julilili42/papers huggingface dataset:
Rotated Ring, Radial and Depth Wise Separable Radial Convolutions
2021-07-18

Simple image rotations significantly reduce the accuracy of deep neural networks. Moreover, training with all possible rotations increases the data set, which also increases the training duration. In this work, we address trainable rotation invariant convolutions as well as the construction of nets, since fully connected layers can only be rotation invariant with a one-dimensional input. On the one hand, we show that our approach is rotationally invariant for different models and on different public data sets. We also discuss the influence of purely rotational invariant features on accuracy. The rotationally adaptive convolution models presented in this work are more computationally intensive than normal convolution models. Therefore, we also present a depth wise separable approach with radial convolution. Link to CUDA code https://atreus.informatik.uni-tuebingen.de/seafile/d/8e2ab8c3fdd444e1a135/
Measuring the Ripeness of Fruit with Hyperspectral Imaging and Deep Learning
2021-07-18

We present a system to measure the ripeness of fruit with a hyperspectral camera and a suitable deep neural network architecture. This architecture did outperform competitive baseline models on the prediction of the ripeness state of fruit. For this, we recorded a data set of ripening avocados and kiwis, which we make public. We also describe the process of data collection in a manner that the adaption for other fruit is easy. The trained network is validated empirically, and we investigate the trained features. Furthermore, a technique is introduced to visualize the ripening process.
Spatio-temporal dynamics of stress-induced network reconfigurations reflect negative affectivity
2021-07-18

Abstract Background Chronic stress is an important risk factor in the etiology of mood and anxiety disorders, but exact pathomechanisms remain to be understood. Mapping individual differences of acute stress-induced neurophysiological changes, especially on the level of neural activation and functional connectivity (FC), could provide important insights in how variation in the individual stress response is linked to disease risk. Methods Using an established psycho-social stress task flanked by two resting-state scans, we measured subjective, physiological, and brain responses to acute stress and recovery in 217 unmedicated participants with and without mood and anxiety disorders. To estimate block-wise changes in stress-induced brain activation and FC, we used hierarchical mixed-effects models based on denoised timeseries within a predefined stress network. We predicted inter- and intra-individual differences in stress phases (anticipation vs. acute stress vs. recovery) and transdiagnostic dimensions of stress reactivity using elastic net and support vector machines. Results We identified four subnetworks showing distinct changes in FC over time. Subnetwork trajectories predicted the stress phase (accuracy: 71%, p perm &lt;.001) and increases in pulse rate ( R 2 =.10, p perm &lt;.001). Critically, individual spatio-temporal trajectories of changes across networks also predicted negative affectivity (Δ R 2 =.08, p perm =.009), but not the presence or absence of a mood and anxiety disorder. Conclusions Spatio-temporal dynamics of brain network reconfiguration induced by stress reflect individual differences in the psychopathology dimension negative affectivity. These results support the idea that vulnerability for mood and anxiety disorders can be conceptualized best at the level of network dynamics, which may pave the way for improved prediction of individual risk.
High-Dimensional Gaussian Process Inference with Derivatives
2021-07-18

Although it is widely known that Gaussian processes can be conditioned on observations of the gradient, this functionality is of limited use due to the prohibitive computational cost of in data points and dimension . The dilemma of gradient observations is that a single one of them comes at the same cost as independent function evaluations, so the latter are often preferred. Careful scrutiny reveals, however, that derivative observations give rise to highly structured kernel Gram matrices for very general classes of kernels (inter alia, stationary kernels). We show that in the low-data regime , the Gram matrix can be decomposed in a manner that reduces the cost of inference to (i.e., linear in the number of dimensions) and, in special cases, to . This reduction in complexity opens up new use-cases for inference with gradients especially in the high-dimensional regime, where the information-to-cost ratio of gradient observations significantly increases. We demonstrate this potential in a variety of tasks relevant for machine learning, such as optimization and Hamiltonian Monte Carlo with predictive gradients.
Stylolites and stylolite networks as primary controls on the geometry and distribution of carbonate diagenetic alterations
2021-07-18

