bluuebunny/crossref_metadata_2025 huggingface dataset:
Channelplate Illumination Correction for Secondary Ion Mass Spectroscopy Images by Solving Apparatus Elasticity Equations
Authors: Stubbings Thomas C. , Pollak Christoph , Hutter Herbert
Published: April 2013

Abstract: The SIMS channelplate used for recording image signals is characterized by local sensitivity differences caused by increasing aging of the central channelplate regions, which are subject to much more intense ion bombardment than the outer regions. These sensitivity differences lead to inhomogenous illumination of the sample, i.e., to images with disturbed intensity distributions. We present here a novel method to correct these illumination discrepancies by using the intensity changes due to sample position shifts to find the interfering background function that can be used to correct the original image. The proposed method has low presuppositions about the regarded images, and is stable with regard to noise and easy to apply. It is suitable not only for correction of channelplate local sensitivity differences but for all sorts of microscopic images that suffer from illumination inhomogeneity.
CT-based post-implant dosimetry for I-125 prostate brachytherapy: a multi-centre audit in the UK and Ireland
Authors: Hayman O. , Palmer A.
Published: April 2013

Background and purpose

To assess the reliability of post-implant CT (PICT) dosimetry for I-125 prostate seed brachytherapy by investigating the variation between centres in performing PICT through a multi-centre audit.

Materials and methods

Computerised tomography data sets from four I-125 prostate brachytherapy patients were circulated to nine participating centres. Centres followed local protocol for PICT outlining and seed identification, dosimetry for D90, V100 and V150 for the prostate was reported. Outlines were compared to determine the variation in: quality parameters (D90, V100 and V150), dose-volume histograms and approach to PICT dosimetry between the centres.

Results

There was significant variation in the prostate outlines drawn by the nine centres; for a prostate with mean volume 43 cm3, the range was 39–57 cm3 which led to variations of D90 of 119–154 Gy (mean 140 Gy) and V100 of 80–93% (mean of 88%). Using automatic seedfinder software reduced discrepancies between centres identifying seeds; overall consistency in seed location was good.

Conclusions

There was a significant uncertainty in the outlining of the prostate volume for PICT dosimetry with an uncertainty value of around ± 20 Gy on D90. PICT is a valuable technique but its accuracy and consistency limitations must be appreciated.
SETI, Evolution and Human History Merged into a Mathematical Model
Authors: Maccone Claudio
Published: April 2013

In this paper we propose a new mathematical model capable of merging Darwinian Evolution, Human History and SETI into a single mathematical scheme:

(1) Darwinian Evolution over the last 3.5 billion years is defined as one particular realization of a certain stochastic process called Geometric Brownian Motion (GBM). This GBM yields the fluctuations in time of the number of species living on Earth. Its mean value curve is an increasing exponential curve, i.e. the exponential growth of Evolution.

(2) In 2008 this author provided the statistical generalization of the Drake equation yielding the number N of communicating ET civilizations in the Galaxy. N was shown to follow the lognormal probability distribution.

(3) We call “b-lognormals” those lognormals starting at any positive time b (“birth”) larger than zero. Then the exponential growth curve becomes the geometric locus of the peaks of a one-parameter family of b-lognormals: this is our way to re-define Cladistics.

(4) b-lognormals may be also be interpreted as the lifespan of any living being (a cell, or an animal, a plant, a human, or even the historic lifetime of any civilization). Applying this new mathematical apparatus to Human History, leads to the discovery of the exponential progress between Ancient Greece and the current USA as the envelope of all b-lognormals of Western Civilizations over a period of 2500 years.

(5) We then invoke Shannon's Information Theory. The b-lognormals' entropy turns out to be the index of “development level” reached by each historic civilization. We thus get a numerical estimate of the entropy difference between any two civilizations, like the Aztec-Spaniard difference in 1519.

(6) In conclusion, we have derived a mathematical scheme capable of estimating how much more advanced than Humans an Alien Civilization will be when the SETI scientists will detect the first hints about ETs.
The treatment of depression and simple phobia through an interpreter in the North East of England: a case study
Authors: Mofrad Layla , Webster Lisa A. D.
Published: April 2013

A 35-year-old Middle Eastern woman, experiencing moderate depression compounded by animal phobia was referred to an Improving Access to Psychological Therapies (IAPT) service. Shared understandings were gradually developed using written functional analyses translated in session. Activity scheduling was integrated with graded exposure to increase access to positive reinforcement. Questionnaires and subjective data indicated a reduction in phobic avoidance and functioning increased. Despite the complexity of working as a triad, a positive therapeutic relationship was achieved with increased mutual cultural understanding. Indirect communication led to difficulties maintaining guided discovery and focus. There is limited evidence to support CBT when delivered through an interpreter. IAPT recommendations suggest staff reflect the community; the North East has one of the lowest foreign-born populations in the UK indicating that IAPT services may be ill prepared to work with ethnic minorities. Learning points for the therapist were: maintain simplicity, take time to formulate incorporation of cultural difference, and use transcultural interventions. The interpreter brought advantages; providing means of communication and understanding of cultural differences. Disadvantages were the potential for bias or lost information, increased time and complexity of delivering therapy. This case indicates a deficit in high intensity training and lack of literature to support therapists.
The Theory of Finance
Authors: King George
Published: April 2013

1. Capital is wealth appropriated to reproductive employment, and, in the words of the late J. S. Mill, “the gross profit on capital may be distinguished into three parts, which are respectively the remuneration for risk, for trouble, and for the capital itself, and may be called insurance, wages of superintendence, and interest.”

