bluuebunny/crossref_metadata_2025 huggingface dataset:
Ecohydrographic constraints on biodiversity and distribution of phytoplankton and zooplankton in coral reefs of the Red Sea, Saudi Arabia
Authors: Kürten Benjamin , Khomayis Hisham S. , Devassy Reny , Audritz Saskia , Sommer Ulrich , Struck Ulrich , El‐Sherbiny Mohsen M. , Al‐Aidaroos Ali M.
Published: October 2014

An integral concept of ecological research is the constraint of biodiversity along latitudinal and environmental gradients. The Red Sea features a natural example of a latitudinal gradient of salinity, temperature and nutrient richness. Coral reefs along the Red Sea coasts are supported with allochthonous resources such as oceanic and neritic phytoplankton and zooplankton; however, relatively little is known about how the ecohydrography correlates with plankton biodiversity and abundance. In this article we present the biodiversity of phytoplankton and zooplankton in Red Sea coral reefs. Oceanographic data (temperature, salinity), water samples for nutrient analysis, particulate organic matter, phytoplankton and zooplankton, the latter with special reference to Copepoda (Crustacea), were collected at nine coral reefs over ~1500 km distance along the Red Sea coast of Saudi Arabia. The trophic state of ambient waters [as indicated by chlorophyll a (Chl a)] changed from strong oligotrophy in the north to mesotrophy in the south and was associated with increasing biomasses of Bacillariophyceae, picoeukaryotes and Synechococcus as indicated by pigment fingerprinting (CHEMTAX) and flow cytometry. Net‐phytoplankton microscopy revealed a Trichodesmium erythraeum (Cyanobacteria) bloom north of the Farasan Islands. Several potentially harmful algae, including Dinophysis miles and Gonyaulax spinifera (Dinophyceae), were encountered in larger numbers in the vicinity of the aquaculture facilities at Al Lith. Changes in zooplankton abundance were mainly correlated to the phytoplankton biomass following the latitudinal gradient. The largest zooplankton abundance was observed at the Farasan Archipelago, despite high abundances of copepodites, veligers (Gastropoda larvae) and Chaetognatha at Al Lith. Although the community composition changed over latitude, biodiversity indices of phytoplankton and zooplankton did not exhibit a systematic pattern. As this study constitutes the first current account of the plankton biodiversity in Red Sea coral reefs at a large spatial scale, the results will be informative for ecosystem‐based management along the coastline of Saudi Arabia.
Decadal changes in common reef coral populations and their associations with algal symbionts (Symbiodinium spp.)
Authors: McClanahan Timothy R. , Starger Craig J. , Baker Andrew C.
Published: October 2014

Decadal populations changes in four coral taxa and their patterns of association with algal symbionts (Symbiodinium spp. – 10 years of sampling) were examined on Kenyan back reefs over a period of climatic disturbances (1991−2009). Some of the better surviving taxa, Pavona and Pocillopora, were associated with variable temperature regimes and >50% of sampled colonies in these taxa had some of the more thermally tolerant Symbiodinium in clade D. In contrast, only around 35% of Acropora and no branching forms of Porites contained detectable levels of clade D, and both taxa experienced high levels of thermally‐induced mortality and poor recovery. Overall, however the relationship between Symbiodinium clade and population‐level success of coral hosts was not strong, and differential success inside and outside fisheries closures suggests that other factors, such as predation on corals, were also influential. Consequently, while Symbiodinium in clade D may contribute to the success of coral hosts across thermal disturbances, multiple ecological factors and additional biological traits also influence their long‐term survival.
Evidence that clade A and clade B head lice live in sympatry and recombine in Algeria
Authors: BOUTELLIS A. , BITAM I. , FEKIR K. , MANA N. , RAOULT D.
Published: October 2014

Pediculus humanus L. (Psocodea: Pediculidae) can be characterized into three deeply divergent lineages (clades) based on mitochondrial DNA. Clade A consists of both head lice and clothing lice and is distributed worldwide. Clade B consists of head lice only and is mainly found in North and Central America, and in western Europe and Australia. Clade C, which consists only of head lice, is found in Ethiopia, Nepal and Senegal. Twenty‐six head lice collected from pupils at different elementary schools in two localities in Algiers (Algeria) were analysed using molecular methods for genotyping lice (cytochrome b and the multi‐spacer typing (MST) method. For the first time, we found clade B head lice in Africa living in sympatry with clade A head lice. The phylogenetic analysis of the concatenated sequences of these populations of head lice showed that clade A and clade B head lice had recombined, suggesting that interbreeding occurs when lice live in sympatry.
Freshwater aquaculture in PR China: trends and prospects
Authors: Wang Qidong , Cheng Lin , Liu Jiashou , Li Zhongjie , Xie Shouqi , De Silva Sena S.
Published: October 2014

It is acknowledged that China is the mainstay in global aquaculture, contributing for example, 65.7 (of 76 321 310 t) and 63.6 (of 38 994 913 t) per cent to total global and freshwater aquaculture production, respectively, in 2011, significantly increasing the corresponding contributions from 36.1 and 38.5% of the global total (7 359 881 t) and global freshwater (2 342 706 t) aquaculture production in 1980. Overall, aquaculture production in China in turn has enabled to reduce our dependence on food fish supplies from a hunted to a farmed origin, like all the other staples. However, there are very few accounts on different subsectors of aquaculture in China and even less on variations in aquaculture developments within the country. This review attempts to trace the development trends in inland aquaculture in China in time and space and includes aspects on production, types and modes of culture, species cultured and marketing. It is evident that though inland aquaculture is practised in most provinces of China, the great bulk of it occurs in the area that lies approximately between 110 and 120 °E and 19 and 35 °N, in the Yangtze and Pearl River basins. The review also addresses emerging issues on freshwater aquaculture and possible ways of achieving sustainability in the long term.
Intricacies of Redoxome Function Demonstrated with a Simple In vitro Chemiluminescence Method, with Special Reference to Vitamin B12 as Antioxidant
Authors: Bøyum A. , Forstrøm R. J. , Sefland I. , Sand K. L. , Benestad H. B.
Published: October 2014

