bluuebunny/crossref_metadata_2025 huggingface dataset:
20S proteasomes secreted by the malaria parasite promote its growth
Authors: Dekel Elya , Yaffe Dana , Rosenhek-Goldian Irit , Ben-Nissan Gili , Ofir-Birin Yifat , Morandi Mattia I. , Ziv Tamar , Sisquella Xavier , Pimentel Matthew A. , Nebl Thomas , Kapp Eugene , Ohana Daniel Yael , Karam Paula Abou , Alfandari Daniel , Rotkopf Ron , Malihi Shimrit , Temin Tal Block , Mullick Debakshi , Revach Or-Yam , Rudik Ariel , Gov Nir S. , Azuri Ido , Porat Ziv , Bergamaschi Giulia , Sorkin Raya , Wuite Gijs J. L. , Avinoam Ori , Carvalho Teresa G. , Cohen Sidney R. , Sharon Michal , Regev-Rudzki Neta
Published: February 2021

Mature red blood cells (RBCs) lack internal organelles and canonical defense mechanisms, making them both a fascinating host cell, in general, and an intriguing choice for the deadly malaria parasite Plasmodium falciparum (Pf), in particular. Pf, while growing inside its natural host, the human RBC, secretes multipurpose extracellular vesicles (EVs), yet their influence on this essential host cell remains unknown. Here we demonstrate that Pf parasites, cultured in fresh human donor blood, secrete within such EVs assembled and functional 20S proteasome complexes (EV-20S). The EV-20S proteasomes modulate the mechanical properties of naïve human RBCs by remodeling their cytoskeletal network. Furthermore, we identify four degradation targets of the secreted 20S proteasome, the phosphorylated cytoskeletal proteins β-adducin, ankyrin-1, dematin and Epb4.1. Overall, our findings reveal a previously unknown 20S proteasome secretion mechanism employed by the human malaria parasite, which primes RBCs for parasite invasion by altering membrane stiffness, to facilitate malaria parasite growth.
Cell non-autonomy amplifies disruption of neurulation by mosaic Vangl2 deletion in mice
Authors: Galea Gabriel L. , Maniou Eirini , Edwards Timothy J. , Marshall Abigail R. , Ampartzidis Ioakeim , Greene Nicholas D. E. , Copp Andrew J.
Published: February 2021

Post-zygotic mutations that generate tissue mosaicism are increasingly associated with severe congenital defects, including those arising from failed neural tube closure. Here we report that neural fold elevation during mouse spinal neurulation is vulnerable to deletion of the VANGL planar cell polarity protein 2 (Vangl2) gene in as few as 16% of neuroepithelial cells.Vangl2-deleted cells are typically dispersed throughout the neuroepithelium, and each non-autonomously prevents apical constriction by an average of fiveVangl2-replete neighbours. This inhibition of apical constriction involves diminished myosin-II localisation on neighbour cell borders and shortening of basally-extending microtubule tails, which are known to facilitate apical constriction.Vangl2-deleted neuroepithelial cells themselves continue to apically constrict and preferentially recruit myosin-II to their apical cell cortex rather than to apical cap localisations. Such non-autonomous effects can explain how post-zygotic mutations affecting a minority of cells can cause catastrophic failure of morphogenesis leading to clinically important birth defects.
Innate immune evasion revealed in a colorectal zebrafish xenograft model
Authors: Póvoa Vanda , Rebelo de Almeida Cátia , Maia-Gil Mariana , Sobral Daniel , Domingues Micaela , Martinez-Lopez Mayra , de Almeida Fuzeta Miguel , Silva Carlos , Grosso Ana Rita , Fior Rita
Published: February 2021

Cancer immunoediting is a dynamic process of crosstalk between tumor cells and the immune system. Herein, we explore the fast zebrafish xenograft model to investigate the innate immune contribution to this process. Using multiple breast and colorectal cancer cell lines and zAvatars, we find that some are cleared (regressors) while others engraft (progressors) in zebrafish xenografts. We focus on two human colorectal cancer cells derived from the same patient that show contrasting engraftment/clearance profiles. Using polyclonal xenografts to mimic intra-tumor heterogeneity, we demonstrate that SW620_progressors can block clearance of SW480_regressors. SW480_regressors recruit macrophages and neutrophils more efficiently than SW620_progressors; SW620_progressors however, modulate macrophages towards a pro-tumoral phenotype. Genetic and chemical suppression of myeloid cells indicates that macrophages and neutrophils play a crucial role in clearance. Single-cell-transcriptome analysis shows a fast subclonal selection, with clearance of regressor subclones associated with IFN/Notch signaling and escaper-expanded subclones with enrichment of IL10 pathway. Overall, our work opens the possibility of using zebrafish xenografts as living biomarkers of the tumor microenvironment.
Characterising open chromatin in chick embryos identifies cis-regulatory elements important for paraxial mesoderm formation and axis extension
Authors: Mok Gi Fay , Folkes Leighton , Weldon Shannon A. , Maniou Eirini , Martinez-Heredia Victor , Godden Alice M. , Williams Ruth M. , Sauka-Spengler Tatjana , Wheeler Grant N. , Moxon Simon , Münsterberg Andrea E.
Published: February 2021

