bluuebunny/crossref_metadata_2025_split huggingface dataset:
A macroscopic object passively cooled into its quantum ground state of motion beyond single-mode cooling
Authors: Cattiaux D. , Golokolenov I. , Kumar S. , Sillanpää M. , Mercier de Lépinay L. , Gazizulin R. R. , Zhou X. , Armour A. D. , Bourgeois O. , Fefferman A. , Collin E. 
Published: October 2021

AbstractThe nature of the quantum-to-classical crossover remains one of the most challenging open question of Science to date. In this respect, moving objects play a specific role. Pioneering experiments over the last few years have begun exploring quantum behaviour of micron-sized mechanical systems, either by passively cooling single GHz modes, or by adapting laser cooling techniques developed in atomic physics to cool specific low-frequency modes far below the temperature of their surroundings. Here instead we describe a very different approach, passive cooling of a whole micromechanical system down to 500 μK, reducing the average number of quanta in the fundamental vibrational mode at 15 MHz to just 0.3 (with even lower values expected for higher harmonics); the challenge being to be still able to detect the motion without disturbing the system noticeably. With such an approach higher harmonics and the surrounding environment are also cooled, leading to potentially much longer mechanical coherence times, and enabling experiments questioning mechanical wave-function collapse, potentially from the gravitational background, and quantum thermodynamics. Beyond the average behaviour, here we also report on the fluctuations of the fundamental vibrational mode of the device in-equilibrium with the cryostat. These reveal a surprisingly complex interplay with the local environment and allow characteristics of two distinct thermodynamic baths to be probed.
Miniature type V-F CRISPR-Cas nucleases enable targeted DNA modification in cells
Authors: Bigelyte Greta , Young Joshua K. , Karvelis Tautvydas , Budre Karolina , Zedaveinyte Rimante , Djukanovic Vesna , Van Ginkel Elizabeth , Paulraj Sushmitha , Gasior Stephen , Jones Spencer , Feigenbutz Lanie , Clair Grace St. , Barone Pierluigi , Bohn Jennifer , Acharya Ananta , Zastrow-Hayes Gina , Henkel-Heinecke Selgar , Silanskas Arunas , Seidel Ralf , Siksnys Virginijus 
Published: October 2021

AbstractClass 2 CRISPR systems are exceptionally diverse, nevertheless, all share a single effector protein that contains a conserved RuvC-like nuclease domain. Interestingly, the size of these CRISPR-associated (Cas) nucleases ranges from >1000 amino acids (aa) for Cas9/Cas12a to as small as 400-600 aa for Cas12f. For in vivo genome editing applications, compact RNA-guided nucleases are desirable and would streamline cellular delivery approaches. Although miniature Cas12f effectors have been shown to cleave double-stranded DNA, targeted DNA modification in eukaryotic cells has yet to be demonstrated. Here, we biochemically characterize two miniature type V-F Cas nucleases, SpCas12f1 (497 aa) and AsCas12f1 (422 aa), and show that SpCas12f1 functions in both plant and human cells to produce targeted modifications with outcomes in plants being enhanced with short heat pulses. Our findings pave the way for the development of miniature Cas12f1-based genome editing tools.
The spatial configuration of biotic interactions shapes coexistence-area relationships in an annual plant community
Authors: García-Callejas David , Bartomeus Ignasi , Godoy Oscar 
Published: October 2021

AbstractThe increase of species richness with area is a universal phenomenon on Earth. However, this observation contrasts with our poor understanding of how these species-area relationships (SARs) emerge from the collective effects of area, spatial heterogeneity, and local interactions. By combining a structuralist approach with five years of empirical observations in a highly-diverse Mediterranean grassland, we show that spatial heterogeneity plays a little role in the accumulation of species richness with area in our system. Instead, as we increase the sampled area more species combinations are realized, and they coexist mainly due to direct pairwise interactions rather than by changes in single-species dominance or by indirect interactions. We also identify a small set of transient species with small population sizes that are consistently found across spatial scales. These findings empirically support the importance of the architecture of species interactions together with stochastic events for driving coexistence- and species-area relationships.
Macrophages in heterotopic ossification: from mechanisms to therapy
Authors: Huang Yifei , Wang Xinyi , Zhou Daixuan , Zhou Wenwen , Dai Fengyi , Lin Hui 
Published: October 2021

