bluuebunny/crossref_metadata_2025_split huggingface dataset:
More frequent extreme climate events stabilize reindeer population dynamics
Authors: Hansen Brage B. , Gamelon Marlène , Albon Steve D. , Lee Aline M. , Stien Audun , Irvine R. Justin , Sæther Bernt-Erik , Loe Leif E. , Ropstad Erik , Veiberg Vebjørn , Grøtan Vidar 
Published: April 2019

AbstractExtreme climate events often cause population crashes but are difficult to account for in population-dynamic studies. Especially in long-lived animals, density dependence and demography may induce lagged impacts of perturbations on population growth. In Arctic ungulates, extreme rain-on-snow and ice-locked pastures have led to severe population crashes, indicating that increasingly frequent rain-on-snow events could destabilize populations. Here, using empirically parameterized, stochastic population models for High-Arctic wild reindeer, we show that more frequent rain-on-snow events actually reduce extinction risk and stabilize population dynamics due to interactions with age structure and density dependence. Extreme rain-on-snow events mainly suppress vital rates of vulnerable ages at high population densities, resulting in a crash and a new population state with resilient ages and reduced population sensitivity to subsequent icy winters. Thus, observed responses to single extreme events are poor predictors of population dynamics and persistence because internal density-dependent feedbacks act as a buffer against more frequent events.
Directly visualizing the sign change of d-wave superconducting gap in Bi2Sr2CaCu2O8+δ by phase-referenced quasiparticle interference
Authors: Gu Qiangqiang , Wan Siyuan , Tang Qingkun , Du Zengyi , Yang Huan , Wang Qiang-Hua , Zhong Ruidan , Wen Jinsheng , Gu G. D. , Wen Hai-Hu 
Published: April 2019

AbstractThe superconducting state is formed by the condensation of Cooper pairs and protected by the superconducting gap. The pairing interaction between the two electrons of a Cooper pair determines the gap function. Thus, it is pivotal to detect the gap structure for understanding the mechanism of superconductivity. In cuprate superconductors, it has been well established that the gap may have a d-wave function. This gap function has an alternative sign change in the momentum space. It is however hard to visualize this sign change. Here we report the measurements of scanning tunneling spectroscopy in Bi2Sr2CaCu2O8+δ and conduct the analysis of phase-referenced quasiparticle interference (QPI). We see the seven basic scattering vectors that connect the octet ends of the banana-shaped contour of Fermi surface. The phase-referenced QPI clearly visualizes the sign change of the d-wave gap. Our results illustrate an effective way for determining the sign change of unconventional superconductors.
Comparative transcriptomics of social insect queen pheromones
Authors: Holman Luke , Helanterä Heikki , Trontti Kalevi , Mikheyev Alexander S. 
Published: April 2019

AbstractQueen pheromones are chemical signals that mediate reproductive division of labor in eusocial animals. Remarkably, queen pheromones are composed of identical or chemically similar compounds in some ants, wasps and bees, even though these taxa diverged >150MYA and evolved queens and workers independently. Here, we measure the transcriptomic consequences of experimental exposure to queen pheromones in workers from two ant and two bee species (genera: Lasius, Apis, Bombus), and test whether they are similar across species. Queen pheromone exposure affected transcription and splicing at many loci. Many genes responded consistently in multiple species, and the set of pheromone-sensitive genes was enriched for functions relating to lipid biosynthesis and transport, olfaction, production of cuticle, oogenesis, and histone (de)acetylation. Pheromone-sensitive genes tend to be evolutionarily ancient, positively selected, peripheral in the gene coexpression network, hypomethylated, and caste-specific in their expression. Our results reveal how queen pheromones achieve their effects, and suggest that ants and bees use similar genetic modules to achieve reproductive division of labor.
Iron and sulfide nanoparticle formation and transport in nascent hydrothermal vent plumes
Authors: Findlay Alyssa J. , Estes Emily R. , Gartman Amy , Yücel Mustafa , Kamyshny Alexey , Luther George W. 
Published: April 2019

