bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved fermentation efficiency of S. cerevisiae by changing glycolytic metabolic pathways with plasma agitation
Authors: Recek Nina , Zhou Renwu , Zhou Rusen , Te’o Valentino Setoa Junior , Speight Robert E. , Mozetič Miran , Vesel Alenka , Cvelbar Uros , Bazaka Kateryna , Ostrikov Kostya
Published: May 2018

Production of ethanol by the yeast Saccharomyces cerevisiae is a process of global importance. In these processes, productivities and yields are pushed to their maximum possible values leading to cellular stress. Transient and lasting enhancements in tolerance and performance have been obtained by genetic engineering, forced evolution, and exposure to moderate levels of chemical and/or physical stimuli, yet the drawbacks of these methods include cost, and multi-step, complex and lengthy treatment protocols. Here, plasma agitation is shown to rapidly induce desirable phenotypic changes in S. cerevisiae after a single treatment, resulting in improved conversion of glucose to ethanol. With a complex environment rich in energetic electrons, highly-reactive chemical species, photons, and gas flow effects, plasma treatment simultaneously mimics exposure to multiple environmental stressors. A single treatment of up to 10 minutes performed using an atmospheric pressure plasma jet was sufficient to induce changes in cell membrane structure, and increased hexokinase 2 activity and secondary metabolite production. These results suggest that plasma treatment is a promising strategy that can contribute to improving metabolic activity in industrial microbial strains, and thus the practicality and economics of industrial fermentations.
Improved thermoelectric performance of solid solution Cu4Sn7.5S16 through isoelectronic substitution of Se for S
Authors: Cui Jiaolin , He Tongtong , Han Zhongkang , Liu Xianglian , Du Zhengliang
Published: May 2018

Cu-Sn-S family of compounds have been considered as very competitive thermoelectric candidates in recent years due to their abundance and eco-friendliness. The first-principles calculation reveals that the density of states (DOS) increases in the vicinity of the Fermi level (Ef) upon an incorporation of Se in the Cu4Sn7.5S16−xSe
x
(x = 0–2.0) system, which indicates the occurrence of resonant states. Besides, the formation of Cu(Sn)-Se network upon the occupation of Se in S site reduces the Debye temperature from 395 K for Cu4Sn7S16 (x = 0) to 180.8 K for Cu4Sn7.5S16−xSe
x
(x = 1.0). Although the point defects mainly impact the phonon scattering, an electron-phonon interaction also bears significance in the increase in phonon scattering and the further reducion of lattice thermal conductivity at high temperatures. As a consequence, the resultant TE figure of merit (ZT) reaches 0.5 at 873 K, which is 25% higher compared to 0.4 for Cu4Sn7.5S16.
PhosContext2vec: a distributed representation of residue-level sequence contexts and its application to general and kinase-specific phosphorylation site prediction
Authors: Xu Ying , Song Jiangning , Wilson Campbell , Whisstock James C.
Published: May 2018

Phosphorylation is the most important type of protein post-translational modification. Accordingly, reliable identification of kinase-mediated phosphorylation has important implications for functional annotation of phosphorylated substrates and characterization of cellular signalling pathways. The local sequence context surrounding potential phosphorylation sites is considered to harbour the most relevant information for phosphorylation site prediction models. However, currently there is a lack of condensed vector representation for this important contextual information, despite the presence of varying residue-level features that can be constructed from sequence homology profiles, structural information, and physicochemical properties. To address this issue, we present PhosContext2vec which is a distributed representation of residue-level sequence contexts for potential phosphorylation sites and demonstrate its application in both general and kinase-specific phosphorylation site predictions. Benchmarking experiments indicate that PhosContext2vec could achieve promising predictive performance compared with several other existing methods for phosphorylation site prediction. We envisage that PhosContext2vec, as a new sequence context representation, can be used in combination with other informative residue-level features to improve the classification performance in a number of related bioinformatics tasks that require appropriate residue-level feature vector representation and extraction. The web server of PhosContext2vec is publicly available at http://phoscontext2vec.erc.monash.edu/.
Spatially organizing biochemistry: choosing a strategy to translate synthetic biology to the factory
Authors: Jakobson Christopher M. , Tullman-Ercek Danielle , Mangan Niall M.
Published: May 2018

Natural biochemical systems are ubiquitously organized both in space and time. Engineering the spatial organization of biochemistry has emerged as a key theme of synthetic biology, with numerous technologies promising improved biosynthetic pathway performance. One strategy, however, may produce disparate results for different biosynthetic pathways. We use a spatially resolved kinetic model to explore this fundamental design choice in systems and synthetic biology. We predict that two example biosynthetic pathways have distinct optimal organization strategies that vary based on pathway-dependent and cell-extrinsic factors. Moreover, we demonstrate that the optimal design varies as a function of kinetic and biophysical properties, as well as culture conditions. Our results suggest that organizing biosynthesis has the potential to substantially improve performance, but that choosing the appropriate strategy is key. The flexible design-space analysis we propose can be adapted to diverse biosynthetic pathways, and lays a foundation to rationally choose organization strategies for biosynthesis.
A Judgement Bias Test to Assess Affective State and Potential Therapeutics in a Rat Model of Chemotherapy-Induced Mucositis
Authors: George Rebecca P. , Barker Timothy H. , Lymn Kerry A. , Bigatton Dylan A. , Howarth Gordon S. , Whittaker Alexandra L.
Published: May 2018

