Constraints on the K_{S}^{0}→μ^{+}μ^{-} Branching Fraction

A search for the decay K_{S}^{0}→μ^{+}μ^{-} is performed using proton-proton collision data, corresponding to an integrated luminosity of 5.6  fb^{-1} and collected with the LHCb experiment during 2016, 2017, and 2018 at a center-of-mass energy of 13 TeV. The observed signal yield is consistent with zero, yielding an upper limit of B(K_{S}^{0}→μ^{+}μ^{-})<2.2×10^{-10} at 90% C.L.. The limit reduces to B(K_{S}^{0}→μ^{+}μ^{-})<2.1×10^{-10} at 90% C.L. once combined with the result from data taken in 2011 and 2012.

Observation of Enhanced Double Parton Scattering in Proton-Lead Collisions at sqrt[s_{NN}]=8.16 TeV

A study of prompt charm-hadron pair production in proton-lead collisions at sqrt[s_{NN}]=8.16  TeV is performed using data corresponding to an integrated luminosity of about 30  nb^{-1}, collected with the LHCb experiment. Production cross sections for different pairs of charm hadrons are measured and kinematic correlations between the two charm hadrons are investigated. This is the first measurement of associated production of two charm hadrons in proton-lead collisions. The results confirm the predicted enhancement of double parton scattering production in proton-lead collisions compared to the single parton scattering production.

RKDOSCNV: A Local Kernel Density-Based Approach to the Detection of Copy Number Variations by Using Next-Generation Sequencing Data

Copy number variations (CNVs) are significant causes of many human cancers and genetic diseases. The detection of CNVs has become a common method by which to analyze human diseases using next-generation sequencing (NGS) data. However, effective detection of insignificant CNVs is still a challenging task. In this study, we propose a new detection method, RKDOSCNV, to meet the need. RKDOSCNV uses kernel density estimation method to evaluate the local kernel density distribution of each read depth segment (RDS) based on an expanded nearest neighbor (k-nearest neighbors, reverse nearest neighbors, and shared nearest neighbors of each RDS) data set, and assigns a relative kernel density outlier score (RKDOS) for each RDS. According to the RKDOS profile, RKDOSCNV predicts the candidate CNVs by choosing a reasonable threshold, which it uses split read approach to correct the boundaries of candidate CNVs. The performance of RKDOSCNV is assessed by comparing it with several current popular methods via experiments with simulated and real data at different tumor purity levels. The experimental results verify that the performance of RKDOSCNV is superior to that of several other methods. In summary, RKDOSCNV is a simple and effective method for the detection of CNVs from whole genome sequencing (WGS) data, especially for samples with low tumor purity.

Dust mite-derived Enterobacterial fimbriae H protein enforces the allergen specific immunotherapy in asthma mice

BACKGROUND

The mite alimentary canal contains plenty of microbiota. It is accepted that some of the microbial products function as adjuvants to speed up immune responses.

OBJECTIVES

We identified five bacterial proteins from dust mite, and Enterobacterial fimbriae H (FimH) was one of them. This study aims to test a hypothesis that the FimH protein enforces immunotherapy in asthmatic mice.

METHODS

Asthmatic mice were treated by allergen specific immunotherapy (ASIT) with rDer f1/f2 or rDer f1/f2 plus FimH. Changes in inflammatory cell infiltration, airway hyperreactivity, frequency of Tregs, splenic CD4⁺IFN-γ⁺ cells, and serum levels of TGF-β, IL-10, IL-13 and IL-17A of asthmatic mice were checked.

RESULTS

ASIT with rDer f1/f2 plus FimH reduced inflammatory cell infiltration, airway hyperreactivity (AHR), and levels of IgE and IgG1 compared to ASIT with rDer f1/f2 alone, but the levels of IgG2a increased. Asthmatic mice that underwent ASIT with rDer f1/f2 plus FimH showed increased frequency of Tregs, splenic CD4⁺IFN-γ⁺ cells, serum levels of TGF-β and IL-10; and deceased splenic CD4⁺IL-4⁺ cells, and serum levels of IL-13 and IL-17A. In vitro study showed FimH triggered IL-10 expression in a concentration dependent manner and facilitated the differentiation of Tregs.

