bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene expression changes triggered by end-of-day far-red light treatment on early developmental stages of Eustoma grandiflorum (Raf.) Shinn.
Authors: Takemura Yoshihiro , Kuroki Katsuou , Katou Masahiro , Kishimoto Masayuki , Tsuji Wataru , Nishihara Eiji , Tamura Fumio 
Published: December 2015

AbstractTo better understand the molecular mechanisms related to growth promotion in the early developmental stages of Eustoma grandiflorum (Raf.) Shinn. under end-of-day far-red light (EOD-FR) treatment, we analyzed the leaf transcriptome of treated (EOD) and untreated plants (Cont) by using RNA-seq technology. EOD-FR treatment for only about 2 weeks in regions with limited sunshine during winter resulted in significantly higher internode length between the 3rd and 4th nodes on the main stem in EOD than in Cont. Among the differentially expressed genes (DEGs) related to synthesis or transport of auxin, higher levels of YUCCA (CL6581) and PIN4 (CL6181) were noted after treatment in EOD than in Cont in the leaf. In addition, high expression levels of GA20ox (Unigene11862) related to gibberellin (GA) synthesis and transcription factor bHLH 135 (CL7761) were observed in the stem of EOD, 3 h after treatment. A vertical section of the stem showed that the pith length of cells at the 4th node was longer in EOD than in Cont. Collectively, these results suggested that EOD-FR treatment increased the expression of DEGs related to GA and auxin biosynthesis, bHLH transcription factor and internodal cell elongation along the longitudinal axis of Eustoma plants.
Bio-inspired heterogeneous composites for broadband vibration mitigation
Authors: Chen Yanyu , Wang Lifeng 
Published: December 2015

AbstractStructural biological materials have developed heterogeneous and hierarchical architectures that are responsible for the outstanding performance to provide protection against environmental threats including static and dynamic loading. Inspired by this observation, this research aims to develop new material and structural concepts for broadband vibration mitigation. The proposed composite materials possess a two-layered heterogeneous architecture where both layers consist of high-volume platelet-shape reinforcements and low-volume matrix, similar to the well-known “brick and mortar” microstructure of biological composites. Using finite element method, we numerically demonstrated that broadband wave attenuation zones can be achieved by tailoring the geometric features of the heterogeneous architecture. We reveal that the resulting broadband attenuation zones are gained by directly superimposing the attenuation zones in each constituent layer. This mechanism is further confirmed by the investigation into the phonon dispersion relation of each layer. Importantly, the broadband wave attenuation capability will be maintained when the mineral platelet orientation is locally manipulated, yet a contrast between the mineral platelet concentrations of the two constituent layers is essential. The findings of this work will provide new opportunities to design heterogeneous composites for broadband vibration mitigation and impact resistance under mechanically challenging environmental conditions.
Seven gene deletions in seven days: Fast generation of Escherichia coli strains tolerant to acetate and osmotic stress
Authors: Jensen Sheila I. , Lennen Rebecca M. , Herrgård Markus J. , Nielsen Alex T. 
Published: December 2015

AbstractGeneration of multiple genomic alterations is currently a time consuming process. Here, a method was established that enables highly efficient and simultaneous deletion of multiple genes in Escherichia coli. A temperature sensitive plasmid containing arabinose inducible lambda Red recombineering genes and a rhamnose inducible flippase recombinase was constructed to facilitate fast marker-free deletions. To further speed up the procedure, we integrated the arabinose inducible lambda Red recombineering genes and the rhamnose inducible FLP into the genome of E. coli K-12 MG1655. This system enables growth at 37 °C, thereby facilitating removal of integrated antibiotic cassettes and deletion of additional genes in the same day. Phosphorothioated primers were demonstrated to enable simultaneous deletions during one round of electroporation. Utilizing these methods, we constructed strains in which four to seven genes were deleted in E. coli W and E. coli K-12. The growth rate of an E. coli K-12 quintuple deletion strain was significantly improved in the presence of high concentrations of acetate and NaCl. In conclusion, we have generated a method that enables efficient and simultaneous deletion of multiple genes in several E. coli variants. The method enables deletion of up to seven genes in as little as seven days.
Perinatal Oxidative Stress May Affect Fetal Ghrelin Levels in Humans
Authors: Luo Zhong-Cheng , Bilodeau Jean-François , Monique Nuyt Anne , Fraser William D. , Julien Pierre , Audibert Francois , Xiao Lin , Garofalo Carole , Levy Emile 
Published: December 2015

