bluuebunny/crossref_metadata_2025_split huggingface dataset:
A quantitative autonomous bioluminescence reporter system with a wide dynamic range for Plant Synthetic Biology
Authors: Calvache Camilo , Vazquez-Vilar Marta , Moreno-Giménez Elena , Orzaez Diego 
Published: February 2023

ABSTRACTEngineered autonomous bioluminescence (EAB) offers many potential applications in Plant Synthetic Biology, notably asin vivoreporter system. Current EAB reporter configurations are limited for quantitative applications due to low dynamic range. We reconfigured theNeonothopanus nambifungal bioluminescence (NeoLuc) pathway to serve as a high-throughput and inexpensive reporter for quantitative analysis of gene expression. We showed that by configuring the first committed step in the pathway (HispS) as the transcriptional entry point instead of the fungal luciferase, the dynamic range of the output increased dramatically, equaling that of the FLuc/RLuc reporter, and outperforming it in high throughput capacity. Furthermore, the inclusion of an enhanced GFP as normalizer allowed transient ratiometric measurements inN. benthamiana. Fast and rich datasets generated by the NeoLuc/eGFP system enabled us to undertake the optimization of new challenging synthetic gene circuits, including a complex agrochemical/optogenetic dual input switch for tight control of engineered metabolic pathways.
Predicting Individual Traits From T1-weighted Anatomical MRI Using the Xception CNN Architecture
Authors: Baratz Zvi , Assaf Yaniv 
Published: February 2023

AbstractModeling individual traits is a long-standing goal of neuroscientific research, as it allows us to gain a more profound understanding of the relationship between brain structure and individual variability. In this article, we used the Keras-Tuner library to evaluate the performance of a tuned Xception convolutional neural network (CNN) architecture in predicting sex and age from a sample of 4,049 T1-weighted anatomical MRI scans originating from 1,594 participants. In addition, we used the same tuning procedure to predict the big five inventory (BFI) personality traits for 415 participants (represented by 1,253 scans), and compared the results with those generated by applying transfer learning (TL) based on the models for sex and age. To minimize the effects of preprocessing procedures, scans were subjected exclusively to brain extraction and linear registration with the 2 mm MNI152 template. Our results suggest that CNNs trained with hyperparameter optimization could be used as an effective and accessible tool for predicting subject traits from anatomical MRI scans, and that TL shows potential for application across target domains. While BFI scores were not found not be predictable from T1-weighted scans, further research is required to assess other preprocessing and prediction workflows.
Near-atomic resolution reconstructions fromin siturevitrified cryo samples
Authors: Bongiovanni Gabriele , Harder Oliver F. , Voss Jonathan M. , Drabbels Marcel , Lorenz Ulrich J. 
Published: February 2023

AbstractWe have recently introduced a microsecond time-resolved version of cryo-electron microscopy (cryo-EM) to enable the observation of the fast conformational motions of proteins. Our technique involves locally melting a cryo sample with a laser beam to allow the proteins to undergo dynamics in liquid phase. When the laser is switched off, the sample cools within just a few microseconds and revitrifies, trapping particles in their transient configurations, in which they can subsequently be imaged. We have previously described two alternative implementations of the technique, using either an optical microscope or performing revitrification experimentsin situ. Here, we show that it is possible to obtain near-atomic resolution reconstructions fromin siturevitrified cryo samples. Moreover, the resulting map is indistinguishable from that obtained from a conventional sample within our spatial resolution. Interestingly, we observe that revitrification leads to a more homogeneous angular distribution of the particles, suggesting that revitrification may potentially be used to overcome issues of preferred particle orientation.SynopsisNear-atomic resolution reconstructions can be obtained fromin situmelted and revitrified cryo samples. Revitrification results in a more homogeneous angular distribution.
Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection
Authors: Illingworth Christopher J. R. , Guerra-Assuncao Jose A. , Gregg Samuel , Charles Oscar , Pang Juanita , Roy Sunando , Abdelnabi Rana , Neyts Johan , Breuer Judith 
Published: February 2023

