Effects of supplemental irrigation on grain yield and water and nitrogen efficiencies of winter wheat in the North China Plain.

BACKGROUND: Aiming at unbalanced coordination of irrigation and fertilization of winter wheat in the eastern North China Plain, this study investigated the effect of fertigation on wheat grain yield, grain quality, and water use efficiency (WUE) and nitrogen use efficiency (NUE) in seven irrigation and nitrogen (N) fertilization treatments. Under the field conditions, the traditional irrigation and fertilization method (total N amount of 240 kg ha-1 , application of 90 kg ha-1 at sowing irrigation at jointing and anthesis, with topdressing N of 150 kg ha-1 at jointing) was used as the control (CK). There were six fertigation treatments to compare with CK. For the fertigation treatments, the total amount of N application was set to 180 kg ha-1 and 90 kg ha-1 was applied at sowing and the remaining N fertilizer was applied through fertigation. The fertigation treatments included the combination of three fertigation frequencies (S2: at jointing and anthesis; S3: at jointing, anthesis, and filling; S4: at jointing, booting, anthesis, and filling) and two soil water replenishment depths (M1: 0-10 cm; M2: 0-20 cm). The six treatments were S4M2, S4M1, S3M2, S3M1, S2M2, and S2M1. RESULT: Compared with CK, three and four irrigations (S3 and S4) maintained higher soil and plant analyzer development value and photosynthetic rate after anthesis. These treatments increased soil water extraction while reducing crop water consumption during the whole growing season, promoted the assimilation and translocation of dry matter into the grain after anthesis, and increased the 1000-grain weight. These fertigation treatments also significantly increased WUE and NUE. At the same time, the high grain protein content and grain protein yield were maintained. Compared with the CK, high wheat yield was maintained by S3M1 (drip irrigation fertilizer at the jointing, anthesis, and filling, and the depth of the moisture replenishment is 10 cm). This fertigation treatment significantly increased yield by 7.6%, WUE by 30%, NUE by 41.4%, and partial factor productivity from applied N by 25.8%; grain yield, grain protein content, and grain protein yield also performed well. CONCLUSION: Consequently, S3M1 treatment was suggested to be a good practice for reducing irrigation water and N input in the eastern North China Plain. © 2023 Society of Chemical Industry.

Recent Advances in Microgels: From Biomolecules to Functionality.

The emerging applications of hydrogel materials at different length scales, in areas ranging from sustainability to health, have driven the progress in the design and manufacturing of microgels. Microgels can provide miniaturized, monodisperse, and regulatable compartments, which can be spatially separated or interconnected. These microscopic materials provide novel opportunities for generating biomimetic cell culture environments and are thus key to the advances of modern biomedical research. The evolution of the physical and chemical properties has, furthermore, highlighted the potentials of microgels in the context of materials science and bioengineering. This review describes the recent research progress in the fabrication, characterization, and applications of microgels generated from biomolecular building blocks. A key enabling technology allowing the tailoring of the properties of microgels is their synthesis through microfluidic technologies, and this paper highlights recent advances in these areas and their impact on expanding the physicochemical parameter space accessible using microgels. This review finally discusses the emerging roles that microgels play in liquid-liquid phase separation, micromechanics, biosensors, and regenerative medicine.

Differences in cytokine and chemokine profiles in cerebrospinal fluid caused by the etiology of cryptococcal meningitis and tuberculous meningitis in HIV patients.

