Quantifying the partial ionization effect of gold in the transition region between condensed matter and warm dense matter.

It is now well known that solids under ultra-high-pressure shock compression will enter the warm dense matter (WDM) regime which connects condensed matter and hot plasma. How condensed matter turns into the WDM, however, remains largely unexplored due to the lack of data in the transition pressure range. In this letter, by employing the unique high-Z three-stage gas gun launcher technique developed recently, we compress gold into TPa shock pressure to fill the gap inaccessible by the two-stage gas gun and laser shock experiments. With the aid of high-precision Hugoniot data obtained experimentally, we observe a clear softening behavior beyond ~560 GPa. The state-of-the-art ab-initio molecular dynamics calculations reveal that the softening is caused by the ionization of 5d electrons in gold. This work quantifies the partial ionization effect of electrons under extreme conditions, which is critical to model the transition region between condensed matter and WDM.

TransMeta simultaneously assembles multisample RNA-seq reads.

Assembling RNA-seq reads into full-length transcripts is crucial in transcriptomic studies and poses computational challenges. Here we present TransMeta, a simple and robust algorithm that simultaneously assembles RNA-seq reads from multiple samples. TransMeta is designed based on the newly introduced vector-weighted splicing graph model, which enables accurate reconstruction of the consensus transcriptome via incorporating a cosine similarity-based combing strategy and a newly designed label-setting path-searching strategy. Tests on both simulated and real data sets show that TransMeta consistently outperforms PsiCLASS, StringTie2 plus its merge mode, and Scallop plus TACO, the most popular tools, in terms of precision and recall under a wide range of coverage thresholds at the meta-assembly level. Additionally, TransMeta consistently shows superior performance at the individual sample level.

Highly efficient clustering of long-read transcriptomic data with GeLuster.

MOTIVATION: The advancement of long-read RNA sequencing technologies leads to a bright future for transcriptome analysis, in which clustering long reads according to their gene family of origin is of great importance. However, existing de novo clustering algorithms require plenty of computing resources. RESULTS: We developed a new algorithm GeLuster for clustering long RNA-seq reads. Based on our tests on one simulated dataset and nine real datasets, GeLuster exhibited superior performance. On the tested Nanopore datasets it ran 2.9-17.5 times as fast as the second-fastest method with less than one-seventh of memory consumption, while achieving higher clustering accuracy. And on the PacBio data, GeLuster also had a similar performance. It sets the stage for large-scale transcriptome study in future. AVAILABILITY AND IMPLEMENTATION: GeLuster is freely available at https://github.com/yutingsdu/GeLuster.

TGF-ß1 and TGF-ßR1 variants are associated with clinical outcomes in smoking-related head and neck cancer patients treated with chemoradiation through modulating microRNA-mediated regulation.

TGF-ß1 and TGF-ßR1 play important roles in immune and inflammatory responses. Genetic variants of TGF-ß1 rs1800470 and TGF-ßR1 rs334348 have emerged as potentially prognostic biomarkers for HPV-related head and neck cancer, while their prognostic effect on survival of smoking-related head and neck cancer remains unknown. This study included 1403 patients with smoking-related head and neck cancer, and all these patients were genotyped for TGF-ß1 rs1800470 and TGF-ßR1 rs334348. Both univariate and multivariate analyses were performed to evaluate associations between the two functional genetic variants in microRNA binding sites of TGF-ß1 and TGF-ßR1 and survivals. Patients with TGF-ß1 rs1800470 CT or CC genotype had 30-35% risk reductions for OS, DSS, and DFS compared to patients with TT genotype among overall patients, ever smokers, and patients administered chemoradiation. Furthermore, patients with TGF-ßR1 rs334348 GA or GG genotype had significant 50-60% risk reductions for OS, DSS, and DFS compared to patients with AA genotype among overall patients and patients administered chemoradiation; among ever smokers, the risk reductions even reached 60-70%. The TCGA dataset was used for validation. These findings suggest that TGF-ß1 rs1800470 and TGF-ßR1 rs334348 significantly affect survival outcomes in patients with smoking-related head and neck cancer, especially in the subgroups of ever smokers and patients treated with chemoradiation. These genetic variants may serve as prognostic indicators for patients with smoking-related head and neck cancer and could play a role in advancing the field of personalized chemoradiation, thereby improving patient survival and quality of life.

