bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants
Authors: Christian Ryan W. , Hewitt Seanna L. , Roalson Eric H. , Dhingra Amit 
Published: May 2020

AbstractPlastids are morphologically and functionally diverse organelles that are dependent on nuclear-encoded, plastid-targeted proteins for all biochemical and regulatory functions. However, how plastid proteomes vary temporally, spatially, and taxonomically has been historically difficult to analyze at a genome-wide scale using experimental methods. A bioinformatics workflow was developed and evaluated using a combination of fast and user-friendly subcellular prediction programs to maximize performance and accuracy for chloroplast transit peptides and demonstrate this technique on the predicted proteomes of 15 sequenced plant genomes. Gene family grouping was then performed in parallel using modified approaches of reciprocal best BLAST hits (RBH) and UCLUST. A total of 628 protein families were found to have conserved plastid targeting across angiosperm species using RBH, and 828 using UCLUST. However, thousands of clusters were also detected where only one species had predicted plastid targeting, most notably in Panicum virgatum which had 1,458 proteins with species-unique targeting. An average of 45% overlap was found in plastid-targeted protein-coding gene families compared with Arabidopsis, but an additional 20% of proteins matched against the full Arabidopsis proteome, indicating a unique evolution of plastid targeting. Neofunctionalization through subcellular relocalization is known to impart novel biological functions but has not been described before on a genome-wide scale for the plastid proteome. Further work to correlate these predicted novel plastid-targeted proteins to transcript abundance and high-throughput proteomics will uncover unique aspects of plastid biology and shed light on how the plastid proteome has evolved to influence plastid morphology and biochemistry.
When open mindedness hinders consensus
Authors: Schawe Hendrik , Hernández Laura 
Published: May 2020

AbstractWe perform a detailed study of the Hegselmann-Krause bounded confidence opinion dynamics model with heterogeneousconfidenceεidrawn from uniform distributions in different intervals [ε1,εu]. The phase diagram reveals a highly complex andnon-monotonous behaviour, with a re-entrant consensus phase in the region where fragmentation into multiple distinct opinionsis expected for the homogeneous case. A careful exploration of the phase diagram, along with an extensive finite-size analysis,allows us to identify the mechanism leading to this counter-intuitive behaviour. This systematic study over system sizes whichgo well beyond those of previous works, is enabled by an efficient algorithm presented in this article.
Tracking the Near Eastern origins and European dispersal of the western house mouse
Authors: Cucchi Thomas , Papayianni Katerina , Cersoy Sophie , Aznar-Cormano Laetitia , Zazzo Antoine , Debruyne Régis , Berthon Rémi , Bălășescu Adrian , Simmons Alan , Valla François , Hamilakis Yannis , Mavridis Fanis , Mashkour Marjan , Darvish Jamshid , Siahsarvi Roohollah , Biglari Fereidoun , Petrie Cameron A. , Weeks Lloyd , Sardari Alireza , Maziar Sepideh , Denys Christiane , Orton David , Jenkins Emma , Zeder Melinda , Searle Jeremy B. , Larson Greger , Bonhomme François , Auffray Jean-Christophe , Vigne Jean-Denis 
Published: May 2020

AbstractThe house mouse (Mus musculus) represents the extreme of globalization of invasive mammals. However, the timing and basis of its origin and early phases of dispersal remain poorly documented. To track its synanthropisation and subsequent invasive spread during the develoment of complex human societies, we analyzed 829Musspecimens from 43 archaeological contexts in Southwestern Asia and Southeastern Europe, between 40,000 and 3,000 cal. BP, combining geometric morphometrics numerical taxonomy, ancient mitochondrial DNA and direct radiocarbon dating. We found that large late hunter-gatherer sedentary settlements in the Levant, c. 14,500 cal. BP, promoted the commensal behaviour of the house mouse, which probably led the commensal pathway to cat domestication. House mouse invasive spread was then fostered through the emergence of agriculture throughout the Near East 12,000 years ago. Stowaway transport of house mice to Cyprus can be inferred as early as 10,800 years ago. However, the house mouse invasion of Europe did not happen until the development of proto urbanism and exchange networks — 6,500 years ago in Eastern Europe and 4000 years ago in Southern Europe — which in turn may have driven the first human mediated dispersal of cats in Europe.
Entomopathogenic nematodes from Mexico that can overcome the resistance mechanisms of the western corn rootworm
Authors: Bruno Pamela , Machado Ricardo A. R. , Glauser Gaétan , Köhler Angela , Campos-Herrera Raquel , Bernal Julio , Toepfer Stefan , Erb Matthias , Robert Christelle A. M. , Arce Carla C. M. , Turlings Ted C. J. 
Published: May 2020