Chemotherapy-induced mucositis is an extremely painful condition that occurs in 40–60% of patients undergoing chemotherapy. As mucositis currently has no effective treatment, and due to the self-limiting nature of the condition, the major treatment aims are to manage symptoms and limit pain with significance placed on improving patient quality of life. Rodent models are frequently used in mucositis research. These investigations typically assess pathological outcomes, yet fail to include a measure of affective state; the key therapeutic goal. Assessment of cognitive biases is a novel approach to determining the affective state of animals. Consequently, this study aimed to validate a cognitive bias test through a judgement bias paradigm to measure affective state in a rat model of chemotherapy-induced intestinal mucositis. Rats with intestinal mucositis demonstrated a negative affective state, which was partially ameliorated by analgesic administration, whilst healthy rats showed an optimistic response. This study concluded that the judgement bias test was able to evaluate the emotional state of rats with chemotherapy-induced mucositis. These findings provide a foundation for future refinement to the experimental design associated with the animal model that will expedite successful transitioning of novel therapeutics to clinical practice, and also improve humane endpoint implementation.
Naturally occurring a loss of a giant plasmid from Mycobacterium ulcerans subsp. shinshuense makes it non-pathogenic
Authors: Nakanaga Kazue , Ogura Yoshitoshi , Toyoda Atsushi , Yoshida Mitsunori , Fukano Hanako , Fujiwara Nagatoshi , Miyamoto Yuji , Nakata Noboru , Kazumi Yuko , Maeda Shinji , Ooka Tadasuke , Goto Masamichi , Tanigawa Kazunari , Mitarai Satoshi , Suzuki Koichi , Ishii Norihisa , Ato Manabu , Hayashi Tetsuya , Hoshino Yoshihiko
Published: May 2018

Mycobacterium ulcerans is the causative agent of Buruli ulcer (BU), a WHO-defined neglected tropical disease. All Japanese BU causative isolates have shown distinct differences from the prototype and are categorized as M. ulcerans subspecies shinshuense. During repeated sub-culture, we found that some M. shinshuense colonies were non-pigmented whereas others were pigmented. Whole genome sequence analysis revealed that non-pigmented colonies did not harbor a giant plasmid, which encodes elements needed for mycolactone toxin biosynthesis. Moreover, mycolactone was not detected in sterile filtrates of non-pigmented colonies. Mice inoculated with suspensions of pigmented colonies died within 5 weeks whereas those infected with suspensions of non-pigmented colonies had significantly prolonged survival (>8 weeks). This study suggests that mycolactone is a critical M. shinshuense virulence factor and that the lack of a mycolactone-producing giant plasmid makes the strain non-pathogenic. We made an avirulent mycolactone-deletion mutant strain directly from the virulent original.
Repeated administration of alpha-galactosylceramide ameliorates experimental lupus nephritis in mice
Authors: Uchida Takahiro , Nakashima Hiroyuki , Yamagata Akira , Ito Seigo , Ishikiriyama Takuya , Nakashima Masahiro , Seki Shuhji , Kumagai Hiroo , Oshima Naoki
Published: May 2018

Lupus nephritis is a crucial complication of systemic lupus erythematosus. In this study, we investigated the roles of mouse natural killer T (NKT) cells in lupus nephritis. From 24 weeks of age, NZB/NZW F1 mice were injected with alpha-galactosylceramide (α-GalCer) or vehicle once a week for four weeks. In the α-GalCer group, the levels of proteinuria and blood urea nitrogen were significantly lower than those in the vehicle group. The histological evaluation showed a decrease in glomerular immune complex deposits and an alleviation of podocyte injury. The proportion of NKT cells in the mononuclear cell (MNC) fraction in the α-GalCer group was significantly decreased in the liver, kidney, and spleen. The proliferation and cytokine production in α-GalCer-stimulated liver MNCs were markedly diminished in the α-GalCer group (anergy). The IFN-γ production in liver MNCs stimulated by concanavalin A or an anti-CD3 antibody did not differ between the two groups, whereas the IL-4 production was significantly lower in the α-GalCer group. In addition, the IgM production in CpG-oligodeoxynucleotide-stimulated spleen MNCs was significantly lower in the α-GalCer group. These results suggest that α-GalCer suppressed Th2 immune responses in NKT cells and B cell function, thereby slowing the progression of lupus nephritis.
Injectable cartilaginous template transformed BMSCs into vascularized bone
Authors: Feng Xiaoke , Li Zhiye , Wei Jianhua , Feng Zhihong , Wu Wei , Zhao Yimin
Published: May 2018

Regeneration of alveolar bone for dental implant remains a major issue, partifcularly for patients suffering from severe bone adsorption and irregular socket trauma. Recapitulating embryological development is becoming an attractive approach for engineer organ or three-dimensional tissues from stem cells. In this study, we aimed to develop an injectable “cartilaginous” graft with adequate mechanical resistance and ideal bone remodelling potential. The cartilaginous graft was composed of a particulate decellularised cartilage matrix (PDCM), chondrogenically primed bone mesenchymal stem cell (BMSC) bricks (CB), and enriched platelet-rich plasma (P) gel. In immunodeficient mice, we found that angiogenesis occurred quickly inside PDCM-CB-P constructs after implantation, thereby improving tissue survival and bone formation. In rabbit tibia bone defects around implants, we confirmed that CBs not only transformed into bone tissue rapidly, but also significantly promoted bone remodelling and replacement of PDCM, thus realising osseointegration of dental implants within 3 months. In conclusion, CBs exhibited the potential for endochondral ossification in vivo, and application of a cartilaginous template composed of PDCM, CB, and P provided a minimally-invasive, “free material residual” approach to regenerate alveolar bone tissues in vivo. This method could have applications in peri-implant bone regeneration.
Role of TREM-1 in pulmonary tuberculosis patients- analysis of serum soluble TREM-1 levels
Authors: Feng Jia-Yih , Su Wei-Juin , Pan Sheng-Wei , Yeh Yi-Chen , Lin Yung-Yang , Chen Nien-Jung
Published: May 2018

