bluuebunny/crossref_metadata_2025_split huggingface dataset:
Super-regional land-use change and effects on the grassland specialist flora
Authors: Auffret Alistair G. , Kimberley Adam , Plue Jan , Waldén Emelie 
Published: August 2018

AbstractHabitat loss through land-use change is the most pressing threat to biodiversity worldwide. European semi-natural grasslands have suffered an ongoing decline since the early twentieth century, but we have limited knowledge of how grassland loss has affected biodiversity across large spatial scales. We quantify land-use change over 50–70 years across a 175,000 km2 super-region in southern Sweden, identifying a widespread loss of open cover and a homogenisation of landscape structure, although these patterns vary considerably depending on the historical composition of the landscape. Analysing species inventories from 46,796 semi-natural grasslands, our results indicate that habitat loss and degradation have resulted in a decline in grassland specialist plant species. Local factors are the best predictors of specialist richness, but the historical landscape predicts present-day richness better than the contemporary landscape. This supports the widespread existence of time-lagged biodiversity responses, indicating that further species losses could occur in the future.
Perrault syndrome type 3 caused by diverse molecular defects in CLPP
Authors: Brodie Erica J. , Zhan Hanmiao , Saiyed Tamanna , Truscott Kaye N. , Dougan David A. 
Published: August 2018

AbstractThe maintenance of mitochondrial protein homeostasis (proteostasis) is crucial for correct cellular function. Recently, several mutations in the mitochondrial protease CLPP have been identified in patients with Perrault syndrome 3 (PRLTS3). These mutations can be arranged into two groups, those that cluster near the docking site (hydrophobic pocket, Hp) for the cognate unfoldase CLPX (i.e. T145P and C147S) and those that are adjacent to the active site of the peptidase (i.e. Y229D). Here we report the biochemical consequence of mutations in both regions. The Y229D mutant not only inhibited CLPP-peptidase activity, but unexpectedly also prevented CLPX-docking, thereby blocking the turnover of both peptide and protein substrates. In contrast, Hp mutations cause a range of biochemical defects in CLPP, from no observable change to CLPP activity for the C147S mutant, to dramatic disruption of most activities for the “gain-of-function” mutant T145P - including loss of oligomeric assembly and enhanced peptidase activity.
The statistical shape of geometric reasoning
Authors: Hart Yuval , Dillon Moira R. , Marantan Andrew , Cardenas Anna L. , Spelke Elizabeth , Mahadevan L. 
Published: August 2018

AbstractGeometric reasoning has an inherent dissonance: its abstract axioms and propositions refer to perfect, idealized entities, whereas its use in the physical world relies on dynamic perception of objects. How do abstract Euclidean concepts, dynamics, and statistics come together to support our intuitive geometric reasoning? Here, we address this question using a simple geometric task – planar triangle completion. An analysis of the distribution of participants’ errors in localizing a fragmented triangle’s missing corner reveals scale-dependent deviations from a deterministic Euclidean representation of planar triangles. By considering the statistical physics of the process characterized via a correlated random walk with a natural length scale, we explain these results and further predict participants’ estimates of the missing angle, measured in a second task. Our model also predicts the results of a categorical reasoning task about changes in the triangle size and shape even when such completion strategies need not be invoked. Taken together, our findings suggest a critical role for noisy physical processes in our reasoning about elementary Euclidean geometry.
Systematic analysis reveals molecular characteristics of ERG-negative prostate cancer
Authors: Xiao Qingyu , Sun Yidi , Dobi Albert , Srivastava Shiv , Wang Wendy , Srivastava Sudhir , Ji Yuan , Hou Jun , Zhao Guo-Ping , Li Yixue , Li Hong 
Published: August 2018

