julilili42/papers huggingface dataset:
Optimally convergent mixed finite element methods for the stochastic Stokes equations
2021-03-15

Abstract We propose some new mixed finite element methods for the time-dependent stochastic Stokes equations with multiplicative noise, which use the Helmholtz decomposition of the driving multiplicative noise. It is known (Langa, J. A., Real, J. &amp; Simon, J. (2003) Existence and regularity of the pressure for the stochastic Navier--Stokes equations. Appl. Math. Optim., 48, 195--210) that the pressure solution has low regularity, which manifests in suboptimal convergence rates for well-known inf-sup stable mixed finite element methods in numerical simulations; see Feng X., &amp; Qiu, H. (Analysis of fully discrete mixed finite element methods for time-dependent stochastic Stokes equations with multiplicative noise. arXiv:1905.03289v2 [math.NA]). We show that eliminating this gradient part from the noise in the numerical scheme leads to optimally convergent mixed finite element methods and that this conceptual idea may be used to retool numerical methods that are well known in the deterministic setting, including pressure stabilization methods, so that their optimal convergence properties can still be maintained in the stochastic setting. Computational experiments are also provided to validate the theoretical results and to illustrate the conceptual usefulness of the proposed numerical approach.
Who Chooses Teacher Education and Why? Evidence From Germany
2021-03-15

Empirically rigorous research on teacher education entry is extremely limited. Evidence on who enters teacher education and why is crucial for identifying undesired gaps in entry and can assist with teacher recruitment. Grounded in prior research, we identified four primary groups of relevant individual-level variables: student/family background, achievement/abilities, personality, and motivation. We empirically tested this conceptual model using rich data from a national cohort of German ninth-graders followed to college/university and their parents. Our study is the first to predict eventual teacher education entry early in secondary school. Although those students who eventually entered teacher education were significantly different from their counterparts across most variables, fewer were conditionally predictive. Social interests, desired working conditions, desire to have children, and students’ parents were particularly influential. Implications for research and teacher recruitment are discussed.
Sensitive Interferometric Plasmon Ruler Based on a Single Nanodimer
2021-03-15

The plasmon ruler has drawn substantial attention for measuring small separations between two plasmonic nanoparticles (NPs), which can be as sensitive as to observe the bending of DNA. Usually, the...
Re-operation rate after surgical treatment of osteochondral lesions of the talus in paediatric and adolescent patients
2021-03-15

Abstract Background The aim of this study is to analyse the re-operation rate after surgical treatment of osteochondral lesions of the talus (OCLTs) in children and adolescents. Methods Between 2009 and 2019, 27 consecutive patients with a solitary OCLT (10 male, 17 female; mean age 16.9 ± 2.2 years; 8 idiopathic vs. 19 traumatic) received primary operative treatment (arthroscopy + bone marrow stimulation [BMS], n = 8; arthroscopy + retrograde drilling, n = 8; autologous chondrocyte implantation [ACI]/autologous bone grafting, n = 9; arthroscopy + BMS + retrograde drilling; n = 1; flake fixation, n = 1). Seventeen OCLTs were located at the medial and ten at the lateral talus. ‘Re-operation’ as the outcome measure was evaluated after a median follow-up of 42 months (range 6–117 months). Patients were further subdivided into groups A (re-operation, n = 7) and B (no re-operation, n = 20). Groups A and B were compared with respect to epidemiological, lesion- and therapy-related variables. Results Seven of 27 patients needed a re-operation (re-operation rate 25.9% after a median interval of 31 months [range 13–61 months]). The following operative techniques were initially used in these seven patients: arthroscopy + BMS n = 2, arthroscopy + retrograde drilling n = 4, ACI + autologous bone grafting n = 1. A comparison of group A with group B revealed different OCLT characteristics between both groups. The intraoperative findings according to the International Cartilage Repair Society (ICRS) classification revealed significantly more advanced cartilage damage in group B than in group A ( p = 0.001). Conclusions We detected a re-operation rate of 25.9% after primary surgical OCLT treatment. Patients with re-operation had significantly lower ICRS classification stages compared to patients without re-operation.
Dinosaur taphonomy of the Jurassic Shishugou Formation (Northern Junggar Basin, NW China) – insights from bioerosional trace fossils on bone
2021-03-15

