bluuebunny/crossref_metadata_2025 huggingface dataset:
Achieving Brazil's Deforestation Target Will Reduce Fire and Deliver Air Quality and Public Health Benefits
Authors: Butt Edward W. , Conibear Luke , Smith Callum , Baker Jessica C. A. , Rigby Richard , Knote Christoph , Spracklen Dominick V.
Published: November 2022

Climate, deforestation, and forest fires are closely coupled in the Amazon, but models of fire that include these interactions are lacking. We trained machine learning models on temperature, rainfall, deforestation, land‐use, and fire data to show that spatial and temporal patterns of fire in the Amazon are strongly modified by deforestation. We find that fire count across the Brazilian Amazon increases by 0.44 percentage points for each percentage point increase in deforestation rate. We used the model to predict that the increased deforestation rate in the Brazilian Amazon from 2013 to 2020 caused a 42% increase in fire counts in 2020. We predict that if Brazil had achieved the deforestation target under the National Policy on Climate Change, there would have been 32% fewer fire counts across the Brazilian Amazon in 2020. Using a regional chemistry‐climate model and exposure‐response associations, we estimate that the improved air quality due to reduced smoke emission under this scenario would have resulted in 2,300 fewer deaths due to reduced exposure to fine particulate matter. Our analysis demonstrates the air quality and public health benefits that would accrue from reducing deforestation in the Brazilian Amazon.
Thermo‐Hydro‐Chemical Simulation of Mid‐Ocean Ridge Hydrothermal Systems: Static 2D Models and Effects of Paleo‐Seawater Chemistry
Authors: DePaolo Donald J. , Sonnenthal Eric L. , Pester Nicholas J.
Published: November 2022

Decades of research have resulted in characterization of the ocean floor manifestations of mid‐ocean ridge (MOR) hydrothermal systems, yet numerical models accounting for the connections between heat transfer, hydrology and geochemistry have been slow to develop. The Thermo‐hydro‐chemical code ToughReact can be used to describe the coupled effects of fluid flow, heat transfer, and fluid‐rock chemical interactions that occur in MOR systems. We describe the results of 2‐dimensional simulations of steady state flow in fractured diabase with mineral‐fluid chemical reactions. Basal heating and specified permeability yield maximum temperature of 400°C. Total fluid flux and high fracture flow velocities are in accord with observations. Fluid chemistry, mineralogical changes and 87Sr/86Sr ratios can be compared to observations to assess and calibrate models. Simulated high temperature fracture fluids have Mg and SO4 near zero, elevated Ca and 87Sr/86Sr of about 0.7040. Total alteration is 10%–50% for simple models of spreading. Anhydrite forms mainly near the base of the upwelling zone and results in substantial local fracture porosity reduction. A calibrated model is used to predict how Sr isotopes and other features of altered oceanic crust would be different in the Cretaceous (95 Ma) early Proterozoic (1,800 Ma) and Archean (3,800 Ma), when seawater may have had high Ca and Sr concentrations, lower pH, higher temperature, and lower Na, Mg, and SO4. The simulations are offered as a start on what ultimately may require a longer‐term community effort to better understand the role of MOR thermo‐hydro‐chemical systems in Earth evolution.
When a Dust Storm Is Not a Dust Storm: Reliability of Dust Records From the Storm Events Database and Implications for Geohealth Applications
Authors: Ardon‐Dryer K. , Gill T. E. , Tong D. Q.
Published: November 2022

Windblown dust impacts human health, air quality, and climate. The National Weather Service Storm Events Database (SED) is a widely used dataset of significant or unusual weather, including dust storms (DS), and resulting deaths, injuries, and material losses in the USA. The SED is frequently used by medical, social, and atmospheric scientists. However, it is uncertain whether this dataset reliably represents spatial and temporal variations and trends of DS. Analyzing the SED from 2000 to 2020 identified 1,167 DS reports; removing reports of the same event from multiple locations left 647 DS in 21 USA states. The number of DS ranged from 12 in 2008 to 53 in 2018, with no strong interannual trends detected (R2was 0.3). By examining the DS events reported in the SED based on meteorological observations including wind speed, visibility, and weather codes, we determined that the SED was not only missing many DS (visibility <1 km), but also included many blowing dust (BLDU) events. 49.9% of 491 reported DS events in SED had visibility >1 km and were incorrectly reported as DS. Underrepresentation of DS and inclusion of BLDU may be partially due to the diverse sources contributing to the SED and a lack of verification of the reports and their consistency. Although the SED is an extremely useful and valuable database of impactful weather, including DS, the issues found in this study warrant caution in use of this dataset for many geohealth applications.
Behavior of Hydrogarnet‐Type Defects in Hydrous Stishovite at Various Temperatures and Pressures
Authors: Palfey William R. , Rossman George R. , Goddard William A.
Published: November 2022

