julilili42/papers huggingface dataset:
BEAST begins: sample characteristics and survey performance of the B-star Exoplanet Abundance Study
2021-01-06

While the occurrence rate of wide giant planets appears to increase with stellar mass at least up through the A-type regime, B-type stars have not been systematically studied in large-scale surveys so far. It therefore remains unclear up to what stellar mass this occurrence trend continues. The B-star Exoplanet Abundance Study (BEAST) is a direct imaging survey with the extreme adaptive optics instrument SPHERE, targeting 85 B-type stars in the young Scorpius-Centaurus (Sco-Cen) region with the aim to detect giant planets at wide separations and constrain their occurrence rate and physical properties. The statistical outcome of the survey will help determine if and where an upper stellar mass limit for planet formation occurs. In this work, we describe the selection and characterization of the BEAST target sample. Particular emphasis is placed on the age of each system, which is a central parameter in interpreting direct imaging observations. We implement a novel scheme for age dating based on kinematic sub-structures within Sco-Cen, which complements and expands upon previous age determinations in the literature. We also present initial results from the first epoch observations, including the detections of ten stellar companions, of which six were previously unknown. All planetary candidates in the survey will need follow up in second epoch observations, which are part of the allocated observational programme and will be executed in the near future.
Vast Amounts of Encoded Items Nullify but Do Not Reverse the Effect of Sleep on Declarative Memory
2021-01-06

Sleep strengthens memories by repeatedly reactivating associated neuron ensembles. Our studies show that although long-term memory for a medium number of word-pairs (160) benefits from sleep, a large number (320) does not. This suggests an upper limit to the amount of information that has access to sleep-dependent declarative memory consolidation, which is possibly linked to the availability of reactivation opportunities. Due to competing processes of global forgetting that are active during sleep, we hypothesized that even larger amounts of information would enhance the proportion of information that is actively forgotten during sleep. In the present study, we aimed to induce such forgetting by challenging the sleeping brain with vast amounts of to be remembered information. For this, 78 participants learned a very large number of 640 word-pairs interspersed with periods of quiet awake rest over the course of an entire day and then either slept or stayed awake during the night. Recall was tested after another night of regular sleep. Results revealed comparable retention rates between the sleep and wake groups. Although this null-effect can be reconciled with the concept of limited capacities available for sleep-dependent consolidation, it contradicts our hypothesis that sleep would increase forgetting compared to the wake group. Additional exploratory analyses relying on equivalence testing and Bayesian statistics reveal that there is evidence against sleep having a detrimental effect on the retention of declarative memory at high information loads. We argue that forgetting occurs in both wake and sleep states through different mechanisms, i.e., through increased interference and through global synaptic downscaling, respectively. Both of these processes might scale similarly with information load.
Autophagy inhibition rescues structural and functional defects caused by the loss of mitochondrial chaperone Hsc70-5 in Drosophila
2021-01-06

We investigated in larval and adult <i>Drosophila</i> models whether loss of the mitochondrial chaperone <i>Hsc70-5</i> is sufficient to cause pathological alterations commonly observed in Parkinson disease. At affected larval neuromuscular junctions, no effects on terminal size, bouton size or number, synapse size, or number were observed, suggesting that we studied an early stage of pathogenesis. At this stage, we noted a loss of synaptic vesicle proteins and active zone components, delayed synapse maturation, reduced evoked and spontaneous excitatory junctional potentials, increased synaptic fatigue, and cytoskeleton rearrangements. The adult model displayed ATP depletion, altered body posture, and susceptibility to heat-induced paralysis. Adult phenotypes could be suppressed by knockdown of <i>dj-1β, Lrrk, DCTN2-p50, DCTN1-p150, Atg1, Atg101, Atg5, Atg7</i>, and <i>Atg12</i>. The knockdown of components of the macroautophagy/autophagy machinery or overexpression of human <i>HSPA9</i> broadly rescued larval and adult phenotypes, while disease-associated <i>HSPA9</i> variants did not. Overexpression of <i>Pink1</i> or promotion of autophagy exacerbated defects.<b>Abbreviations:</b> AEL: after egg laying; AZ: active zone; brp: bruchpilot; Csp: cysteine string protein; dlg: discs large; eEJPs: evoked excitatory junctional potentials; GluR: glutamate receptor; H<sub>2</sub>O<sub>2</sub>: hydrogen peroxide; mEJP: miniature excitatory junctional potentials; MT: microtubule; NMJ: neuromuscular junction; PD: Parkinson disease; <i>Pink1</i>: PTEN-induced putative kinase 1; PSD: postsynaptic density; SSR: subsynaptic reticulum; SV: synaptic vesicle; VGlut: vesicular glutamate transporter.
Comparison of Methods for Estimating Retinal Shape: Peripheral Refraction vs. Optical Coherence Tomography
2021-01-06

