bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel Hormone Receptors Present in Apocrine Cystadenoma of the Eyelid
Authors: Brown Sarah E. , Friedman Alan H. , Phelps Robert G. , Bleiweiss Ira J. , Wu Albert Y.
Published: February 2015

A 53-year-old woman presented with an apocrine cystadenoma of the right upper eyelid. Histologic examination revealed proliferating epithelial cells with apocrine snouts and occasional mitotic figures. Immunohistochemical analysis revealed a Ki-67 index of 15% and positive staining for synaptophysin, chromogranin, estrogen receptor, progesterone receptor, gross cystic disease fluid protein (GCDFP)-15, and mammoglobin. The complement of positive immunomarkers in this case reinforces the importance of total excision and careful histologic assessment.
Quantifying the reliability of dispersal paths in connectivity networks
Authors: Hock Karlo , Mumby Peter J.
Published: February 2015

Many biological systems, from fragmented landscapes to host populations, can be represented as networks of connected habitat patches. Links between patches in these connectivity networks can represent equally diverse processes, from individuals moving through the landscape to pathogen transmissions or successive colonization events in metapopulations. Any of these processes can be characterized as stochastic, with functional links among patches that exist with various levels of certainty. This stochasticity then needs to be reflected in the algorithms that aim to predict the dispersal routes in these networks. Here we adapt the concept of reliability to characterize the likelihood that a specific path will be used for dispersal in a probabilistic connectivity network. The most reliable of the paths that connect two patches will then identify the most likely sequence of intermediate steps between these patches. Path reliability will be sensitive to targeted disruptions of individual links that form the path, and this can then be used to plan the interventions aimed at either preserving or disrupting the dispersal along that path. The proposed approach is general, and can be used to identify the most likely dispersal routes in various contexts, such as predicting patterns of migrations, colonizations, invasions and epidemics.
A new enigmatic Late Miocene mylodontoid sloth from northern South America
Authors: Rincón Ascanio D. , McDonald H. Gregory , Solórzano Andrés , Flores Mónica Núñez , Ruiz-Ramoni Damián
Published: February 2015

A new genus and species of sloth (Eionaletherium tanycnemiusgen. et sp. nov.) recently collected from the Late Miocene Urumaco Formation, Venezuela (northern South America) is herein described based on a partial skeleton including associated femora and tibiae. In order to make a preliminary analysis of the phylogenetic affinities of this new sloth we performed a discriminate analysis based on several characters of the femur and tibia of selected Mylodontoidea and Megatherioidea sloths. The consensus tree produced indicates that the new sloth,E. tanycnemius, is a member of the Mylodontoidea. Surprisingly, the new taxon shows some enigmatic features among Neogene mylodontoid sloths, e.g. femur with a robust lesser trochanter that projects medially and the straight distinctly elongated tibia. The discovery ofE. tanycnemiusincreases the diversity of sloths present in the Urumaco sequence to ten taxa. This taxon supports previous studies of the sloth assemblage from the Urumaco sequence as it further indicates that there are several sloth lineages present that are unknown from the better sampled areas of southern South America.
Detection dog efficacy for collecting faecal samples from the critically endangered Cross River gorilla (Gorilla gorilla diehli) for genetic censusing
Authors: Arandjelovic Mimi , Bergl Richard A. , Ikfuingei Romanus , Jameson Christopher , Parker Megan , Vigilant Linda
Published: February 2015

Population estimates using genetic capture–recapture methods from non-invasively collected wildlife samples are more accurate and precise than those obtained from traditional methods when detection and resampling rates are high. Recently, detection dogs have been increasingly used to find elusive species and their by-products. Here we compared the effectiveness of dog- and human-directed searches for Cross River gorilla (Gorilla gorilla diehli) faeces at two sites. The critically endangered Cross River gorilla inhabits a region of high biodiversity and endemism on the border between Nigeria and Cameroon. The rugged highland terrain and their cryptic behaviour make them difficult to study and a precise population size for the subspecies is still lacking. Dog-directed surveys located more fresh faeces with less bias than human-directed survey teams. This produced a more reliable population estimate, although of modest precision given the small scale of this pilot study. Unfortunately, the considerable costs associated with use of the United States-based detection dog teams make the use of these teams financially unfeasible for a larger, more comprehensive survey. To realize the full potential of dog-directed surveys and increase cost-effectiveness, we recommend basing dog-detection teams in the countries where they will operate and expanding the targets the dogs are trained to detect.
Damping-induced interplay between vibrations and waves in a forced non-dispersive elastic continuum with asymmetrically placed local attachments
Authors: Blanchard A. , McFarland D. M. , Bergman L. A. , Vakakis A. F.
Published: February 2015

We study the dynamics of a linear, uniform, undamped string under harmonic base excitation, with an attachment consisting of either a spring–dashpot system or a vibration absorber. Mode complexity caused by the local damping of the attachment can lead to coexistence of vibrations and waves in the string. We consider either identical harmonic base motions at both ends or harmonic base excitation at one end. In the case of double harmonic base excitation, it is possible to choose the parameters of the attachment, so that the mode complexity is maximal in one part of the string (leading to travelling waves and elimination of vibrations) and almost zero in the other part (with standing waves or vibration modes). Similarly, for single base excitation, we analytically predict the parameters of the attachment that maximize mode complexity and enhance the interplay of vibrations and travelling waves in the string. Under such conditions, the system acts as a passive vibration confinement device, with induced energy being transmitted through travelling waves to a region where it is confined in the form of standing waves. Our results can be used for predictive design and reveal an unexpected new application of the classical linear vibration absorber.
Laplace's equation on convex polyhedra via the unified method
Authors: Ashton A. C. L.
Published: February 2015

