julilili42/papers huggingface dataset:
Von der Stöchiometrie zur Kontrolle metabolischer Netzwerke
2021-02-01

Abstract Cellular metabolism is very complex and extensively regulated. For many organisms we know almost the complete set of biochemical reactions in their metabolic network. However, it is not well understood how these reactions are regulated and how they interact in order to enable cellular functions. In this review, we describe recent methodological advances to study metabolic networks with a focus on bacterial metabolism.
Predicting Lifestyle and Host From Positive Selection Data and Genome Properties in Oomycetes
2021-02-01

<title>Abstract</title> <bold>Background:</bold> Host and niche shifts are a source of genomic and phenotypic diversi_cation as evidenced in parasitism. Most characteristic is core metabolism reduction as parasites adapt to a particular host, while the accessory genome often maintains a high degree of diversi_cation. However, selective pressures acting on the genome of such organisms are not fully understood. <bold>Results:</bold> Here, we developed a comparative genomic approach to study underlying adaptive trends in oomycetes, a eukaryotic phylum with a broad range of economically important plant and animal parasitic lifestyles. Our analysis reveals converging evolution on biological processes for oomycetes inhabiting similar niches. We _nd that certain functions, in particular carbohydrate metabolism, transport, and signaling, are important for host and environmental adaption in oomycetes. <bold>Discussion:</bold> Given the high correlation of lifestyle to genome properties in our oomycete dataset and the convergent evolution of fungal and oomycete genomes, we have developed a model that predicts plant pathogen lifestyles with high accuracy. Understanding how genomes and selective pressures correlate with lifestyle may be crucial to identify new emerging diseases and pandemic threats.
Alertness Training Increases Visual Processing Speed in Healthy Older Adults
2021-02-02

In this study, we investigated whether alertness training in healthy older adults increases visual processing speed (VPS) and whether functional connectivity in the cingulo-opercular network predicts training gain. Using the theory of visual attention, we derived quantitative estimates of VPS before and after training. In Study 1, 75 healthy older adults participated in alertness training, active-control training, or no training ( n = 25 each). A significant Group × Session interaction indicated an increase in VPS in the alertness-training group but not in the control group, despite VPS not differing significantly between groups before training. In Study 2, 29 healthy older adults underwent resting-state functional MRI and then participated in alertness training. Pretraining functional connectivity in the cingulo-opercular network correlated with the individual training-induced change in VPS. In conclusion, results indicate that alertness training improves visual processing in older adults and that functional connectivity in the cingulo-opercular network provides a neural marker for predicting individual training gain.
Learning to Dress 3D People in Generative Clothing
2021-02-02

Three-dimensional human body models are widely used in the analysis of human pose and motion. Existing models, however, are learned from minimally-clothed 3D scans and thus do not generalize to the complexity of dressed people in common images and videos. Additionally, current models lack the expressive power needed to represent the complex non-linear geometry of pose-dependent clothing shapes. To address this, we learn a generative 3D mesh model of clothed people from 3D scans with varying pose and clothing. Specifically, we train a conditional Mesh-VAE-GAN to learn the clothing deformation from the SMPL body model, making clothing an additional term in SMPL. Our model is conditioned on both pose and clothing type, giving the ability to draw samples of clothing to dress different body shapes in a variety of styles and poses. To preserve wrinkle detail, our Mesh-VAE-GAN extends patchwise discriminators to 3D meshes. Our model, named CAPE, represents global shape and fine local structure, effectively extending the SMPL body model to clothing. To our knowledge, this is the first generative model that directly dresses 3D human body meshes and generalizes to different poses. The model, code and data are available for research purposes at https://cape.is.tue.mpg.de.
OmicsTIDE: Interactive Exploration of Trends in Multi-Omics Data
2021-02-02

