bluuebunny/crossref_metadata_2025 huggingface dataset:
Robustness of purity of quantum channels
Authors: Wang Ying , Luo Yu , Xi Zhengjun
Published: April 2021

Quantifying purity is a basic problem in quantum information theory. When a quantum state passes through a quantum channel, its purity may be changed. In order to explore what role the quantum channel plays in this process, it is necessary to study the purity of quantum channels. In this paper, we formulate the quantum resource theory for channel purity. There are two basic elements in the quantum resource theory for channel purity: free channels and free superchannels. The free channels are completely randomizing channels which neither store nor output purity. The free superchannels are the uniformity preserving superchannels which do not generate resource channels from free ones. We also provide a method for the realization of a uniformity preserving superchannel. We quantify the purity of quantum channels by the robustness and show that the robustness of purity of a quantum channel (RPC) is a purity monotone. We obtain the efficient numerical calculation of RPC through semidefinite programming. Moreover, we find that the RPC has operational significance as the best advantage that one can obtain in the ensemble of quantum state discrimination games. As an application, we also study the RPC for some single-qubit channels.
The influence of Tm3+ to enhance 2.7 μm mid-infrared emission of Er3+ in CaLaGa3O7 crystal
Authors: Liu Yunyun , Pan Fei , Wang Xihu , Gao Ju
Published: April 2021

Er3+/Tm3+:CaLaGa3O7 (abbr. as Er3+/Tm3+:CLGO) crystal was grown successfully by Czochralski technology and detailed spectroscopic analyses were carried out. The effects of Tm3+ on the spectroscopic properties and mutual energy transfer mechanisms were investigated. It is found that the more suitable pumping scheme for laser applications at 2.7 μm laser is 980 nm excitation for Er3+/Tm3+ co-doped CLGO crystal. Under 980 nm excitation, the introductions of Tm3+ are helpful to achieve enhanced mid-infrared (MIR) emissions, as well as reduced near-infrared emissions. Furthermore, the introducing Tm3+ depopulated the lower laser lever through energy transfer and thus reduced the fluorescence lifetime of Er3+ : 4I13/2, without significantly affecting the fluorescence lifetime of the upper laser level Er3+ : 4I11/2, which reduces the self-saturation problem to a great degree. It concludes that this Er3+/Tm3+:CLGO crystal could be a potential MIR gain media for enhanced 2.7 μm laser under 980 nm pumping.
Radiative decay of the Ξ(1620) in a hadronic molecule picture *
Authors: Huang Yin , Yang Feng , Zhu HongQiang
Published: April 2021

Last year, the

state, which is cataloged in the Particle Data Group (PDG) with only one star, was reported again in the

final state by the Belle Collaboration. Its properties, such as the spectroscopy and decay width, cannot be simply explained in the context of conventional constituent quark models. This inspires an active discussion on the structure of this resonance. In this paper, we study the radiative decays of the newly observed

assuming that it is a meson-baryon molecular state of

and

with spin-parity

developed in our previous study. The partial decay widths of the

molecular state into

and

final states through hadronic loops are evaluated using effective Lagrangians. The partial widths for

is evaluated to be approximately

keV, which may be accessible for the LHCb experiment. If

is a

molecule, the radiative transition strength

is considerably small and the decay width is of the order of 0.01 eV. Future experimental measurements of these processes can be useful to test the molecule interpretations of the

.
Tested Performance of JUNO 20” PMTs
Authors: Zhang Haiqiong , Wang Zhimin , Wang Wei , Qin Zhonghua , Olshevskiy Alexander , Anfimov Nikolay , Wonsak Björn , Denis Korablev , Lachenmaier Tobias , Sterr Tobias , Tietzsch Alexander , Wang Jun , Hu Hang , Zhao Rao , Guo Jingyuan
Published: April 2021

The physics goal of the Jiangmen Underground Neutrino Observatory (JUNO) is mainly to determine the neutrino mass hierarchy by precisely measuring the oscillation spectrum with

3
%
/

E

v
i
s

(
M
e
V
)

energy resolution.Totally, about 20, 000 large area 20” tubes with high photon detection efficiency will be used to achieve this requirement, including 5,000 Hamamatsu dynode PMTs and 15,000 NNVT MCP PMTs. The JUNO collaboration has built two systems to check the performances of these tubes, which have been running since July 2017 and about 14000 tubes have been tested, so far. The key parameters compared with vendor data, including operating voltage, photon detection efficiency, dark count rate, rise time, fall time are presented. The selected PMTs meet all the requirements of the JUNO detector.
Tomographic imaging with Compton PET modules: ideal case and first implementation
Authors: Peng P. , Zhang M. , Zeraatkar N. , Qi J. , Cherry S.R.
Published: April 2021