Somites arising from paraxial mesoderm are a hallmark of the segmented vertebrate body plan. They form sequentially during axis extension and generate musculoskeletal cell lineages. How paraxial mesoderm becomes regionalised along the axis and how this correlates with dynamic changes of chromatin accessibility and the transcriptome remains unknown. Here, we report a spatiotemporal series of ATAC-seq and RNA-seq along the chick embryonic axis. Footprint analysis shows differential coverage of binding sites for several key transcription factors, including CDX2, LEF1 and members of HOX clusters. Associating accessible chromatin with nearby expressed genes identifies cis-regulatory elements (CRE) for TCF15 and MEOX1. We determine their spatiotemporal activity and evolutionary conservation in Xenopus and human. Epigenome silencing of endogenous CREs disrupts TCF15 and MEOX1 gene expression and recapitulates phenotypic abnormalities of anterior–posterior axis extension. Our integrated approach allows dissection of paraxial mesoderm regulatory circuits in vivo and has implications for investigating gene regulatory networks.
EARLY BUD-BREAK 1 and EARLY BUD-BREAK 3 control resumption of poplar growth after winter dormancy
Authors: Azeez Abdul , Zhao Yiru Chen , Singh Rajesh Kumar , Yordanov Yordan S. , Dash Madhumita , Miskolczi Pal , Stojkovič Katja , Strauss Steve H. , Bhalerao Rishikesh P. , Busov Victor B.
Published: February 2021

Bud-break is an economically and environmentally important process in trees and shrubs from boreal and temperate latitudes, but its molecular mechanisms are poorly understood. Here, we show that two previously reported transcription factors, EARLY BUD BREAK 1 (EBB1) and SHORT VEGETATIVE PHASE-Like (SVL) directly interact to control bud-break. EBB1 is a positive regulator of bud-break, whereas SVL is a negative regulator of bud-break. EBB1 directly and negatively regulates SVL expression. We further report the identification and characterization of the EBB3 gene. EBB3 is a temperature-responsive, epigenetically-regulated, positive regulator of bud-break that provides a direct link to activation of the cell cycle during bud-break. EBB3 is an AP2/ERF transcription factor that positively and directly regulates CYCLIND3.1 gene. Our results reveal the architecture of a putative regulatory module that links temperature-mediated control of bud-break with activation of cell cycle.
Colossal switchable photocurrents in topological Janus transition metal dichalcogenides
Authors: Xu Haowei , Wang Hua , Zhou Jian , Guo Yunfan , Kong Jing , Li Ju
Published: February 2021

Nonlinear optical properties, such as bulk photovoltaic effects, possess great potential in energy harvesting, photodetection, rectification, etc. To enable efficient light–current conversion, materials with strong photo-responsivity are highly desirable. In this work, we predict that monolayer Janus transition metal dichalcogenides (JTMDs) in the 1T′ phase possess colossal nonlinear photoconductivity owing to their topological band mixing, strong inversion symmetry breaking, and small electronic bandgap. 1T′ JTMDs have inverted bandgaps on the order of 10 meV and are exceptionally responsive to light in the terahertz (THz) range. By first-principles calculations, we reveal that 1T′ JTMDs possess shift current (SC) conductivity as large as 2300 nm μA V−2, equivalent to a photo-responsivity of 2800 mA/W. The circular current (CC) conductivity of 1T′ JTMDs is as large as ∼104 nm μA V−2. These remarkable photo-responsivities indicate that the 1T′ JTMDs can serve as efficient photodetectors in the THz range. We also find that external stimuli such as the in-plane strain and out-of-plane electric field can induce topological phase transitions in 1T′ JTMDs and that the SC can abruptly flip their directions. The abrupt change of the nonlinear photocurrent can be used to characterize the topological transition and has potential applications in 2D optomechanics and nonlinear optoelectronics.
Code interoperability extends the scope of quantum simulations
Authors: Govoni Marco , Whitmer Jonathan , de Pablo Juan , Gygi Francois , Galli Giulia
Published: February 2021

The functionality of many materials is critically dependent on the integration of dissimilar components and on the interfaces that arise between them. The description of such heterogeneous components requires the development and deployment of first principles methods, coupled to appropriate dynamical descriptions of matter and advanced sampling techniques, in order to capture all the relevant length and time scales of importance to the materials’ performance. It is thus essential to build simple, streamlined computational schemes for the prediction and design of multiple properties of broad classes of materials, by developing interoperable codes which can be efficiently coupled to each other to perform complex tasks. We discuss the use of interoperable codes to simulate the structural and spectroscopic characterization of materials, including chemical reactions for catalysis, the description of defects for quantum information science, and heat and charge transport.
Genetic characteristics and epidemiology of inherited retinal degeneration in Taiwan
Authors: Chen Ta-Ching , Huang Ding-Siang , Lin Chao-Wen , Yang Chang-Hao , Yang Chung-May , Wang Victoria Y. , Lin Jou-Wei , Luo Allen Chilun , Hu Fung-Rong , Chen Pei-Lung
Published: February 2021

