julilili42/papers huggingface dataset:
Developmental changes resemble stochastic optimization
2022-04-04

Analogies to stochastic optimization are common in developmental psychology, describing a gradual reduction in randomness ("cooling off") over the lifespan. Yet for lack of concrete empirical comparison, there is ambiguity in interpreting this analogy. Using data from n=281 participants ages 5 to 55, we show that `"cooling off'" does not only apply to the single dimension of randomness. Rather, development resembles an optimization process along multiple dimensions of learning (i.e., reward generalization, uncertainty-directed exploration, and decision temperature). What begins as large tweaks in the parameters that define learning during childhood plateaus and converges to efficient parameter constellations in adulthood. The developmental trajectory of human parameters is strikingly similar to several stochastic optimization algorithms, yet we observe intriguing differences in convergence. Notably, none of the optimization algorithms discovered reliably better regions of the strategy space than adult participants, suggesting a remarkable efficiency of human development.
A note on the modeling of the effects of experimental time in psycholinguistic experiments
2022-04-04

Abstract Thul et al. (2020) called attention to problems that arise when chronometric experiments implementing specific factorial designs are analysed with the generalized additive mixed model (GAMM), using factor smooths to capture trial-to-trial dependencies. From a series of simulations incorporating such dependencies, they conclude that GAMMs are inappropriate for between-subject designs. They argue that in addition GAMMs come with too many modeling possibilities, and advise using the linear mixed model (LMM) instead. As clarified by the title of their paper, their conclusion is: “Using GAMMs to model trial-by-trial fluctuations in experimental data: More risks but hardly any benefit”. We address the questions raised by Thul et al. (2020) , who clearly demonstrated that problems can indeed arise when using factor smooths in combination with factorial designs. We show that the problem does not arise when using by-smooths. Furthermore, we have traced a bug in the implementation of factor smooths in the mgcv package, which will have been removed from version 1.8–36 onwards. To illustrate that GAMMs now produce correct estimates, we report simulation studies implementing different by-subject longitudinal effects. The maximal LMM emerges as slightly conservative compared to GAMMs, and GAMMs provide estimated coefficients that can be less variable across simulation runs. We also discuss two datasets where time-varying effects interact with numerical predictors in a theoretically informative way.
Morphological association between muscle attachments and ossification sites in the late cartilaginous skull of tuatara embryos
2022-04-04

Abstract During development, the embryonic cartilaginous skull in most vertebrates is partially replaced by bones with endochondral and perichondral ossifications. Muscle attachments are thought to influence the patterns of ossification and, hence, the differentiation of the skull. To investigate the association between muscle attachments and early ossifications of reptilian embryos, we conducted digital 3D reconstructions of the cranium, the head, and the neck musculature from a histological section series of a late term embryonic tuatara, Sphenodon punctatus , with a total body length of 52 mm. As the sole living rhynchocephalian species, it is an important outgroup in comparative studies of squamate evolution. We found that head and neck muscles are largely associated with early ossification of the basal plate and the palatoquadrate, and with three other ossifications in an older specimen with a total body length of 72 mm. These results suggest that tensile forces resulting from embryonic muscle contraction are largely, but not exclusively, correlated with the area of endochondral ossification in the chondrocranium and palatoquadrate in tuatara. Beyond little‐known genetic factors, the complexity of chondrocranial architecture, the progress of its development, and the effect of multiple muscle transmitting forces in the chondrocranium must be considered to provide a more comprehensive discussion of the mechanical properties of the embryonic skull.
Stereo viewing upsets cinematic continuity: Filmic cuts are more salient in 3D than in 2D movies.
2022-04-04

Filmmakers have established editing rules that aim to create cinematic continuity across filmic cuts, thereby avoiding viewers' confusion despite the abrupt changes in perception.In our present project, we investigated the impact of 3D films, as opposed to 2D films, on the salience of filmic cuts.We employed a cut detection task and focused on within-scene cuts with mere changes in camera perspective.We presented short video clips to our participants and asked them to press a key whenever they noticed a filmic cut, and we measured their cut detection performance.In addition to viewing mode (2D vs. 3D presentation), we considered cross-modal auditory influences (visual vs. audiovisual presentation) on the salience of filmic cuts.Participants detected cuts more accurately and faster when the video clips were presented in 3D rather than in 2D and when the video clips were presented only visually (without soundtrack) rather than audiovisually (with soundtrack).Both factors influenced cut detection performance independently.We conclude that while the regular audiovisual presentation of films supports the filmmakers' mission to achieve cinematic continuity, filmmakers should also be aware of the additional salience of cuts that comes with 3D film presentation and consider its effects on cinematic continuity.
ACKR3 regulates platelet activation and ischemia-reperfusion tissue injury
2022-04-05

