julilili42/papers huggingface dataset:
Interaction between Crustal-Scale Darcy and Hydrofracture Fluid Transport: A Numerical Study
2020-11-05

Crustal-scale fluid flow can be regarded as a bimodal transport mechanism. At low hydraulic head gradients, fluid flow through rock porosity is slow and can be described as diffusional. Structures such as hydraulic breccias and hydrothermal veins both form when fluid velocities and pressures are high, which can be achieved by localized fluid transport in space and time, via hydrofractures. Hydrofracture propagation and simultaneous fluid flow can be regarded as a “ballistic” transport mechanism, which is activated when transport by diffusion alone is insufficient to release the local fluid overpressure. The activation of a ballistic system locally reduces the driving force, through allowing the escape of fluid. We use a numerical model to investigate the properties of the two transport modes in general and the transition between them in particular. We developed a numerical model in order to study patterns that result from bimodal transport. When hydrofractures are activated due to low permeability relative to fluid flux, many hydrofractures form that do not extend through the whole system. These abundant hydrofractures follow a power-law size distribution. A Hurst factor of ~0.9 indicates that the system self-organizes. The abundant small-scale hydrofractures organize the formation of large-scale hydrofractures that ascend through the whole system and drain fluids in large bursts. As the relative contribution of porous flow increases, escaping fluid bursts become less frequent, but more regular in time and larger in volume. We propose that metamorphic rocks with abundant veins, such as in the Kodiak accretionary prism (Alaska) and Otago schists (New Zealand), represent regions with abundant hydrofractures near the fluid source, while hydrothermal breccias are formed by the large fluid bursts that can ascend the crust to shallower levels.
Bio-impedance measurement allows displaying the early stages of neutrophil extracellular traps
2020-11-05

Neutrophils are the most abundant immune cells in the blood. Besides common immune defense mechanisms, releasing their DNA covered with antimicrobial proteases and histones represent another strong defense mechanism: neutrophil extracellular traps. In vitro the two most common inducers of these, so called, NETs are calcium ionophores (CI) and PMA (Phorbol 12-myristate 13-acetate). Following stimulation monitoring of NET release is necessary. For now, the methods of choice are quantification of free DNA by fluorescent dyes or analysis of immunofluorescence images. As a new method we tested bio-impedance monitoring of neutrophils after stimulation with the two inducers PMA and CI in gold-electrode coated plates. Bio-impedance (cell index) was measured over time. Results were compared to the monitoring of NETs by the fluorescent DNA-binding dye Sytox Green and immunofluorescence analysis. Cell index peaked about 25 min faster following CI stimulation than following PMA stimulation. The activation in Sytox Green Assay was significantly later detectable for PMA (+ approx. 90 min) but not for CI stimulation. The earlier and faster activation by CI was also confirmed by immunofluorescence staining. Our data suggest that bio-impedance measurement allows an easy online tracking of early neutrophil activation. This offers new opportunities to monitor early phases and stimuli-dependent dynamics of NETosis.
Smaller spared subcortical nuclei are associated with worse post-stroke sensorimotor outcomes in 28 cohorts worldwide
2020-11-05

