Observation of a Resonant Structure near the D_{s}^{+}D_{s}^{-} Threshold in the B^{+}→D_{s}^{+}D_{s}^{-}K^{+} Decay

An amplitude analysis of the B^{+}→D_{s}^{+}D_{s}^{-}K^{+} decay is carried out to study for the first time its intermediate resonant contributions, using proton-proton collision data collected with the LHCb detector at center-of-mass energies of 7, 8, and 13 TeV. A near-threshold peaking structure, referred to as X(3960), is observed in the D_{s}^{+}D_{s}^{-} invariant-mass spectrum with significance greater than 12 standard deviations. The mass, width, and the quantum numbers of the structure are measured to be 3956±5±10  MeV, 43±13±8  MeV, and J^{PC}=0^{++}, respectively, where the first uncertainties are statistical and the second systematic. The properties of the new structure are consistent with recent theoretical predictions for a state composed of cc[over ¯]ss[over ¯] quarks. Evidence for an additional structure is found around 4140 MeV in the D_{s}^{+}D_{s}^{-} invariant mass, which might be caused either by a new resonance with the 0^{++} assignment or by a J/ψϕ↔D_{s}^{+}D_{s}^{-} coupled-channel effect.

Evidence for Modification of b Quark Hadronization in High-Multiplicity pp Collisions at sqrt[s]=13 TeV

The production rate of B_{s}^{0} mesons relative to B^{0} mesons is measured by the LHCb experiment in pp collisions at a center-of-mass energy sqrt[s]=13  TeV over the forward rapidity interval 2 Collapse

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Test of Lepton Universality in b→sℓ^{+}ℓ^{-} Decays

The first simultaneous test of muon-electron universality using B^{+}→K^{+}ℓ^{+}ℓ^{-} and B^{0}→K^{*0}ℓ^{+}ℓ^{-} decays is performed, in two ranges of the dilepton invariant-mass squared, q^{2}. The analysis uses beauty mesons produced in proton-proton collisions collected with the LHCb detector between 2011 and 2018, corresponding to an integrated luminosity of 9  fb^{-1}. Each of the four lepton universality measurements reported is either the first in the given q^{2} interval or supersedes previous LHCb measurements. The results are compatible with the predictions of the Standard Model.

Prediction of DNA Methylation based on Multi-dimensional feature encoding and double convolutional fully connected convolutional neural network

DNA methylation takes on critical significance to the regulation of gene expression by affecting the stability of DNA and changing the structure of chromosomes. DNA methylation modification sites should be identified, which lays a solid basis for gaining more insights into their biological functions. Existing machine learning-based methods of predicting DNA methylation have not fully exploited the hidden multidimensional information in DNA gene sequences, such that the prediction accuracy of models is significantly limited. Besides, most models have been built in terms of a single methylation type. To address the above-mentioned issues, a deep learning-based method was proposed in this study for DNA methylation site prediction, termed the MEDCNN model. The MEDCNN model is capable of extracting feature information from gene sequences in three dimensions (i.e., positional information, biological information, and chemical information). Moreover, the proposed method employs a convolutional neural network model with double convolutional layers and double fully connected layers while iteratively updating the gradient descent algorithm using the cross-entropy loss function to increase the prediction accuracy of the model. Besides, the MEDCNN model can predict different types of DNA methylation sites. As indicated by the experimental results,the deep learning method based on coding from multiple dimensions outperformed single coding methods, and the MEDCNN model was highly applicable and outperformed existing models in predicting DNA methylation between different species. As revealed by the above-described findings, the MEDCNN model can be effective in predicting DNA methylation sites.

