Divergent effects of short-term and continuous anthropogenic noise exposure on Western Bluebird parental care behavior
Sensory environments are rapidly changing due to increased human activity in urban and non-urban areas alike. For instance, natural and anthropogenic sounds can interfere with parent-offspring communication and mask cues reflective of predation risk, resulting in elevated vigilance at the cost of provisioning. Here we present data from two separate studies involving anthropogenic noise and nestling provisioning behavior in Western Bluebirds (Sialia mexicana): one in response to short-term (1 h) experimental noise playback and a second in the context of nests located along a gradient of exposure to continuous noise. In the short-term playback experiment, nests were sequentially exposed to trials with either traffic noise or a silent audio track. The effect of the playback type interacted with the effect of the order in which trials were presented. The outcome was that provisioning rates during second trials with the silent track playback were higher than provisioning rates during noise playback on first or second trials, but not first trials with the silent track playback. Additionally, failed provisioning attempts only occurred during noise trials. In contrast, provisioning rates increased with the amplitude of noise among nests located in a gradient of continuous noise exposure. For nests along the noise gradient, the latency to resume provisioning behavior following human disturbance from approaching the nest negatively covaried with noise exposure amplitude. Specifically, birds resumed provisioning behavior more quickly with increased noise amplitude. Collectively, both studies demonstrate that noise can influence avian parental care of offspring, but the direction of the effect of noise are opposite. This difference could reflect variation in populations, noise characteristics or latent environmental contexts, or different ages of nestlings. However, it is also possible that the divergent responses reflect important differences in organismal responses to short-term versus long-term noise exposure. The possibility of mismatches in responses to short-term versus long-term noise exposure should be the focus of additional research, especially because short-term noise exposure experiments are often used to understand the consequences of noise pollution for organisms living in noisy environments.
Ozkan et al. (2024) Divergent effects of short-term and continuous anthropogenic noise exposure on Western Bluebird parental care behavior. PeerJ 12:e18558 https://doi.org/10.7717/peerj.18558
Evaluation of nutrient content of different harvest stages in switchgrass (Panicum virgatum L.) cultivars
Panicum virgatum L., also known as switchgrass, is a warm season short-day, C4-perennial crop gaining attention in feedstock production. The harvest stage of the forage crops and the cultivars used directly affect the feed quality as animal feed. In this study, differences were evaluated in various macro element contents of switchgrass (Panicum virgatum L.) cultivars at different harvest stages. Eight different switchgrass cultivars (Alamo, BoMaster, Kanlow, Cave in Rock, Long Island, Shawnee, Shelter, and Trailblazer) were evaluated in the study. According to the results of the study, significant differences were found among the cultivars studied for phosphate (P), potassium (K), calcium (Ca), and magnesium (Mg). The Long Island cultivar had the highest mineral concentration (0.223% P, 1.049% K, 0.581% Ca, and 0.201% Mg). As harvest proceeded, the levels of P and K in the plants decreased while the levels of Ca and Mg increased. The highest P (0.223%) and K (1.030%) values were obtained from plants harvested at the pre-flowering stage, while the highest Ca (0.538%) and Mg (0.183%) values were obtained from plants harvested at the full flowering stage. Switchgrass cultivars were found to be insufficient to meet animal needs for P and Ca content throughout the plant’s harvest stages. Mg was found to be sufficient in all harvest stages, while K was sufficient in the first two harvest stages, pre-flowering and 50% flowering, but insufficient in the full flowering stage. The dry matter’s Ca/P ratio, regardless of cultivar or harvest stage, posed no risk to animal health. The K/(Ca+Mg) ratio varied between 0.807 and 1.235 depending on the cultivar and harvest stage. This ratio does not pose any risk to animal health. Based on these results, it would be appropriate to supplement feed rations with materials containing P and Ca or to use switchgrass in animal feeding together with feeds rich in these minerals when using dry matter obtained from switchgrass cultivars alone as roughage. In general, although Panicum virgatum has an important potential as a feed source in animal nutrition, it needs to be supplemented with nutrient-containing additives. It would also be appropriate to determine the nutrient content of these varieties under different ecological conditions.
