bluuebunny/crossref_metadata_2025_split huggingface dataset:
Independent regulation of age associated fat accumulation and longevity
Authors: Beas Anthony O. , Gordon Patricia B. , Prentiss Clara L. , Olsen Carissa Perez , Kukurugya Matthew A. , Bennett Bryson D. , Parkhurst Susan M. , Gottschling Daniel E. 
Published: June 2020

AbstractAge-dependent changes in metabolism can manifest as cellular lipid accumulation, but how this accumulation is regulated or impacts longevity is poorly understood. We find that Saccharomyces cerevisiae accumulate lipid droplets (LDs) during aging. We also find that over-expressing BNA2, the first Biosynthesis of NAD+ (kynurenine) pathway gene, reduces LD accumulation during aging and extends lifespan. Mechanistically, this LD accumulation during aging is not linked to NAD+ levels, but is anti-correlated with metabolites of the shikimate and aromatic amino acid biosynthesis (SA) pathways (upstream of BNA2), which produce tryptophan (the Bna2p substrate). We provide evidence that over-expressed BNA2 skews glycolytic flux from LDs towards the SA-BNA pathways, effectively reducing LDs. Importantly, we find that accumulation of LDs does not shorten lifespan, but does protect aged cells against stress. Our findings reveal how lipid accumulation impacts longevity, and how aging cell metabolism can be rewired to modulate lipid accumulation independently from longevity.
A SAM-I riboswitch with the ability to sense and respond to uncharged initiator tRNA
Authors: Tang Dong-Jie , Du Xinyu , Shi Qiang , Zhang Jian-Ling , He Yuan-Ping , Chen Yan-Miao , Ming Zhenhua , Wang Dan , Zhong Wan-Ying , Liang Yu-Wei , Liu Jin-Yang , Huang Jian-Ming , Zhong Yun-Shi , An Shi-Qi , Gu Hongzhou , Tang Ji-Liang 
Published: June 2020

AbstractAll known riboswitches use their aptamer to senese one metabolite signal and their expression platform to regulate gene expression. Here, we characterize a SAM-I riboswitch (SAM-IXcc) from the Xanthomonas campestris that regulates methionine synthesis via the met operon. In vitro and in vivo experiments show that SAM-IXcc controls the met operon primarily at the translational level in response to cellular S-adenosylmethionine (SAM) levels. Biochemical and genetic data demonstrate that SAM-IXcc expression platform not only can repress gene expression in response to SAM binding to SAM-IXcc aptamer but also can sense and bind uncharged initiator Met tRNA, resulting in the sequestering of the anti-Shine-Dalgarno (SD) sequence and freeing the SD for translation initiation. These findings identify a SAM-I riboswitch with a dual functioning expression platform that regulates methionine synthesis through a previously unrecognized mechanism and discover a natural tRNA-sensing RNA element. This SAM-I riboswitch appears to be highly conserved in Xanthomonas species.
Single-cell transcriptomic analysis identifies the conversion of zebrafish Etv2-deficient vascular progenitors into skeletal muscle
Authors: Chestnut Brendan , Casie Chetty Satish , Koenig Andrew L. , Sumanas Saulius 
Published: June 2020

AbstractCell fate decisions involved in vascular and hematopoietic embryonic development are still poorly understood. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we report a single-cell transcriptomic analysis of hematovascular development in wild-type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors are identified using an etv2ci32Gt gene trap line, in which the Gal4 transcriptional activator is integrated into the etv2 gene locus. We observe a cell population with a skeletal muscle signature in etv2-deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells differentiate as skeletal muscle cells instead of contributing to vasculature in etv2-deficient embryos. Wnt and FGF signaling promote the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors, thus restricting these cells to a vascular endothelial fate.
Traceless native chemical ligation of lipid-modified peptide surfactants by mixed micelle formation
Authors: Jin Shuaijiang , Brea Roberto J. , Rudd Andrew K. , Moon Stuart P. , Pratt Matthew R. , Devaraj Neal K. 
Published: June 2020