The homeostatic control of the redox system (the redoxome) in mammalian cells depends upon a large number of interacting molecules, which tend to buffer the electronegativity of cells against oxidants or reductants. Some of these components kill – at high concentration – microbes and by‐stander normal cells, elaborated by professional phagocytes. We examined whether a simple, in vitro chemiluminescence set‐up, utilizing redox components from human polymorphonuclear neutrophils (PMN) and red blood cells (RBC), could clarify some unexplained workings of the redoxome. PMN or purified myeloperoxidase (MPO) triggers formation of reactive oxygen species (ROS), quantified by light emission from oxidized luminol. Both PMN and RBC can generate abundant amounts of ROS, necessitating the presence of a high‐capacity redoxome to keep the cellular electronegativity within physiological limits. We obtained proof‐of‐principle evidence that our assay could assess redox effects, but also demonstrated the intricacies of redox reactions. Simple dose–responses were found, as for the PMN proteins S100A9 (A9) and S100A8 (A8), and the system also revealed the reducing capacity of vitamin B12 (Cbl) and lutein. However, increased concentrations of oxidants in the assay mixture could decrease the chemiluminescence. Even more remarkable, A9 and NaOCl together stimulated the MPO response, but alone they inhibited MPO chemiluminescence. Biphasic responses were also recorded for some dose–response set‐ups and are tentatively explained by a ‘balance hypothesis’ for the redoxome.
Inhibition of Human γδ T Cell Proliferation and Effector Functions by Neutrophil Serine Proteases
Authors: Fazio J. , Kalyan S. , Wesch D. , Kabelitz D.
Published: October 2014

Human peripheral blood γδ T cells expressing the Vγ9Vδ2 T cell receptor are activated by microbial or endogenous pyrophosphate antigens and indirectly by nitrogen‐containing bisphosphonates. Apart from proliferation, such phosphoantigens induce proinflammatory cytokine production including TNF‐α and IFN‐γ and trigger cytotoxic effector function. Neutrophil granulocytes are known to modulate T cell activation. The neutrophil serine proteases proteinase 3, elastase and cathepsin G have multiple potential targets and promote microbial killing. In this study, we investigated the effect of the three serine proteases on the in vitro proliferation and effector functions of γδ T cells cultured in serum‐free medium. All three proteases inhibited the proliferative activity, suppressed the cytokine production and decreased the cytotoxicity of γδ T cells. Further studies indicated that proteolytic cleavage of IL‐2 and modulation of butyrophilin 3A1 (CD277) expression might contribute to the overall inhibition.
Soluble CD163, a Specific Macrophage Activation Marker, is Decreased by Anti‐TNF‐α Antibody Treatment in Active Inflammatory Bowel Disease
Authors: Dige A. , Støy S. , Thomsen K. L. , Hvas C. L. , Agnholt J. , Dahlerup J. F. , Møller H. J. , Grønbæk H.
Published: October 2014

Activated macrophages shed the haemoglobin–haptoglobin scavenger receptor CD163 into the circulation as soluble(s)‐CD163. We measured sCD163 as an in vivo macrophage activation marker in patients with Crohn's disease (CD) or ulcerative colitis (UC) receiving antitumour necrosis factor (TNF)‐α antibody or prednisolone treatment. We also investigated the CD163 expression on circulating monocytes. 58 patients with CD, 40 patients with UC and 90 healthy controls (HC) were included. All patients had active disease at inclusion and were followed for 6 weeks of anti‐TNF‐α antibody or prednisolone treatment. We measured plasma sCD163 levels at baseline, 1 day, 1 week and 6 weeks after initiating treatment. CD163 expression on circulating CD14+ monocytes was measured in 21 patients with CD receiving anti‐TNF‐α antibody treatment. Baseline sCD163 levels were elevated in patients with CD [1.99 (1.80–2.18) mg/l] and in patients with UC [2.07 (1.82–2.32) mg/l] compared with HC [1.51 (1.38–1.63) mg/l] (P < 0.001). Anti‐TNF‐α antibody treatment induced a rapid decrease in sCD163 levels in patients with CD and in patients with UC 1 day after treatment initiation (P < 0.05). One week of prednisolone treatment did not induce a reduction in sCD163 levels. Anti‐TNF‐α treatment normalized sCD163 levels in patients with UC, whereas patients with CD exhibited sustained increased sCD163 levels. In patients with CD, CD163 expression on CD14+ monocytes was increased compared with HC. This study highlights that active CD and UC are associated with increased macrophage activation, as indicated by elevated sCD163 levels and monocytic CD163 expression. Anti‐TNF‐α antibody treatment induced a rapid decrease in sCD163 levels, suggesting a specific effect on macrophage activation in inflammatory bowel diseases.
Dendritic Cells in Bone Marrow at Diagnosis and after Chemotherapy in Adult Patients with Acute Myeloid Leukaemia
Authors: Derolf Å. R. , Laane E. , Björklund E. , Saft L. , Björkholm M. , Porwit Anna
Published: October 2014