The roles of cytokines and chemokines in HIV-associated cryptococcal meningitis (HCM) and HIV-associated tuberculous meningitis (HTBM) are debatable. In sum, 34 HIV-infected patients without meningitis, 44 HCM patients and 27 HTBM patients were enrolled for study. The concentrations of 22 cytokines/chemokines in cerebrospinal fluid (CSF) were assayed at admission. Principal component analysis (PCA), Pearson's and logistic regression analyses were used to assess the role of cytokines/chemokines in HCM and HTBM. We found the levels of T helper (Th)17, Th1 [interleukin (IL)-12p40, interferon (IFN)-γ, tumor necrosis factor (TNF)-α and TNF-ß and Th2 (IL-2/4/5/6/10)] cytokines were elevated in patients with meningitis compared with those in HIV-infected patients without central nervous system (CNS) infection. Furthermore, the IL-1Ra, IL-12p40, IL-17α and monocyte chemotactic protein-1 (MCP-1) levels were higher in HCM patients, while the IFN-γ, regulated upon activation, normal T cell expressed and secreted (RANTES) and interferon-inducible protein-10 (IP)-10 levels were higher in HTBM patients. Elevated CSF concentrations of IL-17a, TNF-ß, IL-5, IL-12p40 and IL-1Rα were closely related to meningitis, but elevated IP-10, MCP-1, RANTES and IFN-γ levels and CSF white blood cells (WBCs) were protective factors against HCM. Our study suggested that HIV-infected patients with low CSF WBCs have a high risk of HCM. Th1, Th2 and Th17 cytokines/chemokines mediate differences in the pathogenesis of HCM and TBM. Overexpressed proinflammatory MCP-1, RANTES, IFN-γ and IP-10 in CSF are protective factors against HCM but not HTBM.

Microfluidic Templating of Spatially Inhomogeneous Protein Microgels.

3D scaffolds in the form of hydrogels and microgels have allowed for more native cell-culture systems to be developed relative to flat substrates. Native biological tissues are, however, usually spatially inhomogeneous and anisotropic, but regulating the spatial density of hydrogels at the microscale to mimic this inhomogeneity has been challenging to achieve. Moreover, the development of biocompatible synthesis approaches for protein-based microgels remains challenging, and typical gelation conditions include UV light, extreme pH, extreme temperature, or organic solvents, factors which can compromise the viability of cells. This study addresses these challenges by demonstrating an approach to fabricate protein microgels with controllable radial density through microfluidic mixing and physical and enzymatic crosslinking of gelatin precursor molecules. Microgels with a higher density in their cores and microgels with a higher density in their shells are demonstrated. The microgels have robust stability at 37 °C and different dissolution rates through enzymolysis, which can be further used for gradient scaffolds for 3D cell culture, enabling controlled degradability, and the release of biomolecules. The design principles of the microgels could also be exploited to generate other soft materials for applications ranging from novel protein-only micro reactors to soft robots.

Lipid-Stabilized Double Emulsions Generated in Planar Microfluidic Devices.

Microemulsions have found a wide range of applications exploiting their chemical and physical properties. Development of microfluidic-based approaches has allowed for the controlled production of highly monodispersed emulsions, including the formation of multiple and hierarchical emulsions. Conventional poly(dimethylsiloxane)-based microfluidic systems require tight spatial control over the surface chemistry when used for double emulsion generation, which can be challenging to achieve on the micrometer scale. Here, we present a two-dimensional device design, which can selectively be surface-treated in a straightforward manner and allows for the formation of uniform water/oil/water double emulsions by combining two distinct hydrophilic and hydrophobic surface properties. These surfaces are sufficiently separated in space to allow for imparting their functionalization without the requirement for lithographic approaches or complex flow control. We demonstrate that a mismatch between the wettability requirements of the continuous phase and the channel wall inherent in this approach can be tolerated over several hundreds of micrometers, opening up the possibility to use simple pressure-driven flows to achieve surface functionalization. The design architecture exhibits robust efficiency in emulsion generation while retaining simple device fabrication. We finally demonstrate the potential of this approach by generating water in oil in water emulsions with lipid molecules acting as surfactants.

Chemokine and Cytokine Cascade Caused by Skewing of the Th1-Th2 Balance Is Associated with High Intracranial Pressure in HIV-Associated Cryptococcal Meningitis.