AbstractHeterotopic ossification (HO) is the formation of extraskeletal bone in non-osseous tissues. It is caused by an injury that stimulates abnormal tissue healing and regeneration, and inflammation is involved in this process. It is worth noting that macrophages are crucial mediators of inflammation. In this regard, abundant macrophages are recruited to the HO site and contribute to HO progression. Macrophages can acquire different functional phenotypes and promote mesenchymal stem cell (MSC) osteogenic differentiation, chondrogenic differentiation, and angiogenesis by expressing cytokines and other factors such as the transforming growth factor-β1 (TGF-β1), bone morphogenetic protein (BMP), activin A (Act A), oncostatin M (OSM), substance P (SP), neurotrophin-3 (NT-3), and vascular endothelial growth factor (VEGF). In addition, macrophages significantly contribute to the hypoxic microenvironment, which primarily drives HO progression. Thus, these have led to an interest in the role of macrophages in HO by exploring whether HO is a “butterfly effect” event. Heterogeneous macrophages are regarded as the “butterflies” that drive a sequence of events and ultimately promote HO. In this review, we discuss how the recruitment of macrophages contributes to HO progression. In particular, we review the molecular mechanisms through which macrophages participate in MSC osteogenic differentiation, angiogenesis, and the hypoxic microenvironment. Understanding the diverse role of macrophages may unveil potential targets for the prevention and treatment of HO.
Vertebrate host phylogeny influences gut archaeal diversity
Authors: Youngblut Nicholas D. , Reischer Georg H. , Dauser Silke , Maisch Sophie , Walzer Chris , Stalder Gabrielle , Farnleitner Andreas H. , Ley Ruth E. 
Published: October 2021

AbstractCommonly used 16S rRNA gene primers do not detect the full range of archaeal diversity present in the vertebrate gut. As a result, several questions regarding the archaeal component of the gut microbiota remain, including which Archaea are host-associated, the specificities of such associations and the major factors influencing archaeal diversity. Using 16S rRNA gene amplicon sequencing with primers that specifically target Archaea, we obtained sufficient sequence data from 185 gastrointestinal samples collected from 110 vertebrate species that span five taxonomic classes (Mammalia, Aves, Reptilia, Amphibia and Actinopterygii), of which the majority were wild. We provide evidence for previously undescribed Archaea–host associations, including Bathyarchaeia andMethanothermobacter, the latter of which was prevalent among Aves and relatively abundant in species with higher body temperatures, although this association could not be decoupled from host phylogeny. Host phylogeny explained archaeal diversity more strongly than diet, while specific taxa were associated with both factors, and cophylogeny was significant and strongest for mammalian herbivores. Methanobacteria was the only class predicted to be present in the last common ancestors of mammals and all host species. Further analysis indicated that Archaea–Bacteria interactions have a limited effect on archaeal diversity. These findings expand our current understanding of Archaea–vertebrate associations.
Liver and brain differential expression of one-carbon metabolism genes during ontogenesis
Authors: Imbard Apolline , Schwendimann Leslie , Lebon Sophie , Gressens Pierre , Blom Henk J. , Benoist Jean-François 
Published: October 2021