First Observation of a Doubly Charged Tetraquark and Its Neutral Partner

A combined amplitude analysis is performed for the decays B^{0}→D[over ¯]^{0}D_{s}^{+}π^{-} and B^{+}→D^{-}D_{s}^{+}π^{+}, which are related by isospin symmetry. The analysis is based on data collected by the LHCb detector in proton-proton collisions at center-of-mass energies of 7, 8, and 13 TeV. The full data sample corresponds to an integrated luminosity of 9  fb^{-1}. Two new resonant states with masses of 2.908±0.011±0.020  GeV and widths of 0.136±0.023±0.013  GeV are observed, which decay to D_{s}^{+}π^{+} and D_{s}^{+}π^{-} respectively. The former state indicates the first observation of a doubly charged open-charm tetraquark state with minimal quark content [cs[over ¯]ud[over ¯]], and the latter state is a neutral tetraquark composed of [cs[over ¯]u[over ¯]d] quarks. Both states are found to have spin-parity of 0^{+}, and their resonant parameters are consistent with each other, which suggests that they belong to an isospin triplet.

Search for Rare Decays of D^{0} Mesons into Two Muons

A search for the very rare D^{0}→μ^{+}μ^{-} decay is performed using data collected by the LHCb experiment in proton-proton collisions at sqrt[s]=7, 8, and 13 TeV, corresponding to an integrated luminosity of 9  fb^{-1}. The search is optimized for D^{0} mesons from D^{*+}→D^{0}π^{+} decays but is also sensitive to D^{0} mesons from other sources. No evidence for an excess of events over the expected background is observed. An upper limit on the branching fraction of this decay is set at B(D^{0}→μ^{+}μ^{-})<3.1×10^{-9} at a 90% C.L. This represents the world's most stringent limit, constraining models of physics beyond the standard model.

Nuclear Modification Factor of Neutral Pions in the Forward and Backward Regions in p-Pb Collisions

The nuclear modification factor of neutral pions is measured in proton-lead collisions collected at a center-of-mass energy per nucleon of 8.16 TeV with the LHCb detector. The π^{0} production cross section is measured differentially in transverse momentum (p_{T}) for 1.5 Collapse

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Observation of a J/ψΛ Resonance Consistent with a Strange Pentaquark Candidate in B^{-}→J/ψΛp[over ¯] Decays

An amplitude analysis of B^{-}→J/ψΛp[over ¯] decays is performed using 4400 signal candidates selected on a data sample of pp collisions recorded at center-of-mass energies of 7, 8, and 13 TeV with the LHCb detector, corresponding to an integrated luminosity of 9  fb^{-1}. A narrow resonance in the J/ψΛ system, consistent with a pentaquark candidate with strangeness, is observed with high significance. The mass and the width of this new state are measured to be 4338.2±0.7±0.4  MeV and 7.0±1.2±1.3  MeV, where the first uncertainty is statistical and the second systematic. The spin is determined to be 1/2 and negative parity is preferred. Because of the small Q-value of the reaction, the most precise single measurement of the B^{-} mass to date, 5279.44±0.05±0.07  MeV, is obtained.

Enabling early detection of knee osteoarthritis using diffusion-relaxation correlation spectrum imaging

AIM

To present a technique that enables detection of early stage OA of the knee using diffusion-relaxation correlation spectrum imaging (DR-CSI).

MATERIALS AND METHODS

Fifty-five early osteoarthritis patients (OA, Kellgren-Lawrence [KL] score 1 to 2; mean age, 56.4 years) and 49 healthy volunteers (mean age, 56.7 years) were underwent magnetic resonance imaging (MRI) with T2-mapping and DR-CSI techniques. Maps of mean apparent diffusion coefficient (ADC), T2 relaxation time and volume fraction Vi for DR-CSI compartment i (A, B, C, D) sensitivity, specificity, and positive and negative likelihood ratio (PLR, NLR) were assessed to determine the diagnostic accuracy for detection of early-stage degeneration of knee articular cartilage. The structural abnormalities of articular cartilage were evaluated using modified Whole-Organ MR Imaging Scores (WORMS).

