bluuebunny/crossref_metadata_2025_split huggingface dataset:
An analysis of 45 large-scale wastewater sites in England to estimate SARS-CoV-2 community prevalence
Authors: Morvan Mario , Jacomo Anna Lo , Souque Celia , Wade Matthew J. , Hoffmann Till , Pouwels Koen , Lilley Chris , Singer Andrew C. , Porter Jonathan , Evens Nicholas P. , Walker David I. , Bunce Joshua T. , Engeli Andrew , Grimsley Jasmine , O’Reilly Kathleen M. , Danon Leon 
Published: July 2022

AbstractAccurate surveillance of the COVID-19 pandemic can be weakened by under-reporting of cases, particularly due to asymptomatic or pre-symptomatic infections, resulting in bias. Quantification of SARS-CoV-2 RNA in wastewater can be used to infer infection prevalence, but uncertainty in sensitivity and considerable variability has meant that accurate measurement remains elusive. Here, we use data from 45 sewage sites in England, covering 31% of the population, and estimate SARS-CoV-2 prevalence to within 1.1% of estimates from representative prevalence surveys (with 95% confidence). Using machine learning and phenomenological models, we show that differences between sampled sites, particularly the wastewater flow rate, influence prevalence estimation and require careful interpretation. We find that SARS-CoV-2 signals in wastewater appear 4–5 days earlier in comparison to clinical testing data but are coincident with prevalence surveys suggesting that wastewater surveillance can be a leading indicator for symptomatic viral infections. Surveillance for viruses in wastewater complements and strengthens clinical surveillance, with significant implications for public health.
Spatial tomography of light resolved in time, spectrum, and polarisation
Authors: Plöschner Martin , Morote Marcos Maestre , Dahl Daniel Stephen , Mounaix Mickael , Light Greta , Rakić Aleksandar D. , Carpenter Joel 
Published: July 2022

AbstractMeasuring polarisation, spectrum, temporal dynamics, and spatial complex amplitude of optical beams is essential to studying phenomena in laser dynamics, telecommunications and nonlinear optics. Current characterisation techniques apply in limited contexts. Non-interferometric methods struggle to distinguish spatial phase, while phase-sensitive approaches necessitate either an auxiliary reference source or a self-reference, neither of which is universally available. Deciphering complex wavefronts of multiple co-propagating incoherent fields remains particularly challenging. We harness principles of spatial state tomography to circumvent these limitations and measure a complete description of an unknown beam as a set of spectrally, temporally, and polarisation resolved spatial state density matrices. Each density matrix slice resolves the spatial complex amplitude of multiple mutually incoherent fields, which over several slices reveals the spectral or temporal evolution of these fields even when fields spectrally or temporally overlap. We demonstrate these features by characterising the spatiotemporal and spatiospectral output of a vertical-cavity surface-emitting laser.
Revisiting stress-corrosion cracking and hydrogen embrittlement in 7xxx-Al alloys at the near-atomic-scale
Authors: López Freixes Martí , Zhou Xuyang , Zhao Huan , Godin Hélène , Peguet Lionel , Warner Timothy , Gault Baptiste 
Published: July 2022

AbstractThe high-strength 7xxx series aluminium alloys can fulfil the need for light, high strength materials necessary to reduce carbon-emissions, and are extensively used in aerospace for weight reduction purposes. However, as all major high-strength materials, these alloys can be sensitive to stress-corrosion cracking (SCC) through anodic dissolution and hydrogen embrittlement (HE). Here, we study at the near-atomic-scale the intra- and inter-granular microstructure ahead and in the wake of a propagating SCC crack. Moving away from model alloys and non-industry standard tests, we perform a double cantilever beam (DCB) crack growth test on an engineering 7xxx Al-alloy. H is found segregated to planar arrays of dislocations and to grain boundaries that we can associate to the combined effects of hydrogen-enhanced localised plasticity (HELP) and hydrogen-enhanced decohesion (HEDE) mechanisms. We report on a Mg-rich amorphous hydroxide on the corroded crack surface and evidence of Mg-related diffusional processes leading to dissolution of the strengthening η-phase precipitates ahead of the crack.
Carbodefluorination of fluoroalkyl ketones via a carbene-initiated rearrangement strategy
Authors: Li Linxuan , Zhang Xinyu , Ning Yongquan , Zhang Xiaolong , Liu Binbin , Zhang Zhansong , Sivaguru Paramasivam , Zanoni Giuseppe , Li Shuang , Anderson Edward A. , Bi Xihe 
Published: July 2022

