julilili42/papers huggingface dataset:
CORRAREA: cross-calibration of the XMM-Newton EPIC pn and MOS effective areas
2020-12-13

The remaining relative uncertainties on the calibration of the XMM-Newton telescope effective areas can still yield differences of the order of ten percent for the astrophysical parameters derived from the EPIC pn and MOS data. The aim of the CORRAREA project is to provide an empirical correction function determined by cross-calibration of the EPIC effective areas. The correction will be integrated as a default multiplicative energy-dependent correction factor to the ARFs in the SAS software package. It is determined by cross-calibrating the on-axis effective areas using a sample of more than 250 bright but non-piled-up observations of point-like sources. A fit-and-stack approach is used for cross-calibration with physically motivated models defined separately for each observation in the sample. Data-to-model ratios are calculated for each of the three detectors by dividing the detector data with the pn model convoluted with the detector response. A fit to the ratio of the MOS and pn data-to-model ratios then yields the correction function. The EPIC pn camera was chosen as the reference instrument as most of its calibration parameters have remained stable over the lifetime of the XMM-Newton mission. A highly automated pipeline was developed to allow for easy recalculation of the correction function to account for any future changes introduced in the XMM-Newton calibration files or SAS. The automated pipeline also allows to easily add future observations to the sample with only two manual tasks per observation: selection of a model and visual screening including the selection of source and background regions.
Revisiting the phosphorite deposit of Fontanarejo (central Spain): new window into the early Cambrian evolution of sponges and into the microbial origin of phosphorites
2020-12-13

Abstract Fossils within early Cambrian phosphorites worldwide are often well preserved due to early diagenetic permineralization. Here, we examine the fossil record contained within phosphorites of the Lower Cambrian Pusa Formation (late Fortunian to Cambrian Stage 2) in Fontanarejo, central Spain. The sedimentology and age of these phosphorites have been controversial and are here reviewed and discussed, providing also a updated geological map. The Pusa Formation is composed of fine clastic sediments that are partly turbiditic, with channels of quartz-rich conglomerates and abundant phosphorites in the upper part of the succession. The microfacies and mineralogy of these channel deposits are studied here for the first time in detail, showing that they are mainly composed of subspherical apatite clasts, with minor mudstone intraclasts, quartzite and mica grains. Numerous sponge spicules, as well as entirely preserved hexactinellid sponges and demosponges, were collected within these phosphorites and likely represent stem groups. In addition to sponges, other fossils, such as small shelly fossils (SSF) of the mollusk Anabarella sp., were found. The phosphorites exhibit multiple evidence of intense microbial activity, including diverse fabrics (phosphatic oncoidal-like microbialites, thrombolites, stromatolites, and cements) and abundant fossils of filamentous microbes that strongly resemble sulfur oxidizing bacteria. Our findings strongly suggest that microbial processes mediated the rapid formation of most of the Fontanarejo apatite, probably accounting for the exceptional preservation of fragile fossils such as sponge skeletons. The apparent presence of taxonomically diverse hexactinellid and demosponge communities by the lowermost Cambrian further corroborates a Precambrian origin of the phylum Porifera.
Apathy in presymptomatic genetic frontotemporal dementia predicts cognitive decline and is driven by structural brain changes
2020-12-14

Abstract Introduction Apathy adversely affects prognosis and survival of patients with frontotemporal dementia (FTD). We test whether apathy develops in presymptomatic genetic FTD, and is associated with cognitive decline and brain atrophy. Methods Presymptomatic carriers of MAPT , GRN or C9orf72 mutations (N = 304), and relatives without mutations (N = 296) underwent clinical assessments and MRI at baseline, and annually for 2 years. Longitudinal changes in apathy, cognition, gray matter volumes, and their relationships were analyzed with latent growth curve modeling. Results Apathy severity increased over time in presymptomatic carriers, but not in non‐carriers. In presymptomatic carriers, baseline apathy predicted cognitive decline over two years, but not vice versa. Apathy progression was associated with baseline low gray matter volume in frontal and cingulate regions. Discussion Apathy is an early marker of FTD‐related changes and predicts a subsequent subclinical deterioration of cognition before dementia onset. Apathy may be a modifiable factor in those at risk of FTD.
Clear cell meningiomas are defined by a highly distinct DNA methylation profile and mutations in SMARCE1
2020-12-14

