bluuebunny/crossref_metadata_2025_split huggingface dataset:
Threshold accumulation of a constitutive protein explainsE. colicell division behavior in nutrient upshifts
Authors: Panlilio Mia , Grilli Jacopo , Tallarico Giorgio , Iuliani Ilaria , Sclavi Bianca , Cicuta Pietro , Lagomarsino Marco Cosentino 
Published: August 2020

AbstractDespite of a boost of recent progress in dynamic single-cell measurements and analyses inE. coli, we still lack a mechanistic understanding of the determinants of the decision to divide. Specifically, the debate is open regarding the processes linking growth and chromosome replication to division, and on the molecular origin of the observed “adder correlations”, whereby cells divide adding roughly a constant volume independent of their initial volume. In order to gain insight into these questions, we interrogate dynamic size-growth behavior of single cells across nutrient upshifts with a high-precision microfluidic device. We find that the division rate changes quickly after nutrients change, much before growth rate goes to a steady state, and in a way that adder correlations are robustly conserved. Comparison of these data to simple mathematical models falsifies proposed mechanisms where replication-segregation or septum completion are the limiting step for cell division. Instead, we show that the accumulation of a putative constitutively expressed “P-sector divisor” protein explains the behavior during the shift.Significance statementThe mechanism leading to cell division in the bacteriumE. coliis unknown, but we know that it results in adding a roughly constant size every cell cycle, regardless of size at birth. While most available studies try to infer information on cell division from steadily dividing cells in constant nutrient conditions, this study leverages on a high-resolution device to monitor single-cell growth division upon nutrient changes. Comparing these data with different mathematical models, the authors are able to discriminate among fundamentally different mechanisms of cell division control, and they show that the data support a model where an unregulated protein accumulates to a threshold and triggers division.
Change in liana density over 30 years in a Bornean rain forest supports the escape hypothesis
Authors: Newbery D. M. , Zahnd C. 
Published: August 2020

AbstractLiana dynamics may influence tree dynamics and vice versa. Only long-term studies can perhaps disentangle them. In two permanent plots of lowland dipterocarp forest at Danum a liana census in 1988 was repeated in 2018. The primary forest was still in a late stage of recovery from an inferred large and natural disturbance in the past. Mean number of lianas per tree decreased by 22 and 34% in plots 1 and 2, and in different ways. By 2018 there were relatively more trees with few lianas and relatively fewer trees with many lianas than in 1988. The redistribution was strongest for overstorey trees of the Dipterocarpaceae (more with no lianas by 2018) and understorey trees of the Euphorbiaceae (many losing high loads in especially plot 2). Proportion of trees with lianas increased overall by 3.5%. Number of lianas per tree showed a quadratic relationship with tree size: maximal for large trees, fewer for smaller and very large trees. Tree survival and stem growth rate were significantly negatively related to the number of lianas after accounting for spatial autocorrelation. Monte Carlo random subsampling of trees in 1988 and 2018, to achieve statistical independence, established significance of change. Dipterocarps and euphorbs clearly differed in their liana dynamics between plots. Regression models had different forms for the two plots, which reflected a complicated structural-spatial variability in host-liana dynamics. Analysis of the abundant tree species individually, highlighted a group of emergent dipterocarps with low liana counts decreasing with time. Building on an earlier hypothesis for this forest type and site, these very large trees appear to have been losing their lianas by branch shedding, as they moved into and out of the main canopy. They were evidently ‘escaping’ from the parasite. The process may in part explain the characteristically very uneven forest canopy at Danum. Change in liana density was therefore contingent on both forest history and site succession, and on plot-level structure and tree dynamics. Liana promotion in the intermittent ENSO dry periods was seemingly being offset by closing of the forest and dominance by dipterocarps in late seral stages.
Greater TMS-evoked frontoparietal effective connectivity is correlated with better cognitive performance
Authors: Morris Timothy P. , Redondo-Camos Maria , Cattaneo Gabriele , Macia Didac , Solana-Sanchez Javier , Espanya-Irla Goretti , Delgado-Gallén Selma , Alviarez-Schulze Vanessa , Pachón-Garcia Catherine , Santarnecchi Emiliano , Tadayon Ehsan , Ozdemir Recep , Muñoz Jose Ma Tormos , Batres-Faz David , Pascual-Leone Alvaro , Shafi Mouhsin M. 
Published: August 2020

