bluuebunny/crossref_metadata_2025 huggingface dataset:
Numerical study of bluntness effects on laminar leading edge separation in hypersonic flow
Authors: Khraibut Amna , Gai S. L. , Neely A. J.
Published: September 2019

Bluntness effects on laminar hypersonic leading edge separation are investigated numerically at Mach number $M\approx 10$, unit Reynolds number $Re=1.3\times 10^{6}~\text{m}^{-1}$, specific enthalpy $h_{o}=3.1~\text{MJ}~\text{kg}^{-1}$ and wall-to-stagnation temperature ratio $T_{w}/T_{o}=0.1$. Such effects are important from an experimental point of view and because bluntness can affect a separated flow favourably or adversely. In this study, two blunt leading edge cases of small radius ($15~\unicode[STIX]{x03BC}\text{m}$) and large radius ($100~\unicode[STIX]{x03BC}\text{m}$) are investigated. A comparison with the idealised sharp leading edge case is also given. General flow features and surface parameters such as the shear stress, pressure and heat flux are presented and analysed. The results have also been interpreted in terms of Cheng’s displacement-bluntness similitude parameter affecting the size of separation. Previous experiments by Holden delineated small and large bluntness effects based on Cheng’s parameter and considering small to moderate separated regions. In this study, leading edge separation was found to suppress the favourable effect of bluntness in delaying separation. Bluntness, furthermore, seemed to promote the appearance of secondary vortices within a main separated region. Analysis of reverse flow boundary layer profiles such as velocity, pressure and temperature is also given. It is shown that bluntness accentuates large transverse gradients. This in turn adversely effects the reverse flow boundary layer leading to the appearance of secondary vortices.
WEAKLY REMARKABLE CARDINALS, ERDŐS CARDINALS, AND THE GENERIC VOPĚNKA PRINCIPLE
Authors: WILSON TREVOR M.
Published: September 2019

We consider a weak version of Schindler’s remarkable cardinals that may fail to be ${{\rm{\Sigma }}_2}$-reflecting. We show that the ${{\rm{\Sigma }}_2}$-reflecting weakly remarkable cardinals are exactly the remarkable cardinals, and that the existence of a non-${{\rm{\Sigma }}_2}$-reflecting weakly remarkable cardinal has higher consistency strength: it is equiconsistent with the existence of an ω-Erdős cardinal. We give an application involving gVP, the generic Vopěnka principle defined by Bagaria, Gitman, and Schindler. Namely, we show that gVP + “Ord is not ${{\rm{\Delta }}_2}$-Mahlo” and ${\text{gVP}}(\underset{\raise0.3em\hbox{$\smash{\scriptscriptstyle\thicksim}$}}{\Pi } _1 )$ + “there is no proper class of remarkable cardinals” are both equiconsistent with the existence of a proper class of ω-Erdős cardinals, extending results of Bagaria, Gitman, Hamkins, and Schindler.
A BETTER COMPARISON OF - AND -COHOMOLOGIES
Authors: KELLY SHANE
Published: September 2019

In order to work with non-Nagata rings which are Nagata “up-to-completely-decomposed-universal-homeomorphism,” specifically finite rank Hensel valuation rings, we introduce the notions ofpseudo-integral closure,pseudo-normalization, andpseudo-Hensel valuation ring. We use this notion to give a shorter and more direct proof that$H_{\operatorname{cdh}}^{n}(X,F_{\operatorname{cdh}})=H_{l\operatorname{dh}}^{n}(X,F_{l\operatorname{dh}})$for homotopy sheaves$F$of modules over the$\mathbb{Z}_{(l)}$-linear motivic Eilenberg–Maclane spectrum. This comparison is an alternative to the first half of the author’s volume Astérisque 391 whose main theorem is a cdh-descent result for Voevodsky motives. The motivating new insight is really accepting that Voevodsky’s motivic cohomology (with$\mathbb{Z}[\frac{1}{p}]$-coefficients) is invariant not just for nilpotent thickenings, but for all universal homeomorphisms.
Poincaré duality and resonance varieties
Authors: Suciu Alexander I.
Published: September 2019

We explore the constraints imposed by Poincaré duality on the resonance varieties of a graded algebra. For a three-dimensional Poincaré duality algebra A, we obtain a fairly precise geometric description of the resonance varieties ${\cal R}^i_k(A)$.
GAPS BETWEEN DIVISIBLE TERMS IN
Authors: CHAN TSZ HO
Published: September 2019

Suppose $a^{2}(a^{2}+1)$ divides $b^{2}(b^{2}+1)$ with $b>a$. We improve a previous result and prove a gap principle, without any additional assumptions, namely $b\gg a(\log a)^{1/8}/(\log \log a)^{12}$. We also obtain $b\gg _{\unicode[STIX]{x1D716}}a^{15/14-\unicode[STIX]{x1D716}}$ under the abc conjecture.
Dynamics of Memory and Religious Nationalism in a Sino-Vietnamese Border Town
Authors: NGO TAM T. T.
Published: September 2019

This article analyses the dynamics of official and unofficial religious nationalism in the Vietnamese border town of Lào Cai. In 1979 it was one of many Vietnamese towns that were reduced to rubble during the short but bloody war between Vietnam and China. The normalization of Sino-Vietnamese relations in 1991 allowed a booming border trade that let Lào Cai prosper, while the painful memory of this war continued to haunt the town and the daily experiences of its residents, both humans and gods. Since the Vietnamese state forbids any official remembrance of the war, Lào Cai residents have found a religious way to deal with their war memories that skilfully evades state control. By analysing narratives about the fate of the gods and goddesses that reign in the Father God Temple and the Mother Goddess Temple—two religious institutions located right next to the border—this article shows that it is in the symbolism of the supernatural that one can find memories of the war and of the changing social landscape of Lào Cai and reconstruct its history.
Deriving natural law from the Decalogue, natural inclination and God's silence
Authors: Lombardo Nicholas E.
Published: September 2019

