bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional transitions in Alphonso mango (Mangifera indica L.) during fruit development and ripening explain its distinct aroma and shelf life characteristics
Authors: Deshpande Ashish B. , Anamika Krishanpal , Jha Vineet , Chidley Hemangi G. , Oak Pranjali S. , Kadoo Narendra Y. , Pujari Keshav H. , Giri Ashok P. , Gupta Vidya S. 
Published: August 2017

AbstractAlphonso is known as the “King of mangos” due to its unique flavor, attractive color, low fiber pulp and long shelf life. We analyzed the transcriptome of Alphonso mango through Illumina sequencing from seven stages of fruit development and ripening as well as flower. Total transcriptome data from these stages ranged between 65 and 143 Mb. Importantly, 20,755 unique transcripts were annotated and 4,611 were assigned enzyme commission numbers, which encoded 142 biological pathways. These included ethylene and flavor related secondary metabolite biosynthesis pathways, as well as those involved in metabolism of starch, sucrose, amino acids and fatty acids. Differential regulation (p-value ≤ 0.05) of thousands of transcripts was evident in various stages of fruit development and ripening. Novel transcripts for biosynthesis of mono-terpenes, sesqui-terpenes, di-terpenes, lactones and furanones involved in flavor formation were identified. Large number of transcripts encoding cell wall modifying enzymes was found to be steady in their expression, while few were differentially regulated through these stages. Novel 79 transcripts of inhibitors of cell wall modifying enzymes were simultaneously detected throughout Alphonso fruit development and ripening, suggesting controlled activity of these enzymes involved in fruit softening.
ATF3 negatively regulates cellular antiviral signaling and autophagy in the absence of type I interferons
Authors: Sood Vikas , Sharma Kiran Bala , Gupta Vishal , Saha Dhurjhoti , Dhapola Parashar , Sharma Manish , Sen Utsav , Kitajima Shigetaka , Chowdhury Shantanu , Kalia Manjula , Vrati Sudhanshu 
Published: August 2017

AbstractStringent regulation of antiviral signaling and cellular autophagy is critical for the host response to virus infection. However, little is known how these cellular processes are regulated in the absence of type I interferon signaling. Here, we show that ATF3 is induced following Japanese encephalitis virus (JEV) infection, and regulates cellular antiviral and autophagy pathways in the absence of type I interferons in mouse neuronal cells. We have identified new targets of ATF3 and show that it binds to the promoter regions of Stat1, Irf9, Isg15 and Atg5 thereby inhibiting cellular antiviral signaling and autophagy. Consistent with these observations, ATF3-depleted cells showed enhanced antiviral responses and induction of robust autophagy. Furthermore, we show that JEV replication was significantly reduced in ATF3-depleted cells. Our findings identify ATF3 as a negative regulator of antiviral signaling and cellular autophagy in mammalian cells, and demonstrate its important role in JEV life cycle.
Seeing biomass recalcitrance through fluorescence
Authors: Auxenfans Thomas , Terryn Christine , Paës Gabriel 
Published: August 2017

AbstractLignocellulosic biomass is the only renewable carbon resource available in sufficient amount on Earth to go beyond the fossil-based carbon economy. Its transformation requires controlled breakdown of polymers into a set of molecules to make fuels, chemicals and materials. But biomass is a network of various inter-connected polymers which are very difficult to deconstruct optimally. In particular, saccharification potential of lignocellulosic biomass depends on several complex chemical and physical factors. For the first time, an easily measurable fluorescence properties of steam-exploded biomass samples from miscanthus, poplar and wheat straw was shown to be directly correlated to their saccharification potential. Fluorescence can thus be advantageously used as a predictive method of biomass saccharification. The loss in fluorescence occurring after the steam explosion pretreatment and increasing with pretreatment severity does not originate from the loss in lignin content, but rather from a decrease of the lignin β-aryl-ether linkage content. Fluorescence lifetime analysis demonstrates that monolignols making lignin become highly conjugated after steam explosion pretreatment. These results reveal that lignin chemical composition is a more important feature to consider than its content to understand and to predict biomass saccharification.
How to achieve Tat transport with alien TatA
Authors: Hauer René Steffen , Freudl Roland , Dittmar Julia , Jakob Mario , Klösgen Ralf Bernd 
Published: August 2017

