title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1109
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Bird-window collisions: different fall and winter risk and protective factors
link: https://peerj.com/articles/9401
last-modified: 2020-06-19
description: BackgroundTo reduce bird fatalities from millions of window collisions each year in North America, it is important to understand how design and landscape elements relate to collision risk. The current study extends prior research that found that buildings near ornamental pear trees (Prunus calleryana) and buildings with mirrored windows significantly increased odds of collisions among eight buildings on the University of Utah campus in winter. The previous study found bird-friendly glass was not related to collision risk, although only one fatality occurred at two buildings with ORNILUX® ultraviolet (UV) or fritted windows. We reasoned that extending data collection to include fall might provide a better test of efficacy. We tested the following three hypotheses: (1) Buildings with mirrored windows would experience more collisions, replicating the original study; (2) the addition of fall migration data would reveal fewer collisions at the buildings with bird-friendly windows; (3) the danger of pear tree proximity would be heightened in winter, when fruit is ripe enough to appeal to frugivores, especially the Cedar Waxwings (Bombycilla cedrorum) that frequent these trees.MethodsTrained observers monitored buildings three times per week in Fall (September 12 to October 27, 2019) and Winter (October 29, 2019 to January 24, 2020). Collisions were photographed and documented in the iNaturalist University of Utah Bird Window Collision Project.ResultsThere were 39 total collisions, from 0 to 14 per building.Using generalized estimating equations, buildings near pear trees had 3.33-fold increased odds, mirrored windows had 5.92-fold increased odds, and bird-friendly windows had an 84% lower odds (Odds ratio = 0.16) of bird window collisions when analyzed separately; all were statistically significant (p < 0.01). A test of all possible combinations of risk and protective factors revealed that the best fit model included pear trees (odds = 2.31) and mirrored windows (odds = 2.33). A separate analysis tested the pear tree by season interaction model; it yielded the deadliest combination, with 40-fold increased odds for buildings near pear trees in winter season.DiscussionThis research provides the first peer-reviewed evidence found for the efficacy of bird-friendly fritted windows and ORNILUX ® UV windows in buildings. In addition, it replicated a study that established the dangers of mirrored windows and fruiting pear trees near buildings. These risks were especially dangerous to Cedar Waxwings, who constituted 62.2% of the identifiable window collision victims. This research highlights how building risks depend on window design, landscape choices, species, and season. If replicated, analyses of risk factors can help identify buildings that require mitigation to make existing windows less deadly. Results also support the installation of bird-friendly glass in new or renovated buildings to reduce fatalities.
creator: Barbara B. Brown
creator: Lia Hunter
creator: Sabrina Santos
uri: https://doi.org/10.7717/peerj.9401
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Brown et al.

title: The common personal behavior and preventive measures among 42 uninfected travelers from the Hubei province, China during COVID-19 outbreak: a cross-sectional survey in Macao SAR, China
link: https://peerj.com/articles/9428
last-modified: 2020-06-19
description: BackgroundThe novel coronavirus diseases 2019 (COVID-19) caused over 1.7 million confirmed cases and cumulative mortality up to over 110,000 deaths worldwide as of 14 April 2020. A total of 57 Macao citizens were obligated to stay in Hubei province, China, where the highest COVID-19 prevalence was noted in the country and a “lockdown” policy was implemented for outbreak control for more than one month. They were escorted from Wuhan City to Macao via a chartered airplane organized by Macao SAR government and received quarantine for 14 days with none of the individual being diagnosed with COVID-19 by serial RNA tests from the nasopharyngeal specimens and sera antibodies. It was crucial to identify common characteristics among these 57 uninfected individuals.MethodsA questionnaire survey was conducted to extract information such as behavior, change of habits and preventive measures.ResultsA total of 42 effective questionnaires were analyzed after exclusion of 14 infants and children with age under fifteen as ineligible for the survey and missing of one questionnaire, with a response rate of 97.7% (42 out of 43). The proportion of female composed more than 70% of this group of returners. The main reason for visiting Hubei in 88.1% of respondents was to visit relatives. Over 88% of respondents did not participate in high-risk activities due to mobility restriction. All (100%) denied contact with suspected or confirmed COVID-19 cases. Comparison of personal hygiene habits before and during disease outbreak showed a significant increase in practice including wearing a mask when outdoor (16.7% and 95.2%, P < 0.001) and often wash hands with soap or liquid soap (85.7% and 100%, P = 0.031).
creator: Chon Fu Lio
creator: Hou Hon Cheong
creator: Chin Ion Lei
creator: Iek Long Lo
creator: Lan Yao
creator: Chong Lam
creator: Iek Hou Leong
uri: https://doi.org/10.7717/peerj.9428
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Lio et al.

