bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isotaphonomy in concept and practice: an exploration of vertebrate microfossil bonebeds in the Upper Cretaceous (Campanian) Judith River Formation, north-central Montana
Authors: Rogers Raymond R. , Carrano Matthew T. , Curry Rogers Kristina A. , Perez Magaly , Regan Anik K. 
Published: February 2017

AbstractVertebrate microfossil bonebeds (VMBs)—localized concentrations of small resilient vertebrate hard parts—are commonly studied to recover otherwise rarely found small-bodied taxa, and to document relative taxonomic abundance and species richness in ancient vertebrate communities. Analyses of taphonomic comparability among VMBs have often found significant differences in size and shape distributions, and thus considered them to be non-isotaphonomic. Such outcomes of “strict” statistical tests of isotaphonomy suggest discouraging limits on the potential for broad, comparative paleoecological reconstruction using VMBs. Yet it is not surprising that sensitive statistical tests highlight variations among VMB sites, especially given the general lack of clarity with regard to the definition of “strict” isotaphonomic comparability. We rigorously sampled and compared six VMB localities representing two distinct paleoenvironments (channel and pond/lake) of the Upper Cretaceous Judith River Formation to evaluate biases related to sampling strategies and depositional context. Few defining distinctions in bioclast size and shape are evident in surface collections, and most site-to-site comparisons of sieved collections are indistinguishable (p≤0.003). These results provide a strong case for taphonomic equivalence among the majority of Judith River VMBs, and bode well for future studies of paleoecology, particularly in relation to investigations of faunal membership and community structure in Late Cretaceous wetland ecosystems. The taphonomic comparability of pond/lake and channel-hosted VMBs in the Judith River Formation is also consistent with a formative model that contends that channel-hosted VMBs were reworked from pre-existing pond/lake assemblages, and thus share taphonomic history.
Predation on feather stars by regular echinoids as evidenced by laboratory and field observations and its paleobiological implications
Authors: Stevenson Angela , Gahn Forest J. , Baumiller Tomasz K. , Sevastopulo George D. 
Published: February 2017

AbstractAmong extant crinoids, the feather stars are the most diverse and occupy the greatest bathymetric range, being especially common in reef environments. Feather stars possess a variety of morphological, behavioral and physiological traits that have been hypothesized to be critical to their success, especially in their ability to cope with predation. However, knowledge of their predators is exceptionally scant, consisting primarily of circumstantial evidence of attacks by fishes. In this study the question whether regular echinoids, recently shown to consume stalked crinoids, also consume feather stars is explored. Aquarium observations indicate that regular echinoids find feather stars palatable, including feather stars known to be distasteful to fish, and that regular echinoids can capture and eat live feather stars, including those known to swim. Gut-content analyses of the echinoidAraeosoma fenestratum(Thomson, 1872), which is commonly observed with large populations of the feather starKoehlermetra porrecta(Carpenter, 1888) in video transects from marine canyons off the coast of France, revealed elements of feather stars in the guts of 6 of 13 individuals. The high proportion of crinoid material (up to 90%), and the presence of articulated crinoid skeletal elements in the gut ofA. fenestratum, suggest that these echinoids consumed at least some live crinoids, although they may have also ingested some postmortem remains found in the sediment. Additionally, photographic evidence from the northeast Atlantic suggests that another regular echinoid,Cidaris cidaris(Linnaeus, 1758), preys on feather stars. Thus in spite of the broad suite of antipredatory adaptations, feather stars are today subject to predation by regular echinoids and may have been since the Mesozoic, when this group of crinoids first appeared.
Needham at the crossroads: history, politics and international science in wartime China (1942–1946)
Authors: MOUGEY THOMAS 
Published: February 2017

