Rock Magnetic and Remanence Properties of Both Synthetic Martian Basaltic Intrusions and Dropstones Along the East Antarctic Margin, to Aid in the Understanding of the Carriers of Crustal Magnetic Anomalies

This thesis examines potential carriers of magnetic anomalies found in remote areas where direct sampling is impossible. The areas examined are the southern hemisphere of Mars and the East Antarctic Margin. We examine the rock magnetic and remanence properties of synthetic Mars basalts and Antarctic dropstones, to predict the type and intensity of anomaly they would produce. The anomalies measured within the Martian crust are entirely remanent magnetization and are remarkably orders of magnitude stronger than the strongest terrestrial anomaly. Two basalt compositions denoted M-type and T-type, deemed relevant to the crust of Mars, were synthesized to examine contrasts in rock magnetic and remanence properties following identical thermal histories and oxygen fugacity conditions. We examine the magnetic mineral assemblages produced and assess if they are efficient remanence carriers. The composition denoted T-type is rich in Al and poor in Fe, reflecting constraints provided by thermal emission spectroscopy that the Martian crust is somewhat terrestrial in character. The M-type composition is poor in Al and rich in Fe, reflecting the composition of basaltic liquid in equilibrium with Martian meteorite phase assemblages. The two compositions are identical with respect to MgO, SÌO2 , and TÌO2 . Batches of each composition were cooled from above 1200 °C to 1070 °C at 4 °C/h and annealed at 1070°C for 100 h, then quenched. Samples were then held at 650°C for periods ranging from 21 to 158 days under quartz-fayalite-magnetite (QFM)/02 buffer conditions, then quenched. The experimental conditions are germane to shallow igneous intrusions, which might be a significant volumetric fraction of the Martian crust and potential carriers of crustal magnetic anomalies, and provide an important contrast to a previous set of fast-cooled (3-230 °C/h) basalts our group performed on the same two compositions. M-type samples contain Fe-Ti-Al-Mg oxide grains 40-50 pm in diameter with skeletal and equant euhedral morphologies. T-type samples contain equant euhedral Fe- Ti-Al-Mg oxides with grain diameters ranging from 15-30 pm as well as elongated anhedral ilmenite grains. For M-type samples both the starting material and the samples annealed at 650 °C have narrow multidomain hysteresis loops. T-type starting materials and samples annealed at 650 °C have pseudo single domain (PSD) hysteresis loops, but the annealed samples plot lower and to the right within the PSD field on a Day plot, indicating coarser magnetic grains. Alternating field demagnetization of anhysteretic remanent magnetization (ARM) shows median destructive fields \u3c 10 mT. M-type samples exhibited higher magnetic susceptibility and intensity of remanence than T-type samples. Both M-type and T-type samples carry an intense natural remanent magnetization (NRM). The NRM is inferred to be a thermoremanent magnetization (TRM) acquired during quenching and air-cooling after the 650 °C anneal. NRM values range from 0.03 to 170 mAm2/kg for M-type samples and 0.005 to 47 mAm2/kg for Ttype samples, values comparable to those observed in rapidly cooled synthetic basalts of the same chemical composition. However, the slow- cooled samples have a much “softer” coercivity spectrum. The multi-domain magnetic mineral assemblage suggests that while intrusions generated by slow-cooled basaltic melts are capable of carrying intense TRMs they may be less stable over geologic time. The second portion of this study presents a catalog of the magnetic and petrographic properties of dropstones collected by United States Antarctic Program cruise NBP01-01. These dropstones provide direct samples of the subglacial geology and provide a range of susceptibility values, intensity of natural remanent magnetization, and description of the carriers of magnetization, which can help in the interpretation of magnetic anomaly surveys. Samples were collect in three main regions along the East Antarctic Margin, including the George V Coast, Prydz Bay, and MacRobertson Land. The samples are examined and classified optically through thin section analysis, and characterized magnetically through magnetic susceptibility, natural remanent magnetization, magnetic hysteresis, scanning electron microscopy and thermomagnetic measurements. The potential for each sample to generate a dominant induced or remnant magnetization was calculated using the Koenigsberger ratio, Q; where Q = Total Remnant Magnetization / Total Induced Magnetization. The majority of magnetic minerals are found in low abundances (\u3c1%) in granitic and metamorphic rocks and displayed Q values less than 1, suggesting they would produce induced dominated anomalies. The exception to this are two mafic igneous rocks, vesicular basalt and dolerite, that possess single domain magnetic minerals and recorded remanences several orders of magnitude higher than other east Antarctic rock types

