bluuebunny/crossref_metadata_2025 huggingface dataset:
Imputation of single‐cell gene expression with an autoencoder neural network
Authors: Badsha Md. Bahadur , Li Rui , Liu Boxiang , Li Yang I. , Xian Min , Banovich Nicholas E. , Qiuyan Fu Audrey
Published: January 2020

Background

Single‐cell RNA‐sequencing (scRNA‐seq) is a rapidly evolving technology that enables measurement of gene expression levels at an unprecedented resolution. Despite the explosive growth in the number of cells that can be assayed by a single experiment, scRNA‐seq still has several limitations, including high rates of dropouts, which result in a large number of genes having zero read count in the scRNA‐seq data, and complicate downstream analyses.

Methods

To overcome this problem, we treat zeros as missing values and develop nonparametric deep learning methods for imputation. Specifically, our LATE (Learning with AuToEncoder) method trains an autoencoder with random initial values of the parameters, whereas our TRANSLATE (TRANSfer learning with LATE) method further allows for the use of a reference gene expression data set to provide LATE with an initial set of parameter estimates.

Results

On both simulated and real data, LATE and TRANSLATE outperform existing scRNA‐seq imputation methods, achieving lower mean squared error in most cases, recovering nonlinear gene‐gene relationships, and better separating cell types. They are also highly scalable and can efficiently process over 1 million cells in just a few hours on a GPU.

Conclusions

We demonstrate that our nonparametric approach to imputation based on autoencoders is powerful and highly efficient.
Hydroiodic Acid Additive Enhanced the Performance and Stability of PbS-QDs Solar Cells via Suppressing Hydroxyl Ligand
Authors: Yang Xiaokun , Yang Ji , Khan Jahangeer , Deng Hui , Yuan Shengjie , Zhang Jian , Xia Yong , Deng Feng , Zhou Xue , Umar Farooq , Jin Zhixin , Song Haisheng , Cheng Chun , Sabry Mohamed , Tang Jiang
Published: January 2020

The recent emerging progress of quantum dot ink (QD-ink) has overcome the complexity of multiple-step colloidal QD (CQD) film preparation and pronouncedly promoted the device performance. However, the detrimental hydroxyl (OH) ligands induced from synthesis procedure have not been completely removed. Here, a halide ligand additive strategy was devised to optimize QD-ink process. It simultaneously reduced sub-bandgap states and converted them into iodide-passivated surface, which increase carrier mobility of the QDs films and achieve thicker absorber with improved performances. The corresponding power conversion efficiency of this optimized device reached 10.78%. (The control device was 9.56%.) Therefore, this stratege can support as a candidate strategy to solve the QD original limitation caused by hydroxyl ligands, which is also compatible with other CQD-based optoelectronic devices.
Evaluation of Relationships Between Ridership Demand and Transit-Oriented Development (TOD) Indicators Focused on Land Use Density, Diversity, and Accessibility: A Case Study of Existing Metro Stations in Bangkok
Authors: Nyunt Khin Thiri Kyaw , Wongchavalidkul Natachai
Published: January 2020

The purpose of this work is to support the transit-oriented development (TOD) in Thailand. The main research objective is to explore the relationship between ridership demand and TOD indicators, which is expected to be the first question that a developer in Thailand must be able to answer in order to direct their development plan in the right direction. Using existing Bangkok metro stations as a case study, 22 variables categorized into three groups (density, diversity, and design) were collected for an 800-m buffer area around the stations. Results of the correlation analysis between transit ridership and other variables show a significant relation with the volume of transit ridership. Bus services have a stronger influence on transit ridership than railway stations and ferries (pier). Also, the interchange stations and park-and-ride buildings are found to be the main variables that correlate directly with the transit ridership numbers. Results from the principal component analysis are used to evaluate factors of TOD characteristics for the existing Bangkok metro stations, categorized into seven factor groups.
CHARACTER LEVELS AND CHARACTER BOUNDS
Authors: GURALNICK ROBERT M. , LARSEN MICHAEL , TIEP PHAM HUU
Published: January 2020

We develop the concept of character level for the complex irreducible characters of finite, general or special, linear and unitary groups. We give characterizations of the level of a character in terms of its Lusztig label and in terms of its degree. Then we prove explicit upper bounds for character values at elements with not-too-large centralizers and derive upper bounds on the covering number and mixing time of random walks corresponding to these conjugacy classes. We also characterize the level of the character in terms of certain dual pairs and prove explicit exponential character bounds for the character values, provided that the level is not too large. Several further applications are also provided. Related results for other finite classical groups are obtained in the sequel [Guralnicket al. ‘Character levels and character bounds for finite classical groups’, Preprint, 2019,arXiv:1904.08070] by different methods.
The Politics of the Hijab in Post-Soviet Azerbaijan
Authors: Bashirov Galib
Published: January 2020

In late 2010, Azerbaijan tried to introduce a ban on hijab in all secondary schools, referring to an article of the new Law of Education that mandated school uniforms. The supporters of the ban argued that the hijab was inimical to Azerbaijani culture and law because it violated the separation of religion and state, was a propaganda tool of Islamist fundamentalists funded from abroad, and was a foreign form of clothing that did not exist in Azerbaijani culture. This article examines why hijab is the focus of controversy in Azerbaijan. The supporters of the ban offered simple oppositions, such as secularism versus theocracy, modernity versus backwardness, and national versus foreign, to explain and justify the ban. However, these dichotomies do not capture the complexities of Islam in Azerbaijan. Rather, they are polemics that blur more than they reveal. In this article, I argue that the debates around the hijab controversy in Azerbaijan are a political discourse aimed at building a nation. The key contribution of this article is to examine the wider historical trajectory of the political discourse that constructed hijab as fundamentalist, backward, threatening, and alien, through discussing the topics of secularism, Islamist politics, modernity, and nationalism.
Investigation of the coronal heating through phase relation of solar activity indexes
Authors: Li K. J. , Xu J. C. , Yin Z. Q. , Xie J. L. , Feng W.
Published: January 2020

