bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic brain activity during associative learning examined with MEG/fMRI co-processing
Authors: Nair Sangeeta , Allendorfer Jane B. , Wang Yingying , Szaflarski Jerzy P. 
Published: September 2021

ABSTRACTBackgroundDue to limitations of individual neuroimaging methods we examine spatial and temporal contributions to self-generation using multimodality imaging with functional magnetic resonance imaging (fMRI) and magnetoencephalography (MEG) within the Bayesian framework Multiple Sparse Priors (MSP).New Method24 healthy participants performed an fMRI and MEG paired-associate learning task. FMRI data were processed within Group ICA fMRI Toolbox. Independent components (ICs) were temporally sorted by task time series (|r|>0.30 threshold identified task-related ICs). Task-positive (“generate”) ICs were retained as spatial priors for MEG analyses. MEG data were processed by averaging trials to increase the signal-to-noise ratio within subjects and with an event-related theta power approach. MEG source reconstructions were constrained within the task-positive ICs for both analytical approaches.ResultsFor fMRI, five networks were identified as task-related. Four ICs underlying active generation spanned bilateral parietal, orbitofrontal, medial frontal and superior temporal regions, and occipital lobe. FMRI-constrained MEG source reconstructions yielded early visual cortex activity followed by left inferior frontal gyrus (IFG) and orbito-frontal cortex (OFC) recruitment to coalesce in the left inferior temporal lobe. For the event-related theta approach, reconstructions showed a progression of activity from bilateral temporal areas to left OFC and middle temporal gyrus, followed by right IFG.Comparison with Existing MethodsMSP analyses informed by fMRI produced more focused regional activity than reconstructions without priors suggesting increased attention and maintenance when selecting relevant semantic information during active generation.ConclusionsConstraining MEG source reconstruction to fMRI priors during active generation implicates interconnected fronto-temporal and fronto-parietal networks across time.
Wild pigs mediate far-reaching agricultural impacts on tropical forest soil microbial communities
Authors: Brearley Francis Q. , Song Hokyung , Tripathi Binu M. , Dong Ke , Zin Noraziah Mohamad , Abdul Rachman Abdul Rahim , Ickes Kalan , Adams Jonathan M. , Luskin Matthew S. 
Published: September 2021

ABSTRACTEdge effects, the altered abiotic and biotic conditions on the borders of natural areas, rarely extend more than a few hundred meters. Edge effects have rarely been linked to altered soil biota, which shape ecosystem processes including carbon storage, biogeochemical cycling, and plant performance. Here, we investigated if agriculturally-mediated increased wildlife populations affect soil biotic communities at a distance well over that of estimated edge effects when they move between agriculture and natural habitats using a 22-year fenced exclusion experiment in a primary rainforest in Peninsular Malaysia. We found that the presence of wildlife (mainly native pigs (Sus scrofa) that crop-raid in nearby oil palm plantations) was associated with higher bacterial diversity, and an altered community composition (mediated by changes in soil pH), and reduced abundances of symbiotic ectomycorrhizal fungi compared to soil in exclosures. There were only minor effects of pigs on soil chemistry or microclimate, so we suggest that changes in soil communities are driven by pigs’ leaf litter removal and alterations to plant composition. Our study highlights that indirect effects from agriculture can be transferred by wildlife >1 km into protected areas and this could have important repercussions for ecosystem processes and plant-soil feedbacks.
The Application of The Skin Virome for Human Identification
Authors: Graham Ema H. , Clarke Jennifer L. , Fernando Samodha C. , Herr Joshua R. , Adamowicz Michael S. 
Published: September 2021

