bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased temperatures may safeguard the nutritional quality of crops under future elevated CO2 concentrations
Authors: Köhler Iris H. , Huber Steven C. , Bernacchi Carl J. , Baxter Ivan R. 
Published: June 2018

SummaryIron (Fe) and zinc (Zn) deficiencies are a global human health problem that may worsen by growth of crops at elevated atmospheric CO2 concentration (eCO2). However, climate change will also involve higher temperature, but it is unclear how the combined effect of eCO2 and higher temperature will affect the nutritional quality of food crops. To begin to address this question, we grew soybean (Glycine max) in a Temperature by Free-Air CO2 Enrichment (T-FACE) experiment in 2014 and 2015 under ambient (400 μmol mol−1) and elevated (600 μmol mol−1) CO2 concentration and under ambient and elevated temperatures (+2.7 °C day and +3.4 °C at night). In our study, eCO2 significantly decreased Fe concentration in soybean seeds in both seasons (−8.7% and −7.7%) and Zn concentration in one season (−8.9%) while higher temperature (at ambient CO2 concentration) had the opposite effect. The combination of eCO2 with elevated temperature generally restored seed Fe and Zn concentrations to levels obtained under ambient CO2 and temperature conditions, suggesting that the potential threat to human nutrition by increasing CO2 concentration may not be realized. In general, seed Fe concentration was negatively correlated with yield suggesting inherent limitations to increasing seed Fe. In addition, we confirm our previous report that the concentration of seed storage products and several minerals varies with node position at which the seeds developed. Overall, these results demonstrate the complexity of predicting climate change effects on food security when various environmental parameters change in an interactive manner.
Inflammation induced by influenza virus impairs innate control of human pneumococcal carriage
Authors: Jochems Simon P. , Marcon Fernando , Carniel Beatriz F. , Holloway Mark , Mitsi Elena , Smith Emma , Gritzfeld Jenna F. , Solórzano Carla , Reiné Jesús , Pojar Sherin , Nikolaou Elissavet , German Esther L. , Hyder-Wright Angie , Hill Helen , Hales Caz , de Steenhuijsen Piters Wouter A.A , Bogaert Debby , Adler Hugh , Zaidi Seher , Connor Victoria , Rylance Jamie , Nakaya Helder I. , Ferreira Daniela M. 
Published: June 2018

AbstractSecondary bacterial pneumonia following influenza infection is a significant cause of mortality worldwide. Upper respiratory tract pneumococcal carriage is important as both determinants of disease and population transmission. The immunological mechanisms that contain pneumococcal carriage are well-studied in mice but remain unclear in humans. Loss of this control of carriage following influenza infection is associated with secondary bacterial pneumonia during seasonal and pandemic outbreaks. We used a human type 6B pneumococcal challenge model to show that carriage acquisition induces early degranulation of resident neutrophils and recruitment of monocytes to the nose. Monocyte function associated with clearance of pneumococcal carriage. Prior nasal infection with live attenuated influenza virus induced inflammation, impaired innate function and altered genome-wide nasal gene responses to pneumococcal carriage. Levels of the cytokine IP-10 promoted by viral infection at the time of pneumococcal encounter was positively associated with bacterial density. These findings provide novel insights in nasal immunity to pneumococcus and viral-bacterial interactions during co-infection.
Pins & Needles: Towards Limb Disownership in Augmented Reality
Authors: Kannape Oliver A , Smith Ethan JT , Moseley Peter , Roy Mark P , Lenggenhager Bigna 
Published: June 2018

