bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcription Termination and Antitermination of Bacterial CRISPR Arrays
Authors: Stringer Anne M. , Baniulyte Gabriele , Lasek-Nesselquist Erica , Seed Kimberley D. , Wade Joseph T. 
Published: August 2018

ABSTRACTA hallmark of CRISPR-Cas immunity systems is the CRISPR array, a genomic locus consisting of short, repeated sequences (“repeats”) interspersed with short, variable sequences (“spacers”). CRISPR arrays are transcribed and processed into individual CRISPR RNAs (crRNAs) that each include a single spacer, and direct Cas proteins to complementary sequence in invading nucleic acid. Most bacterial CRISPR array transcripts are unusually long for untranslated RNA, suggesting the existence of mechanisms to prevent premature transcription termination by Rho, a conserved bacterial transcription termination factor that rapidly terminates untranslated RNA. We show that Rho termination functionally limits the length of bacterial CRISPR arrays, and we identify a widespread antitermination mechanism that antagonizes Rho to facilitate complete transcription of CRISPR arrays. Thus, our data highlight the importance of Rho termination in the evolution of bacterial CRISPR-Cas systems.
F-actin dynamics transform filopodial bridges into intercellular nanotubes capable of distant cell communication
Authors: Chang Minhyeok , Oh Jaeho , Doh Junsang , Lee Jong-Bong 
Published: August 2018

AbstractA novel actin-based bridge connecting cells has been recognized as a new pathway for the distant transport of cytoplasmic components, viruses, or pathogenic substances between cells. However, it is not yet known how such a fine structure extends over several hundred micrometres and remains robust for several hours. Using optical fluorescence imaging methods, we found that random contact promotes the formation of filopodial bridges through N-cadherin interactions between filopodia, which are slender actin-rich plasma membrane protrusions. These filopodial bridges eventually evolve into a single actin-based bridge (intercellular nanotube) that connects two cells via an intermediate state that involves a helical structure. Surprisingly, the twisting of two filopodia is likely to result from the rotational motion of actin filaments inside the filopodia by myosin V. The accumulated torsion of the filopodia triggers the release of one of the paired filopodia, whose end is attached to the other cell body by an N-cadherin cluster. The resulting retraction of the filopodium by retrograde F-actin flow leaves a single bridge. The N-cadherin/catenin cluster is likely to form a synapse between the intercellular nanotube and the cell body. This study sheds light on the formation mechanism of the filopodial bridge-based intercellular nanotubes for long-distance communication between cells.
Dogs, but not wolves, lose their sensitivity towards novelty with age
Authors: Hansen Wheat Christina , van der Bijl Wouter , Temrin Hans 
Published: August 2018

AbstractSelection on behavioural traits holds a prominent role in the domestication of animals, with reductions in fear behaviour considered to be a key component. Specifically, there is a general assumption that domesticated species express reduced fear and reactivity towards novel stimuli compared to their ancestral species. However, very few studies have explicitly tested this proposed link between domestication and reduced fear responses. Of the limited number of studies experimentally addressing the alterations of fear during domestication, the majority have been done on canids. Previous work in foxes, wolves and dogs has led to the suggestion that decreased expression of fear in domesticated animals is linked to a domestication driven delay in the first onset of fearful behaviour during early ontogeny. Thus, wolves are expected to express exaggerated fearfulness earlier during ontogeny compared to dogs. However, while adult dogs are less fearful towards novelty than adult wolves and wolf-dog hybrids, consensus is lacking on when differences in fear expression arise in wolves and dogs. Here we present the first extended examination of fear development in hand-raised dogs and European grey wolves, using repeated novel object tests from six to 26 weeks of age. Contrary to expectations, we found no evidence in support of an increase in fearfulness in wolves with age or a delayed onset of fear response in dogs compared to wolves. Instead, we found that dogs strongly reduced their fear response in the period between six and 26 weeks of age, resulting in a significant species difference in fear expression towards novelty at 26 weeks. Critically, as wolves did not differ in their fear response towards novelty over time, the detected species difference was caused solely by a progressive reduced fear response in dogs. Our results thereby suggest that species differences in fear of novelty between wolves and dogs are not caused by a domestication driven shift in the first onset of fear response. Instead, we suggest that a loss of sensitivity towards novelty with age in dogs causes the difference in fear expression towards novelty in wolves and dogs.
ECM deposition is driven by caveolin1-dependent regulation of exosomal biogenesis and cargo sorting
Authors: Albacete-Albacete Lucas , Navarro-Lérida Inmaculada , Lopez Juan Antonio , Martín-Padura Inés , Astudillo Alma M. , Van-Der-Heyden Michael , Balsinde Jesús , Orend Gertraud , Vazquez Jesús , Ángel del Pozo Miguel 
Published: August 2018

