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Years of massive applications of high-throughput atomistic modeling tools such as molecular docking and end-point free energy calculations in the drug industry and academic exploration have made them indispensable parts of hierarchical screening. While the similarities between host–guest and protein–ligand complexes lead to the direct extension of techniques for protein–ligand screening to host–guest systems, the practical performance of these hit identification tools remains unclear in host-–-guest binding. Recent reports on specific host–guest complexes suggest that the experience on the accuracy ladder accumulated from protein–ligand cases could be invalid in host–guest complexes, which makes it an urgent need to perform a systematic benchmark to secure solid numerical supports and guidance of practical setups. Concerning molecular docking, there still lacks a comprehensive benchmark considering popular docking programs. As for end-point reranking, quantitative and rigorous free energy estimation via end-point formulism requires establishing statistically meaningful measurements of uncertainties due to finite sampling, which is neglected or underestimated by a significant portion in almost all main-stream applications. Further, a face-to-face comparison between different screening tools is required for the design of a hierarchical workflow. To fill the above-mentioned critical gaps, in this work, using a dataset containing tens of host–guest complexes involving basket-like macromolecular hosts from the octa acid family, we extensively benchmark seven academic docking protocols and perform post-docking end-point rescoring with twenty protocols. The resulting comprehensive benchmark provides conclusive pictures of the practical value of docking and end-point screening in OA host–guest binding.

Abstract The dissolution of silicate glasses has implications in diverse fields ranging from the immobilization of radioactive waste to the development of sustainable alternatives to Portland cement. Here, we used ab initio molecular dynamics simulations biased with well-tempered metadynamics to study Si-O-T bridge dissociation in calcium aluminosilicate glasses, crucial for understanding their dissolution. In a departure from the conventional Michalske-Freiman model, our findings reveal a nucleophilic substitution reaction mechanism characterized by a short-lived, 5-fold coordinated Si intermediate or transition state, depending on the Si bridge coordination, with a near-trigonal bipyramidal geometry. We find that the reorganization required for reaching this state causes the activation energy barriers to be dependent on the Si bridge coordination, with Si Q3 species serving as the rate-limiting step in the dissolution reaction. Our findings not only challenge long-standing theoretical models but also pave the way for more accurate and comprehensive frameworks for understanding the dissolution of silicate glasses in various applications.

Elevated lactate levels are common in sepsis patients. This study aimed to assess the effect of dynamic changes in lactate levels within the first 24 hours following admission on patient prognosis. We extracted data from the Medical Information Mart for Intensive Care (MIMIC)-IV database and classified patients using latent class growth analysis (LCGA). This analysis classified sepsis patients into different groups based on dynamic changes in lactate levels during the initial 24 hours post-admission, dividing this time frame into four periods (0–3 h, 3–6 h, 6–12 h, and 12–24 h). The highest lactate level recorded in each period was then used for patient classification. We subsequently compared the baseline characteristics and outcomes between these different groups. Our study encompassed 7,830 patients, whom LCGA successfully divided into two classes: class 1 (steady lactate class) and class 2 (increasing lactate class). Class 2 demonstrated a worse clinical status at baseline, as indicated by vital signs, disease severity scores, and laboratory results. Importantly, class 2 also had a significantly higher 28-day mortality rate than class 1 (55.6% vs 13.5%, P < 0.001). In conclusion, LCGA effectively categorized sepsis patients into two distinct groups based on their dynamic changes in lactate levels during the first 24 hours post-admission. This methodology has potential utility in clinical practice for managing sepsis patients.

