ScCAEs: deep clustering of single-cell RNA-seq via convolutional autoencoder embedding and soft K-means

Clustering and cell type classification are a vital step of analyzing scRNA-seq data to reveal the complexity of the tissue (e.g. the number of cell types and the transcription characteristics of the respective cell type). Recently, deep learning-based single-cell clustering algorithms become popular since they integrate the dimensionality reduction with clustering. But these methods still have unstable clustering effects for the scRNA-seq datasets with high dropouts or noise. In this study, a novel single-cell RNA-seq deep embedding clustering via convolutional autoencoder embedding and soft K-means (scCAEs) is proposed by simultaneously learning the feature representation and clustering. It integrates the deep learning with convolutional autoencoder to characterize scRNA-seq data and proposes a regularized soft K-means algorithm to cluster cell populations in a learned latent space. Next, a novel constraint is introduced to the clustering objective function to iteratively optimize the clustering results, and more importantly, it is theoretically proved that this objective function optimization ensures the convergence. Moreover, it adds the reconstruction loss to the objective function combining the dimensionality reduction with clustering to find a more suitable embedding space for clustering. The proposed method is validated on a variety of datasets, in which the number of clusters in the mentioned datasets ranges from 4 to 46, and the number of cells ranges from 90 to 30 302. The experimental results show that scCAEs is superior to other state-of-the-art methods on the mentioned datasets, and it also keeps the satisfying compatibility and robustness. In addition, for single-cell datasets with the batch effects, scCAEs can ensure the cell separation while removing batch effects.

[The comparison of prognosis and risk factors after radical resection for pancreatic ductal adenocarcinoma between China Pancreas Data Center and SEER]

Objectives: To compare the prognosis of patients underwent radical resection for pancreatic ductal adenocarcinoma(PDAC) in Surveillance, Epidemiology, and End Results(SEER) and China Pancreas Data Center(CPDC), and to compare the prognostic factors for PDAC in both databases. Methods: The data of patients underwent radical resection for PDAC in CPDC database from January 2016 to December 2017 and SEER database from January 2014 to December 2015 were retrospectively analyzed. The prognosis of patients in both databases was analyzed by the Kaplan-Meier method, Log-rank method, and propensity score matching, and the Cox proportional hazard regression was used to analyze the independent prognosis factors for PDAC. Results: There were 1 977 cases and 2 220 cases of pancreatic cancer that underwent radical resection from CPDC and SEER, respectively. There were more male patients(60.90%,1 204/1 977) than female patients(39.10%,773/1 977) in CPDC, while nearly 1∶1 ratio(male:1 112 cases,female:1108)was observed between male and female in SEER(χ²=48.977,P<0.01). The proportion of patients under 45 years old was the smallest in both databases, and the age group with the most significant proportion was 60 to 74 years old. The ratio of patients over 75 years old in the SEER(24.28%,539/2 220) was higher than that of CPDC(7.89%,156/1 977)(χ²=202.090,P<0.01), while the proportion of patients between 45 and 59 years old in CPDC(33.69%,666/1 977) was higher than that in SEER(19.77%,439/2 220)(χ²=103.640,P<0.01). There were more pancreatic head cancers than body and tail cancers in both databases, and no statistical difference was found in tumor size between the two databases (W=2 181 502,P=0.740). More positive and examined lymph nodes were found in SEER patients (W=3 265 131,W=2 954 363,all P<0.01); and the proportion of patients who had at least 15 lymph nodes dissected was higher in SEER(63.24%,1 404/2 220)(χ²=532.130,P<0.01). There were more patients without neoadjuvant or adjuvant therapy in CPDC(57.16%,1 130/1 977) than that in SEER(24.91%,553/2 220)(χ²=451.390,P<0.01). After propensity score matching, the overall survival for CPDC was better than that for SEER(Log-rank test:χ²=4.500,P=0.034), and the median overall survival was 24 months and 23 months respectively. Cox regressional analysis showed the common independent prognosis factors in both databases were ≥75 years old, pancreatic head cancer, poorly differentiated and undifferentiated tumors, T stage, N stage(All P<0.05). Neoadjuvant or adjuvant therapy was a protective factor in both databases(CPDC:Wald=27.082;SEER:Wald=212.285, all P<0.01) and 45 to 59 years old was protective factor in the SEER database(Wald=5.212,P=0.020). Conclusions: The data in both databases have a good consistency. However, in terms of data quality, examined lymph nodes count, and neoadjuvant/adjuvant therapy rate, the CPDC differs greatly from the SEER.

Study on Catalytic Oxidation, Flocculation and Sedimentation of Acidizing and Fracturing Wastewater

The acidizing and fracturing waste fluid in a wellsite in northern Shaanxi was treated by catalytic oxidation and flocculation precipitation. It investigated the effect of different coagulants and their dosage and the wastewater pH on coagulation precipitation. As for chemical oxidation experiment, it investigated the effect of oxidant dosage and reaction time on its treatment effect. The results showed that when 30% hydrogen peroxide (volume percentage) was added at the dosage of 0.3% and oxidized for 50 min, the pH was adjusted to 7.5 and 350 mg/L polyaluminum chloride (PAC) and 4 mg/L polyacrylamide were added (PAM); after processing the waste liquid, total iron, chemical oxygen demand (COD), chromaticity, and average corrosion rate were reduced from 252.75 mg/L, 3427.50 mg/L, 624.15°, and 0.1226 mm/a to 0.12 mg/L, 275.18 mg/L, 125° and 0.0217 mm/a, respectively; effective removal of iron and color, reduced COD, and controlled corrosion was achieved.

