bluuebunny/crossref_metadata_2025 huggingface dataset:
Ab Initio molecular dynamics with screened Lorentz forces. II. Efficient propagators and rovibrational spectra in strong magnetic fields
Authors: Peters Laurens D. M. , Culpitt Tanner , Monzel Laurenz , Tellgren Erik I. , Helgaker Trygve
Published: July 2021

Strong magnetic fields have a large impact on the dynamics of molecules. In addition to the changes in the electronic structure, the nuclei are exposed to the Lorentz force with the magnetic field being screened by the electrons. In this work, we explore these effects using ab initio molecular dynamics simulations based on an effective Hamiltonian calculated at the Hartree–Fock level of theory. To correctly include these non-conservative forces in the dynamics, we have designed a series of novel propagators that show both good efficiency and stability in test cases. As a first application, we analyze simulations of He and H2 at two field strengths characteristic of magnetic white dwarfs (0.1 B0 = 2.35 × 104 T and B0 = 2.35 × 105 T). While the He simulations clearly demonstrate the importance of electron screening of the Lorentz force in the dynamics, the extracted rovibrational spectra of H2 reveal a number of fascinating features not observed in the field-free case: couplings of rotations/vibrations with the cyclotron rotation, overtones with unusual selection rules, and hindered rotations that transmute into librations with increasing field strength. We conclude that our presented framework is a powerful tool to investigate molecules in these extreme environments.
Pushbutton-activated microfluidic cartridge as a user-friendly sample preparation tool for diagnostics
Authors: Park Juhwan , Park Je-Kyun
Published: July 2021

Microfluidic technologies have several advantages in sample preparation for diagnostics but suffer from the need for an external operation system that hampers user-friendliness. To overcome this limitation in microfluidic technologies, a number of user-friendly methods utilizing capillary force, degassed poly(dimethylsiloxane), pushbutton-driven pressure, a syringe, or a pipette have been reported. Among these methods, the pushbutton-driven, pressure-based method has a great potential to be widely used as a user-friendly sample preparation tool for point-of-care testing or portable diagnostics. In this Perspective, we focus on the pushbutton-activated microfluidic technologies toward a user-friendly sample preparation tool. The working principle and recent advances in pushbutton-activated microfluidic technologies are briefly reviewed, and future perspectives for wide application are discussed in terms of integration with the signal analysis system, user-dependent variation, and universal and facile use.
High-efficiency single-pixel imaging using discrete Hartley transform
Authors: Ma Mengchao , Sun Qianzhen , Gao Xicheng , Wang Guan , Deng Huaxia , Zhang Yi , Guan Qingtian , Zhong Xiang
Published: July 2021

Single-pixel imaging technology is popular with invisible wavelengths and low light environments. However, the time-consuming steps hindered the development of single-pixel imaging technology. To improve imaging efficiency, a high-efficiency one-step single-pixel imaging method based on the discrete Hartley transform is proposed. The proposed method does not require a large number of fringe patterns and only requires a real-number calculation. The number of fringe patterns required for the proposed method is only half of that required for the four-step phase-shift Fourier method at the same sampling rate. Although a one-step method, it also uses the idea of differential measurements and adds upsampling processing strategies, which simultaneously improve the signal-to-noise ratio of the recovered image. The simulation shows that the peak signal-to-noise ratio and structural similarity index of the recovered target scene exceed 20 dB and 80%, respectively, when the sampling rate is 30%. Only 20 164 patterns are needed to reconstruct a (256 × 256)-pixel image. After defocusing the gray stripe pattern into a binary pattern, it only takes milliseconds to project these patterns into the target. It can be seen that the experimental results of the proposed method are significantly better than those of the two-step phase-shift method under dramatical noise interference. With the rapid development of advanced equipment, this method will represent significant progress in the real-time reconstruction of single-pixel imaging.
Effect of torsional spring and shape on the performance of bioinspired caudal fin
Authors: Lin Xingjian , Wu Jie , Zhang Tongwei
Published: July 2021

The swimming ability of fish is greatly influenced by the hydrodynamics of their caudal fins. In this paper, the effects of flexibility and shape on the performance of a bioinspired panel are numerically studied. The flexibility is simplified as a torsional spring, and three typical shapes (i.e., square, convex, and concave shapes) are considered. The results are obtained based on three-dimensional numerical simulations of flapping panels at Re = 1000 and St = 0.5. It is shown that the flexibility can significantly affect the performance of pitching panels, by changing the phase lag between the motions of the fore and hind parts. When the phase lag is in the range of 0.1π–0.6π, the performance improvement can be obtained by the flexible panels, as compared with the rigid panel. Moreover, the maximum thrust (or efficiency) can be achieved by a flexible panel when the phase lag is approximately 0.35π (or 0.24π). On the other hand, it is found that the convex shape is optimal for thrust generation, but the square shape is optimal for propulsive efficiency. Moreover, the mechanism by which flexibility and shape can influence the performance of the pitching panel is analyzed. The results obtained here may provide some light on designing the efficient propulsor for microunderwater robots.
Collaborative assessments in Mandarin conversation
Authors: Fang Di
Published: July 2021