We provide a new method to study the classical Dirichlet problem for Laplace's equation on a convex polyhedron. This new approach was motivated by Fokas’ unified method for boundary value problems. The central object in this approach is the global relation: an integral equation which couples the known boundary data and the unknown boundary values. This integral equation depends holomorphically on two complex parameters, and the resulting analysis takes place on a Banach space of complex analytic functions closely related to the classical Paley–Wiener space. We write the global relation in the form of an operator equation and prove that the relevant operator is bounded below using some novel integral identities. We give a new integral representation to the solution to the underlying boundary value problem which serves as a concrete realization of the fundamental principle of Ehrenpreis.
Ocean acidification with (de)eutrophication will alter future phytoplankton growth and succession
Authors: Flynn Kevin J. , Clark Darren R. , Mitra Aditee , Fabian Heiner , Hansen Per J. , Glibert Patricia M. , Wheeler Glen L. , Stoecker Diane K. , Blackford Jerry C. , Brownlee Colin
Published: February 2015

Human activity causes ocean acidification (OA) though the dissolution of anthropogenically generated CO
2
into seawater, and eutrophication through the addition of inorganic nutrients. Eutrophication increases the phytoplankton biomass that can be supported during a bloom, and the resultant uptake of dissolved inorganic carbon during photosynthesis increases water-column pH (bloom-induced basification). This increased pH can adversely affect plankton growth. With OA, basification commences at a lower pH. Using experimental analyses of the growth of three contrasting phytoplankton under different pH scenarios, coupled with mathematical models describing growth and death as functions of pH and nutrient status, we show how different conditions of pH modify the scope for competitive interactions between phytoplankton species. We then use the models previously configured against experimental data to explore how the commencement of bloom-induced basification at lower pH with OA, and operating against a background of changing patterns in nutrient loads, may modify phytoplankton growth and competition. We conclude that OA and changed nutrient supply into shelf seas with eutrophication or de-eutrophication (the latter owing to pollution control) has clear scope to alter phytoplankton succession, thus affecting future trophic dynamics and impacting both biogeochemical cycling and fisheries.
New insights on postglacial colonization in western Europe: the phylogeography of the Leisler's bat (Nyctalus leisleri)
Authors: Boston Emma S. M. , Ian Montgomery W. , Hynes Rosaleen , Prodöhl Paulo A.
Published: February 2015

Despite recent advances in the understanding of the interplay between a dynamic physical environment and phylogeography in Europe, the origins of contemporary Irish biota remain uncertain. Current thinking is that Ireland was colonized post-glacially from southern European refugia, following the end of the last glacial maximum (LGM), some 20 000 years BP. The Leisler's bat (Nyctalus leisleri), one of the few native Irish mammal species, is widely distributed throughout Europe but, with the exception of Ireland, is generally rare and considered vulnerable. We investigate the origins and phylogeographic relationships of Irish populations in relation to those across Europe, including the closely related speciesN. azoreum. We use a combination of approaches, including mitochondrial and nuclear DNA markers, in addition to approximate Bayesian computation and palaeo-climatic species distribution modelling. Molecular analyses revealed two distinct and diverse European mitochondrial DNA lineages, which probably diverged in separate glacial refugia. A western lineage, restricted to Ireland, Britain and the Azores, comprises Irish and BritishN. leisleriandN. azoreumspecimens; an eastern lineage is distributed throughout mainland Europe. Palaeo-climatic projections indicate suitable habitats during the LGM, including known glacial refugia, in addition to potential novel cryptic refugia along the western fringe of Europe. These results may be applicable to populations of many species.
Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal
Authors: Sharma Prashant P. , Fernández Rosa , Esposito Lauren A. , González-Santillán Edmundo , Monod Lionel
Published: February 2015

Scorpions represent an iconic lineage of arthropods, historically renowned for their unique bauplan, ancient fossil record and venom potency. Yet, higher level relationships of scorpions, based exclusively on morphology, remain virtually untested, and no multilocus molecular phylogeny has been deployed heretofore towards assessing the basal tree topology. We applied a phylogenomic assessment to resolve scorpion phylogeny, for the first time, to our knowledge, sampling extensive molecular sequence data from all superfamilies and examining basal relationships with up to 5025 genes. Analyses of supermatrices as well as species tree approaches converged upon a robust basal topology of scorpions that is entirely at odds with traditional systematics and controverts previous understanding of scorpion evolutionary history. All analyses unanimously support a single origin of katoikogenic development, a form of parental investment wherein embryos are nurtured by direct connections to the parent's digestive system. Based on the phylogeny obtained herein, we propose the following systematic emendations: Caraboctonidae is transferred to Chactoideanew superfamilial assignment; superfamily Bothriuroidearevalidatedis resurrected and Bothriuridae transferred therein; and Chaerilida and Pseudochactida are synonymized with Buthidanew parvordinal synonymies.
Loss of
Drosophila
pheromone reverses its role in sexual communication in
Drosophila suzukii
Authors: Dekker Teun , Revadi Santosh , Mansourian Suzan , Ramasamy Sukanya , Lebreton Sebastien , Becher Paul G. , Angeli Sergio , Rota-Stabelli Omar , Anfora Gianfranco
Published: February 2015

