bluuebunny/crossref_metadata_2025 huggingface dataset:
EFFECT OF GLOBULAR CARBON ADDITION ON RHEOLOGICAL PROPERTIES OF COAL-WATER SUSPENSION
Authors: Emelyanova Tatyana Yu. , Kashkina Lyudmila V. , Kulagin Vladimir A. , Stebeleva Olesya P. , Petrakovskaya Eleanorа A. , Nemcev Ivan V. , Redkin Victor E.
Published: July 2018

The physical-mechanical properties was studied for the composite material (the highly concentrated suspension based on distilled water, ultra fine brown coal, nano particles of the globular carbon T-900). It was found that carbon nano particles at low concentrations (0.04, 0.08 2 wt.%) can be dispersing agents. Under certain cavitation modes the surface segregation of oxygen impurities was detected in the nano carbon particles. The combustion kinetics of dispersed phase powder of suspension with the addition of 2 wt.% nano carbon differs from the original coal combustion.
EFFECT OF CHEMICAL TREATMENT ON PROPERTIES OF CARBON-MINERAL MATERIALS FROM SAPROPEL
Authors: Terekhova Elena N. , Lavrenov Alexandr V. , Krivonos Oksana I.
Published: July 2018

We investigated the possibility of producing porous carbon-mineral materials based on sapropel, and also the variation of their textural characteristics and the chemical state of the surface by acidic, alkaline treatment and processing with water vapor. Prepared carbon-mineral-supported cobalt-molybdenum catalyst tested in the reaction of hydrotransformation of 2,4 – dibenzothiophene and α - methylnaphthalene.
FORMATION OF NANO STRUCTURES IN RESULT OF HOMOGENOUS NUCLEATION OF CARBON OBTAINED IN THERMAL PLASMA UNDER ATMOSPHERIC PRESSURE
Authors: Shavelkina Marina B. , Amirov Ravil Kh. , Borodina Tatyana I. , Kiselev Viktor I. , Shatalova Tatiana B. , Rabadanov Kamille S.
Published: July 2018

Thermal plasma processing of carbon sources using a plasma jet with high heat capacity is one of the most promising methods for the synthesis of new materials. This paper describes the low-temperature deposition of carbon nanomaterials by remote plasma-enhanced chemical vapor deposition (PECVD) in the absence of catalysts. The remote PECVD process differs from conventional and direct PECVD process in two ways: (a) only a subset of the process reactants and/or diluents are directly plasma excited; and (b) thin film deposition takes place on a substrate that is outside of the plasma glow region. In conventional CVD methods, carbon is produced from the decomposition of carbon sources such as hydrocarbons, carbon monoxide, alcohols, and so on, over a metal catalyst. The unavoidable metal species remaining in carbon nanomaterials would lead to obvious disadvantages for property characterization and application exploration. Despite sustained efforts, it is still an intractable problem to remove metal catalysts completely from carbon nanomaterials samples without introducing defects and contaminations. Good reactor design allowed to overcome problems of chemical and structural purity, and poor process robustness in terms of phase composition of product from run to run. For the synthesis of graphene materials, carbon black, carbon nanotubes, nanowires we used the thermal plasma generator which is a high current divergent anode-channel DC plasma torch. The experiment involved a simultaneous input of hydrocarbons (methane, propane, butane, acetylene) with the plasma forming gas (helium, argon, nitrogen) into the plasma torch, wherein heating and decompositions occurred in the plasma jet and in the region of the arc discharge, followed by condensation of the synthesis product on metallic surfaces. The deposition rate was varied with distance from the plasma. Consumption of carbon source, plasma forming gas and plasma torch power were changed independently from each other. For the experimental conditions the electric power of plasma torch was set up to 40 kW. Regularities of formation of carbon thread-like nanostructures and graphene in the course of hydrocarbons pyrolysis in thermal plasma without participation of catalytic particles were studied by means of electron microscopy, X-ray diffraction, IR-spectrometry and thermogravimetry. Depending on the pyrolytic synthesis parameters, different proportions of crystal carbon and soot may be obtained. It has been demonstrated that the phase composition is varied by hydrocarbons flow rate, plasma forming gas pressure and dc plasma torch power. It has been established through the experiments that carbon nucleation is volumetric and proceeds according to the model of explosive soot formation.
PROPERTIES AND PHASE COMPOSITION OF DETONATION NANODIAMONDS SURFACE
Authors: Shevchenko Nikolay V. , Gorbachev Valentin A. , Chobanyan Vladimir A. , Sigalaev Sergey K. , Rizahanov Razhudin N. , Golubev Alexandr A. , Kirichenko Alexey N. , Efremov Vladimir P.
Published: July 2018

The characteristics, properties and phase composition of surface of nano- and microdiamond crystals obtained by detonation synthesis were researched. In blend composition of nano diamonds the carbine presence was revealed. On the surface of the nano diamond microcrystals and after chemical treatment the presence of sp2 and sp3 carbon phases with the predominant content of sp3crystal phase was revealed. Together with that the presence on the surface of the sp3 amorpohous phase was established for nano diamonds.
DETONATION NANODIAMOND AS PROSPECTIVE COMPONENT OF COMPOSITE SOLID PROPELLANTS
Authors: Gorbachev Valentin A. , Ubey - Volk Evgeniy Yu. , Shevchenko Nikolay V. , Golubev Alexandr A.
Published: July 2018

