julilili42/papers huggingface dataset:
Regulation of mitochondrial cargo-selective autophagy by posttranslational modifications
2021-10-22

Mitochondria are important organelles in eukaryotes. Turnover and quality control of mitochondria are regulated at the transcriptional and posttranslational level by several cellular mechanisms. Removal of defective mitochondrial proteins is mediated by mitochondria resident proteases or by proteasomal degradation of individual proteins. Clearance of bulk mitochondria occurs via a selective form of autophagy termed mitophagy. In yeast and some developing metazoan cells (e.g., oocytes and reticulocytes), mitochondria are largely removed by ubiquitin-independent mechanisms. In such cases, the regulation of mitophagy is mediated via phosphorylation of mitochondria-anchored autophagy receptors. On the other hand, ubiquitin-dependent recruitment of cytosolic autophagy receptors occurs in situations of cellular stress or disease, where dysfunctional mitochondria would cause oxidative damage. In mammalian cells, a well-studied ubiquitin-dependent mitophagy pathway induced by mitochondrial depolarization is regulated by the mitochondrial protein kinase PINK1, which upon activation recruits the ubiquitin ligase parkin. Here, we review mechanisms of mitophagy with an emphasis on posttranslational modifications that regulate various mitophagy pathways. We describe the autophagy components involved with particular emphasis on posttranslational modifications. We detail the phosphorylations mediated by PINK1 and parkin-mediated ubiquitylations of mitochondrial proteins that can be modulated by deubiquitylating enzymes. We also discuss the role of accessory factors regulating mitochondrial fission/fusion and the interplay with pro- and antiapoptotic Bcl-2 family members. Comprehensive knowledge of the processes of mitophagy is essential for the understanding of vital mitochondrial turnover in health and disease.
Characterization of the complete chloroplast genome of Zephyranthes phycelloides (Amaryllidaceae, tribe Hippeastreae) from Atacama region of Chile
2021-10-22

Sporadic rains in the Atacama Desert reveal a high biodiversity of plant species that only occur there. One of these rare species is the "Red añañuca" (<i>Zephyranthes phycelloides</i>), formerly known as <i>Rhodophiala phycelloides</i>. Many species of <i>Zephyranthes</i> in the Atacama Desert are dangerously threatened, due to massive extraction of bulbs and cutting of flowers. Therefore, studies of the biodiversity of these endemic species, which are essential for their conservation, should be conducted sooner rather than later. There are some chloroplast genomes available for <i>Amaryllidaceae</i> species, however there is no complete chloroplast genome available for any of the species of <i>Zephyranthes</i> subgenus <i>Myostemma</i>. The aim of the present work was to characterize and analyze the chloroplast of <i>Z. phycelloides</i> by NGS sequencing. The chloroplast genome of the <i>Z. phycelloides</i> consists of 158,107 bp, with typical quadripartite structures: a large single copy (LSC, 86,129 bp), a small single copy (SSC, 18,352 bp), and two inverted repeats (IR, 26,813 bp). One hundred thirty-seven genes were identified: 87 coding genes, 8 rRNA, 38 tRNA and 4 pseudogenes. The number of SSRs was 64 in <i>Z. phycelloides</i> and a total of 43 repeats were detected. The phylogenetic analysis of <i>Z. phycelloides</i> shows a distinct subclade with respect to <i>Z. mesochloa</i>. The average nucleotide variability (<i>Pi</i>) between <i>Z. phycelloides</i> and <i>Z. mesochloa</i> was of 0.02000, and seven loci with high variability were identified: <i>psbA</i>, <i>trnS<sup>GCU</sup>-trnG<sup>UCC</sup>, trnD<sup>GUC</sup>-trnY<sup>GUA</sup>, trnL<sup>UAA</sup>-trnF<sup>GAA</sup>, rbcL, psbE-petL</i> and <i>ndhG-ndhI</i>. The differences between the species are furthermore confirmed by the high amount of SNPs between these two species. Here, we report for the first time the complete cp genome of one species of the <i>Zephyranthes</i> subgenus <i>Myostemma</i>, which can be used for phylogenetic and population genomic studies.
NAP-XPS as a new tool for in-situ studies of SMOX gas sensors
2021-10-22

