Minimum Spanning Tree under Explorable Uncertainty in Theory and Experiments

We consider the minimum spanning tree (MST) problem in an uncertainty model where uncertain edge weights can be explored at extra cost. The task is to find an MST by querying a minimum number of edges for their exact weight. This problem has received quite some attention from the algorithms theory community. In this paper, we conduct the first practical experiments for MST under uncertainty, theoretically compare three known algorithms, and compare theoretical with practical behavior of the algorithms. Among others, we observe that the average performance and the absolute number of queries are both far from the theoretical worst-case bounds. Furthermore, we investigate a known general preprocessing procedure and develop an implementation thereof that maximally reduces the data uncertainty. We also characterize a class of instances that is solved completely by our preprocessing. Our experiments are based on practical data from an application in telecommunications and uncertainty instances generated from the standard TSPLib graph library

Haley Johnson, interviewed by Nicole Vazquez

Haley Johnson graduated with a Bachelor\u27s degree in Interdisciplinary Arts for Children and a minor in Studio Arts. She worked as a Residence Assistant throughout her time as an undergraduate student. Since her graduation she has worked as a Residence Hall Director at Bramley, Thompson, and Mortimer Hall. As of November 2019, she currently holds that position at Mortimer Hall

Breaking the paradigm: Dr Insight empowers signature-free, enhanced drug repurposing

Motivation: Transcriptome-based computational drug repurposing has attracted considerable interest by bringing about faster and more cost-effective drug discovery. Nevertheless, key limitations of the current drug connectivity-mapping paradigm have been long overlooked, including the lack of effective means to determine optimal query gene signatures. Results: The novel approach Dr Insight implements a frame-breaking statistical model for the ‘hand-shake’ between disease and drug data. The genome-wide screening of concordantly expressed genes (CEGs) eliminates the need for subjective selection of query signatures, added to eliciting better proxy for potential disease-specific drug targets. Extensive comparisons on simulated and real cancer datasets have validated the superior performance of Dr Insight over several popular drug-repurposing methods to detect known cancer drugs and drug–target interactions. A proof-of-concept trial using the TCGA breast cancer dataset demonstrates the application of Dr Insight for a comprehensive analysis, from redirection of drug therapies, to a systematic construction of disease-specific drug-target networks

Methods for Scarless, Selection-Free Generation of Human Cells and Allele-Specific Functional Analysis of Disease-Associated SNPs and Variants of Uncertain Significance.

With the continued emergence of risk loci from Genome-Wide Association studies and variants of uncertain significance identified from patient sequencing, better methods are required to translate these human genetic findings into improvements in public health. Here we combine CRISPR/Cas9 gene editing with an innovative high-throughput genotyping pipeline utilizing KASP (Kompetitive Allele-Specific PCR) genotyping technology to create scarless isogenic cell models of cancer variants in ~1 month. We successfully modeled two novel variants previously identified by our lab in the PALB2 gene in HEK239 cells, resulting in isogenic cells representing all three genotypes for both variants. We also modeled a known functional risk SNP of colorectal cancer, rs6983267, in HCT-116 cells. Cells with extremely low levels of gene editing could still be identified and isolated using this approach. We also introduce a novel molecular assay, ChIPnQASO (Chromatin Immunoprecipitation and Quantitative Allele-Specific Occupation), which uses the same technology to reveal allele-specific function of these variants at the DNA-protein interaction level. We demonstrated preferential binding of the transcription factor TCF7L2 to the rs6983267 risk allele over the non-risk. Our pipeline provides a platform for functional variant discovery and validation that is accessible and broadly applicable for the progression of efforts towards precision medicine

Extramedullary plasmacytoma of the uterine cervix arising in an asymptomatic 46-year-old female

An extramedullary plasmacytoma is a rare type of plasma cell tumour that can be found in soft tissues throughout the body. The most common location for an extramedullary plasmacytoma is in the head and neck region. Few case reports have previously documented patients with an extramedullary plasmacytoma within the female genital tract. We report a case of a healthy and asymptomatic 46-year-old female who presented to Colposcopy Clinic with a finding of low-grade squamous intraepithelial lesion seen on a routine Pap smear. She was found to have a cervical polyp that was excised. Pathology revealed diffuse sheets of atypical plasma cells with lambda light chain restriction. She was referred to Hematology for extensive work-up as the pathology finding was concerning for a plasma cell neoplasm. Staging investigations, including bone marrow biopsy, skeletal survey, whole body PET-CT scan, serum protein electrophoresis, and serum free light chain testing, were all negative. Surgical resection with a hysterectomy was recommended as the most appropriate course of management. The treatment approach is consistent with guidelines outlined in the literature, whereby extramedullary plasmacytomas, which arise outside of the head and neck region and have clear margins, should undergo surgical resection. Extramedullary plasmacytomas carry a risk of progressing to systemic disease, such as multiple myeloma, making it crucial that these patients be followed with routine surveillance to achieve the most optimal long term survival outcome

Tour de Franzia

Tour de France? Kind of boring. Tour de Franzia? Definitely not boring. Allow me to introduce you to the best drinking game on two wheels

Examining the dynamics of social cohesion: A call for a different perspective on scaling impacts of real-world laboratories

Social cohesion is an important impact category for scaling real-world laboratory experiments. This idea has been largely overlooked in the transformative research debate. Based on observations within real-world laboratories that focused on iterative, co-creative, and practice-based climate change adaptation, we identify social cohesion, first, as a prerequisite for real-world laboratory impacts. Second, social cohesion can itself be an impact, enhancing the scaling potential of real-world laboratories. Cooperation can pave the way for amplifying real-world laboratories’ activities temporally and spatially

Wirkung verschiedener Insektizide bei Ober- und Unterblattapplikation gegen die Kohlmottenschildlaus Aleurodes proletella in biologischem Rosenkohl

Versuchsbericht zur Wirkung verschiedener Insektizide bei Ober- und Unterblattapplikation gegen die Kohlmottenschildlaus Aleurodes proletella in biologischem Rosenkoh