bluuebunny/crossref_metadata_2025 huggingface dataset:
Global and local reduced models for interacting, heterogeneous agents
Authors: Thiem Thomas N. , Kemeth Felix P. , Bertalan Tom , Laing Carlo R. , Kevrekidis Ioannis G.
Published: July 2021

Large collections of coupled, heterogeneous agents can manifest complex dynamical behavior presenting difficulties for simulation and analysis. However, if the collective dynamics lie on a low-dimensional manifold, then the original agent-based model may be approximated with a simplified surrogate model on and near the low-dimensional space where the dynamics live. Analytically identifying such simplified models can be challenging or impossible, but here we present a data-driven coarse-graining methodology for discovering such reduced models. We consider two types of reduced models: globally based models that use global information and predict dynamics using information from the whole ensemble and locally based models that use local information, that is, information from just a subset of agents close (close in heterogeneity space, not physical space) to an agent, to predict the dynamics of an agent. For both approaches, we are able to learn laws governing the behavior of the reduced system on the low-dimensional manifold directly from time series of states from the agent-based system. These laws take the form of either a system of ordinary differential equations (ODEs), for the globally based approach, or a partial differential equation (PDE) in the locally based case. For each technique, we employ a specialized artificial neural network integrator that has been templated on an Euler time stepper (i.e., a ResNet) to learn the laws of the reduced model. As part of our methodology, we utilize the proper orthogonal decomposition (POD) to identify the low-dimensional space of the dynamics. Our globally based technique uses the resulting POD basis to define a set of coordinates for the agent states in this space and then seeks to learn the time evolution of these coordinates as a system of ODEs. For the locally based technique, we propose a methodology for learning a partial differential equation representation of the agents; the PDE law depends on the state variables and partial derivatives of the state variables with respect to model heterogeneities. We require that the state variables are smooth with respect to model heterogeneities, which permit us to cast the discrete agent-based problem as a continuous one in heterogeneity space. The agents in such a representation bear similarity to the discretization points used in typical finite element/volume methods. As an illustration of the efficacy of our techniques, we consider a simplified coupled neuron model for rhythmic oscillations in the pre-Bötzinger complex and demonstrate how our data-driven surrogate models are able to produce dynamics comparable to the dynamics of the full system. A nontrivial conclusion is that the dynamics can be equally well reproduced by an all-to-all coupled and by a locally coupled model of the same agents.
Radio frequency mixing modules for superconducting qubit room temperature control systems
Authors: Xu Yilun , Huang Gang , Santiago David I. , Siddiqi Irfan
Published: July 2021

As the number of qubits in nascent quantum processing units increases, the connectorized RF (radio frequency) analog circuits used in first generation experiments become exceedingly complex. The physical size, cost, and electrical failure rate all become limiting factors in the extensibility of control systems. We have developed a series of compact RF mixing boards to address this challenge by integrating I/Q quadrature mixing, intermediate frequency/LO (local oscillator)/RF power level adjustments, and direct current bias fine tuning on a 40 × 80 mm2 four-layer printed circuit board with electromagnetic interference shielding. The RF mixing module is designed to work with RF and LO frequencies between 2.5 and 8.5 GHz. The typical image rejection and adjacent channel isolation are measured to be ∼27 dBc and ∼50 dB. By scanning the drive phase in a loopback test, the module short-term amplitude and phase linearity are typically measured to be 5 ×10−4 (Vpp/Vmean) and 1 ×10−3 radian (pk–pk). The operation of the RF mixing board was validated by integrating it into the room temperature control system of a superconducting quantum processor and executing randomized benchmarking characterization of single and two qubit gates. We measured a single-qubit process infidelity of 9.3(3) × 10−4 and a two-qubit process infidelity of 2.7(1) × 10−2.
Anharmonic vibration of Ag atom in low lattice thermal conductivity chain structure phosphide Ag3SnP7
Authors: Miyata Masanobu
Published: July 2021

This study investigates the phonon-transport properties of transition metal phosphide Ag3SnP7, experimentally and theoretically. Polycrystalline Ag3SnP7 is synthesized using a chemical vapor transport technique with iodine as the transport agent. The experimental lattice thermal conductivity κlat of Ag3SnP7 is low, at approximately 1.5 W K−1 m−1. The phonon properties of Ag3SnP7 are calculated using self-consistent phonon (SCPH) calculation with a fourth-order interatomic force constant (IFC). The value of κlat from SCPH calculation corresponds with that of experimentally obtained κlat, demonstrating that using a fourth-order IFC is important for phonon transport in the Ag3SnP7 system. The shape of the energy potential of Ag at a 4f site is distinctly non-parabolic, suggesting that atomic-Ag vibration originates from the anharmonicity of phonon modes in the Ag3SnP7 system. The estimated phonon lifetime in Ag3SnP7 at 300 K using a logarithmic plot of κlat vs Cpvm2 (the specific heat is Cp, the mean speed of sound is vm) is very small at 0.24 ps, beyond that of Bi2Te3 and other phosphides. Results show that the low value of κlat originates from a short phonon lifetime caused by the anharmonic vibration of Ag at the 4f site.
3D-printed terahertz metamaterial absorber based on vertical split-ring resonator
Authors: Li Shengnan , Zhang Liuyang , Chen Xuefeng
Published: July 2021