Abstract The development of near ambient pressure x-ray photoelectron spectroscopy (NAP-XPS) allows scientists to perform spectroscopic investigations of solid–gas interfaces at elevated pressures in a defined gas atmosphere. Due to the high surface sensitivity and element specificity, this technique promises to be a valuable and powerful tool in gas sensor research. A Pt doped SnO 2 sample was studied to explore a variety of phenomena in sensor research that can be addressed using NAP-XPS at a synchrotron. The change of several parameters, including chemical shifts, band bending, and valence band structure, could be observed in-situ and highlights the enormous potential of the method in this field. Furthermore, a series of DC resistance measurements has been performed to study the impact of pressure. The decrease of resistance at low pressure strongly indicates that both the electronic characteristics as well as the surface composition under the conditions of NAP-XPS are dissimilar to operando conditions at atmospheric pressure.
Evaluation of Parameters for Fetal Behavioural State Classification
2021-10-22

Abstract Fetal behavioural states (fBS) describe periods of fetal wakefulness and sleep and are commonly defined by features such as body and eye movements and heart rate. Automatic state detection through algorithms relies on different parameters and thresholds derived from both the cardiogram and the actogram, which are highly dependent on the specific datasets and are prone to artefacts. Furthermore, the development of the fetal states is dynamic over the gestational period and the evaluation usually only separated into early and late gestation (before and after 32 weeks). In the current work, fBS were classified in 120 fetal magnetocardiographic data segments, between 27 and 39 weeks of gestational age, by both a classification algorithm and visual inspection. To identify how automated fBS detection could be improved, we first identified commonly used parameters for fBS classification in both the cardiogram and the actogram, and investigated their distribution across the different fBS. Then, we calculated a Receiver Operating Characteristics (ROC) curve to determine the performance of each parameter in the fBS classification. Finally, we investigated the development of parameters over gestation through linear regression. As a result, the parameters derived from the cardiogram have a higher classification accuracy compared to those derived from the body movement as defined by the actogram. However, the overlapping distributions of several parameters across states limit a clear separation of states based on these parameters. The changes over gestation of the cardiogram parameters reflect the maturation of the fetal autonomous nervous system. Given the higher classification accuracy of the cardiogram in comparison to the actogram, we suggest to focus further research on the cardiogram. Furthermore, we propose to develop a probabilistic fBS classification approaches to improve classification in less prototypical datasets.
Nomad-FAIR North-Remote-Tool Example Dataset Electron Microscopy
2021-10-22

<strong>Dataset.Objective.Aperture.Energy.Slit.cdf.nx5.zip<br> Dataset.Objective.Aperture.Energy.Slit.dm3.cdf.zip<br> parser-focalseries-gatandm-cdf2nx5.py</strong><br> An example dataset for focus-series reconstruction (in-line holography).<br> The dataset supplements/comes from a research study https://doi.org/10.1016/j.ultramic.2021.113264 <strong>em-sprint09-example.zip</strong> This archive contains an example YAML file how metadata to e.g. 1613_Si_HAADF_610_kx.emd<br> (see below) are stored internally in a NOMAD OASIS when saving entries into the customized<br> ELN schema of the EM example that was developed in Sprint09 Area B in the FAIRmat project.<br> This eln_data.yaml file serves as an input to the dataconverter/em reader tool to supplement<br> the numerical data from the 1613_Si_HAADF_610_kx.emd file with metadata during the creation<br> of the emd.nxs file. Furtermore, this archive contains a Bruker BCF, a Velox EMD, and a Digital Micrograph v3 DM3<br> file. These file formats can be used as input to the dataconverter/em reader tool to inject<br> specific numerical data while creating an instance of an NXem-compliant NeXus file. The files have the following SHA256 checksum to verify their integriety: sha256sum eln_data.yaml<br> c0fd230336ce7cd8e2715445ea6af404202b4ab9d7e7186838748bd0559d536f sha256sum 46_ES-LP_L1_brg.bcf<br> bf5ca0f862af49726b848a8a60d73af6f1669990131288ac4b4ca6cb57e58aff sha256sum 1613_Si_HAADF_610_kx.emd<br> 6ed0e8b8c170a0ed307e5c877fd891767a38e636f4680632e9b00c46a2b963b9 sha256sum EELS_map_2_ROI_1_location_4.dm3<br> b97850f6c6b100740813c34d20eda294ef66a6130daa42a6cf975c4572ff599c
Hyaluronic Acid-Functionalized Hybrid Gelatin–Poly-L-Lactide Scaffolds with Tunable Hydrophilicity
2021-10-23