ABSTRACT Background and Purpose Up to two-thirds of stroke survivors experience persistent sensorimotor impairments. Recovery relies on the integrity of spared brain areas to compensate for damaged tissue. Subcortical regions play critical roles in the control and regulation of sensorimotor circuits. The goal of this work is to identify associations between volumes of spared subcortical nuclei and sensorimotor behavior at different timepoints after stroke. Methods We pooled high-resolution T1-weighted MRI brain scans and behavioral data in 828 individuals with unilateral stroke from 28 cohorts worldwide. Cross-sectional analyses using linear mixed-effects models related post-stroke sensorimotor behavior to non-lesioned subcortical volumes (Bonferroni-corrected, p&lt;0.004). We tested subacute (≤90 days) and chronic (≥180 days) stroke subgroups separately, with exploratory analyses in early stroke (≤21 days) and across all time. Sub-analyses in chronic stroke were also performed based on class of sensorimotor deficits (impairment, activity limitations) and side of lesioned hemisphere. Results Worse sensorimotor behavior was associated with a smaller ipsilesional thalamic volume in both early (n=179; d =0.68) and subacute (n=274, d =0.46) stroke. In chronic stroke (n=404), worse sensorimotor behavior was associated with smaller ipsilesional putamen ( d =0.52) and nucleus accumbens ( d =0.39) volumes, and a larger ipsilesional lateral ventricle ( d =-0.42). Worse chronic sensorimotor impairment specifically (measured by the Fugl-Meyer Assessment; n=256) was associated with smaller ipsilesional putamen ( d =0.72) and larger lateral ventricle ( d =-0.41) volumes, while several measures of activity limitations (n=116) showed no significant relationships. In the full cohort across all time (n=828), sensorimotor behavior was associated with the volumes of the ipsilesional nucleus accumbens ( d =0.23), putamen ( d =0.33), thalamus ( d =0.33), and lateral ventricle ( d =-0.23). Conclusions We demonstrate significant relationships between post-stroke sensorimotor behavior and reduced volumes of subcortical gray matter structures that were spared by stroke, which differ by time and class of sensorimotor measure. These findings may provide additional targets for improving post-stroke sensorimotor outcomes.
Data for "Bayesian inference for biophysical neuron models enables stimulus optimization for retinal neuroprosthetics"
2020-11-05

Experimental and precomputed data for the paper "Bayesian inference for biophysical neuron models enables stimulus optimization for retinal neuroprosthetics" by Oesterle et al. 2020 (DOI: 10.7554/eLife.54997). The cone bipolar cell data has been described and published in the paper "Inhibition decorrelates visual feature representations in the inner retina" by Franke et al. 2017 (DOI: 10.1038/nature21394). This data is both a supplement to the Oesterle et al. paper and the code for this paper. The code is available in this GitHub repository. We recommend downloading the GitHub repository and to follow the instructions there.
The Margins of the Language Network in the Brain
2020-11-06

This review paper summarizes the various brain modules that are involved in speech and language communication in addition to a left-dominant “core” language network that, for the present purpose, has been restricted to elementary formal-linguistic and more or less disembodied functions such as abstract phonology, syntax, and very basic lexical functions. This left-dominant perisylvian language network comprises parts of inferior frontal gyrus, premotor cortex, and upper temporal lobe, and a temporoparietal interface. After introducing this network, first, the various roles of neighboring and functionally connected brain regions are discussed. As a second approach, entire additional networks were considered rather than single regions, mainly motivated by resting-state studies indicating more or less stable connectivity patterns within these networks. Thirdly, some examples are provided for language tasks with functional demands exceeding the operating domain of the core language network. The rationale behind this approach is to present some outline of how the brain produces and perceives language, accounting, first, for a bulk of clinical studies showing typical forms of aphasia in case of left-hemispheric lesions in the core language network and second, for wide-spread activation patterns beyond this network in various experimental studies with language tasks. Roughly, the brain resources that complement the core language system in a task-specific way can be described as a number of brain structures and networks that are related to (1) motor representations, (2) sensory-related representations, (3) non-verbal memory structures, (4) affective/emotional processing, (5) social cognition and theory of mind, (6) meaning in context, and (7) cognitive control. After taking into account all these aspects, first, it seems clear that natural language communication cannot really work without additional systems. Second, it also becomes evident that during language acquisition the core language network has to be built up from outside, that is, from various neuronal activations that are related to sensory input, motor imitation, nursing, pre-linguistic sound communication, and pre-linguistic pragmatics. Furthermore, it might be worth considering that also in cases of aphasia the language network might be restored by being trained from outside.
HDAC inhibition ameliorates cone survival in retinitis pigmentosa mice
2020-11-06

Abstract Cone photoreceptor cell death in inherited retinal diseases, such as Retinitis Pigmentosa (RP), leads to the loss of high acuity and color vision and, ultimately to blindness. In RP, a vast number of mutations perturb the structure and function of rod photoreceptors, while cones remain initially unaffected. Extensive rod loss in advanced stages of the disease triggers cone death by a mechanism that is still largely unknown. Here, we show that secondary cone cell death in animal models for RP is associated with increased activity of histone deacetylates (HDACs). A single intravitreal injection of an HDAC inhibitor at late stages of the disease, when the majority of rods have already degenerated, was sufficient to delay cone death and support long-term cone survival in two mouse models for RP, affected by mutations in the phosphodiesterase 6b gene. Moreover, the surviving cones remained light-sensitive, leading to an improvement in visual function. RNA-seq analysis of protected cones demonstrated that HDAC inhibition initiated multi-level protection via regulation of different pro-survival pathways, including MAPK, PI3K-Akt, and autophagy. This study suggests a unique opportunity for targeted pharmacological protection of secondary dying cones by HDAC inhibition and creates hope to maintain vision in RP patients even in advanced disease stages.
An extreme particle accelerator in the Galactic plane: HESSJ1826-130
2020-11-06