AbstractMutagenic antiviral drugs have shown promising results against multiple viruses, yet concerns have been raised about whether their use might promote the emergence of new and harmful viral variants. Here, we examine the genetic consequences of effective and suboptimal dosing of favipiravir and molnupiravir in the treatment of SARS-CoV-2 infection in a hamster model. We identify a dose-dependent effect upon the mutational load in a viral population, with molnupiravir having a greater potency than favipiravir per mg/kg of treatment. The emergence of de novo variants was largely driven by stochastic processes, with evidence of compensatory adaptation but not of the emergence of drug resistance or novel immune phenotypes. Effective doses for favipiravir and molunpiravir correspond to similar levels of mutational load. Combining both drugs had an increased impact on both efficacy and mutational load. Our results suggest the potential for mutational load to provide a marker for clinical efficacy.
Human-aided dispersal and population bottlenecks facilitate parasitism escape in the most invasive mosquito species
Authors: Girard Maxime , Martin Edwige , Vallon Laurent , Van Van Tran , Carvalho Camille Da Silva , Sack Justine , Bontemps Zélia , BaltenNeck Julie , Colin Florence , Duval Pénélope , Malassigné Simon , Hennessee Ian , Vizcaino Lucrecia , Romer Yamila , Dada Nsa , Kim Khan Ly Huynh , Thuy Trang Huynh Thi , Bellet Christophe , Lambert Gregory , Raharimalala Fara Nantenaina , Jupatanakul Natapong , Goubert Clement , Boulesteix Matthieu , Mavingui Patrick , Desouhant Emmanuel , Luis Patricia , Cazabet Rémy , Hay Anne-Emmanuelle , Moro Claire Valiente , Minard Guillaume 
Published: February 2023

AbstractDuring biological invasion process, species encounter new environments and partially escape some ecological constraints they faced in their native range, while they face new ones. The Asian tiger mosquitoAedes albopictusis one of the most iconic invasive species introduced in every inhabited continent due to international trade. It has also been shown to be infected by a prevalent yet disregarded microbial entomoparasiteAscogregarina taiwanensis. In this study, we aimed at deciphering the factors that shape the global dynamics ofAs. taiwanensisinfection in naturalAe. albopictuspopulations. We showed thatAe. albopictuspopulations are highly colonized by several parasite genotypes but recently introduced ones are escaping it. We further performed experiments based on the invasion process to explain such pattern. To that end, we hypothesized that (i) mosquito passive dispersal (i.e.human-aided egg transportation) may affect the parasite infectiveness, (ii) founder effects (i.e.population establishment by a small number of mosquitoes) may influence the parasite dynamics and (iii) unparasitized mosquitoes are more prompt to found new populations through active flight dispersal. The two first hypotheses were supported as we showed that parasite infection decreases over time when dry eggs are stored and that experimental increase in mosquitoes’ density improves the parasite horizontal transmission to larvae. Surprisingly, parasitized mosquitoes tend to be more active than their unparasitized relatives. Finally, this study highlights the importance of global trade as a driver of biological invasion of the most invasive arthropod vector species.SignificanceGlobal trade expansion has facilitated the introduction of invasive species such as the Asian tiger mosquitoAedes albopictus. Eventually, invasive species might escape their natural enemies and this phenomenon exemplifies their invasion success. In this study, we combined field observations and laboratory experiments to decipher the ecological consequences of the invasion process on the interaction dynamics betweenAe. albopictusand its most prevalent natural parasiteAs. taiwanensis. We observed a decrease in parasitism in recently introduced populations and provide experimental evidence to explain how human-aided mosquito transportation and mosquito population bottlenecks were a burden for the parasite.
Pan-genotypic probe-based enrichment to improve efficiency of Hepatitis B virus sequencing
Authors: Lumley Sheila F , Jennings Daisy , Waddilove Elizabeth , Trebes Amy , Delphin Marion , Downs Louise O , MacIntyre-Cockett George , Wu Yanxia , Chaudron Sandra , de Lara Catherine , Chai Haiting , Maponga Tongai G , Martin Jacqueline , Collier Jane , Ip Camilla LC , Barnes Eleanor , Bonsall David , Piazza Paolo , Ansari M. Azim , Matthews Philippa C 
Published: February 2023

