bluuebunny/crossref_metadata_2025_split huggingface dataset:
Do Neotropical adult dobsonflies (Megaloptera, Corydalidae) feed on solid material in the nature? Information from a gut content study
Authors: Álvarez Hugo Alejandro , de Figueroa José Manuel Tierno , Cebada-Ruiz Jorge Alejandro 
Published: April 2022

ABSTRACTFemales of two species of corydalids (Megaloptera),Corydalus magnusContreras-Ramos, 1998 andPlatyneuromus soror(Hagen, 1861), are studied with the aim to determine if solid food is present in their guts, which would indicate the existence of feeding on solid food during the imaginal life in nature. Gut anatomical architecture is also studied and described for females of both species, showing no peculiarities regarding the existing information in other close related species and confirming that digestive morphology is conserved in Megaloptera, as previously reported in literature. No significant solid food was detected in any of the species, so in the nature, they may rely more on liquid sources and/or fat reserves produced in the larval stage for the energetic requirements of adult life.
Estimation of microtubule-generated forces using a DNA origami nanospring
Authors: Maleki Ali Nick , Huis in’t Veld Pim J. , Akhmanova Anna , Dogterom Marileen , Volkov Vladimir A. 
Published: April 2022

AbstractMicrotubules are dynamic cytoskeletal filaments that can generate forces when polymerizing and depolymerizing. Proteins that follow growing or shortening microtubule ends and couple forces to cargo movement are important for a wide range of cellular processes. Quantifying these forces and the composition of protein complexes at dynamic microtubule ends is challenging and requires sophisticated instrumentation. Here we present an experimental approach to estimate microtubule-generated forces through the extension of a fluorescent spring-shaped DNA origami molecule. Optical readout of the spring extension enables recording of force production simultaneously with single-molecule fluorescence of proteins getting recruited to the site of force generation. DNA nanosprings enable multiplexing of force measurements and only require a fluorescence microscope and basic laboratory equipment. We validate the performance of DNA nanosprings against results obtained using optical trapping. Finally, we demonstrate the use of the nanospring to study proteins that couple microtubule growth and shortening to force generation.
Bats as ecosystem engineers in iron ore caves in the Carajás National Forest, Brazilian Amazonia
Authors: Piló Luis B. , Calux Allan , Scherer Rafael , Bernard Enrico 
Published: April 2022

AbstractEcosystem engineers are organisms able to modify their environment by changing the distribution of materials and energy, with effects on biotic and abiotic ecosystem components. Several ecosystem engineers are known, but for most of them the mechanisms behind their influence are poorly known. We detail the role of bats as ecosystem engineers in iron ore caves in the Carajás National Forest, Brazilian Amazonia, an area with > 1,500 caves, some holding ∼150,000 bats. We analyzed the chemical composition of guano deposits in bat caves, radiocarbon-dated those deposits, and elucidated the chemical mechanisms involved and the role the bat guano has on structuring those caves. The insect-composed guano was rich in organic matter, with high concentrations of carbon, nitrogen, phosphorus pentoxide and ferric oxide, plus potassium oxide, calcium and sulfur trioxide. Radiocarbon dating indicated guano deposits between 22,000 and 1,800 years old. The guano pH was mainly acid (from 2.1 to 5.6). Percolating waters in those bat caves were also acid (pH reaching 1.5), with the presence of phosphate, iron, calcium, nitrate and sulfate. Acid solutions due to guano decomposition and possible microbial activity produced various forms of corrosion on the caveś floor and walls, resulting in their enlargement. Caves with active or inactive bat colonies had, on average, horizontal projections 4.5 times larger, areas 4.4 times larger, and volumes 5.0 times bigger than the reginal average, plus more abundant, diversified and bigger speleothems. In an example of bioengineering, the long-term presence of bats (> 22,000 years) and the guano deposits they produce, mediated by biological and chemical interactions along millennia, resulted in very unique ecological, evolutionary and geomorphological processes, whose working are just beginning to be better understood by science. However, the current expansion of mineral activities coupled with the loosening of licensing and cave protection rules is a real conservation threat to the bat caves in Carajás. The destruction of those caves would represent and unacceptable loss of both speleological and biological heritage and we urge that, whenever they occur, bat caves and their colonies must be fully protected and left off-limits of mineral extraction.
The stoichiometric interaction model for mesoscopic molecular dynamics simulations of liquid-liquid phase separation
Authors: Murata Yutaka , Niina Toru , Takada Shoji 
Published: April 2022

