bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dry and hot: the hydraulic consequences of a climate change–type drought for Amazonian trees
Authors: Fontes Clarissa G. , Dawson Todd E. , Jardine Kolby , McDowell Nate , Gimenez Bruno O. , Anderegg Leander , Negrón-Juárez Robinson , Higuchi Niro , Fine Paul V. A. , Araújo Alessandro C. , Chambers Jeffrey Q. 
Published: October 2018

How plants respond physiologically to leaf warming and low water availability may determine how they will perform under future climate change. In 2015–2016, an unprecedented drought occurred across Amazonia with record-breaking high temperatures and low soil moisture, offering a unique opportunity to evaluate the performances of Amazonian trees to a severe climatic event. We quantified the responses of leaf water potential, sap velocity, whole-tree hydraulic conductance (Kwt), turgor loss and xylem embolism, during and after the 2015–2016 El Niño for five canopy-tree species. Leaf/xylem safety margins (SMs), sap velocity andKwtshowed a sharp drop during warm periods. SMs were negatively correlated with vapour pressure deficit, but had no significant relationship with soil water storage. Based on our calculations of canopy stomatal and xylem resistances, the decrease in sap velocity andKwtwas due to a combination of xylem cavitation and stomatal closure. Our results suggest that warm droughts greatly amplify the degree of trees' physiological stress and can lead to mortality. Given the extreme nature of the 2015–2016 El Niño and that temperatures are predicted to increase, this work can serve as a case study of the possible impact climate warming can have on tropical trees.This article is part of a discussion meeting issue ‘The impact of the 2015/2016 El Niño on the terrestrial tropical carbon cycle: patterns, mechanisms and implications’.
Actin dynamics drive microvillar motility and clustering during brush border assembly
Authors: Meenderink Leslie M , Tyska Matthew J. 
Published: October 2018

SUMMARYDuring differentiation, transporting epithelial cells generate large arrays of microvilli known as a brush borders to enhance functional capacity. To develop our understanding of brush border formation, we used live cell imaging to visualize apical surface remodeling during early stages of this process. Strikingly, we found that individual microvilli exhibit persistent active motility, translocating across the cell surface at ~0.2 μm/min. Perturbation studies with inhibitors and photokinetic experiments revealed that microvillar motility is driven by actin assembly at the barbed-ends of core bundles, which in turn is linked to robust treadmilling of these structures. Because the apical surface of differentiating epithelial cells is crowded with nascent microvilli, persistent motility promotes collisions between protrusions and ultimately leads to their clustering and consolidation into higher order arrays. Thus, microvillar motility represents a previously unrecognized driving force for apical surface remodeling and maturation during epithelial differentiation.
The blind choreographer: evolution of social norms and correlated equilibria
Authors: Morsky Bryce , Akçay Erol 
Published: October 2018

AbstractSocial norms regulate and coordinate most aspects of human social life, yet they emerge and change as a result of individual behaviours, beliefs, and expectations. A satisfactory account for the evolutionary dynamics of social norms therefore has to link individual beliefs and expectations to population-level dynamics, where individual norms change according to their consequences for individuals. Here we present a new model of evolutionary dynamics of social norms that encompasses this objective and addresses the emergence of social norms. In this model, a norm is a set of behavioural prescriptions and a set of environmental descriptions that describe the expected behaviours of those with whom the norm holder will interact. These pre-scriptions and descriptions are functions of exogenous environmental events. These events have no intrinsic meaning or effect on the payoffs to individuals, yet beliefs/- superstitions regarding them can effectuate coordination. Though a norm's prescriptions and descriptions are dependent upon one another, we show how they emerge from random accumulations of beliefs. We categorize the space of social norms into several natural classes and study the evolutionary competition between these classes of norms. We apply our model to the Game of Chicken and the Nash Bargaining Game. Further, we show how the space of norms and evolutionary stability is dependent upon the correlation structure of the environment, and under which such correlation structures social dilemmas can be ameliorated or exacerbated.
Genomic Bayesian confirmatory factor analysis and Bayesian network to characterize a wide spectrum of rice phenotypes
Authors: Yu Haipeng , Campbell Malachy T. , Zhang Qi , Walia Harkamal , Morota Gota 
Published: October 2018

