bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aneuploidy tolerance caused by BRG1 loss allows chromosome gains and recovery of fitness
Authors: Schiavoni Federica , Zuazua-Villar Pedro , Roumeliotis Theodoros I. , Benstead-Hume Graeme , Pardo Mercedes , Pearl Frances M. G. , Choudhary Jyoti S. , Downs Jessica A. 
Published: April 2022

AbstractAneuploidy results in decreased cellular fitness in many species and model systems. However, aneuploidy is commonly found in cancer cells and often correlates with aggressive growth, suggesting that the impact of aneuploidy on cellular fitness is context dependent. The BRG1 (SMARCA4) subunit of the SWI/SNF chromatin remodelling complex is frequently lost in cancer. Here, we use a chromosomally stable cell line to test the effect of BRG1 loss on the evolution of aneuploidy. BRG1 deletion leads to an initial loss of fitness in this cell line that improves over time. Notably, we find increased tolerance to aneuploidy immediately upon loss of BRG1, and the fitness recovery over time correlates with chromosome gain. These data show that BRG1 loss creates an environment where karyotype changes can be explored without a fitness penalty. At least in some genetic backgrounds, therefore, BRG1 loss can affect the progression of tumourigenesis through tolerance of aneuploidy.
Bridging the gap between atomically thin semiconductors and metal leads
Authors: Cai Xiangbin , Wu Zefei , Han Xu , Chen Yong , Xu Shuigang , Lin Jiangxiazi , Han Tianyi , He Pingge , Feng Xuemeng , An Liheng , Shi Run , Wang Jingwei , Ying Zhehan , Cai Yuan , Hua Mengyuan , Liu Junwei , Pan Ding , Cheng Chun , Wang Ning 
Published: April 2022

AbstractElectrically interfacing atomically thin transition metal dichalcogenide semiconductors (TMDSCs) with metal leads is challenging because of undesired interface barriers, which have drastically constrained the electrical performance of TMDSC devices for exploring their unconventional physical properties and realizing potential electronic applications. Here we demonstrate a strategy to achieve nearly barrier-free electrical contacts with few-layer TMDSCs by engineering interfacial bonding distortion. The carrier-injection efficiency of such electrical junction is substantially increased with robust ohmic behaviors from room to cryogenic temperatures. The performance enhancements of TMDSC field-effect transistors are well reflected by the low contact resistance (down to 90 Ωµm in MoS2, towards the quantum limit), the high field-effect mobility (up to 358,000 cm2V−1s−1 in WSe2), and the prominent transport characteristics at cryogenic temperatures. This method also offers possibilities of the local manipulation of atomic structures and electronic properties for TMDSC device design.
Enantioselective functionalization at the C4 position of pyridinium salts through NHC catalysis
Authors: Choi Hangyeol , Mathi Gangadhar Rao , Hong Seonghyeok , Hong Sungwoo 
Published: April 2022

AbstractA catalytic method for the enantioselective and C4-selective functionalization of pyridine derivatives is yet to be developed. Herein, we report an efficient method for the asymmetric β-pyridylations of enals that involve N-heterocyclic carbene (NHC) catalysis with excellent control over enantioselectivity and pyridyl C4-selectivity. The key strategy for precise stereocontrol involves enhancing interactions between the chiral NHC-bound homoenolate and pyridinium salt in the presence of hexafluorobenzene, which effectively differentiates the two faces of the homoenolate radical. Room temperature is sufficient for this transformation, and reaction efficiency is further accelerated by photo-mediation. This methodology exhibits broad functional group tolerance and enables facile access to a diverse range of enantioenriched β-pyridyl carbonyl compounds under mild and metal-free conditions.
Morphological evolution of creek networks in 10 restored coastal wetlands in the UK
Authors: Chirol C. , Haigh I. D. , Pontee N. , Thompson C. E. L , Gallop S. L. 
Published: April 2022

