Phase transition of DNA knotting in spherical space.

Knots have been discovered in various biological systems, such as DNA. The knotting probability of DNA in free space depends non-monotonically on its bending rigidity and has a prominent peak. The current work aims to understand the underlying mechanism of the non-monotonic dependence of DNA knotting probability on bending rigidity. Monte Carlo simulations are performed on a closed DNA molecule confined in spherical space described by a worm-like chain model and a flexible kink model, respectively. The closed DNA's contour length and the spherical space radius both increase knotting probability, but also alter the unimodal dependence of knotting probability on bending rigidity. This is generalized using universal phase diagrams based on the two models. Under the flexible kink model, the total knotting probability of closed DNA is obviously increased at a relatively high excited energy. This supports the expectation that the entropy effect of knot size favours knot formation at a relatively low bending rigidity. In a given spherical space, the increasing contour length of closed DNA described by the worm-like chain model results in a visible shift in the knotting probability distribution. At the same time, the gyration radius of non-trivial closed DNA becomes comparable to that of trivial closed DNA, so that their ratio is not anti-correlated with average knot length. For closed DNA of various contour lengths, the relationship between average knot length and bending rigidity has a universal behaviour: the average knot length decreases to a local minimum at a bending rigidity of ∼5 and then gradually increases to a constant value. The existence of the local minimum is determined by the cut-off distance in repulsive Lennard-Jones potential. The bending rigidity corresponding to the beginning of the constant average knot length is consistent with that at the peak in the knotting distribution. At this point, the knot-size effect balances with the fragment free-energy effect and, at an even greater bending rigidity, knot length breathes around the average knot length value.

Chinese version of the clinical supervision self-assessment tool: Assessment of reliability and validity.

BACKGROUND: Cultivating the professional knowledge and professional identity of nursing students is important for nursing education. The degree of professional identity of nursing students will directly affect their career options and work performance after graduation. Clinical practice is a learning process of combining the knowledge and the practical techniques of nursing. It is the important way to cultivate the students' comprehensive ability, professional attitude and professional emotion. Effective clinical supervision during the clinical practice plays an important role in guaranteeing clinial practice quality and cultivating professional nursing students. Active teaching supervision is helpful to achieve the expected learning effect. Therefore, it is vital to evaluate the clinical supervision ability of the clinical nursing teachers. However, there is no special assessment instrument available in China. OBJECTIVES: To assess the validity and reliability of the Chinese version of the modified Clinical Supervision Self-Assessment Tool (mCAST). DESIGN: A cross sectional survey design with a convenience sample was used in this study. This cross-sectional psychometric instrumental study determined the reliability and validity of the Chinese version of the modified Clinical Supervision Self-Assessment Tool (mCAST). SETTINGS: Twelve hospitals in Tianjin, China. PARTICIPANTS: A total of 350 registered nurses who perform teaching tasks in clinical practice were recruited. METHODS: The Chinese version of the mCSAT was translated and tested by obtaining the authorization of the developer of the mCAST using Brislin's model (that is, translation, back translation, cultural adaptation and pilot study). A total of 350 registered nurses who perform teaching tasks in clinical practice were recruited by convenience sampling for the assessment of construct validity using exploratory factor analysis (EFA). Moreover, item analysis, internal correlation coefficients, Cronbach's alpha coefficients, test-retest realibility and split-half reliability were conducted to test the psychometric properties of the Chinese version of the mCSAT. RESULTS: The Chinese version of the mCSAT contained 2 subscales, namely, mCSAT-Knowledge and mCSAT-Skills. Exploratory factor analysis of the knowledge and skills subscales explained 63.26% and 63.60% of the total variances, respectively. The mCSAT-Knowledge subscale contains 3 dimensions, namely, evaluating learning (10 items), facilitating learning (9 items) and problem solving (10 items); the mCSAT-Skills subscale contains 3 dimensions, namely, evaluating learning (10 items), facilitating learning (9 items) and problem solving (10 items). The Cronbach's α coefficients of the mCSAT-Knowledge and mCSAT-Skills subscales were both 0.95. The split-half reliability of the mCSAT-Knowledge and mCSAT-Skills subscales were 0.88 and 0.89, respectively. CONCLUSION: The Chinese version of the mCSAT was reliable and valid in the evaluation of the knowledge and skills for the clinical supervision of registered nurses. Further validation of the Chinese version of the mCSAT requires a more representative and larger sample. Also, the confirmatory factor analysis should be conducted in future study.