Abstract Motivation The increasing amount of data produced by omics technologies has significantly improved the understanding of how biological information is transferred across different omics layers and to which extent it is involved in the manifestation of a given phenotype. Besides data-driven analysis strategies, interactive visualization tools have been developed to make the analysis in the multi-omics field more transparent. However, most state-of-the-art tools do not reconstruct the impact of a given omics layer on the final integration result. In general, the amount of omics data analyses strategies and the fields of applications lack a clearer classification of the different approaches. Results We developed a classification for omics data focusing on different aspects of multi-omics data sets, such as data type and experimental design. Based on this classification we developed the Omics Trend-comparing Interactive Data Explorer ( OmicsTIDE ), an interactive visualization tool developed to address the limitations of current visualization approaches in the multi-omics field. The tool consists of an automated part that clusters omics data to determine trends and an interactive visualization. The trends are visualized as profile plots and are connected by a Sankey diagram that allows an interactive pairwise trend comparison to discover concordant and discordant trends. Moreover, large-scale omics data sets are broken down into small subsets of concordant and discordant regulatory trends within few analysis steps. We demonstrate the interactive analysis using OmicsTIDE with two case studies focusing on different types of experimental designs. Availability OmicsTIDE is a web tool and available via http://tuevis.informatik.uni-tuebingen.de/ Contact kay.nieselt@uni-tuebingen.de
Calvarial Lesions: Overview of Imaging Features and Neurosurgical Management
2021-02-02

<title>Abstract</title> <bold>Objective</bold>Calvarial lesions are rare and can present as a variety of different diseases. The lesions can be palpable on the skin, cause local pain and paraesthesia and, depending on the location, neurological deficits can also occur. This research aims to present an overview of typical imaging features as well as neurosurgical management. <bold>Methods</bold>We examined the charts of patients who underwent surgery on a calvarial lesion in our department between 2004 and 2017 (n=133). Retrospectively, the pre-, intra- and postoperative data were analyzed with morphological and histological findings and compared with each other.<bold>Results</bold>Pain, swelling, cosmetically disturbing and neurological deficits were the main complaints. Seventy-seven lesions were limited to the bone, while another 56 lesions showed an infiltrating growth in the adjacent tissue. Depending on the clinical signs and suspected diagnosis, a biopsy, a partial removal or a complete resection was performed. Histiocytosis (n=20), meningiomas (n=20), metastases (n=19) and osteomas (n=16) were the most common lesions. Fibrous dysplasia (n=6) and intraosseous hemangioma (n=9) were less common; other lesions were present only in isolated cases. <bold>Conclusion</bold>Imaging gives a hint, but the diagnosis can be only confirmed by histological examination. The surgical strategy depends on the complaints, location of the lesion and suspected diagnosis. Adjuvant treatment should be initiated according to the histological findings.
Environmental enrichment induces epigenomic and genome organization changes relevant for cognitive function
2021-02-02

Summary In early development, the environment triggers mnemonic epigenomic programs resulting in memory and learning experiences to confer cognitive phenotypes into adulthood. To uncover how environmental stimulation impacts the epigenome and genome organization, we used the paradigm of environmental enrichment (EE) in young mice constantly receiving novel stimulation. We profiled epigenome and chromatin architecture in whole cortex and sorted neurons by deep-sequencing techniques. Specifically, we studied chromatin accessibility, gene and protein regulation, and 3D genome conformation, combined with predicted enhancer and chromatin interactions. We identified increased chromatin accessibility, transcription factor binding including CTCF-mediated insulation, differential occupancy of H3K36me3 and H3K79me2, and changes in transcriptional programs required for neuronal development. EE stimuli led to local genome re-organization by inducing increased contacts between chromosomes 7 and 17 ( inter- chromosomal). Our findings support the notion that EE-induced learning and memory processes are directly associated with the epigenome and genome organization. Highlights - Environmental enrichment (EE) alters chromatin conformation, CTCF binding, and spatially 3D genome changes, thereby regulating cognitive function during the first steps of life after birth. - Transcription-associated gene body marks H3K79me2 and H3K36me3 are differently influenced by EE in cortical brain cells and binding is exacerbated upon stimulation in an age-dependent manner. - EE-induced changes of 3D genome organization increase inter- chromosomal interactions of genes associated with synaptic transmission and AMPA receptor genes on chromosomes 7 and 17.
A forgotten piece of transnationalism in religious education: Harold Loukes’ influence on ‘problem-oriented RE‘ in Germany
2021-02-02

