bluuebunny/crossref_metadata_2025_split huggingface dataset:
Frugivore gut passage increases seed germination: an updated meta-analysis
Authors: Rogers Haldre S. , Cavazos Brittany R. , Gawel Ann Marie , Karnish Alex , Ray Courtenay A. , Rose Ethan , Thierry Hugo , Fricke Evan C. 
Published: October 2021

ABSTRACTMany plants rely on animal mutualists for reproduction. Quantifying how animal mutualists impact plant performance provides a foundation for modelling how change in animal communities affects the composition and functioning of plant communities. We performed a meta-analysis of 2539 experiments, 6 times more than the last comprehensive meta-analysis, examining how gut passage by frugivores influences seed germination. We simultaneously analyzed multiple predictor variables related to study methodology, location, and frugivore identity to disentangle methodological from ecological impacts on effect sizes. We found that gut passage by birds, fish, reptiles, bats, primates, and other mammals on average increased seed germination, but that the magnitude varied across vertebrate groups. The positive effects of gut passage were largely explained by the de-inhibitory effects of pulp removal rather than by the scarification of seed tissues. Some previous studies and meta-analyses that found no effect of gut passage only tested scarification or did not distinguish between these tests of scarification and pulp removal. We found that, for a typical fleshy-fruited plant species, the lack of gut passage reduces germination by 60%. From an evolutionary perspective, this indicates a large risk associated with reliance on animal mutualists that is balanced against the benefits of animal-mediated seed dispersal. From a conservation perspective, this highlights the potential for large demographic consequences of frugivore declines on plant populations. Our database and findings advance quantitative predictions for the role of fruit-frugivore interactions in shaping plant communities in the Anthropocene.
Dynamic remodeling of ribosomes and endoplasmic reticulum in axon terminals of motoneurons
Authors: Deng Chunchu , Moradi Mehri , Reinhard Sebastian , Ji Changhe , Jablonka Sibylle , Hennlein Luisa , Lüningschrör Patrick , Doose Sören , Sauer Markus , Sendtner Michael 
Published: October 2021

AbstractIn neurons, endoplasmic reticulum forms a highly dynamic network that enters axons and presynaptic terminals and plays a central role in Ca2+ homeostasis and synapse maintenance. However, the underlying mechanisms involved in regulation of its dynamic remodeling as well as its function in axon development and presynaptic differentiation remain elusive. Here, we used high resolution microscopy and live cell imaging to investigate rapid movements of endoplasmic reticulum and ribosomes in axons of cultured motoneurons after stimulation with Brain-derived neurotrophic factor. Our results indicate that the endoplasmic reticulum extends into axonal growth cone filopodia where its integrity and dynamic remodeling are regulated mainly by actin and its motor protein myosin VI. Additionally, we found that in axonal growth cones, ribosomes assemble into 80S subunits within seconds and associate with ER in response to extracellular stimuli which describes a novel function of axonal ER in dynamic regulation of local translation.Summary statementIn axonal growth cones of motoneurons, dynamic remodeling of ER is coordinated through drebrin A-mediated actin and microtubule crosstalk and contributes to local translation as response to BDNF stimulation.
Social and asocial learning in zebrafish are encoded by a shared brain network that is differentially modulated by local activation
Authors: Pinho Júlia , Cunliffe Vincent , Petri Giovanni , Oliveira Rui F. 
Published: October 2021