PURPOSE: Serum cytokines/chemokines play important roles in cryptococcal meningitis, but it is unclear whether cytokines/chemokines in cerebrospinal fluid (CSF) contribute to high intracranial pressure (HICP) in HIV-associated cryptococcal meningitis (HCM). METHODS: CSF cytokines/chemokines were assayed in 17 HIV-uninfected patients, 26 HIV-infected patients without CNS infection, and 39 HCM patients at admission. Principal component analysis and correlation and logistic regression analyses were used to assess the relationships between these parameters. RESULTS: The CSF Th1, Th2, and macrophage cytokines showed an obvious increase in HCM patients as compared to the HIV-uninfected patients and HIV-infected patients without CNS infection. CSF IL-6, GM-CSF, and IL-8 were positively correlated with CSF fungal burden. Serum CD4 count, CSF Th1 cytokines (TNF-α, TNF-ß, IL-12, IL-1ß, IL-12, IL-1α, TNF-α, TNF-ß, IL-12, IL-1γ, and IL-12) and Th2 cytokines (IL-4 and IL-10) contribute to HICP. CONCLUSION: Overall, the present findings indicated that both pro- and anti-inflammatory cytokines of Th1, Th2, and macrophage origin contributed to the development of HCM. Specifically, the chemokine and cytokine cascade caused by skewing of the Th1-Th2 balance and reduced CD4 count were found to be important contributors to HICP. Summary. Our research suggested that chemokine and cytokine cascade caused by skewing of the Th1-Th2 balance in HIV-infected patients played more important role than Cryptococcus numbers and size in CSF on the development of high intracranial pressure in HIV-associated cryptococcal meningitis, providing a new understanding of mechanisms of HCM.

Characterization of HIV-1 subtypes and transmitted drug resistance among treatment-naive HIV-infected individuals in Zhejiang, China, 2014-2017.

In recent years, transmitted drug resistance (TDR) has adversely impacted upon first-line therapy for HIV-infected individuals. To understand the current subtype distribution and TDR level in Zhejiang, China we performed phylogenetic analysis and genotypic drug resistance testing of treatment-naive HIV-infected individuals. A total of 153 HIV-1 Pol genes were successfully amplified. The distribution of HIV-1 genotypes was as follows: CRF01_AE (43.8%); CRF07_BC (37.9%); subtype B/B' (7.2%); CRF08_BC (5.2%); and others (5.9%). Drug resistance analysis demonstrated that 11.1% of isolates contained at least one NRTI or NNRTI resistance-associated mutations while 2.0% were identified to be resistant to PIs. These findings enhance our understanding of the genetic diversity of HIV-1 strains circulating in Zhejiang and provide some guidelines for HIV initial treatment therapy.

Fluid and cell behaviors along a 3D printed alginate/gelatin/fibrin channel.

Three-dimensional (3D) cell manipulation is available with the integration of microfluidic technology and rapid prototyping techniques. High-Fidelity (Hi-Fi) constructs hold enormous therapeutic potential for organ manufacturing and regenerative medicine. In the present paper we introduced a quasi-three-dimensional (Q3D) model with parallel biocompatible alginate/gelatin/fibrin hurdles. The behaviors of fluids and cells along the microfluidic channels with various widths were studied. Cells inside the newly designed microfluidic channels attached and grew well. Morphological changes of adipose-derived stem cells (ADSCs) in both two-dimensional (2D) and 3D milieu were found on the printed constructs. Endothelialization occurred with the co-cultures of ADSCs and hepatocytes. This study provides insights into the interactions among fluids, cells and biomaterials, the behaviors of fluids and cells along the microfluidic channels, and the applications of Q3D techniques.

Toe Box Shape of Running Shoes Affects In-Shoe Foot Displacement and Deformation: A Randomized Crossover Study.

BACKGROUND: Long-distance running is popular but associated with a high risk of injuries, particularly toe-related injuries. Limited research has focused on preventive measures, prompting exploration into the efficacy of raised toe box running shoes. PURPOSE: This study aimed to investigate the effect of running shoes with raised toe boxes on preventing toe injuries caused by distance running. METHODS: A randomized crossover design involved 25 male marathon runners (height: 1.70 ± 0.02 m, weight: 62.6 + 4.5 kg) wearing both raised toe box (extended by 8 mm along the vertical axis and 3 mm along the sagittal axis) and regular toe box running shoes. Ground reaction force (GRF), in-shoe displacement, and degree of toe deformation (based on the distance change between the toe and the metatarsal head) were collected. RESULTS: Wearing raised toe box shoes resulted in a significant reduction in vertical (p = 0.001) and antero-posterior (p = 0.015) ground reaction forces during the loading phase, with a notable increase in vertical ground reaction force during the toe-off phase (p < 0.001). In-shoe displacement showed significant decreased movement in the forefoot medial (p < 0.001) and rearfoot (medial: p < 0.001, lateral: p < 0.001) and significant increased displacement in the midfoot (medial: p = 0.002, lateral: p < 0.001). Impact severity on the hallux significantly decreased (p < 0.001), while impact on the small toes showed no significant reduction (p = 0.067). CONCLUSIONS: Raised toe box running shoes offer an effective means of reducing toe injuries caused by long-distance running.

