bluuebunny/crossref_metadata_2025_split huggingface dataset:
The MAPKKK gene family in cassava: Genome-wide identification and expression analysis against drought stress
Authors: Ye Jianqiu , Yang Hai , Shi Haitao , Wei Yunxie , Tie Weiwei , Ding Zehong , Yan Yan , Luo Ying , Xia Zhiqiang , Wang Wenquan , Peng Ming , Li Kaimian , Zhang He , Hu Wei 
Published: October 2017

AbstractMitogen-activated protein kinase kinase kinases (MAPKKKs), an important unit of MAPK cascade, play crucial roles in plant development and response to various stresses. However, little is known concerning the MAPKKK family in the important subtropical and tropical crop cassava. In this study, 62 MAPKKK genes were identified in the cassava genome, and were classified into 3 subfamilies based on phylogenetic analysis. Most of MAPKKKs in the same subfamily shared similar gene structures and conserved motifs. The comprehensive transcriptome analysis showed that MAPKKK genes participated in tissue development and response to drought stress. Comparative expression profiles revealed that many MAPKKK genes were activated in cultivated varieties SC124 and Arg7 and the function of MeMAPKKKs in drought resistance may be different between SC124/Arg7 and W14. Expression analyses of the 7 selected MeMAPKKK genes showed that most of them were significantly upregulated by osmotic, salt and ABA treatments, whereas slightly induced by H2O2 and cold stresses. Taken together, this study identified candidate MeMAPKKK genes for genetic improvement of abiotic stress resistance and provided new insights into MAPKKK -mediated cassava resistance to drought stress.
Clinical evaluation of final impressions from three-dimensional printed custom trays
Authors: Sun Yuchun , Chen Hu , Li Hong , Deng Kehui , Zhao Tian , Wang Yong , Zhou Yongsheng 
Published: October 2017

AbstractThis study aimed to evaluate the quality of the final impressions taken by three-dimensional printed custom trays for edentulous patients. Custom trays were designed with or without saddle-shaped tissue stops and fabricated by three-dimensional printing techniques. Manually made trays with photocurable materials were produced as controls. Both 3D printed custom trays and manually made ones were used to take impressions from edentulous patients. After 3D scanning of the final impression, the impression materials were removed, thus the underneath tray surfaces were able to be scanned, allowing the thickness of the impression materials to be measured. Final impressions obtained by pre-border-molded 3D printed trays were scanned as references, to which the flange extension deviations and morphology deviations of the impressions taken by both 3D printed trays and manually made ones were calculated. The results showed that (1) impressions from 3D printed custom trays had better thickness distribution than that of manually made ones; (2) impression morphology deviations in non-marginal area were neither statistic different between 3D printed trays and manually made trays, nor between trays with and without tissue stops; and (3) final impressions taken by custom trays without pre-border-molding were tended to have insufficient flange extensions.
On-Chip Glass Microspherical Shell Whispering Gallery Mode Resonators
Authors: Zhang Chenchen , Cocking Alexander , Freeman Eugene , Liu Zhiwen , Tadigadapa Srinivas 
Published: October 2017

AbstractArrays of on-chip spherical glass shells of hundreds of micrometers in diameter with ultra-smooth surfaces and sub-micrometer wall thicknesses have been fabricated and have been shown to sustain optical resonance modes with high Q-factors of greater than 50 million. The resonators exhibit temperature sensitivity of −1.8 GHz K−1 and can be configured as ultra-high sensitivity thermal sensors for a broad range of applications. By virtue of the geometry’s strong light-matter interaction, the inner surface provides an excellent on-chip sensing platform that truly opens up the possibility for reproducible, chip scale, ultra-high sensitivity microfluidic sensor arrays. As a proof of concept we demonstrate the sensitivity of the resonance frequency as water is filled inside the microspherical shell and is allowed to evaporate. By COMSOL modeling, the dependence of this interaction on glass shell thickness is elucidated and the experimentally measured sensitivities for two different shell thicknesses are explained.
Tuning the motility and directionality of self-propelled colloids
Authors: Gomez-Solano Juan Ruben , Samin Sela , Lozano Celia , Ruedas-Batuecas Pablo , van Roij René , Bechinger Clemens 
Published: October 2017

