[Application and comparison of three occupational health risk assessment methods in an automobile manufacturing industry]

Objective: Three occupational health risk assessment methods were used to assess the occupational health risk of noise exposed posts in an automobile manufacturing enterprise. According to the results, the selection of risk assessment methods and risk management of such occupational noise enterprises were provided. Methods: Form April to November 2021, The occupational health field survey was carried out in an automobile manufacturing industry in Tianjin. The occupational health MES risk assessment method, occupational health risk index risk assessment method and Australian occupational hazard risk assessment method were used to evaluate the occupational health risk of noise-exposed posts in this enterprise, and the evaluation results of different methods were analyzed and compared. Results: The average value of L(Aeq, 8 h) in the four workshops of automobile manufacturing industry was 82.95 dB (A) , and the noise detection exceeding rate was 22.41% (26/116) . The LAeq, 8h and exceeding rate noise of welding workshop were higher than those of other workshops (χ(2)=23.56, 32.94, P<0.01) . The three occupational health risk assessment methods have the same risk assessment results for the four major workshops. The assembly and painting workshops are level 4 risk (possible risk) , and the stamping and welding workshops are level 3 risk (significant risk) . Conclusion: Occupational noise has certain potential hazards to workers in automobile manufacturing enterprises. Therefore, in the future work, corresponding organizational management measures should be taken to improve the working environment and reduce the actual exposure level of workers in order to protect the health of occupational workers.

Thyroid Hormone Receptor Agonistic and Antagonistic Activity of Newly Synthesized Dihydroxylated Polybrominated Diphenyl Ethers: An In Vitro and In Silico Coactivator Recruitment Study

Dihydroxylated polybrominated diphenyl ethers (DiOH-PBDEs) could be the metabolites of PBDEs of some organisms or the natural products of certain marine bacteria and algae. OH-PBDEs may demonstrate binding affinity to thyroid hormone receptors (TRs) and can disrupt the functioning of the systems modulated by TRs. However, the thyroid hormone disruption mechanism of diOH-PBDEs remains elusive due to the absence of diOH-PBDEs standards. This investigation explores the potential disruptive effects of OH/diOH-PBDEs on thyroid hormones via competitive binding and coactivator recruitment with TRα and TRβ. At levels of 5000 nM and 25,000 nM, 6-OH-BDE-47 demonstrated significant recruitment of steroid receptor coactivator (SRC), whereas none of the diOH-PBDEs exhibited SRC recruitment within the range of 0.32-25,000 nM. AutoDock CrankPep (ADCP) simulations suggest that the conformation of SRC and TR-ligand complexes, particularly their interaction with Helix 12, rather than binding affinity, plays a pivotal role in ligand agonistic activity. 6,6'-diOH-BDE-47 displayed antagonistic activity towards both TRα and TRβ, while the antagonism of 3,5-diOH-BDE-100 for TRα and TRβ was concentration-dependent. 3,5-diOH-BDE-17 and 3,5-diOH-BDE-51 exhibited no discernible agonistic or antagonistic activities. Molecular docking analysis revealed that the binding energy of 3,3',5-triiodo-L-thyronine (T3) surpassed that of OH/diOH-PBDEs. 3,5-diOH-BDE-100 exhibited the highest binding energy, whereas 6,6'-diOH-BDE-47 displayed the lowest. These findings suggest that the structural determinants influencing the agonistic and antagonistic activities of halogen phenols may be more intricate than previously proposed, involving factors beyond high-brominated PBDEs or hydroxyl group and bromine substitutions. It is likely that the agonistic or antagonistic propensities of OH/diOH-PBDEs are instigated by protein conformational changes rather than considerations of binding energy.

Deriving aquatic PNECs of endocrine disruption effects for PFOS and PFOA by combining species sensitivity weighted distributions and adverse outcome pathway networks

Perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA), as emerging endocrine-disrupting chemicals (EDCs), pose adverse effects on aquatic organisms. Conventional ecological risk assessment (ERA) not fully considering the mode of toxicity action of PFOS and PFOA, may result in an underestimation of risks and confuse decision-makers. In the study, we developed species sensitivity weighted distribution (SSWD) models based on adverse outcome pathway (AOP) networks for deriving predicted no-effect concentrations (PNECs). Three kinds of weighting criteria (intraspecies variation, trophic level abundance, and data quality) and weighted log-normal distribution methods were adopted. The developed models considered the inter/intraspecies variation and integrated nontraditional endpoints of endocrine-disrupting effects. The PNECs of endocrine disruption effects were derived as 2.52 μg/L (95% confidence intervals 0.667-9.85 μg/L) for PFOS and 18.7 μg/L (5.40-71.0 μg/L) for PFOA, which were more conservative than those derived from the SSD method and were comparable with the values in the literature based on the chronic toxicity data. For PFOS, the effect of growth and development was the most sensitive; however, for PFOA, the effect of reproduction was the most sensitive in the effects of growth and development, reproduction, biochemistry and genetics, and survival. The endocrine-disrupting effects of PFOS and PFOA are significant and need to be fully recognized in the ERA. This study provided an ERA framework that can improve the ecological relevance and reduce the uncertainty of PNECs of EDCs.

[The application of 3D bioprinting in ophthalmology]

On the basis of 3D printing technology, 3D bioprinting has emerged with great development potential and good prospects in the field of medicine and tissue engineering. With this technique, different types of cells and biomaterials can be precisely incorporated into 3D anatomical structures, achieving tissue substitutes with superior structures or functions. In recent years, great progress has been made in the application of 3D bioprinting in ophthalmology. This article reviews not only the differences between 3D printing and 3D bioprinting, but also the development, types, characteristics, application, and prospects of 3D bioprinting in the production of eye tissue engineering materials.

Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment

We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average ~70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.

[Impact of different diagnostic criteria for assessing mild micro-hepatic encephalopathy in liver cirrhosis: an analysis based on a prospective, multicenter, real-world study]

Objective: To compare the differences in the prevalence of mild micro-hepatic encephalopathy (MHE) among patients with cirrhosis by using the psychometric hepatic encephalopathy score (PHES) and the Stroop smartphone application (Encephal App) test. Methods: This prospective, multi-center, real-world study was initiated by the National Clinical Medical Research Center for Infectious Diseases and the Portal Hypertension Alliance and registered with International ClinicalTrials.gov (NCT05140837). 354 cases of cirrhosis were enrolled in 19 hospitals across the country. PHES (including digital connection tests A and B, digital symbol tests, trajectory drawing tests, and serial management tests) and the Stroop test were conducted in all of them. PHES was differentiated using standard diagnostic criteria established by the two studies in China and South Korea. The Stroop test was evaluated based on the criteria of the research and development team. The impact of different diagnostic standards or methods on the incidence of MHE in patients with cirrhosis was analyzed. Data between groups were differentiated using the t-test, Mann-Whitney U test, and χ (2) test. A kappa test was used to compare the consistency between groups. Results: After PHES, the prevalence of MHE among 354 cases of cirrhosis was 78.53% and 15.25%, respectively, based on Chinese research standards and Korean research normal value standards. However, the prevalence of MHE was 56.78% based on the Stroop test, and the differences in pairwise comparisons among the three groups were statistically significant (kappa = -0.064, P < 0.001). Stratified analysis revealed that the MHE prevalence in three groups of patients with Child-Pugh classes A, B, and C was 74.14%, 83.33%, and 88.24%, respectively, according to the normal value standards of Chinese researchers, while the MHE prevalence rates in three groups of patients with Child-Pugh classes A, B, and C were 8.29%, 23.53%, and 38.24%, respectively, according to the normal value standards of Korean researchers. Furthermore, the prevalence rates of MHE in the three groups of patients with Child-Pugh grades A, B, and C were 52.68%, 58.82%, and 73.53%, respectively, according to the Stroop test standard. However, among the results of each diagnostic standard, the prevalence of MHE showed an increasing trend with an increasing Child-Pugh grade. Further comparison demonstrated that the scores obtained by the number connection test A and the number symbol test were consistent according to the normal value standards of the two studies in China and South Korea (Z = -0.982, -1.702; P = 0.326, 0.089), while the other three sub-tests had significant differences (P < 0.001). Conclusion: The prevalence rate of MHE in the cirrhotic population is high, but the prevalence of MHE obtained by using different diagnostic criteria or methods varies greatly. Therefore, in line with the current changes in demographics and disease spectrum, it is necessary to enroll a larger sample size of a healthy population as a control. Moreover, the establishment of more reliable diagnostic scoring criteria will serve as a basis for obtaining accurate MHE incidence and formulating diagnosis and treatment strategies in cirrhotic populations.