AbstractTatA is an essential and structurally conserved component of all known Twin-arginine transport (Tat) machineries which are able to catalyse membrane transport of fully folded proteins. Here we have investigated if bacterial TatA, or chimeric pea/E. coli TatA derivatives, are capable of replacing thylakoidal TatA in function. While authentic E. coli TatA does not show any transport activity in thylakoid transport experiments, TatA chimeras comprising the transmembrane helix (TMH) of pea TatA are fully active. For minimal catalytic activity it is even sufficient to replace three residues within TMH of E. coli TatA by the corresponding pea residues. Almost any further substitution within TMH gradually raises transport activity in the thylakoid system, while functional characterization of the same set of TatA derivatives in E. coli yields essentially inverse catalytic activities. Closer inspection of the substituted residues suggests that the two transport systems have deviating demands with regard to the hydrophobicity of the transmembrane helix.
Rapid Dwarfing of an Insular Mammal – The Feral Cattle of Amsterdam Island
Authors: Rozzi Roberto , Lomolino Mark V. 
Published: August 2017

AbstractThe island rule describes a graded trend in insular populations of vertebrates from gigantism in small species to dwarfism in large species. The dwarfing of large mammals on islands has been observed both in the present fauna and in the fossil record. Elephants, hippopotami, deer, and other species became dwarfed on islands scattered all over the world, from the Mediterranean Sea to Indonesia, from the Eastern to Western Pacific Ocean, from the Caribbean to Canary Islands. The most rapid and well documented cases of island dwarfing known thus far took place over thousands of years. Here, we describe a rapid example of dwarfing of a large mammal - the feral cattle of Amsterdam Island, southern Indian Ocean, which dwarfed to about three quarters of its body size in slightly more than one century. This population provides us with a rare opportunity to assess the rapidity of demographic, life history, and morphological responses of large mammals to a very isolated and ecologically simple, insular environment.
Multi-tissue interactions in an integrated three-tissue organ-on-a-chip platform
Authors: Skardal Aleksander , Murphy Sean V. , Devarasetty Mahesh , Mead Ivy , Kang Hyun-Wook , Seol Young-Joon , Shrike Zhang Yu , Shin Su-Ryon , Zhao Liang , Aleman Julio , Hall Adam R. , Shupe Thomas D. , Kleensang Andre , Dokmeci Mehmet R. , Jin Lee Sang , Jackson John D. , Yoo James J. , Hartung Thomas , Khademhosseini Ali , Soker Shay , Bishop Colin E. , Atala Anthony 
Published: August 2017

AbstractMany drugs have progressed through preclinical and clinical trials and have been available – for years in some cases – before being recalled by the FDA for unanticipated toxicity in humans. One reason for such poor translation from drug candidate to successful use is a lack of model systems that accurately recapitulate normal tissue function of human organs and their response to drug compounds. Moreover, tissues in the body do not exist in isolation, but reside in a highly integrated and dynamically interactive environment, in which actions in one tissue can affect other downstream tissues. Few engineered model systems, including the growing variety of organoid and organ-on-a-chip platforms, have so far reflected the interactive nature of the human body. To address this challenge, we have developed an assortment of bioengineered tissue organoids and tissue constructs that are integrated in a closed circulatory perfusion system, facilitating inter-organ responses. We describe a three-tissue organ-on-a-chip system, comprised of liver, heart, and lung, and highlight examples of inter-organ responses to drug administration. We observe drug responses that depend on inter-tissue interaction, illustrating the value of multiple tissue integration for in vitro study of both the efficacy of and side effects associated with candidate drugs.
Thermal acclimation mitigates cold-induced paracellular leak from the Drosophila gut
Authors: MacMillan Heath A. , Yerushalmi Gil Y. , Jonusaite Sima , Kelly Scott P. , Donini Andrew 
Published: August 2017

