bluuebunny/crossref_metadata_2025 huggingface dataset:
Construction with digital twin information systems
Authors: Sacks Rafael , Brilakis Ioannis , Pikas Ergo , Xie Haiyan Sally , Girolami Mark
Published: November 2020

The concept of a “digital twin” as a model for data-driven management and control of physical systems has emerged over the past decade in the domains of manufacturing, production, and operations. In the context of buildings and civil infrastructure, the notion of a digital twin remains ill-defined, with little or no consensus among researchers and practitioners of the ways in which digital twin processes and data-centric technologies can support design and construction. This paper builds on existing concepts of Building Information Modeling (BIM), lean project production systems, automated data acquisition from construction sites and supply chains, and artificial intelligence to formulate a mode of construction that applies digital twin information systems to achieve closed loop control systems. It contributes a set of four core information and control concepts for digital twin construction (DTC), which define the dimensions of the conceptual space for the information used in DTC workflows. Working from the core concepts, we propose a DTC information system workflow—including information stores, information processing functions, and monitoring technologies—according to three concentric control workflow cycles. DTC should be viewed as a comprehensive mode of construction that prioritizes closing the control loops rather than an extension of BIM tools integrated with sensing and monitoring technologies.
THE REVOLUTIONARY AIMS OF IRELAND'S FORGOTTEN DIPLOMATS, 1919–1922
Authors: O'BRIEN ANN MARIE
Published: November 2020

In the last twenty years, the involvement of women's organizations in the campaign for Irish independence has featured prominently in publications and public discourse. But this article asks, did women serve the cause for independence in other ways? This article focuses on the careers of Irish women who worked for the Irish Department of Foreign Affairs in the period 1919–22, pressing Ireland's case for autonomy from British rule. The work of these early women abroad has been largely ignored by historians who have concentrated on the diplomatic activities of men in this period. This article first argues that these women who worked towards achieving independence for Ireland through the use of diplomacy and propaganda merit attention, but secondly they can be considered providing further insights into how women's work for the cause of Irish freedom did not warrant them a place in the diplomatic service in the new Irish Free State.
Orange juice industry by-product silage can increase fat and protein in Holstein cow's milk
Authors: Ítavo Luís Carlos Vinhas , Kozerski Noemila Débora , Ítavo Camila Celeste Brandão Ferreira , Dias Alexandre Menezes , Petit Hélène Veronique , Benchaar Chaouki , Voltolini Tadeu Vinhas , Jobim Cloves Cabreira , dos Santos Geraldo Tadeu
Published: November 2020

We aimed to evaluate the effect of replacing corn silage by orange peel silage on nutrient intake, ruminal parameters and milk production of multiparous lactating Holstein cows. Eight fistulated Holstein cows averaging 587.5 ± 39.6 kg and 111 ± 22 d in milking were randomly assigned to a double 4 × 4 Latin square design carried out two times to determine the effects of feeding with orange peel silage (OPS) in substitution of whole plant corn silage (WPCS). The treatments were a control diet with WPCS only or diets with OPS replacing WPCS in the total mixed diet (250, 500, or 750 g/kg DM). All cows were fed the same 750 : 250 g/kg roughage : concentrate ratio. The DM intake and milk production were reduced with the OPS inclusion, with decreases in consumption of neutral detergent fibre and increased consumption of non-fibrous carbohydrates. Diets with 250 and 500 g/kg OPS showed similar milk production and protein content in milk to the standard WCPS diet, whilst 750 g/kg orange peel silage as roughage increased fat and protein contents significantly. The orange peel silage as a substitute for corn silage for feeding dairy cows did not show adverse changes in the rumen environment and showed promising results in the increase of fat in milk of Holstein cows.
The standing stock and CaCO3 contribution of Halimeda macroloba in the tropical seagrass-dominated ecosystem in Dongsha Island, the main island of Dongsha Atoll, South China Sea
Authors: Mayakun Jaruwan , Liao Chen-Pan , Liu Shao-Lun
Published: November 2020

Calcareous green alga in the genus Halimeda are important contributors to the marine carbonate budget. Dongsha Island is located in the northernmost South China Sea and is a seagrass-dominated ecosystem with intermixed Halimeda macroloba patches, making it an excellent system to better examine the extent of carbonate contribution by H. macroloba in such an ecosystem. To this end, we examined the standing stock and actual CaCO3 contribution of H. macroloba in the seagrass-dominated ecosystem (herein Dongsha Island) and compared them with those in Halimeda-dominated ecosystems. The density, growth rate, calcification rate and CaCO3 content of H. macroloba at four life stages were investigated. The mean density of H. macroloba was around 8.82 ± 1.57 thalli m−2 and the estimated standing stock was 61,740 to 72,730 thalli. Thalli produced 1 to 2 new segments day−1, giving a growth rate of 0.003 ± 0.001 g dry weight thallus−1 day−1. Calculated algal biomass and annual areal production were 0.03 g m−2 and 9.66 g m−2 year−1. In each square metre of this area, H. macroloba produced 8.82 to 17.64 new segments day−1, accumulating 0.002 ± 0.001 g CaCO3 thallus−1 day−1 or around 6.44 g CaCO3 m−2 year−1. Mean CaCO3 content was 0.32 ± 0.05 g thallus−1. As expected, the growth rate and CaCO3 production of H. macroloba in Dongsha Island were lower than in other studies from Halimeda tropical ecosystems. Overall, this work provides the baseline of carbonate production of H. macroloba in Dongsha Island and relevant systems where the ecosystem is dominated by seagrasses.
Provisioning thePosho: Labor Migration and Working-Class Food Systems on the Early-Colonial Kenyan Coast
Authors: Smart Devin
Published: November 2020

