julilili42/papers huggingface dataset:
Use of extracorporeal circulation (ECLS/ECMO) for cardiac and circulatory failure –A clinical practice Guideline Level 3
2021-11-22

Abstract Aims Worldwide applications of extracorporeal circulation for mechanical support in cardiac and circulatory failure, which are referred to as extracorporeal life support (ECLS) or veno‐arterial extracorporeal membrane oxygenation (va‐ECMO), have dramatically increased over the past decade. In spite of the expanding use and the immense medical as well as socio‐economic impact of this therapeutic approach, there has been a lack of interdisciplinary recommendations considering the best available evidence for ECLS treatment. Methods and Results In a multiprofessional, interdisciplinary scientific effort of all scientific societies involved in the treatment of patients with acute cardiac and circulatory failure, the first evidence‐ and expert consensus‐based guideline (level S3) on ECLS/ECMO therapy was developed in a structured approach under regulations of the AWMF (Association of the Scientific Medical Societies in Germany) and under use of GRADE (Grading of Recommendations Assessment, Development and Evaluation) criteria. This article presents all recommendations created by the expert panel, addressing a multitude of aspects for ECLS initiation, continuation, weaning and aftercare as well as structural and personnel requirements. Conclusions This first evidence‐ and expert consensus‐based guideline (level S3) on ECLS/ECMO therapy should be used to apply the best available care nationwide. Beyond clinical practice advice, remaining important research aspects for future scientific efforts are formulated.
Experience with polyethylene glycol allergy‐guided risk management for COVID‐19 vaccine anaphylaxis
2021-11-22

Abstract Background Polyethylene glycol (PEG) may elicit anaphylaxis to COVID‐19 mRNA vaccines, and guidance for patients at risk is needed. Methods In retrospective patients with PEG allergy collected from 2006 till 2019, clinical, skin, and basophil activation test (BAT) characteristics discriminative for PEG allergy were analyzed and compared with the literature. In 421 prospective real‐life patients asking for allergy workup for COVID‐19 vaccine hypersensitivity in 2020/2021, risk assessment was performed and tolerance of the recommended vaccination approach was assessed. Results Ten patients with PEG allergy were found in the retrospective cohort. Patients reacted with immediate anaphylaxis (100%) not only to PEG‐based laxatives/bowel preparations or injections, but also to cold medication, antiseptics, analgetics, or antibiotics. Skin tests ± BAT with PEG ± elicitors were positive in 10/10. Provocation tests were positive in 7/9 patients. From the prospective cohort, 370/421 patients self‐reporting increased risk for vaccine allergy lacked criteria necessitating allergy workup and were recommended for routine vaccination. A total of 51/421 patients were tested, and three (6%) with PEG allergy were identified, whereas 48 patients remained negative in skin tests. Vaccination was recommended in all those patients. No hypersensitivity reactions were reported to vaccination including six PEG‐allergic patients tolerating COVID‐19 vaccination. Conclusions Taking a detailed history excluded PEG allergy in most referred patients and enabled direct safe vaccination. Immediate urticaria/anaphylaxis to typical elicitors identified patients requiring PEG allergy workup. Skin tests ± BAT identified PEG allergy and helped to select the vaccine and the vaccination approach. Even PEG‐allergic patients can tolerate COVID‐19 vaccines.
Increasing Success in Higher Education: The Relationships of Online Course Taking With College Completion and Time-to-Degree
2021-11-22

Online courses provide flexible learning opportunities, but research suggests that students may learn less and persist at lower rates compared to face-to-face settings. However, few studies have investigated more distal effects of online education. In this study, we analyzed 6 years of institutional data for three cohorts of students in 13 large majors (N = 10,572) at a public research university to examine distal effects of online course participation. Using online course offering as an instrumental variable for online course taking, we find that online course taking of major-required courses leads to higher likelihood of successful 4-year graduation and slightly accelerated time-to-degree. These results suggest that offering online courses may help students to more efficiently graduate college.
A restaurant process with cocktail bar and relations to the three-parameter Mittag–Leffler distribution
2021-11-22

