julilili42/papers huggingface dataset:
Inflationary phenomenology of Einstein Gauss-Bonnet gravity compatible with GW170817
2019-08-21

In this work we shall study Einstein Gauss-Bonnet theories and we investigate\\nwhen these can have their gravitational wave speed equal to the speed of light,\\nwhich is unity in natural units, thus becoming compatible with the striking\\nevent GW170817. We demonstrate how this is possible and we show that if the\\nscalar coupling to the Gauss-Bonnet invariant is constrained to satisfy a\\ndifferential equation, the gravitational wave speed becomes equal to one.\\nAccordingly, we investigate the inflationary phenomenology of the resulting\\nrestricted Einstein Gauss-Bonnet model, by assuming that the slow-roll\\nconditions hold true. As we demonstrate, the compatibility with the\\nobservational data coming from the Planck 2018 collaboration, can be achieved,\\neven for a power-law potential. We restricted ourselves to the study of the\\npower-law potential, due to the lack of analyticity, however more realistic\\npotentials can be used, in this case though the calculations are not easy to be\\nperformed analytically. We also pointed out that a string-corrected extension\\nof the Einstein Gauss-Bonnet model we studied, containing terms of the form\\n can also provide a\\ntheory with gravity waves speed in natural units, if the function\\n is appropriately constrained, however in the absence of the\\nGauss-Bonnet term the gravity waves speed can\\nnever be . Finally, we discuss which extensions of the above models\\ncan provide interesting cosmologies, since any combination of \\ngravities with the above string-corrected Einstein Gauss-Bonnet models can\\nyield , with .\\n
NuSTAR observations of wind-fed X-ray pulsar GX 301–2 during unusual spin-up event
2019-08-21

We report on NuSTAR observations of the well-known wind-accreting X-ray pulsar GX 301–2 during a strong spin-up episode that took place in January–March 2019. A measurement of high luminosity of the source in the most recent observation allowed us to detect a positive correlation of the cyclotron line energy with luminosity. Beyond that, only minor differences in spectral and temporal properties of the source during the spin-up, presumably associated with the formation of a transient accretion disk, and the normal wind-fed state could be detected. Finally, we discuss conditions for the formation of the disk and possible reasons for lack of any appreciable variations in most of the observed source properties induced by the change of the accretion mechanism, and conclude that the bulk of the observed X-ray emission is still likely powered by direct accretion from the wind.
The temporal structure of the inner retina at a single glance
2019-08-21

Abstract The retina decomposes visual stimuli into parallel channels that encode different features of the visual environment. Central to this computation is the synaptic processing in a dense and thick layer of neuropil, the so-called inner plexiform layer (IPL). Here, different types of bipolar cells stratifying at distinct depths relay the excitatory feedforward drive from photoreceptors to amacrine and ganglion cells. Current experimental techniques for studying processing in the IPL do not allow imaging the entire IPL simultaneously in the intact tissue. Here, we extend a two-photon microscope with an electrically tunable lens allowing us to obtain optical vertical slices of the IPL, which provide a complete picture of the response diversity of bipolar cells at a “single glance”. The nature of these axial recordings additionally allowed us to isolate and investigate batch effects, i.e. inter-experimental variations resulting in systematic differences in response speed. As a proof of principle, we developed a simple model that disentangles biological from experimental causes of variability, and allowed us to recover the characteristic gradient of response speeds across the IPL with higher precision than before. Our new framework will make it possible to study the computations performed in the central synaptic layer of the retina more efficiently.
Correction to "Detecting distortions of peripherally presented letter stimuli under crowded conditions"
2019-08-21

We discovered a bug in the code producing radial frequency distortions for our paper Wallis, T. S. A., Tobias, S., Bethge, M., &amp; Wichmann, F. A. (2017). Detecting distortions of peripherally presented letter stimuli under crowded conditions. Attention, Perception, &amp; Psychophysics. https://doi.org/10.3758/s13414-016-1245-x In this correction, we fixed the bug, remeasured data for Experiment 1 from the paper, and found that our substantive conclusions remain.
Affinity proteomics identifies novel functional modules related to adhesion GPCRs
2019-08-22