Engaging questions about social reproduction, migrant labor, and food provisioning, this article examines the emergence of a working-class food system on the coast of Kenya during the early decades of the twentieth century. Like elsewhere in Africa, labor migrants in Kenya's port city of Mombasa and on nearby plantations were provisioned with food rations, which were part of what Patrick Harries calls a “racial paternalism” that structured many labor relations during the colonial period. The article starts in rural Kenya, but then follows labor migrants to their places of employment to examine the formation of this new food system. In upcountry rural societies, women had primarily produced and then exclusively prepared their communities’ food. However, as migrants, men received a ration (posho) of maize meal or rice as part of their pay, used their cash wages to purchase foodstuffs from nearby markets, and some plantation workers were also able to grow their own vegetables on plots allocated by their employers. After acquiring their food through these wage-labor relations, men then had to cook their meals themselves. In addition the cuisine created by labor migration was one of extreme monotony compared to what these migrants ate in their rural communities, but I also show how food became a point of conflict between management and labor. The article demonstrates how workers successfully pressured their employers to improve the quantity and quality of their rations from the 1910s to the 1920s, while also raising their wages that allowed them to purchase better food. I additionally argue that during this period an “urban” or “rural” context did not fundamentally define how migrant workers acquired their food, as those laboring in both city and countryside received these rations. However, the article concludes by examining how after 1930, economic transformations changed Mombasa's food system so that workers became almost entirely reliant on cash and credit as the way they acquired their daily meals, while paternalism continued to infuse the food systems of rural migrant laborers. In sum, this article is a local study of coastal Kenya that is also concerned with global questions about how food provisioning fits into the social reproduction of working classes in industrial and colonial capitalism.
The Caledon Lockout: Revolution and Counter-Revolution in Rural Ulster, 1918–1922
Authors: Mac Bhloscaidh Fearghal
Published: November 2020

This paper examines an unsuccessful strike by Irish Catholic and Protestant workers at a woolen mill in 1919. The location, Caledon in County Tyrone, is renowned as a stronghold of Ulster Unionism and Orangeism, yet in the context of the revolutionary period in Ireland from 1916–1926, traditional sectarian divisions briefly abated in the face of working-class solidarity. In this respect, the analysis offers something of a corrective to assumptions regarding the immutability of sectarian divisions in Ulster. The article also places Caledon within the context of a widespread and sustained movement of unskilled workers in the main provincial city, Belfast, and across much of rural Ulster between 1918–1920. Nevertheless, the manner in which the employer defeated the strike and the village's subsequent history of violent sectarianism offers valuable insights into the creation and consolidation of Northern Ireland, or what many local Catholics called “the Orange State,” which celebrates its centenary in 2020.
Representing the Worker in Postsocialist Public Space: Art and Politics under Neoliberalism
Authors: Isto Raino
Published: November 2020

Across former Eastern Europe, the transition from state socialism toward neoliberal capitalism has been accompanied by a marked reduction in emphasis on working-class identities. Because of the centrality of class to socialist-era identity-construction projects, the recent and relatively sudden ascendancy of various forms of individualist, consumption-oriented subjectivity in postrevolutionary societies has produced conflicts that are often more visible than in societies where capitalism has been the accepted economic paradigm for much longer. This shift can be seen in the realm of art and visual culture: Images of the worker once dominated public spaces under state socialism, competing in number with representations of leaders and communist ideologues, but since 1989 they have often been vandalized, dismantled, or else relocated to decay in relative obscurity. Where new public images of the worker do appear in postsocialist neoliberal conditions, they frequently serve as nexuses of controversy, where generational and ideological conflicts regarding current labor conditions and the legacy of worker solidarity play out. The debates surrounding representations of workers in postsocialism are both part of a global history of postsocialist art and part of the history of labor and its relation to contemporary urban space. This article examines artistic representations of the worker sited in public space in postsocialist Albania, in order to map the political and artistic discourses that animate engagements with working-class identity in conditions of neoliberal social transformation.
Working-class and Memory Policy in Post-Industrial Cities: Łódź, Poland, and Tampere, Finland, Compared
Authors: Rek-Woźniak Magdalena , Woźniak Wojciech
Published: November 2020

Łódź and Tampere share an industrial and political past. Part of the Russian empire, the cities became major textile hubs crucial for Tsarist industrial economy.1 The cities were also Red strongholds. Historically, they can be seen as socio-economic “experiments” and “islands of modernization” within largely rural societies. Since the 1980s (in case of Tampere) and the 1990s (in case of Łódź) both cities have undergone substantial social and economic transformations connected with the collapse or decline of traditional industries. How do the two cities choose to represent their working-class heritage today? This essay compares how city museums in Tampere and Łódź represent their working-class history in selective and contradictory ways.
The expansinEXP1gene in the elongation zone is induced during soybean embryonic axis germination and differentially expressed in response to ABA and PEG treatments
Authors: Montechiarini Nidia H. , Delgado Luciana , Morandi Eligio N. , Carrillo Néstor J. , Gosparini Carlos O.
Published: November 2020

