bluuebunny/crossref_metadata_2025 huggingface dataset:
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

Brown 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

In 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

The 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

In 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

We 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

Osteoarthritis (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

Bondarzewia 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.
Characterization of N⋯O non-covalent interactions involving σ-holes: “electrostatics” or “dispersion”
Authors: Shukla Rahul , Chopra Deepak
Published: September 2016

Exploring the possibility of formation of pnicogen bonds or chalcogen bonds by utilizing the σ-holes present on nitrogen and oxygen atoms in per-halo substituted complexes.
Transition metal-catalysed couplings between arenes and strained or reactive rings: combination of C–H activation and ring scission
Authors: Wang Fen , Yu Songjie , Li Xingwei
Published: September 2016

Transition metal-catalysed systems of C–H activation of arenes in combination with opening of strained or reactive three, four, and five membered rings are summarized in this review.
Transformation of mackinawite to greigite by trichloroethylene and tetrachloroethylene
Authors: Lan Ying , Elwood Madden Andrew S. , Butler Elizabeth C.
Published: September 2016

Trichloroethylene and tetrachloroethylene transform mackinawite to greigite.
Annihilation upconversion in nanoconfinement: solving the oxygen quenching problem
Authors: Baluschev Stanislav , Katta Kartheek , Avlasevich Yuri , Landfester Katharina
Published: September 2016

Step by step concepts of triplet–triplet annihilation photon energy upconversion in nanoconfinement are summarized and reviewed.
Regioselective synthesis of functionalized dihydroisoquinolines from o-alkynylarylaldimines via the Reformatsky reaction
Authors: Chaudhari Tohasib Yusub , Urvashi Urvashi , Ginotra Sandeep K. , Yadav Pooja , Kumar Gulshan , Tandon Vibha
Published: September 2016

A novel approach for the synthesis of functionalized 1,2-dihydroisoquinolines from o-alkynylarylaldimines via the Reformatsky reaction without the aid of an external Lewis acid has been described.
Catalytic aerobic oxidation of 5-hydroxymethylfurfural into 2,5-diformylfuran over VO2+and Cu2+immobilized on amino-functionalized core–shell magnetic Fe3O4@SiO2
Authors: Liao Longfei , Liu Ying , Li Zengyong , Zhuang Junping , Zhou Yanbin , Chen Size
Published: September 2016

Amino modified Fe3O4@SiO2(Fe3O4@SiO2–NH2) was used to immobilize Cu2+and VO2+for preparing Fe3O4@SiO2–NH2–Cu2+and Fe3O4@SiO2–NH2–VO2+catalysts.
Optical, dielectric, electronic and morphological study of biologically synthesized zinc sulphide nanoparticles using Moringa oleifera leaf extract and quantitative analysis of chemical components present in the leaf extract
Authors: Sur Ujjal Kumar , Ankamwar Balaprasad
Published: September 2016

The biosynthesis of zinc sulphide nanoparticles with ∼30 nm diameter using the leaf extract of Moringa oleifera is reported here.
Orbital moment probed spin orbit coupling effects on anisotropy and damping in CoFeB thin films
Authors: Jhajhria Deepika , Pandya Dinesh K. , Chaudhary Sujeet
Published: September 2016

Spin orbit coupling based direct correlation between magnetic anisotropy and damping is established in CoFeB thin films on compositional and stress variations.
Highly efficient continuous-flow oxidative coupling of amines using promising nanoscale CeO2–M/SiO2 (M = MoO3 and WO3) solid acid catalysts
Authors: Rao Bolla Govinda , Sudarsanam Putla , Mallesham Baithy , Reddy Benjaram M.
Published: September 2016

Nanoscale CeO2–MoO3/SiO2 solid acid shows an outstanding catalytic performance in the oxidative coupling of amines under industrially-favourable conditions.
Controllable synthesis of hierarchical NiCo2S4@Ni3S2 core–shell nanotube arrays with excellent electrochemical performance for aqueous asymmetric supercapacitors
Authors: He Taobin , Wang Senlin , Lu Fengxia , Zhang Mucan , Zhang Xiao , Xu Lin
Published: September 2016