AbstractThe use of skin virome for human identification purposes offers a unique approach to instances where a viable and statistically relevant human DNA profile is unavailable. The human skin virome may act as an alternative DNA profile and/or an additional form of probative genetic material. To date, no study has attempted to investigate the human virome over a time series across various physical locations of the body to identify its potential as a tool for human identification. For this study, we set out to evaluate the stability, diversity, and individualization of the human skin virome. An additional goal was to identify viral signatures that can be used in conjunction with traditional forensic STR loci. In order to accomplish this, human virome metagenomes were collected and sequenced from 42 individuals at three anatomical locations (left hand, right hand, and scalp) across multiple collections periods over a 6-month window of time. Assembly dependent and independent bioinformatic approaches were employed, along with a database-based assessment, which resulted in three sets of stable putative viral markers. In total, with the three sets combined, 59 viral species and uncharacterized viral genome assemblies were identified as being significantly stable (P=5.3×10-15). Viral diversity, based on presence or absence, is significantly different across subjects (P<0.001). Here we demonstrate that not only is the human virome applicable to be used for human identification, but we have identified many viral signatures that can be used for forensic applications, thus providing a foundation to the novel field of forensic virology.HighlightsHere we provide the largest human skin virome study, to date. Our study revealed novel diversity findings of high abundance for certain viral taxa, for example, the Cress-like DNA phages, that have not previously been characterized in human skin viral ecology studies.There were 59 putative human skin viral biomarkers suitable for human identification from the core stable human skin virome of 42 subjects.The putative markers we identified were significantly stable over a 6-month period of time within individuals and across three autosomal locations of left hand, right hand, and scalp.Diversity of profiles, based on the presence and absence of our putative marker data set, were significantly different across test subjects.
STAYGREEN-mediated chlorophyll a catabolism is critical for photosystem stability upon heat stress in ryegrass
Authors: Zhang Jing , Li Hui , Huang Xinru , Xing Jing , Yao Jiaming , Jiang Jiafu , Wang Puchang , Xu Bin 
Published: September 2021

AbstractChlorophyll (Chl) loss is one of the most visible symptoms of heat-induced leaf senescence, especially for cool-season grass species. Suppression of the Chl a Me-dechelatase gene,SGR(also named asnye1), blocked the degradation of Chl a and resulted in the ‘stay-green’ trait during leaf senescence. However, effect of Chl a catabolism on plant tolerance to long-term moderate heat stress (35-40°C) remains unclear. In this study, we suppressed the expression of Chl a catabolic gene,LpSGR, in both constitutive and inducible manners in perennial ryegrass. Constitutive suppression ofLpSGRaggravated heat stress-induced chloroplast structure and photosystem damages, disrupted energy utilization/dissipation during photosynthesis, activated ROS generation with weakened ROS-scavenging enzyme activities. Transcriptome comparison among wildtype (WT) and transgenic RNAi plants under either the optimum or high temperature conditions also emphasized the effect of Chl a catabolism on expression of genes encoding photosynthesis system, ROS-generation and scavenging system, and heat shock transcription factors. Furthermore, making use of a modified ethanol-inducible system, we generated stable transgenic perennial ryegrass to suppressLpSGRin an inducible manner. Without ethanol induction, these transgenic lines exhibited the same growth and heat tolerance traits to WT, while under the induction of ethanol spray, the transgenic lines also showed compromised heat tolerance. Taken together, our data suggest that Chl a catabolism is critical for energy dissipation and electron transfer in photosynthesis, ROS-balancing and chloroplast membrane system stability upon long-term moderate heat stress.
Quercetin prevents insulin dysfunction in hypertensive animals
Authors: Serra Cristiane Alves , dos Reis Alexandre Freire , Calsa Bruno , Bueno Cintia Sena , Helaehil Júlia Venturini , de Souza Suelen Aparecida Ribeiro , de Oliveira Camila Andrea , Vanzella Emerielle Cristine , do Amaral Maria Esméria Corezola 
Published: September 2021

AbstractAngiotensin II induced increase in hypertension enhances oxidative stress and compromises insulin action and pancreatic function. Quercetin-rich foods are beneficial for hypertensive and diabetic animals owing to their antioxidant function. The aim of this study was to evaluate the antioxidant effects of quercetin in hypertensive rats on insulin action, signaling, and secretion. Wistar rats were randomly divided into three groups: sham, hypertensive rats (H), and hypertensive rats supplemented with quercetin (HQ). After three months of initial hypertension, quercetin was administered at 50 mg/kg/day for 30 days. Our results indicate that hypertension and serum lipid peroxidation levels were reduced by quercetin supplementation. We observed increased insulin sensitivity in adipose tissue, corroborating the insulin tolerance test, HOMA index, and improvements in lipid profile. Despite normal insulin secretion at 2.8 and 20 mM of glucose, animals treated with quercetin exhibited increased number of islets per section; increased protein expression of muscarinic receptor type 3, VEGF, and catalase in islets; and hepatic mRNA levels of Ide were normalized. In conclusion, supplementation with quercetin improved insulin action and prevented pancreatic and metabolic dysfunction.
Orientations of Mistaken Point fronds indicate morphology impacted ability to survive turbulence
Authors: Vixseboxse Philip B. , Kenchington Charlotte G. , Dunn Frances S. , Mitchell Emily G. 
Published: September 2021