AbstractIn vitro cell model studies have shown that oxidative stress may affect beta-cell function. It is unknown whether oxidative stress may affect metabolic health in human fetuses/newborns. In a singleton pregnancy cohort (n = 248), we studied maternal (24–28 weeks gestation) and cord plasma biomarkers of oxidative stress [malondialdehyde (MDA), F2-isoprostanes] in relation to fetal metabolic health biomarkers including cord plasma glucose-to-insulin ratio (an indicator of insulin sensitivity), proinsulin-to-insulin ratio (an indicator of beta-cell function), insulin, IGF-I, IGF-II, leptin, adiponectin and ghrelin concentrations. Strong positive correlations were observed between maternal and cord plasma biomarkers of oxidative stress (r = 0.33 for MDA, r = 0.74 for total F2-isoprostanes, all p < 0.0001). Adjusting for gestational age at blood sampling, cord plasma ghrelin concentrations were consistently negatively correlated to oxidative stress biomarkers in maternal (r = −0.32, p < 0.0001 for MDA; r = −0.31, p < 0.0001 for F2-isoprostanes) or cord plasma (r = −0.13, p = 0.04 for MDA; r = −0.32, p < 0.0001 for F2-isoprostanes). Other fetal metabolic health biomarkers were not correlated to oxidative stress. Adjusting for maternal and pregnancy characteristics, similar associations were observed. Our study provides the first preliminary evidence suggesting that oxidative stress may affect fetal ghrelin levels in humans. The implications in developmental “programming” the vulnerability to metabolic syndrome related disorders remain to be elucidated.
Orthogonal-band-multiplexed offset-QAM optical superchannel generation and coherent detection
Authors: Zheng Zhennan , Wang Dan , Zhu Xiaoqi , Lv Xin , Zou Kaiheng , Zhu Yixiao , Zhang Fan , Chen Zhangyuan 
Published: December 2015

AbstractNowadays the Internet not only has fast growing data traffic, but also has a fast growing number of on-line devices. This leads to high demand of capacity and flexibility of the future networks. The conventional Orthogonal Frequency Division Multiplexing (OFDM) and Nyquist pulse shaping signals have the advantage of high spectral efficiency when consisting of superchannels in the Wavelength-Division-Multiplexing (WDM) way. However, they face a cost issue when the spectral granularity of the superchannel is decreased to support more users. This paper proposes for the first time the scheme of Orthogonal-band-multiplexed offset-Quadrature Amplitude Modulation (OBM-OQAM) superchannel. OBM-OQAM superchannel provides large capacity and high spectral efficiency. Furthermore, it has the advantage of offering subbands of variable symbol rate without changing the system configuration. We provide a proof-of-principle demonstration of OBM-OQAM superchannel transmission. In our experiment, 400 Gbps 16 Quadrature Amplitude Modulation (QAM) OBM-OQAM superchannel transmission over 400 km Standard Single Mode Fiber (SSMF) is conducted. The experimental results show that the OBM-OQAM signal has low penalty in multi-band aggregation.
Ultra-sensitive detection of tumorigenic cellular impurities in human cell-processed therapeutic products by digital analysis of soft agar colony formation
Authors: Kusakawa Shinji , Yasuda Satoshi , Kuroda Takuya , Kawamata Shin , Sato Yoji 
Published: December 2015

AbstractContamination with tumorigenic cellular impurities is one of the most pressing concerns for human cell-processed therapeutic products (hCTPs). The soft agar colony formation (SACF) assay, which is a well-known in vitro assay for the detection of malignant transformed cells, is applicable for the quality assessment of hCTPs. Here we established an image-based screening system for the SACF assay using a high-content cell analyzer termed the digital SACF assay. Dual fluorescence staining of formed colonies and the dissolution of soft agar led to accurate detection of transformed cells with the imaging cytometer. Partitioning a cell sample into multiple wells of culture plates enabled digital readout of the presence of colonies and elevated the sensitivity for their detection. In practice, the digital SACF assay detected impurity levels as low as 0.00001% of the hCTPs, i.e. only one HeLa cell contained in 10,000,000 human mesenchymal stem cells, within 30 days. The digital SACF assay saves time, is more sensitive than in vivo tumorigenicity tests and would be useful for the quality control of hCTPs in the manufacturing process.
Ultrafast Thermal Nonlinearity
Authors: Khurgin Jacob B. , Sun Greg , Chen Wei Ting , Tsai Wei-Yi , Tsai Din Ping 
Published: December 2015