The coronal heating problem is a long-standing perplexing issue. In this study, 13 solar activity indexes are used to investigate their phase relation with the sunspot number (SSN). Only three of them are found to statistically significantly lag the SSN (large-scale magnetic activity) by about one solar rotation period; the three indexes are total solar irradiance (TSI), the modified coronal index, and the solar wind velocity; the former two indexes may represent the long-term variation of energy quantity of the heated photosphere and corona, respectively. The Mount Wilson Sunspot Index (MWSI) and the Magnetic Plage Strength Index (MPSI), which reflect the large- and small-scale magnetic field activities, respectively, are also utilised to investigate their phase relations with the three indexes. The three indexes are found to be much more intimately related to MPSI than to MWSI, and MWSI statistically significantly leads TSI by about one rotation period. The heated corona is found to pulse perfectly in step with the small-scale magnetic activity rather than the large-scale magnetic activity; furthermore, combined with observations, our statistical evidence should thus attribute coronal heating firmly to small-scale magnetic activity phenomena, such as spicules, micro-flares, nano-flares, and others. The photosphere and the corona are synchronously heated, which should seemingly prefer magnetic reconnection heating to wave heating. In the long term, such a coronal heating way is inferred effective. Statistically, it is also small-scale magnetic activity phenomena that produce TSI enhancement. Coronal heating and solar wind acceleration are found to be synchronous, as standard models require.
Ambedkar on the Haughty Face of Dignity
Authors: Cabrera Luis
Published: January 2020

Can a concept such as dignity, with roots in hierarchy and exclusion, serve as the constitutional basis for advancing egalitarian justice within a democratic political community? This article highlights some concerns, via engagement with the work of Indian constitutional architect and anti-caste champion B.R. Ambedkar. Ambedkar strongly associates dignity with upper-caste status in Hinduism, and with dispositions to haughtiness or arrogance toward lower-status persons. His analysis has implications for recent treatments which frame dignity as a property which is possessed equally by all persons and is suitable for grounding egalitarian justice within political communities. In such accounts, dignity is shown to entail a defensive disposition and indignation against others as potential rights violators. This introduces tensions between the dignitarian foundation and in some cases very expansive social justice aims. Ambedkar offers an alternative conception of innate worth or worthiness, entailing dispositions to openness and inclusiveness, rendered as fraternity, Deweyan social endosmosis, and ultimately the Buddhist maitri. Such an approach avoids some tensions between dignity/indignation and egalitarian aims, while also offering a way to conceptualize human and non-human animal relations that avoids simply reinscribing status hierarchies.
Indikatoren schulischen Wohlbefindens bei gesunden und chronisch kranken Kindern: Psychometrische Prüfung und Validierung adaptierter FEESS-Skalen
Authors: Schnick-Vollmer Kathleen , Diefenbach Christiane , Gräf Christine , Hoffmann Dorle , Hoffmann Isabell , Imhof Margarete , Kiefer Thomas , König Jochem , Schlecht Jennifer , Schmidt Martina F. , Urschitz Michael S.
Published: January 2020

Zusammenfassung. Das schulbezogene Wohlbefinden (SBWB) ist eine wichtige Voraussetzung für schulischen Erfolg. Trotzdem existieren – insbesondere mit Blick auf die Erfassung des SBWB von Erstklässlern – im deutschsprachigen Raum nur vereinzelt Studien. Dies lässt sich möglicherweise durch das Fehlen geeigneter Instrumente begründen. Dies gilt auch und insbesondere dann, wenn der Gesundheitszustand der Kinder berücksichtigt werden soll. Das Ziel der vorliegenden Arbeit besteht in der Validierung des adaptierten Fragebogens zur Erfassung von emotionalen und sozialen Schulerfahrungen (FEESS 1 – 2; Rauer & Schuck, 2004 ) mit Fokus auf die Eignung des Instruments für chronisch kranke und gesunde Kinder. Dafür wird zunächst das Konstrukt Wohlbefinden (WB) resp. SBWB definiert und in einschlägige Theorien – die Selbstbestimmungstheorie nach Deci und Ryan (1985) und das Erwartung-mal-Wert-Modell nach Wigfield und Eccles (2000) – eingebettet. Die Bedeutung der verwendeten FEESS-Skalen und ihr Zusammenhang zum schulischen Erfolg werden aufgezeigt. 1491 Kinder wurden zu ihrer Lernfreude (LF), sozialen Integration (SI) und zu ihrem schulbezogenen Fähigkeitsselbstkonzept (SK) befragt. Die Erfassung des Gesundheitszustands wurde über Elternfragebögen und Schuleingangsuntersuchungen eruiert. Zudem wurden die Eltern zur gesundheitsbezogenen Lebensqualität (LQ) ihrer Kinder mit Hilfe eines Fragebogens zur Erfassung der Lebensqualität von Kindern (KINDL; Bullinger, Mackensen & Kirchberger, 1994 ) befragt. Die psychometrische Qualität der adaptierten FEESS-Skalen wurde für beide Gruppen (erkrankt / gesund) auf Skalen- und Itemebene untersucht. Hierzu kamen sowohl klassische Verfahren als auch Verfahren der Item-Response-Theorie zum Einsatz. Die Ergebnisse untermauern die Validität des Konstruktes SBWB und stützen die Annahme der Dreidimensionalität (LF, SI, SK). Alle drei Skalen zeigen eine zufriedenstellende bis sehr gute Reliabilität. Die Items zeigen sehr gute MNSQ-Werte (weighted mean-square; gewichtete Abweichungsquadrate) und geeignete Trennschärfen. Die externe Validität, für deren Berechnung der Zusammenhang zwischen den Angaben der Kinder und den Angaben der Eltern zur gesundheitsbezogenen LQ untersucht wurde, konnte noch nicht ausreichend nachgewiesen werden. Bis auf diese Einschränkung kann mit Hilfe der adaptierten FEESS-Skalen im nächsten Schritt das SBWB von gesunden und erkrankten Kindern verglichen werden, um mögliche Chancenungleichheiten auszugleichen.
Tidal Wetland Gross Primary Production Across the Continental United States, 2000–2019
Authors: Feagin R. A. , Forbrich I. , Huff T. P. , Barr J. G. , Ruiz‐Plancarte J. , Fuentes J. D. , Najjar R. G. , Vargas R. , Vázquez‐Lule A. , Windham‐Myers L. , Kroeger K. D. , Ward E. J. , Moore G. W. , Leclerc M. , Krauss K. W. , Stagg C. L. , Alber M. , Knox S. H. , Schäfer K. V. R. , Bianchi T. S. , Hutchings J. A. , Nahrawi H. , Noormets A. , Mitra B. , Jaimes A. , Hinson A. L. , Bergamaschi B. , King J. S. , Miao G.
Published: January 2020

