bluuebunny/crossref_metadata_2025_split huggingface dataset:
Was the Ediacaran–Cambrian radiation a unique evolutionary event?
Authors: Erwin Douglas H. 
Published: March 2015

AbstractThe extent of morphologic innovation during the Ediacaran–Cambrian diversification of animals was unique in the history of metazoan life. This episode was also associated with extensive changes in the redox state of the oceans, in the structure of benthic and pelagic marine ecosystems, in the nature of marine sediments, and in the complexity of developmental interactions in Eumetazoa. But did the phylogenetic and morphologic breadth of this episode simply reflect the unusual outcome of recurrent evolutionary processes, or was it the unique result of circumstances, whether in the physical environment, in developmental mechanisms, or in ecological interactions? To better characterize the uniqueness of the events, I distinguish among these components on the basis of the extent of sensitivity to initial conditions and unpredictability, which generates a matrix of possibilities from fully contingent to fully deterministic. Discriminating between these differences is important for informing debates over determinism versus the contingency in the history of life, for understanding the nature of evolutionary theory, and for interpreting historically unique events.
Taphonomic biases in the insect fossil record: shifts in articulation over geologic time
Authors: Karr Jered A. , Clapham Matthew E. 
Published: March 2015

AbstractInsect taphonomy is a topic that has drawn interest because of its potential biases on diversity patterns and the ecological information recorded by ancient insect faunas. Other than the onset of common amber fossilization in the Cretaceous, very little is known about long-term trends in the nature and quality of insect preservation and, as a result, the effects of taphonomic biases are poorly constrained. We assembled a database of nearly 7000 Carboniferous–Pliocene insect adpression (compression and impression) species from the primary literature to assess changes in insect taphonomy over time and test biotic and environmental controls on preservation. We grouped the fossils into 10-Myr bins and scored preservation of holotype specimens as either articulated bodies or isolated wings; articulated specimens with a body implied a generally higher quality of preservation. Paleozoic and Triassic insect holotypes are known overwhelmingly from isolated wings (only 12% articulated bodies), but our database shows a significant increase in the percentage preserved as articulated bodies, to more than 70%, beginning about 160 Myr ago in the Late Jurassic. This transition could reflect variations in the robustness of different insect orders and shifts in the taxonomic composition of insect faunas, but all the major orders in the database exhibit significant increases in articulation. Instead, a shift to increased preservation in lacustrine paleoenvironments, which contain a greater proportion of articulated body fossils, explains most of the trend. The pronounced Late Jurassic increase in articulation has implications for evolutionary and ecological reconstructions, for example, suggesting that preserved insect diversity may be biased downward in the earlier part of their history when articulation was poor.
A morphospace of planktonic marine diatoms. II. Sampling standardization and spatial disparity partitioning
Authors: Kotrc Benjamin , Knoll Andrew H. 
Published: March 2015

AbstractMorphospace occupation through time provides a view of diversification distinct from the more familiar taxonomic tabulations. However, this view is subject to the same geological biases long recognized in studies of taxonomic diversification, where techniques for correcting secular bias in sampling have become standard practice. In this study, we apply sampling standardization techniques to a morphospace investigation to test whether observed stratigraphic trends in morphospace occupation are artifacts of trends in sampling. When sampling bias is corrected by randomized subsampling, all disparity metrics show stationary patterns, or at most directional changes of small magnitude. Metrics describing the average dispersion of taxa in morphospace are less subject to sampling bias than those describing the total extent of morphospace occupied. We also investigate a measure of disparity that is insensitive to sampling intensity, introducing a geographic component of morphological disparity. By analogy to α and β components of taxonomic diversity, we suggest the notions of α and β disparity, and find that α disparity remains roughly constant through time. Our analysis also allows us to present the first taxonomic diversity curve of diatoms under shareholder quorum subsampling (SQS), showing similar results to previously published subsampling methods: a roughly twofold rise over the Cenozoic, with peak diversity around the Eocene/Oligocene boundary. Tests for methodological bias from choices in ordination method and data culling during morphospace construction indicate that our results are relatively insensitive to both factors: Cenozoic occupation of planktonic diatom morphospace is largely unchanging. We find a similarly stationary pattern when we directly analyze the morphological data, seeing no change in the prevalence of taxa with different sets of morphological characters. More broadly, our results make clear that a complete view of morphological disparity must consider sampling biases, which can be addressed with wellestablished, quantitative methods in morphospaces populated using occurrence-level data.
Testing for escalation in Lower Mississippian camerate crinoids
Authors: Thompson Jeffrey R. , Ausich William I. 
Published: March 2015

