bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acacetin inhibits Streptococcus pneumoniae virulence by targeting pneumolysin
Authors: Li Shufang , Lv Qianghua , Sun Xiaodi , Tang Tianzhong , Deng Xuming , Yin Yunhou , Li Li 
Published: May 2020

Abstract

Objectives
Streptococcus pneumoniae (S. pneumoniae) is an important commensal and pathogenic bacterium responsible for pneumonia, meningitis and other invasive diseases. Pneumolysin (PLY) is the major virulence factor that contributes significantly to the interaction between S. pneumoniae and the host.

Key findings
In this study, the results of antibacterial analysis, the haemolysis test and the Western blotting assay showed that acacetin inhibited PLY-mediated pore-forming activity caused by S. pneumoniae culture precipitates and purified PLY without anti-S. pneumoniae activity. In addition, acacetin treatment inhibited PLY oligomerization without affecting the expression of PLY in S. pneumoniae culture supernatants. Live/dead cells and cytotoxicity assays suggested that acacetin significantly enhanced the survival rate of injured cells by inhibiting the biological toxicity of PLY without cytotoxicity in the coculture system. The in vivo mouse model of S. pneumoniae infection further demonstrated that acacetin treatment could significantly reduce the levels of inflammatory factors (INF-γ and IL-β) in bronchoalveolar lavage fluid (BALF) and alleviate the pathological damage of lung injury.

Conclusions
Taken together, the results presented in this study indicated that acacetin inhibited the pore-forming activity of PLY and reduced the virulence of S. pneumoniae in vivo and in vitro, which may provide a leading compound for the treatment of S. pneumoniae infection.
Moving beyond the riverine barrier vicariant paradigm
Authors: Naka Luciano N. , Pil Maria W. 
Published: May 2020

AbstractOne of the main goals of evolutionary biology is to understand the processes behind current patterns of biodiversity. Shared geographic distributions among unrelated species may result from a common history, providing a unique opportunity to assess the evolution of the landscape and the origins of biodiversity. Until recently, vicariance prevailed as the main evolutionary model to be tested, and the riverine barrier hypothesis the null model for taxa with river‐bounded distributions. In recent years, however, multispecies comparative approaches have unveiled idiosyncratic scenarios among codistributed species, suggesting that rivers may or may not play a role in the speciation process. In a From the Cover article in this issue of Molecular Ecology, Kopuchian et al. (2020) explore predictions of the riverine barrier hypothesis in a major subtropical river system, evaluating the degree of mitochondrial and nuclear genomic differentiation in seven bird species with allegedly morphological differentiation across the Paraná‐Paraguay river system. The authors show that in only one case, the genetic differentiation was concordant with the river. Interestingly, pairs presented disparate divergence times and/or distinct demographic histories. In most cases, putative contact zones broadly coincided with the transition of different ecoregions, such as the Espinal/Chaco ecological ecotone. These findings argue against the role of the Paraná‐Paraguay river system as a major biogeographic barrier and highlight the need to explore the role of ecology in species diversification. Here, we feature different perspectives for studying the processes governing species divergence and suggest a basic protocol to advance the study of riverine barriers.
Gut‐brain axis serotonergic responses to acute stress exposure are microbiome‐dependent
Authors: Lyte Joshua M. , Gheorghe Cassandra E. , Goodson Michael S. , Kelley‐Loughnane Nancy , Dinan Timothy G. , Cryan John F. , Clarke Gerard 
Published: May 2020

