bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vibrio algicola sp. nov., isolated from the surface of coralline algae
Authors: Geng Yu-Hui , He Xiao-Yan , Li Na , Li Jian , Gu Tie-Ji , Sun Xiao-Meng , Song Xiao-Yan , Chen Xiu-Lan , Zhang Yu-Zhong , Qin Qi-Long , Zhang Xi-Ying 
Published: August 2020

A Gram-stain-negative, oxidase- and catalase-positive, facultative anaerobic and rod-shaped bacterium, designated strain SM1977T, was isolated from the surface of coralline algae collected from the intertidal zone at Qingdao, PR China. The strain grew at 10–35 °C, pH 4.5–8.5 and with 1–8.5% (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed Tween 20 and DNA. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SM1977T was affiliated with the genus

Vibrio

, having the highest sequence similarity (97.6 %) to the type strain of

Vibrio casei

, followed by those of another five species (95.6–97.6 %) in the Rumoiensis clade of the genus

Vibrio

. However, the in silico DNA–DNA hybridization (75.3–75.9 %) and average nucleotide identity (21.6–22.8 %) values of SM1977T against these close relatives were all below the corresponding thresholds to discriminate bacterial species. The major fatty acids were summed feature 3 (C16:1
ω7c and/or C16:1
ω6c), C16:0 and summed feature 8 (C18:1
ω6c and /or C18:1
ω7c). The predominant polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The sole respiratory quinone was Q-8. The genomic DNA G+C content of strain SM1977T, determined from the obtained whole genomic sequence, was 42.3 mol%. On the basis of the polyphasic results obtained in this study, strain SM1977T is considered to represent a novel species within the genus

Vibrio

, for which the name Vibrio algicola sp. nov. is proposed. The type strain is SM1977T (=MCCC 1K04351T=KCTC 72847T).
Aeromedical retrieval diagnostic trends during a period of Coronavirus 2019 lockdown
Authors: Gardiner Fergus W , Gillam Marianne , Churilov Leonid , Sharma Pritish , Steere Mardi , Hanna Michelle , Hooper Andrew , Quinlan Frank 
Published: August 2020

AbstractBackgroundWe aimed to compare the pre, lockdown, and post-lockdown aeromedical retrieval (AR) diagnostic reasons and patient demographics during a period of Coronavirus 2019 (COVID-19) social isolation.MethodsAn observational study with retrospective data collection, consisting of Australians who received an AR between the 26 January to the 23 June 2020. The main outcome measures were patient diagnostic category proportions and trends prior (28 January to 15 March), during (16 March to 4 May), and following (5 May to 23 June 2020) social isolation restrictions.ResultsThere were 16981 ARs consisting of 1959 (11.5) primary evacuations (PE) and 12724 (88.5) inter-hospital transfer (IHT), with a population median age of 52 years old (interquartile range [IQR]29.0–69.0), with 49.0% (n = 8283) of the cohort being male and 38.0% (n = 6399) being female. There were a total of 6 confirmed and 209 suspected cases of COVID-19, with the majority of cases (n = 114;53.0%) in the social isolation period. As compared to pre-restriction, the odds of retrieval for the restriction and post-restriction period differed across time between the major diagnostic groups. This included, an increase in cardiovascular retrieval for both restriction and post-restriction periods (OR 1.12 95% CI 1.02-1.24 and OR 1.18 95% CI 1.08-1.30 respectively), increases in neoplasm in the post restriction period (OR 1.31 95% CI 1.04-1.64), and increases for congenital conditions in the restriction period (OR 2.56 95% CI 1.39-4.71). Cardiovascular and congenital conditions had increased rates of priority 1 patients in the restriction and post restriction periods. There was a decrease in endocrine and metabolic disease retrievals in the restriction period (OR 0.72 95% CI 0.53-0.98). There were lower odds during the post-restriction period for a retrievals of the respiratory system (OR 0.78 95% CI 0.67-0.93), and disease of the skin (OR 0.78 95% CI 0.6-1.0). Distribution between the 2019 and 2020 time periods differed (p< 0.05), with the lockdown period resulting in a significant reduction in activity.ConclusionThe lockdown period resulted in increased AR rates of circulatory and congenital conditions. However, this period also resulted in a reduction of overall activity, possibly due to a reduction in other infectious disease rates, such as influenza, due to social distancing.
Towards chronomic medicine: Enrichment and linkage of chronotype markers with rare disease associated genes
Authors: Malik Basimah T , Hearn Timothy J 
Published: August 2020