AbstractOne-carbon metabolism (1C metabolism) is of paramount importance for cell metabolism and mammalian development. It is involved in the synthesis or modification of a wide variety of compounds such as proteins, lipids, purines, nucleic acids and neurotransmitters. We describe here the evolution of expression of genes related to 1C metabolism during liver and brain ontogeny in mouse. The level of expression of 30 genes involved in 1C metabolism was quantified by RT-qPCR in liver and brain tissues of OF1 mice at E9, E11, E13, E15, E17, P0, P3, P5, P10, P15 developmental stages and in adults. In the liver, hierarchical clustering of the gene expression patterns revealed five distinct clades of genes with a first bifurcating hierarchy distinguishing two main developmental stages before and after E15. In the brain most of the 1C metabolism genes are expressed but at a lower levels. The gene expression of enzymes involved in 1C metabolism show dramatic changes during development that are tissue specific. mRNA expression patterns of all major genes involved in 1C metabolism in liver and brain provide clues about the methylation demand and methylation pathways during embryonic development.
Catechol thwarts virulent dimorphism in Candida albicans and potentiates the antifungal efficacy of azoles and polyenes
Authors: Jothi Ravi , Sangavi Ravichellam , Kumar Ponnuchamy , Pandian Shunmugiah Karutha , Gowrishankar Shanmugaraj 
Published: October 2021

AbstractThe present study was deliberately focused to explore the antivirulence efficacy of a plant allelochemical—catechol against Candida albicans, and attempts were made to elucidate the underlying mechanisms as well. Catechol at its sub-MIC concentrations (2–256 μg/mL) exhibited a dose dependent biofilm as well as hyphal inhibitory efficacies, which were ascertained through both light and fluorescence microscopic analyses. Further, sub-MICs of catechol displayed remarkable antivirulence efficacy, as it substantially inhibited C. albicans’ virulence enzymes i.e. secreted hydrolases. Notably, FTIR analysis divulged the potency of catechol in effective loosening of C. albicans’ exopolymeric matrix, which was further reinforced using EPS quantification assay. Although, catechol at BIC (256 μg/mL) did not disrupt the mature biofilms of C. albicans, their initial adherence was significantly impeded by reducing their hydrophobic nature. Besides, FTIR analysis also unveiled the ability of catechol in enhancing the production of farnesol—a metabolite of C. albicans, whose accumulation naturally blocks yeast-hyphal transition. The qPCR data showed significant down-regulation of candidate genes viz., RAS1, HWP1 and ALS3 which are the key targets of Ras-cAMP-PKA pathway -the pathway that contribute for C. albicans’ pathogenesis. Interestingly, the up-regulation of TUP1 (a gene responsible for farnesol-mediated hyphal inhibition) during catechol exposure strengthen the speculation of catechol triggered farnesol-mediated hyphal inhibition. Furthermore, catechol profusely enhanced the fungicidal efficacy of certain known antifungal agent’s viz., azoles (ketoconazole and miconazole) and polyenes (amphotericin-B and nystatin).
Unraveling the complexity of faba bean (Vicia faba L.) transcriptome to reveal cold-stress-responsive genes using long-read isoform sequencing technology
Authors: Lyu Jae Il , Ramekar Rahul , Kim Jung Min , Hung Nguyen Ngoc , Seo Ji Su , Kim Jin-Baek , Choi Ik-Young , Park Kyong-Cheul , Kwon Soon-Jae 
Published: October 2021

AbstractFaba bean (Vicia faba L.), a globally important grain legume providing a stable source of dietary protein, was one of the earliest plant cytogenetic models. However, the lack of draft genome annotations and unclear structural information on mRNA transcripts have impeded its genetic improvement. To address this, we sequenced faba bean leaf transcriptome using the PacBio single-molecule long-read isoform sequencing platform. We identified 28,569 nonredundant unigenes, ranging from 108 to 9669 bp, with a total length of 94.5 Mb. Many unigenes (3597, 12.5%) had 2–20 isoforms, indicating a highly complex transcriptome. Approximately 96.5% of the unigenes matched sequences in public databases. The predicted proteins and transcription factors included NB-ARC, Myb_domain, C3H, bHLH, and heat shock proteins, implying that this genome has an abundance of stress resistance genes. To validate our results, we selected WCOR413-15785, DHN2-12403, DHN2-14197, DHN2-14797, COR15-14478, and HVA22-15 unigenes from the ICE-CBF-COR pathway to analyze their expression patterns in cold-treated samples via qRT-PCR. The expression of dehydrin-related genes was induced by cold stress. The assembled data provide the first insights into the deep sequencing of full-length RNA from faba bean at the single-molecule level. This study provides an important foundation to improve gene modeling and protein prediction.
Whole-exome sequencing of the mummified remains of Cangrande della Scala (1291–1329 CE) indicates the first known case of late-onset Pompe disease
Authors: Iadarola Barbara , Lavezzari Denise , Modi Alessandra , Degli Esposti Chiara , Beltrami Cristina , Rossato Marzia , Zaro Valentina , Napione Ettore , Latella Leonardo , Lari Martina , Caramelli David , Salviati Alessandro , Delledonne Massimo 
Published: October 2021