title: Shape of attachment structures in parasitic isopodan crustaceans: the influence of attachment site and ontogeny
link: https://peerj.com/articles/9181
last-modified: 2020-06-18
description: Many fields of modern systematic biology are adult-centred. This is unfortunately also the case for Cymothoidae, an ingroup of parasitic forms of Isopoda, with fishes as hosts. Different ingroups of Cymothoidae have specialised appendages that enable their fish associated lifestyles, attaching to different sites on the body of the host. The extent to which these structures vary among species and in relation different sites of attachment, and between different ontogenetic stages, is explored here. This study presents the detailed descriptions, illustrations, comparisons, and analysis of a variety of attachment structures of 13 adult and immature specimens representing three major groups Ceratothoa, Elthusa and Anilocra, along with full focus, detailed photographs of all the examined life stages. The three groups exhibit different strategies attaching to mouth, gill and externally, respectively. A statistical representation of the morphology of the dactyli, used for attaching to the host, was performed. This included a critical comparison of 10 additional species documented in literature. This is the first comprehensive description and photographs of specialised appendage morphology of immatures of Ceratothoa, as well as the first detailed micrographs of embryonic stages of Cymothoidae, and the first lateral and ventral views of immature stages of the examined species. Immature specimens possess morphological characters that can be used to distinguish between different species, but cannot be accurately identified based on diagnostic characters of adults. Quantitative analysis indicates that ontogeny plays a major role in the shape of the attachment structures (e.g. dactyli).
creator: Serita van der Wal
creator: Joachim T. Haug
uri: https://doi.org/10.7717/peerj.9181
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 van der Wal and Haug

title: Structural analysis of leucine, lysine and tryptophan mitochondrial tRNA of nesting turtles Caretta caretta (Testudines: Chelonioidea) in the Colombian Caribbean
link: https://peerj.com/articles/9204
last-modified: 2020-06-18
description: The understanding of the functional properties of mitochondrial transfer RNA (mt tRNAs) depend on the knowledge of its structure. tRNA acts as an interface between polynucleotides and polypeptides thus, they are key molecules in protein biosynthesis. The tRNA molecule has a functional design and, given its importance in the translation of mitochondrial genes, it is plausible that modifications of the structure can affect the synthesis of proteins and the functional properties of the mitochondria. In a previous work, the mitochondrial genome of an individual of the nesting Caretta caretta of the Colombian Caribbean was obtained, where specific mutations were identified in the only tRNALeu (CUN), tRNATrp and tRNALys genes. In order to analyze the effect of these mutations on these three mt tRNAs, the prediction of 2D and 3D structures was performed. Genes were sequenced in 11 nesting loggerhead turtles from the Colombian Caribbean. Two-dimensional structures were inferred using the ARWEN program, and three-dimensional structures were obtained with the RNA Composer 3D program. Two polymorphisms were identified in tRNATrp and another one was located in tRNALys, both specific to C. caretta. The thymine substitution in nucleotide position 14 of tRNATrp could constitute an endemic polymorphism of the nesting colony of the Colombian Caribbean. Two 2D and three 3D patterns were obtained for tRNATrp. In the case of tRNALys and tRNALeu 2D and 3D structures were obtained respectively, which showed compliance to canonical structures, with 4 bp in the D-arm, 4–5 bp in the T-arm, and 5 bp in the anticodon arm. Moderate deviations were found, such as a change in the number of nucleotides, elongation in loops or stems and non-Watson–Crick base pairing: adenine–adenine in stem D of tRNATrp, uracil–uracil and adenine–cytosine in the acceptor arm of the tRNALys and cytosine–cytosine in the anticodon stem of the tRNALeu. In addition, distortions or lack of typical interactions in 3D structures gave them unique characteristics. According to the size of the variable region (4–5 nt), the three analyzed tRNAs belong to class I. The interactions in the three studied tRNAs occur mainly between D loop—variable region, and between spacer bases—variable region, which classifies them as tRNA of typology II. The polymorphisms and structural changes described can, apparently, be post-transcriptionally stabilized. It will be crucial to perform studies at the population and functional levels to elucidate the synthetic pathways affected by these genes. This article analyses for the first time the 1D, 2D and 3D structures of the mitochondrial tRNALys, tRNATrp and tRNALeu in the loggerhead turtle.
creator: Harvey Infante-Rojas
creator: Leonardo Marino-Ramirez
creator: Javier Hernández-Fernández
uri: https://doi.org/10.7717/peerj.9204
license: https://creativecommons.org/publicdomain/zero/1.0/
rights: 