AbstractChill susceptible insects suffer tissue damage and die at low temperatures. The mechanisms that cause chilling injury are not well understood but a growing body of evidence suggests that a cold-induced loss of ion and water homeostasis leads to hemolymph hyperkalemia that depolarizes cells, leading to cell death. The apparent root of this cascade is the net leak of osmolytes down their concentration gradients in the cold. Many insects, however, are capable of adjusting their thermal physiology, and cold-acclimatedDrosophilacan maintain homeostasis and avoid injury better than warm-acclimated flies. Here, we test whether chilling causes a loss of epithelial barrier function in female adultDrosophila, and provide the first evidence of cold-induced epithelial barrier failure in an invertebrate. Flies had increased rates of paracellular leak through the gut epithelia at 0 °C, but cold acclimation reduced paracellular permeability and improved cold tolerance. Improved barrier function was associated with changes in the abundance of select septate junction proteins and the appearance of a tortuous ultrastructure in subapical intercellular regions of contact between adjacent midgut epithelial cells. Thus, cold causes paracellular leak in a chill susceptible insect and cold acclimation can mitigate this effect through changes in the composition and structure of transepithelial barriers.
Mineralization and Preservation of an extremotolerant Bacterium Isolated from an Early Mars Analog Environment
Authors: Gaboyer F. , Le Milbeau C. , Bohmeier M. , Schwendner P. , Vannier P. , Beblo-Vranesevic K. , Rabbow E. , Foucher F. , Gautret P. , Guégan R. , Richard A. , Sauldubois A. , Richmann P. , Perras A. K. , Moissl-Eichinger C. , Cockell C. S. , Rettberg P. , Marteinsson  , Monaghan E. , Ehrenfreund P. , Garcia-Descalzo L. , Gomez F. , Malki M. , Amils R. , Cabezas P. , Walter N. , Westall F. 
Published: August 2017

AbstractThe artificial mineralization of a polyresistant bacterial strain isolated from an acidic, oligotrophic lake was carried out to better understand microbial (i) early mineralization and (ii) potential for further fossilisation. Mineralization was conducted in mineral matrixes commonly found on Mars and Early-Earth, silica and gypsum, for 6 months. Samples were analyzed using microbiological (survival rates), morphological (electron microscopy), biochemical (GC-MS, Microarray immunoassay, Rock-Eval) and spectroscopic (EDX, FTIR, RAMAN spectroscopy) methods. We also investigated the impact of physiological status on mineralization and long-term fossilisation by exposing cells or not to Mars-related stresses (desiccation and radiation). Bacterial populations remained viable after 6 months although the kinetics of mineralization and cell-mineral interactions depended on the nature of minerals. Detection of biosignatures strongly depended on analytical methods, successful with FTIR and EDX but not with RAMAN and immunoassays. Neither influence of stress exposure, nor qualitative and quantitative changes of detected molecules were observed as a function of mineralization time and matrix. Rock-Eval analysis suggests that potential for preservation on geological times may be possible only with moderate diagenetic and metamorphic conditions. The implications of our results for microfossil preservation in the geological record of Earth as well as on Mars are discussed.
Helical edge states and edge-state transport in strained armchair graphene nanoribbons
Authors: Liu Zheng-Fang , Wu Qing-Ping , Chen Ai-Xi , Xiao Xian-Bo , Liu Nian-Hua , Miao Guo-Xing 
Published: August 2017

AbstractA helical type edge state, which is generally supported only on graphene with zigzag boundaries, is found to also appear in armchair graphene nanoribbons in the presence of intrinsic spin-orbit coupling and a suitable strain. At a critical strain, there appears a quantum phase transition from a quantum spin Hall state to a trivial insulator state. Further investigation shows that the armchair graphene nanoribbons with intrinsic spin-orbit coupling, Rashba spin-orbit coupling, effective exchange fields and strains also support helical-like edge states with a unique spin texture. In such armchair graphene nanoribbons, the spin directions of the counterpropogating edge states on the same boundary are always opposite to each other, while is not conserved and the spins are canted away from the -direction due to the Rashba spin-orbit coupling, which is different from the case of the zigzag graphene nanoribbons. Moreover, the edge-state energy gap is smaller than that in zigzag graphene nanoribbons, even absent in certain cases.
Co-Registration of ex vivo Surgical Histopathology and in vivo T2 weighted MRI of the Prostate via multi-scale spectral embedding representation
Authors: Li Lin , Pahwa Shivani , Penzias Gregory , Rusu Mirabela , Gollamudi Jay , Viswanath Satish , Madabhushi Anant 
Published: August 2017

