bluuebunny/crossref_metadata_2025 huggingface dataset:
Mercury Evidence of Intense Volcanism Preceded Oceanic Anoxic Event 1d
Authors: Yao Hanwei , Chen Xi , Yin Runsheng , Grasby Stephen E. , Weissert Helmut , Gu Xue , Wang Chengshan
Published: February 2021

Geochemical studies of marine sediments indicate that most Oceanic Anoxic Events (OAEs) appear coincident with Large Igneous Province (LIP) volcanism. OAE 1d records peculiar paleoceanographic changes and global carbon cycle perturbations, however, its association with volcanism has not yet been supported by robust geochemical evidence. To examine the potential role of volcanism we investigated the mercury (Hg) concentration and isotopic record of OAE 1d interval at the Youxia section, southern Tibet. The interval prior to OAE 1d is marked by a combined positive Δ199Hg and Hg content shift, which suggests a volcanic Hg source. These findings are consistence with a prominent increase in sea surface temperatures and atmospheric CO2 before OAE 1d. We suggest that eruption of the central portion of the Kerguelen LIP may have been the main source of the Hg anomaly and resulted in global environment perturbations that drove the onset of the anoxia event.
Winter Precipitation Changes in California Under Global Warming: Contributions of CO2, Uniform SST Warming, and SST Change Patterns
Authors: Dong Lu , Leung L. Ruby
Published: February 2021

Climate models project a wetting winter over California, distinct from the drying in all other Mediterranean climate regions under warming. Dynamic effect via an eastward extension of the westerly jet stream over the North Pacific is the root cause for the wetting California. Utilizing four sets of prescribed‐SST (sea surface temperature) simulations, the relative effects of direct CO2 radiative forcing, uniform SST warming, and SST change patterns are investigated. The wetting winter is dominated by uniform SST warming mainly through its effect on the jet extension. As a fundamental response to the enhanced upper‐tropospheric warming in the tropics, the jet extension in coupled simulations is well reproduced under uniform SST warming and robust among models. An El Niño‐like SST warming pattern has a secondary contribution to the jet extension via atmospheric teleconnection, but with large inter‐model spread. Relative to the SST forcing, the direct CO2 radiative effect is negligible.
Changing Lengths of the Four Seasons by Global Warming
Authors: Wang Jiamin , Guan Yuping , Wu Lixin , Guan Xiaodan , Cai Wenju , Huang Jianping , Dong Wenjie , Zhang Banglin
Published: February 2021

How long will the four seasons be by 2100? Increasing evidence suggests that the length of a single season or in regional scales has changed under global warming, but a hemispherical‐scale response of the four seasons in the past and future remains unknown. We find that summer in the Northern Hemisphere midlatitudes has lengthened, whereas winter has shortened, owing to shifts in their onsets and withdrawals, accompanied by shorter spring and autumn. Such changes in lengths and onsets can be mainly attributed to greenhouse‐warming. Even if the current warming rate does not accelerate, changes in seasons will still be exacerbated in the future. Under the business‐as‐usual scenario, summer is projected to last nearly half a year, but winter less than 2 months by 2100. The changing seasonal clock signifies disturbed agriculture seasons and rhythm of species activities, more frequent heat waves, storms and wildfires, amounting to increased risks to humanity.
Physical Origin of Short Scale Plasma Structures in the Auroral F Region
Authors: Bisai N. , Sen A.
Published: February 2021

The drift instability in the auroral F region of the ionosphere is known to create long scale finger like plasma structures in the presence of a density inhomogeneity and an ambient electric field. These structures elongate mainly along the density inhomogeneity direction. In situ measurements as well as scattering experiments have also revealed the existence of small scale structures in this region. The authors propose that such structures are created due to the breakup of the long scale structures on account of their differential stretching from sheared electric fields. Using heuristic physical arguments and dimensional analysis the authors derive a general criterion for the onset of such breakups. The analytic results are validated from numerical simulations of the full set of basic nonlinear equations describing the instability and should prove useful in the prediction and interpretation of the spread F in the high latitude region.
Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions
Authors: Krainer Georg , Welsh Timothy J. , Joseph Jerelle A. , Espinosa Jorge R. , Wittmann Sina , de Csilléry Ella , Sridhar Akshay , Toprakcioglu Zenon , Gudiškytė Giedre , Czekalska Magdalena A. , Arter William E. , Guillén-Boixet Jordina , Franzmann Titus M. , Qamar Seema , George-Hyslop Peter St , Hyman Anthony A. , Collepardo-Guevara Rosana , Alberti Simon , Knowles Tuomas P. J.
Published: February 2021

Liquid–liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.
Inference and analysis of cell-cell communication using CellChat
Authors: Jin Suoqin , Guerrero-Juarez Christian F. , Zhang Lihua , Chang Ivan , Ramos Raul , Kuan Chen-Hsiang , Myung Peggy , Plikus Maksim V. , Nie Qing
Published: February 2021

