julilili42/papers huggingface dataset:
A Diagnostic Approach to the Identification of Burkitt-like Lymphoma With 11q Aberration in Aggressive B-Cell Lymphomas
2020-10-30

Rare cases of aggressive B-cell lymphomas with a morphology similar to Burkitt lymphoma (BL) present with the BL-typical immunophenotype, but lacked MYC translocation ( MYC -negative Burkitt-like lymphoma: mnBLL). A proportion of those with an imbalance pattern in chromosome 11q has been designated Burkitt-like lymphoma with 11q aberration in the recent update of the World Health Organization (WHO) classification. Because of the problems in the identification of Burkitt-like lymphoma with 11q aberration, our goal was to retrospectively analyze their frequency in a cohort of “candidate” aggressive lymphomas (cohort 1, n=35) such as mnBLL (n=16), diffuse large B-cell lymphoma with similarities to Burkitt lymphoma (DLBCL-BL; n=3), high-grade B-cell lymphomas, not otherwise specified (NOS) (n=16), as well as in a cohort of MYC -negative diffuse large B-cell lymphoma NOS (cohort 2, n=62). In total, 17/33 cohort 1 cases (52%) harbored the typical 11q aberration pattern, predominantly those that had been classified as mnBLL (12/16, 75%), but also as DLBCL-BL (2/3, 67%) and high-grade B-cell lymphomas, NOS (3/14; 21%). The specimens with this typical 11q aberration pattern were usually negative for the BCL2 protein. Of interest and as a new finding, samples harboring the 11q aberration pattern were often characterized by strikingly coarse apoptotic debris within starry sky macrophages facilitating their recognition. In contrast, only 1 of 62 garden variety DLBCL, NOS was positive for the 11q aberration pattern. In 2 DLBCL-BL, a dual MYC translocation/11q aberration pattern was detected. As a diagnostic algorithm, we, therefore, propose analysis of 11q status in MYC -negative high-grade lymphomas with features of BL, especially showing BCL2 negativity and a conspicuous coarse apoptotic debris in starry sky macrophages.
Facilitating collaborative reflective inquiry amongst teachers: What do we currently know?
2020-10-30

Collaborative teacher learning is thought to improve teaching practice and student outcomes. Key to such learning is Reflective Professional Inquiry (RPI); seen as vital if practitioners are to engage effectively with new knowledge and ideas. Yet RPI is under-conceptualised and little is known about how to facilitate effective RPI. With this study we engage in a meta-narrative literature review, covering a range of disciplines (including education, medicine, and psychology), in an attempt to fill these knowledge gaps. Findings indicate that there are no existing interventions designed to foster RPI that have been rigorously evaluated. Consequently, there are no approaches that could be employed as part of collaborative teacher learning, with the expectation that practice or student outcomes will subsequently improve.
Geographically structured genomic diversity of non-human primate-infecting Treponema pallidum subsp. pertenue
2020-10-30

Many non-human primate species in sub-Saharan Africa are infected with Treponema pallidum subsp. pertenue , the bacterium causing yaws in humans. In humans, yaws is often characterized by lesions of the extremities and face, while T. pallidum subsp. pallidum causes venereal syphilis and is typically characterized by primary lesions on the genital, anal or oral mucosae. It remains unclear whether other T. pallidum subspecies found in humans also occur in non-human primates and how the genomic diversity of non-human primate T. pallidum subsp. pertenue lineages is distributed across hosts and space. We observed orofacial and genital lesions in sooty mangabeys ( Cercocebus atys ) in Taï National Park, Côte d’Ivoire and collected swabs and biopsies from symptomatic animals. We also collected non-human primate bones from 8 species in Taï National Park and 16 species from 11 other sites across sub-Saharan Africa. Samples were screened for T. pallidum DNA using polymerase chain reactions (PCRs) and we used in-solution hybridization capture to sequence T. pallidum genomes. We generated three nearly complete T. pallidum genomes from biopsies and swabs and detected treponemal DNA in bones of six non-human primate species in five countries, allowing us to reconstruct three partial genomes. Phylogenomic analyses revealed that both orofacial and genital lesions in sooty mangabeys from Taï National Park were caused by T. pallidum subsp. pertenue . We showed that T. pallidum subsp. pertenue has infected non-human primates in Taï National Park for at least 28 years and has been present in two non-human primate species that had not been described as T. pallidum subsp. pertenue hosts in this ecosystem, western chimpanzees ( Pan troglodytes verus ) and western red colobus ( Piliocolobus badius ), complementing clinical evidence that started accumulating in Taï National Park in 2014. More broadly, simian T. pallidum subsp. pertenue strains did not form monophyletic clades based on host species or the symptoms caused, but rather clustered based on geography. Geographical clustering of T. pallidum subsp. pertenue genomes might be compatible with cross-species transmission of T. pallidum subsp. pertenue within ecosystems or environmental exposure, leading to the acquisition of closely related strains. Finally, we found no evidence for mutations that confer antimicrobial resistance.
Nanocellulose and Elastin Act as Plasticizers of Electrospun Bioinspired Scaffolds
2020-10-30

