bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of influential spreaders in complex networks using HybridRank algorithm
Authors: Ahajjam Sara , Badir Hassan 
Published: August 2018

AbstractIdentifying the influential spreaders in complex networks is crucial to understand who is responsible for the spreading processes and the influence maximization through networks. Targeting these influential spreaders is significant for designing strategies for accelerating the propagation of information that is useful for various applications, such as viral marketing applications or blocking the diffusion of annoying information (spreading of viruses, rumors, online negative behaviors, and cyberbullying). Existing methods such as local centrality measures like degree centrality are less effective, and global measures like closeness and betweenness centrality could better identify influential spreaders but they have some limitations. In this paper, we propose the HybridRank algorithm using a new hybrid centrality measure for detecting a set of influential spreaders using the topological features of the network. We use the SIR spreading model for simulating the spreading processes in networks to evaluate the performance of our algorithm. Empirical experiments are conducted on real and artificial networks, and the results show that the spreaders identified by our approach are more influential than several benchmarks.
Clock gene expression and locomotor activity predict death in the last days of life in Drosophila melanogaster
Authors: Zhao Jia , Warman Guy Robert , Cheeseman James Frederick 
Published: August 2018

AbstractThe importance of the circadian clock for the regulation of behaviour and physiology, and the molecular control of these rhythms by a set of clock genes are well defined. The circadian clock deteriorates with advancing age but the mechanism underlying is unclear. Here we recorded the expression of two key clock genes in young, middle-aged and old Drosophila using transgenic luciferase lines reporting period and timeless in vivo. We report a novel marker of imminent death in the expression of TIMELESS. In the days immediately preceding death TIMELESS expression increased to at least 150% of previous acrophase values (88.0% of n = 217) and lost circadian rhythmicity, which predicted death equally well in flies of different ages and under light and temperature cycles. We suggest this transient aberrant clock-gene expression is central to the mechanism of the disturbance in circadian behaviour before death (82.7% of n = 342). We also find that PERIOD expression in central-clock neurons remained robust with age, however PERIOD and TIMELESS in peripheral clocks showed a reduction in both expression level and rhythmicity. In conclusion, as flies age the molecular clock gradually declines at the peripheral level but continues to function at the central until days before death.
Significant enhancement of nitrous oxide energy yields from wastewater achieved by bioaugmentation with a recombinant strain of Pseudomonas aeruginosa
Authors: Lin Ziyu , Sun Dezhi , Dang Yan , Holmes Dawn E. 
Published: August 2018

AbstractNitrous oxide (N2O) is formed during wastewater nitrogen removal processes. It is a strong greenhouse gas, however, if properly captured it can also be used as a renewable energy source. In this study, a nosZ-deficient strain of Pseudomonas aeruginosa was constructed. During growth under denitrifying conditions, the nosZ-deficient strain was more highly transcribing other genes from the denitrification pathway (narG, nirS, and norB) than the wild-type strain. This strain could also convert 85% of NO2−-N to N2O when it was grown with acetate compared to <0.6% by the wild-type strain. When a bioreactor treating synthetic wastewater with high NO2−-N concentrations (700 mg/L) was inoculated with this strain, the N2O conversion efficiencies were >73% and N2O comprised 73~81% of the biogas being generated. The energy yield from wastewater in bioaugmented reactors also reached levels as high as 1260 kJ/m3. These results are significant and show that bioaugmentation of reactors during denitrification treatment processes with nosZ-deficient strains of Pseudomonas or other core denitrifying bacteria might be an effective way to enhance N2O recovery.
c-Src regulates cargo transit via the Golgi in pancreatic acinar cells
Authors: Kostenko Sergiy , Heu Chan C. , Yaron Jordan R. , Singh Garima , de Oliveira Cristiane , Muller William J. , Singh Vijay P. 
Published: August 2018

