bluuebunny/crossref_metadata_2025_split huggingface dataset:
Apparent diet digestibility of captive colobines in relation to stomach types with special reference to fibre digestion
Authors: Hoshino Satoru , Seino Satoru , Funahashi Takashi , Hoshino Tomonori , Clauss Marcus , Mastuda Ikki , Yayota Masato 
Published: March 2021

AbstractColobine monkeys are known for the anatomical complexity of their stomachs, making them distinct within the primate order. Amongst foregut fermenters, they appear peculiar because of the occurrence of two different stomach types, having either three (‘tripartite’) or four (‘quadripartite’, adding the praesaccus) chambers. The functional differences between tri and quadripartite stomachs largely remain to be explained. In this study, we aim to compare the apparent digestibility (aD) in tripartite and quadripartite colobines. Hence, we measured the aD in two colobine species,Nasalis larvatus(quadripartite) andTrachypithecus cristatus(tripartite), in two zoos. We also included existing colobine literature data on the aD and analysed whether the aD of fibre components is different between the stomach types to test the hypothesis of whether quadripartite colobines show higher aD of fibre components than tripartite colobines did. Our captiveN. larvatusspecimen had a more distinctively varying nutrient intake across seasons with a larger seasonal variation in aD than that of a pair ofT. cristatus, which mostly consumed commercial foods with a lower proportion of browse and less seasonal variation. We observed higher aD of dry matter (DM), neutral detergent fibre (NDF) and acid detergent fibre (ADF) in theN. larvatusspecimen, suggesting a higher gut capacity ofN. larvatusprovided by the additional praesaccus forestomach chamber. Based on the analysis of literature data for aD, we also found that quadripartite species achieved higher fibre digestibility at similar dietary fibre levels compared with tripartite species, supporting the hypothesis that the additional gut capacity offered by the praesaccus facilitates a longer retention and hence more thorough microbial fermentation of plant fibre.
Development and Validation of LAMP Primer Sets for Rapid and Correct Identification of Aspergillus fumigatus Carrying the cyp51A TR46 Azole Resistance Gene
Authors: Trabasso Plinio , Matsuzawa Tetsuhiro , Arai Teppei , Hagiwara Daisuke , Mikami Yuzuru , Moretti Maria Luiza , Watanabe Akira 
Published: March 2021

ABSTRACTInfections due to triazole resistant Aspergillus fumigatus are increasingly reported worldwide and are associated with treatment failure and mortality. The principal class of azole resistant isolates is characterized by the presence of tandem repeats of 34 bp or 46 bp (TR34 or TR46) within the promoter region of the cyp51A gene. Loop-mediated isothermal amplification (LAMP) is a widely used nucleic acid amplification system with high rapidity and specificity. In this paper, we report a new LAMP assay method to detect the 46 bp tandem repeat insertion in the cyp51A gene promoter region, named TR46-LAMP assay, based on the use of a newly designed specific LAMP primer sets. TR46 is a high-prevalence allele which is associated with the occurrence of multi-triazole resistance of A. fumigatus in patients as well as isolates from the environment. This newly designed TR46-LAMP assay was validated as a useful method for specific detection of azole-resistant A. fumigatus isolates bearing TR462 as well as TR463 in cyp51A gene promoter region. It could also differentiate azole-resistant isolates of TR46 tandem repeats from those with TR34 tandem repeats in cyp51A genes. These results showed this TR46-LAMP method is specific, rapid, and also provides crucial insights to enable development of novel antifungal therapeutic strategies against severe fungal infections due to A. fumigatus with TR46 tandem repeats.
Dissecting CD8+ T cell pathology of severe SARS-CoV-2 infection by single-cell epitope mapping
Authors: Schreibing Felix , Hannani Monica , Ticconi Fabio , Fewings Eleanor , Nagai James S , Begemann Matthias , Kuppe Christoph , Kurth Ingo , Kranz Jennifer , Frank Dario , Anslinger Teresa M , Ziegler Patrick , Kraus Thomas , Enczmann Jürgen , Balz Vera , Windhofer Frank , Balfanz Paul , Kurts Christian , Marx Gernot , Marx Nikolaus , Dreher Michael , Schneider Rebekka K , Saez-Rodriguez Julio , Costa Ivan , Kramann Rafael 
Published: March 2021