Triggering receptor expressed on myeloid cells 1 (TREM-1) amplifies inflammatory responses and is upregulated during sepsis and pulmonary infection. The association between serum soluble TREM-1 (sTREM-1) level and pulmonary tuberculosis (PTB) disease deserves investigation. In the present study, patients with PTB, latent TB infection (LTBI), and non-TB, non-LTBI subjects were prospectively enrolled and serum levels of sTREM-1, sTREM-2, and C-reactive protein (CRP) were measured. We correlated serum biomarkers and clinical presentations and treatment outcomes of PTB cases. We also utilized immunohistochemistry (IHC) to visualize TREM-1-expressing cells in lung tissues from PTB patients. A total of 86 PTB, 41 LTBI, and 20 non-TB, non-LTBI subjects were enrolled. Serum levels of sTREM-1 and CRP significantly increased in PTB patients; these higher serum levels were correlated with more advanced involvement in chest films and higher bacteria burden in sputum. In multivariate analysis, serum levels of sTREM-1 >260 pg/mL and CRP >2.6 mg/L were independent predictors for on-treatment mortality. Abundant TREM-1-expressing macrophages were identified in lung tissues from PTB samples. In conclusion, serum levels of sTREM-1 correlated with disease severity and treatment outcomes in PTB patients.
Bacterial Communities Changes during Food Waste Spoilage
Authors: Wu Shanghua , Xu Shengjun , Chen Xi , Sun Haishu , Hu Mingli , Bai Zhihui , Zhuang Guoqiang , Zhuang Xuliang
Published: May 2018

Food waste is an important component of municipal solid waste worldwide. There are various ways to treat or utilize food waste, such as, biogas fermentation, animal feed, etc. but pathogens and mycotoxins that accumulate in the process of spoilage can present a health hazard. However, spoilage of food waste has not yet been studied, and there are no reports of the bacterial communities present in this waste. In this research, food waste was collected and placed at two different temperatures. We investigated the spoilage microbiota by using culture-independent methods and measured the possible mycotoxins may appear in the spoilage process. The results showed that lactic acid bacteria are the most important bacteria in the food waste community, regardless of the temperature. Few microbial pathogens and aflatoxins were found in the spoilage process. This suggests that if food waste is stored at a relatively low temperature and for a short duration, there will be less risk for utilization.
Categorical and Geographical Separation in Science
Authors: Sienkiewicz Julian , Soja Krzysztof , Hołyst Janusz A. , Sloot Peter M. A.
Published: May 2018

We study scientific collaboration at the level of universities. The scope of this study is to answer two fundamental questions: (i) can one indicate a category (i.e., a scientific discipline) that has the greatest impact on the rank of the university and (ii) do the best universities collaborate with the best ones only? Restricting ourselves to the 100 best universities from year 2009 we show how the number of publications in certain categories correlates with the university rank. Strikingly, the expected negative trend is not observed in all cases – for some categories even positive values are obtained. After applying Principal Component Analysis we observe clear categorical separation of scientific disciplines, dividing the papers into almost separate clusters connected to natural sciences, medicine and arts and humanities. Moreover, using complex networks analysis, we give hints that the scientific collaboration is still embedded in the physical space and the number of common papers decays with the geographical distance between them.
Dimethyl fumarate induces a persistent change in the composition of the innate and adaptive immune system in multiple sclerosis patients
Authors: Montes Diaz G. , Fraussen J. , Van Wijmeersch B. , Hupperts R. , Somers V.
Published: May 2018

The effects of dimethyl fumarate (DMF) on the immune system in multiple sclerosis (MS) are not completely elucidated. In this study, an extensive immunophenotypic analysis of innate and adaptive immune cells of DMF-treated MS patients was performed. Peripheral blood immune cell phenotypes were determined using flow cytometry in a follow-up study of 12 MS patients before, after 3 and 12 months of DMF treatment and a cross-sectional study of 25 untreated and 64 DMF-treated MS patients. Direct effects of DMF on B cells were analyzed in vitro. After 12 months of DMF treatment, percentages of monocytes, natural killer cells, naive T and B cells and transitional B cells increased. Percentages of (effector) memory T cells, (non) class-switched memory B cells and double negative B cells decreased together with CD4+ T cells expressing interferon-γ (IFN-γ), granulocyte macrophage colony-stimulating factor (GM-CSF) and interleukin-17 (IL-17). DMF treatment was fully effective as of 6 months and directly induced apoptosis and decreased expression of costimulatory CD40, antigen presentation molecule MHCII and B cell activating factor receptor (BAFFR) on B cells. DMF induced a persistent change of the immune system of MS patients, directly induced apoptosis and reduced expression of functional markers on B cells.
Excitation and injury of adult ventricular cardiomyocytes by nano- to millisecond electric shocks
Authors: Semenov Iurii , Grigoryev Sergey , Neuber Johanna U. , Zemlin Christian W. , Pakhomova Olga N. , Casciola Maura , Pakhomov Andrei G.
Published: May 2018

Intense electric shocks of nanosecond (ns) duration can become a new modality for more efficient but safer defibrillation. We extended strength-duration curves for excitation of cardiomyocytes down to 200 ns, and compared electroporative damage by proportionally more intense shocks of different duration. Enzymatically isolated murine, rabbit, and swine adult ventricular cardiomyocytes (VCM) were loaded with a Ca2+ indicator Fluo-4 or Fluo-5N and subjected to shocks of increasing amplitude until a Ca2+ transient was optically detected. Then, the voltage was increased 5-fold, and the electric cell injury was quantified by the uptake of a membrane permeability marker dye, propidium iodide. We established that: (1) Stimuli down to 200-ns duration can elicit Ca2+ transients, although repeated ns shocks often evoke abnormal responses, (2) Stimulation thresholds expectedly increase as the shock duration decreases, similarly for VCMs from different species, (3) Stimulation threshold energy is minimal for the shortest shocks, (4) VCM orientation with respect to the electric field does not affect the threshold for ns shocks, and (5) The shortest shocks cause the least electroporation injury. These findings support further exploration of ns defibrillation, although abnormal response patterns to repetitive ns stimuli are of a concern and require mechanistic analysis.
The degree of prevalence of similarity between outer tropical cyclone rainbands and squall lines
Authors: Yu Cheng-Ku , Lin Che-Yu , Cheng Lin-Wen , Luo Jhang-Shuo , Wu Chun-Chieh , Chen Ying
Published: May 2018