It is with the last of these, Interest, that we have at present to do.

2. In civilized communities wealth is measured in money, and therefore in our investigations it is of money that we shall speak; but evidently it is immaterial, in laying down general propositions, whether the standard units are of one actual value or of another, so long as we remain consistent with ourselves, and use the same standard throughout. We shall therefore, as the most convenient course to suit all currencies, treat of units of value, without specifying to what currency these units belong.
The Present Position of the Silver Question
Authors: Nicholson J. Shield
Published: April 2013

The Silver Question, as it is called, like the Land Question and the Labour Question, is really a group of several complex and difficult problems, and it would be absurd to attempt to give in an address of a popular kind an adequate account even of the main issues in the controversy. I have used the term popular with some trepidation, for after many attempts I doubt if it is possible—at any rate for me—to give even the semblance of popularity to the intricacies of the currency. In the whole subject there is, I believe, only one recognised joke, namely, that any considerable attention given to it is sure to end in lunacy, and a good many people imagine that this is not a joke at all, but a very solemn warning. Again, there is no scope for quoting little bits of poetry which are often so effective in popular discourses. The only lines I ever felt inclined to quote are those of the well-worn couplet—He that complies against his will Is of his own opinion still.

There is no one so stubborn in opinion as the budding lunatic of currency. It is obvious that a problem which in some parts can be most clearly explained by the use of algebraic symbols will not readily lend itself to eloquence, and the statistics of foreign countries are not likely to arouse enthusiasm in the insular mind. In fact, a careful survey of the different devices for making an address popular leads to the conclusion that in currency only one is available. Being the only one, it has naturally been very widely adopted.
The Evolution of Premium Rates, a chapter in the History of Life Insurance
Authors: Sorley James
Published: April 2013

Gentlemen,—For the honour which you have done me by electing me Honorary President of our Society for the new Session which we inaugurate to-night, I return you my most sincere and cordial thanks. All the more do I appreciate the compliment in that, during the greater portion of my business life, I have been more or less intimately connected with the Societ, and have learned much from the many important papers which have been read at its meetings, and from the discussions which have taken place upon them.

It has occurred to me that a fitting subject for this evening would be an historical sketch of the rates of premiums charged for Life Assurances, and a consideration of the grounds upon which such premiums have from time to time been adjusted, together with an examination of tendencies at work which may yet lead to further modifications in our methods or our results.

Life Assurance appears to have been practised to a limited extent in the seventeenth century, and earlier part of the eighteenth, as a simple branch of underwriting. Those whose business it was to insure ships against loss at sea, came in due course to be asked to insure also masters of vessels—not against death, but against the risk of their being taken by the Moorish or Turkish pirates, etc., in order that, in such an event, a fund might be available to pay their ransom.
Forms of Life Office Books
Authors: Nicol William Smith
Published: April 2013

Eleven years have elapsed since anything on the subject of Office Books was before you. Mr. M'Lauchlan's paper, which was read in April 1886, has long since become a classic, and has been of incalculable service as a text-book for the Faculty and Institute Examinations. All-embracing as it is, however, its great scope rendered it impossible to treat, within the limits of one paper, all aspects of Life Office Book-keeping and its kindred topic Life Office Records, so fully as may be done by taking the subjects in sections. I shall be glad, therefore, if my contribution be looked upon as a practical tribute of my sense of indebtedness to Mr. M'Lauchlan's paper, and as an attempt to expand a small portion of it. I hope my example may be the means of inducing others to do likewise.

Mr. R. P. Hardy recently said (J.I.A., vol. xxxii, p. 443) that to frame a scheme of books and forms that were at once analytical and interlocking, presenting at the same time the maximum of convenience for the needs of to-day, encumbered by the mere minimum of what was indispensable for the emerging wants of the future, was in itself a liberal and highly stimulating education.
Weibliche Libido – eine Frage der Hormone?
Authors: Leeners Brigitte
Published: April 2013

Die Lust auf Sexualität bei Frauen entsteht aus einem komplexen Netzwerk regulierender psycho-sexueller und körperlicher Faktoren. Während Östrogen eine entscheidende Rolle bei den körperlichen Voraussetzungen für die weibliche Libido spielt, ist die Bedeutung in Bezug auf spezifische sexuelle Parameter unklar. Ein Absinken des Testosteronspiegels ist nur in Einzelfällen die Ursache eines Libidoverlustes bei Frauen, d. h. eine Testosteronsubstitution als Therapieversuch bei reduzierter Libido sollte ausgewählten Patientinnen vorbehalten bleiben. Bei der Auswahl einer oralen Kontrazeption sollten Partialwirkungen von Gestagenen in Bezug auf die Libido berücksichtigt werden. Obwohl die zerebralen Mechanismen bei der Regulation der weiblichen Libido derzeit noch unzureichend geklärt sind, deuten aktuelle Untersuchungsergebnisse auf einen entscheidenden Einfluss von Prolaktin. Insgesamt stellen Hormone jedoch nur einen von mehreren Faktoren, welche die weibliche Lust auf Sexualität beeinflussen, dar.
Der Zahn im Auge – Die erste in der Schweiz eingebrachte Osteo-Odonto-Keratoprothese
Authors: Berg Britt-Isabelle , Hilber Nicole , Hille Konrad , Kunz Christoph , Goldblum David
Published: April 2013

