Publications by authors named "Jennifer M Allen"

12 Publications

  • Page 1 of 1

Psychosocial collaboration fosters connection in times of isolation.

J Psychosoc Oncol 2021 Mar 9:1-4. Epub 2021 Mar 9.

Department of Psychology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.

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http://dx.doi.org/10.1080/07347332.2021.1894525DOI Listing
March 2021

Pseudogymnoascus destructans growth in wood, soil and guano substrates.

Sci Rep 2021 Jan 12;11(1):763. Epub 2021 Jan 12.

Department of Fisheries and Wildlife, Oregon State University, 2820 SW Campus Way, Nash Hall, Corvallis, OR, 97331, USA.

Understanding how a pathogen can grow on different substrates and how this growth impacts its dispersal are critical to understanding the risks and control of emerging infectious diseases. Pseudogymnoascus destructans (Pd) causes white-nose syndrome (WNS) in many bat species and can persist in, and transmit from, the environment. We experimentally evaluated Pd growth on common substrates to better understand mechanisms of pathogen persistence, transmission and viability. We inoculated autoclaved guano, fresh guano, soil, and wood with live Pd fungus and evaluated (1) whether Pd grows or persists on each (2) if spores of the fungus remain viable 4 months after inoculation on each substrate, and (3) whether detection and quantitation of Pd on swabs is sensitive to the choice to two commonly used DNA extraction kits. After inoculating each substrate with 460,000 Pd spores, we collected ~ 0.20 g of guano and soil, and swabs from wood every 16 days for 64 days to quantify pathogen load through time using real-time qPCR. We detected Pd on all substrates over the course of the experiment. We observed a tenfold increase in pathogen loads on autoclaved guano and persistence but not growth in fresh guano. Pathogen loads increased marginally on wood but declined ~ 60-fold in soil. After four months, apparently viable spores were harvested from all substrates but germination did not occur from fresh guano. We additionally found that detection and quantitation of Pd from swabs of wood surfaces is sensitive to the DNA extraction method. The commonly used PrepMan Ultra Reagent protocol yielded substantially less DNA than did the QIAGEN DNeasy Blood and Tissue Kit. Notably the PrepMan Ultra Reagent failed to detect Pd in many wood swabs that were detected by QIAGEN and were subsequently found to contain substantial live conidia. Our results indicate that Pd can persist or even grow on common environmental substrates with results dependent on whether microbial competitors have been eliminated. Although we observed clear rapid declines in Pd on soil, viable spores were harvested four months after inoculation. These results suggest that environmental substrates and guano can in general serve as infectious environmental reservoirs due to long-term persistence, and even growth, of live Pd. This should inform management interventions to sanitize or modify structures to reduce transmission risk as well early detection rapid response (EDRR) planning.
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http://dx.doi.org/10.1038/s41598-020-80707-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7804951PMC
January 2021

Psychosocial Factors and Psychological Interventions: Implications for Chronic Post-Surgical Pain in Pediatric Patients with Osteosarcoma.

J Clin Psychol Med Settings 2020 Nov 10. Epub 2020 Nov 10.

Division of Anesthesiology, Department of Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN, USA.

This study retrospectively investigated psychological factors contributing to chronic post-surgical pain (CPSP) in pediatric patients after limb-sparing or amputation surgery for extremity osteosarcoma. Psychological factors were identified and analyzed by the Wilcoxon rank-sum and median two-sample tests. Univariate and multivariate Cox regressions were performed using gender, age, psychological factors, and psychological interventions related to CPSP duration as covariates. Duration of pain treatment was significantly longer in patients resistant to psychological interventions (p = 0.01) than those receptive to interventions. Shorter duration of pain treatment was associated with older age (p = 0.03) and receptiveness to psychological interventions (HR = 4.19, 95% CI [1.22, 14.35]). Older age and receptiveness to psychological interventions as part of pain management care are associated with needing a shorter duration of pain treatment. Our results highlight the importance of prospective investigations evaluating motivation to engage in psychotherapy and psychological interventions and identify risk factors for CPSP in pediatric oncology.
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http://dx.doi.org/10.1007/s10880-020-09748-yDOI Listing
November 2020

Environmental DNA facilitates accurate, inexpensive, and multiyear population estimates of millions of anadromous fish.

