title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=766
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: No evidence of conditioning of pupillary constriction despite overtraining
link: https://peerj.com/articles/12948
last-modified: 2022-02-15
description: Eyeblink conditioning is the most popular paradigm for studying classical conditioning in humans. But the fact that eyelids are under voluntary control means it is ultimately impossible to ascertain whether a blink response is ‘conditioned’ or a timed ‘voluntary’ blink response. In contrast, the pupillary response is an autonomic response, not under voluntary control. By conditioning the pupillary response, one might avoid potential volition-related confounds. Several attempts have been made to condition the pupillary constriction and dilation responses, with the earliest published attempts dating back to the beginning of the 20th century. While a few early studies reported successful conditioning of pupillary constriction, later studies have failed to replicate this. The apparatus for recording pupil size, the type of stimuli used and the interval between the stimuli has varied in previous attempts—which may explain the inconsistent results. Moreover, measuring the pupil size used to be cumbersome compared with today when an eyetracker can continuously measure pupil size non-invasively. Here we used an eyetracker to test whether it is possible to condition the autonomic pupillary constriction response by pairing a tone (CS) and a light (US) with a 1s CS-US interval. Unlike in previous studies, our subjects went through multiple training sessions to ensure that any potential lack of conditioning would not be due to too little training. A total of 10 participants went through 2–12 conditioning sessions, each lasting approximately 20 min. One training session consisted of 75 paired, tone + light, trials and 25 randomly interspersed CS alone trials. The eyetracker (Tobii Pro Nano), continuously measured participants’ pupil size. To test statistically whether conditioning of the pupillary response occurred we compared the pupil size after the tone on the first session and the last session. The results showed a complete lack of evidence of conditioning. Though the pupil size varied slightly between participants, the size did not change as a result of the training—irrespective of the number of training sessions. The data replicate previous findings that pupillary constriction does not show conditioning. We conclude that it is not possible to condition pupillary constriction—at least not by pairing a tone and a light. One hypothesis is that when pupillary conditioning has been observed in previous studies, it has been mediated by conditioning of an emotional response.
creator: Diederick C. Niehorster
creator: Stina Bengtsson
creator: Niklas Brodin
creator: Anders Rasmussen
uri: https://doi.org/10.7717/peerj.12948
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Niehorster et al.

title: Factors of balance determining the risk of falls in physically active women aged over 50 years
link: https://peerj.com/articles/12952
last-modified: 2022-02-15
description: BackgroundBalance disorders are believed to be one of the main reasons for falls in older adults. They are related to natural processes of ageing, resulting in deterioration of information integration and processing from the vestibular, somatosensory and visual systems. The consequence is an increased number of postural sways, which are some of balance factors. Balance control in static and dynamic activities is an essential element of daily functioning of older citizens. It seems that balance assessment is essential to determine the risk of falls, as well as to determine which factors of balance have greatest impact on the risk of falls.MethodsThe study involved physically active female students (n = 36, mean age 67,11 ± 5,35) of a University of the Third Age. We used the Balance System SD platform to assess their balance in four tests with eyes open and with eyes closed and to determine the risk of falls. We assessed the relationships between individual balance indices (overall stability index, anterior/posterior stability index, medial/lateral stability index) and the falls risk index. We also determined those factors which predicted the risk of falls the most.ResultsThe studied subjects had low risk of falls for their age category. In most measurements there were relationships between the risk of falls and the size of sways in the coronal plane and the overall stability index. We also found that the overall stability index calculated in measurements with eyes closed predicted the risk of falls of the studied physically active females most accurately (R2 0.391 F(1.34)=23.475; <0.000). The subjects were physically active and their falls risk index was low - this allowed us to presume that there was a relationship between these two factors. Preventive programmes should include exercise performed with eyes closed, and tests conducted with eyes closed seem to be most sensitive in determining balance disorders in physically active women.
creator: Grzegorz Bednarczuk
creator: Izabela Rutkowska
uri: https://doi.org/10.7717/peerj.12952
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Bednarczuk and Rutkowska

