bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strong regulatory effects of vgll3 genotype on reproductive axis gene expression in immature male Atlantic salmon
Authors: Ahi Ehsan Pashay , Sinclair-Waters Marion , Moustakas-Verho Jacqueline , Jansouz Shadi , Primmer Craig R. 
Published: August 2021

AbstractAge at maturity is a major contributor to the diversity of life history strategies in organisms. The process of maturation is influenced by both genetics and the environment, and includes changes in levels of sex hormones and behavior, but the specific factors leading to variation in maturation timing are not well understood. gnrh1 regulates the transcription of gonadotropin genes at the onset of puberty in many species, but this gene is lacking in certain teleost species including Atlantic salmon (Salmo salar), which raises the possibility of the involvement of other important regulatory factors during this process. Earlier research has reported a strong association of alternative alleles of the vgll3 gene with maturation timing in Atlantic salmon, suggesting it as a potential candidate regulating reproductive axis genes. Here, we investigated the expression of reproductive axis genes in immature Atlantic salmon males with different vgll3 genotypes during the spawning period. We detected strong vgll3 genotype-dependent differential expression of reproductive axis genes (such as fshb, lhb, amh and igf3) tested in the pituitary, and testis of one-year-old immature male Atlantic salmon. In addition, we observed differential expression of jun (ap1) and nr5a1b (sf1), potential upstream regulators of gonadotropins in the pituitary, as well as axin2, id3, insl3, itch, ptgs2a and ptger4b, the downstream targets of amh and igf3 in the testis. Hereby, we provide evidence of strong vgll3 genotype-dependent transcriptional regulation of reproductive axis genes prior to sexual maturation together with models for distinct actions of vgll3 genotypes on the molecular processes controlling spermatogenesis in Atlantic salmon.
A warmer growing season triggers earlier following spring phenology
Authors: Gu Hongshuang , Qiao Yuxin , Xi Zhenxiang , Rossi Sergio , Smith Nicholas G. , Liu Jianquan , Chen Lei 
Published: August 2021

AbstractUnder global warming, advances in spring phenology due to the rising temperature have been widely reported. However, the physiological mechanisms underlying the warming-induced earlier spring phenology remain poorly understood. Here, using multiple long-term and large-scale phenological datasets between 1951 and 2018, we show that warmer temperatures during the previous growing season between May and September led to earlier spring phenology in the Northern Hemisphere. We also found that warming-induced increases in maximum photosynthetic rate in the previous year advanced spring phenology, with an average of 2.50 days °C-1. Furthermore, we found a significant decline in the advancing effect of warming during the previous growing season on spring phenology from cold to warm periods over the past decades. Our results suggest that the observed warming-induced earlier spring phenology may be driven by increased photosynthetic carbon assimilation in the previous season, while the slowdown in the advanced spring phenology arise likely from decreased carbon assimilation when warming exceeding the optimal temperatures for photosynthesis. Our study highlights the vital role of photosynthetic carbon assimilation during growing season in spring phenology under global warming.
Distinct progressions of neuronal activity changes underlie the formation and consolidation of a gustatory associative memory
Authors: Arieli Elor , Younis Nadia , Moran Anan 
Published: August 2021

AbstractAcquiring new memories is a multi-stage process. Ample of studies have convincingly demonstrated that initially acquired memories are labile, and only stabilized by later consolidation processes. These multiple phases of memory formation are known to involve modification of both cellular excitability and synaptic connectivity, which in turn change neuronal activity at both the single neuron and ensemble levels. However, the specific mapping between the known phases of memory and the observed changes in neuronal activity remains unknown. Here we address this unknown in the context of conditioned taste aversion learning by continuously tracking gustatory cortex (GC) neuronal taste responses from alert rats in the 24 hours following a taste-malaise pairing. We found that the progression of neuronal activity changes in the GC depend on the neuronal organizational level. The population response changed continuously; these changes, however, were only reflected in the population mean amplitude during the acquisition and consolidation phases, and in the known quickening of the ensemble state dynamics after the time of consolidation. Together our results demonstrate how complex dynamics in different representational level of cortical activity underlie the formation and stabilization of memory within the cortex.Significant StatementMemories are formed through a multi-phase process; an early initial acquired memory consolidates into a stable form over hours and days. While the underlying phase-specific molecular pathways are fairly known, the neuronal activity changes during these different phases remain elusive. Here we studied this unknown by tracking cortical neuronal activity over 24h as the taste becomes aversive following association with malaise. We found that that the progression of activity changes is organization-level dependent: The population response changed continuously; the population mean amplitude was time-locked to the acquisition and consolidation phases, and the quickening of the known ensemble state dynamics appear only after consolidation. Our results reveal the complex organizational-level neuronal interactions that underlie the progression of memory formation.
Improving the analysis of biological ensembles through extended similarity measures
Authors: Chang Liwei , Perez Alberto , Miranda-Quintana Ramón Alain 
Published: August 2021

