bluuebunny/crossref_metadata_2025_split huggingface dataset:
Welding of Semiconductor Nanowires by Coupling Laser-Induced Peening and Localized Heating
Authors: Rickey Kelly M. , Nian Qiong , Zhang Genqiang , Chen Liangliang , Suslov Sergey , Bhat S. Venkataprasad , Wu Yue , Cheng Gary J. , Ruan Xiulin 
Published: November 2015

AbstractWe demonstrate that laser peening coupled with sintering of CdTe nanowire films substantially enhances film quality and charge transfer while largely maintaining basic particle morphology. During the laser peening phase, a shockwave is used to compress the film. Laser sintering comprises the second step, where a nanosecond pulse laser beam welds the nanowires. Microstructure, morphology, material content and electrical conductivities of the films are characterized before and after treatment. The morphology results show that laser peening can decrease porosity and bring nanowires into contact and pulsed laser heating fuses those contacts. Multiphysics simulations coupling electromagnetic and heat transfer modules demonstrate that during pulsed laser heating, local EM field enhancement is generated specifically around the contact areas between two semiconductor nanowires, indicating localized heating. The characterization results indicate that solely laser peening or sintering can only moderately improve the thin film quality; however, when coupled together as laser peen sintering (LPS), the electrical conductivity enhancement is dramatic. LPS can decrease resistivity up to a factor of ~10,000, resulting in values on the order of ~105 Ω-cm in some cases, which is comparable to CdTe thin films. Our work demonstrates that LPS is an effective processing method to obtain high-quality semiconductor nanocrystal films.
Biochemical and structural characterization of a novel ubiquitin-conjugating enzyme E2 from Agrocybe aegeria reveals Ube2w family-specific properties
Authors: Qi Chao , Li De-Feng , Feng Lei , Hou Yanjie , Sun Hui , Wang Da-Cheng , Liu Wei 
Published: November 2015

AbstractUbiquitination is a post-translational modification that is involved in myriad cellar regulation and disease pathways. The ubiquitin-conjugating enzyme (E2) is an important player in the ubiquitin transfer pathway. Although many E2 structures are available, not all E2 families have known structures and three-dimensional structures from fungal organisms other than yeast are lacking. We report here the crystal structure of UbcA1, which is a novel ubiquitin-conjugating enzyme identified from the edible and medicinal mushroom Agrocybe aegerita and displays potential antitumor properties. The protein belongs to the Ube2w family and shows similar biochemical characteristics to human Ube2w, including monomer-dimer equilibrium in solution, α-NH2 ubiquitin-transfer activity and a mechanism to recognize backbone atoms of intrinsically disordered N-termini in substrates. Its structure displays a unique C-terminal conformation with an orientation of helix α3 that is completely different from the reported E2 structures but similar to a recently reported NMR ensemble of Ube2w. A mutagenesis study on this novel enzyme revealed that an intact C-terminus is significant for protein dimerization and enzymatic activity. As the first crystallized full-length protein of this family, UbcA1 may supersede the truncated X-ray structure of Ube2w (PDB entry 2A7L) as the representative structure of the Ube2w family.
A novel approach combining self-organizing map and parallel factor analysis for monitoring water quality of watersheds under non-point source pollution
Authors: Zhang Yixiang , Liang Xinqiang , Wang Zhibo , Xu Lixian 
Published: November 2015

AbstractHigh content of organic matter in the downstream of watersheds underscored the severity of non-point source (NPS) pollution. The major objectives of this study were to characterize and quantify dissolved organic matter (DOM) in watersheds affected by NPS pollution and to apply self-organizing map (SOM) and parallel factor analysis (PARAFAC) to assess fluorescence properties as proxy indicators for NPS pollution and labor-intensive routine water quality indicators. Water from upstreams and downstreams was sampled to measure dissolved organic carbon (DOC) concentrations and excitation-emission matrix (EEM). Five fluorescence components were modeled with PARAFAC. The regression analysis between PARAFAC intensities (Fmax) and raw EEM measurements indicated that several raw fluorescence measurements at target excitation-emission wavelength region could provide similar DOM information to massive EEM measurements combined with PARAFAC. Regression analysis between DOC concentration and raw EEM measurements suggested that some regions in raw EEM could be used as surrogates for labor-intensive routine indicators. SOM can be used to visualize the occurrence of pollution. Relationship between DOC concentration and PARAFAC components analyzed with SOM suggested that PARAFAC component 2 might be the major part of bulk DOC and could be recognized as a proxy indicator to predict the DOC concentration.
Electrodeposited Ultrathin TiO2 Blocking Layers for Efficient Perovskite Solar Cells
Authors: Su Tzu-Sen , Hsieh Tsung-Yu , Hong Cheng-You , Wei Tzu-Chien 
Published: November 2015

