julilili42/papers huggingface dataset:
Quantification of Facial Fat Compartment Variations: A Three-Dimensional Morphometric Analysis of the Cheek
2023-03-06

Background: Cheek contour is a main determinant of facial attractiveness. The aim of this study was to evaluate the relationship between age, sex, and body mass index (BMI) and cheek fat volume in a large cohort to better understand and treat facial aging. Methods: The authors performed a retrospective review of the archives of the Department of Diagnostic and Interventional Radiology, University Hospital of Tübingen. Epidemiologic data and medical history were assessed. Cheek superficial and deep fat compartment volumes were measured on magnetic resonance images. Statistical analyses were performed using SPSS and SAS statistical software. Results: A total of 87 patients with a mean age of 46 years (range, 18 to 81 years) were included. The superficial and deep fat compartment volumes of the cheek increased with BMI ( P &lt; 0.001 and P = 0.005), but there was no significant relationship between age and volume. The ratio of superficial versus deep fat did not change with age. No significant difference of the superficial or deep fat compartments was found between men and women in a regression analysis ( P = 0.931 and P = 0.057). Conclusions: Cheek fat volume measurements on magnetic resonance imaging scans using reconstruction software suggest that the fat volume of the cheek increases with BMI but does not change significantly with age. Further studies are needed to elucidate the role of age-related changes of bone structures or sagging of the fat compartments.
Back to the future: breast surgery with tumescent local anesthesia (TLA)?
2023-03-06

Abstract Purpose Breast surgery is usually performed under general anesthesia. Tumescent local anesthesia (TLA) offers the possibility to anesthetize large areas with highly diluted local anesthetic. Methods In this paper, the implementation, and experiences with TLA in the field of breast surgery are discussed. Conclusion For carefully selected indications, breast surgery in TLA represents an alternative to ITN.
Chemical Doping by Fluorination and Its Impact on All Energy Levels of π-Conjugated Systems
2023-03-06

Halogenation of organic molecules causes chemical shifts of C1s core-level binding energies that are commonly used as fingerprints to identify chemical species. Here, we use synchrotron-based X-ray photoelectron spectroscopy and density functional theory calculations to unravel such chemical shifts by examining different partially fluorinated pentacene derivatives. Core-level shifts occur even for carbon atoms distant from the fluorination positions, yielding a continuous shift of about 1.8 eV with increasing degree of fluorination for pentacenes. Since also their LUMO energies shift markedly with the degree of fluorination of the acenes, core-level shifts result in a nearly constant excitation energy of the leading π* resonance as obtained in complementary recorded K-edge X-ray absorption spectra, hence demonstrating that local fluorination affects the entire π-system, including valence and core levels. Our results thus challenge the common picture of characteristic chemical core-level energies as fingerprint signatures of fluorinated π-conjugated molecules.
Bioinformatics-Guided Discovery of Biaryl-Tailored Lasso Peptides
2023-03-06

Abstract Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) that feature an isopeptide bond and a distinct lariat fold. A growing number of secondary modifications have been described that further decorate lasso peptide scaffolds. Using genome mining, we have discovered a pair of lasso peptide biosynthetic gene clusters (BGCs) that include cytochrome P450 genes. Here, we report the structural characterization of two unique examples of (C-N) biaryl-containing lasso peptides. Nocapeptin A, from Nocardia terpenica, is tailored with Trp-Tyr crosslink while longipepetin A, from Longimycelium tulufanense, features Trp-Trp linkage. Besides the unusual bicyclic frame, longipepetin A receives an S-methylation by a new Met methyltransferase resulting in unprecedented sulfonium-bearing RiPP. Our bioinformatic survey revealed P450(s) and further maturating enzyme(s)-containing lasso BGCs awaiting future characterization.
Stress-induced brain responses are associated with BMI in women
2023-03-06

Abstract Background Stress is associated with elevated risk for overweight and obesity, especially in women. Since body mass index (BMI) is correlated with increased inflammation and reduced baseline cortisol, obesity may lead to altered stress responses. However, it is not well understood whether stress-induced changes in brain function scale with BMI and if peripheral inflammation contributes to this. Methods We investigated the subjective, autonomous, endocrine, and neural stress response in a transdiagnostic sample (N=192, 120 women, M BMI =23.7±4.0 kg/m 2 ; N=148, 89 women, with cytokines). First, we used regression models to examine effects of BMI on stress reactivity. Second, we predicted BMI based on stress-induced changes in activation and connectivity using cross-validated elastic-nets. Third, to link stress responses with inflammation, we quantified the association of BMI-related cytokines with model predictions. Results BMI was associated with higher negative affect after stress and an increased response to stress in the substantia nigra and the bilateral posterior insula ( p FWE &lt;.05). Moreover, stress-induced changes in activation of the hippocampus, dACC, and posterior insula predicted BMI in women ( p perm &lt;.001), but not in men. BMI was associated with higher baseline cortisol while cytokines were not associated with predicted BMI scores. Conclusions Stress-induced changes in the hippocampus and posterior insula predicted BMI in women, indicating that acute brain responses to stress might be more strongly related to a higher BMI in women compared to men. Altered stress-induced changes were associated with baseline cortisol but independent of cytokines, suggesting that the endocrine system and not inflammation contributes to stress-related changes in BMI.
UmetaFlow: An untargeted metabolomics workflow for high-throughput data processing and analysis
2023-03-06

