bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surface Kinetic Temperatures and Nontronite Single Scattering Albedo Spectra From Mars Reconnaissance Orbiter CRISM Hyperspectral Imaging Data Over Glen Torridon, Gale Crater, Mars
Authors: He L. , Arvidson R. E. , OʼSullivan J. A. , Morris R. V. , Condus T. , Hughes M. N. , Powell K. E. 
Published: March 2022

AbstractThe Mars Reconnaissance Orbiter Compact Imaging Spectrometer for Mars (CRISM) covers the spectral range from 0.362 to 3.92 μm with a midafternoon local solar time data acquisition. For equatorial to midlatitudes, depending on the season and surface materials, wavelengths longer than ∼2.65 μm exhibit spectral radiances on sensor that include sunlight and thermal‐emission related terms. We developed a radiative transfer based neural network approach to model both solar and emitted terms in which surface kinetic temperatures are retrieved for each image pixel, together with single scattering albedo spectra, over the full CRISM wavelength range. We applied the method to along‐track oversampled scene FRT00021C92 over Glen Torridon within Gale Crater, where the Curiosity rover traversed and acquired remote sensing and in‐situ data. Synergistic analysis of orbital and rover‐based data, coupled with laboratory analyses of ferric‐rich smectites, provide a self‐consistent set of results for the presence of desiccated nontronite associated with Murray formation mudstones exposed as periodic bedrock ridges located just to the south of Vera Rubin ridge. The desiccated nature is consistent with Curiosity's CheMin data, which for Glen Torridon drill samples indicate an abundance of nontronite having a collapsed structure resulting from loss of interlayer H2O.
Using an Explainable Machine Learning Approach to Characterize Earth System Model Errors: Application of SHAP Analysis to Modeling Lightning Flash Occurrence
Authors: Silva Sam J. , Keller Christoph A. , Hardin Joseph 
Published: March 2022

AbstractComputational models of the Earth System are critical tools for modern scientific inquiry. Efforts toward evaluating and improving errors in representations of physical and chemical processes in these large computational systems are commonly stymied by highly nonlinear and complex error behavior. Recent work has shown that these errors can be effectively predicted using modern Artificial Intelligence (A.I.) techniques. In this work, we go beyond these previous studies to apply an explainable A.I. technique to not only predict model errors but also move toward understanding the underlying reasons for successful error prediction. We use XGBoost classification trees and SHapley Additive exPlanations analysis to explore the errors in the prediction of lightning occurrence in the NASA Goddard Earth Observing System model, a widely used Earth System Model. This explainable error prediction system can effectively predict the model error and indicates that the errors are strongly related to convective processes and the characteristics of the land surface.
A flexible, multifunctional, optoelectronic anticounterfeiting device from high-performance organic light-emitting paper
Authors: Pan Teng , Liu Shihao , Zhang Letian , Xie Wenfa , Yu Cunjiang 
Published: March 2022

AbstractAs a primary anticounterfeiting technology, most paper anticounterfeiting devices take advantage of photoresponsive behaviors of certain security materials or structures, thus featuring low-security threshold, which has been a critical global issue. To incorporate optoelectronic devices into existing anticounterfeiting technology suggests a feasible avenue to address this challenge. Here we report a high-performance organic light-emitting paper-based flexible anticounterfeiting (FAC) device with multiple stimuli-responsiveness, including light, electricity, and their combination. Without sacrificing the preexisted security information on the paper, we fabricate FAC device in a facile, low-cost yet high-fidelity fashion by integrating patterned electro-responsive and photo-responsive organic emitters onto paper substrates. By introducing optical microcavities, the FAC device shows considerable color shift upon different viewing angle and applied voltage, which is easily discernible by naked eyes. Notably, the FAC device is bendable, unclonable, and durable (a half-lifetime over 4000 hours at 100 cd m−2).
Evaluation of selective bone scan staging in prostate cancer – external validation of current strategies and decision-curve analysis
Authors: Hiwase Mrunal D. , Jay Alex , Bulamu Norma , Teh Johnathan , Paterson Felix , Kichenadasse Ganessan , Vincent Andrew D. , O’Callaghan Michael ,   South Australian Prostate Cancer Clinical Outcomes Collaborative (SA-PCCOC), Kopsaftis Tina , Walsh Scott 
Published: March 2022

Abstract
Background
Recommendations for staging newly diagnosed prostate cancer patients vary between guidelines and literature.

