bluuebunny/crossref_metadata_2025_split huggingface dataset:
IBSE-Type Astronomy Projects Using Real Data
Authors: Lewis Fraser 
Published: December 2021

AbstractI present three examples of IBSE (Inquiry-Based Science Education) type activities for students and teachers using data and resources from the Faulkes Telescope Project and the National Schools’ Observatory. Both projects have recently celebrated their 15th anniversary and both provide free access via the internet to 2-metre robotic telescopes to educational users throughout the World. Each activity contains supporting material and sample datasets in several aspects of astronomy as well as instructions on how to analyse data. These activities are designed to be ‘teacher-free’, extended projects for students.They include the study of open clusters via astronomical images and population studies of exoplanets. I also present a Citizen Science project using data from Type Ia supernovae as discovered by the Gaia Alerts consortium. These data allow citizen scientists to develop their own Hubble Plot and begin to understand the link between Type Ia supernovae and the age of the Universe.
SonoUno: a user-centred approach to sonification
Authors: Casado Johanna , De La Vega Gonzalo , Díaz-Merced Wanda , Gandhi Poshak , García Beatriz 
Published: December 2021

AbstractThough there are a variety of astronomy sonification software packages, none of them shown high granularity evidence of having been designed with a user-centric focus. SonoUno is a sonification package created taking into account the user from the beginning, and incorporates end user contact feedback for continuous improvements to the software. In this contribution, SonoUno user cases are presented with the soft corresponding updates, as well as the first description of a recent web page development.
Effects of maternal exposure to acute stress on birth outcomes: a quasi-experiment study
Authors: Ahmed Asma , King Suzanne , Elgbeili Guillaume , Laplante David P. , Yang Seungmi 
Published: December 2021

AbstractNumerous studies have shown associations between maternal stress and poor birth outcomes, but evidence is unclear for causal inference. Natural disasters provide an opportunity to study effects of quasi-randomized hardship with an accurate measure of onset and duration. In a population-based quasi-experimental study, we examined the effect of maternal exposure to the January 1998 Québec ice storm on birth outcomes by comparing pregnant mothers who lived in an area hard hit by the ice storm with those in two unaffected regions. In a total of 147,349 singleton births between 1995 and 2001, we used a difference-in-differences method to estimate the effects of the ice storm on gestational age at delivery (GA), preterm birth (PTB), weight-for-gestational-age z-scores (BWZ), large for gestational age (LGA), and small for gestational age (SGA). After adjusting for maternal and sociodemographic characteristics, there were no differences between the exposed and the unexposed mothers for birth outcomes. The estimated differences (exposed vs. unexposed) were 0.01 SDs (95% CI: −0.02, 0.05) for BWZ; 0.10% point (95% CI: −0.95%, 1.16%) for SGA; 0.25% point (95% CI: −0.78%, 1.28%) for LGA; −0.01 week (95% CI: −0.07, 0.05) for GA; and 0.16% point (95% CI: −0.66%, 0.97%) for PTB. Neither trimester-specific nor dose–response associations were observed. Overall, exposure to the 1998 Québec ice storm as a proxy for acute maternal stress in pregnancy was not associated with poor birth outcomes. Our results suggest that acute maternal hardship may not have a substantial effect on adverse birth outcomes.
Post‐Seismic to Co‐Seismic Moment Ratios for the 2016 Moderate Earthquakes Along Chaman Fault
Authors: Furuya Masato , Matsumoto Fumiko 
Published: December 2021

AbstractPostseismic‐to‐coseismic moment ratios (PCMR) for strong (M > 6) earthquakes typically do not exceed ∼0.3, but there have been limited estimates for moderate‐to‐small earthquakes. Three M5‐class earthquakes and one M4.7 earthquake occurred along the Chaman fault, Pakistan, on May 13 and July 10, 2016. Using Sentinel‐1A InSAR time‐series from October 2014 to August 2018, we estimate spatial‐temporal evolution of the co‐ and post‐seismic fault slip and its velocity. Because of the long‐lasting (>1 year) afterslip, the estimated PCMRs of the M5‐class events and M4.7 event were 0.7 ± 0.2 and 8.3 ± 2.2, respectively, which are both larger than those of M > 6 earthquakes but consistent with previous events that occurred on the Chaman Fault System. Unlike in case of large earthquakes, geodetic inversions are not able to resolve spatial relationships between coseismic slip and afterslip. In case of a non‐complementary slip distribution, one explanation might be heterogeneity of friction properties on the fault surface, while other interpretations are possible.
Did Modern Precipitation Drivers Influence Centennial Trends in the Highlands of the Atacama Desert During the Most Recent Millennium?
Authors: Jara Ignacio A. , Maldonado Antonio , de Porras María Eugenia 
Published: December 2021

