bluuebunny/crossref_metadata_2025 huggingface dataset:
Measurement and modeling of neutral, radical, and ion densities in H2-N2-Ar plasmas
Authors: Sode M. , Jacob W. , Schwarz-Selinger T. , Kersten H.
Published: February 2015

A comprehensive experimental investigation of absolute ion and neutral species densities in an inductively coupled H2-N2-Ar plasma was carried out. Additionally, the radical and ion densities were calculated using a zero-dimensional rate equation model. The H2-N2-Ar plasma was studied at a pressure of 1.5 Pa and an rf power of 200 W. The N2 partial pressure fraction was varied between fN2=0% and 56% by a simultaneous reduction of the H2 partial pressure fraction. The Ar partial pressure fraction was held constant at about 1%. NH3 was found to be produced almost exclusively on the surfaces of the chamber wall. NH3 contributes up to 12% to the background gas. To calculate the radical densities with the rate equation model, it is necessary to know the corresponding wall loss times twrad of the radicals. twrad was determined by the temporal decay of radical densities in the afterglow with ionization threshold mass spectrometry during pulsed operation and based on these experimental data the absolute densities of the radical species were calculated and compared to measurement results. Ion densities were determined using a plasma monitor (mass and energy resolved mass spectrometer). H3+ is the dominant ion in the range of 0.0≤fN2<3.4%. For 3.4<fN2<40%, NH3+ and NH4+ are the most abundant ions and agree with each other within the experimental uncertainty. For fN2=56%, N2H+ is the dominant ion, while NH3+ and NH4+ have only a slightly lower density. Ion species with densities in the range between 0.5% and 10% of ni,tot are H2+, ArH+, and NH2+. Ion species with densities less than 0.5% of ni,tot are H+, Ar+, N+, and NH+. Our model describes the measured ion densities of the H2-N2-Ar plasma reasonably well. The ion chemistry, i.e., the production and loss processes of the ions and radicals, is discussed in detail. The main features, i.e., the qualitative abundance of the ion species and the ion density dependence on the N2 partial pressure fraction, are well reproduced by the model.
Ferromagnetic tunnel contacts to graphene: Contact resistance and spin signal
Authors: Cubukcu M. , Martin M.-B. , Laczkowski P. , Vergnaud C. , Marty A. , Attané J.-P. , Seneor P. , Anane A. , Deranlot C. , Fert A. , Auffret S. , Ducruet C. , Notin L. , Vila L. , Jamet M.
Published: February 2015

We report spin transport in CVD graphene-based lateral spin valves using different magnetic contacts. We compared the spin signal amplitude measured on devices where the cobalt layer is directly in contact with the graphene to the one obtained using tunnel contacts. Although a sizeable spin signal (up to ∼2 Ω) is obtained with direct contacts, the signal is strongly enhanced (∼400 Ω) by inserting a tunnel barrier. In addition, we studied the resistance-area product (R.A) of a variety of contacts on CVD graphene. In particular, we compared the R.A products of alumina and magnesium oxide tunnel barriers grown by sputtering deposition of aluminum or magnesium and subsequent natural oxidation under pure oxygen atmosphere or by plasma. When using an alumina tunnel barrier on CVD graphene, the R.A product is high and exhibits a large dispersion. This dispersion can be highly reduced by using a magnesium oxide tunnel barrier, as for the R.A value. This study gives insight in the material quest for reproducible and efficient spin injection in CVD graphene.
Enhanced magnetic hysteresis in Ni-Mn-Ga single crystal and its influence on magnetic shape memory effect
Authors: Heczko O. , Drahokoupil J. , Straka L.
Published: February 2015

Enhanced magnetic hysteresis due to boron doping in combination with magnetic shape memory effect in Ni-Mn-Ga single crystal results in new interesting functionality of magnetic shape memory (MSM) alloys such as mechanical demagnetization. In Ni50.0Mn28.5Ga21.5 single crystal, the boron doping increased magnetic coercivity from few Oe to 270 Oe while not affecting the transformation behavior and 10 M martensite structure. However, the magnetic field needed for MSM effect also increased in doped sample. The magnetic behavior is compared to undoped single crystal of similar composition. The evidence from the X-ray diffraction, magnetic domain structure, magnetization loops, and temperature evolution of the magnetic coercivity points out that the enhanced hysteresis is caused by stress-induced anisotropy.
Mechanism of sign crossover of the anisotropic magneto-resistance in La0.7−xPrxCa0.3MnO3 thin films
Authors: Alagoz H. S. , Desomberg J. , Taheri M. , Razavi F. S. , Chow K. H. , Jung J.
Published: February 2015

Magneto-resistive anisotropy (AMR) has been studied in 45 nm thick La0.7−xPrxCa0.3MnO3 (LPCMO) manganite films (with Pr doping x between 0 and 0.40) deposited on LaAlO3 (LAO) and SrTiO3 (STO) substrates. The AMR in compressively strained films undergoes a sign change from positive to negative at low temperatures, whereas its sign does not change in films subjected to tensile strain. Temperature dependence of magnetization in a magnetic field applied parallel and perpendicular to the (100)-plane of the films shows that at low temperatures strain-induced rotation of the easy-axis magnetization determines the sign of the AMR. At higher temperatures near the TMI the sign of the AMR is the same in both LPCMO/LAO and LPCMO/STO films, suggesting the dominating influence of percolative transport in the plane of these films at these temperatures.
An intuitive method to probe phase structure by upconversion photoluminescence of Er3+ doped in ferroelectric Pb(Mg1/3Nb2/3)O3-PbTiO3
Authors: Yao Yongjie , Luo Laihui , Li Weiping , Zhou Jun , Wang Feifei
Published: February 2015

