bluuebunny/crossref_metadata_2025 huggingface dataset:
The impact of autophagy modulation on phenotype and survival of cardiac stromal cells under metabolic stress
Authors: Chimenti Isotta , Picchio Vittorio , Pagano Francesca , Schirone Leonardo , Schiavon Sonia , D’Ambrosio Luca , Valenti Valentina , Forte Maurizio , di Nonno Flavio , Rubattu Speranza , Peruzzi Mariangela , Versaci Francesco , Greco Ernesto , Calogero Antonella , De Falco Elena , Frati Giacomo , Sciarretta Sebastiano
Published: April 2022

Cardiac stromal cells (CSCs) embrace multiple phenotypes and are a contributory factor in tissue homeostasis and repair. They can be exploited as therapeutic mediators against cardiac fibrosis and remodeling, but their survival and cardioprotective properties can be decreased by microenvironmental cues. We evaluated the impact of autophagy modulation by different pharmacological/genetic approaches on the viability and phenotype of murine CSCs, which had been subjected to nutrient deprivation or hyperglycemia, in order to mimic relevant stress conditions and risk factors of cardiovascular diseases. Our results show that autophagy is activated in CSCs by nutrient deprivation, and that autophagy induction by trehalose or autophagy-related protein 7 (ATG7)-overexpression can significantly preserve CSC viability. Furthermore, autophagy induction is associated with a higher proportion of primitive, non-activated stem cell antigen 1 (Sca1)-positive cells, and with a reduced fibrotic fraction (positive for the discoidin domain-containing receptor 2, DDR2) in the CSC pool after nutrient deprivation. Hyperglycemia, on the other hand, is associated with reduced autophagic flux in CSCs, and with a significant reduction in primitive Sca1+ cells. Autophagy induction by adenoviral-mediated ATG7-overexpression maintains a cardioprotective, anti-inflammatory and pro-angiogenic paracrine profile of CSCs exposed to hyperglycemia for 1 week. Finally, autophagy induction by ATG7-overexpression during hyperglycemia can significantly preserve cell viability in CSCs, which were subsequently exposed to nutrient deprivation, reducing hyperglycemia-induced impairment of cell resistance to stress. In conclusion, our results show that autophagy stimulation preserves CSC viability and function in response to metabolic stressors, suggesting that it may boost the beneficial functions of CSCs in cardiac repair mechanisms.
Cyclic 5-membered disulfides are not selective substrates of thioredoxin reductase, but are opened nonspecifically
Authors: Felber Jan G. , Poczka Lena , Scholzen Karoline C. , Zeisel Lukas , Maier Martin S. , Busker Sander , Theisen Ulrike , Brandstädter Christina , Becker Katja , Arnér Elias S. J. , Thorn-Seshold Julia , Thorn-Seshold Oliver
Published: April 2022

The cyclic five-membered disulfide 1,2-dithiolane has been widely used in chemical biology and in redox probes. Contradictory reports have described it either as nonspecifically reduced in cells, or else as a highly specific substrate for thioredoxin reductase (TrxR). Here we show that 1,2-dithiolane probes, such as “TRFS” probes, are nonspecifically reduced by thiol reductants and redox-active proteins, and their cellular performance is barely affected by TrxR inhibition or knockout. Therefore, results of cellular imaging or inhibitor screening using 1,2-dithiolanes should not be interpreted as reflecting TrxR activity, and previous studies may need re-evaluation. To understand 1,2-dithiolanes’ complex behaviour, probe localisation, environment-dependent fluorescence, reduction-independent ring-opening polymerisation, and thiol-dependent cellular uptake must all be considered; particular caution is needed when co-applying thiophilic inhibitors. We present a general approach controlling against assay misinterpretation with reducible probes, to ensure future TrxR-targeted designs are robustly evaluated for selectivity, and to better orient future research.
The promotion effect of π-π interactions in Pd NPs catalysed selective hydrogenation
Authors: Guo Miao , Jayakumar Sanjeevi , Luo Mengfei , Kong Xiangtao , Li Chunzhi , Li He , Chen Jian , Yang Qihua
Published: April 2022

The utilization of weak interactions to improve the catalytic performance of supported metal catalysts is an important strategy for catalysts design, but still remains a big challenge. In this work, the weak interactions nearby the Pd nanoparticles (NPs) are finely tuned by using a series of imine-linked covalent organic frameworks (COFs) with different conjugation skeletons. The Pd NPs embedded in pyrene-COF are ca. 3 to 10-fold more active than those in COFs without pyrene in the hydrogenation of aromatic ketones/aldehydes, quinolines and nitrobenzene, though Pd have similar size and surface structure. With acetophenone (AP) hydrogenation as a model reaction, systematic studies imply that the π-π interaction of AP and pyrene rings in the vicinity of Pd NPs could significantly reduce the activation barrier in the rate-determining step. This work highlights the important role of non-covalent interactions beyond the active sites in modulating the catalytic performance of supported metal NPs.
Imaging vesicle formation dynamics supports the flexible model of clathrin-mediated endocytosis
Authors: Nawara Tomasz J. , Williams Yancey D. , Rao Tejeshwar C. , Hu Yuesong , Sztul Elizabeth , Salaita Khalid , Mattheyses Alexa L.
Published: April 2022

