bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cross‐comparison of convergence algorithms to solve trip‐based dynamic traffic assignment problems
Authors: Ameli Mostafa , Lebacque Jean‐Patrick , Leclercq Ludovic 
Published: January 2020

AbstractSolving a dynamic traffic assignment problem in a transportation network is a computational challenge. This study first reviews the different algorithms in the literature used to numerically calculate the user equilibrium (UE) related to dynamic network loading. Most of them are based on iterative methods to solve a fixed‐point problem. Two elements must be computed: the path set and the optimal path flow distribution between all origin–destination pairs. In a generic framework, these two steps are referred to as the outer and the inner loops, respectively. The goal of this study is to assess the computational performance of the inner loop methods that calculate the path flow distribution for different network settings (mainly network size and demand levels). Several improvements are also proposed to speed up convergence: four new swapping algorithms and two new methods for the step size initialization used in each descent iteration. All these extensions significantly reduce the number of iterations to obtain a good convergence rate and drastically speed up the overall simulations. The results show that the performance of different components of the solution algorithm is sensitive to the network size and saturation. Finally, the best algorithms and settings are identified for all network sizes with particular attention being given to the largest scale.
Discriminant haplotypes of avirulence genes of Phytophthora sojae lead to a molecular assay to predict phenotypes
Authors: Dussault‐Benoit Chloé , Arsenault‐Labrecque Geneviève , Sonah Humira , Belzile François , Bélanger Richard R. 
Published: January 2020

AbstractThe soybean–Phytophthora sojae interaction operates on a gene‐for‐gene relationship, where the product of a resistance gene (Rps) in the host recognizes that of an avirulence gene (Avr) in the pathogen to generate an incompatible reaction. To exploit this form of resistance, one must match with precision the appropriate Rps gene with the corresponding Avr gene. Currently, this association is evaluated by phenotyping assays that are labour‐intensive and often imprecise. To circumvent this limitation, we sought to develop a molecular assay that would reveal the avirulence allele of the seven main Avr genes (Avr1a, Avr1b, Avr1c, Avr1d, Avr1k, Avr3a, and Avr6) in order to diagnose with precision the pathotypes of P. sojae isolates. For this purpose, we analysed the genomic regions of these Avr genes in 31 recently sequenced isolates with different virulence profiles and identified discriminant mutations between avirulence and virulence alleles. Specific primers were designed to generate amplicons of a distinct size, and polymerase chain reaction conditions were optimized in a final assay of two parallel runs. When tested on the 31 isolates of known virulence, the assay accurately revealed all avirulence alleles. The test was further assessed and compared to a phenotyping assay on 25 isolates of unknown virulence. The two assays matched in 97% (170/175) of the interactions studied. Interestingly, the sole cases of discrepancy were obtained with Avr3a, which suggests a possible imperfect interaction with Rps3a. This molecular assay offers a powerful and reliable tool to exploit and study with greater precision soybean resistance against P. sojae.
Fibre‐specific regulation of lignin biosynthesis improves biomass quality in Populus
Authors: Gui Jinshan , Lam Pui Ying , Tobimatsu Yuki , Sun Jiayan , Huang Cheng , Cao Shumin , Zhong Yu , Umezawa Toshiaki , Li Laigeng 
Published: January 2020

Summary

Lignin is a major component of cell wall biomass and decisively affects biomass utilisation. Engineering of lignin biosynthesis is extensively studied, while lignin modification often causes growth defects.

We developed a strategy for cell‐type‐specific modification of lignin to achieve improvements in cell wall property without growth penalty. We targeted a lignin‐related transcription factor, LTF1, for modification of lignin biosynthesis. LTF1 can be engineered to a nonphosphorylation form which is introduced into Populus under the control of either a vessel‐specific or fibre‐specific promoter.

The transgenics with lignin suppression in vessels showed severe dwarfism and thin‐walled vessels, while the transgenics with lignin suppression in fibres displayed vigorous growth with normal vessels under phytotron, glasshouse and field conditions. In‐depth lignin structural analyses revealed that such cell‐type‐specific downregulation of lignin biosynthesis led to the alteration of overall lignin composition in xylem tissues reflecting the population of distinctive lignin polymers produced in vessel and fibre cells.

