julilili42/papers huggingface dataset:
Earliest evidence for hunter-gatherer impacts on raven diet and ecology in the Gravettian of Southern Moravia
2022-09-15

<title>Abstract</title> The Early Gravettian of Southern Moravia – the Pavlovian – is notable for its corvid-rich faunal assemblages dominated by common ravens (<italic>Corvus corax</italic>). Based on the available zooarchaeological and settlement data from the Pavlovian, it has been hypothesized that ravens were attracted by human domestic activities and subsequently captured by Pavlovian people for food and feathers. Here, we report independent <italic>δ</italic><sup>15</sup>N, <italic>δ</italic><sup>13</sup>C and <italic>δ</italic><sup>34</sup>S isotope data obtained from twelve adult common ravens from the Pavlovian key sites of Předmostí I, Pavlov I and Dolní Věstonice I. We show that these ravens had diets surprisingly rich in mammoth, thus strongly aligning in feeding preferences with contemporary early <italic>Homo sapiens</italic> foragers. We isolate two groups of ravens with distinct dietary profiles and argue that these opportunistic-generalist feeders were both attracted from adjacent regions and encouraged locally through human activity. These data provide the earliest direct evidence for incipient synanthropism among Upper Palaeolithic ravens. We suggest that subtle anthropogenic ecosystem engineering, including carrion supply dynamics, furnishes unique contexts for the emergence of synanthropism, affirming deep-historical roots in Late Pleistocene hunter-gatherer contexts. The coalescence of synanthropic niches can promote novel foraging opportunities and human-environment feedback dynamics and is thus important for understanding early human ecosystem impacts.
N‐terminal domain of ARF‐GEF GNOM prevents heterodimerization with functionally divergent GNL1 in Arabidopsis
2022-09-15

SUMMARY Evolutionary change following gene duplication can lead to functionally divergent paralogous proteins. If comprising identical subunits their random assortment would also form potentially detrimental heteromeric proteins. In Arabidopsis, the ARF GTPase guanine‐nucleotide exchange factor GNOM is essential for polar recycling of auxin‐efflux transporter PIN1 from endosomes to the basal plasma membrane whereas its paralog GNL1 mediates retrograde Golgi‐endoplasmic reticulum traffic. Here we show that both GNOM and GNL1 form homodimers but no heterodimers. To assess the biological significance of this, we generated transgenic plants expressing engineered heterodimer‐compatible GNOM variants. Those plants showed developmental defects such as the failure to produce lateral roots. To identify mechanisms underlying heterodimer prevention, we analyzed interactions of the N‐terminal dimerization and cyclophilin‐binding (DCB) domain. Each DCB domain interacted with the complementary fragment (ΔDCB) both of their own and of the paralogous protein. However, only DCB GNOM interacted with itself whereas DCB GNL1 failed to interact with itself and with DCB GNOM . GNOM variants in which the DCB domain was removed or replaced by DCB GNL1 revealed a role for DCB‐DCB interaction in the prevention of GNOM‐GNL1 heterodimers whereas DCB‐ΔDCB interaction was essential for dimer formation and GNOM function. Our data suggest a model of early DCB‐DCB interaction that facilitates GNOM homodimer formation, indirectly precluding formation of detrimental heterodimers.
Microglial colonisation of the developing brain is facilitated by clonal expansion of highly proliferative progenitors and follows an allometric scaling
2022-09-15

SUMMARY Microglia are the resident immune cells of the brain and arise from yolk sac-derived macrophages during early embryogenesis. On entering the brain, microglia undergo in situ proliferation and eventually colonise the entire brain by the second and third postnatal weeks in mice. However, the intricate dynamics of their developmental expansion remain unclear. Here, we examine and characterise the proliferative dynamics of microglia during embryonic and postnatal development. Using complementary fate-mapping techniques, we demonstrate that the developmental colonisation of the brain by microglia is facilitated by clonal expansion of highly proliferative microglial progenitors that occupy spatial niches throughout the brain. We also find that the distribution of microglia switches from a clustered to a random pattern between embryonic and late postnatal development. Moreover, the developmental increase in microglia follows the proportional growth of the brain in an allometric manner with the density of microglia eventually stabilising when the mosaic distribution has been established. Overall, our findings offer insight into how the competition for space acts as a driving force for microglial colonisation by clonal expansion during development.
Platelet phosphatidylserine is the critical mediator of thrombosis in heparin-induced thrombocytopenia
2022-09-15