AbstractIn 1946, the British biochemist Joseph Needham returned from a four-year stay in China. Needham scholars have considered this visit as a revelatory period that paved the way for his famous book seriesScience and Civilization in China(SCC). Surprisingly, however, Needham's actual time in China has remained largely unstudied over the last seventy years. As director of the Sino-British Scientific Cooperation Office, Needham travelled throughout Free China to promote cooperation between British and Chinese scientists to contain the Japanese invasion during the Second World War. By rediscovering Needham's peregrinations, this paper re-examines the origins of his fascination for China. First, it contests the widely held idea that this Chinese episode is quite separate and different from Needham's first half-life as a leftist scientist. Second, it demonstrates how the political and philosophical commitments he inherited from the social relations of science movement, and his biochemical research, shaped his interest in China's past. Finally, this paper recounts these forgotten years to reveal their implications for his later pursuits as historian of science and as director of the natural-science division of UNESCO. It highlights how, while in China, Needham co-constituted the philosophical tenets of his scientific programme at UNESCO and the conceptual foundations of hisSCC.
Alternating direction implicit type preconditioners for the steady state inhomogeneous Vlasov equation
Authors: Gasteiger Markus , Einkemmer Lukas , Ostermann Alexander , Tskhakaya David 
Published: February 2017

The purpose of the current work is to find numerical solutions of the steady state inhomogeneous Vlasov equation. This problem has a wide range of applications in the kinetic simulation of non-thermal plasmas. However, the direct application of either time stepping schemes or iterative methods (such as Krylov-based methods such as the generalized minimal residual method (GMRES) or relaxation schemes) is computationally expensive. In the former case the slowest time scale in the system forces us to perform a long time integration while in the latter case a large number of iterations is required. In this paper we propose a preconditioner based on an alternating direction implicit type splitting method. This preconditioner is then combined with both GMRES and Richardson iteration. The resulting numerical schemes scale almost ideally (i.e. the computational effort is proportional to the number of grid points). Numerical simulations conducted show that this can result in a speed-up of close to two orders of magnitude (even for intermediate grid sizes) with respect to the unpreconditioned case. In addition, we discuss the characteristics of these numerical methods and show the results for a number of numerical simulations.
Tracking and predicting hand, foot, and mouth disease (HFMD) epidemics in China by Baidu queries
Authors: XIAO Q. Y. , LIU H. J. , FELDMAN M. W. 
Published: February 2017

SUMMARYHand, foot, and mouth disease (HFMD) is highly prevalent in China, and more efficient methods of epidemic detection and early warning need to be developed to augment traditional surveillance systems. In this paper, a method that uses Baidu search queries to track and predict HFMD epidemics is presented, and the outbreaks of HFMD in China during the 60-month period from January 2011 to December 2015 are predicted. The Pearson correlation coefficient (R) of the predictive model and the mean absolute percentage errors between observed HFMD case counts and the predicted number show that our predictive model gives excellent fit to the data. This implies that Baidu search queries can be used in China to track and reliably predict HFMD epidemics, and can serve as a supplement to official systems for HFMD epidemic surveillance.
Towards consumer-driven meat supply chains: opportunities and challenges for differentiation by taste
Authors: Schulze-Ehlers Birgit , Anders Sven 
Published: February 2017

AbstractThis paper investigates the state of pork supply as to its neglect of developing innovations and mechanisms for delivering superior eating quality to consumers. We explore reasons behind pork supply chains’ predominant focus on mass production combined with traceability and food safety, while only little attention has been given to potentially lucrative niche markets focused on intrinsic quality cues. Using established analytical frameworks of hedonic pricing and transactions costs economics we discuss alternative strategies for the segregation and promotion of intrinsic sensory differentiated pork. Growing empirical evidence in the literature underpins the importance of eating experience in delivering utility to consumers and in stabilizing declining demand trends in major markets. Building on current consumer behavioral literature and organizational developments in meat supply chains in Europe and Australia, we critically discuss opportunities to overcome this supposedly suboptimal situation.
The case for taking account of labor in sustainable food systems in the United States
Authors: Minkoff-Zern Laura-Anne 
Published: February 2017

AbstractThis commentary argues for strengthening research and analysis of food workers' rights as part of a more comprehensive sustainable food systems approach. Starting with a broad definition of sustainability, one which includes social, as well as ecological, and economic elements, the author outlines current critiques of alternative food movement actors. She then looks at existing food labor activism and successes, providing them as examples for how sustainable food movement actors and researchers should move forward.
Exercise-induced irisin in bone and systemic irisin administration reveal new regulatory mechanisms of bone metabolism
Authors: Zhang Jin , Valverde Paloma , Zhu Xiaofang , Murray Dana , Wu Yuwei , Yu Liming , Jiang Hua , Dard Michel M , Huang Jin , Xu Zhiwei , Tu Qisheng , Chen Jake 
Published: February 2017

