bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stock delineation of striped snakehead, Channa striata using multivariate generalised linear models with otolith shape and chemistry data
Authors: Khan Salman , Schilling Hayden T. , Khan Mohammad Afzal , Patel Devendra Kumar , Maslen Ben , Miyan Kaish 
Published: April 2021

AbstractOtoliths are commonly used to discriminate between fish stocks, through both elemental composition and otolith shape. Typical studies also have a large number of elemental compositions and shape measures relative to the number of otolith samples, with these measures exhibiting strong mean–variance relationships. These properties make otolith composition and shape data highly suitable for use within a multivariate generalised linear model (MGLM) framework, yet MGLMs have never been applied to otolith data. Here we apply both a traditional distance based permutational multivariate analysis of variance (PERMANOVA) and MGLMs to a case study of striped snakehead (Channa striata) in India. We also introduce the Tweedie and gamma distributions as suitable error structures for the MGLMs, drawing similarities to the properties of Biomass data. We demonstrate that otolith elemental data and combined otolith elemental and shape data violate the assumption of homogeneity of variance of PERMANOVA and may give misleading results, while the assumptions of the MGLM with Tweedie and gamma distributions are shown to be satisfied and are appropriate for both otolith shape and elemental composition data. Consistent differences between three groups ofC. striatawere identified using otolith shape, otolith chemistry and a combined otolith shape and chemistry dataset. This suggests that future research should be conducted into whether there are demographic differences between these groups which may influence management considerations. The MGLM method is widely applicable and could be applied to any multivariate otolith shape or elemental composition dataset.
A Raman probe of phonons and electron–phonon interactions in the Weyl semimetal NbIrTe4
Authors: Shojaei Iraj Abbasian , Pournia Seyyedesadaf , Le Congcong , Ortiz Brenden R. , Jnawali Giriraj , Zhang Fu-Chun , Wilson Stephen D. , Jackson Howard E. , Smith Leigh M. 
Published: April 2021

AbstractThere is tremendous interest in measuring the strong electron–phonon interactions seen in topological Weyl semimetals. The semimetal NbIrTe4 has been proposed to be a Type-II Weyl semimetal with 8 pairs of opposite Chirality Weyl nodes which are very close to the Fermi energy. We show using polarized angular-resolved micro-Raman scattering at two excitation energies that we can extract the phonon mode dependence of the Raman tensor elements from the shape of the scattering efficiency versus angle. This van der Waals semimetal with broken inversion symmetry and 24 atoms per unit cell has 69 possible phonon modes of which we measure 19 modes with frequencies and symmetries consistent with Density Functional Theory calculations. We show that these tensor elements vary substantially in a small energy range which reflects a strong variation of the electron–phonon coupling for these modes.
Optimisation of a PC12 cell-based in vitro stroke model for screening neuroprotective agents
Authors: Chua PinFen , Lim William K. 
Published: April 2021

AbstractStroke causes death and disability globally but no neuroprotectant is approved for post-stroke neuronal injury. Neuroprotective compounds can be identified using oxygen glucose deprivation (OGD) of neuronal cells as an in vitro stroke model. Nerve growth factor (NGF)-differentiated PC12 pheochromocytoma cells are frequently used. However, investigators often find their clonal variant undifferentiable and are uncertain of optimal culture conditions. Hence we studied 3 commonly used PC12 variants: PC12 Adh, PC12 from Riken Cell Bank (PC12 Riken) and Neuroscreen-1 (NS-1) cells. We found DMEM the optimal media for PC12 Riken and NS-1 cells. Using a novel serum-free media approach, we identified collagen IV as the preferred adhesive substrate for both cell lines. We found PC12 Adh cells cannot attach without serum and is unable to differentiate using NGF. NS-1 cells differentiated to a maximal 72.7 ± 5.2% %, with substantial basal differentiation. We optimised differentiated NS-1 cells for an in vitro stroke model using 3 h of OGD resulting in ~ 70% viable cells. We screened 5 reported neuroprotectants and provide the first report that serotonin is antiapoptotic in a stroke model and the 5-HT1A agonist 8-hydroxy-2-(di-n-propylamino) tetralin (8-OH-DPAT) is neuroprotective in PC12 cells. Thus we demonstrate the optimisation and validation for a PC12 cell-based in vitro stroke model.
Lymphedema alters lipolytic, lipogenic, immune and angiogenic properties of adipose tissue: a hypothesis-generating study in breast cancer survivors
Authors: Koc Michal , Wald Martin , Varaliová Zuzana , Ondrůjová Barbora , Čížková Terezie , Brychta Milan , Kračmerová Jana , Beranová Lenka , Pala Jan , Šrámková Veronika , Šiklová Michaela , Gojda Jan , Rossmeislová Lenka 
Published: April 2021