Bioerosional trace fossils can offer invaluable insights into taphonomic processes, ecosystem dynamics and environmental conditions that are not obtainable by other lines of evidence. Here, we describe the first invertebrate trace fossils on dinosaur bone from the Upper Jurassic Shishugou Formation of the northeastern Junggar Basin. The traces occur as spherical holes in the bone, closely resembling boreholes attributed to either indeterminate insects or dermestid beetles and thus they are here likewise ascribed to feeding and/or pupation by necrophagous insects. Such bioerosional trace fossils have several taphonomical and palaeoecological implications for they are only inflicted on subaerially exposed tissues and preferentially when carcasses are desiccated. We, therefore, conclude that the dinosaur carcass was exposed for at least several weeks under a semi-arid and seasonal climate before it was buried by sediment. This supports the general palaeoclimatological and paleoenvironmental reconstructions for the Shishugou Formation from sedimentological data. Moreover, this is the first evidence for invertebrate–vertebrate interactions from the Late Jurassic of Asia, offering a novel glimpse into the diverse biotic relationships of this ancient Jurassic ecosystem.
The ROS scavenger PDTC affects adaptation to treadmill running in mice: distinct effects on murine body mass, resting heart rate and skeletal muscle fiber type composition
2021-03-15

ABSTRACT Regular exercise induces a broad spectrum of adaptation reactions in a variety of tissues and organs. However, the respective mechanisms are incompletely understood. In the context of their analysis, animal model systems, specifically rodent treadmill running protocols, play an important role. However, few researchers have studied different aspects of adaptation, such as cardiorespiratory and skeletal muscle training effects, within one set of experiments. Here, we analyzed physiological adaptation to 10 weeks of regular, moderate-intensity, uphill treadmill running in mice, a widely used model for endurance exercise training. To study the effects of reactive oxygen species (ROS), which have been suggested to be major regulators of training adaptation, a subgroup of mice was treated with the ROS scavenger PDTC (pyrrolidine dithiocarbamate). We found that mass gain in mice that exercised under PDTC treatment lagged behind that of all other experimental groups. In addition, both exercise and PDTC significantly and additively decreased resting heart rate. Furthermore, there was a trend towards an enhanced proportion of type 2A skeletal muscle fibers and differential expression of metabolism-associated genes, indicating metabolic and functional adaptation of skeletal muscle fibers. By contrast, there were no effects on grip strength and relative mass of individual muscles, suggesting that our protocol of uphill running did not increase skeletal muscle hypertrophy and strength. Taken together, our data suggest that a standard protocol of moderate-intensity uphill running induces adaptation reactions at multiple levels, part of which might be modulated by ROS, but does not enhance skeletal muscle hypertrophy and force.
Are Violations of Student Privacy “Quick and Easy"? Implications of K-12 Educational Institutions’ Posts on Facebook
2021-03-15

As the use of social media increases in daily life, it has also increased for institutions in the field of education. While there may be benefits for schools to use this media outlet, the privacy of students within those schools may be at risk when their names and photos are shared on such a publicly accessible domain. In this study, we analyzed the extent to which students’ privacy is protected by qualitatively coding a random sample of 100 Facebook posts made by U.S. school districts from a population of over 9.3 million photo posts that we collected. Using inferential techniques, we found that students are somewhat protected compared to teachers and community members, with only 2.67% of students’ detected faces able to be identified by name. These numbers at first appear small, but if applied to the entire population, this could potentially leave between 153,218 and 1,l53,844 students identifiable to anyone on the Internet; the number of photos of students posted by schools and districts is much greater still, between 15.2 and 20.3 million. The same measure for staff and community members were 4.6% and 16%, respectively. We discuss the severity and scale of these privacy threats and make recommendations for research on student privacy in social media and other informal education-related contexts. In all, these could represent the largest publicly available collection of identifiable photos of students (and children) in the United States and could seriously threaten the privacy of those identified.
Potential origin of the state-dependent high-energy tail in the black hole microquasar Cygnus X-1 as seen with INTEGRAL
2021-03-15

0.1-10 MeV observations of the black hole microquasar Cygnus X-1 have shown the presence of a spectral feature in the form of a power law in addition to the standard black body and Comptonization components observed by INTEGRAL. This so-called "high-energy tail" has recently been shown to be strong in its hard spectral state and interpreted as high-energy part of the emission from a compact jet. This result was, however, obtained from a data set dominated by hard state observations. In the soft state, only upper limits on the presence and hence the potential parameters of a high-energy tail could be derived. Using an extended data set we aim at obtaining better constraints on the properties of this spectral component in both states. We make use of data obtained from 15 years of observations with the INTEGRAL satellite. The data set is separated into the different states and we analyse stacked state-resolved spectra obtained from the X-ray monitors, the gamma-ray imager, and the gamma-ray spectrometer onboard. A high-energy component is detected in both states confirming its earlier detection in the hard state and its suspected presence in the soft state with INTEGRAL. We first characterize the high-energy tail components in the two states through a model-independent, phenomenological analysis. We then apply physical models based on hybrid Comptonization. The spectra are well modeled in all cases, with a similar goodness of the fits. While in the phenomenological approach the high-energy tail has similar indices in both states, the fits with the physical models seem to indicate different properties. We discuss the potential origins of the high-energy components in both states, and favor an interpretation where the part of the high-energy component is due to a compact jet in the hard state and hybrid Comptonization in either a magnetised or non-magnetised corona in the soft state.
Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager
2021-03-16

