Swapping Events Research Articles

CDK4 is co-amplified with either TP53 promoter gene fusions or MDM2 through distinct mechanisms in osteosarcoma

Amplification of the MDM2 and CDK4 genes on chromosome 12 is commonly associated with low-grade osteosarcomas. In this study, we conducted high-resolution genomic and transcriptomic analyses on 33 samples from 25 osteosarcomas, encompassing both high- and low-grade cases with MDM2 and/or CDK4 amplification. We discerned four major subgroups, ranging from nearly intact genomes to heavily rearranged ones, each harbouring CDK4 and MDM2 amplification or CDK4 amplification with TP53 structural alterations. While amplicons involving MDM2 exhibited signs of an initial chromothripsis event, no evidence of chromothripsis was found in TP53-rearranged cases. Instead, the initial disruption of the TP53 locus led to co-amplification of the CDK4 locus. Additionally, we observed recurring promoter swapping events involving the regulatory regions of the FRS2, PLEKHA5, and TP53 genes. These events resulted in ectopic expression of partner genes, with the ELF1 gene being upregulated by the FRS2 and TP53 promoter regions in two distinct cases.

Exploring the role of community-based enterprises in consumers’ voluntary clothing disposition via UK swapping events using theory of social practice

Purpose This paper aims to explore consumers’ voluntary disposition practices through swapping events organised by community-based enterprises. The paper investigates consumers’ decision-making strategies and factors affecting voluntary clothing disposition via public swapping events across the UK. Design/methodology/approach This paper investigates UK swapping events, through conducting 18 semi-structured consumer interviews. Data were transcribed and analysed using the seven-step guide proposed by Easterby-Smith et al. (2018). Findings Findings indicate that within community-based enterprises an implicit social contract emerges between the enterprises and swappers which has an influence on the clothing brought to swaps, thereby impacting the competence and meaning elements of practice. This is linked to peer-pressure susceptibility which affects consumers’ participation in swapping. The findings further reveal an emerging consumer strategy aiding decision-making process regarding items brought to swaps. The use of a particular strategy is found to be linked with the respective level of swapping expertise. Research limitations/implications Though the interviews provide a rich narrative, this paper is limited by its sample size meaning data cannot be generalised. Although the data is limited by singular country perspective, research participants were recruited from across the UK, thus, offering a broad picture of the swapping practice. Originality/value This paper contributes to and advances an understanding of swapping events organised by community-based enterprises. The theory of social practice lens offers a unique viewpoint on the elements influencing the consumers’ decision-making process with reference to voluntary disposition.

Short-term electric vehicle battery swapping demand prediction: Deep learning methods

Battery swap stations have become an important alternative to general charging posts. Predicting battery swapping demand at the station level would be helpful for real-time operation of stations. This paper first provided insights into battery swapping demand patterns by analyzing a real-world dataset which contained 2,529 battery swapping events collected from 36 battery swap stations in Beijing from 31st July to 20th August 2019. Further, we developed a series of deep learning methods to predict the EV battery swapping demand, particularly considering temporal demand patterns obtained from the dataset. The deep learning models were Long Short-Term Memory, Bidirectional Long Short-Term Memory, Gated Recurrent Units, and Bidirectional Gated Recurrent Units. The results showed that the four deep learning models outperformed typical machine learning methods (e.g., support vector regression). An ablation study indicated that incorporating temporal battery swapping demand patterns into the deep learning methods could greatly improve model performance.

Birth Death Swap population in random environment and aggregation with two timescales

This paper deals with the stochastic modeling of a class of heterogeneous population in random environment, structured by discrete subgroups, and called birth–death–swap. In addition to demographic events modifying the population size, swap events, i.e. moves between subgroups, occur in the population. Event intensities are random functionals of the population. In the first part, we show that the complexity of the problem is significantly reduced by modeling the jump measure of the population as a multivariate counting process. This process is defined as the solution of a stochastic differential system with random coefficients, driven by a multivariate Poisson random measure. The solution is obtained under weak assumptions, by the thinning of a strongly dominating point process generated by the same Poisson measure. This key construction relies on a general strong comparison result, of independent interest.The second part is dedicated to averaging results when swap events are significantly more frequent than demographic events. An important ingredient is the stable convergence, which is well-adapted to the general random environment. The pathwise construction by domination yields tightness results straightforwardly. At the limit, the demographic intensity functionals are averaged against random kernels resulting from swap events. Finally, under a natural assumption, we show the convergence of the aggregated population to a birth–death process in random environment, with non-linear intensity functionals.

