bluuebunny/crossref_metadata_2025_split huggingface dataset:
Natural killer cell activation by respiratory syncytial virus-specific antibodies is decreased in infants with severe respiratory infections and correlates with Fc-glycosylation
Authors: van Erp Elisabeth A. , Lakerveld Anke J. , de Graaf Erik , Larsen Mads D. , Schepp Rutger M. , Hipgrave Ederveen Agnes L. , Ahout Inge M. L. , de Haan Cornelis A. M. , Wuhrer Manfred , Luytjes Willem , Ferwerda Gerben , Vidarsson Gestur , van Kasteren Puck B. 
Published: August 2019

AbstractBackgroundRespiratory syncytial virus (RSV) is a major cause of severe lower respiratory tract infections in infants and there is no vaccine available. In early life, the most important contributors to protection against infectious diseases are the innate immune system and maternal antibodies. However, the mechanisms by which antibodies can protect against RSV disease are incompletely understood, as both antibody levels and neutralization capacity correlate poorly with protection. We therefore asked whether antibody-mediated natural killer (NK) cell activation correlates with RSV disease.MethodsWe performed an observational case-control study including infants hospitalized for RSV infection (n=43, cases), hernia surgery (n=16, controls), or RSV-negative viral respiratory tract infections (n=18, controls). First, we determined RSV antigen-specific antibody levels in infant plasma using a multiplex immunoassay. Subsequently, we measured the capacity of these antibodies to activate NK cells. Finally, we assessed Fc-glycosylation of the RSV-specific antibodies by mass spectrometry.ResultsWe found that RSV-specific maternal antibodies potently activate NK cellsin vitro. While the concentrations of RSV-specific antibodies did not differ between cases and controls, antibodies from infants hospitalized for severe lower respiratory tract infections (RSV and/or other) induced significantly less NK cell interferon gamma production than those from uninfected controls. Furthermore, NK cell activation correlated with Fc-fucosylation of RSV-specific antibodies, but their glycosylation status did not significantly differ between cases and controls.ConclusionsOur results suggest that Fc-dependent antibody function and quality, exemplified by NK cell activation and glycosylation, contribute to protection against severe RSV disease and warrant further studies to evaluate the potential of harnessing these activities to develop an effective vaccine.
Multi-modal communication: Song sparrows increase signal redundancy in noise
Authors: Akçay Çağlar , Beecher Michael D. 
Published: August 2019

AbstractAlthough the effects of anthropogenic noise on animal communication have been studied widely, most research on the effect of noise in communication has been on communication in a single modality. Consequently, how multimodal communication is affected by anthropogenic noise is relatively poorly understood. Here we ask whether song sparrows (Melospiza melodia) show evidence of plasticity in response to noise in two aggressive signals in acoustic and visual modalities. We test two hypotheses: (1) that song sparrows will shift signaling effort to the visual modality (the multi-modal shift hypothesis), and (2) that they will increase redundancy of their multi-modal signaling (the back-up hypothesis). We presented male song sparrows with song playback and a taxidermic mount with or without a low-frequency acoustic noise from a nearby speaker. We found that males did not switch their signaling effort to visual modality (i.e., wing waves) in response to the noise. However, the correlation between warbled soft songs and wing waves increased in the noise treatment, i.e. signals became more redundant. These results suggest that when faced with anthropogenic noise, song sparrows can increase redundancy of their multi-modal signals, which may aid in robustness of the communication system.
Heart-Brain Interactions Shape Somatosensory Perception and Evoked Potentials
Authors: Al Esra , Iliopoulos Fivos , Forschack Norman , Nierhaus Till , Grund Martin , Motyka Paweł , Gaebler Michael , Nikulin Vadim V. , Villringer Arno 
Published: August 2019

