bluuebunny/crossref_metadata_2025_split huggingface dataset:
High light can alleviate chilling stress in maize
Authors: Cackett Lee , Burnett Angela C. , Royles Jessica , Hibberd Julian M. , Kromdijk Johannes 
Published: March 2023

AbstractChilling stress has the potential to significantly decrease growth and yield of sensitive crop plants such as maize. Based on previous work, high light during chilling may exacerbate stress via enhanced photoinhibition but may also aid acclimation responses to chilling. To further understand molecular processes behind responses to chilling with and without high light, two maize accessions with contrasting tolerance (B73 and F7) were exposed to three treatments: chilling, chilling combined with high light and high light alone. Transcriptome data indicated that the chilling treatment resulted in the largest stress response. Addition of high light to chilling stress had a mitigating, rather than additive effect on stress, as evident from alleviated repression of photosynthesis-related genes and less induction of stress-related pathways such as abscisic acid signalling and senescence compared with the response to chilling alone. Five transcription factors belonging to well-known stress-related transcription factor families were identified as candidates for driving the transcriptional changes behind the high-light induced mitigation of chilling stress. Physiological measurements of non-photochemical quenching and the maximum quantum efficiency of photosystem II corroborated the transcriptome results, showing that the addition of high light alleviated photoinhibition and membrane damage caused by chilling. High light alone had little effect on the plant transcriptome or physiological response. Overall, this study overturns previous reports, offers a new outlook on the impact of high light during chilling stress and has the potential to provide clearer targets for crop engineering.
Effect of number of diffusion encoding directions in Neonatal Diffusion Tensor Imaging using Tract-Based Spatial Statistical analysis
Authors: Merisaari Harri , Karlsson Linnea , Scheinin Noora M. , Shulist Satu , Lewis John D. , Karlsson Hasse , Tuulari Jetro J. 
Published: March 2023

AbstractDiffusion Tensor Imaging (DTI) has been used to study the developing brain in early childhood, infants andin uterostudies. In infants, number of used diffusion encoding directions has traditionally been smaller in earlier studies down to the minimum of 6 orthogonal directions. While the more recent studies often involve more directions, number of used directions remains an issue when acquisition time is optimized without compromising on data quality and in retrospective studies. Variability in the number of used directions may introduce bias and uncertainties to the DTI scalar estimates that affect cross-sectional and longitudinal study of the brain.We analyzed DTI images of 133 neonates, each data having 54 directions after quality control, to evaluate the effect of number of diffusion weighting directions from 6 to 54 with interval of 6 to the DTI scalars with Tract-based spatial statistics (TBSS) analysis. The TBSS analysis was applied to DTI scalar maps, and the mean Region of Interest (ROI) values were extracted using JHU atlas.We found significant bias in ROI mean values when only 6 directions were used (positive in FA, negative in MD, AD, RD), while when using 24 directions and above, the difference to scalar values calculated from 54 direction DTI was negligible.Using DTI measurements from data with at least 24 directions may be used in comparisons with DTI measurements from data with higher numbers of directions.
Hypertonic lactate infusion reduces vasopressor requirement and biomarkers of brain and cardiac injury after experimental cardiac arrest
Authors: Annoni Filippo , Su Fuhong , Peluso Lorenzo , Lisi Ilaria , Caruso Enrico , Pischiutta Francesca , Gouvea Bogossian Elisa , Garcia Bruno , Njimi Hassane , Vincent Jean-Louis , Gaspard Nicolas , Ferlini Lorenzo , Creteur Jacques , Zanier Elisa R , Taccone Fabio Silvio 
Published: March 2023