Inherited retinal degenerations (IRDs) are a group of phenotypically and genotypically heterogeneous disorders with substantial socioeconomic impact. In this cohort study, we tried to address the genetic characteristics and epidemiology of IRDs in Taiwan. Totally, 312 families with IRDs were identified and recruited and genetic testing was performed via probe capture-based NGS targeting 212 IRD-related genes. Statistical analysis was based on the proband of each affected family. Disease-causing genotypes were identified in 178 families (57.1%). ABCA4 variants were the most common cause of disease in this cohort (27 families, 15.2%), whereas CYP4V2 variants were the most common cause for the single phenotype—Bietti’s crystalline dystrophy (12 families, 3.8%). Some variants such as ABCA4:c.1804C>T, CYP4V2:c.802-8_810delinsGC, and EYS:c6416G>A were population-specific disease-causing hotspots. Probands affected by ABCA4, RPGR, RP1L1, and CEP290 sought medical help earlier while patients affected by EYS and CYP4V2 visited our clinic at an older age. To evaluate the representativeness of our cohort in the genetic epidemiology of IRDs in Taiwan, our demographic data were compared with that of the total IRD population in Taiwan, obtained from the National Health Insurance Research Database. This is currently the largest-scale, comprehensive study investigating the genetic characteristics and epidemiology of IRD in Taiwan. These data could help patients and caregivers to adopt precision genomic medicine and novel gene therapies in near future.
Single-bubble EHD behavior into water two-phase flow under electric-field stress and gravitational acceleration using PFM
Authors: Mianmahale Maryam Aliakbary , Mehrabani-Zeinabad Arjomand , Zare Masoud Habibi , Ghadiri Mahdi
Published: February 2021

In this study, single-bubble electro-hydrodynamic effects on the two-phase laminar flow of water under electric field stress are investigated using numerical modeling. A 2D axisymmetric model is also developed to study the growth and departure of a single bubble. The phase-field method is applied to track the interphase between liquid and gas. The growth of the attached vapor bubble nucleus to a superheat at 7.0 °C and 8.5 °C are evaluated with 50° and 90° contact angles. The results show that the enhancement of the contact angle changes the velocity and temperature fields around the bubble. It is observed that the growing size and base of the bubble is increased with increasing the wall superheat, but the bubble departure diameter and time are decreased. The electric field results in raising the number of detached bubbles from the superheat at a certain time interval but decreasing the bubbles departure size. Additionally, the formation of stretched bubbles enhances the rate of heat flux and there is a non-linear relationship between the applied voltage and heat flux.
Author Correction: A global moderate resolution dataset of gross primary production of vegetation for 2000–2016
Authors: Zhang Yao , Xiao Xiangming , Wu Xiaocui , Zhou Sha , Zhang Geli , Qin Yuanwei , Dong Jinwei
Published: February 2021

A Correction to this paper has been published: https://doi.org/10.1038/s41597-021-00854-6.
Female fertile phase synchrony, and male mating and reproductive skew, in the crested macaque
Authors: Higham James P. , Heistermann Michael , Agil Muhammad , Perwitasari-Farajallah Dyah , Widdig Anja , Engelhardt Antje
Published: February 2021

High social status is the primary determinant of reproductive success among group-living male mammals. Primates living in multimale–multifemale groups show the greatest variation in the strength of this link, with marked variation in reproductive skew by male dominance among species, dependent on the degree of female fertile phase synchrony, and the number of competing males. Here, we present data on two groups of wild crested macaques (Macaca nigra), living in the Tangkoko Reserve, Sulawesi, Indonesia. We investigated male monopolization of fertile females in 31 cycles of 19 females, and genetic paternity of 14 offspring conceived during the study period. We show that female fertile phase synchrony was low, that females had few mating partners in their fertile phase, and that dominant males monopolized a high proportion of consortships and matings, resulting in marked and steep mating and reproductive skew. We conclude that female cycle asynchrony provides the opportunity for strong direct male–male competition in crested macaques, resulting in monopolization of females by dominant males, consistent with their marked sexual dimorphism. Our study provides a test of the underlying factors that determine the relative occurrence and strength of different mechanisms of sexual selection, and the phenotypes that evolve as a result.
Convection heat mass transfer and MHD flow over a vertical plate with chemical reaction, arbitrary shear stress and exponential heating
Authors: Sehra  , Haq Sami Ul , Shah Syed Inayat Ali , Nisar Kottakkaran Sooppy , Jan Saeed Ullah , Khan Ilyas
Published: February 2021

The present research article is directed to study the heat and mass transference analysis of an incompressible Newtonian viscous fluid. The unsteady MHD natural convection flow over an infinite vertical plate with time dependent arbitrary shear stresses has been investigated. In heat and mass transfer analysis the chemical molecular diffusivity effects have been studied. Moreover, the infinite vertical plate is subjected to the phenomenon of exponential heating. For this study, we formulated the problem into three governing equations along with their corresponding initial and boundary conditions. The Laplace transform method has been used to gain the exact analytical solutions to the problem. Special cases of the obtained solutions are investigated. It is noticed that some well-known results from the published literature are achieved from these special cases. Finally, different physical parameters’ responses are investigated graphically through Mathcad software.
A high-throughput RNA-Seq approach to elucidate the transcriptional response of Piriformospora indica to high salt stress
Authors: Nivedita  , Rawoof Abdul , Ramchiary Nirala , Abdin Malik Z.
Published: February 2021

