bluuebunny/crossref_metadata_2025_split huggingface dataset:
A combined morphometric and phylogenetic revision of the Late Ordovician brachiopod generaEochonetesandThaerodonta
Authors: Bauer Jennifer E. , Stigall Alycia L. 
Published: September 2016

AbstractSystematic revision of the Late Ordovician brachiopod generaEochonetesReed, 1917 andThaerodontaWang, 1949 was conducted utilizing specimen-based morphometric and species-level phylogenetic analyses. Previous studies had recognizedThaerodontaandEochonetesas either distinct taxonomic entities or synonyms. New multivariate and phylogenetic analyses confirm the synonymy ofThaerodontawithEochonetesand provide a framework to assess evolutionary and ecological patterns within the clade. Multivariate analyses were employed to delineate species in morphospace and provided information on potential species relationships. Phylogenetic analysis was used to produce an evolutionary framework for taxonomic revision and identify character evolution within the clade. Most species previously assigned toThaerodontaare transferred toEochonetes, and three others are excluded fromEochonetesand provisionally referred to other sowerbyellid genera. Three new species (Eochonetes maearumnew species,E. voldemortusnew species,E. minervanew species) are described, one species (Leptaena saxeaSardeson, 1892) is synonymized withE. recedensSardeson, 1892, and one subspecies (Thaerodonta mucronata scabraHowe, 1965) is rejected. This study demonstrates that a combination of complementary approaches and data types has the potential to advance interpretations beyond analyses confined to single analytical tools. Specifically, multivariate analyses provide constraints on species boundaries, whereas species-level phylogenetic analyses provide frameworks to examine morphological, ecological, and biogeographic evolution within a clade.
First Cretaceous (Albian) invertebrate fossil assemblage from Batavia Knoll, Perth Abyssal Plain, eastern Indian Ocean: taxonomy and paleoecological significance
Authors: Wild Toban J. , Stilwell Jeffrey D. 
Published: September 2016

AbstractThe first sedimentary rocks from Batavia Knoll, on the western edge of the Perth Abyssal Plain, eastern Indian Ocean, have been recovered, yielding an assemblage of invertebrate fossils hitherto undocumented from this part of the world. The fauna consists of 22 species of Mollusca, including new gastropods, a calliotropidPlanolateralus acanthanodusn. sp.; a margaritidIgonoia levimargaritan. sp.; a procerithiidProcerithium arenacollicolan. sp.; and aporrhaidsDrepanocheilus bataviensisn. sp. andAnchura pelsaertin. sp. In addition, pleurotomariid, ringiculid, and architectonicid gastropod taxa were recovered. Bivalves are represented by members of the Nuculanidae, Inoceramidae, Pinnidae, Buchiidae, Lucinidae, Veneridae, and Hiatellidae. Scaphopods (Dentaliidae) and ammonites (two taxa, of Desmoceratidae and Hamitidae) are also present. Further recovered were one species of Serpulidae (Polychaeta), two of Trachyleberididae (Ostracoda), and a probable echinoid fragment. The fossil assemblage was dominated by shallow marine suspension-feeding taxa (39% of the suite). Detritivorous and herbivorous taxa comprised 22% and 9%, respectively, with nektic and epifaunal carnivores amounting to 30%. Taphonomic analyses of these fossils and their host sedimentary facies revealed the Batavia Knoll sandstone was deposited in a shallow marine environment during a mass-flow event. Biostratigraphic range data of the preserved macro- and microfossil assemblages imply an age of latest Albian, contemporaneous with the rifting of Batavia Knoll from Greater India during the broader India–Australia–Antarctica breakup in the mid-Cretaceous.
CONSTRUCTING MANY ATOMIC MODELS IN ℵ1
Authors: BALDWIN JOHN T. , LASKOWSKI MICHAEL C. , SHELAH SAHARON 
Published: September 2016

AbstractWe introduce the notion of pseudoalgebraicity to study atomic models of first order theories (equivalently models of a complete sentence of ${L_{{\omega _1},\omega }}$). Theorem: Let T be any complete first-order theory in a countable language with an atomic model. If the pseudominimal types are not dense, then there are 2ℵ0 pairwise nonisomorphic atomic models of T, each of size ℵ1.
GENERALISED IMAGINARIES AND GALOIS COHOMOLOGY
Authors: SUSTRETOV DMITRY 
Published: September 2016