In our previous studies, we demonstrated that the Compton PET module, a layer structure PET detector with side readout, can provide high performance in terms of spatial/energy/timing resolution, as well as high gamma ray detection efficiency. In this study, we investigate how to translate the high performance of the detector module into good quality reconstructed tomographic images. This study is performed using GATE simulation, as well as with physical experiments. Similar detector geometry is used in the simulation and experiment: two identical 4-layer detector modules are placed with face to face distance of 56 mm. In the simulation study, each layer consists of a 1-mm-pitch pixelated crystal array. In the experimental study, each layer is a monolithic crystal, which is virtually binned into 1 mm^2 cells to group single events according to the gamma ray interaction locations. A customized Derenzo phantom was placed between the two detector modules. By rotating the phantom using a motorized rotary stage, data along lines of response (LORs) at different angles were collected for reconstructing the tomographic image. The same reconstruction algorithm was used for both simulation and experimental studies. The results demonstrate that the simulation study could resolve 0.8 mm rods while the experimental study was able to resolve 1.0 mm rods.
Expanding number of Western US urban centers face declining summertime air quality due to enhanced wildland fire activity
Authors: Wilmot T Y , Hallar A G , Lin J C , Mallia D V
Published: April 2021

Combining multiple sources of information on atmospheric composition, wildland fire emissions, and fire area burned, we link decadal air quality trends in Western US urban centers with wildland fire activity during the months of August and September for the years 2000–2019. We find spatially consistent trends in extreme levels (upper quantile) of fine particulate matter (PM2.5), organic carbon, and absorption aerosol optical depth centered on the US Pacific Northwest during the month of August. Emerging trends were also found across the Pacific Northwest, western Montana, and Wyoming in September. Furthermore, we identify potential wildfire emission ‘hotspots’ from trends in wildfire derived PM2.5 emissions and burned area. The spatial correspondence between wildfire emissions hotspots and extreme air quality trends, as well as their concomitant spatial shift from August to September supports the hypothesis that wildfires are driving extreme air quality trends across the Western US. We derive further evidence of the influence of wildland fires on air quality in Western US urban centers from smoke induced PM2.5 enhancements calculated through statistical modeling of the PM2.5-meteorology relationship at 18 Western US cities. Our results highlight the significant risk of increased human exposure to wildfire smoke in August at these Western US population centers, while also pointing to the potential danger of emerging trends in Western US population growth, wildfire emissions, and extreme air quality in September.
Hybrid algorithm for multi artifact removal from single channel EEG
Authors: Noorbasha Sayedu Khasim , Florence Sudha Gnanou
Published: April 2021

Electroencephalogram (EEG) signals recorded from the ambulatory systems are mostly contaminated by various artifacts like, electrooculogram (EOG), motion artifacts (MA) and electrocardiogram (ECG) artifacts. These artifacts limit the accuracy in further analysis of EEG in practise. So far, several existing methods have been proposed with the combination of decomposition techniques and independent component analysis (ICA) to remove single artifacts and only few methods to remove multiple artifacts from the single channel EEG. As improperly denoised EEG signals can result in wrong diagnosis, in this work, Singular Spectrum Analysis (SSA) and ICA are jointly combined with Generalized Moreau Envelope Total Variation (GMETV) technique to simultaneously remove combinations of different artifacts from single channel EEG. In this work, the SSA is used to decompose the contaminated single channel EEG, while the ICA is employed to separate the various hidden sources as independent components (ICs). Although the ICA is adequate in source separation, there is still, some essential EEG signal data appearing as artifact in the IC. Hence, eliminating this would allow EEG signal information to be lost. The GMETV approach is proposed in this paper, to estimate the actual artifacts in order to address these issues. The estimated actual artifacts are subtracted from the artifact ICs providing the residue of wanted component of EEG. This residue is added back to the remaining ICs, to obtain the denoised EEG. Simulation results demonstrated that the proposed technique performs better compared to the existing techniques. The Relative Root Mean Square Error (RRMSE) is reduced by 12.02% and 7.22% compared to SSA-ICA and SSA-ICA-thresholding respectively. Similarly, the Correlation Coefficient (CC) is increased by 21.48% and 8.25% with respect to SSA-ICA and SSA-ICA-thresholding respectively.
A two-dimensional air streamer discharge modified model based on artificial stability term under non-uniform electric field at low temperature and sub-atmospheric pressure
Authors: ZHAO Zhihang , WEI Xinlao , SONG Shuang , CUI Lin , YANG Kailun , ZHANG Zhonghua
Published: April 2021

In this paper, an improved air discharge fluid model under non-uniform electric field is constructed based on the plasma module COMSOL Multiphysics with artificial stability term, and the boundary conditions developed in the previous paper are applied to the calculation of photoionization rate. Based on the modified model, the characteristics of low temperature sub-atmospheric air discharge under 13 kV direct current voltage are discussed, including needle-plate and needle-needle electrode structures. Firstly, in order to verify the reliability of the model, a numerical example and an experimental verification were carried out for the modified model respectively. Both verification results show that the model can ensure the accuracy and repeatability of the calculation. Secondly, according to the calculation results of the modified model, under the same voltage and spacing, the reduced electric field under low temperature sub-atmosphere pressure is larger than that under normal temperature and atmospheric pressure. The high electric field leads to the air discharge at low temperature and sub atmospheric pressure entering the streamer initiation stage earlier, and has a faster propagation speed in the streamer development stage, which shortens the overall discharge time. Finally, the discharge characteristics of the two electrode structures are compared, and it is found that the biggest difference between them is that there is a pre-ionization region near the cathode in the needle-needle electrode structure. When the pre-ionization level reaches 1013 cm−3, the propagation speed of the positive streamer remains unchanged throughout the discharge process, and is no longer affected by the negative streamer. The peak value of electric field decreases with the increase of pre-ionization level, and tends to be constant during streamer propagation. Based on the previous paper, this paper constructs the air discharge model under non-uniform electric field, complements with the previous paper, and forms a relatively complete set of air discharge simulation system under low temperature and sub atmospheric pressure, which provides a certain reference for future research.
Elastic behavior analysis of multilayers by finite element method
Authors: Roa Simón , Sirena Martín
Published: April 2021

