bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate localization microscopy by intrinsic aberration calibration
Authors: Copeland Craig R. , McGray Craig D. , Ilic B. Robert , Geist Jon , Stavis Samuel M. 
Published: June 2021

AbstractA standard paradigm of localization microscopy involves extension from two to three dimensions by engineering information into emitter images, and approximation of errors resulting from the field dependence of optical aberrations. We invert this standard paradigm, introducing the concept of fully exploiting the latent information of intrinsic aberrations by comprehensive calibration of an ordinary microscope, enabling accurate localization of single emitters in three dimensions throughout an ultrawide and deep field. To complete the extraction of spatial information from microscale bodies ranging from imaging substrates to microsystem technologies, we introduce a synergistic concept of the rigid transformation of the positions of multiple emitters in three dimensions, improving precision, testing accuracy, and yielding measurements in six degrees of freedom. Our study illuminates the challenge of aberration effects in localization microscopy, redefines the challenge as an opportunity for accurate, precise, and complete localization, and elucidates the performance and reliability of a complex microelectromechanical system.
Allosteric modulation of ghrelin receptor signaling by lipids
Authors: Damian Marjorie , Louet Maxime , Gomes Antoniel Augusto Severo , M’Kadmi Céline , Denoyelle Séverine , Cantel Sonia , Mary Sophie , Bisch Paulo M. , Fehrentz Jean-Alain , Catoire Laurent J. , Floquet Nicolas , Banères Jean-Louis 
Published: June 2021

AbstractThe membrane is an integral component of the G protein-coupled receptor signaling machinery. Here we demonstrate that lipids regulate the signaling efficacy and selectivity of the ghrelin receptor GHSR through specific interactions and bulk effects. We find that PIP2 shifts the conformational equilibrium of GHSR away from its inactive state, favoring basal and agonist-induced G protein activation. This occurs because of a preferential binding of PIP2 to specific intracellular sites in the receptor active state. Another lipid, GM3, also binds GHSR and favors G protein activation, but mostly in a ghrelin-dependent manner. Finally, we find that not only selective interactions but also the thickness of the bilayer reshapes the conformational repertoire of GHSR, with direct consequences on G protein selectivity. Taken together, this data illuminates the multifaceted role of the membrane components as allosteric modulators of how ghrelin signal could be propagated.
Order-by-disorder from bond-dependent exchange and intensity signature of nodal quasiparticles in a honeycomb cobaltate
Authors: Elliot M. , McClarty P. A. , Prabhakaran D. , Johnson R. D. , Walker H. C. , Manuel P. , Coldea R. 
Published: June 2021

AbstractRecent theoretical proposals have argued that cobaltates with edge-sharing octahedral coordination can have significant bond-dependent exchange couplings thus offering a platform in 3d ions for such physics beyond the much-explored realisations in 4d and 5d materials. Here we present high-resolution inelastic neutron scattering data within the magnetically ordered phase of the stacked honeycomb magnet CoTiO3 revealing the presence of a finite energy gap and demonstrate that this implies the presence of bond-dependent anisotropic couplings. We also show through an extensive theoretical analysis that the gap further implies the existence of a quantum order-by-disorder mechanism that, in this material, crucially involves virtual crystal field fluctuations. Our data also provide an experimental observation of a universal winding of the scattering intensity in angular scans around linear band-touching points for both magnons and dispersive spin-orbit excitons, which is directly related to the non-trivial topology of the quasiparticle wavefunction in momentum space near nodal points.
PGRL2 triggers degradation of PGR5 in the absence of PGRL1
Authors: Rühle Thilo , Dann Marcel , Reiter Bennet , Schünemann Danja , Naranjo Belen , Penzler Jan-Ferdinand , Kleine Tatjana , Leister Dario 
Published: June 2021

