bluuebunny/crossref_metadata_2025_split huggingface dataset:
Information content and acoustic structure of male African elephant social rumbles
Authors: Stoeger Angela S. , Baotic Anton 
Published: June 2016

AbstractUntil recently, the prevailing theory about male African elephants (Loxodonta africana) was that, once adult and sexually mature, males are solitary and targeted only at finding estrous females. While this is true during the state of ‘musth’ (a condition characterized by aggressive behavior and elevated androgen levels), ‘non-musth’ males exhibit a social system seemingly based on companionship, dominance and established hierarchies. Research on elephant vocal communication has so far focused on females and very little is known about the acoustic structure and the information content of male vocalizations. Using the source and filter theory approach, we analyzed social rumbles of 10 male African elephants. Our results reveal that male rumbles encode information about individuality and maturity (age and size), with formant frequencies and absolute fundamental frequency values having the most informative power. This first comprehensive study on male elephant vocalizations gives important indications on their potential functional relevance for male-male and male-female communication. Our results suggest that, similar to the highly social females, future research on male elephant vocal behavior will reveal a complex communication system in which social knowledge, companionship, hierarchy, reproductive competition and the need to communicate over long distances play key roles.
Anticipatory Manoeuvres in Bird Flight
Authors: Vo Hong D. , Schiffner Ingo , Srinivasan Mandyam V. 
Published: June 2016

AbstractIt is essential for birds to be agile and aware of their immediate environment, especially when flying through dense foliage. To investigate the type of visual signals and strategies used by birds while negotiating cluttered environments, we presented budgerigars with vertically oriented apertures of different widths. We find that, when flying through narrow apertures, birds execute their maneuvers in an anticipatory fashion, with wing closures, if necessary, occurring well in advance of the aperture. When passing through an aperture that is narrower than the wingspan, the birds close their wings at a specific, constant distance before the aperture, which is independent of aperture width. In these cases, the birds also fly significantly higher, possibly pre-compensating for the drop in altitude. The speed of approach is largely constant and independent of the width of the aperture. The constancy of the approach speed suggests a simple means by which optic flow can be used to gauge the distance and width of the aperture and guide wing closure.
Distinct characteristics of asymmetric magnetic reconnections: Observational results from the exhaust region at the dayside magnetopause
Authors: Zhang Y. C. 
Published: June 2016

AbstractMagnetic reconnection plays a key role in the conversion of magnetic energy into the thermal and kinetic energy of plasma. On either side of the diffusion region in space plasma, the conditions for the occurrence of reconnections are usually not symmetric. Previous theoretical studies have predicted that reconnections under asymmetric conditions will bear different features compared with those of symmetric reconnections, and numerical simulations have verified these distinct features. However, to date, the features of asymmetric reconnections have not been thoroughly investigated using in situ observations; thus, some results from theoretical studies and simulations have not been tested with observations sufficiently well. Here, spacecraft observations are used in a statistical investigation of asymmetric magnetic reconnection exhaust at the dayside magnetopause. The resulting observational features are consistent with the theoretical predictions. The results presented here advance our understanding of the development of reconnections under asymmetric conditions.
Resonantly Enhanced Betatron Hard X-rays from Ionization Injected Electrons in a Laser Plasma Accelerator
Authors: Huang K. , Li Y. F. , Li D. Z. , Chen L. M. , Tao M. Z. , Ma Y. , Zhao J. R. , Li M. H. , Chen M. , Mirzaie M. , Hafz N. , Sokollik T. , Sheng Z. M. , Zhang J. 
Published: June 2016

AbstractUltrafast betatron x-ray emission from electron oscillations in laser wakefield acceleration (LWFA) has been widely investigated as a promising source. Betatron x-rays are usually produced via self-injected electron beams, which are not controllable and are not optimized for x-ray yields. Here, we present a new method for bright hard x-ray emission via ionization injection from the K-shell electrons of nitrogen into the accelerating bucket. A total photon yield of 8 × 108/shot and 108 photons with energy greater than 110 keV is obtained. The yield is 10 times higher than that achieved with self-injection mode in helium under similar laser parameters. The simulation suggests that ionization-injected electrons are quickly accelerated to the driving laser region and are subsequently driven into betatron resonance. The present scheme enables the single-stage betatron radiation from LWFA to be extended to bright γ-ray radiation, which is beyond the capability of 3rd generation synchrotrons.
Rapid Synthesis of Thin and Long Mo17O47 Nanowire-Arrays in an Oxygen Deficient Flame
Authors: Allen Patrick , Cai Lili , Zhou Lite , Zhao Chenqi , Rao Pratap M. 
Published: June 2016

