bluuebunny/crossref_metadata_2025 huggingface dataset:
Revising the Effects of Local and Remote Atmospheric Forcing on the Atlantic Jet and Western Alboran Gyre Dynamics
Authors: Bolado‐Penagos M. , Sala I. , Gomiz‐Pascual J. J. , Romero‐Cózar J. , González‐Fernández D. , Reyes‐Pérez J. , Vázquez A. , Bruno M.
Published: January 2021

The main objective of the present study is to gain insight into the response of the Atlantic Jet (AJ) to the atmospheric forcing, in order to understand the hydrodynamic processes behind its disconnection from the Western Alboran Gyre (WAG) and the eastward displacement of the latter. An analysis was carried out based on observations of high frequency radar (HFR) derived currents and sea level, numerical model simulations and satellite imagery, with particular focus on the events of intense and endured easterlies. Among the main factors that characterize the atmospheric forcing linked to intense and persistent easterly wind events, the conjugation of the direct local wind forcing effect on the Atlantic Inflow (AI) on the eastern side of the Strait of Gibraltar and the response of the coastal waters in the northwestern (NW) corner of the Alboran Sea to the wind forcing over the Alboran Sea are of particular interest. In addition, the effect of the elevation surges in the Strait coming from the western Mediterranean Sea on reducing the AI intensity must be taken into account. These surges appear in coincidence with the establishment of persistent and intense easterlies over the Alboran Sea. The alteration of the AJ‐WAG system in response to this forcing causes important changes in the phytoplankton distributions in the Alboran Sea. After the events of persistent and intense easterlies the phytoplankton accumulations in the NW Alboran Sea are displaced offshore and the phytoplankton transported with the AJ is injected toward the central zone of the WAG.
Validation and Calibration of Nadir SWH Products From CFOSAT and HY‐2B With Satellites and In Situ Observations
Authors: Li Xiuzhong , Xu Ying , Liu Baochang , Lin Wenming , He Yijun , Liu Jianqiang
Published: January 2021

The China France Oceanography Satellite (CFOSAT) and Haiyang‐2B (HY‐2B) satellites were successively launched in China on the 29th and 25th of October 2018, respectively. HY‐2 B carries the second Chinese radar altimeter along with three other microwave sensors, whereas CFOSAT contains the first Surface Waves Investigation and Monitoring (SWIM) instrument and a fan beam rotating scatterometer. As missions for measuring the dynamic marine environment, both satellites can measure the nadir significant wave height (SWH). For data obtained from a newly launched satellite to be utilized with confidence, the quality of SWH from the two satellites requires validation. In this study, the HY‐2B altimeter and CFOSAT nadir SWHs have been validated against the National Data Buoy Center (NDBC) buoys and the Jason‐3 altimeter SWH data, respectively, which resulted in CFOSAT nadir SWH having the best accuracy and HY‐2B having the best precision. The SWHs of the two missions are also calibrated by Jason‐3 and NDBC buoys. Following calibration, the root mean square error (RMSE) of CFOSAT and HY‐2B are 0.21 and 0.27 m, respectively, when compared to Jason‐3, and 0.23 and 0.30 m, respectively, compared to the buoys. Our results show that the two missions can provide good‐quality SWH and can be relied upon as a new data resource of global SWH.
An Overview of Atmospheric Features Over the Western North Atlantic Ocean and North American East Coast—Part 2: Circulation, Boundary Layer, and Clouds
Authors: Painemal David , Corral Andrea F. , Sorooshian Armin , Brunke Michael A. , Chellappan Seethala , Afzali Gorooh Vesta , Ham Seung‐Hee , O'Neill Larry , Smith William L. , Tselioudis George , Wang Hailong , Zeng Xubin , Zuidema Paquita
Published: January 2021

The Western North Atlantic Ocean (WNAO) is a complex land‐ocean‐atmosphere system that experiences a broad range of atmospheric phenomena, which in turn drive unique aerosol transport pathways, cloud morphologies, and boundary layer variability. This work, Part 2 of a 2‐part paper series, provides an overview of the atmospheric circulation, boundary layer variability, three‐dimensional cloud structure, and precipitation over the WNAO; the companion paper (Part 1) focused on chemical characterization of aerosols, gases, and wet deposition. Seasonal changes in atmospheric circulation and sea surface temperature explain a clear transition in cloud morphologies from small shallow cumulus clouds, convective clouds, and tropical storms in summer, to stratus/stratocumulus and multilayer cloud systems associated with winter storms. Synoptic variability in cloud fields is estimated using satellite‐based weather states, and the role of postfrontal conditions (cold‐air outbreaks) in the development of stratiform clouds is further analyzed. Precipitation is persistent over the ocean, with a regional peak over the Gulf Stream path, where offshore sea surface temperature gradients are large and surface fluxes reach a regional peak. Satellite data show a clear annual cycle in cloud droplet number concentration with maxima (minima) along the coast in winter (summer), suggesting a marked annual cycle in aerosol‐cloud interactions. Compared with satellite cloud retrievals, four climate models qualitatively reproduce the annual cycle in cloud cover and liquid water path, but with large discrepancies across models, especially in the extratropics. The paper concludes with a summary of outstanding issues and recommendations for future work.
Persistent Increases in Nighttime Heat Stress From Urban Expansion Despite Heat Island Mitigation
Authors: Huang Kangning , Lee Xuhui , Stone Brian , Knievel Jason , Bell Michelle L. , Seto Karen C.
Published: January 2021

