bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid simultaneous acquisition of macromolecular tissue volume, susceptibility, and relaxometry maps
Authors: Yu Fang Frank , Huang Susie Yi , Witzel Thomas , Kumar Ashwin , Liao Congyu , Duval Tanguy , Cohen-Adad Julien , Bilgic Berkin 
Published: June 2021

AbstractPurposeA major obstacle to the clinical implementation of quantitative MR is the lengthy acquisition time required to derive multi-contrast parametric maps. We sought to reduce the acquisition time for quantitative susceptibility mapping (QSM) and macromolecular tissue volume (MTV) by acquiring both contrasts simultaneously by leveraging their redundancies. The Joint Virtual Coil concept with generalized autocalibrating partially parallel acquisitions (JVC-GRAPPA) was applied to reduce acquisition time further.MethodsThree adult volunteers were imaged on a 3T scanner using a multi-echo 3D GRE sequence acquired at three head orientations. MTV, QSM, R2*, T1, and proton density maps were reconstructed. The same sequence (GRAPPA R=4) was performed in subject #1 with a single head orientation for comparison. Fully sampled data was acquired in subject #2, from which retrospective undersampling was performed (R=6 GRAPPA and R=9 JVC-GRAPPA). Prospective undersampling was performed in subject #3 (R=6 GRAPPA and R=9 JVC-GRAPPA) using gradient blips to shift k-space sampling in later echoes.ResultsSubject #1’s multi-orientation and single-orientation MTV maps were not significantly different based on RMSE. For subject #2, the retrospectively undersampled JVC-GRAPPA and GRAPPA generated similar results as fully sampled data. This approach was validated with the prospectively undersampled images in subject #3. Using QSM, R2*, and MTV, the contributions of myelin and iron content to susceptibility was estimated.ConclusionWe have developed a novel strategy to simultaneously acquire data for the reconstruction of five intrinsically co-registered 1-mm isotropic resolution multi-parametric maps, with a scan time of 6 minutes using JVC-GRAPPA.
Leveraging host-genetics and gut microbiota to determine immunocompetence in pigs
Authors: Ramayo-Caldas Yuliaxis , Zingaretti Laura M. , Pérez-Pascual David , Alexandre Pamela A. , Reverter Antonio , Dalmau Toni , Quintanilla Raquel , Ballester Maria 
Published: June 2021

AbstractThe aim of the present work was to identify microbial biomarkers linked to immunity traits and to characterize the contribution of host-genome and gut microbiota to the immunocompetence in healthy pigs. To achieve this goal, we undertook a combination of network, mixed model and microbial-wide association studies (MWAS) for 21 immunity traits and the relative abundance of gut bacterial communities in 389 pigs genotyped for 70K SNPs. The heritability (h2; proportion of phenotypic variance explained by the host genetics) and microbiability (m2; proportion of variance explained by the microbial composition) showed similar values for most of the analyzed immunity traits, except for both IgM and IgG in plasma that were dominated by the host genetics, and the haptoglobin in serum which was the trait with larger m2 (0.275) compared to h2 (0.138). Results from the MWAS suggested a polymicrobial nature of the immunocompetence in pigs and revealed associations between pigs gut microbiota composition and 15 of the analyzed traits. The lymphocytes phagocytic capacity (quantified as mean fluorescence) and the total number of monocytes in blood were the traits associated with the largest number of taxa (6 taxa). Among the associations identified by MWAS, 30% were confirmed by an information theory network approach. The strongest confirmed associations were between Fibrobacter and phagocytic capacity of lymphocytes (r=0.37), followed by correlations between Streptococcus and the percentage of phagocytic lymphocytes (r=-0.34) and between Megasphaera and serum concentration of haptoglobin (r=0.26). In the interaction network, Streptococcus and percentage of phagocytic lymphocytes were the keystone bacterial and immune-trait, respectively. Overall, our findings reveal an important connection between immunity traits and gut microbiota in pigs and highlight the need to consider both sources of information, host genome and microbial levels, to accurately characterize immunocompetence in pigs.
Beyond demographic buffering: Context dependence in demographic strategies across animals
Authors: Lenzi Omar , Ozgul Arpat , Salguero-Gómez Roberto , Paniw Maria 
Published: June 2021

