bluuebunny/crossref_metadata_2025 huggingface dataset:
A Pythagorean tree fractal shape stub-loaded resonator as a UWB bandpass filter with wide stopband
Authors: Kumari Puja , Sarkar Pankaj , Ghatak Rowdra
Published: January 2021

A compact ultrawideband (UWB) bandpass filter (BPF) is designed by harnessing the efficacy of a Pythagorean tree fractal shape stub-loaded resonator. The design inherently provides the passband transmission poles, which make it convenient to be used in wide passband filtering circuits. The number and the position of the resonating modes can be controlled by increasing the iterations of the Pythagorean tree, as analyzed using odd- and even-mode analysis. Design steps of the BPF are detailed. The designed UWB BPF takes up a small circuit area of (12.13 × 9.59) mm2. The proposed design is fabricated and measured to verify the simulated results. The stopband is extended up to 17.5 GHz with a maximum attenuation of 15 dB.
TheArgentineAllusion:On the Significance of the Southern Cone in Early Twentieth-Century São Paulo
Authors: Woodard James P.
Published: January 2021

This article examines a much cited but little understood aspect of the Latin American intellectual and cultural ferment of the 1910s and 1920s: the frequency with which intellectuals from the southeastern Brazilian state of São Paulo referred to developments in post Sáenz Peña Argentina, and to a lesser extent in Uruguay and Chile. In books, pamphlets, speeches, and the pages of a vibrant periodical press—all key sources for this article—São Paulo intellectuals extolled developments in the Southern Cone, holding them out for imitation, especially in their home state. News of such developments reached São Paulo through varied sources, including the writings of foreign travelers, which reached intellectuals and their publics through different means. Turning from circuits and sources to motives and meanings, the Argentine allusion conveyed aspects of how these intellectuals were thinking about their own society. The sense that São Paulo, in particular, might be “ready” for reform tending toward democratization, as had taken place in Argentina, Uruguay, and Chile, was accompanied by a belief in the difference of their southeastern state from other Brazilian states and its affinities with climactically temperate and racially “white” Spanish America. While these imagined affinities were soon forgotten, that sense of difference—among other legacies of this crucial period—would remain.
Two Atmospheric Responses to Winter Sea Ice Decline Over the Barents‐Kara Seas
Authors: Jiang Zhina , Feldstein Steven B. , Lee Sukyoung
Published: January 2021

The intraseasonal atmospheric responses to winter sea ice decline over the Barents‐Kara Seas are examined by dividing rapid sea ice decline events into two categories, based on the direction (upward vs. downward) of the anomalous surface turbulent heat flux (ASTHF) after the sea ice loss. The upward ASTHF events, which could potentially have a large impact on the overlying atmosphere, are characterized by anomalously negative total column water and surface air temperature minus skin temperature, and anomalously positive surface wind speed following the sea ice loss. The downward ASTHF events show opposite features. Both types of events are linked to the Madden‐Julian Oscillation and subsequent circulation anomalies. This result indicates that on the intraseasonal time scale, not all sea ice decline events influence the atmosphere, and caution is called for when designing transient model experiments using observed sea ice decline.
Future Changes in the Hadley Circulation: The Role of Ocean Heat Transport
Authors: Chemke R.
Published: January 2021

The projected widening and weakening of the Hadley circulation hold large societal impacts at low and subtropical latitudes. Previous studies suggested that ocean heat transport (OHT) might play a central role in future circulation's changes. Here, using ensembles of model integrations, we quantify the role of OHT in the evolution of the Hadley cell over the 20th and 21st centuries. We find that by the end of the current century OHT reduces the widening of the circulation by ∼35% (0.42°) and its weakening by ∼60% (1.3 × 1010 kg s−1). As a result, OHT delays the emergence from internal variability of the widening by 30 years and of the weakening by 20 years. Lastly, while oceanic heat uptake accounts for most of the reduced widening, and thus merely delays it by reducing surface warming, horizontal heat transport and net heat uptake have comparable impacts to reduce the weakening of the circulation.
Mode Coupling From Kinetic Alfvén Waves to Electron Acoustic Waves in the Topside Ionosphere
Authors: Shi Run , Liang Jun , Ni Binbin
Published: January 2021

The propagation and energy transfer of kinetic Alfvén waves (KAWs) in the topside ionosphere are investigated based on a drift kinetic model. We examine the dependence of the generation of electron acoustic waves (EAWs) on the perpendicular wavelength and on the hot electron temperature. With decreasing perpendicular wavelength and increasing hot electron temperature, the coupling of KAWs to EAWs becomes increasingly important. The Landau damping of the EAWs is strong except in the transition region, where the nonlinear dissipation can be important. With increasing wave amplitude, the generated electron acoustic mode waves become unsustainable when the depletion of cold electron density is comparable to the initial background cold electron density. These findings indicate that electron acoustic mode waves play an important role at kinetic scales in the topside ionosphere.
The Unstable Relationship Between the Precipitation Dipole Pattern in the Tibetan Plateau and Summer NAO
Authors: Liu Yong , Chen Huopo , Hu Xiaoyu
Published: January 2021

