bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cerebellar Atrophy in Adult Survivors of Childhood Cerebellar Tumor
Authors: Ailion Alyssa S. , King Tricia Z. , Wang Liya , Fox Michelle, E. , Mao Hui , Morris Robin M. , Crosson Bruce 
Published: March 2016

AbstractObjectives: The cerebellum (CB) is known for its role in supporting processing speed (PS) and cognitive efficiencies. The CB often sustains damage from treatment and resection in pediatric patients with posterior fossa tumors. Limited research suggests that CB atrophy may be associated with the radiation treatment experienced during childhood. The purpose of the study was to measure cerebellar atrophy to determine its neurobehavioral correlates. Methods: Brain magnetic resonance images were collected from 25 adult survivors of CB tumors and age- and gender-matched controls (Mage=24 years (SD=5), 52% female). Average age at diagnosis was 9 years (SD=5) and average time since diagnosis was 15 years (SD=5). PS was measured by the Symbol Digit Modality Test. To quantify atrophy, an objective formula was developed based on prior literature, in which Atrophy=[(CB White+CB Gray Volume)/Intracranial Vault (ICV)]controls-[(CB White+CB Gray+Lesion Size Volume)/ICV]survivors. Results: Regression analyses found that the interaction term (age at diagnosis*radiation) predicts CB atrophy; regression equations included the Neurological Predictor Scale, lesion size, atrophy, and the interaction term and accounted for 33% of the variance in oral PS and 48% of the variance in written PS. Both interactions suggest that individuals with smaller CB lesion size but a greater degree of CB atrophy had slower PS, whereas individuals with a larger CB lesion size and less CB atrophy were less affected. Conclusion: The results of the current study suggest that young age at diagnosis and radiation is associated with CB atrophy, which interacts with lesion size to impact both written and oral PS. (JINS, 2016, 23, 1–11)
Microstructural Characterization of Aluminum-Carbon Nanotube Nanocomposites Produced Using Different Dispersion Methods
Authors: Simões Sónia , Viana Filomena , Reis Marcos A. L. , Vieira Manuel F. 
Published: March 2016

AbstractThis research focuses on characterization of the impact of dispersion methods on aluminum-carbon nanotubes (Al-CNTs) nanocomposite structure. Nanocomposites were produced by a conventional powder metallurgy process after the dispersion of the CNTs on the Al powders, using two approaches: (1) the dispersion of CNTs and mixture with Al powders were performed in a single step by ultrasonication; and (2) the CNTs were previously untangled by ultrasonication and then mixed with Al powders by ball milling. Microstructural characterization of Al-CNT nanocomposites was performed by optical microscopy, scanning and transmission electron microscopy, electron backscatter diffraction, and high-resolution transmission electron microscopy (HRTEM). Microstructural characterization revealed that the use of ball milling for mixing CNTs with Al powders promoted the formation of CNT clusters of reduced size, more uniformly dispersed in the matrix, and a nanocomposite of smaller grain size. However, the results of HRTEM and Raman spectroscopy show that ball milling causes higher damage to the CNT structure. The strengthening effect of the CNT is attested by the increase in hardness and tensile strength of the nanocomposites.
Genetic polymorphisms among and between blast disease resistant and susceptible finger millet,Eleusine coracana(L.) Gaertn.
Authors: Saha Dipnarayan , Rana Rajeev Singh , Arya Lalit , Verma Manjusha , Gowda M. V. Channabyre , Upadhyaya Hari D. 
Published: March 2016

AbstractFungal blast disease is one of the major constraints in finger millet production. Breeding for disease resistance in finger millet, needs characterization of genetic polymorphism among and between the resistant and susceptible genotypes. In total, 67 finger millet genotypes, which are resistant or susceptible to fungal blast disease, were analysed using sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR) markers to assess genetic variations and select diverse parents. Twelve each of SRAP and SSR primers produced 95.1 and 93.1% polymorphic bands and grouped them into unweighted pair-group method with arithmetic average clusters. Two of the finger millet genotypes, IE 4709 (blast resistant) and INDAF 7 (susceptible) were distinguished as most diverse genotypes as parents. Several genotype-specific bands observed with SSR primers are potential in developing genotype-specific markers. A high genetic diversity within the resistant and susceptible genotypes, rather than between them, was revealed through Nei's gene diversity (h) index and analysis of molecular variance. The finding helps us to understand the extent of genetic polymorphism between blast disease resistant and susceptible finger millet genotypes to exploit in resistance breeding programs.
Factors shaping the legal implications of increasingly autonomous military systems
Authors: McFarland Tim 
Published: March 2016