AbstractWith the advent of high-throughput phenotyping platforms, plant breeders have a means to assess many traits for large breeding populations. However, understanding the genetic interdependencies among high-dimensional traits in a statistically robust manner remains a major challenge. Since multiple phenotypes likely share mutual relationships, elucidating the interdependencies among economically important traits can better inform breeding decisions and accelerate the genetic improvement of plants. The objective of this study was to leverage confirmatory factor analysis and graphical modeling to elucidate the genetic interdependencies among a diverse agronomic traits in rice. We used a Bayesian network to depict conditional dependencies among phenotypes, which can not be obtained by standard multitrait analysis. We utilized Bayesian confirmatory factor analysis which hypothesized that 48 observed phenotypes resulted from six latent variables including grain morphology, morphology, flowering time, physiology, yield, and morphological salt response. This was followed by studying the genetics of each latent variable, which is also known as factor, using single nucleotide polymorphisms. Bayesian network structures involving the genomic component of six latent variables were established by fitting four algorithms (i.e., Hill Climbing, Tabu, Max-Min Hill Climbing, and General 2-Phase Restricted Maximization algorithms). Physiological components influenced the flowering time and grain morphology, and morphology and grain morphology influenced yield. In summary, we show the Bayesian network coupled with factor analysis can provide an effective approach to understand the interdependence patterns among phenotypes and to predict the potential influence of external interventions or selection related to target traits in the interrelated complex traits systems.
TIN2 functions with TPP1/POT1 to stimulate telomerase processivity
Authors: Pike Alexandra M. , Strong Margaret A. , Ouyang John Paul T. , Connelly Carla J. , Greider Carol W. 
Published: October 2018

AbstractTelomere length maintenance is crucial for cells that divide many times. TIN2 is an important regulator of telomere length, and mutations in TINF2, the gene encoding TIN2, cause short telomere syndromes. While the genetics underscore the importance of TIN2, the mechanism through which TIN2 regulates telomere length remains unclear. Here, we characterize the effects of TIN2 on telomerase activity. We identified a new isoform in human cells, TIN2M, that is expressed at similar levels to previously studied TIN2 isoforms. Additionally, we found that all three TIN2 isoforms stimulated telomerase processivity beyond the previously characterized stimulation by TPP1/POT1. Mutations in the TPP1 TEL-patch abrogated this stimulation, implicating TIN2 as a component of the TPP1/POT1 processivity complex. All three TIN2 isoforms localized to telomeres in vivo but had distinct effects on telomere length, suggesting they are functionally distinct. These data contrast previous descriptions of TIN2 a simple scaffolding protein, showing that TIN2 isoforms directly regulate telomerase.
Human telomere repeat binding factor TRF1 replaces TRF2 bound to shelterin core hub TIN2 when TPP1 is absent
Authors: Janovič Tomáš , Stojaspal Martin , Veverka Pavel , Horáková Denisa , Hofr Ctirad 
Published: October 2018

AbstractHuman telomeric repeat binding factors TRF1, TRF2 along with TIN2 form a core of shelterin complex that protects chromosome ends against unwanted end-joining and DNA repair. We applied a single-molecule approach to assess TRF1-TIN2-TRF2 complex formation in solution at physiological conditions. Fluorescence Cross-Correlation Spectroscopy (FCCS) was used to describe the complex formation by analyzing how coincident fluctuations of differently labeled TRF1 and TRF2 correlate when they move together through the confocal volume of the microscope. We observed, at the single-molecule level, that TRF1 effectively substituted TRF2 on TIN2. We assessed the effect of another telomeric factor TPP1 that recruits telomerase to telomeres. We found that TPP1 upon binding to TIN2 induces allosteric changes that expand TIN2 binding capacity, such that TIN2 can accommodate both TRF1 and TRF2 simultaneously. We suggest a molecular model that explains why TPP1 is essential for the stable formation of TRF1-TIN2-TRF2 core complex.
Physical and functional interaction between SET1/COMPASS complex component CFP-1 and a Sin3 HDAC complex
Authors: Beurton F. , Stempor P. , Caron M. , Appert A. , Dong Y. , Chen R. , Cluet D. , Couté Y. , Herbette M. , Huang N. , Polveche H. , Spichty M. , Bedet C. , Ahringer J. , Palladino F. 
Published: October 2018