In this articlethe the possibility of application of detonation nanodiamond (DND) as a prospective component of composite solid propellants (CSP) and additive approach to optimization of fuel compositions based on binary fuel compositions is considered. The introduction to the fuel composition of DND allows creating a metal-free CSP with increased energy-to-mass characteristics. Usage of the additive approach for calculations when creating new prospective compositions of CSP allows reducing significantly the volume of work to optimize the fuel compositions and to simplify the process of thermodynamic engineering.
ROLE OF STRUCTURING VOLUME AND SURFACE OF OPTICAL MATERIALS AT MODIFICATION OF THEIR BASIC MACROPARAMETERS
Authors: Kamanina Natalia V.
Published: July 2018

In the current paper the results on change of main macroparameters of optical materials at structuring both their bulk and surface are briefly presented at application of laser technologies. The changes in transmission and reflection spectra in mechanical and refractive parameters of materials were established and were explained including the changes in their photo conductivity properties. The broadening of application areas of thin film organic systems in comparison with volime electro-optical inorganic structures is discussed.
DISCRETE STEPS OF DIAMOND-GRAPHITE PHASE TRANSITION AT ANNEALING OF NANODIAMONDS IN WIDE TEMPERATURE RANGE
Authors: Kornienko Nikolay E. , Kirichenko Alexey N.
Published: July 2018

We present the short review of the works on a problem of phase transitions (PT) which are distributed in the temperature range ΔТ of PT.  Experimental studies of Raman spectra (laser wavelength 514.5 nm) of nanodiamonds after annealing at 900-2000 °C and their detailed numerical analysis with decomposition of the allocated oscillatory D and G bands on the compound spectral components D and G, D (k) and G (k’) relating to various states of Brillouin’s zones were conducted. Detection of temperature maxima of intensities, frequencies and full width at half maximum (FWHM) of individual Raman components as well as intensity of a background defines discrete steps of PT of diamond - onion-shaped carbon in temperature ranges of 940-1200 °C and 1500-2000 °C.
COMPARISON OF EFFECTIVENESS OF CARBON NANO- AND MICROFIBERS FOR FORMATION OF PHYSICAL-MECHANICAL AND TRIBOLOTECHNICAL PARAMETERS OF POLYMER COMPOSITES BASED ON HIGH MOLECULAR WEIGHT MATRIX
Authors: Panin Sergey V. , Kornienko Lyudmila A. , Aleksenko Vladislav O. , Ivanova Larisa R. , Shilko Sergey V. , Buslovich Dmitriy G.
Published: July 2018

The mechanical and tribo-technical parameters of composite materials of mixtures on the bases of super- molecular polyethylene (SMPE) at conditions of dry friction and abrasive wear were studied for comparative estimation of solid- grease properties of nano and micro fibers of carbon. It was shown that wear resistance of polymer compositions of SMPE+0.5 weight% the percent of C(nano) increases by a factor 6.6 and for  SMPE+5 weight% the percent of C(micro) increases by a factor 2.5 at conditions of dry friction of slip. At conditions of abrasive wear the resistance of composites mentioned above increases by a factor about 2 for both types of fillers. The role of nano and micro fibers of carbon is discussed as solid grease in tribo- conjugated polymer compositions based on SMPE for application at various conditions of operation.
BEHAVIOR OF CARBON AND URANIUM AT RADIOACTIVE GRAPHITE HEATING IN WATER VAPOR. THERMODYNAMIC MODELING
Authors: Barbin Nikolaiy M. , Kobelev Anton M. , Terent’ev Dmiriy I. , Alexeev Sergeiy G.
Published: July 2018

The behavior of radioactive graphite was studied by the method of thermodynamic modeling at high temperature in water vapor. The distribution of radioactive carbon and uranium on phase states is given.
CO-CRYSTALLIZATION OF C60 AND С70 FULLERENES IN CRYSTAL-SOLVATE [(C70)X+(С60)Y]• TMTSeF•2(C6H6) (х+у=3)
Authors: Blagov Maksim A. , Spitsina Nataliya G. , Konovalikhin Sergei V.
Published: July 2018

The compexation of (С70/C60) fullerenes with organic p-donor of electrons tetramethyl-(tetra selenium)fulvalene (TMTSeF) in benzene (С6Н6) was studied. Comparison of experimental and calculated X-ray patterns showed that in the investigated single crystals of [(C70)x+(С60)y]· TMTSeF·2(C6H6) (х+у=3) (1) С70 and C60 fullerens are co-crystallized. IR spectral data and electroconductivity of 1 indicate the absence of the charge transfer on fullerene molecule for complexes under study.
CAVITATIONAL SYNTHESIS OF CARBON NANOFORMS BY WATER HAMMER
Authors: Dushenko Nikita V. , Voropaev Sergey A. , Ponomareva Ekaterina A. , Dnestrovskiy Alexey Yu. , Shkinev Valery M , Aronin Alexandr S. , Galimov Erik M.
Published: July 2018

We consider features of the carbon composite nano-particles formation at cavitation by means of the hydro impact. The comparison of given method with existing methods of synthesis in nanotechnology was carried out. The crystal structure of the various carbon nanoforms synthesized by hydrodynamic cavitation in a mixture of water and isopropyl alcohol was investigated using the methods of electron diffraction. Such polymorphs of carbon as the nano-diamond, nanographite and composites were revealed. The lattices characteristics of the synthesized carbon nano forms were analyzed. Applications of results for microelectronics were considered.
Diş Hekimliğinde Trombosit Konsantrasyonlarinin Tarihsel Gelişimi ve Özellikleri
Authors: KIZILTOPRAK Mehmet , USLU Mustafa özay
Published: July 2018

