bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phytochromes measure photoperiod in Brachypodium
Authors: Gao Mingjun , Geng Feng , Klose Cornelia , Staudt Anne-Marie , Huang He , Nguyen Duy , Lan Hui , Mockler Todd C. , Nusinow Dmitri A. , Hiltbrunner Andreas , Schäfer Eberhard , Wigge Philip A. , Jaeger Katja E. 
Published: July 2019

SummaryDaylength is a key seasonal cue for animals and plants. In cereals, photoperiodic responses are a major adaptive trait, and alleles of clock genes such asPHOTOPERIOD DEPENDENT1 (PPD1)andEARLY FLOWERING3 (ELF3)have been selected for in breeding barley and wheat for more northern latitudes (Faure et al., 2012; Turner, Beales, Faure, Dunford, & Laurie, 2005). How monocot plants sense photoperiod and integrate this information into growth and development is not well understood. We show that inBrachypodium distachyon, phytochrome C (phyC) acts as a molecular timer, directly communicating information to the circadian clock protein ELF3. In this way, ELF3 levels integrate night length information. ELF3 is a central regulator of photoperiodism in Brachypodium, andelf3mutants display a constitutive long day transcriptome. Conversely, conditions that result in higher levels of ELF3 suppress long day responses. We are able to show that these effects are direct, as ELF3 and phyC occur in a common complex, and they associate with the promoters of a number of conserved regulators of photoperiodism, includingPPD1. Consistent with observations in barley, we are able to show thatPPD1overexpression accelerates flowering in SD and is necessary for rapid flowering in response to LD. These findings provide a conceptual framework for understanding observations in the photoperiodic responses of key crops, including wheat, barley and rice.
Revealing the Assembly of Filamentous Proteins with Scanning Transmission Electron Microscopy
Authors: Martinez-Torres Cristina , Burla Federica , Alkemade Celine , Koenderink Gijsje H. 
Published: July 2019

ABSTRACTFilamentous proteins are responsible for the superior mechanical strength of our cells and tissues. The remarkable mechanical properties of protein filaments are tied to their complex molecular packing structure. However, since these filaments have widths of several to tens of nanometers, it has remained challenging to quantitatively probe their molecular mass density and three-dimensional packing order. Scanning transmission electron microscopy (STEM) is a powerful tool to perform simultaneous mass and morphology measurements on filamentous proteins at high resolution, but its applicability has been greatly limited by the lack of automated image processing methods. Here, we demonstrate a semi-automated tracking algorithm that is capable of analyzing the molecular packing density of intra- and extracellular protein filaments over a broad mass range from STEM images. We prove the wide applicability of the technique by analyzing the mass densities of two cytoskeletal proteins (actin and microtubules) and of the main protein in the extracellular matrix, collagen. The high-throughput and spatial resolution of our approach allow us to quantify the internal packing of these filaments and their polymorphism by correlating mass and morphology information. Moreover, we are able to identify periodic mass variations in collagen fibrils that reveal details of their axially ordered longitudinal self-assembly. STEM-based mass mapping coupled with our tracking algorithm is therefore a powerful technique in the characterization of a wide range of biological and synthetic filaments.
Cardiac valve regeneration in adult zebrafish: importance of TGFß signaling in new tissue formation
Authors: Bensimon-Brito Anabela , Ramkumar Srinath , Boezio Giulia L. M. , Guenther Stefan , Kuenne Carsten , Sánchez-Iranzo Héctor , Iloska Dijana , Piesker Janett , Pullamsetti Soni , Mercader Nadia , Beis Dimitris , Stainier Didier Y. R. 
Published: July 2019