title: Identification of hydatidosis-related modules and key regulatory genes
link: https://peerj.com/articles/9280
last-modified: 2020-06-18
description: BackgroundEchinococcosis caused by larval of Echinococcus is prevalent all over the world. Although clinical experience showed that the presence of tapeworms could not be found in liver lesions, the repeated infection and aggravation of lesions still occur in the host. Here, this study constructed a multifactor-driven disease-related dysfunction network to explore the potential molecular pathogenesis mechanism in different hosts after E.multilocularis infection.MethodFirst, iTRAQ sequencing was performed on human liver infected with E.multilocularis. Second, obtained microRNAs(miRNAs) expression profiles of humans and canine infected with Echinococcus from the GEO database. In addition, we also performed differential expression analysis, protein interaction network analysis, enrichment analysis, and crosstalk analysis to obtain genes and modules related to E.multilocularis infection. Pivot analysis is used to calculate the potential regulatory effects of multiple factors on the module and identify related non-coding RNAs(ncRNAs) and transcription factors(TFs). Finally, we screened the target genes of miRNAs of Echinococcus to further explore its infection mechanism.ResultsA total of 267 differentially expressed proteins from humans and 3,635 differentially expressed genes from canine were obtained. They participated in 16 human-related dysfunction modules and five canine-related dysfunction modules, respectively. Both human and canine dysfunction modules are significantly involved in BMP signaling pathway and TGF-beta signaling pathway. In addition, pivot analysis found that 1,129 ncRNAs and 110 TFs significantly regulated human dysfunction modules, 158 ncRNAs and nine TFs significantly regulated canine dysfunction modules. Surprisingly, the Echinococcus miR-184 plays a role in the pathogenicity regulation by targeting nine TFs and one ncRNA in humans. Similarly, miR-184 can also cause physiological dysfunction by regulating two transcription factors in canine.ConclusionThe results show that the miRNA-184 of Echinococcus can regulate the pathogenic process through various biological functions and pathways. The results laid a solid theoretical foundation for biologists to further explore the pathogenic mechanism of Echinococcosis.
creator: Jijun Song
creator: Mingxin Song
uri: https://doi.org/10.7717/peerj.9280
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Song and Song

title: How caged salmon respond to waves depends on time of day and currents
link: https://peerj.com/articles/9313
last-modified: 2020-06-18
description: Disease, pest control, and environmental factors such as water quality and carrying capacity limit growth of salmon production in existing farm areas. One way to circumvent such problems is to move production into more exposed locations with greater water exchange. Farming in exposed locations is better for the environment, but may carry unforeseen costs for the fish in those farms. Currents may be too strong, and waves may be too large with a negative impact on growth and profit for farmers and on fish welfare. This study employed two major fish monitoring methods to determine the ability of Atlantic Salmon (Salmo salar) to cope with wavy conditions in exposed farms. Echosounders were used to determine vertical distribution and horizontal preference of fish during different wave and current conditions as well as times of day. Video cameras were used to monitor shoal cohesion, swimming effort, and fish prevalence in locations of interest. The results indicate complex interacting effects of wave parameters, currents, and time of day on fish behaviour and vertical distribution. During the day, hydrodynamic conditions had stronger effects on vertical distribution than during the night. In weak currents, fish generally moved further down in taller waves, but stronger currents generally caused fish to move upwards regardless of wave conditions. Long period waves had unpredictable effects on vertical distribution with fish sometimes seeking deeper water and other times moving up to shallower water. It is unclear how much the cage bottom restricted vertical distribution and whether movement upwards in the water columns was related to cage deformation. In extreme cases, waves can reach below the bottom of a salmon cage, preventing fish from moving below the waves and cage deformation could exacerbate this situation. Farmers ought to take into consideration the many interacting effects on salmon behaviour within a cage as well as the potential for cage deformation when they design their farms for highly exposed locations. This will ensure that salmon are able to cope when storms and strong currents hit at the same time.
creator: Ása Johannesen
creator: Øystein Patursson
creator: Jóhannus Kristmundsson
creator: Signar Pæturssonur Dam
creator: Pascal Klebert
uri: https://doi.org/10.7717/peerj.9313
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Johannesen et al.

