bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive genomic analysis of Bacillus subtilis 9407 reveals its biocontrol potential against bacterial fruit blotch
Authors: Gu Xiaofei , Zeng Qingchao , Wang Yu , Li Jishun , Zhao Yu , Li Yan , Wang Qi 
Published: February 2021

AbstractBacillus subtilis, a plant-beneficial bacterial species exhibiting good biocontrol capabilities, has been widely used in agricultural production. The endophytic strain 9407 can efficiently control bacterial fruit blotch (BFB) caused by the gram-negative bacterium Acidovorax citrulli. However, the mechanism underlying its biocontrol ability remains poorly understood. Given the genomic diversity of B. subtilis, strain 9407 was sequenced and assembled in this study to determine the genome information associated with its biocontrol traits. A combination of core genome phylogenetic analysis and average nucleotide identity (ANI) analysis demonstrated that the 9407 strain belonged to B. subtilis. Various functional genes related to biocontrol traits, i.e., biofilm formation, motility, pathogen inhibition, plant growth promotion, and induction of systemic resistance, were identified in B. subtilis 9407. Four secondary metabolite biosynthesis gene clusters with antibacterial ability were also found in the B. subtilis 9407 genome, including newly identified subtilosin A, bacilysin, and bacillaene, and the previously reported surfactin. Mutants lacking sboA or bacG, which are defective in synthesizing subtilosin A or bacilysin, showed decreased inhibitory activity against A. citrulli MH21, and the triple mutant with deleted sboA, bacG, and srfAB almost completely lost its inhibitory activity. The biofilm formation and swarming motility of the sboA and bacG mutants also decreased, in turn leading to decreased colonization on melon roots and leaves. Under greenhouse conditions, the biocontrol efficacy of the sboA and bacG mutants against BFB on melon leaves decreased by 21.4 and 32.3%, respectively. Here, we report a new biocontrol pathway of B. subtilis 9407 against BFB, in which subtilosin A and bacilysin contributed to the biocontrol efficacy by improving antibacterial activity and colonization ability of the strain. The comprehensive genomic analysis of B. subtilis 9407 improves our understanding of the biocontrol mechanisms of B. subtilis, providing support for further research of its biocontrol mechanisms and field applications.
Surveilling COVID-19 Emotional Contagion on Twitter by Sentiment Analysis
Authors: Crocamo Cristina , Viviani Marco , Famiglini Lorenzo , Bartoli Francesco , Pasi Gabriella , Carrà Giuseppe 
Published: February 2021

Abstract

Background
The fight against the COVID-19 pandemic seems to encompass a social media debate, possibly resulting in emotional contagion and the need for novel surveillance approaches. In the current study, we aimed to examine the flow and content of tweets, exploring the role of COVID-19 key events on the popular Twitter platform.

Methods
Using representative freely available data, we performed a focused, social media-based analysis to capture COVID-19 discussions on Twitter, considering sentiment and longitudinal trends between January 19 and March 3, 2020. Different populations of users were considered. Core discussions were explored measuring tweets’ sentiment, by both computing a polarity compound score with 95% Confidence Interval and using a transformer-based model, pretrained on a large corpus of COVID-19-related Tweets. Context-dependent meaning and emotion-specific features were considered.

Results
We gathered 3,308,476 tweets written in English. Since the first World Health Organization report (January 21), negative sentiment proportion of tweets gradually increased as expected, with amplifications following key events. Sentiment scores were increasingly negative among most active users. Tweets content and flow revealed an ongoing scenario in which the global emergency seems difficult to be emotionally managed, as shown by sentiment trajectories.

Conclusions
Integrating social media like Twitter as essential surveillance tools in the management of the pandemic and its waves might actually represent a novel preventive approach to hinder emotional contagion, disseminating reliable information and nurturing trust. There is the need to monitor and sustain healthy behaviors as well as community supports also via social media-based preventive interventions.
Prevalence and correlates of suicidal ideation among the general population in China during the COVID-19 pandemic
Authors: Shi Le , Que Jian-Yu , Lu Zheng-An , Gong Yi-Miao , Liu Lin , Wang Yun-He , Ran Mao-Sheng , Ravindran Nisha , Ravindran Arun V. , Fazel Seena , Bao Yan-Ping , Shi Jie , Lu Lin 
Published: February 2021

Abstract

Background
The coronavirus disease 2019 (COVID-19) pandemic is a major threat to the public. However, the comprehensive profile of suicidal ideation among the general population has not been systematically investigated in a large sample in the age of COVID-19.