Tropical cyclone rainbands (TCRs) are not only one of the most striking and persistent features of tropical cyclones (TCs) but also one of the major causes for extreme floods as TCs approach or encounter the land area. TCRs have been traditionally considered as manifestations of atmospheric waves initiated near the eyewall or close to the TC center. However, the limited evidence from recent studies showed the possibility for TCRs to develop squall-line-like characteristics in the outer region of TCs. In this study, the degree of the prevalence for this similarity is explored by radar and surface observations from a large set of 50 outer TCRs associated with 22 TCs as they approached Taiwan. The results indicate that around 58% of outer TCRs are similar to squall lines. These outer TCRs are generally characterized by convective precipitation, an obvious convergence zone between the band-relative rear-to-front flow and front-to-rear flow at low levels, either frontward or rearward tilting updrafts, and a surface cold pool signature. The frequent similarity between the outer TCRs and squall lines documented provides important insights into the formation of organized, heavy precipitation associated with TCs.
Homodimerisation-independent cleavage of dsRNA by a pestiviral nicking endoribonuclease
Authors: Lussi Carmela , Sauter Kay-Sara , Schweizer Matthias
Published: May 2018

The glycoprotein Erns plays a central role in the biology of the pestivirus bovine viral diarrhea virus (BVDV). This soluble endonuclease mediates the escape from an interferon (IFN) response in the infected fetus, thereby permitting the establishment of persistent infection. Viral single-stranded (ss) and double-stranded (ds) RNA act as potent IFN inducing signals and we previously showed that Erns efficiently cleaves these substrates, thereby inhibiting an IFN response that is crucial for successful fetal infection. Considering that a large variety of RNases and DNases require dimerisation to cleave double-stranded substrates, the activity of Erns against dsRNA was postulated to depend on homodimer formation mediated by disulfide bonds involving residue Cys171. Here, we show that monomeric Erns is equally able to cleave dsRNA and to inhibit dsRNA-induced IFN synthesis as the wild-type form. Furthermore, both forms were able to degrade RNA within a DNA/RNA- as well as within a methylated RNA/RNA-hybrid, with the DNA and the methylated RNA strand being resistant to degradation. These results support our model that Erns acts as ‘nicking endoribonuclease’ degrading ssRNA within double-stranded substrates. This efficiently prevents the activation of IFN and helps to maintain a state of innate immunotolerance in persistently infected animals.
Patterns of species richness and the center of diversity in modern Indo-Pacific larger foraminifera
Authors: Förderer Meena , Rödder Dennis , Langer Martin R.
Published: May 2018

Symbiont-bearing Larger Benthic Foraminifera (LBF) are ubiquitous components of shallow tropical and subtropical environments and contribute substantially to carbonaceous reef and shelf sediments. Climate change is dramatically affecting carbonate producing organisms and threatens the diversity and structural integrity of coral reef ecosystems. Recent invertebrate and vertebrate surveys have identified the Coral Triangle as the planet’s richest center of marine life delineating the region as a top priority for conservation. We compiled and analyzed extensive occurrence records for 68 validly recognized species of LBF from the Indian and Pacific Ocean, established individual range maps and applied Minimum Convex Polygon (MCP) and Species Distribution Model (SDM) methodologies to create the first ocean-wide species richness maps. SDM output was further used for visualizing latitudinal and longitudinal diversity gradients. Our findings provide strong support for assigning the tropical Central Indo-Pacific as the world’s species-richest marine region with the Central Philippines emerging as the bullseye of LBF diversity. Sea surface temperature and nutrient content were identified as the most influential environmental constraints exerting control over the distribution of LBF. Our findings contribute to the completion of worldwide research on tropical marine biodiversity patterns and the identification of targeting centers for conservation efforts.
An orthogonal system for heterologous expression of actinobacterial lasso peptides in Streptomyces hosts
Authors: Mevaere Jimmy , Goulard Christophe , Schneider Olha , Sekurova Olga N. , Ma Haiyan , Zirah Séverine , Afonso Carlos , Rebuffat Sylvie , Zotchev Sergey B. , Li Yanyan
Published: May 2018

Lasso peptides are ribosomally synthesized and post-translationally modified peptides produced by bacteria. They are characterized by an unusual lariat-knot structure. Targeted genome scanning revealed a wide diversity of lasso peptides encoded in actinobacterial genomes, but cloning and heterologous expression of these clusters turned out to be problematic. To circumvent this, we developed an orthogonal expression system for heterologous production of actinobacterial lasso peptides in Streptomyces hosts based on a newly-identified regulatory circuit from Actinoalloteichus fjordicus. Six lasso peptide gene clusters, mainly originating from marine Actinobacteria, were chosen for proof-of-concept studies. By varying the Streptomyces expression hosts and a small set of culture conditions, three new lasso peptides were successfully produced and characterized by tandem MS. The newly developed expression system thus sets the stage to uncover and bioengineer the chemo-diversity of actinobacterial lasso peptides. Moreover, our data provide some considerations for future bioprospecting efforts for such peptides.
Optimum Sowing Date and Genotype Testing for Upland Rice Production in Brazil
Authors: Ferrari Samuel , Pagliari Paulo , Trettel Juliana
Published: May 2018

