bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of habitat configuration in shaping animal population processes: a framework to generate quantitative predictions
Authors: He Peng , Montiglio Pierre-Olivier , Somveille Marius , Cantor Mauricio , Farine Damien R. 
Published: July 2020

AbstractBy shaping where individuals move, habitat configuration can fundamentally structure animal populations. Yet, we currently lack a framework for generating quantitative predictions about the role of habitat configuration in modulating population outcomes. For example, it is well known that the social structure of animal populations can shape spreading dynamics, but it remains underexplored to what extent such dynamics are determined by the underlying habitat configuration. To address this gap, we propose a framework and model inspired by studies using networks to characterize habitat connectivity. We first define animal habitat networks, explain how they can integrate information about the different configurational features of animals’ habitats, and highlight the need for a bottom-up generative model that can depict realistic variations in habitat structural connectivity. Second, we describe a model for simulating animal habitat networks (available in the R packageAnimalHabitatNetwork), and demonstrate its ability to generate alternative habitat configurations based on empirical data, which forms the basis for exploring the consequences of alternative habitat structures. Finally, we use our framework to demonstrate how transmission properties, such as the spread of a pathogen, can be impacted by both local connectivity and landscape-level characteristics of the habitat. Our study highlights the importance of considering the underlying habitat configuration in studies linking social structure with population-level outcomes.
Statistical image processing quantifies the changes in cytoplasmic texture associated with aging inCaenorhabditis elegansoocytes
Authors: Imakubo Momoko , Takayama Jun , Okada Hatsumi , Onami Shuichi 
Published: July 2020

AbstractBackgroundOocyte quality decreases with aging, thereby increasing errors in fertilization, chromosome segregation, and embryonic cleavage. Oocyte appearance also changes with aging, suggesting a functional relationship between oocyte quality and appearance. However, no methods are available to objectively quantify age-associated changes in oocyte appearance.ResultsWe show that statistical image processing of Nomarski differential interference contrast microscopy images can be used to quantify age-associated changes inCaenorhabditis elegansoocyte appearance. Max-min Value (mean difference between the maximum and minimum intensities within each moving window) quantitatively characterized the difference in oocyte cytoplasmic texture between 1- and 3-day-old adults (Day 1 and Day 3 oocytes, respectively). With an appropriate parameter set, the gray level co-occurrence matrix (GLCM)-based texture featureCorrelation(COR) more sensitively characterized this difference than the Max-min Value. Manipulating the smoothness of and/or adding irregular structures to the cytoplasmic texture of Day 1 oocyte images reproduced the difference in Max-min Value but not in COR between Day 1 and Day 3 oocytes. Increasing the size of granules in synthetic images recapitulated the age-associated changes in COR. Manual measurements validated that the cytoplasmic granules in oocytes become larger with aging.ConclusionsThe Max-min Value and COR objectively quantify age-related changes inC. elegansoocyte in Nomarski DIC microscopy images. Our methods provide new opportunities for understanding the mechanism underlying oocyte aging.
Transcriptomic signatures of ageing vary in solitary and social forms of an orchid bee
Authors: Séguret Alice C. , Stolle Eckart , Fleites-Ayil Fernando A. , Quezada-Euán José Javier G. , Hartfelder Klaus , Meusemann Karen , Harrison Mark , Soro Antonella , Paxton Robert J. 
Published: July 2020

