bluuebunny/crossref_metadata_2025 huggingface dataset:
An event-driven approach for studying gene block evolution in bacteria
Authors: Ream David C. , Bankapur Asma R. , Friedberg Iddo
Published: February 2015

Motivation: Gene blocks are genes co-located on the chromosome. In many cases, gene blocks are conserved between bacterial species, sometimes as operons, when genes are co-transcribed. The conservation is rarely absolute: gene loss, gain, duplication, block splitting and block fusion are frequently observed. An open question in bacterial molecular evolution is that of the formation and breakup of gene blocks, for which several models have been proposed. These models, however, are not generally applicable to all types of gene blocks, and consequently cannot be used to broadly compare and study gene block evolution. To address this problem, we introduce an event-based method for tracking gene block evolution in bacteria.

Results: We show here that the evolution of gene blocks in proteobacteria can be described by a small set of events. Those include the insertion of genes into, or the splitting of genes out of a gene block, gene loss, and gene duplication. We show how the event-based method of gene block evolution allows us to determine the evolutionary rateand may be used to trace the ancestral states of their formation. We conclude that the event-based method can be used to help us understand the formation of these important bacterial genomic structures.

Availability and implementation: The software is available under GPLv3 license on http://github.com/reamdc1/gene_block_evolution.git. Supplementary online material: http://iddo-friedberg.net/operon-evolution

Contact:  i.friedberg@miamioh.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Combined application of biophysical habitat mapping and systematic conservation planning to assess efficiency and representativeness of the existing High Seas MPA network in the Northeast Atlantic
Authors: Evans Jon L. , Peckett Frances , Howell Kerry L.
Published: February 2015

The High Seas are increasingly the subject of exploitation. Although Marine Protected Areas (MPAs) are seen as a useful tool in the sustainable management of the oceans, progress in the implementation of MPA networks in areas beyond national jurisdiction has been limited. Specifically, the criteria of “representativeness” has received little consideration. This study uses the systematic conservation planning software Marxan coupled with a biologically meaningful biophysical habitat map to investigate representative MPA network scenarios and to assess the efficiency and representativeness of the existing High Seas MPA network in the Northeast Atlantic. Habitat maps were created based on the layers of water mass structure and seabed topography resulting in 30 different habitats, in six distinct regions. Conservation targets were set at 10 and 30% representation of each habitat within the final network. Two portfolios were created. The first portfolio (P1) ignored the presence of the existing MPA network within the study area allowing a non-biased selection of planning units (PUs) or sites to be chosen. The second (P2) enforced the selection of areas within the existing MPA network. Efficiency was measured as the difference in the percentage area contained within the “best scenario” MPAs from the un-bias run (P1) compared with (P2). Representativety of the existing network was assessed through the investigation of the properties of PUs included within MPAs in the “best scenario” Marxan output of P2. The results suggest that the current MPA network is neither efficient nor representative. There were clear differences in the spatial distribution of PUs selected in P1 compared with P2. The area required to be protected to achieve that the representation of 10 and 30% of each habitat was 8–10 and 1–4% higher, respectively, in P2 compared with P1. Abyssal areas in all regions are underrepresented within the current MPA network.
Sverdrup critical depth and the role of water clarity in Norwegian Coastal Water
Authors: Aksnes D. L.
Published: February 2015

The critical depth concept was first recognized by Gran and Braarud (1935). During summer, in the Bay of Fundy, they observed an unexpected no bloom situation. Their interpretation was that high amounts of detritus of terrestrial origin caused too murky water and insufficient light for the tidally mixed phytoplankton. Almost 20 years later, this was elaborated by Sverdrup (1953) into a hypothesis for the initiation of the spring bloom in the North Atlantic Water (NAW) masses. Since then, variations in mixed layer depth have been a key in phytoplankton modelling. As illustrated by the study of Gran and Braarud, variation in the non-phytoplankton light attenuation coefficient is also a key to understand phytoplankton bloom conditions. Due to lack of accurate parameterizations, however, non-phytoplankton light attenuation is often assumed invariant in phytoplankton modelling. Here, I report spatial variation in a proxy for the pre-bloom light attenuation in Norwegian Coastal Water (NCW). It is shown that this variation can be partially accounted for by variations in salinity and dissolved oxygen. The light attenuation coefficient at 440 nm increased by 0.041 and 0.032 m−1 with drops in salinity and dissolved oxygen of 1PSU and 1 ml O2 l−1, respectively. Consequences for the euphotic depth, Sverdrup critical depth, and the nutricline depth are discussed. I conclude that phytoplankton modelling, particularly across coastal and oceanic waters, such as NCW and NAW, needs to account for variations in the non-phytoplankton light attenuation and that salinity might be a useful proxy for regional parameterizations.
Visualizing collaborative electronic health record usage for hospitalized patients with heart failure
Authors: Soulakis Nicholas D , Carson Matthew B , Lee Young Ji , Schneider Daniel H , Skeehan Connor T , Scholtens Denise M
Published: February 2015

Objective To visualize and describe collaborative electronic health record (EHR) usage for hospitalized patients with heart failure.

Materials and methods We identified records of patients with heart failure and all associated healthcare provider record usage through queries of the Northwestern Medicine Enterprise Data Warehouse. We constructed a network by equating access and updates of a patient’s EHR to a provider-patient interaction. We then considered shared patient record access as the basis for a second network that we termed the provider collaboration network. We calculated network statistics, the modularity of provider interactions, and provider cliques.