AbstractThe objective of this article is to characterise elimination of finite generalised imaginaries as defined in [9] in terms of group cohomology. As an application, I consider series of Zariski geometries constructed [10, 23, 24] by Hrushovski and Zilber and indicate how their nondefinability in algebraically closed fields is connected to eliminability of certain generalised imaginaries.
Tooth occlusal morphology in the durophagous marine reptiles, Placodontia (Reptilia: Sauropterygia)
Authors: Crofts Stephanie B. , Neenan James M. , Scheyer Torsten M. , Summers Adam P. 
Published: September 2016

AbstractPlacodontia were a group of marine reptiles that lived in shallow nearshore environments during the Triassic. Based on tooth morphology it has been inferred that they were durophagous, but tooth morphology differs among species: placodontoid placodonts have teeth described as hemispherical, and the teeth of more highly nested taxa within the cyamodontoid placodonts have been described as flat. In contrast, the sister taxon to the placodonts, Palatodonta bleekeri, like many other marine reptiles, has tall pointed teeth for eating soft-bodied prey. The goals of this paper are to quantify these different tooth morphologies and compare tooth shape among taxa and with a functionally “optimal” tooth. To quantify tooth morphology we measured the radius of curvature (RoC) of the occlusal surface by fitting spheres to 3D surface scans or computed microtomographic scans. Large RoCs correspond to flatter teeth, while teeth with smaller RoCs are pointier; positive RoCs have convex occlusal surfaces, and a negative RoC indicates that the occlusal surface of the tooth is concave. We found the placodontoid taxa have teeth with smaller RoCs than more highly nested taxa, and palatine teeth tend to be flatter and closer to the optimal morphology than maxillary teeth. Within one well-nested clade, the placochelyids, the rearmost palatine teeth have a more complex morphology than the predicted optimal tooth, with an overall concave occlusal surface with a small, medial cusp. These findings are in keeping with the hypothesis that placodonts were specialized durophagous predators with teeth modified to break hard prey items while resisting tooth failure.
Reactivity to uncertain threat as a familial vulnerability factor for alcohol use disorder
Authors: Gorka S. M. , Hee D. , Lieberman L. , Mittal V. A. , Phan K. L. , Shankman S. A. 
Published: September 2016

BackgroundWhen sober, problematic drinkers display exaggerated reactivity to threats that are uncertain (U-threat). Since this aversive affective state can be alleviated via acute alcohol intoxication, it has been posited that individuals who exhibit heightened reactivity to U-threat at baseline are motivated to use alcohol as a means of avoidance-based coping, setting the stage for excessive drinking. To date, however, no study has attempted to characterize the dispositional nature of exaggerated reactivity to U-threat and test whether it is a vulnerability factor or exclusively a disease marker of problematic alcohol use.MethodThe current investigation utilized a family study design to address these gaps by examining whether (1) reactivity to U-threat is associated with risk for problematic alcohol use, defined by family history of alcohol use disorder (AUD) and (2) reactivity to U-threat is correlated amongst adult biological siblings. A total of 157 families, and 458 individuals, participated in the study and two biological siblings completed a threat-of-shock task designed to probe reactivity to U-threat and predictable threat (P-threat). Startle potentiation was collected as an index of aversive responding.ResultsWithin biological siblings, startle potentiation to U-threat [intraclass correlation (ICC) = 0.35] and P-threat (ICC = 0.63) was significantly correlated. In addition, independent of an individuals’ own AUD status, startle potentiation to U-threat, but not P-threat, was positively associated with risk for AUD (i.e. AUD family history).ConclusionThis suggests that heightened reactivity to U-threat may be a familial vulnerability factor for problematic drinking and a novel prevention target for AUD.
Who is Beck? Sonic markers as a compositional tool in pop production
Authors: Askeroi Eirik 
Published: September 2016

AbstractThroughout the history of music recording, the use of certain technologies and instruments has left distinctive marks on recordings – marks that imply an intrinsic relationship between an era and a sound. At the same time, producers and artists have taken advantage of this relationship, constructing and otherwise exploiting what I have elsewhere conceptualised as sonic markers. This study explores how Beck's use of sound as a compositional tool constructs sonic markers that have in turn contributed profoundly to the formation of his musical identity. First, I take into account Beck's use of various pop aesthetics to explore how sonic markers are constructed through appropriation. Second, I offer an assessment of the ways in which Beck's musical identity has been formed from his play with the sonic markers of other eras. Third, I provide an analytical account of ‘Sexx Laws’ (1999) to illustrate how Beck's play with sonic markers of time also informs individual song structure and composition.
Live mediation: performing concerts using studio technology
Authors: Kjus Yngvar , Danielsen Anne 
Published: September 2016