The broadening utilisation of ancient DNA to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and scale of analyses being performed. In the context of this heterogeneous landscape, we present an advanced, and entirely redesigned and extended version of the EAGER pipeline for the analysis of ancient genomic data. This Nextflow pipeline aims to address three main themes: accessibility and adaptability to different computing configurations, reproducibility to ensure robust analytical standards, and updating the pipeline to the latest routine ancient genomic practices. The new version of EAGER has been developed within the nf-core initiative to ensure high-quality software development and maintenance support; contributing to a long-term life-cycle for the pipeline. nf-core/eager will assist in ensuring that a wider range of ancient DNA analyses can be applied by a diverse range of research groups and fields.
Results of endovascular aortic arch repair using the Relay Branch system
2021-03-16

Abstract OBJECTIVES Our goal was to evaluate results of endovascular aortic arch repair using the Relay Branch system. METHODS Forty-three patients with thoracic aortic pathology involving the aortic arch have been treated with the Relay Branch system (Terumo Aortic, Sunrise, FL, USA) in 10 centres. We assessed in-hospital mortality, neurological injury, treatment success according to current reporting standards and the need for secondary interventions. In addition, outcome was analysed according to the underlying pathology: non-dissective disease versus residual aortic dissection (RAD) (defined as remaining dissection after previous type A repair, chronic type B aortic dissections). RESULTS In-hospital mortality was 9% (0% in patients with RAD). Disabling stroke occurred in 7% (0% in patients with RAD); non-disabling stroke occurred in 19% (7% in patients with RAD). Early type IA and B endoleak formation occurred in 4%. Median follow-up was 16 ± 18 months. During the follow-up period, 23% of the patients died. Aortic-related deaths were low (3% in patients with RAD). CONCLUSIONS The results of endovascular aortic arch repair using the Relay Branch system in a selected patient population with regard to technical success are good. In-hospital mortality is acceptable, the number of disabling strokes is low and technical success is high. Non-disabling stroke is a major concern, and every effort has to be taken to reduce this to a minimum. The best outcome is seen in patients with underlying RAD. Finally, more data are needed.
Five points to check when comparing visual perception in humans and machines
2021-03-16

With the rise of machines to human-level performance in complex recognition tasks, a growing amount of work is directed toward comparing information processing in humans and machines. These studies are an exciting chance to learn about one system by studying the other. Here, we propose ideas on how to design, conduct, and interpret experiments such that they adequately support the investigation of mechanisms when comparing human and machine perception. We demonstrate and apply these ideas through three case studies. The first case study shows how human bias can affect the interpretation of results and that several analytic tools can help to overcome this human reference point. In the second case study, we highlight the difference between necessary and sufficient mechanisms in visual reasoning tasks. Thereby, we show that contrary to previous suggestions, feedback mechanisms might not be necessary for the tasks in question. The third case study highlights the importance of aligning experimental conditions. We find that a previously observed difference in object recognition does not hold when adapting the experiment to make conditions more equitable between humans and machines. In presenting a checklist for comparative studies of visual reasoning in humans and machines, we hope to highlight how to overcome potential pitfalls in design and inference.
Dynamics of the nonrotating and rotating black hole scalarization
2021-03-16

Even though black hole scalarization is extensively studied recently, little has been done in the direction of understanding the dynamics of this process, especially in the rapidly rotating regime. In the present paper, we focus exactly on this problem by considering the nonlinear dynamics of the scalar field while neglecting the backreaction on the spacetime metric. This approach has proven to give good results in various scenarios and we have explicitly demonstrated its accuracy for nonrotating black holes especially close to the bifurcation point. We have followed the evolution of a black hole from a small initial perturbation, throughout the exponential growth of the scalar field followed by a subsequent saturation to an equilibrium configuration. As expected, even though the emitted signal and the time required to scalarize the black hole are dependent on the initial perturbation, the final stationary state that is reached is independent on the initial data.
Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing
2021-03-16