ABSTRACTThe Ediacaran organisms of the Mistaken Point E surface have provided crucial insight into early animal communities, including how they reproduced, the importance of Ediacaran height and what the most important factors were to their community dynamics. Here, we use this iconic community to investigate how morphological variation between eight taxa affected their ability to withstand different flow conditions. For each of Beothukis, Bradgatia, Charniodiscus procerus, Charniodiscus spinosus, Plumeropriscum, Primocandelabrum and Fractofusus we measured the orientation and length of their stems (if present) and their fronds. We statistically tested each taxon’s stem and frond orientation distributions to see whether they displayed a uniform or multimodal distribution. Where multimodal distributions were identified, the stem/frond length of each cohort was tested to identify if there were differences in size between different orientation groups. We find that Bradgatia and Thectardis show a bimodal felling direction, and infer that they were felled by the turbulent head of the felling flow. In contrast, the frondose rangeomorphs including Beothukis, Plumeropriscum, Primocandelabrum, and the arboreomorphs were felled in a single direction, indicating that they were upright in the water column, and were likely felled by the laminar tail of the felling flow. These differences in directionality suggests that an elongate habit, and particularly possession of a stem, lent greater resilience to frondose taxa against turbulent flows, suggesting that such taxa would have had improved survivability in conditions with higher background turbulence than taxa like Bradgatia and Thectardis, which lacked a stem and which had a higher centre of mass, which may have fared better in quieter water conditions.
Modeling the underlying environmental factors of milky sea case and luminous bacteria presence in Java Southern Sea in 2019
Authors: Wibowo Andri 
Published: September 2021

AbstractThe milky sea is one of the unique natural phenomena caused by the presence of luminousVibriobacteria in marine ecosystems. Recently a milky sea has been reported frequently included in the Java Southern Sea. Simultaneously, numerous remote sensing based approaches have been developed to detect the presence of luminous bacteria and the milky sea. Despite this state of the art, the information of detrimental factors of the marine bioluminescence was still limited. Then this research aims to model the underlying environmental factors causing the milky sea and luminous bacteria presence in the Java Southern Sea in 2019. The remote sensing assessment for the period of July 29-August 6, 2019 shows that the magnitude of bioluminescence measured in radiance was having a maximum value of 255 nanoW/cm2/sr and an average of 107 nanoW/cm2/sr/day (95%CI: 71.9 to 142 nanoW/cm2/sr/day). The milky sea size increased and reached its peak with a size of 44,124 km2and then declined. The average milky sea size was 37,942 km2(95% CI: 33,400 to 42,500 km2) and increased with average rate of 16.01% (95%CI: 5.41% to 26.66%). While Akaike Information Criterion (AIC) indicates that the best model to infer the relationship of bacterial bioluminescence with its environmental factors contained Chlorophyll a followed by sea surface temperature factors with AICcvalues of 101.16 (AICweight: 0.50) and 101.95 (AICweight: 0.34). This indicates that low temperature and high plankton cells is the limiting factors of the bacterial bioluminescence.
Vasoactive Intestinal Peptide Amphiphile Micelle Chemical Structure and Hydrophobic Domain Influence Immunomodulatory Potentiation
Authors: Wang Xiaofei , Zhang Rui , Lindaman Bryce D. , Leeper Caitlin N. , Schrum Adam G. , Ulery Bret D. 
Published: September 2021