ABSTRACTHuman perception either refers to the external world, exteroception, or internal body parts such as the heart, interoception. How these two types of perception interact is poorly understood. Using electroencephalography, we identify two heartbeat-related modulations of conscious somatosensory perception: (i) When stimulus timing coincided with systole of the cardiac cycle, participants were less likely to detect and localize somatosensory stimuli, and late components (P300) of the somatosensory-evoked potential (SEP) were attenuated. (ii) The amplitude of the heartbeat-evoked potential (HEP) negatively correlated with detection bias (criterion) and localization accuracy. Furthermore, higher HEP amplitudes were followed by decreases in both early and late SEP amplitudes. Both heartbeat-related effects were independent of the alpha oscillations’ influence on somatosensory processing. We conclude that internal signals are integrated into our conscious perception of the world, and connect our results to predictive processing (heartbeat-coupled stimulus timing) and attentional shifts between exteroception and interoception (HEP amplitude).
Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data
Authors: Jarmusch Alan K. , Wang Mingxun , Aceves Christine M. , Advani Rohit S. , Aguire Shaden , Aksenov Alexander A. , Aleti Gajender , Aron Allegra T. , Bauermeister Anelize , Bolleddu Sanjana , Bouslimani Amina , Rodriguez Andres Mauricio Caraballo , Chaar Rama , Coras Roxana , Elijah Emmanuel O. , Ernst Madeleine , Gauglitz Julia M. , Gentry Emily C. , Husband Makhai , Jarmusch Scott A. , Jones Kenneth L. , Kamenik Zdenek , Le Gouellec Audrey , Lu Aileen , McCall Laura-Isobel , McPhail Kerry L. , Meehan Michael J. , Melnik Alexey V. , Menezes Riya C. , Giraldo Yessica Alejandra Montoya , Nguyen Ngoc Hung , Nothias Louis Felix , Nothias-Esposito Mélissa , Panitchpakdi Morgan , Petras Daniel , Quinn Robert , Sikora Nicole , van der Hooft Justin J.J. , Vargas Fernando , Vrbanac Alison , Weldon Kelly , Knight Rob , Bandeira Nuno , Dorrestein Pieter C. 
Published: August 2019

AbstractMetabolomics data are difficult to find and reuse, even in public repositories. We, therefore, developed the Reanalysis of Data User (ReDU) interface (https://redu.ucsd.edu/), a community- and data-driven approach that solves this problem at the repository scale. ReDU enables public data discovery and co- or re-analysis via uniformly formatted, publicly available MS/MS data and metadata in the Global Natural Product Social Molecular Networking Platform (GNPS), consistent with findable, accessible, interoperable, and reusable (FAIR) principles.1
Targeting effector pathways in RAC1P29S-driven malignant melanoma
Authors: Uribe-Alvarez Cristina , Guerrero-Rodríguez Sandra Lucía , Rhodes Jennifer , Cannon Alexa , Chernoff Jonathan , Araiza-Olivera Daniela 
Published: August 2019

AbstractMalignant melanoma is characterized by mutations in a number of driver genes, most notablyBRAFandNRAS. Recently, genomic analyses revealed that 4-9% of sun-exposed melanoma bear activating mutations inRAC1, which encodes a small GTPase that is known to play key roles in cell proliferation, survival, and migration. The RAC1 protein activates several effector pathways, including Group A p21-activated kinases (PAKs), phosphoinositol-3-kinases (PI3Ks), in particular the beta isoform, and the serum-response factor/myocardin-related transcription factor (SRF/MRTF). Having previously shown that inhibition of Group A PAKs impedes oncogenic signaling from RAC1P29S, we here extend this analysis to examine the roles of PI3Ks and SRF/MITF in melanocytes and/or in a zebrafish model. We demonstrate that a selective Group A PAK inhibitor (Frax-1036) and certain PI3Ks inhibitors (BKM120, TGX221, GSK2636771) impede the growth of melanoma cells driven by mutant RAC1 but not mutant BRAF, however other PI3K inhibitors, including PI3Kα-selective inhibitors are less effective. Similar results were seenin vivo, using embryonic zebrafish development as a readout, but now including an SRF/MRTF inhibitor (CCG-203971). These results suggest that targeting Group A PAKs and/or SRF/MRTF represent promising approach to suppress RAC1 signaling in malignant melanoma.
Sterol regulatory element binding protein and Sp1 is required for transcriptional activation of a freshwater carnivorous fish (Channa striata) elovl5 elongase
Authors: Goh Pei-Tian , Kuah Meng-Kiat , Chew Yen-Shan , Teh Hui-Ying , Shu-Chien Alexander Chong 
Published: August 2019