ABSTRACTThe composition and physical properties of the extracellular matrix (ECM) critically influence tumour cell behaviour, and ECM deposition and remodelling by stromal fibroblast populations is therefore pivotal for tumour progression. The molecular mechanisms by which stromal and tumour cell populations regulate ECM layering are poorly understood. Tumour-stroma interaction is critically dependent on cell-cell communication mediated by exosomes, small vesicles secreted by most cell types and generated within multivesicular bodies (MVBs). Here, we show that caveolin-1 (Cav1), an essential regulator of stromal remodelling and tumour cell fate, plays a central role in modulating both exosome biogenesis and exosomal protein cargo sorting through cholesterol-dependent mechanisms. Quantitative proteomics profiling revealed that a major share of Cav1-dependent exosomal cargoes are compsed of ECM proteins, one of the most important components being tenascin-C (TnC). Comparative functional assays demonstrated that Cav1 is required for fibroblast-derived exosomes to depose ECM and promote tumour cell invasiveness. Exosomes purified from Cav1WT cells, but not those from Cav1-null cells, were able to nucleate distant stromal niches in different organs in vivo. These findings suggest a key role for Cav1 as a cholesterol rheostat in MVBs, and seems to determine ECM deposition by eliciting ECM component sorting into specific exosome pools. These results, together with previous work, support a model in which Cav1 is a central regulatory hub for tumour-stroma interactions through a novel exosome-dependent ECM deposition mechanism.
Icariin induces MC3T3-E1 cell proliferation and differentiation via the BMP-2/Smads/Runx2 signal pathway
Authors: An Qing , Gou Bo , Ma Shaocheng , Goh En Lin , Liu GuoXiong , Sah Bikash Kumar , Cao Hong 
Published: August 2018

AbstractIcariin, the main active ingredient of Epimedium, has played an important role in bone anabolism. However, the molecular mechanism for this effect was not convincingly reported yet. In this paper, the role of icariin on cell morphology, viability, cell cycling and the activity of alkaline phosphatase (ALP) were studied, and the molecular mechanism of icariin induced osteogenic effect was also investigated. Icariin with different concentrations (10, 20 and 40 ng/ml) was used to modify the pre-osteoblastic MC3T3-E1 cells for 48, 72 and 96 h, and the proliferation, morphology, and the cell cycle of the cells were evaluated by Cell Counting Kit-8 (CCK-8), microscopy and flow cytometry, respectively. Bone morphogenic protein-2 (BMP-2), bone morphogenic protein receptor-2 (BMPR-2), Smad4, Smadl/5/8 proteins expression levels were obtained by Western blotting and the expression levels of runt-related transcription factor 2 (Runx2) mRNA was examined by reverse transcription-polymerase chain reaction (RT-PCR). In this study, we found that icariin could promote the proliferation and differentiation of MC3T3-E1 cells in a dose - and time-dependent manner. Icariin could stimulate the expression of the BMP-2, BMPR-2, Smad4 and Smadl/5/8 proteins. Furthermore, icariin could upregulate the expression of Runx2 mRNA. These results showed that icariin played an important role in upregulating BMP-2 expression to activate the BMP-2/Smads/Runx2 signal pathway for increasing both the proliferation and differentiation of the MC3T3-E1 cells. However, the osteogenic effects of icariin can be suppressed by the BMP-2 antagonist (Noggin). In conclusion, we demonstrate that icariin is an osteoinductive factor that exerts its osteogenic effect by regulating the BMP-2/Smads/Runx2 signal pathway in MC3T3-E1 cells.
Optimizing motor decision-making through competition with opponents
Authors: Ota Keiji , Tanae Mamoru , Ishii Kotaro , Takiyama Ken 
Published: August 2018

