julilili42/papers huggingface dataset:
Identification and characterization of Entyloma eschscholziae , a recently introduced pathogen in Europe, and its segregate Entyloma dendromeconis sp. nov.
2023-09-28

Abstract Entyloma includes pathogenic and saprobic species that infect or colonize dicotyledonous host plants. Although most Entyloma species are known only from native areas of occurrence, some species were introduced with their host plants and spread outside their natural areas. The identification of introduced species is important for detection and management of invasive species. In this study, the morphology, phylogeny and species boundaries of Entyloma eschscholziae , recently introduced from North America to Europe, are revisited. Morphology was similar among the type and other specimens of E. eschscholziae analysed on Eschscholzia californica . Both asexual and sexual morphs were observed. The rDNA ITS1‐5.8S‐ITS2 sequences of the E. eschscholziae specimens from Europe and New Zealand and the environmental sequence obtained from grassland soil in California, United States, were identical. Morphological and molecular analyses confirm that the causative agents of white smut on E. californica in native (North America) and introduced (Europe, New Zealand) areas belong to the same species. DNA barcodes obtained in this study (especially ITS sequence from the designated epitype specimen) could be used to facilitate its molecular identification. Specimens on Dendromecon rigida , previously assigned to E. eschscholziae , are morphologically distinct. An attempt to obtain DNA barcode data from degraded holotype material was not successful and no more recent material is available. However, based on the morphological differences and high host specificity found in Entyloma spp., it is appropriate to describe a new species, Entyloma dendromeconis , for this smut pathogen.
Piecewise-Stationary Combinatorial Semi-Bandit with Causally Related Rewards
2023-09-28

We study the piecewise stationary combinatorial semi-bandit problem with causally related rewards. In our nonstationary environment, variations in the base arms’ distributions, causal relationships between rewards, or both, change the reward generation process. In such an environment, an optimal decision-maker must follow both sources of change and adapt accordingly. The problem becomes aggravated in the combinatorial semi-bandit setting, where the decision-maker only observes the outcome of the selected bundle of arms. The core of our proposed policy is the Upper Confidence Bound (UCB) algorithm. We assume the agent relies on an adaptive approach to overcome the challenge. More specifically, it employs a change-point detector based on the Generalized Likelihood Ratio test. Besides, we introduce the notion of group restart as a new alternative restarting strategy in the decision making process in structured environments. Finally, our algorithm integrates a mechanism to trace the variations of the underlying graph structure, which captures the causal relationships between the rewards in the bandit setting. Theoretically, we establish a regret upper bound that reflects the effects of the number of structural- and distribution changes on the performance. The outcome of our numerical experiments in real-world scenarios exhibits applicability and superior performance of our proposal compared to the state-of-the-art benchmarks.
Archaeopedological reconstruction of Middle Bronze Age subsistence farming in SW-Germany from sedimentary archives in the Western Allgäu
2023-09-28

In the northern Alpine foreland, there was a shift at the transition from the Early Bronze Age (EBA, 2200–1600 BCE) to the Middle Bronze Age (MBA, 1600–1250 BCE). This shift was associated with a widespread abandonment of the pile-dwelling settlements around the pre-Alpine lakes and an expansion and intensification of low- and mid-altitude inland settlements. A research gap exists regarding the nature of MBA subsistence in these inland areas, which are considered unfavourable for agriculture. We analysed multi-layered colluvial and alluvial deposits in the agriculturally unfavourable Western Allgäu region to gain insights into MBA subsistence farming. Phases of deposition were determined by optically stimulated luminescence (OSL) technique and AMS radiocarbon (14C) measurements of charcoal. They provide a chronostratigraphic framework that is correlated to the local archaeological record. Subsistence farming was reconstructed using land use proxies such as phytoliths, charcoal spectra, urease activity to microbial biomass carbon (Cmic) ratios, faecal biomarkers, polycyclic aromatic hydrocarbons (PAHs) and heavy metals. The OSL and 14C ages indicate phases of deposition and land use during the MBA. They correlate with two recently excavated MBA inland settlements in the Western Allgäu. Human-induced vegetation change promoted open woodland comprising of Juniperus and Quercus at the expense of Abies and Fagus. The accumulation of charcoal and PAHs in MBA related colluvial horizons is most likely associated with the use of fire to maintain an open landscape. Partially increased urease activity to Cmic ratios and the appearance of Juniperus indicate the importance of livestock farming within the MBA subsistence. Our results show that there was an extensive and diversified subsistence economy in the Western Allgäu during the MBA. They thus reflect an adaptation of MBA farmers to the harsher climatic conditions of the Western Allgäu, where crop yields were certainly less predictable than, for example, in regions near Lake Constance.
On the Nature of the Energy-dependent Morphology of the Composite Multi-TeV Gamma-Ray Source J1702-204
2023-09-28