Clathrin polymerization and changes in plasma membrane architecture are necessary steps in forming vesicles to internalize cargo during clathrin-mediated endocytosis (CME). Simultaneous analysis of clathrin dynamics and membrane structure is challenging due to the limited axial resolution of fluorescence microscopes and the heterogeneity of CME. This has fueled conflicting models of vesicle assembly and obscured the roles of flat clathrin assemblies. Here, using Simultaneous Two-wavelength Axial Ratiometry (STAR) microscopy, we bridge this critical knowledge gap by quantifying the nanoscale dynamics of clathrin-coat shape change during vesicle assembly. We find that de novo clathrin accumulations generate both flat and curved structures. High-throughput analysis reveals that the initiation of vesicle curvature does not directly correlate with clathrin accumulation. We show clathrin accumulation is preferentially simultaneous with curvature formation at shorter-lived clathrin-coated vesicles (CCVs), but favors a flat-to-curved transition at longer-lived CCVs. The broad spectrum of curvature initiation dynamics revealed by STAR microscopy supports multiple productive mechanisms of vesicle formation and advocates for the flexible model of CME.
Long-chain ceramides are cell non-autonomous signals linking lipotoxicity to endoplasmic reticulum stress in skeletal muscle
Authors: McNally Ben D. , Ashley Dean F. , Hänschke Lea , Daou Hélène N. , Watt Nicole T. , Murfitt Steven A. , MacCannell Amanda D. V. , Whitehead Anna , Bowen T. Scott , Sanders Francis W. B. , Vacca Michele , Witte Klaus K. , Davies Graeme R. , Bauer Reinhard , Griffin Julian L. , Roberts Lee D.
Published: April 2022

The endoplasmic reticulum (ER) regulates cellular protein and lipid biosynthesis. ER dysfunction leads to protein misfolding and the unfolded protein response (UPR), which limits protein synthesis to prevent cytotoxicity. Chronic ER stress in skeletal muscle is a unifying mechanism linking lipotoxicity to metabolic disease. Unidentified signals from cells undergoing ER stress propagate paracrine and systemic UPR activation. Here, we induce ER stress and lipotoxicity in myotubes. We observe ER stress-inducing lipid cell non-autonomous signal(s). Lipidomics identifies that palmitate-induced cell stress induces long-chain ceramide 40:1 and 42:1 secretion. Ceramide synthesis through the ceramide synthase 2 de novo pathway is regulated by UPR kinase Perk. Inactivation of CerS2 in mice reduces systemic and muscle ceramide signals and muscle UPR activation. The ceramides are packaged into extracellular vesicles, secreted and induce UPR activation in naïve myotubes through dihydroceramide accumulation. This study furthers our understanding of ER stress by identifying UPR-inducing cell non-autonomous signals.
Kerr reversal in Josephson meta-material and traveling wave parametric amplification
Authors: Ranadive Arpit , Esposito Martina , Planat Luca , Bonet Edgar , Naud Cécile , Buisson Olivier , Guichard Wiebke , Roch Nicolas
Published: April 2022

Josephson meta-materials have recently emerged as very promising platform for superconducting quantum science and technologies. Their distinguishing potential resides in ability to engineer them at sub-wavelength scales, which allows complete control over wave dispersion and nonlinear interaction. In this article we report a versatile Josephson transmission line with strong third order nonlinearity which can be tuned from positive to negative values, and suppressed second order non linearity. As an initial implementation of this multipurpose meta-material, we operate it to demonstrate reversed Kerr phase-matching mechanism in traveling wave parametric amplification. Compared to previous state of the art phase matching approaches, this reversed Kerr phase matching avoids the presence of gaps in transmission, can reduce gain ripples, and allows in situ tunability of the amplification band over an unprecedented wide range. Besides such notable advancements in the amplification performance with direct applications to superconducting quantum computing and generation of broadband squeezing, the in-situ tunability with sign reversal of the nonlinearity in traveling wave structures, with no counterpart in optics to the best of our knowledge, opens exciting experimental possibilities in the general framework of microwave quantum optics, single-photon detection and quantum limited amplification.
The future poleward shift of Southern Hemisphere summer mid-latitude storm tracks stems from ocean coupling
Authors: Chemke Rei
Published: April 2022

The latitudinal position of mid-latitude storm tracks has large climate impacts affecting the distribution of precipitation, temperature, humidity, and winds over the extratropics. By the end of this century, climate models project a poleward shift of summer mid-latitude storm tracks in the Southern Hemisphere. Most previous mechanisms for the poleward shift of the storm tracks focused on the role of atmospheric temperature changes. However, the relative roles of other climate system components in the projected storm tracks’ shift have not been examined to date. Here it is shown that thermodynamic ocean coupling is responsible for the future poleward shift of the storm tracks as it overcomes the effect of dynamic ocean coupling to shift the storm tracks equatorward. These results stress the importance of using full-physics ocean models to investigate the future shift of the storm tracks, and of better monitoring ocean coupling processes to improve our preparedness for future climate changes.
High failure rate of ChAdOx1-nCoV19 immunization against asymptomatic infection in healthcare workers during a Delta variant surge
Authors: Ujjainiya Rajat , Tyagi Akansha , Sardana Viren , Naushin Salwa , Bhatheja Nitin , Kumar Kartik , Barman Joydeb , Prakash Satyartha , Kutum Rintu , Bhaskar Akash Kumar , Singh Prateek , Chaudhary Kumardeep , Loomba Menka , Khanna Yukti , Walecha Chestha , Ahmed Rizwan , Yadav Ashutosh , Bajaj Archana , Malik Gaurav , Qureshi Sahar , Waghdhare Swati , Siddiqui Samreen , Trehan Kamal Krishan , Mani Manju , Dang Rajiv , Das Poonam , Dougall Pankaj , Mahajan Monica , Sonar Sudipta , Jakhar Kamini , Kumar Reema , Tiwari Mahima , Mani Shailendra , Bhattacharyya Sankar , Budhiraja Sandeep , Agrawal Anurag , Dash Debasis , Jha Sujeet , Sengupta Shantanu
Published: April 2022