Results We identified 548 patient records accessed by 5113 healthcare providers in 2012. The provider collaboration network had 1504 nodes and 83 998 edges. We identified 7 major provider collaboration modules. Average clique size was 87.9 providers. We used a graph database to demonstrate an ad hoc query of our provider-patient network.

Discussion Our analysis suggests a large number of healthcare providers across a wide variety of professions access records of patients with heart failure during their hospital stay. This shared record access tends to take place not only in a pairwise manner but also among large groups of providers.

Conclusion EHRs encode valuable interactions, implicitly or explicitly, between patients and providers. Network analysis provided strong evidence of multidisciplinary record access of patients with heart failure across teams of 100+ providers. Further investigation may lead to clearer understanding of how record access information can be used to strategically guide care coordination for patients hospitalized for heart failure.
Astrochemistry at work in the L1157-B1 shock: acetaldehyde formation
Authors: Codella C. , Fontani F. , Ceccarelli C. , Podio L. , Viti S. , Bachiller R. , Benedettini M. , Lefloch B.
Published: February 2015

The formation of complex organic molecules (COMs) in protostellar environments is a hotly debated topic. In particular, the relative importance of the gas phase processes as compared to a direct formation of COMs on the dust grain surfaces is so far unknown. We report here the first high-resolution images of acetaldehyde (CH3CHO) emission towards the chemically rich protostellar shock L1157-B1, obtained at 2 mm with the IRAM Plateau de Bure interferometer. Six blueshifted CH3CHO lines with Eu = 26–35 K have been detected. The acetaldehyde spatial distribution follows the young (∼ 2000 yr) outflow cavity produced by the impact of the jet with the ambient medium, indicating that this COM is closely associated with the region enriched by iced species evaporated from dust mantles and released into the gas phase. A high CH3CHO relative abundance, 2–3 × 10−8, is inferred, similarly to what found in hot corinos. Astrochemical modelling indicates that gas phase reactions can produce the observed quantity of acetaldehyde only if a large fraction of carbon, of the order of 0.1 per cent, is locked into iced hydrocarbons.
Formation of complex organic molecules in cold objects: the role of gas-phase reactions
Authors: Balucani Nadia , Ceccarelli Cecilia , Taquet Vianney
Published: February 2015

While astrochemical models are successful in reproducing many of the observed interstellar species, they have been struggling to explain the observed abundances of complex organic molecules. Current models tend to privilege grain surface over gas-phase chemistry in their formation. One key assumption of those models is that radicals trapped in the grain mantles gain mobility and react on lukewarm ( ≳ 30 K) dust grains. Thus, the recent detections of methyl formate (MF) and dimethyl ether (DME) in cold objects represent a challenge and may clarify the respective role of grain-surface and gas-phase chemistry. We propose here a new model to form DME and MF with gas-phase reactions in cold environments, where DME is the precursor of MF via an efficient reaction overlooked by previous models. Furthermore, methoxy, a precursor of DME, is also synthesized in the gas phase from methanol, which is desorbed by a non-thermal process from the ices. Our new model reproduces fairly well the observations towards L1544. It also explains, in a natural way, the observed correlation between DME and MF. We conclude that gas-phase reactions are major actors in the formation of MF, DME and methoxy in cold gas. This challenges the exclusive role of grain-surface chemistry and favours a combined grain-gas chemistry.
X-ray coherent pulsations during a sub-luminous accretion disc state of the transitional millisecond pulsar XSS J12270−4859
Authors: Papitto A. , de Martino D. , Belloni T. M. , Burgay M. , Pellizzoni A. , Possenti A. , Torres D. F.
Published: February 2015

We present the first detection of X-ray coherent pulsations from the transitional millisecond pulsar XSS J12270−4859, while it was in a sub-luminous accretion disc state characterized by a 0.5–10 keV luminosity of 5 × 1033 erg s−1 (assuming a distance of 1.4 kpc). Pulsations were observed by XMM–Newton at an rms amplitude of (7.7 ± 0.5) per cent with a second harmonic stronger than the fundamental frequency, and were detected when the source is neither flaring nor dipping. The most likely interpretation of this detection is that matter from the accretion disc was channelled by the neutron star magnetosphere and accreted on to its polar caps. According to standard disc accretion theory, for pulsations to be observed the mass inflow rate in the disc was likely larger than the amount of plasma actually reaching the neutron star surface; an outflow launched by the fast rotating magnetosphere then probably took place, in agreement with the observed broad-band spectral energy distribution. We also report about the non-detection of X-ray pulsations during a recent observation performed while the source behaved as a rotationally-powered radio pulsar.
Association of Pigmentary Glaucoma and Nonsenile Nuclear Cataracts
Authors: Mosaed Sameh , Haider Asghar , Kim Deborah , Zhang Zina
Published: February 2015

Purpose:

To describe a new association between nonsenile nuclear cataracts and pigmentary glaucoma in patients with controlled intraocular pressure (IOP).

Design:

Retrospective consecutive case series of nonsenile nuclear cataracts seen in patients with pigmentary glaucoma with controlled IOP in a single glaucoma specialist practice. Eight eyes of 7 patients with pigmentary glaucoma and visually significant cataract who underwent cataract removal were reviewed.