Potentially functional variants of CHMP4A and PANX1 in the pyroptosis-related pathway predict survival of patients with non-oropharyngeal head and neck squamous cell carcinoma.

BACKGROUND: Pyroptosis has been implicated in the advancement of various cancers. Triggering pyroptosis within tumors amplifies the immune response, thereby fostering an antitumor immune environment. Nonetheless, few published studies have evaluated associations between functional variants in the pyroptosis-related genes and clinical outcomes of patients with non-oropharyngeal head and neck squamous cell carcinoma (NON-ORO HNSCC). METHODS: We conducted an association study of 985 NON-ORO HNSCC patients who were randomly divided into two groups: the discovery group of 492 patients and the replication group of 493 patients. We used Cox proportional hazards regression analysis to examine associations between genetic variants of the pyroptosis-related genes and survival of patients with NON-ORO HNSCC. Bayesian false discovery probability (BFDP) was used for multiple testing correction. Functional annotation was applied to the identified survival-associated genetic variants. RESULTS: There are 8254 single-nucleotide polymorphisms (SNPs) located in 82 pyroptosis-related genes, of which 202 SNPs passed multiple testing correction with BFDP < 0.8 in the discovery and six SNPs retained statistically significant in the replication. In subsequent stepwise multivariable Cox regression analysis, two independent SNPs (CHMP4A rs1997996 G > A and PANX1 rs56175344 C > G) remained significant with an adjusted hazard ratios (HR) of 1.31 (95% confidence interval [CI] = 1.09-1.57, p = 0.004) and 0.65 (95% CI = 0.51-0.83, p = 0.0005) for overall survival (OS), respectively. Further analysis of the combined genotypes revealed progressively worse OS associated with the number of unfavorable genotypes (ptrend < 0.0001 and 0.021 for OS and disease-specific survival, respectively). Moreover, both PANX1 rs56175344G and CHMP4A rs1997996A alleles were correlated with reduced mRNA expression levels. CONCLUSIONS: Genetic variants in the pyroptosis pathway genes may predict the survival of NON-ORO HNSCC patients, likely by reducing the gene expression, but our findings need to be replicated by larger studies.

Expression of RIPK1 and FADD are associated with chemosensitivity and survival in head and heck squamous cell carcinoma via tanshinone IIA-mediated modulation of the RIPK1-FADD-Caspase 8 complex.

Tanshinone IIA (Tan IIA), a main active ingredient of salvia miltiorrhiza, has a wide range of antitumor effects, while its specific role and mechanism in head and neck squamous cell carcinomas (HNSCC) is not fully understood. Totally 59 primary HNSCC patients underwent two courses of induction chemotherapy before surgery. The association between expression of Fas-Associated Death Domain (FADD) and receptor interacting protein kinase 1 (RIPK1) and chemotherapy resistance and survival were evaluated. The cell counting kit-8 was used to detect the effect of Tan IIA on the activity of cisplatin in chemoresistant HNSCC cells through a series of in vitro experiments. The quantitative real-time reverse-transcription polymerase chain reaction, Western blot analysis and flow cytometry were used. FADD and RIPK1 expressions were differentially expressed in Chemosensitive and drug-resistant patients. Furthermore, patients with tumors exhibiting high expression of FADD and RIPK1 had significantly greater risk for chemoresistance and mortality than patients with tumors that had low levels of these proteins. Moreover, Tan IIA reduced the expression of RIPK1 and FADD in HNSCC chemoresistant cell lines, which could increase the chemosensitivity of cisplatin and promote apoptosis. Overexpression of RIPK1 led to attenuation of therapeutic effects of Tan IIA, which were mainly realized through regulation of the RIPK1-FADD-Caspase 8 complex. This study is the first to demonstrate the clinical value and role of FADD and RIPK1 in the treatment of HNSCC. This work establishes the proapoptotic effects of Tan IIA and its potential to enhance chemosensitivity in HNSCC by modulating the RIPK1-FADD-Caspase 8 complex.

Genetic variations associated with telomere length predict the risk of recurrence of non-oropharyngeal head and neck squamous cell carcinoma.