AbstractIntroductionPrognosis after resuscitated cardiac arrest (CA) remains poor with high morbidity and mortality due to extensive cardiac and brain injuries and the lack of effective treatments. Hypertonic sodium lactate (HSL) could be beneficial after CA by buffering severe metabolic acidosis, increasing brain perfusion and cardiac performance, reducing cerebral swelling, and serving as alternative energetic cellular substrate. The aim of this study was therefore to test the effects of HSL infusion on brain and cardiac injury in an experimental model of CA.MethodsAfter a 10-min electrically induced CA followed by 5 min of cardiopulmonary resuscitation maneuvers, adult swine (n=35) were randomly assigned to receive either balanced crystalloids (controls, n=11) or HSL infusion, either starting during cardiopulmonary resuscitation (CPR, Intra-arrest, n=12) or after return of spontaneous circulation (Post-ROSC, n=11) for the following 12 hours. In all animals, extensive multimodal neurological and cardiovascular monitoring was implemented. All animals were treated with target temperature management at 34°C.Results34 out of 35 (97.1%) animals achieved ROSC and one animal in the Intra-arrest group deceased before completing the observation period. Arterial pH, lactate, sodium concentrations and plasma osmolarity were higher in treated animals then in controls (p<0.001), while potassium concentrations were lower (p=0.004). HSL infusion either Intra-arrest or Post-ROSC improved hemodynamic compared to controls, as shown by reduced vasopressors need to maintain mean arterial pressure target above 65 mmHg (p=0.005 for interaction; p=0.01 for groups). Moreover, plasmatic troponin-I levels and glial fibrillary acid protein (GFAP) concentrations were lower in treated groups at several time-points than in controls.ConclusionsIn this experimental CA model, HSL infusion was associated with reduced vasopressor requirements and decreased plasmatic levels of biomarkers of cardiac and cerebral injury.
A temporal hierarchy of object processing in human visual cortex
Authors: Xu Rui , Zhou Wenjing , Xu Xin , Ling Zhipei , Liu Hesheng , Hong Bo 
Published: March 2023

ABSTRACTOur brain constructs increasingly sophisticated representations along the ventral visual pathway to support object recognition. To understand how these representations unfold over time, we recorded human intracranial electroencephalography responses to 120 object images at five consecutive stages of the ventral pathway from V1 to occipitotemporal areas. Using representational similarity analysis, we confirmed that response patterns were more strongly driven by low-order stimulus properties at early stages and high-order category information at late stages, respectively. Interestingly, response patterns also became less stimulus-driven and more categorical at all stages over time, from ∼100 to 200 ms post-stimulus. During this period, we found significant noise correlation between single-trial response patterns across stages, indicating tight inter-areal coupling. Thus, multi-areal recurrent processes may be essential in building high-order object representations.
Synaptic changes in pallidostriatal circuits observed in parkinsonian model triggers abnormal beta synchrony with accurate spatio-temporal properties across the basal ganglia
Authors: Azizpour Lindi Shiva , Mallet Nicolas P. , Leblois Arthur 
Published: March 2023

Excessive oscillatory activity across basal ganglia (BG) nuclei in theβfrequencies (12–30Hz) is a hallmark of Parkinson’s disease (PD). While the link between oscillations and symptoms remains debated, exaggeratedβoscillations constitute an important biomarker for therapeutic effectiveness in PD. The neuronal mechanisms ofβ-oscillation generation however remain unknown. Many existing models rely on a central role of the subthalamic nucleus (STN) or cortical inputs to BG. Contrarily, neural recordings and optogenetic manipulations in normal and parkinsonian rats recently highlighted the central role of the external pallidum (GPe) in abnormalβoscillations, while showing that the integrity of STN or motor cortex is not required. Here, we evaluate the mechanisms for the generation of abnormalβoscillations in a BG network model where neuronal and synaptic time constants, connectivity, and firing rate distributions are strongly constrained by experimental data. Guided by a mean-field approach, we show in a spiking neural network that several BG sub-circuits can drive oscillations. Strong recurrent STN-GPe connections or collateral intra-GPe connections drive gamma oscillations (>40Hz), whereas strong pallidostriatal loops drive low-β(10-15Hz) oscillations. We show that pathophysiological strengthening of striatal and pallidal synapses following dopamine depletion leads to the emergence of synchronized oscillatory activity in the mid-βrange with spike-phase relationships between BG neuronal populations in-line with experiments. Furthermore, inhibition of GPe, contrary to STN, abolishes oscillations. Our modeling study uncovers the neural mechanisms underlying PDβoscillations and may thereby guide the future development of therapeutic strategies.Significance statementIn Parkinson’s disease, neural activity in subcortical nuclei called the basal ganglia displays abnormal oscillatory synchronization that constitutes an important biomarker for therapeutic effectiveness. The neural mechanisms for the generation of these oscillations remain unknown. Here, in a theoretical neuronal network model strongly constrained by anatomical and physiological data, we show that specific circuit modifications in basal ganglia connectivity during Parkinson’s disease lead to the emergence of synchronized oscillatory activity in the network with properties that strongly agree with available experimental evidence. This and future theoretical investigations of the neural mechanisms underlying abnormal neuronal activity in Parkinson’s disease are necessary to guide the future development of therapeutic strategies to ameliorate symptoms.
A multi-omics genome-and-transcriptome single-cell atlas of human preimplantation embryogenesis reveals the cellular and molecular impact of chromosome instability
Authors: Gallardo Elia Fernandez , Sifrim Alejandro , Chappell Joel , Demeulemeester Jonas , Herrmann Jennifer Clara , Vermotte Robin , Kerremans Alison , Van der Haegen Michiel , Herck Jens Van , Vanuytven Sebastiaan , Vandereyken Katy , Macaulay Iain C. , Vermeesch Joris Robert , Peeraer Karen , Debrock Sophie , Pasque Vincent , Voet Thierry 
Published: March 2023