Unique NiCo2S4@Ni3S2 core–shell nanotube arrays with a hierarchical structure, as promising positive electrodes for supercapacitors, were designed and synthesized on the surface of Ni foam via a hydrothermal reaction and electrodeposition method.
Aluminum derivative peroxides in the (t-BuO)3Al–2t-BuOOH catalytic system as a source of electron-excited dioxygen: a quantum chemical study on a model
Authors: Gadzhiev Oleg B. , Dodonov Victor A. , Petrov Alexander I.
Published: September 2016

The t-BuOOH catalytic decomposition leads to reactive oxygen species including chemically activated and chemically excited (O2(b1Σ+g) and O2(1Δg)) dioxygen.
Improved preparation of 4(5)-aryl-2-(β-d-glucopyranosyl)-imidazoles, the most efficient glucose analogue inhibitors of glycogen phosphorylase
Authors: Szennyes Eszter , Bokor Éva , Batta Gyula , Docsa Tibor , Gergely Pál , Somsák László
Published: September 2016

Large scale (up to 20 g) preparation ofIandIIallowed the best inhibitors of glycogen phosphorylaseIIIto be synthesized in close to 60% overall yields fromI.
Antimicrobial activity and cytotoxicity of polyketides isolated from the mushroom Xerula sp. BCC56836
Authors: Sadorn Karoon , Saepua Siriporn , Boonyuen Nattawut , Laksanacharoen Pattiyaa , Rachtawee Pranee , Pittayakhajonwut Pattama
Published: September 2016

Thirteen new polyketides (1, 3, 5–12, and 14–16) together with nine known compounds were isolated from the mushroom Xerula sp. BCC56836.
Spirocyclic quaternary ammonium cations for alkaline anion exchange membrane applications: an experimental and theoretical study
Authors: Gu Liang , Dong Huilong , Sun Zhe , Li Youyong , Yan Feng
Published: September 2016

Spirocyclic quaternary ammonium cation based alkaline anion exchange membranes were synthesized and studied by both experimental and theoretical analysis.
Glucagon-like peptide-1 loaded phospholipid micelles for the treatment of type 2 diabetes: improved pharmacokinetic behaviours and prolonged glucose-lowering effects
Authors: Cui Xu , Meng Qinghua , Chu Yingying , Gu Xiaoke , Tang Yan , Zhou Feng , Fei Yingying , Fu Junjie , Han Jing
Published: September 2016

GLP-1-SSM, a sterically stabilized GLP-1 in phospholipid micelles, exhibited improved hypoglycemic activity and long-acting antidiabetic ability.
Effect of zinc cations on the kinetics of supramolecular assembly and the chirality of porphyrin J-aggregates
Authors: Romeo A. , Castriciano M. A. , Zagami R. , Pollicino G. , Monsù Scolaro L. , Pasternack R. F.
Published: September 2016

The key role of adventitious zinc(ii) ions, extracted from glass and quartz surfaces, in the kinetics of porphyrin aggregation and in the subsequent expression of their chirality is discussed herein.
Modified separators coated with a Ca(OH)2–carbon framework derived from crab shells for lithium–sulfur batteries
Authors: Shao Hongyuan , Huang Bicheng , Liu Naiqiang , Wang Weikun , Zhang Hao , Wang Anbang , Wang Feng , Huang Yaqin
Published: September 2016

Synthesis of a Ca(OH)2–carbon framework from crab shells and the polysulfide-trapping mechanisms of the modified separator for Li–S batteries.
Amphiphilic block copolymers from a renewable ε-decalactone monomer: prediction and characterization of micellar core effects on drug encapsulation and release
Authors: Kakde Deepak , Taresco Vincenzo , Bansal Kuldeep K. , Magennis E. Peter , Howdle Steven M. , Mantovani Giuseppe , Irvine Derek J. , Alexander Cameron
Published: September 2016

Block co-polymers with a block derived from a sustainable monomer source are used to encapsulate and release the drug indomethacin.
Vacancy formation in MoO3: hybrid density functional theory and photoemission experiments
Authors: Akande Salawu Omotayo , Chroneos Alexander , Vasilopoulou Maria , Kennou Stella , Schwingenschlögl Udo
Published: September 2016

Molybdenum oxide (MoO3) is an important material that is being considered for numerous technological applications, including catalysis and electrochromism.
Impulse space charge and dielectric characteristics of an Al2O3 nanoparticle suspension in propylene carbonate using various electrode materials
Authors: Yang Qing , Jin Yang , Sima Wenxia , Liu Mengna
Published: September 2016