AbstractCrinoids were relatively unaffected by the end-Devonian Hangenberg mass extinction event. Major clades of Devonian durophagous fishes suffered significant extinctions, however, and the dominant surviving clades were biting or nipping predators. In part as a response to the Hangenberg event, early Mississippian crinoids underwent an adaptive radiation, while fish clades with a shell-crushing durophagous strategy diversified. Durophagous predators are inferred to have been more effective predators on camerate crinoids; and it is hypothesized, following the predictions of escalation, that through the early Mississippian, camerate crinoids evolved more effective anti-predatory strategies in response. We test this hypothesis of escalation by examining the changes in spinosity and plate convexity among camerate crinoids throughout this interval. A new method was formulated to test for an increase in convexity of the tegmen plates. Traits inAgaricocrinus,Aorocrinus, andDorycrinus(Family Coelocrinidae) were tested for congruence to the escalation hypothesis, and results were mixed. Convexity of tegmen plates inAgaricocrinus, spine length/calyx diameter inAorocrinus, calyx size inAorocrinus, central spine length inDorycrinus, and spine width inDorycrinusdid not have size increase trends supporting escalation. Rather than an increase in convexity, the variance of convexity inAgaricocrinustegmen plates narrowed, which could reflect an optimum. Alternatively, morphological change consistent with the escalation hypothesis occurred in calyx size ofAgaricocrinusand in lateral spine length and calyx size inDorycrinus. Furthermore, central and lateral spine length, parameters of the spine width, and size trends support escalation whenAorocrinusandDorycrinusare treated as a lineage. Thus, inferred escalation acted on traits differently within a single lineage and was relevant for both speciation and the diversification of a new genus.
Geographic variation of parasitic and predatory traces on mollusks in the northern Adriatic Sea, Italy: implications for the stratigraphic paleobiology of biotic interactions
Authors: Warren Huntley John , Scarponi Daniele 
Published: March 2015

AbstractParasitic trematode worms leave characteristic pits in their bivalve mollusk hosts and represent an ideal system for analyzing parasite-host interactions through space and time with statistically meaningful sample sizes. Previous work in Late Pleistocene–Holocene sequences from the Po plain revealed significant long-term fluctuations in trematode prevalence values: higher prevalence in retrogradational environments (TST) and negligible prevalence in progradational environments (HST). Here we expand upon this work by investigating traces of parasitism, kleptoparasitism, and predation on mollusk death assemblages from two domains along the northern Adriatic coastline. The domain north of the Po delta (TST-like) and the southern domain (including the Po delta; HST-like) comprise environments comparable to those recovered in late Holocene (<6 Kyr) subsurface progradational deposits. We collected 17,299 specimens representing 111 species from 11 locations on the northern Adriatic coast of Italy. Our results reveal high predation pressure, a high diversity of host taxa, and widespread presence of trematode infestation in starved, oligotrophic, environmentally more stable (i.e., TST-like) settings north of the Po delta. Immediately south of the Po delta, in settings with strong and variable sedimentary input, almost no infestation is recorded. The reappearance of infestation is evident in the southern portion of the study area (i.e., Cattolica-Montemarciano), relatively far from the highly stressed environments south of the Po River. There is no significant difference in trematode prevalence values between fossil and modern samples. The distribution of spionid traces (an indicator of stressed environments) was nearly the opposite of that displayed by trematodes. Drilling frequency is highest in TST-like environments and is not correlated with diversity indices. These results suggest that temporal trends of trematode prevalence (and possibly also other biotic interactions) in sedimentary successions are controlled by environmental changes driven by glacio-eustatic dynamics, and reaffirm the importance of interpreting temporal trends in the context of spatial variation.
Robust Focus Measure Operator Using Adaptive Log-Polar Mapping for Three-Dimensional Shape Recovery
Authors: Lee Ik-Hyun , Mahmood Muhammad Tariq , Choi Tae-Sun 
Published: March 2015