Abstract HESS J1702-420 is a multi-TeV gamma-ray source with an unusual energy-dependent morphology. The recent H.E.S.S. observations suggest that the emission is well described by a combination of the point-like HESS J1702-420A (dominating at highest energies, ≳30 TeV) and diffuse (∼0.°3) HESS J1702-420B (dominating below ≲5 TeV) sources with very hard (Γ ∼ 1.5) and soft (Γ ∼ 2.6) power-law spectra, respectively. Here, we propose a model that postulates that the proton accelerator is located at the position of HESS J1702-420A and is embedded into a dense molecular cloud that coincides with HESS J1702-420B. In the proposed model, the very-high-energy radiation of HESS J1702-420 is explained by pion-decay emission from the continuously injected relativistic protons propagating through a dense cloud. The energy-dependent morphology is defined by the diffusive nature of the low-energy proton propagation, transiting sharply to (quasi) ballistic propagation at higher energies. Adopting a strong energy dependence of the diffusion coefficient, D ∝ E β with β ≥ 1, we argue that HESS J1702-420 as a system of two gamma-ray sources is the result of the propagation effect. Protons injected by a single accelerator at a rate <?CDATA ?> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:msub> <mml:mrow> <mml:mi>Q</mml:mi> </mml:mrow> <mml:mrow> <mml:mn>0</mml:mn> </mml:mrow> </mml:msub> <mml:mo>≃</mml:mo> <mml:msup> <mml:mrow> <mml:mn>10</mml:mn> </mml:mrow> <mml:mrow> <mml:mn>38</mml:mn> </mml:mrow> </mml:msup> <mml:mspace width="0.25em" /> <mml:msup> <mml:mrow> <mml:mo stretchy="false">(</mml:mo> <mml:msub> <mml:mrow> <mml:mi>n</mml:mi> </mml:mrow> <mml:mrow> <mml:mn>0</mml:mn> </mml:mrow> </mml:msub> <mml:mrow> <mml:mo stretchy="true">/</mml:mo> </mml:mrow> <mml:mn>100</mml:mn> <mml:mspace width="0.25em" /> <mml:mspace width="0.25em" /> <mml:msup> <mml:mrow> <mml:mi>cm</mml:mi> </mml:mrow> <mml:mrow> <mml:mo>−</mml:mo> <mml:mn>3</mml:mn> </mml:mrow> </mml:msup> <mml:mo stretchy="false">)</mml:mo> </mml:mrow> <mml:mrow> <mml:mo>−</mml:mo> <mml:mn>1</mml:mn> </mml:mrow> </mml:msup> <mml:mspace width="0.25em" /> <mml:msup> <mml:mrow> <mml:mo stretchy="false">(</mml:mo> <mml:mi>d</mml:mi> <mml:mrow> <mml:mo stretchy="true">/</mml:mo> </mml:mrow> <mml:mn>0.25</mml:mn> <mml:mspace width="0.25em" /> <mml:mi>kpc</mml:mi> <mml:mo stretchy="false">)</mml:mo> </mml:mrow> <mml:mrow> <mml:mo>−</mml:mo> <mml:mn>1</mml:mn> </mml:mrow> </mml:msup> <mml:mspace width="0.25em" /> <mml:mi>erg</mml:mi> <mml:mspace width="0.25em" /> <mml:msup> <mml:mrow> <mml:mi mathvariant="normal">s</mml:mi> </mml:mrow> <mml:mrow> <mml:mo>−</mml:mo> <mml:mn>1</mml:mn> </mml:mrow> </mml:msup> </mml:math> can reasonably reproduce the morphology and fluxes of the two gamma-ray components.
Cooperative Thresholded Lasso for Sparse Linear Bandit
2023-09-28