SummaryCardiac valve disease can lead to severe cardiac dysfunction and is thus a frequent cause of morbidity and mortality. Its main treatment is valve replacement, which is currently greatly limited by the poor recellularization and tissue formation potential of the implanted valves. As we still lack suitable animal models to identify modulators of these processes, here we used the adult zebrafish and found that, upon valve decellularization, they initiate a striking regenerative program that leads to the formation of new functional valves. After injury, endothelial and kidney marrow-derived cells undergo cell cycle re-entry and differentiate into new extracellular matrix-secreting valve cells. The Transforming Growth Factor beta (TGFβ) signaling pathway promotes this process by enhancing progenitor cell proliferation as well as valve cell differentiation. These findings reveal a key role for TGFβ signaling in valve regeneration and also establish the zebrafish as a model to identify and test factors promoting valve recellularization and growth.
TRF1 prevents permissive DNA damage response, recombination and Break Induced Replication at telomeres
Authors: Porreca Rosa Maria , Law Pui Pik , Herrera-Moyano Emilia , Gonzalez-Franco Roser , Montoya Alex , Faull Peter , Kramer Holger , Vannier Jean-Baptiste 
Published: July 2019

AbstractTelomeres are a significant challenge to DNA replication and are prone to replication stress and telomere fragility. The shelterin component TRF1 facilitates telomere replication but the molecular mechanism remains uncertain. By interrogating the proteomic composition of telomeres, we show that telomeres lacking TRF1 undergo protein composition reorganisation associated with a DNA damage response and chromatin remodelers. Surprisingly, TRF1 suppresses the accumulation of promyelocytic leukemia (PML) protein, BRCA1 and the SMC5/6 complex at telomeres, which is associated with increased Homologous Recombination (HR) and TERRA transcription. We uncovered a previously unappreciated role for TRF1 in the suppression of telomere recombination, dependent on SMC5 and also POLD3 dependent Break Induced Replication at telomeres. We propose that TRF1 facilitates S-phase telomeric DNA synthesis to prevent illegitimate mitotic DNA recombination and chromatin rearrangement.
An annotation dataset facilitates automatic annotation of whole-brain activity imaging ofC. elegans
Authors: Toyoshima Yu , Wu Stephen , Kanamori Manami , Sato Hirofumi , Jang Moon Sun , Oe Suzu , Murakami Yuko , Teramoto Takayuki , Park ChanHyun , Iwasaki Yuishi , Ishihara Takeshi , Yoshida Ryo , Iino Yuichi 
Published: July 2019

AbstractAnnotation of cell identity is an essential process in neuroscience that allows for comparing neural activities across different animals. InC. elegans, although unique identities have been assigned to all neurons, the number of annotatable neurons in an intact animal is limited in practice and comprehensive methods for cell annotation are required. Here we propose an efficient annotation method that can be integrated with the whole-brain imaging technique. We systematically identified neurons in the head region of 311 adult worms using 35 cell-specific promoters and created a dataset of the expression patterns and the positions of the neurons. The large positional variations illustrated the difficulty of the annotation task. We investigated multiple combinations of cell-specific promoters to tackle this problem. We also developed an automatic annotation method with human interaction functionality that facilitates annotation for whole-brain imaging.
A mathematical model of ephaptic interactions in neuronal fiber pathways: could there be more than transmission along the tracts?
Authors: Sheheitli Hiba , Jirsa Viktor K. 
Published: July 2019

AbstractIn the past several decades, there has been numerous experimental and modeling efforts to study ephaptic interactions in neuronal systems. While studies on the matter have looked at either axons of the peripheral nervous system or cortical neuronal structures, no attention has be given to the possibility of ephaptic interactions in the white matter tracts of the brain. Inspired by the highly organized and tightly packed geometry of axons in neuronal fiber pathways, we aim to theoretically investigate the potential effects of ephaptic interactions along these structures that are resilient to experimental probing. For that end, we use axonal cable theory to derive a minimal model of a sheet of N ephaptically coupled axons. We numerically solve the equations and explore the dynamics of the system as the ephaptic coupling parameter is varied. We demonstrate that ephaptic interactions can lead to local phase locking between impulses traveling along adjacent axons. As ephaptic coupling is increased, traveling impulses trigger new impulses along adjacent axons resulting in finite size traveling fronts. For strong enough coupling, impulses propagate laterally and backwards, resulting in complex spatio-temporal patterns. While it is common for large scale brain network models to assume the role of brain fiber pathways to be that of mere transmission of signals between different brain regions, our work calls for a closer re-examination of the validity of such a view. The results suggest that in the presence of significant ephaptic interactions the brain fiber tracts can act as a dynamic active medium.Author summaryStarting from local circuit theory and the Fitzhugh-Nagumo cable model of an axon, we derive a system of nonlinear coupled partial differential equations (PDE’s) to model a sheet of N ephaptically coupled axons. We also put forward a continuous limit approximation that transforms the model into a field equation in the form of a two-dimensional PDE that allows for the extension of the model to a 3D domain. We numerically solve the equations and explore the dynamic responses as the ephaptic coupling strength is varied. We observe that ephaptic interaction allows for phase locking of adjacent impulses and coordination of subthreshold dynamics. In addition, when strong enough, ephaptic interaction can lead to the generation of new impulses along the axons as well as lateral and backward propagation in the form of traveling fronts and complex spatio-temporal patterns. The transition between different dynamic regimes happens abruptly at critical values of the parameter. We also compare the dynamics of the two models and find good qualitative correspondence in certain parameter regimes. The results put into question the validity of assuming the role of fiber pathways to be that of mere interneuronal transmission and calls for further investigation of the matter.
Rag1D600A, a novel catalytically inactive RAG mouse model
Authors: Wong Jason B , Skok Jane A 
Published: July 2019