AbstractAlthough present‐day precipitation variability in the southern Altiplano and adjacent Andean margins (15–25°S) is well understood, past drivers and mechanisms remain little‐explored. We analyzed the pollen assemblages of 31 fossil rodent middens to reconstruct precipitation change during the most recent millennium in the highlands of the Atacama Desert (22°S), on the western foothills of the Altiplano. Variations in low and high elevation pollen types reveal reduced (increased) precipitation between 930 and 550 BP (510 and 440 BP) (BP = before present; taken as Common Era 1950). Variable pollen assemblages prevailed from 390 to 90 BP, followed by a drying trend that persists until present times. Similarities with proxy records from the Altiplano, the tropical Andes and the equatorial Pacific suggest that centennial‐scale wet/dry phases in the Atacama highlands were associated with changes in the strength of the South American monsoon system, most likely influenced by changes akin to modern El Niño Southern Oscillation variability.
Comments on “Stochastic TEC Structure Characterization” by Charles Rino, Yu Morton, Brian Breitsch, and Charles Carrano, Journal of Geophysical Research: Space Physics, 124, https://doi.org/10.1029/2019JA026958
Authors: McCaffrey Anthony , Jayachandran P. T. 
Published: December 2021

AbstractRino et al. (2019, https://doi.org/10.1029/2019JA026958) has recently explored the effects of refractive (total electron content [TEC]) and stochastic/diffractive (scintillation) on the GPS carrier phase observable, with the intent to show that the scintillation portion of the total ionospheric effect on the carrier phase is negligible. A major portion of the manuscript is based on “stochastic TEC,” a new term that is not well defined by the authors. If the authors meant this as variations in the phase that does not scale with carrier frequency, then it is not TEC at all. One cannot measure TEC, using phase, if the variations do not scale with frequency. In the data‐driven portion of the paper, there are claims and assumptions made that are incorrect, or not well explained. These include the claim that the TEC and scintillation portions of the carrier phase observable cannot be separated, but previous work has shown that it is possible (McCaffrey & Jayachandran, 2019, https://doi.org/10.1029/2018ja025759); the use of the C/N0 in calculating the S4 scintillation index, despite C/N0's sensitivity to the phase and amplitude of the carrier; and the negligence of the higher‐order effects of the TEC calculation.
Transport Path of Cold‐Dense Plasmas in the Dusk Magnetotail Plasma Sheet: MMS Observations
Authors: Nishino M. N. , Hasegawa H. , Saito Y. , Kitamura N. , Miyashita Y. , Nagai T. , Yokota S. , Russell C. T. , Gershman D. J. , Giles B. L. 
Published: December 2021

AbstractThe near‐Earth plasma sheet becomes cold and dense under northward interplanetary magnetic field (IMF) condition, which suggests efficient solar wind plasma entry into the magnetosphere across the magnetopause for northward IMF and a possible contribution of ionospheric oxygen ion outflow. The cold and dense characteristics of the plasma sheet are more evident in the magnetotail flank regions that are the interface between cold solar wind plasma and hot magnetospheric plasma. Several physical mechanisms have been proposed to explain the solar wind plasma entry across the magnetopause and resultant formation of the cold‐dense plasma sheet (CDPS) in the tail flank regions. However, the transport path of the cold‐dense plasma inside the magnetotail has not been understood yet. Here, we present a case study of the CDPS in the dusk magnetotail by magnetospheric multiscale (MMS) spacecraft under strongly northward IMF and high‐density solar wind conditions. The ion distribution function consists of high‐ and low‐energy components, and the low‐energy one intermittently shows energy dispersion in the directions parallel and antiparallel to the local magnetic field. The time‐of‐flight analysis of the energy‐dispersed low‐energy ions suggests that these ions originate in the region farther down the tail, move along the magnetic field toward the ionosphere and then come back to the magnetotail by the mirror reflection. The pitch‐angle dispersion analysis gives consistent results on the traveling time and path length of the energy‐dispersed ions. Based on these observations, we discuss possible generation mechanisms of the energy‐dispersed structure of the low‐energy ions during the northward IMF.
Gradient Winds and Neutral Flow Dawn‐Dusk Asymmetry in the Auroral Oval During Geomagnetically Disturbed Conditions
Authors: Larsen M. F. , Pfaff R. F. , Mesquita R. , Kaeppler S. R. 
Published: December 2021