AbstractVasoactive intestinal peptide (VIP) is a neuropeptide capable of downregulating innate immune responses in antigen presenting cells (APCs) by suppressing their pro-inflammatory cytokine secretion and cell surface marker expression. Though VIP’s bioactivity could possibly be leveraged as a treatment for autoimmune disorders and transplant tolerance, drug delivery innovation is required to overcome its intrinsically limited cellular delivery capacity due to its shortin vivolifetime. One option is to employ peptide amphiphiles (PAs) which are lipidated peptides capable of self-assembling into micelles in water that can enhance cellular association. With this approach in mind, a series of triblock VIP amphiphiles (VIPAs) has been synthesized to explore the influence of block arrangement and hydrophobicity on micelle biocompatibility and bioactivity. VIPA formulation has been found to influence the shape, size, and surface charge of VIPA micelles (VIPAMs) as well as their cytotoxicity and immunomodulatory effects. Specifically, the enclosed work provides strong evidence that cylindrical VIPAMs with aspect ratios of 1.5 - 150 and moderate positive surface charge are able to potentiate the bioactivity of VIP limiting TNF-α secretion and MHC II and CD86 surface expression on APCs. With this criteria, we have identified PalmK-(EK)4-VIP as our lead formulation, which showed comparable or enhanced anti-inflammatory effects relative to the unmodified VIP at all dosages evaluated. Additionally, the relationships between peptide block location and lipid block size provide further information on the chemistry-structure-function relationships of peptide amphiphile micelles for the delivery of VIP as well as potentially for other peptides more broadly.
Effectors from a Bacterial Vector-Borne Pathogen Exhibit Diverse Subcellular Localization, Expression Profiles and Manipulation of Plant Defense
Authors: Reyes-Caldas PA , Zhu Jie , Breakspear A , Thapa SP , Toruño TY , Perilla-Henao L , Casteel C , Faulkner C , Coaker G 
Published: September 2021

SUMMARYClimate change is predicted to increase the prevalence of vector borne disease due to expansion of insect populations. Candidatus Liberibacter solanacearum (CLso) is a phloem-limited pathogen associated with multiple economically important diseases in Solanaceous crops. Little is known about the strategies and pathogenicity factors CLso uses to colonize vector and host. We determined the CLso effector repertoire by predicting SEC secreted proteins across four different CLso haplotypes, investigated effector localization in planta, and profiled effector expression in vector and host. The localization of CLso effectors in Nicotiana revealed diverse eukaryotic subcellular targets. The majority of tested effectors were unable to suppress plant immune responses, indicating they possess unique activities. Expression profiling in tomato and the psyllid Bactericera cockerelli indicated CLso differentially interacts with its host and vector and can switch effector expression in response to the environment. This study reveals CLso effectors possess complex expression patterns, target diverse host organelles and the majority are unable to suppress host immune responses. A mechanistic understanding of Lso effector function will reveal novel targets and provide insight into phloem biology.
A-Prot: Protein structure modeling using MSA transformer
Authors: Hong Yiyu , Lee Juyong , Ko Junsu 
Published: September 2021

AbstractIn this study, we propose a new protein 3D structure modeling method, A-Prot, using MSA Transformer, one of the state-of-the-art protein language models. For a given MSA, an MSA feature tensor and row attention maps are extracted and converted into 2D residue-residue distance and dihedral angle predictions. We demonstrated that A-Prot predicts long-range contacts better than the existing methods. Additionally, we modeled the 3D structures of the free modeling and hard template-based modeling targets of CASP14. The assessment shows that the A-Prot models are more accurate than most top server groups of CASP14. These results imply that A-Prot captures evolutionary and structural information of proteins accurately with relatively low computational cost. Thus, A-Prot can provide a clue for the development of other protein property prediction methods.
iCn3D: From Web-based 3D Viewer to Structural Analysis Tool in Batch Mode
Authors: Wang Jiyao , Youkharibache Philippe , Marchler-Bauer Aron , Lanczycki Christopher , Zhang Dachuan , Lu Shennan , Madej Thomas , Marchler Gabriele H. , Cheng Tiejun , Chong Li Chuin , Zhao Sarah , Yang Kevin , Lin Jack , Cheng Zhiyu , Dunn Rachel , Malkaram Sridhar Acharya , Tai Chin-Hsien , Enoma David , Busby Ben , Johnson Nicholas L. , Tabaro Francesco , Song Guangfeng , Ge Yuchen 
Published: September 2021