ABSTRACTHepatitis B Virus (HBV) genome sequencing can be used to provide more complete genetic information at the population and individual level to shed light on the limitations of current interventions, and inform new strategies for elimination. HBV sequencing is challenging due to the partially dsDNA genome, high diversity, low viral loads and presence of large amounts of host genetic material in clinical samples. Here we describe the design and use of a pan-genotypic panel of 74 HBV specific capture-probes and nuclease treatment in improving sequencing efficiency. We processed 20 plasma samples (viral loads 1.98 to 4.07 log10, genotypes A-E) and three positive controls (human total brain RNA and bacteriophage lambda DNA) in triplicate to compare DNAse vs. RNAse vs. no nuclease treatment. We prepared libraries using the Takara Bio SMARTer Stranded Total RNA-Seq Kit v3, split the library in two, enriching half with the custom-designed probe panel and xGen Hybridization and Wash Kit (IDT), the other half was not enriched. Both libraries were sequenced on the NovaSeq6000 platform with 2×150nt paired-end reads. Capture resulted in a 47,970 fold increase in the number of reads mapped to the HBV genome in the “no nuclease” arm (243 HBV reads per million reads sequenced in the capture pool vs. 5×10−3reads per million in the no-capture pool). Out of 20 samples, only 1 without capture generated HBV reads (viral load 3.89 log10IU/ml) vs. 19 samples with capture. HBV sequence yield was increased in the capture arm and resulted in 2.30 log10(95% confidence interval 1.99 - 2.48 log10) increase in HBV reads (per million reads sequenced) per log10increase in viral load. The proportion of HBV reads increased a median of 12 fold with RNAse treatment. We developed a targeted pan-genotypic sequencing method using a custom panel of biotinylated oligos that increases the sequencing efficacy of HBV. This method will allow us to gain a better insight into HBV diversity.
Synthetic cell armor made of DNA origami
Authors: Wang Weitao , Hayes Peter R. , Ren Xi , Taylor Rebecca E. 
Published: February 2023

AbstractTherapeutic and bioengineering applications of cells, such as cell printing and cell delivery, are directly limited by cell damage and death due to harsh mechanical conditions. Improved cellular robustness thus motivates investigations into cell encapsulation that provides essential protection. Here we target the cell-surface glycocalyx and crosslink two layers of DNA origami nanorods on the cellular plasma membrane to form a nanoscale protective shell. This modular and programmable approach enables fine control over the layering and composition of membrane-deposited nanorods. We show that the DNA origami nanoshell modulates the biophysical properties of cell membranes by enhancing membrane stiffness and lowering lipid fluidity. Moreover, the nanoshell serves as armor, protecting cells, limiting swelling and ultimately improving their viability against mechanical stress from osmotic imbalance and centrifugal forces. Our results demonstrate the potential of the nanoshell, not only as a cellular protection strategy, but also as a platform for manipulating and studying plasma membrane mechanics.
Integrating simultaneous motor imagery and spatial attention for EEG-BCI control
Authors: Forenzo Dylan , Liu Yixuan , Kim Jeehyun , Ding Yidan , Yoon Taehyung , He Bin 
Published: February 2023