AbstractThird order nonlinear optical phenomena explored in the last half century have been predicted to find wide range of applications in many walks of life, such as all-optical switching, routing and others, yet this promise has not been fulfilled primarily because the strength of nonlinear effects is too low when they are to occur on the picosecond scale required in today’s signal processing applications. The strongest of the third-order nonlinearities, engendered by thermal effects, is considered to be too slow for the above applications. In this work we show that when optical fields are concentrated into the volumes on the scale of few tens of nanometers, the speed of the thermo-optical effects approaches picosecond scale. Such a sub-diffraction limit concentration of field can be accomplished with the use of plasmonic effects in metal nanoparticles impregnating the thermo-optic dielectric (e.g. amorphous Si) and leads to phase shifts sufficient for all optical switching on ultrafast scale.
Impacts of impervious surface expansion on soil organic carbon – a spatially explicit study
Authors: Yan Yan , Kuang Wenhui , Zhang Chi , Chen Chunbo 
Published: December 2015

AbstractThe rapid expansion of impervious surface areas (ISA) threatens soil organic carbon (SOC) pools in urbanized areas globally. The paucity of field observations on SOC under ISA (SOCISA), especially in dryland areas has limited our ability to assess the ecological impacts of ISA expansion. Based on systematically measured SOCISA(0–80 cm depth) of a dryland city and land-use and land-cover change data derived from remotely sensed data, we investigated the magnitude and vertical/horizontal patterns of SOCISAand mapped the impact of ISA expansion on SOC storage. The mean SOCISAin the city was 5.36 ± 0.51 kg C m−2, lower than that observed in humid cities but much higher than that assumed in many regional carbon assessments. SOCISAdecreased linearly as the soil depth or the horizontal distance from the open area increased. SOCISAaccounted for over half of the city’s SOC stock, which decreased by 16% (primarily in the converted croplands) because of ISA expansion from 1990 to 2010. The impacts of the ISA expansion varied spatially, depending on the land- use and converted land-cover type.
Discriminating Active Tuberculosis from Latent Tuberculosis Infection by flow cytometric measurement of CD161-expressing T cells
Authors: Yang Qianting , Xu Qian , Chen Qi , Li Jin , Zhang Mingxia , Cai Yi , Liu Haiying , Zhou Yiping , Deng Guofang , Deng Qunyi , Zhou Boping , Kornfeld Hardy , Chen Xinchun 
Published: December 2015

AbstractInterferon-gamma Release Assays (IGRAs) significantly increases the possibility for early diagnosis of tuberculosis, but IGRAs alone cannot discriminate active TB from LTBI. Therefore, fast and reliable discrimination of active tuberculosis, especially bacteriology negative tuberculosis, from LTBI is a great necessity. Here we established an assay based on flow cytometric multiparameter assay assessing expression of CD161 along with CD3, CD4 and CD8, whereby a set of indices formulated by the percentages of CD3+CD161+, CD3+CD4+CD161+ and CD3+CD8+CD161+ T cells multiplied with lymphocyte/monocyte ratio were established. Application of the CD3+CD8+CD161+ index to compare a cohort of active tuberculosis with a cohort of LTBI or health control yielded 0.7662 (95% confidence interval [CI] 0.6559–0.8552) or 0.7922 (95%  CI 0.6846–0.8763) for sensitivity and 0.9048 (95%  CI 0.8209–0.9580) or 0.8939 (95% CI 0.8392–0.9349) for specificity when the TB cohort was AFB+; the corresponding results were 0.7481 (95%  CI 0.6648–0.8198) or 0.7557 (95%  CI 0.6730–0.8265) for sensitivity and 0.8571 (95%  CI 0.7637–0.9239) or 0.8603 (95%  CI 0.8008–0.9075) for specificity when the TB cohort was AFB−. Our results reveal that in combination with IGRAs, CD161-based indices provide a novel, fast diagnostic solution addressing the limitation of current tuberculosis diagnostics.
A novel multiplex isothermal amplification method for rapid detection and identification of viruses
Authors: Nyan Dougbeh-Chris , Swinson Kevin L. 
Published: December 2015

