Undergraduate Library Internships and Professional Success

This poster reports on an assessment completed of former undergraduate library interns to explore the impact their internship had on the development of career goals, acceptance to and preparation for graduate education, and their early career. Through an online survey (n= 45) and six semi-structured telephone interviews, respondents reported a positive impact on the above areas

Undergraduate Library Internships at Musselman Library, Gettysburg College

In 2015-2016, Musselman Library at Gettysburg College participated in Cohort 3 of the Association of College and Research Libraries’ Assessment in Action program. This report outlines an assessment completed of former undergraduate library interns in order to explore the impact their internship experience had on the development of career goals, acceptance to and preparation for graduate education, and their early career. Through an online survey (n= 45) and six semi-structured telephone interviews, respondents reported a positive impact on the above areas

The Effect of Arbuscular Mycorrhizae on Milkweed Growth and its Implications for Western Monarchs

Western monarch butterfly (Danaus plexippus plexippus) populations in the Pacific Northwest have decreased by approximately 99% in recent decades due in part to the destruction of milkweed (Asclepias spp.) habitat. Milkweeds are one of the only plant genera upon which monarchs will lay eggs and the larvae will feed, so milkweed habitat restoration is critical for the future survival and rehabilitation of western monarch butterfly populations. This research aimed to investigate the effect of the root symbiont arbuscular mycorrhizal fungus (AMF) on growth for two species of milkweed native to Oregon’s Willamette Valley. In showy milkweed (A. speciosa), four of the five growth parameters were significantly affected (two increased and two decreased), while in narrow-leaf milkweed (A. fascicularis) only one was affected (decreased). Our results suggest further testing of different milkweed species, as well as different AMF species, would be valuable in evaluating AMF’s relationship with milkweeds to help restore habitat for the highly imperiled western monarch

The Effect of Residual Roundup on Showy Milkweed Growth and Cardenolide Production

Western monarch butterfly populations have sharply declined over the last three decades largely due to destruction of their habitat and larval food source, milkweed (Asclepias spp.). In order to aid reestablishment of milkweed habitat in support of Western monarch populations, the effects of soil pollutants and additives on the plant’s growth and toxin production should be examined. We evaluated five growth parameters and cardenolide concentration of showy milkweed (A. speciosa) exposed to various soil treatments of Roundup and arbuscular mycorrhizal fungi in controlled greenhouse conditions. Our results suggest that residual Roundup in soil does not affect cardenolide concentrations in showy milkweed but may interact with arbuscular mycorrhizal fungus symbionts to affect growth. More research is needed in order to understand the relationship between Roundup and mycorrhizal symbionts, but our results suggest that Roundup pollutants remaining in soil will not adversely affect milkweed restoration efforts in support of the imperiled Western monarch butterfly

The Effect of Species Diversity and Shade on Milkweed Growth and Cardenolide Concentration

Monarch butterflies (Danaus plexippus) rely upon milkweed plants for survival, as it is the only plant upon which female monarchs oviposit and it is the sole food supply for monarch larvae. Additionally, cardenolide, a defense toxin within milkweed tissue, is sequestered by monarchs, making them unpalatable to most predators. Eastern and Western monarch populations in the United States are in sharp decline, in part due to the growing scarcity of milkweed, and reestablishing milkweed habitat is crucial to the monarch’s long-term survival. This study aimed to study the effects of plant species diversity and shade on the growth and cardenolide content of two species of milkweed common in the Pacific Northwest (PNW). Milkweed plants were grown outdoors over three summers at the University of Portland, under varying levels of plant species diversity and shade. Four growth measurements and cardenolide concentration were analyzed. Species diversity affected several growth measurements but not cardenolide concentration. Medium shade conditions resulted in increases in three growth measurements and cardenolide concentration compared to low and high shade conditions. The results suggest PNW milkweed can grow under more diverse conditions than previously known, which may be useful information for reestablishment of milkweed habitat supporting the highly imperiled Western monarch population

Design considerations for workflow management systems use in production genomics research and the clinic

Abstract The changing landscape of genomics research and clinical practice has created a need for computational pipelines capable of efficiently orchestrating complex analysis stages while handling large volumes of data across heterogeneous computational environments. Workflow Management Systems (WfMSs) are the software components employed to fill this gap. This work provides an approach and systematic evaluation of key features of popular bioinformatics WfMSs in use today: Nextflow, CWL, and WDL and some of their executors, along with Swift/T, a workflow manager commonly used in high-scale physics applications. We employed two use cases: a variant-calling genomic pipeline and a scalability-testing framework, where both were run locally, on an HPC cluster, and in the cloud. This allowed for evaluation of those four WfMSs in terms of language expressiveness, modularity, scalability, robustness, reproducibility, interoperability, ease of development, along with adoption and usage in research labs and healthcare settings. This article is trying to answer, which WfMS should be chosen for a given bioinformatics application regardless of analysis type?. The choice of a given WfMS is a function of both its intrinsic language and engine features. Within bioinformatics, where analysts are a mix of dry and wet lab scientists, the choice is also governed by collaborations and adoption within large consortia and technical support provided by the WfMS team/community. As the community and its needs continue to evolve along with computational infrastructure, WfMSs will also evolve, especially those with permissive licenses that allow commercial use. In much the same way as the dataflow paradigm and containerization are now well understood to be very useful in bioinformatics applications, we will continue to see innovations of tools and utilities for other purposes, like big data technologies, interoperability, and provenance

