julilili42/papers huggingface dataset:
Data for "A systematic evaluation of interneuron morphology representations for cell type discrimination"
2020-02-14

data_v1.1 contains all the data to reproduce the figures of the publication <em>A systematic evaluation of interneuron morphology representations for cell type discrimination (</em>https://doi.org/10.1101/591370<em>).</em> statistic_descriptions.csv : links each feature's statistic_id with a short description classification: This folder holds the multi-class and the pairwise classification performances of all feature representations (relevant for figure 4 and figure 5). It also holds the pickled multi-class models trained on morphometric statistics which coefficients are visualized in figure S5. embedding_data: This folder holds all the data used for the t-SNE visualizations of figure 8 and S4. features: This folder holds all computed feature representations of each data set and each modality (full, axon, dendrite). Features are indexed by a statistic id. Some example features are shown in figure 2. Careful, this folder is large (~6GB)! reconstructions: This folder contains all the neural reconstructions used for figure 1. final morphologies: contains all pre-processed reconstructions used in this study.
Data for "A systematic evaluation of interneuron morphology representations for cell type discrimination"
2020-02-14

This folder contains all the data to reproduce the figures of the publication <em>A systematic evaluation of interneuron morphology representations for cell type discrimination (</em>https://doi.org/10.1101/591370<em>).</em> statistic_descriptions.csv : links each feature's statistic_id with a short description classification: This folder holds the multi-class and the pairwise classification performances of all feature representations (relevant for figure 4 and figure 5). It also holds the pickled multi-class models trained on morphometric statistics which coefficients are visualized in figure S5. embedding_data: This folder holds all the data used for the t-SNE visualizations of figure 8 and S4. features: This folder holds all computed feature representations of each data set and each modality (full, axon, dendrite). Features are indexed by a statistic id. Some example features are shown in figure 2. Careful, this folder is large (~6GB)! reconstructions: This folder contains all the neural reconstructions used for figure 1.
Influence of Physical Perturbation on Fe(II) Supply in Coastal Marine Sediments
2020-02-15

Iron (Fe) biogeochemistry in marine sediments is driven by redox transformations creating Fe(II) and Fe(III) gradients. As sediments are physically mixed by wave action or bioturbation, Fe gradients re-establish regularly. In order to identify the response of dissolved Fe(II) (Fe<sup>2+</sup>) and Fe mineral phases toward mixing processes, we performed voltammetric microsensor measurements, sequential Fe extractions, and Mössbauer spectroscopy of 12 h light-dark cycle incubated marine coastal sediment. Fe<sup>2+</sup> decreased during 7 days of undisturbed incubation from approximately 400 to 60 μM. In the first 2-4 days of incubation, Fe<sup>2+</sup> accumulated up to 100 μM in the top 2 mm due to Fe(III) photoreduction. After physical perturbation at day 7, Fe<sup>2+</sup> was re-mobilized reaching concentrations of 320 μM in 30 mm depth, which decreased to below detection limit within 2 days afterward. Mössbauer spectroscopy showed that the relative abundance of metastable iron-sulfur mineral phases (FeS<i><sub>x</sub></i>) increased during initial incubation and decreased together with pyrite (FeS<sub>2</sub>) after perturbation. We show that Fe<sup>2+</sup> mobilization in marine sediments is stimulated by chemical changes caused by physical disturbances impacting the Fe redox distribution. Our study suggests that, in addition to microbial and abiotic Fe(III) reduction, including Fe(III) photoreduction, physical mixing processes induce chemical changes providing sediments and the inhabiting microbial community with Fe<sup>2+</sup>.
FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2
2020-02-15

