bluuebunny/crossref_metadata_2025 huggingface dataset:
A large dataset of protein dynamics in the mammalian heart proteome
Authors: Lau Edward , Cao Quan , Ng Dominic C.M. , Bleakley Brian J. , Dincer T. Umut , Bot Brian M. , Wang Ding , Liem David A. , Lam Maggie P.Y. , Ge Junbo , Ping Peipei
Published: March 2016

Protein stability is a major regulatory principle of protein function and cellular homeostasis. Despite limited understanding on mechanisms, disruption of protein turnover is widely implicated in diverse pathologies from heart failure to neurodegenerations. Information on global protein dynamics therefore has the potential to expand the depth and scope of disease phenotyping and therapeutic strategies. Using an integrated platform of metabolic labeling, high-resolution mass spectrometry and computational analysis, we report here a comprehensive dataset of the in vivo half-life of 3,228 and the expression of 8,064 cardiac proteins, quantified under healthy and hypertrophic conditions across six mouse genetic strains commonly employed in biomedical research. We anticipate these data will aid in understanding key mitochondrial and metabolic pathways in heart diseases, and further serve as a reference for methodology development in dynamics studies in multiple organ systems.
The FAIR Guiding Principles for scientific data management and stewardship
Authors: Wilkinson Mark D. , Dumontier Michel , Aalbersberg IJsbrand Jan , Appleton Gabrielle , Axton Myles , Baak Arie , Blomberg Niklas , Boiten Jan-Willem , da Silva Santos Luiz Bonino , Bourne Philip E. , Bouwman Jildau , Brookes Anthony J. , Clark Tim , Crosas Mercè , Dillo Ingrid , Dumon Olivier , Edmunds Scott , Evelo Chris T. , Finkers Richard , Gonzalez-Beltran Alejandra , Gray Alasdair J.G. , Groth Paul , Goble Carole , Grethe Jeffrey S. , Heringa Jaap , ’t Hoen Peter A.C , Hooft Rob , Kuhn Tobias , Kok Ruben , Kok Joost , Lusher Scott J. , Martone Maryann E. , Mons Albert , Packer Abel L. , Persson Bengt , Rocca-Serra Philippe , Roos Marco , van Schaik Rene , Sansone Susanna-Assunta , Schultes Erik , Sengstag Thierry , Slater Ted , Strawn George , Swertz Morris A. , Thompson Mark , van der Lei Johan , van Mulligen Erik , Velterop Jan , Waagmeester Andra , Wittenburg Peter , Wolstencroft Katherine , Zhao Jun , Mons Barend
Published: March 2016

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.
Development of a double-antibody sandwich ELISA for rapid detection of Bacillus Cereus in food
Authors: Zhu Longjiao , He Jing , Cao Xiaohan , Huang Kunlun , Luo Yunbo , Xu Wentao
Published: March 2016

Bacillus cereus is increasingly recognized as one of the major causes of food poisoning in the industrialized world. In this paper, we describe a sensitive double-antibody sandwich enzyme-linked immunosorbent assay (ELISA) that was developed for rapid detection of B. cereus in food to minimize the risk of contamination. The polyclonal antibody (pAb) and monoclonal antibodies (mAbs) specific to B. cereus were generated from rabbit antiserum and mouse ascites, respectively, using the octanoic acid/saturated ammonium sulfate precipitation method and protein A-sepharose columns. IgG-isotype mAbs were specially developed to undergo a novel peripheral multiple sites immunization for rapid gain of hybridomas and a subtractive screen was used to eliminate cross reactivity with closely related species such as Bacillus thuringiensis, B. subtilis, B. licheniformis and B. perfringens. The linear detection range of the method was approximately 1 × 104–2.8 × 106 cells/mL with a detection limit (LOD) of 0.9 × 103 cells/mL. The assay was able to detect B. cereus when the samples were prepared in meat with various pathogens. The newly developed analytical method provides a rapid method to sensitively detect B. cereus in food specimens.
Clinical Practice Pattern of Immediate Intravesical Chemotherapy following Transurethral Resection of a Bladder Tumor in Korea: National Health Insurance Database Study
Authors: Seo Gi Hyeon , Kim Jae Heon , Ku Ja Hyeon
Published: March 2016

We evaluated the frequency and practice pattern of immediate postoperative intravesical chemotherapy (PIC) after transurethral resection of a bladder tumor (TURBT) in suspected non-muscle-invasive bladder cancer (NMIBC). Information from the Health Insurance Review and Assessment Service database from January 1, 2008 to December 31, 2013 was used. Patients with bladder cancer who received TURBT were considered as the cases (37,941 patients and 59,568 cases). The time of PIC after TURBT, types of PIC regimens, and the potential effect of PIC on the delay for additional treatment were analyzed. The study cohort included 23,726 subjects and 30,473 cases with a mean age of 66.8 ± 12.0 years, including 19,362 (81.6%) male patients. The rate of immediate PIC was 11.0% of cases (3,359 cases). There was significant difference in the frequency rate of additional treatment among patients with immediate PIC and patients without immediate PIC within 1 year from the first TURBT (15.2% vs 16.6%, p = 0.035). However, no difference was revealed for whole observational period (33.7% vs 34.5%, p = 0.373). The frequency rate of immediate PIC after TURBT for suspected NMIBC was low in real clinical practice. More efforts are needed to improve the usage rate of PIC after TURBT for suspected NMIBC.
A generic screening platform for inhibitors of virus induced cell fusion using cellular electrical impedance
Authors: Watterson Daniel , Robinson Jodie , Chappell Keith J. , Butler Mark S. , Edwards David J. , Fry Scott R. , Bermingham Imogen M. , Cooper Matthew A. , Young Paul R.
Published: March 2016

