julilili42/papers huggingface dataset:
Closing the loop: autonomous experiments enabled by machine-learning-based online data analysis in synchrotron beamline environments
2023-09-11

Recently, there has been significant interest in applying machine-learning (ML) techniques to the automated analysis of X-ray scattering experiments, due to the increasing speed and size at which datasets are generated. ML-based analysis presents an important opportunity to establish a closed-loop feedback system, enabling monitoring and real-time decision-making based on online data analysis. In this study, the incorporation of a combined one-dimensional convolutional neural network (CNN) and multilayer perceptron that is trained to extract physical thin-film parameters (thickness, density, roughness) and capable of taking into account prior knowledge is described. ML-based online analysis results are processed in a closed-loop workflow for X-ray reflectometry (XRR), using the growth of organic thin films as an example. Our focus lies on the beamline integration of ML-based online data analysis and closed-loop feedback. Our data demonstrate the accuracy and robustness of ML methods for analyzing XRR curves and Bragg reflections and its autonomous control over a vacuum deposition setup.
Sensing the formaldehyde pollutant by an enhanced BNC18 fullerene: DFT outlook
2023-09-11

An enhanced boron nitrogen decorated carbon fullerene with the formula BNC18 (BNC) was investigated for sensing the formaldehyde (FMA) pollutant. Density functional theory (DFT) calculations were performed to optimize the pure C fullerene and the BNC one to prepare a comparative study of facile detection of FMA substance through the formation of FMA@C and FMA@BNC complexes. The details of complexes were re-recognized by the additional quantum theory of atoms in molecule (QTAIM) analyses, in which the formations of both of FMA@C and FMA@BNC were confirmed. However, the BN-decoration enhancement provided a better interacting surface for the BNC fullerene towards the FMA substance in comparison with the pure C fullerene. Moreover, the electronic molecular orbitals features indicated a significant sensing function for the BNC model by improving the semiconductivity for recognizing the adsorbed substance. In this regard, the BNC fullerene was found suitable for successfully approaching two terms of “recovery time” and “conductance rate” for sensing the FMA pollutant.
Redox state and altered pyruvate metabolism contribute to a dose-dependent metformin-induced lactate production of human myotubes
2023-09-11

Metformin shifts the equilibrium of lactate dehydrogenase (LDH) reaction by low dose-induced phosphorylation of pyruvate dehydrogenase (PDH) resulting in inhibition of pyruvate oxidation and high dose-induced increase in NADH, which explains the dose-dependent lactate production of differentiated human skeletal muscle cells.
The evolution of hierarchically structured communication
2023-09-11

Human language sentences are standardly understood as exhibiting considerable hierarchical structure: they can and typically do contain parts that in turn contain parts, etc. In other words, sentences are thought to generally exhibit significant nested part-whole structure. As far as we can tell, this is not a feature of the gestural or vocal communication systems of our great ape relatives. So, one of the many challenges we face in providing a theory of human language evolution is to explain the evolution of hierarchically structured communication in our line. This article takes up that challenge. More specifically, I first present and motivate an account of hierarchical structure in language that departs significantly from the orthodox conception of such structure in linguistics and evolutionary discussions that draw on linguistic theory. On the account I propose, linguistic structure, including hierarchical structure, is treated as a special case of structured action. This account is rooted in the cognitive neuroscience of action, as opposed to (formal) linguistic theory. Among other things, such an account enables us to see how selection for enhanced capacities of act organization and act control in actors, and for act interpretation in observers, might have constructed the brain machinery necessary for the elaborate forms of hierarchically structured communication that we humans engage in. I flesh out this line of thought, emphasizing in particular the role of hominin technique and technology, and the social learning thereof, as evolutionary drivers of this brain machinery.
The ‘Behavioral Balance Model’: A new perspective on the aetiology and therapy of obesity
2023-09-11

Abstract Obesity is a debilitating disease of global proportions that necessitates refined, concept‐driven therapeutic approaches. Policy makers, the public and even health care professionals, but also individuals with obesity harbour many misconceptions regarding this disease, which leads to prejudice, negative attitudes, stigmatization, discrimination, self‐blame, and failure to provide and finance adequate medical care. Decades of intensive, successful scientific research on obesity have only had a very limited effect on this predicament. We propose a science‐based, easy‐to‐understand conceptual model that synthesizes the complex pathogenesis of obesity including biological, psychological, social, economic and environmental aspects with the aim to explain and communicate better the nature of obesity and currently available therapeutic modalities. According to our integrative ‘Behavioral Balance Model’, ‘top‐down cognitive control’ strategies are implemented (often with limited success) to counterbalance the increased ‘bottom‐up drive’ to gain weight, which is triggered by biological, psycho‐social and environmental mechanisms in people with obesity. Besides offering a deeper understanding of obesity, the model also highlights why there is a strong need for multimodal therapeutic approaches that may not only increase top‐down control but also reduce a pathologically increased bottom‐up drive.
NCBench: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for DNA-sequencing-based variant calling
2023-09-11