The
Drosophila
pheromone
cis
-11-octadecenyl acetate (
c
VA) is used as pheromone throughout the
melanogaster
group and fulfils a primary role in sexual and social behaviours. Here, we found that
Drosophila suzukii
, an invasive pest that oviposits in undamaged ripe fruit, does not produce
c
VA. In fact, its production site, the ejaculatory bulb, is atrophied. Despite loss of
c
VA production, its receptor, Or67d, and cognate sensillum, T1, which are essential in
c
VA-mediated behaviours, were fully functional. However, T1 expression was dramatically reduced in
D. suzukii
, and the corresponding antennal lobe glomerulus, DA1, minute. Behavioural responses to
c
VA depend on the input balance of Or67d neurons (driving
c
VA-mediated behaviours) and Or65a neurons (inhibiting
c
VA-mediated behaviours). Accordingly, the shifted input balance in
D. suzukii
has reversed
c
VA's role in sexual behaviour: perfuming
D. suzukii
males with
Drosophila melanogaster
equivalents of
c
VA strongly reduced mating rates.
c
VA has thus evolved from a generic sex pheromone to a heterospecific signal that disrupts mating in
D. suzukii
, a saltational shift, mediated through offsetting the input balance that is highly conserved in congeneric species. This study underlines that dramatic changes in a species' sensory preference can result from rather ‘simple’ numerical shifts in underlying neural circuits.
The transition from subsonic to supersonic cracks
Authors: Behn Chris , Marder M.
Published: February 2015

We present the full analytical solution for steady-state in-plane crack motion in a brittle triangular lattice. This allows quick numerical evaluation of solutions for very large systems, facilitating comparisons with continuum fracture theory. Cracks that propagate faster than the Rayleigh wave speed have been thought to be forbidden in the continuum theory, but clearly exist in lattice systems. Using our analytical methods, we examine in detail the motion of atoms around a crack tip as crack speed changes from subsonic to supersonic. Subsonic cracks feature displacement fields consistent with a stress intensity factor. For supersonic cracks, the stress intensity factor disappears. Subsonic cracks are characterized by small-amplitude, high-frequency oscillations in the vertical displacement of an atom along the crack line, while supersonic cracks have large-amplitude, low-frequency oscillations. Thus, while supersonic cracks are no less physical than subsonic cracks, the connection between microscopic and macroscopic behaviour must be made in a different way. This is one reason supersonic cracks in tension had been thought not to exist.
Microstructural aspects of fatigue in Ni-base superalloys
Authors: Antolovich Stephen D.
Published: February 2015

Nickel-base superalloys are primarily used as components in jet engines and land-based turbines. While compositionally complex, they are microstructurally simple, consisting of small (50–1000 nm diameter), ordered, coherent Ni3(Al,Ti)-type L12or Ni3Nb-type DO22precipitates (calledγ′andγ′′, respectively) embedded in an FCC substitutional solid solution consisting primarily of Ni and other elements which confer desired properties depending upon the application. The grain size may vary from as small as 2 μm for powder metallurgy alloys used in discs to single crystals the actual size of the component for turbine blades. The fatigue behaviour depends upon the microstructure, deformation mode, environment and cycle time. In many cases, it can be controlled or modified through small changes in composition which may dramatically change the mechanism of damage accumulation and the fatigue life. In this paper, the fundamental microstructural, compositional, environmental and deformation mode factors which affect fatigue behaviour are critically reviewed. Connections are made across a range of studies to provide more insight. Modern approaches are pointed out in which the wealth of available microstructural, deformation and damage information is used for computerized life prediction. The paper ends with a discussion of the very important and highly practical subject of thermo-mechanical fatigue (TMF). It is shown that physics-based modelling leads to significantly improved life prediction. Suggestions are made for moving forward on the critical subject of TMF life prediction in notched components.
Nesterenkonia populi sp. nov., an actinobacterium isolated from Populus euphratica
Authors: Liu Jia-Meng , Tuo Li , Habden Xugela , Guo Lin , Jiang Zhong-Ke , Liu Xian-Fu , Chen Li , Zhang Yu-Qin , Sun Cheng-Hang
Published: February 2015

An alkaliphilic and moderately halophilic actinobacterium, designated strain GP10-3T, was isolated from Populus euphratica collected from the southern edge of Taklimakan desert, Xinjiang, China. Cells of this strain were Gram-stain-positive, non-motile and non-spore-forming short rods. Strain GP10-3T grew optimally at 37 °C on LB agar media in the presence of 5–10 % (w/v) NaCl at pH 9.0. The menaquinones were MK-7, MK-8 and MK-9. The major fatty acids (>10 %) were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C16 : 0. The peptidoglycan type was variation A4α, l-Lys-l-Glu. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylglycolipid, phosphatidylcholine, phosphatidylinositol, glycolipid and an unidentified phospholipid. The DNA G+C content was 67.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain GP10-3T belonged to the genus

Nesterenkonia

, sharing 94.6–96.9 % sequence similarity with the type strains of species within this genus with validly published names. Based on the evidence of the polyphasic taxonomic study, strain GP10-3T represents a novel species of the genus