AbstractFronto-parietal activity has been related to fluid intelligence and flexible cognitive control. However, causal insights on this relation are lacking. We used real-time integration of MRI-guided TMS and EEG to characterize the spatial and temporal properties of signal propagation between these two regions and relate them to cognitive performance.31 healthy adults (55 ±6 years, 20 female) underwent TMS-EEG and a full cognitive assessment. Local and propagated current from 5 source space-reconstructed scouts ipsilateral to two stimulation sites (pre frontal cortex (PFC) and inferior parietal lobule (IPL)) was quantified in two-time windows (15-40ms and 40-80ms) and related to domain-general (global cognition) and domain-specific (memory, working memory, reasoning, flexibility, lexical access and visuo-spatial) cognitive functions.TMS-evoked activity from stimulation of the PFC and the IPL resulted in local and distributed activity across frontoparietal regions. TMS-evoked activity in local regions was not correlated with cognitive functions. In response to TMS of the PFC, propagated current to the distal superior parietal scout in the first 15-40ms was significantly associated with global cognition (β = 2.63, SE = .898,p= .008, R2= .31). Similarly, following TMS of the IPL, propagation to the middle prefrontal gyrus scout (15-40ms) was significantly associated with global cognition (β = 2.67, SE = 1.289,p= .025, R2= .27). In an exploratory step, domain-specific correlations were seen in the PFC condition.Locally evoked activity measured via source space reconstruction from TMS of two association hubs is not associated with cognitive functions. However, the propagation of the TMS pulse through frontoparietal connections is associated with overall cognitive ability. These associations are driven by a number of cognitive domains in the PFC stimulation condition.
SARS-CoV-2 ORF6 disrupts nucleocytoplasmic transport through interactions with Rae1 and Nup98
Authors: Addetia Amin , Lieberman Nicole A. P. , Phung Quynh , Xie Hong , Roychoudhury Pavitra , Shrestha Lasata , Loprieno Michelle , Huang Meei-Li , Jerome Keith R. , Greninger Alexander L. 
Published: August 2020

AbstractRNA viruses that replicate in the cytoplasm often disrupt nucleocytoplasmic transport to preferentially translate their own transcripts and prevent host antiviral responses. TheSarbecovirusaccessory protein ORF6 has previously been shown to be the major inhibitor of interferon production in both SARS-CoV and SARS-CoV-2. SARS-CoV-2 ORF6 was recently shown to co-purify with the host mRNA export factors Rae1 and Nup98. Here, we demonstrate SARS-CoV-2 ORF6 strongly represses protein expression of co-transfected reporter constructs and imprisons host mRNA in the nucleus, which is associated with its ability to co-purify with Rae1 and Nup98. These protein-protein interactions map to the C-terminus of ORF6 and can be abolished by a single amino acid mutation in Met58. Overexpression of Rae1 restores reporter expression in the presence of SARS-CoV-2 ORF6. We further identify an ORF6 mutant containing a 9-amino acid deletion, ORF6 Δ22-30, in multiple SARS-CoV-2 clinical isolates that can still downregulate the expression of a co-transfected reporter and interact with Rae1 and Nup98. SARS-CoV ORF6 also interacts with Rae1 and Nup98. However, SARS-CoV-2 ORF6 more strongly co-purifies with Rae1 and Nup98 and results in significantly reduced expression of reporter proteins compared to SARS-CoV ORF6, a potential mechanism for the delayed symptom onset and pre-symptomatic transmission uniquely associated with the SARS-CoV-2 pandemic.ImportanceSARS-CoV-2, the causative agent of COVID-19, is an RNA virus with a large genome that encodes accessory proteins. While these accessory proteins are not required for growthin vitro, they can contribute to the pathogenicity of the virus. One of SARS-CoV-2’s accessory proteins, ORF6, was recently shown to co-purify with two host proteins, Rae1 and Nup98, involved in mRNA nuclear export. We demonstrate SARS-CoV-2 ORF6 interaction with these proteins is associated with reduced expression of a reporter protein and accumulation of poly-A mRNA within the nucleus. SARS-CoV ORF6 also shows the same interactions with Rae1 and Nup98. However, SARS-CoV-2 ORF6 more strongly represses reporter expression and co-purifies with Rae1 and Nup98 compared to SARS-CoV ORF6. The ability of SARS-CoV-2 ORF6 to more strongly disrupt nucleocytoplasmic transport than SARS-CoV ORF6 may partially explain critical differences in clinical presentation between the two viruses.
Exploring the boundaries of microbial habitability in soil
Authors: Dragone Nicholas B. , Diaz Melisa A. , Hogg Ian , Lyons W. Berry , Jackson W. Andrew , Wall Diana H. , Adams Byron J. , Fierer Noah 
Published: August 2020