AbstractEusocial insect queens are remarkable in their ability to maximise both fecundity and longevity, thus escaping the typical trade-off between these two traits. In species exhibiting complex eusocial behaviour, several mechanisms have been proposed to underlie the remoulding of the trade-off, such as reshaping of the juvenile hormone pathway, or caste-specific susceptibility to oxidative stress. However, it remains a challenge to disentangle the molecular mechanisms underlying the remoulding of the trade-off in eusocial insects from caste-specific physiological attributes that have subsequently arisen due to their different life histories. Socially plastic species such as the orchid beeEuglossa viridissimarepresent excellent models to address the role of socialityper sein longevity as they allow direct comparisons of solitary and social individuals within a common genetic background. We present data on gene expression and juvenile hormone levels from young and old bees, from both solitary and social nests. We found 940 genes to be differentially expressed with age in solitary females,versusonly 14 genes in social dominant females, and seven genes in subordinate females. We performed a weighted gene co-expression network analysis to further highlight candidate genes related to ageing in this species. Primary “ageing gene” candidates were related to protein synthesis, gene expression, immunity and venom production. Remarkably, juvenile hormone titres did not vary with age or social status. These results represent an important step in understanding the proximate mechanisms underlying the remodeling of the fecundity/longevity trade-off that accompanies the evolutionary transition from solitary life to eusociality.Significance statementThe remarkably long lifespan of the queens of eusocial insects despite their high reproductive output suggests that they are not subject to the widespread trade-off between fecundity and longevity that governs solitary animal life histories, yet surprisingly little is known of the molecular mechanisms underpinning their longevity. Using a socially plastic bee in which some individuals of a population are social whilst others are solitary, we identified hundreds of candidate genes and related gene networks that are involved in the remoulding of the fecundity/longevity tradeoff. As well as identifying candidate ageing genes, our data suggest that even in incipient stages of sociality there is a marked reprogramming of ageing; long live the queen.
Exceptional stability of a perilipin on lipid droplets depends on its polar residues, suggesting multimeric assembly
Authors: Giménez-Andrés Manuel , Emeršič Tadej , Antoine-Bally Sandra , Antonny Bruno , Derganc Jure , Čopič Alenka 
Published: July 2020

AbstractNumerous proteins target lipid droplets (LDs) through amphipathic helices (AHs). It is generally assumed that AHs insert bulky hydrophobic residues in packing defects at the LD surface. However, this model does not explain the targeting of perilipins, the most abundant and specific amphipathic proteins of LDs. The gigantic Plin4 contains a highly repetitive AH that lacks bulky hydrophobic residues, and its LD targeting depends strongly on its length. We show that Plin4 forms a remarkably immobile protein layer at the surface of cellular or artificial LDs, making them stable over days. This Plin4 AH feature is not shared with the AHs of other perilipins, which display much faster dynamics on lipid surfaces. Plin4 AH stability on LDs is exquisitely sensitive to the nature and distribution of its polar residues. These results suggest that Plin4 forms stable arrangements of adjacent AHs via polar interactions.
INTERMEDIUM-Cmediates the shade-induced bud growth arrest in barley
Authors: Wang Hongwen , Seiler Christiane , Sreenivasulu Nese , von Wirén Nicolaus , Kuhlmann Markus 
Published: July 2020

AbstractTiller formation is a key agronomic determinant for grain yield in cereal crops. The modulation of this trait is controlled by transcriptional regulators and plant hormones, tightly regulated by external environmental conditions. While endogenous (genetics) and exogenous (environmental factors) triggers for tiller formation have mostly been investigated separately, it has remained elusive how they are integrated into the developmental program of this trait. The transcription factorINTERMEDIUM-C (INT-C), which is the barley ortholog of the maize domestication geneTEOSINTE BRANCHED1 (TB1)has a prominent role in regulating tiller bud outgrowth. Here we show thatINT-Cis expressed in tiller buds, required for bud growth arrest in response to shade. In contrast to wild type plants,int-cmutant plants are impaired in their shade response and do not stop tiller production after shading. Gene expression levels ofINT-Care up-regulated under light-limiting growth conditions, and down-regulated after decapitation. Transcriptome analysis of wild-type andint-cbuds under control and shading conditions identified target genes of INT-C that belong to auxin and gibberellin biosynthesis and signaling pathways. Our study identifies INT-C as integrator of the shade response into tiller formation, which is prerequisite for implementing shading responses in the breeding of cereal crops.
Nuclear pores constrict upon energy depletion
Authors: Zimmerli Christian E. , Allegretti Matteo , Rantos Vasileios , Goetz Sara K. , Obarska-Kosinska Agnieszka , Zagoriy Ievgeniia , Halavatyi Aliaksandr , Mahamid Julia , Kosinski Jan , Beck Martin 
Published: July 2020

