bluuebunny/crossref_metadata_2025 huggingface dataset:
How Can Abstract Objects of Mathematics Be Known?†
Authors: Kvasz Ladislav
Published: July 2019

The aim of the paper is to answer some arguments raised against mathematical structuralism developed by Michael Resnik. These arguments stress the abstractness of mathematical objects, especially their causal inertness, and conclude that mathematical objects, the structures posited by Resnik included, are inaccessible to human cognition. In the paper I introduce a distinction between abstract and ideal objects and argue that mathematical objects are primarily ideal. I reconstruct some aspects of the instrumental practice of mathematics, such as symbolic manipulations or ruler-and-compass constructions, and argue that instrumental practice can secure epistemic access to ideal objects of mathematics.
Legal challenges of artificial intelligence: modelling the disruptive features of emerging technologies and assessing their possible legal impact
Authors: Ballell Teresa Rodríguez de las Heras
Published: July 2019

The extensive use of artificial intelligence (AI) tools and systems and its extraordinary relevance in a multitude of social and economic domains must be framed into the broader context of a second wave of digital transformation. AI embodies the transformative force and the disruptive potential of a second generation of technologies that are ushering in a new stage of the digital evolution of our societies and economies. The acceleration and accumulation of technological developments pose unforeseen challenges to the twenty-first century's law. A systematic, extensive, and wisely combined application of these emerging technologies, such as AI and advanced robotics, Internet-of-Things (IoT), and DLT, offers fascinating possibilities and announces great disruptive effects. The aim of this article is to devise an analytical framework to identify the disruptive features of AI, as one of the most illustrative exponents of the second-generation technologies, and assess the potential impact on certain existing principles, rules and concepts.
Integrating Online Georeferenced Epidemiological Analysis and Visualization into a Telemedicine Infrastructure – First Results
Authors: von Wangenheim Aldo , Savaris Alexandre , Borgatto Adriano Ferretti , de Souza Inácio Andrei
Published: July 2019

With the objective to perform a first evaluation of the impact of the integration of a graphic spatial epidemiology tool that allows quasi-realtime georeferenced data visualization into a telemedicine infrastructure, this work presents GISTelemed, an online module specialized on indexing structured and semi-structured data, as well as querying the indexed content using structured and free-text search.

We evaluated GISTelemed accordingly to the guidelines published by the US Centers for Disease Control and Prevention and input provided by a questionnaire customized according to AdEQUATE (questionnAire for Evaluation of QUAlity in TElemedicine systems).

39 healthcare professionals from 13 municipalities participated in the evaluation. We analyzed data from questionnaires using descriptive statistics, being Lernability and Comfort the characteristics that received the best evaluation. Quantitative evaluation based upon leprosis cases detected through tele-dermatology showed a sensitivity and PPV of respectively 77.2% and 95.3%. 22.8% of the cases detected were un-notified cases.

Results from our case study show a good evaluation regarding the perceived software quality”. We conclude that the integration of spatial epidemiology tools to the STT/SC system, besides enabling visualization of data in maps, allowed users to analyze the evolution of morbidities and their co-occurrences.
Phylogenomics provides new insights into gains and losses of selenoproteins among Archaeplastida
Authors: Liang Hongping , Wei Tong , Xu Yan , Li Linzhou , Sahu Sunil Kumar , Wang Hongli , Li Haoyuan , Fu Xian , Zhang Gengyun , Melkonian Michael , Liu Xin , Wang Sibo , Liu Huan
Published: July 2019

Selenoproteins that contain selenocysteine (Sec) are found in all kingdoms of life. Although they constitute a small proportion of the proteome, selenoproteins play essential roles in many organisms. In photosynthetic eukaryotes, selenoproteins have been found in algae but are missing in land plants (embryophytes). In this study, we explored the evolutionary dynamics of Sec incorporation by conveying a genomic search for the Sec machinery and selenoproteins across Archaeplastida. We identified a complete Sec machinery and variable sizes of selenoproteomes in the main algal lineages. However, the entire Sec machinery was missing in the BV clade (Bangiophyceae-Florideophyceae) of Rhodoplantae (red algae) and only partial machinery was found in three species of Archaeplastida, indicating parallel loss of Sec incorporation in different groups of algae. Further analysis of genome and transcriptome data suggests that all major lineages of streptophyte algae display a complete Sec machinery, although the number of selenoproteins is low in this group, especially in subaerial taxa. We conclude that selenoproteins tend to be lost in Archaeplastida upon adaptation to a subaerial or acidic environment. The high number of redox-active selenoproteins found in some bloom-forming marine microalgae may be related to defense against viral infections. Some of the selenoproteins in these organisms may have been gained by horizontal gene transfer from bacteria.
Consciousness & Brain Functional Complexity in Propofol Anaesthesia
Authors: Varley TF , Luppi A , Pappas I , Naci L , Adapa R , Owen A , Menon DK , Stamatakis EA
Published: July 2019