Seed soaking with melatonin promotes seed germination under chromium stress via enhancing reserve mobilization and antioxidant metabolism in wheat

Chromium (Cr) pollution has serious harm to crop growth, while little is known on the role of melatonin (MT) on seed germination and physiology in Cr-stressed wheat. The effects of seed soaking with MT on growth, reserve mobilization, osmotic regulation and antioxidant capacity of wheat seeds during germination under hexavalent chromium (100 μM) stress were investigated. The results indicated that Cr toxicity decreased the seed germination rate by 16% and suppressed the growth of germinated seeds compared to unstressed seeds. MT in the concentration-dependent manner increased germination rate and promoted subsequent growth when seeds were exposed to Cr stress, but the effect could be counteracted at high concentration. Seed soaking with MT (100 μM) markedly decreased Cr accumulation in seeds, radicals and coleoptiles by 15%, 6% and 15%, respectively, and enhanced α-amylase activity and soluble sugar and free amino acids content in seeds to improve reserve mobilization under Cr stress, compared with Cr treatment. Furthermore, decreasing the level of osmotic regulators (soluble sugar and soluble protein) in radicles under MT combined with Cr treatment confirmed the reduction of osmotic stress caused by Cr stress. Importantly, MT pretreatment reduced H₂O₂ content by 19% and O₂·^- release rate by 45% in radicles under Cr toxicity compared with Cr-stressed wheat, in terms of promoting scavenging ability and decreasing production ability, which was to upregulate the activities and encoding genes expression levels of superoxide dismutase (SOD), catalase (CAT), ascorbic acid peroxidase (APX) and peroxidase (POD) and to downregulate plasma membrane-bound NADPH oxidase (NOX) encoding genes (TaRbohD, TaRbohF) expression, respectively. In all, these results provided evidence that seed soaking with MT could be a potentially method to protect wheat seeds from Cr toxicity, which effectively ameliorated germination under Cr stress by enhancing reserve mobilization and antioxidant metabolism in wheat.

[Mesenchymal Stem Cells Cultured in 3D System Inhibit Non-small Cell Lung Cancer Cells Through p38 MAPK and CXCR4/AKT Pathways by IL-24 Regulating]

Non-small cell lung cancer (NSCLC) is prevalent worldwide and has a high mortality rate. Even if mesenchymal stem cells (MSCs) are suggested as cancer treatment, the studies of their effects on NSCLC cells contradict each other, mainly due to utilization of two-dimensional (2D) culture system. Three-dimensional (3D) culture systems resemble tissue organization in vivo. Here we comprehensively explore the inhibitory effects of MSCs on NSCLC cells in a 3D culture system. We confirmed that the inhibitory effects of 3D-cultured MSCs (3D-MSCs) on the proliferation and migration of NSCLC cells are greater than that of the 2D-cultured MSCs. 3D-MSCs overexpress IL-24, which serve as the key factor enhancing antitumor effects of MSCs. In these cells, IL-24 affects p38 MAPK and CXCR4/AKT pathways. Overall, this study provides the support for use of MSCs in tumor.

Hydroxyethyl starch-new indocyanine green conjugates for enhanced cancer photodynamic therapy

In the present work, hydroxyethyl starch-new indocyanine green (HES-IR-820) conjugates were developed for enhanced cancer photodynamic therapy. HES-IR-820 conjugates were prepared by the condensation reaction between IR-820 and amino groups modified HES. HES-IR-820 conjugates with IR-820 loading content of 2.0% (HES-IR-820_2.0) and 3.2% (HES-IR-820_3.2) were prepared and characterized by ¹H NMR, FT-IR, HPLC, and UV-Vis. HES-IR-820_2.0 and HES-IR-820_3.2 are monomolecular nanosized particles with hydrodynamic diameters of around 10 nm. HES-IR-820_2.0 and HES-IR-820_3.2 exhibit significantly enhanced stability in pH 7.4 PBS buffer and pH 7.4 PBS buffer containing 10% fetal bovine serum as compared to free IR-820. HES-IR-820_2.0 and HES-IR-820_3.2 show limited drug release in pH 7.4 and pH 5.0 PBS buffer. HES-IR-820_2.0 and HES-IR-820_3.2 exhibit enhanced singlet oxygen generation under 808 nm laser irradiation and reduced cellular uptake amount as compared to free IR-820. The cellular uptake pathway study reveals that the lipid raft-mediated endocytosis and macropinocytosis are involved in the cellular uptake of HES-IR-820_2.0 and HES-IR-820_3.2. Compared to free IR-820, HES-IR-820_2.0 and HES-IR-820_3.2 show reduced cytotoxicity, enhanced in vitro antitumor effect under 0.3 W/cm² 808 nm laser irradiation, and similar in vitro antitumor effect under 0.6 W/cm² 808 nm laser irradiation. HES-IR-820 conjugates show significant potential for cancer photodynamic therapy.

Autophagy Modulators From Chinese Herbal Medicines: Mechanisms and Therapeutic Potentials for Asthma

Asthma has become a global health issue, suffering more than 300 million people in the world, which is a heterogeneous disease, usually characterized by chronic airway inflammation and airway hyperreactivity. Combination of inhaled corticosteroids (ICS) and long acting β-agonists (LABA) can relieve asthma symptoms and reduce the frequency of exacerbations, especially for patients with refractory asthma, but there are limited treatment options for people who do not gain control on combination ICS/LABA. The increase in ICS dose generally provides little additional benefit, and there is an increased risk of side effects. Therefore, therapeutic interventions integrating the use of different agents that focus on different targets are needed to overcome this set of diseases. Some findings suggest autophagy is closely correlated with the severity of asthma through eosinophilic inflammation, and its modulation may provide novel therapeutic approaches for severe allergic asthma. The chinese herbal medicine (CHM) have been demonstrated clinically as potent therapeutic interventions for asthma. Moreover some reports have found that the bioactive components isolated from CHM could modulate autophagy, and exhibit potent Anti-inflammatory activity. These findings have implied the potential for CHMs in asthma or allergic inflammation therapy via the modulation of autophagy. In this review, we discuss the basic pathomechanisms underpinning asthma, and the potential role of CHMs in treating asthma with modulating autophagy.

[Association of sepM gene mutation with mutacin Ⅳ production by Streptococcus mutans]

OBJECTIVE

To investigate the types of sepM gene mutations and their distribution in clinical isolates of Streptococcus mutans (S. mutans) and explore the association of sepM gene mutation with the capacity of mutacin Ⅳ production by S. mutans.

OBJECTIVE

We assessed the capacity of mutacin Ⅳ production in 80 clinical isolates of S. mutans using an inhibition zone assay. The minimum spanning tree and phylogenetic tree of these isolates were constructed using core genome multilocus sequence typing and maximum likelihood method, respectively. GeneMarkS software was used to predict the coding genes of these isolates, and the predicted genes were blasted against the sepM gene sequence of the reference genome UA159 to determine sepM gene mutations and their distribution characteristics in the clinical isolates. The mutation types affecting mutacin Ⅳ production were identified by analyzing the differentially distributed mutations between mutacin Ⅳ-producing isolates and mutacin Ⅳ-free isolates and by comparing the inhibition zones between isolates with sepM gene mutations and those without mutations.

