bluuebunny/crossref_metadata_2025_split huggingface dataset:
A low-cost molecular test for SARS-CoV-2 detection suitable for variant discrimination and community testing using saliva
Authors: da Silva Sofia M. , Amaral Catarina , Luís Cláudia , Grilo Diana , Duarte Américo , Morais Inês , Afonso Gonçalo , Faria Nuno , Antunes Wilson , Gomes Inês , Sá-Leão Raquel , Miragaia Maria , Serrano Mónica , Pimentel Catarina 
Published: July 2023

AbstractThe gold standard for COVID-19 diagnostic testing relies on RNA extraction from naso/oropharyngeal swab followed by amplification through RT-PCR with fluorogenic probes. While the test is extremely sensitive and specific, its high cost and the potential discomfort associated with specimen collection make it suboptimal for public health screening purposes.In this study, we developed an equally reliable, but cheaper and less invasive alternative test based on a one-step RT-PCR with the DNA-intercalating dye SYBR Green, which enables the detection of SARS-CoV-2 directly from saliva samples or RNA isolated from nasopharyngeal swabs. Importantly, we found that this type of testing can be fine-tuned to discriminate SARS-CoV-2 variants of concern.The saliva RT-PCR SYBR Green test was successfully used in a mass-screening initiative targeting nearly 4500 asymptomatic children under the age of 12. Testing was performed at a reasonable cost of less than € 0.8 per child, and in some cases, the saliva test outperformed nasopharyngeal rapid antigen tests in identifying infected children. Whole genome sequencing revealed that the antigen testing failure could not be attributed to a specific lineage of SARS-CoV-2.To further reduce testing costs, we produced all the necessary enzymes and established a new RT-PCR protocol based on the EvaGreen dye. Overall, this work strongly supports the view that RT-PCR saliva tests based on DNA-intercalating dyes represent a powerful strategy for community screening of SARS-CoV-2. The tests can be easily applied to other infectious agents and, therefore, constitute a powerful resource for an effective response to future pandemics.
Functional Connectivity Development along the Sensorimotor-Association Axis Enhances the Cortical Hierarchy
Authors: Luo Audrey , Sydnor Valerie J. , Pines Adam , Larsen Bart , Alexander-Bloch Aaron F. , Cieslak Matthew , Covitz Sydney , Chen Andrew , Esper Nathalia Bianchini , Feczko Eric , Franco Alexandre R. , Gur Raquel E. , Gur Ruben C. , Houghton Audrey , Hu Fengling , Keller Arielle S. , Kiar Gregory , Mehta Kahini , Salum Giovanni A. , Tapera Tinashe , Xu Ting , Zhao Chenying , Fair Damien A. , Salo Taylor , Shinohara Russell T. , Milham Michael P. , Satterthwaite Theodore D. 
Published: July 2023

ABSTRACTHuman cortical maturation has been posited to be organized along the sensorimotor-association (S-A) axis, a hierarchical axis of brain organization that spans from unimodal sensorimotor cortices to transmodal association cortices. Here, we investigate the hypothesis that the development of functional connectivity during childhood through adolescence conforms to the cortical hierarchy defined by the S-A axis. We tested this pre-registered hypothesis in four large-scale, independent datasets (total n = 3,355; ages 5-23 years): the Philadelphia Neurodevelopmental Cohort (n = 1,207), Nathan Kline Institute-Rockland Sample (n = 397), Human Connectome Project: Development (n = 625), and Healthy Brain Network (n = 1,126). In each dataset, the development of functional connectivity systematically varied along the S-A axis. Connectivity in sensorimotor regions increased, whereas connectivity in association cortices declined, refining and reinforcing the cortical hierarchy. These robust and generalizable results establish that the sensorimotor-association axis of cortical organization encodes the dominant pattern of functional connectivity development.
Visuomotor prediction during action planning in the human frontoparietal cortex and cerebellum
Authors: Quirmbach Felix , Limanowski Jakub 
Published: July 2023