Urban areas generally have higher near‐surface air temperature and lower air humidity than rural areas. Little is known about how heat stress, the combined effect of high air temperature and high humidity on human physiology, will be affected by future urban land expansion. Here we use a mesoscale numerical weather prediction model to examine the effects of urban land expansion from 2000 to 2050 on heat stress (measured as wet‐bulb globe temperature, WBGT) in the urban areas of China, India, and Nigeria, which are projected to account for one‐third of global urban population growth through 2050. Our results show that urban expansion slightly reduces heat stress during the day (∼0.2°C) but substantially intensifies it at night, by ∼1°C on average and by up to 2–3°C in five mega‐urban regions (MURs). These effects exist with or without climate change induced by rising concentrations of greenhouse gases (GHGs). Installing cool roofs—an urban heat island mitigation measures—can reduce the daytime WBGT by 0.5–1°C, partially offsetting the heat stress conditions caused by GHG‐induced climate change. However, even with cool roofs, the nighttime WBGTs are higher by 0.3–0.9°C over the whole countries studied, and by 1–2°C in the MURs under the urban expansion scenario, compared to the situation in which urban areas remain unchanged. These results show that future urban expansion and heat island mitigation can result in potential daytime benefits but also persistent nighttime risks.
Improved Simulations of Global Black Carbon Distributions by Modifying Wet Scavenging Processes in Convective and Mixed‐Phase Clouds
Authors: Liu Mingxu , Matsui Hitoshi
Published: January 2021

In‐cloud wet scavenging dominates the wet removal of aerosols in the atmosphere, but is not well represented in climate models. Aircraft measurements of black carbon (BC) concentrations suggest that models commonly overestimate BC concentrations in the upper troposphere of the tropics by more than one order of magnitude but underestimate BC burdens in polar latitudes. In this study, we improved the in‐cloud wet scavenging parameterizations for convective clouds and mixed‐phase clouds to better characterize BC abundances in the remote atmosphere (remote oceans and polar regions) with a global model, CAM5‐ATRAS2. The modified wet scavenging processes in the model achieved a more realistic simulation of BC concentrations over both the tropics and the Arctic. The new, unified scheme for vertical transport and wet removal during deep convection generally reproduced the observed low mixing ratios (about 0.1 ng kg−1) of BC in the middle and upper troposphere over the tropics, and the Wegener–Bergeron–Findeisen process (WBF) lowered the wet removal efficiency of BC from mixed‐phase clouds and consequently increased BC burdens in the Arctic by about a factor of 2. The BC direct radiative forcings increased by 20% globally (from 0.26 to 0.31 W m−2), and more importantly by a factor of 2 in the Arctic (from 0.09 to 0.18 W m−2). Our results indicated that good agreement between modeled and observed BC concentrations could be obtained in the remote atmosphere without requiring the relatively short global BC lifetime (∼4 days) suggested by previous studies.
Influence of Large‐Scale Circulation Patterns on Compound Dry and Hot Events in China
Authors: Wu Xinying , Hao Zengchao , Hao Fanghua , Zhang Xuan , Singh Vijay P. , Sun Cheng
Published: January 2021

Compound weather and climate events, which may cause devastating impacts on economic and social development, have become major threats in the twenty‐first century, especially to countries with complex climate and terrain like China. A better understanding of the driving factors of compound weather and climate events is essential for reducing their impacts, which remains overall lacking. In this study, we evaluate the potential influence of large‐scale circulation patterns on compound dry and hot events (CDHEs) during summer for the period 1921–2016 in mainland China using the composite analysis. Furthermore, the logistic regression model and correlation analysis are also used to confirm the result. The Atlantic Multidecadal Oscillation is found to affect CDHEs for about 18.52% of mainland China, followed by North Atlantic Oscillation and Pacific Decadal Oscillation accounting for about 14.64% and 12.96%, respectively. El Niño–Southern Oscillation affects CDHEs for small areas (about 5.27%). In general, regions with significant impacts of these indices from the three methods are overall consistent (mainly shown in northern parts of mainland China) with relatively larger areas estimated from the correlation analysis. These results are expected to be helpful for understanding occurrences of CDHEs and mitigating their negative impacts in China.
On the Effect of Magnetospheric Shielding on the Lunar Hydrogen Cycle
Authors: Tucker O. J. , Farrell W. M. , Poppe A. R.
Published: January 2021

The global distribution of surficial hydroxyl on the Moon is hypothesized to be derived from the implantation of solar wind protons. As the Moon traverses the geomagnetic tail, it is generally shielded from the solar wind; therefore, the concentration of hydrogen is expected to decrease during full Moon. A Monte Carlo approach is used to model the diffusion of implanted hydrogen atoms in the regolith as they form metastable bonds with O atoms, and the subsequent degassing of H2 into the exosphere. We quantify the expected change in the surface OH and the H2 exosphere using averaged SW proton flux obtained from the Acceleration, Reconnection, Turbulence, and Electrodynamics of the Moon's Interaction with the Sun (ARTEMIS) measurements. At lunar local noon, there is a small difference <∼10 ppm between the surface concentrations in the tail compared to out. However, the cumulative effect of traversing the magnetotail is a surface concentration depleted by ∼60 ppm for a region of the surface that spends most of its time in the lunar wake (waning gibbous to waxing crescent) on the nightside during time periods when Moon is exposed to unperturbed solar wind. The H2 exosphere decreased by approximately an order of magnitude while in the magnetotail due to the decreased proton flux. The model results are consistent with preliminary exospheric observations obtained by both the (Lyman Alpha Mapping Project on the Lunar Reconnaissance Orbiter) LAMP observations and mass spectrometer measurements by the Chandrayaan‐I Altitudinal Composition Explorer (CHACE).
An Evolving Understanding of Enigmatic Large Ripples on Mars
Authors: Lapôtre Mathieu G. A. , Ewing Ryan C. , Lamb Michael P.
Published: January 2021