There is an ongoing debate on whether stylolites act as barriers or conduits for fluids, or even play no role in terms of fluid transport. This problem can be tackled by examining the spatial and temporal relationships between stylolites and other diagenetic products at multiple scales. Using the well-known Lower Cretaceous Benicàssim case study (Maestrat Basin, E Spain), we provide new field and petrographic observations of how bedding-parallel stylolites can influence different diagenetic processes during the geological evolution of a basin. The results reveal that stylolites can serve as baffles or inhibitors for different carbonate diagenetic reactions, and act as fronts for dolomitization, dolomite recrystallization and calcitization processes. Anastomosing stylolites, which pre-date burial dolomitization, likely acted as a collective baffle for dolomitization fluids in the study area, resulting in stratabound replacement geometries at the metre-to-kilometre scale. The dolomitization front weaves up and down following consecutive anastomosing stylolites, which are typical of mud-dominated facies that characterize limestone-dolostone transition zones. Contrarily, dolostone bodies tend to correspond to grain-dominated facies characterized by parallel (non-anastomosing) stylolites. The same stylolites subsequently acted as fluid flow conduits and barriers again when the burial and stress conditions changed. Stylolites within dolostones close to faults are found corroded and filled with saddle dolomite riming the stylolite pore, and high-temperature blocky calcite cements filling the remaining porosity. The fluids responsible for these reactions were likely released from below at high pressure, causing hydraulic brecciation, and were channelised through stylolites, which acted as fluid conduits. Stylolites are also found acting as baffles for subsequent calcitization reactions and occasionally appear filled with iron oxides released by calcitization. This example demonstrates how the same type of stylolites can act as barriers/inhibitors and/or conduits for different types of diagenetic reactions through time, and how important it is to consider their collective role when they form networks.
Continuous Decoding of Daily-Life Hand Movements from Forearm Muscle Activity for Enhanced Myoelectric Control of Hand Prostheses
2021-07-18

State-of-the-art motorized hand prostheses are endowed with actuators able to provide independent and proportional control of as many as six degrees of freedom (DOFs). The control signals are derived from residual electromyographic (EMG) activity, recorded concurrently from relevant forearm muscles. Nevertheless, the functional mapping between forearm EMG activity and hand kinematics is only known with limited accuracy. Therefore, no robust method exists for the reliable computation of control signals for the independent and proportional actuation of more than two DOFs. A common approach to deal with this limitation is to pre-program the prostheses for the execution of a restricted number of behaviors (e.g., pinching, grasping, and wrist rotation) that are activated by the detection of specific EMG activation patterns. However, this approach severely limits the range of activities users can perform with the prostheses during their daily living. In this work, we introduce a novel method, based on a long short-term memory (LSTM) network, to continuously map forearm EMG activity onto hand kinematics. Critically, unlike previous work, which often focuses on simple and highly controlled motor tasks, we tested our method on a dataset of activities of daily living (ADLs): the KIN-MUS UJI dataset. To the best of our knowledge, ours is the first reported work on the prediction of hand kinematics that uses this challenging dataset. Remarkably, we show that our network is able to generalize to novel untrained ADLs. Our results suggest that the presented method is suitable for the generation of control signals for the independent and proportional actuation of the multiple DOFs of state-of-the-art hand prostheses.
Anti–platelet factor 4 antibodies causing VITT do not cross-react with SARS-CoV-2 spike protein
2021-07-19

Abstract Vaccine-induced immune thrombotic thrombocytopenia (VITT) is a severe adverse effect of ChAdOx1 nCoV-19 COVID-19 vaccine (Vaxzevria) and Janssen Ad26.COV2.S COVID-19 vaccine, and it is associated with unusual thrombosis. VITT is caused by anti-platelet factor 4 (PF4) antibodies activating platelets through their FcγRIIa receptors. Antibodies that activate platelets through FcγRIIa receptors have also been identified in patients with COVID-19. These findings raise concern that vaccination-induced antibodies against anti-SARS-CoV-2 spike protein cause thrombosis by cross-reacting with PF4. Immunogenic epitopes of PF4 and SARS-CoV-2 spike protein were compared using in silico prediction tools and 3D modeling. The SARS-CoV-2 spike protein and PF4 share at least 1 similar epitope. Reactivity of purified anti-PF4 antibodies from patients with VITT was tested against recombinant SARS-CoV-2 spike protein. However, none of the affinity-purified anti-PF4 antibodies from 14 patients with VITT cross-reacted with SARS-CoV-2 spike protein. Sera from 222 polymerase chain reaction–confirmed patients with COVID-19 from 5 European centers were tested by PF4-heparin enzyme-linked immunosorbent assays and PF4-dependent platelet activation assays. We found anti-PF4 antibodies in sera from 19 (8.6%) of 222 patients with COVID-19. However, only 4 showed weak to moderate platelet activation in the presence of PF4, and none of those patients developed thrombotic complications. Among 10 (4.5%) of 222 patients who had COVID-19 with thrombosis, none showed PF4-dependent platelet-activating antibodies. In conclusion, antibodies against PF4 induced by vaccination do not cross-react with the SARS-CoV-2 spike protein, indicating that the intended vaccine-induced immune response against SARS-CoV-2 spike protein is not the trigger of VITT. PF4-reactive antibodies found in patients with COVID-19 in this study were not associated with thrombotic complications.
A Narrative Review on the Role of AMPK on De Novo Lipogenesis in Non-Alcoholic Fatty Liver Disease: Evidence from Human Studies
2021-07-19