Piriformospora indica, a root endophytic fungus, augments plant nutrition and productivity as well as protects plants against pathogens and abiotic stresses. High salinity is a major problem faced by plants as well as by microbes. Until now, the precise mechanism of salt stress tolerance in P. indica has remained elusive. In this study, the transcriptomes of control and salt-treated (0.5 M NaCl) P. indica were sequenced via the RNA-seq approach. A total of 30,567 transcripts and 15,410 unigenes for P. indica were obtained from 7.3 Gb clean reads. Overall 661 differentially expressed genes (DEGs) between control and treated samples were retrieved. Gene ontology (GO) and EuKaryotic Orthologous Groups (KOG) enrichments revealed that DEGs were specifically involved in metabolic and molecular processes, such as “response to salt stress”, “oxidoreductase activity”, “ADP binding”, “translation, ribosomal structure and biogenesis”, “cytoskeleton”, and others. The unigenes involved in “cell wall integrity”, “sterol biosynthesis”, and “oxidative stress” such as Rho-type GTPase, hydroxymethylglutaryl-CoA synthase, and thioredoxin peroxidase were up-regulated in P. indica subjected to salt stress. The salt-responsive DEGs have shown that they might have a potential role in salt stress regulation. Our study on the salt-responsive DEGs established a foundation for the elucidation of molecular mechanisms related to P. indica stress adaptation and a future reference for comparative functional genomics studies of biotechnologically important fungal species.
Integrins mediate placental extracellular vesicle trafficking to lung and liver in vivo
Authors: Nguyen Sean L. , Ahn Soo Hyun , Greenberg Jacob W. , Collaer Benjamin W. , Agnew Dalen W. , Arora Ripla , Petroff Margaret G.
Published: February 2021

Membrane-bound extracellular vesicles (EVs) mediate intercellular communication in all organisms, and those produced by placental mammals have become increasingly recognized as significant mediators of fetal-maternal communication. Here, we aimed to identify maternal cells targeted by placental EVs and elucidate the mechanisms by which they traffic to these cells. Exogenously administered pregnancy-associated EVs traffic specifically to the lung; further, placental EVs associate with lung interstitial macrophages and liver Kupffer cells in an integrin-dependent manner. Localization of EV to maternal lungs was confirmed in unmanipulated pregnancy using a transgenic reporter mouse model, which also provided in situ and in vitro evidence that fetally-derived EVs, rarely, may cause genetic alteration of maternal cells. These results provide for the first time direct in vivo evidence that placental EVs target maternal immune cells, and further, that EVs can alter cellular phenotype.
Characterization of HIV-1 recombinant and subtype B near full-length genome among men who have sex with men in South Korea
Authors: Ryou Sangmi , Yoo Myeongsu , Kim Kisoon , Kim Sangsoo , Kim Sang Il , Kim Youn Jeong , Park Dae Won , Choi Jun Yong , Kim Hyo Youl , Kim Jung Ho , Song Joon Young , Kim Shin-Woo , Chang Hyun-Ha , Choi Bo Youl , Kee Mee-Kyung
Published: February 2021

In Korea, subtype B is the predominant variant of HIV-1, but full genome sequencing and analysis of its viral variants are lacking. We performed near full-length genome (NFLG) sequencing and phylogenetic and recombination analyses of fifty plasma samples from HIV-positive men who have sex with men (MSM) from a Korea HIV/AIDS cohort study. Viral genomes were amplified and the near-full-length sequences were determined using next-generation sequencing (NGS) and Sanger sequencing. We focused on the HIV-1 subtype classification and identification of HIV recombinants. Twelve HIV-1 NFLGs were determined: ten were subtyped as pure HIV-1 subtype B and two recombinant strains as a common subtype CRF07_BC, and a novel subtype CRF43_02G recombined with CRF02_AG again, or a new CRF02_AG and subtype G recombinant. For the ten NFLGs determined by NGS, “the novel recombinant emerged at approximately 2003 and the other nine subtype B about 2004 or 2005”. This is the first report analyzing HIV-1 NFLG, including recombinants and clinical characteristics, by subtype among MSM in Korea. Our results provide novel insights for understanding the recombinants in the HIV-1 epidemic in Korea.
Antibody mediated activation of natural killer cells in malaria exposed pregnant women
Authors: Damelang Timon , Aitken Elizabeth H. , Hasang Wina , Lopez Ester , Killian Martin , Unger Holger W. , Salanti Ali , Shub Alexis , McCarthy Elizabeth , Kedzierska Katherine , Lappas Martha , Kent Stephen J. , Rogerson Stephen J. , Chung Amy W.
Published: February 2021

Immune effector responses against Plasmodium falciparum include antibody-mediated activation of innate immune cells, which can induce Fc effector functions, including antibody-dependent cellular cytotoxicity, and the secretion of cytokines and chemokines. These effector functions are regulated by the composition of immunoglobulin G (IgG) Fc N-linked glycans. However, a role for antibody-mediated natural killer (NK) cells activation or Fc N-linked glycans in pregnant women with malaria has not yet been established. Herein, we studied the capacity of IgG antibodies from pregnant women, with placental malaria or non-placental malaria, to induce NK cell activation in response to placental malaria-associated antigens DBL2 and DBL3. Antibody-mediated NK cell activation was observed in pregnant women with malaria, but no differences were associated with susceptibility to placental malaria. Elevated anti-inflammatory glycosylation patterns of IgG antibodies were observed in pregnant women with or without malaria infection, which were not seen in healthy non-pregnant controls. This suggests that pregnancy-associated anti-inflammatory Fc N-linked glycans may dampen the antibody-mediated activation of NK cells in pregnant women with malaria infection. Overall, although anti-inflammatory glycans and antibody-dependent NK cell activation were detected in pregnant women with malaria, a definitive role for these antibody features in protecting against placental malaria remains to be proven.
Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community
Authors: Lee Hye Kyung , Knabl Ludwig , Pipperger Lisa , Volland Andre , Furth Priscilla A. , Kang Keunsoo , Smith Harold E. , Knabl Ludwig , Bellmann Romuald , Bernhard Christina , Kaiser Norbert , Gänzer Hannes , Ströhle Mathias , Walser Andreas , von Laer Dorothee , Hennighausen Lothar
Published: February 2021