Abstract Background Patient satisfaction is an important outcome measure of health service and is one of the main reasons for the gradual deterioration of doctor–patient relationships in China. This study used the standardized patient (SP) method to explore patient satisfaction and its health provider-related determinants among primary health facilities in rural China. Methods The dataset comprised 1138 clinic cases in 728 rural primary health facilities in 31 counties, spread across four provinces. Information regarding the consultation interaction between the unannounced SPs and primary physicians was recorded. Patient satisfaction was gathered from the feedback of SPs after the visit. Results The overall average score of SP satisfaction with rural primary health facilities was only 13.65 (SD = 3.22) out of 20. The SP scores were found to be consistent with those of real patients. After controlling variances in patient population via the SP method, the regression analysis demonstrated that health provider-related factors, such as physician-level characteristics, consultation process, affordability, and convenience, have a significant correlation with patient satisfaction among primary physicians. Among factors relating to physician-level characteristics, affordability, convenience and the consultation process of the visit, the quality of the consultation process (e.g., consultation time, proactively providing necessary instructions and other crucial information) were found to be the prominent determinants. Conclusions This study revealed the need to improve patient satisfaction in primary health facilities in rural China. To solve this issue, we recommend that policies to increase medical service quality be implemented in rural primary healthcare systems.

Measurement(s) ab initio energies and forces of hydrogen combustion Technology Type(s) density functional theory • ab initio molecular dynamics • normal modes Factor Type(s) cartesian coordinates

DeAMPylation, as a reversible reaction of AMPylation and mediated by the endoplasmic reticulum-localized enzyme FICD (filamentation induced by cAMP domain protein, also known as HYPE), is an important process in protein posttranslational modifications (PTMs). Elucidating the function and catalytic details of FICD is of vital importance to provide a comprehensive understanding of protein folding homeostasis. However, the detailed deAMPylation mechanism is still unclear. Furthermore, the role of a conserved glutamine (Glu234), that plays an inhibitory role in the AMPylation response, is still an open question in the deAMPylation process. In the present work, the elaborated deAMPylation mechanisms with AMPylation-inhibitory/assistant forms of FICD (wild type and Glu234Ala mutant) were investigated based on the QM(DFT)/MM MD approach. The results revealed that deAMPylation was triggered by proton transfer from protonated histidine (His363) to AMPylated threonine, instead of a nucleophilic attack of water molecules adding to the phosphorus of AMP. The free energy barrier of deAMPylation in the wild type (∼17.3 kcal/mol) is consistent with that in the Glu234Ala mutant of FICD (∼17.1 kcal/mol), suggesting that the alteration of the Glu234 residue does not affect the deAMPylation reaction and indirectly verifying the inducement of deAMPylation in FICD. In the wild type, the proton in the nucleophilic water molecule is transferred to Glu234, whereas it is delivered to Asp367 through the hydrogen-bond network of coordinated water molecules in the Glu234Ala mutant. The present findings were inspirational for understanding the catalytic and inhibitory mechanisms of FICD-mediated AMP transfer, paving the way for further studies on the physiological role of FICD protein.

Some researches to facilitate wound healing by using electrical stimulation are based on electric current stimulation, which may cause secondary damage and the imbalance of the microenvironment in vivo. In this study, alternating capacitive electric field (ACEF) was applied via a self-designed system so as to avoid direct contact with cells and to maintain stable microenvironment for cell growth. The influences of 58 ​mV/mm ACEFs with various frequencies of 10, 60 and 110 ​Hz on epidermal cells, fibroblasts and macrophages which involve in wound healing were comprehensively explored. The results suggested that ACEFs of 10, 60 and 110 ​Hz all significantly promoted the proliferation of human dermal fibroblasts (HDFs) and human epidermal keratinocyte cell line (HaCaT) cells, and 60 ​Hz ACEF furtherly accelerated the migration of these two kinds of cells. Moreover, ACEFs of all different studied frequencies facilitated M2-type polarization of macrophages, and YAP/TAZ expression of macrophages were enhanced under the stimulations of 10 and 60 ​Hz ACEFs. The enhancements in cell activity, migration rate and M2-type polarizability indicated that 58 ​mV/mm ACEFs especially at 60 ​Hz possessing potentially affirmative applications for wound healing without the risks of secondary damage and microenvironment imbalance.