Volume changes and brain-behavior relationships in white matter and subcortical gray matter in children with prenatal alcohol exposure: Volume Changes and Brain-Behavior in Children with PAE

Children with prenatal alcohol exposure (PAE) may have cognitive, behavioral and brain abnormalities. Here, we compare rates of white matter and subcortical gray matter volume change in PAE and control children, and examine relationships between annual volume change and arithmetic ability, behavior, and executive function. Participants (n=75 PAE/64 control; age: 7.1–15.9 years) each received two structural magnetic resonance scans, ~2 years apart. Assessments included Wechsler Intelligence Scale for Children (WISC-IV), the Child Behavior Checklist (CBCL) and the Behavior Rating Inventory of Executive Function (BRIEF). Subcortical white and gray volumes were extracted for each hemisphere. Group volume differences were tested using false discovery rate (FDR, q<0.05). Analyses examined group-by-age interactions and group-score interactions for correlations between change in volume and raw behavioral scores. Results showed that subjects with PAE had smaller volumes than control subjects across the brain. Significant group-score interactions were found in temporal and parietal regions for WISC arithmetic scores and in frontal and parietal regions for behavioral measures. Poorer cognitive/ behavioral outcomes were associated with larger volume increases in PAE, while control subjects generally showed no significant correlations. In contrast with previous results demonstrating different trajectories of cortical volume change in PAE, our results show similar rates of subcortical volume growth in subjects with PAE and control subjects. We also demonstrate abnormal brain-behavior relationships in subjects with PAE, suggesting different use of brain resources. Our results are encouraging in that, due to the stable volume differences, there may be an extended window of opportunity for intervention in children with PAE

Regional brain volume reductions relate to facial dysmorphology and neurocognitive function in fetal alcohol spectrum disorders

Individuals with heavy prenatal alcohol exposure can experience significant deficits in cognitive and psychosocial functioning and alterations in brain structure that persist into adulthood. In this report, data from 99 participants collected across three sites (Los Angeles and San Diego, California, and Cape Town, South Africa) were analyzed to examine relationships between brain structure, neurocognitive function, facial morphology, and maternal reports of quantities of alcohol consumption during the first trimester. Across study sites, we found highly significant volume reductions in the FASD group for all of the brain regions evaluated. After correcting for scan location, age, and total brain volume, these differences remained significant in some regions of the basal ganglia and diencephalon. In alcohol-exposed subjects, we found that smaller palpebral fissures were significantly associated with reduced volumes in the diencephalon bilaterally, that greater dysmorphology of the philtrum predicted smaller volumes in basal ganglia and diencephalic structures, and that lower IQ scores were associated with both smaller basal ganglia volumes and greater facial dysmorphology. In subjects from South Africa, we found a significant negative correlation between intracranial volume and total number of drinks per week in the first trimester. These results corroborate previous reports that prenatal alcohol exposure is particularly toxic to basal ganglia and diencephalic structures. We extend previous findings by illustrating relationships between specific measures of facial dysmorphology and the volumes of particular subcortical structures, and for the first time show that continuous measures of maternal alcohol consumption during the first trimester relates to overall brain volume reduction

Abnormal Cortical Thickness Alterations in Fetal Alcohol Spectrum Disorders and Their Relationships with Facial Dysmorphology

Accumulating evidence from structural brain imaging studies on individuals with fetal alcohol spectrum disorder (FASD) has supported links between prenatal alcohol exposure and brain morphological deficits. Although global and regional volumetric reductions appear relatively robust, the effects of alcohol exposure on cortical thickness and relationships with facial dysmorphology are not yet known. The structural magnetic resonance imaging data from 69 children and adolescents with FASD and 58 nonexposed controls collected from 3 sites were examined using FreeSurfer to detect cortical thickness changes across the entire brain in FASD and their associations with facial dysmorphology. Controlling for brain size, subjects with FASD showed significantly thicker cortices than controls in several frontal, temporal, and parietal regions. Analyses conducted within site further revealed prominent group differences in left inferior frontal cortex within all 3 sites. In addition, increased inferior frontal thickness was significantly correlated with reduced palpebral fissure length. Consistent with previous reports, findings of this study are supportive of regional increases in cortical thickness serving as a biomarker for disrupted brain development in FASD. Furthermore, the significant associations between thickness and dysmorphic measures suggest that the severity of brain anomalies may be reflected by that of the face

Callosal Thickness Reductions Relate to Facial Dysmorphology in Fetal Alcohol Spectrum Disorders: CALLOSAL THICKNESS REDUCTIONS IN FASD

Structural abnormalities of the corpus callosum (CC), such as reduced size and increased shape variability, have been documented in individuals with fetal alcohol spectrum disorders (FASD). However, the regional specificity of altered CC structure, which may point to the timing of neurodevelopmental disturbances and/or relate to specific functional impairments, is unclear. Further, associations between facial dysmorphology and callosal structure remain undetermined