Methods
A national online cross-sectional survey was conducted between February 28, 2020 and March 11, 2020 in a representative sample of Chinese adults aged 18 years and older. Suicidal ideation was assessed using item 9 of the Patient Health Questionnaire-9. The prevalence of suicidal ideation and its risk factors was evaluated.

Results
A total of 56,679 participants (27,149 males and 29,530 females) were included. The overall prevalence of suicidal ideation was 16.4%, including 10.9% seldom, 4.1% often, and 1.4% always suicidal ideation. The prevalence of suicidal ideation was higher in males (19.1%) and individuals aged 18–24 years (24.7%) than in females (14.0%) and those aged 45 years and older (11.9%). Suicidal ideation was more prevalent in individuals with suspected or confirmed infection (63.0%), frontline workers (19.2%), and people with pre-existing mental disorders (41.6%). Experience of quarantine, unemployed, and increased psychological stress during the pandemic were associated with an increased risk of suicidal ideation and its severity. However, paying more attention to and gaining a better understanding of COVID-19-related knowledge, especially information about psychological interventions, could reduce the risk.

Conclusions
The estimated prevalence of suicidal ideation among the general population in China during COVID-19 was significant. The findings will be important for improving suicide prevention strategies during COVID-19.
Cardiometabolic Profile of Different Body Composition Phenotypes in Children
Authors: Ong Yi Ying , Huang Jonathan Y , Michael Navin , Sadananthan Suresh Anand , Yuan Wen Lun , Chen Ling-Wei , Karnani Neerja , Velan S Sendhil , Fortier Marielle V , Tan Kok Hian , Gluckman Peter D , Yap Fabian , Chong Yap-Seng , Godfrey Keith M , Chong Mary F-F , Chan Shiao-Yng , Lee Yung Seng , Tint Mya-Thway , Eriksson Johan G 
Published: February 2021

Abstract

Context
Cardiometabolic profiles of different body composition phenotypes are poorly characterized in young children, where it is well established that high adiposity is unfavorable, but the role of lean mass is unclear.

Objective
We hypothesized that higher lean mass attenuates cardiometabolic risk in children with high fat mass.

Methods
In 6-year-old children (n = 377) from the Growing Up in Singapore Towards healthy Outcomes (GUSTO) prospective birth cohort, whole-body composition was measured by quantitative magnetic resonance, a novel validated technology. Based on fat mass index (FMI) and lean mass index (LMI), 4 body composition phenotypes were derived: low FMI-low LMI (LF-LL), low FMI-high LMI (LF-HL), high FMI-low LMI (HF-LL), high FMI-high LMI (HF-HL).

Main Outcome Measures
Body mass index (BMI) z-score, fasting plasma glucose, insulin resistance, metabolic syndrome risk score, fatty liver index, and blood pressure

Results
Compared with the LF-HL group, children in both high FMI groups had increased BMI z-score (HF-HL: 1.43 units 95% CI [1.11,1.76]; HF-LL: 0.61 units [0.25,0.96]) and metabolic syndrome risk score (HF-HL: 1.64 [0.77,2.50]; HF-LL: 1.28 [0.34,2.21]). The HF-HL group also had increased fatty liver index (1.15 [0.54,1.77]). Girls in HF-HL group had lower fasting plasma glucose (–0.29 mmol/L [–0.55,–0.04]) and diastolic blood pressure (–3.22 mmHg [–6.03,–0.41]) than girls in the HF-LL group. No similar associations were observed in boys.

