Miracle-dz/UniFAR-FTUs huggingface dataset:
Postlaunch assessment of the response versus scan angle for the thermal emissive bands of visible infrared imaging radiometer suite on-board the Suomi national polar-orbiting partnership satellite

Abstract. The visible infrared imaging radiometer suite (VIIRS) is a key sensor carried on the Suomi national polar-orbiting partnership (S-NPP) satellite, which was launched in October 2011. It has several on-board calibration components, including a solar diffuser and a solar diffuser stability monitor for the reflective solar bands, a V-groove blackbody for the thermal emissive bands (TEB), and a space view port for background subtraction. These on-board calibrators are located at fixed scan angles. The VIIRS response versus scan angle (RVS) was characterized prelaunch in lab ambient conditions and is currently used to characterize the on-orbit response for all scan angles relative to the calibrator scan angle. Since the RVS is vitally important to the quality of calibrated radiance products, several independent studies were performed to analyze the prelaunch RVS measurement data. A spacecraft level pitch maneuver was scheduled during the first 3 months of intensive Cal/Val. The S-NPP pitch maneuver provided a rare opportunity for VIIRS to make observations of deep space over the entire range of Earth view scan angles, which can be used to characterize the TEB RVS. This study provides our analysis of the pitch maneuver data and assessment of the derived TEB RVS by comparison with prelaunch results. In addition, the stability of the RVS after the first 5 years of operation is examined using observed brightness temperatures (BT) over a clear ocean at various angles of incidence (AOI). To reduce the impact of variations in the BT measurements, the daily overpasses collected over the ocean are screened for cloud contamination, normalized to the results obtained at the blackbody AOI, and averaged each year.
Determination of Isoprene and α-/β-Pinene Oxidation Products in Boreal Forest Aerosols from Hyytiälä, Finland: Diel Variations and Possible Link with Particle Formation Events

: Biogenic volatile organic compounds (VOCs), such as isoprene and a -/ b -pinene, are photo-oxidized in the atmosphere to non-volatile species resulting in secondary organic aerosol (SOA). The goal of this study was to examine time trends and diel variations of oxidation products of isoprene and a -/ b -pinene in order to investigate whether they are linked with meteorological parameters or trace gases. Separate day-night aerosol samples (PM 1 ) were collected in a Scots pine dominated forest in southern Finland during 28 July–11 August 2005 and analyzed with gas chromatography/mass spectrometry (GC/MS). In addition, inorganic trace gases (SO 2 , CO, NO x , and O 3 ), meteorological parameters, and the particle number concentration were monitored. The median total concentration of terpenoic acids (i.e., pinic acid, norpinic acid, and two novel compounds, 3-hy-droxyglutaric acid and 2-hydroxy-4-isopropyladipic acid) was 65 ng m –3 , while that of isoprene oxidation products (i.e., 2-methyltetrols and C 5 alkene triols) was 17.2 ng m –3 . The 2-meth-yltetrols exhibited day/night variations with maxima during day-time, while a -/ b -pinene oxidation products did not show any diel variation. The sampling period was marked by a relatively high condensation sink, caused by pre-existing aerosol particles, and no nucleation events. In general, the concentration trends of the SOA compounds reflected those of the inorganic trace gases, meteorological parameters, and condensation sink. Both the isoprene and a -/ b -pinene SOA products were strongly influenced by SO 2 , which is consistent with earlier reports that acidity plays a role in SOA formation. The results support previous proposals that oxygenated VOCs contribute to particle growth processes above boreal forest.
Coding dynamics of the striatal networks during learning

The rat dorsomedial (DMS) and dorsolateral striatum (DMS), equivalent to caudate nucleus and putamen in primates, are generally required for goal-directed and habit behaviour, respectively. However, it is still unclear whether and how this functional dychotomy emerges in the course of learning. In this study we investigated this issue by recording DMS and DLS single neuron activity in rats performing a continuous spatial alternation task, from the acquisition to optimized performance. We first applied a classical analytical approach to identify task-related activity based on the modifications of single neuron firing rate in relation to specific task events or maze trajectories. We then used an innovative approach based on Hawkes process to reconstruct a directed connectivity graph of simultaneously recorded neurons, that was used to decode animal behavior. This approach enabled us to better unravel the role of DMS and DLS neural networks across learning stages. We showed that DMS and DLS display different task-related activity throughout learning stages, and the proportion of coding neurons over time decreases in the DMS and increases in the DLS. Despite theses major differences, the decoding power of both networks increases during learning. These results suggest that DMS and DLS neural networks gradually reorganize in different ways in order to progressively increase their control over the behavioral performance.
A digital approach to quantum theory