Understanding global communications among cells requires accurate representation of cell-cell signaling links and effective systems-level analyses of those links. We construct a database of interactions among ligands, receptors and their cofactors that accurately represent known heteromeric molecular complexes. We then develop CellChat, a tool that is able to quantitatively infer and analyze intercellular communication networks from single-cell RNA-sequencing (scRNA-seq) data. CellChat predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Through manifold learning and quantitative contrasts, CellChat classifies signaling pathways and delineates conserved and context-specific pathways across different datasets. Applying CellChat to mouse and human skin datasets shows its ability to extract complex signaling patterns. Our versatile and easy-to-use toolkit CellChat and a web-based Explorer (http://www.cellchat.org/) will help discover novel intercellular communications and build cell-cell communication atlases in diverse tissues.
Population-specific causal disease effect sizes in functionally important regions impacted by selection
Authors: Shi Huwenbo , Gazal Steven , Kanai Masahiro , Koch Evan M. , Schoech Armin P. , Siewert Katherine M. , Kim Samuel S. , Luo Yang , Amariuta Tiffany , Huang Hailiang , Okada Yukinori , Raychaudhuri Soumya , Sunyaev Shamil R. , Price Alkes L.
Published: February 2021

Many diseases exhibit population-specific causal effect sizes with trans-ethnic genetic correlations significantly less than 1, limiting trans-ethnic polygenic risk prediction. We develop a new method, S-LDXR, for stratifying squared trans-ethnic genetic correlation across genomic annotations, and apply S-LDXR to genome-wide summary statistics for 31 diseases and complex traits in East Asians (average N = 90K) and Europeans (average N = 267K) with an average trans-ethnic genetic correlation of 0.85. We determine that squared trans-ethnic genetic correlation is 0.82× (s.e. 0.01) depleted in the top quintile of background selection statistic, implying more population-specific causal effect sizes. Accordingly, causal effect sizes are more population-specific in functionally important regions, including conserved and regulatory regions. In regions surrounding specifically expressed genes, causal effect sizes are most population-specific for skin and immune genes, and least population-specific for brain genes. Our results could potentially be explained by stronger gene-environment interaction at loci impacted by selection, particularly positive selection.
Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome
Authors: Chen Congying , Zhou Yunyan , Fu Hao , Xiong Xinwei , Fang Shaoming , Jiang Hui , Wu Jinyuan , Yang Hui , Gao Jun , Huang Lusheng
Published: February 2021

Gut microbiota plays an important role in pig health and production. Still, availability of sequenced genomes and functional information for most pig gut microbes remains limited. Here we perform a landscape survey of the swine gut microbiome, spanning extensive sample sources by deep metagenomic sequencing resulting in an expanded gene catalog named pig integrated gene catalog (PIGC), containing 17,237,052 complete genes clustered at 90% protein identity from 787 gut metagenomes, of which 28% are unknown proteins. Using binning analysis, 6339 metagenome-assembled genomes (MAGs) were obtained, which were clustered to 2673 species-level genome bins (SGBs), among which 86% (2309) SGBs are unknown based on current databases. Using the present gene catalog and MAGs, we identified several strain-level differences between the gut microbiome of wild boars and commercial Duroc pigs. PIGC and MAGs provide expanded resources for swine gut microbiome-related research.
Van der Waals engineering of ferroelectric heterostructures for long-retention memory
Authors: Wang Xiaowei , Zhu Chao , Deng Ya , Duan Ruihuan , Chen Jieqiong , Zeng Qingsheng , Zhou Jiadong , Fu Qundong , You Lu , Liu Song , Edgar James H. , Yu Peng , Liu Zheng
Published: February 2021

The limited memory retention for a ferroelectric field-effect transistor has prevented the commercialization of its nonvolatile memory potential using the commercially available ferroelectrics. Here, we show a long-retention ferroelectric transistor memory cell featuring a metal-ferroelectric-metal-insulator-semiconductor architecture built from all van der Waals single crystals. Our device exhibits 17 mV dec−1 operation, a memory window larger than 3.8 V, and program/erase ratio greater than 107. Thanks to the trap-free interfaces and the minimized depolarization effects via van der Waals engineering, more than 104 cycles endurance, a 10-year memory retention and sub-5 μs program/erase speed are achieved. A single pulse as short as 100 ns is enough for polarization reversal, and a 4-bit/cell operation of a van der Waals ferroelectric transistor is demonstrated under a 100 ns pulse train. These device characteristics suggest that van der Waals engineering is a promising direction to improve ferroelectronic memory performance and reliability for future applications.
Active-site loop variations adjust activity and selectivity of the cumene dioxygenase
Authors: Heinemann Peter M. , Armbruster Daniel , Hauer Bernhard
Published: February 2021

Active-site loops play essential roles in various catalytically important enzyme properties like activity, selectivity, and substrate scope. However, their high flexibility and diversity makes them challenging to incorporate into rational enzyme engineering strategies. Here, we report the engineering of hot-spots in loops of the cumene dioxygenase fromPseudomonas fluorescensIP01 with high impact on activity, regio- and enantioselectivity. Libraries based on alanine scan, sequence alignments, and deletions along with a novel insertion approach result in up to 16-fold increases in activity and the formation of novel products and enantiomers. CAVER analysis suggests possible increases in the active pocket volume and formation of new active-site tunnels, suggesting additional degrees of freedom of the substrate in the pocket. The combination of identified hot-spots with the Linker In Loop Insertion approach proves to be a valuable addition to future loop engineering approaches for enhanced biocatalysts.
Tuning nonlinear damping in graphene nanoresonators by parametric–direct internal resonance
Authors: Keşkekler Ata , Shoshani Oriel , Lee Martin , van der Zant Herre S. J. , Steeneken Peter G. , Alijani Farbod
Published: February 2021