Trombositler hemostaz ve yara iyileşmesinde çok önemli bir rol oynamakta ve ihtiva ettikleri büyüme faktörleri ve sitokinler sayesinde rejeneratif tedavinin potansiyel hücreleri arasında yer almaktadırlar. Bu durum, rejeneratif tedavide, trombosit ve trombosit konsantrasyonlarına olan ilgiyi arttırmıştır. Geçmişten günümüze kadar çeşitli trombosit konsantrasyonları elde edilmiş ve bu ürünler tek başına veya başka biomateryallerle kombine kullanıldığında, iyileşme sürecine olan olumlu katkıları görülmüştür. Trombosit konsantrasyonları, sert ve yumuşak doku ile ilgili cerrahi prosedürlerde kullanıldığında, içeriğinde bulunan yoğun sitokin ve büyüme faktörlerinin kontrollü salınımı sağlar. Bu durum doğal yara iyileşme sürecini hızlandırmaktadır. Ayrıca, otojen kaynaklı olduklarından herhangi bir immünolojik reaksiyon ve enfeksiyona yol açmamaları en önemli avantajlarıdır. Tam kan farklı devirlerde ve farklı sürelerde santrifüj edildiğinde içeriği birbirinden farklı olan trombosit kaynaklı ürünler elde edilmiştir. PRP, PRGF, PRF ve CGF gibi ürünlere bakıldığında yeni keşfedilen her ürünün bir öncekine göre daha gelişmiş özellikleri olduğu görülmektedir.  Bu derlemenin amacı; PRP, PRGF, PRF ve CGF gibi trombosit konsantrasyonlarının tarihsel gelişimi ve özellikleri hakkında bilgi vermektir.
Fabrikasyon ve Döküm Manyetik Ataşmanların Korozyon Dirençlerinin İncelenmesi
Authors: Coşkun Mehmet Emre , Özdemir Ali Kemal
Published: July 2018

Amaç: Bu çalışmanın amacı, protetik
tedavilerde kullanılan döküm ve fabrikasyon manyetik ataşman sistemlerinin,
korozyona karşı dirençlerinin incelenmesidir. Gereç ve Yöntem: Korozyon testi için, ağırlıkça
%39,5 platin, %59,75 demir ve %0,75 niobyum içeren döküm manyetik ataşmanlar
ile neodmiyum, demir ve boron içeriğe sahip fabrikasyon Hilop manyetik ataşman
sistemleri, %1’ lik laktik asit ve %0,9’ luk NaCl solüsyon içerisinde 14 gün
boyunca bekletilmiş (n:8). Örneklerden solüsyonlar içerisine salınan demir,
platin, neodimyum, bor ve niobyum iyonlarının miktarı indüktif olarak eşleşmiş
plazma kütle spektroskopi (ICP-MS) yöntemiyle tayin edilmiştir. Bulgular: Her iki manyetik ataşman
sisteminde de en fazla solüsyon içerisine salınan ve korozyona neden olan
element demir olarak tespit edilmiştir. Ayrıca her iki ortamda da döküm manyetik
ataşman sistemi korozyona karşı en dirençli sistem olarak tespit edilmiştir.

Sonuç: Paslanmaz çelik ile kaplama
fabrikasyon manyetik ataşman sistemlerini korozyona karşı korusada döküm
mıknatısların içeriğindeki yüksek orandaki platin malzemeyi korozyona karşı
daha dirençli hale getirmiştir.
Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites
Authors: Chen Guoling , Zheng Chenqing , Wan Nelson , Liu Daoqiang , Fu Vivian Wing Kan , Yang Xu , Yu Yat-tung , Liu Yang
Published: July 2018

Background. Understanding genetic diversity and population structure is critically important for the conservation and management of endangered species. These factors are particularly relevant for species with small populations and/or restricted ranges, such as the critically endangered Blue-crowned Laughingthrush, Garrulax courtoisi, which has only two wild populations left in Wuyuan, Jiangxi and Simao, Yunnan, China.

Methods. In this study, novel microsatellites markers were developed using whole-genome sequencing of the target species. We genotyped 14 and nine individuals from the Oceanic Park of Hong Kong, which are of unknown origin, and the Nanchang Zoo, which were introduced from the wild Wuyuan population, respectively, using the novel microsatellite markers. The genetic diversity of captive Blue-crowned Laughingthrush populations was estimated based on genetic polymorphisms revealed by a new microsatellite data set and mitochondrial sequences.Then, we characterised the population structure using STRUCTURE, principal coordinates analysis, population assignment test using the microsatellite data, and haplotype analysis of mitochondrial data. Additionally, we quantified genetic relatednessbased on the microsatellite data with ML-Relate.

Results. This is the first study to describe this novel set of 12 microsatellite markers for Blue-crowned Laughingthrush. Our results based on the microsatellite dataset and mitochondrial sequences showed equally low levels of genetic diversity of the two captive Blue-crowned Laughingthrush populations. The population structure analysis, population assignment test using the microsatellite data, and haplotype analysis of the mitochondrial data showed some population structuring between these two populations. The average pairwise relatedness coefficient was not significant, and their genetic relatedness was quantified.

Discussion. This study provided a genetic tool which allowed the first estimate of captive population genetic diversity and relatedness for a critically endangered bird species. Furthermore, our results indicate that we cannot exclude the possibility that the origin of the Hong Kong captive population was the wild Wuyuan population. These results provide valuable knowledge that can help improve conservation management and planning for both captive and wild Blue-crowned Laughingthrush populations.
Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon
Authors: Vickrey Anna I , Bruders Rebecca , Kronenberg Zev , Mackey Emma , Bohlender Ryan J , Maclary Emily T , Maynez Raquel , Osborne Edward J , Johnson Kevin P , Huff Chad D , Yandell Mark , Shapiro Michael D
Published: July 2018