(0.97-x)Pb(Mg1/3Nb2/3)O3-xPbTiO3-0.03Pb(Er1/2Nb1/2)O3 (PMN-xPT:Er) ceramics with different PT contents are prepared. The dielectric, piezoelectric, ferroelectric, and upconversion (UC) photoluminescence properties of the ceramics are investigated. The crystal structure of PMN-xPT:Er evolves from rhombohedral to the morphotropic phase boundary (MPB), and then to the tetragonal phase as the PT content increases. The ratio of red to green emission intensities of UC emission is strongly correlated with the phase structure of the host PMN-xPT:Er ceramic. The origin of this correlation is discussed based on Judd-Ofelt theory. Furthermore, based on the evolution of crystal symmetry of the PMN-xPT:Er ceramics, the crystal structure of the MPB phase of PMN-xPT is suggested.
The use of call imitation to establish territory occupancy by Leadbeater's possum (Gymnobelideus leadbeateri)
Authors: Harley Dan
Published: February 2015

Leadbeater’s possum (Gymnobelideus leadbeateri) is a cryptic, endangered species that is notoriously difficult to detect using conventional mammal survey methods. However, the imitation of the species’ social contact and/or alarm calls has previously been found to attract resident animals. Call imitation was employed as a secondary survey method to confirm ongoing site occupancy by Leadbeater’s possum at Yellingbo Nature Conservation Reserve. All call imitation reported here was conducted at sites currently or previously known to be occupied by particular family groups. The results indicate that the method has considerable promise as a tool to facilitate broad-scale surveys targeting this species. However, ‘false negatives’ did occur during the surveys at Yellingbo, highlighting that additional testing is required to adequately characterise the species’ response patterns, in particular variation in the response rate in occupied territories and the distance over which animals will respond. A detailed understanding of these factors is essential to permit reliable interpretation of survey findings.
Does typographic design of examination materials affect performance?
Authors: Lonsdale Maria dos Santos
Published: February 2015

The present paper reports three experiments investigating the effect typographic design of examination materials has on performance. Significant differences in performance were always found in all three experiments. These differences were always in favour of text and/or question and answer sheet layouts conforming to legibility guidelines. Participants also considered the questions with these layouts easy to answer. The main conclusion was that text and question and answer sheet layouts displaying a combination of typographic features intended to improve legibility facilitate efficient search reading and answering of questions at the perceptual level of reading. The effect of typographic layout on performance should therefore be considered in order to construct valid and reliable examination materials.
5. Definitions, types, domains
Authors: Stephenson Barry
Published: February 2015

The word “ritual” is used in three different, though related, ways. First, ritual is conceived as a kind of action. Second, ritual is a cultural domain, arena, stage, or field, in and out of which people act and are acted upon. Third, ritual is sometimes conceived as an actor in its own right. ‘Definitions, types, domains’ explains the limitations of definitions and assesses the wide-ranging scholarship on what ritual is. There are three concepts that can be distinguished from one another, though their usage tends to overlap: ritualization, rites, and ritual. The differences between religious ritual (liturgy) and political ritual and civil religion, often referred to as ceremony, are also discussed.
Following Up on Smallholder Farmers and Supermarkets in Kenya
Authors: Andersson Camilla I.M. , Chege Christine G.K. , Rao Elizaphan J.O. , Qaim Matin
Published: February 2015

In many developing countries, supermarkets are expanding rapidly. This affects farmers’ marketing options. Previous studies have analyzed welfare effects of smallholder participation in supermarket channels from a static perspective, using cross‐section data. We develop a conceptual framework and use panel data to better understand participation and impact dynamics. The analysis focuses on vegetable producers in Kenya. Participation in supermarket channels is associated with income gains. However, many farmers have dropped out of the supermarket channel due to various constraints. The initial income gains cannot be sustained when returning to the traditional market. Organizational support may be needed to avoid widening income disparities.
Numerical simulation of the December 4, 2007 landslide-generated tsunami in Chehalis Lake, Canada
Authors: Wang Jiajia , Ward Steven N. , Xiao Lili
Published: February 2015

On December 4, 2007, a three million cubic metres landslide impacted Chehalis Lake, 80 km east of Vancouver, Canada. The failed mass rushed into the lake and parented a tsunami that ran up 38 m on the opposite shore, destroyed trees, roads and campsite facilities. Armed with field surveys and multihigh-tech observations from SONAR, LiDAR and orthophotographs, we apply the newly developed ‘Tsunami Squares’ method to simulate the Chehalis Lake landslide and its generated tsunami. The landslide simulation shows a progressive failure, flow speeds up to ∼60 m s–1, and a slide mass stoppage with uniform repose angle on the lakebed. Tsunami products suggest that landslide velocity and spatial scale influence the initial wave size, while wave energy decay and inundation heights are affected by a combination of distance to the landslide, bathymetry and shoreline orientation relative to the wave direction.
Evaluation of intermittent preventive treatment of malaria against group B Streptococcus colonization in pregnant women: a nested analysis of a randomized controlled clinical trial of sulfadoxine/pyrimethamine versus mefloquine
Authors: Capan-Melser Mesküre , Mombo Ngoma Ghyslain , Akerey-Diop Daisy , Basra Arti , Würbel Heike , Groger Mirjam , Mackanga Jean R. , Zoleko-Manego Rella , Schipulle Ulla , Schwing Julia , Lötsch Felix , Rehman Khalid , Matsiegui Pierre-Blaise , Agnandji Selidji T. , Adegnika Ayôla A. , Bélard Sabine , González Raquel , Kremsner Peter G. , Menendez Clara , Ramharter Michael
Published: February 2015