AbstractThis article identifies five factors that will shape the legal implications of the use of autonomous military systems. It contends that the systems which present legal challenges are those programmed to “make decisions” that are regulated by law. In so doing, they transfer control of, and responsibility for, those decisions away from those who have been traditionally seen as decision-makers to persons responsible for developing and deploying the system. The article also suggests that there may be limits to the extent to which the rules of international humanitarian law can appropriately regulate the altered relationship between soldiers and their increasingly autonomous weapon systems.
Conserved regulators of Rag GTPases orchestrate amino acid-dependent TORC1 signaling
Authors: Powis Katie , De Virgilio Claudio 
Published: March 2016

AbstractThe highly conserved target of rapamycin complex 1 (TORC1) is the central component of a signaling network that couples a vast range of internal and external stimuli to cell growth, proliferation and metabolism. TORC1 deregulation is associated with a number of human pathologies, including many cancers and metabolic disorders, underscoring its importance in cellular and organismal growth control. The activity of TORC1 is modulated by multiple inputs; however, the presence of amino acids is a stimulus that is essential for its activation. Amino acid sufficiency is communicated to TORC1 via the highly conserved family of Rag GTPases, which assemble as heterodimeric complexes on lysosomal/vacuolar membranes and are regulated by their guanine nucleotide loading status. Studies in yeast, fly and mammalian model systems have revealed a multitude of conserved Rag GTPase modulators, which have greatly expanded our understanding of amino acid sensing by TORC1. Here we review the major known modulators of the Rag GTPases, focusing on recent mechanistic insights that highlight the evolutionary conservation and divergence of amino acid signaling to TORC1.
Regulatory (pan-)genome of an obligate intracellular pathogen in the PVC superphylum
Authors: de Barsy Marie , Frandi Antonio , Panis Gaël , Théraulaz Laurence , Pillonel Trestan , Greub Gilbert , Viollier Patrick H 
Published: March 2016

Abstract
Like other obligate intracellular bacteria, the Chlamydiae feature a compact regulatory genome that remains uncharted owing to poor genetic tractability. Exploiting the reduced number of transcription factors (TFs) encoded in the chlamydial (pan-)genome as a model for TF control supporting the intracellular lifestyle, we determined the conserved landscape of TF specificities by ChIP-Seq (chromatin immunoprecipitation-sequencing) in the chlamydial pathogen Waddlia chondrophila. Among 10 conserved TFs, Euo emerged as a master TF targeting &gt;100 promoters through conserved residues in a DNA excisionase-like winged helix-turn-helix-like (wHTH) fold. Minimal target (Euo) boxes were found in conserved developmentally-regulated genes governing vertical genome transmission (cytokinesis and DNA replication) and genome plasticity (transposases). Our ChIP-Seq analysis with intracellular bacteria not only reveals that global TF regulation is maintained in the reduced regulatory genomes of Chlamydiae, but also predicts that master TFs interpret genomic information in the obligate intracellular α-proteobacteria, including the rickettsiae, from which modern day mitochondria evolved.
The microbiome of coral surface mucus has a key role in mediating holobiont health and survival upon disturbance
Authors: Glasl Bettina , Herndl Gerhard J , Frade Pedro R 
Published: March 2016

