bluuebunny/crossref_metadata_2025_split huggingface dataset:
Origin and evolution of lysyl oxidases
Authors: Grau-Bové Xavier , Ruiz-Trillo Iñaki , Rodriguez-Pascual Fernando 
Published: May 2015

AbstractLysyl oxidases (LOX) are copper-dependent enzymes that oxidize primary amine substrates to reactive aldehydes. The best-studied role of LOX enzymes is the remodeling of the extracellular matrix (ECM) in animals by cross-linking collagens and elastin, although intracellular functions have been reported as well. Five different LOX enzymes have been identified in mammals, LOX and LOX-like (LOXL) 1 to 4, showing a highly conserved catalytic carboxy terminal domain and more divergence in the rest of the sequence. Here we have surveyed a wide selection of genomes in order to infer the evolutionary history of LOX. We identified LOX proteins not only in animals, but also in many other eukaryotes, as well as in bacteria and archaea – which reveals a pre-metazoan origin for this gene family. LOX genes expanded during metazoan evolution resulting in two superfamilies, LOXL2/L3/L4 and LOX/L1/L5. Considering the current knowledge on the function of mammalian LOX isoforms in ECM remodeling, we propose that LOXL2/L3/L4 members might have preferentially been involved in making cross-linked collagen IV-based basement membrane, whereas the diversification of LOX/L1/L5 forms contributed to chordate/vertebrate-specific ECM innovations, such as elastin and fibronectin. Our work provides a novel view on the evolution of this family of enzymes.
Surface Plasmon Resonance-Induced Stiffening of Silver Nanowires
Authors: Ben Xue , Park Harold S. 
Published: May 2015

AbstractWe report the results of a computational, atomistic electrodynamics study of the effects of electromagnetic waves on the mechanical properties and specifically the Young’s modulus of silver nanowires. We find that the Young’s modulus of the nanowires is strongly dependent on the optical excitation energy, with a peak enhancement occurring at the localized surface plasmon resonance frequency. When the nanowire is excited at the plasmon resonance frequency, the Young’s modulus is found to increase linearly with increasing nanowire aspect ratio, with a stiffening of nearly 15% for a 2 nm cross section silver nanowire with an aspect ratio of 3.5. Furthermore, our results suggest that this plasmon resonance-induced stiffening is stronger for larger diameter nanowires for a given aspect ratio. Our study demonstrates a novel approach to actively tailoring and enhancing the mechanical properties of metal nanowires.
Vacancy-controlled ultrastable nanoclusters in nanostructured ferritic alloys
Authors: Zhang Z. W. , Yao L. , Wang X.-L. , Miller M. K. 
Published: May 2015

AbstractA new class of advanced structural materials, based on the Fe-O-vacancy system, has exceptional resistance to high-temperature creep and excellent tolerance to extremely high-dose radiation. Although these remarkable improvements in properties compared to steels are known to be associated with the Y-Ti-O-enriched nanoclusters, the roles of vacancies in facilitating the nucleation of nanoclusters are a long-standing puzzle, due to the experimental difficulties in characterizing vacancies, particularly in-situ while the nanoclusters are forming. Here we report an experiment study that provides the compelling evidence for the presence of significant concentrations of vacancies in Y-Ti-O-enriched nanoclusters in a nanostructured ferritic alloy using a combination of state-of-the-art atom-probe tomography and in situ small angle neutron scattering. The nucleation of nanoclusters starts from the O-enriched solute clustering with vacancy mediation. The nanoclusters grow with an extremely low growth rate through attraction of vacancies and O:vacancy pairs, leading to the unusual stability of the nanoclusters.
Structural transition in Bcl-xL and its potential association with mitochondrial calcium ion transport
Authors: Rajan Sreekanth , Choi Minjoo , Nguyen Quoc Toan , Ye Hong , Liu Wei , Toh Hui Ting , Kang CongBao , Kamariah Neelagandan , Li Chi , Huang Huiya , White Carl , Baek Kwanghee , Grüber Gerhard , Yoon Ho Sup 
Published: May 2015