Substantial progress has been made in understanding the relationship between summer precipitation in the Tibetan Plateau (TP) and North Atlantic Oscillation (NAO), but impacts of the summer NAO on precipitation spatial pattern remain controversial. Using the long‐term observational and reanalysis datasets, we have identified the intimate relationship between summer NAO and TP precipitation dipole pattern has been weakened since the late 1990s. Changes in regional atmospheric circulation induced by the asymmetrical wave propagation structure along the Eurasian continent are responsible for this weakened linkage. Further analyses revealed that the wave propagation anomalies are mainly induced by interdecadal change of summer NAO, which is attributed to the Atlantic multidecadal oscillation (AMO) variations. Moreover, the model simulations derived from the Geophysical Fluid Dynamics Laboratory (GFDL AM2.1) provide direct evidence to demonstrate that the AMO phase transition contributes to the unstable relationship between the summer NAO and precipitation dipole pattern in the eastern TP.
Modeling the Radiative Effect on Microphysics in Cirrus Clouds Against Satellite Observations
Authors: Zeng Xiping , Gong Jie , Li Xiaowen , Wu Dong L.
Published: January 2021

The radiative effect on microphysics (REM) plays an important role in the dew/frost formation near the surface. How REM impacts cirrus clouds is investigated in this study, using bin microphysical model simulations and coincident data of the CloudSat and Global Precipitation Measurement (GPM) satellites. REM affects ice crystal spectrum with two types: radiative cooling and warming. Radiative cooling, as predicted by the bin‐model simulations, favors the formation of horizontally oriented ice crystals (HOICs), but radiative warming does not. Hence, a test of REM can be transformed to a test of HOICs, because HOICs can be measured by the microwave polarization observations of the GPM Microwave Imager (GMI) at 166 GHz. To analyze the GMI data for their HOIC distribution, clouds are sorted into four groups with different optical depth and altitude, based on the radiative cooling/warming ratio (or eta) computed with satellite‐retrieved ice water content. Their HOIC distributions (e.g., the midlevel thick clouds have more HOICs than the high‐level ones) agree well with those predicted by the bin‐model simulations. The general agreement between the GMI observations and bin‐model simulations suggests that REM is common in cirrus clouds and impacts cirrus clouds significantly.
Combining Remote Sensing and Crop Models to Assess the Sustainability of Stakeholder‐Driven Groundwater Management in the US High Plains Aquifer
Authors: Deines Jillian M. , Kendall Anthony D. , Butler James J. , Basso Bruno , Hyndman David W.
Published: January 2021

Nonrenewable groundwater contributes ∼20% of global irrigation water. As a result, key agricultural regions around the world are on unsustainable trajectories due to aquifer depletion, threatening food production and local economies. With increasing resource scarcity in the central High Plains Aquifer in the United States, an innovative stakeholder‐driven groundwater management framework emerged in Kansas referred to as the Local Enhanced Management Area (LEMA) program. This framework enables groups of irrigators to join together to implement measures to conserve groundwater. Here, we assessed the efficacy of the first LEMA to move the region toward sustainability with a process‐based crop model driven by well records and satellite‐derived annual land use. We found increased irrigation efficiency under the LEMA program reduced groundwater extraction by 25% (40 million m3). However, only 22% of pumping reductions benefitted the net water balance (9 million m3) due to decreased irrigation return flow resulting from increased irrigation efficiency. We then estimated economic impacts using simulated crop yields, commodity prices, and estimated energy saved from reduced groundwater pumping. Cost savings from reduced pumping were about 4.5 times greater than the income lost from minor yield penalties. This suggests that the program promotes both economic and water sustainability, but water targets may need to be more strict to stabilize groundwater levels. As aquifer depletion threatens crop production in many parts of the world, approaches that integrate dynamic process‐based models with in situ and satellite data can inform economically and hydrologically sustainable management strategies. Our work highlights the need to consider both economic factors and root zone processes when evaluating irrigation conservation programs.
Sowing Seeds of Food Security in Africa
Authors: Nakalembe Catherine , Justice Christina , Kerner Hannah , Justice Christopher , Becker-Reshef Inbal
Published: January 2021

An innovative program focused on collaboration and capacity building is looking to improve outcomes for smallholder farmers, reduce hunger, and alleviate food insecurity in sub-Saharan Africa.
Climate Change Uproots Global Agriculture
Authors: Cartier Kimberly
Published: January 2021

Climate change is shifting where ideal growing conditions exist and is leaving farmers behind. How can we secure our future food supply and support the people who grow it?
Enhancing Food Security Through Earth Science Data
Authors: Brown M.
Published: January 2021

When most agriculture in the world is rural, getting crucial geoscience information to farmers is a technical challenge that a few organizations are just starting to figure out.
Vitamin D and schizophrenia: 20 years on
Authors: Cui Xiaoying , McGrath John J. , Burne Thomas H. J. , Eyles Darryl W.
Published: January 2021

Many epidemiological studies have highlighted the link between vitamin D deficiency and schizophrenia. In particular, two prominent studies report an association between neonatal vitamin D deficiency and an increased risk of schizophrenia. In parallel, much has been learnt about the role of vitamin D in the developing central nervous system over the last two decades. Studies in rodent models of developmental vitamin D (DVD)-deficiency describe how brain development is altered leading to a range of neurobiological and behavioral phenotypes of interest to schizophrenia. While glutamate and gamma aminobutyric acid (GABA) systems have been little investigated in these models, alterations in developing dopamine systems are frequently reported. There have been far more studies reporting patients with schizophrenia have an increased risk of vitamin D deficiency compared to well controls. Here we have conducted a systematic review and meta-analysis that basically confirms this association and extends this to first-episode psychosis. However, patients with schizophrenia also have poorer general health, poorer diets, are frequently less active and also have an increased risk of other medical conditions, all factors which reduce circulating vitamin D levels. Therefore, we would urge caution in any causal interpretation of this association. We also summarize the inconsistent results from existing vitamin D supplementation trials in patients with schizophrenia. In respect to animal models of adult vitamin D deficiency, such exposures produce subtle neurochemical alterations and effects on cognition but do not appear to produce behavioral phenotypes of relevance to schizophrenia. We conclude, the hypothesis that vitamin D deficiency during early life may increase the risk of schizophrenia remains plausible and warrants ongoing research.
The prevalence of depressive and anxiety symptoms and their associations with quality of life among clinically stable older patients with psychiatric disorders during the COVID-19 pandemic
Authors: Li Wen , Zhao Na , Yan Xiaona , Zou Siyun , Wang Huan , Li Yulong , Xu Xiuying , Du Xiangdong , Zhang Lan , Zhang Qinge , Cheung Teris , Ungvari Gabor S. , Ng Chee H. , Xiang Yu-Tao
Published: January 2021