Deep transfer learning for inter-chain contact predictions of transmembrane protein complexes

Membrane proteins are encoded by approximately a quarter of human genes. Inter-chain residue-residue contact information is important for structure prediction of membrane protein complexes and valuable for understanding their molecular mechanism. Although many deep learning methods have been proposed to predict the intra-protein contacts or helix-helix interactions in membrane proteins, it is still challenging to accurately predict their inter-chain contacts due to the limited number of transmembrane proteins. Addressing the challenge, here we develop a deep transfer learning method for predicting inter-chain contacts of transmembrane protein complexes, named DeepTMP, by taking advantage of the knowledge pre-trained from a large data set of non-transmembrane proteins. DeepTMP utilizes a geometric triangle-aware module to capture the correct inter-chain interaction from the coevolution information generated by protein language models. DeepTMP is extensively evaluated on a test set of 52 self-associated transmembrane protein complexes, and compared with state-of-the-art methods including DeepHomo2.0, CDPred, GLINTER, DeepHomo, and DNCON2_Inter. It is shown that DeepTMP considerably improves the precision of inter-chain contact prediction and outperforms the existing approaches in both accuracy and robustness.

Assessment of heavy metal contamination of an electrolytic manganese metal industrial estate in northern China from an integrated chemical and magnetic investigation

Heavy metal concentrations (Al, V, Mn, Fe, Co, Ni, Cu, Zn, and Pb) and the magnetic properties of soil and sediment samples in/around an electrolytic manganese metal (EMM) industrial estate in northern China were investigated. Potential enrichment of Mn, Zn, and Pb was found in/around the core area of the EMM industrial estate; however, the pollution load index (PLI) values did not indicate severely polluted levels. For adults, all hazard index (HI) values of noncarcinogenic risks in the soil samples were below the safe level of 1.00. For children, none of the HI values exceeded the safe level, except Mn (HI = 1.23) in one industrial estate sample. The particle size of magnetic materials was mostly in the range of stable single-domain, and coarser ferrimagnetic phases enhanced the magnetic parameters in the industrial estate soils. Highly positive correlations were found between magnetic parameters, heavy metal concentrations, and PLI values, demonstrating that the magnetic parameters are an efficient proxy for assessing heavy metal contamination. Enrichment of Mn, Zn, and Pb was mainly derived from the EMM industry. The data showed that the EMM industrial estate under cleaner production had limited adverse impacts on the adjacent environment from the perspective of heavy metal contamination.

The association between thyroid homeostasis parameters and obesity in subjects with euthyroidism

The relationship between thyroid homeostasis parameters and obesity remains poorly understood in subjects with euthyroidism. This retrospective study aimed to investigate the association between the thyroid homeostasis and obesity in a population with euthyroidism. A total of 201 adult participants with euthyroidism (age range: 27-85 years) were enrolled. Clinical measurements, including obesity indices and biochemical analyses, were conducted. Thyroid homeostasis parameters were calculated. Multiple linear regression analysis was used to analyze the associations between thyroid function, thyroid homeostasis parameters, and obesity measurements. There was a positive correlation between thyroid-stimulating hormone (TSH), free triiodothyronine (fT3), Jostel's thyrotropin index (TSHI), standard TSH index (sTSHI), thyrotroph thyroid hormone sensitivity index (TTSI), sum activity of peripheral deiodinase (SPINA-GD), and body mass index (BMI) in participants with euthyroidism and a negative correlation between thyroid's secretory capacity (SPINA-GT) and BMI (all P<0.05). Only the fT3, TSHI, and sTSHI had a positive correlation with waist circumference (all P<0.05). We concluded that BMI was positively associated with pituitary thyrotropic function parameters and SPINA-GD, and negatively correlated with SPINA-GT in adults with euthyroidism.

The association between thyroid homeostasis parameters and obesity in subjects with euthyroidism

The relationship between thyroid homeostasis parameters and obesity remains poorly understood in subjects with euthyroidism. This retrospective study aimed to investigate the association between the thyroid homeostasis and obesity in a population with euthyroidism. A total of 201 adult participants with euthyroidism (age range: 27-85 years) were enrolled. Clinical measurements, including obesity indices and biochemical analyses, were conducted. Thyroid homeostasis parameters were calculated. Multiple linear regression analysis was used to analyze the associations between thyroid function, thyroid homeostasis parameters, and obesity measurements. There was a positive correlation between thyroid-stimulating hormone (TSH), free triiodothyronine (fT3), Jostel's thyrotropin index (TSHI), standard TSH index (sTSHI), thyrotroph thyroid hormone sensitivity index (TTSI), sum activity of peripheral deiodinase (SPINA-GD), and body mass index (BMI) in participants with euthyroidism and a negative correlation between thyroid's secretory capacity (SPINA-GT) and BMI (all P<0.05). Only the fT3, TSHI, and sTSHI had a positive correlation with waist circumference (all P<0.05). We concluded that BMI was positively associated with pituitary thyrotropic function parameters and SPINA-GD, and negatively correlated with SPINA-GT in adults with euthyroidism.

Occurrence and ecological risk assessment of 2,2',4,4'-tetrabromodiphenyl ether and decabromodiphenyl ether in surface waters across China

Polybrominated diphenyl ethers (PBDEs) are efficient brominated flame retardants and are released into various environmental media via usage, recycling and disposal. This study investigated the concentrations and ecological risks of two typical PBDEs, 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) and decabromodiphenyl ether (BDE-209), in surface waters across China from 2011 to 2018. The results showed that the concentration of BDE-209 (8.25 ng L^-1) was higher than that of BDE-47 (1.02 ng L^-1), and the concentrations of BDE-47 and BDE-209 in the lakes (2.56 ng L^-1 and 22.19 ng L^-1, respectively) were higher than those in the rivers (0.58 ng L^-1 and 7.05 ng L^-1, respectively). In addition, the concentration of BDE-209 in the wet season (2.61 ng L^-1) was lower than that in the dry season (10.83 ng L^-1), whereas the concentration of BDE-47 in the wet season (0.24 ng L^-1) was a little lower than that in the dry season (0.99 ng L^-1). BDE-47 and BDE-209 concentrations showed a gradual decrease in surface waters across China during the eight-year period. Based on the species sensitivity distribution (SSD) models, the 5% hazardous concentration (HC₅) and predicted no-effect concentration (PNEC) values were derived using the acute and chronic toxicity data of BDE-47 and BDE-209. Results showed that the PNEC values based on the acute and chronic toxicity data were 2.08 μg L^-1 and 0.52 μg L^-1 for BDE-47, respectively and 370 μg L^-1 and 0.34 μg L^-1 for BDE-209, respectively. The risk quotient (RQ) values of BDE-47 in surface waters across China were far smaller than 0.1 (low ecological risk). Similarly, the RQ values of BDE-209 were also smaller than 0.1, except for those at Baiyangdian Lake and Chaohu Lake, where the probability of 0.1 ≤ RQ < 1.0 (medium ecological risk) was approximately 10% based on 10,000 Monte Carlo simulations.

A tiered probabilistic approach to assess antibiotic ecological and resistance development risks in the fresh surface waters of China

Exposure to antibiotics can result in not only ecotoxicity on aquatic organisms but also the development of antibiotic resistance. In the study, the ecotoxicity data and minimum inhibitory concentrations of the antibiotics were screened to derive predicted no-effect concentrations of ecological (PNEC_eco) and resistance development risks (PNEC_res) for 36 antibiotics in fresh surface waters of China. The derived PNEC_eco and PNEC_res values were ranged from 0.00175 to 2351 μg/L and 0.037-50 μg/L, respectively. Antibiotic ecological and resistance development risks were geographically widespread, especially in the Yongding River, Daqing River, and Ziya River basins of China. Based on the risk quotients, 11 and 14 of 36 target antibiotics were at high ecological risks and high resistance development risks in at least one basin, respectively. The higher tiered assessments provided more detailed risk descriptions by probability values and β-lactams (penicillin and amoxicillin) were present at the highest levels for ecological and resistance development risks. Although there was uncertainty based on the limited data and existing methods, this study can indicate the overall situation of the existing risk levels and provide essential insights and data supporting antibiotic management.