AbstractTemporal variation in vital rates (e.g., survival, reproduction) can decrease the long-term mean performance of a population. Species are therefore expected to evolve demographic strategies that counteract the negative effects of vital rate variation on the population growth rate. One key strategy, demographic buffering, is reflected in a low temporal variation in vital rates critical to population dynamics. However, comparative studies in plants have found little evidence for demographic buffering, and little is known about the prevalence of buffering in animal populations. Here, we used vital rate estimates from 31 natural populations of 29 animal species to assess the prevalence of demographic buffering. We modeled the degree of demographic buffering using a standard measure of correlation between the standard deviation of vital rates and the sensitivity of the population growth rate to changes in such vital rates across populations. We also accounted for the effects of life-history traits, i.e., age at first reproduction and spread of reproduction across the life cycle, on these correlation measures. We found no strong or consistent evidence of demographic buffering across the study populations. Instead, key vital rates could vary substantially depending on the specific environmental context populations experience. We suggest that it is time to look beyond concepts of demographic buffering when studying natural populations towards a stronger focus on the environmental context-dependence of vital-rate variation.
Saccades and pre-saccadic stimulus repetition alter cortical network topology and dynamics: evidence from EEG and graph theoretical analysis
Authors: Ghaderi Amirhossein , Niemeier Matthias , Crawford John Douglas 
Published: June 2021

AbstractParietal and frontal cortex are involved in saccade generation, but their output signals also modify visual signals throughout cortex. These signals produce well-documented behavioral phenomena (saccades, saccadic suppression, various perisaccadic perceptual distortions) but their underlying influence on cortical network dynamics is not known. Here, we combined electroencephalography (EEG) with frequency-dependent source localization and graph theory analysis (GTA) to understand how saccades and pre-saccadic visual stimuli interactively alter cortical network dynamics in humans. 21 participants viewed series of 1-3 vertical or horizontal grids, followed by grid with the opposite orientation just before a horizontal saccade or continued fixation. EEG signals from the presaccadic interval (cue + 200ms, or equivalent fixation period) were used for source localization. Source localization (saccade – fixation) identified bilateral dorsomedial frontoparietal activity across frequency bands, whereas stimulus repetition produced band-specific modulations in left prefrontal, posterior parietal, and central-superior frontal and/or parietal cortex, with significant saccade-repetition interactions in frontal and parietal regions. GTA analysis revealed a saccade-specific functional network with major hubs in inferior parietal cortex (alpha) and the frontal eye fields (beta), and major saccade-repetition interactions in left prefrontal (theta) and supramarginal gyrus (gamma). Overall, quantitative measures of whole-brain network topology and dynamics (segregation, integration, synchronization, complexity) were enhanced during the presaccadic interval, but repetition interactions reduced synchronization and complexity. These results show that presaccadic signals have widespread, coherent influence on cortical network dynamics, likely responsible for both saccade production and the perceptual phenomena associated with saccades.HighlightsSource localization & graph theory were used to analyze presaccadic EEG signalsPresaccadic signals produced band-specific modulations/hubs in parietofrontal cortexFrontal/parietal eye fields showed extensive functional connectivity across all lobesPresaccadic stimulus repetition further modulated functional network connectivitySaccades and repetition both influenced network clustering, integration, & complexity
High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads
Authors: Wang Bo , Yang Xiaofei , Jia Yanyan , Xu Yu , Jia Peng , Dang Ningxin , Wang Songbo , Xu Tun , Zhao Xixi , Gao Shenghan , Dong Quanbin , Ye Kai 
Published: June 2021

