bluuebunny/crossref_metadata_2025_split huggingface dataset:
Taphonomic features of benthic foraminifera in a temperate setting: experimental and field observations on the role of abrasion, solution and microboring in the destruction of foraminiferal tests
Authors: Shroba Cynthia S. 
Published: January 2018

Benthic foraminifera recovered from sediments in the waters surrounding San Juan Island, Washington, were examined to assess taphonomic damage and to compare magnitude of the taphonomic agents of abrasion, solution and microboring to studies done in tropical environments. Abrasion experiments of 24, 72, 120 and 240 hour duration were run on Elphidiella and Islandiella, two benthic foraminifera common in the Puget Sound region. Results show that styles of taphonomic damage observed in field sediment samples, including impact pitting, scratching, caving and exfoliation, were produced on experimentally manipulated groups in as few as 24 hours. Elphidiella appears slightly more resistant to abrasive reduction compared to Islandiella, which produced a wide range of abrasive features within 3 days.A control group of Elphidiella and Islandiella was placed in a mesh bag for 240 hours to assess taphonomic alteration by solution, boring and encrustation, removed from the effects of abrasion. These specimens showed no significant solution reduction, but within 3 days were covered with algal filaments and diatoms. Taphonomic damage observed in field specimens can be divided into destructive and constructive agents. Destructive features include breakage, pitting, boring, scratching, and exfoliation. Constructive features include pyritization and encrustation by diatoms and other algae. Although several naturally occurring abrasion features were produced in the experimental abrasion runs, the magnitude of taphonomic damage seen in field specimens was not achieved experimentally. Features of extreme taphonomic damage include complete removal of the outer chamber walls, as well as removal of all but the umbilical regions of planispiral forms. Solution and predation are largely responsible for such severely damaged tests.
Rudists as successful sediment-dwellers, not reef-builders, on Cretaceous carbonate platforms
Authors: Skelton Peter W. , Gili Eulàlia , Masse Jean-Pierre 
Published: January 2018

The claim that rudist bivalves competitively displaced corals from reef frameworks in the Cretaceous combines two assertions: (1) that rudist formations commonly developed as reefs; and (2) that the autecology of rudists was convergent with that of hermatypic corals. We dispute both assertions, and thus reject the hypothesis of competitive displacement. We argue instead that mobile sediments, rather than frameworks, dominated the margins of most of the extensive carbonate platforms of the period, and that it was on these non-reefal biotopes that the rudists flourished.Definitions of reefs tend to combine two major elements: (1) a robust biogenic framework (with accompanying sedimentary and diagenetic components); and (2) topographical relief. Such definitions are clearly rooted in Recent coral reefs, in which endosymbiotic zooxanthellae permit the extensive growth of colonial coral frameworks in shallow but relatively nutrient-poor waters and topography is largely the legacy of Pleistocene changes in sea-level. In rudist formations, in contrast, individual rudist aggregations are volumetrically limited, relative to sediment, often loosely constructed, and evidently showed little relief. Tabular and small lenticular units predominate.Differences in structure and palaeoenvironmental situation between rudist and coralgal associations are the effect of the different autecologies of the constituent organisms. While the clonal growth of corals predisposed them to framework development, the aclonal development of rudists was better suited to the opportunistic occupation of a variety of temporarily available substrata. Moreover, the tolerances and growth responses of rudists to such factors as water turbidity, nutrients and current regime were quite different from those of hermatypic corals. Despite repeated assertions in the literature that rudists possessed zooxanthellae, only a few species show any evidence for such a symbiosis and other evidence suggests that most lacked them.Rudist/coral competition is therefore doubtful, even though members of both groups co-occur in many areas. The relative demise and migration into deeper water of coral frameworks in the Cretaceous was thus probably independently caused.
Hierarchical factor analysis and the derivation of phylogenetic skull shape characters in canids
Authors: Stevens William P. 
Published: January 2018

