julilili42/papers huggingface dataset:
The ROCEEH Out of Africa Database (ROAD): A large-scale research database serves as an indispensable tool for human evolutionary studies
2023-08-01

Large scale databases are critical for helping scientists decipher long-term patterns in human evolution. This paper describes the conception and development of such a research database and illustrates how big data can be harnessed to formulate new ideas about the past. The Role of Culture in Early Expansions of Humans (ROCEEH) is a transdisciplinary research center whose aim is to study the origins of culture and the multifaceted aspects of human expansions across Africa and Eurasia over the last three million years. To support its research, the ROCEEH team developed an online tool named the ROCEEH Out of Africa Database (ROAD) and implemented its web-based applications. ROAD integrates geographical data as well as archaeological, paleoanthropological, paleontological and paleobotanical content within a robust chronological framework. In fact, a unique feature of ROAD is its ability to dynamically link scientific data both spatially and temporally, thereby allowing its reuse in ways that were not originally conceived. The data stem from published sources spanning the last 150 years, including those generated by the research team. Descriptions of these data rely on the development of a standardized vocabulary and profit from online explanations of each table and attribute. By synthesizing legacy data, ROAD facilitates the reuse of heritage data in novel ways. Database queries yield structured information in a variety of interoperable formats. By visualizing data on maps, users can explore this vast dataset and develop their own theories. By downloading data, users can conduct further quantitative analyses, for example with Geographic Information Systems, modeling programs and artificial intelligence. In this paper, we demonstrate the innovative nature of ROAD and show how it helps scientists studying human evolution to access datasets from different fields, thereby connecting the social and natural sciences. Because it permits the reuse of “old” data in new ways, ROAD is now an indispensable tool for researchers of human evolution and paleogeography.
PowerBEV: A Powerful Yet Lightweight Framework for Instance Prediction in Bird’s-Eye View
2023-08-01

Accurately perceiving instances and predicting their future motion are key tasks for autonomous vehicles, enabling them to navigate safely in complex urban traffic. While bird’s-eye view (BEV) representations are commonplace in perception for autonomous driving, their potential in a motion prediction setting is less explored. Existing approaches for BEV instance prediction from surround cameras rely on a multi-task auto-regressive setup coupled with complex post-processing to predict future instances in a spatio-temporally consistent manner. In this paper, we depart from this paradigm and propose an efficient novel end-to-end framework named PowerBEV, which differs in several design choices aimed at reducing the inherent redundancy in previous methods. First, rather than predicting the future in an auto-regressive fashion, PowerBEV uses a parallel, multi-scale module built from lightweight 2D convolutional networks. Second, we show that segmentation and centripetal backward flow are sufficient for prediction, simplifying previous multi-task objectives by eliminating redundant output modalities. Building on this output representation, we propose a simple, flow warping-based post-processing approach which produces more stable instance associations across time. Through this lightweight yet powerful design, PowerBEV outperforms state-of-the-art baselines on the NuScenes Dataset and poses an alternative paradigm for BEV instance prediction. We made our code publicly available at: https://github.com/EdwardLeeLPZ/PowerBEV.
The Vanishing of the Primary Emission Region in PKS 1510–089
2023-08-01

Abstract In 2021 July, PKS 1510−089 exhibited a significant flux drop in the high-energy γ -ray (by a factor 10) and optical (by a factor 5) bands and remained in this low state throughout 2022. Similarly, the optical polarization in the source vanished, resulting in the optical spectrum being fully explained through the steady flux of the accretion disk and the broad-line region. Unlike the aforementioned bands, the very-high-energy γ -ray and X-ray fluxes did not exhibit a significant flux drop from year to year. This suggests that the steady-state very-high-energy γ -ray and X-ray fluxes originate from a different emission region than the vanished parts of the high-energy γ -ray and optical jet fluxes. The latter component has disappeared through either a swing of the jet away from the line of sight or a significant drop in the photon production efficiency of the jet close to the black hole. Either change could become visible in high-resolution radio images.
Impact of Biogenic Magnetite Formation and Transformation on Biogeochemical Cycles
2023-08-01