We mapped tidal wetland gross primary production (GPP) with unprecedented detail for multiple wetland types across the continental United States (CONUS) at 16‐day intervals for the years 2000–2019. To accomplish this task, we developed the spatially explicit Blue Carbon (BC) model, which combined tidal wetland cover and field‐based eddy covariance tower data into a single Bayesian framework, and used a super computer network and remote sensing imagery (Moderate Resolution Imaging Spectroradiometer Enhanced Vegetation Index). We found a strong fit between the BC model and eddy covariance data from 10 different towers (r2 = 0.83, p < 0.001, root‐mean‐square error = 1.22 g C/m2/day, average error was 7% with a mean bias of nearly zero). When compared with NASA's MOD17 GPP product, which uses a generalized terrestrial algorithm, the BC model reduced error by approximately half (MOD17 had r2 = 0.45, p < 0.001, root‐mean‐square error of 3.38 g C/m2/day, average error of 15%). The BC model also included mixed pixels in areas not covered by MOD17, which comprised approximately 16.8% of CONUS tidal wetland GPP. Results showed that across CONUS between 2000 and 2019, the average daily GPP per m2 was 4.32 ± 2.45 g C/m2/day. The total annual GPP for the CONUS was 39.65 ± 0.89 Tg C/year. GPP for the Gulf Coast was nearly double that of the Atlantic and Pacific Coasts combined. Louisiana alone accounted for 15.78 ± 0.75 Tg C/year, with its Atchafalaya/Vermillion Bay basin at 4.72 ± 0.14 Tg C/year. The BC model provides a robust platform for integrating data from disparate sources and exploring regional trends in GPP across tidal wetlands.
Heat Content Anomaly and Decay of Warm‐Core Rings: the Case of the Gulf of Mexico
Authors: Meunier Thomas , Sheinbaum Julio , Pallàs‐Sanz Enric , Tenreiro Miguel , Ochoa José , Ruiz‐Angulo Angel , Carton Xavier , de Marez Charly
Published: January 2020

In this study, we harness the 25‐year satellite‐altimeter record, in concert with a vast array of in situ measurements, to estimate the heat content anomaly of 32 warm‐core rings in the Gulf of Mexico (GoM). The decay rate of these mesoscale eddies is studied in detail, and it is shown that they release the majority of their heat as they drift in the central GoM (away from topographic obstacles). The surface heat fluxes from the eddies are shown to be small in comparison to the total rate of heat loss from the eddies, suggesting that heat is primarily released toward the surrounding water masses. Integrating the total heat evolution equation over the warm‐core rings yields an estimate of their effective lateral diffusivity coefficient. The long‐term impact of warm‐core rings on heat and salt balance in the GoM is also discussed.
Millimeter‐Scale Tsunami Detected by a Wide and Dense Observation Array in the Deep Ocean: Fault Modeling of an Mw 6.0 Interplate Earthquake off Sanriku, NE Japan
Authors: Kubota T. , Saito T. , Suzuki W.
Published: January 2020

A new dense and widely distributed tsunami observation network installed off northeast Japan detected millimeter‐scale tsunamis from an Mw 6.0 shallow interplate earthquake on 20 August 2016. Based on the fault model deduced from this data set, we obtained a stress drop of 1.5 MPa for this event, similar to those associated with typical interplate earthquakes. The rupture area was unlikely to overlap with regions where slow earthquakes occur, such as low‐frequency‐tremors and very‐low‐frequency‐earthquakes. The results demonstrated that this new network has dramatically increased the detectability of millimeter‐scale tsunamis. Some near‐source stations were contaminated by large pressure offset signals irrelevant to tsunami, and we must therefore be careful when analyzing these data. Nonetheless, the new array enables estimations of the stress drops of moderate offshore earthquakes and can be used to elucidate the spatial variation of mechanical properties along the plate interface with much higher resolution than previously possible.
Detection of Gas Hydrates in Faults Using Azimuthal Seismic Velocity Analysis, Vestnesa Ridge, W‐Svalbard Margin
Authors: Singhroha Sunny , Bünz Stefan , Plaza‐Faverola Andreia , Chand Shyam
Published: January 2020