Character independence is an important assumption in parsimony-based phylogenetic analysis. For taxa with extant representatives, the analysis of within-species covariation of quantitative characters provides a basis for assessing character independence. One promising approach is to use mean species scores on factors of within-species covariation as phylogenetic characters, but the use of common morphometric factor models leads to problems with either the independence or the interpretability of such characters. Principal components and principal factors, whether rotated or not, may be constrained to be orthogonal but may be difficult to interpret since the effects of each factor are spread over all variables. In Wright-style factor analysis the restriction of secondary factors to subsets of variables facilitates their interpretation, but the factors may be highly correlated.An alternative approach is to adopt a hierarchical factor model in which correlated first-order factors are restricted to subsets of the variables. Size is modelled as a second-order factor inducing correlation of the primary factors, in contrast to the common morphometric procedure of attempting to partial out size in the first stage of analysis. The size-independent components of the primary factors provide shape characters which are interpretable as the deviations of regional growth from their predictions based on size. Hierarchical factor models have been widely used in psychometric studies since their introduction by Thurstone in the 1930's, but have been little used in morphometric analyses.The hierarchical model is applied to the covariances of interlandmark trusses measured on skulls of extant canids using a video-based stereophotogrammetric system. Preliminary results indicate that the canid skull may be partitioned into discrete regions of relatively independent local growth.
Eurasian and North American phylogeny of Turolian hipparionine horses (Perissodactyla, Mammalia) in China
Authors: Watabe Mahito 
Published: January 2018

The late Miocene Chinese hipparions are morphologically diversified showing similarity to both western Old World's and North American forms. Two Chinese taxa that are phylogenetically related to western Old World's forms are Hipparion fossatum (= H. forstende) from Baode (Shanxi) and H. hippidiodus from Qingyang (Gansu) and Baode. The former is related to H. mediterraneum and the latter to H. urmiense - platygenys from the Turolian localities in the western Old World. H. fossatum and H. hippidiodus are associated with the “dorcadoides” (open-land) and “mixed” faunas in northern China. Hipparion fossatum that is characterized by POF located close to the orbit co-occurs with large and morphologically specialized form, H. dermatorhinum in Baode (Loc.30). H. hippidiodus with reduced POF is discovered with smaller H. coelophyes in Loc. 43, 44 (Baode) and Loc. 115 (Gansu).The hipparions associated with the “gaudryi” (forest) fauna are characterized by well defined and small POF located far from the orbit. Those forms are: H. platyodus from Loc. 70; H. ptychodus from Loc. 73; H. tylodus from Hsi-Liang in Yushe - Wuxiang basins; and H. sefvei from Loc. 12 at Xin-an in Henan province. H. coelophyes from Baode (Loc.43 & 44) and Qingyang (Loc. 115) also show similar facial morphology to the these forms, although it has small size and shallow POF. Those forms are similar in facial and dental morphology to Hipparion sensu stricto and some species of Cormohipparion in North America.The assemblages of Chinese hipparions are composed of two groups whose members are phylogenetically similar to the forms from both western part of Eurasia and North America. The “gaudryi” fauna is considered younger than the other two on the basis of faunal analyses. The similarity in hipparionine taxonomy between northern China and North America in the latest Miocene is an evidences for possible faunal interchange(s) occurred during that period, as suggested by taxonomic analyses on carnivores and proboscideans in eastern half of Eurasia and North America.
Reconstruction of the enigmatic Late Cambrian

Climactichnites
Authors: Yochelson E.L. , Parrish M. 
Published: January 2018

Climactichnites Logan, 1860, is known only from its large trail up to 20 cm in width, a trace superficially resembling a rope ladder. Prominent lateral ridges are parallel throughout the length of the trail; they may be smooth and hemispherical in cross-section or crenulated, much like a pie crust. Between these ridges is a series of raised dune-like bars and furrows dug into the substrate. The bars and furrows show considerable individual variation between trails and also variation along a trail. Ovoid impressions are known which occur at the start of trails. The posterior of these impressions is well rounded; the anterior is triangular, and for a short distance from the impression, the trail is developed on only one side. One exceptionally preserved impression shows curved, closely spaced, fine lines parallel to the posterior.The trails are found only in sandstone, and where they are present, they are abundant. Slightly equivocable evidence indicates a Dresbachian (early Late Cambrian) age for the occurrences in New York, Missouri, and Wisconsin; trails in Ontario and Quebec are less certainly dated. Desiccation cracks and air escape hole suggest that the trail was fully exposed to the atmosphere.From this data, a large number of sketches were made to reconstruct an animal able to make such a trail. Each attempt produced new speculation on the morphology. In the final rendition, the animal is bilaterally symmetrical, broad and low. The integument is tough, and the sole bears a subcentral mouth anteriorward. Lateral flaps scraped and compressed damp sand to make the parallel ridges. The anterior was strongly musculated and thin. This anterior flap grasped the sediment, alternating on either side of the animal to pull the form forward when the lateral flaps were relaxed. Curved rows of cilia on the posterior moved loose sand into dunes between the furrows formed by the anterior flaps.This reconstruction is like that of no other animal known in the Vendian or the Phanerozoic.
Associations between body mass index and the risk of renal events in patients with type 2 diabetes
Authors: Mohammedi Kamel , Chalmers John , Herrington William , Li Qiang , Mancia Giuseppe , Marre Michel , Poulter Neil , Rodgers Anthony , Williams Bryan , Perkovic Vlado , Coresh Josef , Woodward Mark 
Published: January 2018