Amanda Perreau-Saussine de Ezcurra saw positive law as a resource for uncovering natural law. She also saw our natural inclinations, especially our natural sociability and our natural tendency toward benevolence, as crucial to a proper understanding of natural law. Drawing on these two foundational ideas of hers, this article will look at the Decalogue, the pre-eminent example of divine positive law, and then our concrete experience of desire, as revelatory of what she called ‘a law-like ordering of the world prior to human thought and action, a natural ordering that constrains practical reasoning’. To her characteristic concerns, it will add attention to God's silence.
English as a linguistic resource
Authors: Zhang Yi
Published: September 2019

With the intensification of globalization and advancement of digital communication, interactions online have gained increasing vitality in our life. Online communication now influences the spread of various languages (e.g., English) and semiotic signs (e.g., emoticons) to many countries, especially for those characterized by Kachru (1986) as belonging to the Expanding Circle (e.g., Japan, China — countries where English is usually practiced as a foreign language). Recent inquiries of digital discourse analysis have researched how English and its features are adopted in countries of the Expanding Circle (e.g., Crystal, 2008; Zhang, 2012). This paper continues to explore the linguistic landscape of English practices online, and specifically focuses on how micro-blogging users in mainland China adopt English as a resource for meaningful multilingual communication.
The use of biosphere reserves by a wide-ranging avian scavenger indicates its significant potential for conservation
Authors: Guido Jorgelina M , Alarcón Pablo AE , Donázar José A , Hiraldo Fernando , Lambertucci Sergio A
Published: September 2019

The framing of environmental conservation has been changing, mainly towards a reconciliation between human needs and nature conservation. A major challenge of biosphere reserves (BRs) is the integration of biodiversity conservation and the sustainable development of local communities. Although these areas are large, they are often not large enough to contain the movements of wide-ranging species. We studied immature Andean condor (Vultur gryphus) movements to evaluate their habitat use in relation to protected areas (PAs). We particularly aimed to determine whether BRs significantly increase the protection of this wide-ranging species. We analysed the movement overlap of 26 GPS-tagged birds with the PAs of Patagonia, and we evaluated preferences for particular landscape categories with a use–availability design. Condors were mainly located in unprotected areas (56.4%), whereas 26.4% of locations were within International Union for Conservation of Nature (IUCN) PAs and 17.2% of locations were in BRs (not including IUCN PAs). When compared to availability, birds preferred BRs over other areas, highlighting the importance of BRs in protecting species that forage in humanized areas. However, the lack of controls and management policies expose condors to several threats, such as poisoning and persecution, in both private lands and BRs. Implementing strict management practices for BRs will help to conserve wide-ranging scavengers that feed in humanized areas.
Autobiographical Voices: Performing Absence in Singers’ Memoirs
Authors: White Kimberly
Published: September 2019

This article explores the emergent genre of singers’ autobiographies in late nineteenth-century France. The moment singers took up the pen is telling, as it coincides with their dislodgement in the operatic marketplace from creator and collaborator to interpreter. In their life writings, Gilbert Duprez and Gustave Roger demonstrate a strong preoccupation with revising their public images and the histories that had been written about them. I argue that what critics felt was a flaw – the tenors’ predominant focus on relationships in their autobiographies, rather than on art – reveals how Duprez and Roger sought to reconstruct their artistic identities beyond the voice, locating their most profound contributions in their exchanges and actions within the musical community.
Determining the Parameters of the Ångström‐Prescott Model for Estimating Solar Radiation in Different Regions of China: Calibration and Modeling
Authors: Liu Yujie , Tan Qinghua , Pan Tao
Published: September 2019

The Ångström‐Prescott model (referred to as the A‐P model) is one of the most accurate and widely used models for estimating global solar radiation (Rs). In the absence of Rs measurements and given the regional discrepancy of model parameters, it is crucial to increase the availability of these parameters and the applicability of parameter‐predicted models in different regions. In this study, we evaluated and compared the applicability and performance of the calibrated model and eight predictive models in terms of A‐P model parameters, using daily Rs and meteorological data from 105 radiation stations in seven natural geographic zones in China. These models were evaluated based on their coefficient of determination (R2), root mean square error, Nash‐Sutcliffe efficiency coefficients, percent bias, and global performance indexes. Results indicated that altitude was the main factor determining the Ångström‐Prescott parameters in most regions. All models performed well, with acceptable accuracy across the whole country; however, their performances varied among regions. The best performing predictive models for the northeast region (Zone 1), north China (Zone 2), central China (Zone 3), south China (Zone 4), Inner Mongolia (Zone 5), northwest region (Zone 6), and Qinghai‐Tibet region (Zone 7) were obtained: These were Models 6, 1, 7, 3, 6, 1, and 7, respectively. The present results support the application of these predictive models for the estimation of daily global Rs in the corresponding regions of China, where measured Rs data are not available, and possibly in other regions with a similar climate.
Distinct Impacts of Light and Heavy Precipitation on PM2.5 Mass Concentration in Beijing
Authors: Sun Yue , Zhao Chuanfeng , Su Yunfei , Ma Zhanshan , Li Jiming , Letu Husi , Yang Yikun , Fan Hao
Published: September 2019

