bluuebunny/crossref_metadata_2025_split huggingface dataset:
Core Imaging Library - Part II: multichannel reconstruction for dynamic and spectral tomography
Authors: Papoutsellis Evangelos , Ametova Evelina , Delplancke Claire , Fardell Gemma , Jørgensen Jakob S. , Pasca Edoardo , Turner Martin , Warr Ryan , Lionheart William R. B. , Withers Philip J. 
Published: July 2021

The newly developed core imaging library (CIL) is a flexible plug and play library for tomographic imaging with a specific focus on iterative reconstruction. CIL provides building blocks for tailored regularized reconstruction algorithms and explicitly supports multichannel tomographic data. In the first part of this two-part publication, we introduced the fundamentals of CIL. This paper focuses on applications of CIL for multichannel data, e.g. dynamic and spectral. We formalize different optimization problems for colour processing, dynamic and hyperspectral tomography and demonstrate CIL’s capabilities for designing state-of-the-art reconstruction methods through case studies and code snapshots.This article is part of the theme issue ‘Synergistic tomographic image reconstruction: part 2’.
Synergistic tomographic image reconstruction: part 2
Authors: Tsoumpas Charalampos , Sauer Jørgensen Jakob , Kolbitsch Christoph , Thielemans Kris 
Published: July 2021

This special issue is the second part of a themed issue that focuses on synergistic tomographic image reconstruction and includes a range of contributions in multiple disciplines and application areas. The primary subject of study lies within inverse problems which are tackled with various methods including statistical and computational approaches. This volume covers algorithms and methods for a wide range of imaging techniques such as spectral X-ray computed tomography (CT), positron emission tomography combined with CT or magnetic resonance imaging, bioluminescence imaging and fluorescence-mediated imaging as well as diffuse optical tomography combined with ultrasound. Some of the articles demonstrate their utility on real-world challenges, either medical applications (e.g. motion compensation for imaging patients) or applications in material sciences (e.g. material decomposition and characterization). One of the desired outcomes of the special issues is to bring together different scientific communities which do not usually interact as they do not share the same platforms such as journals and conferences.
This article is part of the theme issue ‘Synergistic tomographic image reconstruction: part 2’.
Impact of cilia-related genes on mitochondrial dynamics during Drosophila spermatogenesis
Authors: Bauerly Elisabeth , Akiyama Takuya , Yi Kexi , Gibson Matthew C. 
Published: July 2021

AbstractSpermatogenesis is a dynamic process of cellular differentiation that generates the mature spermatozoa required for reproduction. Errors that arise during this process can lead to sterility due to low sperm counts and malformed or immotile sperm. While is estimated that 1 out of 7 couples encounter infertility, the underlying cause of male infertility can only be identified in 50% of cases. Here, we describe and examine the genetic requirements for missing minor mitochondria (mmm), sterile affecting ciliogenesis (sac), and testes of unusual size (tous), three previously uncharacterized genes that are predicted to be components of the flagellar axoneme. Using Drosophila, we demonstrate that these genes are essential for male fertility and that loss of mmm, sac, or tous results in complete immotility of the sperm flagellum. Cytological examination uncovered additional roles for sac and tous during cytokinesis and transmission electron microscopy of developing spermatids in mmm, sac, and tous mutant animals revealed defects associated with mitochondria and the accessory microtubules required for the proper elongation of the mitochondria and flagella during ciliogenesis. This study highlights the complex interactions of cilia-related proteins within the cell body and advances our understanding of male infertility by uncovering novel mitochondrial defects during spermatogenesis.
Dopaminergic axon tracts within a hyaluronic acid hydrogel encasement for implantation to restore the nigrostriatal pathway
Authors: Gordián-Vélez Wisberty J. , Browne Kevin D. , Galarraga Jonathan H. , Duda John E. , España Rodrigo A. , Chen H. Isaac , Burdick Jason A. , Cullen D. Kacy 
Published: July 2021