We tested the impulse breakdown voltage of Al2O3 “nano-modified” propylene carbonate between different electrode materials. At any given concentration, the breakdown voltage was highest with stainless steel electrodes, followed by copper, and then aluminum. The space charge and electric field distributions were measured too. Results show that less space charge was injected by the electrodes, and the electric field was less distorted, than in pure propylene carbonate. However, the hoped-for reduction of the influence of the electrodes did not take place. Substantial differences in the space charge density and electric field distortion remained between the different electrode materials.
Synthesis and characterization of Ar-annealed zinc oxide nanostructures
Authors: Kuthirummal Narayanan , Smith Gregory M. , Lopez Leisha , Podila Ramakrishna , Howell Jason , Dun Chaochao , Rao Apparao M.
Published: September 2016

Nanostructured zinc oxide samples were synthesized through CVD and annealed in argon. The samples were investigated using SEM, TEM, XRD, and UV/VIS/FTIR photoacoustic spectroscopy. The SEM/TEM images show relatively spherical particles that form elongated, connected domains post-anneal. XRD measurements indicate a typical wurtzite structure and reveal an increase in average grain size from 16.3 nm to 21.2 nm in Ar-annealed samples over pristine samples. Visible photoacoustic spectra reveal the contribution of defect levels on the absorption edge of the fundamental gap of zinc oxide. The steepness parameter of the absorption edge, which is inversely proportional to the width of the absorption edge, decreased from 0.1582 (pristine) to 0.1539 (annealed for 90 minutes) revealing increased density of defect states upon annealing. The FTIR photoacoustic spectra show an intense peak at 412 cm-1 and a shoulder at 504 cm-1 corresponding to the two transverse optical stretching modes of ZnO. These results may indicate a self-assembly mechanism upon anneal under Ar atmosphere leading to early-stage nanorod growth.
Concomitant emergence of the antisense protein gene of HIV-1 and of the pandemic
Authors: Cassan Elodie , Arigon-Chifolleau Anne-Muriel , Mesnard Jean-Michel , Gross Antoine , Gascuel Olivier
Published: September 2016

Significance

HIV-1 is commonly assumed to have nine genes. However, in 1988 a 10th gene was suggested, overlapped by the
env
gene, but read on the antisense strand. The corresponding protein was named AntiSense Protein (ASP). Several pieces of evidence argue in favor of ASP expression in vivo, but its function is still unknown. We performed the first evolutionary study of ASP, using a very large number of HIV-1 and SIV (simian) sequences. Our results show that ASP is specific to group M of HIV-1, which is responsible for the pandemic. Moreover, we demonstrated that evolutionary forces act to maintain the
asp
gene within the M sequences and showed a striking correlation of
asp
with the spread of the pandemic.
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

This 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.
Intraflagellar transport protein IFT20 is essential for male fertility and spermiogenesis in mice
Authors: Zhang Zhengang , Li Wei , Zhang Yong , Zhang Ling , Teves Maria E. , Liu Hong , Strauss Jerome F. , Pazour Gregory J. , Foster James A. , Hess Rex A. , Zhang Zhibing
Published: September 2016

Intraflagellar transport (IFT) is a conserved mechanism believed to be essential for the assembly and maintenance of cilia and flagella. However, little is known about its role in mammalian sperm flagella formation. To fill this gap, we disrupted the Ift20 gene in male germ cells. Homozygous mutant mice were infertile, with significantly reduced sperm counts and motility. In addition, abnormally shaped, elongating spermatid heads and bulbous, round spermatids were found in the lumen of the seminiferous tubules. Electron microscopy revealed increased cytoplasmic vesicles, fiber-like structures, abnormal accumulation of mitochondria, and a decrease in mature lysosomes. The few developed sperm had disrupted axonemes, and some retained cytoplasmic lobe components on the flagella. ODF2 and SPAG16L, two sperm flagella proteins, failed to be incorporated into sperm tails of the mutant mice, and in the germ cells, both were assembled into complexes with lighter density in the absence of IFT20. Disrupting IFT20 did not significantly change expression levels of IFT88, a component of the IFT-B complex, and IFT140, a component of the IFT-A complex. Even though the expression level of an autophagy core protein that associates with IFT20, ATG16, was reduced in the testis of the Ift20 mutant mice, expression levels of other major autophagy markers, including LC3 and ubiquitin, were not changed. Our studies suggest that IFT20 is essential for male fertility and spermiogenesis in mice, and its major function is to transport cargo proteins for sperm flagella formation. It also appears to be involved in removing excess cytoplasmic components.
Molecular basis of Kar9-Bim1 complex function during mating and spindle positioning
Authors: Manatschal Cristina , Farcas Ana-Maria , Degen Miriam Steiner , Bayer Mathias , Kumar Anil , Landgraf Christiane , Volkmer Rudolf , Barral Yves , Steinmetz Michel O.
Published: September 2016