The brain is possibly the most complex system known to mankind, and its complexity has been called upon to explain the emergence of consciousness. However, complexity can take many forms: here, we investigate measures of algorithmic and process complexity in both the temporal and topological dimension, testing them on functional MRI data obtained from individuals undergoing various levels of sedation with the anaesthetic agent propofol, in two separate datasets. We demonstrate that the various measures are differently able to discriminate between levels of sedation, with temporal measures showing higher sensitivity. Further, we show that all measures are strongly related to a single underlying construct explaining most of the variance, as assessed by Principal Component Analysis, which we interpret as a measure of overall complexity of our data. This overall complexity was also able to discriminate between levels of sedation, supporting the hypothesis that consciousness is related to complexity - independent of how the latter is measured.
Genome-wide transposon screen of aPseudomonas syringae mexBmutant reveals the substrates of efflux transporters
Authors: Helmann Tyler C. , Ongsarte Caitlin L. , Lam Jennifer , Deutschbauer Adam M. , Lindow Steven E.
Published: July 2019

Bacteria express numerous efflux transporters that confer resistance to diverse toxicants present in their environment. Due to a high level of functional redundancy of these transporters, it is difficult to identify those that are of most importance in conferring resistance to specific compounds. The resistance-nodulation-division (RND) protein family is one such example of redundant transporters that are widespread among Gram-negative bacteria. Within this family, the MexAB-OprM protein complex is highly-expressed and conserved amongPseudomonasspecies. We exposed barcoded transposon mutant libraries in isogenic wild-type and ΔmexBbackgrounds inP. syringaeB728a to diverse toxic compoundsin vitroto identify mutants with increased susceptibility to these compounds. Mutants in genes encoding both known and novel redundant transporters, but with partially overlapping substrate specificities were observed in a ΔmexBbackground. Psyr_0228, an uncharacterized member of the Major Facilitator Superfamily of transporters, preferentially contributes to tolerance of acridine orange and acriflavine. Another transporter located in the inner membrane, Psyr_0541, contributes to tolerance to acriflavine and berberine. The presence of multiple redundant, genomically encoded, efflux transporters appears to enable bacterial strains to tolerate a diversity of environmental toxins. This genome-wide screen in a hyper-susceptible mutant strain revealed numerous transporters that would otherwise be dispensable in these conditions. Bacterial strains such asP. syringaethat likely encounter diverse toxins in their environment such as in association with many different plant species, probably benefit from possessing multiple redundant transporters that enable versatility to tolerate novel toxicants.
CryoFold: determining protein structures and ensembles from cryo-EM data
Authors: Shekhar Mrinal , Terashi Genki , Gupta Chitrak , Sarkar Daipayan , Debussche Gaspard , Sisco Nicholas J. , Nguyen Jonathan , Mondal Arup , Zook James , Vant John , Fromme Petra , Van Horn Wade D. , Tajkhorshid Emad , Kihara Daisuke , Dill Ken , Perez Alberto , Singharoy Abhishek
Published: July 2019

Cryo-EM is a powerful method for determining protein structures. But it requires computational assistance. Physics-based computations have the power to give low-free-energy structures and ensembles of populations, but have been computationally limited to only small soluble proteins. Here, we introduce CryoFold. By integrating data of varying sparsity from electron density maps of 3–5 Å resolution with coarse-grained physical knowledge of secondary and tertiary interactions, CryoFold determines ensembles of protein structures directly from sequence. We give six examples showing its broad capabilities, over proteins ranging from 72 to 2000 residues, including membrane and multi-domain proteins, and including results from two EMDB competitions. The ensembles CryoFold predicts starting from the density data of a single known protein conformation encompass multiple low-energy conformations, all of which are experimentally validated and biologically relevant.
Rolling stones gather moss: Movement and longevity of moss balls on an Alaskan glacier
Authors: Hotaling Scott , Bartholomaus Timothy C. , Gilbert Sophie L.
Published: July 2019

Glaciers support diverse ecosystems that are largely comprised of microbial life. However, at larger, macroscopic scales, glacier moss balls (sometimes called “glacier mice”) can develop from impurities on ice surfaces and represent a relatively rare biological phenomenon. These ovoid-shaped conglomerations of dirt and moss are only found on some glacier surfaces and provide key habitats for invertebrate colonization. Yet, despite their development and presence being widely reported, no targeted studies of their movement and persistence across years have been conducted. This knowledge gap is particularly important when considering the degree to which glacier moss balls may represent viable, long-term biotic habitats on glaciers, perhaps complete with their own ecological succession dynamics. Here, we describe the movement and persistence of glacier moss balls on the Root Glacier in southcentral Alaska, USA. We show that glacier moss balls move an average of 2.5 cm per day in herd-like fashion, and their movements are positively correlated with glacier ablation. Surprisingly, the dominant moss ball movement direction does not align with the prevailing wind or downslope directions, nor with any dominant direction of solar radiation. After attaining a mature size, glacier moss balls persist for many years, likely in excess of 6 years. Finally, we observed moss ball formation on the Root Glacier to occur within a narrow, low albedo stripe downwind of a nunatuk, a potential key source of moss spores and/or fine-grained sediment that interact to promote their formation.
Volume and intramuscular fat content of upper extremity muscles in individuals with chronic hemiparetic stroke
Authors: Garmirian Lindsay R. P. , Acosta Ana Maria , Schmid Ryan , Dewald Jules P. A.
Published: July 2019

