bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation, nucleotide sequencing and genomic comparison of a Novel SXT/R391 ICE mobile genetic element isolated from a municipal wastewater environment
Authors: Slattery Shannon , Tony Pembroke J. , Murnane John G. , Ryan Michael P. 
Published: May 2020

AbstractIntegrative Conjugative Elements (ICE’s) of the SXT/R391 family have largely been detected in clinical or environmental isolates of Gammaproteobacteria, particularly Vibrio and Proteus species. As wastewater treatment plants accumulate a large and diverse number of such species, we examined raw water samples taken from a municipal wastewater treatment plant initially using SXT/R391 family integrase gene-specific PCR probes to detect the presence of such elements in a directed approach. A positive amplification occurred over a full year period and a subsequent Restriction Fragment Length Polymorphism (RFLP) analysis revealed a very limited diversity in the treatment plant examined. Samples demonstrating positive amplification were cultured using Vibrio and Proteus selective media and PCR amplification tracking was utilized to monitor SXT/R391-ICE family containing strains. This screening procedure resulted in the isolation and identification of a Proteus mirabilis strain harbouring an ICE. Whole-genome sequencing of this ICE containing strain using Illumina sequencing technology revealed a novel 81 kb element that contained 75 open reading frames on annotation but contained no antibiotic or metal resistance determinants. Comparative genomics revealed the element contained a conserved ICE core with one of the insertions containing a novel bacteriophage defence mechanism. This directed isolation suggests that ICE elements are present in the environment without apparent selective pressure but may contain adaptive functions allowing survival in particular environments such as municipal wastewater which are reservoirs for large bacterial phage populations.
Using an Innovation Arena to compare wild-caught and laboratory Goffin’s cockatoos
Authors: Rössler Theresa , Mioduszewska Berenika , O’Hara Mark , Huber Ludwig , Prawiradilaga Dewi M. , Auersperg Alice M. I. 
Published: May 2020

AbstractThe ability to innovate, i.e., to exhibit new or modified learned behaviours, can facilitate adaptation to environmental changes or exploiting novel resources. We hereby introduce a comparative approach for studying innovation rate, the ‘Innovation Arena’ (IA), featuring the simultaneous presentation of 20 interchangeable tasks, which subjects encounter repeatedly. The new design allows for the experimental study of innovation per time unit and for uncovering group-specific problem-solving abilities – an important feature for comparing animals with different predispositions and life histories. We applied the IA for the first time to investigate how long-term captivity affects innovative capacities in the Goffin’s cockatoo, an avian model species for animal innovation. We found that fewer temporarily-captive wild birds are inclined to consistently interact with the apparatus in comparison to laboratory-raised birds. However, those that are interested solve a similar number of tasks at a similar rate, indicating no difference in the cognitive ability to solve technical problems. Our findings thus provide a contrast to previous literature, which suggested enhanced cognitive abilities and technical problem-solving skills in long-term captive animals. We discuss the impact and discrepancy between motivation and cognitive ability on innovation rate. Our findings contribute to the debate on how captivity affects innovation in animals.
Design and Analysis of Active Metamaterial Modulated by RF Power Level
Authors: Phon Ratanak , Lim Sungjoon 
Published: May 2020

AbstractIn this paper, a radio frequency (RF)-power-modulated active metamaterial loaded with a nonlinear Schottky diode is presented. Its operating mode is a function of the incident power level. It is switched by a change in the operating state (i.e., on/off) of the Schottky diode, which is directly triggered by a change in the incident power level. For instance, when a low-power RF radiation is incident on the proposed metamaterial, the Schottky diode is turned off, and the metamaterial passes a 2 GHz signal in the pass-band mode. By contrast, when a high RF power is incident, the diode is turned on, and the metamaterial reflects all frequencies in the reflection mode. The proposed active metamaterial was analysed by performing numerical simulations for both low- and high-power modes, and the proposed concept was successfully demonstrated by circuit analysis, full-wave simulation, and experimental results.
Developmental stage-specific distribution and phosphorylation of Mblk-1, a transcription factor involved in ecdysteroid-signaling in the honey bee brain
Authors: Kumagai Hitomi , Kunieda Takekazu , Nakamura Korefumi , Matsumura Yasuhiro , Namiki Manami , Kohno Hiroki , Kubo Takeo 
Published: May 2020