AbstractThe C–F bond cleavage and C–C bond formation (i.e., carbodefluorination) of readily accessible (per)fluoroalkyl groups constitutes an atom-economical and efficient route to partially fluorinated compounds. However, the selective mono-carbodefluorination of trifluoromethyl (CF3) groups remains a challenge, due to the notorious inertness of C–F bond and the risk of over-defluorination arising from C–F bond strength decrease as the defluorination proceeds. Herein, we report a carbene-initiated rearrangement strategy for the carbodefluorination of fluoroalkyl ketones with β,γ-unsaturated alcohols to provide skeletally and functionally diverse α-mono- and α,α-difluoro-γ,δ-unsaturated ketones. The reaction starts with the formation of silver carbenes from fluoroalkylN-triftosylhydrazones, followed by nucleophilic attack of a β,γ-unsaturated alcohol to form key silver-coordinated oxonium ylide intermediates, which triggers selective C–F bond cleavage by HF elimination and C–C bond formation through Claisen rearrangement of in situ generated difluorovinyl ether. The origin of chemoselectivity and the reaction mechanism are determined by experimental and DFT calculations. Collectively, this strategy by an intramolecular cascade process offers significant advances over existing stepwise strategies in terms of selectivity, efficiency, functional group tolerance, etc.
Warming and redistribution of nitrogen inputs drive an increase in terrestrial nitrous oxide emission factor
Authors: Harris E. , Yu L. , Wang Y-P. , Mohn J. , Henne S. , Bai E. , Barthel M. , Bauters M. , Boeckx P. , Dorich C. , Farrell M. , Krummel P. B. , Loh Z. M. , Reichstein M. , Six J. , Steinbacher M. , Wells N. S. , Bahn M. , Rayner P. 
Published: July 2022

AbstractAnthropogenic nitrogen inputs cause major negative environmental impacts, including emissions of the important greenhouse gas N2O. Despite their importance, shifts in terrestrial N loss pathways driven by global change are highly uncertain. Here we present a coupled soil-atmosphere isotope model (IsoTONE) to quantify terrestrial N losses and N2O emission factors from 1850-2020. We find that N inputs from atmospheric deposition caused 51% of anthropogenic N2O emissions from soils in 2020. The mean effective global emission factor for N2O was 4.3 ± 0.3% in 2020 (weighted by N inputs), much higher than the surface area-weighted mean (1.1 ± 0.1%). Climate change and spatial redistribution of fertilisation N inputs have driven an increase in global emission factor over the past century, which accounts for 18% of the anthropogenic soil flux in 2020. Predicted increases in fertilisation in emerging economies will accelerate N2O-driven climate warming in coming decades, unless targeted mitigation measures are introduced.
Therapeutic targeting of ATR in alveolar rhabdomyosarcoma
Authors: Dorado García Heathcliff , Pusch Fabian , Bei Yi , von Stebut Jennifer , Ibáñez Glorymar , Guillan Kristina , Imami Koshi , Gürgen Dennis , Rolff Jana , Helmsauer Konstantin , Meyer-Liesener Stephanie , Timme Natalie , Bardinet Victor , Chamorro González Rocío , MacArthur Ian C. , Chen Celine Y. , Schulz Joachim , Wengner Antje M. , Furth Christian , Lala Birgit , Eggert Angelika , Seifert Georg , Hundsoerfer Patrick , Kirchner Marieluise , Mertins Philipp , Selbach Matthias , Lissat Andrej , Dubois Frank , Horst David , Schulte Johannes H. , Spuler Simone , You Daoqi , Dela Cruz Filemon , Kung Andrew L. , Haase Kerstin , DiVirgilio Michela , Scheer Monika , Ortiz Michael V. , Henssen Anton G. 
Published: July 2022

AbstractDespite advances in multi-modal treatment approaches, clinical outcomes of patients suffering from PAX3-FOXO1 fusion oncogene-expressing alveolar rhabdomyosarcoma (ARMS) remain dismal. Here we show that PAX3-FOXO1-expressing ARMS cells are sensitive to pharmacological ataxia telangiectasia and Rad3 related protein (ATR) inhibition. Expression of PAX3-FOXO1 in muscle progenitor cells is not only sufficient to increase sensitivity to ATR inhibition, but PAX3-FOXO1-expressing rhabdomyosarcoma cells also exhibit increased sensitivity to structurally diverse inhibitors of ATR. Mechanistically, ATR inhibition leads to replication stress exacerbation, decreased BRCA1 phosphorylation and reduced homologous recombination-mediated DNA repair pathway activity. Consequently, ATR inhibitor treatment increases sensitivity of ARMS cells to PARP1 inhibition in vitro, and combined treatment with ATR and PARP1 inhibitors induces complete regression of primary patient-derived ARMS xenografts in vivo. Lastly, a genome-wide CRISPR activation screen (CRISPRa) in combination with transcriptional analyses of ATR inhibitor resistant ARMS cells identifies the RAS-MAPK pathway and its targets, the FOS gene family, as inducers of resistance to ATR inhibition. Our findings provide a rationale for upcoming biomarker-driven clinical trials of ATR inhibitors in patients suffering from ARMS.
The architecture of kinesin-3 KLP-6 reveals a multilevel-lockdown mechanism for autoinhibition
Authors: Wang Wenjuan , Ren Jinqi , Song Weiye , Zhang Yong , Feng Wei 
Published: July 2022