We present a novel approach to address the multi-agent sparse contextual linear bandit problem, in which the feature vectors have a high dimension d whereas the reward function depends on only a limited set of features - precisely s0 ≪ d. Furthermore, the learning follows under information-sharing constraints. The proposed method employs Lasso regression for dimension reduction, allowing each agent to independently estimate an approximate set of main dimensions and share that information with others depending on the network’s structure. The information is then aggregated through a specific process and shared with all agents. Each agent then resolves the problem with ridge regression focusing solely on the extracted dimensions. We represent algorithms for both a star-shaped network and a peer-to-peer network. The approaches effectively reduce communication costs while ensuring minimal cumulative regret per agent. Theoretically, we show that our proposed methods have a regret bound of order O(s0 log d + s0 √T) with high probability, where T is the time horizon. To our best knowledge, it is the first algorithm that tackles row-wise distributed data in sparse linear bandits, achieving comparable performance compared to the state-of-the-art single and multi-agent methods. Besides, it is widely applicable to high-dimensional multi-agent problems where efficient feature extraction is critical for minimizing regret. To validate the effectiveness of our approach, we present experimental results on both synthetic and real-world datasets.
Creation rate of Dirac particles at a point source
2023-09-28

Abstract Only recently has it been possible to construct a self-adjoint Hamiltonian that involves the creation of Dirac particles at a point source in 3d space. Its definition makes use of an interior-boundary condition. Here, we develop for this Hamiltonian a corresponding theory of the Bohmian configuration. That is, we (non-rigorously) construct a Markov jump process <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:mo stretchy="false">(</mml:mo> <mml:msub> <mml:mi>Q</mml:mi> <mml:mi>t</mml:mi> </mml:msub> <mml:mrow> <mml:msub> <mml:mo stretchy="false">)</mml:mo> <mml:mrow> <mml:mi>t</mml:mi> <mml:mo>∈</mml:mo> <mml:mrow> <mml:mi mathvariant="double-struck">R</mml:mi> </mml:mrow> </mml:mrow> </mml:msub> </mml:mrow> </mml:math> in the configuration space of a variable number of particles that is <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:mrow> <mml:mo>|</mml:mo> </mml:mrow> <mml:msub> <mml:mi>ψ</mml:mi> <mml:mi>t</mml:mi> </mml:msub> <mml:msup> <mml:mrow> <mml:mo>|</mml:mo> </mml:mrow> <mml:mn>2</mml:mn> </mml:msup> </mml:math> -distributed at every time t and follows Bohmian trajectories between the jumps. The jumps correspond to particle creation or annihilation events and occur either to or from a configuration with a particle located at the source. The process is the natural analog of Bell’s jump process, and a central piece in its construction is the determination of the rate of particle creation. The construction requires an analysis of the asymptotic behavior of the Bohmian trajectories near the source. We find that the particle reaches the source with radial speed 0, but orbits around the source infinitely many times in finite time before absorption (or after emission).
Multiepitope-based vaccine design against DiiA inStreptococcus pneumoniae, An immunoinformatics approach
2023-09-28

