title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1097 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The metabolic profile of Asinara (albino) and Sardo donkeys (pigmented) (Equus asinus L., 1758) points to unequivocal breed assignment of individuals link: https://peerj.com/articles/9297 last-modified: 2020-07-08 description: This study pointed to explore if variations in circulating levels of metabolites in the blood stream of no. 25 feral donkeys occur in view of the different coat color between specimens of Asinara (albino, no. 8) vs. Sardo (dun-grey, no. 17) breed. All individuals involved in this investigation are living in the nature, at Mediterranean latitudes and roam in the same areas all over the National Park of Capo Caccia, where they feed on spontaneous vegetation sources. The study was conducted during the positive photoperiod of the boreal hemisphere (peak in the month of June, 2019) to maximize the effect of exposure to the natural sun radiation and thus elicit the coping ability of albino (Asinara) in comparison with pigmented donkeys (Sardo). The biochemical profile of all donkeys was used in a Discriminant Analysis (DA) to explore if circulating levels of metabolites could point to metabolic markers for breed assignment of individuals following a canonical discriminant analysis (CANDISC). The biochemical investigation included also the determination of the circulating Vitamin E (alpha tocopherol, α-TOH), as an essential biologically active compound involved in antioxidant mechanisms, and its respective status (circulating α-TOH to total triglycerides and total cholesterol ratio). In the CANDISC, the distance between the two breeds was not significant. However, it pointed to different metabolites (UREA, total protein, total triglycerides, Zn) capable of describing biochemical patterns on each respective breed (Asinara vs. Sardo). The multivariate analysis DA carried out using 22 metabolites correctly assigned individuals to the two breeds in the 100% of cases. In view of such metabolic background, circulating α-TOH found in the bloodstream of Asinara vs. Sardo donkeys under free grazing conditions turned out to reach similar values (2.114 vs. 1.872 µg/ml, respectively, p = 0.676). It is worth noting that significant differences were observed as to circulating lactate dehydrogenase (LDH, p = 0.022) levels, in association with increased creatine phosphokinase (CPK, p = 0.076), both above the upper limit of the physiological range reported in other donkey breeds, and found in the totality of Asinara (albino) donkeys solely, still apparently clinically healthy. creator: Maria Grazia Cappai creator: Corrado Dimauro creator: Giovanni Paolo Biggio creator: Raffaele Cherchi creator: Francesca Accioni creator: Flavia Pudda creator: Gianpiero Boatto creator: Walter Pinna uri: https://doi.org/10.7717/peerj.9297 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Cappai et al. title: pulseTD: RNA life cycle dynamics analysis based on pulse model of 4sU-seq time course sequencing data link: https://peerj.com/articles/9371 last-modified: 2020-07-08 description: The life cycle of intracellular RNA mainly involves transcriptional production, splicing maturation and degradation processes. Their dynamic changes are termed as RNA life cycle dynamics (RLCD). It is still challenging for the accurate and robust identification of RLCD under unknow the functional form of RLCD. By using the pulse model, we developed an R package named pulseTD to identify RLCD by integrating 4sU-seq and RNA-seq data, and it provides flexible functions to capture continuous changes in RCLD rates. More importantly, it also can predict the trend of RNA transcription and expression changes in future time points. The pulseTD shows better accuracy and robustness than some other methods, and it is available on the GitHub repository (https://github.com/bioWzz/pulseTD_0.2.0). creator: Xin Wang creator: Siyu He creator: Jian Li creator: Jun Wang creator: Chengyi Wang creator: Mingwei Wang creator: Danni He creator: Xingfeng Lv creator: Qiuyan Zhong creator: Hongjiu Wang creator: Zhenzhen Wang uri: https://doi.org/10.7717/peerj.9371 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: Open Access uptake by universities worldwide link: https://peerj.com/articles/9410 last-modified: 2020-07-08 description: The implementation of policies promoting the adoption of an open science (OS) culture must be accompanied by indicators that allow monitoring the uptake of such policies and their potential effects on research publishing and sharing practices. This study presents indicators of open access (OA) at the institutional level for universities worldwide. By combining data from Web of Science, Unpaywall and the Leiden Ranking disambiguation of institutions, we track OA coverage of universities’ output for 963 institutions. This paper presents the methodological challenges, conceptual discrepancies and limitations and discusses further steps needed to move forward the discussion on fostering OA and OS practices and policies. creator: Nicolas Robinson-Garcia creator: Rodrigo Costas creator: Thed N. van Leeuwen uri: https://doi.org/10.7717/peerj.9410 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Robinson-Garcia et al. title: Exceptionally preserved ‘skin’ in an Early