Mechanical sources of nonlinear damping play a central role in modern physics, from solid-state physics to thermodynamics. The microscopic theory of mechanical dissipation suggests that nonlinear damping of a resonant mode can be strongly enhanced when it is coupled to a vibration mode that is close to twice its resonance frequency. To date, no experimental evidence of this enhancement has been realized. In this letter, we experimentally show that nanoresonators driven into parametric-direct internal resonance provide supporting evidence for the microscopic theory of nonlinear dissipation. By regulating the drive level, we tune the parametric resonance of a graphene nanodrum over a range of 40–70 MHz to reach successive two-to-one internal resonances, leading to a nearly two-fold increase of the nonlinear damping. Our study opens up a route towards utilizing modal interactions and parametric resonance to realize resonators with engineered nonlinear dissipation over wide frequency range.
Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells
Authors: Kim Chuna , Sung Sanghyun , Kim Jong-Seo , Lee Hyunji , Jung Yoonseok , Shin Sanghee , Kim Eunkyeong , Seo Jenny J. , Kim Jun , Kim Daeun , Niida Hiroyuki , Kim V. Narry , Park Daechan , Lee Junho
Published: February 2021

Telomeres are part of a highly refined system for maintaining the stability of linear chromosomes. Most telomeres rely on simple repetitive sequences and telomerase enzymes to protect chromosomal ends; however, in some species or telomerase-defective situations, an alternative lengthening of telomeres (ALT) mechanism is used. ALT mainly utilises recombination-based replication mechanisms and the constituents of ALT-based telomeres vary depending on models. Here we show that mouse telomeres can exploit non-telomeric, unique sequences in addition to telomeric repeats. We establish that a specific subtelomeric element, the mouse template for ALT (mTALT), is used for repairing telomeric DNA damage as well as for composing portions of telomeres in ALT-dependent mouse embryonic stem cells. Epigenomic and proteomic analyses before and after ALT activation reveal a high level of non-coding mTALT transcripts despite the heterochromatic nature of mTALT-based telomeres. After ALT activation, the increased HMGN1, a non-histone chromosomal protein, contributes to the maintenance of telomere stability by regulating telomeric transcription. These findings provide a molecular basis to study the evolution of new structures in telomeres.
Depth-dependent peridotite-melt interaction and the origin of variable silica in the cratonic mantle
Authors: Tomlinson Emma L. , Kamber Balz S.
Published: February 2021

Peridotites from the thick roots of Archaean cratons are known for their compositional diversity, whose origin remains debated. We report thermodynamic modelling results for reactions between peridotite and ascending mantle melts. Reaction between highly magnesian melt (komatiite) and peridotite leads to orthopyroxene crystallisation, yielding silica-rich harzburgite. By contrast, shallow basalt-peridotite reaction leads to olivine enrichment, producing magnesium-rich dunites that cannot be generated by simple melting. Komatiite is spatially and temporally associated with basalt within Archaean terranes indicating that modest-degree melting co-existed with advanced melting. We envisage a relatively cool mantle that experienced episodic hot upwellings, the two settings could have coexisted if roots of nascent cratons became locally strongly extended. Alternatively, deep refractory silica-rich residues could have been detached from shallower dunitic lithosphere prior to cratonic amalgamation. Regardless, the distinct Archaean melting-reaction environments collectively produced skewed and multi-modal olivine distributions in the cratonic lithosphere and bimodal mafic-ultramafic volcanism at surface.
Correlating Josephson supercurrents and Shiba states in quantum spins unconventionally coupled to superconductors
Authors: Küster Felix , Montero Ana M. , Guimarães Filipe S. M. , Brinker Sascha , Lounis Samir , Parkin Stuart S. P. , Sessi Paolo
Published: February 2021

Local spins coupled to superconductors give rise to several emerging phenomena directly linked to the competition between Cooper pair formation and magnetic exchange. These effects are generally scrutinized using a spectroscopic approach which relies on detecting the in-gap bound modes arising from Cooper pair breaking, the so-called Yu-Shiba-Rusinov (YSR) states. However, the impact of local magnetic impurities on the superconducting order parameter remains largely unexplored. Here, we use scanning Josephson spectroscopy to directly visualize the effect of magnetic perturbations on Cooper pair tunneling between superconducting electrodes at the atomic scale. By increasing the magnetic impurity orbital occupation by adding one electron at a time, we reveal the existence of a direct correlation between Josephson supercurrent suppression and YSR states. Moreover, in the metallic regime, we detect zero bias anomalies which break the existing framework based on competing Kondo and Cooper pair singlet formation mechanisms. Based on first-principle calculations, these results are rationalized in terms of unconventional spin-excitations induced by the finite magnetic anisotropy energy. Our findings have far reaching implications for phenomena that rely on the interplay between quantum spins and superconductivity.
Mapping ticks and tick-borne pathogens in China
Authors: Zhao Guo-Ping , Wang Yi-Xing , Fan Zheng-Wei , Ji Yang , Liu Ming-jin , Zhang Wen-Hui , Li Xin-Lou , Zhou Shi-Xia , Li Hao , Liang Song , Liu Wei , Yang Yang , Fang Li-Qun
Published: February 2021