AbstractGroup living animals can use social and asocial cues to predict the presence of a reward or a punishment in the environment through associative learning. The degree to which social and asocial learning share the same mechanisms is still a matter of debate, and, so far, studies investigating the neuronal basis of these two types of learning are scarce and have been restricted to primates, including humans, and rodents. Here we have used a Pavlovian fear conditioning paradigm in which a social (fish image) or an asocial (circle image) conditioned stimulus (CS) have been paired with an unconditioned stimulus (US=food), and we have used the expression of the immediate early gene c-fos to map the neural circuits associated with social and asocial learning. Our results show that the learning performance is similar with social (fish image) and asocial (circle image) CSs. However, the brain regions involved in each learning type are distinct. Social learning is associated with an increased expression of c-fos in olfactory bulbs, ventral zone of ventral telencephalic area, ventral habenula and ventromedial thalamus, whereas asocial learning is associated with a decreased expression of c-fos in dorsal habenula and anterior tubercular nucleus. Using egonetworks, we further show that each learning type has an associated pattern of functional connectivity across brain regions. Moreover, a community analysis of the network data reveals four segregated functional submodules, which seem to be associated with different cognitive functions involved in the learning tasks: a generalized attention module, a visual response module, a social stimulus integration module and a learning module. Together, these results suggest that, although there are localized differences in brain activity between social and asocial learning, the two learning types share a common learning module and social learning also recruits a specific social stimulus integration module. Therefore, our results support the occurrence of a common general-purpose learning module, that is differentially modulated by localized activation in social and asocial learning.
Modelling homing suppression gene drive in haplodiploid organisms
Authors: Liu Yiran , Champer Jackson 
Published: October 2021

AbstractGene drives have shown great promise for suppression of pest populations. These engineered alleles can function by a variety of mechanisms, but the most common is the CRISPR homing drive, which converts wild-type alleles to drive alleles in the germline of heterozygotes. Some potential target species are haplodiploid, in which males develop from unfertilized eggs and thus have only one copy of each chromosome. This prevents drive conversion, a substantial disadvantage compared to diploids where drive conversion can take place in both sexes. Here, we study homing suppression gene drives in haplodiploids and find that a drive targeting a female fertility gene could still be successful. However, such drives are less powerful than in diploids and suffer more from functional resistance alleles. They are substantially more vulnerable to high resistance allele formation in the embryo due to maternally deposited Cas9 and gRNA and also to somatic cleavage activity. Examining spatial models where organisms move over a continuous landscape, we find that haplodiploid suppression drives surprisingly perform nearly as well as in diploids, possibly due to their ability to spread further before inducing strong suppression. Together, these results indicate that gene drive can potentially be used to effectively suppress haplodiploid populations.
Mapping tumor spheroid mechanics in dependence of 3D microenvironment stiffness and degradability by Brillouin microscopy
Authors: Mahajan Vaibhav , Beck Timon , Gregorczyk Paulina , Ruland André , Alberti Simon , Guck Jochen , Werner Carsten , Schlüßler Raimund , Taubenberger Anna V. 
Published: October 2021

AbstractAltered biophysical properties of cancer cells and of their microenvironment contribute to cancer progression. While the relationship between microenvironmental stiffness and cancer cell mechanical properties and responses has been previously studied using two-dimensional (2D) systems, much less is known about it in a physiologically more relevant 3D context and in particular for multicellular systems. To investigate the influence of microenvironment stiffness on tumor spheroid mechanics, we first generated MCF-7 tumor spheroids within matrix metalloproteinase (MMP)-degradable 3D polyethylene glycol (PEG)-heparin hydrogels, where spheroids showed reduced growth in stiffer hydrogels. We then quantitatively mapped the mechanical properties of tumor spheroids in situ using Brillouin microscopy. Maps acquired for tumor spheroids grown within stiff hydrogels showed elevated Brillouin frequency shifts (hence increased longitudinal elastic moduli) with increasing hydrogel stiffness. Maps furthermore revealed spatial variations of the mechanical properties across the spheroids’ cross-sections. When hydrogel degradability was blocked, comparable Brillouin frequency shifts of the MCF-7 spheroids were found in both compliant and stiff hydrogels, along with similar levels of growth-induced compressive stress. Under low compressive stress, single cells or free multicellular aggregates showed consistently lower Brillouin frequency shifts compared to spheroids growing within hydrogels. Thus, the spheroids’ mechanical properties were modulated by matrix stiffness and degradability as well as multicellularity, and also to the associated level of compressive stress felt by tumor spheroids. Spheroids generated from a panel of invasive breast, prostate and pancreatic cancer cell lines within degradable stiff hydrogels, showed higher Brillouin frequency shifts and less cell invasion compared to those in compliant hydrogels. Taken together, our findings contribute to a better understanding of the interplay between cancer cells and microenvironment mechanics and degradability, which is relevant to better understand cancer progression.
From compartments to gene loops: Functions of the 3D genome in the human brain
Authors: Rahman Samir , Dong Pengfei , Apontes Pasha , Fernando Michael B. , Townsley Kayla G. , Girdhar Kiran , Bendl Jaroslav , Shao Zhiping , Misir Ruth , Tsankova Nadia , Kleopoulos Steven P. , Brennand Kristen J. , Fullard John F. , Roussos Panos 
Published: October 2021