AbstractLong-chain polyunsaturated fatty acid (LC-PUFA) biosynthesis involves the activities of two groups of enzymes, the fatty acyl desaturases (Fads) and elongases of very long-chain fatty acid (Elovl). Fish are major source of beneficial n-3 LC-PUFA in human diet and there is a considerable interest to elucidate the mechanism and regulatory aspects of LC-PUFA biosynthesis in farmed fish species. The promoter of elovl5 elongase, which catalyze the rate limiting reaction of adding two carbons to the C18 PUFA have been previously described and characterized from several marine and diadromous teleost species. We report here the cloning and characterization of the elovl5 promoter from two freshwater fish species, the carnivorous snakehead fish (Channa striata) and zebrafish. Results show the importance of sterol regulatory element binding protein (Srebp) and the corresponding sterol responsive element (SRE) in the core regulatory region of both promoters. Mutagenesis luciferase and electrophoretic mobility shift assays confirm that SRE is indispensable for basal transcriptional activation in both species. In addition, several Sp1 binding sites located in close proximity with SRE were present in the snakehead promoter, with one having a potential synergy with SRE in regulating elovl5 expression. The core elovl5 promoter fragments of both species also directed in vivo expression in the yolk syncytial layer of developing zebrafish embryos. This study is the first functional promoter analysis of Elovl5 in freshwater teleost.
Diffusion tubes: a method for the mass culture of ctenophores and other pelagic marine invertebrates
Authors: Patry Wyatt L. , Bubel Mac Kenzie , Hansen Cypress , Knowles Thomas 
Published: August 2019

AbstractThe culture of pelagic marine invertebrates, especially the ctenophore Mnemiopsis leidyi, has been demonstrated in past studies dating back to the 1960’s, however the mass culture of delicate pelagic invertebrates has remained elusive. By using a pair of acrylic tubes and enabling water diffusion between them, we have been able to reliably and cost effectively mass culture several genera of ctenophores (Pleurobrachia, Hormiphora, Bolinopsis, Mnemiopsis, and Leucothea), one species of siphonophore (Nanomia) and one species of larvacean (Oikopleura). The simple, compact method is effective enough to support two permanent exhibits of ctenophores at the Monterey Bay Aquarium while minimizing live food culture requirements with the potential to support further investigation of pelagic marine invertebrate ontogeny, ecology and genomics.
Inhibitory effect ofBacillus subtilisWL-2 and its IturinA lipopeptides againstPhytophthora infestans
Authors: Wang Youyou , Zhang Congying , Wu Lufang , Wang Le , Gao Wenbin , Jiang Jizhi , Wu Yanqing 
Published: August 2019

ABSTRACTPotato late blight triggered byPhytophthora infestans((Mont.) de Bary) represents a great food security threat worldwide and is difficult to control. Currently,Bacillusspp. have been considered biocontrol agents to control many fungal diseases. Here,Bacillus subtilisWL-2 was selected as the antifungal strain with the most potential againstP. infestansmycelium growth. Additionally, the functional metabolites extracted from WL-2 were identified as IturinA-family cyclic lipopeptides (CLPs) via high-performance liquid chromatography (HPLC) and electrospray ionization mass spectrometry (ESI-MS). Analyses using scanning and transmission electron microscopy (SEM and TEM) revealed that IturinA caused a change in the mycelial surface and damage to the internal cell structure, including cell membrane disruption and irregular organelle formation. Moreover, propidium iodide staining and nucleic acid and protein release were detected to clarify the cell membrane damage caused by IturinA. Additionally, IturinA triggered reactive oxygen species (ROS) generation and malondialdehyde (MDA) production. Mitochondrial membrane potential (MMP), mitochondrial respiratory chain complexes activity (MRCCA), respiratory control rate (RCR), and oxidative phosphorylation efficiency (P/O) assays indicated thatP. infestansmitochondria affected by IturinA were so seriously damaged that the MMP and MRCCA declined remarkably and that mitochondrial ATP production ability was weakened. Therefore, IturinA induces cell membrane damage, oxidative stress, and dysfunction of mitochondria, resulting inP. infestanshyphal cell death. As such, the results highlight thatB. subtilisWL-2 and IturinA have great potential as candidates for inhibitingP. infestansmycelium growth and controlling potato late blight.IMPORTANCEPotato (Solanum tuberosumL.) is the fourth most common global food crop, and its planting area and yield increase yearly. Notably, in 2015, China initiated a potato staple food conversion strategy, and by 2020, approximately 50% of potatoes will be consumed as a staple food. The plant pathogen fungusPhytophthora infestans((Mont.) de Bary) is the culprit of potato late blight; however, biological agents rather than chemicals are highly necessary to control this threatening disease. In this study, we discovered an antifungal substance, IturinA, a lipopeptide produced byBacillus subtilisWL-2. Moreover, our research revealed the actual mechanism of IturinA againstP. infestansmycelium growth and clarified the potential ofB. subtilisWL-2 and IturinA as a biocontrol agent againstP. infestansmycelium growth as well as for controlling the development of late blight in potato cultivation.
The aminoalkylindole, BML-190, negatively regulates chitosan synthesis via the cAMP/PKA1 pathway in Cryptococcus neoformans
Authors: Maybruck Brian T. , Lam Woei C. , Specht Charles A. , Ilagan Ma Xenia G. , Donlin Maureen J. , Lodge Jennifer K. 
Published: August 2019

