bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early Cambrian sponges of the Sirius Passet Biota, North Greenland
Authors: Botting Joseph P. , Peel John S. 
Published: June 2016

AbstractThe Sirius Passet Biota of the Buen Formation in North Greenland is one of the key Burgess Shale‐type faunas, as it represents the only diverse early Cambrian (Stage 2, Series 3) biota from Laurentia. The sponges are one of the major components of the fauna, although they appear to be much less abundant than arthropods, based on the available collections. At least 13 species are described here, including the new taxaHamptonia limatulasp. nov.,Lenica perversasp. nov.,Saetaspongia procerasp. nov.,Constellatispongia canismajoriigen. et sp. nov. andCrassicoactum cucumisgen. et sp. nov. An additional new species,Ratcliffespongia freuchenensissp. nov., is described from the upper part of the Buen Formation. The assemblage is dominated by a major lineage of protomonaxonids, together with rarer reticulosans and demosponges. Some taxa, such as the anthaspidellid lithistidFieldospongia bellilineata, were previously known only from Laurentian faunas; others, such asSaetospongia densa,Solactiniellacf. plumataandLenica unica, were previously recognized from South China and/or Siberia. The described assemblage confirms the cosmopolitan distribution of Cambrian sponges generally, and suggests that the differences between Laurentian and Chinese assemblages are due more to a taxonomic overturn during Cambrian Series 2, Stage 4, than to the geographical separation. Furthermore, crown‐group demosponges appear to have occupied shallow‐water (perhaps dominantly platform) environments at this time, and may have been much more diversified and widespread than is currently recognized during the early Cambrian.
TGFβ-Responsive HMOX1 Expression Is Associated with Stemness and Invasion in Glioblastoma Multiforme
Authors: Ghosh Dhiman , Ulasov Ilya V. , Chen LiPing , Harkins Lualhati E. , Wallenborg Karolina , Hothi Parvinder , Rostad Steven , Hood Leroy , Cobbs Charles S. 
Published: June 2016

AbstractGlioblastoma multiforme (GBM) is the most common and lethal adult brain tumor. Resistance to standard radiation and chemotherapy is thought to involve survival of GBM cancer stem cells (CSCs). To date, no single marker for identifying GBM CSCs has been able to capture the diversity of CSC populations, justifying the needs for additional CSC markers for better characterization. Employing targeted mass spectrometry, here we present five cell-surface markers HMOX1, SLC16A1, CADM1, SCAMP3, and CLCC1 which were found to be elevated in CSCs relative to healthy neural stem cells (NSCs). Transcriptomic analyses of REMBRANDT and TCGA compendiums also indicated elevated expression of these markers in GBM relative to controls and non-GBM diseases. Two markers SLC16A1 and HMOX1 were found to be expressed among pseudopalisading cells that reside in the hypoxic region of GBM, substantiating the histopathological hallmarks of GBM. In a prospective study (N = 8) we confirmed the surface expression of HMOX1 on freshly isolated primary GBM cells (P0). Employing functional assays that are known to evaluate stemness, we demonstrate that elevated HMOX1 expression is associated with stemness in GBM and can be modulated through TGFβ. siRNA-mediated silencing of HMOX1 impaired GBM invasion—a phenomenon related to poor prognosis. In addition, surgical resection of GBM tumors caused declines (18% ± 5.1SEM) in the level of plasma HMOX1 as measured by ELISA, in 8/10 GBM patients. These findings indicate that HMOX1 is a robust predictor of GBM CSC stemness and pathogenesis. Further understanding of the role of HMOX1 in GBM may uncover novel therapeutic approaches.
Calcium, Strontium and Barium Homogeneous Catalysts for Fine Chemicals Synthesis
Authors: Sarazin Yann , Carpentier Jean‐François 
Published: June 2016

