bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global Characterization of the Varying Responses of the Standardized Precipitation Evapotranspiration Index to Atmospheric Evaporative Demand
Authors: Tomas‐Burguera M. , Vicente‐Serrano S. M. , Peña‐Angulo D. , Domínguez‐Castro F. , Noguera I. , El Kenawy A. 
Published: August 2020

AbstractThe standardized precipitation evapotranspiration index (SPEI) is one of the well‐established drought metrics worldwide. It is simply computed using precipitation and atmospheric evaporative demand (AED) data. Although AED is considered a key driver of drought variability worldwide, it could have less impact on drought in specific regions and for particular times as a function of the magnitude of precipitation. Specifically, the influence of the AED might overestimate drought severity during both normal and humid periods, resulting in “false alarms” about drought impacts on physical and human environments. Here, we provided a global characterization of the sensitivity of the SPEI to changes of the AED. Results demonstrate that the contribution of AED to drought severity is largely impacted by the spatial and temporal variability of precipitation. Specifically, the impact of AED on drought severity was more pronounced during periods of low precipitation, compared to wet periods. Interestingly, drought severity in humid regions (as revealed by SPEI) also showed low sensitivity to AED under drier conditions. These results highlight the skill of SPEI in identifying the role of AED in drought evolution, especially in arid and semiarid regions whose climate is characterized typically by low precipitation. This advantage was also evident for humid environments, where SPEI did not overestimate drought severity due to the increased AED. These findings highlight the broader applicability of SPEI to accurately characterize drought severity worldwide.
Minocycline differentially modulates human spatial memory systems
Authors: Berens Sam C. , Bird Chris M. , Harrison Neil A. 
Published: August 2020

AbstractMicroglia play a critical role in many processes fundamental to learning and memory in health and are implicated in Alzheimer’s pathogenesis. Minocycline, a centrally-penetrant tetracycline antibiotic, inhibits microglial activation and enhances long-term potentiation, synaptic plasticity, neurogenesis and hippocampal-dependent spatial memory in rodents, leading to clinical trials in human neurodegenerative diseases. However, the effects of minocycline on human memory have not previously been investigated. Utilising a double-blind, randomised crossover study design, we recruited 20 healthy male participants (mean 24.6 ± 5.0 years) who were each tested in two experimental sessions: once after 3 days of Minocycline 150 mg (twice daily), and once 3 days of placebo (identical administration). During each session, all completed an fMRI task designed to tap boundary- and landmark-based navigation (thought to rely on hippocampal and striatal learning mechanisms respectively). Given the rodent literature, we hypothesised that minocycline would selectively modulate hippocampal learning. In line with this, minocycline biased use of boundary- compared to landmark-based information (t980 = 3.140, p = 0.002). However, though this marginally improved performance for boundary-based objects (t980 = 1.972, p = 0.049), it was outweighed by impaired landmark-based navigation (t980 = 6.374, p < 0.001) resulting in an overall performance decrease (t980 = 3.295, p = 0.001). Furthermore, against expectations, minocycline significantly reduced activity during memory encoding in the right caudate (t977 = 2.992, p = 0.003) and five other cortical regions, with no significant effect in the hippocampus. In summary, minocycline impaired human spatial memory performance, likely through disruption of striatal processing resulting in greater biasing towards reliance on boundary-based navigation.
NRIP3 upregulation confers resistance to chemoradiotherapy in ESCC via RTF2 removal by accelerating ubiquitination and degradation of RTF2
Authors: Suo Daqin , Wang Ling , Zeng Tingting , Zhang Hui , Li Lei , Liu Jinyun , Yun Jingping , Guan Xin-Yuan , Li Yan 
Published: August 2020