The Co3O4 hollow dodecahedron (Co3O4@CN) was prepared by calcining ZIF-67 in N2 and then air atmosphere. In the Co3O4@CN compound material, Co3O4 nanoparticles (Co3O4 NPs) are anchored in the carbon skeleton, solving the aggregation problem of Co3O4 NPs. Because Co3O4@CN retains the porous structure of ZIF-67, and the presence of Co2+ and Co3+ favors electron transfer between the enzyme substrates, it has excellent peroxidase-like (POD-like) activity. Enzymatic kinetic tests show that Co3O4@CN has approximately six times more affinity for TMB than HRP and the maximal reaction rate is approximately three times that of HRP. The cholesterol sensor was constructed with Co3O4@CN, and its linear range was 20-1000 μM, and the detection limit was 14.33 μM. The application of Co3O4@CN to the detection of human serum cholesterol will be a valuable research direction.

The overuse of chromium (Cr) has significantly negatively impacted human life and environmental sustainability. Recently, the employment of nano zero-valent iron (nZVI) for Cr(VI) removal is becoming an emerging approach. In this study, carbonized melamine foam-supported nZVI composites, prepared by a simple impregnation–carbonization–reduction method, were assessed for efficient Cr(VI) removal. The prepared composites were characterized by XPS, SEM, TEM, BET and XRD. Batch experiments at different conditions revealed that the amount of iron added, the temperature of carbonization and the initial Cr(VI) concentration were critical factors. Fe@MF-12.5-800 exhibited the highest removal efficiency of 99% Cr(VI) (10 mg/L) at neutral pH among the carbonized melamine foam-supported nZVI composites. Its iron particles were effectively soldered onto the carbonaceous surfaces within the pore networks. Moreover, Fe@MF-12.5-800 demonstrated remarkable stability (60%, 7 days) in an open environment compared with nZVI particles.

Objective: Cellular repressor of E1A-stimulated genes (CREG), a vasculoprotective molecule, is significantly downregulated in atherosclerotic vessels through unclear mechanisms. While epigenetic regulation is involved in atherosclerosis development, it is not known if the CREG gene is epigenetically regulated. The aim of this study was to assess the potential role of CREG methylation in contributing to atherosclerosis. Approach and results: Overexpression of DNA methyltransferase (DNMT)3B significantly inhibited CREG expression in human umbilical vein endothelial cells (HUVECs) and human coronary aortic endothelial cells (HCAECs).Conversely, inhibition of DNA methylation with 5-aza-2′-deoxycytidine (5-aza-dC) dose-dependently increased CREG expression. A CREG promoter analysis identified +168 to +255 bp as a key regulatory region and the CG site at +201/+202 bp as a key methylation site. The transcription factor GR-α could bind to the +201/+202 bp CG site promoting CREG transcription, a process significantly inhibited by DNMT3B overexpression. Treatment of cells with oxidized low-density lipoprotein (ox-LDL), a critical atherosclerogenic factor, significantly increased DNMT3B expression, increasing CREG promotor methylation, blocking GR-α binding, and inhibiting CREG expression. Consistently, CG sites in the CREG promoter fragment were hyper-methylated in human atherosclerotic arteries, and CREG expression was significantly reduced. A negative correlation between DNMT3B and CREG expression levels was observed in human atherosclerotic arteries. Finally, Ox-LDL-induced endothelium dysfunction was significantly attenuated by both 5-aza-dC and an anti-oxidative molecular N-acetylcysteine (NAC) administration through rescue the expression of CREG and activation of the p-eNOS/NO pathway. Conclusions: Our study provides the first direct evidence that DNMT3B-mediated CREG gene hypermethylation is a novel mechanism that contributes to endothelial dysfunction and atherosclerosis development. Blocking CREG methylation may represent a novel therapeutic approach to treat ox-LDL-induced atherosclerosis.

Damage of axon and glial scars formation both inhibit nerve regenerative growth during nerve injury. In addition, mechanical stretch at high displacement rates of 10% tensile strain can cause marked nerve injury, it is important for finding a proper nano biomaterial to repair nerve injury. Nano-hydroxyapatite (n-HA) has excellent biocompatibility and high bioactivity, which is a good candidate for biomedical engineering applications. But the certain mechanism of n-HA on the injured nerve is seldom reported. In this study, we determined the role of n-HA on the mechanical stretch-induced nerve injury at adult rat spine. Mechanical stretch under strain 10% at displacement rates of 60 ​mm/min can cause marked broken vessels and edema in spinal cord and dorsal root ganglion tissue in haematoxylin-eosin (HE) staining. However, n-HA application can reverse hemorrhage and edema triggered by high rates of 60 ​mm/min stretch. Moreover, n-HA can promote positive staining of Netrin-1 increase significantly in spinal cord and dorsal root ganglion tested by immunohistochemistry (IHC) staining. In general, our study indicated that n-HA can repair mechanical stretch-induced nerve injury, it may provide a new approach to block injury and accelerate nerve regeneration in future.