AbstractArabidopsis thaliana is an important and long-established model species for plant molecular biology, genetics, epigenetics, and genomics. However, the latest version of reference genome still contains significant number of missing segments. Here, we report a high-quality and almost complete Col-0 genome assembly with two gaps (Col-XJTU) using combination of Oxford Nanopore Technology ultra-long reads, PacBio high-fidelity long reads, and Hi-C data. The total genome assembly size is 133,725,193 bp, introducing 14.6 Mb of novel sequences compared to the TAIR10.1 reference genome. All five chromosomes of Col-XJTU assembly are highly accurate with consensus quality (QV) scores > 60 (ranging from 62 to 68), which are higher than those of TAIR10.1 reference (QV scores ranging from 45 to 52). We have completely resolved chromosome (Chr) 3 and Chr5 in a telomere-to-telomere manner. Chr4 has been completely resolved except the nucleolar organizing regions, which comprise long repetitive DNA fragments. The Chr1 centromere (CEN1), reportedly around 9 Mb in length, is particularly challenging to assemble due to the presence of tens of thousands of CEN180 satellite repeats. Using the cutting-edge sequencing data and novel computational approaches, we assembled about 4 Mb of sequence for CEN1 and a 3.5-Mb-long CEN2. We investigated the structure and epigenetics of centromeres. We detected four clusters of CEN180 monomers, and found that the centromere-specific histone H3-like protein (CENH3) exhibits a strong preference for CEN180 cluster 3. Moreover, we observed hypomethylation patterns in CENH3-enriched regions. We believe that this high-quality genome assembly, Col-XJTU, would serve as a valuable reference to better understand the global pattern of centromeric polymorphisms, as well as genetic and epigenetic features in plants.
Typical resting state activity of the brain requires visual input during an early sensitive period
Authors: Rączy Katarzyna , Hölig Cordula , Guerreiro Maria J. S. , Lingareddy Sunitha , Kekunnaya Ramesh , Röder Brigitte 
Published: June 2021

AbstractSensory deprivation, following a total loss of one sensory modality e.g. vision, has been demonstrated to result in intra- and cross-modal plasticity. It is yet not known to which extent intra- and cross-modal plasticity as a consequence of blindness reverse if sight is restored.Here, we used functional magnetic resonance imaging to acquire blood oxygen level dependent (BOLD) resting state activity during an eyes open and an eyes closed state in congenital cataract-reversal individuals, developmental cataract-reversal individuals, congenitally permanently blind individuals and sighted controls. The amplitude of low frequency fluctuations (ALFF) of the BOLD signal - a neural marker of spontaneous brain activity during rest - was analyzed.As has been shown before, in normally sighted controls we observed an increase in ALFF during rest with the eyes open compared to rest with eyes closed in visual association areas and in parietal cortex but a decrease in auditory and sensorimotor regions. In congenital cataract-reversal individuals, we found an increase of the amplitude of slow BOLD fluctuations in visual cortex during rest with eyes open compared to rest with eyes closed too but this increase was larger in amplitude than in normally sighted controls. At the same time, congenital cataract-reversal individuals lagged a similar increase in parietal regions and did not show the typical decrease of ALFF in auditory and sensorimotor cortex. Congenitally blind individuals displayed an overall higher amplitude in slow BOLD fluctuations in visual cortex compared to sighted individuals and compared to congenital cataract-reversal individuals in the eyes closed condition.Higher ALFF in visual cortex of congenital cataract-reversal individuals than in normally sighted controls during eyes open might indicate an altered excitatory-inhibitory balance of visual neural circuits. By contrast, the lower parietal increase and the missing downregulation in auditory and sensorimotor regions suggest a reduced influence of the visual system on multisensory and the remaining sensory systems after restoring sight in congenitally blind individuals. These results demonstrate a crucial dependence of multisensory neural networks on visual experience during a sensitive phase in human brain development.
Cross-species comparative hippocampal transcriptomics in Alzheimer’s disease
Authors: De Bastiani Marco Antônio , Bellaver Bruna , Carello-Collar Giovanna , Zimmermann Maria , Kunach Peter , Lima-Filho Ricardo A. S. , Forner Stefania , Martini Alessandra Cadete , Pascoal Tharick A. , Lourenco Mychael V. , Rosa-Neto Pedro , Zimmer Eduardo R. 
Published: June 2021