During soybean seed germination, the expansive growth potential of the embryonic axes is driven by water uptake while cell wall loosening occurs in cells from the elongation zone (EZ). Expansins are regarded as primary promoters of cell wall remodelling in all plant expansion processes, with the expression profiles of the soybean expansins supporting their cell or tissue specificity. Therefore, we used embryonic axes isolated from whole seed and focused on the EZ to study seed germination. Using a suite of degenerate primers, we amplified an abundantly expressed expansin gene at the EZ during soybean embryonic axis germination, which was identified asEXP1byin silicoanalyses. Expression studies showed thatEXP1was induced under germination conditions in distilled water and down-regulated by abscisic acid (ABA), which inhibits soybean germination by physiologically restraining expansion. Moreover, we also identified a time window of ABA responsiveness within the first 6 h of incubation in water, after which ABA lost control of bothEXP1expression and embryonic axis germination, thus confirming the early role ofEXP1in the EZ during this process. By contrast,EXP1levels in the EZ increased even when germination was impaired by osmotically limiting the water availability required to develop the embryonic axes’ growth potential. We propose that these higherEXP1levels are involved in the fast germination of soybean embryonic axes as soon as water availability is re-established. Taken together, our results show strongEXP1expression in the EZ and postulateEXP1as a target candidate for soybean seed germination control.
A compact polarization reconfigurable stacked microstrip antenna for WiMAX application
Authors: Shaw Murari , Mandal Niranjan , Gangopadhyay Malay
Published: November 2020

In this paper, a stacked microstrip patch antenna with polarization reconfigurable property has been proposed for worldwide interoperability for microwave access (WiMAX) application. The proposed antenna has two substrate layers: upper and lower layers with two radiating patches connected with the coaxial probe. Without the upper layer the lower square-shaped substrate layer having regular hexagonal radiating patch with probe fed acts as a linear polarized antenna with impedance bandwidth for (S11 ≤ −10 dB) is 370 MHz 10.56% (3.32–3.69 GHz) cover WiMAX (3.4–3.69 GHz) application band. The hexagonal radiating patch is perturbed with an optimum rectangular slot to enhance the impedance bandwidth of the antenna. The lower substrate layer having hexagonal patch with the same probe position is stacked with the upper square-shaped substrate layer with same sized square patch and the upper patch soldered with the coaxial probe. The overall stacked antenna generates a circularly polarized band when the opposite corner of the top square radiating patch of the upper layer is truncated with optimum size. In order to generate another circularly polarized band and to improve the input impedance matching of the stacked antenna, the top radiating patch is perturbed with two slots and a slit. The stacked circularly polarized antenna generates impedance bandwidth of 12.75% (3.23–3.67 GHz) for (S11 ≤ −10 dB) with two circularly polarized bands (3.34–3.37 GHz) and (3.66–3.70 GHz) as per (axial ratio ≤ 3 dB) for WiMAX application. Therefore, the proposed antenna can be used as linearly polarized or dual band circularly polarized according to requirement.
Rattail fescue (Vulpia myuros) interference and seed production as affected by sowing time and crop density in winter wheat
Authors: Akhter Muhammad Javaid , Kudsk Per , Mathiassen Solvejg Kopp , Melander Bo
Published: November 2020

Field experiments were conducted in the growing seasons of 2017 to 2018 and 2018 to 2019 to evaluate the competitive effects of rattail fescue [Vulpia myuros (L.) C.C. Gmel.] in winter wheat (Triticum aestivum L.) and to assess whether delayed crop sowing and increased crop density influence the emergence, competitiveness, and fecundity of V. myuros. Cumulative emergence showed the potential of V. myuros to emerge rapidly and under a wide range of climatic conditions with no effect of crop density and variable effects of sowing time between the two experiments. Grain yield and yield components were negatively affected by increasing V. myuros density. The relationship between grain yield and V. myuros density was not influenced by sowing time or by crop density, but crop–weed competition was strongly influenced by growing conditions. Due to very different weather conditions, grain yield reductions were lower in the growing season of 2017 to 2018 than in 2018 to 2019, with maximum grain yield losses of 22% and 50% in the two growing seasons, respectively. The yield components, number of crop ears per square meter, and 1,000-kernel weight were affected almost equally, reflecting that V. myuros’s competition with winter wheat occurred both early and late in the growing season. Seed production of V. myuros was suppressed by delaying sowing and increasing crop density. The impacts of delayed sowing and increasing crop density on seed production of V. myuros highlight the potential of these cultural weed control tactics in the long-term management programs of this species.
Fluid Circulation Along an Oceanic Detachment Fault: Insights From Fluid Inclusions in Silicified Brecciated Fault Rocks (Mid‐Atlantic Ridge at 13°20′N)
Authors: Verlaguet A. , Bonnemains D. , Mével C. , Escartín J. , Andreani M. , Bourdelle F. , Boiron M‐C. , Chavagnac V.
Published: November 2020

