bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuropil contraction in relation to Complement C4 gene copy numbers in independent cohorts of adolescent-onset and young adult-onset schizophrenia patients–a pilot study
Authors: Prasad Konasale M. , Chowdari Kodavali V. , D’Aiuto Leonardo A. , Iyengar Satish , Stanley Jeffrey A. , Nimgaonkar Vishwajit L. 
Published: July 2018

AbstractA recent report suggestedComplement 4 (C4A)gene copy numbers (GCN) as risk factors for schizophrenia. Rodent model showed association ofC4with synaptic pruning suggesting its pathophysiological significance (Sekar, A. et al. (2016)). We, therefore, predicted thatC4AGCN would be positively correlated with neuropil contraction in the human brain among schizophrenia patients showing more prominent correlations in ventral regions among young adults and dorsal regions among adolescents since neuromaturation progresses dorsoventrally. Whole-brain, multi-voxel, in vivo phosphorus magnetic resonance spectroscopy (31P MRS) assessed neuropil changes by estimating levels of membrane phospholipid (MPL) precursors and catabolites. Increased MPL catabolites and/or decreased MPL precursors indexed neuropil contraction. Digital droplet PCR-based assay was used to estimateC4AandC4BGCN. We evaluated two independent cohorts (young adult-onset early-course schizophrenia (YASZ = 15) and adolescent-onset schizophrenia (AOSZ = 12) patients), and controls matched for each group,n = 22 and 15, respectively. Separate forward stepwise linear regression models with Akaike information Criterion were built for MPL catabolites and precursors.YASZ cohort:Consistent with the rodent model (Sekar, A. et al. 2016)),C4AGCN positively correlated with neuropil contraction (increased pruning/decreased formation) in the inferior frontal cortex and inferior parietal lobule.AOSZ cohort: C4AGCN positively correlated with neuropil contraction in the dorsolateral prefrontal cortex and thalamus. Exploratory analysis ofC4BGCN showed positive correlation with neuropil contraction in the cerebellum and superior temporal gyrus among YASZ while AOSZ showed neuropil contraction in the prefrontal and subcortical structures. Thus,C4A and C4BGCN are associated with neuropil contraction in regions often associated with schizophrenia, and may be neuromaturationally dependent.
Widespread anti-CRISPR proteins in virulent bacteriophages inhibit a range of Cas9 proteins
Authors: Hynes Alexander P. , Rousseau Geneviève M. , Agudelo Daniel , Goulet Adeline , Amigues Beatrice , Loehr Jeremy , Romero Dennis A. , Fremaux Christophe , Horvath Philippe , Doyon Yannick , Cambillau Christian , Moineau Sylvain 
Published: July 2018

AbstractCRISPR-Cas systems are bacterial anti-viral systems, and bacterial viruses (bacteriophages, phages) can carry anti-CRISPR (Acr) proteins to evade that immunity. Acrs can also fine-tune the activity of CRISPR-based genome-editing tools. While Acrs are prevalent in phages capable of lying dormant in a CRISPR-carrying host, their orthologs have been observed only infrequently in virulent phages. Here we identify AcrIIA6, an Acr encoded in 33% of virulent Streptococcus thermophilus phage genomes. The X-ray structure of AcrIIA6 displays some features unique to this Acr family. We compare the activity of AcrIIA6 to those of other Acrs, including AcrIIA5 (also from S. thermophilus phages), and characterize their effectiveness against a range of CRISPR-Cas systems. Finally, we demonstrate that both Acr families from S. thermophilus phages inhibit Cas9-mediated genome editing of human cells.
Electrically driven three-dimensional solitary waves as director bullets in nematic liquid crystals
Authors: Li Bing-Xiang , Borshch Volodymyr , Xiao Rui-Lin , Paladugu Sathyanarayana , Turiv Taras , Shiyanovskii Sergij V. , Lavrentovich Oleg D. 
Published: July 2018

AbstractElectric field-induced collective reorientation of nematic molecules is of importance for fundamental science and practical applications. This reorientation is either homogeneous over the area of electrodes, as in displays, or periodically modulated, as in electroconvection. The question is whether spatially localized three-dimensional solitary waves of molecular reorientation could be created. Here we demonstrate that the electric field can produce particle-like propagating solitary waves representing self-trapped “bullets” of oscillating molecular director. These director bullets lack fore-aft symmetry and move with very high speed perpendicularly to the electric field and to the initial alignment direction. The bullets are true solitons that preserve spatially confined shapes and survive collisions. The solitons are topologically equivalent to the uniform state and have no static analogs, thus exhibiting a particle–wave duality. Their shape, speed, and interactions depend strongly on the material parameters, which opens the door for a broad range of future studies.
Broadband Bending of Flexural Waves: Acoustic Shapes and Patterns
Authors: Darabi Amir , Zareei Ahmad , Alam Mohammad-Reza , Leamy Michael J. 
Published: July 2018

