julilili42/papers huggingface dataset:
Two novel heteropolymer‐forming proteins maintain the multicellular shape of the cyanobacterium Anabaena sp. PCC 7120
2020-11-18

Polymerizing and filament‐forming proteins are instrumental for numerous cellular processes such as cell division and growth. Their function in stabilization and localization of protein complexes and replicons is achieved by a filamentous structure. Known filamentous proteins assemble into homopolymers consisting of single subunits – for example, MreB and FtsZ in bacteria – or heteropolymers that are composed of two subunits, for example, keratin and α/β tubulin in eukaryotes. Here, we describe two novel coiled‐coil‐rich proteins (CCRPs) in the filament‐forming cyanobacterium Anabaena sp. PCC 7120 (hereafter Anabaena ) that assemble into a heteropolymer and function in the maintenance of the Anabaena multicellular shape (termed trichome). The two CCRPs – Alr4504 and Alr4505 (named ZicK and ZacK) – are strictly interdependent for the assembly of protein filaments in vivo and polymerize nucleotide independently in vitro , similar to known intermediate filament (IF) proteins. A Δ zicK Δ zacK double mutant is characterized by a zigzagged cell arrangement and hence a loss of the typical linear Anabaena trichome shape. ZicK and ZacK interact with themselves, with each other, with the elongasome protein MreB, the septal junction protein SepJ and the divisome associate septal protein SepI. Our results suggest that ZicK and ZacK function in cooperation with SepJ and MreB to stabilize the Anabaena trichome and are likely essential for the manifestation of the multicellular shape in Anabaena . Our study reveals the presence of filament‐forming IF‐like proteins whose function is achieved through the formation of heteropolymers in cyanobacteria.
SEMITONES: Single-cEll Marker IdentificaTiON by Enrichment Scoring
2020-11-18

Abstract Identification of markers is an essential step in single-cell analytic. Current marker identification strategies typically rely on cluster assignments of cells. Cluster assignment, in particular of development data, is non-trivial, potentially arbitrary and commonly relies on prior knowledge. Yet, cluster uncertainty is not commonly taken into account. In response, we present SEMITONES, a principled method for cluster-free marker identification. We showcase its application on healthy haematopoiesis data as 1) a robust alternative to highly variable gene selection, 2) for marker gene and regulatory region identification, and 3) for the construction of co-enrichment networks that reveal regulators of cell identity.
Analyzing Coping Strategies and Adaptation after Resettlement—Case Study of Ekondo Kondo, Cameroon and Ekondo Kondo Model of Adaptation
2020-11-18

This article centrally deals with the resettlement of the Cameroonian village Ekondo Kondo. In the following paper, I present resettlements as catastrophic events for the relocated populations. Research was conducted in the resettled Cameroonian village of Ekondo Kondo. The objectives of the research were to find out what kind of changes and challenges (positive and negative) people faced after relocation, whether these changes and challenges illustrated aspects of adaptation after resettlement which are lacking in the literature, and whether they could be included in the existing models of adaptation after resettlement to provide an enhanced framework for resettlement-linked projects. I demonstrate the consequences of the relocation for women and men. Whereas women developed coping strategies, adapted to the new village (site) 13 years after the relocation, and were able to emancipate themselves, men are still struggling with the relocation’s changes including threats to their former social role as hunters. These results support my argument that the existing adaptation models in the literature do not depict all key challenges the relocated populations have to go through. According to the fieldwork results, there are several adaptation processes in different key areas which do not follow one another or run homogenously but overlap and sometimes happen at the same time and on different levels. Additionally, there are significant gender specific differences which can be depicted in these key areas. Further predispositions of social groups, such as interests or experiences, can influence the processes of coping and adaptation as well. For this reason, I present and introduce the Ekondo Kondo Model of adaptation after relocation, which can be helpful both for difficult adaptation following disasters and adaptation processes when people develop fast coping strategies and get positive results.
Follicular lymphoma t(14;18)-negative is genetically a heterogeneous disease
2020-11-19