AbstractBackgroundUnderstanding the mechanisms underpinning the response to acute stress is critical for determining how this can be modulated in both health and disease and across sexes. Stress can markedly alter the microbiome and gut‐brain axis signaling with the serotonergic system being particularly sensitive to acute stress. As the impact of acute stress on regional serotonergic dynamics in the gut‐brain axis and the contribution of the microbiome to this are poorly appreciated, we used microbiota‐deficient mice to assess whether the serotonergic response to acute stress exposure is microbiome dependent.MethodsAdult male and female conventional, germ‐free, and colonized germ‐free mice underwent a single acute stressor and samples were harvested immediately or 45 minutes following stress. Serotonin and related metabolites and serotonergic gene expression were determined.Key ResultsOur data clearly show the microbiota influenced gastrointestinal serotonergic response to acute stress in a sex‐ and region‐dependent manner. Male‐specific poststress increases in colonic serotonin were absent in germ‐free mice but normalized following colonization. mRNA serotonergic gene expression was differentially expressed in colon and ileum of germ‐free mice on a sex‐dependent basis. Within the frontal cortex, absence of the microbiome altered basal serotonin, its main metabolite 5‐hydroxyindoleacetic acid, and prevented stress‐induced increases in serotonin turnover.Conclusions and InferencesThe gut microbiome influences the set points of the brain and gastrointestinal serotonergic systems and affected their response to acute stress in a sex‐ and region‐dependent manner.
TGFam‐Finder: a novel solution for target‐gene family annotation in plants
Authors: Kim Seungill , Cheong Kyeongchae , Park Jieun , Kim Myung‐Shin , Kim Jihyun , Seo Min‐Ki , Chae Geun Young , Jang Min Jeong , Mang Hyunggon , Kwon Sun‐Ho , Kim Yong‐Min , Koo Namjin , Min Cheol Woo , Kim Kwang‐Soo , Oh Nuri , Kim Ki‐Tae , Jeon Jongbum , Kim Hyunbin , Lee Yoon‐Young , Sohn Kee Hoon , McCann Honour C. , Ye Sang‐Kyu , Kim Sun Tae , Park Kyung‐Soon , Lee Yong‐Hwan , Choi Doil 
Published: May 2020

Summary

Whole‐genome annotation error that omits essential protein‐coding genes hinders further research.

We developed Target Gene Family Finder (TGFam‐Finder), an alternative tool for the structural annotation of protein‐coding genes containing target domain(s) of interest in plant genomes. TGFam‐Finder took considerably reduced annotation run‐time and improved accuracy compared to conventional annotation tools.

Large‐scale re‐annotation of 50 plant genomes identified an average of 150, 166 and 86 additional far‐red‐impaired response 1, nucleotide‐binding and leucine‐rich‐repeat, and cytochrome P450 genes, respectively, that were missed in previous annotations. We detected significantly higher number of translated genes in the new annotations using mass spectrometry data from seven plant species compared to previous annotations.

TGFam‐Finder along with the new gene models can provide an optimized platform for comprehensive functional, comparative, and evolutionary studies in plants.
Gemma cup and gemma development in Marchantia polymorpha
Authors: Kato Hirotaka , Yasui Yukiko , Ishizaki Kimitsune 
Published: May 2020

SummaryThe basal land plant Marchantia polymorpha efficiently propagates in favourable environments through clonal progeny called gemmae. Gemmae develop in cup‐shaped receptacles known as gemma cups, which are formed on the gametophyte body. Anatomical studies have described the developmental processes involved over a century ago; however, little is known about the underlying molecular mechanisms. Recent studies have started to unravel the mechanism underlying genetic and hormonal regulation of gemma cup and gemma development, showing that it shares some regulatory mechanisms with several sporophytic organs in angiosperms. Further study of these specialized organs will contribute to our understanding of the core regulatory modules underlying organ development in land plants and how these became so diversified morphologically over the course of evolution.
Prevention of left atrium esophagus fistula: Appraisal of existing technologies and strategies
Authors: Jiang Ruhong , Zei Paul C. , Jiang Chenyang 
Published: May 2020

AbstractCatheter ablation has emerged as an effective treatment for atrial fibrillation (AF). Atrial esophageal fistula (AEF) is a rare, but feared complication. With increasing utilization of ablation therapy for AF, the understanding of the relationship between AEF and ablation has been improved in recent years. Efforts to reduce the risk of AEF have focused on decreasing the risk of severe esophageal injury (EI) and the presumed subsequent progression from EI to AEF, including esophageal temperature monitoring, esophageal cooling systems, esophageal deviation devices, and decreasing and/or curtailing ablation energy delivery. Periprocedural assessment may help identify higher risk patients and detect early esophageal lesions. This review systematically summarizes and evaluates the current strategies and techniques utilized to reduce the risk of AEF in the clinical workflow for AF ablation. We expect that this review will help clinicians to better understand the principles, advantages, and disadvantages of these methods, and to find suitable strategies using current available tools.
Singular troubles with singleton socrates
Authors: Krämer Stephan 
Published: May 2020

