julilili42/papers huggingface dataset:
Modeling disk fragmentation and multiplicity in massive star formation
2020-11-27

\\nContext. There is growing evidence that massive stars grow by disk accretion in a similar way to their low-mass counterparts. Early in evolution, these disks can achieve masses that are comparable to the current stellar mass, and therefore the forming disks are highly susceptible to gravitational fragmentation.\\nAims. We investigate the formation and early evolution of an accretion disk around a forming massive protostar, focussing on its fragmentation physics. To this end, we follow the collapse of a molecular cloud of gas and dust, the formation of a massive protostar, the formation of its circumstellar disk, and the formation and evolution of the disk fragments.\\nMethods. We used a grid-based, self-gravity radiation hydrodynamics code including a sub-grid module for stellar evolution and dust evolution. We purposely do not use a sub-grid module for fragmentation such as sink particles to allow for all paths of fragment formation and destruction, but instead we keep the spatial grid resolution high enough to properly resolve the physical length scales of the problem, namely the pressure scale height and Jeans length of the disk. Simulations are performed on a grid in spherical coordinates with a logarithmic spacing of the grid cells in the radial direction and a cosine distribution of the grid cells in the polar direction, focusing the spatial resolution on the disk midplane. As a consequence, roughly 25% of the total number of grid cells, corresponding to ~26 million grid cells, are used to model the disk physics. These constitute the highest resolution simulations performed up to now on disk fragmentation around a forming massive star with the physics considered here. For a better understanding of the effects of spatial resolution and to compare our high-resolution results with previous lower resolution studies in the literature, we perform the same simulation at five different resolutions, each run differing in resolution from its predecessor by a factor of two.\\nResults. The cloud collapses and a massive (proto)star is formed in its center surrounded by a fragmenting Keplerian-like accretion disk with spiral arms. The fragments have masses of ~1 M⊙, and their continuous interactions with the disk, spiral arms, and other fragments result in eccentric orbits. Fragments form hydrostatic cores surrounded by secondary disks with spiral arms that also produce new fragments. We identified several mechanisms of fragment formation, interaction, and destruction. Central temperatures of the fragments can reach the hydrogen dissociation limit, form second Larson cores, and evolve into companion stars. Based on this, we study the multiplicity predicted by the simulations and find approximately six companions at different distances from the primary: from possible spectroscopic multiples, to companions at distances between 1000 and 2000 au. \\n
The influence of infall on the properties of protoplanetary discs
2020-11-27

Context. The properties of protoplanetary discs determine the conditions for planet formation. In addition, planets can already form during the early stages of infall. Aims. We constrain physical quantities such as the mass, radius, lifetime, and gravitational stability of protoplanetary discs by studying their evolution from formation to dispersal. Methods. We perform a population synthesis of protoplanetary discs with a total of 50 000 simulations using a 1D vertically integrated viscous evolution code, studying a parameter space of final stellar mass from 0.05 to 5 M ⊙ . Each star-and-disc system is set up shortly after the formation of the protostar and fed by infalling material from the parent molecular cloud core. Initial conditions and infall locations are chosen based on the results from a radiation-hydrodynamic population synthesis of circumstellar discs. We also consider a different infall prescription based on a magnetohydrodynamic (MHD) collapse simulation in order to assess the influence of magnetic fields on disc formation. The duration of the infall phase is chosen to produce a stellar mass distribution in agreement with the observationally determined stellar initial mass function. Results. We find that protoplanetary discs are very massive early in their lives. When averaged over the entire stellar population, the discs have masses of ~0.3 and 0.1 M ⊙ for systems based on hydrodynamic or MHD initial conditions, respectively. In systems characterised by a final stellar mass ~1 M ⊙ , we find disc masses of ~0.7 M ⊙ for the “hydro” case and ~0.2 M ⊙ for the “MHD” case at the end of the infall phase. Furthermore, the inferred total disc lifetimes are long, ≈5–7 Myr on average. This is despite our choice of a high value of 10 −2 for the background viscosity α -parameter. In addition, we find that fragmentation is common in systems that are simulated using hydrodynamic cloud collapse, with more fragments of larger mass formed in more massive systems. In contrast, if disc formation is limited by magnetic fields, fragmentation may be suppressed entirely. Conclusions. Our work draws a picture quite different from the one often assumed in planet formation studies: protoplanetary discs are more massive and live longer. This means that more mass is available for planet formation. Additionally, when fragmentation occurs, it can affect the disc’s evolution by transporting large amounts of mass radially. We suggest that the early phases in the lives of protoplanetary discs should be included in studies of planet formation. Furthermore, the evolution of the central star, including its accretion history, should be taken into account when comparing theoretical predictions of disc lifetimes with observations.
#EEGManyLabs: Investigating the Replicability of Influential EEG Experiments
2020-11-27