Abstract
Microbes are well-recognized members of the coral holobiont. However, little is known about the short-term dynamics of mucus-associated microbial communities under natural conditions and after disturbances, and how these dynamics relate to the host’s health. Here we examined the natural variability of prokaryotic communities (based on 16S ribosomal RNA gene amplicon sequencing) associating with the surface mucus layer (SML) of Porites astreoides, a species exhibiting cyclical mucus aging and shedding. Shifts in the prokaryotic community composition during mucus aging led to the prevalence of opportunistic and potentially pathogenic bacteria (Verrucomicrobiaceae and Vibrionaceae) in aged mucus and to a twofold increase in prokaryotic abundance. After the release of aged mucus sheets, the community reverted to its original state, dominated by Endozoicimonaceae and Oxalobacteraceae. Furthermore, we followed the fate of the coral holobiont upon depletion of its natural mucus microbiome through antibiotics treatment. After re-introduction to the reef, healthy-looking microbe-depleted corals started exhibiting clear signs of bleaching and necrosis. Recovery versus mortality of the P. astreoides holobiont was related to the degree of change in abundance distribution of the mucus microbiome. We conclude that the natural prokaryotic community inhabiting the coral SML contributes to coral health and that cyclical mucus shedding has a key role in coral microbiome dynamics.
Drift transport of helical spin coherence with tailored spin–orbit interactions
Authors: Kunihashi Y. , Sanada H. , Gotoh H. , Onomitsu K. , Kohda M. , Nitta J. , Sogawa T. 
Published: March 2016

AbstractMost future information processing techniques using electron spins in non-magnetic semiconductors will require both the manipulation and transfer of spins without their coherence being lost. The spin–orbit effective magnetic field induced by drifting electrons enables us to rotate the electron spins in the absence of an external magnetic field. However, the fluctuations in the effective magnetic field originating from the random scattering of electrons also cause undesirable spin decoherence, which limits the length scale of the spin transport. Here we demonstrate the drift transport of electron spins adjusted to a robust spin structure, namely a persistent spin helix. We find that the persistent spin helix enhances the spatial coherence of drifting spins, resulting in maximized spin decay length near the persistent spin helix condition. Within the enhanced distance of the spin transport, the transport path of electron spins can be modulated by employing time-varying in-plane voltages.
Extinction of fish-shaped marine reptiles associated with reduced evolutionary rates and global environmental volatility
Authors: Fischer Valentin , Bardet Nathalie , Benson Roger B. J. , Arkhangelsky Maxim S. , Friedman Matt 
Published: March 2016

AbstractDespite their profound adaptations to the aquatic realm and their apparent success throughout the Triassic and the Jurassic, ichthyosaurs became extinct roughly 30 million years before the end-Cretaceous mass extinction. Current hypotheses for this early demise involve relatively minor biotic events, but are at odds with recent understanding of the ichthyosaur fossil record. Here, we show that ichthyosaurs maintained high but diminishing richness and disparity throughout the Early Cretaceous. The last ichthyosaurs are characterized by reduced rates of origination and phenotypic evolution and their elevated extinction rates correlate with increased environmental volatility. In addition, we find that ichthyosaurs suffered from a profound Early Cenomanian extinction that reduced their ecological diversity, likely contributing to their final extinction at the end of the Cenomanian. Our results support a growing body of evidence revealing that global environmental change resulted in a major, temporally staggered turnover event that profoundly reorganized marine ecosystems during the Cenomanian.
Anomalous correlation effects and unique phase diagram of electron-doped FeSe revealed by photoemission spectroscopy
Authors: Wen C. H. P. , Xu H. C. , Chen C. , Huang Z. C. , Lou X. , Pu Y. J. , Song Q. , Xie B. P. , Abdel-Hafiez Mahmoud , Chareev D. A. , Vasiliev A. N. , Peng R. , Feng D. L. 
Published: March 2016

AbstractFeSe layer-based superconductors exhibit exotic and distinctive properties. The undoped FeSe shows nematicity and superconductivity, while the heavily electron-doped KxFe2−ySe2 and single-layer FeSe/SrTiO3 possess high superconducting transition temperatures that pose theoretical challenges. However, a comprehensive study on the doping dependence of an FeSe layer-based superconductor is still lacking due to the lack of a clean means of doping control. Through angle-resolved photoemission spectroscopy studies on K-dosed thick FeSe films and FeSe0.93S0.07 bulk crystals, here we reveal the internal connections between these two types of FeSe-based superconductors, and obtain superconductivity below ∼46 K in an FeSe layer under electron doping without interfacial effects. Moreover, we discover an exotic phase diagram of FeSe with electron doping, including a nematic phase, a superconducting dome, a correlation-driven insulating phase and a metallic phase. Such an anomalous phase diagram unveils the remarkable complexity, and highlights the importance of correlations in FeSe layer-based superconductors.
Manipulation of prenylation reactions by structure-based engineering of bacterial indolactam prenyltransferases
Authors: Mori Takahiro , Zhang Lihan , Awakawa Takayoshi , Hoshino Shotaro , Okada Masahiro , Morita Hiroyuki , Abe Ikuro 
Published: March 2016

