bluuebunny/crossref_metadata_2025_split huggingface dataset:
Formation of droplet interface bilayers in a Teflon tube
Authors: Walsh Edmond , Feuerborn Alexander , Cook Peter R. 
Published: September 2016

AbstractDroplet-interface bilayers (DIBs) have applications in disciplines ranging from biology to computing. We present a method for forming them manually using a Teflon tube attached to a syringe pump; this method is simple enough it should be accessible to those without expertise in microfluidics. It exploits the properties of interfaces between three immiscible liquids and uses fluid flow through the tube to pack together drops coated with lipid monolayers to create bilayers at points of contact. It is used to create functional nanopores in DIBs composed of phosphocholine using the protein α-hemolysin (αHL), to demonstrate osmotically-driven mass transfer of fluid across surfactant-based DIBs and to create arrays of DIBs. The approach is scalable and thousands of DIBs can be prepared using a robot in one hour; therefore, it is feasible to use it for high throughput applications.
Detecting individual extracellular vesicles using a multicolor in situ proximity ligation assay with flow cytometric readout
Authors: Löf Liza , Ebai Tonge , Dubois Louise , Wik Lotta , Ronquist K. Göran , Nolander Olivia , Lundin Emma , Söderberg Ola , Landegren Ulf , Kamali-Moghaddam Masood 
Published: September 2016

AbstractFlow cytometry is a powerful method for quantitative and qualitative analysis of individual cells. However, flow cytometric analysis of extracellular vesicles (EVs) and the proteins present on their surfaces has been hampered by the small size of the EVs – in particular for the smallest EVs, which can be as little as 40 nm in diameter, the limited number of antigens present and their low refractive index. We addressed these limitations for detection and characterization of EV by flow cytometry through the use of multiplex and multicolor in situ proximity ligation assays (in situ PLA), allowing each detected EV to be easily recorded over background noise using a conventional flow cytometer. By targeting sets of proteins on the surface that are specific for distinct classes of EVs, the method allows for selective recognition of populations of EVs in samples containing more than one type of EVs. The method presented herein opens up for analyses of EVs using flow cytometry for their characterization and quantification.
Map-based Cloning and Characterization of the BPH18 Gene from Wild Rice Conferring Resistance to Brown Planthopper (BPH) Insect Pest
Authors: Ji Hyeonso , Kim Sung-Ryul , Kim Yul-Ho , Suh Jung-Pil , Park Hyang-Mi , Sreenivasulu Nese , Misra Gopal , Kim Suk-Man , Hechanova Sherry Lou , Kim Hakbum , Lee Gang-Seob , Yoon Ung-Han , Kim Tae-Ho , Lim Hyemin , Suh Suk-Chul , Yang Jungil , An Gynheung , Jena Kshirod K. 
Published: September 2016

AbstractBrown planthopper (BPH) is a phloem sap-sucking insect pest of rice which causes severe yield loss. We cloned the BPH18 gene from the BPH-resistant introgression line derived from the wild rice species Oryza australiensis. Map-based cloning and complementation test revealed that the BPH18 encodes CC-NBS-NBS-LRR protein. BPH18 has two NBS domains, unlike the typical NBS-LRR proteins. The BPH18 promoter::GUS transgenic plants exhibited strong GUS expression in the vascular bundles of the leaf sheath, especially in phloem cells where the BPH attacks. The BPH18 proteins were widely localized to the endo-membranes in a cell, including the endoplasmic reticulum, Golgi apparatus, trans-Golgi network, and prevacuolar compartments, suggesting that BPH18 may recognize the BPH invasion at endo-membranes in phloem cells. Whole genome sequencing of the near-isogenic lines (NILs), NIL-BPH18 and NIL-BPH26, revealed that BPH18 located at the same locus of BPH26. However, these two genes have remarkable sequence differences and the independent NILs showed differential BPH resistance with different expression patterns of plant defense-related genes, indicating that BPH18 and BPH26 are functionally different alleles. These findings would facilitate elucidation of the molecular mechanism of BPH resistance and the identified novel alleles to fast track breeding BPH resistant rice cultivars.
Assembling non-ferromagnetic materials to ferromagnetic architectures using metal-semiconductor interfaces
Authors: Ma Ji , Liu Chunting , Chen Kezheng 
Published: September 2016