AbstractIrisin is a polypeptide hormone derived from the proteolytic cleavage of fibronectin-type III domain-containing 5 (FNDC5) protein. Once released to circulation upon exercise or cold exposure, irisin stimulates browning of white adipose tissue (WAT) and uncoupling protein 1 (UCP1) expression, leading to an increase in total body energy expenditure by augmented UCP1-mediated thermogenesis. It is currently unknown whether irisin is secreted by bone upon exercise or whether it regulates bone metabolism in vivo. In this study, we found that 2 weeks of voluntary wheel-running exercise induced high levels of FNDC5 messenger RNA as well as FNDC5/irisin protein expression in murine bone tissues. Increased immunoreactivity due to exercise-induced FNDC5/irisin expression was detected in different regions of exercised femoral bones, including growth plate, trabecular bone, cortical bone, articular cartilage, and bone–tendon interface. Exercise also increased expression of osteogenic markers in bone and that of UCP1 in WAT, and led to bodyweight loss. Irisin intraperitoneal (IP) administration resulted in increased trabecular and cortical bone thickness and osteoblasts numbers, and concurrently induced UCP1 expression in subcutaneous WAT. Lentiviral FNDC5 IP administration increased cortical bone thickness. In vitro studies in bone cells revealed irisin increases osteoblastogenesis and mineralization, and inhibits receptor activator of nuclear factor-kB ligand (RANKL)-induced osteoclastogenesis. Taken together, our findings show that voluntary exercise increases irisin production in bone, and that an increase in circulating irisin levels enhances osteogenesis in mice.
C-edge loops of arrestin function as a membrane anchor
Authors: Lally Ciara C M. , Bauer Brian , Selent Jana , Sommer Martha E 
Published: February 2017

AbstractG-protein-coupled receptors are membrane proteins that are regulated by a small family of arrestin proteins. During formation of the arrestin–receptor complex, arrestin first interacts with the phosphorylated receptor C terminus in a pre-complex, which activates arrestin for tight receptor binding. Currently, little is known about the structure of the pre-complex and its transition to a high-affinity complex. Here we present molecular dynamics simulations and site-directed fluorescence experiments on arrestin-1 interactions with rhodopsin, showing that loops within the C-edge of arrestin function as a membrane anchor. Activation of arrestin by receptor-attached phosphates is necessary for C-edge engagement of the membrane, and we show that these interactions are distinct in the pre-complex and high-affinity complex in regard to their conformation and orientation. Our results expand current knowledge of C-edge structure and further illuminate the conformational transitions that occur in arrestin along the pathway to tight receptor binding.
An integrative approach unveils FOSL1 as an oncogene vulnerability in KRAS-driven lung and pancreatic cancer
Authors: Vallejo Adrian , Perurena Naiara , Guruceaga Elisabet , Mazur Pawel K. , Martinez-Canarias Susana , Zandueta Carolina , Valencia Karmele , Arricibita Andrea , Gwinn Dana , Sayles Leanne C. , Chuang Chen-Hua , Guembe Laura , Bailey Peter , Chang David K. , Biankin Andrew , Ponz-Sarvise Mariano , Andersen Jesper B. , Khatri Purvesh , Bozec Aline , Sweet-Cordero E. Alejandro , Sage Julien , Lecanda Fernando , Vicent Silve 
Published: February 2017

AbstractKRAS mutated tumours represent a large fraction of human cancers, but the vast majority remains refractory to current clinical therapies. Thus, a deeper understanding of the molecular mechanisms triggered by KRAS oncogene may yield alternative therapeutic strategies. Here we report the identification of a common transcriptional signature across mutant KRAS cancers of distinct tissue origin that includes the transcription factor FOSL1. High FOSL1 expression identifies mutant KRAS lung and pancreatic cancer patients with the worst survival outcome. Furthermore, FOSL1 genetic inhibition is detrimental to both KRAS-driven tumour types. Mechanistically, FOSL1 links the KRAS oncogene to components of the mitotic machinery, a pathway previously postulated to function orthogonally to oncogenic KRAS. FOSL1 targets include AURKA, whose inhibition impairs viability of mutant KRAS cells. Lastly, combination of AURKA and MEK inhibitors induces a deleterious effect on mutant KRAS cells. Our findings unveil KRAS downstream effectors that provide opportunities to treat KRAS-driven cancers.
Understanding the glacial methane cycle
Authors: Hopcroft Peter O. , Valdes Paul J. , O’Connor Fiona M. , Kaplan Jed O. , Beerling David J. 
Published: February 2017