Immunization is expected to confer protection against infection and severe disease for vaccines while reducing risks to unimmunized populations by inhibiting transmission. Here, based on serial serological studies of an observational cohort of healthcare workers, we show that during a Severe Acute Respiratory Syndrome -Coronavirus 2 Delta-variant outbreak in Delhi, 25.3% (95% Confidence Interval 16.9-35.2) of previously uninfected, ChAdOx1-nCoV19 double vaccinated, healthcare workers were infected within less than two months, based on serology. Induction of anti-spike response was similar between groups with breakthrough infection (541 U/ml, Inter Quartile Range 374) and without (342 U/ml, Inter Quartile Range 497), as was the induction of neutralization activity to wildtype. This was not vaccine failure since vaccine effectiveness estimate based on infection rates in an unvaccinated cohort were about 70% and most infections were asymptomatic. We find that while ChAdOx1-nCoV19 vaccination remains effective in preventing severe infections, it is unlikely to be completely able to block transmission and provide herd immunity.
Temporal and spatial characterisation of protein liquid-liquid phase separation using NMR spectroscopy
Authors: Bramham Jack E. , Golovanov Alexander P.
Published: April 2022

Liquid-liquid phase separation (LLPS) of protein solutions is increasingly recognised as an important phenomenon in cell biology and biotechnology. However, opalescence and concentration fluctuations render LLPS difficult to study, particularly when characterising the kinetics of the phase transition and layer separation. Here, we demonstrate the use of a probe molecule trifluoroethanol (TFE) to characterise the kinetics of protein LLPS by NMR spectroscopy. The chemical shift and linewidth of the probe molecule are sensitive to local protein concentration, with this sensitivity resulting in different characteristic signals arising from the dense and lean phases. Monitoring of these probe signals by conventional bulk-detection19F NMR reports on the formation and evolution of both phases throughout the sample, including their concentrations and volumes. Meanwhile, spatially-selective19F NMR, in which spectra are recorded from smaller slices of the sample, was used to track the distribution of the different phases during layer separation. This experimental strategy enables comprehensive characterisation of the process and kinetics of LLPS, and may be useful to study phase separation in protein systems as a function of their environment.
Platicon microcomb generation using laser self-injection locking
Authors: Lihachev Grigory , Weng Wenle , Liu Junqiu , Chang Lin , Guo Joel , He Jijun , Wang Rui Ning , Anderson Miles H. , Liu Yang , Bowers John E. , Kippenberg Tobias J.
Published: April 2022

The past decade has witnessed major advances in the development and system-level applications of photonic integrated microcombs, that are coherent, broadband optical frequency combs with repetition rates in the millimeter-wave to terahertz domain. Most of these advances are based on harnessing of dissipative Kerr solitons (DKS) in microresonators with anomalous group velocity dispersion (GVD). However, microcombs can also be generated with normal GVD using localized structures that are referred to as dark pulses, switching waves or platicons. Compared with DKS microcombs that require specific designs and fabrication techniques for dispersion engineering, platicon microcombs can be readily built using CMOS-compatible platforms such as thin-film (i.e., thickness below 300 nm) silicon nitride with normal GVD. Here, we use laser self-injection locking to demonstrate a fully integrated platicon microcomb operating at a microwave K-band repetition rate. A distributed feedback (DFB) laser edge-coupled to a Si3N4 chip is self-injection-locked to a high-Q ( > 107) microresonator with high confinement waveguides, and directly excites platicons without sophisticated active control. We demonstrate multi-platicon states and switching, perform optical feedback phase study and characterize the phase noise of the K-band platicon repetition rate and the pump laser. Laser self-injection-locked platicons could facilitate the wide adoption of microcombs as a building block in photonic integrated circuits via commercial foundry service.
Dual-wavelength switchable single-mode lasing from a lanthanide-doped resonator
Authors: Jin Limin , Chen Xian , Wu Yunkai , Ai Xiangzhe , Yang Xiaoli , Xiao Shumin , Song Qinghai
Published: April 2022

The development of multi-wavelength lasing, particularly with the wavelength tuning in a wide spectral range, is challenging but highly desirable for integrated photonic devices due to its dynamic switching functionality, high spectral purity and contrast. Here, we propose a general strategy, that relies on the simultaneous design on the electronic states and the optical states, to demonstrate dynamically switchable single-mode lasing spanning beyond the record range (300 nm). This is achieved through integrating the reversely designed nanocrystals with two size-mismatched coupled microcavities. We show an experimental validation of a crosstalk-free violet-to-red single-mode behavior through collective control of asymmetric excitation and excitation wavelength. The single-mode action persists for a wide power range, and presents significant enhancement when compared with that in the microdisk laser. These findings enlighten the reverse design of luminescent materials. Given the remarkable doping flexibility, our results may create new opportunities in a variety of frontier applications.
Stereoselective intermolecular radical cascade reactions of tryptophans or ɤ-alkenyl-α-amino acids with acrylamides via photoredox catalysis
Authors: Li Jiang-Tao , Luo Jian-Nan , Wang Jia-Le , Wang De-Ku , Yu Yi-Zhe , Zhuo Chun-Xiang
Published: April 2022