Abstract Heparin-induced thrombocytopenia (HIT) is a severe immune-mediated prothrombotic disorder caused by antibodies reactive to complexes of platelet factor 4 and heparin. Platelets (PLTs) and their interaction with different immune cells contribute to prothrombotic conditions in HIT. However, the exact mechanisms and the role of different PLT subpopulations to this prothrombotic enviroment remain poorly understood. In this study, we observed that HIT patient antibodies (Abs) induce relevant changes in PLT phenotype, with the key features being increased P-Selectin expression and procoagulant phosphatidylserine (PS) externalization. Formation of procoagulant PLTs was dependent on engagement of PLT Fc-gamma-RIIA by HIT Abs and resulted in significant increase of thrombin generation on the PLT surface. Using an ex vivo thrombosis model and multi-parameter assessment of thrombus formation, we observed that HIT Ab-induced procoagulant PLTs propagated formation of large PLT aggregates, leukocyte recruitment and most importantly, fibrin network generation. These prothrombotic conditions were prevented via the upregulation of PLTs intracellular cAMP with Iloprost, a clinically approved prostacyclin analogue. Additionally, the functional relevance of high P-Selectin and PS levels on procoagulant PLTs was dissected. While inhibition of P-Selectin did not affect thrombus formation, the specific blockade of PS with Lactadherin prevented HIT Ab-mediated thrombin generation and most importantly procoagulant PLT-mediated thrombus formation ex vivo. Taken together, our findings indicate that procoagulant PLTs are critical mediators of prothrombotic conditions in HIT. Upregulation of cAMP with Iloprost or PS targeting specifc therapeutics could be a promising approach to prevent thromboembolic events in HIT patients. Key points - HIT immune complexes drive procoagulant platelet formation - Phosphatidylserine blockade prevents HIT antibody-induced thrombus formation
Electronic appendix to: Spectral Induced Polarization (SIP) of Denitrification-Driven Microbial Activity in Column Experiments Packed with Calcareous Aquifer Sediments
2022-09-15

&lt;p&gt;This is the electronic appendix of the publication&nbsp;&lt;br&gt; C. Strobel, S. Abramov, J. A. Huisman, O.A. Cirpka, A. Mellage (2022): Spectral Induced Polarization (SIP) of Denitrification-Driven Microbial Activity in Column Experiments Packed with Calcareous Aquifer Sediments (submitted)&lt;/p&gt;
Electronic appendix to: Spectral Induced Polarization (SIP) of Denitrification-Driven Microbial Activity in Column Experiments Packed with Calcareous Aquifer Sediments
2022-09-15

This is the electronic appendix of the publication C. Strobel, S. Abramov, J. A. Huisman, O.A. Cirpka, A. Mellage (2022): Spectral Induced Polarization (SIP) of Denitrification-Driven Microbial Activity in Column Experiments Packed with Calcareous Aquifer Sediments (submitted)
Gravitational Waves from Accretion-Induced Descalarization in Massive Scalar-Tensor Theory
2022-09-16