AbstractLater stages of secondary lymphedema are associated with the massive deposition of adipose tissue (AT). The factors driving lymphedema-associated AT (LAT) expansion in humans remain rather elusive. We hypothesized that LAT expansion could be based on alterations of metabolic, adipogenic, immune and/or angiogenic qualities of AT. AT samples were acquired from upper limbs of 11 women with unilateral breast cancer-related lymphedema and 11 healthy women without lymphedema. Additional control group of 11 female breast cancer survivors without lymphedema was used to assess systemic effects of lymphedema. AT was analysed for adipocyte size, lipolysis, angiogenesis, secretion of cytokines, immune and stem cell content and mRNA gene expression. Further, adipose precursors were isolated and tested for their proliferative and adipogenic capacity. The effect of undrained LAT- derived fluid on adipogenesis was also examined. Lymphedema did not have apparent systemic effect on metabolism and cytokine levels, but it was linked with higher lymphocyte numbers and altered levels of several miRNAs in blood. LAT showed higher basal lipolysis, (lymph)angiogenic capacity and secretion of inflammatory cytokines when compared to healthy AT. LAT contained more activated CD4+ T lymphocytes than healthy AT. mRNA levels of (lymph)angiogenic markers were deregulated in LAT and correlated with markers of lipolysis. In vitro, adipose cells derived from LAT did not differ in their proliferative, adipogenic, lipogenic and lipolytic potential from cells derived from healthy AT. Nevertheless, exposition of preadipocytes to LAT-derived fluid improved their adipogenic conversion when compared with the effect of serum. This study presents results of first complex analysis of LAT from upper limb of breast cancer survivors. Identified LAT alterations indicate a possible link between (lymph)angiogenesis and lipolysis. In addition, our in vitro results imply that AT expansion in lymphedema could be driven partially by exposition of adipose precursors to undrained LAT-derived fluid.
In situ novel environment assay reveals acoustic exploration as a repeatable behavioral response in migratory bats
Authors: Schabacker Theresa , Lindecke Oliver , Rizzi Sofia , Marggraf Lara , Pētersons Gunārs , Voigt Christian C. , Snijders Lysanne 
Published: April 2021

AbstractIntegrating information on species-specific sensory perception with spatial activity provides a high-resolution understanding of how animals explore environments, yet frequently used exploration assays commonly ignore sensory acquisition as a measure for exploration. Echolocation is an active sensing system used by hundreds of mammal species, primarily bats. As echolocation call activity can be reliably quantified, bats present an excellent model system to investigate intraspecific variation in environmental cue sampling. Here, we developed an in situ roost-like novel environment assay for tree-roosting bats. We repeatedly tested 52 individuals of the migratory bat species,Pipistrellus nathusii, across 24 h, to examine the role of echolocation when crawling through a maze-type arena and test for consistent intraspecific variation in sensory-based exploration. We reveal a strong correlation between echolocation call activity and spatial activity. Moreover, we show that during the exploration of the maze, individuals consistently differed in spatial activity as well as echolocation call activity, given their spatial activity, a behavioral response we term ’acoustic exploration’. Acoustic exploration was correlated with other exploratory behaviors, but not with emergence latency. We here present a relevant new measure for exploration behavior and provide evidence for consistent (short-term) intra-specific variation in the level at which wild bats collect information from a novel environment.
Land use in urban areas impacts the composition of soil bacterial communities involved in nitrogen cycling. A case study from Lefkosia (Nicosia) Cyprus
Authors: Stephanou Coralea , Omirou Michalis , Philippot Laurent , Zissimos Andreas M. , Christoforou Irene C. , Trajanoski Slave , Oulas Anastasis , Ioannides Ioannis M. 
Published: April 2021

