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The aim of this study was to develop and externally validate a simple-to-use nomogram for predicting the survival of hospitalised human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) patients (hospitalised person living with HIV/AIDS (PLWHAs)). Hospitalised PLWHAs (n = 3724) between January 2012 and December 2014 were enrolled in the training cohort. HIV-infected inpatients (n = 1987) admitted in 2015 were included as the external-validation cohort. The least absolute shrinkage and selection operator method was used to perform data dimension reduction and select the optimal predictors. The nomogram incorporated 11 independent predictors, including occupation, antiretroviral therapy, pneumonia, tuberculosis, Talaromyces marneffei, hypertension, septicemia, anaemia, respiratory failure, hypoproteinemia and electrolyte disturbances. The Likelihood χ2 statistic of the model was 516.30 (P = 0.000). Integrated Brier Score was 0.076 and Brier scores of the nomogram at the 10-day and 20-day time points were 0.046 and 0.071, respectively. The area under the curves for receiver operating characteristic were 0.819 and 0.828, and precision-recall curves were 0.242 and 0.378 at two time points. Calibration plots and decision curve analysis in the two sets showed good performance and a high net benefit of nomogram. In conclusion, the nomogram developed in the current study has relatively high calibration and is clinically useful. It provides a convenient and useful tool for timely clinical decision-making and the risk management of hospitalised PLWHAs.
Combining different swine populations in genomic prediction can be an important tool, leading to an increased accuracy of genomic prediction using single nucleotide polymorphism (SNP) chip data compared with within-population genomic. However, the expected higher accuracy of multi-population genomic prediction has not been realized. This may be due to an inconsistent linkage disequilibrium (LD) between SNPs and quantitative trait loci (QTL) across populations, and the weak genetic relationships across populations. In this study, we determined the impact of different genomic relationship matrices, SNP density and pre-selected variants on prediction accuracy using a combined Yorkshire pig population. Our objective was to provide useful strategies for improving the accuracy of genomic prediction within a combined population. Results showed that the accuracy of genomic best linear unbiased prediction (GBLUP) using imputed whole-genome sequencing (WGS) data in the combined population was always higher than that within populations. Furthermore, the use of imputed WGS data always resulted in a higher accuracy of GBLUP than the use of 80K chip data for the combined population. Additionally, the accuracy of GBLUP with a non-linear genomic relationship matrix was markedly increased (0.87% to 15.17% for 80K chip data, and 0.43% to 4.01% for imputed WGS data) compared with that obtained with a linear genomic relationship matrix, except for the prediction of XD population in the combined population using imputed WGS data. More importantly, the application of pre-selected variants based on fixation index (Fst) scores improved the accuracy of multi-population genomic prediction, especially for 80K chip data. For BLUP|GA (BLUP approach given the genetic architecture), the use of a linear method with an appropriate weight to build a weight-relatedness matrix led to a higher prediction accuracy compared with the use of only pre-selected SNPs for genomic evaluations, especially for the total number of piglets born. However, for the non-linear method, BLUP|GA showed only a small increase or even a decrease in prediction accuracy compared with the use of only pre-selected SNPs. Overall, the best genomic evaluation strategy for reproduction-related traits for a combined population was found to be GBLUP performed with a non-linear genomic relationship matrix using variants pre-selected from the 80K chip data based on Fst scores.
Chlamydia trachomatis (CT) infection has been a major public health threat globally. Monitoring and prediction of CT epidemic status and trends are important for programme planning, allocating resources and assessing impact; however, such activities are limited in China. In this study, we aimed to apply a seasonal autoregressive integrated moving average (SARIMA) model to predict the incidence of CT infection in Shenzhen city, China. The monthly incidence of CT between January 2008 and June 2019 in Shenzhen was used to fit and validate the SARIMA model. A seasonal fluctuation and a slightly increasing pattern of a long-term trend were revealed in the time series of CT incidence. The monthly CT incidence ranged from 4.80/100 000 to 21.56/100 000. The mean absolute percentage error value of the optimal model was 8.08%. The SARIMA model could be applied to effectively predict the short-term CT incidence in Shenzhen and provide support for the development of interventions for disease control and prevention.