AbstractMo17O47 nanowire-arrays are promising active materials and electrically-conductive supports for batteries and other devices. While high surface area resulting from long, thin, densely packed nanowires generally leads to improved performance in a wide variety of applications, the Mo17O47 nanowire-arrays synthesized previously by electrically-heated chemical vapor deposition under vacuum conditions were relatively thick and short. Here, we demonstrate a method to grow significantly thinner and longer, densely packed, high-purity Mo17O47 nanowire-arrays with diameters of 20–60 nm and lengths of 4–6 μm on metal foil substrates using rapid atmospheric flame vapor deposition without any chamber or walls. The atmospheric pressure and 1000 °C evaporation temperature resulted in smaller diameters, longer lengths and order-of-magnitude faster growth rate than previously demonstrated. As explained by kinetic and thermodynamic calculations, the selective synthesis of high-purity Mo17O47 nanowires is achieved due to low oxygen partial pressure in the flame products as a result of the high ratio of fuel to oxidizer supplied to the flame, which enables the correct ratio of MoO2 and MoO3 vapor concentrations for the growth of Mo17O47. This flame synthesis method is therefore a promising route for the growth of composition-controlled one-dimensional metal oxide nanomaterials for many applications.
Origin of Shear Stability and Compressive Ductility Enhancement of Metallic Glasses by Metal Coating
Authors: Sun B. A. , Chen S. H. , Lu Y. M. , Zhu Z. G. , Zhao Y. L. , Yang Y. , Chan K. C. , Liu C. T. 
Published: June 2016

AbstractMetallic glasses (MGs) are notorious for the poor macroscopic ductility and to overcome the weakness various intrinsic and extrinsic strategies have been proposed in past decades. Among them, the metal coating is regarded as a flexible and facile approach, yet the physical origin is poorly understood due to the complex nature of shear banding process. Here, we studied the origin of ductile enhancement in the Cu-coating both experimentally and theoretically. By examining serrated shear events and their stability of MGs, we revealed that the thin coating layer plays a key role in stopping the final catastrophic failure of MGs by slowing down shear band dynamics and thus retarding its attainment to a critical instable state. The mechanical analysis on interplay between the coating layer and shear banding process showed the enhanced shear stability mainly comes from the lateral tension of coating layer induced by the surface shear step and the bonding between the coating layer and MGs rather than the layer thickness is found to play a key role in contributing to the shear stability.
Cool?
Authors: Parker Becky 
Published: June 2016

The original paper
‘Cool?’ was first published in Physics Education in 1969 (Mpemba and Osborne 1969 Phys. Educ.
4

172). Written by Erasto Mpemba and Denis Osborne this paper has been cited 26 times to date, has led to hundreds of articles being written and has a story behind it to inspire every student. We asked Becky Parker, the director of and inspiration behind the Institute for Research in Schools (www.researchinschools.org/), to write a commentary.
Harnessing Molecular Motors for Nanoscale Pulldown in Live Cells
Authors: Bird Jonathan E. , Barzik Melanie , Drummond Meghan C. , Sutton Daniel C. , Goodman Spencer M. , Morozko Eva L. , Cole Stacey M. , Skidmore Jennifer , Syam Diana , Wilson Elizabeth A. , Fitzgerald Tracy , Rehman Atteeq U. , Martin Donna M. , Boger Erich T. , Belyantseva Inna A. , Friedman Thomas B. 
Published: June 2016