AbstractThe different types of land-use and soil lithology in urban and peri-urban areas of modern cities compose a complex mosaic of soil ecosystems. It is largely unknown how these differences result in changes in bacterial community composition and structure as well as in functional guilds involved in N cycling. To investigate the bacterial composition and the proportion of denitrifiers in agricultural, forested, schoolyard and industrial areas, 24 samples were collected from urban and peri-urban sites of Lefkosia. Bacterial diversity and the proportion of denitrifiers were assessed by NGS and qPCR, respectively. Proteobacteria, Actinobacteria, Bacteriodetes, Chloroflexi, Acidobacteria and Planctomycetes were identified as the most dominant phyla across all sites, while agricultural sites exhibited the highest bacterial diversity. Heavy metals such as Co, Pb, V and Al were identified as key factors shaping bacterial composition in industrial and schoolyard sites, while the bacterial assemblages in agricultural and forested sites were associated with Ca. Variance partitioning analysis showed that 10.2% of the bacterial community variation was explained by land use management, 5.1% by chemical elements due to soil lithology, and 1.4% by sampling location. The proportion of denitrifiers varied with land use management. In industrial and schoolyard sites, the abundance of thenosZII bacterial community increased whilenirK abundance declined. Our data showed that land use and lithology have a moderate impact on the bacterial assemblages in urban and peri-urban areas of Lefkosia. As thenosZII bacterial community is important to the N2O sink capacity of soils, it would be interesting to elucidate the factors contributing to the proliferation of thenosZII clade in these soils.
Impact of clinical targeted sequencing on endocrine responsiveness in estrogen receptor-positive, HER2-negative metastatic breast cancer
Authors: Hagio Kanako , Amano Toraji , Hayashi Hideyuki , Takeshita Takashi , Oshino Tomohiro , Kikuchi Junko , Ohhara Yoshihito , Yabe Ichiro , Kinoshita Ichiro , Nishihara Hiroshi , Yamashita Hiroko 
Published: April 2021

AbstractClinical targeted sequencing allows for the selection of patients expected to have a better treatment response, and reveals mechanisms of resistance to molecular targeted therapies based on actionable gene mutations. We underwent comprehensive genomic testing with either our original in-house CLHURC system or with OncoPrime. Samples from 24 patients with estrogen receptor-positive, human epidermal growth factor receptor 2-negative metastatic breast cancer underwent targeted sequencing between 2016 and 2018. Germline and somatic gene alterations and patients’ prognosis were retrospectively analyzed according to the response to endocrine therapy. All of the patients had one or more germline and/or somatic gene alterations. Four patients with primary or secondary endocrine-resistant breast cancer harbored germline pathogenic variants of BRCA1, BRCA2, or PTEN. Among somatic gene alterations, TP53, PIK3CA, AKT1, ESR1, and MYC were the most frequently mutated genes. TP53 gene mutation was more frequently observed in patients with primary endocrine resistance compared to those with secondary endocrine resistance or endocrine-responsive breast cancer. Recurrent breast cancer patients carrying TP53-mutant tumors had significantly worse overall survival compared to those with TP53-wild type tumors. Our 160-gene cancer panel will be useful to identify clinically actionable gene alterations in breast cancer in clinical practice.
Identification and functional analysis of a biflavone as a novel inhibitor of transient receptor potential vanilloid 4-dependent atherogenic processes
Authors: Alharbi Mazen O. , Dutta Bidisha , Goswami Rishov , Sharma Shweta , Lei Kai Y. , Rahaman Shaik O. 
Published: April 2021