Abstract In addition to the features of the two-parameter Chinese restaurant process (CRP), the restaurant under consideration has a cocktail bar and hence allows for a wider range of (bar and table) occupancy mechanisms. The model depends on three real parameters, , , and , fulfilling certain conditions. Results known for the two-parameter CRP are carried over to this model. We study the number of customers at the cocktail bar, the number of customers at each table, and the number of occupied tables after n customers have entered the restaurant. For the number of occupied tables, properly scaled, is asymptotically three-parameter Mittag–Leffler distributed as n tends to infinity. We provide representations for the two- and three-parameter Mittag–Leffler distribution leading to efficient random number generators for these distributions. The proofs draw heavily from methods known for exchangeable random partitions, martingale methods known for generalized Pólya urns, and results known for the two-parameter CRP.
Revealing the Three-Dimensional Orientation and Interplay between Plasmons and Interband Transitions for Single Gold Bipyramids by Photoluminescence Excitation Pattern Imaging
2021-11-22

Gold bipyramids (AuBPs) attract significant attention due to the large enhancement of the electric field around their sharp tips and well-defined tunability of their plasmon resonances. Excitation patterns of single AuBPs are recorded using raster-scanning confocal microscopy combined with radially and azimuthally polarized laser beams. Photoluminescence spectra (PL) and excitation patterns of the same AuBP are acquired with three different excitation wavelengths. Here, the isotropic excitation patterns suggest that the AuBPs are mainly excited by interband transitions with 488/530 nm radiation, while excitation patterns created with a 633 nm laser exhibit a double lobed shape that indicates a single dipole excitation process associated with the longitudinal plasmon resonance mode. We are able to determine the three-dimensional orientation of single AuBPs nonperturbatively by comparing experimental patterns with theoretical simulations. The asymmetric patterns show that the AuBPs are lying on the substrate with an out-of-plane tilt angle of around 10° to 15°.
Comparative transcriptional analysis of the satellite glial cell injury response
2021-11-22

Abstract Satellite glial cells (SGCs) tightly surround and support primary sensory neurons in the peripheral nervous system and are increasingly recognized for their involvement in the development of neuropathic pain following nerve injury. The SGCs are difficult to investigate due to their flattened shape and tight physical connection to neurons in vivo and their rapid changes in phenotype and protein expression when cultured in vitro . Consequently, several aspects of SGC function under normal conditions as well as after a nerve injury remain to be explored. The recent advance in single cell RNAseq technologies has enabled a new approach to investigate SGCs. Here we publish a dataset from mice subjected to sciatic nerve injury as well as a dataset from dorsal root ganglia cells after 3 days in culture. We use a meta-analysis approach to compare the injury response with that in other published datasets and conclude that SGCs share a common signature following sciatic nerve crush and sciatic ligation, involving transcriptional regulation of cholesterol biosynthesis. We also observed a considerable transcriptional change when culturing SGCs, suggesting that some differentiate into a specialised in vitro state, while others start resembling Schwann cell-like precursors. The datasets are available via the Broad Institute Single Cell Portal.
Systematic assessment of the accuracy of subunit counting in biomolecular complexes using automated single molecule brightness analysis
2021-11-22

ABSTRACT Analysis of single molecule brightness allows subunit counting of high-order oligomeric biomolecular complexes. Although the theory behind the method has been extensively assessed, systematic analysis of the experimental conditions required to accurately quantify the stoichiometry of biological complexes remains challenging. In this work, we develop a high-throughput, automated computational pipeline for single molecule brightness analysis that requires minimal human input. We use this strategy to systematically quantify the accuracy of counting under a wide range of experimental conditions in simulated ground-truth data and then validate its use on experimentally obtained data. Our approach defines a set of conditions under which subunit counting by brightness analysis is designed to work optimally and helps establishing the experimental limits in quantifying the number of subunits in a complex of interest. Finally, we combine these features into a powerful, yet simple, software that can be easily used for the stoichiometry analysis of such complexes.
A COVID-19 peptide vaccine for the induction of SARS-CoV-2 T cell immunity
2021-11-23