AbstractThe CFP1 CXXC zinc finger protein targets the SET1/COMPASS complex to non-methylated CpG rich promoters to implement tri-methylation of histone H3 Ly4 (H3K4me3). Although H3K4me3 is widely associated with gene expression, the effects of CFP1 loss depend on chromatin context, so it is important to understand the relationship between CFP1 and other chromatin factors. Using a proteomics approach, we identified an unexpected link betweenC. elegansCFP-1 and a Rpd3/Sin3 histone deacetylase complex. We find that mutants of CFP-1, SIN-3, and the catalytic subunit SET-2/SET1 have similar phenotypes and misregulate common genes. CFP-1 directly binds SIN-3 through a region including the conserved PAH1 domain and recruits SIN-3 and the HDA-1/HDAC subunit to H3K4me3 enriched promoters. Our results reveal a novel role for CFP-1 in mediating interaction between SET1/COMPASS and a Sin3 HDAC complex at promoters and uncover coordinate regulation of gene expression by chromatin complexes having distinct activities.
A complete chromosome substitution mapping panel reveals genome-wide epistasis in Arabidopsis
Authors: Wijnen Cris L. , Botet Ramon , van de Belt José , Deurhof Laurens , de Jong Hans , de Snoo C. Bastiaan , Dirks Rob , Boer Martin P. , van Eeuwijk Fred A. , Wijnker Erik , Keurentjes Joost J.B. 
Published: October 2018

AbstractChromosome substitution lines (CSLs) are tentatively supreme resources to investigate non-allelic genetic interactions. However, the difficulty of generating such lines in most species largely yielded imperfect CSL panels, prohibiting a systematic dissection of epistasis. Here, we present the development and use of a unique and complete panel of CSLs inArabidopsis thaliana, allowing the full factorial analysis of epistatic interactions. A first comparison of reciprocal single chromosome substitutions revealed a dependency of QTL detection on different genetic backgrounds. The subsequent analysis of the complete panel of CSLs enabled the mapping of the genetic interactors and identified multiple two- and three-way interactions for different traits. Some of the detected epistatic effects were as large as any observed main effect, illustrating the impact of epistasis on quantitative trait variation. We, therefore, have demonstrated the high power of detection and mapping of genome-wide epistasis, confirming the assumed supremacy of comprehensive CSL sets.One sentence summaryDevelopment of a complete panel of chromosome substitution lines enables high power mapping of epistatic interactions inArabidopsis thaliana.
Composition is the core driver of the language-selective network
Authors: Mollica Francis , Diachek Evgeniia , Mineroff Zachary , Kean Hope , Siegelman Matthew , Piantadosi Steven T. , Futrell Richard , Qian Peng , Fedorenko Evelina 
Published: October 2018

AbstractThe fronto-temporal language network responds robustly and selectively to sentences. But the features of linguistic input that drive this response and the computations these language areas support remain debated. Two key features of sentences are typically confounded in natural linguistic input: words in sentences a) are semantically and syntactically combinable into phrase- and clause-level meanings, and b) occur in an order licensed by the language’s grammar. Inspired by recent psycholinguistic work establishing that language processing is robust to word order violations, we hypothesized that the core linguistic computation is composition, and, thus, can take place even when the word order violates the grammatical constraints of the language. This hypothesis predicts that a linguistic string should elicit a sentence-level response in the language network as long as the words in that string can enter into dependency relationships as in typical sentences. We tested this prediction across two fMRI experiments (total N=47) by introducing a varying number of local word swaps into naturalistic sentences, leading to progressively less syntactically well-formed strings. Critically, local dependency relationships were preserved because combinable words remained close to each other. As predicted, word order degradation did not decrease the magnitude of the BOLD response in the language network, except when combinable words were so far apart that composition among nearby words was highly unlikely. This finding demonstrates that composition is robust to word order violations, and that the language regions respond as strongly as they do to naturalistic linguistic input as long as composition can take place.
Characterization of the gastric motility response to human motilin and erythromycin in human motilin receptor-expressing transgenic mice
Authors: Kato Shinichi , Takahashi Aoi , Shindo Mai , Yoshida Ayano , Kawamura Tomoe , Matsumoto Kenjiro , Matsuura Bunzo 
Published: October 2018