Results:

Patients with pigmentary glaucoma developed rapidly progressing, nonsenile nuclear cataracts, with resulting myopic shifts between 4 and 13 D from baseline in <2 years. The patients had controlled IOP and there were no associations between medication use and cataract development.

Conclusions:

A new association between pigmentary glaucoma and nonsenile nuclear cataracts is described. In these patients, the IOP remains controlled and no association is seen between the cataract and medication use. The cataract is rapidly progressive and can cause a myopic shift between 4 and 13 D. Awareness of the purely nuclear cataract and its’ clinical presentation can assist the clinician when approaching the patient with pigment dispersion and decreasing vision. To the best of our knowledge, this is a new association and warrants further investigation.
Comparison of Optical Coherence Tomography Findings in Patients With Primary Open-angle Glaucoma and Parkinson Disease
Authors: Eraslan Muhsin , Balci Sevcan Y. , Cerman Eren , Temel Ahmet , Suer Devran , Elmaci Nese T.
Published: February 2015

Purpose:

To evaluate the peripapillary retinal nerve fiber layer (RNFL), ganglion cell complex, and macular thickness as well as their correlation with the severity of diseases.

Materials and Methods:

This is a cross-sectional study and comparing both eyes of 26 patients with primary open-angle glaucoma, 25 patients with Parkinson disease (PD), and 23 healthy subjects. RNFL, ganglion cell complex, and macular thickness were measured and analyzed with optical coherence tomography (OCT) in all cases and correlation with severity of the disease was assessed in PD group.

Results:

The mean RNFL of PD was significantly thinner compared with controls (P=0.002). In glaucoma group, the mean RNFL was significantly thinner (96.28±12.49 μm) than PD (105.43±13.45 μm) and the controls (113.75±8.53 μm) (P<0.001;P<0.001, respectively). The global loss volume (GLV) rates in the glaucoma and PD group were significantly higher than controls, respectively (P=0.006;P<0.001/P=0.002,P=0.013). However, the GLV rate was significantly lower in PD group compared with glaucoma group (P=0.001). There was no significant correlation between OCT measurements and disease duration or severity in the PD patients.

Conclusions:

Although RNFL thickness and GLV changes may show the ganglion cell loss in both disease but none of the OCT parameters are correlated with the severity of PD. OCT may help to reveal the ganglion cell damage but may not help in determination of severity during the clinical follow-up of PD patients.
Vascular Endothelial Growth Factor is Increased in Aqueous Humor of Acute Primary Angle-Closure Eyes
Authors: Huang Wenbin , Gao Xinbo , Chen Shida , Li Xingyi , Zhang Xinyu , Zhang Xiulan
Published: February 2015

Purpose:

To measure and compare the levels of vascular endothelial growth factor (VEGF) in the aqueous humor of patients with acute primary angle closure (APAC), primary angle-closure glaucoma (PACG), and normal cataract (controls).

Methods:

Aqueous humor samples were prospectively collected from 38 APAC eyes, 36 PACG eyes, and 25 nonglaucomatous cataract control eyes. The levels of aqueous humor VEGF were measured using enzyme-linked immunoassays. The clinical characteristics of participants were also collected for correlation analysis.

Results:

VEGF was detected in aqueous humor samples of 35 of 38 APAC patients (mean±SE of the mean, 935±258 pg/mL), 30 of 36 PACG patients (165±37.5 pg/mL), and 16 of 25 cataract controls (69.5±13.5 pg/mL). The mean concentration of VEGF in APAC eyes was 13.5 and 5.7 times higher than that in controls and PACG eyes, respectively, and these differences were statistically significant (both P<0.0167). In the correlation analysis that included all participants, the aqueous humor VEGF level was found to correlate negatively with axial length (ρ=−0.342, P=0.001), and positively with intraocular pressure (ρ=0.434, P<0.001).

Conclusions:

VEGF was significantly increased in aqueous humor of APAC eyes. An increase in aqueous humor VEGF may be the result of the characteristic ocular ischemia and hypoxia observed in APAC eyes as a consequence of sudden excessive increases in intraocular pressure during the acute episode.
Prescriptions for Bedtime Sedatives After the Introduction of a General Admission Order Set at an Academic Health Center: The Potential and Pitfalls of Order Sets
Authors: Kara Areeba , Isaacs Alex N. , Nisly Sarah A.
Published: February 2015

Objective

This study describes the impact of modifications to a general admission order set on physician prescribing of 2 as-needed or pro re nata (PRN) bedtime sedatives.

Methods

The hospitalists at our institution have used a general medical admission order set since 2005. Zolpidem was the only as-needed (PRN) bedtime sedative option on the order set until trazodone was added in December 2008. Trazodone is preferred over zolpidem in the geriatric population. We identified patients admitted by the hospitalists between January 2007 and August 2013 who were prescribed with either zolpidem or trazodone as a PRN sedative. Patient demographics, date and time of the order, and number of sedative doses administered during the hospitalization were recorded. Orders placed within 12 hours of admission were attributed to admission orders.

Results

Between 2007 and 2013, the number of patients admitted by the hospitalists with an order for PRN trazodone on admission increased by 18-fold. During the same period, the number of admissions by the hospitalists increased by 2.3 times. Zolpidem orders exceeded those for trazodone in all age groups until 2008. After the addition of trazodone, its use exceeded that of zolpidem. Almost half (48%) of all patients did not have a dose of the PRN trazodone administered.

