Cirolana westbyi, (Isopoda: Cirolanidae) a new species in the ‘Cirolana parva-group’ from the Turneffe Atoll, Belize

Figure 9. Maximum Likelihood phylogenetic comparison of several members in the Cirolanidae, including the newly sequenced 18S genes of Cirolana westbyi n. sp. and Cirolana parva.Published as part of Jennings, Lucas A., Bojko, Jamie, Rotjan, Randi D. & Behringer, Donald C., 2021, Cirolana westbyi, (Isopoda: Cirolanidae) a new species in the 'Cirolana parva-group' from the Turneffe Atoll, Belize, pp. 2053-2069 in Journal of Natural History 54 (31-32) on page 2065, DOI: 10.1080/00222933.2020.1837273, http://zenodo.org/record/502898

Systematic assessment of the Panopeidae and broader Eubrachyura (Decapoda: Brachyura) using mitochondrial genomics

Abstract This study provides a broad phylogenetic analysis for the Eubrachyura, with the inclusion of three new Panopeidae mitochondrial genomes: Eurypanopeus depressus (flatback mud crab) (15,854bp), Panopeus herbstii (Atlantic mud crab) (15,812bp) and Rhithropanopeus harrisii (Harris, or ‘white-fingered’ mud crab) (15,892bp). These new mitogenomes were analyzed alongside all available brachyuran mitochondrial genomes (n = 113), comprising 80 genera from 29 families, to provide an updated phylogenetic analysis of the infra-order Brachyura (“true crabs”). Our analyses support the subsection Potamoida within the Eubrachyura as the sister group to Thoracotremata. The family Panopeidae aligns with the family Xanthidae to form the Xanthoidea branch, which is supported by current morphological and genetic taxonomy. A unique gene arrangement termed ‘XanGO’ was identified for the panopeids and varies relative to other members of the subsection Heterotremata (within the Eubrachyura) via a transposition of the trnV gene. This gene arrangement is novel and is shared between several Xanthoidea species, including Etisus anaglyptus (hairy spooner crab), Atergatis floridus (brown egg crab), and Atergatis integerrimus (red egg crab), suggesting that it is a conserved gene arrangement within the Xanthoidea superfamily. Our study further reveals a need for taxonomic revision of some brachyuran groups, particularly the Sesarmidae. The inclusion of panopeid mitogenomes into the greater brachyuran phylogeny increases our understanding of crab evolution and higher level Eubrachyuran systematics

Patterns of microchromosome organization remain highly conserved throughout avian evolution

The structure and organization of a species genome at a karyotypic level, and in interphase nuclei, have broad functional significance. Although regular sized chromosomes are studied extensively in this regard, microchromosomes, which are present in many terrestrial vertebrates, remain poorly explored. Birds have more cytologically indistinguishable microchromosomes (~ 30 pairs) than other vertebrates; however, the degree to which genome organization patterns at a karyotypic and interphase level differ between species is unknown. In species where microchromosomes have fused to other chromosomes, they retain genomic features such as gene density and GC content; however, the extent to which they retain a central nuclear position has not been investigated. In studying 22 avian species from 10 orders, we established that, other than in species where microchromosomal fusion is obvious (Falconiformes and Psittaciformes), there was no evidence of microchromosomal rearrangement, suggesting an evolutionarily stable avian genome (karyotypic) organization. Moreover, in species where microchromosomal fusion has occurred, they retain a central nuclear location, suggesting that the nuclear position of microchromosomes is a function of their genomic features rather than their physical size

Influence of the scattering potential model on low energy electron diffraction from Cu(001)−c(2 × 2)-Pb

A dynamical LEED intensity analysis is reported for Cu(001)−c(2 × 2)-Pb. The adsorbate layer distance from the substrate is determined as 2.29 Å, and the topmost interlayer spacing for the substrate is the same as in bulk Cu, in contrast to a contraction for clean Cu(001). This structural result is, within the accuracy reached, insensitive to changes in the assumed scattering potential models. The r-factors suggest a weak preference for an energy-dependent exchange correlation and a moderate one for adding a localized adsorption part inside the muffin-tin spheres. The sensitivity of spectra and r-factors to changes in the assumed isotropic Debye temperature for Pb suggests that vibrational anisotropy should be taken into account in order to improve the accuracy of the analysis. Calculated spin polarization spectra are very sensitive to the exchange approximation, the localized absorption and the Debye temperature. Together with experimental data, they should be useful in particular for determining the vibrational anisotropy

A shallow though extensive H2 2.12 micron imaging survey of Taurus-Auriga-Perseus: I. NGC1333, L1455, L1448 and B1