CONCLUSION

Used as an adjuvant, FimH enforces the effect of ASIT in asthmatic mice via augmenting Tregs.

A coded aperture microscope for X-ray fluorescence full-field imaging

The design and construction of an instrument for full-field imaging of the X-ray fluorescence emitted by a fully illuminated sample are presented. The aim is to produce an X-ray microscope with a few micrometers spatial resolution, which does not need to scan the sample. Since the fluorescence from a spatially inhomogeneous sample may contain many fluorescence lines, the optic which will provide the magnification of the emissions must be achromatic, i.e. its optical properties must be energy-independent. The only optics which fulfill this requirement in the X-ray regime are mirrors and pinholes. The throughput of a simple pinhole is very low, so the concept of coded apertures is an attractive extension which improves the throughput by having many pinholes, and retains the achromatic property. Modified uniformly redundant arrays (MURAs) with 10 µm openings and 50% open area have been fabricated using gold in a lithographic technique, fabricated on a 1 µm-thick silicon nitride membrane. The gold is 25 µm thick, offering good contrast up to 20 keV. The silicon nitride is transparent down into the soft X-ray region. MURAs with various orders, from 19 up to 73, as well as their respective negative (a mask where open and closed positions are inversed compared with the original mask), have been made. Having both signs of mask will reduce near-field artifacts and make it possible to correct for any lack of contrast.

Molecular Basis for Craniofacial Phenotypes Caused by Sclerostin Deletion

Some genetic disorders are associated with distinctive facial features, which can aid in diagnosis. While considerable advances have been made in identifying causal genes, relatively little progress has been made toward understanding how a particular genotype results in a characteristic craniofacial phenotype. An example is sclerosteosis/van Buchem disease, which is caused by mutations in the Wnt inhibitor sclerostin (SOST). Affected patients have a high bone mass coupled with a distinctive appearance where the mandible is enlarged and the maxilla is foreshortened. Here, mice carrying a null mutation in Sost were analyzed using quantitative micro-computed tomographic (µCT) imaging and histomorphometric analyses to determine the extent to which the size and shape of craniofacial skeleton were altered. Sost^-/- mice exhibited a significant increase in appositional bone growth, which increased the height and width of the mandible and reduced the diameters of foramina. In vivo fluorochrome labeling, histology, and immunohistochemical analyses indicated that excessive bone deposition in the premaxillary suture mesenchyme curtailed overall growth, leading to midfacial hypoplasia. The amount of bone extracellular matrix produced by Sost^-/- cells was significantly increased; as a consequence, osteoid seams were evident throughout the facial skeleton. Collectively, these analyses revealed a remarkable fidelity between human characteristics of sclerosteosis/van Buchem disease and the Sost^-/- phenotype and provide clues into the conserved role for sclerostin signaling in modulating craniofacial morphology.

The Junctional Epithelium Is Maintained by a Stem Cell Population

The most fundamental function of an epithelial tissue is to act as a barrier, regulating interactions between the external environment and the body. This barrier function typically requires a contiguous cell layer but since teeth penetrate the oral epithelium, a modified barrier has evolved, called the junctional epithelium (JE). In health, the JE attaches to the tooth, sealing the inside of the body against oral micro-organisms. Breakdown of the JE barrier results in periodontal ligament (PDL) disintegration, alveolar bone resorption, and ultimately tooth loss. Using lineage tracing and DNA pulse-chase analyses, we identified an anatomical location in the JE that supported both fast- and slow-cycling Wnt-responsive stem cells that contributed to self-renewal of the tissue. Stem cells produced daughter cells with an extraordinarily high rate of turnover that maintained JE integrity for 1.4 y in mice. Blocking cell proliferation via a chemotherapeutic agent 5-fluorouracil (5-Fu) eliminated fast-cycling stem cells, which caused JE degeneration, PDL destruction, and bone resorption. Upon removal of 5-Fu, slow-cycling stem cells regenerated both the structure and barrier function of the JE. Taken together, our studies identified a stem cell population in the JE and have potential clinical implications for prevention and treatment of periodontitis.