AbstractParkinson’s disease (PD) affects 10 million patients worldwide, making it the second most prevalent neurodegenerative disease. Motor symptoms emerge from the loss of dopamine in the striatum after the death of dopaminergic neurons and the long-projecting axons of the nigrostriatal pathway. Current treatments, such as dopamine replacement, deep brain stimulation or cell therapies, disregard the loss of this pathway at the core of symptoms. We sought to address this by improving our tissue-engineered nigrostriatal pathway (TE-NSP) technology, which consists of a tubular hydrogel with a collagen/laminin core that encases an aggregate of dopaminergic neurons and their axons in a way that resembles the nigrostriatal pathway. These constructs can be implanted to replace the lost neurons and axons with fidelity to the pathway, and thus provide dopamine according to feedback from the host circuitry. While TE-NSPs have been traditionally fabricated with agarose, here we utilized a hyaluronic acid (HA) hydrogel to expand the functionality of the encasement and our control over its properties. Using rat ventral midbrain neurons, we found that TE-NSPs exhibited longer and faster neurite growth with HA relative to agarose, with no differences observed in electrically-evoked dopamine release. When transplanted, HA hydrogels reduced host neuron loss and inflammation around the implant compared to agarose, and the cells and axons within TE-NSPs survived and maintained their cytoarchitecture for at least 2 weeks.HighlightsWe fabricated engineered dopaminergic axons encased in a tubular hydrogel.We made hydrogels from methacrylated hyaluronic acid and compared them to agarose.Axons in HA hydrogels had longer and faster axon growth and displayed evoked dopamine release.HA hydrogels reduced the host inflammatory response and supported neuron and axon survival in vivo.This platform may be used to reconstruct the nigrostriatal pathway to treat Parkinson’s disease.
Deleting in vivo β-catenin degradation domain in mouse hepatocytes drives hepatocellular carcinoma or hepatoblastoma-like tumors
Authors: Loesch Robin , Caruso Stefano , Paradis Valérie , Godard Cecile , Gougelet Angélique , Picard Simon , Perret Christine , Taketo Makoto Mark , Zucman-Rossi Jessica , Colnot Sabine 
Published: July 2021

AbstractBackground and aimsOne-third of hepatocellular carcinomas (HCCs) have mutations that activate the β-catenin pathway with mostly CTNNB1 mutations. Mouse models using Adenomatous polyposis coli (Apc) loss-of-functions (LOF) are widely used to mimic β-catenin-dependent tumorigenesis. Considering the low prevalence of APC mutations in human HCCs we aimed to generate hepatic tumors through CTNNB1 exon 3 deletion (βcatΔex3) and to compare them to hepatic tumors with Apc LOF engineered through a frameshift in exon 15 (Apcfs-ex15).MethodsWe used hepatic-specific and inducible Cre-lox mouse models as well as a hepatic-specific in vivo CRISPR/Cas9 approach using AAV vectors, to generate Apcfs-ex15 and βcatΔex3 hepatic tumors harboring activation of the β-catenin pathway. Tumors generated by the Cre-lox models were analyzed phenotypically using immunohistochemistry and were selected for transcriptomic analysis using RNA-sequencing. Mouse RNAseq data were compared to human RNAseq data (normal tissues (8), HCCs (48) and hepatoblastomas (9)) in an integrative analysis. Tumors generated via CRISPR were analyzed using DNA sequencing and immunohistochemistry.ResultsMice with βcatΔex3 alteration in hepatocytes developed liver tumors. Generated tumors were indistinguishable from those arising in Apcfs-ex15 mice. Both Apcfs-ex15 and βcatΔex3 mouse models induced two phenotypically distinct tumors (differentiated or undifferentiated). Integrative analysis of human and mouse tumors showed that mouse differentiated tumors are close to human well differentiated CTNNB1-mutated tumors, while undifferentiated ones are closer to human mesenchymal hepatoblastomas, and are activated for YAP signaling.ConclusionApcfs-ex15 and βcatΔex3 mouse models similarly induce tumors transcriptionally close to either well differentiated β-Catenin activated human HCCs or mesenchymal hepatoblastomas.
Based on the identification of tumor antigens and immune subtypes in renal clear cell carcinoma for mRNA vaccine development
Authors: Zhang Shichao , Xiong Yu , Kang Shijing , Mao Chengju , Wang Yue , Zeng Zhu , Peng Jian , Ouyang Yan 
Published: July 2021