Retinal shape presents a clinical parameter of interest for myopia, and has commonly been inferred indirectly from peripheral refraction (PRX) profiles. Distortion-corrected optical coherence tomography (OCT) scans offer a new and direct possibility for retinal shape estimation. The current study compared retinal curvatures derived from OCT scans vs. PRX measurements in three refractive profiles (0° and 90° meridians, plus spherical equivalent) for 25 participants via Bland–Altman analysis. The radial differences between both procedures were correlated to axial length using Pearson correlation. In general, PRX- and OCT-based retinal radii showed low correlation (all intraclass correlation coefficients &lt; 0.21). PRX found flatter retinal curvatures compared to OCT, with the highest absolute agreement found with the 90° meridian (mean difference +0.08 mm) and lowest in the 0° meridian (mean difference +0.89 mm). Moreover, a negative relation between axial length and the agreement of both methods was detected especially in the 90° meridian (R = −0.38, p = 0.06). PRX measurements tend to underestimate the retinal radius with increasing myopia when compared to OCT measurements. Therefore, future conclusions from PRX on retinal shape should be made cautiously. Rather, faster and more clinically feasible OCT imaging should be performed for this purpose.
Understanding condensation domain selectivity in non-ribosomal peptide biosynthesis: structural characterization of the acceptor bound state
2021-01-06

Abstract Non-ribosomal peptide synthetases are important enzymes for the assembly of complex peptide natural products. Within these multi-modular assembly lines, condensation domains perform the central function of chain assembly, typically by forming a peptide bond between two peptidyl carrier protein (PCP)-bound substrates. In this work, we report the first structural snapshots of a condensation domain in complex with an aminoacyl-PCP acceptor substrate. These structures allow the identification of a mechanism that controls access of acceptor substrates to the active site in condensation domains. The structures of this previously uncharacterized complex also allow us to demonstrate that condensation domain active sites do not contain a distinct pocket to select the side chain of the acceptor substrate during peptide assembly but that residues within the active site motif can instead serve to tune the selectivity of these central biosynthetic domains.
Spin-Induced Black Hole Scalarization in Einstein-Scalar-Gauss-Bonnet Theory
2021-01-07

We construct black hole solutions with spin-induced scalarization in a class of models where a scalar field is quadratically coupled to the topological Gauss-Bonnet term. Starting from the tachyonically unstable Kerr solutions, we obtain families of scalarized black holes such that the scalar field has either even or odd parity, and we investigate their domain of existence. The scalarized black holes can violate the Kerr rotation bound. We identify "critical" families of scalarized black hole solutions such that the expansion of the metric functions and of the scalar field at the horizon no longer allows for real coefficients. For the quadratic coupling considered here, solutions with spin-induced scalarization are entropically favored over Kerr solutions with the same mass and angular momentum.
Feasibility and physics potential of detecting 8B solar neutrinos at JUNO *
2021-01-07