AbstractAutoinhibition of kinesin-3 ensures the proper spatiotemporal control of the motor activity for intracellular transport, but the underlying mechanism remains elusive. Here, we determine the full-length structure of kinesin-3 KLP-6 in a compact self-folded state. Unexpectedly, all the internal coiled-coil segments and domains in KLP-6 cooperate to successively lock down the neck and motor domains. The first coiled-coil segment is melted into several short helices that work with the motor domain to restrain the entire neck domain. The second coiled-coil segment associates with its neighboring FHA and MBS domains and integrates with the tail MATH domain to form a supramodule that synergistically wraps around the motor domain to trap the nucleotide and hinder the microtubule binding. This multilevel-lockdown mechanism for autoinhibition could be applicable to other kinesin-3 motors.
Transition from sub-Rayleigh anticrack to supershear crack propagation in snow avalanches
Authors: Trottet Bertil , Simenhois Ron , Bobillier Gregoire , Bergfeld Bastian , van Herwijnen Alec , Jiang Chenfanfu , Gaume Johan 
Published: July 2022

AbstractSnow slab avalanches, characterized by a distinct, broad fracture line, are released following anticrack propagation in highly porous weak snow layers buried below cohesive slabs. The anticrack mechanism is driven by the volumetric collapse of the weak layer, which leads to the closure of crack faces and to the onset of frictional contact. Here, on the basis of snow fracture experiments, full-scale avalanche measurements and numerical simulations, we report the existence of a transition from sub-Rayleigh anticrack to supershear crack propagation. This transition follows the Burridge–Andrews mechanism, in which a supershear daughter crack nucleates ahead of the main fracture front and eventually propagates faster than the shear wave speed. Furthermore, we show that the supershear propagation regime can exist even if the shear-to-normal stress ratio is lower than the static friction coefficient as a result of the loss of frictional resistance during collapse. This finding shows that snow slab avalanches have fundamental similarities with strike-slip earthquakes.
Self-supervised deep learning encodes high-resolution features of protein subcellular localization
Authors: Kobayashi Hirofumi , Cheveralls Keith C. , Leonetti Manuel D. , Royer Loic A. 
Published: July 2022

AbstractExplaining the diversity and complexity of protein localization is essential to fully understand cellular architecture. Here we present cytoself, a deep-learning approach for fully self-supervised protein localization profiling and clustering. Cytoself leverages a self-supervised training scheme that does not require preexisting knowledge, categories or annotations. Training cytoself on images of 1,311 endogenously labeled proteins from the OpenCell database reveals a highly resolved protein localization atlas that recapitulates major scales of cellular organization, from coarse classes, such as nuclear and cytoplasmic, to the subtle localization signatures of individual protein complexes. We quantitatively validate cytoself’s ability to cluster proteins into organelles and protein complexes, showing that cytoself outperforms previous self-supervised approaches. Moreover, to better understand the inner workings of our model, we dissect the emergent features from which our clustering is derived, interpret them in the context of the fluorescence images, and analyze the performance contributions of each component of our approach.
Cereal grain mineral micronutrient and soil chemistry data from GeoNutrition surveys in Ethiopia and Malawi
Authors: Kumssa D. B. , Mossa A. W. , Amede T. , Ander E. L. , Bailey E. H. , Botoman L. , Chagumaira C. , Chimungu J. G. , Davis K. , Gameda S. , Haefele S. M. , Hailu K. , Joy E. J. M. , Lark R. M. , Ligowe I. S. , McGrath S. P. , Milne A. , Muleya P. , Munthali M. , Towett E. , Walsh M. G. , Wilson L. , Young S. D. , Haji I. R. , Broadley M. R. , Gashu D. , Nalivata P. C. 
Published: July 2022