Wir berichten über die erste in der Schweiz eingesetzte Osteo-Odonto-Keratoprothese (OOKP). Die Operation wird bei bilateralem kornealem Visusverlust durchgeführt. Beim zweizeitigen Eingriff wird ein Zahn mit umgebenden Knochen entnommen, und ein optischer Zylinder eingesetzt. Dieser Zahn-Knochen-Plexiglaskomplex wird für drei Monate infraorbital in eine Weichteiltasche implantiert. Danach wird der Zahnknochenplexiglaskomplex entnommen und die darunterliegende Hornhaut wird für die Aufnahme der Optik trepaniert, Linse, Iris und der vordere Glaskörper werden entfernt und die Prothese auf den Bulbus fixiert. Unser Patient sieht aktuell bestkorrigiert 0,7.
Fit für die ambulante Pflege?
Authors: Koch Lee F. , Lehrer Viktoria , Pölitz Christiane , Reichhardt Anna , Selinger Yvonne
Published: April 2013

In einem Forschungsprojekt wurden bundesweit Praxisanleiter ambulanter Pflegedienste befragt, inwieweit Berufseinsteiger durch ihre Ausbildung auf die Anforderungen im Berufsalltag vorbereitet sind.
Den Theorie-Praxis-Transfer unterstützen
Authors: Biehl Maria
Published: April 2013

Die Berufsfachschule Altenpflege Langwedel – ein Schulstandort des Bildungs- und Privatschulträgers ibs Institut für Berufs- und Sozialpädagogik e. V. – erarbeitete gemeinsam mit Praxisanleiterinnen der kooperierenden Einrichtungen einen Rahmenplan für die praktische Ausbildung.
The Making of Institutions of Information Governance: The Case of the Internet Governance Forum
Authors: Epstein Dmitry
Published: April 2013

Histories of information systems are inseparable from the histories of their governance. In the case of the Internet, governance structures informally developed during its early design were substantially different from the typical mechanisms resulting from public policy decision-making. Traditionally, global information systems, such as telecommunication systems, were governed through state-centric mechanisms that would set treaty-based framework for non-state actors to operate within. Legitimate participation in these traditional governance structures was the prerogative of states that possessed sole decision-making authority. In the case of the Internet, non-state-actor-driven governance frameworks were developed outside of those traditional mechanisms. They relied on a different conception of legitimacy and authority. This paper discusses how the state and non-state actors were forced to cooperate around the creation of institutions that could accommodate the variety of views on authority, legitimacy, and decision-making processes in Internet governance. It tracks the creation of the Internet Governance Forum as a case where notions of legitimacy and authority were redefined for policy deliberations of complex information systems. The paper concludes with whether those changes lead to the emergence of new institutions that contribute to the sustainability of the network by enabling coexistence of competing political interests and values; and what this could mean for the future of the network.
Ferromagnetism in cluster free, transition metal doped high κ dilute magnetic oxides: Films and nanocrystals
Authors: Wu C. N. , Wu T. S. , Huang S. Y. , Lee W. C. , Chang Y. H. , Soo Y. L. , Hong M. , Kwo J.
Published: April 2013

The structural and magnetic properties of high κ dilute magnetic oxides (DMOs) have been studied in two types of samples: thin films and nanocrystals, including Co doped HfO2 films, Co doped Y2O3 films, Co doped Y2O3 nanocrystals, and Mn doped Y2O3 nanocrystals. The characterizations were conducted by extended x-ray absorption fine structure, x-ray absorption near edge structure, and superconducting quantum interference device vibrating sample magnetometer. Oxygen vacancies are shown to play a crucial role in ferromagnetic ordering, as defect centers in the bound magnetic polaron model to account for DMOs with medium band gap and low carrier concentration. The observation of room temperature ferromagnetism in tri-valence oxide of Y2O3 as well as in tetra-valence oxide of HfO2 suggests a generic feature of transition metal doped high κ oxides as good candidates for DMO. The ability to modulate the magnetic behavior of DMO via oxygen vacancy concentration by means of post anneals can be exploited for potential applications in spintronics.
Packings of Os layers for the development of L10 order of FePt in nanoscale [Os-FePt]n multilayer systems
Authors: Su T. T. , Hsiao Ching-Hung , Lo Shen-Chuan , Ouyang Wen , Li Tzu-Yuan , Ouyang H. , Yao Y. D.
Published: April 2013