It is probably no coincidence that the essay written by Terence Copley (1947–2011) and published posthumously in this issue on how to re-appreciate Loukes’ work did not refer to Loukes’ internation...
Development of Attention and Accuracy in Learning a Categorization Task
2021-02-02

Being able to categorize objects as similar or different is an essential skill. An important aspect of learning to categorize is learning to attend to relevant features (i.e., features that determine category membership) and ignore irrelevant features of the to-be-categorized objects. Feature variability across objects of different categories is informative, because it allows inferring the rules underlying category membership. In this study, participants learned to categorize fictitious creatures (i.e., aliens). We measured attention to the aliens during learning using eye-tracking and calculated the attentional focus as the ratio of attention to relevant versus irrelevant features. As expected, participants’ categorization accuracy improved with practice; however, in contrast to our expectations, their attentional focus did not improve with practice. When computing the attentional focus, attention to the aliens’ eyes was disregarded, because while eyes attract a lot of attention, they did not vary across aliens (non-informative feature). Yet, an explorative analysis of attention to eyes suggested that participants’ attentional focus did become somewhat more efficient in that over time they learned to ignore the eyes. Results are discussed in the context of the need for instructional methods to improve attentional focus in learning to categorize.
Streptoneury Is Independent From Ontogenetic Torsion in the Caenogastropod Snail Marisa Cornuarietis
2021-02-02

Abstract A hallmark in snails’ anatomy is the conspicuous crossing of the pleurovisceral nerve cords present in all but the most derived gastropod clades. This feature is called streptoneury and hitherto near-universally believed to derive from the process of torsion which is, ontogenetically, visible by a 180° rotation of the visceral sac relative to the cephalopodium, being also responsible for the formation of a cranially bent gut and the location of gills in a mantle cavity that opens to the anterior. However, the mechanical link between the ontogenetic rotation of the visceropallium and streptoneury has never been demonstrated directly. After suppressing ontogenetic torsion in the freshwater apple snail Marisa cornuarietis, we could show in a 3D reconstruction based on serial sectioning that the nervous system of the non-torted snail almost identically mirrored the classical organization of a normally developed individual and showed all features of streptoneury in this species. Furthermore, confocal laser scanning microscopy revealed the pleurovisceral cords not to be fully shaped after completion of ontogenetic torsion. We therefore conclude that, ontogenetically, and potentially also phylogenetically, torsion is not an implicit prerequisite for streptoneury, thereby fundamentally challenging a century-old ‘certainty’ in molluscan developmental biology and evolution.
CD4+ T Cells: Multitasking Cells in the Duty of Cancer Immunotherapy
2021-02-03

Cancer immunotherapy activates the immune system to specifically target malignant cells. Research has often focused on CD8+ cytotoxic T cells, as those have the capacity to eliminate tumor cells after specific recognition upon TCR-MHC class I interaction. However, CD4+ T cells have gained attention in the field, as they are not only essential to promote help to CD8+ T cells, but are also able to kill tumor cells directly (via MHC-class II dependent recognition) or indirectly (e.g., via the activation of other immune cells like macrophages). Therefore, immunotherapy approaches have shifted from only stimulating CD8+ T cells to targeting and assessing both, CD4+ and CD8+ T cell subsets. Here, we discuss the various subsets of CD4+ T cells, their plasticity and functionality, their relevance in the antitumor immune response in patients affected by cancer, and their ever-growing role in therapeutic approaches for human cancer.
Functional synergy recruitment index as a reliable biomarker of motor function and recovery in chronic stroke patients
2021-02-03