Genetic factors underlying lymphocyte telomere length (LTL) may provide insights into genomic stability and integrity, with direct links to susceptibility to cancer recurrence. Polymorphisms in telomere-associated genes are strongly associated with LTL and cancer risk, while few large studies have explored the associations between LTL-related polymorphisms and recurrence risk of non-oropharyngeal head and neck squamous cell carcinoma (non-OPHNSCC). Totally 1403 non-OPHNSCC patients were recruited and genotyped for 16 LTL-related polymorphisms identified by genome-wide association studies. Univariate and multivariate analyzes were performed to evaluate associations between the polymorphisms and non-OPHNSCC recurrence risk. Patients carrying rs755017 GA/GG, rs2487999 TC/TT, rs2736108 TC/TT, or rs6772228 AT/AA genotypes exhibited shorter DFS than those with the rs755017 AA, rs2487999 CC, rs2736108 CC, or s6772228 TT genotypes, respectively (all log-rank p < 0.05). Multivariable analysis confirmed an increased risk of recurrence for patients carrying rs755017 GA/GG, rs2487999 TC/TT, rs2736108 TC/TT, or rs6772228 AT/AA genotypes (adjusted hazard ratio [aHR]: 1.66, 95% confidence interval [CI]: 1.32-2.07; aHR: 1.77, 95% CI: 1.41-2.23; aHR: 1.56, 95% CI: 1.22-1.99; aHR: 1.52, 95% CI: 1.20-1.93, respectively). Further stratified analysis revealed stronger associations between these genotypes and recurrence risk in ever-smokers and patients undergoing chemoradiotherapy. The similar but particularly pronounced results were observed for the combined risk genotypes of the four significant polymorphisms. This is the first large study on non-OPHNSCC patients showing that LTL-related polymorphisms may modify risk of non-OPHNSCC recurrence individually and jointly, particularly when analyzed in the context of smoking status and personized treatment. Larger studies are needed to validate these results.

Early clinical efficacy of pegylated interferon treatment in patients with different phases of chronic HBV infection: A real-world analysis.

Although there are therapeutic advantages for hepatitis B virus (HBV) withpegylated interferon alpha (peg-IFNα) treatment compared with nucleos(t)ide analog (NAs) therapy, the effect difference in infected population at different phases has not been well established. We studied the clinical efficacy of peg-IFNα in two populations with HBV infection, including inactive HBsAg carrier (IHC) and chronic hepatitis B (CHB). A total of 328 HBV-infected patients were included in this real-world analysis. Patients were divided into two groups according to the infected stages. Peg-IFNα monotherapy or combination therapy with NAs were used in IHCs, and peg-IFNα added-on NAs therapy was applied to patients with CHB. The primary efficacy endpoint was HBsAg loss at Week 24. Results: The Kaplan-Meier cumulative rates of HBsAg loss were 39.50% (n = 47/119) in IHC group and 28.71% (n = 60/209) in CHB group at Week 24 (p < .05). After Propensity Score Matching (PSM), the HBsAg loss rates were 36.84% (n = 35/95) and 32.63% (n = 31/95), respectively (p > .05). Patients with baseline HBsAg level < 100 IU/ml achieved higher rates of HBsAg clearance in IHC and CHB group (before PSM: 47.44% vs. 42.86%, after PSM: 49.12% vs. 45.83%, all p values > .05). Baseline HBsAg level and its level decline from baseline to Week 12 can be as the predictors for HBsAg loss at Week 24 in both groups. Hence, the efficacy of HBsAg clearance was broadly similar between IHCs and NA-treated CHB patients during the early peg-IFNα therapy. A significant downward trend of HBsAg level was observed in both groups during peg-IFNα therapy.

Joint effect of human papillomavirus exposure, smoking and alcohol on risk of oral squamous cell carcinoma.

BACKGROUND: Smoking, alcohol consumption, and human papillomavirus (HPV) infection are known risk factors for oral squamous cell carcinoma (OSCC) including SCC of oropharynx (SCCOP) and SCC of oral cavity (SCCOC). Researchers have examined each of these risk factors independently, but few have observed the potential risk of their interaction. This study investigated the interactions among these risk factors and risk of OSCC. METHODS: Totally 377 patients with newly diagnosed SCCOP and SCCOC and 433 frequency-matched cancer-free controls by age and sex were included. Multivariable logistic regression was performed to calculate ORs and 95% CIs. RESULTS: We found that overall OSCC risk was independently associated with smoking (adjusted OR(aOR), 1.4; 95%CI, 1.0-2.0), alcohol consumption (aOR, 1.6; 95%CI, 1.1-2.2), and HPV16 seropositivity (aOR, 3.3; 95%CI, 2.2-4.9), respectively. Additionally, we found that HPV16 seropositivity increased the risk of overall OSCC in ever-smokers (aOR, 6.8; 95%CI, 3.4-13.4) and ever-drinkers (aOR, 4.8; 95%CI, 2.9-8.0), while HPV16-seronegative ever-smokers and ever-drinkers had less than a twofold increase in risk of overall OSCC (aORs, 1.2; 95%CI, 0.8-1.7 and 1.8; 95%CI, 1.2-2.7, respectively). Furthermore, the increased risk was particularly high for SCCOP in HPV16-seropositive ever-smokers (aOR, 13.0; 95%CI, 6.0-27.7) and in HPV16-seropositive ever-drinkers (aOR, 10.8; 95%CI, 5.8-20.1), while the similar increased risk was not found in SCCOC. CONCLUSION: These results suggest a strong combined effect of HPV16 exposure, smoking, and alcohol on overall OSCC, which may indicate a strong interaction between HPV16 infection and smoking and alcohol consumption, particularly for SCCOP.