Birds and other vertebrates display stunning variation in pigmentation patterning, yet the genes controlling this diversity remain largely unknown. Rock pigeons (Columba livia) are fundamentally one of four color pattern phenotypes, in decreasing order of melanism: T-check, checker, bar (ancestral), or barless. Using whole-genome scans, we identified NDP as a candidate gene for this variation. Allele-specific expression differences in NDP indicate cis-regulatory divergence between ancestral and melanistic alleles. Sequence comparisons suggest that derived alleles originated in the speckled pigeon (Columba guinea), providing a striking example of introgression. In contrast, barless rock pigeons have an increased incidence of vision defects and, like human families with hereditary blindness, carry start-codon mutations in NDP. In summary, we find that both coding and regulatory variation in the same gene drives wing pattern diversity, and post-domestication introgression supplied potentially advantageous melanistic alleles to feral populations of this ubiquitous urban bird.
A protein secreted by the Salmonella type III secretion system controls needle filament assembly
Authors: Kato Junya , Dey Supratim , Soto Jose E , Butan Carmen , Wilkinson Mason C , De Guzman Roberto N , Galan Jorge E
Published: July 2018

Type III protein secretion systems (T3SS) are encoded by several pathogenic or symbiotic bacteria. The central component of this nanomachine is the needle complex. Here we show in a Salmonella Typhimurium T3SS that assembly of the needle filament of this structure requires OrgC, a protein encoded within the T3SS gene cluster. Absence of OrgC results in significantly reduced number of needle substructures but does not affect needle length. We show that OrgC is secreted by the T3SS and that exogenous addition of OrgC can complement a ∆orgC mutation. We also show that OrgC interacts with the needle filament subunit PrgI and accelerates its polymerization into filaments in vitro. The structure of OrgC shows a novel fold with a shared topology with a domain from flagellar capping proteins. These findings identify a novel component of T3SS and provide new insight into the assembly of the type III secretion machine.
Matrin 3-dependent neurotoxicity is modified by nucleic acid binding and nucleocytoplasmic localization
Authors: Malik Ahmed M , Miguez Roberto A , Li Xingli , Ho Ye-Shih , Feldman Eva L , Barmada Sami J
Published: July 2018

Abnormalities in nucleic acid processing are associated with the development of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Mutations in Matrin 3 (MATR3), a poorly understood DNA- and RNA-binding protein, cause familial ALS/FTD, and MATR3 pathology is a feature of sporadic disease, suggesting that MATR3 dysfunction is integrally linked to ALS pathogenesis. Using a rat primary neuron model to assess MATR3-mediated toxicity, we noted that neurons were bidirectionally vulnerable to MATR3 levels, with pathogenic MATR3 mutants displaying enhanced toxicity. MATR3’s zinc finger domains partially modulated toxicity, but elimination of its RNA recognition motifs had no effect on survival, instead facilitating its self-assembly into liquid-like droplets. In contrast to other RNA-binding proteins associated with ALS, cytoplasmic MATR3 redistribution mitigated neurodegeneration, suggesting that nuclear MATR3 mediates toxicity. Our findings offer a foundation for understanding MATR3-related neurodegeneration and how nucleic acid binding functions, localization, and pathogenic mutations drive sporadic and familial disease.
Insights into the ubiquitin transfer cascade catalyzed by the Legionella effector SidC
Authors: Wasilko David Jon , Huang Qingqiu , Mao Yuxin
Published: July 2018

The causative agent of Legionnaires’ disease, Legionella pneumophila, delivers more than 330 virulent effectors to its host to establish an intracellular membrane-bound organelle called the Legionella containing vacuole. Among the army of Legionella effectors, SidC and its paralog SdcA have been identified as novel bacterial ubiquitin (Ub) E3 ligases. To gain insight into the molecular mechanism of SidC/SdcA as Ub ligases, we determined the crystal structures of a binary complex of the N-terminal catalytic SNL domain of SdcA with its cognate E2 UbcH5C and a ternary complex consisting of the SNL domain of SidC with the Ub-linked E2 UbcH7. These two structures reveal the molecular determinants governing the Ub transfer cascade catalyzed by SidC. Together, our data support a common mechanism in the Ub transfer cascade in which the donor Ub is immobilized with its C-terminal tail locked in an extended conformation, priming the donor Ub for catalysis.
Cytokinin transfer by a free-living mirid to Nicotiana attenuata recapitulates a strategy of endophytic insects
Authors: Brütting Christoph , Crava Cristina Maria , Schäfer Martin , Schuman Meredith C , Meldau Stefan , Adam Nora , Baldwin Ian T
Published: July 2018

Endophytic insects provide the textbook examples of herbivores that manipulate their host plant’s physiology, putatively altering source/sink relationships by transferring cytokinins (CK) to create ‘green islands’ that increase the nutritional value of infested tissues. However, unambiguous demonstrations of CK transfer are lacking. Here we show that feeding by the free-living herbivore Tupiocoris notatus on Nicotiana attenuata is characterized by stable nutrient levels, increased CK levels and alterations in CK-related transcript levels in attacked leaves, in striking similarity to endophytic insects. Using 15N-isotope labeling, we demonstrate that the CK N6-isopentenyladenine (IP) is transferred from insects to plants via their oral secretions. In the field, T. notatus preferentially attacks leaves with transgenically increased CK levels; plants with abrogated CK-perception are less tolerant of T. notatus feeding damage. We infer that this free-living insect uses CKs to manipulate source/sink relationships to increase food quality and minimize the fitness consequences of its feeding.
Wnt/β-catenin regulates an ancient signaling network during zebrafish scale development
Authors: Aman Andrew J , Fulbright Alexis N , Parichy David M
Published: July 2018