In order to map quantitative trait loci (QTLs) for allometries of body compositions and metabolic traits in chicken, we phenotypically characterize the allometric growths of multiple body components and metabolic traits relative to BWs using joint allometric scaling models and then establish random regression models (RRMs) to fit genetic effects of markers and minor polygenes derived from the pedigree on the allometric scalings. Prior to statistically inferring the QTLs for the allometric scalings by solving the RRMs, the LASSO technique is adopted to rapidly shrink most of marker genetic effects to zero. Computer simulation analysis confirms the reliability and adaptability of the so-called LASSO-RRM mapping method. In the F2 population constructed by multiple families, we formulate two joint allometric scaling models of body compositions and metabolic traits, in which six of nine body compositions are tested as significant, while six of eight metabolic traits are as significant. For body compositions, a total of 14 QTLs, of which 9 dominant, were detected to be associated with the allometric scalings of drumstick, fat, heart, shank, liver and spleen to BWs; while for metabolic traits, a total of 19 QTLs also including 9 dominant be responsible for the allometries of T4, IGFI, IGFII, GLC, INS, IGR to BWs. The detectable QTLs or highly linked markers can be used to regulate relative growths of the body components and metabolic traits to BWs in marker-assisted breeding of chickens.
Guangxi, a province in southwestern China, has the second highest reported number of HIV/AIDS cases in China. This study aimed to develop an accurate and effective model to describe the tendency of HIV and to predict its incidence in Guangxi. HIV incidence data of Guangxi from 2005 to 2016 were obtained from the database of the Chinese Center for Disease Control and Prevention. Long short-term memory (LSTM) neural network models, autoregressive integrated moving average (ARIMA) models, generalised regression neural network (GRNN) models and exponential smoothing (ES) were used to fit the incidence data. Data from 2015 and 2016 were used to validate the most suitable models. The model performances were evaluated by evaluating metrics, including mean square error (MSE), root mean square error, mean absolute error and mean absolute percentage error. The LSTM model had the lowest MSE when the N value (time step) was 12. The most appropriate ARIMA models for incidence in 2015 and 2016 were ARIMA (1, 1, 2) (0, 1, 2)12 and ARIMA (2, 1, 0) (1, 1, 2)12, respectively. The accuracy of GRNN and ES models in forecasting HIV incidence in Guangxi was relatively poor. Four performance metrics of the LSTM model were all lower than the ARIMA, GRNN and ES models. The LSTM model was more effective than other time-series models and is important for the monitoring and control of local HIV epidemics.
Alanyl-glutamine (Ala-Gln), a highly soluble and stable glutamine dipeptide, is known to improve gut integrity and function. The aim of this study was to evaluate whether dietary Ala-Gln supplementation could improve growth performance, intestinal development and digestive-absorption function in weaned piglets. A total of 100 purebred Yorkshire piglets weaned at 21 days of age were assigned randomly to four dietary treatment groups and fed a basal diet (control group) or a basal diet containing 0.15%, 0.30% and 0.45% Ala-Gln, respectively. Compared with the control group, piglets fed the Ala-Gln diets had higher average daily gain and lower feed : gain and diarrhea rate (P < 0.05). Moreover, dietary Ala-Gln supplementation increased villous height and villous height : crypt depth ratio in duodenum and jejunum (P < 0.05), as well as the activities of maltase and lysozyme in jejunum mucosa (P < 0.05). In addition, a decrease in serum diamine oxidase activity and crypt depth in duodenum and jejunum was observed in piglets fed the Ala-Gln diets (P < 0.05). Serum cytosolic phospholipase A2 (cPLA2) concentration and gene expression of cPLA2, Na+-dependent glucose transporter 1, glucose transporter 2 and peptide transporter 1 in jejunum were increased by feeding Ala-Gln diets relative to control diet (P < 0.05). These results indicated that feeding Ala-Gln diet has beneficial effects on the growth performance of weaned piglets, which associated with maintaining intestinal morphology and digestive-absorption function.