AbstractMulti-modal image co-registration via optimizing mutual information (MI) is based on the assumption that intensity distributions of multi-modal images follow a consistent relationship. However, images with a substantial difference in appearance violate this assumption, thus MI directly based on image intensity alone may be inadequate to drive similarity based co-registration. To address this issue, we introduce a novel approach for multi-modal co-registration called Multi-scale Spectral Embedding Registration (MSERg). MSERg involves the construction of multi-scale spectral embedding (SE) representations from multimodal images via texture feature extraction, scale selection, independent component analysis (ICA) and SE to create orthogonal representations that decrease the dissimilarity between the fixed and moving images to facilitate better co-registration. To validate the MSERg method, we aligned 45 pairs of in vivo prostate MRI and corresponding ex vivo histopathology images. The dataset was split into a learning set and a testing set. In the learning set, length scales of 5 × 5, 7 × 7 and 17 × 17 were selected. In the independent testing set, we compared MSERg with intensity-based registration, multi-attribute combined mutual information (MACMI) registration and scale-invariant feature transform (SIFT) flow registration. Our results suggest that multi-scale SE representations generated by MSERg are found to be more appropriate for radiology-pathology co-registration.
Drought and exogenous abscisic acid alter hydrogen peroxide accumulation and differentially regulate the expression of two maize RD22-like genes
Authors: Phillips Kyle , Ludidi Ndiko 
Published: August 2017

AbstractIncreased biosynthesis of abscisic acid (ABA) occurs in plants in response to water deficit, which is mediated by changes in the levels of reactive oxygen species such as H2O2. Water deficit and ABA induce expression of some RD22-like proteins. This study aimed to evaluate the effect of water deficit and exogenous ABA (50 µM ABA applied every 24 hours for a total of 72 hours) on H2O2 content in Zea mays (maize) and to characterise genes encoding two putative maize RD22-like proteins (designated ZmRD22A and ZmRD22B). The expression profiles of the two putative maize RD22-like genes in response to water deficit and treatment with ABA were examined in leaves. In silico analyses showed that the maize RD22-like proteins share domain organisation with previously characterized RD22-like proteins. Both water deficit and exogenous ABA resulted in increased H2O2 content in leaves but the increase was more pronounced in response to water deficit than to exogenous ABA. Lignin content was not affected by exogenous ABA, whereas it was decreased by water deficit. Expression of both RD22-like genes was up-regulated by drought but the ZmRD22A gene was not influenced by exogenous ABA, whereas ZmRD22B was highly responsive to exogenous ABA.
CDKAL1 rs7756992 is associated with diabetic retinopathy in a Chinese population with type 2 diabetes
Authors: Peng Danfeng , Wang Jie , Zhang Rong , Jiang Feng , Tam Claudia H. T. , Jiang Guozhi , Wang Tao , Chen Miao , Yan Jing , Wang Shiyun , Yan Dandan , He Zhen , Ma Ronald C. W. , Bao Yuqian , Hu Cheng , Jia Weiping 
Published: August 2017

AbstractDiabetic retinopathy (DR) is a major microvascular complication of diabetes. Susceptibility genes for type 2 diabetes may also impact the susceptibility of DR. This case-control study investigated the effects of 88 type 2 diabetes susceptibility loci on DR in a Chinese population with type 2 diabetes performed in two stages. In stage 1, 88 SNPs were genotyped in 1,251 patients with type 2 diabetes, and we found that ADAMTS9-AS2 rs4607103, WFS1 rs10010131, CDKAL1 rs7756992, VPS26A rs1802295 and IDE-KIF11-HHEX rs1111875 were significantly associated with DR. The association between CDKAL1 rs7756992 and DR remained significant after Bonferroni correction for multiple comparisons (corrected P = 0.0492). Then, the effect of rs7756992 on DR were analysed in two independent cohorts for replication in stage 2. Cohort (1) consisted of 380 patients with DR and 613 patients with diabetes for ≥5 years but without DR. Cohort (2) consisted of 545 patients with DR and 929 patients with diabetes for ≥5 years but without DR. A meta-analysis combining the results of stage 1 and 2 revealed a significant association between rs7756992 and DR, with the minor allele A conferring a lower risk of DR (OR 0.824, 95% CI 0.743–0.914, P = 2.46 × 10−4).
High operating temperature in V-based superconducting quantum interference proximity transistors
Authors: Ligato Nadia , Marchegiani Giampiero , Virtanen Pauli , Strambini Elia , Giazotto Francesco 
Published: August 2017