ABSTRACTThe frequent acquisition of genomic abnormalities in human preimplantation embryos is a leading cause of pregnancy loss, but does not necessarily prohibit healthy offspring. However, the impact of genomic abnormalities on cellular states and development of the early human embryo remains largely unclear. Here, we characterise aneuploidy and reconstruct gene regulatory networks in human preimplantation embryos, and investigate gene expression and developmental perturbations instigated by aneuploidy using single-cell genome-and-transcriptome sequencing (G&T-seq). At the genomic level, we show that acquired numerical and structural chromosomal aberrations are frequent across all stages of early embryogenesis and in all cell lineages. At the transcriptome level, we identify regulators of cell identity and uncover a network of 248 transcription factors from 10 major gene regulatory modules that characterise the distinct lineages of human preimplantation embryos. By integrating single-cell DNA-with RNA-information, we unveil how expression levels are affected by losses or gains of the corresponding genes in embryonic cells across human preimplantation development, as well as how copy-number aberrant transcription factor genes perturb the expression of their cognate target genes in euploid regions. Furthermore, we reveal a majority of aneuploid cells show a developmental delay and reduced fitness, indicating cell competition within the mosaic diploid-aneuploid embryo, which may contribute to selection against aneuploid cells and the birth of healthy offspring from mosaic diploid-aneuploid embryos. In summary, our multi-modal analyses provide unprecedented insights into early human embryo development.
Short-term transcutaneous vagus nerve stimulation increases pupil size but does not affect EEG alpha power: a replication
Authors: Lloyd Beth , Wurm Franz , de Kleijn Roy , Nieuwenhuis Sander 
Published: March 2023