AbstractThe Pedersen component of the Lorentz force produces an acceleration that is generally in the zonal direction in much of the dawn and dusk sectors in the auroral oval. During geomagnetically disturbed conditions, as the neutral flow begins to accelerate through the ion drag force and the flow speeds increase, a balance develops in the meridional direction between the Coriolis, curvature, and pressure gradient forces, which are dominant in the lower thermosphere. The gradient wind equation that describes this balance predicts that the cyclonic flow on the dawn side is limited to the so‐called regular solution, which has a maximum value of twice the geostrophic wind speed. The anticyclonic flow on the dusk side, on the other hand, can satisfy either the regular or anomalous solution with a transition at twice the geostrophic wind speed. The anomalous flow solutions have wind speeds significantly greater than the transition value, but are limited by the inertial wind value, that is, the value that corresponds to a balance between the curvature and Coriolis forces. The analysis is carried out to show this result, which indicates that a significant quantitative asymmetry is expected between the dawn‐ and dusk‐side flow, as is observed and has been shown in both observations and a number of numerical modeling studies. Implications for the wind distribution of perturbed pressure gradients and inertial instability are discussed.
Mapping the Thermal Structure of the Amazon Craton to Constrain the Tectonic Domains
Authors: Correa R. T. , Vidotti R. M. , Guedes V. J. C. B. , Scandolara J. E. 
Published: December 2021

AbstractRheology of solids is primarily a function of temperature. Mapping depth to the bottom of the magnetic layer (DBML), which is assumed as a proxy for the depth to Curie temperature, can be used to constrain the thermal structure of the lithosphere. Heat flow data are commonly used to address the thermal structure of the lithosphere. However, these data are scarce for the Amazon Craton. Therefore, as an alternative, DBML was calculated using fractal magnetic source distribution. The Amazon craton is usually described in terms of geochronological provinces models. Nevertheless, geophysical data are poorly discussed in these models. We provide a DBML model that was integrated with the potential field, seismic tomography, and crustal thickness data to address this issue. Our model varies from 10 to 80 km, and almost 90% of the estimates are in the 20‐50 km range. The recurrence of long‐wavelength features on independent datasets supports the assessment that the model is robust and recovered real geophysical signals. Our model suggests that the limits between Carajás and Bacajás domains should be revisited as well as the limits between Tapajós and Iriri Xingú domains. Moreover, we also correlate the model with main mineral deposits. Further, the identified DBML anomaly suggests the mantle is serpentinized in the eastern Carajás domain. This feature is highly correlated with high p‐wave velocity indicating fertile mantle conditions, thus making this region favorable for world‐class mineral deposits.
Scarless excision of an insertion sequence restores capsule production and virulence in Acinetobacter baumannii
Authors: Whiteway Clémence , Valcek Adam , Philippe Chantal , Strazisar Mojca , De Pooter Tim , Mateus Ivan , Breine Anke , Van der Henst Charles 
Published: December 2021

Abstract
We identify a new mechanism mediating capsule production and virulence in the WHO and CDC priority ESKAPE pathogen Acinetobacter baumannii. Non-capsulated and avirulent bacteria can revert into a capsulated and virulent state upon scarless excision of an ISAba13 insertion sequence under stress conditions. Reversion events fully restore capsule production and in vivo virulence. This increases our knowledge about A. baumannii genome dynamics, and the regulation of capsule production, virulence and resistance.
Intravitreal injections as a leading cause of acute postoperative endophthalmitis—a regional survey in England
Authors: Ong Ariel Yuhan , Rigaudy Axelle , Toufeeq Shafak , Robins Julian , Shalchi Zaid , Bindra Mandeep Singh , Charbel Issa Peter 
Published: December 2021

Abstract
Background
To evaluate the characteristics, treatment patterns and outcomes of acute postoperative endophthalmitis.

Methods
Patients presenting with acute postoperative endophthalmitis between January 2017 to December 2019 were identified from hospital records in this multicentre retrospective cohort study. Clinical records were reviewed for visual acuity (VA) at various timepoints, cause of endophthalmitis, microbiological results, treatments and complications.