This study demonstrates that fibre‐specific suppression of lignin biosynthesis resulted in the improvement of wood biomass quality and saccharification efficiency and presents an effective strategy to precisely regulate lignin biosynthesis with desired growth performance.
miRNA precursor‐derived SSR marker‐mediated genotyping of tea (Camellia sinensis) cultivars with varying health benefit traits
Authors: Hazra Anjan , Dasgupta Nirjhar , Kumar Rakesh , Sengupta Chandan , Das Sauren 
Published: January 2020

AbstractBesides its popular refreshing value, tea is globally consumed as a potential health beverage. Health benefit traits primarily rely on some regulatory networks of different metabolic pathways. In tea, the trait‐specific simple sequence repeat (SSR) markers are still insufficient, which could be used for marker‐assisted breeding technique. MicroRNAs are endogenous, non‐coding, short RNAs directly involved in regulating gene expressions at the post‐transcriptional level. It has been found that differences in miRNA precursor gene sequences interfere their structure formation and obstruct subsequent function. SSR motifs within the putative miRNA precursor genes have been identified followed by experimental validation of their existence and variation exclusively in tea. Simultaneously, diverse commercial accessions of Indian tea were undergone rigorous phenotyping during three plucking seasons to assess 20 chemotypic traits by high‐throughput techniques. Six miRNA‐SSR marker‐generated bands consisted the putative trait‐associated loci. Newly developed microRNAs (mi408, miR5021a and miR2863) precursor‐derived SSR markers, miSSR‐03, miSSR‐11 and miSSR‐14, executed convincing results in distinguishing tea cultivars with contrasting health benefit traits. This is in accordance with the earlier reports where mi408, miR5021a and miR2863 have been found to be involved in cellular pathways conferring tolerance to oxidative stress. Consequently, these markers can be used further as suitable choice to select promising tea genotypes with sound antioxidant quality.
Extracellular vesicles released by melanocytes after UVA irradiation promote intercellular signaling via miR21
Authors: Wäster Petra , Eriksson Ida , Vainikka Linda , Öllinger Karin 
Published: January 2020

AbstractSkin pigmentation is controlled by complex crosstalk between melanocytes and keratinocytes and is primarily induced by exposure to ultraviolet (UV) irradiation. Several aspects of UVA‐induced signaling remain to be explored. In skin cells, UVA induces plasma membrane damage, which is repaired by lysosomal exocytosis followed by instant shedding of extracellular vesicles (EVs) from the plasma membrane. The released EVs are taken up by neighboring cells. To elucidate the intercellular crosstalk induced by UVA irradiation, EVs were purified from UVA‐exposed melanocytes and added to keratinocytes. Transcriptome analysis of the keratinocytes revealed the activation of TGF‐β and IL‐6/STAT3 signaling pathways and subsequent upregulation of microRNA (miR)21. EVs induced phosphorylation of ERK and JNK, reduced protein levels of PDCD4 and PTEN, and augment antiapoptotic signaling. Consequently, keratinocyte proliferation and migration were stimulated and UV‐induced apoptosis was significantly reduced. Interestingly, melanoma cells and melanoma spheroids also generate increased amounts of EVs with capacity to stimulate proliferation and migration upon UVA. In conclusion, we present a novel intercellular crosstalk mediated by UVA‐induced lysosome‐derived EVs leading to the activation of proliferation and antiapoptotic signaling via miR21.
Theoretical Study of the Wavelength Selection for the Photocleavage of Coumarin‐caged D‐luciferin
Authors: Usukura Junko , Hiyama Miyabi , Kurata Maki , Hazama Yuji , Qiu Xing‐Ping , Winnik Francoise M. , Akiyama Hidefumi , Koga Nobuaki 
Published: January 2020