Fusion of the viral envelope with host cell membranes is an essential step in the life cycle of all enveloped viruses. Despite such a clear target for antiviral drug development, few anti-fusion drugs have progressed to market. One significant hurdle is the absence of a generic, high-throughput, reproducible fusion assay. Here we report that real time, label-free measurement of cellular electrical impedance can quantify cell-cell fusion mediated by either individually expressed recombinant viral fusion proteins, or native virus infection. We validated this approach for all three classes of viral fusion and demonstrated utility in quantifying fusion inhibition using antibodies and small molecule inhibitors specific for dengue virus and respiratory syncytial virus.
Development of a method for detection and quantification of B. brongniartii and B. bassiana in soil
Authors: Canfora L. , Malusà E. , Tkaczuk C. , Tartanus M. , Łabanowska B.H. , Pinzari F.
Published: March 2016

A culture independent method based on qPCR was developed for the detection and quantification of two fungal inoculants in soil. The aim was to adapt a genotyping approach based on SSR (Simple Sequence Repeat) marker to a discriminating tracing of two different species of bioinoculants in soil, after their in-field release. Two entomopathogenic fungi, Beauveria bassiana and B. brongniartii, were traced and quantified in soil samples obtained from field trials. These two fungal species were used as biological agents in Poland to control Melolontha melolontha (European cockchafer), whose larvae live in soil menacing horticultural crops. Specificity of SSR markers was verified using controls consisting of: i) soil samples containing fungal spores of B. bassiana and B. brongniartii in known dilutions; ii) the DNA of the fungal microorganisms; iii) soil samples singly inoculated with each fungus species. An initial evaluation of the protocol was performed with analyses of soil DNA and mycelial DNA. Further, the simultaneous detection and quantification of B. bassiana and B. brongniartii in soil was achieved in field samples after application of the bio-inoculants. The protocol can be considered as a relatively low cost solution for the detection, identification and traceability of fungal bio-inoculants in soil.
Pharyngeal pumping in Caenorhabditis elegans depends on tonic and phasic signaling from the nervous system
Authors: Trojanowski Nicholas F. , Raizen David M. , Fang-Yen Christopher
Published: March 2016

Rhythmic movements are ubiquitous in animal locomotion, feeding and circulatory systems. In some systems, the muscle itself generates rhythmic contractions. In others, rhythms are generated by the nervous system or by interactions between the nervous system and muscles. In the nematode Caenorhabditis elegans, feeding occurs via rhythmic contractions (pumping) of the pharynx, a neuromuscular feeding organ. Here, we use pharmacology, optogenetics, genetics and electrophysiology to investigate the roles of the nervous system and muscle in generating pharyngeal pumping. Hyperpolarization of the nervous system using a histamine-gated chloride channel abolishes pumping and optogenetic stimulation of pharyngeal muscle in these animals causes abnormal contractions, demonstrating that normal pumping requires nervous system function. In mutants that pump slowly due to defective nervous system function, tonic muscle stimulation causes rapid pumping, suggesting tonic neurotransmitter release may regulate pumping. However, tonic cholinergic motor neuron stimulation, but not tonic muscle stimulation, triggers pumps that electrophysiologically resemble typical rapid pumps. This suggests that pharyngeal cholinergic motor neurons are normally rhythmically and not tonically active. These results demonstrate that the pharynx generates a myogenic rhythm in the presence of tonically released acetylcholine and suggest that the pharyngeal nervous system entrains contraction rate and timing through phasic neurotransmitter release.
A novel framework of classical and quantum prisoner’s dilemma games on coupled networks
Authors: Deng Xinyang , Zhang Qi , Deng Yong , Wang Zhen
Published: March 2016

Evolutionary games on multilayer networks are attracting growing interest. While among previous studies, the role of quantum games in such a infrastructure is still virgin and may become a fascinating issue across a myriad of research realms. To mimick two kinds of different interactive environments and mechanisms, in this paper a new framework of classical and quantum prisoner’s dilemma games on two-layer coupled networks is considered. Within the proposed model, the impact of coupling factor of networks and entanglement degree in quantum games on the evolutionary process has been studied. Simulation results show that the entanglement has no impact on the evolution of the classical prisoner’s dilemma, while the rise of the coupling factor obviously impedes cooperation in this game and the evolution of quantum prisoner’s dilemma is greatly impacted by the combined effect of entanglement and coupling.
Towards understanding of heat effects in metallic glasses on the basis of macroscopic shear elasticity
Authors: Mitrofanov Y. P. , Wang D. P. , Makarov A. S. , Wang W. H. , Khonik V. A.
Published: March 2016

It is shown that all heat effects taking place upon annealing of a metallic glass within the glassy and supercooled liquid states, i.e. heat release below the glass transition temperature and heat absorption above it, as well as crystallization-induced heat release, are related to the macroscopic shear elasticity. The underlying physical reason can be understood as relaxation in the system of interstitialcy-type ”defects” (elastic dipoles) frozen-in from the melt upon glass production.
Universally Conserved Relationships between Nuclear Shape and Cytoplasmic Mechanical Properties in Human Stem Cells
Authors: Lozoya Oswaldo A. , Gilchrist Christopher L. , Guilak Farshid
Published: March 2016

