bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep Sequencing of Random Mutant Libraries Reveals the Active Site of the Narrow Specificity CphA Metallo-β-Lactamase is Fragile to Mutations
Authors: Sun Zhizeng , Mehta Shrenik C. , Adamski Carolyn J. , Gibbs Richard A. , Palzkill Timothy 
Published: September 2016

AbstractCphA is a Zn2+-dependent metallo-β-lactamase that efficiently hydrolyzes only carbapenem antibiotics. To understand the sequence requirements for CphA function, single codon random mutant libraries were constructed for residues in and near the active site and mutants were selected for E. coli growth on increasing concentrations of imipenem, a carbapenem antibiotic. At high concentrations of imipenem that select for phenotypically wild-type mutants, the active-site residues exhibit stringent sequence requirements in that nearly all residues in positions that contact zinc, the substrate, or the catalytic water do not tolerate amino acid substitutions. In addition, at high imipenem concentrations a number of residues that do not directly contact zinc or substrate are also essential and do not tolerate substitutions. Biochemical analysis confirmed that amino acid substitutions at essential positions decreased the stability or catalytic activity of the CphA enzyme. Therefore, the CphA active - site is fragile to substitutions, suggesting active-site residues are optimized for imipenem hydrolysis. These results also suggest that resistance to inhibitors targeted to the CphA active site would be slow to develop because of the strong sequence constraints on function.
Effects of allergic diseases and age on the composition of serum IgG glycome in children
Authors: Pezer Marija , Stambuk Jerko , Perica Marija , Razdorov Genadij , Banic Ivana , Vuckovic Frano , Gospic Adrijana Miletic , Ugrina Ivo , Vecenaj Ana , Bakovic Maja Pucic , Lokas Sandra Bulat , Zivkovic Jelena , Plavec Davor , Devereux Graham , Turkalj Mirjana , Lauc Gordan 
Published: September 2016

AbstractIt is speculated that immunoglobulin G (IgG) plays a regulatory role in allergic reactions. The glycans on the Fc region are known to affect IgG effector functions, thereby possibly having a role in IgG modulation of allergic response. This is the first study investigating patients’ IgG glycosylation profile in allergic diseases. Subclass specific IgG glycosylation profile was analyzed in two cohorts of allergen sensitized and non-sensitized 3- to 11-year-old children (conducted at University of Aberdeen, UK and Children’s Hospital Srebrnjak, Zagreb, Croatia) with 893 subjects in total. IgG was isolated from serum/plasma by affinity chromatography on Protein G. IgG tryptic glycopeptides were analyzed by liquid chromatography electrospray ionization mass spectrometry. In the Zagreb cohort IgG glycome composition changed with age across all IgG subclasses. In both cohorts, IgG glycome composition did not differ in allergen sensitized subjects, nor children sensitized to individual allergens, single allergen mean wheal diameter or positive wheal sum values. In the Zagreb study the results were also replicated for high total serum IgE and in children with self-reported manifest allergic disease. In conclusion, our findings demonstrate no association between serum IgG glycome composition and allergic diseases in children.
Grain Boundary Induced Bias Instability in Soluble Acene-Based Thin-Film Transistors
Authors: Nguyen Ky V. , Payne Marcia M. , Anthony John E. , Lee Jung Hun , Song Eunjoo , Kang Boseok , Cho Kilwon , Lee Wi Hyoung 
Published: September 2016