Stroke survivors often experience upper extremity deficits that make activities of daily living (ADLs) like dressing, cooking and bathing difficult or impossible. Survivors experience paresis, the inability to efficiently and fully activate muscles, which combined with decreased use of the upper extremity, will lead to muscle atrophy and potentially an increase in intramuscular fat. Muscle atrophy has been linked to weakness post stroke and is an important contributor to upper extremity deficits. However, the extent of upper extremity atrophy post hemiparetic stroke is unknown and a better understanding of these changes is needed to inform the direction of intervention-based research. In this study, the volume of contractile tissue and intramuscular fat in the elbow and wrist flexors and extensors were quantified in the paretic and non-paretic upper limb using MRI and the Dixon technique for the first time. Total muscle volume (p≤0.0005) and contractile element volume (p≤0.0005) were significantly smaller in the paretic upper extremity, for all muscle groups studied. The average percent difference between limbs and across participants was 21.3% for muscle volume and 22.9% for contractile element volume. We also found that while the percent intramuscular fat was greater in the paretic limb compared to the non-paretic (p≤0.0005), however, the volume of intramuscular fat was not significantly different between upper limbs (p=0.231). The average volumes of intramuscular fat for the elbow flexors/extensors and wrist flexors/extensors were 28.1, 28.8 and 19.9, 8.8 cm3 in the paretic limb and 29.6, 27.7 and 19.7, 8.8 cm3 in the non-paretic limb. In short, these findings indicate a decrease in muscle volume and not an increase in intramuscular fat, which will contribute to the reduction in strength in the paretic upper limb.
Structure and functional analysis of theLegionellachitinase ChiA reveals a novel mechanism of metal-dependent mucin degradation
Authors: Richardson Katherine H. , Grigoryeva Lubov S. , Corsini Paula , White Richard C. , Shaw Rosie , Portlock Theo J. , Dorgan Benjamin , Fornili Arianna , Cianciotto Nicholas P. , Garnett James A.
Published: July 2019

Chitinases are important enzymes that contribute to the generation of carbon and nitrogen from chitin, a long chain polymer of N-acetylglucosamine that is abundant in insects, fungi, invertebrates and fish. Although mammals do not produce chitin, chitinases have been identified in bacteria that are key virulence factors in severe respiratory, gastrointestinal and urinary diseases. However, it is unclear how these enzymes are able to carry out this dual function.Legionella pneumophilais the causative agent of Legionnaires’ disease, an often-fatal pneumonia and its chitinase ChiA is essential for the survival ofL. pneumophilain the lung. Here we report the first atomic resolution insight into the pathogenic mechanism of a bacterial chitinase. We derive an experimental model of intact ChiA and show how its N-terminal region targets ChiA to the bacterial surface after its secretion. We provide the first evidence thatL. pneumophilacan bind mucins on its surface but this is not dependent onchiA. This demonstrates that additional peripheral mucin binding proteins are also expressed inL. pneumophila. Finally, we show that the ChiA C-terminal chitinase domain has novel metal-dependent peptidase activity against mammalian mucins. These findings suggest that ChiA facilitates bacterial penetration of the alveolar mucosa and ChiA may be a promising target for vaccine development.
Brain regions with positive and negative task-evoked responses engage in cooperative rather than competitive interactions
Authors: Csumitta Kelsey D. , Ossowski Alexandra , Gilmore Adrian W. , Gotts Stephen J. , Martin Alex
Published: July 2019

Brain regions displaying task-induced decreases in activity, sometimes referred to as “Task-Negative”, have been proposed to reflect cortico-cortical competition from regions showing task-induced increases in activity, sometimes referred to as “Task-Positive”. If these functional networks are competitive, trial-level fMRI BOLD responses across voxels exhibiting Positive and Negative responses should be anti-correlated. Additionally, the correlation between the BOLD response and behavior in Positive and Negative regions should have opposite sign. Here, we test these predictions using trial-to-trial variability in an object naming task. In contrast to the negative coupling proposed by a competition model, we find positive coupling between Positive and Negative regions and show that this coupling aligns with trial-level behavioral correlations. We provide evidence that these cooperative interactions are not due to a non-specific global factor and discuss alternative proposals, such as thalamo-cortical gating.

Highlights

Tested competitive interactions among positive and negative task-evoked regions

Positive and negative regions exhibited positive coupling at trial and run levels

Smaller competitive effects seen in BOLD-behavior correlations

Strong cooperative effects not due to a non-specific common global factor

eTOC

Csumitta et al. show that positive and negative BOLD responses do not exhibit cortical competition among corresponding brain regions. Rather, these networks display positive coupling. The spatial distribution of positive coupling aligned with behavioral correlations, suggesting normal, cooperative network interactions.
Specific lid-base contacts in the 26S proteasome control the conformational switching required for substrate engagement and degradation
Authors: Greene Eric R. , Goodall Ellen A. , de la Peña Andres H. , Matyskiela Mary E. , Lander Gabriel C. , Martin Andreas
Published: July 2019