ABSTRACTThe seemingly stable construct of our bodily self depends on the continued, successful integration of multisensory feedback about our body, rather than its purely physical composition. Accordingly, pathological disruption of such neural processing is linked to striking alterations of the bodily self, ranging from limb misidentification to disownership, and even the desire to amputate a healthy limb. While previous embodiment research has relied on experimental setups using supernumerary limbs in variants of the Rubber Hand Illusion, we here used Augmented Reality to directly manipulate the feeling of ownership for one’s own, biological limb. Using a Head-Mounted Display, participants received visual feedback about their own arm, from an embodied first-person perspective. In a series of three studies, in independent cohorts, we altered embodiment by providing visuotactile feedback that could be synchronous (control condition) or asynchronous (400ms delay, Real Hand Illusion). During the illusion, participants reported a significant decrease in ownership of their own limb, along with a lowered sense of agency. Supporting the right-parietal body network, we found an increased illusion strength for the left upper limb as well as a modulation of the feeling of ownership during anodal transcranial direct current stimulation. Extending previous research, these findings demonstrate that a controlled, visuotactile conflict about one’s own limb can be used to directly and systematically modulate ownership – without a proxy. This not only corroborates the malleability of body representation but questions its permanence. These findings warrant further exploration of combined VR and neuromodulation therapies for disorders of the bodily self.
TORC1 modulation in adipose tissue is required for organismal adaptation to hypoxia inDrosophila
Authors: Lee Byoungchun , Barretto Elizabeth C. , Grewal Savraj S. 
Published: June 2018

ABSTRACTAnimals often develop in conditions where environmental conditions such as food, oxygen and temperature fluctuate. The ability to adapt their metabolism to these fluctuations is important to ensure normal development and viability. In most animals, low oxygen (hypoxia) is deleterious, however some animals can alter their physiology to thrive under hypoxia. Here we show that TORC1 modulation in adipose tissue is required for organismal adaptation to hypoxia inDrosophila. We find that hypoxia rapidly suppresses TORC1 kinase signalling in Drosophila larvae via TSC-mediated inhibition of Rheb. We show that this hypoxia-mediated inhibition of TORC1 specifically in the larval fat body is essential for viable development to adulthood. Moreover, we find that these effects of TORC1 inhibition on hypoxia tolerance are mediated through remodeling of fat body lipid droplets and lipid storage. These studies identify the larval adipose tissue as a key hypoxia sensing tissue that coordinates whole-body development and survival to changes in environmental oxygen by modulating TORC1 and lipid storage.
High glucose-induced ubiquitylation of G6PD leads to the injury of podocyte
Authors: Wang Meng , Hu Ji , Yan Linling , Yang Yeping , He Min , Guo Shizhe , Wu Meng , Li Qin , Gong Wei , Yang Yang , Handy Diane E. , Lu Bin , Hao Chuanming , Wang Qinghua , Li Yiming , Hu Ronggui , Stanton Robert C. , Zhang Zhaoyun 
Published: June 2018

AbstractOxidative stress contributes substantially to podocyte injury in diabetic kidney disease. The mechanism of hyperglycemia-induced oxidative stress in podocytes is not fully understood. Glucose-6-phosphate dehydrogenase is critical in maintaining NADPH, an important cofactor for antioxidant system. Here, we hypothesized that high glucose induces ubiquitylation and degradation of G6PD, which injures podocytes by reactive oxygen species (ROS) accumulation. We found that both G6PD protein expression and G6PD activity was decreased in kidneys of both diabetic patients and diabetic rodents. Overexpressing G6PD reversed redox imbalance and podocyte apoptosis induced by high glucose and palmitate. Inhibition of G6PD induced podocyte apoptosis. In G6PD deficient mice, podocyte apoptosis was also largely increased. High glucose had no effect on G6PD mRNA level but it caused decreased G6PD protein expression, which was mediated by the ubiquitin proteasome pathway. Furthermore, von Hippel−Lindau (VHL), an E3 ubiquitin ligase subunit, directly bound to G6PD and degraded G6PD through ubiquitylating G6PD on lysine residues 366/403. Our data suggest that high glucose induces ubiquitylation of G6PD by VHL, which leads to ROS accumulation and podocyte injury.
Timed collinear activation of Hox genes during gastrulation controls the avian forelimb position
Authors: Moreau Chloe , Caldarelli Paolo , Rocancourt Didier , Roussel Julian , Denans Nicolas , Pourquie Olivier , Gros Jerome 
Published: June 2018