Cretaceous fish from Colombia link: https://peerj.com/articles/9479 last-modified: 2020-07-08 description: Studies of soft tissue, cells and original biomolecular constituents preserved in fossil vertebrates have increased greatly in recent years. Here we report preservation of ‘skin’ with chemical and molecular characterization from a three-dimensionally preserved caudal portion of an aspidorhynchid Cretaceous fish from the equatorial Barremian of Colombia, increasing the number of localities for which exceptional preservation is known. We applied several analytical techniques including SEM-EDS, FTIR and ToF-SIMS to characterize the micromorphology and molecular and elemental composition of this fossil. Here, we show that the fossilized ‘skin’ exhibits similarities with those from extant fish, including the wrinkles after suffering compression stress and flexibility, as well as architectural and tissue aspects of the two main layers (epidermis and dermis). This similarity extends also to the molecular level, with the demonstrated preservation of potential residues of original proteins not consistent with a bacterial source. Our results show a potential preservation mechanism where scales may have acted as an external barrier and together with an internal phosphate layer resulting from the degradation of the dermis itself creating an encapsulated environment for the integument. creator: Andrés Alfonso-Rojas creator: Edwin-Alberto Cadena uri: https://doi.org/10.7717/peerj.9479 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Alfonso-Rojas and Cadena title: Successful promotion of physical activity among students of medicine through motivational interview and Web-based intervention link: https://peerj.com/articles/9495 last-modified: 2020-07-08 description: BackgroundRegular physical activity supports healthy behavior and contributes to the reduction of preventable diseases. Students in their social transition period are the ideal groups for interventions. The higher education period, associated with demanding changes and poor time management, results in a low level of physical activity. In this age, social media usually are a suitable channel of communication and multicomponent interventions are the most desirable. It has not been sufficiently investigated how effective a Web-based approach is among university students when it comes to physical activity in the long-term period. We combined a Web-based approach with motivational interviews and tested these two interventions together and separate to assess their impact on improving the physical activity of medical students 1 year after the intervention.MethodsAll 514 first-year students at the Faculty of Medicine in Belgrade were invited to fill in a baseline questionnaire. Also, they underwent measurement of weight, height and waist circumference. After that, students selected a 6 months intervention according to their preference: Intervention through social media (Facebook) (Group 1) or combined with a motivational interview (Group 2). Group 3 consisted of students without any intervention. One year after completion of the 6 months intervention period, all students were invited to a second comprehensive assessment. Analyses were performed employing a wide range of statistical testing, including direct logistic regression, to identify determinants of increased physical activity measured by an average change of Metabolic Equivalent of Task (MET). This outcome measure was defined as the difference between the values at baseline and one year after completion of the 6 months intervention period.ResultsDue to a large number of potential determinants of the change of MET, three logistic regression models considered three groups of independent variables: basic socio-demographic and anthropometric data, intervention and willingness for change, and health status with life choices. The only significant model comprised parameters related to the interventions (p < 0.001). It accurately classified 73.5% of cases. There is a highly significant overall effect for type of intervention (Wald = 19.5, df = 2, p < 0.001) with high odds for the increase of physical activity. Significant relationship between time and type of intervention also existed (F = 7.33, p < 0.001, partial η2 = 0.091). The influence of both factors (time and interventions) led to a change (increase) in the dependent variable MET.ConclusionOur study confirmed the presence of low-level physical activity among students of medicine and showed that multicomponent interventions have significant potential for positive change. The desirable effects of the Web-based intervention are higher if an additional booster is involved, such as a motivational interview. creator: Dubravka Mandic creator: Vesna Bjegovic-Mikanovic creator: Dejana Vukovic creator: Bosiljka Djikanovic creator: Zeljka Stamenkovic creator: Nebojsa M. Lalic uri: https://doi.org/10.7717/peerj.9495 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Mandic et al. title: The effects of knee extensor moment biofeedback on gait biomechanics and quadriceps contractile behavior link: https://peerj.com/articles/9509 last-modified: 2020-07-08 description: Individuals with knee joint pathologies exhibit quadriceps dysfunction that, during walking, manifests as smaller peak knee extensor moment (pKEM) and reduced knee flexion excursion. These changes persist despite muscle strengthening and may alter stance phase knee joint loading considered relevant to osteoarthritis risk. Novel rehabilitation strategies that more directly augment quadriceps mechanical output during functional movements are needed to reduce this risk. As an important first step, we tested the efficacy of real-time biofeedback during walking to prescribe changes of ±20% and ±40% of normal walking pKEM values in 11 uninjured young adults. We simultaneously recorded knee joint kinematics, ground reaction forces, and, via ultrasound, vastus lateralis (VL) fascicle length change behavior. Participants successfully responded to real-time biofeedback and averaged up to 55% larger and 51% smaller than normal pKEM values with concomitant and potentially favorable changes in knee flexion excursion. While the VL muscle-tendon unit (MTU) lengthened, VL fascicles accommodated weight acceptance during walking largely through isometric, or even slight concentric, rather than eccentric action as is commonly presumed. Targeted pKEM biofeedback may be a useful rehabilitative and/or scientific tool to elicit desirable changes in knee joint biomechanics considered relevant to the development of osteoarthritis. creator: Amanda E. Munsch creator: Brian Pietrosimone creator: Jason R. Franz uri: https://doi.org/10.7717/peerj.9509 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Munsch et al. title: Motor expertise affects the unconscious processing of geometric forms link: https://peerj.com/articles/9520 last-modified: 2020-07-08 description: BackgroundThe unconscious processing of information is an important skill used by competitive athletes to handle the rapidly changing movements of opponents and equipment. Previous studies have shown that unconscious information processing among athletes is better than that among non-athletes in the sports-specific domain. However, it is not yet clear whether athletes also show superior unconscious information processing in the general cognitive domain.MethodsTwenty-five competitive table tennis players (athletes) and 26 aged-matched non-athletic college students (non-athlete controls) were recruited for this study. Participants first performed a masked priming task that used geometric shapes as primes and targets to examine unconscious information processing in the general cognitive domain. As a control, participants then completed a prime identification task to determine whether they could consciously detect the priming geometric forms. Reaction times and error rates were analyzed to examine whether motor expertise influenced unconscious information processing in the general domain. Nineteen athletes and 17 non-athletes from our present study, which used general stimuli, also participated in our previous study, which used sport-specific stimuli. The strength of the unconscious response priming effect was analyzed to examine whether the effect of motor expertise on unconscious processing could be transferred from a sports-specific domain to a general domain.ResultsSignal detection analyses indicated that neither athletes nor non-athletes could consciously perceive the priming stimuli. Two-way repeated-measures analyses of variance followed by simple main effects analyses of the masked priming performance, indicating that athletes responded faster and committed fewer errors when the priming stimulus was congruent with the target stimulus. These results suggested that athletes exhibited a significant unconscious response priming effect of geometric forms. By contrast, non-athletes did not respond faster or commit fewer errors for congruent vs. incongruent conditions. No significant difference was detected between athletes and non-athletes in error rates for congruent trials, but athletes committed significantly more errors than non-athletes on incongruent trials. The strength of the unconscious response priming effect that athletes exhibited was greater than that for non-athletes, both in the present study with general stimuli and in our previous study with sport-specific stimuli.ConclusionThe results indicated that motor expertise facilitated the unconscious processing of geometric forms, suggesting that the influence of motor expertise on unconscious information processing occurs not only for the sports-specific domain but also transfers to the general cognitive domain. creator: Jiaxian Geng creator: Fanying Meng creator: Chao Wang creator: Hanna Haponenko creator: Anmin Li uri: https://doi.org/10.7717/peerj.9520 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Geng et al. title: Metoprolol rescues endothelial progenitor cell dysfunction in diabetes link: https://peerj.com/articles/9306 last-modified: 2020-07-07 description: Added risk portended by diabetes in addition to hypertension has been related to an amplification of endothelial dysfunction. β-blockers are widely used for cardiovascular diseases and improve the endothelial function compared with a placebo. However, the effect of β-blockers on the endothelial progenitor cells (EPCs) function in diabetes is still unknown. Five β-blockers (metoprolol, atenolol, propranolol, bisoprolol, and nebivolol) were tested in EPC functional screening. Metoprolol improved EPC function significantly