bluuebunny/crossref_metadata_2025_split huggingface dataset:
Graded sensitivity to structure and meaning throughout the human language network
Authors: Shain Cory , Kean Hope , Casto Colton , Lipkin Benjamin , Affourtit Josef , Siegelman Matthew , Mollica Francis , Fedorenko Evelina 
Published: November 2021

AbstractHuman language has a remarkable capacity to encode complex ideas. This capacity arises because language iscompositional: the form and arrangement of words in sentences (structure) determine the conceptual relations that hold between the words’ referents (meaning). A foundational question in human cognition is whether the brain regions that support language are similarly factored into structure-selective and meaning-selective areas. In an influential study, Pallier et al. (2011, PNAS) used fMRI to investigate the brain response to sequences of real words and pseudowords and reported a sharp dissociation between structure-selective and meaning-selective brain regions. In the present study, we argue that no such dissociation emerges when individual differences in brain anatomy are considered. We report three experiments (including a close conceptual replication of Pallier et al.’s original study) that use precision fMRI methods to capture separation or overlap of function in the brains of individual participants. Our results replicate Pallier et al.’s finding that the brain’s response is modulated by the sequential structure of language but paint a different picture with respect to the structure-meaning relationship. Instead of distinct structure-selective and meaning-selective brain areas, we find distributed sensitivity to both linguistic structure and meaning throughout a broad frontotemporal brain network. Our results join a growing body of evidence for an integrated network for language in the human brain within which internal specialization is primarily a matter of degree rather than kind, in contrast with influential proposals that advocate distinct specialization of different brain areas for different types of linguistic functions.Significance StatementUsing fMRI, we show that a broad network of frontal and temporal areas in the left hemisphere of the human brain is sensitive to both the structure of language and the meaning that it encodes. This finding challenges many current theories of the neurobiology of language, which propose a sharp separation between areas that encode structure and areas that encode meaning. Instead, results support a broad distribution of word- and sentence-level processing across an integrated brain network for language.This PDF file includes:Main TextFigures 1 to 3Tables 1 to 1
Scaling between DNA and cell size governs bacterial growth homeostasis and resource allocation
Authors: Li Boyan , Zhang Songyuan , Zhang Le , Qiao Xiaoying , Shi Yiqiang , Li Cheng , Ouyang Qi , Wei Ping , Qian Long 
Published: November 2021

AbstractBacteria maintain a stable cell size and a certain DNA content through proliferation as described by classic growth laws. How cells behave when this inherent scaling is broken, however, has rarely been interrogated. Here we engineered Escherichia coli cells with extremely low DNA contents using a tunable synthetic tool CRISPRori that temporarily inhibited chromosome replication initiation. A detailed mechanistic model coupling DNA replication, cell growth, and division revealed a fundamental DNA-centric growth law, which was validated by two observations. First, lineage dynamics were robust to large CRISPRori perturbations with division cycles rapidly restoring through a timer mechanism rather than the adder rule. Second, cellular growth transitioned into a linear regime at low DNA-cytoplasm ratios. Experiments and theory showed that in this regime, cellular resource was redirected to plasmid-borne gene expression. Together with the ability of CRISPRori to bi-directionally modulate plasmid copy numbers, these findings suggest a novel strategy for bio-production enhancement.
Rapid and efficient generation of antigen-specific isogenic T cells from cryopreserved blood samples
Authors: Eerkens AL , Vledder A , van Rooij N , Foijer F , Nijman HW , de Bruyn M 
Published: November 2021