A better understanding of widespread agricultural practices adopted in the region of Ribeira Valley, São Paulo, Brazil for upland rice (Oryza sativa L.) production is needed. The objectives of this study were to determine the optimum sowing date and highest yielding genotypes for rice production. Treatments included four upland rice genotypes (ANA 5011, AN-Cambará, Moti-Amarelo, and Moti-Branco) and four sowing dates (October, November, December, and January) in 2011 and 2012. The results of the study showed that genotype ANA 5011 had the earliest maturity, while the Moti genotypes had the latest maturity in all sowing dates. The Moti genotypes were found to have greater plant height and 1,000-grain weight than the other two genotypes. In contrast, the Moti genotypes had fewer panicles m−2, fewer total filled and total numbers of spikelets panicle−1, and lower final yield. The genotype AN-Cambará had the highest number of tillers, filled and total number of spikelets panicle−1, panicle m−2, and the highest yield. Sowing in either November or December was found to be the most suitable dates for rice cultivation for all genotypes. In conclusion, the AN-Cambará genotype was found to have the highest yield potential for the region among all genotypes studied.
Daily morning light therapy is associated with an increase in choroidal thickness in healthy young adults
Authors: Read Scott A. , Pieterse Emily C. , Alonso-Caneiro David , Bormann Rebekah , Hong Seentinie , Lo Chai-Hoon , Richer Rhiannon , Syed Atif , Tran Linda
Published: May 2018

Ambient light exposure is one environmental factor thought to play a role in the regulation of eye growth and refractive error development, and choroidal thickness changes have also been linked to longer term changes in eye growth. Therefore in this study we aimed to examine the influence of a 1-week period of morning light therapy upon choroidal thickness. Twenty two healthy young adult subjects had a series of macular choroidal thickness measurements collected with spectral domain optical coherence tomography before, and then following a 7-day period of increased daily light exposure. Increased light exposure was delivered through the use of commercially available light therapy glasses, worn for 30 minutes in the morning each day. A significant increase in subfoveal choroidal thickness (mean increase of +5.4 ± 10.3 µm) was found following 7-days of increased daily light exposure (p = 0.02). An increase in choroidal thickness was also observed associated with light therapy across the central 5 mm macular region. This study provides the first evidence in the human eye that daily morning light therapy results in small magnitude but statistically significant increases in choroidal thickness. These changes may have implications for our understanding of the impact of environmental factors upon eye growth.
Evapotranspiration and favorable growing degree-days are key to tree height growth and ecosystem functioning: Meta-analyses of Pacific Northwest historical data
Authors: Liu Yang , El-Kassaby Yousry A.
Published: May 2018

While temperature and precipitation comprise important ecological filtering for native ranges of forest trees and are predisposing factors underlying forest ecosystem dynamics, the extent and severity of drought raises reasonable concerns for carbon storage and species diversity. Based on historical data from common garden experiments across the Pacific Northwest region, we developed non-linear niche models for height-growth trajectories of conifer trees at the sapling stage using annual or seasonal climatic variables. The correlations between virtual tree height for each locality and ecosystem functions were respectively assessed. Best-fitted models were composed of two distinct components: evapotranspiration and the degree-days disparity for temperature regimes between 5 °C and 18 °C (effective temperature sum and growth temperature, respectively). Tree height prediction for adaptive generalists (e.g., Pinus monticola, Thuja plicata) had smaller residuals than for specialists (e.g., Pinus contorta, Pseudotsuga menziesii), albeit a potential confounding factor – tree age. Discernably, there were linearly positive patterns between tree height growth and ecosystem functions (productivity, biomass and species diversity). Additionally, there was a minor effect of tree diversity on height growth in coniferous forests. This study uncovers the implication of key ecological filtering and increases our integrated understanding of how environmental cues affect tree stand growth, species dominance and ecosystem functions.
Genotype by Yield*Trait (GYT) Biplot: a Novel Approach for Genotype Selection based on Multiple Traits
Authors: Yan Weikai , Frégeau-Reid Judith
Published: May 2018

Genotype selection based on multiple traits is a key issue in plant breeding; it has been dependent on setting a subjective weight for each trait in index selection and a subjective truncation point for each trait in independent culling, and the weights and truncation points can be highly subjective. In this paper we proposed and demonstrated a novel approach for genotype selection based on multiple traits, the genotype by yield*trait (GYT) biplot, where “trait” can be any breeding objective other than yield; it may be an agronomic trait, a grain quality, processing quality, or nutritional quality trait, or a disease resistance. The GYT biplot ranks genotypes based on their levels in combining yield with other target traits and at the same time shows their trait profiles, i.e., their strengths and weaknesses. Compared to existing methods, this approach is graphical, objective, effective, and straightforward. Underlying the GYT biplot approach is the paradigm shift that genotypes should be evaluated by their levels in combining yield with other traits as opposed to by their levels in individual traits. An oat dataset from multi-year multi-locations trials was used to demonstrate the GYT biplot approach.
Transient and local two-phase heat transport at macro-scales to nano-scales
Authors: Mehrvand Mehrdad , Putnam Shawn A.
Published: May 2018