We studied the elastic properties of free-standing multilayered systems using finite element analysis with a rigid spherical indenter. To model and simulate the elastic response of these systems a 2-dimensional axisymmetric solid model was used. In particular, multilayered systems with a total thickness of 10 [μm] and composed by a periodic bilayer array were studied. The bilayers thickness in each multilayered system, as well as the isotropic elastic constants (Young´s modulus and Poisson´s ratio) of each thin film, were fixed to be constant in all the cases. The influence on the mechanical properties of different relative thickness ratios (from 0.11 up to 9) between the two films in the bilayer was carefully studied. Our results indicated that changes in the relative thickness ratios can produce considerable changes in the elastic mechanical response of the multilayered systems, observing important variations up to 19% (for displacements lower than 10% of the first film thickness) on the magnitude of the effective Young´s modulus. The interplay between the structural properties of the layers gives place to the nonlinear behavior of the Young modulus as a function of the volume fraction of the different layers. Due to the non-homogenous nature of the system, a strong dependence of the sample Young´s modulus with respect to the indentation depth was observed. This work contributes to qualitatively understand the impact of different characteristics of multilayered systems, such as the elastic properties and the proportion of the composing materials, on its elastic behavior.
Numerical simulation with experimental validation of the structural reaction injection moulding of 3D continuous fibre reinforced polyurethane foam
Authors: Schäfer Kay , Nestler Daisy , Jahn Kristina , Niedziela Dariusz , Ireka Ikenna , Steiner Konrad , Kroll Lothar
Published: April 2021

Sandwich composite materials are established in the industry. Polyurethane foam reinforced with spacer fabric represents an innovative solution for a core in this field. It is manufactured in the Structural Reaction Injection Moulding (SRIM). This paper describes new investigations that provide the base for component and process design when using this Interpenetrating Phase Composite (IPC). Filling studies were carried out for this purpose in three moulding tools with different cavities with and without spacer fabric. It is shown that the PUR foam expansion and the foam bulk density are clearly influenced by the sprue type, cavity design and spacer fabric. Simulations are necessary to investigate all process-structure-property relationships in detail and to enable a user-friendly and efficient design of material and process. Adequate mathematical models to simulate the transport of mass, heat and momentum in the SRIM are presented in this paper. The resistance to the expansion process caused by the porous structures in the domain were taken into account. The transport of momentum in the mould is described with the Navier–Stokes-Brinkman equations which in the limit of the permeability tensor reduces to the Navier–Stokes equation. The model equations are solved numerically and the results show reasonable agreement with the experimental data.
Strategies for the construction of machine-learning potentials for accurate and efficient atomic-scale simulations
Authors: Miksch April M , Morawietz Tobias , Kästner Johannes , Urban Alexander , Artrith Nongnuch
Published: April 2021

Recent advances in machine-learning interatomic potentials have enabled the efficient modeling of complex atomistic systems with an accuracy that is comparable to that of conventional quantum-mechanics based methods. At the same time, the construction of new machine-learning potentials can seem a daunting task, as it involves data-science techniques that are not yet common in chemistry and materials science. Here, we provide a tutorial-style overview of strategies and best practices for the construction of artificial neural network (ANN) potentials. We illustrate the most important aspects of (a) data collection, (b) model selection, (c) training and validation, and (d) testing and refinement of ANN potentials on the basis of practical examples. Current research in the areas of active learning and delta learning are also discussed in the context of ANN potentials. This tutorial review aims at equipping computational chemists and materials scientists with the required background knowledge for ANN potential construction and application, with the intention to accelerate the adoption of the method, so that it can facilitate exciting research that would otherwise be challenging with conventional strategies.
Single step synthesis of WO3 nanoparticles by wire explosion process and its photocatalytic behaviour
Authors: Ranjan Prem , Suematsu H. , Sarathi R.
Published: April 2021

Tungsten (W) wires are exploded in oxygen ambience to get tungsten oxide (WO3) nanoparticles (NPs). Energy stored in the capacitors (EC) is used to overcome the sublimation energy of wire. Energy ratio (K, ratio of EC and sublimation energy) and oxygen pressure (P) are two control parameters for the particle phase and morphology in the wire explosion process. X-ray diffraction (XRD) patterns confirmed the partial oxidation of W for low values of K. For K = 2, oxidation increases with increase in P. For K = 10, complete oxidation was achieved irrespective of P. Particles are spherical in shape as observed from scanning electron microscope (SEM) and transmission electron microscope (TEM) micrographs. Particle size follows a log-normal distribution with a least mean size of 24.1 nm. UV-vis diffuse reflectance spectroscopy (DRS) was used to measure the absorbance of NPs (complete WO3 with least mean size) for band gap measurement. The band gap was found to be 2.92 eV (visible region). NPs are used as photocatalyst to degrade aqueous solution of methylene blue (MB) under visible light irradiation. 500 mg l−1 of WO3 NPs were optimum to degrade 10 mg l−1 MB in 120 min.
Supported Binary and Ternary Nanoalloy Nanoparticle Catalysts-A Green Processing Approach using the Leidenfrost layer as Nanoreactor
Authors: Es-Souni Mohammed
Published: April 2021