AbstractAlthough optimal decision-making is essential for sports performance and fine motor control, it has been repeatedly confirmed that humans show a strong risk-seeking bias, selecting a risky strategy over an optimal solution. Despite such evidence, the ideal method to promote optimal decision-making remains unclear. Here, we propose that interactions with other people can influence motor decision-making and improve risk-seeking bias. We developed a competitive reaching game (a variant of the “chicken game”) in which aiming for greater rewards increased the risk of no reward and subjects competed for the total reward with their opponent. The game resembles situations in sports, such as a penalty kick in soccer, service in tennis, the strike zone in baseball, or take-off in ski jumping. In five different experiments, we demonstrated that, at the beginning of the competitive game, the subjects robustly switched their risk-seeking strategy to a risk-averse strategy. Following the reversal of the strategy, the subjects achieved optimal decision-making when competing with risk-averse opponents. This optimality was achieved by a non-linear influence of an opponent’s decisions on a subject’s decisions. These results suggest that interactions with others can alter human motor decision strategies and that competition with a risk-averse opponent is key for optimizing motor decision-making.
Hi-D: Nanoscale mapping of nuclear dynamics in single living cells
Authors: Shaban Haitham A. , Barth Roman , Recoules Ludmila , Bystricky Kerstin 
Published: August 2018

ABSTRACTBulk chromatin motion has not been analysed at high resolution. We present Hi-D, a method to quantitatively map dynamics of chromatin and abundant nuclear proteins for every pixel simultaneously over the entire nucleus from fluorescence image series. Hi-D combines reconstruction of chromatin motion, and classification of local diffusion processes by Bayesian inference. We show that DNA dynamics in the nuclear interior are spatially partitioned into 0.3 – 3 μm domains in a mosaic-like pattern, uncoupled from chromatin compaction. This pattern was remodelled in response to transcriptional activity. Hi-D can be applied to any dense and bulk structures opening new perspectives towards understanding motion of nuclear molecules.
ganon: precise metagenomics classification against large and up-to-date sets of reference sequences
Authors: Piro Vitor C. , Dadi Temesgen H. , Seiler Enrico , Reinert Knut , Renard Bernhard Y. 
Published: August 2018

AbstractMotivationThe exponential growth of assembled genome sequences greatly benefits metagenomics studies. However, currently available methods struggle to manage the increasing amount of sequences and their frequent updates. Indexing the current RefSeq can take days and hundreds of GB of memory on large servers. Few methods address these issues thus far, and even though many can theoretically handle large amounts of references, time/memory requirements are prohibitive in practice. As a result, many studies that require sequence classification use often outdated and almost never truly up-to-date indices.ResultsMotivated by those limitations we created ganon, a k-mer based read classification tool that uses Interleaved Bloom Filters in conjunction with a taxonomic clustering and a k-mer counting/filtering scheme. Ganon provides an efficient method for indexing references, keeping them updated. It requires less than 55 minutes to index the complete RefSeq of bacteria, archaea, fungi and viruses. The tool can further keep these indices up-to-date in a fraction of the time necessary to create them. Ganon makes it possible to query against very large reference sets and therefore it classifies significantly more reads and identifies more species than similar methods. When classifying a high-complexity CAMI challenge dataset against complete genomes from RefSeq, ganon shows strongly increased precision with equal or better sensitivity compared with state-of-the-art tools. With the same dataset against the complete RefSeq, ganon improved the F1-Score by 65% at the genus level. It supports taxonomy- and assembly-level classification, multiple indices and hierarchical classification.AvailabilityThe software is open-source and available at: https://gitlab.com/rki_bioinformatics/ganonContactbernhard.renard@hpi.de
Imaging spectroscopy predicts variable distance decay across contrasting Amazonian tree communities
Authors: Draper Frederick C. , Baraloto Christopher , Brodrick Philip G. , Phillips Oliver L. , Martinez Rodolfo Vasquez , Honorio Coronado Euridice N. , Baker Timothy R. , Zárate Gómez Ricardo , Amasifuen Guerra Carlos A. , Flores Manuel , Garcia Villacorta Roosevelt , V. A. Fine Paul , Freitas Luis , Monteagudo‐Mendoza Abel , J. W Brienen Roel , Asner Gregory P. 
Published: August 2018