The ability of cells to proliferate, differentiate, transduce extracellular signals and assemble tissues involves structural connections between nucleus and cytoskeleton. Yet, how the mechanics of these connections vary inside stem cells is not fully understood. To address those questions, we combined two-dimensional particle-tracking microrheology and morphological measures using variable reduction techniques to measure whether cytoplasmic mechanics allow for discrimination between different human adherent stem cell types and across different culture conditions. Here we show that nuclear shape is a quantifiable discriminant of mechanical properties in the perinuclear cytoskeleton (pnCSK) of various stem cell types. Also, we find the pnCSK is a region with different mechanical properties than elsewhere in the cytoskeleton, with heterogeneously distributed locations exhibiting subdiffusive features and which obeys physical relations conserved among various stem cell types. Finally, we offer a prospective basis to discriminate between stem cell types by coupling perinuclear mechanical properties to nuclear shape.
EMD in periodontal regenerative surgery modulates cytokine profiles: A randomised controlled clinical trial
Authors: Villa Oscar , Wohlfahrt Johan C. , Koldsland Odd Carsten , Brookes Steven J. , Lyngstadaas Staale P. , Aass Anne M. , Reseland Janne E.
Published: March 2016

The enamel matrix derivative (EMD) contains hundreds of peptides in different levels of proteolytic processing that may provide a range of biological effects of importance in wound healing. The aim of the present study was to compare the effect of EMD and its fractions on the cytokine profiles from human gingival fibroblasts in vitro and in gingival crevicular fluid (GCF) in a randomized controlled split-mouth clinical study (n = 12). Levels of cytokines in cell culture medium and in GCF were measured by Luminex over a 2-week period. In the clinical study, levels of pro-inflammatory cytokines and chemokines were increased, whereas the levels of transforming growth factor-α (TGF-α) and platelet-derived growth factor-BB (PDGF-BB) were reduced. The in vitro study showed that EMD and its high and low molecular weight fractions reduced the secretion of pro-inflammatory cytokines and chemokines compared to untreated cells. EMD had an effect on levels of cytokines related to fibroplasia, angiogenesis, inflammation and chemotaxis both in vitro and in vivo, however, the anti-inflammatory effect induced by EMD observed in the in vitro study could not be confirmed clinically.
Self-assembled hydrophobin for producing water-soluble and membrane permeable fluorescent dye
Authors: Wang Kunpeng , Xiao Yunjie , Wang Yanyan , Feng Yaqing , Chen Cheng , Zhang Jie , Zhang Qian , Meng Shuxian , Wang Zefang , Yang Haitao
Published: March 2016

Low water solubility and poor membrane permeability are major disadvantages that compromise applications of most fluorescent dyes. To resolve these problems, herein, using Boron-dipyrromethene (BODIPY) as a model fluorescent dye, for the first time, we provide a new strategy for the rapid and efficient production of a water-soluble and membrane-permeable dye by mixing with an amphiphilic protein named hydrophobin. Data shows BODIPY could be effectively solubilized and dispersed in 200 μg/mL hydrophobin by simple mixing and sonication. Subsequent experiments indicated that hydrophobin self-assembled into a protein film on the surface of BODIPY forming stable hydrophobin-BODIPY complexes with a size range of 10–30 nm. Furthermore, we demonstrated hydrophobin-functionalized BODIPY are toxicity free to cells. The hydrophobin-BODIPY complex could pass through both the cell plasma membrane and nuclear membrane efficiently. Our work opens a novel route to modify and functionalize fluorescent dyes and may be developed as a general strategy for broadening their applications.
Gene expression profiling gut microbiota in different races of humans
Authors: Chen Lei , Zhang Yu-Hang , Huang Tao , Cai Yu-Dong
Published: March 2016

The gut microbiome is shaped and modified by the polymorphisms of microorganisms in the intestinal tract. Its composition shows strong individual specificity and may play a crucial role in the human digestive system and metabolism. Several factors can affect the composition of the gut microbiome, such as eating habits, living environment and antibiotic usage. Thus, various races are characterized by different gut microbiome characteristics. In this present study, we studied the gut microbiomes of three different races, including individuals of Asian, European and American races. The gut microbiome and the expression levels of gut microbiome genes were analyzed in these individuals. Advanced feature selection methods (minimum redundancy maximum relevance and incremental feature selection) and four machine-learning algorithms (random forest, nearest neighbor algorithm, sequential minimal optimization, Dagging) were employed to capture key differentially expressed genes. As a result, sequential minimal optimization was found to yield the best performance using the 454 genes, which could effectively distinguish the gut microbiomes of different races. Our analyses of extracted genes support the widely accepted hypotheses that eating habits, living environments and metabolic levels in different races can influence the characteristics of the gut microbiome.
Association between Testicular Cancer and Epididymoorchitis: A Population-Based Case-Control Study
Authors: Kao Li-Ting , Lin Herng-Ching , Chung Shiu-Dong , Huang Chao-Yuan
Published: March 2016

Even though epididymoorchitis and testicular cancer (TC) may have similar pathophysiological pathways, no prior study has attempted to determine the association between these two diseases. This case-control study investigated the relationship between TC and prior epididymoorchitis by using a large population-based database. We used the Taiwan Longitudinal Health Insurance Database 2005 to select 372 patients who had received a diagnosis of TC and 3,720 age-matched controls without TC. We found that of the total sample of 4,092 patients, 53 (1.3%) had received a diagnosis of epididymoorchitis prior to the index date. Patients with TC had a higher prevalence of prior epididymoorchitis than that of patients without TC (11.0% vs. 0.3%,p < 0.001). Conditional logistic regression showed that prior epididymoorchitis was significantly associated with TC (crude OR = 38.24, 95% CI = 19.91–73.46). The association remained statistically significant even after adjustment for the other variables (OR = 47.17, 95% CI = 23.83–93.40). This study showed that patients with TC have higher odds of prior epididymoorchitis than do those without TC even after adjustment for potential confounders.
Nitrate fertilisation does not enhance CO2 responses in two tropical seagrass species
Authors: Ow Y. X. , Vogel N. , Collier C. J. , Holtum J. A. M. , Flores F. , Uthicke S.
Published: March 2016