AbstractAtherosclerosis, a chronic inflammatory disease of large arteries, is the major contributor to the growing burden of cardiovascular disease-related mortality and morbidity. During early atherogenesis, as a result of inflammation and endothelial dysfunction, monocytes transmigrate into the aortic intimal areas, and differentiate into lipid-laden foam cells, a critical process in atherosclerosis. Numerous natural compounds such as flavonoids and polyphenols are known to have anti-inflammatory and anti-atherogenic properties. Herein, using a fluorometric imaging plate reader-supported Ca2+ influx assay, we report semi high-throughput screening-based identification of ginkgetin, a biflavone, as a novel inhibitor of transient receptor potential vanilloid 4 (TRPV4)-dependent proatherogenic and inflammatory processes in macrophages. We found that ginkgetin (1) blocks TRPV4-elicited Ca2+ influx into macrophages, (2) inhibits oxidized low-density lipoprotein (oxLDL)-induced foam cell formation by suppressing the uptake but not the binding of oxLDL in macrophages, and (3) attenuates oxLDL-induced phosphorylation of JNK2, expression of TRPV4 proteins, and induction of inflammatory mRNAs. Considered all together, the results of this study show that ginkgetin inhibits proatherogenic/inflammatory macrophage function in a TRPV4-dependent manner, thus strengthening the rationale for the use of natural compounds for developing therapeutic and/or chemopreventive molecules.
Managed honeybees and South American bumblebees exhibit complementary foraging patterns in highbush blueberry
Authors: Estravis-Barcala M. Cecilia , Palottini Florencia , Macri Ivana , Nery Denise , Farina Walter M. 
Published: April 2021

AbstractDespiteApis melliferabeing the most widely managed pollinator to enhance crop production, they are not the most suitable species for highbush blueberries, which possess restrictive floral morphology and require buzz-pollination. Thus, the South American bumblebeeBombus pauloensisis increasingly managed as an alternative species in this crop alongside honeybees. Herein, we evaluated the foraging patterns of the two species, concerning the potential pollen transfer between two blueberry co-blooming cultivars grown under open high tunnels during two seasons considering different colony densities. Both managed pollinators showed different foraging patterns, influenced by the cultivar identity which varied in their floral morphology and nectar production. Our results demonstrate that both species are efficient foragers on highbush blueberry and further suggest that they contribute positively to its pollination in complementary ways: while bumblebees were more effective at the individual level (visited more flowers and carried more pollen), the greater densities of honeybee foragers overcame the difficulties imposed by the flower morphology, irrespective of the stocking rate. This study supports the addition of managed native bumblebees alongside honeybees to enhance pollination services and emphasizes the importance of examining behavioural aspects to optimize management practices in pollinator-dependent crops.
Nitric oxide attenuated transforming growth factor-β induced myofibroblast differentiation of human keratocytes
Authors: Park Joo-Hee , Kim Martha , Yim Bora , Park Choul Yong 
Published: April 2021

AbstractNitric oxide (NO) has the potential to modulate myofibroblast differentiation. In this study, we investigated the effect of exogenous NO on the myofibroblast differentiation of human keratocytes using sodium nitrite as a NO donor. Myofibroblasts were induced by exposing resting keratocytes to transforming growth factor (TGF)-β1. N-cadherin and α-smooth muscle actin (αSMA) were used as myofibroblast markers. Both resting keratocytes and -stimulated keratocytes were exposed to various concentrations of sodium nitrite (1 μM to 1000 mM) for 24 to 72 h. Exposure to sodium nitrite did not alter keratocytes’ viability up to a 10 mM concentration for 72 h. However, significant cytotoxicity was observed in higher concentrations of sodium nitrite (over 100 mM). The expression of αSMA and N-cadherin was significantly increased in keratocytes by TGF-β1 stimulation after 72 h incubation. The addition of sodium nitrite (1 mM) to TGF-β1-stimulated keratocytes significantly decreased αSMA and N cadherin expression. Smad3 phosphorylation decreased after sodium nitrite (1 mM) exposure in TGF-β1-stimulated keratocytes. The effect of NO was reversed when NO scavenger, 2-4-carboxyphenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO) was added in the culture medium. Application of sodium nitrite resulted in significant decrease of corneal opacity when measured at 2 weeks after the chemical burn in the mouse. These results verified the potential therapeutic effect of NO to decrease myofibroblast differentiation of human keratocytes and corneal opacity after injury.
The fragility of opinion formation in a complex world
Authors: Medo Matúš , Mariani Manuel S. , Lü Linyuan 
Published: April 2021