Dendritic cells (DCs) develop in the bone marrow from haematopoietic progenitor cells. Two subsets, plasmacytoid DCs (pDCs) and myeloid DCs (mDCs), have been identified. Little is known regarding DC levels in bone marrow of patients with acute myeloid leukaemia (AML) before and after chemotherapy. We investigated relative pDC and mDC levels in bone marrow from 37 hospital controls and 60 patients with AML [at diagnosis, complete remission (CR) and follow‐up] using four‐colour flow cytometry. The pDC immunophenotype was characterized as lin‐/HLA‐DR+/CD123 +  and mDC as lin‐/HLA‐DR+/CD11c+. In 69% of patients with AML, no DCs were detected at diagnosis. At CR, mDC levels were the same in patients with AML and hospital controls while pDC levels were slightly lower. There was no association between minimal residual disease or survival rates and DC levels. Patients with low mDC levels at CR were more likely to suffer from complicated infections, although the difference was not statistically significant. Altogether, there was a profound decrease in DC levels in patients with AML at diagnosis. DC levels increased at CR and were higher than in hospital controls after post‐remission therapy, suggesting that DCs recover after repeated chemotherapy. There may be an association between mDC levels and infectious complications.
Differential Cytokine Expression and Regulatory Cells in Patients with Primary and Secondary Sjögren's Syndrome
Authors: Furuzawa‐Carballeda J. , Sánchez‐Guerrero J. , Betanzos J. L. , Enriquez A. B. , Avila‐Casado C. , Llorente L. , Hernández‐Molina G.
Published: October 2014

Sjögren's syndrome (SS) is an autoimmune disease characterized by lymphocytic infiltration of the salivary and lacrimal glands. The aim of the study was to characterize and compare the presence of diverse cytokines and regulatory T and B cells in lip minor salivary gland (MSG) biopsies from patients with primary Sjögren's syndrome (pSS), secondary SS (sSS), and patients with connective tissue disease (CTD) without (w/o) SS. We included samples of MSG from 15 pSS, 24 sSS (six scleroderma, nine rheumatoid arthritis and nine lupus patients) and 15 patients with CTD w/o SS. Tissues were examined by an indirect immunoperoxidase technique (goat polyclonal anti‐human IL‐19, goat polyclonal anti‐human IL‐22 or mouse monoclonal anti‐human IL‐24). To determine the subpopulation of CD4+/IL‐17A+‐, CD4+/IL‐4+‐, CD4+/IFN‐ɣ+‐expressing T cells, CD25+/Foxp3+ Treg cells and CD20+/IL‐10+‐producing B cell subset, a double‐staining procedure was performed. We estimated the mean percentage of positively staining cells in two fields per sample. CD4+/IFN‐ɣ+, CD4+/IL‐4+ and IL‐22+ cell percentages were elevated in both SS varieties; however, the cells were more prevalent in pSS. Patients with pSS had a high number of CD4+/IL‐17A+ and IL‐19+ T cells and a lower percentage of IL‐24+ cells (P < 0.05). The Treg and IL‐10‐producing B cells were increased in pSS (P < 0.05). Concluding, in our patients, a pro‐inflammatory and regulatory balance coexists in SS, being both responses more intense in pSS. The explanation of these differences may be related to disease activity, disease duration and treatment.
Patterns of Presentation for Attempted Suicide: Analysis of a Cohort of Individuals Who Subsequently Died by Suicide
Authors: Mallon Sharon , Rosato Michael , Galway Karen , Hughes Lynette , Rondon‐Sulbaran Janeet , McConkey Sam , Leavey Gerard
Published: October 2014

All suicides and related prior attempts occurring in Northern Ireland over two years were analyzed, focusing on number and timing of attempts, method, and mental health diagnoses. Cases were derived from coroner's records, with 90% subsequently linked to associated general practice records. Of those included, 45% recorded at least one prior attempt (with 59% switching from less to more lethal methods between attempt and suicide). Compared with those recording one attempt, those with 2+  attempts were more likely to have used less lethal methods at the suicide (OR = 2.77: 95% CI = 1.06, 7.23); and those using less lethal methods at the attempts were more likely to persist with these into the suicide (OR = 3.21: 0.79, 13.07). Finally, those with preexisting mental problems were more likely to use less lethal methods in the suicide: severe mental illness (OR = 7.88: 1.58, 39.43); common mental problems (OR = 3.68: 0.83, 16.30); and alcohol/drugs related (OR = 2.02: 0.41, 9.95). This analysis uses readily available data to highlight the persisting use of less lethal methods by visible and vulnerable attempters who eventually complete their suicide. Further analysis of such conditions could allow more effective prevention strategies to be developed.
Concealed Carry in the Show‐Me State: Do Voters in Favor of Right‐to‐Carry Legislation End Up Packing Heat?*
Authors: Ghent Linda S. , Grant Alan P.
Published: October 2014

Objectives

The objectives of this study were to examine the relationship between a public vote on the right to carry (RTC) concealed weapons in the state of Missouri and the subsequent demand for concealed‐carry permits.

Methods

Weighted logit analysis of the referendum vote and the proportion of the population holding concealed‐carry permits was performed to investigate the factors that influence them.

Results

We find vast differences in the factors that significantly influenced the vote and the decision to hold a concealed‐carry permit. Crime rates are positively related to the vote, but have no influence on the decision to carry.

