bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatio-temporal spawning patterns and early growth of Japanese sardine in the western North Pacific during the recent stock increase
Authors: Niino Yohei , Furuichi Sho , Kamimura Yasuhiro , Yukami Ryuji 
Published: December 2020

AbstractSpatio-temporal patterns in spawning influence growth and survival by affecting the environment experienced by offspring during their early life stages. Therefore, identifying changes in spawning patterns can help researchers understand population dynamics and recruitment fluctuations. The Japanese sardineSardinops melanostictusis a small pelagic fish that undergoes large stock fluctuations. Although spawning patterns are known to change spatially and temporally with stock abundance, little information is available on the processes underlying stock increases. This study aimed to describe changes in spawning pattern and early growth of Japanese sardine during the recent period of stock increase, and to clarify the effects of different spawning periods on offspring growth. We examined trends in egg abundance in the western North Pacific in 2004–2018 and analyzed hatch dates and growth trajectories by otolith microstructure analysis of juveniles from the Kuroshio–Oyashio transitional region (the species’ main nursery area). During the study period, the main spawning area shifted from the western to the eastern part of this region off Japan, and spawning in the eastern part roughly coincided with juvenile hatch dates. Hatch dates also shifted from mid-March at the earliest to February and early March from 2013 onwards. Although early-hatched cohorts (which originate offshore of eastern Japan) experienced slower initial growth, they likely played an important role in the recent stock increase. Successful recruitment of these cohorts may have been facilitated by factors such as early hatching and transport to the nursery, which reduces the frequency of predator encounters.
Precise base editing for thein vivostudy of developmental signaling and human pathologies in zebrafish
Authors: Rosello Marion , Vougny Juliette , Czarny François , Mione Maria Caterina , Concordet Jean-Paul , Albadri Shahad , Del Bene Filippo 
Published: December 2020

ABSTRACTWhile zebrafish is emerging as a new model system to study human diseases, an efficient methodology to generate precise point mutations at high efficiency is still lacking. Here we show that base editors can generate C-to-T point mutations with high efficiencies without other unwanted on-target mutations. In addition, we established a new editor variant recognizing an NAA PAM, expanding the base editing possibilities in zebrafish. Using these approaches, we first generated a base change in the ctnnb1 gene, mimicking oncogenic mutations of the human gene known to result in constitutive activation of endogenous Wnt signaling. Additionally, we precisely targeted several cancer-associated genes among which cbl. With this last target we created a new zebrafish dwarfism model. Together our findings expand the potential of zebrafish as a model system allowing new approaches for the endogenous modulation of cell signaling pathways and the generation of precise models of human genetic disease associated-mutations.
Genome based analyses reveals the presence of heterotypic synonyms and subspecies in Bacteria and Archaea
Authors: Madhaiyan Munusamy , Saravanan Venkatakrishnan Sivaraj , See-Too Wah-Seng 
Published: December 2020

AbstractTerm heterotypic synonym refers to different names have been associated with different type strains, however from the opinion of a bacteriologist, different names belongs to the same taxon and term subspecies refers to strains and genetically close organisms that were diverging phenotypically. In this study, sequenced and publicly available genomes in the Edgar 2.0 server were carefully analysed and based on high (>98 %) amino acid identity value, synonyms were putatively identified. The 16S rRNA gene sequence of those species were used for the construction of maximum likelihood based phylogenetic trees to infer the genetic closeness or distance by examining the tree topology and clustering of the organisms within clades. They were further subjected to overall genome related indices like digital DNA-DNA hybridization, average nucleotide identity to confirm the presence of synonyms or subspecies with phenotypic data support. The outcome of this polyphasic taxonomic re-analysis was identification of 40 later heterotypic synonyms and 13 subspecies spread over phylumActinobacteria,Bacteroidetes,Firmicutes,Nitrospirae,ProteobacteriaandThermotogaeand in domainArchaea.
TM6SF2/PNPLA3/MBOAT7 loss-of-function genetic variants impact on NAFLD development and progression both in patients and inin vitromodels
Authors: Longo Miriam , Meroni Marica , Erconi Veronica , Carli Fabrizia , Macchi Chiara , Fortunato Francesco , Ronchi Dario , Sabatini Silvia , Paolini Erika , De Caro Emilia Rita , Alisi Anna , Miele Luca , Soardo Giorgio , Comi Giacomo Pietro , Valenti Luca , Ruscica Massimiliano , Fracanzani Anna L , Gastaldelli Amalia , Dongiovanni Paola 
Published: December 2020