AbstractNatural enemies of herbivores are expected to adapt to the defence strategies of their preys or hosts. Such adaptations may also include their capacity to cope with plant metabolites that herbivores sequester as a defence. In this study, we evaluated the ability of Mexican entomopathogenic nematodes (EPN) to resist benzoxazinoids that are sequestered from maize roots by the western corn rootworm (WCR,Diabrotica virgifera virgifera;Coleoptera: Chrysomelidae), an important maize pest in America and Europe. From maize fields throughout Mexico, we retrieved 40 EPN isolates belonging to five different species, with a majority identified asHeterorhabditis bacteriophora. In the laboratory, all nematodes readily infected non-sequestering larvae of the banded cucumber beetle (D. balteata), while infectivity varied strongly for WCR larvae. While someH. bacteriophoraisolates seemed negatively affected by benzoxazinoids, most showed to be resistant. Thus, EPN from Mexican maize fields can cope with these plant defence metabolites, but the results also indicate that WCR larvae possess other mechanisms that help to resist EPN. This work contributes to a better understanding of the capacity of herbivore natural enemies to resist plant defence metabolites. Furthermore, it identifies several benzoxazinoid-resistant EPN isolates that may be used to control this important maize pest.
Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase FO motor
Authors: Kubo Shintaroh , Niina Toru , Takada Shoji 
Published: May 2020

AbstractThe FO motor in FOF1 ATP synthase rotates its rotor driven by the proton motive force. While earlier studies elucidated basic mechanisms therein, recent advances in high-resolution cryo-electron microscopy enabled to investigate proton-transfer coupled FO rotary dynamics at structural details. Here, taking a hybrid Monte Carlo/molecular dynamics simulation method, we studied reversible dynamics of a yeast mitochondrial FO. We obtained the 36°-stepwise rotations of FO per one proton transfer in the ATP synthesis mode and the proton pumping in the ATP hydrolysis mode. In both modes, the most prominent path alternatively sampled states with two and three deprotonated glutamates in c-ring, by which the c-ring rotates one step. The free energy transduction efficiency in the model FO motor reached ~ 90% in optimal conditions. Moreover, mutations in key glutamate and a highly conserved arginine increased proton leakage and markedly decreased the coupling, in harmony with previous experiments. This study provides a simple framework of simulations for chemical-reaction coupled molecular dynamics calling for further studies in ATP synthase and others.
CDH6 and HAGH protein levels in plasma associate with Alzheimer’s disease in APOE ε4 carriers
Authors: Ahmad Shahzad , Milan Marta del Campo , Hansson Oskar , Demirkan Ayse , Agustin Ruiz , Sáez Maria E. , Giagtzoglou Nikolaos , Cabrera-Socorro Alfredo , Bakker Margot H. M. , Ramirez Alfredo , Hankemeier Thomas , Stomrud Erik , Mattsson-Carlgren Niklas , Scheltens Philip , van der Flier Wiesje M. , Ikram M. Arfan , Malarstig Anders , Teunissen Charlotte E. , Amin Najaf , van Duijn Cornelia M. 
Published: May 2020