AbstractIn the honey bee, the mushroom bodies (MBs), a higher-order center in insect brain, comprise interneurons termed Kenyon cells (KCs). We previously reported that Mblk-1, which encodes a transcription factor involved in ecdysteroid-signaling, is expressed preferentially in the large-type KCs (lKCs) in the pupal and adult worker brain and that phosphorylation by the Ras/MAPK pathway enhances the transcriptional activity of Mblk-1 in vitro. In the present study, we performed immunoblotting and immunofluorescence studies using affinity-purified anti-Mblk-1 and anti-phosphorylated Mblk-1 antibodies to analyze the distribution and phosphorylation of Mblk-1 in the brains of pupal and adult workers. Mblk-1 was preferentially expressed in the lKCs in both pupal and adult worker brains. In contrast, some Mblk-1 was phosphorylated almost exclusively in the pupal stages, and phosphorylated Mblk-1 was preferentially expressed in the MB neuroblasts and lKCs in pupal brains. Immunofluorescence studies revealed that both Mblk-1 and phosphorylated Mblk-1 are located in both the cytoplasm and nuclei of the lKC somata in the pupal and adult worker brains. These findings suggest that Mblk-1 plays a role in the lKCs in both pupal and adult stages and that phosphorylated Mblk-1 has pupal stage-specific functions in the MB neuroblasts and lKCs in the honey bee brain.
Chronic within-hive video recordings detect altered nursing behaviour and retarded larval development of neonicotinoid treated honey bees
Authors: Siefert Paul , Hota Rudra , Ramesh Visvanathan , Grünewald Bernd 
Published: May 2020

AbstractRisk evaluations for agricultural chemicals are necessary to preserve healthy populations of honey bee colonies. Field studies on whole colonies are limited in behavioural research, while results from lab studies allow only restricted conclusions on whole colony impacts. Methods for automated long-term investigations of behaviours within comb cells, such as brood care, were hitherto missing. In the present study, we demonstrate an innovative video method that enables within-cell analysis in honey bee (Apis mellifera) observation hives to detect chronic sublethal neonicotinoid effects of clothianidin (1 and 10 ppb) and thiacloprid (200 ppb) on worker behaviour and development. In May and June, colonies which were fed 10 ppb clothianidin and 200 ppb thiacloprid in syrup over three weeks showed reduced feeding visits and duration throughout various larval development days (LDDs). On LDD 6 (capping day) total feeding duration did not differ between treatments. Behavioural adaptation was exhibited by nurses in the treatment groups in response to retarded larval development by increasing the overall feeding timespan. Using our machine learning algorithm, we demonstrate a novel method for detecting behaviours in an intact hive that can be applied in a versatile manner to conduct impact analyses of chemicals, pests and other stressors.
Image-Based Single Cell Sorting Automation in Droplet Microfluidics
Authors: Sesen Muhsincan , Whyte Graeme 
Published: May 2020

AbstractThe recent boom in single-cell omics has brought researchers one step closer to understanding the biological mechanisms associated with cell heterogeneity. Rare cells that have historically been obscured by bulk measurement techniques are being studied by single cell analysis and providing valuable insight into cell function. To support this progress, novel upstream capabilities are required for single cell preparation for analysis. Presented here is a droplet microfluidic, image-based single-cell sorting technique that is flexible and programmable. The automated system performs real-time dual-camera imaging (brightfield & fluorescent), processing, decision making and sorting verification. To demonstrate capabilities, the system was used to overcome the Poisson loading problem by sorting for droplets containing a single red blood cell with 85% purity. Furthermore, fluorescent imaging and machine learning was used to load single K562 cells amongst clusters based on their instantaneous size and circularity. The presented system aspires to replace manual cell handling techniques by translating expert knowledge into cell sorting automation via machine learning algorithms. This powerful technique finds application in the enrichment of single cells based on their micrographs for further downstream processing and analysis.
Whole blood transcriptome profile at hospital admission discriminates between patients with ST-segment elevation and non-ST-segment elevation acute myocardial infarction
Authors: Chiesa Mattia , Piacentini Luca , Bono Elisa , Milazzo Valentina , Campodonico Jeness , Marenzi Giancarlo , Colombo Gualtiero I. 
Published: May 2020

