julilili42/papers huggingface dataset:
Semi-supervised learning for increasing transferability of machine learning in digital soil mapping&#160;
2021-04-28

&amp;lt;p&amp;gt;The most critical aspect of application of digital soil mapping is its limited transferability. Modelling soil properties for regions where no or only sparse soil information is available is highly uncertain, when using the low-cost geo-spatial environmental covariates alone. To overcome this drawback, transfer learning has been introduced in different environmental sciences, including soil science. The general idea behind extrapolation of soil information with transfer learning in soil science is that the target area to transfer to is alike, e.g. in terms of soil-forming factors, and the same machine learning rules can be applied. Supervised machine learning, so far, has been used to transfer the soil information from the reference to the target areas with very similar environmental characteristics between both. Hence, it is unclear how machine learning can perform for other target regions with different environmental characteristics. Semi-supervised learning is an approach to machine learning that combines a small amount of labeled data (reference area) with a large amount of unlabeled data (target area) during training. In this study, we explored if semi-supervised learning could improve the transferability of digital soil mapping relative to supervised learning methods. Soil data for two arid regions and associated environmental covariates were obtained. Semi-supervised learning and supervised learning models were trained based on the data in the reference area and then tested based on the data in the target area. The results of this study indicated the higher power of semi-supervised learning for transferring soil information from one area to another in comparison to the supervised learning method.&amp;amp;#160;&amp;amp;#160;&amp;amp;#160;&amp;lt;/p&amp;gt;
Stramenopile dataset for positive selection
2021-04-28

This repository contains the data (sequences, annotations, and intermediary files) collected and produced during the preparation of the following preprint: https://doi.org/10.1101/2021.01.12.426341. Description of files: The samples.zip file contains for each taxa: The functional annotations from Interproscan with extension ".tsv" in a TSV format. The genome annotations with extension ".gff" in a gff3 format. The protein sequences with extension ".faa" in a fasta format. The corresponding coding DNA sequences with extension ".fna" in a fasta format. The all_ann.csv file contains all annotations from the tested genes with added information for positive selection and orthology status in a CSV format. The go_mapping.csv file contains the mapping of GO terms to protein accessions of the dataset in a CSV format. The protein_families.poff.tsv contains the proteinortho output file corresponding to the classification of the genes in the dataset into ortholog groups in a TSV format. The families.zip file contains the intermediary files for each of the selected orthogroups: Tree files in newick format in the folder "trees". Protein sequences in the folder "faas". Coding DNA sequences in the folder "fnas". Log outputs from the FUBAR analysis in the folder "logs". Codon alignments in the folder "codon_alns" The families_fubar.zip file contains the same files as before for the subset of orthogroups with a positive result in the FUBAR analysis plus log output from the aBSREL analysis in the log folder.
Distribution patterns of intramyocellular and extramyocellular fat by magnetic resonance imaging in subjects with diabetes, prediabetes and normoglycaemic controls
2021-04-29

Abstract Aim To evaluate the distribution of intramyocellular lipids (IMCLs) and extramyocellular lipids (EMCLs) as well as total fat content in abdominal skeletal muscle by magnetic resonance imaging (MRI) using a dedicated segmentation algorithm in subjects with type 2 diabetes (T2D), prediabetes and normoglycaemic controls. Materials and Methods Subjects from a population‐based cohort were classified with T2D, prediabetes or as normoglycaemic controls. Total myosteatosis, IMCLs and EMCLs were quantified by multiecho Dixon MRI as proton‐density fat‐fraction (in %) in abdominal skeletal muscle. Results Among 337 included subjects (median age 56.0 [IQR: 49.0‐64.0] years, 56.4% males, median body mass index [BMI]: 27.2 kg/m 2 ), 129 (38.3%) were classified with an impaired glucose metabolism (T2D: 49 [14.5%]; prediabetes: 80 [23.7%]). IMCLs were significantly higher than EMCLs in subjects without obesity (5.7% [IQR: 4.8%‐7.0%] vs. 4.1% [IQR: 2.7%‐5.8%], P &lt; .001), whereas the amounts of IMCLs and EMCLs were shown to be equal and significantly higher in subjects with obesity (both 6.7%, P &lt; .001). Subjects with prediabetes and T2D had significantly higher amounts of IMCLs and EMCLs compared with normoglycaemic controls ( P &lt; .001). In univariable analysis, prediabetes and T2D were significantly associated with both IMCLs (prediabetes: β: 0.76, 95% CI: 0.28‐1.24, P = .002; T2D: β: 1.56, 95% CI: 0.66‐2.47, P &lt; .001) and EMCLs (prediabetes: β: 1.54, 95% CI: 0.56‐2.51, P = .002; T2D: β: 2.15, 95% CI: 1.33‐2.96, P &lt; .001). After adjustment for age and gender, the association of IMCLs with prediabetes attenuated ( P = 0.06), whereas for T2D, both IMCLs and EMCLs remained significantly and positively associated ( P &lt; .02). Conclusion There are significant differences in the amount and distribution ratio of IMCLs and EMCLs between subjects with T2D, prediabetes and normoglycaemic controls. Therefore, these patterns of intramuscular fat distribution by MRI might serve as imaging biomarkers in both normal and impaired glucose metabolism.
Individual differences in cognitive offloading: a comparison of intention offloading, pattern copy, and short-term memory capacity
2021-04-29