AbstractBcl-2 family proteins are key regulators for cellular homeostasis in response to apoptotic stimuli. Bcl-xL, an antiapoptotic Bcl-2 family member, undergoes conformational transitions, which leads to two conformational states: the cytoplasmic and membrane-bound. Here we present the crystal and small-angle X-ray scattering (SAXS) structures of Bcl-xL treated with the mild detergent n-Octyl β-D-Maltoside (OM). The detergent-treated Bcl-xL forms a dimer through three-dimensional domain swapping (3DDS) by swapping helices α6-α8 between two monomers. Unlike Bax, a proapoptotic member of the Bcl-2 family, Bcl-xL is not converted to 3DDS homodimer upon binding BH3 peptides and ABT-737, a BH3 mimetic drug. We also designed Bcl-xL mutants which cannot dimerize and show that these mutants reduced mitochondrial calcium uptake in MEF cells. This illustrates the structural plasticity in Bcl-xL providing hints toward the probable molecular mechanism for Bcl-xL to play a regulatory role in mitochondrial calcium ion transport.
Properties of Water Confined in Ionic Liquids
Authors: Saihara Koji , Yoshimura Yukihiro , Ohta Soichi , Shimizu Akio 
Published: May 2015

AbstractThe varying states of water confined in the nano-domain structures of typical room temperature ionic liquids (ILs) were investigated by 1H NMR and by measurements of self-diffusion coefficients while systematically varying the IL cations and anions. The NMR peaks for water in BF4-based ILs were clearly split, indicating the presence of two discrete states of confined water (H2O and HOD). Proton and/or deuterium exchange rate among the water molecules was very slowly in the water-pocket. Notably, no significant changes were observed in the chemical shifts of the ILs. Self-diffusion coefficient results showed that water molecules exhibit a similar degree of mobility, although their diffusion rate is one order of magnitude faster than that of the IL cations and anions. These findings provide information on a completely new type of confinement, that of liquid water in soft matter.
Quantum Anomalous Hall Effect in Graphene-based Heterostructure
Authors: Zhang Jiayong , Zhao Bao , Yao Yugui , Yang Zhongqin 
Published: May 2015

AbstractQuantum anomalous Hall (QAH) effect, with potential applications in low-power-consumption electronics, is predicted in the heterostructure of graphene on the (001) surface of a real antiferromagnetic insulator RbMnCl3, based on density-functional theory and Wannier function methods. Due to the interactions from the substrate, a much large exchange field (about 280 meV) and an enhanced Rashba spin-orbit coupling are induced in graphene, leading to a topologically nontrivial QAH gap opened in the system. The avenues of enhancing the nontrivial gap are also proposed, from which nearly a gap one order large is achieved. Our work demonstrates that this graphene-based heterostructure is an appropriate candidate to be employed to experimentally observe the QAH effect and explore the promising applications.
Drosophila Rif1 is an essential gene and controls late developmental events by direct interaction with PP1-87B
Authors: Sreesankar Easwaran , Bharathi Vellaichamy , Mishra Rakesh K. , Mishra Krishnaveni 
Published: May 2015

AbstractRif1, identified as a regulator of telomerase in yeast, is an evolutionarily conserved protein and functions in diverse processes including telomere length regulation, epigenetic gene regulation, anti-checkpoint activity, DNA repair and establishing timing of firing at replication origins. Previously we had identified that all Rif1 homologues have PP1 interacting SILK-RVxF motif. In the present study, we show that Drosophila Rif1 is essential for normal fly development and loss of dRif1 impairs temporal regulation of initiation of DNA replication. In multiple tissues dRif1 colocalizes with HP1, a protein known to orchestrate timing of replication in fly. dRif1 associates with chromosomes in a mitotic stage-dependent manner coinciding with dephosphorylation of histones. Ectopic expression of dRif1 causes enlarged larval imaginal discs and early pupal lethality which is completely reversed by co-expression of PP1 87B, the major protein phosphatase in Drosophila, indicating genetic and functional interaction. These findings suggest that dRif1 is an adaptor for PP1 and functions by recruiting PP1 to multiple sites on the chromosome.
The proteome of Hypobaric Induced Hypoxic Lung: Insights from Temporal Proteomic Profiling for Biomarker Discovery
Authors: Ahmad Yasmin , Sharma Narendra K. , Ahmad Mohammad Faiz , Sharma Manish , Garg Iti , Srivastava Mousami , Bhargava Kalpana 
Published: May 2015