AbstractCoastal wetlands provide crucial ecosystem services including flood protection and carbon storage, but are being lost rapidly worldwide to the combined effects of sea-level rise, erosion and coastal urbanisation. Managed Realignment (MR) aims to mitigate for these losses by restoring reclaimed land to tidal influence. Data of creek evolution is critical to assess the performance of design strategies and improve design and implementation practices. This data descriptor provides a dataset of the horizontal morphological evolution of creek systems from various initial conditions in 10 MR schemes across the UK. Using a semi-automated workflow, morphological creek parameters were extracted from 52 lidar datasets at 1 m horizontal resolution spanning 2 to 20 years post-breach. This constitutes the most comprehensive systematic monitoring of MR creek morphology to date. The dataset will assist future MR design and provide baseline morphological information for ecological and biogeochemical surveying.
Association of comorbidities and medications with risk of asthma exacerbation in pediatric patients: a retrospective study using Japanese claims data
Authors: Maeda Shotaro , Kobayashi Shigetoshi , Takahashi Kenzo , Miyata Satoshi 
Published: April 2022

AbstractAsthma exacerbation impairs the quality of life of pediatric patients and negatively impacts future respiratory function and health economics. Several risk factors associated with exacerbations have been identified; however, most studies report the risk of each factor. Therefore, this study aimed to evaluate the risk of each factor and a combination of factors. We performed a retrospective cohort study using Japanese claims data and extracted factors associated with exacerbations using multivariate Cox proportional hazards regression and stepwise method. Risk scores were then calculated from the extracted factors and validated by tenfold cross validation. Of the 1,748,111 asthma patients in the database, the data of 14,980 were extracted, and 1988 (13.3%) had exacerbation. Factors associated with asthma exacerbation were age of 3–5 years, exacerbation history before cohort entry date, allergic rhinitis, chronic sinusitis, otitis externa, blepharitis, upper respiratory infections, urticaria, LTRA prescription, were determined. A four-level risk score was calculated from 9-factors and the AUC derived from cross validation was 0.700. Most factors extracted in our study are consistent with those of previous studies. We showed that combining each factor is more helpful in assessing the increased risk of asthma exacerbation than assessing each factor alone.
Metabonomics analysis of flavonoids in seeds and sprouts of two Chinese soybean cultivars
Authors: Bi Weiwei , Zhao Guixing , Zhou Yutong , Xia Xiaoyu , Wang Jinsheng , Wang Guangjin , Lu Shuwen , He Wenjin , Bi Taifei , Li Jinrong 
Published: April 2022

AbstractA popular food in China, soybean seeds and sprouts contained many biologically active substances which are beneficial to the human body, such as flavonoids. Northeast of China is the main producing area of soybean. The experimental materials came from the main soybean producing areas in Northeast China, this study compared flavonoids of two China cultivars of soybeans, Heinong52(HN52) and Heinong71(HN71). Here, we also considered the effects of germination on the chemical profile of flavonoids. Using a LC–ESI–MS/MS system, 114 differential flavonoid metabolites were identified. A total of 18 metabolites were significantly different between the two soybean varieties before germination, of which 14 were up-regulated and 4 were down-regulated. After germination, 33 significantly different metabolites were found in the two soybean sprouts, of which 19 were up-regulated and 14 were down-regulated. These experimental results revealed significant up-regulation of metabolites in soybean sprouts compared with soybean seeds, thus suggesting that soybean germination may increase content of flavonoid metabolites. There are six main pathways for the synthesis of flavonoids: isoflavonoid biosynthesis, flavonoid biosynthesis, flavone and flavonol biosynthesis, biosynthesis of secondary metabolites, and biosynthesis of phenylpropanoids. Soybean seeds lack flavone and flavanol biosynthesis and develop the capacity for this biosynthetic pathway after germination as sprouts. Isoflavonoid biosynthesis is the most abundantly utilized pathway.
Exploring the performances of the vibrating barriers for the seismic protection of the Zoser pyramid
Authors: Cacciola P. , Shadlou M. , Ayoub A. , Rashed Y. F. , Tombari A. 
Published: April 2022