Abstract T cell immunity is central for the control of viral infections. CoVac-1 is a peptide-based vaccine candidate, composed of SARS-CoV-2 T cell epitopes derived from various viral proteins 1,2 , combined with the Toll-like receptor 1/2 agonist XS15 emulsified in Montanide ISA51 VG, aiming to induce profound SARS-CoV-2 T cell immunity to combat COVID-19. Here we conducted a phase I open-label trial, recruiting 36 participants aged 18–80 years, who received a single subcutaneous CoVac-1 vaccination. The primary end point was safety analysed until day 56. Immunogenicity in terms of CoVac-1-induced T cell response was analysed as the main secondary end point until day 28 and in the follow-up until month 3. No serious adverse events and no grade 4 adverse events were observed. Expected local granuloma formation was observed in all study participants, whereas systemic reactogenicity was absent or mild. SARS-CoV-2-specific T cell responses targeting multiple vaccine peptides were induced in all study participants, mediated by multifunctional T helper 1 CD4 + and CD8 + T cells. CoVac-1-induced IFNγ T cell responses persisted in the follow-up analyses and surpassed those detected after SARS-CoV-2 infection as well as after vaccination with approved vaccines. Furthermore, vaccine-induced T cell responses were unaffected by current SARS-CoV-2 variants of concern. Together, CoVac-1 showed a favourable safety profile and induced broad, potent and variant of concern-independent T cell responses, supporting the presently ongoing evaluation in a phase II trial for patients with B cell or antibody deficiency.
Growth-Promoting Gold Nanoparticles Decrease Stress Responses in Arabidopsis Seedlings
2021-11-23

The global economic success of man-made nanoscale materials has led to a higher production rate and diversification of emission sources in the environment. For these reasons, novel nanosafety approaches to assess the environmental impact of engineered nanomaterials are required. While studying the potential toxicity of metal nanoparticles (NPs), we realized that gold nanoparticles (AuNPs) have a growth-promoting rather than a stress-inducing effect. In this study we established stable short- and long-term exposition systems for testing plant responses to NPs. Exposure of plants to moderate concentrations of AuNPs resulted in enhanced growth of the plants with longer primary roots, more and longer lateral roots and increased rosette diameter, and reduced oxidative stress responses elicited by the immune-stimulatory PAMP flg22. Our data did not reveal any detrimental effects of AuNPs on plants but clearly showed positive effects on growth, presumably by their protective influence on oxidative stress responses. Differential transcriptomics and proteomics analyses revealed that oxidative stress responses are downregulated whereas growth-promoting genes/proteins are upregulated. These omics datasets after AuNP exposure can now be exploited to study the underlying molecular mechanisms of AuNP-induced growth-promotion.
Improving 3D convolutional neural network comprehensibility via interactive visualization of relevance maps: evaluation in Alzheimer's disease.
2021-11-23