AbstractIn plants, inactivation of either of the thylakoid proteins PGR5 and PGRL1 impairs cyclic electron flow (CEF) around photosystem I. Because PGR5 is unstable in the absence of the redox-active PGRL1, but not vice versa, PGRL1 is thought to be essential for CEF. However, we show here that inactivation of PGRL2, a distant homolog of PGRL1, relieves the need for PGRL1 itself. Conversely, high levels of PGRL2 destabilize PGR5 even when PGRL1 is present. In the absence of both PGRL1 and PGRL2, PGR5 alters thylakoid electron flow and impairs plant growth. Consequently, PGR5 can operate in CEF on its own, and is the target of the CEF inhibitor antimycin A, but its activity must be modulated by PGRL1. We conclude that PGRL1 channels PGR5 activity, and that PGRL2 triggers the degradation of PGR5 when the latter cannot productively interact with PGRL1.
Bioactivity descriptors for uncharacterized chemical compounds
Authors: Bertoni Martino , Duran-Frigola Miquel , Badia-i-Mompel Pau , Pauls Eduardo , Orozco-Ruiz Modesto , Guitart-Pla Oriol , Alcalde Víctor , Diaz Víctor M. , Berenguer-Llergo Antoni , Brun-Heath Isabelle , Villegas Núria , de Herreros Antonio García , Aloy Patrick 
Published: June 2021

AbstractChemical descriptors encode the physicochemical and structural properties of small molecules, and they are at the core of chemoinformatics. The broad release of bioactivity data has prompted enriched representations of compounds, reaching beyond chemical structures and capturing their known biological properties. Unfortunately, bioactivity descriptors are not available for most small molecules, which limits their applicability to a few thousand well characterized compounds. Here we present a collection of deep neural networks able to infer bioactivity signatures for any compound of interest, even when little or no experimental information is available for them. Our signaturizers relate to bioactivities of 25 different types (including target profiles, cellular response and clinical outcomes) and can be used as drop-in replacements for chemical descriptors in day-to-day chemoinformatics tasks. Indeed, we illustrate how inferred bioactivity signatures are useful to navigate the chemical space in a biologically relevant manner, unveiling higher-order organization in natural product collections, and to enrich mostly uncharacterized chemical libraries for activity against the drug-orphan target Snail1. Moreover, we implement a battery of signature-activity relationship (SigAR) models and show a substantial improvement in performance, with respect to chemistry-based classifiers, across a series of biophysics and physiology activity prediction benchmarks.
Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells
Authors: Cannoodt Robrecht , Saelens Wouter , Deconinck Louise , Saeys Yvan 
Published: June 2021

AbstractWe present dyngen, a multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. dyngen is more flexible than current single-cell simulation engines, and allows better method development and benchmarking, thereby stimulating development and testing of computational methods. We demonstrate its potential for spearheading computational methods on three applications: aligning cell developmental trajectories, cell-specific regulatory network inference and estimation of RNA velocity.
Unsplit superconducting and time reversal symmetry breaking transitions in Sr2RuO4 under hydrostatic pressure and disorder
Authors: Grinenko Vadim , Das Debarchan , Gupta Ritu , Zinkl Bastian , Kikugawa Naoki , Maeno Yoshiteru , Hicks Clifford W. , Klauss Hans-Henning , Sigrist Manfred , Khasanov Rustem 
Published: June 2021

AbstractThere is considerable evidence that the superconducting state of Sr2RuO4 breaks time reversal symmetry. In the experiments showing time reversal symmetry breaking, its onset temperature, TTRSB, is generally found to match the critical temperature, Tc, within resolution. In combination with evidence for even parity, this result has led to consideration of a dxz ± idyz order parameter. The degeneracy of the two components of this order parameter is protected by symmetry, yielding TTRSB = Tc, but it has a hard-to-explain horizontal line node at kz = 0. Therefore, s ± id and d ± ig order parameters are also under consideration. These avoid the horizontal line node, but require tuning to obtain TTRSB ≈ Tc. To obtain evidence distinguishing these two possible scenarios (of symmetry-protected versus accidental degeneracy), we employ zero-field muon spin rotation/relaxation to study pure Sr2RuO4 under hydrostatic pressure, and Sr1.98La0.02RuO4 at zero pressure. Both hydrostatic pressure and La substitution alter Tc without lifting the tetragonal lattice symmetry, so if the degeneracy is symmetry-protected, TTRSB should track changes in Tc, while if it is accidental, these transition temperatures should generally separate. We observe TTRSB to track Tc, supporting the hypothesis of dxz ± idyz order.
The origin of the high electrochemical activity of pseudo-amorphous iridium oxides
Authors: Elmaalouf Marine , Odziomek Mateusz , Duran Silvia , Gayrard Maxime , Bahri Mounib , Tard Cédric , Zitolo Andrea , Lassalle-Kaiser Benedikt , Piquemal Jean-Yves , Ersen Ovidiu , Boissière Cédric , Sanchez Clément , Giraud Marion , Faustini Marco , Peron Jennifer 
Published: June 2021