AbstractEsophageal squamous cell carcinoma (ESCC) is a common malignant cancer worldwide. Despite recent improvements in surgical techniques and adjuvant therapies, the prognosis of patients with advanced ESCC remains poor. Resistance to chemoradiotherapy (CRT) remains a major cause of treatment failure for advanced ESCC patients. Here, we report that NRIP3 (nuclear receptor interacting protein 3) promotes ESCC tumor cell growth and resistance to CRT in ESCC cells by increasing and binding to DDI1 (DNA-damage inducible 1 homolog 1) and RTF2 (homologous toSchizosaccharomycespombeRtf2), and accelerating the removal of RTF2, which is a key determinant for the ability of cells to manage replication stress. In addition, we found that NRIP3 could increase DDI1 expression via PPARα. The NRIP3-PPARα-DDI1-RTF2 axis represents a protective molecular pathway in ESCC cells that mediates resistance to replication stress signals induced by chemoradiotherapy. In addition, elevated NRIP3 is associated with the poor clinical outcome of ESCC patients receiving radiotherapy and/or cisplatin-based chemotherapy. Our study therefore reveals that NRIP3 is a prognostic factor in ESCC and could have some predictive value to select patients who benefit from CRT treatment. A common mechanism that protects ESCC tumor cells from DNA damage induced by CRT is also revealed in this study.
NEDDylation negatively regulates ERRβ expression to promote breast cancer tumorigenesis and progression
Authors: Naik Sanoj K. , Lam Eric W.-F. , Parija Monalisa , Prakash Surya , Jiramongkol Yannasittha , Adhya Amit K. , Parida Dilip K. , Mishra Sandip K. 
Published: August 2020

AbstractEstrogen-related receptor beta (ERRβ) is downregulated in breast cancer cells and its overexpression in breast cancer patients is positively correlated with an improved prognosis and prolonged relapse-free survival. Here, we unravelled a molecular mechanism for ERRβ downregulation in breast cancer. We found that ERRβ is a key substrate of the SCF complex and that NEDDylation can activate the Cullin subunits of the SCF complex to target ERRβ for degradation in breast cancer. Consistently, using in vitro and in vivo models, we demonstrated that MLN4924, a specific small molecule inhibitor of NEDDylation, can restore ERRβ expression and culminate in a reduction in cell proliferation and migration of breast cancer cells. We also showed that increased ERRβ expression promotes the upregulation of its target genes, including the tumour suppressors p21Cip1/Waf1 and E-cadherin, involved in cell proliferation and migration arrest at the gene promoter level. Interestingly, this tumour suppressive role of ERRβ does not depend on the expression of ERα in breast cancer. Moreover, our data revealed that the ERRβ recruits the transcription co-activator p300 to its targeted gene promoters to upregulate their expression. Collectively, our work revealed that restoration of ERRβ expression using the NEDDylation inhibitor MLN4924 can be a novel and effective strategy for breast cancer treatment.
De novo design of an intercellular signaling toolbox for multi-channel cell–cell communication and biological computation
Authors: Du Pei , Zhao Huiwei , Zhang Haoqian , Wang Ruisha , Huang Jianyi , Tian Ye , Luo Xudong , Luo Xunxun , Wang Min , Xiang Yanhui , Qian Long , Chen Yihua , Tao Yong , Lou Chunbo 
Published: August 2020

AbstractIntercellular signaling is indispensable for single cells to form complex biological structures, such as biofilms, tissues and organs. The genetic tools available for engineering intercellular signaling, however, are quite limited. Here we exploit the chemical diversity of biological small molecules to de novo design a genetic toolbox for high-performance, multi-channel cell–cell communications and biological computations. By biosynthetic pathway design for signal molecules, rational engineering of sensing promoters and directed evolution of sensing transcription factors, we obtain six cell–cell signaling channels in bacteria with orthogonality far exceeding the conventional quorum sensing systems and successfully transfer some of them into yeast and human cells. For demonstration, they are applied in cell consortia to generate bacterial colony-patterns using up to four signaling channels simultaneously and to implement distributed bio-computation containing seven different strains as basic units. This intercellular signaling toolbox paves the way for engineering complex multicellularity including artificial ecosystems and smart tissues.
Efficient open cultivation of cyanidialean red algae in acidified seawater
Authors: Hirooka Shunsuke , Tomita Reiko , Fujiwara Takayuki , Ohnuma Mio , Kuroiwa Haruko , Kuroiwa Tsuneyoshi , Miyagishima Shin-ya 
Published: August 2020

AbstractMicroalgae possess high potential for producing pigments, antioxidants, and lipophilic compounds for industrial applications. However, their open pond cultures are often contaminated by other undesirable organisms, including their predators. In addition, the cost of using freshwater is relatively high, which limits the location and scale of cultivation compared with using seawater. It was previously shown that Cyanidium caldarium and Galdieria sulphuraria, but not Cyanidioschyzon merolae grew in media containing NaCl at a concentration equivalent to seawater. We found that the preculture of C. merolae in the presence of a moderate NaCl concentration enabled the cells to grow in the seawater-based medium. The cultivation of cyanidialean red algae in the seawater-based medium did not require additional pH buffering chemicals. In addition, the combination of seawater and acidic conditions reduced the risk of contamination by other organisms in the nonsterile open culture of C. merolae more efficiently than the acidic condition alone.
Gut bacteria-derived peptidoglycan induces a metabolic syndrome-like phenotype via NF-κB-dependent insulin/PI3K signaling reduction in Drosophila renal system
Authors: Zugasti Olivier , Tavignot Raphäel , Royet Julien 
Published: August 2020