Dense polymorphs of silica have been demonstrated experimentally to incorporate from 1.5 wt% to as much as 11.6 wt% H2O as OH groups, with implications for the hydrogen budgets of Earth and other planets. This OH is thought to enter the SiO2 structure via a charge‐balanced substitution in which silicon vacancies (VSi) are compensated by protonating four of the surrounding six oxygen atoms, often referred to as a hydrogarnet‐type defect. There are many possible configurations for this defect structure in dense silica, but the nature of these configurations and whether they can be distinguished experimentally is unknown. We present here density functional theory calculations that systematically assess the possible configurations of a hydrogarnet‐type defect in stishovite (rutile‐type SiO2), with direct comparisons to experimental vibrational spectroscopy data. We predict that stishovite synthesized at 450 K and 10 GPa quenched to room temperature is dominated by a single defect type with tetrahedral geometry. This leads to OH stretching modes (2,500–3,000 cm−1) and SiOH bending modes (∼1,400–1,450 cm−1) largely consistent with experimentally observed modes. One remaining issue is that our calculations produce results compatible with experimental data on H to D exchange, but do not explain why a considerable fraction of the 1,420 cm−1 mode shifts by only 40 cm−1 in deuterated samples. At elevated pressures and temperatures, we find that a second square planar defect configuration also becomes favorable, leading to modes that should allow differentiation from the tetrahedral configuration.
Reply to Comment by I. van Zelst on “Estimates on the Frequency of Volcanic Eruptions on Venus”
Authors: Byrne Paul K. , Krishnamoorthy Siddharth
Published: November 2022

In their 2022 study, Byrne and Krishnamoorthy (https://doi.org/10.1029/2021je007040) extrapolated to Venus the most comprehensive record of eruptions on Earth, to estimate the frequency of volcanic events on the second planet. The approach underlying this extrapolation is necessarily based on assumptions for which there is little supporting evidence; moreover, the eruptive record on Earth is far from complete because, for example, submarine events are considerably undercounted. Byrne and Krishnamoorthy (2022, https://doi.org/10.1029/2021je007040) discussed at length the limitations of their study, cautioning that their estimates on the frequency of volcanic eruptions on Venus are simply that—estimates, albeit amenable to testing by future missions to the planet. The comment by van Zelst on the Byrne and Krishnamoorthy (2022, https://doi.org/10.1029/2021je007040) study identified a calculation error in one specific scenario considered in that earlier study. The other points raised in the van Zelst comment are either consistent with the range of uncertainties discussed in, or focus on topics that have no bearing on, the Byrne and Krishnamoorthy (2022, https://doi.org/10.1029/2021je007040) study. The scientific conclusions of the Byrne and Krishnamoorthy study remain unchanged.
Delineating the dynamic evolution from preneoplasia to invasive lung adenocarcinoma by integrating single-cell RNA sequencing and spatial transcriptomics
Authors: Zhu Jianfei , Fan Yue , Xiong Yanlu , Wang Wenchen , Chen Jiakuan , Xia Yanmin , Lei Jie , Gong Li , Sun Shiquan , Jiang Tao
Published: November 2022

The cell ecology and spatial niche implicated in the dynamic and sequential process of lung adenocarcinoma (LUAD) from adenocarcinoma in situ (AIS) to minimally invasive adenocarcinoma (MIA) and subsequent invasive adenocarcinoma (IAC) have not yet been elucidated. Here, we performed an integrative analysis of single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) to characterize the cell atlas of the invasion trajectory of LUAD. We found that the UBE2C + cancer cell subpopulation constantly increased during the invasive process of LUAD with remarkable elevation in IAC, and its spatial distribution was in the peripheral cancer region of the IAC, representing a more malignant phenotype. Furthermore, analysis of the TME cell type subpopulation showed a constant decrease in mast cells, monocytes, and lymphatic endothelial cells, which were implicated in the whole process of invasive LUAD, accompanied by an increase in NK cells and MALT B cells from AIS to MIA and an increase in Tregs and secretory B cells from MIA to IAC. Notably, for AIS, cancer cells, NK cells, and mast cells were colocalized in the cancer region; however, for IAC, Tregs colocalized with cancer cells. Finally, communication and interaction between cancer cells and TME cell-induced constitutive activation of TGF-β signaling were involved in the invasion of IAC. Therefore, our results reveal the specific cellular information and spatial architecture of cancer cells and TME subpopulations, as well as the cellular interaction between them, which will facilitate the identification and development of precision medicine in the invasive process of LUAD from AIS to IAC.
Rapid, noncontact, sensitive, and semiquantitative characterization of buffered hydrogen-fluoride-treated silicon wafer surfaces by terahertz emission spectroscopy
Authors: Yang Dongxun , Mannan Abdul , Murakami Fumikazu , Tonouchi Masayoshi
Published: November 2022

Advances in modern semiconductor integrated circuits have always demanded faster and more sensitive analytical methods on a large-scale wafer. The surface of wafers is fundamentally essential to start building circuits, and quantitative measures of the surface potential, defects, contamination, passivation quality, and uniformity are subject to inspection. The present study provides a new approach to access those by means of terahertz (THz) emission spectroscopy. Upon femtosecond laser illumination, THz radiation, which is sensitive to the surface electric fields of the wafer, is generated. Here, we systematically research the THz emission properties of silicon surfaces under different surface conditions, such as the initial surface with a native oxide layer, a fluorine-terminated surface, and a hydrogen-terminated surface. Meanwhile, a strong doping concentration dependence of the THz emission amplitude from the silicon surface has been revealed in different surface conditions, which implies a semiquantitative connection between the THz emission and the surface band bending with the surface dipoles. Laser-induced THz emission spectroscopy is a promising method for evaluating local surface properties on a wafer scale.
CD147 contributes to SARS-CoV-2-induced pulmonary fibrosis
Authors: Wu Jiao , Chen Liang , Qin Chuan , Huo Fei , Liang Xue , Yang Xu , Zhang Kui , Lin Peng , Liu Jiangning , Feng Zhuan , Zhou Jiansheng , Pei Zhuo , Wang Yatao , Sun Xiu-Xuan , Wang Ke , Geng Jiejie , Zheng Zhaohui , Fu Xianghui , Liu Man , Wang Qingyi , Zhang Zheng , Bian Huijie , Zhu Ping , Chen Zhi-Nan
Published: November 2022