The MAR 13°20′N corrugated detachment fault is composed of pervasively silicified mafic cataclastic breccias, instead of ultramafics and gabbros commonly found at other detachments. These breccias record overplating of hangingwall diabases, with syntectonic silicification due to important influx of silica‐iron‐rich fluids, able to leach alkalis and calcium. Fluids trapped in quartz inclusions show important salinity variations (2.1–10 wt.% NaCl eq.) indicating supercritical phase separation. Fluid inclusions also contain minor amounts of H2 ± CO2 ± CH4 ± H2S, with high H2/CO2 and H2/H2S ratios, signatures typical of ultramafic‐hosted vent fluids. We propose that seawater infiltrated the hangingwall upper crust at the axis adjacent to the active detachment, reaching a reaction zone at the dyke complex base (∼2 km). At >500°C, fluids become Si‐rich during diabase alteration (amphibolite‐facies alteration in clasts), and undergo phase separation. Brines, preferentially released in the nearby detachment fault during diabase brecciation, mix with serpentinite‐derived fluids bearing H2 and CH4. Cooling during detachment deformation and fluid upward migration triggers silica precipitation at greenschist‐facies conditions (quartz + Fe‐rich‐chlorite ± pyrite). Important variations in fluid inclusion salinity and gas composition at both sample and grain scales record heterogeneous fluid circulation at small spatial and short temporal scales. This heterogeneous fluid circulation operating at <2 km depth, extending both along‐axis and over time, is inconsistent with models of fluids channeled along detachments from heat sources at the base of the crust at the fault root. Present‐day venting at detachment footwall, including Irinovskoe, is instead likely underlain by fluid circulation within the footwall, with outflow crossing the inactive detachment fault near‐surface.
On the Unsteady Steepening of Short Gravity Waves Near the Crests of Longer Waves in the Absence of Generation or Dissipation
Authors: Peureux Charles , Ardhuin Fabrice , Guimarães Pedro Veras
Published: November 2020

The wave action equation provides a general framework that has been applied to the conservative hydrodynamic interactions between short and long surface waves. So far, only a limited range of solutions have been investigated. Here, we show that the wave action equation predicts that groups of short waves propagating over long monochromatic waves are unstable. We demonstrate theoretically and numerically, a new ratchet‐type instability that progressively condenses short wave action around the long wave crests due to the correlation of phase speed and action fluctuations. This instability is of particular interest because it may lead to a higher probability of breaking for short waves propagating in directions within ±35 degrees of the dominant waves direction. This preferred breaking could has a strong impact on cross‐ and down‐wind slope statistics and thus air‐sea exchanges and remote sensing.
Partitioning of Crystalline and Amorphous Phases During Freezing of Simulated Enceladus Ocean Fluids
Authors: Fox‐Powell Mark G. , Cousins Claire R.
Published: November 2020

Saturn's ice‐covered moon Enceladus may contain the requisite conditions for life. Its potentially habitable subsurface ocean is vented into space as large cryovolcanic plumes that can be sampled by spacecraft, acting as a window to the ocean below. However, little is known about how Enceladus’ ocean fluids evolve as they freeze. Using cryo‐imaging techniques, we investigated solid phases produced by freezing simulated Enceladean ocean fluids at endmember cooling rates. Our results show that under flash‐freezing conditions (>10 K s−1), Enceladus‐relevant fluids undergo segregation, whereby the precipitation of ice templates the formation of brine vein networks. The high solute concentrations and confined nature of these brine veins means that salt crystallization is kinetically inhibited and glass formation (vitrification) can occur at lower cooling rates than typically required for vitrification of a bulk solution. Crystalline salts also form if flash‐frozen fluids are re‐warmed. The 10 µm‐scale distribution of salt phases produced by this mechanism differs markedly from that of gradually cooled (∼1 K min−1) fluids, showing that they inherit a textural signature of their formation conditions. The mineralogy of cryogenic carbonates can be used as a probe for cooling rate and parent fluid pH. Our findings reveal possible endmember routes for solid phase production from Enceladus’ ocean fluids and mechanisms for generating compositional heterogeneity within ice particles on a sub‐10 µm scale. This has implications for understanding how Enceladus' ocean constituents are incorporated into icy particles and delivered to space.
Emission of Greenhouse Gases From Water Tracks Draining Arctic Hillslopes
Authors: Harms Tamara K. , Rocher‐Ros Gerard , Godsey Sarah E.
Published: November 2020

Experimental and ambient warming of Arctic tundra results in emissions of greenhouse gases to the atmosphere, contributing to a positive feedback to climate warming. Estimates of gas emissions from lakes and terrestrial tundra confirm the significance of aquatic fluxes in greenhouse gas budgets, whereas few estimates describe emissions from fluvial networks. We measured dissolved gas concentrations and estimated emissions of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) from water tracks, vegetated depressions that hydrologically connect hillslope soils to lakes and streams. Concentrations of trace gases generally increased as ground thaw deepened through the growing season, indicating active production of greenhouse gases in thawed soils. Wet antecedent conditions were correlated with a decline in CO2 and CH4 concentrations. Dissolved N2O in excess of atmospheric equilibrium occurred in drier water tracks, but on average water tracks took up N2O from the atmosphere at low rates. Estimated CO2 emission rates for water tracks were among the highest observed for Arctic aquatic ecosystems, whereas CH4 emissions were of similar magnitude to streams. Despite occupying less than 1% of total catchment area, surface waters within water tracks were an estimated source of up to 53–85% of total CH4 emissions from their catchments and offset the terrestrial C sink by 5–9% during the growing season. Water tracks are abundant features of tundra landscapes that contain warmer soils and incur deeper thaw than adjacent terrestrial ecosystems and as such might contribute to ongoing and accelerating release of greenhouse gases from permafrost soils to the atmosphere.
Bioinformatics identification and pharmacological validation of Kcnn3/KCa2 channels as a mediator of negative affective behaviors and excessive alcohol drinking in mice
Authors: Padula Audrey E. , Rinker Jennifer A. , Lopez Marcelo F. , Mulligan Megan K. , Williams Robert W. , Becker Howard C. , Mulholland Patrick J.
Published: November 2020