OBJECTIVE

Among the 80 clinical isolates of S. mutans, 25 isolates were capable of mutacin Ⅳ production and 55 did not produce mutacin Ⅳ. The minimum spanning tree showed that the allelic differences were less among the mutacin Ⅳproducing isolates than among the mutacin Ⅳ-free isolates, and the origins of the mutacin Ⅳ-producing isolates were similar. We identified a total of 34 single base mutations in the 80 clinical isolates, and among them, C31T (P=0.001), G533A (P < 0.001), C756T (P=0.025), and C1036T (P=0.003) showed significant differential distributions between the mutacin Ⅳ-producing and mutacin Ⅳ-free isolates. These differentially distributed mutations were positively correlated with the capacity of mutacin Ⅳ production of the bacteria.

OBJECTIVE

sepM gene mutations that affect the capacity of mutacin Ⅳ production are present in the clinical strains of S. mutans.

Nano-TiO2 particles inhibit the biological behavior and mineralization of bone marrow mesenchymal stem cells transfected with CXCR4

OBJECTIVE

Bone marrow mesenchymal stem cells (BMSC) are widely used as experimental cells with potential differentiation function. Nanomaterials are currently a research hotspot. We assessed nano-TiO2 particles' effect on the biological behavior and mineralization of CXCR4 transfected BMSCs.

PATIENTS AND METHODS

After transfection of BMSC with CXCR4, cells were divided into blank group (no transfection), control group (transfection with CXCR4) and observe group (transfection with CXCR4 containing nanoparticles). Then, cell proliferation and ALP staining were measured along with analysis of Runx2 and BGP level by Western blot or RT-PCR and mineralization detection.

RESULTS

With increased culture time, the observed fractionation on day 14 showed significantly reduced activity; 3 mn nano-TiO2 particles significantly inhibited cell proliferation and bone formation after CXCR4 transfection with an inhibitory effect on the osteogenic ability of CXCR4-transfected BMCS cells in a time-dependent manner. The longer the culture time, the more significantly inhibitory effect; 3 mn nano-TiO2 particles can inhibit the mineralization of BMSCs after transfection of CXCR4 to a certain extent.

CONCLUSIONS

TiO2 nanoparticles have an inhibitory effect on the biological behavior and mineralization of BMSC cells transfected with CXCR4. The longer the culture time, the greater the inhibitory effect on osteogenic differentiation of BMSC cells transfected with CXCR4.

CD38 deficiency alleviates Ang II-induced vascular remodeling by inhibiting small extracellular vesicle-mediated vascular smooth muscle cell senescence in mice

CD38 is the main enzyme for nicotinamide adenine dinucleotide (NAD) degradation in mammalian cells. Decreased NAD levels are closely related to metabolic syndromes and aging-related diseases. Our study showed that CD38 deficiency significantly alleviated angiotensin II (Ang II)-induced vascular remodeling in mice, as shown by decreased blood pressures; reduced vascular media thickness, media-to-lumen ratio, and collagen deposition; and restored elastin expression. However, our bone marrow transplantation assay showed that CD38 deficiency in lymphocytes led to lack of protection against Ang II-induced vascular remodeling, suggesting that the effects of CD38 on Ang II-induced vascular remodeling might rely primarily on vascular smooth muscle cells (VSMCs), not lymphocytes. In addition, we observed that CD38 deficiency or NAD supplementation remarkably mitigated Ang II-induced vascular senescence by suppressing the biogenesis, secretion, and internalization of senescence-associated small extracellular vesicles (SA-sEVs), which facilitated the senescence of neighboring non-damaged VSMCs. Furthermore, we found that the protective effects of CD38 deficiency on VSMC senescence were related to restoration of lysosome dysfunction, particularly with respect to the maintenance of sirtuin-mediated mitochondrial homeostasis and activation of the mitochondria-lysosomal axis in VSMCs. In conclusion, our findings demonstrated that CD38 and its associated intracellular NAD decline are critical for Ang II-induced VSMC senescence and vascular remodeling.

pH-Sensitive, Cerebral Vasculature-Targeting Hydroxyethyl Starch Functionalized Nanoparticles for Improved Angiogenesis and Neurological Function Recovery in Ischemic Stroke

Angiogenesis, an essential restorative process following ischemia, is a promising therapeutic approach to improve neurological deficits. However, overcoming the blood-brain barrier (BBB) and effective drug enrichment are challenges for conventional drug delivery methods, which has limited the development of treatment strategies. Herein, a dual-targeted therapeutic strategy is reported to enable pH-sensitive drug release and allow cerebral ischemia targeting to improve stroke therapeutic efficacy. Targeted delivery is achieved by surface conjugation of Pro-His-Ser-Arg-Asn (PHSRN) peptides, which binds to integrin α₅ β₁ enriched in the cerebral vasculature of ischemic tissue. Subsequently, smoothened agonist (SAG), an activator of sonic hedgehog (Shh) signaling, is coupled to PHSRN-HES by pH-dependent electrostatic adsorption. SAG@PHSRN-HES nanoparticles can sensitively release more SAG in the acidic environment of ischemic brain tissue. More importantly, SAG@PHSRN-HES exerts the synergistic mechanisms of PHSRN and SAG to promote angiogenesis and BBB integrity, thus improving neuroplasticity and neurological function recovery. This study proposes a new approach to improve the delivery of medications in the ischemic brain. Dual-targeted therapeutic strategies have excellent potential to treat patients suffering from cerebral infarction.

Similarities and Differences in Interoceptive Bodily Awareness Between US-American and Japanese Cultures: A Focus-Group Study in Bicultural Japanese-Americans

Interoceptive awareness is the conscious perception of sensations that create a sense of the physiological condition of the body. A validation study for the Japanese translation of the Multidimensional Assessment of Interoceptive Awareness (MAIA) surprised with a factor structure different from the original English-language version by eliminating two of eight scales. This prompted an exploration of the similarities and differences in interoceptive bodily awareness between Japanese and European Americans. Bicultural Japanese-Americans discussed concepts and experiences in the two cultures. We conducted focus groups and qualitative thematic analyses of transcribed recordings. 16 participants illustrated cross-cultural differences in interoceptive bodily awareness: switching between languages changes embodied experience; external versus internal attention focus; social expectations and body sensations; emphasis on form versus self-awareness; personal space; and mind-body relationship; context dependency of bodily awareness and self-construal. The participants explained key concepts that present challenges for a Japanese cultural adaptation of the MAIA, specifically the concept of self-regulation lost in the factor analysis. In Japanese culture, self-regulation serves the purpose of conforming to social expectations, rather than achieving an individual self-comforting sense of homeostasis. Our findings will inform the next phase of improving the MAIA's cross-cultural adaptation.

