julilili42/papers huggingface dataset:
State-dependent effects of natural forcing on global and local climate variability
2022-02-24

Earth and Space Science Open Archive This preprint has been submitted to and is under consideration at Geophysical Research Letters. ESSOAr is a venue for early communication or feedback before peer review. Data may be preliminary.Learn more about preprints preprintOpen AccessYou are viewing the latest version by default [v1]State-dependent effects of natural forcing on global and local climate variabilityAuthorsBeatriceEllerhoffiDMoritz JohannesKirschneriDElisaZieglerMax DanielHollowayiDLouise CSimeKiraRehfeldSee all authors Beatrice EllerhoffiDGeo- and Environmental Research Center, Universität TübingenDepartment of Physics and Department of Geosciences, Universität TübingeniDhttps://orcid.org/0000-0002-3200-8280view email addressThe email was not providedcopy email addressMoritz Johannes KirschneriDInstitute of Environmental PhysicsiDhttps://orcid.org/0000-0003-3946-2395view email addressThe email was not providedcopy email addressElisa ZieglerGeo- and Environmental Research CenterDepartment of Physics and Department of Geoscience, Universität TübingenRuprecht Karls Universität Heidelberg, Heidelberg Universityview email addressThe email was not providedcopy email addressMax Daniel HollowayiDBritish Antarctic SurveyiDhttps://orcid.org/0000-0003-0709-3644view email addressThe email was not providedcopy email addressLouise C SimeBritish Antarctic Surveyview email addressThe email was not providedcopy email addressKira RehfeldCorresponding Author• Submitting AuthorGeo- and Environmental Research CenterDepartment of Geoscience and Department of PhysicsUniversität Tübingenview email addressThe email was not providedcopy email address
Adiabatic theorem in the thermodynamic limit: Systems with a uniform gap
2022-02-24

We show that recent results on adiabatic theory for interacting gapped many-body systems on finite lattices remain valid in the thermodynamic limit. More precisely, we prove a generalised super-adiabatic theorem for the automorphism group describing the infinite volume dynamics on the quasi-local algebra of observables. The key assumption is the existence of a sequence of gapped finite volume Hamiltonians which generates the same infinite volume dynamics in the thermodynamic limit. Our adiabatic theorem holds also for certain perturbations of gapped ground states that close the spectral gap (so it is an adiabatic theorem also for resonances and in this sense `generalised'), and it provides an adiabatic approximation to all orders in the adiabatic parameter (a property often called `super-adiabatic'). In addition to existing results for finite lattices, we also perform a resummation of the adiabatic expansion and allow for observables that are not strictly local. Finally, as an application, we prove the validity of linear and higher order response theory for our class of perturbations also for infinite systems. While we consider the result and its proof as new and interesting in itself, they also lay the foundation for the proof of an adiabatic theorem for systems with a gap only in the bulk, which will be presented in a follow-up article.
Nanobodies as allosteric modulators of Parkinson’s disease–associated LRRK2
2022-02-25

Significance Parkinson’s disease (PD) is the second-most common neurodegenerative disorder. Mutations leading to overactivation of LRRK2 are a leading cause of familial PD, and this protein is therefore considered as an appealing target for drug design. Here, we describe the discovery and characterization of a diverse set of LRRK2-targeting nanobodies. A subset of these nanobodies inhibit LRRK2 via a mechanism that differs from the commonly used LRRK2 kinase inhibitors. Importantly, some of these nanobodies selectively inhibit certain LRRK2 activities (Rab phosphorylation) while leaving other activities (autophosphorylation) unaffected. We anticipate that these nanobodies will find multiple applications as research tools and will open up opportunities for the development of new PD diagnostics and therapeutics in parallel to other currently pursued strategies.
CSF and Serum Levels of Inflammatory Markers in PD: Sparse Correlation, Sex Differences and Association With Neurodegenerative Biomarkers
2022-02-25