Two scales of ripples form in fine sand on Mars. The larger ripples were proposed to have an equilibrium size set by an aerodynamic process, making them larger under thinner atmospheres and distinct from smaller impact ripples. Sullivan et al. (2020, https://doi.org/10.1029/2020JE006485) show that large ripples can develop in a numerical model due to Mars’ low atmospheric pressure. Although their proposed growth‐limiting mechanism is consistent with an aerodynamic process, they argue that the ripples in their model are simply large versions of impact ripples, not a separate class of ripples. Here, we explore this debate by synthesizing recent advances in large‐ripple formation (including initiation and subsequent evolution to equilibrium). Although significant knowledge gaps remain, it is clear that large Martian ripples in well sorted sand are larger under thinner atmospheres, and thus remain a powerful paleoclimate indicator.
A Parameterization of Turbulent Dissipation and Pressure Damping Time Scales in Stably Stratified Inversions, and its Effects on Low Clouds in Global Simulations
Authors: Guo Zhun , Griffin Brian M. , Domke Steffen , Larson Vincent E.
Published: January 2021

It is difficult for coarse‐resolution global models of the atmosphere to accurately simulate the observed distribution of low clouds. In particular, it is difficult for moist turbulence closure models to simulate sufficiently bright near‐coastal stratocumulus (Sc) without simulating overly bright marine shallow cumuli (Cu). To parameterize bright Sc, a turbulence parameterization must damp the turbulent fluxes of heat and moisture above cloud top in order to prevent excessive entrainment of dry air into cloud top. To parameterize dim shallow Cu, the subgrid variances of temperature and moisture must remain large, in order to permit partial cloudiness. However, damping the fluxes but not the variances just above cloud top is difficult if a parameterization uses a single “master” time scale to damp both. In nature, the above‐cloud fluxes are damped by pressure fluctuations, whereas scalar variances are damped by a different process, namely, turbulent dissipation. In a stably stratified inversion above cloud, pressure damping is large but turbulent dissipation is small. To avoid this problem, a multitime scale parameterization for damping has been developed. The damping parameterization has been implemented in a global model and evaluated. The parameterization is capable of dimming shallow Cu while producing adequately bright Sc.
Estimation of the carrier frequencies and proportions of potential patients by detecting causative gene variants associated with autosomal recessive bone dysplasia using a whole-genome reference panel of Japanese individuals
Authors: Nagaoka Shinichi , Yamaguchi-Kabata Yumi , Shiga Naomi , Tachibana Masahito , Yasuda Jun , Tadaka Shu , Tamiya Gen , Fuse Nobuo , Kinoshita Kengo , Kure Shigeo , Murotsuki Jun , Yamamoto Masayuki , Yaegashi Nobuo , Sugawara Junichi
Published: January 2021

Bone dysplasias are a group of rare hereditary diseases, with up to 436 disease types. Perinatal diagnosis is clinically important for adequate personalized management and counseling. There are no reports focused on pathogenic variants of bone dysplasias in the general population. In this study, we focused on autosomal recessive bone dysplasias. We identified pathogenic variants using whole-genome reference panel data from 3552 Japanese individuals. For the first time, we were able to estimate the carrier frequencies and the proportions of potential patients. For autosomal recessive bone dysplasias, we detected 198 pathogenic variants of 54 causative genes. We estimated the variant carrier frequencies and the proportions of potential patients with variants associated with four clinically important bone dysplasias: osteogenesis imperfecta (OI), hypophosphatasia (HPP), asphyxiating thoracic dysplasia (ATD), and Ellis–van Creveld syndrome (EvC). The proportions of potential patients with OI, ATD, and EvC based on pathogenic variants classified as “pathogenic” and “likely pathogenic” by InterVar were closer to the reported incidence rates in Japanese subjects. Furthermore, the proportions of potential patients with HPP variants classified as “pathogenic” and “likely pathogenic” in InterVar and “pathogenic” in ClinVar were closer to the reported incidence rates. For bone dysplasia, the findings of this study will provide a better understanding of the variant types and frequencies in the Japanese general population, and should be useful for clinical diagnosis, genetic counseling, and personalized medicine.
Irreversibility in dynamical phases and transitions
Authors: Seara Daniel S. , Machta Benjamin B. , Murrell Michael P.
Published: January 2021

Living and non-living active matter consumes energy at the microscopic scale to drive emergent, macroscopic behavior including traveling waves and coherent oscillations. Recent work has characterized non-equilibrium systems by their total energy dissipation, but little has been said about how dissipation manifests in distinct spatiotemporal patterns. We introduce a measure of irreversibility we term the entropy production factor to quantify how time reversal symmetry is broken in field theories across scales. We use this scalar, dimensionless function to characterize a dynamical phase transition in simulations of the Brusselator, a prototypical biochemically motivated non-linear oscillator. We measure the total energetic cost of establishing synchronized biochemical oscillations while simultaneously quantifying the distribution of irreversibility across spatiotemporal frequencies.
Cell culture NAIL-MS allows insight into human tRNA and rRNA modification dynamics in vivo
Authors: Heiss Matthias , Hagelskamp Felix , Marchand Virginie , Motorin Yuri , Kellner Stefanie
Published: January 2021