Results
Forty-six eyes of 46 patients were included. Intravitreal injections were the leading cause of acute postoperative endophthalmitis (n = 29; 63%), followed by cataract surgery (n = 8; 17%), vitreoretinal surgery (n = 7; 15%), and secondary intraocular lens insertion (n = 2, 4%). The absolute risk of endophthalmitis was 0.024% (1:4132) for intravitreal injections, 0.016% (1:6096) for cataract surgery, and 0.072% (1:1385) for vitreoretinal surgery. The majority of patients (n = 38; 83%) had better VA at 6 months compared to presentation, although fewer (n = 13; 28%) maintained similar or better VA compared to before the precipitating surgery. Twenty-four cases yielded positive culture results, of which staphylococcus epidermidis was the most commonly isolated organism. Microbiological yield was not associated with better final visual outcomes. Patients who underwent therapeutic vitrectomy (n = 15; 33%) had poorer VA at presentation, but subsequently achieved visual outcomes comparable to those who received medical treatment alone. There was no difference in time to presentation, visual outcome and retinal detachment rates among the different causative procedures.

Conclusion
Intravitreal injections were the most common cause of endophthalmitis in our region, primarily because of their higher frequency compared to other intraocular procedures. In this cohort, the primary procedure had no effect on presentation, management or visual outcomes.
Carbon flux through photosynthesis and central carbon metabolism show distinct patterns between algae, C3 and C4 plants
Authors: Treves Haim , Küken Anika , Arrivault Stéphanie , Ishihara Hirofumi , Hoppe Ines , Erban Alexander , Höhne Melanie , Moraes Thiago Alexandre , Kopka Joachim , Szymanski Jedrzej , Nikoloski Zoran , Stitt Mark 
Published: December 2021

AbstractPhotosynthesis-related pathways are regarded as a promising avenue for crop improvement. Whilst empirical studies have shown that photosynthetic efficiency is higher in microalgae than in C3 or C4 crops, the underlying reasons remain unclear. Using a tailor-made microfluidics labelling system to supply 13CO2 at steady state, we investigated in vivo labelling kinetics in intermediates of the Calvin Benson cycle and sugar, starch, organic acid and amino acid synthesis pathways, and in protein and lipids, in Chlamydomonas reinhardtii, Chlorella sorokiniana and Chlorella ohadii, which is the fastest growing green alga on record. We estimated flux patterns in these algae and compared them with published and new data from C3 and C4 plants. Our analyses identify distinct flux patterns supporting faster growth in photosynthetic cells, with some of the algae exhibiting faster ribulose 1,5-bisphosphate regeneration and increased fluxes through the lower glycolysis and anaplerotic pathways towards the tricarboxylic acid cycle, amino acid synthesis and lipid synthesis than in higher plants.
Spatial structure governs the mode of tumour evolution
Authors: Noble Robert , Burri Dominik , Le Sueur Cécile , Lemant Jeanne , Viossat Yannick , Kather Jakob Nikolas , Beerenwinkel Niko 
Published: December 2021

AbstractCharacterizing the mode—the way, manner or pattern—of evolution in tumours is important for clinical forecasting and optimizing cancer treatment. Sequencing studies have inferred various modes, including branching, punctuated and neutral evolution, but it is unclear why a particular pattern predominates in any given tumour. Here we propose that tumour architecture is key to explaining the variety of observed genetic patterns. We examine this hypothesis using spatially explicit population genetics models and demonstrate that, within biologically relevant parameter ranges, different spatial structures can generate four tumour evolutionary modes: rapid clonal expansion, progressive diversification, branching evolution and effectively almost neutral evolution. Quantitative indices for describing and classifying these evolutionary modes are presented. Using these indices, we show that our model predictions are consistent with empirical observations for cancer types with corresponding spatial structures. The manner of cell dispersal and the range of cell–cell interactions are found to be essential factors in accurately characterizing, forecasting and controlling tumour evolution.
Climatic and soil factors explain the two-dimensional spectrum of global plant trait variation
Authors: Joswig Julia S. , Wirth Christian , Schuman Meredith C. , Kattge Jens , Reu Björn , Wright Ian J. , Sippel Sebastian D. , Rüger Nadja , Richter Ronny , Schaepman Michael E. , van Bodegom Peter M. , Cornelissen J. H. C. , Díaz Sandra , Hattingh Wesley N. , Kramer Koen , Lens Frederic , Niinemets Ülo , Reich Peter B. , Reichstein Markus , Römermann Christine , Schrodt Franziska , Anand Madhur , Bahn Michael , Byun Chaeho , Campetella Giandiego , Cerabolini Bruno E. L. , Craine Joseph M. , Gonzalez-Melo Andres , Gutiérrez Alvaro G. , He Tianhua , Higuchi Pedro , Jactel Hervé , Kraft Nathan J. B. , Minden Vanessa , Onipchenko Vladimir , Peñuelas Josep , Pillar Valério D. , Sosinski Ênio , Soudzilovskaia Nadejda A. , Weiher Evan , Mahecha Miguel D. 
Published: December 2021