AbstractBackground and aimsThe I148M PNPLA3, the rs641738 inMBOAT7/TMC4locus and the E167K TM6SF2 polymorphisms represent the main predisposing factors to non-alcoholic fatty liver disease (NAFLD) development and progression. We previously generated a full knockout ofMBOAT7in HepG2 cells (MBOAT7-/-), homozygous for the I148M PNPLA3. Therefore, we aimed to:1) investigate the synergic impact of the 3 at-risk variants on liver injury and hepatocellular carcinoma (HCC) in a large cohort of NAFLD patients;2) createin vitromodels of genetic NAFLD by silencingTM6SF2in both HepG2 and MBOAT7-/-cells.MethodsNAFLD patients (n=1380) of whom 121 had HCC were stratified with a semi-quantitative score ranging from 0 to 3 according to the number ofPNPLA3,TM6SF2andMBOAT7at-risk variants.TM6SF2was silenced in HepG2 (TM6SF2-/-) and MBOAT7-/-(MBOAT7-/-TM6SF2-/-) through CRISPR/Cas9.ResultsIn NAFLD patients, the additive weight of these mutations was associated with liver disease severity and increased risk to develop HCC. In HepG2 cells,TM6SF2silencing altered lipid composition and induced the accumulation of micro-vesicular LDs, whereas the MBOAT7-/-TM6SF2-/-cells showed a mixed micro/macro pattern of LDs.TM6SF2deletion strongly affected endoplasmic reticulum (ER) and mitochondria ultrastructures thus increasing ER/oxidative stress. Mitochondrial number raised in both TM6SF2-/-and MBOAT7-/-TM6SF2-/-models, suggesting an unbalancing in mitochondrial dynamics and the silencing of bothMBOAT7andTM6SF2impaired mitochondrial activity with a shift towards anaerobic glycolysis. MBOAT7-/-TM6SF2-/-cells also showed the highest proliferation rate.ConclusionsThe co-presence of the 3 at-risk variants impacts on NAFLD course, in both patients and experimental models affecting LDs accumulation, mitochondrial functionality and metabolic reprogramming towards HCC.
Wildfire affects circulating hormone levels and the expression of male sexual plumage in a tropical songbird
Authors: Boersma Jordan , Barron Douglas G. , Baldassarre Daniel T. , Webster Michael S. , Schwabl Hubert 
Published: December 2020

ABSTRACTNatural disturbances like drought and wildfires are expected to increase in prevalence, so understanding how organisms are affected is a key goal for conservationists and biologists alike. While many studies have illustrated long-term effects of perturbations on survival and reproduction, little is known of short-term effects to physiology and sexual signal expression. Ornamental traits have been proposed as reliable indicators of environmental health, yet studies are lacking in the context of natural disturbances. Here we present short-term responses of male Red-backed Fairywrens (Malurus melanocephalus) to wildfire near the onset of the typical breeding season. Males of this species are characterized by plastic expression of sexual plumage phenotypes in their first breeding season. Using two populations with Fairywren captures before and after separate wildfires we illustrate that wildfire suppressed molt into ornamented plumage, including in third year males that typically show little plasticity in ornamentation. Baseline plasma corticosterone was elevated in males sampled after fire, but condition (furcular fat stores) was unaffected. Although testosterone levels did not decrease following fire, we found a positive correlation between testosterone and plumage ornamentation. In addition, males molting in ornamental plumage had higher circulating levels of testosterone than males molting in unornamented plumage following fire. Collectively, these findings suggest that wildfires inhibit or greatly delay acquisition of ornamentation in young males without exerting obvious effects on condition, but rather through subtle effects on testosterone and corticosterone circulation. This natural experiment also reveals that expression of alternative male reproductive phenotypes in this species is sensitive to environmental conditions and more plastic than previously assumed.
Gating transitions and modulation of a hetero-octameric AMPA glutamate receptor
Authors: Zhang Danyang , Watson Jake F. , Matthews Peter M. , Cais Ondrej , Greger Ingo H. 
Published: December 2020