Understanding ecological niches of major tick species and prevalent tick-borne pathogens is crucial for efficient surveillance and control of tick-borne diseases. Here we provide an up-to-date review on the spatial distributions of ticks and tick-borne pathogens in China. We map at the county level 124 tick species, 103 tick-borne agents, and human cases infected with 29 species (subspecies) of tick-borne pathogens that were reported in China during 1950−2018.Haemaphysalis longicornisis found to harbor the highest variety of tick-borne agents, followed byIxodes persulcatus,Dermacentor nutalliandRhipicephalus microplus. Using a machine learning algorithm, we assess ecoclimatic and socioenvironmental drivers for the distributions of 19 predominant vector ticks and two tick-borne pathogens associated with the highest disease burden. The model-predicted suitable habitats for the 19 tick species are 14‒476% larger in size than the geographic areas where these species were detected, indicating severe under-detection. Tick species harboring pathogens of imminent threats to public health should be prioritized for more active field surveillance.
Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface
Authors: Ding Xinqiang , Lin Xingcheng , Zhang Bin
Published: February 2021

The three-dimensional organization of chromatin is expected to play critical roles in regulating genome functions. High-resolution characterization of its structure and dynamics could improve our understanding of gene regulation mechanisms but has remained challenging. Using a near-atomistic model that preserves the chemical specificity of protein-DNA interactions at residue and base-pair resolution, we studied the stability and folding pathways of a tetra-nucleosome. Dynamical simulations performed with an advanced sampling technique uncovered multiple pathways that connect open chromatin configurations with the zigzag crystal structure. Intermediate states along the simulated folding pathways resemble chromatin configurations reported from in situ experiments. We further determined a six-dimensional free energy surface as a function of the inter-nucleosome distances via a deep learning approach. The zigzag structure can indeed be seen as the global minimum of the surface. However, it is not favored by a significant amount relative to the partially unfolded, in situ configurations. Chemical perturbations such as histone H4 tail acetylation and thermal fluctuations can further tilt the energetic balance to stabilize intermediate states. Our study provides insight into the connection between various reported chromatin configurations and has implications on the in situ relevance of the 30 nm fiber.
Bedside functional monitoring of the dynamic brain connectivity in human neonates
Authors: Baranger Jerome , Demene Charlie , Frerot Alice , Faure Flora , Delanoë Catherine , Serroune Hicham , Houdouin Alexandre , Mairesse Jerome , Biran Valerie , Baud Olivier , Tanter Mickael
Published: February 2021

Clinicians have long been interested in functional brain monitoring, as reversible functional losses often precedes observable irreversible structural insults. By characterizing neonatal functional cerebral networks, resting-state functional connectivity is envisioned to provide early markers of cognitive impairments. Here we present a pioneering bedside deep brain resting-state functional connectivity imaging at 250-μm resolution on human neonates using functional ultrasound. Signal correlations between cerebral regions unveil interhemispheric connectivity in very preterm newborns. Furthermore, fine-grain correlations between homologous pixels are consistent with white/grey matter organization. Finally, dynamic resting-state connectivity reveals a significant occurrence decrease of thalamo-cortical networks for very preterm neonates as compared to control term newborns. The same method also shows abnormal patterns in a congenital seizure disorder case compared with the control group. These results pave the way to infants’ brain continuous monitoring and may enable the identification of abnormal brain development at the bedside.
Lysates of Methylococcus capsulatus Bath induce a lean-like microbiota, intestinal FoxP3+RORγt+IL-17+ Tregs and improve metabolism
Authors: Jensen Benjamin A. H. , Holm Jacob B. , Larsen Ida S. , von Burg Nicole , Derer Stefanie , Sonne Si B. , Pærregaard Simone I. , Damgaard Mads V. , Indrelid Stine A. , Rivollier Aymeric , Agrinier Anne-Laure , Sulek Karolina , Arnoldussen Yke J. , Fjære Even , Marette André , Angell Inga L. , Rudi Knut , Treebak Jonas T. , Madsen Lise , Åkesson Caroline Piercey , Agace William , Sina Christian , Kleiveland Charlotte R. , Kristiansen Karsten , Lea Tor E.
Published: February 2021

Interactions between host and gut microbial communities are modulated by diets and play pivotal roles in immunological homeostasis and health. We show that exchanging the protein source in a high fat, high sugar, westernized diet from casein to whole-cell lysates of the non-commensal bacterium Methylococcus capsulatus Bath is sufficient to reverse western diet-induced changes in the gut microbiota to a state resembling that of lean, low fat diet-fed mice, both under mild thermal stress (T22 °C) and at thermoneutrality (T30 °C). Concomitant with microbiota changes, mice fed the Methylococcus-based western diet exhibit improved glucose regulation, reduced body and liver fat, and diminished hepatic immune infiltration. Intake of the Methylococcu-based diet markedly boosts Parabacteroides abundances in a manner depending on adaptive immunity, and upregulates triple positive (Foxp3+RORγt+IL-17+) regulatory T cells in the small and large intestine. Collectively, these data point to the potential for leveraging the use of McB lysates to improve immunometabolic homeostasis.
A digital single-molecule nanopillar SERS platform for predicting and monitoring immune toxicities in immunotherapy
Authors: Li Junrong , Wuethrich Alain , Sina Abu A. I. , Cheng Han-Hao , Wang Yuling , Behren Andreas , Mainwaring Paul N. , Trau Matt
Published: February 2021

