julilili42/papers huggingface dataset:
Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq)
2020-07-02

Abstract Regulatory sRNAs in photosynthetic cyanobacteria have been reported, but the lack of plausible RNA chaperones involved in this regulation appears enigmatic. Here, we analyzed the full ensemble of cellular RNAs and proteins using gradient profiling by sequencing (Grad-seq) in Synechocystis 6803. Complexes with overlapping subunits such as the CpcG1-type versus the CpcL-type phycobilisomes or the PsaK1 versus PsaK2 photosystem I pre(complexes) could be distinguished supporting a high quality of the approach. Clustering of the in-gradient distribution profiles followed by several additional criteria yielded a short list of potential RNA chaperones that include a YlxR homolog and a cyanobacterial homolog of the KhpA/B complex. The data suggest previously undetected complexes between accessory proteins and CRISPR-Cas systems, such as a Csx1-Csm6 ribonucleolytic defense complex. Moreover, the exclusive association of either RpoZ or 6S RNA with the core RNA polymerase complex and the existence of a reservoir of inactive sigma-antisigma complexes is suggested. The Synechocystis Grad-seq resource is available online at https://sunshine.biologie.uni-freiburg.de/GradSeqExplorer/ , providing a comprehensive resource for the functional assignment of RNA-protein complexes and multisubunit protein complexes in a photosynthetic organism. One-sentence summary We provide the first global analysis of a cyanobacterium using Grad-seq, providing a comprehensive resource for the in-depth analysis of the complexome in a photosynthetic organism.
Digital Learning and the Humanities
2020-07-02

The current research and funding situation with regards to digital teaching and learning will be a starting point to further inquire about the mission, intent and self-styling of the humanities and the field of English. The proliferation of digital opportunities makes knowledge globally available and universally transferable in a technological sense. Yet, what about the changes that digitalization triggers in epistemology or cultural techniques of information management? And, what are the stakes of the humanities and their way of making meaning and creation of knowledge? Can the knowledge of the humanities or the field of English – here particularly language, narrative literature and culture – be communicated, taught or learned with digital means? The humanities make it their designated task to provide orientation and evaluation for the increasingly complex and fast-paced global developments and their diverse cultural, societal and educative contexts. It should be in the interest of the humanities and its disciplines, to find answers to the questions of benefits that can be provided by digitalization of educational fields. Puentedura's SAMR matrix (substitution, amplification, modification, redefinition) will be introduced to allow for an evaluation of digitalization processes and tools.
Connectivity patterns of task-specific brain networks allow individual prediction of cognitive symptom dimension of schizophrenia and link to molecular architecture
2020-07-02

Abstract Background Despite the marked inter-individual variability in the clinical presentation of schizophrenia, it remains unclear the extent to which individual dimensions of psychopathology may be reflected in variability across the collective set of functional brain connections. Here, we address this question using network-based predictive modeling of individual psychopathology along four data-driven symptom dimensions. Follow-up analyses assess the molecular underpinnings of predictive networks by relating them to neurotransmitter-receptor distribution patterns. Methods We investigated resting-state fMRI data from 147 schizophrenia patients recruited at seven sites. Individual expression along negative, positive, affective, and cognitive symptom dimensions was predicted using relevance vector machine based on functional connectivity within 17 meta-analytic task-networks following a repeated 10-fold cross-validation and leave-one-site-out analyses. Results were validated in an independent sample. Networks robustly predicting individual symptom dimensions were spatially correlated with density maps of nine receptors/transporters from prior molecular imaging in healthy populations. Results Ten-fold and leave-one-site-out analyses revealed five predictive network-symptom associations. Connectivity within theory-of-mind, cognitive reappraisal, and mirror neuron networks predicted negative, positive, and affective symptom dimensions, respectively. Cognitive dimension was predicted by theory-of-mind and socio-affective-default networks. Importantly, these predictions generalized to the independent sample. Intriguingly, these two networks were positively associated with D 1 dopamine receptor and serotonin reuptake transporter densities as well as dopamine-synthesis-capacity. Conclusions We revealed a robust association between intrinsic functional connectivity within networks for socio-affective processes and the cognitive dimension of psychopathology. By investigating the molecular architecture, the present work links dopaminergic and serotonergic systems with the functional topography of brain networks underlying cognitive symptoms in schizophrenia.
The emerging spectrum of COVID-19 neurology: clinical, radiological and laboratory findings
2020-07-03