Lluı́s Masanes,1 Markus P. Müller,2 Remigiusz Augusiak,1 and David Pérez-Garcı́a3 ICFO-Institut de Ciències Fotòniques, Mediterranean Technology Park, 08860 Castelldefels (Barcelona), Spain Perimeter Institute for Theoretical Physics, 31 Caroline Street North, Waterloo, ON N2L 2Y5, Canada Dpto. Analisis Matemático and IMI, Universidad Complutense de Madrid, 28040 Madrid, Spain (Dated: August 3, 2012)
Sources of prey availability data alter interpretation of outputs from prey choice null networks

Null models provide an invaluable baseline against which to test fundamental ecological hypotheses and highlight patterns in foraging choices that cannot be explained by neutral processes or sampling artefacts. In this way, null models can advance our understanding beyond simplistic dietary descriptions to identify drivers of interactions. This method, however, requires estimates of resource availability, which are generally imperfect representations of highly dynamic systems. Optimising method selection is crucial for study design, but the precise effects of different resource availability data on the efficacy of null models are poorly understood. Using spider-prey networks as a model, we used prey abundance (suction sample) and activity density (sticky trap) data, and combinations of the two, to simulate null networks. We compared null diet composition, network properties (e.g., connectance and nestedness) and deviations of simulations from metabarcoding-based spider dietary data (to ascertain how different prey availability data alter ecological interpretation. Different sampling methods produced different null networks and inferred distinct prey selectivity. Null networks based on prey abundance and combined frequency-of-occurrence data more closely resembled the observed diet composition, and those based on prey abundance, activity density and proportionally combined data generated network properties most like dietary metabarcoding networks. We show that survey method choice impacts all aspects of null network analyses, the precise effects varying between methods but ultimately altering ecological interpretation by increasing disparity in network properties or trophic niches between null and directly constructed networks. Merging datasets can generate more complete prey availability data but is not a panacea because it introduces different biases. The choice of method should reflect the research hypotheses and study system being investigated. Ultimately, survey methods should emulate the foraging mode of the focal predator as closely as possible, informed by the known ecology, natural history and behaviour of the predator.
Deep mutational scanning quantifies DNA binding and predicts clinical outcomes of PAX6 variants

Nonsense and missense mutations in the transcription factor PAX6 cause a wide range of eye development defects, including aniridia, microphthalmia and coloboma. To understand how changes of PAX6:DNA binding cause these phenotypes, we combined saturation mutagenesis of the paired domain of PAX6 with a yeast one-hybrid (Y1H) assay in which expression of a PAX6-GAL4 fusion gene drives antibiotic resistance. We quantified binding of more than 2,700 single amino-acid variants to two DNA sequence elements. Mutations in DNA-facing residues of the N-terminal subdomain and linker region were particularly detrimental, as were mutations to prolines and to negatively charged residues. Many variants caused molecular gain-of-function effects, including variants in position Ile71 that increased binding to the LE9 enhancer but decreased binding to a SELEX-derived binding site. Benchmarking against known patient variants and applying ACMG/AMP guidelines to variant classification, we obtained supporting to moderate evidence to suggest that 1,306 variants are likely benign, and 977, likely pathogenic. Our analysis shows that most pathogenic mutations in the paired domain of PAX6 can be explained simply by the effects of these mutations on PAX6:DNA association, and establishes Y1H as a generalisable assay for the interpretation of variant effects in transcription factors.
Combined representation of visual features in the scene-selective cortex

Visual features of separable dimensions like color and shape conjoin to represent an integrated entity. We investigated how visual features bind to form a complex visual scene. Specifically, we focused on features important for visually guided navigation: direction and distance. Previously, separate works have shown that directions and distances of navigable paths are coded in the occipital place area (OPA). Using functional magnetic resonance imaging (fMRI), we tested how separate features are concurrently represented in the OPA. Participants saw eight different types of scenes, in which four of them had one path and the other four had two paths. In single-path scenes, path direction was either to the left or to the right. In double-path scenes, both directions were present. Each path contained a glass wall located either near or far, changing the navigational distance. To test how the OPA represents paths in terms of direction and distance features, we took three approaches. First, the independent-features approach examined whether the OPA codes directions and distances independently in single-path scenes. Second, the integrated-features approach explored how directions and distances are integrated into path units, as compared to pooled features, using double-path scenes. Finally, the integrated-paths approach asked how separate paths are combined into a scene. Using multi-voxel pattern similarity analysis, we found that the OPA’s representations of single-path scenes were similar to other single-path scenes of either the same direction or the same distance. Representations of double-path scenes were similar to the combination of two constituent single-paths, as a combined unit of direction and distance rather than pooled representation of all features. These results show that the OPA combines the two features to form path units, which are then used to build multiple-path scenes. Altogether, these results suggest that visually guided navigation may be supported by the OPA that automatically and efficiently combines multiple features relevant for navigation and represent a navigation file.
A step in the deep evolution of Alvinellidae (Annelida: Polychaeta): a phylogenomic comparative approach based on transcriptomes