Acikbas (2024) Evaluation of nutrient content of different harvest stages in switchgrass (Panicum virgatum L.) cultivars. PeerJ 12:e18570 https://doi.org/10.7717/peerj.18570
Phase angle as a predictor of mortality in elderly patients with multimorbidity: a matched case-control study
Background We aimed to investigate the value of phase angle (PhA) as a prognostic marker for mortality in elderly patients with multimorbidity using a matched case-control study. Methods This study was conducted with patients 70 years of age or older with multimorbidity at Beijing Geriatric Hospital. The body composition parameters including PhA were determined using bioelectrical impedance analysis. Common hematological indices were determined using blood tests. The outcome was mortality 1 year after admission. A multivariate logistic regression analysis was employed to identify independent risk factors for death. A receiver-operating characteristic (ROC) curve analysis was used to evaluate the performance of risk factors in predicting death. Results A total of 30 deceased patients were included in the death group. The living patients were matched 1:1 with the deceased patients in age, gender, and Cumulative Illness Rating Scale-Geriatric score to generate a survival group of 30. The death group exhibited higher levels of blood urea nitrogen and extracellular water to total body water ratio and lower levels of PhA and prealbumin than the survival group. The multivariate logistic regression analysis identified PhA as the only independent risk factor for mortality (OR = 3.296, 95% CI [1.201–9.044], P < 0.05). For the ROC curve analysis, PhA had an area of 0.854 (95% CI [0.755–0.955], P = 000). The Youden index was 0.700, and the optimal cutoff value associated with the Youden index was 2.45°. Conclusion PhA serves as a good prognostic marker for mortality in elderly patients with multimorbidity.
Wang et al. (2024) Phase angle as a predictor of mortality in elderly patients with multimorbidity: a matched case-control study. PeerJ 12:e18592 https://doi.org/10.7717/peerj.18592
Nuclear eDNA metabarcoding primers for anthozoan coral biodiversity assessment
The distributions of anthozoan corals are undercharacterized due to their wide bathymetric ranges, occurrences in remote locales, and difficulties of identification from morphology alone. Environmental DNA (eDNA) sequencing promises to be a noninvasive strategy to complement conventional approaches for mapping and monitoring the distribution and biodiversity of coral communities. Primers for eDNA metabarcoding have been designed to amplify nuclear and mitochondrial DNA barcodes in shallow scleractinians and mitochondrial MutS in deep-sea octocorals. However, a comprehensive method for eDNA metabarcoding of all anthozoan corals, including black corals, has not been developed. We leveraged a sequence database of global coral collections, from shallow water to the deep sea, to design new PCR primers for coral eDNA sequencing that target the 28S rRNA gene (28S rDNA). We tested the performance of these primers by amplifying and sequencing eDNA from water samples collected in the Gulf of Mexico near mesophotic and deep-sea corals that were also imaged, sampled, and sequenced. Sequencing libraries produced using the primers were highly enriched in eDNA from octocorals, black corals and scleractinians, with up to 99.9% of the reads originating from these corals. Further, the 28S barcode amplified using the primers distinguished coral genera and species in many cases, like previously developed methods that target eDNA in only octocorals or scleractinians. We recovered amplicon sequencing variants (ASVs) identical to DNA barcodes derived from Sanger sequencing and genome skimming of corals sampled at the same field sites. This new eDNA metabarcoding strategy permits targeted eDNA sequencing of black corals, octocorals, and scleractinians at sites where they co-occur and expands our current toolkit for mapping and monitoring coral communities in shallow coral reefs and the deep sea.
McCartin et al. (2024) Nuclear eDNA metabarcoding primers for anthozoan coral biodiversity assessment. PeerJ 12:e18607 https://doi.org/10.7717/peerj.18607
Ferroptosis and its implications in bone-related diseases
Ferroptosis, a recently recognized form of regulated cell death (RCD) characterized by iron-dependent lipid peroxide accumulation, has emerged as a noteworthy regulator in various bone-related diseases, including osteoporosis (OP), osteoarthritis (OA), and osteosarcoma (OS). OS primarily afflicts the elderly, rendering them susceptible to fractures due to increased bone fragility. OA represents the most prevalent arthritis in the world, often observed in the aging population. OS predominantly manifests during adolescence, exhibiting an aggressive nature and bearing a significantly unfavorable prognosis. In this review article, we present an overview of the characteristics and mechanism of ferroptosis and its involvement in bone-related diseases, with a particular focus on OP, OA, and OS. Furthermore, we summarize chemical compounds or biological factors that impact bone-related diseases by regulating ferroptosis. Through an in-depth exploration of ferroptosis based on current research findings, this review provides promising insights for potential therapeutic approaches to effectively manage and mitigate the impact of these bone-related pathological conditions.