AbstractCombining high activity and stability, iridium oxide remains the gold standard material for the oxygen evolution reaction in acidic medium for green hydrogen production. The reasons for the higher electroactivity of amorphous iridium oxides compared to their crystalline counterpart is still the matter of an intense debate in the literature and, a comprehensive understanding is needed to optimize its use and allow for the development of water electrolysis. By producing iridium-based mixed oxides using aerosol, we are able to decouple the electronic processes from the structural transformation, i.e. Ir oxidation from IrO2 crystallization, occurring upon calcination. Full characterization using in situ and ex situ X-ray absorption spectroscopy, X-ray photoelectron spectroscopy, X-ray diffraction and transmission electron microscopy allows to unambiguously attribute their high electrochemical activity to structural features and rules out the iridium oxidation state as a critical parameter. This study indicates that short-range ordering, corresponding to sub-2nm crystal size for our samples, drives the activity independently of the initial oxidation state and composition of the calcined iridium oxides.
Frontopolar theta oscillations link metacognition with prospective decision making
Authors: Soutschek Alexander , Moisa Marius , Ruff Christian C. , Tobler Philippe N. 
Published: June 2021

AbstractProspective decision making considers the future consequences of actions and therefore requires agents to represent their present subjective preferences reliably across time. Here, we test the link of frontopolar theta oscillations to both metacognitive ability and prospective choice behavior. We target these oscillations with transcranial alternating current stimulation while participants make decisions between smaller-sooner and larger-later monetary rewards and rate their choice confidence after each decision. Stimulation designed to enhance frontopolar theta oscillations increases metacognitive accuracy in reports of subjective uncertainty in intertemporal decisions. Moreover, the stimulation also enhances the willingness of participants to restrict their future access to short-term gratification by strengthening the awareness of potential preference reversals. Our results suggest a mechanistic link between frontopolar theta oscillations and metacognitive knowledge about the stability of subjective value representations, providing a potential explanation for why frontopolar cortex also shields prospective decision making against future temptation.
Approximate Bayesian Computation of radiocarbon and paleoenvironmental record shows population resilience on Rapa Nui (Easter Island)
Authors: DiNapoli Robert J. , Crema Enrico R. , Lipo Carl P. , Rieth Timothy M. , Hunt Terry L. 
Published: June 2021

AbstractExamining how past human populations responded to environmental and climatic changes is a central focus of the historical sciences. The use of summed probability distributions (SPD) of radiocarbon dates as a proxy for estimating relative population sizes provides a widely applicable method in this research area. Paleodemographic reconstructions and modeling with SPDs, however, are stymied by a lack of accepted methods for model fitting, tools for assessing the demographic impact of environmental or climatic variables, and a means for formal multi-model comparison. These deficiencies severely limit our ability to reliably resolve crucial questions of past human-environment interactions. We propose a solution using Approximate Bayesian Computation (ABC) to fit complex demographic models to observed SPDs. Using a case study from Rapa Nui (Easter Island), a location that has long been the focus of debate regarding the impact of environmental and climatic changes on its human population, we find that past populations were resilient to environmental and climatic challenges. Our findings support a growing body of evidence showing stable and sustainable communities on the island. The ABC framework offers a novel approach for exploring regions and time periods where questions of climate-induced demographic and cultural change remain unresolved.
Chronic obstructive pulmonary disease as a risk factor in primary care: a Canadian retrospective cohort study
Authors: Cave Andrew , Pham Anh , Lindeman Cliff , Soos Boglarka , Williamson Tyler , Drummond Neil 
Published: June 2021