Metabolomics experiments generate highly complex datasets, which are time and work-intensive, sometimes even error-prone if inspected manually. Therefore, new methods for automated, fast, reproducible, and accurate data processing and dereplication are required. Here, we present UmetaFlow, a computational workflow for untargeted metabolomics that combines algorithms for data pre-processing, spectral matching, molecular formula and structural predictions, and an integration to the GNPS workflows Feature-Based Molecular Networking and Ion Identity Molecular Networking for downstream analysis. UmetaFlow is implemented as a Snakemake workflow, making it easy to use, scalable, and reproducible. For more interactive computing, visualization, as well as development, the workflow is also implemented in Jupyter notebooks using the Python programming language and a set of Python bindings to the OpenMS algorithms (pyOpenMS). Finally, UmetaFlow is also offered as a web-based Graphical User Interface for parameter optimization and processing of smaller-sized datasets. UmetaFlow was validated with in-house LC-MS/MS datasets of actinomycetes producing known secondary metabolites, as well as commercial standards, and it detected all expected features and accurately annotated 76% of the molecular formulas and 65% of the structures. As a more generic validation, the publicly available MTBLS733 and MTBLS736 datasets were used for benchmarking, and UmetaFlow detected more than 90% of all ground truth features and performed exceptionally well in quantification and discriminating marker selection. We anticipate that UmetaFlow will provide a useful platform for the interpretation of large metabolomics datasets.
The neurocellular implementation of representational geometry in primate prefrontal cortex
2023-03-06

Summary Modern neuroscience has seen the rise of a population-doctrine that represents cognitive variables using geometrical structures in activity space. Representational geometry does not, however, account for how individual neurons implement these representations. Here, leveraging the principle of sparse coding, we present a framework to dissect representational geometry into biologically interpretable components that retain links to single neurons. Applied to extracellular recordings from the primate prefrontal cortex in a working memory task with interference, the identified components revealed disentangled and sequential memory representations including the recovery of memory content after distraction, signals hidden to conventional analyses. Each component was contributed by small subpopulations of neurons with distinct electrophysiological properties and response dynamics. Modelling showed that such sparse implementations are supported by recurrently connected circuits as in prefrontal cortex. The perspective of neuronal implementation links representational geometries to their cellular constituents, providing mechanistic insights into how neural systems encode and process information.
Role of immune responses in the development of NAFLD-associated liver cancer and prospects for therapeutic modulation
2023-03-07

The liver is the central metabolic organ of the body, regulating energy and lipid metabolism, while also having potent immunological functions. Overwhelming the metabolic capacity of the liver via obesity and a sedentary lifestyle leads to hepatic lipid accumulation, chronic necro-inflammation, enhanced mitochondrial/endoplasmic reticulum stress and development of non-alcoholic fatty liver disease (NAFLD), and its more severe form non-alcoholic steatohepatitis (NASH). Based on an improved understanding of pathophysiological mechanisms, specifically targeting metabolic pathways to prevent or slow down the progression of NAFLD to liver cancer will become possible. Genetic/environmental factors are also known to contribute to the development of NASH and progression to liver cancer. The complex pathophysiology of NAFLD-NASH is reflected by environmental factors, particularly the gut microbiome and its metabolic products. NAFLD-associated HCC most often occurs in the context of a chronically inflamed and cirrhotic liver. Recognition of environmental alarmins or metabolites derived from the gut microbiota and the metabolically injured liver create a strong inflammatory milieu supported by innate and adaptive immunity. Several recent studies indicate that chronic steatosis induces auto-aggressive CD8+CXCR6+PD1+ T cells that eliminate parenchymal and non-parenchymal cells in an antigen-independent manner. This promotes chronic liver damage and a pro-tumorigenic environment. CD8+CXCR6+PD1+ T cells possess an exhausted, hyperactivated, resident phenotype; they trigger the NASH to HCC transition and might be responsible for weaker responses to immune checkpoint inhibitors - in particular atezolizumab/bevacizumab. Here, we provide an overview of NASH-related inflammation/pathogenesis, focusing on new discoveries on the role of T cells. This review discusses preventive measures to halt disease progression to liver cancer and therapeutic strategies to manage patients with NASH-HCC.
Pseudospectrum of horizonless compact objects: A bootstrap instability mechanism
2023-03-07