AbstractAtmospheric methane (CH4) varied with climate during the Quaternary, rising from a concentration of 375 p.p.b.v. during the last glacial maximum (LGM) 21,000 years ago, to 680 p.p.b.v. at the beginning of the industrial revolution. However, the causes of this increase remain unclear; proposed hypotheses rely on fluctuations in either the magnitude of CH4 sources or CH4 atmospheric lifetime, or both. Here we use an Earth System model to provide a comprehensive assessment of these competing hypotheses, including estimates of uncertainty. We show that in this model, the global LGM CH4 source was reduced by 28–46%, and the lifetime increased by 2–8%, with a best-estimate LGM CH4 concentration of 463–480 p.p.b.v. Simulating the observed LGM concentration requires a 46–49% reduction in sources, indicating that we cannot reconcile the observed amplitude. This highlights the need for better understanding of the effects of low CO2 and cooler climate on wetlands and other natural CH4 sources.
NO3− anions can act as Lewis acid in the solid state
Authors: Bauzá Antonio , Frontera Antonio , Mooibroek Tiddo J. 
Published: February 2017

AbstractIdentifying electron donating and accepting moieties is crucial to understanding molecular aggregation, which is of pivotal significance to biology. Anions such as NO3− are typical electron donors. However, computations predict that the charge distribution of NO3− is anisotropic and minimal on nitrogen. Here we show that when the nitrate’s charge is sufficiently dampened by resonating over a larger area, a Lewis acidic site emerges on nitrogen that can interact favourably with electron rich partners. Surveys of the Cambridge Structural Database and Protein Data Bank reveal geometric preferences of some oxygen and sulfur containing entities around a nitrate anion that are consistent with this ‘π-hole bonding’ geometry. Computations reveal donor–acceptor orbital interactions that confirm the counterintuitive Lewis π–acidity of nitrate.
Tumour and host cell PD-L1 is required to mediate suppression of anti-tumour immunity in mice
Authors: Lau Janet , Cheung Jeanne , Navarro Armando , Lianoglou Steve , Haley Benjamin , Totpal Klara , Sanders Laura , Koeppen Hartmut , Caplazi Patrick , McBride Jacqueline , Chiu Henry , Hong Rebecca , Grogan Jane , Javinal Vincent , Yauch Robert , Irving Bryan , Belvin Marcia , Mellman Ira , Kim Jeong M. , Schmidt Maike 
Published: February 2017

AbstractExpression of PD-L1, the ligand for T-cell inhibitory receptor PD-1, is one key immunosuppressive mechanism by which cancer avoids eradication by the immune system. Therapeutic use of blocking antibodies to PD-L1 or its receptor PD-1 has produced unparalleled, durable clinical responses, with highest likelihood of response seen in patients whose tumour or immune cells express PD-L1 before therapy. The significance of PD-L1 expression in each cell type has emerged as a central and controversial unknown in the clinical development of immunotherapeutics. Using genetic deletion in preclinical mouse models, here we show that PD-L1 from disparate cellular sources, including tumour cells, myeloid or other immune cells can similarly modulate the degree of cytotoxic T-cell function and activity in the tumour microenvironment. PD-L1 expression in both the host and tumour compartment contribute to immune suppression in a non-redundant fashion, suggesting that both sources could be predictive of sensitivity to therapeutic agents targeting the PD-L1/PD-1 axis.
Stellera chamaejasme and its constituents induce cutaneous wound healing and anti-inflammatory activities
Authors: Kim Myungsuk , Lee Hee Ju , Randy Ahmad , Yun Ji Ho , Oh Sang-Rok , Nho Chu Won 
Published: February 2017

