumen epithelium, the small-tailed Han sheep showed higher utilisation of the ketogenesis pathway than Tibetan sheep; however, Tibetan sheep had greater regulation capacity in SCFA metabolism pathways. These differences between breeds allowed the Tibetan sheep to have greater capability of absorbing SCFA and better capacity to regulate the metabolism of SCFA, which would allow them to cope with low energy intake better than small-tailed Han sheep.

Effect of dietary energy on digestibilities, rumen fermentation, urinary purine derivatives and serum metabolites in Tibetan and small-tailed Han sheep.

Tibetan sheep are indigenous to the Qinghai-Tibetan Plateau, graze the grassland all year round without supplementation and are well-adapted to the harsh conditions. Small-tailed Han sheep were introduced to the plateau and are raised mainly in feedlots. Based on their different backgrounds, we hypothesized that the ability to cope with poor diets would be better in Tibetan than in Han sheep. To test our prediction, we examined the effect of dietary energy on apparent digestibilities, rumen fermentation, urinary purine derivatives and serum metabolites by using a 4 × 4 Latin square design in each sheep breed. Four diets were formulated to be low in crude protein (~7%) but to differ in metabolizable energy concentration. Average daily gain was greater in Tibetan than in Han sheep (p < 0.01) and increased linearly with an increase in energy intake (p < 0.001). The digestibilities of dry matter, organic matter, gross energy, and neutral and acid detergent fibres were greater in Tibetan than in Han sheep (p < 0.05). Ruminal pH was lower (p < 0.05), while volatile fatty acids (VFAs), urea-N, ammonia-N and soluble protein-N concentrations were higher (p < 0.05) in Tibetan than in Han sheep. As a molar proportion of total VFA, acetate decreased (p < 0.001) with an increase in dietary energy whereas propionate and butyrate increased (p < 0.05). Urinary purine derivative excretion was greater in Tibetan than in Han sheep (p < 0.01), as was microbial nitrogen production; both parameters increased with dietary energy (p < 0.01). Serum concentrations of glucose, insulin and insulin-like growth factor-1 increased (p < 0.05) as energy level increased, while non-esterified fatty acids and growth hormone decreased (p < 0.05). It was concluded that Tibetan sheep were better able to cope with low-protein, low-energy diets and, consequently, our prediction was supported.

[Correlation between the liver injury and the expression of interleukin-10 in severe acute pancreatitis at high altitude: a rat experimental result].