AbstractDeep-sea hydrothermal vents are a significant source of dissolved metals to the global oceans, producing midwater plumes enriched in metals that are transported thousands of kilometers from the vent source. Particle precipitation upon emission of hydrothermal fluids controls metal speciation and the magnitude of metal export. Here, we document metal sulfide particles, including pyrite nanoparticles, within the first meter of buoyant plumes from three high-temperature vents at the East Pacific Rise. We observe a zone of particle settling 10–20 cm from the orifice, indicated by stable sulfur isotopes; however, we also demonstrate that nanoparticulate pyrite (FeS2) is not removed from the plume and can account for over half of the filtered Fe (≤0.2 µm) up to one meter from the vent orifice. The persistence of nanoparticulate pyrite demonstrates that it is an important mechanism for near-vent Fe stabilisation and highlights the potential role of nanoparticles in element transport.
An artificial triazole backbone linkage provides a split-and-click strategy to bioactive chemically modified CRISPR sgRNA
Authors: Taemaitree Lapatrada , Shivalingam Arun , El-Sagheer Afaf H. , Brown Tom 
Published: April 2019

AbstractAs the applications of CRISPR-Cas9 technology diversify and spread beyond the laboratory to diagnostic and therapeutic use, the demands of gRNA synthesis have increased and access to tailored gRNAs is now restrictive. Enzymatic routes are time-consuming, difficult to scale-up and suffer from polymerase-bias while existing chemical routes are inefficient. Here, we describe a split-and-click convergent chemical route to individual or pools of sgRNAs. The synthetic burden is reduced by splitting the sgRNA into a variable DNA/genome-targeting 20-mer, produced on-demand and in high purity, and a fixed Cas9-binding chemically-modified 79-mer, produced cost-effectively on large-scale, a strategy that provides access to site-specific modifications that enhance sgRNA activity and in vivo stability. Click ligation of the two components generates an artificial triazole linkage that is tolerated in functionally critical regions of the sgRNA and allows efficient DNA cleavage in vitro as well as gene-editing in cells with no unexpected off-target effects.
Sec14l3 potentiates VEGFR2 signaling to regulate zebrafish vasculogenesis
Authors: Gong Bo , Li Zhihao , Xiao Wanghua , Li Guangyuan , Ding Shihui , Meng Anming , Jia Shunji 
Published: April 2019

AbstractVascular endothelial growth factor (VEGF) regulates vasculogenesis by using its tyrosine kinase receptors. However, little is known about whether Sec14-like phosphatidylinositol transfer proteins (PTP) are involved in this process. Here, we show that zebrafish sec14l3, one of the family members, specifically participates in artery and vein formation via regulating angioblasts and subsequent venous progenitors’ migration during vasculogenesis. Vascular defects caused by sec14l3 depletion are partially rescued by restoration of VEGFR2 signaling at the receptor or downstream effector level. Biochemical analyses show that Sec14l3/SEC14L2 physically bind to VEGFR2 and prevent it from dephosphorylation specifically at the Y1175 site by peri-membrane tyrosine phosphatase PTP1B, therefore potentiating VEGFR2 signaling activation. Meanwhile, Sec14l3 and SEC14L2 interact with RAB5A/4A and facilitate the formation of their GTP-bound states, which might be critical for VEGFR2 endocytic trafficking. Thus, we conclude that Sec14l3 controls vasculogenesis in zebrafish via the regulation of VEGFR2 activation.
SNAREs define targeting specificity of trafficking vesicles by combinatorial interaction with tethering factors
Authors: Koike Seiichi , Jahn Reinhard 
Published: April 2019

AbstractMembrane traffic operates by vesicles that bud from precursor organelles and are transported to their target compartment where they dock and fuse. Targeting requires tethering factors recruited by small GTPases and phosphoinositides whereas fusion is carried out by SNARE proteins. Here we report that vesicles containing the Q-SNAREs syntaxin 13 (Stx13) and syntaxin 6 (Stx6) together are targeted to a different endosomal compartment than vesicles containing only Stx6 using injection of artificial vesicles. Targeting by Stx6 requires Vps51, a component of the GARP/EARP tethering complexes. In contrast, targeting by both Stx6 and Stx13 is governed by Vps13B identified here as tethering factor functioning in transport from early endosomes to recycling endosomes. Vps13B specifically binds to Stx13/Stx6 as well as to Rab14, Rab6, and PtdIns(3)P. We conclude that SNAREs use a combinatorial code for recruiting tethering factors, revealing a key function in targeting that is independent of SNARE pairing during fusion.
Acute exposure to diesel exhaust induces central nervous system stress and altered learning and memory in honey bees
Authors: Reitmayer Christine M. , Ryalls James M. W. , Farthing Emily , Jackson Christopher W. , Girling Robbie D. , Newman Tracey A. 
Published: April 2019