AbstractIn this paper we aim to investigate the use of the Vibrating Barrier (ViBa) as a potential strategy to mitigate the effects of the seismic action on the Zoser Pyramid. The Vibrating Barrier is a structure buried in the soil that is able to absorb a significant portion of the dynamic energy arising from the ground motion. The working principle exploits the dynamic interaction among vibrating structures resting on a compliant semi-infinite space, namely the structure–soil–structure interaction. A reliable numerical simulation of the Zoser Pyramid and the surrounding soil undergoing stochastic ground motion excitations representing the seismicity in Saqqara is presented. Due to the unique structural form, the ViBa is herein optimized through an ad-hoc procedure to minimize a response strain energy spectral density used as a synthetic performance parameter. Various layouts of the ViBa have been considered and presented in the paper. The efficiency of the ViBa is assessed by numerical simulation of the finite element model of the ViBa-Soil-Pyramid system and by laboratory testing. Results from a pertinent Monte Carlo study show an evident reduction of the stresses in the Pyramid manifesting the feasibility of this novel strategy to protect historic structures from earthquake-induced ground motion. Experimental results on a 1:500 gelatine model of the pyramid and the surrounding area highlighted the efficiency and efficacy of the proposed approach.
Equivalency of four research-grade movement sensors to assess movement behaviors and its implications for population surveillance
Authors: Migueles Jairo H. , Molina-Garcia Pablo , Torres-Lopez Lucia V. , Cadenas-Sanchez Cristina , Rowlands Alex V. , Ebner-Priemer Ulrich W. , Koch Elena D. , Reif Andreas , Ortega Francisco B. 
Published: April 2022

Abstract the benefits of physical activity (PA) and sleep for health, accurate and objective population-based surveillance is important. Monitor-based surveillance has potential, but the main challenge is the need for replicable outcomes from different monitors. This study investigated the agreement of movement behavior outcomes assessed with four research-grade activity monitors (i.e., Movisens Move4, ActiGraph GT3X+, GENEActiv, and Axivity AX3) in adults. Twenty-three participants wore four monitors on the non-dominant wrist simultaneously for seven days. Open-source software (GGIR) was used to estimate the daily time in sedentary, light, moderate-to-vigorous PA (MVPA), and sleep (movement behaviors). The prevalence of participants meeting the PA and sleep recommendations were calculated from each monitor’s data. Outcomes were deemed equivalent between monitors if the absolute standardized difference and its 95% confidence intervals (CI95%) fell within ± 0.2 standard deviations (SD) of the mean of the differences. The participants were mostly men (n = 14, 61%) and aged 36 (SD = 14) years. Pairwise confusion matrices showed that 83–87% of the daily time was equally classified into the movement categories by the different pairs of monitors. The between-monitor difference in MVPA ranged from 1 (CI95%: − 6, 7) to 8 (CI95%: 1, 15) min/day. Most of the PA and sleep metrics could be considered equivalent. The prevalence of participants meeting the PA and the sleep guidelines was 100% consistent across monitors (22 and 5 participants out of the 23, respectively). Our findings indicate that the various research-grade activity monitors investigated show high inter-instrument reliability with respect to sedentary, PA and sleep-related estimates when their raw data are processed in an identical manner. These findings may have important implications for advancement towards monitor-based PA and sleep surveillance systems.
Early Triassic ichthyopterygian fossils from the Russian Far East
Authors: Nakajima Yasuhisa , Shigeta Yasunari , Houssaye Alexandra , Zakharov Yuri D. , Popov Alexander M. , Sander P. Martin 
Published: April 2022

AbstractIchthyopterygia is a major clade of reptiles that colonized the ocean after the end-Permian mass extinction, with the oldest fossil records found in early Spathian substage (late Olenekian, late Early Triassic) strata in the western USA. Here, we describe reptilian remains found in situ in the early Spathian Neocolumbites insignis ammonoid zone of South Primorye in the Russian Far East. Specimen NSM PV 23854 comprises fragmentary axial elements exhibiting a combination of morphological characteristics typical of Ichthyopterygia. The cylindrical centra suggest that the specimen represents a basal ichthyopterygian, and its size is comparable to that of Utatsusaurus. Specimen NSM PV 24995 is represented by a single limb bone, which is tentatively identified as an ichthyopterygian humerus. With a body length of approximately 5 m estimated from the humeral length, NSM PV 24995 represents one of the largest specimens of early Spathian marine reptiles known to date. Such size variation among the earliest ichthyopterygians might suggest an explosive diversification in size immediately after the end-Permian mass extinction. Both vertebrae and humerus specimens exhibit an extremely cancellous inner structure, suggesting a high degree of aquatic adaptation in ichthyopterygians, despite their short history of evolution in the ocean.
Cryogenic TEM imaging of artificial light harvesting complexes outside equilibrium
Authors: Krishnaswamy Sundar Raj , Gabrovski Ivo A. , Patmanidis Ilias , Stuart Marc C. A. , de Vries Alex H. , Pshenichnikov Maxim S. 
Published: April 2022