Macromolecule crowding effects on the phase separation of semi-flexible polymer in spherical confined space.

Current works focus on detecting macromolecule crowding effects on the phase separation of the mixture between semi-flexible polymer and crowders (hydrophilic polymers) in confined space by Monte Carlo simulations. With the increasing addition of crowders into the spherical confined space, the semi-flexible polymer was first compressed into a condensed state from the initial coil state, and then the condensed conformation expanded and deposited on the inner surface of the spherical confined space with an extended state. The phase diagram in the phase space of the volume fraction of crowders and the scaled radius of spherical confined space by crowder diameter, and the direct conformation transition of semi-flexible polymer have validated the phase transition process successfully. In addition, the deposition of extended conformation on the inner surface of the spherical confined space was qualified by the vertex density, its curve shifted along the radial direction with the increasing volume fraction of crowder. During the phase separation process, the critical volume fraction φ∗ relates to the crowder diameter approximately linearly and the relation between the critical volume fraction and the crowder diameter strongly depends on the size of the spherical confined space.

Frailty among older people in a community setting in China.

Frailty is the most common manifestation of serious health issues in the world, and it is becoming more prevalent worldwide as the aging population grows. Changes that occur in an individual during the aging process have physical, psychological, social, and environmental aspects that make an individual more frail. In China, older people may live in communities for aging individuals. This study aimed to describe the presence and severity of frailty and to analyze influencing factors among this population in China. The Frailty Index 35 (FI-35) scale, which includes 35 items in physical, psychological, social, and environmental domains, was used to investigate frailty. The FI-35 score ranges from zero to one, with a score closer to one indicating greater frailty. Biographical, socioeconomic, and lifestyle factors were measured as potential determinants of frailty. We relied on the November 2017-February 2018 waves of the Chinese cross-sectional study survey that comprised a sample of 513 adults, aged 60 or older, who were living in China. Linear regression was performed to identify factors associated with FI-35 scores. We categorized the determinants of frailty into three models: Model 1: biographical variables; Model 2: biographical and socioeconomic variables; and Model 3: biographical, economic, and lifestyle variables. Frailty scores ranged from 0.00 to 0.89, with a median of 0.31, and the prevalence of frailty was 67.6%. The final model obtained after variable selection included age, minority status, marriage status, income, diet, and exercise. The adjusted R-squared indicated that the analysis explained 13.8% of the variance in frailty scores. Adding household, marriage status, education level, medical insurance, and income as elements in Model 2 explained 25.7%. Adding diet, smoking, drinking, exercise, and hobbies in Model 3 explained 27.9%. The degree of frailty varies considerably among Chinese community-dwelling older people and is partly determined by biographical, socioeconomic, and lifestyle factors.

Health Risk Assessment Indicators for the Left-Behind Elderly in Rural China: A Delphi Study.

In China, many young and middle-aged rural residents move to urban areas each year. The rural elderly are left behind. The number of the rural left-behind elderly is increasing with urbanization, but it is unclear which indicators can be used to assess their health condition. The health risk assessment index system was developed to improve the health level of the rural left-behind elderly. A two-round web-based Delphi process was used to organize the recommendations from fifteen Chinese experts in geriatrics, health management, social psychology who participated in this study. Meaningfulness, importance, modifiability, and comprehensive value of the health risk assessment indicators in the index system were evaluated. The effective recovery rates of the two-round Delphi were 86.67% and 92.31%, respectively. The judgement coefficient and the authority coefficient were 0.87 and 0.82, respectively. The expert familiarity was 0.76. Ultimately, the health risk assessment index system for the rural left-behind elderly consisted of five first-level indicators, thirteen second-level indicators, and sixty-six third-level indicators. The final indicators can be used to evaluate the health of the rural left-behind elderly and provide the basis for additional health risk interventions.

LOVD-DASH: A comprehensive LOVD database coupled with diagnosis and an at-risk assessment system for hemoglobinopathies.