The co-production of a sentence is a phenomenon that is widely observed in talk-in-interaction across languages. However, with a few notable exceptions, there is still much room for the investigation of how the co-production of sentences is put to the service of specific actions and activities in different language communities. This paper, using 10 hours of video-recorded data, examines the co-production of assessments (“collaborative assessments”) in Mandarin conversation. It is found that speakers can use syntactic, prosodic, and bodily-visual devices to realize assessment collaboration, and that the functions of collaborative assessment include (1) helping provide a candidate assessment term and facilitating the assessment; (2) articulating/specifying ‘vague’ assessments; (3) helping complete the foreshadowing of a negative assessment term; and (4) co-participation in the assessment activity. This paper also discusses the design features of co-completion and subsequent responses on the basis of the continuum of speakers’ epistemic authority and agency in collaborative assessment sequences and concludes with some implications of this study for grammar as practice.
Real-potential-driven anti-

PT

-symmetry breaking in non-Hermitian Su–Schrieffer–Heeger model
Authors: Zhao Xuedong , Xing Yan , Qi Lu , Liu Shutian , Zhang Shou , Wang Hong-Fu
Published: July 2021

Non-Hermitian Hamiltonians with anti-

PT

symmetry show distinct discrepancies compared to

PT

-symmetric systems. Here we investigate the non-Hermitian Su–Schrieffer–Heeger (SSH) model and reveal the interplay between anti-

PT

symmetry and different topological phases, in which the anti-

PT

symmetry is triggered by introducing real chemical potential and imaginary nearest-neighbor hopping. Three types of anti-

PT

-symmetric SSH models with different on-site configurations are investigated, and the effect of each on-site configuration on the energy spectrum of system is analyzed and discussed. We find that the type of on-site configuration affects the energy spectrum of the same topological region significantly and each on-site configuration has distinguishable impacts on the energy spectra of different topological regions. Moreover, the spontaneous anti-

PT

-symmetry-breaking transitions undergone in both of the topologically trivial and nontrivial regions are also clarified. Furthermore, we address the corresponding eigenstates of some specific eigenvalues and some interesting localized phenomena are observed. Our results enrich the study of non-Hermitian topological phases and broaden the understanding of anti-

PT

-symmetric systems.
Conservative constraints on the effective theory of dark matter-nucleon interactions from IceCube: the impact of operator interference
Authors: Brenner Anja , Ibarra Alejandro , Rappelt Andreas
Published: July 2021

We present a method to derive conservative upper limits on
the coupling constants of the effective theory of dark
matter-nucleon interactions, taking into account the interference
among operators. The method can be applied in any basis, and can be
easily particularized to any UV complete model. To illustrate our
method, we use the IceCube constraints on an exotic neutrino flux
from dark matter annihilations in the Sun to derive conservative
upper limits on the dark matter-nucleon coupling constants of the
effective theory, as well as to derive conservative upper limits on
the dark matter-proton and dark matter-neutron scattering
cross-sections.
Cosmic no-hair theorems for viscous contracting Universes
Authors: Ganguly Chandrima
Published: July 2021

A cosmic no-hair theorem for all initially contracting, spatially homogeneous, orthogonal Bianchi Cosmologies is derived - which shows that all such Universes asymptote to a spatially flat, isotropic Universe with the inclusion of a shear viscous stress. This establishes a new mechanism of isotropisation in a contracting Universe, which does not take recourse to an ekpyrosis-like mechanism using an effective ultra-stiff equation of state fluid, that is, one in which the pressure is much greater than the energy density.
Improved sensitivity of the DRIFT-IId directional dark matter experiment using machine learning
Authors: Battat J.B.R. , Eldridge C. , Ezeribe A.C. , Gaunt O.P. , Gauvreau J.-L. , Marcelo Gregorio R.R. , Habich E.K.K. , Hall K.E. , Harton J.L. , Ingabire I. , Lafler R. , Loomba D. , Lynch W.A. , Paling S.M. , Pan A.Y. , Scarff A. , Schuckman II F.G. , Snowden-Ifft D.P. , Spooner N.J.C. , Toth C. , Xu A.A.
Published: July 2021

We demonstrate a new type of analysis for the DRIFT-IId
directional dark matter detector using a machine learning algorithm
called a Random Forest Classifier. The analysis labels events as
signal or background based on a series of selection parameters,
rather than solely applying hard cuts. The analysis efficiency is
shown to be comparable to our previous result at high energy but
with increased efficiency at lower energies. This leads to a
projected sensitivity enhancement of one order of magnitude below a
WIMP mass of 15 GeV c-2 and a projected sensitivity limit that
reaches down to a WIMP mass of 9 GeV c-2, which is a first for
a directionally sensitive dark matter detector.
MIKE: a new computational tool for investigating radiation, optical and physical properties of prototyped shielding materials
Authors: Hussein K.I. , Alqahtani M.S. , Algarni H. , Zahran H. , Yaha I.S. , Grelowska I. , Reben M. , Yousef E.S.
Published: July 2021