AbstractChronic obstructive pulmonary disease (COPD) is a complex disease that is predicted to be the third most common cause of death by 2030. In Canada, the care and management of chronic conditions is largely provided by primary care providers. Although there is emerging research and initiatives that describe the prevalence of COPD in Canadian primary care settings, to our knowledge, there have been no efforts to use a large pan-Canadian database to analyze COPD as a risk factor for other common chronic conditions managed in primary care. We report the risk of developing comorbidities after the onset of COPD, that is, the extent to which COPD is a risk factor for developing common chronic conditions (heart failure, depression, anxiety, coronary artery disease, diabetes, anemia, hypertension, ischemic heart disease, underweight, and osteoporosis). After adjusting for age, sex, urban vs rural residence, and smoking status, the relative risks for patients with COPD at baseline were significantly higher for subsequent incidence of anemia, anxiety, diabetes, depression, heart failure, ischemic heart disease, lung cancer, osteoporosis, sleep apnea, underweight, and hypertension than patients without COPD. Using a cut-point of a 200% increase in relative risk as indicative of particular clinical relevance, COPD has a statistically and clinically significant association with developing lung cancer, becoming underweight, and developing heart failure.
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome
Authors: Nayfach Stephen , Páez-Espino David , Call Lee , Low Soo Jen , Sberro Hila , Ivanova Natalia N. , Proal Amy D. , Fischbach Michael A. , Bhatt Ami S. , Hugenholtz Philip , Kyrpides Nikos C. 
Published: June 2021

AbstractBacteriophages have important roles in the ecology of the human gut microbiome but are under-represented in reference databases. To address this problem, we assembled the Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available human stool metagenomes. Over 75% of genomes represent double-stranded DNA phages that infect members of the Bacteroidia and Clostridia classes. Based on sequence clustering we identified 54,118 candidate viral species, 92% of which were not found in existing databases. The Metagenomic Gut Virus catalogue improves detection of viruses in stool metagenomes and accounts for nearly 40% of CRISPR spacers found in human gut Bacteria and Archaea. We also produced a catalogue of 459,375 viral protein clusters to explore the functional potential of the gut virome. This revealed tens of thousands of diversity-generating retroelements, which use error-prone reverse transcription to mutate target genes and may be involved in the molecular arms race between phages and their bacterial hosts.
Dataset and validation of the approaches to study skills inventory for students
Authors: Dedos Skarlatos G. , Fouskakis Dimitris 
Published: June 2021

AbstractThere exists a vast amount of research on how students, in higher education, approach their studying and learning. Such research resulted in a multitude of questionnaires and tools to capture the way students perform in higher education institutions. One of these tools is the Approaches to Study Skills Inventory for Students (ASSIST) that was developed in the ’80 s and ’90 s. This inventory broadly classifies students, as approaching their study, in a deep, a strategic and/or a surface manner. Although it has gone through rigorous validation in many studies, there exist no publicly available dataset of the results of these studies and so the raw datasets cannot be re-used or integrated with other similar datasets. Here, we report and make publicly available the raw data of an 8-year longitudinal survey using this inventory in a cohort study of 1181 students from a department of a higher education institution. We validated our dataset using reliability analyses that confirmed, and compared well, with the results of previous studies.
Radiocarbon dating of lead white: novel application in the study of polychrome sculpture
Authors: Sá Sara , Hendriks Laura , Pombo Cardoso Isabel , Hajdas Irka 
Published: June 2021