Conclusion
In a multi-ethnic Asian cohort, lean mass seemed to protect against some cardiometabolic risk markers linked with adiposity, but only in girls. The FMI seemed more important than lean mass index in relation to cardiometabolic profiles of young children.
Impaired Suppression of Glucagon in Obese Subjects Parallels Decline in Insulin Sensitivity and Beta-Cell Function
Authors: Chen Xi , Maldonado Enrique , DeFronzo Ralph A , Tripathy Devjit 
Published: February 2021

AbstractAimTo examine the relationship between plasma glucagon levels and insulin sensitivity and insulin secretion in obese subjects.MethodsSuppression of plasma glucagon was examined in 275 obese Hispanic Americans with varying glucose tolerance. All subjects received a 2-hour oral glucose tolerance test (OGTT) and a subset (n = 90) had euglycemic hyperinsulinemic clamp. During OGTT, we quantitated suppression of plasma glucagon concentration, Matsuda index of insulin sensitivity, and insulin secretion/insulin resistance (disposition) index. Plasma glucagon suppression was compared between quartiles of insulin sensitivity and beta-cell function.ResultsFasting plasma glucagon levels were similar in obese subjects with normal glucose tolerance (NGT), prediabetes, and type 2 diabetes (T2D), but the fasting glucagon/insulin ratio decreased progressively from NGT to prediabetes to T2D (9.28 ± 0.66 vs 6.84 ± 0.44 vs 5.84 ± 0.43; P &lt; 0.001). Fasting and 2-hour plasma glucagon levels during OGTT progressively increased and correlated positively with severity of insulin resistance (both Matsuda index and euglycemic hyperinsulinemic clamp). The fasting glucagon/insulin ratio declined with worsening insulin sensitivity and beta-cell function, and correlated with whole-body insulin sensitivity (Matsuda index, r = 0.81; P &lt; 0.001) and beta-cell function (r = 0.35; P &lt; 0.001). The glucagon/insulin ratio also correlated and with beta-cell function during OGTT at 60 and 120 minutes (r = −0.47; P &lt; 0.001 and r = −0.32; P &lt; 0.001).ConclusionInsulin-mediated suppression of glucagon secretion in obese subjects is impaired with increasing severity of glucose intolerance and parallels the severity of insulin resistance and beta-cell dysfunction.
Nuclear upregulation of class I phosphoinositide 3-kinase p110β correlates with high 47S rRNA levels in cancer cells
Authors: Mazloumi Gavgani Fatemeh , Karlsson Thomas , Tangen Ingvild L. , Morovicz Andrea Papdiné , Arnesen Victoria Smith , Turcu Diana C. , Ninzima Sandra , Spang Katharina , Krakstad Camilla , Guillermet-Guibert Julie , Lewis Aurélia E. 
Published: February 2021

ABSTRACT
The class I phosphoinositide 3-kinase (PI3K) catalytic subunits p110α and p110β are ubiquitously expressed but differently targeted in tumours. In cancer, PIK3CB (encoding p110β) is seldom mutated compared with PIK3CA (encoding p110α) but can contribute to tumorigenesis in certain PTEN-deficient tumours. The underlying molecular mechanisms are, however, unclear. We have previously reported that p110β is highly expressed in endometrial cancer (EC) cell lines and at the mRNA level in primary patient tumours. Here, we show that p110β protein levels are high in both the cytoplasmic and nuclear compartments in EC cells. Moreover, high nuclear:cytoplasmic staining ratios were detected in high-grade primary tumours. High levels of phosphatidylinositol (3,4,5)-trisphosphate [PtdIns(3,4,5)P3] were measured in the nucleus of EC cells, and pharmacological and genetic approaches showed that its production was partly dependent upon p110β activity. Using immunofluorescence staining, p110β and PtdIns(3,4,5)P3 were localised in the nucleolus, which correlated with high levels of 47S pre-rRNA. p110β inhibition led to a decrease in both 47S rRNA levels and cell proliferation. In conclusion, these results present a nucleolar role for p110β that may contribute to tumorigenesis in EC.
This article has an associated First Person interview with Fatemeh Mazloumi Gavgani, joint first author of the paper.
Quantitative intravital imaging in zebrafish reveals in vivo dynamics of physiological-stress-induced mitophagy
Authors: Wrighton Paul J. , Shwartz Arkadi , Heo Jin-Mi , Quenzer Eleanor D. , LaBella Kyle A. , Harper J. Wade , Goessling Wolfram 
Published: February 2021