When a nanocarbon substrate is heated between 300 °C and 320 °C that is slightly above the Leidenfrost temperature and subsequently quenched in an aqueous solution containing a mixture of noble metal ions, a high density of nanoalloy nanoparticles (NPs) form on the surface. Large surface areas can be decorated in this way by nanoalloy NPs of the system (Au, Pt, Pd). Both binary AuPt, AuPd and PtPd as well as ternary nanoalloys are obtained. The chemical composition of the nanoalloys can be tuned by varying the ion mixture ratio of the solutions. The simultaneous reduction of the noble metal ions on the surface occurs without the need of any reducing agent, presumably owing to charge transfer from ionized species during the quenching process. The method yields nanocarbon-supported, highly adherent nanoalloy NPs, is materials efficient and cost effective because only the surface is modified with the costly noble metals. The supported nanoalloy NPs are exemplary applied to the electrooxidation of methanol and formic acid in acidic solutions, and show an overall high performance.
Lessons from recent medical history: an obsolete anti-reflux device in an older patient with variable gastrointestinal symptoms
Authors: Squires Charlotte , Porter Ross J , Ward Benjamin M
Published: April 2021

A frail 93-year-old lady presented with delirium, on a background of heart failure, cerebrovascular disease, constipation and osteoporosis. A computed tomography (CT) pulmonary angiography, undertaken due to persistent hypoxia, identified no pathology aside from an unusual appearance of the left hypochondrium, necessitating further elucidation with CT abdomen. This unexpectedly reported the presence of a gastric band, leading us to consider possible misidentification. Perusing her General Practitioner (GP) records demonstrated that she underwent surgical insertion of an Angelchik prosthesis in 1984. Angelchik prostheses were anti-reflux devices used for a short period, before falling from favour due to increasing evidence around late developing complications. A collateral history from family revealed that this patient had experienced multiple longstanding symptoms including bloating, reflux and constipation, potentially linked to her prosthesis, a previously unestablished link.
Deciphering the evolution of the ovule genetic network through expression analyses in Gnetum gnemon
Authors: Zumajo-Cardona Cecilia , Ambrose Barbara A
Published: April 2021

Background and aims

The ovule is a synapomorphy of all seed plants (gymnosperms and angiosperms); however, there are some striking differences in ovules among the major seed plant lineages, such as the number of integuments or the orientation of the ovule. The genetics involved in ovule development have been well studied in the model species Arabidopsis thaliana, which has two integuments and anatropous orientation. This study is approached from what is known in arabidopsis, focusing on the expression patterns of homologues of four genes known to be key for the proper development of the integuments in arabidopsis: AINTEGUMENTA (ANT), BELL1, (BEL1), KANADIs (KANs) and UNICORN (UCN).

Methods

We used histology to describe the morphoanatomical development from ovules to seeds in Gnetum gnemon. We carried out spatiotemporal expression analyses in G. gnemon, a gymnosperm, which has a unique ovule morphology with an integument covering the nucellus, two additional envelopes where the outermost becomes fleshy as the seed matures, and an orthotropous orientation.

Key Results

Our anatomical and developmental descriptions provide a framework for expression analyses in the ovule of G. gnemon. Our expression results show that although ANT, KAN and UCN homologues are expressed in the inner integument, their spatiotemporal patterns differ from those found in angiosperms. Furthermore, all homologues studied here are expressed in the nucellus, revealing major differences in seed plants. Finally, no expression of the studied homologues was detected in the outer envelopes.

Conclusions

Altogether, these analyses provide significant comparative data that allows us to better understand the functional evolution of these gene lineages, providing a compelling framework for evolutionary and developmental studies of seeds. Our findings suggest that these genes were most likely recruited from the sporangium development network and became restricted to the integuments of angiosperm ovules.
Cloning, expression, and characterization of Baeyer–Villiger monooxygenases from eukaryotic Exophiala jeanselmei strain KUFI-6N
Authors: Yamamoto Taisei , Kobayashi Kento , Hasegawa Yoshie , Iwaki Hiroaki
Published: April 2021

The fungus Exophiala jeanselmei strain KUFI-6N produces a unique cycloalkanone monooxygenase (ExCAMO) that displays an uncommon substrate spectrum of Baeyer–Villiger oxidation of 4-10-membered ring ketones. In this study, we aimed to identify and sequence the gene encoding ExCAMO from KUFI-6N and overexpress the gene in Escherichia coli. We found that the primary structure of ExCAMO is most closely related to the cycloalkanone monooxygenase from Cylindrocarpon radicicola ATCC 11011, with 54.2% amino acid identity. ExCAMO was functionally expressed in E. coli and its substrate spectrum and kinetic parameters were investigated. Substrate profiling indicated that ExCAMO is unusual among known Baeyer–Villiger monooxygenases owing to its ability to accept a variety of substrates, including C4-C12 membered ring ketones. ExCAMO has high affinity and catalytic efficiency toward cycloalkanones, the highest being toward cyclohexanone. Five other genes encoding Baeyer–Villiger monooxygenases were also cloned and expressed in E. coli.
Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections
Authors: Khan Jamshed , Patro Rob
Published: April 2021