The introduction of immune checkpoint inhibitors has demonstrated significant improvements in survival for subsets of cancer patients. However, they carry significant and sometimes life-threatening toxicities. Prompt prediction and monitoring of immune toxicities have the potential to maximise the benefits of immune checkpoint therapy. Herein, we develop a digital nanopillar SERS platform that achieves real-time single cytokine counting and enables dynamic tracking of immune toxicities in cancer patients receiving immune checkpoint inhibitor treatment - broader applications are anticipated in other disease indications. By analysing four prospective cytokine biomarkers that initiate inflammatory responses, the digital nanopillar SERS assay achieves both highly specific and highly sensitive cytokine detection down to attomolar level. Significantly, we report the capability of the assay to longitudinally monitor 10 melanoma patients during immune inhibitor blockade treatment. Here, we show that elevated cytokine concentrations predict for higher risk of developing severe immune toxicities in our pilot cohort of patients.
Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework
Authors: Kirschner Philipp , Arthofer Wolfgang , Pfeifenberger Stefanie , Záveská Eliška , Schönswetter Peter ,   The STEPPE Consortium, Frajman Božo , Gamisch Alexander , Hilpold Andreas , Paun Ovidiu , Sanmartín Isabel , Trucchi Emiliano , Steiner Florian M. , Schlick-Steiner Birgit C.
Published: February 2021

Multi-locus genetic data are pivotal in phylogenetics. Today, high-throughput sequencing (HTS) allows scientists to generate an unprecedented amount of such data from any organism. However, HTS is resource intense and may not be accessible to wide parts of the scientific community. In phylogeography, the use of HTS has concentrated on a few taxonomic groups, and the amount of data used to resolve a phylogeographic pattern often seems arbitrary. We explore the performance of two genetic marker sampling strategies and the effect of marker quantity in a comparative phylogeographic framework focusing on six species (arthropods and plants). The same analyses were applied to data inferred from amplified fragment length polymorphism fingerprinting (AFLP), a cheap, non-HTS based technique that is able to straightforwardly produce several hundred markers, and from restriction site associated DNA sequencing (RADseq), a more expensive, HTS-based technique that produces thousands of single nucleotide polymorphisms. We show that in four of six study species, AFLP leads to results comparable with those of RADseq. While we do not aim to contest the advantages of HTS techniques, we also show that AFLP is a robust technique to delimit evolutionary entities in both plants and animals. The demonstrated similarity of results from the two techniques also strengthens biological conclusions that were based on AFLP data in the past, an important finding given the wide utilization of AFLP over the last decades. We emphasize that whenever the delimitation of evolutionary entities is the central goal, as it is in many fields of biodiversity research, AFLP is still an adequate technique.
Safety envelope of pedestrians upon motor vehicle conflicts identified via active avoidance behaviour
Authors: Nie Bingbing , Li Quan , Gan Shun , Xing Bobin , Huang Yuan , Li Shengbo Eben
Published: February 2021

Human reaction plays a key role in improved protection upon emergent traffic situations with motor vehicles. Understanding the underlying behaviour mechanisms can combine active sensing system on feature caption and passive devices on injury mitigation for automated vehicles. The study aims to identify the distance-based safety boundary (“safety envelope”) of vehicle–pedestrian conflicts via pedestrian active avoidance behaviour recorded in well-controlled, immersive virtual reality-based emergent traffic scenarios. Via physiological signal measurement and kinematics reconstruction of the complete sequence, we discovered the general perception-decision-action mechanisms under given external stimulus, and the resultant certain level of natural harm-avoidance action. Using vision as the main information source, 70% pedestrians managed to avoid the collision by adapting walking speeds and directions, consuming overall less “decision” time (0.17–0.24 s vs. 0.41 s) than the collision cases, after that, pedestrians need enough “execution” time (1.52–1.84 s) to take avoidance action. Safety envelopes were generated by combining the simultaneous interactions between the pedestrian and the vehicle. The present investigation on emergent reaction dynamics clears a way for realistic modelling of biomechanical behaviour, and preliminarily demonstrates the feasibility of incorporating in vivo pedestrian behaviour into engineering design which can facilitate improved, interactive on-board devices towards global optimal safety.
Contrasting effects of male immigration and rainfall on rank-related patterns of miscarriage in female olive baboons
Authors: Bailey Andrea , Eberly Lynn E. , Packer Craig
Published: February 2021