ABSTRACTLiquid-liquid phase separation (LLPS) has received considerable attention in recent years for explaining the formation of cellular biomolecular condensates. The fluidity and the complexity of their components make molecular simulation approaches indispensable for gaining structural insights. Domain-resolution mesoscopic model simulations have been explored for case in which condensates are formed by multivalent proteins with tandem domains. One problem with this approach is that interdomain pairwise interactions cannot regulate the valency of the binding domains. To overcome this problem, we propose a new potential, the stoichiometric interaction (SI) potential. First, we verified that the SI potential maintained the valency of the interacting domains for the test systems. We then examined a well-studied LLPS model system containing tandem repeats of SH3 domains and proline-rich motifs. We found that the SI potential alone cannot reproduce the phase diagram of LLPS quantitatively. We had to combine the SI and a pairwise interaction; the former and the latter represent the specific and non-specific interactions, respectively. Biomolecular condensates with the mixed SI and pairwise interaction exhibited fluidity, whereas those with the pairwise interaction alone showed no detectable diffusion. We also compared the phase diagrams of the systems containing different numbers of tandem domains with those obtained from the experiments, and found quantitative agreement in all but one case.SIGNIFICANCECells organize their interior structures as not only membrane-bound organelles but also as membrane-less organelles. Membrane-less organelles, such as stress granules, Cajal bodies, and postsynaptic density, are biomolecular condensates in which many biomolecules are gathered owing to their interactions. In some cases, biomolecular condensates are formed by tandemly connected multidomain proteins. In such cases, a mesoscopic simulation model representing each domain as a particle is effective; however, the problem with this approach is that a domain-domain pairwise interaction cannot regulate the well-defined valency. To overcome this problem, in this study, we have developed a new potential, viz. the stoichiometric interaction potential, and confirmed that this potential can reproduce the liquid-liquid phase separation of multidomain proteins, a hallmark of the membrane-less organelles.
Deciphering the roadmap of in vivo reprogramming towards pluripotency
Authors: Chondronasiou Dafni , Martínez de Villareal Jaime , Melendez Elena , Lynch Cian J. , Kovatcheva Marta , Aguilera Mònica , Prats Neus , Real Francisco X. , Serrano Manuel 
Published: April 2022

SummaryDifferentiated cells can be converted to pluripotent stem cells (iPSCs) upon ectopic expression of transcription factors OCT4, SOX2, KLF4 and MYC (OSKM) in a process known as reprogramming. Great efforts have been made to dissect intermediate states of in vitro reprogramming and how they are affected by culture conditions, while the roadmap of in vivo reprogramming remains unexplored. Here, we use single cell RNA sequencing to capture cells undergoing reprogramming in the adult pancreas. We identify markers along the trajectory from acinar identity to pluripotency, which allow in situ visualization of the intermediate states of reprogramming. Importantly, different tissues expressing OSKM, such as pancreas, stomach and colon, share markers of intermediate reprogramming, suggesting a conserved in vivo reprogramming path. Our in vivo roadmap defines landmarks along in vivo reprogramming that could be useful for applications in tissue regeneration and cellular rejuvenation based on intermediate reprogramming states.
Vitis vinifera plants edited in DMR6 genes show improved resistance to downy mildew
Authors: Giacomelli Lisa , Zeilmaker Tieme , Scintilla Simone , Salvagnin Umberto , van der Voort Jeroen Rouppe , Moser Claudio 
Published: April 2022