AbstractSince the grain boundaries (GBs) within the semiconductor layer of organic field-effect transistors (OFETs) have a strong influence on device performance, a substantial number of studies have been devoted to controlling the crystallization characteristics of organic semiconductors. We studied the intrinsic effects of GBs within 5,11-bis(triethylsilylethynyl) anthradithiophene (TES-ADT) thin films on the electrical properties of OFETs. The GB density was easily changed by controlling nulceation event in TES-ADT thin films. When the mixing time was increased, the number of aggregates in as-spun TES-ADT thin films were increased and subsequent exposure of the films to 1,2-dichloroethane vapor led to a significant increase in the number of nuleation sites, thereby increasing the GB density of TES-ADT spherulites. The density of GBs strongly influences the angular spread and crystallographic orientation of TES-ADT spherulites. Accordingly, the FETs with higher GB densities showed much poorer electrical characteristics than devices with lower GB density. Especially, GBs provide charge trapping sites which are responsible for bias-stress driven electrical instability. Dielectric surface treatment with a polystyrene brush layer clarified the GB-induced charge trapping by reducing charge trapping at the semiconductor-dielectric interface. Our study provides an understanding on GB induced bias instability for the development of high performance OFETs.
miR-224-3p inhibits autophagy in cervical cancer cells by targeting FIP200
Authors: Fang Wang , Shu Shan , Yongmei Li , Endong Zhu , Lirong Yin , Bei Sun 
Published: September 2016

AbstractCervical cancer (CC) is a malignant solid tumor, which is one of the main causes of morbidity and mortality in women. Persistent High-risk human papillomavirus (hrHPV) infection is closely related to cervical cancer and autophagy has been suggested to inhibit viral infections. miRNAs have been reported to regulate autophagy in many solid tumors with many studies implicating miR-224-3p in the regulation of autophagy. In this study, we performed a miRNA microarray analysis on CC tissues and found that a large number of miRNAs with differential expressions in hrHPV-infected tissues. We identified miR-224-3p as a candidate miRNA selectively up regulated in HPV-infected tissues and cell lines. Further analysis revealed that miR-224-3p regulates autophagy in cervical cancer tissues and cell lines. While the overexpression of miR-224-3p inhibits autophagy in HPV-infected cells, knocking down endogenous miR-224-3p increases autophagy activity in the same cells. In addition, we found that miR-224-3p directly inhibits the expression of autophagy related gene, FAK family-interacting protein of 200 kDa (FIP200). In summary, we found that miR-224-3p regulates autophagy in hrHPV-induced cervical cancer cells through targeting FIP200 expression.
Regulation of cell-cell fusion by nanotopography
Authors: Padmanabhan Jagannath , Augelli Michael J. , Cheung Bettina , Kinser Emily R. , Cleary Barnett , Kumar Priyanka , Wang Renhao , Sawyer Andrew J. , Li Rui , Schwarz Udo D. , Schroers Jan , Kyriakides Themis R. 
Published: September 2016

AbstractCell-cell fusion is fundamental to a multitude of biological processes ranging from cell differentiation and embryogenesis to cancer metastasis and biomaterial-tissue interactions. Fusogenic cells are exposed to biochemical and biophysical factors, which could potentially alter cell behavior. While biochemical inducers of fusion such as cytokines and kinases have been identified, little is known about the biophysical regulation of cell-cell fusion. Here, we designed experiments to examine cell-cell fusion using bulk metallic glass (BMG) nanorod arrays with varying biophysical cues, i.e. nanotopography and stiffness. Through independent variation of stiffness and topography, we found that nanotopography constitutes the primary biophysical cue that can override biochemical signals to attenuate fusion. Specifically, nanotopography restricts cytoskeletal remodeling-associated signaling, which leads to reduced fusion. This finding expands our fundamental understanding of the nanoscale biophysical regulation of cell fusion and can be exploited in biomaterials design to induce desirable biomaterial-tissue interactions.
Design methodology for a confocal imaging system using an objective microlens array with an increased working distance
Authors: Choi Woojae , Shin Ryung , Lim Jiseok , Kang Shinill 
Published: September 2016