AbstractMummified remains of relevant historical figures are nowadays an important source of information to retrace data concerning their private life and health, especially when historical archives are not available. Next-generation-sequencing was proved to be a valuable tool to unravel the characteristics of these individuals through their genetic heritage. Using the strictest criteria currently available for the validation of ancient DNA sequences, whole-genome and whole-exome sequencing were generated from the mummy remains of an Italian nobleman died almost 700 years ago, Cangrande della Scala. While its genome sequencing could not yield sufficient coverage for in depth investigation, exome sequencing could overcome the limitations of this approach to achieve significantly high coverage on coding regions, thus allowing to perform the first extensive exome analysis of a mummy genome. Similar to a standard “clinical exome analysis” conducted on modern DNA, an in-depth variant annotation, high-quality filtering and interpretation was performed, leading to the identification of a genotype associated with late-onset Pompe disease (glycogen storage disease type II). This genetic diagnosis was concordant with the limited clinical history available for Cangrande della Scala, who likely represents the earliest known case of this autosomal recessive metabolic disorder.
Multiparametric analysis of geometric features of fibrotic textures leading to cardiac arrhythmias
Authors: Nezlobinsky T. , Okenov A. , Panfilov A. V. 
Published: October 2021

AbstractOne of the important questions in cardiac electrophysiology is to characterise the arrhythmogenic substrate; for example, from the texture of the cardiac fibrosis, which is considered one of the major arrhythmogenic conditions. In this paper, we perform an extensive in silico study of the relationships between various local geometric characteristics of fibrosis on the onset of cardiac arrhythmias. In order to define which texture characteristics have better predictive value, we induce arrhythmias by external stimulation, selecting 4363 textures in which arrhythmia can be induced and also selecting 4363 non-arrhythmogenic textures. For each texture, we determine such characteristics as cluster area, solidity, mean distance, local density and zig-zag propagation path, and compare them in arrhythmogenic and non-arrhythmogenic cases. Our study shows that geometrical characteristics, such as cluster area or solidity, turn out to be the most important for prediction of the arrhythmogenic textures. Overall, we were able to achieve an accuracy of 67% for the arrhythmogenic texture-classification problem. However, the accuracy of predictions depends on the size of the region chosen for the analysis. The optimal size for the local areas of the tissue was of the order of 0.28 of the wavelength of the arrhythmia. We discuss further developments and possible applications of this method for characterising the substrate of arrhythmias in fibrotic textures.
Epidemiology of mutant Plasmodium falciparum parasites lacking histidine-rich protein 2/3 genes in Eritrea 2 years after switching from HRP2-based RDTs
Authors: Mihreteab Selam , Anderson Karen , Pasay Cielo , Smith David , Gatton Michelle L. , Cunningham Jane , Berhane Araia , Cheng Qin 
Published: October 2021