Abstract
Background/objectives
We aimed to evaluate the relationship between BMI and the risk of renal disease in patients with type 2 diabetes in the Action in Diabetes and Vascular Disease: PreterAx and DiamicroN Modified-Release Controlled Evaluation (ADVANCE) study.

Subjects/methods
Participants were divided into six baseline BMI categories: <18.5 (underweight, n = 58); ≥18.5 to <25 (normal, n = 2894); ≥25 to <30 (overweight, n = 4340); ≥30 to <35 (obesity grade 1, n = 2265); ≥35 to <40 (obesity grade 2, n = 744); and ≥40 kg/m2 (obesity grade 3, n = 294); those underweight were excluded. The composite outcome “major renal event” was defined as development of new macroalbuminuria, doubling of creatinine, end stage renal disease, or renal death. These outcomes and development of new microalbuminuria were considered individually as secondary endpoints.

Results
During 5-years of follow-up, major renal events occurred in 487 (4.6%) patients. The risk increased with higher BMI. Multivariable-adjusted HRs (95% CIs), compared to normal weight, were: 0.91 (0.72–1.15) for overweight; 1.03 (0.77–1.37) for obesity grade 1; 1.42 (0.98–2.07) for grade 2; and 2.16 (1.34–3.48) for grade 3 (p for trend = 0.006). These findings were similar across subgroups by randomised interventions (intensive versus standard glucose control and perindopril-indapamide versus placebo). Every additional unit of BMI over 25 kg/m2 increased the risk of major renal events by 4 (1–6)%. Comparable results were observed with the risk of secondary endpoints.

Conclusions
Higher BMI is an independent predictor of major renal events in patients with type 2 diabetes. Our findings encourage weight loss to improve nephroprotection in these patients.
Biological rejuvenation of iron oxides in bioturbated marine sediments
Authors: Beam Jacob P , Scott Jarrod J , McAllister Sean M , Chan Clara S , McManus James , Meysman Filip J R , Emerson David 
Published: January 2018

Abstract
The biogeochemical cycle of iron is intricately linked to numerous element cycles. Although biological processes that catalyze the reductive side of the iron cycle are established, little is known about microbial oxidative processes on iron cycling in sedimentary environments—resulting in the formation of iron oxides. Here we show that a potential source of sedimentary iron oxides originates from the metabolic activity of iron-oxidizing bacteria from the class Zetaproteobacteria, presumably enhanced by burrowing animals in coastal sediments. Zetaproteobacteria were estimated to be a global total of 1026 cells in coastal, bioturbated sediments, and predicted to annually produce 8 × 1015 g of Fe in sedimentary iron oxides—55 times larger than the annual flux of iron oxides deposited by rivers. These data suggest that iron-oxidizing Zetaproteobacteria are keystone organisms in marine sedimentary environments—despite their low numerical abundance—yet exert a disproportionate impact via the rejuvenation of iron oxides.
Novel hydrogenases from deep-sea hydrothermal vent metagenomes identified by a recently developed activity-based screen
Authors: Adam Nicole , Perner Mirjam 
Published: January 2018

Abstract
Hydrogen is one of the most common elements on Earth. The enzymes converting molecular hydrogen into protons and electrons are the hydrogenases. Hydrogenases are ubiquitously distributed in all three domains of life where they play a central role in cell metabolism. So far, the recovery of hydrogenases has been restricted to culture-dependent and sequence-based approaches. We have recently developed the only activity-based screen for seeking H2-uptake enzymes from metagenomes without having to rely on enrichment and isolation of hydrogen-oxidizing microorganisms or prior metagenomic sequencing. When screening 14,400 fosmid clones from three hydrothermal vent metagenomes using this solely activity-based approach, four clones with H2-uptake activity were identified with specific activities of up to 258 ± 19 nmol H2/min/mg protein of partially purified membrane fractions. The respective metagenomic fragments exhibited mostly very low or no similarities to sequences in the public databases. A search with hidden Markov models for different hydrogenase groups showed no hits for three of the four metagenomic inserts, indicating that they do not encode for classical hydrogenases. Our activity-based screen serves as a powerful tool for the discovery of (novel) hydrogenases which would not have been identified by the currently available techniques. This screen can be ideally combined with culture- and sequence-based approaches to investigate the tremendous hydrogen-converting potential in the environment.
Oridonin exerts anticancer effect on osteosarcoma by activating PPAR-γ and inhibiting Nrf2 pathway
Authors: Lu Ying , Sun Yang , Zhu Jianwei , Yu Lisha , Jiang Xiubo , Zhang Jie , Dong Xiaochen , Ma Bo , Zhang Qi 
Published: January 2018