Using hourly observation data of precipitation and PM2.5 at 12 sites in Beijing from 2015 to 2017, this study investigates the impacts of different types of precipitation on PM2.5 mass concentration, along with the characteristics of precipitation and PM2.5. There were totally 91–123 precipitation events annually, 69.7–79.4% of which has precipitation amount less than 5 mm. By investigating the differences of PM2.5 mass concentration between 1 hr after and before the precipitation events, this study finds distinct impacts of different types of precipitation on PM2.5 mass concentration. For precipitation events with amount of 0.1–0.5 mm, PM2.5 mass concentration increased with precipitation amount with a rate of 0.85 μg/m3 per 0.1 mm. For precipitation events with amount of 0.5–10 mm, there was no clear relationship between precipitation amount and PM2.5 mass concentration. For precipitation events with amount larger than 10 mm, PM2.5 mass concentration decreased with precipitation amount with a rate of 0.17 μg/m3 per 1 mm. Further analysis shows that weak precipitation less than 10 mm increased PM10, and heavy precipitation larger than 10 mm decreased PM10. The aerosol amount also affects the response of PM2.5 to precipitation, with weak pollution prone to increase with precipitation and heavy pollution prone to decrease with precipitation. Likely mechanisms are discussed, which include the aerosol hygroscopic growth and gas‐particle conversion that increase aerosol amount and precipitation scavenging that decreases aerosol amount. Shortly, the mechanisms that increase (decrease) aerosol amount more probably dominate when precipitation is light (heavy).
House Passes Measure to Protect Arctic National Wildlife Refuge
Authors: Showstack Randy
Published: September 2019

The measure, which would repeal an oil and gas development program in the refuge, now needs to pass the Senate, where there is stiff opposition.
Tidal Responses to Future Sea Level Trends on the Yellow Sea Shelf
Authors: Feng Xi , Feng Hui , Li Huichao , Zhang Fan , Feng Weibing , Zhang Wei , Yuan Jinjin
Published: September 2019

Quantifying how tides evolve with coupling between future sea level rise (SLR) and different coastline configurations is imperative for proposing appropriate coastal defense strategies. By using numerical models, we investigated tidal changes and determined a realistic trend of SLR on the Jiangsu coastal area and adjacent sea on the Yellow Sea shelf. A notable decrease in tidal range occurs in the northern shelf, and the tide increases mainly in the southern shelf. Tidal changes are of both signs, while the increase in sea level is unidirectional. Thus, the SLR effect on tide is not additive in all locations. We also explored the nonlinearity and spatial similarity in tidal range in response to the SLR considering uniform SLR scenarios with multiple levels and allowing inundation of the natural coastline. The patterns of change in tide evolution on the study domain remain linear until the SLR exceeds 2.0 m. Simulations and comparisons are further conducted between the responses of hardened and natural shoreline configurations to SLR. Hardened shoreline introduces both local and remote spatial variability in tidal responses. On the regional scale, SLR induces a shift in the tidal system in the offshore region, which controls the net energy flux into the embayment upon the coast. On the local scale, tidal dynamics are mainly a competition between net energy flux and tidal dissipation and are plausibly influenced by tidal reflection, which depends on whether a basin is tidally reflective.
Characteristics of Ice Clouds Over Mountain Regions Detected by CALIPSO and CloudSat Satellite Observations
Authors: Seiki Tatsuya , Kodama Chihiro , Satoh Masaki , Hagihara Yuichiro , Okamoto Hajime
Published: September 2019

This study examines the characteristics of orographic ice clouds in steep mountain regions using 3 years of CloudSat and CALIPSO satellite products. A combination of radar and lidar cloud fraction data is used to identify ice cloud systems. Additionally, the retrieved ice water content (IWC) and ice number concentration (NI) are used to analyze the dominant ice cloud microphysics in convective‐ and cirrus‐type clouds. The analysis shows that temporally averaged values of the IWC and NI are larger in mountain regions than in land and ocean regions. For convective clouds over mountains, both the IWC and NI have larger values at atmospheric temperatures warmer than 250 K, suggesting a dominant role for the freezing of supercooled liquid water. For cirrus clouds over mountains, however, only the NI has larger values at atmospheric temperatures colder than 240 K, indicating the importance of homogeneous ice nucleation. These characteristics of ice‐phase clouds in terms of the IWC and NI in mountain regions are distinct, with a horizontal scale smaller than 300 km. This study suggests that it is useful to categorize ice clouds in mountain regions in addition to ocean and land regions to evaluate the microphysical properties (mass and number) of such ice clouds in atmospheric models.
A Numerical Study on the Formation and Maintenance of a Long‐Lived Rainband in Typhoon Longwang (2005)
Authors: Li Yuanlong , Lin Yanluan , Wang Yuqing
Published: September 2019

A 14‐hr long‐lasting spiral rainband of landfalling Typhoon Longwang (2005) was investigated based on a high‐resolution simulation using the Advanced Research version of the Weather Research and Forecasting model. This rainband was previously suggested to be triggered and maintained by vortex‐Rossby wave (VRW) dynamics based on available observations. The simulation results in the present study further suggest that the rainband originated from a previously existing wavenumber‐2 VRW. The wave amplified via a positive feedback between Ekman pumping and diabatic heating. The wavenumber‐1 convective forcing induced by the deep‐layer environmental vertical wind shear also contributed to the amplification of the rainband after its formation. Although both observations and simulation showed the long‐lived (greater than 10 hr) rainband with leading stratiform precipitation, unlike in observations, the rainband in the simulation showed a transition from an inner rainband to an outer rainband when the simulated rainband moved beyond the VRW stagnation radius at about 140 km from the storm center. As a result, in the band's later stages, VRW dynamics could not contribute to the maintenance of the rainband. Instead, both cold‐pool dynamics and vertical wind shear‐induced wavenumber‐1 convective forcing played key roles in the further maintenance of the rainband.
Evaluation of the Mesospheric Polar Vortices in WACCM
Authors: Harvey V. Lynn , Randall Cora E. , Becker Erich , Smith Anne K. , Bardeen Charles G. , France Jeff A. , Goncharenko Larisa P.
Published: September 2019