AbstractThe role of the circadian clock is becoming apparent in many aspects of human health and disease. Large scale GWAS studies have delivered high numbers of genetic markers for chronotype, which can be used to find links to Mendelian disorders. We used the variants in the 1,000 genomes study to estimate linkage disequilibrium for these chronotype markers. We analysed genes in high linkage disequilibrium with the chronotype markers for enrichment of disease-causing genes, and looked for enrichment of common HPO terms in the wider disease associated genes. We identified that two cardiovascular disorders, cardiomyopathy, and the inherited cardiac arrhythmia Long QT Syndrome, along with the immune system disorder complement component 2 deficiency were significantly enriched MIM diseases. In contrast the most common HPO terms were developmental and neurological terms. This analysis provides a starting point for identifying the circadian contribution to disease outside of the core circadian clock genes, by providing candidate conditions and loci for identifying circadian modifier variants.
Role of necroptosis in chronic hepatic inflammation and liver disease in Cu/Zn superoxide dismutase deficient mice
Authors: Mohammed Sabira , Nicklas Evan H , Thadathil Nidheesh , Selvarani Ramasamy , Royce Gordon H , Richardson Arlan , Deepa Sathyaseelan S. 
Published: August 2020

AbstractMice deficient in the antioxidant enzyme Cu/Zn-superoxide dismutase (Sod1−/−or Sod1KO mice) develop spontaneous hepatocellular carcinoma (HCC) with age. Similar to humans, HCC development in Sod1KO mice progresses from fatty liver disease to non-alcoholic steatohepatitis (NASH) with fibrosis, which eventually progresses to HCC. Because liver inflammation is the main mechanism that drives the disease progression in chronic liver disease (CLD) and because necroptosis is a major source of inflammation, we tested the hypothesis that increased necroptosis in the liver plays a role in increased inflammation and progression to fibrosis and HCC in Sod1KO mice. Phosphorylation of MLKL (P-MLKL), a well-accepted marker of necroptosis, and expression of MLKL protein were significantly increased in the livers of Sod1KO mice compared to WT mice indicating increased necroptosis. Similarly, phosphorylation of RIPK3 and RIPK3 protein levels were also significantly increased. Markers of pro-inflammatory M1 macrophages, NLRP3 inflammasome, and transcript levels of pro-inflammatory cytokines and chemokines, e.g., TNFα, IL-6, IL-1β, and Ccl2 that are associated with human NASH and HCC, were significantly increased. Markers of fibrosis and oncogenic transcription factor STAT3 were also upregulated in the livers of Sod1KO mice. Short term treatment of Sod1KO mice with necrostatin-1s (Nec-1s), a necroptosis inhibitor, significantly reduced necroptosis, pro-inflammatory cytokines, fibrosis markers and STAT3 activation. Our data show for the first time that necroptosis-mediated inflammation contributes to fibrosis and HCC progression in Sod1KO mice, a mouse model of accelerated aging and progressive HCC development. These findings suggest that necroptosis might be a target for treating NASH and HCC.
The effect of whey protein on viral infection and replication of SARS-CoV-2 and pangolin coronavirus in vitro
Authors: Fan Huahao , Luo Yuqian , Hong Bixia , Wang Liqin , Jin Xiangshu , Chen Yangzhen , Hu Yunjia , Li Tong , Zhuang Hui , Zhou Yi-Hua , Tong Yigang , Xiang Kuanhui 
Published: August 2020

AbstractSince the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breastmilk, little is known about the antiviral property of human breastmilk to SARS-CoV-2 and its related pangolin coronavirus (GX_P2V). Here we present for the first time that whey protein from human breastmilk effectively inhibited both SARS-CoV-2 and GX_P2V by blocking viral attachment, entry and even post-entry viral replication. Moreover, human whey protein inhibited infectious virus production proved by the plaque assay. We found that whey protein from different species such as cow and goat also showed anti-coronavirus properties. And commercial bovine milk also showed similar activity. Interestingly, the main antimicrobial components of breastmilk, such as Lactoferrin and IgA antibody, showed limited anti-coronavirus activity, indicating that other factors of breastmilk may play the important anti-coronavirus role. Taken together, we reported that whey protein inhibits SARS-CoV-2 and its related virus of GX_P2V. These results rule out whey protein as a direct-acting inhibitor of SARS-CoV-2 and GX_P2V infection and replication and further investigation of its molecular mechanism of action in the context of COVID-19.
Origin of exponential growth in nonlinear reaction networks
Authors: Lin Wei-Hsiang , Kussell Edo , Young Lai-Sang , Jacobs-Wagner Christine 
Published: August 2020