AbstractMicroorganisms are able to overcome the thermal randomness of their surroundings by harvesting energy to navigate in viscous fluid environments. In a similar manner, synthetic colloidal microswimmers are capable of mimicking complex biolocomotion by means of simple self-propulsion mechanisms. Although experimentally the speed of active particles can be controlled by e.g. self-generated chemical and thermal gradients, an in-situ change of swimming direction remains a challenge. In this work, we study self-propulsion of half-coated spherical colloids in critical binary mixtures and show that the coupling of local body forces, induced by laser illumination, and the wetting properties of the colloid, can be used to finely tune both the colloid’s swimming speed and its directionality. We experimentally and numerically demonstrate that the direction of motion can be reversibly switched by means of the size and shape of the droplet(s) nucleated around the colloid, depending on the particle radius and the fluid’s ambient temperature. Moreover, the aforementioned features enable the possibility to realize both negative and positive phototaxis in light intensity gradients. Our results can be extended to other types of half-coated microswimmers, provided that both of their hemispheres are selectively made active but with distinct physical properties.
Impact of blood urea nitrogen to creatinine ratio on mortality and morbidity in hemodialysis patients: The Q-Cohort Study
Authors: Tanaka Shigeru , Ninomiya Toshiharu , Taniguchi Masatomo , Tokumoto Masanori , Masutani Kosuke , Ooboshi Hiroaki , Kitazono Takanari , Tsuruya Kazuhiko 
Published: October 2017

AbstractThe association between blood urea nitrogen to creatinine ratio (UCR) and survival is uncertain in hemodialysis patients. We examined the influence of UCR on mortality and morbidity in hemodialysis patients. A total of 3,401 hemodialysis patients were prospectively followed for 4 years. The association between UCR with overall survival was analyzed using a Cox regression model. During a 4-year follow-up period, 545 patients died from any cause and 582 experienced MACE, 392 with coronary heart disease (CHD), 114 with infection-related death, 77 with hemorrhagic stroke, 141 with ischemic stroke, and 107 with cancer death. Every 1 increase in UCR level was significantly associated with an increased risk for all-cause mortality (hazard ratio [HR] 1.07; 95% confidence interval [CI] 1.03–1.12), CHD (HR 1.08; 95% CI 1.02–1.14), and infection-related death (HR 1.11; 95% CI 1.02–1.21). There was no evidence of a significant association between UCR and death from cancer, and incidence of stroke. A high UCR was significantly associated with an increased risk for all-cause mortality, infection-related death and incidence of CHD in hemodialysis patients.
Dinuclear Metal-Mediated Homo Base Pairs with Metallophilic Interactions: Theoretical Studies of G2M2
2+ (M = Cu, Ag, and Au) Ions
Authors: Cao Guo-Jin 
Published: October 2017

AbstractDinuclear metal-mediated homo base pairs are interesting clusters with highly symmetric structures and significant stabilities. The geometric and electronic structures of G2M22+ (G = Guanine, M = Cu, Ag or Au) cluster ions were studied with quantum chemical calculations. The lowest-energy isomers of G2M22+ cluster ions have C2h symmetries with an approximately antiparallel alignment of two sets of N-M∙∙∙O groups being formed in the planar structures. The M-M distances are shorter than the sum of van der Waals radii of corresponding two homo coinage metal atoms, showing that metallophilic interactions significantly exist in these complexes. They have the large HOMO−LUMO gaps of about 5.80 eV at the DFT level and the bond dissociation energies of more than 5.60 eV at the DFT/B3LYP level, indicating that these cluster dications are highly stable. The second lowest-energy isomers stabilized by an approximately parallel alignment of one set of O-M-O group and one set of N-M-N group are found to be close to the lowest-energy isomers in energy. The barrier between the two isomers of G2M22+ cluster ions is significantly large, also showing that these lowest-energy isomers are very stable.
Anion-conducting channelrhodopsins with tuned spectra and modified kinetics engineered for optogenetic manipulation of behavior
Authors: Wietek Jonas , Rodriguez-Rozada Silvia , Tutas Janine , Tenedini Federico , Grimm Christiane , Oertner Thomas G. , Soba Peter , Hegemann Peter , Wiegert J. Simon 
Published: October 2017