Staphylococcal Complement Evasion Protein Sbi Stabilises C3d Dimers by Inducing an N-Terminal Helix Swap.

Staphylococcus aureus is an opportunistic pathogen that is able to thwart an effective host immune response by producing a range of immune evasion molecules, including S. aureus binder of IgG (Sbi) which interacts directly with the central complement component C3, its fragments and associated regulators. Recently we reported the first structure of a disulfide-linked human C3d17C dimer and highlighted its potential role in modulating B-cell activation. Here we present an X-ray crystal structure of a disulfide-linked human C3d17C dimer, which undergoes a structurally stabilising N-terminal 3D domain swap when in complex with Sbi. These structural studies, in combination with circular dichroism and fluorescence spectroscopic analyses, reveal the mechanism underpinning this unique helix swap event and could explain the origins of a previously discovered N-terminally truncated C3dg dimer isolated from rat serum. Overall, our study unveils a novel staphylococcal complement evasion mechanism which enables the pathogen to harness the ability of dimeric C3d to modulate B-cell activation.

The Longitudinal Superdiffusive Motion of Block Copolymer in a Tight Nanopore.

The structure and dynamic properties of polymer chains in a confined environment were studied by means of the Monte Carlo method. The studied chains were represented by coarse-grained models and embedded into a simple 3D cubic lattice. The chains stood for two-block linear copolymers of different energy of bead–bead interactions. Their behavior was studied in a nanotube formed by four impenetrable surfaces. The long-time unidirectional motion of the chain in the tight nanopore was found to be correlated with the orientation of both parts of the copolymer along the length of the nanopore. A possible mechanism of the anomalous diffusion was proposed on the basis of thermodynamics of the system, more precisely on the free energy barrier of the swapping of positions of both parts of the chain and the impulse of temporary forces induced by variation of the chain conformation. The mean bead and the mass center autocorrelation functions were examined. While the former function behaves classically, the latter indicates the period of time of superdiffusive motion similar to the ballistic motion with the autocorrelation function scaling with the exponent t5/3. A distribution of periods of time of chain diffusion between swapping events was found and discussed. The influence of the nanotube width and the chain length on the polymer diffusivity was studied.

Systematic investigation of promoter substitutions resulting from somatic intrachromosomal structural alterations in diverse human cancers

One of the ways in which genes can become activated in tumors is by somatic structural genomic rearrangements leading to promoter swapping events, typically in the context of gene fusions that cause a weak promoter to be substituted for a strong promoter. While identifiable by whole genome sequencing, limited availability of this type of data has prohibited comprehensive study of the phenomenon. Here, we leveraged the fact that copy number alterations (CNAs) arise as a result of structural alterations in DNA, and that they may therefore be informative of gene rearrangements, to pinpoint recurrent promoter swapping at a previously intractable scale. CNA data from nearly 9500 human tumors was combined with transcriptomic sequencing data to identify several cases of recurrent activating intrachromosomal promoter substitution events, either involving proper gene fusions or juxtaposition of strong promoters to gene upstream regions. Our computational screen demonstrates that a combination of CNA and expression data can be useful for identifying novel fusion events with potential driver roles in large cancer cohorts.

Traces of cultural and personal values on sustainable consumption: An analysis of a small local swap event in Izmir, Turkey

AbstractA shift to the use of more eco‐friendly products and production methods is not sufficient to reverse the negative impacts of the Anthropocene period. Irrational overconsumption and production patterns should be abolished and redesigned to remain within the Earth's carrying capacity. Over‐consumption in Turkey is a part of the problem. At the juncture of Europe and Asia, Turkey has a wide variety of consumer behaviors, ranging from conservative habits to shopping sprees, especially with the rapid transition to an open economy in developing cities with contemporized lifestyles. On the one hand, consumption and material culture have quickly diffused among the younger population, who have an important share in the demographic structure and who adopt new information technologies and follow global trends. On the other hand, sharing and collaboration are core elements of the established culture. With that notion in mind, Karsiyaka municipality and the alternative education cooperation BBOM Izmir organized a swap event. The aim of the research, was to discover the views of participants on sustainability and swapping as an alternative collaborative consumption method. The results of the interviews and observations from the swap event revealed the traces of personal and cultural values on the participants' perspectives on sustainability concept and swapping. The results also showed correlations and differences with the literature. The perceptions and expectations of local consumers about swap and the concept of sustainability are mismatched with what we profoundly need for our goal of sustainability.

