Growth and annual survival estimates to examine the ecology of larval lamprey and the implications of ageing error in fitting models.

This study used existing western brook lamprey Lampetra richardsoni age information to fit three different growth models (i.e. von Bertalanffy, Gompertz and logistic) with and without error in age estimates. Among these growth models, there was greater support for the logistic and Gompertz models than the von Bertalanffy model, regardless of ageing error assumptions. The von Bertalanffy model, however, appeared to fit the data well enough to permit survival estimates; using length-based estimators, annual survival varied between 0·64 (95% credibility interval: 0·44-0·79) and 0·81 (0·79-0·83) depending on ageing and growth process error structure. These estimates are applicable to conservation and management of L. richardsoni and other western lampreys (e.g. Pacific lamprey Entosphenus tridentatus) and can potentially be used in the development of life-cycle models for these species. These results also suggest that estimators derived from von Bertalanffy growth models should be interpreted with caution if there is high uncertainty in age estimates.

TEM investigations on the local microstructure of electrodeposited galfenol nanowires.

The local microstructure of Fe-Ga nanowires is investigated considering dependence on the deposition technique. Using a complexed electrolyte, smooth and homogeneous Fe80Ga20 nanowires are deposited into anodic aluminum oxide templates by either applying pulse potential or potentiostatic deposition technique. At optimized deposition conditions the wires show the desired composition of Fe80±2Ga20±2 without a gradient along the growth direction. Composition distribution, structure and microstructure are examined in detail and reveal only minor differences. Line EELS and crystal lattice measurements reveal a negligible oxygen content for both preparation routines. Neither Fe/Ga oxides nor hydroxides were found. Both potentiostatically deposited as well as pulse deposited nanowires exhibit a preferred 〈110〉orientation, the latter with slightly larger crystals. Different contrast patterns were found by TEM that appear more pronounced in the case of pulse deposited wires. High resolution transmission electron microscopy analysis and comparison of differently prepared focused ion beam lamellas reveal that these contrasts are caused by defects in the alternating potential deposition itself and are not induced during the TEM preparation process. The alternating potential mode causes periodic growth thereby inducing different layers with reduced wire thickness/defects at the layer interfaces.

Structure of shikimate kinase, an in vivo essential metabolic enzyme in the nosocomial pathogen Acinetobacter baumannii, in complex with shikimate.

Acinetobacter baumannii is an opportunistic Gram-negative pathogen that is an important cause of healthcare-associated infections exhibiting high mortality rates. Clinical isolates of multidrug-resistant (MDR) and extremely drug-resistant (XDR) A. baumannii strains are increasingly being observed. Compounding this concern is the dearth of new antibacterial agents in late-stage development that are effective against MDR and XDR A. baumannii. As part of an effort to address these concerns, two genes (aroA and aroC) of the shikimate pathway have previously been determined to be essential for the growth and survival of A. baumannii during host infection (i.e. to be essential in vivo). This study expands upon these results by demonstrating that the A. baumannii aroK gene, encoding shikimate kinase (SK), is also essential in vivo in a rat soft-tissue infection model. The crystal structure of A. baumannii SK in complex with the substrate shikimate and a sulfate ion that mimics the binding interactions expected for the ß-phosphate of ATP was then determined to 1.91 Å resolution and the enzyme kinetics were characterized. The flexible shikimate-binding domain and LID region are compared with the analogous regions in other SK crystal structures. The impact of structural differences and sequence divergence between SKs from pathogenic bacteria that may influence antibiotic-development efforts is discussed.

Infrared spectroscopy and density functional theory investigation of calcite, chalk, and coccoliths--do we observe the mineral surface?