COVID‐19 patients can develop clinical and histopathological features associated with fibrosis, but the pathogenesis of fibrosis remains poorly understood. CD147 has been identified as a universal receptor for SARS-CoV-2 and its variants, which could initiate COVID-19-related cytokine storm. Here, we systemically analyzed lung pathogenesis in SARS-CoV-2- and its delta variant-infected humanized CD147 transgenic mice. Histopathology and Transmission Electron Microscopy revealed inflammation, fibroblast expansion and pronounced fibrotic remodeling in SARS-CoV-2-infected lungs. Consistently, RNA-sequencing identified a set of fibrosis signature genes. Furthermore, we identified CD147 as a crucial regulator for fibroblast activation induced by SARS-CoV-2. We found conditional knockout of CD147 in fibroblast suppressed activation of fibroblasts, decreasing susceptibility to bleomycin-induced pulmonary fibrosis. Meplazumab, a CD147 antibody, was able to inhibit the accumulation of activated fibroblasts and the production of ECM proteins, thus alleviating the progression of pulmonary fibrosis caused by SARS-CoV-2. In conclusion, we demonstrated that CD147 contributed to SARS-CoV-2-triggered progressive pulmonary fibrosis and identified CD147 as a potential therapeutic target for treating patients with post-COVID-19 pulmonary fibrosis.
MYC and MET cooperatively drive hepatocellular carcinoma with distinct molecular traits and vulnerabilities
Authors: Sequera Celia , Grattarola Margherita , Holczbauer Agnes , Dono Rosanna , Pizzimenti Stefania , Barrera Giuseppina , Wangensteen Kirk J. , Maina Flavio
Published: November 2022

Enhanced activation of the transcription factor MYC and of the receptor tyrosine kinase MET are among the events frequently occurring in hepatocellular carcinoma (HCC). Both genes individually act as drivers of liver cancer initiation and progression. However, their concomitant alteration in HCC has not been explored, nor functionally documented. Here, we analysed databases of five independent human HCC cohorts and found a subset of patients with high levels of MYC and MET (MYChigh/METhigh) characterised by poor prognosis. This clinical observation drove us to explore the functionality of MYC and MET co-occurrence in vivo, combining hydrodynamic tail vein injection for MYC expression in the R26stopMet genetic setting, in which wild-type MET levels are enhanced following the genetic deletion of a stop cassette. Results showed that increased MYC and MET expression in hepatocytes is sufficient to induce liver tumorigenesis even in the absence of pre-existing injuries associated with a chronic disease state. Intriguingly, ectopic MYC in MET tumours increases expression of the Mki67 proliferation marker, and switches them into loss of Afp, Spp1, Gpc3, Epcam accompanied by an increase in Hgma1, Vim, and Hep-Par1 levels. We additionally found a switch in the expression of specific immune checkpoints, with an increase in the Ctla-4 and Lag3 lymphocyte co-inhibitory responses, and in the Icosl co-stimulatory responses of tumour cells. We provide in vitro evidence on the vulnerability of some human HCC cell lines to combined MYC and MET targeting, which are otherwise resistant to single inhibition. Mechanistically, combined blockage of MYC and MET converts a partial cytostatic effect, triggered by individual blockage of MYC or MET, into a cytotoxic effect. Together, these findings highlight a subgroup of HCC characterised by MYChigh/METhigh, and document functional cooperativity between MYC and MET in liver tumorigenesis. Thus, the MYC-R26Met model is a relevant setting for HCC biology, patient classification and treatment.
Naa10p promotes cell invasiveness of esophageal cancer by coordinating the c-Myc and PAI1 regulatory axis
Authors: Pan Ke-Fan , Liu Yu-Cheng , Hsiao Michael , Cheng Tsu-Yao , Hua Kuo-Tai
Published: November 2022

N-α-acetyltransferase 10 protein, Naa10p, is involved in various cellular functions impacting tumor progression. Due to its capacity to acetylate a large spectrum of proteins, both oncogenic and tumor-suppressive roles of Naa10p have been documented. Here, we report an oncogenic role of Naa10p in promoting metastasis of esophageal cancer.NAA10is more highly expressed in esophageal cancer tissues compared to normal tissues. HigherNAA10expression also correlates with poorer survival of esophageal cancer patients. We found thatNAA10expression was transcriptionally regulated by the critical oncogene c-Myc in esophageal cancer. Furthermore, activation of the c-Myc-Naa10p axis resulted in upregulated cell invasiveness of esophageal cancer. This increased cell invasiveness was also elucidated to depend on the enzymatic activity of Naa10p. Moreover, Naa10p cooperated with Naa15p to interact with the protease inhibitor, PAI1, and prevent its secretion. This inhibition of PAI1 secretion may derive from the N-terminal acetylation effect of the Naa10p/Naa15p complex. Our results establish the significance of Naa10p in driving metastasis in esophageal cancer by coordinating the c-Myc-PAI1 axis, with implications for its potential use as a prognostic biomarker and therapeutic target for esophageal cancer.
The prognostic implication of visual acuity at the time of uveal melanoma diagnosis
Authors: Asplund Elin , Fili Maria , Pansell Tony , Brautaset Rune , Nilsson Maria , Stålhammar Gustav
Published: November 2022

Background

Visual outcomes after primary tumour treatment of uveal melanoma (UM) have been investigated repeatedly. This study evaluates the correlation between best-corrected visual acuity (BCVA) before treatment with clinicopathological factors and patient survival.