Abstract Fifty-five cases of t(14;18)− follicular lymphoma (FL) were genetically characterized by targeted sequencing and copy number (CN) arrays. t(14;18)− FL predominated in women (M/F 1:2); patients often presented during early clinical stages (71%), and had excellent prognoses. Overall, t(14;18)− FL displayed CN alterations (CNAs) and gene mutations carried by conventional t(14;18)+ FL (cFL), but with different frequencies. The most frequently mutated gene was STAT6 (57%) followed by CREBBP (49%), TNFRSF14 (39%), and KMT2D (27%). t(14;18)− FL showed significantly more STAT6 mutations and lacked MYD88, NOTCH2, MEF2B, and MAP2K1 mutations compared with cFL, nodal marginal zone lymphoma (NMZL), and pediatric-type FL (PTFL). We identified 2 molecular clusters. Cluster A was characterized by TNFRSF14 mutations/1p36 alterations (96%) and frequent mutations in epigenetic regulators, with recurrent loss of 6q21-24 sharing many features with cFL. Cluster B showed few genetic alterations; however, a subgroup with STAT6 mutations concurrent with CREBBP mutations/16p alterations without TNFRSF14 and EZH2 mutations was noted (65%). These 2 molecular clusters did not distinguish cases by inguinal localization, growth pattern, or presence of STAT6 mutations. BCL6 rearrangements were demonstrated in 10 of 45 (22%) cases and did not cluster together. Cases with predominantly inguinal presentation (20 of 50; 40%) had a higher frequency of diffuse growth pattern, STAT6 mutations, CD23 expression, and a lower number of CNAs, in comparison with noninguinal cases (5.1 vs 9.1 alterations per case; P &amp;lt; .05). STAT6 mutations showed a positive correlation with CD23 expression (P &amp;lt; .001). In summary, t(14;18)− FL is genetically a heterogeneous disorder with features that differ from cFL, NMZL, and PTFL.
Application of a Novel Iterative Denoising and Image Enhancement Technique in T1-Weighted Precontrast and Postcontrast Gradient Echo Imaging of the Abdomen
2020-11-19

Objectives The aim of this study was to investigate the impact of a novel iterative denoising and image enhancement technique in T1-weighted precontrast and postcontrast volume-interpolated breath-hold examination (VIBE) of the abdomen on image quality, noise levels, and diagnostic confidence without change of acquisition parameters. Materials and Methods Fifty patients were included in this retrospective, monocentric, institutional review board–approved study after clinically indicated magnetic resonance imaging of the abdomen including T1-weighted precontrast and postcontrast imaging. After acquisition of the standard VIBE (VIBE S ), images were processed with a novel reconstruction algorithm using the same raw data as for VIBE S , resulting in a denoised and enhanced dataset (VIBE DE ). Two different radiologists evaluated both datasets in a randomized order regarding sharpness of organs as well as vessels, noise levels, artifacts, overall image quality, and diagnostic confidence using a Likert scale ranging from 1 to 4 with 4 being the best. Furthermore, in the presence of focal liver lesions, the largest lesion was measured in the postcontrast dataset, and lesion detectability was analyzed using a Likert scale (1–4). Results Precontrast and postcontrast sharpness of organs and sharpness of vessels were rated significantly superior by both readers in VIBE DE with a median of 4 (interquartile range, 0) compared with VIBE S with a median of 3 (1) (all P 's &lt; 0.0001). Precontrast and postcontrast noise levels were also rated superior by both readers in VIBE DE with a median of 4 (0) compared with VIBE S with a median of 3 (1) for precontrast and a median of 3 (0) (median of 3 [1] for reader 2) for postcontrast imaging (all P 's &lt; 0.0001). Overall image quality was also rated higher with a median of 4 (0) in VIBE DE versus 3 (1) in VIBE S ( P &lt; 0.0001). Twenty-seven imaging studies contained liver lesions. There was no difference regarding the number and localization between the readers and between VIBE S and VIBE DE . Lesion detectability was rated by both readers significantly better in VIBE DE with a median of 4 (0) compared with a median of 4 (1) for reader 1 and a median of 3 (1) for reader 2 ( P = 0.001 for reader 1; P &lt; 0.001 for reader 2). Consequently, diagnostic confidence was also significantly superior in VIBE DE versus VIBE S with a median of 4 (0) for both ( P = 0.001). Interreader agreement resulted in a Cohen κ of 0.76 for precontrast analysis as well as of 0.76 for postcontrast analysis. Conclusions Application of a novel iterative denoising and image enhancement technique in T1-weighted VIBE precontrast and postcontrast imaging of the abdomen is feasible, providing superior image quality, noise levels, and diagnostic confidence.
Game-based learning environments affect frontal brain activity
2020-11-19