The development of new, advanced shielding materials has attracted great interest among scientists and engineers. Recently, various shielding materials have been developed, which could replace the toxic, heavy, and costly conventional shielding materials. In this paper, we present our new computational software, MIKE, to assist researchers in the process of calculating and analyzing different radiation shielding parameters, such as the linear attenuation coefficient, mass attenuation coefficient, and half-value layer. The shielding parameter equations were coded using MATLAB. Additionally, the computational tool can be used to calculate the physical and optical properties of the selected composition, such as the average molar weight, molar volume, and molar electronic polarizability. Moreover, this tool allows the user to analyze the shielding parameters and the transmission factors for a selected material against a wide range of ionizing radiation energies. The newly developed computational software has been compared with existing radiation-shielding codes, including Phy-X/PSD and WinXcom, in addition to the available experimental data in the literature. The computed values produced using the MIKE software show good agreement with values calculated using the available competitor software programs (WinXcom, Phy-X/PSD, and the Monte Carlo method) with percentage differences of less than 0.2%. Our user-friendly computational software could help researchers evaluate whether various shielding materials meet the requirements of radiation applications, such as diagnostic and therapy applications including mammography, general radiography, computed tomography (CT), nuclear medicine, and high-energy photons used in radiotherapy applications.
Landscape-scale characterization of Arctic tundra vegetation composition, structure, and function with a multi-sensor unoccupied aerial system
Authors: Yang Dedi , Morrison Bailey D , Hantson Wouter , Breen Amy L , McMahon Andrew , Li Qianyu , Salmon Verity G , Hayes Daniel J , Serbin Shawn P
Published: July 2021

The Arctic is experiencing some of the most rapid climate change on Earth, with strong impacts on tundra ecosystems that are characterized by high land-surface and vegetation heterogeneity. Previous studies have explored this complexity using satellite remote sensing, however these typically coarse spatial resolution data have generally missed sub-pixel heterogeneity, leaving critical gaps in our understanding of tundra vegetation dynamics from the community to landscape scales. To address these gaps, we collected very high-resolution (1–5 cm) optical, structural, and thermal data at three low-Arctic tundra sites on the Seward Peninsula, Alaska, using a multi-sensor unoccupied aerial system (UAS). We examined the application of these data to studying tundra vegetation dynamics, by quantifying (a) canopy height and thermoregulation (leaf–air temperature) of representative plant functional types (PFTs), (b) fine-scale patterns of vegetation composition across landscapes, and (c) impacts of fine-scale vegetation composition on landscape-scale variation of canopy height and thermoregulation. Our results show that deciduous tall shrubs (those that can potentially grow >2 m) had a strong cooling effect, with canopy temperatures significantly lower than local air temperatures and other PFTs. Increased cover of tall shrubs also had the potential to reduce the cover of low-stature PFTs across the landscape, potentially associated with their closed canopy (i.e. increased light competition) and strong thermoregulation. To understand the connections between fine-scale vegetation composition and large-scale ecosystem processes, we produced a random forest model which showed that fine-scale PFT composition accounted for 86.8% and 74.2% of the landscape-scale variation in canopy height and thermoregulation, respectively. These findings highlight the importance of spatially detailed characterization of tundra PFTs to improve our ecological understanding and model representation of tundra vegetation, also transcend our study to show the need for continued collection of similar datasets to better understand the impacts of surface heterogeneity on the mapping and modeling of tundra ecosystem dynamics, as well as assist with conservation management and biodiversity monitoring strategies.
Labrador Slope Water connects the subarctic with the Gulf Stream
Authors: New A L , Smeed D A , Czaja A , Blaker A T , Mecking J V , Mathews J P , Sanchez-Franks A
Published: July 2021

Labrador Slope Water (LSLW) is a relatively fresh and cool water mass that originates from the Labrador Current in the subarctic and is known to occur in the Eastern Slope Sea on the US-Canadian shelf-slope north of the Gulf Stream. It has potential densities of 27.4–27.65 kg m−3. Using ocean observations, we show here that the LSLW penetrates as a boundary current deeply into the Western Slope Sea (west of 66°W) as a salinity minimum between 400 and 600 m, bringing it into close proximity with the Gulf Stream. The LSLW at Line W (near 69°W) also spreads across, and brings fresher and thicker waters to, the Slope Sea north of the Gulf Stream. A high-resolution ocean model simulation shows that the spreading of the LSLW occurs throughout the entire Slope Sea through the extrusion of fine-scale filaments from the boundary current following interaction with Gulf Stream meanders and eddies. At Line W, the LSLW is also found to be fresher and thicker between 2003 and 2008, when the Atlantic Meridional Overturning Circulation (AMOC) at 26°N is higher (by 3 Sv), and the Shelf Slope Front is further south (by 0.7°), compared to AMOC low conditions in 2009–2014. The thicker LSLW causes lighter isopycnals to rise over the shelf slope, and through increasing the lateral density gradient contributes an additional 1.3 Sv to the Gulf Stream transport. These changes to the LSLW and the Shelf Slope Front are likely to result from an enhanced flow of the Labrador Current into the Slope Sea, caused by changes in the wind stress in the subpolar gyre. The transport of the LSLW (as opposed to the deeper Labrador Sea Water) thereby offers a potential new mechanism for decadal variability in the Atlantic climate system, through connecting changes in the subarctic with subsequent variability in the Gulf Stream and AMOC.
Comparative evaluation of shape retrieval methods on macromolecular surfaces: an application of computer vision methods in structural bioinformatics
Authors: Machat Mohamed , Langenfeld Florent , Craciun Daniela , Sirugue Léa , Labib Taoufik , Lagarde Nathalie , Maria Maxime , Montes Matthieu
Published: July 2021

Motivation

The investigation of the structure of biological systems at the molecular level gives insights about their functions and dynamics. Shape and surface of biomolecules are fundamental to molecular recognition events. Characterizing their geometry can lead to more adequate predictions of their interactions. In the present work, we assess the performance of reference shape retrieval methods from the computer vision community on protein shapes.