Background!#!Although convolutional neural networks (CNNs) achieve high diagnostic accuracy for detecting Alzheimer's disease (AD) dementia based on magnetic resonance imaging (MRI) scans, they are not yet applied in clinical routine. One important reason for this is a lack of model comprehensibility. Recently developed visualization methods for deriving CNN relevance maps may help to fill this gap as they allow the visualization of key input image features that drive the decision of the model. We investigated whether models with higher accuracy also rely more on discriminative brain regions predefined by prior knowledge.!##!Methods!#!We trained a CNN for the detection of AD in N = 663 T1-weighted MRI scans of patients with dementia and amnestic mild cognitive impairment (MCI) and verified the accuracy of the models via cross-validation and in three independent samples including in total N = 1655 cases. We evaluated the association of relevance scores and hippocampus volume to validate the clinical utility of this approach. To improve model comprehensibility, we implemented an interactive visualization of 3D CNN relevance maps, thereby allowing intuitive model inspection.!##!Results!#!Across the three independent datasets, group separation showed high accuracy for AD dementia versus controls (AUC ≥ 0.91) and moderate accuracy for amnestic MCI versus controls (AUC ≈ 0.74). Relevance maps indicated that hippocampal atrophy was considered the most informative factor for AD detection, with additional contributions from atrophy in other cortical and subcortical regions. Relevance scores within the hippocampus were highly correlated with hippocampal volumes (Pearson's r ≈ -0.86, p &amp;amp;lt; 0.001).!##!Conclusion!#!The relevance maps highlighted atrophy in regions that we had hypothesized a priori. This strengthens the comprehensibility of the CNN models, which were trained in a purely data-driven manner based on the scans and diagnosis labels. The high hippocampus relevance scores as well as the high performance achieved in independent samples support the validity of the CNN models in the detection of AD-related MRI abnormalities. The presented data-driven and hypothesis-free CNN modeling approach might provide a useful tool to automatically derive discriminative features for complex diagnostic tasks where clear clinical criteria are still missing, for instance for the differential diagnosis between various types of dementia.
Effects of immune cells on mesenchymal stem cells during fracture healing
2021-11-23

In vertebrates, bone is considered an osteoimmune system which encompasses functions of a locomotive organ, a mineral reservoir, a hormonal organ, a stem cell pool and a cradle for immune cells. This osteoimmune system is based on cooperatively acting bone and immune cells, cohabitating within the bone marrow. They are highly interdependent, a fact that is confounded by shared progenitors, mediators, and signaling pathways. Successful fracture healing requires the participation of all the precursors, immune and bone cells found in the osteoimmune system. Recent evidence demonstrated that changes of the immune cell composition and function may negatively influence bone healing. In this review, first the interplay between different immune cell types and osteoprogenitor cells will be elaborated more closely. The separate paragraphs focus on the specific cell types, starting with the cells of the innate immune response followed by cells of the adaptive immune response, and the complement system as mediator between them. Finally, a brief overview on the challenges of preclinical testing of immune-based therapeutic strategies to support fracture healing will be given.
I see something you do not: Eye movement modelling examples do not improve anomaly detection in interpreting medical images
2021-11-23

Abstract Background When interpreting medical images such as dental panoramic radiographs (Orthopanthomogram, OPT), errors are frequent. Previous research has shown that eye movement modelling examples (EMME) are a supportive training method for medical image interpretation to reduce errors. To date, EMME support for OPTs has not been verified. Objectives We investigated whether a training with EMME and verbal explanations supports dental students in evaluating OPTs. Methods Dental students were randomly assigned to an intervention ( N = 42) or a control group ( N = 41). The intervention group received the EMME between pre‐ and post‐test. In a laboratory study, we measured students' gaze behaviour during evaluating OPTs and the detection rate of anomalies. Results and conclusions The training led to fewer, shorter, and later fixations on anomalies and no difference in visual coverage of the OPT. The detection rate of anomalies did not improve. We replicated the latter finding in an online study ( N = 31). Students may not have been able to apply the information from the EMME to detect anomalies. The image reading processes changed to more efficient rather than deeper visual search. Major takeaways This study evaluated a training method with EMME for anomaly detection of OPTs. EMMEs did not improve the anomaly detection of dental students and changed their visual search process toward a more efficient rather than a deeper search.
Long-Term Humoral Immune Response against SARS-CoV-2 after Natural Infection and Subsequent Vaccination According to WHO International Binding Antibody Units (BAU/mL)
2021-11-23