AbstractThe TMPRSS2:ERG gene fusion is the most prevalent early driver gene activation in prostate cancers of European ancestry, while the fusion frequency is much lower in Africans and Asians. The genomic characteristics and mechanisms for patients lacking ERG fusion are still unclear. In this study, we systematically compared the characteristics of gene fusions, somatic mutations, copy number alterations and gene expression signatures between 201 ERG fusion positive and 296 ERG fusion negative prostate cancer samples. Both common and group-specific genomic alterations were observed, suggesting shared and different mechanisms of carcinogenesis in prostate cancer samples with or without ERG fusion. The genomic alteration patterns detected in ERG-negative group showed similarities with 77.5% of tumor samples of African American patients. These results emphasize that genomic and gene expression features of the ERG-negative group may provide a reference for populations with lower ERG fusion frequency. While the overall expression patterns were comparable between ERG-negative and ERG-positive tumors, we found that genomic alterations could affect the same pathway through distinct genes in the same pathway in both groups of tumor types. Altogether, the genomic and molecular characteristics revealed in our study may provide new opportunities for molecular stratification of ERG-negative prostate cancers.
Generalized Haldane models on laser-coupling optical lattices
Authors: Liu Wanli , Lin Zhi , Wang Z. D. , Chen Yan 
Published: August 2018

AbstractWe propose two generalized Haldane models on laser-coupling optical lattices. Laser-assisted nearest neighbour tunnelings generate artificial staggered magnetic flux, facilitating the realization of topological nontrivial band structures. As generalizations of Haldane model, these models support topological insulator and semimetal phases featuring high Chern numbers. We show simple rules for computing Chern numbers of our models and display the phase diagrams. Moreover, numerical calculations of energy spectra are in perfect agreement with our theoretical expectations. Our models may serve as two new family members for generalizing Haldane model on optical lattices.
Roles of aberrant hemichannel activities due to mutant connexin26 in the pathogenesis of KID syndrome
Authors: Taki T. , Takeichi T. , Sugiura K. , Akiyama M. 
Published: August 2018

AbstractGermline missense mutations inGJB2encoding connexin (Cx) 26 have been found in keratitis, ichthyosis and deafness (KID) syndrome. We explored the effects of three mouse Cx26 mutants (Cx26-G12R, -G45E and -D50N) corresponding to KID syndrome-causative human mutants on hemichannel activities leading to cell death and the expression of immune response-associated genes. We analyzed the 3D images of cells expressing wild-type (WT) or mutant Cx26 molecules to demonstrate clearly the intracellular localization of Cx26 mutants and hemichannel formation. High extracellular Ca2+conditions lead to the closure of gap junction hemichannels in Cx26-G12R or Cx26-G45E expressing cells, resulting in prohibition of the Cx26 mutant-induced cell death. Fluorescent dye uptake assays revealed that cells with Cx26-D50N had aberrantly high hemichannel activities, which were abolished by a hemichannel blocker, carbenoxolone and 18α-Glycyrrhetinic acid. These results further support the idea that abnormal hemichannel activities play important roles in the pathogenesis of KID syndrome. Furthermore, we revealed that the expressions ofIL15,CCL5,IL1A,IL23RandTLR5are down-regulated in keratinocytes expressing Cx26-D50N, suggesting that immune deficiency in KID syndrome expressing Cx26-D50N might be associated not only with skin barrier defects, but also with the down-regulated expression of immune response-related genes.
SiNWs Biophysically Regulate the Fates of Human Mesenchymal Stem Cells
Authors: Lin Hsin-I , Kuo Shu-Wen , Yen Ta-Jen , Lee Oscar K. 
Published: August 2018

AbstractWhile biophysical stimuli from polymeric matrices are known to significantly affect the fates of human mesenchymal stem cells (hMSCs), the stimulatory effects of nano-sized silicon-based matrices on hMSCs have not been thoroughly investigated. We previously demonstrated that vertically aligned, single-crystalline silicon nanowires (SiNWs) can control the osteogenicity of hMSCs via controllable spring constants from SiNWs matrix. However, other possible differentiation fates of hMSCs on SiNWs have not been explored. We hypothesize that tunable spring constant from artificial SiNWs matrices can direct different types of hMSC differentiations. The spring constants of tunable SiNW matrices can be consistently controlled by tuning the SiNW length. The results of gene expression and cell stiffness suggest that hMSCs differentiations are sensitive to our distinguishable spring constants from the SiNWs groups, and simultaneously conduct osteogenicity and adipogenicity. These findings suggest that SiNW matrices can regulate the fates of hMSCs when the SiNW characteristics are carefully tuned.
Exercise in pregnancy: 1-year and 7-year follow-ups of mothers and offspring after a randomized controlled trial
Authors: Chiavaroli Valentina , Hopkins Sarah A. , Derraik José G. B. , Biggs Janene B. , Rodrigues Raquel O. , Brennan Christine H. , Seneviratne Sumudu N. , Higgins Chelsea , Baldi James C. , McCowan Lesley M. E. , Cutfield Wayne S. , Hofman Paul L. 
Published: August 2018