We have measured infrared spectra from several types of calcite: chalk, freshly cultured coccoliths produced by three species of algae, natural calcite (Iceland Spar), and two types of synthetic calcite. The most intense infrared band, the asymmetric carbonate stretch vibration, is clearly asymmetric for the coccoliths and the synthetic calcite prepared using the carbonation method. It can be very well fitted by two peaks: a narrow Lorenzian at lower frequency and a broader Gaussian at higher frequency. These two samples both have a high specific surface area. Density functional theory for bulk calcite and several calcite surface systems allows for assignment of the infrared bands. The two peaks that make up the asymmetric carbonate stretch band come from the bulk (narrow Lorenzian) and from a combination of two effects (broad Gaussian): the surface or near surface of calcite and line broadening from macroscopic dielectric effects. We detect water adsorbed on the high surface area synthetic calcite, which permits observation of the chemistry of thin liquid films on calcite using transmission infrared spectroscopy. The combination of infrared spectroscopy and density functional theory also allowed us to quantify the amount of polysaccharides associated with the coccoliths. The amount of polysaccharides left in chalk, demonstrated to be present in other work, is below the IR detection limit, which is 0.5% by mass.

Neuroticism and post-traumatic stress disorder: a prospective investigation.

BACKGROUND: Neuroticism has been consistently correlated with the post-traumatic stress disorder (PTSD) response to traumatic events. Interpretation of these findings is limited by the retrospective nature of these findings: neuroticism was measured after the trauma had occurred. The prospective association of neuroticism with PTSD has not been examined (the relationship of neuroticism with PTSD symptoms was examined in a few prospective studies). We evaluate prospectively the relationship of neuroticism, measured at baseline, with the cumulative occurrence of PTSD during the subsequent 10 years, using data from a longitudinal epidemiological study of young adults. METHOD: A sample of 1007 young adults randomly selected from the membership of a large health maintenance organization in southeast Michigan was assessed at baseline and followed up at 3, 5 and 10 years later. We conducted a series of multinomial logistic regressions to estimate the relative risk (RR) of exposure to trauma and PTSD by neuroticism at baseline, adjusting for history of major depression (n = 990). RESULTS: During the 10-year follow-up, 50.2% of the sample experienced traumatic events and 5.2% developed PTSD. Neuroticism score at baseline increased significantly the RR of PTSD response to trauma. Additional analysis revealed that, among persons with history of major depression at baseline, RR for PTSD associated with neuroticism was equal to the null value of 1, but was increased significantly among those with no history of major depression. CONCLUSIONS: The results confirm the role of neuroticism as diathesis in the PTSD response to traumatic experiences.

Probing the energy barriers and magnetization reversal processes of nanoperforated membrane based percolated media.

Magnetization reversal processes in Co/Pt multilayers prepared on nanoperforated templates are probed by magnetization relaxation measurements. The signature of pinning controlled domain wall movement as expected for percolated media is identified. This contrasts with the nucleation-type reversal mechanism of a Co/Pt reference film prepared on a smooth substrate. A zero field energy barrier of 93kBT is determined by fluctuation field measurements and is elucidated by micromagnetic calculations using the nudged elastic band method. This value is sufficiently large to qualify the material as a promising percolated medium.

Quantitative measurement of the surface self-diffusion on Au nanoparticles by aberration-corrected transmission electron microscopy.

We present a method that allows for a quantitative measurement of the surface self-diffusion on nanostructures, such as nanoparticles, at the atomic scale using aberration-corrected high-resolution transmission electron microscopy (HRTEM). The diffusion coefficient can be estimated by measuring the fluctuation of the atom column occupation at the surface of Au nanoparticles, which is directly observable in temporal sequences of HRTEM images. Both a Au icosahedron and a truncated Au octahedron are investigated, and their diffusion coefficients are found to be in the same order of magnitude, D = 10(-17) to 10(-16) cm(2)/s. It is to be assumed that the measured surface diffusion is affected by the imaging electron beam. This assumption is supported by the observed instability of a (5 × 1) surface reconstruction on a {100} Au facet.

Understanding the metal-carbon interface in FePt catalyzed carbon nanotubes.

Any tip functionalization of carbon nanotubes, for which the relative orientation between their (metallic) catalyst particle and the nanotube axis is essential, requires a detailed knowledge of the nature of the internal interface between the particle and the outgrown tube. In the present work, this interface is characterized with atomic precision using state-of-the-art low-voltage aberration-corrected transmission electron microscopy in combination with molecular dynamics simulations for the case of hard-magnetically terminated carbon nanotubes. Our results indicate that the physical principle based upon which the interfacial metal facet is chosen is a reduction of the desorption energy for carbon.