AbstractRecently, radiocarbon dating underwent considerable technological advances allowing unprecedented sample size downscaling. These achievements introduced novel opportunities in dating cultural heritage objects. Within this pioneering research, the possibility of a direct 14C dating of lead white pigment and organic binder in paint samples was investigated on polychrome sculptures, a foremost artistic expression in human history. The polychromy, an indivisible part of polychrome sculpture, holds a key role in the interpretation and understanding of these artworks. Unlike in other painted artworks, the study of polychromies is repeatedly hampered by repaints and degradation. The omnipresence of lead white within the original polychromy was thus pursued as dating proxy. Thermal decomposition allowed bypassing geologic carbonate interferences caused by the object's support material, while an added solvent extraction successfully removed conservation products. This radiocarbon dating survey of the polychromy from 16 Portuguese medieval limestone sculptures confirmed that some were produced within the proposed chronologies while others were revised. Within this multidisciplinary study, the potential of radiocarbon dating as a complementary source of information about these complex paint systems guiding their interpretation is demonstrated. The challenges of this innovative approach are highlighted and improvements on sampling and sample preparation are discussed.
The best temperature range to acquire reliable thermal infrared spectra from orbit
Authors: Nestola F. , Ferrari S. , Pamato M. G. , Redhammer G. , Helbert J. , Alvaro M. , Domeneghetti M. C. 
Published: June 2021

AbstractSolar System bodies undergo to daily and periodical variations of temperature that mainly depend on their closeness to the Sun. It is known that mineral expansion and contraction due to such variations modify the thermal infrared spectra acquired on solid surfaces. Therefore, it becomes crucial to know the best temperature range at which the acquisition itself should be carried out to get reliable information on the mineralogy of such bodies. Here we provide the thermal expansion of olivine between 20 and 298 K determined by X-ray diffraction. Our data reveal the non-linear behaviour of silicates that undergo to low temperatures, where volume variations appear positively correlated with temperatures. Subtle bond-length variations occurring at low temperatures are then expected to minimally affect vibrational absorption positions. We suggest that thermal infrared spectra of those Solar-System surfaces that are not exceeding 300 K provide reliable information about not only the silicate mineral identification but also on their chemical composition, regardless of the instantaneous temperature.
The mineralocorticoid receptor leads to increased expression of EGFR and T-type calcium channels that support HL-1 cell hypertrophy
Authors: Stroedecke Katharina , Meinel Sandra , Markwardt Fritz , Kloeckner Udo , Straetz Nicole , Quarch Katja , Schreier Barbara , Kopf Michael , Gekle Michael , Grossmann Claudia 
Published: June 2021

AbstractThe EGF receptor (EGFR) has been extensively studied in tumor biology and recently a role in cardiovascular pathophysiology was suggested. The mineralocorticoid receptor (MR) is an important effector of the renin–angiotensin–aldosterone-system and elicits pathophysiological effects in the cardiovascular system; however, the underlying molecular mechanisms are unclear. Our aim was to investigate the importance of EGFR for MR-mediated cardiovascular pathophysiology because MR is known to induce EGFR expression. We identified a SNP within the EGFR promoter that modulates MR-induced EGFR expression. In RNA-sequencing and qPCR experiments in heart tissue of EGFR KO and WT mice, changes in EGFR abundance led to differential expression of cardiac ion channels, especially of the T-type calcium channel CACNA1H. Accordingly, CACNA1H expression was increased in WT mice after in vivo MR activation by aldosterone but not in respective EGFR KO mice. Aldosterone- and EGF-responsiveness of CACNA1H expression was confirmed in HL-1 cells by Western blot and by measuring peak current density of T-type calcium channels. Aldosterone-induced CACNA1H protein expression could be abrogated by the EGFR inhibitor AG1478. Furthermore, inhibition of T-type calcium channels with mibefradil or ML218 reduced diameter, volume and BNP levels in HL-1 cells. In conclusion the MR regulates EGFR and CACNA1H expression, which has an effect on HL-1 cell diameter, and the extent of this regulation seems to depend on the SNP-216 (G/T) genotype. This suggests that the EGFR may be an intermediate for MR-mediated cardiovascular changes and that SNP analysis can help identify subgroups of patients that will benefit most from MR antagonists.