Recently, studies about RNA modification dynamics in human RNAs are among the most controversially discussed. As a main reason, we identified the unavailability of a technique which allows the investigation of the temporal processing of RNA transcripts. Here, we present nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS) for efficient, monoisotopic stable isotope labeling in both RNA and DNA in standard cell culture. We design pulse chase experiments and study the temporal placement of modified nucleosides in tRNAPhe and 18S rRNA. In existing RNAs, we observe a time-dependent constant loss of modified nucleosides which is masked by post-transcriptional methylation mechanisms and thus undetectable without NAIL-MS. During alkylation stress, NAIL-MS reveals an adaptation of tRNA modifications in new transcripts but not existing ones. Overall, we present a fast and reliable stable isotope labeling strategy which allows in-depth study of RNA modification dynamics in human cell culture.
Temporal changes in global soil respiration since 1987
Authors: Lei Jiesi , Guo Xue , Zeng Yufei , Zhou Jizhong , Gao Qun , Yang Yunfeng
Published: January 2021

As the second-largest terrestrial carbon (C) flux, soil respiration (RS) has been stimulated by climate warming. However, the magnitude and dynamics of such stimulations of soil respiration are highly uncertain at the global scale, undermining our confidence in future climate projections. Here, we present an analysis of globalRSobservations from 1987–2016.RSincreased (P < 0.001) at a rate of 27.66 g C m−2 yr−2(equivalent to 0.161 Pg C yr−2) in 1987–1999 globally but became unchanged in 2000–2016, which were related to complex temporal variations of temperature anomalies and soil C stocks. However, global heterotrophic respiration (Rh) derived from microbial decomposition of soil C increased in 1987–2016 (P < 0.001), suggesting accumulated soil C losses. Given the warmest years on records after 2015, our modeling analysis shows a possible resuscitation of globalRSrise. This study of naturally occurring shifts inRSover recent decades has provided invaluable insights for designing more effective policies addressing future climate challenges.
High-pressure phase diagrams of FeSe1−xTex: correlation between suppressed nematicity and enhanced superconductivity
Authors: Mukasa K. , Matsuura K. , Qiu M. , Saito M. , Sugimura Y. , Ishida K. , Otani M. , Onishi Y. , Mizukami Y. , Hashimoto K. , Gouchi J. , Kumai R. , Uwatoko Y. , Shibauchi T.
Published: January 2021

The interplay among magnetism, electronic nematicity, and superconductivity is the key issue in strongly correlated materials including iron-based, cuprate, and heavy-fermion superconductors. Magnetic fluctuations have been widely discussed as a pairing mechanism of unconventional superconductivity, but recent theory predicts that quantum fluctuations of nematic order may also promote high-temperature superconductivity. This has been studied in FeSe1−xSx superconductors exhibiting nonmagnetic nematic and pressure-induced antiferromagnetic orders, but its abrupt suppression of superconductivity at the nematic end point leaves the nematic-fluctuation driven superconductivity unconfirmed. Here we report on systematic studies of high-pressure phase diagrams up to 8 GPa in high-quality single crystals of FeSe1−xTex. When Te composition x(Te) becomes larger than 0.1, the high-pressure magnetic order disappears, whereas the pressure-induced superconducting dome near the nematic end point is continuously found up to x(Te) ≈ 0.5. In contrast to FeSe1−xSx, enhanced superconductivity in FeSe1−xTex does not correlate with magnetism but with the suppression of nematicity, highlighting the paramount role of nonmagnetic nematic fluctuations for high-temperature superconductivity in this system.
The p63 C-terminus is essential for murine oocyte integrity
Authors: Lena Anna Maria , Rossi Valerio , Osterburg Susanne , Smirnov Artem , Osterburg Christian , Tuppi Marcel , Cappello Angela , Amelio Ivano , Dötsch Volker , De Felici Massimo , Klinger Francesca Gioia , Annicchiarico-Petruzzelli Margherita , Valensise Herbert , Melino Gerry , Candi Eleonora
Published: January 2021

The transcription factor p63 mediates distinct cellular responses, primarily regulating epithelial and oocyte biology. In addition to the two amino terminal isoforms, TAp63 and ΔNp63, the 3’-end of p63 mRNA undergoes tissue-specific alternative splicing that leads to several isoforms, including p63α, p63β and p63γ. To investigate in vivo how the different isoforms fulfil distinct functions at the cellular and developmental levels, we developed a mouse model replacing the p63α with p63β by deletion of exon 13 in the Trp63 gene. Here, we report that whereas in two organs physiologically expressing p63α, such as thymus and skin, no abnormalities are detected, total infertility is evident in heterozygous female mice. A sharp reduction in the number of primary oocytes during the first week after birth occurs as a consequence of the enhanced expression of the pro-apoptotic transcriptional targets Puma and Noxa by the tetrameric, constitutively active, TAp63β isoform. Hence, these mice show a condition of ovary dysfunction, resembling human primary ovary insufficiency. Our results show that the p63 C-terminus is essential in TAp63α-expressing primary oocytes to control cell death in vivo, expanding the current understanding of human primary ovarian insufficiency.
The challenges of containing SARS-CoV-2 via test-trace-and-isolate
Authors: Contreras Sebastian , Dehning Jonas , Loidolt Matthias , Zierenberg Johannes , Spitzner F. Paul , Urrea-Quintero Jorge H. , Mohr Sebastian B. , Wilczek Michael , Wibral Michael , Priesemann Viola
Published: January 2021