&amp;lt;p&amp;gt;The novel coronavirus (SARS-CoV-2) currently spreads worldwide, causing the disease COVID-19. The number of infections increases&amp;nbsp;daily, without any approved antiviral therapy. The recently released viral nucleotide sequence enables the identification of therapeutic&amp;nbsp;targets, e.g., by analyzing integrated human-virus metabolic models. Investigations of changed metabolic processes after virus&amp;nbsp;infections and the effect of knock-outs on the host and the virus can reveal new potential targets.&amp;lt;/p&amp;gt;\\n\\n&amp;lt;p&amp;gt;We generated an integrated host-virus genome-scale metabolic model of human alveolar macrophages and SARS-CoV-2. Analyses of&amp;nbsp;stoichiometric and metabolic changes between uninfected and infected host cells using flux balance analysis (FBA) highlighted the&amp;nbsp;different requirements of host and virus.&amp;lt;/p&amp;gt;\\n\\n&amp;lt;p&amp;gt;Consequently, alterations in the metabolism can have different effects on host and virus, leading to potential antiviral targets. One of&amp;nbsp;these potential targets is guanylate kinase (GK1). In FBA analyses, the knock-out of the guanylate kinase decreased the growth of the&amp;nbsp;virus to zero, while not affecting the host. As GK1 inhibitors are described in the literature, its potential therapeutic effect for SARS-CoV&amp;nbsp;2 infections needs to be verified in&amp;nbsp;&amp;lt;em&amp;gt;in-vitro&amp;lt;/em&amp;gt;&amp;nbsp;experiments.&amp;lt;/p&amp;gt;
The relationship between trainers’ media‐didactical competence and media‐didactical self‐efficacy, attitudes and use of digital media in training
2020-02-16

The ongoing digitalization in the training sector produces new demands on the media‐didactical competence of trainers. We conducted an online survey of 279 trainers in Germany to investigate the relationships among media‐didactical competence, media‐didactical self‐efficacy, attitudes toward the use of digital media and the actual use of digital media in training. Furthermore, we compared trainers who attended a course on digital media with trainers who did not attend such a course. The analysis of the theoretically expected correlations between the variables resulted in not all hypotheses being accepted. The analysis of the group differences showed that the trainers who attended a course on digital media had higher media‐didactical competence and media‐didactical self‐efficacy scores and used digital media more often in training. There was no significant difference in negative attitudes. The implications for the promotion of the media‐didactical competence of trainers are discussed.
Reformist Buddhist Groups in the Late Meiji Era and Their Relationship to Christianity
2020-02-16

This paper explores the attitude towards Christianity among the so-called “New Buddhists” in the late Meiji era, i.e. members and sympathizers of the reformist Buddhist groups Keiikai and Bukkyō seito dōshikai. Whereas an anti-Christian attitude prevailed among Buddhist intellectuals up to the 1880s and 1890s, the New Buddhists advocated religious tolerance and the unbiased study of religions. By analysing the writings of Furukawa Rōsen and prominent members of the Bukkyō seito dōshikai, particularly Sakaino Kōyō and Katō Genchi, this paper reconstructs how these Buddhist groups approached Christianity on the basis of comparative and historical studies, and based on their conviction that religion should serve societal goals and be compatible with the scientific knowledge of their times.
An Agenda for Open Science in Communication
2020-02-17

Abstract In the last 10 years, many canonical findings in the social sciences appear unreliable. This so-called “replication crisis” has spurred calls for open science practices, which aim to increase the reproducibility, replicability, and generalizability of findings. Communication research is subject to many of the same challenges that have caused low replicability in other fields. As a result, we propose an agenda for adopting open science practices in Communication, which includes the following seven suggestions: (1) publish materials, data, and code; (2) preregister studies and submit registered reports; (3) conduct replications; (4) collaborate; (5) foster open science skills; (6) implement Transparency and Openness Promotion Guidelines; and (7) incentivize open science practices. Although in our agenda we focus mostly on quantitative research, we also reflect on open science practices relevant to qualitative research. We conclude by discussing potential objections and concerns associated with open science practices.
A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry
2020-02-17

Abstract The field of epitranscriptomics continues to reveal how post-transcriptional modification of RNA affects a wide variety of biological phenomena. A pivotal challenge in this area is the identification of modified RNA residues within their sequence contexts. Mass spectrometry (MS) offers a comprehensive solution by using analogous approaches to shotgun proteomics. However, software support for the analysis of RNA MS data is inadequate at present and does not allow high-throughput processing. Existing software solutions lack the raw performance and statistical grounding to efficiently handle the numerous modifications found on RNA. We present a free and open-source database search engine for RNA MS data, called NucleicAcidSearchEngine (NASE), that addresses these shortcomings. We demonstrate the capability of NASE to reliably identify a wide range of modified RNA sequences in four original datasets of varying complexity. In human tRNA, we characterize over 20 different modification types simultaneously and find many cases of incomplete modification.
Spatial monitoring of grassland management using multi-temporal satellite imagery
2020-02-17