Nitrogen metabolism in mycobacteria: the key genes and targeted antimicrobials.

Nitrogen metabolism is an important physiological process that affects the survival and virulence of Mycobacterium tuberculosis. M. tuberculosis's utilization of nitrogen in the environment and its adaptation to the harsh environment of acid and low oxygen in macrophages are closely related to nitrogen metabolism. In addition, the dormancy state and drug resistance of M. tuberculosis are closely related to nitrogen metabolism. Although nitrogen metabolism is so important, limited research was performed on nitrogen metabolism as compared with carbon metabolism. M. tuberculosis can use a variety of inorganic or organic nitrogen sources, including ammonium salts, nitrate, glutamine, asparagine, etc. In these metabolic pathways, some enzymes encoded by key genes, such as GlnA1, AnsP2, etc, play important regulatory roles in the pathogenesis of TB. Although various small molecule inhibitors and drugs have been developed for different nitrogen metabolism processes, however, long-term validation is needed before their practical application. Most importantly, with the emergence of multidrug-resistant strains, eradication, and control of M. tuberculosis will still be very challenging.

The central nervous system is a potential reservoir and possible origin of drug resistance in hepatitis B infection.

Background: The significance of hepatitis B virus (HBV) in cerebrospinal fluid (CSF) is unclear. Methods: Synchronous serum and CSF samples were collected from 13 patients. HBV DNA, full-length genome, quasispecies, phylogenetic tree, compartmentalization and mutation of the reverse transcriptase (RT) region were performed based on PCR and sequencing methods. Results: HBV DNA was detected in the CSF of 3 antiviral-naïve individuals and 1 individual after successful antiviral therapy. Complete full-length HBV genomes were isolated from the CSF of 5 individuals, including 2 with undetectable serum HBV DNA. Ten individuals exhibited distinct CSF-serum quasispecies, 8 harbored independent CSF-serum genetic compartmentalization and phylogenetic trees, and 5 lamivudine/entecavir-associated resistance mutations only in the CSF. The frequencies of rtL180M and rtM204I/V mutations in both serum and CSF were higher in HIV-HBV-coinfected individuals than in the HBV-monoinfected ones (serum: rtL180M: 3.9% vs. 0, P = 0.004; rtM204I/V: 21.3% vs. 0, P < 0.001; CSF: rtL180M: 7.6% vs. 0, P = 0.026; rtM204I/V 7.6% vs. 1.6%, P = 0.097). Conclusion: CSF is a potential HBV reservoir, and HBV in CSF harbors distinct evolution and mutation characteristics from those in serum. HIV infection increases the possibility of HBV rtL180M and rtM204I/V mutations in both serum and CSF.

Training of Deep Learning Pipelines on Memory-Constrained GPUs via Segmented Fused-Tiled Execution.

Training models with massive inputs is a significant challenge in the development of Deep Learning pipelines to process very large digital image datasets as required by Whole Slide Imaging (WSI) in computational pathology and analysis of brain fMRI images in computational neuroscience. Graphics Processing Units (GPUs) represent the primary workhorse in training and inference of Deep Learning models. In order to use GPUs to run inference or training on a neural network pipeline, state-of-the-art machine learning frameworks like PyTorch and TensorFlow currently require that the collective memory on the GPUs must be larger than the size of the activations at any stage in the pipeline. Therefore, existing Deep Learning pipelines for these use cases have been forced to develop sub-optimal "patch-based" modeling approaches, where images are processed in small segments of an image. In this paper, we present a solution to this problem by employing tiling in conjunction with check-pointing, thereby enabling arbitrarily large images to be directly processed, irrespective of the size of global memory on a GPU and the number of available GPUs. Experimental results using PyTorch demonstrate enhanced functionality/performance over existing frameworks.