SARS-CoV-2 infection ranges from asymptomatic to severe with lingering symptomatology in some. This prompted investigation of whether or not asymptomatic disease results in measurable immune activation post-infection. Immune activation following asymptomatic SARS-CoV-2 infection was characterized through a comparative investigation of the immune cell transcriptomes from 43 asymptomatic seropositive and 52 highly exposed seronegative individuals from the same community 4–6 weeks following a superspreading event. Few of the 95 individuals had underlying health issues. One seropositive individual reported Cystic Fibrosis and one individual reported Incontinentia pigmenti. No evidence of immune activation was found in asymptomatic seropositive individuals with the exception of the Cystic Fibrosis patient. There were no statistically significant differences in immune transcriptomes between asymptomatic seropositive and highly exposed seronegative individuals. Four positive controls, mildly symptomatic seropositive individuals whose blood was examined 3 weeks following infection, showed immune activation. Negative controls were four seronegative individuals from neighboring communities without COVID-19. All individuals remained in their usual state of health through a five-month follow-up after sample collection. In summary, whole blood transcriptomes identified individual immune profiles within a community population and showed that asymptomatic infection within a super-spreading event was not associated with enduring immunological activation.
One-dimensional diffusion of TrpR along DNA enhances its affinity for the operator by chemical ratchet mechanism
Authors: Kinebuchi Takashi , Shimamoto Nobuo
Published: February 2021

Several DNA-binding proteins show the affinities for their specific DNA sites that positively depend on the length of DNA harboring the sites, i. e. antenna effect. DNA looping can cause the effect for proteins with two or more DNA binding sites, i. e. the looping mechanism. One-dimensional diffusion also has been suggested to cause the effect for proteins with single DNA sites, the diffusion mechanism, which could violate detailed balance. We addressed which mechanism is possible for E. coli TrpR showing 104-fold antenna effect with a single DNA binding site. When a trpO-harboring DNA fragment was connected to a nonspecific DNA with biotin-avidin connection, the otherwise sevenfold antenna effect disappeared. This result denies the looping mechanism with an unknown second DNA binding site. The 3.5-fold repression by TrpR in vivo disappeared when a tight LexA binding site was introduced at various sites near the trpO, suggesting that the binding of LexA blocks one-dimensional diffusion causing the antenna effect. These results are consistent with the chemical ratchet recently proposed for TrpR-trpO binding to solve the deviation from detailed balance, and evidence that the antenna effect due to one-dimensional diffusion exists in cells.
Enabling deeper learning on big data for materials informatics applications
Authors: Jha Dipendra , Gupta Vishu , Ward Logan , Yang Zijiang , Wolverton Christopher , Foster Ian , Liao Wei-keng , Choudhary Alok , Agrawal Ankit
Published: February 2021

The application of machine learning (ML) techniques in materials science has attracted significant attention in recent years, due to their impressive ability to efficiently extract data-driven linkages from various input materials representations to their output properties. While the application of traditional ML techniques has become quite ubiquitous, there have been limited applications of more advanced deep learning (DL) techniques, primarily because big materials datasets are relatively rare. Given the demonstrated potential and advantages of DL and the increasing availability of big materials datasets, it is attractive to go for deeper neural networks in a bid to boost model performance, but in reality, it leads to performance degradation due to the vanishing gradient problem. In this paper, we address the question of how to enable deeper learning for cases where big materials data is available. Here, we present a general deep learning framework based on Individual Residual learning (IRNet) composed of very deep neural networks that can work with any vector-based materials representation as input to build accurate property prediction models. We find that the proposed IRNet models can not only successfully alleviate the vanishing gradient problem and enable deeper learning, but also lead to significantly (up to 47%) better model accuracy as compared to plain deep neural networks and traditional ML techniques for a given input materials representation in the presence of big data.
Avoiding gauge ambiguities in cavity quantum electrodynamics
Authors: Rouse Dominic M. , Lovett Brendon W. , Gauger Erik M. , Westerberg Niclas
Published: February 2021

Systems of interacting charges and fields are ubiquitous in physics. Recently, it has been shown that Hamiltonians derived using different gauges can yield different physical results when matter degrees of freedom are truncated to a few low-lying energy eigenstates. This effect is particularly prominent in the ultra-strong coupling regime. Such ambiguities arise because transformations reshuffle the partition between light and matter degrees of freedom and so level truncation is a gauge dependent approximation. To avoid this gauge ambiguity, we redefine the electromagnetic fields in terms of potentials for which the resulting canonical momenta and Hamiltonian are explicitly unchanged by the gauge choice of this theory. Instead the light/matter partition is assigned by the intuitive choice of separating an electric field between displacement and polarisation contributions. This approach is an attractive choice in typical cavity quantum electrodynamics situations.
Brain functional connectivity differs when viewing pictures from natural and built environments using fMRI resting state analysis
Authors: Kühn Simone , Forlim Caroline Garcia , Lender Anja , Wirtz Janina , Gallinat Jürgen
Published: February 2021