AbstractGenetic engineering of natural light-gated ion channels has proven a powerful way to generate optogenetic tools for a wide variety of applications. In recent years, blue-light activated engineered anion-conducting channelrhodopsins (eACRs) have been developed, improved, and were successfully applied in vivo. We asked whether the approaches used to create eACRs can be transferred to other well-characterized cation-conducting channelrhodopsins (CCRs) to obtain eACRs with a broad spectrum of biophysical properties. We generated 22 variants using two conversion strategies applied to 11 CCRs and screened them for membrane expression, photocurrents and anion selectivity. We obtained two novel eACRs, Phobos and Aurora, with blue- and red-shifted action spectra and photocurrents similar to existing eACRs. Furthermore, step-function mutations greatly enhanced the cellular operational light sensitivity due to a slowed-down photocycle. These bi-stable eACRs can be reversibly toggled between open and closed states with brief light pulses of different wavelengths. All new eACRs reliably inhibited action potential firing in pyramidal CA1 neurons. In Drosophila larvae, eACRs conveyed robust and specific light-dependent inhibition of locomotion and nociception.
GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison
Authors: Faisal Fazle E. , Newaz Khalique , Chaney Julie L. , Li Jun , Emrich Scott J. , Clark Patricia L. , Milenković Tijana 
Published: October 2017

AbstractInitial protein structural comparisons were sequence-based. Since amino acids that are distant in the sequence can be close in the 3-dimensional (3D) structure, 3D contact approaches can complement sequence approaches. Traditional 3D contact approaches study 3D structures directly and are alignment-based. Instead, 3D structures can be modeled as protein structure networks (PSNs). Then, network approaches can compare proteins by comparing their PSNs. These can be alignment-based or alignment-free. We focus on the latter. Existing network alignment-free approaches have drawbacks: 1) They rely on naive measures of network topology. 2) They are not robust to PSN size. They cannot integrate 3) multiple PSN measures or 4) PSN data with sequence data, although this could improve comparison because the different data types capture complementary aspects of the protein structure. We address this by: 1) exploiting well-established graphlet measures via a new network alignment-free approach, 2) introducing normalized graphlet measures to remove the bias of PSN size, 3) allowing for integrating multiple PSN measures, and 4) using ordered graphlets to combine the complementary PSN data and sequence (specifically, residue order) data. We compare synthetic networks and real-world PSNs more accurately and faster than existing network (alignment-free and alignment-based), 3D contact, or sequence approaches.
Potential for social involvement modulates activity within the mirror and the mentalizing systems
Authors: Begliomini Chiara , Cavallo Andrea , Manera Valeria , Becchio Cristina , Stramare Roberto , Miotto Diego , Castiello Umberto 
Published: October 2017

AbstractProcessing biological motion is fundamental for everyday life activities, such as social interaction, motor learning and nonverbal communication. The ability to detect the nature of a motor pattern has been investigated by means of point-light displays (PLD), sets of moving light points reproducing human kinematics, easily recognizable as meaningful once in motion. Although PLD are rudimentary, the human brain can decipher their content including social intentions. Neuroimaging studies suggest that inferring the social meaning conveyed by PLD could rely on both the Mirror Neuron System (MNS) and the Mentalizing System (MS), but their specific role to this endeavor remains uncertain. We describe a functional magnetic resonance imaging experiment in which participants had to judge whether visually presented PLD and videoclips of human-like walkers (HL) were facing towards or away from them. Results show that coding for stimulus direction specifically engages the MNS when considering PLD moving away from the observer, while the nature of the stimulus reveals a dissociation between MNS -mainly involved in coding for PLD- and MS, recruited by HL moving away. These results suggest that the contribution of the two systems can be modulated by the nature of the observed stimulus and its potential for social involvement.
Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi
Authors: Meiser Anjuli , Otte Jürgen , Schmitt Imke , Grande Francesco Dal 
Published: October 2017