Spatial monitoring of grassland management is crucial for ecosystem assessment and the establishment of sustainable agriculture. Switzerland is covered by large areas of small structured grassland parcels differing in management practices and use intensities, making the mapping of grassland management challenging. We present a monitoring tool to map grassland management, distinguishing between mowing- and grazing practice, and between different use intensities for Swiss agroecosystems. By analyzing pixelwise spectral time series of 2015, derived from satellite imagery of the Landsat archive, we estimated the number of management events and biomass productivity. Both estimates were used to map classes of dominant management practices and use intensities following a stepwise clustering approach. The grassland management (GM) classes were evaluated relative to established spectral and topographical patterns of grassland use intensity, and in terms of spatial conformity with available regional land use data. The GM classes were also analyzed with respect to management related vegetation plot data on species diversity, as well as on indicator values for nutrient supply and management tolerance. The stepwise clustering gave three use intensity classes for each dominant management practice of grazing (pasture) and mowing (meadow). Use intensity was higher for meadows than pastures with a distinct intensity gradient for each grassland practice. The GM classes reproduced established spectral and topographical patterns of grassland use intensity, indicated by increased standard deviations (SD) of spectral time series profiles (e.g. mean SD of 0.048 for pastures and 0.054 for meadows) and lower slopes (e.g. mean slopes of 10° for pastures and 7° for meadows). The averaged spatial conformity of the GM classes with a cantonal land use map was 82% for meadows and 97% for pastures. The GM classes spatially matched with land use patterns of three subregions, e.g. with an areal proportion of 73% pasture classes for a subregion dominated by grazing. Moreover, the GM classes reproduced established vegetation patterns of grassland use intensity along the GM intensity gradient, showing a mean decrease in species richness (33%), as well as a mean increase in indicator values for nutrient supply (5%), grazing tolerance (4%), and mowing tolerance (6%).
GNAQ and GNA 11 mutant nonuveal melanoma: a subtype distinct from both cutaneous and uveal melanoma
2020-02-17

Our findings suggest that GNAQ/11 mutant nonuveal melanomas are a subtype of melanoma that is both clinically and genetically distinct from cutaneous and uveal melanoma. As they respond poorly to available treatment regimens, novel effective therapeutic approaches for affected patients are urgently needed. What is already known about this topic? The rare occurrence of GNAQ/11 mutations in nonuveal melanoma has been documented. GNAQ/11 mutant nonuveal melanomas also harbour genetic alterations in EIF1AX, SF3B1 and BAP1 that are of prognostic relevance in uveal melanoma. What does this study add? GNAQ/11 mutant nonuveal melanomas show metastatic spread reminiscent of cutaneous melanoma, but not uveal melanoma. GNAQ/11 mutant nonuveal melanomas have a low tumour mutational burden that is higher than uveal melanoma, but lower than cutaneous melanoma. What is the translational message? Primary GNAQ/11 mutant nonuveal melanomas are a subtype of melanoma that is clinically and genetically distinct from both cutaneous and uveal melanoma. As metastatic GNAQ/11 mutant nonuveal melanomas respond poorly to available systemic therapies, including immune checkpoint inhibition, novel therapeutic approaches for these tumours are urgently needed. Linked Comment: Rafei-Shamsabadi. Br J Dermatol 2020; 183:806-807.
Greater male than female variability in regional brain structure across the lifespan
2020-02-17