AbstractWhether ST-segment (STEMI) and non-ST-segment elevation myocardial infarction (NSTEMI) should be regarded as distinct pathophysiological entities is a matter of debate. We tested the hypothesis that peripheral blood gene-expression profiles at presentation distinguish STEMI from NSTEMI. We performed a case-control study collecting whole-blood from 60 STEMI and 58 NSTEMI (defined according to the third universal definition of MI) consecutive patients on hospital admission. We used RNA-sequencing for the discovery phase, comparing 15 STEMI vs. 15 NSTEMI patients, matched for age, sex, and cardiovascular risk factors, and quantitative PCR in the remaining unmatched patients for validating top-significant genes. Gene-level differential expression analysis identified significant differences in the expression of 323 genes: 153 genes withstood correction for admission cardiac troponin I (cTnI), differentiating the two conditions independently of myocardial necrosis extent. Functional annotation analysis uncovered divergent modulation in leukocyte and platelet activation, cell migration, and mitochondrial respiratory processes. Linear regression analysis revealed gene expression patterns on admission predicting infarct size, as indexed by cTnI peak (R2 = 0.58–0.75). Our results unveil distinctive pathological traits for these two MI subtypes and provide insights into the early assessment of injury extent. This could translate into RNA-based disease-specific biomarkers for precision diagnosis and risk stratification.
Electric Fields at Breast Cancer and Cancer Cell Collective Galvanotaxis
Authors: Zhu Kan , Hum Nicholas R. , Reid Brian , Sun Qin , Loots Gabriela G. , Zhao Min 
Published: May 2020

AbstractCancer growth interferes with local ionic environments, membrane potentials, and transepithelial potentials, resulting in small electrical changes in the tumor microenvironment. Electrical fields (EFs) have significant effects on cancer cell migration (galvanotaxis/electrotaxis), however, their role as a regulator of cancer progression and metastasis is poorly understood. Here, we employed unique probe systems to characterize the electrical properties of cancer cells and their migratory ability under an EF. Subcutaneous tumors were established from a triple-negative murine breast cancer cell line (4T1), electric currents and potentials of tumors were measured using vibrating probe and glass microelectrodes, respectively. Steady outward and inward currents could be detected at different positions on the tumor surface and magnitudes of the electric currents on the tumor surface strongly correlated with tumor weights. Potential measurements also showed the non-homogeneous intratumor electric potentials. Cancer cell migration was then surveyed in the presence of EFs in vitro. Parental 4T1 cells and metastatic sublines in isolation showed random migration in EFs of physiological strength, whereas cells in monolayer migrated collectively to the anode. Our data contribute to an improved understanding of breast cancer metastasis, providing new evidence in support of an electrical mechanism that promotes this phenomenon.
2-Hydroxypropyl-gamma-cyclodextrin overcomes NPC1 deficiency by enhancing lysosome-ER association and autophagy
Authors: Singhal Ashutosh , Krystofiak Evan S. , Jerome W. Gray , Song Byeongwoon 
Published: May 2020

AbstractNiemann-Pick type C (NPC) disease is a fatal neurodegenerative disorder caused by mutations in NPC1 and NPC2 genes that result in an accumulation of cholesterol in lysosomes. The majority of children with NPC die in adolescence. Currently, no FDA-approved therapies exist for NPC and the mechanisms of NPC disease are not fully understood. Our recent study and the reports from other laboratories showed that 2-hydroxypropyl-γ-cyclodextrin (HPγCD) alleviates cholesterol accumulation in NPC1-deficient cells in spite of its low binding affinity for cholesterol. In this study, we explored the cellular changes that are induced upon HPγCD treatment in NPC1 patient-derived fibroblasts. We show that HPγCD treatment increases lysosome-ER association and enhances autophagic activity. Our study indicates that HPγCD induces an activation of the transcription factor EB (TFEB), a master regulator of lysosomal functions and autophagy. Lysosome-ER association could potentially function as conduits for cholesterol transport from lysosomes to the ER. Accumulating evidence suggests a role for autophagy in rescuing the cholesterol accumulation in NPC and other degenerative diseases. Collectively, our findings suggest that HPγCD restores cellular homeostasis in NPC1-deficient cells via enhancing lysosomal dynamics and functions. Understanding the mechanisms of HPγCD-induced cellular pathways could contribute to effective NPC therapies.
Predicting miRNA-based disease-disease relationships through network diffusion on multi-omics biological data
Authors: Sumathipala Marissa , Weiss Scott T. 
Published: May 2020

