bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy of Low‐Cost, Side‐Scan Sonar for Surveying Alligator Gars
Authors: Paul Fleming B. , Daugherty Daniel J. , Smith Nathan G. , Betsill Robert K. 
Published: February 2018

AbstractSide‐scan sonar (SSS) provides an efficient, nonintrusive sampling tool for many fisheries applications. Professional‐grade systems have proven useful for species‐specific detection of large, distinctive fishes; however, these systems are often cost prohibitive for widespread use. Lower‐cost, consumer‐grade systems are becoming increasingly popular for fisheries applications and have been used extensively to map aquatic habitat. However, these systems often produce lower‐resolution imagery that may limit species‐specific applications. We used experimental ponds stocked with known fish assemblages and a field‐based mark–recapture study to determine the efficacy of a consumer‐grade SSS system in surveying Alligator Gars Atractosteus spatula. Three ponds were stocked with known abundances of Alligator Gars and other sympatric fishes. A fourth pond remained unstocked to assess false positives; a fifth was stocked only with other species to quantify misidentification. Replicate sonar images of each pond were then recorded using a Humminbird 998c system. For the field‐based application, we used gill nets to mark and recapture Alligator Gars and estimate population size within a closed backwater of the Guadalupe River, Texas. Following final recapture, we recorded replicate imagery of the backwater. Imagery from both evaluations was interpreted by three independent readers of varying experience without knowledge of image origin. The results from the ponds indicated a low rate of false detection (7%) and misidentification (4%). The number of Alligator Gars identified was positively related to density; however, the probability of detection varied among readers (range, 0.27–0.71) and was positively related to experience. In contrast, all readers estimated Alligator Gar abundance in the backwater within 10% of the population estimated from the mark–recapture data. Our results suggest that low‐cost SSS can provide an effective, noninvasive alternative to traditional sampling techniques for Alligator Gars.
Mutually exclusive alternative splicing of pre‐mRNAs
Authors: Jin Yongfeng , Dong Haiyang , Shi Yang , Bian Lina 
Published: February 2018

Pre‐mRNA alternative splicing is an important mechanism used to expand protein diversity in higher eukaryotes, and mutually exclusive splicing is a specific type of alternative splicing in which only one of the exons in a cluster is included in functional transcripts. The most extraordinary example of this is the Drosophila melanogaster Down’s syndrome cell adhesion molecule gene (Dscam), which potentially encodes 38,016 different isoforms through mutually exclusive splicing. Mutually exclusive splicing is a unique and challenging model that can be used to elucidate the evolution, regulatory mechanism, and function of alternative splicing. The use of new approaches has not only greatly expanded the mutually exclusive exome, but has also enabled the systematic analyses of single‐cell alternative splicing during development. Furthermore, the identification of long‐range RNA secondary structures provides a mechanistic framework for the regulation of mutually exclusive splicing (i.e., Dscam splicing). This article reviews recent insights into the identification, underlying mechanism, and roles of mutually exclusive splicing.This article is categorized under:

RNA Processing > Splicing Regulation/Alternative Splicing
RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems
A New Experimental Design to Study the Kinetics of Solid Dissolution into Liquids at Elevated Temperature
Authors: Wang Huijun , White Jesse F. , Sichen Du 
Published: February 2018

Abstract
A new method was developed to study the dissolution of a solid cylinder in a liquid under forced convection at elevated temperature. In the new design, a rotating cylinder was placed concentrically in a crucible fabricated by boring four holes into a blank material for creating an internal volume with a quatrefoil profile. A strong flow in the radial direction in the liquid was created, which was evidently shown by computational fluid dynamic (CFD) calculations and experiments at both room temperature and elevated temperature. The new setup was able to freeze the sample as it was at experimental temperature, particularly the interface between the solid and the liquid. This freezing was necessary to obtain reliable information for understanding the reaction mechanism. This was exemplified by the study of dissolution of a refractory in liquid slag. The absence of flow in the radial direction in the traditional setup using a symmetrical cylinder was also discussed. The differences in the findings by past investigators using the symmetrical cylinder are most likely due to the extent of misalignment of the cylinder in the containment vessel.
The effective diffusivity of ordered and freely evolving bubbly suspensions
Authors: Loisy Aurore , Naso Aurore , Spelt Peter D. M. 
Published: February 2018