AbstractPlant functional traits can predict community assembly and ecosystem functioning and are thus widely used in global models of vegetation dynamics and land–climate feedbacks. Still, we lack a global understanding of how land and climate affect plant traits. A previous global analysis of six traits observed two main axes of variation: (1) size variation at the organ and plant level and (2) leaf economics balancing leaf persistence against plant growth potential. The orthogonality of these two axes suggests they are differently influenced by environmental drivers. We find that these axes persist in a global dataset of 17 traits across more than 20,000 species. We find a dominant joint effect of climate and soil on trait variation. Additional independent climate effects are also observed across most traits, whereas independent soil effects are almost exclusively observed for economics traits. Variation in size traits correlates well with a latitudinal gradient related to water or energy limitation. In contrast, variation in economics traits is better explained by interactions of climate with soil fertility. These findings have the potential to improve our understanding of biodiversity patterns and our predictions of climate change impacts on biogeochemical cycles.
Rapid, efficient and activation-neutral gene editing of polyclonal primary human resting CD4+ T cells allows complex functional analyses
Authors: Albanese Manuel , Ruhle Adrian , Mittermaier Jennifer , Mejías-Pérez Ernesto , Gapp Madeleine , Linder Andreas , Schmacke Niklas A. , Hofmann Katharina , Hennrich Alexandru A. , Levy David N. , Humpe Andreas , Conzelmann Karl-Klaus , Hornung Veit , Fackler Oliver T. , Keppler Oliver T. 
Published: December 2021

AbstractCD4+T cells are central mediators of adaptive and innate immune responses and constitute a major reservoir for human immunodeficiency virus (HIV) in vivo. Detailed investigations of resting human CD4+T cells have been precluded by the absence of efficient approaches for genetic manipulation limiting our understanding of HIV replication and restricting efforts to find a cure. Here we report a method for rapid, efficient, activation-neutral gene editing of resting, polyclonal human CD4+T cells using optimized cell cultivation and nucleofection conditions of Cas9–guide RNA ribonucleoprotein complexes. Up to six genes, including HIV dependency and restriction factors, were knocked out individually or simultaneously and functionally characterized. Moreover, we demonstrate the knock in of double-stranded DNA donor templates into different endogenous loci, enabling the study of the physiological interplay of cellular and viral components at single-cell resolution. Together, this technique allows improved molecular and functional characterizations of HIV biology and general immune functions in resting CD4+T cells.
Benchmarking atlas-level data integration in single-cell genomics
Authors: Luecken Malte D. , Büttner M. , Chaichoompu K. , Danese A. , Interlandi M. , Mueller M. F. , Strobl D. C. , Zappia L. , Dugas M. , Colomé-Tatché M. , Theis Fabian J. 
Published: December 2021

AbstractSingle-cell atlases often include samples that span locations, laboratories and conditions, leading to complex, nested batch effects in data. Thus, joint analysis of atlas datasets requires reliable data integration. To guide integration method choice, we benchmarked 68 method and preprocessing combinations on 85 batches of gene expression, chromatin accessibility and simulation data from 23 publications, altogether representing >1.2 million cells distributed in 13 atlas-level integration tasks. We evaluated methods according to scalability, usability and their ability to remove batch effects while retaining biological variation using 14 evaluation metrics. We show that highly variable gene selection improves the performance of data integration methods, whereas scaling pushes methods to prioritize batch removal over conservation of biological variation. Overall, scANVI, Scanorama, scVI and scGen perform well, particularly on complex integration tasks, while single-cell ATAC-sequencing integration performance is strongly affected by choice of feature space. Our freely available Python module and benchmarking pipeline can identify optimal data integration methods for new data, benchmark new methods and improve method development.