The impact of the COVID-19 pandemic on clinically stable older patients with psychiatric disorders is unclear. This study examined the prevalence of depressive and anxiety symptoms, and their associations with quality of life (QOL) in clinically stable older patients with psychiatric disorders during the COVID-19 pandemic. This was a multicenter, cross-sectional study. Depressive and anxiety symptoms, insomnia, pain, and QOL were assessed with standardized instruments. A total of 1063 patients were included. The prevalence of depressive and anxiety symptoms, and combined depressive and anxiety symptoms were 62.3% (95%CI = 59.4–65.2%), 52.4% (95%CI = 49.3–55.4%), and 45.9% (95%CI = 42.9–48.9%), respectively. Patients with depressive and anxiety symptoms had significantly lower QOL than those without (P < 0.01). Binary logistic regression analyses revealed that having depressive symptoms was positively associated with more severe insomnia (OR = 1.29, P < 0.01) and pain (OR = 1.14, P < 0.01), and was negatively associated with other psychiatric diagnoses (except for major depressive disorder, schizophrenia, and organic mental disorder; OR = 0.50, P < 0.01), while having anxiety symptoms was positively associated with severe physical diseases (OR = 1.57, P = 0.02), poor adherence to treatment (OR = 1.50, P < 0.01), and more severe insomnia (OR = 1.15, P < 0.01) and pain (OR = 1.11, P < 0.01). Having combined depression and anxiety symptoms was positively associated with poor adherence to treatment (OR = 1.42, P = 0.02) and more severe insomnia (OR = 1.19, P < 0.01) and pain (OR = 1.15, P < 0.01), and was negatively associated with the diagnosis of schizophrenia (OR = 0.50, P = 0.04) and others (OR = 0.53, P < 0.01). Depressive and anxiety symptoms were common in clinically stable older patients with psychiatric disorders during the COVID-19 pandemic. Considering the negative impact of these symptoms on QOL, regular screening and appropriate treatment are recommended for this population.
PGC7 promotes tumor oncogenic dedifferentiation through remodeling DNA methylation pattern for key developmental transcription factors
Authors: Yan Qian , Zhang Yu , Fang Xiaona , Liu Beilei , Wong Tin Lok , Gong Lanqi , Liu Shan , Yu Dandan , Liu Ming , Jiang Lingxi , Wang Xia , Wei Ting , Jia Yongxu , Li Lei , Sun Liangzhan , Tang Ying , Zhou Ningning , Yuan Yun-Fei , Li Yan , Ma Stephanie , Guan Xin-Yuan
Published: January 2021

Poorly differentiated tumors usually exhibit phenotypes similar to that of their developmental precursor cells. Tumor cells that acquire the lineage progenitor cells feature usually exploit developmental signaling to potentiate cancer progression. However, the underlying molecular events remain elusive. In this study, based on analysis of an in vitro hepatocyte differentiation model, the maternal factor PGC7 (also known as DPPA3, STELLA) was found closely associated with liver development and tumor differentiation in hepatocellular carcinoma (HCC). Expression of PGC7 decreased during hepatocyte maturation and increased progressively from well-differentiated HCCs to poorly differentiated HCCs. Whole-genome methylation sequencing found that PGC7 could induce promoter demethylation of genes related to development. Pathway-based network analysis indicated that downstream targets of PGC7 might form networks associated with developmental transcription factor activation. Overexpression of PGC7 conferred progenitor-like features of HCC cells both in vitro and in vivo. Mechanism studies revealed that PGC7 could impede nuclear translocation of UHRF1, and thus facilitate promoter demethylation of GLI1 and MYCN, both of which are important regulators of HCC self-renewal and differentiation. Depletion or inhibition of GLI1 effectively downregulated MYCN, abolished the effect of PGC7, and sensitized HCC cells to sorafenib treatment. In addition, we found a significant correlation of PGC7 with GLI1/MYCN and lineage differentiation markers in clinical HCC patients. PGC7 expression might drive HCC toward a “dedifferentiated” progenitor lineage through facilitating promoter demethylation of key developmental transcription factors; further inhibition of PGC7/GLI1/MYCN might reverse poorly differentiated HCCs and provide novel therapeutic strategies.
The HSP-RTK-Akt axis mediates acquired resistance to Ganetespib in HER2-positive breast cancer
Authors: Eyermann Christopher E. , Haley John D. , Alexandrova Evguenia M.
Published: January 2021