SUMMARYProtein-protein interactions (PPIs) regulate signal transduction and cellular behavior, yet studying PPIs within live cells remains fundamentally challenging. We have miniaturized the affinity pulldown, a gold-standard PPI interrogation technique, for use within live cells. Our assay hijacks endogenous myosin motors to forcibly traffic, or pulldown, macromolecular complexes within the native cytosolic environment. Macromolecules captured by nanoscale pulldown (NanoSPD) are optically interrogatedin situby tagging individual protein components. Critically, continuous motor trafficking concentrates query complexes into nanoscopic subcellular compartments, providing fluorescence enhancement and allowing nanoscale pulldowns to be visualized and quantified by standard microscopy. Nanoscale pulldown is compatible with nuclear, membrane-associated and cytoplasmic proteins and can investigate functional effects of protein truncations or amino acid substitutions. Moreover, binding hierarchies in larger complexes can be quickly examined within the natural cytosol, making nanoscale pulldown a powerful new optical platform for quantitative high-content screening of known and novel PPIs that act within macromolecular assemblies.
The Quick and the Dead: Microbial Demography at the Yeast Thermal Limit
Authors: Maxwell Colin S. , Magwene Paul M. 
Published: June 2016

AbstractThe niche of microorganisms is determined by where their populations can expand. Populations can fail to grow because of high death or low birth rates, but these are challenging to measure in microorganisms. We developed a novel technique that enables single cell measurement of age-structured birth and death rates in the budding yeast, Saccharomyces cerevisiae, and used this method to study responses to heat stress in a genetically diverse panel of strains. We find that individual cells show significant heterogeneity in their rates of birth and death during heat stress. Genotype-by-environment effects on processes that regulate asymmetric cell division contribute to this heterogeneity. These lead to either premature senescence or early life mortality during heat stress, and we find that a mitochondrial inheritance defect explains the early life mortality phenotype of one of the strains we studied. This study demonstrates how the interplay of physiology, genetic variation, and environmental variables influences where microbial populations survive and flourish.
Identification of polymorphic and off-target probe binding sites on the Illumina Infinium MethylationEPIC BeadChip
Authors: McCartney Daniel L. , Walker Rosie M. , Morris Stewart W. , McIntosh Andrew M. , Porteous David J. , Evans Kathryn L. 
Published: June 2016

AbstractGenome-wide analysis of DNA methylation has now become a relatively inexpensive technique thanks to array-based methylation profiling technologies. The recently developed Illumina Infinium MethylationEPIC BeadChip interrogates methylation at over 850,000 sites across the human genome, covering 99% of RefSeq genes. This array supersedes the widely used Infinium HumanMethylation450 BeadChip, which has permitted insights into the relationship between DNA methylation and a wide range of conditions and traits. Previous research has identified issues with certain probes on both the HumanMethylation450 BeadChip and its predecessor, the Infinium HumanMethylation27 BeadChip, which were predicted to affect array performance. These issues concerned probe-binding specificity and the presence of polymorphisms at target sites. Usingin silicomethods, we have identified probes on the Infinium MethylationEPIC BeadChip that are predicted to (i) measure methylation at polymorphic sites and (ii) hybridise to multiple genomic regions. We intend these resources to be used for quality control procedures when analysing data derived from this platform.
Decoding of generic mental representations from functional MRI data using word embeddings
Authors: Pereira Francisco , Lou Bin , Pritchett Brianna , Kanwisher Nancy , Botvinick Matthew , Fedorenko Evelina 
Published: June 2016

AbstractSeveral different groups have demonstrated the feasibility of building forward models of functional MRI data in response to concrete stimuli such as pictures or video, and of using these models to decode or reconstruct stimuli shown while acquiring test fMRI data. In this paper, we introduce an approach for building forward models of conceptual stimuli, concrete or abstract, and for using these models to carry out decoding of semantic information from new imaging data. We show that this approach generalizes to topics not seen in training, and provides a straightforward path to decoding from more complex stimuli such as sentences or paragraphs.
Stabilizing membrane domains antagonizes n-alcohol anesthesia
Authors: Machta B.B. , Grey E. , Nouri M. , McCarthy N.L.C. , Gray E.M. , Miller A.L. , Brooks N.J. , Veatch S.L. 
Published: June 2016