AbstractThe concept of forward models in the brain, classically applied to describing on-line motor control, can in principle be extended to action planning; i.e., assuming forward sensory predictions are issued during the mere preparation of movements. To test this idea, we combined a delayed movement task with a virtual reality based manipulation of visuomotor congruence during functional magnetic resonance imaging (fMRI). Participants executed simple hand movements after a delay. During the delay, two aspects of the upcoming movement could be cued: the movement type and the visuomotor mapping (i.e., (in)congruence of executed hand movements and visual movement feedback by a glove- controlled virtual hand). Frontoparietal areas showed increased delay period activity when preparing pre-specified movements (cued > uncued). The cerebellum showed increased activity during the preparation for incongruent > congruent visuomotor mappings. The left anterior intraparietal sulcus (aIPS) showed an interaction effect, responding most strongly when a pre-specified (cued) movement was prepared under expected visuomotor incongruence. These results suggest that motor planning entails a forward prediction of visual body movement feedback, which can be adjusted in anticipation of nonstandard visuomotor mappings, and which is likely computed by the cerebellum and integrated with state estimates for (planned) control in the aIPS.
Sugar co-ordinates plant defence signalling
Authors: Yamada Kohji , Mine Akira 
Published: July 2023

AbstractRecognition of microbial molecules triggers energy-intensive defence systems. Although successful defence should therefore depend on energy availability, whether and, if so, how cellular metabolic information is molecularly input into defence remains unclear. We show that sugar, especially glucose-6-phosphate (G6P), plays a key role in regulating the types and amplitudes of defence outputs inArabidopsis thaliana. Under sugar-sufficient conditions, protein and phosphorylation levels of calcium-dependent protein kinase 5 (CPK5) are elevated by induced expression and G6P-mediated suppression of protein phosphatases, priming defence responses. Furthermore, recognition of bacterial flagellin activates sugar transporters, leading to increased cellular G6P, which elicits CPK5-independent signalling promoting synthesis of the phytohormone salicylic acid (SA) involved in anti-bacterial defence. In contrast, while perception of fungal chitin does not promote sugar influx or SA accumulation, chitin-induced synthesis of the anti-fungal compound camalexin requires basal sugar influx activity. These results suggest that, by monitoring G6P levels, plants determine defence priming levels and execute appropriate outputs against bacterial and fungal pathogens. Together, our findings provide a comprehensive view of the roles of sugar in plant defence.
Copy number variations shape genomic structural diversity underpinning ecological adaptation in the wild tomatoSolanum chilense
Authors: Wei Kai , Stam Remco , Tellier Aurélien , Silva-Arias Gustavo A 
Published: July 2023

AbstractCopy Number Variations (CNVs) are genomic structural variations constituting genetic diversity and underpinning rapid ecological adaptation. The timing and target genes of adaptation by means of CNVs are yet to be explored at the population level in the tomato clade. Therefore, we characterize the CNV landscape ofSolanum chilense, a wild tomato species, using whole-genome data of 35 individuals from seven populations. We identify 212,207 CNVs, including 160,926 deletions and 51,281 duplications. We find CNVs for both intergenic and coding regions, and a higher number of CNVs in recently diverged populations occupying more recently colonized habitats. Population structure analyses based on CNVs and single nucleotide polymorphisms are in agreement, highlighting that the distribution of CNVs is shaped by past demographic and colonization events. Furthermore, we identify 3,539 candidate genes with highly divergent copy number profiles across populations. These genes are functionally associated with response to abiotic stimuli and stress and linked to multiple pathways of flowering time regulation. Gene copy number variation exhibits two evolutionary trends: a contraction with gene loss in central and southern coast populations, and an expansion with gene gain in the southern highland group. Genome-environments association ultimately links the dynamics of gene copy number to six climatic variables and suggests that natural selection has likely shaped patterns of CNV in response to the climatic changes during the southward range expansion ofS. chilense. Our findings provide insights into the role of CNVs underlying ecological adaptation to recently colonized habitats.
Synthetic Eco-Evolutionary Dynamics in Simple Molecular Environment
Authors: Casiraghi Luca , Mambretti Francesco , Tovo Anna , Paraboschi Elvezia Maria , Suweis Samir , Bellini Tommaso 
Published: July 2023

