Increasing STEM Literacy Through Directed Outreach

5th Annual Engagement and Service-Learning Summit: Connecting Through Listening and Scholarship, Thursday February 28th, 2019, Hosted by the Office of Engagement and Purdue Honors Colleg

Unveiling the diversity of tree growth patterns in boreal old-growth forests reveals the richness of their dynamics

Research Highlights: Radial growth patterns of trees growing in old-growth boreal forests in eastern Canada can be grouped into a small number of simple patterns that are specific to different old-growth forest types or successional stages. Background and Objectives: Identifying the main radial growth trends in old-growth forests could help to develop silvicultural treatments that mimic the complex dynamics of old-growth forests. Therefore, this study aimed to identify the main radial growth patterns and determine how their frequencies change during forest succession in old-growth forests, focusing on boreal landscapes in eastern Canada. Materials and Methods: We used dendrochronological data sampled from 21 old-growth stands in the province of Quebec, Canada. Tree-ring chronologies were simplified into chronologies of equal length to retain only primary growth trends. We used k-means clustering to identify individual growth patterns and the difference in growth-pattern frequency within the studied stands. We then used non-parametric analyses of variance to compare tree or stand characteristics among the clusters. Results: We identified six different growth patterns corresponding to four old-growth forest types, from stands at the canopy breakup stage to true old-growth stands (i.e., when all the pioneer cohort had disappeared). Secondary disturbances of low or moderate severity drove these growth patterns. Overall, the growth patterns were relatively simple and could be generally separated into two main phases (e.g., a phase of limited radial increment size due to juvenile suppression and a phase of increased radial increment size following a growth release). Conclusions: The complexity of old-growth forest dynamics was observed mainly at the stand level, not at the tree level. The growth patterns observed in true old-growth forests were similar to those observed following partial or stem-selection cuts in boreal stands; thus, these silvicultural treatments may be effective in mimicking old-growth dynamics

Adaptive and Safe Bayesian Optimization in High Dimensions via One-Dimensional Subspaces

Bayesian optimization is known to be difficult to scale to high dimensions, because the acquisition step requires solving a non-convex optimization problem in the same search space. In order to scale the method and keep its benefits, we propose an algorithm (LineBO) that restricts the problem to a sequence of iteratively chosen one-dimensional sub-problems that can be solved efficiently. We show that our algorithm converges globally and obtains a fast local rate when the function is strongly convex. Further, if the objective has an invariant subspace, our method automatically adapts to the effective dimension without changing the algorithm. When combined with the SafeOpt algorithm to solve the sub-problems, we obtain the first safe Bayesian optimization algorithm with theoretical guarantees applicable in high-dimensional settings. We evaluate our method on multiple synthetic benchmarks, where we obtain competitive performance. Further, we deploy our algorithm to optimize the beam intensity of the Swiss Free Electron Laser with up to 40 parameters while satisfying safe operation constraints

Analysis of the Effects of Dietary Pattern on the Oral Microbiome of Elite Endurance Athletes

Although the oral microbiota is known to play a crucial role in human health, there are few studies of diet x oral microbiota interactions, and none in elite athletes who may manipulate their intakes of macronutrients to achieve different metabolic adaptations in pursuit of optimal endurance performance. The aim of this study was to investigate the shifts in the oral microbiome of elite male endurance race walkers from Europe, Asia, the Americas and Australia, in response to one of three dietary patterns often used by athletes during a period of intensified training: a High Carbohydrate (HCHO; = 9; with 60% energy intake from carbohydrates; ~8.5 g kg day carbohydrate, ~2.1 g kg day protein, 1.2 g kg day fat) diet, a Periodised Carbohydrate (PCHO; = 10; same macronutrient composition as HCHO, but the intake of carbohydrates is different across the day and throughout the week to support training sessions with high or low carbohydrate availability) diet or a ketogenic Low Carbohydrate High Fat (LCHF; = 10; 0.5 g kg day carbohydrate; 78% energy as fat; 2.1 g kg day protein) diet. Saliva samples were collected both before (Baseline; BL) and after the three-week period (Post treatment; PT) and the oral microbiota profiles for each athlete were produced by 16S rRNA gene amplicon sequencing. Principal coordinates analysis of the oral microbiota profiles based on the weighted UniFrac distance measure did not reveal any specific clustering with respect to diet or athlete ethnic origin, either at baseline (BL) or following the diet-training period. However, discriminant analyses of the oral microbiota profiles by Linear Discriminant Analysis (LDA) Effect Size (LEfSe) and sparse Partial Least Squares Discriminant Analysis (sPLS-DA) did reveal changes in the relative abundance of specific bacterial taxa, and, particularly, when comparing the microbiota profiles following consumption of the carbohydrate-based diets with the LCHF diet. These analyses showed that following consumption of the LCHF diet the relative abundances of and spp. were decreased, and the relative abundance of spp. was increased. Such findings suggest that diet, and, in particular, the LCHF diet can induce changes in the oral microbiota of elite endurance walkers

Tuning Particle Accelerators with Safety Constraints using Bayesian Optimization

Tuning machine parameters of particle accelerators is a repetitive and time-consuming task, that is challenging to automate. While many off-the-shelf optimization algorithms are available, in practice their use is limited because most methods do not account for safety-critical constraints that apply to each iteration, including loss signals or step-size limitations. One notable exception is safe Bayesian optimization, which is a data-driven tuning approach for global optimization with noisy feedback. We propose and evaluate a step size-limited variant of safe Bayesian optimization on two research faculties of the Paul Scherrer Institut (PSI): a) the Swiss Free Electron Laser (SwissFEL) and b) the High-Intensity Proton Accelerator (HIPA). We report promising experimental results on both machines, tuning up to 16 parameters subject to more than 200 constraints

CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing

The CRISPR–Cas system is a powerful genome editing tool that functions in a diverse array of organisms and cell types. The technology was initially developed to induce targeted mutations in DNA, but CRISPR–Cas has now been adapted to target nucleic acids for a range of purposes. CHOPCHOP is a web tool for identifying CRISPR–Cas single guide RNA (sgRNA) targets. In this major update of CHOPCHOP, we expand our toolbox beyond knockouts. We introduce functionality for targeting RNA with Cas13, which includes support for alternative transcript isoforms and RNA accessibility predictions. We incorporate new DNA targeting modes, including CRISPR activation/repression, targeted enrichment of loci for long-read sequencing, and prediction of Cas9 repair outcomes. Finally, we expand our results page visualization to reveal alternative isoforms and downstream ATG sites, which will aid users in avoiding the expression of truncated proteins. The CHOPCHOP web tool now supports over 200 genomes and we have released a command-line script for running larger jobs and handling unsupported genomes. CHOPCHOP v3 can be found at https://chopchop.cbu.uib.nopublishedVersio

Dense bottom gravity currents and their impact on pelagic methanotrophy at oxic/anoxic transition zones

We show that inflows of oxygenated waters into sulfidic layers have a strong impact on biogeochemical transformation at oxic/anoxic transition zones. Taking the pelagic methane dynamics in the Gotland Basin as an example, we performed our studies when one of the largest inflows ever recorded entered the Baltic Sea in March 2015. An inflowing gravity current transported oxic waters into the sulfidic deep layers and freshly generated a near-bottom secondary redox interface. At the upper slope, where the inflowing water masses were vigorously turbulent and the main and secondary redox interfaces in close contact to each other, methane oxidation rates inside the transition zone were found to be higher compared to the weakly turbulent basin interior. At the main redox interface in the basin center, lateral intrusions of oxygenated waters into intermediate water depth may have stimulated the growth of the methanotrophic community and their activity

Centering Proximity: Why giving platforms should center the organizations on the frontlines of social change

Social change happens in communities. And proximate organizations make that change happen.Proximate organizations are those closest to the causes and the communities they're directly serving.They are these communities.Proximate organizations are often (not always) small in size. Though nonprofits with less than $1M in budget represent 92% of nonprofits, they only receive around 20% of individual donations.More and more giving is happening online-- increasing by over 42% in the past three years alone. Online giving platforms are also growing, playing an increasingly important role in facilitating those donations.Imagine a world where online giving platforms channeled more of the power and promise of generosity to these proximate organizations.This publication focuses on that possibility.It is the output of listening to 25 leaders of proximate organizations - just a microcosm of the thousands of leaders working in communities around the country

TailFindR: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing

Polyadenylation at the 3′-end is a major regulator of messenger RNA and its length is known to affect nuclear export, stability, and translation, among others. Only recently have strategies emerged that allow for genome-wide poly(A) length assessment. These methods identify genes connected to poly(A) tail measurements indirectly by short-read alignment to genetic 3′-ends. Concurrently, Oxford Nanopore Technologies (ONT) established full-length isoform-specific RNA sequencing containing the entire poly(A) tail. However, assessing poly(A) length through base-calling has so far not been possible due to the inability to resolve long homopolymeric stretches in ONT sequencing. Here we present tailfindr, an R package to estimate poly(A) tail length on ONT long-read sequencing data. tailfindr operates on unaligned, base-called data. It measures poly(A) tail length from both native RNA and DNA sequencing, which makes poly(A) tail studies by full-length cDNA approaches possible for the first time. We assess tailfindr’s performance across different poly(A) lengths, demonstrating that tailfindr is a versatile tool providing poly(A) tail estimates across a wide range of sequencing conditions.publishedVersio

Effects of cold winters and roost site stability on population development of non-native Asian ring-necked parakeets (Alexandrinus manillensis) in temperate Central Europe – Results of a 16-year census

Asian ring-necked parakeets (Alexandrinus manillensis, formerly Psittacula krameri, hereafter RNP) first bred in Germany in 1969. Since then, RNP numbers increased in all three major German subpopulations (Rhineland, Rhine-Main, Rhine-Neckar) over the period 2003–2018. In the Rhine-Neckar region, the population increased to more than fivefold within only 15 years. Interestingly, there was no significant breeding range expansion of  RNP in the period 2010–2018. In 2018, the total number of RNP in Germany amounted to >16,200 birds. Differences in RNP censuses between years were evident. Surprisingly, cold winters (extreme value, −13.7 °C) and cold weather conditions in the breeding season (coldest month average, −1.36 °C) were not able to explain between-year variation. This finding suggests that in general winter mortality is low – with exceptions for winters 2008/2009 and 2009/2010, and a population-relevant loss of broods is low in our study population. Surprisingly, the social behaviour in terms of spatio-temporal stability of roost sites could well explain positive and negative population trends. Years of spatially stable and regularly used roost sites seem to correlate with increasing population sizes. In contrast, known shifts of RNP among different roost sites or the formations of new roost sites by split are related to population stagnation or a decrease in numbers. Climate change may lead to further range expansion as cities not suitable yet for RNP may become so in the near future.