Without a cure, vaccine, or proven long-term immunity against SARS-CoV-2, test-trace-and-isolate (TTI) strategies present a promising tool to contain its spread. For any TTI strategy, however, mitigation is challenged by pre- and asymptomatic transmission, TTI-avoiders, and undetected spreaders, which strongly contribute to ”hidden" infection chains. Here, we study a semi-analytical model and identify two tipping points between controlled and uncontrolled spread: (1) the behavior-driven reproduction number$${R}_{t}^{H}$$RtHof the hidden chains becomes too large to be compensated by the TTI capabilities, and (2) the number of new infections exceeds the tracing capacity. Both trigger a self-accelerating spread. We investigate how these tipping points depend on challenges like limited cooperation, missing contacts, and imperfect isolation. Our results suggest that TTI alone is insufficient to contain an otherwise unhindered spread of SARS-CoV-2, implying that complementary measures like social distancing and improved hygiene remain necessary.
Publisher Correction: Enhancer remodeling promotes tumor-initiating activity in NRF2-activated non-small cell lung cancers
Authors: Okazaki Keito , Anzawa Hayato , Liu Zun , Ota Nao , Kitamura Hiroshi , Onodera Yoshiaki , Alam Md. Morshedul , Matsumaru Daisuke , Suzuki Takuma , Katsuoka Fumiki , Tadaka Shu , Motoike Ikuko , Watanabe Mika , Hayasaka Kazuki , Sakurada Akira , Okada Yoshinori , Yamamoto Masayuki , Suzuki Takashi , Kinoshita Kengo , Sekine Hiroki , Motohashi Hozumi
Published: January 2021

A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-20927-9.
Comparison of two fluorescent probes in preclinical non-invasive imaging and image-guided debridement surgery of Staphylococcal biofilm implant infections
Authors: Park Howard Y. , Zoller Stephen D. , Hegde Vishal , Sheppard William , Burke Zachary , Blumstein Gideon , Hamad Christopher , Sprague Marina , Hoang John , Smith Ryan , Romero Pastrana Francisco , Czupryna Julie , Miller Lloyd S. , López-Álvarez Marina , Bispo Mafalda , van Oosten Marleen , van Dijl Jan Maarten , Francis Kevin P. , Bernthal Nicholas M.
Published: January 2021

Implant-associated infections are challenging to diagnose and treat. Fluorescent probes have been heralded as a technologic advancement that can improve our ability to non-invasively identify infecting organisms, as well as guide the inexact procedure of surgical debridement. This study’s purpose was to compare two fluorescent probes for their ability to localize Staphylococcus aureus biofilm infections on spinal implants utilizing noninvasive optical imaging, then assessing the broader applicability of the more successful probe in other infection animal models. This was followed by real-time, fluorescence image-guided surgery to facilitate debridement of infected tissue. The two probe candidates, a labelled antibiotic that targets peptidoglycan (Vanco-800CW), and the other, a labelled antibody targeting the immunodominant Staphylococcal antigen A (1D9-680), were injected into mice with spine implant infections. Mice were then imaged noninvasively with near infrared fluorescent imaging at wavelengths corresponding to the two probe candidates. Both probes localized to the infection, with the 1D9-680 probe showing greater fidelity over time. The 1D9-680 probe was then tested in mouse models of shoulder implant and allograft infection, demonstrating its broader applicability. Finally, an image-guided surgery system which superimposes fluorescent signals over analog, real-time, tissue images was employed to facilitate debridement of fluorescent-labelled bacteria.
Inhibition of mitochondrial complex II in neuronal cells triggers unique pathways culminating in autophagy with implications for neurodegeneration
Authors: Ranganayaki Sathyanarayanan , Jamshidi Neema , Aiyaz Mohamad , Rashmi Santhosh-Kumar , Gayathri Narayanappa , Harsha Pulleri Kandi , Padmanabhan Balasundaram , Srinivas Bharath Muchukunte Mukunda
Published: January 2021

Mitochondrial dysfunction and neurodegeneration underlie movement disorders such as Parkinson’s disease, Huntington’s disease and Manganism among others. As a corollary, inhibition of mitochondrial complex I (CI) and complex II (CII) by toxins 1-methyl-4-phenylpyridinium (MPP+) and 3-nitropropionic acid (3-NPA) respectively, induced degenerative changes noted in such neurodegenerative diseases. We aimed to unravel the down-stream pathways associated with CII inhibition and compared with CI inhibition and the Manganese (Mn) neurotoxicity. Genome-wide transcriptomics of N27 neuronal cells exposed to 3-NPA, compared with MPP+ and Mn revealed varied transcriptomic profile. Along with mitochondrial and synaptic pathways, Autophagy was the predominant pathway differentially regulated in the 3-NPA model with implications for neuronal survival. This pathway was unique to 3-NPA, as substantiated by in silico modelling of the three toxins. Morphological and biochemical validation of autophagy markers in the cell model of 3-NPA revealed incomplete autophagy mediated by mechanistic Target of Rapamycin Complex 2 (mTORC2) pathway. Interestingly, Brain Derived Neurotrophic Factor (BDNF), which was elevated in the 3-NPA model could confer neuroprotection against 3-NPA. We propose that, different downstream events are activated upon neurotoxin-dependent CII inhibition compared to other neurotoxins, with implications for movement disorders and regulation of autophagy could potentially offer neuroprotection.
Tryptophan-derived metabolites and BAK1 separately contribute to Arabidopsis postinvasive immunity against Alternaria brassicicola
Authors: Kosaka Ayumi , Pastorczyk Marta , Piślewska-Bednarek Mariola , Nishiuchi Takumi , Ono Erika , Suemoto Haruka , Ishikawa Atsushi , Frerigmann Henning , Kaido Masanori , Mise Kazuyuki , Bednarek Paweł , Takano Yoshitaka
Published: January 2021