Machine learning and predicting the time-dependent dynamics of local yielding in dry foams

The authors use convolutional neural networks to extract information in neighbor swap events in sheared foams

Kinship identification based on rare severe variants from trio whole exome sequencing

Background: To automatic identify potential sample swaps or kinship label errors for inter-family or intra-family whole exome sequencing (WES) data, this study added a kinship quality control module to the current trio WES analysis pipeline. Methods: The study involved 105 trio WES, including 323 samples in total. The module used total variants data (total variants) or the rare, severe variants data during data processing (feature variants) to evaluate the similarity between samples. Then, the module identified different kinships based on sample similarity, including setting thresholds to distinguish related and non-related kinship and thresholds to reconstruct the level of kinship (first-, second-, and third-degree kinship). Results: Based on total variants, no clear threshold of sample similarity could be set to identify the kinship. In contrast, sample similarity scores based on feature variants could not only accurately identify whether there is relationship between samples, but also reconstruct the pedigree tree among samples. At last, the study simulated sample swap events for two trios to test whether feature variants could accurately identify the swapped samples. Conclusions: We developed a kinship quality control module into a pre-published NGS data processing pipeline (Fudan pipeline 2.0) to automate the identification of kinship or sample swap events.

Second-hand clothing acquisition: The motivations and barriers to clothing swaps for Chinese consumers

Textile wastes have been identified as a major threat to the environment, especially in China, which has the world’s largest population and where a large number of textile wastes are generated each year. Clothing swaps provide a way for consumers to extend the lifespan of their existing clothes by exchanging them with others, which also gives consumers a chance to find something different than their existing wardrobe and to have some fresh items. The purpose of this study is to identify the motivations and barriers to participating in clothing swaps for Chinese consumers and to discover whether the influential factors are different for attending swapping events versus swapping with familiar family members and friends. A sample of 321 Chinese men and women was collected through an online survey. The structural equation modeling (SEM) was utilized for data analysis, which illustrated that both social shopping value and perceived enjoyment have a positive influence on Chinese consumers’ intention to swap clothing items with family members or friends and to attend clothing swapping events; the results also confirmed the negative influences of performance risk and social risk on Chinese consumers’ intention to swap clothing items with family or friends. This study is the first attempt to investigate the relationships between shopping values and perceived risks with the intention to clothing swap among Chinese consumers. The study results are expected to provide in-depth insights to better understand Chinese consumers’ swapping behavior.

Swap-Driven Self-Adhesion and Healing of Vitrimers

Vitrimers are covalent network materials, comparable in structure to classical thermosets. Unlike normal thermosets, they possess a chemical bond swap mechanism that makes their structure dynamic and suitable for activated welding and even autonomous self-healing. The central question in designing such materials is the trade-off between autonomy and material stability: the swap mechanism facilitates the healing, but it also facilitates creep, which makes the perfectly stable self-healing solid a hard goal to reach. Here, we address this question for the case of self-healing vitrimers made from star polymers. Using coarse-grained molecular dynamics simulations, we studied the adhesion of two vitrimer samples and found that they bond together on timescales that are much shorter than the stress relaxation time. We showed that the swap mechanism allows the star polymers to diffuse through the material through coordinated swap events, but the healing process is much faster and does not depend on this mobility.