AbstractThe 3D genome plays a key role in the regulation of gene expression. However, little is known about the spatiotemporal organization of chromatin during human brain development. We investigated the 3D genome in human fetal cortical plate and in adult prefrontal cortical neurons and glia. We found that neurons have weaker compartments than glia that emerge during fetal development. Furthermore, neurons form loop domains whereas glia form compartment domains. We show through CRISPRi on CNTNAP2 that transcription is coupled to loop domain insulation. Gene regulation during neural development involves increased use of enhancer-promoter and repressor-promoter loops. Finally, transcription is associated with gene loops. Altogether, we provide novel insights into the relationship between gene expression and different scales of chromatin organization in the human brain.
Deep learning models of cognitive processes constrained by human brain connectomes
Authors: Zhang Yu , Farrugia Nicolas , Bellec Pierre 
Published: October 2021

AbstractDecoding cognitive processes from recordings of brain activity has been an active topic in neuroscience research for decades. Traditional decoding studies focused on pattern classification in specific regions of interest and averaging brain activity over many trials. Recently, brain decoding with graph neural networks has been shown to scale at fine temporal resolution and on the full brain, achieving state-of-the-art performance on the human connectome project benchmark. The reason behind this success is likely the strong inductive connectome prior that enables the integration of distributed patterns of brain activity. Yet, the nature of such inductive bias is still poorly understood. In this work, we investigate the impact of the inclusion of multiple path lengths (through high-order graph convolution), the homogeneity of brain parcels (graph nodes), and the type of interactions (graph edges). We evaluate the decoding models on a large population of 1200 participants, under 21 different experimental conditions, acquired from the Human Connectome Project database. Our findings reveal that the optimal choice for large-scale cognitive decoding is to propagate neural dynamics within empirical functional connectomes and integrate brain dynamics using high-order graph convolutions. In this setting, the model exhibits high decoding accuracy and robustness against adversarial attacks on the graph architecture, including randomization in functional connectomes and lesions in targeted brain regions and networks. The trained model relies on biologically meaningful features for the prediction of cognitive states and generates task-specific graph representations resembling task-evoked activation maps. These results demonstrate that a full-brain integrative model is critical for the large-scale brain decoding. Our study establishes principles of how to effectively leverage human connectome constraints in deep graph neural networks, providing new avenues to study the neural substrates of human cognition at scale.
Single-cell transcriptomics reveals expression profiles of Trypanosoma brucei sexual stages
Authors: Howick Virginia M. , Peacock Lori , Kay Chris , Collett Clare , Gibson Wendy , Lawniczak Mara K.N. 
Published: October 2021

AbstractEarly diverging lineages such as trypanosomes can provide clues to the evolution of sexual reproduction in eukaryotes. In Trypanosoma brucei, the pathogen that causes Human African Trypanosomiasis, sexual reproduction occurs in the salivary glands of the insect host, but analysis of the molecular signatures that define these sexual forms is complicated because they mingle with more numerous, mitotically-dividing developmental stages. We used single-cell RNA-sequencing (scRNAseq) to profile 388 individual trypanosomes from midgut, proventriculus, and salivary glands of infected tsetse flies allowing us to identify tissue-specific cell types. Further investigation of salivary gland parasite transcriptomes revealed fine-scale changes in gene expression over a developmental progression from putative sexual forms through metacyclics expressing variant surface glycoprotein genes. The cluster of cells potentially containing sexual forms was characterized by high level transcription of the gamete fusion protein HAP2, together with an array of surface proteins and several genes of unknown function. We linked these expression patterns to distinct morphological forms using immunofluorescence assays and reporter gene expression to demonstrate that the kinetoplastid-conserved gene Tb927.10.12080 is exclusively expressed at high levels by meiotic intermediates and gametes. We speculate that this protein, currently of unknown function, plays a role in gamete formation and/or fusion.
Making Genomic Surveillance Deliver: A Lineage Classification and Nomenclature System to Inform Rabies Elimination
Authors: Campbell K. , Gifford R.J. , Singer J. , Hill V. , O’Toole A. , Rambaut A. , Hampson K. , Brunker K. 
Published: October 2021