AbstractThe current COVID-19 pandemic represents a global challenge. A better understanding of the immune response against SARS-CoV-2 is key to unveil the differences in disease severity and to develop future vaccines targeting novel SARS-CoV-2 variants. Feature barcode technology combined with CITE-seq antibodies and DNA-barcoded peptide-MHC I Dextramer reagents enabled us to identify relevant SARS-CoV-2-derived epitopes and compare epitope-specific CD8+T cell populations between mild and severe COVID-19. We identified a strong CD8+T cell response against an S protein-derived epitope. CD8+effector cells in severe COVID-19 displayed hyperactivation, T cell exhaustion and were missing characteristics of long-lived memory T cells. We identify A*0101 WTAGAAAYY as an immunogenic CD8+T cell epitope with the ability to drive clonal expansion. We provide an in-depth characterization of the CD8+T cell-mediated response to SARS-CoV-2 infection which will be relevant for the development of molecular and targeted therapies and potential adjustments of vaccination strategies.
Paralogous gene modules derived from ancient hybridization drive vesicle traffic evolution in yeast
Authors: Purkanti Ramya , Thattai Mukund 
Published: March 2021

AbstractModules of interacting proteins regulate vesicle budding and fusion in eukaryotes. Distinct paralogous copies of these modules act at distinct sub-cellular locations. The processes by which such large gene modules are duplicated and retained remain unclear. Here we show that interspecies hybridization is a potent source of paralogous gene modules. We study the dynamics of paralog doublets derived from the 100-million-year-old hybridization event that gave rise to the whole genome duplication clade of budding yeast. We show that paralog doublets encoding vesicle traffic proteins are convergently retained across species. Vesicle coats and adaptors involved in secretory and early-endocytic pathways are retained as doublets, while tethers and other machinery involved in intra-Golgi traffic and later endocytic steps are reduced to singletons. These patterns reveal common selective pressures that have sculpted traffic pathways in diverse yeast species. They suggest that hybridization may have played a pivotal role in the expansion of the endomembrane system.
The connectome spectrum as a canonical basis for a sparse representation of fast brain activity
Authors: Rué-Queralt Joan , Glomb Katharina , Pascucci David , Tourbier Sebastien , Carboni Margherita , Vulliémoz Serge , Plomp Gijs , Hagmann Patric 
Published: March 2021

AbstractThe functional organization of neural processes is constrained by the brain’ s intrinsic structural connectivity. Here, we explore the potential of exploiting this structure in order to improve the signal representation properties of brain activity and its dynamics. Using a multi-modal imaging dataset (electroencephalography, structural MRI and diffusion MRI), we represent electrical brain activity at the cortical surface as a time-varying composition of harmonic modes of structural connectivity. The harmonic modes are termed connectome harmonics, and their representation is known as the connectome spectrum of the signal. We found that: first, the brain activity signal is more compactly represented by the connectome spectrum than by the traditional area-based representation; second, the connectome spectrum characterizes fast brain dynamics in terms of signal broadcasting profile, revealing different temporal regimes of integration and segregation that are consistent across participants. And last, the connectome spectrum characterises fast brain dynamics with fewer degrees of freedom than area-based signal representations. Specifically, we show that with the connectome spectrum representation, fewer dimensions are needed to capture the differences between low-level and high-level visual processing, and the topological properties of the signal. In summary, this work provides statistical, functional and topological evidence supporting that by accounting for the brain’ s structural connectivity fosters a more comprehensive understanding of large-scale dynamic neural functioning.
Geroprotective effects ofAronia melanocarpafruit extract onDrosophila melanogaster
Authors: Platonova Elena Y. , Zemskaya Nadezhda V. , Shaposhnikov Mikhail V. , Golubev Denis A. , Kukuman Daria V. , Pakshina Natalya R. , Ulyasheva Natalia S. , Punegov Vasily V. , Patov Sergey A. , Moskalev Alexey A. 
Published: March 2021