In this study, we describe the production of hybrid gelatin-poly-L-lactide electrospun scaffolds whose hydrophilicity was controlled by binding increasing concentrations of hyaluronic acid (HA). We show that cross-linking has advantages over coating when aiming to functionalize the scaffolds with HA. The here described scaffolds structurely mimicked the complexity of the extracellular matrix, and when excited by second harmonic generation, they produced a signal that is typical of collagen-containing biological fibers. Fluorescence lifetime imaging microscopy (FLIM) was used to marker-independently monitor the growth of human dermal fibroblasts on the electrospun scaffolds using reduced (phosphorylated) nicotinamide adenine dinucleotide as target. Benefitting from the different fluorescence lifetimes of the polymer and the endogenous cellular fluorophore, we were able to distinguish and separate the signals produced by the cells from the signals generated by the electrospun scaffolds. FLIM further allowed the detection of metabolic differences in the cells seeded on the HA-functionalized scaffolds compared with cells that were cultured on nonfunctionalized control scaffolds.
Half‐Sandwich Complexes [Cp′4Ln4I8]4 (Ln=Ce, Pr):Emergence of Donor‐Free Organolanthanide Nanowheels
2021-10-24

Abstract Slow diffusion of Me 3 SiI into an n ‐hexane solution of lanthanide half‐sandwich complexes [Cp′Ln(AlMe 4 ) 2 ] (Ln=Ce, Pr; Cp′=C 5 H 4 SiMe 3 ) gives access to the hexadecalanthanide ring‐cluster hybrids [Cp′ 4 Ln 4 I 8 ] 4 , along with the cyclopentadienyl‐bridged {Ce 8 } cluster [Cp′ 4 Ce 4 I 7 ( μ 2 ‐Cp)] 2 . On the contrary, direct addition of the halogenating reagent to complex [Cp′Ce(AlMe 4 ) 2 ] in solution affords the spherical dodecanuclear cluster [Cp′CeI 2 ] 12 in addition to [Cp′ 4 Ln 4 I 8 ] 4 . The isostructural bromide and chloride clusters [Cp′LnX 2 ] 12 (X=Cl, Br) were isolated via the same solution synthesis protocol, using the mild halogenido transfer reagents Me 3 GeX (X=Cl, Br). The reaction [Cp′Ce(AlMe 4 ) 2 ]/Me 3 GeCl yielded the decanuclear heteroaluminato derivative [Cp′ 5 Ce 5 Cl 9 (AlCl 2 Me 2 )] 2 as a coproduct. Attempts to isolate any intermediate species by performing the reaction at low temperature resulted in incomplete AlMe 4 /iodido exchange, affording the hexanuclear homoaluminate cluster [Cp′ 6 Pr 6 I 8 (AlMe 4 ) 4 ]. All cerium clusters show bright photoluminescence under UV light. The luminescence properties of the dodecanuclear clusters [Cp′CeX 2 ] 12 (X=Cl, Br, I) were closer investigated.
Cell-derived and enzyme-based decellularized extracellular matrix exhibit compositional and structural differences that are relevant for its use as a biomaterial
2021-10-24

Due to its availability and minimal invasive harvesting human adipose tissue-derived extracellular matrix (dECM) is often used as a biomaterial in various tissue engineering and healthcare applications. Next to dECM, cell-derived ECM (cdECM) can be generated by and isolated from in vitro cultured cells. So far both types of ECM were investigated extensively towards their application as (bio)material in tissue engineering and healthcare. However, a systematic characterization and comparison of soft tissue dECM and cdECM is still missing. In this study, we characterized dECM from human adipose tissue, as well as cdECM from human adipose-derived stem cells (ASCs), towards their molecular composition, structural characteristics, and biological purity. The dECM was found to exhibit higher levels of collagens and lower levels of sulfated glycosaminoglycans (sGAGs) compared to cdECMs. Structural characteristics revealed an immature state of the fibrous part of cdECM samples. By the identified differences, we aim to support researchers in the selection of a suitable ECM-based biomaterial for their specific application and the interpretation of obtained results.
Cnm1 mediates nucleus–mitochondria contact site formation in response to phospholipid levels
2021-10-25