Abstract Preliminary clinical data indicate that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is associated with neurological and neuropsychiatric illness. Responding to this, a weekly virtual coronavirus disease 19 (COVID-19) neurology multi-disciplinary meeting was established at the National Hospital, Queen Square, in early March 2020 in order to discuss and begin to understand neurological presentations in patients with suspected COVID-19-related neurological disorders. Detailed clinical and paraclinical data were collected from cases where the diagnosis of COVID-19 was confirmed through RNA PCR, or where the diagnosis was probable/possible according to World Health Organization criteria. Of 43 patients, 29 were SARS-CoV-2 PCR positive and definite, eight probable and six possible. Five major categories emerged: (i) encephalopathies (n = 10) with delirium/psychosis and no distinct MRI or CSF abnormalities, and with 9/10 making a full or partial recovery with supportive care only; (ii) inflammatory CNS syndromes (n = 12) including encephalitis (n = 2, para- or post-infectious), acute disseminated encephalomyelitis (n = 9), with haemorrhage in five, necrosis in one, and myelitis in two, and isolated myelitis (n = 1). Of these, 10 were treated with corticosteroids, and three of these patients also received intravenous immunoglobulin; one made a full recovery, 10 of 12 made a partial recovery, and one patient died; (iii) ischaemic strokes (n = 8) associated with a pro-thrombotic state (four with pulmonary thromboembolism), one of whom died; (iv) peripheral neurological disorders (n = 8), seven with Guillain-Barré syndrome, one with brachial plexopathy, six of eight making a partial and ongoing recovery; and (v) five patients with miscellaneous central disorders who did not fit these categories. SARS-CoV-2 infection is associated with a wide spectrum of neurological syndromes affecting the whole neuraxis, including the cerebral vasculature and, in some cases, responding to immunotherapies. The high incidence of acute disseminated encephalomyelitis, particularly with haemorrhagic change, is striking. This complication was not related to the severity of the respiratory COVID-19 disease. Early recognition, investigation and management of COVID-19-related neurological disease is challenging. Further clinical, neuroradiological, biomarker and neuropathological studies are essential to determine the underlying pathobiological mechanisms that will guide treatment. Longitudinal follow-up studies will be necessary to ascertain the long-term neurological and neuropsychological consequences of this pandemic.
Tailoring Electronic and Magnetic Properties of Graphene by Phosphorus Doping
2020-07-03

The electronic and magnetic properties of graphene can be modulated by doping it with other elements, especially those with a different number of valence electrons. In this article, we first provide a three-dimensional reconstruction of the atomic structure of a phosphorus substitution in graphene using aberration-corrected scanning transmission electron microscopy. Turning then to theoretical calculations based on the density functional theory (DFT), we show that doping phosphorus in various bonding configurations can induce magnetism in graphene. Our simulations reveal that the electronic and magnetic properties of P-doped (Gr-P) and/or phosphono-functionalized graphene (Gr-PO<sub>3</sub>H<sub>2</sub>) can be controlled by both the phosphorus concentration and configurations, ultimately leading to ferromagnetic (FM) and/or antiferromagnetic (AFM) features with the transition temperature up to room temperature. We also calculate core-level binding energies of variously bonded P to facilitate X-ray photoelectron spectroscopy-based identification of its chemical form present in P-doped graphene-based structures. These results may enable the design of graphene-based organic magnets with tailored properties for future magnetic or spintronic applications.
A (distributional) semantic perspective on the processing of morphologically complex words
2020-07-03

Abstract While morphemes are theoretically defined as linguistic units linking form and meaning, semantic effects in morphological processing are not reported consistently in the literature on derived and compound words. The lack of consistency in this line of research has often been attributed to methodological differences between studies or contextual effects. In this paper, we advance a different proposal where semantic effects emerge quite consistently if semantics is defined in a dynamic and flexible way, relying on distributional semantics approaches. In this light, we revisit morphological processing, taking a markedly cognitive perspective, as allowed by models that focus on morphology as systematic meaning transformation or that focus on the mapping between the orthographic form of words and their meanings.
Discovery of Highly Active Recombinant PNGase H+ Variants Through the Rational Exploration of Unstudied Acidobacterial Genomes
2020-07-03

Peptide-<i>N</i> <sup>4</sup>-(<i>N</i>-acetyl-β-glucosaminyl) asparagine amidases (PNGases, <i>N</i>-glycanases, EC 3.5.1.52) are indispensable tools in releasing <i>N</i>-glycans from glycoproteins. So far, only a limited number of PNGase candidates are available for the structural analysis of glycoproteins and their glycan moieties. Herein, a panel of 13 novel PNGase H<sup>+</sup> candidates (the suffix H<sup>+</sup> refers to the acidic pH optimum of these acidobacterial PNGases) was tested in their recombinant form for their deglycosylation performance. One candidate (originating from the bacterial species <i>Dyella japonica</i>) showed superior properties both in solution-phase and immobilized on amino-, epoxy- and nitrilotriacetate resins when compared to currently acidic available PNGases. The high expression yield compared to a previously described PNGase H<sup>+</sup>, broad substrate specificity, and good storage stability of this novel <i>N</i>-glycanase makes it a valuable tool for the analysis of protein glycosylation.
Comparisons of Natural and Cultivated Populations of Corydalis yanhusuo Indicate Divergent Patterns of Genetic and Epigenetic Variation
2020-07-03