Background An involvement of the central-nervous and peripheral, innate and adaptive immune system in the pathogenesis of Parkinson's disease (PD) is nowadays well established. Objectives We face several open questions in preparation of clinical trials aiming at disease-modification by targeting the immune system: Do peripheral (blood) inflammatory profiles reflect central (CSF) inflammatory processes? Are blood/CSF inflammatory markers associated with CSF levels of neurodegenerative/PD-specific biomarkers? Methods Using a multiplex assay we assessed 41 inflammatory markers in CSF/serum pairs in 453 sporadic PD patients. We analyzed CSF/serum correlation as well as associations of inflammatory markers with clinical outcome measures (UPDRS-III, H&amp;amp;Y, MoCA) and with CSF levels of α-synuclein, Aβ 1−42 , t- Tau, p181-Tau and NFL. All analyses were stratified by sex as the immune system shows relevant sex-specific differences. Results Correlations between CSF and serum were sparse and detected in only 25% (9 out of 36) of the analysable inflammatory markers in male PD patients and in only 38% (12 out of 32) of female PD patients. The most important pro-inflammatory mediators associated with motor and cognitive decline as well as with neurodegenerative/PD-specific biomarkers were FABP, ICAM-1, IL-8, MCP-1, MIP-1-beta, and SCF. Results were more robust for CSF than for serum. Interpretation Levels of central-nervous and peripheral inflammatory markers might be regulated independently of each other with CSF inflammatory markers reflecting CNS pathology more accurately than peripheral markers. These findings along with sex-specific characteristics have to be considered when designing clinical trials aiming at disease-modification by targeting the immune system.
Open-Shell Early Lanthanide Terminal Imides
2022-02-25

Group 3- and 4f-element organometallic chemistry and reactivity are decisively driven by the rare-earth-metal/lanthanide (Ln) ion size and associated electronegativity/ionicity/Lewis acidity criteria. For these reasons, the synthesis of terminal "unsupported" imides [Ln═NR] of the smaller, closed-shell Sc(III), Lu(III), Y(III), and increasingly covalent Ce(IV) has involved distinct reaction protocols while derivatives of the "early" large Ln(III) have remained elusive. Herein, we report such terminal imides of open-shell lanthanide cations Ce(III), Nd(III), and Sm(III) according to a new reaction protocol. Lewis-acid-stabilized methylidene complexes [Tp<sup><i>t</i>Bu,Me</sup>Ln(μ<sub>3</sub>-CH<sub>2</sub>){(μ<sub>2</sub>-Me)MMe<sub>2</sub>}<sub>2</sub>] (Ln = Ce, Nd, Sm; M = Al, Ga) react with 2,6-diisopropylaniline (H<sub>2</sub>NAr<sup><i>i</i>Pr</sup>) via methane elimination. The formation of arylimide complexes is governed by the Ln(III) size, the Lewis acidity of the group 13 metal alkyl, steric factors, the presence of a donor solvent, and the sterics and acidity (p<i>K</i><sub>a</sub>) of the aromatic amine. Crucially, terminal arylimides [Tp<sup><i>t</i>Bu,Me</sup>Ln(═NAr<sup><i>i</i>Pr</sup>)(THF)<sub>2</sub>] (Ln = Ce, Nd, Sm) are formed only for M = Ga, and for M = Al, the Lewis-acid-stabilized imides [Tp<sup><i>t</i>Bu,Me</sup>Ln(NAr<sup><i>i</i>Pr</sup>)(AlMe<sub>3</sub>)] (Ln = Ce, Nd, Sm) are persistent. In stark contrast, the [GaMe<sub>3</sub>]-stabilized imide [Tp<sup><i>t</i>Bu,Me</sup>Ln(NAr<sup><i>i</i>Pr</sup>)(GaMe<sub>3</sub>)] (Ln = Nd, Sm) is reversibly formed in noncoordinating solvents.
Open-Source, Adaptable, All-in-One Smartphone-Based System for Quantitative Analysis of Point-of-Care Diagnostics
2022-02-25

Point-of-care (POC) diagnostics, in particular lateral flow assays (LFA), represent a great opportunity for rapid, precise, low-cost and accessible diagnosis of disease. Especially with the ongoing coronavirus disease 2019 (COVID-19) pandemic, rapid point-of-care tests are becoming everyday tools for identification and prevention. Using smartphones as biosensors can enhance POC devices as portable, low-cost platforms for healthcare and medicine, food and environmental monitoring, improving diagnosis and documentation in remote, low-resource locations. We present an open-source, all-in-one smartphone-based system for quantitative analysis of LFAs. It consists of a 3D-printed photo box, a smartphone for image acquisition, and an R Shiny software package with modular, customizable analysis workflow for image editing, analysis, data extraction, calibration and quantification of the assays. This system is less expensive than commonly used hardware and software, so it could prove very beneficial for diagnostic testing in the context of pandemics, as well as in low-resource countries.
Certifiably Adversarially Robust Detection of Out-of-Distribution Data
2022-02-25