AbstractI identify a problem for Kit Fine’s truthmaker semantics for ground: it excludes a range of plausible structures of grounding hierarchies. Specifically, there is an attractive view about the grounds of the existence of individual singleton sets which is inconsistent under the truthmaker account. I then develop a modification of the truthmaker account which avoids this difficulty and show that it preserves most of the desirable features of the original account, such as the propositional logic of ground it yields.
Neural correlates of fluctuations in the intermediate band for heart rate and respiration are related to interoceptive perception
Authors: Keller Micha , Pelz Holger , Perlitz Volker , Zweerings Jana , Röcher Erik , Baqapuri Halim Ibrahim , Mathiak Klaus 
Published: May 2020

AbstractSupratentorial brain structures such as the insula and the cingulate cortex modulate the autonomic nervous system (ANS). The neural underpinnings of separate frequency bands for variability in cardiac and respiratory data have been suggested in explaining parasympathetic and sympathetic ANS modulation. As an extension, an intermediate (IM) band in peripheral physiology has been considered to reflect psychophysiological states during rest. Using functional magnetic resonance imaging (fMRI), we investigated the neural correlates associated with IM band variability in cardiac and respiratory rate and identified dissociable networks for LF, IM, and HF bands in both modalities. Cardiac and respiratory IM band fluctuations correlated with blood oxygen level‐dependent (BOLD) signal in the mid and posterior insula and the secondary somatosensory area, that is, regions related to interoceptive perception. These data suggest that in addition to the commonly considered LF and HF bands, other frequency components represent relevant physiological constituents. The IM band may be instrumental for assessment of the CNS‐ANS interaction. In particular, the relation between the IM band and interoception may be of physiological and clinical interest.
The spatial frequency spectrum of fearful faces modulates early and mid‐latency ERPs but not the N170
Authors: Bruchmann Maximilian , Schindler Sebastian , Straube Thomas 
Published: May 2020

AbstractPrioritized processing of fearful compared to neutral faces is reflected in behavioral advantages such as lower detection thresholds, but also in enhanced early and late event‐related potentials (ERPs). Behavioral advantages have recently been associated with the spatial frequency spectrum of fearful faces, better fitting the human contrast sensitivity function than the spectrum of neutral faces. However, it is unclear whether and to which extent early and late ERP differences are due to low‐level spatial frequency spectrum information or high‐level representations of the facial expression. In this pre‐registered EEG study (N = 38), the effects of fearful‐specific spatial frequencies on event‐related ERPs were investigated by presenting faces with fearful and neutral expressions whose spatial frequency spectra were manipulated so as to contain either the average power spectra of neutral, fearful, or both expressions combined. We found an enlarged N170 to fearful versus neutral faces, not interacting with spatial frequency. Interactions of emotional expression and spatial frequencies were observed for the P1 and Early Posterior Negativity (EPN). For both components, larger emotion differences were observed when the spectrum contained neutral as opposed to fearful frequencies. Importantly, for the EPN, fearful and neutral expressions did not differ anymore when inserting fearful frequencies into neutral expressions, whereas typical emotion differences were found when faces contained average or neutral frequencies. Our findings show that N170 emotional modulations are unaffected by expression‐specific spatial frequencies. However, expression‐specific spatial frequencies alter early and mid‐latency ERPs. Most notably, the EPN to neutral expressions is boosted by adding fearful spectra—but not vice versa.
The re‐occurrence of violations in occupational safety and health administration inspections
Authors: Mendeloff John , Gray Wayne B. , Armour Philip , Neuhauser Frank 
Published: May 2020

AbstractHow well do firms in the United States maintain compliance with occupational safety and health administration (OSHA) standards after being cited for a violation? How and why does this vary among standards? This paper identifies serious violations of 91 frequently cited standards at manufacturing plants during 1992–2002 and tracks compliance with that standard in later inspections over 10 years. While formal measures of Repeat violations are quite low, we find considerably higher re‐violation rates for some standards once we look separately at how often health standards are cited in later health inspections and safety standards cited in later safety inspections. Characteristics of the standards affect re‐violation rates, but not always in the expected direction. Standards whose violations are rated as more hazardous or which received higher initial penalties tend to have more re‐violations. These findings could reflect inspector behavior, with those standards getting more attention and thus being cited more frequently. When, as in the case of OSHA and other enforcement agencies, we know about violations only when inspectors cite them, we need to consider bureaucratic behavior as well as employers' incentives.
Malignant pleural effusion survival prognostication in an Asian population
Authors: Quek Jonathan Caleb , Tan Qiao Li , Allen John Carson , Anantham Devanand 
Published: May 2020