There is growing awareness across the neuroscience community that the replicability of findings on the relationship between brain activity and cognitive phenomena can be improved by conducting studies with high statistical power that adhere to well-defined and standardized analysis pipelines. Inspired by efforts from the psychological sciences, and with the desire to examine some of the foundational findings using electroencephalography (EEG), we have launched #EEGManyLabs, a large-scale international collaborative replication effort. Since its discovery in the early 20th century, EEG has had a profound influence on our understanding of human cognition, but there is limited evidence on the replicability of some of the most highly cited discoveries. After a systematic search and selection process, we have identified 27 of the most influential and continually cited studies in the field. We plan to directly test the replicability of key findings from 20 of these studies in teams of at least three independent laboratories. The design and protocol of each replication effort will be submitted as a Registered Report and peer-reviewed prior to data collection. Prediction markets, open to all EEG researchers, will be used as a forecasting tool to examine which findings the community expects to replicate. This project will update our confidence in some of the most influential EEG findings and generate a large open access database that can be used to inform future research practices. Finally, through this international effort, we hope to create a cultural shift towards inclusive, high-powered multi-laboratory collaborations.
Definition and validation of a radiomics signature for loco-regional tumour control in patients with locally advanced head and neck squamous cell carcinoma
2020-11-27

Purpose: To develop and validate a CT-based radiomics signature for the prognosis of loco-regional tumour control (LRC) in patients with locally advanced head and neck squamous cell carcinoma (HNSCC) treated by primary radiochemotherapy (RCTx) based on retrospective data from 6 partner sites of the German Cancer Consortium - Radiation Oncology Group (DKTK-ROG). Material and methods: Pre-treatment CT images of 318 patients with locally advanced HNSCC were collected. Four-hundred forty-six features were extracted from each primary tumour volume and then filtered through stability analysis and clustering. First, a baseline signature was developed from demographic and tumour-associated clinical parameters. This signature was then supplemented by CT imaging features. A final signature was derived using repeated 3-fold cross-validation on the discovery cohort. Performance in external validation was assessed by the concordance index (C-Index). Furthermore, calibration and patient stratification in groups with low and high risk for loco-regional recurrence were analysed. Results: For the clinical baseline signature, only the primary tumour volume was selected. The final signature combined the tumour volume with two independent radiomics features. It achieved moderately good discriminatory performance (C-Index [95% confidence interval]: 0.66 [0.55–0.75]) on the validation cohort along with significant patient stratification (p = 0.005) and good calibration. Conclusion: We identified and validated a clinical-radiomics signature for LRC of locally advanced HNSCC using a multi-centric retrospective dataset. Prospective validation will be performed on the primary cohort of the HNprädBio trial of the DKTK-ROG once follow-up is completed.
Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples
2020-11-27

Shotgun metagenomic sequencing (SMg) enables the simultaneous detection and characterization of viruses in human, animal and environmental samples. However, lack of sensitivity still poses a challenge and may lead to poor detection and data acquisition for detailed analysis. To improve sensitivity, we assessed a broad scope targeted sequence capture (TSC) panel (ViroCap) in both human and animal samples. Moreover, we adjusted TSC for the Oxford Nanopore MinION and compared the performance to an SMg approach. TSC on the Illumina NextSeq served as the gold standard. Overall, TSC increased the viral read count significantly in challenging human samples, with the highest genome coverage achieved using the TSC on the MinION. TSC also improved the genome coverage and sequencing depth in clinically relevant viruses in the animal samples, such as influenza A virus. However, SMg was shown to be adequate for characterizing a highly diverse animal virome. TSC on the MinION was comparable to the NextSeq and can provide a valuable alternative, offering longer reads, portability and lower initial cost. Developing new viral enrichment approaches to detect and characterize significant human and animal viruses is essential for the One Health Initiative.
Direct‐Push Color Logging Images Spatial Heterogeneity of Organic Carbon in Floodplain Sediments
2020-11-27

Abstract In soils and sediments, large amounts of total organic carbon (TOC) mark reducing conditions. As dark sediment colors are good predictors for high‐TOC zones, they indicate hot spots of biogeochemical turnover and microbial activity. Traditionally, obtaining the sediment color or TOC at depth requires costly core sampling, resulting in poor horizontal resolution and related uncertainty caused by interpolation. We suggest using a direct‐push tool for optical screening of the sediment color to acquire multiple high‐resolution vertical color profiles and demonstrate its applicability to a biogeochemical transition zone in floodplain sediments, dominated by tufa. We use Gaussian mixture models for a cluster analysis of 35 color logs in the International Commission on Illumination (CIE) L * a * b * color space to identify three colorfacies that differ in lithology and TOC content: a dark colorfacies that agrees well with peat layers, a gray colorfacies associated with clay, and a creamy‐brown facies made of autochthonous carbonate precipitates. We test different approaches either to infer the TOC content from color metrics, namely, the lightness and chroma, across all facies, or to identify TOC ranges for each colorfacies. Given the high variability in TOC due to organic carbon specks in the tufa, the latter approach appears more realistic. In our application we map the 3‐D distribution of organic matter in a floodplain in distinct facies over 20,000 m 2 down to 12 m depth. While we relate the sediment color only to the TOC content, direct‐push color logging may also be used for in situ mapping of other biogeochemically relevant properties, such as the ferric‐iron content or sedimentary structure.
Evaluation of Ethylated Phenylcarbamoylazinane‐1,2,4‐Triazole Amides Derivatives as 15‐Lipoxygenase Inhibitors Together with Cytotoxic, ADME and Molecular Modeling Studies
2020-11-27