SummaryAlzheimer’s disease (AD) is a multifactorial pathology, with most cases having a sporadic origin. Recently, knock-in (KI) models have been developed with the promise of resembling better sporadic human AD, such as the novel hAβ-KI mouse. Here, we compared hippocampal publicly available transcriptomic profiles of transgenic (5xFAD and APP/PS1) and KI (hAβ-KI) mouse models with early- (EOAD) and late- (LOAD) onset AD patients. Experimental validation of consistently dysregulated genes revealed four altered in mice (SLC11A1, S100A6, CD14, CD33, C1QB) and three in humans (S100A6, SLC11A1, KCNK). Additionally, the three mouse models presented more Gene Ontology biological processes terms and enriched signaling pathways in common with LOAD than with EOAD individuals. Finally, we identified 17 transcription factors potentially acting as master regulators of AD. Our cross-species analyses revealed that the three mouse models presented a remarkable similarity to LOAD, with the hAβ-KI being the more specific one.
DNA damage response at telomeres boosts the transcription of SARS-CoV-2 receptor ACE2 during aging
Authors: Sepe Sara , Rossiello Francesca , Cancila Valeria , Iannelli Fabio , Matti Valentina , Cicio Giada , Cabrini Matteo , Marinelli Eugenia , Alabi Busola , di Lillo Alessia , Di Napoli Arianna , Shay Jerry W. , Tripodo Claudio , d’Adda di Fagagna Fabrizio 
Published: June 2021

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is known to be more common in the elderly, who show also more severe symptoms and a higher risk of hospitalization and death. Here we show that the expression of the Angiotensin Converting Enzyme 2 (ACE2), the SARS-CoV2 cell receptor, increases during aging in mouse and human lungs, and following telomere shortening or dysfunction in mammalian cells and in mouse models. This increase is regulated at the transcription level, and Ace2 promoter activity is DNA damage response (DDR)-dependent. Indeed, ATM inhibition or the selective inhibition of telomeric DDR, through the use of antisense oligonucleotides, prevents Ace2 upregulation following telomere damage, in cultured cells and in mice.We propose that during aging telomeric shortening, by triggering DDR activation, causes the upregulation of ACE2, the SARS-CoV2 cell receptor, thus making the elderly likely more susceptible to the infection.
Segmentation of Pancreatic Ductal Adenocarcinoma (PDAC) and surrounding vessels in CT images using deep convolutional neural networks and texture descriptors
Authors: Mahmoudi Tahereh , Kouzahkanan Zahra Mousavi , Radmard Amir Reza , Kafieh Raheleh , Salehnia Aneseh , Davarpanah Amir H. , Arabalibeik Hossein , Ahmadian Alireza 
Published: June 2021

AbstractFully automated and volumetric segmentation of critical tumors may play a crucial role in diagnosis and surgical planning. One of the most challenging tumor segmentation tasks is localization of Pancreatic Ductal Adenocarcinoma (PDAC). Exclusive application of conventional methods does not appear promising. Deep learning approaches has achieved great success in the computer aided diagnosis, especially in biomedical image segmentation. This paper introduces a framework based on convolutional neural network (CNN) for segmentation of PDAC mass and surrounding vessels in CT images by incorporating powerful classic features, as well. First, a 3D-CNN architecture is used to localize the pancreas region from the whole CT volume using 3D Local Binary Pattern (LBP) map of the original image. Segmentation of PDAC mass is subsequently performed using 2D attention U-Net and Texture Attention U-Net (TAU-Net). TAU-Net is introduced by fusion of dense Scale-Invariant Feature Transform (SIFT) and LBP descriptors into the attention U-Net. An ensemble model is then used to cumulate the advantages of both networks using a 3D-CNN. In addition, to reduce the effects of imbalanced data, a new loss function is proposed as a weighted combination of three classic losses including Generalized Dice Loss (GDL), Weighted Pixel-Wise Cross Entropy loss (WPCE) and boundary loss. Due to insufficient sample size for vessel segmentation, we used the above-mentioned pre-trained networks and fin-tuned them. Experimental results show that the proposed method improves the Dice score for PDAC mass segmentation in portal-venous phase by 7.52% compared to state-of-the-art methods (from 53.08% to 60.6%) in term of DSC. Besides, three dimensional visualization of the tumor and surrounding vessels can facilitate the evaluation of PDAC treatment response.
Minimizer-space de Bruijn graphs
Authors: Ekim Barış , Berger Bonnie , Chikhi Rayan 
Published: June 2021