AbstractDiverse molecules induce general anesthesia with potency strongly correlated both with their hydrophobicity and their effects on certain ion channels. We recently observed that several n-alcohol anesthetics inhibit heterogeneity in plasma membrane derived vesicles by lowering the critical temperature (Tc) for phase separation. Here we exploit conditions that stabilize membrane heterogeneity to further test the correlation between the anesthetic potency of n-alcohols and effects onTc. First we show that hexadecanol acts oppositely to n-alcohol anesthetics on membrane mixing and antagonizes ethanol induced anesthesia in a tadpole behavioral assay. Second, we show that two previously described ‘intoxication reversers’ raiseTcand counter ethanol’s effects in vesicles, mimicking the findings of previous electrophysiological and behavioral measurements. Third, we find that hydrostatic pressure, long known to reverse anesthesia, also raises Tc in vesicles with a magnitude that counters the effect of butanol at relevant concentrations and pressures. Taken together,these results demonstrate that ΔTcpredicts anesthetic potency for n-alcohols better than hydrophobicity in a range of contexts, supporting a mechanistic role for membrane heterogeneity in general anesthesia.
Dark diversity illuminates the dim side of conservation and restoration
Authors: Moeslund Jesper Erenskjold , Brunbjerg Ane Kirstine , Clausen Kevin Kuhlmann , Dalby Lars , Flojgaard Camilla , Juel Anders , Lenoir Jonathan 
Published: June 2016

Summary1Dark diversityis a promising concept for prioritizing management efforts as it focuses on missing species, i.e., species present in the regional pool, but locally absent despite suitable environmental conditions.2We applied the concept to a massive national plant diversity database (236,923 records from 15,160 surveys involving 564 species) to provide the first geographically comprehensive assessment of dark diversity across a large area (43,000 km2), at a spatial scale (~75 m2) relevant for conservation and restoration planning and across multiple terrestrial habitats, thus maximising its practical application potential. The likelihood for a given plant species to belong to the dark diversity pool was computed and logistically regressed against its ecological preferences (nutrient availability, pH etc.), strategies (competitor, stress tolerance, ruderal), mycorrhizal dependence and infection percentage, seed mass and maximum dispersal distance.3Forty-six percent of the species were absent in >95 % of the suitable sites, whereas 7 % of the species were absent in less than 60 % of sites that were deemed suitable.4Species that were more likely to belong to the dark diversity tended to depend on mycorrhiza, were mostly adapted to low light and nutrient levels, had poor dispersal abilities, were ruderals and had a low stress tolerance.Synthesis and applicationsOur findings have important implications for the planning and management of natural ecosystems requiring detailed knowledge of what triggers the presence/absence of individual plant species in a seemingly suitable habitat. We conclude that practitioners may need to carefully consider mycorrhizal inoculations with a suitable assemblage of fungi for certain plant species to become established. Also assisted migration might be necessary to help poor dispersers although spatial and temporal processes are also important to have in mind. Finally, it is important to vary nutrient loads making room for plant species to colonise both nutrient-poor and nutrient-rich localities.
A Dormant Microbial Component in the Development of Pre-Eclampsia1
Authors: Kell Douglas B. , Kenny Louise C. 
Published: June 2016