AbstractIn this study, a design methodology for a multi-optical probe confocal imaging system was developed. To develop an imaging system that has the required resolving power and imaging area, this study focused on a design methodology to create a scalable and easy-to-implement confocal imaging system. This system overcomes the limitations of the optical complexities of conventional multi-optical probe confocal imaging systems and the short working distance using a micro-objective lens module composed of two microlens arrays and a telecentric relay optical system. The micro-objective lens module was fabricated on a glass substrate using backside alignment photolithography and thermal reflow processes. To test the feasibility of the developed methodology, an optical system with a resolution of 1 μm/pixel using multi-optical probes with an array size of 10 × 10 was designed and constructed. The developed system provides a 1 mm × 1 mm field of view and a sample scanning range of 100 μm. The optical resolution was evaluated by conducting sample tests using a knife-edge detecting method. The measured lateral resolution of the system was 0.98 μm.
Spin excitations in hole-overdoped iron-based superconductors
Authors: Horigane K. , Kihou K. , Fujita K. , Kajimoto R. , Ikeuchi K. , Ji S. , Akimitsu J. , Lee C. H. 
Published: September 2016

AbstractUnderstanding the overall features of magnetic excitation is essential for clarifying the mechanism of Cooper pair formation in iron-based superconductors. In particular, clarifying the relationship between magnetism and superconductivity is a central challenge because magnetism may play a key role in their exotic superconductivity. BaFe2As2 is one of ideal systems for such investigation because its superconductivity can be induced in several ways, allowing a comparative examination. Here we report a study on the spin fluctuations of the hole-overdoped iron-based superconductors Ba1-xKxFe2As2 (x = 0.5 and 1.0; Tc = 36 K and 3.4 K, respectively) over the entire Brillouin zone using inelastic neutron scattering. We find that their spin spectra consist of spin wave and chimney-like dispersions. The chimney-like dispersion can be attributed to the itinerant character of magnetism. The band width of the spin wave-like dispersion is almost constant from the non-doped to optimum-doped region, which is followed by a large reduction in the overdoped region. This suggests that the superconductivity is suppressed by the reduction of magnetic exchange couplings, indicating a strong relationship between magnetism and superconductivity in iron-based superconductors.
Orbital Angular Momentum-based Space Division Multiplexing for High-capacity Underwater Optical Communications
Authors: Ren Yongxiong , Li Long , Wang Zhe , Kamali Seyedeh Mahsa , Arbabi Ehsan , Arbabi Amir , Zhao Zhe , Xie Guodong , Cao Yinwen , Ahmed Nisar , Yan Yan , Liu Cong , Willner Asher J. , Ashrafi Solyman , Tur Moshe , Faraon Andrei , Willner Alan E. 
Published: September 2016

AbstractTo increase system capacity of underwater optical communications, we employ the spatial domain to simultaneously transmit multiple orthogonal spatial beams, each carrying an independent data channel. In this paper, we show up to a 40-Gbit/s link by multiplexing and transmitting four green orbital angular momentum (OAM) beams through a single aperture. Moreover, we investigate the degrading effects of scattering/turbidity, water current, and thermal gradient-induced turbulence, and we find that thermal gradients cause the most distortions and turbidity causes the most loss. We show systems results using two different data generation techniques, one at 1064 nm for 10-Gbit/s/beam and one at 520 nm for 1-Gbit/s/beam; we use both techniques since present data-modulation technologies are faster for infrared (IR) than for green. For the 40-Gbit/s link, data is modulated in the IR, and OAM imprinting is performed in the green using a specially-designed metasurface phase mask. For the 4-Gbit/s link, a green laser diode is directly modulated. Finally, we show that inter-channel crosstalk induced by thermal gradients can be mitigated using multi-channel equalisation processing.
A Hiatus of the Greenhouse Effect
Authors: Song Jinjie , Wang Yuan , Tang Jianping 
Published: September 2016

