julilili42/papers huggingface dataset:
RANBP2 Mutation Mimicking Viral Encephalitis
2022-04-05

A 10-month-old boy presented with fever, vomiting, and treatment-refractory status epilepticus. Viral encephalitis was suspected, however, blood and cerebrospinal fluid tests as well as multiplex polymerase chain reaction for detection of respiratory viruses were unremarkable. Laboratory investigations including liver function parameters revealed no abnormalities. Brain magnetic resonance imaging showed multifocal T2-hyperintense cortical and subcortical lesions including both thalami ([Fig. 1]). Exome sequencing revealed a heterozygous mutation in RANBP2 (ENST00000283195.6: c.1754C > T,p.Thr585Met) causing acute necrotizing encephalopathy (ANE1).[1] [2] A second episode with fever-triggered encephalopathy occurred at the age of 12 months. Methylprednisolone therapy was initiated (20 mg/kg body weight per day for three consecutive days), leading to rapid clinical improvement (subsidence of seizures, vigilance improvement). The case underlines the importance of neurogenetic diseases as differential diagnosis in cases of suspected neuroinflammation.
A novel proxy for tracking the provenance of dust based on paired E1'-peroxy paramagnetic defect centres in fine-grained quartz
2022-04-05

&lt;p&gt;Crystal lattice defects in quartz have long been exploited for age determination, yet also show potential for sediment provenance studies. Here we introduce a novel method for tracking aeolian dust provenance by utilising the natural accumulation of E&lt;sub&gt;1&lt;/sub&gt;&rsquo; and peroxy defect centres in quartz. Our approach is based on the previously observed premise that E&lt;sub&gt;1&lt;/sub&gt;&rsquo; and peroxy centres arise from Frenkel defect pairs, and that their concentration increases with age of the quartz-bearing source rock. We propose that these defect centres can be utilised as a characteristic feature of the source rock and consequently, for fingerprinting sediments derived from it. We successfully apply our new protocol to distinguish fine-grained quartz extracted from loess deposits from two regions in Central Asia which are known to derive from different source material of differing age. Our method offers strong potential for identifying variability in source, both spatially and through time down sedimentary sequences.&lt;/p&gt; &lt;p&gt;&nbsp;&lt;/p&gt;
Additional file 3 of Effects of caloric restriction on the gut microbiome are linked with immune senescence
2022-04-05

Additional file 2. The three supplementary Excel files, for colon (colon_cca_xlsx), spleen (spleen_cca_xlsx), and liver(liver_cca_xlsx), comprise each four spreadsheets: The sheets “corr.matrix” and “corr.fdr” contain estimated coefficients of the latent cross-correlation matrix (as shown in Fig. 6 and Supplementary Figure 5 heatmaps) and corresponding FDR-adjusted P-values, respectively. The sheet “asv.cca” contains for all ASVs (with the same order as in the correlation matrix) FDR-adjusted P-values and log-fold change values (columns C, D) from DESeq2 differential abundance testing (as shown in heatmap Fig. 1 C), the corresponding taxonomy table including seven taxonomic ranks (columns E-K), taxa labels used for heatmaps (column L) and two columns indicating the top (upper and lower) ASVs that were highlighted in correlation heatmap and circular chord diagrams (column M) and that were selected by sparse canonical correlation analysis using the Bayesian information criterion (column N), with sparse coefficients’ weights provided in column O. The sheet “imm.cca” contains for all immunological parameters (with the same order as in the correlation matrix) that were assessed in a given organ, FDR-adjusted P-values from GLMM and non-parametric (Wilcoxon-Mann-Whitney) differential abundance testing (columns C, D) between AdLib and CalRes groups. Columns E indicates type of parameter, i.e., whether absolute cell counts, or cell frequencies were determined. Column F denotes which cell population served as input for cluster-based analyses or was manually gated. Columns G – I provide cell subset IDs including prepended cluster numbers, manually annotated population names, and differentiation state. Columns J – L contain labels as displayed in correlation heatmap and circular chord diagrams for subset name, differentiation/antigen-experience, and lineage membership, respectively. Columns M – O indicate the top left and right immune parameters in the correlation heatmap, those selected by sparse canonical correlation analysis using the Bayesian information criterion, and sparse coefficients’ weights, respectively.
The Best of Two Worlds: A Systematic Review on Combining Real and Virtual Experiments in Science Education
2022-04-06

