Characteristics and usefulness of trunk muscle endurance tests on the Roman chair in healthy adults
Background Adequate trunk muscle endurance is considered to be an important indicator of good low back stability; therefore, its assessment is needed when determining an individual’s risk for back pain. Optimal tests to assess each trunk muscle group separately are difficult to find. The objective of this study was to verify if two groups of trunk muscle endurance tests (standard and alternative) show comparable results in terms of muscle endurance ratios, holding times and rated perceived effort to perform each test. Methods The study was designed as a quasi-experimental repeated-measures design. There was a single group of participants who took part in two different trunk muscle endurance testing. Sixty-eight healthy adult volunteers, aged 20–45 years (31.9 ± 7.2 years), without recent musculoskeletal injury or disorder participated in the study. All participants finished the study. Trunk muscle endurance tests as tested on the Roman chair (B tests) were compared with standard tests as suggested by McGill (A tests). Each group of tests consisted of an endurance test for trunk extensors, trunk flexors, and lateral trunk muscles for left and right side. The order of tests’ performances was randomly assigned to each participant, whereby a participant did perform A and B tests in the same order. In each test of A and B the holding time was recorded and a perceived effort in each test performance was also assessed by participants. Post testing performance the four ratios of trunk muscles endurance comparison were calculated for each group of tests to determine if there is a good or poor ratio between muscles. Results of each participant were compared for trunk muscle endurance ratio calculations, holding times and rated perceived effort for A and B tests. Results Results showed comparable trunk muscle endurance ratios in the three ratios observed, except for the flexors:extensors ratio (AFL:EX: 1.2 (IQR: 0.7–1.6) vs. BFL:EX: 0.6 (IQR: 0.3–0.8); p < 0.001). As compared to A tests, holding times were significantly longer in B tests for the extensors (AEX: 125.5 s (IQR: 104.8–182.8 s) vs. BEX: 284.0 s (IQR: 213.0–342.3 s); p < 0.001) and lateral trunk muscles (AL-LM: 61.0 s (IQR: 48.3–80.8 s) vs. BL-LM: 131.5 s (IQR: 95.5–158.5 s); AR-LM: 63.5 s (IQR: 45.8–77.3 s) vs. BR-LM: 113.0 s (IQR: 86.3–148.8 s); p < 0.001), both were also rated as slightly easier to perform in the extensors (ARPE-EX: 13 (IQR: 12.0–14.0) vs BRPE-EX: 11 (IQR: 10.0–13.0); pRPE-EX < 0.001) and lateral muscles testing (ARPE-LM: 14.0 (IQR: 12.3–15.8) vs. BRPE-LM: 13.0 (IQR: 12.0–15.0); pRPE-LM = 0.001). Conclusions A and B tests are comparable in three of four trunk muscle endurance ratios, while longer holding times and lower perceived effort to perform were observed in most of the B tests. The Roman chair tests could be used as an alternative to standard tests.
Petrič et al. (2022) Characteristics and usefulness of trunk muscle endurance tests on the Roman chair in healthy adults. PeerJ 10:e14469 https://doi.org/10.7717/peerj.14469
Sex ratio and relatedness in the Griffon vulture (Gyps fulvus) population of Serbia
Background Once a widespread species across the region of Southeast Europe, the Griffon vulture is now confined to small and isolated populations across the Balkan Peninsula. The population from Serbia represents its biggest and most viable population that can serve as an important reservoir of genetic diversity from which the birds can be used for the region’s reintroduction programmes. The available genetic data for this valuable population are scarce and as a protected species that belongs to the highly endangered vulture group, it needs to be well described so that it can be properly managed and used as a restocking population. Considering the serious recent bottleneck event that the Griffon vulture population from Serbia experienced we estimated the overall relatedness among the birds from this population. Sex ratio, another important parameter that shows the vitality and strength of the population was evaluated as well. Methods During the annual monitoring that was performed in the period from 2013–2021, we collected blood samples from individual birds that were marked in the nests. In total, 169 samples were collected and each was used for molecular sexing while 58 presumably unrelated birds from different nests were used for inbreeding and relatedness analyses. The relatedness was estimated using both biparentally (10 microsatellite loci) and uniparentally (Cytb and D-loop I of mitochondrial DNA) inherited markers. Results The level of inbreeding was relatively high and on average it was 8.3% while the mean number of relatives for each bird was close to three. The sex ratio was close to 1:1 and for the analysed period of 9 years, it didn’t demonstrate a statistically significant deviation from the expected ratio of 1:1, suggesting that this is a stable and healthy population. Our data suggest that, even though a relatively high level of inbreeding can be detected among the individual birds, the Griffon vulture population from Serbia can be used as a source population for restocking and reintroduction programmes in the region. These data combined with previously observed genetic differentiation between the populations from the Iberian and Balkan Peninsulas suggest that the introduction of foreign birds should be avoided and that local birds should be used instead.