Human beings evolved in “natural” environments. Many intervention studies have shown that exposure to natural environments (compared to built/urban environments) reduces stress and increases cognitive functioning. We set out to test differences in fMRI functional connectivity while showing participants photographs from natural versus built environments (matched in terms of scenicness ratings). No differences in self-reported perceived stress, rumination, valence, arousal or dominance were observed. However, functional connectivity was significantly higher when participants saw natural rather than built environmental photographs in circuits consisting of dorsal attention network (DAN) and ventral attention network (VAN), DAN and default mode network (DMN) and DMN and Somatomotor connections. In addition, we observed lower functional connectivity during the natural environment condition correlated with more years that individuals spent in major cities during upbringing. Future studies, linking changes in cognitive functioning due to nature exposure and alterations in functional connectivity, are warranted.
Atorvastatin treatment does not abolish inflammatory mediated cardiovascular risk in subjects with chronic kidney disease
Authors: Hoogeveen Renate M. , Verweij Simone L. , Kaiser Yannick , Kroon Jeffrey , Verberne Hein J. , Vogt Liffert , Moens Sophie J. Bernelot , Stroes Erik S. G.
Published: February 2021

Individuals with chronic kidney disease are at an increased risk for cardiovascular disease. This risk may partially be explained by a chronic inflammatory state in these patients, reflected by increased arterial wall and cellular inflammation. Statin treatment decreases cardiovascular risk and arterial inflammation in non-CKD subjects. In patients with declining kidney function, cardiovascular benefit resulting from statin therapy is attenuated, possibly due to persisting inflammation. In the current study, we assessed the effect of statin treatment on arterial wall and cellular inflammation. Fourteen patients with chronic kidney disease stage 3 or 4, defined by an estimated Glomerular Filtration Rate between 15 and 60 mL/min/1.73 m2, without cardiovascular disease were included in a single center, open label study to assess the effect of atorvastatin 40 mg once daily for 12 weeks (NTR6896). At baseline and at 12 weeks of treatment, we assessed arterial wall inflammation by 18F-fluoro-deoxyglucose positron-emission tomography computed tomography (18F-FDG PET/CT) and the phenotype of circulating monocytes were assessed. Treatment with atorvastatin resulted in a 46% reduction in LDL-cholesterol, but this was not accompanied by an attenuation in arterial wall inflammation in the aorta or carotid arteries, nor with changes in chemokine receptor expression of circulating monocytes. Statin treatment does not abolish arterial wall or cellular inflammation in subjects with mild to moderate chronic kidney disease. These results imply that CKD-associated inflammatory activity is mediated by factors beyond LDL-cholesterol and specific anti-inflammatory interventions might be necessary to further dampen the inflammatory driven CV risk in these subjects.
Population decline in a ground-nesting solitary squash bee (Eucera pruinosa) following exposure to a neonicotinoid insecticide treated crop (Cucurbita pepo)
Authors: Willis Chan D. Susan , Raine Nigel E.
Published: February 2021

Insect pollinators are threatened by multiple environmental stressors, including pesticide exposure. Despite being important pollinators, solitary ground-nesting bees are inadequately represented by pesticide risk assessments reliant almost exclusively on honeybee ecotoxicology. Here we evaluate the effects of realistic exposure via squash crops treated with systemic insecticides (Admire-imidacloprid soil application, FarMore FI400-thiamethoxam seed-coating, or Coragen-chlorantraniliprole foliar spray) for a ground-nesting bee species (Hoary squash bee, Eucera pruinosa) in a 3-year semi-field experiment. Hoary squash bees provide essential pollination services to pumpkin and squash crops and commonly nest within cropping areas increasing their risk of pesticide exposure from soil, nectar, and pollen. When exposed to a crop treated at planting with soil-applied imidacloprid, these bees initiated 85% fewer nests, left 5.3 times more pollen unharvested, and produced 89% fewer offspring than untreated controls. No measurable impacts on bees from exposure to squash treated with thiamethoxam as a seed-coating or foliage sprayed with chlorantraniliprole were found. Our results demonstrate important sublethal effects of field-realistic exposure to a soil-applied neonicotinoid (imidacloprid) on bee behaviour and reproductive success. Soil must be considered a potential route of pesticide exposure in risk assessments, and restrictions on soil-applied insecticides may be justified, to mitigate impacts on ground-nesting solitary bee populations and the crop pollination services they provide.
Topological structures, spontaneous symmetry breaking and energy spectra in dipole hexagonal lattices
Authors: Batle Josep
Published: February 2021

The interplay between the special triangular/hexagonal two dimensional lattice and the long range dipole–dipole interaction gives rise to topological defects, specifically the vortex, formed by a particular arrangement of the interacting classic dipoles. The nature of such vortices has been traditionally explained on the basis of numerical evidence. Here we propose the emerging formation of vortices as the natural minimum energy configuration of interacting (in-plane) two-dimensional dipoles based on the mechanism of spontaneous symmetry breaking. As opposed to the quantal case, where spin textures such as skyrmions or bimerons occur due to non-linearities in their Hamiltonian, it is still possible to witness classic topological structures due only to the nature of the dipole–dipole force. We shall present other (new) topological structures for the in-plane honeycomb lattice, as well as for two-dimensional out-of-plane dipoles. These structures will prove to be essential in the minimum energy configurations for three-dimensional simple hexagonal and hexagonal-closed-packed structures, whose energies in the bulk are obtained for the first time.
Relevant methane emission to the atmosphere from a geological gas manifestation
Authors: Mazzini Adriano , Sciarra Alessandra , Etiope Giuseppe , Sadavarte Pankaj , Houweling Sander , Pandey Sudhanshu , Husein Alwi
Published: February 2021