AbstractThe metagenome skimming approach, i.e. low coverage shotgun sequencing of multi-species assemblages and subsequent reconstruction of individual genomes, is increasingly used for in-depth genomic characterization of ecological communities. This approach is a promising tool for reconstructing genomes of facultative symbionts, such as lichen-forming fungi, from metagenomic reads. However, no study has so far tested accuracy and completeness of assemblies based on metagenomic sequences compared to assemblies based on pure culture strains of lichenized fungi. Here we assembled the genomes ofEvernia prunastriandPseudevernia furfuraceabased on metagenomic sequences derived from whole lichen thalli. We extracted fungal contigs using two different taxonomic binning methods, and performed gene prediction on the fungal contig subsets. We then assessed quality and completeness of the metagenome-based assemblies using genome assemblies as reference which are based on pure culture strains of the two fungal species. Our comparison showed that we were able to reconstruct fungal genomes from uncultured lichen thalli, and also cover most of the gene space (86–90%). Metagenome skimming will facilitate genome mining, comparative (phylo)genomics, and population genetics of lichen-forming fungi by circumventing the time-consuming, sometimes unfeasible, step of aposymbiotic cultivation.
KIXBASE: A comprehensive web resource for identification and exploration of KIX domains
Authors: Yadav Archana , Thakur Jitendra K. , Yadav Gitanjali 
Published: October 2017

AbstractThe KIX domain has emerged in the last two decades as a critical site of interaction for transcriptional assembly, regulation and gene expression. Discovered in 1994, this conserved, triple helical globular domain has been characterised in various coactivator proteins of yeast, mammals and plants, including the p300/CBP (a histone acetyl transferase), MED15 (a subunit of the mediator complex of RNA polymerase II), and RECQL5 helicases. In this work, we describe the first rigorous meta analysis of KIX domains across all forms of life, leading to the development of KIXBASE, a predictive web server and global repository for detection and analysis of KIX domains. To our knowledge, KIXBASE comprises the largest online collection of KIX sequences, enabling assessments at the level of both sequence and structure, incorporating PSIPRED and MUSTER at the backend for further annotation and quality assessment. In addition, KIXBASE provides useful information about critical aspects of KIX domains such as their intrinsic disorder, hydrophobicity profiles, functional classification and annotation based on domain architectures. KIXBASE represents a significant enrichment of the currently annotated KIX dataset, especially in the plant kingdom, thus highlighting potential targets for biochemical characterization. The KIX webserver and database are both freely available to the scientific community, athttp://www.nipgr.res.in/kixbase/home.php.
Optical Assets of In situ Electro-assembled Platinum Black Nanolayers
Authors: Stanca S. E. , Hänschke F. , Zieger G. , Dellith J. , Ihring A. , Undisz A. , Meyer H.-G. 
Published: October 2017

AbstractOptoelectronic technology has been increasingly driven towards miniaturization. In this regard, maintaining the optical properties of the bulk materials while reducing their size is a critical need. How thin must the film be to preserve the bulk material´s optical absorbance and reflectance characteristics? This is the central question for our study of the in situ electro-assembly broad band optical absorber films of platinum in non-aqueous solution of PtCl4. By reducing the in situ constructed film to sub-visible-wavelength thicknesses, the measured reflectance in the region from the ultraviolet to the infrared remained close to that exhibited by the micrometre-width films. These platinum black films broadly absorb electromagnetic waves at a sub-incident-wavelength thickness owing to their plasmonically increased absorbance cross-section. Simulation of various incident energy electron trajectories gives insights into the electron depth through the porous platinum black of ρ = 1.6 g/cm3 and previews the optical behaviour close to the atomic thickness.
Hodgkin Lymphoma has a seasonal pattern of incidence and mortality that depends on latitude
Authors: Borchmann Sven , Müller Horst , Engert Andreas 
Published: October 2017

AbstractSeasonal variations in incidence and mortality after a Hodgkin lymphoma (HL) diagnosis have been previously described with partly conflicting results. The goal of this analysis is to provide a comprehensive analysis of these seasonal variations. In total, 41,405 HL cases diagnosed between 1973 and 2012 in the 18 Surveillance, Epidemiology, and End Results registries were included. Cosinor analysis and Cox proportional-hazards models were employed to analyze seasonality of incidence and mortality, respectively. HL shows a sinusoid seasonal incidence pattern (p < 0.001). Estimated incidence in March is 15.4% [95%-CI: 10.8-20.0] higher than in September. This sinusoid pattern is more pronounced at higher latitudes (p = 0.023). The risk of dying within the first three years after a HL diagnosis in winter is significantly increased compared to a HL diagnosis in summer at higher latitudes (HR = 1.082 [95%-CI: 1.009-1.161], p = 0.027). Furthermore, increasing northern latitude increases the additional mortality risk conferred by a diagnosis in winter (pinteraction0.033). The seasonality patterns presented here provide epidemiological evidence that Vitamin D might play a protective role in HL. Further evidence on the direct association between Vitamin D levels and the clinical course of HL needs to be collected to advance the understanding of the role of Vitamin D in HL.
Turbulent transport reduction induced by transition on radial electric field shear and curvature through amplitude and cross-phase in torus plasma
Authors: Kobayashi T. , Itoh K. , Ido T. , Kamiya K. , Itoh S.-I. , Miura Y. , Nagashima Y. , Fujisawa A. , Inagaki S. , Ida K. 
Published: October 2017