AbstractThere are limited data on long-term outcomes of mothers or their offspring following exercise interventions during pregnancy. We assessed long-term effects of an exercise intervention (home-based stationary cycling) between 20–36 weeks of gestation on anthropometry and body composition in mothers and offspring after 1 and 7 years. 84 women were randomised to intervention or usual activity, with follow-up data available for 61 mother-child pairs (38 exercisers) at 1 year and 57 (33 exercisers) at 7 years. At 1 year, there were no observed differences in measured outcomes between mothers and offspring in the two groups. At the 7-year follow-up, mothers were mostly similar, except that exercisers had lower systolic blood pressure (−6.2 mmHg; p = 0.049). However, offspring of mothers who exercised during pregnancy had increased total body fat (+3.2%; p = 0.034) and greater abdominal (+4.1% android fat; p = 0.040) and gynoid (+3.5% gynoid fat; p = 0.042) adiposity compared with controls. Exercise interventions beginning during pregnancy may be beneficial to long-term maternal health. However, the initiation of exercise during pregnancy amongst sedentary mothers may be associated with adverse effects in the offspring during childhood. Larger follow-up studies are required to investigate long-term effects of exercise in pregnancy.
Experimental evidence for the preservation of U-Pb isotope ratios in mantle-recycled crustal zircon grains
Authors: Bea Fernando , Montero Pilar , Palma Jose Francisco Molina 
Published: August 2018

AbstractZircon of crustal origin found in mantle-derived rocks is of great interest because of the information it may provide about crust recycling and mantle dynamics. Consideration of this requires understanding of how mantle temperatures, notably higher than zircon crystallization temperatures, affected the recycled zircon grains, particularly their isotopic clocks. Since Pb2+ diffuses faster than U4+ and Th+4, it is generally believed that recycled zircon grains lose all radiogenic Pb after a few million years, thus limiting the time range over which they can be detected. Nonetheless, this might not be the case for zircon included in mantle minerals with low Pb2+ diffusivity and partitioning such as olivine and orthopyroxene because these may act as zircon sealants. Annealing experiments with natural zircon embedded in cristobalite (an effective zircon sealant) show that zircon grains do not lose Pb to their surroundings, although they may lose some Pb to molten inclusions. Diffusion tends to homogenize the Pb concentration in each grain changing the U-Pb and Th-Pb isotope ratios proportionally to the initial 206Pb, 207Pb and 208Pb concentration gradients (no gradient-no change) but in most cases the original age is still recognizable. It seems, therefore, that recycled crustal zircon grains can be detected, and even accurately dated, no matter how long they have dwelled in the mantle.
Removal of choroidal vasculature using concurrently applied ultrasound bursts and nanosecond laser pulses
Authors: Zhang Haonan , Xie Xinyi , Li Jia , Qin Yu , Zhang Wei , Cheng Qian , Yuan Songtao , Liu Qinghuai , Paulus Yannis M. , Wang Xueding , Yang Xinmai 
Published: August 2018

AbstractPathologic microvasculature plays a crucial role in innumerable diseases causing death and major organ impairment. A major clinical challenge is the development of selective therapies to remove these diseased microvessels without damaging surrounding tissue. This report describes our development of novel photo-mediated ultrasound therapy (PUT) technology for precisely removing choroidal blood vessels in the eye. PUT selectively removes microvessels by concurrently applying nanosecond laser pulses with ultrasound bursts. In PUT experiments on rabbit eyes in vivo, we applied 55–75 mJ/cm2 of light fluence at the retinochoroidal surface at 532-nm and 0.5 MPa of ultrasound pressure at 0.5 MHz. PUT resulted in significantly reduced blood perfusion in the choroidal layer which persisted to four weeks without causing collateral tissue damage, demonstrating that PUT is capable of removing choroidal microvasculature safely and effectively. With its unique advantages, PUT holds potential for the clinical management of eye diseases associated with microvessels and neovascularization.
Modeling of inhomogeneous electromagnetic fields in the nervous system: a novel paradigm in understanding cell interactions, disease etiology and therapy
Authors: Isakovic Jasmina , Dobbs-Dixon Ian , Chaudhury Dipesh , Mitrecic Dinko 
Published: August 2018