AbstractThe exocrine pancreatic acinar cell is unique for its rapid protein synthesis and packaging in zymogen granules (ZGs). However, while crucial to the pathogenesis of pancreatitis, the signaling involved in the transit of proteins via the Golgi is poorly understood in these cells. Noting the evidence of c-Src in regulating transit of cargo via the Golgi in other systems, we explored this in acinar cells. Stimulation of ZG formation with dexamethasone activated Src and increased the Golgi area in acinar cells. c-Src localized to the microsomes of acinar cells on immunofluorescence and subcellular fractionation. While other Src family members had no effect on the Golgi markers P115 and GM130, active c-Src increased the Golgi area these stained, extending them into the ER. Src inhibition reduced amylase staining outside the Golgi and increased it in a stack like Golgi morphology. In vivo pharmacologic inhibition or acinar specific genetic deletion of c-Src reduced ZG number and staining of amylase in ZGs along with increasing amylase retention in the microsomal fraction. Morphologically this was associated with smaller Golgi stacks, and dilation of the endoplasmic reticulum. Therefore the role c-Src regulated Golgi function, ZG formation and microsomal zymogen transit in acinar cells needs to be explored in pancreatitis.
Suboptimal Coding Metasurfaces for Terahertz Diffuse Scattering
Authors: Moccia Massimo , Koral Can , Papari Gian Paolo , Liu Shuo , Zhang Lei , Wu Rui Yuan , Castaldi Giuseppe , Cui Tie Jun , Galdi Vincenzo , Andreone Antonello 
Published: August 2018

AbstractCoding metasurfaces, composed of only two types of elements arranged according to a binary code, are attracting a steadily increasing interest in many application scenarios. In this study, we apply this concept to attain diffuse scattering at THz frequencies. Building up on previously derived theoretical results, we carry out a suboptimal metasurface design based on a simple, deterministic and computationally inexpensive algorithm that can be applied to arbitrarily large structures. For experimental validation, we fabricate and characterize three prototypes working at 1 THz, which, in accordance with numerical predictions, exhibit significant reductions of the radar cross-section, with reasonably good frequency and angular stability. Besides the radar-signature control, our results may also find potentially interesting applications to diffusive imaging, computational imaging, and (scaled to optical wavelengths) photovoltaics.
A single N1-methyladenosine on the large ribosomal subunit rRNA impacts locally its structure and the translation of key metabolic enzymes
Authors: Sharma Sunny , Hartmann Johannes David , Watzinger Peter , Klepper Arvid , Peifer Christian , Kötter Peter , Lafontaine Denis L. J. , Entian Karl-Dieter 
Published: August 2018

AbstractThe entire chemical modification repertoire of yeast ribosomal RNAs and the enzymes responsible for it have recently been identified. Nonetheless, in most cases the precise roles played by these chemical modifications in ribosome structure, function and regulation remain totally unclear. Previously, we demonstrated that yeast Rrp8 methylates m1A645 of 25S rRNA in yeast. Here, using mung bean nuclease protection assays in combination with quantitative RP-HPLC and primer extension, we report that 25S/28S rRNA of S. pombe, C. albicans and humans also contain a single m1A methylation in the helix 25.1. We characterized nucleomethylin (NML) as a human homolog of yeast Rrp8 and demonstrate that NML catalyzes the m1A1322 methylation of 28S rRNA in humans. Our in vivo structural probing of 25S rRNA, using both DMS and SHAPE, revealed that the loss of the Rrp8-catalyzed m1A modification alters the conformation of domain I of yeast 25S rRNA causing translation initiation defects detectable as halfmers formation, likely because of incompetent loading of 60S on the 43S-preinitiation complex. Quantitative proteomic analysis of the yeast Δrrp8 mutant strain using 2D-DIGE, revealed that loss of m1A645 impacts production of specific set of proteins involved in carbohydrate metabolism, translation and ribosome synthesis. In mouse, NML has been characterized as a metabolic disease-associated gene linked to obesity. Our findings in yeast also point to a role of Rrp8 in primary metabolism. In conclusion, the m1A modification is crucial for maintaining an optimal 60S conformation, which in turn is important for regulating the production of key metabolic enzymes.
Genome wide identification and experimental validation of Pseudomonas aeruginosa Tat substrates
Authors: Gimenez Maxime Rémi , Chandra Govind , Van Overvelt Perrine , Voulhoux Romé , Bleves Sophie , Ize Bérengère 
Published: August 2018