Motivation

The construction of the compacted de Bruijn graph from collections of reference genomes is a task of increasing interest in genomic analyses. These graphs are increasingly used as sequence indices for short- and long-read alignment. Also, as we sequence and assemble a greater diversity of genomes, the colored compacted de Bruijn graph is being used more and more as the basis for efficient methods to perform comparative genomic analyses on these genomes. Therefore, time- and memory-efficient construction of the graph from reference sequences is an important problem.

Results

We introduce a new algorithm, implemented in the tool Cuttlefish, to construct the (colored) compacted de Bruijn graph from a collection of one or more genome references. Cuttlefish introduces a novel approach of modeling de Bruijn graph vertices as finite-state automata, and constrains these automata’s state-space to enable tracking their transitioning states with very low memory usage. Cuttlefish is also fast and highly parallelizable. Experimental results demonstrate that it scales much better than existing approaches, especially as the number and the scale of the input references grow. On a typical shared-memory machine, Cuttlefish constructed the graph for 100 human genomes in under 9 h, using ∼29 GB of memory. On 11 diverse conifer plant genomes, the compacted graph was constructed by Cuttlefish in under 9 h, using ∼84 GB of memory. The only other tool completing these tasks on the hardware took over 23 h using ∼126 GB of memory, and over 16 h using ∼289 GB of memory, respectively.

Availability and implementation

Cuttlefish is implemented in C++14, and is available under an open source license at https://github.com/COMBINE-lab/cuttlefish.

Supplementary information

Supplementary data are available at Bioinformatics online.
Visual exploration of large metabolic models
Authors: Aichem Michael , Czauderna Tobias , Zhu Yan , Zhao Jinxin , Klapperstück Matthias , Klein Karsten , Li Jian , Schreiber Falk
Published: April 2021

Motivation

Large metabolic models, including genome-scale metabolic models, are nowadays common in systems biology, biotechnology and pharmacology. They typically contain thousands of metabolites and reactions and therefore methods for their automatic visualization and interactive exploration can facilitate a better understanding of these models.

Results

We developed a novel method for the visual exploration of large metabolic models and implemented it in LMME (Large Metabolic Model Explorer), an add-on for the biological network analysis tool VANTED. The underlying idea of our method is to analyze a large model as follows. Starting from a decomposition into several subsystems, relationships between these subsystems are identified and an overview is computed and visualized. From this overview, detailed subviews may be constructed and visualized in order to explore subsystems and relationships in greater detail. Decompositions may either be predefined or computed, using built-in or self-implemented methods. Realized as add-on for VANTED, LMME is embedded in a domain-specific environment, allowing for further related analysis at any stage during the exploration. We describe the method, provide a use case and discuss the strengths and weaknesses of different decomposition methods.

Availability and implementation

The methods and algorithms presented here are implemented in LMME, an open-source add-on for VANTED. LMME can be downloaded from www.cls.uni-konstanz.de/software/lmme and VANTED can be downloaded from www.vanted.org. The source code of LMME is available from GitHub, at https://github.com/LSI-UniKonstanz/lmme.
Differential gene expression analysis for multi-subject single-cell RNA-sequencing studies withaggregateBioVar
Authors: Thurman Andrew L , Ratcliff Jason A , Chimenti Michael S , Pezzulo Alejandro A
Published: April 2021

Motivation

Single-cell RNA-sequencing (scRNA-seq) provides more granular biological information than bulk RNA-sequencing; bulk RNA sequencing remains popular due to lower costs which allows processing more biological replicates and design more powerful studies. As scRNA-seq costs have decreased, collecting data from more than one biological replicate has become more feasible, but careful modeling of different layers of biological variation remains challenging for many users. Here, we propose a statistical model for scRNA-seq gene counts, describe a simple method for estimating model parameters and show that failing to account for additional biological variation in scRNA-seq studies can inflate false discovery rates (FDRs) of statistical tests.

Results

First, in a simulation study, we show that when the gene expression distribution of a population of cells varies between subjects, a naïve approach to differential expression analysis will inflate the FDR. We then compare multiple differential expression testing methods on scRNA-seq datasets from human samples and from animal models. These analyses suggest that a naïve approach to differential expression testing could lead to many false discoveries; in contrast, an approach based on pseudobulk counts has better FDR control.

Availability and implementation

A software package, aggregateBioVar, is freely available on Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/aggregateBioVar.html) to accommodate compatibility with upstream and downstream methods in scRNA-seq data analysis pipelines.

Supplementary information

Raw gene-by-cell count matrices for pig scRNA-seq data are available as GEO accession GSE150211. Supplementary data are available at Bioinformatics online.
Alignment free sequence comparison methods and reservoir host prediction
Authors: Lee Bill , Smith David K , Guan Yi
Published: April 2021

Motivation

The emergence and subsequent pandemic of the SARS-CoV-2 virus raised urgent questions about its origin and, particularly, its reservoir host. These types of questions are long-standing problems in the management of emerging infectious diseases and are linked to virus discovery programs and the prediction of viruses that are likely to become zoonotic. Conventional means to identify reservoir hosts have relied on surveillance, experimental studies and phylogenetics. More recently, machine learning approaches have been applied to generate tools to swiftly predict reservoir hosts from sequence data.