Inclusion of game elements in learning environments to increase motivation and learning outcome is becoming increasingly popular. However, underlying mechanisms of game-based learning have not been studied sufficiently yet. In the present study, we investigated effects of game-based learning environments on a neurofunctional level. In particular, 59 healthy adults completed a game-based version (including game elements such as a narrative and virtual incentives) as well as a non-game-based version of a number line estimation task, to improve fractional knowledge, while their brain activity was monitored using near-infrared spectroscopy. Behavioral performance was comparable across the two versions, although there was a tendency that less errors were made in the game-based version. However, subjective user experience differed significantly between versions. Participants rated the game-based version as more attractive, novel, and stimulating but less efficient than the non-game-based version. Additionally, positive affect was reported to be higher while engaging in the game-based as compared to the non-game-based task version. Corroborating these user reports, we identified increased brain activation in areas associated with emotion and reward processing while playing the game-based version, which might be driven by rewarding elements of the game-based version. Moreover, frontal areas associated with attention were also more activated in the game-based version of the task. Hence, we observed converging evidence on a user experience and neurofunctional level indicating that the game-based version was more rewarding as well as emotionally and attentionally engaging. These results underscore the potential of game-based learning environments to promote more efficient learning by means of attention and reward up-tuning.
Face Tuning in Depression
2020-11-19

Abstract The latest COVID-19 pandemic reveals that unexpected changes elevate depression bringing people apart, but also calling for social sharing. Yet the impact of depression on social cognition and functioning is not well understood. Assessment of social cognition is crucial not only for a better understanding of major depressive disorder (MDD), but also for screening, intervention, and remediation. Here by applying a novel experimental tool, a Face-n-Food task comprising a set of images bordering on the Giuseppe Arcimboldo style, we assessed the face tuning in patients with MDD and person-by-person matched controls. The key benefit of these images is that single components do not trigger face processing. Contrary to common beliefs, the outcome indicates that individuals with depression express intact face responsiveness. Yet, while in depression face sensitivity is tied with perceptual organization, in typical development, it is knotted with social cognition capabilities. Face tuning in depression, therefore, may rely upon altered behavioral strategies and underwriting brain mechanisms. To exclude a possible camouflaging effect of female social skills, we examined gender impact. Neither in depression nor in typical individuals had females excelled in face tuning. The outcome sheds light on the origins of the face sensitivity and alterations in social functioning in depression and mental well-being at large. Aberrant social functioning in depression is likely to be the result of deeply-rooted maladaptive strategies rather than of poor sensitivity to social signals. This has implications for mental well-being under the current pandemic conditions.
Enthusiasm
2020-11-19