Deep neural networks are known to be overconfident when applied to out-of-distribution (OOD) inputs which clearly do not belong to any class. This is a problem in safety-critical applications since a reliable assessment of the uncertainty of a classifier is a key property, allowing the system to trigger human intervention or to transfer into a safe state. In this paper, we aim for certifiable worst case guarantees for OOD detection by enforcing not only low confidence at the OOD point but also in an -ball around it. For this purpose, we use interval bound propagation (IBP) to upper bound the maximal confidence in the -ball and minimize this upper bound during training time. We show that non-trivial bounds on the confidence for OOD data generalizing beyond the OOD dataset seen at training time are possible. Moreover, in contrast to certified adversarial robustness which typically comes with significant loss in prediction performance, certified guarantees for worst case OOD detection are possible without much loss in accuracy.
Nx4 attenuated stress‐induced activity of the anterior cingulate cortex—A post‐hoc analysis of a randomized placebo‐controlled crossover trial
2022-02-25

Abstract Objective Stress‐related symptoms are associated with significant health and economic burden. Several studies suggest Nx4 for the pharmacological management of the stress response and investigated the underlying neural processes. Here we hypothesized that Nx4 can directly affect the stress response in a predefined stress network, including the anterior cingulate cortex (ACC), which is linked to various stress‐related symptoms in patients. Methods In a randomized, placebo‐controlled, double‐blind, crossover trial, 39 healthy males took a single dose of placebo or Nx4. Psychosocial stress was induced by the ScanSTRESS paradigm inside an MRI scanner, and stress network activation was analyzed in brain regions defined a priori. Results Using the placebo data only, we could validate the activation of a distinct neural stress pattern by the ScanSTRESS paradigm. For Nx4, we provide evidence of an attenuating effect on this stress response. A statistically significant reduction in differential stress‐induced activation in the right supracallosal ACC was observed for the rotation stress task of the ScanSTRESS paradigm. The results add to previously published results of Nx4 effects on emotion regulation. Conclusions Our results strengthen the hypothesis that Nx4 modulates the stress response by reducing the activation in parts of the neural stress network, particularly in the ACC. Trial registration: NCT02602275; ClinicalTrials.gov
NCMW: A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome
2022-02-25

The human upper respiratory tract is the reservoir of a diverse community of commensals and potential pathogens (pathobionts), including Streptococcus pneumoniae (pneumococcus), Haemophilus influenzae , Moraxella catarrhalis , and Staphylococcus aureus , which occasionally turn into pathogens causing infectious diseases, while the contribution of many nasal microorganisms to human health remains undiscovered. To better understand the composition of the nasal microbiome community, we create a workflow of the community model, which mimics the human nasal environment. To address this challenge, constraint-based reconstruction of biochemically accurate genome-scale metabolic models (GEMs) networks of microorganisms is mandatory. Our workflow applies constraint-based modeling (CBM), simulates the metabolism between species in a given microbiome, and facilitates generating novel hypotheses on microbial interactions. Utilizing this workflow, we hope to gain a better understanding of interactions from the metabolic modeling perspective. This article presents nasal community modeling workflow (NCMW)—a python package based on GEMs of species as a starting point for understanding the composition of the nasal microbiome community. The package is constructed as a step-by-step mathematical framework for metabolic modeling and analysis of the nasal microbial community. Using constraint-based models reduces the need for culturing species in vitro , a process that is not convenient in the environment of human noses. Availability: NCMW is freely available on the Python Package Index (PIP) via pip install NCMW. The source code, documentation, and usage examples (Jupyter Notebook and example files) are available at https://github.com/manuelgloeckler/ncmw .
Endovascular Aneurysm Repair With AFX Stent-Grafts or Tube Grafts for Sacciform Infrarenal Pathologies in a Narrow Aortic Anatomy
2022-02-25