Methods
Our objective was to validate and compare prediction models selecting newly diagnosed prostate cancer patients for bone scan staging. To achieve this, we validated eleven models in a population-based cohort of 10,721 patients diagnosed with prostate cancer between 2005 and 2019. The primary outcome was net-benefit. This was assessed at different balances of conservatism and tolerance, represented by preference ratio and number-willing-to-test (NWT). Secondary outcomes included calibration slope, calibration-in-the-large (intercept), and discrimination measured by Area-under-the-receiver-operator-characteristics curve (AUC).

Results
For preference ratios less than 1:39 (NWT greater than 40), scanning everyone provided greater net-benefit than selective staging. For preference ratios 1:39 to 3:97 (NWT 33–40), the European Association of Urology (EAU) 2020 guideline recommendation was the best approach. For preference ratios 3:97–7:93 (NWT 14–33), scanning EAU high-risk patients only was preferable. For preference ratios 7:93–1:9 (NWT 10–13), scanning only Gnanapragasam Group 5 patients was best. All models had similar fair discrimination (AUCs 0.68–0.80), but most had poor calibration.

Conclusions
We identified three selective staging strategies that outperformed all other approaches but did so over different ranges of conservatism and tolerance. Scanning only EAU high-risk patients provided the greatest net-benefit over the greatest range of preference ratios and scenarios, but other options may be preferable depending upon the local healthcare system’s degree of conservatism and tolerance.
Autophagy-associated circRNA circATG7 facilitates autophagy and promotes pancreatic cancer progression
Authors: He Zhiwei , Cai Kun , Zeng Zhirui , Lei Shan , Cao Wenpeng , Li Xiaowu 
Published: March 2022

AbstractDysregulation of autophagy and circular RNAs (circRNAs) are involved in the pancreatic cancer (PC) progression. However, the regulatory network between circRNAs, autophagy, and PC progression remains unknown. Herein, we demonstrated that autophagy-associated circRNA circ-autophagy related 7 (circATG7) was elevated in PC tissues compared to adjacent tissues, and in PC cells treated with EBSS and hypoxia. circATG7 expression was positively associated with tumor diameter and lymph node invasion in patients with PC. circATG7 overexpression promoted PC cell proliferation, mobility, and autophagy in vitro, while circATG7 knockdown induced the opposite effects. ATG7 inhibition attenuated the effects of circATG7 on the biological functions of PC cells. CircATG7 is located in the cell cytoplasm and nucleus. Cytoplasmic circATG7 sponged miR-766-5p and decreased its expression, and increased the expression of ATG7, a target gene of miR-766-5p. Nuclear circATG7 acted as a scaffold to increase the interaction between the human antigen R protein and ATG7 mRNA and enhanced ATG mRNA stability. Furthermore, we demonstrated that circATG7 regulates PC cell proliferation and metastasis in vivo via ATG7-dependent autophagy. In conclusion, our results demonstrated that circATG7 accelerates PC progression via miR-766-5p/ATG7 and that HUR/ATG7 depends on autophagic flux. Thus, circATG7 may be a potential therapeutic target for PC.
A systematic review and meta-analysis of gene therapy with hematopoietic stem and progenitor cells for monogenic disorders
Authors: Tucci Francesca , Galimberti Stefania , Naldini Luigi , Valsecchi Maria Grazia , Aiuti Alessandro 
Published: March 2022