This work evaluates the wintertime mesospheric polar vortices in the Whole Atmosphere Community Climate Model. Mesospheric altitudes are where high‐top models underestimate the concentration of nitrogen oxides produced by energetic particle precipitation. For this reason, we seek to determine the extent to which the observed mesospheric vortex size and frequency of occurrence is reproduced by the model. We compare 13 years (2005–2017) of “specified dynamics” Whole Atmosphere Community Climate Model (where meteorology in the troposphere and stratosphere is constrained by observations) to Sounding of the Atmosphere using Broadband Emission Radiometry and Mesospheric Limb Sounder observations. Near 75 km, the model reproduces observed winter mesospheric vortex frequency of occurrence rates and size reasonably well. The simulated Antarctic mesospheric vortex is displaced toward the Pacific longitude sector, and the Arctic mesospheric vortex is present 10–20% less often over the pole but ~5% more often in midlatitudes, particularly over the continents. These differences are attributed to larger planetary waves in the model. There are significant differences between the modeled and observed mean polar winter circulation near 90 km. Model‐measurement differences suggest that the simulated Antarctic mesospheric vortex does not extend to high enough altitudes, and the Arctic mesospheric vortex is too displaced from the pole. Despite these differences, the model accurately captures the evolution of structural changes to the mesospheric vortex following prolonged sudden stratospheric warmings. Thus, we conclude that model underestimates of nitrogen oxides produced by energetic particle precipitation after these warmings are not due to a misrepresentation of the mesospheric vortex strength and size below 80 km.
A High‐Resolution Simulation of Roll Convection Over the Yellow Sea During a Cold Air Outbreak
Authors: Chen Yong , Yuan Huiling , Gao Shanhong
Published: September 2019

Horizontal convective rolls (HCRs) are significant for vertical transport of momentum, heat, and moisture, which is not fully understood partly due to lack of adequate observations. Previous high‐resolution modeling studies of roll convection mainly focused on idealized simulations. This study is one of the first simulations of HCRs with high‐resolution numerical weather prediction models in the real world, aiming to assess the modeling ability of realistic roll structure and investigate the characteristics of roll‐to‐cell transition. A real case of roll convection over the Yellow Sea during a cold air outbreak has been simulated, using the Weather Research and Forecasting (WRF) model at resolutions of 1 (WRF1) and 3 km (WRF3). Compared with the WRF3 simulation, the cloud water, vertical velocity, and the fine‐scale secondary circulations of HCRs are enhanced in WRF1 simulation, and the geometrical and physical parameters are consistent with the observations of satellite images (viewed as cloud streets) or previous studies. In this case, the 1‐km WRF simulation is able to reproduce the HCRs with a roll size of ~5 km. When the rolls transform to open cells downstream, the friction velocity and sensible heat flux gradually reduce following the prevailing wind, and the stability parameter –zi/L (the ratio of planetary boundary layer depth to Obukhov length) tends to increase with larger variances. During the roll‐to‐cell transition, the associated thermodynamic conditions are well simulated, with an average –zi/L ~ 22. In the future, reliable high‐resolution simulations can serve as an alternative to quantitatively investigate roll characteristics when observations are sparse or unavailable.
The Role of Interactive SST in the Cloud‐Resolving Simulations of Aggregated Convection
Authors: Chen Yan‐Ting , Wu Chien‐Ming
Published: September 2019

This study investigates the role of interactive sea surface temperature (SST) in the early development of aggregated convection using a vector vorticity equation cloud‐resolving model coupled to a slab ocean. The simulations are initialized by a mock Walker circulation driven by initial SST gradient in the elongated x axis, with an average of 300 K and sinusoidal variation of amplitude ranging from 1.5 to 3 K. According to large‐scale perturbation strength, which is caused by SST variation, the results can be divided into two groups. Under weak perturbation, convection‐SST feedback efficiently eliminates SST gradient and moisture anomaly. The large‐scale environment is homogenized within 2 days. Even though SST in the group with stronger perturbation undergoes a similar process, significant moist static energy (MSE) advection in the boundary produces enough moisture difference to introduce virtual temperature effect and aggregation is triggered. Once dry zone starts to expand, radiative and convective effects regenerate SST gradient, which intensifies circulation and accelerates the process. We further show that the evolution of aggregation or not is captured by the trend of MSE‐EIS (estimated inversion strength) variance. The results highlight the boundary layer processes on the formation of aggregated convection in the tropics.
Perioperative use of renin-angiotensin system inhibitors and outcomes in patients undergoing cardiac surgery
Authors: Ding Qian , Zhang Zugui , Liu Hong , Nie Huang , Berguson Mark , Goldhammer Jordan E. , Young Nilas , Boyd Douglas , Morris Rohinton , Sun Jianzhong
Published: September 2019