Nesterenkonia

, for which the name Nesterenkonia populi sp. nov. is proposed. The type strain is GP10-3T ( = DSM 27959T = KCTC 29119T).
Pseudohalocynthiibacter aestuariivivens gen. nov., sp. nov., isolated from a tidal flat
Authors: Won Sung-Min , Park Sooyeon , Park Ji-Min , Kim Byung-Chan , Yoon Jung-Hoon
Published: February 2015

A Gram-stain-negative, non-motile, aerobic and coccoid, ovoid or rod-shaped bacterial strain, designated BS-W9T, was isolated from a tidal flat of the South Sea, South Korea. Strain BS-W9T grew optimally at 25–30 °C, at pH 7.0–8.0 and in the presence of approximately 2.0 % (w/v) NaCl. Phylogenetic trees, based on 16S rRNA gene sequences, revealed that strain BS-W9T clustered with the type strain of

Halocynthiibacter namhaensis

, showing a highest sequence similarity of 97.3 %. It exhibited sequence similarity values of less than 95.6 % to the type strains of other species with validly published names. Strain BS-W9T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The major polar lipids of strain BS-W9T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. The fatty acid and polar lipid profiles of strain BS-W9T were distinguished from those of the type strains of

H. namhaensis

and other phylogenetically related genera. The DNA G+C content of strain BS-W9T was 53.2 mol% and its mean DNA–DNA relatedness value with

H. namhaensis

RA2-3T was 14 %. On the basis of the phylogenetic, chemotaxonomic and other phenotypic properties, strain BS-W9T is considered to represent a novel genus and species within the family

Rhodobacteraceae

, for which the name Pseudohalocyntiibacter aestuariivivens gen. nov., sp. nov. is proposed. The type strain of Pseudohalocyntiibacter aestuariivivens is BS-W9T ( = KCTC 42348T = CECT 8726T).
Actinomycetospora rhizophila sp. nov., an actinomycete isolated from rhizosphere soil of a peace lily (Spathi phyllum Kochii)
Authors: He Hairong , Zhang Yuejing , Ma Zhaoxu , Li Chuang , Liu Chongxi , Zhou Ying , Li Lianjie , Wang Xiangjing , Xiang Wensheng
Published: February 2015

A novel actinomycete, designated strain NEAU-B-8T, was isolated from the rhizosphere soil of a peace lily (Spathi phyllum Kochii) collected from Heilongjiang province, north-east China. Key morphological and physiological characteristics as well as chemotaxonomic features of strain NEAU-B-8T were congruent with the description of the genus

Actinomycetospora

, such as the major fatty acids, the whole-cell hydrolysates, the predominant menaquinone and the phospholipid profile. The 16S rRNA gene sequence analysis revealed that strain NEAU-B-8T shared the highest sequence similarities with

Actinomycetospora lutea

JCM 17982T (99.3 % 16S rRNA gene sequence similarity),

Actinomycetospora chlora

TT07I-57T (98.4 %),

Actinomycetospora straminea

IY07-55T (98.3 %) and

Actinomycetospora chibensis

TT04-21T (98.2 %); similarities to type strains of other species of this genus were lower than 98 %. The phylogenetic tree based on 16S rRNA gene sequences showed that strain NEAU-B-8T formed a distinct branch with

A. lutea

JCM 17982T that was supported by a high bootstrap value of 97 % in the neighbour-joining tree and was also recovered with the maximum-likelihood algorithm. However, the DNA–DNA relatedness between strain NEAU-B-8T and

A. lutea

JCM 17982T was found to be 50.6±1.2 %. Meanwhile, strain NEAU-B-8T differs from other most closely related strains in phenotypic properties, such as maximum NaCl tolerance, hydrolysis of aesculin and decomposition of urea. On the basis of the morphological, physiological, chemotaxonomic, phylogenetic and DNA–DNA hybridization data, we conclude that strain NEAU-B-8T represents a novel species of the genus

Actinomycetospora

, named Actinomycetospora rhizophila sp. nov. The type strain is NEAU-B-8T. ( = CGMCC 4.7134T = DSM 46673T).
Croceicoccus naphthovorans sp. nov., a polycyclic aromatic hydrocarbons-degrading and acylhomoserine-lactone-producing bacterium isolated from marine biofilm, and emended description of the genus Croceicoccus
Authors: Huang Yili , Zeng Yanhua , Feng Hao , Wu Yuehong , Xu Xuewei
Published: February 2015

A polycyclic aromatic hydrocarbons-degrading and acylhomoserine-lactone-producing marine bacterium, designated strain PQ-2T, was isolated from marine biofilm collected from a boat shell at a harbour of Zhoushan island in Zhejiang Province, PR China. Strain PQ-2T is Gram-stain-negative, yellow-pigmented, non-motile and short rod-shaped. Optimal growth of strain PQ-2T was observed at 32 °C, at pH 7.0 and in 2 % (w/v) NaCl. The 16S rRNA gene sequence of strain PQ-2T showed highest similarity to

Croceicoccus marinus

E4A9T (96.3 %) followed by

Novosphingobium malaysiense

MUSC 273T (95.6 %) and

Altererythrobacter marinus

H32T (95.6 %). Phylogenetic analysis with all species of the family

Erythrobacteraceae

with validly published names revealed that strain PQ-2T formed a phyletic line with

