bluuebunny/crossref_metadata_2025_split huggingface dataset:
Embryonic origin and genetic basis of cave associated phenotypes in the isopod crustacean Asellus aquaticus
Authors: Mojaddidi Hafasa , Fernandez Franco E. , Erickson Priscilla A. , Protas Meredith E. 
Published: November 2018

AbstractCharacteristics common to animals living in subterranean environments include the reduction or absence of eyes, lessened pigmentation and enhanced sensory systems. How these characteristics have evolved is poorly understood for the majority of cave dwelling species. In order to understand the evolution of these changes, this study uses an invertebrate model system, the freshwater isopod crustacean, Asellus aquaticus, to examine whether adult differences between cave and surface dwelling individuals first appear during embryonic development. We hypothesized that antennal elaboration, as well as eye reduction and pigment loss, would be apparent during embryonic development. We found that differences in pigmentation, eye formation, and number of segments of antenna II were all present by the end of embryonic development. In addition, we found that cave and surface hatchlings do not significantly differ in the relative size of antenna II and the duration of embryonic development. To investigate whether the regions responsible for eye and pigment differences could be genetically linked to differences in article number, we genotyped F2 hybrids for the four previously mapped genomic regions associated with eye and pigment differences and phenotyped these F2 hybrids for antenna II article number. We found that the region previously known to be responsible for both presence versus absence of pigment and eye size also was significantly associated with article number. Future experiments will address whether pleiotropy and/or genetic linkage play a role in the evolution of cave characteristics in Asellus aquaticus.
Effect of Early Calf-Hood Nutrition on the Transcriptional Regulation of the Hypothalamic-Pituitary-Testicular axis in Holstein-Friesian Bull Calves
Authors: English A. M. , Byrne C. J. , Cormican P , Waters S. M. , Fair S. , Kenny D. A. 
Published: November 2018

AbstractThe aim of this study was to investigate the effect of early calf-hood nutrition on the transcriptomic profile of the arcuate nucleus of the hypothalamus, anterior pituitary and testes in Holstein-Friesian bulls. Holstein-Friesian bull calves with a mean (±S.D.) age and bodyweight of 19 (±8.2) days and 47.5 (±5.3) kg, respectively, were offered a high (n = 10) or low (n = 10) plane of nutrition in order to achieve an overall growth rate of 1.2 and 0.5 kg/day. At 126 (±3) days of age, calves were euthanized, hypothalamus (arcuate region), anterior pituitary and testicular parenchyma samples were harvested and RNAseq analysis was performed. There were 0, 49 and 1,346 genes differentially expressed in the arcuate nucleus, anterior pituitary and testicular tissue of bull calves on the low relative to the high plane of nutrition, respectively (P < 0.05; False Discovery Rate <0.05). Cell cycle processes in the anterior pituitary were down regulated in the low relative to the high plane of nutrition; there was no differential expression of genes related to reproductive processes. Gene expression involved in cholesterol and androgen biosynthesis in the testes were down regulated in animals on the low plane of nutrition. This study provides insight into the effect of early life plane of nutrition on the regulation of the HPT axis.
Critical Drip Size and Blue Flame Shedding of Dripping Ignition in Fire
Authors: Huang Xinyan 
Published: November 2018

AbstractDripping of molten fuels is a widely observed fire phenomenon, and, by igniting other fuels, it can promote fire spread and increase fire hazards. In this work, dripping phenomena from fires of horizontally oriented wires, coated with polyethylene (PE), are investigated in the laboratory. It is found that as long as a flame is attached to the drip, thin tissue paper can be ignited by a single drip. Below a minimum diameter (Dmin = 0.63 mm), the drip floats up. Above a critical diameter (Dcrt = 2.3 mm), a flame can remain attached to the drip and ignite tissue paper as it falls through a distance of at least 2.6 m, thereby posing a significant fire hazard. A falling burning drip appears to the eye to be a blue chain of flame as a result of persistence of vision. Photographic evidence identifies a flame-shedding process, most likely associated with continual sequential ignition of fuel vapor within a von Karman vortex street generated behind the falling burning drip. The frequency of flame shedding agrees with both the frequency of modeled vortex shedding and the frequency of the unexpected sound that is heard during the process. This is the first time that combustion characteristics of dripping fire phenomena have been studied in detail, and this helps to better evaluate the risk and hazards of wire and façade fires.
Extensions to Michaelis-Menten Kinetics for Single Parameters
Authors: Ariyawansha R. T. K. , Basnayake B. F. A. , Karunarathna A. K. , Mowjood M. I. M. 
Published: November 2018