Critical current scaling and anisotropy in oxypnictide superconductors.

Having succeeded in the fabrication of epitaxial superconducting LaFeAsO(1-x)F(x) thin films we performed an extensive study of electrical transport properties. In the face of multiband superconductivity we can demonstrate that an anisotropic Ginzburg-Landau scaling of the angular dependent critical current densities can be adopted, although being originally developed for single band superconductors. In contrast with single band superconductors the mass anisotropy of LaFeAsO(1-x)F(x) is temperature dependent. A very steep increase of the upper critical field and the irreversibility field can be observed at temperatures below 6 K, indicating that the band with the smaller gap is in the dirty limit. This temperature dependence can be theoretically described by two dominating bands responsible for superconductivity. A pinning force scaling provides insight into the prevalent pinning mechanism and can be specified in terms of the Kramer model.

Morphologic magnetic resonance imaging features of therapy-induced cerebral necrosis.

To describe the morphologic magnetic resonance imaging (MRI) findings in histologically proven therapy-induced cerebral necrosis. We retrospectively reviewed the morphologic MRI findings in patients with therapy-induced cerebral necrosis. Images were reviewed for size, location, and characteristics of signal intensity abnormalities and T1-contrast enhancement. Images were also assessed for mass effect, necrosis, cyst, atrophy, cortical thinning, and leukoencephalopathy. The individual imaging characteristics were correlated with clinical and treatment variables. There were 44 patients. Seventy percent had a glioma, all patients had received radiation, and 57% had received chemotherapy in close proximity to radiation. All images demonstrated contrast enhancement, predominantly in the white matter. Enhancement was present in the periventricular/subependymal region in 50% of cases and the corpus callosum in 27%. The most common pattern of lesion peripheral enhancement was "spreading wavefront" and of interior enhancement was "Swiss cheese/soap bubble." The enhancing lesion was single in 60% of cases. Mass effect was present in 93% of patients. Location and patterns of enhancement were significantly associated with the interval from brain radiation to the diagnosis of therapy-induced cerebral necrosis, tumor histology, patient age, type of radiation, and administration of systemic chemotherapy. This is the largest study of the morphologic conventional MRI findings in pathologically confirmed therapy-induced cerebral necrosis. We characterized the imaging findings in a variety of tumor types following a variety of radiation treatments and other antineoplastic therapy. These findings may be of value in identifying therapy-induced cerebral necrosis in patients treated for a brain tumor.

Localized primary melanoma of male urethra with a 4-year follow up.

The objective is to perform a case report of primary melanoma of urethra in a male patient from a Teaching Hospital in Campinas, SP - Brazil. Male, 79 years of age, with blackened lesion on the meatus of the urethra with 1.5 cm of dimension, that could be palpated on the fossa navicularis region associated to an irregular lesion on the region of and the foreskin. The biopsy showed a malignant neoplasia. A partial penectomy with oncological margin of 2 cm was performed with a bilateral deep inguinal linfadenectomy. A follow up showed no recurrence of the disease.

The K1 capsular polysaccharide of Acinetobacter baumannii strain 307-0294 is a major virulence factor.

Acinetobacter baumannii is a pathogen of increasing medical importance with a propensity to be multidrug resistant, thereby making treatment challenging. Little is known of virulence traits in A. baumannii. To identify virulence factors and potential drug targets, random transposon (Tn) mutants derived from the A. baumannii strain AB307-0294 were screened to identify genes essential for growth in human ascites fluid in vitro, an inflammatory exudative fluid. These studies led to the identification of two genes that were predicted to be required for capsule polymerization and assembly. The first, ptk, encodes a putative protein tyrosine kinase (PTK), and the second, epsA, encodes a putative polysaccharide export outer membrane protein (EpsA). Monoclonal antibodies used in flow cytometric and Western analyses confirmed that these genes are required for a capsule-positive phenotype. A capsule-positive phenotype significantly optimized growth in human ascites fluid, survival in human serum, and survival in a rat soft tissue infection model. Importantly, the clearance of the capsule-minus mutants AB307.30 (ptk mutant, capsule minus) and AB307.45 (epsA mutant, capsule minus) was complete and durable. These data demonstrated that the K1 capsule from AB307-0294 was an important protectin. Further, these data suggested that conserved proteins, which contribute to the capsule-positive phenotype, are potential antivirulence drug targets. Therefore, the results from this study have important biologic and translational implications and, to the best of our knowledge, are the first to address the role of capsule in the pathogenesis of A. baumannii infection.