Drug delivery systems (DDSs) limited to a single function or single-drug loading are struggling to meet the requirements of clinical medical applications. It is of great significance to fabricate DDSs with multiple functions such as magnetic targeting or fluorescent labeling, as well as with multiple-drug loading for enhancing drug efficacy and accelerating actions. In this study, inspired by the dual-chamber structure of rapeseed pods, biomimetic magnetic–luminescent bifunctional drug delivery carriers (DDCs) of 1.9 ± 0.3 μm diameter and 19.6 ± 4.4 μm length for dual drug release were fabricated via double-needle electrospraying. Morphological images showed that the rapeseed pod-like DDCs had a rod-like morphology and Janus dual-chamber structure. Magnetic nanoparticles and luminescent materials were elaborately designed to be dispersed in two different chambers to endow the DDCs with excellent magnetic and luminescent properties. Synchronously, the Janus structure of DDCs promoted the luminescent intensity by at least threefold compared to single-chamber DDCs. The results of the hemolysis experiment and cytotoxicity assay suggested the great blood and cell compatibilities of DDCs. Further inspired by the core–shell structure of rapeseeds containing oil wrapped in rapeseed pods, DDCs were fabricated to carry benzimidazole molecules and doxorubicin@chitosan nanoparticles in different chambers, realizing the sequential release of benzimidazole within 12 h and of doxorubicin from day 3 to day 18. These rapeseed pod-like DDSs with excellent magnetic and luminescent properties and sequential release of dual drugs have potential for biomedical applications such as targeted drug delivery, bioimaging, and sustained treatment of diseases.

AMPylation is a prevalent posttranslational modification that involves the addition of adenosine monophosphate (AMP) to proteins. Exactly how Huntingtin-associated yeast-interacting protein E (HYPE), as the first human protein, is involved in the transformation of the AMP moiety to its substrate target protein (the endoplasmic reticulum chaperone binding to immunoglobulin protein (BiP)) is still an open question. Additionally, a conserved glutamine plays a vital key role in the AMPylation reaction in most filamentation processes induced by the cAMP (Fic) protein. In the present work, the detailed catalytic AMPylation mechanisms in HYPE were determined based on the density functional theory (DFT) method. Molecular dynamics (MD) simulations were further used to investigate the exact role of the inhibitory glutamate. The metal center, Mg2+, in HYPE has been examined in various coordination configurations, including 4-coordrinated, 5-coordinated and 6-coordinated. DFT calculations revealed that the transformation of the AMP moiety of HYPE with BiP followed a sequential pathway. The model with a 4-coordinated metal center had a barrier of 14.7 kcal/mol, which was consistent with the experimental value and lower than the 38.7 kcal/mol barrier of the model with a 6-coordinated metal center and the 31.1 kcal/mol barrier of the model with a 5-coordinated metal center. Furthermore, DFT results indicated that Thr518 residue oxygen directly attacks the phosphorus, while the His363 residue acts as H-bond acceptor. At the same time, an MD study indicated that Glu234 played an inhibitory role in the α-inhibition helix by regulating the hydrogen bond interaction between Arg374 and the Pγ of the ATP molecule. The revealed sequential pathway and the inhibitory role of Glu234 in HYPE were inspirational for understanding the catalytic and inhibitory mechanisms of Fic-mediated AMP transfer, paving the way for further studies on the physiological role of Fic enzymes.