AbstractExposure to high altitude induces physiological responses due to hypoxia. Lungs being at the first level to face the alterations in oxygen levels are critical to counter and balance these changes. Studies have been done analysing pulmonary proteome alterations in response to exposure to hypobaric hypoxia. However, such studies have reported the alterations at specific time points and do not reflect the gradual proteomic changes. These studies also identify the various biochemical pathways and responses induced after immediate exposure and the resolution of these effects in challenge to hypobaric hypoxia. In the present study, using 2-DE/MS approach, we attempt to resolve these shortcomings by analysing the proteome alterations in lungs in response to different durations of exposure to hypobaric hypoxia. Our study thus highlights the gradual and dynamic changes in pulmonary proteome following hypobaric hypoxia. For the first time, we also report the possible consideration of SULT1A1, as a biomarker for the diagnosis of high altitude pulmonary edema (HAPE). Higher SULT1A1 levels were observed in rats as well as in humans exposed to high altitude, when compared to sea-level controls. This study can thus form the basis for identifying biomarkers for diagnostic and prognostic purposes in responses to hypobaric hypoxia.
Resilience to orthostasis and haemorrhage: A pilot study of common genetic and conditioning mechanisms
Authors: Davydov Dmitry M. , Zhdanov Renad I. , Dvoenosov Vladimir G. , Kravtsova Olga A. , Voronina Elena N. , Filipenko Maxim L. 
Published: May 2015

AbstractA major challenge presently is not only to identify the genetic polymorphisms increasing risk to diseases, but to also find out factors and mechanisms, which can counteract a risk genotype by developing a resilient phenotype. The objective of this study was to examine acquired and innate vagal mechanisms that protect against physical challenges and haemorrhages in 19 athletes and 61 non-athletes. These include examining change in heart rate variability (HF-HRV; an indicator of vagus activity) in response to orthostatic challenge, platelet count (PLT), mean platelet volume (MPV) and single-nucleotide polymorphisms in genes that encode several coagulation factors, PAI-1 and MTHFR. Individual differences in PLT and MPV were significant predictors, with opposite effects, of the profiles of the HF-HRV changes in response to orthostasis. Regular physical training of athletes indirectly (through MPV) modifies the genetic predisposing effects of some haemostatic factors (PAI-1 and MTHFR) on vagal tone and reactivity. Individual differences in vagal tone were also associated with relationships between Factor 12 C46T and Factor 11 C22771T genes polymorphisms. This study showed that genetic predispositions for coagulation are modifiable. Its potential significance is promoting advanced protection against haemorrhages in a variety of traumas and injuries, especially in individuals with coagulation deficits.
Development of biodegradable Zn-1X binary alloys with nutrient alloying elements Mg, Ca and Sr
Authors: Li H. F. , Xie X. H. , Zheng Y. F. , Cong Y. , Zhou F. Y. , Qiu K. J. , Wang X. , Chen S. H. , Huang L. , Tian L. , Qin L. 
Published: May 2015

AbstractBiodegradable metals have attracted considerable attentions in recent years. Besides the early launched biodegradable Mg and Fe metals, Zn, an essential element with osteogenic potential of human body, is regarded and studied as a new kind of potential biodegradable metal quite recently. Unfortunately, pure Zn is soft, brittle and has low mechanical strength in the practice, which needs further improvement in order to meet the clinical requirements. On the other hand, the widely used industrial Zn-based alloys usually contain biotoxic elements (for instance, ZA series contain toxic Al elements up to 40 wt.%), which subsequently bring up biosafety concerns. In the present work, novel Zn-1X binary alloys, with the addition of nutrition elements Mg, Ca and Sr were designed (cast, rolled and extruded Zn-1Mg, Zn-1Ca and Zn-1Sr). Their microstructure and mechanical property, degradation andin vitroandin vivobiocompatibility were studied systematically. The results demonstrated that the Zn-1X (Mg, Ca and Sr) alloys have profoundly modified the mechanical properties and biocompatibility of pure Zn. Zn-1X (Mg, Ca and Sr) alloys showed great potential for use in a new generation of biodegradable implants, opening up a new avenue in the area of biodegradable metals.
SUMO1 Affects Synaptic Function, Spine Density and Memory
Authors: Matsuzaki Shinsuke , Lee Linda , Knock Erin , Srikumar Tharan , Sakurai Mikako , Hazrati Lili-Naz , Katayama Taiichi , Staniszewski Agnieszka , Raught Brian , Arancio Ottavio , Fraser Paul E. 
Published: May 2015