The element osmium (Os), with high melting and boiling points, plays a crucial role in the development of the L10 order for FePt in [Os(5 nm)/FePt(25 nm)]4 and [Os(1 nm)/FePt(5 nm)]20 systems. The large mismatches of lattice constants between Os and FePt, with specific epitaxial relations, induce a great strain in the [Os(5 nm) /FePt(25 nm)]4 system with fixed total thicknesses for the FePt and Os layers. Due to this large strain effect, the L10 order in a FePt structure can be enhanced through an application of stressing along the c axis for the face-centered cubic structure, which results in a higher coercivity. However, a smaller degree of average strain was observed in the 5 nm-thickness FePt system due to the existence of pinholes.
Surface hopping modeling of two-dimensional spectra
Authors: Tempelaar Roel , van der Vegte Cornelis P. , Knoester Jasper , Jansen Thomas L. C.
Published: April 2013

Recently, two-dimensional (2D) electronic spectroscopy has become an important tool to unravel the excited state properties of complex molecular assemblies, such as biological light harvesting systems. In this work, we propose a method for simulating 2D electronic spectra based on a surface hopping approach. This approach self-consistently describes the interaction between photoactive chromophores and the environment, which allows us to reproduce a spectrally observable dynamic Stokes shift. Through an application to a dimer, the method is shown to also account for correct thermal equilibration of quantum populations, something that is of great importance for processes in the electronic domain. The resulting 2D spectra are found to nicely agree with hierarchy of equations of motion calculations. Contrary to the latter, our method is unrestricted in describing the interaction between the chromophores and the environment, and we expect it to be applicable to a wide variety of molecular systems.
Spectral properties of a confined nonlinear quantum oscillator in one and three dimensions
Authors: Schulze-Halberg Axel , Gordon Christopher R.
Published: April 2013

We analyze the spectral behaviour of a nonlinear quantum oscillator model under confinement. The underlying potential is given by a harmonic oscillator interaction plus a nonlinear term that can be weakened or strengthened through a parameter. Numerical eigenvalues of the model in one and three dimensions are presented. The asymptotic behaviour of the eigenvalues for confinement relaxation and for vanishing nonlinear term in the potential is investigated. Our findings are compared with existing results.
Relation between occupation in the first coordination shells and Widom line in core-softened potentials
Authors: Salcedo Evy , Barraz Ney M. , Barbosa Marcia C.
Published: April 2013

Three core-softened families of potentials are checked for the presence of density and diffusion anomalies. These potentials exhibit a repulsive core with a softening region and at larger distances an attractive well. We found that the region in the pressure-temperature phase diagram in which the anomalies are present increases if the slope between the core-softened scale and the attractive part of the potential decreases. The anomalous region also increases if the range of the core-softened or of the attractive part of the potential decreases. We also show that the presence of the density anomaly is consistent with the non-monotonic changes of the radial distribution function at each one of the two scales when temperature and density are varied. Then, using this anomalous behavior of the structure we show that the pressure and the temperature at which the radial distribution function of one of the two length scales equals the radial distribution function of the other length scales identify the Widom line.
Propagation of hydrodynamic interactions between particles in a compressible fluid
Authors: Tatsumi Rei , Yamamoto Ryoichi
Published: April 2013

Hydrodynamic interactions are transmitted by viscous diffusion and sound propagation, and the temporal evolution of hydrodynamic interactions by both mechanisms is studied using direct numerical simulation in this paper. The hydrodynamic interactions for a system of two particles in a fluid are estimated using the velocity correlation of the particles. In an incompressible fluid, hydrodynamic interactions propagate instantaneously at the infinite speed of sound followed by a temporal evolution due to viscous diffusion. Conversely, sound propagates in a compressible fluid at a finite speed, which affects the temporal evolution of the hydrodynamic interactions through an order-of-magnitude relationship between the time scales of viscous diffusion and sound propagation. The hydrodynamic interactions are characterized by introducing the ratio of these time scales as an interactive compressibility factor.
Single cell rheometry with a microfluidic constriction: Quantitative control of friction and fluid leaks between cell and channel walls
Authors: Preira Pascal , Valignat Marie-Pierre , Bico José , Théodoly Olivier
Published: April 2013

We report how cell rheology measurements can be performed by monitoring the deformation of a cell in a microfluidic constriction, provided that friction and fluid leaks effects between the cell and the walls of the microchannels are correctly taken into account. Indeed, the mismatch between the rounded shapes of cells and the angular cross-section of standard microfluidic channels hampers efficient obstruction of the channel by an incoming cell. Moreover, friction forces between a cell and channels walls have never been characterized. Both effects impede a quantitative determination of forces experienced by cells in a constriction. Our study is based on a new microfluidic device composed of two successive constrictions, combined with optical interference microscopy measurements to characterize the contact zone between the cell and the walls of the channel. A cell squeezed in a first constriction obstructs most of the channel cross-section, which strongly limits leaks around cells. The rheological properties of the cell are subsequently probed during its entry in a second narrower constriction. The pressure force is determined from the pressure drop across the device, the cell velocity, and the width of the gutters formed between the cell and the corners of the channel. The additional friction force, which has never been analyzed for moving and constrained cells before, is found to involve both hydrodynamic lubrication and surface forces. This friction results in the existence of a threshold for moving the cells and leads to a non-linear behavior at low velocity. The friction force can nevertheless be assessed in the linear regime. Finally, an apparent viscosity of single cells can be estimated from a numerical prediction of the viscous dissipation induced by a small step in the channel. A preliminary application of our method yields an apparent loss modulus on the order of 100 Pa s for leukocytes THP-1 cells, in agreement with the literature data.
Evidence for boron diffusion into sub-stoichiometric MgO (001) barriers in CoFeB/MgO-based magnetic tunnel junctions
Authors: Harnchana V. , Hindmarch A. T. , Sarahan M. C. , Marrows C. H. , Brown A. P. , Brydson R. M. D.
Published: April 2013

