bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human subcortical pathways automatically detect collision trajectory without attention and awareness
Authors: Guo Fanhua , Zou Jinyou , Wang Ye , Fang Boyan , Zhou Huafen , Wang Dajiang , He Sheng , Zhang Peng 
Published: February 2023

AbstractDetecting imminent collisions is essential for our survival and is likely supported by evolutionarily conserved mechanisms in the brain. Using high-resolution 7T fMRI, we investigated subcortical pathways for detecting collision trajectories in healthy human subjects and hemianopic patients. When healthy participants focused their attention on a central fixation task, their superior colliculus (SC), ventromedial pulvinar (vmPul) and ventral tegmental area (VTA) elicited stronger responses to a peripheral object approaching on head-collision courses compared to near-miss trajectories. Correlation and path analyses of collision-sensitive responses revealed collision sensitivity in the SC-vmPul and SC-VTA pathways without attention and cortical influence. Both behavioral performance and SC responses showed higher sensitivity to looming stimuli from the upper visual field. For hemianopic patients with unilateral lesions of the geniculostriate pathway, the ipsilesional SC, vmPul and VTA showed collision sensitivity to looming stimuli in their blind visual field, in the absence of their awareness. Stronger responses in the SC were also associated with better detection performance of the collision events. These findings clearly demonstrate that human tectofugal pathways, without attention and awareness, automatically detects approaching objects on a collision course, supporting blindsight to impending visual threats.HighlightsSC-vmPul and SC-VTA pathways show collision sensitivity without attention and cortical influence in healthy participants.Both behavioral performance and SC responses show higher sensitivity to looming stimuli from the upper visual field.The ipsilesional SC, vmPul and VTA of hemianopic patients automatically detects collision trajectories in their blind visual field without awareness.SC response is associated with “blindsight” detection of impending collisions.
Eggplant’s foliar chlorogenic acid provides resistance against the tropical armyworm
Authors: Kumar Manish , Umesh K.P. , Pandey Prashasti P. , Firake D. M. , Pandit Sagar S 
Published: February 2023

AbstractLepidopteran pests are the major crop devastators. Farmers have to resort to heavy synthetic pesticide application for their control. It increases the pesticide residue contamination on produce and causes health hazards. Synthetic pesticides also endanger beneficial insects and pollute the environment. Therefore, the use of safe and eco-friendly botanicals as biopesticides is rapidly increasing. Despite their high demand, only a few botanicals are commercially available. Consequently, biopesticide discovery research boomed in the last decade.Spodoptera lituraFabricius (armyworm) is a polyphagous multi-insecticide-resistant lepidopteran pest. It is a serious concern for several commercially important crops. In this study, we employed a chemical ecology approach to discover a biopesticide against it. As a biopesticide source, we explored secondary metabolite-richSolanum melongenaL. (eggplant), one of the armyworm’s hosts. We found that the armyworm larvae show differential occurrence on seven eggplant varieties; the Himalayan eggplant variety RC-RL-22 (RL22) showed no armyworm infestation. When reared in a no-choice condition on RL22, larval mortality was two-fold higher, and mass was three-fold lower than the varieties showing high infestation. We tested whether RL22’s secondary metabolite(s) were associated with this hampered larval performance. Using LC-ESI-QTOF-based non-targeted metabolomics of eggplant varieties, we identified candidate metabolites. 5-O-caffeoylquinic acid (chlorogenic acid; CGA) showed a strong negative correlation (r= -0.88;p= 0.008) with the larval performance. CGA-spiked (average physiological concentration) artificial diet (CGA-AD)-fed larvae showed a three-fold mass reduction and two-fold mortality increase than the control artificial diet (AD)-fed larvae; pupation and eclosion also significantly reduced (1.3-fold and 1.4-fold, respectively) in the CGA-ingested larvae. We used a reverse genetics approach to assess thein plantainsecticidal potential of CGA. When RL22’s CGA biosynthesis gene hydroxycinnamoyl-CoA quinate transferase (SmHQT) was silenced using virus-induced gene silencing (VIGS), CGA levels decreased by three-fold. This CGA depletion rendered RL22 two-fold armyworm-susceptible than controls. Foliar CGA application restored RL22’s armyworm resistance.Overall, this study showed that CGA exhibits larvicidal properties against the armyworm. It is also safe for beneficial organisms. CGA is a well-known dietary supplement and an antioxidant for humans. Thus, it is safe for human consumption. Together, high CGA-containing varieties can be used to reduce the armyworm infestation risk. CGA is a promising biopesticide candidate for the field trial phase against the lepidopteran pests, especially armyworm. If successful, it can be integrated into the pest control measures.
Temporal Dynamics of Normalization Reweighting
Authors: Baker Daniel H. , Marinova Daniela , Aveyard Richard , Hargreaves Lydia J. , Renton Alice , Castellani Ruby , Hall Phoebe , Harmens Miriam , Holroyd Georgia , Nicholson Beth , Williams Emily L. , Hobson Hannah M. , Wade Alex R. 
Published: February 2023