AbstractExponentially growing systems are prevalent in nature, spanning all scales from biochemical reaction networks in single cells to food webs of ecosystems. How exponential growth emerges in nonlinear systems is mathematically unclear. Here, we describe a general theoretical framework that reveals underlying principles of long-term growth: scalability of flux functions and ergodicity of the rescaled systems. Our theory shows that nonlinear fluxes can generate not only balanced growth, but also oscillatory or chaotic growth modalities, explaining non-equilibrium dynamics observed in cell cycles and ecosystems. Our mathematical framework is broadly useful in predicting long-term growth rates from natural and synthetic networks, analyzing the effects of system noise and perturbations, validating empirical and phenomenological laws on growth rate, and studying autocatalysis and network evolution.SignificanceNatural systems (e.g., cells, ecosystems) generally consist of reaction networks (e.g., metabolic networks, food webs) with nonlinear flux functions (e.g., Michaelis-Menten kinetics, density-dependent selection). Despite their complex nonlinearities, these systems often exhibit simple exponential growth in the long term. How exponential growth emerges from nonlinear networks remains elusive. Our work demonstrates mathematically how two principles, multivariate scalability of flux functions and ergodicity of the rescaled system, guarantee a well-defined rate of growth. By connecting ergodic theory, a powerful branch of mathematics, to the study of growth in biology, our theoretical framework can recapitulate various growth modalities (from balanced growth to periodic, quasi-periodic or even chaotic behaviors), greatly expanding the types of growing systems that can be studied.
Single-cell atlas of tumor clonal evolution in liver cancer
Authors: Ma Lichun , Wang Limin , Chang Ching-Wen , Heinrich Sophia , Dominguez Dana , Forgues Marshonna , Candia Julián , Hernandez Maria O. , Kelly Michael , Zhao Yongmei , Tran Bao , Hernandez Jonathan M. , Davis Jeremy L. , Kleiner David E. , Wood Bradford J. , Greten Tim F. , Wang Xin Wei 
Published: August 2020

SUMMARYTumor evolution is a key feature of tumorigenesis and plays a pivotal role in driving intratumor heterogeneity, treatment failure and patients’ prognosis. Here we performed single-cell transcriptome profiling of 46 primary liver cancers from 37 patients enrolled for interventional studies. We surveyed the landscape of ~57,000 malignant and non-malignant cells and determined tumor cell clonality by developing a machine learning-based consensus clustering method. We found evidence of tumor cell branching evolution using hierarchical clustering, RNA velocity as well as reverse graph embedding methods. Interestingly, an increasing tumor cell clonality was tightly linked to patients’ prognosis, accompanied by a polarized immune cell landscape. We identified osteopontin as a key player for tumor cell evolution and microenvironmental reprogramming. Our study offers insight into the collective behavior of tumor cell communities in liver cancer as well as potential drivers for tumor evolution in response to therapy.
Longitudinal changes in aperiodic and periodic activity in electrophysiological recordings in the first seven months of life
Authors: Schaworonkow Natalie , Voytek Bradley 
Published: August 2020

AbstractNeuronal oscillations emerge in early human development. These periodic oscillations are thought to rapidly change in infancy and stabilize during maturity. Given their numerous connections to physiological and cognitive processes, as well as their pathological divergence, understanding the trajectory of oscillatory development is important for understanding healthy human brain development. This understanding is complicated by recent evidence that assessment of periodic neuronal oscillations is confounded by aperiodic neuronal activity, which is an inherent feature of electrophysiological neuronal recordings. Recent cross-sectional evidence shows that this aperiodic signal progressively shifts from childhood through early adulthood, and from early adulthood into later life. None of these studies, however, have been performed in infants, nor have they been examined longitudinally. Here, we analyzed non-invasive EEG data from 22 typically developing infants, across multiple time points, ranging between 38 and 203 days old. We show that the progressive flattening of the EEG power spectrum begins in very early development, continuing through the first several months of life. These results highlight the importance of separating the periodic and aperiodic neuronal signals, because the aperiodic signal can bias measurement of neuronal oscillations. Given the infrequent, bursting nature of oscillations in infants, we recommend the use of quantitative time domain approaches that isolate bursts and uncover changes in waveform properties of oscillatory bursts.
Influence of climate forecasts, data assimilation, and uncertainty propagation on the performance of near-term phenology forecasts
Authors: Taylor Shawn D. , White Ethan P. 
Published: August 2020