AbstractA rapid multiplex isothermal amplification assay has been developed for detection and identification of multiple blood-borne viruses that infect millions of people world-wide. These infections may lead to chronic diseases or death if not diagnosed and treated in a timely manner. Sets of virus-specific oligonucleotides and oligofluorophores were designed and used in a reverse-transcription loop-mediated multiplexed isothermal amplification reaction for detection and gel electrophoretic identification of human Immunodeficiency virus (HIV), hepatitis-B virus (HBV), hepatitis-C virus (HCV), hepatitis-E virus (HEV), dengue virus (DENV) and West Nile (WNV) virus infection in blood plasma. Amplification was catalyzed with two thermostable enzymes for 30–60 minutes under isothermal condition, utilizing a simple digital heat source. Electrophoretic analysis of amplified products demonstrated simultaneous detection of 6 viruses that were distinctly identified by unique ladder-like banding patterns. Naked-eye fluorescent visualization of amplicons revealed intensely fluorescing products that indicated positive detection. The test demonstrated a 97% sensitivity and a 100% specificity, with no cross-reaction with other viruses observed. This portable detection tool may have clinical and field utility in the developing and developed world settings. This may enable rapid diagnosis and identification of viruses for targeted therapeutic intervention and prevention of disease transmission.
Discovery of symbiotic nitrogen fixation and chemoautotrophy in cold-water corals
Authors: Middelburg Jack J. , Mueller Christina E. , Veuger Bart , Larsson Ann I. , Form Armin , Oevelen Dick van 
Published: December 2015

AbstractCold-water corals (CWC) are widely distributed around the world forming extensive reefs at par with tropical coral reefs. They are hotspots of biodiversity and organic matter processing in the world’s deep oceans. Living in the dark they lack photosynthetic symbionts and are therefore considered to depend entirely on the limited flux of organic resources from the surface ocean. While symbiotic relations in tropical corals are known to be key to their survival in oligotrophic conditions, the full metabolic capacity of CWC has yet to be revealed. Here we report isotope tracer evidence for efficient nitrogen recycling, including nitrogen assimilation, regeneration, nitrification and denitrification. Moreover, we also discovered chemoautotrophy and nitrogen fixation in CWC and transfer of fixed nitrogen and inorganic carbon into bulk coral tissue and tissue compounds (fatty acids and amino acids). This unrecognized yet versatile metabolic machinery of CWC conserves precious limiting resources and provides access to new nitrogen and organic carbon resources that may be essential for CWC to survive in the resource-depleted dark ocean.
Microplastics profile along the Rhine River
Authors: Mani Thomas , Hauk Armin , Walter Ulrich , Burkhardt-Holm Patricia 
Published: December 2015

AbstractMicroplastics result from fragmentation of plastic debris or are released to the environment as pre-production pellets or components of consumer and industrial products. In the oceans, they contribute to the ‘great garbage patches’. They are ingested by many organisms, from protozoa to baleen whales and pose a threat to the aquatic fauna. Although as much as 80% of marine debris originates from land, little attention was given to the role of rivers as debris pathways to the sea. Worldwide, not a single great river has yet been studied for the surface microplastics load over its length. We report the abundance and composition of microplastics at the surface of the Rhine, one of the largest European rivers. Measurements were made at 11 locations over a stretch of 820 km. Microplastics were found in all samples, with 892,777 particles km −2 on average. In the Rhine-Ruhr metropolitan area, a peak concentration of 3.9 million particles km −2 was measured. Microplastics concentrations were diverse along and across the river, reflecting various sources and sinks such as waste water treatment plants, tributaries and weirs. Measures should be implemented to avoid and reduce the pollution with anthropogenic litter in aquatic ecosystems.
Acute Appendicitis Is Associated with Peptic Ulcers: A Population-based Study
Authors: Tsai Ming-Chieh , Kao Li-Ting , Lin Herng-Ching , Chung Shiu-Dong , Lee Cha-Ze 
Published: December 2015