AbstractThe equilibrium structures and optical properties of the photolabile caged luciferin, (7‐diethylaminocoumarin‐4‐yl)methyl caged D‐luciferin (DEACM‐caged D‐luciferin), in aqueous solution were investigated via quantum chemical calculations. The probable conformers of DEACM‐caged D‐luciferin were determined by potential energy curve scans and structural optimizations. We identified 40 possible conformers of DEACM‐caged D‐luciferin in water by comparing the Gibbs free energy of the optimized structures. Despite the difference in their structures, the conformers were similar in terms of assignments, oscillator strengths and energies of the three low‐lying excited states. From the concentrations of the conformers and their oscillator strengths, we obtained a theoretical UV/Vis spectrum of DEACM‐caged D‐luciferin that has two main bands of shape nearly identical to the experimental UV/Vis spectrum. The absorption bands with maxima ~ 384 and 339 nm were attributed to the electronic excitations of the caged group and the luciferin moiety, respectively, by analysis of the theoretical UV/Vis spectrum. Furthermore, the analysis showed that DEACM‐caged D‐luciferin is excited in the caged group only by light of wavelength ranging within 400–430 nm, which is in the long‐wavelength tail of the 384 nm band. This should be tested to lower damage upon photocleavage.
Effect of Photobiomodulation on C2C12 Myoblasts Cultivated in M1 Macrophage‐conditioned Media
Authors: dos Santos Tainá Caroline , de Brito Sousa Kaline , Andreo Lucas , Martinelli Andreia , Rodrigues Maria Fernanda Setubal Destro , Bussadori Sandra Kalil , Fernandes Kristianne Porta Santos , Mesquita‐Ferrari Raquel Agnelli 
Published: January 2020

AbstractModerate levels of a proinflammatory macrophages phenotype are indispensable and play an important role in the skeletal muscle repair process since this response depends on their secreted products concentration to influence and modulate muscle inflammation as well as the differentiation of myoblasts. This study investigated the effects of photobiomodulation (PBM) on undifferentiated and differentiation‐induced C2C12 myoblasts cultivated in different concentrations of M1 phenotype macrophage‐conditioned media of J774 cells (MCM1) also submitted to PBM using the same irradiation parameters. Irradiation was performed once with low‐level laser (780 nm, 70 mW, 1 J) and was evaluated cell viability, proliferation and differentiation, nitric oxide (NO) synthesis and IL‐6 and TNF‐α protein levels 24 and 48 h after C2C12 irradiation. PBM treatment in undifferentiated myoblasts exhibited lower IL‐6 levels in the presence of nonirradiated MCM1 at both concentrations. Myoblasts in proliferation condition cultivated with irradiated MCM1 showed lower IL‐6 and TNF‐α levels after 48 h in the presence of both concentrations evaluated. PBM induced a decrease in the synthesis of NO on undifferentiated and differentiation‐induced myoblasts. PBM was able to reduce the level of proinflammatory protein and markers, which are important to allow the differentiation of myoblasts during the muscle repair process.
Probability Size Matters: The Effect of Foreground‐Only versus Foreground+Background Graphs on Risk Aversion Diminishes with Larger Probabilities
Authors: Okan Yasmina , Stone Eric R. , Parillo Jonathan , Bruine de Bruin Wändi , Parker Andrew M. 
Published: January 2020

AbstractGraphs are increasingly recommended for improving decision‐making and promoting risk‐avoidant behaviors. Graphs that depict only the number of people affected by a risk (“foreground‐only” displays) tend to increase perceived risk and risk aversion (e.g., willingness to get vaccinated), as compared to graphs that also depict the number of people at risk for harm (“foreground+background” displays). However, previous research examining these “foreground‐only effects” has focused on relatively low‐probability risks (<10%), limiting generalizability to communications about larger risks. In two experiments, we systematically investigated the moderating role of probability size on foreground‐only effects, using a wide range of probability sizes (from 0.1% to 40%). Additionally, we examined the moderating role of the size of the risk reduction, that is, the extent to which a protective behavior reduces the risk. Across both experiments, foreground‐only effects on perceived risk and risk aversion were weaker for larger probabilities. Experiment 2 also revealed that foreground‐only effects were weaker for smaller risk reductions, while foreground‐only displays decreased understanding of absolute risk magnitudes independently of probability size. These findings suggest that the greater effectiveness of foreground‐only versus foreground+background displays for increasing perceived risk and risk aversion diminishes with larger probability sizes and smaller risk reductions. Moreover, if the goal is to promote understanding of absolute risk magnitudes, foreground+background displays should be used rather than foreground‐only displays regardless of probability size. Our findings also help to refine and extend existing theoretical accounts of foreground‐only effects to situations involving a wide range of probability sizes.
Efficient Data Augmentation for Multivariate Probit Models with Panel Data: An Application to General Practitioner Decision Making about Contraceptives
Authors: Chin Vincent , Gunawan David , Fiebig Denzil G. , Kohn Robert , Sisson Scott A. 
Published: January 2020