Mitochondrial functions are tightly regulated by nuclear activity, requiring extensive communication between these organelles. One way by which organelles can communicate is through contact sites, areas of close apposition held together by tethering molecules. While many contacts have been characterized in yeast, the contact between the nucleus and mitochondria was not previously identified. Using fluorescence and electron microscopy in S. cerevisiae, we demonstrate specific areas of contact between the two organelles. Using a high-throughput screen, we uncover a role for the uncharacterized protein Ybr063c, which we have named Cnm1 (contact nucleus mitochondria 1), as a molecular tether on the nuclear membrane. We show that Cnm1 mediates contact by interacting with Tom70 on mitochondria. Moreover, Cnm1 abundance is regulated by phosphatidylcholine, enabling the coupling of phospholipid homeostasis with contact extent. The discovery of a molecular mechanism that allows mitochondrial crosstalk with the nucleus sets the ground for better understanding of mitochondrial functions in health and disease.
Long-term Occupational Consequences for Families of Children With Type 1 Diabetes: The Mothers Take the Burden
2021-10-25

OBJECTIVE To investigate the occupational and financial consequences for parents following the onset of type 1 diabetes in their child. RESEARCH DESIGN AND METHODS A questionnaire assessing occupational and financial situations before and in the first year after the onset of diabetes was distributed to all families with a child ≤14 years of age at diagnosis with a diabetes duration of at least 12 months in nine German pediatric diabetes centers. RESULTS Data of 1,144 children (mean age at diagnosis 6.7 [3.6] years; 46.5% female) and their families were obtained. Mothers’ occupational status reflected in paid working hours was significantly reduced in the first year after their child's diabetes diagnosis (P &amp;lt; 0.001). Overall, 15.1% of mothers stopped working, and 11.5% reduced working hours. Mothers of preschool children were particularly affected. Fathers’ working status hardly changed (P = 0.75). Nearly half of the families (46.4%) reported moderate to severe financial losses. Compared with an earlier similar study in 2003, significant negative occupational consequences for mothers and financial burden on families remained unchanged in 2018 (P = 0.59 and 0.31, respectively). CONCLUSIONS Mothers of young children with newly diagnosed diabetes experienced negative consequences in their occupational situation. This inequality for mothers can have long-term negative consequences for their mental health and future economic situation. There is an urgent need for action to reduce the burden on families and to provide professional, social, and regulatory support, especially for mothers of young children with diabetes.
MOSES: A Novel Observation System to Monitor Dynamic Events across Earth Compartments
2021-10-25

Abstract Modular Observation Solutions of Earth Systems (MOSES) is a novel observation system that is specifically designed to unravel the impact of distinct, dynamic events on the long-term development of environmental systems. Hydrometeorological extremes such as the recent European droughts or the floods of 2013 caused severe and lasting environmental damage. Modeling studies suggest that abrupt permafrost thaw events accelerate Arctic greenhouse gas emissions. Short-lived ocean eddies seem to comprise a significant share of the marine carbon uptake or release. Although there is increasing evidence that such dynamic events bear the potential for major environmental impacts, our knowledge on the processes they trigger is still very limited. MOSES aims at capturing such events, from their formation to their end, with high spatial and temporal resolution. As such, the observation system extends and complements existing national and international observation networks, which are mostly designed for long-term monitoring. Several German Helmholtz Association centers have developed this research facility as a mobile and modular “system of systems” to record energy, water, greenhouse gas, and nutrient cycles on the land surface, in coastal regions, in the ocean, in polar regions, and in the atmosphere—but especially the interactions between the Earth compartments. During the implementation period (2017–21), the measuring systems were put into operation and test campaigns were performed to establish event-driven campaign routines. With MOSES’s regular operation starting in 2022, the observation system will then be ready for cross-compartment and cross-discipline research on the environmental impacts of dynamic events.
Note-taking in consecutive interpreting. On the reconstruction of an individualised language
2021-10-25