Conclusions

Although order sets can be leveraged to align practitioners with established guidelines, the expediency of using medications on an order set may overcome physicians' clinical judgment. The content of an order set therefore deserves careful scrutiny before implementation.
Baby on board: olfactory cues indicate pregnancy and fetal sex in a non-human primate
Authors: Crawford Jeremy Chase , Drea Christine M.
Published: February 2015

Olfactory cues play an integral, albeit underappreciated, role in mediating vertebrate social and reproductive behaviour. These cues fluctuate with the signaller's hormonal condition, coincident with and informative about relevant aspects of its reproductive state, such as pubertal onset, change in season and, in females, timing of ovulation. Although pregnancy dramatically alters a female's endocrine profiles, which can be further influenced by fetal sex, the relationship between gestation and olfactory cues is poorly understood. We therefore examined the effects of pregnancy and fetal sex on volatile genital secretions in the ring-tailed lemur (
Lemur catta
), a strepsirrhine primate possessing complex olfactory mechanisms of reproductive signalling. While pregnant, dams altered and dampened their expression of volatile chemicals, with compound richness being particularly reduced in dams bearing sons. These changes were comparable in magnitude with other, published chemical differences among lemurs that are salient to conspecifics. Such olfactory ‘signatures’ of pregnancy may help guide social interactions, potentially promoting mother–infant recognition, reducing intragroup conflict or counteracting behavioural mechanisms of paternity confusion; cues that also advertise fetal sex may additionally facilitate differential sex allocation.
Norway rats reciprocate help according to the quality of help they received
Authors: Dolivo Vassilissa , Taborsky Michael
Published: February 2015

Direct reciprocity, according to the decision rule ‘help someone who has helped you before’, reflects cooperation based on the principle of postponed benefits. A predominant factor influencing
Homo sapiens
' motivation to reciprocate is an individ­ual's perceived benefit resulting from the value of received help. But hitherto it has been unclear whether other species also base their decision to cooperate on the quality of received help. Previous experiments have demonstrated that Norway rats,
Rattus norvegicus
, cooperate using direct reciprocity decision rules in a variant of the iterated Prisoner's Dilemma, where they preferentially help cooperators instead of defectors. But, as the quality of obtained benefits has not been varied, it is yet unclear whether rats use the value of received help as decision criterion to pay help back. Here, we tested whether rats distinguish between different cooperators depending purely on the quality of their help. Our data show that a rat's propensity to reciprocate help is, indeed, adjusted to the perceived quality of the partner's previous help. When cooperating with two conspecific partners expending the same effort, rats apparently rely on obtained benefit to adjust their level of returned help.
Coupling human mobility and social ties
Authors: Toole Jameson L. , Herrera-Yaqüe Carlos , Schneider Christian M. , González Marta C.
Published: February 2015

Studies using massive, passively collected data from communication technologies have revealed many ubiquitous aspects of social networks, helping us understand and model social media, information diffusion and organizational dynamics. More recently, these data have come tagged with geographical information, enabling studies of human mobility patterns and the science of cities. We combine these two pursuits and uncover reproducible mobility patterns among social contacts. First, we introduce measures of mobility similarity and predictability and measure them for populations of users in three large urban areas. We find individuals' visitations patterns are far more similar to and predictable by social contacts than strangers and that these measures are positively correlated with tie strength. Unsupervised clustering of hourly variations in mobility similarity identifies three categories of social ties and suggests geography is an important feature to contextualize social relationships. We find that the composition of a user's ego network in terms of the type of contacts they keep is correlated with mobility behaviour. Finally, we extend a popular mobility model to include movement choices based on social contacts and compare its ability to reproduce empirical measurements with two additional models of mobility.
Three-dimensional topology of the SMC2/SMC4 subcomplex from chicken condensin I revealed by cross-linking and molecular modelling
Authors: Barysz Helena , Kim Ji Hun , Chen Zhuo Angel , Hudson Damien F. , Rappsilber Juri , Gerloff Dietlind L. , Earnshaw William C.
Published: February 2015

SMC proteins are essential components of three protein complexes that are important for chromosome structure and function. The cohesin complex holds replicated sister chromatids together, whereas the condensin complex has an essential role in mitotic chromosome architecture. Both are involved in interphase genome organization. SMC-containing complexes are large (more than 650 kDa for condensin) and contain long anti-parallel coiled-coils. They are thus difficult subjects for conventional crystallographic and electron cryomicroscopic studies. Here, we have used amino acid-selective cross-linking and mass spectrometry combined with structure prediction to develop a full-length molecular draft three-dimensional structure of the SMC2/SMC4 dimeric backbone of chicken condensin. We assembled homology-based molecular models of the globular heads and hinges with the lengthy coiled-coils modelled in fragments, using numerous high-confidence cross-links and accounting for potential irregularities. Our experiments reveal that isolated condensin complexes can exist with their coiled-coil segments closely apposed to one another along their lengths and define the relative spatial alignment of the two anti-parallel coils. The centres of the coiled-coils can also approach one another closely
in situ
in mitotic chromosomes. In addition to revealing structural information, our cross-linking data suggest that both H2A and H4 may have roles in condensin interactions with chromatin.
Mechanical analysis of avian feet: multiarticular muscles in grasping and perching
Authors: Backus Spencer B. , Sustaita Diego , Odhner Lael U. , Dollar Aaron M.
Published: February 2015