Abstract Streptococcus pneumoniae (SPN) infection has resulted in significant morbidity and mortality worldwide in children and adults. It is responsible for colonizing the human nasopharynx and can also cause diseases, including otitis media, pneumonia, bacteraemia, and meningitis. SPN is exhibiting resistance to multiple antibiotics and current vaccines have a number of limitations including poor immunogenicity and limited effectiveness against all pneumococcal serotypes. Here, we explain the design of a novel multi-epitope vaccine using Dimorphic invasion-involved protein A (DiiA) as a target protein. For designing the vaccine, the sequence of DiiA was obtained and various bioinformatics tools were employed to predict multiple CTL, HTL, B lymphocyte epitopes of DiiA. After evaluating antigenicity, allergenicity, toxicity, and immunogenicity, the most promising epitopes were chosen for constructing the vaccine, followed by an analysis of their physicochemical and immunological characteristics.The prediction, refinement, and validation of the 3D structure of the vaccine were carried out. Molecular docking, molecular dynamic simulation, and immune simulation were executed to examine the binding affinities and biological interactions at the atomic level between the vaccine and Toll-like receptor (TLR4). Vaccine translation, codon optimization were performed and expression efficiency was assessed through an in-silico cloning experiment performed to transfer into pET28a(+) plasmid vector.The obtained results proved that the vaccine maintained structural stability and possessed the capability to stimulate an efficient immune response against S. pneumoniae infection. The constructed vaccine has the potential for subsequent wet lab experimentation, leading to the development of an innovative vaccine.
Reviewer #1 (Public Review): The retina uncouples glycolysis and oxidative phosphorylation via Cori-, Cahill-, and mini-Krebs-cycle
2023-09-28

The retina consumes massive amounts of energy, yet its metabolism and substrate exploitation remain poorly understood. Here, we used a murine explant model to manipulate retinal energy metabolism under entirely controlled conditions and utilized 1H-NMR spectroscopy-based metabolomics, in situ enzyme detection, and cell viability readouts to uncover the pathways of retinal energy production. Our experimental manipulations resulted in varying degrees of photoreceptor degeneration, while the inner retina and retinal pigment epithelium were essentially unaffected. This selective vulnerability of photoreceptors suggested very specific adaptations in their energy metabolism. Rod photoreceptors were found to rely strongly on oxidative phosphorylation, but only mildly on glycolysis. Conversely, cone photoreceptors were highly dependent on glycolysis but insensitive to electron transport chain decoupling. Importantly, photoreceptors were able to uncouple glycolytic and Krebs-cycle metabolism via three different pathways: 1) the mini-Krebs-cycle, fueled by glutamine and branched-chain amino acids, generating N-acetylaspartate; 2) the alanine-generating Cahill-cycle; 3) the lactate-releasing Cori-cycle. Moreover, the metabolomic data indicated a shuttling of taurine and hypotaurine between the retinal pigment epithelium and photoreceptors, resulting in an additional net transfer of reducing power to photoreceptors. These findings expand our understanding of retinal physiology and pathology and shed new light on neuronal energy homeostasis and the pathogenesis of neurodegenerative diseases.Retinal photoreceptors employ both glucose and glutamate as fuels. While rod photoreceptors rely strongly on oxidative phosphorylation and the N-acetylaspartate producing mini-Krebs-cycle, cone photoreceptors rely on the lactate-producing Cori cycle and the oxidative, alanine-producing Cahill cycle.
The Legal and Data Protection Concept for the Operation of the German Human Genome-Phenome Archive (GHGA)
2023-09-28

&lt;p&gt;In this white paper we will describe the legal and data protection concept for GHGA, and how its development was shaped by the legal and data protection obligations under which GHGA operates.&lt;/p&gt;
Logarithmic negativity in out-of-equilibrium open free-fermion chains: An exactly solvable case
2023-09-29

We derive the quasiparticle picture for the fermionic logarithmic negativity in a tight-binding chain subject to gain and loss dissipation. We focus on the dynamics after the quantum quench from the fermionic Néel state. We consider the negativity between both adjacent and disjoint intervals embedded in an infinite chain. Our result holds in the standard hydrodynamic limit of large subsystems and long times, with their ratio fixed. Additionally, we consider the weakly-dissipative limit, in which the dissipation rates are inversely proportional to the size of the intervals. We show that the negativity is proportional to the number of entangled pairs of quasiparticles that are shared between the two intervals, as is the case for the mutual information. Crucially, in contrast with the unitary case, the negativity content of quasiparticles is not given by the Rényi entropy with Rényi index 1/2 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mn>1</mml:mn><mml:mi>/</mml:mi><mml:mn>2</mml:mn></mml:mrow></mml:math> , and it is in general not easily related to thermodynamic quantities.
School-to-Work Transitions under Unequal Conditions: A Regionalised Perspective on the ‘Discouraged Worker’ Hypothesis
2023-09-29