AbstractThe use of computers is continuously changing the sound of records but also increasingly challenging established forms of live concert aesthetics. So what becomes of creativity and expressivity in the live performance? In this study, we present an artist-oriented approach to this question through interviews with artists invested in performing studio works on stage, as well as improvising musicians using studio technology in their concerts. We find that challenges to creative authorship and expressive agency are constantly negotiated through evolving practices of up- and down-scaling particular aspects of studio works on stage, as well as designing technological setups tailored to individual forms of improvisation. While these practices challenge deep-rooted notions of the ‘right’ or appropriate bond between musician and music, the appropriation of studio technology in live performance has clearly become an integral part of many artists’ continual exploration of their musical agency.
‘Distilling More than 2,000 Years of History into 161,000 Square Feet of Display Space’: Limiting Britishness and the Failure to Create a Museum of British History
Authors: CARTER TOM , ROBERTSON IAIN 
Published: September 2016

Abstract:National museums both mediate and inculcate official and formal versions of national culture and by this means make and maintain national identity. Three times in the course of the twentieth century, various groups have attempted, and failed, to establish a national museum, identified variously as British or English. This paper explores just one of those attempts: the Museum of British History Project, first proposed in 1996 and finally killed off in 2008. The focus here is, therefore, on failure and on the role of the conflation of Britishness and Englishness in that failure as well as the nature of British identity construction more generally.All three attempts to create a national museum placed the rural idyll at the heart of the project. In the course of a detailed investigation of the Museum of British History project, this paper will pay particular attention to the proposed designs for a ‘British Landscape Gallery’ and the project's hegemonic, ruralised and Anglocentric perspectives. The gallery was the principal way in which established constructs of England and Englishness became conflated in the museum with Britain and Britishness and served to perpetuate the dominance of the ‘rural idyll’ in hegemonic manifestations of the nation. But the project remained stillborn in the face of the new museology: a failure which undoubtedly demonstrates the limits to the cultural power of the rural idyll.
A systematic review of methods to assess intake of fruits and vegetables among healthy European adults and children: a DEDIPAC (DEterminants of DIet and Physical Activity) study
Authors: Riordan Fiona , Ryan Kathleen , Perry Ivan J , Schulze Matthias B , Andersen Lene Frost , Geelen Anouk , van’t Veer Pieter , Eussen Simone , Dagnelie Pieter , Wijckmans-Duysens Nicole , Harrington Janas M 
Published: September 2016

AbstractObjectiveEvidence suggests that health benefits are associated with consuming recommended amounts of fruits and vegetables (F&V), yet standardised assessment methods to measure F&V intake are lacking. The current review aims to identify methods to assess F&V intake among children and adults in pan-European studies and inform the development of the DEDIPAC (DEterminants of DIet and Physical Activity) toolbox of methods suitable for use in future European studies.DesignA literature search was conducted using three electronic databases and by hand-searching reference lists. English-language studies of any design which assessed F&V intake were included in the review.SettingStudies involving two or more European countries were included in the review.SubjectsHealthy, free-living children or adults.ResultsThe review identified fifty-one pan-European studies which assessed F&V intake. The FFQ was the most commonly used (n42), followed by 24 h recall (n11) and diet records/diet history (n7). Differences existed between the identified methods; for example, the number of F&V items on the FFQ and whether potatoes/legumes were classified as vegetables. In total, eight validated instruments were identified which assessed F&V intake among adults, adolescents or children.ConclusionsThe current review indicates that an agreed classification of F&V is needed in order to standardise intake data more effectively between European countries. Validated methods used in pan-European populations encompassing a range of European regions were identified. These methods should be considered for use by future studies focused on evaluating intake of F&V.
The oncometabolite 2-hydroxyglutarate activates the mTOR signalling pathway
Authors: Carbonneau Mélissa , M. Gagné Laurence , Lalonde Marie-Eve , Germain Marie-Anne , Motorina Alena , Guiot Marie-Christine , Secco Blandine , Vincent Emma E. , Tumber Anthony , Hulea Laura , Bergeman Jonathan , Oppermann Udo , Jones Russell G. , Laplante Mathieu , Topisirovic Ivan , Petrecca Kevin , Huot Marc-Étienne , Mallette Frédérick A. 
Published: September 2016