AbstractOsteosarcoma is the most common high-grade human primary malignant bone sarcoma with lower survival in the past decades. Oridonin, a bioactive diterpenoid isolated from Rabdosia rubescens, has been proved to possess potent anti-cancer effects. However, its potential mechanism still remains not fully clear nowadays. In this study, we investigated the anticancer effect of oridonin on human osteosarcoma and illuminated the underlying mechanisms. In vitro, oridonin inhibited the cell viability of various osteosarcoma cells. We demonstrated that oridonin induced mitochondrial-mediated apoptosis by increasing Bax/Bcl-2 ratio, loss of mitochondrial membrane potential (MMP), triggering reactive oxygen species (ROS) generation and activating caspase-3 and caspase-9 cleavage in MG-63 and HOS cells. Moreover, we found that oridonin triggered ROS by inhibiting NF-E2-related factor 2 (Nrf2) pathway and induced mitochondrial apoptosis via inhibiting nuclear factor-κB (NF-κB) activation by activating Peroxisome Proliferator-Activated Receptor γ (PPAR-γ) in MG-63 and HOS cells. We further confirmed the results by PPAR-γ inhibitor GW9662, PPAR-γ siRNA as well as overexpression of PPAR-γ and Nrf2 in vitro. Furthermore, our in vivo study showed that oridonin inhibited tumor growth with high safety via inducing apoptosis through activating PPAR-γ and inhibiting Nrf2 activation in xenograft model inoculated HOS tumor. Taken together, oridonin exerted a dramatic pro-apoptotic effect by activating PPAR-γ and inhibiting Nrf2 pathway in vitro and in vivo. Therefore, oridonin may be a promising and effective agent for human osteosarcoma in the future clinical applications.
CKAMP44 modulates integration of visual inputs in the lateral geniculate nucleus
Authors: Chen Xufeng , Aslam Muhammad , Gollisch Tim , Allen Kevin , von Engelhardt Jakob 
Published: January 2018

AbstractRelay neurons in the dorsal lateral geniculate nucleus (dLGN) receive excitatory inputs from retinal ganglion cells (RGCs). Retinogeniculate synapses are characterized by a prominent short-term depression of AMPA receptor (AMPAR)-mediated currents, but the underlying mechanisms and its function for visual integration are not known. Here we identify CKAMP44 as a crucial auxiliary subunit of AMPARs in dLGN relay neurons, where it increases AMPAR-mediated current amplitudes and modulates gating of AMPARs. Importantly, CKAMP44 is responsible for the distinctive short-term depression in retinogeniculate synapses by reducing the rate of recovery from desensitization of AMPARs. Genetic deletion of CKAMP44 strongly reduces synaptic short-term depression, which leads to increased spike probability of relay neurons when activated with high-frequency inputs from retinogeniculate synapses. Finally, in vivo recordings reveal augmented ON- and OFF-responses of dLGN neurons in CKAMP44 knockout (CKAMP44−/−) mice, demonstrating the importance of CKAMP44 for modulating synaptic short-term depression and visual input integration.
Full-field thermal imaging of quasiballistic crosstalk reduction in nanoscale devices
Authors: Ziabari Amirkoushyar , Torres Pol , Vermeersch Bjorn , Xuan Yi , Cartoixà Xavier , Torelló Alvar , Bahk Je-Hyeong , Koh Yee Rui , Parsa Maryam , Ye Peide D. , Alvarez F. Xavier , Shakouri Ali 
Published: January 2018