Magnetite is a redox-active mineral that can form from both abiotic and biotic processes, and plays an active role in different biogeochemical cycles. Biogenic magnetite particles have properties that differ from their abiogenic counterparts in a variety of ways, including their size, chemical purity, magnetic properties, and association with biomass-derived organic matter. These properties directly influence magnetite reactivity—in particular its sorbent and redox behavior—affecting its association with metals, oxyanions, and other compounds in the environment. Biogenic (and abiogenic) magnetite particles are involved in redox processes by storing electrons, functioning as biogeobatteries, and by transferring electrons between microbial cells or between cells and inorganic constituents. Thus, magnetite influences the fate of contaminants and nutrients in the environment.
Area deprivation and demographic factors associated with diabetes technology use in adults with type 1 diabetes in Germany
2023-08-01

Introduction Diabetes technology improves glycemic control and quality of life for many people with type 1 diabetes (T1D). However, inequalities in access to diabetes technology exist in many countries. In Germany, disparities in technology use have been described in pediatric T1D, but no data for adults are available so far. We therefore aimed to analyze whether demographic factors and area deprivation are associated with technology use in a representative population of adults with T1D. Materials and methods In adults with T1D from the German prospective diabetes follow-up registry (DPV), we analyzed the use of continuous subcutaneous insulin infusion (CSII), continuous glucose monitoring (CGM), and sensor augmented pump therapy (SAP, with and without automated insulin delivery) in 2019-2021 by age group, gender, migration background, and area deprivation using multiple adjusted regression models. Area deprivation, defined as a relative lack of area-based resources, was measured by quintiles of the German index of Multiple Deprivation (GIMD 2015, from Q1, least deprived, to Q5, most deprived districts). Results Among 13,351 adults with T1D, the use of technology decreased significantly with older age: CSII use fell from 56.1% in the 18−&amp;lt;25-year age group to 3.1% in the ≥80-year age group, CGM use from 75.3% to 28.2%, and SAP use from 45.1% to 1.5% (all p for trend &amp;lt;0.001). The use of technology was also significantly higher in women than in men (CSII: 39.2% vs. 27.6%; CGM: 61.9% vs. 58.0%; SAP: 28.7% vs. 19.6%, all p &amp;lt;0.001), and in individuals without migration background than in those with migration background (CSII: 38.8% vs. 27.6%; CGM: 71.1% vs. 61.4%; SAP: 30.5% vs. 21.3%, all p &amp;lt;0.001). Associations with area deprivation were not linear: the use of each technology decreased only from Q2 to Q4. Discussion Our real-world data provide evidence that higher age, male gender, and migration background are currently associated with lower use of diabetes technology in adults with T1D in Germany. Associations with area deprivation are more complex, probably due to correlations with other factors, like the higher proportion of migrants in less deprived areas or the federal structure of the German health care system.
TCR-engaging scaffolds selectively expand antigen-specific T-cells with a favorable phenotype for adoptive cell therapy
2023-08-01