Terahertz metamaterials have received significant attention for their unprecedented abilities to modulate the terahertz wave effectively. The traditional manufacturing of terahertz metamaterials has been mainly relying on the micro–nanofabrication technique due to the micro-scale characteristic size of the unit cell. However, the fabrication usually involves multi-step and time-consuming processes, as well as expensive equipment. To overcome these shortcomings, here we used projection micro-stereolithography 3D printing followed by the magnetron sputtering to additively manufacture terahertz metamaterials. A vertical split-ring resonator-based metamaterial absorber is taken into account as the prototype to demonstrate the simplicity of the proposed fabrication technique. Both terahertz time-domain spectroscopy measurement and simulation indicate that the 3D printed absorber has a near-unity narrow-band absorption peak at 0.8 THz. The absorption mechanism is clearly clarified by the coupled mode and impedance matching theory and electromagnetic field distribution at the resonant frequency. A 3D printed narrow-band absorber also demonstrates great potential for highly efficient biosensing of lactose and galactose. It can be estimated that 3D printing provides an easy-going fabrication approach for THz metamaterials and shed light on its foreseeable application for the versatile design and manufacturing of functional THz devices.
Hydrodynamic models of astrophysical wormholes: The general concept
Authors: Churilov Semyon , Stepanyants Yury
Published: July 2021

We study the amplification of shallow-water waves in the course of their propagation in a duct of a variable cross section with a spatially inhomogeneous flow. We derive the basic set of equations for the wave propagation and present the asymptotic analysis of solutions in the neighborhood of critical points where the wave speed coincides with the speed of the current. The considered model represents a kinematic analog of astrophysical event horizons occurring in the vicinity of the black holes (BH) or white holes (WH). We study then the wave propagation in the flow with two critical points (two horizons) when the flow transits first the BH horizon and then the WH one or vice versa. In the former case, the region between the critical points mimics a wormhole in general relativity. The theoretical results are illustrated by numerical calculations of wave propagation through the critical points. It is shown that the wave amplification after passing the active zone between the horizons takes place in BH–WH arrangements only and can occur for different relationships between the subcritical and supercritical flow velocities. The frequency dependence of the amplification factor is obtained and quantified in terms of the velocity ratio within and outside the “wormhole domain.”
Analytic derivation of the inertial range of compressible turbulence
Authors: Goldman I.
Published: July 2021

An analytic model for steady state turbulence is employed to obtain the inertial range power spectrum of compressible turbulence. We assume that for homogeneous turbulence, the timescales controlling the energy injected at a given wavenumber from all smaller wavenumbers are equal for each spatial component. However, the longitudinal component energy is diverted into compression, so the rate controlling the energy that is transferred to all larger wavenumbers by the turbulent viscosity is reduced. The resulting inertial range is a power law with an index of −2. Indeed, such power spectra were observed in various astrophysical settings and also in numerical simulations.
Electron holes in a κ distribution background with singularities
Authors: Haas Fernando
Published: July 2021

The pseudo-potential method is applied to derive diverse propagating electron–hole structures in a nonthermal or κ particle distribution function background. The associated distribution function Ansatz reproduces the Schamel distribution of [H. Schamel, Phys. Plasmas 22, 042301 (2015)] in the Maxwellian (κ→∞) limit, providing a significant generalization of it for plasmas where superthermal electrons are ubiquitous, such as space plasmas. The pseudo-potential and the nonlinear dispersion relation are evaluated. The role of the spectral index κ on the nonlinear dispersion relation is investigated, in what concerns the wave amplitude, for instance. The energy-like first integral from Poisson's equation is applied to analyze the properties of diverse classes of solutions: with the absence of trapped electrons, with a non-analytic distribution of trapped electrons, or with a surplus of trapped electrons. Special attention is, therefore, paid to the non-orthodox case where the electrons distribution function exhibits strong singularities, being discontinuous or non-analytic.
Immediate impact of the COVID-19 pandemic on the work and personal lives of Australian hospital clinical staff
Authors: Holton Sara , Wynter Karen , Trueman Melody , Bruce Suellen , Sweeney Susan , Crowe Shane , Dabscheck Adrian , Eleftheriou Paul , Booth Sarah , Hitch Danielle , Said Catherine M. , Haines Kimberley J. , Rasmussen Bodil
Published: July 2021