We investigate the dispersion of a passive scalar such as the concentration of a chemical species, or temperature, in homogeneous bubbly suspensions, by determining an effective diffusivity tensor. Defining the longitudinal and transverse components of this tensor with respect to the direction of averaged bubble rise velocity in a zero mixture velocity frame of reference, we focus on the convective contribution thereof, this being expected to be dominant in commonly encountered bubbly flows. We first extend the theory of Kochet al.(J. Fluid Mech., vol. 200, 1989, pp. 173–188) (which is for dispersion in fixed beds of solid particles under Stokes flow) to account for weak inertial effects in the case of ordered suspensions. In the limits of low and of high Péclet number, including the inertial effect of the flow does not affect the scaling of the effective diffusivity with respect to the Péclet number. These results are confirmed by direct numerical simulations performed in different flow regimes, for spherical or very deformed bubbles and from vanishingly small to moderate values of the Reynolds number. Scalar transport in arrays of freely rising bubbles is considered by us subsequently, using numerical simulations. In this case, the dispersion is found to be convectively enhanced at low Péclet number, like in ordered arrays. At high Péclet number, the Taylor dispersion scaling obtained for ordered configurations is replaced by one characterizing a purely mechanical dispersion, as in random media, even if the level of disorder is very low.
Factors related to reducing free sugar intake among white ethnic adults in the UK: a qualitative study
Authors: Rawahi Said Harith Al , Asimakopoulou Koula , Newton Jonathon Timothy 
Published: February 2018

Abstract
Objective/Aims:
To determine the barriers and enablers to behavioural change to reduce free sugar intake related to dental caries in a sample of UK adults who identify their ethnicity as White.

Materials and methods:
Qualitative study comprising semi-structured interviews of 27 participants. Interviews were recorded, transcribed and analysed using thematic analysis methods. The Capability-Opportunity-Motivation-Behaviour model (COM-B) and the Theoretical Domains Framework (TDF) were used to guide the derivation of themes.

Results:
Data saturation occurred at 27 interviews. The COM-B Model and TDF domains captured various factors that may influence the consumption of free sugar. TDF elements which are reflected in the study are: Knowledge; Psychological skills; Memory, attention, and decision processes; Behavioural regulation; Physical skills; Social influence; Environmental context and resources; Social and professional role and identity; Beliefs about capabilities; Beliefs about consequence; Intentions and goals reinforcement; and Emotions. COM-B Model elements which are reflected in the study are: psychological capabilities, physical capabilities, social opportunities, physical opportunities, reflective motivation, and automatic motivation.

Discussion and conclusion:
The COM-B model and TDF framework provided a comprehensive account of the barriers and facilitators of reducing sugar intake among white ethnic groups.
The role of disease-linked residue glutamine-913 in support of the structure and function of the human electrogenic sodium/bicarbonate cotransporter NBCe1-A
Authors: Myers Evan J. , Marshall Aniko , Parker Mark D. 
Published: February 2018

AbstractMutations in the sodium bicarbonate cotransporter NBCe1 (SLC4A4) cause proximal renal tubular acidosis (pRTA). We recently described a novel pRTA mutation p.Gln913Arg (Q913R), inherited in compound heterozygous form with p.Arg510His (R510H). Q913R causes intracellular retention of NBCe1 and a ‘gain of function’ Cl− leak. To learn more about the importance of glutamine at position 913, we substituted a variety of alternative amino-acid residues (Cys, Glu, Lys, Leu, Ser) at position 913. Studying cRNA-injected Xenopus oocytes by voltage clamp, we find that most de novo mutants exhibit close-to-normal NBCe1 activity; only Q913K expresses a Cl− leak. Studying transiently-transfected, polarised kidney cells by fluorescence microscopy we find that most de novo mutants (except Q913E) are intracellularly retained. A 3D homology model predicts that Gln913 is located in the gating domain of NBCe1 and neighbours the 3D space occupied by another pRTA-associated residue (Arg881), highlighting an important and conformationally-sensitive region of NBCe1. We conclude that the intracellular retention of Q913R is caused by the loss of Gln at position 913, but that the manifestation of the Cl− leak is related to the introduction of Arg at position 913. Our findings will inform future studies to elucidate the nature and the consequences of the leak.
Diamond FinFET without Hydrogen Termination
Authors: Huang Biqin , Bai Xiwei , Lam Stephen K. , Tsang Kenneth K. 
Published: February 2018