AbstractMicrobes are widely assumed to be capable of colonizing even the most challenging terrestrial surface environments on Earth given enough time. We would not expect to find surface soils uninhabited by microbes as soils typically harbor diverse microbial communities and viable microbes have been detected in soils exposed to even the most inhospitable conditions. However, if uninhabited soils do exist, we might expect to find them in Antarctica. We analyzed 204 ice-free soils collected from across a remote valley in the Transantarctic Mountains (84 – 85°S, 174 – 177°W) and were able to identify a potential limit of microbial habitability. While most of the soils we tested contained diverse microbial communities, with fungi being particularly ubiquitous, microbes could not be detected in many of the driest, higher elevation soils - results that were confirmed using cultivation-dependent, cultivation-independent, and metabolic assays. While we cannot confirm that this subset of soils is completely sterile and devoid of microbial life, our results do show that microbial habitability and activity can be restricted by near-continuous exposure to cold, dry, and salty conditions, establishing the environmental conditions that constrain habitability in terrestrial surface environments. Constant exposure to these conditions for thousands of years has generated uninhabited surface soil environments, with either no detectable microbes or conditions which are not suitable to sustain microbial activity. Such uninhabited soils are unlikely to be unique to the studied region with this work challenging expectations about where microbes might, or might not, be able to thrive on Earth and other planets.Significance StatementCertain surface soils in Antarctica have remained effectively uninhabited due to a near-continuous exposure to cold-dry-salty conditions. This is an unexpected result because soils, even those in hyper-arid deserts, typically contain detectable microorganisms. Additionally, the prevalence of fungi at the colder, drier, higher elevation sites suggests that certain fungi may in fact be better adapted than bacteria or archaea to some of the most challenging soil environments on Earth.
Noise-robust recognition of objects by humans and deep neural networks
Authors: Jang Hojin , McCormack Devin , Tong Frank 
Published: August 2020

AbstractDeep neural networks (DNNs) for object classification have been argued to provide the most promising model of the visual system, accompanied by claims that they have attained or even surpassed human-level performance. Here, we evaluated whether DNNs provide a viable model of human vision when tested with challenging noisy images of objects, sometimes presented at the very limits of visibility. We show that popular state-of-the-art DNNs perform in a qualitatively different manner than humans – they are unusually susceptible to spatially uncorrelated white noise and less impaired by spatially correlated noise. We implemented a noise-training procedure to determine whether noise-trained DNNs exhibit more robust responses that better match human behavioral and neural performance. We found that noise-trained DNNs provide a better qualitative match to human performance; moreover, they reliably predict human recognition thresholds on an image-by-image basis. Functional neuroimaging revealed that noise-trained DNNs provide a better correspondence to the pattern-specific neural representations found in both early visual areas and high-level object areas. A layer-specific analysis of the DNNs indicated that noise training led to broad-ranging modifications throughout the network, with greater benefits of noise robustness accruing in progressively higher layers. Our findings demonstrate that noise-trained DNNs provide a viable model to account for human behavioral and neural responses to objects in challenging noisy viewing conditions. Further, they suggest that robustness to noise may be acquired through a process of visual learning.
Detection of alternative splicing inDiabrotica virgifera virgiferaLeConte, in association with Bt resistance using RNA-seq and PacBio Iso-Seq
Authors: Zhao Zixiao , Elsik Christine G. , Hibbard Bruce E. , Shelby Kent S. 
Published: August 2020

AbstractBackgroundAlternative splicing is one of the major mechanisms that increases transcriptome diversity in eukaryotes, including insect species that have gained resistance to pesticides and Bt toxins. In western corn rootworm (Diabrotica virgifera virgiferaLeConte), neither alternative splicing nor its role in resistance to Bt toxins has been studied.ResultsTo investigate the mechanisms of Bt resistance we carried out single-molecule real-time (SMRT) transcript sequencing and Iso-seq analysis on resistant, eCry3.1Ab-selected and susceptible, unselected, western corn rootworm neonate midguts which fed on seedling maize with and without eCry3.1Ab for 12 and 24 hours. We present transcriptome-wide alternative splicing patterns of western corn rootworm midgut in response to feeding on eCry3.1Ab-expressing corn using a comprehensive approach that combines both RNA-seq and SMRT transcript sequencing techniques. We found that 67.73% of multi-exon genes are alternatively spliced, which is consistent with the high transposable element content of the genome. One of the alternative splicing events we identified was a novel peritrophic matrix protein with two alternative splicing isoforms. Analysis of differential exon usage between resistant and susceptible colonies showed that in eCry3.1Ab-resistant western corn rootworm, expression of one isoform was significantly higher than in the susceptible colony, while no significant differences between colonies were observed with the other isoform.ConclusionOur results provide the first survey of alternative splicing in western corn rootworm and suggest that the observed alternatively spliced isoforms of peritrophic matrix protein may be associated with eCry3.1Ab resistance in western corn rootworm.
Genome-wide association study of TP53 R249S mutation in hepatocellular carcinoma with aflatoxin B1 exposure and hepatitis B virus infection in Guangxi
Authors: Han Chuangye , Yu Tingdong , Qin Wei , Liao Xiwen , Huang Jianlu , Liu Zhengtao , Yu Long , Liu Xiaoguang , Chen Zhiwei , Yang Chengkun , Wang Xiangkun , Mo Shutian , Zhu Guangzhi , Su Hao , Mo Zengnan , Peng Tao 
Published: August 2020