Recent investigations of the pseudospectrum in black hole spacetimes have shown that quasinormal mode frequencies suffer from spectral instabilities. This phenomenon may severely affect gravitationalwave spectroscopy and limit precision tests of general relativity. We extend the pseudospectrum analysis to horizonless exotic compact objects that possess a reflective surface arbitrarily close to the Schwarzschild radius and find that their quasinormal modes also suffer from an overall spectral instability. Even though all the modes themselves decay monotonically, the pseudospectrum contours of equal resonance magnitude around the fundamental mode and the lowest overtones can cross the real axis into the unstable regime of the complex plane, unveiling the existence of nonmodal pseudoresonances. A pseudospectrum analysis further predicts that fluctuations to the system may destabilize the object when next to leading-order effects are considered, as the triggering of pseudoresonant growth can break the order expansion of black hole perturbation theory.
Using Species Knowledge to Promote Pro-Environmental Attitudes? The Association among Species Knowledge, Environmental System Knowledge and Attitude towards theEnvironment in Secondary School Students
2023-03-07

Scientists and conservationists suggest species knowledge as a possible starting point when it comes to creating deeper knowledge and awareness of nature, the environment, and biodiversity. The aim of this work was to analyze secondary school students’ species knowledge of vertebrates and invertebrates. This is one of the first studies that also draws on invertebrates. Furthermore, we investigated whether knowledge of species forms a basis for the formation of environmental knowledge and attitude towards the environment. For this purpose, a questionnaire on species knowledge was developed. In addition, a questionnaire was used to measure environmental system knowledge, and the 2-MEV Attitude Scale to measure attitude towards the environment. The questionnaires were completed by 103 seventh and eighth-grade (age: 12–13) students of a secondary German school (Gymnasium, highest stratification level). The students identified more vertebrates than invertebrates (50.15% vs. 36.7%). The structural equation model with the latent variables species knowledge, environmental system knowledge, and attitude towards the environment showed that species knowledge has a highly significant influence on the two other latent variables. More precisely species knowledge explained 28% of the variance in environmental systems knowledge and 17% of the variance in attitude towards the environment. This study can therefore draw attention to the relevance of teaching species knowledge in the sense of Education for Sustainable Development, in order not to promote decreasing biodiversity through dwindling species knowledge.
Charismatic Species and Birdwatching: Advanced Birders Prefer Small, Shy, Dull, and Rare Species
2023-03-07

Studies about charismatic bird species have been carried out using the general public; among the most common charismatic attributes are body mass and coloration. However, research on birders as a target population is lacking. Birders are people who identify bird species based on visual or acoustic cues. It is important to study this group directly because they invest a lot of time and effort in citizen science projects and donate money to the conservation of nature. Identifying charismatic species for birders can help to determine the optimal flagship species for this group. Because some studies show that preferences for certain species and their attributes may be dependent on the personal characteristics of the respondents, we decided to study the preferences of different types of birder (casual, intermediate, advanced). We surveyed 2,303 German birders and found advanced birders to prefer species with a lower body mass and less coloration/brightness, compared with casual and intermediate birders. Moreover, advanced birders prefer species that are difficult to detect: that is, nocturnal species, species with larger flight distances, species with smaller population sizes, and nonurban birds. Because birders differ from the public in species preferences, this should be taken into account when species are chosen for conservation purposes, initiating citizen science projects, or management plans.
Cladribine treatment specifically affects peripheral blood memory B cell clones and clonal expansion in multiple sclerosis patients
2023-03-07