ABSTRACT
Mitophagy, the selective recycling of mitochondria through autophagy, is a crucial metabolic process induced by cellular stress, and defects are linked to aging, sarcopenia and neurodegenerative diseases. To therapeutically target mitophagy, the fundamental in vivo dynamics and molecular mechanisms must be fully understood. Here, we generated mitophagy biosensor zebrafish lines expressing mitochondrially targeted, pH-sensitive fluorescent probes, mito-Keima and mito-EGFP–mCherry, and used quantitative intravital imaging to illuminate mitophagy during physiological stresses, namely, embryonic development, fasting and hypoxia. In fasted muscle, volumetric mitolysosome size analyses documented organelle stress response dynamics, and time-lapse imaging revealed that mitochondrial filaments undergo piecemeal fragmentation and recycling rather than the wholesale turnover observed in cultured cells. Hypoxia-inducible factor (Hif) pathway activation through physiological hypoxia or chemical or genetic modulation also provoked mitophagy. Intriguingly, mutation of a single mitophagy receptor (bnip3) prevented this effect, whereas disruption of other putative hypoxia-associated mitophagy genes [bnip3la (nix), fundc1, pink1 or prkn (Parkin)] had no effect. This in vivo imaging study establishes fundamental dynamics of fasting-induced mitophagy and identifies bnip3 as the master regulator of Hif-induced mitophagy in vertebrate muscle.
Do endotherms have thermal performance curves?
Authors: Levesque Danielle L. , Marshall Katie E. 
Published: February 2021

ABSTRACTTemperature is an important environmental factor governing the ability of organisms to grow, survive and reproduce. Thermal performance curves (TPCs), with some caveats, are useful for charting the relationship between body temperature and some measure of performance in ectotherms, and provide a standardized set of characteristics for interspecific comparisons. Endotherms, however, have a more complicated relationship with environmental temperature, as endothermy leads to a decoupling of body temperature from external temperature through use of metabolic heat production, large changes in insulation and variable rates of evaporative heat loss. This has impeded our ability to model endothermic performance in relation to environmental temperature as well as to readily compare performance between species. In this Commentary, we compare the strengths and weaknesses of potential TPC analogues (including other useful proxies for linking performance to temperature) in endotherms and suggest several ways forward in the comparative ecophysiology of endotherms. Our goal is to provide a common language with which ecologists and physiologists can evaluate the effects of temperature on performance. Key directions for improving our understanding of endotherm thermoregulatory physiology include a comparative approach to the study of the level and precision of body temperature, measuring performance directly over a range of body temperatures and building comprehensive mechanistic models of endotherm responses to environmental temperatures. We believe the answer to the question posed in the title could be ‘yes’, but only if ‘performance’ is well defined and understood in relation to body temperature variation, and the costs and benefits of endothermy are specifically modelled.
Continuous body 3-D reconstruction of limbless animals
Authors: Fu Qiyuan , Mitchel Thomas W. , Kim Jin Seob , Chirikjian Gregory S. , Li Chen 
Published: February 2021

ABSTRACT
Limbless animals such as snakes, limbless lizards, worms, eels and lampreys move their slender, long bodies in three dimensions to traverse diverse environments. Accurately quantifying their continuous body's 3-D shape and motion is important for understanding body–environment interactions in complex terrain, but this is difficult to achieve (especially for local orientation and rotation). Here, we describe an interpolation method to quantify continuous body 3-D position and orientation. We simplify the body as an elastic rod and apply a backbone optimization method to interpolate continuous body shape between end constraints imposed by tracked markers. Despite over-simplifying the biomechanics, our method achieves a higher interpolation accuracy (∼50% error) in both 3-D position and orientation compared with the widely used cubic B-spline interpolation method. Beyond snakes traversing large obstacles as demonstrated, our method applies to other long, slender, limbless animals and continuum robots. We provide codes and demo files for easy application of our method.
Olfactory tracking strategies in a neotropical fruit bat
Authors: Brokaw Alyson F. , Smotherman Michael 
Published: February 2021