AbstractIn bacteria, the twin-arginine translocation (Tat) pathway allows the export of folded proteins through the inner membrane. Proteins targeted to this system are synthesized with N-terminal signal peptides bearing a conserved twin-arginine motif. The Tat pathway is critical for many bacterial processes including pathogenesis and virulence. However, the full set of Tat substrates is unknown in many bacteria, and the reliability ofin silicoprediction methods largely uncertain. In this work, we performed a combination ofin silicoanalysis and experimental validation to identify a core set of Tat substrates in the opportunistic pathogenPseudomonas aeruginosa.In silicoanalysis predicted 44 putative Tat signal peptides in theP. aeruginosaPA14 proteome. We developed an improved amidase-based Tat reporter assay to show that 33 of these are real Tat signal peptides. In addition,in silicoanalysis of the full translated genome revealed a Tat candidate with a missassigned start codon. We showed that it is a new periplasmic protein inP. aeruginosa. Altogether we discovered and validated 34 Tat substrates. These show little overlap withEscherichia coliTat substrates, and functional analysis points to a general role for theP. aeruginosaTat system in the colonization of environmental niches and pathogenicity.
Topical administration of EGF suppresses immune response and protects skin barrier in DNCB-induced atopic dermatitis in NC/Nga mice
Authors: Kim Young-Je , Choi Mi Ji , Bak Dong-Ho , Lee Byung Chul , Ko Eun Jung , Ahn Ga Ram , Ahn Seung Won , Kim Moo Joong , Na Jungtae , Kim Beom Joon 
Published: August 2018

AbstractAtopic dermatitis (AD) is a common inflammatory skin disease characterized by a complex, heterogeneous pathogenesis including skin barrier dysfunction, immunology, and pruritus. Although epidermal growth factor (EGF) is essential for epithelial homeostasis and wound healing, the effect of EGF on AD remains to be explored. To develop a new therapy for AD, the anti-AD potential of EGF was investigated by inducing AD-like skin lesions in NC/Nga mice using 2,4-dinitrochlorobenzene (DNCB). EGF was administrated to NC/Nga mice to evaluate its therapeutic effect on DNCB-induced AD. EGF treatment improved dermatitis score, ear thickness, epidermal hyperplasia, serum total immunoglobulin E level, and transepidermal water loss in NC/Nga mice with DNCB-induced AD. In addition, levels of skin barrier-related proteins such as filaggrin, involucrin, loricrin, occludin, and zonula occludens-1 (ZO-1) were increased by EGF treatment. These beneficial effects of EGF on AD may be mediated by EGF regulation of Th1/Th2-mediated cytokines, mast cell hyperplasia, and protease activated receptor-2 (PAR-2) and thymic stromal lymphopoietin (TSLP), which are triggers of AD. Taken together, our findings suggest that EGF may potentially protect against AD lesional skin via regulation of skin barrier function and immune response.
Isobenzofuranone derivative JVPH3, an inhibitor of L. donovani topoisomerase II, disrupts mitochondrial architecture in trypanosomatid parasites
Authors: Chowdhury Somenath Roy , Godinho Joseane Lima Prado , Vinayagam Jayaraman , Zuma Aline Araujo , Silva Sara Teixeira De Macedo , Jaisankar Parasuraman , Rodrigues Juliany Cola Fernandes , De Souza Wanderley , Majumder Hemanta K. 
Published: August 2018