Mood disorders are often comorbid with alcohol use disorder (AUD) and play a considerable role in the development and maintenance of alcohol dependence and relapse. Because of this high comorbidity, it is necessary to determine shared and unique genetic factors driving heavy drinking and negative affective behaviors. In order to identify novel pharmacogenetic targets, a bioinformatics analysis was used to quantify the expression of amygdala K+ channel genes that covary with anxiety-related phenotypes in the well-phenotyped and fully sequenced family of BXD strains. We used a model of stress-induced escalation of drinking in alcohol-dependent mice to measure negative affective behaviors during abstinence. A pharmacological approach was used to validate the key bioinformatics findings in alcohol-dependent, stressed mice. Amygdalar expression of Kcnn3 correlated significantly with 40 anxiety-associated phenotypes. Further examination of Kcnn3 expression revealed a strong eigentrait for anxiety-like behaviors and negative correlations with binge-like and voluntary alcohol drinking. Mice treated with chronic intermittent alcohol exposure and repeated swim stress consumed more alcohol in their home cages and showed hypophagia on the novelty-suppressed feeding test during abstinence. Pharmacologically targeting Kcnn gene products with the KCa2 (SK) channel-positive modulator 1-EBIO decreased drinking and reduced feeding latency in alcohol-dependent, stressed mice. Collectively, these validation studies provide central nervous system links into the covariance of stress, negative affective behaviors, and AUD in the BXD strains. Further, the bioinformatics discovery tool is effective in identifying promising targets (i.e., KCa2 channels) for treating alcohol dependence exacerbated by comorbid mood disorders.
Pharmacological blockage of transforming growth factor-β signalling by a Traf2- and Nck-interacting kinase inhibitor, NCB-0846
Authors: Sugano Teppei , Masuda Mari , Takeshita Fumitaka , Motoi Noriko , Hirozane Toru , Goto Naoko , Kashimoto Shigeki , Uno Yuko , Moriyama Hideki , Sawa Masaaki , Nagakawa Yuichi , Tsuchida Akihiko , Seike Masahiro , Gemma Akihiko , Yamada Tesshi
Published: November 2020

Background

Metastasis is the primary cause of death in cancer patients, and its management is still a major challenge. Epithelial to mesenchymal transition (EMT) has been implicated in the process of cancer metastasis, and its pharmacological interference holds therapeutic promise.

Methods

Traf2- and Nck-interacting kinase (TNIK) functions as a transcriptional coregulator of Wnt target genes. Given the convergence of Wnt and transforming growth factor-β (TGFβ) signalling, we examined the effects of a small-molecule TNIK inhibitor (named NCB-0846) on the TGFβ1-induced EMT of lung cancer cells.

Results

NCB-0846 inhibited the TGFβ1-induced EMT of A549 cells. This inhibition was associated with inhibition of Sma- and Mad-Related Protein-2/3 (SMAD2/3) phosphorylation and nuclear translocation. NCB-0846 abolished the lung metastasis of TGFβ1-treated A549 cells injected into the tail veins of immunodeficient mice. The inhibition of EMT was mediated by suppression of the TGFβ receptor type-I (TGFBR1) gene, at least partly through the induction of microRNAs targeting the TGFBR1 transcript [miR-320 (a, b and d) and miR-186].

Conclusions

NCB-0846 pharmacologically blocks the TGFβ/SMAD signalling and EMT induction of lung cancer cells by transcriptionally downregulating TGFBRI expression, representing a potentially promising approach for prevention of metastasis in lung cancer patients.
A Cas-embedding strategy for minimizing off-target effects of DNA base editors
Authors: Liu Yajing , Zhou Changyang , Huang Shisheng , Dang Lu , Wei Yu , He Jun , Zhou Yingsi , Mao Shaoshuai , Tao Wanyu , Zhang Yu , Yang Hui , Huang Xingxu , Chi Tian
Published: November 2020

DNA base editors, typically comprising editing enzymes fused to the N-terminus of nCas9, display off-target effects on DNA and/or RNA, which have remained an obstacle to their clinical applications. Off-target edits are typically countered via rationally designed point mutations, but the approach is tedious and not always effective. Here, we report that the off-target effects of both A > G and C > T editors can be dramatically reduced without compromising the on-target editing simply by inserting the editing enzymes into the middle of nCas9 at tolerant sites identified using a transposon-based genetic screen. Furthermore, employing this Cas-embedding strategy, we have created a highly specific editor capable of efficient C > T editing at methylated and GC-rich sequences.
The structural basis of promiscuity in small multidrug resistance transporters
Authors: Kermani Ali A. , Macdonald Christian B. , Burata Olive E. , Ben Koff B. , Koide Akiko , Denbaum Eric , Koide Shohei , Stockbridge Randy B.
Published: November 2020