AbstractAMPA glutamate receptors (AMPARs) mediate the majority of excitatory transmission in the brain, and enable synaptic plasticity that underlies learning1. A diverse array of AMPAR signaling complexes are established by receptor auxiliary subunits, associating in various combinations to modulate trafficking, gating and synaptic strength2. However, their mechanisms of action are poorly understood. Here, we determine cryo-electron microscopy structures of the heteromeric GluA1/2 receptor assembled with both TARP-γ8 and CNIH2, the predominant AMPAR complex in the forebrain, in both resting and active states (at 3.2 and 3.7 Å, respectively). Consequential for gating regulation, two γ8 and two CNIH2 subunits lodge at distinct sites beneath the ligand-binding domains of the receptor tetramer, with site-specific lipids shaping each interaction. Activation leads to a stark asymmetry between GluA1 and GluA2 along the ion conduction path, and an outward expansion of the channel triggers counter-rotations of both auxiliary subunit pairs, that promotes the active-state conformation. In addition, both γ8 and CNIH2 pivot towards the pore exit on activation, extending their reach for cytoplasmic receptor elements. CNIH2 achieves this through its uniquely extended M2 helix, which has transformed this ER-export factor into a powerful positive AMPAR modulator, capable of providing hippocampal pyramidal neurons with their integrative synaptic properties.
The RelA hydrolase domain: a molecular switch for (p)ppGpp synthesis
Authors: Sinha Anurag Kumar , Winther Kristoffer Skovbo 
Published: December 2020

AbstractBacteria synthesize guanosine tetra- and penta phosphate (commonly referred to as (p)ppGpp) in response to environmental stresses. (p)ppGpp reprograms cell physiology and is essential for stress survival, virulence and antibiotic tolerance. Proteins of the RSH superfamily (RelA/SpoT Homologues) are ubiquitously distributed and hydrolyze or synthesize (p)ppGpp. Structural studies have suggested that the shift between hydrolysis and synthesis is governed by conformational antagonism between the two active sites in RSHs. RelA proteins of γ-proteobacteria exclusively synthesize (p)ppGpp and encode an inactive pseudo-hydrolase domain.Escherichia coliRelA synthesizes (p)ppGpp in response to amino acid starvation with cognate uncharged tRNA at the ribosomal A-site, however, mechanistic details to the regulation of the enzymatic activity remain elusive. Here, we show a role of the enzymatically inactive hydrolase domain in modulating the activity of the synthetase domain of RelA. Using mutagenesis screening and functional studies, we identify a loop region (residues 114-130) in the hydrolase domain, which controls the synthetase activity. We show that a synthetase-inactive loop mutant of RelA is not affected for tRNA binding, but binds the ribosome less efficiently than wildtype RelA. Our data support the model that the hydrolase domain acts as a molecular switch to regulate the synthetase activity.
Synchrotron radiation X-ray microtomography for the visualization of intra-cochlear anatomy in human temporal bones implanted with a perimodiolar cochlear implant electrode array
Authors: Sismono Fergio , Mancini Lucia , Leblans Marc , Goyens Jana , De Greve Glynnis , Schneiders Sara , Beckers Karen , Dirckx Joris , De Foer Bert , Zarowski Andrzej 
Published: December 2020