Croceicoccus marinus

E4A9T that was distinct from other members of the family

Erythrobacteraceae

. The sole respiratory quinone was ubiquinone 10 (Q-10). The predominant fatty acids were C18 : 1ω7c, C17 : 1ω6c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The genomic DNA G+C content was 61.7 mol%. In the polar lipid profile, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, one unidentified phospholipid and one sphingoglycolipid were the major compounds; and another sphingoglycolipid was present in a minor amount. Based on the genotypic and phenotypic data, strain PQ-2T represents a novel species of the genus

Croceicoccus

, for which the name Croceicoccus
naphthovorans sp. nov. is proposed. The type strain is PQ-2T ( = CGMCC 1.12805T = NBRC 110381T). In addition, emended descriptions for the genus

Croceicoccus

and the species

C. marinus

are given.
Bradymonas sediminis gen. nov., sp. nov., isolated from coastal sediment, and description of Bradymonadaceae fam. nov. and Bradymonadales ord. nov.
Authors: Wang Zong-Jie , Liu Qian-Qian , Zhao Li-Hua , Du Zong-Jun , Chen Guan-Jun
Published: February 2015

A novel Gram-stain-negative, rod-shaped, gliding, facultatively anaerobic, oxidase-negative and catalase-positive bacterium, designated FA350T, was isolated from coastal sediment from Xiaoshi Island, Weihai, China. Strain FA350T showed growth on modified nutrient agar supplemented with 0.1 % d-(+)-trehalose and with distilled water replaced by seawater. Optimal growth occurred at 33 °C and pH 8.5 with 4 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain FA350T belongs to a novel bacterial order in the class

Deltaproteobacteria

, and the most closely related type strains belong to the order

Desulfuromonadales

, with 85.1–85.6 % 16S rRNA gene sequence similarity. The polar lipid profile of the novel strain consisted of phosphatidylethanolamine, phosphatidylglycerol and two unknown phospholipids. Major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω10c and menaquinone MK-7 was the sole respiratory quinone. The DNA G+C content of strain FA350T was 60.3 mol%. The isolate and closely related environmental clones formed a novel order-level clade in the class

Deltaproteobacteria

. Comparative analysis of 16S rRNA gene sequences and characterization indicated that strain FA350T may represent a novel order of the

Deltaproteobacteria

. Here, we propose the name Bradymonas sediminis gen. nov., sp. nov. to accommodate strain FA350T. The type strain of Bradymonas sediminis is FA350T ( = DSM 28820T = CICC 10904T); Bradymonadales ord. nov. and Bradymonadaceae fam. nov. are also proposed to accommodate the novel taxon.
Occultifur tropicalis f.a., sp. nov., a novel cystobasidiomycetous yeast species isolated from tropical regions
Authors: Khunnamwong Pannida , Surussawadee Janjira , Jindamorakot Sasitorn , Ribeiro José R. A. , Hagler Allen N. , Limtong Savitree
Published: February 2015

Five strains representing a single novel anamorphic yeast species were isolated from sugar cane. Two strains were from tissue (DMKU-SE38, DMKU-SE59T) and two from the external surface (DMKU-SP385, DMKU-SP403) of leaves collected in Thailand and the fifth (IMUFRJ 52020) from the rhizoplane of sugar cane in an organically cultivated field in Brazil. On the basis of sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, they were classified as representing a single species of the genus Occultifur. The sequences of the D1/D2 region of the LSU rRNA genes and the ITS regions of the five strains were either identical or differed from each other by only one nucleotide substitution. The novel species was related most closely to Occultifur brasiliensis f.a. CBS 12687T but with 0.7–1.0 % nucleotide substitutions (4–6 nt) in the D1/D2 region of the LSU rRNA gene and 2.5–2.7 % nucleotide substitutions (14–15 nt) in the ITS region. The name Occultifur tropicalis f.a., sp. nov. is proposed. The type strain is DMKU-SE59T ( = BCC 61184T = NBRC 109696T = CBS 13389 T).
Paenibacillus tibetensis sp. nov., a psychrophilic bacterium isolated from alpine swamp meadow soil
Authors: Han Li-Li , He Ji-Zheng , Zheng Yuan-Ming , Zeng Jun , Zhang Li-Mei
Published: February 2015

A novel psychrophilic strain, SSB001T, was isolated from an alpine swamp meadow soil in Tibet, China, and identified as a representative of a novel phylogenetic subclade in the genus

Paenibacillus

, with

Paenibacillus antarcticus

(96.2 %),

Paenibacillus macquariensis

(96.53 %) and

Paenibacillus glacialis

(96.2 %) as the most closely related species on the basis of 16S rRNA gene sequence analyses. The strain was distinguished from defined species of the genus

Paenibacillus

by further study of rpoB gene sequences, phenotypic characterization, cellular fatty acid composition, quinones, polar lipids and meso-diaminopimelic acid in the peptidoglycan. Based upon these results, we propose the strain as a representative of a novel species named Paenibacillus tibetensis sp. nov., with SSB001T ( = ACCC 19728T = DSM 29321T) as the type strain. The DNA G+C content (mol%) of strain SSB001T was 40.18 mol% (HPLC).
Rufibacter immobilis sp. nov., isolated from a high-altitude saline lake
Authors: Polkade Ashish V. , Ramana V. Venkata , Joshi Amaraja , Pardesi Larrisa , Shouche Yogesh S.
Published: February 2015

Two pinkish-red, Gram-stain-negative, non-motile aerobic bacterial strains (MCC P1T and MCC P2), capable of growing at low temperatures (15 °C), were isolated from water of a saline lake located in the western Himalayas of India. The strains were capable of growth in the presence of 0–2.0 % NaCl and at pH 6.5–9.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed the closest similarity of 96.3 % to the type strain of the only species of the genus