Many classes of extended scalar-tensor theories predict that dynamical instabilities can take place at high energies, leading to the formation of scalarized neutron stars. Depending on the theory parameters, stars in a scalarized state can form a solution-space branch that shares a lot of similarities with the so-called mass twins in general relativity appearing for equations of state containing first-order phase transitions. Members of this scalarized branch have a lower maximum mass and central energy density compared to Einstein ones. In such cases, a scalarized star could potentially overaccrete beyond the critical mass limit, thus triggering a gravitational phase transition where the star sheds its scalar hair and migrates over to its nonscalarized counterpart. Such an event resembles, but is distinct from, a nuclear or thermodynamic phase transition. We dynamically track a gravitational transition by first constructing hydrostatic, scalarized equilibria for realistic equations of state, and then allowing additional material to fall onto the stellar surface. The resulting bursts of monopolar radiation are dispersively stretched to form a quasicontinuous signal that persists for decades, carrying strains of order ≳10^{-22} (kpc/L)^{3/2} Hz^{-1/2} at frequencies of ≲300 Hz, detectable with the existing interferometer network out to distances of L≲10 kpc, and out to a few hundred kpc with the inclusion of the Einstein Telescope. Electromagnetic signatures of such events, involving gamma-ray and neutrino bursts, are also considered.
Short-Time Transport Properties of Bidisperse Suspensions of Immunoglobulins and Serum Albumins Consistent with a Colloid Physics Picture
2022-09-16

The crowded environment of biological systems such as the interior of living cells is occupied by macromolecules with a broad size distribution. This situation of polydispersity might influence the dependence of the diffusive dynamics of a given tracer macromolecule in a monodisperse solution on its hydrodynamic size and on the volume fraction. The resulting size dependence of diffusive transport crucially influences the function of a living cell. Here, we investigate a simplified model system consisting of two constituents in aqueous solution, namely, of the proteins bovine serum albumin (BSA) and bovine polyclonal gamma-globulin (Ig), systematically depending on the total volume fraction and ratio of these constituents. From high-resolution quasi-elastic neutron spectroscopy, the separate apparent short-time diffusion coefficients for BSA and Ig in the mixture are extracted, which show substantial deviations from the diffusion coefficients measured in monodisperse solutions at the same total volume fraction. These deviations can be modeled quantitatively using results from the short-time rotational and translational diffusion in a two-component hard sphere system with two distinct, effective hydrodynamic radii. Thus, we find that a simple colloid picture well describes short-time diffusion in binary mixtures as a function of the mixing ratio and the total volume fraction. Notably, the self-diffusion of the smaller protein BSA in the mixture is faster than the diffusion in a pure BSA solution, whereas the self-diffusion of Ig in the mixture is slower than in the pure Ig solution.
Children’s sport opportunities and parental support in single-parent families with a lower socio-economic status. An ecological perspective
2022-09-16

Single parents tend to face particular challenges in supporting their children's sport activity. Informed by an ecological perspective, a qualitative interview study was conducted to get an in-depth understanding about how barriers and facilitators shape children's sport opportunities in Swiss single-parent families with lower socio-economic status (SES). In order to estimate the extent to which situations are specific to lower SES single parents, they were contrasted with lower SES two-parent families. Semi-structured interviews with six single parents and five parents from two-parent families were conducted. The findings indicate that lower SES single parents are far more likely to perceive restrictions of parental support in comparison to interviewees from two-parent families. A lack of financial means and a lack of time due to work responsibilities were often found to significantly restrict children's sport opportunities. At the same time, a case-wise analysis revealed great differences among single-parent families, which resulted from a complex interplay of various ecological factors. Barriers and facilitators were identified on the individual level (e.g. parental sport-related beliefs, parental physical health, and children's interest in sport activities), the family level (e.g. the presence of siblings), the meso level (e.g. social support for single parents), and the macro level (e.g. sport opportunities in proximity to the family's home). The results of this study are of relevance to (sport) political actors.
A plant growth model to test for changes in plant–plant interaction over a growing season: the case of kin competition
2022-09-16