AbstractDirecting and controlling flexural waves in thin plates along a curved trajectory over a broad frequency range is a significant challenge that has various applications in imaging, cloaking, wave focusing, and wireless power transfer circumventing obstacles. To date, all studies appeared controlling elastic waves in structures using periodic arrays of inclusions where these structures are narrowband either because scattering is efficient over a small frequency range, or the arrangements exploit Bragg scattering bandgaps, which themselves are narrowband. Here, we design and experimentally test a wave-bending structure in a thin plate by smoothly varying the plate’s rigidity (and thus its phase velocity). The proposed structures are (i) broadband, since the approach is frequency-independent and does not require bandgaps, and (ii) capable of bending elastic waves along convex trajectories with an arbitrary curvature.
Gut Bacterial Microbiota and its Resistome Rapidly Recover to Basal State Levels after Short-term Amoxicillin-Clavulanic Acid Treatment in Healthy Adults
Authors: MacPherson Chad W. , Mathieu Olivier , Tremblay Julien , Champagne Julie , Nantel André , Girard Stéphanie-Anne , Tompkins Thomas A. 
Published: July 2018

AbstractClinical effects of antimicrobials and probiotics in combination have been reported, however, little is known about their impact on gut microbiota and its resistome. In this study 16S rRNA gene amplicon, shotgun metagenomics sequencing and antibiotic resistance (ABR) microarray were used on fecal samples of 70 healthy participants, taken at four time points in probiotic (Lactobacillus rhamnosus R0011 and Lactobacillus helveticus R0052) and placebo groups to profile the gut bacterial microbiota and its resistome following administration of amoxicillin-clavulanic acid for one week. Significant shifts in microbiota family composition caused by the antimicrobial in both groups that included decreases in the proportion of Lachnospiraceae, Coriobacteriaceae and unidentified Clostridiales; and notable increases for the proportion of Enterobacteriaceae, Bacteroidaceae and Porphyromonadaceae compared to baseline levels. Resistome showed a corresponding enrichment of ABR genes compared to baseline from such classes as aminoglycosides and beta-lactams that were linked, by in silico inference, to the enrichment of the family Enterobacteriaceae. Despite perturbations caused by short-term antibiotic treatment, both gut microbiota and resistome showed prompt recovery to baseline levels one week after cessation of the antimicrobial. This rapid recovery may be explained by the hypothesis of community resilience.
Visible–Near-Infrared Spectroscopy can predict Mass Transport of Dissolved Chemicals through Intact Soil
Authors: Katuwal Sheela , Knadel Maria , Moldrup Per , Norgaard Trine , Greve Mogens H. , de Jonge Lis W. 
Published: July 2018

AbstractThe intensification of agricultural production to meet the growing demand for agricultural commodities is increasing the use of chemicals. The ability of soils to transport dissolved chemicals depends on both the soil’s texture and structure. Assessment of the transport of dissolved chemicals (solutes) through soils is performed using breakthrough curves (BTCs) where the application of a solute at one site and its appearance over time at another are recorded. Obtaining BTCs from laboratory studies is extremely expensive and time- and labour-consuming. Visible–near-infrared (vis–NIR) spectroscopy is well recognized for its measurement speed and for its low data acquisition cost and can be used for quantitative estimation of basic soil properties such as clay and organic matter. In this study, for the first time ever, vis–NIR spectroscopy was used to predict dissolved chemical breakthrough curves obtained from tritium transport experiments on a large variety of intact soil columns. Averaged across the field, BTCs were estimated with a high degree of accuracy. So, with vis-NIR spectroscopy, the mass transport of dissolved chemicals can be measured, paving the way for next-generation measurements and monitoring of dissolved chemical transport by spectroscopy.
Ultra-lightweight superconducting wire based on Mg, B, Ti and Al
Authors: Kováč P. , Hušek I. , Rosová A. , Kulich M. , Kováč J. , Melišek T. , Kopera L. , Balog M. , Krížik P. 
Published: July 2018