Rufibacter

,

Rufibacter tibetensis

CCTCC AB 208084T. Strains MCC P1T and MCC P2 shared 99.0 % 16S rRNA gene sequence similarity and 88.6 % DNA–DNA relatedness. The major cellular fatty acids were iso-C15 : 0, C17 : 1ω6c, summed feature 3 (C16 : 1ω6c/C16 : 1ω7c) and summed feature 4 (anteiso-C17 : 1 B/iso-C17 : 1 I). Predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The respiratory quinone was MK-7. The DNA G+C content of the strains was 52.6–52.8 mol%. Based on morphological, physiological, chemotaxonomical and molecular characteristics, strains MCC P1T and MCC P2 represent a novel species of the genus

Rufibacter

, for which the name Rufibacter immobilis sp. nov. is proposed. The type strain is MCC P1T ( = MCC 2268T = CCTCC AB 2013351T).
Microbial aetiology of acute diarrhoea in children under five years of age in Khartoum, Sudan
Authors: Saeed Amir , Abd Hadi , Sandstrom Gunnar
Published: February 2015

Diarrhoea is one of leading causes of morbidity and mortality worldwide. Recent estimations suggested the number of deaths is close to 2.5 million. This study examined the causative agents of diarrhoea in children under 5 years of age in suburban areas of Khartoum, Sudan. A total of 437 stool samples obtained from children with diarrhoea were examined by culture and PCR for bacteria, by microscopy and PCR for parasites and by immunoassay for detection of rotavirus A. Of the 437 samples analysed, 211 (48 %) tested positive for diarrhoeagenic Escherichia coli, 96 (22 %) for rotavirus A, 36 (8 %) for Shigella spp., 17 (4 %) for Salmonella spp., 8 (2 %) for Campylobacter spp., 47 (11 %) for Giardia intestinalis and 22 (5 %) for Entamoeba histolytica. All isolates of E. coli (211, 100 %) and Salmonella (17, 100 %), and 30 (83 %) isolates of Shigella were sensitive to chloramphenicol; 17 (100 %) isolates of Salmonella, 200 (94 %) isolates of E. coli and (78 %) 28 isolates of Shigella spp. were sensitive to gentamicin. In contrast, resistance to ampicillin was demonstrated in 100 (47 %) isolates of E. coli and 16 (44 %) isolates of Shigella spp. In conclusion, E. coli proved to be the main cause of diarrhoea in young children in this study, followed by rotavirus A and protozoa. Determination of diarrhoea aetiology and antibiotic susceptibility patterns of diarrhoeal pathogens and improved hygiene are important for clinical management and controlled strategic planning to reduce the burden of infection.
Hepatitis C virus infection of cholangiocarcinoma cell lines
Authors: Fletcher Nicola F. , Humphreys Elizabeth , Jennings Elliott , Osburn William , Lissauer Samantha , Wilson Garrick K. , van IJzendoorn Sven C. D. , Baumert Thomas F. , Balfe Peter , Afford Simon , McKeating Jane A.
Published: February 2015

Hepatitis C virus (HCV) infects the liver and hepatocytes are the major cell type supporting viral replication. Hepatocytes and cholangiocytes derive from a common hepatic progenitor cell that proliferates during inflammatory conditions, raising the possibility that cholangiocytes may support HCV replication and contribute to the hepatic reservoir. We screened cholangiocytes along with a panel of cholangiocarcinoma-derived cell lines for their ability to support HCV entry and replication. While primary cholangiocytes were refractory to infection and lacked expression of several entry factors, two cholangiocarcinoma lines, CC-LP-1 and Sk-ChA-1, supported efficient HCV entry; furthermore, Sk-ChA-1 cells supported full virus replication. In vivo cholangiocarcinomas expressed all of the essential HCV entry factors; however, cholangiocytes adjacent to the tumour and in normal tissue showed a similar pattern of receptor expression to ex vivo isolated cholangiocytes, lacking SR-BI expression, explaining their inability to support infection. This study provides the first report that HCV can infect cholangiocarcinoma cells and suggests that these heterogeneous tumours may provide a reservoir for HCV replication in vivo.
Phen-Gen: Combining Phenotype and Genotype to Analyze Rare Disorders
Authors: Javed Asif , Agrawal Saloni , Ng Pauline C.
Published: February 2015

We introduce Phen-Gen, a method which combines patient’s disease symptoms and sequencing data with prior domain knowledge to identify the causative gene(s) for rare disorders. Simulations reveal that the causal variant is ranked first in 88% cases when it is coding; which is 52% advantage over a genotype-only approach and outperforms existing methods by 13-58%. If disease etiology is unknown, the causal variant is assigned top-rank in 71% of simulations.
The Cyst Nematode Effector Protein 10A07 Targets and Recruits Host Posttranslational Machinery to Mediate Its Nuclear Trafficking and to Promote Parasitism in Arabidopsis
Authors: Hewezi Tarek , Juvale Parijat S. , Piya Sarbottam , Maier Tom R. , Rambani Aditi , Rice J. Hollis , Mitchum Melissa G. , Davis Eric L. , Hussey Richard S. , Baum Thomas J.
Published: February 2015