AbstractMotilin is a gastrointestinal peptide hormone that stimulates gastrointestinal motility. Motilin is produced primarily in the duodenum and jejunum. Motilin receptors (MTLRs) are G protein-coupled receptors that may represent a clinically useful pharmacological target as they can be activated by erythromycin. The functions of motilin are highly species-dependent and remain poorly understood. As a functional motilin system is absent in rodents such as rats and mice, these species are not commonly used for basic studies. In this study, we examine the usefulness of human MTLR-overexpressing transgenic (hMTLR-Tg) mice by identifying the mechanisms of the gastric motor response to human motilin and erythromycin.The distribution of hMTLR was examined immunohistochemically in male wild-type (WT) and hMTLR-Tg mice. The contractile response of gastric strips was measured isometrically in an organ bath, while gastric emptying was determined using phenol red.hMTLR expression was abundant in the gastric smooth muscle layer but more potently expressed in the myenteric plexus of hMTLR-Tg mice but not WT mice. hMTLR was not co-localized with vesicular acetylcholine transporter, a marker of cholinergic neurons in the myenteric plexus. Treatment with human motilin and erythromycin caused concentration-dependent contraction of gastric strips obtained from hMTLR-Tg mice but not from WT mice.The contractile response to human motilin and erythromycin in hMTLR-Tg mice was affected by neither atropine nor tetrodotoxin and was totally absent in Ca2+-free conditions. Furthermore, intraperitoneal injection of erythromycin significantly promoted gastric emptying in hMTLR-Tg mice but not in WT mice.Human motilin and erythromycin stimulate the gastric motor response in hMTLR-Tg mice. This action is mediated by direct contraction of smooth muscle via the influx of extracellular Ca2+. Thus, hMTLR-Tg mice may be useful for the evaluation of MTLR agonists as gastric prokinetic agents.
Sufficient therapeutic effect of cryopreserved frozen adipose-derived regenerative cells on burn wounds
Authors: Kaita Yasuhiko , Tarui Takehiko , Yoshino Hideaki , Matsuda Takeaki , Yamaguchi Yoshihiro , Nakagawa Takatoshi , Asahi Michio , Ii Masaaki 
Published: October 2018

AbstractThe purpose of this study was to evaluate whether cryopreserved (frozen) adipose-derived regenerative cells (ADRCs) have a therapeutic effect on burn wound healing as well as freshly isolated (fresh) ADRCs.Full thickness burns were created on dorsum of nude mice and burn wound was excised. The wound was covered by artificial dermis with; (i) fresh ADRCs, (ii) frozen ADRCs, and (iii) PBS (control). The assessment for wound healing was performed by morphological, histopathological and immunohistochemical analyses.In vivo analyses exhibited the significant therapeutic effect of frozen ADRCs on burn wound healing up to the similar or higher level of fresh ADRCs. There were significant differences of wound closure, epithelized tissue thickness, and neovascularization between the treatment groups and control group. Although there was no significant difference of therapeutic efficacy between fresh ADRC group and frozen ADRC group, frozen ADRCs improved burn wound healing process in dermal regeneration with increased great type I collagen synthesis compared with fresh ADRCs.These findings indicate that frozen ADRCs allow us to apply not only quickly but also for multiple times, and the cryopreserved ADRCs could therefore be useful for the treatment of burn wounds in clinical settings.
The predictive value of quantitative nucleic acid amplification detection ofClostridium difficiletoxin gene for faecal sample toxin status and patient outcome
Authors: Davies Kerrie A , Planche Tim , Wilcox Mark H 
Published: October 2018