Two-phase cooling has become a promising method for improving the sustainability and efficiency of high energy-density and power-density devices. Fundamentally, however, two-phase thermal transport is not well understood for local, transient processes, especially at critical to near-critical heat fluxes at the macro, micro, and nano-scales. Here we report spatiotemporal characterization of the single-bubble ebullition cycle in a hot-spot heating configuration with heat fluxes approaching 3 kW cm−2. In particular, we experimentally reconstruct the spatiotemporal heat transfer coefficient in terms of its proportionality at both the macro-scale (l >> 1 μm) and the micro-to-nanoscale (l < 1 μm). We show that the maximum rates of heat transfer occur during the microlayer evaporation stage of the ebullition cycle, corresponding to critical maxima in the heat transfer coefficient of ~160 ± 40 kW m−2 K−1 and ~5300 ± 300 kW m−2 K−1 at the macro-scale and micro-to-nanoscale, respectively.
The asthma mobile health study, smartphone data collected using ResearchKit
Authors: Chan Yu-Feng Yvonne , Bot Brian M. , Zweig Micol , Tignor Nicole , Ma Weiping , Suver Christine , Cedeno Rafhael , Scott Erick R. , Gregory Hershman Steven , Schadt Eric E. , Wang Pei
Published: May 2018

Widespread adoption of smart mobile platforms coupled with a growing ecosystem of sensors including passive location tracking and the ability to leverage external data sources create an opportunity to generate an unprecedented depth of data on individuals. Mobile health technologies could be utilized for chronic disease management as well as research to advance our understanding of common diseases, such as asthma. We conducted a prospective observational asthma study to assess the feasibility of this type of approach, clinical characteristics of cohorts recruited via a mobile platform, the validity of data collected, user retention patterns, and user data sharing preferences. We describe data and descriptive statistics from the Asthma Mobile Health Study, whereby participants engaged with an iPhone application built using Apple's ResearchKit framework. Data from 6346 U.S. participants, who agreed to share their data broadly, have been made available for further research. These resources have the potential to enable the research community to work collaboratively towards improving our understanding of asthma as well as mobile health research best practices.
Ratiometric fluorescence detection of trace water in organic solvents based on aggregation-induced emission enhanced Cu nanoclusters
Authors: Song Shanliang , Zhang Yuping , Yang Yizhou , Wang Chuanxi , Zhou Ying , Zhang Chuan , Zhao Yueqi , Yang Minghui , Lin Quan
Published: May 2018

A novel dual-emission fluorescent nanocomposite material, CDs/Cu NCs, was fabricated for detecting trace water in organic solvents (DMSO, DMF, THF, and ACN).
Detection of cystic fibrosis transmembrane conductance regulator ΔF508 gene mutation using a paper-based nucleic acid hybridization assay and a smartphone camera
Authors: Malhotra Karan , Noor M. Omair , Krull Ulrich J.
Published: May 2018

QD-FRET nucleic acid bioassay for the detection of CFTR ΔF508 gene mutation using a paper-based platform and smartphone imaging.
Production and characterization of a single-chain variable fragment-alkaline phosphatase fusion protein for glycocholic acid detection in a one-step enzyme-linked immunosorbent assay
Authors: Cui Xiping , He Qiyi , Shen Ding , Jiang Zhengyun , Chen Yingshan , Zhao Suqing , Hammock Bruce D.
Published: May 2018

One-step enzyme-linked immunosorbent assay for glycocholic acid based on single-chain variable fragment-alkaline phosphatase fusion protein.
Quantification of combined color and shade changes in colorimetry and image analysis: water pH measurement as an example
Authors: Wang Ying , Liu Yue , Liu Wen , Tang Wenhao , Shen Li , Li Zhilin , Fan Meikun
Published: May 2018

Color quantization which contains both color and shade changes with high accuracy has been achieved.
Polystyrene-impregnated paper substrates for direct mass spectrometric analysis of proteins and peptides in complex matrices
Authors: Li Jin , Zheng Yajun , Mi Wei , Muyizere Theoneste , Zhang Zhiping
Published: May 2018

Direct analysis of proteins and peptides in complex matrices is of significant importance for biological, medicinal and toxicological studies.
Reconstitution of full-length P450BM3 with an artificial metal complex by utilising the transpeptidase Sortase A
Authors: Omura Keita , Aiba Yuichiro , Onoda Hiroki , Stanfield Joshua Kyle , Ariyasu Shinya , Sugimoto Hiroshi , Shiro Yoshitsugu , Shoji Osami , Watanabe Yoshihito
Published: May 2018

Mn-substituted full-length P450BM3 was constructed by transpeptidase Sortase A, showing catalytic hydroxylation of aliphatic C–H bonds with molecular oxygen.
CsPbX3/Cs4PbX6 core/shell perovskite nanocrystals
Authors: Jia Chao , Li Hui , Meng Xianwei , Li Hongbo
Published: May 2018

The synthesis of 3D/0D core/shell lead halide perovskite nanocrystals has been realized using the seeded growth approach for the first time.
Bimodal coordination of fused arenes to a Pd3 cluster site
Authors: Sugawa Tsuyoshi , Yamamoto Koji , Murahashi Tetsuro
Published: May 2018

We report bimodal coordination of fused arenes to a Pd3 cluster site. The oxidative π-addition mode of anthracene and tetracene as well as the π-coordination mode of triphenylene and fluoranthene were identified.
2D organic–inorganic nanosheets via self-assembly of a pillar[6]arene and polyoxometalate for enhanced degradation efficiency
Authors: Cheng Ni , Chen Yong , Wu Xuan , Liu Yu
Published: May 2018

Pillar[6]arene induced the aggregation of 2D nanosheets and enhanced the degradation efficiency of the polyoxometalate.
Facile synthesis of Pd@Ru nanoplates with controlled thickness as efficient catalysts for hydrogen evolution reaction
Authors: Han Yu , Yan Yucong , Wu Zhemin , Jiang Yi , Li Xiao , Xu Qingfeng , Yang Xiaofang , Zhang Hui , Yang Deren
Published: May 2018