Planting the seeds of a quiet activism

While traditional academic accounts of activism emphasise vocal, antagonistic and demonstrative forms of protest, geographers have begun to expand the category of activism to include modest, quotidian acts of kindness, connection and creativity. This paper outlines ‘quiet activism’ as small, everyday, embodied acts, often of making and creating, that can be either implicitly or explicitly political in nature. This concept is explored with seed savers, gardeners who cultivate fruits and vegetables and then select and save seed to provide future generations of plants for themselves and others. It draws on ethnographic research with individuals involved in a national seed conservation network (The Heritage Seed Library) and a local seed swap event (Seedy Sunday, Brighton) in the UK. These organisations connect individual seed savers and frame their quiet acts of growing and sharing as part of a broad movement to conserve biodiversity and challenge the corporate control of food and seed systems. The paper unpicks the implications of embodied activisms performed at varying volumes, and it highlights the need for scholars to attend to the differing embodiments called for by various modes of activism in order to trace their particular impacts, emotions and affects. The experiences of seed savers elucidate the particular power of small and quiet acts of making and doing to critique, subvert and rework dominant modes of production and consumption.

Guaranteed Performance in the FRI Setting

Finite Rate of Innovation (FRI) sampling theory has shown that it is possible to sample and perfectly reconstruct classes of non-bandlimited signals such as streams of Diracs. In the case of noisy measurements, FRI methods achieve the optimal performance given by the Cramer-Rao bound up to a certain PSNR and breaks down for smaller PSNRs. To the best of our knowledge, the precise anticipation of the breakdown event in FRI settings is still an open problem. In this letter, we address this issue by investigating the subspace swap event which has been broadly recognised as the reason for performance breakdown in SVD-based parameter estimation algorithms. We work out at which noise level the absence of subspace swap is guaranteed and this gives us an accurate prediction of the breakdown PSNR which we also relate to the sampling rate and the distance between adjacent Diracs. Simulation results validate the reliability of our analysis.

Threshold Effects in Parameter Estimation From Compressed Data

In this paper, we investigate threshold effects associated with swapping of signal and noise subspaces in estimating signal parameters from compressed noisy data. The term threshold effect refers to a sharp departure of mean-squared error from the Cramer-Rao bound when the signal-to-noise ratio falls below a threshold SNR. In many cases, the threshold effect is caused by a subspace swap event, when the measured data (or its sample covariance) is better approximated by a subset of components of an orthogonal subspace than by the components of a signal subspace. We derive analytical lower bounds on the probability of a subspace swap in compressively measured noisy data. These bounds guide our understanding of threshold effects and performance breakdown for parameter estimation using compression. As a case study, we investigate threshold effects in maximum likelihood (ML) estimation of directions of arrival of two closely-spaced sources using co-prime subsampling. Our results show the impact of compression on threshold SNR. A rule of thumb is that every doubling of compression ratio brings a penalty in threshold SNR of 3 dB.

GRM1 is upregulated through gene fusion and promoter swapping in chondromyxoid fibroma

Glutamate receptors are well-known actors in the central and peripheral nervous systems, and altered glutamate signaling is implicated in several neurological and psychiatric disorders. It is increasingly recognized that such receptors may also have a role in tumor growth. Here we provide direct evidence of aberrant glutamate signaling in the development of a locally aggressive bone tumor, chondromyxoid fibroma (CMF). We subjected a series of CMFs to whole-genome mate-pair sequencing and RNA sequencing and found that the glutamate receptor gene GRM1 recombines with several partner genes through promoter swapping and gene fusion events. The GRM1 coding region remains intact, and 18 of 20 CMFs (90%) showed a more than 100-fold and up to 1,400-fold increase in GRM1 expression levels compared to control tissues. Our findings unequivocally demonstrate that direct targeting of GRM1 is a necessary and highly specific driver event for CMF development.

The Crystal Structure of Giardia duodenalis 14-3-3 in the Apo Form: When Protein Post-Translational Modifications Make the Difference

The 14-3-3s are a family of dimeric evolutionary conserved pSer/pThr binding proteins that play a key role in multiple biological processes by interacting with a plethora of client proteins. Giardia duodenalis is a flagellated protozoan that affects millions of people worldwide causing an acute and chronic diarrheal disease. The single giardial 14-3-3 isoform (g14-3-3), unique in the 14-3-3 family, needs the constitutive phosphorylation of Thr214 and the polyglycylation of its C-terminus to be fully functional in vivo. Alteration of the phosphorylation and polyglycylation status affects the parasite differentiation into the cyst stage. To further investigate the role of these post-translational modifications, the crystal structure of the g14-3-3 was solved in the unmodified apo form. Oligomers of g14-3-3 were observed due to domain swapping events at the protein C-terminus. The formation of filaments was supported by TEM. Mutational analysis, in combination with native PAGE and chemical cross-linking, proved that polyglycylation prevents oligomerization. In silico phosphorylation and molecular dynamics simulations supported a structural role for the phosphorylation of Thr214 in promoting target binding. Our findings highlight unique structural features of g14-3-3 opening novel perspectives on the evolutionary history of this protein family and envisaging the possibility to develop anti-giardial drugs targeting g14-3-3.