Abstract Clear cell meningioma represents an uncommon variant of meningioma that typically affects children and young adults. Although an enrichment of loss-of-function mutations in the SMARCE1 gene has been reported for this subtype, comprehensive molecular investigations are lacking. Here we describe a molecularly distinct subset of tumors ( n = 31), initially identified through genome-wide DNA methylation screening among a cohort of 3093 meningiomas, of which most were diagnosed histologically as clear cell meningioma. This cohort was further supplemented by an additional 11 histologically diagnosed clear cell meningiomas for analysis ( n = 42). Targeted DNA sequencing revealed SMARCE1 mutations in 33/34 analyzed samples, accompanied by a nuclear loss of expression determined via immunohistochemistry and a decreased SMARCE1 transcript expression in the tumor cells. Analysis of time to progression or recurrence of patients within the clear cell meningioma group ( n = 14) in comparison to those with meningioma WHO grade 2 ( n = 220) revealed a similar outcome and support the assignment of WHO grade 2 to these tumors. Our findings indicate the existence of a highly distinct epigenetic signature of clear cell meningiomas, separate from all other variants of meningiomas, with recurrent mutations in the SMARCE1 gene. This suggests that these tumors may arise from a different precursor cell population than the broad spectrum of the other meningioma subtypes.
Collapse and rescue of evolutionary food webs under global warming
2020-12-14

Abstract Global warming is severely impacting ecosystems and threatening ecosystem services as well as human well‐being. While some species face extinction risk, several studies suggest the possibility that fast evolution may allow species to adapt and survive in spite of environmental changes. We assess how such evolutionary rescue extends to multitrophic communities and whether evolution systematically preserves biodiversity under global warming. More precisely, we expose simulated trophic networks of co‐evolving consumers to warming under different evolutionary scenarios, which allows us to assess the effect of evolution on diversity maintenance. We also investigate how the evolution of body mass and feeding preference affects coexistence within a simplified consumer–resource module. Our simulations predict that the long‐term diversity loss triggered by warming is considerably higher in scenarios where evolution is slowed down or switched off completely, indicating that eco‐evolutionary feedback indeed helps to preserve biodiversity. However, even with fast evolution, food webs still experience vast disruptions in their structure and functioning. Reversing warming may thus not be sufficient to restore previous structures. Our findings highlight how the interaction between evolutionary rescue and changes in trophic structures constrains ecosystem responses to warming with important implications for conservation and management policies.
Long term measures of vestibulo-ocular reflex function in high level male gymnasts and its possible role during context specific rotational tasks
2020-12-14

In a prior publication, we described a previously unknown eye movement phenomenon during the execution of actively performed multiaxial rotations in high level gymnasts. This phenomenon was consistently observed during the phase of fast free flight rotations and was marked by a prolonged and complete suppression of nystagmus and gaze stabilizing “environment referenced eye movements” (EREM; such as the vestibulo-ocular reflex, optokinetic reflex, smooth pursuit and others). Instead, these eye movements were coupled with intersegmental body movements. We have therefore called it “spinal motor-coupled eye movements” (SCEM) and have interpreted the phenomenon to likely be caused by anti-compensatory functions of more proprioceptive mediated reflexes and perhaps other mechanisms (e.g., top-down regulation as part of a motor plan) to effectively cope with a new-orientation in space, undisturbed by EREM functions. In the phase before landing, the phenomenon was replaced again by the known gaze-stabilizing EREM functions. The present study specifically evaluated long-term measures of vestibulo-ocular reflex functions (VOR) in high level gymnasts and controls during both passively driven monoaxial rotations and context-specific multiaxial somersault simulations in a vestibular lab. This approach provided further insights into the possible roles of adaptive or mental influences concerning the VOR function and how they are associated with the described phenomenon of SCEM. Results showed high inter-individual variability of VOR function in both gymnasts and controls, but no systematic adaptation of the VOR in gymnasts, neither compared to controls nor over a period of three years. This might generally support the hypothesis that the phenomenon of SCEM might indeed be driven more by proprioceptively mediated and situationally dominant eye movement functions than by adaptative processes of the VOR.
Parking planets in circumbinary discs
2020-12-15