Breast cancer is the leading cause of cancer-related death in women worldwide. Human epidermal growth factor receptor 2 (HER2)-positive subtype comprises 20% of sporadic breast cancers and is an aggressive disease. While targeted therapies have greatly improved its management, primary and acquired resistance remain a major roadblock to making it a curable malignancy. Ganetespib, an Hsp90 (Heat shock protein 90) small molecule inhibitor, shows preferential efficacy in HER2-positive breast cancer, including therapy-refractory cases, and has an excellent safety profile in ongoing clinical trials (38 in total, six on breast cancer). However, Ganetespib itself evokes acquired resistance, which is a significant obstacle to its clinical advancement. Here, we show that Ganetespib potently, albeit temporarily, suppresses HER2-positive breast cancer in genetic mouse models, but the animals eventually succumb via acquired resistance. We found that Ganetespib-resistant tumors upregulate several compensatory HSPs, as well as a wide network of phospho-activated receptor tyrosine kinases (RTKs), many of which are HSP clients. Downstream of p-RTKs, the MAPK pathway remains suppressed in the resistant tumors, as is HER2 itself. In contrast, the p-RTK effector Akt is stabilized and phospho-activated. Notably, pharmacological inhibition of Akt significantly delays acquired Ganetespib resistance, by 50%. These data establish Akt as a unifying actionable node downstream of the broadly upregulated HSP/p-RTK resistance program and suggests that Akt co-targeting with Ganetespib may be a superior therapeutic strategy in the clinic.
TROAP switches DYRK1 activity to drive hepatocellular carcinoma progression
Authors: Li Lei , Wei Jia-Ru , Song Ye , Fang Shuo , Du Yanyu , Li Zhuo , Zeng Ting-Ting , Zhu Ying-Hui , Li Yan , Guan Xin-Yuan
Published: January 2021

Hepatocellular carcinoma (HCC) is one of the common malignancy and lacks effective therapeutic targets. Here, we demonstrated that ectopic expression of trophinin-associated protein (TROAP) dramatically drove HCC cell growth assessed by foci formation in monolayer culture, colony formation in soft agar and orthotopic liver transplantation in nude mice. Inversely, silencing TROAP expression with short-hairpin RNA attenuated the malignant proliferation of HCC cells in vitro and in vivo. Next, mechanistic investigation revealed that TROAP directly bound to dual specificity tyrosine phosphorylation regulated kinase 1A/B (DYRK1A/B), resulting in the cytoplasmic retention of proteins DYRK1A/B and promoting cell cycle process via activation of Akt/GSK-3β signaling. Combination of cisplatin with an inhibitor of DYRK1 AZ191 effectively inhibited tumor growth in mouse model for HCC cells with high level of TROAP. Clinically, TROAP was significantly upregulated by miR-142-5p in HCC tissues, which predicted the poor survival of patients with HCC. Therefore, TROAP/DYRK1/Akt axis may be a promising therapeutic target and prognostic indicator for patients with HCC.
Zika virus infection induces endoplasmic reticulum stress and apoptosis in placental trophoblasts
Authors: Muthuraj Philma Glora , Sahoo Prakash K. , Kraus Madison , Bruett Taylor , Annamalai Arun S. , Pattnaik Aryamav , Pattnaik Asit K. , Byrareddy Siddappa N. , Natarajan Sathish Kumar
Published: January 2021

Zika virus (ZIKV) infection to a pregnant woman can be vertically transmitted to the fetus via the placenta leading to Congenital Zika syndrome. This is characterized by microcephaly, retinal defects, and intrauterine growth retardation. ZIKV induces placental trophoblast apoptosis leading to severe abnormalities in the growth and development of the fetus. However, the molecular mechanism behind ZIKV-induced apoptosis in placental trophoblasts remains unclear. We hypothesize that ZIKV infection induces endoplasmic reticulum (ER) stress in the trophoblasts, and sustained ER stress results in apoptosis. HTR-8 (HTR-8/SVneo), a human normal immortalized trophoblast cell and human choriocarcinoma-derived cell lines (JEG-3 and JAR) were infected with ZIKV. Biochemical and structural markers of apoptosis like caspase 3/7 activity and percent apoptotic nuclear morphological changes, respectively were assessed. ZIKV infection in placental trophoblasts showed an increase in the levels of CHOP mRNA and protein expression, which is an inducer of apoptosis. Next, we also observed increased levels of ER stress markers such as phosphorylated forms of inositol-requiring transmembrane kinase/endoribonuclease 1α (P-IRE1α), and its downstream target, the spliced form of XBP1 mRNA, phosphorylated eukaryotic initiation factor 2α (P-eIF2α), and activation of cJun N-terminal Kinase (JNK) and p38 mitogen activated protein kinase (MAPK) after 16–24 h of ZIKV infection in trophoblasts. Inhibition of JNK or pan-caspases using small molecule inhibitors significantly prevented ZIKV-induced apoptosis in trophoblasts. Further, JNK inhibition also reduced XBP1 mRNA splicing and viral E protein staining in ZIKV infected cells. In conclusion, the mechanism of ZIKV-induced placental trophoblast apoptosis involves the activation of ER stress and JNK activation, and the inhibition of JNK dramatically prevents ZIKV-induced trophoblast apoptosis.
Complex hereditary spastic paraplegia associated with episodic visual loss caused by ACO2 variants
Authors: Tozawa Takenori , Nishimura Akira , Ueno Tamaki , Shikata Akane , Taura Yoshihiro , Yoshida Takeshi , Nakagawa Naoko , Wada Takahito , Kosugi Shinji , Uehara Tomoko , Takenouchi Toshiki , Kosaki Kenjiro , Chiyonobu Tomohiro
Published: January 2021