title: Parents know best: transgenerational predator recognition through parental effects
link: https://peerj.com/articles/9340
last-modified: 2020-06-18
description: In highly biodiverse systems, such as coral reefs, prey species are faced with predatory threats from numerous species. Recognition of predators can be innate, or learned, and can help increase the chance of survival. Research suggests that parental exposure to increased predatory threats can affect the development, behaviour, and ultimately, success of their offspring. Breeding pairs of damselfish (Acanthochromis polyacanthus) were subjected to one of three olfactory and visual treatments (predator, herbivore, or control), and their developing embryos were subsequently exposed to five different chemosensory cues. Offspring of parents assigned to the predator treatment exhibited a mean increase in heart rate two times greater than that of offspring from parents in herbivore or control treatments. This increased reaction to a parentally known predator odour suggests that predator-treated parents passed down relevant threat information to their offspring, via parental effects. This is the first time transgenerational recognition of a specific predator has been confirmed in any species. This phenomenon could influence predator-induced mortality rates and enable populations to adaptively respond to fluctuations in predator composition and environmental changes.
creator: Jennifer A. Atherton
creator: Mark I. McCormick
uri: https://doi.org/10.7717/peerj.9340
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Atherton and McCormick

title: Spatial patterns of bat diversity overlap with woodpecker abundance
link: https://peerj.com/articles/9385
last-modified: 2020-06-18
description: Woodpecker diversity is usually higher in natural forests rich in dead wood and old trees than in managed ones, thus this group of birds is regarded as an indicator of forest biodiversity. Woodpeckers excavate cavities which can be subsequently used by several bird species. As a consequence, their abundance indicates high avian abundance and diversity in forests. However, woodpecker-made holes may be also important for other animals, for example, mammals but it has seldom been investigated so far. Here, we examine how well one species, the Great Spotted Woodpecker, predicts species richness, occurrence and acoustic activity of bats in Polish pine forests. In 2011 we conducted woodpecker and bat surveys at 63 point-count sites in forests that varied in terms of stand age, structure and amount of dead wood. From zero to five Great Spotted Woodpeckers at a point-count site were recorded. The total duration of the echolocation calls during a 10-min visit varied from 0 to 542 s and the number of bat species/species groups recorded during a visit ranged between zero to five. The local abundance of the woodpecker was positively correlated with bat species richness (on the verge of significance), bat occurrence and pooled bat activity. The occurrence of Eptesicus and Vespertilio bats and Nyctalus species was positively related with the abundance of the Great Spotted Woodpecker. The activity of Pipistrellus pygmaeus, Eptesicus and Vespertilio bats and a group of Myotis species was not associated with the woodpecker abundance, but echolocation calls of Nyctalus species, P. nathusii and P.pipistrellus were more often at sites with many Great Spotted Woodpeckers. Moreover, the probability of bat presence and the activity of bats was generally higher shortly after dusk and in middle of the summer than in late spring. We suggest that the observed correlations can be driven by similar roosting habitats (e.g., woodpeckers can provide breeding cavities for bats) or possibly by associated invertebrate food resources of woodpeckers and bats. The abundance of Great Spotted Woodpecker seems to be a good positive indicator of bat species richness, occurrence and activity, thus adding a group of relatively cryptic forest species that are indicated by the presence of the Great Spotted Woodpecker.
creator: Dorota Kotowska
creator: Marcin Zegarek
creator: Grzegorz Osojca
creator: Andrzej Satory
creator: Tomas Pärt
creator: Michał Żmihorski
uri: https://doi.org/10.7717/peerj.9385
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Kotowska et al.