1AbstractFor decades, neural suppression in early visual cortex has been thought to be fixed. But recent work has challenged this assumption by showing that suppression can bereweightedbased on recent history; when pairs of stimuli are repeatedly presented together, suppression between them strengthens. Here we investigate the temporal dynamics of this process using a steady-state visual evoked potential (SSVEP) paradigm that provides a time-resolved, direct index of suppression between pairs of stimuli flickering at different frequencies (5 and 7Hz). Our initial analysis of an existing EEG dataset (N=100) indicated that suppression increases substantially during the first 2-5 seconds of stimulus presentation (with some variation across stimulation frequency). We then collected new EEG data (N=100) replicating this finding for both monocular and dichoptic mask arrangements in a preregistered study designed to measure reweighting. A third experiment (N=20) used source localized MEG, and found that these effects are apparent in primary visual cortex (V1), consistent with results from neurophysiological work. Because long-standing theories propose inhibition/excitation differences in autism, we also compared reweighting between individuals with high vs low autistic traits, and with and without an autism diagnosis, across our 3 data sets (total N=220). We find no compelling differences in reweighting that are associated with autism. Our results support the normalization reweighting model, and indicate that for prolonged stimulation, increases in suppression occur on the order of 2-5 seconds after stimulus onset.
A Horizontal View of Primary Metabolomes in Vegetative Desiccation Tolerance
Authors: Dace Halford J.W. , Reus Robbin , Ricco Celeste Righi , Hall Robert , Farrant Jill M. , Hilhorst Henk W.M. 
Published: February 2023

AbstractVegetative desiccation tolerance (VDT), the ability of such tissues to survive the near complete loss of cellular water, is a rare but polyphyletic phenotype. It is a complex multifactorial trait, typified by some near universal (core) factors but with many and varied adaptations due to plant architecture, biochemistry and biotic/abiotic dynamics of particular ecological niches. The ability to enter into a quiescent biophysically stable state is what ultimately determines desiccation tolerance. Thus, understanding of the metabolomic complement of plants with VDT gives insight into the nature of survival as well as evolutionary aspects of VDT. In this study we measured the soluble carbohydrate profiles and the polar, TMS-derivatisable metabolomes of 7 phylogenetically diverse species with VDT, in contrast with 3 desiccation sensitive (DS) species, under conditions of full hydration, severe water deficit stress, and desiccated.Our study confirmed the existence of core mechanisms of VDT systems relying on either constitutively abundant trehalose, or the accumulation of raffinose family oligosaccharides and sucrose, with threshold ratios conditioned by other features of the metabolome. DS systems did not meet these ratios. Considerable chemical variations among VDT species suggest that similar stresses, e.g. photosynthetic stress, are dealt with using different chemical regimes. Furthermore, differences in timing of metabolic shifts suggest there is not a single “desiccation programme”, but that subprocesses are coordinated differently at different phases of drying. There is likely to be constraints on the composition of a viable dry state and how different adaptive strategies interact with the biophysical constraints of VDT.
The Genome of the Soybean Gall Midge (Resseliella maxima)
Authors: Melotto Gloria , Jones Megan W. , Bosley Kathryn , Flack Nicole , Frank Lexi E. , Jacobson Emily , Kipp Evan J. , Nelson Sally , Ramirez Mauricio , Walls Carrie , Koch Robert L. , Lindsey Amelia R. I. , Faulk Christopher 
Published: February 2023