AbstractIn this study, the electrodeposition (ED) of ultrathin, compact TiO2 blocking layers (BLs) on fluorine-doped tin oxide (FTO) glass for perovskite solar cells (PSCs) is evaluated. This bottom-up method allows for controlling the morphology and thickness of TiO2 films by simply manipulating deposition conditions. Compared with BLs produced using the spin-coating (SC) method, BLs produced using ED exhibit satisfactory surface coverage, even with a film thickness of 29 nm. Evidence from cyclic voltammetry shows that an ED BL suppresses interfacial recombination more profoundly than an SC BL does, consequently improving the photovoltaic properties of the PSC significantly. A PSC equipped with an ED TiO2 BL having a 13.6% power conversion efficiency is demonstrated.
Neurotoxicity induced by zinc oxide nanoparticles: age-related differences and interaction
Authors: Tian Lei , Lin Bencheng , Wu Lei , Li Kang , Liu Huanliang , Yan Jun , Liu Xiaohua , Xi Zhuge 
Published: November 2015

AbstractThis study mainly investigated the neurotoxicity induced by zinc oxide nanoparticle (ZnO NP) in different-aged mice and the interaction between age and ZnO NP exposure. Sixty adult and old male C57BL/6J mice were assigned to four groups based on a two-factor (age and ZnO NP exposure) design. Results showed that ZnO NPs (5.6 mg/kg, intraperitoneal) induced increased production of pro-inflammatory cytokines in the serum and the brain of mice. A synergistic reaction between aging and ZnO NP exposure occurred regarding serum interleukin 1 (IL-1) and interleukin 6 (IL-6). In the brain, increased oxidative stress level, impaired learning and memory abilities and hippocampal pathological changes were identified, especially in old mice, following ZnO NP exposure. Then, a potential mechanism of cognitive impairment was examined. The contents of hippocampal cAMP response element binding protein (CREB), phosphorylated CREB, synapsin I and cAMP were decreased in an age-dependent manner and the most substantial decrease occurred in old mice treated with ZnO NPs. These findings demonstrated for the first time that aging and ZnO NP exposure synergistically influenced systemic inflammation and indicated old individuals were more susceptible to ZnO NP-induced neurotoxicity. One of the mechanisms might due to the supression of cAMP/CREB signaling.
The role of host genetic factors in respiratory tract infectious diseases: systematic review, meta-analyses and field synopsis
Authors: Patarčić Inga , Gelemanović Andrea , Kirin Mirna , Kolčić Ivana , Theodoratou Evropi , Baillie Kenneth J. , de Jong Menno D. , Rudan Igor , Campbell Harry , Polašek Ozren 
Published: November 2015

AbstractHost genetic factors have frequently been implicated in respiratory infectious diseases, often with inconsistent results in replication studies. We identified 386 studies from the total of 24,823 studies identified in a systematic search of four bibliographic databases. We performed meta-analyses of studies on tuberculosis, influenza, respiratory syncytial virus, SARS-Coronavirus and pneumonia. One single-nucleotide polymorphism from IL4 gene was significant for pooled respiratory infections (rs2070874; 1.66 [1.29–2.14]). We also detected an association of TLR2 gene with tuberculosis (rs5743708; 3.19 [2.03–5.02]). Subset analyses identified CCL2 as an additional risk factor for tuberculosis (rs1024611; OR = 0.79 [0.72–0.88]). The IL4-TLR2-CCL2 axis could be a highly interesting target for translation towards clinical use. However, this conclusion is based on low credibility of evidence - almost 95% of all identified studies had strong risk of bias or confounding. Future studies must build upon larger-scale collaborations, but also strictly adhere to the highest evidence-based principles in study design, in order to reduce research waste and provide clinically translatable evidence.
Transgenerational Developmental Programming of Ovarian Reserve
Authors: Aiken C. E. , Tarry-Adkins J. L. , Ozanne S. E. 
Published: November 2015