Abstract The Jiangmen Underground Neutrino Observatory (JUNO) features a 20 kt multi-purpose underground liquid scintillator sphere as its main detector. Some of JUNO's features make it an excellent location for B solar neutrino measurements, such as its low-energy threshold, high energy resolution compared with water Cherenkov detectors, and much larger target mass compared with previous liquid scintillator detectors. In this paper, we present a comprehensive assessment of JUNO's potential for detecting B solar neutrinos via the neutrino-electron elastic scattering process. A reduced 2 MeV threshold for the recoil electron energy is found to be achievable, assuming that the intrinsic radioactive background U and Th in the liquid scintillator can be controlled to 10 g/g. With ten years of data acquisition, approximately 60,000 signal and 30,000 background events are expected. This large sample will enable an examination of the distortion of the recoil electron spectrum that is dominated by the neutrino flavor transformation in the dense solar matter, which will shed new light on the inconsistency between the measured electron spectra and the predictions of the standard three-flavor neutrino oscillation framework. If eV , JUNO can provide evidence of neutrino oscillation in the Earth at approximately the 3 (2 ) level by measuring the non-zero signal rate variation with respect to the solar zenith angle. Moreover, JUNO can simultaneously measure using B solar neutrinos to a precision of 20% or better, depending on the central value, and to sub-percent precision using reactor antineutrinos. A comparison of these two measurements from the same detector will help understand the current mild inconsistency between the value of reported by solar neutrino experiments and the KamLAND experiment.
In-Line and Off-Line Monitoring of Skin Penetration Profiles Using Confocal Raman Spectroscopy
2021-01-07

Ex-vivo and in-vivo skin analysis has been extensively evaluated by confocal Raman spectroscopy (CRS). The off-line measurement with a CRS-suited skin-mounted device after Franz-cell incubations is the most popular choice. However, real-time monitoring of in-line measurement has clear advantages for obtaining dynamic and more timely results. In our study, a custom-built setup suitable for in-line measurements was implemented, which ensures constant skin incubation and in-situ skin detections. We aim to compare the differences between using in-line and off-line devices for monitoring skin drug penetrations. A well-assessed formulation gel with procaine-HCl as the active ingredient was used as reference. The PEG-23 lauryl ether was added to the formulation as a penetration enhancer to evaluate the enhancement effects of procaine on skin. After incubation times of 14, 20, and 24 h, skin penetration profiles were assessed. Comparable results between off-line and in-line measurements were obtained. Remarkable improvements in penetrated procaine amount and depth were observed. Based on the significant differences of their enhanced penetration amounts, fairly similar estimations were achieved from both methods. A slight difference of 14 h incubation between these two setups can still be found, which may be due to the different detection conditions and affected skin properties. Overall, in-line measurements could provide a more time- and labor-saving alternative for off-line measurements in ex-vivo study.
On the Application of Advanced Machine Learning Methods to Analyze Enhanced, Multimodal Data from Persons Infected with COVID-19
2021-01-07

The current COVID-19 pandemic, caused by the rapid worldwide spread of the SARS-CoV-2 virus, is having severe consequences for human health and the world economy. The virus affects different individuals differently, with many infected patients showing only mild symptoms, and others showing critical illness. To lessen the impact of the epidemic, one problem is to determine which factors play an important role in a patient’s progression of the disease. Here, we construct an enhanced COVID-19 structured dataset from more than one source, using natural language processing to add local weather conditions and country-specific research sentiment. The enhanced structured dataset contains 301,363 samples and 43 features, and we applied both machine learning algorithms and deep learning algorithms on it so as to forecast patient’s survival probability. In addition, we import alignment sequence data to improve the performance of the model. Application of Extreme Gradient Boosting (XGBoost) on the enhanced structured dataset achieves 97% accuracy in predicting patient’s survival; with climatic factors, and then age, showing the most importance. Similarly, the application of a Multi-Layer Perceptron (MLP) achieves 98% accuracy. This work suggests that enhancing the available data, mostly basic information on patients, so as to include additional, potentially important features, such as weather conditions, is useful. The explored models suggest that textual weather descriptions can improve outcome forecast.
Expanding the phenotype of PIGS‐associated early onset epileptic developmental encephalopathy
2021-01-07