The Kepler space mission has discovered about a dozen planets orbiting around binary stars systems. Most of these circumbinary planets lie near their instability boundaries, at about three to five binary separations. Past attempts to match these final locations through an inward migration process were only shown to be successful for the Kepler-16 system. Here, we study ten circumbinary systems and attempt to match the final parking locations and orbital parameters of the planets with a disc-driven migration scenario. We performed 2D locally isothermal hydrodynamical simulations of circumbinary discs with embedded planets and followed their migration evolution using different values for the disc viscosity and aspect ratio. We found that for the six systems with intermediate binary eccentricities (0.1 ≤ e bin ≤ 0.21), the final planetary orbits matched the observations closely for a single set of disc parameters, specifically, a disc viscosity of α = 10 −4 and an aspect ratio of H ∕ r ~ 0.04. For these systems the planet masses are large enough to open at least a partial gap in their discs as they approach the binary, forcing the discs to become circularised and allowing for further migration towards the binary – ultimately leading to a good agreement with the observed planetary orbital parameters. For systems with very small or large binary eccentricities, the match was not as good as the very eccentric discs and the large inner cavities in these cases prevented close-in planet migration. In test simulations with higher than observed planet masses, a better agreement was found for those systems. The good agreement for six out of the ten modelled systems, where the relative difference between observed and simulated final planet orbit is ≤10% strongly supports the idea that planet migration in the disc brought the planets to their present locations.
Evidence and implications of pre‐existing humoral cross‐reactive immunity to SARS‐CoV‐2
2020-12-15

Abstract Background Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has emerged throughout the world. Building knowledge around Covid‐19 is crucial to devise facts based approaches to respond efficiently against this pandemic. Aim We aimed to investigate pre‐existing humoral cross‐reactive immunity to SARS‐CoV‐2. Method We have tested the reactivity against SARS‐CoV‐2 nucleocapsid (N) antigen of sera collected from healthy healthcare volunteers in 2014. We assessed immunoglobulins reactive against SARS‐CoV‐2 N‐antigen using a well‐validated serological platform; Elecsys assay. Results Sera from 32 subjects (out of 135 [23.7%]) were reactive to SARS‐CoV‐2 N‐antigen, suggesting the presence of anti‐SARS‐CoV‐2 N‐antigen antibodies. Conclusion Although the clinical relevance of the observed reactivity can only be speculated and needs to be investigated, the implication of this finding for coronavirus disease 2019 seroepidemiological survey and vaccines' clinical trials is critical.
Biological Maturity Status in Elite Youth Soccer Players: A Comparison of Pragmatic Diagnostics With Magnetic Resonance Imaging
2020-12-15