AbstractThe energy transport in natural light-harvesting complexes can be explored in laboratory conditions via self-assembled supramolecular structures. One such structure arises from the amphiphilic dye C8S3 molecules, which self-assemble in an aqueous medium to a double-wall cylindrical nanotube reminiscent of natural light-harvesting complexes found in green sulphur bacteria. In this paper, we report a way to investigate the structure of inner nanotubes (NTs) alone by dissolving the outer NTs in a microfluidic setting. The resulting thermodynamically unstable system was rapidly frozen, preventing the reassembly of the outer NT from the dissolved molecules, and imaged using cryogenic transmission electron microscopy (cryo-TEM). The experimental cryo-TEM images and the molecular structure were compared by simulating high-resolution TEM images, which were based on the molecular modelling of C8S3 NTs. We found that the inner NT with outer walls removed during the flash-dilution process had a similar size to the parent double-walled NTs. Moreover, no structural inhomogeneity was observed in the inner NT after flash-dilution. This opens up exciting possibilities for functionalisation of inner NTs before the reassembly of the outer NT occurs, which can be broadly extended to modify the intra-architecture of other self-assembled nanostructures.
Direct and latent effects of ocean acidification on the transition of a sea urchin from planktonic larva to benthic juvenile
Authors: Dorey Narimane , Butera Emanuela , Espinel-Velasco Nadjejda , Dupont Sam 
Published: April 2022

AbstractOngoing ocean acidification is expected to affect marine organisms and ecosystems. While sea urchins can tolerate a wide range of pH, this comes at a high energetic cost, and early life stages are particularly vulnerable. Information on how ocean acidification affects transitions between life-history stages is scarce. We evaluated the direct and indirect effects of pH (pHT8.0, 7.6 and 7.2) on the development and transition between life-history stages of the sea urchinStrongylocentrotusdroebachiensis,from fertilization to early juvenile. Continuous exposure to low pH negatively affected larval mortality and growth. At pH 7.2, formation of the rudiment (the primordial juvenile) was delayed by two days. Larvae raised at pH 8.0 and transferred to 7.2 after competency had mortality rates five to six times lower than those kept at 8.0, indicating that pH also has a direct effect on older, competent larvae. Latent effects were visible on the larvae raised at pH 7.6: they were more successful in settling (45% at day 40 post-fertilization) and metamorphosing (30%) than larvae raised at 8.0 (17 and 1% respectively). These direct and indirect effects of ocean acidification on settlement and metamorphosis have important implications for population survival.
A multi-omics approach to elucidate the mechanisms of action of a dietary muramidase administered to broiler chickens
Authors: Brugaletta Giorgio , De Cesare Alessandra , Laghi Luca , Manfreda Gerardo , Zampiga Marco , Oliveri Chiara , Pérez-Calvo Estefanía , Litta Gilberto , Lolli Susanna , Sirri Federico 
Published: April 2022

AbstractA novel dietary muramidase has been shown to have positive effects on broiler chickens. However, very little is known about its mechanisms of action. The present multi-omics investigation sought to address this knowledge gap. A total of 2,340 day-old male broilers were assigned to 3 groups (12 replicates each) fed, from 0 to 42 d, a basal diet (control group—CON) or the basal diet supplemented with muramidase at 25,000 (low-dose group—MUL) or 45,000 LSU(F)/kg feed (high-dose group—MUH). MUH significantly outperformed CON in terms of cumulative feed intake (4,798vs4,705 g), body weight (2,906vs2,775 g), and feed conversion ratio (1.686vs1.729), while MUL exhibited intermediate performance. At caecal level, MUH showed the lowest alpha diversity, a significantly different beta diversity, a reduction in Firmicutes, and a rise in Bacteroidetes, especially compared with MUL. MUH also exhibited a considerable decrease in Clostridiaceae and an overrepresentation of Bacteroidaceae and Lactobacillaceae. At blood level, MUH had lower hypoxanthine—probably due to its drop at caecal level—histidine, and uracil, while greater pyruvate, 2-oxoglutarate, and glucose. This study sheds light on the mode of action of this muramidase and lays the groundwork for future investigations on its effects on the intestinal ecosystem and systemic metabolism of broiler chickens.
Metabolomics approach to assess the effect of siphonal autotomy on metabolic characteristics of razor clam Solen grandis
Authors: Wu Yangping , Chen Aihua , Zhang Yu , Zhang Zhidong , Cao Yi , Chen Suhua , Tian Zhen , Li Qiujie 
Published: April 2022