By providing broad resistance to environmental biocides, transporters from the small multidrug resistance (SMR) family drive the spread of multidrug resistance cassettes among bacterial populations. A fundamental understanding of substrate selectivity by SMR transporters is needed to identify the types of selective pressures that contribute to this process. Using solid-supported membrane electrophysiology, we find that promiscuous transport of hydrophobic substituted cations is a general feature of SMR transporters. To understand the molecular basis for promiscuity, we solved X-ray crystal structures of a SMR transporter Gdx-Clo in complex with substrates to a maximum resolution of 2.3 Å. These structures confirm the family’s extremely rare dual topology architecture and reveal a cleft between two helices that provides accommodation in the membrane for the hydrophobic substituents of transported drug-like cations.
Hypocretinergic interactions with the serotonergic system regulate REM sleep and cataplexy
Authors: Seifinejad Ali , Li Sha , Possovre Marie-Laure , Vassalli Anne , Tafti Mehdi
Published: November 2020

Loss of muscle tone triggered by emotions is called cataplexy and is the pathognomonic symptom of narcolepsy, which is caused by hypocretin deficiency. Cataplexy is classically considered to be an abnormal manifestation of REM sleep and is treated by selective serotonin (5HT) reuptake inhibitors. Here we show that deleting the 5HT transporter in hypocretin knockout mice suppressed cataplexy while dramatically increasing REM sleep. Additionally, double knockout mice showed a significant deficit in the buildup of sleep need. Deleting one allele of the 5HT transporter in hypocretin knockout mice strongly increased EEG theta power during REM sleep and theta and gamma powers during wakefulness. Deleting hypocretin receptors in the dorsal raphe neurons of adult mice did not induce cataplexy but consolidated REM sleep. Our results indicate that cataplexy and REM sleep are regulated by different mechanisms and both states and sleep need are regulated by the hypocretinergic input into 5HT neurons.
Quantification of purified endogenous miRNAs with high sensitivity and specificity
Authors: Shin Soochul , Jung Yoonseok , Uhm Heesoo , Song Minseok , Son Soomin , Goo Jiyoung , Jeong Cherlhyun , Song Ji-Joon , Kim V. Narry , Hohng Sungchul
Published: November 2020

MicroRNAs (miRNAs) are short (19–24 nt) non-coding RNAs that suppress the expression of protein coding genes at the post-transcriptional level. Differential expression profiles of miRNAs across a range of diseases have emerged as powerful biomarkers, making a reliable yet rapid profiling technique for miRNAs potentially essential in clinics. Here, we report an amplification-free multi-color single-molecule imaging technique that can profile purified endogenous miRNAs with high sensitivity, specificity, and reliability. Compared to previously reported techniques, our technique can discriminate single base mismatches and single-nucleotide 3′-tailing with low false positive rates regardless of their positions on miRNA. By preloading probes in Thermus thermophilus Argonaute (TtAgo), miRNAs detection speed is accelerated by more than 20 times. Finally, by utilizing the well-conserved linearity between single-molecule spot numbers and the target miRNA concentrations, the absolute average copy numbers of endogenous miRNA species in a single cell can be estimated. Thus our technique, Ago-FISH (Argonaute-based Fluorescence In Situ Hybridization), provides a reliable way to accurately profile various endogenous miRNAs on a single miRNA sensing chip.
High frequency atomic tunneling yields ultralow and glass-like thermal conductivity in chalcogenide single crystals
Authors: Sun Bo , Niu Shanyuan , Hermann Raphael P. , Moon Jaeyun , Shulumba Nina , Page Katharine , Zhao Boyang , Thind Arashdeep S. , Mahalingam Krishnamurthy , Milam-Guerrero JoAnna , Haiges Ralf , Mecklenburg Matthew , Melot Brent C. , Jho Young-Dahl , Howe Brandon M. , Mishra Rohan , Alatas Ahmet , Winn Barry , Manley Michael E. , Ravichandran Jayakanth , Minnich Austin J.
Published: November 2020

Crystalline solids exhibiting glass-like thermal conductivity have attracted substantial attention both for fundamental interest and applications such as thermoelectrics. In most crystals, the competition of phonon scattering by anharmonic interactions and crystalline imperfections leads to a non-monotonic trend of thermal conductivity with temperature. Defect-free crystals that exhibit the glassy trend of low thermal conductivity with a monotonic increase with temperature are desirable because they are intrinsically thermally insulating while retaining useful properties of perfect crystals. However, this behavior is rare, and its microscopic origin remains unclear. Here, we report the observation of ultralow and glass-like thermal conductivity in a hexagonal perovskite chalcogenide single crystal, BaTiS3, despite its highly symmetric and simple primitive cell. Elastic and inelastic scattering measurements reveal the quantum mechanical origin of this unusual trend. A two-level atomic tunneling system exists in a shallow double-well potential of the Ti atom and is of sufficiently high frequency to scatter heat-carrying phonons up to room temperature. While atomic tunneling has been invoked to explain the low-temperature thermal conductivity of solids for decades, our study establishes the presence of sub-THz frequency tunneling systems even in high-quality, electrically insulating single crystals, leading to anomalous transport properties well above cryogenic temperatures.
Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome
Authors: Fang He , Bonora Giancarlo , Lewandowski Jordan P. , Thakur Jitendra , Filippova Galina N. , Henikoff Steven , Shendure Jay , Duan Zhijun , Rinn John L. , Deng Xinxian , Noble William S. , Disteche Christine M.
Published: November 2020