We discuss wide-field near-IR imaging of the NGC1333, L1448, L1455 and B1 star forming regions in Perseus. The observations have been extracted from a much larger narrow-band imaging survey of the Taurus-Auriga-Perseus complex. These H2 2.12 micron observations are complemented by broad-band K imaging, mid-IR imaging and photometry from the Spitzer Space Telescope, and published submillimetre CO J=3-2 maps of high-velocity molecular outflows. We detect and label 85 H2 features and associate these with 26 molecular outflows. Three are parsec-scale flows, with a mean flow lobe length exceeding 11.5 arcmin. 37 (44%) of the detected H2 features are associated with a known Herbig-Haro object, while 72 (46%) of catalogued HH objects are detected in H2 emission. Embedded Spitzer sources are identified for all but two of the 26 molecular outflows. These candidate outflow sources all have high near-to-mid-IR spectral indices (mean value of alpha ~ 1.4) as well as red IRAC 3.6-4.5 micron and IRAC/MIPS 4.5-24.0 micron colours: 80% have [3.6]-[4.5] > 1.0 and [4.5]-[24] > 1.5. These criteria - high alpha and red [4.5]-[24] and [3.6]-[4.5] colours - are powerful discriminants when searching for molecular outflow sources. However, we find no correlation between alpha and flow length or opening angle, and the outflows appear randomly orientated in each region. The more massive clouds are associated with a greater number of outflows, which suggests that the star formation efficiency is roughly the same in each region.Comment: 23 pages (including Appoendix); 11 main text figures, 5 colour appendix figs uploaded as gifs; accepted by MNRAS; for higher-resolution figures please visit http://www.jach.hawaii.edu/~cdavis

The structure of protostellar envelopes derived from submillimeter continuum images

High dynamic range imaging of submillimeter dust emission from the envelopes of eight young protostars in the Taurus and Perseus star-forming regions has been carried out using the SCUBA submillimeter camera on the James Clerk Maxwell Telescope. Good correspondence between the spectral classifications of the protostars and the spatial distributions of their dust emission is observed, in the sense that those with cooler spectral energy distributions also have a larger fraction of the submillimeter flux originating in an extended envelope compared with a disk. This results from the cool sources having more massive envelopes rather than warm sources having larger disks. Azimuthally-averaged radial profiles of the dust emission are used to derive the power-law index of the envelope density distributions, p (defined by rho proportional to r^-p), and most of the sources are found to have values of p consistent with those predicted by models of cloud collapse. However, the youngest protostars in our sample, L1527 and HH211-mm, deviate significantly from the theoretical predictions, exhibiting values of p somewhat lower than can be accounted for by existing models. For L1527 heating of the envelope by shocks where the outflow impinges on the surrounding medium may explain our result. For HH211-mm another explanation is needed, and one possibility is that a shallow density profile is being maintained in the outer envelope by magnetic fields and/or turbulence. If this is the case star formation must be determined by the rate at which the support is lost from the cloud, rather than the hydrodynamical properties of the envelope, such as the sound speed.Comment: Accepted for publication in the Astrophysical Journa

Chromosome-level assembly reveals extensive rearrangement in sakar falcon and budgerigar, but not ostrich, genomes

Background: The number of de novo genome sequence assemblies is increasing exponentially; however, relatively few contain one scaffold/contig per chromosome. Such assemblies are essential for studies of genotype-to-phenotype association, gross genomic evolution, and speciation. Inter-species differences can arise from chromosomal changes fixed during evolution, and we previously hypothesized that a higher fraction of elements under negative selection contributed to avian-specific phenotypes and avian genome organization stability. The objective of this study is to generate chromosome-level assemblies of three avian species (saker falcon, budgerigar, and ostrich) previously reported as karyotypically rearranged compared to most birds. We also test the hypothesis that the density of conserved non-coding elements is associated with the positions of evolutionary breakpoint regions. Results: We used reference-assisted chromosome assembly, PCR, and lab-based molecular approaches, to generate chromosome-level assemblies of the three species. We mapped inter- and intrachromosomal changes from the avian ancestor, finding no interchromosomal rearrangements in the ostrich genome, despite it being previously described as chromosomally rearranged. We found that the average density of conserved non-coding elements in evolutionary breakpoint regions is significantly reduced. Fission evolutionary breakpoint regions have the lowest conserved non-coding element density, and intrachromomosomal evolutionary breakpoint regions have the highest. Conclusions: The tools used here can generate inexpensive, efficient chromosome-level assemblies, with > 80% assigned to chromosomes, which is comparable to genomes assembled using high-density physical or genetic mapping. Moreover, conserved non-coding elements are important factors in defining where rearrangements, especially interchromosomal, are fixed during evolution without deleterious effects

Responses and adverse effects of carboplatin-based chemotherapy for pediatric intracranial germ cell tumors