AbstractIn this letter we report the first diamond fin field-effect transistor (diamond FinFET) without a hydrogen-terminated channel. The device operates with hole accumulation by metal-oxide-semiconductor (MOS) structures built on fins to maintain effective control of the channel conduction. Devices with 100-nm—wide fins were designed and fabricated to ensure that the channel pinched off at zero gate bias. The transfer characteristic of FinFET showed a greater than 3000 on/off ratio, successfully demonstrating the transistor behavior. Devices were characterized at room temperature and at 150 °C, showing 30 mA/mm current density at 150 °C, 35 times more than current density at room temperature. The diamond FinFET, which leverages the fin concept from the silicon industry and the material advance of diamond, enables a new class of diamond transistors for applications from digital to power and radio frequency (RF) electronics.
Human subarachnoid space width oscillations in the resting state
Authors: Gruszecki Marcin , Lancaster Gemma , Stefanovska Aneta , Neary J. Patrick , Dech Ryan T. , Guminski Wojciech , Frydrychowski Andrzej F. , Kot Jacek , Winklewski Pawel J. 
Published: February 2018

AbstractAbnormal cerebrospinal fluid (CSF) pulsatility has been implicated in patients suffering from various diseases, including multiple sclerosis and hypertension. CSF pulsatility results in subarachnoid space (SAS) width changes, which can be measured with near-infrared transillumination backscattering sounding (NIR-T/BSS). The aim of this study was to combine NIR-T/BSS and wavelet analysis methods to characterise the dynamics of the SAS width within a wide range of frequencies from 0.005 to 2 Hz, with low frequencies studied in detail for the first time. From recordings in the resting state, we also demonstrate the relationships between SAS width in both hemispheres of the brain, and investigate how the SAS width dynamics is related to the blood pressure (BP). These investigations also revealed influences of age and SAS correlation on the dynamics of SAS width and its similarity with the BP. Combination of NIR-T/BSS and time-frequency analysis may open up new frontiers in the understanding and diagnosis of various neurodegenerative and ageing related diseases to improve diagnostic procedures and patient prognosis.
Loss of the homeostatic protein BPIFA1, leads to exacerbation of otitis media severity in the Junbo mouse model
Authors: Mulay Apoorva , Hood Derek W. , Williams Debbie , Russell Catherine , Brown Steve D. M. , Bingle Lynne , Cheeseman Michael , Bingle Colin D. 
Published: February 2018

AbstractOtitis Media (OM) is characterized by epithelial abnormalities and defects in innate immunity in the middle ear (ME). Although, BPIFA1, a member of the BPI fold containing family of putative innate defence proteins is abundantly expressed by the ME epithelium and SNPs in Bpifa1 have been associated with OM susceptibility, its role in the ME is not well characterized. We investigated the role of BPIFA1 in protection of the ME and the development of OM using murine models. Loss of Bpifa1 did not lead to OM development. However, deletion of Bpifa1 in Evi1Jbo/+ mice, a model of chronic OM, caused significant exacerbation of OM severity, thickening of the ME mucosa and increased collagen deposition, without a significant increase in pro-inflammatory gene expression. Our data suggests that BPIFA1 is involved in maintaining homeostasis within the ME under steady state conditions and its loss in the presence of inflammation, exacerbates epithelial remodelling leading to more severe OM.
Predictive Biomarkers of Gastroesophageal Reflux Disease and Barrett’s Esophagus in World Trade Center Exposed Firefighters: a 15 Year Longitudinal Study
Authors: Haider Syed H. , Kwon Sophia , Lam Rachel , Lee Audrey K. , Caraher Erin J. , Crowley George , Zhang Liqun , Schwartz Theresa M. , Zeig-Owens Rachel , Liu Mengling , Prezant David J. , Nolan Anna 
Published: February 2018