In this work, we produced cross-linked electrospun hybrid scaffolds composed of gelatin/poly-D,L-lactide, gelatin/poly-D,L-lactide/nanocellulose and gelatin/poly-D,L-lactide/cellulose nanocrystals/elastin. Fourier-Transform Infrared Spectroscopy, X-Ray Diffraction, and High Performance Liquid Chromatography demonstrated the complete embedding of each com-ponent in the hybrid scaffolds. Degree of cross-linking was quantified by using a 2,4,6-trinitrobenzenesulfonic acid assay and Attenuated Total Reflectance Spectroscopy revealed the effectiveness of cross-linking reaction. Noteworthy, the interconnected porous structure revelead in un-cross-linked scaffolds endured even after cross-linking. Scaffolds were characterized in water through contact angle showing total wettability. We throughout investigated mechanical properties by Uniaxial Tensile Testing showing that even in the dry-state nanocellulose and elastin containing scaffolds exhibit higher elongation at rupture compared to pure gelatin/poly-D,L-lactide. Therefore, we succeed in tuning the toughness of the scaffolds by modulating composition. In order to use scaffolds as medical devices, we assayed fibroblasts on scaffolds extraction media establishing that they were non-cytotoxic. Finally the attachment and proliferation of fibroblasts on the surface of different scaffolds was evaluated
Resilience of Micropollutant and Biological Effect Removal in an Aerated Horizontal Flow Treatment Wetland
2020-10-30

The performance of an aerated horizontal subsurface flow treatment wetland was investigated before, during and after a simulated aeration failure. Conventional wastewater parameters (e.g., carbonaceous biological oxygen demand, total nitrogen, and Escherichia coli) as well as selected micropollutants (caffeine, ibuprofen, naproxen, benzotriazole, diclofenac, acesulfame, and carbamazepine) were investigated. Furthermore, the removal of biological effects was investigated using in vitro bioassays. The six bioassays selected covered environmentally relevant endpoints (indicative of activation of aryl hydrocarbon receptor, AhR; binding to the peroxisome proliferator-activated receptor gamma, PPARγ; activation of estrogen receptor alpha, ERα; activation of glucocorticoid receptor, GR; oxidative stress response, AREc32; combined algae test, CAT). During the aeration interruption phase, the water quality deteriorated to a degree comparable to that of a conventional (non-aerated) horizontal subsurface flow wetland. After the end of the aeration interruption, the analytical and biological parameters investigated recovered at different time periods until their initial treatment performance. Treatment efficacy for conventional parameters was recovered within a few days, but no complete recovery of treatment efficacy could be observed for bioassays AhR, AREc32 and CAT in the 21 days following re-start of the aeration system. Furthermore, the removal efficacy along the flow path for most of the chemicals and bioassays recovered as it was observed in the baseline phase. Only for the activation of AhR and AREc32 there was a shift of the internal treatment profile from 12.5% to 25% (AhR) and 50% (AREc32) of the fractional length.
Task-Irrelevant Visual Forms Facilitate Covert and Overt Spatial Selection
2020-10-30