[Current clinical application of lacrimal gland injection of botulinum toxin type A in inhibiting lacrimal secretion]

Lacrimal gland injection of botulinum toxin type A inhibits the secretion of tears. As a new method to treat or alleviate the symptom of tears or epiphora, it has the characteristics of simple operation, definite curative effect, repeatable treatment and no irreversible complications. It provides an optional treatment scheme for many patients with refractory tears or epiphora. This article reviews the pharmacological characteristics of botulinum toxin type A, the mechanism of inhibiting tear secretion, the method and dose of lacrimal gland injection, indications and contraindications, clinical efficacy evaluation, complications, existing problems to be solved and prospects for reference.

Docking cyclic peptides formed by a disulfide bond through a hierarchical strategy

MOTIVATION

Cyclization is a common strategy to enhance the therapeutic potential of peptides. Many cyclic peptide drugs have been approved for clinical use, in which the disulfide-driven cyclic peptide is one of the most prevalent categories. Molecular docking is a powerful computational method to predict the binding modes of molecules. For protein-cyclic peptide docking, a big challenge is considering the flexibility of peptides with conformers constrained by cyclization.

RESULTS

Integrating our efficient peptide 3D conformation sampling algorithm MODPEP2.0 and knowledge-based scoring function ITScorePP, we have proposed an extended version of our hierarchical peptide docking algorithm, named HPEPDOCK2.0, to predict the binding modes of the peptide cyclized through a disulfide against a protein. Our HPEPDOCK2.0 approach was extensively evaluated on diverse test sets and compared with the state-of-the-art cyclic peptide docking program AutoDock CrankPep (ADCP). On a benchmark dataset of 18 cyclic peptide-protein complexes, HPEPDOCK2.0 obtained a native contact fraction of above 0.5 for 61% of the cases when the top prediction was considered, compared with 39% for ADCP. On a larger test set of 25 cyclic peptide-protein complexes, HPEPDOCK2.0 yielded a success rate of 44% for the top prediction, compared with 20% for ADCP. In addition, HPEPDOCK2.0 was also validated on two other test sets of 10 and 11 complexes with apo and predicted receptor structures, respectively. HPEPDOCK2.0 is computationally efficient and the average running time for docking a cyclic peptide is about 34 min on a single CPU core, compared with 496 min for ADCP. HPEPDOCK2.0 will facilitate the study of the interaction between cyclic peptides and proteins and the development of therapeutic cyclic peptide drugs.

AVAILABILITY AND IMPLEMENTATION

http://huanglab.phys.hust.edu.cn/hpepdock/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Potentiation of Vancomycin: Creating Cooperative Membrane Lysis through a "Derivatization-for-Sensitization" Approach

Gram-negative bacteria, especially the ones with multidrug resistance, post dire challenges to antibiotic treatments due to the presence of the outer membrane (OM), which blocks the entry of many antibiotics. Current solutions for such permeability issues, namely lipophilic-cationic derivatization of antibiotics and sensitization with membrane-active agents, cannot effectively potentiate the large, globular, and hydrophilic antibiotics such as vancomycin, due to ineffective disruption of the OM. Here, we present our solution for high-degree OM binding of vancomycin via a hybrid "derivatization-for-sensitization" approach, which features a combination of LPS-targeting lipo-cationic modifications on vancomycin and OM disruption activity from a sensitizing adjuvant. 10⁶- to 10⁷-fold potentiation of vancomycin and 20-fold increase of the sensitizer's effectiveness were achieved with a combination of a vancomycin derivative and its sensitizer. Such potentiation is the result of direct membrane lysis through cooperative membrane binding for the sensitizer-antibiotic complex, which strongly promotes the uptake of vancomycin and adds to the extensive antiresistance effectiveness. The potential of such derivatization-for-sensitization approach was also supported by the combination's potent in vivo antimicrobial efficacy in mouse model studies, and the expanded application of such strategy on other antibiotics and sensitizer structures.

Tiered ecological risk assessment of nonylphenol and tetrabromobisphenol A in the surface waters of China based on the augmented species sensitivity distribution models

The ecological risks of nonylphenol (NP) and tetrabromobisphenol A (TBBPA) have received continued attention owing to their large consumption, frequently detection, adverse effects on the reproductive fitness, and lack of risk assessment technical systems. The geometric mean of the median concentrations of NP in the 22 surface waters was 0.278 μg/L, and TBBPA in the seven surface waters was 0.014 μg/L in China. The species sensitivity distribution (SSD) models were augmented by extrapolated reproductive toxicity data of native species to reduce uncertainty. The SSD models and the hazardous concentrations for 5% of species exhibited good robustness and reliability using the bootstrap method and minimum sample size determination. The acute and reproductive predicted no-effect concentrations (PNECs) were derived as 9.88 and 0.187 μg/L for NP, and 56.6 and 0.0878 μg/L for TBBPA, respectively. The risk quotients indicated that 11 of 22 locations for NP, and 3 of 7 locations for TBBPA were at high ecological risk levels based on the reproductive PNECs. Furthermore, the higher tier ecological risk assessment (ERA) based on potential affected fraction and joint probability curves indicated that the ecological risks in the four of above locations needed further concern. The ERA based on both the acute and reproductive toxicity is essential for assessing the ecological risks of NP and TBBPA, otherwise using acute PNECs only may result in an underestimation of ecological risk. The developed tiered ERA method and its framework can provide accurate, detailed, quantitative, locally applicable, and economically technical support for ERA of typical endocrine-disrupting chemicals in China.

Efficient Enzymatic Incorporation of Dehydroalanine Based on SAMDI-Assisted Identification of Optimized Tags for OspF/SpvC

Site-specific modification of proteins has important applications in biological research and drug development. Reactive tags such as azide, alkyne, and tetrazine have been used extensively to achieve the abovementioned goal. However, bulky side-chain "ligation scars" are often left after the labeling and may hinder the biological application of such engineered protein products. Conjugation chemistry via dehydroalanine (Dha) may provide an opportunity for "traceless" ligation because the activated alkene moiety on Dha can then serve as an electrophile to react with radicalophile, thiol/amine nucleophile, and reactive phosphine probe to introduce a minimal linker in the protein post-translational modifications. In this report, we present a mild and highly efficient enzymatic approach to incorporate Dha with phosphothreonine/serine lyases, OspF and SpvC. These lyases originally catalyze an irreversible elimination reaction that converts a doubly phosphorylated substrate with phosphothreonine (pT) or phosphoserine (pS) to dehydrobutyrine (Dhb) or Dha. To generate a simple monophosphorylated tag for these lyases, we conducted a systematic approach to profile the substrate specificity of OspF and SpvC using peptide arrays and self-assembled monolayers for matrix-assisted laser desorption/ionization mass spectrometry. The optimized tag, [F/Y/W]-pT/pS-[F/Y/W] (where [F/Y/W] indicates an aromatic residue), results in a ∼10-fold enhancement of the overall peptide labeling efficiency via Dha chemistry and enables the first demonstration of protein labeling as well as live cell labeling with a minimal ligation linker via enzyme-mediated incorporation of Dha.

A QSAR-ICE-SSD Model Prediction of the PNECs for Per- and Polyfluoroalkyl Substances and Their Ecological Risks in an Area of Electroplating Factories

Per- and polyfluoroalkyl substances (PFASs) are a class of highly fluorinated aliphatic compounds that are persistent and bioaccumulate, posing a potential threat to the aquatic environment. The electroplating industry is considered to be an important source of PFASs. Due to emerging PFASs and many alternatives, the acute toxicity data for PFASs and their alternatives are relatively limited. In this study, a QSAR–ICE–SSD composite model was constructed by combining quantitative structure-activity relationship (QSAR), interspecies correlation estimation (ICE), and species sensitivity distribution (SSD) models in order to obtain the predicted no-effect concentrations (PNECs) of selected PFASs. The PNECs for the selected PFASs ranged from 0.254 to 6.27 mg/L. The ΣPFAS concentrations ranged from 177 to 983 ng/L in a river close to an electroplating industry in Shenzhen. The ecological risks associated with PFASs in the river were below 2.97 × 10⁻⁴.

Docking and scoring for nucleic acid-ligand interactions: Principles and current status

Nucleic acid (NA)-ligand interactions have crucial roles in many cellular processes and, thus, are increasingly attracting therapeutic interest in drug discovery. Molecular docking is a valuable tool for studying molecular interactions. However, because NAs differ significantly from proteins in both their physical and chemical properties, traditional docking algorithms and scoring functions for protein-ligand interactions might not be applicable to NA-ligand docking. Therefore, various sampling strategies and scoring functions for NA-ligand interactions have been developed. Here, we review the basic principles and current status of docking algorithms and scoring functions for DNA/RNA-ligand interactions. We also discuss challenges and limitations of current docking and scoring approaches.