RNANetMotif: Identifying sequence-structure RNA network motifs in RNA-protein binding sites.

RNA molecules can adopt stable secondary and tertiary structures, which are essential in mediating physical interactions with other partners such as RNA binding proteins (RBPs) and in carrying out their cellular functions. In vivo and in vitro experiments such as RNAcompete and eCLIP have revealed in vitro binding preferences of RBPs to RNA oligomers and in vivo binding sites in cells. Analysis of these binding data showed that the structure properties of the RNAs in these binding sites are important determinants of the binding events; however, it has been a challenge to incorporate the structure information into an interpretable model. Here we describe a new approach, RNANetMotif, which takes predicted secondary structure of thousands of RNA sequences bound by an RBP as input and uses a graph theory approach to recognize enriched subgraphs. These enriched subgraphs are in essence shared sequence-structure elements that are important in RBP-RNA binding. To validate our approach, we performed RNA structure modeling via coarse-grained molecular dynamics folding simulations for selected 4 RBPs, and RNA-protein docking for LIN28B. The simulation results, e.g., solvent accessibility and energetics, further support the biological relevance of the discovered network subgraphs.

HYOU1 promotes cell proliferation, migration, and invasion via the PI3K/AKT/FOXO1 feedback loop in bladder cancer.

BACKGROUND: Hypoxia up-regulated 1 (HYOU1) was identified as a proto-oncogene and involved in tumorigenesis and progression in several cancer. Nonetheless, the biological function and mechanism of HYOU1 in bladder cancer (BCa) remian unclear. METHODS: The HYOU1 level in BCa tissues and cells was examined using RT-qPCR and western blot methods. The relationship between HYOU1 expression and clinicopathologic characteristics of BCa was analyzed. The biological role of HYOU1 on BCa cell proliferation, apoptosis, migration and invasion were analyzed via counting kit-8 (CCK-8), flow cytometry, wound healing and Transwell assays, respectively. The association between HYOU1 and the PI3K/AKT/Forkhead box O1 (FOXO1) signalling was assessed via western blot assay, meanwhile the the association of FOXO1 with HYOU1 was also investigated. RESULTS: HYOU1 was up-regulated in BCa tissues and cell lines, and the high level of HYOU1 was associated with bladder cancer histological grade and pathologic stage. Moreover, patients with high expression of HYOU1 showed poor overall survival from Kaplan-Meier Plotter. HYOU1 depletion impeded cell proliferation, migration and invasion, and induced cell apoptosis, while HYOU1 overexpression promoted cell proliferation, migration and invasion. Mechanically, our results showed that HYOU1 knockdown repressed PI3K/AKT/FOXO1 pathway and HYOU1 was negative regulated by FOXO1 in BCa. Significantly, we confirmed that the HYOU1/PI3K-AKT/FOXO1 negative feedback loop was involved in BCa cell proliferation, migration and invasion. CONCLUSION: These findings revealed that HYOU1 acted as a pro-oncogene on BCa progression, and it will be a possible target for BCa treatment.

Three-dimensional multiphysics coupling numerical simulation of a proton conductor solid oxide fuel cell based on multi-defect transport.