ABSTRACTThe production and cultivation of vines (Vitis vinifera) tolerant or resistant to diseases such as downy mildew (DM) is a promising strategy to reduce fungicides and help viticulture sustainability. In many crops, generation of knock-out mutants in host genes controlling susceptibility to DM, such as Downy Mildew Resistant 6 (DMR6) is a strategy of proven success to obtain resistant plants, while the effect of mutations in DMR6 genes has yet to be demonstrated in grapevine. In addition, small mutations in genes governing important traits can be obtained by gene-editing while maintaining the genetic background of commercially important clones. Moreover, very recent advances in the technology of gene-editing allowed to produce non-transgenic grapevine mutants, by regeneration of protoplasts previously edited with the CRISPR-Cas9 ribonucleoprotein. This approach may revolutionize the production of new grapevine varieties and clones, but it requires knowledge on the targets, and an extensive evaluation of the impact of their mutation on plant phenotype and fitness. In this work we generated single and double knock-out mutants in DMR6 susceptibility (S) genes in multiple grapevine cultivars with improved resistance to DM.
Intercellular collectivity is governed by enzyme secretion strategies in marine polysaccharide degrading bacteria
Authors: D’Souza Glen , Ebrahimi Ali , Stubbusch Astrid , Daniels Michael , Keegstra Johannes , Stocker Roman , Cordero Otto , Ackermann Martin 
Published: April 2022

AbstractPolysaccharide breakdown by bacteria requires the activity of enzymes that degrade polymers extracellularly. This generates a localized pool of breakdown products that are accessible to the enzyme producers themselves as well as to other organisms. Marine bacterial taxa often show marked differences in the production and secretion of degradative enzymes that break down polysaccharides. These differences can have profound effects on the pool of diffusible breakdown products and hence on the ecological dynamics. However, the consequences of differences in enzymatic secretions on cellular growth dynamics and interactions are unclear. Here we combine experiments and models to study the growth dynamics of single cells within populations of marine Vibrionaceae strains that grow on the abundant marine polymer alginate, using microfluidics coupled to quantitative single-cell analysis and mathematical modelling. We find that strains that have low extracellular secretions of alginate lyases show stronger aggregative behaviors compared to strains that secrete high levels of enzymes. One plausible reason for this observation is that low secretors require a higher cellular density to achieve maximal growth rates in comparison with high secretors. Our findings indicate that increased aggregation increases intercellular synergy amongst cells of low-secreting strains. By mathematically modelling the impact of the level of degradative enzyme secretion on the rate of oligomer loss to diffusion, we find that enzymatic capability modulates the propensity of cells within clonal populations to cooperate or compete with each other. Our experiments and models demonstrate that marine bacteria display distinct aggregative behaviors and intercellular interactions based on their enzymatic secretion capabilities when growing on polysaccharides.
Predicting gene expression from cell morphology in human induced pluripotent stem cells
Authors: Wakui Takashi , Negishi Mitsuru , Murakami Yuta , Tominaga Shunsuke , Shiraishi Yasushi , Carpenter Anne E. , Singh Shantanu , Segawa Hideo 
Published: April 2022

AbstractPurification is essential before differentiating human induced pluripotent stem cells (hiPSCs) into cells that fully express particular differentiation marker genes. High-quality iPSC clones are typically purified through gene expression profiling or visual inspection of the cell morphology; however, the relationship between the two methods remains unclear. We investigated the relationship between gene expression levels and morphology by analyzing live-cell phase-contrast images and mRNA profiles collected during the purification process. We employed this data and an unsupervised image feature extraction method to build a model that predicts gene expression levels from morphology. As a benchmark, we confirmed that the method can predict the gene expression levels from tissue images for cancer genes, performing as well as state-of-the-art methods. We then applied the method to iPSCs and identified two genes that are well-predicted from cell morphology. Although strong batch effects resulting from the reprogramming process preclude the ability to use the same model to predict across batches, prediction within a reprogramming batch is sufficiently robust to provide a practical approach for estimating expression levels of a few genes and monitoring the purification process.
Motor outcomes congruent with intentions may sharpen metacognitive representations
Authors: Charalampaki Angeliki , Peters Caroline , Maurer Heiko , Maurer Lisa K. , Müller Hermann , Verrel Julius , Filevich Elisa 
Published: April 2022