AbstractThe RAG complex (RAG1 and RAG2) can bind to recombination signal sequences of antigen receptor loci gene segments and coordinate V(D)J recombination which is the primary method of generating antigen receptor diversity. Previous biochemistry studies discovered RAG1 D600, D708 and E962 residues as essential for catalytic DNA nicking and hairpin forming activity of the RAG complex. Neutralization of each of the acidic residues does not impair DNA binding to recombination signal sequence containing DNA substrates, but cleavage of the substrates is severely compromised. These three acidic residues are thought to comprise a DDE motif that is responsible for binding to a divalent cation that is necessary for cleavage activity. Although a Rag1-/-; RAG1-D708A transgenic mouse model system has been used to study dynamics of RAG activity, transgenic expression may not precisely mimic expression from the endogenous locus. In order to improve upon this model, we created Rag1D600A mice that lack B and T cells and demonstrate a developmental block at the pro-B and DN stages, respectively. Thus, Rag1D600A mice provide a novel mouse model system for studying the poorly understood noncanonical functions of RAG1.
Mapping Cumulative Impacts to Coastal Ecosystem Services in British Columbia
Authors: Singh Gerald G. , Eddy Ian M.S. , Halpern Benjamin S. , Neslo Rabin , Satterfield Terre , Chan Kai M.A. 
Published: July 2019

AbstractEcosystem services are impacted through restricting service supply, through limiting people from accessing services, and by affecting the quality of services. We map cumulative impacts to 8 different ecosystem services in coastal British Columbia using InVEST models, spatial data, and expert elicitation to quantify risk to each service from anthropogenic activities. We find that impact to service access and quality as well as impact to service supply results in greater severity of impact and a greater diversity of causal processes of impact than only considering impact to service supply. This suggests that limiting access to services and impacts to service quality may be important and understanding these kinds of impacts may complement our knowledge of impacts to biophysical systems that produce services. Some ecosystem services are at greater risk from climate stressors while others face greater risk from local activities. Prominent causal pathways of impact include limiting access and affecting quality. Mapping cumulative impacts to ecosystem services can yield rich insights, including highlighting areas of high impact and understanding causes of impact, and should be an essential management tool to help maintain the flow of services we benefit from.
Monitoring and characterizing soluble and membrane-bound ectonucleotidases CD73 and CD39
Authors: Goueli Said A. , Hsiao Kevin 
Published: July 2019