AbstractBiochemical transformation kinetics is based on the formation of enzyme-substrate complexes. We developed a robust scheme based on unit productions of enzymes and reactants in cyclic events to comply with mass action law to form enzyme-substrate complexes. The developed formalism supports a successful application of Michaelis-Menten kinetics in all biochemical transformations of single parameters. It is an essential tool to overcome some challenging healthcare and environmental issues. In developing the formalism, we defined the substrate [S]= [Product]3/4 and rate of reaction based on rate and time perspectives. It allowed us to develop two quadratic equations. The first, represents a body entity that gave a useful relationship of enzyme E = 2S0.33, and the second nutrients/feed, each giving [Enzymes] and [Enzyme-substrate complexes], simulating rate of reaction, [substrate], and their differentials. By combining [Enzymes] and [Enzyme-substrate complexes] values, this quadratic equation derives a Michaelis-Menten hyperbolic function. Interestingly, we can derive the proportionate rate of reaction and [Enzymes] values of the quadratics resulting in another Michaelis-Menten hyperbolic. What is clear from these results is that between these two hyperbolic functions, in-competitive inhibitions exist, indicating metabolic activities and growth in terms of energy levels. We validated these biochemical transformations with examples applicable to day to day life.
Sirtuin 1 genetic variation, energy balance and colorectal cancer risk by sex and subsite in the Netherlands Cohort Study
Authors: Simons C. C. J. M. , Schouten L. J. , Godschalk R. W. , van Schooten F. J. , van den Brandt P. A. , Weijenberg M. P. 
Published: November 2018

AbstractSirtuin 1 (SIRT1) is an energy-sensing protein, which may affect tumorigenesis. We used SIRT1 variants as time-independent indicators of SIRT1 involvement in carcinogenesis and we studied two tagging SIRT1 variants in relation to colorectal cancer (CRC) risk. We also evaluated known energy balance-related CRC risk factors within SIRT1 genotype strata. The Netherlands Cohort Study includes 120,852 individuals and has 20.3 years follow-up (case-cohort: nsubcohort = 5000; nCRC cases = 4667). At baseline, participants self-reported weight, weight at age 20, height, trouser/skirt size reflecting waist circumference, physical activity, and early life energy restriction. SIRT1 rs12778366 and rs10997870 were genotyped in toenail DNA available for ~75% of the cohort. Sex- and subsite-specific Cox hazard ratios (HRs) showed that the rs12778366 CC versus TT genotype decreased CRC and colon cancer risks in women (HRCRC = 0.53, 95% confidence interval: 0.30–0.94) but not men. Multiplicative interactions were observed between SIRT1 variants and energy balance-related factors in relation to CRC endpoints, but the direction of associations was not always conform expectation nor specific to one genotype stratum. In conclusion, these results support SIRT1 involvement in colon cancer development in women. No conclusions could be made regarding a modifying effect of SIRT1 variants on associations between energy balance-related factors and CRC risk.
Pili mediated intercellular forces shape heterogeneous bacterial microcolonies prior to multicellular differentiation
Authors: Pönisch Wolfram , Eckenrode Kelly B. , Alzurqa Khaled , Nasrollahi Hadi , Weber Christoph , Zaburdaev Vasily , Biais Nicolas 
Published: November 2018

AbstractMicrocolonies are aggregates of a few dozen to a few thousand cells exhibited by many bacteria. The formation of microcolonies is a crucial step towards the formation of more mature bacterial communities known as biofilms, but also marks a significant change in bacterial physiology. Within a microcolony, bacteria forgo a single cell lifestyle for a communal lifestyle hallmarked by high cell density and physical interactions between cells potentially altering their behaviour. It is thus crucial to understand how initially identical single cells start to behave differently while assembling in these tight communities. Here we show that cells in the microcolonies formed by the human pathogen Neisseria gonorrhoeae (Ng) present differential motility behaviors within an hour upon colony formation. Observation of merging microcolonies and tracking of single cells within microcolonies reveal a heterogeneous motility behavior: cells close to the surface of the microcolony exhibit a much higher motility compared to cells towards the center. Numerical simulations of a biophysical model for the microcolonies at the single cell level suggest that the emergence of differential behavior within a multicellular microcolony of otherwise identical cells is of mechanical origin. It could suggest a route toward further bacterial differentiation and ultimately mature biofilms.
Effects of rotation on temperature fluctuations in turbulent thermal convection on a hemisphere
Authors: Meuel T. , Coudert M. , Fischer P. , Bruneau C. H. , Kellay H. 
Published: November 2018