AbstractNuclear pore complexes (NPCs) fuse the inner and outer nuclear membranes and mediate nucleocytoplasmic exchange. They are made of 30 different nucleoporins that form an intricate cylindrical architecture around an aqueous central channel. This architecture is highly dynamic in space and time. Variations in NPC diameter were reported, but the physiological circumstances and the molecular details remain unknown. Here we combined cryo-electron tomography and subtomogram averaging with integrative structural modeling to capture a molecular movie of the respective large-scale conformational changesin cellulo. While actively transporting NPCs adopt a dilated conformation, they strongly constrict upon cellular energy depletion. Fluorescence recovery after photo bleaching experiments show that NPC constriction is concomitant with reduced diffusion and active transport across the nuclear envelope. Our data point to a model where the energy status of cells is linked to the conformation of NPC architecture.
Global RNA sequencing reveals enhanced photosynthetic activity and auxin response inBrassica napustreated withPseudomonas chlororaphisPA23
Authors: Wan Joey C , Becker Michael G , Bolaji Ayooluwa , Walker Philip L , Gray Emma , de Kievit Teresa R , Fernando WG Dilantha , Belmonte Mark F 
Published: July 2020

AbstractPlant growth promoting bacteria (PGPB) are a growing subset of agricultural adjuncts which can be used to increase crop yield and plant productivity. Although substantial research has been conducted on the metabolites and active molecules secreted by PGPBs, relatively little is known about their effects on the global transcriptome of the host plant. The present study was carried out to investigate changes in the gene expression landscape of early vegetativeBrassica napusfollowing treatment withPseudomonas chlororaphisPA23. This PGPB was isolated from the soybean rhizosphere and has been extensively studied as a biocontrol agent. However, little is known about its effects on plant growth and development. Using a combination of RNA-sequencing and physiological analyses, we identified increased abundance of mRNA transcripts associated with photosynthesis and phytohormone response.Phenotypically we observed increased photosynthetic rates and larger root and shoot systems inB. napusfollowingP. chlororaphisPA23 treatment. Lastly, we identified auxin production byP. chlororaphisPA23 which likely contributes to changes in gene expression and the observed phenotypic differences in root and shoot structures. Together, the results of our study suggest that PA23 is a potent plant growth promoting agent with the potential for field applications as an agricultural adjunct.
Fragile X Mental Retardation Protein modulates somatic D-type K+channels and action potential threshold in the mouse prefrontal cortex
Authors: Kalmbach Brian E. , Brager Darrin H. 
Published: July 2020

ABSTRACTAxo-somatic K+channels control action potential output in part by acting in concert with voltage-gated Na+channels to set action potential threshold. Slowly inactivating, D-type K+channels are enriched at the axo-somatic region of cortical pyramidal neurons of the prefrontal cortex where they regulate action potential firing. We previously demonstrated that D-type K+channels are down regulated in extratelencephalic-projecting L5 neurons (ET) in the prefrontal cortex of thefmr1knockout mouse model of Fragile X syndrome (FX mice), resulting in a hyperpolarized action potential threshold. To test whether K+channel alterations are regulated in a cell autonomous manner in FXS, we used a viral-mediated approach to restore expression of Fragile X Mental Retardation Protein (FMRP) in a small population of prefrontal neurons in male FX mice. Outside-out voltage clamp recordings revealed a higher D-type K+conductance in FMRP-positive ET neurons compared to nearby FMRP-negative ET neurons. FMRP did not affect either rapidly inactivating A-type or non-inactivating K+conductance. ET neuron patches recorded with FMRP1-298, a truncated form of FMRP which lacks mRNA binding domains, included in the pipette solution had larger D-type K+conductance compared to heat-inactivated controls. Viral expression of FMRP in FX mice depolarized action potential threshold to near wild type levels in ET neurons. These results suggest that FMRP influences the excitability of ET neurons in the mPFC by regulating somatic D-type K+channels in a cell autonomous, protein-protein dependent manner.
Dystrophic microglia are a disease associated microglia morphology in the human brain
Authors: Shahidehpour Ryan K. , Higdon Rebecca E. , Crawford Nicole G. , Neltner Janna H. , Ighodaro Eseosa T. , Patel Ela , Price Douglas , Nelson Peter T. , Bachstetter Adam 
Published: July 2020