Joint analysis of electrical resistivity and seismic velocity data is primarily used to detect the presence of gas hydrate‐filled faults and fractures. In this study, we present a novel approach to infer the occurrence of structurally controlled gas hydrate accumulations using azimuthal seismic velocity analysis. We perform this analysis using ocean‐bottom seismic data at two sites on Vestnesa Ridge, W‐Svalbard Margin. Previous geophysical studies inferred the presence of gas hydrates at shallow depths (up to ~190–195 m below the seafloor) in marine sediments of Vestnesa Ridge. We analyze azimuthal P‐wave seismic velocities in relation with steeply dipping near‐surface faults to study structural controls on gas hydrate distribution. This unique analysis documents directional changes in seismic velocities along and across faults. P‐wave velocities are elevated and reduced by ~0.06–0.08 km/s in azimuths where the raypath plane lies along the fault plane in the gas hydrate stability zone (GHSZ) and below the base of the GHSZ, respectively. The resulting velocities can be explained with the presence of gas hydrate‐ and free gas‐filled faults above and below the base of the GHSZ, respectively. Moreover, the occurrence of elevated and reduced (>0.05 km/s) seismic velocities in groups of azimuths bounded by faults suggests compartmentalization of gas hydrates and free gas by fault planes. Results from gas hydrate saturation modeling suggest that these observed changes in seismic velocities with azimuth can be due to gas hydrate saturated faults of thickness greater than 20 cm and considerably smaller than 300 cm.
Multidecadal Basal Melt Rates and Structure of the Ross Ice Shelf, Antarctica, Using Airborne Ice Penetrating Radar
Authors: Das Indrani , Padman Laurie , Bell Robin E. , Fricker Helen A. , Tinto Kirsty J. , Hulbe Christina L. , Siddoway Christine S. , Dhakal Tejendra , Frearson Nicholas P. , Mosbeux Cyrille , Cordero S. Isabel , Siegfried Matthew R.
Published: January 2020

Basal melting of ice shelves is a major source of mass loss from the Antarctic Ice Sheet. In situ measurements of ice shelf basal melt rates are sparse, while the more extensive estimates from satellite altimetry require precise information about firn density and characteristics of near‐surface layers. We describe a novel method for estimating multidecadal basal melt rates using airborne ice penetrating radar data acquired during a 3‐year survey of the Ross Ice Shelf. These data revealed an ice column with distinct upper and lower units whose thicknesses change as ice flows from the grounding line toward the ice front. We interpret the lower unit as continental meteoric ice that has flowed across the grounding line and the upper unit as ice formed from snowfall onto the relatively flat ice shelf. We used the ice thickness difference and strain‐induced thickness change of the lower unit between the survey lines, combined with ice velocities, to derive basal melt rates averaged over one to six decades. Our results are similar to satellite laser altimetry estimates for the period 2003–2009, suggesting that the Ross Ice Shelf melt rates have been fairly stable for several decades. We identify five sites of elevated basal melt rates, in the range 0.5–2 m a−1, near the ice shelf front. These hot spots indicate pathways into the sub‐ice‐shelf ocean cavity for warm seawater, likely a combination of summer‐warmed Antarctic Surface Water and modified Circumpolar Deep Water, and are potential areas of ice shelf weakening if the ocean warms.
Preterm birth is associated with epigenetic programming of transgenerational hypertension in mice
Authors: Dumeige Laurence , Nehlich Mélanie , Viengchareun Say , Perrot Julie , Pussard Eric , Lombès Marc , Martinerie Laetitia
Published: January 2020

Renal and cardiovascular complications of prematurity are well established, notably the development of hypertension in adulthood. However, the underlying molecular mechanisms remain poorly understood. Our objective was to investigate the impact of prematurity on the ontogenesis of renal corticosteroid pathways, to evaluate its implication in perinatal renal complications and in the emergence of hypertension in adulthood. Swiss CD1 pregnant mice were injected with lipopolysaccharides at 18 days of gestation (E18) to induce prematurity at E18.5. Pups were sacrificed at birth, 7 days and 6 months of life. Second (F2) and third (F3) generations, established by mating prematurely born adult females with wild-type males, were also analyzed. Former preterm males developed hypertension at M6 (P < 0.0001). We found robust activation of renal corticosteroid target gene transcription at birth in preterm mice (αENaC (+45%), Gilz (+85%)), independent of any change in mineralocorticoid or glucocorticoid receptor expression. The offspring of the preterm group displayed increased blood pressure in F2 and F3, associated with increased renal Gilz mRNA expression, despite similar MR or GR expression and plasma corticosteroid levels measured by LC-MS/MS. Gilz promoter methylation measured by methylated DNA immunoprecipitation-qPCR was reduced with a negative correlation between methylation and expression (P = 0.0106). Our study demonstrates prematurity-related alterations in renal corticosteroid signaling pathways, with transgenerational inheritance of blood pressure dysregulation and epigenetic Gilz regulation up to the third generation. This study provides a better understanding of the molecular mechanisms involved in essential hypertension, which could partly be due to perinatal epigenetic programming from previous generations.
FeO–CeO2 nanocomposites: an efficient and highly selective catalyst system for photothermal CO2 reduction to CO
Authors: Zhao Jiaqing , Yang Qi , Shi Run , Waterhouse Geoffrey I. N. , Zhang Xin , Wu Li-Zhu , Tung Chen-Ho , Zhang Tierui
Published: January 2020