Abstract Platelet activation plays a critical role in thrombosis. Inhibition of platelet activation is a cornerstone in treatment of acute organ ischemia. Platelet ACKR3 surface expression is independently associated with all-cause mortality in CAD patients. In a novel genetic mouse strain, we show that megakaryocyte/platelet-specific deletion of ACKR3 results in enhanced platelet activation and thrombosis in vitro and in vivo. Further, we performed ischemia/reperfusion experiments (transient LAD-ligation and tMCAO) in mice to assess the impact of genetic ACKR3 deficiency in platelets on tissue injury in ischemic myocardium and brain. Loss of platelet ACKR3 enhances tissue injury in ischemic myocardium and brain and aggravates tissue inflammation. Activation of platelet-ACKR3 via specific ACKR3 agonists inhibits platelet activation and thrombus formation and attenuates tissue injury in ischemic myocardium and brain. Here we demonstrate that ACKR3 is a critical regulator of platelet activation, thrombus formation and organ injury following ischemia/reperfusion.
Climate warming can reduce biocontrol efficacy and promote plant invasion due to both genetic and transient metabolomic changes
2022-04-05

Abstract Climate change may affect plant–herbivore interactions and their associated ecosystem functions. In an experimental evolution approach, we subjected replicated populations of the invasive Ambrosia artemisiifolia to a combination of simulated warming and herbivory by a potential biocontrol beetle. We tracked genomic and metabolomic changes across generations in field populations and assessed plant offspring phenotypes in a common environment. Using an integrated Bayesian model, we show that increased offspring biomass in response to warming arose through changes in the genetic composition of populations. In contrast, increased resistance to herbivory arose through a shift in plant metabolomic profiles without genetic changes, most likely by transgenerational induction of defences. Importantly, while increased resistance was costly at ambient temperatures, warming removed this constraint and favoured both vigorous and better defended plants under biocontrol. Climate warming may thus decrease biocontrol efficiency and promote Ambrosia invasion, with potentially serious economic and health consequences.
Current clinical practice and outcome of neoadjuvant chemotherapy for early breast cancer: analysis of individual data from 94,638 patients treated in 55 breast cancer centers
2022-04-05

Abstract Neoadjuvant chemotherapy (NACT) is frequently used in patients with early breast cancer. Randomized controlled trials have demonstrated similar survival after NACT or adjuvant chemotherapy (ACT). However, certain subtypes may benefit more when NACT contains regimes leading to high rates of pathologic complete response (pCR) rates. In this study we analyzed data using the OncoBox research from 94,638 patients treated in 55 breast cancer centers to describe the current clinical practice of and outcomes after NACT under routine conditions. These data were compared to patients treated with ACT. 40% of all patients received chemotherapy. The use of NACT increased over time from 5% in 2007 up to 17.3% in 2016. The proportion of patients receiving NACT varied by subtype. It was low in patients with HR-positive/HER2-negative breast cancer (5.8%). However, 31.8% of patients with triple-negative, 31.9% with HR-negative/HER2-positive, and 26.5% with HR-positive/HER2-positive breast cancer received NACT. The rates of pCR were higher in patients with HR-positive/HER2-positive, HR-negative/HER2-positive and triple-negative tumors (36, 53 and 38%) compared to HR-positive/HER2-negative tumors (12%). PCR was achieved more often in HER2-positive and triple-negative tumors over time. This is the largest study on use and effects of NACT in German breast cancer centers. It demonstrates the increased use of NACT based on recommendations in current clinical guidelines. An improvement of pCR was shown in particular in HER2-positive and triple-negative breast cancer, which is consistent with data from randomized controlled trails.
The “Greta Effect”: Networked Mobilization and Leader Identification Among Fridays for Future Protesters
2022-04-05

Drawing on walking interviews with 19 Fridays for Future (FFF) activists in Germany, this study focuses on Greta Thunberg by researching strikers’ perception, identification, and online networking practices with the movement’s central figure. With respect to protest mobilization and collective identity formation, this study finds that participants primarily identify with Thunberg via her class standing. While male activists highlight Thunberg’s gender as a mobilizing factor, female and non-binary activists often dismiss it, thereby distancing themselves from FFF’s feminized public image. Participants believe that Thunberg’s disability gives her an “edge” to generate media attention for FFF, calling it an asset to the cause. Although all participants engage with Thunberg via social media, many downplay her leadership role in the movement. Similarly, local organizers actively use Thunberg’s posts to build up their own online networks while routinely emphasizing FFF’s leaderlessness. The findings thus nuance assumptions about identity-based mobilization, explore the construction of networked leadership, and chart digital organizing practices in a transnational youth climate movement.
Self‐concept but not prior knowledge moderates effects of different implementations of computer‐assisted inquiry learning activities on students' learning
2022-04-05