Abstract The cognitive load of many everyday life tasks exceeds known limitations of short-term memory. One strategy to compensate for information overload is cognitive offloading which refers to the externalization of cognitive processes such as reminder setting instead of memorizing. There appears to be remarkable variance in offloading behavior between participants which poses the question whether there is a common factor influencing offloading behavior across different tasks tackling short-term memory processes. To pursue this question, we studied individual differences in offloading behavior between two well-established offloading paradigms: the intention offloading task which tackles memory for intentions and the pattern copy task which tackles continuous short-term memory load. Our study also included an unrelated task measuring short-term memory capacity. Each participant completed all tasks twice on two consecutive days in order to obtain reliability scores. Despite high reliability scores, individual differences in offloading behavior were uncorrelated between the two offloading tasks. In both tasks, however, individual differences in offloading behavior were correlated with the individual differences in an unrelated short-term memory task. Our results therefore show that offloading behavior cannot simply be explained in terms of a single common factor driving offloading behavior across tasks. We discuss the implications of this finding for future research investigating the interrelations of offloading behavior across different tasks.
Platelet Activation and Plasma Levels of Furin Are Associated With Prognosis of Patients With Coronary Artery Disease and COVID-19
2021-04-29

Objective: Patients with coronary artery disease (CAD) are at increased risk for cardiac death and respiratory failure following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Platelets are crucially involved in pathogenesis of CAD and might also contribute to pathophysiology of SARS-CoV-2 infection. Approach and Results: We enrolled a cohort of 122 participants from February 2020 to July 2020 including 55 patients with preexisting CAD and acute SARS-CoV-2 infection (CAD-SARS-CoV-2 positive ), 28 patients with CAD and without SARS-CoV-2 (CAD-SARS-CoV-2 negative ), and 39 healthy controls. Clinical and cardiac examination of the CAD-SARS-CoV-2 positive group included blood sampling, echocardiography, and electrocardiography within 24 hours after hospital admission. Phenotyping of platelets was performed by flow cytometry; plasma levels of chemokines were analyzed by ELISA. Respiratory failure of patients was stratified by the Horovitz index as moderately/severely impaired when Horovitz index &lt;200 mm Hg. The clinical end point was defined as Horovitz index &lt;200 mm Hg with subsequent mechanical ventilation within a follow-up of 60 days. CAD-SARS-CoV-2 positive patients display a significant enhanced platelet activation and hyper-inflammation early at time of hospital admission. Circulating platelet/leukocyte co-aggregates correlate with plasma levels of cytokines/chemokines like IL (interleukin)-6, CCL2, and CXCL10 (chemokine [C-X-C motif] ligand) as well as activation of platelets is associated with CCL5 and elevation of pulmonary artery pressure. Furthermore, furin is stored and released from activated platelets. High furin plasma levels are associated with poor clinical prognosis in CAD-SARS-CoV-2 positive patients. Conclusions: Patients with CAD and SARS-CoV-2 infection exhibit elevated systemic platelet activation and enhanced plasma levels of the subtilisin-like proprotein convertase furin, which may contribute to an unfavorable clinical prognosis.
The missing link in gravitational-wave astronomy
2021-04-29