AbstractAlthough microbiome–host interactions are usual at steady state, gut microbiota dysbiosis can unbalance the physiological and behavioral parameters of the host, mostly via yet not understood mechanisms. Using the Drosophila model, we investigated the consequences of a gut chronic dysbiosis on the host physiology. Our results show that adult flies chronically infected with the non-pathogenic Erwinia carotorova caotovora bacteria displayed organ degeneration resembling wasting-like phenotypes reminiscent of Metabolic Syndrome associated pathologies. Genetic manipulations demonstrate that a local reduction of insulin signaling consecutive to a peptidoglycan-dependent NF-κB activation in the excretory system of the flies is responsible for several of the observed phenotypes. This work establishes a functional crosstalk between bacteria-derived peptidoglycan and the immune NF-κB cascade that contributes to the onset of metabolic disorders by reducing insulin signal transduction. Giving the high degree of evolutionary conservation of the mechanisms and pathways involved, this study is likely to provide a helpful model to elucidate the contribution of altered intestinal microbiota in triggering human chronic kidney diseases.
Kinetic analysis of effects of temperature and time on the regulation of venom expression in Bungarus multicinctus
Authors: Yin Xianmei , Guo Shuai , Gao Jihai , Luo Lu , Liao Xuejiao , Li Mingqian , Su He , Huang Zhihai , Xu Jiang , Pei Jin , Chen Shilin 
Published: August 2020

AbstractVenom gland is a highly efficient venom production system to maintain their predatory arsenal. Venom toxins mRNA has been shown to increase abruptly in snake after venom expenditure, while the dynamics of venom accumulation during synthesis are poorly understood. Here, PacBio long-read sequencing, Illumina RNA sequencing (RNA-seq), and label-free proteome quantification were used to investigate the composition landscape and time- and temperature-dependent dynamics changes of the Bungarus multicinctus venom gland system. Transcriptome data (19.5223 Gb) from six adult B. multicinctus tissues were sequenced using PacBio RS II to generate a reference assembly, and average 7.28 Gb of clean RNA-seq data was obtained from venom glands by Illumina sequencing. Differentially expressed genes (DEGs) mainly were protein processing rather than venom toxins. Post-translational modifications provided the evidence of the significantly different proportions of toxins in the venom proteome with the changing of replenishment time and temperature, but constant of venom toxins mRNA in the venom gland transcriptome. Dynamic of toxins and genes involved in venom gland contraction suggesting the formation of the mature venom gland system would take at least 9 days. In addition, 59 toxin processing genes were identified, peptidylprolyl isomerase B of which underwent positive selection in Toxicofera. These results provide a reference for determining the extraction time of venom, production of polyclonal and monoclonal antibody for precise treatment plans of venomous snakebites, and construction of an in vitro synthesis system for snake venom protein.
Genome editing with the donor plasmid equipped with synthetic crRNA-target sequence
Authors: Ishibashi Riki , Abe Kota , Ido Nanami , Kitano Satsuki , Miyachi Hitoshi , Toyoshima Fumiko 
Published: August 2020

AbstractCRISPR/Cas-mediated genome editing is a powerful tool for generating genetically mutated cells and organisms. Linearisation of donor cassettes with this system has been shown to facilitate both transgene donor insertion and targeted knock-in. Here, we developed a donor plasmid that we name pCriMGET (plasmid of syntheticCRISPR coded RNA target sequence-equipped donor plasmid-mediatedgenetargeting), in which an off-target free synthetic CRISPR coded RNA-target sequence (syn-crRNA-TS) is incorporated with a multi-cloning site, where a donor cassette can be inserted. With co-expression of Cas9 and the syn-crRNA-TS guide RNA (gRNA), pCriMGET provides a linearised donor cassette in vivo, thereby promoting the transgene donor insertion and targeted knock-in. When co-injected with Cas9 protein and gRNA into murine zygotes, pCriMGET yielded around 20% transgene insertion in embryos. This method also achieved more than 25% in-frame knock-in at the mouseTbx3gene locus without predicted insertion–deletion mutations using a transgene donor with 400-bp homology arms. pCriMGET is therefore useful as a versatile CRISPR/Cas9-cleavable donor plasmid for efficient integration and targeted knock-in of exogenous DNA in mice.
Lateralization of social signal brain processing correlates with the degree of social integration in a songbird
Authors: Cousillas Hugo , Henry Laurence , George Isabelle , Marchesseau Schedir , Hausberger Martine 
Published: August 2020