SummaryThe paper considers the problem of estimating a multivariate probit model in a panel data setting with emphasis on sampling a high dimensional correlation matrix and improving the overall efficiency of the data augmentation approach. We reparameterize the correlation matrix in a principled way and then carry out efficient Bayesian inference by using Hamiltonian Monte Carlo sampling. We also propose a novel antithetic variable method to generate samples from the posterior distribution of the random effects and regression coefficients, resulting in significant gains in efficiency. We apply the methodology by analysing stated preference data obtained from Australian general practitioners evaluating alternative contraceptive products. Our analysis suggests that the joint probability of discussing combinations of contraceptive products with a patient shows medical practice variation among the general practitioners, which indicates some resistance even to discuss these products, let alone to recommend them.
Informality and Latino‐Owned Businesses: A National Portrait of Unregistered Latino‐Owned Businesses
Authors: Pisani Michael J. , Morales Alfonso 
Published: January 2020

ObjectiveThis study provides the first nationally representative portrait of unregistered (informal) Latino‐owned businesses (LOBs) in the United States.MethodsWe employ data from the 2018 Stanford Latino Entrepreneurship Initiative Survey of 4,024 U.S. LOBs. We estimate the determinants of unregistered LOBs through a set of independent variables derived from entrepreneur demographics/firm characteristics utilizing a binomial logistic regression to predict the odds of group membership between (un)registered LOBs.ResultsApproximately one‐third of LOBs across the United States operate as unregistered enterprises. We find that LOB firm registration is associated with higher levels of education of the entrepreneur and larger size of the LOB. We uncover further links between entrepreneur acculturation and gender, and firm product offering and clientele ethnicity, with firm registration.ConclusionFor the first time, we are able to establish a quantitative baseline for informality and firm registration among LOBs using a nationally representative sample.
Photosynthesis in the fleeting shadows: an overlooked opportunity for increasing crop productivity?
Authors: Wang Yu , Burgess Steven J. , de Becker Elsa M. , Long Stephen P. 
Published: January 2020

SummaryPhotosynthesis measurements are traditionally taken under steady‐state conditions; however, leaves in crop fields experience frequent fluctuations in light and take time to respond. This slow response reduces the efficiency of carbon assimilation. Transitions from low to high light require photosynthetic induction, including the activation of Rubisco and the opening of stomata, whereas transitions from high to low light require the relaxation of dissipative energy processes, collectively known as non‐photochemical quenching (NPQ). Previous attempts to assess the impact of these delays on net carbon assimilation have used simplified models of crop canopies, limiting the accuracy of predictions. Here, we use ray tracing to predict the spatial and temporal dynamics of lighting for a rendered mature Glycine max (soybean) canopy to review the relative importance of these delays on net cumulative assimilation over the course of both a sunny and a cloudy summer day. Combined limitations result in a 13% reduction in crop carbon assimilation on both sunny and cloudy days, with induction being more important on cloudy than on sunny days. Genetic variation in NPQ relaxation rates and photosynthetic induction in parental lines of a soybean nested association mapping (NAM) population was assessed. Short‐term NPQ relaxation (<30 min) showed little variation across the NAM lines, but substantial variation was found in the speeds of photosynthetic induction, attributable to Rubisco activation. Over the course of a sunny and an intermittently cloudy day these would translate to substantial differences in total crop carbon assimilation. These findings suggest an unexplored potential for breeding improved photosynthetic potential in our major crops.
Is a de novo nonsense variant in the ASPDH gene the cause of ulcerative skin lesions in a Holstein calf?
Authors: Brunner Magdalena A. T. , Veiga Inês M. B. , Niggeler Allegra , Häfliger Irene M. , Stettler Manuela , Meylan Mireille , Welle Monika , Drögemüller Cord 
Published: January 2020