Hemoglobinopathies are the most common monogenic disorders worldwide. Substantial effort has been made to establish databases to record complete mutation spectra causing or modifying this group of diseases. We present a variant database which couples an online auxiliary diagnosis and at-risk assessment system for hemoglobinopathies (DASH). The database was integrated into the Leiden Open Variation Database (LOVD), in which we included all reported variants focusing on a Chinese population by literature peer review-curation and existing databases, such as HbVar and IthaGenes. In addition, comprehensive mutation data generated by high-throughput sequencing of 2,087 hemoglobinopathy patients and 20,222 general individuals from southern China were also incorporated into the database. These sequencing data enabled us to observe disease-causing and modifier variants responsible for hemoglobinopathies in bulk. Currently, 371 unique variants have been recorded; 265 of 371 were described as disease-causing variants, whereas 106 were defined as modifier variants, including 34 functional variants identified by a quantitative trait association study of this high-throughput sequencing data. Due to the availability of a comprehensive phenotype-genotype data set, DASH has been established to automatically provide accurate suggestions on diagnosis and genetic counseling of hemoglobinopathies. LOVD-DASH will inspire us to deal with clinical genotyping and molecular screening for other Mendelian disorders.

Biopharmaceutical Industry Practices for Sequence Variant Analyses of Recombinant Protein Therapeutics.

The application of advanced methodologies such as next-generation sequencing (NGS) and mass spectrometry (MS) to the characterization of cell lines and recombinant proteins has enabled the highly sensitive detection of sequence variants (SVs). However, although these approaches can be leveraged to provide deep insight into product microheterogeneity caused by SVs, they are not used in a standardized manner across the industry. Currently, there is little clarity and consensus on the utilization, timing, and significance of SV findings. This white paper addresses the current practices, logistics, and strategies for the analysis of SVs using a benchmarking survey coordinated by the International Consortium for Innovation & Quality in Pharmaceutical Development (IQ) as well as a series of deliberations among a panel of experts assembled from across the biopharmaceutical industry. Discussion includes current industry experiences including approaches for detection and quantitation of SVs during cell-line and process development, risk assessments, and regulatory feedback. Although SVs are a potential issue for all recombinant protein therapeutics, the scope of this discussion will be limited to SVs produced in mammalian cells. Ultimately, it is our hope that the findings from the survey and deliberations of the committee are useful to decision makers in industry and positions them to respond to findings of SVs in recombinant proteins that are destined for clinical or commercial use in a strategic manner.LAY ABSTRACT: This white paper addresses the current practices, logistics, and strategies for the analysis of amino acid sequence variants using a benchmarking survey coordinated by the International Consortium for Innovation & Quality in Pharmaceutical Development (IQ) as well as a series of deliberations among a panel of experts assembled from across the biopharmaceutical industry. Discussion includes current industry experiences regarding detection and quantitation of SVs during cell-line and process development, risk assessments, and regulatory feedback.

realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta).

With over 6000 species in seven classes, red algae (Rhodophyta) have diverse economic, ecological, experimental and evolutionary values. However, red algae are usually absent or rare in comparative analyses because genomic information of this phylum is often under-represented in various comprehensive genome databases. To improve the accessibility to the ome data and omics tools for red algae, we provided 10 genomes and 27 transcriptomes representing all seven classes of Rhodophyta. Three genomes and 18 transcriptomes were de novo assembled and annotated in this project. User-friendly BLAST suit, Jbrowse tools and search system were developed for online analyses. Detailed introductions to red algae taxonomy and the sequencing status are also provided. In conclusion, realDB (realDB.algaegenome.org) provides a platform covering the most genome and transcriptome data for red algae and a suite of tools for online analyses, and will attract both red algal biologists and those working on plant ecology, evolution and development.Database URL: http://realdb.algaegenome.org/.

Dynamic Cerebral Autoregulation Assessment Using Extracranial Internal Carotid Artery Doppler Ultrasonography.