AbstractPrenylation reactions play crucial roles in controlling the activities of biomolecules. Bacterial prenyltransferases, TleC from Streptomyces blastmyceticus and MpnD from Marinactinospora thermotolerans, catalyse the ‘reverse’ prenylation of (−)-indolactam V at the C-7 position of the indole ring with geranyl pyrophosphate or dimethylallyl pyrophosphate, to produce lyngbyatoxin or pendolmycin, respectively. Using in vitro analyses, here we show that both TleC and MpnD exhibit relaxed substrate specificities and accept various chain lengths (C5–C25) of the prenyl donors. Comparisons of the crystal structures and their ternary complexes with (−)-indolactam V and dimethylallyl S-thiophosphate revealed the intimate structural details of the enzyme-catalysed ‘reverse’ prenylation reactions and identified the active-site residues governing the selection of the substrates. Furthermore, structure-based enzyme engineering successfully altered the preference for the prenyl chain length of the substrates, as well as the regio- and stereo-selectivities of the prenylation reactions, to produce a series of unnatural novel indolactams.
Using mutability landscapes of a promiscuous tautomerase to guide the engineering of enantioselective Michaelases
Authors: van der Meer Jan-Ytzen , Poddar Harshwardhan , Baas Bert-Jan , Miao Yufeng , Rahimi Mehran , Kunzendorf Andreas , van Merkerk Ronald , Tepper Pieter G. , Geertsema Edzard M. , Thunnissen Andy-Mark W. H. , Quax Wim J. , Poelarends Gerrit J. 
Published: March 2016

AbstractThe Michael-type addition reaction is widely used in organic synthesis for carbon–carbon bond formation. However, biocatalytic methodologies for this type of reaction are scarce, which is related to the fact that enzymes naturally catalysing carbon–carbon bond-forming Michael-type additions are rare. A promising template to develop new biocatalysts for carbon–carbon bond formation is the enzyme 4-oxalocrotonate tautomerase, which exhibits promiscuous Michael-type addition activity. Here we present mutability landscapes for the expression, tautomerase and Michael-type addition activities, and enantioselectivity of 4-oxalocrotonate tautomerase. These maps of neutral, beneficial and detrimental amino acids for each residue position and enzyme property provide detailed insight into sequence–function relationships. This offers exciting opportunities for enzyme engineering, which is illustrated by the redesign of 4-oxalocrotonate tautomerase into two enantiocomplementary ‘Michaelases’. These ‘Michaelases’ catalyse the asymmetric addition of acetaldehyde to various nitroolefins, providing access to both enantiomers of γ-nitroaldehydes, which are important precursors for pharmaceutically active γ-aminobutyric acid derivatives.
A general approach to visualize protein binding and DNA conformation without protein labelling
Authors: Song Dan , Graham Thomas G. W. , Loparo Joseph J. 
Published: March 2016

AbstractSingle-molecule manipulation methods, such as magnetic tweezers and flow stretching, generally use the measurement of changes in DNA extension as a proxy for examining interactions between a DNA-binding protein and its substrate. These approaches are unable to directly measure protein–DNA association without fluorescently labelling the protein, which can be challenging. Here we address this limitation by developing a new approach that visualizes unlabelled protein binding on DNA with changes in DNA conformation in a relatively high-throughput manner. Protein binding to DNA molecules sparsely labelled with Cy3 results in an increase in fluorescence intensity due to protein-induced fluorescence enhancement (PIFE), whereas DNA length is monitored under flow of buffer through a microfluidic flow cell. Given that our assay uses unlabelled protein, it is not limited to the low protein concentrations normally required for single-molecule fluorescence imaging and should be broadly applicable to studying protein–DNA interactions.
Lithium Protects Against Anaesthesia Neurotoxicity In The Infant Primate Brain
Authors: Noguchi Kevin K. , Johnson Stephen A. , Kristich Lauren E. , Martin Lauren D. , Dissen Gregory A. , Olsen Emily A. , Olney John W. , Brambrink Ansgar M. 
Published: March 2016