Mol Ecol Resour 2020 Mar 31;20(2):457-467. Epub 2019 Dec 31.

Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA.

Although environmental DNA shed from an organism is now widely used for species detection in a wide variety of contexts, mobilizing environmental DNA for management requires estimation of population size and trends in addition to assessing presence or absence. However, the efficacy of environmental-DNA-based indices of abundance for long-term population monitoring have not yet been assessed. Here we report on the relationship between six years of mark-recapture population estimates for eulachon (Thaleichthys pacificus) and "eDNA rates" which are calculated from the product of stream flow and DNA concentration. Eulachon are a culturally and biologically important anadromous fish that have significantly declined in the southern part of their range but were historically rendered into oil and traded. Both the peak eDNA rate and the area under the curve of the daily eDNA rate were highly predictive of the mark-recapture population estimate, explaining 84.96% and 92.53% of the deviance, respectively. Even in the absence of flow correction, the peak of the daily eDNA concentration explained an astonishing 89.53% while the area under the curve explained 90.74% of the deviance. These results support the use of eDNA to monitor eulachon population trends and represent a >80% cost savings over mark-recapture, which could be further increased with automated water sampling, reduced replication, and focused temporal sampling. Due to its logistical ease and affordability, eDNA sampling can facilitate monitoring a larger number of rivers and in remote locations where mark-recapture is infeasible.
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http://dx.doi.org/10.1111/1755-0998.13123DOI Listing
March 2020

Beyond clinical practice in pediatric psychology: Illustrative experiences in influencing practice changes, public opinion, and governmental policies.

Psychol Serv 2019 Aug 5. Epub 2019 Aug 5.

Department of Psychology.

Consistent with the core underpinnings of advocacy within the field of pediatrics, the discipline of pediatric psychology places an emphasis on advocating for children through clinical and research efforts as well as through a systems approach of interdisciplinary collaboration and partnering with others. In the current article, the role of advocacy efforts for pediatric psychologists within children's hospitals are highlighted. Various forms and models of advocacy are discussed, particularly as they relate to individual and organizational advocacy within children's hospitals, as well as interdisciplinary collaboration and shared advocacy with other health care providers and leadership. Training of pediatric psychologists in advocacy is also addressed, including limitations in development and application of advocacy skills for pediatric psychologists. Examples of policy change at the hospital/institutional, state, and national levels are also provided. While pediatric psychologists are in unique positions to advocate for their patients within interdisciplinary health care settings, challenges in advocacy exist. Future directions for improving advocacy for pediatric psychologists are explored. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
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http://dx.doi.org/10.1037/ser0000385DOI Listing
August 2019

Environmental DNA for the enumeration and management of Pacific salmon.

Mol Ecol Resour 2019 May 10;19(3):597-608. Epub 2019 Apr 10.

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.

Pacific salmon are a keystone resource in Alaska, generating annual revenues of well over ~US$500 million/year. Due to their anadromous life history, adult spawners distribute amongst thousands of streams, posing a huge management challenge. Currently, spawners are enumerated at just a few streams because of reliance on human counters and, rarely, sonar. The ability to detect organisms by shed tissue (environmental DNA, eDNA) promises a more efficient counting method. However, although eDNA correlates generally with local fish abundances, we do not know if eDNA can accurately enumerate salmon. Here we show that daily, and near-daily, flow-corrected eDNA rate closely tracks daily numbers of returning sockeye and coho spawners and outmigrating sockeye smolts. eDNA thus promises accurate and efficient enumeration, but to deliver the most robust numbers will need higher-resolution stream-flow data, at-least-daily sampling, and a focus on species with simple life histories, since shedding rate varies amongst jacks, juveniles, and adults.
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http://dx.doi.org/10.1111/1755-0998.12987DOI Listing
May 2019

Environmental DNA from Residual Saliva for Efficient Noninvasive Genetic Monitoring of Brown Bears (Ursus arctos).

PLoS One 2016 9;11(11):e0165259. Epub 2016 Nov 9.

Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, United States of America.