The 26S proteasome is essential for protein homeostasis and the regulation of vital cellular processes through ATP-dependent degradation of ubiquitinated substrates. To accomplish the multi-step reaction of protein degradation, the proteasome’s regulatory particle, consisting of the lid and base subcomplexes, undergoes major conformational changes whose origin and control are largely unknown. Investigating the Saccharomyces cerevisiae 26S proteasome, we found that peripheral interactions between the lid subunit Rpn5 and the base AAA+ ATPase ring play critical roles in stabilizing the substrate-engagement-competent state and coordinating the conformational switch to processing states after a substrate has been engaged. Disrupting these interactions perturbs the conformational equilibrium and interferes with degradation initiation, while later steps of substrate processing remain unaffected. Similar defects in the early degradation steps are also observed when eliminating hydrolysis in the ATPase subunit Rpt6, whose nucleotide state seems to control conformational transitions of the proteasome. These results provide important insight into the network of interactions that coordinate conformational changes with various stages of proteasomal degradation, and how modulators of conformational equilibria may influence substrate turnover.
Generative modelling of the thalamo-cortical circuit mechanisms underlying the neurophysiological effects of ketamine
Authors: Shaw Alexander D , Muthukumaraswamy Suresh D , Saxena Neeraj , Sumner Rachael L , Adams Natalie , Moran Rosalyn J , Singh Krish D
Published: July 2019

Cortical recordings of task-induced oscillations following subanaesthetic ketamine administration demonstrate alterations in amplitude, including increases at high-frequencies (gamma) and reductions at low frequencies (theta, alpha). To investigate the population-level interactions underlying these changes, we implemented a thalamo-cortical model (TCM) capable of recapitulating broadband spectral responses. Compared with an existing cortex-only 4-population model, Bayesian Model Selection preferred the TCM. The model was able to accurately and significantly recapitulate ketamine-induced reductions in alpha amplitude and increases in gamma amplitude. Parameter analysis revealed no change in receptor time-constants but significant increases in select synaptic connectivity with ketamine. Significantly increased connections included both AMPA and NMDA mediated connections from layer 2/3 superficial pyramidal cells to inhibitory interneurons and both GABAA and NMDA mediated within-population gain control of layer 5 pyramidal cells. These results support the use of extended generative models for explaining oscillatory data and provide in silico support for ketamine’s ability to alter local coupling mediated by NMDA, AMPA and GABA-A.
Realistic modeling of ephaptic fields in the human brain
Authors: Ruffini Giulio , Salvador Ricardo , Tadayon Ehsan , Sanchez-Todo Roser , Pascual-Leone Alvaro , Santarnecchi Emiliano
Published: July 2019

Several decades of research suggest that weak electric fields may influence neural processing, including those induced by neuronal activity and recently proposed as substrate for a potential new cellular communication system, i.e., ephaptic transmission. Here we aim to map ephaptic activity in the human brain and explore its trajectory during aging by characterizing the macroscopic electric field generated by cortical dipoles using realistic finite element modeling. We find that modeled endogenous field magnitudes are comparable to those in measurements of weak but functionally relevant endogenous fields and to those generated by noninvasive transcranial brain stimulation, therefore possibly able to modulate neuronal activity. Then, to evaluate the role of self-generated ephaptic fields in the human cortex, we adapt an interaction approximation that considers the relative orientation of neuron and field to derive the membrane potential perturbation in pyramidal cells. Building on this, we define a simplified metric (EMOD1) that weights dipole coupling as a function of distance and relative orientation between emitter and receiver and evaluate it in a sample of 401 realistic human brain models from subjects aged 16-83. Results reveal that ephaptic modulation follows gyrification patterns in the human brain, and significantly decreases with age, with higher involvement of sensorimotor regions and medial brain structures. By providing the means for fast and direct interaction between neurons, ephaptic modulation likely contributes to the complexity of human function for cognition and behavior, and its modification across the lifespan and in response to pathology.
The Norepinephrine Metabolite DOPEGAL Confers Locus Coeruleus Tau Vulnerability and Propagation via Asparagine Endopeptidase
Authors: Kang Seong Su , Liu Xia , Ahn Eun Hee , Xiang Jie , Manfredsson Fredric P. , Yang Xifei , Luo Hongbo R. , Liles L. Cameron , Weinshenker David , Ye Keqiang
Published: July 2019

Aberrant Tau inclusions in the locus coeruleus (LC) are the earliest detectable Alzheimer’s disease (AD)-like neuropathology in the human brain; however, why LC neurons are selectively vulnerable to developing early Tau pathology and degenerating later in disease and whether the LC might seed the stereotypical spread of Tau pathology to the rest of the brain remain unclear. Here we show that 3,4-dihydroxyphenylglycolaldehyde (DOPEGAL), which is produced exclusively in noradrenergic neurons by monoamine oxidase A (MAO-A) metabolism of norepinephrine (NE), activates asparagine endopeptidase (AEP) that cleaves Tau at residue N368 into aggregation- and propagation-prone forms, thereby leading to LC degeneration and the spread of Tau pathology. DOPEGAL triggers AEP-cleaved Tau aggregationin vitroand in intact cells, resulting in LC neurotoxicity and propagation of pathology to the forebrain. Thus, our findings reveal a novel molecular mechanism underlying the selective vulnerability of LC neurons in AD.
Biased neural representation of feature-based attention in the human brain
Authors: Gong Mengyuan , Liu Taosheng
Published: July 2019