AbstractBackgroundTranscutaneous auricular vagus nerve stimulation (taVNS) is a promising brain stimulation method for the treatment of pharmaco-resistant epilepsy and depression. Its clinical efficacy is thought to depend on taVNS-induced activation of the locus coeruleus. However, unlike for invasive VNS, there is little evidence for an effect of taVNS on noradrenergic activity.ObjectiveWe attempted to replicate recently published findings by Sharon et al. (2021), showing that short bursts of taVNS transiently increased pupil size and decreased EEG alpha power, two correlates of central noradrenergic activity.MethodsFollowing the original study, we used a single-blind, sham-controlled, randomized cross-over design. We applied short-term (3.4 s) taVNS in healthy human volunteers (n=29), while collecting resting-state pupil-size and EEG data. To analyze the data, we used scripts provided by Sharon and colleagues.ResultsConsistent with Sharon et al. (2021), pupil dilation was significantly larger during taVNS than during sham stimulation (p= .009; Bayes factor supporting the difference = 7.45). However, we failed to replicate the effect of taVNS on EEG alpha power (p= .37); the data were four times more likely under the null hypothesis (BF10= 0.28).ConclusionOur findings support the effectiveness of short-term taVNS in inducing transient pupil dilation, a correlate of phasic noradrenergic activity. However, we failed to replicate the recent finding by Sharon et al. (2021) that taVNS attenuates EEG alpha activity. Overall, this study highlights the need for continued research on the neural mechanisms underlying taVNS efficacy and its potential as a treatment option for pharmaco-resistant conditions. It also highlights the need for direct replications of influential taVNS studies.
Spatial transcriptomic analysis of virtual prostate biopsy reveals confounding effect of heterogeneity on genomic signature scoring
Authors: Figiel Sandy , Yin Wencheng , Doultsinos Dimitrios , Erickson Andrew , Poulose Ninu , Singh Reema , Magnussen Anette , Anbarasan Thineskrishna , Teague Renuka , He Mengxiao , Lundeberg Joakim , Loda Massimo , Verrill Clare , Colling Richard , Gill Pelvender S. , Bryant Richard J. , Hamdy Freddie C. , Woodcock Dan J. , Mills Ian G. , Cussenot Olivier , Lamb Alastair D. 
Published: March 2023

AbstractGenetic signatures have added a molecular dimension to prognostics and therapeutic decision-making. However, tumour heterogeneity in prostate cancer and current sampling methods could confound accurate assessment. Based on previously published spatial transcriptomic data from multifocal prostate cancer, we created virtual biopsy models that mimic conventional biopsy placement and core size. We then analysed the gene expression of different prognostic signatures (OncotypeDx®, Decipher®, Prostadiag®) using a step-wise approach increasing resolution from pseudo-bulk analysis of the whole biopsy, to differentiation by tissue subtype (benign, stroma, tumour), followed by distinct tumour grade and finally clonal resolution. The gene expression profile of virtual tumour biopsies revealed clear differences between grade groups and tumour clones, compared to a benign control, which were not reflected in bulk analyses. This suggests that bulk analyses of whole biopsies or tumour-only areas, as used in clinical practice, may provide an inaccurate assessment of gene profiles. The type of tissue, the grade of the tumour and the clonal composition all influence the gene expression in a biopsy. Clinical decision making based on biopsy genomics should be made with caution while we await more precise targeting and cost-effective spatial analyses.Patient summaryProstate cancers are very variable, including within a single tumour. Current genetic scoring systems, which are sometimes used to make decisions for how to treat patients with prostate cancer, are based on sampling methods which do not reflect these variations. We found, using state-of-the-art spatial genetic technology to simulate accurate assessment of variation in biopsies, that the current approaches miss important details which could negatively impact clinical decisions.Take home messageVirtual biopsies from spatial transcriptomic analysis of a whole prostate reveal that current genomic risk scores potentially deliver misleading results as they are based on bulk analysis of prostate biopsies and ignore tumour heterogeneity.
Comparative Genomics of Firmicutes reveals probable adaptations for xylose fermentation in Thermoanaerobacterium saccharolyticum
Authors: Fiamenghi Mateus B. , Prodonoff Juliana S. , Borelli Guilherme , Carazzolle Marcelo F. , Pereira Gonçalo A. G. , José Juliana 
Published: March 2023

AbstractSecond-generation (2G) ethanol is one potential biofuel that could be used to achieve the goal of reducing greenhouse gas emissions. Many challenges still need to be overcome for the feasibility of this technology, most of them related to consumption of xylose, a pentose sugar not easily metabolized by industrial microorganisms. Thus, exploring genes, pathways and other organisms that can ferment xylose is a strategy implemented to solve industrial bottlenecks.Thermoanaerobacterium saccharolyticum(T. sac) is an organism from the firmicutes phylum, capable of naturally fermenting compounds of industrial interest, such as xylan and xylose. Understanding evolutionary adaptations may help not only to solidify this bacterium as a potential substitute to the yeastSaccharomyces cerevisiaein industry, but also bring novel genes and information that can be used for yeast, enhance its fermenting capabilities, and increase production of current bio-platforms. This study presents a deep evolutionary study of members of the firmicutes clade, focusing on adaptations that may be related to overall fermentation metabolism, especially for xylose fermentation. One highlight is the finding of positive selection on a xylose binding protein of the xylFGH operon, close to the annotated sugar binding site, with this protein already being found to be expressed in xylose fermenting conditions in a previous study. Results from this study can serve as basis for searching for candidate genes to use in industrial strains or to improveT. sacas a new microbial cell factory, which may help to solve current problems found in the biofuels industry.
Continuous assembly required: perpetual species turnover in two trophic level ecosystems
Authors: Spaak Jurg W. , Adler Peter B. , Ellner Stephen P. 
Published: March 2023