The radical cascade reaction is considered as one of the most powerful methods to build molecular complexity. However, highly stereoselective intermolecular radical cascade reactions that can produce complex cyclic compounds bearing multiple stereocenters via visible-light-induced photocatalysis have been challenging yet desirable. Herein we report a facile and efficient synthesis of multi-substituted trans-fused hexahydrocarbazoles via a stereoselective intermolecular radical cascade reaction of readily available tryptophans and acrylamides enabled by visible-light-induced photoredox catalysis. The trans-fused hexahydrocarbazoles with up to five stereocenters including two quaternary ones can be accessed in up to 82% yield, >20/1 diastereoselectivity, and 96% ee. Interestingly, the tetrahydrocarbazoles are favorably formed when the reaction is performed under air. Moreover, by simply switching the starting material from tryptophans to ɤ-alkenyl substituted α-amino acids, this protocol can be further applied to the stereoselective syntheses of 1,3,5-trisubstituted cyclohexanes which are otherwise challenging to access. Preliminary mechanistic studies suggest that the reaction goes through radical addition cascade and radical-polar crossover processes.
Therapeutic and immunomodulatory potential of pazopanib in malignant phyllodes tumor
Authors: Ng Dave Yong Xiang , Li Zhimei , Lee Elizabeth , Kok Jessica Sook Ting , Lee Jing Yi , Koh Joanna , Ng Cedric Chuan-Young , Lim Abner Herbert , Liu Wei , Ng Sheng Rong , Lim Kah Suan , Huang Xi Xiao , Hong Jing Han , Guan Peiyong , Sim Yirong , Thike Aye Aye , Nasir Nur Diyana Md , Li Shang , Tan Puay Hoon , Teh Bin Tean , Chan Jason Yongsheng
Published: April 2022

Malignant phyllodes tumors (PT) are rare aggressive fibroepithelial neoplasms with high metastatic potential and lack effective therapy. We established a patient-derived xenograft (PDX) and cell line model (designated MPT-S1) of malignant PT which demonstrated clinical response to pazopanib. Whole exome sequencing identified somatic mutations in TP53, RB1, MED12, and KMT2D. Immunohistochemistry and genomic profiles of the tumor, PDX and cell line were concordant. In keeping with clinical observation, pazopanib reduced cell viability in a dose-dependent manner and evoked apoptosis, and led to significant abrogation of in vivo tumor growth. Whole transcriptomic analysis revealed that pazopanib decreased expression of genes involved in oncogenic and apoptosis signaling. We also observed decreased expression of ENPP1, with known roles in cancer invasion and metastasis, as well as STING pathway upregulation. Accordingly, pazopanib induced micronuclei formation, and evoked phospho-TBK1 and PD-L1 expression. In an additional cohort of malignant PT (n = 14), six (42.9%) showed comparable or higher levels of ENPP1 relative to MPT-S1, highlighting its potential role as a therapeutic target. In conclusion, we established MPT-S1, a new PDX and cell line model, and provided evidence for the clinical efficacy of pazopanib in malignant PT.
Cryogenic spray quenching of simulated propellant tank wall using coating and flow pulsing in microgravity
Authors: Chung J. N. , Dong Jun , Wang Hao , Darr S. R. , Hartwig J. W.
Published: April 2022

In-space cryogenic propulsion will play a vital role in NASA’s return to the Moon mission and future mission to Mars. The enabling of in-space cryogenic engines and cryogenic fuel depots for these future manned and robotic space exploration missions begins with the technology development of advanced cryogenic thermal-fluid management systems for the propellant transfer lines and storage system. Before single-phase liquid can flow to the engine or spacecraft receiver tank, the connecting transfer line and storage tank must first be chilled down to cryogenic temperatures. The most direct and simplest method to quench the line and the tank is to use the cold propellant itself that results in the requirement of minimizing propellant consumption during chilldown. In view of the needs stated above, a highly efficient thermal-fluid management technology must be developed to consume the minimum amount of cryogen during chilldown of a transfer line and a storage tank. In this paper, we suggest the use of the cryogenic spray for storage tank chilldown. We have successfully demonstrated its feasibility and high efficiency in a simulated space microgravity condition. In order to maximize the storage tank chilldown efficiency for the least amount of cryogen consumption, the technology adopted included cryogenic spray cooling, Teflon thin-film coating of the simulated tank surface, and spray flow pulsing. The completed flight experiments successfully demonstrated that spray cooling is the most efficient cooling method for the tank chilldown in microgravity. In microgravity, Teflon coating alone can improve the efficiency up to 72% and the efficiency can be improved up to 59% by flow pulsing alone. However, Teflon coating together with flow pulsing was found to substantially enhance the chilldown efficiency in microgravity for up to 113%.
Multi-modality machine learning predicting Parkinson’s disease
Authors: Makarious Mary B. , Leonard Hampton L. , Vitale Dan , Iwaki Hirotaka , Sargent Lana , Dadu Anant , Violich Ivo , Hutchins Elizabeth , Saffo David , Bandres-Ciga Sara , Kim Jonggeol Jeff , Song Yeajin , Maleknia Melina , Bookman Matt , Nojopranoto Willy , Campbell Roy H. , Hashemi Sayed Hadi , Botia Juan A. , Carter John F. , Craig David W. , Van Keuren-Jensen Kendall , Morris Huw R. , Hardy John A. , Blauwendraat Cornelis , Singleton Andrew B. , Faghri Faraz , Nalls Mike A.
Published: April 2022