Objectives

Streptococcus agalactiae constitutes an important cause of neonatal infections in sub-Saharan Africa. Sulfadoxine/pyrimethamine—the current intermittent preventive treatment of malaria in pregnancy (IPTp)—has proven in vitro activity against group B Streptococcus (GBS). Because of specific drug resistance to sulfadoxine/pyrimethamine, mefloquine—an antimalarial without in vitro activity against GBS—was evaluated as a potential alternative. This study assessed the potential of sulfadoxine/pyrimethamine-IPTp to reduce the prevalence of GBS colonization in pregnant women in Gabon when compared with the inactive control mefloquine-IPTp.

Methods

Pregnant women participating in a randomized controlled clinical trial evaluating mefloquine-IPTp versus sulfadoxine/pyrimethamine-IPTp were invited to participate and recto-vaginal swabs were collected at delivery for detection of GBS colonization. Prevalence of recto-vaginal GBS colonization was compared between IPTp regimens and risk factor and birth outcome analyses were computed.

Results

Among 549 participants, 106 were positive for GBS colonization at delivery (19%; 95% CI = 16%–23%). Prevalence of maternal GBS colonization showed no significant difference between the two IPTp regimens (mefloquine-IPTp: 67 of 366 women = 18%; 95% CI = 14%–22%; sulfadoxine/pyrimethamine-IPTp: 39 of 183 women = 21%; 95% CI = 15%–27%). Risk factor analysis for GBS colonization demonstrated a significant association with illiteracy (adjusted OR = 2.03; 95% CI = 1.25–3.30). GBS colonization had no impact on birth outcome, anaemia at delivery, gestational age and birth weight.

Conclusions

Sulfadoxine/pyrimethamine did not reduce colonization rates when used as the IPTp drug during pregnancy. Illiteracy was associated with GBS colonization.
Chemical Clearance in Infants and Children With Acid Reflux in the Physiologic Range
Authors: Woodley Frederick W. , Machado Rodrigo , Di Lorenzo Carlo , Mousa Hayat
Published: February 2015

Background and Aim:

We reported that chemical clearance (CC) of acid gastroesophageal reflux (AGER) is relatively prolonged in children with cystic fibrosis (CF). Disparity in CC values within our CF cohort sparked curiosity as to what CC looks like in infants and children with AGER in the physiologic range. The aim of the study was to assess CC in infants and children with normal AGER.

Methods:

Impedance‐pH tracings from our database for infants (≤12 months) and children (>12 months–18 years) were manually scanned for 2‐phase AGER episodes. Tracings were excluded for patients who had AGER Indices >3% (children) or >6% (infants), had positive GER‐symptom associations, were on antireflux medications, had a fundoplication, or had impedance studies shorter than 18 hour. In addition to medians (25%–75% interquartile range), we calculated the 95th percentile for the CC duration and the fifth percentile for the CC rate.

Results:

Two‐phase AGER episodes were detected in 44 infants and 60 children. The median CC duration was 64.3 seconds (51.0–91.6 seconds) for infants and 37.5 seconds (27.7–52.4 seconds) for children. The median CC rate was 0.0622 pH units/second (PU/second) (0.0354–0.0946 PU/second) for infants and 0.0928 PU/second (0.0631–0.2057 PU/second) for children. The CC duration at the 95th percentile was 148.5 seconds for infants and 114.4 seconds for children. The CC rate at the fifth percentile was 0.0088 PU/second for infants and 0.0465 PU/second for children.

Conclusions:

We report reference values for CC in infants and children who have normal acid reflux. These values should not be used as “cutoff values” because they were derived from infant and children cohorts that did not include individuals with intermediate AGER.
Development of a Medication Safety and Quality Survey for Small Rural Hospitals
Authors: Winterstein Almut G. , Johns Thomas E. , Campbell Kyle N , Libby Joel , Pannell Bob
Published: February 2015

Purpose

We summarize the development and initial implementation of a survey tool to assess medication safety in small rural hospitals.

As part of an ongoing rural hospital medication safety improvement program, we developed a survey tool in all 13 critical access hospitals (CAHs) in Florida. The survey was compiled from existing medication safety assessments and standards, clinical practice guidelines, and published literature. Survey items were selected based on considerations regarding practicality and relevance to the CAH setting.

The final survey instrument included 134 items representing 17 medication safety domains. Overall hospital scores ranged from 41% to 95%, with a median of 59%. Most hospitals showed large variation in scores across domains, with 5 hospitals having at least 1 domain with scores less than 10%. Highest scores across all facilities were seen for safety procedures concerning high-alert or look-alike medications and the assembly of emergency carts. The lowest median scores included availability and consistent use of standardized order sets and the effective implementation of medication safety committees. Most hospitals used the survey results to identify and prioritize quality improvement activities.