AbstractExposure of infant animals, including non-human primates (NHPs), to anaesthetic drugs causes apoptotic death of neurons and oligodendrocytes (oligos) and results in long-term neurodevelopmental impairment (NDI). Moreover, retrospective clinical studies document an association between anaesthesia exposure of human infants and significant increase in NDI. These findings pose a potentially serious dilemma because millions of human infants are exposed to anaesthetic drugs every year as part of routine medical care. Lithium (Li) at clinically established doses is neuroprotective in various cerebral injury models. We therefore investigated whether Li also protects against anaesthesia neurotoxicity in infant NHPs. On postnatal day 6 NHPs were anaesthetized with the widely used anaesthetic isoflurane (ISO) for 5 h employing the same standards as in a human pediatric surgery setting. Co-administration of Li completely prevented the acute ISO-induced neuroapoptosis and significantly reduced ISO-induced apoptosis of oligodendroglia. Our findings are highly encouraging as they suggest that a relatively simple pharmacological manipulation might protect the developing primate brain against the neurotoxic action of anaesthetic drugs while not interfering with the beneficial actions of these drugs. Further research is needed to determine Li’s potential to prevent long-term NDI resulting from ISO anaesthesia and to establish its safety in human infants.
Tropical secondary forests regenerating after shifting cultivation in the Philippines uplands are important carbon sinks
Authors: Mukul Sharif A. , Herbohn John , Firn Jennifer 
Published: March 2016

AbstractIn the tropics, shifting cultivation has long been attributed to large scale forest degradation, and remains a major source of uncertainty in forest carbon accounting. In the Philippines, shifting cultivation, locally known as kaingin, is a major land-use in upland areas. We measured the distribution and recovery of aboveground biomass carbon along a fallow gradient in post-kaingin secondary forests in an upland area in the Philippines. We found significantly higher carbon in the aboveground total biomass and living woody biomass in old-growth forest, while coarse dead wood biomass carbon was higher in the new fallow sites. For young through to the oldest fallow secondary forests, there was a progressive recovery of biomass carbon evident. Multivariate analysis indicates patch size as an influential factor in explaining the variation in biomass carbon recovery in secondary forests after shifting cultivation. Our study indicates secondary forests after shifting cultivation are substantial carbon sinks and that this capacity to store carbon increases with abandonment age. Large trees contribute most to aboveground biomass. A better understanding of the relative contribution of different biomass sources in aboveground total forest biomass, however, is necessary to fully capture the value of such landscapes from forest management, restoration and conservation perspectives.
Quantitative proteomics study of the neuroprotective effects of B12 on hydrogen peroxide-induced apoptosis in SH-SY5Y cells
Authors: Zhong Lijun , Zhou Juntuo , Chen Xi , Lou Yaxin , Liu Dan , Zou Xiajuan , Yang Bin , Yin Yuxin , Pan Yan 
Published: March 2016

AbstractB12 belongs to the coumarin class of compounds that have been shown to have various physiological and pharmacological activities including anti-inflammatory, antibacterial and antioxidant. In the present study, we characterised the neuroprotective effects of B12 against H2O2-induced neuronal cell damage in SH-SY5Y cells. Protein expression profiling in combination with pathway analysis was deployed to investigate the molecular events associated with the neuroprotective effects in human neuronal cells using a label-free quantitative proteomics approach. A total of 22 proteins were significantly differentially expressed in H2O2-damaged cells with or without B12 treatment. Bioinformatics analysis using the Cytoscape platform indicated that poly pyrimidine tract binding protein 1 (PTBP1) was highly associated with the protective effect and western blotting verified that PTBP1 was up-regulated in H2O2 + B12 treatment group, compared with the H2O2 treated group. PTBP RNAi experiments knocked down PTBP expression, which cancelled out the protective effect of B12 on cell viability. Thus, we infer that B12 neuroprotective activity involves up-regulation of PTBP1 and its associated signalling networks following H2O2-induced apoptosis in SH-SY5Y cells. B12 or related compounds may prove to be useful therapeutic agents for the treatment of neurodegenerative diseases such as Alzheimer’s and Parkinson’s.