Objective This study was performed to investigate the potential of a modified puncture method to decrease the incidence of intravenous indwelling needle-related complications in inpatients with cardiovascular disease. Methods From February 2017 to July 2017, 436 consecutive inpatients with cardiovascular disease requiring infusion treatment were recruited and randomly divided into the control group and the treatment group. The standard infusion puncture method was applied in the control group, and a modified puncture method was applied in the treatment group. The incidence of complications and necessary positional adjustments of the intravenous indwelling needle in the two groups were observed. Results The incidence of necessary positional adjustments of the intravenous indwelling needle was significantly lower in the treatment group than control group (16.5% versus 5.0%, respectively). The incidences of redness at the puncture point and oozing of blood or fluid at the puncture point were also significantly lower in the treatment group than control group (18.6% versus 4.5% and 12.7% versus 5.5%, respectively). Conclusions The modified puncture method for intravenous indwelling needles can significantly decrease the incidence of complications and positional adjustments during application, which relieves patients’ pain and lightens nurses’ workload.

Many pairwise additive force fields are in active use for intrinsically disordered proteins (IDPs) and regions (IDRs), some of which modify energetic terms to improve the description of IDPs/IDRs but are largely in disagreement with solution experiments for the disordered states. This work considers a new direction—the connection to configurational entropy—and how it might change the nature of our understanding of protein force field development to equally well encompass globular proteins, IDRs/IDPs, and disorder-to-order transitions. We have evaluated representative pairwise and many-body protein and water force fields against experimental data on representative IDPs and IDRs, a peptide that undergoes a disorder-to-order transition, for seven globular proteins ranging in size from 130 to 266 amino acids. We find that force fields with the largest statistical fluctuations consistent with the radius of gyration and universal Lindemann values for folded states simultaneously better describe IDPs and IDRs and disorder-to-order transitions. Hence, the crux of what a force field should exhibit to well describe IDRs/IDPs is not just the balance between protein and water energetics but the balance between energetic effects and configurational entropy of folded states of globular proteins.

Cellular repressor of E1A-stimulated genes 1 (CREG1) is a small glycoprotein whose physiological function is unknown. In cell culture studies, CREG1 promotes cellular differentiation and maturation. To elucidate its physiological functions, we deleted the Creg1 gene in mice and found that loss of CREG1 leads to early embryonic death, suggesting that it is essential for early development. In the analysis of Creg1 heterozygous mice, we unexpectedly observed that they developed obesity as they get older. In this study, we further studied this phenotype by feeding wild type (WT) and Creg1 heterozygote (Creg1+/-) mice a high fat diet (HFD) for 16 weeks. Our data showed that Creg1+/- mice exhibited a more prominent obesity phenotype with no change in food intake compared with WT controls when challenged with HFD. Creg1 haploinsufficiency also exacerbated HFD-induced liver steatosis, dyslipidemia and insulin resistance. In addition, HFD markedly increased pro-inflammatory cytokines in plasma and epididymal adipose tissue in Creg1+/- mice as compared with WT controls. The activation level of NF-κB, a major regulator of inflammatory response, in epididymal adipose tissue was also elevated in parallel with the cytokines in Creg1+/- mice. These pro-inflammatory responses elicited by CREG1 reduction were confirmed in 3T3-L1-derived adipocytes with CREG1 depletion by siRNA transfection. Given that adipose tissue inflammation has been shown to play a key role in obesity-induced insulin resistance and metabolic syndrome, our results suggest that Creg1 haploinsufficiency confers increased susceptibility of adipose tissue to inflammation, leading to aggravated obesity and insulin resistance when challenged with HFD. This study uncovered a novel function of CREG1 in metabolic disorders.