AbstractAll major processes in the nervous system depend on interactions between cells and nerve fibers. In this work we present a novel model of inhomogeneous electromagnetic fields originating from nerve fibers and delineate their influence on cells. By expanding Hodgkin-Huxley’s applied current into axial current, governed by$${J}_{i}^{j+1}=K\times {J}_{i}^{j}$$

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, we reveal that cell-with-neuron interactions are regulated by the strength of the electromagnetic fields, which are homogeneous up to 2.066 μm or 6.606 μm away from neurilemma and axolemma, respectively. At the nodes of Ranvier, these fields reach strengths of 3.0 × 10−12T, while at the myelinated segments they only peak at 2.3 × 10−12T. These are the same fields which are, due to inhomogeneity, detected as 1,000 times weaker by magnetoencephalography. Considering the widespread occurrence of neurodegenerative disorders, our model reveals that a 50% demyelination increases the field strength by 0.35 × 10−12T, while a complete demyelination increases it by 0.7 × 10−12T. Since this suggests that the inhomogeneous electromagnetic fields around neurons play a role in physiological and pathological processes, including cell-to-neuron and cell-to-cell communication, their improved understanding opens up new therapeutic strategies based on electromagnetic field modulation or cell’s surface charge alteration.
Transcriptional shifts account for divergent resource allocation in feed efficient broiler chickens
Authors: Reyer Henry , Metzler-Zebeli Barbara U. , Trakooljul Nares , Oster Michael , Muráni Eduard , Ponsuksili Siriluck , Hadlich Frieder , Wimmers Klaus 
Published: August 2018

AbstractConsiderable variation in feed efficiency (FE) has been observed in indigenous and selected meat-type chicken populations. Although this variation could be partially linked to extrinsic factors like diet, housing environment and microbiota, it further illustrates the existence of strong molecular mechanisms enabling the differential allocation of resources for various physiological processes. To further deepen the molecular basis of individual allocation capacity in male and female broilers, an RNA-seq experiment was conducted which based on a phenotyped chicken population divergent in FE. Transcriptional differences linked to FE were pronounced in intestinal and muscular tissue sites of male animals. Specifically, signalling pathways of farnesoid X receptor (FXR) and retinoid X receptor (RXR) might contribute to mediate individual FE. The transcriptional profiles suggested ACSBG2 (muscular lipid utilisation), ASBT (intestinal bile salt transport), CLEC2B (natural killer cell activation), HMGCS2 (jejunal, duodenal and muscular ketogenesis), and SCARB1 (jejunal lipid uptake) as potential mediators driving FE. Results indicate that improvements in FE exploit shifts in resource allocation which might occur at the expense of general immune responsiveness in high efficient male chickens. Consequently, to further improve FE traits and to explore causative molecular patterns, effects originating from sex-dimorphism in chickens need to be taken into consideration.
The splicing factor SRSF3 is functionally connected to the nuclear RNA exosome for intronless mRNA decay
Authors: Mure Fabrice , Corbin Antoine , Benbahouche Nour El Houda , Bertrand Edouard , Manet Evelyne , Gruffat Henri 
Published: August 2018

AbstractThe RNA exosome fulfills important functions in the processing and degradation of numerous RNAs species. However, the mechanisms of recruitment to its various nuclear substrates are poorly understood. Using Epstein-Barr virus mRNAs as a model, we have discovered a novel function for the splicing factor SRSF3 in the quality control of nuclear mRNAs. We have found that viral mRNAs generated from intronless genes are particularly unstable due to their degradation by the nuclear RNA exosome. This effect is counteracted by the viral RNA-binding protein EB2 which stabilizes these mRNAs in the nucleus and stimulates both their export to the cytoplasm and their translation. In the absence of EB2, SRSF3 participates in the destabilization of these viral RNAs by interacting with both the RNA exosome and its adaptor complex NEXT. Taken together, our results provide direct evidence for a connection between the splicing machinery and mRNA decay mediated by the RNA exosome. Our results suggest that SRSF3 aids the nuclear RNA exosome and the NEXT complex in the recognition and degradation of certain mRNAs.
Visualizing the hydrodynamics in sieve-based lateral displacement systems
Authors: Dijkshoorn J. P. , de Valença J. C. , Wagterveld R. M. , Boom R. M. , Schutyser M. A. I. 
Published: August 2018