The grasping capability of birds' feet is a hallmark of their evolution, but the mechanics of avian foot function are not well understood. Two evolutionary trends that contribute to the mechanical complexity of the avian foot are the variation in the relative lengths of the phalanges and the subdivision and variation of the digital flexor musculature observed among taxa. We modelled the grasping behaviour of a simplified bird foot in response to the downward and upward forces imparted by carrying and perching tasks, respectively. Specifically, we compared the performance of various foot geometries performing these tasks when actuated by distally inserted flexors only, versus by both distally inserted and proximally inserted flexors. Our analysis demonstrates that most species possess relative phalanx lengths that are conducive to grasps actuated only by a single distally inserted tendon per digit. Furthermore, proximally inserted flexors are often required during perching, but the distally inserted flexors are sufficient when grasping and carrying objects. These results are reflected in differences in the relative development of proximally and distally inserted digital flexor musculature among ‘perching’ and ‘grasping’ taxa. Thus, our results shed light on the relative roles of variation in phalanx length and digit flexor muscle distribution in an integrative, mechanical context.
Uncomfortable images produce non-sparse responses in a model of primary visual cortex
Authors: Hibbard Paul B. , O'Hare Louise
Published: February 2015

The processing of visual information by the nervous system requires significant metabolic resources. To minimize the energy needed, our visual system appears to be optimized to encode typical natural images as efficiently as possible. One consequence of this is that some atypical images will produce inefficient, non-optimal responses. Here, we show that images that are reported to be uncomfortable to view, and that can trigger migraine attacks and epileptic seizures, produce relatively non-sparse responses in a model of the primary visual cortex. In comparison with the responses to typical inputs, responses to aversive images were larger and less sparse. We propose that this difference in the neural population response may be one cause of visual discomfort in the general population, and can produce more extreme responses in clinical populations such as migraine and epilepsy sufferers.
Homogenization of two fluid flow in porous media
Authors: Daly K. R. , Roose T.
Published: February 2015

The macroscopic behaviour of air and water in porous media is often approximated using Richards' equation for the fluid saturation and pressure. This equation is parametrized by the hydraulic conductivity and water release curve. In this paper, we use homogenization to derive a general model for saturation and pressure in porous media based on an underlying periodic porous structure. Under an appropriate set of assumptions, i.e. constant gas pressure, this model is shown to reduce to the simpler form of Richards' equation. The starting point for this derivation is the Cahn–Hilliard phase field equation coupled with Stokes equations for fluid flow. This approach allows us, for the first time, to rigorously derive the water release curve and hydraulic conductivities through a series of cell problems. The method captures the hysteresis in the water release curve and ties the macroscopic properties of the porous media with the underlying geometrical and material properties.
Energy control of inhomogeneous nonlinear lattices
Authors: Udwadia Firdaus E. , Mylapilli Harshavardhan
Published: February 2015

This paper considers energy control of an
n
-d.f. inhomogeneous nonlinear lattice with fixed–fixed and fixed–free ends. The lattice consists of dissimilar masses wherein each mass is connected to its nearest neighbour by a nonlinear or linear memoryless spring element. The potential functions of the nonlinear spring elements are assumed to be qualitatively different. Each potential is described by a twice continuously differentiable, strictly convex function, possessing a global minimum at zero displacement, with zero curvature possibly only at zero displacement. The energy control requirement is viewed from an analytical dynamics perspective and is recast as a constraint on the motion of the dynamical system. No linearizations and/or approximations of the nonlinear dynamical system or the controller are made. Given the set of masses at which control is to be applied, explicit closed form expressions for the nonlinear control forces are obtained. Global asymptotic convergence to any desired non-zero energy state is guaranteed provided that the first mass, or the last mass or, alternatively, any two consecutive masses in the lattice are included in the subset of masses that are controlled. Numerical simulations involving a 101-mass nonlinear lattice demonstrate the simplicity and efficacy of the approach.
Cumulants, free cumulants and half-shuffles
Authors: Ebrahimi-Fard Kurusch , Patras Frédéric
Published: February 2015

Free cumulants were introduced as the proper analogue of classical cumulants in the theory of free probability. There is a mix of similarities and differences, when one considers the two families of cumulants. Whereas the combinatorics of classical cumulants is well expressed in terms of set partitions, that of free cumulants is described and often introduced in terms of non-crossing set partitions. The formal series approach to classical and free cumulants also largely differs. The purpose of this study is to put forward a different approach to these phenomena. Namely, we show that cumulants, whether classical or free, can be understood in terms of the algebra and combinatorics underlying commutative as well as non-commutative (half-)shuffles and (half-) unshuffles. As a corollary, cumulants and free cumulants can be characterized through linear fixed point equations. We study the exponential solutions of these linear fixed point equations, which display well the commutative, respectively non-commutative, character of classical and free cumulants.
A Miocene hyperdiverse crocodylian community reveals peculiar trophic dynamics in proto-Amazonian mega-wetlands
Authors: Salas-Gismondi Rodolfo , Flynn John J. , Baby Patrice , Tejada-Lara Julia V. , Wesselingh Frank P. , Antoine Pierre-Olivier
Published: February 2015