Conducting experiments fosters conceptual understanding in science education. In various studies, combinations of real (hands-on) and virtual (computer-simulated) experiments have been shown to be especially helpful for gaining conceptual understanding. The present systematic review, based on 42 experimental studies, focuses on the following: (1) What is the relative effectiveness of combining real and virtual experiments compared with a single type of experimentation? (2) Which sequence of real and virtual experiments is most effective? The results indicate that (1) in most cases combinations of real and virtual experiments promote conceptual understanding better than a single type of experimentation, and (2) there is no evidence for the superiority of a particular sequence. We conclude that for combining real and virtual experiments, apart from the individual affordances and the learning objectives of the different experiment types, especially their specific function for the learning task must be considered.
An integrative skeletal and paleogenomic analysis of stature variation suggests relatively reduced health for early European farmers
2022-04-06

Significance Subsistence shifts from hunting and gathering to agriculture over the last 12,000 y have impacted human culture, biology, and health. Although past human health cannot be assessed directly, adult stature variation and skeletal indicators of nonspecific stress can serve as proxies for health during growth and development. By integrating paleogenomic genotype and osteological stature data on a per-individual basis for 167 prehistoric Europeans, we observe relatively shorter than expected statures among early farmers after correcting for individual genetic contributions to stature. Poorer nutrition and/or increased disease burdens for early agriculturalists may partly underscore this result. Our integrated osteological–genetic model has exciting potential for studies of past human health and expansion into various other contexts.
Cytotoxic activity of Nep1‐like proteins on monocots
2022-04-06

Summary Necrosis‐ and ethylene‐inducing peptide 1 (Nep1)‐like proteins (NLPs) are found throughout several plant‐associated microbial taxa and are typically considered to possess cytolytic activity exclusively on dicot plant species. However, cytolytic NLPs are also produced by pathogens of monocot plants such as the onion ( Allium cepa ) pathogen Botrytis squamosa . We determined the cytotoxic activity of B . squamosa Bs Nep1, as well as other previously characterized NLPs, on various monocot plant species and assessed the plant plasma membrane components required for NLP sensitivity. Leaf infiltration of NLPs showed that onion cultivars are differentially sensitive to NLPs, and analysis of their sphingolipid content revealed that the GIPC series A : series B ratio did not correlate to NLP sensitivity. A tri‐hybrid population derived from a cross between onion and two wild relatives showed variation in NLP sensitivity within the population. We identified a quantitative trait locus (QTL) for NLP insensitivity that colocalized with a previously identified QTL for B . squamosa resistance and the segregating trait of NLP insensitivity correlated with the sphingolipid content. Our results demonstrate the cytotoxic activity of NLPs on several monocot plant species and legitimize their presence in monocot‐specific plant pathogens.
Model-based assessment of shallow landslides susceptibility at a petrochemical site in Brazil
2022-04-06

The Serra do Mar mountain range is the main site of shallow-landslides occurrence in Brazil. The application of physically-based models is an effective method to predict landslide susceptibility, which is of great importance in hazard assessments and urban-planning studies. Thus, the objective of this study is to compare landslide susceptibility scenarios created with SHALSTAB and SINMAP at two large watersheds (Mogi and Perequê) in Cubatão, Latin America’s largest petrochemical site. Model calibration is based on the landslide scars inventory of the 1985 event, the geotechnical parameters derived from soil samples and the topography sourced from a 5 m resolution DEM. Using the Receiver Operating Characteristics (ROC) analysis to assess model performance, SHALSTAB emerges as the best-fit model for both watersheds due to higher concentration of landslide scars in unstable areas (true positive results) and higher global accuracy. Even though SINMAP had similar degree of success, it was slightly less accurate and failed more often in the identification of potentially unstable areas. Comparative performance studies of physically-based models are fundamental to support effective and reliable hazard assessments in mountain regions, providing an outlook in how to proceed with more detailed studies.
Sex classification using the human sacrum: Geometric morphometrics versus conventional approaches
2022-04-06