Solar-driven catalysis is a promising strategy for transforming CO2 into fuels and valuable chemical feedstocks, with current research focusing primarily on increasing CO2 conversion efficiency and product selectivity. Herein, a series of FeO–CeO2 nanocomposite catalysts were successfully prepared by H2 reduction of Fe(OH)3-Ce(OH)3 precursors at temperatures (x) ranging from 200 to 600 °C (the obtained catalysts are denoted as FeCe-x). An FeCe-300 catalyst with an Fe:Ce molar ratio of 2:1 demonstrated outstanding performance for photothermal CO2 conversion to CO in the presence of H2 under Xe lamp irradiation (CO2 conversion, 43.63%; CO selectivity, 99.87%; CO production rate, 19.61 mmol h−1 gcat−1; stable operation over 50 h). Characterization studies using powder X-ray diffraction and high-resolution transmission electron microscopy determined that the active catalyst comprises FeO and CeO2 nanoparticles. The selectivity to CO of the FeCe-x catalysts decreased as the reduction temperature (x) increased in the range of 300–500 °C due to the appearance of metallic Fe0, which introduced an additional reaction pathway for the production of CH4. In situ diffuse reflectance infrared Fourier transform spectroscopy identified formate, bicarbonate and methanol as important reaction intermediates during light-driven CO2 hydrogenation over the FeCe-x catalysts, providing key mechanistic information needed to explain the product distributions of CO2 hydrogenation on the different catalysts.
Lanthanide doping in metal halide perovskite nanocrystals: spectral shifting, quantum cutting and optoelectronic applications
Authors: Mir Wasim J. , Sheikh Tariq , Arfin Habibul , Xia Zhiguo , Nag Angshuman
Published: January 2020

Lanthanides have been widely explored as optically active dopants in inorganic crystal lattices, which are often insulating in nature. Doping trivalent lanthanide (Ln3+) into traditional semiconductor nanocrystals, such as CdSe, is challenging because of their tetrahedral coordination. Interestingly, CsPbX3 (X = Cl, Br, I) perovskite nanocrystals provide the octahedral coordination suitable for Ln3+ doping. Over the last two years, tremendous success has been achieved in doping Ln3+ into CsPbX3 nanocrystals, combining the excellent optoelectronic properties of the host with the f-f electronic transitions of the dopants. For example, the efficient quantum cutting phenomenon in Yb3+-doped CsPb(Cl,Br)3 nanocrystals yields a photoluminescence quantum yield close to 200%. Other approaches of Ln3+ doping and codoping have enabled promising proof-of-principle demonstration of solid-state lighting and solar photovoltaics. In this perspective article, we highlight the salient features of the material design (including doping in Pb-free perovskites), optical properties and potential optoelectronic applications of lanthanide-doped metal halide perovskite nanocrystals. While review articles on doping different metal ions into perovskite nanocrystals are present, the present review-type article is solely dedicated to lanthanide-doped metal halide perovskite nanocrystals.
Topological–chiral magnetic interactions driven by emergent orbital magnetism
Authors: Grytsiuk S. , Hanke J.-P. , Hoffmann M. , Bouaziz J. , Gomonay O. , Bihlmayer G. , Lounis S. , Mokrousov Y. , Blügel S.
Published: January 2020

Two hundred years ago, Ampère discovered that electric loops in which currents of electrons are generated by a penetrating magnetic field can mutually interact. Here we show that Ampère’s observation can be transferred to the quantum realm of interactions between triangular plaquettes of spins on a lattice, where the electrical currents at the atomic scale are associated with the orbital motion of electrons in response to the non-coplanarity of neighbouring spins playing the role of a magnetic field. The resulting topological orbital moment underlies the relation of the orbital dynamics with the topology of the spin structure. We demonstrate that the interactions of the topological orbital moments with each other and with the spins form a new class of magnetic interactions $$-$$− topological–chiral interactions $$-$$− which can dominate over the Dzyaloshinskii–Moriya interaction, thus opening a path for realizing new classes of chiral magnetic materials with three-dimensional magnetization textures such as hopfions.
Single AAV-mediated mutation replacement genome editing in limited number of photoreceptors restores vision in mice
Authors: Nishiguchi Koji M. , Fujita Kosuke , Miya Fuyuki , Katayama Shota , Nakazawa Toru
Published: January 2020

Supplementing wildtype copies of functionally defective genes with adeno-associated virus (AAV) is a strategy being explored clinically for various retinal dystrophies. However, the low cargo limit of this vector allows its use in only a fraction of patients with mutations in relatively small pathogenic genes. To overcome this issue, we developed a single AAV platform that allows local replacement of a mutated sequence with its wildtype counterpart, based on combined CRISPR-Cas9 and micro-homology-mediated end-joining (MMEJ). In blind mice, the mutation replacement rescued approximately 10% of photoreceptors, resulting in an improvement in light sensitivity and an increase in visual acuity. These effects were comparable to restoration mediated by gene supplementation, which targets a greater number of photoreceptors. This strategy may be applied for the treatment of inherited disorders caused by mutations in larger genes, for which conventional gene supplementation therapy is not currently feasible.
Structure and mechanism of a Type III CRISPR defence DNA nuclease activated by cyclic oligoadenylate
Authors: McMahon Stephen A. , Zhu Wenlong , Graham Shirley , Rambo Robert , White Malcolm F. , Gloster Tracey M.
Published: January 2020