Covert and overt spatial selection behaviors are guided by both visual saliency maps derived from early visual features as well as priority maps reflecting high-level cognitive factors. However, whether mid-level perceptual processes associated with visual form recognition contribute to covert and overt spatial selection behaviors remains unclear. We hypothesized that if peripheral visual forms contribute to spatial selection behaviors, then they should do so even when the visual forms are task-irrelevant. We tested this hypothesis in male and female human subjects as well as in male macaque monkeys performing a visual detection task. In this task, subjects reported the detection of a suprathreshold target spot presented on top of one of two peripheral images, and they did so with either a speeded manual button press (humans) or a speeded saccadic eye movement response (humans and monkeys). Crucially, the two images, one with a visual form and the other with a partially phase-scrambled visual form, were completely irrelevant to the task. In both manual (covert) and oculomotor (overt) response modalities, and in both humans and monkeys, response times were faster when the target was congruent with a visual form than when it was incongruent. Importantly, incongruent targets were associated with almost all errors, suggesting that forms automatically captured selection behaviors. These findings demonstrate that mid-level perceptual processes associated with visual form recognition contribute to covert and overt spatial selection. This indicates that neural circuits associated with target selection, such as the superior colliculus, may have privileged access to visual form information. SIGNIFICANCE STATEMENT Spatial selection of visual information either with (overt) or without (covert) foveating eye movements is critical to primate behavior. However, it is still not clear whether spatial maps in sensorimotor regions known to guide overt and covert spatial selection are influenced by peripheral visual forms. We probed the ability of humans and monkeys to perform overt and covert target selection in the presence of spatially congruent or incongruent visual forms. Even when completely task-irrelevant, images of visual objects had a dramatic effect on target selection, acting much like spatial cues used in spatial attention tasks. Our results demonstrate that traditional brain circuits for orienting behaviors, such as the superior colliculus, likely have privileged access to visual object representations.
Self-Regulation and Mathematics Performance in German and Iranian Students of More and Less Math-Related Fields of Study
2020-10-30

Self-regulation is a multidimensional construct that is positively related to academic achievement, such as successful mathematics performance. However, this relation of self-regulation and mathematics performance has mainly been investigated in Western countries with similar cultural contexts, although self-regulation is assumed to be context-sensitive. Therefore, the present study investigated the relation of self-regulation and mathematics performance across two different countries (Germany vs. Iran) in college students. The relation of self-regulation and mathematics performance was expected to be weaker in students of math-related fields, such as Engineering/Informatics, as they are assumed to need less self-regulation to solve the mathematics problems than students of less math-related fields, such as Human Sciences. In total, 122 undergraduate students (German = 60; Iranian = 62) of Human Sciences or Engineering/Informatics participated in this study. We measured self-regulation with the Brief Self-Control Scale (Tangney et al., 2004) and mathematics performance with a complex multiplication test. Results showed that self-regulation did not predict multiplication performance in German or Iranian students, in general. However, when the field of study was considered, self-regulation predicted multiplication performance in the subgroup of German and Iranian students studying Human Sciences within each country. We conclude that cultural context does not seem to play a dominant role in moderating the relation between self-regulation and math performance, however, field of study and more generally familiarity with math may be an important factor to consider in single or cross-cultural studies.
Detecting the re-emergent COVID-19 pandemic after elimination: modelling study of combined primary care and hospital surveillance.
2020-10-30

This model-based analysis suggests that a surveillance system with a very high level of routine testing is probably required to detect an emerging or re-emerging SARS-CoV-2 outbreak within five weeks of a border control failure in a nation that had previously eliminated COVID-19. Nevertheless, there are plausible strategies to enhance testing yield and cost-effectiveness and potential supplementary surveillance systems such as the testing of town/city sewerage systems for the pandemic virus.
Alpha entrainment drives pain relief using visual stimulation in a sample of chronic pain patients. A proof-of-concept controlled study.
2020-10-30