Acoustic Droplet-Assisted Superhydrophilic-Superhydrophobic Microarray Platform for High-Throughput Screening of Patient-Derived Tumor Spheroids

Cell-based high-throughput screening is a key step in the current disease-based research, drug development, and precision medicine. However, it is challenging to establish a rapid culture and screening platform for rare cells (patient-derived) due to the obvious differences between the traditional 2D cell model and the tumor microenvironment, as well as the lack of a low-consumption screening platform for low numbers of cells. Here, we developed an acoustic drop-assisted superhydrophilic-superhydrophobic microarray platform for the rapid culture and screening of a few cells. By employing hydrophilic and hydrophobic microarrays, we can automatically distribute the cell suspension into uniform droplets, and these cells can spontaneously form compact 3D cell spheroids within 36 h (similar to the microenvironment of tumors in vivo). By using the acoustic droplet ejection device, we can accurately inject a drug solution with a volume of ∼pL to ∼nL into the droplet, and the whole process can be completed within 20 ms (one print). By using three different cell lines (Caco-2, MCF-7, and HeLa) to optimize the platform, the culture and screening of five patients' colon cancer were subsequently realized. Using three conventional chemotherapeutics (5-fluorouracil, cetuximab, and panitumumab) of various concentrations, the best treatment was screened out and compared with the actual treatment effect of the patients, and the results were extremely similar. As a proof-of-concept application, we have proved that our platform can quickly cultivate patient samples and effectively screen the best treatment methods, highlighting its wide application in precision medicine, basic tumor research, and drug development.

Efficient Four-Component Dirac-Coulomb-Gaunt Hartree-Fock in the Pauli Spinor Representation

Four-component Dirac-Hartree-Fock is an accurate mean-field method for treating molecular systems where relativistic effects are important. However, the computational cost and complexity of the two-electron interaction make this method less common, even though we can consider the Dirac-Hartree-Fock Hamiltonian the "ground truth" of the electronic structure, barring explicit quantum electrodynamical effects. Being able to calculate these effects is then vital to the design of lower scaling methods for accurate predictions in computational spectroscopy and properties of heavy element complexes that must include relativistic effects for even qualitative accuracy. In this work, we present a Pauli quaternion formalism of maximal component and spin separation for computing the Dirac-Coulomb-Gaunt Hartree-Fock ground state, with a minimal floating point operation count algorithm. This approach also allows one to explicitly separate different spin physics from the two-body interactions, such as spin-free, spin-orbit, and spin-spin contributions. Additionally, we use this formalism to examine relativistic trends in the periodic table and analyze the basis set dependence of atomic gold and gold dimer systems.

Yak milk-derived exosomes alleviate lipopolysaccharide-induced intestinal inflammation by inhibiting PI3K/AKT/C3 pathway activation

Intestinal epithelial cells (IEC) are important parts of the mucosal barrier, whose function can be impaired upon various injury factors such as lipopolysaccharide. Although food-derived exosomes are preventable against intestinal barrier injuries, there have been few studies on the effect of yak milk-derived exosomes and the underlying mechanism that remains poorly understood. This study aimed to characterize the effect of exosomal proteins derived from yak and cow milk on the barrier function of IEC-6 treated with lipopolysaccharide and the relevant mechanism involved. Proteomics study revealed 392 differentially expressed proteins, with 58 higher expressed and 334 lower expressed in yak milk-derived exosomes than those in cow exosomes. Additionally, the top 20 proteins with a relatively consistent higher expression in yak milk exosomes than cow milk exosomes were identified. Protein CD46 was found to be a regulator for alleviating inflammatory injury of IEC-6. In vitro assay of the role of yak milk exosomes on survival of IEC-6 in inflammation by 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyl tetrazolium bromide assay confirmed the effectiveness of yak milk exosomes to increase IEC-6 survival up to 18% for 12 h compared with cow milk exosomes (up to 12%), indicating a therapeutic effect of yak milk exosomes in the prevention of intestinal inflammation. Furthermore, yak and cow milk exosomes were shown to activate the PI3K/AKT/C3 signaling pathway, thus promoting IEC-6 survival. Our findings demonstrated an important relationship between yak and cow milk exosomes and intestinal inflammation, facilitating further understanding of the mechanisms of inflammation-driven epithelial homeostasis. Interestingly, compared with cow milk exosomes, yak milk exosomes activated the PI3K/AKT/C3 signaling pathway more to lower the incidence and severity of intestine inflammation, which might represent a potential innovative therapeutic option for intestinal inflammation.

A mild method to prepare nitrogen-rich interlaced porous carbon nanosheets for high-performance supercapacitors

In this work, a non-toxic and mild strategy was presented to efficiently fabricate porous and nitrogen-doped carbon nanosheets. Silkworm cocoon (SCs) acted as carbon source and original nitrogen source. Sodium carbonate (Na₂CO₃) could facilitate the SCs to expose silk protein and played a catalytic role in the subsequent activation of calcium chloride (CaCl₂). Calcium chloride served as pore-making agent. The as-obtained carbon materials with protuberant porous nanosheets exhibit high specific surface area of 731 m² g^-1, rich native nitrogen-doped of 7.91 atomic %, wide pore size distribution from 0.5 to 65 nm, and thus possessing high areal specific capacitances of 34 μF cm^-2 as well as excellent retention rate of 97% after 20 000 cycles at a current density of 20 A g^-1 in 6 M KOH electrolyte. The assembled carbon nanosheet-based supercapacitor displays a maximum energy density of 21.06 Wh kg^-1 at the power density of 225 W kg^-1 in 1 M Na₂SO₄ electrolyte. Experimental results show that a mild and non-toxic treatment of biomass can be an effective and extensible method for preparing optimal porous carbon for electrochemical energy storage.