Recently, synchrotron radiation computed microtomography (SRµCT) has emerged as a promising tool for non-destructive, in situ visualization of cochlear implant electrode arrays inserted into a human cochlea. Histological techniques have been the `gold standard' technique for accurate localization of cochlear implant electrodes but are suboptimal for precise three-dimensional measurements. Here, an SRµCT experimental setup is proposed that offers the benefit of a high spatial and contrast resolution (isotropic voxel size = 4.95 µm and propagation-based phase-contrast imaging), while visualizing the soft-tissue structures and electrode array of the cochlear implant simultaneously. In this work, perimodiolar electrode arrays have been tested, which incorporate thick and closely spaced platinum–iridium contacts and wiring. These data can assist cochlear implant and hearing research, can be used to verify electrode segmentation techniques for clinical computed tomography or could be utilized to evaluate cochlear implant electrode array designs.
Advanced X-ray polarimeter design for nuclear resonant scattering
Authors: Marx-Glowna Berit , Uschmann Ingo , Schulze Kai S. , Marschner Heike , Wille Hans-Christian , Schlage Kai , Stöhlker Thomas , Röhlsberger Ralf , Paulus Gerhard G. 
Published: December 2020

This work presents the improvements in the design and testing of polarimeters based on channel-cut crystals for nuclear resonant scattering experiments at the 14.4 keV resonance of 57Fe. By using four asymmetric reflections at asymmetry angles of α1 = −28°, α2 = 28°, α3 = −28° and α4 = 28°, the degree of polarization purity could be improved to 2.2 × 10−9. For users, an advanced polarimeter without beam offset is now available at beamline P01 of the storage ring PETRA III.
Precise and parallel segmentation model (PPSM) via MCET using hybrid distributions
Authors: Rawas Soha , El-Zaart Ali 
Published: December 2020

PurposeImage segmentation is one of the most essential tasks in image processing applications. It is a valuable tool in many oriented applications such as health-care systems, pattern recognition, traffic control, surveillance systems, etc. However, an accurate segmentation is a critical task since finding a correct model that fits a different type of image processing application is a persistent problem. This paper develops a novel segmentation model that aims to be a unified model using any kind of image processing application. The proposed precise and parallel segmentation model (PPSM) combines the three benchmark distribution thresholding techniques to estimate an optimum threshold value that leads to optimum extraction of the segmented region: Gaussian, lognormal and gamma distributions. Moreover, a parallel boosting algorithm is proposed to improve the performance of the developed segmentation algorithm and minimize its computational cost. To evaluate the effectiveness of the proposed PPSM, different benchmark data sets for image segmentation are used such as Planet Hunters 2 (PH2), the International Skin Imaging Collaboration (ISIC), Microsoft Research in Cambridge (MSRC), the Berkley Segmentation Benchmark Data set (BSDS) and Common Objects in COntext (COCO). The obtained results indicate the efficacy of the proposed model in achieving high accuracy with significant processing time reduction compared to other segmentation models and using different types and fields of benchmarking data sets.Design/methodology/approachThe proposed PPSM combines the three benchmark distribution thresholding techniques to estimate an optimum threshold value that leads to optimum extraction of the segmented region: Gaussian, lognormal and gamma distributions.FindingsOn the basis of the achieved results, it can be observed that the proposed PPSM–minimum cross-entropy thresholding (PPSM–MCET)-based segmentation model is a robust, accurate and highly consistent method with high-performance ability.Originality/valueA novel hybrid segmentation model is constructed exploiting a combination of Gaussian, gamma and lognormal distributions using MCET. Moreover, and to provide an accurate and high-performance thresholding with minimum computational cost, the proposed PPSM uses a parallel processing method to minimize the computational effort in MCET computing. The proposed model might be used as a valuable tool in many oriented applications such as health-care systems, pattern recognition, traffic control, surveillance systems, etc.
Exploring the barriers to upscaling the production capacity of the edible insect sector in the United Kingdom
Authors: Yang Ying , Cooke Christopher 
Published: December 2020