AbstractThe rate at which the global average surface temperature is increasing has slowed down since the end of the last century. This study investigates whether this warming hiatus results from a change in the well-known greenhouse effect. Using long-term, reliable, and consistent observational data from the Earth’s surface and the top of the atmosphere (TOA), two monthly gridded atmospheric and surface greenhouse effect parameters (Ga and Gs) are estimated to represent the radiative warming effects of the atmosphere and the surface in the infrared range from 1979 to 2014. The atmospheric and surface greenhouse effect over the tropical monsoon-prone regions is found to contribute substantially to the global total. Furthermore, the downward tendency of cloud activity leads to a greenhouse effect hiatus after the early 1990 s, prior to the warming pause. Additionally, this pause in the greenhouse effect is mostly caused by the high number of La Niña events between 1991 and 2014. A strong La Niña indicates suppressed convection in the tropical central Pacific that reduces atmospheric water vapor content and cloud volume. This significantly weakened regional greenhouse effect offsets the enhanced warming influence in other places and decelerates the rising global greenhouse effect. This work suggests that the greenhouse effect hiatus can be served as an additional factor to cause the recent global warming slowdown.
Mussel-inspired approach to constructing robust cobalt-embedded N-doped carbon nanosheet toward enhanced sulphate radical-based oxidation
Authors: Zeng Tao , Zhang Haiyan , He Zhiqiao , Chen Jianmeng , Song Shuang 
Published: September 2016

AbstractHeterogeneous sulphate radical based advanced oxidation processes (SR-AOPs) have lately been raised as a promising candidate for water treatment. Despite the progress made, either the stability or the performance of the current catalysts is still far from satisfactory for practical applications. Herein, using polydopamine-cobalt ion complex that inspired by mussel proteins as medium, we facilely fabricate a robust SR-AOPs catalyst with cobalt nanoparticles (NPs) embedded in nitrogen-doped reduced graphene oxide matrix (NRGO@Co). The NRGO scaffold with high porosity and surface area not only stabilizes the NPs but also greatly facilitates the accessibility and adsorption of substrates to the active sites. With the synergistic effect arising from the NRGO and Co NPs, the NRGO@Co hybrid catalyst exhibits enhanced catalytic activity for activation of peroxymonosulfate (PMS) to degrade organic pollutants in water. Furthermore, taking advantage of the favorable magnetic properties, the catalyst can be easily recycled and reused for at least 4 runs with negligible loss of activity. Coupled with systematic investigation in terms of influential factors, mineralization, and radicals identification, make the catalyst hold significant potential for application in remediation of organic pollutants in water.
The rise and fall of a change from below in Early Modern Spanish
Authors: Blas Arroyo José Luis 
Published: September 2016

AbstractThis article deals with the patterns of variation and change undergone by a syntactic variable in Early Modern Spanish grammar, namely the alternation betweendeber‘have to, must, should’ anddeber de + infinitive ‘have to, must, should’ as a modal periphrasis. Based on a 1,500,000-word corpus of immediacy texts (private letters, memories) the results of this variationist study suggest that throughout the 16th century, but more especially during its second half, the prepositional periphrasis gradually became more common, above all in stylistic contexts predominated by the spontaneity and proximity of the relationships between the interlocutors. It was also more frequently found in contexts involving members of northern speech communities, particularly males, the young and the middle-low social strata, the incidence being especially high at the points where some of these groups intersect. All this suggests a change from below in the Golden Age period, which reached considerable dimensions in a relatively short time but was destined to stagnate and later decline just as quickly in the centuries that followed as a result of some structural features, such as the special “visibility” of the preposition, which could have led to the stigmatization of the periphrasis in a similar way to what happened in other Spanish syntactic phenomena.
DM-BLD: differential methylation detection using a hierarchical Bayesian model exploiting local dependency
Authors: Wang Xiao , Gu Jinghua , Hilakivi-Clarke Leena , Clarke Robert , Xuan Jianhua 
Published: September 2016

Abstract

Motivation
The advent of high-throughput DNA methylation profiling techniques has enabled the possibility of accurate identification of differentially methylated genes for cancer research. The large number of measured loci facilitates whole genome methylation study, yet posing great challenges for differential methylation detection due to the high variability in tumor samples.