OBJECTIVE: To observe the indexes of liver injury and the expression of inflammation-related factor interleukin-10 (IL-10) in rats with severe acute pancreatitis (SAP), and to discuss the correlation between the expression of IL-10 and the related factors of liver injury in SAP rats at different altitudes. METHODS: 280 male Wistar rats with SPF grade aged 5 to 6 months were divided into four groups according to random number table with 70 rats in each group, and the rats were placed in different altitudes such as Xi'an (at an altitude of 1 027 m), Xining (at an altitude of 2 260 m), Xinghai (at an altitude of 3 300 m) and Wenquan (at an altitude of 3 950 m). The rats in each altitude were randomly divided into sham operation group (Sham group, n = 10) and SAP 1, 6, 12, 24 hours groups (all n = 15). SAP rat model was reproduced by injecting sodium cholate into the posterior membrane of pancreas, and the rats of Sham group were only turned pancreas over several times after opening the abdomen and then closed the abdomen. The rats were sacrificed at the corresponding time points after model reproduction in SAP groups, and rats in Sham group were sacrificed at 6 hours after sham operation. At the same time, the abdominal aorta blood was harvested, and the contents of serum amylase (AMY), alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were determined by automatic biochemical analyzer. Liver tissues were harvested, and the expression level of IL-10 was determined by immunohistochemistry. Pancreatic tissues were harvested, and hematoxylin-eosin (HE) staining was performed to observe the pathological changes under light microscopy. The correlations among the indicators were analyzed by Pearson correlation. RESULTS: At different altitudes, no significant abnormality was found in the pancreas of Sham group, but significant pathological changes were found in the pancreas of all SAP groups, mainly manifested as pancreatic acinar swelling, inflammatory cell infiltration, vascular congestion and hemorrhage, acinar cell degeneration and dissolution, changes in glandular lobule structure, peri-pancreatic fat necrosis, and continuous aggravation with the increasing of time and altitude. At the same altitude, the pancreatic pathology score, the serum AMY, ALT and AST levels, and the hepatic IL-10 expression were all significantly increased in all the SAP groups as compared with those in Sham group, and they were continuously increased with time. In Sham group, there was no statistically significant difference in pancreatic pathology score, AMY, ALT, AST, or IL-10 level among different altitudes. At the corresponding time point after model reproduction, the pancreatic pathology score, AMY, ALT, AST and IL-10 levels in the SAP groups were also shown a continuous rising tendency with altitude increase, and the differences in above parameters of SAP 24 hours group in Wenquan area were statistically significant as compared with those of Sham group [pathology score: 11.06±0.94 vs. 0.23±0.15, AMY (mmol/L): 2 706.6±208.3 vs. 336.5±94.3, ALT (U/L): 267.00±5.37 vs. 52.00±4.84, AST (U/L): 465.88±11.02 vs. 139.00±11.61, IL-10 (A value): 0.579±0.006 vs. 0.281±0.006, all P < 0.05]. It was shown by correlation analysis that IL-10 of SAP rats at different altitudes was positively correlated with pancreatic pathology score, AMY, ALT and AST, the correlation coefficient (r value) between IL-10 and the above indicators in the Wenquan area with the highest altitude was 0.959, 0.928, 0.977, 0.983, respectively (all P < 0.01). CONCLUSIONS: The severity of SAP rats was positively correlated with altitude. IL-10 was involved in the pathological expression process of SAP liver damage, and its expression level was positively correlated with altitude and the degree of SAP liver damage.

How to prevent the infection of contaminated abdominal incisions.

BACKGROUND: Surgical site infection is one of the most common complications of conventional laparoscopic surgery. Preventing infection of the incision is particularly important. OBJECTIVE: To discuss how to prevent the occurrence of surgical site infection after contaminated abdominal surgery. METHODS: Five hundred and fifty-one surgery patients with ``contaminated abdominal incisions'' from January 2011 to May 2013 were analyzed in terms of the preventative treatment, and summarized for surgical site infection. Subcutaneous tissue flushed with normal saline + hydrogen peroxide before suturing in the intervention 1 group; subcutaneous tissue flushed with normal saline + 0.5% povidone-iodine before suturing in the intervention 2 group. RESULTS: When subcutaneous fat was contaminated to a depth of ≤ 2.5 cm, the rates of surgical site infection in the control group and the intervention groups showed no significant difference (P > 0.05). When subcutaneous fat was contaminated to a depth of ≥ 3.0 cm, the rate of surgical site infection in the control group compared with the intervention one group was not statistically different (P > 0.05). The rate of surgical site infection in the control group compared with the intervention two group was statistical significant (P < 0.05). The rate of surgical site infection in the intervention one group compared with the intervention two group was statistical significant (P < 0.05). CONCLUSIONS: Preoperative control of the blood sugar; correction of anemia and the hypoalbuminemia; use of intraoperative the high-frequency electrotome; irrigation of the incision with plenty of physiological saline +$ iodophor before suturing the subcutaneous fat layer were key to effectively preventing infection in contaminated abdominal incisions.

[Method of Remote Sensing Identification for Mineral Types Based on Multiple Spectral Characteristic Parameters Matching].

The traditional mineral mapping methods with remote sensing data, based on spectral reflectance matching techniques, shows low accuracy, for obviously being affected by the image quality, atmospheric and other factors. A new mineral mapping method based on multiple types of spectral characteristic parameters is presented in this paper. Various spectral characteristic parameters are used together to enhanced the stability in the situation of atmosphere and environment background affecting. AVIRIS (Airborne Visible Infrared Imaging Spectrometer) data of Nevada Cuprite are selected to determine the mineral types with this method. Typical mineral spectral data are also obtained from USGS (United States Geological Survey) spectral library to calculate the spectral characteristic parameters. A mineral identification model based on multiple spectral characteristic parameters is built by analyzing the various characteristic parameters, and is applied in the mineral mapping experiment in Cuprite area. The mineral mapping result produced by Clark et al. in 1995 is used to evaluate the effect of this method, results show, that mineral mapping results with this method can obtain a high precision, the overall mineral identification accuracy is 78.96%.