AbstractBackground/AimsDietary aflatoxin B1 (AFB1) exposure, which induces DNA damage and codon 249 mutation of the TP53 gene, is one of the major risk factors for hepatocellular carcinoma (HCC). Hepatitis B virus (HBV) infection and AFB1 exert synergistic effects to promote carcinogenesis and TP53 R249S mutation in HCC.MethodsA genome-wide association study (GWAS) was conducted on 485 cases of HCC with chronic HBV infection, followed by a two-stage replication study on 270 cases with chronic HBV infection. Susceptibility variants for the TP53 R249S mutation in HCC were identified based on both GWAS and replication analysis. The associations of identified variants with expression levels of their located genes were validated in 20 paired independent samples.ResultsOur results showed that TP53 R249S was significantly associated with ADAMTS18 rs9930984 (adjustedP= 4.84×10−6), WDR49 rs75218075 (adjustedP= 7.36 × 10−5) and SLC8A3 rs8022091 (adjustedP= 0.042). Additionally, ADAMTS18 mRNA expression was significantly higher in HCC tissue, compared with paired non-tumor tissue (P= 0.041) and patients carrying the TT genotype at rs9930984 showed lower ADAMTS18 expression in non-tumor tissue, compared with those carrying the GT genotype (P= 0.0028).ConclusionsTP53 expression is significantly associated with R249S mutation in HCC. Our collective results suggest that rs9930984, rs75218075 and rs8022091 are associated with susceptibility to the R249S mutation in cases of HCC exposed to AFB1 and HBV infection.
The impact of the COVID-19 lockdown on maternal mental health and coping in the UK: Data from the COVID-19 New Mum Study
Authors: Dib Sarah , Rougeaux Emeline , Vázquez Adriana , Wells Jonathan , Fewtrell Mary 
Published: August 2020

AbstractBackgroundDepression and anxiety affect up to 20% of new and expectant mothers during the perinatal period; this rate may have increased due to COVID-19 and lockdown measures. This analysis aimed to assess how mothers are feeling and coping during lockdown, and to identify the potential pathways that can assist them.Methods1329 women living in the UK aged ≥18 years with an infant ≤12 months of age completed an anonymous online survey. Descriptive analysis of maternal mental health, coping, support received, activities undertaken and consequences of lockdown was conducted. Linear regression was used to predict maternal mental health and coping, using activities, support, and consequences of the lockdown as predictors, while adjusting for age, gestational age, ethnicity, income, marital status and number of children.ResultsMore than half of the participants reported feeling down (56%), lonely (59%), irritable (62%) and worried (71%), to some or high extent since lockdown began. Despite this, 70% felt able to cope with the situation. Support with her own health (95% CI .004,235), contacting infant support groups (95% CI -.003, .252), and higher infant gestational age (95% CI .000, .063) predicted better mental health. Travelling for work (95% CI -.680, - .121), lockdown having a major impact on the ability to afford food (95% CI -1.202, -.177), and having an income lower than 30k (95% CI -.475, -.042) predicted poorer mental health. Support with her own health and more equal division of household chores were associated with better coping.ConclusionDuring lockdown, a large proportion of new mothers experienced symptoms of poor mental health; mothers of infants with lower gestational age, with low income, and who are travelling to work were particularly at risk. However, greater support for maternal health and with household chores showed positive associations with maternal mental health and coping. These findings highlight the urgent need to assess maternal mental health, and to identify prevention strategies for mothers during different stages of lockdown.
Fragrances' luxury brand extension: consumer behaviour and influences
Authors: Figueiredo Jose , Eiriz Vasco 
Published: August 2020

PurposeThis article aims to understand the influences surrounding the consumption of fragrances, especially if these products fit as a brand extension of luxury brands. More specifically, it aims at identifying the main reasons behind the process of buying fragrances and the main features associated with the consumption of fragrances.Design/methodology/approachThis research adopts a qualitative approach in the form of 15 in-depth interviews with consumers of fragrances, seeking to assess attitudes and influences in the consumption of fragrances as a brand extension of luxury brands.FindingsThis research shows that the emotional use of fragrances as a luxury product is much more important than their functionality, the relationship between the studied consumers and fragrances depends on the occasion of consumption (season of the year; day or night) and the aroma and the durability of the aroma is the main decision criterion for the purchase of fragrances. Respondents have also mentioned comfort, elegance and sophistication as attributes to choose a fragrance as a luxury product.Originality/valueThis article adds to the current knowledge on the topics of luxury brand management and buying behaviour by providing a better understanding of attitudes and influences towards the use of fragrances. This research recognizes the importance of a brand extension strategy for luxury brands, especially in the case of fragrances.