Technical note: The effects of five different defaunation methods on biogeochemical properties of intertidal sediment

Various methods have been used to remove organisms from sediments to investigate structure and function of faunal assemblages in intertidal habitats. Nevertheless, little is known about how these treatments affect properties of the sediments themselves, although changing these properties may cause changes in the assemblages, independently of other hypotheses being tested. This study assesses the efficacy of defaunation and effect on selected biogeochemical properties of five different methods of defaunating soft muddy sediments in an estuary. The methods were removal and freezing of sediment, removal and oven-heating, freezing in situ with liquid N2, spraying with formalin and spraying with hydrogen peroxide. The first four of these methods have been used in previous studies, whilst the fifth was considered to be a potentially useful defaunator because it does not leave toxic residues. The first two methods required sediment to be brought back to the lab, disrupting the natural structure of the sediment; the last three were done in situ, with much less disturbance.  Variables measured to assess effects of the treatments on the sediment were amount of water, grain size, total carbohydrate, suspension index (relative erosion rate), erosion threshold, chlorophyll a and b, colloidal carbohydrate, Fo (minimal fluorescence) and Fv/ Fm (photosynthetic yield). There were no significant effects of any treatment on the first four variables. For the others, effects of defaunation varied from treatment to treatment and with time after treatment. Generally, the greatest disturbance was to the microphytobenthos (MPB, measured by chlorophyll and fluorescence) and related variables. For most treatments, recovery was rapid, but the effects of formalin and H2O2 persisted for a few days. Effects on physical properties of the sediment were mostly minor and insignificant. Removal and freezing or heating, however, caused major changes to the sediments because of the disturbances involved. Choosing the appropriate method of defaunation is very important if interpretations are not to be confounded between the effects of defaunation per se and any effects of changes to other biota (such as microphytobenthos) and/or the properties of sediments caused by the method used to defaunate experimental areas

Navier-Stokes transport coefficients of dd-dimensional granular binary mixtures at low density

The Navier-Stokes transport coefficients for binary mixtures of smooth inelastic hard disks or spheres under gravity are determined from the Boltzmann kinetic theory by application of the Chapman-Enskog method for states near the local homogeneous cooling state. It is shown that the Navier-Stokes transport coefficients are not affected by the presence of gravity. As in the elastic case, the transport coefficients of the mixture verify a set of coupled linear integral equations that are approximately solved by using the leading terms in a Sonine polynomial expansion. The results reported here extend previous calculations [V. Garz\'o and J. W. Dufty, Phys. Fluids {\bf 14}, 1476 (2002)] to an arbitrary number of dimensions. To check the accuracy of the Chapman-Enskog results, the inelastic Boltzmann equation is also numerically solved by means of the direct simulation Monte Carlo method to evaluate the diffusion and shear viscosity coefficients for hard disks. The comparison shows a good agreement over a wide range of values of the coefficients of restitution and the parameters of the mixture (masses and sizes).Comment: 6 figures, to be published in J. Stat. Phy

What do people know about the heritability of sleep?

Study Objectives Twin studies have provided data about the relative weight of genetic and environmental factors on sleep variables over the last few decades. However, heritability is a non-intuitive concept and it is often misunderstood even amongst the scientific community. This study aimed to analyze: (1) understanding of the meaning of heritability of insomnia; (2) the accuracy of estimations of heritability in the general population regarding three sleep traits (sleep duration, sleep quality and insomnia); (3) perceptions of the effectiveness of different treatments for insomnia depending on how the disorder is presented (i.e. having an environmental or genetic etiology) and whether the subject’s estimate of genetic influence on sleep traits impacted beliefs about the effectiveness of different treatments. Methods Participants (N = 3658) completed a survey which included: questions about general genetic knowledge; a specific question about the meaning of heritability; estimates of heritability of three different sleep traits; and the effectiveness of different treatments for insomnia depending on how the etiology of this condition was presented. Results Fewer than 25% of the participants selected the correct description of the heritability of insomnia. Almost half of the sample incorrectly believed that heritability refers to the chance of passing a disorder onto their children. We also found that participants provided different estimates for the effectiveness of different treatments depending on the presumed etiology of the disorder. Conclusion Most people do not have accurate knowledge about the concept of heritability. People’s assumptions about the etiology of a disorder may influence which treatments they consider most effective

Cryptic loxP sites in mammalian genomes: genome-wide distribution and relevance for the efficiency of BAC/PAC recombineering techniques