AbstractBiology utilizes multiple strategies, including sequestration in lipid vesicles, to raise the rate and specificity of chemical reactions through increases in effective molarity of reactants. We show that micelle-assisted reaction can facilitate native chemical ligations (NCLs) between a peptide-thioester – in which the thioester leaving group contains a lipid-like alkyl chain – and a Cys-peptide modified by a lipid-like moiety. Hydrophobic lipid modification of each peptide segment promotes the formation of mixed micelles, bringing the reacting peptides into close proximity and increasing the reaction rate. The approach enables the rapid synthesis of polypeptides using low concentrations of reactants without the need for thiol catalysts. After NCL, the lipid moiety is removed to yield an unmodified ligation product. This micelle-based methodology facilitates the generation of natural peptides, like Magainin 2, and the derivatization of the protein Ubiquitin. Formation of mixed micelles from lipid-modified reactants shows promise for accelerating chemical reactions in a traceless manner.
The transcriptional repressor Blimp1/PRDM1 regulates the maternal decidual response in mice
Authors: Goolam Mubeen , Xypolita Maria-Eleni , Costello Ita , Lydon John P. , DeMayo Francesco J. , Bikoff Elizabeth K. , Robertson Elizabeth J. , Mould Arne W. 
Published: June 2020

AbstractThe transcriptional repressor Blimp1 controls cell fate decisions in the developing embryo and adult tissues. Here we describe Blimp1 expression and functional requirements within maternal uterine tissues during pregnancy. Expression is robustly up-regulated at early post-implantation stages in the primary decidual zone (PDZ) surrounding the embryo. Conditional inactivation results in defective formation of the PDZ barrier and abnormal trophectoderm invasion. RNA-Seq analysis demonstrates down-regulated expression of genes involved in cell adhesion and markers of decidualisation. In contrast, genes controlling immune responses including IFNγ are up-regulated. ChIP-Seq experiments identify candidate targets unique to the decidua as well as those shared across diverse cell types including a highly conserved peak at the Csf-1 gene promoter. Interestingly Blimp1 inactivation results in up-regulated Csf1 expression and macrophage recruitment into maternal decidual tissues. These results identify Blimp1 as a critical regulator of tissue remodelling and maternal tolerance during early stages of pregnancy.
The characterization of Mediator 12 and 13 as conditional positive gene regulators in Arabidopsis
Authors: Liu Qikun , Bischof Sylvain , Harris C. Jake , Zhong Zhenhui , Zhan Lingyu , Nguyen Calvin , Rashoff Andrew , Barshop William D. , Sun Fei , Feng Suhua , Potok Magdalena , Gallego-Bartolome Javier , Zhai Jixian , Wohlschlegel James A. , Carey Michael F. , Long Jeffrey A. , Jacobsen Steven E. 
Published: June 2020

AbstractMediator 12 (MED12) and MED13 are components of the Mediator multi-protein complex, that facilitates the initial steps of gene transcription. Here, in an Arabidopsis mutant screen, we identify MED12 and MED13 as positive gene regulators, both of which contribute broadly to morc1 de-repressed gene expression. Both MED12 and MED13 are preferentially required for the expression of genes depleted in active chromatin marks, a chromatin signature shared with morc1 re-activated loci. We further discover that MED12 tends to interact with genes that are responsive to environmental stimuli, including light and radiation. We demonstrate that light-induced transient gene expression depends on MED12, and is accompanied by a concomitant increase in MED12 enrichment during induction. In contrast, the steady-state expression level of these genes show little dependence on MED12, suggesting that MED12 is primarily required to aid the expression of genes in transition from less-active to more active states.
Vertical datum transformation grids for Mexico
Authors: Carrera-Hernández Jaime J. 
Published: June 2020

AbstractMexico has used two vertical datums—the U.S. National Geodetic Vertical Datum of 1929 (NGVD29) and the North American Vertical Datum of 1988 (NAVD88). Because Mexico started using the NAVD88 as its vertical datum in 2015, most of Mexico’s data is referenced to the NGVD29 and recent high resolution data are referenced to the NAVD88. Compounding this situation, satellite-derived Digital Elevation Models (DEMs) are referenced to the Earth Gravimetric Model 96 (EGM96), and no tools are currently available in Mexico to transform elevation data between the aforementioned vertical datums. To overcome this problem, this work presents the development of two surfaces to transform orthometric heights between the NGVD29 and NAVD88 or between the NGVD29 and EGM96 in Mexico. These surfaces can be used by any interested user to transform orthometric heights referenced to the aforementioned datums.
Efficient Closed-loop Maximization of Carbon Nanotube Growth Rate using Bayesian Optimization
Authors: Chang Jorge , Nikolaev Pavel , Carpena-Núñez Jennifer , Rao Rahul , Decker Kevin , Islam Ahmad E. , Kim Jiseob , Pitt Mark A. , Myung Jay I. , Maruyama Benji 
Published: June 2020