The Kar9 pathway promotes nuclear fusion during mating and spindle alignment during metaphase in budding yeast. How Kar9 supports the different outcome of these two divergent processes is an open question. Here, we show that three sites in the C-terminal disordered domain of Kar9 mediate tight Kar9 interaction with the C-terminal dimerization domain of Bim1 (EB1 orthologue). Site1 and Site2 contain SxIP motifs; however, Site3 defines a novel type of EB1-binding site. Whereas Site2 and Site3 mediate Kar9 recruitment to microtubule tips, nuclear movement, and karyogamy, only Site2 functions in spindle positioning during metaphase. Site1 in turn plays an inhibitory role during mating. Additionally, the Kar9-Bim1 complex is involved in microtubule-independent activities during mating. Together, our data reveal how multiple and partially redundant EB1-binding sites provide a microtubule-associated protein with the means to modulate its biochemical properties to promote different molecular processes during cell proliferation and differentiation.
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

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

Motivation

Gene 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.

Results

The 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 Implementation

EGSEA 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 information

Supplementary 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

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

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.
Introduction
Authors: Wynn Gary H. , Benedek David M.
Published: September 2016

The driving force behind this textbook was recognition of the increasing need for more consolidated information on complementary and alternative medicine (CAM) for posttraumatic stress disorder (PTSD). During the past decade, may of the contributors to this book have seen an increasing number of individuals returning from military deployment suffering from PTSD, alongside the rising use and interest in CAM. This increased interest has led to significant strides forward in research, including some attention devoted to various CAM modalities. When looking across the clinical and research landscape, it was an easy decision to move forward with a project dedicated to consolidating the growing wealth of current information on CAM and PTSD. The hope is that this book provides easily digestible information that assists clinicians, advocates, patients, and students in their pursuit of better understanding of this important and growing topic.
Meditation Techniques for Posttraumatic Stress Disorder
Authors: Khusid Marina
Published: September 2016

Although there is currently insufficient evidence to support meditation as a first-line treatment for posttraumatic stress disorder (PTSD), the evidence base for meditation used adjunctively in the management of PTSD and related psychiatric comorbidities is rapidly expanding. The 2010 Veterans Administration/Department of Defense (VA/DoD) clinical practice guideline (CPG) for management of PTSD states that mind–body approaches may be considered adjunctive treatment for hyperarousal symptoms. Although several reviews support the conclusions reflected in the CPG, others suggest meditation interventions may be more useful in managing PTSD than originally speculated. Meditation may help reduce intrusive memories, avoidance, and anger; and increase self-esteem, pain tolerance, energy, and ability to relax and cope with stress. One comparative effectiveness review concluded that mindfulness meditation is beneficial in reducing psychological stress consequences, such as depression, pain, and mental health-related quality of life.
Acupuncture
Authors: Balog Daniel J. , Koffman Robert , Helms Joseph M.
Published: September 2016

People who acquire posttraumatic stress disorder (PTSD) after experiencing a traumatic event endure a constellation of debilitating symptoms, including intrusion, avoidance, negative mood alteration, and marked increases in reactivity. They have difficulty falling or staying asleep, and often have comorbid physical and pain-related diagnoses secondary to their trauma. Despite evolving definitions and measures, estimates of prevalence of lifetime PTSD in U.S. population have remained quite consistent since the advent of theDiagnostic and Statistical Manual of Mental Disorders(DSM), third edition, revised (III-R). In civilian populations, lifetime DSM-III-R PTSD prevalence rates of 9.2%; DSM, fourth edition, PTSD prevalence rates of 6.8%; and DSM, fifth edition, PTSD estimate rates of 5.4% have been reported. In U.S. military populations, prevalence rates as high as 17% after combat deployments have been reported. Importantly, persons with PTSD experience higher prevalence of other psychiatric and physical comorbid conditions, including mood, substance use, and pain disorders.
Computed Tomography for Minor Head Injury
Authors: Lee Christoph I.
Published: September 2016