The unidentified very-high-energy (VHE; E>0.1 TeV)γ-ray source, HESS J1826−130, was discovered with the High Energy Stereoscopic System(HESS) in the Galactic plane. The analysis of 215 h of HESS data has revealed a steadyγ-ray flux from HESS J1826−130, which appears extendedwith a half-width of 0.21◦±0.02◦stat±0.05◦sys. The source spectrum is best fit with either a power-law function with a spectral indexΓ =1.78±0.10stat±0.20sysand an exponential cut-offat 15.2+5.5−3.2TeV, or a broken power-law withΓ1=1.96±0.06stat±0.20sys,Γ2=3.59±0.69stat±0.20sysfor energies below and aboveEbr=11.2±2.7 TeV, respectively. The VHE flux from HESS J1826−130 is contaminated by the extended emission ofthe bright, nearby pulsar wind nebula (PWN), HESS J1825−137, particularly at the low end of the energy spectrum. Leptonic scenarios for theorigin of HESS J1826−130 VHE emission related to PSR J1826−1256 are confronted by our spectral and morphological analysis. In a hadronicframework, taking into account the properties of dense gas regions surrounding HESS J1826−130, the source spectrum would imply an astrophysicalobject capable of accelerating the parent particle population up to&200 TeV. Our results are also discussed in a multiwavelength context, accountingfor both the presence of nearby supernova remnants (SNRs), molecular clouds, and counterparts detected in radio, X-rays, and TeV energies
TIM-3 Genetic Variants Are Associated with Altered Clinical Outcome and Susceptibility to Gram-Positive Infections in Patients with Sepsis
2020-11-06

Background: Previous studies have reported the fundamental role of immunoregulatory proteins in the clinical phenotype and outcome of sepsis. This study investigated two functional single nucleotide polymorphisms (SNPs) of T cell immunoglobulin and mucin domain-containing protein 3 (TIM-3), which has a negative stimulatory function in the T cell immune response. Methods: Patients with sepsis (n = 712) were prospectively enrolled from three intensive care units (ICUs) at the University Medical Center Goettingen since 2012. All patients were genotyped for the TIM-3 SNPs rs1036199 and rs10515746. The primary outcome was 28-day mortality. Disease severity and microbiological findings were secondary endpoints. Results: Kaplan–Meier survival analysis demonstrated a significantly lower 28-day mortality for TIM-3 rs1036199 AA homozygous patients compared to C-allele carriers (18% vs. 27%, p = 0.0099) and TIM-3 rs10515746 CC homozygous patients compared to A-allele carriers (18% vs. 26%, p = 0.0202). The TIM-3 rs1036199 AA genotype and rs10515746 CC genotype remained significant predictors for 28-day mortality in the multivariate Cox regression analysis after adjustment for relevant confounders (adjusted hazard ratios: 0.67 and 0.70). Additionally, patients carrying the rs1036199 AA genotype presented more Gram-positive and Staphylococcus epidermidis infections, and rs10515746 CC homozygotes presented more Staphylococcus epidermidis infections. Conclusion: The studied TIM-3 genetic variants are associated with altered 28-day mortality and susceptibility to Gram-positive infections in sepsis.
Truncated moment sequences and a solution to the channel separability problem
2020-11-06

We consider the problem of separability of quantum channels via the Choi matrix representation given by the Choi-Jamio{\\l}kowski isomorphism. We explore three classes of separability across different cuts between systems and ancillae and we provide a solution based on the mapping of the coordinates of the Choi state (in a fixed basis) to a truncated moment sequence (tms) . This results in an algorithm which gives a separability certificate using semidefinite programming. The computational complexity and the performance of it depend on the number of variables in the tms and on the size of the moment matrix of order . We exploit the algorithm to numerically investigate separability of families of 2-qubit and single-qutrit channels; in the latter case we can provide an answer for examples explored earlier through the criterion based on the negativity , a criterion which remains inconclusive for Choi matrices with .
Migration jumps of planets in transition discs
2020-11-06