Davidović et al. (2022) Sex ratio and relatedness in the Griffon vulture (Gyps fulvus) population of Serbia. PeerJ 10:e14477 https://doi.org/10.7717/peerj.14477
Catalases in the pathogenesis of Sporothrix schenckii research
Pathogenic fungal infection success depends on the ability to escape the immune response. Most strategies for fungal infection control are focused on the inhibition of virulence factors and increasing the effectiveness of antifungal drugs. Nevertheless, little attention has been focused on their physiological resistance to the host immune system. Hints may be found in pathogenic fungi that also inhabit the soil. In nature, the saprophyte lifestyle of fungi is also associated with predators that can induce oxidative stress upon cell damage. The natural sources of nutrients for fungi are linked to cellulose degradation, which in turn generates reactive oxygen species (ROS). Overall, the antioxidant arsenal needed to thrive both in free-living and pathogenic lifestyles in fungi is fundamental for success. In this review, we present recent findings regarding catalases and oxidative stress in fungi and how these can be in close relationship with pathogenesis. Additionally, special focus is placed on catalases of Sporothrix schenckii as a pathogenic model with a dual lifestyle. It is assumed that catalase expression is activated upon exposure to H2O2, but there are reports where this is not always the case. Additionally, it may be relevant to consider the role of catalases in S. schenckii survival in the saprophytic lifestyle and why their study can assess their involvement in the survival and therefore, in the virulence phenotype of different species of Sporothrix and when each of the three catalases are required. Also, studying antioxidant mechanisms in other isolates of pathogenic and free-living fungi may be linked to the virulence phenotype and be potential therapeutic and diagnostic targets. Thus, the rationale for this review to place focus on fungal catalases and their role in pathogenesis in addition to counteracting the effect of immune system reactive oxygen species. Fungi that thrive in soil and have mammal hosts could shed light on the importance of these enzymes in the two types of lifestyles. We look forward to encouraging more research in a myriad of areas on catalase biology with a focus on basic and applied objectives and placing these enzymes as virulence determinants.
Vargas-Maya et al. (2022) Catalases in the pathogenesis of Sporothrix schenckii research. PeerJ 10:e14478 https://doi.org/10.7717/peerj.14478
Estimation of common percentile of rainfall datasets in Thailand using delta-lognormal distributions
Weighted percentiles in many areas can be used to investigate the overall trend in a particular context. In this article, the confidence intervals for the common percentile are constructed to estimate rainfall in Thailand. The confidence interval for the common percentile help to indicate intensity of rainfall. Herein, four new approaches for estimating confidence intervals for the common percentile of several delta-lognormal distributions are presented: the fiducial generalized confidence interval, the adjusted method of variance estimates recovery, and two Bayesian approaches using fiducial quantity and approximate fiducial distribution. The Monte Carlo simulation was used to evaluate the coverage probabilities and average lengths via the R statistical program. The proposed confidence intervals are compared in terms of their coverage probabilities and average lengths, and the results of a comparative study based on these metrics indicate that one of the Bayesian confidence intervals is better than the others. The efficacies of the approaches are also illustrated by applying them to daily rainfall datasets from various regions in Thailand.
Thangjai et al. (2022) Estimation of common percentile of rainfall datasets in Thailand using delta-lognormal distributions. PeerJ 10:e14498 https://doi.org/10.7717/peerj.14498
Symbiotic association of microalgae and plants in a deep water culture system
In this study, microalgae culture (Chlorella vulgaris) and mint seedlings (Mentha spp.) were combined in a hydroponic system to improve plant growth. Mint seedlings were grown both in microalgae-containing and in microalgae-free trial groups, and both groups were subjected to aerated and non-aerated conditions to show the effect of aeration and microalgae co-cultivation on the mint weight and height. The plant quality was also determined with color measurements of the mint leaves. The increase in the weight of the plants was the highest in microalgae-containing and aerated group (0.47 g) and the lowest in microalgae-free and non-aerated group (0.22 g). On the other hand, the variation in the plant height was not significant between the groups, the growth was lateral. The best quality mint leaves were also produced in microalgae-containing and aerated group. Our results have revealed the symbiotic life of the mint plant placed in the hydroponic system with microalgae and demonstrated improved mint growth and quality. This co-cultivation system is also potentially more environmentally friendly compared to growing microalgae and mint independently because of lower cost of aeration and mixing for microalgae cultivation, higher nutrient consumption efficiency, and reduced nutrient outflow.