Abstract Enthusiasm seeks to contribute to a culturally and historically nuanced understanding of how emotions secure and ratify the truth of convictions. More than just pure affective intensity, enthusiasm is about something: a certainty, clarity, or truth. Neither as clearly negative as “fanaticism” nor as general as “passion,” “enthusiasm” specifically entails belief. For this reason, Enthusiasm takes its starting point in religion, the social arena in which the concept was first debated and to which the term still gestures. Empirically based in modern German Protestantism, where religious emotion is intensely cultivated but also subject to vigorous scrutiny, this book combines historical and ethnographic methods to show how enthusiasm has been negotiated and honed as a practice in Protestant denominations ranging from liberal to charismatic. The nexus of religion and emotion and how it relates to central concepts of modernity such as rationality, knowledge, interiority, and sincerity are key to understanding why moderns are so ambivalent about enthusiasm. Grounded in practice theory, Enthusiasm assumes that emotions are not an affective state we “have” but mind–body activations we “do,” having learned to perform them in culturally specific ways. This book shows that, when understood as an emotional practice, enthusiasm has different styles, inflected by historical traditions, social milieus, and knowledge (even ideologies) about emotions and how they work. Finally, Enthusiasm also provides insight into how this feeling works in secular humanism as well as in politics, and why it is so contested as a practice in any context.
Early results of a low-profile stent-graft for thoracic endovascular aortic repair
2020-11-19

Purpose To assess outcomes of a low-profile thoracic stent-graft in the treatment of thoracic aortic pathologies. Methods A retrospective analysis of all consecutive patients with aortic thoracic pathologies treated with the RelayPro device in two university hospitals between October 2018 and July 2019. Results 23 patients (65% men; mean age 63.4 ± 15 years) were treated. Pathologies included aortic dissections (n = 10), 5 residual type A (22%) and 5 type B (22%), 6 degenerative aortic aneurysms (26%), 4 penetrating aortic ulcers (17%), and aortic erosion, intramural hematoma and aortic rupture (n = 1 and 4% in each case). Two cases (9%) were emergent and two urgent. Proximal landing was achieved in zones 0 (4%), 1 (4%), 2 (43%), and 3 (26%). Five grafts were frozen elephant trunk extensions. Technical success was 100% with accurate device deployment in the intended landing zone of the aortic arch in all 23 patients and with no Ia/III endoleaks and three (13%) type II endoleaks. Apposition was adequate in 96%. Two patients had post-implantation syndromes (one fever, one leukocytosis). Mean follow-up was 11.6 ± 3.7 months (range, 2–16) with no other complications, secondary interventions or conversions to open surgery. There was no 30-day mortality and no aortic-related mortality; all-cause mortality was 4% during follow-up. Conclusion A 3–4 French reduced profile in the current generation of stent-grafts facilitates TEVAR particularly in patients with smaller vessels access. Early safety and effectiveness outcomes are favorable, even in endpoints such as deployment accuracy and apposition which may be surrogates for longer-term clinical success and durability.
Open Science in Psychophysiology: An Overview of Challenges and Emerging Solutions
2020-11-19

The present review is the result of a one-day workshop on open science, held at the Annual Meeting of the Society for Psychophysiological Research in Washington, DC, September 2019. The contributors represent psychophysiological researchers at different career stages and from a wide spectrum of institutions. The state of open science in psychophysiology is discussed from different perspectives, highlighting key challenges, potential benefits, and emerging solutions that are intended to facilitate open science practices. Three domains are emphasized: data sharing, preregistration, and multi-site studies. In the context of these broader domains, we present potential implementations of specific open science procedures such as data format harmonization, power analysis, data, presentation code and analysis pipeline sharing, suitable for psychophysiological research. Practical steps are discussed that may be taken to facilitate the adoption of open science practices in psychophysiology. These steps include (1) promoting broad and accessible training in the skills needed to implement open science practices, such as collaborative research and computational reproducibility initiatives, (2) establishing mechanisms that provide practical assistance in sharing of processing pipelines, presentation code, and data in an efficient way, and (3) improving the incentive structure for open science approaches. Throughout the manuscript, we provide references and links to available resources for those interested in adopting open science practices in their research.
Investigating holistic face processing within and outside of face-responsive brain regions
2020-11-19