AbstractKinetoplast DNA (kDNA) bearing unusual mitochondrion of trypanosomatid parasites offers a new paradigm in chemotherapy modality. Topoisomerase II of Leishmania donovani (LdTopII), a key enzyme associated with kDNA replication, is emerging as a potential drug target. However, mode of action of LdTopII targeted compounds in the parasites at sub-cellular level remains largely unknown. Previously, we reported that an isobenzofuranone derivative, namely 3,5-bis(4-chlorophenyl)-7-hydroxyisobenzofuran-1(3H)-one (JVPH3), targets LdTopII and induces apoptosis-like cell death in L. donovani. Here, we elucidate the phenotypic changes and the events occurring at sub-cellular level caused by JVPH3 in L. donovani. In addition, we have evaluated the cytotoxicity and ultrastructural alterations caused by JVPH3 in two brazilian trypanosomatid pathogens viz. L. amazonensis and Trypanosoma cruzi. Despite killing these parasites, JVPH3 caused significantly different phenotypes in L. donovani and L. amazonensis. More than 90% population of parasites showed altered morphology. Mitochondrion was a major target organelle subsequently causing kinetoplast network disorganization in Leishmania. Altered mitochondrial architecture was evident in 75–80% Leishmania population being investigated. Quantification of mitochondrial function using JC-1 fluorophore to measure a possible mitochondrial membrane depolarization further confirmed the mitochondrion as an essential target of the JVPH3 corroborating with the phenotype observed by electron microscopy. However, the impact of JVPH3 was lesser on T. cruzi than Leishmania. The molecule caused mitochondrial alteration in 40% population of the epimastigotes being investigated. To our knowledge, this is the first report to evaluate the proliferation pattern and ultrastructural alterations caused in Brazilian kinetoplastid pathogens by a synthetic LdTopII inhibitor previously established to have promising in vivo activity against Indian strain of L. donovani.
Functional near-infrared spectroscopy for monitoring macaque cerebral motor activity during voluntary movements without head fixation
Authors: Yamada Toru , Kawaguchi Hiroshi , Kato Junpei , Matsuda Keiji , Higo Noriyuki 
Published: August 2018

AbstractWe developed an fNIRS system for monitoring macaque cerebral motor activity during voluntary movements without head fixation. fNIRS data at 27 channels in 7.5 mm spatial interval were calibrated by simulating light propagation through the macaque cranial tissues. The subject was instructed to repeatedly (75 times) retrieve a food pellet with alternating left or right hands from a food well for each session. We detected significant increases in oxygenated hemoglobin (Hb) and decrease in deoxygenated Hb in the primary motor area (M1) contralateral to the hand used. In more rostral and ventral regions in both hemispheres, the hemodynamic similarly changed regardless of used hand. Direct feeding to the mouth eliminated activity in the hand M1 whereas that at bilateral ventral regions (mouth M1 area) remained. Statistical analyses for the hemodynamics between left/right-hand use revealed the location of each hand M1 in either hemisphere. In these regions, the maximum amplitude and time of the maximum amplitude in the hemodynamic response evoked by food retrieval were highly correlated with the time associated with food retrieval. We could assign each channel to an appropriate functional motor area, providing proof of principle for future studies involving brain damage models in freely moving macaque monkeys.
Riverbed erosion of the final 565 kilometers of the Yangtze River (Changjiang) following construction of the Three Gorges Dam
Authors: Zheng Shuwei , Xu Y. Jun , Cheng Heqin , Wang Bo , Xu Wei , Wu Shuaihu 
Published: August 2018

AbstractThe world’s largest hydropower dam, the Three Gorges Dam (TGD), spans the upper Yangtze River in China, creating a 660-km long and 1.1-km wide reservoir upstream. Several recent studies reported a considerable decline in sediment load of the Lowermost Yangtze River (LmYR) and a rapid erosion in the subaqueous delta of the river mouth after the closure of the TGD in 2003. However, it is unknown if the TGD construction has also affected river channel and bed formation of the LmYR. In this study, we compared bathymetric data of the last 565 kilometers of the Yangtze River’s channel between 1998 and 2013. We found severe channel erosion following the TGD closure, with local riverbed erosion up to 10 m deep. The total volume of net erosion from the 565-km channel amounted to 1.85 billion m3, an equivalent of 2.59 billion metric tons of sediment, assuming a bulk density of 1.4 t/m3for the riverbed material. The largest erosion occurred in a 100-km reach close to the Yangtze River mouth, contributing up to 73% of the total net eroded channel volume.
Behavioural patterns of electrolyte repletion in intensive care units: lessons from a large electronic dataset
Authors: Joseph Thomas T. , DiMeglio Matthew , Huffenberger Annmarie , Laudanski Krzysztof 
Published: August 2018