AbstractCryptococcus neoformans can cause fatal meningoencephalitis in patients with AIDS or other immune-compromising conditions. Current antifungals are suboptimal to treat this disease, therefore, novel targets and new therapies are needed. Previously, we have shown that chitosan is a critical component of the cryptococcal cell wall, is required for survival in the mammalian host, and that chitosan deficiency results in rapid clearance from the mammalian host. We had also identified several specific proteins that were required for chitosan biosynthesis, and we hypothesize that screening for compounds that inhibit chitosan biosynthesis would identify additional genes/proteins that influence chitosan biosynthesis.To identify these compounds we developed a robust and novel cell-based flow cytometry screening method to identify small molecule inhibitors of chitosan production. We screened the ICCB Known Bioactives library and identified 8 compounds that reduced chitosan in C. neoformans. We used flow cytometry-based counter and confirmatory screens, followed by a biochemical secondary screen to refine our primary screening hits to 2 confirmed hits.One of the confirmed hits that reduced chitosan content was the aminoalkylindole, BML-190, a known inverse agonist of mammalian cannabinoid receptors. We demonstrated that BML-190 likely targets the C. neoformans G-protein coupled receptor, Gpr4, and via the cAMP/PKA signaling pathway, contributes to an intracellular accumulation of cAMP that results in decreased chitosan. Our discovery suggests that this approach could be used to identify additional compounds and pathways that reduce chitosan biosynthesis, and could lead to potential novel therapeutics against C. neoformans.ImportanceCryptococcus neoformans is a fungal pathogen that kills ∼200,000 people every year. The cell wall is an essential organelle that protects fungus from the environment. Chitosan, the deacetylated form of chitin, has been shown to be an essential component of cryptococcal cells wall during infection of a mammalian host. In this study, we screened a set of 480 compounds, which are known to have defined biological activities, for activity that reduced chitosan production in C. neoformans. Two of these compounds were validated using an alternative method of measuring chitosan, and one of these was demonstrated to impact the cAMP signal transduction pathway. This work demonstrates that the cAMP pathway regulates chitosan in C. neoformans, and validates that this screening approach could be used to find potential antifungal agents.
Impact of C-terminal amino acid composition on protein expression in bacteria
Authors: Weber Marc , Burgos Raul , Yus Eva , Yang Jae-Seong , Lluch-Senar Maria , Serrano Luis 
Published: August 2019

AbstractThe C-terminal sequence of a protein is involved in processes such as efficiency of translation termination and protein degradation. However, the general relationship between features of this C-terminal sequence and levels of protein expression remains unknown. Here, we identified C-terminal amino acid biases that are ubiquitous across the bacterial taxonomy (1582 genomes). We showed that the frequency is higher for positively charged amino acids (lysine, arginine) while hydrophobic amino acids and threonine are lower. In highly abundant proteins, the C-terminal residue is more conserved. We then studied the impact of C-terminal composition on protein levels in a library ofM. pneumoniaemutants, covering all possible combinations of the two last codons. We found that charged and polar residues, in particular lysine, led to higher expression, while hydrophobic and aromatic residues led to lower expression, with a difference in protein levels up to 4-fold. Our results demonstrate that the identity of the last amino acids has a strong influence on protein expression levels and is under selective pressure in highly expressed proteins.
Can internal factors improve innovation performance via innovation culture in SMEs?
Authors: Hanifah Haniruzila , Halim Hasliza Abdul , Ahmad Noor Hazlina , Vafaei-Zadeh Ali 
Published: August 2019

Purpose
Innovation performance is an issue that has a profound effect not only on Malaysian large companies but also among small and medium enterprises (SMEs) especially Bumiputera SMEs. The purpose of this paper is to explore the theoretical review of innovation culture pertaining to innovation performance by conducting a literature review on SME studies. The previous reference on innovation performance in Malaysian SMEs is still scarce, even though it is the key benchmark to measure firm performance. It has been demonstrated by the literature that innovation culture is significantly associated with innovation performance. Nonetheless, its effect on Bumiputera SMEs is still underexplored. Thus, this study examines the importance of internal factors (specific human capital and social capital) to innovation culture in driving innovation performance.