Wang et al. (2024) Ferroptosis and its implications in bone-related diseases. PeerJ 12:e18626 https://doi.org/10.7717/peerj.18626
Effect of basal luteinizing hormone/follicle-stimulating hormone ratio on clinical outcome of In Vitro fertilization in patients with polycystic ovarian syndrome: a retrospective cohort study
Background The basal luteinizing hormone (LH) and the prior LH to follicle-stimulating hormone (FSH) ratio (LH/FSH) in polycystic ovarian syndrome (PCOS) are generally higher than those in non-PCOS patients and the general population. The potential negative effects of elevated LH on human reproductive function are highly controversial, as are the effects of down-regulation of LH on reproductive function. The purpose of this study was to evaluate the effect of the basal LH/FSH ratio on the live birth rate of PCOS patients undergoing in vitro fertilization (IVF) cycles. Methods A retrospective analysis was conducted on 698 patients with polycystic ovary syndrome undergoing IVF treatments with a mild stimulation protocol (n = 95) and a gonadotropin-releasing hormone (GnRH) agonist protocol (n = 603). The basal LH/FSH ratio of 2 was used as the cut-off value for further subgroup analysis. The demographic properties, controlled ovarian hyperstimulation (COH) processes, and clinical pregnancy outcomes were compared between groups under each ovulation stimulation protocol. Results The live birth rate for patients with a LH/FSH ratio ≥ 2 group (56.38%, n = 149) was not statistically different from that of the ones with a ratio < 2 (53.74%, n = 454) in the GnRH agonist protocol (P = 0.576). Correspondingly, the live birth rate for the LH/FSH ratio ≥ 2 group (43.48%, n = 23) also showed no statistical difference from the ratio < 2 group (48.61%, n = 72) in the mild stimulation protocol (P = 0.668). Additionally, LH/FSH ratios had no significant effect on the live birth rate after adjusting for confounders both in the GnRH agonist protocol (adjusted OR: 1.111; 95% CI [0.467–2.642], P = 0.812) and in the mild stimulation protocol (adjusted OR: 4.057; 95% CI [0.431–38.195], P = 0.221). Furthermore, there was no significant difference in the live birth rate between different ovulation stimulation protocols in PCOS patients with the LH/FSH ratio ≥ 2. Conclusions The live birth rate in IVF outcomes was not affected by an elevated basal LH/FSH ratio in patients with polycystic ovary syndrome. The choice of the GnRH agonist protocol or mild stimulation protocol for ovulation stimulation does not affect the final clinical outcomes either for PCOS patients with a basal LH/FSH ratio ≥ 2.
Shan et al. (2024) Effect of basal luteinizing hormone/follicle-stimulating hormone ratio on clinical outcome of In Vitro fertilization in patients with polycystic ovarian syndrome: a retrospective cohort study. PeerJ 12:e18635 https://doi.org/10.7717/peerj.18635
Method selection affects the estimates of residency and site fidelity in bottlenose dolphins: testing sensitivity and performance of different methods using mark-resight data
Residency (R) and site fidelity (SF) are important parameters in population ecology, yet their quantification poses challenges in marine mammals. Based on a previous review, this study used simulated and empirical mark-resight data to assess the variations and performance of the most used R (n = 8) and SF (n = 11) indices in peer-reviewed literature under different scenarios. We applied the Jolly-Seber model to simulate thousands of bottlenose dolphin populations varying resighting (p) and survival (Phi) probabilities, and performed calibration, sensitivity, and validation analyses. Our results underscore the effects of p and Phi on individual categorization within the diverse simulated conditions, representing the often-overlooked heterogeneity in residency classification for Tursiops populations. All SF indices showed similar and consistent performance (>0.70 Gower’s distance) across the simulated scenarios, even when compared to field study data from wild dolphin populations (i.e., Savannah, USA, and Alvarado, Mexico); thus, SF should be a critical parameter for interstudy comparisons. Conversely, R indices were remarkably different based on their definitions and classification criteria. The different thresholds among definitions largely biased the proportion of residents and transient individuals (or occasional visitors) even leading to counterintuitive outcomes. This emphasizes the importance of considering trade-offs in R index selection aligned with project goals, specific sampling efforts, and population dynamics. For instance, the simplified binomial categorization of R defined by Conway (2017) (https://digitalcommons.coastal.edu/etd/10/) easier to interpret but R indices incorporating temporal components (e.g., monthly, seasonal, and annual) outperformed (>0.70 Gower’s distance) other R indices lacking such criteria. This allowed for a more detailed representation of the temporal structure of the population, and higher consistency and accuracy while classifying individuals. Also, although the residency categories proposed by Möller, Allen & Harcourt (2002) (DOI 10.1071/AM02011) did not perform as well, these seemed to fit better when dealing with data gaps across spatial and temporal scales. Our results contribute to the ongoing discussion on methodological implications for the interpretation of ecological patterns, facilitating a nuanced understanding of population dynamics, aiding scientists, and conservation agencies in making informed decisions for bottlenose dolphin populations worldwide.