AbstractSmall ubiquitin-like modifier-1 (SUMO1) plays a number of roles in cellular events and recent evidence has given momentum for its contributions to neuronal development and function. Here, we have generated a SUMO1 transgenic mouse model with exclusive overexpression in neurons in an effort to identify in vivo conjugation targets and the functional consequences of their SUMOylation. A high-expressing line was examined which displayed elevated levels of mono-SUMO1 and increased high molecular weight conjugates in all brain regions. Immunoprecipitation of SUMOylated proteins from total brain extract and proteomic analysis revealed ~95 candidate proteins from a variety of functional classes, including a number of synaptic and cytoskeletal proteins. SUMO1 modification of synaptotagmin-1 was found to be elevated as compared to non-transgenic mice. This observation was associated with an age-dependent reduction in basal synaptic transmission and impaired presynaptic function as shown by altered paired pulse facilitation, as well as a decrease in spine density. The changes in neuronal function and morphology were also associated with a specific impairment in learning and memory while other behavioral features remained unchanged. These findings point to a significant contribution of SUMO1 modification on neuronal function which may have implications for mechanisms involved in mental retardation and neurodegeneration.
Transmission of Tomato Yellow Leaf Curl Virus by Bemisia tabaci as Affected by Whitefly Sex and Biotype
Authors: Ning Wenxi , Shi Xiaobin , Liu Baiming , Pan Huipeng , Wei Wanting , Zeng Yang , Sun Xinpei , Xie Wen , Wang Shaoli , Wu Qingjun , Cheng Jiaxu , Peng Zhengke , Zhang Youjun 
Published: May 2015

AbstractBemisia tabaci is a serious pest of vegetables and other crops worldwide. The most damaging and predominant B. tabaci biotypes are B and Q and both are vectors of tomato yellow leaf curl virus (TYLCV). Previous research has shown that Q outperforms B in many respects but comparative research is lacking on the ability of B and Q to transmit viruses. In the present study, we tested the hypothesis that B and Q differ in their ability to transmit TYLCV and that this difference helps explain TYLCV outbreaks. We compared the acquisition, retention and transmission of TYLCV by B and Q females and males. We found that Q females are more efficient than Q males, B females and B males at TYLCV acquisition and transmission. Although TYLCV acquisition and transmission tended to be greater for B females than B males, the differences were not statistically significant. Based on electrical penetration graphs determination of phloem sap ingestion parameters, females fed better than males and Q females fed better than Q males, B females, or B males. These results are consistent with the occurrences of TYLCV outbreaks in China, which have been associated with the spread of Q rather than B.
Agrobacterium-mediated transient MaFT expression in mulberry (Morus alba L.) leaves
Authors: Wu Su-Li , Yang Xiao-Bing , Liu Li-Qun , Jiang Tao , Wu Hai , Su Chao , Qian Yong-Hua , Jiao Feng 
Published: May 2015

Abstract
To optimize Agrobacterium-mediated transient transformation assay in mulberry (Morus alba L.), various infiltration methods, Agrobacterium tumefaciens (A. tumefaciens) strains, and bacterial concentrations were tested in mulberry seedlings. Compared with LBA4404, GV3101 harboring pBE2133 plasmids presented stronger GUS signals at 3 days post infiltration using syringe. Recombinant plasmids pBE2133:GFP and pBE2133:GFP:MaFT were successfully constructed. Transient expression of MaFT:GFP protein was found in leaves, petiole (cross section), and shoot apical meristem (SAM) of mulberry according to the GFP signal. Moreover, MaFT:GFP mRNA was also detected in leaves and SAM via RT-PCR and qRT-PCR. An efficient transient transformation system could be achieved in mulberry seedlings by syringe using A. tumefaciens GV3101 at the OD600 of 0.5. The movement of MaFT expression from leaves to SAM might trigger the precocious flowering of mulberry.
β-Galactosidase from Ginkgo biloba seeds active against β-galactose-containing N-glycans: purification and characterization
Authors: Rahman Md Ziaur , Maeda Megumi , Kimura Yoshinobu 
Published: May 2015