AbstractDespite some studies having indicated a possible association between appendicitis and duodenal ulcers, this association was mainly based on regional samples or limited clinician experiences and as such, did not permit unequivocal conclusions. In this case-control study, we examined the association of acute appendicitis with peptic ulcers using a population-based database. We included 3574 patients with acute appendicitis as cases and 3574 sex- and age-matched controls. A Chi-squared test showed that there was a significant difference in the prevalences of prior peptic ulcers between cases and controls (21.7% vs. 16.8%, p < 0.001). The adjusted odds ratio (OR) of prior peptic ulcers for cases was 1.40 (95% confidence interval [CI]: 1.24~1.54, p < 0.001) compared to controls. The results further revealed that younger groups demonstrated higher ORs for prior peptic ulcers among cases than controls. In particular, the adjusted OR for cases < 30 years old was as high as 1.65 (95% CI = 1.25~2.19; p < 0.001) compared to controls. However, we failed to observe an association of acute appendicitis with peptic ulcers in the ≥ 60-year age group (OR = 1.19, 95% CI = 0.93~1.52). We concluded that there is an association between acute appendicitis and a previous diagnosis of peptic ulcers.
A cheap and non-destructive approach to increase coverage/loading of hydrophilic hydroxide on hydrophobic carbon for lightweight and high-performance supercapacitors
Authors: Zhang Liuyang , Gong Hao 
Published: December 2015

AbstractCarbon-based substrates offer unprecedented advantages in lightweight supercapacitors. However, it is still challenging to achieve high coverage or loading. Different from the traditional belief that a lack of defects or functional groups is the cause of poor growth on carbon-based substrates, we reckon that the major cause is the discrepancy between the hydrophilic nature of the metal oxide/hydroxide and the hydrophobic nature of carbon. To solve this incompatibility, we introduced ethanol into the precursor solution. The method to synthesize nickel copper hydroxide on carbon fiber paper employs only water and ethanol, in addition to nickel acetate and copper acetate. The results revealed good growth and tight adhesion of active materials on carbon fiber paper substrates. The specific capacitance and energy density per total weight of the active material plus substrate (carbon fiber paper, current collector) reached 770 F g−1and 33 Wh kg−1(1798 F g−1and 54 Wh kg−1per weight of the active materials), owing to the high loading of active material and the light weight of carbon fiber paper. These results signified the achievability of light, cheap and high-performance supercapacitors by an environmental-friendly approach.
Structural analysis of APOB variants, p.(Arg3527Gln), p.(Arg1164Thr) and p.(Gln4494del), causing Familial Hypercholesterolaemia provides novel insights into variant pathogenicity
Authors: Fernández-Higuero J. A. , Etxebarria A. , Benito-Vicente A. , Alves A. C. , Arrondo J. L. R. , Ostolaza H. , Bourbon M. , Martin C. 
Published: December 2015

AbstractFamilial hypercholesterolaemia (FH) is an inherited autosomal dominant disorder resulting from defects in the low-density lipoprotein receptor (LDLR), in the apolipoprotein B (APOB) or in the proprotein convertase subtilisin/kexin type 9 (PCSK9) genes. In the majority of the cases FH is caused by mutations occurring within LDLR, while only few mutations in APOB and PCSK9 have been proved to cause disease. p.(Arg3527Gln) was the first mutation in APOB being identified and characterized. Recently two novel pathogenic APOB variants have been described: p.(Arg1164Thr) and p.(Gln4494del) showing impaired LDLR binding capacity and diminished LDL uptake. The objective of this work was to analyse the structure of p.(Arg1164Thr) and p.(Gln4494del) variants to gain insight into their pathogenicity. Secondary structure of the human ApoB100 has been investigated by infrared spectroscopy (IR) and LDL particle size both by dynamic light scattering (DLS) and electron microscopy. The results show differences in secondary structure and/or in particle size of p.(Arg1164Thr) and p.(Gln4494del) variants compared with wild type. We conclude that these changes underlie the defective binding and uptake of p.(Arg1164Thr) and p.(Gln4494del) variants. Our study reveals that structural studies on pathogenic variants of APOB may provide very useful information to understand their role in FH disease.