among the five β-blockers and was chosen for the in vivo tests in STZ induced diabetic mice. Reactive hyperemia peripheral arterial tonometry (RH-PAT) measurements were performed using the Endo-PAT2000 device in diabetic patients. Metoprolol, but not other β-blockers, improved EPC function in both tube formation and migration assay. EPC function was significantly decreased in diabetic mice, and metoprolol treatment restored damaged EPC migration capabilities and circulation EPC number. Metoprolol treatment promoted wound healing and stimulated angiogenesis in diabetic mice. Furthermore, metoprolol significantly enhanced eNOS phosphorylation and decreased O2− levels in EPCs of diabetic mice. In clinical trials, the RH-PAT index was significantly higher in metoprolol-treated versus bisoprolol-treated diabetics. Metoprolol could accelerate wound healing in diabetic mice and improve endothelial function in diabetic subjects, which may be mediated in part by improving impaired EPC function. creator: Lang Yan creator: Yi-fan Dong creator: Tao-lin Qing creator: Ya-ping Deng creator: Xue Han creator: Wen-jing Shi creator: Jin-feng Li creator: Fang-yuan Gao creator: Xiao-fang Zhang creator: Yi-jun Tian creator: Xiao-yu Dai creator: Jiang-bo Zhu creator: Ji-kuai Chen uri: https://doi.org/10.7717/peerj.9306 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yan et al. title: Three-dimensional thoracic and pelvic kinematics and arm swing maximum velocity in older adults using inertial sensor system link: https://peerj.com/articles/9329 last-modified: 2020-07-07 description: Understanding characteristics of torso motion and arm swing of older adults is important. A comprehensive database of three-dimensional thoracic and pelvic kinematics and arm swing maximum velocity of older adults during overground walking is still lacking. Moreover, the relationships between these variables are not fully understood. Therefore, we investigated age and gender effects of three-dimensional thoracic and pelvic ranges of motion and arm swing maximum velocity in 113 healthy old adults (aged 60–89 years) in a 2-min walk test using APDM Movement Monitoring inertial sensor system by two-way ANOVA, and post hoc Bonferroni correction was applied for multiple comparisons between age groups. A paired t-test was used to study the side preference of arm swing maximum velocity. The relationships between variables were investigated via multiple linear regression models. In general, thoracic and pelvic motions showed reduced amplitude with aging. Gait speed, pelvis coronal plane motion and arm swing maximum velocity significantly declined with age. Only the pelvic sagittal plane motion showed a gender main effect. Coronal plane motions of the thorax and pelvis were closely associated, as were sagittal plane motions. Thoracic coronal plane motion was the significant variable influencing pelvic transverse plane motion and vice versa. Gait speed, pelvic coronal and transverse plane motions and thorax sagittal plane motion were significant independent variables that influenced dominant arm maximum velocity. A larger maximum velocity was seen in the left arm. This investigation is valuable for better understanding of gait phenomena and will contribute to identification of gait dysfunction and development of rehabilitation measures. creator: Xin Fang creator: Zhongli Jiang uri: https://doi.org/10.7717/peerj.9329 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Fang and Jiang title: Universality vs experience: a cross-cultural pilot study on the consonance effect in music at different altitudes link: https://peerj.com/articles/9344 last-modified: 2020-07-07 description: BackgroundPrevious studies have shown that music preferences are influenced by cultural “rules”, and some others have suggested a universal preference for some features over others.MethodsWe investigated cultural differences on the “consonance effect”, consisting in higher pleasantness judgments for consonant compared to dissonant chords—according to the Western definition of music: Italian and Himalayan participants were asked to express pleasantness judgments for consonant and dissonant chords. An Italian and a Nepalese sample were tested both at 1,450 m and at 4,750 m of altitude, with the further aim to evaluate the effect of hypoxia on this task. A third sample consisted of two subgroups of Sherpas: lowlanders (1,450 m of altitude), often exposed to Western music, and highlanders (3,427 m of altitude), less exposed to Western music. All Sherpas were tested where they lived.ResultsIndependently from the altitude, results confirmed the consonance effect in the Italian sample, and the absence of such effect in the Nepalese sample. Lowlander Sherpas revealed the consonance effect, but highlander Sherpas did not show this effect.ConclusionsResults of this pilot study show that neither hypoxia (altitude), nor demographic features (age, schooling, or playing music), nor ethnicity per se influence the consonance effect. We conclude that music preferences are attributable to music exposure. creator: Giulia Prete creator: Danilo Bondi creator: Vittore Verratti creator: Anna Maria Aloisi creator: Prabin Rai creator: Luca Tommasi uri: https://doi.org/10.7717/peerj.9344 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Prete et al.