Conclusions

Our analysis shows that most voters do not appear to vote for the RTC based on a latent desire to carry concealed weapons. Instead, our evidence suggests that voters in favor of concealed carry may be voting for moral or philosophical reasons, and that they may be hoping to free ride on the concealed carry of others.
The Damnedest Mess: An Empirical Evaluation of the 1966 Georgia Gubernatorial Election*
Authors: Bullock Charles S. , Hood M. V.
Published: October 2014

Objective

The 1966 gubernatorial campaign provides an interesting retrospective examination of Georgia politics during a period of seismic change that included the dawn of two‐party competition, black enfranchisement, and legislative determination of the chief executive.

Method

This article provides an empirical evaluation of the 1966 gubernatorial election in Georgia, including action that occurred in the General Assembly following the election.

Results

Our findings clearly define the various coalitions supporting the three gubernatorial candidates and also explain why the plurality popular winner loses the legislative vote.

Conclusion

The 1966 election is not only interesting as a case study in its own right, but one that had a major impact on two‐party politics and legislative‐executive relations in Georgia for decades to come.
Split quantification and the status of adjunction in the theory of grammar
Authors: Authier J.‐Marc
Published: October 2014

This article provides new evidence in favor of recognizing adjunction as a grammatical operation distinct from complementation. I first introduce a case of split quantification in French that has received little attention in the literature. It consists of a quantificational expression the restriction of which is made up of the elementcomme‘as’ followed by a bare common noun. I refer to this construct asQCN. I then compareQCNwith two well‐known cases of split quantification: quantification at a distance in French (QAD) and the so‐calledwas‐für/wat voorsplit quantification construction found in German and Dutch. I argue that a coherent account of those properties of FrenchQCNthat contrast with those of FrenchQADand Germanwas‐fürsentences can only emerge from a theory of phrase structure that recognizes that arguments and adjuncts are subject to different requirements within the workspace. I show that if one assumes thatQCNrestrictor phrases areQP‐modifying adjuncts that need not be present in the derivation while theirQPhost is undergoing Merge or Move (but can be introduced at a later stage in the derivation when their host is acting as the complement or specifier of some other projection), the patterns of locality restrictions observed forQCNas well as the scopal properties of this construction can be accounted for. This, I claim, constitute strong evidence against theories of phrase structure that do not recognize adjunction as a grammatical operation distinct from complementation.
Strong modality and truth disposability in syntactic subordination: What is the locus of the phase edge validating modal adverbials?
Authors: Abraham Werner
Published: October 2014

This paper investigates modality elements in German dependent clauses. We demonstrate that although modal adverbial elements can appear freely in matrix clauses, they have a limited distribution in dependent clauses – showing up, for example, in non‐factive complement clauses, but not in factive complement clauses. More generally, the modality potential comes to exist, in ways still to be explained, in what may be called ‘peripheral’ subordinate clauses rather than ‘central’ dependent clauses. To explain this distribution, we argue that for this distinction of dependent clauses phasehood should be extended beyondCPto embrace Force. From this point we continue to distinguish a proper left edge to the Force phase from a defective one with the result that the empirical status of dependent clauses is accounted for appropriately in Minimalist terms.
Complete genomic sequence of KIR3DL1*0150102
Authors: Yindom L.‐M. , Wong G. , de Silva T. I. , Rowland‐Jones S. L.
Published: October 2014

Full‐length sequence of KIR3DL1*0150102 differs from that of KIR3DL1*0150101 in intron 6.
How much of seed dormancy in weeds can be related to seed traits?
Authors: Gardarin A , Colbach N
Published: October 2014

Seed dormancy contributes to species persistence in unpredictable environments and is a key process to be taken into account in weed dynamics models. As the level of seed dormancy, photosensitivity and the dates of dormancy induction and release are difficult to measure, our objective was to relate weed seed dormancy with morphological, chemical or physiological seed traits and with expert knowledge. Dormancy of four species was studied experimentally during a 2‐year seed burial experiment. Experiments were supplemented with data from the literature to increase the number of species analysed, resulting in a data set of 29 species. Proportions of non–dormant seeds were higher for elongated than spherical seeds, even when accounting for phylogenetic relatedness between species. Elongated seeds, which tend to remain on the soil surface in undisturbed habitats, may have been selected for lack of dormancy and immediate germination to limit mortality due to predation. Dormancy increased with seed coat thickness, which can act as a chemical and physical barrier to germination, while no relation was found with seed lipid or protein content. No correlation was found between photosensitivity parameters and any of the species traits analysed. Variations in dormancy dates (induction and release) were highly correlated with average field emergence season estimated from expert knowledge. The observed correlations suggest that the level of dormancy results both from direct and from indirect effects of traits being involved in trade‐offs together with seed mortality.
Vertical directionality-controlled metal-assisted chemical etching for ultrahigh aspect ratio nanoscale structures
Authors: Tiberio Richard C. , Rooks Michael J. , Chang Chieh , F. Knollenberg Clifford , Dobisz Elizabeth A. , Sakdinawat Anne
Published: October 2014

High aspect ratio nanoscale features are becoming increasingly important in a wide range of applications. In this paper, the authors describe the concepts of vertical directionality-controlled metal-assisted chemical etching (V-MaCE) and demonstrate resolution and fabrication capabilities for V-MaCE in the context of x-ray diffractive optics. The authors fabricate x-ray grating structures having a period of 50 nm, 25 nm lines, and 25 nm spaces, with a thickness of 1.26 μm, and achieve an aspect ratio of ∼50:1. In order to maintain the vertical etching profiles of these deep structures, the authors demonstrate the design and usage of adjacent, outrigger, gratings to balance the electron-hole concentration.
Infrared spectroscopy study of adsorption and photodecomposition of formic acid on reduced and defective rutile TiO2 (110) surfaces
Authors: Mattsson Andreas , Hu Shuanglin , Hermansson Kersti , Österlund Lars
Published: October 2014