AbstractWith critical roles in regulating gene expression, miRNAs are strongly implicated in the pathophysiology of many complex diseases. Experimental methods to determine disease related miRNAs are time consuming and costly. Computationally predicting miRNA-disease associations has potential applications in finding miRNA therapeutic pathways and in understanding the role of miRNAs in disease-disease relationships. In this study, we propose the MiRNA-disease Association Prediction (MAP) method, anin-silicomethod to predict and prioritize miRNA-disease associations. The MAP method applies a network diffusion approach, starting from the known disease genes in a heterogenous network constructed from miRNA-gene associations, protein-protein interactions, and gene-disease associations. Validation using experimental data on miRNA-disease associations demonstrated superior performance to two current state-of-the-art methods, with areas under the ROC curve all over 0.8 for four types of cancer. MAP is successfully applied to predict differential miRNA expression in four cancer types. Most strikingly, disease-disease relationships in terms of shared miRNAs revealed hidden disease subtyping comparable to that of previous work on shared genes between diseases, with applications for multi-omics characterization of disease relationships.
Oral administration of ferulic acid or ethyl ferulate attenuates retinal damage in sodium iodate-induced retinal degeneration mice
Authors: Kohno Masayuki , Musashi Kunihiro , Ikeda Hanako Ohashi , Horibe Tomohisa , Matsumoto Aki , Kawakami Koji 
Published: May 2020

AbstractEpidemiological studies indicate that the daily intake of antioxidants from a traditional Asian diet reduces the risk of developing age-related macular degeneration. Many of the phytochemicals that are abundant in whole grains exhibit a wide variety of biological activity such as antioxidant, anti-inflammatory, and neuroprotective effects. Ferulic acid (FA) is a phenolic acid found in vegetables and grains that has therapeutic potential for diabetes mellitus, Alzheimer’s disease, and other diseases. We investigated the retinal protective effect of FA in a sodium iodate (NaIO3)-induced model of retinal degeneration. In a human retinal pigment epithelial cell line, FA attenuated H2O2-induced injury and lipopolysaccharide- or 7-ketocholesterol-induced inflammation. In mice, the oral administration of FA or its analog, ethyl ferulate, attenuated the morphological and functional features of NaIO3-induced retinal degeneration according to optical coherence tomography and electroretinography. Our results demonstrate that the oral administration of FA provides protective effects to the retina, suggesting that the intake of FA as a daily supplement or daily healthy diet containing rich vegetables and whole grains may prevent age-related macular degeneration.
Genetic dissection of Rift Valley fever pathogenesis: Rvfs2 locus on mouse chromosome 11 enables survival to early-onset hepatitis
Authors: Batista Leandro , Jouvion Gregory , Simon-Chazottes Dominique , Houzelstein Denis , Burlen-Defranoux Odile , Boissière Magali , Tokuda Satoko , do Valle Tania Zaverucha , Cumano Ana , Flamand Marie , Montagutelli Xavier , Panthier Jean-Jacques 
Published: May 2020

AbstractInfection of mice with Rift Valley fever virus (RVFV) reproduces major pathological features of severe human disease, notably the early-onset hepatitis and delayed-onset encephalitis. We previously reported that the Rvfs2 locus from the susceptible MBT/Pas strain reduces survival time after RVFV infection. Here, we used BALB/cByJ (BALB) mice congenic for Rvfs2 (C.MBT-Rvfs2) to investigate the pathophysiological mechanisms impacted by Rvfs2. Clinical, biochemical and histopathological features indicated similar liver damage in BALB and C.MBT-Rvfs2 mice until day 5 after infection. However, while C.MBT-Rvfs2 mice succumbed from acute liver injury, most BALB mice recovered and died later of encephalitis. Hepatocytes of BALB infected liver proliferated actively on day 6, promoting organ regeneration and recovery from liver damage. By comparison with C.MBT-Rvfs2, BALB mice had up to 100-fold lower production of infectious virions in the peripheral blood and liver, strongly decreased RVFV protein in liver and reduced viral replication in primary cultured hepatocytes, suggesting that the BALB Rvfs2 haplotype limits RVFV pathogenicity through decreased virus replication. Moreover, bone marrow chimera experiments showed that both hematopoietic and non-hematopoietic cells are required for the protective effect of the BALB Rvfs2 haplotype. Altogether, these results indicate that Rvfs2 controls critical events which allow survival to RVFV-induced hepatitis.
Supercooled water confined in a metal-organic framework
Authors: Fischer Jonas K. H. , Sippel Pit , Denysenko Dmytro , Lunkenheimer Peter , Volkmer Dirk , Loidl Alois 
Published: May 2020