Background Adoptive cell therapy (ACT) has shown promising results for the treatment of cancer and viral infections. Successful ACT relies on ex vivo expansion of large numbers of desired T-cells with strong cytotoxic capacity and in vivo persistence, which constitutes the greatest challenge to current ACT strategies. Here, in this study, we present a novel technology for ex vivo expansion of antigen-specific T-cells; artificial antigen-presenting scaffolds (Ag-scaffolds) consisting of a dextran-polysaccharide backbone, decorated with combinations of peptide-Major Histocompatibility Complex (pMHC), cytokines and co-stimulatory molecules, enabling coordinated stimulation of antigen-specific T-cells. Methods The capacity of Ag-scaffolds to expand antigen-specific T-cells was explored in ex vivo cultures with peripheral blood mononuclear cells from healthy donors and patients with metastatic melanoma. The resulting T-cell products were assessed for phenotypic and functional characteristics. Results We identified an optimal Ag-scaffold for expansion of T-cells for ACT, carrying pMHC and interleukin-2 (IL-2) and IL-21, with which we efficiently expanded both virus-specific and tumor-specific CD8+ T cells from peripheral blood of healthy donors and patients, respectively. The resulting T-cell products were characterized by a high frequency of antigen-specific cells with high self-renewal capacity, low exhaustion, a multifunctional cytokine profile upon antigen-challenge and superior tumor killing capacity. This demonstrates that the coordinated stimuli provided by an optimized stoichiometry of TCR engaging (pMHC) and stimulatory (cytokine) moieties is essential to obtain desired T-cell characteristics. To generate an ‘off-the-shelf’ multitargeting Ag-scaffold product of relevance to patients with metastatic melanoma, we identified the 30 most frequently recognized shared HLA-A0201-restricted melanoma epitopes in a cohort of 87 patients. By combining these in an Ag-scaffold product, we were able to expand tumor-specific T-cells from 60–70% of patients with melanoma, yielding a multitargeted T-cell product with up to 25% specific and phenotypically and functionally improved T cells. Conclusions Taken together, the Ag-scaffold represents a promising new technology for selective expansion of antigen-specific CD8+ T cells directly from blood, yielding a highly specific and functionally enhanced T-cell product for ACT.
Timing and origin of skarn-, greisen-, and vein-hosted tin mineralization at Geyer, Erzgebirge (Germany)
2023-08-01

Abstract This contribution presents new insights into the origin and age relationships of the Geyer tin deposit in the Erzgebirge, Germany. Tin mineralization occurs in skarns, greisen, and in cassiterite-bearing fluorite-quartz veins. Skarn alteration replaces marble layers of the Cambrian Jáchymov Group and occurs in two clearly distinct stages. The first skarn stage forms skarnoid textured assemblages of clinopyroxene, garnet, and wollastonite with no tin phases recognized. Garnet U-Pb ages of this skarn stage (~322 Ma) relate the earlier skarn stage to the emplacement of the Ehrenfriedersdorf granite (~324 to 317 Ma). The second stage of skarn alteration is marked by the occurrence of malayaite and cassiterite associated with garnet recording ages of 307 to 301 Ma. Greisen- and skarn-hosted cassiterite-bearing veins provide U-Pb ages in the range of 308 to 305 Ma, relating greisenization and vein formation to the same magmatic-hydrothermal event as the second skarn stage. This suggests that tin mineralization at Geyer is related to a distinctly younger magmatic-hydrothermal event, clearly postdating the Ehrenfriedersdorf granite, which was previously assumed as the source of the tin-rich fluids. Fluid inclusions show salinities in the range of 1.0 to 31.5 % eq. w(NaCl±CaCl 2 ) and homogenization temperatures between 255 and 340 °C. Cassiterite-associated fluid inclusions show indications for heterogeneous entrapment and dilution of hydrothermal with meteoric fluids. Dilution of high-salinity fluids with low-salinity fluids and cooling of the system was probably a decisive process in the precipitation of cassiterite in the Geyer Sn system.
Fetal Assessment in Pregnancy (Indication and Methodology for Fetal Monitoring in a Low-risk Population). Guideline of the DGGG, DEGUM, OEGGG and SGGG (S3-Level, AWMF Registry No. 015/089, February 2023)
2023-08-01