<ns3:p>We present the results of the human genomic small variant calling benchmarking initiative of the German Research Foundation (DFG) funded Next Generation Sequencing Competence Network (NGS-CN) and the German Human Genome-Phenome Archive (GHGA).</ns3:p><ns3:p> In this effort, we developed NCBench, a continuous benchmarking platform for the evaluation of small genomic variant callsets in terms of recall, precision, and false positive/negative error patterns. NCBench is implemented as a continuously re-evaluated open-source repository.</ns3:p><ns3:p> We show that it is possible to entirely rely on public free infrastructure (Github, Github Actions, Zenodo) in combination with established open-source tools. NCBench is agnostic of the used dataset and can evaluate an arbitrary number of given callsets, while reporting the results in a visual and interactive way.</ns3:p><ns3:p> </ns3:p><ns3:p> We used NCBench to evaluate over 40 callsets generated by various variant calling pipelines available in the participating groups that were run on three exome datasets from different enrichment kits and at different coverages.</ns3:p><ns3:p> While all pipelines achieve high overall quality, subtle systematic differences between callers and datasets exist and are made apparent by NCBench.These insights are useful to improve existing pipelines and develop new workflows.</ns3:p><ns3:p> </ns3:p><ns3:p> NCBench is meant to be open for the contribution of any given callset. Most importantly, for authors, it will enable the omission of repeated re-implementation of paper-specific variant calling benchmarks for the publication of new tools or pipelines, while readers will benefit from being able to (continuously) observe the performance of tools and pipelines at the time of reading instead of at the time of writing.</ns3:p>
The impact of gender on the self-confidence of practical and surgical skills among OBGYN residents: a trinational survey
2023-09-11

Abstract Introduction Gender disparities exist in the OBGYN discipline. This study investigates, for the first time, whether gender impacts on the confidence of practical and surgical skills among OBGYN residents, and of being prepared to work as a specialist. Methods The gynecological societies of Austria, Germany, and Switzerland established a web-based survey of 30 questions that was sent to all registered OBGYN members-in-training from August to September 2020. Data collection, controlling and analysis were performed by the Swiss Federal Institute of Technology in Zurich (ETH). Results A total of 422 participants took part in the survey, of which 375 (88.9%) were female, 46 (10.9%) were male, and one (0.2%) was divers. The diverse participant was excluded from further analyses. The gender distribution was comparable in all three countries. Multiple regression analyses showed that gender is an independent variable significantly impacting on the confidence levels in performing standard gynaecological ( p = 0.03) and obstetric ( p &lt; 0.001) procedures. Similarly, the feeling of confidence in being prepared for working as a specialist in a clinic showed to be gender-dependent ( p &lt; 0.001), however, not the feeling of being prepared for working as specialist in an outpatient setting ( p = 0.37). The “female factor” significantly decreases the confidence rating for surgical and practical skills and for working in a hospital. Covariates including year of training, country, workload, receiving regular feedback, and implemented simulation training were included in all analyses. Discussion Improvements of residency programs to promote female doctors to overcome factors reducing their confidence in their own OBGYN skills are highly warranted.
Microfluidic Isolation of Disseminated Tumor Cells from the Bone Marrow of Breast Cancer Patients
2023-09-11

Disseminated tumor cells (DTCs) in the bone marrow (BM) of breast cancer (BC) patients are putative precursors of metastatic disease, and their presence is associated with an adverse clinical outcome. To achieve the personalization of therapy on a clinical routine level, the characterization of DTCs and in vitro drug testing on DTCs are of great interest. Therefore, biobanking methods, as well as novel approaches to DTC isolation, need to be developed. In this study, we established a protocol for the biobanking of BM samples and evaluated a microfluidic-based separation system (Parsortix®) for the enrichment of cryopreserved DTCs. We were able to successfully isolate viable DTCs after the prior cryopreservation of BM samples. We calculated a significant increase of up to 90-fold in harvested DTCs with the proposed method compared to the current standard techniques, opening up new analysis possibilities for DTCs. Our advanced method further presents options for 3D DTC cultures, enabling the individualized testing of targeted therapies for BC patients. In conclusion, we present a novel approach for DTC enrichment, with possibilities for future clinical implications.
Stacking of PRRs in potato to achieve enhanced resistance againstPhytophthora infestans
2023-09-11