AbstractGastroesophageal reflux disease (GERD) and Barrett’s Esophagus (BE), which are prevalent in the World Trade Center (WTC) exposed and general populations, negatively impact quality of life and cost of healthcare. GERD, a risk factor of BE, is linked to obstructive airways disease (OAD). We aim to identify serum biomarkers of GERD/BE, and assess the respiratory and clinical phenotype of a longitudinal cohort of never-smoking, male, WTC-exposed rescue workers presenting with pulmonary symptoms. Biomarkers collected soon after WTC-exposure were evaluated in optimized predictive models of GERD/BE. In the WTC-exposed cohort, the prevalence of BE is at least 6 times higher than in the general population. GERD/BE cases had similar lung function, D
LCO
, bronchodilator response and long-acting β-agonist use compared to controls. In confounder-adjusted regression models, TNF-α ≥ 6 pg/mL predicted both GERD and BE. GERD was also predicted by C-peptide ≥ 360 pg/mL, while BE was predicted by fractalkine ≥ 250 pg/mL and IP-10 ≥ 290 pg/mL. Finally, participants with GERD had significantly increased use of short-acting β-agonist compared to controls. Overall, biomarkers sampled prior to GERD/BE presentation showed strong predictive abilities of disease development. This study frames future investigations to further our understanding of aerodigestive pathology due to particulate matter exposure.
Botulinum neurotoxin–encoding plasmids can be conjugatively transferred to diverse clostridial strains
Authors: Nawrocki Erin M. , Bradshaw Marite , Johnson Eric A. 
Published: February 2018

AbstractMost Group I Clostridium botulinum strains harbor botulinum neurotoxin (bont) genes on their chromosome, while some carry these genes (including bont/a, bont/b, and bont/f) on large plasmids. Prior work in our laboratory demonstrated that Group I BoNT plasmids were mobilized to C. botulinum recipient strains containing the Tn916 transposon. Here, we show that Tn916 is nonessential for plasmid transfer. Relying on an auxotrophic donor phenotype and a plasmid-borne selectable marker, we observed the transfer of pCLJ, a 270 kb plasmid harboring two bont genes, from its host strain to various clostridia. Transfer frequency was greatest to other Group I C. botulinum strains, but the plasmid was also transferred into traditionally nontoxigenic species, namely C. sporogenes and C. butyricum. Expression and toxicity of BoNT/A4 was confirmed in transconjugants by immunoblot and mouse bioassay. These data indicate that conjugation within the genus Clostridium can occur across physiological Groups of C. botulinum, supporting horizontal gene transfer via bont-bearing plasmids. The transfer of plasmids possessing bont genes to resistant Clostridium spp. such as C. sporogenes could impact biological safety for animals and humans. These plasmids may play an environmental role in initiating death in vertebrates, leading to decomposition and nutrient recycling of animal biomass.
Mesoporous silica nanocarriers encapsulated antimalarials with high therapeutic performance
Authors: Amolegbe Saliu Alao , Hirano Yui , Adebayo Joseph Oluwatope , Ademowo Olusegun George , Balogun Elizabeth Abidemi , Obaleye Joshua Ayoola , Krettli Antoniana Ursine , Yu Chengzhong , Hayami Shinya 
Published: February 2018

AbstractThe use of nanocarriers in drug delivery is a breakeven research and has received a clarion call in biomedicine globally. Herein, two newly nano-biomaterials: MCM-41 encapsulated quinine (MCM-41 ⊃ QN) (1) and 3-phenylpropyl silane functionalized MCM-41 loaded QN (pMCM-41 ⊃ QN) (2) were synthesized and well characterized. 1 and 2 along with our two already reported nano-antimalarial drugs (MCM-41 ⊃ ATS) (3) and 3-aminopropyl silane functionalized MCM-41 contained ATS (aMCM-41 ⊃ ATS) (4) were screened in vitro for their activity against P. falciparium W2 strain, cytotoxicity against BGM cells and in vivo for their activity against Plasmodium bergheiNK65. 1 has the highest antimalarial activity in vivo against P. berghei NK65, (ED50: < 0.0625 mg/kg body weight) and higher mean survival time compared to the other nano biomaterials or unencapsulated drugs at doses higher than 0.0625 mg/kg body weight. This encapsulation strategy of MCM-41 ⊃ QN (1) stands very useful and effective in delivering the drug to the target cells compared to other delivery systems and therefore, this encapsulated drug may be considered for rational drug design.
Decreased succinate dehydrogenase B in human hepatocellular carcinoma accelerates tumor malignancy by inducing the Warburg effect
Authors: Tseng Po-Lin , Wu Wei-Hsuan , Hu Tsung-Hui , Chen Chih-Wei , Cheng Hung-Chi , Li Chien-Feng , Tsai Wen-Hui , Tsai Hui-Ju , Hsieh Meng-Che , Chuang Jiin-Haur , Chang Wen-Tsan 
Published: February 2018