Abstract Purpose The aim of this guideline was to find evidence on whether carrying out Doppler examinations and CTGs in low-risk cohorts of pregnant women improves outcomes. Methods First, a systematic search for guidelines was carried out. Identified guidelines were evaluated using the DELPHI instrument of the AWMF. Three guidelines were found to be suitable to evaluate CTG. Two DEGUM best practice guidelines were judged suitable to describe the methods. All studies on this issue were additionally analyzed using 8 PICO questions. A structured consensus of the participating professional societies was achieved using a nominal group process and a structured consensus conference moderated by an independent moderator. Recommendations No antepartum Doppler sonography examinations should be carried out in low-risk cohorts in the context of antenatal care. No antepartum CTG should be carried out in low-risk cohorts. Note The guideline will be published simultaneously in the official journals of both professional societies (i.e., Geburtshilfe und Frauenheilkunde for the DGGG and Ultraschall in der Medizin/European Journal of Ultrasound for the DEGUM).
Interactive cognitive maps support flexible behavior under threat
2023-08-01

In social environments, survival can depend upon inferring and adapting to other agents' goal-directed behavior. However, it remains unclear how humans achieve this, despite the fact that many decisions must account for complex, dynamic agents acting according to their own goals. Here, we use a predator-prey task (total n = 510) to demonstrate that humans exploit an interactive cognitive map of the social environment to infer other agents' preferences and simulate their future behavior, providing for flexible, generalizable responses. A model-based inverse reinforcement learning model explained participants' inferences about threatening agents' preferences, with participants using this inferred knowledge to enact generalizable, model-based behavioral responses. Using tree-search planning models, we then found that behavior was best explained by a planning algorithm that incorporated simulations of the threat's goal-directed behavior. Our results indicate that humans use a cognitive map to determine other agents' preferences, facilitating generalized predictions of their behavior and effective responses.
Association of MTHFR Polymorphisms With Leukoencephalopathy Risk in Patients With Primary CNS Lymphoma Treated With Methotrexate-Based Regimens
2023-08-01

The <i>MTHFR</i> 1298A→C genotype may serve to identify patients with PCNSL at elevated risk of HD-MTX-induced leukoencephalopathy. This seems to translate into reduced survival, potentially due to decreased functional status.
Impact of a recent wildfire on tortoises at Cape Point, South Africa, and implications for the interpretation of heated bones in the archaeological record
2023-08-01

Abstract Heat-altered bones are a common occurrence in the archaeological record, and their analysis can provide detailed insights into past fire use behaviors and subsistence strategies. Heat-altered bones, however, may also result from natural fire events such as wildfires that are unrelated to human activity. We currently lack robust reference materials from natural fire events, analyzed using the same methodological approaches as we apply them to archaeological assemblages, that can be used to differentiate between natural and anthropogenic origins of heated materials. Here, we studied an assemblage of 50 tortoises that perished in a brushfire in Cape Point, South Africa. We used a combination of (1) zooarchaeological assessments of heating pattern and (2) infrared spectroscopy including a heating experiment to reconstruct heating temperatures with the aim to document the fire impact on the tortoise remains. For both approaches, we used statistical models to develop and test predictions that can also be applied to archaeological material. Our analyses suggest a quickly moving and low temperature brushfire in the study region with a generally low and superficial heating impact on the tortoise remains. However, we also observed several high-temperature alterations with calcination and speculate that naturally occurring fuel sources controlled the severity of the fire impact. The evidence of heating on the tortoise was unpatterned. We conclude that temperature alone presents a low confidence deciding factor between wildfires and campfires while skeletal heating pattern, in concert with other contextual analysis, may be able to facilitate this distinction with more localized heating signatures for campfires.
A drought year favored drier‐adapted origins over local origins in a reciprocal transplant experiment along a rainfall gradient
2023-08-01