A new synthetic method toward a key intermediate in the total synthesis of alkannin and shikonin

In the present work, a new synthetic method toward a key intermediate in the total synthesis of alkannin and shikonin is developed. The key intermediate, 4-methyl-1-(naphtho[1,8- de:4,5- d’e’]bis([1,3]dioxine)-4-yl)pent-3-en-1-one (5), is synthesized via the reaction of 1,8:4,5-bis(methylenedioxy)naphthalene-2-carboxylic acid N-methoxy- N-methylamide with prenyllithium. This synthetic approach avoids the use of N-methoxy- N,4-dimethylpent-3-enamide, which is not easy to obtain, and the toxic reagent sodium cyanide.

[Chaihu Guizhi decoction produces antidepressant-like effects via sirt1-p53 signaling pathway]

OBJECTIVE

To investigate the mechanism of the antidepressant-like effects of Chaihu Guizhi decoction (CGD).

OBJECTIVE

Chaihu Guizhi decoction at the daily dose of 17 g/kg and solvent vehicle were administered by gavage in 12 and 14 male C57BL/6J mice for 7 consecutive days, respectively. Forced swimming test (FST), elevated plus maze (EPM) test, open field test (OFT) and novelty-suppressed feeding test (NSF) were performed to assess the depression- and anxiety-like behaviors and motor ability of the mice. We further used chronic social defeat stress (CSDS) and social interaction test to evaluate the antidepressant-like effects of CGD in comparison with the solvent vehicle. Western blotting and RT-qPCR were performed to detect the expressions of sirt1, p53, acetylated p53, and the neuron plasticity-related genes including synapsin I (Syn1), Rab4B, SNAP25 and tubulin beta4b in the hippocampus of the mice.

OBJECTIVE

In FST, the immobility time of CGDtreated mice was decreased significantly (P < 0.05); no significant differences were found in the performances in EPM, NSF and OFT tests between the two groups. In social interaction test, the mouse models of CSDS treated with CGD showed significantly increased time in the interaction zone (P < 0.05). Compared with those in the vehicle group, the CGD-treated mouse models exhibited significantly increased protein level of SIRT1 and decreased p53 acetylation (P < 0.05) with up-regulated synapsin I mRNA expression in the hippocampus (P < 0.05); no significant difference were found in Rab (P=0.813), SNAP (P=0.820), or Tubb mRNA expressions (P=0.864) between the two groups.

OBJECTIVE

CGD produces antidepressant-like effects in mice possibly through the sirt1-p53 signaling pathway and synaptic plasticity.

Profiling of immune-cancer interactions at the single-cell level using a microfluidic well array

Cancer immunotherapy has achieved great success in hematological cancers. However, immune cells are a highly heterogeneous population and can vary highly in clonal expansion, migration and function status, making it difficult to evaluate and predict patient response to immune therapy. Conventional technologies only yield information on the average population information of the treatment, masking the heterogeneity of the individual T cell activation status, the formation of immune synapse, as well as the efficacy of tumor cell killing at the single-cell level. To fully interrogate these single-cell events in detail, herein, we present a microfluidic microwell array device that enables the massive parallel analysis of the immunocyte's heterogeneity upon its interaction pairs with tumor cells at the single-cell level. By precisely controlling the number and ratio of tumor cells and T cells, our technique can interrogate the dynamics of the CD8+ T cell and leukemia cell interaction inside 6400 microfluidic wells simultaneously. We have demonstrated that by investigating the interactions of T cell and tumor cell pairs at the single-cell level using our microfluidic chip, details hidden in bulk investigations, such as heterogeneity in T cell killing capacity, time-dependent killing dynamics, as well as drug treatment-induced dynamic shifts, can be revealed. This method opens up avenues to investigate the efficacy of cancer immunotherapy and resistance at the single-cell level and can explore our understanding of fundamental cancer immunity as well as determine cancer immunotherapy efficacy for personalized therapy.

Thermal Stability and Cation Composition of Hybrid Organic-Inorganic Perovskites

One of the great challenges of hybrid organic-inorganic perovskite photovoltaics is the material's stability at elevated temperatures. Over the past years, significant progress has been achieved in the field by compositional engineering of perovskite semiconductors, e.g., using multiple-cation perovskites. However, given the large variety of device architectures and nonstandardized measurement protocols, a conclusive comparison of the intrinsic thermal stability of different perovskite compositions is missing. In this work, we systematically investigate the role of cation composition on the thermal stability of perovskite thin films. The cations in focus of this study are methylammonium (MA), formamidinium (FA), cesium, and the most common mixtures thereof. We compare the thermal degradation of these perovskite thin films in terms of decomposition, optical losses, and optoelectronic changes when stressed at 85 °C for a prolonged time. Finally, we demonstrate the effect of thermal stress on perovskite thin films with respect to their performance in solar cells. We show that all investigated perovskite thin films show signs of degradation under thermal stress, though the decomposition is more pronounced in methylammonium-based perovskite thin films, whereas the stoichiometry in methylammonium-free formamidinium lead iodide (FAPbI₃) and formamidinium cesium lead iodide (FACsPbI₃) thin films is much more stable. We identify compositions of formamidinium and cesium to result in the most stable perovskite compositions with respect to thermal stress, demonstrating remarkable stability with no decline in power conversion efficiency when stressed at 85 °C for 1000 h. Thereby, our study contributes to the ongoing quest of identifying the most stable perovskite compositions for commercial application.

Imaging and Analysis of Isomeric Unsaturated Lipids through Online Photochemical Derivatization of Carbon-Carbon Double Bonds*

Unraveling the complexity of the lipidome requires the development of novel approaches for the structural characterization of lipid species with isomer-level discrimination. Herein, we introduce an online photochemical approach for lipid isomer identification through selective derivatization of double bonds by reaction with singlet oxygen. Lipid hydroperoxide products are generated promptly after laser irradiation. Fragmentation of these species in a mass spectrometer produces diagnostic fragments revealing the C=C locations in the unreacted lipids. This approach uses an inexpensive light source and photosensitizer making it easy to incorporate into any lipidomics workflow. We demonstrate the utility of this approach for the shotgun profiling of C=C locations in different lipid classes present in tissue extracts using electrospray ionization (ESI) and ambient imaging of lipid species differing only by the location of C=C bonds using nanospray desorption electrospray ionization (nano-DESI).