ABSTRACTBackground and objectiveLENT and PROMISE scores prognosticate survival in patients with MPE. Prognostication guides the selection of interventions and management. However, the predictive value of these scores and their refinements (modified‐LENT) in Asians remain unclear. We aim to evaluate the performance of LENT, modified‐LENT and clinical PROMISE scores; identify predictors of survival; and develop an alternative prognostication tool should current scores lack accuracy.MethodsRetrospective medical record review of an Asian pleuroscopy database from 2011 to 2018 of patients with MPE was conducted. The prognostic capability of current available scores were evaluated using C‐statistics. Demographic and clinical variables as predictors of survival were assessed, and an alternative model was developed using logistic regression.ResultsIn 130 patients, the C‐statistics for modified‐LENT was not significantly different from LENT (0.59 (95% CI: 0.52–0.67) vs 0.56 (95% CI: 0.49–0.63); P = 0.403). In 57 patients, the PROMISE C‐statistics was 0.72 (95% CI: 0.53–0.91). In our alternative prognostication model (n = 147), Sex, Eastern Cooperative Oncology Group status, Leukocyte count, EGFR mutation, Chemotherapy and primary Tumour type (SELECT) were predictors of 90‐day mortality (C‐statistic = 0.87 (95% CI: 0.79–0.95)). SELECT sensitivity, specificity, positive and negative predictive values, and positive and negative likelihood ratios using a predicted probability of 90‐day mortality cut‐off point of 10% were 0.91, 0.68, 0.34, 0.98, 2.83 and 0.13, respectively.ConclusionThe LENT, modified‐LENT and PROMISE scores have poor accuracy of survival prognostication in Asian patients with MPE undergoing pleuroscopy. The proposed SELECT prognostication model is accurate at identifying patients with high probability of survival at 90 days.
Arabidopsis REM16 acts as a B3 domain transcription factor to promote flowering time via directly binding to the promoters of SOC1 and FT
Authors: Yu Yanchong , Qiao Longfei , Chen Jiacai , Rong Yongheng , Zhao Yuhang , Cui Xiankui , Xu Jinpeng , Hou Xiaomin , Dong Chun‐Hai 
Published: May 2020

SummaryActin depolymerizing factor (ADF) is a key modulator for dynamic organization of actin cytoskeleton. Interestingly, it was found that the ADF1 gene silencing delays flowering, but its mechanism remains unclear. In this study, ADF1 was used as a bait to screen its interacting proteins by the yeast two‐hybrid (Y2H) system. One of them, the REM16 transcription factor was identified. As one of the AP2/B3‐like transcriptional factor family members, the REM16 contains two B3 domains and its transcript levels kept increasing during the floral transition stage. Overexpression of REM16 accelerates flowering while silencing of REM16 delays flowering. Gene expression analysis indicated that the key flowering activation genes such as CONSTANS (CO), FLOWERING LOCUS T (FT), LEAFY (LFY) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS (SOC1) were upregulated in the REM16 overexpression lines, while the transcription of the flowering suppression gene FLOWERING LOCUS C (FLC) was decreased. In contrast, the REM16 gene silencing lines contained lower transcript levels of the CO, FT, LFY and SOC1 but higher transcript levels of the FLC compared with the wild‐type plants. It was proved that REM16 could directly bind to the promoter regions of SOC1 and FT by in vitro and in vivo assays. Genetic analysis supported that REM16 acts upstream of SOC1 and FT in flowering pathways. All these studies provided strong evidence demonstrating that REM16 promotes flowering by directly activating SOC1 and FT.
A draft genome of sweet cherry (Prunus avium L.) reveals genome‐wide and local effects of domestication
Authors: Pinosio Sara , Marroni Fabio , Zuccolo Andrea , Vitulo Nicola , Mariette Stephanie , Sonnante Gabriella , Aravanopoulos Filippos A. , Ganopoulos Ioannis , Palasciano Marino , Vidotto Michele , Magris Gabriele , Iezzoni Amy , Vendramin Giovanni G. , Morgante Michele 
Published: May 2020