AbstractFor effective foraging, many insect pollinators rely on the ability to learn and recall floral odours, behaviours that are associated with a complex suite of cellular processes. Here, we investigated how acute exposure to a high-dose of diesel exhaust (containing 19.8 and 17.5 ppm of NO and NO2, respectively) affected associative learning behaviour of honey bees (Apis mellifera) and expression of a ubiquitous heat shock protein, HSP70, in their central nervous system (CNS). To determine whether exposure to diesel exhaust would alter their tolerance to a subsequent abiotic stress, we further subjected individuals to heat stress. Diesel exhaust exposure decreased honey bees’ ability to learn and recall a conditioned odour stimulus. Whilst there was no significant difference in CNS HSP70 expression between honey bees exposed to either diesel exhaust or clean air across the entire duration of the experiment (3.5 h), there was a significant effect of time and a significant interaction between exposure treatment and time. This interaction was investigated using correlation analyses, which demonstrated that only in the diesel exhaust exposed honey bees was there a significant positive correlation between HSP70 expression and time. Furthermore, there was a 44% reduction in honey bee individuals that were able to recall the odour 72 h after diesel exposure compared with clean air control individuals. Moreover, diesel exhaust affected A. mellifera in a way that reduced their ability to survive a second subsequent stressor. Such negative effects of air pollution on learning, recall, and stress tolerance has potential to reduce foraging efficiency and pollination success of individual honey bees.
A marker of glutathione S-transferase-mediated resistance to insecticides is associated with higher Plasmodium infection in the African malaria vector Anopheles funestus
Authors: Tchouakui Magellan , Chiang Mu-Chun , Ndo Cyrille , Kuicheu Carine K. , Amvongo-Adjia Nathalie , Wondji Murielle J. , Tchoupo Micareme , Kusimo Michael O. , Riveron Jacob M. , Wondji Charles S. 
Published: April 2019

AbstractMetabolic resistance to insecticides is threatening malaria control in Africa. However, the extent to which it impacts malaria transmission remains unclear. Here, we investigated the association between a marker of glutathione S-transferase mediated metabolic resistance and Plasmodium infection in field population of Anopheles funestus s.s. in comparison to the A296S-RDL target site mutation. The 119F-GSTe2 resistant allele was present in southern (Obout) (56%) and central (Mibellon) (25%) regions of Cameroon whereas the 296S-RDL resistant allele was detected at 98.5% and 15% respectively. The whole mosquito Plasmodium and sporozoite infection rates were 57% and 14.8% respectively in Obout (n = 508) and 19.7% and 5% in Mibellon (n = 360). No association was found between L119F-GSTe2 genotypes and whole mosquito infection status. However, when analyzing oocyst and sporozoite infection rates separately, the resistant homozygote 119F/F genotype was significantly more associated with Plasmodium infection in Obout than both heterozygote (OR = 2.5; P = 0.012) and homozygote susceptible (L/L119) genotypes (OR = 2.10; P = 0.013). In contrast, homozygote RDL susceptible mosquitoes (A/A296) were associated more frequently with Plasmodium infection than other genotypes (OR = 4; P = 0.03). No additive interaction was found between L119F and A296S. Sequencing of the GSTe2 gene showed no association between the polymorphism of this gene and Plasmodium infection. Glutathione S-transferase metabolic resistance is potentially increasing the vectorial capacity of resistant An. funestus mosquitoes. This could result in a possible exacerbation of malaria transmission in areas of high GSTe2-based metabolic resistance to insecticides.
Anisotropy vs isotropy in living cell indentation with AFM
Authors: Efremov Yuri M. , Velay-Lizancos Mirian , Weaver Cory J. , Athamneh Ahmad I. , Zavattieri Pablo D. , Suter Daniel M. , Raman Arvind 
Published: April 2019