It has been shown that human faces are processed holistically (i.e. as indecomposable wholes, rather than by their component parts) and this holistic face processing is linked to brain activity in face-responsive brain regions. Although several brain regions outside of the face-responsive network are also sensitive to relational processing and perceptual grouping, whether these non-face-responsive regions contribute to holistic processing remains unclear. Here, we investigated holistic face processing in the composite face paradigm both within and outside of face-responsive brain regions. We recorded participants' brain activity using fMRI while they performed a composite face task. Behavioural results indicate that participants tend to judge the same top face halves as different when they are aligned with different bottom face halves but not when they are misaligned, demonstrating a composite face effect. Neuroimaging results revealed significant differences in responses to aligned and misaligned faces in the lateral occipital complex (LOC), and trends in the anterior part of the fusiform face area (FFA2) and transverse occipital sulcus (TOS), suggesting that these regions are sensitive to holistic versus part-based face processing. Furthermore, the retrosplenial cortex (RSC) and the parahippocampal place area (PPA) showed a pattern of neural activity consistent with a holistic representation of face identity, which also correlated with the strength of the behavioural composite face effect. These results suggest that neural activity in brain regions both within and outside of the face-responsive network contributes to the composite-face effect.
Fostering Knowledge of Computer Viruses among Children
2020-11-19

Children increasingly use computing devices. However, it is unclear whether they have basic knowledge of security-related issues such as computer viruses and, in case they do not, what they can learn about them. It was found previously that Czech 8-year-olds have only limited knowledge of computer viruses, but neither naïve understanding of older children nor what they can learn has been researched. Here, we first examined preconceptions of computer viruses among Czech 5-6-graders (N = 14) and German 3-4-graders (N = 28) by means of a written test. Second, the German sample (experimental group), but not the Czech one (control group), received an intervention to learn about computer viruses, antiviruses, and software updates by means of a 45-min lesson combining a cartoon series on viruses, frontal instruction, and discussion. Both groups again completed the written test. A joint analysis of both samples indicated that Czech and German children already knew key points concerning computer viruses. These included, for instance, that viruses harm our computers (88% of the total sample). However, overall, their knowledge was patchy, and children also had misconceptions such as that viruses can only infect devices connected to the Internet (57%), and antiviruses can delete viruses from the Internet (40%). Due to the intervention, the experimental group improved from pre to posttest (d = 1.06), while this was not the case for the control group. A more in-depth analysis indicated that knowledge gains were mostly related to information repeatedly mentioned during the lesson, but it was less clear whether the lesson helped correct previously held misconceptions. Taken together, the results indicated that knowledge of computer viruses should and can be taught to primary school children, but attention must be paid to existing preconceptions.
Modeling Maltese Noun Plural Classes without Morphemes
2020-11-19

Word and Paradigm morphology proposes that morphologically complex words are stored as wholes in the mental lexicon, and by doing so it avoids problems that are related to the notion of the morpheme. However, it is not yet clear to what degree it is possible to computationally model classification and production of complex word forms without morphemes.We take up this question by modeling the classification and production of the Maltese noun plural system. Maltese is a Semitic language that has two broad classes of plurals: concatenative ones and non-concatenative ones. We model the classification in two models, and the production in a third one. The first model for classification, the Tilburg Memory Based Learner (TiMBL), is a computational implementation of exemplar models. TiMBL is impartial as to the existence of morphemes in the mental lexicon, and allows us to directly compare the classification with and without morphemes. It turns out that the classification with and without morphemes of Maltese nouns is equally good. The second classification model is the Naive Discriminative Learner (NDL). NDL is a computational implementation of discriminative learning. It can be understood as an implementation of the Word and Paradigm model and thus eschews morphemes. It differs from TiMBL in its assumptions about learning, and they way in which the classifications are obtained. NDL, too, classifies Maltese nouns well. A classification task is very different from a production task, and therefore we used neural networks to model the production of plurals. In these models we address the question whether the production of a plural noun for a given singular can be modeled without recourse to morphemes. We used two neural networks architectures (LSTM and GRU) that have been applied to linguistic phenomena, and find that they are able to correctly produce plurals, without making use of morphemes.We conclude that the Maltese noun plural system can be modeled on the basis of whole words alone without morphemes. These results, therefore, support the Word and Paradigm theory of the mental lexicon.