Effect of platelet-rich fibrin on the control of alveolar osteitis, pain, trismus, soft tissue healing, and swelling following mandibular third molar surgery: an updated systematic review and meta-analysis

The purpose of this study was to estimate the effect of platelet-rich fibrin (PRF) on the control of alveolar osteitis (AO), pain, trismus, soft tissue healing, and swelling following mandibular third molar surgery. A comprehensive search of the literature was conducted through PubMed, Embase, Web of Science, and Cochrane Library up to May 2019. Randomized controlled studies conforming to the inclusion criteria were included. The record screening and data extraction were conducted by two authors independently. The risk of bias assessment was performed according to the guidelines recommended by the Cochrane Collaboration. The quantitative analysis was performed using RevMan version 5.3. Nineteen studies were included in the systematic review and 17 studies were eligible for the meta-analysis. The use of PRF significantly reduced the incidence of AO and postoperative pain when compared to the controls (AO: relative risk 0.43, 95% confidence interval (CI) 0.28 to 0.65, Z=3.90, P<0.0001 (I²=0%); pain: day 1, standardized mean difference (SMD) -1.12, 95% CI -1.87 to -0.37, Z=2.93, P=0.003 (I²=95%); day 3, SMD -0.93, 95% CI -1.48 to -0.38, Z=3.30, P=0.001 (I²=92%); day 7, SMD -1.84, 95% CI -2.98 to -0.71, Z=3.19, P=0.001 (I²=97%)). Additionally, the result showed a better soft tissue healing when PRF was used (mean difference -0.63, 95% CI -1.08 to -0.18, Z=2.76, P=0.006 (I²=90%)). The use of PRF reduced the incidence of AO and postoperative pain following third molar surgery. Furthermore, PRF may also improve the postoperative soft tissue healing.

Inferring subgroup-specific driver genes from heterogeneous cancer samples via subspace learning with subgroup indication

MOTIVATION

Detecting driver genes from gene mutation data is a fundamental task for tumorigenesis research. Due to the fact that cancer is a heterogeneous disease with various subgroups, subgroup-specific driver genes are the key factors in the development of precision medicine for heterogeneous cancer. However, the existing driver gene detection methods are not designed to identify subgroup specificities of their detected driver genes, and therefore cannot indicate which group of patients is associated with the detected driver genes, which is difficult to provide specifically clinical guidance for individual patients.

RESULTS

By incorporating the subspace learning framework, we propose a novel bioinformatics method called DriverSub, which can efficiently predict subgroup-specific driver genes in the situation where the subgroup annotations are not available. When evaluated by simulation datasets with known ground truth and compared with existing methods, DriverSub yields the best prediction of driver genes and the inference of their related subgroups. When we apply DriverSub on the mutation data of real heterogeneous cancers, we can observe that the predicted results of DriverSub are highly enriched for experimentally validated known driver genes. Moreover, the subgroups inferred by DriverSub are significantly associated with the annotated molecular subgroups, indicating its capability of predicting subgroup-specific driver genes.