AbstractSpatiotemporal evolutions of radial electric field and turbulence are measured simultaneously in the H-mode transition, which is a prototypical example of turbulence structure formation in high-temperature plasmas. In the dynamical phase where transport barrier is established abruptly, the time-space-frequency-resolved turbulent particle flux is obtained. Here we report the validation of the mechanism of transport barrier formation quantitatively. It is found that the particle flux is suppressed predominantly by reducing density fluctuation amplitude and cross phase between density fluctuation and potential fluctuation. Both radial electric field shear and curvature are responsible for the amplitude suppression as was predicted by theory. Turbulence amplitude reduction immediately responds to the growth of the radial electric field non-uniformity and saturates, while cross phase continuously approaches zero.
Functionalized vertical GaN micro pillar arrays with high signal-to-background ratio for detection and analysis of proteins secreted from breast tumor cells
Authors: Choi Mun-Ki , Kim Gil-Sung , Jeong Jin-Tak , Lim Jung-Taek , Lee Won-Yong , Umar Ahmad , Lee Sang-Kwon 
Published: October 2017

AbstractThe detection of cancer biomarkers has recently attracted significant attention as a means of determining the correct course of treatment with targeted therapeutics. However, because the concentration of these biomarkers in blood is usually relatively low, highly sensitive biosensors for fluorescence imaging and precise detection are needed. In this study, we have successfully developed vertical GaN micropillar (MP) based biosensors for fluorescence sensing and quantitative measurement of CA15-3 antigens. The highly ordered vertical GaN MP arrays result in the successful immobilization of CA15-3 antigens on each feature of the arrays, thereby allowing the detection of an individual fluorescence signal from the top surface of the arrays owing to the high regularity of fluorophore-tagged MP spots and relatively low background signal. Therefore, our fluorescence-labeled and CA15-3 functionalized vertical GaN-MP-based biosensor is suitable for the selective quantitative analysis of secreted CA15-3 antigens from MCF-7 cell lines, and helps in the early diagnosis and prognosis of serious diseases as well as the monitoring of the therapeutic response of breast cancer patients.
Character-based DNA barcoding for authentication and conservation of IUCN Red listed threatened species of genus Decalepis (Apocynaceae)
Authors: Mishra Priyanka , Kumar Amit , Sivaraman Gokul , Shukla Ashutosh K. , Kaliamoorthy Ravikumar , Slater Adrian , Velusamy Sundaresan 
Published: October 2017

AbstractThe steno-endemic species of genusDecalepisare highly threatened by destructive wild harvesting. The medicinally important fleshy tuberous roots ofDecalepis hamiltoniiare traded as substitute, to meet the international market demand ofHemidesmus indicus. In addition, the tuberous roots of all three species ofDecalepispossess similar exudates and texture, which challenges the ability of conventional techniques alone to perform accurate species authentication. This study was undertaken to generate DNA barcodes that could be utilized in monitoring and curtailing the illegal trade of these endangered species. The DNA barcode reference library was developed in BOLD database platform for candidate barcodesrbcL,matK,psbA-trnH,ITSandITS2. The average intra-specific variations (0–0.27%) were less than the distance to nearest neighbour (0.4–11.67%) withmatKandITS. Anchoring the coding regionrbcLin multigene tiered approach, the combinationrbcL + matK + ITSyielded 100% species resolution, using the least number of loci combinations either with PAUP or BLOG methods to support a character-based approach. Species-specific SNP position (230 bp) in thematKregion that is characteristic ofD.hamiltoniicould be used to design specific assays, enhancing its applicability for direct use in CITES enforcement for distinguishing it fromH.indicus.