Nonhost resistance of Arabidopsis thaliana against the hemibiotrophic fungus Colletotrichum tropicale requires PEN2-dependent preinvasive resistance and CYP71A12 and CYP71A13-dependent postinvasive resistance, which both rely on tryptophan (Trp) metabolism. We here revealed that CYP71A12, CYP71A13 and PAD3 are critical for Arabidopsis’ postinvasive basal resistance toward the necrotrophic Alternaria brassicicola. Consistent with this, gene expression and metabolite analyses suggested that the invasion by A. brassicicola triggered the CYP71A12-dependent production of indole-3-carboxylic acid derivatives and the PAD3 and CYP71A13-dependent production of camalexin. We next addressed the activation of the CYP71A12 and PAD3-dependent postinvasive resistance. We found that bak1-5 mutation significantly reduced postinvasive resistance against A. brassicicola, indicating that pattern recognition contributes to activation of this second defense-layer. However, the bak1-5 mutation had no detectable effects on the Trp-metabolism triggered by the fungal penetration. Together with this, further comparative gene expression analyses suggested that pathogen invasion in Arabidopsis activates (1) CYP71A12 and PAD3-related antifungal metabolism that is not hampered by bak1-5, and (2) a bak1-5 sensitive immune pathway that activates the expression of antimicrobial proteins.
Prevalence of different comorbidities in chronic obstructive pulmonary disease among Shahrekord PERSIAN cohort study in southwest Iran
Authors: Kiani Fatemeh Zeynab , Ahmadi Ali
Published: January 2021

Comorbidities are common in chronic obstructive pulmonary disease (COPD) patients. This study was conducted to determine the prevalence of common comorbidities in patients with COPD compared with people without COPD. This cross-sectional, population-based study was performed on 6961 adults aged 35–70 years enrolled in the Shahrekord PERSIAN cohort study. Data (demographic and clinical characteristics, comorbidities, anthropometric and blood pressure measurements, laboratory, and spirometry tests) collection was performed according to the cohort protocol from 2015 to 2019. In the present study, 215 (3.1%) patients were diagnosed with COPD and 1753 (25.18%) ones with restrictive lung patterns. The mean age of COPD patients was 52.5 ± 9.76 years. 55.8% of patients were male, 17.7% were current smokers and 12.1% had a history of smoking or were former smokers. 5.6% of patients had no comorbidity and 94.5% had at least one comorbidity. The most common comorbidities in COPD patients were dyslipidemia (70.2%), hypertension (30.2%), metabolic syndrome (22.8%), and diabetes (16.7%). The most common comorbidities in individuals with a restrictive spirometry pattern were dyslipidemia (68.9%), metabolic syndrome (27.2%), hypertension (26.1%), depression (17.6%), and fatty liver (15.5%). The logistic regression analysis with 95% confidence interval (95%CI) of odds ratio (OR) showed that comorbidities of chronic lung diseases (OR = 2.12, 95% CI 1.30–3.44), diabetes (OR = 1.54, 95%CI 1.03–2.29), cardiovascular disease (OR = 1.52, 95%CI 1.17–2.43), and hypertension (OR = 1.4, 95%CI 1.02–1.99) were more likely to occur in COPD patients than in healthy individuals. Knowing these prevalence rates and related information provides new insights on comorbidities to reduce disease burden and develop preventive interventions and to regulate health care resources to meet the needs of patients in primary health care.
Crop nutrient management using Nutrient Expert improves yield, increases farmers’ income and reduces greenhouse gas emissions
Authors: Sapkota Tek B. , Jat Mangi L. , Rana Dharamvir S. , Khatri-Chhetri Arun , Jat Hanuman S. , Bijarniya Deepak , Sutaliya Jhabar M. , Kumar Manish , Singh Love K. , Jat Raj K. , Kalvaniya Kailash , Prasad Gokul , Sidhu Harminder S. , Rai Munmun , Satyanarayana T. , Majumdar Kaushik
Published: January 2021

Reduction of excess nutrient application and balanced fertilizer use are the key mitigation options in agriculture. We evaluated Nutrient Expert (NE) tool-based site-specific nutrient management (SSNM) in rice and wheat crops by establishing 1594 side-by-side comparison trials with farmers’ fertilization practices (FFP) across the Indo-Gangetic Plains (IGP) of India. We found that NE-based fertilizer management can lower global warming potential (GWP) by about 2.5% in rice, and between 12 and 20% in wheat over FFP. More than 80% of the participating farmers increased their crop yield and farm income by applying the NE-based fertilizer recommendation. We also observed that increased crop yield and reduced fertilizer consumption and associated greenhouse gas (GHG) emissions by using NE was significantly influenced by the crop type, agro-ecology, soil properties and farmers’ current level of fertilization. Adoption of NE-based fertilizer recommendation practice in all rice and wheat acreage in India would translate into 13.92 million tonnes (Mt) more rice and wheat production with 1.44 Mt less N fertilizer use, and a reduction in GHG of 5.34 Mt CO2e per year over farmers’ current practice. Our study establishes the utility of NE to help implement SSNM in smallholder production systems for increasing crop yields and farmers’ income while reducing GHG emissions.
Isolation of the South China Sea from the North Pacific Subtropical Gyre since the latest Miocene due to formation of the Luzon Strait
Authors: Yin Shaoru , Hernández-Molina F. Javier , Lin Lin , Chen Jiangxin , Ding Weifeng , Li Jiabiao
Published: January 2021