AbstractThe dataset comprises primary data for the concentration of 29 mineral micronutrients in cereal grains and up to 84 soil chemistry properties from GeoNutrition project surveys in Ethiopia and Malawi. The work provided insights on geospatial variation in the micronutrient concentration in staple crops, and the potential influencing soil factors. In Ethiopia, sampling was conducted in Amhara, Oromia, and Tigray regions, during the late-2017 and late-2018 harvest seasons. In Malawi, national-scale sampling was conducted during the April–June 2018 harvest season. The concentrations of micronutrients in grain were measured using inductively coupled plasma mass spectrometry (ICP-MS). Soil chemistry properties reported include soil pH; total soil nitrogen; total soil carbon (C); soil organic C; effective cation exchange capacity and exchangeable cations; a three-step sequential extraction scheme for the fractionation of sulfur and selenium; available phosphate; diethylenetriaminepentaacetic acid (DTPA)-extractable trace elements; extractable trace elements using 0.01 M Ca(NO3)2 and 0.01 M CaCl2; and isotopically exchangeable Zn. These data are reported here according to FAIR data principles to enable users to further explore agriculture-nutrition linkages.
Learning to sense three-dimensional shape deformation of a single multimode fiber
Authors: Wang Xuechun , Wang Yufei , Zhang Ketao , Althoefer Kaspar , Su Lei 
Published: July 2022

AbstractOptical fiber bending, deformation or shape sensing are important measurement technologies and have been widely deployed in various applications including healthcare, structural monitoring and robotics. However, existing optical fiber bending sensors require complex sensor structures and interrogation systems. Here, inspired by the recent renewed interest in information-rich multimode optical fibers, we show that the multimode fiber (MMF) output speckles contain the three-dimensional (3D) geometric shape information of the MMF itself. We demonstrate proof-of-concept 3D multi-point deformation sensing via a single multimode fiber by using k-nearest neighbor (KNN) machine learning algorithm, and achieve a classification accuracy close to 100%. Our results show that a single MMF based deformation sensor is excellent in terms of system simplicity, resolution and sensitivity, and can be a promising candidate in deformation monitoring or shape-sensing applications.
Characterization of methylation patterns associated with lifestyle factors and vitamin D supplementation in a healthy elderly cohort from Southwest Sweden
Authors: Cruz Maria Araceli Diaz , Ulfenborg Benjamin , Blomstrand Peter , Faresjö Maria , Ståhl Fredrik , Karlsson Sandra 
Published: July 2022

AbstractNumerous studies have shown that lifestyle factors, such as regular physical activity and vitamin D intake, may remarkably improve overall health and mental wellbeing. This is especially important in older adults whose vitamin D deficiency occurs with a high prevalence. This study aimed to examine the influence of lifestyle and vitamin D on global DNA methylation patterns in an elderly cohort in Southwest of Sweden. We also sought to examine the methylation levels of specific genes involved in vitamin D's molecular and metabolic activated pathways. We performed a genome wide methylation analysis, using Illumina Infinium DNA Methylation EPIC 850kBeadChip array, on 277 healthy individuals from Southwest Sweden at the age of 70–95. The study participants also answered queries on lifestyle, vitamin intake, heart medication, and estimated health. Vitamin D intake did not in general affect methylation patterns, which is in concert with other studies. However, when comparing the group of individuals taking vitamin supplements, including vitamin D, with those not taking supplements, a difference in methylation in the solute carrier family 25 (SCL25A24)gene was found. This confirms a previous finding, where changes in expression ofSLC25A24were associated with vitamin D treatment in human monocytes. The combination of vitamin D intake and high physical activity increased methylation of genes linked to regulation of vitamin D receptor pathway, the Wnt pathway and general cancer processes. To our knowledge, this is the first study detecting epigenetic markers associated with the combined effects of vitamin D supplementation and high physical activity. These results deserve to be further investigated in an extended, interventional study cohort, where also the levels of 25(OH)D3can be monitored.
Finite element and in vitro study on biomechanical behavior of endodontically treated premolars restored with direct or indirect composite restorations
Authors: Maravić Tatjana , Comba Allegra , Mazzitelli Claudia , Bartoletti Luca , Balla Irene , di Pietro Elisabetta , Josić Uroš , Generali Luigi , Vasiljević Darko , Blažić Larisa , Breschi Lorenzo , Mazzoni Annalisa 
Published: July 2022