One-third of the population in the UK and worldwide struggle with chronic pain. Entraining brain alpha activity through non-invasive visual stimulation has been shown to reduce experimental pain in healthy volunteers. Neural oscillations entrainment offers a potential non-invasive and non-pharmacological intervention for patients with chronic pain, which can be delivered in the home setting and has the potential to reduce use of medications. However, evidence supporting its use in patients with chronic pain is lacking. This study explores whether a) alpha entrainment increase alpha power in patients and b) whether this increase in alpha correlates with analgesia.28 patients with chronic pain sat in a comfortable position and underwent 4-minute visual stimulation using customised goggles at 10 Hz (alpha) and 7 Hz (control) frequency blocks in a randomised cross-over design. 64-channel Electroencephalography (EEG) and 11-point Numeric Rating Scale (NRS) pain intensity and pain unpleasantness scores were recorded before and after stimulation.EEG analysis revealed frontal alpha power was significantly higher when stimulating at 10 Hz when compared to 7 Hz. There was a significant positive correlation between increased frontal alpha and reduction in pain intensity (r=0.33, p&amp;lt;0.05) and pain unpleasantness (r=0.40, p&amp;lt;0.05) in the 10 Hz block.This study provides the first proof of concept that changes in alpha power resulting from entrainment correlate with an analgesic response in patients with chronic pain. Further studies are warranted to investigate dose-response parameters and equivalence to analgesia provided by medications.
COMPARATIVE TAPHONOMY OF DEEP-SEA AND SHALLOW-MARINE ECHINOIDS OF THE GENUS ECHINOCYAMUS
2020-10-30

ABSTRACT The infaunal living clypeasteroid echinoid genus Echinocyamus is considered a model organism for various ecological and paleontological studies since its distribution ranges from the polar regions to the tropics, and from shallow-marine settings to the deep-sea. Deep-sea analyses of this genus are rare, but imperative for the understanding and function of these important ecosystems. During the 2012 Southern Surveyor expedition, 35 seamounts off the east coast of Australia were dredged in depths greater than 800 m. Of these, six dredges contained a total of 18 deep-sea Echinocyamus tests. The tests have been analyzed for taphonomic alterations including abrasion patterns, macro-borings, micro-borings, depressions on the test, test staining, test filling, encrustation, and fragmentation. Findings are interpreted in the context of the deep-sea setting and are compared to Echinocyamus samples from shallow-water environments. Results show that abrasion in deep-sea environments is generally high, especially in ambulacral and genital pores indicating that tests can persist for a long time on the seafloor. This contrasts with shallow-water Echinocyamus that show lower abrasion due to early test destruction. Macro-borings are present as single or paired holes with straight vertical profiles resembling Lithophaga borings. Micro-borings are abundant and most likely the result of sponge or fungal activity. Depressions on the tests, such as scars or pits, are likely the result of trauma or malformation during ontogeny. Test staining is common, but variable, and is associated with FE/Mn oxidation and authigenic clays based on elemental analyses. Test filling occurs as loose or lithified sediment. Encrustation is present in the form of rudimentary crusts and biofilms. No macro-organisms were found on the tests. Biofilm composition differs from shallow-water environments in that organisms captured in the biofilm reflect aphotic conditions or sedimentation of particles from higher in the water column (e.g., coccoliths). Fragmentation is restricted to the apical system and pore regions. Results of this first comparative study on deep-sea Echinocyamus from Australian seamounts show that the minute tests can survive for a long time in these settings and undergo environmental specific taphonomic processes reflected in various taphonomic alterations.
TuLeD. Tupían Lexical Database
2020-10-30

Cite the source of the dataset as: Fabrício Ferraz Gerardi, Stanislav Reichert, Carolina Aragon, Johann-Mattis List, &amp; Tim Wientzek. (2021). TuLeD: Tupían lexical database. Max Planck Institute for Evolutionary Anthropology: Leipzig
Acceptance of near-natural greenspace management relates to ecological and socio-cultural assigned values among European urbanites
2020-10-31