AbstractBackgroundCancer vaccine based on mRNA is considered as a promising strategy and has become a new hot spot in cancer immunotherapy. However, its application to KIRC is not clear. A growing body of research has shown that immunotyping can reflect the comprehensive immune status and immune microenvironment of tumor, which is closely related to treatment response and vaccination potential. The aim of this study was to identify the potential antigens of KIRC for the development of anti-KIRC mRNA vaccines, and to further differentiate the immune subtypes of KIRC to construct an immune landscape for the selection of appropriate patients for vaccination.MethodsGene expression profiles and corresponding clinical information of 265 KIRC patients and RNA-seq data of 539 KIRC patients were retrieved from were collected from GEO and TCGA. cBioPortal was used to visualize and compare genetic alterations, while GEPIA2 was used to calculate the prognostic index of selected antigens. The relationship between the infiltration of antigen presenting cells and the expression of the identified antigen was visualized with TIMER, and consensus clustering analysis was used to determine the immune subtypes. Finally, the immune landscape of KIRC is visualized through the dimensionality reduction analysis based on graph learning.ResultsTwo tumor antigens associated with prognostic and antigen-presenting infiltrating cells were identified in KIRC, including LRP2, and DOCK8. KIRC patients were classified into six immune subtypes based on different molecular, cellular, and clinical characteristics. Patients with IS5 and IS6 tumors had an immune “hot” and immunosuppressive phenotype, which was associated with better survival compared to other subtypes, whereas patients with IS1-4 tumors had an immune “cold” phenotype, which was associated with a higher tumor mutation burden. In addition, the expression of immune checkpoints and immunogenic cell death modulators differed significantly in different immunosubtypes of tumors. Finally, the immune landscape of KIRC shows a high degree of heterogeneity across patients.ConclusionsLRP2 and FEM2 are potential KIRC antigens for mRNA vaccine development, and patients with immune subtypes IS1-4 are suitable for vaccination.
Detection ofRamularia collo-cygnifrom barley (Hordeum vulgare) in Australia using triplex quantitative and digital PCR
Authors: Knight N. L. , Moslemi A. , Begum F. , Dodhia K. N. , Covarelli L. , Hills A. L. , Lopez-Ruiz F. J. 
Published: July 2021

AbstractRamularia leaf spot (RLS), caused byRamularia collo-cygni, is an emerging threat to barley (Hordeum vulgare) production. RLS has been reported in Australia; however only minimal information is available regarding its detection and distribution. Due to initial asymptomatic growthin planta, slow growthin vitroand symptomatic similarities to net blotch and physiological leaf spots, detection of this pathogen can be challenging. Quantitative PCR-based methods forR. collo-cygni-specific identification and detection have been described, however these assays (based upon the internal transcribed spacer [ITS] region) have been demonstrated to lack specificity. False-positive detections may have serious implications, thus we aimed to design a robustR. collo-cygni-specific PCR method. Using the phylogenetically informative RNA polymerase II second largest subunit (rpb2) and translation elongation factor 1-α (tef1-α) genes, along with thetef1-αgene ofH. vulgare, a triplex assay was developed for both quantitative and digital PCR. The triplex assay was used to assess DNA of barley leaves from New South Wales, South Australia, Tasmania, Victoria and Western Australia, along with DNA of seeds from Western Australia. Detection ofR. collo-cygniDNA was confirmed for leaf samples from New South Wales, South Australia, Tasmania, Victoria and Western Australia, indicating a distribution ranging across the southern barley growing regions of Australia. NoR. collo-cygniDNA was detected in seed from Western Australia. TheR. collo-cygni-specific assay will be a valuable tool to assist with monitoring the distribution ofR. collo-cygniin Australia and other regions.
Selection drives the evolution of convergent gene expression changes during transitions to co-sexuality in haploid sexual systems
Authors: Cossard Guillaume G. , Godfroy Olivier , Nehr Zofia , Cruaud Corinne , Cock J. Mark , Lipinska Agnieszka , Coelho Susana M. 
Published: July 2021