Abstract
In this study, we purified an acidic β-galactosidase to homogeneity from Ginkgo biloba seeds (β-Gal’ase Gb-1) with approximately 270-fold purification. A molecular mass of the purified β-Gal’ase Gb-1 was estimated about 35 kDa by gel filtration and 32 kDa by SDS-PAGE under non-reducing condition, respectively. On the other hand, β-Gal’ase Gb-1 produced a single band with a molecular mass of 16 kDa by SDS-PAGE under reducing condition. The N-terminal amino acid sequences of 32 kDa and 16 kDa molecules were the same and identified as H-K-A-N-X-V-T-V-A-F-V-M-T-Q-H-, suggesting that β-Gal’ase Gb-1 may function as a homodimeric structure in vivo. When complex-type N-glycans containing β-galactosyl residues were used as substrates, β-Gal’ase Gb-1 showed substantial activity for β1-4 galactosyl residue and modest activity for β1-3 galactosyl residue with an optimum pH near 5.0. Based on these results, the involvement of β-Gal’ase Gb-1 in the degradation of plant complex-type N-glycans is discussed.
QVZ: lossy compression of quality values
Authors: Malysa Greg , Hernaez Mikel , Ochoa Idoia , Rao Milind , Ganesan Karthik , Weissman Tsachy 
Published: May 2015

Abstract

Motivation
Recent advancements in sequencing technology have led to a drastic reduction in the cost of sequencing a genome. This has generated an unprecedented amount of genomic data that must be stored, processed and transmitted. To facilitate this effort, we propose a new lossy compressor for the quality values presented in genomic data files (e.g. FASTQ and SAM files), which comprise roughly half of the storage space (in the uncompressed domain). Lossy compression allows for compression of data beyond its lossless limit.

Results
The proposed algorithm QVZ exhibits better rate-distortion performance than the previously proposed algorithms, for several distortion metrics and for the lossless case. Moreover, it allows the user to define any quasi-convex distortion function to be minimized, a feature not supported by the previous algorithms. Finally, we show that QVZ-compressed data exhibit better performance in the genotyping than data compressed with previously proposed algorithms, in the sense that for a similar rate, a genotyping closer to that achieved with the original quality values is obtained.

Availability and implementation
QVZ is written in C and can be downloaded from https://github.com/mikelhernaez/qvz.

Contact
mhernaez@stanford.edu or gmalysa@stanford.edu or iochoa@stanford.edu

Supplementary information
Supplementary data are available at Bioinformatics online.
“Lordy, Lordy, Look Who’s 40!” The Journal of Consumer Research Reaches a Milestone
Authors: Rapp Justine M. , Hill Ronald Paul 
Published: May 2015

Abstract
The Journal of Consumer Research has completed four decades as one of the top journals in the larger field of marketing as well as the premier outlet for research on consumer behavior. This elite status is based, in part, on its stated objective as a multidisciplinary journal that allows for a variety of topics, methods, and populations that are central to collectives of scholars from many social sciences and methodological orientations. While a few articles have reviewed the level of diversity within the journal and among its peers, none to date has taken an expansive look at what is studied, how it is examined, and which consumers are used to determine the validity of our theoretical contributions. Thus this article looks across the life span of JCR to address these issues and finds considerable progress along with major areas that should be addressed by the community of researchers that constitutes our field.
The Value of Time
Authors: Festjens Anouk , Janiszewski Chris 
Published: May 2015

Abstract
Ten studies are used to document that time is valued in accordance with a double-kinked value function. There is a zone of indifference for small time gains (losses), increasing marginal utility (disutility) for moderate time gains (losses), and diminishing marginal utility (disutility) for large time gains (losses). Moderate amounts of time exhibit increasing marginal utility (disutility) because larger blocks of time provide a more diverse set of usage opportunities. It is only when it is difficult to imagine how more (less) time would be beneficial (detrimental) that there is diminishing marginal utility (disutility) for time. Thus time valuation shows increasing marginal utility when there is a time deficit, but diminishing marginal utility when there is a time surplus. These findings have implications for how other resources might be valued.
CMR—basic principles
Authors: Wright Jeremy , Bogaert Jan 
Published: May 2015

Abstract
Recent advances have enabled CMR to come close to the goal of a complete examination of the cardiovascular system by a single modality. It can provide relevant information on most aspects of heart structure, global and regional ventricular function, valve function, flow patterns, myocardial perfusion, coronary anatomy, and myocardial viability, all obtained non-invasively in a single study in 30–60 min. The aim of this chapter is to describe the physics and practical aspects of CMR and then explore the available pulse sequences, so that the clinical utility of CMR can be maximized.