Objective This study investigated the short-term psychosocial effects of the COVID-19 pandemic on hospital clinical staff, specifically their self-reported concerns and perceived impact on their work and personal lives. Methods Nurses, midwives, doctors and allied health staff at a large metropolitan tertiary health service in Melbourne, Australia, completed an anonymous online cross-sectional survey between 15 May and 10 June 2020. The survey assessed respondents’ COVID-19 contact status, concerns related to COVID-19 and other effects of COVID-19. Space was provided for free-text comments. Results Respondents were mostly concerned about contracting COVID-19, infecting family members and caring for patients with COVID-19. Concerns about accessing and using personal protective equipment, redeployment and their ability to provide high-quality patient care during the pandemic were also reported. Pregnant staff expressed uncertainty about the possible impact of COVID-19 on their pregnancy. Despite their concerns, few staff had considered resigning, and positive aspects of the pandemic were also described. Conclusion The COVID-19 pandemic has had a considerable impact on the work and personal lives of hospital clinical staff. Staff, particularly those who are pregnant, would benefit from targeted well-being and support initiatives that address their concerns and help them manage their work and personal lives. What is known about the topic? The COVID-19 pandemic is having an impact on healthcare workers’ psychological well-being. Little is known about their COVID-19-related concerns and the perceived impact of the pandemic on their work and personal lives, particularly hospital clinical staff during the ‘first wave’ of the pandemic in Australia. What does this paper add? This paper contributes to a small but emerging evidence base about the impact of the COVID-19 pandemic on the work and personal lives of hospital clinical staff. Most staff were concerned about their own health and the risk to their families, friends and colleagues. Despite their concerns, few had considered resigning. Uncertainty about the possible impact of COVID-19 on pregnancy was also reported. What are the implications for practitioners? During the current and future pandemics, staff, especially those who are pregnant, would benefit from targeted well-being and support initiatives that address their concerns and help them manage the impact on their health, work and personal lives.
Introducing Pseudoramps and Mixed Ramp-Gaussian Jensen Basis Sets for Better Nuclear Densities
Authors: Cox Claudia S. , McKemmish Laura K.
Published: July 2021

Gaussian basis sets dominate quantum chemistry but struggle to model near-core electron densities and thus nuclear magnetic resonance (NMR) spectral properties. Mixed ramp-Gaussian (RG) basis sets show significant promise for these core properties due to the inclusion of a ramp-function with a non-zero nuclear-electron cusp. To enable quicker testing of the potential of RG basis sets for core chemistry, here we approximate ramps as a large linear combination of Gaussians called pseudoramps, thus enabling standard quantum chemistry packages to be used to approximate RG basis set results. We produce and test rampified general-purpose segmented Jensen basis sets. These basis sets retain the valence chemistry of their parent all-Gaussian basis sets, as desired, but unfortunately fail to show significantly improved performance in core chemistry. Crucially, for NMR spin-spin couplings (the most promising potential application of RG basis sets), general-purpose basis sets are so poorly performing that results cannot be interpreted. For chemical shifts, P-ramps are likely required for improved performance. We conclude that the use of pseudoramps to test the performance of ramp-Gaussian basis sets is extremely helpful, decoupling methodology development and evaluation from implementation, but that more sophisticated basis set optimisation will be required to identify potential advantages of ramp-Gaussian basis sets over all-Gaussian basis sets.
Complexes of humic acid with cationic surfactants support the supramolecular view of extracted humic matter
Authors: Chaaban Abdul Amir , Lartiges Bruno , El Hayek Eliane , Kazpard Veronique , Plisson-Chastang Celia , Vicendo Patricia , Caillet Celine
Published: July 2021

Environmental context The molecular organisation of humic substances is key to understanding various natural and engineered processes, such as metal speciation and bioavailability. Two main models have been proposed: polymeric organisation and supramolecular organisation. A physicochemical approach, based on the interaction of humic acid with increasing amounts of cationic surfactants, leads to a sequence of molecular structures that provides support to the supramolecular view of humic organisation. Abstract The structural organisation of extracted humic matter, polymeric or supramolecular, has been a long-standing controversial issue. In this paper, we show that the interaction between a reference humic material, the Suwannee River Humic Acid (SRHA), and a homologous series of cationic surfactants (n-alkyl trimethyl ammonium chloride) provides key insights to resolve the controversy. By combining measurements of turbidity, electrophoretic mobility, surface tension and cryogenic transmission electron microscopy, we show that: (i) the binding of cationic surfactant to the anionic humic acid is initially triggered by electrostatic interactions; (ii) the contrasting evolution of turbidity–surfactant concentration curves implies that the surfactant alkyl chain interacts with the hydrophobic moieties of humic matter from very low concentrations of surfactant; (iii) a drastic restructuring of humic matter occurs on surfactant binding, which brings out supplementary anionic humic sites; (iv) in the presence of C12 cationic surfactant, SRHA spontaneously forms stable nanoscale unilamellar vesicles, which, in addition to the high surface activity of complexes, could be of interest in the remediation of oil-contaminated environments; (v) the sequence of molecular structures obtained from SRHA with increasing amounts of C12-cationic surfactant – humic-rich vesicles, aggregates, surfactant-rich vesicles – bears striking similarities with the phase behaviour of aqueous mixtures of anionic and cationic surfactants, thus supporting the supramolecular view of humic structure.
Temperature effects on RNA polymerase initiation kinetics reveal which open complex initiates and that bubble collapse is stepwise
Authors: Plaskon Dylan M. , Henderson Kate L. , Felth Lindsey C. , Molzahn Cristen M. , Evensen Claire , Dyke Sarah , Shkel Irina A. , Record M. Thomas
Published: July 2021