AbstractCo-sexuality has evolved repeatedly from ancestors with separate sexes across a wide range of taxa. The switch to co-sexuality is expected to involve major molecular readjustments at the level of gene expression patterns, as modified males or females will express the opposite sexual function for which their phenotypes have been optimized. However, the molecular changes underpinning this important transition remain unknown, particularly in organisms with haploid sexual systems such as bryophytes, red and brown algae. Here, we explore four independent events of emergence of co-sexuality from uni-sexual (dioicous) ancestors in brown algal clades in order to examine the nature, evolution and degree of convergence of gene expression changes that accompany the breakdown of dioicy. The amount of male versus female phenotypic differences in dioicous species were not correlated with the extent of sex-biased gene expression, in strike contrast to what is observed in animals. Although sex-biased genes exhibited a high turnover rate during brown alga diversification, their predicted functions were remarkably conserved. Transition to co-sexuality consistently involved adaptive gene expression shifts and rapid sequence evolution, particularly of male-biased genes. The gene expression profiles of co-sexual species were more similar to those of females than to males of related dioicous species, suggesting that the former may have arisen from ancestral females. Finally, we identified extensive convergent gene expression changes associated with the transition to co-sexuality, and these changes appear to be driven by selection. Together, our observations provide novel insights on how co-sexual systems arise from ancestral, haploid UV sexual systems.
Topography-induced large-scale anti-parallel collective migration in vascular endothelium
Authors: Leclech Claire , Gonzalez-Rodriguez David , Villedieu Aurélien , Lok Thévy , Déplanche Anne-Marie , Barakat Abdul I 
Published: July 2021

AbstractCollective migration of vascular endothelial cells is central for embryonic development, angiogenesis, and wound closure. Although physical confinement of cell assemblies has been shown to elicit specific patterns of collective movement in various cell types, endothelial migration in vivo often occurs without confinement. Here we show that unconfined endothelial cell monolayers on microgrooved substrates that mimic the anisotropic organization of the extracellular matrix exhibit a new type of collective movement that takes the form of a periodic pattern of anti-parallel cell streams. We further establish that the development of these streams requires intact cell-cell junctions and that stream sizes are particularly sensitive to groove depth. Finally, we show that modeling the endothelial cell sheet as an active fluid with the microgrooves acting as constraints on cell orientation predicts the occurrence of the periodic anti-parallel cell streams as well as their lengths and widths. We posit that in unconfined cell assemblies, physical factors that constrain or bias cellular orientation such as anisotropic extracellular matrix cues or directed flow-derived shear forces dictate the pattern of collective cell movement.
Generation, quality control, and analysis of the first genomically humanised knock-in mice for the ALS/FTD genes SOD1, TARDBP (TDP-43), and FUS
Authors: Devoy Anny , Price Georgia , Giorgio Francesca De , Bunton-Stasyshyn Rosie , Thompson David , Gasco Samanta , Allan Alasdair , Codner Gemma F. , Nair Remya R. , Tibbit Charlotte , McLeod Ross , Ali Zeinab , Noda Judith , Marrero-Gagliardi Alessandro , Brito-Armas José M , Simon Michelle , O’Neill Edward , Harrison Jackie , Atkins Gemma , Corrochano Silvia , Stewart Michelle , Teboul Lydia , Acevedo-Arozena Abraham , Fisher Elizabeth M.C , Cunningham Thomas J. 
Published: July 2021

SUMMARYAmyotrophic lateral sclerosis - frontotemporal dementia spectrum disorder (ALS/FTD) is a complex neurodegenerative disease; up to 10% of cases are familial, usually arising from single dominant mutations in >30 causative genes. Transgenic mouse models that overexpress human ALS/FTD causative genes have been the preferred organism for in vivo modelling. However, while conferring human protein biochemistry, these overexpression models are not ideal for dosage-sensitive proteins such as TDP-43 or FUS.We have created three next-generation genomically humanised knock-in mouse models for ALS/FTD research, by replacing the entire mouse coding region of Sod1, Tardbp (TDP-43) and Fus, with their human orthologues to preserve human protein biochemistry, with exons and introns intact to enable future modelling of coding or non-coding mutations and variants and to preserve human splice variants. In generating these mice, we have established a new-standard of quality control: we demonstrate the utility of indirect capture for enrichment of a region of interest followed by Oxford Nanopore sequencing for robustly characterising large knock-in alleles. This approach confirmed that targeting occurred at the correct locus and to map homologous recombination events. Furthermore, extensive expression data from the three lines shows that homozygous humanised animals only express human protein, at endogenous levels. Characterisation of humanised FUS animals showed that they are phenotypically normal compared to wildtype littermates throughout their lifespan.These humanised mouse strains are critically needed for preclinical assessment of interventions, such as antisense oligonucleotides (ASOs), to modulate expression levels in patients, and will serve as templates for the addition of human ALS/FTD mutations to dissect disease pathomechanisms.
The Dilemma Of Disobedience: An ERP study
Authors: Fabre Eve F. , Causse Mickaël , Othon Maryel , Van Der Henst Jean-Baptiste 
Published: July 2021