Abstract Background Engaging students in computer‐assisted guided inquiry learning has great potential to scaffold their scientific understanding: Students are expected to improve their scientific problem‐solving skills, and at the same time gain a deep conceptual understanding of the subject‐matter. Additional generative activities such as creating video explanations subsequent to inquiry learning activities can also further deepen students' knowledge. Objectives In this experiment, we therefore compared the effectiveness of computer‐based direct instruction (to mimic traditional classroom teaching) versus computer‐based inquiry learning. Methods University students ( N = 118) either received video‐based direct instruction (direct instruction), including the demonstration of a virtual experiment, or conducted the virtual experiment themselves supported by prompts (inquiry learning). A third group of students additionally generated a video explanation as consolidation activity subsequent to conducting the virtual experiment (inquiry learning + generative activity). Results and Conclusions Contrarily to our hypotheses, the direct instruction condition outperformed the inquiry learning conditions. There were no significant differences between the inquiry learning and the inquiry learning + generative activity condition. Moderation analyses revealed that the effectiveness of direct instruction predominantly held true for students with low levels of domain‐specific self‐concept. All in all, our present study contributes to a better understanding of effects of direct instruction versus guided inquiry learning in computer‐based science education settings. Importantly, our findings show that the effectiveness of instructional approaches may depend on students' domain‐specific self‐concept as a motivational prerequisite. As such it is up for further research in science education to identify motivating instructional strategies to enhance students' learning.
The effect of formation processes on the frequency of palaeolithic cave sites in semiarid zones: Insights from Kazakhstan
2022-04-05

Abstract Central Asian caves with Palaeolithic deposits are few, but they provide a rich record of human fossils and cultural assemblages that has been used to model Late Pleistocene hominin dispersals. However, previous research has not yet systematically evaluated the formation processes that influence the frequency of Palaeolithic cave sites in the region. To address this deficiency, we combined field survey and micromorphological analyses in the piedmont zone of south Kazakhstan. Here, we present our preliminary results focusing on selected sites of the Qaratau mountains. Sediment cover varies among the surveyed caves, and loess‐like sediments dominate the cave sequences. The preservation of cave deposits is influenced by reworking of cave sediments within the caves but also by the broader erosional processes that shape semiarid landscapes. Ultimately, deposits of potentially Pleistocene age are scarce. Our study provides new data in the geoarchaeologically neglected region of Central Asia and demonstrates that micromorphology has great analytical potential even within the limitations of rigorous survey projects. We outline some of the processes that influence the formation and preservation of cave deposits in Kazakhstan, as well as broader implications for the distribution of Palaeolithic cave sites in Central Asia and other semiarid environments.
Towards an understanding of mobility in social policy research
2022-04-05

Over recent years, there has been increasing attention to migration in social policy research. Uniting this research has been a focus on cross-national migration, and predominantly immigration. In the meantime, the relationship between human mobility and social policy at other scales and sites has gained much less attention. This is in spite of the salience of multiple forms of mobility and measures for restricting, facilitating or promoting mobility not confined to the territorial borders of the nation-state. This article proposes an alternative mobility perspective for social policy research that moves us beyond the limitations of current migration approaches. To do so, we draw on interdisciplinary mobilities theory and research. Empirically, we apply a mobility perspective to examine how systems of social provision are shaped by and shape mobility and immobility, in restricting, facilitating or promoting the movement of people. We argue that such an approach allows us to frame and address questions that place mobility and immobility as central to the social relations of welfare, advancing our understanding of how social policies can reduce or reinforce the inequalities of mobility.
Aspirin improves transplant-free survival after TIPS implantation in patients with refractory ascites: a retrospective multicentre cohort study
2022-04-05

Abstract Background and aims Transjugular intrahepatic portosystemic shunt (TIPS) implantation is an established procedure to treat portal hypertension. Impact of administration of aspirin on transplant-free survival after TIPS remains unknown. Methods A multicenter retrospective analysis including patients with TIPS implantation between 2011 and 2018 at three tertiary German Liver Centers was performed. N = 583 patients were included. Survival analysis was performed in a matched cohort after propensity score matching. Patients were grouped according to whether aspirin was ( PSM-aspirin-cohort ) or was not ( PSM-no-aspirin-cohort ) administered after TIPS. Primary endpoint of the study was transplant-free survival at 12 months after TIPS. Results Aspirin improved transplant-free survival 12 months after TIPS with 90.7% transplant-free survival compared to 80.0% ( p = 0.001) after PSM. Separated by TIPS indication, aspirin did improve transplant-free survival in patients with refractory ascites significantly (89.6% vs. 70.6% transplant-free survival, p &lt; 0.001), while no significant effect was observed in patients with refractory variceal bleeding (91.1% vs. 92.2% transplant-free survival, p = 0.797). Conclusion This retrospective multicenter study provides first data indicating a beneficial effect of aspirin on transplant-free survival after TIPS implantation in patients with refractory ascites.
Therapeutic Efficacy of Pharmacological Ascorbate on Braf Inhibitor Resistant Melanoma Cells In Vitro and In Vivo
2022-04-05