ABSTRACTEvaluation of ecological forecasts is a vital step in the continuous improvement of near-term ecological forecasts. Here we performed a thorough evaluation of a near-term phenological forecast system which has been operating for several years. We evaluated point forecast accuracy and the reliability of the prediction intervals. We also tested the contribution of upstream climate forecasts on phenology forecast proficiency. We found that 9 month climate forecasts contributed little skill overall, though some species did benefit from them. The assimilation of observed winter and spring temperature provided the largest improvement of forecast skill throughout the spring. We also found that phenology forecast prediction intervals were most robust when uncertainty was propagated from climate, phenological model, and model parameters as opposed to using climate uncertainty alone. Our analysis points the way toward several potential improvements to the forecasting system, which can be re-evaluated at a future date in a continuous cycle of forecast refinement.
Spontaneous activity competes externally evoked responses in sensory cortex
Authors: Karvat Golan. , Alyahyay Mansour , Diester Ilka 
Published: August 2020

SummaryThe functional role of spontaneous brain activity, especially in relation to external events, is a longstanding key question in neuroscience. Intrinsic and externally-evoked activities were suggested to be anticorrelated, yet inferring an antagonistic mechanism between them remains a challenge. Here, we used beta-band (15-30 Hz) power as a proxy of spontaneous activity in the rat somatosensory cortex during a detection task. Beta-power anticorrelated with sensory-evoked-responses, and high rates of spontaneously occurring beta-bursts predicted reduced detection. By applying a burst-rate detection algorithm in real-time and trial-by-trial stimulus-intensity adjustment, this influence could be counterbalanced. Mechanistically, bursts in all bands indicated transient synchronization of cell assemblies, but only beta-bursts were followed by a reduction in firing-rate. Our findings reveal that spontaneous beta-bursts reflect a dynamic state that competes with external stimuli.
Protein Plasticity and its Role in Cellular Functions
Authors: Ilyas Sidra , Manan Abdul 
Published: August 2020

ABSTRACTThe contribution of redox active properties of cysteines in intrinsically disordered regions (IDRs) of proteins is not very well acknowledged. Despite of providing structural stability and rigidity, intrinsically disordered cysteines are exceptional redox sensors and the redox status of the protein defines its structure. Experimental evidence suggests that the conformational heterogeneity of cysteines in intrinsically disordered proteins (IDPs) is related to numerous functions including regulation, structural changes and fuzzy complex formation. The unusual plasticity of IDPs make them suitable candidate to interact with many clients under specific conditions. Binding capabilities, dimerization and folding or unfolding nature of IDPs upon interaction with multiple clients assign distinct conformational changes associated with disulfide formation. Here we are going to focus on redox activity of IDPs, their dramatic roles that are not only restricted to cellular redox homeostasis and signaling pathways but also provide antioxidant, anti-apoptotic, binding and interactive power.
Mecp2 Deficiency Alters M1/M2 Gene Expresion in Bone Marrow-Derived Macrophages Upon Stimulation
Authors: Zalosnik M.I , De Filippis B , De Simone R. , Pietraforte D. , Laviola G. , Degano A.L 
Published: August 2020

ABSTRACTRett Syndrome (RTT) is a neurodevelopmental disorder mostly caused by mutations in the X-linked gene, MeCP2, which encodes for methyl-CpG binding protein 2 (MeCP2). MeCP2 is member of a family of methyl binding proteins that control the expression of several genes according to the genomic context. Emerging evidence suggests that immune dysfunctions would actively contribute to the pathogenesis of RTT. Macrophages are key effector cells that participate in several critical aspects of immune responses. The aim of our work was to assess the response of macrophagesin vitroin the context of polarizing stimuli. We used bone marrow-derived macrophages (BMDM) obtained from MeCP2308/ymice, a mouse model that carries a truncated form of MeCP2. Since MeCP2 is expressed as a “partially functional” protein in humans with RTT it becomes crucial to establish how the presence of a mutant form of MeCP2 affects immune responses to support the normal homeostasis of individuals. MeCP2 deficiency induced exacerbation of pro-inflammatory mediators and deficient immune regulatory responses under polarizing conditions. These findings suggest that MeCP2 plays a role in the establishment of macrophage polarization in the context of immune activation. Present results may have important implications in understanding RTT pathogenesis and for developing potential treatments.Conflict of interestThe authors declare no conflicts of interest.
STRATEGIC IDENTIFICATION OF NEW GENETIC DIVERSITY TO EXPAND LENTILLens culinarisMedik. PRODUCTION USING NEPAL AS AN EXAMPLE
Authors: Neupane Sandesh , Dhakal Rajeev , Wright Derek M. , Shrestha Deny Kumar , Dhakal Bishnu , Bett Kirstin E. 
Published: August 2020