title: KIT is involved in melanocyte proliferation, apoptosis and melanogenesis in the Rex Rabbit
link: https://peerj.com/articles/9402
last-modified: 2020-06-18
description: BackgroundMelanocytes play an extremely important role in the process of skin and coat colors in mammals which is regulated by melanin-related genes. Previous studies have demonstrated that KIT is implicated in the process of determining the color of the coat in Rex rabbits. However, the effect of KIT on the proliferation and apoptosis of melanocytes and melanogenesis has not been clarified.MethodsThe mRNA and protein expression levels of KIT were quantified in different coat colored rabbits by qRT-PCR and a Wes assay. To identify whether KIT functions by regulating of melanogenesis, KIT overexpression and knockdown was conducted in melanocytes, and KIT mRNA expression and melanin-related genes TYR, MITF, PMEL and DCT were quantified by qRT-PCR. To further confirm whether KIT influences melanogenesis in melanocytes, melanin content was quantified using NaOH lysis after overexpression and knockdown of KIT. Melanocyte proliferation was estimated using a CCK-8 assay at 0, 24, 48 and 72 h after transfection, and the rate of apoptosis of melanocytes was measured by fluorescence-activated cell sorting.ResultsKITmRNA and protein expression levels were significantly different in the skin of Rex rabbits with different color coats (P < 0.05), the greatest levels observed in those with black skin. The mRNA expression levels of KIT significantly affected the mRNA expression of the pigmentation-related genes TYR, MITF, PMEL and DCT (P < 0.01). Melanin content was evidently regulated by the change in expression patterns of KIT (P < 0.01). In addition, KIT clearly promoted melanocyte proliferation, but inhibited apoptosis.ConclusionsOur results reveal that KIT is a critical gene in the regulation of melanogenesis, controlling proliferation and apoptosis in melanocytes, providing additional evidence for the mechanism of pigmentation of animal fur.
creator: Shuaishuai Hu
creator: Yang Chen
creator: Bohao Zhao
creator: Naisu Yang
creator: Shi Chen
creator: Jinyu Shen
creator: Guolian Bao
creator: Xinsheng Wu
uri: https://doi.org/10.7717/peerj.9402
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Hu et al.

title: Habitual and ready positions in female table tennis players and their relation to the prevalence of back pain
link: https://peerj.com/articles/9170
last-modified: 2020-06-17
description: BackgroundThe current body of knowledge shows that there is very little research into the occurrence and scale of asymmetry or postural defects in table tennis. It is interesting which regions of the spine are exposed to the greatest changes in the shape of its curvatures and whether the asymmetrical position of the shoulder and pelvic girdles in table tennis players changes when adopting the ready position. Consequently, can overload occur in certain parts of the spine and can the asymmetry deepen as a response of adopting this position? The reply to these questions may be an indication of the need for appropriate compensatory or corrective measures. Therefore, the aim of the study was to evaluate the effect of body position during play on the change in the shape of anterior–posterior spinal curvatures and trunk asymmetry in table tennis players.MethodsTo evaluate body posture the photogrammetric method based on the Moiré phenomenon with equipment by CQ electronic was applied. The study involved 22 female players practicing competitive table tennis (the age of 17 ± 4.5, with the average training experience of 7 ± 4.3 years, body mass of 47.8 ± 15.8, and body height of 161.2 ± 10.4). Each participant completed an author’s own questionnaire on spinal pain. The shape of curvatures in the sagittal and frontal plane was evaluated in the participant in the habitual standing position and in the table tennis ready position. Descriptive statistical analysis was performed and the significance of differences was tested using the Mann–Whitney U test.Results and ConclusionsThis study demonstrated the dominance of kyphotic body posture in table tennis players, which can be caused by many hours of using the ready position during playing. After adopting this position, there are significant differences in the angles of anterior and posterior spinal curvatures compared to the habitual posture. This may be the cause of overloads and pain complaints reported by the study participants. Adopting the ready position is also associated with an increase in asymmetry in the position (rotation) of the pelvis and spinous processes (frontal plane). Therefore, training programs should be extended with exercises that relieve the spine in the vertical line and exercises that improve symmetry of the work of the upper limbs, body trunk muscles and the pelvis.
creator: Ziemowit Bańkosz
creator: Katarzyna Barczyk-Pawelec
uri: https://doi.org/10.7717/peerj.9170
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Bańkosz and Barczyk-Pawelec