AbstractUnderstanding nanoscale thermal transport is of substantial importance for designing contemporary semiconductor technologies. Heat removal from small sources is well established to be severely impeded compared to diffusive predictions due to the ballistic nature of the dominant heat carriers. Experimental observations are commonly interpreted through a reduction of effective thermal conductivity, even though most measurements only probe a single aggregate thermal metric. Here, we employ thermoreflectance thermal imaging to directly visualise the 2D temperature field produced by localised heat sources on InGaAs with characteristic widths down to 100 nm. Besides displaying effective thermal performance reductions up to 50% at the active junctions in agreement with prior studies, our steady-state thermal images reveal that, remarkably, 1–3 μm adjacent to submicron devices the crosstalk is actually reduced by up to fourfold. Submicrosecond transient imaging additionally shows responses to be faster than conventionally predicted. A possible explanation based on hydrodynamic heat transport, and some open questions, are discussed.
Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels
Authors: Jiang Xia , O’Reilly Paul F. , Aschard Hugues , Hsu Yi-Hsiang , Richards J. Brent , Dupuis Josée , Ingelsson Erik , Karasik David , Pilz Stefan , Berry Diane , Kestenbaum Bryan , Zheng Jusheng , Luan Jianan , Sofianopoulou Eleni , Streeten Elizabeth A. , Albanes Demetrius , Lutsey Pamela L. , Yao Lu , Tang Weihong , Econs Michael J. , Wallaschofski Henri , Völzke Henry , Zhou Ang , Power Chris , McCarthy Mark I. , Michos Erin D. , Boerwinkle Eric , Weinstein Stephanie J. , Freedman Neal D. , Huang Wen-Yi , Van Schoor Natasja M. , van der Velde Nathalie , Groot Lisette C. P. G. M. de , Enneman Anke , Cupples L. Adrienne , Booth Sarah L. , Vasan Ramachandran S. , Liu Ching-Ti , Zhou Yanhua , Ripatti Samuli , Ohlsson Claes , Vandenput Liesbeth , Lorentzon Mattias , Eriksson Johan G. , Shea M. Kyla , Houston Denise K. , Kritchevsky Stephen B. , Liu Yongmei , Lohman Kurt K. , Ferrucci Luigi , Peacock Munro , Gieger Christian , Beekman Marian , Slagboom Eline , Deelen Joris , Heemst Diana van , Kleber Marcus E. , März Winfried , de Boer Ian H. , Wood Alexis C. , Rotter Jerome I. , Rich Stephen S. , Robinson-Cohen Cassianne , den Heijer Martin , Jarvelin Marjo-Riitta , Cavadino Alana , Joshi Peter K. , Wilson James F. , Hayward Caroline , Lind Lars , Michaëlsson Karl , Trompet Stella , Zillikens M. Carola , Uitterlinden Andre G. , Rivadeneira Fernando , Broer Linda , Zgaga Lina , Campbell Harry , Theodoratou Evropi , Farrington Susan M. , Timofeeva Maria , Dunlop Malcolm G. , Valdes Ana M. , Tikkanen Emmi , Lehtimäki Terho , Lyytikäinen Leo-Pekka , Kähönen Mika , Raitakari Olli T. , Mikkilä Vera , Ikram M. Arfan , Sattar Naveed , Jukema J. Wouter , Wareham Nicholas J. , Langenberg Claudia , Forouhi Nita G. , Gundersen Thomas E. , Khaw Kay-Tee , Butterworth Adam S. , Danesh John , Spector Timothy , Wang Thomas J. , Hyppönen Elina , Kraft Peter , Kiel Douglas P. 
Published: January 2018

AbstractVitamin D is a steroid hormone precursor that is associated with a range of human traits and diseases. Previous GWAS of serum 25-hydroxyvitamin D concentrations have identified four genome-wide significant loci (GC, NADSYN1/DHCR7, CYP2R1, CYP24A1). In this study, we expand the previous SUNLIGHT Consortium GWAS discovery sample size from 16,125 to 79,366 (all European descent). This larger GWAS yields two additional loci harboring genome-wide significant variants (P = 4.7×10−9 at rs8018720 in SEC23A, and P = 1.9×10−14 at rs10745742 in AMDHD1). The overall estimate of heritability of 25-hydroxyvitamin D serum concentrations attributable to GWAS common SNPs is 7.5%, with statistically significant loci explaining 38% of this total. Further investigation identifies signal enrichment in immune and hematopoietic tissues, and clustering with autoimmune diseases in cell-type-specific analysis. Larger studies are required to identify additional common SNPs, and to explore the role of rare or structural variants and gene–gene interactions in the heritability of circulating 25-hydroxyvitamin D levels.