Personalized medicine promises individualized disease prediction and treatment. The convergence of machine learning (ML) and available multimodal data is key moving forward. We build upon previous work to deliver multimodal predictions of Parkinson’s disease (PD) risk and systematically develop a model using GenoML, an automated ML package, to make improved multi-omic predictions of PD, validated in an external cohort. We investigated top features, constructed hypothesis-free disease-relevant networks, and investigated drug–gene interactions. We performed automated ML on multimodal data from the Parkinson’s progression marker initiative (PPMI). After selecting the best performing algorithm, all PPMI data was used to tune the selected model. The model was validated in the Parkinson’s Disease Biomarker Program (PDBP) dataset. Our initial model showed an area under the curve (AUC) of 89.72% for the diagnosis of PD. The tuned model was then tested for validation on external data (PDBP, AUC 85.03%). Optimizing thresholds for classification increased the diagnosis prediction accuracy and other metrics. Finally, networks were built to identify gene communities specific to PD. Combining data modalities outperforms the single biomarker paradigm. UPSIT and PRS contributed most to the predictive power of the model, but the accuracy of these are supplemented by many smaller effect transcripts and risk SNPs. Our model is best suited to identifying large groups of individuals to monitor within a health registry or biobank to prioritize for further testing. This approach allows complex predictive models to be reproducible and accessible to the community, with the package, code, and results publicly available.
Viruses affect picocyanobacterial abundance and biogeography in the North Pacific Ocean
Authors: Carlson Michael. C. G. , Ribalet François , Maidanik Ilia , Durham Bryndan P. , Hulata Yotam , Ferrón Sara , Weissenbach Julia , Shamir Nitzan , Goldin Svetlana , Baran Nava , Cael B. B. , Karl David M. , White Angelicque E. , Armbrust E. Virginia , Lindell Debbie
Published: April 2022

The photosynthetic picocyanobacteria Prochlorococcus and Synechococcus are models for dissecting how ecological niches are defined by environmental conditions, but how interactions with bacteriophages affect picocyanobacterial biogeography in open ocean biomes has rarely been assessed. We applied single-virus and single-cell infection approaches to quantify cyanophage abundance and infected picocyanobacteria in 87 surface water samples from five transects that traversed approximately 2,200 km in the North Pacific Ocean on three cruises, with a duration of 2–4 weeks, between 2015 and 2017. We detected a 550-km-wide hotspot of cyanophages and virus-infected picocyanobacteria in the transition zone between the North Pacific Subtropical and Subpolar gyres that was present in each transect. Notably, the hotspot occurred at a consistent temperature and displayed distinct cyanophage-lineage composition on all transects. On two of these transects, the levels of infection in the hotspot were estimated to be sufficient to substantially limit the geographical range of Prochlorococcus. Coincident with the detection of high levels of virally infected picocyanobacteria, we measured an increase of 10–100-fold in the Synechococcus populations in samples that are usually dominated by Prochlorococcus. We developed a multiple regression model of cyanophages, temperature and chlorophyll concentrations that inferred that the hotspot extended across the North Pacific Ocean, creating a biological boundary between gyres, with the potential to release organic matter comparable to that of the sevenfold-larger North Pacific Subtropical Gyre. Our results highlight the probable impact of viruses on large-scale phytoplankton biogeography and biogeochemistry in distinct regions of the oceans.
A dataset of non-pharmaceutical interventions on SARS-CoV-2 in Europe
Authors: Altman George , Ahuja Janvi , Monrad Joshua Teperowski , Dhaliwal Gurpreet , Rogers-Smith Charlie , Leech Gavin , Snodin Benedict , Sandbrink Jonas B. , Finnveden Lukas , Norman Alexander John , Oehm Sebastian B. , Sandkühler Julia Fabienne , Kulveit Jan , Flaxman Seth , Gal Yarin , Mishra Swapnil , Bhatt Samir , Sharma Mrinank , Mindermann Sören , Brauner Jan Markus
Published: April 2022

During the second half of 2020, many European governments responded to the resurging transmission of SARS-CoV-2 with wide-ranging non-pharmaceutical interventions (NPIs). These efforts were often highly targeted at the regional level and included fine-grained NPIs. This paper describes a new dataset designed for the accurate recording of NPIs in Europe’s second wave to allow precise modelling of NPI effectiveness. The dataset includes interventions from 114 regions in 7 European countries during the period from the 1st August 2020 to the 9th January 2021. The paper includes NPI definitions tailored to the second wave following an exploratory data collection. Each entry has been extensively validated by semi-independent double entry, comparison with existing datasets, and, when necessary, discussion with local epidemiologists. The dataset has considerable potential for use in disentangling the effectiveness of NPIs and comparing the impact of interventions across different phases of the pandemic.
A spatially-explicit harmonized global dataset of critical infrastructure
Authors: Nirandjan Sadhana , Koks Elco E. , Ward Philip J. , Aerts Jeroen C. J. H.
Published: April 2022