ABSTRACTObjectivesCRISPR/Cas9-mediated gene editing has been leveraged for the modification of human and mouse T cells. However, limited experience is available on the application of CRISPR/Cas9 electroporation in cryopreserved T cells collected during e.g. clinical trials.MethodsPBMCs from healthy donors were used to generate knockout T cell models for interferon-γ (IFNγ), Cbl Proto-Oncogene B (CBLB), Fas cell surface death receptor (Fas) and T cell receptor (TCRαβb) genes. The effect of CRISPR-cas9-mediated gene editing on T cells was evaluated using apoptosis assays, cytokine bead arrays and ex vivo and in vitro stimulation assays.ResultsOur results demonstrate that CRISPR/Cas9-mediated gene editing of ex vivo T cells is efficient and does not overtly affect T cell viability. Cytokine release and T cell proliferation were not affected in gene edited T cells. Interestingly, memory T cells were more susceptible to CRISPR/Cas9 gene editing than naïve T cells. Ex vivo and in vitro stimulation with antigens resulted in equivalent antigen-specific T cell responses in gene-edited and untouched control cells; making CRISPR/Cas9-mediated gene editing compatible with clinical antigen-specific T cell activation and expansion assays.ConclusionHere, we report an optimized protocol for rapid, viable and highly efficient genetic modification in ex vivo human antigen specific T cells, for subsequent functional evaluation and/or expansion. Our platform extends CRISPR/Cas9-mediated gene editing for use in gold-standard clinically-used immune-monitoring pipelines and serves as a starting point for development of analogous approaches such as those including transcriptional activators and or epigenetic modifiers.
Identification and Characterization of Long Non-Coding RNA in Tomato Roots under Salt Stress
Authors: Li Ning , Wang Zhongyu , Wang Baike , Wang Juan , Xu Ruiqiang , Yang Tao , Huang Shaoyong , Yu Qinghui , Wang Huan , Gao Jie 
Published: November 2021

AbstractAs one of the most important vegetable crops in the world, the production of tomatoes was restricted by salt stress. Therefore, it is of great interest to analyze the salt stress tolerance genes. As the non-coding RNAs (ncRNAs) with a length of more than 200 nucleotides, long non-coding RNAs (lncRNAs) lack the ability of protein-coding, but they can play crucial roles in plant development and response to abiotic stresses by regulating gene expression. Nevertheless, there are few studies on the roles of salt-induced lncRNAs in tomatoes. Therefore, we selected wild tomato Solanum pennellii (S. pennellii) and cultivated tomato M82 to be materials. By high-throughput sequencing, 1044 putative lncRNAs were identified here. Among them, 154 and 137 lncRNAs were differentially expressed in M82 and S. pennellii, respectively. Through functional analysis of target genes of differentially expressed lncRNAs (DE-lncRNAs), some genes were found to respond positively to salt stress by participating in Abscisic Acid (ABA) signaling pathway, brassinosteroid (BR) signaling pathway, ethylene (ETH) signaling pathway and anti-oxidation process. We also construct a salt-induced lncRNA-mRNA co-expression network to dissect the putative mechanisms of high salt tolerance in S. pennellii. We analyze the function of salt-induced lncRNAs in tomato roots at the genome-wide levels for the first time. These results will contribute to understanding the molecular mechanisms of salt tolerance in tomatoes from the perspective of lncRNAs.
Phage-encoded sigma factors alter bacterial dormancy
Authors: Schwartz DA , Lehmkuhl BK , Lennon JT 
Published: November 2021

ABSTRACTBy entering a reversible state of reduced metabolic activity, dormant microorganisms are able to tolerate suboptimal conditions that would otherwise reduce their fitness. Dormancy may also benefit bacteria by serving as a refuge from parasitic infections. Here we focus on dormancy in the Firmicutes, where endospore development is transcriptionally regulated by the expression of sigma factors. A disruption of this process could influence the survivorship and reproduction of phages that infect spore-forming hosts with implications for coevolutionary dynamics. Here, we characterized the distribution and diversity of sigma factors in nearly 3,500 phage genomes. Homologs of sporulation-specific sigma factors were identified in phages that infect spore-forming hosts. Unlike sigma factors required for phage reproduction, the sporulation-like sigma factors were non-essential for lytic infection. However, when expressed in the spore-forming Bacillus subtilis, sigma factors from phages activated the bacterial sporulation gene network and reduced spore yield. Our findings suggest that the acquisition of host-like transcriptional regulators may allow phages to manipulate a complex and ancient trait in one of the most abundant cell types on Earth.
Genome Compartmentalization with Nuclear Landmarks: Random yet Precise
Authors: Kamat Kartik , Qi Yifeng , Wang Yuchuan , Ma Jian , Zhang Bin 
Published: November 2021