Simulation of Fluid Flow during Egg Pickling under Different Inlet and Outlet Conditions in a Pulsed Pressure Tank with Liquid Circulation.

Pulsed pressure pickling is an emerging highly efficient osmotic dehydration technique. However, the immobility of the pickling liquid and the material, the formation of layers, and the uneven pickling efficiency in different sections make it difficult to use industrially. This work aims at improving and optimizing the conditions of fluid flow in the pickling tank with a liquid-cycle system to reduce the unevenness in the production process. Fluid flow around the eggs was numerically investigated by solving three-dimensional Reynolds-averaged Navier-Stokes equations within the flow regime, adopting different angles and positions at the inlet and outlet. The simulation results show that the inlet with a radial deflection of 35° and the outlet with axial direction were characterized by the best flow efficiency. Under these conditions, the average flow velocity and the global uniformity index were 0.153 m/s and 0.407, respectively. Furthermore, the experiments were carried out using an equivalent scale model of the pulsed pressure equipment with liquid circulation. The experimental results showed that, under optimal conditions, the salt content in all four layers of the egg white was about 2.8% after 48 h. This study provides a solution to ensure the constant salinity of different layers of pickled eggs and to improve pickling efficiency, especially in industrial-scale production.

Intrapatient Development of Multi-Class Drug Resistance in an Individual Infected with HIV-1 CRF01_AE.

The rapid expansion of access to antiretroviral therapy (ART) has led to the emergence of multi-class drug resistance (MDR) in people living with HIV (PLWH). However, the viral evolutionary dynamics of the development of MDR has not been well documented. For this study, plasma and peripheral blood mononuclear cells (PBMC) were longitudinally collected at different time points from a PLWH who suffered several periods of ART failure. Next generation sequencing (NGS) was used to analyze the distribution and percent of drug resistance mutations in PBMC and plasma. The results showed the gradual replacement of the wild type protease and integrase genotype by protease inhibitors (PI) and integrase strand transfer inhibitor (INSTI) drug resistant mutations when patient's ART regimen was changed - driving the increase of genetic variability in HIV DNA. Sampling for this study was initiated after the patient was first diagnosed with ART failure, five years after ART treatment was first initiated. By that time, mutants resistant to the reverse transcriptase inhibitor nevirapine (NVP) had already replaced almost 100% of wild type. After the introduction of the protease inhibitor lopinavir/ritonavir (LPV/r) to the patient's ART, resistant protease inhibitor (PI) mutants developed slowly. After one month, none were found in PMBC DNA; after sixteen months, less than 20% were mutants; and after three years (two months prior to the patient's death) PI mutants were still under 50%. However, integrase strand transfer inhibitor (INSTI) mutations evolved much more quickly, replacing approximately 75% of the wild genotype in HIV DNA one year after addition of the integrase inhibitor raltegravir to the patient's ART, and almost 100% after two years. In summary, our dataset provides the first analysis of the distribution and percent of drug resistance mutations in PBMC and plasma during the development of a four-class drug resistant HIV-1 CRF01_AE virion. The study also showed that months before drug resistant mutants could be found in plasma, NGS identified them in HIV DNA, demonstrating that this can be a very effective tool for early detection of the development of drug resistance.

Intrapatient Evolutionary Dynamics in an Individual Infected with HIV-1 CRF01_AE Who Experienced Periods of Treatment Failure.

