bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of self-seeding and crystal post-selection on the quality of Monte Carlo-integrated SFX data
Authors: Barends Thomas , White Thomas A. , Barty Anton , Foucar Lutz , Messerschmidt Marc , Alonso-Mori Roberto , Botha Sabine , Chapman Henry , Doak R. Bruce , Galli Lorenzo , Gati Cornelius , Gutmann Matthias , Koglin Jason , Markvardsen Anders , Nass Karol , Oberthur Dominik , Shoeman Robert L. , Schlichting Ilme , Boutet Sébastien
Published: April 2015

Serial femtosecond crystallography (SFX) is an emerging method for data collection at free-electron lasers (FELs) in which single diffraction snapshots are taken from a large number of crystals. The partial intensities collected in this way are then combined in a scheme called Monte Carlo integration, which provides the full diffraction intensities. However, apart from having to perform this merging, the Monte Carlo integration must also average out all variations in crystal quality, crystal size, X-ray beam properties and other factors, necessitating data collection from thousands of crystals. Because the pulses provided by FELs running in the typical self-amplified spontaneous emission (SASE) mode of operation have very irregular, spiky spectra that vary strongly from pulse to pulse, it has been suggested that this is an important source of variation contributing to inaccuracies in the intensities, and that, by using monochromatic pulses produced through a process called self-seeding, fewer images might be needed for Monte Carlo integration to converge, resulting in more accurate data. This paper reports the results of two experiments performed at the Linac Coherent Light Source in which data collected in both SASE and self-seeded mode were compared. Importantly, no improvement attributable to the use of self-seeding was detected. In addition, other possible sources of variation that affect SFX data quality were investigated, such as crystal-to-crystal variations reflected in the unit-cell parameters; however, these factors were found to have no influence on data quality either. Possibly, there is another source of variation as yet undetected that affects SFX data quality much more than any of the factors investigated here.
Optical laser systems at the Linac Coherent Light Source
Authors: Minitti Michael P. , Robinson Joseph S. , Coffee Ryan N. , Edstrom Steve , Gilevich Sasha , Glownia James M. , Granados Eduardo , Hering Philippe , Hoffmann Matthias C. , Miahnahri Alan , Milathianaki Despina , Polzin Wayne , Ratner Daniel , Tavella Franz , Vetter Sharon , Welch Marc , White William E. , Fry Alan R.
Published: April 2015

Ultrafast optical lasers play an essential role in exploiting the unique capabilities of recently commissioned X-ray free-electron laser facilities such as the Linac Coherent Light Source (LCLS). Pump–probe experimental techniques reveal ultrafast dynamics in atomic and molecular processes and reveal new insights in chemistry, biology, material science and high-energy-density physics. This manuscript describes the laser systems and experimental methods that enable cutting-edge optical laser/X-ray pump–probe experiments to be performed at LCLS.
A posterioridetermination of the useful data range for small-angle scattering experiments on dilute monodisperse systems
Authors: Konarev Petr V. , Svergun Dmitri I.
Published: April 2015

Small-angle X-ray and neutron scattering (SAXS and SANS) experiments on solutions provide rapidly decaying scattering curves, often with a poor signal-to-noise ratio, especially at higher angles. On modern instruments, the noise is partially compensated for by oversampling, thanks to the fact that the angular increment in the data is small compared with that needed to describe adequately the local behaviour and features of the scattering curve. Given a (noisy) experimental data set, an important question arises as to which part of the data still contains useful information and should be taken into account for the interpretation and model building. Here, it is demonstrated that, for monodisperse systems, the useful experimental data range is defined by the number of meaningful Shannon channels that can be determined from the data set. An algorithm to determine this number and thus the data range is developed, and it is tested on a number of simulated data sets with various noise levels and with different degrees of oversampling, corresponding to typical SAXS/SANS experiments. The method is implemented in a computer program and examples of its application to analyse the experimental data recorded under various conditions are presented. The program can be employed to discard experimental data containing no useful information in automated pipelines, in modelling procedures, and for data deposition or publication. The software is freely accessible to academic users.
Serial snapshot crystallography for materials science with SwissFEL
Authors: Dejoie Catherine , Smeets Stef , Baerlocher Christian , Tamura Nobumichi , Pattison Philip , Abela Rafael , McCusker Lynne B.
Published: April 2015

New opportunities for studying (sub)microcrystalline materials with small unit cells, both organic and inorganic, will open up when the X-ray free electron laser (XFEL) presently being constructed in Switzerland (SwissFEL) comes online in 2017. Our synchrotron-based experiments mimicking the 4%-energy-bandpass mode of the SwissFEL beam show that it will be possible to record a diffraction pattern of up to 10 randomly oriented crystals in a single snapshot, to index the resulting reflections, and to extract their intensities reliably. The crystals are destroyed with each XFEL pulse, but by combining snapshots from several sets of crystals, a complete set of data can be assembled, and crystal structures of materials that are difficult to analyze otherwise will become accessible. Even with a single shot, at least a partial analysis of the crystal structure will be possible, and with 10–50 femtosecond pulses, this offers tantalizing possibilities for time-resolved studies.
Crystal structure of 3-(4-methoxyphenyl)-2,3-dihydro-1H-naphtho[2,1-b]pyran-1-one
Authors: Vasanthi R. , Reuben Jonathan D. , Elizhlarasi K. S. , Revathi B. K. , Usha G.
Published: April 2015