Defective lymphopoiesis in bone marrow of motheaten (me/me) and viable motheaten (mev/mev) mutant mice. I. Analysis of development of prothymocytes, early B lineage cells, and terminal deoxynucleotidyl transferase-positive cells.

This study identifies defects in the early stages of lymphopoiesis that may contribute to the abnormalities in the development and/or function of peripheral T and B lymphocytes in mice homozygous for the motheaten (me/me) and viable motheaten (mev/mev) mutations. The results indicate that in me/me and mev/mev mice prothymocytes in bone marrow are present in essentially normal numbers, as determined by intrathymic injection, but apparently lack the ability to home effectively to the thymus, as determined by intravenous transfer; early B lineage cells in bone marrow, identified by the B220 antigen, are markedly depleted, including immature B cells (sIg+), pre-B cells (cIg+, sIg-), and pro-B cells (B220+, cIg-, sIg-); TdT+ bone marrow cells, especially a subset that expresses the B220 B lineage antigen, are markedly depleted by two weeks of age; normal numbers of TdT+ thymocytes are present during the first 3 wk of postnatal life, but rapidly decrease thereafter. The results further indicate that neither the defective thymus homing capacity of prothymocytes nor the deficiency of TdT+ bone marrow cells is due to autoantibodies. The possible relationship of the defective development of lymphoid precursor cells to the premature onset of thymic involution and to the abnormalities of peripheral T and B lymphocytes in me/me and mev/mev mice is discussed; as are the results of in vitro studies (presented in a companion paper), which suggest that a primary defect in the stromal microenvironment of the bone marrow is responsible for the abnormal development of the lymphoid precursor cells.

Severe acute respiratory syndrome coronavirus nsp9 dimerization is essential for efficient viral growth.

The severe acute respiratory syndrome coronavirus (SARS-CoV) devotes a significant portion of its genome to producing nonstructural proteins required for viral replication. SARS-CoV nonstructural protein 9 (nsp9) was identified as an essential protein with RNA/DNA-binding activity, and yet its biological function within the replication complex remains unknown. Nsp9 forms a dimer through the interaction of parallel alpha-helices containing the protein-protein interaction motif GXXXG. In order to study the role of the nsp9 dimer in viral reproduction, residues G100 and G104 at the helix interface were targeted for mutation. Multi-angle light scattering measurements indicated that G100E, G104E, and G104V mutants are monomeric in solution, thereby disrupting the dimer. However, electrophoretic mobility assays revealed that the mutants bound RNA with similar affinity. Further experiments using fluorescence anisotropy showed a 10-fold reduction in RNA binding in the G100E and G104E mutants, whereas the G104V mutant had only a 4-fold reduction. The structure of G104E nsp9 was determined to 2.6-A resolution, revealing significant changes at the dimer interface. The nsp9 mutations were introduced into SARS-CoV using a reverse genetics approach, and the G100E and G104E mutations were found to be lethal to the virus. The G104V mutant produced highly debilitated virus and eventually reverted back to the wild-type protein sequence through a codon transversion. Together, these data indicate that dimerization of SARS-CoV nsp9 at the GXXXG motif is not critical for RNA binding but is necessary for viral replication.

Adaptive modulations of martensites.

Modulated phases occur in numerous functional materials like giant ferroelectrics and magnetic shape-memory alloys. To understand the origin of these phases, we employ and generalize the concept of adaptive martensite. As a starting point, we investigate the coexistence of austenite, adaptive 14M phase, and tetragonal martensite in Ni-Mn-Ga magnetic shape-memory alloy epitaxial films. We show that the modulated martensite can be constructed from nanotwinned variants of the tetragonal martensite phase. By combining the concept of adaptive martensite with branching of twin variants, we can explain key features of modulated phases from a microscopic view. This includes metastability, the sequence of 6M-10M-14M-NM intermartensitic transitions, and the magnetocrystalline anisotropy.