Abstract Plants employ pattern recognition receptors (PRRs) to sense pathogen-associated molecular patterns (PAMPs) or apoplastic effectors at the plant cell surface, as well as nucleotide-binding domain leucine-rich-repeat-containing receptors (NLRs) to sense effectors inside the plant cell. Breeding for potato resistance to P. infestans has focused on the use of NLRs, however, these genes are typically quickly overcome since the matching avirulence genes evolve exceptionally quickly. Here, we stacked two PRRs, PERU and RLP23 , that recognize the rather conserved Phytophthora PAMPs Pep-13/25 and nlp20, respectively, in the potato cultivar Atlantic, and evaluated their effect on P. infestans resistance. We found that PERU and RLP23 cooperate for the early immune responses like the accumulation of reactive oxygen species (ROS) and production of ethylene by recognizing their corresponding PAMPs. Furthermore, we show that potato plants overexpressing these two PRRs are slightly less affected by P. infestans compared to the single transformants. Together, our data suggest that pyramiding of surface receptors can provide additional enhanced resistance against pathogens, however, more effective or synergistic combinations that may include intracellular NLR receptors should be explored.
Reduced expression of fMRI subsequent memory effects with increasing severity across the Alzheimer’s disease risk spectrum
2023-09-11

Abstract In functional magnetic resonance imaging (fMRI) studies, episodic memory is commonly investigated with the subsequent memory paradigm in which brain activity is recorded during encoding and analyzed as a function of subsequent remembering and forgetting. Impaired episodic memory is common in individuals with or at risk for Alzheimer’s disease (AD), but only few studies have reported subsequent memory effects in AD or its risk states like mild cognitive impairment (MCI). One reason for this might be that subsequent memory responses may be blunted in AD or MCI and thus less likely to manifest in fMRI signal differences. Here, we used Bayesian model selection of single-subject fMRI general linear models (GLMs) for a visual novelty and memory encoding experiment to compare the model performance of categorical and parametric subsequent memory models as well as memory-invariant models in a clinical cohort (N = 468) comprising healthy controls (HC) as well as individuals with subjective cognitive decline (SCD), MCI, and AD, plus healthy relatives of AD patients (AD-rel). We could replicate the previously reported superiority of parametric subsequent memory models over categorical models (Soch et al., 2021a) in the HC and also in the SCD and AD-rel groups. However, memory-invariant models outperformed any model assuming subsequent memory effects in the MCI and AD groups. In the AD group, we additionally found substantially lower model preference for models assuming novelty compared to models not differentiating between novel and familiar stimuli. Our results suggest that voxel-wise memory-related fMRI activity patterns in AD and also MCI should be interpreted with caution and point to the need for additional or alternative approaches to investigate memory function.
Developmental trajectories of achievement emotions in mathematics during adolescence
2023-09-12

Abstract This study examined how adolescents' emotions in mathematics develop over time. Growth curve modeling was applied to longitudinal data collected annually from 2002 to 2006 (Grades 5–9; N = 3425 German adolescents; M age = 11.7, 15.6 years at the first and last waves, respectively; 50.0% female). Results indicated that enjoyment and pride decreased over time (Glass's Δ s = −.86, −.71). In contrast, negative emotions exhibited more complex patterns: Anger, boredom, and hopelessness increased (Δ s = .52, .79, .26), shame decreased (Δ = −.12), and anxiety remained stable (Δ = .00). These change trajectories of emotions were associated with change trajectories of perceived control, intrinsic value, achievement value, and achievement in mathematics. Implications and future directions are discussed.
An exploratory study of cell stiffness as a mechanical label-free biomarker across multiple musculoskeletal sarcoma cells
2023-09-12

Abstract Background Cancer cells are characterized by changes in cell cytoskeletal architecture and stiffness. Despite advances in understanding the molecular mechanisms of musculoskeletal cancers, the corresponding cellular mechanical properties remain largely unexplored. The aim of this study was to investigate the changes in cellular stiffness and the associated cytoskeleton configuration alterations in various musculoskeletal cancer cells. Methods Cell lines from five main sarcoma types of the musculoskeletal system (chondrosarcoma, osteosarcoma, Ewing sarcoma, fibrosarcoma and rhabdomyosarcoma) as well as their healthy cell counterparts (chondrocytes, osteoblasts, mesenchymal stem cells, fibroblasts, skeletal muscle cells) were subjected to cell stiffness measurements via atomic force microscopy (AFM). Biochemical and structural changes of the cytoskeleton (F-actin, β-tubulin and actin-related protein 2/3) were assessed by means of fluorescence labelling, ELISA and qPCR. Results While AFM stiffness measurements showed that the majority of cancer cells (osteosarcoma, Ewing sarcoma, fibrosarcoma and rhabdomyosarcoma) were significantly less stiff than their corresponding non-malignant counterparts (p &lt; 0.001), the chondrosarcoma cells were significant stiffer than the chondrocytes (p &lt; 0.001). Microscopically, the distribution of F-actin differed between malignant entities and healthy counterparts: the organisation in well aligned stress fibers was disrupted in cancer cell lines and the proteins was mainly concentrated at the periphery of the cell, whereas β-tubulin had a predominantly perinuclear localization. While the F-actin content was lower in cancer cells, particularly Ewing sarcoma (p = 0.018) and Fibrosarcoma (p = 0.023), this effect was even more pronounced in the case of β-tubulin for all cancer-healthy cell duos. Interestingly, chondrosarcoma cells were characterized by a significant upregulation of β-tubulin gene expression (p = 0.005) and protein amount (p = 0.032). Conclusion Modifications in cellular stiffness, along with structural and compositional cytoskeleton rearrangement, constitute typical features of sarcomas cells, when compared to their healthy counterpart. Notably, whereas a decrease in stiffness is typically a feature of malignant entities, chondrosarcoma cells were stiffer than chondrocytes, with chondrosarcoma cells exhibiting a significantly upregulated β-tubulin expression. Each Sarcoma entity may have his own cellular-stiffness and cytoskeleton organisation/composition fingerprint, which in turn may be exploited for diagnostic or therapeutic purposes.
Urbanization gradient, diet, and gut microbiota in Sub-Saharan Africa: a systematic review
2023-09-12