AbstractThe understanding of eco-evolutionary dynamics, and in particular the mechanism of coexistence of species, is still fragmentary and in need of test bench model systems. To this aim we developed a variant of SELEX in-vitro selection to study the evolution of a population of ∼ 1015single-strand DNA oligonucleotide ‘individuals’. We begin with a seed of random sequences which we select via affinity capture from ∼ 1012DNA oligomers of fixed sequence (‘resources’) over which they compete. At each cycle (‘generation’), the ecosystem is replenished via PCR amplification of survivors. Massive parallel sequencing indicates that across generations the variety of sequences (‘species’) drastically decreases, while some of them become populous and dominate the ecosystem. The simplicity of our approach, in which survival is granted by hybridization, enables a quantitative investigation of fitness through a statistical analysis of binding energies. We find that the strength of individual-resource binding dominates the selection in the first generations, while inter and intra-individual interactions become important in later stages, in parallel with the emergence of prototypical forms of mutualism and parasitism.
Increased thermal tolerance under anoxic conditions in an extremophile fish from hot sulfur springs in Mexico
Authors: Pacher Korbinian , Hernández-Román Natalia , Juarez-Lopez Alejandro , Jiménez-Jiménez Jesús Emmanuel , Lukas Juliane , Sevinchan Yunus , Krause Jens , Arias-Rodríguez Lenin , Bierbach David 
Published: July 2023

AbstractThe thermal ecology of ectotherm animals has gained considerable attention in the face of human induced climate change. Particularly in aquatic species the experimental assessment of critical thermal limits (CTminand CTmax) may help to predict possible effects of global warming on habitat suitability and ultimately species survival. Here we present data on the thermal limits of two endemic and endangered extremophile fish species, inhabiting a geothermally-heated and sulfur-rich spring system in Southern Mexico: The sulfur molly (Poecilia sulphuraria) and the widemouth gambusia (Gambusia eurystoma). Besides physiological challenges induced by toxic hydrogen sulfide and related severe hypoxia during the day, water temperatures have been previously reported to exceed those of nearby clearwater streams. We now present temperature data for various locations and years in the sulphur spring complex and conducted laboratory thermal tolerance tests (CTminand CTmax) both under normoxic as well as sever hypoxic conditions in both species. Average CTmaxlimits did not differ between species under normoxic conditions. SurprisinglyP. sulphurariawas found to reach a higher critical temperature (CTmax= 43.2°C) when tested under hypoxic conditions, whileG. eurystomaon average had a lower CTmaxwhen oxygen was absent. Based on this data we calculated both species’ thermal safety margins and used a TDT (thermal death time) model framework to relate our experimental data to observed temperatures in the natural habitat. Our findings suggest, that both species live near their thermal limits during the annual dry season and are locally already exposed to temperatures above their critical thermal limits. We discuss these findings in the light of possible physiological adaptions of the sulfur-adapted fish species and the anthropogenic threats for this unique system.
Computational and neural mechanisms underlying the influence of action affordances on value learning
Authors: Yi Sanghyun , O’Doherty John P. 
Published: July 2023

AbstractWhen encountering a novel situation, an intelligent agent needs to find out which actions are most beneficial for interacting with that environment. One purported mechanism for narrowing down the scope of possible actions is the concept of action affordance. Here, we delve into the neuro-computational mechanisms accounting for how action affordance shapes value-based learning in a novel environment by utilizing a novel task alongside computational modeling of behavioral and fMRI data collected in humans. Our findings indicate that rather than simply exerting an initial or persistent bias on value-driven choices, action affordance is better conceived of as an independent system that concurrently guides action-selection alongside value-based decision-making. These two systems engage in a competitive process to determine final action selection, governed by a dynamic meta controller. We find that the pre-supplementary motor area and anterior cingulate cortex plays a central role in exerting meta-control over the two systems while the posterior parietal cortex integrates the predictions from these two controllers of what action to select, so that the action-selection process dynamically takes into account both the expected value and appropriateness of particular actions for a given scenario.
Highly accurate estimation of cell type abundance in bulk tissues based on single-cell reference and domain adaptive matching
Authors: Guo Xin-Yang , Huang Zhao-Yang , Ju Fen , Zhao Chen-Guang , Yu Liang 
Published: July 2023

