The complex AGM, periods of elliptic curves over C and complex elliptic logarithms

We give an account of the complex Arithmetic-Geometric Mean (AGM), as first studied by Gauss, together with details of its relationship with the theory of elliptic curves over \C, their period lattices and complex parametrisation. As an application, we present efficient methods for computing bases for the period lattices and elliptic logarithms of points, for arbitrary elliptic curves defined over \C. Earlier authors have only treated the case of elliptic curves defined over the real numbers; here, the multi-valued nature of the complex AGM plays an important role. Our method, which we have implemented in both \Magma\ and \Sage, is illustrated with several examples using elliptic curves defined over number fields with real and complex embeddings.Comment: The addional file elog_ex.sage contains a Sage script for the examples in the last section of the paper, and the file elog_ex.out contains the result of running that script with Sage version 5.

Performance and robustness analysis for structured uncertainty

This paper introduces a nonconservative measure of performance for linear feedback systems in the face of structured uncertainty. This measure is based on a new matrix function, which we call the Structured Singular Value

A cancer cell-line titration series for evaluating somatic classification.

BackgroundAccurate detection of somatic single nucleotide variants and small insertions and deletions from DNA sequencing experiments of tumour-normal pairs is a challenging task. Tumour samples are often contaminated with normal cells confounding the available evidence for the somatic variants. Furthermore, tumours are heterogeneous so sub-clonal variants are observed at reduced allele frequencies. We present here a cell-line titration series dataset that can be used to evaluate somatic variant calling pipelines with the goal of reliably calling true somatic mutations at low allele frequencies.ResultsCell-line DNA was mixed with matched normal DNA at 8 different ratios to generate samples with known tumour cellularities, and exome sequenced on Illumina HiSeq to depths of >300×. The data was processed with several different variant calling pipelines and verification experiments were performed to assay >1500 somatic variant candidates using Ion Torrent PGM as an orthogonal technology. By examining the variants called at varying cellularities and depths of coverage, we show that the best performing pipelines are able to maintain a high level of precision at any cellularity. In addition, we estimate the number of true somatic variants undetected as cellularity and coverage decrease.ConclusionsOur cell-line titration series dataset, along with the associated verification results, was effective for this evaluation and will serve as a valuable dataset for future somatic calling algorithm development. The data is available for further analysis at the European Genome-phenome Archive under accession number EGAS00001001016. Data access requires registration through the International Cancer Genome Consortium's Data Access Compliance Office (ICGC DACO)

Database management and analysis of fisheries in Illinois: Final report, 1 March 1999-28 February 2002

Issued May 2002; F-69-RReport issued on: May 200

Regional perturbation of gene transcription is associated with intrachromosomal rearrangements and gene fusion transcripts in high grade ovarian cancer.

Genomic rearrangements are a hallmark of cancer biology and progression, allowing cells to rapidly transform through alterations in regulatory structures, changes in expression patterns, reprogramming of signaling pathways, and creation of novel transcripts via gene fusion events. Though functional gene fusions encoding oncogenic proteins are the most dramatic outcomes of genomic rearrangements, we investigated the relationship between rearrangements evidenced by fusion transcripts and local expression changes in cancer using transcriptome data alone. 9,953 gene fusion predictions from 418 primary serious ovarian cancer tumors were analyzed, identifying depletions of gene fusion breakpoints within coding regions of fused genes as well as an N-terminal enrichment of breakpoints within fused genes. We identified 48 genes with significant fusion-associated upregulation and furthermore demonstrate that significant regional overexpression of intact genes in patient transcriptomes occurs within 1 megabase of 78 novel gene fusions that function as central markers of these regions. We reveal that cancer transcriptomes select for gene fusions that preserve protein and protein domain coding potential. The association of gene fusion transcripts with neighboring gene overexpression supports rearrangements as mechanism through which cancer cells remodel their transcriptomes and identifies a new way to utilize gene fusions as indicators of regional expression changes in diseased cells with only transcriptomic data