title: Identification of novel prophage regions in Xenorhabdus nematophila genome and gene expression analysis during phage-like particle induction
link: https://peerj.com/articles/12956
last-modified: 2022-02-15
description: BackgroundEntomopathogenic Xenorhabdus bacteria are endosymbionts of Steinernema nematodes and together they form an insecticidal mutualistic association that infects a wide range of insect species. Xenorhabdus produce an arsenal of toxins and secondary metabolites that kill the insect host. In addition, they can induce the production of diverse phage particles. A few studies have focused on one integrated phage responsible for producing a phage tail-like bacteriocin, associated with an antimicrobial activity against other Xenorhabdus species. However, very little is known about the diversity of prophage regions in Xenorhabdus species.MethodsIn the present study, we identified several prophage regions in the genome of Xenorhabdus nematophila AN6/1. We performed a preliminary study on the relative expression of genes in these prophage regions. We also investigated some genes (not contained in prophage region) known to be involved in SOS bacterial response (recA and lexA) associated with mitomycin C and UV exposure.ResultsWe described two integrated prophage regions (designated Xnp3 and Xnp4) not previously described in the genome of Xenorhabdus nematophila AN6/1. The Xnp3 prophage region appears very similar to complete Mu-like bacteriophage. These prophages regions are not unique to X. nematophila species, although they appear less conserved among Xenorhabdus species when compared to the previously described p1 prophage region. Our results showed that mitomycin C exposure induced an up-regulation of recA and lexA suggesting activation of SOS response. In addition, mitomycin C and UV exposure seems to lead to up-regulation of genes in three of the four integrated prophages regions.
creator: Emilie Lefoulon
creator: Natalie Campbell
creator: S. Patricia Stock
uri: https://doi.org/10.7717/peerj.12956
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Lefoulon et al.

title: Validity and inter-rater reliability of ankle motion observed during a single leg squat
link: https://peerj.com/articles/12990
last-modified: 2022-02-15
description: BackgroundThe single leg squat (SLS) test is a clinical functional test commonly used to evaluate clinically aberrant movement patterns of the knee. The SLS could be an interesting option to analyze ankle control in the frontal plane during dynamic load analysis. However, to date, there are no studies that have analyzed the associations between the increased subtalar joint pronation by navicular drop (ND) test and ankle control with single leg squat (SLSankle) using a three-point scale. The purpose of this study was to evaluate the reliability of a clinical observation method to assess and determine the relationship between navicular drop (ND) and ankle control on the SLSankle score.MethodsA total of fifty-five healthy, physically active (31 females and 24 males) volunteers participated in this study. The degree of subtalar pronation was assessed through the ND test, and the ankle control was defined as the ankle displacement in the frontal plane during the SLS.ResultsWe found good intra-rater and inter-rater agreement during SLSankle, with Kappa values from 0.731 to 0.750. The relationship between the SLSankle and ND was significant ; the Spearman’s rank correlation coefficient was 0.504 (p < 0.05).ConclusionsThe SLSankle score supplied the clinical practice with a reliable and valid alternative for quantifying foot mobility in comparison to the ND test.
creator: Paloma Guillén-Rogel
creator: Cristina San Emeterio
creator: Pedro J. Marín
uri: https://doi.org/10.7717/peerj.12990
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Guillén-Rogel et al.

title: The shadow model: how and why small choices in spatially explicit species distribution models affect predictions
link: https://peerj.com/articles/12783
last-modified: 2022-02-14
description: The use of species distribution models (SDMs) has rapidly increased over the last decade, driven largely by increasing observational evidence of distributional shifts of terrestrial and aquatic populations. These models permit, for example, the quantification of range shifts, the estimation of species co-occurrence, and the association of habitat to species distribution and abundance. The increasing complexity of contemporary SDMs presents new challenges—as the choices among modeling options increase, it is essential to understand how these choices affect model outcomes. Using a combination of original analysis and literature review, we synthesize the effects of three common model choices in semi-parametric predictive process species distribution modeling: model structure, spatial extent of the data, and spatial scale of predictions. To illustrate the effects of these choices, we develop a case study centered around sablefish (Anoplopoma fimbria) distribution on the west coast of the USA. The three modeling choices represent decisions necessary in virtually all ecological applications of these methods, and are important because the consequences of these choices impact derived quantities of interest (e.g., estimates of population size and their management implications). Truncating the spatial extent of data near the observed range edge, or using a model that is misspecified in terms of covariates and spatial and spatiotemporal fields, led to bias in population biomass trends and mean distribution compared to estimates from models using the full dataset and appropriate model structure. In some cases, these suboptimal modeling decisions may be unavoidable, but understanding the tradeoffs of these choices and impacts on predictions is critical. We illustrate how seemingly small model choices, often made out of necessity or simplicity, can affect scientific advice informing management decisions—potentially leading to erroneous conclusions about changes in abundance or distribution and the precision of such estimates. For example, we show how incorrect decisions could cause overestimation of abundance, which could result in management advice resulting in overfishing. Based on these findings and literature gaps, we outline important frontiers in SDM development.
creator: Christian J. C. Commander
creator: Lewis A. K. Barnett
creator: Eric J. Ward
creator: Sean C. Anderson
creator: Timothy E. Essington
uri: https://doi.org/10.7717/peerj.12783
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Commander et al.