Critical infrastructure (CI) is fundamental for the functioning of a society and forms the backbone for socio-economic development. Natural and human-made threats, however, pose a major risk to CI. Therefore, geospatial data on the location of CI are fundamental for in-depth risk analyses, which are required to inform policy decisions aiming to reduce risk. We present a first-of-its-kind globally harmonized spatial dataset for the representation of CI. In this study, we: (1) collect and harmonize detailed geospatial data of the world’s main CI systems into a single geospatial database; and (2) develop the Critical Infrastructure Spatial Index (CISI) to express the global spatial intensity of CI. The CISI aggregates high-resolution geospatial OpenStreetMap (OSM) data of 39 CI types that are categorized under seven overarching CI systems. The detailed geospatial data are rasterized into a harmonized and consistent dataset with a resolution of 0.10 × 0.10 and 0.25 × 0.25 degrees. The dataset can be applied to explore the current landscape of CI, identify CI hotspots, and as exposure input for large-scale risk assessments.
A biologging database of juvenile white sharks from the northeast Pacific
Authors: O’Sullivan John , Lowe Christopher G. , Sosa-Nishizaki Oscar , Jorgensen Salvador J. , Anderson James M. , Farrugia Thomas J. , García-Rodríguez Emiliano , Lyons Kady , McKinzie Megan K. , Oñate-González Erick C. , Weng Kevin , White Connor F. , Winkler Chuck , Van Houtan Kyle S.
Published: April 2022

Species occurrence records are vital data streams in marine conservation with a wide range of important applications. From 2001–2020, the Monterey Bay Aquarium led an international research collaboration to understand the life cycle, ecology, and behavior of white sharks (Carcharodon carcharias) in the southern California Current. The collaboration was devoted to tagging juveniles with animal-borne sensors, also known as biologging. Here we report the full data records from 59 pop-up archival (PAT) and 20 smart position and temperature transmitting (SPOT) tags that variously recorded pressure, temperature, and light-level data, and computed depth and geolocations for 63 individuals. Whether transmitted or from recovered devices, raw data files from successful deployments (n = 70) were auto-ingested from the manufacturer into the United States (US) Animal Telemetry Network’s (ATN) Data Assembly Center (DAC). There they have attributed a full suite of metadata, visualized within their public-facing data portal, compiled for permanent archive under the DataONE Research Workspace member node, and are accessible for download from the ATN data portal.
A hierarchical inventory of the world’s mountains for global comparative mountain science
Authors: Snethlage Mark A. , Geschke Jonas , Ranipeta Ajay , Jetz Walter , Yoccoz Nigel G. , Körner Christian , Spehn Eva M. , Fischer Markus , Urbach Davnah
Published: April 2022

A standardized delineation of the world’s mountains has many applications in research, education, and the science-policy interface. Here we provide a new inventory of 8616 mountain ranges developed under the auspices of the Global Mountain Biodiversity Assessment (GMBA). Building on an earlier compilation, the presented geospatial database uses a further advanced and generalized mountain definition and a semi-automated method to enable globally standardized, transparent delineations of mountain ranges worldwide. The inventory is presented on EarthEnv at various hierarchical levels and allows users to select their preferred level of regional aggregation from continents to small subranges according to their needs and the scale of their analyses. The clearly defined, globally consistent and hierarchical nature of the presented mountain inventory offers a standardized resource for referencing and addressing mountains across basic and applied natural as well as social sciences and a range of other uses in science communication and education.
Trait rumination and social anxiety separately influence stress-induced rumination and hemodynamic responses
Authors: Laicher Hendrik , Int-Veen Isabell , Torka Florian , Kroczek Agnes , Bihlmaier Isabel , Storchak Helena , Velten-Schurian Kerstin , Dresler Thomas , Täglich Ramona , Fallgatter Andreas J. , Ehlis Ann-Christine , Rosenbaum David
Published: April 2022

We aimed to investigate stress-reactive rumination in response to social stress and its association with social anxiety and trait rumination. From previous investigations we know that people with a certain vulnerability to rumination show increased stress-reactive rumination. However, up to date the possible influence of social anxiety on this relationship is still unclear. Therefore, we reanalyzed the data of two of our previous studies assessing healthy low and high trait ruminators and depressed patients performing the Trier Social Stress Test (TSST). We measured cortical oxygenation using functional Near-Infrared Spectroscopy (fNIRS) as well as different behavioral outcome measures (subjective stress levels, negative affect, state rumination). On a behavioral level, we found an influence of both, social anxiety and trait rumination, on state rumination, even when correcting for the other factor, respectively, implying two potentially independent factors of influence. On a neural level, we observed reduced activation in brain regions of the cognitive control network (CCN) for higher social anxiety and trait rumination, which might be a result of reduced cognitive and attentional control. Results indicate a specific role of social anxiety, at least on a behavioral level, and therefore implicate a crucial factor to be considered in the treatment of depression.
Longitudinal relationship of liver injury with inflammation biomarkers in COVID-19 hospitalized patients using a joint modeling approach
Authors: Diaz-Louzao Carla , Barrera-Lopez Lucia , Lopez-Rodriguez Maria , Casar Clara , Vazquez-Agra Nestor , Pernas-Pardavila Hadrian , Marques-Afonso Ana , Vidal-Vazquez Martin , Montoya Jonathan G. , Andrade Ariadna H. , Fernandez-Castro Ivan , Varela Pablo , Gonzalez-Quintela Arturo , Otero Esteban , Gude Francisco , Cadarso-Suarez Carmen , Tome Santiago
Published: April 2022