AbstractAging and its consequences is one of the main problems of humanity. Phytochemicals such as polyphenols, flavonoids, anthocyanins have great potential as geroprotectors. Plants including Aronia used as dietary supplements are an excellent source of these compounds. We have studied the effects of the ethanol extract from Aronia fruits onDrosophila melanogasterlifespan, locomotor activity, stress resistance (oxidative stress, heat shock and starvation). And also, in order to reveal the influence of Aronia extract applied to different life cycles ofDrosophila melanogaster, we selected different dietary schemes for imago: throughout life, during the first two weeks (1 – 2) and during average age (4 – 6 weeks). It was revealed that the ethanol extract of chokeberry increases the median life expectancy in males and females by 5% whenDrosophila melanogasteris added to the diet for 4 – 6 weeks of life. This suggests that intervention even in old age is sufficient to increase lifespan. In addition, no harmful effects of ABE on locomotor activity were found as an indicator of fly health. We showed that Aronia extract increased stress resistance to hyperthermia and oxidative stress. At the same time, Aronia extract did not significantly affect the resistance of flies to starvation. ABE supplementation has increased expression of heat shock proteins (Hsp27, Hsp68, Hsp83), oxidative stress resistance genes (Keap1, NRF, Sod1), some circadian clock genes (Clk, per) and gene of longevitySirt1.
A Machine Learning Approach to Unmask Novel Gene Signatures and Prediction of Alzheimer’s Disease Within Different Brain Regions
Authors: Sharma Abhibhav , Dey Pinki 
Published: March 2021

AbstractAlzheimer’s disease (AD) is a progressive neurodegenerative disorder whose aetiology is currently unknown. Although numerous studies have attempted to identify the genetic risk factor(s) of AD, the interpretability and/or the prediction accuracies achieved by these studies remained unsatisfactory, reducing their clinical significance. Here, we employ the ensemble of random-forest and regularized regression model (LASSO) to the AD-associated microarray datasets from four brain regions - Prefrontal cortex, Middle temporal gyrus, Hippocampus, and Entorhinal cortex- to discover novel genetic biomarkers through a machine learning-based feature-selection classification scheme. The proposed scheme unrevealed the most optimum and biologically significant classifiers within each brain region, which achieved by far the highest prediction accuracy of AD in 5-fold cross-validation (99% average). Interestingly, along with the novel and prominent biomarkers including CORO1C, SLC25A46, RAE1, ANKIB1, CRLF3, PDYN, numerous non-coding RNA genes were also observed as discriminator, of which AK057435 and BC037880 are uncharacterized long non-coding RNA genes.
Genome-wide identification of genetic requirements ofPseudomonas aeruginosaPAO1 for rat cardiomyocyte (H9C2) infection by insertion sequencing
Authors: Ranjani Jothi , Sivakumar Ramamoorthy , Gunasekaran Paramasamy , Rajendhran Jeyaprakash 
Published: March 2021

AbstractPseudomonas aeruginosais the major infectious agent among Gram-negative bacteria which causes both acute and chronic infections without any tissue specificity. Infections due toP. aeruginosaare hard to treat, as it entails various strategies like virulence factors synthesis, drug efflux systems & resistance and protein secretion systems during pathogenesis. Despite extensive research inPseudomonaspathogenesis, novel drug targets and potential therapeutic strategies are inevitable. In this study, we investigated the genetic requirements ofP.aeruginosaPAO1 for rat cardiomyocyte (H9C2) infection by insertion sequencing (INSeq). A mutant library comprising ~70,000 mutants of PAO1 was generated and the differentiated form of H9C2 cells (d-H9C2) was infected with the library. The infected d-H9C2 cells were maintained with antibiotic-protection and without any antibiotics in the growth media for 24 h. Subsequently, DNA library for INSeq was prepared, sequenced and fitness analysis was performed. A-One hundred and thirteen mutants were negatively selected in the infection condition with antibiotic-protection, whereas 143 mutants were negatively selected in antibiotic-free condition. Surprisingly, a higher number of mutants showed enriched fitness than the mutants of reduced fitness during the infection. We demonstrated that the genes associated with flagella and T3SS are important for adhesion and invasion of cardiomyocytes, while pili and proteases are conditionally essential during host cell lysis.Take away✓Fitness ofP.aeruginosamutants were analyzed during cardiomyocyte infection✓Genes involve amino acid transport & metabolism and signal transduction are important during intracellular lifestyle✓OMVs play a crucial role during infection and pathogenesis✓Flagella and T3SS are conditionally essential for adhesion and invasion, whereas pili and proteases are conditionally essential during host cell lysis
Dopaminergic signaling supports auditory social learning
Authors: Paraouty Nihaad , Rizzuto Catherine R. , Sanes Dan H. 
Published: March 2021