Plant-parasitic cyst nematodes synthesize and secrete effector proteins that are essential for parasitism. One such protein is the 10A07 effector from the sugar beet cyst nematode, Heterodera schachtii, which is exclusively expressed in the nematode dorsal gland cell during all nematode parasitic stages. Overexpression of H. schachtii 10A07 in Arabidopsis thaliana produced a hypersusceptible phenotype in response to H. schachtii infection along with developmental changes reminiscent of auxin effects. The 10A07 protein physically associates with a plant kinase and the IAA16 transcription factor in the cytoplasm and nucleus, respectively. The interacting plant kinase (IPK) phosphorylates 10A07 at Ser-144 and Ser-231 and mediates its trafficking from the cytoplasm to the nucleus. Translocation to the nucleus is phosphorylation dependent since substitution of Ser-144 and Ser-231 by alanine resulted in exclusive cytoplasmic accumulation of 10A07. IPK and IAA16 are highly upregulated in the nematode-induced syncytium (feeding cells), and deliberate manipulations of their expression significantly alter plant susceptibility to H. schachtii in an additive fashion. An inactive variant of IPK functioned antagonistically to the wild-type IPK and caused a dominant-negative phenotype of reduced plant susceptibility. Thus, exploitation of host processes to the advantage of the parasites is one mechanism by which cyst nematodes promote parasitism of host plants.
Preliminary evaluation of a forensic dual diagnosis intervention
Authors: Tibber Marc Samuel , Piek Nicola , Boulter Sara
Published: February 2015

Purpose

– This study is apost hocservice level investigation into the efficacy of a forensic dual diagnosis intervention. The treatment programme incorporated the principles of cognitive behavioural therapy and Motivational Interviewing, and was comprised of three stages: psycho-education into the links between mental/physical health, substance use and offending, the cultivation of coping strategies and relapse prevention planning. The paper aims to discuss these issues.

Design/methodology/approach

– Treatment outcome was tracked using pre- and post- stage 1 and 2 measures, and included self-report questionnaires that probed service users’ readiness for change, motivations for treatment and perceived effectiveness of coping strategies (n=80 and 37 patients for stages 1 and 2, respectively). In addition, service users undertook a knowledge “quiz”, which probed information retention.

Findings

– The results show that whilst psycho-education (stage 1) increased service users’ knowledge of key issues, this had no parallel effects on other measures. In contrast, completion of stage 2 led to an increase in external motivation for treatment, although this did not translate into a shift in service users’ readiness for change.

Research limitations/implications

– These findings are consistent with the Motivational Interviewing literature and highlight the need for a shift in internalised motivation for treatment if change is to be elicited. Further, they point towards the viability of using self-report measures to monitor treatment outcome in a secure forensic setting.

Originality/value

– These findings have a number of implications for the design and on-going evaluation of forensic dual diagnosis services, an area of research that is currently under-represented in the literature.
Dual diagnosis among veterans in the United States
Authors: Crane Cory A. , Schlauch Robert C. , Easton Caroline J.
Published: February 2015

Purpose

– Over the course of their service, veterans are exposed to elevated levels of chronic stress that contribute to a greater prevalence of mental illness than observed in the general population. When mental illness is present, comorbidity is normative. Convergent evidence suggests that co-occurring substance use and mental illness is among the most prevalent forms of comorbidity within veteran samples. The purpose of this paper is to explore issues associated with dual diagnoses among veterans in the USA.

Design/methodology/approach

– Research on dual diagnoses among veterans was reviewed and consolidated for presentation into three substantive content areas consisting of prevalence, associated conditions, and treatment of dual diagnoses.

Findings

– Dually diagnosed veterans represent a group at particularly high risk for myriad adverse biopsychosocial and treatment outcomes, including poor health, suicidality, violence or aggressive behavior, arrest, homelessness, and unemployment. A comprehensive strategy has been implemented within the Veterans Health Administration to address dual diagnosis and related problems. Additional research is required to more readily identify co-occurring substance use and mental illness and to refine integrated intervention approaches to minimize burden while improving treatment outcomes for veterans and their families.

Originality/value

– The current review includes a wide range of research spanning more than two decades and describing dual diagnosis among combat veterans of all modern eras. Areas in need of further research (e.g. dual diagnosis among female veterans; early detection of psychopathology and fully integrated care among returning veterans) are identified and discussed.
Factors associated with smoking and smoking cessation among primary care patients with depression: a naturalistic cohort study
Authors: Gilchrist Gail , Davidson Sandra , Middleton Aves , Herrman Helen , Hegarty Kelsey , Gunn Jane
Published: February 2015

Purpose

– People with a history of depression are more likely to smoke and less likely to achieve abstinence from smoking long term. The purpose of this paper is to understand the factors associated with smoking and smoking cessation among patients with depression.

Design/methodology/approach

– This paper reports on smoking prevalence and cessation in a cohort of 789 primary care attendees with depressive symptoms (Centre for Epidemiologic Studies Depression Scale score of=16) recruited from 30 randomly selected Primary Care Practices in Victoria, Australia in 2005.

Findings

– At baseline, 32 per cent of participants smoked. Smokers were more likely to be male, unmarried, receive government benefits, have difficulty managing on available income, have emphysema, a chronic illness, poor self-rated health, to have more severe depressive and anxiety symptoms, to be taking anti-depressants, to be hazardous drinkers, to report suicidal ideation and to have experienced childhood physical or sexual abuse. At 12 months, 20 participants reported quitting. Females and people with good or better self-rated health were significantly more likely to have quit, while people with a chronic illness or suicidal ideation were less likely to quit. Smoking cessation was not associated with increases in depression or anxiety symptoms. Only six participants remained quit over four years.