AbstractObjective: EEG-based brain-computer interfaces (BCI) are non-invasive approaches for replacing or restoring motor functions in impaired patients, and direct brain-to-device communication in the general population. Motor imagery (MI) is one of the most used BCI paradigms, but its performance varies across individuals and certain users require substantial training to develop control. In this study, we propose to integrate a MI paradigm simultaneously with a recently proposed Overt Spatial Attention (OSA) paradigm, to accomplish BCI control. Methods: We evaluated a cohort of 25 human subjects’ ability to control a virtual cursor in one- and two-dimensions over 5 BCI sessions. The subjects used 5 different BCI paradigms: MI alone, OSA alone, MI and OSA simultaneously towards the same target (MI+OSA), and MI for one axis while OSA controls the other (MI/OSA and OSA/MI). Results: Our results show that MI+OSA reached the highest average online performance in 2D tasks at 49% Percent Valid Correct (PVC), statistically outperforms MI alone (42%), and was higher, but not statistically significant, than OSA alone (45%). MI+OSA had a similar performance to each subject’s best individual method between MI alone and OSA alone (50%) and 9 subjects reached their highest average BCI performance using MI+OSA. Conclusion: Integrating MI and OSA leads to improved performance over MI alone at the group level and is the best BCI paradigm option for some subjects. Significance: This work proposes a new BCI control paradigm that integrates two existing paradigms and demonstrates its value by showing that it can improve users’ BCI performance.
Establishing cordgrass plants cluster their shoots to avoid ecosystem engineering
Authors: van de Ven Clea N. , Reijers Valérie C. , Lammers Carlijn , van Belzen Jim , Chung Yeyeong , Bouma Tjeerd J. , van der Heide Tjisse 
Published: February 2023

Abstract

Vegetated coastal ecosystems such as salt marshes, dunes and seagrass meadows occur at the land–sea interface—a dynamic environment typified by harsh growing conditions. These ecosystems are known as biogeomorphic landscapes because their functioning depends on biophysical interactions by which organisms engineer landforms to their own benefit. The strength of such biogeomorphic feedbacks depends on plant traits, such as stem flexibility and shoot density.

Recent work demonstrated that dune grasses with similar morphological traits can build contrasting landscapes due to differences in their spatial shoot organization. However, in contrast to dune grasses that trap and stabilize sand particles in aeolian landscapes, flow attenuation in aquatic environments can generate scouring around plant stems and cause uprooting, leading to establishment thresholds for young plants.

Yet, it remains unknown how findings from aeolian landscapes translate to aquatic systems and how young clonally expanding plants in hydrodynamically exposed conditions overcome these establishment thresholds by optimizing shoot placement.

Here, we measured shoot patterns of 90 establishing cordgrass patches Spartina anglica at 18 European field sites that cover a broad range of hydrodynamic conditions. Next, we carried out a field experiment to investigate how observed spatial shoot patterns affect plant–sediment feedbacks.

Surprisingly, field survey analyses reveal highly consistent clustered shoot patterns, regardless of environmental conditions. Experimental results demonstrate that this clustered pattern minimizes scouring compared to densely clumped organizations typically observed in established patches.

Synthesis. In contrast to earlier findings highlighting that establishing dune grasses optimize their landscape engineering capacity via a flexible shoot placement strategy, we find that cordgrass instead follows a fixed strategy that minimizes engineering effects in its early life stages. We suggest that marsh grasses avoid physical stress and associated establishment thresholds in their early life stage, and switch to an ecosystem engineering strategy once established. These findings shed new light on how plant traits interact with their environment to shape the landscape and pave the way for improved restoration designs by mimicking the natural shoot organization of establishing vegetation.

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Impacts of the Ukraine–Russia Conflict on the Global Food Supply Chain and Building Future Resilience
Authors: Dyson Ellen , Helbig Rachel , Avermaete Tessa , Halliwell Kate , Calder Philip C. , Brown Lynn R. , Ingram John , Popping Bert , Verhagen Hans , Boobis Alan R. , Guelinckx Isabelle , Dye Louise , Boyle Neil 
Published: February 2023