In the title compound, C20H16O3, the hydropyran ring adopts a distorted half-chair conformation with the methine C atom and the ring O atom displaced by −0.554 (2) and 0.158 (1) Å, respectively, from the plane of the other four atoms (r.m.s. deviation = 0.020 Å). Its mean plane (all atoms) is inclined to the naphthalene ring system at a dihedral angle of 11.67 (1)°. The dihedral angle between the napthalene ring system and the phenyl ring is 71.84 (1)°. In the crystal, no diectional interactions beyond van der Waals contacts could be identified.
Crystal structure of 3-bromo-2-hydroxybenzoic acid
Authors: Laus Gerhard , Kahlenberg Volker , Gelbrich Thomas , Nerdinger Sven , Schottenberger Herwig
Published: April 2015

Mutual carboxyl–carboxyl O—H...O hydrogen bonds link the molecules of the title compound, C7H5BrO3, into centrosymmetric dimers which display a centralR22(8) ring motif. In addition, there is an intramolecular hydroxyl–carboxyl O—H...O interaction present. A comparison with the crystal structures of 59 other substituted derivatives of salicylic acid shows that both the centrosymmetric carboxyl–carboxyl O—H...O dimer and the stacking mode of molecules along the shortaaxis observed in the title structure are frequent packing motifs in this set.
Crystal structure of 2-(11-oxo-10H,11H-indeno[1,2-b]chromen-10-yl)-2,3-dihydro-1H-indene-1,3-dione
Authors: Mague Joel T. , Mohamed Shaaban K. , Akkurt Mehmet , Abdelhamid Antanr A. , Albayati Mustafa R.
Published: April 2015

In the title molecule, C25H14O4, the fused-ring system consisting of four rings is approximately planar, with a dihedral angle of 9.62 (5)° between the planes of the indene ring system and the benzene ring. The dihydroindene-1,3-dione unit makes a dihedral angle of 63.50 (2)° with the mean plane of the fused-ring system. A weak C—H...O interaction organizes the molecules into a helical chain along thebaxis. In addition, there is a π–π stacking interaction between the five-membered rings of adjacent fused-ring systems, with a centroid–centroid distance of 3.666 (1) Å.
Crystal structure of tetrakis(μ3-2-{[1,1-bis(hydroxymethyl)-2-oxidoethyl]iminomethyl}phenolato)tetracopper(II) ethanol monosolvate 2.5-hydrate
Authors: Wang Weilun , Ran Jingwen
Published: April 2015

The title compound, [Cu4(C11H13NO4)4]·CH3CH2OH·2.5H2O, is an electronically neutral tetranuclear copper(II) complex with a cubane-like Cu4O4core. The complete molecule has point group symmetry 2. The phenol hydroxy group and one of the three alcohol hydroxy groups of each 2-{[tris(hydroxymethyl)methyl]iminomethyl}phenol ligand are deprotonated, while the secondary amine and the other two hydroxy groups remain unchanged. The CuIIatoms in the Cu4O4core are connected by four μ3-O atoms from the deprotonated alcohol hydroxy groups. Each of the pentacoordinated CuIIions has an NO4distorted square-pyramidal environment through coordination to the tridentate Schiff base ligands. The Cu—N/O bond lengths span the range 1.902 (4)–1.955 (4) Å, similar to values reported for related structures. There are O—H...O hydrogen-bond interactions between the complex molecules and the ethanol and water solvent molecules, leading to the formation of a three-dimensional network. The ethanol solvent molecule is disordered about a twofold rotation axis. One of the two independent water molecules is also located on this twofold rotation axis and shows half-occupancy.
Crystal structure of bis[1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene]silver(I) chloride tetrahydrofuran monosolvate
Authors: Sänger Inge , Lerner Hans-Wolfram , Bolte Michael
Published: April 2015

In the title salt, [Ag(C27H36N2)2]Cl·C4H8O, the AgIatom is coordinated by two 1,3-bis(2,6-dimethylphenyl)imidazol-2-ylidene ligands. The imidazole rings are inclined to one another by 46.69 (13)° and the benzene rings in each ligand are almost normal to the imdazole ring to which they are attached, with dihedral angles varying from 82.39 (13) to 88.27 (12)°. There are C—H...π interactions present in the cation, involving the two ligands, and the solvent molecule is linked to the cationviaa C—H...O hydrogen bond. In the crystal, molecules are linked by trifurcated C—H...(Cl,Cl,Cl) hydrogen bonds, forming slabs parallel to (101). One isopropyl group is disordered over two sets of sites with an occupancy ratio of 0.447 (17):0.553 (17) and the THF molecule is disordered over two positions with an occupancy ratio of 0.589 (6):0.411 (6).
A proposed contribution model for general Islamic insurance industry
Authors: Olorogun Lukman Ayinde
Published: April 2015

Purpose

– This paper aims to consider a contribution model of a general Islamic insurance industry which allowed the return of underwriting profit to the Islamic insurance participants. The objective is to create a justified and equitable means of computing contribution which maximises the expected ownership right of the Islamic insurance fund.