PurposeCisplatin-based chemotherapy has been commonly used for the treatment of intracranial germ cell tumors (IC-GCTs). However, this treatment exhibits some adverse effects such as renal problems and hearing difficulty. Carboplatin-based chemotherapy was administered to pediatric patients with IC-GCTs from August 2004 at the Samsung Medical Center. In this study, we assessed the responses and adverse effects of carboplatin-based chemotherapy in pediatric IC-GCTs patients according to the risk group, and compared the results with those of the previous cisplatin-based chemotherapy.MethodsWe examined 35 patients (27 men and 8 women) diagnosed with IC-GCTs between August 2004 and April 2008 and received risk-adapted carboplatin-based chemotherapy at the Samsung Medical Center. Patients were divided into either low-risk (LR) or high-risk (HR) groups and a retrospective analysis was performed using information from the medical records.ResultsAlthough hematological complications were common, hearing difficulties or grade 3 or 4 creatinine level elevation were not observed in patients who underwent carboplatin-based chemotherapy. The frequency of febrile neutropenia did not differ between the risk groups. The overall survival was 100% and event-free survival (EFS) was 95.7%. The EFS rate was 100% in the LR group and 90% in the HR group, respectively.ConclusionDespite their common occurrence in high-risk patients, no lethal hematological complications were associated with carboplatin-based treatment. The current carboplatin-based chemotherapy protocol is safe and effective for the treatment of pediatric patients with IC-GCTs

The linear polarisation of southern bright stars measured at the parts-per-million level

We report observations of the linear polarisation of a sample of 50 nearby southern bright stars measured to a median sensitivity of ~4.4 x 10^{-6}. We find larger polarisations and more highly polarised stars than in the previous PlanetPol survey of northern bright stars. This is attributed to a dustier interstellar medium in the mid-plane of the Galaxy, together with a population containing more B-type stars leading to more intrinsically polarised stars, as well as using a wavelength more sensitive to intrinsic polarisation in late-type giants. Significant polarisation had been identified for only six stars in the survey group previously, whereas we are now able to deduce intrinsic polarigenic mechanisms for more than twenty. The four most highly polarised stars in the sample are the four classical Be stars (alpha Eri, alpha Col, eta Cen and alpha Ara). For the three of these objects resolved by interferometry, the position angles are consistent with the orientation of the circumstellar disc determined. We find significant intrinsic polarisation in most B stars in the sample; amongst these are a number of close binaries and an unusual binary debris disk system. However these circumstances do not account for the high polarisations of all the B stars in the sample and other polarigenic mechanisms are explored. Intrinsic polarisation is also apparent in several late type giants which can be attributed to either close, hot circumstellar dust or bright spots in the photosphere of these stars. Aside from a handful of notable debris disk systems, the majority of A to K type stars show polarisation levels consistent with interstellar polarisation.Peer reviewe

Permeability Prediction in Tight Carbonate Rocks using Capillary Pressure Measurements

The prediction of permeability in tight carbonate reservoirs presents ever more of a challenge in the hydrocarbon industry today. It is the aim of this paper to ascertain which models have the capacity to predict permeability reliably in tight carbonates, and to develop a new one, if required. This paper presents (i) the results of laboratory Klinkenberg-corrected pulse decay measurements of carbonates with permeabilities in the range 65 nD to 0.7 mD, (ii) use of the data to assess the performance of 16 permeability prediction models, (iii) the development of an improved prediction model for tight carbonate rocks, and (iv) its validation using an independent data set. Initial measurements including porosity, permeability and mercury injection capillary pressure measurements (MICP) were carried out on a suite of samples of Kometan limestone from the Kurdistan region of Iraq. The prediction performance of sixteen different percolation-type and Poiseuille-type permeability prediction models were analysed with the measured data. Analysis of the eight best models is included in this paper and the analysis of the remainder is provided in supplementary material. Some of the models were developed especially for tight gas sands, while many were not. Critically, none were developed for tight gas carbonates. Predictably then, the best prediction was obtained from the generic model and the RGPZ models (R2 = 0.923, 0.920 and 0.915, respectively), with other models performing extremely badly. In an attempt to provide a better model for use with tight carbonates, we have developed a new model based on the RGPZ theoretical model by adding an empirical scaling parameter to account for the relationship between grain size and pore throat size in carbonates. The generic model, the 28 new RGPZ Carbonate model and the two original RGPZ models have been tested against independent data from a suite of 42 samples of tight Solnhofen carbonates. All four models performed very creditably with the generic and the new RGPZ Carbonate models performing well (R2 = 0.840 and 0.799, respectively). It is clear from this study that the blind application of conventional permeability prediction techniques to carbonates, and particularly to tight carbonates, will lead to gross errors and that the development of new methods that are specific to tight carbonates is unavoidable