Subjects/Methods

Pre-treatment BCVA was examined in relation to tumour dimensions and location, and survival in a retrospective cohort of 1809 patients who underwent plaque brachytherapy. BCVA was also correlated to tumour histological factors in a second cohort of 137 enucleated eyes.

Results

The mean BCVA of the tumour eye prior to plaque brachytherapy was LogMAR 0.42 (SD 0.46). Patients with low BCVA (LogMAR ≥ 1.00) did not differ in age (p = 0.19) and had similar frequency of ciliary body involvement (p = 0.99) but had tumours with greater apical thickness (p < 0.0001), greater diameter (p < 0.0001) and shorter distance to the optic disc and fovea (p < 0.0001). There were no significant relations between low BCVA and any of 13 examined tumour histological factors at a Bonferroni-corrected significance level (p > 0.004). Patients with low BCVA had greater incidence of UM-related mortality in competing risk analysis (p = 0.0019) and shorter overall survival (p < 0.0001). Low BCVA was also associated with increased hazard ratio (HR) for UM-related mortality in univariate analysis (HR 1.5, 95% confidence interval 1.2 to 1.9), but not in multivariate analysis with tumour size and location as covariates.

Conclusions

UM patients with low BCVA before primary tumour treatment have a worse prognosis, likely related to increased tumour dimensions. Future studies should examine the prognostic significance of BCVA in relation to macula-involving retinal detachment and genetic factors.
Restoring cellular magnesium balance through Cyclin M4 protects against acetaminophen-induced liver damage
Authors: González-Recio Irene , Simón Jorge , Goikoetxea-Usandizaga Naroa , Serrano-Maciá Marina , Mercado-Gómez Maria , Rodríguez-Agudo Rubén , Lachiondo-Ortega Sofía , Gil-Pitarch Clàudia , Fernández-Rodríguez Carmen , Castellana Donatello , Latasa Maria U. , Abecia Leticia , Anguita Juan , Delgado Teresa C. , Iruzubieta Paula , Crespo Javier , Hardy Serge , Petrov Petar D. , Jover Ramiro , Avila Matías A. , Martín César , Schaeper Ute , Tremblay Michel L. , Dear James W. , Masson Steven , McCain Misti Vanette , Reeves Helen L. , Andrade Raul J. , Lucena M. Isabel , Buccella Daniela , Martínez-Cruz Luis Alfonso , Martínez-Chantar Maria L
Published: November 2022

Acetaminophen overdose is one of the leading causes of acute liver failure and liver transplantation in the Western world. Magnesium is essential in several cellular processess. The Cyclin M family is involved in magnesium transport across cell membranes. Herein, we identify that among all magnesium transporters, only Cyclin M4 expression is upregulated in the liver of patients with acetaminophen overdose, with disturbances in magnesium serum levels. In the liver, acetaminophen interferes with the mitochondrial magnesium reservoir via Cyclin M4, affecting ATP production and reactive oxygen species generation, further boosting endoplasmic reticulum stress. Importantly, Cyclin M4 mutant T495I, which impairs magnesium flux, shows no effect. Finally, an accumulation of Cyclin M4 in endoplasmic reticulum is shown under hepatoxicity. Based on our studies in mice, silencing hepatic Cyclin M4 within the window of 6 to 24 h following acetaminophen overdose ingestion may represent a therapeutic target for acetaminophen overdose induced liver injury.
Integration of single-cell transcriptomes and biological function reveals distinct behavioral patterns in bone marrow endothelium
Authors: Kim Young-Woong , Zara Greta , Kang HyunJun , Branciamore Sergio , O’Meally Denis , Feng Yuxin , Kuan Chia-Yi , Luo Yingjun , Nelson Michael S. , Brummer Alex B. , Rockne Russell , Chen Zhen Bouman , Zheng Yi , Cardoso Angelo A. , Carlesso Nadia
Published: November 2022

Heterogeneity of endothelial cell (EC) populations reflects their diverse functions in maintaining tissue’s homeostasis. However, their phenotypic, molecular, and functional properties are not entirely mapped. We use the Tie2-CreERT2;Rosa26-tdTomato reporter mouse to trace, profile, and cultivate primary ECs from different organs. As paradigm platform, we use this strategy to study bone marrow endothelial cells (BMECs). Single-cell mRNA sequencing of primary BMECs reveals that their diversity and native molecular signatures is transitorily preserved in an ex vivo culture that conserves key cell-to-cell microenvironment interactions. Macrophages sustain BMEC cellular diversity and expansion and preserve sinusoidal-like BMECs ex vivo. Endomucin expression discriminates BMECs in populations exhibiting mutually exclusive properties and distinct sinusoidal/arterial and tip/stalk signatures. In contrast to arterial-like, sinusoidal-like BMECs are short-lived, form 2D-networks, contribute to in vivo angiogenesis, and support hematopoietic stem/progenitor cells in vitro. This platform can be extended to other organs’ ECs to decode mechanistic information and explore therapeutics.
Inference of hyperedges and overlapping communities in hypergraphs
Authors: Contisciani Martina , Battiston Federico , De Bacco Caterina
Published: November 2022