Noninvasive genetic sampling is an important tool in wildlife ecology and management, typically relying on hair snaring or scat sampling techniques, but hair snaring is labor and cost intensive, and scats yield relatively low quality DNA. New approaches utilizing environmental DNA (eDNA) may provide supplementary, cost-effective tools for noninvasive genetic sampling. We tested whether eDNA from residual saliva on partially-consumed Pacific salmon (Oncorhynchus spp.) carcasses might yield suitable DNA quality for noninvasive monitoring of brown bears (Ursus arctos). We compared the efficiency of monitoring brown bear populations using both fecal DNA and salivary eDNA collected from partially-consumed salmon carcasses in Southeast Alaska. We swabbed a range of tissue types from 156 partially-consumed salmon carcasses from a midseason run of lakeshore-spawning sockeye (O. nerka) and a late season run of stream-spawning chum (O. keta) salmon in 2014. We also swabbed a total of 272 scats from the same locations. Saliva swabs collected from the braincases of salmon had the best amplification rate, followed by swabs taken from individual bite holes. Saliva collected from salmon carcasses identified unique individuals more quickly and required much less labor to locate than scat samples. Salmon carcass swabbing is a promising method to aid in efficient and affordable monitoring of bear populations, and suggests that the swabbing of food remains or consumed baits from other animals may be an additional cost-effective and valuable tool in the study of the ecology and population biology of many elusive and/or wide-ranging species.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0165259PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5102439PMC
July 2017

Sleep and Pain in Pediatric Illness: A Conceptual Review.

CNS Neurosci Ther 2016 11 15;22(11):880-893. Epub 2016 Jul 15.

Department of Psychology, St. Jude Children's Research Hospital, Memphis, TN, USA.

Background: Sleep disruption is a common comorbidity of pediatric pain. Consequences of pain and disrupted sleep, evidence for the pain-sleep relation, and how aspects of illness, treatment, and pharmacological pain management may contribute to or exacerbate these issues are presented.

Aims: This conceptual review explored the relation between pain and sleep in children diagnosed with chronic medical or developmental conditions. The goal of this review is to expand upon the literature by examining common themes in sleep disturbances associated with painful conditions across multiple pediatric illnesses. Populations reviewed include youth with intellectual and developmental disabilities (IDD), migraines, cystic fibrosis (CF), sickle cell disease (SCD), cancer, juvenile idiopathic arthritis (JIA), juvenile fibromyalgia (JFM), and functional gastrointestinal disorders (FGIDs).

Results: Consistent evidence demonstrates that children with medical or developmental conditions are more vulnerable to experiencing pain and subjective sleep complaints than healthy peers. Objective sleep concerns are common but often under-studied. Evidence of the pain-sleep relationship exists, particularly in pediatric SCD, IDD, and JIA, with a dearth of studies directly examining this relation in pediatric cancer, JFM, CF, and FGIDs. Findings suggest that assessing and treating pain and sleep disruption is important when optimizing functional outcomes.

Conclusion: It is essential that research further examine objective sleep, elucidate the pain-sleep relationship, consider physiological and psychosocial mechanisms of this relationship, and investigate nonpharmacological interventions aimed at improving pain and sleep in vulnerable pediatric populations.
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http://dx.doi.org/10.1111/cns.12583DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6492850PMC
November 2016

Differential use of salmon by vertebrate consumers: implications for conservation.

PeerJ 2015 4;3:e1157. Epub 2015 Aug 4.

Center for Integrated Spatial Research, Department of Environmental Studies, University of California , Santa Cruz, CA , USA.

Salmon and other anadromous fish are consumed by vertebrates with distinct life history strategies to capitalize on this ephemeral pulse of resource availability. Depending on the timing of salmon arrival, this resource may be in surplus to the needs of vertebrate consumers if, for instance, their populations are limited by food availability during other times of year. However, the life history of some consumers enables more efficient exploitation of these ephemeral resources. Bears can deposit fat and then hibernate to avoid winter food scarcity, and highly mobile consumers such as eagles, gulls, and other birds can migrate to access asynchronous pulses of salmon availability. We used camera traps on pink, chum, and sockeye salmon spawning grounds with various run times and stream morphologies, and on individual salmon carcasses, to discern potentially different use patterns among consumers. Wildlife use of salmon was highly heterogeneous. Ravens were the only avian consumer that fed heavily on pink salmon in small streams. Eagles and gulls did not feed on early pink salmon runs in streams, and only moderately at early sockeye runs, but were the dominant consumers at late chum salmon runs, particularly on expansive river flats. Brown bears used all salmon resources far more than other terrestrial vertebrates. Notably, black bears were not observed on salmon spawning grounds despite being the most frequently observed vertebrate on roads and trails. From a conservation and management perspective, all salmon species and stream morphologies are used extensively by bears, but salmon spawning late in the year are disproportionately important to eagles and other highly mobile species that are seasonally limited by winter food availability.
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http://dx.doi.org/10.7717/peerj.1157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4558068PMC
September 2015

Quantifying plasmid copy number to investigate plasmid dosage effects associated with directed protein evolution.