AbstractRotation is present in many physical and geophysical systems and its role in determining flow properties and modifying turbulent fluctuations is of crucial importance. Here we focus on the role of rotation on temperature fluctuations in turbulent thermal convection. The system used consists of a rotating half soap bubble heated from below. This system has features, curvature and a quasi two dimensional character, which are reminiscent of atmospheric and planetary systems. Our experiments and numerical simulations show that rotation changes the nature of turbulent fluctuations and a new scaling regime is obtained for the temperature field. This change in the scaling behavior of temperature fluctuations, due to rotation, is put forth by studying the so called second moment of temperature differences across different scales. For high enough rotation rates, these temperature differences display a transition from Bolgiano Obukhov scaling to a new scaling regime. This scaling is at odds with expectations from theory, numerics, and experiments in three dimensions, suggesting that the effects of rotation on turbulent flows depend strongly on geometry and spatial dimension.
Bottle beam generation from a frequency-doubled Nd:YVO4 laser
Authors: Tung J. C. , Ma Y. Y. , Miyamoto K. , Chen Y. F. , Omatsu T. 
Published: November 2018

AbstractWe demonstrate, for the first time, the direct generation of a bottle beam with a well-isolated three-dimensional zero-intensity dark core (high potential barrier) from a compact intracavity frequency-doubled Nd:YVO4 laser with a nearly hemispherical cavity. We also numerically calculate the physical properties of the generated bottle beam using a coherent superposition of a series of frequency-locked Laguerre–Gaussian modes.
Structural Studies based on two Lysine Dioxygenases with Distinct Regioselectivity Brings Insights Into Enzyme Specificity within the Clavaminate Synthase-Like Family
Authors: Bastard Karine , Isabet Tatiana , Stura Enrico A. , Legrand Pierre , Zaparucha Anne 
Published: November 2018

AbstractIron(II)/α-ketoacid-dependent oxygenases (αKAOs) are enzymes that catalyze the oxidation of unactivated C-H bonds, mainly through hydroxylation. Among these, those that are active towards amino-acids and their derivatives are grouped in the Clavaminate Synthase Like (CSL) family. CSL enzymes exhibit high regio- and stereoselectivities with strict substrate specificity. This study reports the structural elucidation of two new regiodivergent members, KDO1 and KDO5, active towards lysine, and the structural and computational analysis of the whole family through modelling and classification of active sites. The structures of KDO1 and KDO5 in complex with their ligands show that one exact position in the active site controls the regioselectivity of the reaction. Our results suggest that the substrate specificity and high stereoselectivity typical of this family is linked to a lid that closes up in order to form a sub-pocket around the side chain of the substrate. This dynamic lid is found throughout the family with varying sequence and length and is associated with a conserved stable dimeric interface. Results from this study could be a starting-point for exploring the functional diversity of the CSL family and direct in vitro screening in the search for new enzymatic activities.
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) shows adaptation of grass pollen composition
Authors: Diehn Sabrina , Zimmermann Boris , Bağcıoğlu Murat , Seifert Stephan , Kohler Achim , Ohlson Mikael , Fjellheim Siri , Weidner Steffen , Kneipp Janina 
Published: November 2018