Hypergraphs, encoding structured interactions among any number of system units, have recently proven a successful tool to describe many real-world biological and social networks. Here we propose a framework based on statistical inference to characterize the structural organization of hypergraphs. The method allows to infer missing hyperedges of any size in a principled way, and to jointly detect overlapping communities in presence of higher-order interactions. Furthermore, our model has an efficient numerical implementation, and it runs faster than dyadic algorithms on pairwise records projected from higher-order data. We apply our method to a variety of real-world systems, showing strong performance in hyperedge prediction tasks, detecting communities well aligned with the information carried by interactions, and robustness against addition of noisy hyperedges. Our approach illustrates the fundamental advantages of a hypergraph probabilistic model when modeling relational systems with higher-order interactions.
Precise tuning of interlayer electronic coupling in layered conductive metal-organic frameworks
Authors: Lu Yang , Zhang Yingying , Yang Chi-Yuan , Revuelta Sergio , Qi Haoyuan , Huang Chuanhui , Jin Wenlong , Li Zichao , Vega-Mayoral Victor , Liu Yannan , Huang Xing , Pohl Darius , Položij Miroslav , Zhou Shengqiang , Cánovas Enrique , Heine Thomas , Fabiano Simone , Feng Xinliang , Dong Renhao
Published: November 2022

Two-dimensional conjugated metal-organic frameworks (2D c-MOFs) have attracted increasing interests for (opto)-electronics and spintronics. They generally consist of van der Waals stacked layers and exhibit layer-depended electronic properties. While considerable efforts have been made to regulate the charge transport within a layer, precise control of electronic coupling between layers has not yet been achieved. Herein, we report a strategy to precisely tune interlayer charge transport in 2D c-MOFs via side-chain induced control of the layer spacing. We design hexaiminotriindole ligands allowing programmed functionalization with tailored alkyl chains (HATI_CX, X = 1,3,4; X refers to the carbon numbers of the alkyl chains) for the synthesis of semiconducting Ni3(HATI_CX)2. The layer spacing of these MOFs can be precisely varied from 3.40 to 3.70 Å, leading to widened band gap, suppressed carrier mobilities, and significant improvement of the Seebeck coefficient. With this demonstration, we further achieve a record-high thermoelectric power factor of 68 ± 3 nW m−1 K−2 in Ni3(HATI_C3)2, superior to the reported holes-dominated MOFs.
U.S. winter wheat yield loss attributed to compound hot-dry-windy events
Authors: Zhao Haidong , Zhang Lina , Kirkham M. B. , Welch Stephen M. , Nielsen-Gammon John W. , Bai Guihua , Luo Jiebo , Andresen Daniel A. , Rice Charles W. , Wan Nenghan , Lollato Romulo P. , Zheng Dianfeng , Gowda Prasanna H. , Lin Xiaomao
Published: November 2022

Climate extremes cause significant winter wheat yield loss and can cause much greater impacts than single extremes in isolation when multiple extremes occur simultaneously. Here we show that compound hot-dry-windy events (HDW) significantly increased in the U.S. Great Plains from 1982 to 2020. These HDW events were the most impactful drivers for wheat yield loss, accounting for a 4% yield reduction per 10 h of HDW during heading to maturity. Current HDW trends are associated with yield reduction rates of up to 0.09 t ha−1 per decade and HDW variations are atmospheric-bridged with the Pacific Decadal Oscillation. We quantify the “yield shock”, which is spatially distributed, with the losses in severely HDW-affected areas, presumably the same areas affected by the Dust Bowl of the 1930s. Our findings indicate that compound HDW, which traditional risk assessments overlooked, have significant implications for the U.S. winter wheat production and beyond.
Induction of cross-neutralizing antibodies by a permuted hepatitis C virus glycoprotein nanoparticle vaccine candidate
Authors: Sliepen Kwinten , Radić Laura , Capella-Pujol Joan , Watanabe Yasunori , Zon Ian , Chumbe Ana , Lee Wen-Hsin , de Gast Marlon , Koopsen Jelle , Koekkoek Sylvie , del Moral-Sánchez Iván , Brouwer Philip J. M. , Ravichandran Rashmi , Ozorowski Gabriel , King Neil P. , Ward Andrew B. , van Gils Marit J. , Crispin Max , Schinkel Janke , Sanders Rogier W.
Published: November 2022

Hepatitis C virus (HCV) infection affects approximately 58 million people and causes ~300,000 deaths yearly. The only target for HCV neutralizing antibodies is the highly sequence diverse E1E2 glycoprotein. Eliciting broadly neutralizing antibodies that recognize conserved cross-neutralizing epitopes is important for an effective HCV vaccine. However, most recombinant HCV glycoprotein vaccines, which usually include only E2, induce only weak neutralizing antibody responses. Here, we describe recombinant soluble E1E2 immunogens that were generated by permutation of the E1 and E2 subunits. We displayed the E2E1 immunogens on two-component nanoparticles and these nanoparticles induce significantly more potent neutralizing antibody responses than E2. Next, we generated mosaic nanoparticles co-displaying six different E2E1 immunogens. These mosaic E2E1 nanoparticles elicit significantly improved neutralization compared to monovalent E2E1 nanoparticles. These results provide a roadmap for the generation of an HCV vaccine that induces potent and broad neutralization.
A resource for automated search and collation of geochemical datasets from journal supplements
Authors: Martin Erin L. , Barrote Vitor R. , Cawood Peter A.
Published: November 2022