Topological organization of whole-brain white matter in HIV infection

Infection with human immunodeficiency virus (HIV) is associated with neuroimaging alterations. However, little is known about the topological organization of whole-brain networks and the corresponding association with cognition. As such, we examined structural whole-brain white matter connectivity patterns and cognitive performance in 29 HIV+ young adults (mean age = 25.9) with limited or no HIV treatment history. HIV+ participants and demographically similar HIV− controls (n = 16) residing in South Africa underwent magnetic resonance imaging (MRI) and neuropsychological testing. Structural network models were constructed using diffusion MRI-based multifiber tractography and T(1)-weighted MRI-based regional gray matter segmentation. Global network measures included whole-brain structural integration, connection strength, and structural segregation. Cognition was measured using a neuropsychological global deficit score (GDS) as well as individual cognitive domains. Results revealed that HIV+ participants exhibited significant disruptions to whole-brain networks, characterized by weaker structural integration (characteristic path length and efficiency), connection strength, and structural segregation (clustering coefficient) than HIV− controls (p < 0.05). GDSs and performance on learning/recall tasks were negatively correlated with the clustering coefficient (p < 0.05) in HIV+ participants. Results from this study indicate disruption to brain network integrity in treatment-limited HIV+ young adults with corresponding abnormalities in cognitive performance

Exome sequencing identifies nonsegregating nonsense ATM and PALB2 variants in familial pancreatic cancer.

We sequenced 11 germline exomes from five families with familial pancreatic cancer (FPC). One proband had a germline nonsense variant in ATM with somatic loss of the variant allele. Another proband had a nonsense variant in PALB2 with somatic loss of the variant allele. Both variants were absent in a relative with FPC. These findings question the causal mechanisms of ATM and PALB2 in these families and highlight challenges in identifying the causes of familial cancer syndromes using exome sequencing

NGOs and the Promotion of the Sexual and Reproductive Rights of Girls and Young Women with Disabilities in Zimbabwe

This case study investigates strategies used by the NGO Leonard Cheshire Disability Zimbabwe (LCDZ) to promote the SRHRs of girls and young women with disabilities in Zimbabwe. The findings show that LCDZ employed a combination of six strategies. These are: (1) building practical knowledge on SRHRs; (2) increasing community awareness and sensitivity; (3) providing SRHRs-related education; (4) enhancing access to justice and related services for survivors of sexual violence; (5) delivering assistive devices; and (6) promoting the livelihoods and economic empowerment. LCDZ made use of multi-stakeholder partnerships to implement these strategies, leveraging complementary skills and experience in the promotion of SRHRs. In each of these strategies, girls and young women with disabilities are the target group, with other stakeholders brought together to support them

Metals and Bacteria Partitioning to Various Size Particles in Ballona Creek Storm Water Runoff

Many storm water best management practice (BMP) devices function primarily by capturing particulate matter to take advantage of the well‐documented association between storm water particles and pollutants. The hydrodynamic separation or settling methods used by most BMP devices are most effective at capturing medium to large particles; however, these may not be the most predominant particles associated with urban runoff. The present study examined particle size distribution in storm water runoff from an urban watershed in southern California and investigated the pollutant–particle associations of metals (Cu, Pb, Ni, and Zn) and bacteria (enterococci and Escherichia coli). During small storm events (≤0.7 cm rain), the highest concentration of pollutants were associated with a \u3c6‐µm filter fraction, which accounted for 70% of the per storm contaminant mass but made up more than 20% of the total particle mass. The pollutant–particle association changed with storm size. Most pollutant mass was associated with \u3e35 µm size particles during a 5‐cm rain event. These results suggest that much of the contaminant load in storm water runoff will not be captured by the most commonly used BMP devices, because most of these devices (e.g., hydrodynamic separators) are unable to capture particles smaller than 75 µm