bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractLow 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

AbstractThe 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

AbstractEven 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

AbstractSeagrasses 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

AbstractThis 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

AbstractIsoliquiritigenin (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

AbstractSalinity 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

AbstractHuman 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

AbstractOrganic 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

AbstractHeat-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

AbstractLeishmania 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

AbstractUbiG 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

AbstractMagnetic 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

AbstractRegeneration 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

AbstractPerinatal 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.