\\nContext. Transition discs form a special class of protoplanetary discs that are characterised by a deficiency of disc material close to the star. In a subgroup, inner holes in these discs can stretch out to a few tens of au while there is still mass accretion onto the central star observed at the same time.\\nAims. We analyse the proposition that this type of wide transition disc is generated by the interaction of the disc with a system of embedded planets.\\nMethods. We performed two-dimensional hydrodynamics simulations of a flat disc. Different equations of state were used including locally isothermal models and more realistic cases that consider viscous heating, radiative cooling, and stellar heating. Two massive planets (with masses of between three and nine Jupiter masses) were embedded in the disc and their dynamical evolution due to disc–planet interaction was followed for over 100 000 yr. The simulations account for mass accretion onto the star and planets. We included models with parameters reminiscent of the system PDS 70. To assess the observability of features in our models we performed synthetic ALMA observations.\\nResults. For systems with a more massive inner planet, there are phases where both planets migrate outward engaged in a 2:1 mean motion resonance via the Masset-Snellgrove mechanism. In sufficiently massive discs, the resulting formation of a vortex and the interaction with it can trigger rapid outward migration of the outer planet where its distance can increase by tens of au in a few thousand years. After another few thousand years, the outer planet rapidly migrates back inwards into resonance with the inner planet. We call this emerging composite phenomenon a migration jump. Outward migration and the migration jumps are accompanied by a high mass accretion rate onto the star. The synthetic images reveal numerous substructures depending on the type of dynamical behaviour.\\nConclusions. Our results suggest that the outward migration of two embedded planets is a prime candidate for the explanation of the observed high stellar mass accretion rate in wide transition discs. The models for PDS 70 indicate it is not currently undergoing a migration jump but might very well be in a phase of outward migration.\\n
Heavy Metal Stress Alters the Response of the Unicellular Cyanobacterium Synechococcus elongatus PCC 7942 to Nitrogen Starvation
2020-11-07

Non-diazotrophic cyanobacteria are unable to fix atmospheric nitrogen and rely on combined nitrogen for growth and development. In the absence of combined nitrogen sources, most non-diazotrophic cyanobacteria, e.g., Synechocystis sp. PCC 6803 or Synechococcus elongatus PCC 7942, enter a dormant stage called chlorosis. The chlorosis process involves switching off photosynthetic activities and downregulating protein biosynthesis. Addition of a combined nitrogen source induces the regeneration of chlorotic cells in a process called resuscitation. As heavy metals are ubiquitous in the cyanobacterial biosphere, their influence on the vegetative growth of cyanobacterial cells has been extensively studied. However, the effect of heavy metal stress on chlorotic cyanobacterial cells remains elusive. To simulate the natural conditions, we investigated the effects of long-term exposure of S. elongatus PCC 7942 cells to both heavy metal stress and nitrogen starvation. We were able to show that elevated heavy metal concentrations, especially for Ni2+, Cd2+, Cu2+ and Zn2+, are highly toxic to nitrogen starved cells. In particular, cells exposed to elevated concentrations of Cd2+ or Ni2+ were not able to properly enter chlorosis as they failed to degrade phycobiliproteins and chlorophyll a and remained greenish. In resuscitation assays, these cells were unable to recover from the simultaneous nitrogen starvation and Cd2+ or Ni2+ stress. The elevated toxicity of Cd2+ or Ni2+ presumably occurs due to their interference with the onset of chlorosis in nitrogen-starved cells, eventually leading to cell death.
Computational Psychiatry for Computers
2020-11-07

Computational psychiatry is a nascent field that attempts to use multi-level analyses of the underlying computational problems that we face in navigating a complex, uncertain and changing world to illuminate mental dysfunction and disease. Two particular foci of the field are the costs and benefits of environmental adaptivity and the danger and necessity of heuristics. Here, we examine the extent to which these foci and others can be used to study the actual and potential flaws of the artificial computational devices that we are increasingly inventing and empowering to navigate this very same environment on our behalf.
The impact ofStaphylococcus aureuscell wall glycosylation on langerin recognition and Langerhans cell activation
2020-11-07