It remains disputable about perioperative use of renin-angiotensin system inhibitors (RASi) and their outcome effects. This multicenter retrospective cohort study examines association between use of perioperative RASi and outcomes in patients undergoing coronary artery bypass graft and/or valve surgery. After the exclusion, the patients are divided into 2 groups with or without preoperative RASi (PreRASi, n = 8581), or 2 groups with or without postoperative RASi (PostRASi, n = 8130). With using of propensity scores matching to reduce treatment selection bias, the study shows that PreRASi is associated with a significant reduction in postoperative 30-day mortality compared with without one (3.41% vs. 5.02%); PostRASi is associated with reduced long-term mortality rate compared with without one (6.62% vs. 7.70% at 2-year; 17.09% vs. 19.95% at 6-year). The results suggest that perioperative use of RASi has a significant benefit for the postoperative and long-term survival among patients undergoing cardiac surgery.
Giant valley splitting in monolayer WS2 by magnetic proximity effect
Authors: Norden Tenzin , Zhao Chuan , Zhang Peiyao , Sabirianov Renat , Petrou Athos , Zeng Hao
Published: September 2019

Lifting the valley degeneracy of monolayer transition metal dichalcogenides (TMDs) would allow versatile control of the valley degree of freedom. We report a giant valley exciton splitting of 16 meV/T for monolayer WS2, using the proximity effect from an EuS substrate, which is enhanced by nearly two orders of magnitude from that obtained by an external magnetic field. More interestingly, a sign reversal of the valley splitting is observed as compared to that of WSe2 on EuS. Using first principles calculations, we investigate the complex behavior of exchange interactions between TMDs and EuS. The sign reversal is attributed to competing ferromagnetic (FM) and antiferromagnetic (AFM) exchange interactions for Eu- and S- terminated EuS surface sites. They act differently on the conduction and valence bands of WS2 compared to WSe2. Tuning the sign and magnitude of the valley exciton splitting offers opportunities for control of valley pseudospin for quantum information processing.
Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer
Authors: Wilson Marcus D. , Renault Ludovic , Maskell Daniel P. , Ghoneim Mohamed , Pye Valerie E. , Nans Andrea , Rueda David S. , Cherepanov Peter , Costa Alessandro
Published: September 2019

Retroviral integrase can efficiently utilise nucleosomes for insertion of the reverse-transcribed viral DNA. In face of the structural constraints imposed by the nucleosomal structure, integrase gains access to the scissile phosphodiester bonds by lifting DNA off the histone octamer at the site of integration. To clarify the mechanism of DNA looping by integrase, we determined a 3.9 Å resolution structure of the prototype foamy virus intasome engaged with a nucleosome core particle. The structural data along with complementary single-molecule Förster resonance energy transfer measurements reveal twisting and sliding of the nucleosomal DNA arm proximal to the integration site. Sliding the nucleosomal DNA by approximately two base pairs along the histone octamer accommodates the necessary DNA lifting from the histone H2A-H2B subunits to allow engagement with the intasome. Thus, retroviral integration into nucleosomes involves the looping-and-sliding mechanism for nucleosomal DNA repositioning, bearing unexpected similarities to chromatin remodelers.
Lhcx proteins provide photoprotection via thermal dissipation of absorbed light in the diatom Phaeodactylum tricornutum
Authors: Buck Jochen M. , Sherman Jonathan , Bártulos Carolina Río , Serif Manuel , Halder Marc , Henkel Jan , Falciatore Angela , Lavaud Johann , Gorbunov Maxim Y. , Kroth Peter G. , Falkowski Paul G. , Lepetit Bernard
Published: September 2019

Diatoms possess an impressive capacity for rapidly inducible thermal dissipation of excess absorbed energy (qE), provided by the xanthophyll diatoxanthin and Lhcx proteins. By knocking out the Lhcx1 and Lhcx2 genes individually in Phaeodactylum tricornutum strain 4 and complementing the knockout lines with different Lhcx proteins, multiple mutants with varying qE capacities are obtained, ranging from zero to high values. We demonstrate that qE is entirely dependent on the concerted action of diatoxanthin and Lhcx proteins, with Lhcx1, Lhcx2 and Lhcx3 having similar functions. Moreover, we establish a clear link between Lhcx1/2/3 mediated inducible thermal energy dissipation and a reduction in the functional absorption cross-section of photosystem II. This regulation of the functional absorption cross-section can be tuned by altered Lhcx protein expression in response to environmental conditions. Our results provide a holistic understanding of the rapidly inducible thermal energy dissipation process and its mechanistic implications in diatoms.
Cell type-specific transcriptional programs in mouse prefrontal cortex during adolescence and addiction
Authors: Bhattacherjee Aritra , Djekidel Mohamed Nadhir , Chen Renchao , Chen Wenqiang , Tuesta Luis M. , Zhang Yi
Published: September 2019

Coordinated activity-induced transcriptional changes across multiple neuron subtypes of the prefrontal cortex (PFC) play a pivotal role in encoding and regulating major cognitive behaviors. Yet, the specific transcriptional programs in each neuron subtype remain unknown. Using single-cell RNA sequencing (scRNA-seq), here we comprehensively classify all unique cell subtypes in the PFC. We analyze transcriptional dynamics of each cell subtype under a naturally adaptive and an induced condition. Adaptive changes during adolescence (between P21 and P60), a highly dynamic phase of postnatal neuroplasticity, profoundly impacted transcription in each neuron subtype, including cell type-specific regulation of genes implicated in major neuropsychiatric disorders. On the other hand, an induced plasticity evoked by chronic cocaine addiction resulted in progressive transcriptional changes in multiple neuron subtypes and became most pronounced upon prolonged drug withdrawal. Our findings lay a foundation for understanding cell type-specific postnatal transcriptional dynamics under normal PFC function and in neuropsychiatric disease states.
Pre- and peri-implantation Zika virus infection impairs fetal development by targeting trophectoderm cells
Authors: Tan Lei , Lacko Lauretta A. , Zhou Ting , Tomoiaga Delia , Hurtado Romulo , Zhang Tuo , Sevilla Ana , Zhong Aaron , Mason Christopher E , Noggle Scott , Evans Todd , Stuhlmann Heidi , Schwartz Robert E. , Chen Shuibing
Published: September 2019