Abstract Since 2015 the gravitational-wave observations of LIGO and Virgo have transformed our understanding of compact-object binaries. In the years to come, ground-based gravitational-wave observatories such as LIGO, Virgo, and their successors will increase in sensitivity, discovering thousands of stellar-mass binaries. In the 2030s, the space-based LISA will provide gravitational-wave observations of massive black holes binaries. Between the <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mo>∼</mml:mo> <mml:mn>10</mml:mn> </mml:math> –10 3 Hz band of ground-based observatories and the <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mo>∼</mml:mo> <mml:mn>1</mml:mn> <mml:msup> <mml:mrow> <mml:mn>0</mml:mn> </mml:mrow> <mml:mrow> <mml:mo>−</mml:mo> <mml:mn>4</mml:mn> </mml:mrow> </mml:msup> </mml:math> –10 − 1 Hz band of LISA lies the uncharted decihertz gravitational-wave band. We propose a Decihertz Observatory to study this frequency range, and to complement observations made by other detectors. Decihertz observatories are well suited to observation of intermediate-mass ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mo>∼</mml:mo> <mml:mn>1</mml:mn> <mml:msup> <mml:mrow> <mml:mn>0</mml:mn> </mml:mrow> <mml:mrow> <mml:mn>2</mml:mn> </mml:mrow> </mml:msup> </mml:math> –10 4 M ⊙ ) black holes; they will be able to detect stellar-mass binaries days to years before they merge, providing early warning of nearby binary neutron star mergers and measurements of the eccentricity of binary black holes, and they will enable new tests of general relativity and the Standard Model of particle physics. Here we summarise how a Decihertz Observatory could provide unique insights into how black holes form and evolve across cosmic time, improve prospects for both multimessenger astronomy and multiband gravitational-wave astronomy, and enable new probes of gravity, particle physics and cosmology.
Structural Insight into Non-Enveloped Virus Binding to Glycosaminoglycan Receptors: A Review
2021-04-29

Viruses are infectious agents that hijack the host cell machinery in order to replicate and generate progeny. Viral infection is initiated by attachment to host cell receptors, and typical viral receptors are cell-surface-borne molecules such as proteins or glycan structures. Sialylated glycans (glycans bearing sialic acids) and glycosaminoglycans (GAGs) represent major classes of carbohydrate receptors and have been implicated in facilitating viral entry for many viruses. As interactions between viruses and sialic acids have been extensively reviewed in the past, this review provides an overview of the current state of structural knowledge about interactions between non-enveloped human viruses and GAGs. We focus here on adeno-associated viruses, human papilloma viruses (HPVs), and polyomaviruses, as at least some structural information about the interactions of these viruses with GAGs is available. We also discuss the multivalent potential for GAG binding, highlighting the importance of charged interactions and positively charged amino acids at the binding sites, and point out challenges that remain in the field.
Nucleoside Analogue Reverse Transcriptase Inhibitors Improve Clinical Outcome in Transcriptional Active Human Parvovirus B19-Positive Patients
2021-04-29

Human parvovirus B19 (B19V) is the predominant cardiotropic virus associated with dilated inflammatory cardiomyopathy (DCMi). Transcriptionally active cardiotropic B19V infection is clinically relevant and triggers adverse long-term mortality. During the study; we evaluated whether antiviral treatment with the nucleoside analogue telbivudine (LTD) is effective in suppressing transcriptional active B19V in endomyocardial biopsies (EMBs) of B19V positive patients and improving clinical outcomes. Seventeen B19V-positive patients (13 male; mean age 45.7 ± 13.9 years; mean left ventricular ejection fraction (LVEF) 37.7 ± 13.5%) with positive B19V DNA and transcriptional activity (B19V mRNA) in EMBs were treated with 600 mg/d LTD over a period of six months. Patients underwent EMBs before and after termination of the LTD treatment. B19V RNA copy numbers remained unchanged in 3/17 patients (non-responder) and declined or disappeared completely in the remaining 14/17 patients (responder) (p ≤ 0.0001). Notably; LVEF improvement was more significant in patients who reduced or lost B19V RNA (responder; p = 0.02) in contrast to non-responders (p = 0.7). In parallel; responder patients displayed statistically significant improvement in quality of life (QoL) questionnaires (p = 0.03) and dyspnea on exertion (p = 0.0006), reflecting an improvement in New York Heart Association (NYHA) Classification (p = 0.001). Our findings demonstrated for the first time that suppression of B19V transcriptional activity by LTD treatment improved hemodynamic and clinical outcome significantly. Thus; the present study substantiates the clinical relevance of detecting B19V transcriptional activity of the myocardium.
A Comparison of Six Transport Models of the MADE‐1 Experiment Implemented With Different Types of Hydraulic Data
2021-04-29