Design/methodology/approach

– The accumulation of funds and claims paid were characterised in form of accumulation and decay function over a period of time. It provides necessary and sufficient conditions for their existence and uniqueness. Mathematical derivative procedures were adopted to derive the underwriting returns to be returned to the Islamic insurance participants. Lastly, this paper recommends the incorporation of underwriting returns’ variable into the traditional actuarial model and provides theoretical justification for the process.

Findings

– Then, the derivation of underwriting returns through convolution of accumulated funds and claims paid views in the form of Laplace Transform led to a conjecture and proved. Thereafter, the proposed and adjusted model was arrived at.

Originality/value

– This study, to the best knowledge of the researcher, is the first attempt in the quantification of Islamic insurance industry. Thus, the model is the first attempt of creating a justified way of calculating the Islamic insurance participants’ contributions.
Development and evaluation of an Internet-based program to improve the mental health and wellbeing of young men
Authors: Ellis Louise A. , McCabe Kathryn , Davenport Tracey , Burns Jane M. , Rahilly Kitty , Nicholas Mariesa , Hickie Ian B
Published: April 2015

Purpose

– This paper aims to describe the development of WorkOut, an Internet-based program designed to help young men overcome the barriers towards help-seeking and to build the skills they need to understand and manage their own mental health. Information and communication technologies (ICT) hold great potential to significantly improve mental health outcomes for hard-to-reach and traditionally underserved groups. Internet-based programs and mobile phone applications may be particularly appealing to young men due to their convenience, accessibility and privacy and they also address the strong desire for independence and autonomy held by most men.

Design/methodology/approach

– In this paper, we describe the design process itself, and the strategies used for multi-disciplinary collaboration. The initial evaluation process and results are also described which consisted of three distinct phases: website statistics; one-on-one user testing; and pilot interviews.

Findings

– The results suggest that WorkOut has the potential to attract young men. However, further work is needed to ensure that users remain engaged with the program.

Originality/value

– The difficulties encountered and lessons learned provide an insight into the factors that should be considered in the design and evaluation of future ICT-based strategies within the mental health domain, as well as their potential applicability to clinical and educational settings.
Customer and employee co-creation of radical service innovations
Authors: Melton Horace , Hartline Michael D.
Published: April 2015

Purpose

– The study demonstrates that firms can effectively involve customers in new service development (NSD) to create radically innovative, high-performing new services. Prior research found no effect of customer involvement on radicalness in NSD programs, but the current study provides evidence that customer involvement in the design stage of NSD projects can increase the radical innovativeness of a new service.

Design/methodology/approach

– Surveys from 160 firms captured information on the development process, participants and outcomes of recent service innovation projects. Direct effect and mediation hypotheses were tested using structural equation modeling.

Findings

– Customer involvement in the NSD process increases the innovativeness of a new service when customers are involved in the design stage and when the influence is mediated by process complexity. Customer involvement in the development stage has no significant effect on service innovativeness. Process complexity also mediates the positive influence of frontline employee and cross-functional team involvement in the NSD process on service innovativeness.

Practical implications

– To produce radically innovative new services, managers should: focus on customer involvement in the design phase and build an understanding of how the customer creates value-in-context, and use a detailed but flexible development process and provide extensive opportunities for interaction of customers, frontline employees and cross-functional teams throughout the NSD process.

Originality/value

– The study draws on complexity theory to explain how a complex NSD process enhances participants’ creativity and learning and increases the innovativeness of a new service.
A view from the street: an exploratory study of consumer attitudes toward offshoring of professional services in the United States
Authors: Koku Paul Sergius
Published: April 2015

Purpose

– The study aims to examine consumer attitudes toward offshore-outsourcing of professional services in the USA. It focuses on the services of accountants, attorneys and doctors to provide a framework for discussing policy and marketing implications.

Design/methodology/approach

– The study reviews a review of the literature on consumer decision-making under uncertainty and attitude formation, and a focus group study to examine consumers’ attitudes toward offshore-outsourcing of professional services.

Findings

– Contrary to reports in the popular press, this paper suggests that consumers do not have a generalized negative attitude toward offshore-outsourcing of all forms of professional services. While consumers do not mind offshore-outsourcings of the services of medical doctors and attorneys, they seem to be concerned about offshore-outsourcings of accounting or financial services. These results suggest that persons engaged in offshore-outsourcings of tax and other related services must re-strategize.

Research limitations/implications

– While the results of this study offer a window into the US consumers’ feelings about offshore-outsourcings of professional services, the results lack generalizability, as they are based on an exploratory study.

Practical implications

– Even though outsourcing has received a lot of media attention and some limited attention from academics, no study, to the best of the authors’ knowledge, has specifically investigated US consumers’ attitudes toward offshore-outsourcings of professional services. Given the fact that the trend is growing instead of abating, a study, such as the current one, that investigates how consumers feel about the practice is not only timely but will also provide valuable information to managers for strategy reformulation and to lawmakers for regulation purposes.