When plant populations show local adaptation along climatic gradients, climate change may displace them from their current fitness optima. Unclear is whether foreign genotypes originating from sites that approximate future climatic conditions can attain higher fitness and support existing populations, because foreign genotypes may lack important adaptations to other local conditions besides climate. We conducted a fully reciprocal transplant experiment with the winter annual Biscutella didyma across four sites along a steep natural rainfall gradient in Israel. It experienced an exceptional drought event that approximated future climatic conditions. This unique opportunity allowed to test whether genotypes transplanted from drier sites outperform local genotypes under a drier climate. The four population origins showed consistent clines in germination fraction, phenology, and vegetative biomass that suggest local adaptation along the rainfall gradient. In terms of fitness (survival, seed number), however, local origins were outperformed by genotypes originating from the next‐drier site along the gradient. Our results suggest that the experienced drought conditions favored origins from drier conditions over local origins despite local biotic interactions. Genotypes originating from drier sites may thus support existing populations and reduce their vulnerability to climate change. Moreover, we conceptualize under which conditions foreign genotypes may benefit local populations in general, which adds to clarify the importance of local adaptation to climatic and nonclimatic factors for populations under climate change.
High Productivity at High Latitudes? Photosynthesis and Leaf Ecophysiology in Arctic Forests of the Eocene
2023-08-01

Abstract The Arctic forests of the Eocene, which thrived under elevated CO 2 , a temperate climate, high precipitation and annually extremely different daylengths, represent a quite spectacular no‐analogue habitat of Earth's greenhouse past. The aim of this study was to improve our understanding of the ecophysiology of Arctic broad‐leaved deciduous forests of the Eocene, by analyzing leaf photosynthesis and tree productivity based on gas exchange modeling for two fossil Eocene sites, Svalbard and Ellesmere Island. For this, a single‐leaf photosynthesis model that includes heat transfer and leaf senescence was derived. Environmental conditions were based on available palaeoclimate data and a CO 2 level of 800 μmol/mol. Additionally, different light regimes (diffusivity and transmissivity) were considered. With this model, annual photosynthesis was calculated on the basis of annual temperature and day lengths (derived by celestial mechanics). To obtain productivity of a whole deciduous broad‐leaved tree, the single leaf data were then upscaled by a canopy model. The results indicate that productivity was enhanced at both high latitude sites by elevated CO 2 , temperature of the growing season and high maximum daylength (24 hr) during late spring and early summer. With productivity values about 30%–60% higher as for a mid‐latitude continental European forest, the results indicate a potential for high productivity at the Eocene polar sites which is in the range of extant tropical forests. In contrast to speculations, no evidence for a selective advantage of large leaf size—as shown by various fossil leaves from high latitude sites—could be found.
The design of functional proteins using tensorized energy calculations
2023-08-01

In protein design, the energy associated with a huge number of sequence-conformer perturbations has to be routinely estimated. Hence, enhancing the throughput and accuracy of these energy calculations can profoundly improve design success rates and enable tackling more complex design problems. In this work, we explore the possibility of tensorizing the energy calculations and apply them in a protein design framework. We use this framework to design enhanced proteins with anti-cancer and radio-tracing functions. Particularly, we designed multispecific binders against ligands of the epidermal growth factor receptor (EGFR), where the tested design could inhibit EGFR activity <i>in vitro</i> and <i>in vivo</i>. We also used this method to design high-affinity Cu<sup>2+</sup> binders that were stable in serum and could be readily loaded with copper-64 radionuclide. The resulting molecules show superior functional properties for their respective applications and demonstrate the generalizable potential of the described protein design approach.
Costs and benefits of voluntary attention in crows
2023-08-01

Behavioural signatures of voluntary, endogenous selective attention have been found in both mammals and birds, but the relationship between performance benefits at attended and costs at unattended locations remains unclear. We trained two carrion crows ( Corvus corone ) on a Posner-like spatial cueing task with dissociated cue and target locations, using both highly predictive and neutral central cues to compare reaction time (RT) and detection accuracy for validly, invalidly and neutrally cued targets. We found robust RT effects of predictive cueing at varying stimulus-onset asynchronies (SOA) that resulted from both advantages at cued locations and costs at un-cued locations. Both crows showed cueing effects around 15–25 ms with an early onset at 100 ms SOA, comparable to macaques. Our results provide a direct assessment of costs and benefits of voluntary attention in a bird species. They show that crows are able to guide spatial attention using associative cues, and that the processing advantage at attended locations impairs performance at unattended locations.