Most patients with homozygous or compound heterozygous pathogenic ACO2 variants present with muscular hypotonia features, namely, infantile cerebellar-retinal degeneration. Recently, two studies reported rare familial cases of ACO2 variants presenting as complex hereditary spastic paraplegia (HSP) with broad clinical spectra. Here, we report the case of a 20-year-old Japanese woman with complex HSP caused by compound heterozygous ACO2 variants, revealing a new phenotype of episodic visual loss during febrile illness.
Uncooled sub-GHz spin bolometer driven by auto-oscillation
Authors: Goto Minori , Yamada Yuma , Shimura Atsushi , Suzuki Tsuyoshi , Degawa Naomichi , Yamane Takekazu , Aoki Susumu , Urabe Junichiro , Hara Shinji , Nomura Hikaru , Suzuki Yoshishige
Published: January 2021

Bolometers are rectification devices that convert electromagnetic waves into direct current voltage through a temperature change. A superconducting bolometer has a responsivity of approximately 106–107 V/W under cryogenic temperatures at infrared wavelengths; however, no devices have realized such a high responsivity in the sub-GHz frequency region. We describe a spin bolometer with a responsivity of (4.40 ± 0.04) × 106 V/W in the sub-GHz region at room temperature using heat generated in magnetic tunnel junctions through auto-oscillation. We attribute the unexpectedly high responsivity to a heat-induced spin-torque. This spin-torque modulates and synchronizes the magnetization precession due to the spin-torque auto-oscillation and produces a large voltage output. In our device, heat-induced spin-torque was obtained because of a large heat-controlled magnetic anisotropy change: −2.7 µJ/Wm, which is significant for enhancing dynamic range and responsivity. This study can potentially lead to the development of highly sensitive microwave detectors in the sub-GHz region.
Role of mutational reversions and fitness restoration in Zika virus spread to the Americas
Authors: Liu Jianying , Liu Yang , Shan Chao , Nunes Bruno T. D. , Yun Ruimei , Haller Sherry L. , Rafael Grace H. , Azar Sasha R. , Andersen Clark R. , Plante Kenneth , Vasilakis Nikos , Shi Pei-Yong , Weaver Scott C.
Published: January 2021

Zika virus (ZIKV) emerged from obscurity in 2013 to spread from Asia to the South Pacific and the Americas, where millions of people were infected, accompanied by severe disease including microcephaly following congenital infections. Phylogenetic studies have shown that ZIKV evolved in Africa and later spread to Asia, and that the Asian lineage is responsible for the recent epidemics in the South Pacific and Americas. However, the reasons for the sudden emergence of ZIKV remain enigmatic. Here we report evolutionary analyses that revealed four mutations, which occurred just before ZIKV introduction to the Americas, represent direct reversions of previous mutations that accompanied earlier spread from Africa to Asia and early circulation there. Our experimental infections ofAedes aegyptimosquitoes, human cells, and mice using ZIKV strains with and without these mutations demonstrate that the original mutations reduced fitness for urban, human-amplifed transmission, while the reversions restored fitness, increasing epidemic risk. These findings include characterization of three transmission-adaptive ZIKV mutations, and demonstration that these and one identified previously restored fitness for epidemic transmission soon before introduction into the Americas. The initial mutations may have followed founder effects and/or drift when the virus was introduced decades ago into Asia.
Orthogonal translation enables heterologous ribosome engineering in E. coli
Authors: Kolber Natalie S. , Fattal Ranan , Bratulic Sinisa , Carver Gavriela D. , Badran Ahmed H.
Published: January 2021

The ribosome represents a promising avenue for synthetic biology, but its complexity and essentiality have hindered significant engineering efforts. Heterologous ribosomes, comprising rRNAs and r-proteins derived from different microorganisms, may offer opportunities for novel translational functions. Such heterologous ribosomes have previously been evaluated in E. coli via complementation of a genomic ribosome deficiency, but this method fails to guide the engineering of refractory ribosomes. Here, we implement orthogonal ribosome binding site (RBS):antiRBS pairs, in which engineered ribosomes are directed to researcher-defined transcripts, to inform requirements for heterologous ribosome functionality. We discover that optimized rRNA processing and supplementation with cognate r-proteins enhances heterologous ribosome function for rRNAs derived from organisms with ≥76.1% 16S rRNA identity to E. coli. Additionally, some heterologous ribosomes undergo reduced subunit exchange with E. coli-derived subunits. Cumulatively, this work provides a general framework for heterologous ribosome engineering in living cells.
Quantum-mechanical exploration of the phase diagram of water
Authors: Reinhardt Aleks , Cheng Bingqing
Published: January 2021

The set of known stable phases of water may not be complete, and some of the phase boundaries between them are fuzzy. Starting from liquid water and a comprehensive set of 50 ice structures, we compute the phase diagram at three hybrid density-functional-theory levels of approximation, accounting for thermal and nuclear fluctuations as well as proton disorder. Such calculations are only made tractable because we combine machine-learning methods and advanced free-energy techniques. The computed phase diagram is in qualitative agreement with experiment, particularly at pressures ≲ 8000 bar, and the discrepancy in chemical potential is comparable with the subtle uncertainties introduced by proton disorder and the spread between the three hybrid functionals. None of the hypothetical ice phases considered is thermodynamically stable in our calculations, suggesting the completeness of the experimental water phase diagram in the region considered. Our work demonstrates the feasibility of predicting the phase diagram of a polymorphic system from first principles and provides a thermodynamic way of testing the limits of quantum-mechanical calculations.
Dynamic electron correlations with charge order wavelength along all directions in the copper oxide plane
Authors: Boschini F. , Minola M. , Sutarto R. , Schierle E. , Bluschke M. , Das S. , Yang Y. , Michiardi M. , Shao Y. C. , Feng X. , Ono S. , Zhong R. D. , Schneeloch J. A. , Gu G. D. , Weschke E. , He F. , Chuang Y. D. , Keimer B. , Damascelli A. , Frano A. , da Silva Neto E. H.
Published: January 2021

