VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

BACKGROUND: RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and cells. The increase in use of RNA-seq technology has led to the continuous development of new tools for every step of analysis from alignment to downstream pathway analysis. However, effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts. RESULTS: Using the workflow management system Snakemake we have developed a user friendly, fast, efficient, and comprehensive pipeline for RNA-seq analysis. VIPER (Visualization Pipeline for RNA-seq analysis) is an analysis workflow that combines some of the most popular tools to take RNA-seq analysis from raw sequencing data, through alignment and quality control, into downstream differential expression and pathway analysis. VIPER has been created in a modular fashion to allow for the rapid incorporation of new tools to expand the capabilities. This capacity has already been exploited to include very recently developed tools that explore immune infiltrate and T-cell CDR (Complementarity-Determining Regions) reconstruction abilities. The pipeline has been conveniently packaged such that minimal computational skills are required to download and install the dozens of software packages that VIPER uses. CONCLUSIONS: VIPER is a comprehensive solution that performs most standard RNA-seq analyses quickly and effectively with a built-in capacity for customization and expansion

A Multidisciplinary Investigation of a Polycythemia Vera Cancer Cluster of Unknown Origin

Cancer cluster investigations rarely receive significant public health resource allocations due to numerous inherent challenges and the limited success of past efforts. In 2008, a cluster of polycythemia vera, a rare blood cancer with unknown etiology, was identified in northeast Pennsylvania. A multidisciplinary group of federal and state agencies, academic institutions, and local healthcare providers subsequently developed a multifaceted research portfolio designed to better understand the cause of the cluster. This research agenda represents a unique and important opportunity to demonstrate that cancer cluster investigations can produce desirable public health and scientific outcomes when necessary resources are available

The Public Repository of Xenografts enables discovery and randomized phase II-like trials in mice

More than 90% of drugs with preclinical activity fail in human trials, largely due to insufficient efficacy. We hypothesized that adequately powered trials of patient-derived xenografts (PDX) in mice could efficiently define therapeutic activity across heterogeneous tumors. To address this hypothesis, we established a large, publicly available repository of well-characterized leukemia and lymphoma PDXs that undergo orthotopic engraftment, called the Public Repository of Xenografts (PRoXe). PRoXe includes all de-identified information relevant to the primary specimens and the PDXs derived from them. Using this repository, we demonstrate that large studies of acute leukemia PDXs that mimic human randomized clinical trials can characterize drug efficacy and generate transcriptional, functional, and proteomic biomarkers in both treatment-naive and relapsed/refractory disease

2017 Research & Innovation Day Program

A one day showcase of applied research, social innovation, scholarship projects and activities.https://first.fanshawec.ca/cri_cripublications/1004/thumbnail.jp

The Seventeenth Data Release of the Sloan Digital Sky Surveys: Complete Release of MaNGA, MaStar and APOGEE-2 Data

This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library (MaStar) accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) survey which publicly releases infra-red spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the sub-survey Time Domain Spectroscopic Survey (TDSS) data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey (SPIDERS) sub-survey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated Value Added Catalogs (VACs). This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper (MWM), Local Volume Mapper (LVM) and Black Hole Mapper (BHM) surveys

Deaminative ring contraction for the synthesis of polycyclic heteroaromatics: a concise total synthesis of toddaquinoline

A concise strategy to prepare polycyclic heteroaromatics involving a deaminative contraction cascade is detailed. The efficient deaminative ring contraction involves the in situ methylation of a biaryl-linked dihydroazepine to form a cyclic ammonium cation that undergoes a base-induced [1,2]-Stevens rearrangement/dehydroamination sequence. The presence of pseudosymmetry guides the retrosynthetic analysis of pyridyl-containing polycyclic heteroaromatics, enabling their construction by the reductive cyclization and deaminative contraction of tertiary amine precursors

Relationships Among Leadership Practices and Employees’ Experiences of Meaningful Work