Photo-active and dynamical properties of hematite (Fe2O3)–water interfaces: an experimental and theoretical study

The dynamical properties of physically and chemically adsorbed water molecules at pristine hematite-(001) surfaces have been studied by means of equilibrium Born-Oppenheimer molecular dynamics (BOMD) in the NVT ensemble at 298 K. The dissociation of water molecules to form chemically adsorbed species was scrutinised, in addition to 'hopping' or swapping events of protons between water molecules. Particular foci have been dynamical properties of the adsorbed water molecules and OH(-) and H3O(+) ions, the hydrogen bonds between protons in water molecules and the bridging oxygen atoms at the hematite surface, as well as the interactions between oxygen atoms in adsorbed water molecules and iron atoms at the hematite surface. Experimental results for photoelectrical current generation complement simulation findings of water dissociation.

Metallothionein-protein interactions.

Metallothioneins (MTs) are a family of universal, small proteins, sharing a high cysteine content and an optimal capacity for metal ion coordination. They take part in a plethora of metal ion-related events (from detoxification to homeostasis, storage, and delivery), in a wide range of stress responses, and in different pathological processes (tumorigenesis, neurodegeneration, and inflammation). The information on both intracellular and extracellular interactions of MTs with other proteins is here comprehensively reviewed. In mammalian kidney, MT1/MT2 interact with megalin and related receptors, and with the transporter transthyretin. Most of the mammalian MT partners identified concern interactions with central nervous system (mainly brain) proteins, both through physical contact or metal exchange reactions. Physical interactions mainly involve neuronal secretion multimers. Regarding metal swap events, brain MT3 appears to control the metal ion load in peptides whose aggregation leads to neurodegenerative disorders, such as Aβ peptide, α-synuclein, and prion proteins (Alzheimer's and Parkinson's diseases, and spongiform encephalopathies, respectively). Interaction with ferritin and bovine serum albumin are also documented. The intercourse of MTs with zinc-dependent enzymes and transcription factors is capable to activate/deactivate them, thus conferring MTs the role of metabolic and gene expression regulators. As some of these proteins are involved in cell cycle and proliferation control (p53, nuclear factor κB, and PKCμ), they are considered in the context of oncogenesis and tumor progression. Only one non-mammalian MT interaction, involving Drosophila MtnA and MtnB major isoforms and peroxiredoxins, has been reported. The prospective use for biomedical applications of the MT-interaction information is finally discussed.

Structure‐based optimization of designed Armadillo‐repeat proteins

The armadillo domain is a right-handed super-helix of repeating units composed of three α-helices each. Armadillo repeat proteins (ArmRPs) are frequently involved in protein-protein interactions, and because of their modular recognition of extended peptide regions they can serve as templates for the design of artificial peptide binding scaffolds. On the basis of sequential and structural analyses, different consensus-designed ArmRPs were synthesized and show high thermodynamic stabilities, compared to naturally occurring ArmRPs. We determined the crystal structures of four full-consensus ArmRPs with three or four identical internal repeats and two different designs for the N- and C-caps. The crystal structures were refined at resolutions ranging from 1.80 to 2.50 Å for the above mentioned designs. A redesign of our initial caps was required to obtain well diffracting crystals. However, the structures with the redesigned caps caused domain swapping events between the N-caps. To prevent this domain swap, 9 and 6 point mutations were introduced in the N- and C-caps, respectively. Structural and biophysical analysis showed that this subsequent redesign of the N-cap prevented domain swapping and improved the thermodynamic stability of the proteins. We systematically investigated the best cap combinations. We conclude that designed ArmRPs with optimized caps are intrinsically stable and well-expressed monomeric proteins and that the high-resolution structures provide excellent structural templates for the continuation of the design of sequence-specific modular peptide recognition units based on armadillo repeats.