AbstractThe cecidomyiid fly, soybean gall midge,Resseliella maximaGagné, is a recently discovered insect that feeds on soybean plants in the Midwest US.Resseliella maximalarvae feed on soybean stems which may induce plant death and can cause considerable yield losses, making it an important agricultural pest. From three pools of 50 adults each, we used long-read nanopore sequencing to assemble aR. maximareference genome. The final genome assembly is 206 Mb with 64.88X coverage, consisting of 1009 contigs with an N50 size of 714 kb. The assembly is high quality with a BUSCO score of 87.8%. Genome-wide GC level is 31.60% and DNA methylation was measured at 1.07%. TheR. maximagenome is comprised of 21.73% repetitive DNA, which is in line with other cecidomyiids. Protein prediction annotated 14,798 coding genes with 89.9% protein BUSCO score. Mitogenome analysis indicated thatR. maximaassembly is a single circular contig of 15,301 bp and shares highest identity to the mitogenome of the Asian rice gall midge,Orseolia oryzae(Wood-Mason). TheR. maximagenome has one of the highest completeness levels for a cecidomyiid and will provide a resource for research focused on the biology, genetics, and evolution of cecidomyiids, as well as plant-insect interactions in this important agricultural pest.
SeqScreen-Nano: a computational platform for rapid, in-field characterization of previously unseen pathogens
Authors: Balaji Advait , Liu Yunxi , Nute Michael G. , Hu Bingbing , Kappell Anthony , LeSassier Danielle S. , Godbold Gene D. , Ternus Krista L. , Treangen Todd J. 
Published: February 2023

ABSTRACTThe COVID-19 pandemic forever underscored the need for biosurveillance platforms capable of rapid detection of previously unseen pathogens. Oxford Nanopore Technology (ONT) couples long-read sequencing with in-field capability, opening the door to real-time, in-field biosurveillance. Though a promising technology, streaming assignment of accurate functional and taxonomic labels with nanopore reads remains challenging given: (i) individual reads can span multiple genes, (ii) individual reads may contain truncated genes, and pseudogenes, (iii) the error rate of the ONT platform that may introduce frameshifts and missense errors, and (iv) the computational costs of read-by-read analysis may exceed that of in-field computational equipment. Altogether, these challenges highlight a need for novel computational approaches. To this end, we describe SeqSeqscreen-Nano, a novel and portable computational platform for the characterization of novel pathogens. Based on results from simulated and synthetic microbial communities, SeqScreen-Nano can identify Open Reading Frames (ORFs) across the length of raw ONT reads and then use the predicted ORFs for accurate functional characterization and taxonomic classification. SeqScreen-Nano can run efficiently in a memory-constrained environment (less than 32GB of RAM), allowing it to be utilized in resource-limited settings. SeqScreen-Nano can also process reads directly from the ONT MinlON sequencing device, enabling rapid, in-field characterization of previously unseen pathogens. SeqScreen-Nano (v4.0) is available on GitLab at:https://gitlab.com/treangenlab/seqscreen
Benchmarking robust spatial transcriptomics approaches to capture the molecular landscape and pathological architecture of archived cancer tissues
Authors: Vo Tuan , Jones Kahli , Yoon Sohye , Lam Pui Yeng , Kao Yung-Ching , Zhou Chenhao , Prakrithi P. , Crawford Joanna , Walters Shaun , Gupta Ishaan , Soyer H. Peter , Khosrotehrani Kiarash , Stark Mitchell S. , Nguyen Quan 
Published: February 2023

AbtractsApplying spatial transcriptomics (ST) to explore a vast amount of formalin-fixed paraffin-embedded (FFPE) archival cancer tissues has been highly challenging due to several critical technical issues. In this work, we optimised ST protocols to generate unprecedented spatial gene expression data for FFPE skin cancer. Skin is among the most challenging tissue types for ST due to its fibrous structure and a high risk of RNAse contamination. We evaluated tissues collected from ten years to two years ago, spanning a range of tissue qualities and complexity. Technical replicates and multiple patient samples were assessed. Further, we integrated gene expression profiles with pathological information, revealing a new layer of molecular information. Such integration is powerful in cancer research and clinical applications. The data allowed us to detect the spatial expression of non-coding RNAs. Together, this work provides important technical perspectives to enable the applications of ST on archived cancer tissues.
Deep sequencing of the T cell Receptor reveals common and reproducible CD8+signatures of response to checkpoint immunotherapy
Authors: Watson Robert A. , Taylor Chelsea A. , Tong Orion , Cooper Rosalin , Jungkurth Elsita , Kumar Sharma Piyush , Storey Bethan , Ye Weiyu , Sun Bo , de los Aires Alba Verge , Matos Santo Flavia , Nassiri Isar , Gilchrist James J. , Ieremia Eleni , Middleton Mark R. , Fairfax Benjamin P. 
Published: February 2023