AbstractAutotomy appendages are fundamental evolutionary adaptations to escape predation. The siphon is an important foraging organ for bivalves. Here, we report the first demonstration of autotomy of the siphon in marine bivalves (razor clam Solen grandis) and the effect of siphonal autotomy in S. grandis on foraging and metabolic characteristics. In this study, the feeding rate and digestive enzyme activities upon siphonal autotomy in razor clams were investigated. Moreover, endogenous metabolites pre/post-autotomy of the siphon were investigated using liquid chromatography tandem-mass spectrometry (LC–MS). The feeding rate and digestive enzyme activities decreased significantly after siphonal autotomy in S. grandis (P < 0.05), suggesting that autotomy of the siphon negatively affected its foraging. These results might be related to the reduction in the foraging radius. Additionally, the effect of autotomy was investigated on a total of 34 differentially abundant metabolites, and pathway analysis indicated that 32 differentially enriched metabolic pathways were worthy of attention. Further integrated key metabolic pathway analysis showed that glycine, serine and threonine metabolism; taurine and hypotaurine metabolism; biotin metabolism; vitamin B6 and thiamine metabolism were significantly relevant pathways in S. grandis pre/post-autotomy of the siphon. The downregulation of glycine, taurine, and hypotaurine is expected to indicate a shortage of intermediate compounds and energy in S. grandis. Therefore, to provide the required energy and materials for siphon regeneration in S. grandis, we anticipated that it would be necessary to supplement these as exogenous metabolites from the daily diet.
Analysis of individual-level data from 2018–2020 Ebola outbreak in Democratic Republic of the Congo
Authors: Vossler Harley , Akilimali Pierre , Pan Yuhan , KhudaBukhsh Wasiur R. , Kenah Eben , Rempała Grzegorz A. 
Published: April 2022

AbstractThe 2018–2020 Ebola virus disease epidemic in Democratic Republic of the Congo (DRC) resulted in 3481 cases (probable and confirmed) and 2299 deaths. In this paper, we use a novel statistical method to analyze the individual-level incidence and hospitalization data on DRC Ebola victims. Our analysis suggests that an increase in the rate of quarantine and isolation that has shortened the infectiousness period by approximately one day during the epidemic’s third and final wave was likely responsible for the eventual containment of the outbreak. The analysis further reveals that the total effective population size or the average number of individuals at risk for the disease exposure in three epidemic waves over the period of 24 months was around 16,000–a much smaller number than previously estimated and likely an evidence of at least partial protection of the population at risk through ring vaccination and contact tracing as well as adherence to strict quarantine and isolation policies.
Growth promotion and antibiotic induced metabolic shifts in the chicken gut microbiome
Authors: Plata Germán , Baxter Nielson T. , Susanti Dwi , Volland-Munson Alyssa , Gangaiah Dharanesh , Nagireddy Akshitha , Mane Shrinivasrao P. , Balakuntla Jayanth , Hawkins Troy B. , Kumar Mahajan Arvind 
Published: April 2022

AbstractAntimicrobial growth promoters (AGP) have played a decisive role in animal agriculture for over half a century. Despite mounting concerns about antimicrobial resistance and demand for antibiotic alternatives, a thorough understanding of how these compounds drive performance is missing. Here we investigate the functional footprint of microbial communities in the cecum of chickens fed four distinct AGP. We find relatively few taxa, metabolic or antimicrobial resistance genes similarly altered across treatments, with those changes often driven by the abundances of core microbiome members. Constraints-based modeling of 25 core bacterial genera associated increased performance with fewer metabolite demands for microbial growth, pointing to altered nitrogen utilization as a potential mechanism of narasin, the AGP with the largest performance increase in our study. Untargeted metabolomics of narasin treated birds aligned with model predictions, suggesting that the core cecum microbiome might be targeted for enhanced performance via its contribution to host-microbiota metabolic crosstalk.