Practical implications

– Rates of smoking were high, and long-term cessation was low among primary care patients with depressive symptoms. Primary care physicians should provide additional monitoring and support to assist smokers with depression quit and remain quit.

Originality/value

– This is the first naturalistic study of smoking patterns among primary care attendees with depressive symptoms.
Clinician experiences of administering the Essen Climate Evaluation Schema (EssenCES) in a forensic intellectual disability service
Authors: Chester Verity , McCathie Julia , Quinn Marian , Ryan Lucy , Popple Jason , Loveridge Camilla , Spall Jamie
Published: February 2015

Purpose

– Social climate (ward atmosphere) affects numerous treatment outcomes. The most commonly used measure is the Essen Climate Evaluation Schema (EssenCES) (Schalast et al., 2008). Though studies have investigated the psychometric properties of EssenCES in intellectual disability populations, few have focused on the clinical utility, or accessibility of the measure. The purpose of this paper is to examine clinician's experiences of using this measure with this population.

Design/methodology/approach

– Clinicians experienced in administering EssenCES with forensic intellectual disability patients completed an open-ended questionnaire, which sought qualitative data on their experiences of using EssenCES with this population. Data were analysed using thematic analysis.

Findings

– A number of issues were raised regarding use of EssenCES with patients with intellectual disability. Four overarching themes arose: Understanding of Language, Commenting on Others, Understanding of Likert Scale, and Scale Positives and Adaptation. Clinicians felt certain items were not uniformly understood by all patients, particularly those that incorporated abstract concepts, double negatives, or complex language.

Originality/value

– Results suggest forensic intellectual disability patients vary in their ability to understand EssenCES items. This resulted in significant further explanation by the administering clinician, a practice which raised concern regarding reliability. Results provide preliminary evidence to indicate EssenCES use requires further consideration in intellectual disability services, or adaptation for this client group.
An examination of factors that influence the number of information security policy violations in Qatari organizations
Authors: Al-Mukahal Hasan M. , Alshare Khaled
Published: February 2015

Purpose

– This paper aims to investigate factors that impact the number of information security policy violations in Qatari organizations and to examine the moderating effect of Hofstede’s cultural dimensions on the relationships between the independent factors and the number of information security policy violations.

Design/methodology/approach

– Grounded in related theories from the fields of criminology, behavioral psychology and theory of planned behavior, two components that affect the number of information security policy violations were identified. A quantitative approach was used by developing a questionnaire survey to collect the data. The research model was tested using 234 employees from different Qatari organizations.

Findings

– The results of the study indicate that trust, the impact of implementing information security policy on work environment and the clarity of the scope of the information security policy were significant factors in predicting the number of information security policy violations. The findings also reveal that cultural dimensions such as uncertainty avoidance and collectivism moderate the relationships between trust, clarity of policy scope and impact of information security policy on work environment and the number information security policy violations.

Research limitations/implications

– The generalizability of the results is limited because the sample of the study was drawn from only one developing country. Therefore, a plausible future research could be testing the proposed model in many developing and developed countries.

Practical implications

– The paper includes practical implications for developing and implementing security measures and policies in diversified work environments.

Originality/value

– This study fulfils a gap in investigating the factors that influence the number of information security policy violations and the moderating effect of cultural dimensions in developing countries such as Qatar.
A new hierarchical intrusion detection system based on a binary tree of classifiers
Authors: Ahmim Ahmed , Ghoualmi Zine Nacira
Published: February 2015

Purpose

– The purpose of this paper is to build a new hierarchical intrusion detection system (IDS) based on a binary tree of different types of classifiers. The proposed IDS model must possess the following characteristics: combine a high detection rate and a low false alarm rate, and classify any connection in a specific category of network connection.

Design/methodology/approach

– To build the binary tree, the authors cluster the different categories of network connections hierarchically based on the proportion of false-positives and false-negatives generated between each of the two categories. The built model is a binary tree with multi-levels. At first, the authors use the best classifier in the classification of the network connections in category A and category G2 that clusters the rest of the categories. Then, in the second level, they use the best classifier in the classification of G2 network connections in category B and category G3 that represents the different categories clustered in G2 without category B. This process is repeated until the last two categories of network connections. Note that one of these categories represents the normal connection, and the rest represent the different types of abnormal connections.

Findings

– The experimentation on the labeled data set for flow-based intrusion detection, NSL-KDD and KDD’99 shows the high performance of the authors' model compared to the results obtained by some well-known classifiers and recent IDS models. The experiments’ results show that the authors' model gives a low false alarm rate and the highest detection rate. Moreover, the model is more accurate than some well-known classifiers like SVM, C4.5 decision tree, MLP neural network and naïve Bayes with accuracy equal to 83.26 per cent on NSL-KDD and equal to 99.92 per cent on the labeled data set for flow-based intrusion detection. As well, it is more accurate than the best of related works and recent IDS models with accuracy equal to 95.72 per cent on KDD’99.

Originality/value

– This paper proposes a novel hierarchical IDS based on a binary tree of classifiers, where different types of classifiers are used to create a high-performance model. Therefore, it confirms the capacity of the hierarchical model to combine a high detection rate and a low false alarm rate.