AbstractThe large alkaline earths (Ae), calcium, strontium and barium, have in the past 15 years yielded a brand new generation of heteroleptic molecular catalysts for the production of fine chemicals. However, the integrity of these complexes is often plagued by ligand redistribution equilibria in solution. This personal account retraces the paths followed in our research group towards the design of stable heteroleptic alkalino‐earth complexes, including the use of intramolecular noncovalent Ae···H–Si and Ae···F–C interactions. Their implementation as homogenous precatalysts for reactions such as the intramolecular and intermolecular hydroamination and hydrophosphination of activated alkenes, the hydrophosphonylation of ketones, and the dehydrogenative coupling of amines and hydrosilanes that enable the efficient and controlled formations of CP, CN, or SiN σ‐bonds, is presented in a synthetic perspective that highlights their overall outstanding catalytic performance.image
An improved spreadsheet for calculating limb length discrepancy and epiphysiodesis timing using the multiplier method
Authors: Mills Gavin , Nelson Scott 
Published: June 2016

Purpose The multiplier method is a technique to predict limb length discrepancy (LLD) at maturity in pediatric patients. Various tools have been developed for performing the multiplier calculations to predict LLD and timing of epiphysiodesis. These include multiplier/growth applications (apps) and a spreadsheet which have helped to facilitate LLC calculations in an efficient and easy manner. We have updated the spreadsheet to improve features for making LLD calculations and facilitate pasting data into electronic medical records (EMRs). Methods Tools currently in use were critically examined for features that limited their function, created possible sources of error or could be more user-friendly. These features were modified and recreated in an improved Excel spreadsheet that uses patient age, sex, limb lengths, and previous lengthening surgeries as inputs to predict LLD at maturity and offer options for timing of epiphysiodesis for both congenital and developmental LLD. Our multiplier spreadsheet function was then compared to manual calculations and other multiplier tools for accuracy and ease of use. Results Our spreadsheet accurately calculates LLD at maturity and timing of epiphysiodesis when compared to other methods. It contains a function to calculate predicted leg lengths after previous lengthenings, and concise single-page worksheets for developmental LLD, congenital LLD, and height prediction. Conclusions This spreadsheet was developed to provide a more efficient and user-friendly method of calculating LLD at maturity and timing of epiphysiodesis. It can easily be pasted into the EMR for ease of documentation. We recommend this method for both clinical practice and educational use.
TACO: Taxonomic prediction of unknown OTUs through OTU co‐abundance networks
Authors: Irannia Zohreh Baharvand , Chen Ting 
Published: June 2016

BackgroundA main goal of metagenomics is taxonomic characterization of microbial communities. Although sequence comparison has been the main method for the taxonomic classification, there is not a clear agreement on similarity calculation and similarity thresholds, especially at higher taxonomic levels such as phylum and class. Thus taxonomic classification of novel metagenomic sequences without close homologs in the biological databases poses a challenge.MethodsIn this study, we propose to use the co‐abundant associations between taxa/operational taxonomic units (OTU) across complex and diverse communities to assist taxonomic classification. We developed a Markov Random Field model to predict taxa of unknown microorganisms using co‐abundant associations.ResultsAlthough such associations are intrinsically functional associations, we demonstrate that they are strongly correlated with taxonomic associations and can be combined with sequence comparison methods to predict taxonomic origins of unknown microorganisms at phylum and class levels.ConclusionsWith the ever‐increasing accumulation of sequence data from microbial communities, we now take the first step to explore these associations for taxonomic identification beyond sequence similarity.Availability and ImplementationSource codes of TACO are freely available at the following URL: https://github.com/baharvand/OTU‐Taxonomy‐Identification implemented in C++, supported on Linux and MS Windows.
THE MODEL COMPANION OF DIFFERENTIAL FIELDS WITH FREE OPERATORS
Authors: SÁNCHEZ OMAR LEÓN , MOOSA RAHIM 
Published: June 2016

AbstractA model companion is shown to exist for the theory of partial differential fields of characteristic zero equipped with free operators that commute with the derivations. The free operators here are those introduced in [R. Moosa and T. Scanlon, Model theory of fields with free operators in characteristic zero, Journal of Mathematical Logic 14(2), 2014]. The proof relies on a new lifting lemma in differential algebra: a differential version of Hensel’s Lemma for local finite algebras over differentially closed fields.
Chronology and Faunal Remains of the Khayrgas Cave (Eastern Siberia, Russia)
Authors: Kuzmin Yaroslav V , Kosintsev Pavel A , Stepanov Aleksandr D , Boeskorov Gennady G , Cruz Richard J 
Published: June 2016