Abstract Adhesion G protein–coupled receptors (ADGRs) have recently become a target of intense research. Their unique protein structure, which consists of a G protein–coupled receptor combined with long adhesive extracellular domains, suggests a dual role in cell signaling and adhesion. Despite considerable progress in the understanding of ADGR signaling over the past years, the knowledge about ADGR protein networks is still limited. For most receptors, only a few interaction partners are known thus far. We aimed to identify novel ADGR‐interacting partners to shed light on cellular protein networks that rely on ADGR function. For this, we applied affinity proteomics, utilizing tandem affinity purifications combined with mass spectrometry. Analysis of the acquired proteomics data provides evidence that ADGRs not only have functional roles at synapses but also at intracellular membranes, namely at the endoplasmic reticulum, the Golgi apparatus, mitochondria, and mitochondria‐associated membranes (MAMs). Specifically, we found an association of ADGRs with several scaffold proteins of the membrane‐associated guanylate kinases family, elementary units of the γ‐secretase complex, the outer/inner mitochondrial membrane, MAMs, and regulators of the Wnt signaling pathways. Furthermore, the nuclear localization of ADGR domains together with their physical interaction with nuclear proteins and several transcription factors suggests a role of ADGRs in gene regulation.
Eikonal quasinormal modes of black holes beyond general relativity
2019-08-22

Much of our physical intuition about black hole quasinormal modes in general relativity comes from the eikonal/geometric optics approximation. According to the well-established eikonal model, the fundamental quasinormal mode represents wavepackets orbiting in the vicinity of the black hole's geodesic photon ring, slowly peeling off towards the event horizon and infinity. Besides its strength as a "visualisation" tool, the eikonal approximation also provides a simple quantitative method for calculating the mode frequency, in close agreement with rigorous numerical results. In this paper we move away from Einstein's theory and its garden-variety black holes and go on to consider spherically symmetric black holes in modified theories of gravity through the lens of the eikonal approximation. The quasinormal modes of such black holes are typically described by a set of coupled wave equations for the various field degrees of freedom. Considering a general, theory-agnostic, system of two equations for two perturbed fields, we derive eikonal formulae for the complex fundamental quasinormal mode frequency. In addition we show that the eikonal modes can be related to the extremum of an effective potential and its associated "photon ring". As an application of our results we consider a specific example of a modified theory of gravity with known black hole quasinormal modes and find that these are well approximated by the eikonal formulae.
Crystallographic and fluid compositional effects on the halogen (Cl, F, Br, I) incorporation in pyromorphite-group minerals
2019-08-22

Abstract Pyromorphite-group minerals (PyGM), mainly pyromorphite [Pb5(PO4)3Cl], mimetite [Pb5(AsO4)3Cl], and vanadinite [Pb5(VO4)3Cl], are common phases that form by supergene weathering of galena. Their formation is strongly influenced by processes at the Earth's surface and in the soil overlying a lead deposit, and they incorporate high amounts of halogens, mostly Cl and, in some cases, F. The abundance of Br and I in natural PyGM and their potential as process tracers during surface and sub-surface fluid-rock interaction processes has not been investigated in detail due to analytical difficulties. We, therefore, developed methods for the simultaneous determination of Cl, F, Br, and I in PyGM for (1) powdered bulk samples via combustion ion chromatography (CIC) and (2) compositionally zoned crystals by means of secondary ion mass spectrometry (SIMS). Our study is based on well-characterized samples of pyromorphite (N = 38), mimetite (N = 16), and vanadinite (N = 2) from Schwarzwald (Germany). Natural pyromorphite incorporates more I (up to 26 μg/g) than mimetite (up to 2 μg/g) and vanadinite (up to 1 μg/g), while Br contents are higher in mimetite (up to 20 μg/g) and vanadinite (up to 13 μg/g) compared to pyromorphite (less than 4 μg/g). These results are unexpected, as mimetite and vanadinite have longer As/V-O bonds giving them larger unit cells and larger polyhedral volumes for the Cl site in the Pb26 octahedron than pyromorphite. Accordingly, pyromorphite was expected to preferentially incorporate Br rather than I, but the opposite is observed. Hence, halogen chemistry of PyGM is probably not governed by a crystal-chemical control (alone) but by fluid composition. However, the exact reasons remain enigmatic. This idea is corroborated by spatially resolved SIMS analyses that show that many pyromorphite-group minerals are strongly zoned with respect to their halogen mass ratios (e.g., Br/Cl, Br/I mass ratios). Furthermore, variations in halogen abundance ratios do not correlate with Ca/Pb, P/As, or P/V ratios and therefore may record alternating and season-dependent environmental parameters including biological activity, vegetation density, physico-chemical soil properties, and rainfall rate. We suggest that the zonation reflects multiple single fluid flow episodes and, hence, records surface processes. However, further experiments concerning the fractionation of halogens between fluid and PyGM are needed before halogen ratios in pyromorphite-group minerals can be used as reliable monitors of fluid-driven processes.
De novo variants in SLC12A6 cause sporadic early-onset progressive sensorimotor neuropathy
2019-08-22