SummaryLimb position along the body is highly consistent within one species but very variable among vertebrates. Despite major advances in our understanding of limb patterning in three dimensions, how limbs reproducibly form along the anteroposterior axis remains largely unknown. Hox genes have long been suspected to control limb position, however supporting evidences are mostly correlative and their role in this process remains unclear. Here we show that Hox genes determine the avian forelimb position in a two-step process: first, their sequential collinear activation during gastrulation controls the relative position of their own successive expression domains along the body axis. Then, within these collinear domains, Hox genes differentially activate or repress the genetic cascade responsible for forelimb initiation. Furthermore, we provide evidences that changes in the timing of collinear Hox gene activation might underlie natural variation in forelimb position between different birds. Altogether our results which characterize the cellular and molecular mechanisms underlying the regulation and natural variation of forelimb position in avians, show a direct and early role for Hox genes in this process.
Measuring narrative engagement: The heart tells the story
Authors: Richardson Daniel C. , Griffin Nicole K. , Zaki Lara , Stephenson Auburn , Yan Jiachen , Curry Thomas , Noble Richard , Hogan John , Skipper Jeremy I. , Devlin Joseph T. 
Published: June 2018

AbstractStories play a fundamental role in human culture. They provide a mechanism for sharing cultural identity, imparting knowledge, revealing beliefs, reinforcing social bonds and providing entertainment that is central to all human societies. Here we investigated the extent to which the delivery medium of a story (audio or visual) affected conscious and subconscious engagement with the narrative. Although participants self-reported greater involvement for watching video relative to listening to auditory scenes, stronger physiological responses were recorded for auditory stories. Sensors placed at their wrists showed higher and more variable heart rates, greater electrodermal activity, and even higher body temperatures. We interpret these findings as physiological evidence that the stories were more cognitively and emotionally engaging when presented in an auditory format. This may be because listening to a story, rather than watching a video, is a more active process of co-creation, and that this imaginative process in the listener’s mind is detectable on the skin at their wrist.
An Equivariant Bayesian Convolutional Network predicts recombination hotspots and accurately resolves binding motifs
Authors: Brown Richard , Lunter Gerton 
Published: June 2018

AbstractMotivationConvolutional neural networks (CNNs) have been trememdously successful in many contexts, particularly where training data is abundant and signal-to-noise ratios are large. However, when predicting noisily observed biological phenotypes from DNA sequence, each training instance is only weakly informative, and the amount of training data is often fundamentally limited, emphasizing the need for methods that make optimal use of training data and any structure inherent in the model.ResultsHere we show how to combine equivariant networks, a general mathematical framework for handling exact symmetries in CNNs, with Bayesian dropout, a version of MC dropout suggested by a reinterpretation of dropout as a variational Bayesian approximation, to develop a model that exhibits exact reverse-complement symmetry and is more resistant to overtraining. We find that this model has increased power and generalizability, resulting in significantly better predictive accuracy compared to standard CNN implementations and state-of-art deep-learning-based motif finders. We use our network to predict recombination hotspots from sequence, and identify high-resolution binding motifs for the recombination-initiation protein PRDM9, which were recently validated by high-resolution assays. The network achieves a predictive accuracy comparable to that attainable by a direct assay of the H3K4me3 histone mark, a proxy for PRDM9 binding.Availabilityhttps://github.com/luntergroup/EquivariantNetworksContactrichard.brown@well.ox.ac.uk, gerton.lunter@well.ox.ac.ukSupplementary informationSupplementary data are available at Bioinformatics online.
Non-invasive ultrasonic modulation of visual evoked response by GABA delivery through the blood brain barrier
Authors: Constans C. , Ahnine H. , Santin M. D. , Lehericy S. , Tanter M. , Pouget P. , Aubry J-F 
Published: June 2018

AbstractWe demonstrate the feasibility of non-invasively modulating the visual cortex activity of non-human primates by local ultrasound-induced delivery of an inhibitory neurotransmitter (GABA). GABA was injected intravenously after the blood brain barrier (BBB) was transiently disrupted with focused ultrasound (FUS) coupled with ultrasound contrast agents (UCA). Visual evoked potentials exhibited a significant and progressive decrease of the activity. Combined effects of neuromodulation and BBB opening were shown to be 8.7 times less important than GABA-induced inhibition. During the sonication, the UCA harmonic response was monitored to estimate the level of stable cavitation (signature of BBB opening efficiency) and to avoid damages due to inertial cavitation (automatic shutdown of the sonication when detected). As recent developments in beam forming have shown that ultrasound beams can be focused non-invasively in deep-seated human brain locations, our results hold promise to explore and treat the brain with a non-invasive, controllable, repeatable and reversible method.
Chromosome polymorphisms track trans-Atlantic divergence, admixture and adaptive evolution in salmon
Authors: Lehnert Sarah J. , Bentzen Paul , Kess Tony , Lien Sigbjørn , Horne John B. , Clément Marie , Bradbury Ian R. 
Published: June 2018