AbstractGroup cohesion relies on the ability of its members to process social signals. Songbirds provide a unique model to investigate links between group functioning and brain processing of social acoustic signals. In the present study, we performed both behavioral observations of social relationships within a group of starlings and individual electrophysiological recordings of HVC neuronal activity during the broadcast of either familiar or unfamiliar individual songs. This allowed us to evaluate and compare preferred partnerships and individual electrophysiological profiles. The electrophysiological results revealed asymmetric neuronal activity in the HVC and higher responsiveness to familiar than to unfamiliar songs. However, most importantly, we found a correlation between strength of cerebral asymmetry and social integration in the group: the more preferred partners a bird had, the more its HVC neuronal activity was lateralized. Laterality is likely to give advantages in terms of survival. Our results suggest that these include social skill advantages. Better knowledge of links between social integration and lateralization of social signal processing should help understand why and how lateralization has evolved.
The value of adjuvant chemotherapy in stage II/III colorectal signet ring cell carcinoma
Authors: Zhao Zhuang , Yan Na , Pan Shu , Wang Dun-wei , Li Zhi-wen 
Published: August 2020

AbstractThis study aimed to assess the benefit of postoperative adjuvant chemotherapy in stage II–III colorectal signet ring cell carcinoma (SRCC). Qualified postoperative patients were extracted from Surveillance, Epidemiology, and End Results (SEER) database from 2004 until 2015. We collected 1675 patients in the research, and 936 patients were subjected to adjuvant chemotherapy group. The proportions of married status, male, rectal cancer, grade III/IV, AJCC stage III and radiotherapy were higher; While, the rates of white race, ≥ 65 years old and located in cecum–transverse colon were lower in patients of chemotherapy group compared to no chemotherapy group (all P < 0.05). K-M plots revealed significantly better OS of adjuvant chemotherapy group than no chemotherapy group (P < 0.001). Meanwhile, there was no significantly different in CSS between the two groups (P = 0.93). However, after adjusting for confounding factors by multivariable Cox regression analysis, receipt of postoperative chemotherapy was still associated with better CSS and OS (CSS: hazard ratio [HR] = 0.719, 95% CI 0.612–0.844, P < 0.001) ; (OS: HR = 0.618, 95% CI 0.537–0.713, P < 0.001). Patients with stage II/III colorectal SRCC could receive survival benefit from postoperative adjuvant chemotherapy.
Social learning exploits the available auditory or visual cues
Authors: Paraouty Nihaad , Charbonneau Joey A. , Sanes Dan H. 
Published: August 2020

AbstractThe ability to acquire a behavior can be facilitated by exposure to a conspecific demonstrator. Such social learning occurs under a range of conditions in nature. Here, we tested the idea that social learning can benefit from any available sensory cue, thereby permitting learning under different natural conditions. The ability of naïve gerbils to learn a sound discrimination task following 5 days of exposure adjacent to a demonstrator gerbil was tested in the presence or absence of visual cues. Naïve gerbils acquired the task significantly faster in either condition, as compared to controls. We also found that exposure to a demonstrator was more potent in facilitating learning, as compared to exposure to the sounds used to perform the discrimination task. Therefore, social learning was found to be flexible and equally efficient in the auditory or visual domains.
Quantifying the evolution of atomic interaction of a complex surface with a functionalized atomic force microscopy tip
Authors: Liebig Alexander , Hapala Prokop , Weymouth Alfred J. , Giessibl Franz J. 
Published: August 2020

AbstractTerminating the tip of an atomic force microscope with a CO molecule allows data to be acquired with a well-known and inert apex. Previous studies have shown conflicting results regarding the electrostatic interaction, indicating in some cases that the negative charge at the apex of the CO dominates, whereas in other cases the positive charge at the end of the metal tip dominates. To clarify this, we investigated $$\hbox {CaF}_{2}$$