Grasslands are widespread elements of urban greenspace providing recreational, psychological and aesthetic benefits to city residents. Two urban grassland types of contrasting management dominate urban greenspaces: frequently mown, species-poor short-cut lawns and less intensively managed, near-natural tall-grass meadows. The higher conservation value of tall-grass meadows makes management interventions such as converting short-cut lawns into tall-grass meadows a promising tool for urban biodiversity conservation. The societal success of such interventions, however, depends on identifying the values urban residents assign to different types of urban grasslands, and how these values translate to attitudes towards greenspace management. Using 2027 questionnaires across 19 European cities, we identify the assigned values that correlate with people's personal greenspace use and their preferences for different types of urban grasslands to determine how these values relate to the agreement with a scenario of converting 50% of their cities' short-cut lawns into tall-grass meadows. We found that most people assigned nature-related values, such as wildness, to tall-grass meadows and utility-related values, such as recreation, to short-cut lawns. Positive value associations of wildness and species richness with tall-grass meadows, and social and nature related greenspace activities, positively correlated with agreeing to convert short-cut lawns into tall-grass meadows. Conversely, disapproval of lawn conversion correlated with positive value associations of cleanliness and recreation potential with short-cut lawns. Here, people using greenspaces for nature-related activities were outstandingly positive about lawn conversion. The results show that the plurality of values assigned to different types of urban grasslands should be considered in urban greenspace planning. For example, tall-grass meadows could be managed to also accommodate the values associated with short-cut lawns, such as tidiness and recreation potential, to support their societal acceptance.
Salt dome related soil salinity in southern Iran: Prediction and mapping with averaging machine learning models
2020-10-31

Abstract In order to manage soil salinity effectively, it is necessary to understand the origin and the spatial distribution of salinity. There are about 120 salt dome outcrops in southern Iran and little is known about their contribution as the potential sources of salts and the spatial pattern of salts around them. Six machine learning algorithms were applied to model topsoil electrical conductivity (EC) and sodium adsorption ratio (SAR) in the Darab Plain (surrounded by six salt domes), Fars Province. Decision trees (DT), k‐nearest neighbours (kNN), support vector machines (SVM), Cubist, random forests (RF) and extreme gradient boosting (XGBoost) were used as primary models and the Granger–Ramanathan (GR) method was used to combine the predictions of these models. The results showed that remotely sensed data contributed more to predict EC and SAR than terrain‐based data. In terms of root mean square errors (RMSE), Cubist followed by the RF model, tended to give the best estimates of EC, whereas for SAR, RF performed best and was followed closely by SVM and Cubist. Compared to the primary models, the GR method on average resulted in a decrease of 6.1% and 3.9% in RMSE and an increase of 10% and 10.9% in R 2 for EC and SAR, respectively. The spatial pattern of SAR and EC suggested that the contribution of salt domes in soil salinization varied significantly according to their hydraulic behaviour in relation to adjacent aquifers and their activity. In general, the model averaging approach showed the potential to improve the estimates of EC and SAR.
Extracellular Matrix-Specific Platelet Activation Leads to a Differential Translational Response and Protein De Novo Synthesis in Human Platelets
2020-10-31

Platelets are exposed to extracellular matrix (ECM) proteins like collagen and laminin and to fibrinogen during acute vascular events. However, beyond hemostasis, platelets have the important capacity to migrate on ECM surfaces, but the translational response of platelets to different extracellular matrix stimuli is still not fully characterized. Using 2D-gel electrophoresis, confocal microscopy, polysome analysis and protein sequencing by mass spectrometry, we demonstrate that platelets show a differential expression profile of newly synthesized proteins on laminin, collagen or fibrinogen. In this context, we observed a characteristic, ECM-dependent translocation phenotype of translation initiation factor eIF4E to the ribosomal site. eIF4E accumulated in polysomes with increased binding of mRNA and co-localization with vinculin, leading to de novo synthesis of important cytoskeletal regulator proteins. As the first study, we included a proteome analysis of laminin-adherent platelets and interestingly identified upregulation of essentially important proteins that mediate cytoskeletal regulation and mobility in platelets, such as filamin A, talin, vinculin, gelsolin, coronin or kindlin-3. In summary, we demonstrate that platelet activation with extracellular matrix proteins results in a distinct stimulus-specific translational response of platelets that will help to improve our understanding of the regulation of platelet mobility and migration.