Significance

To transcribe DNA sequences into RNA, RNA polymerase (RNAP) first binds to promoter DNA. The promoter sequence dictates both binding strength and rate of remodeling the DNA duplex by RNAP to open 13 base pairs in the start site region. This open “bubble” allows complementary nucleotides to pair with template-strand bases and be incorporated into RNA. All sequence-specific, RNAP-promoter contacts must break for RNAP to escape and elongate the RNA, but how this occurs is not well understood. Here, we report rate constants for each initiation step at the λPR promoter at different temperatures. We analyze these data to obtain insights into which open complex initiates and when RNAP-promoter contacts are disrupted, allowing bubble collapse, duplex formation, and promoter escape.
Evolution of a σ–(c-di-GMP)–anti-σ switch
Authors: Schumacher Maria A. , Gallagher Kelley A. , Holmes Neil A. , Chandra Govind , Henderson Max , Kysela David T. , Brennan Richard G. , Buttner Mark J.
Published: July 2021

Significance

Diverse bacterial lifestyle transitions are controlled by the nucleotide second messenger c-di-GMP, including virulence, motility, and biofilm formation. To control such fundamentally distinct processes, the set of genes under c-di-GMP control must have gone through several shifts during bacterial evolution. Here we show that the same σ–(c-di-GMP)–anti-σ switch has been co-opted during evolution to regulate distinct biological functions in unicellular and filamentous bacteria, controlling type IV pilus production in the genusRubrobacterand the differentiation of reproductive hyphae into spores inStreptomyces. Moreover, we show that the anti-σ likely originated as a homodimer and evolved to become a monomer through an intragenic duplication event. This study thus describes the structural and functional evolution of a c-di-GMP regulatory switch.
Tight electrostatic regulation of the OH production rate from the photolysis of hydrogen peroxide adsorbed on surfaces
Authors: Ruiz-López Manuel F. , Martins-Costa Marilia T. C. , Francisco Joseph S. , Anglada Josep M.
Published: July 2021

Significance

The photolysis of hydrogen peroxide produces OH radicals and has enormous environmental and technological relevance. Experiments have shown that the absorption cross-sections beyond 290 nm (solar radiation reaching the Earth’s surface) are not very different in the gas phase and in bulk water solution, and hence comparable photolytic rate constants are found in these two media. Computer simulations reported in the present article reveal, however, that the situation changes dramatically when hydrogen peroxide is adsorbed on surfaces. The results emphasize the role of the local electric field and describe a nonlinear variation of the absorption cross-sections with field strength. The implications of this finding are discussed.
Preparation for assembly and commissioning of ITER
Authors: Bigot B.
Published: July 2021

Progress is described on the construction of infrastructure and plant systems, and on the manufacturing of the ITER tokamak components and their assembly since the IAEA FEC 2018. Major achievements in this period have been the completion of the tokamak building and installation of the cryostat base and lower section that mark the start of tokamak assembly in 2020. This has been followed by the arrival of key core tokamak components to enable assembly of the first tokamak sector, which is made up of one vacuum vessel (VV) sector, 2 toroidal field (TF) coils and the corresponding thermal shield (TS), and the completion of manufacturing and testing of the first two poloidal field (PF) coils (PF5 and PF6). In parallel with this, the tools required for assembly have been commissioned and plant systems required for operations have progressed in construction and have started or will start commissioning in the near future. The remaining core tokamak components (e.g. the remaining eight VV sectors, TF coils, PF coils and central solenoid (CS) modules) are in advanced manufacturing state or already completed and under testing, as required for the assembly plan to first plasma (FP). In parallel with machine assembly, systems to support plasma operation during the FP and later phases of the ITER research plan (IRP) have made significant progress as well. This includes the plasma control system, for which the final design for FP has been completed, the electron cyclotron heating (ECH) system, diagnostic systems, plasma protection components for FP and the disruption mitigation system (DMS). The IRP itself has also been consolidated and specific issues identified where R&D support by the ITER Members’ fusion communities may refine it further. The consolidation of the IRP has involved changes to the upgrade paths considered in the baseline by the identification of MHD stable plasma scenarios that can meet ITER’s Q = 5 steady-state fusion power goal with neutral beam heating (NBI) and ECH thus removing the need for the installation of a lower hybrid current drive (LHCD) system previously included as an upgrade in the baseline for this specific purpose.
Corrigendum: Study of water discharge in the Ulee Lheue Port Channel, Indonesia (IOP Conf. Ser.: Earth Environ. Sci. 429 012013)
Authors: Setiawan I , Isbah F , Muhammad M , Yuni S M , Purnawan S , Akram A , Ilhamsyah Y
Published: July 2021

Page 2:

In the section 2., the following text appears:

“2. Materials and metodhs”

This should read:

“2. Materials and methods”

In the 2.2. Research procedure section, the following text appears:

“This velocity measurement was held four times a day at the three depths, as presented in Figure 2.”

This should read:

“This velocity measurement was held four times a day at the three depths, as presented in Figure 1.”

Page 3:

In the 3.1. Water depth section, the following text appears:

“The data concerning water depth from the week I to IV are presented in Figure 3 to 6.”

This should read:

“The data concerning water depth from the week I to IV are presented in Figure 2 to 5.”

Page 5:

In the 3.2. The current velocity section, the following text appears:

“Figure 7 shows that is the current velocity of the 5th day at 03:00 pm was the highest in the first week, that was 0.26 m/s.”