The association between opportunistic infection (OI) and anaemia among HIV-infected patients remains to be studied. We investigated the prevalence and risk factors of anaemia in hospitalised HIV-infected patients to reveal the association between OI and anaemia. We conducted a retrospective study of HIV-positive hospitalised patients from June 2016 to December 2017 in Mengchao Hepatobiliary Hospital of Fujian Medical University. Patients’ information on socio-demographic and clinical characteristics were carefully collected. The comparison of anaemia prevalence between groups was conducted with χ2 test. A logistic regression model was carried out to analyse the predictors of anaemia. The total prevalence of anaemia in hospitalised HIV-infected patients was 55.15%. The prevalence of mild, moderate and severe anaemia was 41.42%, 11.08% and 2.64%, respectively. Predictors independently associated with anaemia were: CD4 counts <50 cells/μl (odds ratio (OR): 6.376, 95% confidence interval (CI) = 1.916–21.215, P = 0.003), CD4 counts 50–199 cells/μl (OR: 6.303, 95% CI = 1.874–21.203, P = 0.003), co-infection with tuberculosis (TB) (OR: 2.703, 95% CI = 1.349–5.414, P = 0.005) or Penicillium marneffei (PM) (OR: 7.162, 95% CI = 3.147–15.299, P < 0.001). In Fujian, China, more than half inpatients with HIV were anaemic, but severe anaemia is infrequent. Lower CD4 counts, co-infection with TB or PM were independent risk factors for anaemia. Chinese HIV patients especially with TB, PM infection and low CD4 level should be routinely detected for anaemia to improve therapy.
Porphyrins are vital pigments involved in biological energy transduction processes. Their abilities to absorb light, then convert it to energy, have raised the interest of using porphyrin nanoparticles as photosensitizers in photodynamic therapy. A recent study showed that self- assembled porphyrin-silica composite nanoparticles can selectively destroy tumor cells, but detection of the cellular uptake of porphyrin-silica composite nanoparticles was limited to imaging microscopy. Here we developed a novel method to rapidly identify porphyrin-silica composite nanoparticles using Atmospheric Solids Analysis Probe-Mass Spectrometry (ASAP-MS). ASAP-MS can directly analyze complex mixtures without the need for sample preparation. Porphyrin-silica composite nanoparticles were vaporized using heated nitrogen desolvation gas, and their thermo-profiles were examined to identify distinct mass- to-charge (M/Z) signatures. HeLa cells were incubated in growth media containing the nanoparticles, and after sufficient washing to remove residual nanoparticles, the cell suspension was loaded onto the end of ASAP glass capillary probe. Upon heating, HeLa cells were degraded and porphyrin-silica composite nanoparticles were released. Vaporized nanoparticles were ionized and detected by MS. The cellular uptake of porphyrin-silica composite nanoparticles was identified using this ASAP-MS method.
Using whole-genome sequence (WGS) data are supposed to be optimal for genome-wide association studies and genomic predictions. However, sequencing thousands of individuals of interest is expensive. Imputation from single nucleotide polymorphisms panels to WGS data is an attractive approach to obtain highly reliable WGS data at low cost. Here, we conducted a genotype imputation study with a combined reference panel in yellow-feather dwarf broiler population. The combined reference panel was assembled by sequencing 24 key individuals of a yellow-feather dwarf broiler population (internal reference panel) and WGS data from 311 chickens in public databases (external reference panel). Three scenarios were investigated to determine how different factors affect the accuracy of imputation from 600 K array data to WGS data, including: genotype imputation with internal, external and combined reference panels; the number of internal reference individuals in the combined reference panel; and different reference sizes and selection strategies of an external reference panel. Results showed that imputation accuracy from 600 K to WGS data were 0.834±0.012, 0.920±0.007 and 0.982±0.003 for the internal, external and combined reference panels, respectively. Increasing the reference size from 50 to 250 improved the accuracy of genotype imputation from 0.848 to 0.974 for the combined reference panel and from 0.647 to 0.917 for the external reference panel. The selection strategies for the external reference panel had no impact on the accuracy of imputation using the combined reference panel. However, if only an external reference panel with reference size >50 was used, the selection strategy of minimizing the average distance to the closest leaf had the greatest imputation accuracy compared with other methods. Generally, using a combined reference panel provided greater imputation accuracy, especially for low-frequency variants. In conclusion, the optimal imputation strategy with a combined reference panel should comprehensively consider genetic diversity of the study population, availability and properties of external reference panels, sequencing and computing costs, and frequency of imputed variants. This work sheds light on how to design and execute genotype imputation with a combined external reference panel in a livestock population.