AbstractThe three-dimensional (3D) organization of eukaryotic genomes plays an important role in genome function. While significant progress has been made in deciphering the folding mechanisms of individual chromosomes, the principles of the dynamic large-scale spatial arrangement of all chromosomes inside the nucleus are poorly understood. We use polymer simulations to model the diploid human genome compartmentalization relative to nuclear bodies such as nuclear lamina, nucleoli, and speckles. We show that a self-organization process based on a co-phase separation between chromosomes and nuclear bodies can capture various features of genome organization, including the formation of chromosome territories, phase separation of A/B compartments, and the liquid property of nuclear bodies. The simulated 3D structures quantitatively reproduce both sequencing-based genomic mapping and imaging assays that probe chromatin interaction with nuclear bodies. Importantly, our model captures the heterogeneous distribution of chromosome positioning across cells, while simultaneously producing well-defined distances between active chromatin and nuclear speckles. Such heterogeneity and preciseness of genome organization can coexist due to the non-specificity of phase separation and the slow chromosome dynamics. Together, our work reveals that the co-phase separation provides a robust mechanism for encoding functionally important 3D contacts without requiring thermodynamic equilibration that can be difficult to achieve.
Experimental and Biophysical Modeling of Transcription and Translation Dynamics in Bacterial- and Mammalian-based Cell-Free Expression Systems
Authors: Zhao Yuwen , Wang Shue 
Published: November 2021

AbstractCell-free expression (CFE) systems have been used extensively in system and synthetic biology as a promising platform for manufacturing proteins and chemicals. Currently, the most widely used CFE system is in vitro protein transcription and translation platform. As the rapidly increased applications and uses, it is crucial to have a standard biophysical model for quantitative studies of gene circuits, which will provide a fundamental understanding of basic working mechanisms of CFE systems. Current modeling approaches mainly focus on the characterization of E. coli-based CFE systems, a computational model that can be utilized to both bacterial- and mammalianbased CFE has not been investigated. Here, we developed a simple ODE (ordinary differential equation)-based biophysical model to simulate transcription and translation dynamics for both bacterial- and mammalian-based CFE systems. The key parameters were estimated and adjusted based on experimental results. We next tested four gene circuits to characterize kinetic dynamics of transcription and translation in E. coli- and HeLa-based CFE systems. The real-time transcription and translation were monitored using Broccoli aptamer, double stranded locked nucleic acid (dsLNA) probe and fluorescent protein. We demonstrated the difference of kinetic dynamics for transcription and translation in both systems, which will provide valuable information for quantitative genomic and proteomic studies. This simple biophysical model and the experimental data for both E. coli- and HeLa-based CFE will be useful for researchers that are interested in genetic engineering and CFE bio-manufacturing.
Key Factors Governing Initial Stages of Lipid Droplet Formation
Authors: Kim Siyoung , Li Chenghan , Farese Robert V. , Walther Tobias C. , Voth Gregory A. 
Published: November 2021

ABSTRACTLipid droplets (LDs) are neutral lipid storage organelles surrounded by a phospholipid (PL) monolayer. LD biogenesis from the endoplasmic reticulum (ER) is driven by phase separation of neutral lipids, overcoming surface tension and membrane deformation. However, the core biophysics of the initial steps of LD formation remain relatively poorly understood. Here, we use a tunable, phenomenological coarse-grained (CG) model to study triacylglycerol (TG) nucleation in a bilayer membrane. We show that PL rigidity has a strong influence on TG lensing and membrane remodeling: When membrane rigidity increases, TG clusters remain more planar with high anisotropy but a minor degree of phase nucleation. This finding is confirmed by free energy sampling simulations that calculate the potential of mean force (PMF) as a function of the degree of nucleation and anisotropy. We also show that asymmetric tension, controlled by the number of PLs on each membrane leaflet, determines the budding direction. A TG lens buds in the direction of the monolayer containing excess PLs to allow for better PL coverage of TG, consistent with reported experiments. Finally, two governing mechanisms of the LD growth, Ostwald ripening and merging, are observed. Taken together, this study characterizes the interplay between two thermodynamic quantities during the initial LD phases, the TG bulk free energy and membrane remodeling energy.
Optogenetic induction of appetitive and aversive taste memories in Drosophila
Authors: Jelen Meghan , Musso Pierre-Yves , Junca Pierre , Gordon Michael D. 
Published: November 2021