AVAILABILITY AND IMPLEMENTATION

The source code is publicly available at https://github.com/JianingXi/DriverSub.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

DINTD: Detection and Inference of Tandem Duplications From Short Sequencing Reads

Tandem duplication (TD) is an important type of structural variation (SV) in the human genome and has biological significance for human cancer evolution and tumor genesis. Accurate and reliable detection of TDs plays an important role in advancing early detection, diagnosis, and treatment of disease. The advent of next-generation sequencing technologies has made it possible for the study of TDs. However, detection is still challenging due to the uneven distribution of reads and the uncertain amplitude of TD regions. In this paper, we present a new method, DINTD (Detection and INference of Tandem Duplications), to detect and infer TDs using short sequencing reads. The major principle of the proposed method is that it first extracts read depth and mapping quality signals, then uses the DBSCAN (Density-Based Spatial Clustering of Applications with Noise) algorithm to find the possible TD regions. The total variation penalized least squares model is fitted with read depth and mapping quality signals to denoise signals. A 2D binary search tree is used to search the neighbor points effectively. To further identify the exact breakpoints of the TD regions, split-read signals are integrated into DINTD. The experimental results of DINTD on simulated data sets showed that DINTD can outperform other methods for sensitivity, precision, F1-score, and boundary bias. DINTD is further validated on real samples, and the experiment results indicate that it is consistent with other methods. This study indicates that DINTD can be used as an effective tool for detecting TDs.

A numerical study of spin torque oscillators based on IMA/PMA bilayer nano-pillars

In this paper, the magnetization dynamics of bilayer structured nano-pillars containing a fixed layer with perpendicular magnetic anisotropy (PMA) and a free layer with in-plane magnetic anisotropy (IMA) are studied using the micro-magnetic simulation method. Unlike typical sandwich-structured spin-torque nano-pillar oscillators (STNOs), the proposed structure does not contain any nonmagnetic spacer layer. It is found that a stable oscillation with a significant amplitude can be established fast after driving out the vortex core by an in-plane magnetic pulse field. The oscillation frequency and amplitude can be easily manipulated by adjusting the side-length of the nanopillar, the thickness and saturation magnetization of the IMA layer, and an applied magnetic field along z axis. In an array with an adequate inter-pillar distance, the mutual interaction between the nano-pillars will lead the oscillations to be phase-locked, resulting in a considerable enhancement of total amplitude. As it is easy to fabricate these kinds of bi-layer nano-pillars and assemble them in arrays, they may have widespread applications in STNOs.

Interspecies Comparison of Alveolar Bone Biology, Part I: Morphology and Physiology of Pristine Bone

INTRODUCTION

Few interspecies comparisons of alveolar bone have been documented, and this knowledge gap raises questions about which animal models most accurately represent human dental conditions or responses to surgical interventions.

OBJECTIVES

The objective of this study was to employ state-of-the-art quantitative metrics to directly assess and compare the structural and functional characteristics of alveolar bone among humans, mini pigs, rats, and mice.

METHODS

The same anatomic location (i.e., the posterior maxillae) was analyzed in all species via micro-computed tomographic imaging, followed by quantitative analyses, coupled with histology and immunohistochemistry. Bone remodeling was evaluated with alkaline phosphatase activity and tartrate-resistant acid phosphatase staining to identify osteoblast and osteoclast activities. In vivo fluorochrome labeling was used as a means to assess mineral apposition rates.

RESULTS

Collectively, these analyses demonstrated that bone volume differed among the species, while bone mineral density was equal. All species showed a similar density of alveolar osteocytes, with a highly conserved pattern of collagen organization. Collagen maturation was equal among mouse, rat, and mini pig. Bone remodeling was a shared feature among the species, with morphologically indistinguishable hemiosteonal appearances, osteocytic perilacunar remodeling, and similar mineral apposition rates in alveolar bone.

CONCLUSIONS

Our analyses demonstrated equivalencies among the 4 species in a plurality of the biological features of alveolar bone. Despite contradictory results from older studies, we found no evidence for the superiority of pig models over rodent models in representing human bone biology.

KNOWLEDGE TRANSFER STATEMENT

Animal models are extensively used to evaluate bone tissue engineering strategies, yet there are few state-of-the-art studies that rigorously compare and quantify the factors influencing selection of a given animal model. Consequently, there is an urgent need to assess preclinical animal models for their predictive value to dental research. Our article addresses this knowledge gap and, in doing so, provides a foundation for more effective standardization among animal models commonly used in dentistry.