CaF
2

(111). $$\hbox {CaF}_{2}$$

CaF
2

is an ionic crystal and the (111) surface does not possess charge inversion symmetry. Far from the surface, the interaction is dominated by electrostatics via the negative charge at the apex. Closer to the surface, Pauli repulsion and CO bending dominate, which leads to an unexpected appearance of the complex 3-atom unit cell. We compare simulated data in which the electrostatics are modeled by point particles versus a charge density calculated by DFT. We also compare modeling Pauli repulsion via individual Lennard–Jones potentials versus a total charge density overlap. In doing so, we determine forcefield parameters useful for future investigations of biochemical processes.
A machine learning tool for interpretation of Mass Transport Deposits from seismic data
Authors: Kumar Priyadarshi Chinmoy , Sain Kalachand 
Published: August 2020

AbstractMachine learning is a tool that allows machines or intelligent systems to learn and get equipped to solve complex problems in predicting reliable outcome. The learning process consists of a set of computer algorithms that are employed to a small segment of data with a view to speed up realistic interpretation from entire data without extensive human intervention. Here we present an approach of supervised learning based on artificial neural network to automate the process of delineating structural distribution of Mass Transport Deposit (MTD) from 3D reflection seismic data. The responses, defined by a set of individual attributes, corresponding to the MTD, are computed from seismic volume and amalgamated them into a hybrid attribute. This generated new attribute, called as MTD Cube meta-attribute, does not only define the subsurface architecture of MTD distinctly but also reduces the human involvement thereby accelerating the process of interpretation. The system, after being fully trained, quality checked and validated, automatically delimits the structural geometry of MTDs within the Karewa prospect in northern Taranaki Basin off New Zealand, where MTDs are evidenced.
New insights on improved growth and biogas production potential of Chlorella pyrenoidosa through intermittent iron oxide nanoparticle supplementation
Authors: Rana Mohit Singh , Bhushan Shashi , Prajapati Sanjeev Kumar 
Published: August 2020

AbstractIn the present work, the effect of α-Fe2O3-nanoparticles (IONPs) supplementation at varying doses (0, 10, 20 and, 30 mg L−1) at the intermittent stage (after 12th day of growth period) was studied on the growth and biogas production potential of Chlorella pyrenoidosa. Significant enhancements in microalgae growth were observed with all the tested IONPs doses, the highest (2.94 ± 0.01 g L−1) being at 20 mg L−1. Consequently, the composition of the biomass was also improved. Based on the precedent determinations, theoretical chemical oxygen demand (CODth) as well as theoretical and stoichiometric methane potential (TMP, and SMP) were also estimated. The CODth, TMP, SMP values indicated IONPs efficacy for improving biogas productivity. Further, the biochemical methane potential (BMP) test was done for IONPs supplemented biomass. The BMP test revealed up to a 25.14% rise in biogas yield (605 mL g–1 VSfed) with 22.4% enhanced methane content for 30 mg L−1 IONPs supplemented biomass over control. Overall, at 30 mg L−1 IONPs supplementation, the cumulative enhancements in biomass, biogas, and methane content proffered a net rise of 98.63% in biomethane potential (≈ 2.86 × 104 m3 ha−1 year−1) compared to control. These findings reveal the potential of IONPs in improving microalgal biogas production.
Organization and function of paraspeckles
Authors: Wang Yang , Chen Ling-Ling 
Published: August 2020

Abstract
Paraspeckles are a type of subnuclear bodies built on the long noncoding RNA NEAT1 (nuclear paraspeckle assembly transcript 1, also known as MEN-ε/β or VINC-1). Paraspeckles are involved in many physiological processes including cellular stress responses, cell differentiation, corpus luteum formation and cancer progression. Recently, ultra-resolution microscopy coupled with multicolor-labeling of paraspeckle components (the NEAT1 RNA and paraspeckle proteins) revealed the exquisite details of paraspeckle structure and function. NEAT1 transcripts are radially arranged to form a core–shell spheroidal structure, while paraspeckle proteins (PSPs) localize within different layers. Functional dissection of NEAT1 shows that the subdomains of NEAT1_2 are important for RNA stability, isoform switching and paraspeckle assembly via a liquid–liquid phase separation (LLPS) mechanism. We review recent progress on structure and organization of paraspeckles as well as how paraspeckles spatiotemporally control gene regulation through sequestration of diverse proteins and RNAs in cells.