Methods Mol Biol 2012 ;834:33-48

Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, CA, USA.

Our laboratory specializes in directed protein evolution, i.e., evolution of proteins under defined selective pressures in the laboratory. Our target genes are encoded in ColE1 plasmids to facilitate the generation of libraries in vivo. We have observed that when random mutations are not restricted to the coding sequence of the target genes, directed evolution results in a strong positive selection of plasmid origin of replication (ori) mutations. Surprisingly, this is true even during evolution of new biochemical activities, when the activity that is being selected was not originally present. The selected plasmid ori mutations are diverse and produce a range of plasmid copy numbers, suggesting a complex interplay between ori and coding mutations rather than a simple enhancement of level of expression of the target gene. Thus, plasmid dosage may contribute significantly to evolution by fine-tuning levels of activity. Here, we present examples illustrating these observations as well as our methods for efficient quantification of plasmid copy number.
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http://dx.doi.org/10.1007/978-1-61779-483-4_3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3804865PMC
April 2012

Examining infants' preferences for tempo in lullabies and playsongs.

Can J Exp Psychol 2011 Sep;65(3):168-72

Department of Psychology, Saint Mary's University, Halifax, Nova Scotia, Canada.

Caregivers around the world sing to their infants. Infants not only prefer to listen to infant-directed singing over adult-directed singing, but infant-directed singing also serves a function, communicating affective information to preverbal infants to aid in adjusting arousal levels. Pitch variation has previously been identified as one performance feature that may help to convey the message. Earlier research has indicated that infants' pitch preferences are context dependent, suggesting that infants are tuned in to the communicative intent of infant-directed singing. However, there are several other performance-based features present in infant-directed singing that may also contribute to the affective message. The current study examined the role of context on infants' tempo preferences in sung playsongs and lullabies. Using a head-turn preference procedure, we measured 24 preverbal infants' natural preferences for foreign language playsongs and lullabies as a function of tempo. Infants showed a preference for fast over slow tempo playsongs, but no such context dependent preference was found within lullabies. Results partially support the role of tempo as a communicative feature of infant directed singing.
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http://dx.doi.org/10.1037/a0023296DOI Listing
September 2011

Roles of DNA polymerase I in leading and lagging-strand replication defined by a high-resolution mutation footprint of ColE1 plasmid replication.

Nucleic Acids Res 2011 Sep 26;39(16):7020-33. Epub 2011 May 26.

Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, 1156 High Street Santa Cruz, CA 95060, USA.

DNA polymerase I (pol I) processes RNA primers during lagging-strand synthesis and fills small gaps during DNA repair reactions. However, it is unclear how pol I and pol III work together during replication and repair or how extensive pol I processing of Okazaki fragments is in vivo. Here, we address these questions by analyzing pol I mutations generated through error-prone replication of ColE1 plasmids. The data were obtained by direct sequencing, allowing an accurate determination of the mutation spectrum and distribution. Pol I's mutational footprint suggests: (i) during leading-strand replication pol I is gradually replaced by pol III over at least 1.3 kb; (ii) pol I processing of Okazaki fragments is limited to ∼20 nt and (iii) the size of Okazaki fragments is short (∼250 nt). While based on ColE1 plasmid replication, our findings are likely relevant to other pol I replicative processes such as chromosomal replication and DNA repair, which differ from ColE1 replication mostly at the recruitment steps. This mutation footprinting approach should help establish the role of other prokaryotic or eukaryotic polymerases in vivo, and provides a tool to investigate how sequence topology, DNA damage, or interactions with protein partners may affect the function of individual DNA polymerases.
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http://dx.doi.org/10.1093/nar/gkr157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3167613PMC
September 2011