Abstract The phosphatidylinositol glycan anchor biosynthesis class S protein ( PIGS) gene has recently been implicated in a novel congenital disorder of glycosylation resulting in autosomal recessive inherited glycosylphosphatidylinositol‐anchored protein (GPI‐AP) deficiency. Previous studies described seven patients with biallelic variants in the PIGS gene, of whom two presented with fetal akinesia and five with global developmental delay and epileptic developmental encephalopathy. We present the molecular and clinical characteristics of six additional individuals from five families with unreported variants in PIGS . All individuals presented with hypotonia, severe global developmental delay, microcephaly, intractable early infantile epilepsy, and structural brain abnormalities. Additional findings include vision impairment, hearing loss, renal malformation, and hypotonic facial appearances with minor dysmorphic features but without a distinctive facial gestalt. Four individuals died due to neurologic complications. GPI anchoring studies performed on one individual revealed a significant decrease in GPI‐APs. We confirm that biallelic variants in PIGS cause vitamin pyridoxine‐responsive epilepsy due to inherited GPI deficiency and expand the genotype and phenotype of PIGS ‐related disorder. Further delineation of the molecular spectrum of PIGS ‐related disorders would improve management, help develop treatments, and encourage the expansion of diagnostic genetic testing to include this gene as a potential cause of neurodevelopmental disorders and epilepsy.
Antibody and Cell-Mediated Immune Responses Are Correlates of Protection against Influenza Infection in Vaccinated Older Adults
2021-01-07

Despite efforts to design better vaccines for older adults, the risk for serious complications of influenza remains disproportionately high. Identifying correlates of vaccine effectiveness and understanding the heterogeneity of health outcomes in older adults are key to the vaccine development pipeline. We sought correlates of protection against laboratory-confirmed influenza illness (LCII) in a 4-year randomized trial of standard versus high-dose influenza vaccination of adults 65 years and older. To this end, we quantified serum hemagglutination-inhibition (HAI) titers and interferon-gamma (IFNγ) and interleukin-10 (IL-10) secretion by virus-challenged peripheral blood mononuclear cells. Of the 608 participants included, 26 developed either A/H3N2-(n = 17) or B-LCII (n = 9) at 10–20 weeks post-vaccination. Antibody titres for A/H3N2 at 4-weeks post-vaccination were significantly associated with protection against LCII, where every 1-standard deviation increase reduced the odds of A/H3N2-LCII by 53%. Although B-titres did not correlate with protection against B-LCII, the fold-increase in IFNγ:IL-10 ratios from pre- to 4-weeks post-vaccination was significantly associated with protection against B-LCII, where every 1-standard deviation increase reduced the odds by 71%. Our results suggest that both antibody and cell-mediated immune measures are valuable and potentially complementary correlates of protection against LCII in vaccinated older adults, although this may depend on the viral type causing infection.
Altered Spatial Composition of the Immune Cell Repertoire in Association to CD34+ Blasts in Myelodysplastic Syndromes and Secondary Acute Myeloid Leukemia
2021-01-07

Background: Myelodysplastic syndromes (MDS) are caused by a stem cell failure and often include a dysfunction of the immune system. However, the relationship between spatial immune cell distribution within the bone marrow (BM), in relation to genetic features and the course of disease has not been analyzed in detail. Methods: Histotopography of immune cell subpopulations and their spatial distribution to CD34+ hematopoietic cells was determined by multispectral imaging (MSI) in 147 BM biopsies (BMB) from patients with MDS, secondary acute myeloid leukemia (sAML), and controls. Results: In MDS and sAML samples, a high inter-tumoral immune cell heterogeneity in spatial proximity to CD34+ blasts was found that was independent of genetic alterations, but correlated to blast counts. In controls, no CD8+ and FOXP3+ T cells and only single MUM1p+ B/plasma cells were detected in an area of ≤10 μm to CD34+ HSPC. Conclusions: CD8+ and FOXP3+ T cells are regularly seen in the 10 μm area around CD34+ blasts in MDS/sAML regardless of the course of the disease but lack in the surrounding of CD34+ HSPC in control samples. In addition, the frequencies of immune cell subsets in MDS and sAML BMB differ when compared to control BMB providing novel insights in immune deregulation.
Balancing the brain of offenders with psychopathy? Resting state EEG and electrodermal activity after a pilot study of brain self-regulation training
2021-01-07