Background Charcot-Marie-Tooth disease (CMT) is a clinically and genetically heterogeneous disorder of the peripheral nervous system. Biallelic variants in SLC12A6 have been associated with autosomal-recessive hereditary motor and sensory neuropathy with agenesis of the corpus callosum (HMSN/ACC). We identified heterozygous de novo variants in SLC12A6 in three unrelated patients with intermediate CMT. Methods We evaluated the clinical reports and electrophysiological data of three patients carrying de novo variants in SLC12A6 identified by diagnostic trio exome sequencing. For functional characterisation of the identified variants, potassium influx of mutated KCC3 cotransporters was measured in Xenopus oocytes. Results We identified two different de novo missense changes (p.Arg207His and p.Tyr679Cys) in SLC12A6 in three unrelated individuals with early-onset progressive CMT. All presented with axonal/demyelinating sensorimotor neuropathy accompanied by spasticity in one patient. Cognition and brain MRI were normal. Modelling of the mutant KCC3 cotransporter in Xenopus oocytes showed a significant reduction in potassium influx for both changes. Conclusion Our findings expand the genotypic and phenotypic spectrum associated with SLC12A6 variants from autosomal-recessive HMSN/ACC to dominant-acting de novo variants causing a milder clinical presentation with early-onset neuropathy.
Cellular and molecular mechanisms of photoreceptor tuning for prey capture in larval zebrafish
2019-08-22

In the eye, the function of same-type photoreceptors must be regionally adjusted to process a highly asymmetrical natural visual world. Here we show that UV-cones in the larval zebrafish area temporalis are specifically tuned for UV-bright prey capture in their upper frontal visual field, which uses the signal from a single cone at a time. For this, UV-detection efficiency is regionally boosted 42-fold. Next, in vivo 2-photon imaging, transcriptomics and computational modelling reveal that these cones use an elevated baseline of synaptic calcium to facilitate the encoding of bright objects, which in turn results from expressional tuning of phototransduction genes. Finally, this signal is further accentuated at the level of glutamate release driving retinal networks. These regional differences tally with variations between peripheral and foveal cones in primates and hint at a common mechanistic origin. Together, our results highlight a rich mechanistic toolkit for the tuning of neurons.
Multiple Radiocarbon Dating of Human remains: Clarifying the Chronology and Sequences of Burials in the late Neolithic Dolmen of Oberbipp (Switzerland)
2019-08-22