Pd@Ru nanoplates with controlled thickness were synthesized and exhibited substantially enhanced properties for the hydrogen evolution reaction relative to commercial catalysts.
Effective photocatalytic and bifunctional electrocatalytic materials based on Keggin arsenomolybdates and different transition metal capped assemblies
Authors: Li Feng-rui , Lv Jing-hua , Yu Kai , Zhang Mao-lin , Wang Kun-peng , Meng Fan-xue , Zhou Bai-bin
Published: May 2018

V, Co, and Cu were introduced into {AsMo12} system to build three Keggin derivatives with different caps, which show excellent photocatalytic activity and bifunctional electrocatalytic behavior.
Mediation of band structure for BiOBrxI1−x hierarchical microspheres of multiple defects with enhanced visible-light photocatalytic activity
Authors: Cai Lei , Zhang Guoqiang , Zhang Yanfeng , Wei Yu
Published: May 2018

The band edge positions are of vital importance due to their direct effect on the redox reactions occurring at the surface of the samples.
The catalytic activity and mechanism of oxygen reduction reaction on P-doped MoS2
Authors: Zhang Xiaoming , Shi Shaodong , Gu Tianwei , Li Leyi , Yu Shansheng
Published: May 2018

The high density of electrons localized at the P–Mo bridge site limits the ORR activity of P-MoS2 through the strong interaction with H atom.
Nano-phase separation and structural ordering in silica-rich mixed network former glasses
Authors: Liu Hao , Youngman Randall E. , Kapoor Saurabh , Jensen Lars R. , Smedskjaer Morten M. , Yue Yuanzheng
Published: May 2018

In the B2O3–Al2O3–SiO2–P2O5glass system, the structural heterogeneity leads to nano-phase separation and structural ordering upon cooling and heating, respectively.
Crystallographic and spectroscopic evidence for intrinsic distortion in the disordered crystal β-NaGdF4
Authors: Jin Jianning , Yu Hua , Guo Liying , Liu Jinjin , Wu Bing , Guo Yuao , Fu Yuting , Zhao Lijuan
Published: May 2018

The local structure of β-NaGdF4 which is a kind of optical material with disorder structure, is clearly depicted by EXAFS.
Dissociation channels, collisional energy transfer, and multichannel coupling effects in the thermal decomposition of CH3F
Authors: Matsugi Akira
Published: May 2018

The multichannel character of the thermal decomposition of CH3F and its dependency on the collisional energy transfer model are elucidated.
Influence of quasi-particle density over polaron mobility in armchair graphene nanoribbons
Authors: Silva Gesiel Gomes , da Cunha Wiliam Ferreira , de Sousa Junior Rafael Timóteo , Almeida Fonseca Antonio Luciano , Ribeiro Júnior Luiz Antônio , e Silva Geraldo Magela
Published: May 2018

An important aspect concerning the performance of armchair graphene nanoribbons (AGNRs) as materials for conceiving electronic devices is related to the mobility of charge carriers in these systems.
Dynamic Monte Carlo algorithm for out-of-equilibrium processes in colloidal dispersions
Authors: Corbett Daniel , Cuetos Alejandro , Dennison Matthew , Patti Alessandro
Published: May 2018

Field-induced isotropic-to-nematic phase transition of colloidal rods studied with Dynamic Monte Carlo simulations.
Density functional study of the phase stability and Raman spectra of Yb2O3, Yb2SiO5 and Yb2Si2O7 under pressure
Authors: Ogawa Takafumi , Otani Noriko , Yokoi Taishi , Fisher Craig A. J. , Kuwabara Akihide , Moriwake Hiroki , Yoshiya Masato , Kitaoka Satoshi , Takata Masasuke
Published: May 2018

The phase stability and Raman spectra of Yb2O3, Yb2SiO5 and Yb2Si2O7 under hydrostatic pressure are investigated using density functional theory calculations.
Doped boron nitride surfaces: potential metal free bifunctional catalysts for non-aqueous Li–O2 batteries
Authors: Chowdhury Chandra , Datta Ayan
Published: May 2018

Novel cathode catalysts for the practical execution of lithium–oxygen (Li–O2) batteries are predicted.
Complexation-assisted reduction: complexes of glutaroimide-dioxime with tetravalent actinides (Np(iv) and Th(iv))
Authors: Zhang Zhicheng , Parker Bernard F. , Lohrey Trevor D. , Teat Simon J. , Arnold John , Rao Linfeng
Published: May 2018

Glutaroimide-dioxime forms strong complexes with Np(iv) and Th(iv) in aqueous solution and in crystals. The formation of Np(iv) complexes from initial Np(v) is interpreted by a complexation-assisted reduction mechanism.
Promoting effect of nickel hydroxide on the electrocatalytic performance of Pt in alkaline solution
Authors: Wang Yao , Qin Yuchen , Zhang Xin , Dai Xiaoping , Zhuo Hongying , Luan Chenglong , Jiang Yan , Zhao Huihui , Wang Hai , Huang Xingliang
Published: May 2018

The introduction of Ni(OH)2 improved the electrocatalytic performance of Pt/Ni(OH)2/N–CNTs for MOR via accelerating water dissociation and oxidizing carbonaceous poison.
Field influence on the slow magnetic relaxation of nickel-based single ion magnets
Authors: Titiš Ján , Rajnák Cyril , Valigura Dušan , Boča Roman
Published: May 2018

A mononuclear complex, [Ni(pydca)(dmpy)]·H2O, exhibits a slow magnetic relaxation under an applied magnetic field with manifold relaxation channels. With an external field of 0.6 T, the low-frequency channel is the dominating relaxation path yielding a relaxation time of 322 ms at 2.0 K. At 1.2 T the relaxation time is as slow as 876 ms.
Important cytotoxic and cytostatic effects of new copper(i)–phosphane compounds with N,N, N,O and N,S bidentate ligands
Authors: Morais Tânia S. , Jousseaume Yann , M. Piedade M. Fátima , Roma-Rodrigues Catarina , Fernandes Alexandra R. , Marques Fernanda , Villa de Brito Maria J. , Garcia M. Helena
Published: May 2018