Abstract Six conceptually different transport models were applied to the macrodispersion experiment (MADE)‐1 field tracer experiment as a first major attempt for model comparison. The objective was to show that complex mass distributions in heterogeneous aquifers can be predicted without calibration of transport parameters, solely making use of structural and flow data. The models differ in their conceptualization of the heterogeneous aquifer structure, computational complexity, and use of conductivity data obtained from various observation methods (direct push injection logging, DPIL, grain size analysis, pumping tests and flowmeter). They share the same underlying physical transport process of advection by the velocity field solely. Predictive capability is assessed by comparing results to observed longitudinal mass distributions of the MADE‐1 experiment. The decreasing mass recovery of the observed plume is attributed to sampling and no physical process like mass transfer is invoked by the models. Measures like peak location and strength are used in comparing the modeled and measured plume mass distribution. Comparison of models reveals that the predictions of the solute plume agree reasonably well with observations, if the models are underlain by a few parameters of close values: mean velocity, a parameter reflecting log‐conductivity variability, and a horizontal length scale related to conductivity spatial correlation. The robustness of the results implies that conservative transport models with appropriate conductivity upscaling strategies of various observation data provide reasonable predictions of plumes longitudinal mass distribution, as long as key features are taken into account.
Effects of Insoluble Cereal Fibre on Body Fat Distribution in the Optimal Fibre Trial
2021-04-29

Scope The Optimal Fibre Trial (OptiFiT) investigates metabolic effects of insoluble cereal fibre in subjects with impaired glucose tolerance (IGT), showing moderate glycemic and anti‐inflammatory benefits, especially in subjects with an obesity‐related phenotype. An OptiFiT sub‐group is analysed for effects on body fat distribution. Methods and results 180 participants with IGT receive a blinded, randomized supplementation with insoluble cereal fibre or placebo for 2 years. Once a year, all subjects undergo fasting blood sampling, oral glucose tolerance test, and anthropometric measurements. A subgroup (n=47) also received magnetic resonance imaging and spectroscopy for quantification of adipose tissue distribution and liver fat content. We compared MR, metabolic and inflammatory outcomes between fibre and placebo group metabolism and inflammation. Visceral and non‐visceral fat, fasting glucose, HbA1c, fasting insulin, insulin resistance, and uric acid decrease only in the fibre group, mirroring effects of the entire cohort. However, after adjustment for weight loss, there are no significant between‐group differences. There is a statistical trend for fibre‐driven liver fat reduction in subjects with confirmed non‐alcoholic fatty liver disease (NAFLD; n = 19). Conclusions Data and evidence on beneficial effects of insoluble cereal fibre on visceral and hepatic fatstorage is limited, but warrants further research. Targeted trials are required.
When unsupervised training benefits category learning
2021-04-29