Zika virus (ZIKV) infection results in an increased risk of spontaneous abortion and poor intrauterine growth although the underlying mechanisms remain undetermined. Little is known about the impact of ZIKV infection during the earliest stages of pregnancy, at pre- and peri-implantation, because most current ZIKV pregnancy studies have focused on post-implantation stages. Here, we demonstrate that trophectoderm cells of pre-implantation human and mouse embryos can be infected with ZIKV, and propagate virus causing neural progenitor cell death. These findings are corroborated by the dose-dependent nature of ZIKV susceptibility of hESC-derived trophectoderm cells. Single blastocyst RNA-seq reveals key transcriptional changes upon ZIKV infection, including nervous system development, prior to commitment to the neural lineage. The pregnancy rate of mice is >50% lower in pre-implantation infection than infection at E4.5, demonstrating that pre-implantation ZIKV infection leads to miscarriage. Cumulatively, these data elucidate a previously unappreciated association of pre- and peri-implantation ZIKV infection and microcephaly.
Comparative fitness analysis of D-cycloserine resistant mutants reveals both fitness-neutral and high-fitness cost genotypes
Authors: Evangelopoulos Dimitrios , Prosser Gareth A. , Rodgers Angela , Dagg Belinda M. , Khatri Bhagwati , Ho Mei Mei , Gutierrez Maximiliano G. , Cortes Teresa , de Carvalho Luiz Pedro S.
Published: September 2019

Drug resistant infections represent one of the most challenging medical problems of our time. D-cycloserine is an antibiotic used for six decades without significant appearance and dissemination of antibiotic resistant strains, making it an ideal model compound to understand what drives resistance evasion. We therefore investigated why Mycobacterium tuberculosis fails to become resistant to D-cycloserine. To address this question, we employed a combination of bacterial genetics, genomics, biochemistry and fitness analysis in vitro, in macrophages and in mice. Altogether, our results suggest that the ultra-low rate of emergence of D-cycloserine resistance mutations is the dominant biological factor delaying the appearance of clinical resistance to this antibiotic. Furthermore, we also identified potential compensatory mechanisms able to minimize the severe fitness costs of primary D-cycloserine resistance conferring mutations.
Selective autophagy maintains centrosome integrity and accurate mitosis by turnover of centriolar satellites
Authors: Holdgaard Søs Grønbæk , Cianfanelli Valentina , Pupo Emanuela , Lambrughi Matteo , Lubas Michal , Nielsen Julie C. , Eibes Susana , Maiani Emiliano , Harder Lea M. , Wesch Nicole , Foged Mads Møller , Maeda Kenji , Nazio Francesca , de la Ballina Laura R. , Dötsch Volker , Brech Andreas , Frankel Lisa B. , Jäättelä Marja , Locatelli Franco , Barisic Marin , Andersen Jens S. , Bekker-Jensen Simon , Lund Anders H. , Rogov Vladimir V. , Papaleo Elena , Lanzetti Letizia , De Zio Daniela , Cecconi Francesco
Published: September 2019

The centrosome is the master orchestrator of mitotic spindle formation and chromosome segregation in animal cells. Centrosome abnormalities are frequently observed in cancer, but little is known of their origin and about pathways affecting centrosome homeostasis. Here we show that autophagy preserves centrosome organization and stability through selective turnover of centriolar satellite components, a process we termed doryphagy. Autophagy targets the satellite organizer PCM1 by interacting with GABARAPs via a C-terminal LIR motif. Accordingly, autophagy deficiency results in accumulation of large abnormal centriolar satellites and a resultant dysregulation of centrosome composition. These alterations have critical impact on centrosome stability and lead to mitotic centrosome fragmentation and unbalanced chromosome segregation. Our findings identify doryphagy as an important centrosome-regulating pathway and bring mechanistic insights to the link between autophagy dysfunction and chromosomal instability. In addition, we highlight the vital role of centriolar satellites in maintaining centrosome integrity.
Structure of the thermo-sensitive TRP channel TRP1 from the alga Chlamydomonas reinhardtii
Authors: McGoldrick Luke L. , Singh Appu K. , Demirkhanyan Lusine , Lin Ting-Yu , Casner Ryan G. , Zakharian Eleonora , Sobolevsky Alexander I.
Published: September 2019

Algae produce the largest amount of oxygen on earth and are invaluable for human nutrition and biomedicine, as well as for the chemical industry, energy production and agriculture. The mechanisms by which algae can detect and respond to changes in their environments can rely on membrane receptors, including TRP ion channels. Here we present a 3.5-Å resolution cryo-EM structure of the transient receptor potential (TRP) channel crTRP1 from the alga Chlamydomonas reinhardtii that opens in response to increased temperature and is positively regulated by the membrane lipid PIP2. The structure of crTRP1 significantly deviates from the structures of other TRP channels and has a unique 2-fold symmetrical rose-shape architecture with elbow domains and ankyrin repeat domains submerged and dipping into the membrane, respectively. Our study provides a structure of a TRP channel from a micro-organism and a structural framework for better understanding algae biology and TRP channel evolution.
UPF1/SMG7-dependent microRNA-mediated gene regulation
Authors: Park Jungyun , Seo Jwa-Won , Ahn Narae , Park Seokju , Hwang Jungwook , Nam Jin-Wu
Published: September 2019