AbstractExplicit rewards are commonly used to reinforce a behavior, a form of learning that engages the dopaminergic neuromodulatory system. In contrast, skill acquisition can display dramatic improvements from a social learning experience, even though the observer receives no explicit reward. Here, we test whether a dopaminergic signal contributes to social learning in naïve gerbils that are exposed to, and learn from, a skilled demonstrator performing an auditory discrimination task. Following five exposure sessions, naïve observer gerbils were allowed to practice the auditory task, and their performance was assessed across days. We first tested the effect of an explicit food reward in the observer’s compartment that was yoked to the demonstrator’s performance during exposure sessions. Naïve observer gerbils with the yoked reward learned the discrimination task significantly faster, as compared to unrewarded observers. The effect of this explicit reward was abolished by administration of a D1/D5 dopamine receptor antagonist during the exposure sessions. Similarly, the D1/D5 antagonist reduced the rate of learning in unrewarded observers. To test whether a dopaminergic signal was sufficient to enhance social learning, we administered a D1/D5 receptor agonist during the exposure sessions in which no reward was present, and found that the rate of learning occurred significantly faster. Finally, a quantitative analysis of observer vocalizations and movements during the exposure sessions suggest behavioral strategies that contribute to social learning. Together, these results are consistent with a dopamine-dependent reward signal during social learning.
Novel anti-repression mechanism of H-NS proteins by a phage “early protein”
Authors: Bdira Fredj Ben , Qin Liang , Volkov Alexander N. , Lippa Andrew M. , Erkelens Amanda M. , Bowring Nicholas , Boyle Aimee L. , Ubbink Marcellus , Dove Simon L. , Dame Remus T. 
Published: March 2021

AbstractH-NS family proteins, bacterial xenogeneic silencers, play central roles in genome organization and in the regulation of foreign genes. It is thought that gene repression is directly dependent on the DNA binding modes of H-NS family proteins. These proteins form lateral protofilaments along DNA. Under specific environmental conditions they switch to bridging two DNA duplexes. This switching is a direct effect of environmental conditions on electrostatic interactions between the oppositely charged DNA binding and N-terminal domains of H-NS proteins. ThePseudomonaslytic phage LUZ24 encodes the early protein gp4, which modulates the DNA binding and function of the H-NS family protein MvaT ofPseudomonas aeruginosa. However, the mechanism by which gp4 modulates MvaT activity remains elusive. In this study, we show that gp4 specifically interferes with the formation and stability of the bridged MvaT-DNA complex. Structural investigations suggest that gp4 acts as an “electrostatic zipper” between the oppositely charged domains of MvaT protomers, and stabilizes a structure resembling their “half-open” conformation, resulting in relief of gene silencing and adverse effects onP. aeruginosagrowth. The ability to control H-NS conformation and thereby its impact on global gene regulation and growth might open new avenues to fightPseudomonasmultidrug resistance.
Modulation of early level EEG signatures by distributed facial emotion cues
Authors: Costa Diana , Dias Camila , Sousa Teresa , Estiveira João , Castelhano João , Figueiredo Verónica , Pereira Andreia , Castelo-Branco Miguel 
Published: March 2021