AbstractHow does the complexity of the world around us affect the reliability of our opinions? Motivated by this question, we quantitatively study an opinion formation mechanism whereby an uninformed observer gradually forms opinions about a world composed of subjects interrelated by a signed network of mutual trust and distrust. We show numerically and analytically that the observer’s resulting opinions are highly inconsistent (they tend to be independent of the observer’s initial opinions) and unstable (they exhibit wide stochastic variations). Opinion inconsistency and instability increase with the world’s complexity, intended as the number of subjects and their interactions. This increase can be prevented by suitably expanding the observer’s initial amount of information. Our findings imply that an individual who initially trusts a few credible information sources may end up trusting the deceptive ones even if only a small number of trust relations exist between the credible and deceptive sources.
Legacies of Indigenous land use shaped past wildfire regimes in the Basin-Plateau Region, USA
Authors: Carter Vachel A. , Brunelle Andrea , Power Mitchell J. , DeRose R. Justin , Bekker Matthew F. , Hart Isaac , Brewer Simon , Spangler Jerry , Robinson Erick , Abbott Mark , Maezumi S. Yoshi , Codding Brian F. 
Published: April 2021

AbstractClimatic conditions exert an important influence on wildfire activity in the western United States; however, Indigenous farming activity may have also shaped the local fire regimes for millennia. The Fish Lake Plateau is located on the Great Basin–Colorado Plateau boundary, the only region in western North America where maize farming was adopted then suddenly abandoned. Here we integrate sedimentary archives, tree rings, and archeological data to reconstruct the past 1200 years of fire, climate, and human activity. We identify a period of high fire activity during the apex of prehistoric farming between 900 and 1400 CE, and suggest that farming likely obscured the role of climate on the fire regime through the use of frequent low-severity burning. Climatic conditions again became the dominant driver of wildfire when prehistoric populations abandoned farming around 1400 CE. We conclude that Indigenous populations shaped high-elevation mixed-conifer fire regimes on the Fish Lake Plateau through land-use practices.
Phytoplankton community structuring and succession in a competition-neutral resource landscape
Authors: Behrenfeld Michael J , Boss Emmanuel S , Halsey Kimberly H 
Published: April 2021

Abstract
Phytoplankton community composition and succession affect aquatic food webs and biogeochemistry. Resource competition is commonly viewed as an important governing factor for community structuring and this perception is imbedded in modern ecosystem models. Quantitative consideration of the physical spacing between phytoplankton cells, however, suggests that direct competition for growth-limiting resources is uncommon. Here we describe how phytoplankton size distributions and temporal successions are compatible with a competition-neutral resource landscape. Consideration of phytoplankton-herbivore interactions with proportional feeding size ranges yields small-cell dominated size distributions consistent with observations for stable aquatic environments, whereas predator–prey temporal lags and blooming physiologies shift this distribution to larger mean cell sizes in temporally dynamic environments. We propose a conceptual mandala for understanding phytoplankton community composition where species successional series are initiated by environmental disturbance, guided by the magnitude of these disturbances and nutrient stoichiometry, and terminated with the return toward a ‘stable solution’. Our conceptual mandala provides a framework for interpreting and modeling the environmental structuring of natural phytoplankton populations.