Introduction B cells are acknowledged as crucial players in the pathogenesis of multiple sclerosis (MS). Several disease modifying drugs including cladribine have been shown to exert differential effects on peripheral blood B cell subsets. However, little is known regarding functional changes within the peripheral B cell populations. In this study, we obtained a detailed picture of B cell repertoire changes under cladribine treatment on a combined immunoglobulin (Ig) transcriptome and proteome level. Methods We performed next-generation sequencing of Ig heavy chain (IGH) transcripts and Ig mass spectrometry in cladribine-treated patients with relapsing-remitting multiple sclerosis (n = 8) at baseline and after 6 and 12 months of treatment in order to generate Ig transcriptome and Ig peptide libraries. Ig peptides were overlapped with the corresponding IGH transcriptome in order to analyze B cell clones on a combined transcriptome and proteome level. Results The analysis of peripheral blood B cell percentages pointed towards a significant decrease of memory B cells and an increase of naive B cells following cladribine therapy. While basic IGH repertoire parameters (e.g. variable heavy chain family usage and Ig subclasses) were only slightly affected by cladribine treatment, a significantly decreased number of clones and significantly lower diversity in the memory subset was noticeable at 6 months following treatment which was sustained at 12 months. When looking at B-cell clones comprising sequences from the different time-points, clones spanning between all three time-points were significantly more frequent than clones including sequences from two time-points. Furthermore, Ig proteome analyses showed that Ig transcriptome specific peptides could mostly be equally aligned to all three time-points pointing towards a proportion of B-cell clones that are maintained during treatment. Discussion Our findings suggest that peripheral B cell related treatment effects of cladribine tablets might be exerted through a reduction of possibly disease relevant clones in the memory B cell subset without disrupting the overall clonal composition of B cells. Our results -at least partially- might explain the relatively mild side effects regarding infections and the sustained immune response after vaccinations during treatment. However, exact disease driving B cell subsets and their effects remain unknown and should be addressed in future studies.
Learning in the workplace: evidence on the role of behavioural job crafting on fostering self-perceived employability
2023-03-07

Purpose Given the instability and volatility of the labour market and the global talent scarcity, placing more attention on job employability is fundamental. In this context, the literature has already extensively examined employability as a crucial individual aspect, identifying some significant antecedents, including the applicability of training on the job. The present study aims to examine the impact that teaching employees to craft their job may have on the levels of applicability of training and if, in turn, this improves self-perceived employability. Design/methodology/approach The authors involved three private organizations that followed three workshops on job crafting behaviour. To empirically assess the intervention, the authors asked participants of the workshop to complete four quantitative diaries on a weekly basis, i.e. one per week, one before the intervention and three after the intervention. The diaries comprised measures of job crafting behaviours, applicability of training and self-perceived employability. Findings Multi-level analysis of data collected provided support to the positive associations between job crafting behaviour and self-perceived employability with the mediating effect of applicability of training. Notably, the applicability of training improves when individuals search for challenges, which indirectly affects perceived employability in terms of organizational sense. Research limitations/implications In the present study, no control group was used with which the results of our intervention could be compared. However, this does not affect the overall results, given the amount of intraindividual variability. Originality/value The paper proposes initial avenues for promoting employability at work via the use of behavioural job crafting intervention.
Sparse Activations for Interpretable Disease Grading
2023-03-07

Abstract Interpreting deep learning models typically relies on post-hoc saliency map techniques. However, these techniques often fail to serve as actionable feedback to clinicians, and they do not directly explain the decision mechanism. Here, we propose an inherently interpretable model that combines the feature extraction capabilities of deep neural networks with advantages of sparse linear models in interpretability. Our approach relies on straight-forward but effective changes to a deep bag-of-local-features model (BagNet). These modifications lead to fine-grained and sparse class evidence maps which, by design, correctly reflect the model’s decision mechanism. Our model is particularly suited for tasks which rely on characterising regions of interests that are very small and distributed over the image. In this paper, we focus on the detection of Diabetic Retinopathy, which is characterised by the progressive presence of small retinal lesions on fundus images. We observed good classification accuracy despite our added sparseness constraint. In addition, our model precisely highlighted retinal lesions relevant for the disease grading task and excluded irrelevant regions from the decision mechanism. The results suggest our sparse BagNet model can be a useful tool for clinicians as it allows efficient inspection of the model predictions and facilitates clinicians’ and patients’ trust.
Serotonergic modulation of local network processing in V1 mirrors previously reported signatures of local network modulation by spatial attention
2023-03-07

Abstract Sensory processing is influenced by neuromodulators such as serotonin, thought to relay behavioural state. Recent work has shown that the modulatory effect of serotonin itself differs with the animal's behavioural state. In primates, including humans, the serotonin system is anatomically important in the primary visual cortex (V1). We previously reported that in awake fixating macaques, serotonin reduces the spiking activity by decreasing response gain in V1. But the effect of serotonin on the local network is unknown. Here, we simultaneously recorded single‐unit activity and local field potentials (LFPs) while iontophoretically applying serotonin in V1 of alert monkeys fixating on a video screen for juice rewards. The reduction in spiking response we observed previously is the opposite of the known increase of spiking activity with spatial attention. Conversely, in the local network (LFP), the application of serotonin resulted in changes mirroring the local network effects of previous reports in macaques directing spatial attention to the receptive field. It reduced the LFP power and the spike–field coherence, and the LFP became less predictive of spiking activity, consistent with reduced functional connectivity. We speculate that together, these effects may reflect the sensory side of a serotonergic contribution to quiet vigilance: The lower gain reduces the salience of stimuli to suppress an orienting reflex to novel stimuli, whereas at the network level, visual processing is in a state comparable to that of spatial attention.