AbstractDNA sequencing data continues to progress towards longer reads with increasingly lower sequencing error rates. We focus on the problem of assembling such reads into genomes, which poses challenges in terms of accuracy and computational resources when using cutting-edge assembly approaches, e.g. those based on overlapping reads using minimizer sketches. Here, we introduce the concept of minimizer-space sequencing data analysis, where the minimizers rather than DNA nucleotides are the atomic tokens of the alphabet. By projecting DNA sequences into ordered lists of minimizers, our key idea is to enumerate what we call k-min-mers, that are k-mers over a larger alphabet consisting of minimizer tokens. Our approach, mdBG or minimizer-dBG, achieves orders-of-magnitude improvement in both speed and memory usage over existing methods without much loss of accuracy. We demonstrate three uses cases of mdBG: human genome assembly, metagenome assembly, and the representation of large pangenomes. For assembly, we implemented mdBG in software we call rust-mdbg, resulting in ultra-fast, low memory and highly-contiguous assembly of PacBio HiFi reads. A human genome is assembled in under 10 minutes using 8 cores and 10 GB RAM, and 60 Gbp of metagenome reads are assembled in 4 minutes using 1 GB RAM. For pangenome graphs, we newly allow a graphical representation of a collection of 661,405 bacterial genomes as an mdBG and successfully search it (in minimizer-space) for anti-microbial resistance (AMR) genes. We expect our advances to be essential to sequence analysis, given the rise of long-read sequencing in genomics, metagenomics and pangenomics.
Landscape and climatic variations of the Quaternary shaped multiple secondary contacts among barn owls (Tyto alba) of the Western Palearctic
Authors: Cumer Tristan , Machado Ana Paula , Dumont Guillaume , Bontzorlos Vasileios , Ceccherelli Renato , Charter Motti , Dichmann Klaus , Martens Hans-Dieter , Kassinis Nicolaos , Lourenço Rui , Manzia Francesca , Prévost Laure , Rakovic Marko , Siverio Felipe , Roulin Alexandre , Goudet Jérôme 
Published: June 2021

AbstractThe combined actions of climatic variations and landscape barriers shape the history of natural populations. When organisms follow their shifting niches, obstacles in the landscape can lead to the splitting of populations, on which evolution will then act independently. When two such populations are reunited, secondary contact occurs in a broad range of admixture patterns, from narrow hybrid zones to the complete dissolution of lineages. A previous study suggested that barn owls colonized the Western Palearctic after the last glaciation in a ring-like fashion around the Mediterranean Sea, and conjectured an admixture zone in the Balkans. Here, we take advantage of whole-genome sequences of 94 individuals across the Western Palearctic to reveal the complex history of the species in the region using observational and modeling approaches. Even though our results confirm that two distinct lineages colonized the region, one in Europe and one in the Levant, they suggest that it predates the last glaciation and identify a narrow secondary contact zone between the two in Anatolia. Nonetheless, we also show that barn owls re-colonized Europe after the glaciation from two distinct glacial refugia: a western one in Iberia and an eastern one in Italy. Both glacial lineages now communicate via eastern Europe, in a wide and permeable contact zone. This complex history of populations enlightens the taxonomy of Tyto alba in the region, highlights the key role played by mountain ranges and large water bodies as barriers and illustrates the power of population genomics in uncovering intricate demographic patterns.
Detection of pigeon circoviruses in ticks of sheep and camels in Inner Mongolia, China
Authors: Kong Yunyi , Yan Chao , Zhang Gang , Cai Yurong , He Biao , Li Yong 
Published: June 2021

AbstractCircovirus is one of the smallest known DNA viruses infecting animals. In this report, circovirus was detected in two tick species- Hyalomma asiaticum and Dermacentor nuttalli collected from sheep and camels in Inner Mongolia, China by high-throughput sequencing. The reverse semi-nested PCR assay revealed a complete genomic sequence of 2042 base pairs of cyclic single-stranded DNA (ssDNA). Evolutionary analysis further revealed that it belonged to circovirus with two major open read frames (ORFs) that putatively encode replicase and capsid proteins, respectively. Sequence and phylogenetic analysis suggested that the circovirus belonged to pigeon circovirus. The results demonstrated the presence of pigeon circovirus in ticks in Inner Mongolia, which provide the basis for future exploration of the prevalence of pigeon circovirus in Inner Mongolia and the pathogens carried by ticks in Inner Mongolia.