The conductivity of the electrolyte of a proton conductor solid oxide fuel cell is not only related to temperature, but also related to the humidity and oxygen partial pressure of the cathode and anode. The gas partial pressure and temperature of the cell have significant inhomogeneity in three-dimensional space, so it is extremely important to develop a multi-field coupled three-dimensional model to explore the electrochemical performance of the cell. In this study, a model is constructed that takes into account macroscopic heat and mass transfer, microscopic defect transport, and the reaction kinetics of defects. The results show that for thin cathodes, the ribs significantly affect the oxygen partial pressure and the concentration of defects on the cathode side. On both sides of the electrolyte membrane, the concentration of hydroxide ions increases with increasing gas humidity. The hydroxide ion concentration increases along the flow direction, but the concentration of O-site small polarons increases on the anode side and decreases on the cathode side. The conductivity of hydroxide ions is more sensitive to the humidity of the anode side, while the conductivity of O-site small polarons is more sensitive to the humidity of the cathode side. Increasing the humidity of the cathode side results in a significant decrease in the conductivity of the O-site small polarons. The contribution of the conductivity of oxygen vacancies to the total conductivity is negligible. The total conductivity on the cathode side is greater than that on the anode side; it is dominated by hydroxide ions on the anode side, and co-dominated by hydroxide ions and O-site small polarons on the cathode side. Increasing temperature significantly increases both partial and total conductivity. When hydrogen depletion occurs, the partial conductivities and the total conductivity exhibit a sharp increase downstream of the cell.

Risk factors for head and neck cancer in more and less developed countries: Analysis from the INHANCE consortium.

OBJECTIVE: We analyzed the pooled case-control data from the International Head and Neck Cancer Epidemiology (INHANCE) consortium to compare cigarette smoking and alcohol consumption risk factors for head and neck cancer between less developed and more developed countries. SUBJECTS AND METHODS: The location of each study was categorized as either a less developed or more developed country. We compared the risk of overall head and neck cancer and cancer of specific anatomic subsites associated with cigarette smoking and alcohol consumption. Additionally, age and sex distribution between categories was compared. RESULTS: The odds ratios for head and neck cancer sites associated with smoking duration differed between less developed and more developed countries. Smoking greater than 20 years conferred a higher risk for oral cavity and laryngeal cancer in more developed countries, whereas the risk was greater for oropharynx and hypopharynx cancer in less developed countries. Alcohol consumed for more than 20 years conferred a higher risk for oropharynx, hypopharynx, and larynx cancer in less developed countries. The proportion of cases that were young (<45 years) or female differed by country type for some HNC subsites. CONCLUSION: These findings suggest the degree of industrialization and economic development affects the relationship between smoking and alcohol with head and neck cancer.

A repeated dose 28-day oral toxicity study of sodium dehydroacetate (DHA-S) in Wistar rats.

Sodium dehydroacetate (DHA-S) is a food additive and preservative. The present study was conducted to investigate the potential toxicity of repeated oral doses of DHA-S. DHA-S was administered orally by gavage to Wistar rats at doses of 0, 50, 100, or 200 mg/kg BW/day for 28 days, after which growth indicators, clinical pathology, organ weights, and histopathology were determined. Body weight and food consumption were significantly reduced at doses of 100 or 200 mg/kg BW, and some hematological indexes and organ weight were significantly affected, particularly in female rats. At a dose of 200 mg/kg BW, the blood coagulation activities were significantly reduced in female rats. At a dose of 100 or 200 mg/kg BW, the main blood biochemical parameters of both sexes were obviously affected. Similar histological changes in the hepatic and renal tissues were observed in both the treated (200 mg/kg BW DHA-S) and control animals. Female rats were more susceptible to most of the toxic effects caused by DHA-S, which further indicating a gender difference in the toxic phenotype profile of rats. Based on these results, the no observed adverse effect level (NOAEL) of DHA-S was determined to be 50 mg/kg BW/day in rats.

The effect of lifting load on the kinematic characteristics of lumbar spinous process in vivo.