In strongly correlated systems the strength of Coulomb interactions between electrons, relative to their kinetic energy, plays a central role in determining their emergent quantum mechanical phases. We perform resonant x-ray scattering on Bi2Sr2CaCu2O8+δ, a prototypical cuprate superconductor, to probe electronic correlations within the CuO2 plane. We discover a dynamic quasi-circular pattern in the x-y scattering plane with a radius that matches the wave vector magnitude of the well-known static charge order. Along with doping- and temperature-dependent measurements, our experiments reveal a picture of charge order competing with superconductivity where short-range domains along x and y can dynamically rotate into any other in-plane direction. This quasi-circular spectrum, a hallmark of Brazovskii-type fluctuations, has immediate consequences to our understanding of rotational and translational symmetry breaking in the cuprates. We discuss how the combination of short- and long-range Coulomb interactions results in an effective non-monotonic potential that may determine the quasi-circular pattern.
Author Correction: Donkey genomes provide new insights into domestication and selection for coat color
Authors: Wang Changfa , Li Haijing , Guo Yu , Huang Jinming , Sun Yan , Min Jiumeng , Wang Jinpeng , Fang Xiaodong , Zhao Zicheng , Wang Shuai , Zhang Yanlin , Liu Qingfeng , Jiang Qiang , Wang Xiuge , Guo Yijun , Yang Chunhong , Wang Yinchao , Tian Fang , Zhuang Guilong , Fan Yanna , Gao Qican , Li Yuhua , Ju Zhihua , Li Jianbin , Li Rongling , Hou Minghai , Yang Guiwen , Liu Guiqin , Liu Wenqiang , Guo Jiao , Pan Shanshan , Fan Guangyi , Zhang Wei , Zhang Ruitao , Yu Jie , Zhang Xinhao , Yin Qi , Ji Chuanliang , Jin Yuanchun , Yue Guidong , Liu Mei , Xu Jiake , Liu Shimin , Jordana Jordi , Noce Antonia , Amills Marcel , Wu Dong Dong , Li Shuaicheng , Zhou Xiangshan , Zhong Jifeng
Published: January 2021

A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-21014-9
Predicting stable crystalline compounds using chemical similarity
Authors: Wang Hai-Chen , Botti Silvana , Marques Miguel A. L.
Published: January 2021

We propose an efficient high-throughput scheme for the discovery of stable crystalline phases. Our approach is based on the transmutation of known compounds, through the substitution of atoms in the crystal structure with chemically similar ones. The concept of similarity is defined quantitatively using a measure of chemical replaceability, extracted by data-mining experimental databases. In this way we build 189,981 possible crystal phases, including 18,479 that are on the convex hull of stability. The resulting success rate of 9.72% is at least one order of magnitude better than the usual success rate of systematic high-throughput calculations for a specific family of materials, and comparable with speed-up factors of machine learning filtering procedures. As a characterization of the set of 18,479 stable compounds, we calculate their electronic band gaps, magnetic moments, and hardness. Our approach, that can be used as a filter on top of any high-throughput scheme, enables us to efficiently extract stable compounds from tremendously large initial sets, without any initial assumption on their crystal structures or chemical compositions.
The complementary graphene growth and etching revealed by large-scale kinetic Monte Carlo simulation
Authors: Kong Xiao , Zhuang Jianing , Zhu Liyan , Ding Feng
Published: January 2021

To fully understand the kinetics of graphene growth, large-scale atomic simulations of graphene islands evolution up to macro sizes (i.e., graphene islands of a few micrometers or with billions of carbon atoms) during growth and etching is essential, but remains a great challenge. In this paper, we developed a low computational cost large-scale kinetic Monte Carlo (KMC) algorithm, which includes all possible events of carbon attachments and detachments on various edge sites of graphene islands. Such a method allows us to simulate the evolution of graphene islands with sizes up to tens of micrometers during either growth or etching with a single CPU core. With this approach and the carefully fitted parameters, we have reproduced the experimentally observed evolution of graphene islands during both growth or etching on Pt(111) surface, and revealed more atomic details of graphene growth and etching. Based on the atomic simulations, we discovered a complementary relationship of graphene growth and etching—the route of graphene island shape evolution during growth is exactly the same as that of the etching of a hole in graphene and that of graphene island etching is exactly same as that of hole growth. The complementary relation brings us a basic principle to understand the growth and etching of graphene, and other 2D materials from atomic scale to macro size and the KMC algorithm is expected to be further developed into a standard simulation package for investigating the growth mechanism of 2D materials on various substrates.
A deep learning-based model for screening and staging pneumoconiosis
Authors: Zhang Liuzhuo , Rong Ruichen , Li Qiwei , Yang Donghan M. , Yao Bo , Luo Danni , Zhang Xiong , Zhu Xianfeng , Luo Jun , Liu Yongquan , Yang Xinyue , Ji Xiang , Liu Zhidong , Xie Yang , Sha Yan , Li Zhimin , Xiao Guanghua
Published: January 2021