AbstractiCn3D was initially developed as a web-based 3D molecular viewer. It then evolved from visualization into a full-featured interactive structural analysis software. It became a collaborative research instrument through the sharing of permanent, shortened URLs that encapsulate not only annotated visual molecular scenes, but also all underlying data and analysis scripts in a FAIR manner. More recently, with the growth of structural databases, the need to analyze large structural datasets systematically led us to use Python scripts and convert the code to be used in Node.js scripts. We showed a few examples of Python scripts at https://github.com/ncbi/icn3d/tree/master/icn3dpython to export secondary structures or PNG images from iCn3D. Users just need to replace the URL in the Python scripts to export other annotations from iCn3D. Furthermore, any interactive iCn3D feature can be converted into a Node.js script to be run in batch mode, enabling an interactive analysis performed on one or a handful of protein complexes to be scaled up to analysis features of large ensembles of structures. Currently available Node.js analysis scripts examples are available at https://github.com/ncbi/icn3d/tree/master/icn3dnode. This development will enable ensemble analyses on growing structural databases such as AlphaFold or RoseTTAFold on one hand and Electron Microscopy on the other. In this paper, we also review new features such as DelPhi electrostatic potential, 3D view of mutations, alignment of multiple chains, assembly of multiple structures by realignment, dynamic symmetry calculation, 2D cartoons at different levels, interactive contact maps, and use of iCn3D in Jupyter Notebook as described at https://pypi.org/project/icn3dpy.
Metagenomic identification of viral sequences in laboratory reagents
Authors: Porter Ashleigh F. , Cobbin Joanna , Li Cixiu , Eden John-Sebastian , Holmes Edward C. 
Published: September 2021

2.AbstractMetagenomic next-generation sequencing has transformed the discovery and diagnosis of infectious disease, with the power to characterize the complete ‘infectome’ (bacteria, viruses, fungi, parasites) of an individual host organism. However, the identification of novel pathogens has been complicated by widespread microbial contamination in commonly used laboratory reagents. Using total RNA sequencing (“metatranscriptomics”) we documented the presence of contaminant viral sequences in multiple libraries of ‘blank’ negative control sequencing libraries that comprise a sterile water and reagent mix. Accordingly, we identified 14 viral sequences in 7 negative control sequencing libraries. As in previous studies, several circular replication-associated protein encoding (CRESS) DNA virus-like sequences were recovered in the blank libraries, as well as contaminating sequences from the RNA virus families Totiviridae, Tombusviridae and Lentiviridae. These data suggest that the contamination of common laboratory reagents is likely widespread and can comprise a wide variety of viruses.3.Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.1.5RepositoriesThe viral genome sequence data generated in this study has been deposited in the NCBI database under accession numbers MZ824225-MZ824237. Sequence reads are available at the public Sequence Read Archive (SRA) database with accession SRX6803604 and under the BioProject accession PRJNA735051 reference numbers SRR14737466-71 and BioSample numbers SAMN20355437-40.
Novel prokaryotic sensing and regulatory system employing previously unknown nucleic acids-based receptors
Authors: Tetz Victor , Tetz George 
Published: September 2021

AbstractThe present study describes a previously unknown universal signaling and regulatory system, which we named TRB receptor system. This system is responsible for sensing, remembering, and regulating cell responses to various chemical, physical or biological stimuli. It controls cell survival, variability, reproduction, adaptation, genome changes, and gene transfer. Importantly, the TRB-receptor system is responsible for the formation and maintenance of cell memory, as well the ability to “forget” preceding events. The system is composed of DNA- and RNA-based receptors located outside the membrane named “TezRs”, as well as reverse transcriptases and integrases. The sensory and regulatory functions of TezRs enable the TRB-receptor system to control all major aspects of bacterial behavior, such as growth, biofilm formation and dispersal, utilization of nutrients including xenobiotics, virulence, chemo- and magnetoreception, response to external factors (e.g., temperature, UV, light and gas content), mutation events, phage-host interaction and recombination activity. Additionally, it supervises the function of other receptor-mediated signaling pathways. Transcriptome analysis revealed that the loss of different TezRs instigates significant alterations in gene expression.HIGHLIGHTSThe TRB-receptor system regulates bacterial sensing and response to various stimuli.The TRB-receptor system is responsible for maintenance and loss of cell memory.The TRB-receptor system comprises DNA- and RNA-based “TezRs” receptors.The TRB-receptor system relies on reverse transcriptases and recombinases.The TRB-receptor system oversees other receptor-mediated signaling pathways.TezRs are implicated in cell mutation and recombination events.