5′AMP-activated protein kinase (AMPK) is known as metabolic sensor in mammalian cells that becomes activated by an increasing adenosine monophosphate (AMP)/adenosine triphosphate (ATP) ratio. The heterotrimeric AMPK protein comprises three subunits, each of which has multiple phosphorylation sites, playing an important role in the regulation of essential molecular pathways. By phosphorylation of downstream proteins and modulation of gene transcription AMPK functions as a master switch of energy homeostasis in tissues with high metabolic turnover, such as the liver, skeletal muscle, and adipose tissue. Regulation of AMPK under conditions of chronic caloric oversupply emerged as substantial research target to get deeper insight into the pathogenesis of non-alcoholic fatty liver disease (NAFLD). Evidence supporting the role of AMPK in NAFLD is mainly derived from preclinical cell culture and animal studies. Dysbalanced de novo lipogenesis has been identified as one of the key processes in NAFLD pathogenesis. Thus, the scope of this review is to provide an integrative overview of evidence, in particular from clinical studies and human samples, on the role of AMPK in the regulation of primarily de novo lipogenesis in human NAFLD.
Acute coronary syndrome is associated with a substantial change in the platelet lipidome
2021-07-19

Abstract Aims Platelets play a key role in the pathophysiology of coronary artery disease (CAD) and patients with enhanced platelet activation are at increased risk to develop adverse cardiovascular events. Beyond reliable cardiovascular risk factors such as dyslipoproteinaemia, significant changes of platelet lipids occur in patients with CAD. In this study, we investigate the platelet lipidome by untargeted liquid chromatography–mass spectrometry, highlighting significant changes between acute coronary syndrome (ACS) and chronic coronary syndrome (CCS) patients. Additionally, we classify the platelet lipidome, spotlighting specific glycerophospholipids as key players in ACS patients. Furthermore, we examine the impact of significantly altered lipids in ACS on platelet-dependent thrombus formation and aggregation. Methods and results In this consecutive study, we characterized the platelet lipidome in a CAD cohort (n = 139) and showed significant changes of lipids between patients with ACS and CCS. We found that among 928 lipids, 7 platelet glycerophospholipids were significantly up-regulated in ACS, whereas 25 lipids were down-regulated compared to CCS. The most prominent up-regulated lipid in ACS, PC18:0 (PC 10:0-8:0), promoted platelet activation and ex vivo platelet-dependent thrombus formation. Conclusions Our results reveal that the platelet lipidome is altered in ACS and up-regulated lipids embody primarily glycerophospholipids. Alterations of the platelet lipidome, especially of medium chain lipids, may play a role in the pathophysiology of ACS.
Phylogenetic Typology
2021-07-19

In this article we propose a novel method to estimate the frequency distribution of linguistic variables while controlling for statistical non-independence due to shared ancestry. Unlike previous approaches, our technique uses all available data, from language families large and small as well as from isolates, while controlling for different degrees of relatedness on a continuous scale estimated from the data. Our approach involves three steps: First, distributions of phylogenies are inferred from lexical data. Second, these phylogenies are used as part of a statistical model to estimate transition rates between parameter states. Finally, the long-term equilibrium of the resulting Markov process is computed. As a case study, we investigate a series of potential word-order correlations across the languages of the world.
Consensus Recommendations of the German Consortium for Hereditary Breast and Ovarian Cancer
2021-07-19

&lt;b&gt;&lt;i&gt;Background:&lt;/i&gt;&lt;/b&gt; The German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC) has established a multigene panel (TruRisk®) for the analysis of risk genes for familial breast and ovarian cancer. &lt;b&gt;&lt;i&gt;Summary:&lt;/i&gt;&lt;/b&gt; An interdisciplinary team of experts from the GC-HBOC has evaluated the available data on risk modification in the presence of pathogenic mutations in these genes based on a structured literature search and through a formal consensus process. &lt;b&gt;&lt;i&gt;Key Messages:&lt;/i&gt;&lt;/b&gt; The goal of this work is to better assess individual disease risk and, on this basis, to derive clinical recommendations for patient counseling and care at the centers of the GC-HBOC from the initial consultation prior to genetic testing to the use of individual risk-adapted preventive/therapeutic measures.
Radiative transitions of charmonium states in the covariant confined quark model
2021-07-19