AbstractEx-vivo gene therapy (GT) with hematopoietic stem and progenitor cells (HSPCs) engineered with integrating vectors is a promising treatment for monogenic diseases, but lack of centralized databases is hampering an overall outcomes assessment. Here we aim to provide a comprehensive assessment of the short and long term safety of HSPC-GT from trials using different vector platforms. We review systematically the literature on HSPC-GT to describe survival, genotoxicity and engraftment of gene corrected cells. From 1995 to 2020, 55 trials for 14 diseases met inclusion criteria and 406 patients with primary immunodeficiencies (55.2%), metabolic diseases (17.0%), haemoglobinopathies (24.4%) and bone marrow failures (3.4%) were treated with gammaretroviral vector (γRV) (29.1%), self-inactivating γRV (2.2%) or lentiviral vectors (LV) (68.7%). The pooled overall incidence rate of death is 0.9 per 100 person-years of observation (PYO) (95% CI = 0.37–2.17). There are 21 genotoxic events out of 1504.02 PYO, which occurred in γRV trials (0.99 events per 100 PYO, 95% CI = 0.18–5.43) for primary immunodeficiencies. Pooled rate of engraftment is 86.7% (95% CI = 67.1–95.5%) for γRV and 98.7% (95% CI = 94.5–99.7%) for LV HSPC-GT (p = 0.005). Our analyses show stable reconstitution of haematopoiesis in most recipients with superior engraftment and safer profile in patients receiving LV-transduced HSPCs.
The arginine methyltransferase PRMT7 promotes extravasation of monocytes resulting in tissue injury in COPD
Authors: Günes Günsel Gizem , Conlon Thomas M. , Jeridi Aicha , Kim Rinho , Ertüz Zeynep , Lang Niklas J. , Ansari Meshal , Novikova Mariia , Jiang Dongsheng , Strunz Maximilian , Gaianova Mariia , Hollauer Christine , Gabriel Christina , Angelidis Ilias , Doll Sebastian , Pestoni Jeanine C. , Edelmann Stephanie L. , Kohlhepp Marlene Sophia , Guillot Adrien , Bassler Kevin , Van Eeckhoutte Hannelore P. , Kayalar Özgecan , Konyalilar Nur , Kanashova Tamara , Rodius Sophie , Ballester-López Carolina , Genes Robles Carlos M. , Smirnova Natalia , Rehberg Markus , Agarwal Charu , Krikki Ioanna , Piavaux Benoit , Verleden Stijn E. , Vanaudenaerde Bart , Königshoff Melanie , Dittmar Gunnar , Bracke Ken R. , Schultze Joachim L. , Watz Henrik , Eickelberg Oliver , Stoeger Tobias , Burgstaller Gerald , Tacke Frank , Heissmeyer Vigo , Rinkevich Yuval , Bayram Hasan , Schiller Herbert B. , Conrad Marcus , Schneider Robert , Yildirim Ali Önder 
Published: March 2022

AbstractExtravasation of monocytes into tissue and to the site of injury is a fundamental immunological process, which requires rapid responses via post translational modifications (PTM) of proteins. Protein arginine methyltransferase 7 (PRMT7) is an epigenetic factor that has the capacity to mono-methylate histones on arginine residues. Here we show that in chronic obstructive pulmonary disease (COPD) patients, PRMT7 expression is elevated in the lung tissue and localized to the macrophages. In mouse models of COPD, lung fibrosis and skin injury, reduced expression of PRMT7 associates with decreased recruitment of monocytes to the site of injury and hence less severe symptoms. Mechanistically, activation of NF-κB/RelA in monocytes induces PRMT7 transcription and consequential mono-methylation of histones at the regulatory elements of RAP1A, which leads to increased transcription of this gene that is responsible for adhesion and migration of monocytes. Persistent monocyte-derived macrophage accumulation leads to ALOX5 over-expression and accumulation of its metabolite LTB4, which triggers expression of ACSL4 a ferroptosis promoting gene in lung epithelial cells. Conclusively, inhibition of arginine mono-methylation might offer targeted intervention in monocyte-driven inflammatory conditions that lead to extensive tissue damage if left untreated.
Apoplastic class III peroxidases PRX62 and PRX69 promote Arabidopsis root hair growth at low temperature
Authors: Pacheco Javier Martínez , Ranocha Philippe , Kasulin Luciana , Fusari Corina M. , Servi Lucas , Aptekmann Ariel. A. , Gabarain Victoria Berdion , Peralta Juan Manuel , Borassi Cecilia , Marzol Eliana , Rodríguez-Garcia Diana Rosa , del Carmen Rondón Guerrero Yossmayer , Sardoy Mariana Carignani , Ferrero Lucía , Botto Javier F. , Meneses Claudio , Ariel Federico , Nadra Alejandro D. , Petrillo Ezequiel , Dunand Christophe , Estevez José M. 
Published: March 2022