The Alvinellidae are a family of worms that are endemic to deep-sea hydrothermal vents in the Pacific and Indian Oceans. These annelid worms, a sister group to the Ampharetidae, occupy a wide range of thermal habitats. The family includes the most thermotolerant marine animals described to date such as the Pompeii worm Alvinella pompejana, and other species living at much lower temperatures such as Paralvinella grasslei or Paralvinella pandorae. The phylogeny of this family has not been studied extensively. It is, however, a complex case where molecular phylogenies give conflicting results, especially concerning the monophyletic or polyphyletic character of the genus Paralvinella. We carried out a comprehensive study of the phylogeny of this family using the best molecular data currently available from RNAseq datasets. The study is based on the assembly of several hundred transcripts for 11 of the 14 species currently described or in description. The results obtained by the most popular phylogenetic inference models (gene concatenation with maximum likelihood, or coalescent-based methods from gene trees) are compared using a series of ampharetid and terebellid outgroups. Our study shows that a high number of gene trees support the hypothesis of the monophyly of the Paralvinella genus, as initially proposed by Desbruyères and Laubier, in which the species Paralvinella pandorae and Paralvinella unidentata are more closely related within the subgenus Nautalvinella. However, the global phylogenetic signal favors the hypothesis of paraphyly for this genus, with P. pandorae being sister species of the other Alvinellidae. Gene trees separated equally between these two hypotheses, making it difficult to draw conclusionsabout the initial split of the MCRA as different genomic regions seem to have very different phylogenetic stories. According to molecular dating, the radiation of the Alvinellidae was rapid and took place in a short period of time between 70 and 80 million years ago. This is reflected at the genomic scale by high rates of incomplete lineage sorting between the first ancestral lineages with probable gene transfers between the ancestors of Alvinella, Nautalvinella, and the rest of the Paralvinella lineages.
Microstructure-Based Nuclear Lamina Constitutive Model

The nuclear lamina is widely recognized as the most crucial component in providing mechanical stability to the nucleus. However, it is still a significant challenge to model the mechanics of this multilayered protein network. We developed a constitutive model of the nuclear lamina network based on its microstructure, which accounts for the deformation phases at the dimer level, as well as the orientational arrangement and density of lamin filaments. Instead of relying on homology modeling in the previous studies, we conducted molecular simulations to predict the force-extension response of a highly accurate lamin dimer structure obtained through X-ray diffraction crystallography experimentation. Furthermore, we devised a semi-flexible worm-like chain extension-force model of lamin dimer as a substitute, incorporating phases of initial stretching, uncoiling of the dimer coiled-coil, and transition of secondary structures. Subsequently, we developed a 2D network continuum model for the nuclear lamina by using our extension-force lamin dimer model and derived stress resultants. By comparing with experimentally measured lamina modulus, we found that the lamina network has sharp initial strain-hardening behavior. This also enabled us to carry out finite element simulations of the entire nucleus with an accurate microstructure-based nuclear lamina model. Finally, we conducted simulations of transendothelial transmigration of a nucleus and investigated the impact of varying network density and uncoiling constants on the critical force required for successful transmigration. The model allows us to incorporate the microstructure characteristics of the nuclear lamina into the nucleus model, thereby gaining insights into how laminopathies and mutations affect nuclear mechanics.
A Representation Theorem for Absolute Confirmation

Proposals for rigorously explicating the concept of confirmation in probabilistic terms abound. To foster discussions on the formal properties of the proposed measures, recent years have seen the upshot of a number of representation theorems that uniquely determine a confirmation measure (up to ordinal equivalence) based on a number of desiderata. However, the results that have been presented so far focus exclusively on the concept of incremental confirmation. This leaves open the question whether similar results can be obtained for the concept of absolute confirmation. This article closes the gap by providing a representation theorem for absolute confirmation measures.
Effects of Elevated Atmospheric CO2 and/or O3 on Intra- and Interspecific Competitive Ability of Aspen