This study aims to develop an artificial intelligence (AI)-based model to assist radiologists in pneumoconiosis screening and staging using chest radiographs. The model, based on chest radiographs, was developed using a training cohort and validated using an independent test cohort. Every image in the training and test datasets were labeled by experienced radiologists in a double-blinded fashion. The computational model started by segmenting the lung field into six subregions. Then, convolutional neural network classification model was used to predict the opacity level for each subregion respectively. Finally, the diagnosis for each subject (normal, stage I, II, or III pneumoconiosis) was determined by summarizing the subregion-based prediction results. For the independent test cohort, pneumoconiosis screening accuracy was 0.973, with both sensitivity and specificity greater than 0.97. The accuracy for pneumoconiosis staging was 0.927, better than that achieved by two groups of radiologists (0.87 and 0.84, respectively). This study develops a deep learning-based model for screening and staging of pneumoconiosis using man-annotated chest radiographs. The model outperformed two groups of radiologists in the accuracy of pneumoconiosis staging. This pioneer work demonstrates the feasibility and efficiency of AI-assisted radiography screening and diagnosis in occupational lung diseases.
Enhanced laser-driven proton acceleration using nanowire targets
Authors: Vallières S. , Salvadori M. , Permogorov A. , Cantono G. , Svendsen K. , Chen Z. , Sun S. , Consoli F. , d’Humières E. , Wahlström C.-G. , Antici P.
Published: January 2021

Laser-driven proton acceleration is a growing field of interest in the high-power laser community. One of the big challenges related to the most routinely used laser-driven ion acceleration mechanism, Target-Normal Sheath Acceleration (TNSA), is to enhance the laser-to-proton energy transfer such as to maximize the proton kinetic energy and number. A way to achieve this is using nanostructured target surfaces in the laser-matter interaction. In this paper, we show that nanowire structures can increase the maximum proton energy by a factor of two, triple the proton temperature and boost the proton numbers, in a campaign performed on the ultra-high contrast 10 TW laser at the Lund Laser Center (LLC). The optimal nanowire length, generating maximum proton energies around 6 MeV, is around 1–2 $$\upmu$$
μ
m. This nanowire length is sufficient to form well-defined highly-absorptive NW forests and short enough to minimize the energy loss of hot electrons going through the target bulk. Results are further supported by Particle-In-Cell simulations. Systematically analyzing nanowire length, diameter and gap size, we examine the underlying physical mechanisms that are provoking the enhancement of the longitudinal accelerating electric field. The parameter scan analysis shows that optimizing the spatial gap between the nanowires leads to larger enhancement than by the nanowire diameter and length, through increased electron heating.
Role of subnetworks mediated by $$\hbox {TNF}\alpha$$, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis
Authors: Pandey Rakesh , Al-Nuaimi Yusur , Mishra Rajiv Kumar , Spurgeon Sarah K. , Goodfellow Marc
Published: January 2021

Psoriasis is a chronic inflammatory skin disease clinically characterized by the appearance of red colored, well-demarcated plaques with thickened skin and with silvery scales. Recent studies have established the involvement of a complex signalling network of interactions between cytokines, immune cells and skin cells called keratinocytes. Keratinocytes form the cells of the outermost layer of the skin (epidermis). Visible plaques in psoriasis are developed due to the fast proliferation and unusual differentiation of keratinocyte cells. Despite that, the exact mechanism of the appearance of these plaques in the cytokine-immune cell network is not clear. A mathematical model embodying interactions between key immune cells believed to be involved in psoriasis, keratinocytes and relevant cytokines has been developed. The complex network formed of these interactions poses several challenges. Here, we choose to study subnetworks of this complex network and initially focus on interactions involving $$\hbox {TNF}_{\alpha }$$

TNF
α

, IL-23/IL-17, and IL-15. These are chosen based on known evidence of their therapeutic efficacy. In addition, we explore the role of IL-15 in the pathogenesis of psoriasis and its potential as a future drug target for a novel treatment option. We perform steady state analyses for these subnetworks and demonstrate that the interactions between cells, driven by cytokines could cause the emergence of a psoriasis state (hyper-proliferation of keratinocytes) when levels of $$\hbox {TNF}_{\alpha }$$

TNF
α

, IL-23/IL-17 or IL-15 are increased. The model results explain and support the clinical potentiality of anti-cytokine treatments. Interestingly, our results suggest different dynamic scenarios underpin the pathogenesis of psoriasis, depending upon the dominant cytokines of subnetworks. We observed that the increase in the level of IL-23/IL-17 and IL-15 could lead to psoriasis via a bistable route, whereas an increase in the level of $$\hbox {TNF}_{\alpha }$$

TNF
α

would lead to a monotonic and gradual disease progression. Further, we demonstrate how this insight, bistability, could be exploited to improve the current therapies and develop novel treatment strategies for psoriasis.
Wettability of semispherical droplets on layered elastic gradient soft substrates
Authors: Yang Yonglin , Li Xing , Wang Wenshuai
Published: January 2021