[Application of fecal DNA methylation biomarkers detection in gastric cancer screening]

Objective: Explore the feasibility of fecal gene methylation for screening gastric cancer and its relationship with clinical characteristics of gastric cancer patients. Methods: One hundred and fifty-six stool samples of patients in general surgery or digestive department of the First Affiliated Hospital of Soochow University from August 2018 to December 2019 were collected, detailed clinical information of gastric cancer patients were recorded. All patients and normal controls were divided into two sets including train sets (n=52)and test sets (n=104). Stool DNA was extracted for detection of methylation (SDC2, SFRP2, RASSF2 and TERT). Meanwhile, hemoglobin in stool samples were detected by immunoassays. A logistic regression model was built to analyze the sensitivity and specificity of single fecal DNA biomarker in detecting gastric cancer by Ct values of each stool-based DNA biomarker; Based on Akaike information criterion (AIC), the gastric cancer early screening model was constructed with each biomarker and the combinations, and evaluate the performance of the model in the test sets. Results: The accuracy of each stool biomarkers and their ranks were showed as SDC2(71.2%)>TERT(67.3%)=RASSF2(67.3%)>Hb(63.5%)>SFRP2(61.5%). By stepwise regression analysis, a combination composed of the methylation of SDC2 and TERT, fecal occult blood testing was well-behaved in the screening of gastric cancer.This combination showed a sensitivity of 66.7% for gastric cancer in train sets and test sets at the specificity of 78.9%. In different stages and parts of gastric cancer samples, the combination of this marker has the highest sensitivity in stage I gastric cancer(78.6%) and gastric body cancer(75.0%). Conclusion: The methylation of SDC2, SFRP2, TERT, RASSF2 has higher accuracy rate in the screening of gastric cancer, which is a potential fecal biomarker of gastric cancer.

Acoustic Droplet Vitrification Method for High-Efficiency Preservation of Rare Cells

Cryopreservation is a key step for current translational medicine including reproductive medicine, regenerative medicine, and cell therapy. However, it is challenging to preserve rare cells for practical applications due to the difficulty in handling low numbers of cells as well as the lack of highly efficient and biocompatible preservation protocols. Here, we developed an acoustic droplet vitrification method for high-efficiency handling and preservation of rare cells. By employing an acoustic droplet ejection device, we can encapsulate rare cells into water-in-air droplets with a volume from ∼pL to ∼nL and deposit these cell-containing droplets into a droplet array onto a substrate. By incorporating a cooling system into the droplet array substrate, we can vitrify hundreds to thousands of rare cells at an ultrafast speed (about ∼2 s) based on the high surface to volume ratio of the droplets. By optimizing this method with three different cell lines (a human lung cancer cell line, A549 cells, a human liver cell line, L02 cells, and a mouse embryonic fibroblast cell line, 3T3-L1 cells), we developed an effective protocol with excellent cell viability (e.g., >85% for days, >70% for months), proliferation, and adhesion. As a proof-of-concept application, we demonstrated that our method can rapidly handle and efficiently preserve rare cells, highlighting its broad applications in species diversity, basic research, and clinical medicine.

Boosting zinc ion energy storage capability of inert MnO cathode by defect engineering

Aqueous zinc ion battery constitutes a safe, stable and promising next-generation energy storage device, but suffers the lack of suitable host compounds for zinc ion storage. Development of a facile way to emerging cathode materials is strongly requested toward superior electrochemical activities and practical applications. Herein, defect engineering, i.e., simultaneous introduction of nitrogen dopant and oxygen vacancy into commercial and low-cost MnO, is proposed as a positive strategy to activate the originally inert phase for kinetically propelling its zinc ion storage capability. Both experimental characterization and theoretical calculations demonstrate that the nitrogen dopant significantly improves the electric conductivity of electrochemical inert MnO. Simultaneously, the oxygen vacancy creates sufficient large inserted channels and available activated adsorption sites for zinc ions storage. These synergistic structural advantages obviously ameliorate the electrochemical performance of inert MnO. Therefore, even without any conductive agent additive, the as-prepared material shows high specific capacity, superb rate capability, prolonged cycling stability and attractive energy density, which are dramatically superior to those of the pristine MnO as well as many other host cathode materials. This work presents fresh insights on the role of defect engineering in the enhancement of the intrinsic electrochemical reactivity of inert cathode, and an effective strategy for scalable fabrication of high-performance cathode for zinc ion battery.

Surface chemical functionality of carbon dots: influence on the structure and energy storage performance of the layered double hydroxide

As a kind of zero-dimensional material, carbon dots (CDs) have become a kind of promising novel material due to their incomparable unique physical and chemical properties. Despite the optical properties of CDs being widely studied, their surface chemical functions are rarely reported. Here we propose an interesting insight into the important role of surface chemical properties of CDs in adjusting the structure of the layered double hydroxide (LDH) and its energy storage performance. It was demonstrated that CDs with positive charge (p-CDs) not only reduce the size of the flower-like LDH through affecting the growth of LDH sheets, but also act as a structure stabilizer. After calcination, the layered double oxide (LDO) maintained the morphology of the LDH and prevented the stacking of layers. And the superiority of the composite in lithium-ion batteries (LIBs) was demonstrated. When used as an anode of LIBs, composites possess outstanding specific capacity, cycle stability and rate performance. It presents the discharge capacity of 1182 mA h g-1 and capacity retention of 94% at the current density of 100 mA g-1 after 100 cycles. Our work demonstrates the important chemical functions of CDs and expands their future applications.

Gene mapping reveals the association between tyrosine protein kinase Abl1 and the silk yield of Bombyx mori

The Z chromosome of the silkworm contains a major gene that influences silk yield. This major locus on chromosome Z accounts for 35.10% of the phenotypic variance. The location and identification of the gene have been a focus of silkworm genetics research. Unfortunately, identification of this gene has been difficult. We used extreme phenotype subpopulations and selected from a backcross population, BC₁ M, which was obtained using the high-yield strain 872B and the low-yield strain IS-Dazao as parents, for mapping the gene on the chromosome Z. The candidate region was narrowed down to 134 kb at the tip of the chromosome. BmAbl1 in this region correlated with silk gland development by spatiotemporal expression analysis. This gene was differentially expressed in the posterior silk glands of the high- and low-yield strains. In BmAbl1, an insertion-deletion (indel) within the 10th exonic region and an SNP within the 6th intronic region were detected and shown to be associated with cocoon shell weight in 84 Bombyx mori strains with different yields. Nucleotide diversity analysis of BmAbl1 and its 50 kb flanking regions indicated that BmAbl1 has experienced strong artificial selection during silkworm domestication. This study is the first to identify the genes controlling silk yield in the major QTL of the Z chromosome using forward genetics.