Selective attention is a core cognitive function for efficient processing of information. Although it is well known that attention can modulate neural responses in many brain areas, the computational principles underlying attentional modulation remain unclear. Contrary to the prevailing view of a high-dimensional, distributed neural representation, here we show a surprisingly simple, biased neural representation for feature-based attention in a large dataset including five human fMRI studies. We found that when participants selected one feature from a compound stimulus, voxels in many cortical areas responded consistently higher to one attended feature over the other. This univariate bias was robust at the level of single brain areas and consistent across brain areas within individual subjects. Importantly, this univariate bias showed a progressively stronger magnitude along the cortical hierarchy. In frontoparietal areas, the bias was strongest and contributed largely to pattern-based decoding, whereas early visual areas lacked such a bias. These findings suggest a gradual transition from a more analog to a more abstract representation of attentional priority along the cortical hierarchy. Biased neural responses in high-level areas likely reflect a low-dimensional neural code that facilitates robust representation and simple read-out of cognitive variables.
PhyloMagnet: Fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics
Authors: Schön Max E. , Eme Laura , Ettema Thijs J.G.
Published: July 2019

Motivation

Metagenomic and metatranscriptomic sequencing analyses have become increasingly popular tools for producing massive amounts of short-read data, often used for the reconstruction of draft genomes or the detection of (active) genes in microbial communities. Unfortunately, sequence assemblies of such datasets generally remain a computationally challenging task. Frequently, researchers are only interested in a specific group of organisms or genes; yet, the assembly of multiple datasets only to identify candidate sequences for a specific question is sometimes prohibitively slow, forcing researchers to select a subset of available datasets to address their question. Here we present PhyloMagnet, a workflow to screen meta-omics datasets for taxa and genes of interest using gene-centric assembly and phylogenetic placement of sequences.

Results

Using PhyloMagnet, we could identify up to 87% of the genera in anin vitromock community with variable abundances, while the false positive predictions per single gene tree ranged from 0% to 23%. When applied to a group of metagenomes for which a set of MAGs have been published, we could detect the majority of the taxonomic labels that the MAGs had been annotated with. In a metatranscriptomic setting the phylogenetic placement of assembled contigs corresponds to that of transcripts obtained from transcriptome assembly.

Availability

PhyloMagnet is built using Nextflow, available atgithub.com/maxemil/PhyloMagnetand is developed and tested on Linux. It is released under the open source GNU GPL license and documentation is available atphylomagnet.readthedocs.io. Version 0.5 of PhyloMagnet was used for all benchmarks experiments.
Outwitting planarian’s antibacterial defence mechanisms:Rickettsialesbacterial trans-infection fromParamecium multimicronucleatumto planarians
Authors: Modeo Letizia , Salvetti Alessandra , Rossi Leonardo , Castelli Michele , Szokoli Franziska , Krenek Sascha , Sabaneyeva Elena , Di Giuseppe Graziano , Fokin Sergei I. , Verni Franco , Petroni Giulio
Published: July 2019

Most of the microorganisms belonging to genera responsible for vector-borne diseases (VBD) have hematophagous arthropods as vector/reservoir. Recently, many new species of microorganisms phylogenetically related to agents of VBD were found in a variety of aquatic eukaryotic hosts, in particular, numerous new bacterial species related to the genusRickettsia(Alphaproteobacteria, Rickettsiales) were discovered in protist ciliates and other unicellular eukaryotes. Although their pathogenicity for humans and terrestrial animals is not known, these bacteria might act as etiological agents of possible VBD of aquatic organisms, with protist as vectors. In the present study, we characterized a novel strain of theRickettsia-Like Organism (RLO) endosymbiont “Candidatus(Ca.) Trichorickettsia mobilis” in the macronucleus of the ciliateParamecium multimicronucleatumthrough FluorescenceIn SituHybridization (FISH) and molecular analyses. Ultrastructural investigations on the presence of flagella confirmed previous studies on the same bacterial species. The potential trans-infection perosof this bacterium to planarians (Dugesia japonica), a widely used model system able to eliminate a wide range of bacteria pathogenic to humans and other Metazoa, was further verified. Ciliate mass cultures were set up, and trans-infection experiments were performed by adding homogenized paramecia to food of antibiotic-treated planarians, performed. Treated and non-treated (i.e. control) planarians were investigated at day 1, 3, and 7 after feeding for endosymbiont presence by means of PCR and ultrastructural analyses. Obtained results were fully concordant and suggest that this RLO endosymbiont can be transferred from ciliates to metazoans, being detected up to day 7 in treated planarian enterocytes inside and, possibly, outside phagosomes.
Current range of Agrilus planipennis Fairmaire, an alien pest of ash trees, in European Russia and Ukraine
Authors: Orlova-Bienkowskaja Marina J. , Drogvalenko Alexander N. , Zabaluev Ilya A. , Sazhnev Alexey S. , Peregudova Elena Y. , Mazurov Sergey G. , Komarov Evgenij V. , Struchaev Vitalij V. , Martynov Vladimir V. , Nikulina Tatyana V. , Bieńkowski Andrzej O.
Published: July 2019

Context

The first detection of A. planipennis in European Russia was in Moscow in 2003, when it began to spread.

Aim

To determine the range of A. planipennis as of 2020.

Methods

In 2017-2020, our Russian-Ukrainian research team examined >7000 F. pennsylvanica trees and >2500 F. excelsior trees in 84 localities of European Russia, Ukraine and Belarus.