The stability and quality of metazoan mRNAs are under microRNA (miRNA)-mediated and nonsense-mediated control. Although UPF1, a core mediator of nonsense-mediated mRNA decay (NMD), mediates the decay of target mRNA in a 3′UTR-length-dependent manner, the detailed mechanism remains unclear. Here, we suggest that 3′UTR-length-dependent mRNA decay is not mediated by nonsense mRNAs but rather by miRNAs that downregulate target mRNAs via Ago-associated UPF1/SMG7. Global analyses of mRNAs in response to UPF1 RNA interference in miRNA-deficient cells reveal that 3′UTR-length-dependent mRNA decay by UPF1 requires canonical miRNA targeting. The destabilization of miRNA targets is accomplished by the combination of Ago2 and UPF1/SMG7, which may recruit the CCR4-NOT deadenylase complex. Indeed, loss of the SMG7-deadenylase complex interaction increases the levels of transcripts regulated by UPF1-SMG7. This UPF1/SMG7-dependent miRNA-mediated mRNA decay pathway may enable miRNA targeting to become more predictable and expand the miRNA-mRNA regulatory network.
A highly dynamic F-actin network regulates transport and recycling of micronemes in Toxoplasma gondii vacuoles
Authors: Periz Javier , Del Rosario Mario , McStea Alexandra , Gras Simon , Loney Colin , Wang Lin , Martin-Fernandez Marisa L. , Meissner Markus
Published: September 2019

The obligate intracellular parasite Toxoplasma gondii replicates in an unusual process, described as internal budding. Multiple dausghter parasites are formed sequentially within a single mother cell, requiring replication and distribution of essential organelles such as micronemes. These organelles are thought to be formed de novo in the developing daughter cells. Using dual labelling of a microneme protein MIC2 and super-resolution microscopy, we show that micronemes are recycled from the mother to the forming daughter parasites using a highly dynamic F-actin network. While this recycling pathway is F-actin dependent, de novo synthesis of micronemes appears to be F-actin independent. The F-actin network connects individual parasites, supports long, multidirectional vesicular transport, and regulates transport, density and localisation of micronemal vesicles. The residual body acts as a storage and sorting station for these organelles. Our data describe an F-actin dependent mechanism in apicomplexans for transport and recycling of maternal organelles during intracellular development.
Materials tactile logic via innervated soft thermochromic elastomers
Authors: Jin Yang , Lin Yiliang , Kiani Abolfazl , Joshipura Ishan D. , Ge Mingqiao , Dickey Michael D.
Published: September 2019

Conventional machines rely on rigid, centralized electronic components to make decisions, which limits complexity and scaling. Here, we show that decision making can be realized on the material-level without relying on semiconductor-based logic. Inspired by the distributed decision making that exists in the arms of an octopus, we present a completely soft, stretchable silicone composite doped with thermochromic pigments and innervated with liquid metal. The ability to deform the liquid metal couples geometric changes to Joule heating, thus enabling tunable thermo-mechanochromic sensing of touch and strain. In more complex circuits, deformation of the metal can redistribute electrical energy to distal portions of the network in a way that converts analog tactile ‘inputs’ into digital colorimetric ‘outputs’. Using the material itself as the active player in the decision making process offers possibilities for creating entirely soft devices that respond locally to environmental interactions or act as embedded sensors for feedback loops.
The paleoclimatic footprint in the soil carbon stock of the Tibetan permafrost region
Authors: Ding Jinzhi , Wang Tao , Piao Shilong , Smith Pete , Zhang Ganlin , Yan Zhengjie , Ren Shuai , Liu Dan , Wang Shiping , Chen Shengyun , Dai Fuqiang , He Jinsheng , Li Yingnian , Liu Yongwen , Mao Jiafu , Arain Altaf , Tian Hanqin , Shi Xiaoying , Yang Yuanhe , Zeng Ning , Zhao Lin
Published: September 2019

Tibetan permafrost largely formed during the late Pleistocene glacial period and shrank in the Holocene Thermal Maximum period. Quantifying the impacts of paleoclimatic extremes on soil carbon stock can shed light on the vulnerability of permafrost carbon in the future. Here, we synthesize data from 1114 sites across the Tibetan permafrost region to report that paleoclimate is more important than modern climate in shaping current permafrost carbon distribution, and its importance increases with soil depth, mainly through forming the soilʼs physiochemical properties. We derive a new estimate of modern soil carbon stock to 3 m depth by including the paleoclimate effects, and find that the stock ($${\mathrm{36}}{\mathrm{.6}}_{{\mathrm{ - 2}}{\mathrm{.4}}}^{{\mathrm{ + 2}}.3}$$
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PgC) is triple that predicted by ecosystem models (11.5 ± 4.2 s.e.m PgC), which use pre-industrial climate to initialize the soil carbon pool. The discrepancy highlights the urgent need to incorporate paleoclimate information into model initialization for simulating permafrost soil carbon stocks.
Histone deacetylase 11 inhibition promotes breast cancer metastasis from lymph nodes
Authors: Leslie Patrick L. , Chao Yvonne L. , Tsai Yi-Hsuan , Ghosh Subrata K. , Porrello Alessandro , Van Swearingen Amanda E. D. , Harrison Emily B. , Cooley Brian C. , Parker Joel S. , Carey Lisa A. , Pecot Chad V.
Published: September 2019