Originality/value

– This paper, to the best of the authors’ knowledge, is the first to specifically examine consumer attitude toward offshoring of the basic professional services – the services of doctors, accountants and attorneys.
Genome and proteome analysis of Pseudomonas chloritidismutans AW‐1T that grows on n‐decane with chlorate or oxygen as electron acceptor
Authors: Mehboob Farrakh , Oosterkamp Margreet J. , Koehorst Jasper J. , Farrakh Sumaira , Veuskens Teun , Plugge Caroline M. , Boeren Sjef , de Vos Willem M. , Schraa Gosse , Stams Alfons J.M. , Schaap Peter J.
Published: April 2015

Growth of Pseudomonas chloritidismutans AW‐1T on C7 to C12 n‐alkanes with oxygen or chlorate as electron acceptor was studied by genome and proteome analysis. Whole genome shotgun sequencing resulted in a 5 Mbp assembled sequence with a G + C content of 62.5%. The automatic annotation identified 4767 protein‐encoding genes and a putative function could be assigned to almost 80% of the predicted proteins. The distinct phylogenetic position of P. chloritidismutans AW‐1T within the Pseudomonas stutzeri cluster became clear by comparison of average nucleotide identity values of sequenced genomes. Analysis of the proteome of P. chloritidismutans AW‐1T showed the versatility of this bacterium to adapt to aerobic and anaerobic growth conditions with acetate or n‐decane as substrates. All enzymes involved in the alkane oxidation pathway were identified. An alkane monooxygenase was detected in n‐decane‐grown cells, but not in acetate‐grown cells. The enzyme was found when grown in the presence of oxygen or chlorate, indicating that under both conditions an oxygenase‐mediated pathway is employed for alkane degradation. Proteomic and biochemical data also showed that both chlorate reductase and chlorite dismutase are constitutively present, but most abundant under chlorate‐reducing conditions.
Early engagement with a Lead Maternity Carer: Results from Growing Up in New Zealand
Authors: Bartholomew Karen , Morton Susan M.B. , Atatoa Carr Polly E. , Bandara Dinusha K. , Grant Cameron C.
Published: April 2015

Background

Timely engagement in antenatal care improves maternal and child health outcomes and is an important element of healthcare performance measurement.

Aims

To describe the timeliness of lead maternity carer (LMC) engagement and identify the factors associated with timely engagement.

Materials and Methods

The Growing Up in New Zealand longitudinal study enrolled a diverse sample of pregnant women during 2009 and 2010. Timely engagement was defined as before ten weeks gestation. Independent associations of LMC type; maternal ethnicity, age, parity and education, and household deprivation with timely engagement were described using odds ratios (OR) and 95% confidence intervals (CIs).

Results

Of the 6822 women enrolled, 6661 (98%) stated they had a LMC. Of these 6661, 6012 (90%) reported the time taken to engage a LMC. Eighty‐six to 92% of women engaged a LMC in a timely manner depending upon the estimate of gestational time used. Factors independently associated with delayed engagement were Māori (odds ratio (OR) = 0.59, 95% CI 0.44–0.80), Pacific (0.63, 0.46–0.86) or Asian (0.51, 0.39–0.67) ethnicity; first pregnancy (0.71, 0.58–0.88); age <20 years (0.62, 0.41–0.94); socio‐economic deprivation (0.69, 0.52–0.92); and LMC type being a hospital midwife (0.47, 0.38–0.60), or a combination of care providers (0.60, 0.42–0.90).

Conclusions

Timeliness of LMC engagement in NZ is poorer for non‐European women, younger women, women in their first pregnancy, and women living in more socioeconomically deprived areas. Improving the timeliness of LMC engagement for these groups of women has the potential to reduce inequalities in maternal and child health outcomes.
Indications of lymphatic endothelial differentiation and endothelial progenitor cell activation in the pathology of proliferative diabetic retinopathy
Authors: Loukovaara Sirpa , Gucciardo Erika , Repo Pauliina , Vihinen Helena , Lohi Jouko , Jokitalo Eija , Salven Petri , Lehti Kaisa
Published: April 2015

Purpose

Proliferative diabetic retinopathy (PDR) is characterized by ischaemia‐ and inflammation‐induced neovascularization, but the pathological vascular differentiation in PDR remains poorly characterized. Here, endothelial progenitor and growth properties, as well as potential lymphatic differentiation, were investigated in the neovascular membrane specimens from vitrectomized patients with PDR.

Methods

The expression of pan‐endothelial CD31 (PECAM‐1), ETS‐related gene (ERG), α‐smooth muscle actin (α‐SMA), and stem/progenitor cell marker CD117 (c‐kit) and cell proliferation marker Ki67 was investigated along with the markers of lymphatic endothelial differentiation (vascular endothelial growth factor receptor (VEGFR)‐3; prospero‐related homeobox gene‐1 (Prox‐1), lymphatic vessel endothelial receptor [LYVE)‐1 and podoplanin (PDPN)] by immunohistochemistry. Lymphocyte antigen CD45 and pan‐macrophage marker CD68 were likewise investigated.

Results

All specimens displayed CD31, ERG and α‐SMA immunoreactivity in irregular blood vessels. Unexpectedly, VEGFR3 and Prox‐1 lymphatic marker positive vessels were also detected in several tissues. Prox‐1 was co‐expressed with CD117 in lumen‐lining endothelial cells and adjacent cells, representing putative endothelial stem/progenitor cells and pro‐angiogenic perivascular cells. Immunoreactivity of CD45 and CD68 was detectable in all investigated diabetic neovessel specimens. PDPN immunoreactivity was also detected in irregular lumen‐forming structures, but these cells lacked CD31 and ERG that mark blood and lymphatic endothelium.