SUMMARYTastes are typically thought to evoke innate appetitive or aversive behaviours, prompting food acceptance or rejection. However, research in Drosophila melanogaster indicates that taste responses can be modified through experience-dependent changes in mushroom body circuits. In this study, we develop a novel taste learning paradigm using closed-loop optogenetics. We find that appetitive and aversive taste memories can be formed by pairing gustatory stimuli with optogenetic activation of sensory or dopaminergic neurons associated with reward or punishment. As with olfactory memories, distinct dopaminergic subpopulations drive the parallel formation of short- and long-term appetitive memories. Long-term memories are protein synthesis-dependent and have energetic requirements that are satisfied by a variety of caloric food sources or by direct stimulation of MB-MP1 dopaminergic neurons. Our paradigm affords new opportunities to probe plasticity mechanisms within the taste system and understand the extent to which taste responses depend on experience.
Biosorption potential and molecular characterization of metal resistant autochthonous microbes from tannery solid waste
Authors: Younas Hajira , Nazir Aisha , Latif Zakia , Thies Janice E. , Shafiq Muhammad , Firdaus-e-Bareen  
Published: November 2021

AbstractThis study encompasses isolation and screening of heavy metal-resistant fungal and bacterial strains from tannery solid waste (TSW). Twelve fungal strains and twenty-five bacterial strains were isolated from TSW. The growth of fungal strains was observed against different heavy metals ranging from 10 mg L-1 to 1050 mg L-1 and the growth of bacteria was observed in metal concentrations ranging from 10 mg L-1 to 1200 mg L-1. Five multi-metal resistant fungal isolates belonging to the genus Trichoderma and ten bacterial isolates belonging to the genus Bacillus showed good metal resistance and biosorption potential. They were identified through molecular techniques, fungi based on ITS region ribotyping, and bacteria based on 16S rRNA ribotyping. The fungal strains were characterized as T. hamatum (TSWF-06), T. harzianum (TSWF-11), T. lixii (TSWF-02) and T. pseudokoningii (TSWF-03, TSWF-10). The bacterial strains were characterized as Bacillus xiamenensis (TSW-02), B. velezensis (TSW-05), B. piscis (TSW-06), B. safensis (TSW-10), B. subtilis (TSW-14, TSW-15, TSW-17) B. licheniformis (TSW-19), B. cereus (TSW-20) and B. thuringiensis (TSW-22). The fungal strains namely, T. pseudokoningii (TSWF-03) and T. harzianum proved to be two multi-metal resistant strains with good biosorption efficiency. Unlike fungi, bacterial strains showed metal specific resistance. The strains Bacillus xiamenensis, B. subtilis (TSW-14) and B. subtilis (TSW-15) showed good biosorption efficiency against Cr, B. safensis against Cu, B. piscis and B. subtilis (TSW-17) against Pb and B. licheniformis and B. thuringiensis against Zn. The autochthonous fungal and bacterial strains can therefore be employed to clean metal contaminated environments.
Does globalisation have an impact on dual banking system productivity in selected Southeast Asian banking industry?
Authors: W Jubilee Ribed Vianneca , Kamarudin Fakarudin , Abdul Latiff Ahmed Razman , Iqbal Hussain Hafezali , Mohamad Anwar Nazratul Aina 
Published: November 2021