In mammalian species with prolonged maternal investment in which high-ranking males gain disproportionate numbers of mating opportunities, males that quickly ascend the hierarchy may benefit from eliminating the dependent offspring of their competitors. In savanna baboons, high-ranking females are the most profitable targets of infanticide or feticide, because their offspring have higher survival rates and their daughters reach sexual maturity at a younger age. However, such patterns may be obscured by environmental stressors that are known to exacerbate fetal losses, especially in lower-ranking females. Using 30 years of data on wild olive baboons (Papio anubis) in Gombe National Park, Tanzania, we found evidence that rapidly-rising immigrant males induced miscarriages in high-ranking females outside of drought conditions. However, miscarriage rates were largely reversed during prolonged periods of low rainfall, suggesting that low-ranking females are particularly vulnerable to low food availability and social instability. Infanticide did not emerge as a recurrent male strategy in this population, likely because of the protective behavior of resident males towards vulnerable juveniles.
Spectrum of mutational signatures in T-cell lymphoma reveals a key role for UV radiation in cutaneous T-cell lymphoma
Authors: Jones Christine L. , Degasperi Andrea , Grandi Vieri , Amarante Tauanne D. ,   Genomics England Research Consortium, Ambrose John C. , Arumugam Prabhu , Baple Emma L. , Bleda Marta , Boardman-Pretty Freya , Boissiere Jeanne M. , Boustred Christopher R. , Brittain Helen , Caulfield Mark J. , Chan Georgia C. , Craig Clare E. H. , Daugherty Louise C. , de Burca Anna , Devereau Andrew , Elgar Greg , Foulger Rebecca E. , Fowler Tom , Furió-Tarí Pedro , Giess Adam , Hackett Joanne M. , Halai Dina , Hamblin Angela , Henderson Shirley , Holman James E. , Hubbard Tim J. P. , Ibáñez Kristina , Jackson Rob , Jones Louise J. , Kasperaviciute Dalia , Kayikci Melis , Kousathanas Athanasios , Lahnstein Lea , Lawson Kay , Leigh Sarah E. A. , Leong Ivonne U. S. , Lopez Javier F. , Maleady-Crowe Fiona , Mason Joanne , McDonagh Ellen M. , Moutsianas Loukas , Mueller Michael , Murugaesu Nirupa , Need Anna C. , O’Donovan Peter , Odhams Chris A. , Orioli Andrea , Patch Christine , Pereira Mariana Buongermino , Perez-Gil Daniel , Polychronopoulos Dimitris , Pullinger John , Rahim Tahrima , Rendon Augusto , Riesgo-Ferreiro Pablo , Rogers Tim , Ryten Mina , Savage Kevin , Sawant Kushmita , Scott Richard H. , Siddiq Afshan , Sieghart Alexander , Smedley Damian , Smith Katherine R. , Smith Samuel C. , Sosinsky Alona , Spooner William , Stevens Helen E. , Stuckey Alexander , Sultana Razvan , Tanguy Mélanie , Thomas Ellen R. A. , Thompson Simon R. , Tregidgo Carolyn , Tucci Arianna , Walsh Emma , Watters Sarah A. , Welland Matthew J. , Williams Eleanor , Witkowska Katarzyna , Wood Suzanne M. , Zarowiecki Magdalena , Mitchell Tracey J. , Nik-Zainal Serena , Whittaker Sean J.
Published: February 2021

T-cell non-Hodgkin’s lymphomas develop following transformation of tissue resident T-cells. We performed a meta-analysis of whole exome sequencing data from 403 patients with eight subtypes of T-cell non-Hodgkin’s lymphoma to identify mutational signatures and associated recurrent gene mutations. Signature 1, indicative of age-related deamination, was prevalent across all T-cell lymphomas, reflecting the derivation of these malignancies from memory T-cells. Adult T-cell leukemia-lymphoma was specifically associated with signature 17, which was found to correlate with the IRF4 K59R mutation that is exclusive to Adult T-cell leukemia-lymphoma. Signature 7, implicating UV exposure was uniquely identified in cutaneous T-cell lymphoma (CTCL), contributing 52% of the mutational burden in mycosis fungoides and 23% in Sezary syndrome. Importantly this UV signature was observed in CD4 + T-cells isolated from the blood of Sezary syndrome patients suggesting extensive re-circulation of these T-cells through skin and blood. Analysis of non-Hodgkin’s T-cell lymphoma cases submitted to the national 100,000 WGS project confirmed that signature 7 was only identified in CTCL strongly implicating UV radiation in the pathogenesis of cutaneous T-cell lymphoma.
An analysis framework for the integration of broadband NIRS and EEG to assess neurovascular and neurometabolic coupling
Authors: Pinti P. , Siddiqui M. F. , Levy A. D. , Jones E. J. H. , Tachtsidis Ilias
Published: February 2021

With the rapid growth of optical-based neuroimaging to explore human brain functioning, our research group has been developing broadband Near Infrared Spectroscopy (bNIRS) instruments, a technological extension to functional Near Infrared Spectroscopy (fNIRS). bNIRS has the unique capacity of monitoring brain haemodynamics/oxygenation (measuring oxygenated and deoxygenated haemoglobin),andmetabolism (measuring the changes in the redox state of cytochrome-c-oxidase). When combined with electroencephalography (EEG), bNIRS provides a unique neuromonitoring platform to explore neurovascular coupling mechanisms. In this paper, we present a novel pipeline for the integrated analysis of bNIRS and EEG signals, and demonstrate its use on multi-channel bNIRS data recorded with concurrent EEG on healthy adults during a visual stimulation task. We introduce the use of the Finite Impulse Response functions within the General Linear Model for bNIRS and show its feasibility to statistically localize the haemodynamic and metabolic activity in the occipital cortex. Moreover, our results suggest that the fusion of haemodynamic and metabolic measures unveils additional information on brain functioning over haemodynamic imaging alone. The cross-correlation-based analysis of interrelationships between electrical (EEG) and haemodynamic/metabolic (bNIRS) activity revealed that the bNIRS metabolic signal offers a unique marker of brain activity, being more closely coupled to the neuronal EEG response.
Plasma phospholipid n-3 polyunsaturated fatty acids and major depressive disorder in Japanese elderly: the Japan Public Health Center-based Prospective Study
Authors: Hamazaki Kei , Matsuoka Yutaka J. , Yamaji Taiki , Sawada Norie , Mimura Masaru , Nozaki Shoko , Shikimoto Ryo , Tsugane Shoichiro
Published: February 2021