Abstract For many traits, males show greater variability than females, with possible implications for understanding sex differences in health and disease. Here, the ENIGMA (Enhancing Neuro Imaging Genetics through Meta-Analysis) Consortium presents the largest-ever mega-analysis of sex differences in variability of brain structure, based on international data spanning nine decades of life. Subcortical volumes, cortical surface area and cortical thickness were assessed in MRI data of 16,683 healthy individuals 1-90 years old (47% females). We observed significant patterns of greater male than female between-subject variance for all subcortical volumetric measures, all cortical surface area measures, and 60% of cortical thickness measures. This pattern was stable across the lifespan for 50% of the subcortical structures, 70% of the regional area measures, and nearly all regions for thickness. Our findings that these sex differences are present in childhood implicate early life genetic or gene-environment interaction mechanisms. The findings highlight the importance of individual differences within the sexes, that may underpin sex-specific vulnerability to disorders.
ORCA study: real-world versus reading centre assessment of disease activity of neovascular age-related macular degeneration (nAMD)
2020-02-17

Background/aims The prospective, non-interventional ORCA module of the OCEAN study (Observation of Treatment Patterns with Lucentis in Approved Indications) evaluated the qualiy of spectral domain-optical coherence tomography (SD-OCT) image interpretation and treatment decisions by clinicians in Germany and the impact on visual outcomes over 24 months in patients with neovascular age-related macular degeneration (nAMD). Methods 2286 SD-OCT scans of 205 eyes were independently evaluated by clinicians and reading centres (RCs) regarding signs of choroidal neovascularisation (CNV) activity, including presence of intraretinal fluid, subretinal fluid, and/or increase in pigment epithelial detachments. Agreement between clinicians and RCs was calculated. Treatment decisions by clinicians and the impact on treatment outcomes were evaluated. Results CNV activity was detected by RCs on 1578 scans (69.0%) and by clinicians on 1392 scans (60.9%), with agreement in 74.9% of cases. Of the 1578 scans with RC detected CNV activity, anti-vascular endothelial growth factor injections were performed by clinicians in only 35.5% (560/1578). In 19.7% of cases (311/1578), lack of treatment was justified by patients request, termination criteria or chronic cystoid spaces without other signs for CNV activity. In 44.8% of cases (707/1578) with RC detected CNV activity, clinicians claimed no treatment was necessary despite having correctly detected CNV activity in about 2/3 of these cases. In 34% of cases with presumed undertreatment, visual acuity declined in the following visit. Conclusion Although broad agreement on CNV activity parameters was observed between clinicians and RCs, correct identification of CNV activity did not always lead to the initiation of (re-)treatment. To preserve vision over time, correct interpretation of SD-OCT scans and careful retreatment decisions are required. Trial registration number NCT02194803 .
Antifibrotic Effects of Amyloid-Beta and Its Loss in Cirrhotic Liver
2020-02-17

The function and regulation of amyloid-beta (Aβ) in healthy and diseased liver remains unexplored. Because Aβ reduces the integrity of the blood-brain barrier we have examined its potential role in regulating the sinusoidal permeability of normal and cirrhotic liver. Aβ and key proteins that generate (beta-secretase 1 and presenilin-1) and degrade it (neprilysin and myelin basic protein) were decreased in human cirrhotic liver. In culture, activated hepatic stellate cells (HSC) internalized Aβ more efficiently than astrocytes and HSC degraded Aβ leading to suppressed expression of α-smooth muscle actin (α-SMA), collagen 1 and transforming growth factor β (TGFβ). Aβ also upregulated sinusoidal permeability marker endothelial NO synthase (eNOS) and decreased TGFβ in cultured human liver sinusoidal endothelial cells (hLSEC). Liver Aβ levels also correlate with the expression of eNOS in transgenic Alzheimer’s disease mice and in human and rodent cirrhosis/fibrosis. These findings suggest a previously unexplored role of Aβ in the maintenance of liver sinusoidal permeability and in protection against cirrhosis/fibrosis via attenuation of HSC activation.
How much total ovarian tissue can be removed without compromising ovarian function? An animal study
2020-02-17