BACKGROUND: There are limited data on the in vivo natural kinematics of the lumbar spinous process. This paper intends to explore the effect of lifting load on the in vivo movement mode of the lumbar spinous process and its biomechanical changes. METHODS: Ten asymptomatic subjects between the ages of 25 and 39 underwent CT scans of the lumbar spine in the supine position, and 3D models of L3-L5 were constructed. Using a Dual Fluoroscopy Imaging System (DFIS), instantaneous orthogonal fluoroscopic images of each subject's flexion-extension, left-right bending, and left-right rotational movements were taken under different loads (0 kg, 5 kg, 10 kg). The supine CT model was matched, using computer software, to the bony contours of the images from the two orthogonal views, so that the instantaneous 3D vertebral position at each location could be quantified. A Cartesian coordinate system was ultimately constructed at the tip of the spinous process to obtain the 6DOF kinematic data of the spinous process. RESULTS: In different postural movements of the trunk, there was no significant difference in the rotation angle and translation range of the lumbar spinous process under different loads (P > 0.05). In flexion to extension motion, spinous processes mainly rotate < 4° along the medial and lateral axes and translate < 4 mm along the craniocaudal direction. In the left-right bending motion, spinous processes mainly rotate < 5° along the anterior and posterior axes, and the translation is mainly coupling < 2 mm. In the rotational motion, the spinous process is mainly coupled motion, the rotation range is less than 3°, and the translation range is less than 2 mm. The distance between spinous processes measured in the supine position was 6.66 ± 2.29 mm at L3/4 and 5.08 ± 1.57 mm at L4/5. CONCLUSION: The in vivo kinematics of the lumbar spinous process will not change significantly with increasing low load. In complex motion, the spinous process is dominated by coupling motion.

Genetic variants in CYP2B6 and HSD17B12 associated with risk of squamous cell carcinoma of the head and neck.

Polycyclic aromatic hydrocarbons (PAH) and tobacco-specific nitrosamines (TSNA) metabolism-related genes play an important role in the development of cancers. We assessed the associations of genetic variants in genes involved in the metabolism of PAHs and TSNA with risk of squamous cell carcinoma of the head and neck (SCCHN) in European populations using two published genome-wide association study datasets. In the single-locus analysis, we identified two SNPs (rs145533669 and rs35246205) in CYP2B6 to be associated with risk of SCCHN (P = 1.57 × 10-4 and .004, respectively), two SNPs (EPHX1 rs117522494 and CYP2B6 rs145533669) to be associated with risk of oropharyngeal cancer (P = .001 and .004, respectively), and one SNP (rs4359199 in HSD17B12) to be associated with risk of oral cancer (P = .006). A significant interaction effect was found between rs4359199 and drinking status on risks of SCCHN and oropharyngeal cancer (P < .05). eQTL and sQTL analyzes revealed that two SNPs (CYP2B6 rs35246205 and HSD17B12 rs4359199) were correlated with alternative splicing or mRNA expression levels of the corresponding genes in liver cells (P < .05 for both). In silico functional annotation suggested that these two SNPs may regulate mRNA expression by affecting the binding of transcription factors. Results from phenome-wide association studies presented significant associations between these genes and risks of other cancers, smoking behavior and alcohol dependence (P < .05). Thus, our study provided some insight into the underlying genetic mechanism of head and neck cancer, which warrants future functional validation.

Robust and ultrafast fiducial marker correspondence in electron tomography by a two-stage algorithm considering local constraints.

MOTIVATION: Electron tomography (ET) has become an indispensable tool for structural biology studies. In ET, the tilt series alignment and the projection parameter calibration are the key steps toward high-resolution ultrastructure analysis. Usually, fiducial markers are embedded in the sample to aid the alignment. Despite the advances in developing algorithms to find correspondence of fiducial markers from different tilted micrographs, the error rate of the existing methods is still high such that manual correction has to be conducted. In addition, existing algorithms do not work well when the number of fiducial markers is high. RESULTS: In this article, we try to completely solve the fiducial marker correspondence problem. We propose to divide the workflow of fiducial marker correspondence into two stages: (i) initial transformation determination, and (ii) local correspondence refinement. In the first stage, we model the transform estimation as a correspondence pair inquiry and verification problem. The local geometric constraints and invariant features are used to reduce the complexity of the problem. In the second stage, we encode the geometric distribution of the fiducial markers by a weighted Gaussian mixture model and introduce drift parameters to correct the effects of beam-induced motion and sample deformation. Comprehensive experiments on real-world datasets demonstrate the robustness, efficiency and effectiveness of the proposed algorithm. Especially, the proposed two-stage algorithm is able to produce an accurate tracking within an average of ⩽ 100 ms per image, even for micrographs with hundreds of fiducial markers, which makes the real-time ET data processing possible. AVAILABILITY AND IMPLEMENTATION: The code is available at https://github.com/icthrm/auto-tilt-pair. Additionally, the detailed original figures demonstrated in the experiments can be accessed at https://rb.gy/6adtk4. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Clustering single-cell RNA-seq data by rank constrained similarity learning.