Huesca-Domínguez et al. (2024) Method selection affects the estimates of residency and site fidelity in bottlenose dolphins: testing sensitivity and performance of different methods using mark-resight data. PeerJ 12:e18329 https://doi.org/10.7717/peerj.18329
Testing the ‘parasite-mediated domestication’ hypothesis: a comparative approach to the wild boar and domestic pig as model species
The mechanisms underlying the domestication process have already been well explained. Starting with Belyaev’s pioneering experiment on silver foxes, which showed that selection for tameness (reduced fear response, changes in the ‘hypothalamic-pituitary-adrenal system’—HPA axis) leads to destabilisation of the regulatory systems that control morphological and behavioural development, resulting in the changes characteristic of the domestication syndrome. Later, the thyroid rhythm hypothesis and the neural crest cell (NCC) hypothesis provided additional explanations. Recently, the parasite-mediated domestication hypothesis (PMD) has been proposed, suggesting an important role of endoparasites in the domestication process. Since parasites either directly or indirectly affect all mechanisms underlying the domestication syndrome (HPA, thyroid, NCC), the PMD proposes that they may be an important trigger of domestication. PMD can be tested either experimentally or comparatively. One of the basic assumptions of PMD is that parasite-susceptible, genetically less resistant/more tolerant wild animals were originally domesticated and that the susceptibility to parasites has been passed on to today’s domestic animals. This can be verified primarily by comparing the parasite susceptibility of existing wild and domestic populations of the same species. We, therefore, followed a systematic comparative approach by analysing the parasite load in wild boar (WB) and free-ranging domestic pig (DP) populations from a comparable environment in a geographically close area. Fresh faeces from WB and DP populations, one each from Slovenia (SI) and Croatia (HR), were sampled. A total of 59 individual faecal samples were collected (SI: 12 WB, 20 DP; HR: 14 WB, 13 DP). Parasitological diagnostics were carried out using the sedimentation and floatation method. Five different taxa were found in WB and seven in DP. Three parasite taxa were found exclusively in DP (Cystoisospora suis, Trichuris sp., Balantidium coli), and one (Strongyloides sp.) only in WB. Of the parasites found in both cohorts, strongyles/Oesophagostomum sp. were significantly more abundant in DP, while Eimeria sp. was found in equal amounts in both (but in HR only in WB). According to the preliminary study presented here, there is evidence to support the PMD baselines in the wild boar—domestic pig association. However, we cannot draw a definitive conclusion as there are many aspects that may bias the interpretation based on parasite load alone, which are also discussed here. Therefore, comparative studies should be supported by a more focussed methodology, including an experimental approach.