AbstractImmune checkpoint blockade (ICB) has markedly improved outcomes across a range of tumours, including metastatic melanoma (MM). However, peripheral biomarkers of response remain lacking and underlying mechanisms of action incompletely described. A number of studies have demonstrated the value of T cell receptor (TCR) repertoire analysis in determining associations with response, however identifying key groups of T cells based on their TCR usage has remained elusive. Here we performed deep sequencing of the TCR of CD8+T cells isolated from peripheral blood of patients receiving ICB for MM (n=91) at multiple time points, along with healthy control samples (n=42) and resected tumour specimens (from n=7 patients). Using the GLIPH2 algorithm to cluster TCR based on putative shared antigen specificity, we describe groups of TCR which expand post-ICB in responding patients which we term ‘Emergent Responder’ (ER) clones. We find that these ER clones are typically large and of a memory phenotype, with increased expression of genes encoding cytotoxic proteins. Analysis of tumours resected in advance of ICB demonstrates ER clones are enriched and expanded within the tumour compared to the periphery at pre-treatment. Significantly, we note the proportion of the peripheral repertoire occupied by ER clones strongly correlates with long-term clinical response. Clinical outcome further associated with HLA type and, crucially, can be validated across replication and independent datasets. This work provides the first-in-kind description of TCR-defined CD8+T cells that mediate the response to ICB in MM, demonstrating the prognostic utility of the peripheral immune repertoire with potential widespread therapeutic and prognostic applications.
The Crown Pearl V2: an improved genome assembly of the European freshwater pearl musselMargaritifera margaritifera(Linnaeus, 1758)
Authors: Gomes-dos-Santos André , Lopes-Lima Manuel , Machado André M. , Forest Thomas , Achaz Guillaume , Teixeira Amílcar , Prié Vincent , Castro L. Filipe C. , Froufe Elsa 
Published: February 2023

AbstractContiguous assemblies are fundamental to decipher the exact composition of extant genomes. In molluscs, this task is considerably challenging owing to their large size, heterozygosity, and widespread content of repetitive content. Consequently, the usage of long-read sequencing technologies is fundamental to achieve high contiguity and quality. The first genome assembly ofMargaritifera margaritifera(Linnaeus, 1758) (Mollusca: Bivalvia: Unionida), a culturally relevant, widespread, and highly threatened species of freshwater mussels, has been produced recently. However, the current genome is highly fragmented since the assembly relied solely on short-read approaches. To overcome this caveat, here, a new improved reference genome assembly is produced using a combination of PacBio CLR long reads and Illumina paired-end short reads. This novel genome assembly is 2.4 Gb long, organized into 1,700 scaffolds with a contig N50 length of 3.4Mbp. Theab initiogene prediction resulted in a total of 48,314 protein-coding genes. This new assembly represents a substantial improvement and is an essential resource for studying this species’ unique biological and evolutionary features that ultimately will help to promote its conservation.
Hierarchical and fine-scale mechanisms of binocular rivalry for conscious perception
Authors: Qian Chencan , Chen Zhiqiang , de Hollander Gilles , Knapen Tomas , Zhang Zihao , He Sheng , Zhang Peng 
Published: February 2023