AbstractCommunity assembly is often treated as deterministic, converging on one or at most a few possible stable endpoints. However, in nature we typically observe continuous change in community composition, which is often ascribed to environmental change. But continuous changes in community composition can also arise in deterministic, time-invariant community models, especially food web models. Our goal was to determine why some models produce continuous assembly and others do not. We investigated a simple two trophic-level community model to show that continuous assembly is driven by the relative niche width of the trophic levels. If predators have a larger niche width than prey, community assembly converges to a stable equilibrium. Conversely, if predators have a smaller niche width than prey, then community composition never stabilizes. Evidence that food webs need not reach a stable equilibrium has important implications, as many ecological theories of community ecology based on equilibria may be difficult to apply to such food webs.
ancIBD - Screening for identity by descent segments in human ancient DNA
Authors: Ringbauer Harald , Huang Yilei , Akbari Ali , Mallick Swapan , Patterson Nick , Reich David 
Published: March 2023

AbstractLong DNA sequences shared between two individuals, known as Identical by descent (IBD) segments, are a powerful signal for identifying close and distant biological relatives because they only arise when the pair shares a recent common ancestor. Existing methods to call IBD segments between present-day genomes cannot be straightforwardly applied to ancient DNA data (aDNA) due to typically low coverage and high genotyping error rates. We present ancIBD, a method to identify IBD segments for human aDNA data implemented as a Python package. Our approach is based on a Hidden Markov Model, using as input genotype probabilities imputed based on a modern reference panel of genomic variation. Through simulation and downsampling experiments, we demonstrate that ancIBD robustly identifies IBD segments longer than 8 centimorgan for aDNA data with at least either 0.25x average whole-genome sequencing (WGS) coverage depth or at least 1x average depth for in-solution enrichment experiments targeting a widely used aDNA SNP set (‘1240k’). This application range allows us to screen a substantial fraction of the aDNA record for IBD segments and we showcase two downstream applications. First, leveraging the fact that biological relatives up to the sixth degree are expected to share multiple long IBD segments, we identify relatives between 10,156 ancient Eurasian individuals and document evidence of long-distance migration, for example by identifying a pair of two approximately fifth-degree relatives who were buried 1410km apart in Central Asia 5000 years ago. Second, by applying ancIBD, we reveal new details regarding the spread of ancestry related to Steppe pastoralists into Europe starting 5000 years ago. We find that the first individuals in Central and Northern Europe carrying high amounts of Steppe-ancestry, associated with the Corded Ware culture, share high rates of long IBD (12-25 cM) with Yamnaya herders of the Pontic-Caspian steppe, signaling a strong bottleneck and a recent biological connection on the order of only few hundred years, providing evidence that the Yamnaya themselves are a main source of Steppe ancestry in Corded Ware people. We also detect elevated sharing of long IBD segments between Corded Ware individuals and people associated with the Globular Amphora culture (GAC) from Poland and Ukraine, who were Copper Age farmers not yet carrying Steppe-like ancestry. These IBD links appear for all Corded Ware groups in our analysis, indicating that individuals related to GAC contexts must have had a major demographic impact early on in the genetic admixtures giving rise to various Corded Ware groups across Europe. These results show that detecting IBD segments in aDNA can generate new insights both on a small scale, relevant to understanding the life stories of people, and on the macroscale, relevant to large-scale cultural-historical events.