AbstractRoot Hairs (RHs) growth is influenced by endogenous and by external environmental signals that coordinately regulate its final cell size. We have recently determined that RH growth was unexpectedly boosted whenArabidopsis thalianaseedlings are cultivated at low temperatures. It was proposed that RH growth plasticity in response to low temperature was linked to a reduced nutrient availability in the media. Here, we explore the molecular basis of this RH growth response by using a Genome Wide Association Study (GWAS) approach usingArabidopsis thaliananatural accessions. We identify the poorly characterized PEROXIDASE 62 (PRX62) and a related protein PRX69 as key proteins under moderate low temperature stress. Strikingly, a cell wall protein extensin (EXT) reporter reveals the effect of peroxidase activity on EXT cell wall association at 10 °C in the RH apical zone. Collectively, our results indicate that PRX62, and to a lesser extent PRX69, are key apoplastic PRXs that modulate ROS-homeostasis and cell wall EXT-insolubilization linked to RH elongation at low temperature.
Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data
Authors: Liu Yunxi , Kearney Joshua , Mahmoud Medhat , Kille Bryce , Sedlazeck Fritz J. , Treangen Todd J. 
Published: March 2022

AbstractInfectious disease monitoring on Oxford Nanopore Technologies (ONT) platforms offers rapid turnaround times and low cost. Tracking low frequency intra-host variants provides important insights with respect to elucidating within-host viral population dynamics and transmission. However, given the higher error rate of ONT, accurate identification of intra-host variants with low allele frequencies remains an open challenge with no viable computational solutions available. In response to this need, we present Variabel, a novel approach and first method designed for rescuing low frequency intra-host variants from ONT data alone. We evaluate Variabel on both synthetic data (SARS-CoV-2) and patient derived datasets (Ebola virus, norovirus, SARS-CoV-2); our results show that Variabel can accurately identify low frequency variants below 0.5 allele frequency, outperforming existing state-of-the-art ONT variant callers for this task. Variabel is open-source and available for download at: www.gitlab.com/treangenlab/variabel.
Mucospheres produced by a mixotrophic protist impact ocean carbon cycling
Authors: Larsson Michaela E. , Bramucci Anna R. , Collins Sinead , Hallegraeff Gustaaf , Kahlke Tim , Raina Jean-Baptiste , Seymour Justin R. , Doblin Martina A. 
Published: March 2022

AbstractMixotrophic protists (unicellular eukaryotes) that engage in both phototrophy (photosynthesis) and phago-heterotrophy (engulfment of particles)—are predicted to contribute substantially to energy fluxes and marine biogeochemical cycles. However, their impact remains largely unquantified. Here we describe the sophisticated foraging strategy of a widespread mixotrophic dinoflagellate, involving the production of carbon-rich ‘mucospheres’ that attract, capture, and immobilise microbial prey facilitating their consumption. We provide a detailed characterisation of this previously undescribed behaviour and reveal that it represents an overlooked, yet quantitatively significant mechanism for oceanic carbon fluxes. Following feeding, the mucospheres laden with surplus prey are discarded and sink, contributing an estimated 0.17–1.24 mg m−2 d−1 of particulate organic carbon, or 0.02–0.15 Gt to the biological pump annually, which represents 0.1–0.7% of the estimated total export from the euphotic zone. These findings demonstrate how the complex foraging behaviour of a single species of mixotrophic protist can disproportionally contribute to the vertical flux of carbon in the ocean.
Benchmarking of SpCas9 variants enables deeper base editor screens of BRCA1 and BCL2
Authors: Sangree Annabel K. , Griffith Audrey L. , Szegletes Zsofia M. , Roy Priyanka , DeWeirdt Peter C. , Hegde Mudra , McGee Abby V. , Hanna Ruth E. , Doench John G. 
Published: March 2022

AbstractNumerous rationally-designed and directed-evolution variants of SpCas9 have been reported to expand the utility of CRISPR technology. Here, we assess the activity and specificity of WT-Cas9 and 10 SpCas9 variants by benchmarking their PAM preferences, on-target activity, and off-target susceptibility in cell culture assays with thousands of guides targeting endogenous genes. To enhance the coverage and thus utility of base editing screens, we demonstrate that the SpCas9-NG and SpG variants are compatible with both A > G and C > T base editors, more than tripling the number of guides and assayable residues. We demonstrate the performance of these technologies by screening for loss-of-function mutations in BRCA1 and Venetoclax-resistant mutations in BCL2, identifying both known and new mutations that alter function. We anticipate that the tools and methodologies described here will facilitate the investigation of genetic variants at a finer and deeper resolution for any locus of interest.
Quantifying and comparing radiation damage in the Protein Data Bank
Authors: Shelley Kathryn L. , Garman Elspeth F. 
Published: March 2022