Introduction As Sub-Saharan Africa (SSA) undergoes rapid urbanization changes in diet and lifestyle have contributed to a rise in non-communicable diseases (NCDs) across the region. Changes in gut microbiota which play an important role in human health may be an underlying driving factor. While evidence suggests that the gut microbiota differs between the extreme levels of economic development (least vs highly developed), it is not well-established which factors along the urbanization gradient are most influential, especially for SSA. This systematic review analyzed published articles from SSA countries that examined the differences in the composition and diversity of gut microbiota along the urbanization gradient. The findings of this review have important implications for understanding the impact of urbanization on human health in the SSA. Methods Peer-reviewed articles that examined the link between the urbanization gradient, dietary patterns, and gut microbiota using culture-independent techniques were included in the review. Results A total of 3,265 studies were identified and screened. Eighty-nine (89) studies underwent full-text review, and 23 studies were extracted and included for final analysis. Among these studies, it was observed that hunter-gatherers had high alpha diversity (within-person variation) and beta diversity (between-person variation) in their gut microbiota compared to rural and urban residents in SSA. However, there were inconsistent differences between rural and urban at the individual taxa levels, potentially due to limited statistical power and large variability in the study techniques and designs. Similarly, there were no clear differences in the relative abundance of genera across the urbanization gradient. Additionally, both diet and intestinal parasites were associated with the composition and diversity of the gut microbiota. Conclusion The review revealed there are variations in both alpha and beta diversity of the gut microbiota across the urbanization gradient with a higher diversity observed in rural areas. However, we did not observe significant differences in the relative abundance at phyla or genus levels consistently across the urbanization gradient. Moreover, our findings suggest that the mode of subsistence, diet, and intestinal parasites play a role in shaping the composition and diversity of the gut microbiota in SSA. Systematic review registration https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42021251006 , identifier CRD42021251006.
Asymmetric distribution of color-opponent response types across mouse visual cortex supports superior color vision in the sky
2023-09-12

Color is an important visual feature that informs behavior, and the retinal basis for color vision has been studied across various vertebrate species. While many studies have investigated how color information is processed in visual brain areas of primate species, we have limited understanding of how it is organized beyond the retina in other species, including most dichromatic mammals. In this study, we systematically characterized how color is represented in the primary visual cortex (V1) of mice. Using large-scale neuronal recordings and a luminance and color noise stimulus, we found that more than a third of neurons in mouse V1 are color-opponent in their receptive field center, while the receptive field surround predominantly captures luminance contrast. Furthermore, we found that color-opponency is especially pronounced in posterior V1 that encodes the sky, matching the statistics of natural scenes experienced by mice. Using unsupervised clustering, we demonstrate that the asymmetry in color representations across cortex can be explained by an uneven distribution of green-On/UV-Off color-opponent response types that are represented in the upper visual field. Finally, a simple model with natural scene-inspired parametric stimuli shows that green-On/UV-Off color-opponent response types may enhance the detection of ‘predatory’-like dark UV-objects in noisy daylight scenes. The results from this study highlight the relevance of color processing in the mouse visual system and contribute to our understanding of how color information is organized in the visual hierarchy across species.
Impact of retraining a deep learning algorithm for improving guideline-compliant aortic diameter measurements on non-gated chest CT
2023-09-12

Re-training of the DL tool improved diameter assessment, resulting in a total of 95.5% correct measurements. Our data suggests that the re-trained DL tool can be applied even in non-ECG-gated chest CT including both, CE and non-CE exams.