Modeling of the Long-Term Epidemic Dynamics of COVID-19 in the United States

Coronavirus 2019 (COVID-19) is causing a severe pandemic that has resulted in millions of confirmed cases and deaths around the world. In the absence of effective drugs for treatment, non-pharmaceutical interventions are the most effective approaches to control the disease. Although some countries have the pandemic under control, all countries around the world, including the United States (US), are still in the process of controlling COVID-19, which calls for an effective epidemic model to describe the transmission dynamics of COVID-19. Meeting this need, we have extensively investigated the transmission dynamics of COVID-19 from 22 January 2020 to 14 February 2021 for the 50 states of the United States, which revealed the general principles underlying the spread of the virus in terms of intervention measures and demographic properties. We further proposed a time-dependent epidemic model, named T-SIR, to model the long-term transmission dynamics of COVID-19 in the US. It was shown in this paper that our T-SIR model could effectively model the epidemic dynamics of COVID-19 for all 50 states, which provided insights into the transmission dynamics of COVID-19 in the US. The present study will be valuable to help understand the epidemic dynamics of COVID-19 and thus help governments determine and implement effective intervention measures or vaccine prioritization to control the pandemic.

Toxicity and accumulation of 6-OH-BDE-47 and newly synthesized 6,6'-diOH-BDE-47 in early life-stages of Zebrafish (Danio rerio)

Dihydroxylated polybrominated diphenyl ethers (diOH-PBDEs) appear to be natural products or metabolites of PBDEs in some marine organisms, yet its toxicity is still largely unknown. With a newly lab-synthesized diOH-PBDE, 6,6'-dihydroxy-2,2',4'4'-tetrabromodiphenyl ether (6,6'-diOH-BDE-47) in hand, the present study has provided the first data set to compare 6-hydroxy-2,2',4'4'- tetrabromodiphenyl ether (6-OH-BDE-47) and 6,6'-diOH-BDE-47 for their acute toxicity and accumulation, and thyroid hormone levels in treated zebrafish larvae. By real time-PCR technique, transcripts of hypothalamic-pituitary-thyroid axis associated genes were also investigated in developing larvae at 96 h post fertilization (96 hpf). Apparently, 6,6'-diOH-BDE-47 was less toxic than that of 6-OH-BDE-47: 1) the 96-h LC₅₀ (96-h median lethal concentration) of 6-OH-BDE-47 and 6,6'-diOH-BDE-47 were 235 nM and 516 nM, respectively; 2) although severe developmental delays and morphological deformities were observed in zebrafish larvae in high exposure doses, at the exposure concentration of 1-50 nM, the accumulated 6-OH-BDE-47 and 6,6'-diOH-BDE-47 is ranged between 226-2279 nmol/g and 123-539 nmol/g in treated larvae; and 3) for 6-OH-BDE-47, its bioconcentration factor (BCF) were 1.83- to 4.30-fold more than that of 6,6'-diOH-BDE-47, suggesting that the lower internal exposure concentration of 6,6'-diOH-BDE-47 may lead to lower toxicity. The increased thyroid hormone levels were recorded for 1 nM of 6-OH-BDE-47 and 20 nM of 6,6'-diOH-BDE-47, and the exposures both significantly increased thyroid gland-specific transcription of thyroglobulin gene, indicating an adverse effect associated with the HPT axis. Therefore, 6,6'-diOH-BDE-47, with lower toxicity compared to that of 6-OH-BDE-47, still possesses hazards and environmental risk.

[Effects of double-catheter epidural analgesia by lidocaine injection respectively on the delivery outcomes and maternal-infant complications for persistent posterior or lateral occipital position of protracted active phase]

Objective: To evaluate the effect of dual-tube epidural segmental injection of lidocaine analgesia on the delivery outcome and maternal and infant complications of persistent posterior occipital position postpartum or lateral occipital position postpartum patients with protracted active phase. Methods: The full and single-term primiparas (n=216, 37 to 42 weeks gestation, 22 to 35 years) diagnosed as persistent posterior or lateral occipital position during the active period were selected from the Department of Obstetrics of Qingdao Municipal Hospital from January 2015 to October 2019. The subjects were randomly assigned into two groups: double-tube epidural block group (n=108) and single-tube epidural block group (n=108), 1% lidocaine was used for epidural analgesia respectively under ultrasound guidance. Senior midwife or obstetricians implement new partogram, and guide women to perform position management, and push or rotate the fetal head in a timely manner. Observation indicators: general condition, the use of non-pharmacological analgesic measures, analgesia related conditions and pain visual analogue scale (VAS) score, delivery-related indicator, cesarean section indication, anesthesia-related indicator, maternal and child complications. Results: (1) General condition: the age, weight, height, gestational age, the ratio of persistent lateral or posterior occipital position, cephalic score, and neonatal birth weight between the two groups of women were not statistically significant (all P>0.05). (2) The use of non-pharmacological analgesic measures: the women's Lamaze breathing method, Doula delivery companionship, percutaneous electrical stimulation, and other measures between two groups were compared, and there were not significant differences (all P>0.05). (3) Analgesia related conditions and VAS scores of women undergoing vaginal delivery: compared with the single-tube epidural block group (n=40), the second-partum time of the women in the double-tube epidural block group (n=59) was significantly shortened [(124±44) vs (86±33) minutes, P<0.01]; after 30 minutes of analgesia (4.4±0.5 vs 0.9±0.5, P<0.01), during forced labor in the second stage of labor (5.7±0.6 vs 1.3±0.4, P<0.01), the VAS scores of pain were also significantly reduced (P<0.01). (4) Labor-related indicators: compared with the single-tube epidural block group, the natural delivery rate (21.3% vs 49.1%) and the delivery experience satisfaction rate (51.9% vs 98.1%) of women in the double-tube epidural block group were significantly increased (all P<0.01), cesarean section rate (63.0% vs 45.4%), instrument assisted rate (15.7% vs 5.6%) decreased significantly (all P<0.05). (5) Cesarean section indications: compared with the single-tube epidural block group, the cesarean section rate caused by prolonged labor or protracted active phase of women in the double-tube epidural block group was significantly reduced (38.0% vs 22.2%； P<0.05), and the fetal distress, intrauterine infection, and social factors caused by cesarean section between the two groups were compared, while the differences were not statistically significant (all P>0.05).(6) Anesthesia related indexes: the block planes of the maternal upper tube administration in the double-tube epidural block group were mostly T7, T8, T9-L2 and L3,While,the block planes in the single-tube epidural block group were mostly T10, T11-S1, S2, S3, and the modified Bromage score were all 0. (7) Maternal and child complications: compared with the single-tube epidural block group, the postpartum hemorrhage rate (18.5% vs 7.4%), the perineal lateral cut rate (20.4% vs 5.6%), the neonatal asphyxia rate (12.0% vs 3.7%), ICU rate of transferred neonates (13.9% vs 4.6%) in the double-tube epidural block group were significantly reduced (all P<0.05). Soft birth canal injury rate, puerperal disease rate and neonatal birth rate between two groups were compared, and there were not statistically significant differences (all P>0.05). Conclusion: Dual-tube epidural segmental injection of lidocaine analgesia could increase the natural delivery rate of women with posterior occipital or lateral occipital position with active stagnation, reduce the rate of cesarean section and the rate of transvaginal instruments, and reduce the complications of mother and child.

Protein-ensemble-RNA docking by efficient consideration of protein flexibility through homology models

MOTIVATION

Given the importance of protein-ribonucleic acid (RNA) interactions in many biological processes, a variety of docking algorithms have been developed to predict the complex structure from individual protein and RNA partners in the past decade. However, due to the impact of molecular flexibility, the performance of current methods has hit a bottleneck in realistic unbound docking. Pushing the limit, we have proposed a protein-ensemble-RNA docking strategy to explicitly consider the protein flexibility in protein-RNA docking through an ensemble of multiple protein structures, which is referred to as MPRDock. Instead of taking conformations from MD simulations or experimental structures, we obtained the multiple structures of a protein by building models from its homologous templates in the Protein Data Bank (PDB).