The CRISPR system provides adaptive immunity against mobile genetic elements in prokaryotes. On binding invading RNA species, Type III CRISPR systems generate cyclic oligoadenylate (cOA) signalling molecules, potentiating a powerful immune response by activating downstream effector proteins, leading to viral clearance, cell dormancy or death. Here we describe the structure and mechanism of a cOA-activated CRISPR defence DNA endonuclease, CRISPR ancillary nuclease 1 (Can1). Can1 has a unique monomeric structure with two CRISPR associated Rossman fold (CARF) domains and two DNA nuclease-like domains. The crystal structure of the enzyme has been captured in the activated state, with a cyclic tetra-adenylate (cA4) molecule bound at the core of the protein. cA4 binding reorganises the structure to license a metal-dependent DNA nuclease activity specific for nicking of supercoiled DNA. DNA nicking by Can1 is predicted to slow down viral replication kinetics by leading to the collapse of DNA replication forks.
Efficient electron transmission in covalent organic framework nanosheets for highly active electrocatalytic carbon dioxide reduction
Authors: Zhu Hong-Jing , Lu Meng , Wang Yi-Rong , Yao Su-Juan , Zhang Mi , Kan Yu-He , Liu Jiang , Chen Yifa , Li Shun-Li , Lan Ya-Qian
Published: January 2020

Efficient conversion of carbon dioxide (CO2) into value-added products is essential for clean energy research. Design of stable, selective, and powerful electrocatalysts for CO2 reduction reaction (CO2RR) is highly desirable yet largely unmet. In this work, a series of metalloporphyrin-tetrathiafulvalene based covalent organic frameworks (M-TTCOFs) are designed. Tetrathiafulvalene, serving as electron donator or carrier, can construct an oriented electron transmission pathway with metalloporphyrin. Thus-obtained M-TTCOFs can serve as electrocatalysts with high FECO (91.3%, −0.7 V) and possess high cycling stability (>40 h). In addition, after exfoliation, the FECO value of Co-TTCOF nanosheets (~5 nm) is higher than 90% in a wide potential range from −0.6 to −0.9 V and the maximum FECO can reach up to almost 100% (99.7%, −0.8 V). The electrocatalytic CO2RR mechanisms are discussed and revealed by density functional theory calculations. This work paves a new way in exploring porous crystalline materials in electrocatalytic CO2RR.
Pt-O bond as an active site superior to Pt0 in hydrogen evolution reaction
Authors: Yu Fei-Yang , Lang Zhong-Ling , Yin Li-Ying , Feng Kun , Xia Yu-Jian , Tan Hua-Qiao , Zhu Hao-Tian , Zhong Jun , Kang Zhen-Hui , Li Yang-Guang
Published: January 2020

The oxidized platinum (Pt) can exhibit better electrocatalytic activity than metallic Pt0 in the hydrogen evolution reaction (HER), which has aroused great interest in exploring the role of oxygen in Pt-based catalysts. Herein, we select two structurally well-defined polyoxometalates Na5[H3Pt(IV)W6O24] (PtW6O24) and Na3K5[Pt(II)2(W5O18)2] (Pt2(W5O18)2) as the platinum oxide model to investigate the HER performance. Electrocatalytic experiments show the mass activities of PtW6O24/C and Pt2(W5O18)2/C are 20.175 A mg−1 and 10.976 A mg−1 at 77 mV, respectively, which are better than that of commercial 20% Pt/C (0.398 A mg−1). The in situ synchrotron radiation experiments and DFT calculations suggest that the elongated Pt-O bond acts as the active site during the HER process, which can accelerate the coupling of proton and electron and the rapid release of H2. This work complements the knowledge boundary of Pt-based electrocatalytic HER, and suggests another way to update the state-of-the-art electrocatalyst.
Super-resolution microscopy compatible fluorescent probes reveal endogenous glucagon-like peptide-1 receptor distribution and dynamics
Authors: Ast Julia , Arvaniti Anastasia , Fine Nicholas H. F. , Nasteska Daniela , Ashford Fiona B. , Stamataki Zania , Koszegi Zsombor , Bacon Andrea , Jones Ben J. , Lucey Maria A. , Sasaki Shugo , Brierley Daniel I. , Hastoy Benoit , Tomas Alejandra , D’Agostino Giuseppe , Reimann Frank , Lynn Francis C. , Reissaus Christopher A. , Linnemann Amelia K. , D’Este Elisa , Calebiro Davide , Trapp Stefan , Johnsson Kai , Podewin Tom , Broichhagen Johannes , Hodson David J.
Published: January 2020

The glucagon-like peptide-1 receptor (GLP1R) is a class B G protein-coupled receptor (GPCR) involved in metabolism. Presently, its visualization is limited to genetic manipulation, antibody detection or the use of probes that stimulate receptor activation. Herein, we present LUXendin645, a far-red fluorescent GLP1R antagonistic peptide label. LUXendin645 produces intense and specific membrane labeling throughout live and fixed tissue. GLP1R signaling can additionally be evoked when the receptor is allosterically modulated in the presence of LUXendin645. Using LUXendin645 and LUXendin651, we describe islet, brain and hESC-derived β-like cell GLP1R expression patterns, reveal higher-order GLP1R organization including membrane nanodomains, and track single receptor subpopulations. We furthermore show that the LUXendin backbone can be optimized for intravital two-photon imaging by installing a red fluorophore. Thus, our super-resolution compatible labeling probes allow visualization of endogenous GLP1R, and provide insight into class B GPCR distribution and dynamics both in vitro and in vivo.
Histidine kinase MHZ1/OsHK1 interacts with ethylene receptors to regulate root growth in rice
Authors: Zhao He , Duan Kai-Xuan , Ma Biao , Yin Cui-Cui , Hu Yang , Tao Jian-Jun , Huang Yi-Hua , Cao Wu-Qiang , Chen Hui , Yang Chao , Zhang Zhi-Guo , He Si-Jie , Zhang Wan-Ke , Wan Xiang-Yuan , Lu Tie-Gang , Chen Shou-Yi , Zhang Jin-Song
Published: January 2020