AbstractIn this work, a facile and versatile solution route was used to fabricate room-temperature ferromagnetic fish bone-like, pteridophyte-like, poplar flower-like, cotton-like Cu@Cu2O architectures and golfball-like Cu@ZnO architecture. The ferromagnetic origins in these architectures were found to be around metal-semiconductor interfaces and defects and the root cause for their ferromagnetism lay in charge transfer processes from metal Cu to semiconductors Cu2O and ZnO. Owing to different metallization at their interfaces, these architectures exhibited different ferromagnetic behaviors, including coercivity, saturation magnetization as well as magnetic interactions.
Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input
Authors: Armstrong Alacia , Valverde Angel , Ramond Jean-Baptiste , Makhalanyane Thulani P. , Jansson Janet K. , Hopkins David W. , Aspray Thomas J. , Seely Mary , Trindade Marla I. , Cowan Don A. 
Published: September 2016

AbstractThe temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.
Casein kinase 1 is recruited to nuclear speckles by FAM83H and SON
Authors: Kuga Takahisa , Kume Hideaki , Adachi Jun , Kawasaki Naoko , Shimizu Maiko , Hoshino Isamu , Matsubara Hisahiro , Saito Youhei , Nakayama Yuji , Tomonaga Takeshi 
Published: September 2016

AbstractIn some fibroblasts, casein kinase 1α (CK1α) is localized to nuclear speckles, which are sub-nuclear compartments supplying splicing factors, whereas it is recruited on keratin filaments in colorectal cancer cells such as DLD1 cells. In order to obtain a deeper understanding of why CK1α is localized to these different subcellular sites, we herein elucidated the mechanisms underlying its localization to nuclear speckles. CK1α and FAM83H were localized to nuclear speckles in RKO and WiDr colorectal cancer cells, which do not express simple epithelial keratins and in DLD1 cells transfected with siRNAs for type I keratins. The localization of FAM83H to nuclear speckles was also detected in colorectal cancer cells with a poorly organized keratin cytoskeleton in colorectal cancer tissues. Using an interactome analysis of FAM83H, we identified SON, a protein present in nuclear speckles, as a scaffold protein to which FAM83H recruits CK1α. This result was supported by the knockdown of FAM83H or SON delocalizing CK1α from nuclear speckles. We also found that CK1δ and ε are localized to nuclear speckles in a FAM83H-dependent manner. These results suggest that CK1 is recruited to nuclear speckles by FAM83H and SON in the absence of an intact keratin cytoskeleton.
Hexagonal Boron Nitride Tunnel Barriers Grown on Graphite by High Temperature Molecular Beam Epitaxy
Authors: Cho Yong-Jin , Summerfield Alex , Davies Andrew , Cheng Tin S. , Smith Emily F. , Mellor Christopher J. , Khlobystov Andrei N. , Foxon C. Thomas , Eaves Laurence , Beton Peter H. , Novikov Sergei V. 
Published: September 2016

AbstractWe demonstrate direct epitaxial growth of high-quality hexagonal boron nitride (hBN) layers on graphite using high-temperature plasma-assisted molecular beam epitaxy. Atomic force microscopy reveals mono- and few-layer island growth, while conducting atomic force microscopy shows that the grown hBN has a resistance which increases exponentially with the number of layers, and has electrical properties comparable to exfoliated hBN. X-ray photoelectron spectroscopy, Raman microscopy and spectroscopic ellipsometry measurements on hBN confirm the formation of sp2-bonded hBN and a band gap of 5.9 ± 0.1 eV with no chemical intermixing with graphite. We also observe hexagonal moiré patterns with a period of 15 nm, consistent with the alignment of the hBN lattice and the graphite substrate.
Inhibition of transforming growth factor β-activated kinase 1 prevents inflammation-related cartilage degradation in osteoarthritis
Authors: Cheng Jin , Hu Xiaoqing , Dai Linghui , Zhang Xin , Ren Bo , Shi Weili , Liu Zhenlong , Duan Xiaoning , Zhang Jiying , Fu Xin , Chen Wenqing , Ao Yingfang 
Published: September 2016