ABSTRACTWe present new algorithms to classify structural ensembles of macromolecules, based on the recently proposed extended similarity measures. Molecular Dynamics provides a wealth of structural information on systems of biologically interest. As computer power increases we capture larger ensembles and larger conformational transitions between states. Typically, structural clustering provides the statistical mechanics treatment of the system to identify relevant biological states. The key advantage of our approach is that the newly introduced extended similiarity indices reduce the computational complexity of assessing the similarity of a set of structures from O(N2) to O(N). Here we take advantage of this favorable cost to develop several highly efficient techniques, including a linear-scaling algorithm to determine the medoid of a set (which we effectively use to select the most representative structure of a cluster). Moreover, we use our extended similarity indices as a linkage criterion in a novel hierarchical agglomerative clustering algorithm. We apply these new metrics to analyze the ensembles of several systems of biological interest such as folding and binding of macromolecules (peptide,protein,DNA -protein). In particular, we design a new workflow that is capable of identifying the most important conformations contributing to the protein folding process. We show excellent performance in the resulting clusters (surpassing traditional linkage criteria), along with faster performance and an efficient cost-function to identify when to merge clusters.
Phyllotaxis Models: from the Inhibition Potential to the Real Plant
Authors: Jean-Paul Walch 
Published: August 2021

AbstractPrevious phyllotaxis models allowed the initiation of new primordia when a threshold of inhibition potential is reached on the meristem front: their adequacy to botanical reality is only qualitative. We formulated the hypothesis that it is not the value of the inhibition threshold that remains constant as the meristem develops, but the difference of the inhibition thresholds during the initiation of two successive primordia. We were thus able to model with accuracy the sequence of plastochron ratios observed by Williams (1975) on the leaf meristem of flax: an outstanding result. More generally, we have shown that the evolution trajectories of the phyllotaxis modes as a function of the plastochron ratios follow the minima of the potential under decreasing plastochron ratios constraint and bifurcate when the number of these minima increases, thus giving physicochemical foundations to the famous van Iterson diagram. This historical representation of rising phyllotaxis shows the trajectories, but doesn’t give the velocity of the movement: our plastochron ratio sequence adds this major dynamical information.
Metataxonomic review to elucidate the role of the microbiome in Celiac disease across the gastrointestinal tract
Authors: Arcila Juliana , Loria-Kohen Viviana , Ramírez de Molina Ana , Carrillo de Santa Pau Enrique , Marcos-Zambrano Laura Judith 
Published: August 2021

AbstractBackgroundDysbiosis of the microbiome has been related to the Celiac disease (CeD) progress, an autoimmune disease characterised by gluten intolerance developed in genetically susceptible individuals under certain environmental factors. The microbiome contributes to CeD pathophysiology modulating the immune response by the action of short-chain fatty acids (SCFA), affecting gut barrier integrity allowing the entrance of gluten derived proteins, and degrading immunogenic peptides of gluten through endoprolyl peptidase enzymes. We reviewed state of the art in taxonomic composition for CeD and compiled the larger dataset of 16S prokaryotic ribosomal RNA (rRNA) gene high-throughput sequencing for consensus profiling. We present for the first time an integrative analysis of metataxonomic data from CeD patients, including samples from different body sites (saliva, pharynx, duodenum, and stool). We found the presence of coordinated changes through the gastrointestinal tract characterised by an increase in Actinobacteria species in the upper tract (pharynx and duodenum), and an increase in Proteobacteria in the lower tract (duodenum and stool), as well as site- specific changes evidencing a dysbiosis in CeD patients’ microbiota. Moreover, we described the effect of adherence to a gluten-free diet (GFD) evidenced by an increase in beneficial bacteria and a decrease in some Betaproteobacteriales but not fully restoring CeD-related dysbiosis. We illustrate that the gut microbiota acts as an enhancer of immune response in CeD through the production of lipopolysaccharides and other bacterial components that activate the immune response and by decrease SCFA producers bacteria. Furthermore, microbial changes observed through the gastrointestinal tract of CeD patients may help manage the disease and follow-up GFD treatment.
How Filopodia Respond to Calcium in the Absence of a Calcium-binding Structural Protein: They Use Rapid Transit
Authors: Heckman C. A. , Ademuyiwa O. M. , Cayer M. L 
Published: August 2021