AbstractRadiation damage remains one of the major bottlenecks to accurate structure solution in protein crystallography. It can induce structural and chemical changes in protein crystals, and is hence an important consideration when assessing the quality and biological veracity of crystal structures in repositories like the Protein Data Bank (PDB). However, detection of radiation damage artefacts has traditionally proved very challenging. To address this, here we introduce the Bnet metric. Bnet summarises in a single value the extent of damage suffered by a crystal structure by comparing the B-factor values of damage-prone and non-damage-prone atoms in a similar local environment. After validating that Bnet successfully detects damage in 23 different crystal structures previously characterised as damaged, we calculate Bnet values for 93,978 PDB crystal structures. Our metric highlights a range of damage features, many of which would remain unidentified by the other summary statistics typically calculated for PDB structures.
Universality, criticality and complexity of information propagation in social media
Authors: Notarmuzi Daniele , Castellano Claudio , Flammini Alessandro , Mazzilli Dario , Radicchi Filippo 
Published: March 2022

AbstractStatistical laws of information avalanches in social media appear, at least according to existing empirical studies, not robust across systems. As a consequence, radically different processes may represent plausible driving mechanisms for information propagation. Here, we analyze almost one billion time-stamped events collected from several online platforms – including Telegram, Twitter and Weibo – over observation windows longer than ten years, and show that the propagation of information in social media is a universal and critical process. Universality arises from the observation of identical macroscopic patterns across platforms, irrespective of the details of the specific system at hand. Critical behavior is deduced from the power-law distributions, and corresponding hyperscaling relations, characterizing size and duration of avalanches of information. Statistical testing on our data indicates that a mixture of simple and complex contagion characterizes the propagation of information in social media. Data suggest that the complexity of the process is correlated with the semantic content of the information that is propagated.
Norway spruce postglacial recolonization of Fennoscandia
Authors: Nota Kevin , Klaminder Jonatan , Milesi Pascal , Bindler Richard , Nobile Alessandro , van Steijn Tamara , Bertilsson Stefan , Svensson Brita , Hirota Shun K. , Matsuo Ayumi , Gunnarsson Urban , Seppä Heikki , Väliranta Minna M. , Wohlfarth Barbara , Suyama Yoshihisa , Parducci Laura 
Published: March 2022

AbstractContrasting theories exist regarding how Norway spruce (Picea abies) recolonized Fennoscandia after the last glaciation and both early Holocene establishments from western microrefugia and late Holocene colonization from the east have been postulated. Here, we show that Norway spruce was present in southern Fennoscandia as early as 14.7 ± 0.1 cal. kyr BP and that the millennia-old clonal spruce trees present today in central Sweden likely arrived with an early Holocene migration from the east. Our findings are based on ancient sedimentary DNA from multiple European sites (N = 15) combined with nuclear and mitochondrial DNA analysis of ancient clonal (N = 135) and contemporary spruce forest trees (N = 129) from central Sweden. Our other findings imply that Norway spruce was present shortly after deglaciation at the margins of the Scandinavian Ice Sheet, and support previously disputed finds of pollen in southern Sweden claiming spruce establishment during the Lateglacial.
Oxidative metabolisms catalyzed Earth’s oxygenation
Authors: Shang Haitao , Rothman Daniel H. , Fournier Gregory P. 
Published: March 2022

AbstractThe burial of organic carbon, which prevents its remineralization via oxygen-consuming processes, is considered one of the causes of Earth’s oxygenation. Yet, higher levels of oxygen are thought to inhibit burial. Here we propose a resolution of this conundrum, wherein Earth’s initial oxygenation is favored by oxidative metabolisms generating partially oxidized organic matter (POOM), increasing burial via interaction with minerals in sediments. First, we introduce the POOM hypothesis via a mathematical argument. Second, we reconstruct the evolutionary history of one key enzyme family, flavin-dependent Baeyer–Villiger monooxygenases, that generates POOM, and show the temporal consistency of its diversification with the Proterozoic and Phanerozoic atmospheric oxygenation. Finally, we propose that the expansion of oxidative metabolisms instigated a positive feedback, which was amplified by the chemical changes to minerals on Earth’s surface. Collectively, these results suggest that Earth’s oxygenation is an autocatalytic transition induced by a combination of biological innovations and geological changes.