Results

The current range exceeds the area of Spain and includes the Luhansk region of Ukraine and 16 regions of ER: Belgorod, Bryansk, Kaluga, Kursk, Lipetsk, Moscow, Orel, Ryazan, Smolensk, Tambov, Tula, Tver, Vladimir, Volgograd, Voronezh, and Yaroslavl. Agrilus planipennis was not detected in Belarus. The overwhelming majority of the infestations were found on F. pennsylvanica. All known cases of infestation of the native species (F. excelsior) are from artificial plantings.

Conclusion

Agrilus planipennis will appear in other European countries soon and damage F. pennsylvanica. Further surveys are necessary to determine whether A. planipennis infests F. excelsior in forests.
Higher Temperatures Generically Favor Slower-Growing Bacterial Species in Multispecies Communities
Authors: Lax Simon , Abreu Clare I. , Gore Jeff
Published: July 2019

Temperature is among the cardinal environmental variables which determine the composition and function of microbial communities. Many culture-independent studies have characterized communities that are affected by changing temperatures, either due to seasonal cycles1-3, long-term warming4-6, or latitudinal/elevational gradients7-8. However, a predictive understanding of how microbial communities respond to such changes in temperature is still lacking, partly because it is not obvious which aspects of microbial physiology determine whether a species should benefit from temperature alteration. Here, we incorporate how microbial growth rates change with temperature to a modified Lotka-Volterra competition model9, and predict that higher temperatures should generically favor slower-growing species in a bacterial community. We experimentally confirm this prediction in pairwise cocultures assembled from a diverse set of species, and we show that these changes to pairwise outcomes with temperature are also predictive of changing outcomes in three-species communities, suggesting our theory may propagate to more complex assemblages. Our results demonstrate that it is possible to predict how bacterial communities will shift with temperature knowing only the growth rates of the community members. These results provide a testable hypothesis for future studies of more complex, natural communities, and we hope that this work will help bridge the gap between ecological theory and the complex dynamics observed in metagenomic surveys.
Epithelial-Mesenchymal Plasticity is regulated by inflammatory signalling networks coupled to cell morphology
Authors: Garcia Mar Arias , Yin Zheng , Roumeliotis Theodoros I. , Butera Francesca , Wang Lin , Rickman Rebecca , Choudhary Jyoti , Wong Stephen T.C. , Yuan Yinyin , Bakal Chris
Published: July 2019

Morphology dictates how cells sense physical and soluble cues in their environment; thus contributing to fate decisions. The differentiation of epithelial cells into mesenchymal forms, or epithelial-mesenchymal plasticity (EMP), is essential for metazoan development and homeostasis. Here we show that the decision to engage EMP is coupled to cell morphology by cell-cell adhesions by microtubule and nuclear organization (MTNO). Using an integrative ‘omic approach we identify Junctional Adhesion Molecule 3 (JAM3) as a new tumour suppressor in breast cancer patients. JAM3 depletion in epithelial cells alters MTNO and causes differentiation into mesenchymal forms. Soluble TGFβ also changes MTNO, and synergizes with JAM3 depletion to promote mesenchymal morphogenesis. Through systematic proteomic analysis we show that changes in MTNO lead to the upregulation of an inflammatory signalling network where YAP/TAZ, FOXO, IKK-NFKB, and JNK pathways are active; but where insulin signalling is suppressed. The actions of the MT-motor Kinesin-1 serve to both change MTNO and promote the upregulation of the core EMP network. Critically, the upregulation of the EMP network predicts the mesenchymal state across cancers.

Graphical Abstract
A geostatistical approach to estimate high resolution nocturnal bird migration densities from a weather radar network
Authors: Nussbaumer Raphaël , Benoit Lionel , Mariethoz Grégoire , Liechti Felix , Bauer Silke , Schmid Baptiste
Published: July 2019

Quantifying nocturnal bird migration at high resolution is essential for (1) understanding the phenology of migration and its drivers, (2) identifying critical spatio-temporal protection zones for migratory birds, and (3) assessing the risk of collision with man-made structures.

We propose a tailored geostatistical model to interpolate migration intensity monitored by a network of weather radars. The model is applied to data collected in autumn 2016 from 69 European weather radars. To cross-validate the model, we compared our results with independent measurements of two bird radars.

Our model estimated bird densities at high resolution (0.2°latitude-longitude, 15min) and assessed the associated uncertainty. Within the area covered by the radar network, we estimated that around 120 million birds were simultaneously in flight [10-90 quantiles: 107-134]. Local estimations can be easily visualized and retrieved from a dedicated interactive website:birdmigrationmap.vogelwarte.ch.