AbstractConscious perception alternates between the two eyes’ images during binocular rivalry. How hierarchical processes in our brain interact to resolve visual competition to generate conscious perception remains unclear. Here we investigated the mesoscale neural circuitry for binocular rivalry in human cortical and subcortical areas using high-resolution functional MRI at 7 Tesla. Eye-specific response modulation in binocular rivalry was strongest in the superficial layers of V1 ocular dominance columns (ODCs), and more synchronized in the superficial and deep layers. The intraparietal sulcus (IPS) generated stronger eye-specific response modulation and increased effective connectivity to the early visual cortex during binocular rivalry compared to monocular “replay” simulations. Although there was no evidence of eye-specific rivalry modulation in the lateral geniculate nucleus (LGN) of the thalamus, strong perceptual rivalry modulation can be found in its parvocellular (P) subdivision. Finally, IPS and ventral pulvinar showed robust perceptual rivalry modulation and increased connectivity to the early visual cortex. These findings demonstrate that local interocular competition arises from lateral mutual inhibition between V1 ODCs, and feedback signals from IPS to visual cortex and visual thalamus further synchronize and resolve visual competition to generate conscious perception.Graphical abstractHighlightsEye-specific rivalry modulation is strongest in the superficial layers of V1 ODCs and more synchronized in superficial and deep layersIPS generates stronger eye-specific response modulation and increases connectivity to V1 during rivalry compared to replayLGN activity shows no evidence of eye-specific rivalry modulation but strong perceptual rivalry modulation in its P subdivisionIPS and ventral pulvinar show robust perceptual rivalry modulation and increased connectivity to the early visual cortex
Impact of aging on the immunological and microbial landscape of the lung during non-tuberculous mycobacterial infection
Authors: Cinco Isaac R. , Rhoades Nicholas S. , Napier Ethan G. , Davies Michael , Allison Derek B. , Kohama Steven G. , Bermudez Luiz , Winthrop Kevin , Fuss Cristina , Spindel Eliot R. , Messaoudi Ilhem 
Published: February 2023

ABSTRACTNontuberculous mycobacteria (NTM) are environmentally ubiquitous and predominately cause pulmonary disease (NTMPD). The incidence of NTMPD has steadily increased and is now more prevalent than that ofMycobacterium tuberculosis(M. tb) in the US. Moreover, the prevalence of NTMPD increases with age; therefore, it is likely that the burden of NTMPD will continue to increase in the coming decades as the number of those over the age of 65 increased in the U.S population. However, the mechanisms leading to higher susceptibility and severity of NTMPD with aging are poorly defined. Here, we used a rhesus macaque model of intrabronchial infection withM. aviumcomplex in young and aged animals to address this knowledge gap. Unilateral infection resulted in a robust inflammatory response predominantly in the inoculated lung, however, immune cell infiltration and antigen-specific T cell responses were detected in both lungs. Nasal, oral, and fecal swabs, and BAL samples were profiled using 16S amplicon sequencing. These data suggested that decompartmentalization of the lower respiratory microbiome was occurring, evidenced by detection of bacterial DNA typically found in the gut and oral-pharyngeal cavity in bronchoalveolar samples following infection. Radiographic studies, gross pathology, and histopathology examination revealed increased disease severity in aged compared to young animals with pulmonary consolidation, edema, and lesions. Finally, single cell RNA sequencing indicated that aged animals generated a dysregulated macrophage and CD8 T cell response to MAC infection.
Evolutionary conserved and divergent responses to copper zinc superoxide dismutase inhibition in plants
Authors: Frohn Stephanie , Haas Fabian B. , Dreyer Bernd H. , Reiss Erik V. , Ziplys Anne , Weichert Heiko , Chavez Benjamin G. , D’Auria John C. , Rensing Stefan A. , Schippers Jos H.M. 
Published: February 2023

AbstractLife evolved in the presence of reactive oxygen species (ROS) and was further challenged by two consecutive great oxidation events. Therefore, ROS are deeply intertwined into the physological, morphological and transcriptional responses of organisms. Copper zinc superoxide dismutases (CuZnSODs) evolved around the first great oxidation event and have next to their classical role in ROS detoxification also important roles in signaling and transcriptional regulation. Here we addressed the role of CuZnSODs in early land plant evolution. We show, that pharmaceutical inhibition of CuZnSODs with Lung Cancer Screen 1 (LCS-1) in different plant species, includingMarchantia polymorphaandPhyscomitrium patens, representing the evolutionary early stages of land plants, andArabidopsis thalianaas a modern vascular plant, lead to impairment of development and growth. Interestingly, Marchantia only possesses the cytosolic CuZnSOD isoform, whereasPhyscomitriumadditionally contains a plastidial isoform and Arabidopsis contains next to that a third peroxisomal isoform. An RNA-seq analysis revealed that the inhibition of CuZnSODs provoked a similar core response in all plant species analyzed, while those that contain more isoforms showed an extended response. In addition, an untargeted metabolomics approach revealed a specific metabolic signature for each plant species. Through the above approach the oxidative stress provoked by LCS-1 in plants can be specified and we argue that CuZnSOD functions are evolutionary conserved and might be important for plant terrestrialization.