PurposeThis study aims to explore the barriers to upscaling the production capacity of the edible insect sector in the UK and to identify the impact of current regulation on the sector's development.Design/methodology/approachA significant proportion of edible insect-producing companies within the UK were identified through an online market research database and contacted via email to invite them to participate in this study. Phone interviews were conducted with ten companies. Thematic analysis was adopted for data analysis.FindingsThere were five themes identified as barriers to the upscaling of the production for the edible insect sector in the UK: insect feeding materials, production capacity, expertise and knowledge, new product development and regulatory uncertainty.Research limitations/implicationsThis research was based on a qualitative study. Further quantitative research is needed to test the extent of the impact of these five themes on upscaling production capacity. In addition to production capacity, marketing and consumers' acceptance, culture and behaviour can also be considered in future studies.Originality/valueThis study makes a significant contribution to the literature by providing insight on the barriers to upscaling production capacity in the edible insect sector.
Does an MBA degree advance business management skill or in fact create horizontal and vertical mismatches?
Authors: Alam Gazi Mahabubul , Parvin Morsheda , Ayub Ahmad Fauzi Bin Mohd , Kader Romana , Rahman Md. Mahfuzur 
Published: December 2020

PurposeAn old saying –“Jack of all trades, master of none”– deliberately asserts that the purpose of a master’s degree program is to generate high level job skills in order to improve a nation's economy, while a bachelor degree produces economically productive graduates. Employment of such graduates is fundamentally important for personal and economic development. There is a link between a bachelor’s and master's degree and how these qualifications are linked to the job market. Both horizontal and vertical mismatches are developed which is the central focus of this research.Design/methodology/approachGiven the differentiated nature of research questions, multiple techniques are used to collect the data. However, this research bears the norms of the qualitative method. Both secondary and primary data are used, and meanwhile secondary data are collected by the banks, Bangladesh Bureau of Educational Information and Statistics (BANBEIS), University Grants Commission (UGC) and by the institutions sampled. Primary data are gathered from interviews with key people. Data were collected from three institutions of higher education and from six commercial banks and from the Central Bank. The academic results of 21,325 MBA graduates and education backgrounds of 750 executives working in banks served as the basis for establishing our arguments.FindingsThis study discovers that MBA graduates who have studied science subjects achieved much better grades in the MBA compared to their counterparts who studied business from secondary provision to first degree. The market-driven MBA programme has become a “business product”. The major revenue of higher education institutions comes from enrolment in MBA courses. For this reason, a science-friendly MBA program is developed to generate more business. If this continues, the philosophy of the master's program would either be lost or will have to be redefined in the 21st century.Originality/valueWhile a few studies have investigated the area of HE in Bangladesh, none covers the impact of MBA degrees on the job market and its contribution to enhancing job skills.
The impact of audit committee attributes on the quality and quantity of environmental, social and governance (ESG) disclosures
Authors: Arif Muhammad , Sajjad Aymen , Farooq Sanaullah , Abrar Maira , Joyo Ahmed Shafique 
Published: December 2020

PurposeThe purpose of this research is to ascertain the impact of audit committee (AC) activism and independence on the quality and quantity of environmental, social and governance (ESG) disclosures for energy sector firms in Australia. This paper aims to understand how AC attributes such as meeting frequency, and the number of independent directors influence the compliance with the global reporting initiative (GRI) guidelines and quantity of ESG disclosures.Design/methodology/approachBloomberg ESG disclosure scores and company reported AC attributes are collected and analysed using the pooled ordinary least square (OLS) regression framework with Petersen’s (2009) technique by using a two-dimensional cluster at the firm and year level. Further, this paper uses a lagged independent variable and two-stage least square approach to address endogeneity concerns.FindingsThe results show a significant positive effect of AC activism and independence on the level of compliance with the GRI guidelines, indicating the favourable effect of AC attributes on ESG reporting quality. Likewise, AC attributes positively affect the quantity of ESG disclosures. Notably, the impact of AC attributes is more pronounced on environmental disclosures.Originality/valueThis paper validates the significance of the management control mechanism in improving the quality and quantity of ESG disclosures for an environmentally sensitive sector, hence offering a potential answer to reduce agency and legitimacy issues for the sensitive industry firms.