Seagrasses are often considered “winners” of ocean acidification (OA); however, seagrass productivity responses to OA could be limited by nitrogen availability, since nitrogen-derived metabolites are required for carbon assimilation. We tested nitrogen uptake and assimilation, photosynthesis, growth, and carbon allocation responses of the tropical seagrasses Halodule uninervis and Thalassia hemprichii to OA scenarios (428, 734 and 1213 μatm pCO2) under two nutrients levels (0.3 and 1.9 μM NO3−). Net primary production (measured as oxygen production) and growth in H. uninervis increased with pCO2 enrichment, but were not affected by nitrate enrichment. However, nitrate enrichment reduced whole plant respiration in H. uninervis. Net primary production and growth did not show significant changes with pCO2 or nitrate by the end of the experiment (24 d) in T. hemprichii. However, nitrate incorporation in T. hemprichii was higher with nitrate enrichment. There was no evidence that nitrogen demand increased with pCO2 enrichment in either species. Contrary to our initial hypothesis, nutrient increases to levels approximating present day flood plumes only had small effects on metabolism. This study highlights that the paradigm of increased productivity of seagrasses under ocean acidification may not be valid for all species under all environmental conditions.
Enhanced Performance of PbS-quantum-dot-sensitized Solar Cells via Optimizing Precursor Solution and Electrolytes
Authors: Tian Jianjun , Shen Ting , Liu Xiaoguang , Fei Chengbin , Lv Lili , Cao Guozhong
Published: March 2016

This work reports a PbS-quantum-dot-sensitized solar cell (QDSC) with power conversion efficiency (PCE) of 4%. PbS quantum dots (QDs) were grown on mesoporous TiO2 film using a successive ion layer absorption and reaction (SILAR) method. The growth of QDs was found to be profoundly affected by the concentration of the precursor solution. At low concentrations, the rate-limiting factor of the crystal growth was the adsorption of the precursor ions and the surface growth of the crystal became the limiting factor in the high concentration solution. The optimal concentration of precursor solution with respect to the quantity and size of synthesized QDs was 0.06 M. To further increase the performance of QDSCs, the 30% deionized water of polysulfide electrolyte was replaced with methanol to improve the wettability and permeability of electrolytes in the TiO2 film, which accelerated the redox couple diffusion in the electrolyte solution and improved charge transfer at the interfaces between photoanodes and electrolytes. The stability of PbS QDs in the electrolyte was also improved by methanol to reduce the charge recombination and prolong the electron lifetime. As a result, the PCE of QDSC was increased to 4.01%.
Isoliquiritigenin Attenuates Adipose Tissue Inflammation in vitro and Adipose Tissue Fibrosis through Inhibition of Innate Immune Responses in Mice
Authors: Watanabe Yasuharu , Nagai Yoshinori , Honda Hiroe , Okamoto Naoki , Yamamoto Seiji , Hamashima Takeru , Ishii Yoko , Tanaka Miyako , Suganami Takayoshi , Sasahara Masakiyo , Miyake Kensuke , Takatsu Kiyoshi
Published: March 2016

Isoliquiritigenin (ILG) is a flavonoid derived from Glycyrrhiza uralensis and potently suppresses NLRP3 inflammasome activation resulting in the improvement of diet-induced adipose tissue inflammation. However, whether ILG affects other pathways besides the inflammasome in adipose tissue inflammation is unknown. We here show that ILG suppresses adipose tissue inflammation by affecting the paracrine loop containing saturated fatty acids and TNF-α by using a co-culture composed of adipocytes and macrophages. ILG suppressed inflammatory changes induced by the co-culture through inhibition of NF-κB activation. This effect was independent of either inhibition of inflammasome activation or activation of peroxisome proliferator-activated receptor-γ. Moreover, ILG suppressed TNF-α-induced activation of adipocytes, coincident with inhibition of IκBα phosphorylation. Additionally, TNF-α-mediated inhibition of Akt phosphorylation under insulin signaling was alleviated by ILG in adipocytes. ILG suppressed palmitic acid-induced activation of macrophages, with decreasing the level of phosphorylated Jnk expression. Intriguingly, ILG improved high fat diet-induced fibrosis in adipose tissue in vivo. Finally, ILG inhibited TLR4- or Mincle-stimulated expression of fibrosis-related genes in stromal vascular fraction from obese adipose tissue and macrophages in vitro. Thus, ILG can suppress adipose tissue inflammation by both inflammasome-dependent and -independent manners and attenuate adipose tissue fibrosis by targeting innate immune sensors.
Physiological and proteomic responses to salt stress in chloroplasts of diploid and tetraploid black locust (Robinia pseudoacacia L.)
Authors: Meng Fanjuan , Luo Qiuxiang , Wang Qiuyu , Zhang Xiuli , Qi Zhenhua , Xu Fuling , Lei Xue , Cao Yuan , Chow Wah Soon , Sun Guangyu
Published: March 2016