Spatial Segmentation of Mass Spectrometry Imaging Data by Combining Multivariate Clustering and Univariate Thresholding

Spatial segmentation partitions mass spectrometry imaging (MSI) data into distinct regions, providing a concise visualization of the vast amount of data and identifying regions of interest (ROIs) for downstream statistical analysis. Unsupervised approaches are particularly attractive, as they may be used to discover the underlying subpopulations present in the high-dimensional MSI data without prior knowledge of the properties of the sample. Herein, we introduce an unsupervised spatial segmentation approach, which combines multivariate clustering and univariate thresholding to generate comprehensive spatial segmentation maps of the MSI data. This approach combines matrix factorization and manifold learning to enable high-quality image segmentation without an extensive hyperparameter search. In parallel, some ion images inadequately represented in the multivariate analysis were treated using univariate thresholding to generate complementary spatial segments. The final spatial segmentation map was assembled from segment candidates that were generated using both techniques. We demonstrate the performance and robustness of this approach for two MSI data sets of mouse uterine and kidney tissue sections that were acquired with different spatial resolutions. The resulting segmentation maps are easy to interpret and project onto the known anatomical regions of the tissue.

A proof-of-concept study of an automated solution for clinical metagenomic next-generation sequencing

AIMS

Metagenomic next-generation sequencing (mNGS) has been utilized for diagnosing infectious diseases. It is a culture-free and hypothesis-free nucleic acid test for diagnosing all pathogens with known genomic sequences, including bacteria, fungi, viruses and parasites. While this technique greatly expands the clinical capacity of pathogen detection, it is a second-line choice due to lengthy procedures and microbial contaminations introduced from wet-lab processes. As a result, we aimed to reduce the hands-on time and exogenous contaminations in mNGS.

METHODS AND RESULTS

We developed a device (NGSmaster) that automates the wet-lab workflow, including nucleic acid extraction, PCR-free library preparation and purification. It shortens the sample-to-results time to 16 and 18·5 h for DNA and RNA sequencing respectively. We used it to test cultured bacteria for validation of the workflow and bioinformatic pipeline. We also compared PCR-free with PCR-based library prep and discovered no differences in microbial reads. Moreover we analysed results by automation and manual testing and found that automation can significantly reduce microbial contaminations. Finally, we tested artificial and clinical samples and showed mNGS results were concordant with traditional culture.

CONCLUSION

NGSmaster can fulfil the microbiological diagnostic needs in a variety of sample types.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study opens up an opportunity of performing in-house mNGS to reduce turnaround time and workload, instead of transferring potentially contagious specimen to a third-party laboratory.

Five Silkworm 30K Proteins Are Involved in the Cellular Immunity against Fungi

Simple Summary

The molecular mechanism of 30K proteins in anti-fungal immunity remains unclear. Here, we examined the mRNA levels of 30K proteins, including BmLP1, BmLP2, BmLP3, BmLP4, and BmLP7, and found that all of these proteins were significantly upregulated after injection of pathogen-associated molecular patterns to the fifth instar larvae, implying their involvement in immune response. The binding assay results showed that only BmLP1 and BmLP4 can bind to both fungal cells and silkworm hemocytes. In vitro, the encapsulation of hemocytes on day 5 of the fifth instar larval stage was promoted by the coating of agarose beads with recombinant BmLP1 and BmLP4. Therefore, these results demonstrate that 30K proteins are involved in the cellular immunity of silkworms by acting as pattern recognition molecules to directly recruit hemocytes to the fungal surface. We believe that our study makes a significant contribution to the literature because it provides insights into the 30K-mediated cellular immunity in silkworms.

Abstract

Background: 30K proteins are a major group of nutrient storage proteins in the silkworm hemolymph. Previous studies have shown that 30K proteins are involved in the anti-fungal immunity; however, the molecular mechanism involved in this immunity remains unclear. Methods: We investigated the transcriptional expression of five 30K proteins, including BmLP1, BmLP2, BmLP3, BmLP4, and BmLP7. The five recombinant 30K proteins were expressed in an Escherichia coli expression system, and used for binding assays with fungal cells and hemocytes. Results: The transcriptional expression showed that the five 30K proteins were significantly upregulated after injection of pathogen-associated molecular patterns to the fifth instar larvae, indicating the possibility of their involvement in immune response. The binding assay showed that only BmLP1 and BmLP4 can bind to both fungal cells and silkworm hemocytes. Furthermore, we found that BmLP1-coated and BmLP4-coated agarose beads promote encapsulation of hemocytes in vitro. The hemocyte encapsulation was blocked when the BmLP1-coated beads were preincubated with BmLP1 specific polyclonal antibodies. Conclusions: These results demonstrate that 30K proteins are involved in the cellular immunity of silkworms by acting as pattern recognition molecules to directly recruit hemocytes to the fungal surface.

Hydroxyethyl starch based smart nanomedicine

In the past decades, the vigorous development of nanomedicine has opened up a new world for drug delivery. Hydroxyethyl starch (HES), a clinical plasma volume expander which has been widely used for years, is playing an attracting role as drug carriers. Compared with all other polysaccharides, HES has proven its unique characteristics for drug delivery platforms, including good manufacture practice, biodegradability, biocompatibility, abundant groups for chemical modification, excellent water solubility, and tailorability. In this review, an overview of various types of HES based drug delivery systems is provided, including HES-drug conjugates, HES-based nano-assemblies, HES-based nanocapsules, and HES-based hydrogels. In addition, the current challenges and future opportunities for design and application of HES based drug delivery systems are also discussed. The available studies show that HES based drug delivery systems has significant potential for clinical translation.