Kin recognition and kin selection have long been known to occur in animals where they shape altruistic behavior towards relatives. More recently, studies have found that kin recognition and altered behavior towards kin can also occur in plants. However, inferring the underlying mechanism responsible for variation in plant performance in experimental studies is challenging as often, results can be explained by alternative and non‐exclusive mechanisms such as niche differences, kin competition avoidance and genetic variation in growth rate and competitive ability. Plant–plant interactions may change with the life stage of plants, and competition is often most intense towards the end of plants growing season. However, changes in plant–plant interaction intensity across plants life cycle are rarely considered in kin interaction studies. Here, we adapt a model of plant growth over time modified to specifically include effects of kin and non‐kin competition. The model decompose competitive interactions at different stages during plant growth from initial growth to the end of the growing season. It estimates genotype specific variation in growth rate, and how sensitive individual genotypes are to competition from neighbors. Furthermore, it estimates size asymmetry among plants accounting for both variation in growth rate, neighbor relatedness and resource variation (here water availability). We use this model to analyze the results from a competition experiment where plants grew in mini‐populations with neighbor plants that were either kin or non‐kin. We find that when applied to our experiments, this approach can disentangle kin effects from other effects caused by genotypic variation in growth rate and competitive response to neighbors, and thus significantly help to detect whether plants exhibit kin‐cooperative behavior.
Age-related Macular Degeneration and Current Therapies
2022-09-16

Age-related macular degeneration (AMD) is degenerative retinal eye disease that affects central vision. It is estimated that by 2040, approximately 288 million people in the world might be affected by AMD. Considering the rapidly aging world population, the need for understanding the mechanism of progressive degeneration and developing appropriate treatment methods are increasing. Retinal degeneration in AMD is directly associated with many factors such as smoking, cardiovascular diseases, nutritional and genetic factors, and genes regulating complement, lipid, angiogenic, and extracellular matrix pathways. Studies on therapy development have limitations due to lack of knowledge of pathophysiological mechanism, multifactorial effects and disease progression is different in different patients. Although some therapy studies promise in treating AMD, huge effort is still needed for future drug development. This review focuses on the classification of AMD, underlying pathological mechanism, currently available and developing new treatment opportunities.
CINWA: Database of Cultivated plants and their names in the indigenous languages of South America
2022-09-16

This repository contains source data for CINWA - Database of Cultivated plants and their names in the indigenous languages of South America <br> If you use these data please cite the database Aguilar Panchi, Evelyn Michelle, Saetbyul Lee, Evgenia Brodetsky, and Matthias Urban (eds.). 2022. CINWA - Database of Cultivated plants and their names in the indigenous languages of South America. Version 0.9. Available online at cinwa.org. <br> If you would like to cite specific data entries, please also acknowledge the original source by consulting the reference that is associated with that entry. For example: Cook, Dorothy M., and Frances L. Gralow. 2001. Diccionario bilingüe koreguaje-español español-koreguaje. Santafé de Bogotá: Editorial Alberto Lleras Camargo. In: Aguilar Panchi, Evelyn Michelle, Saetbyul Lee, Evgenia Brodetsky, and Matthias Urban (eds.). 2022. CINWA - Database of Cultivated plants and their names in the indigenous languages of South America. Version 0.9. Available online at cinwa.org.
OASIS: Only Adversarial Supervision for Semantic Image Synthesis
2022-09-17

Abstract Despite their recent successes, generative adversarial networks (GANs) for semantic image synthesis still suffer from poor image quality when trained with only adversarial supervision. Previously, additionally employing the VGG-based perceptual loss has helped to overcome this issue, significantly improving the synthesis quality, but at the same time limited the progress of GAN models for semantic image synthesis. In this work, we propose a novel, simplified GAN model, which needs only adversarial supervision to achieve high quality results. We re-design the discriminator as a semantic segmentation network, directly using the given semantic label maps as the ground truth for training. By providing stronger supervision to the discriminator as well as to the generator through spatially- and semantically-aware discriminator feedback, we are able to synthesize images of higher fidelity and with a better alignment to their input label maps, making the use of the perceptual loss superfluous. Furthermore, we enable high-quality multi-modal image synthesis through global and local sampling of a 3D noise tensor injected into the generator, which allows complete or partial image editing. We show that images synthesized by our model are more diverse and follow the color and texture distributions of real images more closely. We achieve a strong improvement in image synthesis quality over prior state-of-the-art models across the commonly used ADE20K, Cityscapes, and COCO-Stuff datasets using only adversarial supervision. In addition, we investigate semantic image synthesis under severe class imbalance and sparse annotations, which are common aspects in practical applications but were overlooked in prior works. To this end, we evaluate our model on LVIS, a dataset originally introduced for long-tailed object recognition. We thereby demonstrate high performance of our model in the sparse and unbalanced data regimes, achieved by means of the proposed 3D noise and the ability of our discriminator to balance class contributions directly in the loss function. Our code and pretrained models are available at https://github.com/boschresearch/OASIS .
Evidence Based Estimation of Macrodispersivity for Groundwater Transport Applications
2022-09-17