Results

Shape retrieval methods are efficient in identifying orthologous proteins and tracking large conformational changes. This work illustrates the interest for the protein surface shape as a higher-level representation of the protein structure that (i) abstracts the underlying protein sequence, structure or fold, (ii) allows the use of shape retrieval methods to screen large databases of protein structures to identify surficial homologs and possible interacting partners and (iii) opens an extension of the protein structure–function paradigm toward a protein structure-surface(s)-function paradigm.

Availabilityand implementation

All data are available online at http://datasetmachat.drugdesign.fr.

Supplementary information

Supplementary data are available at Bioinformatics online.
Efficient gradient-based parameter estimation for dynamic models using qualitative data
Authors: Schmiester Leonard , Weindl Daniel , Hasenauer Jan
Published: July 2021

Motivation

Unknown parameters of dynamical models are commonly estimated from experimental data. However, while various efficient optimization and uncertainty analysis methods have been proposed for quantitative data, methods for qualitative data are rare and suffer from bad scaling and convergence.

Results

Here, we propose an efficient and reliable framework for estimating the parameters of ordinary differential equation models from qualitative data. In this framework, we derive a semi-analytical algorithm for gradient calculation of the optimal scaling method developed for qualitative data. This enables the use of efficient gradient-based optimization algorithms. We demonstrate that the use of gradient information improves performance of optimization and uncertainty quantification on several application examples. On average, we achieve a speedup of more than one order of magnitude compared to gradient-free optimization. In addition, in some examples, the gradient-based approach yields substantially improved objective function values and quality of the fits. Accordingly, the proposed framework substantially improves the parameterization of models from qualitative data.

Availability and implementation

The proposed approach is implemented in the open-source Python Parameter EStimation TOolbox (pyPESTO). pyPESTO is available at https://github.com/ICB-DCM/pyPESTO. All application examples and code to reproduce this study are available at https://doi.org/10.5281/zenodo.4507613.

Supplementary information

Supplementary data are available at Bioinformatics online.
The Transformative Power of Trust: Exploring Tertiary Desistance in Reinventive Prisons
Authors: Ugelvik Thomas
Published: July 2021

While prisons are often described as places of pain, despair and hopelessness, studies show that some prisoners under certain conditions report positive life changes happening in prison. This paper explores the connections between trust and desistance processes, specifically between the experience of being trusted and ‘tertiary desistance’. I argue that trust can be an engine of positive change in prison and that the experience of being trusted might even acquire additional value from the low-trust and risk-sensitive environment that most prisons normally offer prisoners. Finally, I discuss whether prisons that manage to get this balance right deserve to be called ‘reinventive prisons’.
Incidence of Respiratory Syncytial Virus Infection Among Hospitalized Adults, 2017–2020
Authors: Branche Angela R , Saiman Lisa , Walsh Edward E , Falsey Ann R , Sieling William D , Greendyke William , Peterson Derick R , Vargas Celibell Y , Phillips Matthew , Finelli Lyn
Published: July 2021

Background

Respiratory syncytial virus (RSV) causes acute respiratory illness (ARI) and triggers exacerbations of cardiopulmonary disease. Estimates of incidence in hospitalized adults range widely, with few data on incidence in adults with comorbidities that increase the risk of severity. We conducted a prospective, population-based, surveillance study to estimate incidence of RSV hospitalization among adults overall and those with specific comorbidities.

Methods

Hospitalized adults aged ≥18 years residing in the surveillance area with ≥2 ARI symptoms or exacerbation of underlying cardiopulmonary disease were screened during the 2017–2018, 2018–2019, and 2019–2020 RSV seasons in 3 hospitals in Rochester, New York and New York City. Respiratory specimens were tested for RSV using polymerase chain reaction assays. RSV incidence per 100 000 was adjusted by market share.

Results

Active and passive surveillance identified 1099 adults hospitalized with RSV. Annual incidence during 3 seasons ranged from 44.2 to 58.9/100 000. Age-group–specific incidence ranged from 7.7 to 11.9/100 000, 33.5 to 57.5/100 000, and 136.9 to 255.6/100 000 in patients ages 18–49, 50–64, and ≥65 years, respectively. Incidence rates in patients with chronic obstructive pulmonary disease, coronary artery disease, and congestive heart failure were 3–13, 4–7, and 4–33 times, respectively, the incidence in patients without these conditions.

Conclusions

We found a high burden of RSV hospitalization in this large prospective study. Notable was the high incidence among older patients and those with cardiac conditions. These data confirm the need for effective vaccines to prevent RSV infection in older and vulnerable adults.
Acute tubulointerstitial nephritis and COVID-19
Authors: Ng Jia H , Zaidan Mohamad , Jhaveri Kenar D , Izzedine Hassan
Published: July 2021