AbstractWithin the so-called “no-man’s land” between about 150 and 235 K, crystallization of bulk water is inevitable. The glass-like freezing and a liquid-to-liquid transition of water, predicted to occur in this region, can be investigated by confining water in nanometer-sized pores. Here, we report the molecular dynamics of water within the pores of a metal-organic framework using dielectric spectroscopy. The detected temperature-dependent dynamics of supercooled water matches that of bulk water as reported outside the borders of the no-man’s land. In confinement, a different type of water is formed, nevertheless still undergoing a glass transition with considerable molecular cooperativity. Two different length scales seem to exist in water: a smaller one, of the order of 2 nm, being the cooperativity length scale governing glassy freezing, and a larger one (> 2 nm), characterizing the minimum size of the hydrogen-bonded network needed to create “real” water with its unique dynamic properties.
Minimizing CO2 emissions with renewable energy: a comparative study of emerging technologies in the steel industry
Authors: Flores-Granobles Marian , Saeys Mark 
Published: May 2020

Implementing CCUS technologies at existing steel plants reduces CO2 emissions by 70%, requiring 1.1 MW h per ton of renewable electricity. H2-based steel-making and CCU technologies require 4 and 8 times more electricity to reach similar reductions.
Methoxylation of quinoidal bithiophene as a single regioisomer building block for narrow-bandgap conjugated polymers and high-performance organic field-effect transistors
Authors: Sun Yunlong , Zhang Yunpeng , Ran Yang , Shi Longxian , Zhang Qingsong , Chen Jinyang , Li Qingyuan , Guo Yunlong , Liu Yunqi 
Published: May 2020

Methoxyl group was introduced to obtain isomer-free methoxylation quinoidal bithiophene building block. Four polymers displayed narrow bandgap (<1.20 eV) and hole mobility of up to 2.70 cm2 V−1 s−1.
Cellular localization of the FMRP in rat retina
Authors: Zhang Ping-Ping , Yao Hui-Hui , Zha An-Hui , Liu Xing-Yue , Fan Ke-Yu , Xu Yue , Yuan Hui-Yao , Li Lei , Wang Lie-Cheng 
Published: May 2020

Abstract
The fragile X mental retardation protein (FMRP) is a regulator of local translation through its mRNA targets in the neurons. Previous studies have demonstrated that FMRP may function in distinct ways during the development of different visual subcircuits. However, the localization of the FMRP in different types of retinal cells is unclear. In this work, the FMRP expression in rat retina was detected by Western blot and immunofluorescence double labeling. Results showed that the FMRP expression could be detected in rat retina and that the FMRP had a strong immunoreaction (IR) in the ganglion cell (GC) layer, inner nucleus layer (INL), and outer plexiform layer (OPL) of rat retina. In the outer retina, the bipolar cells (BCs) labeled by homeobox protein ChX10 (ChX10) and the horizontal cells (HCs) labeled by calbindin (CB) were FMRP-positive. In the inner retina, GABAergic amacrine cells (ACs) labeled by glutamate decarbonylase colocalized with the FMRP. The dopaminergic ACs (tyrosine hydroxylase marker) and cholinergic ACs (choline acetyltransferase (ChAT) marker) were co-labeled with the FMRP. In most GCs (labeled by Brn3a) and melanopsin-positive intrinsically photosensitive retinal GCs (ipRGCs) were also FMRP-positive. The FMRP expression was observed in the cellular retinal binding protein-positive Müller cells. These results suggest that the FMRP could be involved in the visual pathway transmission.