The North Pacific subtropical gyre (NPSG) plays a major role in present global ocean circulation. At times, the gyre has coursed through the South China Sea, but its role in the evolutionary development of that Sea remains uncertain. This work systematically describes a major shift in NPSG paleo-circulation evident from sedimentary features observed in seismic and bathymetric data. These data outline two contourite depositional systems—a buried one formed in the late Miocene, and a latest Miocene to present-day system. The two are divided by a prominent regional discontinuity that represents a major shift in paleo-circulation during the latest Miocene (~ 6.5 Ma). The shift coincides with the further restriction of the South China Sea with respect to the North Pacific due to the formation of the Luzon Strait as a consequence of further northwest movement of the Philippine Sea plate. Before that restriction, data indicate vigorous NPSG circulation in the South China Sea. Semi-closure, however, established a new oceanographic circulation regime in the latest Miocene. This work demonstrates the significant role of recent plate tectonics, gateway development, and marginal seas in the establishment of modern global ocean circulation.
Benchtop micro-mashing: high-throughput, robust, experimental beer brewing
Authors: Kerr Edward D. , Caboche Christopher H. , Josh Peter , Schulz Benjamin L.
Published: January 2021

Brewing science is undergoing a renaissance with the use of modern analytical chemistry and microbiology techniques. However, these modern analytical tools and techniques are not necessarily aligned with the scale and scope of brewing science. In particular, brewing processes can be time consuming, ingredient intensive, and require specialised technical equipment. These drawbacks compound with the need for appropriate numbers of replicates for adequately powered experimental design. Here, we describe a micro-scale mash method that can be performed using a common laboratory benchtop shaker/incubator, allowing for high throughput mashing and easy sample replication for statistical analysis. Proteomic profiles at both the protein and peptide levels were consistent between the 1 mL micro-mash and a 23 L Braumeister mash, and both mash scales produced wort with equivalent fermentable sugar and free amino acid profiles. The experimental flexibility offered by our micro-mash method allowed us to investigate the effects of altered mash parameters on the beer brewing proteome.
Biodiversity response to forest management intensity, carbon stocks and net primary production in temperate montane forests
Authors: Asbeck Thomas , Sabatini Francesco , Augustynczik Andrey L. D. , Basile Marco , Helbach Jan , Jonker Marlotte , Knuff Anna , Bauhus Jürgen
Published: January 2021

Managed forests are a key component of strategies aimed at tackling the climate and biodiversity crises. Tapping this potential requires a better understanding of the complex, simultaneous effects of forest management on biodiversity, carbon stocks and productivity. Here, we used data of 135 one-hectare plots from southwestern Germany to disentangle the relative influence of gradients of management intensity, carbon stocks and forest productivity on different components of forest biodiversity (birds, bats, insects, plants) and tree-related microhabitats. We tested whether the composition of taxonomic groups varies gradually or abruptly along these gradients. The richness of taxonomic groups was rather insensitive to management intensity, carbon stocks and forest productivity. Despite the low explanatory power of the main predictor variables, forest management had the greatest relative influence on richness of insects and tree-related microhabitats, while carbon stocks influenced richness of bats, birds, vascular plants and pooled taxa. Species composition changed relatively abruptly along the management intensity gradient, while changes along carbon and productivity gradients were more gradual. We conclude that moderate increases in forest management intensity and carbon stocks, within the range of variation observed in our study system, might be compatible with biodiversity and climate mitigation objectives in managed forests.
A pilot study: effectiveness of local injection of autologous platelet-rich plasma in treating women with stress urinary incontinence
Authors: Long Cheng-Yu , Lin Kun-Ling , Shen Chin-Ru , Ker Chin-Ru , Liu Yi-Yin , Loo Zi-Xi , Hsiao Hui-Hua , Lee Yung-Chin
Published: January 2021

The study aims to evaluate the effectiveness of local injection of autologous platelet rich plasma (A-PRP) as a treatment for women suffering from stress urinary incontinence (SUI). In a prospective intervention study, twenty consecutive women suffering from SUI were treated with A-PRP injection at anterior vaginal wall where mid-urethra locates. Self-reported questionnaires were used to measure pre-treatment, 1 month and 6 months post-treatment symptom severity. Secondary outcomes of sexual function and treatment effect sorted by age were analyzed with valid statistical methods. A-PRP is effective in relieving SUI symptoms at both 1 month and 6 months post-treatment without significant adverse reactions reported. It seems to have a trend that treatment success rate with cured and improved symptoms was slightly higher in the younger group, although it did not reach statistical significance (P = 0.07). No significant changes in sexual function before and after the treatment were reported by the patients. This pilot study is the first to report A-PRP treatment effect for SUI in women. The result suggested that A-PRP is a considerable treatment option for mild to moderate SUI cases. It also opens up further research opportunities for A-PRP’s clinical applications.
Thiamethoxam exposure deregulates short ORF gene expression in the honey bee and compromises immune response to bacteria
Authors: Decio Pâmela , Ustaoglu Pinar , Derecka Kamila , Hardy Ian C. W. , Roat Thaisa C. , Malaspina Osmar , Mongan Nigel , Stöger Reinhard , Soller Matthias
Published: January 2021