The influence of biological maturity status (BMS) on talent identification and development within elite youth soccer is critically debated. During adolescence, maturity-related performance differences within the same age group may cause greater chances of being selected for early maturing players. Therefore, coaches need to consider players' BMS. While standard methods for assessing BMS in adolescents are expensive and time-consuming imaging techniques (i.e., X-ray and MRI), there also exist more pragmatic procedures. This study aimed to evaluate commonly used methods to assess BMS within a highly selected sample of youth soccer players. A total of N = 63 elite male soccer players (U12 and U14) within the German Soccer Association's talent promotion program completed a test battery assessing BMS outcomes. Utilizing MRI diagnostics, players' skeletal age (SA MRI ) was determined by radiologists and served as the reference method. Further commonly used methods included skeletal age measured by an ultrasound device (SA US ), the maturity offset (MO MIR ), and the percentage of adult height (PAH KR ). The relation of these alternative BMS outcomes to SA MRI was examined using different perspectives: performing bivariate correlation analyses (1), modeling BMS as a latent variable (BMS lat ) based on the multiple alternative diagnostics (2), and investigating individual differences in agreement (3). (1) Correlations of SA MRI and the further BMS variables ranked from r = 0.80 to r = 0.84 for the total sample and were lower for U12 (0.56 ≤ r ≤ 0.66), and U14 (0.61 ≤ r ≤ 0.74) (2). The latent structural equation modeling (SEM) ( R 2 = 51%) revealed a significant influence on BMS lat for MO MIR (β = 0.51, p &amp;lt;0.05). The additional contribution of PAH KR (β = 0.27, p = 0.06) and SA US (β = −0.03, p = 0.90) was rather small (3). The investigation of individual differences between the reference method and alternative diagnostics indicated a significant bias for MO MIR ( p &amp;lt;0.01). The results support the use of economical and time-efficient methods for assessing BMS within elite youth soccer. Bivariate correlation analyses as well as the multivariate latent variable approach highlight the measures' usefulness. However, the observed individual level differences for some of the utilized procedures led to the recommendation for practitioners to use at least two alternative assessment methods in order to receive more reliable information about players' BMS within the talent promotion process.
Abnormal Regional and Global Connectivity Measures in Subjective Cognitive Decline Depending on Cerebral Amyloid Status
2020-12-15

Background: Amyloid-β accumulation was found to alter precuneus-based functional connectivity (FC) in mild cognitive impairment (MCI) and Alzheimer’s disease (AD) dementia, but its impact is less clear in subjective cognitive decline (SCD), which in combination with AD pathologic change is theorized to correspond to stage 2 of the Alzheimer’s continuum in the 2018 NIA-AA research framework. Objective: This study addresses how amyloid pathology relates to resting-state fMRI FC in SCD, especially focusing on the precuneus. Methods: From the DELCODE cohort, two groups of 24 age- and gender-matched amyloid-positive (SCDAβ+) and amyloidnegative SCD (SCDβ−) patients were selected according to visual [18F]-Florbetaben (FBB) PET readings, and studied with resting-state fMRI. Local (regional homogeneity [ReHo], fractional amplitude of low-frequency fluctuations [fALFF]) and global (degree centrality [DC], precuneus seed-based FC) measures were compared between groups. Follow-up correlation analyses probed relationships of group differences with global and precuneal amyloid load, as measured by FBB standard uptake value ratios (SUVR=⫖FBB). Results: ReHo was significantly higher (voxel-wise p &lt; 0.01, cluster-level p &lt; 0.05) in the bilateral precuneus for SCDAβ+patients, whereas fALFF was not altered between groups. Relatively higher precuneus-based FC with occipital areas (but no altered DC) was observed in SCDAβ+ patients. In this latter cluster, precuneus-occipital FC correlated positively with global (SCDAβ+) and precuneus SUVRFBB (both groups). Conclusion: While partial confounding influences due to a higher APOE ε4 carrier ratio among SCDAβ+ patients cannot be excluded, exploratory results indicate functional alterations in the precuneus hub region that were related to amyloid-β load, highlighting incipient pathology in stage 2 of the AD continuum.
Hidden in plain sight: A microanalytical study of a Middle Stone Age ochre piece trapped inside a micromorphological block sample
2020-12-15