Abstract The scope of this work is to discuss the proper choice of macrodispersion coefficients in modeling contaminant transport through the advection dispersion equation (ADE). It is common to model solute concentrations in transport by groundwater with the aid of the ADE. Spreading is quantified by macrodispersivity coefficients, which are much larger than the laboratory observed pore‐scale dispersivities. In the frame of stochastic theory, longitudinal macrodispersivity is related to the hydraulic conductivity spatial variability via its statistical moments (mean, variance, integral scales), which are generally determined by geostatistical analysis of field measurements. In many cases, especially for preliminary assessment of contaminant spreading, these data are not available and ad hoc values are adopted by practitioners. The present study aims at recommending dispersivity values based on a thorough analysis of tens of field experiments. Aquifers are classified as of weak, medium, and high heterogeneity and for each class a range of macrodispersivity values is recommended. Much less data are available for the transverse macrodispersivities, which are significantly smaller than the longitudinal one. Nevertheless, a few realistic values based on field data, are recommended for applications. Transport models using macrodispersivities can predict mean concentrations, different from the local ones. They can be used for estimation of robust measures, like plumes spatial moments, longitudinal mass distribution and breakthrough curves at control planes.
Chitinase 6 is required for procuticle thickening and organ shape in Drosophila wing
2022-09-17

Abstract The polysaccharide chitin is a major scaffolding molecule in the insect cuticle. In order to be functional, both chitin amounts and chitin organization have been shown to be important parameters. Despite great advances in the past decade, the molecular mechanisms of chitin synthesis and organization are not fully understood. Here, we have characterized the function of the Chitinase 6 (Cht6) in the formation of the wing, which is a simple flat cuticle organ, in the fruit fly Drosophila melanogaster . Reduction of Cht6 function by RNA interference during wing development does not affect chitin organization, but entails a thinner cuticle suggesting reduced chitin amounts. This phenotype is opposed to the one reported recently to be caused by reduction of Cht10 expression. Probably as a consequence, cuticle permeability to xenobiotics is enhanced in Cht6‐less wings. We also observed massive deformation of these wings. In addition, the shape of the abdomen is markedly changed upon abdominal suppression of Cht6. Finally, we found that suppression of Cht6 transcript levels influences the expression of genes coding for enzymes of the chitin biosynthesis pathway. This finding indicates that wing epidermal cells respond to activity changes of Cht6 probably trying to adjust chitin amounts. Together, in a working model, we propose that Cht6‐introduced modifications of chitin are needed for chitin synthesis to proceed correctly. Cuticle thickness, according to our hypothesis, is in turn required for correct organ or body part shape. The molecular mechanisms of this processes shall be characterized in the future.
Metacognitive Information Theory
2022-09-18

The capacity that subjects have to rate confidence in their choices is a form of metacognition, and can be assessed according to bias, sensitivity and efficiency. Rich networks of domain-specific and domain-general regions of the brain are involved in the rating, and are associated with its quality and its use for regulating the processes of thinking and acting. Sensitivity and efficiency are often measured by quantities called meta-d' and the M-ratio that are based on reverse engineering the potential accuracy of the original, primary, choice that is implied by the quality of the confidence judgements. Here, we advocate a straightforward measure of efficiency, called meta-I, which assesses the mutual information between the accuracy of the subject's choices and the confidence reports., and two normalized versions of this measure that quantify efficiency in different regimes. Unlike most other measures, meta-I-based quantities increase with the number of correctly assessed bins with which confidence is reported. We illustrate meta-I on data from a perceptual decision-making task, and via a simple form of simulated second-order metacognitive observer.