SummaryThe reverberations of the Ukraine–Russia conflict have been keenly felt in 2022 as the impacts of Russia's invasion of Ukraine quickly cascaded across the globe, significantly exacerbating existing pressures on global systems. The vulnerabilities of the global food system have been particularly laid bare with significant disruptions to food and fertiliser supply chains instigating profound shocks on global food supply – disproportionately affecting poorer and vulnerable populations of the Global South. The immediate concerns and potential solutions to the global impacts of the Ukraine–Russia conflict were recently discussed by a panel of industry, academic and civil society experts convened by the European branch of the International Life Sciences Institute, all of whom are authors of this manuscript. The key concerns: the reduced affordability of food – focussing on those most vulnerable to its effects; the socio‐political implications of reduced food security; food safety; and nutrition security are all discussed in this Point de Vue. The authors voice the need for improved resilience to future shocks and stress on the food system.
Dasatinib, a selective tyrosine kinase inhibitor, prevents joint destruction in rheumatoid arthritis animal model
Authors: Min Hong Ki , Kim Se Hee , Won Ji‐Yeon , Kim Kyoung‐Woon , Lee Ji‐Yeon , Lee Sang‐Heon , Kim Hae‐Rim 
Published: February 2023

AbstractAimWe aimed to evaluate the preventive role of the tyrosine kinase inhibitor dasatinib in an animal model of rheumatoid arthritis (RA).MethodsDBA/1J mice were injected with bovine type II collagen to induce arthritis (collagen‐induced arthritis [CIA]). There were four experimental groups of mice, namely negative control (non‐CIA), vehicle‐treated CIA, dasatinib‐pretreated CIA, and dasatinib‐treated CIA. After collagen immunization, arthritis progression in the mice was clinically scored twice weekly for 5 weeks. Flow cytometry was used to evaluate in vitro CD4+T‐cell differentiation and ex vivo mast cell/CD4+T‐cell differentiation. Osteoclast formation was evaluated using tartrate‐resistant acid phosphatase (TRAP) staining and by estimating the resorption pit area.ResultsWe found that the clinical arthritis histological scores were lower in the dasatinib pretreatment group than in the vehicle and dasatinib post‐treatment groups. Flow cytometry showed that FcεR1+cells were downregulated and regulatory T cells were upregulated in splenocytes of the dasatinib pretreatment group compared with those in the vehicle group. Additionally, there was a decline in IL‐17+ CD4+T‐cell differentiation and an increase in CD4+ CD24high Foxp3+T‐cell differentiation with in vitro dasatinib treatment of human CD4+T cells. The number of TRAP+osteoclasts and the area of the resorption were decreased in the bone marrow cells derived from dasatinib‐pretreated mice compared with those derived from vehicle group.ConclusionDasatinib protected against arthritis in an animal model of RA by regulating the differentiation of regulatory T cells and IL‐17+ CD4+T cells and inhibiting osteoclastogenesis, indicating the therapeutic potential of dasatinib in the treatment of early RA.
Correlating variables with different scale types: A new framework based on matrix comparisons
Authors: Podani János , Schmera Dénes , Bagella Simonetta 
Published: February 2023

AbstractEcological variables may be expressed on four basic measurement scales (nominal, ordinal, interval or ratio), whereas circular variables and those combining a nominal state with other scale types are also common. However, existing methods are not suited to calculate correlations between all pairwise combinations of such variables, preventing the application of standard multivariate techniques.The essence of the new approach is to derive a so‐called difference semimatrix for all pairs of observations for each variable, and then to calculate the matrix correlation based on two such semimatrices. The advantage of this function, termedd‐correlation, is that comparisons are made on the same logical basis regardless of the measurement scale, allowing for the use of principal components analysis to visualize interrelationships among many variables simultaneously. Further advantages are that missing values in the data are tolerated and that the Gower index of dissimilarity between objects may also be computed.The use of the method is demonstrated on a small toy matrix, an artificial plant trait matrix and a large dataset summarizing ecological features of all vascular plant species of Sardinia, Italy. The source code in R and FORTRAN, and applications for three different operation systems, are provided for computations with results serving as input for other statistical software.The new computational framework will allow the comparison of any types of ecological traits in a mathematically meaningful manner. This option was not available earlier in the field of multivariate statistics, and the method is expected to receive applications in other subject areas as well in which many objects are described in terms of variables expressed on different measurement scales.