AbstractPleistocene glaciations drove repeated range contractions and expansions shaping contemporary intraspecific diversity. Atlantic salmon (Salmo salar) from the western and eastern Atlantic range diverged >600K YBP, with each clade isolated in independent southern refugia during glacial maxima, driving trans-Atlantic genomic and karyotypic differences. Here, we investigate genomic consequences of glacial isolation and transAtlantic secondary contact using a 220K single nucleotide polymorphism (SNP) array genotyped in 80 North American and European populations. Throughout North America, we identified large inter-individual variation and discrete linkage blocks within and between chromosomes with known rearrangements: Ssa01/Ssa23 translocation and Ssa08/Ssa29 fusion. Spatial genetic analyses suggest independence of rearrangements, with Ssa01/Ssa23 showing high European introgression (>50%) in northern populations indicative of post-glacial trans-Atlantic secondary contact, contrasting low European ancestry genome-wide (3%). Ssa08/Ssa29 showed greater intra-population diversity suggesting a derived chromosome fusion polymorphism within North America. Evidence of selection on both regions suggests adaptive variation associated with karyotypes. Our study highlights how Pleistocene glaciations can drive large-scale intraspecific variation in genomic architecture of northern species.
Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion
Authors: Gutierrez Jahir M. , Feizi Amir , Li Shangzhong , Kallehauge Thomas B. , Hefzi Hooman , Grav Lise M. , Ley Daniel , Hizal Deniz Baycin , Betenbaugh Michael J. , Voldborg Bjorn , Kildegaard Helene Faustrup , Lee Gyun Min , Palsson Bernhard O. , Nielsen Jens , Lewis Nathan E. 
Published: June 2018

AbstractIn mammalian cells, >25% of synthesized proteins are exported through the secretory pathway. The pathway complexity, however, obfuscates its impact on the secretion of different proteins. Unraveling its impact on diverse proteins is particularly important for biopharmaceutical production. Here we delineate the core secretory pathway functions and integrate them with genome-scale metabolic reconstructions of human, mouse, and Chinese hamster cells. The resulting reconstructions enable the computation of energetic costs and machinery demands of each secreted protein. By integrating additional omics data, we find that highly secretory cells have adapted to reduce expression and secretion of other expensive host cell proteins. Furthermore, we predict metabolic costs and maximum productivities of biotherapeutic proteins and identify protein features that most significantly impact protein secretion. Finally, the model successfully predicts the increase in secretion of a monoclonal antibody after silencing a highly expressed selection marker. This work represents a knowledgebase of the mammalian secretory pathway that serves as a novel tool for systems biotechnology.
The genome and metabolome of the tobacco tree, Nicotiana glauca: a potential renewable feedstock for the bioeconomy
Authors: Usade Björn , Tohge Takayuki , Scossa Federico , Sierro Nicolas , Schmidt Maximilian , Vogel Alexander , Bolger Anthony , Kozlo Amanda , Enfissi Eugenia MA , Morrel Kris , Regenauer Manuel , Hallab Asis , Ruprecht Colin , Gundlach Heidrun , Spannagl Manuel , Koram Yaw , Mayer Klaus FX , Boerjan Wout , Fraser Paul D. , Persson Staffan , Ivanov Nikolai V. , Fernie Alisdair R. 
Published: June 2018