AbstractBackgroundLaboratory diagnosis ofClostridium difficileinfection (CDI) remains unsettled, despite updated guidelines. We investigated the potential utility of quantitative data from a nucleic acid amplification test (NAAT) forC. difficiletoxin gene (tg) for patient management.MethodsUsing data from the largest everC. difficilediagnostic study (8853 diarrhoeal samples from 7335 patients), we determined the predicative value of C. difficile tgNAAT (Cepheid Xpert C.diff) low cycle threshold (CT) value for patient toxin positive status, CDI severity, mortality and CDI recurrence. Reference methods for CDI diagnosis were cytotoxicity assay (CTA) and cytotoxigenic culture (CTC).ResultsOf 1281 tgNAAT positive faecal samples, 713 and 917 were CTA and CTC positive, respectively. The median tgNAAT CT for patients who died was 25.5 vs 27.5 for survivors (p = 0.021); for toxin-positivity was 24.9 vs 31.6 for toxin-negative samples (p<0.001) and for patients with a recurrence episode was 25.6 vs 27.3 for those who did not have a recurrent episode (p = 0.111). Following optimal cut-off determination, low CT was defined as ≤25 and was significantly associated with a toxin-positive result (P<0.001, positive predictive value 83.9%), presence of PCR-ribotype 027 (P=0.025), and mortality (P=0.032). Recurrence was not associated with low CT (p 0.111).ConclusionsLow tgNAAT CT could indicate CTA positive patients, have more severe infection, increased risk of mortality and possibly recurrence. Although, the limited specificity of tgNAAT means it cannot be used as a standalone test, it could augment a more timely diagnosis, and optimise management of these at-risk patients.
Soleus muscle weakness in Cerebral Palsy: muscle architecture revealed with Diffusion Tensor Imaging
Authors: Sahrmann Annika S. , Stott Ngaire Susan , Besier Thor F. , Fernandez Justin W. , Handsfield Geoffrey G. 
Published: October 2018

ABSTRACTCerebral palsy (CP) is associated with movement disorders and reduced muscle size. This latter phenomenon has been observed by computing muscle volumes from conventional MRI, with most studies reporting significantly reduced volumes in leg muscles. This indicates impaired muscle growth, but without knowing muscle fiber orientation, it is not clear whether muscle growth in CP is impaired in the along-fiber direction (indicating shortened muscles and limited range of motion) or the cross-fiber direction (indicating weak muscles and impaired strength). Using Diffusion Tensor Imaging (DTI) we can determine muscle fiber orientation and construct 3D muscle architectures to examine along-fiber length and cross-sectional area separately. Such an approach has not been undertaken in CP. Here, we use advanced DTI sequences with fast imaging times to capture fiber orientations in the soleus muscle of children with CP and age-matched, able-bodied controls. Physiological cross sectional areas (PCSA) were reduced (37 ± 11%) in children with CP compared to controls, indicating impaired muscle strength. Along-fiber muscle lengths were not different between groups, but we observed large variance in length within CP group. This study is the first to demonstrate functional strength deficits using DTI and implicates impaired cross-sectional muscle growth in children with cerebral palsy.
Evaluating an Upper Respiratory Disease Panel on the Portable MinION Sequencer
Authors: Lyon Wanda J. , Smith Zachary K. , Grier Brian , Baldwin James , Starr Clarise R. 
Published: October 2018

AbstractThe MinION was used to evaluate upper respiratory disease infections using both whole genome amplification (WGA), targeted sequencing, and was found to have tremendous potential for field use. The MinION nanopore sequencer was been released to community testers for evaluation using a variety of sequencing applications. The MinION was used to evaluate upper respiratory disease infections using both whole genome amplification and targeted sequencing, and was found to have tremendous potential for field use. In this study, we tested the ability of the MinION nanopore sequencer to accurately identify and differentiate clinical bacterial and viral samples via targeted sequencing and whole genome sequencing. The current nanopore technology has limitations with respect to error rate but has steadily improved with development of new flow cells and kits. Upper respiratory disease organisms were successfully identified and differentiated down to the strain level with 87-98% alignment to our reference genome database. The ability to differentiate strains by amplicon and whole genome sequencing on the MinION was accomplished despite the observed average per 100-base error rate averaged 1.2E-01. This study offers evidence of the utility of sequencing to identify and differentiate both viral and bacterial species present within clinical samples.