Abstract Purpose Until now, it is not clear how much total ovarian tissue can be removed without affecting ovarian functions. Aim to investigate impact of stepwise removed ovarian tissue on endocrine hormone levels reflecting ovarian function, follicle morphology and weight in rats. Methods The study was performed with six groups of animals, each consisting of six ten-week-old Sprague-Dawley rats. A blood test was performed on the day of surgery (baseline) and fortnightly thereafter to assess serum hormones reflecting ovarian function: estradiol (E2), progesterone (P), follicle-stimulating hormone (FSH), anti-Müllerian hormone (AMH), inhibin B (INHB); weight was also assessed. The ovaries obtained from surgical resection and from the rats sacrificed 12 weeks after surgery were stained with hematoxylin-eosin. Surgeries in the groups; [%] of remaining total ovarian tissue: Group 1, non-ovariectomized [100% tissue]. Group 2, half of left ovary excised [75% tissue]. Group 3, left ovary excised [50% tissue]. Group 4, left ovary + half of right ovary excised [25% tissue]. Group 5, left ovary + three quarters of right ovary excised [12.5% tissue]. Group 6, bilateral ovariectomy [0% tissue]. Results During the 12 weeks, group 4, 5 and 6 had higher FSH and lower AMH and INHB values compared to the control (group 1) ( p &lt;0.05), but in group 4 production of E2 and P was not significantly different from control ( p &gt;0.05). All ovarian function parameters completely stopped in group 5, i.e. the same as the bilateral ovariectomized rats (group 6). Weight significantly increased in group 6 ( p &lt;0.05). Follicle morphology at baseline and 12 weeks after surgery in groups 2-5 was not significantly different to the control. Conclusions Our animal study confirms that removal of one ovary maintains the remaining ovarian tissue's potency for normal hormone production, as already suggested in clinical studies. However, to our knowledge, we demonstrate here for the first time that even up to 75% of total ovarian tissue can be removed without impact on E2 and P production, which if confirmed in women would mean that hazardous hormone replacement therapy is not required to avoid the negative consequences of hormone depletion.
Short stem hip arthroplasty provides a more physiological load transfer: a comparative finite element analysis study
2020-02-17

Abstract Background: Short stem total hip arthroplasty (SHA) preserves femoral bone stock and is supposed to provide a more natural load transfer compared to standard stem total hip arthroplasty (THA). As comparative biomechanical reference data are rare we used a finite element analysis (FEA) approach to compare cortical load transfer after implantations of a cementless short and standard stem in native biomechanical femora. Methods: The subject specific finite element models of biomechanical femora, one native and two with implanted SHA (Metha, B.Braun Aesculap) and standard THA (CLS, Zimmer-Biomet), were generated from computed tomography datasets. The loading configuration was performed with an axial force of 1400 N. Von Mises stress was used to investigate the change of cortical stress distribution. Results: Compared to the native femur, a considerable reduction of cortical stress was recorded after implantation of SHA and standard THA. The SHA showed less reduction proximally with a significant higher metaphyseal cortical stress compared to standard THA. Moreover, the highest peak stresses were observed metaphyseal for the SHA stem while for the standard THA high stress pattern was observed more distally. Conclusions: Both, short and standard THA, cause unloading of the proximal femur. However, SHA features a clearly favorable pattern in terms of a lower reduction proximally and improved metaphyseal loading, while standard THA shows a higher proximal unloading and more distal load transfer. These load pattern implicate a reduced stress shielding proximally for SHA and might be able to translate in a better bone preservation.
Offshore wind farm wake recovery: Airborne measurements and its representation in engineering models
2020-02-18

Abstract We present an analysis of wind measurements from a series of airborne campaigns conducted to sample the wakes from two North Sea wind farm clusters, with the aim of determining the dependence of the downstream wind speed recovery on the atmospheric stability. The consequences of the stability dependence of wake length on the expected annual energy yield of wind farms in the North Sea are assessed by an engineering model. Wakes are found to extend for significantly longer downstream distances (&gt;50 km) in stable conditions than in neutral and unstable conditions ( 15 km). The parameters of one common engineering model are modified to reproduce the observed wake decay at downstream distances 30 km. More significant effects on the energy yield are expected for wind farms separated by distances 30 km, which is generally the case in the North Sea, but additional data would be required to validate the suggested parameter modifications within the engineering model. A case study is accordingly performed to show reductions in the farm efficiency downstream of a wind farm. These results emphasize not only the importance of understanding the impact of atmospheric stability on offshore wind farms but also the need to update the representation of wakes in current industry models to properly include wake‐induced energy losses, especially in large offshore clusters.