Understanding how patterning influences cell behaviors to generate three dimensional morphologies is a central goal of developmental biology. Additionally, comparing these regulatory mechanisms among morphologically diverse tissues allows for rigorous testing of evolutionary hypotheses. Zebrafish skin is endowed with a coat of precisely patterned bony scales. We use in-toto live imaging during scale development and manipulations of cell signaling activity to elucidate core features of scale patterning and morphogenesis. These analyses show that scale development requires the concerted activity of Wnt/β-catenin, Ectodysplasin (Eda) and Fibroblast growth factor (Fgf) signaling. This regulatory module coordinates Hedgehog (HH) dependent collective cell migration during epidermal invagination, a cell behavior not previously implicated in skin appendage morphogenesis. Our analyses demonstrate the utility of zebrafish scale development as a tractable system in which to elucidate mechanisms of developmental patterning and morphogenesis, and suggest a single, ancient origin of skin appendage patterning mechanisms in vertebrates.
A selective gut bacterial bile salt hydrolase alters host metabolism
Authors: Yao Lina , Seaton Sarah Craven , Ndousse-Fetter Sula , Adhikari Arijit A , DiBenedetto Nicholas , Mina Amir I , Banks Alexander S , Bry Lynn , Devlin A Sloan
Published: July 2018

The human gut microbiota impacts host metabolism and has been implicated in the pathophysiology of obesity and metabolic syndromes. However, defining the roles of specific microbial activities and metabolites on host phenotypes has proven challenging due to the complexity of the microbiome-host ecosystem. Here, we identify strains from the abundant gut bacterial phylum Bacteroidetes that display selective bile salt hydrolase (BSH) activity. Using isogenic strains of wild-type and BSH-deleted Bacteroides thetaiotaomicron, we selectively modulated the levels of the bile acid tauro-β-muricholic acid in monocolonized gnotobiotic mice. B. thetaiotaomicron BSH mutant-colonized mice displayed altered metabolism, including reduced weight gain and respiratory exchange ratios, as well as transcriptional changes in metabolic, circadian rhythm, and immune pathways in the gut and liver. Our results demonstrate that metabolites generated by a single microbial gene and enzymatic activity can profoundly alter host metabolism and gene expression at local and organism-level scales.
A brighter force gauge for cells
Authors: Ma Victor Pui-Yan , Salaita Khalid
Published: July 2018

An improved biosensor sheds new light on tension within proteins.
Setting the bar
Authors: Feigin Charles Y , Mallarino Ricardo
Published: July 2018

Analyzing the genomes of rock pigeons demonstrates that genetic variation comes in many forms and can have unexpected origins.
Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced loci
Authors: de Medeiros Bruno A. S. , Farrell Brian D.
Published: July 2018

Whole-genome amplification by multiple displacement amplification (MDA) is a promising technique to enable the use of samples with only limited amount of DNA for the construction of RAD-seq libraries. Previous work has shown that, when the amount of DNA used in the MDA reaction is large, double-digest RAD-seq (ddRAD) libraries prepared with amplified genomic DNA result in data that are indistinguishable from libraries prepared directly from genomic DNA. Based on this observation, here we evaluate the quality of ddRAD libraries prepared from MDA-amplified genomic DNA when the amount of input genomic DNA and the coverage obtained for samples is variable. By simultaneously preparing libraries for five species of weevils (Coleoptera, Curculionidae), we also evaluate the likelihood that potential contaminants will be encountered in the assembled dataset. Overall, our results indicate that MDA may not be able to rescue all samples with small amounts of DNA, but it does produce ddRAD libraries adequate for studies of phylogeography and population genetics even when conditions are not optimal. We find that MDA makes it harder to predict the number of loci that will be obtained for a given sequencing effort, with some samples behaving like traditional libraries and others yielding fewer loci than expected. This seems to be caused both by stochastic and deterministic effects during amplification. Further, the reduction in loci is stronger in libraries with lower amounts of template DNA for the MDA reaction. Even though a few samples exhibit substantial levels of contamination in raw reads, the effect is very small in the final dataset, suggesting that filters imposed during dataset assembly are important in removing contamination. Importantly, samples with strong signs of contamination and biases in heterozygosity were also those with fewer loci shared in the final dataset, suggesting that stringent filtering of samples with significant amounts of missing data is important when assembling data derived from MDA-amplified genomic DNA. Overall, we find that the combination of MDA and ddRAD results in high-quality datasets for population genetics as long as the sequence data is properly filtered during assembly.
Integrated analysis of differentially expressed profiles and construction of a competing endogenous long non-coding RNA network in renal cell carcinoma
Authors: Xing Qianwei , Huang Yeqing , Wu You , Ma Limin , Cai Bo
Published: July 2018

Background

Long non-coding RNAs (lncRNAs) play crucial roles in the initiation and progression of renal cell carcinoma (RCC) by competing in binding to miRNAs, and related competitive endogenous RNA (ceRNA) networks have been constructed in several cancers. However, the coexpression network has been poorly explored in RCC.

Methods

We collected RCC RNA expression profile data and relevant clinical features from The Cancer Genome Atlas (TCGA). A cluster analysis was explored to show different lncRNA expression patterns. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses and gene set enrichment analysis (GSEA) were performed to analyze the functions of the intersecting mRNAs. Targetscan and miRanda bioinformatics algorithms were used to predict potential relationships among RNAs. Univariate Cox proportional hazards regression was conducted to determine the RNA expression levels and survival times.

Results

Bioinformatics analysis revealed that the expression profiles of hundreds of aberrantly expressed lncRNAs, miRNAs, and mRNAs were significantly changed between different stages of tumors and non-tumor groups. By combining the data predicted by databases with intersection RNAs, a ceRNA network consisting of 106 lncRNAs, 26 miRNAs and 69 mRNAs was established. Additionally, a protein interaction network revealed the main hub nodes (VEGFA, NTRK2, DLG2, E2F2, MYB and RUNX1). Furthermore, 63 lncRNAs, four miRNAs and 31 mRNAs were significantly associated with overall survival.