Synthesis of new phosphane–Cu(i) complexes with bidentate ligands displaying cytotoxic and cytostatic effects that make them attractive as anticancer agents.
On verdigris, part II: synthesis of the 2-1-5 phase, Cu3(CH3COO)4(OH)2·5H2O, by long-term crystallisation from aqueous solution at room temperature
Authors: Bette Sebastian , Kremer Reinhard K. , Eggert Gerhard , Dinnebier Robert E.
Published: May 2018

Long-term crystallisation led to the formation of the 2-1-5 verdigris phase (Cu3(CH3COO)4(OH)2·5H2O). The crystal structure, as well as magnetic, thermal and spectroscopic properties, was investigated.
Bacterial bioreporter detection of arsenic associated with iron oxides
Authors: van Genuchten Case M. , Finger Amanda , van der Meer Jan R. , Peña Jasquelin
Published: May 2018

The mineral properties that govern the detection of surface-bound As(v) by bacterial bioreporters are identified.
Reaction of bisphenol A with synthetic and commercial MnOx(s): spectroscopic and kinetic study
Authors: Shaikh Nabil , Zhang Huichun , Rasamani Kowsalya , Artyushkova Kateryna , Ali Abdul-Mehdi S. , Cerrato José M.
Published: May 2018

The reaction of bisphenol A (BPA) using laboratory synthesized (Syn-MnOx) and commercially available (Com-MnOx) MnOx(s) media was investigated using spectroscopic and aqueous chemistry methods.
Hydroxyl radical scavenging by cerium oxide nanoparticles improves Arabidopsis salinity tolerance by enhancing leaf mesophyll potassium retention
Authors: Wu Honghong , Shabala Lana , Shabala Sergey , Giraldo Juan Pablo
Published: May 2018

Nanoceria ROS scavenging is a key tool for understanding and improving plant tolerance to salinity, a stress that severely limits crop yield worldwide.
Natural reaction channels in H + CHD3 → H2 + CD3
Authors: Ellerbrock Roman , Mantheuwe Uwe
Published: May 2018

Natural reaction channels control the mode-specific chemistry of methane and its isotopomeres.
Correction: Protection of COOH and OH groups in acid, base and salt free reactions
Authors: Zhu Xiaotao , Qian Bo , Wei Rongbiao , Huang Jian-Dong , Bao Hongli
Published: May 2018

Correction for ‘Protection of COOH and OH groups in acid, base and salt free reactions’ by Xiaotao Zhu et al., Green Chem., 2018, 20, 1444–1447.
Label-free, high-throughput detection ofP. falciparuminfection in sphered erythrocytes with digital holographic microscopy
Authors: Ugele Matthias , Weniger Markus , Leidenberger Maria , Huang Yiwei , Bassler Michael , Friedrich Oliver , Kappes Barbara , Hayden Oliver , Richter Lukas
Published: May 2018

Label-free, high-throughput holographic microscopy enables malaria detection at the ring stage and distinction ofP. falciparumlife cycle stages.
A lighter-than-water deep eutectic-solvent-based dispersive liquid-phase microextraction method in a U-shaped homemade device
Authors: Jouyban Abolghasem , Farajzadeh Mir Ali , Afshar Mogaddam Mohammad Reza
Published: May 2018

A new microextraction method, termed glass-filter-based dispersive liquid-phase microextraction using a lighter-than-water deep eutectic solvent, was developed for the extraction and preconcentration of different classes of pesticides from fruit juice and vegetable samples.
A PDDA functionalized nitrogen and sulphur doped graphene composite as the counter electrode for dye-sensitized solar cells
Authors: Raji Karunagaran Jhanani , Janakiraman Manokaran , Jonna Narendranath , Natesan Balasubramanian , Nallamuthu Prabhu
Published: May 2018

Poly-diallyldimethylammonium chloride (PDDA) functionalized nitrogen and sulphur doped graphene (SN-Gp) was synthesized as a Pt-free counter electrode (CE) for developing highly efficient and low cost dye sensitized solar cells (DSSCs).
Highly uniform supramolecular nano-films derived from carbazole-containing perylene diimide via surface-supported self-assembly and their electrically bistable memory behavior
Authors: Khan Qudrat Ullah , Tian Guofeng , Bao Lin , Qi Shengli , Wu Dezhen
Published: May 2018

For electrical memory applications, two perylenetetracarboxylic diimide (PDI) derivatives were synthesized and their surface-supported self-assembly behaviors were investigated.
Co-sensitization of Ru(ii) complex with terthiophene-based D–π–π–A metal-free organic dyes for highly efficient dye-sensitized solar cells: influence of anchoring group on molecular geometry and photovoltaic performance
Authors: Elmorsy Mohamed R. , Su Rui , Fadda Ahmed A. , Etman H. A. , Tawfik Eman H. , El-Shafei Ahmed
Published: May 2018

In this work, we studied the photovoltaic performance of two novel metal-free organic dyes carrying the same donor but with different anchoring moieties.
Active targeted dual-modal CT/MR imaging of VX2 tumors using PEGylated BaGdF5 nanoparticles conjugated with RGD
Authors: Wang Tao , Jia Guorong , Cheng Chao , Wang Qiuhu , Li Xiao , Liu Yanyan , He Chaofan , Chen Luguang , Sun Gaofeng , Zuo Changjing
Published: May 2018

RGD-PEG-BaGdF5 NPs can be used as CT/MR dual-modality contrast agents of solid tumors via the RGD-mediated tumor vasculature targeting strategy.