Abstract New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes from complex microbial communities. Using long read data (ONT MinION) obtained from an ensemble of activated sludge enrichment bioreactors we recover 22 closed or complete genomes of community members, including several species known to play key functional roles in wastewater bioprocesses, specifically microbes known to exhibit the polyphosphate- and glycogen-accumulating organism phenotypes (namely Candidatus Accumulibacter and Dechloromonas , and Micropruina , Defluviicoccus and Candidatus Contendobacter, respectively), and filamentous bacteria ( Thiothrix ) associated with the formation and stability of activated sludge flocs. Additionally we demonstrate the recovery of close to 100 circularised plasmids, phages and small microbial genomes from these microbial communities using long read assembled sequence. We describe methods for validating long read assembled genomes using their counterpart short read metagenome-assembled genomes, and assess the influence of different correction procedures on genome quality and predicted gene quality. Our findings establish the feasibility of performing long read metagenome-assembled genome recovery for both chromosomal and non-chromosomal replicons, and demonstrate the value of parallel sampling of moderately complex enrichment communities to obtaining high quality reference genomes of key functional species relevant for wastewater bioprocesses.
Multiplexed Serum Antibody Screening Platform Using Virus Extracts from Endemic Coronaviridae and SARS-CoV-2
2021-03-16

The presence of antibodies against endemic coronaviruses has been linked to disease severity after SARS-CoV-2 infection. Assays capable of concomitantly detecting antibodies against endemic coronaviridae such as OC43, 229E, NL63, and SARS-CoV-2 may help to elucidate this question. We developed a serum screening platform using a bead-based Western blot system called DigiWest, capable of running hundreds of assays using microgram amounts of protein prepared directly from different viruses. Characterization of the immunoassay for detection of SARS-CoV-2 specific antibodies revealed a sensitivity of 90.3% and a diagnostic specificity of 98.1%. Concordance analysis with the SARS-CoV-2 immunoassays available by Roche, Siemens, and Euroimmun indicates comparable assay performances (Cohen's κ ranging from 0.8874 to 0.9508). Analogous assays for OC43, 229E, and NL63 were established and combined into one multiplex with the SARS-CoV-2 assay. Seroreactivity for different coronaviruses was detected with high incidence, and the multiplex assay was adapted for serum screening.
Prediction and error in early infant speech learning: a speech acquisition model
2021-03-16

In the last two decades, statistical clustering models have emerged as a dominant model of how infants learn the sounds of their language. However, recent empirical and computational evidence suggests that purely statistical clustering methods may not be sufficient to explain speech sound acquisition. To model early development of speech perception, the present study used a two-layer network trained with Rescorla-Wagner learning equations, an implementation of discriminative, error-driven learning. The model contained no a priori linguistic units, such as phonemes or phonetic features. Instead, expectations about the upcoming acoustic speech signal were learned from the surrounding speech signal, with spectral components extracted from an audio recording of child-directed speech as both inputs and outputs of the model. To evaluate model performance, we simulated infant responses in the high-amplitude sucking paradigm using vowel and fricative pairs and continua. The simulations were able to discriminate vowel and consonant pairs and predicted the infant speech perception data. The model also showed the greatest amount of discrimination in the expected spectral frequencies. These results suggest that discriminative error-driven learning may provide a viable approach to mod- elling early infant speech sound acquisition.
SPIRO – the automated Petri plate imaging platform designed by biologists, for biologists
2021-03-16

Abstract Phenotyping of model organisms grown on Petri plates is often carried out manually, despite the procedures being time-consuming and laborious. The main reason for this is the limited availability of automated phenotyping facilities, whereas constructing a custom automated solution can be a daunting task for biologists. Here, we describe SPIRO, the Smart Plate Imaging Robot, an automated platform that acquires time-lapse photos of up to four vertically oriented Petri plates in a single experiment, corresponding to 192 seedlings for a typical root growth assay and up to 2500 seeds for a germination assay. SPIRO is catered specifically to biologists’ needs, requiring no engineering or programming expertise for assembly and operation. Its small footprint is optimized for standard incubators, the inbuilt green LED enables imaging under dark conditions, and remote control provides access to the data without interfering with sample growth. SPIRO’s excellent image quality is suitable for automated image processing, which we demonstrate on the example of seed germination and root growth assays. Furthermore, the robot can be easily customized for specific uses, as all information about SPIRO is released under open-source licenses. Importantly, uninterrupted imaging allows considerably more precise assessment of seed germination parameters and root growth rates compared to manual assays. Moreover, SPIRO enables previously technically challenging assays such as phenotyping in the dark. We illustrate the benefits of SPIRO in proof-of-concept experiments which yielded a novel insight on the interplay between autophagy, nitrogen sensing and photoblastic response.