AbstractBackgroundGiven its tolerance to stress and its richness in particular secondary metabolites, the tobacco tree, Nicotiana glauca, has been considered a promising biorefinery feedstock that would not be competitive with food and fodder crops.ResultsHere we present a 3.5 Gbp draft sequence and annotation of the genome of N. glauca spanning 731,465 scaffold sequences, with an N50 size of approximately 92 kbases. Furthermore, we supply a comprehensive transcriptome and metabolome analysis of leaf development comprising multiple techniques and platforms.The genome sequence is predicted to cover nearly 80% of the estimated total genome size of N. glauca. With 73,799 genes predicted and a BUSCO score of 94.9%, we have assembled the majority of gene-rich regions successfully. RNA-Seq data revealed stage-and/or tissue-specific expression of genes, and we determined a general trend of a decrease of tricarboxylic acid cycle metabolites and an increase of terpenoids as well as some of their corresponding transcripts during leaf development.ConclusionThe N. glauca draft genome and its detailed transcriptome, together with paired metabolite data, constitute a resource for future studies of valuable compound analysis in tobacco species and present the first steps towards a further resolution of phylogenetic, whole genome studies in tobacco.
Retrospective cues mitigate information loss in human cortex during working memory storage
Authors: Ester Edward F. , Nouri Asal , Rodriguez Laura 
Published: June 2018

AbstractWorking memory (WM) enables the flexible representation of information over short intervals. It is well-established that WM performance can be enhanced by a retrospective cue presented during storage, yet the neural mechanisms responsible for this benefit are unclear. Here, we tested several explanations for retro-cue benefits by quantifying changes in spatial WM representations reconstructed from alpha-band (8-12 Hz) EEG activity recorded from human participants (both sexes) before and after presentation of a retrospective cue. This allowed us to track cue-related changes in WM representations with high temporal resolution (tens of milliseconds). Participants encoded the locations of two colored discs for subsequent report. During neutral trials an uninformative cue instructed participants to remember the locations of both discs across a blank delay, and we observed a monotonic decrease in the fidelity of reconstructed spatial WM representations with time. During valid trials a 100% reliable cue indicated the color of the disc participants would be probed to report. Critically, valid cues were presented immediately after termination of the encoding display (“valid early”, or VE trials) or midway through the delay period (“valid late” or VL trials). During VE trials the gradual loss of location-specific information observed during neutral trials was eliminated, while during VL trials it was partially reversed. Our findings suggest that retro-cues engage several different mechanisms that together serve to mitigate information loss during WM storage.Significance StatementWorking memory (WM) performance can be improved by a cue presented during storage. This effect, termed a retrospective cue benefit, has been used to explore the limitations of attentional prioritization in WM. However, the mechanisms responsible for retrospective cue benefits are unclear. Here we tested several explanations for retrospective cue benefits by examining how they influence WM representations reconstructed from human EEG activity. This approach allowed us to visualize, quantify, and track the effects of retrospective cues with high temporal resolution (on the order of tens of milliseconds). We show that under different circumstances retrospective cues can both eliminate and even partially reverse information loss during WM storage, suggesting that retrospective cue benefits have manifold origins.
Cuticular hydrocarbon divergence in Drosophila melanogaster populations evolving under differential operational sex ratios
Authors: Dutta Rochishnu , Chechi Tejinder Singh , Yadav Ankit , Prasad Nagaraj Guru 
Published: June 2018

AbstractThe ability of interlocus sexual conflict to facilitate reproductive isolation is widely anticipated. However, very few experimental evolutionary studies have convincingly demonstrated the evolution of reproductive isolation due to sexual conflict. Recently a study on replicate populations of Drosophila melanogaster under differential sexual conflict found that divergent mate preference evolved among replicate populations under high sexual conflict regime. The precopulatory isolating mechanism underlying such divergent mate preference could be sexual signals such as cuticular hydrocarbons since they evolve rapidly and are involved in D. melanogaster mate recognition. Using D. melanogaster replicates used in the previous study, we investigate whether cuticular hydrocarbon divergence bears signatures of sexually antagonistic coevolution that led to reproductive isolation among replicates of high sexual conflict regime. We found that D. melanogaster cuticular hydrocarbon profiles are sexually dimorphic. Although replicate populations under high sexual conflict displayed assortative mating, we found no significant differences in the cuticular hydrocarbon profile between the high and low sexual conflict regimes. Instead we find cuticular hydrocarbon divergence patterns to be suggestive of the Buridan’s Ass regime which is one of the six possible mechanisms to resolve sexual conflict. Sexual selection that co-vary between populations under high and low sexual conflict regimes may also have contributed to the evolution of cuticular hydrocarbons. This study indicates that population differentiation as a result of cuticular hydrocarbon divergence cannot be credited to sexual conflict despite high sexual conflict regime evolving divergent cuticular hydrocarbon profiles.