Abstract

The forests of Amazonia are among the most biodiverse on Earth, yet accurately quantifying how species composition varies through space (i.e., beta‐diversity) remains a significant challenge. Here, we use high‐fidelity airborne imaging spectroscopy from the Carnegie Airborne Observatory to quantify a key component of beta‐diversity, the distance decay in species similarity through space, across three landscapes in Northern Peru. We then compared our derived distance decay relationships to theoretical expectations obtained from a Poisson Cluster Process, known to match well with empirical distance decay relationships at local scales.

We used an unsupervised machine learning approach to estimate spatial turnover in species composition from the imaging spectroscopy data. We first validated this approach across two landscapes using an independent dataset of forest composition in 49 forest census plots (0.1–1.5 ha). We then applied our approach to three landscapes, which together represented terra firme clay forest, seasonally flooded forest and white‐sand forest. We finally used our approach to quantify landscape‐scale distance decay relationships and compared these with theoretical distance decay relationships derived from a Poisson Cluster Process.

We found a significant correlation of similarity metrics between spectral data and forest plot data, suggesting that beta‐diversity within and among forest types can be accurately estimated from airborne spectroscopic data using our unsupervised approach. We also found that estimated distance decay in species similarity varied among forest types, with seasonally flooded forests showing stronger distance decay than white‐sand and terra firme forests. Finally, we demonstrated that distance decay relationships derived from the theoretical Poisson Cluster Process compare poorly with our empirical relationships.

Synthesis. Our results demonstrate the efficacy of using high‐fidelity imaging spectroscopy to estimate beta‐diversity and continuous distance decay in lowland tropical forests. Furthermore, our findings suggest that distance decay relationships vary substantially among forest types, which has important implications for conserving these valuable ecosystems. Finally, we demonstrate that a theoretical Poisson Cluster Process poorly predicts distance decay in species similarity as conspecific aggregation occurs across a range of nested scales within larger landscapes.
Australia Demonstrates the Rise of Populism is About More than Economics
Authors: Wood Danielle , Daley John , Chivers Carmela 
Published: August 2018

AbstractVotes for established centre‐right and centre‐left political parties are falling across the developed world. Australia is not immune from this trend: in the 2016 federal election, more people voted for minor parties than at any point since the Second World War. Australia is an interesting case study for the rest of the world on the origins of populist support. Political scientists have struggled to separate the effects of cultural shifts and poor economic outcomes (low wages and rising inequality) in many countries because these shifts have occurred simultaneously. However, in Australia the economy was relatively healthy during the period of rising minor party support. Our analysis suggests that falling trust in government and a backlash against the pace of social change explain much of the collapse in support for the political mainstream.
The Rule of Law and the Rule of Empire: A.V. Dicey in Imperial Context
Authors: Lino Dylan 
Published: August 2018

AbstractThe idea of the rule of law, more ubiquitous globally today than ever before, owes a lasting debt to the work of Victorian legal theorist A. V. Dicey. But for all of Dicey's influence, little attention has been paid to the imperial entanglements of his thought, including on the rule of law. This article seeks to bring the imperial dimensions of Dicey's thinking about the rule of law into view. On Dicey's account, the rule of law represented a distinctive English civilisational achievement, one that furnished a liberal justification for British imperialism. And yet Dicey was forced to acknowledge that imperial rule at times required arbitrariness and formal inequality at odds with the rule of law. At a moment when the rule of law has once more come to license all sorts of transnational interventions by globally powerful political actors, Dicey's preoccupations and ambivalences are in many ways our own.
Protecting Free Speech and Academic Freedom in Universities
Authors: Cram Ian , Fenwick Helen 
Published: August 2018