AbstractActually, MgB2 is the lightest superconducting compound. Its connection with lightweight metals like Ti (as barrier) and Al (as outer sheath) would result in a superconducting wire with the minimal mass. However, pure Al is mechanically soft metal to be used in drawn or rolled composite wires, especially if applied for the outer sheath, where it cannot provide the required densification of the boron powder inside. This study reports on a lightweight MgB2 wire sheathed with aluminum stabilized by nano-sized γ-Al2O3 particles (named HITEMAL) and protected against the reaction with magnesium by Ti diffusion barrier. Electrical and mechanical properties of single-core MgB2/Ti/HITEMAL wire made by internal magnesium diffusion (IMD) into boron were studied at low temperatures. It was found that the ultra-lightweight MgB2 wire exhibited high critical current densities and also tolerances to mechanical stress. This predetermines the potential use of such lightweight superconducting wires for aviation and space applications, and for powerful offshore wind generators, where reducing the mass of the system is required.
Landscape limits gene flow and drives population structure in Agassiz’s desert tortoise (Gopherus agassizii)
Authors: Sánchez-Ramírez Santiago , Rico Yessica , Berry Kristin H. , Edwards Taylor , Karl Alice E. , Henen Brian T. , Murphy Robert W. 
Published: July 2018

AbstractDistance, environmental heterogeneity and local adaptation can strongly influence population structure and connectivity. Understanding how these factors shape the genomic landscape of threatened species is a major goal in conservation genomics and wildlife management. Herein, we use thousands (6,859) of single nucleotide polymorphism markers and spatial data from hundreds of individuals (n = 646) to re-evaluate the population structure of Agassiz’s desert tortoise (Gopherus agassizii). Analyses resolve from 4 to 8 spatially well-defined clusters across the range. Western, central, and southern populations within the Western Mojave recovery unit are consistent throughout, while analyses sometimes merge other recovery units depending on the level of clustering. Causal modeling consistently associates genetic connectivity with least-cost distance, based on multiple landscape features associated with tortoise habitat, better than geographic distance. Some features include elevation, soil depth, rock volume, precipitation, and vegetation coverage, suggesting that physical, climatic, and biotic landscape features have played a strong evolutionary role restricting gene flow between populations. Further, 12 highly differentiated outlier loci have associated functions that may be involved with neurogenesis, wound healing, lipid metabolism, and possibly vitellogenesis. Together, these findings have important implications for recovery programs, such as translocations, population augmentation, reproduction in captivity and the identification of ecologically important genes, opening new venues for conservation genomics in desert tortoises.
Species Richness, Molecular Taxonomy and Biogeography of the Radicine Pond Snails (Gastropoda: Lymnaeidae) in the Old World
Authors: Aksenova Olga V. , Bolotov Ivan N. , Gofarov Mikhail Yu. , Kondakov Alexander V. , Vinarski Maxim V. , Bespalaya Yulia V. , Kolosova Yulia S. , Palatov Dmitry M. , Sokolova Svetlana E. , Spitsyn Vitaly M. , Tomilova Alena A. , Travina Oksana V. , Vikhrev Ilya V. 
Published: July 2018

AbstractThe radicine pond snails represent a species-rich and widely distributed group, many species of which are key vectors of human and animal trematodoses. Here we clarify the taxonomy, distribution and evolutionary biogeography of the radicine lymnaeids in the Old World based on the most comprehensive multi-locus molecular dataset sampled to date. We show that the subfamily Amphipepleinae is monophyletic and contains at least ten genus-level clades:RadixMontfort, 1810,AmpullaceanaServain, 1881,PeregrianaServain, 1881,TibetoradixBolotov, Vinarski & Aksenovagen.nov.,KamtschaticanaKruglov & Starobogatov, 1984,OrientogalbaKruglov & Starobogatov, 1985,CerasinaKobelt, 1881,MyxasG. B. Sowerby I, 1822,BullastraBergh, 1901, andAustropepleaCotton, 1942. With respect to our phylogeny, species-delimitation model and morphological data, the Old World fauna includes 35 biological species of radicines. Tibet and Eastern Europe harbor the richest faunas, while East Asia and Africa appear to be the most species-poor areas. The radicine clade could have originated near the Cretaceous – Paleocene boundary. The Miocene great lakes in Eurasia seems to be the most important evolutionary hotspots shaping spatial patterns of recent species richness. Finally, we present the first DNA barcode reference library for the reliable molecular identification of species within this group.
Gonadal steroid levels in rock pigeon eggs do not represent adequately maternal allocation
Authors: Kumar Neeraj , van Faassen Martijn , de Vries Bonnie , Kema Ido , Gahr Manfred , Groothuis Ton G. G. 
Published: July 2018