Salinity is an important abiotic stressor that negatively affects plant growth. In this study, we investigated the physiological and molecular mechanisms underlying moderate and high salt tolerance in diploid (2×) and tetraploid (4×) Robinia pseudoacacia L. Our results showed greater H2O2 accumulation and higher levels of important antioxidative enzymes and non-enzymatic antioxidants in 4× plants compared with 2× plants under salt stress. In addition, 4× leaves maintained a relatively intact structure compared to 2× leaves under a corresponding condition. NaCl treatment didn’t significantly affect the photosynthetic rate, stomatal conductance or leaf intercellular CO2 concentrations in 4× leaves. Moreover, proteins from control and salt treated 2× and 4× leaf chloroplast samples were extracted and separated by two-dimensional gel electrophoresis. A total of 61 spots in 2× (24) and 4× (27) leaves exhibited reproducible and significant changes under salt stress. In addition, 10 proteins overlapped between 2× and 4× plants under salt stress. These identified proteins were grouped into the following 7 functional categories: photosynthetic Calvin-Benson Cycle (26), photosynthetic electron transfer (7), regulation/defense (5), chaperone (3), energy and metabolism (12), redox homeostasis (1) and unknown function (8). This study provides important information of use in the improvement of salt tolerance in plants.
Deletion of endogenous Tau proteins is not detrimental in Drosophila
Authors: Burnouf Sylvie , Grönke Sebastian , Augustin Hrvoje , Dols Jacqueline , Gorsky Marianna Karina , Werner Jennifer , Kerr Fiona , Alic Nazif , Martinez Pedro , Partridge Linda
Published: March 2016

Human Tau (hTau) is a highly soluble and natively unfolded protein that binds to microtubules within neurons. Its dysfunction and aggregation into insoluble paired helical filaments is involved in the pathogenesis of Alzheimer’s disease (AD), constituting, together with accumulated β-amyloid (Aβ) peptides, a hallmark of the disease. Deciphering both the loss-of-function and toxic gain-of-function of hTau proteins is crucial to further understand the mechanisms leading to neurodegeneration in AD. As the fruit fly Drosophila melanogaster expresses Tau proteins (dTau) that are homologous to hTau, we aimed to better comprehend dTau functions by generating a specific tau knock-out (KO) fly line using homologous recombination. We observed that the specific removal of endogenous dTau proteins did not lead to overt, macroscopic phenotypes in flies. Indeed, survival, climbing ability and neuronal function were unchanged in tau KO flies. In addition, we did not find any overt positive or negative effect of dTau removal on human Aβ-induced toxicity. Altogether, our results indicate that the absence of dTau proteins has no major functional impact on flies and suggests that our tau KO strain is a relevant model to further investigate the role of dTau proteins in vivo, thereby giving additional insights into hTau functions.
Controlled Growth of Rubrene Nanowires by Eutectic Melt Crystallization
Authors: Chung Jeyon , Hyon Jinho , Park Kyung-Sun , Cho Boram , Baek Jangmi , Kim Jueun , Lee Sang Uck , Sung Myung Mo , Kang Youngjong
Published: March 2016

Organic semiconductors including rubrene, Alq3, copper phthalocyanine and pentacene are crystallized by the eutectic melt crystallization. Those organic semiconductors form good eutectic systems with the various volatile crystallizable additives such as benzoic acid, salicylic acid, naphthalene and 1,3,5-trichlorobenzene. Due to the formation of the eutectic system, organic semiconductors having originally high melting point (Tm > 300 °C) are melted and crystallized at low temperature (Te = 40.8–133 °C). The volatile crystallizable additives are easily removed by sublimation. For a model system using rubrene, single crystalline rubrene nanowires are prepared by the eutectic melt crystallization and the eutectic-melt-assisted nanoimpinting (EMAN) technique. It is demonstrated that crystal structure and the growth direction of rubrene can be controlled by using different volatile crystallizable additives. The field effect mobility of rubrene nanowires prepared using several different crystallizable additives are measured and compared.
Flexible heat-flow sensing sheets based on the longitudinal spin Seebeck effect using one-dimensional spin-current conducting films
Authors: Kirihara Akihiro , Kondo Koichi , Ishida Masahiko , Ihara Kazuki , Iwasaki Yuma , Someya Hiroko , Matsuba Asuka , Uchida Ken-ichi , Saitoh Eiji , Yamamoto Naoharu , Kohmoto Shigeru , Murakami Tomoo
Published: March 2016

Heat-flow sensing is expected to be an important technological component of smart thermal management in the future. Conventionally, the thermoelectric (TE) conversion technique, which is based on the Seebeck effect, has been used to measure a heat flow by converting the flow into electric voltage. However, for ubiquitous heat-flow visualization, thin and flexible sensors with extremely low thermal resistance are highly desired. Recently, another type of TE effect, the longitudinal spin Seebeck effect (LSSE), has aroused great interest because the LSSE potentially offers favourable features for TE applications such as simple thin-film device structures. Here we demonstrate an LSSE-based flexible TE sheet that is especially suitable for a heat-flow sensing application. This TE sheet contained a Ni0.2Zn0.3Fe2.5O4 film which was formed on a flexible plastic sheet using a spray-coating method known as “ferrite plating”. The experimental results suggest that the ferrite-plated film, which has a columnar crystal structure aligned perpendicular to the film plane, functions as a unique one-dimensional spin-current conductor suitable for bendable LSSE-based sensors. This newly developed thin TE sheet may be attached to differently shaped heat sources without obstructing an innate heat flux, paving the way to versatile heat-flow measurements and management.
Single-molecule analysis of DNA replication reveals novel features in the divergent eukaryotes Leishmania and Trypanosoma brucei versus mammalian cells
Authors: Stanojcic Slavica , Sollelis Lauriane , Kuk Nada , Crobu Lucien , Balard Yves , Schwob Etienne , Bastien Patrick , Pagès Michel , Sterkers Yvon
Published: March 2016