Maximizing crop yields relies on the use of agrochemicals to control insect pests. One of the most widely used classes of insecticides are neonicotinoids that interfere with signalling of the neurotransmitter acetylcholine, but these can also disrupt crop-pollination services provided by bees. Here, we analysed whether chronic low dose long-term exposure to the neonicotinoid thiamethoxam alters gene expression and alternative splicing in brains of Africanized honey bees, Apis mellifera, as adaptation to altered neuronal signalling. We find differentially regulated genes that show concentration-dependent responses to thiamethoxam, but no changes in alternative splicing. Most differentially expressed genes have no annotated function but encode short Open Reading Frames, a characteristic feature of anti-microbial peptides. As this suggested that immune responses may be compromised by thiamethoxam exposure, we tested the impact of thiamethoxam on bee immunity by injecting bacteria. We show that intrinsically sub-lethal thiamethoxam exposure makes bees more vulnerable to normally non-pathogenic bacteria. Our findings imply a synergistic mechanism for the observed bee population declines that concern agriculturists, conservation ecologists and the public.
Baseline local hemodynamics as predictor of lumen remodeling at 1-year follow-up in stented superficial femoral arteries
Authors: Colombo Monika , He Yong , Corti Anna , Gallo Diego , Casarin Stefano , Rozowsky Jared M. , Migliavacca Francesco , Berceli Scott , Chiastra Claudio
Published: January 2021

In-stent restenosis (ISR) is the major drawback of superficial femoral artery (SFA) stenting. Abnormal hemodynamics after stent implantation seems to promote the development of ISR. Accordingly, this study aims to investigate the impact of local hemodynamics on lumen remodeling in human stented SFA lesions. Ten SFA models were reconstructed at 1-week and 1-year follow-up from computed tomography images. Patient-specific computational fluid dynamics simulations were performed to relate the local hemodynamics at 1-week, expressed in terms of time-averaged wall shear stress (TAWSS), oscillatory shear index and relative residence time, with the lumen remodeling at 1-year, quantified as the change of lumen area between 1-week and 1-year. The TAWSS was negatively associated with the lumen area change (ρ = − 0.75, p = 0.013). The surface area exposed to low TAWSS was positively correlated with the lumen area change (ρ = 0.69, p = 0.026). No significant correlations were present between the other hemodynamic descriptors and lumen area change. The low TAWSS was the best predictive marker of lumen remodeling (positive predictive value of 44.8%). Moreover, stent length and overlapping were predictor of ISR at follow-up. Despite the limited number of analyzed lesions, the overall findings suggest an association between abnormal patterns of WSS after stenting and lumen remodeling.
Identification and genetic diversity analysis of a male-sterile gene (MS1) in Japanese cedar (Cryptomeria japonica D. Don)
Authors: Hasegawa Yoichi , Ueno Saneyoshi , Wei Fu-Jin , Matsumoto Asako , Uchiyama Kentaro , Ujino-Ihara Tokuko , Hakamata Tetsuji , Fujino Takeshi , Kasahara Masahiro , Bino Takahiro , Yamaguchi Katsushi , Shigenobu Shuji , Tsumura Yoshihiko , Moriguchi Yoshinari
Published: January 2021

Identifying causative genes for a target trait in conifer reproduction is challenging for species lacking whole-genome sequences. In this study, we searched for the male-sterility gene (MS1) inCryptomeria japonica, aiming to promote marker-assisted selection (MAS) of male-sterileC. japonicato reduce the pollinosis caused by pollen dispersal from artificialC. japonicaforests in Japan. We searched for mRNA sequences expressed in male strobili and found the gene CJt020762, coding for a lipid transfer protein containing a 4-bp deletion specific to male-sterile individuals. We also found a 30-bp deletion by sequencing the entire gene of another individual with thems1. All nine breeding materials with the allelems1had either a 4-bp or 30-bp deletion in gene CJt020762, both of which are expected to result in faulty gene transcription and function. Furthermore, the 30-bp deletion was detected from three of five individuals in the Ishinomaki natural forest. From our findings, CJt020762 was considered to be the causative gene ofMS1. Thus, by performing MAS using two deletion mutations as a DNA marker, it will be possible to find novel breeding materials ofC. japonicawith the allelems1adapted to the unique environment of each region of the Japanese archipelago.
Generation of highly amenable cellulose-Iβ via selective delignification of rice straw using a reusable cyclic ether-assisted deep eutectic solvent system
Authors: Thulluri Chiranjeevi , Balasubramaniam Ravi , Velankar Harshad Ravindra
Published: January 2021

Cellulolytic enzymes can readily access the cellulosic component of lignocellulosic biomass after the removal of lignin during biomass pretreatment. The enzymatic hydrolysis of cellulose is necessary for generating monomeric sugars, which are then fermented into ethanol. In our study, a combination of a deep eutectic (DE) mixture (of 2-aminoethanol and tetra-n-butyl ammonium bromide) and a cyclic ether (tetrahydrofuran) was used for selective delignification of rice straw (RS) under mild conditions (100 °C). Pretreatment with DE-THF solvent system caused ~ 46% delignification whereas cellulose (~ 91%) and hemicellulose (~ 67%) recoveries remained higher. The new solvent system could be reused upto 10 subsequent cycles with the same effectivity. Interestingly, the DE-THF pretreated cellulose showed remarkable enzymatic hydrolysability, despite an increase in its crystallinity to 72.3%. Contrary to conventional pretreatments, we report for the first time that the enzymatic hydrolysis of pretreated cellulose is enhanced by the removal of lignin during DE-THF pretreatment, notwithstanding an increase in its crystallinity. The current study paves way for the development of newer strategies for biomass depolymerization with DES based solvents.