The human pelvis shows marked sexual dimorphism that stems from the conflicting selective pressures of bipedal locomotion and parturition. The sacrum is thought to reflect this dimorphism as it makes up a significant portion of the pelvic girdle. However, reported sexual classification accuracies vary considerably depending on the method and reference sample (54%-98%). We aim to explore this inconsistency by quantifying sexual dimorphism and sex classification accuracies in a geographically heterogeneous sample by comparing 3D geometric morphometrics with the more commonly employed linear metric and qualitative assessments. Our sample included 164 modern humans from Africa, Europe, Asia, and America. The geometric morphometric analysis was based on 44 landmarks and 56 semilandmarks. Linear dimensions included sacral width, corpus depth and width, and the corresponding indices. The qualitative inspection relied on traditional macroscopic features such as proportions between the corpus of the first sacral vertebrae and the alae, and sagittal and coronal curvature of the sacrum. Classification accuracy was determined using linear discriminant function analysis for the entire sample and for the largest subsamples (i.e., Europeans and Africans). Male and female sacral shapes extensively overlapped in the geometric morphometric investigation, leading to a classification accuracy of 72%. Anteroposterior corpus depth was the most powerful discriminating linear parameter (83%), followed by the corpus-area index (78%). Qualitative inspection yielded lower accuracies (64–76%). Classification accuracy was higher for the Central European subsample and diminished with increasing geographical heterogeneity of the subgroups. Although the sacrum forms an integral part of the birth canal, our results suggest that its sex-related variation is surprisingly low. Morphological variation thus seems to be driven also by other factors, including body size, and sacrum shape is therefore likely under stronger biomechanical rather than obstetric selection.
Utility of serum complement factors C3 and C4 as biomarkers during therapeutic management of giant cell arteritis
2022-04-06

There is a strong unmet need for biomarkers in giant cell arteritis (GCA), as C-reactive protein (CRP) may be unreliable in patients treated with Tocilizumab (TCZ). We aimed to assess whether C3 and C4 are useful biomarkers in GCA patients, particularly in those treated with TCZ. We retrospectively enrolled all patients who underwent C3 and C4 measurement at baseline. All patients were evaluated at 3, 6, 12, and 24 months after diagnosis, as part of routine follow-up. Two assessments after the end of the observational period, in case of further relapses, were also included. At baseline, mean ± sd levels (mg/dL) of C3 (133 ± 28.99) and C4 (25.9 ± 9.04) were within normal ranges. During follow-up, C3 and C4 decreased in patients attaining remission (107.07 ± 19.86, p = 0.0006; 19.86 ± 10.27, p = 0.01, respectively) and sustained remission (95.85 ± 18.04, p = 0.001; 15.61 ± 9.75, p = 0.006). In TCZ-treated patients, even stronger decreases in C3 (83.11 ± 19.66, p = 0.001) and C4 (8.26 ± 3.83, p &lt; 0.0001) were observed, and their values were not correlated with CRP or erythrocyte sedimentation rate. C3 and C4 do not seem useful in the diagnosis of GCA, as normal values do not rule out active vasculitis. However, C3 and C4 correlate with disease activity. As the low C4 levels found in TCZ-treated patients are not correlated with CRP, C4 should be evaluated as a potential biomarker of disease activity and treatment response.
PEP7 is a ligand for receptor kinase SIRK1 to regulate aquaporins and root growth
2022-04-06

Abstract Plant receptor kinases constitute a large protein family that regulate various aspects of development and responses to external biotic and abiotic cues. Functional characterization of this protein family and particularly the identification of their ligands remains a major challenge in plant biology. Previously, we identified plasma membrane-intrinsic SUCROSE INDUCED RECEPTOR KINASE 1 (SIRK1) and QIAN SHOU KINASE 1 (QSK1) as a receptor / co-receptor pair involved in regulation of aquaporins in response to osmotic conditions induced by sucrose. Here, we identified a member of the Elicitor Peptide (PEP) family, namely PEP7, as the specific ligand of receptor kinase SIRK1. PEP7 binds to the extracellular domain of SIRK1 with a binding constant of 1.44±0.79 μM and is secreted to the apoplasm specifically in response to sucrose treatment. Stabilization of a signaling complex involving SIRK1, QSK1 and aquaporins as substrates is mediated by alterations in the external sucrose concentration or by PEP7 application. Moreover, the presence of PEP7 induces the phosphorylation of aquaporins in vivo and enhance water influx into protoplasts. The loss-of-function mutant of SIRK1 is not responsive to external PEP7 treatment regarding kinase activity, aquaporin phosphorylation and water influx activity. Our data indicate that the PEP7/SIRK1/QSK1 complex represents a crucial perception and response module mediating sucrose-controlled water flux in plants.
Feasibility of an accelerated 2D-multi-contrast knee MRI protocol using deep-learning image reconstruction: a prospective intraindividual comparison with a standard MRI protocol
2022-04-07