AbstractA major technological challenge in materials research is the large and complex parameter space, which hinders experimental throughput and ultimately slows down development and implementation. In single-walled carbon nanotube (CNT) synthesis, for instance, the poor yield obtained from conventional catalysts is a result of limited understanding of input-to-output correlations. Autonomous closed-loop experimentation combined with advances in machine learning (ML) is uniquely suited for high-throughput research. Among the ML algorithms available, Bayesian optimization (BO) is especially apt for exploration and optimization within such high-dimensional and complex parameter space. BO is an adaptive sequential design algorithm for finding the global optimum of a black-box objective function with the fewest possible measurements. Here, we demonstrate a promising application of BO in CNT synthesis as an efficient and robust algorithm which can (1) improve the growth rate of CNT in the BO-planner experiments over the seed experiments up to a factor 8; (2) rapidly improve its predictive power (or learning); (3) Consistently achieve good performance regardless of the number or origin of seed experiments; (4) exploit a high-dimensional, complex parameter space, and (5) achieve the former 4 tasks in just over 100 hundred experiments (~8 experimental hours) – a factor of 5× faster than our previously reported results.
Generalized Maxwell projections for multi-mode network Photonics
Authors: Makarenko M. , Burguete-Lopez A. , Getman F. , Fratalocchi A. 
Published: June 2020

AbstractThe design of optical resonant systems for controlling light at the nanoscale is an exciting field of research in nanophotonics. While describing the dynamics of few resonances is a relatively well understood problem, controlling the behavior of systems with many overlapping states is considerably more difficult. In this work, we use the theory of generalized operators to formulate an exact form of spatio-temporal coupled mode theory, which retains the simplicity of traditional coupled mode theory developed for optical waveguides. We developed a fast computational method that extracts all the characteristics of optical resonators, including the full density of states, the modes quality factors, and the mode resonances and linewidths, by employing a single first principle simulation. This approach can facilitate the analytical and numerical study of complex dynamics arising from the interactions of many overlapping resonances, defined in ensembles of resonators of any geometrical shape and in materials with arbitrary responses.
Human BDNF/TrkB variants impair hippocampal synaptogenesis and associate with neurobehavioural abnormalities
Authors: Sonoyama Takuhiro , Stadler Lukas K. J. , Zhu Mingyan , Keogh Julia M. , Henning Elana , Hisama Fuki , Kirwan Peter , Jura Magdalena , Blaszczyk Beata K. , DeWitt David C. , Brouwers Bas , Hyvönen Marko , Barroso Inês , Merkle Florian T. , Appleyard Suzanne M. , Wayman Gary A. , Farooqi I. Sadaf 
Published: June 2020

AbstractBrain-derived neurotrophic factor (BDNF) signals through its high affinity receptor Tropomyosin receptor kinase-B (TrkB) to regulate neuronal development, synapse formation and plasticity. In rodents, genetic disruption of Bdnf and TrkB leads to weight gain and a spectrum of neurobehavioural phenotypes. Here, we functionally characterised a de novo missense variant in BDNF and seven rare variants in TrkB identified in a large cohort of people with severe, childhood-onset obesity. In cells, the E183K BDNF variant resulted in impaired processing and secretion of the mature peptide. Multiple variants in the kinase domain and one variant in the extracellular domain of TrkB led to a loss of function through multiple signalling pathways, impaired neurite outgrowth and dominantly inhibited glutamatergic synaptogenesis in hippocampal neurons. BDNF/TrkB variant carriers exhibited learning difficulties, impaired memory, hyperactivity, stereotyped and sometimes, maladaptive behaviours. In conclusion, human loss of function BDNF/TrkB variants that impair hippocampal synaptogenesis may contribute to a spectrum of neurobehavioural disorders.
Prognostic value and therapeutic potential of the long noncoding RNA TP73-AS1 in cancers: A systematic review and meta-analysis
Authors: Zhong Yuan , Zhao Meng , Yu Yang , Li Quanpeng , Wang Fei , Wu Peiyao , Zhang Wen , Miao Lin 
Published: June 2020