AbstractThe availability of pathogen sequence data and use of genomic surveillance is rapidly increasing. Genomic tools and classification systems need updating to reflect this. Here, rabies virus is used as an example to showcase the potential value of updated genomic tools to enhance surveillance to better understand epidemiological dynamics and improve disease control. Previous studies have described the evolutionary history of rabies virus; however, the resulting taxonomy lacks the definition necessary to identify incursions, lineage turnover and transmission routes at high resolution. Here we propose a lineage classification system based on the dynamic nomenclature used for SARS-CoV-2, defining a lineage by phylogenetic methods, for tracking virus spread and comparing sequences across geographic areas. We demonstrate this system through application to the globally distributed Cosmopolitan clade of rabies virus, defining 73 total lineages within the clade, beyond the 22 previously reported. We further show how integration of this tool with a new rabies virus sequence data resource (RABV-GLUE) enables rapid application, for example, highlighting lineage dynamics relevant to control and elimination programmes, such as identifying importations and their sources, and areas of persistence and transmission, including transboundary incursions. This system and the tools developed should be useful for coordinating and targeting control programmes and monitoring progress as we work towards eliminating dog-mediated rabies, as well as having potential for broad application to the surveillance of other viruses.Author SummaryThe importance of the ability to track the diversity and spread of viruses in a universal way that can be clearly communicated has been highlighted during the SARS-CoV-2 pandemic. This, accompanied with the increase in the availability and use of pathogen sequence data, means the development of new genomic tools and classification systems can strengthen outbreak response and disease control. Here, we present an easy-to-use objective and transferable classification tool for tracking viruses at high resolution. We use rabies virus, a neglected zoonotic disease that causes around 59,000 human deaths each year, as an example use case of this tool. Applying our tool to a global clade of rabies virus, we find an over 200% increase in the definition at which we can classify the virus, allowing us to identify areas of persistence and transmission that were not previously apparent, and patterns of virus spread. Insights from the application of this tool should prove valuable in targeting vaccination campaigns and improving surveillance as countries work towards the elimination of dog-mediated rabies.
scINSIGHT for interpreting single-cell gene expression from biologically heterogeneous data
Authors: Qian Kun , Fu Shiwei , Li Hongwei , Li Wei Vivian 
Published: October 2021

AbstractThe increasing number of scRNA-seq data emphasizes the need for integrative analysis to interpret similarities and differences between single-cell samples. Even though different batch effect removal methods have been developed, none of the existing methods is suitable for het-erogeneous single-cell samples coming from multiple biological conditions. To address this challenge, we propose a method named scINSIGHT to learn coordinated gene expression patterns that are common among or specific to different biological conditions, offering a unique chance to identify cellular identities and key biological processes across single-cell samples. We have evaluated scINSIGHT in comparison with state-of-the-art methods using simulated and real data, which consistently demonstrate its improved performance. In addition, our results show the applicability of scINSIGHT in diverse biomedical and clinical problems.
In vivo mitochondrial matrix proteome profiling reveals RTN4IP1/OPA10 as an antioxidant NADPH oxidoreductase
Authors: Park Isaac , Kim Kwang-eun , Kim Jeesoo , Bae Subin , Jung Minkyo , Choi Jinhyuk , Kwak Chulhwan , Kang Myeong-Gyun , Yoo Chang-Mo , Mun Ji Young , Liu Kwang-Hyeon , Kim Jong-Seo , Suh Jae Myoung , Rhee Hyun-Woo 
Published: October 2021