RESULTS

Our approach can not only avoid the reliability issue of structures from MD simulations but also circumvent the limited number of experimental structures for a target protein in the PDB. Tested on 68 unbound-bound and 18 unbound-unbound protein-RNA complexes, our MPRDock/DITScorePR considerably improved the docking performance and achieved a significantly higher success rate than single-protein rigid docking whether pseudo-unbound templates are included or not. Similar improvements were also observed when combining our ensemble docking strategy with other scoring functions. The present homology model-based ensemble docking approach will have a general application in molecular docking for other interactions.

AVAILABILITY AND IMPLEMENTATION

http://huanglab.phys.hust.edu.cn/mprdock/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

[A multicenter randomized prospective study of concurrent chemoradiation with 60 Gy versus 50 Gy for inoperable esophageal squamous cell carcinoma]

Objective: To determine whether 60 Gy is superior to standard 50 Gy for definitive concurrent chemoradiation(CCRT) in esophageal squamous cell carcinoma (ESCC) using modern radiation technology in a phase Ⅲ prospective randomized trial. Methods: From April 2013 to May 2017, 331 patients from 22 hospitals who were pathologically confirmed with stage ⅢA-ⅣA ESCC were randomized to 60 Gy or 50 Gy with random number table. Total of 305 patients were analyzed, including 152 in 60 Gy group and 153 in 50 Gy group. The median age was 63 years, 242(79.3%) males and 63(20.7%) females. The median length of primary tumor was 5.6 cm. The clinical characteristics between two groups were comparable. All patients were delivered 2 Gy per fraction, 5 fractions per week. Concurrent weekly chemotherapy with docetaxel (25 mg/m(2)) and cisplatin (25 mg/m(2)) and 2 cycles consolidation chemotherapy with docetaxel (70 mg/m(2)) and cisplatin (25 mg/m(2), d1-3) were administrated. The primary endpoint was local/regional progression-free survival (LRPFS). The data were compared with Pearson chi-square test or Fisher's exact test. Results: At a median follow-up of 27.3 months, the disease progression rate was 37.5% (57/152), 43.8% (67/153) in the high and standard-dose group, respectively (χ(2)=1.251, P=0.263). The 1, 2, 3-year LRPFS rate was 75.4%, 56.8%, 52.1% and 74.2%, 58.4%, 50.1%, respectively (HR: 0.95, 95%CI: 0.69-1.31, P=0.761). The 1, 2, 3-year overall survival rate was 84.1%, 64.8%, 54.1% and 85.4%, 62.9%, 54.0%, respectively (HR: 0.98, 95%CI: 0.71-1.38, P=0.927). The 1, 2, 3-year progression-free survival rate was 70.8%, 54.2%, 48.5% and 65.5%, 51.9%, 45.1%, respectively (HR: 0.93, 95%CI: 0.68-1.26, P=0.621). The incidence rates in toxicities between the two groups were similar except for higher rate of severe pneumonitis in high dose group (χ(2)=11.596, P=0.021). Conclusions: The efficacy in disease control is similar between 60 Gy and 50 Gy using modern radiation technology concurrent with chemotherapy for ESCC. The 50 Gy should be recommended as the regular radiation dose with CCRT for ESCC.

HNADOCK: a nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures

Interactions between nuclide acids (RNA/DNA) play important roles in many basic cellular activities like transcription regulation, RNA processing, and protein synthesis. Therefore, determining the complex structures between RNAs/DNAs is crucial to understand the molecular mechanism of related RNA/DNA-RNA/DNA interactions. Here, we have presented HNADOCK, a user-friendly web server for nucleic acid (NA)-nucleic acid docking to model the 3D complex structures between two RNAs/DNAs, where both sequence and structure inputs are accepted for RNAs, while only structure inputs are supported for DNAs. HNADOCK server was tested through both unbound structure and sequence inputs on the benchmark of 60 RNA-RNA complexes and compared with the state-of-the-art algorithm SimRNA. For structure input, HNADOCK server achieved a high success rate of 71.7% for top 10 predictions, compared to 58.3% for SimRNA. For sequence input, HNADOCK server also obtained a satisfactory performance and gave a success rate of 83.3% when the bound RNA templates are included or 53.3% when excluding those bound RNA templates. It was also found that inclusion of the inter-RNA base-pairing information from RNA-RNA interaction prediction can significantly improve the docking accuracy, especially for the top prediction. HNADOCK is fast and can normally finish a job in about 10 minutes. The HNADOCK web server is available at http://huanglab.phys.hust.edu.cn/hnadock/.

Improving Protein-Peptide Docking Results via Pose-Clustering and Rescoring with a Combined Knowledge-Based and MM-GBSA Scoring Function

Protein-peptide docking, which predicts the complex structure between a protein and a peptide, is a valuable computational tool in peptide therapeutics development and the mechanistic investigation of peptides involved in cellular processes. Although current peptide docking approaches are often able to sample near-native peptide binding modes, correctly identifying those near-native modes from decoys is still challenging because of the extremely high complexity of the peptide binding energy landscape. In this study, we have developed an efficient postdocking rescoring protocol using a combined scoring function of knowledge-based ITScorePP potentials and physics-based MM-GBSA energies. Tested on five benchmark/docking test sets, our postdocking strategy showed an overall significantly better performance in binding mode prediction and score-rmsd correlation than original docking approaches. Specifically, our postdocking protocol outperformed original docking approaches with success rates of 15.8 versus 10.5% for pepATTRACT on the Global_57 benchmark, 5.3 versus 5.3% for CABS-dock on the Global_57 benchmark, 17.0 versus 11.3% for FlexPepDock on the LEADS-PEP data set, 40.3 versus 33.9% for HPEPDOCK on the Local_62 benchmark, and 64.2 versus 52.8% for HPEPDOCK on the LEADS-PEP data set when the top prediction was considered. These results demonstrated the efficacy and robustness of our postdocking protocol.

Molecular Mechanism of Evolution and Human Infection with SARS-CoV-2

The outbreak of a novel coronavirus, which was later formally named the severe acute respiratory coronavirus 2 (SARS-CoV-2), has caused a worldwide public health crisis. Previous studies showed that SARS-CoV-2 is highly homologous to SARS-CoV and infects humans through the binding of the spike protein to ACE2. Here, we have systematically studied the molecular mechanisms of human infection with SARS-CoV-2 and SARS-CoV by protein-protein docking and MD simulations. It was found that SARS-CoV-2 binds ACE2 with a higher affinity than SARS-CoV, which may partly explain that SARS-CoV-2 is much more infectious than SARS-CoV. In addition, the spike protein of SARS-CoV-2 has a significantly lower free energy than that of SARS-CoV, suggesting that SARS-CoV-2 is more stable and may survive a higher temperature than SARS-CoV. This provides insights into the evolution of SARS-CoV-2 because SARS-like coronaviruses have originated in bats. Our computation also suggested that the RBD-ACE2 binding for SARS-CoV-2 is much more temperature-sensitive than that for SARS-CoV. Thus, it is expected that SARS-CoV-2 would decrease its infection ability much faster than SARS-CoV when the temperature rises. These findings would be beneficial for the disease prevention and drug/vaccine development of SARS-CoV-2.

[A preliminary study on the safety of berberine solution in rabbit eyes with topical application]