title: Uptake of a plasticizer (di-n-butyl phthalate) impacts the biochemical and physiological responses of barley
link: https://peerj.com/articles/12859
last-modified: 2022-02-14
description: BackgroundDBP is one of the most commonly used plasticizers for imparting desirable properties to polymers. The introduction of phthalates is reported to have occurred in the late 1920s, and there has been a significant rise in their release into the environment in past decades due to a lack of covalent bonding with the parent matrix. Because of their numerous applications in day-to-day life, phthalates have become ubiquitous and also classified as endocrine disruptors. Hence, several studies have been conducted to investigate the phthalate-mediated toxicities in animals; however, plants have not been explored to the same amount.MethodsTherefore, in the present study, the accumulation and translocation along with morpho-physiological perturbations in barley plants after 15, 30, 60, and 120 days of exposure to di-n-butyl phthalate (DBP) are investigated using standard protocols.ResultsThe maximal accumulation and translocation of DBP in the roots and shoots of barley plants was observed after 60 days of exposure. The exposure of DBP from 15 to 120 days was recorded to decline all the morphological indices (i.e., dry weight, net primary productivity, seed number per spike, and seed weight) of barley plants. The pigments content declined under DBP treatment for all exposure durations except 120 days exposure. Carbohydrate content increased after 15–30 days of exposure afterward it was observed to be decreased under 60 and 120 days of exposure. The protein content was declined in DBP stressed plants for 15–120 days. Proline content was increased in all exposure durations and maximal percent increase was recorded in 120 days of exposure. MDA content showed an increase at earlier exposure durations then followed by a decline in long-term exposure. Hydrogen peroxide content increased at all exposure durations. There were significant alterations observed in the activities of all antioxidative enzymes in comparison to the control. Furthermore, DBP stressed plants after 60 days were analyzed for the macromolecular variations using Fourier transform infrared spectroscopy (FTIR).ConclusionThus, the outcomes of the current work provide an appraisal of phthalates’ uptake and translocation mediated phytotoxic responses in barley plants. These observations can help in developing genetically modified edible plants that are resistant to phthalates uptake, thereby ensuring food security.
creator: Arpna Kumari
creator: Rajinder Kaur
uri: https://doi.org/10.7717/peerj.12859
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Kumari and Kaur