AbstractMicroglia activation—typically described in terms of hypertrophic appearance—is a well-established feature of aging. Recent studies have suggested that microglia dystrophy, not activation, may increase the propagation of progressive neurodegenerative diseases such as Alzheimer’s disease (AD). Yet, a clear understanding of cause and consequences of dystrophic microglia is lacking. Although frequently observed in diseased brains, the appearance of dystrophic microglia in the hippocampus of individuals free of cognitive impairment suggests that microglia may be undergoing senescence with age, leading to dystrophy. Therefore, we hypothesized that chronological age could be a significant contributor to the presence of dystrophic microglia. To investigate this relationship, we employed stereological counts of total microglia, hypertrophic, and dystrophic microglia across the decades of the human lifespan. The microglia counts were performed in the frontal cortex gray and white matter and the CA1 subregion of the hippocampus in individuals without known neurodegenerative disease. There was age-associated increase in the number of dystrophic microglia in the CA1 region and the frontal cortex gray matter related to age. However, the increase in dystrophic microglia was proportional to the age-related increase in the total number of microglia, suggesting that aging alone was not sufficient to explain the presence of dystrophic microglia. We next tested if dystrophic microglia could be a disease-associated microglia phenotype. Compared to controls without neuropathology, the number of dystrophic microglia was significantly greater in aged-matched cases with either AD, dementia with Lewy bodies, or LATE-NC. These results provide evidence that healthy aging is only associated with a modest increase in dystrophic microglia and suggest that dystrophic microglia may be a disease-associated microglia phenotype. Finally, we found strong evidence for iron homeostasis changes, with increases in ferritin light chain, in dystrophic microglia compared to ramified or hypertrophic microglia. Based on our findings, microglia dystrophy, and not hypertrophic microglia, are the disease-associated microglia morphology. Future work is required to understand the links between the increase in dystrophic microglia and neurodegenerative disorders.
Single cell transcriptomics reveal disrupted kidney filter cell-cell interactions after early and selective podocyte injury
Authors: Clark Abbe R. , Marshall Jamie , Zhou Yiming , Montesinos Monica S. , Chen Haiqi , Nguyen Lan , Chen Fei , Greka Anna 
Published: July 2020

AbstractThe health of the kidney filtration barrier requires communication between podocytes, endothelial cells and mesangial cells. Disruption of these cell-cell interactions is thought to contribute to disease progression in chronic kidney diseases (CKD). We recently demonstrated that podocyte ablation via doxycycline-inducible deletion of an essential endogenous molecule, CTCF (iCTCFpod-/-), is sufficient to drive progressive CKD. However, the earliest events connecting podocyte injury to disrupted intercellular communication within the kidney filter remain unclear. Here we performed single-cell RNA sequencing of kidney tissue from iCTCFpod-/-mice after one week of doxycycline induction to generate a map of the earliest transcriptional effects of podocyte injury on cell-cell interactions at single cell resolution. A subset of podocytes showed the earliest signs of injury due to disrupted gene programs for cytoskeletal regulation and mitochondrial function. Surviving podocytes upregulated Col4a5, causing reactive changes in integrin expression in endothelial populations and mesangial cells. Intercellular interaction analysis revealed several receptor-ligand-target gene programs as drivers of endothelial cell injury and abnormal matrix deposition. This analysis reveals the earliest disruptive changes within the kidney filter, pointing to new, actionable targets within a therapeutic window that may allow us to maximize the success of much needed therapeutic interventions for CKD.
RDMA data transfer and GPU acceleration methods for high-throughput online processing of serial crystallography images
Authors: Ponsard Raphael , Janvier Nicolas , Kieffer Jerome , Houzet Dominique , Fristot Vincent 
Published: July 2020