Amazonia contains one of the world's richest biotas, but origins of this diversity remain obscure. Onset of the Amazon River drainage at approximately 10.5 Ma represented a major shift in Neotropical ecosystems, and proto-Amazonian biotas just prior to this pivotal episode are integral to understanding origins of Amazonian biodiversity, yet vertebrate fossil evidence is extraordinarily rare. Two new species-rich bonebeds from late Middle Miocene proto-Amazonian deposits of northeastern Peru document the same hyperdiverse assemblage of seven co-occurring crocodylian species. Besides the large-bodied
Purussaurus
and
Mourasuchus
, all other crocodylians are new taxa, including a stem caiman—
Gnatusuchus pebasensis
—bearing a massive shovel-shaped mandible, procumbent anterior and globular posterior teeth, and a mammal-like diastema. This unusual species is an extreme exemplar of a radiation of small caimans with crushing dentitions recording peculiar feeding strategies correlated with a peak in proto-Amazonian molluscan diversity and abundance. These faunas evolved within dysoxic marshes and swamps of the long-lived Pebas Mega-Wetland System and declined with inception of the transcontinental Amazon drainage, favouring diversification of longirostrine crocodylians and more modern generalist-feeding caimans. The rise and demise of distinctive, highly productive aquatic ecosystems substantially influenced evolution of Amazonian biodiversity hotspots of crocodylians and other organisms throughout the Neogene.
Did shifting seawater sulfate concentrations drive the evolution of deep-sea methane-seep ecosystems?
Authors: Kiel Steffen
Published: February 2015

The origin and evolution of the faunas inhabiting deep-sea hydrothermal vents and methane seeps have been debated for decades. These faunas rely on a local source of sulfide and other reduced chemicals for nutrition, which spawned the hypothesis that their evolutionary history is independent from that of photosynthesis-based food chains and instead driven by extinction events caused by deep-sea anoxia. Here I use the fossil record of seep molluscs to show that trends in body size, relative abundance and epifaunal/infaunal ratios track current estimates of seawater sulfate concentrations through the last 150 Myr. Furthermore, the two main faunal turnovers during this time interval coincide with major changes in seawater sulfate concentrations. Because sulfide at seeps originates mostly from seawater sulfate, variations in sulfate concentrations should directly affect the base of the food chain of this ecosystem and are thus the likely driver of the observed macroecologic and evolutionary patterns. The results imply that the methane-seep fauna evolved largely independently from developments and mass extinctions affecting the photosynthesis-based biosphere and add to the growing body of evidence that the chemical evolution of the oceans had a major impact on the evolution of marine life.
Rapid, generalized adaptation to asynchronous audiovisual speech
Authors: Van der Burg Erik , Goodbourn Patrick T.
Published: February 2015

The brain is adaptive. The speed of propagation through air, and of low-level sensory processing, differs markedly between auditory and visual stimuli; yet the brain can adapt to compensate for the resulting cross-modal delays. Studies investigating temporal recalibration to audiovisual speech have used prolonged adaptation procedures, suggesting that adaptation is sluggish. Here, we show that adaptation to asynchronous audiovisual speech occurs rapidly. Participants viewed a brief clip of an actor pronouncing a single syllable. The voice was either advanced or delayed relative to the corresponding lip movements, and participants were asked to make a synchrony judgement. Although we did not use an explicit adaptation procedure, we demonstrate rapid recalibration based on a single audiovisual event. We find that the point of subjective simultaneity on each trial is highly contingent upon the modality order of the preceding trial. We find compelling evidence that rapid recalibration generalizes across different stimuli, and different actors. Finally, we demonstrate that rapid recalibration occurs even when auditory and visual events clearly belong to different actors. These results suggest that rapid temporal recalibration to audiovisual speech is primarily mediated by basic temporal factors, rather than higher-order factors such as perceived simultaneity and source identity.
Brittle fracture in structural steels: perspectives at different size-scales
Authors: Knott John
Published: February 2015

This paper describes characteristics of transgranular cleavage fracture in structural steel, viewed at different size-scales. Initially, consideration is given to structures and the service duty to which they are exposed at themacroscale, highlighting failure by plastic collapse and failure by brittle fracture. This is followed by sections describing the use of fracture mechanics and materials testing in carrying-out assessments of structural integrity. Attention then focuses on themicroscale, explaining how values of the local fracture stress in notched bars or of fracture toughness in pre-cracked test-pieces are related to features of the microstructure: carbide thicknesses in wrought material; the sizes of oxide/silicate inclusions in weld metals. Effects of a microstructure that is ‘heterogeneous’ at themesoscaleare treated briefly, with respect to the extraction of test-pieces from thick sections and to extrapolations of data to low failure probabilities. The values of local fracture stress may be used to infer a local ‘work-of-fracture’ that is found experimentally to be a few times greater than that of two free surfaces. Reasons for this are discussed in the conclusion section onnano-scale events. It is suggested that, ahead of a sharp crack, it is necessary to increase the compliance by a cooperative movement of atoms (involving extra work) to allow the crack-tip bond to displace sufficiently for the energy of attraction between the atoms to reduce to zero.
Crossing grain boundaries in metals by slip bands, cleavage and fatigue cracks
Authors: Pineau André
Published: February 2015