AbstractMaternal hormones deposited in the egg can provide a powerful model for the study of maternal effects. The differential amount of maternal hormones in the yolk of freshly laid eggs is assumed to represent differential maternal allocation. However, some evidence suggests that these amounts do not reflect maternal allocation that in fact takes place before ovulation. We compared the amounts of a wide array of gonadal steroids and their metabolites in the yolk of pre-ovulatory follicles with those of freshly laid eggs of rock pigeons using mass spectrometry. We found that between the follicle and egg stages the levels of progesterone increase whereas androstenedione and testosterone decrease in which the strength of decrease was dependent on the laying order of the egg. For conjugated estrone the change between follicle and egg differed in direction for first and second laying position yielding a significant interaction effect. For conjugated testosterone the interaction did not reach but was close to significance. This extremely early steroid metabolism was not due to maternal enzymes in the yolk as indicated by incubation of pre-ovulatory yolks treated with proteinase-K, a protein digesting enzyme. The results have significant consequences for the functional and evolutionary interpretation as well as experimental manipulation of hormone-mediated maternal effects.
Structural determinants of the catalytic mechanism of Plasmodium CCT, a key enzyme of malaria lipid biosynthesis
Authors: Guca Ewelina , Nagy Gergely N. , Hajdú Fanni , Marton Lívia , Izrael Richard , Hoh François , Yang Yinshan , Vial Henri , Vértessy Beata G. , Guichou Jean-François , Cerdan Rachel 
Published: July 2018

AbstractThe development of the malaria parasite, Plasmodium falciparum, in the human erythrocyte, relies on phospholipid metabolism to fulfil the massive need for membrane biogenesis. Phosphatidylcholine (PC) is the most abundant phospholipid in Plasmodium membranes. PC biosynthesis is mainly ensured by the de novo Kennedy pathway that is considered as an antimalarial drug target. The CTP:phosphocholine cytidylyltransferase (CCT) catalyses the rate-limiting step of the Kennedy pathway. Here we report a series of structural snapshots of the PfCCT catalytic domain in its free, substrate- and product-complexed states that demonstrate the conformational changes during the catalytic mechanism. Structural data show the ligand-dependent conformational variations of a flexible lysine. Combined kinetic and ligand-binding analyses confirm the catalytic roles of this lysine and of two threonine residues of the helix αE. Finally, we assessed the variations in active site residues between Plasmodium and mammalian CCT which could be exploited for future antimalarial drug design.
Metabolomic analysis of mouse prefrontal cortex reveals upregulated analytes during wakefulness compared to sleep
Authors: Bourdon Allen K. , Spano Giovanna Maria , Marshall William , Bellesi Michele , Tononi Giulio , Serra Pier Andrea , Baghdoyan Helen A. , Lydic Ralph , Campagna Shawn R. , Cirelli Chiara 
Published: July 2018

AbstractBy identifying endogenous molecules in brain extracellular fluid metabolomics can provide insight into the regulatory mechanisms and functions of sleep. Here we studied how the cortical metabolome changes during sleep, sleep deprivation and spontaneous wakefulness. Mice were implanted with electrodes for chronic sleep/wake recording and with microdialysis probes targeting prefrontal and primary motor cortex. Metabolites were measured using ultra performance liquid chromatography-high resolution mass spectrometry. Sleep/wake changes in metabolites were evaluated using partial least squares discriminant analysis, linear mixed effects model analysis of variance, and machine-learning algorithms. More than 30 known metabolites were reliably detected in most samples. When used by a logistic regression classifier, the profile of these metabolites across sleep, spontaneous wake, and enforced wake was sufficient to assign mice to their correct experimental group (pair-wise) in 80–100% of cases. Eleven of these metabolites showed significantly higher levels in awake than in sleeping mice. Some changes extend previous findings (glutamate, homovanillic acid, lactate, pyruvate, tryptophan, uridine), while others are novel (D-gluconate, N-acetyl-beta-alanine, N-acetylglutamine, orotate, succinate/methylmalonate). The upregulation of the de novo pyrimidine pathway, gluconate shunt and aerobic glycolysis may reflect a wake-dependent need to promote the synthesis of many essential components, from nucleic acids to synaptic membranes.
The histone chaperone NAP1L3 is required for haematopoietic stem cell maintenance and differentiation
Authors: Heshmati Yaser , Kharazi Shabnam , Türköz Gözde , Chang David , Kamali Dolatabadi Esmat , Boström Johan , Krstic Aleksandra , Boukoura Theodora , Wagner Emma , Kadri Nadir , Månsson Robert , Altun Mikael , Qian Hong , Walfridsson Julian 
Published: July 2018