Against the background of considerable regional disparities, we test the “discouraged worker” hypothesis, which postulates that poor regional socioeconomic conditions foster students’ aspirations for more education, ultimately leading to an extension of their educational careers. Our two dependent variables are (i) whether students aspire to prolong their general school careers or enter vocational training and (ii) whether they in fact prolong their school careers. To that end, we link regional-level data to individual-level data from the German National Educational Panel Study (NEPS). To describe regional conditions adequately, we illustrate geographical patterns in socioeconomic conditions relevant for school-to-work transitions (e.g., labour market conditions and availability of vocational training opportunities). We compare two operationalisations of regional areas: (i) administrative districts and (ii) public transport areas. Our results show that students are more likely to aspire to prolong their general school careers in socioeconomically deprived regions. Moreover, the effects are stronger when school-based vocational training opportunities are scarce. The effects on actual transitions vary according to the school track attended and the availability of educational alternatives in the general school system. Finally, the operationalisation of regions varies regarding effect sizes and corresponding levels of statistical significance.
Number Express: a Digital Game to Improve Early Numeracy
2023-09-29

Early numeracy (including basic skills like counting, order processing, etc.) has repeatedly been observed to predict later scholastic but also vocational prospects. As such, it seems sensible to foster it early on during development. In this article, we describe the development and initial evaluation of Number Express, a digital game designed to facilitate numerical skills in pre-and primary school considering the latest evidence from research on order processing. The game consists of a train with six carriages for the player to fill in with numbers in the correct order. The game progresses in difficulty across several levels, moving from smaller to larger numbers and sequences in steps of 2, 5, and 10. Informative feedback helps players in case they respond wrongly. Associating numbers to carriages in the correct order earns the player points, with which they can buy items in a virtual shop, providing additional experience with calculating with money. During the design phase, we sought feedback from researchers, teachers, and an education consultant specialising in the learning and teaching of primary mathematics. Piloting will involve testing the game with a small group of preschool children to evaluate its playability and ease of use and to resolve any remaining technical issues. Additionally, we will gather feedback from children to identify any areas of the game that might be improved or made more engaging. In the next step, the game will be implemented in an intervention study to determine its effectiveness in improving children's early numeracy skills. In case the game proves to be effective in improving children's early numeracy skills, it has the potential to be a valuable tool for educators and parents in supporting their children's numerical development.
Acute and chronic psychosocial stress by the brain-derived neurotrophic factor in male humans: a highly standardized and controlled study
2023-09-29

Abstract Objective The neurotrophic protein brain-derived neurotrophic factor (BDNF) plays a pivotal role in brain function and is affected by acute and chronic stress. We here investigate the patterns of BDNF and cortisol stress reactivity and recovery under the standardized stress protocol of the TSST and the effect of perceived chronic stress on the basal BDNF levels in healthy young men. Methods Twenty-nine lean young men underwent the Trier Social Stress Test (TSST) and a resting condition. Serum BDNF and cortisol were measured before and repeatedly after both conditions. The perception of chronic stress was assessed by the Trier Inventory for Chronic Stress (TICS). Results After the TSST, there was a significant increase over time for BDNF and cortisol. Stronger increase in cortisol in response to stress was linked to an accelerated BDNF decline after stress. Basal resting levels of BDNF was significantly predicted by chronic stress perception. Conclusions The increased BDNF level following psychosocial stress suggest a stress-induced neuroprotective mechanism. The presumed interplay between BDNF and the HPA-axis indicates an antagonistic relationship of cortisol on BDNF recovery post-stress. Chronically elevated high cortisol levels, as present in chronic stress, could thereby contribute to reduced neurogenesis, and an increased risk of neurodegenerative conditions in persons suffering from chronic stress. Highlights Acute psychosocial stress increases serum BDNF and cortisol Stress-induced cortisol secretion may accelerate the decline of BDNF after stress. Chronic stress is linked to lower basal serum BDNF levels