Although investigation of the brains of criminals began quite early in the history of psychophysiological research, little is known about brain plasticity of offenders with psychopathy. Building on our preliminary study reporting successful brain self-regulation using slow cortical potential (SCP) neurofeedback in offenders with psychopathy, we investigated the central nervous and autonomic peripheral changes occurring after brain self-regulation in a group of severe male offenders with psychopathy. Regarding the central nervous system, an overall suppression of the psychopathic overrepresentation of slow frequency bands was found, such as delta and theta band activity, after EEG neurofeedback. In addition, an increase in alpha band activity could be observed after the SCP self-regulation training. Electrodermal activity adaptively changed according to the regulation task, and this flexibility improved over training time. The results of this study point towards a constructive learning process and plasticity in neural and peripheral measures of offenders with psychopathy.
From tree to architecture: how functional morphology of arborescence connects plant biology, evolution and physics
2021-01-07

Abstract Trees are the fundamental element of forest ecosystems, made possible by their mechanical qualities and their highly sophisticated conductive tissues. The evolution of trees, and thereby the evolution of forests, were ecologically transformative and affected climate and biogeochemical cycles fundamentally. Trees also offer a substantial amount of ecological niches for other organisms, such as epiphytes, creating a vast amount of habitats. During land plant evolution, a variety of different tree constructions evolved and their constructional principles are a subject of ongoing research. Understanding the “natural construction” of trees benefits strongly from methods and approaches from physics and engineering. Plant water transport is a good example for the ongoing demand for interdisciplinary efforts to unravel form-function relationships on vastly differing scales. Identification of the unique mechanism of water long-distance transport requires a solid basis of interfacial physics and thermodynamics. Studying tree functions by using theoretical approaches is, however, not a one-sided affair: The complex interrelationships between traits, functionality, trade-offs and phylogeny inspire engineers, physicists and architects until today.
Resection of cerebellar tumours causes widespread and functionally relevant white matter impairments
2021-01-07

Abstract Several diffusion tensor imaging studies reveal that white matter (WM) lesions are common in children suffering from benign cerebellar tumours who are treated with surgery only. The clinical implications of WM alterations that occur as a direct consequence of cerebellar disease have not been thoroughly studied. Here, we analysed structural and diffusion imaging data from cerebellar patients with chronic surgical lesions after resection for benign cerebellar tumours. We aimed to elucidate the impact of focal lesions of the cerebellum on WM integrity across the entire brain, and to investigate whether WM deficits were associated with behavioural impairment in three different motor tasks. Lesion symptom mapping analysis suggested that lesions in critical cerebellar regions were related to deficits in savings during an eyeblink conditioning task, as well as to deficits in motor action timing. Diffusion imaging analysis of cerebellar WM indicated that better behavioural performance was associated with higher fractional anisotropy (FA) in the superior cerebellar peduncle, cerebellum's main outflow path. Moreover, voxel‐wise analysis revealed a global pattern of WM deficits in patients within many cerebral WM tracts critical for motor and non‐motor function. Finally, we observed a positive correlation between FA and savings within cerebello‐thalamo‐cortical pathways in patients but not in controls, showing that saving effects partly depend on extracerebellar areas, and may be recruited for compensation. These results confirm that the cerebellum has extended connections with many cerebral areas involved in motor/cognitive functions, and the observed WM changes likely contribute to long‐term clinical deficits of posterior fossa tumour survivors.