Evidence of boron diffusion into the MgO barrier of a CoFeB/MgO based magnetic tunnel junction has been identified using analytical scanning transmission electron microscopy (STEM) and X-ray photoelectron spectroscopy. Structures were deposited by DC/RF-magnetron sputtering, where defective, sub-stoichiometric MgO barriers degrading device performance have been previously mitigated against by deposition of thin Mg layers prior to MgO deposition. We show that despite the protection offered by the Mg layer, disorder in the MgO barrier is still evident by STEM analysis and is a consequence of the oxidation of the Co40Fe40B20 surface during MgO deposition. Evidence of boron diffusion from CoFeB into the MgO barrier in the as-deposited and annealed structure is also presented, which in the as-deposited case we suggest results from the defective structures at the barrier interfaces. Annealing at 375 °C results in the presence of B in the trigonal coordination of [BO3]3− in the MgO barrier and partial crystallization of the top electrode (we presume there is also some boron diffusion into the Ta capping layer). The bottom electrode, however, fails to crystallize and much of the boron is retained in this thicker electrode. A higher annealing temperature or lower initial boron content is required to crystallize the bottom electrode.
Control of energy deposition in femtosecond laser dielectric interactions
Authors: Peng Jiahui , Grojo David , Rayner David M. , Corkum Paul B.
Published: April 2013

There are natural limits to the spatial resolution and the deposited energy densities that can be achieved in femtosecond laser dielectric modification. These arise because of the threshold-like nature of nonlinear absorption. We use two-pulse experiments to show that both limits can be exceeded by taking advantage of absorption seeded by free electrons or self-trapped excitons, depending on the pulse separation.
Spectral response of magnetic nanofluid to toxic cations
Authors: Mahendran V. , Philip John
Published: April 2013

We probe the spectral response of a magnetically polarizable nanofluid in the presence of different toxic metal cations. In the presence of cations like Ni2+, Mn2+, Pb2+, and Cd2+, the nanofluid shows large blue shift in the diffracted Bragg peak and a visually perceivable color change due to changes in the interparticle spacing of the self-assembled nano-arrays. The observed spectral response of the nanofluid offers the possibility of rapid and selective detections of cations optically. Because the emulsion used is easy to produce and inexpensive, this approach may find several interesting applications in rapid detection of cations.
Spectroscopic analysis of phase constitution of high quality VO2 thin film prepared by facile sol-gel method
Authors: Wu Y. F. , Fan L. L. , Chen S. M. , Chen S. , Zou C. W. , Wu Z. Y.
Published: April 2013

VO2 thin films with large-area were prepared on Al2O3 substrates by a simple sol-gel method. After an annealing treatment under low vacuum condition, all the VO2 films showed a preferred growth direction and exhibited excellent semiconductor-metal transition (SMT) characteristics. The structure and electrical properties of the obtained VO2 films were investigated systematically. Raman spectra, X-ray diffraction and X-ray absorption spectra measurements pointed out that the VO2 film on ${\rm A}{\rm l}_{\rm 2} {\rm O}_{\rm 3} ( {{\rm 10}\overline {\rm 1} {\rm 0}})$Al2O3(101¯0) substrate showed a M1 phase instead of M2 phase as reported in previous studies. Based on the experiment results, it was suggested that the strained structure of oriented VO2 films could be a mechanism for the formation of the intermediate M2 phase, whereas it is difficult to access the pure M2 phase of undoped VO2 films. VO2 film on ${\rm A}{\rm l}_{\rm 2} {\rm O}_{\rm 3} \left( {{\rm 10}\overline {\rm 1} {\rm 0}} \right)$Al2O3101¯0 substrate showed a lower SMT temperature compared to VO2 film on Al2O3 (0001), which can be mostly attributed to the differences of both lattice mismatch and thermal stress. The present results confirm and make clear the relevance of the substrate orientation in the growth of VO2 film and their different contributions to the SMT characteristics in vanadate systems.
Spatial distribution patterns, abundance and population structure of deep-sea crab Chaceon macphersoni, based on complementary analyses of trap and trawl data
Authors: Groeneveld Johan C. , Everett Bernadine I. , Fennessy Sean T. , Kirkman Stephen P. , Santos Jorge , Robertson Wendy D.
Published: April 2013