The beneficial effects of n-3 polyunsaturated fatty acids (PUFAs) such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) on depression are not definitively known. In a previous population-based prospective cohort study, we found a reverse J-shaped association of intake of fish and docosapentaenoic acid (DPA), the intermediate metabolite of EPA and DHA, with major depressive disorder (MDD). To examine the association further in a cross-sectional manner, in the present study we analyzed the level of plasma phospholipid n-3 PUFAs and the risk of MDD in 1,213 participants aged 64–86 years (mean 72.9 years) who completed questionnaires and underwent medical check-ups, a mental health examination, and blood collection. In multivariate logistic regression analysis, odds ratios and 95% confidence intervals were calculated for MDD according to plasma phospholipid n-3 PUFA quartiles. MDD was diagnosed in 103 individuals. There were no significant differences in any n-3 PUFAs (i.e., EPA, DHA, or DPA) between individuals with and without MDD. Multivariate logistic regression analysis showed no significant association between any individual n-3 PUFAs and MDD risk. Overall, based on the results of this cross-sectional study, there appears to be no association of plasma phospholipid n-3 PUFAs with MDD risk in the elderly Japanese population.
Highly stretchable large area woven, knitted and robust braided textile based interconnection for stretchable electronics
Authors: Yun Min Ju , Sim Yeon Hyang , Lee Dong Yoon , Cha Seung I.
Published: February 2021

With the rapid development of stretchable and wearable technologies, stretchable interconnection technology also demanded along it. Stretchable interconnections should have high stretchability and stable conductivity for use as an electrode. In addition, to develop to commercialization scale from research scale, a simple fabrication process that can be scaled up, and the stretchable interconnection should be able to be electrically connected to devices or modules directly. To date, printable conductor inks, liquid metals and stretchable structured interconnections have been reported for stretchable interconnections. These approaches have demonstrated high stretchability and conductivity, but in aspect of scale, it is appropriate to apply in micro-scale devices. For requirements of stretchability, conductivity and direct integration into meso- or centimeter-scale electronic devices or modules, here we introduce stretchable interconnections with a textile structure composed of metal fibers. The stretchable woven and knitted textiles show 67% strain and stable conductivity, and the cylindrical textile shows more than 700% strain with high strength. The stretchable textiles were fabricated using a weaving, knitting and braiding machine that can be used to produce textiles without any limit to length or area. These textiles exhibit high and stable conductivity even under deformation, and can be directly integrated into devices or modules by soldering. These high-performance stretchable textiles have great potential for commercial applications.
Impaired NEPHRIN localization in kidney organoids derived from nephrotic patient iPS cells
Authors: Ohmori Tomoko , De Shankhajit , Tanigawa Shunsuke , Miike Koichiro , Islam Mazharul , Soga Minami , Era Takumi , Shiona Shinichi , Nakanishi Koichi , Nakazato Hitoshi , Nishinakamura Ryuichi
Published: February 2021

Mutations in the NPHS1 gene, which encodes NEPHRIN, cause congenital nephrotic syndrome, resulting from impaired slit diaphragm (SD) formation in glomerular podocytes. We previously reported NEPHRIN and SD abnormalities in the podocytes of kidney organoids generated from patient-derived induced pluripotent stem cells (iPSCs) with an NPHS1 missense mutation (E725D). However, the mechanisms underlying the disease may vary depending on the mutations involved, and thus generation of iPSCs from multiple patients is warranted. Here we established iPSCs from two additional patients with different NPHS1 mutations and examined the podocyte abnormalities in kidney organoids derived from these cells. One patient had truncating mutations, and NEPHRIN was undetectable in the resulting organoids. The other patient had a missense mutation (R460Q), and the mutant NEPHRIN in the organoids failed to accumulate on the podocyte surface to form SD precursors. However, the same mutant protein behaved normally when overexpressed in heterologous cells, suggesting that NEPHRIN localization is cell context-dependent. The localization of another SD-associated protein, PODOCIN, was impaired in both types of mutant organoids in a cell domain-specific manner. Thus, the new iPSC lines and resultant kidney organoids will be useful resources for dissecting the disease mechanisms, as well as for drug development for therapies.
Exploring the edible gum (galactomannan) biosynthesis and its regulation during pod developmental stages in clusterbean using comparative transcriptomic approach
Authors: Sharma Sandhya , Tyagi Anshika , Srivastava Harsha , Ramakrishna G. , Sharma Priya , Sevanthi Amitha Mithra , Solanke Amolkumar U. , Sharma Ramavtar , Singh Nagendra Kumar , Sharma Tilak Raj , Gaikwad Kishor
Published: February 2021