PurposeGlobalisation has influenced many countries, over the last few decades with financial globalisation and liberalisation bringing regulatory reforms in the banking sector. Thus, this study aims to fill a gap in the literature by examining the influence of globalisation on Islamic and conventional bank productivity in Southeast Asia.Design/methodology/approachThe sample comprised 155 banks (23 Islamic and 132 conventional) from 4 countries from 2008 to 2017. Panel data techniques will be used, together with data envelopment analysis (DEA)-based Malmquist productivity index (MPI), to investigate the impact of chosen main determinants on bank productivity. A panel regression analysis will be performed after generating the productivity index from the DEA-based MPI frontier.FindingsAccording to the findings, Islamic banks are statistically significantly more productive than conventional banks, and the findings of the t-test are corroborated by the findings of nonparametric tests. Furthermore, the findings of the panel regression model reveal that bank specific factors and macroeconomic variables are significant determinants to bank productivity. Surprisingly, the findings also show that the influence of social globalisation elements tends to be negatively related to conventional bank productivity.Originality/valueThis study adds to the existing literature by bridging the globalisation gap in the productivity of the dual banking industry, particularly in the specific context of Southeast Asia, given that the area is representative of Islamic and finance globally.
The more envious the consumer, the more impulsive? The moderating role of self-monitoring and product type
Authors: Cui Jinsheng , Zhang Mengwei , Yin Chaonan , Li Li , Zhong Jianan 
Published: November 2021

Purpose This paper aimed to explore the influence of envy on impulsive consumption from aspects of the internal psychological mechanism and boundary conditions.Design/methodology/approach Based on social comparison theory, four studies were conducted in this research: The first study explored the effect of envy on impulsive consumption; the second study explored the moderating effect of self-monitoring and the mediating effect of materialism; the third study explored the moderating effect of product type and the fourth study explored the effectiveness of social comparison contexts on the arousal of envy.Findings Study 1 showed that envy could significantly trigger consumers' impulsive consumption. Study 2 indicated that participants experiencing self-monitoring had a higher level of materialism and a stronger propensity to consume impulsively once the emotion of envy emerged. Study 3 suggested that when participants were more envious, their levels of materialism increased with more impulsivity to buy material products. Study 4 revealed that upward comparisons led to a higher level of envy and re-validated the mediating role of materialism between envy and impulsive consumption.Research limitations/implications This study provides evidence for the association between envy and consumer behaviour and clarifies the underlying mechanisms of the relationship between envy and impulsive consumption.Practical implications Marketers could take advantage of consumers' envy after social comparisons without damaging brand image.Originality/value First, this study extended the effects of envy on consumer decisions, suggesting that envy stimulates impulsive consumption by increasing consumers' materialism. Second, this study revealed the boundary condition of product type, namely, material and experiential.
Workplace incivility and bystanders’ helping intentions
Authors: Jungert Tomas , Holm Kristoffer 
Published: November 2021

Purpose
Using observational and experimental designs, the purpose of this study was to explore if the power relation between the offender and the victim of incivility and the level of perceived severity of the incivility were associated with bystanders’ intentions to help when witnessing workplace incivility.

Design/methodology/approach
In Study 1, 160 participants completed a questionnaire where they described a recent uncivil incident they had witnessed, and completed measures of perceived severity and measures of their behavioural response as bystanders. In Study 2, 183 participants were randomised to read one of two vignettes (a manager being uncivil towards a subordinate or vice versa), and completed measures of perceived severity and of their motivation to intervene. The authors investigated whether the power relation between perpetrator and victim, and the perceived severity of the uncivil exchange, were associated with prosocial bystander behaviours in Study 1 and with motivation to defend the victim of incivility in Study 2.

Findings
Higher perpetrator power was significantly associated with the incident being perceived as more severe, and higher perpetrator power was directly related to greater tendency to confront, and lower tendency to avoid, the perpetrator. Perpetrator power was indirectly associated with social support according to the perceived severity. A supervisor acting in an uncivil manner was rated as more severe than a subordinate acting in such a way. Perceived severity mediated the relationship between perpetrator power and the witness’s introjected, identified and intrinsic motivation to intervene.

Originality/value
This study extends previous work by investigating how the perpetrator’s power influences both the bystander’s prosocial behaviour and their motivation to defend the victim. Furthermore, previous research has not considered how perceptions of severity might mediate the relationship between power, behaviour and motivation.