Conclusions

Although the inner part of human eye is physiologically devoid of lymphatic vessels, lymphatic differentiation associated with endothelial stem/progenitor cell activation may be involved in the pathogenesis of human PDR. Further studies are warranted to elucidate whether targeting lymphatic factors could be beneficial in the treatment of patients with the sight‐threatening forms of DR.
Transparency in Research involving Animals: The Basel Declaration and new principles for reporting research in BJP manuscripts
Authors: McGrath John C , McLachlan Elspeth M , Zeller Rolf
Published: April 2015

This article discusses the background to the need for change in the reporting of experiments involving animals, including a report of a consensus meeting organised by the Basel Declaration Society and Understanding Animal Research UK that sought to Internationalise guidelines for reporting experiments involving animals. A commentary on the evolution of BJP's attempts to implement the ARRIVE guidelines and details of our new guidance for authors is published separately (McGrath, 2014).

This is one of a series of editorials discussing updates to the BJP Instructions to Authors

Linked Editorials

This Editorial is the first in a series. The other Editorials in this series will be published in the forthcoming issues. To view them, visit: http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1476‐5381
An occupancy‐based quantification of the highly imperiled status of desert fishes of the southwestern United States
Authors: Budy Phaedra , Conner Mary M. , Salant Nira L. , Macfarlane William W.
Published: April 2015

Desert fishes are some of the most imperiled vertebrates worldwide due to their low economic worth and because they compete with humans for water. An ecological complex of fishes, 2 suckers (Catostomus latipinnis, Catostomus discobolus) and a chub (Gila robusta) (collectively managed as the so‐called three species) are endemic to the U.S. Colorado River Basin, are affected by multiple stressors, and have allegedly declined dramatically. We built a series of occupancy models to determine relationships between trends in occupancy, local extinction, and local colonization rates, identify potential limiting factors, and evaluate the suitability of managing the 3 species collectively. For a historical period (1889–2011), top performing models (AICc) included a positive time trend in local extinction probability and a negative trend in local colonization probability. As flood frequency decreased post‐development local extinction probability increased. By the end of the time series, 47% (95% CI 34‐61) and 15% (95% CI 6‐33) of sites remained occupied by the suckers and the chub, respectively, and models with the 2 species of sucker as one group and the chub as the other performed best. For a contemporary period (2001−2011), top performing (based on AICc) models included peak annual discharge. As peak discharge increased, local extinction probability decreased and local colonization probability increased. For the contemporary period, results of models that split all 3 species into separate groups were similar to results of models that combined the 2 suckers but not the chub. Collectively, these results confirmed that declines in these fishes were strongly associated with water development and that relative to their historic distribution all 3 species have declined dramatically. Further, the chub was distinct in that it declined the most dramatically and therefore may need to be managed separately. Our modeling approach may be useful in other situations in which targeted data are sparse and conservation status and best management approach for multiple species are uncertain.
Are the data on delayed school entry compelling enough to change policy … or even pediatrician recommendations?
Authors: Fastenau Philip S
Published: April 2015

This commentary is on the original article by Jaekel et al. on pages 652–659 of this issue.
Impairments in musical abilities reflected in the auditory brainstem: evidence from congenital amusia
Authors: Lehmann Alexandre , Skoe Erika , Moreau Patricia , Peretz Isabelle , Kraus Nina
Published: April 2015

Congenital amusia is a neurogenetic condition, characterized by a deficit in music perception and production, not explained by hearing loss, brain damage or lack of exposure to music. Despite inferior musical performance, amusics exhibit normal auditory cortical responses, with abnormal neural correlates suggested to lie beyond auditory cortices. Here we show, using auditory brainstem responses to complex sounds in humans, that fine‐grained automatic processing of sounds is impoverished in amusia. Compared with matched non‐musician controls, spectral amplitude was decreased in amusics for higher harmonic components of the auditory brainstem response. We also found a delayed response to the early transient aspects of the auditory stimulus in amusics. Neural measures of spectral amplitude and response timing correlated with participants' behavioral assessments of music processing. We demonstrate, for the first time, that amusia affects how complex acoustic signals are processed in the auditory brainstem. This neural signature of amusia mirrors what is observed in musicians, such that the aspects of the auditory brainstem responses that are enhanced in musicians are degraded in amusics. By showing that gradients of music abilities are reflected in the auditory brainstem, our findings have implications not only for current models of amusia but also for auditory functioning in general.
Life‐history characteristics of ide Leuciscus idus in the Eastern Baltic Sea
Authors: Rohtla M. , Svirgsden R. , Taal I. , Saks L. , Eschbaum R. , Vetemaa M.
Published: April 2015

Otolith Sr:Ca and Ba:Ca profiles were used in parallel with age data to investigate the life‐history characteristics of ide, Leuciscus idus (L.) (n = 111), in the Väinameri Sea, West Estonia. Sr:Ca profiles were more variable and useful than Ba:Ca profiles. Flexible life‐history patterns were observed within and among the three study sites. Most of the individuals (72%) hatched in semi‐enclosed bays that are fresh water during spring spawning but are often flooded with brackish water during other seasons. The importance of lotic spawning varied among sites and was the highest (88%) in Matsalu Bay, moderate in Saunja Bay (33%) and lowest (0%) in Käina Bay. Young of the year emigrated from natal sites and entered the sea within the first summer; 95% did so during the first month post‐hatch. Juvenile ide undertook non‐spawning, freshwater migrations in the following spring; however, the reasons behind this phenomenon remain unknown. As the importance of lotic spawning has significantly decreased and multiple historically important ide spawning rivers lack anadromous runs altogether, it is suggested that actions should be taken to aid the recovery of those imperilled spawning stocks.
Substratum‐dependent responses of ciliate assemblages to temperature: a natural experiment in Icelandic streams
Authors: Plebani Marco , Fussmann Katarina E. , Hansen Dennis M. , O'Gorman Eoin J. , Stewart Rebecca I. A. , Woodward Guy , Petchey Owen L.
Published: April 2015