The mechanisms underlying liver disease in patients with COVID-19 are not entirely known. The aim is to investigate, by means of novel statistical techniques, the changes over time in the relationship between inflammation markers and liver damage markers in relation to survival in COVID-19. The study included 221 consecutive patients admitted to the hospital during the first COVID-19 wave in Spain. Generalized additive mixed models were used to investigate the influence of time and inflammation markers on liver damage markers in relation to survival. Joint modeling regression was used to evaluate the temporal correlations between inflammation markers (serum C-reactive protein [CRP], interleukin-6, plasma D-dimer, and blood lymphocyte count) and liver damage markers, after adjusting for age, sex, and therapy. The patients who died showed a significant elevation in serum aspartate transaminase (AST) and alkaline phosphatase levels over time. Conversely, a decrease in serum AST levels was observed in the survivors, who showed a negative correlation between inflammation markers and liver damage markers (CRP with serum AST, alanine transaminase [ALT], and gamma-glutamyl transferase [GGT]; and D-dimer with AST and ALT) after a week of hospitalization. Conversely, most correlations were positive in the patients who died, except lymphocyte count, which was negatively correlated with AST, GGT, and alkaline phosphatase. These correlations were attenuated with age. The patients who died during COVID-19 infection displayed a significant elevation of liver damage markers, which is correlated with inflammation markers over time. These results are consistent with the role of systemic inflammation in liver damage during COVID-19.
Returning long-range PM2.5 transport into the leeward of East Asia in 2021 after Chinese economic recovery from the COVID-19 pandemic
Authors: Itahashi Syuichi , Yamamura Yuki , Wang Zhe , Uno Itsushi
Published: April 2022

Changes in the aerosol composition of sulfate (SO42−) and nitrate (NO3−) from 2012 to 2019 have been captured as a paradigm shift in the region downwind of China. Specifically, SO42− dramatically decreased and NO3− dramatically increased over downwind locations such as western Japan due to the faster reduction of SO2 emissions than NOx emissions and the almost constant trend of NH3 emissions from China. Emissions from China sharply decreased during COVID-19 lockdowns in February–March 2020, after which China’s economic situation seemed to recover going into 2021. Given this substantial change in Chinese emissions, it is necessary to clarify the impact of long-range PM2.5 transport into the leeward of East Asia. In this study, ground-based aerosol compositions observed at three sites in western Japan were analysed. The concentrations of PM2.5, SO42− and NO3− decreased in 2020 (during COVID-19) compared with 2018–2019 (before COVID-19). In 2021 (after COVID-19), PM2.5 and NO3− increased and SO42− was unchanged. This suggests the returning long-range PM2.5 transport in 2021. From numerical simulations, the status of Chinese emissions during COVID-19 did not explain this returning impact in 2021. This study shows that the status of Chinese emissions in 2021 recovered to that before COVID-19.
Determination and dietary intake risk assessment of 35 pesticide residues in cowpea (Vigna unguiculata [L.] Walp) from Hainan province, China
Authors: Zhang Qun , Ma Chen , Duan Yun , Wu Xiaopeng , Lv Daizhu , Luo Jinhui
Published: April 2022

The presence of pesticide residues in cowpea raises serious health concerns. In this study, a novel, sensitive, high-performance method was developed to simultaneously analyze the residues of 35 pesticides in cowpea samples from growing areas in the Hainan province of China, from November 2018 to June 2021. The method employs modified QuEChERS sample pretreatment coupled with gas chromatography-tandem mass spectrometry. The limits of quantification of the 35 pesticides in the cowpea matrix ranged from 1.0 to 8.0 μg/kg. Twenty-seven of the 35 pesticides were detected, twelve of which are banned for use on legumes in China. Residues for ten pesticides in 17.1% of the samples exceeded their MRLs, with the highest exceedance of 380% observed in difenoconazole. Moreover, 80.8% of the samples contained one or more pesticide residues, with the most frequently detected pesticide being chlorfenapyr with a detection rate of 46.3%. In addition, the pesticide triazophos was detected through different years and regions. Notably, the chronic dietary exposure risk (%ADI) of the detected pesticides, evaluated from the national estimated acceptable daily intake, was lower than 100% in Chinese people of different age groups.
A general framework to link theory and empirics in opinion formation models
Authors: Kozitsin Ivan V.
Published: April 2022

We introduce a minimal opinion formation model that is quite flexible and can reproduce a wide variety of the existing micro-influence assumptions and models. The model can be easily calibrated on real data, upon which it imposes only a few requirements. From this perspective, our model can be considered as a bridge, connecting theoretical studies on opinion formation models and empirical research on social dynamics. We investigate the model analytically by using mean-field approximation and numerically via Monte Carlo simulations. Our analysis is exemplified by recently reported empirical data drawn from an online social network. We demonstrate that the model calibrated on these data may reproduce fragmented and polarizing social systems. Furthermore, we manage to generate an artificial society that features properties quantitatively and qualitatively similar to those observed empirically at the macro scale. This ability became possible after we had advanced the model with two important communication features: selectivity and personalization algorithms.
Alteration in molecular structure of alkali activated slag with various water to binder ratios under accelerated carbonation
Authors: Nguyen Thi Nhan , Phung Quoc Tri , Yu Ziyou , Frederickx Lander , Jacques Diederik , Sakellariou Dimitrios , Dauzeres Alexandre , Elsen Jan , Pontikes Yiannis
Published: April 2022