The size and the character (low and large angle, special boundaries, tilt and twist boundaries, twins) of the grain boundaries (GBs) in polycrystalline materials influence their strength and their fracture toughness. Recent studies devoted to nanocrystalline (NC) materials have shown a deviation from the Hall–Petch law. Special GBs formed by Σ3 twins in face-centred cubic metals are also known to have a strong effect on the mechanical behaviour of these metals, in particular their work-hardening rate. Grain orientation influences also crack path, the fracture toughness of body-centred cubic (BCC) metals and the fatigue crack growth rate of microstructurally short cracks. This paper deals both with slip transfer at GBs and with the interactions between propagating cracks with GBs. In the analysis of slip transfer, the emphasis is placed on twin boundaries (TBs) for which the dislocation reactions during slip transfer are analysed theoretically, experimentally and using the results of atomic molecular simulations published in the literature. It is shown that in a number of situations this transfer leads to a normal motion of the TB owing to the displacement of partial dislocations along the TB. This motion can generate a de-twinning effect observed in particular in NC metals. Crack propagation across GBs is also considered. It is shown that cleavage crack path behaviour in BCC metals is largely dependent on the twist component of the GBs. A mechanism for the propagation of these twisted cracks involving a segmentation of the crack front and the existence of intergranular parts is discussed and verified for a pressure vessel steel. A similar segmentation seems to occur for short fatigue cracks although, quite surprisingly, this crossing mechanism for fatigue cracks does not seem to have been examined in very much detail in the literature. Metallurgical methods used to improve the strength of the materials, via grain boundaries, are briefly discussed.
Marivirga atlantica sp. nov., isolated from seawater and emended description of the genus
Marivirga
Authors: Lin Chao-Yi , Zhang Xi-Ying , Liu Ang , Liu Chang , Song Xiao-Yan , Su Hai-Nan , Qin Qi-Long , Xie Bin-Bin , Zhang Yu-Zhong
Published: February 2015

A novel Gram-stain-negative, aerobic, orange-pigmented, non-flagellated, gliding, rod-shaped bacterium, designated strain SM1354T was isolated from surface seawater of the Atlantic Ocean. The strain hydrolysed gelatin and DNA but did not reduce nitrate. It grew at 4–40 °C and with 0.5–11 % (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene sequences revealed that strain SM1354T belonged to the genus

Marivirga

with 96.0–96.2 % sequence similarities to known species of the genus

Marivirga

. The major fatty acids of strain SM1354T were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 03-OH and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 02-OH). Polar lipids of strain SM1354T included phosphatidylethanolamine, three unidentified lipids and one unidentified aminolipid and aminophospholipid. The major respiratory quinone of strain SM1354T was menaquinone 7 (MK-7). The genomic DNA G+C content of strain SM1354T was 33.9±0.4 mol%. On the basis of the results of the polyphasic characterization in this study, it is proposed that strain SM1354T represents a novel species of the genus

Marivirga

, namely Marivirga atlantica sp. nov. The type strain of Marivirga atlantica is SM1354T ( = CCTCC AB 2014242T = JCM 30305T). An emended description of the genus

Marivirga

is also proposed.
Rhizobium metallidurans sp. nov., a symbiotic heavy metal resistant bacterium isolated from the Anthyllis vulneraria Zn-hyperaccumulator
Authors: Grison Claire M. , Jackson Stephen , Merlot Sylvain , Dobson Alan , Grison Claude
Published: February 2015

A Gram-stain-negative, aerobic, rod-shaped, non-spore-forming bacterium (ChimEc512T) was isolated from 56 host seedlings of the hyperaccumulating Anthyllis vulneraria legume, which was on an old zinc mining site at Les Avinières, Saint-Laurent-Le-Minier, Gard, South of France. On the basis of 16S rRNA gene sequence similarities, strain ChimEc512T was shown to belong to the genus

Rhizobium

and to be most closely related to

Rhizobium endophyticum

CCGE 2052T (98.4 %),

Rhizobium tibeticum

CCBAU 85039T (98.1 %),

Rhizobium grahamii

CCGE 502T (98.0 %) and

Rhizobium mesoamericanum

CCGE 501T (98.0 %). The phylogenetic relationships of ChimEc512T were confirmed by sequencing and analyses of recA and atpD genes. DNA–DNA relatedness values of strain ChimEc512T with

R. endophyticum

CCGE 2052T,

R. tibeticum

CCBAU 85039T,

R. mesoamericanum

CCGE 52T,

Rhizobium grahamii

CCGE 502T,

Rhizobium etli

CCBAU 85039T and

Rhizobium radiobacter

KL09-16-8-2T were 27, 22, 16, 18, 19 and 11 %, respectively. The DNA G+C content of strain ChimEc512T was 58.9 mol%. The major cellular fatty acid was C18 : 1ω7c, characteristic of the genus

Rhizobium

. The polar lipid profile included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine and moderate amounts of aminolipids, phospholipid and sulfoquinovosyl diacylglycerol. Although ChimEc512T was able to nodulate A. vulneraria, the nodC and nifH genes were not detected by PCR. The rhizobial strain was tolerant to high concentrations of heavy metals: up to 35 mM Zn and up to 0.5 mM Cd and its growth kinetics was not impacted by Zn. The results of DNA–DNA hybridizations and physiological tests allowed genotypic and phenotypic differentiation of strain ChimEc512T from species of the genus