Abstract Objectives The aim of this study was to evaluate the image quality and diagnostic performance of a deep-learning (DL)–accelerated two–dimensional (2D) turbo spin echo (TSE) MRI of the knee at 1.5 and 3 T in clinical routine in comparison to standard MRI. Material and methods Sixty participants, who underwent knee MRI at 1.5 and 3 T between October/2020 and March/2021 with a protocol using standard 2D–TSE (TSE S ) and DL–accelerated 2D–TSE sequences (TSE DL ), were enrolled in this prospective institutional review board–approved study. Three radiologists assessed the sequences regarding structural abnormalities and evaluated the images concerning overall image quality, artifacts, noise, sharpness, subjective signal-to-noise ratio, and diagnostic confidence using a Likert scale (1–5, 5 = best). Results Overall image quality for TSE DL was rated to be excellent (median 5, IQR 4–5), significantly higher compared to TSE S (median 5, IQR 4 – 5, p &lt; 0.05), showing significantly lower extents of noise and improved sharpness ( p &lt; 0.001). Inter- and intra-reader agreement was almost perfect ( κ = 0.92–1.00) for the detection of internal derangement and substantial to almost perfect ( κ = 0.58–0.98) for the assessment of cartilage defects. No difference was found concerning the detection of bone marrow edema and fractures. The diagnostic confidence of TSE DL was rated to be comparable to that of TSE S (median 5, IQR 5–5, p &gt; 0.05). Time of acquisition could be reduced to 6:11 min using TSE DL compared to 11:56 min for a protocol using TSE S . Conclusion TSE DL of the knee is clinically feasible, showing excellent image quality and equivalent diagnostic performance compared to TSE S , reducing the acquisition time about 50%. Key Points • Deep-learning reconstructed TSE imaging is able to almost halve the acquisition time of a three-plane knee MRI with proton density and T1-weighted images, from 11:56 min to 6:11 min at 3 T. • Deep-learning reconstructed TSE imaging of the knee provided significant improvement of noise levels (p &lt; 0.001), providing higher image quality (p &lt; 0.05) compared to conventional TSE imaging. • Deep-learning reconstructed TSE imaging of the knee had similar diagnostic performance for internal derangement of the knee compared to standard TSE.
Long-Term Consequences of Repeated School Closures During the COVID-19 Pandemic for Reading and Mathematics Competencies
2022-04-07

School closures during the first wave of the COVID-19 pandemic in early 2020 were associated with attenuated learning gains compared to pre-pandemic years. In Germany, two further pandemic waves led to school closures and periods of remote learning between December 2020 and May 2021. The present study investigates the academic achievement of all incoming fifth-graders in the federal state of Baden-Württemberg before and during the pandemic, using educational large-scale assessment results in reading and mathematics. Each year, the assessments took place at the beginning of the school year in September (each n &amp;gt; 84,000). The comparison of average competence levels in 2021 with pre-pandemic years (2017–2019) indicates that the downward trend that was observed after the first pandemic wave in 2020 came to a halt in the domain of reading and continued at a slower rate in the domain of mathematical operations. Achievements in the mathematical domain of numbers even rebounded to pre-pandemic levels. Longer periods of school closures were associated with larger learning losses. Additional analyses showed larger learning losses for the group of low-achieving students and for schools with less socio-cultural capital. The partial rebound of learning outcomes suggests that most teachers and students successfully adapted to the pandemic situation in 2021. Still, disadvantaged student groups are at high risk of further substantial learning losses due to school closures that may negatively affect their future education. Accordingly, disadvantaged student groups in particular should receive additional support to compensate for the loss of learning opportunities in the classroom.
Testing gravity with black hole shadow subrings
2022-04-07