Adsorption and photodecomposition of formic acid on rutile TiO2 (110) have been investigated with infrared reflection–absorption spectroscopy (IRRAS) employing p- and s-polarized light along the [001] and [11¯0] crystal directions. The single crystal surfaces were prepared either by sputtering and annealing in ultrahigh vacuum (UHV) to obtain a reduced surface (r-TiO2), or by sputtering without annealing to create a rough, highly defective surface (sp-TiO2). Results are compared with corresponding measurements on rutile nanocrystals performed in synthetic air. IRRAS spectra obtained on r-TiO2 and rutile nanocrystals are very similar, and show that in both cases formic acid dissociates and is predominately adsorbed as a bridging bidentate formate species, and that the formate adsorption structure on the nanocrystals is dominated by interactions with majority (110) surfaces. In contrast, the IRRAS spectra on sp-TiO2 are different, with only minor spectral features associated with (110) surfaces and lost azimuthal symmetry, both of which imply changed adsorption geometry due to bonding to low-coordinated Ti atoms with lower valences. The UV-induced rate of formate photodecomposition is about 30 times higher on rutile nanocrystals in synthetic air compared with sp-TiO2 under UHV conditions, and even larger than on r-TiO2. These differences are explained by the lack of oxygen and limited hydroxyl coverage under UHV conditions. The difference in reactivity between the r-TiO2 and sp-TiO2 surfaces is attributed to a high concentration of strongly bonded bridging bidentate formate species on the (110) surface, which lowers its reactivity. The results point to a pressure gap where the availability of molecular oxygen and the hydroxyl concentration limit the photoreactivity in UHV leading to an almost 20-fold decrease of the formate degradation rate in UHV. In contrast, the structure represented by the single crystal (110) surface is shown to capture the essential structural properties, which dictates the formic acid adsorption and adsorption structure of rutile nanocrystals.
Deep ultraviolet photopumped stimulated emission from partially relaxed AlGaN multiple quantum well heterostructures grown on sapphire substrates
Authors: Asif Fatima , Lachab Mohamed , Coleman Antwon , Ahmad Iftikhar , Zhang Bin , Adivarahan Vinod , Khan Asif
Published: October 2014

A low threshold optical power density of 240 kW/cm2 is achieved for room temperature stimulated emission at 276 nm in AlGaN/AlGaN multiple quantum well (MQW) structures over AlN/sapphire templates. The heterostructures were grown by low-pressure metalorganic chemical vapor deposition whereas a pulsed ArF excimer laser (λexc = 193 nm) was used as the pumping source for photoluminescence measurements in edge configuration. The light emitted from the MQWs above threshold exhibits a minimum linewidth of 1.2 nm and is dominated by transverse electric polarization above threshold. The optical confinement factor in the active region was calculated to be about 2%.
On the nucleation and crystallization of nanoparticles in continuous-flow nonthermal plasma reactors
Authors: Lopez Thomas , Mangolini Lorenzo
Published: October 2014

The use of nonthermal plasmas for the processing of nanomaterials remains the focus of ongoing investigations because of the many advantageous properties of this class of processes. Silicon nanoparticles in particular are easily produced using continuous flow nonthermal plasma reactors. This has become a technologically relevant technique especially because silicon is an earth-abundant material with important applications in many energy-related fields. Still, there are significant gaps of knowledge in the dynamics of nucleation, growth, and structural evolution of nanoparticles in continuous flow nonthermal plasma reactors. In this contribution, the authors address these issues by performing in-situ infrared absorption measurements to monitor the rate with which the silicon precursor, silane, is consumed by the plasma. At the same time, the authors extract nanoparticles from the plasma volume at different stages of their growth and monitor their structural evolution. The authors find that particle nucleation occurs rapidly and that as soon as the silane is fully consumed the particles have grown to almost their final size. At the end of this phase, the particles have an amorphous structure. The crystallization then occurs in the plasma on a time scale of 120 ms for the conditions used for this study. By using an experimentally determined crystallization rate for free-standing silicon nanopowders, the authors estimate the particle temperature in the plasma. The authors find that the plasma heats the particle to a temperature of over 1100 K, exceeding estimates based on the reaction between the nanoparticle surface and plasma-generated ions and radicals.
Solid-state fabrication of ultrathin freestanding carbon nanotube–graphene hybrid structures for field emission applications
Authors: Van Hai Hoang , Zhang Mei
Published: October 2014

A solid-state method was developed to fabricate field emission (FE) devices composed of freestanding and ultrathin carbon nanotube (CNT)–graphene nanoribbon (GNRs) hybrid emitter arrays that function as cathodes. The array was made by using a laser to irradiate the freestanding 200 nm-thick CNT films. The FE devices had lateral structures with the electron beam being generated by the 1D emitter arrays. The device was able to generate an emission current of 846 μA, which is equivalent to one emitter generating 150 nA at 200 V. The high FE performance is attributed to the ultrathin nature of the array coupled with the well-separated emitters. This remarkably improved the field penetration and effectively reduced the screening effect. Additionally, the emitter array had the hybrid structure of double-walled CNTs and GNRs, both of which have exceptional electron emission ability due to their unique graphitic structures. The influence of the anode–cathode distance (AC distance) on the FE performance was investigated. When the AC distance increased, the plot of emission current against applied voltage shifted toward higher voltage. However, the plot of current density against electric field (that is, the voltage normalized by the AC distance) shifted to the lower field regime. Therefore, the threshold field at which the current density reached 1 mA/cm2 decreased as the AC distance increased. This resulted from the increase in the corresponding field enhancement factor.
Influence of interfacial layer thickness on frequency dependent dielectric properties and electrical conductivity in Al/Bi4Ti3O12/p-Si structures
Authors: Durmuş Perihan , Yıldırım Mert
Published: October 2014