RESULTS

All intra- and interobserver agreements for DR-CSI compartment volume fractions and modified WORMS of cartilage were excellent. Early OA versus the controls had higher V_C, lower V_A and V_B (p<0.001), but comparable V_D (p>0.05). V_A, V_B and V_C had a moderate association with WORMS. No significant correlation was identified between V_D and WORMS. V_C had better ability than V_A,V_B, V_D, T2 and ADC to discriminate early OA patients from healthy controls (area under the curve, 0.898). Sensitivity, specificity, PLR, and NLR of V_C with a cut-off value of 29.9% were 81.8% (95% confidence interval [CI], 69.1-90.9%), 95.9% (86-99.5%), 20.05% (5.13-78.34%), and 0.19% (0.11-0.33%).

CONCLUSIONS

DR-CSI compartment volume fractions may be sensitive indicators for detecting early-stage degeneration in knee articular cartilage.

Single-scan ultrafast laser inscription of waveguides in IG2 for type-I and type-II operation in the mid-infrared

We demonstrate, for the first time to our knowledge, single-scan ultrafast laser inscription and performance of mid-infrared waveguiding in IG2 chalcogenide glass in the type-I and type-II configurations. The waveguiding properties at 4550 nm are studied as a function of pulse energy, repetition rate, and additionally separation between the two inscribed tracks for type-II waveguides. Propagation losses of ∼1.2 dB/cm in a type-II waveguide and ∼2.1 dB/cm in a type-I waveguide have been demonstrated. For the latter type, there is an inverse relation between the refractive index contrast and the deposited surface energy density. Notably, type-I and type-II waveguiding have been observed at 4550 nm within and between the tracks of two-track structures. In addition, although type-II waveguiding has been observed in the near infrared (1064 nm) and mid infrared (4550 nm) in two-track structures, type-I waveguiding within each track has only been observed in the mid infrared.

scRNASequest: an ecosystem of scRNA-seq analysis, visualization, and publishing

BACKGROUND

Single-cell RNA sequencing is a state-of-the-art technology to understand gene expression in complex tissues. With the growing amount of data being generated, the standardization and automation of data analysis are critical to generating hypotheses and discovering biological insights.

RESULTS

Here, we present scRNASequest, a semi-automated single-cell RNA-seq (scRNA-seq) data analysis workflow which allows (1) preprocessing from raw UMI count data, (2) harmonization by one or multiple methods, (3) reference-dataset-based cell type label transfer and embedding projection, (4) multi-sample, multi-condition single-cell level differential gene expression analysis, and (5) seamless integration with cellxgene VIP for visualization and with CellDepot for data hosting and sharing by generating compatible h5ad files.

CONCLUSIONS

We developed scRNASequest, an end-to-end pipeline for single-cell RNA-seq data analysis, visualization, and publishing. The source code under MIT open-source license is provided at https://github.com/interactivereport/scRNASequest . We also prepared a bookdown tutorial for the installation and detailed usage of the pipeline: https://interactivereport.github.io/scRNAsequest/tutorial/docs/ . Users have the option to run it on a local computer with a Linux/Unix system including MacOS, or interact with SGE/Slurm schedulers on high-performance computing (HPC) clusters.

High Electron Mobility Hot-Exciton Induced Delayed Fluorescent Organic Semiconductors

The development of high mobility emissive organic semiconductors is of great significance for the fabrication of miniaturized optoelectronic devices, such as organic light emitting transistors. However, great challenge exists in designing key materials, especially those who integrates triplet exciton utilization ability. Herein, dinaphthylanthracene diimides (DNADIs), with 2,6-extended anthracene donor, and 3'- or 4'-substituted naphthalene monoimide acceptors were designed and synthesized. By introducing acceptor-donor-acceptor structure, both materials show high electron mobility. Moreover, by fine-tuning of substitution sites, good integration with high solid state photoluminescence quantum yield of 26 %, high electron mobility of 0.02 cm²  V^-1  s^-1 , and the feature of hot-exciton induced delayed fluorescence were obtained in 4'-DNADI. This work opens a new avenue for developing high electron mobility emissive organic semiconductors with efficient utilization of triplet excitons.