ABSTRACT
Many studies have characterized olfactory-tracking behaviors in animals, and it has been proposed that search strategies may be generalizable across a wide range of species. Olfaction is important for fruit- and nectar-feeding bats, but it is uncertain whether existing olfactory search models can predict the strategies of flying mammals that emit echolocation pulses through their nose. Quantitative assessments of how well echolocating bats track and localize odor sources are lacking, so we developed a behavioral assay to characterize the olfactory detection and tracking behavior of crawling northern yellow-shouldered bats (Sturnira parvidens), a common neotropical frugivore. Trained bats were presented with a choice between control and banana-odor-infused solutions in a series of experiments that confirmed that bats are able to locate a reward based on odor cues alone and examined the effect of odor concentration on olfactory search behaviors. Decision distance (the distance from which bats made their change in direction before directly approaching the target) was distinctly bimodal, with an observed peak that coincided with an inflection point in the odor concentration gradient. We observed two main search patterns that are consistent with both serial sampling and learned route-following strategies. These results support the hypothesis that bats can combine klinotaxis with spatial awareness of experimental conditions to locate odor sources, similar to terrestrial mammals. Contrary to existing models, bats did not display prominent head-scanning behaviors during their final approach, which may be due to constraints of nasal-emitted biosonar for orientation.
Accounting for body mass effects in the estimation of field metabolic rates from body acceleration
Authors: Byrnes Evan E. , Lear Karissa O. , Brewster Lauran R. , Whitney Nicholas M. , Smukall Matthew J. , Armstrong Nicola J. , Gleiss Adrian C. 
Published: February 2021

ABSTRACT
Dynamic body acceleration (DBA), measured through animal-attached tags, has emerged as a powerful method for estimating field metabolic rates of free-ranging individuals. Following respirometry to calibrate oxygen consumption rate (ṀO2) with DBA under controlled conditions, predictive models can be applied to DBA data collected from free-ranging individuals. However, laboratory calibrations are generally performed on a relatively narrow size range of animals, which may introduce biases if predictive models are applied to differently sized individuals in the field. Here, we tested the mass dependence of the ṀO2–DBA relationship to develop an experimental framework for the estimation of field metabolic rates when organisms differ in size. We performed respirometry experiments with individuals spanning one order of magnitude in body mass (1.74–17.15 kg) and used a two-stage modelling process to assess the intraspecific scale dependence of the ṀO2–DBA relationship and incorporate such dependencies into the coefficients of ṀO2 predictive models. The final predictive model showed scale dependence; the slope of the ṀO2–DBA relationship was strongly allometric (M1.55), whereas the intercept term scaled closer to isometry (M1.08). Using bootstrapping and simulations, we evaluated the performance of this coefficient-corrected model against commonly used methods of accounting for mass effects on the ṀO2–DBA relationship and found the lowest error and bias in the coefficient-corrected approach. The strong scale dependence of the ṀO2–DBA relationship indicates that caution must be exercised when models developed using one size class are applied to individuals of different sizes.
Temperature adaptations of the thermophilic snail Echinolittorina malaccana: insights from metabolomic analysis
Authors: Chen Ya-qi , Wang Jie , Liao Ming-ling , Li Xiao-xu , Dong Yun-wei 
Published: February 2021

ABSTRACT
The periwinkle snail Echinolittorina malaccana, for which the upper lethal temperature is near 55°C, is one of the most heat-tolerant eukaryotes known. We conducted a multi-level investigation – including cardiac physiology, enzyme activity, and targeted and untargeted metabolomic analyses – that elucidated a spectrum of adaptations to extreme heat in this organism. All systems examined showed heat intensity-dependent responses. Under moderate heat stress (37–45°C), the snail depressed cardiac activity and entered a state of metabolic depression. The global metabolomic and enzymatic analyses revealed production of metabolites characteristic of oxygen-independent pathways of ATP generation (lactate and succinate) in the depressed metabolic state, which suggests that anaerobic metabolism was the main energy supply pathway under heat stress (37–52°C). The metabolomic analyses also revealed alterations in glycerophospholipid metabolism under extreme heat stress (52°C), which likely reflected adaptive changes to maintain membrane structure. Small-molecular-mass organic osmolytes (glycine betaine, choline and carnitine) showed complex changes in concentration that were consistent with a role of these protein-stabilizing solutes in protection of the proteome under heat stress. This thermophilic species can thus deploy a wide array of adaptive strategies to acclimatize to extremely high temperatures.