AbstractExposure to an adverse early-life environment leads to long-term health problems, many of which are recapitulated in subsequent generations. The female reproductive tract is particularly sensitive to early-life influences and plays a pivotal role in programming the conceptus. We examine the influence of suboptimal grandmaternal diet on reproductive potential of granddaughters in the absence of any further dietary manipulations in the daughters in a rat low-protein diet model. Exposure to low-protein grand-maternal diet leads to decreased ovarian reserve and increased intra-abdominal fat mass in granddaughters, accompanied by accelerated accumulation of oxidative stress and mtDNA copy number instability in the ovaries. Ovarian telomere length declines more rapidly in the exposed granddaughters, indicating accelerated ageing in the reproductive tract. Thus, we demonstrate that suboptimal grandmaternal diet during pregnancy accelerates reproductive ageing across subsequent generations. These findings have important implications for understanding both individual rates of decline in fertility with age and the clinical impact of current global trends towards delayed childbearing.
High throughput optical lithography by scanning a massive array of bowtie aperture antennas at near-field
Authors: Wen X. , Datta A. , Traverso L. M. , Pan L. , Xu X. , Moon E. E. 
Published: November 2015

AbstractOptical lithography, the enabling process for defining features, has been widely used in semiconductor industry and many other nanotechnology applications. Advances of nanotechnology require developments of high-throughput optical lithography capabilities to overcome the optical diffraction limit and meet the ever-decreasing device dimensions. We report our recent experimental advancements to scale up diffraction unlimited optical lithography in a massive scale using the near field nanolithography capabilities of bowtie apertures. A record number of near-field optical elements, an array of 1,024 bowtie antenna apertures, are simultaneously employed to generate a large number of patterns by carefully controlling their working distances over the entire array using an optical gap metrology system. Our experimental results reiterated the ability of using massively-parallel near-field devices to achieve high-throughput optical nanolithography, which can be promising for many important nanotechnology applications such as computation, data storage, communication and energy.
Chorionic Villus Sampling in Assisted Versus Spontaneous Conception Twins
Authors: Daskalakis Georgios , Antsaklis Panagiotis , Gourounti Kleanthi , Theodora Mariana , Sindos Michail , Papantoniou Nikolaos , Loutradis Dimitrios 
Published: November 2015

Abstract
Purpose To compare the outcome of chorionic villus sampling (CVS) in twin pregnancies following assisted reproduction technology (ART) versus twins that have been conceived spontaneously.
Materials and Methods Retrospective analysis of dichorionic twin pregnancies that underwent CVS between 1986 and 2013 at our department which is a tertiary center for fetal medicine. 32 twin pregnancies after ART and 130 spontaneously conceived twin pregnancies, which underwent CVS, were analyzed.
Results No difference was observed in the pregnancy loss rate between the two groups (0 % in the ART group vs. 3 % in the spontaneous twins group). The rate of preterm delivery before 28 weeks was higher in the ART group (18.8 %) compared to the control group (1.6 %). The perinatal mortality rate was similar in the two groups.
Conclusion The pregnancy loss rate following CVS is similar in ART twins and in spontaneous twins. However, the risk of prematurity before 28 weeks is significantly higher in the ART group.
3.1 Dihydroxylation of Aromatics and Alkenes
Authors: Allen C. C. R. 
Published: November 2015