To facilitate the process of consecutive interpreting, professional interpreters typically use a special system of note-taking. In the approaches developed on the basis of practical interpreting experience, these notations are commonly regarded as a note-taking technique, and in relevant specialist literature they are often conceived as a language-independent instrument. Against the background of a cognitive approach, however, it can be shown that the so¬called note-taking TECHNIQUE can adequately be described by means of the theoretical constructs LANGUAGE and DISCOURSE. The language dimension is explored with regard to word meanings, word formation and inflection, semantic relations at sentence and text level as well as pragmatic functions. The discourse dimension is mainly discussed from the perspective of rele¬vance theory with a particular emphasis on the balance between the explicit and the implicit.
Coexistence of Ion Pairs and Charge-Transfer Complexes and Their Impact on Pentacene Singlet Fission
2021-10-25

Pentacene (PEN) is a prototypical small-molecule organic semiconductor and a singlet fission (SF) material, but the details of its charge-transfer (CT) interactions with electron acceptors are still under debate. Here, we revisit the CT interactions in thin film blends of PEN and 2,3,5,6-tetrafluoro-7,7,8,8,-tetracyanoquinodimethane (F4-TCNQ) and find experimental evidence for the coexistence of integer CT (ICT) and charge-transfer complex (CTC) formation, with the relative amount depending on the mixing ratio. In contrast, in blends of PEN and 2,2′-(perfluoronaphthalene-2,6-diylidene)dimalononitrile (F6-TCNNQ), only ICT is found, illustrating the special behavior of PEN/F4-TCNQ at the border between CTC formation and ICT. We further study the photophysics of these donor/acceptor blends with respect to the importance of PEN as a SF material and find that SF is robust against moderate amounts of acceptors in the blends. Triplet pair formation and separation, as well as CT from PEN triplets to CTCs and acceptor molecules, is observed.
Learning of affective meaning: revealing effects of stimulus pairing and stimulus exposure
2021-10-25

Charles E. Osgood's theory of affective meaning defines affect as interplay of three meaning dimensions - evaluation, potency, and activity - that represent the central constituents of our affective ecology. Based on a rigorous Brunswikian sampling procedure, we selected a representative set of stimuli that mirror this ecology. A germane informative analysis explicates and corroborates the sampling approach. We then report two experiments testing whether these dimensions of affective meaning can be learnt by means of stimulus pairing and stimulus exposure. Our findings yield evidence for (1) stimulus pairing effects on evaluation and activity, and (2) stimulus exposure effects on potency and activity. Overall, the findings reveal that stimulus pairing and stimulus exposure differentially influence the learning of dimensions of affective meaning. We discuss implications of this research for current emotion theories as well as its contribution to research in the cognition-emotion interface. Finally, we argue that the implementation of representative design by virtue of Brunswikian sampling promotes theory development and opens new research avenues for an original and creative science of cognition and emotion.
The Effect of TNF-α Inhibitors on Nail Psoriasis and Psoriatic Arthritis—Real-World Data from Dermatology Practice
2021-10-25

Patients with psoriatic arthritis (PsA) often develop joint symptoms years after their initial diagnosis of psoriasis disease; therefore, dermatologists should test for and detect PsA early. In this study, we focused on patients with psoriasis with both nail and joint disease being treated with tumor necrosis factor-α inhibitors by dermatologists. We performed a noninterventional, prospective, multicenter, and open-label study to evaluate the effectiveness of adalimumab, etanercept, or infliximab over 24 months of continuous therapy in patients with moderate to severe plaque-type psoriasis (Pso) and PsA. Disease assessments with the Psoriasis Area and Severity Index, Nail Psoriasis Severity Index (NAPSI), joint assessment, Dermatology Life Quality Index (DLQI), and Health Assessment Questionnaire (HAQ) instruments were performed every 3 months for the first year and twice annually thereafter. The cohort included 100 patients with Pso, nail psoriasis, and PsA. A significant reduction of NAPSI was observed 3 months after therapy initiation compared with the baseline (mean ± SD, 22.9 ± 17.8 vs. 33.8 ± 21.4; p &lt; 0.001). Similarly, the mean ± SD number of both tender and swollen joints decreased significantly within the first 3 months of treatment, from 10.8 ± 11.5 to 6.4 ± 10.3 (p &lt; 0.001) and from 6.4 ± 9.5 to 3.1 ± 7.2 (p &lt; 0.001), respectively. Additionally, the distal interphalangeal joint involvement improved throughout the observation time, and DLQI and HAQ scores decreased. Improvements in control of skin, nail, and joint symptoms were seen, as well as in patients’ quality of life and functionality. Dermatologists have an important role not only in PsA diagnosis but also in PsA long-term care.