Epigenetic variation may contribute to traits that are important in domestication, but how patterns of genetic and epigenetic variation differ between cultivated and wild plants remains poorly understood. In particular, we know little about how selection may shape epigenetic variation in natural and cultivated populations. In this study, we investigated 11 natural populations and 6 major cultivated populations using amplified fragment length polymorphism (AFLP) and methylation-sensitive AFLP (MS-AFLP or MSAP) markers to identify patterns of genetic and epigenetic diversity among <i>Corydalis yanhusuo</i> populations. We further explored correlations among genetic, epigenetic, alkaloidal, and climatic factors in natural and cultivated <i>C. yanhusuo</i>. We found support for a single origin for all cultivated populations, from a natural population which was differentiated from the other natural populations. The magnitude of <i>F</i> <sub>ST</sub> based on AFLP was significantly correlated with that for MSAP in pairwise comparisons in both natural and cultivated populations, suggesting a relationship between genetic and epigenetic variation in <i>C. yanhusuo</i>. This relationship was further supported by dbRDA (distance-based redundancy analyses) where some of the epigenetic variation could be explained by genetic variation in natural and cultivated populations. Genetic variation was slightly higher in natural than cultivated populations, and exceeded epigenetic variation in both types of populations. However, epigenetic differentiation exceeded that of genetic differentiation among cultivated populations, while the reverse was observed among natural populations. The differences between wild and cultivated plants may be partly due to processes inherent to cultivation and in particular the differences in mode of reproduction. The importance of epigenetic compared to genetic modifications is thought to vary depending on reproductive strategies, and <i>C. yanhusuo</i> usually reproduces sexually in natural environments, while the cultivated <i>C. yanhusuo</i> are propagated clonally. In addition, alkaloid content of <i>C. yanhusuo</i> varied across cultivated populations, and alkaloid content was significantly correlated to climatic variation, but also to genetic (6.89%) and even more so to epigenetic (14.09%) variation in cultivated populations. Our study demonstrates that epigenetic variation could be important in cultivation of <i>C. yanhusuo</i> and serve as a source of variation for response to environmental conditions.
Constituent polysemy and interpretational diversity in attested English novel compounds
2020-07-03

Abstract We explore variation in the interpretation of attested novel compound nouns in English, especially the contribution of constituent polysemy to this diversity. Our results show that effects of polysemy are pervasive in compound interpretation, contributing both to interpretational diversity and to perceived difficulty of interpretation. The higher the uncertainty about the concept represented by the head noun, based on existing compounds with that head, the greater the diversity of interpretations across speakers and the more difficult, on average, they find it to come up with a meaning.
Word Usage in German Texts on Women’s Suffrage around 1900. Corpus Building, Lexical Documentation and the CLARIN-D Infrastructure
2020-07-03

The paper presents core aspects of a project that examines word usage in the German controversy on women's suffrage around 1900.The investigation is based on a variety of written texts (including journal articles, books, and pamphlets) that began to condense in the 1880s and developed into a complex thematic network until the introduction of women's suffrage in 1918.The focus of this paper is the presentation of two infrastructure aspects.First, the corpus compilation (ongoing and already published to some extent) is accomplished in the CLARIN-D infrastructure component German Text Archive ("Deutsches Textarchiv", hereafter DTA).This project exemplifies a basic user need: to make new corpus texts available from the very beginning of a project which can then be analyzed for the project's purposes with the powerful search tool architecture of the DTA.This kind of strategy is a win-win situation for the author, for the infrastructure, and for the whole research community.Second, the dissertation and the text corpus will be accompanied by a lexical documentation on word usage in the discourse domain.This component relies heavily on standards and best practices adopted in the CLARIN-D community and in the ZHistLex-project.The results are to be published and hosted by one of the German CLARIN centers.This project is a use case with solutions that can be seen as generic for similar kinds of projects, be it dissertations, term papers or larger research projects.
Experimental Transmission of Plasmodium malariae to Anopheles gambiae
2020-07-03

Abstract Our current knowledge of the clinical burden, biology, and transmission of Plasmodium malariae is extremely scarce. To start addressing some of those questions, we experimentally infected Anopheles gambiae mosquitoes with fresh P. malariae isolates obtained from asymptomatic individuals in Lambaréné, Gabon. The proportion of mosquitoes infected via direct membrane feeding assay with either P. malariae monoinfections (16% [19 of 121]) or coinfections (28% [31 of 112]) was higher after serum replacement than in parallel groups without serum replacement (4% [4 of 102] and 4% [2 of 45], respectively; P &amp;lt; .01). Our results show that isolates from asymptomatic carriers can be used for experimental studies of P. malariae transmission.
Die Gold-Frontier in Südafrika
2020-07-03