AbstractFace perception plays an important role in our daily social interactions, as it is essential to recognize emotions. The N170 Event Related Potential (ERP) component has been widely identified as a major face-sensitive neuronal marker. However, despite extensive investigations conducted to examine this electroencephalographic pattern, there is yet no agreement regarding its sensitivity to the content of facial expressions.Here, we aim to clarify the EEG signatures of the recognition of facial expressions by investigating ERP components that we hypothesize to be associated with this cognitive process. We asked the question whether the recognition of facial expressions is encoded by the N170 as weel as at the level of P100 and P250. In order to test this hypothesis, we analysed differences in amplitudes and latencies for the three ERPs, in a sample of 20 participants. A visual paradigm requiring explicit recognition of happy, sad and neutral faces was used. The facial cues were explicitly controlled to vary only regarding mouth and eye components. We found that non neutral emotion expressions elicit a response difference in the amplitude of N170 and P250. In contrast with the P100, there by excluding a role for low level factors.Our study brings new light to the controversy whether emotional face expressions modulate early visual response components, which have been often analysed apart. The results support the tenet that neutral and emotional faces evoke distinct N170 patterns, but go further by revealing that this is also true for P250, unlike the P100.
Profitability, risk and cash flow deficit for beginning cow–calf producers
Authors: Trejo-Pech Carlos J.O. , Bruhin Jared , Boyer Christopher N. , Smith S. Aaron 
Published: March 2021

PurposeThe purpose of this study is to estimate the amount of cash flow deficit, if any, needed to maintain the operating costs and service debt of a startup cow–calf enterprise. The study compares long-term profitability and risk between starting small and building a herd to full carrying capacity or by starting at desired herd capacity.Design/methodology/approachA dynamic cattle growth model was developed to capture expanding and maintaining the desired herd size. Discounted cash flow (DCF) models over a 15-year period were calculated to estimate net present value (NPV), modified internal rate of return (MIRR) and cash flow deficit to keep the business operating and service debt. Simulation analyses were conducted considering price and production risk.FindingsStarting at the desired herd size was preferred, according to NPV/MIRR and cash flow deficit, but the differences were not substantial. Assuming the operation is liquidated at book values, there was a 36.3% probability of this enterprise having a zero or positive NPV. If the conservative terminal value assumption is relaxed up to feasible market values, the cow–calf enterprise is economically attractive at an estimated 2.4% opportunity cost of capital. However, the producer would experience a cash flow deficit during the first seven years, which was simulated to be $14,892 and $15,985 annual for both strategies.Originality/valueInnovative methods used in this study include varying the annual opportunity cost of capital as a function of financing decisions, stochastic prices by cattle type and stochastic weaning weights that are a function of a dynamic cattle model.
The assessment of the attitude of Sicilian consumers towards wild and farmed seafood products – a sample survey
Authors: Allegro Rosalinda , Calagna Antonino , Lo Monaco Daniela , Ciprì Valentina , Bongiorno Carmelo , Cammilleri Gaetano , Battaglia Luisa , Sadok Saloua , Benfante Viviana , Tliba Ines , Di Bella Calogero 
Published: March 2021

PurposeThe purpose of the paper was to know and evaluate consumption, preferences and the knowledge of labelling legislation about wild and farmed seafood products.Design/methodology/approachA sample survey on Sicilian families was conducted through a direct interviews between October 2015 and October 2016 to study the attitudes of Sicilian consumers towards wild and farmed fish and seafood products. A stratified two-stage sampling design was chosen with variable probability of inclusion of the units of first stage and 1,700 subjects were interviewed.FindingsThe results obtained showed that the 69.4% of respondent ate fresh fish at least once a week and the 86% of respondents consumed aquaculture products at least once a month. Also, the 77.3% of respondents did not know the current legislation on the labelling. Multiple correspondence analysis allowed to identified three profiles of Sicilian families and binary logit model was used to examine the factors that influenced different frequency of fresh fish consumption in general and farmed seafood products in particular.Research limitations/implicationsExtending the research throughout the Italian territory would have allowed further comparisons at the national level.Practical implicationsThe research provides useful information on Sicilian consumers that could be used by policymakers and by marketing communications company.Social implicationsThis research, on a restricted group of European consumers (Sicilian), characterised by living in an island, reinforce the knowledge regarding seafood consumers.Originality/valueThis study used a probabilistic sampling design and a face-to-face questionnaire which produce results more robust in compare to surveys used more frequently such as non-probabilistic sampling design.