A flow corridor is a new class of trajectory-based airspace that encloses groups of flights which fly along the same path in one direction and accept responsibility for separation from each other. A well-designed corridor could reduce the airspace complexity, decrease the workload of air traffic controllers and increase the airspace capacity. This paper analyses the impact of different self-separation parameters on capacity and conflicts of the flow corridor. Both the quantitative impact and interaction effects of pairs of parameters are evaluated using the combined discrete-continuous model and Monte Carlo simulation method. The simulation results show that although the initial separation is the dominating factor, the interactions between initial separation and separation buffer, minimum separation, extra switch buffer, extra threshold buffer and velocity difference threshold also have some significant impacts on the capacity and conflicts for the flow corridor.
In the quest for dynamic multimodal probing of a material’s structure and functionality, it is critical to be able to quantify the chemical state on the atomic-/nanoscale using element-specific electronic and structurally sensitive tools such as electron energy-loss spectroscopy (EELS). Ultrafast EELS, with combined energy, time, and spatial resolution in a transmission electron microscope, has recently enabled transformative studies of photoexcited nanostructure evolution and mapping of evanescent electromagnetic fields. This article aims to describe state-of-the-art experimental techniques in this emerging field and its major uses and future applications.
To optimise patients’ outcomes and gain insight into transmitted drug resistance (TDR) among human immunodeficiency virus (HIV)-1 treatment-naive patients in Beijing, the prevalence of TDR was assessed. Demographic and clinical data of 1241 treatment-naive patients diagnosed between April 2014 and February 2015 were collected. TDR was defined using the Stanford University HIV drug resistance mutations database. The risk factors were evaluated by multi-logistic regression analysis. Among 932 successfully amplified cases, most were male (96.78%) and infected through men having sex with men (91.74%). Genotype were CRF01_AE (56.44%), B (20.60%), CRF07_BC (19.96%), C (1.61%) and other genotypes (1.39%). The overall prevalence of TDR was 6.12%. Most frequent mutations occurred in non-nucleoside reverse transcriptase inhibitors (NNRTIs) (3.11%), followed by protease inhibitors (PIs) (2.25%) and nucleoside reverse transcriptase inhibitors (NRTIs) (1.32%). Furthermore, HIV-1 genotype was associated with high risk of resistance, in which genotype C and other genotype may have higher risk for resistance. The prevalence among treatment-naive patients in Beijing was low. Resistance to NNRTIs was higher than with PIs or NRTIs. Continuous monitoring of regional levels of HIV-1 TDRs would contribute to improve treatment outcomes and prevent failures.
The variation of transitional flow features past a micro-ramp is investigated when the Reynolds number is decreased approaching the critical regime. Experiments are conducted in the incompressible flow spanning from supercritical to subcritical roughness-height-based Reynolds number (
, 730, 460 and 320) with tomographic particle image velocimetry. The effect of
on three-dimensional flow behaviour is analysed in a domain encompassing 73 ramp heights in the streamwise direction. Above the critical
, the primary vortex pair and induced central low-speed region in the mean flow field are active over longer range when decreasing
. In the instantaneous flow, at
, the hairpin vortices induced by Kelvin–Helmholtz (K–H) instability progress gradually from close to the micro-ramp into the region where the overall shear layer is destabilized, indicating the correlation between the K–H instability and the onset of transition. The breakdown of K–H vortices as observed at
, does not occur at lower
, the secondary vortex structures make their first appearance significantly downstream, postponing the formation of sideward disturbances, which destabilize the local shear layer by ejection events. Two major types of eigenmodes with symmetric and asymmetric spatial distribution of velocity fluctuations in the near wake are clearly identified by proper orthogonal decomposition. The symmetric and asymmetric modes correspond to the presence of vortex shedding and a sinuous wiggling motion respectively. It is found that
is the key factor determining the importance of the symmetric mode. At
, the disturbance energy of the symmetric mode decays before the onset of transition, suggesting that it is relatively insignificant in the process. However, decreasing
to 730 and 460, the symmetric mode produces continuous growth of high level disturbance energy, leading to transition.