AbstractOsteoarthritis (OA) is a common debilitating joint disorder, there’s still no available disease-modifying drug for OA currently. This study aims to explore the role of TAK1 in OA pathogenesis and therapeutic efficiency of TAK1 inhibition for OA. The contribution of TAK1 to OA pathogenesis was investigated by intra-articular injection of TAK1-encoding adenovirus in rats. TAK1 inhibitor 5Z-7-induced expression changes of extracellular matrix (ECM)-related genes were detected by real-time PCR. The protective effect of 5Z-7 against OA progression was evaluated in a post-traumatic OA rat model. Our results showed that intra-articular injection of Ad-Tak1 induced cartilage destruction and OA-related cytokine secretion in rat joints. TAK1 inhibition by 5Z-7 efficiently blocked NF-κB, JNK and p38 pathways activation in OA chondrocytes and synoviocytes, Meanwhile, 5Z-7 significantly decreased the expression of matrix-degrading enzymes and pro-inflammatory cytokine, while increased ECM protein expression, which are all crucial components in OA. 5Z-7 also ameliorated ECM loss in OA cartilage explants. More importantly, 5Z-7 significantly protected against cartilage destruction in a rat model of OA. In conclusion, our findings provide the first in vivo evidence that TAK1 contributes to OA by disrupting cartilage homeostasis, thus represents an ideal target for OA treatment, with 5Z-7 as a candidate therapeutic.
Phylogeny and biogeography of the remarkable genus Bondarzewia (Basidiomycota, Russulales)
Authors: Song Jie , Chen Jia-Jia , Wang Min , Chen Yuan-Yuan , Cui Bao-Kai 
Published: September 2016

AbstractBondarzewia is a conspicuous and widely distributed mushroom genus, but little is known about its origin and biogeography. Here, we investigated the systematics and biogeography of Bondarzewia species using multi-locus phylogenetic analysis. Four genetic markers, including the internal transcribed spacer (ITS), large nuclear ribosomal RNA subunit (nLSU), elongation factor 1-α (tef1) and mitochondrial small subunit rDNA (mtSSU), were used to infer the phylogenetic relationships of Bondarzewia. We performed Bayesian evolutionary analysis on the gene datasets of the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2). From the results, we inferred that the maximum crown age of Bondarzewia is approximately 25.5 million-years-ago (Mya) and that tropical East Asia is likely to be its ancestral area, with three possible expansions leading to its distribution in North America, Europe and Oceania.
Structure-guided enzymology of the lipid A acyltransferase LpxM reveals a dual activity mechanism
Authors: Dovala Dustin , Rath Christopher M. , Hu Qijun , Sawyer William S. , Shia Steven , Elling Robert A. , Knapp Mark S. , Metzger Louis E. 
Published: September 2016

Significance
Lysophospholipid acyltransferase (LPLAT) proteins are required for many essential biological activities involving the transfer of acyl chains. One LPLAT, LpxM, is necessary for the biosynthesis of lipid A, which comprises the outer leaflet of the outer membrane in Gram-negative bacteria. Lipid A is important because it is a potent activator of the innate immune system and because of its role in preventing xenobiotics from permeating Gram-negative bacteria. In this work, we structurally and mechanistically characterize LpxM, providing insights that may enable the targeted discovery of inhibitors that prevent lipid A maturation; these might potentiate the uptake of extant antibiotics whose clinical efficacy is hitherto limited by poor permeability. Our insights into the mechanism of LpxM may facilitate the study of diverse LPLATs.
Time transient validation of residual stress prediction models for aluminium alloy quenching
Authors: Tanner D. A. , Robinson J. S. 
Published: September 2016