Abstract A complete Middle Stone Age ochre piece was unintentionally collected and fully preserved within a micromorphological block sample intended to characterise a 74 ± 3 ka occupation horizon at Blombos Cave, South Africa. Previously recovered ochre pieces from the same stratigraphic context (Still Bay) have displayed intricate modification patterns with significant behavioural implications. Yet, in the case of the trapped ochre, a direct visual assessment of its surfaces was impossible due to its impregnated state. In this study, we demonstrate how we successfully reconstructed three‐dimensionally and characterised the block‐sampled ochre piece using high‐resolution microcomputed tomography scanning coupled with a range of microanalytical techniques, including optical petrography, micro‐Fourier transform infra‐red spectroscopy, micro‐X‐ray fluorescence and micro‐Raman spectroscopy. Through a morphometric analysis of the score marks present on the trapped ochre's reconstructed surface, we were able to assess the types of modifications and the nature of the actions that created them. Our results show that a block sample‐based study of archaeological artefacts allows for a comprehensive assessment of their depositional and microcontextual setting, their external morphology and microtopography, as well as their internal texture and geochemical properties. We suggest that this type of context‐sensitive, multiscalar and multidisciplinary investigation may also prove beneficial in the study of conventionally recovered archaeological artefacts.
Research Progress of the Application of Hypothermia in the Eye
2020-12-15

Hypothermia is widely used in the medical field to protect organs or tissues from damage. Different research fields have different explanations of the protection mechanism of hypothermia. Hypothermia is also widely used in the field of ophthalmology, for example, in the eye bank, the preservation of corneal tissue and the preservation of the eyeball. Low temperature can also be applied to some ophthalmic diseases, such as allergic conjunctivitis, retinal ischemia, and retinal hypoxia. It is used to relieve eye symptoms or reduce tissue damage. Hypothermic techniques have important applications in ophthalmic surgery, such as corneal refractive surgery, vitrectomy surgery, and ciliary body cryotherapy for end-stage glaucoma. Hypothermia can reduce the inflammation of the cornea and protect the retinal tissue. The eyeball is a complex organ, including collagen tissue of the eyeball wall and retinal nerve tissue and retinal blood vessels. The mechanism of low temperature protecting eye tissue is complicated. It is important to understand the mechanism of hypothermia and its applications in ophthalmology. This review introduces the mechanism of hypothermia and its application in the eye banks, eye diseases (allergic conjunctivitis, retinal ischemia, and hypoxia), and eye surgeries (corneal transplant surgery, corneal refractive surgery, and vitrectomy).
AN IMPORTANT STIMULATORY ROLE FOR THE cGMP-DEPENDENT PROTEIN KINASE II IN PLATELET ACTIVATION, IN VIVO THROMBOSIS AND HAEMOSTASIS
2020-12-15

Background and Purpose: The intracellular second messenger cGMP mediates signals by activating two types of cGMP-dependent protein kinases (PKG), PKG I and PKG II, differentially expressed in different cells. In platelets, cGMP mediates biphasic signals that stimulate and inhibit platelet activation, and the downstream signaling of cGMP is mediated by PKG I, the only PKG known to be expressed in platelets. However, functional defects of PKG I knockout platelets did not fully explain the roles of cGMP and the effect of PKG inhibitors on platelet activation. Experimental Approach: To determine if PKG II is present in platelets and plays a role in platelet activation, we performed RT-PCR and isolation of PKG II protein using cGMP-conjugated beads. We further determined platelet aggregation and ATP release in vitro, and FeCl3-injured carotid artery thrombosis as well as tail bleeding time in vivo. Key Results: PKG II is expressed in platelets and plays an important role in selectively stimulating platelet activation but not in the negative regulatory role of cGMP. Collagen-induced platelet aggregation and ATP secretion were reduced in PKG II-deficient mice but not PKG I-deficient mice. In contrast, low-dose thrombin-induced platelet activation depended on PKG I but not PKG II. Tail bleeding time and FeCl3-induced artery thrombus formation were significantly prolonged in PKG II knockout mice. Conclusion and Implication: PKG II-mediated cGMP signals are important in platelet activation, thrombosis and haemostasis in vitro and in vivo.
Number Fluctuations Induce Persistent Congestion
2020-12-15

The capacity of a street segment quantifies the maximal density of vehicles before congestion arises. Here we show in a simple mathematical model that fluctuations in the instantaneous number of vehicles entering a street segment are sufficient to induce persistent congestion. Congestion emerges even if the average flow is below the segment’s capacity where congestion is absent without fluctuations. We explain how this fluctuation-induced congestion emerges due to a self-amplifying reduction of the average vehicle velocities.