Leishmania and Trypanosoma are unicellular parasites that possess markedly original biological features as compared to other eukaryotes. The Leishmania genome displays a constitutive ‘mosaic aneuploidy’, whereas in Trypanosoma brucei, the megabase-sized chromosomes are diploid. We accurately analysed DNA replication parameters in three Leishmania species and Trypanosoma brucei as well as mouse embryonic fibroblasts (MEF). Active replication origins were visualized at the single molecule level using DNA molecular combing. More than one active origin was found on most DNA fibres, showing that the chromosomes are replicated from multiple origins. Inter-origin distances (IODs) were measured and found very large in trypanosomatids: the mean IOD was 160 kb in T. brucei and 226 kb in L. mexicana. Moreover, the progression of replication forks was faster than in any other eukaryote analyzed so far (mean velocity 1.9 kb/min in T. brucei and 2.4–2.6 kb/min in Leishmania). The estimated total number of active DNA replication origins in trypanosomatids is ~170. Finally, 14.4% of unidirectional replication forks were observed in T. brucei, in contrast to 1.5–1.7% in Leishmania and 4% in MEF cells. The biological significance of these original features is discussed.
Structural insights into the methyl donor recognition model of a novel membrane-binding protein UbiG
Authors: Zhu Yuwei , Jiang Xuguang , Wang Chongyuan , Liu Yang , Fan Xiaojiao , Zhang Linjuan , Niu Liwen , Teng Maikun , Li Xu
Published: March 2016

UbiG is a SAM-dependent O-methyltransferase, catalyzing two O-methyl transfer steps for ubiquinone biosynthesis in Escherichia coli. UbiG possesses a unique sequence insertion between β4 and α10, which is used for membrane lipid interaction. Interestingly, this sequence insertion also covers the methyl donor binding pocket. Thus, the relationship between membrane binding and entrance of the methyl donor of UbiG during the O-methyl transfer process is a question that deserves further exploration. In this study, we reveal that the membrane-binding region of UbiG gates the entrance of methyl donor. When bound with liposome, UbiG displays an enhanced binding ability toward the methyl donor product S-adenosylhomocysteine. We further employ protein engineering strategies to design UbiG mutants by truncating the membrane interacting region or making it more flexible. The ITC results show that the binding affinity of these mutants to SAH increases significantly compared with that of the wild-type UbiG. Moreover, we determine the structure of UbiG∆165–187 in complex with SAH. Collectively, our results provide a new angle to cognize the relationship between membrane binding and entrance of the methyl donor of UbiG, which is of benefit for better understanding the O-methyl transfer process for ubiquinone biosynthesis.
Voltage Controlled Magnetic Skyrmion Motion for Racetrack Memory
Authors: Kang Wang , Huang Yangqi , Zheng Chentian , Lv Weifeng , Lei Na , Zhang Youguang , Zhang Xichao , Zhou Yan , Zhao Weisheng
Published: March 2016

Magnetic skyrmion, vortex-like swirling topologically stable spin configurations, is appealing as information carrier for future nanoelectronics, owing to the stability, small size and extremely low driving current density. One of the most promising applications of skyrmion is to build racetrack memory (RM). Compared to domain wall-based RM (DW-RM), skyrmion-based RM (Sky-RM) possesses quite a few benefits in terms of energy, density and speed etc. Until now, the fundamental behaviors, including nucleation/annihilation, motion and detection of skyrmion have been intensively investigated. However, one indispensable function, i.e., pinning/depinning of skyrmion still remains an open question and has to be addressed before applying skyrmion for RM. Furthermore, Current research mainly focuses on physical investigations, whereas the electrical design and evaluation are still lacking. In this work, we aim to promote the development of Sky-RM from fundamental physics to realistic electronics. First, we investigate the pinning/depinning characteristics of skyrmion in a nanotrack with the voltage-controlled magnetic anisotropy (VCMA) effect. Then, we propose a compact model and design framework of Sky-RM for electrical evaluation. This work completes the elementary memory functionality of Sky-RM and fills the technical gap between the physicists and electronic engineers, making a significant step forward for the development of Sky-RM.
REGene: a literature-based knowledgebase of animal regeneration that bridge tissue regeneration and cancer
Authors: Zhao Min , Rotgans Bronwyn , Wang Tianfang , Cummins S. F.
Published: March 2016

Regeneration is a common phenomenon across multiple animal phyla. Regeneration-related genes (REGs) are critical for fundamental cellular processes such as proliferation and differentiation. Identification of REGs and elucidating their functions may help to further develop effective treatment strategies in regenerative medicine. So far, REGs have been largely identified by small-scale experimental studies and a comprehensive characterization of the diverse biological processes regulated by REGs is lacking. Therefore, there is an ever-growing need to integrate REGs at the genomics, epigenetics and transcriptome level to provide a reference list of REGs for regeneration and regenerative medicine research. Towards achieving this, we developed the first literature-based database called REGene (REgeneration Gene database). In the current release, REGene contains 948 human (929 protein-coding and 19 non-coding genes) and 8445 homologous genes curated from gene ontology and extensive literature examination. Additionally, the REGene database provides detailed annotations for each REG, including: gene expression, methylation sites, upstream transcription factors and protein-protein interactions. An analysis of the collected REGs reveals strong links to a variety of cancers in terms of genetic mutation, protein domains and cellular pathways. We have prepared a web interface to share these regeneration genes, supported by refined browsing and searching functions at http://REGene.bioinfo-minzhao.org/.
Cardiomyocytes in Young Infants With Congenital Heart Disease: a Three-Month Window of Proliferation
Authors: Ye Lincai , Qiu Lisheng , Zhang Haibo , Chen Huiwen , Jiang Chuan , Hong Haifa , Liu Jinfen
Published: March 2016