The continual evolution of photon sources and high-performance detectors drives cutting-edge experiments that can produce very high throughput data streams and generate large data volumes that are challenging to manage and store. In these cases, efficient data transfer and processing architectures that allow online image correction, data reduction or compression become fundamental. This work investigates different technical options and methods for data placement from the detector head to the processing computing infrastructure, taking into account the particularities of modern modular high-performance detectors. In order to compare realistic figures, the future ESRF beamline dedicated to macromolecular X-ray crystallography, EBSL8, is taken as an example, which will use a PSI JUNGFRAU 4M detector generating up to 16 GB of data per second, operating continuously during several minutes. Although such an experiment seems possible at the target speed with the 100 Gb s−1 network cards that are currently available, the simulations generated highlight some potential bottlenecks when using a traditional software stack. An evaluation of solutions is presented that implements remote direct memory access (RDMA) over converged ethernet techniques. A synchronization mechanism is proposed between a RDMA network interface card (RNIC) and a graphics processing unit (GPU) accelerator in charge of the online data processing. The placement of the detector images onto the GPU is made to overlap with the computation carried out, potentially hiding the transfer latencies. As a proof of concept, a detector simulator and a backend GPU receiver with a rejection and compression algorithm suitable for a synchrotron serial crystallography (SSX) experiment are developed. It is concluded that the available transfer throughput from the RNIC to the GPU accelerator is at present the major bottleneck in online processing for SSX experiments.
Incipient stall characterization from skin-friction maps
Authors: Miozzi Massimo , Capone Alessandro , Klein Christian , Costantini Marco 
Published: July 2020

Purpose
The purpose of this study is the characterization of the dramatic variation in the flow scenario occurring at incipient stall conditions on a NACA0015 hydrofoil at moderate Reynolds numbers via the experimental analysis of time- and space-resolved skin-friction maps. The examined flow conditions are relevant for a variety of applications, including renewable energy production and unmanned and micro-aerial vehicles.

Design/methodology/approach
Grounding on the global temperature data acquired via temperature-sensitive paint, the proposed methodology adopts two approaches: one to obtain time-resolved, relative skin-friction vector fields by means of an optical-flow-based algorithm and the other one to extract quantitative, time-averaged skin-friction maps after minimization of the dissimilarity between the observed passive transport of temperature fluctuations and that suggested by the Taylor hypothesis.

Findings
Through the synergistic application of the proposed methods, the time-dependent evolution of the incipient stall over the hydrofoil suction side is globally described by firstly identifying the trailing edge separation at an angle of attack (AoA) AoA = 11.5°, and then by capturing the onset of upstream oriented, mushroom-like structures at AoA = 13°. The concomitant occurrence of both scenarios is found at the intermediate incidence AoA = 12.2°.

Originality/value
The qualitative, time-resolved skin-friction topology, combined with the quantitative, time-averaged distribution of the streamwise friction velocity, enables to establish a portrait of the complex, three-dimensional, unsteady scenario occurring at the examined flow conditions, thus providing new, fundamental information for a deeper understanding of the incipient stall development and for its control.
Corruption, public debt and economic growth – evidence from developing countries
Authors: Ibrahim Carole 
Published: July 2020

Purpose
The purpose of this paper is to empirically examine the effect of corruption on public debt and economic growth in 20 developing countries over the period 1996-2018.

Design/methodology/approach
This study makes use of the autoregressive distributed lag (ARDL) model to detect the long-term relationships, on the one hand, between corruption and public debt and, on the other hand, between corruption and economic growth.

Findings
The empirical results reveal that corruption increases the debt-to-GDP ratio and that the interactions between corruption and public revenues and between corruption and public spending have a positive influence on public debt in the long run. The estimations also show that high corruption hampers long-term economic growth and increases the negative effect of public debt on economic growth in developing countries.

Originality/value
While corruption is a prevalent phenomenon in most developing countries, the literature still lacks empirical examination of its economic effects. This study fills this gap with the aim of highlighting that high corruption hinders development in developing nations. This study also examines the impact of the interactions between corruption and components of the fiscal balance on public debt. Moreover, while the existing empirical literature uses regression techniques, this paper uses a panel ARDL approach to detect the long-term effects of corruption.