Purpose: The objective of this study was to compare the outcomes of patients treated with tube grafts and AFX stent-graft in the narrow infrarenal aortic anatomy. Materials and Methods: Patients with penetrating aortic ulcers (PAUs) or sacciform aneurysms of the infrarenal aorta and an aortic bifurcation diameter ≤20 mm who underwent endovascular aneurysm repair (EVAR) with bifurcated AFX or tube stent-grafts (TUBE) between 2012 and 2020 were included. Demographic data and the outcome of the AFX group were compared with the TUBE group. All morphological measurements in the preoperative and postoperative computed tomography scans were performed in the aortic centerline. Results: Fifty-one patients (female: 12/51; 29%; median age: 72 years [63, 77]) with a median follow-up of 10 (3, 39) months, were included, of whom 35/51 (69%) had PAUs and 11/51 were symptomatic (22%). The aortic bifurcation diameter was 17 mm (15, 18) with severe calcifications in 25/51 (49%). The distal aortic landing zone was longer in the TUBE group (9 mm vs 24 mm; p&lt;0.001). The technical success was 96% with a median aneurysm shrinkage of 8% (3, 13), which was comparable between the groups (p=0.264). Periprocedural mortality, conversion to open surgery, myocardial infarction, and stroke were not observed. Two type Ia endoleaks (EL) and 2 type Ib EL occurred, all in the TUBE group (Type 1 EL; 19 vs 0%; p=0.013). The limb patency in the AFX group was 100%. One patient with a tube graft developed an infrarenal aortic thrombosis 40 months after the intervention. The reintervention rate in the TUBE group was higher (14 vs 0%; p=0.032) and included 3 aortic cuff implantations and 1 covered endovascular aortic reconstruction of aortic bifurcation (CERAB). Conclusion: AFX stent-graft showed a lower rate of type I endoleaks and reinterventions in sacciform infrarenal aortic pathologies during the early and midterm follow-up.
Radiography in high mass X-ray binaries -- Micro-structure of the stellar wind through variability of the column density
2022-02-25

In high mass X-ray binaries (HMXBs), an accreting compact object orbits a high mass star which loses mass through a dense and inhomogeneous wind. Using the compact object as an X-ray backlight, the time variability of the absorbing column density in the wind can be exploited in order to shed light on the micro-structure of the wind and obtain unbiased stellar mass loss rates for high mass stars. We explore the impact of clumpiness on the variability of the column density with a simplified wind model. In particular, we focus on the standard deviation of the column density and the characteristic duration of enhanced absorption episodes, and compare them with analytical predictions based on the porosity length. We identified the favorable systems and orbital phases to determine the wind micro-structure. The coherence time scale of the column density is shown to be the self-crossing time of a clump in front of the compact object. We provide a recipe to get accurate measurements of the size and of the mass of the clumps, purely based on the observable time variability of the column density. The coherence time scale grants direct access to the size of the clumps while their mass can be deduced separately from the amplitude of the variability. If it is due to unaccreted passing-by clumps, the high column density variations in some HMXBs requires high mass clumps to reproduce the observed peak-to-peak amplitude and coherence time scales. These clump properties are hardly compatible with the ones derived from first principles. Alternatively, other components could contribute to the variability of the column density: larger orbital scale structures produced by a mechanism still to be identified, or a dense environment in the immediate vicinity of the accretor such as an accretion disk, an outflow or a spherical shell around the magnetosphere of the accreting neutron star.
Reply to Nielsen et al.: Social mindfulness is associated with countries’ environmental performance and individual environmental concern
2022-02-25

Nielsen et al. (1) argue that Van Doesum et al. (2) need to consider three points for their interpretation of a positive association between individual-level social mindfulness (SoMi) and environmental performance (EPI) at the country level (3). The association is weaker when 1) it is controlled for GDP and 2) when the data of three countries are removed; also, 3) the data do not address the association between SoMi and individual-level environmental concern. We discuss these points in turn.
Benchmarking Unsupervised Object Representations for Video Sequences
2022-02-25