Lymph node (LN) metastases correspond with a worse prognosis in nearly all cancers, yet the occurrence of cancer spreading from LNs remains controversial. Additionally, the mechanisms explaining how cancers survive and exit LNs are largely unknown. Here, we show that breast cancer patients frequently have LN metastases that closely resemble distant metastases. In addition, using a microsurgical model, we show how LN metastasis development and dissemination is regulated by the expression of a chromatin modifier, histone deacetylase 11 (HDAC11). Genetic and pharmacologic blockade of HDAC11 decreases LN tumor growth, yet substantially increases migration and distant metastasis formation. Collectively, we reveal a mechanism explaining how HDAC11 plasticity promotes breast cancer growth as well as dissemination from LNs and suggest caution with the use of HDAC inhibitors.
Publisher Correction: Shape and fluctuations of frustrated self-assembled nano ribbons
Authors: Zhang Mingming , Grossman Doron , Danino Dganit , Sharon Eran
Published: September 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Label-free assessment of pre-implantation embryo quality by the Fluorescence Lifetime Imaging Microscopy (FLIM)-phasor approach
Authors: Ma Ning , Mochel Nabora Reyes de , Pham Paula Duyen , Yoo Tae Yeon , Cho Ken W. Y. , Digman Michelle A.
Published: September 2019

Development of quantitative, safe and rapid techniques for assessing embryo quality provides significant advances in Assisted Reproductive Technologies (ART). Instead of assessing the embryo quality by the standard morphologic evaluation, we apply the phasor-FLIM (Fluorescence Lifetime Imaging Microscopy) method to capture endogenous fluorescent biomarkers of pre-implantation embryos as a non-morphological caliber for embryo quality. Here, we identify, under hypoxic and non-hypoxic conditions, the unique spectroscopic trajectories at different stages of mouse pre-implantation development, which is referred to as the developmental, or “D-trajectory”, that consists of fluorescence lifetime from different stages of mouse pre-implantation embryos. The D-trajectory correlates with intrinsic fluorescent species from a distinctive energy metabolism and oxidized lipids, as seen with Third Harmonic Generation (THG) that changes over time. In addition, we have defined a non-morphological Embryo Viability Index (EVI) to distinguish pre-implantation embryo quality using the Distance Analysis (DA), a machine learning algorithm to process the fluorescence lifetime distribution patterns. We show, under our experimental conditions, that the phasor-FLIM approach provides a much-needed non-invasive quantitative technology for identifying healthy embryos at the early compaction stage with 86% accuracy. The DA and phasor-FLIM method may provide the opportunity to improve implantation success rates forin vitrofertilization clinics.
Spatial and Temporal Variability of Ambient Underwater Sound in the Baltic Sea
Authors: Mustonen Mirko , Klauson Aleksander , Andersson Mathias , Clorennec Dominique , Folegot Thomas , Koza Radomił , Pajala Jukka , Persson Leif , Tegowski Jarosław , Tougaard Jakob , Wahlberg Magnus , Sigray Peter
Published: September 2019

During last decades, anthropogenic underwater sound and its chronic impact on marine species have been recognised as an environmental protection challenge. At the same time, studies on the spatial and temporal variability of ambient sound, and how it is affected by biotic, abiotic and anthropogenic factors are lacking. This paper presents analysis of a large-scale and long-term underwater sound monitoring in the Baltic Sea. Throughout the year 2014, sound was monitored in 36 Baltic Sea locations. Selected locations covered different natural conditions and ship traffic intensities. The 63 Hz, 125 Hz and 2 kHz one-third octave band sound pressure levels were calculated and analysed. The levels varied significantly from one monitoring location to another. The annual median sound pressure level of the quietest and the loudest location differed almost 50 dB in the 63 Hz one-third octave band. Largest difference in the monthly medians was 15 dB in 63 Hz one-third octave band. The same monitoring locations annual estimated probability density functions for two yearly periods show strong similarity. The data variability grows as the averaging time period is reduced. Maritime traffic elevates the ambient sound levels in many areas of the Baltic Sea during extensive time periods.
Artificial neural network analysis of the oxygen saturation signal enables accurate diagnostics of sleep apnea
Authors: Nikkonen Sami , Afara Isaac O. , Leppänen Timo , Töyräs Juha
Published: September 2019

The severity of obstructive sleep apnea (OSA) is classified using apnea-hypopnea index (AHI). Accurate determination of AHI currently requires manual analysis and complicated registration setup making it expensive and labor intensive. Partially for these reasons, OSA is a heavily underdiagnosed disease as only 7% of women and 18% of men suffering from OSA have diagnosis. To resolve these issues, we introduce an artificial neural network (ANN) that estimates AHI and oxygen desaturation index (ODI) using only the blood oxygen saturation signal (SpO2), recorded during ambulatory polygraphy, as an input. Therefore, hypopneas associated only with an arousal were not considered in this study. SpO2 signals from 1692 patients were used for training and 99 for validation. Two test sets were used consisting of 198 and 1959 patients. In the primary test set, the median absolute errors of ANN estimated AHI and ODI were 0.78 events/hour and 0.68 events/hour respectively. Based on the ANN estimated AHI and ODI, 90.9% and 94.4% of the test patients were classified into the correct OSA severity category. In conclusion, AHI and ODI can be reliably determined using neural network analysis of SpO2 signal. The developed method may enable a more affordable screening of OSA.