The conceptualization of meaningful work as both positive and necessary for human thriving has inspired a steady stream of theory-building and empirical inquiry, seeking to both explain what meaningful work is and identify its antecedents and positive individual and organizational consequences (e.g., Chalofsky, 2003; Lysova et al., 2019; Pratt & Ashforth, 2003; Rosso et al., 2010; Schnell, Höge, & Pollet, 2013; Steger, Dik, & Duffy, 2012; Wrzesniewski, 2003). However, while the understanding of factors that contribute to and result from the experience of meaningful work burgeons, knowledge of how people come to experience meaningful work in everyday work-life, and what that experience is like, remains limited (Bailey & Madden, 2019; Lips-Wiersma, Souter, & Wright, 2014; Mitra & Buzzanell, 2017). The consensus among meaningful work theorists agrees that leadership practices are key influencers on the process of experiencing meaningfulness (i.e., Frémeaux & Pavageau, 2020; Lysova et al., 2019). Several dimensions have been generally theorized as leadership practices that positively influence meaningful work, including moral correctness, values-based hiring practices, investment in learning and development, value-bounded autonomy, recognition, positive relationships, and purpose (e.g., Adams & Myles, 2020; Frémeaux & Pavageau, 2020; Isaksen, 2000; Morin 2008; Lips-Wiersma & Morris 2009). However, limited empirical inquiry into the nature of how these theorized practices affect meaningfulness and other associated positive outcomes exists. To better understand how leadership practices influence the experience of meaningfulness, we used exploratory factor analysis to build a 36-item Meaningful Leadership Scale (MLS) that captures the extent to which organizational leaders (from the perspective of employees) vary when it comes to theorized leadership practices of acting with integrity (Integrity), encouraging employees’ personal development (Potential), talking about why the work matters for society (Impact), talking about values during the hiring and onboarding process (Beginnings), fostering a connection with personal lives (Connection), and trusting workers with values-bounded autonomy (Freedom). Research Questions: 1. Do the leadership practices of acting with integrity, talking to employees about personal development, talking about why the work matters for society, talking about values during the hiring and onboarding process, fostering a connection with employees’ personal lives, and trusting workers with values-bounded autonomy positively correlate with the experience of meaningfulness in work? 2. How do MLS subscales (perceived leadership practices) and total scores predict unique variance in the experience of meaningfulness in work? 3. Do MLS subscales and total scores positively correlate with work variables mattering, intrinsic work motivation, job satisfaction, and employee perceptions of standards for environmental, social, and governance standards, and negatively correlate to withdrawal intentions and extrinsic work motivations? 4. How do the above relationships vary across demographic variables

Analysis of Parasites Found in Ducks of the Mississippi Flyway by Parasite Type, Host Gender, Mass, and Species: A Parasitology Class Project

It is important to be aware of the potential parasitic load in any animal which may be used for human consumption. The purpose of this project was to investigate if there was any one factor, such as size, sex, location, or species of duck, which had a significant effect on the amount or type of parasite found. One hundred and nine ducks were legally harvested and donated by hunters from Buffalo and Trempealeau County, WI, and Winona County, MN, then examined for total parasites via necroscopy. The parasites found were then categorized by location within the duck and type of parasite (louse, nematode, trematode, cestode or acanthocephalan), along with the sex, species, and size of the duck. It was predicted that female ducks, along with ducks with higher mass, were more likely to have a higher parasite load. Statistical analysis will be performed on all variables with help from the WSU Statistical Consulting Center. These findings could help identify which factors may increase the chances of a duck having a high parasitic load, which could influence which ducks are targeted by hunters specifically for meat

The Effect of Musical Experience and Autism Spectrum Disorder on the Encoding of Dynamic Audiovisual Temporal Information

Musical training has been associated with a wide variety of benefits in speech, memory, audiovisual integration and attention; however, understanding how musical expertise affects the encoding of environmental stimuli remains under investigation. While much research has shown auditory processing benefits from musical experience, the overall effects on multisensory integration (MSI) and unisensory visual processing remains unknown. Additionally, musicians have been proven to have more precise temporal acuity and sharper temporal windows. In comparison, increased autism symptomatology has been associated with a broader temporal window and a lack of multisensory neural enhancement in auditory-tactile tasks. We investigated whether musical experience and autism spectrum disorder (ASD) influence the encoding of dynamic audiovisual stimuli using event-related potentials (ERPs) through electroencephalogy (EEG). Additionally, superadditivity is used as a measure of MSI. In line with previous findings, our results indicate that experienced musicians are more accurate in detecting asynchrony compared to non-musicians, specifically when the auditory is faster than the visual. In terms of autism symptomatology, those with low autistic symptomatology are better at detecting asynchrony compared to those with high symptomatology, specifically when the auditory is faster than the visual. Preliminary EEG findings suggest that musical experience and autism spectrum disorder may affect encoding at resonant frequencies. Future work on this project will investigate interactions between musical experience and autism symptomatology in order to understand its use as a therapeutic tool in addressing some of the impairments to temporal encoding