Perceiving the world in terms of objects and tracking them through time is a crucial prerequisite for reasoning and scene understanding. Recently, several methods have been proposed for unsupervised learning of object-centric representations. However, since these models were evaluated on different downstream tasks, it remains unclear how they compare in terms of basic perceptual abilities such as detection, figure-ground segmentation and tracking of objects. To close this gap, we design a benchmark with four data sets of varying complexity and seven additional test sets featuring challenging tracking scenarios relevant for natural videos. Using this benchmark, we compare the perceptual abilities of four object-centric approaches: ViMON, a video-extension of MONet, based on recurrent spatial attention, OP3, which exploits clustering via spatial mixture models, as well as TBA and SCALOR, which use explicit factorization via spatial transformers. Our results suggest that the architectures with unconstrained latent representations learn more powerful representations in terms of object detection, segmentation and tracking than the spatial transformer based architectures. We also observe that none of the methods are able to gracefully handle the most challenging tracking scenarios despite their synthetic nature, suggesting that our benchmark may provide fruitful guidance towards learning more robust object-centric video representations.
Ethical behavior in humans and machines -- Evaluating training data quality for beneficial machine learning
2022-02-25

Machine behavior that is based on learning algorithms can be significantly influenced by the exposure to data of different qualities. Up to now, those qualities are solely measured in technical terms, but not in ethical ones, despite the significant role of training and annotation data in supervised machine learning. This is the first study to fill this gap by describing new dimensions of data quality for supervised machine learning applications. Based on the rationale that different social and psychological backgrounds of individuals correlate in practice with different modes of human-computer-interaction, the paper describes from an ethical perspective how varying qualities of behavioral data that individuals leave behind while using digital technologies have socially relevant ramification for the development of machine learning applications. The specific objective of this study is to describe how training data can be selected according to ethical assessments of the behavior it originates from, establishing an innovative filter regime to transition from the big data rationale n = all to a more selective way of processing data for training sets in machine learning. The overarching aim of this research is to promote methods for achieving beneficial machine learning applications that could be widely useful for industry as well as academia.
Interior-Boundary Conditions for the Dirac Equation at Point Sources in 3 Dimensions
2022-02-25

A recently proposed approach for avoiding the ultraviolet divergence of Hamiltonians with particle creation is based on interior-boundary conditions (IBCs). The approach works well in the non-relativistic case, that is, for the Laplacian operator. Here, we study how the approach can be applied to Dirac operators. While this has been done successfully already in 1 space dimension, and more generally for codimension-1 boundaries, the situation of point sources in 3 dimensions corresponds to a codimension-3 boundary. One would expect that, for such a boundary, Dirac operators do not allow for boundary conditions because they are known not to allow for point interactions in 3d, which also correspond to a boundary condition. And indeed, we confirm this expectation here by proving that there is no self-adjoint operator on (a truncated) Fock space that would correspond to a Dirac operator with an IBC at configurations with a particle at the origin. However, we also present a positive result showing that there are self-adjoint operators with IBC (on the boundary consisting of configurations with a particle at the origin) that are, away from those configurations, given by a Dirac operator plus a sufficiently strong Coulomb potential.
Stellar laboratories. X. New Cu IV - VII oscillator strengths and the first detection of copper and indium in hot white dwarfs
2022-02-25

Accurate atomic data is an essential ingredient for the calculation of reliable non-local thermodynamic equilibrium (NLTE) model atmospheres that are mandatory for the spectral analysis of hot stars. We aim to search for and identify for the first time spectral lines of copper (atomic number Z = 29) and indium (Z = 49) in hot white dwarf (WD) stars and to subsequently determine their photospheric abundances. Oscillator strengths of Cu IV - VII were calculated to include radiative and collisional bound-bound transitions of Cu in our NLTE model-atmosphere calculations. Oscillator strengths of In IV - VI were compiled from the literature. We newly identified 1 Cu IV, 51 Cu V, 2 Cu VI, and 5 In Vlines in the ultraviolet (UV) spectrum of DO-type WD RE 0503-289. We determined the photospheric abundances of 9.3 X 10**-5 (mass fraction, 132 times solar) and 3.0 X 10**-5 (56 600 times solar), respectively; we also found Cu overabundances in the DA-type WD G191-B2B (6.3 X 10**-6, 9 times solar). All identified Cu IV - VI lines in the UV spectrum of RE 0503-289 were simultaneously well reproduced with our newly calculated oscillator strengths. With the detection of Cu and In in RE 0503-289, the total number of trans-iron elements (Z &gt; 28) in this extraordinary WD reaches an unprecedented number of 18.