Transcranial Doppler ultrasonography of the middle cerebral artery (MCA) is frequently used to assess dynamic cerebral autoregulation (dCA); however, this is difficult in patients with poor temporal bone windows. In the study described here, we investigated the agreement and sensitivity of dCA indices determined from the extracranial internal carotid artery (ICA) and those determined from the MCA. Measurements for 32 stroke patients and 59 controls were analyzed. Measurement of the mean flow correlation index (Mx) and transfer function analysis based on spontaneous blood pressure fluctuation were simultaneously performed for the extracranial ICA and MCA. The mean values of Mx and phase shift did not significantly differ between the ICA and MCA (mean difference: Mx = 0.01; phase shift of very low frequency [VLF] = 0.7°, low frequency [LF] = 3.3° and high frequency = 4.5°), but the gains in VLF and LF in the ICA were significantly lower than those in the MCA (mean difference: gain of VLF = -0.13, gain of LF = -0.10). The intra-class correlation coefficient between the dCA indices of the ICA and MCA was favorable in Mx (0.76) and the phase shift of VLF (0.72). The area under the receiver operating characteristic curve for stroke diagnosis did not differ among the dCA indices. We conclude that dCA assessed from the ICA is as effective as that from the MCA, but the results are not interchangeable.

Optimal dosing regimen of biapenem in Chinese patients with lower respiratory tract infections based on population pharmacokinetic/pharmacodynamic modelling and Monte Carlo simulation.

In this study, a population pharmacokinetic (PPK) model of biapenem in Chinese patients with lower respiratory tract infections (LRTIs) was developed and optimal dosage regimens based on Monte Carlo simulation were proposed. A total of 297 plasma samples from 124 Chinese patients were assayed chromatographically in a prospective, single-centre, open-label study, and pharmacokinetic parameters were analysed using NONMEN. Creatinine clearance (CLCr) was found to be the most significant covariate affecting drug clearance. The final PPK model was: CL (L/h)=9.89+(CLCr-66.56)×0.049; Vc (L)=13; Q (L/h)=8.74; and Vp (L)=4.09. Monte Carlo simulation indicated that for a target of ≥40% T>MIC (duration that the plasma level exceeds the causative pathogen's MIC), the biapenem pharmacokinetic/pharmacodynamic (PK/PD) breakpoint was 4µg/mL for doses of 0.3g every 6h (3-h infusion) and 1.2g (24-h continuous infusion). For a target of ≥80% T>MIC, the PK/PD breakpoint was 4µg/mL for a dose of 1.2g (24-h continuous infusion). The probability of target attainment (PTA) could not achieve ≥90% at the usual biapenem dosage regimen (0.3g every 12h, 0.5-h infusion) when the MIC of the pathogenic bacteria was 4µg/mL, which most likely resulted in unsatisfactory clinical outcomes in Chinese patients with LRTIs. Higher doses and longer infusion time would be appropriate for empirical therapy. When the patient's symptoms indicated a strong suspicion of Pseudomonas aeruginosa or Acinetobacter baumannii infection, it may be more appropriate for combination therapy with other antibacterial agents.

Efficacy and safety of biapenem against lower respiratory tract infections in elderly Chinese patients and optimal dosing regimen based on pharmacokinetic/pharmacodynamic analysis.

The present study evaluated the efficacy and safety of biapenem in elderly Chinese patients with lower respiratory tract infections (LRTIs) and proposed optimal dosage regimen on the basis of pharmacokinetic/pharmacodynamic (PK/PD) analysis. The clinical efficacy, bacterial eradication and comprehensive therapeutic effect rates of biapenem were 70.3 (78/111), 68.5 (37/54) and 61.1% (33/54), respectively. Drug-related adverse reactions were seen in 12.6% of patients (14/111). The total protein level, Acute Physiology and Chronic Health Evaluation (APACHE) II score, %fT>MIC, fAUC24/MIC and fCmax/MIC values of patients had significant impacts (P < 0.05) on clinical and bacteriological efficacy. However, logistic regression analysis showed that only %fT>MIC independently influenced comprehensive therapeutic effect (P < 0.01, odds ratio = 1.064). The cut-off value for predicting comprehensive therapeutic effect using %fT>MIC was 75.0%; the sensitivity and specificity were 87.9 and 85.7%, respectively. Monte Carlo simulations revealed that the usual dosage regimen (300 mg every 12 hours, 0.5 hour infusion) was considered to be insufficient to obtain satisfactory therapeutic outcomes against low susceptible pathogens for elderly Chinese patients with LRTIs (CLcr = 70 ml/min).