AbstractChanges in TCA cycle enzymes or respiratory activity are possible mechanisms of aerobic glycolysis that contributes to tumor progression. To clarify whether the decrease of succinate dehydrogenase B (SDHB) alters energy metabolism, induces the Warburg effect and results in tumor malignancy, SDHB expression was examined and modulated in hepatocellular carcinoma (HCC) tissues and cells, respectively. SDHB level was often decreased in malignant HCC cells and tissues. Furthermore, the reduced SDHB expression was associated with advanced tumor stage and poor survival rate. Moreover, silencing of SDHB altered energy metabolism switched from aerobic respiration to glycolysis, resulted in the Warburg effect, and enhanced cell proliferation and motility. In contrast, the SDHB overexpression deregulated bioenergetic metabolism and decreased cell growth and migration. In mouse xenograft models, subcutaneous implantation and tail vein injection with SDHB knockdown cells resulted in a larger tumor volume and accelerated cancer metastasis, respectively. A mutation or decrease in SDHB induced the switch from aerobic respiration to glycolysis. This metabolic alteration was associated with tumor cell dedifferentiation, proliferation, motility and overall patient survival in HCC.
Structural elucidation of a polysaccharide from Flammulina velutipes and its immunomodulation activities on mouse B lymphocytes
Authors: Wang Wen-Han , Zhang Jing-Song , Feng Ting , Deng Jing , Lin Chi-Chung , Fan Hua , Yu Wen-Juan , Bao Hai-Ying , Jia Wei 
Published: February 2018

AbstractA novel polysaccharide FVPB2 was purified from fruiting bodies of Flammulina velutipes. Its structure was elucidated by monosaccharide composition and methylation analyses, UV-Visible and FTIR spectroscopy as well as NMR. FVPB2 was a homogeneous heteropolysaccharide (molecular weight ~ 1.50 × 104 Da) containing D-galactose, D-mannose, L-fucose, and D-glucose at molar ratio of 1.9:1.2:1:2.5. In vitro immunomodulatory studies showed FVPB2 induced proliferation of mouse spleen lymphocytes in a dose-dependent manner. The levels of IgM and IgG, secreted by B cells, increased after FVPB2 treatment. So FVPB2 has potential to be a new important immunomodulatory nutraceutical.
Molecular dynamics study of strengthening mechanism of nanolaminated graphene/Cu composites under compression
Authors: Weng Shayuan , Ning Huiming , Fu Tao , Hu Ning , Zhao Yinbo , Huang Cheng , Peng Xianghe 
Published: February 2018

AbstractMolecular dynamics simulations of nanolaminated graphene/Cu (NGCu) and pure Cu under compression are conducted to investigate the underlying strengthening mechanism of graphene and the effect of lamella thickness. It is found that the stress-strain curves of NGCu undergo 3 regimes i.e. the elastic regime I, plastic strengthening regime II and plastic flow regime III. Incorporating graphene monolayer is proved to simultaneously contribute to the strength and ductility of the composites and the lamella thickness has a great effect on the mechanical properties of NGCu composites. Different strengthening mechanisms play main role in different regimes, the transition of mechanisms is found to be related to the deformation behavior. Graphene affected zone is developed and integrated with rule of mixtures and confined layer slip model to describe the elastic properties of NGCu and the strengthening effect of the incorporated graphene.
Measurements of complex refractive index change of photoactive yellow protein over a wide wavelength range using hyperspectral quantitative phase imaging
Authors: Lee KyeoReh , Kim Youngmin , Jung JaeHwang , Ihee Hyotcherl , Park YongKeun 
Published: February 2018

AbstractA novel optical holographic technique is presented to simultaneously measure both the real and imaginary components of the complex refractive index (CRI) of a protein solution over a wide visible wavelength range. Quantitative phase imaging was employed to precisely measure the optical field transmitted from a protein solution, from which the CRIs of the protein solution were retrieved using the Fourier light scattering technique. Using this method, we characterized the CRIs of the two dominant structural states of a photoactive yellow protein solution over a broad wavelength range (461–582 nm). The significant CRI deviation between the two structural states was quantified and analysed. The results of both states show the similar overall shape of the expected rRI obtained from the Kramers–Kronig relations.