Objective: To study the safety of topical berberine solution in rabbit eyes and its effect on corneal epithelial repair in rabbit eyes. Methods: Experimental Study. Ninety-two Japanese rabbits were randomly divided into two groups by random number table method: the general group (32 rabbits, 64 eyes) and the corneal injury group (60 rabbits, 60 eyes).The general groups were further divided into 4 groups by random number table method, and each group has 8 rabbits (16 eyes). According to the administration of deionized water or 0.5, 1.0, 1.5 mg/ml berberine solution, they were divided into the general control group and the general A, B, and C group. Dosing with both eyes, each eye was given a single dose, and then it was given multiple times for 4 weeks after observation for 72h. After the corneal epithelium injury model made in the right eye of rabbits in the corneal injury groups, they were divided into a corneal injury control group and a corneal injury group A, B, and C according to the administration of deionized water or 0.5, 1.0, 1.5 mg/ml berberine solution. there were 5 rabbits (15 eyes) in each group, and the solutions were given continuously for 1 week. The rabbits in the general group were observed their behavioral changes, ocular surface and iris were scored by Draize eye irritation test scoring system. IOP was measured at different time points. Electroretinogram (ERG) was used to detect b-wave amplitude. In the corneal injury group, corneal epithelial defect repairment was observed at 1, 2, 3, 4, 5, 6, and 7 days after the corneal defect. Corneal histopathology observation after discontinuation of all rabbits. The pH value of rabbit tears was described by the paired t test, and the score of Draize eye irritation test were described by the rank-sum test. The analysis of variance and SNK-q were used for IOP, electroretinogram b-wave amplitude, corneal epithelial injury area and repair time. Results: No abnormal behavior was observed in the general group rabbits after single and multiple administration. There was no significant difference in the Draize eye irritation score among the general control group and the general group A, B, C at 1, 2, and 4 weeks of multiple administrations. Among them, the Draize eye irritation score of the general group C was 7 (0, 12), 6 (0, 10), 6 (0, 16) points (χ(2)=1.640, 0.265, 1.963, 1.381; P>0.05).There were no significant difference in IOP at different times among the general control group and the general group A, B, C at different times (F=0.065, 0.292, 0.015, 0.041; P>0.05). Before multiple administrations and after administration at 2, 4 weeks, the b-wave amplitudes of the general control group were (127.75±17.12), (129.18±15.83), (128.81±13.58) μV, and the general group A were (130.68).±18.75), (131.38±16.96), (130.62±12.18) μV,and the general group B were (128.00±16.74), (128.44±16.64), (129.06±16.16) μV, and the general group C were (131.81±19.37), (132.13±18.36), (129.94±12.60) μV. There was no statistically significant difference in b-wave amplitude in the groups at different times before and after administration (F=0.037, 0.011, 0.017, 0.702; P>0.05). There was no significant difference in the results of corneal histopathology among the general control group and the general group A, B, C. The area of corneal epithelial defect in each corneal injury group was statistically significant at different time (F=5.316, 25.864, 127.613; P<0.05). The corneal injury control group compared with the corneal injury group A, B, C, the corneal epithelial defect area in the corneal injury group C was significantly larger than the other three groups, with statistical differences (q=5.153, 10.313, 6.976; P<0.05). The repair time of corneal epithelial in control group and the group A,B,C of corneal injury were (83.0±1.85), (82.9±2.07), (83.7±2.09) and (101.6±2.20) h. The corneal epithelium defect repair time in group C was longer and the difference was statistically significant (F=301.437, P=0.000). Comparing the corneal injury control group and corneal injury group A and B, there was no statistical difference in the repair time of corneal epithelial defect (F=0.813, P=0.450). After repair, there was no significant difference in the pathological results of the corneal tissue between the corneal injury groups. Conclusions: Berberine solution in rabbit eyes with topical application was safety, and has no obvious toxic effect on the ocular surface and ERG of normal rabbits. 1.5 mg/ml berberine solution delayed the repair of experimental corneal epithelial defect, but had no effect on the integrity of corneal tissue after repair. (Chin J Ophthalmol, 2020, 56: 131-137).

Asprosin and type 2 diabetes mellitus: a novel potential therapeutic implication

Diabetes is a group of metabolic disorders that is characterized by hyperglycemia which increases the risks of cardiovascular, microvascular, and macrovascular complications. Innovative therapeutic trials regarding diabetes control and management are continually being undertaken. The present review was aimed to explore the potential effects and mechanisms that lead to the pathogenesis of type 2 diabetes mellitus (T2DM) and its relation with asprosin. Asprosin is a newly discovered hormone that is encoded by protein fibrillin 1 (FBN1 gene), secreted by white adipose during fasting conditions at 5-10 nM levels, which acts on the liver through cell membrane receptors and activates the G protein cAMP- PKA pathway. Asprosin secretion is increased during fasting as the compensatory mechanism in hypoglycemia. Asprosin concentration is higher in patients with T2DM and impaired glucose regulation compared to healthy subjects. Genetic deficiency of asprosin may cause problems of poor appetite and extreme leanness in humans. Attenuating asprosin activity or depleting asprosin may serve as a novel therapeutic innovation for the treatment of T2DM and obesity. Hence, asprosin may serve as a beacon for the target of a future therapy in diabetes management.

Challenges and opportunities of automated protein-protein docking: HDOCK server vs human predictions in CAPRI Rounds 38-46

Protein-protein docking plays an important role in the computational prediction of the complex structure between two proteins. For years, a variety of docking algorithms have been developed, as witnessed by the critical assessment of prediction interactions (CAPRI) experiments. However, despite their successes, many docking algorithms often require a series of manual operations like modeling structures from sequences, incorporating biological information, and selecting final models. The difficulties in these manual steps have significantly limited the applications of protein-protein docking, as most of the users in the community are nonexperts in docking. Therefore, automated docking like a web server, which can give a comparable performance to human docking protocol, is pressingly needed. As such, we have participated in the blind CAPRI experiments for Rounds 38-45 and CASP13-CAPRI challenge for Round 46 with both our HDOCK automated docking web server and human docking protocol. It was shown that our HDOCK server achieved an "acceptable" or higher CAPRI-rated model in the top 10 submitted predictions for 65.5% and 59.1% of the targets in the docking experiments of CAPRI and CASP13-CAPRI, respectively, which are comparable to 66.7% and 54.5% for human docking protocol. Similar trends can also be observed in the scoring experiments. These results validated our HDOCK server as an efficient automated docking protocol for nonexpert users. Challenges and opportunities of automated docking are also discussed.

Determination of newly synthesized dihydroxylated polybrominated diphenyl ethers in sea fish by gas chromatography-tandem mass spectrometry

Dihydroxylated polybrominated diphenyl ethers (diOH-PBDEs) can be natural products of marine organisms or the metabolites of PBDEs. The optimal determination method and concentration of diOH-PBDEs in seafood are unknown due to a lack of commercially available standards. In the present study, diOH-PBDEs were synthesized, and an efficient measurement method for OH-PBDEs and diOH-PBDEs in sea fish muscle samples, including extraction, clean-up and gas chromatography-tandem mass spectrometry (GC-MS/MS) analysis, was established. Pressurized liquid extraction (PLE) followed by partitioning with a KOH solution and florisil cartridge clean-up proved to be a reliable and robust method for detecting all OH-PBDEs/diOH-PBDEs. GC-MS/MS with an electron ionization (EI) source analysis was a sensitive analytical instrument for OH-PBDEs/diOH-PBDEs. The recovery using this method ranged from 19% to 101%, 28%-88% and 42%-90% for 10 ng, 20 ng and 40 ng spiking levels, respectively. The equipment detection limits (EDLs) were in the range of 0.31-2.78 pg/μL, and the limits of detection (LOD) for the method were in the range of 5.07-38.74 pg/g wet weight. Concentrations of diOH-PBDEs in the marine fish muscle samples were in the range of 32.43-1528.63 pg/g wet weight. Similar compositions of OH-PBDEs/diOH-PBDEs were found within the same family of marine fish.

[Retrospective investigation of spontaneous bloody tears: a report of 27 cases]

Objective: To summarize clinical experience on the clinical feature, etiology and treatment of patients with spontaneous bloody tears as the initial symptom. Methods: Retrospective series of case studies. The clinical data and follow-up data of 27 cases of bloody tears as the first symptom in Lacrimal Center of Ophthalmology, the Third Medical Center of Chinese PLA General Hospital from June 2015 to December 2018 were reviewed. The clinical feature, specific cause, diagnosis, treatment and prognosis of these cases were evaluated. Results: A total of 27 cases were collected in this study. The patients were 10 males (37.0%) and 17 females (63.0%), including 21 adults (≥ 18 years old, 77.8%) and 6 minors (<18 years old, 22.2%). There were 22 monocular cases (81.5%) and 5 binocular cases (18.5%). Five cases (18.5%) were bleeding from the eye and other parts of the body, and 22 cases (81.5%) were bleeding only from the eye. There were 19 cases (70.4%) with hematic epiphora and secretions from the punctum, 3 cases (11.1%) with blood-stained tears, and 7 cases (25.9%) with blood-like tears. With regard to etiology, 6 cases (22.2%) were combined with systemic lesions, one of which was granulomatosis with polyangiitis and five of which (<18 years old) were idiopathic bloody tears. Twenty-one cases (77.8%) were local lesions, including 18 cases only involving the lacrimal system, 2 cases only involving the ocular surface, and 1 case involving both the lacrimal system and the ocular surface. Among the 21 cases with local lesions, 5 cases were induced by foreign body, 6 cases were induced by simple inflammation, and 10 cases were induced by tumor including 1 case with conjunctival benign tumor and 9 cases with tumor of the lacrimal system (5 with malignant tumor and 4 with benign tumor). Patients with idiopathic bloody tears received psychological and medical treatment, and interictal discharge was lengthened. One case of granulomatosis with polyangiitis was treated by trans-nasal endoscopic dacryocystorhinostomy. With the recurrence of granulomatosis and polyangiitis, bloody tears recurred after surgery. One patient with conjunctival hemangioma was untreated. Lesions in the lacrimal duct system were removed and dacryocystorhinostomy was performed. In this study, 2 patients (1 with small cell neuroendocrine carcinoma and 1 with adenoid cystic adenocarcinoma) died and the other had a good prognosis. Conclusions: Among the cases of bloody tears, adults and local lesions are more common. Most of the lesions are located in the lacrimal system and are tumors. The main treatment is to remove the lesions, and if necessary, to expand the resection and reconstruct the lacrimal duct. Idiopathic bloody tears occur in minors, who are gave psychotherapy and necessary medical treatment. (Chin J Ophthalmol, 2020, 56: 53-58).