This article presents a resource for automated search, extraction and collation of geochemical and geochronological data from the Figshare repository using web scraping code. To answer fundamental questions about the Earth’s evolution, such as spatial and temporal evolution and interrelationships between the planet’s solid and surficial reservoirs, researchers must utilize global geochemical datasets. Due to the volume of data being published, these datasets become quickly outdated. We present a resource that allows researchers to rapidly curate and update their own databases from existing published data. We use open-source Python code to web scrape the Figshare repository for journal supplementary files using the application programming interface, allowing for the collection and download of hundreds of supplementary files and metadata in minutes. Use of this web scraping tool is demonstrated here by collation of a zircon geochronology and chemistry database of >150,000 analyses. The database is consistent in reproducing trends in other published zircon compilations. Providing a resource for automated collection of Figshare data files will encourage data sharing and reuse.
MaHPIC malaria systems biology data from Plasmodium cynomolgi sporozoite longitudinal infections in macaques
Authors: DeBarry Jeremy D. , Nural Mustafa V. , Pakala Suman B. , Nayak Vishal , Warrenfeltz Susanne , Humphrey Jay , Lapp Stacey A. , Cabrera-Mora Monica , Brito Cristiana F. A. , Jiang Jianlin , Saney Celia L. , Hankus Allison , Stealey Hannah M. , DeBarry Megan B. , Lackman Nicolas , Legall Noah , Lee Kevin , Tang Yan , Gupta Anuj , Trippe Elizabeth D. , Bridger Robert R. , Weatherly Daniel Brent , Peterson Mariko S. , Jiang Xuntian , Tran ViLinh , Uppal Karan , Fonseca Luis L. , Joyner Chester J. , Karpuzoglu Ebru , Cordy Regina J. , Meyer Esmeralda V. S. , Wells Lance L. , Ory Daniel S. , Lee F. Eun-Hyung , Tirouvanziam Rabindra , Gutiérrez Juan B. , Ibegbu Chris , Lamb Tracey J. , Pohl Jan , Pruett Sarah T. , Jones Dean P. , Styczynski Mark P. , Voit Eberhard O. , Moreno Alberto , Galinski Mary R. , Kissinger Jessica C.
Published: November 2022

Plasmodium cynomolgi causes zoonotic malarial infections in Southeast Asia and this parasite species is important as a model for Plasmodium vivax and Plasmodium ovale. Each of these species produces hypnozoites in the liver, which can cause relapsing infections in the blood. Here we present methods and data generated from iterative longitudinal systems biology infection experiments designed and performed by the Malaria Host-Pathogen Interaction Center (MaHPIC) to delve deeper into the biology, pathogenesis, and immune responses of P. cynomolgi in the Macaca mulatta host. Infections were initiated by sporozoite inoculation. Blood and bone marrow samples were collected at defined timepoints for biological and computational experiments and integrative analyses revolving around primary illness, relapse illness, and subsequent disease and immune response patterns. Parasitological, clinical, haematological, immune response, and -omic datasets (transcriptomics, proteomics, metabolomics, and lipidomics) including metadata and computational results have been deposited in public repositories. The scope and depth of these datasets are unprecedented in studies of malaria, and they are projected to be a F.A.I.R., reliable data resource for decades.
Field test study on the evaluation of the microvibration controlling capacity of a mass concrete layer
Authors: Zheng Ming , Zhuang Liangdong , Fan Jiansheng , Liu Yufei , Ren Jinlong , Rong Muning , Zhai Wei
Published: November 2022

Microvibration induced by natural disturbance and human activities has an adverse effect on the operation of the large-scale and ultraprecise facilities in the world. Under such circumstances, a passive vibration control method is generally deployed for such vibration-sensitive facilities, taking the High Energy Photo Source (HEPS) in Beijing as an example, a 3 m-thick mass concrete layer forming a ring foundation was cast at the facility, where a 1 m-thick reinforced concrete slab (RC slab) lies. Since microvibration control plays a crucial role in the operation of such large-scale scientific and ultraprecise facilities and few studies have been reported for large-scale concrete layer as antimicrovibration devices, this paper presents four field tests in Beijing, China, to evaluate the vibration control capacity of a mass concrete layer. Based on a large number of field tests, the effect of applying the concrete layer is discussed, and a reference is provided for the construction of similar facilities. The vibration signals, generated by shock excitation and ambient excitation, are measured through a highly sensitive and high-accuracy vibration acquisition system. It is concluded that the existence of the 1 m-thick RC slab has little influence on the microvibration signal frequency distribution in the vertical direction and that the signals from the concrete layer and subsoil differ by approximately 10 Hz in the vertical direction while differing by approximately 5 Hz in the horizontal direction. The microvibration control ability of the concrete layer is favorable in a higher frequency band over 20 ~ 30 Hz and more than 50% attenuation can be gained through the concrete layer; however, the microvibration control ability is not significant below 20 ~ 30 Hz. The vibration levels across different heights of the concrete layer section are the same. To prevent adverse vibration disturbance below 20 ~ 30 Hz, it is suggested that the traffic and road surface conditions should be taken into consideration when choosing the construction location. In addition, a long-term monitoring shows that 75% vibration energy at the site is firmly related to the construction activities which are approximately 1.4 km from the site.
Manipulations of Libet clock parameters affect intention timing awareness
Authors: Ivanof Bianca E. , Terhune D. B. , Coyle D. , Moore J. W.
Published: November 2022