Abstract Staphylococcus aureus is the leading cause of skin and soft tissue infections. It remains incompletely understood how skin-resident immune cells respond to S. aureus invasion and contribute to an effective immune response. Langerhans cells (LCs), the only professional antigen-presenting cell type in the epidermis, sense S. aureus through their pattern-recognition receptor langerin, triggering a pro-inflammatory response. Langerin specifically recognizes the β-1,4-linked N -acetylglucosamine (β-GlcNAc) modification, which requires the glycosyltransferase TarS, on the cell wall glycopolymer Wall Teichoic Acid (WTA). Recently, an alternative WTA glycosyltransferase, TarP, was identified in methicillin-resistant S. aureus strains belonging to clonal complexes (CC) 5 and CC398. TarP also modifies WTA with β-GlcNAc but at the C-3 position of the WTA ribitol phosphate (RboP) subunit. Here, we aimed to unravel the impact of β-GlcNAc linkage position for langerin binding and LC activation. In addition, we performed structure-binding studies using a small panel of unique chemically-synthesized WTA molecules to assess langerin-WTA binding requirements. Using FITC-labeled recombinant human langerin and genetically-modified S. aureus strains, we observed that langerin similarly recognized bacteria that produce either TarS- or TarP-modified WTA. Furthermore, using chemically-synthesized WTA, representative of the different S. aureus WTA glycosylation patterns, established that β-GlcNAc is sufficient to confer langerin binding. Functionally, tarP -expressing S. aureus induce increased cytokine production and maturation of in vitro -generated LCs compared to tarS expressing S. aureus . Overall, our data suggest that LCs are able to sense all β-GlcNAc-WTA producing S. aureus strains, likely performing an important role as first responders upon S. aureus skin invasion.
Diagnostic Confidence and Feasibility of a Deep Learning Accelerated HASTE Sequence of the Abdomen in a Single Breath-Hold
2020-11-08

Objective The aim of this study was to evaluate the feasibility of a single breath-hold fast half-Fourier single-shot turbo spin echo (HASTE) sequence using a deep learning reconstruction (HASTE DL ) for T2-weighted magnetic resonance imaging of the abdomen as compared with 2 standard T2-weighted imaging sequences (HASTE and BLADE). Materials and Methods Sixty-six patients who underwent 1.5-T liver magnetic resonance imaging were included in this monocentric, retrospective study. The following T2-weighted sequences in axial orientation and using spectral fat suppression were compared: a conventional respiratory-triggered BLADE sequence (time of acquisition [TA] = 4:00 minutes), a conventional multiple breath-hold HASTE sequence (HASTE S ) (TA = 1:30 minutes), as well as a single breath-hold HASTE with deep learning reconstruction (HASTE DL ) (TA = 0:16 minutes). Two radiologists assessed the 3 sequences regarding overall image quality, noise, sharpness, diagnostic confidence, and lesion detectability as well as lesion characterization using a Likert scale ranging from 1 to 4 with 4 being the best. Comparative analyses were conducted to assess the differences between the 3 sequences. Results HASTE DL was successfully acquired in all patients. Overall image quality for HASTE DL was rated as good (median, 3; interquartile range, 3–4) and was significantly superior to HASTE s ( P &lt; 0.001) and inferior to BLADE ( P = 0.001). Noise, sharpness, and artifacts for HASTE DL reached similar levels to BLADE ( P ≤ 0.176) and were significantly superior to HASTE s ( P &lt; 0.001). Diagnostic confidence for HASTE DL was rated excellent by both readers and significantly superior to HASTE s ( P &lt; 0.001) and inferior to BLADE ( P = 0.044). Lesion detectability and lesion characterization for HASTE DL reached similar levels to those of BLADE ( P ≤ 0.523) and were significantly superior to HASTE s ( P &lt; 0.001). Concerning the number of detected lesions and the measured diameter of the largest lesion, no significant differences were found comparing BLADE, HASTE S , and HASTE DL ( P ≤ 0.912). Conclusions The single breath-hold HASTE DL is feasible and yields comparable image quality and diagnostic confidence to standard T2-weighted TSE BLADE and may therefore allow for a remarkable time saving in abdominal imaging.