[A preliminary study on optical coherence tomography of the lacrimal punctum in normal adults]

Objective: To study the imaging characteristics and accumulate data of optical coherence tomography (OCT) of the lacrimal punctum in normal adults. Methods: From September to November 2018, 59 healthy adults (90 eyes) with normal lacrimal punctum structure were enrolled in this cross-sectional study conducted at the Lacrimal Center of Ophthalmology, Third Medical Center of PLA General Hospital, including 21 males (34 eyes) and 38 females (56 eyes), aged 18-65 years. All the subjects were examined by slit lamp microscopy to measure the maximum transverse diameter. OCT was performed to observe the inferior lacrimal punctum, including the external punctal diameter, the punctal diameter at 100 μm and 200 μm depth. The difference in the diameter of different parts of the punctum was analyzed. Independent sample t test and single factor analysis of variance were used for statistical analysis. Results: In normal adults, the maximum transverse diameter under a slit lamp was (545.6±149.3) μm, the external punctal diameter on OCT images was (548.4±130.5) μm, and the punctal width at 100 μm and 200 μm depth on OCT images was (262.8±120.8) μm and (179.2±110.0) μm, respectively. There was no significant difference between the maximum transverse diameter of the punctum under a slit lamp microscope and the OCT outer diameter of the punctum (t=0.133, P=0.894). There were significant differences between the diameter of the lacrimal punctum in the different scanning sites of the OCT (F=213.237, P<0.01). There was significant difference between the punctal width at 100 μm and the external punctal diameter on OCT images (t=15.229, P<0.01). There was significant difference between the punctal width at 200 μm and the external punctal diameter on OCT images (t=20.517, P<0.01). There was significant difference between the punctal width at 100 μm and 200 μm depth on OCT images (t=4.855, P<0.01). Conclusion: The width of different parts of the lacrimal punctum in healthy adults is different on OCT images, and the punctal width at 200 μm depth is the narrowest. (Chin J Ophthalmol, 2019, 55: 695-699).

PepBDB: a comprehensive structural database of biological peptide-protein interactions

Summary

A structural database of peptide-protein interactions is important for drug discovery targeting peptide-mediated interactions. Although some peptide databases, especially for special types of peptides, have been developed, a comprehensive database of cleaned peptide-protein complex structures is still not available. Such cleaned structures are valuable for docking and scoring studies in structure-based drug design. Here, we have developed PepBDB-a curated Peptide Binding DataBase of biological complex structures from the Protein Data Bank (PDB). PepBDB presents not only cleaned structures but also extensive information about biological peptide-protein interactions, and allows users to search the database with a variety of options and interactively visualize the search results.

Availability and implementation

PepBDB is available at http://huanglab.phys.hust.edu.cn/pepbdb/.

Mesoporous TiO2/carbon catalytic ozonation for degradation of p-chloronitrobenzene

In this study, a mesoporous TiO₂/carbon catalyst (TiO₂/C) was prepared by a facile impregnation-carbonization approach to catalyze ozonation of p-chloronitrobenzene (p-CNB). The catalyst was well characterized and the catalytic efficiency under various conditions was systematically evaluated. TiO₂/C has a disordered mesostructure with a high specific surface area. 92.8% of p-CNB (2 μmol/L) can be degraded within 20 min in the TiO₂/C/O₃ system in the presence of 1 mg/L O₃, 100 mg/L catalyst, at pH = 5. Based on the evaluation of the effect of basic parameters, it could be deduced that the removal of p-CNB relied on the synthetic effect of catalysis by TiO₂/C and the autocatalytic induction of p-CNB. The removal efficiency of p-CNB, the structure change and the leaching of Ti ions were also evaluated in five cycles, indicating TiO₂/C is stable and recyclable for catalytic ozonation in water treatment.

Application of Multiple Genetic Markers in Determination of Full and Half Sibling Relationship： A Case Report

Abstract

Objective To investigate the application of the comprehensive use of multiple genetic markers in full and half sibling relationship testing through the identification of a case of suspected sibling relationship. Methods Genomic DNA were extracted from bloodstain samples from 4 subjects （ZHANG-1, ZHANG-2, male; ZHANG-3, ZHANG-4, female）. Autosomal STR loci, X-STR, Y-STR loci and polymorphisms of mtDNA HV-Ⅰ and Ⅱwere genotyped by EX20 STR kit, X19 kit, Data Y24 STR kit, and Sanger sequencing, respectively. Results According to autosomal STR based IBS scoring results, full sibling relationships were indicated among ZHANG-2, ZHANG-3 and ZHANG-4, but those were not indicated between ZHANG-1 and ZHANG-2 or ZHANG-3 or ZHANG-4. According to autosomal STR based FSI and HSI, with ITO method and discriminant function method, full sibling relationships among ZHANG-2, ZHANG-3 and ZHANG-4 were indicated, and half sibling relationships between ZHANG-1 and ZHANG-2 or ZHANG-3 or ZHANG-4 were also indicated. X-STR and mtDNA sequencing results showed that all the 4 samples came from a same maternal line, and Y-STR results showed that ZHANG-1 and ZHANG-2 did not come from a same paternal line, which supported the half sibling relationship between ZHANG-1 and ZHANG-2 or ZHANG-3 or ZHANG-4, verified by parental genotype reconstruction based on autosomal STR genotyping. Conclusion For the identification of sibling relationships, it is effective to have reliable results with the mutual verification and support of multiple genetic markers （autosomal STR, sex chromosomal STR and mtDNA sequence） and calculations （IBS, ITO, discriminant function method and family reconstruction）.

Dynamics and Mechanisms in the Recruitment and Transference of Histone Chaperone CIA/ASF1

The recruitment and transference of proteins through protein-protein interactions is a general process involved in various biological functions in cells. Despite the importance of this general process, the dynamic mechanism of how proteins are recruited and transferred from one interacting partner to another remains unclear. In this study, we investigated the dynamic mechanisms of recruitment and translocation of histone chaperone CIA/ASF1 for nucleosome disassembly by exploring the conformational space and the free energy profile of unbound DBD(CCG1) and CIA/ASF1-bound DBD(CCG1) systems through extensive molecular dynamics simulations. It was found that there exists three metastable conformational states for DBD(CCG1), an unbound closed state, a CIA/ASF1-bound half-open state, and an open state. The free energy landscape shows that the closed state and the half-open state are separated by a high free energy barrier, while the half-open state and the open state are connected with a moderate free energy increase. The high free energy barrier between the closed and half-open states explains why DBD(CCG1) can recruit CIA/ASF1 and remain in the binding state during the transportation. In addition, the asymmetric binding of CIA/ASF1 on DBD(CCG1) allows DBD(CCG1) to adopt the open state by moving one of its two domains, such that the exposed domain of DBD(CCG1) is able to recognize the acetylated histone H4 tails. As such, CIA/ASF1 has a chance to translocate from DBD(CCG1) to histone, which is also facilitated by the moderate energy increase from the bound half-open state to the open state of DBD(CCG1). These findings suggest that the recruitment and transference of histone chaperone CIA/ASF1 is highly favored by its interaction with DBD(CCG1) via conformational selection and asymmetric binding, which may represent a general mechanism of similar biological processes.

Abstract P1-02-10: Early stage breast cancer screening using an emerging novel liquid biopsy screening technology

Background: An emerging novel liquid biopsy technology called Cancer Differentiation Analysis (CDA) has been evaluated as a viable early stage breast cancer screening tool. CDA technology is a blood-sample based, multi-level, multi-parameter diagnostic method which detects signals from both protein, cellular, and to some extent, molecular levels, in which multiple aspects of information can be collected to improve diagnostic accuracy, even for early stage of cancer. Improving capability to screen breast cancer is an important on-going research effort, as breast cancer represents a leading cancer with high incidence rate.