Conclusions

The survey can be used to conduct a short medication safety assessment specific to a limited number of areas and services in CAHs. It showed good ability to discriminate medication safety levels across participating sites and highlighted opportunities for improvement. It may need modification if case mix or services differ in other states or if the status quo of medication safety in CAHs or related standards advance. The described process of survey development might be helpful to support such modifications.
Gene expression, chromosome heterogeneity and the fast-X effect in mammals
Authors: Nguyen Linh-Phuong , Galtier Nicolas , Nabholz Benoit
Published: February 2015

The higher rate of non-synonymous over synonymous substitutions (dN/dS) of the X chromosome compared with autosomes is often interpreted as a consequence of X hemizygosity. However, other factors, such as gene expression, are also known to vary between X and autosomes. Analysing 4800 orthologues in six mammals, we found that gene expression levels, associated with GC content, fully account for the variation in dN/dS between X and autosomes with no detectable effect of hemizygosity. We also report an extensive variance in dN/dS and gene expression between autosomes.
Chromosome interaction over a distance in meiosis
Authors: Brady Mary , Paliulis Leocadia V.
Published: February 2015

The challenge of cell division is to distribute partner chromosomes (pairs of homologues, pairs of sex chromosomes or pairs of sister chromatids) correctly, one into each daughter cell. In the ‘standard’ meiosis, this problem is solved by linking partners together via a chiasma and/or sister chromatid cohesion, and then separating the linked partners from one another in anaphase; thus, the partners are kept track of, and correctly distributed. Many organisms, however, properly separate chromosomes in the absence of any obvious physical connection, and movements of unconnected partner chromosomes are coordinated at a distance. Meiotic distance interactions happen in many different ways and in different types of organisms. In this review, we discuss several different known types of distance segregation and propose possible explanations for non-random segregation of distance-segregating chromosomes.
The series elastic shock absorber: tendon elasticity modulates energy dissipation by muscle during burst deceleration
Authors: Konow Nicolai , Roberts Thomas J.
Published: February 2015

During downhill running, manoeuvring, negotiation of obstacles and landings from a jump, mechanical energy is dissipated via active lengthening of limb muscles. Tendon compliance provides a ‘shock-absorber’ mechanism that rapidly absorbs mechanical energy and releases it more slowly as the recoil of the tendon does work to stretch muscle fascicles. By lowering the rate of muscular energy dissipation, tendon compliance likely reduces the risk of muscle injury that can result from rapid and forceful muscle lengthening. Here, we examine how muscle–tendon mechanics are modulated in response to changes in demand for energy dissipation. We measured lateral gastrocnemius (LG) muscle activity, force and fascicle length, as well as leg joint kinematics and ground-reaction force, as turkeys performed drop-landings from three heights (0.5–1.5 m centre-of-mass elevation). Negative work by the LG muscle–tendon unit during landing increased with drop height, mainly owing to greater muscle recruitment and force as drop height increased. Although muscle strain did not increase with landing height, ankle flexion increased owing to increased tendon strain at higher muscle forces. Measurements of the length–tension relationship of the muscle indicated that the muscle reached peak force at shorter and likely safer operating lengths as drop height increased. Our results indicate that tendon compliance is important to the modulation of energy dissipation by active muscle with changes in demand and may provide a mechanism for rapid adjustment of function during deceleration tasks of unpredictable intensity.
Influence of structural hierarchy on the fracture behaviour of tooth enamel
Authors: Yilmaz Ezgi D. , Schneider Gerold A. , Swain Michael V.
Published: February 2015

Tooth enamel has the critical role of enabling the mastication of food and also of protecting the underlying vital dentin and pulp structure. Unlike most vital tissue, enamel has no ability to repair or remodel and as such has had to develop robust damage tolerance to withstand contact fatigue events throughout the lifetime of a species. To achieve such behaviour, enamel has evolved a complex hierarchical structure that varies slightly between different species. The major component of enamel is apatite in the form of crystallite fibres with a nanometre-sized diameter that extend from the dentin–enamel junction to the oral surface. These crystallites are bound together by proteins and peptides into a range of hierarchical structures from micrometre diameter prisms to 50–100 μm diameter bundles of prisms known as Hunter–Schreger bands. As a consequence of such complex structural organization, the damage tolerance of enamel increases through various toughening mechanisms in the hierarchy but at the expense of fracture strength. This review critically evaluates the role of hierarchy on the development of the R-curve and the stress–strain behaviour. It attempts to identify and quantify the multiple mechanisms responsible for this behaviour as well as their impact on damage tolerance.
Driving force for indentation cracking in glass: composition, pressure and temperature dependence
Authors: Rouxel Tanguy
Published: February 2015

The occurrence of damage at the surface of glass parts caused by sharp contact loading is a major issue for glass makers, suppliers and end-users. Yet, it is still a poorly understood problem from the viewpoints both of glass science and solid mechanics. Different microcracking patterns are observed at indentation sites depending on the glass composition and indentation cracks may form during both the loading and the unloading stages. Besides, we do not know much about the fracture toughness of glass and its composition dependence, so that setting a criterion for crack initiation and predicting the extent of the damage yet remain out of reach. In this study, by comparison of the behaviour of glasses from very different chemical systems and by identifying experimentally the individual contributions of the different rheological processes leading to the formation of the imprint—namely elasticity, densification and shear flow—we obtain a fairly straightforward prediction of the type and extent of the microcracks which will most likely form, depending on the physical properties of the glass. Finally, some guidelines to reduce the driving force for microcracking are proposed in the light of the effects of composition, temperature and pressure, and the areas for further research are briefly discussed.
Paracoccus
panacisoli sp. nov., isolated from a forest soil cultivated with Vietnamese ginseng
Authors: Nguyen Ngoc-Lan , Kim Yeon-Ju , Hoang Van-An , Tran Bao-Tram , Pham Huong-Son , Yang Deok-Chun
Published: February 2015