Rhizobium

with validly published names. Strain ChimEc512T, therefore, represents a novel species, for which the name Rhizobium metallidurans sp. nov. is proposed, with the type strain ChimEc512T ( = DSM 26575 = CIP 110550T).
Bacillus crassostreae sp. nov., isolated from an oyster (Crassostrea hongkongensis)
Authors: Chen Jin-Hua , Tian Xiang-Rong , Ruan Ying , Yang Ling-Ling , He Ze-Qiang , Tang Shu-Kun , Li Wen-Jun , Shi Huazhong , Chen Yi-Guang
Published: February 2015

A novel Gram-stain-positive, motile, catalase- and oxidase-positive, endospore-forming, facultatively anaerobic rod, designated strain JSM 100118T, was isolated from an oyster (Crassostrea hongkongensis) collected from the tidal flat of Naozhou Island in the South China Sea. Strain JSM 100118T was able to grow with 0–13 % (w/v) NaCl (optimum 2–5 %), at pH 5.5–10.0 (optimum pH 7.5) and at 5–50 °C (optimum 30–35 °C). The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant respiratory quinone was menaquinone-7 and the major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C16 : 0 and C16 : 1ω11c. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown glycolipid and an unknown phospholipid. The genomic DNA G+C content was 35.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 100118T belonged to the genus

Bacillus

, and was most closely related to

Bacillus litoralis

SW-211T (98.9 % 16S rRNA gene sequence similarity),

Bacillus halosaccharovorans

E33T (98.3 %),

Bacillus niabensis

4T19T (97.8 %) and

Bacillus herbersteinensis

D-1,5aT (97.1 %). The combination of results from the phylogenetic analysis, DNA–DNA hybridization, and phenotypic and chemotaxonomic characterization supported the conclusion that strain JSM 100118T represents a novel species of the genus

Bacillus

, for which the name Bacillus crassostreae sp. nov. is proposed. The type strain is JSM 100118T ( = CCTCC AB 2010452T = DSM 24486T = JCM 17523T).
Mameliella phaeodactyli sp. nov., a member of the family Rhodobacteraceae isolated from the marine algae Phaeodactylum tricornutum
Authors: Chen Zhangran , Zhang Jingyan , Lei Xueqian , Lai Qiliang , Yang Luxi , Zhang Huajun , Li Yi , Zheng Wei , Tian Yun , Yu Zhiming , Xu Hong , Zheng Tianling
Published: February 2015

A novel Gram-staining-negative, aerobic, rod-shaped, non-motile, yellow bacterium designated strain KD53T, was isolated from a culture of the alga Phaeodactylum tricornutum from Xiamen, Fujian Province, China. 16S rRNA gene sequence comparison showed that strain KD53T was a member of the Roseobacter clade within the family

Rhodobacteraceae

, forming a distinct lineage with species of the genus

Mameliella

. The 16S rRNA gene sequence similarities between strain KD53T and other strains examined were all less than 97.0 %. Strain KD53T was found to grow optimally at 28 °C, at pH 7.5–8.0 and in the presence of 3 % (w/v) NaCl. The dominant fatty acids of strain KD53T were C18 : 1ω6c and/or C18 : 1ω7c, C18 : 0 and C16 : 0. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 65 mol% and the major respiratory quinone was ubiquinone 10 (Q-10). On the basis of phenotypic data and phylogenetic inference, strain KD53T represents a novel member of the genus

Mameliella

, then the name Mameliella phaeodactyli sp. nov. is proposed. The type strain is KD53T ( = MCCC 1K00273T = KCTC 42178T).
Nocardioides deserti sp. nov., an actinobacterium isolated from desert soil
Authors: Tuo Li , Dong Yan-Ping , Habden Xugela , Liu Jia-Meng , Guo Lin , Liu Xian-Fu , Chen Li , Jiang Zhong-Ke , Liu Shao-Wei , Zhang Yu-Bin , Zhang Yu-Qin , Sun Cheng-Hang
Published: February 2015

A rod- or coccus-shaped, non-spore-forming actinobacterium, designated strain SC8A-24T, was isolated from a soil sample collected from the rhizosphere of Alhagi sparsifolia on the southern edge of the Taklimakan desert, Xinjiang, China, and examined by a polyphasic approach to clarify its taxonomic position. This actinobacterium was Gram-staining-positive and aerobic. Substrate and aerial mycelia were not observed, and no diffusible pigments were observed on the media tested. Strain SC8A-24T grew optimally without NaCl at 28–30 °C and pH 7.0–8.0. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain SC8A-24T belonged to the genus

Nocardioides

and shared the highest 16S rRNA gene sequence similarity with

Nocardioides salarius

CL-Z59T (96.51 %),

N. pyridinolyticus

OS4T (96.43 %) and

N. ginsengagri

BX5-10T (96.37 %). The DNA G+C content of strain SC8A-24T was 71 mol%. The cell-wall peptidoglycan contained ll-2,6-diaminopimelic acid, and MK-8(H4) was the predominant menaquinone. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid and an unidentified phospholipid. The major fatty acids were C17 : 1ω8c, 10-methyl C17 : 0 and C18 : 1ω9c. On the basis of phylogenetic analysis and phenotypic and chemotaxonomic characteristics, strain SC8A-24T represents a novel species of the genus

Nocardioides

, for which the name Nocardioides deserti sp. nov. is proposed. The type strain is SC8A-24T ( = DSM 26045T = CGMCC 4.7183T).