AbstractThe Khayrgas Cave in Yakutia (eastern Siberia) is one of the most important Upper Paleolithic sites in northern Asia, and has been the subject of extensive 14C dating and study of mammal bones. The upper part of the cave sequence (Layers 2–4) dates to the Holocene (~4100–8200 BP), and the lower part (Layers 5–7) to the Late Pleistocene (~13,100–21,500 BP). In Layers 2–4, only extant animal species are known; ecologically they belong to a forest-type ecosystem. In Layers 5–7, several extinct species were identified, and the environment at that time corresponded to open and semi-open ecosystems. The Khayrgas Cave provides rare but reliable evidence of human occupation in the deep continental region of eastern Siberia at the Last Glacial Maximum, ~20,700–21,500 BP.
Self-reference in psychosis and depression: a language marker of illness
Authors: Fineberg S. K. , Leavitt J. , Deutsch-Link S. , Dealy S. , Landry C. D. , Pirruccio K. , Shea S. , Trent S. , Cecchi G. , Corlett P. R. 
Published: June 2016

BackgroundLanguage use is of increasing interest in the study of mental illness. Analytical approaches range from phenomenological and qualitative to formal computational quantitative methods. Practically, the approach may have utility in predicting clinical outcomes. We harnessed a real-world sample (blog entries) from groups with psychosis, strong beliefs, odd beliefs, illness, mental illness and/or social isolation to validate and extend laboratory findings about lexical differences between psychosis and control subjects.MethodWe describe the results of two experiments using Linguistic Inquiry and Word Count software to assess word category frequencies. In experiment 1, we compared word use in psychosis and control subjects in the laboratory (23 per group), and related results to subject symptoms. In experiment 2, we examined lexical patterns in blog entries written by people with psychosis and eight comparison groups. In addition to between-group comparisons, we used factor analysis followed by clustering to discern the contributions of strong belief, odd belief and illness identity to lexical patterns.ResultsConsistent with others’ work, we found that first-person pronouns, biological process words and negative emotion words were more frequent in psychosis language. We tested lexical differences between bloggers with psychosis and multiple relevant comparison groups. Clustering analysis revealed that word use frequencies did not group individuals with strong or odd beliefs, but instead grouped individuals with any illness (mental or physical).ConclusionsPairing of laboratory and real-world samples reveals that lexical markers previously identified as specific language changes in depression and psychosis are probably markers of illness in general.
The ground beneath their feet: building continuity at Neolithic Çukuriçi Höyük
Authors: Brami Maxime , Horejs Barbara , Ostmann Felix 
Published: June 2016

AbstractA Neolithic structure was rebuilt three times at Çukuriçi Höyük, on the central Anatolian Aegean coast, despite its unfavourable location on unsettled fill. We draw upon this seemingly incongruous case to make inference about the siting of buildings in Neolithic times. Through detailed cross-comparison with other sequences of vertically superimposed buildings in Anatolia and the Aegean region, we retrace the contours of a Neolithic practice aimed at maintaining occupation in one place. Over time, building continuity transformed into a strategy by some households to claim authority over a place and appropriate it for their own benefit. With regard to the location of Neolithic buildings, we conclude that choices about location dominated over practical considerations. Once a commitment to place was made, there was no turning back, even when this meant living in an unstable house that needed to be rebuilt repeatedly.
Cosmopolitanism, communality and the appropriation of Mycenaean pottery in western Anatolia
Authors: Vaessen Rik 
Published: June 2016

AbstractThe presence of imported and locally produced Mycenaean pottery in western Anatolia has long caught the attention of scholars, and various explanatory models have been proposed to explain the apparent attractiveness of the pottery. In most cases, however, emphasis is placed on the (stylistic) differences between Mycenaean pottery and the various local plain wares, and it is assumed that these differences were actively recognised by local communities and exploited in the formation of social identities. This paper, however, pilots a different approach that focuses not on the stylistic differences between Mycenaean pottery and the various Anatolian wares but on the (perceived) common ground(s) between them and argues that the attractiveness of Mycenaean, and previously Minoan pottery, lay not so much in its cultural origins or its ‘foreignness’ as in its potential to fit in with existing local material assemblages and enhance a sense of communality among cosmopolitan communities.
Prospective Memory in Posttraumatic Stress Disorder
Authors: Scott J. Cobb , Woods Steven Paul , Wrocklage Kristen M. , Schweinsburg Brian C. , Southwick Steven M. , Krystal John H. 
Published: June 2016