Results

Here, we extend a recent work that combined sequence alignment and a mixture of alignment-free approaches using a gradient boosting machines machine learning model, which integrates genomic traits and phylogenetic neighbourhood signatures to predict reservoir hosts. We add a more uniform approach by applying Machine Learning with Digital Signal Processing-based structural patterns. The extended model was applied to an existing virus/reservoir host dataset and to the SARS-CoV-2 and related viruses and generated an improvement in prediction accuracy.

Availability and implementation

The source code used in this work is freely available at https://github.com/bill1167/hostgbms.

Supplementary information

Supplementary data are available at Bioinformatics online.
Dnmt2-null sperm block maternal transmission of a paramutant phenotype†
Authors: Yu Tian , Xie Yeming , Tang Chong , Wang Yue , Yuan Shuiqiao , Zheng Huili , Yan Wei
Published: April 2021

Previous studies have shown that Dnmt2-null sperm block the paternal transmission (through sperm) of certain acquired traits, e.g., high-fat diet–induced metabolic disorders or white tails due to a Kit paramutation. Here, we report that DNMT2 is also required for the transmission of a Kit paramutant phenotype (white tail tip) through the female germline (i.e., oocytes). Specifically, ablation of Dnmt2 led to aberrant profiles of tRNA-derived small RNAs (tsRNAs) and other small noncoding RNAs (sncRNAs) in sperm, which correlate with altered mRNA transcriptomes in pronuclear zygotes derived from wild-type oocytes carrying the Kit paramutation and a complete blockage of transmission of the paramutant phenotype through oocytes. Together, the present study suggests that both paternal and maternal transmissions of epigenetic phenotypes require intact DNMT2 functions in the male germline.
Movement-Related Gamma Synchrony Differentially Predicts Behavior in the Presence of Visual Interference Across the Lifespan
Authors: Spooner Rachel K , Arif Yasra , Taylor Brittany K , Wilson Tony W
Published: April 2021

The ability to allocate neural resources to task-relevant stimuli, while inhibiting distracting information in the surrounding environment (i.e., selective attention) is critical for high-level cognitive function, and declines in this ability have been linked to functional deficits in later life. Studies of age-related declines in selective attention have focused on frontal circuitry, with almost no work evaluating the contribution of motor cortical dynamics to successful task performance. Herein, we examined 69 healthy adults (23–72 years old) who completed a flanker task during magnetoencephalography (MEG). MEG data were imaged in the time-frequency domain using a beamformer to evaluate the contribution of motor cortical dynamics to age-related increases in behavioral interference effects. Our results showed that gamma oscillations in the contralateral motor cortex (M1) were a robust predictor of reaction time, regardless of interference level. Additionally, we observed condition-wise differences in gamma-by-age interactions, such that in younger adults, increases in M1 gamma power were predictive of faster reaction times during incongruent trials, while older adults did not receive this same behavioral benefit. Importantly, these data indicate that M1 gamma oscillations are differentially predictive of behavior in the presence, but not absence of visual interference, resulting in exhausted compensatory strategies with age.
Recurrent massive pulmonary embolism following catheter directed thrombolysis in a 21-year-old with COVID-19: a case report
Authors: Hirschbaum Julian H , Bradley C Pierce , Kingsford Philip , Mehra Anilkumar , Kwan Wilson
Published: April 2021

Background

Coronavirus Disease-2019 (COVID-19) has been associated with increased incidence of pulmonary embolism (PE), even among patients at low risk for venous thrombo-embolic (VTE) events.

Case summary

We present the case of a 21-year-old male, with no previous medical history, who presented with cough, fevers, shortness of breath, pleuritic chest pain, and 1 day of dizziness with near syncope as well as acutely worsened dyspnoea. He was subsequently diagnosed with COVID-19 and massive PE. He underwent successful catheter-directed thrombolysis (CDT), and his clinical status improved. One day following initial CDT, he developed acute respiratory failure and hypotension and was diagnosed with recurrent massive PE. He was treated with repeat CDT and extracorporeal membrane oxygenation (ECMO) to provide time for right ventricular recovery. The patient was able to be weaned off ECMO after 9 days and was eventually extubated and discharged to an acute rehabilitation facility.

Discussion

Beyond COVID-19, no hypercoagulable risk factors were identified despite thorough investigation. This case highlights the thrombogenic potential and morbid sequelae of SARS-CoV-2 infection, even in young patients. It also highlights the use of CDT and ECMO among patients with massive PE and COVID-19. To date, this is the youngest reported patient to develop massive PE in the setting of COVID-19.
Bail-out edge-to-edge mitral repair for an acute single leaflet device attachment: a case report
Authors: Kitamura Mitsunobu , Besler Christian , Lurz Philipp , Noack Thilo
Published: April 2021

Background

An acute single leaflet device attachment (SLDA) may occur during transcatheter mitral valve edge-to-edge repair (TMVr), if an inadequate grasping of the target leaflet and/or a leaflet injury are concomitant. The bail-out TMVr often fails due to the complex pathophysiology.