Abstract Searching the organic compound as anti‐inflammatory agent is a fruitful effort to treat inflammatory disorders such as asthma, arthritis, psoriasis, and especially cancer. These disorders can be cured by lipoxygenase (LOX) inhibitors, which have the ability to stop the development and progression of inflammation. The present research described the synthesis of fifteen new N ‐alkyl/aralkyl/aryl derivatives ( 7 a – o ) of 2‐(4‐ethyl‐5‐(1‐phenylcarbamoyl)piperidine‐4 H ‐1,2,4‐triazol‐3‐ylthio)acetamide by the continuous conversions of ethyl piperidine‐4‐carboxylate ( a ) into phenylcarbamoyl derivative ( 1 ) hydrazide ( 2 ), semicarbazide ( 3 ) and finally the N ‐ethylated 5‐(1‐phenylcarbamoyl)piperidine‐1,2,4‐triazole ( 4 ). The target molecules ( 7 a–o ) were formed by the reaction of 4 with various electrophiles ( 6 a – o ), in methanolic potassium hydroxide. These synthetic analogues were characterized by FTIR, 1 H, 13 C NMR spectroscopy, EIMS, and HREIMS spectrometry. The compounds 7 a – o were screened for their inhibitory potential against 15‐lipoxygenase. Compounds 7 b , 7 e , 7 c and 7 g displayed the potent inhibitory potential (IC 50 17.52±0.67, 35.61±0.81, 36.24±0.83 &amp; 36.52±0.58 μM, respectively), whereas, moderate inhibition was shown by 7 h, 7 a , 7 d with IC 50 values between 42.95±0.73 to 45.67±0.75 μM, respectively. Some compounds exhibited drug‐like characteristics due to their lower cytotoxic and good ADME profiles and supported by molecular modeling studies where one of the NH groups was found engaged through hydrogen bonding with Ala672. The carbonyl group amide and Asn554 were connected by a hydrogen bond, whereas the second NH group was also linked through hydrogen bonds with Gln363.
Time-dependent acoustic scattering from generalized impedance boundary conditions via boundary elements and convolution quadrature
2020-11-27

Abstract Generalized impedance boundary conditions are effective approximate boundary conditions that describe scattering of waves in situations where the wave interaction with the material involves multiple scales. In particular, this includes materials with a thin coating (with the thickness of the coating as the small scale) and strongly absorbing materials. For the acoustic scattering from generalized impedance boundary conditions, the approach taken here first determines the Dirichlet and Neumann boundary data from a system of time-dependent boundary integral equations with the usual boundary integral operators, and then the scattered wave is obtained from the Kirchhoff representation. The system of time-dependent boundary integral equations is discretized by boundary elements in space and convolution quadrature in time. The well-posedness of the problem and the stability of the numerical discretization rely on the coercivity of the Calderón operator for the Helmholtz equation with frequencies in a complex half-plane. Convergence of optimal order in the natural norms is proved for the full discretization. Numerical experiments illustrate the behaviour of the proposed numerical method.
Differential host response to a herpesvirus: Marek’s disease virus peptides on chicken MHC class II molecules are derived from only a few genes and illustrate a new mode of peptide binding
2020-11-27