RNASequest: An End-to-End Reproducible RNAseq Data Analysis and Publishing Framework

We present RNASequest, a customizable RNA sequencing (RNAseq) analysis, app management, and result publishing framework. Its three-in-one RNAseq data analysis ecosystem consists of (1) a reproducible, configurable expression analysis (EA) module, (2) multi-faceted result presentation in R Shiny, a Bookdown document and an online slide deck, and (3) a centralized data management system. In principle, following up our well-received omics data visualization tool Quickomics, RNASequest automates the differential gene expression analysis step, eases statistical model design by built-in covariates testing module, and further provides a web-based tool, ShinyOne, to manage apps powered by Quickomics and reports generated by running the pipeline on multiple projects in one place. Researchers can experience the functionalities by exploring demo data sets hosted at http://shinyone.bxgenomics.com or following the tutorial, https://interactivereport.github.io/RNASequest/tutorial/docs/introduction.html to set up the framework locally to process private RNAseq datasets. The source code released under MIT open-source license is provided at https://github.com/interactivereport/RNASequest.

Efficient pump-probe sampling with a single-cavity dual-comb laser: Application in ultrafast photoacoustics

Ultrafast pump-probe measurements are used to characterize various samples, such as biological cells, bulk, and thin-film structures. However, typical implementations of the pump-probe apparatus are either slow or complex and costly hindering wide deployment. Here we combine a single-cavity dual-comb laser with a simple experimental setup to obtain pump-probe measurements with ultra-high sensitivity, fast acquisition, and high timing precision over long optical delay scan ranges of 12.5 ns that would correspond to a mechanical delay of about 3.75 m. We employ digital signal balancing to obtain shot-noise-limited detection compatible with pump-probe microscopy deployment. Here we demonstrate ultrafast photoacoustics for thin-film sample characterization. We measured a tungsten layer thickness of (700 ± 4) Å with shot-noise-limited detection. Such single-cavity dual-comb lasers can be used for any pump-probe measurements and are especially well-suited for ultrafast photoacoustic studies such as involving ultrasonic echoes, Brillouin oscillations, surface acoustic waves and thermal dynamics.

Voltage-dependent anion channel 2 (VDAC2) facilitates the accumulation of rice stripe virus in the vector Laodelphax striatellus

Rice stripe virus (RSV) causes enormous losses in rice production and is transmitted by the small brown planthopper, Laodelphax striatellus, in a persistent-propagative manner. RSV accumulation within the gut lumen of the vector is indispensable for the successful transmission to rice and insects. In this study, we obtained a 1464 bp full-length cDNA of a voltage-dependent anion channel 2 from L. striatellus (LsVDAC2), which encodes a 283 amino acid protein. RSV infection increased the expression of LsVDAC2 in the midguts and ovaries of L. striatellus by 260% and 228%, respectively. Silencing of LsVDAC2 resulted in a 88% reduction of RSV loads at 24 h after RNAi, indicating that LsVDAC2 facilitates RSV accumulation in the vector. Yeast two-hybrid and GST pulldown assays demonstrated that LsVDAC2 interacted with RSV RNA-dependent RNA polymerase, RdRp. Furthermore, experiments in vivo and in vitro showed that LsVDAC2 induced the apoptotic response in RSV-infected insects and tissues. Silencing of LsVDAC2 via RNAi significantly reduced the expression of genes for apoptosis-related caspases 1a and 1c by 62% and 78%, respectively, in RSV-infected vectors. Whether LsVDAC2-induced RSV accumulation is related to RSV RdRp and LsVDAC2-induced cell apoptosis deserves further investigation.

Dynapenic Abdominal Obesity and Risk of Heart Disease among Middle-Aged and Older Adults: A Prospective Cohort Study

OBJECTIVES

The vicious cycle of dynapenia and abdominal obesity may have synergistic detrimental impacts on health. We aim to investigate the prospective association between dynapenic abdominal obesity and the risk of heart disease among middle-aged and older adults.

DESIGN

A prospective cohort study.

SETTING

English Longitudinal Study of Ageing, 2002-2019.

PARTICIPANTS

A total of 4734 participants aged 50 years and older were included.

