Doublets are prevalent in single-cell sequencing data and can lead to artifactual findings. A number of strategies have therefore been proposed to detect them. Building on the strengths of existing ...approaches, we developed
scDblFinder, a fast, flexible and accurate Bioconductor-based doublet detection method. Here we present the method, justify its design choices, demonstrate its performance on both single-cell RNA and accessibility sequencing data, and provide some observations on doublet formation, detection, and enrichment analysis. Even in complex datasets,
scDblFinder can accurately identify most heterotypic doublets, and was already found by an independent benchmark to outcompete alternatives.
HDECAY: Twenty++ years after Djouadi, Abdelhak; Kalinowski, Jan; Mühlleitner, Margarete ...
Computer physics communications,
05/2019, Volume:
238
Journal Article
Peer reviewed
Open access
The program HDECAY determines the partial decay widths and branching ratios of the Higgs bosons within the Standard Model with three and four generations of fermions, including the case when the ...Higgs couplings are rescaled, a general two-Higgs doublet model where the Higgs sector is extended and incorporates five physical states and its most studied incarnation, the minimal supersymmetric Standard Model (MSSM) with real soft SUSY-breaking parameters. The program addresses all decay channels including the dominant higher-order effects such as radiative corrections and multi-body channels. Since the first launch of the program, more than twenty years ago, important aspects and new ingredients have been incorporated. In this update of the program description, some of the developments are summarized while others are discussed in some detail.
Program Title: HDECAY
Program Files doi:http://dx.doi.org/10.17632/3ggyvkjz95.1
Licensing provisions: GPLv2
Programming language: FORTRAN77
Journal reference of previous version: Comp. Phys. Comm. 108 (1998) 56-74.
Does the new version supersede the previous version?: Yes
Reasons for the new version: Major updates and extensions
Summary of revisions: Since the first release of the original version of the program some bugs have been fixed, a number of improvements and new theoretical calculations have been implemented. The logbook of all modifications and the most recent version 6.52 of the program can be found on the web page http://tiger.web.psi.ch/hdecay/.
Nature of problem: Decay widths and branching ratios for Higgs bosons decays in the Standard Model with three and four generations of fermions and rescaled couplings, a general two-Higgs doublet model and the Minimal Supersymmetric Standard Model are calculated numerically, including loop corrections according to the current theoretical knowledge.
Solution method: One- and two-dimensional numerical integration of analytic formulae for Higgs boson decays into off-shell particles. All other decay widths are calculated analytically. The transition between off-shell and on-shell decays is performed by a linear interpolation.
Single-cell RNA-sequencing has become a widely used, powerful approach for studying cell populations. However, these methods often generate multiplet artifacts, where two or more cells receive the ...same barcode, resulting in a hybrid transcriptome. In most experiments, multiplets account for several percent of transcriptomes and can confound downstream data analysis. Here, we present Single-Cell Remover of Doublets (Scrublet), a framework for predicting the impact of multiplets in a given analysis and identifying problematic multiplets. Scrublet avoids the need for expert knowledge or cell clustering by simulating multiplets from the data and building a nearest neighbor classifier. To demonstrate the utility of this approach, we test Scrublet on several datasets that include independent knowledge of cell multiplets. Scrublet is freely available for download at github.com/AllonKleinLab/scrublet.
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•We define two multiplet errors in single-cell RNA-seq data: “embedded” and “neotypic”•Neotypic errors can lead to misidentification of cell types or transitional states•Scrublet code identifies neotypic doublets and predicts the overall doublet rate•The algorithm is tested against several experimental methods for labeling multiplets
Single-cell RNA-sequencing experiments generate “multiplet errors” when multiple cells are labeled with the same barcode. Wolock et al. describe Scrublet, a method for predicting the effects of multiplets on downstream analyses and identifying problematic multiplets. They validate the method by applying Scrublet to several datasets with independent knowledge of multiplets.
•Megathrust structure variations controlled the rupture of a M7.8 inter-plate event.•The M7.6 earthquake was likely triggered by the M7.8 co- and/or post-seismic slip.•Trench-normal subducted ocean ...lithosphere structures can reactivate in earthquakes.
In 2020, an earthquake doublet, a M7.8 on July 22nd and a M7.6 on October 19th, struck the Alaska-Aleutian subduction zone beneath the Shumagin Islands. This is the first documented earthquake doublet involving a megathrust event and a strike-slip event. The first event partially ruptured a seismic gap, which has not hosted large earthquakes since 1917, and the second event was unusual as it broke a trench-perpendicular fault within the incoming oceanic slab. We used an improved Bayesian geodetic inversion method to estimate the fault slip distributions of the major earthquakes using Interferometric Synthetic Aperture Radar (InSAR) wrapped phase and Global Navigation Satellite Systems (GNSS) offsets data. The geodetic inversions reveal that the Shumagin seismic gap is multi-segmented, and the M7.8 earthquake ruptured the eastern segment from 14 km down to 44 km depth. The coseismic slip occurred along a more steeply, 26∘ dipping segment, and was bounded up-dip by a bend of the megathrust interface to a shallower 8∘ dip angle connecting to the trench. The model for the M7.6 event tightly constrained the rupture depth extent to 19-39 km, within the depth range of the M7.8 coseismic rupture area. We find that the M7.6 event ruptured the incoming slab across its full seismogenic thickness, potentially reactivating subducted Kula-Resurrection seafloor-spreading ridge structures. Coulomb stress transfer models suggest that coseismic and/or postseismic slip of the M7.8 event could have triggered the M7.6 event. We conclude that the segmented megathrust structure and the location of intraslab fault structures limited the rupture dimensions of the M7.8 event and are responsible for the segmentation of the Shumagin seismic gap. Our study suggests that the western and shallower up-dip segments of the seismic gap did not fail and remain potential seismic and tsunami hazard sources. The unusual earthquake doublet provides a unique opportunity to improve our understanding of the role of the subducting lithosphere structure in the segmentation of subduction zones.