The Gold Frontier in South Africa. This paper uses the concept of commodity frontiers to compare the expansions and contractions of the South African gold frontier. Similarities and differences to its counterparts in the USA or Australia become visible in the South African gold frontier’s rapid industrialization, massive exploitation of low-skilled workers and tremendous damage to the natural environment. In addition to these regional factors, the approach also shows to what extent the gold economy has its own specific functional interrelations. Finally, the study also demonstrates how global changes and local dynamics can interact in very different and sometimes unexpected ways.
To move or not to move: roles and specificity of plant RNA mobility
2020-07-04

Intercellular communication in plants coordinates cellular functions during growth and development, and in response to environmental cues. RNAs figure prominently among the mobile signaling molecules used. Many hundreds of RNA species move over short and long distances, and can be mutually exchanged in biotic interactions. Understanding the specificity determinants of RNA mobility and the physiological relevance of this phenomenon are areas of active research. Here, we highlight the recent progress in our knowledge of small RNA and messenger RNA movement. Particular emphasis is given to novel insight into the specificity determinants of messenger RNA mobility, the role of small RNA movement in development, and the specificity of RNA exchange in plant-plant and plant-microbe interactions.
The Response of Maize to Inoculation with Arthrobacter sp. and Bacillus sp. in Phosphorus-Deficient, Salinity-Affected Soil
2020-07-04

Salinity and phosphorus (P) deficiency are among the most serious soil factors constraining crop productivity. A proposed strategy for alleviating these stresses is supporting plants by inoculation with growth-promoting rhizobacteria (PGPR). Here, a comparison of the ability of two maize composite and two F1 hybrid varieties to tolerate a P deficiency in either a saline or a non-saline environment showed that the uptake of nutrients by all four entries was significantly reduced by the imposition of both soil salinity and P deficiency, and that their growth was compromised to a similar extent. Subsequently, the ameliorative effect of inoculation with three strains of either Arthrobacter sp. or Bacillus sp. in an environment, which suffered simultaneously from salinity and P deficiency, was investigated. Inoculation with each of the strains was found to limit the plants’ uptake of sodium cations, to increase their uptake of potassium cations, and to enhance their growth. The extent of the growth stimulation was more pronounced for the composite varieties than for the F1 hybrid ones, although the amount of biomass accumulated by the latter, whether the plants had been inoculated or not, was greater than that of the former varieties. When the bacterial strains were cultured in vitro, each of them was shown as able to produce the phytohormones auxin, abscisic acid, gibberellins, and cytokinins. The implication is that since the presence in the rhizospere of both Arthrobacter sp. and Bacillus sp. strains can support the growth of maize in salinity-affected and P deficient soils in a genotype-dependent fashion, it is important to not only optimize the PGPR strain used for inoculation, but also to select maize varieties which can benefit most strongly from an association with these bacteria.
Zinc Determines Dynamical Properties and Aggregation Kinetics of Human Insulin
2020-07-04

Abstract Protein aggregation is a widespread process leading to deleterious consequences in the organism, with amyloid aggregates being important not only in biology but also for drug design and biomaterial production. Insulin is a protein largely used in diabetes treatment and its amyloid aggregation is at the basis of the so-called insulin-derived amyloidosis. Here we uncover the major role of zinc in both insulin dynamics and aggregation kinetics at low pH, where the formation of different amyloid superstructures (fibrils and spherulites) can be thermally induced. Amyloid aggregation is accompanied by zinc release and the suppression of water-sustained insulin dynamics, as shown by particle-induced X-ray emission and X-ray absorption spectroscopy and by neutron spectroscopy, respectively. Our study shows that zinc binding stabilizes the native form of insulin by facilitating hydration of this hydrophobic protein and suggests that introducing new binding sites for zinc can improve insulin stability and tune its aggregation propensity. Statement of Significance Localized amyloidosis occurs at insulin injection sites for diabetes treatment, leading to deleterious inflammations known as insulin-derived amyloidosis. Amyloid superstructures are also promising candidates in the field of biomaterials. Here we revealed that zinc, coordinated to insulin in the native form, is released upon amyloid aggregation, when insulin forms superstructures known as fibrils and spherulites. Zinc release leads to a full suppression of functionally essential protein dynamics through a modification of the protein’s hydration properties and completely modifies insulin amyloid kinetics. The results suggest that changes in protein hydration upon zinc binding/release modifies both stability and dynamics of insulin and might then be a general strategy to control protein stability and tune protein aggregation into amorphous and ordered superstructures.