Measurement of CP-Averaged Observables in the B^{0}→K^{*0}μ^{+}μ^{-} Decay

An angular analysis of the B^{0}→K^{*0}(→K^{+}π^{-})μ^{+}μ^{-} decay is presented using a dataset corresponding to an integrated luminosity of 4.7  fb^{-1} of pp collision data collected with the LHCb experiment. The full set of CP-averaged observables are determined in bins of the invariant mass squared of the dimuon system. Contamination from decays with the K^{+}π^{-} system in an S-wave configuration is taken into account. The tension seen between the previous LHCb results and the standard model predictions persists with the new data. The precise value of the significance of this tension depends on the choice of theory nuisance parameters.

CONDEL: Detecting Copy Number Variation and Genotyping Deletion Zygosity from Single Tumor Samples Using Sequence Data

Characterizing copy number variations (CNVs) from sequenced genomes is a both feasible and cost-effective way to search for driver genes in cancer diagnosis. A number of existing algorithms for CNV detection only explored part of the features underlying sequence data and copy number structures, resulting in limited performance. Here, we describe CONDEL, a method for detecting CNVs from single tumor samples using high-throughput sequence data. CONDEL utilizes a novel statistic in combination with a peel-off scheme to assess the statistical significance of genome bins, and adopts a Bayesian approach to infer copy number gains, losses, and deletion zygosity based on statistical mixture models. We compare CONDEL to six peer methods on a large number of simulation datasets, showing improved performance in terms of true positive and false positive rates, and further validate CONDEL on three real datasets derived from the 1000 Genomes Project and the EGA archive. CONDEL obtained higher consistent results in comparison with other three single sample-based methods, and exclusively identified a number of CNVs that were previously associated with cancers. We conclude that CONDEL is a powerful tool for detecting copy number variations on single tumor samples even if these are sequenced at low-coverage.

MFCNV: A New Method to Detect Copy Number Variations From Next-Generation Sequencing Data

Copy number variation (CNV) is a very important phenomenon in tumor genomes and plays a significant role in tumor genesis. Accurate detection of CNVs has become a routine and necessary procedure for a deep investigation of tumor cells and diagnosis of tumor patients. Next-generation sequencing (NGS) technique has provided a wealth of data for the detection of CNVs at base-pair resolution. However, such task is usually influenced by a number of factors, including GC-content bias, sequencing errors, and correlations among adjacent positions within CNVs. Although many existing methods have dealt with some of these artifacts by designing their own strategies, there is still a lack of comprehensive consideration of all the factors. In this paper, we propose a new method, MFCNV, for an accurate detection of CNVs from NGS data. Compared with existing methods, the characteristics of the proposed method include the following: (1) it makes a full consideration of the intrinsic correlations among adjacent positions in the genome to be analyzed, (2) it calculates read depth, GC-content bias, base quality, and correlation value for each genome bin and combines them as multiple features for the evaluation of genome bins, and (3) it addresses the joint effect among the factors via training a neural network algorithm for the prediction of CNVs. We test the performance of the MFCNV method by using simulation and real sequencing data and make comparisons with several peer methods. The results demonstrate that our method is superior to other methods in terms of sensitivity, precision, and F1-score and can detect many CNVs that other methods have not discovered. MFCNV is expected to be a complementary tool in the analysis of mutations in tumor genomes and can be extended to be applied to the analysis of single-cell sequencing data.