Single-cell RNA sequencing (scRNA-seq) data often contain doublets, where a doublet manifests as 1 cell barcode that corresponds to combined gene expression of two or more cells. Existence of ...doublets can lead to spurious biological interpretations. Here, we present s ingle- c ell MO del-driven D oublet D etection ( scMODD ), a model-driven algorithm to detect doublets in scRNA-seq data. ScMODD achieved similar performance compared to existing doublet detection algorithms which are primarily data-driven, showing the promise of model-driven approach for doublet detection. When implementing scMODD in simulated and real scRNA-seq data, we tested both the negative binomial (NB) model and the zero-inflated negative binomial (ZINB) model to serve as the underlying statistical model for scRNA-seq count data, and observed that incorporating zero inflation did not improve detection performance, suggesting that consideration of zero inflation is not necessary in the context of doublet detection in scRNA-seq.
A doublet earthquake event including two main shocks with a magnitude larger than Mw 6.0 occurred on 1 July 2022 in the Zagros fold‐and‐thrust belt, southeast Iran. The coseismic InSAR deformation ...field shows that this event caused significant surface uplift due to fault‐related folding in the seismic zone. The estimated preferred faulting model suggests that a higher dip angle fault (maximum slip of ∼1.1 m), and an overlying gentle dipping fault (maximum slip of ∼1.2 m) within the Bandar‐e‐Lengeh Anticline, are responsible for the first and second main shocks, respectively. The calculated Coulomb failure stress change suggests that the first main shock and its Mw 5.7 aftershock have a significantly positive triggering effect in the second main shock. The accumulated interseismic strain should have been partly released by the two main shocks. Finally, the salt diapir activity may affect the generation of the earthquake in the seismic zone.
Plain Language Summary
The doublet earthquake frequently occurred in the southeast part of the Zagros fold‐and‐thrust belt in the past years. In this study, we first adopted the Synthetic Aperture Radar images captured by Sentinel‐1 satellite to map the coseismic surface deformation of the 2022 Hormozgan doublet earthquake. The uplift of fault‐related folding controls the coseismic surface motion of these events from blind thrusting. Moreover, the two main shocks are caused by the rupture of two faults within the Bandar‐e‐Lengeh Anticline. Furthermore, the first main shock increased the stress in the source area of the second main shock, and positive triggered the rupture of the seismogenic fault of the second main shock. The interseismic surface deformation suggests that the 2022 Hormozgan doublet earthquake may have released the accumulated interseismic strain for the past ∼104 years. In addition, salt diapir activity in the southeast part of the seismic zone may contribute to the 2022 Hormozgan doublet earthquake.
Key Points
A doublet earthquake occurred in the southeastern of Zagros fold‐and‐thrust belt with a significant salt layers activity
A combination of steep and shallow blind faults is responsible for the 2022 Hormozgan doublet earthquake
The interseismic strain accumulation and salt diapir activity in the southeast of the seismic zone may cause this doublet earthquake
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•Q(J)-branch vibration-inversion-rotation transitions of NH3 probed at 6.2 µm.•First experimental investigation of air-broadening for the probed transitions.•N2, He, Ar, and O2 ...broadening coefficients measured for the probed transitions.
In this experimental investigation, collision broadening effects on the Q(J)-branch vibration-inversion-rotation spectral lines of ammonia (NH3) within the fundamental ν4 asymmetric bending vibrational band in the 6.2 µm mid-IR region are reported. A continuous-wave external-cavity quantum cascade laser coupled with a high-sensitive cavity ring-down spectrometer was employed to selectively probe 10 transitions in high-resolution, including few inversion doublets of gaseous NH3. Pressure-broadening coefficients, γNH3-Xi (Xi = He, Ar, N2, O2, zero-air) in cm−1 atm−1, characterizing the collision interaction between NH3 and various external perturbing gases, including helium, argon, nitrogen, oxygen, and zero-air, were determined at room temperature (296 K). Mean collision times and optical collision diameters of each collision partner were explored to gain deeper insight into the perturber-induced collision dynamics. This investigation elucidates the intricate intermolecular interactions and collision phenomena induced by various foreign perturbers with NH3, with potential implications for future spectroscopic and atmospheric research of this polyatomic molecule.
Nitrogen dioxide (14NO2) exhibits a unique doublet structure due to the presence of its unpaired electron, which results in a nonzero electronic angular momentum in the ground electronic state of the ...molecule. In this study, an investigation into high-resolution rovibrational spectral features associated with the spin-rotation doublets of 14NO2 was conducted using an external-cavity quantum cascade laser (EC-QCL)-coupled cavity ring-down spectrometer operating at 6.2 μm. Four spin-split doublets belonging to the RR branch of the (001)-(000) fundamental band were probed in the mid-IR spectral region. The air broadening and self-broadening coefficients were reported explicitly for each doublet component for the first time, to the best of our knowledge. The line-intensities were also quantified, and they were compared to the HITRAN database, revealing good agreement (<4% discrepancy).
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