Cre is widely used for DNA tailoring and, in combination with recombineering techniques, to modify BAC/PAC sequences for generating transgenic animals. However, mammalian genomes contain recombinase recognition sites (cryptic loxP sites) that can promote illegitimate DNA recombination and damage when cells express the Cre recombinase gene. We have created a new bioinformatic tool, FuzznucComparator, which searches for cryptic loxP sites and we have applied it to the analysis of the whole mouse genome. We found that cryptic loxP sites occur frequently and are homogeneously distributed in the genome. Given the mammalian nature of BAC/PAC genomic inserts, we hypothesised that the presence of cryptic loxP sites may affect the ability to grow and modify BAC and PAC clones in E. coli expressing Cre recombinase. We have observed a defect in bacterial growth when some BACs and PACs were transformed into EL350, a DH10B-derived bacterial strain that expresses Cre recombinase under the control of an arabinose-inducible promoter. In this study, we have demonstrated that Cre recombinase expression is leaky in un-induced EL350 cells and that some BAC/PAC sequences contain cryptic loxP sites, which are active and mediate the introduction of single-strand nicks in BAC/PAC genomic inserts

Atom focusing by far-detuned and resonant standing wave fields: Thin lens regime

The focusing of atoms interacting with both far-detuned and resonant standing wave fields in the thin lens regime is considered. The thin lens approximation is discussed quantitatively from a quantum perspective. Exact quantum expressions for the Fourier components of the density (that include all spherical aberration) are used to study the focusing numerically. The following lens parameters and density profiles are calculated as functions of the pulsed field area $\theta$: the position of the focal plane, peak atomic density, atomic density pattern at the focus, focal spot size, depth of focus, and background density. The lens parameters are compared to asymptotic, analytical results derived from a scalar diffraction theory for which spherical aberration is small but non-negligible ($\theta \gg 1$). Within the diffraction theory analytical expressions show that the focused atoms in the far detuned case have an approximately constant background density $0.5(1-0.635\theta ^{- 1/2})$ while the peak density behaves as $$, the focal distance or time as $\theta ^{-1}(1+1.27\theta ^{- 1/2})$, the focal spot size as $0.744\theta ^{-3/4}$, and the depth of focus as $1.91\theta ^{- 3/2}$. Focusing by the resonant standing wave field leads to a new effect, a Rabi- like oscillation of the atom density. For the far-detuned lens, chromatic aberration is studied with the exact Fourier results. Similarly, the degradation of the focus that results from angular divergence in beams or thermal velocity distributions in traps is studied quantitatively with the exact Fourier method and understood analytically using the asymptotic results. Overall, we show that strong thin lens focusing is possible with modest laser powers and with currently achievable atomic beam characteristics.Comment: 21 pages, 11 figure

The Horizontal Component of Photospheric Plasma Flows During the Emergence of Active Regions on the Sun

The dynamics of horizontal plasma flows during the first hours of the emergence of active region magnetic flux in the solar photosphere have been analyzed using SOHO/MDI data. Four active regions emerging near the solar limb have been considered. It has been found that extended regions of Doppler velocities with different signs are formed in the first hours of the magnetic flux emergence in the horizontal velocity field. The flows observed are directly connected with the emerging magnetic flux; they form at the beginning of the emergence of active regions and are present for a few hours. The Doppler velocities of flows observed increase gradually and reach their peak values 4-12 hours after the start of the magnetic flux emergence. The peak values of the mean (inside the +/-500 m/s isolines) and maximum Doppler velocities are 800-970 m/s and 1410-1700 m/s, respectively. The Doppler velocities observed substantially exceed the separation velocities of the photospheric magnetic flux outer boundaries. The asymmetry was detected between velocity structures of leading and following polarities. Doppler velocity structures located in a region of leading magnetic polarity are more powerful and exist longer than those in regions of following polarity. The Doppler velocity asymmetry between the velocity structures of opposite sign reaches its peak values soon after the emergence begins and then gradually drops within 7-12 hours. The peak values of asymmetry for the mean and maximal Doppler velocities reach 240-460 m/s and 710-940 m/s, respectively. An interpretation of the observable flow of photospheric plasma is given.Comment: 20 pages, 10 figures, 3 tables. The results of article were presented at the ESPM-13 (12-16 September 2011, Rhodes, Greece, Abstract Book p. 102, P.4.12, http://astro.academyofathens.gr/espm13/documents/ESPM13_abstract_programme_book.pdf

Computed tomographic features of feline sino-nasal and sino-orbital aspergillosis

Feline upper respiratory tract aspergillosis (URTA) occurs as two distinct anatomic forms, sinonasal aspergillosis (SNA) and sino-orbital aspergillosis (SOA). An emerging pathogen, Aspergillus felis is frequently involved. The pathogenesis of URTA, in particular, the relationship between the infecting isolate and outcome, is poorly understood. Computed tomography was used to investigate the route of fungal infection and extension in 16 cases (SNA n=7, SOA n=9) where the infecting isolate had been identified by molecular testing. All cases had nasal cavity involvement except one cat with SNA that had unilateral frontal sinus changes. A strong association between the infecting species and anatomic form was identified. A. fumigatus infections remained within the sino-nasal cavity. Cryptic species infections were associated with orbital and paranasal soft-tissue involvement and with orbital lysis. These species were further associated with a mass in the nasal cavity, paranasal sinuses or nasopharynx. Orbital masses showed heterogeneous contrast enhancement, with central coalescing hypoattenuating foci and peripheral rim enhancement. Severe, cavitated turbinate lysis, typical of canine SNA, was present only in cats with SNA. These findings support that the nasal cavity is the portal of entry for fungal spores in feline URTA and that the route of extension to involve the orbit is via direct naso-orbital communication from bone lysis. Additionally, a pathogenic role for A. wyomingensis and a sinolith in a cat with A. udagawae infection are reported for the first time. Keywords: Aspergillus felis; Aspergillosis; Cats; Sino-nasal; Sino-orbita