AbstractObjectives:Neuropsychological studies of posttraumatic stress disorder (PTSD) have revealed deficits in attention/working memory, processing speed, executive functioning, and retrospective memory. However, little is known about prospective memory (PM) in PTSD, a clinically relevant aspect of episodic memory that supports the encoding and retrieval of intentions for future actions.Methods:Here we examined PM performance in 40 veterans with PTSD compared to 38 trauma comparison (TC) veterans who were exposed to combat but did not develop PTSD. All participants were administered the Memory for Intentions Test (MIST; Raskin, Buckheit, & Sherrod, 2010), a standardized and validated measure of PM, alongside a comprehensive neurocognitive battery, structured diagnostic interviews for psychiatric conditions, and behavioral questionnaires.Results:Veterans with PTSD performed moderately lower than TC on time-based PM, with errors primarily characterized as PM failure errors (i.e., omissions). However, groups did not differ in event-based PM, ongoing task performance, or post-test recognition of PM intentions for each trial. Lower time-based PM performance was specifically related to hyperarousal symptoms of PTSD. Time-based-performance was also associated with neuropsychological measures of retrospective memory and executive functions in the PTSD group. Nevertheless, PTSD was significantly associated with poorer PM above and beyond age and performance in retrospective memory and executive functions.Discussion:Results provide initial evidence of PM dysfunction in PTSD, especially in strategic monitoring during time-based PM tasks. Findings have potential implications for everyday functioning and health behaviors in persons with PTSD, and deserve replication and future study. (JINS, 2016,22, 724–734)
The FNIP co-chaperones decelerate the Hsp90 chaperone cycle and enhance drug binding
Authors: Woodford Mark R. , Dunn Diana M. , Blanden Adam R. , Capriotti Dante , Loiselle David , Prodromou Chrisostomos , Panaretou Barry , Hughes Philip F. , Smith Aaron , Ackerman Wendi , Haystead Timothy A. , Loh Stewart N. , Bourboulia Dimitra , Schmidt Laura S. , Marston Linehan W. , Bratslavsky Gennady , Mollapour Mehdi 
Published: June 2016

AbstractHeat shock protein-90 (Hsp90) is an essential molecular chaperone in eukaryotes involved in maintaining the stability and activity of numerous signalling proteins, also known as clients. Hsp90 ATPase activity is essential for its chaperone function and it is regulated by co-chaperones. Here we show that the tumour suppressor FLCN is an Hsp90 client protein and its binding partners FNIP1/FNIP2 function as co-chaperones. FNIPs decelerate the chaperone cycle, facilitating FLCN interaction with Hsp90, consequently ensuring FLCN stability. FNIPs compete with the activating co-chaperone Aha1 for binding to Hsp90, thereby providing a reciprocal regulatory mechanism for chaperoning of client proteins. Lastly, downregulation of FNIPs desensitizes cancer cells to Hsp90 inhibitors, whereas FNIPs overexpression in renal tumours compared with adjacent normal tissues correlates with enhanced binding of Hsp90 to its inhibitors. Our findings suggest that FNIPs expression can potentially serve as a predictive indicator of tumour response to Hsp90 inhibitors.
Magnetic assembly of transparent and conducting graphene-based functional composites
Authors: Le Ferrand Hortense , Bolisetty Sreenath , Demirörs Ahmet F. , Libanori Rafael , Studart André R. , Mezzenga Raffaele 
Published: June 2016