High temperature fiber optic microphone having a pressure-sensing reflective membrane under tensile stress

A fiber optic microphone is provided for measuring fluctuating pressures. An optical fiber probe having at least one transmitting fiber for transmitting light to a pressure-sensing membrane and at least one receiving fiber for receiving light reflected from a stretched membrane is provided. The pressure-sensing membrane may be stretched for high frequency response. Further, a reflecting surface of the pressure-sensing membrane may have dimensions which substantially correspond to dimensions of a cross section of the optical fiber probe. Further, the fiber optic microphone can be made of materials for use in high temperature environments, for example greater than 1000 F. A fiber optic probe is also provided with a backplate for damping membrane motion. The backplate further provides a means for on-line calibration of the microphone

Microevolution of serial clinical isolates of Cryptococcus neoformans var. grubii and C. gattii

This is the final version. Available from the publisher via the DOI in this record.The pathogenic species of Cryptococcus are a major cause of mortality owing to severe infections in immunocompromised as well as immunocompetent individuals. Although antifungal treatment is usually effective, many patients relapse after treatment, and in such cases, comparative analyses of the genomes of incident and relapse isolates may reveal evidence of determinative, microevolutionary changes within the host. Here, we analyzed serial isolates cultured from cerebrospinal fluid specimens of 18 South African patients with recurrent cryptococcal meningitis. The time between collection of the incident isolates and collection of the relapse isolates ranged from 124 days to 290 days, and the analyses revealed that, during this period within the patients, the isolates underwent several genetic and phenotypic changes. Considering the vast genetic diversity of cryptococcal isolates in subSaharan Africa, it was not surprising to find that the relapse isolates had acquired different genetic and correlative phenotypic changes. They exhibited various mechanisms for enhancing virulence, such as growth at 39°C, adaptation to stress, and capsule production; a remarkable amplification of ERG11 at the native and unlinked locus may provide stable resistance to fluconazole. Our data provide a deeper understanding of the microevolution of Cryptococcus species under pressure from antifungal chemotherapy and host immune responses. This investigation clearly suggests a promising strategy to identify novel targets for improved diagnosis, therapy, and prognosis.Wellcome TrustNational Institute of Allergy and Infectious Disease

Self-similarity, small-world, scale-free scaling, disassortativity, and robustness in hierarchical lattices

In this paper, firstly, we study analytically the topological features of a family of hierarchical lattices (HLs) from the view point of complex networks. We derive some basic properties of HLs controlled by a parameter $q$. Our results show that scale-free networks are not always small-world, and support the conjecture that self-similar scale-free networks are not assortative. Secondly, we define a deterministic family of graphs called small-world hierarchical lattices (SWHLs). Our construction preserves the structure of hierarchical lattices, while the small-world phenomenon arises. Finally, the dynamical processes of intentional attacks and collective synchronization are studied and the comparisons between HLs and Barab{\'asi}-Albert (BA) networks as well as SWHLs are shown. We show that degree distribution of scale-free networks does not suffice to characterize their synchronizability, and that networks with smaller average path length are not always easier to synchronize.Comment: 26 pages, 8 figure

Tracing Genetic Exchange and Biogeography of Cryptococcus neoformans var. grubii at the Global Population Level.