The new WHO reference standard allows for the definition of serum antibodies against various SARS-CoV-2 antigens in terms of binding antibody units (BAU/mL) and thus to compare the results of different ELISA systems. In this study, the concentration of antibodies (ABs) against both the S- and the N-protein of SARS-CoV-2 as well as serum neutralization activity were evaluated in three patients after a mild course of COVID-19. Serum samples were collected frequently during a period of over one year. Furthermore, in two individuals, the effects of an additional vaccination with a mRNA vaccine containing the S1-RBD sequence on these antibodies were examined. After natural infection, the antibodies (IgA, IgG) against the S1-protein remained elevated above the established cut-off to positivity (S-IgA 60 BAU/mL and S-IgG 50 BAU/mL, respectively) for over a year in all patients, while this was not the case for ABs against the N-protein (cut-off N-IgG 40 BAU/mL, N-IgA 256 BAU/mL). Sera from all patients retained the ability to neutralize SARS-CoV-2 for more than a year. Vaccination resulted in a rapid boost of antibodies to S1-protein but, as expected, not to the N-protein. Most likely, the wide use of the WHO reference preparation will be very useful in determining the individual immune status of patients after an infection with SARS-CoV-2 or after vaccination.
Generating visual explanations with natural language
2021-11-23

Abstract We generate natural language explanations for a fine‐grained visual recognition task. Our explanations fulfill two criteria. First, explanations are class discriminative , meaning they mention attributes in an image which are important to identify a class. Second, explanations are image relevant , meaning they reflect the actual content of an image. Our system, composed of an explanation sampler and phrase‐critic model, generates class discriminative and image relevant explanations. In addition, we demonstrate that our explanations can help humans decide whether to accept or reject an AI decision.
Autonomic Symptoms in Older Adults Are Common and Associated With Health-Related Quality of Life
2021-11-23

Background: Autonomic symptoms are common in older adults, and a large body of literature focusing on age-related diseases shows that autonomic symptoms in these diseases constrain Health-Related Quality of Life (HRQoL). To our best knowledge, the association between autonomic symptoms in older adults, independent of specific diseases, and HRQoL has not yet been assessed. Aim: To assess the frequency and the effect of autonomic symptoms in general, as well as orthostatic intolerance, vasomotor, secretomotor, gastrointestinal, bladder, and pupillomotor symptoms, on HRQoL in older adults. Methods: Cross-sectional data of the fourth visit of the Tübinger evaluation of Risk factors for Early detection of Neurodegeneration (TREND) study were included. Autonomic symptoms, as assessed with the Composite Autonomic Symptom Score 31 (COMPASS 31), were quantified and compared with HRQoL, as assessed with the EuroQol five-level version (EQ-5D-5L). Statistical analyses included Spearman's rank correlation and multiple linear regression analysis. Results: The analysis included 928 participants with a median of 68 years; 47% were women. Of those, 85% reported at least one autonomic symptom. Gastrointestinal and secretomotor symptoms were most common. The COMPASS 31 total score and all subdomains were significantly associated with reduced HRQoL. Among the subdomains, the strongest correlations with HRQoL were found for gastrointestinal and bladder symptoms. Overall, autonomic symptoms alone explained 20% of the variance of HRQoL; when depressive mood was added, the model explained 32%. Conclusion: Autonomic symptoms are associated with HRQoL and depressive symptoms in older adults.
On the extraction of purely motor EEG neural correlates during an upper limb visuomotor task
2021-11-23

Abstract Deciphering and analyzing the neural correlates of different movements from the same limb using electroencephalography (EEG) would represent a notable breakthrough in the field of sensorimotor neurophysiology. Functional movements involve concurrent posture co-ordination and head and eye movements, which create electrical activity that affects EEG recordings. In this paper, we revisit the identification of brain signatures of different reaching movements using EEG and present, test, and validate a protocol to separate the effect of head and eye movements from a reaching task-related visuomotor brain activity. Ten healthy participants performed reaching movements under two different conditions: avoiding head and eye movements and moving with no constrains. Reaching movements can be identified from EEG with unconstrained eye and head movement, whereas the discriminability of the signals drops to chance level otherwise. These results show that neural patterns associated with different arm movements could only be extracted from EEG if the eye and head movements occurred concurrently with the task, polluting the recordings. Although these findings do not imply that brain correlates of reaching directions cannot be identified from EEG, they show the consequences that ignoring these events can have in any EEG study that includes a visuomotor task.