AbstractEritrea was the first African country to complete a nationwide switch in 2016 away from HRP2-based RDTs due to high rates of false-negative RDT results caused by Plasmodium falciparum parasites lacking hrp2/hrp3 genes. A cross-sectional survey was conducted during 2019 enrolling symptomatic malaria patients from nine health facilities across three zones consecutively to investigate the epidemiology of P. falciparum lacking hrp2/3 after the RDT switch. Molecular analyses of 715 samples revealed the overall prevalence of hrp2-, hrp3-, and dual hrp2/3-deleted parasites as 9.4% (95%CI 7.4–11.7%), 41.7% (95% CI 38.1–45.3%) and 7.6% (95% CI 5.8–9.7%), respectively. The prevalence of hrp2- and hrp3-deletion is heterogeneous within and between zones: highest in Anseba (27.1% and 57.9%), followed by Gash Barka (6.4% and 37.9%) and Debub zone (5.2% and 43.8%). hrp2/3-deleted parasites have multiple diverse haplotypes, with many shared or connected among parasites of different hrp2/3 status, indicating mutant parasites have likely evolved from multiple and local parasite genetic backgrounds. The findings show although prevalence of hrp2/3-deleted parasites is lower 2 years after RDT switching, HRP2-based RDTs remain unsuitable for malaria diagnosis in Eritrea. Continued surveillance of hrp2/3-deleted parasites in Eritrea and neighbouring countries is required to monitor the trend.
Prognostic efficacy of the RTN1 gene in patients with diffuse large B-cell lymphoma
Authors: Zamani-Ahmadmahmudi Mohamad , Nassiri Seyed Mahdi , Asadabadi Amir 
Published: October 2021

AbstractGene expression profiling has been vastly used to extract the genes that can predict the clinical outcome in patients with diverse cancers, including diffuse large B-cell lymphoma (DLBCL). With the aid of bioinformatics and computational analysis on gene expression data, various prognostic gene signatures for DLBCL have been recently developed. The major drawback of the previous signatures is their inability to correctly predict survival in external data sets. In other words, they are not reproducible in other datasets. Hence, in this study, we sought to determine the gene(s) that can reproducibly and robustly predict survival in patients with DLBCL. Gene expression data were extracted from 7 datasets containing 1636 patients (GSE10846 [n = 420], GSE31312 [n = 470], GSE11318 [n = 203], GSE32918 [n = 172], GSE4475 [n = 123], GSE69051 [n = 157], and GSE34171 [n = 91]). Genes significantly associated with overall survival were detected using the univariate Cox proportional hazards analysis with a P value < 0.001 and a false discovery rate (FDR) < 5%. Thereafter, significant genes common between all the datasets were extracted. Additionally, chromosomal aberrations in the corresponding region of the final common gene(s) were evaluated as copy number alterations using the single nucleotide polymorphism (SNP) data of 570 patients with DLBCL (GSE58718 [n = 242], GSE57277 [n = 148], and GSE34171 [n = 180]). Our results indicated that reticulon family gene 1 (RTN1) was the only gene that met our rigorous pipeline criteria and associated with a favorable clinical outcome in all the datasets (P < 0.001, FDR < 5%). In the multivariate Cox proportional hazards analysis, this gene remained independent of the routine international prognostic index components (i.e., age, stage, lactate dehydrogenase level, Eastern Cooperative Oncology Group [ECOG] performance status, and number of extranodal sites) (P < 0.0001). Furthermore, no significant chromosomal aberration was found in the RTN1 genomic region (14q23.1: Start 59,595,976/End 59,870,966).
Groundwater in sedimentary basins as potential lithium resource: a global prospective study
Authors: Dugamin Elza J. M. , Richard Antonin , Cathelineau Michel , Boiron Marie-Christine , Despinois Frank , Brisset Anne 
Published: October 2021

AbstractElectric cars will require to increase the production of lithium dramatically (up to 2 Mtons lithium equivalent carbonate per year by 2030). However, conventional hard-rock and salar mining are facing environmental and social concerns. Therefore, alternative lithium resources may help meeting the global demand for the next decades. Here, we provide a systematic analysis of published lithium concentration in about 3000 samples of groundwater from 48 sedimentary basins worldwide. The highest lithium concentrations (> 102 mg l−1) are primarily found in high salinity waters (Total Dissolved Solids > 105 mg l−1) and are in the same range as brines from the most productive salars. Conservative estimations based on fluid volume and lithium concentration in selected reservoirs indicate that these lithium resources are comparable to salars and hard-rock mines (0.1–10 Mtons lithium). Therefore, lithium in groundwater from sedimentary basins could be a significant potential resource for the next decades.