AbstractStudies published in recent years have demonstrated that abnormal long noncoding RNA (lncRNA) antisense RNA to TP73 gene (TP73-AS1) expression is markedly associated with tumorigenesis, cancer progression and the prognosis of cancer patients. We aimed to explore the prognostic value of TP73-AS1 in multiple cancers. We comprehensively searched PubMed, Embase, Web of Science and the Cochrane Library (up to February 21, 2019). Hazard ratios (HRs), odds ratios (ORs) and the corresponding 95% confidence intervals (95% CIs) were calculated to estimate the association of TP73-AS1 with survival and clinicopathological features. The potential targets and pathways of TP73-AS1 in multiple cancers were summarized. Nineteen studies that involved thirteen types of cancers and 1329 cancer patients were identified as eligible for this meta-analysis. The results showed that high TP73-AS1 expression was significantly correlated with shorter overall survival (OS) (HR = 1.962, 95% CI 1.630-2.362) and disease-free survival (DFS) (HR = 2.050, 95% CI 1.293-3.249). The summary HRs of OS were 2.101 (95% CI 1.516-2.911) for gastric cancer (GC) and 1.920 (95% CI 1.253-2.942) for osteosarcoma. Subgroup analysis of OS demonstrated that the differential expression of TP73-AS1 in cancer tissues was a potential source of heterogeneity. Furthermore, increased TP73-AS1 expression was markedly associated with larger tumor size (OR = 2.759, 95% CI 1.759-4.330), advanced histological grade (OR = 2.394, 95% CI 1.231-4.656), lymph node metastasis (OR = 2.687, 95% CI 1.211-5.962), distant metastasis (OR = 4.145, 95% CI 2.252-7.629) and advanced TNM stage (OR = 2.633, 95% CI 1.507-4.601). The results of Egger’s test and sensitivity analysis verified the robustness of the original results. High TP73-AS1 expression can predict poor survival and poor clinicopathological features in cancer patients and TP73-AS1 might be a potential biomarker and therapeutic target.
A Quantum secure sharing protocol for Cloud data based on proxy re-encryption
Authors: Chang Yan , Zhang Shi-Bin , Yan Li-Li , Wan Guo-gen 
Published: June 2020

AbstractA quantum scheme for cloud data sharing based on proxy re-encryption is proposed. The user Alice stores the cipher-text of her data on cloud data center. When Alice wants to share her data with another user Bob, Alice is called the delegator and Bob is called the delegatee. The cloud service provider (called the proxy) can convert the delegator’s cipher-text into the delegatee’s cipher-text without decrypting the former, so that the delegatee can get the plain-text of Alice’s data with his private key. The proxy cannot obtain the plain-text of the user’s data stored on cloud data center. Delegator in the protocol should have the ability of producing Bell states, performing Bell basis and Z-basis measurements, and storing qubits. The quantum requirements for the delegatee are reduced. The delegatee needs to have the ability of reflecting and performing Z-basis measurement. One secret at a time (one-time one-pad) is theoretically implemented, especially when the same data is shared multiple times. The anti-selection plain-text attack security and the anti-selective cipher-text attack security are realized. Fine-granularity secret data sharing is achieved flexibly.
Can Thermodynamic Behavior of Alice’s Particle Affect Bob’s Particle?
Authors: Soltanmanesh Ali , Naeij Hamid Reza , Shafiee Afshin 
Published: June 2020

AbstractWe propose an experiment to investigate the possibility of long-distance thermodynamic relationships between two entangled particles. We consider a pair of spin-$$\frac{1}{2}$$

1
2

particles prepared in an entangled singlet state in which one particle is sent to Alice and the other to her distant mate Bob, who are spatially separated. Our proposed experiment consists of three different setups: First, both particles are coupled to two heat baths with various temperatures. In the second setup, only Alice’s particle is coupled to a heat bath and finally, in the last setup, only Bob’s particle is coupled to a heat bath. We study the evolution of an open quantum system using the first law of thermodynamics based on the concepts of ergotropy, adiabatic work, and operational heat, in a quantum fashion. We analyze and compare ergotropy and heat transfer in three setups. Our results show that the heat transfer for each entangled particle is not independent of the thermalization process that occurs for the other one. We prove that the existence of quantum correlations affects the thermodynamic behavior of distant particles in an entangled state.
Signals of selection in the mitogenome provide insights into adaptation mechanisms in heterogeneous habitats in a widely distributed pelagic fish
Authors: Sebastian Wilson , Sukumaran Sandhya , Zacharia P. U. , Muraleedharan K. R. , Dinesh Kumar P. K. , Gopalakrishnan A. 
Published: June 2020