Oleinic et al. (2024) Testing the ‘parasite-mediated domestication’ hypothesis: a comparative approach to the wild boar and domestic pig as model species. PeerJ 12:e18463 https://doi.org/10.7717/peerj.18463
Effect of kinematics on ground reaction force during single-leg jump landing in children: a causal decomposition approach in jumpers and non-jumpers
Background The interaction between joint kinematics and kinetics is usually assessed by linear correlation analysis, which does not imply causality. Understanding the causal links between these variables may help develop landing interventions to improve technique and create joint-specific strengthening programs to reduce reaction forces and injury risk. Objective Therefore, the aim of this study was to analyze the causal interaction between lower limb sagittal kinematics and vertical ground reaction force (VGRF) during single-leg jump landing in children who are jumpers (volleyball and gymnastics) and non-jumpers, using the causal empirical decomposition method. Our hypothesis is that children who participate in jumping sports, compared to those who do not, employ a different joint strategy to regulate ground reaction forces during landing, particularly at the ankle level. Methods Two groups were compared: the jumpers group (n = 14) and the non-jumpers (control group, n = 11). The causal interaction between sagittal kinematics and VGRF was assessed using ensemble empirical mode decomposition (EEMD) and time series instantaneous phase dependence in bi-directional causality. The relative causal strength (RCS) between the time series was quantified as the relative ratio of absolute cause strength between kinematics and VGRF. Results A significant interaction between joint and group was found for RCS (p = 0.035, η2p = 0.14). The post-hoc analysis showed the jumpers group had higher ankle-to-VGRF RCS than the control group (p = 0.017, d = 1.03), while in the control group the hip-to-VGRF RCS was higher than the ankle-to-VGRF RCS (p = 0.004, d = 0.91). Conclusion Based on the causal decomposition approach, our results indicate that practicing jumping sports increases the causal effect of ankle kinematics on ground reaction forces in children. While non-jumper children rely more on the hip to modulate reaction forces, jumper children differ from non-jumpers by their greater use of the ankle joint. These findings could be used to develop specific training programs to improve landing techniques according to practice level, potentially helping to reduce the risk of injury in both athletes and non-athletes.
Cruz-Montecinos et al. (2024) Effect of kinematics on ground reaction force during single-leg jump landing in children: a causal decomposition approach in jumpers and non-jumpers. PeerJ 12:e18502 https://doi.org/10.7717/peerj.18502
Analysis of differential expression of hair follicle tissue transcriptome in Hetian sheep undergoing different periodic changes
Background This study provides new information on long non-coding RNA (lncRNA) and messenger RNA (mRNA) expression profiles in the hair follicles of Hetian sheep via the sequencing and analysis of the transcriptome of skin hair follicles during three periods of periodicity change. This is important for improving the quality of carpet wool, providing a preliminary basis for further research on the targeting relationship of these mRNAs and their target genes, and providing a scientific basis for marker-assisted selection of Hetian sheep. Methods The periodic variation of anagen (P I, May, n = 3), catagen (p II, October, n = 3), and telogen (p III, January, n = 3) of the skin hair follicle tissue of three Hetian sheep ewes were selected. Skin samples were collected from the right mid-side of each sampled sheep at three hair follicle developmental stages. The three sheep were used for each developmental stage as biological and technical replicates for transcriptome sequencing and analysis. Results The statistical power of this experimental design, calculated in RNASeqPower, was 0.92. Differential expression analysis revealed 81 lncRNAs that were differentially expressed (46 up-regulated and 35 down-regulated) and 129 mRNAs that were differentially expressed (46 up-regulated and 83 down-regulated) during the PI and PII periods. Between the PI and PIII periods, a total of 144 differentially expressed lncRNAs and 693 differentially expressed mRNAs were identified. Of these, 73 lncRNAs were significantly up-regulated and 71 were significantly down-regulated, while 474 mRNAs were significantly up-regulated and 219 were down-regulated. Additionally, a total of 87 lncRNAs were found to be differentially expressed, with 40 up-regulated and 47 down-regulated, along with 39 differentially expressed mRNAs (23 up-regulated and 16 down-regulated), between the PII and PIII stages. The functional assessment revealed that the mRNA expressed in the cells is related to the membrane, cell processes, metabolism, extracellular region, and other GO items. It is enriched in thyroid hormone synthesis, choline metabolism, cancer, AMPK, Hedgehog, and other signaling pathways. Conclusion A total of 2,286 lncRNAs (including 965 known and 1,321 novel lncRNAs) and 20,879 mRNAs were identified. These co-expressed differentially expressed genes could be used as candidate genes for studying the periodic changes of the hair follicles in Hetian sheep.
Chen et al. (2024) Analysis of differential expression of hair follicle tissue transcriptome in Hetian sheep undergoing different periodic changes. PeerJ 12:e18542 https://doi.org/10.7717/peerj.18542