We have studied the dominant radiative transitions of the charmonium -and -wave states within the covariant confined quark model. The gauge invariant leading-order transition amplitudes have been expressed by using either the conventional Lorentz structures, or the helicity amplitudes, where it was effective. The renormalization couplings of the charmonium states have been strictly fixed by the compositeness conditions that excludes the constituent degrees of freedom from the space of physical states. We use the basic model parameters for the constituent c-quark mass GeV and the global infrared cutoff GeV. We additionally introduce only one adjustable parameter common for the charmonium states , , , , , and to describe the quark distribution inside the hadron. This parameter describes the ratio between the charmonium size and its physical mass. The optimal value has been fixed by fitting the latest data for the partial widths of the one-photon radiative decays of the triplet . Then, we calculate corresponding fractional widths for states and . Estimated results are in good agreement with the latest data. By using the fraction data from PDG2020 and our estimated partial decay width for we recalculate the theoretical full width MeV in comparison with latest data MeV. We also repeated our calculations by gradually decreasing the global cutoff parameter and revealed that the results do not change for any GeV up to the deconfinement limit.
Characteristics and Injury Patterns of Road Traffic Injuries in Urban and Rural Uganda—A Retrospective Medical Record Review Study in Two Hospitals
2021-07-19

In the ongoing Second Decade of Action for Road Safety, road traffic crashes pose a considerable threat especially in low-income countries. Uganda shows a vast burden of non-fatal injuries and resides at the top range of countries with the highest death rates due to unsafe roads. However, little is known about the differences in road traffic associated injuries between urban and rural areas and potential influence factors. Here, we used a cross-sectional study conducted by a retrospective medical record review from trauma cases admitted in 2016 to hospitals in rural and urban areas in Uganda. Injury severity scores were calculated and descriptive analysis was carried out while multivariate logistic regression was applied to assess significant covariates. According to the 1683 medical records reviewed, the mean age of trauma patients in the dataset under investigation was 30.8 years with 74% male. The trauma in-hospital mortality was 4% while prevalence of traumatic injuries is 56.4%. Motorcycle users (49.6%) and pedestrians (33.7%) were identified as the most vulnerable groups in both urban and rural setting while mild injuries of extremities (61.6%) and the head/neck-region (42.0%) were registered most. The frequency of road traffic injuries was homogenous in the urban and rural hospitals investigated in this study; interventions should therefore be intensified ubiquitously. The identification of significant differences in road traffic crash and injury characteristics provides the opportunity for specific programmes to decrease the socio-economic and health burden of unsafe roads. In addition to law enforcement and introduction of a Systems Thinking approach to road safety including infrastructural and educational concepts, the strengthening of trauma care and health resources is recommended.
TRAF6 Phosphorylation Prevents Its Autophagic Degradation and Re-Shapes LPS-Triggered Signaling Networks
2021-07-19

The ubiquitin E3 ligase TNF Receptor Associated Factor 6 (TRAF6) participates in a large number of different biological processes including innate immunity, differentiation and cell survival, raising the need to specify and shape the signaling output. Here, we identify a lipopolysaccharide (LPS)-dependent increase in TRAF6 association with the kinase IKKε (inhibitor of NF-κB kinase subunit ε) and IKKε-mediated TRAF6 phosphorylation at five residues. The reconstitution of TRAF6-deficient cells, with TRAF6 mutants representing phosphorylation-defective or phospho-mimetic TRAF6 variants, showed that the phospho-mimetic TRAF6 variant was largely protected from basal ubiquitin/proteasome-mediated degradation, and also from autophagy-mediated decay in autolysosomes induced by metabolic perturbation. In addition, phosphorylation of TRAF6 and its E3 ligase function differentially shape basal and LPS-triggered signaling networks, as revealed by phosphoproteome analysis. Changes in LPS-triggered phosphorylation networks of cells that had experienced autophagy are partially dependent on TRAF6 and its phosphorylation status, suggesting an involvement of this E3 ligase in the interplay between metabolic and inflammatory circuits.
Are cognition, motivation, and emotion the same or different?: Let’s abandon that thinking
2021-07-19

This is a short essay that answers a question posed by the editors --- Can you distinguish motivation, cognition, and emotion? My answer is that searching for the commonalities and boundaries between motivation, cognition, and emotion may not be a particularly productive way to advance our understanding of the human mind. This is because they are just mental categories that we psychologically construct based on our subjective feelings and post-hoc interpretation of behaviors. Motivation, cognition, and emotion are not things that define and influence our mental and neural processes. On the contrary, they are a consequence of our interpretation based on the output of mental and neural processes. As such, these categories have, at most, only limited information about mental dynamics.
Supplementary data and research materials for "Is large-scale rapid CoV-2 testing a substitute for lockdowns?"
2021-07-19

This project folder contains supplementary data files and software codes (Stata and Matlab) to replicate the estimation and simulation results documented in:<br>"Is large-scale rapid CoV-2 testing a substitute for lockdowns?"<br>written by Diederichs, M., Kremsner, P.G., Mitze, T., Müller, G.J., Papies, D., Glawion, R., Schulz, F. and Wälde, K. (this version: January 2022).<br><br>An earlier working paper version of this research can be downloaded from medRxiv preprint series at: https://doi.org/10.1101/2021.04.26.21256094.