Design/methodology/approach
A questionnaire-based survey was conducted to gather data from Bumiputera SMEs. A total of 140 responses were obtained and analyses were carried out using Smart-PLS software to produce interesting findings.

Findings
The findings indicate that social capital (relational capital and social network) has a significant impact on innovation culture and indirectly impacts innovation performance. The findings also reveal that specific human capital does not have significant impact on innovation culture and innovation performance. This paper shows the importance of social capital and how it directly influences Bumiputera SMEs and innovation performance. This result will be encouraging to firms in other developing countries.

Practical implications
Although SMEs play an important role in economic development, their contribution to innovation is small and marginal. This study makes an important contribution by providing information to the Malaysian SMEs, especially those that are of Bumiputera status on the factors that could enhance innovation performance and nurture innovation culture in their organisations. Thus, it is hoped that this study will generate interest among researchers to attain more conclusive evidence about the practice of innovation culture among Malaysian SMEs.

Originality/value
This paper is one of the first to address the mediating effect of innovation culture on specific human capital, social capital and innovation performance.
A positivity-preserving nonlinear finite volume scheme for radionuclide transport calculations in geological radioactive waste repository
Authors: Peng Gang , Gao Zhiming , Yan Wenjing , Feng Xinlong 
Published: August 2019

Purpose
This paper aims to consider numerical simulation for radionuclide transport calculations in geological radioactive waste repository.

Design/methodology/approach
The nonlinear two-point flux approximation is used to discretize the diffusion flux and has a fixed stencil. The cell-vertex unknowns are applied to define the auxiliary unknowns and can be interpolated by the cell-centered unknowns. The approximation of convection flux is based on the second-order upwind method with a slope limiter.

Findings
Numerical results illustrate that the positivity-preserving is satisfied in solving this convection-diffusion system and has a second-order convergence rate on the distorted meshes.

Originality/value
A new positivity-preserving nonlinear finite volume scheme is proposed to simulate the far-field model used in the geological radioactive waste repository. Numerical results illustrate that the positivity-preserving is satisfied in solving this convection-diffusion system and has a second-order convergence rate on the distorted meshes.
Numerical simulation of forced convection in a bi-disperse porous medium channel by creating new porous micro-channels inside the porous macro-blocks
Authors: Rajabzadeh Behnam , Hojaji Mohammad , Karimipour Arash 
Published: August 2019

Purpose
Porous medium has always been introduced as an environment for increasing heat transfer in cooling systems. However, increase in heat transfer and resolving pressure drop in the fluid flow have been focused on by researchers.The purpose of this paper is to study the effects of creating porous micro-channels inside porous macro-blocks to optimize system performance in channels.

Design/methodology/approach
To simulate flow field, a developed numerical code that solves Navier–Stokes equations by finite volume method and semi-implicit method for pressure linked equations (SIMPLE) algorithm will be used together with bi-disperse porous medium (BDPM) method. Working fluid is air with Pr = 0.7 in laminar state. Influence of permeability changes by creation of micro-channels containing porous medium in vertical, horizontal and cross-shape patterns will be investigated.

Findings
By creating porous micro-channels inside macro-blocks, not only does the heat transfer increase significantly but the pressure also drops remarkably. Increase in performance evaluation criteria (PEC) is more evident in lower Reynolds numbers that can increase the PEC to 75 per cent by creating cross-shape micro-channels. By changing the permeability of micro-channels, PEC will increase by reducing the pressure drop but it has minor changes in Nu.

Research limitations/implications
The current work is applicable to optimizing system performance by decreasing the pressure drop and increasing the heat transfer.

Practical implications
The developed patterns are useful in increasing the system performance including the increase in heat transfer and decrease in pressure drop in systems such as air coolers required in electrical circuits.

Originality/value
Development and optimization of system performance by new patterns using BDPM in comparison to the previous patterns.