Özer Uyar et al. (2022) Symbiotic association of microalgae and plants in a deep water culture system. PeerJ 10:e14536 https://doi.org/10.7717/peerj.14536
N-mixture model-based estimate of relative abundance of sloth bear (Melursus ursinus) in response to biotic and abiotic factors in a human-dominated landscape of central India
Reliable estimation of abundance is a prerequisite for a species’ conservation planning in human-dominated landscapes, especially if the species is elusive and involved in conflicts. As a means of population estimation, the importance of camera traps has been recognized globally, although estimating the abundance of unmarked, cryptic species has always been a challenge to conservation biologists. This study explores the use of the N-mixture model with three probability distributions, i.e., Poisson, negative binomial (NB) and zero-inflated Poisson (ZIP), to estimate the relative abundance of sloth bears (Melursus ursinus) based on a camera trapping exercise in Sanjay Tiger Reserve, Madhya Pradesh from December 2016 to April 2017. We used environmental and anthropogenic covariates to model the variation in the abundance of sloth bears. We also compared null model estimates (mean site abundance) obtained from the N-mixture model to those of the Royle-Nichols abundance-induced heterogeneity model (RN model) to assess the application of similar site-structured models. Models with Poisson distributions produced ecologically realistic and more precise estimates of mean site abundance (λ = 2.60 ± 0.64) compared with other distributions, despite the relatively high Akaike Information Criterion value. Area of mixed and sal forest, the photographic capture rate of humans and distance to the nearest village predicted a higher relative abundance of sloth bears. Mean site abundance estimates of sloth bears obtained from the N-mixture model (Poisson distribution) and the RN model were comparable, indicating the overall utility of these models in this field. However, density estimates of sloth bears based on spatially explicit methods are essential for evaluating the efficacy of the relatively more cost-effective N-mixture model. Compared to commonly used index/encounter-based methods, the N-mixture model equipped with knowledge on governing biotic and abiotic factors provides better relative abundance estimates for a species like the sloth bear. In the absence of absolute abundance estimates, the present study could be insightful for the long-term conservation and management of sloth bears.
Chaudhuri et al. (2022) N-mixture model-based estimate of relative abundance of sloth bear (Melursus ursinus) in response to biotic and abiotic factors in a human-dominated landscape of central India. PeerJ 10:e13649 https://doi.org/10.7717/peerj.13649
Hypoxia-induced factor and its role in liver fibrosis
Liver fibrosis develops as a result of severe liver damage and is considered a major clinical concern throughout the world. Many factors are crucial for liver fibrosis progression. While advancements have been made to understand this disease, no effective pharmacological drug and treatment strategies have been established that can effectively prevent liver fibrosis or even could halt the fibrotic process. Most of those advances in curing liver fibrosis have been aimed towards mitigating the causes of fibrosis, including the development of potent antivirals to inhibit the hepatitis virus. It is not practicable for many individuals; however, a liver transplant becomes the only suitable alternative. A liver transplant is an expensive procedure. Thus, there is a significant need to identify potential targets of liver fibrosis and the development of such agents that can effectively treat or reverse liver fibrosis by targeting them. Researchers have identified hypoxia-inducible factors (HIFs) in the last 16 years as important transcription factors driving several facets of liver fibrosis, making them possible therapeutic targets. The latest knowledge on HIFs and their possible role in liver fibrosis, along with the cell-specific activities of such transcription factors that how they play role in liver fibrosis progression, is discussed in this review.