Case summary

We report a case of an acute SLDA after TMVr with the PASCAL Repair System for severe mitral regurgitation (MR) with mixed aetiology, i.e., a thin-appeared posterior leaflet and pseudo-prolapse of the anterior mitral leaflet due to mitral annular dilatation. An acute SLDA occurred 2 min after the deployment, with device detachment of the posterior leaflet. A bail-out TMVr with the MitraClip XTR system led to an optimal MR reduction with the PASCAL stabilized. Despite an adequate leaflet insertion of the 1st device achieved, the posterior leaflet was tear due to its fragile tissue characteristics. At discharge, echocardiography confirmed an optimal MR reduction to mild grade with both devices stabilized.

Discussion

The pathology of the mitral valve leaflet is essential to achieve successful TMVr procedure using edge-to-edge repair device. Since the mechanical stress to the target leaflet appears to vary according to the edge-to-edge repair devices, the leaflet tissue characteristics should be respected during device selection.
Management of ascending aorta perforation during transseptal puncture for left atrial appendage closure: a case report
Authors: Schamroth Pravda Nili , Codner Pablo , Vaknin Assa Hana , Hirsch Rafael
Published: April 2021

Background

An 82-year-old female with a history of atrial fibrillation and repeated episodes of major bleeding on direct oral anticoagulant therapy, with a high risk for thromboembolism and was referred for left atrial appendage closure.

Case summary

During the procedure, an unrecognized puncture of the aorta by the transseptal puncture (TSP) needle and inadvertent advancement of the sheath resulted in ascending aorta perforation. This perforation was closed percutaneously using an Amplatzer™ Duct Occluder (ADO). Reversal of heparinization with protamine sulphate was given to avoid intractable bleeding. However, this resulted in thrombus formation and subsequent embolization causing an ST-elevation myocardial infarction. This was treated with balloon dilatation and thrombus aspiration with subsequent Thrombolysis in Myocardial Infarction 3 flow.

Discussion

Inadvertent ascending aorta perforation is a rare yet serious complication that can occur during TSP. Percutaneous closure using an ADO is a viable management option. The reversal of heparin carries a risk of thrombus formation and should be avoided in cases where there is no evidence of overt bleeding.
Impact of closed loop stimulation on prognostic cardiopulmonary variables in patients with chronic heart failure and severe chronotropic incompetence: a pilot, randomized, crossover study
Authors: Proff Joachim , Merkely Béla , Papp Roland , Lenz Corinna , Nordbeck Peter , Butter Christian , Meyerhoefer Juergen , Doering Michael , MacCarter Dean J , Ingel Katharina , Thouet Thomas , Landmesser Ulf , Roser Mattias J
Published: April 2021

Aims

Clinical effects of rate-adaptive pacing in heart failure patients with chronotropic incompetence (CI) undergoing cardiac resynchronization therapy (CRT) remain unclear. Closed loop stimulation (CLS) is a new rate-adaptive sensor in CRT devices. We evaluated the effectiveness of CLS in CRT patients with severe CI, focusing primarily on key prognostic variables assessed by cardiopulmonary exercise (CPX) testing.

Methods and results

In the randomized, crossover, multicentre BIO|CREATE study, 20 CRT patients with severe CI and NYHA Class II/III (60%/40%) were randomized 1:1 to the sequence DDD-40 mode to DDD-CLS mode, or the sequence DDD-CLS mode to DDD-40 mode (1 month in each mode). Patients underwent symptom-limited treadmill-based CPX test in each mode. An improvement (decrease) of the ventilatory efficiency (VE) slope of ≥5% during CLS was regarded as positive response to CLS. Seventeen patients with full data sets had a mean intra-individual VE slope change of −1.8 ± 3.0 (−4.1%) with CLS (P = 0.23). Eight patients (47%) were CLS responders, with a −6.1 ± 2.7 (−16.4%) slope change (P = 0.029). Compared to non-responders, CLS responders had a higher left ventricular (LV) ejection fraction (46 ± 3 vs. 36 ± 9%; P = 0.0070), smaller end-diastolic LV volume (121 ± 34 vs. 181 ± 41 mL; P = 0.0085), smaller end-systolic LV volume (65 ± 23 vs. 114 ± 39 mL; P = 0.0076), and were predominantly in NYHA Class II (P = 0.0498).