Three Al/Bi4Ti3O12/p-Si structures were fabricated with different interfacial layer thickness values (10, 25, and 53 nm) and admittance measurements of the structures were carried out between 1 kHz and 1 MHz in order to investigate the influence of interfacial layer thickness on dielectric properties of these structures. For the structure with thicker interfacial layer, higher dielectric constant (ε′) and dielectric loss (ε″) values were obtained at low frequencies. At high frequencies, these parameters tend to be saturated and become almost constant. Loss tangent versus frequency plots exhibit a peak and magnitude of the peak weakens with increasing frequency and shifts toward high frequency region. The dispersion in ε′ and ε″ with varying thickness at low frequencies was ascribed to interfacial polarization. In addition, obtained ε″ values indicated higher energy dissipation in the structure with thicker interfacial layer. Admittance data of the structures were also considered in terms of modulus formalism to interpret the relaxation processes in the structures. Moreover, dc electrical conductivity values were derived using frequency dependent ac electrical conductivity of the structures.
X-ray Photoelectron Spectroscopy Analyses of the Electronic Structure of Polycrystalline Ti1-xAlxN Thin Films with 0 ≤ x ≤ 0.96
Authors: Greczynski Grzegorz , Jensen Jens , Greene J. E. , Petrov Ivan , Hultman Lars
Published: October 2014

Metastable Ti1-xAlxN (0 ≤ x ≤ 0.96) alloy thin films are grown by reactive magnetron sputter deposition using a combination of high-power pulsed magnetron (HIPIMS) and DC magnetron sputtering (DCMS). Layers are deposited from elemental Ti and Al targets onto Si(001) substrates at 500 °C. All Ti1-xAlxN film surfaces are analyzed by x-ray photoelectron spectroscopy (XPS) employing monochromatic Al Kα radiation (hν = 1486.6 eV). Prior to spectra acquisition, TiAlN surfaces are sputter-cleaned in-situ with 4 keV Ar+ ions incident at an angle of 70° with respect to the surface normal. XPS results reveal satellite structures on the high binding energy side of the Ti 2p, Ti 3s, and Ti 3p core-level signals. The intensities of the primary Ti features (Ti 2p, Ti 3s, and Ti 3p) decrease with increasing AlN concentration such that the satellite peaks dominate spectra from films with x ≥ 0.67. The density-of-states at the Fermi level also decrease with increasing x indicating that the satellite peaks are due to screening of core holes created by the photoionization event. Film compositions, obtained using XPS sensitivity factors, agree to within ±3% with values determined by time-of-flight elastic recoil detection analyses.
CT imaging during microwave ablation: Analysis of spatial and temporal tissue contraction
Authors: Liu Dong , Brace Christopher L.
Published: October 2014

Purpose:

To analyze the spatial distribution and temporal development of liver tissue contraction during high‐temperature ablation by using intraprocedural computed tomography (CT) imaging.

Methods:

A total of 46 aluminum fiducial markers were positioned in a 60 × 45 mm grid, in a single plane, around a microwave ablation antenna in each of six ex vivo bovine liver samples. Ablations were performed for 10 min at 100 W. CT data of the liver sample were acquired every 30 s during ablation. Fiducial motion between acquisitions was tracked in postprocessing and used to calculate measures of tissue contraction and contraction rates. The spatial distribution and temporal evolution of contraction were analyzed.

Results:

Fiducial displacement indicated that the zone measured postablation was 8.2 ± 1.8 mm (∼20%) smaller in the radial direction and 7.1 ± 1.0 mm (∼10%) shorter in the longitudinal direction than the preablation tissue dimension. Therefore, the total ablation volume was reduced from its preablation value by approximately 45%. Very little longitudinal contraction was noted in the distal portion of the ablation zone. Central tissues contracted more than 60%, which was near an estimated limit of ∼70% based on initial water content. More peripheral tissues contracted only 15% in any direction. Contraction rates peaked during the first 60 s of heating with a roughly exponential decay over time.

Conclusions:

Ablation zones measured posttreatment are significantly smaller than the pretreatment tissue dimensions. Tissue contraction is spatially dependent, with the greatest effect occurring in the central ablation zone. Contraction rate peaks early and decays over time.
Sensitivity study of voxel‐based PET image comparison to image registration algorithms
Authors: Yip Stephen , Chen Aileen B. , Aerts Hugo J. W. L. , Berbeco Ross
Published: October 2014

Purpose:

Accurate deformable registration is essential for voxel‐based comparison of sequential positron emission tomography (PET) images for proper adaptation of treatment plan and treatment response assessment. The comparison may be sensitive to the method of deformable registration as the optimal algorithm is unknown. This study investigated the impact of registration algorithm choice on therapy response evaluation.

Methods:

Sixteen patients with 20 lung tumors underwent a pre‐ and post‐treatment computed tomography (CT) and 4D FDG‐PET scans before and after chemoradiotherapy. All CT images were coregistered using a rigid and ten deformable registration algorithms. The resulting transformations were then applied to the respective PET images. Moreover, the tumor region defined by a physician on the registered PET images was classified into progressor, stable‐disease, and responder subvolumes. Particularly, voxels with standardized uptake value (SUV) decreases >30% were classified as responder, while voxels with SUV increases >30% were progressor. All other voxels were considered stable‐disease. The agreement of the subvolumes resulting from difference registration algorithms was assessed by Dice similarity index (DSI). Coefficient of variation (CV) was computed to assess variability of DSI between individual tumors. Root mean square difference (RMSrigid) of the rigidly registered CT images was used to measure the degree of tumor deformation. RMSrigidand DSI were correlated by Spearman correlation coefficient (R) to investigate the effect of tumor deformation on DSI.