Conclusion

Our results identified cancer-specific lncRNAs and constructed a ceRNA network for RCC. A survival analysis related to the RNAs revealed candidate biomarkers for further study in RCC.
Espaço, geograficidades e ação política comunitária na Resex Marinha de Canavieiras-BA
Authors: Santos Mario Alberto
Published: July 2018

A criação da Resex Marinha de Canavieiras-BA em 2006 foi resultado das mobilizações de pescadores e marisqueiras artesanais, com o apoio de instituições da sociedade civil e também de órgãos do Governo Federal. Como obra da ação política e dos saberes, a criação da Resex desencadeou outros processos de transformações sociais e políticas positivas. O fortalecimento comunitário e a construção da coesão na organização do tecido social se destacam. Esse amadurecimento e a criação de um corpo político fizeram surgir também questionamentos do modelo de cogestão do SNUC e do comportamento do ICMBio em relação às suas corresponsabilidades na gestão da unidade. Deste modo, há um debate colocado. A questão da autonomia das comunidades tradicionais na gestão territorial tem entre os beneficiários da Resex em Canavieiras o desejo de uma ressignificação profunda, o que criou um retorno às reinvindicações presentes entre as comunidades tradicionais antes do SNUC. Os papeis da ação política e da educação são essenciais para as alterações necessárias no funcionamento do ICMBio e no comportamento de seus analistas. É fundamental o Estado brasileiro admitir o sentido de Ser e suas geograficidades para pensar sua colaboração na gestão das Resex.

Resumé

ESPACE, GÉOGRAPHICITÉS E ACTION POLITIQUE COMMUNAUTAIRE DANS LA RÉSERVE EXTRATIVISTE MARINE DE CANAVIEIRAS-BA

La création de la réserve de collecte (réserve extrativiste ou resex en abrégé) marine de Canavieiras-BA en 2006 fut le résultat des mobilisations de pêcheurs artisanaux et de collecteuses de mollusques et crustacés, avec l’appui d’institutions de la société civile et d’organismes du gouvernement fédéral. En tant qu’oeuvre d’action politique et de savoirs, la création de la resex déclencha d’autres processos de transformations sociales et politiques positives. La consolidation communautaire et la création de la cohésion dans l’organisation du tissu social se distinguent. Ce mûrissement et la créatin d’un corps politique firent surgir aussi des remises en question du modèle de co-gestion et du comportement de l’organisme environnemental, ICMBio, eu égard à ses co-responsabilités dans la gestion de l’aire protégée. Ainsi, il existe un débat ouvert. La question de l’autonomie des communautés traditionnelles dans la gestion territoriale se pose pour les bénéficiaires de la resex à Canavieiras tel le désir d’une profonde ressignification, ce qui cria un retour aux revendications présentes parmi les communautés traditionnelles avant l’adoption du Système National d’Unités de Conservation (SNUC). Les rôles de l’action politique et de l’éducation sont essentiels pour les altérations nécessaires dans le fonctionnement de l’ICMBio et dans le comportements de ses analystes environnementaux. Il est fondamental que l’Etat brésilien admette le sens de l’Etre et ses géographicités pour penser sa collaboration dans la gestion des resex.
Divisão territorial do trabalho e transporte rodoviário interestadual de passageiros: o município de Londrina/PR como um nó para essa circulação
Authors: Santos Bruno Candido dos
Published: July 2018

O transporte rodoviário interestadual de passageiros é uma atividade econômica que elucida a divisão territorial do trabalho, pois é uma expressão de parte dos deslocamentos de pessoas pelo território nacional e, portanto, ilustra as articulações entre variados centros. Com o avanço da urbanização brasileira e a ampliação da demanda de passageiros o transporte rodoviário acompanha tais processos, pois exerce função social central ao efetuar ligações diversas entre pontos distintos no território nacional e reflete em última instância as dinâmicas da rede urbana e as interações espaciais ocorridas nela. Diante de tais prerrogativas, o município de Londrina, localizado no norte do estado do Paraná, funciona como um nó da rede do transporte rodoviário interestadual de passageiros, pois se trata da segunda cidade mais populosa do estado do Paraná. São dezenas de linhas interestaduais que atingem estados nas macrorregiões Norte, Centro Oeste, Sudeste e Sul, com maior participação das duas últimas.

Abstract

TERRITORIAL DIVISION OF LABOR AND INTERSTATE ROAD TRANSPORT OF PASSENGERS: THE MUNICIPALITY OF LONDRINA/PR AS A NODE FOR THIS CIRCULATION

The interstate road transport of passengers is an economic activity that clarifies the territorial division of labor, it illustrates part of displacement throughout the country and therefore the joints between different centers. With the advancement of Brazilian urbanization and the expansion of the passengers demand the road passenger transport follows these processes, as it exerts a central social function by making diverse connections between distinct points in the national territory and ultimately reflects the dynamics of the urban network and the spatial interactions occurring in it. In view of such prerogatives, the municipality of Londrina, located in the northern part of the Paraná state, functions as a node of the interstate road transport of passengers, because it is the second most populous city in the state of Paraná. There are dozens of interstate lines that reach states in the North, Central-West, Southeast and South macro-regions, with greater participation of the latter two.
Single channel informed signal separation using artificial‐stereophonic mixtures and exemplar‐guided matrix factor deconvolution
Authors: Al‐Tmeme Ahmed , Woo W. L. , Dlay S. S. , Gao Bin
Published: July 2018