Ciliate assemblages play a significant role in the microbial food web. The effects of environmental temperature on assemblage composition may be influenced by abiotic factors such as seasonality and disturbance, but the effects of temperature on ciliate assemblages found on different substrata have not been explored. Sandy bottoms and submerged rocks harbour dissimilar ciliate assemblages, and it might be expected that their ciliate assemblages will respond differently to temperature.

We studied how alpha diversity, beta diversity and total biomass of ciliate protist assemblages found on sandy bottoms and submerged rocks differed in 13 geothermally heated streams in Iceland whose mean temperatures range from 5 to 20 °C. We recorded number of operational taxonomic units (OTUs) and measured the size of cells in ciliate assemblages from both substrata.

Effects of temperature on natural ciliate assemblages were substratum dependent. On rock surfaces, both total ciliate biomass and alpha diversity declined with increasing temperature, and beta diversity increased with increasing temperature difference due to OTU nestedness (assemblages from warm streams being composed chiefly of subsets of the OTUs found in colder streams). In sandy substrata, however, ciliate assemblage composition was independent of temperature.

Substratum‐specific responses may be due to differences in mechanical disturbance, nutrient availability or exposure to invertebrate grazers. Rock‐surface assemblages may be more exposed to the flow and retain less nutrient than those of sandy substratum; thus, they may be more strongly resource limited and more responsive to direct effects of temperature on metabolism. Alternatively, rock‐surface assemblages may be more exposed to grazing by invertebrates, which intensifies with temperature.

Our study highlights the need to account for environmental context such as substratum type to fully understand the effect of temperature on microbial assemblages in streams. Future increases in global temperatures may affect fresh waters differently depending on their prevalent substratum. Those dominated by hard substrata may have their ciliate assemblages, and thus, food‐web structures and ecosystem functioning more strongly affected by warming relative to systems dominated by soft substrata.
The severity of wheat diseases increases when plants and pathogens are acclimatized to elevated carbon dioxide
Authors: Váry Zsolt , Mullins Ewen , McElwain Jennifer C. , Doohan Fiona M.
Published: April 2015

Wheat diseases present a constant and evolving threat to food security. We have little understanding as to how increased atmospheric carbon dioxide levels will affect wheat diseases and thus the security of grain supply. Atmospheric CO2 exceeded the 400 ppmv benchmark in 2013 and is predicted to double or even treble by the end of the century. This study investigated the impact of both pathogen and wheat acclimation to elevated CO2 on the development of Fusarium head blight (FHB) and Septoria tritici blotch (STB) disease of wheat. Here, plants and pathogens were cultivated under either 390 or 780 ppmv CO2 for a period (two wheat generations, multiple pathogen subcultures) prior to standard disease trials. Acclimation of pathogens and the wheat cultivar Remus to elevated CO2 increased the severity of both STB and FHB diseases, relative to ambient conditions. The effect of CO2 on disease development was greater for FHB than for STB. The highest FHB disease levels and associated yield losses were recorded for elevated CO2‐acclimated pathogen on elevated CO2‐acclimated wheat. When similar FHB experiments were conducted using the disease‐resistant cultivar CM82036, pathogen acclimation significantly enhanced disease levels and yield loss under elevated CO2 conditions, thereby indicating a reduction in the effectiveness of the defence pathways innate to this wheat cultivar. We conclude that acclimation to elevated CO2 over the coming decades will have a significant influence on the outcome of plant–pathogen interactions and the durability of disease resistance.
Salicylic acid deposition from wash‐off products: comparison of in vivo and porcine deposition models
Authors: Davies M. A.
Published: April 2015

Synopsis

Objective

Salicylic acid (SA) is a widely used active in anti‐acne face wash products. Only about 1–2% of the total dose is actually deposited on skin during washing, and more efficient deposition systems are sought. The objective of this work was to develop an improved method, including data analysis, to measure deposition of SA from wash‐off formulae.

Methods

Full fluorescence excitation–emission matrices (EEMs) were acquired for non‐invasive measurement of deposition of SA from wash‐off products. Multivariate data analysis methods – parallel factor analysis and N‐way partial least‐squares regression – were used to develop and compare deposition models on human volunteers and porcine skin.

Results

Although both models are useful, there are differences between them. First, the range of linear response to dosages of SA was 60 μg cm−2 in vivo compared to 25 μg cm−2 on porcine skin. Second, the actual shape of the SA band was different between substrates.