AbstractMALDI time-of-flight mass spectrometry (MALDI-TOF MS) has become a widely used tool for the classification of biological samples. The complex chemical composition of pollen grains leads to highly specific, fingerprint-like mass spectra, with respect to the pollen species. Beyond the species-specific composition, the variances in pollen chemistry can be hierarchically structured, including the level of different populations, of environmental conditions or different genotypes. We demonstrate here the sensitivity of MALDI-TOF MS regarding the adaption of the chemical composition of three Poaceae (grass) pollen for different populations of parent plants by analyzing the mass spectra with partial least squares discriminant analysis (PLS-DA) and principal component analysis (PCA). Thereby, variances in species, population and specific growth conditions of the plants were observed simultaneously. In particular, the chemical pattern revealed by the MALDI spectra enabled discrimination of the different populations of one species. Specifically, the role of environmental changes and their effect on the pollen chemistry of three different grass species is discussed. Analysis of the group formation within the respective populations showed a varying influence of plant genotype on the classification, depending on the species, and permits conclusions regarding the respective rigidity or plasticity towards environmental changes.
Experiment of GBR for repair of peri-implant alveolar defects in beagle dogs
Authors: Li HuiPing , Zheng JiSi , Zhang Shanyong , Yang Chi , Kwon Yong-Dae , Kim Yong-Jin 
Published: November 2018

AbstractTo guide barrier membrane choice in the treatment of peri-implant alveolar bone defects, we evaluated guided bone regeneration (GBR) using titanium (Ti) mesh or Bio-Gide membrane, independently or in combination, for repair of alveolar bone defects in Beagle dogs. Six months after extraction of the mandibular premolars and first molars from three beagle dogs, we inserted implants assigned into 3 groups and covered with the following membrane combinations: Group A: Implant + Bio-Oss + Ti-mesh, Group B: Implant + Bio-Oss + Bio-Gide, and Group C: Implant + Bio-Oss + Ti-mesh + Bio-Gide. At 6 months, micro-CT revealed that bone volume/total volume (BV/TV), trabecular number (Tb.N), and trabecular thickness (Tb.Th) was significantly greater in Group C than the other two groups, while trabecular separation (Tb.Sp) was significantly lower, suggesting improved bone regeneration. The distance between bands of three fluorescent tracking dyes was significantly greater in Group C, indicating faster deposition of new bone. The Bio-Oss particles were ideally integrated with newly deposited bone and bone thickness was significantly larger in Group C. These findings suggest that combination of Bio-Gide membrane and titanium mesh can effectively repair peri-implant alveolar bone defects, achieving enhanced bone regeneration compared to titanium mesh or Bio-Gide alone, and therefore providing a novel treatment concept for clinical implant surgery.
Assessment of coding region variants in Kuwaiti population: implications for medical genetics and population genomics
Authors: John Sumi Elsa , Antony Dinu , Eaaswarkhanth Muthukrishnan , Hebbar Prashantha , Channanath Arshad Mohamed , Thomas Daisy , Devarajan Sriraman , Tuomilehto Jaakko , Al-Mulla Fahd , Alsmadi Osama , Thanaraj Thangavel Alphonse 
Published: November 2018

AbstractConsanguineous populations of the Arabian Peninsula have been underrepresented in global efforts that catalogue human exome variability. We sequenced 291 whole exomes of unrelated, healthy native Arab individuals from Kuwait to a median coverage of 45X and characterised 170,508 single-nucleotide variants (SNVs), of which 21.7% were ‘personal’. Up to 12% of the SNVs were novel and 36% were population-specific. Half of the SNVs were rare and 54% were missense variants. The study complemented the Greater Middle East Variome by way of reporting many additional Arabian exome variants. The study corroborated Kuwaiti population genetic substructures previously derived using genome-wide genotype data and illustrated the genetic relatedness among Kuwaiti population subgroups, Middle Eastern, European and Ashkenazi Jewish populations. The study mapped 112 rare and frequent functional variants relating to pharmacogenomics and disorders (recessive and common) to the phenotypic characteristics of Arab population. Comparative allele frequency data and carrier distributions of known Arab mutations for 23 disorders seen among Arabs, of putative OMIM-listed causal mutations for 12 disorders observed among Arabs but not yet characterized for genetic basis in Arabs, and of 17 additional putative mutations for disorders characterized for genetic basis in Arab populations are presented for testing in future Arab studies.
CD200 facilitates the isolation of corneal epithelial cells derived from human pluripotent stem cells
Authors: Hayashi Ryuhei , Ishikawa Yuki , Katayama Tomohiko , Quantock Andrew J. , Nishida Kohji 
Published: November 2018