AbstractThe identification of cancer-associated mutations in the tricarboxylic acid (TCA) cycle enzymes isocitrate dehydrogenases 1 and 2 (IDH1/2) highlights the prevailing notion that aberrant metabolic function can contribute to carcinogenesis. IDH1/2 normally catalyse the oxidative decarboxylation of isocitrate into α-ketoglutarate (αKG). In gliomas and acute myeloid leukaemias, IDH1/2 mutations confer gain-of-function leading to production of the oncometabolite R-2-hydroxyglutarate (2HG) from αKG. Here we show that generation of 2HG by mutated IDH1/2 leads to the activation of mTOR by inhibiting KDM4A, an αKG-dependent enzyme of the Jumonji family of lysine demethylases. Furthermore, KDM4A associates with the DEP domain-containing mTOR-interacting protein (DEPTOR), a negative regulator of mTORC1/2. Depletion of KDM4A decreases DEPTOR protein stability. Our results provide an additional molecular mechanism for the oncogenic activity of mutant IDH1/2 by revealing an unprecedented link between TCA cycle defects and positive modulation of mTOR function downstream of the canonical PI3K/AKT/TSC1-2 pathway.
PKA inhibits WNT signalling in adrenal cortex zonation and prevents malignant tumour development
Authors: Drelon Coralie , Berthon Annabel , Sahut-Barnola Isabelle , Mathieu Mickaël , Dumontet Typhanie , Rodriguez Stéphanie , Batisse-Lignier Marie , Tabbal Houda , Tauveron Igor , Lefrançois-Martinez Anne-Marie , Pointud Jean-Christophe , Gomez-Sanchez Celso E. , Vainio Seppo , Shan Jingdong , Sacco Sonia , Schedl Andreas , Stratakis Constantine A. , Martinez Antoine , Val Pierre 
Published: September 2016

AbstractAdrenal cortex physiology relies on functional zonation, essential for production of aldosterone by outer zona glomerulosa (ZG) and glucocorticoids by inner zona fasciculata (ZF). The cortex undergoes constant cell renewal, involving recruitment of subcapsular progenitors to ZG fate and subsequent lineage conversion to ZF identity. Here we show that WNT4 is an important driver of WNT pathway activation and subsequent ZG differentiation and demonstrate that PKA activation prevents ZG differentiation through WNT4 repression and WNT pathway inhibition. This suggests that PKA activation in ZF is a key driver of WNT inhibition and lineage conversion. Furthermore, we provide evidence that constitutive PKA activation inhibits, whereas partial inactivation of PKA catalytic activity stimulates β-catenin-induced tumorigenesis. Together, both lower PKA activity and higher WNT pathway activity lead to poorer prognosis in adrenocortical carcinoma (ACC) patients. These observations suggest that PKA acts as a tumour suppressor in the adrenal cortex, through repression of WNT signalling.
The importance of copy number variation in congenital heart disease
Authors: Costain Gregory , Silversides Candice K , Bassett Anne S 
Published: September 2016

AbstractCongenital heart disease (CHD) is the most common class of major malformations in humans. The historical association with large chromosomal abnormalities foreshadowed the role of submicroscopic rare copy number variations (CNVs) as important genetic causes of CHD. Recent studies have provided robust evidence for these structural variants as genome-wide contributors to all forms of CHD, including CHD that appears isolated without extra-cardiac features. Overall, a CNV-related molecular diagnosis can be made in up to one in eight patients with CHD. These include de novo and inherited variants at established (chromosome 22q11.2), emerging (chromosome 1q21.1), and novel loci across the genome. Variable expression of rare CNVs provides support for the notion of a genetic spectrum of CHD that crosses traditional anatomic classification boundaries. Clinical genetic testing using genome-wide technologies (e.g., chromosomal microarray analysis) is increasingly employed in prenatal, paediatric and adult settings. CNV discoveries in CHD have translated to changes to clinical management, prognostication and genetic counselling. The convergence of findings at individual gene and at pathway levels is shedding light on the mechanisms that govern human cardiac morphogenesis. These clinical and research advances are helping to inform whole-genome sequencing, the next logical step in delineating the genetic architecture of CHD.
Refinement of the androgen response element based on ChIP-Seq in androgen-insensitive and androgen-responsive prostate cancer cell lines
Authors: Wilson Stephen , Qi Jianfei , Filipp Fabian V. 
Published: September 2016