AbstractRepletion of electrolytes often depends on provider-specific behavior and hospital policy. We examined the pattern of electrolyte repletion across several intensive care units (ICU) in a large healthcare system from 2010–2015. This included 109 723 potassium repletions, 51 833 magnesium repletions, 2 306 calcium repletions, 8 770 phosphate repletions, and 3 128 249 visit-days over 332 018 visits. Potassium, magnesium, and calcium were usually repleted within the institutional reference range. In contrast, the bulk of phosphate repletion was done with pre-repletion serum level below the reference range. The impact of repletion on post-repletion levels was significant but uniformly small. The pre-repletion serum level had a significant inverse correlation with the post-repletion level of each electrolyte. Potassium, magnesium and phosphate follow-up labs were scheduled in 9–10 hours after their repletion. In contrast, calcium was rechecked in less than 20 minutes. Routine repletion of potassium, magnesium and calcium had no effect on the incidence of tachyarrhythmias. We estimated the expense from electrolyte repletion within the reference range was approximately $1.25 million. Absent a specific clinical indication, repleting electrolytes when the serum concentration are within normative values may represent an avenue for cost savings, staff burden unload and potential reduction in frequency of complications in the ICUs.
Feasibility of autologous plasma gel for tonsil-derived stem cell therapeutics in hypoparathyroidism
Authors: Jung Soo Yeon , Kim Ha Yeong , Oh Hyun Ju , Choi Euno , Cho Min Sun , Kim Han Su 
Published: August 2018

AbstractHypoparathyroidism is a deficiency of the parathyroid hormone (PTH) in the body. We previously reported the possibility of treating it using tonsil-derived mesenchymal stem cells (TMSCs) differentiated into PTH-releasing cells. The purpose of this study was to evaluate the feasibility of using autologous plasma gel as scaffold material in treatment of hypoparathyroidism with TMSC. We obtained plasma by venous sampling of autologous blood and centrifuged and fabricated the plasma gel using a sinusoidal pattern heating machine. After we created the hypoparathyroidism animal model, we administered undifferentiated TMSCs and TMSCs differentiated into parathyroid cells at each rat dorsum by intramuscular injection with and without the plasma gel. In the plasma gel groups, intact PTH was detected from on day 21 after TMSC injection; we did not detect intact PTH in the groups that were only transplanted with TMSCs during the entire experimental period. Serum calcium was higher and phosphorous was lower in the TMSC with plasma gel groups than in the groups with TMSCs alone. We detected PTH and chromogranin A in the TMSC-plasma gel-transplanted areas on immunohistochemistry and immunofluorescence stain. Plasma gel can be considered as a cell-delivery scaffold for treating hypoparathyroidism with tonsil-derived mesenchymal stem cells.
Metabolomic changes in the mouse retina after optic nerve injury
Authors: Sato Kota , Saigusa Daisuke , Saito Ritsumi , Fujioka Amane , Nakagawa Yurika , Nishiguchi Koji M , Kokubun Taiki , Motoike Ikuko N. , Maruyama Kazuichi , Omodaka Kazuko , Shiga Yukihiro , Uruno Akira , Koshiba Seizo , Yamamoto Masayuki , Nakazawa Toru 
Published: August 2018

AbstractIn glaucoma, although axonal injury drives retinal ganglion cell (RGC) death, little is known about the underlying pathomechanisms. To provide new mechanistic insights and identify new biomarkers, we combined latest non-targeting metabolomics analyses to profile altered metabolites in the mouse whole retina 2, 4, and 7 days after optic nerve crush (NC). Ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry and liquid chromatography Fourier transform mass spectrometry covering wide spectrum of metabolites in combination highlighted 30 metabolites that changed its concentration after NC. The analysis displayed similar changes for purine nucleotide and glutathione as reported previously in another animal model of axonal injury and detected multiple metabolites that increased after the injury. After studying the specificity of the identified metabolites to RGCs in histological sections using imaging mass spectrometry, two metabolites, i.e., L-acetylcarnitine and phosphatidylcholine were increased not only preceding the peak of RGC death in the whole retina but also at the RGC layer (2.3-fold and 1.2-fold, respectively). These phospholipids propose novel mechanisms of RGC death and may serve as early biomarkers of axonal injury. The combinatory metabolomics analyses promise to illuminate pathomechanisms, reveal biomarkers, and allow the discovery of new therapeutic targets of glaucoma.