Methods: In this single-blind study, 22 breast cancer patients and 25 healthy individuals were recruited at Changhai Hospital of Shanghai. Histopathological examination results of breast cancer patients were collected, 22 cases were diagnosed as infiltrating ductal carcinoma of breast, of which 10 patients were stage I breast cancer. 25 individuals were confirmed healthy after physical examinations. Peripheral blood was drawn in EDTA tubes For CDA tests. CDA data of 22 breast cancer patients and 25 healthy individuals were conducted using SPSS, and the results were shown in the table below.

Results: The average CDA of breast cancer, stageIbreast cancer, and controls were 43.20, 44.17 and 36.17 (rel. units) respectively as shown in Table 1. Both breast cancer and stage I breast cancer could be significantly distinguished from the control (p = 0.000, p = 0.001, respectively). For stage I breast cancer vs. control group, Area under ROC curve was 0.876, sensitivity and specificity were both 80.0% (Table 2). In contrast to traditional breast cancer screening methodologies which have relatively low sensitivity and high false positives for stage I detection, often with radiation side effects and high costs, advantages of CDA technology include ability to detect early stage cancer with relatively high sensitivity and specificity, and it is also highly cost effective without side effects.

Conclusions: Initial results showed that CDA technology could effectively distinguish stageIbreast cancer from healthy individuals, CDA could be a potential candidate for breast cancer screening.

Table 1Summary of CDA test resultsGroupSample SizeAge RangeAge MeanAge MedianCDA Mean (rel. units)CDA Median (rel. units)CDA STDEVControl2523 - 67413735.6336.176.98Breast Cancer2239 - 78545343.2042.304.18Stage I Breast Cancer1043 - 78595944.1743.254.29Stage II Breast Cancer839 - 55474941.2840.303.06Stage III Breast Cancer255555542.2042.202.12Stage IV Breast Cancer251 - 64585847.0047.007.78

Table 2AUC, Sensitivity and Specificity of Control vs. Stage I breast cancerStage I Breast Cancer vs. ControlArea Under the CurveSensitivitySpecificity 0.87680.0%80.0%

Citation Format: Liu C, Dou J, Sheng Y, Wu J, Hu W, Li Y, Lin Y, Tao H, Tang X, Du X, Yu C. Early stage breast cancer screening using an emerging novel liquid biopsy screening technology [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-02-10.

Abstract P1-02-09: CDA screening technology for multi-ethnic group, early stage breast cancer screening

Background: Breast cancer is the second leading cause of death from cancer in American women. Current breast cancer screening technologies have issues with poor sensitivity for early stage breast cancer, high false positives, radiation side effects, etc. Cancer Differentiation Analysis (CDA) technology is a blood-sample based, multi-level, multi-parameter diagnostic method which detects signals from both proteins, cells, and to some extent, molecular level, in which multiple aspects of information are collected to improve diagnostic accuracy. CDA technology has been investigated as a viable clinical utility in breast cancer screening, particularly for early stage breast screening with clear advantages (both whole blood and serum can be used, ability to detect early, easy, simple, no side effects, and high degree of sensitivity and specificity).

Methods: In this study, the human subjects involved are Caucasians, with serum samples of 44 pathologically confirmed breast cancer patients and 34 healthy individuals from 3 blood bank centers in the USA, of which 40 cases were stageIbreast cancer, 2 cases were stageII, and the other 2 cases were stage III breast cancer. CDA data of 44 breast cancer patients and 34 healthy individuals were collected in US lab and analyzed using SPSS, and the results were shown in the table below. Results from the above study was compared with a clinical study on Asian group with data collected in lab in China using CDA technology.

Results: The average CDA value of all breast cancer and stageIbreast cancer samples, and controls were 45.99, 45.76 and 42.36 (rel. units) respectively (see Table 1). Both breast cancer and stageIbreast cancer could be significantly distinguished from the control group (p &lt; 0.001) (Table 2). For stageIbreast cancer vs. control group, Area under ROC curve was 0.727, sensitivity and specificity were 62.5% and 82.4% respectively, which is higher than a typical mammogram. To compare with different ethnic groups, data collected on an Asian group is also shown in Table 2, which showed that overall, AUC, sensitivity and specificity are comparable (some difference may be attributed to sample type difference (whole blood vs. serum)) for early stage breast cancer patients for those two ethnic groups, demonstrating that CDA technology can be extended to multiple ethnic groups.

Conclusions: CDA screening can be extended to different ethnic group including Caucasian and Asian with good sensitivity and specificity for stageIbreast cancer.

We thank Ugur Basmaci, Sunsil Pandit and Sharon Vorse-Yu for their support.

Table 1Summary of CDA Test ResultsGroupSample SizeAge RangeAge MeanAge MedianCDA Mean (rel. units)CDA Median (rel. units)CDA STDEVControl3436 -79575742.3642.652.75Breast Cancer4436 – 77606145.9946.504.22Stage I Breast Cancer4036 – 77606145.7645.554.26Stage II Breast Cancer251 – 64585847.0547.054.88Stage III Breast Cancer262 – 75696949.5049.502.55

Table 2AUC, Sensitivity and Specificity of Control vs. Stage I Breast CancerStage I Breast Cancer vs. ControlArea Under the CurveSensitivitySpecificityCaucasian (Stage I)0.72762.5%82.4%Asian# (Stage I)0.87680.0%80.0%# Whole blood samples. 10 stage I breast cancer samples and 25 control samples

Citation Format: Tao H, Lin Y, Liu C, Dou J, Sheng Y, Wu J, Hu W, Li Y, Tang X, Yu C, Du X. CDA screening technology for multi-ethnic group, early stage breast cancer screening [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-02-09.

Correlation between SPARC, TGFβ1, Endoglin and angiogenesis mechanism in lung cancer

To study the relationship between Secreted protein, acidic and rich in cysteine (SPARC), Transforming growth factorβ1 (TGFβ1), Endoglin and angiogenesis in lung cancer, 40 cases of lung cancer specimens and 40 adjacent normal lung tissues specimens were collected and 10 cases from each were selected for preparation of tissue chip. CD34 (endothelial cell marker), Endoglin human α-Smooth muscle actin, and (α-SMA) markers were performed by immunohistochemical staining, and the immuno-phenotype and the relationship between different morphologies of the microvascular wall components were evaluated. The expression of SPARC mRNA and protein, TGFβ1 mRNA and protein and Endoglin in the remaining 30 cases of lung cancer were detected by immunohistochemistry and in-situ hybridization. The result shows that the positive rates of SPARC, TGFβ1 and Endoglin in lung cancer tissues were significantly higher than those in adjacent normal lung tissues (P less than 0.05). The expression of SPARC and TGFβ1 was negatively correlated with lung cancer. When the positive expression of SPARC increased, the micro-vessel density (MVD) marked by Endoglin decreased gradually; while the positive expression of TGFβ1 increased, MVD increased gradually, and SPARC, TGFβ1 and MVD were correlated (P less than0.05). High SPARC mRNA expression in lung cancer tissues could inhibit the progression of lung cancer, while high TGFβ1 mRNA expression can promote the progression of lung cancer and participate in the metastasis of lung cancer. To sum up, the angiogenesis of lung cancer may be related to the interaction of SPARC, TGFβ1 and Endoglin.

HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry

A major subclass of protein-protein interactions is formed by homo-oligomers with certain symmetry. Therefore, computational modeling of the symmetric protein complexes is important for understanding the molecular mechanism of related biological processes. Although several symmetric docking algorithms have been developed for Cn symmetry, few docking servers have been proposed for Dn symmetry. Here, we present HSYMDOCK, a web server of our hierarchical symmetric docking algorithm that supports both Cn and Dn symmetry. The HSYMDOCK server was extensively evaluated on three benchmarks of symmetric protein complexes, including the 20 CASP11-CAPRI30 homo-oligomer targets, the symmetric docking benchmark of 213 Cn targets and 35 Dn targets, and a nonredundant test set of 55 transmembrane proteins. It was shown that HSYMDOCK obtained a significantly better performance than other similar docking algorithms. The server supports both sequence and structure inputs for the monomer/subunit. Users have an option to provide the symmetry type of the complex, or the server can predict the symmetry type automatically. The docking process is fast and on average consumes 10∼20 min for a docking job. The HSYMDOCK web server is available at http://huanglab.phys.hust.edu.cn/hsymdock/.