Conclusion

The methods employed in this work highlight the utility of the use of EEMs, in conjunction with multivariate analysis tools such as parallel factor analysis and multiway partial least‐squares calibration, in determining sources of spectral variability in skin and quantification of exogenous species deposited on skin. The human model exhibited the widest range of linearity, but porcine model is still useful up to deposition levels of 25 μg cm−2 or used with nonlinear calibration models.
Characterisation of jellyfish protein films with added transglutaminase and wasabi extract
Authors: Lee Ji‐Hyun , Lee Ji‐Hyeon , Yang Hyun‐Ju , Won Misun , Song Kyung Bin
Published: April 2015

The physical, optical, antimicrobial and antioxidant properties of jellyfish protein (JFP) films with added transglutaminase (TGase) and wasabi extract (WE) were studied. Among the plasticisers, 30% sorbitol was the most desirable. The optimal physical properties of the JFP films were obtained when 15 U transglutaminase g−1 JFP was added. The incorporation of WE affected the physical properties of the JFP films. The tensile strength (21.68–35.25 MPa), elongation at break (10.85–13.25%) and Young's modulus (920.18–1278.9 MPa) of the films increased as WE concentration increased from 0.5% to 1.5%. The thermal gravimetric analysis results revealed that the thermal stability of the JFP films increased with increasing concentrations of WE. The inhibition zones against Escherichia coli O157:H7 and Listeria monocytogenes and antioxidant activity also increased as the concentration of WE increased. Thus, antimicrobial and antioxidant JFP films could be prepared by the addition of WE.
Nosocomial Infections after Aneurysmal Subarachnoid Hemorrhage: Time Course and Causative Pathogens
Authors: Laban Kamil G. , Rinkel Gabriel J. E. , Vergouwen Mervyn D. I.
Published: April 2015

Background

Nosocomial infections after aneurysmal subarachnoid hemorrhage (aSAH) are associated with prolonged length of stay and poor functional outcome. It remains unclear if infections result in prolonged length of stay or, vice versa, if prolonged length of stay results in more infections. Before strategies can be designed to reduce infections after aneurysmal subarachnoid hemorrhage, more data are needed on time course and causative pathogens of infections.

Aim

To investigate the time course of infection onset and bacterial microorganisms that cause nosocomial infections after aSAH.

Methods

In consecutive patients with aneurysmal subarachnoid hemorrhage admitted to the University Medical Center Utrecht between 2009 and 2011, we analyzed the proportion of patients with infections, day of infection onset, and culture results.

Results

Of the 291 included patients, 107 (37%) patients developed 115 nosocomial infections. Fifty-six patients (19%) developed an infection within the first week. Median day of infection onset was for pneumonia ( n = 49; 17%) day 4 (interquartile range 3–9), respiratory tract infection ( n = 16; 6%) day 4 (interquartile range 1–7), urinary tract infection ( n = 27; 9%) day 11 (interquartile range 7–14), and meningitis/ventriculitis ( n = 10; 3%) day 19 (interquartile range 9–33). Cultures of infections mostly yielded Staphylococcus aureus (20%), Haemophilus influenzae (15%), and Escherichia coli (14%),

Conclusion

Nosocomial infections after subarachnoid hemorrhage are common and mostly occur in the first week after ictus. Future studies should investigate if general hygienic measures, infection awareness, minimizing the duration of mechanical ventilation and use of catheters/drains, or prophylactic antibiotics reduce infections and improve functional outcome.
Influence of complement on neutrophil extracellular trap release induced by bacteria
Authors: Palmer L. J. , Damgaard C. , Holmstrup P. , Nielsen C. H.
Published: April 2015

Background and Objectives

Neutrophil extracellular trap (NET) release has generally been studied in the absence of serum, or at low concentrations of untreated or heat‐inactivated serum. The influence of serum complement on NET release therefore remains unclear. We examined the DNA release induced by Staphylococcus aureus and three oral bacteria: Actinomyces viscosus, Aggregatibacter actinomycetemcomitans and Fusobacterium nucleatum subsp. vincettii.

Material and Methods

Bacteria‐stimulated NET release from the neutrophils of healthy donors was measured fluorometrically. Various complement containing and complement blocking conditions were used, including heat inactivation of the serum and antibody blockade of complement receptors 1 (CR1, CD35) and 3 (CR3, CD11b/CD18).

Results

While the presence of serum markedly enhanced NET release induced by S. aureus, A. actinomycetemcomitans, and to a lesser extent by A. viscosus, there was no enhancement of NET release induced by F. nucleatum. The serum‐mediated enhancement of NET release by A. actinomycetemcomitans was neutralized by heat inactivation of serum complement, while this was not the case for S. aureus. Blockade of CR1, significantly reduced NET release induced by S. aureus, A. actinomycetemcomitans and A. viscosus, while blockade of CR3, had no effect. However, opsonization of S. aureus with antibodies may also have contributed to the enhancing effect of serum, independently of complement, in that purified IgG promoted NET release.