This chapter, found in the headache section of the book, provides a succinct synopsis of a key study examining the use of computed tomography (CT) scans for minor head injury using the New Orleans criteria. This summary outlines the study methodology and design, major results, limitations and criticisms, related studies and additional information, and clinical implications. The study showed that head CT scans for patients with minor head injury can be safely limited to those presenting with at least 1 of 7 specific clinical findings. In addition to outlining the most salient features of the study, a clinical vignette and imaging example are included in order to provide relevant clinical context.
MRI versus CT for Detecting Acute Intracerebral Hemorrhage in Stroke Patients
Authors: Lee Christoph I.
Published: September 2016

This chapter, found in the headache section of the book, provides a succinct synopsis of a key study comparing the use of computed tomography (CT) and magnetic resonance imaging (MRI) scans for detecting acute intracerebral hemorrhage in stroke patients. This summary outlines the study methodology and design, major results, limitations and criticisms, related studies and additional information, and clinical implications. The researchers found that MRI is as accurate as CT for detecting acute hemorrhage in suspected stroke and is more accurate than CT for detecting chronic intracerebral hemorrhage. In addition to outlining the most salient features of the study, a clinical vignette and imaging example are included in order to provide relevant clinical context.
Imaging Tests for Diagnosis of Carotid Artery Stenosis
Authors: Lee Christoph I.
Published: September 2016

This chapter, found in the headache section of the book, provides a succinct synopsis of a key study examining the use of duplex ultrasound (DUS), magnetic resonance angiography (MRA), and digital subtraction angiography for diagnosing carotid artery stenosis. This summary outlines the study methodology and design, major results, limitations and criticisms, related studies and additional information, and clinical implications. The study showed that both DUS and MRA are very accurate for detecting carotid artery occlusion; however, MRA is more accurate than DUS in diagnosing 70%–99% carotid artery stenosis. In addition to outlining the most salient features of the study, a clinical vignette and imaging example are included in order to provide relevant clinical context.
CT Angiography for Discharge of Acute Coronary Syndrome
Authors: Lee Christoph I.
Published: September 2016

This chapter, found in the chest pain section of the book, provides a succinct synopsis of a key study examining the use of computed tomography (CT) angiography for discharging patients with acute coronary syndrome from the emergency department. This summary outlines the study methodology and design, major results, limitations and criticisms, related studies and additional information, and clinical implications. The study showed that a negative coronary CT angiography examination can be used to safely expedite the discharge of low-to-intermediate risk patients who present to emergency department with possible acute coronary syndrome. In addition to outlining the most salient features of the study, a clinical vignette and imaging example are included in order to provide relevant clinical context.
Imaging Appendicitis in Children
Authors: Lee Christoph I.
Published: September 2016

This chapter, found in the abdominal and pelvic pain section of the book, provides a succinct synopsis of a key study examining the use of ultrasound and computed tomography (CT) among children with suspected appendicitis. This summary outlines the study methodology and design, major results, limitations and criticisms, related studies and additional information, and clinical implications. The study showed that CT with contrast after a negative or indeterminate pelvic ultrasound leads to very high accuracy in diagnosing acute appendicitis in children. In addition to outlining the most salient features of the study, a clinical vignette and imaging example are included in order to provide relevant clinical context.
Imaging for Suspected Nephrolithiasis
Authors: Lee Christoph I.
Published: September 2016

This chapter, found in the abdominal and pelvic pain section of the book, provides a succinct synopsis of a key study examining the use of ultrasound and computed tomography for suspected nephrolithiasis. This summary outlines the study methodology and design, major results, limitations and criticisms, related studies and additional information, and clinical implications. The study found that initial imaging with ultrasonography for suspected nephrolithiasis has similar diagnostic accuracy and short-term patient outcomes, but is associated with lower cumulative radiation exposure, compared to initial imaging with CT for suspected nephrolithiasis. Thus, ultrasound should be used as the initial diagnostic imaging test for patients with suspected renal colic, with additional imaging performed as needed. In addition to outlining the most salient features of the study, a clinical vignette and imaging example are included in order to provide relevant clinical context.
Repeat Bone Mineral Density Screening and Osteoporotic Fracture Prediction
Authors: Lee Christoph I.
Published: September 2016