Firre encodes a lncRNA involved in nuclear organization. Here, we show that Firre RNA expressed from the active X chromosome maintains histone H3K27me3 enrichment on the inactive X chromosome (Xi) in somatic cells. This trans-acting effect involves SUZ12, reflecting interactions between Firre RNA and components of the Polycomb repressive complexes. Without Firre RNA, H3K27me3 decreases on the Xi and the Xi-perinucleolar location is disrupted, possibly due to decreased CTCF binding on the Xi. We also observe widespread gene dysregulation, but not on the Xi. These effects are measurably rescued by ectopic expression of mouse or human Firre/FIRRE transgenes, supporting conserved trans-acting roles. We also find that the compact 3D structure of the Xi partly depends on the Firre locus and its RNA. In common lymphoid progenitors and T-cells Firre exerts a cis-acting effect on maintenance of H3K27me3 in a 26 Mb region around the locus, demonstrating cell type-specific trans- and cis-acting roles of this lncRNA.
An expanded palette of improved SPLICS reporters detects multiple organelle contacts in vitro and in vivo
Authors: Vallese Francesca , Catoni Cristina , Cieri Domenico , Barazzuol Lucia , Ramirez Omar , Calore Valentina , Bonora Massimo , Giamogante Flavia , Pinton Paolo , Brini Marisa , Calì Tito
Published: November 2020

Membrane contact sites between virtually any known organelle have been documented and, in the last decades, their study received momentum due to their importance for fundamental activities of the cell and for the subtle comprehension of many human diseases. The lack of tools to finely image inter-organelle proximity hindered our understanding on how these subcellular communication hubs mediate and regulate cell homeostasis. We develop an improved and expanded palette of split-GFP-based contact site sensors (SPLICS) for the detection of single and multiple organelle contact sites within a scalable distance range. We demonstrate their flexibility under physiological conditions and in living organisms.
A mechanically adaptive hydrogel with a reconfigurable network consisting entirely of inorganic nanosheets and water
Authors: Sano Koki , Igarashi Naoki , Ebina Yasuo , Sasaki Takayoshi , Hikima Takaaki , Aida Takuzo , Ishida Yasuhiro
Published: November 2020

Although various biomimetic soft materials that display structural hierarchies and stimuli responsiveness have been developed from organic materials, the creation of their counterparts consisting entirely of inorganic materials presents an attractive challenge, as the properties of such materials generally differ from those of living organisms. Here, we have developed a hydrogel consisting of inorganic nanosheets (14 wt%) and water (86 wt%) that undergoes thermally induced reversible and abrupt changes in its internal structure and mechanical elasticity (23-fold). At room temperature, the nanosheets in water electrostatically repel one another and self-assemble into a long-periodic lamellar architecture with mutually restricted mobility, forming a physical hydrogel. Upon heating above 55 °C, the electrostatic repulsion is overcome by competing van der Waals attraction, and the nanosheets rearrange into an interconnected 3D network of another hydrogel. By doping the gel with a photothermal-conversion agent, the gel-to-gel transition becomes operable spatiotemporally on photoirradiation.
Single particle tunneling spectrum of superconducting Nd1-xSrxNiO2 thin films
Authors: Gu Qiangqiang , Li Yueying , Wan Siyuan , Li Huazhou , Guo Wei , Yang Huan , Li Qing , Zhu Xiyu , Pan Xiaoqing , Nie Yuefeng , Wen Hai-Hu
Published: November 2020

The pairing mechanism in cuprates remains as one of the most challenging issues in condensed matter physics. Recently, superconductivity was discovered in thin films of the infinite-layer nickelate Nd1-xSrxNiO2 (x = 0.12–0.25) which is believed to have the similar 3d9 orbital electrons as that in cuprates. Here we report single-particle tunneling measurements on the superconducting nickelate thin films. We find predominantly two types of tunneling spectra, one shows a V-shape feature which can be fitted well by a d-wave gap function with gap maximum of about 3.9 meV, another one exhibits a full gap of about 2.35 meV. Some spectra demonstrate mixed contributions of these two components. Combining with theoretical calculations, we attribute the d-wave gap to the pairing potential of the $${\mathrm{Ni - }}3d_{x^2 - y^2}$$
Ni-
3

d

x

2

−

y

2

orbital. Several possible reasons are given for explaining the full gap feature. Our results indicate both similarities and distinctions between the newly found Ni-based superconductors and cuprates.
Tunable analog thermal material
Authors: Xu Guoqiang , Dong Kaichen , Li Ying , Li Huagen , Liu Kaipeng , Li Longqiu , Wu Junqiao , Qiu Cheng-Wei
Published: November 2020

Naturally-occurring thermal materials usually possess specific thermal conductivity (κ), forming a digital set of κ values. Emerging thermal metamaterials have been deployed to realize effective thermal conductivities unattainable in natural materials. However, the effective thermal conductivities of such mixing-based thermal metamaterials are still in digital fashion, i.e., the effective conductivity remains discrete and static. Here, we report an analog thermal material whose effective conductivity can be in-situ tuned from near-zero to near-infinity κ. The proof-of-concept scheme consists of a spinning core made of uncured polydimethylsiloxane (PDMS) and fixed bilayer rings made of silicone grease and steel. Thanks to the spinning PDMS and its induced convective effects, we can mold the heat flow robustly with continuously changing and anisotropic κ. Our work enables a single functional thermal material to meet the challenging demands of flexible thermal manipulation. It also provides platforms to investigate heat transfer in systems with moving components.
Analysis of inositol phosphate metabolism by capillary electrophoresis electrospray ionization mass spectrometry
Authors: Qiu Danye , Wilson Miranda S. , Eisenbeis Verena B. , Harmel Robert K. , Riemer Esther , Haas Thomas M. , Wittwer Christopher , Jork Nikolaus , Gu Chunfang , Shears Stephen B. , Schaaf Gabriel , Kammerer Bernd , Fiedler Dorothea , Saiardi Adolfo , Jessen Henning J.
Published: November 2020