[Study of blood oxygen saturation, heart rate changes and plateau reaction of the Antarctic Kunlun station investigation team in different plateau environments].

OBJECTIVE: To explore the blood oxygen saturation and heart rate changes of the Antarctic explorers. METHODS: During August 2010 to April 2011, the changes in blood oxygen saturation, heart rate and plateau reaction of 16 Antarctic expedition team in different plateau environments (Tibetan plateau versus Antarctic plateau) were monitored with the noninvasive pulse oximeter MD300-C. The extent of acute mountain sickness was determined according to the Lake Louise Consensus acute mountain reaction symptom scores and judgment method. RESULTS: The changes of blood oxygen saturation, heart rate at different altitudes of 110, 3650, 4300 m (96.8% ± 1.2%,89.1% ± 1.2%, 86.1% ± 2.0%, (75.0 ± 5.4) times/min, (104.0 ± 4.3) times/min, (113.0 ± 5.2) times/min,F = 214.155, 240.088,both P < 0.05). With rising latitude and elevation gradient in Antarctic plateau, the changes of blood oxygen saturation, heart rate at different altitudes of 2000, 2500, 3000, 3500 and 4087 m(91.9% ± 1.3%,90.5% ± 1.3%,87.6% ± 1.4%,85.0% ± 1.8%,81.5% ± 2.2%, (85.9 ± 3.2) times/min, (90.6 ± 2.8) times/min, (97.8 ± 4.1) times/min, (102.0 ± 3.4) times/min, (106.3 ± 3.9) times/min, F = 105.418, 90.174, both P < 0.05). Levels of blood oxygen saturation and heart rate were both correlated with the risk of altitude sickness (r = -0.446 and 0.565, both P < 0.05). CONCLUSIONS: As the increases of altitude, there are significant changes in oxygen saturation, heart rate of the Antarctic explorers. And with the increases of altitude, the risk of altitude sickness gradually increases.

[The relationship between systemic inflammatory response syndrome and severity of acute pancreatitis combined with plateau erythrocythemia].

OBJECTIVE: To explore the relationship between systemic inflammatory response syndrome(SIRS) and severity of acute pancreatitis combined with plateau erythrocythemia in the high altitude. METHODS: A retrospective analysis on the clinical data which involved acute pancreatitis combined with plateau erythrocythemia (n = 40) and without plateau erythrocythemia (n = 40) admitted from September 2006 to September 2009 was conducted. According to the unified standards, these cases were divided into plateau erythrocythemia group and no plateau erythrocythemia group. The patients in plateau erythrocythemia group were further divided into severe group and mild group according to scores of APACHEII. The data was analyzed according to the patient with (or without) SIRS, SIRS's standard indicators, diagnostic parameter and relation of severity and duration of SIRS in acute pancreatitis combined with plateau erythrocythemia. RESULTS: There was significantly discrepancy between plateau erythrocythemia group and no plateau erythrocythemia group not only in the incidence of patients who developed SIRS, but also in two items of patients fulfilling or not fulfilling diagnostic criteria of SIRS (P < 0.05). There was significant statistical difference in three items of diagnostic parameter of SIRS between plateau erythrocythemia group and no plateau erythrocythemia group (P < 0.05). Significant difference in two and three diagnostic parameter was found on severity of SIRS in acute pancreatitis combined with plateau erythrocythemia (P < 0.05). The more severity acute pancreatitis combined with plateau erythrocythemia was, the longer duration of SIRS was. CONCLUSION: SIRS is highly correlated with the severity of SIRS in acute pancreatitis combined with plateau erythrocythemia in the high altitude.