Marine species such as deep-sea geryonid crabs often exhibit high spatio-temporal variability in abundance and size over depth, substratum type and season, therefore data collected from a single gear type may not represent the whole population. Complementary data from trawl (soft substratum) and trap (hard substratum) fisheries were analysed within a general linear modelling (GLM) framework to assess distribution, abundance and population structure of Chaceon macphersoni off eastern South Africa. Catch rates, mean size, maturation size and sex ratio were modelled relative to year, month, depth, latitude and gear effects. Trap and trawl analyses indicated higher abundance as depth increased up to 500 m, and during the austral spring and summer. The mean size of crabs remained constant at all depths sampled, and sex ratios were skewed towards females. Females were smaller than males, and achieved maturity at a smaller size. A standardised index based on trawl data (1988–2010) showed a long-term decline in abundance, with some recovery after 2002, whereas the trap index showed recent local depletions on hard substrata. Using data from two gear types confirmed broad gradients in abundance, but also emphasised subtle trends, such as local depletions on hard substrata, that would not have been apparent from trawl data only.
Estimates of carbon emissions from forest fires in Japan, 1979–2008
Authors: Goto Yoshiaki , Suzuki Satoru
Published: April 2013

Emissions from forest fires directly affect the global and regional carbon cycles by increasing atmospheric carbon as well as affecting carbon sequestration by forests. We have estimated the release of total carbon, carbon-based trace gases (CO2, CO, CH4) and non-methane hydrocarbons (NMHC) emitted from forest fires in Japan during a 30-year period from 1979 through 2008. The area burnt varied widely from year to year but has gradually diminished since the 1980s. The mean annual area burnt during the period was 1878 ha. The mean annual estimate of direct carbon emissions from forest fires in Japan was 15.8 Gg C year–1 and ranged between 2.7 and 60.4 Gg C year–1. The mean annual trace gas emissions were 49.4 Gg CO2 year–1, 3.4 Gg CO year–1, 0.15 Gg CH4 year–1 and 0.18 Gg NMHC year–1. Although the carbon emissions varied widely from year to year based on the area burnt, they decreased dramatically from the 1980s onward. The interannual variations in trace gases parallel the total carbon emissions. The direct emissions from forest fires in Japan were substantially lower compared with the mean annual net primary production of Japanese forests or the carbon release in other countries and regions. However, the average annual carbon released per unit area burnt was comparable to that estimated in other regions and rose gradually with the increasing age of plantations.
Scale-dependent habitat selection by reintroduced Eld’s deer (Cervus eldi) in a human-dominated landscape
Authors: Yan Wen-Bo , Zeng Zhi-Gao , Pan Duo , Wang Tie-Jun , Zhang Qiong , Fu Yun-Nan , Lin Xian-Mei , Song Yan-Ling
Published: April 2013

Context
Knowledge of the habitat selection of reintroduced species is crucial to successful re-establishment of viable populations and effective conservation decision-making.

Aims
The aim of our research was to examine habitat selection by reintroduced Eld’s deer (Cervus eldi) in a human-dominated landscape.

Methods
The study was conducted during the period from July 2005 to November 2007 in the Chihao region, a human-dominated area located in western Hainan Island, China. Radio-telemetry was used to monitor 15 collared deer to gain their location information. Resource selection functions were used to quantify habitat selection of the study population at the landscape and home-range scales in both wet and dry seasons.

Key results
At the landscape scale, Eld’s deer showed selection for habitats with scrubland, high elevation, gentle slope, close to water sources and roads. At the home-range scale, Eld’s deer showed selection for habitats with dense forest, scrubland, grassland, low elevation and far away from roads, but they randomly used habitats without special consideration to the distance to water sources. At both landscape and home-range scales, Eld’s deer showed strong avoidance of villages. In addition, Eld’s deer showed increased selection of sparse forests and decreased use of grasslands in the dry season, as compared with the wet season at both spatial scales. Sexual differences in habitat selection existed in reintroduced Eld’s deer. Males showed stronger avoidance to human disturbance, whereas females selected vegetation with higher forage availability but poor hiding cover, especially during the antler-growing period (i.e. wet season).

Conclusions
The habitat selection of reintroduced Eld’s deer was scale-dependent. As a non-fatal anthropogenic factor, human disturbance had a strong influence on habitat selection of Eld’s deer. They more strongly selected slope habitats at relatively high elevations. However, our results also indicated that the reintroduced Eld’s deer had certain adaptive ability and tolerance to the disturbed environment.

Implications
This work provides insight into the habitat selection of reintroduced Eld’s deer in a human-dominated landscape. If the essential food resources are available, the regions at a relatively high elevation with low human disturbance can be considered as potential sites of future Eld’s deer reintroduction.
Microhomology-mediated End Joining and Homologous Recombination share the initial end resection step to repair DNA double-strand breaks in mammalian cells
Authors: Truong Lan N. , Li Yongjiang , Shi Linda Z. , Hwang Patty Yi-Hwa , He Jing , Wang Hailong , Razavian Niema , Berns Michael W. , Wu Xiaohua
Published: April 2013