AbstractDuring directional locomotion, cells must reorient themselves in response to attractive or repulsive cues. Filopodia are narrow actin-based protrusions whose prevalence at the leading edge of a migrating cell is related to the persistence of locomotion. Although there is a marked absence of calcium-binding components in their structure, they responded to store-operated calcium entry (SOCE). Here, we used a two-phase protocol to determine how they responded. In the first phase, extracellular calcium was removed and ER calcium lowered by blocking reuptake through the calcium pump. This was known to activate stromal interacting molecule (STIM) and cause its microtubule-mediated translocation to the cell surface. In the second phase, extracellular calcium and calcium influx into the ER were restored. ER depletion caused filopodia to increase, followed by a spontaneous decrease that was blocked by inhibiting endocytosis. The intracellular calcium concentration increased during depletion, while the size of the exchangeable compartment of vesicles, measured by fluid-phase marker uptake, shrank. When SOCE mediators and the aquaporin, AQP4, were localized, STIM and transient receptor potential canonical (TPRC) channels occupied vesicular profiles side-by-side in linear arrays. STIM1 was translocated, as expected. TRPC1 was initially in a rapidly recycling pool (RRP) where it partially colocalized with Vamp2. Calcium restoration caused TRPC1 exocytosis, while STIM1 reverted toward its original pattern associated with the ER. The exchangeable compartment was restored and this enabled filopodia extension, which was blocked by inhibitors of TRPC1/4/5 and endocytosis. That vesicle recycling was essential for extension during calcium readdition was indicated by reversal of the effect of endocytosis inhibitors in the depletion and readdition phases. The results suggest that SOCE regulates the size of the RRP in epithelial cells, and vesicle recycling is the immediate mechanism affecting filopodia extension. The conclusions are discussed in light of factors regulating protrusion formation, namely surface tension and vesicle trafficking.
Physiologically relevant miRNAs in mammalian oocytes are rare and highly abundant
Authors: Kataruka Shubhangini , Kinterova Veronika , Horvat Filip , Kanka Jiri , Svoboda Petr 
Published: August 2021

AbstractmiRNAs, ~22nt small RNAs associated with Argonaute (AGO) proteins, are important negative regulators of gene expression in mammalian cells. However, mammalian maternal miRNAs show negligible repressive activity and the miRNA pathway is dispensable for oocytes and maternal-to-zygotic transition. The stoichiometric hypothesis proposed that this is caused by dilution of maternal miRNAs during oocyte growth. As the dilution affects miRNAs but not mRNAs, it creates unfavorable miRNA:mRNA stoichiometry for efficient repression of cognate mRNAs. Here we report that porcine ssc-miR-205 and bovine bta-miR-10b are exceptional miRNAs, which resist the diluting effect of oocyte growth and can efficiently suppress gene expression. Additional analysis of ssc-miR-205 shows that it has higher stability, reduces expression of endogenous targets, and contributes to porcine oocyte-to-embryo transition. Consistent with the stoichiometric hypothesis, our results show that the endogenous miRNA pathway in mammalian oocytes is intact and that maternal miRNAs can efficiently suppress gene expression when a favorable miRNA:mRNA stoichiometry is established.
Study on microstructure and properties of Zn-Sn coating on sintered Nd-Fe-B magnets by grain boundary diffusion process
Authors: Hu Zhihua 
Published: August 2021

Purpose
The microstructure and properties of Zn-Sn coating on sintered Nd-Fe-B magnets were investigated by the grain boundary diffusion process, to improve the corrosion resistance of magnet surface and explore the feasibility of realizing the lower-temperature grain boundary diffusion.

Design/methodology/approach
The Zn-Sn coating was deposited on sintered Nd-Fe-B magnets by magnetron sputtering, and then the Zn-Sn coated magnets were put into the vacuum tube furnace for grain boundary diffusion process. The morphology and structure of Zn-Sn coating as well as its mechanical properties and corrosion resistance were investigated.

Findings
Results showed that the particle size of vacuum diffusion-treated Zn-Sn coating increased and the particle agglomeration was weakened with increasing diffusion temperature, and the non-vacuum diffusion-treated Zn-Sn coating was oxidized to generate SnO2 and ZnO compounds. The binding force of coating first increased and then decreased with increasing diffusion temperature, and the maximum binding force was obtained at 540 °C. The binding force and corrosion resistance of non-vacuum diffusion-treated Zn-Sn coating were higher than the vacuum diffusion-treated Zn-Sn coating at the same diffusion temperature.