AbstractThe present experiment aimed at investigating the decision-making and the associated event-related potentials (ERPs) of subordinates under hierarchical pressure. Participants (N = 33) acted as UAV operators and had to decide to crash their defective drone either on a civilian site killing all civilians present on the site or on a military site destroying military material but preventing any human losses. While in the no-command condition, participants decided according to their own preferences, in the command condition they were ordered to protect the military material at the expense of civilians for undisclosed strategic reasons. The results revealed that in the no-command condition participants almost always crashed the drone on the military site (96%), whereas in the command condition they chose to obey orders and sacrifice civilians to protect the military material 33% of the time. In the command condition, participants were longer to make their decisions, mobilizing greater attentional and cognitive resources (i.e., greater P300 responses) to resolve the conflict between their internal moral values and the orders they were given (i.e., greater N200 responses) than in the no-command condition, where they automatically applied the “you shall not kill” rule. Participants also showed a greater negative affective response (i.e., greater P260 amplitudes) after choosing to disobey than to obey orders. This result suggests that disobeying authority could be perceived as a greater moral violation than obeying and sacrificing civilians, suggesting that individuals may sometimes choose to obey malevolent authority to avoid the negative affective reaction triggered by disobedience.
Perceptions and beliefs influencing intention to use solar energy solutions in Zambian households
Authors: Zulu Sambo Lyson , Chabala Mwansa , Zulu Ephraim 
Published: July 2021

PurposeThe study examined perceptions and beliefs that influence the intention to adopt solar energy solutions in the Zambian Housing Sector. This is important because empirical evidence for measures aimed at improving the adoption of solar energy solutions with SSA in general or a Zambian context, in particular, are largely missing from the literature.Design/methodology/approachHierarchical multiple linear regression was used to analyse quantitative data collected through an online questionnaire survey. A total of 947 valid responses were obtained from a convenient sample of household heads.FindingsThe results show that attitude towards solar energy solutions, subjective norms, perceived benefits, perceived trust, knowledge about solar energy solutions, load-shedding and social norms, in that order of magnitude, influence the intention to adopt solar energy solutions. Perceived behavioural control, perceived risk and perceived cost did not influence the intention to adopt solar energy solutions.Originality/valueThe results provide empirical evidence of important factors to drive the adoption of solar energy solutions in Zambia. The results further show that knowledge about available solar energy solutions, rather than general knowledge about renewable energy, influence the adoption intention of solar energy solutions.
Does wage bonus positively impact the economy?
Authors: Le-Van Cuong , To-The Nguyen 
Published: July 2021

PurposeTotal factor productivity (TFP), for a country and for a firm as well, is a crucial element for economic growth by inducing high output. Actually, workers' effort is among the important factors that positively influence the TFP.Design/methodology/approachIn this paper, the authors assume that the wage bonus enhances the worker's effort. Wage bonus is an incentive mechanism and plays a role in the TFP as is shown in a recent paper by Le Van and Pham (2021). The firm will maximize its profits. The supplies of capital and workers are exogenous. At equilibrium, the authors obtain that wage bonus has positive effects on output, labor productivity and price of the output.FindingsThe wage bonus system can make the optimal sequence of outputs grow without bounds. And if the optimal sequence converges to a steady state, this one can be characterized by higher output per capita than that in the steady state without the bonus.Originality/valueIn particular, the result show if, thanks to the wage bonus externality effect, the production may become of increasing returns and if the incentive mechanism is very strong, any optimal path of physical capitals will converge to infinity.