Although previous studies have analyzed cross-level CRF01_AE viral genomic data in populations, less is known about intrapatient viral evolutionary dynamics during antiretroviral therapy (ART) failure. We longitudinally sampled plasma and peripheral blood mononuclear cells (PBMC) at different time points from one human immunodeficiency virus type 1 infected patient. The evolution of viral quasispecies was inferred from viral phylogenies. Before treatment, no drug-resistant mutations were found in this patient's plasma, and all viruses had C-C chemokine receptor type 5 (CCR5) tropism. Two months after treatment, the majority of the virus population in plasma and PBMC were drug resistant and X4-tropic. By 5 months after treatment, the viral load increased significantly, and viruses reversed tropism from X4 to R5 in plasma and PBMC. During treatment failure, the effective population of the pol DNA reservoir in PBMC remained stable, whereas the env DNA reservoir increased. The effective population of the R5 tropism virus increased more rapidly than that of the X4 tropism virus. The ratio of non-synonymous to synonymous substitutions in the env gene of R5 tropism virus (0.43) was lower than X4 tropism (0.52). However, four env positive selection sites were identified in R5 tropism viruses (HXB2: 364, 398, 399, and 400) but none were identified in X4 tropism viruses. Our data demonstrated the different intrapatient evolutionary dynamics patterns of env and pol genes in an individual who experienced periods of ART failure. Our findings also suggest the importance of the R5 tropism virus in the DNA reservoir during ART failure.

Liquid-Liquid Phase-Separated Systems from Reversible Gel-Sol Transition of Protein Microgels.

Liquid-liquid phase-separated biomolecular systems are increasingly recognized as key components in the intracellular milieu where they provide spatial organization to the cytoplasm and the nucleoplasm. The widespread use of phase-separated systems by nature has given rise to the inspiration of engineering such functional systems in the laboratory. In particular, reversible gelation of liquid-liquid phase-separated systems could confer functional advantages to the generation of new soft materials. Such gelation processes of biomolecular condensates have been extensively studied due to their links with disease. However, the inverse process, the gel-sol transition, has been less explored. Here, a thermoresponsive gel-sol transition of an extracellular protein in microgel form is explored, resulting in an all-aqueous liquid-liquid phase-separated system with high homogeneity. During this gel-sol transition, elongated gelatin microgels are demonstrated to be converted to a spherical geometry due to interfacial tension becoming the dominant energetic contribution as elasticity diminishes. The phase-separated system is further explored with respect to the diffusion of small particles for drug-release scenarios. Together, this all-aqueous system opens up a route toward size-tunable and monodisperse synthetic biomolecular condensates and controlled liquid-liquid interfaces, offering possibilities for applications in bioengineering and biomedicine.

Inactivation of Latent HIV-1 Proviral DNA Using Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Treatment and the Assessment of Off-Target Effects.

Viral DNA integrated in host cells is a major barrier to completely curing HIV-1. However, genome editing using the recently developed technique of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 has the potential to eradicate HIV-1. The present study aimed to use a lentiviral vector-based CRISPR/Cas9 system combined with dual-small/single guide RNAs (sgRNAs) to attack HIV-1 DNA in the latency reactivation model J-Lat 10.6 cell line and to assess off-target effects using whole-genome sequencing (WGS). We designed 12 sgRNAs targeting HIV-1 DNA, and selected high-efficiency sgRNAs for further pairwise combinations after a preliminary evaluation of the editing efficiency. Three combinations of dual-sgRNAs/Cas9 with high editing efficiency were screened successfully from multiple combinations. Among these combinations, the incidences of insertions and deletions in the sgRNA-targeted regions reached 76% and above, and no credible off-target sites were detected using WGS. The results provided comprehensive basic experimental evidence and methodological recommendations for future personalized HIV-1 treatment using CRISPR/Cas9 genome editing technology.

From Protein Building Blocks to Functional Materials.

Proteins are the fundamental building blocks for high-performance materials in nature. Such materials fulfill structural roles, as in the case of silk and collagen, and can generate active structures including the cytoskeleton. Attention is increasingly turning to this versatile class of molecules for the synthesis of next-generation green functional materials for a range of applications. Protein nanofibrils are a fundamental supramolecular unit from which many macroscopic protein materials are formed. In this Review, we focus on the multiscale assembly of such protein nanofibrils formed from naturally occurring proteins into new supramolecular architectures and discuss how they can form the basis of material systems ranging from bulk gels, films, fibers, micro/nanogels, condensates, and active materials. We review current and emerging approaches to process and assemble these building blocks in a manner which is different to their natural evolutionarily selected role but allows the generation of tailored functionality, with a focus on microfluidic approaches. We finally discuss opportunities and challenges for this class of materials, including applications that can be involved in this material system which consists of fully natural, biocompatible, and biodegradable feedstocks yet has the potential to generate materials with performance and versatility rivalling that of the best synthetic polymers.