Perinatal reduction in cardiomyocyte cell cycle activity is well established in animal models and humans. However, cardiomyocyte cell cycle activity in infants with congenital heart disease (CHD) is unknown and may provide important information to improve treatment. Human right atrial specimens were obtained from infants during routine surgery to repair ventricular septal defects. The specimens were divided into three groups: group A (age 1–3 months); group B (age, 4–6 months); and group C (age 7–12 months). A dramatic fall in the number of Ki67 -positive CHD cardiac myocytes occurred after three months. When cultured in vitro, young CHD myocytes (≤3 months) showed more abundant Ki67-positive cardiomyocytes and greater incorporation of EdU, indicating enhanced proliferation. YAP1 and NICD—important transcript factors in cardiomyocyte development and proliferation—decreased with age and β-catenin increased with age. Compared with those of older infants, cardiomyocytes of young CHD infants (≤3 months) have a higher proliferating capacity in vivo and in vitro. From the perspective of cardiac muscle regeneration, CHD treatment at a younger age (≤3 months) may be more optimal.
MiR-582-5p/miR-590-5p targeted CREB1/CREB5–NF-κB signaling and caused opioid-induced immunosuppression in human monocytes
Authors: Long X , Li Y , Qiu S , Liu J , He L , Peng Y
Published: March 2016

Chronic opioid abusers are more susceptible to bacterial and viral infections, but the molecular mechanism underlying opioid-induced immunosuppression is unknown. MicroRNAs (miRNAs) are emerging as key players in the control of biological processes, and may participate in immune regulation. In this study, we investigated the molecular mechanisms in opioid-induced and miRNA-mediated immunosuppression, in the context of miRNA dysregulation in opioid abusers. Blood samples of heroin abusers were collected and analyzed using miRNA microarray analysis and quantitative PCR validation. The purified primary human monocytes were cultured in vitro to explore the underlying mechanism. We found that morphine and its derivative heroin significantly decreased the expression levels of miR-582-5p and miR-590-5p in monocytes. cAMP response element-binding protein 1 (CREB1) and CREB5 were detected as direct target genes of miR-582-5p and miR-590-5p, respectively, by using dual-luciferase assay and western bolt. Functional studies showed that knockdown of CREB1/CREB5 increased tumor necrosis factor alpha (TNF-α) level and enhanced expression of phospho–NF-κB p65 and NF-κB p65. Our results demonstrated that miR-582-5p and miR-590-5p play important roles in opioid-induced immunosuppression in monocytes by targeting CREB1/CREB5–NF-κB signaling pathway.
Performance assessment of solvent extraction coupled with gas chromatography-mass spectrometry for the analysis of volatile components from Syringa flowers
Authors: Zheng Weiying , Li Fengqin , Yu Zhigang , Zhang Guiling , Chen Yanhui , Li Xiaoxia , Yan Hong
Published: March 2016

Using gas chromatography-mass spectrometry (GC-MS) as a means of separation and identification, a solvent extraction (SE) method was first developed and used for isolating and concentrating the volatile components fromSyringaflowers.
A colorimetric multilayer sensor for discriminating red wine and green tea by measurement of antioxidant activity
Authors: Li Junjie , Fu Beibei , Hou Changjun , Huo Danqun , Yang Mei , Shen Caihong , Luo Huibo
Published: March 2016

A sensor was fabricated by alternative assembly of chitosan, Fe3+ complexes and alginate sodium on filter paper modified with a TiO2 membrane. The sensor has good super-hydrophobicity and polyphenols in aqueous samples can be pre-concentrated on its surface, providing improved sensor sensitivity.
A quinone mediator drives oxidations catalysed by alcohol dehydrogenase-containing cell lysates
Authors: Haas Julian , Schätzle Michael A. , Husain Syed M. , Schulz-Fincke Johannes , Jung Manfred , Hummel Werner , Müller Michael , Lüdeke Steffen
Published: March 2016

Addition of the quinone lawsone is sufficient to drive oxidations catalysed by recombinant alcohol dehydrogenases in E. coli cell lysates.
Neuraminidase inhibition of Dietary chlorogenic acids and derivatives – potential antivirals from dietary sources
Authors: Gamaleldin Elsadig Karar Mohamed , Matei Marius-Febi , Jaiswal Rakesh , Illenberger Susanne , Kuhnert Nikolai
Published: March 2016

Plants rich in chlorogenic acids (CGAs), caffeic acids and their derivatives have been found to exert antiviral effects against influenza virus neuroaminidase.
A cyclosporine derivative is a substrate of the oligopeptide transporter PepT1
Authors: Foley David W. , Bermudez Isabel , Bailey Patrick D. , Meredith David
Published: March 2016

Cyclosporine was attached to a thiodipeptide carrier, yielding conjugate 7; this is a substrate for PepT1 with oral bioavailability potential.
Microwave-accelerated direct synthesis of 3-picoline from glycerol through a liquid phase reaction pathway
Authors: Luo Cai-Wu , Feng Xiao-Yan , Chao Zi-Sheng
Published: March 2016

A high yield of 3-picoline over a catalyst pair (HAc + TiO2) is obtained under microwave irradiation.
Charge transfer complexes of 4-isopropyl-2-benzyl-1,2,5-thiadiazolidin-3-one1,1-dioxide with DDQ and TCNE: experimental and DFT studies
Authors: Seridi Saida , Dinar Karim , Seridi Achour , Berredjem Malika , Kadri Mekki
Published: March 2016

We investigated the interaction between sulfahydantoin and two acceptors (DDQ and TCNE) in the liquid phase and in the solid state.
Continuous synthesis of nanostructured silica based materials in a gas–liquid segmented flow tubular reactor
Authors: Knossalla Johannes , Mezzavilla Stefano , Schüth Ferdi
Published: March 2016

Synthesizing core–shell particles SiO2@mSiO2, mSiO2and Au@SiO2in a continuous tubular segmented reactor.
Rapid formation of highly stretchable and notch-insensitive hydrogels
Authors: Su Qiang , Wang Yajun , Guan Shuang , Zhang Huixuan , Gao Guang Hui , Zhu Xinyuan
Published: March 2016