AbstractHere we report the fabrication and characterization of fully superconducting quantum interference proximity transistors (SQUIPTs) based on the implementation of vanadium (V) in the superconducting loop. At low temperature, the devices show high flux-to-voltage (up to 0.52 mV/Φ0) and flux-to-current (above 12 nA/Φ0) transfer functions, with the best estimated flux sensitivity ~ 2.6 μΦ0/(Hz)1/2 reached under fixed voltage bias, where Φ0 is the flux quantum. The interferometers operate up to Tbath
$$\simeq $$
≃
2 K, with an improvement of 70% of the maximal operating temperature with respect to early SQUIPTs design. The main features of the V-based SQUIPT are described within a simplified theoretical model. Our results open the way to the realization of SQUIPTs that take advantage of the use of higher-gap superconductors for ultra-sensitive nanoscale applications that operate at temperatures well above 1 K.
Experimental Study of Rheological Properties and Oil Displacement Efficiency in Oilfields for a Synthetic Hydrophobically Modified Polymer
Authors: Liu Pengcheng , Mu Zhenbao , Wang Chao , Wang Yanling 
Published: August 2017

AbstractIn a previous study, we developed a synthetic hydrophobically modified hydroxyethyl cellulose (HEC) using bromododecane (BD), which we denote as BD-HMHEC. In this work, we continually investigate the rheological properties and its oil displacement efficiency in PuTao well area in Daqing oilfields, China. Results show that BD-HMHEC solution has good viscosification, thermal-resistance, salt-tolerance, shear resistance, and acid/alkali resistance. The storage modulus (G’) and the loose modulus (G”) of the BD-HMHEC solutions increase significantly with increasing BD-HMHEC concentration, and the solution becomes viscoelastic at a sufficiently high BD-HMHEC concentration. The core flooding results showed BD-HMHEC flooding improves oil recovery by 7–14% in comparison with HEC flooding at concentrations of 4,000 mg/L under equivalent conditions. Moreover, BD-HMHEC flooding improves oil recovery by 7–8% after conducting water and hydrolyzed polyacrylamide (HPAM) flooding. The oil displacement mechanism of BD-HMHEC solutions is discussed based on a visual evaluation. The results indicate that BD-HMHEC flooding is a feasible means for improving oil recovery after water/HPAM flooding.
Potential health risk of heavy metals in the leather manufacturing industries in Sialkot, Pakistan
Authors: Junaid Muhammad , Hashmi Muhammad Zaffar , Tang Yu-Mei , Malik Riffat Naseem , Pei De-Sheng 
Published: August 2017

AbstractThis is a systematical report on the potential health risk of heavy metals from the leather industries in Pakistan based on multiple biological matrices of the exposed workers and indoor dust samples. The adverse impacts of heavy metals on the oxidative enzyme and their risks to workers’ health were also explored. Our results indicated that the level of Cr in indoor industrial dust was more than twice, compared to the background household dust. Blood, urine and hair samples of exposed workers showed significantly high concentrations of heavy metals, compared to those in the control group. Superoxide dismutase (SOD) level in the blood samples expressed significant positive correlation with Cr and Ni. Total hazard quotients (HQs)/hazard index (HI) were >1, and Cr (VI) exhibited higher cancer risks than that of Cd in the exposed workers. In addition, the PCA-MLR analysis confirmed that the industrial sections; cutting, shivering/crusting, and stitching were the principal contributors of heavy metals in the biological entities of the workers. Taken together, our results highlighted the occupationally exposed groups would likely to experience the potential health risks due to excessive exposure to the heavy metals from the leather industries.
Machine learning quantum phases of matter beyond the fermion sign problem
Authors: Broecker Peter , Carrasquilla Juan , Melko Roger G. , Trebst Simon 
Published: August 2017

AbstractState-of-the-art machine learning techniques promise to become a powerful tool in statistical mechanics via their capacity to distinguish different phases of matter in an automated way. Here we demonstrate that convolutional neural networks (CNN) can be optimized for quantum many-fermion systems such that they correctly identify and locate quantum phase transitions in such systems. Using auxiliary-field quantum Monte Carlo (QMC) simulations to sample the many-fermion system, we show that the Green’s function holds sufficient information to allow for the distinction of different fermionic phases via a CNN. We demonstrate that this QMC + machine learning approach works even for systems exhibiting a severe fermion sign problem where conventional approaches to extract information from the Green’s function, e.g. in the form of equal-time correlation functions, fail.