A review of the effects and molecular mechanisms of dimethylcurcumin (ASC-J9) on androgen receptor-related diseases

Dimethylcurcumin (ASC-J9) is a curcumin analogue capable of inhibiting prostate cancer cell proliferation. The mechanism is associated with the unique role of ASC-J9 in enhancing androgen receptor (AR) degradation. So far, ASC-J9 has been investigated in typical AR-associated diseases such as prostate cancer, benign prostatic hypertrophy, bladder cancer, renal diseases, liver diseases, cardiovascular diseases, cutaneous wound, spinal and bulbar muscular atrophy, ovarian cancer and melanoma, exhibiting great potentials in disease control. In this review, the effects and molecular mechanisms of ASC-J9 on various AR-associated diseases are summarized. Importantly, the effects of ASC-J9 and AR antagonists enzalutamide/bicalutamide on prostate cancer are compared in detail and crucial differences are highlighted. At last, the pharmacological effects of ASC-J9 are summarized and the future applications of ASC-J9 in AR-associated disease control are discussed.

The KMT2A gene: mRNA differential expression in the ovary and a novel 13-nt nucleotide sequence variant associated with litter size in cashmere goats

A genome-wide association study had shown that lysine methyltransferase 2A (KMT2A), which encodes the histone 3 lysine 4 methyltransferase and reportedly can regulate gametogenesis, steroidogenesis, and development as well as other biological processes, is a potential candidate gene influencing litter size in the dairy goat, suggesting its key function in animal reproduction. Here, we aimed to explore the genetic effects of the KMT2A gene on litter size in females of the Chinese indigenous cashmere goat, using a large sample size (n > 1,000), based on their levels of RNA transcription and DNA variation. First, mRNA expression levels of this gene in ovarian tissues between the low-prolific group (first-born litter size = 1) and high-prolific group (first-born litter size ≥2) were significantly different, revealing the potential functioning of KMT2A in goat prolific. Moreover, a novel 13-nt nucleotide sequence variant was identified in Shaanbei white cashmere goats (n = 1,616). In accordance with the independent chi-square (χ²) analysis, the distribution of genotypes (P = 2.57 × 10^-9) and allelotypes (P = 3.00 × 10^-7) between the low- and high-prolific groups differed significantly, indicating the 13-nt mutation was associated with litter size. Further analysis showed that the insertion/insertion (II) genotype was significantly different with insertion/deletion (ID) (P = 1.76 × 10^-9) and deletion/deletion (DD) (P = 7.00 × 10^-6), with goats having the DD genotype producing an average litter size larger than the other genotypes. Taken together, these findings suggest KMT2A can serve as a candidate gene for breeding goats, which may have implications for improving the future development of the goat industry.

Pivotal role of H2 in the isomerisation of isosorbide over a Ru/C catalyst

DFT calculations combined with experiments unveil the key role of the H2 coverage on Ru/C catalyst in the isomerization of isosorbide.

KCl-assisted activation: Moringa oleifera branch-derived porous carbon for high performance supercapacitor

Porous carbons with a high specific surface area (2314–3470 m² g⁻¹) are prepared via a novel KCl-assisted activation strategy for high-performance supercapacitor.

Relationship between serum hepcidin levels and cardiovascular disease in patients with maintenance hemodialysis

Background

To investigate the serum level of hepcidin and its relationship with cardiovascular disease (CVD) in maintenance hemodialysis (MHD) patients.

Methods

Blood was obtained from 75 MHD patients before undergoing hemodialysis and 20 healthy controls. Serum hepcidin, advanced oxidation protein products (AOPP) and interleukin (IL)-6 were measured by enzyme-linked immunosorbant assay (ELISA). Spearman correlation, and binary logistic regression linear regression analyses were used to assess the relationship between serum hepcidin and other parameters.

Results

The serum level of hepcidin, AOPP and IL-6 was significantly up-regulated in MHD patients compared with the control (P < 0.05). Furthermore, serum hepcidin levels in patients with CVD were higher than those in patients without CVD (P < 0.05). In all MHD patients, serum hepcidin level was correlated positively with erythropoietin (EPO) dose per week (ρ = 0.251, P = 0.030), EPO resistance index (ρ = 0.268, P = 0.020), ferritin (ρ = 0.814, P < 0.001), transferin saturation (TSAT, ρ = 0.263, P = 0.023), AOPP (ρ = 0.280, P = 0.049), high sensitive C reactive protein (ρ = 0.151, P = 0.006), IL-6 (ρ = 0.340, P = 0.003) and left ventricular mass index (LVMI, ρ = 0.290, P = 0.033). Moreover, it was negatively correlated with serum pre-albumin (ρ = -0.266, P = 0.021), total iron-binding capacity (TIBC, ρ = -0.458, P < 0.001), unsaturated iron-binding capacity (UIBC, ρ = -0.473, P < 0.001) and transferrin (ρ = -0.487, P < 0.001). Linear regression analysis showed that ferritin (β = 0.708, P < 0.001), TIBC (β = -0.246, P = 0.032) and IL-6 (β = 0.209, P = 0.041) were independently associated with hepcidin. Results of binary logistic regression analysis suggested that higher serum hepcidin level (>249.2 ng/mL) was positively and independently related to CVD (OR = 1.32, 95% CI [1.20-9.56], P = 0.043).

Conclusions

Serum hepcidin level is associated with CVD in MHD patients, indicating that hepcidin may be a novel biomarker and therapeutic target for CVD.

Efficient Intermolecular Energy Exchange and Soft Ionization of Water at Nanoplatelet Interfaces

X-ray, energetic photon, and electron irradiation can ionize and electronically excite target atoms and molecules. These excitations undergo complicated relaxation and energy-transfer processes that ultimately determine the manifold system responses to the deposited excess energy. In weakly bound gas- and solution-phase samples, intermolecular Coulomb decay (ICD) and electron-transfer-mediated decay (ETMD) can occur with neighboring atoms or molecules, leading to efficient transfer of the excess energy to the surroundings. In ionic solids such as metal oxides, intra- and interatomic Auger decay produces localized final states that lead to lattice damage and typically the removal of cations from the substrate. The relative importance of Auger-stimulated damage (ASD) versus ICD and ETMD in microsolvated nanoparticle interfaces is not known. Though ASD is generally expected, essentially no lattice damage resulting from the ionization and electronic excitation of microsolvated boehmite (AlOOH) nanoplatelets has been detected. Rather efficient energy transfer and soft ionization of interfacial water molecules has been observed. This is likely a general phenomenon at gas-oxyhydroxide nanoparticle interfaces where the density of states of the ionized chemisorbed species significantly overlaps with the core hole states of the solid.