Coronavirus disease 2019 (COVID-19) is an ongoing pandemic that to date has spread to >100 countries. Acute kidney injury is not uncommon with this disease. The most common kidney biopsy finding is acute tubular injury. Glomerular diseases such as collapsing glomerulopathy and vasculitis, and thrombotic microangiopathy have been reported. Viral inclusion particles with distinctive spikes in the tubular epithelium and podocytes, and endothelial cells of the glomerular capillary loops, have been visualized by electron microscopy by some but disputed by others as non-viral structures. Interstitial infiltrates have not commonly been described in the published kidney biopsy series from patients with COVID-19. Medications used to treat COVID-19 can lead to interstitial nephritis, but very few have been reported. In summary, interstitial kidney disease is a rare finding in COVID-19.
Interleukin-5-induced eosinophil population improves cardiac function after myocardial infarction
Authors: Xu Jun Yan , Xiong Yu Yan , Tang Rui Jie , Jiang Wen Yang , Ning Yu , Gong Zhao Ting , Huang Pei Sen , Chen Gui Hao , Xu Jun , Wu Chun Xiao , Hu Meng Jin , Xu Jing , Xu Yi , Huang Cun Rong , Jin Chen , Lu Xiao Tong , Qian Hai Yan , Li Xiang Dong , Yang Yue Jin
Published: July 2021

Aims

Interleukin (IL)-5 mediates the development of eosinophils (EOS) that are essential for tissue post-injury repair. It remains unknown whether IL-5 plays a role in heart repair after myocardial infarction (MI). This study aims to test whether IL-5-induced EOS population promotes the healing and repair process post-MI and to reveal the underlying mechanisms.

Methods and results

MI was induced by permanent ligation of the left anterior descending coronary artery in wild-type C57BL/6 mice. Western blot and real-time polymerase chain reaction revealed elevated expression of IL-5 in the heart at 5 days post-MI. Immunohistostaining indicated that IL-5 was secreted mainly from macrophages and CD127+ cells in the setting of experimental MI. External supply of recombinant mouse IL-5 (20 min, 1 day, and 2 days after MI surgery) reduced the infarct size and increased ejection fraction and angiogenesis in the border zone. A significant expansion of EOS was detected in both the peripheral blood and infarcted myocardium after IL-5 administration. Pharmacological depletion of EOS by TRFK5 pretreatment muted the beneficial effects of IL-5 in MI mice. Mechanistic studies demonstrated that IL-5 increased the accumulation of CD206+ macrophages in infarcted myocardium at 7 days post-MI. In vitro co-culture experiments showed that EOS shifted bone marrow-derived macrophage polarization towards the CD206+ phenotypes. This activity of EOS was abolished by IL-4 neutralizing antibody, but not IL-10 or IL-13 neutralization. Western blot analyses demonstrated that EOS promoted the macrophage downstream signal transducer and activator of transcription 6 (STAT6) phosphorylation.

Conclusion

IL-5 facilitates the recovery of cardiac dysfunction post-MI by promoting EOS accumulation and subsequent CD206+ macrophage polarization via the IL-4/STAT6 axis.
Deep-sea hydrothermal vent sediments reveal diverse fungi with antibacterial activities
Authors: Keeler Emma , Burgaud Gaëtan , Teske Andreas , Beaudoin David , Mehiri Mohamed , Dayras Marie , Cassand Jacquelin , Edgcomb Virginia
Published: July 2021

Relatively little is known about the diversity of fungi in deep-sea, hydrothermal sediments. Less thoroughly explored environments are likely untapped reservoirs of unique biodiversity with the potential to augment our current arsenal of microbial compounds with biomedical and/or industrial applications. In this study, we applied traditional culture-based methods to examine a subset of the morphological and phylogenetic diversity of filamentous fungi and yeasts present in 11 hydrothermally influenced sediment samples collected from eight sites on the seafloor of Guaymas Basin, Mexico. A total of 12 unique isolates affiliating with Ascomycota and Basidiomycota were obtained and taxonomically identified on the basis of morphological features and analyses of marker genes including actin, β-tubulin, small subunit ribosomal DNA (18S rRNA), internal transcribed spacer (ITS) and large subunit ribosomal DNA (26S rRNA) D1/D2 domain sequences (depending on taxon). A total of 11 isolates possess congeners previously detected in, or recovered from, deep-sea environments. A total of seven isolates exhibited antibacterial activity against human bacterial pathogens Staphylococcus aureus ATCC-35556 and/or Escherichia coli ATCC-25922. This first investigation suggests that hydrothermal environments may serve as promising reservoirs of much greater fungal diversity, some of which may produce biomedically useful metabolites.
Ultralong Oxford Nanopore Reads Enable the Development of a Reference-Grade Perennial Ryegrass Genome Assembly
Authors: Frei Daniel , Veekman Elisabeth , Grogg Daniel , Stoffel-Studer Ingrid , Morishima Aki , Shimizu-Inatsugi Rie , Yates Steven , Shimizu Kentaro K , Frey Jürg E , Studer Bruno , Copetti Dario
Published: July 2021

Despite the progress made in DNA sequencing over the last decade, reconstructing telomere-to-telomere genome assemblies of large and repeat-rich eukaryotic genomes is still difficult. More accurate basecalls or longer reads could address this issue, but no current sequencing platform can provide both simultaneously. Perennial ryegrass (Lolium perenne L.) is an example of an important species for which the lack of a reference genome assembly hindered a swift adoption of genomics-based methods into breeding programs. To fill this gap, we optimized the Oxford Nanopore Technologies’ sequencing protocol, obtaining sequencing reads with an N50 of 62 kb—a very high value for a plant sample. The assembly of such reads produced a highly complete (2.3 of 2.7 Gb), correct (QV 45), and contiguous (contig N50 and N90 11.74 and 3.34 Mb, respectively) genome assembly. We show how read length was key in determining the assembly contiguity. Sequence annotation revealed the dominance of transposable elements and repeated sequences (81.6% of the assembly) and identified 38,868 protein coding genes. Almost 90% of the bases could be anchored to seven pseudomolecules, providing the first high-quality haploid reference assembly for perennial ryegrass. This protocol will enable producing longer Oxford Nanopore Technology reads for more plant samples and ushering forage grasses into modern genomics-assisted breeding programs.
Effects of urbanization on vulnerability to heat-related mortality in urban and rural areas in South Korea: a nationwide district-level time-series study
Authors: Lee Whanhee , Choi Munjeong , Bell Michelle L , Kang Cinoo , Jang Jeongju , Song Insung , Kim Yong-Ook , Ebi Kristie , Kim Ho
Published: July 2021