title: Assessment of the effects of storage temperature on fatty acid analysis using dried blood spot cards from managed southern white rhinoceroses (Ceratotherium simum simum): implications for field collection and nutritional care
link: https://peerj.com/articles/12896
last-modified: 2022-02-14
description: BackgroundSouthern white rhinoceroses (Ceratotherium simum simum) are an endangered species in decline due to poaching and negative habitat changes. Conservation of the species has become increasingly important and a focus on better human management has become prevalent. One area of management that impacts southern white rhinoceroses is nutritional health monitoring, which is often conducted through blood analysis. Blood analysis conducted during field research can be difficult due to temperature, distance, and limited technological resources, so new methods of fast, and relatively stable blood collection are being pursued. One method that has been used in humans for many years is beginning to make its way into wildlife studies: the use of dried blood spot (DBS) cards. These cards are used as a tool to store single drops of whole blood on specialized filter paper and, once dried, can be used for nutritional biomarker analysis. An area of interest for southern white rhinoceroses and nutrition is monitoring fatty acid percentages for cardiovascular, immune, and reproductive health. The time and temperature limitations for storing blood fractions or liquid whole blood when analyzing fatty acids have been investigated, but few studies have performed storage studies on DBS cards colder than −20 °C or in non-human species.MethodsIn order to better understand the limitations of DBS cards and the impact of temperature on fatty acid DBS samples in long-term storage, triplicate samples from seven adult southern white rhinoceroses at the North Carolina Zoo were collected and subjected to three storage treatments (immediate, room temperature (23 °C), or frozen (−80 °C) for 1 year).ResultsStearidonic (18:4w3) (Δ 0.3%), arachdic (20:0) (Δ 0.1%), eicosatetraenoic (20:4w3) (Δ 0.2%), and erucic acid (22:1w9) (Δ 0.1%) were in higher concentration in frozen than initial. Fatty acids in higher concentrations in the initial samples than frozen were myristic (14:0) (Δ 0.2%), mead (20:3w9) (Δ 0.1%), docosatetraenoic (22:4w6) (Δ 0.2%), nervonic (24:1) (Δ 0.1%), and total highly unsaturated fatty acids (HUFAs) (Δ 0.7%). Stearic (18:0) (Δ 2.2%), stearidonic (18:4w3) (Δ 0.3%), arachdic (20:0) (Δ 0.2%), paullinic (20:1w7) (Δ 0.4%), eicosatetraenoic (20:4w3) (Δ 0.1%), eicosapentaenoic (20:5w3) (Δ 0.1%), docosatetraenoic (22:4w6) (Δ 0.2%), nervonic acid (24:1) (Δ 0.2%), monoenes (Δ 1.9%), and total saturates (Δ 3.6%) had higher concentrations in room temperature than initial. Linoleic (18:2w6) (Δ 4.9%), mead acid (20:3w9) (Δ 0.1%), total polyunsaturated fatty acids (5.3%), and total omega-6 fatty acids (Δ 4.8%) had higher concentrations in initial compared to room temperature. Arachidonic (20:4w6) (Δ 0.4%) and omega-3 docosapentaenoic acid (22:5w3) (Δ 0.1%), had higher concentrations in frozen than in room temperature.DiscussionThe frozen samples had the fewest statistical differences compared to room temperature samples and essential omega-3 and -6 fatty acids were stable with freezing up to 1 year. While more research is still warranted, current results suggest that DBS samples are best utilized when immediate analysis or −80 °C storage is available.
creator: Jordan Wood
creator: Larry J. Minter
creator: Doug Bibus
creator: Troy N. Tollefson
creator: Kimberly Ange-van Heugten
uri: https://doi.org/10.7717/peerj.12896
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Wood et al.

title: Quantification of human enteric viruses as alternative indicators of fecal pollution to evaluate wastewater treatment processes
link: https://peerj.com/articles/12957
last-modified: 2022-02-14
description: We investigated the potential use and quantification of human enteric viruses in municipal wastewater samples of Winnipeg (Manitoba, Canada) as alternative indicators of contamination and evaluated the processing stages of the wastewater treatment plant. During the fall 2019 and winter 2020 seasons, samples of raw sewage, activated sludge, effluents, and biosolids (sludge cake) were collected from the North End Sewage Treatment Plant (NESTP), which is the largest wastewater treatment plant in the City of Winnipeg. DNA (Adenovirus and crAssphage) and RNA enteric viruses (Pepper mild mottle virus, Norovirus genogroups GI and GII, Rotavirus Astrovirus, and Sapovirus) as well as the uidA gene found in Escherichia coli were targeted in the samples collected from the NESTP. Total nucleic acids from each wastewater treatment sample were extracted using a commercial spin-column kit. Enteric viruses were quantified in the extracted samples via quantitative PCR using TaqMan assays. Overall, the average gene copies assessed in the raw sewage were not significantly different (p-values ranged between 0.1023 and 0.9921) than the average gene copies assessed in the effluents for DNA and RNA viruses and uidA in terms of both volume and biomass. A significant reduction (p-value ≤ 0.0438) of Adenovirus and Noroviruses genogroups GI and GII was observed in activated sludge samples compared with those for raw sewage per volume. Higher GCNs of enteric viruses were observed in dewatered sludge samples compared to liquid samples in terms of volume (g of sample) and biomass (ng of nucleic acids). Enteric viruses found in gene copy numbers were at least one order of magnitude higher than the E. coli marker uidA, indicating that enteric viruses may survive the wastewater treatment process and viral-like particles are being released into the aquatic environment. Viruses such as Noroviruses genogroups GI and GII, and Rotavirus were detected during colder months. Our results suggest that Adenovirus, crAssphage, and Pepper mild mottle virus can be used confidently as complementary viral indicators of human fecal pollution.
creator: Audrey Garcia
creator: Tri Le
creator: Paul Jankowski
creator: Kadir Yanaç
creator: Qiuyan Yuan
creator: Miguel I. Uyaguari-Diaz
uri: https://doi.org/10.7717/peerj.12957
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Garcia et al.