A novel bacterial strain, designated DCY94T, was isolated from forest soil cultivated with ginseng in Vietnam. The strain was Gram-reaction-negative, facultatively anaerobic, non-motile, rod-shaped and catalase- and oxidase-positive. 16S rRNA gene sequence analysis demonstrated that strain DCY94T was closely related to

Paracoccus sphaerophysae

Zy-3T (97.5 % 16S rRNA gene sequence similarity) and

Paracoccus caeni

MJ17T (96.9 %). The fatty acid profile of strain DCY94T contained a predominant amount of summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 88.4 %) and moderate to small quantities of C8 : 0 3-OH (1.0 %), C10 : 0 3-OH (2.8 %) and C18 : 0 (5.2 %). Phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and one unidentified glycolipid were major polar lipids; one unidentified aminolipid, one unidentified aminophospholipid, one unidentified phospholipid and four unidentified polar lipids were minor components. The polyamine pattern comprised the major compounds putrescine and spermidine and minor amounts of sym-homospermidine and spermine. The ubiquinone of the strain was Q-10 and the G+C content of its genomic DNA was 68.3 mol%. All these results support the placement of strain DCY94T within the genus

Paracoccus

. Levels of DNA–DNA relatedness between strain DCY94T and

P. sphaerophysae

HAMBI 3106T and

P. caeni

KCTC 22480T were 52 and 50 %, respectively. The results of phylogenetic analysis, phenotypic tests, chemotaxonomic characterization and DNA–DNA relatedness studies distinguished strain DCY94T from the closest recognized species of the genus

Paracoccus

, suggesting that this strain represents a novel species, for which the name Paracoccus panacisoli sp. nov. is proposed. The type strain is DCY94T ( = KCTC 42086T = JCM 30337T).
Aliiglaciecola aliphaticivorans sp. nov., an aliphatic hydrocarbon-degrading bacterium, isolated from a sea-tidal flat and emended description of the genus Aliiglaciecola Jean et al. 2013
Authors: Jin Hyun Mi , Jeong Hye Im , Jeon Che Ok
Published: February 2015

A Gram-stain-negative heterotrophic bacterium, designated GSD6T, capable of growth on aliphatic hydrocarbons as a sole carbon and energy source, was isolated from sea-tidal flat sediment of the Yellow Sea, South Korea. Cells were facultatively aerobic, catalase- and oxidase-positive, motile rods with a single polar flagellum. Growth of strain GSD6T was observed at 4–37 °C (optimum 30 °C), at pH 5.5–9.0 (optimum pH 6.5–7.5) and in the presence of 1–9 % (w/v) NaCl (optimum 2 %). Strain GSD6T contained ubiquinone-8 (Q-8) as the sole isoprenoid quinone and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1ω7c, C17 : 0 10-methyl and C17 : 1ω8c as the major fatty acids. Phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids. The G+C content of the genomic DNA was 44.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GSD6T formed a phylogenetic lineage with members of the genus

Aliiglaciecola

. Strain GSD6T was most closely related to

Aliiglaciecola lipolytica

E3T with a 16S rRNA gene sequence similarity of 97.4 %, but their DNA–DNA hybridization value was 39.1±7.1 %. On the basis of phenotypic, chemotaxonomic and molecular features, strain GSD6T represents a novel species of the genus

Aliiglaciecola

, for which the name Aliiglaciecola aliphaticivorans sp. nov. is proposed. The type strain is GSD6T ( = KACC 18129T = JCM 30133T). An emended description of the genus

Aliiglaciecola

is also proposed.
Algibacter amylolyticus sp. nov., isolated from intertidal sediment
Authors: Zhang De-Chao , Wu Jiang , Neuner Kathrin , Yao Jianting , Margesin Rosa
Published: February 2015

A Gram-reaction-negative, rod-shaped, yellow-pigmented, motile by gliding bacterial strain, designated RU-4-M-4T, was isolated from intertidal sediment of Sakhalin Island in Russia. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RU-4-M-4T was related to the genus

Algibacter

and had highest 16S rRNA gene sequence similarity with

Algibacter pectinivorans

KACC 14153T (97.2 %). The major cellular fatty acids were iso-C15 : 0 3-OH, C15 : 0 and iso-C15 : 1 G. The predominant menaquinone was MK-6. The polar lipid profile contained phosphatidylethanolamine, three unidentified aminolipids and two unidentified lipids. The genomic DNA G+C content of strain RU-4-M-4T was 36.4 mol%. Combined data from phenotypic, phylogenetic and DNA–DNA relatedness studies demonstrated that strain RU-4-M-4T is a representative of a novel species of the genus