Cryptococcus neoformans var. grubii is the causative agent of cryptococcal meningitis, a significant source of mortality in immunocompromised individuals, typically HIV/AIDS patients from developing countries. Despite the worldwide emergence of this ubiquitous infection, little is known about the global molecular epidemiology of this fungal pathogen. Here we sequence the genomes of 188 diverse isolates and characterized the major subdivisions, their relative diversity and the level of genetic exchange between them. While most isolates of C. neoformans var. grubii belong to one of three major lineages (VNI, VNII, and VNB), some haploid isolates show hybrid ancestry including some that appear to have recently interbred, based on the detection of large blocks of each ancestry across each chromosome. Many isolates display evidence of aneuploidy, which was detected for all chromosomes. In diploid isolates of C. neoformans var. grubii (serotype A/A) and of hybrids with C. neoformans var. neoformans (serotype A/D) such aneuploidies have resulted in loss of heterozygosity, where a chromosomal region is represented by the genotype of only one parental isolate. Phylogenetic and population genomic analyses of isolates from Brazil reveal that the previously 'African' VNB lineage occurs naturally in the South American environment. This suggests migration of the VNB lineage between Africa and South America prior to its diversification, supported by finding ancestral recombination events between isolates from different lineages and regions. The results provide evidence of substantial population structure, with all lineages showing multi-continental distributions demonstrating the highly dispersive nature of this pathogen

Genetic diversity and microevolution in clinical Cryptococcus isolates from Cameroon.

Cryptococcal meningitis is the second most common cause of death in people living with HIV/AIDS, yet we have a limited understanding of how cryptococcal isolates change over the course of infection. Cryptococcal infections are environmentally acquired, and the genetic diversity of these infecting isolates can also be geographically linked. Here, we employ whole genome sequences for 372 clinical Cryptococcus isolates from 341 patients with HIV-associated cryptococcal meningitis obtained via a large clinical trial, across both Malawi and Cameroon, to enable population genetic comparisons of isolates between countries. We see that isolates from Cameroon are highly clonal, when compared to those from Malawi, with differential rates of disruptive variants in genes with roles in DNA binding and energy use. For a subset of patients (22) from Cameroon, we leverage longitudinal sampling, with samples taken at days 7 and 14 post enrolment, to interrogate the genetic changes that arise over the course of infection, and the genetic diversity of isolates within patients. We see disruptive variants arising over the course of infection in several genes, including the phagocytosis regulating transcription factor GAT204. In addition, in 13% of patients sampled longitudinally we see evidence for mixed infections. This approach identifies geographically linked genetic variation, signatures of microevolution, and evidence for mixed infections across a clinical cohort of patients affected by cryptococcal meningitis in Central Africa

Comparing genomic variant identification protocols for Candida auris.

Genomic analyses are widely applied to epidemiological, population genetic and experimental studies of pathogenic fungi. A wide range of methods are employed to carry out these analyses, typically without including controls that gauge the accuracy of variant prediction. The importance of tracking outbreaks at a global scale has raised the urgency of establishing high-accuracy pipelines that generate consistent results between research groups. To evaluate currently employed methods for whole-genome variant detection and elaborate best practices for fungal pathogens, we compared how 14 independent variant calling pipelines performed across 35 Candida auris isolates from 4 distinct clades and evaluated the performance of variant calling, single-nucleotide polymorphism (SNP) counts and phylogenetic inference results. Although these pipelines used different variant callers and filtering criteria, we found high overall agreement of SNPs from each pipeline. This concordance correlated with site quality, as SNPs discovered by a few pipelines tended to show lower mapping quality scores and depth of coverage than those recovered by all pipelines. We observed that the major differences between pipelines were due to variation in read trimming strategies, SNP calling methods and parameters, and downstream filtration criteria. We calculated specificity and sensitivity for each pipeline by aligning three isolates with chromosomal level assemblies and found that the GATK-based pipelines were well balanced between these metrics. Selection of trimming methods had a greater impact on SAMtools-based pipelines than those using GATK. Phylogenetic trees inferred by each pipeline showed high consistency at the clade level, but there was more variability between isolates from a single outbreak, with pipelines that used more stringent cutoffs having lower resolution. This project generated two truth datasets useful for routine benchmarking of C. auris variant calling, a consensus VCF of genotypes discovered by 10 or more pipelines across these 35 diverse isolates and variants for 2 samples identified from whole-genome alignments. This study provides a foundation for evaluating SNP calling pipelines and developing best practices for future fungal genomic studies