AbstractAccurately identifying the cellular composition of complex tissues is critical for understanding disease pathogenesis, early diagnosis, and prevention. However, current methods for deconvoluting bulk RNA sequencing (RNA-seq) typically rely on matched single-cell RNA sequencing (scRNA-seq) as a reference, which can be limiting due to differences in sequencing distribution and the potential for invalid information from single-cell references. To overcome these limitations, we introduced SCROAM, a novel computational method that overcomes these challenges. SCROAM transforms scRNA-seq and bulk RNA-seq into a shared feature space, effectively eliminating distributional differences in the latent space. We then generate cell-type-specific expression matrices from scRNA-seq, enabling accurate identification of cell types in bulk tissues. We evaluated the performance of SCROAM by benchmarking it against simulated datasets and human breast cancer and peripheral blood datasets, demonstrating its accuracy and robustness. To further validate SCROAM’s performance, we conducted single-cell and bulk RNA-seq experiments on mouse spinal cord tissue and applied SCROAM to identify bulk tissue cell types. Our results indicate that SCROAM is a highly effective tool for identifying similar cell types, surpassing the performance of existing methods. We then performed an integrated analysis of liver cancer and primary glioblastoma to investigate the relationship between cell type composition and clinical outcomes in various tumor types, highlighting the significance of SCROAM for understanding cellular heterogeneity in complex diseases. Overall, our work presents a novel perspective to accurately infer cellular composition and expression in bulk RNA-seq, offering valuable insights into disease pathogenesis and potential therapeutic strategies.
Ecological assessment of the Amazon sailfin catfish (Pterygoplichthysspecies) within the Indian freshwaters: a mesocosm-based approach
Authors: Mallick Suman , Hussan Ajmal , Sundaray Jitendra Kumar , Ghosal Ratna 
Published: July 2023

ABSTRACTAmazon sailfin catfish is relatively a recent invader to the open waters of India, and studies on ecological assessment of the species within the Indian freshwaters are lacking. In the present study, to assess the ecological impact of catfish, we established mesocosms mimicking the Indian freshwaters within natural ponds of eastern India using three species of native fish, rohu, catla and mrigal, and for two size classes, small (10-20 cm length) and large (20-30 cm length) native fishes. Mesocosms were maintained with (test) and without the catfish (control), and length and weight of native fish, zooplankton abundance, and several hydrological and soil parameters were measured at a monthly interval for a period of 120-days. The catfish had a significant (P<0.05) negative impact on growth of small-size rohu only. However, we found no significant (P>0.05) differences in abiotic parameters and zooplankton abundance between control and test ponds for the small-size class. We speculate that reduced growth of rohu could be due to competition from catfish in the context of feeding, and not due to modification of abiotic environment. Thus, we emphasize upon the need for behavioral studies to further assess the impact of the catfish.
Development of Specific barcodes for identification ofAloe speciesbased on chloroplast DNA barcoding
Authors: Das Subrata K. , Joshi Alpana 
Published: July 2023

ABSTRACTDNA barcoding is currently an effective and extensively used tool for species identification. The chloroplast matK (maturase K) and rbcL (Ribulose-bisphosphate large subunit) are one of the most variable coding genes of angiosperms and have been recommended as a universal barcode for land plants.Aloeis a large genus of around 500 species, and most species are widely used for traditional medicinal purposes worldwide,viz.,Aloe vera, Aloe ferox, Aloe arborescens, andAloe maculate. This study evaluated the two chloroplast DNA barcodes (matK and rbcL) to develop a theoretical base for species identification and germplasm conservation ofAloespecies. The Maximum Parsimony analysis was conducted to study the evolutionary relatedness ofAloesequences using matK and rbcL sequences retrieved from the NCBI database. The results revealed that 49Aloeaccessions were segregated into four major clades based on the matK sequence. Likewise, the 29Aloeaccessions were distributed into two major clades based on the rbcL sequence. SNP (Single Nucleotide Polymorphism) site analysis was conducted to obtain the specific barcode ofAloespecies and generate the corresponding DNA QR code that electronic devices could immediately recognize. This study provides innovative research methods for efficient species identification of the genusAloeand indicates the possibility of correctly identifying, discriminating, and documenting theAloespecies.
Surprising variety in the USP deubiquitinase catalytic mechanism
Authors: Keijzer Niels , Priyanka Anu , Stijf-Bultsma Yvette , Fish Alexander , Gersch Malte , Sixma Titia K. 
Published: July 2023