W judgments are a widely used intention timing awareness estimate. These judgments are typically obtained by using the classic Libet-style paradigm whereby participants are asked to estimate the time they become aware of their intention to act by using the location of a rotating object on a clock face. There is an inconsistency in the Libet clock parameters used in previous studies, and it is unclear whether this variability impacts W judgments and other outcome measures, with implications for the construct validity of this measure and the generalisability of results across studies. Here, we present a four-experiment study that systematically manipulated the Libet clock speed, number of clock markings, length of the clock hand and type of clock radius in order to examine whether these parameter manipulations affect intention timing awareness estimates. Our results demonstrate W judgments can be significantly influenced by the clock speed and number of clock markings. The meaning and implications of these results are discussed.
The role of age inequalities in cause of death in the slow pace of epidemiological transition in India
Authors: Yadav Suryakant , Perianayagam Arokiasamy , Patel Shivani Anil , Cunningham Solveig Argeseanu
Published: November 2022

In developed countries, low disparity in lifespan contributed by the reduction in the burden of noncommunicable diseases (NCDs) is the key to advances in epidemiological transition. Contrarily, India passing through a phase of the dual burden of CDs and NCDs shows a heavy burden of NCDs responsible for the high disparity in lifespan. The Gini coefficient was decomposed for examining the contribution of 22 causes of death and their repercussions for inequality in age at death for 30 years between 1990–1994 and 2015–2019, using Global Burden of Disease data. The outcomes of the study reveal that India’s epidemiological transition has been just modest on account of high inequality in mortality by NCDs emplaced in the middle through old age despite a consistent mortality decline at infant through old age for communicable diseases (CDs). The structural changes in causes of death structure is shaped by CDs rather than NCDs, but overall bolstered by the adult mortality decline, especially in women. However, the process is restrained by the small contribution of the middle age group and a benign contribution of old mortality decline owing to the low threshold age. India needs to target health interventions in seeking significant mortality decline in the middle age group of 50–69 years that is warranted for epidemiological transition apace as evident in the developed nations.
Joint analysis of structured and semi-structured community science data improves precision of relative abundance but not trends in birds
Authors: Schindler Alexander R. , Cunningham Stephanie A. , Schafer Toryn L. J. , Sinnott Emily A. , Clements Sarah J. , DiDonato Frances M. , Mosloff Alisha R. , Walters Clay M. , Shipley Amy A. , Weegman Mitch D. , Zhao Qing
Published: November 2022

Estimating absolute and relative abundance of wildlife populations is critical to addressing ecological questions and conservation needs, yet obtaining reliable estimates can be challenging because surveys are often limited spatially or temporally. Community science (i.e., citizen science) provides opportunities for semi-structured data collected by the public (e.g., eBird) to improve capacity of relative abundance estimation by complementing structured survey data collected by trained observers (e.g., North American breeding bird survey [BBS]). We developed two state-space models to estimate relative abundance and population trends: one using BBS data and the other jointly analyzing BBS and eBird data. We applied these models to seven bird species with diverse life history characteristics. Joint analysis of eBird and BBS data improved precision of mean and year-specific relative abundance estimates for all species, but the BBS-only model produced more precise trend estimates compared to the joint model for most species. The relative abundance estimates of the joint model were particularly more precise than the BBS-only estimates in areas where species detectability was low resulting from either low BBS survey effort or low abundance. These results suggest that community science data can be a valuable resource for cost-effective improvement in wildlife abundance estimation.
A single mutation in the E2 glycoprotein of hepatitis C virus broadens the claudin specificity for its infection
Authors: Shirasago Yoshitaka , Fukazawa Hidesuke , Nagase Shotaro , Shimizu Yoshimi , Mizukami Tomoharu , Wakita Takaji , Suzuki Tetsuro , Tani Hideki , Kondoh Masuo , Kuroda Takuya , Yasuda Satoshi , Sato Yoji , Hanada Kentaro , Fukasawa Masayoshi
Published: November 2022

Entry of the hepatitis C virus (HCV) into host cells is a multistep process mediated by several host factors, including a tight junction protein claudin-1 (CLDN1). We repeatedly passaged HCV-JFH1-tau, an HCV substrain with higher infectivity, on Huh7.5.1-8 cells. A multi-passaged HCV-JFH1-tau lot was infectious to CLDN1-defective S7-A cells, non-permissive to original HCV-JFH1-tau infection. We identified a single mutation, M706L, in the E2 glycoprotein of the HCV-JFH1-tau lot as an essential mutation for infectivity to S7-A cells. The pseudovirus JFH1/M706L mutant could not infect human embryonic kidney 293 T (HEK293T) cells lacking CLDN family but infected HEK293T cells expressing CLDN1, CLDN6, or CLDN9. Thus, this mutant virus could utilize CLDN1, and other CLDN6 and CLDN9, making HCV possible to infect cells other than hepatocytes. iPS cells, one of the stem cells, do not express CLDN1 but express CLDN6 and other host factors required for HCV infection. We confirmed that the HCV-JFH1-tau-derived mutant with an M706L mutation infected iPS cells in a CLDN6-dependent manner. These results demonstrated that a missense mutation in E2 could broaden the CLDN member specificity for HCV infection. HCV may change its receptor requirement through a single amino acid mutation and infect non-hepatic cells.
Distributed time-varying out formation-containment tracking of multi-UAV systems based on finite-time event-triggered control
Authors: Cai Xin , Zhu Xiaozhou , Yao Wen
Published: November 2022