Originality/value
The Zn-Sn coating after diffusion treatment can provide complete protection, and the coating elements diffusion can be carried out at the same temperature as the secondary aging of sintered Nd-Fe-B magnets. Simultaneously, further diffusion process optimization needs to be completed because the diffusion depth is very low and only about 10 µm, which does not meet the requirements of traditional grain boundary diffusion method.
Entire functions of restricted hyper-order sharing a set of two small functions IM with their linear c-shift operators
Authors: Banerjee Abhijit , Roy Arpita 
Published: August 2021

PurposeThe paper aims to build the relationship between an entire function of restricted hyper-order with its linear c-shift operator.Design/methodology/approachStandard methodology for papers in difference and shift operators and value distribution theory have been used.FindingsThe relation between an entire function of restricted hyper-order with its linear c-shift operator was found under the periphery of sharing a set of two small functions IM (ignoring multiplicities) when exponent of convergence of zeros is strictly less than its order. This research work is an improvement and extension of two previous papers.Originality/valueThis is an original research work.
Latent class analysis and individuals' preferences mapping: the new consumption orientations and perspectives for craft beer in North-West Italy
Authors: Massaglia Stefano , Merlino Valentina Maria , Blanc Simone , Bargetto Aurora , Borra Danielle 
Published: August 2021

PurposeIn Italy, the craft beer (CB) market has undergone a trend of exponential growth in recent years, showing, at the same time, differences among different geographical areas. This research aimed to define the consumer preferences towards different CB attributes by involving a sample of individuals from Piedmont (from North-West Italy). Furthermore, the experimentation was designed to distinguish heterogeneous individuals' consumption profiles each characterised by different CB preferences, drinking habits and socio-demographic characteristics.Design/methodology/approachThe exploration of individuals' preferences towards 12 CB quality attributes was made throughout a choice experiment based on the Best-Worst Scaling (BWS) methodology approach. In addition, the BWS results were employed in the latent class analysis to identify the best sample segmentation in relation to attributes preferences.FindingsThe “Brand knowledge”, “I have already tried it” were the most important attributes for CB choice. On the contrary, the “Type of packaging” and “Price” were the least important for CB choice. The “Loyal”, “Attentive to quality composition” and “Territorial brand” clusters were defined in function of CB consumers preferences and described in terms of individuals consumption habits and socio-demographic characteristics.Originality/valueThe BWS methodology allowed the definition of a preference index for each selected CB attributes. These indications could have concrete importance on production and marketing choices in an increasingly extended and globalised market, also at large-scale distribution level. Furthermore, the definition of different consumption profiles allowed to highlight the heterogeneity of consumption (preferences and habits) towards CB.
Comparative analysis of online fresh food shopping behavior during normal and COVID-19 crisis periods
Authors: Lu Miaojia , Wang Ran , Li Peiyang 
Published: August 2021

PurposeOnline fresh food shopping has become increasingly popular in recent years, especially during the COVID-19 crisis. Online fresh food shopping provides consumers with an alternative to shopping in a traditional market, while also enabling procurement of such goods at a reduced risk of infection. The purpose of this study is to investigate whether online fresh food shopping behaviors change during public health emergency periods.Design/methodology/approachThe data were collected through a web-based survey (508 respondents in China). Descriptive analysis, ordinal logistic regression analysis, and the Apriori algorithm were employed to explore what characteristics influence purchase frequency as well as food and delivery time preferences among different customer groups.FindingsBased on the survey data, this study found that purchase frequency grew 71.2% during the COVID-19 crisis. City type and online shopping frequency of respondents are positively correlated with purchase frequency in normal and COVID-19 crisis periods. Number of daily hours worked by respondents only showed a significant impact for the normal period. People perceiving the risk of infection from going out are more willing to purchase fresh food online.Originality/valueThis is the first study to explore and compare online fresh food shopping behaviors during normal and COVID-19 crisis periods with a sample from China. The findings indicate a key role that online fresh food shopping can perform during a crisis and contribute to our understanding of fresh food online shopping behaviors during other possible public health emergency scenarios.
Antecedents and consequences of consumers' attitudes toward product placements: evidence from India
Authors: Kaur Ravineet , Sharma Rakesh Kumar , Bakshi Apurva 
Published: August 2021

PurposeAdvertising clutter has fueled the rise of nontraditional advertising methods. The current study, conducted in India, adopted the consumer socialization framework to assess product placement attitudes and behaviors.Design/methodology/approachA questionnaire-based survey was conducted to gauge consumers' responses to product placements. Structural equation modeling (SEM) was applied to analyze the relationship between different variables.FindingsThe results revealed that young Indian adults are positive about product placements as they believe that incorporating brands into the content adds realism. The authors found that socialization agents significantly impact viewers' attitudes toward product placements which in turn influence their purchase intentions. The authors also found that product acceptability impacts consumers' purchase intentions.Practical implicationsThis paper provides important insights into consumers' perceptions of product placements. Based on the findings, marketers can formulate effective product placement strategies.Originality/valueMost of the studies existing in this area have been conducted in the developed markets except a few which have been conducted in the emerging markets. Hence, the present study is an attempt to fill this research gap. This study is among the first to establish a relationship between product acceptability and consumers' purchase intentions.