AbstractShape from focus (SFF) is a passive optical technique that reconstructs object shape from a sequence of image taken at different focus levels. In SFF techniques, computing focus measurement for each pixel in the image sequence, through a focus measure operator, is the fundamental step. Commonly used focus measure operators compute focus quality in Cartesian space and suffer from erroneous focus quality and lack in robustness. Thus, they provide erroneous depth maps. In this paper, we introduce a new focus measure operator that computes focus quality in log-polar transform (LPT) Properties of LPT, such as biological inspiration, data selection, and edge invariance, enable computation of better focus quality in the presence of noise. Moreover, instead of using a fixed patch of the image, we suggest the use of an adaptive window. The focus quality is assessed by computing variation in LPT. The effectiveness of the proposed technique is evaluated by conducting experiments using image sequences of different simulated and real objects. The comparative analysis shows that the proposed method is robust and effective in the presence of various types of noise.
Genomic and phenotypic differentiation among Methanosarcina mazei populations from Columbia River sediment
Authors: Youngblut Nicholas D , Wirth Joseph S , Henriksen James R , Smith Maria , Simon Holly , Metcalf William W , Whitaker Rachel J 
Published: March 2015

Abstract
Methanogenic archaea are genotypically and phenotypically diverse organisms that are integral to carbon cycling in anaerobic environments. Owing to their genetic tractability and ability to be readily cultivated, Methanosarcina spp. have become a powerful model system for understanding methanogen biology at the cellular systems level. However, relatively little is known of how genotypic and phenotypic variation is partitioned in Methanosarcina populations inhabiting natural environments and the possible ecological and evolutionary implications of such variation. Here, we have identified how genomic and phenotypic diversity is partitioned within and between Methanosarcina mazei populations obtained from two different sediment environments in the Columbia River Estuary (Oregon, USA). Population genomic analysis of 56 M. mazei isolates averaging &lt;1% nucleotide divergence revealed two distinct clades, which we refer to as ‘mazei-T’ and ‘mazei-WC’. Genomic analyses showed that these clades differed in gene content and fixation of allelic variants, which point to potential differences in primary metabolism and also interactions with foreign genetic elements. This hypothesis of niche partitioning was supported by laboratory growth experiments that revealed significant differences in trimethylamine utilization. These findings improve our understanding of the ecologically relevant scales of genomic variation in natural systems and demonstrate interactions between genetic and ecological diversity in these easily cultivable and genetically tractable model methanogens.
Brown fat activation reduces hypercholesterolaemia and protects from atherosclerosis development
Authors: Berbée Jimmy F. P. , Boon Mariëtte R , Khedoe P. Padmini S. J. , Bartelt Alexander , Schlein Christian , Worthmann Anna , Kooijman Sander , Hoeke Geerte , Mol Isabel M. , John Clara , Jung Caroline , Vazirpanah Nadia , Brouwers Linda P.J. , Gordts Philip L.S.M. , Esko Jeffrey D. , Hiemstra Pieter S. , Havekes Louis M. , Scheja Ludger , Heeren Joerg , Rensen Patrick C.N. 
Published: March 2015

AbstractBrown adipose tissue (BAT) combusts high amounts of fatty acids, thereby lowering plasma triglyceride levels and reducing obesity. However, the precise role of BAT in plasma cholesterol metabolism and atherosclerosis development remains unclear. Here we show that BAT activation by β3-adrenergic receptor stimulation protects from atherosclerosis in hyperlipidemic APOE*3-Leiden.CETP mice, a well-established model for human-like lipoprotein metabolism that unlike hyperlipidemic Apoe−/− and Ldlr−/− mice expresses functional apoE and LDLR. BAT activation increases energy expenditure and decreases plasma triglyceride and cholesterol levels. Mechanistically, we demonstrate that BAT activation enhances the selective uptake of fatty acids from triglyceride-rich lipoproteins into BAT, subsequently accelerating the hepatic clearance of the cholesterol-enriched remnants. These effects depend on a functional hepatic apoE-LDLR clearance pathway as BAT activation in Apoe−/− and Ldlr−/− mice does not attenuate hypercholesterolaemia and atherosclerosis. We conclude that activation of BAT is a powerful therapeutic avenue to ameliorate hyperlipidaemia and protect from atherosclerosis.
Cenpj/CPAP regulates progenitor divisions and neuronal migration in the cerebral cortex downstream of Ascl1
Authors: Garcez Patricia P. , Diaz-Alonso Javier , Crespo-Enriquez Ivan , Castro Diogo , Bell Donald , Guillemot François 
Published: March 2015