Abstract The black hole shadow, first observed by the Event Horizon Telescope in 2017, is the newest method for studying black holes and understanding gravity. Much work has gone into understanding the shadow of a Kerr black hole, including all of the complex astrophysics of the accretion disk, and there are numerous studies of the ideal shadow in non-Kerr black holes and exotic compact objects. This paper presents one of the first studies of the black hole shadow of non-Kerr black holes when the illumination source is an accretion disk. In particular, the ability of current and future very long baseline interferometers to estimate the physical parameters of the black hole spacetime and accretion disk is investigated using two different parametrized black hole metrics that encode a number of possible deviations from Kerr. Both the full shadow image and the individual subrings of the shadow are analyzed as the higher order subrings are weakly dependent on the disk physics and may be a more viable observable for studying the spacetime. The results suggest that with current telescope capabilities and any future earth-based telescopes it will be quite difficult to place strong constraints on departures from the Kerr spacetime, primarily due to the low resolution and strong degeneracies between the spacetime parameters. More optimistically, space-based interferometers may be capable of testing the Kerr nature of black holes and general relativity to comparable or better precision than is currently possible with other observations.
The role of the individual TOM subunits in the association of PINK1 with depolarized mitochondria
2022-04-07

Abstract Mitochondria dysfunction is involved in the pathomechanism of many illnesses including Parkinson’s disease. PINK1, which is mutated in some cases of familial Parkinsonism, is a key component in the degradation of damaged mitochondria by mitophagy. The accumulation of PINK1 on the mitochondrial outer membrane (MOM) of compromised organelles is crucial for the induction of mitophagy, but the molecular mechanism of this process is still unresolved. Here, we investigate the association of PINK1 with the TOM complex. We demonstrate that PINK1 heavily relies on the import receptor TOM70 for its association with mitochondria and directly interacts with this receptor. The structural protein TOM7 appears to play only a moderate role in PINK1 association with the TOM complex, probably due to its role in stabilizing this complex. PINK1 requires the TOM40 pore lumen for its stable interaction with the TOM complex and apparently remains there during its further association with the MOM. Overall, this study provides new insights on the role of the individual TOM subunits in the association of PINK1 with the MOM of depolarized mitochondria. Key messages TOM70 is the main receptor for the import of PINK1 into mitochondria. TOM20 plays only a minor role in PINK1 recognition at the organellar outer membrane. PINK1 association with the TOM complex is reduced upon knock-down of TOM7. The lumen of the TOM pore is crucial for PINK1 association with the outer membrane. TcPINK1 blocks the TOM pore in depolarized mitochondria.
Low-Basis Weight Polyacrylonitrile/Polyvinylpyrrolidone Blend Nanofiber Membranes for Efficient Particulate Matter Capture
2022-04-07

Particulate matter (PM) in air frequently poses a serious threat to human health. Smaller PM can easily enter into the alveolus and blood vessels with airflow. This work reports the first polyacrylonitrile (PAN)/polyvinylpyrrolidone (PVP) polymer blend nanofiber filter media for effectively capturing PM. Density functional theory (DFT) calculations are used to investigate the effect of the blending of two polymers on the dipole moment and the electrostatic potential. Based on the DFT calculations of the intermolecular interactions between nanofibers and PM, the PAN/PVP heteromolecular percentage is considered for experimental synthesis, which can provide better performance in the filtration of pollutants. The composite PAN/PVP fiber network was successfully developed and optimized to cope with complex environments during the actual filtration process. The role of the blending ratio of PAN and PVP in wt % was explored on PM2.5 capture, and the refined ratio overcame the conflict between high filtration efficiency and low air pressure resistance. The air filter medium PAN/PVP (6:2) possesses an extremely high air filtration efficiency of 92% under a very low pressure drop of 18 Pa for a 0.5 g m–2 basis weight. Both polar and nonpolar functional groups in blend nanofibers promoted significantly the electrostatic attraction and improved the filtration efficiency under static and dynamic airflow. The PAN/PVP nanofiber membranes maintain outstanding air filtration under different temperature and humidity conditions. This study will shed light on the fabrication of high-efficiency low-basis weight nanofiber filter media as an end product.