Background

Although urbanization is often an important topic in climate change studies, the complex effect of urbanization on heat vulnerability in urban and rural areas has rarely been studied. We investigated the disparate effects of urbanization on heat vulnerability in urban and rural areas, using nationwide data.

Methods

We collected daily weather data for all 229 administrative districts in South Korea (2011–17). Population density was applied as an urbanization indicator. We calculated the heat-mortality risk using a distributed lag nonlinear model and analysed the relationship with population density. We also examined district characteristics that can be related to the spatial heterogeneity in heat-mortality risk.

Results

We found a U-shaped association between population density and heat-mortality risk, with the highest risk for rural populations; in urban areas, risk increases with increasing population density. Higher heat-mortality risk was associated with a lower number of hospital beds per person and higher percentage of people requiring recuperation. The association between hospital beds and heat-mortality risk was prominent in high-density urban areas, whereas the association between the percentage of people requiring recuperation and heat-mortality risk was pronounced in rural areas.

Conclusions

Our findings indicate that the association between population density and heat-mortality risk is different in urban and rural areas, and that district characteristics related to heat-mortality risk also differ by urbanicity. These results can contribute to understanding the complex role of urbanization on heat vulnerability and can provide evidence to policy makers for prioritizing resources.
Occurrence and Distribution of Nonfalciparum Malaria Parasite Species Among Adolescents and Adults in Malawi
Authors: Gumbo Austin , Topazian Hillary M , Mwanza Alexis , Mitchell Cedar L , Puerto-Meredith Sydney , Njiko Ruth , Kayange Michael , Mwalilino David , Mvula Bernard , Tegha Gerald , Mvalo Tisungane , Hoffman Irving , Juliano Jonathan J
Published: July 2021

Background

Plasmodium falciparum malaria dominates throughout sub-Saharan Africa, but the prevalence of Plasmodium malariae, Plasmodium ovale spp., and Plasmodium vivax increasingly contribute to infection in countries that control malaria using P. falciparum-specific diagnostic and treatment strategies.

Methods

We performed quantitative polymerase chain reaction (qPCR) on 2987 dried blood spots from the 2015–2016 Malawi Demographic and Health Survey to identify presence and distribution of nonfalciparum infection. Bivariate models were used to determine species-specific associations with demographic and environmental risk factors.

Results

Nonfalciparum infections had broad spatial distributions. Weighted prevalence was 0.025 (SE, 0.004) for P. malariae, 0.097 (SE, 0.008) for P. ovale spp., and 0.001 (SE, 0.0005) for P. vivax. Most infections (85.6%) had low-density parasitemias ≤ 10 parasites/µL, and 66.7% of P. malariae, 34.6% of P. ovale spp., and 40.0% of P. vivax infections were coinfected with P. falciparum. Risk factors for P. malariae were like those known for P. falciparum; however, there were few risk factors recognized for P. ovale spp. and P. vivax, perhaps due to the potential for relapsing episodes.

Conclusions

The prevalence of any nonfalciparum infection was 11.7%, with infections distributed across Malawi. Continued monitoring of Plasmodium spp. becomes critical as nonfalciparum infections become important sources of ongoing transmission.
Sub-Lethal Effects of λ-Cyhalothrin on Behavior and Development of the ParasitoidAphidius colemani(Hymenoptera: Braconidae) onkdr-Resistant and Susceptible Green Peach Aphid,Myzus persicae(Hemiptera: Aphididae)
Authors: Alfaro-Tapia Armando , Alvarez-Baca Jeniffer K , Figueroa Christian C , Fuentes-Contreras Eduardo
Published: July 2021

The green peach aphid, Myzus persicae (Sulzer), is a pest mainly controlled with insecticides, and it can acquire resistance through different mechanisms. Pyrethroids can select the knock down resistance (kdr) mutation in M. persicae and can also produce lethal and sub-lethal effects on its main parasitoid, Aphidius colemani Viereck. However, kdr-resistant M. persicae exhibits a reduced response to alarm pheromone and increased vulnerability to natural enemies. To study the effects of sub-lethal concentrations of a pyrethroid on the aphid-parasitoid interaction, kdr-resistant and susceptible M. persicae were confronted with A. colemani with residual sub-lethal concentrations of λ-cyhalothrin. The behavior, survival, and development of parasitoids were evaluated after exposure to λ-cyhalothrin LC20 for adult parasitoids (0.52 mg/liter) for susceptible (Mp-SS, 0.56 mg/liter) and kdr-resistant M. persicae (Mp-RR, 12.15 mg/liter). The foraging and oviposition behaviors of the parasitoids were not affected by the lower parasitoid or Mp-SS LC20. Conversely, the higher Mp-RR LC20 significantly reduced parasitoid walking, the frequency of sting attempts, and successful stings, as well as aphid defensive behaviors, such as walking, kicking, and jerking. Therefore, the higher vulnerability of kdr-resistant M. persicae could not be capitalized by A. colemani parasitoids under a high concentration of λ-cyhalothrin. Similarly, the parasitism rate, survival of progeny, productivity, sex ratio (proportion of females), longevity, and adult body mass were reduced, and the development time increased with a higher Mp-RR LC20. Our results suggest that A. colemani could efficiently control kdr-resistant and susceptible M. persicae only at lower λ-cyhalothrin concentrations.
Local border reforms and economic activity
Authors: Egger Peter H , Koethenbuerger Marko , Loumeau Gabriel
Published: July 2021