AbstractThe proneural factor Ascl1 controls multiple steps of neurogenesis in the embryonic brain, including progenitor division and neuronal migration. Here we show that Cenpj, also known as CPAP, a microcephaly gene, is a transcriptional target of Ascl1 in the embryonic cerebral cortex. We have characterized the role of Cenpj during cortical development by in utero electroporation knockdown and found that silencing Cenpj in the ventricular zone disrupts centrosome biogenesis and randomizes the cleavage plane orientation of radial glia progenitors. Moreover, we show that downregulation of Cenpj in post-mitotic neurons increases stable microtubules and leads to slower neuronal migration, abnormal centrosome position and aberrant neuronal morphology. Moreover, rescue experiments shows that Cenpj mediates the role of Ascl1 in centrosome biogenesis in progenitor cells and in microtubule dynamics in migrating neurons. These data provide insights into genetic pathways controlling cortical development and primary microcephaly observed in humans with mutations in Cenpj.
Defective podocyte insulin signalling through p85-XBP1 promotes ATF6-dependent maladaptive ER-stress response in diabetic nephropathy
Authors: Madhusudhan Thati , Wang Hongjie , Dong Wei , Ghosh Sanchita , Bock Fabian , Thangapandi Veera Raghavan , Ranjan Satish , Wolter Juliane , Kohli Shrey , Shahzad Khurrum , Heidel Florian , Krueger Martin , Schwenger Vedat , Moeller Marcus J. , Kalinski Thomas , Reiser Jochen , Chavakis Triantafyllos , Isermann Berend 
Published: March 2015

AbstractEndoplasmic reticulum (ER) stress is associated with diabetic nephropathy (DN), but its pathophysiological relevance and the mechanisms that compromise adaptive ER signalling in podocytes remain unknown. Here we show that nuclear translocation of the transcription factor spliced X-box binding protein-1 (sXBP1) is selectively impaired in DN, inducing activating transcription factor-6 (ATF6) and C/EBP homology protein (CHOP). Podocyte-specific genetic ablation of XBP1 or inducible expression of ATF6 in mice aggravates DN. sXBP1 lies downstream of insulin signalling and attenuating podocyte insulin signalling by genetic ablation of the insulin receptor or the regulatory subunits phosphatidylinositol 3-kinase (PI3K) p85α or p85β impairs sXBP1 nuclear translocation and exacerbates DN. Corroborating our findings from murine DN, the interaction of sXBP1 with p85α and p85β is markedly impaired in the glomerular compartment of human DN. Thus, signalling via the insulin receptor, p85, and XBP1 maintains podocyte homeostasis, while disruption of this pathway impairs podocyte function in DN.
Comparison between single-molecule and X-ray crystallography data on yeast F1-ATPase
Authors: Steel Bradley C. , Nord Ashley L. , Wang Yamin , Pagadala Vijayakanth , Mueller David M. , Berry Richard M. 
Published: March 2015

AbstractSingle molecule studies in recent decades have elucidated the full chemo-mechanical cycle of F1-ATPase, mostly based on F1 from thermophilic bacteria. In contrast, high-resolution crystal structures are only available for mitochondrial F1. Here we present high resolution single molecule rotational data on F1 from Saccharomyces cerevisiae, obtained using new high throughput detection and analysis tools. Rotational data are presented for the wild type mitochondrial enzyme, a “liver” isoform and six mutant forms of yeast F1 that have previously been demonstrated to be less efficient or partially uncoupled. The wild-type and “liver” isoforms show the same qualitative features as F1 from Escherichia coli and thermophilic bacteria. The analysis of the mutant forms revealed a delay at the catalytic dwell and associated decrease in Vmax, with magnitudes consistent with the level of disruption seen in the crystal structures. At least one of the mutant forms shows a previously un-observed dwell at the ATP binding angle, potentially attributable to slowed release of ADP. We discuss the correlation between crystal structures and single molecule results.
Nicotinic Acid is a Common Regulator of Heat-Sensing TRPV1-4 Ion Channels
Authors: Ma Linlin , Lee Bo Hyun , Clifton Heather , Schaefer Saul , Zheng Jie 
Published: March 2015