BACKGROUND:Endothelial cell (EC) apoptosis plays a vital role in the pathogenesis of atherosclerosis in patients with diabetes mellitus (DM), but the underlying mechanism remains unclear. Cellular repressor of E1A-stimulated genes (CREG) is a novel gene reported to be involved in maintaining the homeostasis of ECs. Therefore, in the present study, we investigated the role of CREG in high glucose/high palmitate-induced EC apoptosis and to decipher the upstream regulatory mechanism underlying the transcriptional regulation of CREG. METHODS:The expression of CREG and the rate of apoptosis were assessed in lower-limb atherosclerotic lesions from patients with type 2 DM (T2DM). Primary human umbilical vein endothelial cells (HUVECs) were isolated and cultured in a high glucose/high palmitate medium (25 mmol/L D-glucose, 0.4 mmol/L palmitate), and the over-expression and knock-down of CREG were performed in HUVECs to determine the role of CREG in EC apoptosis. The upstream regulatory mechanism of CREG was identified using a promoter-binding transcription-factor profiling array, chromatin immunoprecipitation (ChIP) assay and a mutation analysis. RESULTS:Compared with normal arteries from non-diabetic patients, reduced CREG expression and increased apoptosis were found in the endothelium of atherosclerotic lesions from patients with T2DM. In vitro treatment of HUVECs with a high glucose/high palmitate medium also resulted in decreased CREG expression and increased apoptosis. Moreover, high glucose/high palmitate induced-HUVEC apoptosis was increased by the knock-down of CREG and rescued by the over-expression of CREG. We also demonstrated that GATA1 was able to bind to the promoter of the human CREG gene. A deletion mutation at -297/-292 in the CREG promoter disrupted GATA1 binding and reduced the activation of CREG transcription by approximately 83.3%. Finally, the overexpression of GATA1 abrogated the high glucose/high palmitate-induced apoptosis in HUVECs. CONCLUSIONS:The over-expression of CREG inhibits high glucose/high palmitate-induced apoptosis in HUVECs. CREG is transcriptionally upregulated by GATA1. Thus, CREG might be a potential therapeutic target for intervention of vascular complications related to diabetes.

The neuropeptide galanin and its receptors (GalR) are found to be up-regulated in brains suffering from nerve injury, but the specific role played by galanin remains unclear. This study aimed to explore the neuroprotective role of galanin after shear stress induced nerve injury in the primary cultured cortical neurons of rats. Our results demonstrated that no significant changes in cell death and viability were found after galanin treatment when subjected to a shear stress of 5 dyn/cm(2) for 12 h, after increasing magnitude of shear stress to 10 dyn/cm(2) for 12 h, cell death was significantly increased, while galanin can inhibit the nerve injury induced by shear stress with 10 dyn/cm(2) for 12 h. Moreover, Gal2-11 (an agonist of GalR2/3) could also effectively inhibit shear stress-induced nerve injury of primary cultured cortical neurons in rats. Although GalR2 is involved in the galanin protection mechanism, there was no GalR3 expression in this system. Moreover, galanin increased the excitatory postsynaptic currents (EPSCs), which can effectively inhibit the physiological effects of shear stress. Galanin was also found to inhibit the activation of p53 and Bax, and further reversed the down regulation of Bcl-2 induced by shear stress. Our results strongly demonstrated that galanin plays a neuroprotective role in injured cortical neurons of rats.

Mesenchymal stem cells (MSCs) are a potential source of material for the generation of tissue-engineered cardiac grafts because of their ability to transdifferentiate into cardiomyocytes after chemical treatments or co-culture with cardiomyocytes. Cardiomyocytes in the body are subjected to cyclic strain induced by the rhythmic heart beating. Whether cyclic strain could regulate rat bone marrow derived MSC (rBMSC) differentiation into cardiomyocyte-like lineage was investigated in this study. A stretching device was used to generate the cyclic strain for rBMSCs. Cardiomyogenic differentiation was evaluated using quantitative real-time reverse transcription polymerase chain reaction (RT-PCR), immunocytochemistry and western-blotting. The results demonstrated that appropriate cyclic strain treatment alone could induce cardiomyogenic differentiation of rBMSCs, as confirmed by the expression of cardiomyocyte-related markers at both mRNA and protein levels. Furthermore, rBMSCs exposed to the strain stimulation expressed cardiomyocyte-related markers at a higher level than the shear stimulation. In addition, when rBMSCs were exposed to both strain and 5-azacytidine (5-aza), expression levels of cardiomyocyte-related markers significantly increased to a degree suggestive of a synergistic interaction. These results suggest that cyclic strain is an important mechanical stimulus affecting the cardiomyogenic differentiation of rBMSCs. This provides a new avenue for mechanistic studies of stem cell differentiation and a new approach to obtain more committed differentiated cells.