AbstractMany Alzheimer’s disease (AD) genes including Apolipoprotein E (APOE) are found to be expressed in blood-derived macrophages and thus may alter blood protein levels. We measured 91 neuro-proteins in plasma from 316 participants of the Rotterdam Study (incident AD = 161) using Proximity Extension Ligation assay. We studied the association of plasma proteins with AD in the overall sample and stratified by APOE. Findings from the Rotterdam study were replicated in 186 AD patients of the BioFINDER study. We further evaluated the correlation of these protein biomarkers with total tau (t-tau), phosphorylated tau (p-tau) and amyloid-beta (Aβ) 42 levels in cerebrospinal fluid (CSF) in the Amsterdam Dementia Cohort (N = 441). Finally, we conducted a genome-wide association study (GWAS) to identify the genetic variants determining the blood levels of AD-associated proteins. Plasma levels of the proteins, CDH6 (β = 0.638, P = 3.33 × 10−4) and HAGH (β = 0.481, P = 7.20 × 10−4), were significantly elevated in APOE ε4 carrier AD patients. The findings in the Rotterdam Study were replicated in the BioFINDER study for both CDH6 (β = 1.365, P = 3.97 × 10−3) and HAGH proteins (β = 0.506, P = 9.31 × 10−7) when comparing cases and controls in APOE ε4 carriers. In the CSF, CDH6 levels were positively correlated with t-tau and p-tau in the total sample as well as in APOE ε4 stratum (P < 1 × 10−3). The HAGH protein was not detected in CSF. GWAS of plasma CDH6 protein levels showed significant association with a cis-regulatory locus (rs111283466, P = 1.92 × 10−9). CDH6 protein is implicated in cell adhesion and synaptogenesis while HAGH protein is related to the oxidative stress pathway. Our findings suggest that these pathways may be altered during presymptomatic AD and that CDH6 and HAGH may be new blood-based biomarkers.
Transplantation of fetal liver tissue coated by ultra-purified alginate gel over liver improves hepatic function in the cirrhosis rat model
Authors: Qiu Rong , Murata Soichiro , Oshiro Katsutomo , Hatada Yumi , Taniguchi Hideki 
Published: May 2020

AbstractIn this study, we used a new coating agent, that is, ultra-purified alginate gel (UPAL), for fetal liver tissue transplantation. This study aims to compare the effect of UPAL with the effect of other coating agents on improving the effect of fetal liver tissue transplantation in a liver cirrhosis rat model. Prior to the transplantation of wild-type ED14 fetal liver tissues, various coating agents were separately applied on the liver surface of rats with cirrhosis. Then, we compared the engraftment area, engraftment rate and liver function level of these rats. As a result, coating the liver surface of a cirrhosis rat with UPAL obtained the best effect in terms of engraftment area and engraftment rate of the transplanted liver tissue and in the recovery of liver function compared with control group. Therefore, UPAL coating may serve as a novel strategy for liver organoid transplantation.
Lead-Halide Scalar Couplings in 207Pb NMR of APbX3 Perovskites (A = Cs, Methylammonium, Formamidinium; X = Cl, Br, I)
Authors: Aebli Marcel , Piveteau Laura , Nazarenko Olga , Benin Bogdan M. , Krieg Franziska , Verel René , Kovalenko Maksym V. 
Published: May 2020

AbstractUnderstanding the structure and dynamics of newcomer optoelectronic materials - lead halide perovskites APbX3 [A = Cs, methylammonium (CH3NH3+, MA), formamidinium (CH(NH2)2+, FA); X = Cl, Br, I] - has been a major research thrust. In this work, new insights could be gained by using 207Pb solid-state nuclear magnetic resonance (NMR) spectroscopy at variable temperatures between 100 and 300 K. The existence of scalar couplings 1JPb-Cl of ca. 400 Hz and 1JPb-Br of ca. 2.3 kHz could be confirmed for MAPbX3 and CsPbX3. Diverse and fast structure dynamics, including rotations of A-cations, harmonic and anharmonic vibrations of the lead-halide framework and ionic mobility, affect the resolution of the coupling pattern. 207Pb NMR can therefore be used to detect the structural disorder and phase transitions. Furthermore, by comparing bulk and nanocrystalline CsPbBr3 a greater structural disorder of the PbBr6-octahedra had been confirmed in a nanoscale counterpart, not readily captured by diffraction-based techniques.
Morphological, genotypic and metabolomic signatures confirm interfamilial hybridization between the ubiquitous kelps Macrocystis (Arthrothamnaceae) and Lessonia (Lessoniaceae)
Authors: Murúa Pedro , Edrada-Ebel RuAngelie , Muñoz Liliana , Soldatou Sylvia , Legrave Nathalie , Müller Dieter G. , Patiño David J. , van West Pieter , Küpper Frithjof C. , Westermeier Renato , Ebel Rainer , Peters Akira F. 
Published: May 2020