The analysis of myo-inositol phosphates (InsPs) and myo-inositol pyrophosphates (PP-InsPs) is a daunting challenge due to the large number of possible isomers, the absence of a chromophore, the high charge density, the low abundance, and the instability of the esters and anhydrides. Given their importance in biology, an analytical approach to follow and understand this complex signaling hub is desirable. Here, capillary electrophoresis (CE) coupled to electrospray ionization mass spectrometry (ESI-MS) is implemented to analyze complex mixtures of InsPs and PP-InsPs with high sensitivity. Stable isotope labeled (SIL) internal standards allow for matrix-independent quantitative assignment. The method is validated in wild-type and knockout mammalian cell lines and in model organisms. SIL-CE-ESI-MS enables the accurate monitoring of InsPs and PP-InsPs arising from compartmentalized cellular synthesis pathways, by feeding cells with either [13C6]-myo-inositol or [13C6]-D-glucose. In doing so, we provide evidence for the existence of unknown inositol synthesis pathways in mammals, highlighting the potential of this method to dissect inositol phosphate metabolism and signalling.
Direct observation of large electron–phonon interaction effect on phonon heat transport
Authors: Zhou Jiawei , Shin Hyun D. , Chen Ke , Song Bai , Duncan Ryan A. , Xu Qian , Maznev Alexei A. , Nelson Keith A. , Chen Gang
Published: November 2020

As a foundational concept in many-body physics, electron–phonon interaction is essential to understanding and manipulating charge and energy flow in various electronic, photonic, and energy conversion devices. While much progress has been made in uncovering how phonons affect electron dynamics, it remains a challenge to directly observe the impact of electrons on phonon transport, especially at environmental temperatures. Here, we probe the effect of charge carriers on phonon heat transport at room temperature, using a modified transient thermal grating technique. By optically exciting electron-hole pairs in a crystalline silicon membrane, we single out the effect of the phonon–carrier interaction. The enhanced phonon scattering by photoexcited free carriers results in a substantial reduction in thermal conductivity on a nanosecond timescale. Our study provides direct experimental evidence of the elusive role of electron–phonon interaction in phonon heat transport, which is important for understanding heat conduction in doped semiconductors. We also highlight the possibility of using light to dynamically control thermal transport via electron–phonon coupling.
UAF1 deubiquitinase complexes facilitate NLRP3 inflammasome activation by promoting NLRP3 expression
Authors: Song Hui , Zhao Chunyuan , Yu Zhongxia , Li Qizhao , Yan Rongzhen , Qin Ying , Jia Mutian , Zhao Wei
Published: November 2020

NOD-like receptor protein 3 (NLRP3) detects microbial infections or endogenous danger signals and activates the NLRP3 inflammasome, which has important functions in host defense and contributes to the pathogenesis of inflammatory diseases, and thereby needs to be tightly controlled. Deubiquitination of NLRP3 is considered a key step in NLRP3 inflammasome activation. However, the mechanisms by which deubiquitination controls NLRP3 inflammasome activation are unclear. Here, we show that the UAF1/USP1 deubiquitinase complex selectively removes K48-linked polyubiquitination of NLRP3 and suppresses its ubiquitination-mediated degradation, enhancing cellular NLRP3 levels, which are indispensable for subsequent NLRP3 inflammasome assembly and activation. In addition, the UAF1/USP12 and UAF1/USP46 complexes promote NF-κB activation, enhance the transcription of NLRP3 and proinflammatory cytokines (including pro-IL-1β, TNF, and IL-6) by inhibiting ubiquitination-mediated degradation of p65. Consequently, Uaf1 deficiency attenuates NLRP3 inflammasome activation and IL-1β secretion both in vitro and in vivo. Our study reveals that the UAF1 deubiquitinase complexes enhance NLRP3 and pro-IL-1β expression by targeting NLRP3 and p65 and licensing NLRP3 inflammasome activation.
Nanorods with multidimensional optical information beyond the diffraction limit
Authors: Wen Shihui , Liu Yongtao , Wang Fan , Lin Gungun , Zhou Jiajia , Shi Bingyang , Suh Yung Doug , Jin Dayong
Published: November 2020

Precise design and fabrication of heterogeneous nanostructures will enable nanoscale devices to integrate multiple desirable functionalities. But due to the diffraction limit (~200 nm), the optical uniformity and diversity within the heterogeneous functional nanostructures are hardly controlled and characterized. Here, we report a set of heterogeneous nanorods; each optically active section has its unique nonlinear response to donut-shaped illumination, so that one can discern each section with super-resolution. To achieve this, we first realize an approach of highly controlled epitaxial growth and produce a range of heterogeneous structures. Each section along the nanorod structure displays tunable upconversion emissions, in four optical dimensions, including color, lifetime, excitation wavelength, and power dependency. Moreover, we demonstrate a 210 nm single nanorod as an extremely small polychromatic light source for the on-demand generation of RGB photonic emissions. This work benchmarks our ability toward the full control of sub-diffraction-limit optical diversities of single heterogeneous nanoparticles.