Mohammad Omar et al. (2022) Hypoxia-induced factor and its role in liver fibrosis. PeerJ 10:e14299 https://doi.org/10.7717/peerj.14299
Stiffness and thickness of the upper trapezius muscle increase after repeated climbing bouts in male climbers
Background Indoor climbing involves overloading the shoulder girdle, including the rotator cuff and upper trapezius muscles. This on the field study aimed to investigate the effects of repeated climbing bouts on morphological and mechanical measures of the upper trapezius muscle. Materials and Methods Fifteen experienced male climbers participated in the study. Rate of perceived exertion (RPE), blood lactate concentration ([La−]b), and stiffness and thickness over four points of the upper trapezius were assessed before and after a repeated climbing exercise. The procedure for the climbing exercise consisted of five climbs for a total time of 5-minutes per climb, followed by a 5-minute rest. Results The analysis showed an increase from baseline to after the 3rd climb (p ≤ 0.01) for RPE and after the 5th climb for [La−]b (p ≤ 0.001). Muscle stiffness and thickness increased at all points (1–2–3–4) after the 5th climb (p ≤ 0.01). We found spatial heterogeneity in muscle stiffness and thickness; muscle stiffness was the highest at Point 4 (p ≤ 0.01), while muscle thickness reached the highest values at points 1–2 (both p ≤ 0.01). Moreover, the analysis between the dominant and non-dominant shoulder showed greater stiffness after the 1st climb at Point 1 (p = 0.004) and after the 5th climb at Point 4 (p ≤ 0.001). Conclusions For muscle thickness, the analysis showed significant changes in time and location between the dominant and the non-dominant shoulder. Bilateral increases in upper trapezius muscle stiffness and thickness, with simultaneous increases in RPE and blood lactate in response to consecutive climbs eliciting fatigue.
Klich et al. (2022) Stiffness and thickness of the upper trapezius muscle increase after repeated climbing bouts in male climbers. PeerJ 10:e14409 https://doi.org/10.7717/peerj.14409
Multi-dimensional feature recognition model based on capsule network for ubiquitination site prediction
Ubiquitination is an important post-translational modification of proteins that regulates many cellular activities. Traditional experimental methods for identification are costly and time-consuming, so many researchers have proposed computational methods for ubiquitination site prediction in recent years. However, traditional machine learning methods focus on feature engineering and are not suitable for large-scale proteomic data. In addition, deep learning methods are mostly based on convolutional neural networks and fuse multiple coding approaches to achieve classification prediction. This cannot effectively identify potential fine-grained features of the input data and has limitations in the representation of dependencies between low-level features and high-level features. A multi-dimensional feature recognition model based on a capsule network (MDCapsUbi) was proposed to predict protein ubiquitination sites. The proposed module consisting of convolution operations and channel attention was used to recognize coarse-grained features in the sequence dimension and the feature map dimension. The capsule network module consisting of capsule vectors was used to identify fine-grained features and classify ubiquitinated sites. With ten-fold cross-validation, the MDCapsUbi achieved 91.82% accuracy, 91.39% sensitivity, 92.24% specificity, 0.837 MCC, 0.918 F-Score and 0.97 AUC. Experimental results indicated that the proposed method outperformed other ubiquitination site prediction technologies.
Li et al. (2022) Multi-dimensional feature recognition model based on capsule network for ubiquitination site prediction. PeerJ 10:e14427 https://doi.org/10.7717/peerj.14427
Mitochondrial genomes assembled from non-invasive eDNA metagenomic scat samples in the endangered Amur tiger Panthera tigris altaica
The Amur or Siberian tiger Panthera tigris altaica (Temminck, 1844) is currently restricted to a small region of its original geographical range in northwestern Asia and is considered ‘endangered’ by the IUCN Red List of Threatened Species. This solitary, territorial, and large top predator is in major need of genomic resources to inform conservation management strategies. This study formally tested if complete mitochondrial genomes of P. tigris altaica can be assembled from non-enriched metagenomic libraries generated from scat eDNA samples using the Illumina sequencing platform and open-access bioinformatics pipelines. The mitogenome of P. tigris altaica was assembled and circularized using the pipeline GetOrganelle with a coverage ranging from 322.7x to 17.6x in four different scat eDNA samples. A nearly complete mitochondrial genome (101x) was retrieved from a fifth scat eDNA sample. The complete or nearly complete mitochondrial genomes of P. tigris altaica were AT-rich and composed of 13 protein coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Synteny observed in all assembled mitogenomes was identical to that reported before for P. tigris altaica and other felids. A phylogenomic analysis based on all PCGs demonstrated that the mitochondrial genomes assembled from scat eDNA reliably identify the sequenced samples as belonging to P. tigris and distinguished the same samples from closely and distantly related congeneric species. This study demonstrates that it is viable to retrieve accurate whole and nearly complete mitochondrial genomes of P. tigris altaica (and probably other felids) from scat eDNA samples without library enrichment protocols and using open-access bioinformatics workflows. This new genomic resource represents a new tool to support conservation strategies (bio-prospecting and bio-monitoring) in this iconic cat.
Baeza (2022) Mitochondrial genomes assembled from non-invasive eDNA metagenomic scat samples in the endangered Amur tiger Panthera tigris altaica. PeerJ 10:e14428 https://doi.org/10.7717/peerj.14428