Algibacter

, for which we propose the name Algibacter amylolyticus sp. nov. (type strain RU-4-M-4T = LMG 28383T = DSM 29199T).
Sediminicola arcticus sp. nov., a psychrophilic bacterium isolated from deep-sea sediment, and emended description of the genus Sediminicola
Authors: Hwang Chung Yeon , Lee Inae , Cho Yirang , Lee Yung Mi , Jung You-Jung , Baek Kiwoon , Nam Seung-Il , Lee Hong Kum
Published: February 2015

A Gram-stain-negative, rod-shaped and non-motile strain, designated PAMC 27266T, was isolated from deep-sea sediment of the Arctic Ocean. Analysis of the 16S rRNA gene sequence of strain PAMC 27266T showed closest affiliation with the genus

Sediminicola

. Phylogenetic analyses revealed that strain PAMC 27266T formed a robust clade with

Sediminicola luteus

CNI-3T, with which it shared 98.9 % 16S rRNA gene sequence similarity. Genomic relatedness analyses based on the average nucleotide identity and genome-to-genome distance showed that strain PAMC 27266T is clearly distinguished from

S. luteus

. Cells of strain PAMC 27266T grew optimally at 15 °C and pH 6.5–7.5 in the presence of 3.5 % (w/v) sea salts. The major polar lipids were phosphatidylethanolamine, two unidentified aminophospholipids and two unidentified lipids. The only respiratory quinone was menaquinone-6. The major cellular fatty acids (>10 %) were C16 : 1ω6c and/or C16 : 1ω7c and C15 : 0. The genomic DNA G+C content was 37.9 mol%. Based on the phylogenetic, genomic, chemotaxonomic and phenotypic data presented, we propose strain PAMC 27266T ( = KCCM 43038T = JCM 19894T) as the type strain of a novel species, with the name Sediminicola arcticus sp. nov.
Halococcus agarilyticus sp. nov., an agar-degrading haloarchaeon isolated from commercial salt
Authors: Minegishi Hiroaki , Echigo Akinobu , Shimane Yasuhiro , Kamekura Masahiro , Itoh Takashi , Ohkuma Moriya , Usami Ron
Published: February 2015

Two agar-degrading halophilic archaeal strains, 62ET and 197A, were isolated from commercial salt samples. Cells were non-motile cocci, approximately 1.2–2.0 µm in diameter and stained Gram-negative. Colonies were pink-pigmented. Strain 62ET was able to grow with 24–30 % (w/v) NaCl (optimum, 27 %), at pH 6.5–8.5 (optimum, pH 7.5) and at 22–47 °C (optimum, 42 °C). The 16S rRNA gene sequences of strains 62ET and 197A were identical, and the level of DNA–DNA relatedness between them was 90 and 90 % (reciprocally). The closest relative was

Halococcus saccharolyticus

JCM 8878T with 99.7 % similarity in 16S rRNA orthologous gene sequences, followed by

Halococcus salifodinae

JCM 9578T (99.6 %), while similarities with other species of the genus

Halococcus

were equal to or lower than 95.1 %. The rpoB′ gene tree strongly supported that the two strains were members of the genus

Halococcus

. Mean DNA–DNA relatedness between strain 62ET and

H. saccharolyticus

JCM 8878T and

H. salifodinae

JCM 9578T was 46 and 44 %, respectively. The major polar lipids were archaeol derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, derived from both C20C20 and C20C25 archaeol, and sulfated diglycosyl archaeol-1. Several unidentified glycolipids were present. Based on the phenotypic and phylogenetic analyses, the isolates are considered to represent a novel species of the genus

Halococcus

, for which the name Halococcus agarilyticus sp. nov. is proposed. The type strain is 62ET ( = JCM 19592T = KCTC 4143T).
Facial subcutaneous phaeohyphomycosis caused by Phialophora verrucosa: successful treatment with itraconazole and local resection
Authors: Zhang Yu , Wang Xiaowen , Li Ruoyu , Kang Yuan , Shi Xianhua , Hagen Ferry , Liu Yahong , Li Guizhen , Kong Xiangjun , Zhang Junling
Published: February 2015

Introduction:

The fungal disease phaeohyphomycosis tends to occur in immunosuppressed individuals and has rarely been reported to be caused by Phialophora verrucosa.

Case presentation:

Here, we report a primary subcutaneous phaeohyphomycosis case caused by P. verrucosa in an immunocompromised Chinese female with a CARD9 mutation that was cured with local resection and further treated with itraconazole. The current case is placed in perspective with a review of the relevant literature. The patient presented with painless dark erythema and a plaque on the right part of her face that had been present for the past 20 years. Histological examinations revealed multiple brown hyphae, bead‐like pseudohyphae and yeast‐like cells either within the giant cell or distributed in the dermis and subcutaneous tissues. The fungal cultures were morphologically identified as P. verrucosa and were confirmed by internal transcribed spacer region nucleotide sequencing. A partial surgical focal excision was performed, and the patient was treated with oral itraconazole 200 mg daily for 1 year as maintenance therapy, resulting in complete resolution of the lesions.

Conclusion:

This case is notable due to the prolonged course before a definitive diagnosis was made, the rarity of P. verrucosa as the cause of subcutaneous phaeohyphomycosis and the dramatic improvement after the focal lesion was excised and treated with itraconazole.
Multidrug‐resistant OXA‐48‐producing Klebsiella pneumoniae mediastinitis treated safely and effectively with imipenem and colistin
Authors: Mnif Basma , Mahjoubi Faouzia , Frikha Imed , Hammami Adnane
Published: February 2015

Introduction:

Post‐operative mediastinitis due to multidrug‐resistant Gram‐negative bacteria has rarely been described and is associated with increased mortality.