AbstractThe success of immunotherapy treatment in oncology ushered a new modality for treating a wide variety of cancers. However, lack of effect in some patients made it imperative to identify other pathways that are exploited by cancer cells to circumvent immune surveillance, and possibly synergize immune checkpoint treatment in those cases. It has been recently recognized that adenosine levels increased significantly in the tumor microenvironment and that adenosine/adenosine receptors play a powerful role as immunosuppressant and attenuating several effector T cell functions. The two main enzymes responsible for generating adenosine in the microenvironment are the ectonucleotidases CD39 and CD73, the former utilizes both ATP and ADP and producing AMP while the latter utilizes AMP and generates adenosine. Thus, these two enzymes combined are the major source for the bulk of adenosine produced in the microenvironment. They were shown to be validated targets in oncology leading to several clinical trials that include small molecules as well as antibodies, showing positive and encouraging results in the preclinical arena. Towards the development of novel drugs to target these enzymes, we have developed a platform that can be utilized to monitor the activities of both enzymes in vitro (biochemical) as well as in cells (cell based) assays. We have developed very sensitive and homogenous assays that enabled us to monitor the activity of both enzymes and demonstrate selectivity of known inhibitors as well as monoclonal antibodies. This should speed up screening for novel inhibitors leading to more effective cancer therapy
Effect of pulsed light on postharvest disease control-related metabolomic variation in melon (Cucumis melo) artificially inoculated with Fusarium pallidoroseum
Authors: Filho Francisco Oiram , de Oliveira Silva Ebenézer , de Almeida Lopes Mônica Maria , Vasconselos Ribeiro Paulo Riceli , Oster Andréia Hansen , Carvalho Guedes Jhonyson Arruda , Nascimento Bordallo Patrícia do , Zocolo Guilherme Julião 
Published: July 2019

AbstractPulsed light, as a postharvest technology, is an alternative to traditional fungicides, and can be used on a wide variety of fruit and vegetables for sanitization or pathogen control. In addition to these applications, other effects also are detected in vegetal cells, including changes in metabolism and production of secondary metabolites, which directly affect disease control response mechanisms. This study aimed to evaluate the possible applications of pulsed ultraviolet light in controlling postharvest rot, mainly caused by Fusarium pallidoroseum in yellow melon ‘Goldex’, in natura, and its implications in the disease control as a function of metabolomic expression to effect fungicidal or fungistatic. The dose of pulsed light (PL) that inhibited F. pallidoroseum growth in melons (Cucumis melo var. Spanish) was 9 KJ m-2. Ultra performance liquid chromatography (UPLC) coupled to a quadrupole time-of-flight (QTOF) mass analyzer identified 12 compounds based on the MS/MS fragmentation patterns. Chemometric analysis by Principal Components Analysis (PCA) and Orthogonal Partial Least Squared Discriminant Analysis (OPLS-DA and S-plot) were used to evaluate the changes in fruit metabolism. PL technology provided protection against postharvest disease in melons, directly inhibiting the growth of F. pallidoroseum through upregulation of specific fruit biomarkers such as pipecolic acid (11), saponarin (7), and orientin (3), which acted as major markers for the defense system against pathogens. PL can thus be proposed as a postharvest technology to avoid chemical fungicides and may be applied to reduce the decay of melon quality during its export and storage.
Agents of alienation: accountants and the land grab of Papua New Guinea
Authors: Finau Glenn , Jacobs Kerry , Chand Satish 
Published: July 2019

Purpose
The purpose of this paper is to explore and examine the role of accounting and accountants in customary land transactions between Indigenous peoples and foreign corporate entities. The paper uses the case of two accountants who utilised accounting technologies in lease agreements to alienate customary land from Indigenous landowners in Papua New Guinea (PNG).

Design/methodology/approach
Employing a case study methodology, the paper draws on contemporary data sets of transcripts related to a Commission of Inquiry established in 2011 to investigate PNG’s Special Agricultural Business Lease system. Analysis of other publicly available data and semi-structured interviews with PNG landowners and other stakeholders supplement and triangulate data from the inquiry transcripts. A Bourdieusian lens was adopted to conceptualise how accounting was used in the struggles for customary land between foreign developers and Indigenous landowners within the wider capitalist field and the traditional Melanesian field.

Findings
This paper reveals how accountants exploited PNG’s customary land registration system, the Indigenous peoples’ lack of financial literacy and their desperation for development to alienate customary land from landowners. The accountants employed accounting technologies in the sublease agreements to reduce their royalty obligations to the landowners and to impose penalty clauses that made it financially impossible for the landowners to cancel the leases. The accountants used accounting to normalise, legitimise and rationalise these exploitative arrangements in formal lease contracts.