This proof-of-concept study demonstrates that a network of weather radar is able to quantify bird migration at high resolution and accuracy. The model presented has the ability to monitor population of migratory birds at scales ranging from regional to continental in space and daily to yearly in time. Near-real-time estimation should soon be possible with an update of the infrastructure and processing software.
mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation
Authors: Werner Johannes , Geron Augustin , Kerssemakers Jules , Matallana-Surget Sabine
Published: July 2019

Metaproteomics allows to decipher the structure and functionality of microbial communities. Despite its rapid development, crucial steps such as the creation of standardized protein search databases and reliable protein annotation remain challenging. To overcome those critical steps, we developed a new program named mPies (metaProteomics in environmental sciences). mPies allows the creation of protein databases derived from assembled or unassembled metagenomes, and/or public repositories based on taxon IDs, gene or protein names. For the first time, mPies facilitates the automatization of reliable taxonomic and functional consensus annotations at the protein group level, minimizing the well-known protein inference issue which is commonly encountered in metaproteomics. mPies’ workflow is highly customizable with regards to input data, workflow steps, and parameter adjustment. mPies is implemented in Python 3/Snakemake and freely available on GitHub: https://github.com/johanneswerner/mPies/.
Kinetic study of the expression of genes related to hepatic steatosis, global intermediate metabolism and cellular stress during overfeeding in mule ducks
Authors: Pioche Tracy , Skiba Fabien , Bernadet Marie-Dominique , Seiliez Iban , Massimino William , Houssier Marianne , Tavernier Annabelle , Ricaud Karine , Davail Stéphane , Skiba-Cassy Sandrine , Gontier Karine
Published: July 2019

Induced by overfeeding, hepatic steatosis is a reversible process exploited for “foie gras” production. To better understand the mechanisms underlying this non-pathological phenomenon, we analysed the physiological responses of the mule duck to cope with 22 carbohydrate meals. A kinetic analysis of intermediate metabolism and cell protection mechanisms was performed during overfeeding. As expected, dietary carbohydrates are up taken mainly by the liver (chrebp, glut1/2/8) and converted into lipids (acox, scd1, acsl1, fas, dgat2). Our study showed an activation of cholesterol biosynthetic pathway with significant correlations between plasma cholesterol, expression of key genes (hmgcr, soat1) and liver weight. Results revealed an activation of insulin and amino acid cell signalling pathway suggesting that ducks boost insulin sensitivity to raise glucose uptake and useviaglycolysis and lipogenesis. Expression ofcpt1a, acad, hadhsuggested an induction of beta-oxidation probably to remove part of newly synthesized lipids and avoid lipotoxicity. Cellular stress analysis revealed an upregulation of autophagy-related gene expression (atg8, atg9, sqstm1) in contrast with an induction ofcyp2e1suggesting that autophagy could be suppressed.Lamp2aandplin2enhanced, conflicting with the idea of an inhibition of lipophagy.Hsbp1overexpression indicated that mechanisms are carried out during overfeeding to limit cellular stress and apoptosis to prevent the switch to pathological state.Atf4andasnsoverexpression reflects the nutritional imbalance during overfeeding. These results permitted to highlight the mechanisms enabling mule ducks to efficiently handle the huge starch overload and reveal potential biomarker candidates of hepatic steatosis as plasma cholesterol for liver weight.
Non-ohmic tissue conduction in cardiac electrophysiology: upscaling the non-linear voltage-dependent conductance of gap junctions
Authors: Hurtado Daniel E. , Jilberto Javiera , Panasenko Grigory
Published: July 2019

Gap junctions are key mediators of the intercellular communication in cardiac tissue, and their function is vital to sustain normal cardiac electrical activity. Conduction through gap junctions strongly depends on the hemichannel arrangement and transjunctional voltage, rendering the intercellular conductance highly non-Ohmic. Despite this marked non-linear behavior, current tissue-level models of cardiac conduction are rooted on the assumption that gap-junctions conductance is constant (Ohmic), which results in inaccurate predictions of electrical propagation, particularly in the low junctional-coupling regime observed under pathological conditions. In this work, we present a novel non-Ohmic multiscale (NOM) model of cardiac conduction that is suitable for tissue-level simulations. Using non-linear homogenization theory, we develop a conductivity model that seamlessly upscales the voltage-dependent conductance of gap junctions, without the need of explicitly modeling gap junctions. The NOM model allows for the simulation of electrical propagation in tissue-level cardiac domains that accurately resemble that of cell-based microscopic models for a wide range of junctional coupling scenarios, recovering key conduction features at a fraction of the computational complexity. A unique feature of the NOM model is the possibility of upscaling the response of non-symmetric gap-junction conductance distributions, which result in conduction velocities that strongly depend on the direction of propagation, thus allowing to model the normal and retrograde conduction observed in certain regions of the heart. We envision that the NOM model will enable organ-level simulations that are informed by sub- and inter-cellular mechanisms, delivering an accurate and predictive in-silico tool for understanding the heart function.

Author summary

The heart relies on the propagation of electrical impulses that are mediated gap junctions, whose conduction properties vary depending on the transjunctional voltage. Despite this non-linear feature, current mathematical models assume that cardiac tissue behaves like an Ohmic (linear) material, thus delivering inaccurate results when simulated in a computer. Here we present a novel mathematical multiscale model that explicitly includes the non-Ohmic response of gap junctions in its predictions. Our results show that the proposed model recovers important conduction features modulated by gap junctions at a fraction of the computational complexity. This contribution represents an important step towards constructing computer models of a whole heart that can predict organ-level behavior in reasonable computing times.
X-ray radiation damage to biological samples: recent progress
Authors: Garman Elspeth F. , Weik Martin
Published: July 2019