AbstractObjectives of the study were to investigate biomechanical properties of severely compromised premolars restored with composite restorations using finite element analysis (FEA), and in vitro fracture resistance test. A 3-D model of an endodontically treated premolar was created in Solidworks. Different composite restorations were modelled (direct restoration-DR; endo-crown-EC; post, core, and crown-C) with two different supporting tissues: periodontal ligament/alveolar bone (B), and polymethyl methacrylate (PMMA). Models were two-point axially loaded occlusally (850 N). Von Mises stresses and strains were calculated. The same groups were further tested for static fracture resistance in vitro (n = 5, 6.0 mm-diameter ball indenter, vertical load). Fracture resistance data were statistically analyzed (p < 0.050). The highest stresses and strains in all FEA models were observed on occlusal and vestibular cervical surfaces, corresponding to fracture propagation demonstrated in vitro. C showed the lowest stress in dentin, while EC showed lower stresses and strains in crown cement. B models demonstrated larger high stress areas in the root than PMMA models. No significant differences in fracture resistance (N) were observed between groups (DR: 747.7 ± 164.0, EC: 867.3 ± 108.1, C: 866.9 ± 126.3; p = 0.307). More conservative restorations seem a feasible alternative for endodontically treated premolars to conventional post-core-crown.
Evidence for correlations between BMI-associated SNPs and circRNAs
Authors: Rajcsanyi Luisa Sophie , Diebels Inga , Pastoors Lydia , Kanber Deniz , Peters Triinu , Volckmar Anna-Lena , Zheng Yiran , Grosse Martin , Dieterich Christoph , Hebebrand Johannes , Kaiser Frank J. , Horsthemke Bernhard , Hinney Anke 
Published: July 2022

AbstractCircular RNAs (circRNAs) are regulators of processes like adipogenesis. Their expression can be modulated by SNPs. We analysed links between BMI-associated SNPs and circRNAs. First, we detected an enrichment of BMI-associated SNPs on circRNA genomic loci in comparison to non-significant variants. Analysis of sex-stratified GWAS data revealed that circRNA genomic loci encompassed more genome-wide significant BMI-SNPs in females than in males. To explore whether the enrichment is restricted to BMI, we investigated nine additional GWAS studies. We showed an enrichment of trait-associated SNPs in circRNAs for four analysed phenotypes (body height, chronic kidney disease, anorexia nervosa and autism spectrum disorder). To analyse the influence of BMI-affecting SNPs on circRNA levels in vitro, we examined rs4752856 located on hsa_circ_0022025. The analysis of heterozygous individuals revealed an increased level of circRNA derived from the BMI-increasing SNP allele. We conclude that genetic variation may affect the BMI partly through circRNAs.
A diffeomorphic aging model for adult human brain from cross-sectional data
Authors: Thottupattu Alphin J. , Sivaswamy Jayanthi , Krishnan Venkateswaran P. 
Published: July 2022

AbstractNormative aging trends of the brain can serve as an important reference in the assessment of neurological structural disorders. Such models are typically developed from longitudinal brain image data—follow-up data of the same subject over different time points. In practice, obtaining such longitudinal data is difficult. We propose a method to develop an aging model for a given population, in the absence of longitudinal data, by using images from different subjects at different time points, the so-called cross-sectional data. We define an aging model as a diffeomorphic deformation on a structural template derived from the data and propose a method that develops topology preserving aging model close to natural aging. The proposed model is successfully validated on two public cross-sectional datasets which provide templates constructed from different sets of subjects at different age points.
Contracted thalamic shape is associated with early development of levodopa-induced dyskinesia in Parkinson’s disease
Authors: Yoo Han Soo , Lee Eun-Chong , Chung Seok Jong , Ye Byoung Seok , Sohn Young H. , Seong Joon-Kyung , Lee Phil Hyu 
Published: July 2022

AbstractLevodopa-induced dyskinesia (LID), a long-term motor complication in Parkinson’s disease (PD), is attributable to both presynaptic and postsynaptic mechanisms. However, no studies have evaluated the baseline structural changes associated with LID at a subcortical level in PD. A total of 116 right-handed PD patients were recruited and based on the LID latency of 5 years, we classified patients into those vulnerable to LID (PD-vLID, n = 49) and those resistant to LID (PD-rLID, n = 67). After adjusting for covariates including dopamine transporter (DAT) availability of the posterior putamen, we compared the subcortical shape between the groups and investigated its association with the onset of LID. The PD-vLID group had lower DAT availability in the posterior putamen, higher parkinsonian motor deficits, and faster increment in levodopa equivalent dose than the PD-rLID group. The PD-vLID group had significant inward deformation in the right thalamus compared to the PD-rLID group. Inward deformation in the thalamus was associated with an earlier onset of LID at baseline. This study suggests that independent of presynaptic dopamine depletion, the thalamus is a major neural substrate for LID and that a contracted thalamic shape at baseline is closely associated with an early development of LID.