Dynamical response and confinement of the electrons at the LaAlO3/SrTiO3 interface.

With infrared ellipsometry and transport measurements we investigated the electrons at the interface between LaAlO3 and SrTiO3. We obtained a sheet carrier concentration of N(s) approximately = 5-9x10(13) cm(-2), an effective mass of m*=3.2+/-0.4m(e), and a strongly frequency dependent mobility. The latter are similar as in bulk SrTi(1-x)Nb(x)O3 and therefore suggestive of polaronic correlations. We also determined the vertical concentration profile which has a strongly asymmetric shape with a rapid initial decay over the first 2 nm and a pronounced tail that extends to about 11 nm.

High upper critical fields and evidence of weak-link behavior in superconducting LaFeAsO1-xFx thin films.

Superconducting LaFeAsO1-xFx thin films were grown on single crystalline LaAlO3 substrates with critical temperatures (onset) up to 28 K. Resistive measurements in high magnetic fields up to 40 T reveal a paramagnetically limited upper critical field mu{0}H{c2}(0) around 77 T and a remarkable steep slope of -6.2 T K-1 near T{c}. From transport measurements we observed weak-link behavior in low magnetic fields and evidence for a broad reversible regime.

Cryptosporidiosis in people: it's not just about the cows.

Cryptosporidiosis is one of the most common causes of infectious diarrhea in people. Although dairy calves are high-risk hosts, the role of other livestock, pets, and humans in the disease should not be underestimated. Some Cryptosporidium species and strains are specific to people, others are specific to animals while some are zoonotic pathogens. Cryptosporidium hominis is the species responsible for the majority of human cases in the United States, Sub-Saharan Africa, and Asia, while Cryptosporidium parvum accounts for more human cases in Europe and particularly in the United Kingdom. A deeper understanding of Cryptosporidium host range, reservoirs, and transmission is needed to develop preventive strategies to protect the general public.

Full tunability of strain along the fcc-bcc bain path in epitaxial films and consequences for magnetic properties.

Strained coherent film growth is commonly either limited to ultrathin films or low strains. Here, we present an approach to achieve high strains in thicker films, by using materials with inherent structural instabilities. As an example, 50 nm thick epitaxial films of the Fe70Pd30 magnetic shape memory alloy are examined. Strained coherent growth on various substrates allows us to adjust the tetragonal distortion from c/a{bct}=1.09 to 1.39, covering most of the Bain transformation path from fcc to bcc crystal structure. Magnetometry and x-ray circular dichroism measurements show that the Curie temperature, orbital magnetic moment, and magnetocrystalline anisotropy change over broad ranges.

p53 binding protein 1 (53BP1) is an early participant in the cellular response to DNA double-strand breaks.

p53 binding protein 1 (53BP1), a protein proposed to function as a transcriptional coactivator of the p53 tumor suppressor, has BRCT domains with high homology to the Saccharomyces cerevisiae Rad9p DNA damage checkpoint protein. To examine whether 53BP1 has a role in the cellular response to DNA damage, we probed its intracellular localization by immunofluorescence. In untreated primary cells and U2OS osteosarcoma cells, 53BP1 exhibited diffuse nuclear staining; whereas, within 5-15 min after exposure to ionizing radiation (IR), 53BP1 localized at discreet nuclear foci. We propose that these foci represent sites of processing of DNA double-strand breaks (DSBs), because they were induced by IR and chemicals that cause DSBs, but not by ultraviolet light; their peak number approximated the number of DSBs induced by IR and decreased over time with kinetics that parallel the rate of DNA repair; and they colocalized with IR-induced Mre11/NBS and gamma-H2AX foci, which have been previously shown to localize at sites of DSBs. Formation of 53BP1 foci after irradiation was not dependent on ataxia-telangiectasia mutated (ATM), Nijmegen breakage syndrome (NBS1), or wild-type p53. Thus, the fast kinetics of 53BP1 focus formation after irradiation and the lack of dependency on ATM and NBS1 suggest that 53BP1 functions early in the cellular response to DNA DSBs.