Highly stretchable and notch-insensitive hydrogels were rapidly prepared using redox initiators.
A “1-methylimidazole-fixation” route to anchor small-sized nitrides on carbon supports as non-Pt catalysts for the hydrogen evolution reaction
Authors: Meng Meichen , Yan Haijing , Jiao Yanqing , Wu Aiping , Zhang Xiaomeng , Wang Ruihong , Tian Chungui
Published: March 2016

Small-sized WN, Mo2N have been grown on various carbon supports based on a robust “1-methylimidazole-fixation” strategy.
Toxicological risks of Rhizoma paridis saponins in rats involved NF-κB and Nrf2 signaling
Authors: Li Jing , Man Shuli , Qiu Peiyu , Fan Wei , Zhang Liming , Gao Wenyuan
Published: March 2016

The aim of the study is to evaluate the safety of long-term use of Rhizoma paridis saponins (RPS).
3D hierarchical porous NiO nanoflowers as an advanced anode material with remarkable lithium storage performance
Authors: Pang Yingping , Zhang Jian , Chen Dairong , Jiao Xiuling
Published: March 2016

A cost-effective but efficient two-step solvothermal calcination strategy for the preparation of novel three-dimensional (3D) open hierarchical NiO nanoflowers was demonstrated. The product showed remarkable lithium storage performance.
Molecular mechanism of cardiolipin-mediated assembly of respiratory chain supercomplexes
Authors: Arnarez C. , Marrink S. J. , Periole X.
Published: March 2016

We reveal the molecular mechanism by which cardiolipin glues respiratory complexes into supercomplexes. This mechanism defines a new biophysico-chemical pathway of protein–lipid interplay, with broad general implications for the dynamic organization of crowded cell membranes.
Structural engineering of porphyrin-based small molecules as donors for efficient organic solar cells
Authors: Wang Hongda , Xiao Liangang , Yan Lei , Chen Song , Zhu Xunjin , Peng Xiaobin , Wang Xingzhu , Wong Wai-Kwok , Wong Wai-Yeung
Published: March 2016

Three A–D–A porphyrin-based small molecules are employed as donors in bulky heterojunction organic solar cells. Striking a delicate balance between solubility, morphology and device fabrication, leads to PCEs of up to 7.7%.
Development of a new in situ analysis technique applying luminescence of local coordination sensors: principle and application for monitoring metal-ligand exchange processes
Authors: Terraschke Huayna , Ruiz Arana Laura , Lindenberg Patric , Bensch Wolfgang
Published: March 2016

In situluminescence analysis of coordination sensors (ILACS) allows studying metal-ligand exchange processes in a fast, sensitive and broadly available fashion.
Nanowire growth kinetics in aberration corrected environmental transmission electron microscopy
Authors: Chou Yi-Chia , Panciera Federico , Reuter Mark C. , Stach Eric A. , Ross Frances M.
Published: March 2016

We visualize atomic level dynamics during Si nanowire growth using aberration corrected environmental transmission electron microscopy, and compare with lower pressure results from ultra-high vacuum microscopy.
Unambiguous characterization of anisotropic foldamer packing in a foldecture with an elongated hexagonal plate shape
Authors: Yoon Eunyoung , Gong Jintaek , Jung Yoonchul , Lee Wonchul , Driver Russell W. , Lee Hee-Seung
Published: March 2016

We report the first complete characterization of the directional molecular packing patterns of individual foldamers within a new foldecture with a well defined hexagonal plate shape.
Diverse tetrahedral tetrazolate frameworks with N-rich surface
Authors: Tang Yu-Huan , Wang Fei , Liu Jin-Xiu , Zhang Jian
Published: March 2016

Three tetrahedral tetrazolate frameworks (TTFs) with SOD, srs and ctn topologies are obtained by using structure-directing agents. The resulting SOD-type TTF-4 shows high chemical stability and high CO2 uptake capacity.
Visible-light-driven photocatalytic water oxidation catalysed by iron-based metal–organic frameworks
Authors: Horiuchi Yu , Toyao Takashi , Miyahara Kenta , Zakary Lionet , Van Dang Do , Kamata Yusuke , Kim Tae-Ho , Lee Soo Wohn , Matsuoka Masaya
Published: March 2016

An iron-based metal–organic framework, MIL-101(Fe), promotes photocatalytic water oxidation to produce oxygen from aqueous silver nitrate solution under visible-light irradiation.
BODIPY-containing nanoscale metal–organic frameworks for photodynamic therapy
Authors: Wang Weiqi , Wang Lei , Li Zhensheng , Xie Zhigang
Published: March 2016

BODIPY-immobilized metal–organic frameworks for photodynamic therapy were developed through solvent-assisted ligand exchange.
Palladium-catalyzed C(sp3)–C(sp2) cross-coupling of homoleptic rare-earth metal trialkyl complexes with aryl bromides: efficient synthesis of functionalized benzyltrimethylsilanes
Authors: Cai Guilong , Huang Yingda , Du Tingting , Zhang Shaowen , Yao Bo , Li Xiaofang
Published: March 2016

The first C(sp3)–C(sp2) cross-coupling of rare-earth metal alkyl complexes with aryl bromides has been developed for an efficient synthesis of benzyltrimethylsilanes with diverse functional groups.
Enhancing the enantioselective recognition and sensing of chiral anions by halogen bonding
Authors: Lim Jason Y. C. , Marques Igor , Ferreira Liliana , Félix Vítor , Beer Paul D.
Published: March 2016

Novel halogen bonding chiral (S)-1,1′-bi-2-naphthol-based receptor molecules significantly enhance enantioselective anion recognition and electrochemical sensing compared to their hydrogen bonding analogues.