Considering the limited communication resources and slow convergence speed of multi-unmanned aerial vehicle (UAV) systems, this paper presents a finite-time even-triggered control framework for multi-UAV systems to achieve formation-containment tracking control. First, a virtual leader with time-varying output is introduced so that the trajectory of the whole system can be manipulated in real time. Second, the finite-time control enables that the systematic error converge to a small neighborhood of origin in finite time. Third, in order to save communication resources, an event-triggering function is developed to generate the control event sequences, which avoids continuous update of the controller. Rigorous proof shows the finite-time stability of the proposed control algorithm, and Zeno behavior is strictly excluded for each UAV. Finally, some numerical simulations are given to verify the effectiveness of the proposed controllers.
Exploring the effects of stationary camera spots on inferences drawn from real-time crash severity models
Authors: Abdi Amirhossein , Seyedabrishami Seyedehsan , Llorca Carlos , Moreno Ana Tsui
Published: November 2022

This study combined crash reports, land use, real-time traffic, and weather data to form an integrated database to analyze the severity of crashes taking place on rural highways. As the traffic cameras are placed at fixed locations, there is a wide range of measured distances between crashes and the selected nearest camera for extracting traffic variables. This may change the significance of traffic variables. For the first time, spacing was introduced as the distance around the detectors in which traffic characteristics are inferred to crashes. Classification and Regression Tree (CART) was employed as an interpretable tool to explore how spacing affects model performance and the significance of traffic variables. Twelve spacing scenarios from 250 to 3000 m were evaluated. Except for short spacings suffering from the low sample size issue, each model has a good predictive performance based on overall accuracy and F2 score in the 1000–3000 m spacings. In this range, three dominant rules emerged: (1) high deviations of speed on the roads surrounded by wastelands are associated with severe crashes; (2) faded markings in residential zones increase the likelihood of severe outcomes; (3) installation of barriers decrease the probability of severe crashes. Comparing the Variable Importance Measure (VIM) reveals that the total importance of traffic variables reduces as the spacing increases. Also, results indicate that average speed is significant until 1750 m; but speed deviation, traffic flow, and percent of heavy vehicles are more stable variables for further spacings. In conclusion, for the first time, spacing scenarios were evaluated systematically and proved that they have a remarkable impact on the significance of variables. This novel research provides guidance not only on the spacing but also on which real-time traffic variables have a greater impact on crash severity, along with design, land use, and environmental variables.
A medication-wide association study (MWAS) on repurposed drugs for COVID-19 with Pre-pandemic prescription medication exposure and pregnancy outcomes
Authors: Davidson Lena , Canelón Silvia P. , Boland Mary Regina
Published: November 2022

Information on effects of medication therapies during pregnancy is lacking as pregnant patients are often excluded from clinical trials. This retrospective study explores the potential of using electronic health record (EHR) data to inform safety profiles of repurposed COVID medication therapies on pregnancy outcomes using pre-COVID data. We conducted a medication-wide association study (MWAS) on prescription medication exposures during pregnancy and the risk of cesarean section, preterm birth, and stillbirth, using EHR data between 2010–2017 on deliveries at PennMedicine. Repurposed drugs studied for treatment of COVID-19 were extracted from ClinicalTrials.gov (n = 138). We adjusted for known comorbidities diagnosed within 2 years prior to birth. Using previously developed medication mapping and delivery-identification algorithms, we identified medication exposure in 2,830 of a total 63,334 deliveries; from 138 trials, we found 31 medications prescribed and included in our cohort. We found 21 (68%) of the 31 medications were not positively associated with increased risk of the outcomes examined. With caution, these medications warrant potential for inclusion of pregnant individuals in future studies, while drugs found to be associated with pregnancy outcomes require further investigation. MWAS facilitates hypothesis-driven evaluation of drug safety across all prescription medications, revealing potential drug candidates for further research.
Performance of the intracerebroventricularly injected streptozotocin Alzheimer’s disease model in a translationally relevant, aged and experienced rat population
Authors: Gáspár Attila , Hutka Barbara , Ernyey Aliz Judit , Tajti Brigitta Tekla , Varga Bence Tamás , Zádori Zoltán Sándor , Gyertyán István
Published: November 2022

The intracerebroventricularly (icv) injected streptozotocin (STZ) induced brain state is a widely used model of sporadic Alzheimer-disease (AD). However, data have been generated in young, naive albino rats. We postulate that the translationally most relevant animal population of an AD model should be that of aged rats with substantial learning history. The objective of the study was thus to probe the model in old rats with knowledge in various cognitive domains. Long-Evans rats of 23 and 10 months age with acquired knowledge in five-choice serial reaction time task (5-CSRTT), a cooperation task, Morris water-maze (MWM) and “pot-jumping” exercise were treated with 3 × 1.5 mg/kg icv. STZ and their performance were followed for 3 months in the above and additional behavioral assays. Both STZ-treated age groups showed significant impairment in the MWM (spatial learning) and novel object recognition test (recognition memory) but not in passive avoidance and fear conditioning paradigms (fear memory). In young STZ treated rats, significant differences were also found in the 5CSRTT (attention) and pot jumping test (procedural learning) while in old rats a significant increase in hippocampal phospho-tau/tau protein ratio was observed. No significant difference was found in the cooperation (social cognition) and pairwise discrimination (visual memory) assays and hippocampal β-amyloid levels. STZ treated old animals showed impulsivity-like behavior in several tests. Our results partly coincide with partly deviate from those published on young, albino, unexperienced rats. Beside the age, strain and experience level of the animals differences can also be attributed to the increased dose of STZ, and the applied food restriction regime. The observed cognitive and non-cognitive activity pattern of icv. STZ in aged experienced rats call for more extensive studies with the STZ model to further strengthen and specify its translational validity.