Abstract Objective . Stroke affects the expression of muscle synergies underlying motor control, most notably in patients with poorer motor function. The majority of studies on muscle synergies have conventionally approached this analysis by assuming alterations in the inner structures of synergies after stroke. Although different synergy-based features based on this assumption have to some extent described pathological mechanisms in post-stroke neuromuscular control, a biomarker that reliably reflects motor function and recovery is still missing. Approach . Based on the theory of muscle synergies, we alternatively hypothesize that functional synergy structures are physically preserved and measure the temporal correlation between the recruitment profiles of healthy modules by paretic and healthy muscles, a feature hereafter reported as the FSRI. We measured clinical scores and extracted the muscle synergies of both ULs of 18 chronic stroke survivors from the electromyographic activity of 8 muscles during bilateral movements before and after 4 weeks of non-invasive BMI controlled robot therapy and physiotherapy. We computed the FSRI as well as features quantifying inter-limb structural differences and evaluated the correlation of these synergy-based measures with clinical scores. Main results . Correlation analysis revealed weak relationships between conventional features describing inter-limb synergy structural differences and motor function. In contrast, FSRI values during specific or combined movement data significantly correlated with UL motor function and recovery scores. Additionally, we observed that BMI-based training with contingent positive proprioceptive feedback led to improved FSRI values during the specific trained finger extension movement. Significance . We demonstrated that FSRI can be used as a reliable physiological biomarker of motor function and recovery in stroke, which can be targeted via BMI-based proprioceptive therapies and adjuvant physiotherapy to boost effective rehabilitation.
Image Quality Improvement of Dynamic Contrast-Enhanced Gradient Echo Magnetic Resonance Imaging by Iterative Denoising and Edge Enhancement
2021-02-03

Objectives The aim of this study was to investigate the impact of a novel edge enhancement and iterative denoising algorithm in 1.5-T T1-weighted dynamic contrast-enhanced (DCE) gradient echo (GRE) magnetic resonance imaging of the abdomen on image quality, noise levels, diagnostic confidence, and lesion detectability. Materials and Methods Fifty patients who underwent a clinically indicated magnetic resonance imaging with DCE imaging of the abdomen between June and August 2020 were included in this retrospective, monocentric, institutional review board–approved study. For DCE imaging, a series of 3 volume interpolated breath-hold examinations (VIBEs) was performed. The raw data of all DCE imaging studies were processed twice, once using standard reconstruction (DCE S ) and again using an edge enhancement and iterative denoising approach (DCE DE ). All imaging studies were randomly reviewed by 2 radiologists independently regarding noise levels, arterial contrast, sharpness of vessels, overall image quality, and diagnostic confidence using a Likert scale ranging from 1 to 4, with 4 being the best. Furthermore, lesion detectability was evaluated using the same ranking system. Results All 50 imaging studies were successfully reconstructed with both methods. Interreader agreement (Cohen κ) was substantial to perfect for both readers. Arterial contrast and sharpness of vessels were rated superior by both readers with a median of 4 in DCE DE versus a median of 3 in DCE S ( P &lt; 0.001). Furthermore, noise levels as well as overall image quality were rated higher with a median of 4 in DCE DE compared with a median of 3 in DCE S ( P &lt; 0.001). Lesion detectability was evaluated to be superior in DCE DE with a median of 4 versus DCE S with a median of 3 ( P &lt; 0.001). Consequently, diagnostic confidence was also rated to be superior in DCE DE with a median of 4 versus DCE S with a median of 3 ( P &lt; 0.001). Conclusions Iterative denoising and edge enhancement are feasible in DCE imaging of the abdomen providing superior arterial contrast, noise levels, and overall image quality. Furthermore, lesion detectability and diagnostic confidence were significantly improved using this novel reconstruction method. Further reduction of acquisition time might be possible via reduction of increased noise levels using this presented method.
Robot Learning With Crash Constraints
2021-02-03