Quantifying natural geological sources of methane (CH4) allows to improve the assessment of anthropogenic emissions to the atmosphere from fossil fuel industries. The global CH4 flux of geological gas is, however, an object of debate. Recent fossil (14C-free) CH4 measurements in preindustrial-era ice cores suggest very low global geological emissions (~ 1.6 Tg year−1), implying a larger fossil fuel industry source. This is however in contrast with previously published bottom-up and top-down geo-emission estimates (~ 45 Tg year−1) and even regional-scale emissions of ~ 1–2 Tg year−1. Here we report on significant geological CH4 emissions from the Lusi hydrothermal system (Indonesia), measured by ground-based and satellite (TROPOMI) techniques. Both techniques indicate a total CH4 output of ~ 0.1 Tg year−1, equivalent to the minimum value of global geo-emission derived by ice core 14CH4 estimates. Our results are consistent with the order of magnitude of the emission factors of large seeps used in global bottom-up estimates, and endorse a substantial contribution from natural Earth’s CH4 degassing. The preindustrial ice core assessments of geological CH4 release may be underestimated and require further study. Satellite measurements can help to test geological CH4 emission factors and explain the gap between the contrasting estimates.
Relationship model between surface strain of concrete and expansion force of reinforcement rust
Authors: Chen Fanxiu , Jin Zuquan , Wang Endong , Wang Lanqin , Jiang Yudan , Guo Pengfei , Gao Xinya , He Xiaoyuan
Published: February 2021

Concrete cracking caused by corrosion of reinforcement could significantly shorten the durability of reinforced concrete structure. It remains critical to investigate the process and mechanism of the corrosion occurring to concrete reinforcement and establish the theoretical prediction model of concrete expansion force for the whole process of corrosion cracking of reinforcement. Under the premise of uniform corrosion of reinforcing steel bars, the elastic mechanics analysis method is adopted to analyze the entire process starting from the corrosion of steel bars to the cracking of concrete due to corrosion. A relationship model between the expansion force of corrosion of steel bars and the surface strain of concrete is established. On the cuboid reinforced concrete specimens with square cross-sections, accelerated corrosion tests are carried out to calibrate and verify the established model. The model can be able to estimate the real-time expansion force of reinforced concrete at any time of the whole process from the initiation of steel corrosion to the end of concrete cracking by measuring the surface strain of concrete. It could be useful for quantitative real-time monitoring of steel corrosion in concrete structures.
One-carbon pathway and cognitive skills in children with Down syndrome
Authors: Antonaros Francesca , Lanfranchi Silvia , Locatelli Chiara , Martelli Anna , Olivucci Giulia , Cicchini Elena , Carosi Diatricch Ludovica , Mannini Elisa , Vione Beatrice , Feliciello Agnese , Ramacieri Giuseppe , Onnivello Sara , Vianello Renzo , Vitale Lorenza , Pelleri Maria Chiara , Strippoli Pierluigi , Cocchi Guido , Pulina Francesca , Piovesan Allison , Caracausi Maria
Published: February 2021

This work investigates the role of metabolite levels in the intellectual impairment of subjects with Down syndrome (DS). Homocysteine, folate, vitamin B12, uric acid (UA), creatinine levels and MTHFR C677T genotype were analyzed in 147 subjects with DS. For 77 subjects, metabolite levels were correlated with cognitive tests. Griffiths-III test was administered to 28 subjects (3.08–6.16 years) and WPPSI-III test was administered to 49 subjects (7.08–16.08 years). Significant correlations were found among some metabolite levels and between homocysteine levels and MTHFR C677T genotype. Moreover, homocysteine, UA and creatinine levels resulted increased with age. We did not find any correlation between metabolites and cognitive test score in the younger group. Homocysteine showed statistically significant correlation with WPPSI-III subtest scores when its level is ≥ 7.35 µmol/L, remaining correlated in higher thresholds only for non-verbal area scores. Vitamin B12 showed correlations with all WPPSI-III subtest scores when its level is < 442 pg/mL. The relevance of the present findings is the detection of a specific metabolite threshold related with a better or worse cognitive score, suggesting that vitamin B12 and homocysteine may have a role in cognitive development in children with DS.
Virus-derived peptide inhibitors of the herpes simplex virus type 1 nuclear egress complex
Authors: Draganova Elizabeth B. , Heldwein Ekaterina E.
Published: February 2021