GeneSearch™ BLN Assay could replace frozen section and touch imprint cytology for intra-operative assessment of breast sentinel lymph nodes.

BACKGROUND: Breast cancer sentinel lymph node (SLN) biopsy has become a common procedure. The GeneSearch™ Breast Lymph Node Assay is a real-time reverse-transcriptase polymerase chain reaction assay for detecting nodal metastases larger than 0.2 mm. The trial is a prospective multi-center clinical trial conducted to validate the assay in China. METHODS: Four hundred and seventy-nine consecutive prospective patients were enrolled from six centers. SLNs were sectioned along the short axis into multiple blocks. Odd blocks were tested by the assay intra-operatively, and even blocks were assessed by post-operative histology. Six 4- to 6-µm-thick sections were taken every 150 µm per block. In addition, intra-operative histological assessments were performed on the even blocks of 214 patients by frozen section (FS) and all blocks of 156 patients by touch imprint cytology (TIC). RESULTS: A total of 1046 SLNs were excised. Overall performance of the assay compared to post-operative histology was accuracy of 91.4 %, sensitivity of 87.5 %, and specificity of 92.9 %. There were no significant differences in assay performance of each center. After a learning curve of about 10 cases, the assay could be performed in a median time of about 35 min. The sensitivity of the assay was similar to the FS (84.9 %, P = 0.885) and was significantly higher than the TIC (70.0 %, P = 0.007) while the specificity of all were comparable. CONCLUSION: The GeneSearch™ Breast Lymph Node Assay is an accurate and rapid intra-operative assay for breast SLNs and it can replace FS and TIC for application.

Comparative study of one-step nucleic acid amplification assay, frozen section, and touch imprint cytology for intraoperative assessment of breast sentinel lymph node in Chinese patients.

UNLABELLED: Conventional procedures for the intraoperative assessment of breast cancer sentinel lymph nodes (SLNs) are frozen section (FS) and touch imprint cytology (TIC). The one-step nucleic acid amplification (OSNA) assay is a novel molecular technique. The aim of this study was to evaluate the optimal approach by comparing OSNA assay, FS, and TIC. Five hundred and fifty-two consecutive patients were enroled from five study centers in China. The SLNs were cut into alternating 2 mm blocks. The odd blocks were tested by the OSNA assay intraoperatively, and the even ones were assessed by postoperative histology (four 4- to 6-µm-thick sections were taken every 200 µm per block). In addition, intraoperative histological assessments were carried out on the even blocks of 211 patients by FS and all blocks of 552 patients by TIC. Overall performance of the assay compared to postoperative histology was: accuracy 91.4%; sensitivity 83.7%; and specificity 92.9%. The sensitivity of the assay was higher than FS (211 patients, 77.6% vs 69.7%; not significant, P = 0.286) and was significantly higher than TIC (552 patients, 83.6% vs 76.2%; P = 0.044). When assessing nodes with micrometastases, the sensitivity of the assay was higher than FS (17 nodes, 47.1% vs 23.5%; not significant, P = 0.289) and was significantly higher than TIC (48 nodes, 62.5% vs 35.4%; P = 0.007). The study indicated that the OSNA assay is an accurate and rapid intraoperative assay for assessing breast SLNs and it can replace FS and TIC for application in general medical practice. The trial was registered as: OSNA assay China Registration Study. CLINICAL TRIAL REGISTRATION NUMBER: China Breast Cancer Clinical Study Group 001c.

Temperature dependence of circular DNA topological states.

Circular double-stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo simulation, we predict the temperature dependence of the linking number distribution of small circular DNAs. Our predictions are based on flexible defect excitations that resulted from local melting or unstacking of DNA base pairs. We found that the reduced bending rigidity alone can lead to measurable changes of the variance of linking number distribution of short circular DNAs. If the defect is accompanied by local unwinding, the effect becomes much more prominent. The predictions can be easily investigated in experiments, providing a new method to study the micromechanics of sharply bent DNAs and the thermal stability of specific DNA sequences. Furthermore, the predictions are directly applicable to the studies of binding of DNA-distorting proteins that can locally reduce DNA rigidity, form DNA kinks, or introduce local unwinding.