In the past decade, numerous machine learning algorithms have been shown to\\nsuccessfully learn optimal policies to control real robotic systems. However,\\nit is common to encounter failing behaviors as the learning loop progresses.\\nSpecifically, in robot applications where failing is undesired but not\\ncatastrophic, many algorithms struggle with leveraging data obtained from\\nfailures. This is usually caused by (i) the failed experiment ending\\nprematurely, or (ii) the acquired data being scarce or corrupted. Both\\ncomplicate the design of proper reward functions to penalize failures. In this\\npaper, we propose a framework that addresses those issues. We consider failing\\nbehaviors as those that violate a constraint and address the problem of\\nlearning with crash constraints, where no data is obtained upon constraint\\nviolation. The no-data case is addressed by a novel GP model (GPCR) for the\\nconstraint that combines discrete events (failure/success) with continuous\\nobservations (only obtained upon success). We demonstrate the effectiveness of\\nour framework on simulated benchmarks and on a real jumping quadruped, where\\nthe constraint threshold is unknown a priori. Experimental data is collected,\\nby means of constrained Bayesian optimization, directly on the real robot. Our\\nresults outperform manual tuning and GPCR proves useful on estimating the\\nconstraint threshold.\\n
Why Do Students Walk or Cycle for Transportation? Perceived Study Environment and Psychological Determinants as Predictors of Active Transportation by University Students
2021-02-03

University students are particularly at risk to suffer from physical and psychological complaints and for not fulfilling health-oriented physical activity (PA) recommendations. Since PA is linked with various benefits for health and educational outcomes, the group of students is of particular interest for PA promotion. Although active commuting has been identified as a relevant domain of PA in order to gain the various benefits of PA, little knowledge is available with respect to university students. This study tested conditions in the study environment, as well as personal motivators and barriers, as determinants for the active transportation of university students. Using a cross-sectional convenience sample of a university in the southwest of Germany (n = 997), we applied factor analyses to bundle relevant information on environmental and psychological determinants (adapted NEWS-G; adapted transport-related items from an Australian university survey) and blockwise hierarchical regressions. The objective was to analyze associations between the bundled determinants and self-reports on PA for transport-related walking and cycling (measured by the EHIS-PAQ). Results revealed associations between transport-related cycling and the perceived study environment (e.g., high automobile traffic) as well as certain personal motivators and barriers (e.g., time effort or weather conditions). The study contributes to the knowledge about determinants that are important for the development and improvement of public health interventions for students in a university setting.
Distinct neural networks for the volitional control of vocal and manual actions in the monkey homologue of Broca's area
2021-02-03

The ventrolateral frontal lobe (Broca's area) of the human brain is crucial in speech production. In macaques, neurons in the ventrolateral prefrontal cortex, the suggested monkey homologue of Broca's area, signal the volitional initiation of vocalizations. We explored whether this brain area became specialized for vocal initiation during primate evolution and trained macaques to alternate between a vocal and manual action in response to arbitrary cues. During task performance, single neurons recorded from the ventrolateral prefrontal cortex and the rostroventral premotor cortex of the inferior frontal cortex predominantly signaled the impending vocal or, to a lesser extent, manual action, but not both. Neuronal activity was specific for volitional action plans and differed during spontaneous movement preparations. This implies that the primate inferior frontal cortex controls the initiation of volitional utterances via a dedicated network of vocal selective neurons that might have been exploited during the evolution of Broca’s area.
Going beyond Pentacene: Photoemission Tomography of a Heptacene Monolayer on Ag(110)
2021-02-03

Longer acenes such as heptacene are promising candidates for optoelectronic applications but are unstable in their bulk structure as they tend to dimerize. This makes the growth of well-defined monolayers and films problematic. In this article, we report the successful preparation of a highly oriented monolayer of heptacene on Ag(110) by thermal cycloreversion of diheptacenes. In a combined effort of angle-resolved photoemission spectroscopy and density functional theory (DFT) calculations, we characterize the electronic and structural properties of the molecule on the surface in detail. Our investigations allow us to unambiguously confirm the successful fabrication of a highly oriented complete monolayer of heptacene and to describe its electronic structure. By comparing experimental momentum maps of photoemission from frontier orbitals of heptacene and pentacene, we shed light on differences between these two acenes regarding their molecular orientation and energy-level alignment on the metal surfaces.