Conclusions

In conclusion, complement opsonization promotes NET release induced by a variety of bacteria, including A. actinomycetemcomitans, and CR1 plays a dominant role in the process. Complement consumption or deficiency may compromise NETosis induced by some bacterial species, including A. actinomycetemcomitans. Within biofilms, the complement‐inactivating abilities of some bacteria may protect other species against NETosis, while these are more vulnerable when adopting a planktonic lifestyle.
Chronic sleep restriction induces long‐lasting changes in adenosine and noradrenaline receptor density in the rat brain
Authors: Kim Youngsoo , Elmenhorst David , Weisshaupt Angela , Wedekind Franziska , Kroll Tina , Mccarley Robert W. , Strecker Robert E. , Bauer Andreas
Published: April 2015

Although chronic sleep restriction frequently produces long‐lasting behavioural and physiological impairments in humans, the underlying neural mechanisms are unknown. Here we used a rat model of chronic sleep restriction to investigate the role of brain adenosine and noradrenaline systems, known to regulate sleep and wakefulness, respectively. The density of adenosine A1 and A2a receptors and β‐adrenergic receptors before, during and following 5 days of sleep restriction was assessed with autoradiography. Rats (n = 48) were sleep‐deprived for 18 h day−1 for 5 consecutive days (SR1–SR5), followed by 3 unrestricted recovery sleep days (R1–R3). Brains were collected at the beginning of the light period, which was immediately after the end of sleep deprivation on sleep restriction days. Chronic sleep restriction increased adenosine A1 receptor density significantly in nine of the 13 brain areas analysed with elevations also observed on R3 (+18 to +32%). In contrast, chronic sleep restriction reduced adenosine A2a receptor density significantly in one of the three brain areas analysed (olfactory tubercle which declined 26–31% from SR1 to R1). A decrease in β‐adrenergic receptors density was seen in substantia innominata and ventral pallidum which remained reduced on R3, but no changes were found in the anterior cingulate cortex. These data suggest that chronic sleep restriction can induce long‐term changes in the brain adenosine and noradrenaline receptors, which may underlie the long‐lasting neurocognitive impairments observed in chronic sleep restriction.
Rhomboid proteases in invasion and replication of Apicomplexa
Authors: Stewart Rebecca J. , Tonkin Christopher J.
Published: April 2015

In this issue of Molecular Microbiology, Rugarabamu and colleagues investigate the role of rhomboid proteases responsible for adhesin shedding during invasion of the apicomplexan parasite Toxoplasma gondii. This study, together with several other recent publications, raises new questions about the function of these rhomboids in Toxoplasma, while also strongly arguing against other recently proposed roles for these proteases.
Carbon catabolite repression by seryl phosphorylated HPr is essential to Streptococcus pneumoniae in carbohydrate‐rich environments
Authors: Fleming Eleanor , Lazinski David W. , Camilli Andrew
Published: April 2015

Carbon catabolite repression (CCR) is a regulatory phenomenon implemented by bacteria to hierarchically organize carbohydrate utilization in order to achieve maximal growth. CCR is likely of great importance to Streptococcus pneumoniae because the human host sites inhabited by this pathogen represent complex carbohydrate environments. In this species, inactivation of the prototypical Gram‐positive CCR master regulator, ccpA, attenuates virulence in mice but does not relieve CCR of most metabolic enzymes, suggesting CcpA‐independent CCR mechanisms predominate. Here we show the activities of three transcriptional regulators constitute the majority of transcriptional CCR of galactose metabolism operons. We determined seryl‐phosphorylated histidine phosphocarrier protein (HPr‐Ser∼P)‐mediated regulation is a major CCR mechanism and an essential activity in the pneumococcus, as an HPr point mutation abolishing HPrK/P‐dependent phosphorylation was not tolerated nor was deletion of hprk/p. The HPr‐Ser∼P phosphomimetic mutant HPr S46D had reduced phosphotransferase system transport rates and limited induction of CCR‐repressed genes. These results support a model of pneumococcal CCR in which HPr‐Ser∼P directly affects the activity of CcpA while indirectly affecting the activity of pathway‐specific transactional regulators. This report describes the first CcpA‐independent CCR mechanism identified in the pneumococcus and the first example of lethality from loss of HPr‐Ser∼P‐mediated CCR in any species.
The Psp system of Mycobacterium tuberculosis integrates envelope stress‐sensing and envelope‐preserving functions
Authors: Datta Pratik , Ravi Janani , Guerrini Valentina , Chauhan Rinki , Neiditch Matthew B. , Shell Scarlet S. , Fortune Sarah M. , Hancioglu Baris , Igoshin Oleg A. , Gennaro Maria Laura
Published: April 2015

The bacterial envelope integrates essential stress‐sensing and adaptive functions; thus, envelope‐preserving functions are important for survival. In Gram‐negative bacteria, envelope integrity during stress is maintained by the multi‐gene Psp response. Mycobacterium tuberculosis was thought to lack the Psp system since it encodes only pspA and no other psp ortholog. Intriguingly, pspA maps downstream from clgR, which encodes a transcription factor regulated by the MprAB‐σE envelope‐stress‐signaling system. clgR inactivation lowered ATP concentration during stress and protonophore treatment‐induced clgR‐pspA expression, suggesting that these genes express Psp‐like functions. We identified a four‐gene set – clgR, pspA (rv2744c), rv2743c, rv2742c – that is regulated by clgR and in turn regulates ClgR activity. Regulatory and protein–protein interactions within the set and a requirement of the four genes for functions associated with envelope integrity and surface‐stress tolerance indicate that a Psp‐like system has evolved in mycobacteria. Among Actinobacteria, the four‐gene module occurred only in tuberculous mycobacteria and was required for intramacrophage growth, suggesting links between its function and mycobacterial virulence. Additionally, the four‐gene module was required for MprAB‐σE stress‐signaling activity. The positive feedback between envelope‐stress‐sensing and envelope‐preserving functions allows sustained responses to multiple, envelope‐perturbing signals during chronic infection, making the system uniquely suited to tuberculosis pathogenesis.