Ethylene plays essential roles during adaptive responses to water-saturating environments in rice, but knowledge of its signaling mechanism remains limited. Here, through an analysis of a rice ethylene-response mutant mhz1, we show that MHZ1 positively modulates root ethylene responses. MHZ1 encodes the rice histidine kinase OsHK1. MHZ1/OsHK1 is autophosphorylated at a conserved histidine residue and can transfer the phosphoryl signal to the response regulator OsRR21 via the phosphotransfer proteins OsAHP1/2. This phosphorelay pathway is required for root ethylene responses. Ethylene receptor OsERS2, via its GAF domain, physically interacts with MHZ1/OsHK1 and inhibits its kinase activity. Genetic analyses suggest that MHZ1/OsHK1 acts at the level of ethylene perception and works together with the OsEIN2-mediated pathway to regulate root growth. Our results suggest that MHZ1/OsHK1 mediates the ethylene response partially independently of OsEIN2, and is directly inhibited by ethylene receptors, thus revealing mechanistic details of ethylene signaling for root growth regulation.
Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain
Authors: Yin Senlin , Lu Keying , Tan Tao , Tang Jie , Wei Jingkuan , Liu Xu , Hu Xinlei , Wan Haisu , Huang Wei , Fan Yong , Xie Dan , Yu Yang
Published: January 2020

The rhesus macaque is a prime model animal in neuroscience. A comprehensive transcriptomic and open chromatin atlas of the rhesus macaque brain is key to a deeper understanding of the brain. Here we characterize the transcriptome of 416 brain samples from 52 regions of 8 rhesus macaque brains. We identify gene modules associated with specific brain regions like the cerebral cortex, pituitary, and thalamus. In addition, we discover 9703 novel intergenic transcripts, including 1701 coding transcripts and 2845 lncRNAs. Most of the novel transcripts are only expressed in specific brain regions or cortical regions of specific individuals. We further survey the open chromatin regions in the hippocampal CA1 and several cerebral cortical regions of the rhesus macaque brain using ATAC-seq, revealing CA1- and cortex-specific open chromatin regions. Our results add to the growing body of knowledge regarding the baseline transcriptomic and open chromatin profiles in the brain of the rhesus macaque.
Endothelial progeria induces adipose tissue senescence and impairs insulin sensitivity through senescence associated secretory phenotype
Authors: Barinda Agian Jeffilano , Ikeda Koji , Nugroho Dhite Bayu , Wardhana Donytra Arby , Sasaki Naoto , Honda Sakiko , Urata Ryota , Matoba Satoaki , Hirata Ken-ichi , Emoto Noriaki
Published: January 2020

Vascular senescence is thought to play a crucial role in an ageing-associated decline of organ functions; however, whether vascular senescence is causally implicated in age-related disease remains unclear. Here we show that endothelial cell (EC) senescence induces metabolic disorders through the senescence-associated secretory phenotype. Senescence-messaging secretomes from senescent ECs induced a senescence-like state and reduced insulin receptor substrate-1 in adipocytes, which thereby impaired insulin signaling. We generated EC-specific progeroid mice that overexpressed the dominant negative form of telomeric repeat-binding factor 2 under the control of the Tie2 promoter. EC-specific progeria impaired systemic metabolic health in mice in association with adipose tissue dysfunction even while consuming normal chow. Notably, shared circulation with EC-specific progeroid mice by parabiosis sufficiently transmitted the metabolic disorders into wild-type recipient mice. Our data provides direct evidence that EC senescence impairs systemic metabolic health, and thus establishes EC senescence as a bona fide risk for age-related metabolic disease.
Variable spin-charge conversion across metal-insulator transition
Authors: Safi Taqiyyah S. , Zhang Pengxiang , Fan Yabin , Guo Zhongxun , Han Jiahao , Rosenberg Ethan R. , Ross Caroline , Tserkovnyak Yaraslov , Liu Luqiao
Published: January 2020

The charge-to-spin conversion efficiency is a crucial parameter in determining the performance of many useful spintronic materials. Usually, this conversion efficiency is predetermined by the intrinsic nature of solid-state materials, which cannot be easily modified without invoking chemical or structural changes in the underlying system. Here we report on successful modulation of charge-spin conversion efficiency via the metal-insulator transition in a quintessential strongly correlated electron compound vanadium dioxide (VO2). By employing ferromagnetic resonance driven spin pumping and the inverse spin Hall effect measurement, we find a dramatic change in the spin pumping signal (decrease by > 80%) and charge-spin conversion efficiency (increase by five times) upon insulator to metal transition. The abrupt change in the structural and electrical properties of this material therefore provides useful insights on the spin related physics in a strongly correlated material undergoing a phase transition.
Atomically resolved Au52Cu72(SR)55 nanoalloy reveals Marks decahedron truncation and Penrose tiling surface
Authors: Song Yongbo , Li Yingwei , Li Hao , Ke Feng , Xiang Ji , Zhou Chuanjun , Li Peng , Zhu Manzhou , Jin Rongchao
Published: January 2020