AbstractThe measurement of local mechanical properties of living cells by nano/micro indentation relies on the foundational assumption of locally isotropic cellular deformation. As a consequence of assumed isotropy, the cell membrane and underlying cytoskeleton are expected to locally deform axisymmetrically when indented by a spherical tip. Here, we directly observe the local geometry of deformation of membrane and cytoskeleton of different living adherent cells during nanoindentation with the integrated Atomic Force (AFM) and spinning disk confocal (SDC) microscope. We show that the presence of the perinuclear actin cap (apical stress fibers), such as those encountered in cells subject to physiological forces, causes a strongly non-axisymmetric membrane deformation during indentation reflecting local mechanical anisotropy. In contrast, axisymmetric membrane deformation reflecting mechanical isotropy was found in cells without actin cap: cancerous cells MDA-MB-231, which naturally lack the actin cap, and NIH 3T3 cells in which the actin cap is disrupted by latrunculin A. Careful studies were undertaken to quantify the effect of the live cell fluorescent stains on the measured mechanical properties. Using finite element computations and the numerical analysis, we explored the capability of one of the simplest anisotropic models – transverse isotropy model with three local mechanical parameters (longitudinal and transverse modulus and planar shear modulus) – to capture the observed non-axisymmetric deformation. These results help identifying which cell types are likely to exhibit non-isotropic properties, how to measure and quantify cellular deformation during AFM indentation using live cell stains and SDC, and suggest modelling guidelines to recover quantitative estimates of the mechanical properties of living cells.
Characterisation of graphene electrodes for microsystems and microfluidic devices
Authors: Del Rosso Michelle , Brodie C. Harrison , Ramalingam Saipriya , Cabral David M. , Pensini Erica , Singh Ashutosh , Collier Christopher M. 
Published: April 2019

AbstractFabrication of microsystems is traditionally achieved with photolithography. However, this fabrication technique can be expensive and non-ideal for integration with microfluidic systems. As such, graphene fabrication is explored as an alternative. This graphene fabrication can be achieved with graphite oxide undergoing optical exposure, using optical disc drives, to impose specified patterns and convert to graphene. This work characterises such a graphene fabrication, and provides fabrication, electrical, microfluidic, and scanning electron microscopy (SEM) characterisations. In the fabrication characterisation, a comparison is performed between traditional photolithography fabrication and the new graphene fabrication. (Graphene fabrication details are also provided.) Here, the minimum achievable feature size is identified and graphene fabrication is found to compare favourably with traditional photolithography fabrication. In the electrical characterisation, the resistivity of graphene is measured as a function of fabrication dose in the optical disc drive and saturation effects are noted. In the microfluidic characterisation, the wetting properties of graphene are shown through an investigation of the contact angle of a microdroplet positioned on a surface that is treated with varying fabrication dose. In the SEM characterisation, the observed effects in the previous characterisations are attributed to chemical or physical effects through measurement of SEM energy dispersive X-ray spectra and SEM images, respectively. Overall, graphene fabrication is revealed to be a viable option for development of microsystems and microfluidics.
Unveiling the potentials of biocompatible silver nanoparticles on human lung carcinoma A549 cells and Helicobacter pylori
Authors: Saravanakumar Kandasamy , Chelliah Ramachandran , MubarakAli Davoodbasha , Oh Deog-Hwan , Kathiresan Kandasamy , Wang Myeong-Hyeon 
Published: April 2019

AbstractSilver nanoparticles (AgNPs) are gaining importance in health and environment. This study synthesized AgNPs using the bark extract of a plant, Toxicodendron vernicifluum (Tv) as confirmed by a absorption peak at 420 nm corresponding to the Plasmon resonance of AgNPs. The AgNPs were spherical, oval-shaped with size range of 2–40 nm as evident by field emission transmission electron microscopy (FE-TEM) and particle size analysis (PSA). The particles formed were crystalline by the presence of (111), (220) and (200) planes, as revealed by X ray diffraction (XRD) and energy dispersive spectroscopy (EDS). The presence of amine, amide, phenolic, and alcoholic aromatics derived from Tv extract was found to be capping and or reducing agents as evident by Fourier-transform infrared spectroscopy (FTIR) spectra. The Tv-AgNPs were observed to be biocompatible to chick embryonic and NIH3T3 cells at various concentrations. Interestingly, Tv-AgNPs at the concentration of 320 µg. mL−1 induced 82.5% of cell death in human lung cancer, A549 cells and further 95% of cell death with annexin V FITC/PI based apoptosis. The Tv-AgNPs selectively targeted and damaged the cancer cells through ROS generation. The Tv-AgNPs displayed minimal inhibitory concentration (MIC) of 8.12 µg.mL−1 and 18.14 µg.mL−1 against STEC and H. pylori respectively. This multi-potent property of Tv-AgNPs was due to shape and size specific property that facilitated easy penetration into the bacterial and cancer cells for targeted therapy.
µSpikeHunter: An advanced computational tool for the analysis of neuronal communication and action potential propagation in microfluidic platforms
Authors: Heiney Kristine , Mateus José C. , Lopes Cátia D. F. , Neto Estrela , Lamghari Meriem , Aguiar Paulo 
Published: April 2019