AbstractThis article is written to disseminate descriptive results obtained from field experiments conducted at Bardiya, Nepal, during winter 2016 and 2017 on 324 diverse lentil (L. culinarisMedik.) genotypes obtained from genebanks and breeding programs around the world. Lentil genotypes were examined for phenological traits related to adaptation, and recommendations for potential incorporation of new exotic genotypes into Nepalese breeding programs are presented. In addition, predictions of days to flowering based on temperature and photoperiod are used to identify genotypes that hold suitability for specific growing regions in Nepal, allowing for the potential expansion of growing regions. From this study we found many potentially adapted genotypes for terai, mid-hill and high hill growing regions, the list consists of a number of large-seeded lines with yellow cotyledons, an entirely new market class of lentils in Nepal. This paper primarily targets lentil breeders and agronomists; furthermore, it can be equally informative to extension workers involved in the pulse crop research and development in Nepal and other countries with similar climatic conditions.
A toolkit to generate inducible and interconvertibleDrosophilatransgenes
Authors: Wendler Franz , Park Sangbin , Hill Claire , Galasso Alessia , Chang Kathleen R. , Awan Iman , Sudarikova Yulia , Bustamante-Sequeiros Mar , Liu Sichen , Sung Ethan , Aisabonoko Gabrielle , Kim Seung K. , Baena-Lopez Luis Alberto 
Published: August 2020

ABSTRACTThe existence of three independent binary systems for conditional gene expression (Gal4/UAS; LexA/LexAop; QF/QUAST) has greatly expanded versatile genetic analyses in the fruit flyDrosophila melanogaster; however, the experimental application of these tools is limited by the need to generate multiple collections of non-interchangeable transgenic fly strains for each inducible gene expression system. To address this practical limitation, we developed a modular vector that contains the regulatory elements from all three binary systems, enabling Gal4-, LexA- or QF-dependent expression of transgenes. Our methods also incorporate DNA elements that facilitate independent site-specific recombination and elimination of regulatory UAS, LexAop or QUAST modules with spatial and temporal control, thus offering unprecedented possibilities and logistical advantages forin vivogenetic modulation and efficient interconversion of overexpression transgenic fly lines.
Rapid Birth or Death of Centromeres on Fragmented Chromosomes in Maize
Authors: Liu Yalin , Su Handong , Zhang Jing , Shi Lindan , Liu Yang , Zhang Bing , Bai Han , Liang Shuang , Gao Zhi , Birchler James A. , Han Fangpu 
Published: August 2020

Abstract
Comparative genomics has revealed common occurrences in karyotype evolution such as chromosomal end-to-end fusions and insertions of one chromosome into another near the centromere, as well as many cases of de novo centromeres that generate positional polymorphisms. However, how rearrangements such as dicentrics and acentrics persist without being destroyed or lost remains unclear. Here, we sought experimental evidence for the frequency and timeframe for inactivation and de novo formation of centromeres in maize (Zea mays). The pollen from plants with supernumerary B chromosomes was gamma-irradiated and then applied to normal maize silks of a line without B chromosomes. In ∼8,000 first-generation seedlings, we found many B–A translocations, centromere expansions, and ring chromosomes. We also found many dicentric chromosomes, but a fraction of these show only a single primary constriction, which suggests inactivation of one centromere. Chromosomal fragments were found without canonical centromere sequences, revealing de novo centromere formation over unique sequences; these were validated by immunolocalization with Thr133-phosphorylated histone H2A, a marker of active centromeres, and chromatin immunoprecipitation-sequencing with the CENH3 antibody. These results illustrate the regular occurrence of centromere birth and death after chromosomal rearrangement during a narrow window of one to potentially only a few cell cycles for the rearranged chromosomes to be recognized in this experimental regime.