AbstractNicotinic acid (NA, a.k.a. vitamin B3 or niacin) can reduce blood cholesterol and low-density lipoproteins whereas increase high-density lipoproteins. However, when NA is used to treat dyslipidemias, it causes a strong side effect of cutaneous vasodilation, commonly called flushing. A recent study showed that NA may cause flushing by lowering activation threshold temperature of the heat-sensitive capsaicin receptor TRPV1 ion channel, leading to its activation at body temperature. The finding calls into question whether NA might also interact with the homologous heat-sensitive TRPV2–4 channels, particularly given that TRPV3 and TRPV4 are abundantly expressed in keratinocytes of the skin where much of the flushing response occurs. We found that NA indeed potentiated TRPV3 while inhibited TRPV2 and TRPV4. Consistent with these gating effects, NA lowered the heat-activation threshold of TRPV3 but elevated that of TRPV4. We further found that activity of TRPV1 was substantially prolonged by extracellular NA, which may further enhance the direct activation effect. Consistent with the broad gating effect on TRPV1–4 channels, evidence from the present study hints that NA may share the same activation pathway as 2-aminoethoxydiphenyl borate (2-APB), a common agonist for these TRPV channels. These findings shed new light on the molecular mechanism underlying NA regulation of TRPV channels.
p53 Suppresses Tetraploid Development in Mice
Authors: Horii Takuro , Yamamoto Masamichi , Morita Sumiyo , Kimura Mika , Nagao Yasumitsu , Hatada Izuho 
Published: March 2015

AbstractMammalian tetraploid embryos die in early development because of defects in the epiblast. Experiments with diploid/tetraploid chimeric mice, obtained via the aggregation of embryonic stem cells, clarified that while tetraploid cells are excluded from epiblast derivatives, diploid embryos with tetraploid extraembryonic tissues can develop to term. Today, this method, known as tetraploid complementation, is usually used for rescuing extraembryonic defects or for obtaining completely embryonic stem (ES) cell-derived pups. However, it is still unknown why defects occur in the epiblast during mammalian development. Here, we demonstrated that downregulation of p53, a tumour suppressor protein, rescued tetraploid development in the mammalian epiblast. Tetraploidy in differentiating epiblast cells triggered p53-dependent cell-cycle arrest and apoptosis, suggesting the activation of a tetraploidy checkpoint during early development. Finally, we found that p53 downregulation rescued tetraploid embryos later in gestation.
Tubular filamentation for laser material processing
Authors: Xie Chen , Jukna Vytautas , Milián Carles , Giust Remo , Ouadghiri-Idrissi Ismail , Itina Tatiana , Dudley John M. , Couairon Arnaud , Courvoisier Francois 
Published: March 2015

AbstractAn open challenge in the important field of femtosecond laser material processing is the controlled internal structuring of dielectric materials. Although the availability of high energy high repetition rate femtosecond lasers has led to many advances in this field, writing structures within transparent dielectrics at intensities exceeding 1013 W/cm2 has remained difficult as it is associated with significant nonlinear spatial distortion. This letter reports the existence of a new propagation regime for femtosecond pulses at high power that overcomes this challenge, associated with the generation of a hollow uniform and intense light tube that remains propagation invariant even at intensities associated with dense plasma formation. This regime is seeded from higher order nondiffracting Bessel beams, which carry an optical vortex charge. Numerical simulations are quantitatively confirmed by experiments where a novel experimental approach allows direct imaging of the 3D fluence distribution within transparent solids. We also analyze the transitions to other propagation regimes in near and far fields. We demonstrate how the generation of plasma in this tubular geometry can lead to applications in ultrafast laser material processing in terms of single shot index writing and discuss how it opens important perspectives for material compression and filamentation guiding in atmosphere.