Results
We have developed a novel probabilistic approach, differential methylation detection using a hierarchical Bayesian model exploiting local dependency (DM-BLD), to detect differentially methylated genes based on a Bayesian framework. The DM-BLD approach features a joint model to capture both the local dependency of measured loci and the dependency of methylation change in samples. Specifically, the local dependency is modeled by Leroux conditional autoregressive structure; the dependency of methylation changes is modeled by a discrete Markov random field. A hierarchical Bayesian model is developed to fully take into account the local dependency for differential analysis, in which differential states are embedded as hidden variables. Simulation studies demonstrate that DM-BLD outperforms existing methods for differential methylation detection, particularly when the methylation change is moderate and the variability of methylation in samples is high. DM-BLD has been applied to breast cancer data to identify important methylated genes (such as polycomb target genes and genes involved in transcription factor activity) associated with breast cancer recurrence.

Availability and Implementation
A Matlab package of DM-BLD is available at http://www.cbil.ece.vt.edu/software.htm.

Supplementary information
Supplementary data are available at Bioinformatics online.
Taste Engineering: An Extended Consumer Model of Cultural Competence Constitution
Authors: Maciel Andre F , Wallendorf Melanie 
Published: September 2016

Abstract
Since industrialization, both beauty and refinement have been highlighted in many consumer markets, including home decoration, clothing, and fine foods and beverages. Consumers whose habitus resonates with these markets often formulate the goal of developing aesthetic expertise in them; they learn complex systems of taste evaluation to judge their aesthetic experiences. Extant research shows these systems’ effects on many aspects of consumer behavior, from information search and memory to strategies for participating in status games. This study extends consumer research by illuminating how these taste evaluation systems are constituted in consumers, after habitus has instilled generic dispositions in them. The multimethod ethnography studies US middle-class, male craft beer aficionados seeking to become connoisseurs. This work makes two main contributions to consumer research. First, it places the often-neglected world of the senses at the center of taste theorizing. It details three learning practices (benchmarking, autodidactics, and scaffolding) that consumers use to bind together the sensory and discursive dimensions of social practices. Second, it reveals interconsumer cooperation as a key mechanism in building consensus on social practices that involve ambiguous aesthetic experiences. This theorization complements prior research on status competition as a dominant type of sociality in taste-centered consumption domains.
Thermally moderated firefly activity is delayed by precipitation extremes
Authors: Hermann Sara L. , Xue Saisi , Rowe Logan , Davidson-Lowe Elizabeth , Myers Andrew , Eshchanov Bahodir , Bahlai Christie A. 
Published: September 2016

AbstractThe timing of events in the life history of temperate insects is most typically primarily cued by one of two drivers: photoperiod or temperature accumulation over the growing season. However, an insect’s phenology can also be moderated by other drivers like rainfall or the phenology of its host plants. When multiple drivers of phenology interact, there is greater potential for phenological asynchronies to arise between an organism and those with which it interacts. We examined the phenological patterns of a highly seasonal group of fireflies (Photinus spp, predominantlyP. pyralis) over a 12-year period (2004–2015) across 10 plant communities to determine if interacting drivers could explain the variability observed in the adult flight activity density (i.e.mating season) of this species. We found that temperature accumulation was the primary driver of phenology, with activity peaks usually occurring at a temperature accumulation of ~800 degree days (base 10°C), however, our model found this peak varied by nearly 180 degree day units among years. This variation could be explained by a quadratic relationship with the accumulation of precipitation in the growing season; in years with either high and low precipitation extremes at our study site, flight activity was delayed. More fireflies were captured in general in herbaceous plant communities with minimal soil disturbance (alfalfa and no-till field crop rotations), but only weak interactions occurred between within-season responses to climatic variables and plant community. The interaction we observed between temperature and precipitation accumulation suggests that, although climate warming has potential to disrupt phenology of many organisms, changes to regional precipitation patterns can magnify these disruptions.