ABSTRACT Undisturbed megalithic burials are extremely rare because in addition to human activities, natural disturbances due to water influence and erosion or faunal activity are likely to occur over time. The dolmen of Oberbipp discovered in 2011 provides a unique opportunity for multidisciplinary research since anthropogenic and natural disturbances are minor. Morphological analysis indicates that approximately 42 individuals were buried in the grave chamber. Using archaeological methods alone, it would not have been possible to determine different occupation periods within the inhumations. Neolithic communities often reused dolmen over centuries. Therefore, radiocarbon ( 14 C) dating is the only method that can solve the question of temporal resolution. Fragments of the same bone element (right femora) were analyzed by two (in some cases three) different laboratories to date all inhumations individually. The aim of this study was threefold: (1) to determine the total occupation time of the dolmen (2) to evaluate the sequence of the burials, and (3) to compare the results of the same skeletal element from different laboratories. In total, 79 radiocarbon dating results from three different laboratories of the right femora (n = 32) were obtained. The total time span of the occupation of the dolmen was between 3350 and 2650 BC. The broad application of radiocarbon dating allowed the determination of two occupation periods within the burial.
Comparison of solitary and collective foraging strategies ofCaenorhabditis elegansin patchy food distributions
2019-08-22

Abstract Collective foraging has been shown to benefit organisms in environments where food is patchily distributed, but whether this is true in the case where organisms do not rely on long-range communications to coordinate their collective behaviour has been understudied. To address this question, we use the tractable laboratory model organism Caenorhabditis elegans , where a social strain ( npr-1 mutant) and a solitary strain (N2) are available for direct comparison of foraging strategies. We first developed an on-lattice minimal model for comparing collective and solitary foraging strategies, finding that social agents benefit from feeding faster and more efficiently simply due to group formation. Our laboratory foraging experiments with npr-1 and N2 worm populations, however, show an advantage for solitary N2 in all food distribution environments that we tested. We incorporated additional strain-specific behavioural parameters of npr-1 and N2 worms into our model and computationally identified N2’s higher feeding rate to be the key factor underlying its advantage, without which it is possible to recapitulate the advantage of collective foraging in patchy environments. Our work highlights the theoretical advantage of collective foraging due to group formation alone without long-range interactions, and the valuable role of modelling to guide experiments.
A global map of orientation tuning in mouse visual cortex
2019-08-23

In primates and most carnivores, neurons in primary visual cortex are spatially organized by their functional properties. For example, neurons with similar orientation preferences are grouped together in iso-orientation domains that smoothly vary over the cortical sheet. In rodents, on the other hand, neurons with different orientation preferences are thought to be spatially intermingled, a feature which has been termed “salt-and-pepper” organization. The apparent absence of any systematic structure in orientation tuning has been considered a defining feature of the rodent visual system for more than a decade, with broad implications for brain development, visual processing, and comparative neurophysiology. Here, we revisited this question using new techniques for wide-field two-photon calcium imaging that enabled us to collect nearly complete population tuning preferences in layers 2-4 across a large fraction of the mouse visual hierarchy. Examining the orientation tuning of these hundreds of thousands of neurons, we found a global map spanning multiple visual cortical areas in which orientation bias was organized around a single pinwheel centered in V1. This pattern was consistent across animals and cortical depth. The existence of this global organization in rodents has implications for our understanding of visual processing and the principles governing the ontogeny and phylogeny of the visual cortex of mammals.
Glissades Are Altered by Lesions to the Oculomotor Vermis but Not by Saccadic Adaptation
2019-08-23

Saccadic eye movements enable fast and precise scanning of the visual field, which is partially controlled by the posterior cerebellar vermis. Textbook saccades have a straight trajectory and a unimodal velocity profile, and hence have well-defined epochs of start and end. However, in practice only a fraction of saccades matches this description. One way in which a saccade can deviate from its trajectory is the presence of an overshoot or undershoot at the end of a saccadic eye movement just before fixation. This additional movement, known as a glissade, is regarded as a motor command error and was characterized decades ago but was almost never studied. Using rhesus macaques, we investigated the properties of glissades and changes to glissade kinematics following cerebellar lesions. Additionally, in monkeys with an intact cerebellum, we investigated whether the glissade amplitude can be modulated using multiple adaptation paradigms. Our results show that saccade kinematics are altered by the presence of a glissade, and that glissades do not appear to have any adaptive function as they do not bring the eye closer to the target. Quantification of these results establishes a detailed description of glissades. Further, we show that lesions to the posterior cerebellum have a deleterious effect on both saccade and glissade properties, which recovers over time. Finally, the saccadic adaptation experiments reveal that glissades cannot be modulated by this training paradigm. Together our work offers a functional study of glissades and provides new insight into the cerebellar involvement in this type of motor error.
The postembryonic transformation of the shell in emydine box turtles
2019-08-23