AbstractWe can monitor our intentional movements, in order to describe how we move our bodies. But it is unclear which information this metacognitive monitoring relies on. For example, when throwing a ball to hit a target, we might use the visual information about how the ball flew to metacognitively assess our performance. Alternatively, we might disregard the ball trajectory — given that it is not directly relevant to our goal — and metacognitively assess our performance based solely on whether we reached the goal of hitting the target. In two experiments we aimed to distinguish between these two alternatives and asked whether the distal outcome of a goal-directed action (hitting or missing a target) informs the metacognitive representations of our own movements. Participants performed a semi-virtual task where they moved their arm to throw a virtual ball at a target. After each throw, participants discriminated which of two ball trajectories displayed on the screen corresponded to the flight path of their throw and then rated their confidence in this decision. The task included two conditions that differed on whether the distal outcome of the two trajectories shown matched (congruent) or differed (incongruent). Participants were significantly more accurate in discriminating between the two trajectories, and responded faster in theincongruentcondition and, accordingly, were significantly more confident on these trials. Crucially, we found significant differences in metacognitive performance (measured as meta-d’/d’) between the two conditions only on successful trials, where the virtual ball had hit the target. These results indicate that participants successfully incorporated information about the outcome of the movement into both their discrimination and confidence responses. However, information about the outcome selectively sharpened the precision of confidence ratings only when the outcome of their throw matched their intention. We argue that these findings underline the separation between the different levels of information that may contribute to body monitoring, and we provide evidence that intentions might play a central role in metacognitive motor representations.HighlightsParticipants threw a virtual ball to hit a targetFollowing their throw participants selected between two plausible trajectoriesOn half the trials, the two alternative trajectories differed in their distal outcome.Discrimination and confidence were higher in trials with different outcome.Metacognitive performance was best in hit trials when the alternative missed.
An intranasal stringent response vaccine targeting dendritic cells as a novel adjunctive therapy against tuberculosis
Authors: Karanika Styliani , Gordy James T. , Neupane Pranita , Karantanos Theodoros , Castillo Jennie Ruelas , Quijada Darla , Comstock Kaitlyn , Sandhu Avinaash Kaur , Hui Yinan , Ayeh Samuel K. , Tasneen Rokeya , Krug Stefanie , Danchik Carina , Wang Tianyin , Schill Courtney , Markham Rirchard B. , Karakousis Petros C. 
Published: April 2022

AbstractLengthy tuberculosis (TB) treatment is required to address the ability of a subpopulation of persistentMycobacterium tuberculosis(Mtb) to remain in a non-replicating, antibiotic-tolerant state characterized by metabolic remodeling, including induction of the RelMtb-mediated stringent response. We developed a novel therapeutic DNA vaccine construct involving fusion of therelMtbgene with the immature dendritic cell-targeting gene encoding chemokine MIP-3α/CCL20. To augment mucosal immune responses, intranasal delivery was also evaluated. We found that the intramuscularMIP-3α/relMtb(fusion) vaccine potentiates isoniazid activity more than a similar DNA vaccine expressingrelMtbalone in a chronic TB mouse model (absolute reduction ofMtbburden: 0.63 log10colony-forming units, P=0.0001), inducing pronouncedMtb-protective immune signatures. The intranasal fusion vaccine, an approach combiningrelMtbfusion to MIP-3α and intranasal delivery, demonstrated the greatest therapeutic effect compared to each approach alone, as evidenced by robust Th1 and Th17 responses systemically and locally and the greatest mycobactericidal activity when combined with isoniazid (absolute reduction ofMtbburden: 1.13 log10, P<0.0001, when compared to the intramuscular vaccine targetingrelMtbalone). This DNA vaccination strategy may be a promising adjunctive approach combined with standard therapy to shorten curative TB treatment, and also serve as proof-of-concept for treating other chronic infections.
Histone methyltransferase Ezh2 coordinates mammalian axon regeneration via epigenetic regulation of key regenerative pathways
Authors: Wang Xue-Wei , Yang Shu-Guang , Hu Ming-Wen , Wang Rui-Ying , Zhang Chi , Kosanam Anish R. , Ochuba Arinze J. , Jiang Jing-Jing , Luo Ximei , Qian Jiang , Liu Chang-Mei , Zhou Feng-Quan 
Published: April 2022