In this paper, a method is proposed to tackle the problem of single channel audio separation. The proposed method leverages on the exemplar source is used to emulate the targeted speech signal. A multicomponent nonnegative matrix factor 2D deconvolution (NMF2D) is proposed to model the temporal and spectral changes and the number of spectral basis of the audio signals. The paper proposes an artificial auxiliary channel to imitate a pair of stereo mixture signals, which is termed as “artificial‐stereophonic mixtures.” The artificial‐stereophonic mixtures and the exemplar source are jointly used to guide the factorization process of the NMF2D. The factorization is adapted under a hybrid framework that combines the generalized expectation–maximization algorithm with multiplicative update adaptation. The proposed algorithm leads to fast and stable convergence and ensures the nonnegativity constraints of the solution are satisfied. Adaptive sparsity has also been introduced on each sparse parameter in the multicomponent NMF2D model when the exemplar deviates from the target signal. Experimental results have shown the competence of the proposed algorithms in comparison with other algorithms.
Limits of control performance for distributed networked control systems in presence of communication delays
Authors: Yan Guoyang , Liu Jinfeng , Huang Biao
Published: July 2018

In terms of computational complexity and fault tolerance, distributed networked control systems (DNCSs) is favorable for large‐scale processes. However, it poses additional limitations on the achievable control performance, especially when communication delay is present. The conventional minimum variance (MV) benchmarks mainly consider the limitations caused by the system itself and can give overly estimates of achievable performance when applied to the systems under distributed networked control. This paper proposes a solution to the MV benchmark for DNCSs considering both system time delays and time‐invariant communication delays. Furthermore, lower and upper bounds of the MV benchmark are proposed to assess the performance of DNCSs when there are time‐varying communication delays. These results are useful for evaluating the potential performance improvement if a DNCS is implemented to replace a decentralized control system. The proposed results are illustrated by a simulation example.
Aggressive Man‐Made Red Blood Cells for Hypoxia‐Resistant Photodynamic Therapy
Authors: Liu Wen‐Long , Liu Tao , Zou Mei‐Zhen , Yu Wu‐Yang , Li Chu‐Xin , He Zu‐Yang , Zhang Ming‐Kang , Liu Miao‐Deng , Li Zi‐Hao , Feng Jun , Zhang Xian‐Zheng
Published: July 2018

Extreme hypoxia of tumors represents the most notable barrier against the advance of tumor treatments. Inspired by the biological nature of red blood cells (RBCs) as the primary oxygen supplier in mammals, an aggressive man‐made RBC (AmmRBC) is created to combat the hypoxia‐mediated resistance of tumors to photodynamic therapy (PDT). Specifically, the complex formed between hemoglobin and enzyme‐mimicking polydopamine, and polydopamine‐carried photosensitizer is encapsulated inside the biovesicle that is engineered from the recombined RBC membranes. The mean corpuscular hemoglobin of AmmRBCs reaches about tenfold as high as that of natural RBCs. Owing to the same origin of outer membranes, AmmRBCs share excellent biocompatibility with parent RBCs. The introduced polydopamine plays the role of the antioxidative enzymes existing inside RBCs to effectively prevent the oxygen‐carrying hemoglobin from the oxidation damage during the circulation. This biomimetic engineering can accumulate in tumors, permit in situ efficient oxygen supply, and impose strong PDT efficacy toward the extremely hypoxic tumor with complete tumor elimination. The man‐made pseudo‐RBC shows potentials as a universal oxygen‐self‐supplied platform to sensitize hypoxia‐limited tumor treatment means, including but not limited to PDT. Meanwhile, this study offers ideas to the production of artificial substitutes of packed RBCs for clinical blood transfusion.
A Liquid‐Metal‐Based Magnetoactive Slurry for Stimuli‐Responsive Mechanically Adaptive Electrodes
Authors: Ren Long , Sun Shuaishuai , Casillas‐Garcia Gilberto , Nancarrow Mitchell , Peleckis Germanas , Turdy Mirzat , Du Kunrong , Xu Xun , Li Weihua , Jiang Lei , Dou Shi Xue , Du Yi
Published: July 2018

Electrical communication between a biological system and outside equipment allows one to monitor and influence the state of the tissue and nervous networks. As the bridge, bioelectrodes should possess both electrical conductivity and adaptive mechanical properties matching the target soft biosystem, but this is still a big challenge. A family of liquid‐metal‐based magnetoactive slurries (LMMSs) formed by dispersing magnetic iron particles in a Ga‐based liquid metal (LM) matrix is reported here. The mechanical properties, viscosity, and stiffness of such materials rapidly respond to the stimulus of an applied magnetic field. By varying the intensity of the magnetic field, regulation within a factor of 1000 of the Young's modulus from ≈kPa to ≈MPa, and the ability to reach GPa with more dense iron particles inside the LMMS are demonstrated. With the advantage of high conductivity of the LM matrix, the functions of the LMMS are not only limited to the soft implanted electrodes or penetrating electrodes in biosystems: the electrical response based on the LMMS electrodes can also be precisely tuned by simply regulating the applied magnetic field.
Integrated Circuits Comprising Patterned Functional Liquids
Authors: Prasad Bhagwati , Pfanzelt Georg , Fillis‐Tsirakis Evangelos , Zachman Michael J. , Kourkoutis Lena F. , Mannhart Jochen
Published: July 2018