AbstractMacrocystis pyrifera and Lessonia spicata are economically and ecologically relevant brown seaweeds that recently have been classified as members of two separated families within Laminariales (kelps). Here we describe for the first time the Macrocystis pyrifera x Lessonia spicata hybridization in the wild (Chiloe Island, Southeastern Pacific), where populations of the two parents exist sympatrically. Externally, this hybrid exhibited typical features of its parents M. pyrifera (cylindrical and flexible distal stipes, serrate frond margins and presence of sporophylls) and L. spicata (rigid and flat main stipe and first bifurcation), as well as intermediate features between them (thick unfused haptera in the holdfast). Histological sections revealed the prevalence of mucilage ducts within stipes and fronds (absent in Lessonia) and fully developed unilocular sporangia in the sporophylls. Molecular analyses confirmed the presence of the two parental genotypes for ITS1 nrDNA and the M. pyrifera genotype for two predominantly maternally inherited cytoplasmic markers (COI and rbcLS spacer) in the tissue of the hybrid. A metabolome-wide approach revealed that this hybrid is more chemically reminiscent to M. pyrifera. Nevertheless, several hits were identified as Lessonia exclusive or more remarkably, not present in any of the parent. Meiospores developed into apparently fertile gametophytes, which gave rise to F1 sporophytes that reached several millimeters before suddenly dying. In-vitro reciprocal crossing of Mar Brava gametophytes from both species revealed that although it is rare, interfamilial hybridization between the two species is possible but mostly overcome by pseudogamy of female gametophytes.
Associations of urinary polymeric immunoglobulin receptor peptides in the context of cardio-renal syndrome
Authors: He Tianlin , Siwy Justyna , Metzger Jochen , Mullen William , Mischak Harald , Schanstra Joost P. , Zürbig Petra , Jankowski Vera 
Published: May 2020

AbstractThe polymeric immunoglobulin receptor (pIgR) transports immunoglobulins from the basolateral to the apical surface of epithelial cells. PIgR was recently shown to be associated with kidney dysfunction. The immune defense is initiated at the apical surface of epithelial cells where the N-terminal domain of pIgR, termed secretory component (SC), is proteolytically cleaved and released either unbound (free SC) or bound to immunoglobulins. The aim of our study was to evaluate the association of pIgR peptides with the cardio-renal syndrome in a large cohort and to obtain information on how the SC is released. We investigated urinary peptides of 2964 individuals available in the Human Urine Proteome Database generated using capillary electrophoresis coupled to mass spectrometry. The mean amplitude of 23 different pIgR peptides correlated negatively with the estimated glomerular filtration rate (eGFR, rho = −0.309, p < 0.0001). Furthermore, pIgR peptides were significantly increased in cardiovascular disease (coronary artery disease and heart failure) after adjustment for eGFR. We further predicted potential proteases involved in urinary peptide generation using the Proteasix algorithm. Peptide cleavage site analysis suggested that several, and not one, proteases are involved in the generation of the SC. In this large cohort, we could demonstrate that pIgR is associated with the cardio-renal syndrome and provided a more detailed insight on how pIgR can be potentially cleaved to release the SC.
Learning to Predict Crystal Plasticity at the Nanoscale: Deep Residual Networks and Size Effects in Uniaxial Compression Discrete Dislocation Simulations
Authors: Yang Zijiang , Papanikolaou Stefanos , Reid Andrew C. E. , Liao Wei-keng , Choudhary Alok N. , Campbell Carelyn , Agrawal Ankit 
Published: May 2020

AbstractThe density and configurational changes of crystal dislocations during plastic deformation influence the mechanical properties of materials. These influences have become clearest in nanoscale experiments, in terms of strength, hardness and work hardening size effects in small volumes. The mechanical characterization of a model crystal may be cast as an inverse problem of deducing the defect population characteristics (density, correlations) in small volumes from the mechanical behavior. In this work, we demonstrate how a deep residual network can be used to deduce the dislocation characteristics of a sample of interest using only its surface strain profiles at small deformations, and then statistically predict the mechanical response of size-affected samples at larger deformations. As a testbed of our approach, we utilize high-throughput discrete dislocation simulations for systems of widths that range from nano- to micro- meters. We show that the proposed deep learning model significantly outperforms a traditional machine learning model, as well as accurately produces statistical predictions of the size effects in samples of various widths. By visualizing the filters in convolutional layers and saliency maps, we find that the proposed model is able to learn the significant features of sample strain profiles.
Flexibility of little auks foraging in various oceanographic features in a changing Arctic
Authors: Jakubas Dariusz , Wojczulanis-Jakubas Katarzyna , Iliszko Lech M. , Kidawa Dorota , Boehnke Rafał , Błachowiak-Samołyk Katarzyna , Stempniewicz Lech 
Published: May 2020