SummaryCurrent clinical treatment for neurodegenerative diseases and neural injuries falls short of success, and one primary reason is that neurons in the mammalian central nervous system (CNS) lose their regeneration ability as they mature. Previous studies indicated that the regeneration ability of neurons is governed by complex signaling networks involving many genes. Therefore, here we investigated the roles of Ezh2, a histone methyltransferase, in regulation of mammalian axon regeneration at the epigenetic level. We found that Ezh2 level was gradually downregulated in the mouse nervous system during maturation but significantly upregulated in mature sensory neurons during spontaneous axon regeneration in the peripheral nerve system (PNS), suggesting its role in supporting axon regeneration. Indeed, Ezh2 loss-of-function in sensory neurons impaired PNS axon regeneration in vitro and in vivo. In contrast, overexpression of Ezh2 in retinal ganglion cells in the CNS induced optic nerve regeneration after optic nerve injury in both methyltransferase-dependent and -independent manners. Mechanistic exploration with multiomics sequencing, together with functional analyses, revealed that Ezh2 supported axon regeneration by systematically silencing the transcription of genes regulating synaptic function and axon regeneration inhibitory signaling, while broadly activating factors promoting axon regeneration. Our study not only reveals that Ezh2 coordinates axon regeneration via epigenetically regulating multiple key regenerative pathways, but also suggests that modulating chromatin accessibility is a promising strategy to promote CNS axon regeneration.
Cluster selection for load balancing in flyingad hocnetworks using an optimal low-energy adaptive clustering hierarchy based on optimization approach
Authors: Sefati Seyed Salar , Halunga Simona , Farkhady Roya Zareh 
Published: April 2022

PurposeFlyingad hocnetworks (FANETs) have a major effect in various areas such as civil projects and smart cities. The facilities of installation and low cost of unmanned aerial vehicles (UAVs) have created a new challenge for researchers. Cluster head (CH) selection and load balancing between the CH are the most critical issues in the FANETs. For CH selection and load balancing in FANETs, this study used efficient clustering to address both problems and overcome these challenges. This paper aims to propose a novel CH selection and load balancing scheme to solve the low energy consumption and low latency in the FANET system.Design/methodology/approachThis paper tried to select the CH and load balancing with the help of low-energy adaptive clustering hierarchy (LEACH) algorithm and bat algorithm (BA). Load balancing and CH selection are NP-hard problems, so the metaheuristic algorithms can be the best answer for these issues. In the LEACH algorithm, UAVs randomly generate numerical, and these numbers are sorted according to those values. To use the load balancing, the threshold of CH has to be considered; if the threshold is less than 0.7, the BA starts working and begins to find new CH according to the emitted pulses.FindingsThe proposed method compares with three algorithms, called bio-inspired clustering scheme FANETs, Grey wolf optimization and ant colony optimization in the NS3 simulator. The proposed algorithm has a good efficiency with respect to the network lifetime, energy consumption and cluster building time.Originality/valueThis study aims to extend the UAV group control concepts to include CH selection and load balancing to improve UAV energy consumption and low latency.
Reputational risk on corporate corruption scandals: evidence from Latin America
Authors: Arbe Roby , Feria-Domínguez José Manuel 
Published: April 2022

PurposeThis paper evaluates how corruption scandals effects corporate reputational risk in main representatives Latin America listed companies. Efficient market hypothesis (EMH) on Standard and Poor’s index is also tried on.Design/methodology/approachFirst it is run a standard event study to evaluate the negative impact of such corruption episodes in terms of abnormal returns (ARs) and cumulative negative abnormal returns (CARs). Secondly, we use the operational loss derived from the corruption scandal divided by the stock's market capitalization (Loss Ratio) to estimate the reputational abnormal returns (RepARs) and its cumulative measure (RepCAR).FindingsIt is found that corporate reputation (CR) does not affect the stock market performance of the companies involved in the corruptions events, at least, in the very short term. The results show positives RepCARs due to still unknown losses of relative size of corruption after the announcement of the scandal, when the market shows greater sensitiveness.Practical implicationsThe behavior of the market on corruption scandals on the Latin American can let explore other options to limit bribery, and the study of this with a perspective of EMH is the significance of this paper.Social implicationsCorruption become major problems in recent years in Latin American and its implications on the stakeholders.Originality/valueObserving in the existing literature, there is no many studies based on the corruption scandals and market price using event methodology.