Finite element models that predict residual stress states in relatively large quenched aluminium alloy products tend to give reliable results. However, even though there is confidence that the predicted stress state is correct, there is no validation indicating that the stress/displacement development during the quench is comparable to the experimental case. Combined with this, finite element predictions for small samples tend to underestimate surface stress. This paper uses a ‘Navy C-Ring’ benchmark design to monitor displacement during quenching. The heat transfer coefficient is found to be the most dominant boundary condition and is critical to ensuring displacement and residual stress predictions that match the experimental case. This paper is part of a Themed Issue on Measurement, modelling and mitigation of residual stress.
The absolute that is not absolute: an alchemical reflection on the caput mortuum, the dark other of logical light
Authors: Marlan Stanton 
Published: September 2016

ABSTRACTThis paper challenges Wolfgang Giegerich’s sometimes sophisticated and at other times sophistic notion of absolute negative interiority. In contrast to his uroboric view of ‘psychology proper’, this author resists the successionist ideas of a post-Jungian, trans-human perspective and asserts the notion of an unassimilable and unsurmountable ‘not’. In this paper, the author revisions the traditional divide between Kant and Hegel, taking the ‘thing-in-itself’ as truly other than existing only for consciousness and arguing against privileging theunityof unity and difference. This paper entertains the alchemical ideas of a residue, acaput mortuum, and an archetypally cumbersome object, a real limit, which remains and unhinges the elevating process of spirit on its path to return to itself in absolute interiority. Rather, it acknowledges an abyss ‘behind the back of consciousness’, a non-reified living unconscious – a dark light, an absolute that is not absolute, but rather a gateway back to the beyond, at the root of imagination, wonder, and transformation.
OMBlast: alignment tool for optical mapping using a seed-and-extend approach
Authors: Leung Alden King-Yung , Kwok Tsz-Piu , Wan Raymond , Xiao Ming , Kwok Pui-Yan , Yip Kevin Y , Chan Ting-Fung 
Published: September 2016

Abstract

Motivation
Optical mapping is a technique for capturing fluorescent signal patterns of long DNA molecules (in the range of 0.1–1 Mbp). Recently, it has been complementing the widely used short-read sequencing technology by assisting with scaffolding and detecting large and complex structural variations (SVs). Here, we introduce a fast, robust and accurate tool called OMBlast for aligning optical maps, the set of signal locations on the molecules generated from optical mapping. Our method is based on the seed-and-extend approach from sequence alignment, with modifications specific to optical mapping.

Results
Experiments with both synthetic and our real data demonstrate that OMBlast has higher accuracy and faster mapping speed than existing alignment methods. Our tool also shows significant improvement when aligning data with SVs.

Availability and Implementation
OMBlast is implemented for Java 1.7 and is released under a GPL license. OMBlast can be downloaded from https://github.com/aldenleung/OMBlast and run directly on machines equipped with a Java virtual machine.

Supplementary information
Supplementary data are available at Bioinformatics online
Combining multiple tools outperforms individual methods in gene set enrichment analyses
Authors: Alhamdoosh Monther , Ng Milica , Wilson Nicholas J , Sheridan Julie M , Huynh Huy , Wilson Michael J , Ritchie Matthew E 
Published: September 2016

AbstractMotivationGene set enrichment (GSE) analysis allows researchers to efficiently extract biological insight from long lists of differentially expressed genes by interrogating them at a systems level. In recent years, there has been a proliferation of GSE analysis methods and hence it has become increasingly difficult for researchers to select an optimal GSE tool based on their particular dataset. Moreover, the majority of GSE analysis methods do not allow researchers to simultaneously compare gene set level results between multiple experimental conditions.ResultsThe ensemble of genes set enrichment analyses (EGSEA) is a method developed for RNA-sequencing data that combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets. EGSEA’s gene set database contains around 25 000 gene sets from sixteen collections. It has multiple visualization capabilities that allow researchers to view gene sets at various levels of granularity. EGSEA has been tested on simulated data and on a number of human and mouse datasets and, based on biologists’ feedback, consistently outperforms the individual tools that have been combined. Our evaluation demonstrates the superiority of the ensemble approach for GSE analysis, and its utility to effectively and efficiently extrapolate biological functions and potential involvement in disease processes from lists of differentially regulated genes.Availability and ImplementationEGSEA is available as an R package at http://www.bioconductor.org/packages/EGSEA/. The gene sets collections are available in the R package EGSEAdata from http://www.bioconductor.org/packages/EGSEAdata/.Supplementary informationSupplementary data are available at Bioinformatics online.
Pro54DB: a database for experimentally verified sigma-54 promoters
Authors: Liang Zhi-Yong , Lai Hong-Yan , Yang Huan , Zhang Chang-Jian , Yang Hui , Wei Huan-Huan , Chen Xin-Xin , Zhao Ya-Wei , Su Zhen-Dong , Li Wen-Chao , Deng En-Ze , Tang Hua , Chen Wei , Lin Hao 
Published: September 2016