AbstractDeterministic lateral displacement (DLD) systems structure suspension flow in so called flow lanes. The width of these flow lanes is crucial for separation of particles and determines whether particles with certain size are displaced or not. In previous research, separation was observed in simplified DLD systems that did not meet the established DLD geometric design criteria, by adjusting the outflow conditions. We here investigated why these simplified DLD systems are able to displace particles, by experimentally investigating the hydrodynamics in the device. Flow lanes were visualized and the local flow velocities were measured using µPIV and compared with 2D fluid dynamics simulations. The size of the flow lanes strongly correlates with the local flow velocity (Vy and Vx), which depends on the hydrodynamics. Therefore, the geometric design criteria of DLD devices is in fact just one method to control the local hydrodynamics, which may also be influenced by other means. These findings give a new perspective on the separation principle, which makes the technique more flexible and easier to translate to industrial scale.
Colloidal nitrogen is an important and highly-mobile form of nitrogen discharging into the Great Barrier Reef lagoon
Authors: Judy Jonathan D. , Kirby Jason K. , Farrell Mark , McLaughlin Mike J. , Wilkinson Scott N. , Bartley Rebecca , Bertsch Paul M. 
Published: August 2018

AbstractSoil-borne colloids have been linked to long-distance transport of radionuclides, metal(loid)s and nutrients. Colloid-associated nitrogen (N) will have different mechanisms of biogeochemical cycling and potential for water-borne transport over longer distances compared to dissolved N. The role that colloids play in the supply and mobility of N within catchments discharging into the Great Barrier Reef (GBR) lagoon is unexplored. Here, we examine water-dispersible clay (WDC) from soil samples collected from gullies and agricultural drains within three different land uses (sugarcane, non-agricultural land and grazing) within the Townsville area. The proportion of soil N associated with WDC was inversely correlated with total soil N, with up to 45% of the total soil N being colloid-associated in low N gully soils. Within the <0.45 µm fraction of the WDC, only 17–25% of the N was truly dissolved (<3 kDa) at the gully sites compared to 58% in the sugarcane sites. Our results demonstrate the importance of colloidal N and the inaccuracy of assuming N < 0.45 µm is dissolved in the sampled areas, as well as providing an alternate explanation for the large amounts of what has previously been defined as dissolved inorganic N in runoff from non-fertilized grazing land. In particular, they describe why non-fertilized land uses can contribute significant N < 0.45 µm, and why catchment models of nutrient export based on soil N concentrations can over-estimate loads of particulate nitrogen derived from monitoring data (N > 0.45 µm). The findings suggest that managing soil erosion may also contribute to managing N < 0.45 µm.
Defining the architecture of KPC-2 Carbapenemase: identifying allosteric networks to fight antibiotics resistance
Authors: Galdadas Ioannis , Lovera Silvia , Pérez-Hernández Guillermo , Barnes Melissa D. , Healy Jess , Afsharikho Hamidreza , Woodford Neil , Bonomo Robert A. , Gervasio Francesco L. , Haider Shozeb 
Published: August 2018

AbstractThe rise of multi-drug resistance in bacterial pathogens is one of the grand challenges facing medical science. A major concern is the speed of development of β-lactamase-mediated resistance in Gram-negative species, thus putting at risk the efficacy of the most recently approved antibiotics and inhibitors, including carbapenems and avibactam, respectively. New strategies to overcome resistance are urgently required, which will ultimately be facilitated by a deeper understanding of the mechanisms that regulate the function of β-lactamases such as the Klebsiella Pneumoniae carbapenemases (KPCs). Using enhanced sampling computational methods together with site-directed mutagenesis, we report the identification of two “hydrophobic networks” in the KPC-2 enzyme, the integrity of which has been found to be essential for protein stability and corresponding resistance. Present throughout the structure, these networks are responsible for the structural integrity and allosteric signaling. Disruption of the networks leads to a loss of the KPC-2 mediated resistance phenotype, resulting in restored susceptibility to different classes of β-lactam antibiotics including carbapenems and cephalosporins. The ”hydrophobic networks” were found to be highly conserved among class-A β-lactamases, which implies their suitability for exploitation as a potential target for therapeutic intervention.