Solid‐state heterostructures are the cornerstone of modern electronics. To enhance the functionality and performance of integrated circuits, the spectrum of materials used in the heterostructures is being expanded by an increasing number of compounds and elements of the periodic table. While the integration of liquids and solid–liquid interfaces into such systems would allow unique and advanced functional properties and would enable integrated nanoionic circuits, solid‐state heterostructures that incorporate liquids have not been considered thus far. Here solid‐state heterostructures with integrated liquids are proposed, realized, and characterized, thereby opening a vast, new phase space of materials and interfaces for integrated circuits. Devices containing tens of microscopic capacitors and field‐effect transistors are fabricated by using integrated patterned NaCl aqueous solutions. This work paves the way to integrated electronic circuits that include highly integrated liquids, thus yielding a wide array of novel research and application opportunities based on microscopic solid/liquid systems.
Light‐Induced Anomalous Resistive Switches Based on Individual Organic–Inorganic Halide Perovskite Micro‐/Nanofibers
Authors: Zhao Jie , Li Shujun , Tong Wenchao , Chen Guanwen , Xiao Yanhe , Lei Shuijin , Cheng Baochang
Published: July 2018

Organic–inorganic halide perovskite (OHP) materials have attracted remarkable attention for the great promise of optoelectronic applications. Unfortunately, hysteresis in the current–voltage response links to the stability and reliability assessment of OHP photovoltaic device that must be addressed. Here, light‐induced antipolar resistive switching (RS) effect is demonstrated in an individual MAPbI3 micro‐/nanofiber–based two‐terminal device after aging for 4 d. The antipolar RS is attributed to reversible electrochemical reactions in the vicinity of Ag electrode, where Ag serves as the work electrode and MAPbI3 acts as the solid electrolyte. That makes conductive behavior of antipolar RS similar with cyclic voltammetry curves of capacitances. Concomitantly, the antipolar RS shows slow dissipation kinetics, which is employed to realize the application of nonvolatile memories. This work establishes the potential for the versatile solid state devices that can efficiently couple interface reaction, charge migration, and photoelectrical effects in an individual micro‐/nanodevice.
Serum free light chain measurements to reduce 24‐h urine monitoring in patients with multiple myeloma with measurable urine monoclonal protein
Authors: Tschautscher Marcella , Rajkumar Vincent , Dispenzieri Angela , Lacy Martha , Gertz Morie , Buadi Francis , Dingli David , Hwa Lisa , Fonder Amie , Hobbs Miriam , Hayman Suzanne , Zeldenrust Stephen , Lust John , Russell Stephen , Leung Nelson , Kapoor Pranshant , Go Ronald , Lin Yi , Gonsalves Wilson , Kourelis Taxiarchis , Warsame Rahma , Kyle Robert , Kumar Shaji
Published: July 2018

Detection of myeloma progression (PD) relies on serial 24‐h urinary M protein measurements in patients without measurable serum M spike. We examined whether serial difference free light chain (dFLC) levels could be used as a surrogate for serial 24‐h urine M protein measurements in monitoring for PD in patients with baseline measurable urine M protein. We studied 122 patients who had serial measurement of urine M protein and serum FLC and had demonstrated PD. The median increase in dFLC with progression as defined by urine M spike was 110% (IQR: 55‐312) and median absolute increase was 74 mg/dL; while 89% of patients had dFLC increase ≥ 25%, 94% had absolute increase in dFLC > 10 mg/dL, and 98% met at least 1 of these 2 criteria at PD. In patients with baseline measurable serum FLC (n = 118), 89% had increase in dFLC ≥ 25%, 97% had dFLC increase of > 10 mg/dL, and 98% had 1 of the 2. We conclude that serial dFLC assessments can be used in place of serial 24‐h urine protein assessments during myeloma surveillance to monitor for PD. Once patients have an absolute increase in dFLC of >10 mg/dL from the nadir, a 24‐h urine collection can then be assessed to document PD as per the International Myeloma Working Group criteria.
A novel FBXO28 frameshift mutation in a child with developmental delay, dysmorphic features, and intractable epilepsy: A second gene that may contribute to the 1q41‐q42 deletion phenotype
Authors: Balak Chris , Belnap Newell , Ramsey Keri , Joss Shelagh , Devriendt Koen , Naymik Marcus , Jepsen Wayne , Siniard Ashley L. , Szelinger Szabolcs , Parker Mary E. , Richholt Ryan , Izatt Tyler , LaFleur Madison , Terraf Panieh , Llaci Lorida , De Both Matt , Piras Ignazio S. , Rangasamy Sampathkumar , Schrauwen Isabelle , Craig David W. , Huentelman Matt , Narayanan Vinodh
Published: July 2018

Chromosome 1q41‐q42 deletions have recently been associated with a recognizable neurodevelopmental syndrome of early childhood (OMIM 612530). Within this group, a predominant phenotype of developmental delay (DD), intellectual disability (ID), epilepsy, distinct dysmorphology, and brain anomalies on magnetic resonance imaging/computed tomography has emerged. Previous reports of patients with de novo deletions at 1q41‐q42 have led to the identification of an evolving smallest region of overlap which has included several potentially causal genes including DISP1, TP53BP2, and FBXO28. In a recent report, a cohort of patients with de novo mutations in WDR26 was described that shared many of the clinical features originally described in the 1q41‐q42 microdeletion syndrome (MDS). Here, we describe a novel germline FBXO28 frameshift mutation in a 3‐year‐old girl with intractable epilepsy, ID, DD, and other features which overlap those of the 1q41‐q42 MDS. Through a familial whole‐exome sequencing study, we identified a de novo FBXO28 c.972_973delACinsG (p.Arg325GlufsX3) frameshift mutation in the proband. The frameshift and resulting premature nonsense mutation have not been reported in any genomic database. This child does not have a large 1q41‐q42 deletion, nor does she harbor a WDR26 mutation. Our case joins a previously reported patient also in whom FBXO28 was affected but WDR26 was not. These findings support the idea that FBXO28 is a monogenic disease gene and contributes to the complex neurodevelopmental phenotype of the 1q41‐q42 gene deletion syndrome.