AbstractUsing GPS-tracked individuals, we compared foraging ecology and reproductive output of a High-Arctic zooplanktivorous seabird, the little auk Alle alle, between three years differing in environmental conditions (sea surface temperature). Despite contrasting environmental conditions, average foraging fights distance and duration were generally similar in all studied years. Also, in all years foraging locations visited by the little auk parents during short trips (ST, for chick provisioning) were significantly closer to the colony compared to those visited during long trips (LTs, mainly for adults’ self-maintenance). Nevertheless, we also found some differences in the little auk foraging behaviour: duration of LTs was the longest in the coldest year suggesting more time for resting for adults compared to warmer years. Besides, birds foraged closer to the colony and in significantly colder water in the coldest year. Interestingly, these differences did not affect chick diet: in all the years, the energy content of food loads was similar, with the Arctic copepod, Calanus glacialis copepodite stage V being the most preferred prey item (>73% of items by number and >67% by energy content). Also chick survival was similar in all the study years. However, when examining chicks growth rate we found that their peak body mass was lower in warmer years suggesting that overall conditions in the two warm years were less favourable. While our results, demonstrate a great foraging flexibility by little auks, they also point out their vulnerability to changing environmental conditions.
Energetic footprints of irreversibility in the quantum regime
Authors: Mohammady M. H. , Auffèves A. , Anders J. 
Published: May 2020

AbstractIn classical thermodynamic processes the unavoidable presence of irreversibility, quantified by the entropy production, carries two energetic footprints: the reduction of extractable work from the optimal, reversible case, and the generation of a surplus of heat that is irreversibly dissipated to the environment. Recently it has been shown that in the quantum regime an additional quantum irreversibility occurs that is linked to decoherence into the energy basis. Here we employ quantum trajectories to construct distributions for classical heat and quantum heat exchanges, and show that the heat footprint of quantum irreversibility differs markedly from the classical case. We also quantify how quantum irreversibility reduces the amount of work that can be extracted from a state with coherences. Our results show that decoherence leads to both entropic and energetic footprints which both play an important role in the optimization of controlled quantum operations at low temperature.
Dehydroeffusol inhibits hypoxia-induced epithelial–mesenchymal transition in non-small cell lung cancer cells through the inactivation of Wnt/β-catenin pathway
Authors: Wei Haitao , Zhang Feng , Wang Jiali , Zhao Min , Hou Tao , Li Li 
Published: May 2020

Abstract
Dehydroeffusol (DHE) is a phenanthrene compound that possesses anti-tumor activity. However, the effect of DHE on non-small cell lung cancer (NSCLC) has not been investigated previously. Therefore, the objective of our study was to explore the role of DHE in NSCLC and the underlying mechanism. Our results showed that DHE significantly inhibited the cell viability of A549 cells in a dose- and time-dependent manner under normoxic condition. Moreover, A549 cells were more sensitive to DHE under hypoxic condition compared with the A549 cells cultured in normoxic condition. Hypoxia-induced increased migration and invasion abilities were mitigated by DHE in A549 cells. Treatment of DHE caused increased E-cadherin expression and decreased N-cadherin expression in hypoxia-induced A549 cells. DHE also suppressed hypoxia-induced increase in both protein and mRNA levels of hypoxia inducible factor-1α (HIF-1α) expression in A549 cells. Furthermore, DHE inhibited hypoxia-induced activation of Wnt/β-catenin pathway in A549 cells. The inhibitory effect of DHE on hypoxia-induced EMT was reversed by LiCl, which is an activator of Wnt/β-catenin signaling pathway. In conclusion, these findings demonstrated that DHE prevented hypoxia-induced EMT in NSCLC cells by inhibiting the activation of Wnt/β-catenin pathway, suggesting that DHE might serve as a therapeutic target for the NSCLC metastasis.
Keratoconus and Ectatic Disease: Evolving Criteria for Diagnosis
Authors: Belin Michael Wellington 
Published: May 2020

AbstractThe approach to corneal ectatic disease has changed dramatically over the last decade with advances in both diagnosis and treatment. Newer treatments, such as corneal cross-linking, have the potential to slow or stop the progression of the disease, but benefit from earlier identification of the disease than had previously been possible or required. The continued use of older diagnostic criteria and ambiguous terminology can lead to erroneous study conclusions that may not be applicable to patients with true pathology.