Case presentation:

We report a case of mediastinitis caused by a multidrug‐resistant OXA‐48‐producing Klebsiella pneumoniae isolate in a patient who underwent coronary artery bypass grafting. Successful treatment consisted of surgical debridement and prolonged administration of imipenem and colistin.

Conclusion:

This result shows that a combination of imipenem/colistin could be used to treat serious infections with carbapenemase‐producing Enterobacteriaceae.
Gammaherpesviruses and canine lymphoma: no evidence for direct involvement in commonly occurring lymphomas
Authors: Waugh Elspeth M. , Gallagher Alice , McAulay Karen A. , Henriques Joaquim , Alves Margarida , Bell Adam J. , Morris Joanna S. , Jarrett Ruth F.
Published: February 2015

Lymphoma is the most common haematopoietic malignancy in dogs, but little is known about the aetiology of this heterogeneous group of cancers. In humans, the Epstein–Barr virus (EBV) is associated with several lymphoma subtypes. Recently, it was suggested that EBV or an EBV-like virus is circulating in dogs. We therefore investigated whether EBV, or a novel herpesvirus, is associated with canine lymphoma using both serological and molecular techniques. In an assay designed to detect antibodies to EBV viral capsid antigens, 41 % of dogs were positive. Dogs with cancers, including lymphoma, were more frequently positive than controls, but no particular association with B-cell lymphoma was noted. EBV-specific RNA and DNA sequences were not detected in lymphoma tissue by in situ hybridization or PCR, and herpesvirus genomes were not detected using multiple degenerate PCR assays with the ability to detect novel herpesviruses. We therefore found no evidence that herpesviruses are directly involved in common types of canine lymphoma although cannot exclude the presence of an EBV-like virus in the canine population.
A Calcium Sensor-Regulated Protein Kinase, CALCINEURIN B-LIKE PROTEIN-INTERACTING PROTEIN KINASE19, Is Required for Pollen Tube Growth and Polarity
Authors: Zhou Liming , Lan Wenzhi , Chen Binqing , Fang Wei , Luan Sheng
Published: February 2015

Calcium plays an essential role in pollen tube tip growth. However, little is known concerning the molecular basis of the signaling pathways involved. Here, we identified Arabidopsis (Arabidopsis thaliana) CALCINEURIN B-LIKE PROTEIN-INTERACTING PROTEIN KINASE19 (CIPK19) as an important element to pollen tube growth through a functional survey for CIPK family members. The CIPK19 gene was specifically expressed in pollen grains and pollen tubes, and its overexpression induced severe loss of polarity in pollen tube growth. In the CIPK19 loss-of-function mutant, tube growth and polarity were significantly impaired, as demonstrated by both in vitro and in vivo pollen tube growth assays. Genetic analysis indicated that disruption of CIPK19 resulted in a male-specific transmission defect. Furthermore, loss of polarity induced by CIPK19 overexpression was associated with elevated cytosolic Ca2+ throughout the bulging tip, whereas LaCl3, a Ca2+ influx blocker, rescued CIPK19 overexpression-induced growth inhibition. Our results suggest that CIPK19 may be involved in maintaining Ca2+ homeostasis through its potential function in the modulation of Ca2+ influx.
The structure of apo ArnA features an unexpected central binding pocket and provides an explanation for enzymatic cooperativity
Authors: Fischer Utz , Hertlein Simon , Grimm Clemens
Published: February 2015

The bacterial protein ArnA is an essential enzyme in the pathway leading to the modification of lipid A with the pentose sugar 4-amino-4-deoxy-L-arabinose. This modification confers resistance to polymyxins, which are antibiotics that are used as a last resort to treat infections with multiple drug-resistant Gram-negative bacteria. ArnA contains two domains with distinct catalytic functions: a dehydrogenase domain and a transformylase domain. The protein forms homohexamers organized as a dimer of trimers. Here, the crystal structure of apo ArnA is presented and compared with its ATP- and UDP-glucuronic acid-bound counterparts. The comparison reveals major structural rearrangements in the dehydrogenase domain that lead to the formation of a previously unobserved binding pocket at the centre of each ArnA trimer in its apo state. In the crystal structure, this pocket is occupied by a DTT molecule. It is shown that formation of the pocket is linked to a cascade of structural rearrangements that emerge from the NAD+-binding site. Based on these findings, a small effector molecule is postulated that binds to the central pocket and modulates the catalytic properties of ArnA. Furthermore, the discovered conformational changes provide a mechanistic explanation for the strong cooperative effect recently reported for the ArnA dehydrogenase function.
Three-dimensional structures ofPlasmodium falciparumspermidine synthase with bound inhibitors suggest new strategies for drug design
Authors: Sprenger Janina , Svensson Bo , Hålander Jenny , Carey Jannette , Persson Lo , Al-Karadaghi Salam
Published: February 2015

