Publications by authors named "S K Krieger"
Background And Objective: The role of genetic variants in response to systemic therapy in muscle-invasive bladder cancer (MIBC) is still elusive. We assessed variations in genes involved in DNA damage repair (DDR) before and after cisplatin-based neoadjuvant chemotherapy (NAC) and correlation of alteration patterns with DNA damage and response to therapy.
Methods: Matched tissue from 46 patients with MIBC was investigated via Ion Torrent-based next-generation sequencing using a self-designed panel of 30 DDR genes.
Spinal cord disease is important in most people with multiple sclerosis, but assessment remains less emphasized in patient care, basic and clinical research and therapeutic trials. The North American Imaging in Multiple Sclerosis Spinal Cord Interest Group was formed to determine and present the contemporary landscape of multiple sclerosis spinal cord evaluation, further existing and advanced spinal cord imaging techniques, and foster collaborative work. Important themes arose: (i) multiple sclerosis spinal cord lesions (differential diagnosis, association with clinical course); (ii) spinal cord radiological-pathological associations; (iii) 'critical' spinal cord lesions; (iv) multiple sclerosis topographical model; (v) spinal cord atrophy; and (vi) automated and special imaging techniques.
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- Solving mRNA transcript structures is challenging with traditional methods, but long-read sequencing addresses this by providing direct sequence information.
- A new targeted enrichment method was developed to capture transcripts of genes related to hereditary breast and ovarian cancer, leading to the identification of 1,231 unique transcripts in eight patients.
- The SOSTAR pipeline successfully annotated transcript structures and discovered key splicing events, including the identification of a retrotransposon related to unexplained inheritance cases.
Perhaps the most fundamental model in synthetic and systems biology for inferring pathways in metabolic reaction networks is a metabolic : a system of reactions that starts from a set of source compounds and produces a set of target molecules, while conserving or not depleting intermediate metabolites. Finding a shortest factory-that minimizes a sum of real-valued weights on its reactions to infer the most likely pathway-is NP-complete. The current state-of-the-art for shortest factories solves a mixed-integer linear program with a major drawback: it requires the user to set a critical parameter, where too large a value can make optimal solutions infeasible, while too small a value can yield degenerate solutions due to numerical error.
View Article and Find Full Text PDFObjective: Evaluate the real-world effect of dimethyl fumarate (DMF) on subclinical biomarkers in patients with relapsing-remitting multiple sclerosis (RRMS) and compare with results from clinical trials.
Methods: Magnetic resonance imaging (MRI) data from 102 RRMS patients were retrospectively collected and processed using icobrain to assess brain atrophy and to assist semi-manual lesion count.
Results: Mean (±SD) annualized percent brain volume change in the first 3 years after DMF-initiation were: -0.