High-dose ascorbate paradoxically acts as a pro-oxidant causing the formation of hydrogen peroxide in an oxygen dependent manner. Tumor cells (in particular melanoma cells) show an increased vulnerability to ascorbate induced reactive oxygen species (ROS). Therefore, high-dose ascorbate is a promising pharmacological approach to treating refractory melanomas, e.g., with secondary resistance to targeted BRAF inhibitor therapy. BRAF mutated melanoma cells were treated with ascorbate alone or in combination with the BRAF inhibitor vemurafenib. Viability, cell cycle, ROS production, and the protein levels of phospho-ERK1/2, GLUT-1 and HIF-1α were analyzed. To investigate the treatment in vivo, C57BL/6NCrl mice were subcutaneously injected with D4M.3A (BrafV600E) melanoma cells and treated with intraperitoneal injections of ascorbate with or without vemurafenib. BRAF mutated melanoma cell lines either sensitive or resistant to vemurafenib were susceptible to the induction of cell death by pharmacological ascorbate. Treatment of BrafV600E melanoma bearing mice with ascorbate resulted in plasma levels in the pharmacologically active range and significantly improved the therapeutic effect of vemurafenib. We conclude that intravenous high-dose ascorbate will be beneficial for melanoma patients by interfering with the tumor’s energy metabolism and can be safely combined with standard melanoma therapies such as BRAF inhibitors without pharmacological interference.
Global Englishes and the pedagogical challenge of developing one’s own voice
2022-04-05

The Standard English (SE) preference firmly anchored in many English teachers' attitudes and practices has been identified as a major problem hindering speaker-learners from developing competence for emancipated Global Englishes (GE) and English as a lingua franca (ELF) communication. The article addresses the issues involved from a social constructivist perspective according to which speaker-learners acquire the language taught by developing their own MY English version in their minds, hearts, and behavior. Orientation and guidance are mediated through their requirements of communicative and communal success and their quest for speaker satisfaction. Critical is not the English taught but what speaker-learners are allowed and encouraged to do with it. Intercultural virtual exchanges enable ELT students of different linguacultural backgrounds to communicate with each other using their English as a pedagogical lingua franca. Communication monitoring and pedagogical mentoring help them develop their own voice. In short, GE/ELF pedagogy meets ELT!
DeepToA: An Ensemble Deep-Learning Approach to Predicting the Theater of Activity of a Microbiome
2022-04-05

Abstract Motivation Metagenomics is the study of microbiomes using DNA sequencing. A microbiome consists of an assemblage of microbes that is associated with a “theater of activity” (ToA). To what degree does the taxonomic and functional content of the former depend on the (details of the) latter? More technically, given a taxonomic and/or functional profile estimated from metagenomic sequencing data, how to predict the associated ToA? Here we present a deep learning approach to this question. We use both taxonomic and functional profiles as input. We apply node2vec to embed hierarchical taxonomic profiles into numerical vectors. We then perform dimension reduction using clustering, to address the sparseness of the taxonomic data and thus make it more amenable to deep learning algorithms. Functional features are combined with textual descriptions of protein families or domains. We present an ensemble deep-learning framework DeepToA for predicting the ‘theater of activity” of microbial community, based on taxonomic and functional profiles. We use SHAP (SHapley Additive exPlanations) values to determine which taxonomic and functional features are important for the prediction. Results Based on 7,560 metagenomic profiles downloaded from MGnify, classified into ten different theaters of activity, we demonstrate that DeepToA has an accuracy of 98.61%. We show that adding textual information to functional features increases the accuracy. Availability Our approach is available at http://ab.inf.uni-tuebingen.de/software/deeptoa . Contact daniel.huson@uni-tuebingen.de Supplementary information Supplementary data are available at Bioinformatics online.
A strangely light neutron star
2022-04-05

<title>Abstract</title> To constrain the equation of state of cold dense matter, astrophysical measurements are essential. These are mostly based on observations of neutron stars in the X-ray band, and, more recently, also on gravitational wave observations. Of particular interest are observations of unusually heavy or light neutron stars which extend the range of central densities probed by observations and thus permit testing nuclear physics predictions over a wider parameter space. Here we report on the analysis of such a star, a central compact object within the supernova remnant HESS J1731-347. We estimate the mass and radius of the neutron star to be M = 0.77(20)Msun and R = 10.4(8) km, respectively, based on modeling of the X-ray spectrum and a robust distance estimate from Gaia observations. Our estimate implies that this object is either the lightest neutron star known, or a "strange star” with a more exotic equation of state. Adopting a standard neutron star matter hypothesis significantly constrains the corresponding equations of state.