AbstractNucleosome assembly proteins (NAPs) are histone chaperones with an important role in chromatin structure and epigenetic regulation of gene expression. We find that high gene expression levels of mouse Nap1l3 are restricted to haematopoietic stem cells (HSCs) in mice. Importantly, with shRNA or CRISPR-Cas9 mediated loss of function of mouse Nap1l3 and with overexpression of the gene, the number of colony-forming cells and myeloid progenitor cells in vitro are reduced. This manifests as a striking decrease in the number of HSCs, which reduces their reconstituting activities in vivo. Downregulation of human NAP1L3 in umbilical cord blood (UCB) HSCs impairs the maintenance and proliferation of HSCs both in vitro and in vivo. NAP1L3 downregulation in UCB HSCs causes an arrest in the G0 phase of cell cycle progression and induces gene expression signatures that significantly correlate with downregulation of gene sets involved in cell cycle regulation, including E2F and MYC target genes. Moreover, we demonstrate that HOXA3 and HOXA5 genes are markedly upregulated when NAP1L3 is suppressed in UCB HSCs. Taken together, our findings establish an important role for NAP1L3 in HSC homeostasis and haematopoietic differentiation.
The effect of pulsatile motion and cardiac-gating on reconstruction and diffusion tensor properties of the corticospinal tract
Authors: Bopp Miriam H. A. , Yang Jia , Nimsky Christopher , Carl Barbara 
Published: July 2018

AbstractPulsatile motion occurs in the cardiac systolic period and leads to significantly larger displacement of water molecules as it is observed during diffusion weighted image acquisition. Obvious pulsatile motion arises in the brain stem and basal ganglia and might affect the corticospinal tract. So far there is no consensus on the real effect of pulsatile motion on diffusion properties, diffusion tensor parameters and fiber tractography and on the role of cardiac-gating to overcome these effects. The present study aimed at detecting effects of pulsatile motion on imaging properties and reconstruction of the corticospinal tract. Non-gated and cardiac-gated data of 22 healthy subjects was acquired using clinical standard protocols and analysed with regard to effects on signal intensities, diffusion tensor properties and tractography results concerning the corticospinal tract. Analyses resulted in obvious effects of pulsatile motion on signal intensities, especially alterations in diffusion tensor properties, compensated by the application of cardiac-gating, whereas no effect on fiber tract volume was seen. Therefore, pulsatile motion and cardiac-gating should be kept in mind as critical aspects when analysing and interpreting diffusion tensor properties within the human brain, but are of minor interest when considering fiber tractography of the corticospinal tract.
Neutrophils enhance early Trypanosoma brucei infection onset
Authors: Caljon Guy , Mabille Dorien , Stijlemans Benoît , De Trez Carl , Mazzone Massimiliano , Tacchini-Cottier Fabienne , Malissen Marie , A. Van Ginderachter Jo , Magez Stefan , De Baetselier Patrick , Van Den Abbeele Jan 
Published: July 2018

AbstractIn this study, Trypanosoma brucei was naturally transmitted to mice through the bites of infected Glossina morsitans tsetse flies. Neutrophils were recruited rapidly to the bite site, whereas monocytes were attracted more gradually. Expression of inflammatory cytokines (il1b, il6), il10 and neutrophil chemokines (cxcl1, cxcl5) was transiently up-regulated at the site of parasite inoculation. Then, a second influx of neutrophils occurred that coincided with the previously described parasite retention and expansion in the ear dermis. Congenital and experimental neutropenia models, combined with bioluminescent imaging, indicate that neutrophils do not significantly contribute to dermal parasite control and elicit higher systemic parasitemia levels during the infection onset. Engulfment of parasites by neutrophils in the skin was rarely observed and was restricted to parasites with reduced motility/viability, whereas live parasites escaped phagocytosis. To our knowledge, this study represents the first description of a trypanosome infection promoting role of early innate immunological reactions following an infective tsetse fly bite. Our data indicate that the trypanosome is not hindered in its early development and benefits from the host innate responses with the neutrophils being important regulators of the early infection, as already demonstrated for the sand fly transmitted Leishmania parasite.