AbstractThe in vitro induction of corneal epithelial cells (CECs) from human induced pluripotent stem cells (iPSCs) represents a new strategy for obtaining CE stem/progenitor cells for the surgical reconstruction of a diseased or injured ocular surface. The clinical promise of this strategy is considerable, but if the approaches’ potential is to be realised, robust methods for the purification of iPSC-derived CE lineage cells need to be developed to avoid contamination with other cells that may carry the risk of unwanted side effects, such as tumorigenesis. Experiments conducted here revealed that during CEC isolation, CD200-negative selection using a cell sorter considerably reduced the contamination of the cell population with various non-CECs compared with what could be achieved using TRA-1-60, a conventional negative marker for CECs. Furthermore, CD200-negative sorting did not affect the yield of CECs nor that of their stem/progenitor cells. Single-cell gene expression analysis for CEC sheets obtained using CD200-negative sorting showed that all analysed cells were CE-lineage cells, expressing PAX6, delta-N p63, and E-cadherin. Non-CECs, on the other hand, expressed non-CEC genes such as FGFR1 and RPE65. CD200, thus, represents a robust negative marker for purification of induced CE lineage cells, which is expressed by undifferentiated iPSCs and non-CECs, including iPSC-derived neural and retinal cells.
Induction of intracellular ferritin expression in embryo-derived Ixodes scapularis cell line (ISE6)
Authors: Hernandez Emmanuel Pacia , Kusakisako Kodai , Talactac Melbourne Rio , Galay Remil Linggatong , Yoshii Kentaro , Tanaka Tetsuya 
Published: November 2018

AbstractIron is a very important nutrient for cells; however, it could also cause fatal effects because of its capability to trigger oxidative stress. Due to high exposure to iron from their blood diet, ticks make use of several mechanisms to cope up with oxidative stress. One mechanism is iron sequestration by ferritin and its control protein (IRP). Since the IRP activity is dependent on the ferrous iron concentration, we tried to induce intracellular ferritin (FER1) protein expression by exposing Ixodes scapularis embryo-derived cell line (ISE6) to different concentrations of ferrous sulphate at different time points. We were able to induce FER1 protein after exposure to 2 mM of ferrous sulphate for 48 h, as observed in both Western blotting and indirect immunofluorescent antibody tests. This could indicate that the FER1 produced could be a product of the release of IRPs from the FER1 mRNA leading to its translation. The RNA interference of FER1, through the transfection of dsRNA, led to an increase in mortality and decrease in the cellular proliferation of ISE6 cells. Overall, ISE6 cells could be a good tool in further understanding the mechanism of FER1 action, not just in Ixodes ticks but in other tick species as well.
Breakdown-induced conductive channel for III-nitride light-emitting devices
Authors: Han Sang-Hyun , Baek Seung-Hye , Lee Hyun-Jin , Kim Hyunsoo , Lee Sung-Nam 
Published: November 2018

AbstractIII-nitride semiconductor-based light-emitting diodes (LEDs) have superior physical properties, such as high thermal stability and brightness, for application to solid-state lighting sources. With the commercialization of GaN-based LEDs, improving LED reliability is important because they can be affected by electrostatic discharge, reverse leakage, and breakdown. However, research on the reverse bias characteristics of GaN-based LEDs is insufficient. We studied the reverse breakdown mechanism and demonstrated that a local breakdown can form a conductive channel in GaN-based LEDs, which can be expanded to a novel planar-type LED structure without an n-contact electrode. Furthermore, we found that this approach can be applied to AC-controllable light-emitting devices without any AC–DC converter.
Exosomes exert cardioprotection in dystrophin-deficient cardiomyocytes via ERK1/2-p38/MAPK signaling
Authors: Gartz Melanie , Darlington Ashley , Afzal Muhammed Zeeshan , Strande Jennifer L. 
Published: November 2018

AbstractAs mediators of intercellular communication, exosomes containing molecular cargo are secreted by cells and taken up by recipient cells to influence cellular phenotype and function. Here we have investigated the effects of exosomes in dystrophin-deficient (Dys) induced pluripotent stem cell derived cardiomyocytes (iCMs). Our data demonstrate that exosomes secreted from either wild type (WT) or Dys-iCMs protect the Dys-iCM from stress-induced injury by decreasing reactive oxygen species and delaying mitochondrial permeability transition pore opening to maintain the mitochondrial membrane potential and decrease cell death. The protective effects of exosomes were dependent on the presence of exosomal surface proteins and activation of ERK1/2 and p38 MAPK signaling. Based on our findings, the acute effects of exosomes on recipient cells can be initiated from exosome membrane proteins and not necessarily their internal cargo.