AbstractThe use of ring-hydroxylating dioxygenase enzymes for the biotransformation of aromatic hydrocarbons, alkenes, and phenols to give chiral cis-dihydrodiol metabolites is of significant potential for the preparation of chiral precursors for organic synthesis. Many products are produced with high enantiomeric excess, and a wide number of biotransformations have been studied. This type of biotransformation is typically used to convert readily available starting materials into single enantiomer bioproducts in a single step. The enzymes are multicomponent systems comprising two or more protein subunits. Furthermore, there is a requirement for reducing equivalents (e.g., NADH) and therefore whole-cell biocatalysts are used, either as wild-type strains, mutants, or clones. Recently, there have been significant developments in the use of molecular biology methods to improve these biocatalysts. This review covers the approaches employed to perform specific types of biotransformation, namely arene, alkene, and phenol hydroxylation.
3.3.1 Oxidation Using Dehydrogenases
Authors: Hollmann F. 
Published: November 2015

AbstractThe use of alcohol dehydrogenases has a number of advantages over traditional chemical methods for the oxidation of alcohols. These include the mild reaction conditions, the avoidance of tedious protecting-group strategies, and the high regio- and chemoselectivites. This review highlights the most important alcohol dehydrogenases used for biocatalysis and discusses the systems used for cofactor regeneration when employing these enzymes. The oxidation of primary alcohols to aldehydes and further to carboxylic acids is presented, along with examples of subsequent cascade reactions (e.g., oxidation–lactonization of diols). The oxidation of secondary alcohols to ketones, including the application of this reaction in kinetic resolutions and deracemizations, is also described.
3.7.1 Isoprenoids, Polyketides, and (Non)ribosomal Peptides
Authors: Quin M. , Flynn C. , Ellinger J. , Schmidt-Dannert C. 
Published: November 2015

AbstractThis chapter describes methods for the biosynthesis and biocatalysis of natural products belonging to the isoprenoids, polyketides (acetate pathway), phenylpropanoids (shikimate pathway), alkaloids, and ribosomal and nonribosomal peptides. Recent advances in genome-sequencing technologies and synthetic biology approaches are discussed, and biological approaches are given where available.
3.8.1 Designed Enzymatic Cascades
Authors: Oroz-Guinea I. , Fernández Lucas J. , Hormigo Cisneros D. , Garcia-Junceda E. 
Published: November 2015

AbstractOne of the major advantages of enzymes as catalysts is that many of them operate under similar conditions of pH, temperature, etc. and thus can be combined in one-pot multistep reaction pathways. The joint action of a sequence of enzymes allows the construction of complex structures from simple elements, a reversible process to be made irreversible, or an equilibrium reaction to be shifted in such a way that enantiomerically pure products can be obtained from racemic or prochiral substrates. This chapter highlights recent developments involving multienzyme cascade reactions for the synthesis of various classes of organic compounds.
Structural basis for the binding of tryptophan-based motifs by δ-COP
Authors: Suckling Richard J. , Poon Pak Phi , Travis Sophie M. , Majoul Irina V. , Hughson Frederick M. , Evans Philip R. , Duden Rainer , Owen David J. 
Published: November 2015

Significance
Eukaryotic cells contain many different organelles between which vesicles traffic material. COPI-coated vesicles mediate essential, evolutionarily conserved retrograde trafficking pathways from the Golgi to the endoplasmic reticulum (ER) and within the Golgi. We have determined structures of the μ-homology domain (MHD) of the COPI δ-COP subunit in complex with tryptophan-based motifs from the ER-resident vesicle-docking/tethering complex Dsl1, giving a mechanistic description of a tether/coat interaction; furthermore we demonstrate that this interaction plays a role in facilitating COPI-coated vesicle transport in vivo. Our work demonstrates the structure of each eukaryotic cell MHD and shows that MHDs are adaptable scaffolds that can interact specifically with a range of proteins and phospholipids at different positions.
Virion-associated phosphatidylethanolamine promotes TIM1-mediated infection by Ebola, dengue, and West Nile viruses
Authors: Richard Audrey Stéphanie , Zhang Adam , Park Sun-Jin , Farzan Michael , Zong Min , Choe Hyeryun 
Published: November 2015