“Based on Figure 8, the current velocity on 12th Jumada I at 09:00 am was 0.35 m/s because the depth of the water also headed towards the tide, resulting in the large current into the port channel.”

This should read:

“Figure 6 shows that is the current velocity of the 5th day at 03:00 pm was the highest in the first week, that was 0.26 m/s.”

“Based on Figure 7, the current velocity on 12th Jumada I at 09:00 am was 0.35 m/s because the depth of the water also headed towards the tide, resulting in the large current into the port channel.”
Retraction: Natural Microalgae Biofilm As A Tool To Clean-Up Mining Wastewater (IOP Conf. Ser.: Earth Environ. Sci.
775 012014)
Authors: Anbu Kumar S. , Gupta Shivam , Kumar Shubham , Meena Pawan Kumar
Published: July 2021

It has come to the attention of IOP Publishing that this article should not have been submitted for publication because of its substantial replication without citation of an earlier-published paper (Adamu Yunusa Ugya, et al 2020, All Life, 13:1, 644-657). Consequently, this paper has been retracted by IOP Publishing. The authors agree to this retraction.

Retraction published: 21 July 2021
Conclusion
Authors: Tyler Amanda L.
Published: July 2021

The book concludes by celebrating aspects of the history of the writ of habeas corpus as a great writ of liberty, observing that the writ has served as a vehicle for securing the freedom of political prisoners and slaves and for the declaration of bedrock constitutional rights in criminal cases. But, the conclusion also notes, it is also the case that habeas corpus has sometimes fallen short, as the World War II mass incarceration of Japanese Americans reveals. Habeas, in other words, is sometimes only as effective as the politics of the time permit. Highlighting the challenges that lie ahead for the future of the storied writ, the conclusion suggests that we would do well to recall the period when the writ earned Blackstone’s praise as a “second magna carta,” for that history tells a story of a habeas writ that could bring even the King of England to his knees before the law.
Characteristics of Work and Employment Related to Leisure-Time Physical Activity: Results of the National Health Survey, Brazil, 2013
Authors: Assunção Ada A , Claro Rafael Moreira
Published: July 2021

Leisure-time physical activity (LTPA) is a crucial behavior to reduce the global burden of disease. The objective of this study was to understand the relationship between LTPA, employment status, and physical workload (PWL). This study analyzed data from 38 449 individuals interviewed in the National Health Survey (NHS), representative of the Brazilian population. This paper examines LTPA in the last 30 days and whether participants achieved the recommended physical activity (≥150 min week−1) according to employment status and PWL utilizing Poisson regression models. One third and ¼ of the participants reported LTPA in the last 30 days and achieved the recommended LTPA, respectively. Intense PWL was reported by 28.7% [95% confidence interval (CI): 27.8–29.6%] of participants; 32.2% among men (95% CI: 31.0–33.5%); 24.3% among women (95% CI: 23.1–25.5%). Precarious employment was associated with a lower prevalence of physical activity among men [adjusted prevalence ratio (PRa) = 0.92; P = 0.016], but not among women (PRa = 1.11; P = 0.039). Employment policies and protection of the work environment are relevant aspects to stimulate physical activity, and may vary by gender.
Hydrogen peroxide induces progranulin expression to control neurite outgrowth in HT22 cells
Authors: Shimoda Ayumu , Tanabe Takemi , Sato Tsubasa , Nedachi Taku
Published: July 2021

Progranulin (PGRN) is a multifunctional growth factor expressed in central nervous system. Although PGRN expression is regulated by various stressors, its precise role(s) and regulatory mechanism(s) remain elusive. In this study, we used HT22 cells to investigate the physiological implications of oxidative stress-induced PGRN expression and the regulation of PGRN expression by oxidative stress. We observed that p38 MAP kinase was activated upon the addition of H2O2, and a selective p38 MAP kinase inhibitor attenuated PGRN induction by H2O2. To explore the physiological role(s) of the PGRN induction, we first confirmed H2O2-dependent responses of HT22 cells and found that the length and number of neurites were increased by H2O2. Pgrn knockdown experiments suggested that these changes were mediated by H2O2-induced PGRN expression, at least in part. Overall, the results suggested that an increase in oxidative stress in HT22 cells induced PGRN expression via p38 MAP kinase pathway, thereby controlling neurite outgrowth.
FlowGrid enables fast clustering of very large single-cell RNA-seq data
Authors: Fang Xiunan , Ho Joshua W K
Published: July 2021

Motivation

Scalable clustering algorithms are needed to analyze millions of cells in single cell RNA-seq (scRNA-seq) data.

Results

Here, we present an open source python package called FlowGrid that can integrate into the Scanpy workflow to perform clustering on very large scRNA-seq datasets. FlowGrid implements a fast density-based clustering algorithm originally designed for flow cytometry data analysis. We introduce a new automated parameter tuning procedure, and show that FlowGrid can achieve comparable clustering accuracy as state-of-the-art clustering algorithms but at a substantially reduced run time for very large single cell RNA-seq datasets. For example, FlowGrid can complete a one-hour clustering task for one million cells in about five min.

Availability and implementation

https://github.com/holab-hku/FlowGrid.