Carbonation of alkali activated materials is one of the main deteriorations affecting their durability. However, current understanding of the structural alteration of these materials exposed to an environment inducing carbonation at the nano/micro scale remains limited. This study examined the evolution of phase assemblages of alkali activated slag mortars subjected to accelerated carbonation (1% CO2, 60% relative humidity, up to 28 day carbonation) using XRD, FTIR and 29Si, 27Al, and 23Na MAS NMR. Samples with three water to binder (w/b) ratios (0.35, 0.45, and 0.55) were investigated. The results show that the phase assemblages mainly consisted of C-A-S-H, a disordered remnant aluminosilicate binder, and a minor hydrotalcite as a secondary product. Upon carbonation, calcium carbonate is mainly formed as the vaterite polymorph, while no sodium carbonate is found after carbonation as commonly reported. Sodium acts primarily as a charge balancing ion without producing sodium carbonate as a final carbonation product in the 28-day carbonated materials. The C-A-S-H structure becomes more cross-linked due to the decalcification of this phase as evidenced by the appearance of Q4 groups, which replace the Q1 and Q2 groups as observed in the 29Si MAS NMR spectra, and the dominance of Al(IV) in 27Al MAS NMR. Especially, unlike cementitious materials, the influence of w/b ratio on the crystalline phase formation and structure of C-A-S-H in the alkali activated mortars before and after carbonation is limited.
Body fat compartment determination by encoder–decoder convolutional neural network: application to amyotrophic lateral sclerosis
Authors: Vernikouskaya Ina , Müller Hans-Peter , Felbel Dominik , Roselli Francesco , Ludolph Albert C. , Kassubek Jan , Rasche Volker
Published: April 2022

The objective of this study was to automate the discrimination and quantification of human abdominal body fat compartments into subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT) from T1-weighted MRI using encoder-decoder convolutional neural networks (CNN) and to apply the algorithm to a diseased patient sample, i.e., patients with amyotrophic lateral sclerosis (ALS). One-hundred-and-fifty-five participants (74 patients with ALS and 81 healthy controls) were split in training (50%), validation (6%), and test (44%) data. SAT and VAT volumes were determined by a novel automated CNN-based algorithm of U-Net like architecture in comparison with an established protocol with semi-automatic assessment as the reference. The dice coefficients between the CNN predicted masks and the reference segmentation were 0.87 ± 0.04 for SAT and 0.64 ± 0.17 for VAT in the control group and 0.87 ± 0.08 for SAT and 0.68 ± 0.15 for VAT in the ALS group. The significantly increased VAT/SAT ratio in the ALS group in comparison to controls confirmed the previous results. In summary, the CNN approach using CNN of U-Net architecture for automated segmentation of abdominal adipose tissue substantially facilitates data processing and offers the opportunity to automatically discriminate abdominal SAT and VAT compartments. Within the research field of neurodegenerative disorders with body composition alterations like ALS, the unbiased analysis of body fat components might pave the way for these parameters as a potential biological marker or a secondary read-out for clinical trials.
Effect of SARs-CoV-2 pandemic on infection prevention behaviors and bacterial burden of high touch surfaces in a medical/surgical setting
Authors: Resendiz Marisol , Blanchard Dawn M. , Lustik Michael B. , Horseman Timothy S. , West Gordon F.
Published: April 2022

This study aimed to determine the longitudinal efficacy of ultraviolet germicidal disinfection (UV-C) in a non-terminal disinfection context. Moreover, factors influencing enhanced infection prevention behaviors during the SARS-CoV-2 pandemic were evaluated. Sixty nursing staff from three medical/surgical wards in a large military hospital were recruited for a survey and microbiological sampling of high-touch surfaces (stethoscope, personal electronic device, common access card, and hospital ID badge) and portable medical equipment (wheelchairs and mobile commodes). Surveys included hand hygiene estimates, frequency/method of cleaning items of interest, perception of UV-C, and factors influencing the use of enhanced disinfection tools. Surveys and microbiological samples were performed prior to and after the installation of a rapid, automated ultraviolet disinfection enclosure for staff use. Both time points preceded the SARS-CoV-2 pandemic in the United States. A final survey/sampling time point was carried out eight months after the declaration of the COVID-19 pandemic. Participants’ hand hygiene frequency did not increase throughout the study, with > 80% reporting a minimum of 4 hand hygiene events per patient hour. The cleaning frequency of high-touch surfaces (non-clinical) but not portable medical equipment increased after installation of a UV-C disinfection tool and was sustained eight months into the COVID-19 pandemic. While a modest decrease in bacterial burden was observed after UV-C intervention, a more significant reduction was observed across all surfaces during pandemic time sampling, though no detectable decrease in pathogenic contamination was observed at either time point. Motivators of UV-C use included fear of SARS-CoV-2 contamination and transmission, ease of device use, and access to rapid, automated disinfection tools while deterrents reported included technical concerns, lack of time, and preference for other disinfection methods. Automated, rapid-cycle UV-C disinfection can be efficacious for high-touch surfaces not currently governed by infection prevention and control guidelines. The introduction of enhanced disinfection tools like UV-C can enhance the overall cleaning frequency and is correlated with mild decreases in bacterial burden of high-touch surfaces, this is enhanced during periods of heightened infection threat. Evidence from this study offers insights into the factors which prompt healthcare workers to internalize/dismiss enhanced infection prevention procedures.