In this article, we make use of large-scale municipal border changes in Germany to provide the first evidence on the effect of local border changes on the distribution of activity in space. To allow for a comparison of economic activity within unique geographical units over time, we use geo-coded light data as well as local land-use data. Applying a difference-in-differences approach, we find evidence that municipalities absorbing their merger partners and hosting the new administrative center experience a significant increase in local activity, while the municipalities that are being absorbed and are losing the administrative center experience a decrease in such activity. The difference between the gains in activity from absorbing municipalities and the losses from absorbed ones is positive. These previously undocumented results point to the importance of distance to the administrative center as a determinant of the spatial distribution of economic activity.
Improving Energy Efficiency: The Significance of Normativity
Authors: Kirk Elizabeth A , Besco Laurel
Published: July 2021

The failure of the global community to effectively address many large-scale environmental challenges calls into question the existing regulatory approaches. A large number of these challenges are diffuse issues which have, over the years been targeted by significant and sizable regulatory frameworks and yet the challenges persist—energy efficiency is one such issue and is the focus of this article. Increasing monitoring or enforcement to achieve improvements in regulatory compliance is too expensive in the context of diffuse problems due to the scale and costs such activities would entail. We suggest a focus on the fit between regulatory frameworks and norm creation may identify more fruitful routes to regulatory reform. Drawing on the ‘interactional account of law’ as a framework, this research uses new empirical data from a survey and a set of interviews to investigate the failure of energy efficiency regulatory frameworks at achieving energy efficient norms of behaviour in industry. We look at Canada and the UK as our case studies and our emphasis is on industry actors as they represent a significant and yet understudied area of society. We find that though existing regulatory structures seem adequate to generate general shared understandings around obligations to engage in energy efficiency actions, more specific shared practice around actually engaging in these actions remains elusive, resulting in a failure to engender norms of behaviour. These failures, we suggest, link directly to an inadequate fit between the regulatory tools and Fuller’s criteria for the internal morality of law.
Platycarya strobilacea Sieb. et Zucc.: a review of its traditional uses, botany, phytochemistry, pharmacology and toxicology
Authors: Zhao Peiyuan , Han Lizhu , Wang Yunlan , Qiu Jinqing , Zhang Xinbo , Tang Zhishu , Duan Xi , Song Xiao
Published: July 2021

Objectives

Platycarya strobilacea Sieb. et Zucc. is the dry infructescence of P. strobilacea, a Juglandaceae plant and is a traditional Chinese medicine with great development potential and utilization value. This study summarizes the research progress on the traditional uses, botany, phytochemistry, extraction methods, pharmacology and toxicology of Platycarya strobilacea Sieb. et Zucc., and provides potential therapeutic uses and drug development prospects for this plant.

Key findings

Phytochemical studies showed that this plant mainly contains volatile constituents, phenols, terpenoids and a carbohydrate. The pharmacological activity of Platycarya strobilacea Sieb. et Zucc. includes antibacterial and anti-inflammatory effects, anti-tumour effects and antioxidant effects. This plant is especially effective in the treatment of allergic rhinitis and chronic sinusitis.

In this review, the phytochemistry and pharmacological effects of Platycarya strobilacea Sieb. et Zucc. are described in detail, which will have guiding significance for the future development of this drug.
Scientific research and product development in the United States to address injuries from a radiation public health emergency
Authors: DiCarlo Andrea L
Published: July 2021

The USA has experienced one large-scale nuclear incident in its history. Lessons learned during the Three-Mile Island nuclear accident provided government planners with insight into property damage resulting from a low-level release of radiation, and an awareness concerning how to prepare for future occurrences. However, if there is an incident resulting from detonation of an improvised nuclear device or state-sponsored device/weapon, resulting casualties and the need for medical treatment could overwhelm the nation’s public health system. After the Cold War ended, government investments in radiation preparedness declined; however, the attacks on 9/11 led to re-establishment of research programs to plan for the possibility of a nuclear incident. Funding began in earnest in 2004, to address unmet research needs for radiation biomarkers, devices and products to triage and treat potentially large numbers of injured civilians. There are many biodosimetry approaches and medical countermeasures (MCMs) under study and in advanced development, including those to address radiation-induced injuries to organ systems including bone marrow, the gastrointestinal (GI) tract, lungs, skin, vasculature and kidneys. Biomarkers of interest in determining level of radiation exposure and susceptibility of injury include cytogenetic changes, ‘omics’ technologies and other approaches. Four drugs have been approved by the US Food and Drug Administration (FDA) for the treatment of acute radiation syndrome (ARS), with other licensures being sought; however, there are still no cleared devices to identify radiation-exposed individuals in need of treatment. Although many breakthroughs have been made in the efforts to expand availability of medical products, there is still work to be done.
Differential degradation of RNA species by autophagy-related pathways in Arabidopsis
Authors: Hickl Daniel , Drews Franziska , Girke Christopher , Zimmer David , Mühlhaus Timo , Hauth Jan , Nordström Karl , Trentmann Oliver , Neuhaus Ekkehard H , Scheuring David , Fehlmann Tobias , Keller Andreas , Simon Martin , Möhlmann Torsten
Published: July 2021