Originality/value
This paper responds to the call for research on accounting and Indigenous peoples that is contemporary rather than historic; examines the role of accountants in Indigenous relations, and examines the emancipatory potential of accounting.
In-flight thrust monitoring: an acoustics-based approach
Authors: Lowe K. Todd , Otero Raul , Ng Wing 
Published: July 2019

Purpose
The purpose of this paper is to present an acoustics-based method for measuring turbofan nozzle exhaust thrust, while assessing the potential of scaling the methods for in-flight measurements.

Design/methodology/approach
Although many methods proposed for achieving in-flight thrust measurements involve complicated, sensitive and expense instruments, an acoustics-based approach is discussed that greatly simplifies the technology development pathway to in-flight applications.

Findings
Results are provided for a minimum set of sensors applied in the exhaust of a research turbofan engine at Virginia Tech, showing the difference in acoustics-measured thrust and nozzle thrust found by integrating thermocouple and Kiel probe measurements to be less than 6 per cent at the maximum fan speed examined.

Practical implications
Measuring accurate thrust values in flight will prove immediately valuable for installed thrust validation and engine health monitoring. Acoustics-based methodologies are attractive because of the robustness and low cost of sensors and sources. The value of in-flight thrust measurements, along with the benefits of acoustic approaches, makes the current topic of great interest for further development.

Originality/value
This paper presents unique applications of a time-of-flight acoustic thrust sensor, while providing an original assessment of technological challenges involved with the progression of the technique for in-flight measurements.
Thermal performance enhancement in a wedge duct with in-line pin fins combined with vortex generators
Authors: Hussain Safeer , Liu Jian , Wang Lei , Sunden Bengt Ake 
Published: July 2019

Purpose
The purpose of this paper is to enhance the heat transfer and thermal performance in the trailing edge region of the vane with vortex generators (VGs).

Design/methodology/approach
This numerical study presents the enhancement of thermal performance in the trailing part of a gas turbine blade. In the trailing part, generally, pin fins are used either in staggered or in-line arrangements to enhance the heat transfer. In this study, based on the idea from heat exchangers, pin fins are combined with VGs. A pair of VGs is embedded in the boundary layer upstream of each pin fin in the first row of the pin fin array having an in-line configuration. The effects of the VG angle relative to the streamwise direction and streamwise distance between the pin fin and VGs are investigated at various Reynolds numbers.

Findings
The results indicated that the endwall heat transfer is enhanced with the addition of VGs and the heat transfer from the surfaces of the pin fins. The level of heat transfer enhancement compared to the case without VGs is more significant at high Reynolds number. The surfaces of the VGs also show a significant amount of heat transfer. Study of the angle of the attack suggested that a high angle of attack is more appropriate for pin fin cooling enhancement whereas an intermediate gap between the VGs and pin fins shows considerable improvement of thermal performance compared to the small and large gaps. The phenomenon of heat transfer augmentation with the VGs is demonstrated by the flow field. It shows that the enhancement of heat transfer is governed by the mixing of the flow as a result of the interaction of vortices generated by the VGs and pin fins.

Originality/value
VGs are used to disturb the thermal boundary layer. It shows that heat transfer is augmented as a result of the interaction of vortices associated with VGs and pin fins.
Comparison of subgrid-scale models for large-eddy simulation of hydrodynamic and magnetohydrodynamic channel flows
Authors: Prinz Sebastian , Schumacher Jörg , Boeck Thomas 
Published: July 2019

Purpose
This paper aims to address the performance of different subgrid-scale models (SGS) for hydro- (HD) and magnetohydrodynamic (MHD) channel flows within a collocated finite-volume scheme.

Design/methodology/approach
First, the SGS energy transfer is analyzed by a priori tests using fully resolved DNS data. Here, the focus lies on the influence of the magnetic field on the SGS energy transport. Second, the authors performed a series of 18 a posteriori model tests, using different grid resolutions and SGS models for HD and MHD channel flows.

Findings
From the a priori analysis, the authors observe a quantitative reduction of the SGS energy transport because of the action of the magnetic field depending on its orientation. The a posteriori model tests show a clear improvement because of the use of mixed-models within the numerical scheme.

Originality/value
This study demonstrates the necessity of improved SGS modeling strategies for magnetohydrodynamic channel flows within a collocated finite-volume scheme.