Supplementary information

Supplementary data are available at Bioinformatics online.
USO1 isoforms differentially promote liver cancer progression by dysregulating the ER–Golgi network
Authors: Yoon Sarah , Choi Ji-Hye , Shah Masaud , Kwon So Mee , Yang Jieun , Park Young Nyun , Wang Hee-Jung , Woo Hyun Goo
Published: July 2021

Alternative splicing of RNA transcripts plays an important role in cancer development and progression. Recent advances in RNA-seq technology have made it possible to identify alternately spliced events in various types of cancer; however, research on hepatocellular carcinoma (HCC) is still limited. Here, by performing RNA-seq profiling of HCC transcripts at isoform level, we identified tumor-specific and molecular subtype-dependent expression of the USO1 isoforms, which we designated as a normal form USO1-N (XM_001290049) and a tumor form USO1-T (NM_003715). The expression of USO1-T, but not USO1-N, was associated with worse prognostic outcomes of HCC patients. We confirmed that the expression of USO1-T promoted an aggressive phenotype of HCC, both in vitro and in vivo. In addition, structural modeling analyses revealed that USO1-T lacks an ARM10 loop encoded by exon 15, which may weaken the dimerization of USO1 and its tethering to GM130. We demonstrated that USO1-T ensured unstacking of the Golgi and accelerated the vesicles trafficking from endoplasmic reticulum (ER) to Golgi and plasma membrane in multiple liver cancer cells. ERK and GRASP65 were found to be involved in the USO1-T-mediated Golgi dysfunction. Conclusively, we provide new mechanophysical insights into the USO1 isoforms that differentially regulate the ER–Golgi network, promoting the heterogeneous HCC progression.
Composing an Oppositional Discourse inCoke Studio Pakistan
Authors: D’Souza Ryan A
Published: July 2021

Coke Studio Pakistan (CSP) is a television show aired in Pakistan and available worldwide on digital platforms. The show features well-known and up-and-coming music artists alongside a studio band who cover contemporary and familiar songs. Some of the popular songs are fusions of traditional compositions and Western instrumentation. The Sufi renditions on the show are popular as well. The music produced on CSP is not necessarily unique to the nation state’s mediascape. Notwithstanding, the music is a novel presentation of Pakistani culture to a transnational audience. The following article positions the show in the dominant Western discourses that construct the nation as an intolerant and orthodox Islamic state harboring terrorists. The author argues that CSP composes an oppositional discourse by showcasing transgressively gendered performances and a mystical and subversive Islam.
Overlapping Functional Representations of Self- and Other-Related Thought are Separable Through Multivoxel Pattern Classification
Authors: Parelman Jacob M , Doré Bruce P , Cooper Nicole , O’Donnell Matthew Brook , Chan Hang-Yee , Falk Emily B
Published: July 2021

Self-reflection and thinking about the thoughts and behaviors of others are important skills for humans to function in the social world. These two processes overlap in terms of the component processes involved, and share overlapping functional organizations within the human brain, in particular within the medial prefrontal cortex (MPFC). Several functional models have been proposed to explain these two processes, but none has directly explored the extent to which they are distinctly represented within different parts of the brain. This study used multivoxel pattern classification to quantify the separability of self- and other-related thought in the MPFC and expanded this question to the entire brain. Using a large-scale mega-analytic dataset, spanning three separate studies (n = 142), we find that self- and other-related thought can be reliably distinguished above chance within the MPFC, posterior cingulate cortex and temporal lobes. We highlight subcomponents of the ventral MPFC that are particularly important in representing self-related thought, and subcomponents of the orbitofrontal cortex robustly involved in representing other-related thought. Our findings indicate that representations of self- and other-related thought in the human brain are described best by a distributed pattern rather than stark localization or a purely ventral to dorsal linear gradient in the MPFC.
Moxifloxacin Pharmacokinetics, Cardiac Safety, and Dosing for the Treatment of Rifampicin-Resistant Tuberculosis in Children
Authors: Radtke Kendra K , Hesseling Anneke C , Winckler J L , Draper Heather R , Solans Belen P , Thee Stephanie , Wiesner Lubbe , van der Laan Louvina E , Fourie Barend , Nielsen James , Schaaf H Simon , Savic Radojka M , Garcia-Prats Anthony J
Published: July 2021

Background

Moxifloxacin is a recommended drug for rifampin-resistant tuberculosis (RR-TB) treatment, but there is limited pediatric pharmacokinetic and safety data, especially in young children. We characterize moxifloxacin population pharmacokinetics and QT interval prolongation and evaluate optimal dosing in children with RR-TB.

Methods

Pharmacokinetic data were pooled from 2 observational studies in South African children with RR-TB routinely treated with oral moxifloxacin once daily. The population pharmacokinetics and Fridericia-corrected QT (QTcF)-interval prolongation were characterized in NONMEM. Pharmacokinetic simulations were performed to predict expected exposure and optimal weight-banded dosing.