BackgroundGenetic skin diseases in cattle are rare.Clinical summaryA 7‐week‐old female Holstein calf was presented with epidermal lesions and alopecia in the caudal region of the ears and on the neck, as well as deep bilateral ulcerative lesions on the palmar aspect of the metacarpi and dorsal aspect of the right metacarpus. Clinical, pathological and histopathological examination of the calf was suggestive of a subepidermal vesicular dermatosis. Genetic analysis identified a de novo non‐sense variant affecting the aspartate dehydrogenase domain containing (ASPDH) gene, which might be associated with the formation of subepidermal vesicles in this case.Conclusion and clinical importanceThe observed phenotype in the calf may represent a novel form of a vesicular skin disorder. Haploinsufficiency of the ASPDH gene might be considered as a possible cause.
Patulous Eustachian tube and palatine defect in a Dachshund with chronic unilateral otitis externa and otitis media
Authors: Koch Sandra N. , Torres Sheila M. F. , Kramek Betty 
Published: January 2020

BackgroundPatulous Eustachian tube (pET) is a rare dysfunction of the Eustachian tube described in humans. It is characterized by failure of the ET to close, resulting in unrestricted passage of air, sound and material between the nasopharynx and the middle ear.ObjectiveTo report a case of pET associated with otitis in a dog.AnimalA 6‐year old‐female spayed Dachshund dog.Methods and materialsOtoscopic examination, cytological evaluation, culture and susceptibility, computerized tomography (CT), video‐otoscopic flushing and surgery.ResultsLeft ear otoscopic examination revealed erythema, purulent frothy discharge, ceruminous gland hyperplasia, stenosis and a partial tear of the tympanum. Cytological evaluation from the left external canal showed neutrophils, macrophages, rods and cocci. Aerobic culture showed predominantly multidrug‐resistant Pseudomonas aeruginosa. The CT findings of the left ear included chronic changes in the external canal, marked lysis of the tympanic bulla and marked dilation of the ET. During video‐otoscope flushing, saline drained through the mouth. Bilateral incomplete hypoplasia of the soft palate was noted. Total ear canal ablation and bulla osteotomy with ET dissection were curative. Histopathological findings were compatible with chronic otitis externa (OE) and media.Conclusion and clinical importanceTo the best of the authors' knowledge, this is the first case of pET described in animals. The ET dysfunction and palatine defect were likely the cause of the otitis in this dog. Clinicians should investigate pET in animals with signs of OE characterized by frothy liquid and food fragments in the ear canal in addition to sneezing after drinking water.
Effect of auriculopalpebral nerve block on equine intraocular pressure measured by rebound tonometry (TonoVet®)
Authors: Diehl Kathryn , Bowden Anna Catherine 
Published: January 2020

AbstractObjectiveTo assess rebound tonometry intraocular pressure (IOP) in unsedated horses without and with auriculopalpebral (AP) nerve blocks.Animals StudiedTwenty‐two client‐ and twenty university‐owned horses (84 total eyes) with unremarkable ophthalmic examinations were evaluated.ProcedureOne eye of each horse was chosen randomly, an AP block performed for that eye, and IOP measured in both eyes with a TonoVet®. The process was repeated for the contralateral eye 72 hours later under the same conditions as the initial measurements. Horses were unsedated for nerve blocks and tonometry. Linear mixed‐effects models were used for comparisons with statistical significance threshold of 0.05.ResultsOverall, blocked eyes had an 0.8 mm Hg lower average IOP than unblocked eyes (P = .039). IOP for client‐owned horses was on average 3.2 mm Hg lower than in UGA‐owned horses (P = .025) and was more impacted by AP block (1.4 mm Hg lower average in client‐owned blocked versus unblocked eyes (P = .006)). Block effectiveness was ranked on a subjective scale (“good”, “poor”, no block/control), and IOP was on average lower in eyes with a good block (P = .008).ConclusionAlthough there were statistically significant differences in IOP between blocked and unblocked eyes, between client‐ and UGA‐owned horses, and between eyes with good and poor AP blocks, these differences were not clinically significant. Thus, AP blocks remain a useful tool for evaluating equine ophthalmic health with minimal impact on IOP assessment.