Results:

Median DSIrigidwas found to be 72%, 66%, and 80%, for progressor, stable‐disease, and responder, respectively. Median DSIdeformablewas 63%–84%, 65%–81%, and 82%–89%. Variability of DSI was substantial and similar for both rigid and deformable algorithms with CV > 10% for all subvolumes. Tumor deformation had moderate to significant impact on DSI for progressor subvolume withRrigid= − 0.60 (p= 0.01) andRdeformable= − 0.46 (p= 0.01–0.20) averaging over all deformable algorithms. For stable‐disease subvolumes, the correlations were significant (p< 0.001) for all registration algorithms withRrigid= − 0.71 andRdeformable= − 0.72. Progressor and stable‐disease subvolumes resulting from rigid registration were in excellent agreement (DSI > 70%) for RMSrigid< 150 HU. However, tumor deformation was observed to have negligible effect on DSI for responder subvolumes with insignificant |R| < 0.26,p> 0.27.

Conclusions:

This study demonstrated that deformable algorithms cannot be arbitrarily chosen; different deformable algorithms can result in large differences of voxel‐based PET image comparison. For low tumor deformation (RMSrigid< 150 HU), rigid and deformable algorithms yield similar results, suggesting deformable registration is not required for these cases.
Technical Note: Influence of the phantom material on the absorbed‐dose energy dependence of the EBT3 radiochromic film for photons in the energy range 3 keV–18 MeV
Authors: Hermida‐López M. , Lüdemann L. , Flühs A. , Brualla L.
Published: October 2014

Purpose:

Water is the reference medium for radiation therapy dosimetry, but for film dosimetry it is more practical to use a solid phantom. As the composition of solid phantoms differs from that of water, the energy dependence of film exposed within solid phantoms may also differ. The energy dependence of a radiochromic film for a given beam quality Q (energy for monoenergetic beams) has two components: the intrinsic energy dependence and the absorbed‐dose energy dependence f(Q), the latter of which can be calculated through a Monte Carlo simulation of radiation transport. The authors used Monte Carlo simulations to study the influence of the phantom material on the f(Q) of the EBT3 radiochromic film (Ashland Specialty Ingredients, Wayne, NJ) for photon beams with energies between 3 keV and 18 MeV.

Methods:

All simulations were carried out with the general‐purpose Monte Carlo code penelope 2011. The geometrical model consisted of a cylindrical phantom, with the film positioned at different depths depending on the initial photon energy. The authors simulated monoenergetic parallel photon beams and x‐ray beams from a superficial therapy system. To validate their choice of simulation parameters, they also calculated f(Q) for older film models, EBT and EBT2, comparing with published results. In addition to water, they calculated f(Q) of the EBT3 film for solid phantom materials commonly used for film dosimetry: RW1 and RW3 (PTW‐Freiburg, Freiburg, Germany), Solid Water (Gammex‐RMI, Madison, WI), and PMMA. Finally, they combined their calculated f(Q) with published overall energy response data to obtain the intrinsic energy dependence of the EBT3 film in water.

Results:

The calculated f(Q) for EBT and EBT2 films was statistically compatible with previously published data. Between 10 keV and 18 MeV, the variation found in f(Q) of the EBT3 film for water was within 2.3%, with a standard statistical uncertainty less than 1%. If the quantity dose‐to‐water in the phantom is considered, which is the common practice in radiation dosimetry, the maximum difference of energy dependence for the solid phantoms with respect to water is about 6%, at an energy of 50 keV.

Conclusions:

The EBT3 film shows a reasonably constant absorbed‐dose energy dependence when irradiated in water. If the dose‐to‐water in the phantom is considered, the maximum difference of EBT3 film energy dependence with the solid phantoms studied with respect to water is about 6% (at an energy of 50 keV). The reported overall energy dependence of the EBT3 film in water at energies below 100 keV is mainly due to the intrinsic energy dependence.
Elongational deformation of wormlike micellar solutions
Authors: Sachsenheimer Dirk , Oelschlaeger Claude , Müller Sonja , Küstner Jan , Bindgen Sebastian , Willenbacher Norbert
Published: October 2014

We have investigated the uniaxial elongation behavior of six different wormlike micelle systems covering a broad range of surfactant concentrations cs and salt/surfactant ratios R using the capillary breakup elongational rheometry (CaBER). In the fast-breaking limit (high cs and R), filament lifetime tfil is controlled by the equilibrium shear modulus G0 and the breakage time λbr obtained from small oscillatory shear according to tfil/G0∝λbr2/3 and relaxation time ratios λe/λs≈1 are found. When reptation dominates (high cs, low R) λe/λs<1 is observed similar as for solutions of covalently bound polymers. In this concentration regime, the micellar structure seems not to be affected by the strong elongational flow. In contrast, high filament lifetimes up to 1000 s and λe/λs values up to 10 are observed at low cs irrespective of R. This indicates the formation of elongation-induced structures (EISs). A minimum viscosity and a minimum initial diameter are required for creating EIS. Additional filament stretching experiments indicate that a critical total deformation has to be exceeded for structure build-up. Finally, our experiments reveal a distinct difference regarding the dependence between solutions of linear and branched micelles of filament lifetime on viscosity suggesting that CaBER is a versatile means to distinguish between these structures.
Molecular Mechanism of Nicotine Degradation by a Newly Isolated Strain, Ochrobactrum sp. Strain SJY1
Authors: Yu Hao , Tang Hongzhi , Zhu Xiongyu , Li Yangyang , Xu Ping
Published: October 2014