MEASUREMENTS

Individuals were divided into non-dynapenia/non-abdominal obesity (ND/NAO), non-dynapenia/abdominal obesity (ND/AO), dynapenia/non-abdominal obesity (D/NAO), and dynapenia/abdominal obesity (D/AO) according to grip strength and waist circumference at baseline. The Cox proportional hazards models were used to obtain the hazard ratios (HRs) of incident heart disease associated with dynapenia and abdominal obesity after adjusting for potential confounding factors.

RESULTS

During a median follow-up of 9.5 years, 1040 cases of heart disease were recorded. Compared with ND/NAO group, the multivariable HRs were 1.05 (0.92, 1.21) for ND/AO group, 1.31 (0.96, 1.81) for D/NAO group, and 1.39 (1.03, 1.88) for D/AO group. The significant association of D/AO with incident heart disease was detected in women but not in men [HR = 1.55 (1.07, 2.24) and 1.06 (0.60, 1.88), respectively]. Among middle-aged adults, significant associations of D/NAO and D/AO with incident heart disease were observed [HR = 2.46 (1.42, 4.29) and 1.74 (1.02, 2.97), respectively].

CONCLUSION

Both D/NAO and D/AO might increase the risk of developing heart disease, highlighting the importance of dynapenia and obesity early screening for heart disease prevention.

Neutrophil extracellular traps facilitate cancer metastasis: cellular mechanisms and therapeutic strategies

Background

The formation of neutrophil extracellular traps (NETs) was initially discovered as a novel immune response against pathogens. Recent studies have also suggested that NETs play an important role in tumor progression. This review summarizes the cellular mechanisms by which NETs promote distant metastasis and discusses the possible clinical applications targeting NETs.

Method

The relevant literature from PubMed and Google Scholar (2001–2021) have been reviewed for this article.

Results

The presence of NETs has been detected in various primary tumors and metastatic sites. NET-associated interactions have been observed throughout the different stages of metastasis, including initial tumor cell detachment, intravasation and extravasation, the survival of circulating tumor cells, the settlement and the growth of metastatic tumor cells. Several in vitro and in vivo studies proved that inhibiting NET formation resulted in anti-cancer effects. The biosafety and efficacy of some NET inhibitors have also been demonstrated in early phase clinical trials.

Conclusions

Considering the role of NETs in tumor progression, NETs could be a promising diagnostic and therapeutic target for cancer management. However, current evidence is mostly derived from experimental models and as such more clinical studies are still needed to verify the clinical significance of NETs in oncological settings.

First Measurement of the Z→μ^{+}μ^{-} Angular Coefficients in the Forward Region of pp Collisions at sqrt[s]=13 TeV

The first study of the angular distribution of μ^{+}μ^{-} pairs produced in the forward rapidity region via the Drell-Yan reaction pp→γ^{*}/Z+X→ℓ^{+}ℓ^{-}+X is presented, using data collected with the LHCb detector at a center-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 5.1  fb^{-1}. The coefficients of the five leading terms in the angular distribution are determined as a function of the dimuon transverse momentum and rapidity. The results are compared to various theoretical predictions of the Z-boson production mechanism and can also be used to probe transverse-momentum-dependent parton distributions within the proton.

Global disease burden of COPD from 1990 to 2019 and prediction of future disease burden trend in China

OBJECTIVES

This study aimed to assess and predict the disease burden attributable to chronic obstructive pulmonary disease (COPD) in a timely, comprehensive, and reliable manner, thereby mitigating the health hazards of COPD.

STUDY DESIGN AND METHODS

Data on the disease burden owing to COPD from 1990 to 2019 were extracted from the Global Burden of Disease (GBD) Study 2019. Linear regression analysis was used to calculate the estimated annual percentage change (EAPC) in the age-standardized rates. Non-parametric tests were used for subgroup analysis. The Bayesian age-period-cohot (BAPC) model integrated nested Laplace approximations to predict the disease burden over the next 25 years. Sensitivity analysis was performed using the Norpred APC model.