Computed tomographic features of feline sino-nasal and sino-orbital aspergillosis

Feline upper respiratory tract aspergillosis (URTA) occurs as two distinct anatomic forms, sinonasal aspergillosis (SNA) and sino-orbital aspergillosis (SOA). An emerging pathogen, Aspergillus felis is frequently involved. The pathogenesis of URTA, in particular, the relationship between the infecting isolate and outcome, is poorly understood. Computed tomography was used to investigate the route of fungal infection and extension in 16 cases (SNA n=7, SOA n=9) where the infecting isolate had been identified by molecular testing. All cases had nasal cavity involvement except one cat with SNA that had unilateral frontal sinus changes. A strong association between the infecting species and anatomic form was identified. A. fumigatus infections remained within the sino-nasal cavity. Cryptic species infections were associated with orbital and paranasal soft-tissue involvement and with orbital lysis. These species were further associated with a mass in the nasal cavity, paranasal sinuses or nasopharynx. Orbital masses showed heterogeneous contrast enhancement, with central coalescing hypoattenuating foci and peripheral rim enhancement. Severe, cavitated turbinate lysis, typical of canine SNA, was present only in cats with SNA. These findings support that the nasal cavity is the portal of entry for fungal spores in feline URTA and that the route of extension to involve the orbit is via direct naso-orbital communication from bone lysis. Additionally, a pathogenic role for A. wyomingensis and a sinolith in a cat with A. udagawae infection are reported for the first time. Keywords: Aspergillus felis; Aspergillosis; Cats; Sino-nasal; Sino-orbita

Clinical activity of ipilimumab for metastatic uveal melanoma: a retrospective review of the Dana-Farber Cancer Institute, Massachusetts General Hospital, Memorial Sloan-Kettering Cancer Center, and University Hospital of Lausanne experience.

BACKGROUND: Uveal melanoma exhibits a high incidence of metastases; and, to date, there is no systemic therapy that clearly improves outcomes. The anticytotoxic T-lymphocyte-associated protein 4 (anti-CTLA-4) antibody ipilimumab is a standard of care for metastatic melanoma; however, the clinical activity of CTLA-4 inhibition in patients with metastatic uveal melanoma is poorly defined. METHODS: To assess ipilimumab in this setting, the authors performed a multicenter, retrospective analysis of 4 hospitals in the United States and Europe. Clinical characteristics, toxicities, and radiographic disease burden, as determined by central, blinded radiology review, were evaluated. RESULTS: Thirty-nine patients with uveal melanoma were identified, including 34 patients who received 3 mg/kg ipilimumab and 5 who received 10 mg/kg ipilimumab. Immune-related response criteria and modified World Health Organization criteria were used to assess the response rate (RR) and the combined response plus stable disease (SD) rate after 12 weeks, after 23 weeks, and overall (median follow-up, 50.4 weeks [12.6 months]). At week 12, the RR was 2.6%, and the response plus SD rate was 46.%; at week 23, the RR was 2.6%, and the response plus SD rate was 28.2%. There was 1 complete response and 1 late partial response (at 100 weeks after initial SD) for an immune-related RR of 5.1%. Immune-related adverse events were observed in 28 patients (71.8%) and included 7 (17.9%) grade 3 and 4 events. Immune-related adverse events were more frequent in patients who received 10 mg/kg ipilimumab than in those who received 3 mg/kg ipilimumab. The median overall survival from the first dose of ipilimumab was 9.6 months (95% confidence interval, 6.3-13.4 months; range, 1.6-41.6 months). Performance status, lactate dehydrogenase level, and an absolute lymphocyte count ≥ 1000 cells/μL at week 7 were associated significantly with survival. CONCLUSIONS: In this multicenter, retrospective analysis of 4 hospitals in the United States and Europe of patients with uveal melanoma, durable responses to ipilimumab and manageable toxicity were observed

Exploring the performance of the spectrometer prisma in heavy zirconium and xenon mass regions

We present results from two recent runs which illustrate the performance of the PRISMA spectrometer in the proximity of the upper limit of its operational interval, namely 96Zr + 124Sn at Elab = 500 MeV and 136Xe + 208Pb at Elab = 930 MeV. In the latter run, the γ array CLARA also allowed us to identify previously unknown γ transitions in the nuclides 136Cs and 134I