A newly isolated strain, SJY1, identified as
Ochrobactrum
sp., utilizes nicotine as a sole source of carbon, nitrogen, and energy. Strain SJY1 could efficiently degrade nicotine via a variant of the pyridine and pyrrolidine pathways (the VPP pathway), which highlights bacterial metabolic diversity in relation to nicotine degradation. A 97-kbp DNA fragment containing six nicotine degradation-related genes was obtained by gap closing from the genome sequence of strain SJY1. Three genes, designated
vppB
,
vppD
, and
vppE
, in the VPP pathway were cloned and heterologously expressed, and the related proteins were characterized. The
vppB
gene encodes a flavin-containing amine oxidase converting 6-hydroxynicotine to 6-hydroxy-
N
-methylmyosmine. Although VppB specifically catalyzes the dehydrogenation of 6-hydroxynicotine rather than nicotine, it shares higher amino acid sequence identity with nicotine oxidase (38%) from the pyrrolidine pathway than with its isoenzyme (6-hydroxy-
l
-nicotine oxidase, 24%) from the pyridine pathway. The
vppD
gene encodes an NADH-dependent flavin-containing monooxygenase, which catalyzes the hydroxylation of 6-hydroxy-3-succinoylpyridine to 2,5-dihydroxypyridine. VppD shows 62% amino acid sequence identity with the hydroxylase (HspB) from
Pseudomonas putida
strain S16, whereas the specific activity of VppD is ∼10-fold higher than that of HspB. VppE is responsible for the transformation of 2,5-dihydroxypyridine. Sequence alignment and phylogenetic analysis suggested that the VPP pathway, which evolved independently from nicotinic acid degradation, might have a closer relationship with the pyrrolidine pathway. The proteins and functional pathway identified here provide a sound basis for future studies aimed at a better understanding of molecular principles of nicotine degradation.
Deciphering the Role of Multiple Betaine-Carnitine-Choline Transporters in the Halophile Vibrio parahaemolyticus
Authors: Ongagna-Yhombi Serge Y. , McDonald Nathan D. , Boyd E. Fidelma
Published: October 2014

Vibrio parahaemolyticus
is a halophile that is the predominant cause of bacterial seafood-related gastroenteritis worldwide. To survive in the marine environment,
V. parahaemolyticus
must have adaptive strategies to cope with salinity changes. Six putative compatible solute (CS) transport systems were previously predicted from the genome sequence of
V. parahaemolyticus
RIMD2210633. In this study, we determined the role of the four putative betaine-carnitine-choline transporter (BCCT) homologues VP1456, VP1723, VP1905, and VPA0356 in the NaCl stress response. Expression analysis of the four BCCTs subjected to NaCl upshock showed that VP1456, VP1905, and VPA0356, but not VP1723, were induced. We constructed in-frame single-deletion mutant strains for all four BCCTs, all of which behaved similarly to the wild-type strain, demonstrating a redundancy of the systems. Growth analysis of a quadruple mutant and four BCCT triple mutants demonstrated the requirement for at least one BCCT for efficient CS uptake. We complemented
Escherichia coli
MHK13, a CS synthesis- and transporter-negative strain, with each BCCT and examined CS uptake by growth analysis and
1
H nuclear magnetic resonance (NMR) spectroscopy analyses. These data demonstrated that VP1456 had the most diverse substrate transport ability, taking up glycine betaine (GB), proline, choline, and ectoine. VP1456 was the sole ectoine transporter. In addition, the data demonstrated that VP1723 can transport GB, proline, and choline, whereas VP1905 and VPA0356 transported only GB. Overall, the data showed that the BCCTs are functional and that there is redundancy among them.
Community Shift from Phototrophic to Chemotrophic Sulfide Oxidation following Anoxic Holomixis in a Stratified Seawater Lake
Authors: Pjevac Petra , Korlević Marino , Berg Jasmine S. , Bura-Nakić Elvira , Ciglenečki Irena , Amann Rudolf , Orlić Sandi
Published: October 2014

Most stratified sulfidic holomictic lakes become oxygenated after annual turnover. In contrast, Lake Rogoznica, on the eastern Adriatic coast, has been observed to undergo a period of water column anoxia after water layer mixing and establishment of holomictic conditions. Although Lake Rogoznica's chemistry and hydrography have been studied extensively, it is unclear how the microbial communities typically inhabiting the oxic epilimnion and a sulfidic hypolimnion respond to such a drastic shift in redox conditions. We investigated the impact of anoxic holomixis on microbial diversity and microbially mediated sulfur cycling in Lake Rogoznica with an array of culture-independent microbiological methods. Our data suggest a tight coupling between the lake's chemistry and occurring microorganisms. During stratification, anoxygenic phototrophic sulfur bacteria were dominant at the chemocline and in the hypolimnion. After an anoxic mixing event, the anoxygenic phototrophic sulfur bacteria entirely disappeared, and the homogeneous, anoxic water column was dominated by a bloom of gammaproteobacterial sulfur oxidizers related to the GSO/SUP05 clade. This study is the first report of a community shift from phototrophic to chemotrophic sulfide oxidizers as a response to anoxic holomictic conditions in a seasonally stratified seawater lake.