title: Defense mechanism responses to COVID-19
link: https://peerj.com/articles/12811
last-modified: 2022-02-11
description: The COVID-19 pandemic has had a wide range of negative physical and mental impacts. This review begins with a theoretical explanation of the psychological defense mechanisms used to deal with the pandemic. It then discusses different categories of defense mechanisms and their roles in managing the impacts of psychological distress. The aim of this review is to highlight the various psychological defense mechanisms individuals use to deal with the pandemic and to discuss how adjustment mechanisms can protect individuals from internal and external threats by shielding the integrity of the ego (the mind) and helping individuals maintain their self-schema.
creator: Nouf Altwaijri
creator: Turki Abualait
creator: Mohammed Aljumaan
creator: Raidah Albaradie
creator: Zahid Arain
creator: Shahid Bashir
uri: https://doi.org/10.7717/peerj.12811
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Altwaijri et al.

title: A synergistic, global approach to revising the trypanorhynch tapeworm family Rhinoptericolidae (Trypanobatoida)
link: https://peerj.com/articles/12865
last-modified: 2022-02-11
description: Since 2010, the trypanorhynch tapeworm family Rhinoptericolidae Carvajal & Campbell, 1975 has housed just two distinctive, monotypic genera (RhinoptericolaCarvajal & Campbell, 1975 and NataliellaPalm, 2010). However, global collections of tapeworms from sharks and rays over the last more than three decades brought to light the need for major revision of the family by suggesting a much greater species-level diversity for the nominal genus Rhinoptericola. Through synonymy and the description of new species, the number of species in the genus is increased from one to eight. A phylogenetic analysis of the D1–D3 gene region of 28S rRNA (28S), including seven of the now nine species of rhinoptericolids, and a broad sampling of the other Trypanobatoida is the first to recover a monophyletic Rhinoptericolidae. In addition to systematic revision, this study allowed for the first evaluation of the degree of intraspecific vs interspecific variation in 28S for adult trypanorhynchs across the various hosts and geographic localities from which they have been reported, suggesting a relatively consistent boundary for Rhinoptericola. It is further suggested that detailed scanning electron microscopy (SEM) images of both the basal and metabasal armatures greatly aid in the interpretation of hook arrangement and shape. A schematic to streamline determination of the tentacular surface presented in scanning electron micrographs and line drawings of trypanorhynchs is presented for species with both two and four bothria. In combination, these methodological refinements can now be used as a model to resolve issues of classification and non-monophyly within both major lineages of the Trypanorhyncha. As a result of the taxonomic work, Rhinoptericola megacanthaCarvajal & Campbell, 1975 (previously only known from the American cownose ray from the Chesapeake Bay and the Ticon cownose ray from the Gulf of Mexico, Venezuela, and Brazil) is now known from an additional species of cownose ray and a species of stingray, and is revealed to have a transatlantic distribution. Data from SEM suggest a simpler interpretation of hook arrangement in the metabasal armature for Rhinoptercola and—in combination with 28S sequence data—support ShirleyrhynchusBeveridge & Campbell, 1988 (a former rhinoptericolid) as its junior synonym. The three species formerly assigned to Shirleyrhynchus are thus transferred to Rhinoptericola. Data from light microscopy on whole-mounted specimens and histological sections, SEM, and 28S showed the eutetrarhynchid Prochristianella jensenaeSchaeffner & Beveridge, 2012b to be morphologically consistent with species of Rhinoptericola and it is thus transferred to the genus. The type series of P. jensenae was determined to be mixed, representing two distinct species which are here redescribed and described as new, respectively. Two additional novel species of Rhinoptericola are described from cownose rays from off Mozambique and the Gulf of California.
creator: Kaylee S. Herzog
creator: Kirsten Jensen
uri: https://doi.org/10.7717/peerj.12865
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Herzog and Jensen