Conclusion

The data of the present pilot study are compatible with the notion that CLS activation may improve VE slope in CRT patients with severe CI and less advanced heart failure. Further research is needed to determine the long-term clinical outcomes of CLS.
Loss of Adam10 Disrupts Ion Transport in Immortalized Kidney Collecting Duct Cells
Authors: Assmus Adrienne , Mullins Linda , Ward Mairi , Dobie Ross , Hunter Robert , Henderson Neil C , Mullins John J
Published: April 2021

The kidney cortical collecting duct (CCD) comprises principal cells (PCs), intercalated cells (IC), and the recently discovered intermediate cell type. Kidney pathology in a mouse model of the syndrome of apparent aldosterone excess revealed plasticity of the CCD, with altered PC:intermediate cell:IC ratio. The self-immortalized mouse CCD cell line, mCCDcl1, shows functional characteristics of PCs, but displays a range of cell types, including intermediate cells, making it ideal to study plasticity. We knocked out Adam10, a key component of the Notch pathway, in mCCDcl1 cells, using CRISPR-Cas9 technology, and isolated independent clones, which exhibited severely affected sodium transport capacity and loss of aldosterone response. Single-cell RNA sequencing revealed significantly reduced expression of major PC-specific markers, such as Scnn1g (γ-ENaC) and Hsd11b2 (11βHSD2), but no significant changes in transcription of components of the Notch pathway were observed. Immunostaining in the knockout clone confirmed the decrease in expression of γ-ENaC and importantly, showed an altered, diffuse distribution of PC and IC markers, suggesting altered trafficking in the Adam10 knockout clone as an explanation for the loss of polarization.
Sequencing, assembly and annotation of the whole-insect genome of Lymantria dispar dispar, the European gypsy moth
Authors: Sparks Michael E , Hebert Francois Olivier , Johnston J Spencer , Hamelin Richard C , Cusson Michel , Levesque Roger C , Gundersen-Rindal Dawn E
Published: April 2021

The European gypsy moth, Lymantria dispar dispar (LDD), is an invasive insect and a threat to urban trees, forests and forest-related industries in North America. For use as a comparator with a previously published genome based on the LD652 pupal ovary-derived cell line, as well as whole-insect genome sequences obtained from the Asian gypsy moth subspecies L. dispar asiatica and L. dispar japonica, the whole-insect LDD genome was sequenced, assembled and annotated. The resulting assembly was 998 Mb in size, with a contig N50 of 662 Kb and a GC content of 38.8%. Long interspersed nuclear elements constitute 25.4% of the whole-insect genome, and a total of 11,901 genes predicted by automated gene finding encoded proteins exhibiting homology with reference sequences in the NCBI NR and/or UniProtKB databases at the most stringent similarity cutoff level (i.e., the gold tier). These results will be especially useful in developing a better understanding of the biology and population genetics of L. dispar and the genetic features underlying Lepidoptera in general.
New Roles for Model Genetic Organisms in Understanding and Treating Human Disease: Report From The 2006 Genetics Society of America Meeting
Authors: Spradling Allan , Ganetsky Barry , Hieter Phil , Johnston Mark , Olson Maynard , Orr-Weaver Terry , Rossant Janet , Sanchez Alejandro , Waterston Robert
Published: April 2021

Fundamental biological knowledge and the technology to acquire it have been immeasurably advanced by past efforts to understand and manipulate the genomes of model organisms. Has the utility of bacteria, yeast, worms, flies, mice, plants, and other models now peaked and are humans poised to become the model organism of the future? The Genetics Society of America recently convened its 2006 meeting entitled “Genetic Analysis: Model Organisms to Human Biology” to examine the future role of genetic research. (Because of time limitations, the meeting was unable to cover the substantial contributions and future potential of research on model prokaryotic organisms.) In fact, the potential of model-organism-based studies has grown substantially in recent years. The genomics revolution has revealed an underlying unity between the cells and tissues of eukaryotic organisms from yeast to humans. No uniquely human biological mechanisms have yet come to light. This common evolutionary heritage makes it possible to use genetically tractable organisms to model important aspects of human medical disorders such as cancer, birth defects, neurological dysfunction, reproductive failure, malnutrition, and aging in systems amenable to rapid and powerful experimentation. Applying model systems in this way will allow us to identify common genes, proteins, and processes that underlie human medical conditions. It will allow us to systematically decipher the gene–gene and gene–environment interactions that influence complex multigenic disorders. Above all, disease models have the potential to address a growing gap between our ability to collect human genetic data and to productively interpret and apply it. If model organism research is supported with these goals in mind, we can look forward to diagnosing and treating human disease using information from multiple systems and to a medical science built on the unified history of life on earth.
Bivalve Molluscs as Model Systems for Studying Mitochondrial Biology
Authors: Ghiselli Fabrizio , Iannello Mariangela , Piccinini Giovanni , Milani Liliana
Published: April 2021

Synopsis

The class Bivalvia is a highly successful and ancient taxon including ∼25,000 living species. During their long evolutionary history bivalves adapted to a wide range of physicochemical conditions, habitats, biological interactions, and feeding habits. Bivalves can have strikingly different size, and despite their apparently simple body plan, they evolved very different shell shapes, and complex anatomic structures. One of the most striking features of this class of animals is their peculiar mitochondrial biology: some bivalves have facultatively anaerobic mitochondria that allow them to survive prolonged periods of anoxia/hypoxia. Moreover, more than 100 species have now been reported showing the only known evolutionarily stable exception to the strictly maternal inheritance of mitochondria in animals, named doubly uniparental inheritance. Mitochondrial activity is fundamental to eukaryotic life, and thanks to their diversity and uncommon features, bivalves represent a great model system to expand our knowledge about mitochondrial biology, so far limited to a few species. We highlight recent works studying mitochondrial biology in bivalves at either genomic or physiological level. A link between these two approaches is still missing, and we believe that an integrated approach and collaborative relationships are the only possible ways to be successful in such endeavor.