AbstractTargeting proximity labeling enzymes to specific cellular locations is a viable strategy for profiling subcellular proteomes. Here, we generated transgenic mice expressing a mitochondrial matrix-targeted ascorbate peroxidase (MAX-Tg) to analyze tissue-specific matrix proteomes. Desthiobiotin-phenol labeling of muscle tissues from MAX-Tg mice allowed for efficient profiling of mitochondrial-localized proteins in these tissues. Comparative analysis of matrix proteomes from MAX-Tg muscle tissues revealed differential enrichment of mitochondrial proteins related to energy production in between different muscle groups. Reticulon 4 interacting protein 1 (RTN4IP1), also known as Optic Atrophy-10 (OPA10), was highly enriched in the cardiac and soleus muscles and was found to localize to the mitochondrial matrix via a strong mitochondrial targeting sequence at its N-terminus. Protein structure analysis revealed that RTN4IP1 is an NADPH oxidoreductase with structural homology to bacterial quinone oxidoreductase. Enzymatic activity assays, interactome analysis, and metabolite profiling confirmed a function for RTN4IP1 in coenzyme Q (CoQ) biosynthesis. Rtn4ip1-knockout C2C12 cells had reduced CoQ9 levels, were vulnerable to oxidative stress, and had decreased oxygen consumption rates and ATP production. Collectively, RTN4IP1 is a mitochondrial antioxidant NADPH oxidoreductase supporting oxidative phosphorylation activity in muscle tissue.
Solvability of nonlinear fractional integro-differential equation with nonlocal condition
Authors: Aicha Sakhri , Merad Ahcene 
Published: October 2021

PurposeThis study describes the applicability of the a priori estimate method on a nonlocal nonlinear fractional differential equation for which the weak solution's existence and uniqueness are proved. The authors divide the proof into two sections for the linear associated problem; the authors derive the a priori bound and demonstrate the operator range density that is generated. The authors solve the nonlinear problem by introducing an iterative process depending on the preceding results.Design/methodology/approachThe functional analysis method is the a priori estimate method or energy inequality method.FindingsThe results show the efficiency of a priori estimate method in the case of time-fractional order differential equations with nonlocal conditions. Our results also illustrate the existence and uniqueness of the continuous dependence of solutions on fractional order differential equations with nonlocal conditions.Research limitations/implicationsThe authors’ work can be considered a contribution to the development of the functional analysis method that is used to prove well-positioned problems with fractional order.Originality/valueThe authors confirm that this work is original and has not been published elsewhere, nor is it currently under consideration for publication elsewhere.
New success factors for construction projects: a systematic review of post-2004 literature
Authors: Charles Shawn H. , Chang-Richards Alice , Yiu (Kenneth) Tak Wing 
Published: October 2021

Purpose
The purpose of this study is to elicit the success factors from empirical evidence, as construction industry requires an improved understanding of factors for managing projects to positive outcomes. Increased stakeholder involvement, including the new technologies, achieving sustainability and safeguarding health and safety, whilst at the same time facing uncertainties, it is crucial to examine whether there are new factors that drive construction projects to succeed, especially from a value-driven perspective.

Design/methodology/approach
Using a systematic review approach, this research reviewed 172 studies published after 2004. When compared to a comprehensive project success factor framework presented by Chan et al. in 2004, 19 factors are considered new since 2004.

Findings
Though several scholarly outputs highlighted significant improvements to project operations and innovations in equipment and techniques, there has not been a comprehensive oversight since Chan’s et al. (2004) conceptual framework. This paper investigates 16 years of industry changes and identified two new success factors categories (innovation and sustainability) and 19 new factors that add to Chan’s et al. (2004) study. Consequently, a new framework of factors affecting project success was developed.

Originality/value
This paper was very specific in its attempt to find the new and additional success factors for managing construction projects. A new conceptual framework, which includes the newly identified factors, was then developed that will create a greater awareness of stakeholders’ concerns and ultimately contribute to significant improvement in developing project objectives and defining success measures.