MOTIVATION: Recent breakthroughs of single-cell RNA sequencing (scRNA-seq) technologies offer an exciting opportunity to identify heterogeneous cell types in complex tissues. However, the unavoidable biological noise and technical artifacts in scRNA-seq data as well as the high dimensionality of expression vectors make the problem highly challenging. Consequently, although numerous tools have been developed, their accuracy remains to be improved. RESULTS: Here, we introduce a novel clustering algorithm and tool RCSL (Rank Constrained Similarity Learning) to accurately identify various cell types using scRNA-seq data from a complex tissue. RCSL considers both local similarity and global similarity among the cells to discern the subtle differences among cells of the same type as well as larger differences among cells of different types. RCSL uses Spearman's rank correlations of a cell's expression vector with those of other cells to measure its global similarity, and adaptively learns neighbor representation of a cell as its local similarity. The overall similarity of a cell to other cells is a linear combination of its global similarity and local similarity. RCSL automatically estimates the number of cell types defined in the similarity matrix, and identifies them by constructing a block-diagonal matrix, such that its distance to the similarity matrix is minimized. Each block-diagonal submatrix is a cell cluster/type, corresponding to a connected component in the cognate similarity graph. When tested on 16 benchmark scRNA-seq datasets in which the cell types are well-annotated, RCSL substantially outperformed six state-of-the-art methods in accuracy and robustness as measured by three metrics. AVAILABILITY AND IMPLEMENTATION: The RCSL algorithm is implemented in R and can be freely downloaded at https://cran.r-project.org/web/packages/RCSL/index.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Real-world study on HBsAg loss of combination therapy in HBeAg-negative chronic hepatitis B patients.

Combination therapy with pegylated interferon (PEG-IFN) and nucleos(t)ide analogues (NAs) can enhance hepatitis B surface antigen (HBsAg) clearance. However, the specific treatment strategy and the patients who would benefit the most are unclear. Therefore, we assessed the HBsAg loss rate of add-on PEG-IFN and explored the factors associated with HBsAg loss in chronic hepatitis B (CHB) patients. This was a real-world cohort study of adults with CHB. Hepatitis B e antigen (HBeAg)-negative NAs-treated patients with baseline HBsAg ≤1500 IU/ml and HBV DNA < the lower limit of detection, or 100 IU/ml, received 48 weeks of add-on PEG-IFN. The primary outcome of the study was the rate of HBsAg loss at 48 weeks of combination treatment. Using multivariable logistic regression analysis, we determined factors associated with HBsAg loss. HBsAg loss in 2579 patients (mean age: 41.2 years; 80.9% male) was 36.7% (947 patients) at 48 weeks. HBsAg loss was highest in patients from south-central and southwestern China (40.0%). Factors independently associated with HBsAg loss included: increasing age (odds ratio = 0.961); being male (0.543); baseline HBsAg level (0.216); HBsAg decrease at 12 weeks (between 0.5 and 1.0 log10 IU/ml [2.405] and >1.0 log10 IU/ml [7.370]); alanine aminotransferase (ALT) increase at 12 weeks (1.365); haemoglobin (HGB) decrease at 12 weeks (1.558). There was no difference in the primary outcomes associated with the combination regimen. In conclusion, HBsAg loss by combination therapy was higher in patients from southern China than those from the north. An increased chance of HBsAg loss was associated with baseline characteristics and dynamic changes in clinical indicators.

Mechanism and Kinetic Study of Cyclodextrin Use to Facilitate NO2 Absorption in Sulfite Solutions.

An innovative strategy to control nitrogen oxide emission from flue gas was developed using the wet flue gas denitrification technology. The use of cyclodextrin (CD) as an additive facilitated NO2 absorption by the sulfite absorbent. Compared with absorption by a sulfite solution (59.12%), the instantaneous absorption efficiencies employing CD improved to 94.57%. Moreover, 48 h of continuous absorption indicated cyclic utilization of CD. The favorable role of CD was ascribed to facilitating the limiting step for the entire NO2 absorption-dissolution process which included both water solubility and gas-liquid mass transfer. Furthermore, we propose a potential mechanism of CD/sulfite mixed solution absorbing NO2, among which the favorable role of the additive is related to its amphiphilic behavior toward gas and liquid phases. Additionally, a kinetic model describing the rates of gas-liquid transfer and macro absorption was established based on various operating conditions. This model explains the absorption improvement in the kinetic aspect and provides theoretical guidance for practical applications.