AbstractUnderstanding neuronal communication is fundamental in neuroscience, but there are few methodologies offering detailed analysis for well-controlled conditions. By interfacing microElectrode arrays with microFluidics (μEF devices), it is possible to compartmentalize neuronal cultures with a specified alignment of axons and microelectrodes. This setup allows the extracellular recording of spike propagation with a high signal-to-noise ratio over the course of several weeks. Addressing these μEF devices, we developed an advanced yet easy-to-use publically available computational tool, μSpikeHunter, which provides a detailed quantification of several communication-related properties such as propagation velocity, conduction failure, spike timings, and coding mechanisms. The combination of μEF devices and μSpikeHunter can be used in the context of standard neuronal cultures or with co-culture configurations where, for example, communication between sensory neurons and other cell types is monitored and assessed. The ability to analyze axonal signals (in a user-friendly, time-efficient, high-throughput manner) opens the door to new approaches in studies of peripheral innervation, neural coding, and neuroregeneration, among many others. We demonstrate the use of μSpikeHunter in dorsal root ganglion neurons where we analyze the presence of both anterograde and retrograde signals in μEF devices. A fully functional version of µSpikeHunter is publically available for download from https://github.com/uSpikeHunter.
Predicting knee osteoarthritis severity: comparative modeling based on patient’s data and plain X-ray images
Authors: Abedin Jaynal , Antony Joseph , McGuinness Kevin , Moran Kieran , O’Connor Noel E. , Rebholz-Schuhmann Dietrich , Newell John 
Published: April 2019

AbstractKnee osteoarthritis (KOA) is a disease that impairs knee function and causes pain. A radiologist reviews knee X-ray images and grades the severity level of the impairments according to the Kellgren and Lawrence grading scheme; a five-point ordinal scale (0–4). In this study, we used Elastic Net (EN) and Random Forests (RF) to build predictive models using patient assessment data (i.e. signs and symptoms of both knees and medication use) and a convolution neural network (CNN) trained using X-ray images only. Linear mixed effect models (LMM) were used to model the within subject correlation between the two knees. The root mean squared error for the CNN, EN, and RF models was 0.77, 0.97 and 0.94 respectively. The LMM shows similar overall prediction accuracy as the EN regression but correctly accounted for the hierarchical structure of the data resulting in more reliable inference. Useful explanatory variables were identified that could be used for patient monitoring before X-ray imaging. Our analyses suggest that the models trained for predicting the KOA severity levels achieve comparable results when modeling X-ray images and patient data. The subjectivity in the KL grade is still a primary concern.
Uncoupling of in-vitro identity of embryonic limb derived skeletal progenitors and their in-vivo bone forming potential
Authors: Verbeeck Louca , Geris Liesbet , Tylzanowski Przemko , Luyten Frank P. 
Published: April 2019

AbstractThe healing of large bone defects remains a major unmet medical need. Our developmental engineering approach consists of the in vitro manufacturing of a living cartilage tissue construct that upon implantation forms bone by recapitulating an endochondral ossification process. Key to this strategy is the identification of the cells to produce such cartilage intermediates efficiently. We applied a cell selection strategy based on published skeletal stem cell markers using mouse embryonic limb cartilage as cell source and analysed their potential to form bone in an in vivo ectopic assay. FGF2 supplementation to the culture media for expansion blocked dedifferentiation of the embryonic cartilage cells in culture and enriched for stem cells and progenitors as quantified using the recently published CD marker set. However, when the stem cells and progenitors were fractionated from expanded embryonic cartilage cells and assessed in the ectopic assay, a major loss of bone forming potential was observed. We conclude that cell expansion appears to affect the association between cell identity based on CD markers and in vivo bone forming capacity.