Differences of cytotoxic T-lymphocyte pressure and divergent evolution of several CRF07_BC clusters circulating in men who have sex with men in China.

The HIV-1 CRF07_BC strain is now the major recombinant form in China among the population of men who have sex with men (MSM), and has critically contributed to the HIV-1 epidemic in recent years. The phylodynamic and virological differences among CRF07_BC clusters circulating in MSM, and the factors that could be driving their evolution, remains unclear. Using the HIV-1 CRF07_BC strains obtained from the Los Alamos HIV database, we undertook a large-scale phylogenetic analysis using the maximum likelihood method of partial gag, pol, and env segments to infer their evolutionary relationships. The demographic histories of clusters were determined using the Bayesian Markov chain Monte Carlo (MCMC) method. For four pol clusters we analyzed the non-synonymous (dN) to synonymous (dS) substitution rates and performed site to site analysis to identify positive selection sites and cytotoxic T-lymphocyte (CTL) escape mutation positions. MSM was found to be the predominant risk factor for all four of the CRF07_BC epidemic pol segment clusters with the largest number of infections. Two of those clusters had higher growth in the effective number of infections, and two clusters had slower growth. Analysis of all four clusters showed no significant differences in the mean substitution rates and dN/dS selection pressure ratios. However, a site to site codon analysis found thirteen significant positive selection sites. Ten of these sites are CTL escape mutations. The two clusters with the higher growth in infections had seven and eight pol segment CTL escape mutation sites respectively, while the two with slower growth had only one or two. Our findings demonstrated differences in the CTL escape mutation and divergent evolution of several CRF07_BC clusters circulating among men who have sex with men in China.

Beijing as the hub of CRF07_BC transmission from the intravenous drug users to men who have sex with men in China.

AIDS Research and Human Retroviruses officially retracts the Instant Online/Just Accepted version of the article entitled, "Beijing as the hub of CRF07_BC transmission from the intravenous drug users to men who have sex with men in China" (epub 7 Dec 2020; doi.org/10.1089/aid.2020.0147). A technical issue caused the unedited, accepted version to post online before all plagiarism checks were finalized. Those checks determined that there was too much duplication from previously published sources which prevented the continuance to final publication. The technical issue that caused the premature posting has since been corrected. AIDS Research and Human Retroviruses and its Publisher are committed to upholding the standards of scientific publishing and the community it serves. BACKGROUND: The HIV-1 CRF07_BC strain has been increasing in frequency in China, is now the major recombination subtype in the men who have sex with men (MSM) population. However, to date, the evolutionary history of CRF07_BC in MSM in China has not been explored in greater detail. METHODS: All available partial gag, pol and env segments of CRF07_BC were obtained from the Los Alamos HIV database. We performed phylogenetic analysis for these fragments by using the Bayesian Markov Chain Monte Carlo method, as implemented in BEAST. We estimated the history of viral migration between different areas over time using the discrete Bayesian phylogeographical method. RESULTS: Spatial reconstruction showed that Yunnan had the highest root state posterior probability (0.89 in pol, 0.60 in gag, 0.87 in env). The virus migrated from Yunnan to Beijing in 1990s through intravenous drug users (IDU). The highest root state posterior probability of MSM cluster is Beijing (0.93 in pol, 0.90 in gag and 0.37 in env). In the beginning of 2000s, Beijing became the primary epicenter as CRF07_BC had expanded their geographical distribution to many provinces in China in MSM population. Guangdong and Shanghai were secondary epicenters, with a large extent of viruses. CONCLUSIONS: This study highlighted the spatial and temporal spread of CRF07_BC in MSM population in China. It revealed that Beijing was the hub of CRF07_BC transmission from IDU to MSM in China.