AbstractRestrictions on speaking events in universities have been created both by recent student‐led efforts at ‘no‐platforming’ and by Part 5 of the Counter‐terrorism and Security Act 2015 which placed aspects of the government's Prevent strategy on a statutory basis. The statutory Prevent duty in universities includes, under the accompanying Guidance, curbing or monitoring events that could have an impact in drawing persons into terrorism. This article places the combined impact of Part 5 and student‐led curbs on campus speech in context by juxtaposing pre‐existing restrictions with the various free speech duties of universities. Focusing on speaking events, it evaluates the resulting state of free speech and academic freedom in universities. It finds potential violations of established free speech norms due to the impact of pre‐emptive strikes against some campus‐linked speech articulating non‐mainstream viewpoints. But it also argues that not all such speech has a strong foundation within such norms.
Clinical utility of red blood cell distribution width in inflammatory and non‐inflammatory joint diseases
Authors: Horta‐Baas Gabriel , Romero‐Figueroa María del Socorro 
Published: August 2018

AbstractAimCurrent studies demonstrate red blood cell distribution width (RDW) as a possible surrogate biomarker of inflammation. The objectives of the present study were to examine RDW in patients with osteoarthritis (OA), fibromyalgia (FM), rheumatoid arthritis (RA) and spondyloarthritis (SpA) and to evaluate its clinical importance.MethodsSix hundred and ninety‐nine ambulatory patients were evaluated. RDW, hemoglobin, erythrocyte sedimentation rate (ESR) and C‐reactive protein (CRP) were assessed. In order to compare groups, a Kruskall–Wallis test with post hoc Dunn's test was applied. A multiple logistic regression analysis was used to evaluate anisocytosis explanatory variables.ResultsRed blood cell distribution width values differed significantly among groups. Post hoc analysis demonstrated a significant increase in RDW within RA versus OA groups (P < 0.001), active SpA versus OA (P < 0.001), RA versus FM (P < 0.001) and active SpA versus FM groups (P = 0.001). Presence of anisocytosis was useful to discriminate between active articular inflammatory versus non‐inflammatory diseases with 48–95% sensitivity and 66–95% specificity. Multivariate analysis showed a six‐fold increase in anisocytosis for the presence of a possible articular inflammatory disease.ConclusionIn subjects with articular pain, RDW interpretation is a useful tool in clinical practice to distinguish between articular inflammatory and non‐inflammatory joint diseases, as with CRP. RDW seems to be a surrogate marker of the inflammatory process.
FOXP3 rs3761548 polymorphism is associated with knee osteoarthritis in a Turkish population
Authors: Cekin Nilgun , Pinarbasi Ergun , Bildirici Aslıhan Esra , Donmez Gonca , Oztemur Zekeriya , Bulut Okay , Arslan Serdal 
Published: August 2018

AbstractAimFunctional polymorphisms located in FOXP3 intron 1 was recently found to be associated with rheumatoid arthritis (RA). Although RA is an autoimmune disease, there is supporting evidence that activated maladaptive responses including pro‐inflammatory pathways play roles in osteoarthritis (OA), similar to RA. The aim of this study was to explore the relationship between rs2232365 (‐924A/G) and rs3761548 (‐3279A/C) polymorphisms as well as possible changes in the 600 bp promoter region of FOXP3 and knee OA.MethodsPatients with primary knee OA (n = 300) and healthy individuals (n = 300) were examined for rs3761548 and rs2232365 FOXP3 gene polymorphisms by the polymerase chain reaction–restriction fragment‐length polymorphism method. The 600 bp promoter region (between −500 and +100) of the gene was also sequenced with direct sequencing in 50 knee OA patients and 50 healthy individuals.ResultsThere were no sequence variants in the promoter region tested both in OA patients and healthy controls. The SNP rs2232365 showed no association with OA susceptibility and severity and the results of other genetic models were also nonsignificant. On the other hand, rs3761548 AC (P = 0.003), AA + CC (P = 0.0014) as well as AC + AA (P = 0.40) genotypes showed association with Grade 4 knee OA patients.ConclusionOur findings indicated that the association between FOXP3 rs2232365 polymorphism and knee OA tended to yield negative results but the FOXP3 rs3761548 C allele was associated with elevated risk of OA in Grade 4 knee OA patients in a Turkish population.