SummarySweet cherry (Prunus avium L.) trees are both economically important fruit crops but also important components of natural forest ecosystems in Europe, Asia and Africa. Wild and domesticated trees currently coexist in the same geographic areas with important questions arising on their historical relationships. Little is known about the effects of the domestication process on the evolution of the sweet cherry genome. We assembled and annotated the genome of the cultivated variety “Big Star*” and assessed the genetic diversity among 97 sweet cherry accessions representing three different stages in the domestication and breeding process (wild trees, landraces and modern varieties). The genetic diversity analysis revealed significant genome‐wide losses of variation among the three stages and supports a clear distinction between wild and domesticated trees, with only limited gene flow being detected between wild trees and domesticated landraces. We identified 11 domestication sweeps and five breeding sweeps covering, respectively, 11.0 and 2.4 Mb of the P. avium genome. A considerable fraction of the domestication sweeps overlaps with those detected in the related species, Prunus persica (peach), indicating that artificial selection during domestication may have acted independently on the same regions and genes in the two species. We detected 104 candidate genes in sweep regions involved in different processes, such as the determination of fruit texture, the regulation of flowering and fruit ripening and the resistance to pathogens. The signatures of selection identified will enable future evolutionary studies and provide a valuable resource for genetic improvement and conservation programs in sweet cherry.
Soluble mediators in packed red blood cells augment lipopolysaccharide‐induced monocyte interleukin‐1β production
Authors: Chong Fenny , Rooks Kelly M , Flower Robert L , Dean Melinda M 
Published: May 2020

AbstractBackground and objectivesSoluble mediators in packed red‐blood‐cell (PRBC) units have been hypothesized as a mechanism associated with transfusion‐related immune modulation. Soluble mediators including damage‐associated molecular patterns (DAMPs) are known to activate inflammasomes. Inflammasome complexes maturate caspase‐1 and interleukin (IL)‐1β. We assessed whether PRBC supernatants (SN) modulated IL‐1β driven inflammation and whether macrophage migration inhibitory factor (MIF) was a contributing factor.Materials and methodsIsolated monocytes were incubated with PRBC‐SN in an in vitro transfusion model. Lipopolysaccharide (LPS) was added in parallel to model a bacterial infection. Separately, recombinant MIF was used in the model to assess its role in IL‐1β driven inflammation. IL‐1β and caspase‐1 were quantified in the PRBC‐SN and culture SN from the in vitro model.ResultsPRBC‐SN alone did not induce IL‐1β production from monocytes. However, PRBC‐SN alone increased caspase‐1 production. LPS alone induced both IL‐1β and caspase‐1 production. PRBC‐SN augmented LPS‐driven IL‐1β and caspase‐1 production. Recombinant MIF did not modulate IL‐1β production in our model.ConclusionsSoluble mediators in PRBC modulate monocyte IL‐1β inflammation, which may be a contributing factor to adverse effects of transfusion associated with poor patient outcomes. While MIF was present in PRBC‐SN, we found no evidence that MIF was responsible for IL‐1β associated immune modulation.
A Microfluidic System to Measure Neonatal Lung Compliance Over Late Stage Development as a Functional Measure of Lung Tissue Mechanics
Authors: Schappell Laurel E. , Minahan Daniel J. , Gleghorn Jason P. 
Published: May 2020

Abstract
Premature birth interrupts the development of the lung, resulting in functional deficiencies and the onset of complex pathologies, like bronchopulmonary dysplasia (BPD), that further decrease the functional capabilities of the immature lung. The dysregulation of molecular targets has been implicated in the presentation of BPD, but there is currently no method to correlate resultant morphological changes observed in tissue histology with these perturbations to differences in function throughout saccular and alveolar lung development. Lung compliance is an aggregate measure of the lung's mechanical properties that is highly sensitive to a number of molecular, cellular, and architectural characteristics, but little is known about compliance in the neonatal mouse lung due to measurement challenges. We have developed a novel method to quantify changes in lung volume and pressure to determine inspiratory and expiratory compliance throughout neonatal mouse lung development. The compliance measurements obtained were validated against compliance values from published studies using mature lungs following enzymatic degradation of the extracellular matrix (ECM). The system was then used to quantify changes in compliance that occurred over the entire span of neonatal mouse lung development. These methods fill a critically important gap connecting powerful mouse models of development and disease to measures of functional lung mechanics critical to respiration and enable insights into the genetic, molecular, and cellular underpinnings of BPD pathology to improve lung function in premature infants.