Research on the wettability of soft matter is one of the most urgently needed studies in the frontier domains, of which the wetting phenomenon of droplets on soft substrates is a hot subject. Scholars have done considerable studies on the wetting phenomenon of single-layer structure, but it is noted that the wetting phenomenon of stratified structure is ubiquitous in nature, such as oil exploitation from geological structural layers and shale gas recovery from shale formations. Therefore, the wettability of droplets on layered elastic gradient soft substrate is studied in this paper. Firstly, considering capillary force, elastic force and surface tension, the constitutive equation of the substrate in the vector function system is derived by using the vector function system in cylindrical coordinates, and the transfer relation of layered structure is obtained. Further, the integral expressions of displacement and stress of double Bessel function are given. Secondly, the numerical results of displacement and stress are obtained by using the numerical formula of double Bessel function integral. The results show that the deformation of the substrate weakens with the increase of the elastic modulus, also the displacement and stress change dramatically near the contact line, while the variation is flat when the contact radius is far away from the droplet radius.
Early production of table olives at a mid-7th millennium BP submerged site off the Carmel coast (Israel)
Authors: Galili E. , Langgut D. , Terral J. F. , Barazani O. , Dag A. , Kolska Horwitz L. , Ogloblin Ramirez I. , Rosen B. , Weinstein-Evron M. , Chaim S. , Kremer E. , Lev-Yadun S. , Boaretto E. , Ben-Barak-Zelas Z. , Fishman A.
Published: January 2021

We present here the earliest evidence for large-scale table olive production from the mid-7thmillennium BP inundated site of Hishuley Carmel on the northern Mediterranean coast of Israel. Olive pit size and fragmentation patterns, pollen as well as the architecture of installations associated with pits from this site, were compared to finds from the nearby and slightly earlier submerged Kfar Samir site. Results indicate that at Kfar Samir olive oil was extracted, while at Hishuley Carmel the data showed that large quantities of table olives, the oldest reported to date, were prepared. This process was most probably facilitated by the site’s proximity to the Mediterranean Sea, which served as a source of both sea water and salt required for debittering/pickling/salting the fruit, as experimentally demonstrated in this study. Comparison of pit morphometry from modern cultivars, wild-growing trees and the archaeological sites, intimates that in pit morphology the ancient pits resemble wild olives, but we cannot totally exclude the possibility that they derive from early cultivated trees. Our findings demonstrate that in this region, olive oil production may have predated table olive preparation, with each development serving as a milestone in the early exploitation of the olive.
High sensitivity rate-integrating hemispherical resonator gyroscope with dead area compensation for damping asymmetry
Authors: Zhao Wanliang , Yang Hao , Liu Fucheng , Su Yan , Li Chong
Published: January 2021

The rate-integrating gyroscope (RIG) operation is considered as the next generation architecture for hemispherical resonator gyroscopes (HRGs) with advantages of direct angle measurement and unlimited dynamic range. However, this RIG operation requires high symmetry for the HRG device and the damping mismatch of the two gyroscopic modes will result in a dead area problem. This work analyzes the error mechanism of the damping asymmetry induced dead area and proposed a novel virtual procession compensation method for HRG RIG. The simulation proves the existence of the dead area as the theory predicted. More importantly, the experimental HRG RIG platform with the proposed compensation method can significantly expand the dynamic range with accurate angle measurement and overcome the problem of dead area. The earth rotation is accurate measured which is the first time that captured by a RIG scheme as a state-of-the-art result.
Chronic BDNF simultaneously inhibits and unmasks superficial dorsal horn neuronal activity
Authors: Alles Sascha R. A. , Odem Max A. , Lu Van B. , Cassidy Ryan M. , Smith Peter A.
Published: January 2021

Brain-derived neurotrophic factor (BDNF) is critically involved in the pathophysiology of chronic pain. However, the mechanisms of BDNF action on specific neuronal populations in the spinal superficial dorsal horn (SDH) requires further study. We used chronic BDNF treatment (200 ng/ml, 5–6 days) of defined-medium, serum-free spinal organotypic cultures to study intracellular calcium ([Ca2+]i) fluctuations. A detailed quantitative analysis of these fluctuations using the Frequency-independent biological signal identification (FIBSI) program revealed that BDNF simultaneously depressed activity in some SDH neurons while it unmasked a particular subpopulation of ‘silent’ neurons causing them to become spontaneously active. Blockade of gap junctions disinhibited a subpopulation of SDH neurons and reduced BDNF-induced synchrony in BDNF-treated cultures. BDNF reduced neuronal excitability assessed by measuring spontaneous excitatory postsynaptic currents. This was similar to the depressive effect of BDNF on the [Ca2+]i fluctuations. This study reveals novel regulatory mechanisms of SDH neuronal excitability in response to BDNF.
Reduction of pTau and APP levels in mammalian brain after low-dose radiation
Authors: Iacono Diego , Murphy Erin K. , Avantsa Soundarya S. , Perl Daniel P. , Day Regina M.
Published: January 2021

Brain radiation can occur from treatment of brain tumors or accidental exposures. Brain radiation has been rarely considered, though, as a possible tool to alter protein levels involved in neurodegenerative disorders. We analyzed possible molecular and neuropathology changes of phosphorylated-Tau (pTau), all-Tau forms, β-tubulin, amyloid precursor protein (APP), glial fibrillary acidic protein (GFAP), ionized calcium binding adaptor molecule 1 (IBA-1), myelin basic protein (MBP), and GAP43 in Frontal Cortex (FC), Hippocampus (H) and Cerebellum (CRB) of swine brains following total-body low-dose radiation (1.79 Gy). Our data show that radiated-animals had lower levels of pTau in FC and H, APP in H and CRB, GAP43 in CRB, and higher level of GFAP in H versus sham-animals. These molecular changes were not accompanied by obvious neurohistological changes, except for astrogliosis in the H. These findings are novel, and might open new perspectives on brain radiation as a potential tool to interfere with the accumulation of specific proteins linked to the pathogenesis of various neurodegenerative disorders.