Results

Eighty-five children contributed pharmacokinetic data (median [range] age of 4.6 [0.8–15] years); 16 (19%) were aged <2 years, and 8 (9%) were living with human immunodeficiency virus (HIV). The median (range) moxifloxacin dose on pharmacokinetic sampling days was 11 mg/kg (6.1 to 17). Apparent clearance was 6.95 L/h for a typical 16-kg child. Stunting and HIV increased apparent clearance. Crushed or suspended tablets had faster absorption. The median (range) maximum change in QTcF after moxifloxacin administration was 16.3 (–27.7 to 61.3) ms. No child had QTcF ≥500 ms. The concentration–QTcF relationship was nonlinear, with a maximum drug effect (Emax) of 8.80 ms (interindividual variability = 9.75 ms). Clofazimine use increased Emax by 3.3-fold. Model-based simulations of moxifloxacin pharmacokinetics predicted that current dosing recommendations are too low in children.

Conclusions

Moxifloxacin doses above 10–15 mg/kg are likely required in young children to match adult exposures but require further safety assessment, especially when coadministered with other QT-prolonging agents.
Induced shifting involvements and cycles of growth and distribution
Authors: Nikiforos Michalis
Published: July 2021

The paper builds on the concept of (shifting) involvements, originally proposed by Albert Hirschman (1982). However, unlike Hirschman, the concept is framed in class terms. A model is presented where income distribution is determined by the involvement of the two classes, capitalists and workers. Higher involvement by capitalists and lower involvement by workers tends to increase the profit share and vice versa. In turn, shifts in involvements are induced by the potential effect of a change in distribution on economic activity and past levels of distribution. On the other hand, as the profit share increases, the economy tends to become more wage led. The dynamics of the resulting model are interesting. The more the two classes prioritise the increase of their income share over economic activity, the more possible it is that the economy is unstable. Under the stable configuration, the most likely outcome is Polanyian predator–prey cycles, which can explain some interesting historical episodes during the twentieth century. Finally, the paper discusses the possibility of conflict and cooperation within each of the distribution-led regimes.
Friends-Based Crowdsourcing: Algorithms For Task Dissemination Over Social Groups
Authors: Li Zhiyao , Liu Wei , Gao Xiaofeng , Chen Guihai
Published: July 2021

Crowdsourcing has become increasingly popular in recent years. In order to achieve the optimal task allocation, one of the most important issues is to select more suitable crowdworkers. By leveraging its pervasiveness, social network can be employed as a novel worker recruitment platform. A robust task allocation scheme over the social network could also consider the word-of-mouth (WoM) mode, in which tasks are delivered from workers to workers. In this paper, we discuss an Non-deterministic Polynomial-Hard (NP-Hard) problem, cost-effective and budget-balanced task allocation (CBTA) problem under the WoM mode in social groups. We propose two heuristic algorithms: CB-greedy and CB-local based on greedy strategy and local search technique, respectively. We also prove that the running time of CB-greedy is $O(m^2\log m)$, whereas CB-local utilizing disjoint-set achieves $O(mn\alpha (m, n))$, where $m$ is the number of edges indicating interactions of social groups, $n$ is the number of social groups and $\alpha $ is the inverse Ackerman function. Extensive experiments validate the efficiency and performance of our proposed algorithms.
Optimization of Climatic Conditions Affecting Determination of the Amount of Water Needed by Plants in Relation to Their Life Cycle with Particle Swarm Optimization, and Determining the Optimum Irrigation Schedule
Authors: Bülbül Mehmet Akif , Öztürk Celal , Işık Mehmet Fatih
Published: July 2021

Plants’ need for water has become a topic of research for the agriculture industry. The fact that plant species are very diverse and each plant’s need for water varies makes it difficult to plan programs with conventional irrigation methods. Plants exhibit different stages from their seed time to harvest season. Each stage is defined within as days, and the amount of water needed by the plant throughout these stages varies. In this study, optimization of the irrigation schedule for each stage of a plant is provided. The amount of water needed by the plant was first figured out by using climatic data, and then, these values were recalculated in relation to the plant type. The amount of water needed at each stage was related to the plant type by using particle swarm optimization. The obtained results revealed the optimal irrigation schedule for each stage with the obtained data.
Designed quadrature to approximate integrals in maximum simulated likelihood estimation
Authors: Bansal Prateek , Keshavarzzadeh Vahid , Guevara Angelo , Li Shanjun , Daziano Ricardo A
Published: July 2021

Maximum simulated likelihood estimation of mixed multinomial logit models requires evaluation of a multidimensional integral. Quasi-Monte Carlo (QMC) methods such as Halton sequences and modified Latin hypercube sampling are workhorse methods for integral approximation. Earlier studies explored the potential of sparse grid quadrature (SGQ), but SGQ suffers from negative weights. As an alternative to QMC and SGQ, we looked into the recently developed designed quadrature (DQ) method. DQ requires fewer nodes to get the same level of accuracy as QMC and SGQ, is as easy to implement, ensures positivity of weights, and can be created on any general polynomial space. We benchmarked DQ against QMC in a Monte Carlo and an empirical study. DQ outperformed QMC in all considered scenarios, is practice ready, and has potential to become the workhorse method for integral approximation.
Cardiac magnetic resonance imaging in unclear cases of ventricular interdependence: a case series
Authors: Moseley Alex , Mazur Wojciech , Ahmad Saad
Published: July 2021

Background 

Diagnosis of constrictive pericarditis requires demonstration of interventricular interdependence which can prove difficult even with invasive haemodynamics. Its treatment requires invasive surgical procedures prior to which diagnostic certainty is necessary. Cardiac magnetic resonance imaging (MRI) is an underutilized tool for identification of this pathology.