RESULTS

Globally, the COPD-related age-standardized incidence rate decreased from 216.48/100,000 in 1990 to 200.49/100,000 in 2019, with an EAPC of -0.33. But the number of new cases increased from 8,722,966 in 1990 to 16, 214, 828 in 2019. Trends in prevalence, deaths, and disability-adjusted life years (DALYs) were the same as incidence. There were significant differences in disease burden between the genders and all age groups (P < 0.05) in China. The projections suggested that the COPD-related number of new cases and deaths in China would increase by approximately 1.5 times over the next 25 years.

CONCLUSIONS

The number of incidence, prevalence, deaths, and DALYs had all increased in China in the past and would continue to grow over the next 25 years. Therefore, measures should be taken to target risk factors and high-risk groups.

Study of the doubly charmed tetraquark [Formula: see text]

Quantum chromodynamics, the theory of the strong force, describes interactions of coloured quarks and gluons and the formation of hadronic matter. Conventional hadronic matter consists of baryons and mesons made of three quarks and quark-antiquark pairs, respectively. Particles with an alternative quark content are known as exotic states. Here a study is reported of an exotic narrow state in the D0D0π+ mass spectrum just below the D*+D0 mass threshold produced in proton-proton collisions collected with the LHCb detector at the Large Hadron Collider. The state is consistent with the ground isoscalar [Formula: see text] tetraquark with a quark content of [Formula: see text] and spin-parity quantum numbers JP = 1+. Study of the DD mass spectra disfavours interpretation of the resonance as the isovector state. The decay structure via intermediate off-shell D*+ mesons is consistent with the observed D0π+ mass distribution. To analyse the mass of the resonance and its coupling to the D*D system, a dedicated model is developed under the assumption of an isoscalar axial-vector [Formula: see text] state decaying to the D*D channel. Using this model, resonance parameters including the pole position, scattering length, effective range and compositeness are determined to reveal important information about the nature of the [Formula: see text] state. In addition, an unexpected dependence of the production rate on track multiplicity is observed.

Recommendations of scRNA-seq Differential Gene Expression Analysis Based on Comprehensive Benchmarking

To guide analysts to select the right tool and parameters in differential gene expression analyses of single-cell RNA sequencing (scRNA-seq) data, we developed a novel simulator that recapitulates the data characteristics of real scRNA-seq datasets while accounting for all the relevant sources of variation in a multi-subject, multi-condition scRNA-seq experiment: the cell-to-cell variation within a subject, the variation across subjects, the variability across cell types, the mean/variance relationship of gene expression across genes, library size effects, group effects, and covariate effects. By applying it to benchmark 12 differential gene expression analysis methods (including cell-level and pseudo-bulk methods) on simulated multi-condition, multi-subject data of the 10x Genomics platform, we demonstrated that methods originating from the negative binomial mixed model such as glmmTMB and NEBULA-HL outperformed other methods. Utilizing NEBULA-HL in a statistical analysis pipeline for single-cell analysis will enable scientists to better understand the cell-type-specific transcriptomic response to disease or treatment effects and to discover new drug targets. Further, application to two real datasets showed the outperformance of our differential expression (DE) pipeline, with unified findings of differentially expressed genes (DEG) and a pseudo-time trajectory transcriptomic result. In the end, we made recommendations for filtering strategies of cells and genes based on simulation results to achieve optimal experimental goals.

Angular Analysis of D^{0}→π^{+}π^{-}μ^{+}μ^{-} and D^{0}→K^{+}K^{-}μ^{+}μ^{-} Decays and Search for CP Violation

The first full angular analysis and an updated measurement of the decay-rate CP asymmetry of the D^{0}→π^{+}π^{-}μ^{+}μ^{-} and D^{0}→K^{+}K^{-}μ^{+}μ^{-} decays are reported. The analysis uses proton-proton collision data collected with the LHCb detector at center-of-mass energies of 7, 8, and 13 TeV. The dataset corresponds to an integrated luminosity of 9  fb^{-1}. The full set of CP -averaged angular observables and their CP asymmetries are measured as a function of the dimuon invariant mass. The results are consistent with expectations from the standard model and with CP symmetry.