Observation of New Ξ_{c}^{0} Baryons Decaying to Λ_{c}^{+}K^{-}

The Λ_{c}^{+}K^{-} mass spectrum is studied with a data sample of pp collisions at a center-of-mass energy of 13 TeV corresponding to an integrated luminosity of 5.6  fb^{-1} collected by the LHCb experiment. Three Ξ_{c}^{0} states are observed with a large significance and their masses and natural widths are measured to be m[Ξ_{c}(2923)^{0}]=2923.04±0.25±0.20±0.14  MeV, Γ[Ξ_{c}(2923)^{0}]=7.1±0.8±1.8  MeV, m[Ξ_{c}(2939)^{0}]=2938.55±0.21±0.17±0.14  MeV, Γ[Ξ_{c}(2939)^{0}]=10.2±0.8±1.1  MeV, m[Ξ_{c}(2965)^{0}]=2964.88±0.26±0.14±0.14  MeV, Γ[Ξ_{c}(2965)^{0}]=14.1±0.9±1.3  MeV, where the uncertainties are statistical, systematic, and due to the limited knowledge of the Λ_{c}^{+} mass. The Ξ_{c}(2923)^{0} and Ξ_{c}(2939)^{0} baryons are new states. The Ξ_{c}(2965)^{0} state is in the vicinity of the known Ξ_{c}(2970)^{0} baryon; however, their masses and natural widths differ significantly.

Evaluation of four disease management programs: evidence from blue cross blue shield of Louisiana

Aims: Chronic diseases impose a substantial healthcare burden. This study sought to evaluate the clinical and economic impact of new disease management (DM) programs, targeting four major chronic disease groups: diabetes, coronary heart disease (CHD)/hypertension (HTN), asthma/chronic obstructive pulmonary disease (COPD), and congestive heart failure (CHF)/chronic kidney disease (CKD).Materials and methods: Between March 1, 2015, and February 28, 2018, members with Blue Cross Blue Shield of Louisiana insurance were contacted and enrolled in a DM program if they were aged 18 years through 64 years, eligible for a DM program, and had not been previously enrolled in a DM program. Active enrollees of a DM program ("IN" group) were compared to members who were not yet enrolled ("OUT" group). Average per member per month (PMPM) costs were aggregated annually to document any descriptive trends. Multivariable model estimates were used to compare PMPM costs for all IN subjects and all OUT subjects. Total medical savings were evaluated for the following time intervals: 1-12 months, 13-24 months, and 25-36 months.Results: For all four DM programs, average costs PMPM trended upward over time for the OUT cohort, while they remained relatively stable for the IN cohort. Some evidence also showed that DM programs improved clinical outcomes, such as hemoglobin A1c values. A difference in difference analysis showed PMPM savings for all four programs combined of $31.61, $50.45, and $53.72 after 1, 2, and 3 years, respectively. Multivariable modeling results showed total savings after 3 years of $14,460,174 for all DM programs combined.Limitations: Although multivariable models adjusted for several clinical, demographic, and economic characteristics; it is possible that some important confounders were missing due to lack of data.Conclusions: DM programs implemented to control diabetes, CHD/HTN, CHF/CKD, and asthma/COPD are cost-effective and show some evidence of improved clinical outcomes.

Search for the Rare Decays B_{s}^{0}→e^{+}e^{-} and B^{0}→e^{+}e^{-}

A search for the decays B_{s}^{0}→e^{+}e^{-} and B^{0}→e^{+}e^{-} is performed using data collected with the LHCb experiment in proton-proton collisions at center-of-mass energies of 7, 8, and 13 TeV, corresponding to integrated luminosities of 1, 2, and 2  fb^{-1}, respectively. No signal is observed. Assuming no contribution from B^{0}→e^{+}e^{-} decays, an upper limit on the branching fraction B(B_{s}^{0}→e^{+}e^{-})<9.4(11.2)×10^{-9} is obtained at 90(95)% confidence level. If no B_{s}^{0}→e^{+}e^{-} contribution is assumed, a limit of B(B^{0}→e^{+}e^{-})<2.5(3.0)×10^{-9} is determined at 90(95)% confidence level. These upper limits are more than one order of magnitude lower than the previous values.