Significance
Many viruses use phosphatidylserine (PS) receptors to gain entry into target cells, and phagocytes use these receptors to clear apoptotic cells. PS receptors mediate these activities by binding PS on the viruses or apoptotic cells. We demonstrate here that phosphatidylethanolamine (PE) is also a ligand for PS receptors, and that PE plays a key role in apoptotic cell clearance and infection of various pathogenic viruses, including West Nile, dengue, and Ebola viruses. This finding provides significant insights; it clarifies how PS receptors promote viral infection, suggests PE is a useful broad-spectrum antiviral target, and deepens our understanding of apoptosis and the process by which apoptotic cells are cleared.
Transition to farming more likely for small, conservative groups with property rights, but increased productivity is not essential
Authors: Gallagher Elizabeth M. , Shennan Stephen J. , Thomas Mark G. 
Published: November 2015

SignificanceThe Neolithic revolution was one of the most influential events in human history, but why and how it occurred are still not fully understood. To try to infer what may have happened, mathematical models have been developed. We describe and implement a method of parameter space exploration when ideal outcomes of a model are known. This method is applied to a published agent-based model for the Neolithic transition, revealing previously unidentified parameter interactions, sensitivities, and complexities. Our results highlight the importance of group structuring, group size, conservatism, and farming-friendly property rights, for the switch to farming around 12,000 years ago. We also find that, although advantageous, it is not essential that farming productivity is greater than foraging productivity.
Facilitation shifts paradigms and can amplify coastal restoration efforts
Authors: Silliman Brian R. , Schrack Elizabeth , He Qiang , Cope Rebecca , Santoni Amanda , van der Heide Tjisse , Jacobi Ralph , Jacobi Mike , van de Koppel Johan 
Published: November 2015

SignificanceRestoration is rapidly becoming a key conservation tool to counteract coastal degradation and enhance biodiversity and the provisioning of ecosystem services. This paper shows that the success of wetland restorations can be significantly enhanced through simple, no-cost design changes that harness positive species interactions. Although 96% of restoration organizations we surveyed plant propagules in dispersed arrangements that seek to reduce competition, our cross-continent study using clumped arrangements to harness facilitation challenges this conventional theory. Harnessing previously untapped, but naturally occurring, facilitation through small adjustments in design resulted in significantly higher yields and survivorship with no additional cost. These results highlight the value for the use of facilitation theory in restoration designs and call for integration of this theory into practice.
Identification and Distribution of Morphologically Conserved Smoothhound Sharks in the Northern Gulf of Mexico
Authors: Giresi Melissa M. , Grubbs R. Dean , Portnoy David S. , Driggers William B. , Jones Lisa , Gold John R. 
Published: November 2015

AbstractIdentification of sharks within the genus Mustelus (smoothhound sharks) is problematic because of extensive overlap in external morphology among species. Consequently, species‐specific management of smoothhound shark resources is difficult when multiple species inhabit the same geographic region. The species identification and distribution of smoothhound sharks in the northern Gulf of Mexico (the Gulf) were assessed using sequences of mitochondrial DNA, nuclear‐encoded microsatellites, and catch data. Phylogenetic analysis of 1,047 base pairs of mitochondrially encoded ND‐2 sequences and Bayesian clustering of multilocus genotypes at 15 microsatellites revealed three genetically distinct monophyletic lineages (clades) of smoothhound sharks in the Gulf. Examination of external morphology revealed characters that distinguished each genetically distinct clade, and based on species descriptions and comparisons with the type and other specimens in established collections, the lineages were identified as Smooth Dogfish Mustelus canis, Florida Smoothhound Mustelus norrisi, and Gulf Smoothhound Mustelus sinusmexicanus. Two hundred and eighty‐seven smoothhound sharks sampled from across the Gulf were then assigned unequivocally, based on genetic data, to one of the three species. Multifactorial analysis and homogeneity tests of species‐specific means versus grand means of spatiotemporal factors (depth, longitude, and month) at capture indicated significant differences among the three species with respect to all three factors. On average, the Smooth Dogfish is found in deeper waters than the Gulf Smoothhound, whereas the Florida Smoothhound inhabits relatively shallow waters. A diagnostic key for the field identification of adult specimens of each species is provided.