Galactomannan is a polymer of high economic importance and is extracted from the seed endosperm of clusterbean (C. tetragonoloba). In the present study, we worked to reveal the stage-specific galactomannan biosynthesis and its regulation in clusterbean. Combined electron microscopy and biochemical analysis revealed high protein and gum content in RGC-936, while high oil bodies and low gum content in M-83. A comparative transcriptome study was performed between RGC-936 (high gum) and M-83 (low gum) varieties at three developmental stages viz. 25, 39, and 50 days after flowering (DAF). Total 209,525, 375,595 and 255,401 unigenes were found at 25, 39 and 50 DAF respectively. Differentially expressed genes (DEGs) analysis indicated a total of 5147 shared unigenes between the two genotypes. Overall expression levels of transcripts at 39DAF were higher than 50DAF and 25DAF. Besides, 691 (RGC-936) and 188 (M-83) candidate unigenes that encode for enzymes involved in the biosynthesis of galactomannan were identified and analyzed, and 15 key enzyme genes were experimentally validated by quantitative Real-Time PCR. Transcription factor (TF) WRKY was observed to be co-expressed with key genes of galactomannan biosynthesis at 39DAF. We conclude that WRKY might be a potential biotechnological target (subject to functional validation) for developing high gum content varieties.
Insecticidal and oviposition deterrent effects of essential oils of Baccharis spp. and histological assessment against Drosophila suzukii (Diptera: Drosophilidae)
Authors: de Souza Michele Trombin , de Souza Mireli Trombin , Bernardi Daniel , de Melo Douglas José , Zarbin Paulo Henrique Gorgatti , Zawadneak Maria Aparecida Cassilha
Published: February 2021

The diverse flora of the Atlantic Forest is fertile ground for discovering new chemical structures with insecticidal activity. The presence of species belonging to the genusBaccharisis of particular interest, as these species have shown promise in pest management applications. The objective of this study is to chemically identify the constituents expressed in the leaves of seven species ofBaccharis(B. anomalaDC.,B. calvescensDC.,B. mesoneuraDC.,B. millefloraDC.,B. oblongifoliaPers.,B. trimera(Less) DC. andB. uncinellaDC.) and to evaluate the toxicological and morphological effects caused by essential oils (EOs) on the larvae and adults ofDrosophila suzukii(Diptera: Drosophilidae). Chemical analysis using gas chromatography-mass spectrometry (GC–MS) indicated that limonene was the main common constituent in allBaccharisspecies. This constituent in isolation, as well as the EOs ofB. calvescens,B. mesoneura, andB. oblongifolia, caused mortality in over 80% of adults ofD. suzukiiat a discriminatory concentration of 80 mg L−1in bioassays of ingestion and topical application. These results are similar to the effect of spinosyn-based synthetic insecticides (spinetoram 75 mg L−1) 120 h after exposure. Limonene and EOs from all species had the lowest LC50and LC90values relative to spinosyn and azadirachtin (12 g L−1) in both bioassays. However, they showed the same time toxicity over time as spinetoram when applied to adults ofD. suzukii(LT50ranging from 4.6 to 8.7 h) in a topical application bioassay. In olfactometry tests, 92% ofD. suzukiifemales showed repellent behavior when exposed to the EOs and limonene. Likewise, the EOs ofB. calvescens,B. mesoneura, andB. oblongifoliasignificantly reduced the number of eggs in artificial fruits (≅ 7.6 eggs fruit−1), differing from the control treatment with water (17.2 eggs fruit−1) and acetone (17.6 eggs fruit−1). According to histological analyses, the L3 larvae ofD. suzukiihad morphological and physiological alterations and deformations after exposure to treatments containing EOs and limonene, which resulted in high larval, pupal, and adult mortality. In view of the results,BaccharisEOs and their isolated constituent, limonene, proved to be promising alternatives for developing bioinsecticides to manage ofD. suzukii.
Antagonist effects of the leek Allium porrum as a companion plant on aphid host plant colonization
Authors: Baudry Xavier , Doury Géraldine , Couty Aude , Fourdrain Yvelise , van Havermaet Robin , Lateur Marc , Ameline Arnaud
Published: February 2021

Combining a non-host plant (companion plant or CP) with a target cultivated plant is considered as a promising strategy to reduce pest pressure. Among the companion plants (CP) commonly used in integrated systems, those belonging to the Amaryllidaceae family (chives, garlic, onion, leek) exhibit characteristics related to certain volatile organic compounds (VOCs) with promising repellent potentialities. The aim of this work was to investigate the potential disruption of sweet pepper (host plant) colonization by the green peach aphid (Myzus persicae) when exposed to leek (Allium porrum) as a CP. Retention/dispersion, EPG and clip-cage/Petri dish laboratory experiments were thus performed to study the effect of leek VOCs on aphid settlement/migration, feeding behavior and life history traits parameters, respectively. This work revealed that leek as a CP had a negative effect on aphid feeding behavior, by disturbing the balance between phloem and xylem sap ingestion, but had no influence concerning aphid settlement. Surprisingly, leek as a CP triggered some unexpected probiotic effects on certain life history traits such as aphid survival, biomass, and fecundity, suggesting a possible hormetic effect of leek VOCs on aphid physiology. The possibility of experience-induced preference of aphids for leek VOCs was also discussed.