AbstractThe USP family of deubiquitinases (DUBs) controls many ubiquitin-dependent signaling events. This generates therapeutic potential, with active-site inhibitors in preclinical and clinical studies.Understanding of the USP active site was so far primarily guided by USP7 data, where the catalytic triad consists of cysteine, histidine and a third residue (first critical residue), which polarizes the histidine through a hydrogen bond. A conserved aspartate (second critical residue) is directly adjacent to this first critical residue.Here we study the roles of these critical residues in a subset of USPs and reveal a remarkable variety in function. While USP7 relies on the first critical residue for catalysis, this residue is dispensable in USP1, USP15, USP40 and USP48. Instead, their second critical residue is vital for catalysis.Interestingly, without their respective vital residue USP7, USP15 and USP40 can still perform nucleophilic attack. The diverging catalytic mechanisms of USP1 and USP7 are independent of substrate and retained in cells for USP1. The unexpected variety of catalytic mechanisms in this well-conserved protein family may generate opportunities for selective targeting of individual USPs.Abstract FigureSynopsisThe roles of the highly conserved critical residues in USP active sites are poorly understood. Here we show that these two residues have varying importance for catalysis between different USPs.Except for USP7, the majority of USPs does not rely on the canonical third catalytic residue (first critical residue). Instead, the USPs tested rely primarily on the highly conserved second critical residue.In some USPs, either critical residues can accommodate nucleophilic attack (USP7, USP40, USP15). USP1 and USP48 are unable to perform the nucleophilic attack without the second critical residue.
Alexa, it is creeping over me – Exploring the impact of privacy concerns on consumer resistance to intelligent voice assistants
Authors: Mou Yupeng , Meng Xiangxue 
Published: July 2023

PurposeWith the upgrade of natural language interaction technology, the simulation extension of intelligent voice assistants (IVAs) and the uncertainty of products and services have received more and more attention. However, most of the existing research focuses on investigating the application of theories to explain consumer behavior related to intention to use and adopt IVAs, while ignoring the impact of its privacy issues on consumer resistance. This article especially examines the negative impact of artificial intelligence-based IVAs’ privacy concerns on consumer resistance, and studies the mediating effect of perceived creepiness in the context of privacy cynicism and privacy paradox and the moderating effect of anthropomorphized roles of IVAs and perceived corporate social responsibility (CSR) of IVAs’ companies. The demographic variables are also included.Design/methodology/approachBased on the theory of human–computer interaction (HCI), this study addresses the consumer privacy concerns of IVAs, builds a model of the influence mechanism on consumer resistance, and then verifies the mediating effect of perceived creepiness and the moderating effect of anthropomorphized roles of IVAs and perceived CSR of IVAs companies. This research explores underlying mechanism with three experiments.FindingsIt turns out that consumers’ privacy concerns are related to their resistance to IVAs through perceived creepiness. The servant (vs. partner) anthropomorphized role of IVAs is likely to induce more privacy concerns and in turn higher resistance. At the same time, when the company’s CSR is perceived high, the impact of the concerns of IVAs’ privacy issues on consumer resistance will be weakened, and the intermediary mechanism of perceiving creepiness in HCI and anthropomorphism of new technology are further explained and verified. The differences between different age and gender are also revealed in the study.Originality/valueThe research conclusions have strategic reference significance for enterprises to build the design framework of IVAs and formulate the response strategy of IVAs’ privacy concerns. And it offers implications for researchers and closes the research gap of IVAs from the perspective of innovation resistance.