[This is a preprint of the manuscript published in Cognition: Bröker, Love, &amp;amp; Dayan (2022).] Humans continuously categorise inputs, but only rarely receive explicit feedback as to whether or not they are correct. This implies that they may be integrating unsupervised information together with their sparse supervised data -- a form of semi-supervised learning. However, experiments testing semi-supervised learning are rare, and are bedevilled with conflicting results about whether the unsupervised information affords any benefit. Here, we suggest that one important factor that has been paid insufficient attention is the alignment between subjects' internal representations of the stimulus material and the experimenter-defined representations that determine success in the tasks. Subjects' representations are shaped by prior biases and experience, and unsupervised learning can only be successful if the alignment suffices. Otherwise, unsupervised learning might harmfully strengthen incorrect assumptions. To test this hypothesis, we conducted an experiment in which subjects initially categorise items along a salient, but task-irrelevant, dimension, and only recover the correct categories when sufficient feedback draws their attention to the subtle, task-relevant, stimulus dimensions. By withdrawing feedback at different stages along this learning curve, we tested whether unsupervised learning improves or worsens performance when internal stimulus representations and task are sufficiently or insufficiently aligned, respectively. Our results demonstrate that unsupervised learning can indeed have opposing effects on subjects' learning. We also discuss factors limiting the degree to which such effects can be predicted from momentary performance. Our work implies that predicting and understanding human category learning in particular tasks requires assessment and consideration of the representational spaces that subjects entertain for the materials involved in those tasks. These considerations not only apply to studies in the lab, but could also help improve the design of tutoring systems and instruction.
Chemical Imaging of Single Anisotropic Polystyrene/Poly (Methacrylate) Microspheres with Complex Hierarchical Architecture
2021-04-29

Monodisperse polystyrene spheres are functional materials with interesting properties, such as high cohesion strength, strong adsorptivity, and surface reactivity. They have shown a high application value in biomedicine, information engineering, chromatographic fillers, supercapacitor electrode materials, and other fields. To fully understand and tailor particle synthesis, the methods for characterization of their complex 3D morphological features need to be further explored. Here we present a chemical imaging study based on three-dimensional confocal Raman microscopy (3D-CRM), scanning electron microscopy (SEM), focused ion beam (FIB), diffuse reflectance infrared Fourier transform (DRIFT), and nuclear magnetic resonance (NMR) spectroscopy for individual porous swollen polystyrene/poly (glycidyl methacrylate-co-ethylene di-methacrylate) particles. Polystyrene particles were synthesized with different co-existing chemical entities, which could be identified and assigned to distinct regions of the same particle. The porosity was studied by a combination of SEM and FIB. Images of milled particles indicated a comparable porosity on the surface and in the bulk. The combination of standard analytical techniques such as DRIFT and NMR spectroscopies yielded new insights into the inner structure and chemical composition of these particles. This knowledge supports the further development of particle synthesis and the design of new strategies to prepare particles with complex hierarchical architectures.
Iron-Catalyzed Cross-Coupling of Thioesters and Organomanganese Reagents
2021-04-29

We report a Fukuyama-type coupling of thioesters with aliphatic organomanganese reagents utilizing a cheap and easily available iron(III) catalyst. The reactions exhibit a wide tolerance of solvents and functional groups (e.g. ketones, esters, aryl(pseudo)halides) allowing for the conversion of thioesters derived from natural products and pharmaceutical compounds. Investigations showed a strong steric influence from each reaction component (carboxylic moiety, thiol substituent and manganese reagent), which enabled regioselective transformation of dithioesters. Tandem transformations combining the coupling with an additional step were observed. Our experiments provide insights into the potential of the employed aliphatic manganese reagents, such as the interaction between iron, manganese and oxygen, which allows for a smooth conversion.
SRG/ART-XC and NuSTAR Observations of the X-Ray pulsar GRO J1008–57 in the Lowest Luminosity State
2021-04-30

Abstract We report results of the first broadband observation of the transient X-ray pulsar GRO J1008−57 performed in the quiescent state. Observations were conducted quasi-simultaneously with NuSTAR and the Mikhail Pavlinsky ART-XC telescope on board SRG right before the beginning of a Type I outburst. GRO J1008−57 was detected in the state with the lowest observed luminosity around several ×10 34 erg s −1 and consequently accreting from the cold disk. Timing analysis allowed us to detect pulsations during this state for the first time. The observed pulsed fraction of about 20% is, however, almost three times lower than in brighter states when the accretion proceeds through the standard disk. We traced the evolution of the broadband spectrum of the source on a scale of three orders of magnitude in luminosity and found that at the lowest luminosities the spectrum transforms into the double-hump structure similarly to other X-ray pulsars accreting at low luminosities (X Persei, GX 304–1, and A 0535+262) reinforcing the conclusion that this spectral shape is typical for these objects.