: Three model communities of trembling aspen (mono-culture, and mixed with either paper birch or sugar maple) were grown for seven years in elevated atmospheric CO 2 and O 3 using Free Air CO 2 Enrichment (FACE) technology. We utilized trends in species’ importance, calculated as an index of volume growth and survival, as indications of shifting community composition. For the pure aspen communities, different clones emerged as having the highest change in relative importance values depending on the pollutant exposure. In the control and elevated CO 2 treatments, clone 42E was rapidly becoming the most successful clone while under elevated O 3 , clone 8 L emerged as the dominant clone. In fact, growth of clone 8 L was greater in the elevated O 3 treatment compared to controls. For the mixed aspen-birch community, importance of aspen and birch changed by – 16% and + 62%, respectively, in the controls. In the treatments, however, importance of aspen and birch changed by – 27% and + 87%, respectively, in elevated O 3 , and by – 10% and + 45%, respectively, in elevated CO 2 . Thus, the presence of elevated O 3 hastened conversion of stands to paper birch, whereas the presence of elevated CO 2 delayed it. Relative importance of aspen and maple changed by – 2% and + 3%, respectively, after seven years in the control treatments. But in elevated O 3 , relative importance of aspen and maple changed by – 2% and + 5%, respectively, and in elevated CO 2 by + 9 and – 20%, respectively. Thus, elevated O 3 slightly increases the rate of conversion of aspen stands to sugar maple, but maple is placed at a competitive disadvantage to aspen under elevated CO 2 .
The Creeping Motion and Deformation of Drops in Solid Constrictions

Axisymmetric boundary-integral (BI) simulations were made for buoyancy-induced squeezing of a deformable drop through a ring constriction. The algorithm uses the Hebeker representation for the solid-particle contribution. A high-order, near-singularity subtraction technique is essential for near-critical squeezing. The drop velocity and minimum drop-solid spacing were determined for different ring and hole sizes, viscosity ratios, and Bond numbers, where the latter is a dimensionless ratio of gravitational to interfacial forces. The drop velocity decelerates typically 100-fold or more, and the drop-solid spacing reduces to typically 0.1%–1% of the nondeformed drop radius as the drop passes through the constriction. The critical Bond number (below which trapping occurs) was determined for different conditions. For supercritical conditions, the nondimensional time required for the drop to pass through the ring increases for a 13 fixed drop-to-hole size with increasing viscosity ratio and decreasing Bond number, but it has a nonmonotonic dependence on the ratio of the radii of the drop and ring cross section. Numerical results indicate that the square of the drop squeezing time is inversely proportional to the Bond number minus the critical Bond number for near-critical squeezing. Another dynamic phenomenon, in addition to drop squeezing, is a drop “dripping” around the outer edge of the ring constriction. The initial stages of drop dripping are numerically simulated using a boundaryintegral method for slightly supercritical Bond numbers. For very large ratios of the drop-to-hole radii, however, a sharp maximum in the critical Bond number is reached, as there is a transition from the drop passing through the inside hole to dripping over the outside edge of the ring for Bond numbers above the critical value.
First Detection of Prominence Material Embedded within a 2 × 106 K CME Front Streaming away at 100–1500 km s−1 in the Solar Corona

Coronal mass ejections (CMEs) are the largest and most dynamic explosions detected in the million degree solar corona, with speeds reaching up to 3000 km s−1 at Earth’s orbit. Triggered by the eruption of prominences, in most cases, one of the outstanding questions pertaining to the dynamic CME-prominence system is the fate of the cool ejected filaments. We present spectroscopic observations acquired during the 2015 March 20 total solar eclipse, which captured a plethora of redshifted plasmoids from Fe xiv emission at . Approximately 10% of these plasmoids enshrouded the same neutral and singly ionized plasma below , observed in prominences anchored at the Sun at that time. This discovery was enabled by the novel design of a dual-channel spectrometer and the exceptionally clear sky conditions on the island of Svalbard during totality. The Doppler redshifts corresponded to speeds ranging from under 100 to over 1500 km s−1. These are the first comprehensive spectroscopic observations to unambiguously detect a filamentary CME front with inclusions of cool prominence material. The CME front covered a projected area of starting from the solar surface. These observations imply that cool prominence inclusions within a CME front maintain their ionic composition during expansion away from the Sun.
Cut-Induced VOC Emissions from Agricultural Grasslands

: The introduction of proton transfer reaction mass spectrometry (PTR-MS) for fast response measurements of volatile organic compounds (VOC) has enabled the use of eddy co-variance methods to investigate VOC fluxes on the ecosystem scale. In this study PTR-MS flux measurements of VOC were performed over agricultural grassland during and after a cut event. Selected masses detected by the PTR-MS showed fluxes of methanol, acetaldehyde, and acetone. They were highest directly after cutting and during the hay drying phase. Simultaneously, significant fluxes of protonated ion masses 73, 81, and 83 were observed. Due to the limited identification of compounds with the PTR-MS technique, GC-MS and GC-FID-PTR-MS techniques were additionally applied. In this way, ion mass 73 could be identified as 2-butanone, mass 81 mainly as (Z)-3-hexenal, and mass 83 mainly as the sum of (Z)-3-hexenol and hexenyl acetates. Hexenal, hexenols, and the hexenyl acetates are mostly related to plant wounding during cutting. It was found that legume plants and forbs emit a higher number of different VOC species than graminoids.