The plant vacuole recycles proteins and RNA delivered to it by autophagy. In this study, by isolating intact vacuoles from Arabidopsis plants, followed by subsequent RNA purification, and deep sequencing, we provide a comprehensive characterization of Arabidopsis vacuolar RNAome. In the vacuolar RNAome, we detected ribosomal RNAs, transfer RNAs, including those of chloroplast origin, and in addition small RNA types. As autophagy is a main mechanism for the transport of RNA to the vacuole, atg5-1 mutants deficient in autophagy were included in our analysis. We observed severely reduced amounts of most chloroplast-derived RNA species in these mutants. Comparisons with cellular RNA composition provided an indication of possible up-regulation of alternative RNA breakdown pathways. By contrast, vacuolar RNA processing and composition in plants lacking vacuolar ribonuclease 2, involved in cellular RNA homeostasis, only showed minor alterations, possibly because of the presence of further so far unknown vacuolar RNase species. Among the small RNA types, we detected mature miRNAs in all vacuolar preparations but at much lower frequency in atg5-1, raising the possibility of a biological role for vacuolar miRNAs.
Parental Equality in Turkey: Understanding Gender Roles Through the Legal Treatment of Working and Divorced Mothers
Authors: Çelebi Özgün
Published: July 2021

This article addresses the position of Turkish law regarding parental equality, with a focus on day-to-day childcare responsibility. It discusses whether the current legal landscape is consistent with the aim of relieving mothers from a disproportionate share of childcare. The article first explains the general legal framework of gender equality in Turkey before offering closer insight into two fields that help understand whether parental equality is embraced or rejected: measures regarding work–life balance and the organisation of child–parent relationships after divorce. The article analyses specific legal measures impacting the delegation of childcare duties by mothers, including leave and flexible work policies and childcare services. It argues that the legal framework concerning working mothers conveys contradictory messages that reinforce the gendered character of childcare duties. Based on recent case law concerning divorced mothers, the article underlines the potential for the evolution towards parental equality but acknowledges the limited impact of such developments due to the attachment to the maternal preference rule. The article concludes that, despite good intentions and legal reforms favouring gender equality, Turkish law is still devoid of a comprehensive policy regarding parental equality and does not offer incentives for fathers to participate in daily childcare.
Highly Replicated Evolution of Parapatric Ecotypes
Authors: James Maddie E , Arenas-Castro Henry , Groh Jeffrey S , Allen Scott L , Engelstädter Jan , Ortiz-Barrientos Daniel
Published: July 2021

Parallel evolution of ecotypes occurs when selection independently drives the evolution of similar traits across similar environments. The multiple origins of ecotypes are often inferred based on a phylogeny that clusters populations according to geographic location and not by the environment they occupy. However, the use of phylogenies to infer parallel evolution in closely related populations is problematic because gene flow and incomplete lineage sorting can uncouple the genetic structure at neutral markers from the colonization history of populations. Here, we demonstrate multiple origins within ecotypes of an Australian wildflower, Senecio lautus. We observed strong genetic structure as well as phylogenetic clustering by geography and show that this is unlikely due to gene flow between parapatric ecotypes, which was surprisingly low. We further confirm this analytically by demonstrating that phylogenetic distortion due to gene flow often requires higher levels of migration than those observed in S. lautus. Our results imply that selection can repeatedly create similar phenotypes despite the perceived homogenizing effects of gene flow.
Three human RNA polymerases interact with TFIIH via a common RPB6 subunit
Authors: Okuda Masahiko , Suwa Tetsufumi , Suzuki Hidefumi , Yamaguchi Yuki , Nishimura Yoshifumi
Published: July 2021

In eukaryotes, three RNA polymerases (RNAPs) play essential roles in the synthesis of various types of RNA: namely, RNAPI for rRNA; RNAPII for mRNA and most snRNAs; and RNAPIII for tRNA and other small RNAs. All three RNAPs possess a short flexible tail derived from their common subunit RPB6. However, the function of this shared N-terminal tail (NTT) is not clear. Here we show that NTT interacts with the PH domain (PH-D) of the p62 subunit of the general transcription/repair factor TFIIH, and present the structures of RPB6 unbound and bound to PH-D by nuclear magnetic resonance (NMR). Using available cryo-EM structures, we modelled the activated elongation complex of RNAPII bound to TFIIH. We also provide evidence that the recruitment of TFIIH to transcription sites through the p62–RPB6 interaction is a common mechanism for transcription-coupled nucleotide excision repair (TC-NER) of RNAPI- and RNAPII-transcribed genes. Moreover, point mutations in the RPB6 NTT cause a significant reduction in transcription of RNAPI-, RNAPII- and RNAPIII-transcribed genes. These and other results show that the p62–RPB6 interaction plays multiple roles in transcription, TC-NER, and cell proliferation, suggesting that TFIIH is engaged in all RNAP systems.