With the continuing development of beamlines for macromolecular crystallography (MX) over the last few years providing ever higher X-ray flux densities, it has become even more important to be aware of the effects of radiation damage on the resulting structures. Nine papers in this issue cover a range of aspects related to the physics and chemistry of the manifestations of this damage, as observed in both MX and small-angle X-ray scattering (SAXS) on crystals, solutions and tissue samples. The reports include measurements of the heating caused by X-ray irradiation in ruby microcrystals, low-dose experiments examining damage rates as a function of incident X-ray energy up to 30 keV on a metallo-enzyme using a CdTe detector of high quantum efficiency as well as a theoretical analysis of the gains predicted in diffraction efficiency using these detectors, a SAXS examination of low-dose radiation exposure effects on the dissociation of a protein complex related to human health, theoretical calculations describing radiation chemistry pathways which aim to explain the specific structural damage widely observed in proteins, investigation of radiation-induced damage effects in a DNA crystal, a case study on a metallo-enzyme where structural movements thought to be mechanism related might actually be radiation-damage-induced changes, and finally a review describing what X-ray radiation-induced cysteine modifications can teach us about protein dynamics and catalysis. These papers, along with some other relevant literature published since the last Journal of Synchrotron Radiation Radiation Damage special issue in 2017, are briefly summarized below.
Crystal structure of two N′-(1-phenylbenzylidene)-2-(thiophen-3-yl)acetohydrazides
Authors: Vu Quoc Trung , Nguyen Ngoc Linh , Tran Thi Thuy Duong , Vu Quoc Manh , Vuong Nguyen Thien , Oanh Doan Thi Yen , Van Meervelt Luc
Published: July 2019

The synthesis, spectroscopic data, crystal and molecular structures of two N′-(1-phenylbenzylidene)-2-(thiophen-3-yl)acetohydrazides, namely N′-[1-(4-hydroxyphenyl)benzylidene]-2-(thiophen-3-yl)acetohydrazide, C13H10N2O2S, (3a), and N′-[1-(4-methoxyphenyl)benzylidene]-2-(thiophen-3-yl)acetohydrazide, C14H14N2O2S, (3b), are described. Both compounds differ in the substituent at the para position of the phenyl ring: –OH for (3a) and –OCH3 for (3b). In (3a), the thiophene ring is disordered over two orientations with occupancies of 0.762 (3) and 0.238 (3). The configuration about the C=N bond is E. The thiophene and phenyl rings are inclined by 84.0 (3) and 87.0 (9)° for the major- and minor-occupancy disorder components in (3a), and by 85.89 (12)° in (3b). Although these dihedral angles are similar, the conformation of the linker between the two rings is different [the C—C—C—N torsion angle is −ac for (3a) and −sc for (3b), while the C6—C7—N9—N10 torsion angle is +ap for (3a) and −sp for (3b)]. A common feature in the crystal packing of (3a) and (3b) is the presence of N—H...O hydrogen bonds, resulting in the formation of chains of molecules running along the b-axis direction in the case of (3a), or inversion dimers for (3b). The most prominent contributions to the surface contacts are those in which H atoms are involved, as confirmed by an analysis of the Hirshfeld surface.
New Geographies of Residential Capitalism: Financialization of the Turkish Housing Market Since the Early 2000s
Authors: Erol Isil
Published: July 2019

The post‐2001 financial crisis era in Turkey gave rise to twin booms in housing construction and credit markets, both of which suffered from the subsequent debt crisis. The financial transformation of the economy in conjunction with state‐led urban legislation reform had significant effects on the housing market in terms of commodification of housing, countrywide construction activities and substantial increases in household debt and construction company loans. The changing role and function of the state as a direct provider of housing can be regarded as actually existing neoliberalism providing favourable conditions for financialization, as it ushered in the commodification of housing. The Turkish government, together with the government‐backed housing agency, metropolitan municipalities and publicly owned real‐estate investment company, has been active in nationwide housing construction and urban regeneration projects. This article argues that there is a lack of synchrony between the commodification of housing and the financialization of the household sector owing to the institutional setting of the mortgage system and structural macroeconomic problems. Rather, housing commodification has been accompanied by the financialization of the corporate sector through a steep rise in the external debt burden of construction companies.
Legal Technologies of Primitive Accumulation: Judicial Robbery and Dispossession‐by‐Restitution in Warsaw
Authors: Kusiak Joanna
Published: July 2019

Among the ‘extra‐economic means’ that facilitate primitive accumulation, or accumulation by dispossession, the law plays a prominent role. But works on neoliberal urban restructuring rarely engage with concrete legal technologies. Analysing judicial property restitution (‘reprivatization’) in Warsaw, this article grasps the machine of accumulation by dispossession at a moment of faltering and exposes the distinctive legal technologies behind its troubleshooting. It makes three contributions to critical urban studies. First, it demonstrates how judicial systems can steal political conflicts that obstruct the cycle of accumulation by dispossession. It thus introduces the notion of ‘judicial robbery’, a non‐legislated expropriation of common property through judicial engineering that simultaneously deprives the public of political agency. Second, it shows that seemingly neutral legal technicalities, usually sheltered from political debate, can become a key locus of urban politics. Third, it examines the agency, scope and spatial patterns of ‘dispossession by restitution’, the term I use for a locally specific form of accumulation by dispossession in Warsaw. Lastly, I raise the question of political struggle against primitive accumulation. Is the judicial robbery reversible? If we can reclaim property, can we also reclaim political conflicts that have been stolen by the law?