AbstractSequence motifs are short, recurring patterns in DNA that can mediate sequence-specific binding for proteins such as transcription factors or DNA modifying enzymes. The androgen response element (ARE) is a palindromic, dihexameric motif present in promoters or enhancers of genes targeted by the androgen receptor (AR). Using chromatin immunoprecipitation sequencing (ChIP-Seq) we refined AR-binding and AREs at a genome-scale in androgen-insensitive and androgen-responsive prostate cancer cell lines. Model-based searches identified more than 120,000 ChIP-Seq motifs allowing for expansion and refinement of the ARE. We classified AREs according to their degeneracy and their transcriptional involvement. Additionally, we quantified ARE utilization in response to somatic copy number amplifications, AR splice-variants, and steroid treatment. Although imperfect AREs make up 99.9% of the motifs, the degree of degeneracy correlates negatively with validated transcriptional outcome. Weaker AREs, particularly ARE half sites, benefit from neighboring motifs or cooperating transcription factors in regulating gene expression. Taken together, ARE full sites generate a reliable transcriptional outcome in AR positive cells, despite their low genome-wide abundance. In contrast, the transcriptional influence of ARE half sites can be modulated by cooperating factors.
Fecal metabolome of the Hadza hunter-gatherers: a host-microbiome integrative view
Authors: Turroni Silvia , Fiori Jessica , Rampelli Simone , Schnorr Stephanie L. , Consolandi Clarissa , Barone Monica , Biagi Elena , Fanelli Flaminia , Mezzullo Marco , Crittenden Alyssa N. , Henry Amanda G. , Brigidi Patrizia , Candela Marco 
Published: September 2016

AbstractThe recent characterization of the gut microbiome of traditional rural and foraging societies allowed us to appreciate the essential co-adaptive role of the microbiome in complementing our physiology, opening up significant questions on how the microbiota changes that have occurred in industrialized urban populations may have altered the microbiota-host co-metabolic network, contributing to the growing list of Western diseases. Here, we applied a targeted metabolomics approach to profile the fecal metabolome of the Hadza of Tanzania, one of the world’s few remaining foraging populations, and compared them to the profiles of urban living Italians, as representative of people in the post-industrialized West. Data analysis shows that during the rainy season, when the diet is primarily plant-based, Hadza are characterized by a distinctive enrichment in hexoses, glycerophospholipids, sphingolipids, and acylcarnitines, while deplete in the most common natural amino acids and derivatives. Complementary to the documented unique metagenomic features of their gut microbiome, our findings on the Hadza metabolome lend support to the notion of an alternate microbiome configuration befitting of a nomadic forager lifestyle, which helps maintain metabolic homeostasis through an overall scarcity of inflammatory factors, which are instead highly represented in the Italian metabolome.
Oscillation of mineral compositions in Core SG-1b, western Qaidam Basin, NE Tibetan Plateau
Authors: Fang Xiaomin , Li Minghui , Wang Zhengrong , Wang Jiuyi , Li Jiao , Liu Xiaoming , Zan Jinbo 
Published: September 2016

AbstractUplift of the Tibetan Plateau since the Late Miocene has greatly affected the nature of sediments deposited in the Qaidam Basin. However, due to the scarcity of continuously dated sediment records, we know little about how minerals responded to this uplift. In order to understand this response, we here present results from the high-resolution mineral profile from a borehole (7.3–1.6 Ma) in the Basin, which shows systematic oscillations of various evaporite and clay minerals that can be linked to the variation of regional climate and tectonic history. In particular, x-ray diffraction (XRD) analyses show that carbonate minerals consist mainly of calcite and aragonite, with minor ankerite and dolomite. Evaporates consist of gypsum, celesite and halite. Clay minerals are principally Fe-Mg illite, mixed layers of illite/smectite and chlorite, with minor kaolinite and smectite. Following implications can be drawn from the oscillations of these minerals phases: (a) the paleolake was brackish with high salinity after 7.3 Ma, while an abrupt change in the chemical composition of paleolake water (e.g. Mg/Ca ratio, SO42− concentration, salinity) occurred at 3.3 Ma; (b) the three changes at ~6.0 Ma, 4.5–4.1 Ma and 3.3 Ma were in response to rapid erosions/uplift of the basin; (c) pore water or fluid was Fe/Mg-rich in 7.3–6.0 Ma, Mg-rich in 6.0–4.5 Ma, and K-rich in 4.1–1.6 Ma; and (d) evaporation rates were high, but weaker than today’s.