AbstractPre-eclampsia (PE) is a complex, multi-system disorder that remains a leading cause of morbidity and mortality in pregnancy. Four main classes of dysregulation accompany PE, and are widely considered to contribute to its severity. These are abnormal trophoblast invasion of the placenta, anti-angiogenic responses, oxidative stress, and inflammation. What is lacking, however, is an explanation of how these themselves are caused.We here develop the unifying idea, and the considerable evidence for it, that the originating cause of PE (and of the four classes of dysregulation) is in fact microbial infection, that most such microbes are dormant and hence resist detection by conventional (replication-dependent) microbiology, and that by occasional resuscitation and growth it is they that are responsible for all the observable sequelae, including the continuing, chronic inflammation. In particular, bacterial products such as lipopolysaccharide (LPS), also known as endotoxin, are well known as highly inflammagenic and stimulate an innate (and possibly trained) immune response that exacerbates the inflammation further. The known need of microbes for free iron can explain the iron dysregulation that accompanies PE. We describe the main routes of infection (gut, oral, urinary tract infection) and the regularly observed presence of microbes in placental and other tissues in PE. Every known proteomic biomarker of “pre-eclampsia” that we assessed has in fact also been shown to be raised in response to infection. An infectious component to PE fulfils the Bradford Hill criteria for ascribing a disease to an environmental cause, and suggests a number of treatments, some of which have in fact been shown to be successful.PE was classically referred to as endotoxaemia or toxaemia of pregnancy, and it is ironic that it seems that LPS and other microbial endotoxins really are involved. Overall, the recognition of an infectious component in the aetiology of PE mirrors that for ulcers and other diseases that were previously considered to lack one.Insight, innovation, integrationMany descriptors of pre-eclampsia are widely accepted (e.g. abnormal trophoblast invasion, oxidative stress, inflammation and altered immune response, and anti-angiogenic responses). However, without knowing what causes them, they do not explain the syndrome. The Biological Insight of this manuscript is that there is considerable evidence to the effect that each of these phenomena (hence PE) are caused by the resuscitation of dormant bacteria that shed (known and potent) inflammagens such as LPS, often as a consequence of iron availability. PE is thus seen as a milder form of sepsis. The Technological Innovations come from the use of molecular markers (of microbes and omics more generally, as well as novel markers of coagulopathies) to measure this. The Benefit of Integration comes from bringing together a huge number of disparate observations into a unifying theme.
tHapMix: simulating tumour samples through haplotype mixtures
Authors: Ivakhno Sergii , Colombo Camilla , Tanner Stephen , Tedder Philip , Berri Stefano , Cox Anthony J. 
Published: June 2016

AbstractMotivationLarge-scale rearrangements and copy number changes combined with different modes of cloevolution create extensive somatic genome diversity, making it difficult to develop versatile and scalable oriant calling tools and create well-calibrated benchmarks.ResultsWe developed a new simulation framework tHapMix that enables the creation of tumour samples with different ploidy, purity and polyclonality features. It easily scales to simulation of hundreds of somatic genomes, while re-use of real read data preserves noise and biases present in sequencing platforms. We further demonstrate tHapMix utility by creating a simulated set of 140 somatic genomes and showing how it can be used in training and testing of somatic copy number variant calling tools.Availability and implementationtHapMix is distributed under an open source license and can be downloaded fromhttps://github.com/Illumina/tHapMix.Contactsivakhno@illumina.comSupplementary informationSupplementary data are available atBioinformaticsonline.
Phylogenetic and structural analyses reveal the determinants of DNA binding specificities of nucleoid-associated proteins HU and IHF
Authors: Dey Debayan , Nagaraja Valakunja , Ramakumar Suryanarayanarao 
Published: June 2016

AbstractNucleoid-associated proteins (NAPs) are chromosome-organizing factors, which affect the transcriptional landscape of a bacterial cell. HU is an NAP, which binds to DNA with a broad specificity while homologous IHF (Integration Host Factor), binds DNA with moderately higher specificity. Specificity and differential binding affinity of HU/IHF proteins towards their target binding sites play a crucial role in their regulatory dynamics. Decades of biochemical and genomic studies have been carried out for HU and IHF like proteins. Yet, questions related to their DNA binding specificity, and differential ability tobendDNA thus affecting the binding site length remained unanswered. In addition, the problem has not been investigated from an evolutionary perspective. Our phylogenetic analysis revealed three major clades belonging to HU, IHFα and IHFβ like proteins with reference toE. coli. We carried out a comparative analysis of three-dimensional structures of HU/IHF proteins to gain insight into the structural basis of clade division. The present study revealed three major features which contribute to differential DNA binding specificity of HU/IHF proteins, I) conformational restriction of DNA binding residues due to salt-bridge formation II) the enrichment of alanine in the DNA binding site increasing conformational space of flexible side chains in its vicinity and III) nature of DNA binding residue (Arg to Lys bias in different clades) which interacts differentially to DNA bases. Differences in the dimer stabilization strategies between HU and IHF were also observed. Our analysis reveals a comprehensive evolutionary picture, which rationalizes the origin of multi-specificity of HU/IHF proteins using sequence and structure-based determinants, which could also be applied to understand differences in binding specificities of other nucleic acid binding proteins.