Gold-copper alloys have rich forms. Here we report an atomically resolved [Au52Cu72(p-MBT)55]+Cl− nanoalloy (p-MBT = SPh-p-CH3). This nanoalloy exhibits unusual structural patterns. First, two Cu atoms are located in the inner 7-atom decahedral kernel (M7, M = Au/Cu). The M7 kernel is then enclosed by a second shell of homogold (Au47), giving rise to a two-shelled M54 (i.e. Au52Cu2) full decahedron. A comparison of the non-truncated M54 decahedron with the truncated homogold Au49 kernel in similar-sized gold nanoparticles provides for the first time an explanation for Marks decahedron truncation. Second, a Cu70(SR)55 exterior cage resembling a 3D Penrose tiling protects the M54 decahedral kernel. Compared to the discrete staple motifs in gold:thiolate nanoparticles, the Cu-thiolate surface of Au52Cu72 forms an extended cage. The Cu-SR Penrose tiling retains the M54 kernel’s high symmetry (D5h). Third, interparticle interactions in the assembly are closely related to the symmetry of the particle, and a “quadruple-gear-like” interlocking pattern is observed.
Genetic diversity and novel lineages in the cosmopolitan copepod Pleuromamma abdominalis in the Southeast Pacific
Authors: González Carolina E. , Goetze Erica , Escribano Rubén , Ulloa Osvaldo , Victoriano Pedro
Published: January 2020

Across boundary currents, zooplankton are subject to strong oceanographic gradients and hence strong selective pressures. How such gradients interact with the speciation process of pelagic organisms is still poorly understood in the open ocean realm. Here we report on genetic diversity within the pelagic copepod Pleuromamma abdominalis in the poorly known Southeast Pacific region, with samples spanning an ocean gradient from coastal upwelling to the oligotrophic South Pacific Subtropical Gyre. We assessed variation in fragments of the mitochondrial (mt) genes cytochrome c oxidase subunit I (COI) and Cytochrome b as well as in the nuclear internal transcribed spacer (ITS) region and 28 S rRNA. Phylogenetic analyses revealed the presence of 8 divergent lineages occurring across the gradient with genetic distances in the range of 0.036 and 0.44 (mt genes), and GMYC species delimitation methods support their inference as distinct (undescribed) species. Genetic lineages occurring across the zonal gradient showed strong genetic structuring, with the presence of at least two new lineages within the coastal upwelling zone, revealing an unexpectedly high level of endemism within the Humboldt Current System. Multivariate analyses found strong correlation between genetic variation and surface chlorophyll-a and salinity, suggesting an important role for hydrographic gradients in maintaining genetic diversity. However, the presence of cryptic lineages within the upwelling zone cannot be easily accounted for by environmental heterogeneity and poses challenging questions for understanding the speciation process for oceanic zooplankton.
Bioremediation of soils saturated with spilled crude oil
Authors: Ali Nedaa , Dashti Narjes , Khanafer Majida , Al-Awadhi Husain , Radwan Samir
Published: January 2020

A desert soil sample was saturated with crude oil (17.3%, w/w) and aliquots were diluted to different extents with either pristine desert or garden soils. Heaps of all samples were exposed to outdoor conditions through six months, and were repeatedly irrigated with water and mixed thoroughly. Quantitative determination of the residual oil in the samples revealed that oil-bioremediation in the undiluted heaps was nearly as equally effective as in the diluted ones. One month after starting the experiment. 53 to 63% of oil was removed. During the subsequent five months, 14 to 24% of the oil continued to be consumed. The dynamics of the hydrocarbonoclastic bacterial communities in the heaps was monitored. The highest numbers of those organisms coordinated chronologically with the maximum oil-removal. Out of the identified bacterial species, those affiliated with the genera Nocardioides (especially N. deserti), Dietzia (especially D. papillomatosis), Microbacterium, Micrococcus, Arthrobacter, Pseudomonas, Cellulomonas, Gordonia and others were main contributors to the oil-consumption. Some species, e.g. D. papillomatosis were minor community constituents at time zero but they prevailed at later phases. Most isolates tolerated up to 20% oil, and D. papillomatosis showed the maximum tolerance compared with all the other studied isolates. It was concluded that even in oil-saturated soil, self-cleaning proceeds at a normal rate. When pristine soil receives spilled oil, indigenous microorganisms suitable for dealing with the prevailing oil-concentrations become enriched and involved in oil-biodegradation.
Autofluorescence mediated red spherulocyte sorting provides insights into the source of spinochromes in sea urchins
Authors: Hira Jonathan , Wolfson Deanna , Andersen Aaron John Christian , Haug Tor , Stensvåg Klara
Published: January 2020

Red spherule cells (RSCs) are considered one of the prime immune cells of sea urchins, but their detailed biological role during immune responses is not well elucidated. Lack of pure populations accounts for one of the major challenges of studying these cells. In this study, we have demonstrated that live RSCs exhibit strong, multi-colour autofluorescence distinct from other coelomocytes, and with the help of fluorescence-activated cell sorting (FACS), a pure population of live RSCs was successfully separated from other coelomocytes in the green sea urchin, Strongylocentrotus droebachiensis. This newly developed RSCs isolation method has allowed profiling of the naphthoquinone content in these cells. With the use of ultra high-performance liquid chromatography, UV absorption spectra, and high-resolution tandem mass spectrometry, it was possible to identify sulphated derivatives of spinochrome C, D, E and spinochrome dimers, which suggests that the RSCs may play an important biological role in the biogenesis of naphthoquinone compounds and regulating their bioactivity.
Experimental subjects do not know what we think they know
Authors: Field Jared M. , Bonsall Michael B.
Published: January 2020

Many biological, psychological and economic experiments have been designed where an organism or individual must choose between two options that have the same expected reward but differ in the variance of reward received. In this way, designed empirical approaches have been developed for evaluating risk preferences. Here, however, we show that if the experimental subject is inferring the reward distribution (to optimize some process), they will rarely agree in finite time that the expected rewards are equal. In turn, we argue that this makes discussions of risk preferences, and indeed the motivations of behaviour, not so simple or straightforward to interpret. We use this particular experiment to highlight the serious need to consider the frame of reference of the experimental subject in studies of behaviour.