Abstract A key trend in the 210‐million‐year‐old history of modern turtles was the evolution of shell kinesis, that is, shell movement during neck and limb retraction. Kinesis is hypothesized to enhance predator defense in small terrestrial and semiaquatic turtles and has evolved multiple times since the early Cretaceous. This complex phenotype is nonfunctional and far from fully differentiated following embryogenesis. Instead, kinesis develops slowly in juveniles, providing a unique opportunity to illustrate the postembryonic origins of an adaptive trait. To this end, we examined ventral shell (plastral) kinesis in emydine box turtles and found that hatchling plastron shape differs from that of akinetic‐shelled relatives, particularly where the hinge that enables kinesis differentiates. We also demonstrated shape changes relative to plastron size in juveniles, coinciding with a shift in the carapace‐plastron structural connection, rearrangement of ectodermal plates, and bone repatterning. Furthermore, because the shell grows larger relative to the head, complete concealment of the head and extremities is only achieved after relative shell proportions increase. Structural alterations that facilitate the box turtle's transformation are probably prepatterned in embryos but require function‐induced changes to differentiate in juveniles. This mode of delayed trait differentiation is essential to phenotypic diversification in turtles and perhaps other tetrapods.
PGRMC1 phosphorylation and cell plasticity 2: genomic integrity and CpG methylation
2019-08-23

SUMMARY Progesterone receptor membrane component 1 (PGRMC1) is often elevated in cancers, and exists in alternative states of phosphorylation. A motif centered on PGRMC1 Y180 was evolutionarily acquired concurrently with the embryological gastrulation organizer that orchestrates vertebrate tissue differentiation. Here, we show that mutagenic manipulation of PGRMC1 phosphorylation alters cell metabolism, genomic stability, and CpG methylation. Each of several mutants elicited distinct patterns of genomic CpG methylation. Mutation of S57A/Y180/S181A led to increased net hypermethylation, reminiscent of embryonic stem cells. Pathways enrichment analysis suggested modulation of processes related to animal cell differentiation status and tissue identity, as well as cell cycle control and ATM/ATR DNA damage repair regulation. We detected different genomic mutation rates in culture. A companion manuscript shows that these cell states dramatically affect protein abundances, cell and mitochondrial morphology, and glycolytic metabolism. We propose that PGRMC1 phosphorylation status modulates cellular plasticity mechanisms relevant to early embryological tissue differentiation.
Advect As challenge: multidisciplinary research on groundwater arsenic dissolution, transport, and retardation under advective flow conditions
2019-08-23

Constant exposure to groundwater contaminated by arsenic (As) constitutes a major health risk for millions of people worldwide. Therefore, the biogeochemical and physical processes responsible for the release, transport and retardation ofAs in groundwater need to be identified to optimize groundwater management strategies, both in rural and urban areas. River delta regions in Asia constitute a relevant spot to study the presence of As in drinking water, due to the interplay among the natural release of As from sediments, the onset of redox fronts in aquifers, which can sharply change the mobility of As, and the anthropogenic increased groundwater extraction for the supply of growing urban areas. The AdvectAs project involves several teams to promote transdisciplinary research on the environmental behaviour and spatial heterogeneity of As in groundwater under advective conditions associated with extensive pumping of pristine groundwater from the city of Hanoi, Red River delta region inVietnam. In autumn 2017 a sampling campaign in the vicinity of Hanoiwas carried out, integrating sediment analyses, geochemical, mineralogical and microbiological studies, hydrogeochemical characterization of groundwater, groundwater dating and transport modelling. The first outcomes of the hydrogeochemical analyses will be presented in this contribution.