Diarrhea is a common cause of morbidity and mortality and the incidence of diarrhea in the world has changed little over the past four decades. To assess the prevalence of and healthcare practices for diarrhea, a cross-sectional study was conducted in Pudong, Shanghai, China. In October 2014, a total of 5324 community residents were interviewed. Respondents were asked if they had experienced diarrhea (defined as ⩾3 passages of watery, loose, bloody, or mucoid stools within a 24-h period) in the previous month prior to the interview. The monthly prevalence of diarrhea was 4·1% (95% CI: 3·3–4·8), corresponding to an incidence rate of 0·54 episodes per person-year. The proportion of individuals with diarrhea who sought healthcare was 21·2% (95% CI: 13·4–29·0). Diarrhea continues to impose a considerable burden on the community and healthcare system in Pudong. Young age and travel were identified as predictors of increased diarrhea occurrence.
A highly efficient parallelization scheme of direct numerical simulation (DNS) for two-dimensional Rayleigh-Bénard convection is presented. By introducing the parallel diagonal dominant (PDD) algorithm to solve the pressure Poisson equation and adjusting the domain decomposition accordingly, all-to-all communication as the usual obstacle to parallel computing can be eliminated. Excellent strong scaling and weak scaling for the parallel efficiency are achieved. Numerical results show that very complex structures in flow exist at very high Ra numbers. The required high resolution both in space and in time can be obtained by the present method at low parallel overhead.
Biological tissues have complex, three-dimensional (3D) organizations of cells and matrix factors that provide the architecture necessary to meet morphogenic and functional demands. Disordered cell alignment is associated with congenital heart disease, cardiomyopathy, and neurodegenerative diseases and repairing or replacing these tissues using engineered constructs may improve regenerative capacity. However, optimizing cell alignment within engineered tissues requires quantitative 3D data on cell orientations and both efficient and validated processing algorithms. We developed an automated method to measure local 3D orientations based on structure tensor analysis and incorporated an adaptive subregion size to account for multiple scales. Our method calculates the statistical concentration parameter, κ, to quantify alignment, as well as the traditional orientational order parameter. We validated our method using synthetic images and accurately measured principal axis and concentration. We then applied our method to confocal stacks of cleared, whole-mount engineered cardiac tissues generated from human-induced pluripotent stem cells or embryonic chick cardiac cells and quantified cardiomyocyte alignment. We found significant differences in alignment based on cellular composition and tissue geometry. These results from our synthetic images and confocal data demonstrate the efficiency and accuracy of our method to measure alignment in 3D tissues.
Pig farmers and veterinarians have high prevalence of methicillin-resistant Staphylococcus aureus (MRSA) due to the occupational livestock exposure, while few reported this association on slaughterhouse workers. We conducted this cross-sectional study to explore the phenotypic and molecular characteristics of S. aureus and MRSA in slaughterhouse pig-related workers and control workers in Guangdong Province, China. Participants were interviewed and provided two nasal swabs. Swabs were tested for S. aureus, and isolates were further tested for antimicrobial susceptibility, virulence genes and multi-locus sequence typing. Compared with control workers, pig-related workers have significantly higher prevalence of MRSA carriage (adjusted odd ratio (aOR) 3·70, 95% CI 1·63–8·40). The proportions of MRSA resistant to clindamycin, erythromycin, tetracycline or chloromycetin were significantly higher in pig-related workers than in control workers. The predominant phenotypes of S. aureus were resistant to penicillin, clindamycin, erythromycin and tetracycline. Three MRSA CC9 isolates with livestock-associated characteristics (resistance to tetracycline and absence of immune evasion cluster (IEC) genes) were detected in pig-related workers but not in control workers. For human-associated CCs (CC7, CC59, CC6, and CC188), there was no significant difference in IEC profile or antimicrobial resistance between the groups. These findings reveal that there may be a potential risk for livestock-to-human transmission of LA-MRSA and human-to-human transmission of human-associated MRSA.
In this paper, we perform an absolute equation of state (EOS) measurement on the principal Hugoniot of aluminum using a near-symmetric impact method. The flyer plates are accelerated to high velocities using the laser-ramp-driven method. An aluminum flyer plate of ~25 µm is accelerated to the velocity range from 4 to 12 km/s. Then the aluminum flyer plate propagates across a vacuum gap and impacts with an aluminum step target. A line-imaging optical recording velocity interferometer for any reflector (ORVIS) is used to measure the aluminum flyer plate and the shock velocity simultaneously. Aluminum EOS data were measured with pressures range from 50 to 200 GPa. This absolute EOS measurement method may be used for studying a variety of materials.