Herpesviruses infect a majority of the human population, establishing lifelong latent infections for which there is no cure. Periodic viral reactivation spreads infection to new hosts while causing various disease states particularly detrimental in the immunocompromised. Efficient viral replication, and ultimately the spread of infection, is dependent on the nuclear egress complex (NEC), a conserved viral heterodimer that helps translocate viral capsids from the nucleus to the cytoplasm where they mature into infectious virions. Here, we have identified peptides, derived from the capsid protein UL25, that are capable of inhibiting the membrane-budding activity of the NEC from herpes simplex virus type 1 in vitro. We show that the inhibitory ability of the peptides depends on their length and the propensity to form an α-helix but not on the exact amino acid sequence. Current therapeutics that target viral DNA replication machinery are rendered ineffective by drug resistance due to viral mutations. Our results establish a basis for the development of an alternative class of inhibitors against nuclear egress, an essential step in herpesvirus replication, potentially expanding the current repertoire of available therapeutics.
Factors influencing scavenger guilds and scavenging efficiency in Southwestern Montana
Authors: Walker Morgan A. , Uribasterra Maria , Asher Valpa , Getz Wayne M. , Ryan Sadie J. , Ponciano José Miguel , Blackburn Jason K.
Published: February 2021

Scavenging of carrion shapes ecological landscapes by influencing scavenger population demography, increasing inter- and intra-specific interactions, and generating ecosystem services such as nutrient cycling and disease moderation. Previous research found the cues promoting, or the constraints limiting, an individual’s propensity or ability to scavenge vary widely, depending on anthropogenic and environmental factors. Here we investigated differences in scavenging patterns in a complex scavenger guild in Southwestern Montana. We used camera traps established at 13 carcass sites to monitor carcass detection, visitation, and consumption times, during 2016–2018 and generalized linear models to explore the influence of carcass characteristics, habitat features, and seasonality, on carcass selection and scavenging efficiency. We found that scavenger species diversity was higher at higher elevations and in grassland habitats. Scavenging efficiency was influencedinter aliaby seasonality, distance to water, and elevation. We found that most carcass consumption was via facultative scavengers (bears, wolves, magpies,Corvusspp.) rather than turkey vultures, the only obligate scavengers in the study area. However, growing populations of turkey vultures may lead to increased competition with facultative scavengers over carrion, and could have cascading effects on food webs in this ecosystem.
Colloidal stability of phytosynthesised gold nanoparticles and their catalytic effects for nerve agent degradation
Authors: Holišová Veronika , Urban Martin , Konvičková Zuzana , Kolenčík Marek , Mančík Pavel , Slabotinský Jiří , Kratošová Gabriela , Plachá Daniela
Published: February 2021

Herein, Tilia sp. bract leachate was used as the reducing agent for Au nanoparticles (Au NPs) phytosynthesis. The colloidal properties of the prepared Au NPs were determined to confirm their stability over time, and the NPs were then used as active catalysts in soman nerve agent degradation. The Au NPs characterisation, reproducibility and stability studies were performed under transmission electron microscopy, ultraviolet visible spectroscopy and with ζ-potential measurements. The reaction kinetics was detected by gas chromatography coupled with mass spectrometry detector and solid-phase micro-extraction to confirm the Au NPs applicability in soman hydrolysis. The ‘green’ phytosynthetic formation of colloidal crystalline Au NPs with dominant quasi-spherical shape and 55 ± 10 nm diameter was successfully achieved, and there were no significant differences in morphology, ζ-potential or absorbance values observed during the 5-week period. This verified the prepared colloids’ long-term stability. The soman nerve agent was degraded to non-toxic substances within 24 h, with 0.2156 h−1 reaction rate constant. These results confirmed bio-nanotechnology’s great potential in preparation of stable and functional nanocatalysts for degradation of hazardous substances, including chemical warfare agents.
Risk of thrombotic events after respiratory infection requiring hospitalization
Authors: Smilowitz Nathaniel R. , Subashchandran Varun , Newman Jonathan , Barfield Michael E. , Maldonado Thomas S. , Brosnahan Shari B. , Yuriditsky Eugene , Horowitz James M. , Shah Binita , Reynolds Harmony R. , Hochman Judith S. , Berger Jeffrey S.
Published: February 2021

Thrombosis is a major concern in respiratory infections. Our aim was to investigate the magnitude and duration of risk for arterial and venous thrombosis following discharge after respiratory infection. Patients with respiratory infections were identified using the United States Nationwide Readmission Database from 2012 to 2014. Patients admitted with asthma or cellulitis served as comparators. Readmissions for acute myocardial infarction (MI) and venous thromboembolism (VTE) were evaluated at 30 to 180 days. The likelihood of a first thrombotic event after discharge was compared with a 30-day period prior to hospitalization. Among 5,271,068 patients discharged after a respiratory infection, 0.56% and 0.78% were readmitted within 30-days with MI and VTE, respectively. Relative to asthma and cellulitis, respiratory infection was associated with a greater age and sex-adjusted hazard of 30-day readmission for MI (adjusted HR [aHR] 1.48 [95% CI 1.42–1.54] vs. asthma; aHR 1.36 [95% CI 1.31–1.41] vs. cellulitis) and VTE (aHR 1.28 [95% CI 1.24–1.33] vs. asthma; aHR 1.26, [95% CI 1.22–1.30] vs. cellulitis). Risks of MI and VTE attenuated over time. In a crossover-cohort analysis, the odds of MI (OR 1.68 [95% CI 1.62–1.73]) and VTE (OR 3.30 [95% 3.19–3.41]) were higher in the 30 days following discharge after respiratory infection than during the 30-day baseline period. Hospitalization for respiratory infection was associated with increased risks of thrombosis that were highest in the first 30-days after discharge and declined over time.