The enzymes of the polyamine-biosynthesis pathway have been proposed to be promising drug targets in the treatment of malaria. Spermidine synthase (SpdS; putrescine aminopropyltransferase) catalyzes the transfer of the aminopropyl moiety from decarboxylatedS-adenosylmethionine to putrescine, leading to the formation of spermidine and 5′-methylthioadenosine (MTA). In this work, X-ray crystallography was used to examine ligand complexes of SpdS from the malaria parasitePlasmodium falciparum(PfSpdS). Five crystal structures were determined ofPfSpdS in complex with MTA and the substrate putrescine, with MTA and spermidine, which was obtained as a result of the enzymatic reaction taking place within the crystals, with dcAdoMet and the inhibitor 4-methylaniline, with MTA and 4-aminomethylaniline, and with a compound predicted in earlierin silicoscreening to bind to the active site of the enzyme, benzimidazol-(2-yl)pentan-1-amine (BIPA). In contrast to the other inhibitors tested, the complex with BIPA was obtained without any ligand bound to the dcAdoMet-binding site of the enzyme. The complexes with the aniline compounds and BIPA revealed a new mode of ligand binding toPfSpdS. The observed binding mode of the ligands, and the interplay between the two substrate-binding sites and the flexible gatekeeper loop, can be used in the design of new approaches in the search for new inhibitors of SpdS.
The rate ofcis–transconformation errors is increasing in low-resolution crystal structures
Authors: Croll Tristan Ian
Published: February 2015

Cis-peptide bonds (with the exception ofX-Pro) are exceedingly rare in native protein structures, yet a check for these is not currently included in the standard workflow for some common crystallography packages nor in the automated quality checks that are applied during submission to the Protein Data Bank. This appears to be leading to a growing rate of inclusion of spuriouscis-peptide bonds in low-resolution structures both in absolute terms and as a fraction of solved residues. Most concerningly, it is possible for structures to contain very large numbers (>1%) of spuriouscis-peptide bonds while still achieving excellent quality reports fromMolProbity, leading to concerns that ignoring such errors is allowing software to overfit maps without producing telltale errors in, for example, the Ramachandran plot.
Radiation damage to macromolecules: kill or cure?
Authors: Garman Elspeth F. , Weik Martin
Published: February 2015

Radiation damage induced by X-ray beams during macromolecular diffraction experiments remains an issue of concern in structural biology. While advances in our understanding of this phenomenon, driven in part by a series of workshops in this area, undoubtedly have been and are still being made, there are still questions to be answered. Eight papers in this volume give a flavour of ongoing investigations, addressing various issues. These range over: a proposed new metric derived from atomicB-factors for identifying potentially damaged amino acid residues, a study of the relative damage susceptibility of protein and DNA in a DNA/protein complex, a report of an indication of specific radiation damage to a protein determined from data collected using an X-ray free-electron laser (FEL), an account of the challenges in FEL raw diffraction data analysis, an exploration of the possibilities of using radiation damage induced phasing to solve structures using FELs, simulations of radiation damage as a function of FEL temporal pulse profiles, results on the influence of radiation damage during scanning X-ray diffraction measurements and, lastly, consideration of strategies for minimizing radiation damage during SAXS experiments. In this short introduction, these contributions are briefly placed in the context of other current work on radiation damage in the field.
Towards a gender-aware understanding of innovation: a three-dimensional route
Authors: Nählinder Johanna , Tillmar Malin , Wigren Caroline
Published: February 2015

Purpose

– The purpose of this study is to discuss the theory of gender bias in innovation studies, to illustrate the gender bias of innovation studies by using empirical means and to suggest what is needed to reduce such bias. Previous studies on innovation have primarily focussed on male-dominated industries. These studies have been biased and hence unable to capture the range of innovations covered by theoretical definitions.

Design/methodology/approach

– An innovation survey was conducted among entrepreneurs in the traditionally “female-labelled” health-care industry, avoiding the “male-labelled” concept of innovation itself in the questionnaire. The authors endeavoured to ascertain whether there is a significant difference between males and females in terms of innovativeness. Quantitative analyses were used to analyse the results and draw comparisons with an ordinary innovation survey.

Findings

– Using a gender-aware operationalisation of innovation, no significant difference in innovativeness was found between men and women. This suggests that more attention is needed to correct the prevailing gender bias in innovation studies. A research model is presented to further understand the gender-biased operationalisations of innovation. Each of its three dimensions has a clear impact upon perceived innovativeness: the gender-label of the sector studied, the gender-neutrality of the operationalisation used in the study and the gender of the actors involved. All dimensions should be taken into account in future innovation studies that aim for gender neutrality.

Practical implications

– Operationalisations for measuring innovations are usually biased. Therefore, women appear less innovative, which, in turn, leads to less visibility.

Originality/value

– Gender perspectives are very seldom employed in innovation studies. In quantitative studies of this sort, it is even rarer. Our empirical evidence from the quantitative study shows the urgency of the need to broaden the concept both in academic, political and public debates. This is not the least for efficiency reasons in resource allocation and public policy.
Government’s civil liability towards individuals’ privacy in cyberspace
Authors: Malmir Ameneh , Malmir Mohammad
Published: February 2015

Purpose

– One of the main manifestations of the application of modern information and communication technologies which is considered by governments is the concept of e-government.

Design/methodology/approach

– Developing economic and social interactions requires the government to interfere in people’s private affairs; the issues that were formerly part of the private rights of citizens are now influenced by public rights and actions resulted by the government’s regulation.

Findings

– To provide their individual freedom and welfare, human beings consider it necessary to respect the privacy of each other; they do not want to be watched over or their personal information and secrets to be revealed.

Originality/value

– Many international laws have been legislated in this regard to respect individuals’ privacy and prohibit natural and legal persons from accessing the information; this must be observed by governments, too.