Case summary 

We present two cases of heart failure due to interventricular interdependence with inconclusive invasive haemodynamic. Prior to recommending invasive surgical treatment, confirmation of the diagnosis was required. This was achieved using cardiac MRI leading to pericardiectomy followed by clinical improvement.

Discussion 

These cases demonstrate the clinical utility, sensitivity, and specificity of cardiac MRI for ventricular interdependence.
Against all odds—late repair of multiple shunt lesions in a patient with Down syndrome: a case report
Authors: Arvanitaki Alexandra , Januszewska Katarzyna , Malec Edward , Baumgartner Helmut , Kehl Hans-Gerd , Lammers Astrid Elisabeth
Published: July 2021

Background

Children with congenital heart defects (CHD) usually undergo elective surgical repair of haemodynamically relevant shunt lesions within the first year of life. Due to susceptibility for pulmonary arterial hypertension (PAH) in patients with Down syndrome, repair is usually aimed for no later than 6 months of life. However, with rising immigration from developing countries to Europe, more patients with unrepaired CHD are diagnosed at a later age. Anatomical repair may be precluded, when advanced pulmonary vascular disease has been established.

Case summary

We report a 39-month-old male patient with Down syndrome with a large non-restrictive perimembranous ventricular septal defect, a large patent ductus arteriosus, and a secundum-type atrial septal defect with a prominent left-to-right shunting. Haemodynamic assessment revealed only a mild increase of pulmonary artery pressures (mPAP) with low pulmonary vascular resistance index (PVRi). Vasodilator testing led to a further increase of the left-to-right shunt and decrease of PVRi, suggesting operability. After careful consideration, the patient underwent complete surgical repair with a good post-operative clinical outcome. Cardiac catheterization 6 months after corrective repair showed a normal mPAP. No signs of PAH have been detected in the medium-term follow-up.

Discussion

Expertise, increased physician awareness, and a thorough pre-operative multidisciplinary evaluation are paramount to determine the best treatment approach for patients, who may present late with multiple shunts, and—in our case—underlying Down syndrome. Long-term close post-surgical follow-up in an expert centre is warranted to promptly diagnose and treat a possible late presentation of PAH appropriately.
MINOCA-induced apical ballooning case report: a diagnostic conundrum
Authors: Dungarwalla Moez , Demetriades Polyvios , Been Martin , Khan Jamal Nasir
Published: July 2021

Background 

Myocardial infarction with non-obstructive coronary arteries (MINOCA) is a recently described phenomenon where no flow-limiting lesions are noted on coronary angiography in a patient with electrocardiogram changes, elevated cardiac biomarkers, and symptoms suggesting acute myocardial infarction. Patients with MINOCA can also potentially develop structural cardiac defects through ischaemic injury. Therefore, the absence of a flow-limiting lesion on angiography coupled with structural defects (e.g. apical ballooning) can very easily result in a diagnosis of Takotsubo cardiomyopathy (TTC). This can lead to potentially serious consequences since treatment options between TTC and MINOCA are different.

Case summary 

We report a case of a patient presenting with features suggestive of TTC but where the final diagnosis was of a MINOCA that induced an apical ventricular septal defect (VSD). Reaching the correct diagnosis proved challenging given that there is no gold standard diagnostic modality for diagnosing MINOCA.

Conclusion 

Imaging adjuncts played a vital role in both diagnosing the underlying MINOCA as well as revealing and planning closure of the resultant VSD. Cardiovascular magnetic resonance imaging played an instrumental role in establishing the patient’s primary pathology and in planning a remediation of the structural defect. Structural myocardial defects in a patient with a diagnosis of TTC should prompt clinicians to further investigate whether there is an underlying infarct aetiology (MINOCA).
Chromosome assembled and annotated genome sequence of Aspergillus flavus NRRL 3357
Authors: Skerker Jeffrey M , Pianalto Kaila M , Mondo Stephen J , Yang Kunlong , Arkin Adam P , Keller Nancy P , Grigoriev Igor V , Glass N Louise
Published: July 2021

Aspergillus flavus is an opportunistic pathogen of crops, including peanuts and maize, and is the second leading cause of aspergillosis in immunocompromised patients. A. flavus is also a major producer of the mycotoxin, aflatoxin, a potent carcinogen, which results in significant crop losses annually. The A. flavus isolate NRRL 3357 was originally isolated from peanut and has been used as a model organism for understanding the regulation and production of secondary metabolites, such as aflatoxin. A draft genome of NRRL 3357 was previously constructed, enabling the development of molecular tools and for understanding population biology of this particular species. Here, we describe an updated, near complete, telomere-to-telomere assembly and re-annotation of the eight chromosomes of A. flavus NRRL 3357 genome, accomplished via long-read PacBio and Oxford Nanopore technologies combined with Illumina short-read sequencing. A total of 13,715 protein-coding genes were predicted. Using RNA-seq data, a significant improvement was achieved in predicted 5’ and 3’ untranslated regions, which were incorporated into the new gene models.