AbstractStellera chamaejasmeL. (Thymelaeaceae) is a perennial herb that is widely used in traditional Chinese medicine to treat tumours, tuberculosis and psoriasis.S. chamaejasmeextract (SCE) possesses anti-inflammatory, analgesic and wound healing activities; however, the effect ofS. chamaejasmeand its active compounds on cutaneous wound healing has not been investigated. We assessed full-thickness wounds of Sprague-Dawley (SD) rats and topically applied SCE for 2 weeks.In vitrostudies were performed using HaCaT keratinocytes, Hs68 dermal fibroblasts and RAW 264.7 macrophages to determine cell viability (MTT assay), cell migration, collagen expression, nitric oxide (NO) production, prostaglandin E2(PGE2) production, inflammatory cytokine expression and β-catenin activation.In vivo, wound size was reduced and epithelisation was improved in SCE-treated SD rats.In vitro, SCE and its active compounds induced keratinocyte migration by regulating the β-catenin, extracellular signal-regulated kinase and Akt signalling pathways. Furthermore, SCE and its active compounds increased mRNA expression of type I and III collagen in Hs68 fibroblasts. SCE and chamechromone inhibited NO and PGE2release and mRNA expression of inflammatory mediators in RAW 264.7 macrophages. SCE enhances the motility of HaCaT keratinocytes and improves cutaneous wound healing in SD rats.
A simple approach for preparation of affinity matrices: Simultaneous purification and reversible immobilization of a streptavidin mutein to agarose matrix
Authors: Wu Sau-Ching , Wang Chris , Hansen Dave , Wong Sui-Lam 
Published: February 2017

AbstractSAVSBPM18 is an engineered streptavidin for affinity purification of both biotinylated biomolecules and recombinant proteins tagged with streptavidin binding peptide (SBP) tags. To develop a user-friendly approach for the preparation of the SAVSBPM18-based affinity matrices, a designer fusion protein containing SAVSBPM18 and a galactose binding domain was engineered. The galactose binding domain derived from the earthworm lectin EW29 was genetically modified to eliminate a proteolytic cleavage site located at the beginning of the domain. This domain was fused to the C-terminal end of SAVSBPM18. It allows the SAVSBPM18 fusions to bind reversibly to agarose and can serve as an affinity handle for purification of the fusion. Fluorescently labeled SAVSBPM18 fusions were found to be stably immobilized on Sepharose 6B-CL. The enhanced immobilization capability of the fusion to the agarose beads results from the avidity effect mediated by the tetrameric nature of SAVSBPM18. This approach allows the consolidation of purification and immobilization of SAVSBPM18 fusions to Sepharose 6B-CL in one step for affinity matrix preparation. The resulting affinity matrix has been successfully applied to purify both SBP tagged β-lactamase and biotinylated proteins. No significant reduction in binding capacity of the column was observed for at least six months.
Heterogeneous nuclear ribonucleoprotein A1 regulates rhythmic synthesis of mouse Nfil3 protein via IRES-mediated translation
Authors: Kim Hyo-Jin , Lee Hwa-Rim , Seo Ji-Young , Ryu Hye Guk , Lee Kyung-Ha , Kim Do-Yeon , Kim Kyong-Tai 
Published: February 2017

AbstractNuclear factor, interleukin 3, regulated (Nfil3, also known as E4 Promoter-Binding Protein 4 (E4BP4)) protein is a transcription factor that binds to DNA and generally represses target gene expression. In the circadian clock system, Nfil3 binds to a D-box element residing in the promoter of clock genes and contributes to their robust oscillation. Here, we show that the 5′-untranslated region (5′-UTR) of Nfil3 mRNA contains an internal ribosome entry site (IRES) and that IRES-mediated translation occurs in a phase-dependent manner. We demonstrate that heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) binds to a specific region of Nfil3 mRNA and regulates IRES-mediated translation. Knockdown of hnRNP A1 almost completely abolishes protein oscillation without affecting mRNA oscillation. Moreover, we observe that intracellular calcium levels, which are closely related to bone formation, depend on Nfil3 levels in osteoblast cell lines. We suggest that the 5′-UTR mediated cap-independent translation of Nfil3 mRNA contributes to the rhythmic expression of Nfil3 by interacting with the RNA binding protein hnRNP A1. These data provide new evidence that the posttranscriptional regulation of clock gene expression is important during bone metabolism.