AbstractOceans are vast, dynamic, and complex ecosystems characterized by fluctuations in environmental parameters like sea surface temperature (SST), salinity, oxygen availability, and productivity. Environmental variability acts as the driver of organismal evolution and speciation as organisms strive to cope with the challenges. We investigated the evolutionary consequences of heterogeneous environmental conditions on the mitogenome of a widely distributed small pelagic fish of Indian ocean, Indian oil sardine, Sardinella longiceps. Sardines were collected from different eco-regions of the Indian Ocean and selection patterns analyzed in coding and non-coding regions. Signals of diversifying selection were observed in key functional regions involved in OXPHOS indicating OXPHOS gene regulation as the critical factor to meet enhanced energetic demands. A characteristic control region with 38–40 bp tandem repeat units under strong selective pressure as evidenced by sequence conservation and low free energy values was also observed. These changes were prevalent in fishes from the South Eastern Arabian Sea (SEAS) followed by the Northern Arabian Sea (NAS) and rare in Bay of Bengal (BoB) populations. Fishes belonging to SEAS exhibited accelerated substitution rate mainly due to the selective pressures to survive in a highly variable oceanic environment characterized by seasonal hypoxia, variable SST, and food availability.
Clinical Characteristics of Infections Caused by Streptococcus Anginosus Group
Authors: Jiang Shenghua , Li Min , Fu Tian , Shan Fenglian , Jiang Luning , Shao Zewei 
Published: June 2020

AbstractThis study aimed to investigate the clinical characteristics, distribution of different strains and risk factors of patients infected withStreptococcus anginosusgroup (SAG). In the population of 463 patients, the male-to-female ratio was 1.95:1, and the patient age ranged from 6 months to 103 years. There were 49 children (10.58%), 311 young and middle-aged adults (67.17%), and 103 elderly adults (22.25%). Approximately 45.4% had underlying conditions, which were mostly malignant tumors and diabetes. Of the 463 specimens, 254 wereS. anginosus(54.86%), 173 wereS. constellatus(37.37%), and 36 wereS. intermedius(7.77%). According to the age distribution, the incidence peaked in the 35–54 year age group. Different sites of infection had statistically significant differences regarding the constituent ratios of these three species. Different age groups also exhibited statistically significant differences in constituent ratios of the pathogenic organisms, as well as organ infections. In our population, 269 were clinically cured, 184 reported satisfactory improvement, and 10 died. SAG, as an opportunistic pathogen, can induce pyogenic infections in patients of all ages and shows no significant gender predilection in any age group. The three pathogenic organisms had differences with respect to patient age and infections of body sites.
Serological and molecular detection of Neospora caninum and Toxoplasma gondii in human umbilical cord blood and placental tissue samples
Authors: Duarte Pâmella Oliveira , Oshiro Leandra Marla , Zimmermann Namor Pinheiro , Csordas Bárbara Guimarães , Dourado Doroty Mesquita , Barros Jacqueline Cavalcante , Andreotti Renato 
Published: June 2020

AbstractNeosporosis primarily affects cattle and dogs and is not currently considered a zoonotic disease. Toxoplasmosis is a zoonosis with a worldwide distribution that is asymptomatic in most cases, but when acquired during pregnancy, it can have serious consequences. The seropositivity rates determined by the indirect fluorescent antibody test for Neospora caninum (N. caninum) and Toxoplasma gondii (T. gondii) were 24.3% (49 samples) and 26.8% (54 samples), respectively. PCR positivity for N. caninum was observed in two samples of cord blood (1%) using the Nc5 and ITS1 gene, positivity for T. gondii was observed in 16 samples using the primer for the B1 gene (5.5% positivity in cord blood and 2.5% positivity in placental tissue). None of the samples showed structures characteristic of tissue cysts or inflammatory infiltrate on histopathology. Significant associations were observed only between N. caninum seropositivity and the presence of domestic animals (p = 0.039) and presence of dogs (p = 0.038) and between T. gondii seropositivity and basic sanitation (p = 0.04). This study obtained important findings regarding the seroprevalence and molecular detection of N. caninum and T. gondii in pregnant women; however, more studies are necessary to establish a correlation between risk factors and infection.