Abstract Viral diseases pose major threats to humans and other animals, including the billions of chickens that are an important food source as well as a public health concern due to zoonotic pathogens. Unlike humans and other typical mammals, the major histocompatibility complex (MHC) of chickens can confer decisive resistance or susceptibility to many viral diseases. An iconic example is Marek’s disease, caused by an oncogenic herpesvirus with over 100 genes. Classical MHC class I and class II molecules present antigenic peptides to T lymphocytes, and it has been hard to understand how such MHC molecules could be involved in susceptibility to Marek’s disease, given the potential number of peptides from over 100 genes. We used a new in vitro infection system and immunopeptidomics to determine peptide motifs for the two class II molecules expressed by the MHC haplotype B2, which is known to confer resistance to Marek’s disease. Surprisingly, we found that the vast majority of viral peptide epitopes presented by chicken class II molecules arise from only four viral genes, nearly all having the peptide motif for BL2, the dominantly-expressed class II molecule in chickens. We expressed BL2 linked to several MDV peptides, and determined one X-ray crystal structure, showing how a single small amino acid in the binding site causes a crinkle in the peptide, leading to core binding peptide of ten amino acids, compared to the nine amino acids in all other reported class II molecules. The limited number of potential T cell epitopes from such a complex virus can explain the differential MHC-determined resistance to MDV, but raises questions of mechanism and opportunities for vaccine targets in this important food species, as well as providing a basis for understanding class II molecules in other species including humans.
Early anthropogenic use of hematite on Aurignacian ivory personal ornaments from Hohle Fels and Vogelherd caves, Germany
2020-11-28

The Aurignacian (ca. 43-35 ka) of southwestern Germany is well known for yielding some of the oldest artifacts related to symbolic behaviors, including examples of figurative art, musical instruments, and personal ornaments. Another aspect of these behaviors is the presence of numerous pieces of iron oxide (ocher); however, these are comparatively understudied, likely owing to the lack of painted artifacts from this region and time period. Several Aurignacian-aged carved ivory personal ornaments from the sites of Hohle Fels and Vogelherd contain traces of what appear to be red ocher residues. We analyzed these beads using a combination of macroanalytical and microanalytical methods, including scanning electron microscopy equipped with energy dispersive spectroscopy and Raman spectroscopy. We found that the residue is composed of the iron oxide mineral hematite (Fe<sub>2</sub>O<sub>3</sub>). Further analyses on associated archaeological sediments by X-ray diffraction revealed the absence of hematite and other iron oxide mineral phases, suggesting that the hematite residues were intentionally applied to the ivory personal ornaments by human agents. These findings have important implications as they represent evidence for the direct application of ocher on portable symbolic objects by early Homo sapiens in Europe. Furthermore, our results reveal shared behavioral practices from two key Aurignacian sites maintained over several millennia and illuminate aspects of pigment use and symbolic practices during a pivotal time in the cultural evolution of humans.
Enabling Violations: Social Class and Sexual Identity in Didier Eribon’s “Returning to Reims”
2020-11-28

Abstract In this paper we explore what we can learn from Didier Eribon’s “Returning to Reims” regarding childhood vulnerability. We argue that the book offers a stimulating perspective on discrimination, humiliation, and injury. Although Eribon is twofold vulnerable due to his class and his sexual identity, his pain and shame does not make him defenceless. It makes him the subject he is: the wound caused by a violent heteronormative order. Therefore, becoming object of violations should not necessarily be conceptualised as the opposite to gaining agency but under certain circumstances can provoke resistance and rebellion. These interpretations are framed by theories of vulnerability mainly drawing on Judith Butler and Gayatri Chakravorty Spivak as well as some thoughts about the new genre of “autosociobiographies” to which “Returning to Reims” belongs.
Caught between a Rock and a Hard Place: The Gap between Rights-related Policies and Educational Opportunities for Unaccompanied Im/migrant Children in Detention
2020-11-29

This research examines the gap between federal and state legal standards and policies related to educational provision for school-age youth detained in the United States, and secondary evidence documenting the educational services that are provided to unaccompanied im/migrant children in federal custody. The educational provision for unaccompanied youth in detention is both defined as a human right and mandated by federal and state law. But, in spite of legislation and policies at the international, national, and state levels, the implementation of education is inconsistent for unaccompanied children in US federal custody at shelters and care facilities nationwide. More specifically, ample evidence suggests there is no system of educational accountability for education provided to unaccompanied minors and other im/migrant children in federal custody at these detention centers, shelters, and care facilities.
FakeNewsPerception: An Eye Movement Dataset on the Perceived Believability of News Stories
2020-11-29

FakeNewsPerception: An Eye Movement Dataset on the Perceived Believability of News Stories Extensive use of the internet has enabled easy access to many different sources, such as news and social media. Content shared on the internet cannot be fully fact-checked, and as a result, misinformation can spread in a fast and easy way. Recently, psychologists and economists have shown in many experiments that prior beliefs, knowledge, and the willingness to think deliberately are important determinants to explain who falls for fake news. Many of these studies only rely on self-reports, which suffer from social desirability, and that we need more objective measures of information processing such as eye movements during reading news. To provide the research community the opportunity to study human behaviors on the news truthness, we propose the FakeNewsPerception dataset. FakeNewsPerception consists of eye movements during reading, perceived believability scores, questionnaires including Cognitive Reflection Test (CRT) and News-Find-Me (NFM) perception, and political orientation, collected from 25 participants with 60 news items. Initial analyses of the eye movements revealed that human perception differs when viewing true and fake news.