Microhomology-mediated end joining (MMEJ) is a major pathway for Ku-independent alternative nonhomologous end joining, which contributes to chromosomal translocations and telomere fusions, but the underlying mechanism of MMEJ in mammalian cells is not well understood. In this study, we demonstrated that, distinct from Ku-dependent classical nonhomologous end joining, MMEJ—even with very limited end resection—requires cyclin-dependent kinase activities and increases significantly when cells enter S phase. We also showed that MMEJ shares the initial end resection step with homologous recombination (HR) by requiring meiotic recombination 11 homolog A (Mre11) nuclease activity, which is needed for subsequent recruitment of Bloom syndrome protein (BLM) and exonuclease 1 (Exo1) to DNA double-strand breaks (DSBs) to promote extended end resection and HR. MMEJ does not require S139-phosphorylated histone H2AX (γ-H2AX), suggesting that initial end resection likely occurs at DSB ends. Using a MMEJ and HR competition repair substrate, we demonstrated that MMEJ with short end resection is used in mammalian cells at the level of 10–20% of HR when both HR and nonhomologous end joining are available. Furthermore, MMEJ is used to repair DSBs generated at collapsed replication forks. These studies suggest that MMEJ not only is a backup repair pathway in mammalian cells, but also has important physiological roles in repairing DSBs to maintain cell viability, especially under genomic stress.
Neutral forces acting on intragenomic variability shape the
Escherichia coli
regulatory network topology
Authors: Ruths Troy , Nakhleh Luay
Published: April 2013

Cis
-regulatory networks (CRNs) play a central role in cellular decision making. Like every other biological system, CRNs undergo evolution, which shapes their properties by a combination of adaptive and nonadaptive evolutionary forces. Teasing apart these forces is an important step toward functional analyses of the different components of CRNs, designing regulatory perturbation experiments, and constructing synthetic networks. Although tests of neutrality and selection based on molecular sequence data exist, no such tests are currently available based on CRNs. In this work, we present a unique genotype model of CRNs that is grounded in a genomic context and demonstrate its use in identifying portions of the CRN with properties explainable by neutral evolutionary forces at the system, subsystem, and operon levels. We leverage our model against experimentally derived data from
Escherichia coli
. The results of this analysis show statistically significant and substantial neutral trends in properties previously identified as adaptive in origin—degree distribution, clustering coefficient, and motifs—within the
E. coli
CRN. Our model captures the tightly coupled genome–interactome of an organism and enables analyses of how evolutionary events acting at the genome level, such as mutation, and at the population level, such as genetic drift, give rise to neutral patterns that we can quantify in CRNs.
Characterizing deformability and surface friction of cancer cells
Authors: Byun Sangwon , Son Sungmin , Amodei Dario , Cermak Nathan , Shaw Josephine , Kang Joon Ho , Hecht Vivian C. , Winslow Monte M. , Jacks Tyler , Mallick Parag , Manalis Scott R.
Published: April 2013

Metastasis requires the penetration of cancer cells through tight spaces, which is mediated by the physical properties of the cells as well as their interactions with the confined environment. Various microfluidic approaches have been devised to mimic traversal in vitro by measuring the time required for cells to pass through a constriction. Although a cell’s passage time is expected to depend on its deformability, measurements from existing approaches are confounded by a cell's size and its frictional properties with the channel wall. Here, we introduce a device that enables the precise measurement of (
i
) the size of a single cell, given by its buoyant mass, (
ii
) the velocity of the cell entering a constricted microchannel (entry velocity), and (
iii
) the velocity of the cell as it transits through the constriction (transit velocity). Changing the deformability of the cell by perturbing its cytoskeleton primarily alters the entry velocity, whereas changing the surface friction by immobilizing positive charges on the constriction's walls primarily alters the transit velocity, indicating that these parameters can give insight into the factors affecting the passage of each cell. When accounting for cell buoyant mass, we find that cells possessing higher metastatic potential exhibit faster entry velocities than cells with lower metastatic potential. We additionally find that some cell types with higher metastatic potential exhibit greater than expected changes in transit velocities, suggesting that not only the increased deformability but reduced friction may be a factor in enabling invasive cancer cells to efficiently squeeze through tight spaces.
Identification and characterization of a previously undescribed family of sequence-specific DNA-binding domains
Authors: Lohse Matthew B. , Hernday Aaron D. , Fordyce Polly M. , Noiman Liron , Sorrells Trevor R. , Hanson-Smith Victor , Nobile Clarissa J. , DeRisi Joseph L. , Johnson Alexander D.
Published: April 2013

Sequence-specific DNA-binding proteins are among the most important classes of gene regulatory proteins, controlling changes in transcription that underlie many aspects of biology. In this work, we identify a transcriptional regulator from the human fungal pathogen
Candida albicans
that binds DNA specifically but has no detectable homology with any previously described DNA- or RNA-binding protein. This protein, named White–Opaque Regulator 3 (Wor3), regulates white–opaque switching, the ability of
C. albicans
to switch between two heritable cell types. We demonstrate that ectopic overexpression of
WOR3
results in mass conversion of white cells to opaque cells and that deletion of
WOR3
affects the stability of opaque cells at physiological temperatures. Genome-wide chromatin immunoprecipitation of Wor3 and gene expression profiling of a
wor3
deletion mutant strain indicate that Wor3 is highly integrated into the previously described circuit regulating white–opaque switching and that it controls a subset of the opaque transcriptional program. We show by biochemical, genetic, and microfluidic experiments that Wor3 binds directly to DNA in a sequence-specific manner, and we identify the set of
cis
-regulatory sequences recognized by Wor3. Bioinformatic analyses indicate that the Wor3 family arose more recently in evolutionary time than most previously described DNA-binding domains; it is restricted to a small number of fungi that include the major fungal pathogens of humans. These observations show that new families of sequence-specific DNA-binding proteins may be restricted to small clades and suggest that current annotations—which rely on deep conservation—underestimate the fraction of genes coding for transcriptional regulators.
Cigarette smoke (CS) and nicotine delay neutrophil spontaneous death via suppressing production of diphosphoinositol pentakisphosphate
Authors: Xu Yuanfu , Li Hongmei , Bajrami Besnik , Kwak Hyunjeong , Cao Shannan , Liu Peng , Zhou Jiaxi , Zhou Yuan , Zhu Haiyan , Ye Keqiang , Luo Hongbo R.
Published: April 2013

