Biology subjects

Perrone, J.

Publications and source records attributed to Perrone, J..

4 recordsLinked to original sources

bioRxiv2023

Adapting to changing methodology in a long-term experiment

Long-term experiments are critical for understanding ecological processes, but their management comes with unique challenges. As time passes, projects may encounter unavoidable changes due to external factors, like availability of materials, affecting aspects of their research methodology. At the Kellogg Biological Station Long-Term Ecological Research Site, one of many National Science Foundation-funded long-term research stations, a three-decade project recently experienced a supply-chain-induced change in insect sampling methodology in their lady beetle observation study. Since 1989, lady beetles (Coleoptera: Coccinellidae) have been sampled weekly over the growing season using yellow sticky cards. In 2021, the original sticky traps were discontinued by the manufacturer and replaced with a similar, but not identical trap. We conducted a 3-year study while the new traps were phased in to examine how the trap change would impact the observed biodiversity patterns at the site. We examined community metrics and individual taxa captures to examine within year and between year differences in performance between the card types. Overall, we noted several small but statistically detectable differences in capture patterns between the two trap types. After accounting for other sources of variation, we observed a difference in Shannon diversity of insects captured on the two card types, but not richness or abundance, in the overall insect community. Yet, these differences were dwarfed by the magnitude of difference observed between years within card types. For individual taxa, similar patterns held: between trap differences could be detected statistically, but the number of differences between capture rates of traps was less than the number of differences observed for the same trap, between years. Thus, we conclude that while subtle changes in methodology could impact data produced in long-term experiments, in this case the magnitude of this change is smaller than other factors such as time and plant treatment. However, if sustained changes in the capture rates of focal taxa are observed, future data users may use our observations to specifically quantify and correct for these shifting patterns related to the protocol change.

ecology↗

bioRxiv2021

Longer study length, standardized sampling techniques, and broader geographic scope leads to higher likelihood of detecting stable abundance patterns in long term deer tick (Ixodes scapularis) studies

BackgroundUnderstanding how study design and monitoring strategies shape inference within, and synthesis across, studies is critical across biological disciplines. Many biological and field studies are short term and limited in scope. Monitoring studies are critical for informing public health about potential vectors of concern, such as Ixodes scapularis (black-legged ticks). Black-legged ticks are a taxon of ecological and human health concern due to their status as primary vectors of Borrelia burgdorferi, which causes Lyme disease. However, variation in black-legged tick monitoring, and gaps in data, are currently considered major barriers to understanding population trends and in turn, predicting Lyme disease risk. To understand how variable methodology in black-legged tick studies may influence which population patterns researchers find, we conducted a data synthesis experiment. Materials and MethodsWe searched for publicly available black-legged tick abundance datasets that had at least 9 years of data, using keywords about ticks in internet search engines, literature databases, data repositories and public health websites. Our analysis included 289 datasets from 7 surveys from locations throughout the US, ranging in length from 9 to 24 years. We used a moving window analysis, which is a kind of non-random resampling approach, to investigate the temporal stability of black-legged tick population trajectories across the US. We then used t-tests to assess differences in stability time across different study parameters. ResultsAll of our sampled datasets required 4 or more years to reach stability. We also found that several study factors can have an impact on the likelihood of a study reaching stability and of data resulting in misleading results if the study does not reach stability. Specifically, datasets collected via dragging reached stability significantly faster than data collected via opportunistic sampling. Datasets that sampled larva reached stability significantly later than those that sampled adults or nymphs. Additionally, datasets collected at the broadest spatial scale (county) reached stability fastest. ConclusionWe used 289 datasets from 7 long term black-legged tick studies to conduct a non-random data resampling experiment, revealing that sampling design does shape inferences in black-legged tick population trajectories and how many years it takes to find stable patterns. Specifically, our results show the importance of study length, sampling technique, life stage, and geographic scope in understanding black-legged tick populations, in the absence of standardized surveillance methods. Current public health efforts based on existing black-legged tick datasets must take monitoring study parameters into account, to better understand if and how to use monitoring data to inform decision making. We also recommend that potential forecasting initiatives consider these parameters when projecting black-legged tick population trends.

bioinformatics↗

bioRxiv2019

Effective buprenorphine use and tapering strategies: Endorsements and insights by people in recovery from opioid use disorder on a Reddit forum

Opioid use disorder (OUD) is a public health emergency in the United States. Over 47,000 overdose-related deaths in 2017 involved opioids. Medication-assisted treatment (MAT), in particular, buprenorphine and buprenorphine combination products such as Suboxone(R), is the most effective, evidence-based treatment for OUD. However, there are a limited number of conclusive scientific studies that provide guidance to medical professionals about strategies for using buprenorphine to achieve stable recovery. In this study, we used data-driven natural language processing methods to mine a total of 16,146 posts about buprenorphine from 1933 unique users on the anonymous social network Reddit. Analysis of a sample of these posts showed that 74% of the posts described users personal experiences and that the top three topics included advice on using Suboxone(R) (55.0%), Suboxone(R) dosage information (35.5%) and information about Suboxone(R) tapering (32.0%). Based on two models, one that incorporated upvoting by other members and one that did not, we found that Reddit users reported more successful recovery with longer tapering schedules, particularly from 2.0 mg to 0.0 mg (median: 93 days; mean: 95 days), as compared to shorter tapering schedules investigated in past clinical trials. Diarrhea, insomnia, restlessness, and fatigue were commonly reported adverse events. Physical exercise, clonidine, and Imodium(R) were frequently reported to help during the recovery process. Due to the difficulties of conducting longer-term clinical trials involving patients with OUD, clinicians should consider other information sources including peer discussions from the abundant, real-time information available on Reddit. Significance StatementOpioid use disorder (OUD) is a national crisis in the United States and buprenorphine is one of the most effective evidence-based treatments. However, few studies have explored successful strategies for using and tapering buprenorphine to achieve stable recovery, particularly due to the difficulties of conducting long-term studies involving patients with OUD. In this study, we show that discussions on the anonymous social network Reddit may be leveraged, via automatic text mining methods, to discover successful buprenorphine use and tapering strategies. We discovered that longer tapering schedules, compared to those investigated in past clinical trials, may lead to (self-reported) sustained recovery. Furthermore, Reddit posts also provide key information regarding buprenorphine withdrawal, cravings, adjunct medications for withdrawal symptoms and relapse prevention strategies.

pharmacology and toxicology↗

bioRxiv2017

Cycledash: a web application for the interactive analysis and exploration of variants

As genomics begins to influence clinical care, validating the result of a somatic variant calling pipeline has become increasingly important. Cycledash is a web application which facilitates the validation and analysis of somatic variants, bringing together and streamlining existing tools and workflows for examining and verifying the existence of variants in patient samples.\n\nAvailabilityThe source code is freely available at https://github.com/hammerlab/cycledash under the Apache 2 License. A public demo (username cycledash password cycledash123) is available at http://cycledash.hammerlab.org. The web application is tested to work in recent version of Firefox, Safari, and Chrome, and the server applications will run on Linux and OS X systems.\n\nContactcorrespondence@hammerlab.org

bioinformatics↗