This chapter, found in the bone, joint, and extremity pain section of the book, provides a succinct synopsis of a key study examining the need for repeat bone densitometry screening and prediction of fractures from osteoporosis. This summary outlines the study methodology and design, major results, limitations and criticisms, related studies and additional information, and clinical implications. The study showed that a repeat bone mineral density test within 4 years adds little additional value beyond the baseline test when assessing hip fracture risk. Moreover, a repeat test within 4 years may not improve fracture risk stratification used for clinical management of osteoporosis. In addition to outlining the most salient features of the study, a clinical vignette and imaging example are included in order to provide relevant clinical context.
Ultrasound for Diagnosing Suspected Symptomatic Deep Venous Thrombosis
Authors: Lee Christoph I.
Published: September 2016

This chapter, found in the bone, joint, and extremity pain section of the book, provides a succinct synopsis of a key study examining the use of Doppler ultrasound for diagnosing suspected lower extremity deep venous thrombosis. This summary outlines the study methodology and design, major results, limitations and criticisms, related studies and additional information, and clinical implications. This study demonstrated that 2-point ultrasonography is equivalent to the whole-leg ultrasonography for diagnosing symptomatic deep venous thrombosis. In addition to outlining the most salient features of the study, a clinical vignette and imaging example are included in order to provide relevant clinical context.
Efficacy of Screening Breast MRI for High-Risk Women
Authors: Lee Christoph I.
Published: September 2016

This chapter, found in the cancer screening and management section of the book, provides a succinct synopsis of a key study examining the efficacy of screening breast magnetic resonance imaging (MRI) for high-risk women. This summary outlines the study methodology and design, major results, limitations and criticisms, related studies and additional information, and clinical implications. Breast MRI screening has higher sensitivity than mammography for high-risk women, but both the specificity and positive predictive value are lower than for mammography screening. In addition to outlining the most salient features of the study, a clinical vignette and imaging example are included in order to provide relevant clinical context.
Breast MRI for Women with Recently Diagnosed Breast Cancer
Authors: Lee Christoph I.
Published: September 2016

This chapter, found in the cancer screening and management section of the book, provides a succinct synopsis of a key study examining the efficacy of breast magnetic resonance imaging for extent of disease evaluation among women with recently diagnosed breast cancer. This summary outlines the study methodology and design, major results, limitations and criticisms, related studies and additional information, and clinical implications. The study showed that breast MRI in newly diagnosed unilateral breast cancer patients can detect contralateral early-stage breast cancers missed by mammography and clinical breast examination. In addition, breast MRI has an extremely high negative predictive value, and may provide helpful information to women and physicians weighing the relative value of prophylactic contralateral mastectomy in the setting of unilateral breast cancer. In addition to outlining the most salient features of the study, a clinical vignette and imaging example are included in order to provide relevant clinical context.
Low-Dose CT Screening for Lung Cancer
Authors: Lee Christoph I.
Published: September 2016

This chapter, found in the cancer screening and management section of the book, provides a succinct synopsis of a key study examining the efficacy of low-dose computed tomography screening for lung cancer. This summary outlines the study methodology and design, major results, limitations and criticisms, related studies and additional information, and clinical implications. The study showed that annual low-dose CT screening among high-risk individuals decreases lung cancer mortality. While the rate of false positives was nearly 3 times higher for those screened by low-dose CT compared to chest radiography, complications from invasive diagnostic evaluation after positive screens were rare. In addition to outlining the most salient features of the study, a clinical vignette and imaging example are included in order to provide relevant clinical context.
Management of Lung Nodules Detected by CT
Authors: Lee Christoph I.
Published: September 2016

This chapter, found in the cancer screening and management section of the book, provides a succinct synopsis of a key study examining the management of lung nodules detected by computed tomography and their risk of developing into lung cancer. This summary outlines the study methodology and design, major results, limitations and criticisms, related studies and additional information, and clinical implications. Virtual colonoscopy, using a primary 3D approach for polyp detection, was shown to be a minimally invasive procedure that is an accurate method for screening average-risk individuals. The likelihood of a clinically significant adenoma being missed on virtual colonoscopy was extremely low given the high negative predictive value. In addition to outlining the most salient features of the study, a clinical vignette and imaging example are included in order to provide relevant clinical context.