Diphosphoinositol pentakisphosphate (InsP7), a higher inositol phosphate containing energetic pyrophosphate bonds, is beginning to emerge as a key cellular signaling molecule. However, the various physiological and pathological processes that involve InsP7 are not completely understood. Here we report that cigarette smoke (CS) extract and nicotine reduce InsP7 levels in aging neutrophils. This subsequently leads to suppression of Akt deactivation, a causal mediator of neutrophil spontaneous death, and delayed neutrophil death. The effect of CS extract and nicotine on neutrophil death can be suppressed by either directly inhibiting the PtdIns(3,4,5)P3/Akt pathway, or increasing InsP7 levels via overexpression of InsP6K1, an inositol hexakisphosphate (InsP6) kinase responsible for InsP7 production in neutrophils. Delayed neutrophil death contributes to the pathogenesis of CS-induced chronic obstructive pulmonary disease. Therefore, disruption of InsP6K1 augments CS-induced neutrophil accumulation and lung damage. Taken together, these results suggest that CS and nicotine delay neutrophil spontaneous death by suppressing InsP7 production and consequently blocking Akt deactivation in aging neutrophils. Modifying neutrophil death via this pathway provides a strategy and therapeutic target for the treatment of tobacco-induced chronic obstructive pulmonary disease.
Uncharted waters: voyages for Education for Sustainable Development in the higher education curriculum
Authors: Ryan Alexandra , Tilbury Daniella
Published: April 2013

The need to embed Education for Sustainable Development (ESD) in the higher education curriculum is well recognised in international sustainable development dialogues. However, early pioneers in this area have met with substantial obstacles and now face the prospect of attempting systemic education change in a new and difficult sector climate. This article explores the potential for engagement with the higher education curriculum by bringing ESD into its quality assurance and quality enhancement system. It builds on insights gained from a national project funded by the Higher Education Funding Council for England, which worked in collaboration with the UK Quality Assurance Agency and a consortium of five universities. It considers the ways that ESD has entered the UK higher education sector and the potential connectivity that exists between ESD and quality. Key findings are shared from the development projects carried out in these universities, including their identification of specific quality‐led pathways for embedding ESD, the differences of perspective uncovered amongst stakeholders and challenges for institutional strategy and implementation. It concludes in reflection on the need to access deeper currents of teaching and learning to make ESD a viable education proposition, as well as the potential transfer to other parts of the education and skills sector.
Has Improved Hand Hygiene Compliance Reduced the Risk of Hospital-Acquired Infections among Hospitalized Patients in Ontario? Analysis of Publicly Reported Patient Safety Data from 2008 to 2011
Authors: DiDiodato Giulio
Published: April 2013

Design.

Prospective, observational, ecological, time series, cross-sectional study examining the association between hand hygiene compliance (HHC) rates and the incidence of hospital-acquired infections.

Setting.

Acute care hospitals (N = 166) located in the province of Ontario, Canada.

Methods.

All data were extracted from the Ontario patient safety indicator database (http://www.hqontario.ca/public-reporting/patient-safety). Complete data were available for 166 acute care hospitals from October 1, 2008, to December 31, 2011. The rates of Clostridium difficile infection (CDI) are reported monthly, methicillin-resistant Staphylococcus aureus (MRSA) bacteremia quarterly, and HHC rates yearly. Trends and associations for each indicator were evaluated by ordinary least squares regression (HHC), zero-inflated Poisson regression (MRSA bacteremia), or Poisson regression (CDI). Dependent variables included in the regression analyses were extracted from the same database and included year, healthcare region, and type of hospital (teaching or small or large community).

Results.

Compared to those in 2008, reported HHC rates improved every year both before and after environment/patient contact (range, 10.6%–25.3%). Compared to those in 2008, there was no corresponding change in the rates of MRSA bacteremia; however, the rates of CDI decreased in 2009 but were not statistically significantly decreased from baseline in either 2010 or 2011. No consistent association was demonstrated between changes in the rates of HHC and these two healthcare-associated infections (HAIs).

Conclusions.

Despite significant improvements in reported rates of HHC among healthcare personnel in Ontario's hospitals, we could not demonstrate a positive ecological impact on rates of these two HAIs.
A Cantor set with hyperbolic complement
Authors: Souto Juan , Stover Matthew
Published: April 2013

We construct a Cantor set in

S

3

\mathbb {S}^3

whose complement admits a complete hyperbolic metric.