Abstract

Summary
In prokaryotes, the σ54 promoters are unique regulatory elements and have attracted much attention because they are in charge of the transcription of carbon and nitrogen-related genes and participate in numerous ancillary processes and environmental responses. All findings on σ54 promoters are favorable for a better understanding of their regulatory mechanisms in gene transcription and an accurate discovery of genes missed by the wet experimental evidences. In order to provide an up-to-date, interactive and extensible database for σ54 promoter, a free and easy accessed database called Pro54DB (σ54 promoter database) was built to collect information of σ54 promoter. In the current version, it has stored 210 experimental-confirmed σ54 promoters with 297 regulated genes in 43 species manually extracted from 133 publications, which is helpful for researchers in fields of bioinformatics and molecular biology.

Availability and Implementation
Pro54DB is freely available on the web at http://lin.uestc.edu.cn/database/pro54db with all major browsers supported.
Father Confessors and Clerical Intervention in Witch-Trials in Seventeenth-Century Lutheran Germany: The Case of Rothenburg, 1692
Authors: Rowlands Alison 
Published: September 2016

Abstract
In 1692 a woman named Barbara Ehness was awaiting execution for attempted murder by poison in the Lutheran imperial city of Rothenburg ob der Tauber. She requested spiritual solace, and three Lutheran clerics duly visited her in gaol. As a result of their intervention, Barbara was, at first, persuaded to admit she was a witch, and that she had attended witches’ gatherings where she had seen several other (named) Rothenburg inhabitants. However, Barbara soon retracted these denunciations, telling the city councillors that she had been forced into making them by one of the three clerics who had visited her in gaol, the territory’s chief ecclesiastical official, Church Superintendent Sebastian Kirchmeier. This article offers a close analysis and contextualisation of this richly detailed trial (which included a lengthy defence of his actions by Kirchmeier), exploring Kirchmeier’s motivations, why the councillors refused to follow his witch-hunting lead, and how the case fitted into the wider context of urban politics. The potentially abusive role of father confessors had already been identified by some seventeenth-century critics of witch-hunts (beginning with Friedrich Spee in 1631), but the confidentiality of the confessor–sinner relationship has usually meant that no record of it is left to us in specific cases. The exposure of Kirchmeier’s intervention in the Ehness trial thus gives us a unique insight into how one father confessor tried (and failed) to use his relationship with a prisoner to influence a trial outcome, and to start a witch-hunt, based on the denunciations of alleged sabbath-attenders whom he suggested to her.
Modelling stellar proton event-induced particle radiation dose on close-in exoplanets
Authors: Atri Dimitra 
Published: September 2016

Abstract
Kepler observations have uncovered the existence of a large number of close-in exoplanets and serendipitously of stellar superflares with emissions several orders of magnitude higher than those observed on the Sun. The interaction between the two and their implications on planetary habitability are of great interest to the community. Stellar proton events (SPEs) interact with planetary atmospheres, generate secondary particles and increase the radiation dose on the surface. This effect is amplified for close-in exoplanets and can be a serious threat to potential planetary life. Monte Carlo simulations are used to model the SPE-induced particle radiation dose on the surface of such exoplanets. The results show a wide range of surface radiation doses on planets in close-in configurations with varying atmospheric column depths, magnetic moments and orbital radii. It can be concluded that for close-in exoplanets with sizable atmospheres and magnetospheres, the radiation dose contributed by stellar superflares may not be high enough to sterilize a planet (for life as we know it) but can result in frequent extinction level events. In light of recent reports, the interaction of hard-spectrum SPEs with the atmosphere of Proxima Centauri b is modelled and their implications on its habitability are discussed.