AbstractInnovative methods producing transparent and flexible electrodes are highly sought in modern optoelectronic applications to replace metal oxides, but available solutions suffer from drawbacks such as brittleness, unaffordability and inadequate processability. Here we propose a general, simple strategy to produce hierarchical composites of functionalized graphene in polymeric matrices, exhibiting transparency and electron conductivity. These are obtained through protein-assisted functionalization of graphene with magnetic nanoparticles, followed by magnetic-directed assembly of the graphene within polymeric matrices undergoing sol–gel transitions. By applying rotating magnetic fields or magnetic moulds, both graphene orientation and distribution can be controlled within the composite. Importantly, by using magnetic virtual moulds of predefined meshes, graphene assembly is directed into double-percolating networks, reducing the percolation threshold and enabling combined optical transparency and electrical conductivity not accessible in single-network materials. The resulting composites open new possibilities on the quest of transparent electrodes for photovoltaics, organic light-emitting diodes and stretchable optoelectronic devices.
Super stretchable hydrogel achieved by non-aggregated spherulites with diameters <5 nm
Authors: Sun Guoxing , Li Zongjin , Liang Rui , Weng Lu-Tao , Zhang Lina 
Published: June 2016

AbstractThe scope of hydrogel applications can be greatly expanded by the improvement of mechanical properties. However, enhancement of nanocomposite hydrogels (NC gels) has been severely limited because the size of crosslinking nanoparticles is too large, at least in one dimension. Here we report a new strategy to synthesize non-aggregated spherulite nanoparticles, with diameters <5 nm, in aqueous solution, and their enhancement to hydrogel. The stress and stretch ratio at rupture of our NC gel are 430 and 121 KPa with only 40-p.p.m. nanoparticle content. The NC gel containing 200-p.p.m. nanoparticles can revert to 90% of its original size after enduring 100-MPa compressive stress. Our results demonstrate that the suppression of nanoparticle size without aggregation helps to establish a super stretchable and high-toughness hydrogel network at very low inorganic content.
Cellular responses to HSV-1 infection are linked to specific types of alterations in the host transcriptome
Authors: Hu Benxia , Li Xin , Huo Yongxia , Yu Yafen , Zhang Qiuping , Chen Guijun , Zhang Yaping , Fraser Nigel W. , Wu Dongdong , Zhou Jumin 
Published: June 2016

AbstractPathogen invasion triggers a number of cellular responses and alters the host transcriptome. Here we report that the type of changes to cellular transcriptome is related to the type of cellular functions affected by lytic infection of Herpes Simplex Virus type I in Human primary fibroblasts. Specifically, genes involved in stress responses and nuclear transport exhibited mostly changes in alternative polyadenylation (APA), cell cycle genes showed mostly alternative splicing (AS) changes, while genes in neurogenesis, rarely underwent these changes. Transcriptome wide, the infection resulted in 1,032 cases of AS, 161 incidences of APA, 1,827 events of isoform changes and up regulation of 596 genes and down regulations of 61 genes compared to uninfected cells. Thus, these findings provided important and specific links between cellular responses to HSV-1 infection and the type of alterations to the host transcriptome, highlighting important roles of RNA processing in virus-host interactions.
Demosaiced pixel super-resolution for multiplexed holographic color imaging
Authors: Wu Yichen , Zhang Yibo , Luo Wei , Ozcan Aydogan 
Published: June 2016

AbstractTo synthesize a holographic color image, one can sequentially take three holograms at different wavelengths, e.g., at red (R), green (G) and blue (B) parts of the spectrum and digitally merge them. To speed up the imaging process by a factor of three, a Bayer color sensor-chip can also be used to demultiplex three wavelengths that simultaneously illuminate the sample and digitally retrieve individual set of holograms using the known transmission spectra of the Bayer color filters. However, because the pixels of different channels (R, G, B) on a Bayer color sensor are not at the same physical location, conventional demosaicing techniques generate color artifacts in holographic imaging using simultaneous multi-wavelength illumination. Here we demonstrate that pixel super-resolution can be merged into the color de-multiplexing process to significantly suppress the artifacts in wavelength-multiplexed holographic color imaging. This new approach, termed Demosaiced Pixel Super-Resolution (D-PSR), generates color images that are similar in performance to sequential illumination at three wavelengths and therefore improves the speed of holographic color imaging by 3-fold. D-PSR method is broadly applicable to holographic microscopy applications, where high-resolution imaging and multi-wavelength illumination are desired.