Τρίτη 27 Μαρτίου 2018
Distinguishing Among Evolutionary Forces Acting on Genome-Wide Base Composition: Computer Simulation Analysis of Approximate Methods for Inferring Site Frequency Spectra of Derived Mutations in Recombining Regions
Inferred ancestral nucleotide states are increasingly employed in analyses of within and between species genome variation. Although numerous studies have focused on ancestral inference among distantly related lineages, approaches to infer ancestral states in polymorphism data have received less attention. Recently developed approaches that employ complex transition matrices allow us to infer ancestral nucleotide sequence in several evolutionary scenarios of base composition. However, the requirement of a single gene tree to calculate a likelihood is an important limitation for conducting ancestral inference using within-species variation in recombining genomes. To resolve this problem, and to extend the applicability of ancestral inference in studies of base composition evolution, we first evaluate three previously proposed methods to infer ancestral nucleotide sequences among within- and between-species sequence variation data. The methods employ a single allele, bifurcation tree, or a star tree for within-species variation data. Using simulated nucleotide sequences, we employ ancestral inference to infer fixations and polymorphisms. We find that all three methods show biased inference. We modify the bifurcating tree method to include weights to adjust for an expected site frequency spectrum, "bifurcating tree with weighting" (BTW). Our simulation analysis show that the BTW method can substantially improve the reliability and robustness of ancestral inference in a range of scenarios, including fixation biases and non-stationarity, in base composition evolution.
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The Draft Genome of the Invasive Walking Stick, Medauroidea extradentata, Reveals Extensive Lineage-Specific Gene Family Expansions of Cell Wall Degrading Enzymes in Phasmatodea
Plant cell wall components are the most abundant macromolecules on Earth. The study of the breakdown of these molecules is thus a central question in biology. Surprisingly, plant cell wall breakdown by herbivores is relatively poorly understood, as nearly all early work focused on the mechanisms used by symbiotic microbes to breakdown plant cell walls in insects such as termites. Recently, however, it has been shown that many organisms make endogenous cellulases. Insects, and other arthropods, in particular have been shown to express a variety of plant cell wall degrading enzymes in many gene families with the ability to break down all the major components of the plant cell wall. Here we report the genome of a walking stick, Medauroidea extradentata, an obligate herbivore that makes uses of endogenously produced plant cell wall degrading enzymes. We present a draft of the 3.3Gbp genome along with an official gene set that contains a diversity of plant cell wall degrading enzymes. We show that at least one of the major families of plant cell wall degrading enzymes, the pectinases, have undergone a striking lineage-specific gene family expansion in the Phasmatodea. This genome will be a useful resource for comparative evolutionary studies with herbivores in many other clades and will help elucidate the mechanisms by which metazoans breakdown plant cell wall components.
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A Bayesian Genomic Regression Model with Skew Normal Random Errors
Genomic selection (GS) has become a tool for selecting candidates in plant and animal breeding programs. In the case of quantitative traits, it is common to assume that the distribution of the response variable can be approximated by a normal distribution. However, it is known that the selection process leads to skewed distributions. There is vast statistical literature on skewed distributions, but the skew normal distribution is of particular interest in this research. This distribution includes a third parameter that drives the skewness, so that it generalizes the normal distribution. We propose an extension of the Bayesian whole-genome regression to skew normal distribution data in the context of GS applications, where usually the number of predictors vastly exceeds the sample size. However, it can also be applied when the number of predictors is smaller than the sample size. We used a stochastic representation of a skew normal random variable, which allows the implementation of standard Markov Chain Monte Carlo (MCMC) techniques to efficiently fit the proposed model. The predictive ability and goodness of fit of the proposed model were evaluated using simulated and real data, and the results were compared to those obtained by the Bayesian Ridge Regression model. Results indicate that the proposed model has a better fit and is as good as the conventional Bayesian Ridge Regression model for prediction, based on the DIC criterion and cross-validation, respectively. A computing program coded in the R statistical package and C programming language to fit the proposed model is available as supplementary material.
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QTL Mapping of Genome Regions Controlling Manganese Uptake in Lentil Seed
This study evaluated Mn concentration in the seeds of 120 RILs of lentil developed from the cross "CDC Redberry" x "ILL7502". Micronutrient analysis using atomic absorption spectrometry indicated mean seed manganese (Mn) concentrations ranging from 8.5 to 26.8 mg/kg, based on replicated field trials grown at three locations in Turkey in 2012 and 2013. A linkage map of lentil was constructed and consisted of seven linkage groups with 5,385 DNA markers. The total map length was 973.1 cM, with an average distance between markers of 0.18 cM. A total of 6 QTLs for Mn concentration were identified using composite interval mapping (CIM). All QTLs were statistically significant and explained 15.3 to 24.1% of the phenotypic variation, with LOD scores ranging from 3.00 to 4.42. The high-density genetic map reported in this study will increase fundamental knowledge of the genome structure of lentil, and will be the basis for the development of micronutrient-enriched lentil genotypes to support biofortification efforts.
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CRITICAL CARE PARAMEDIC - Community Ambulance
Community Ambulance is a 911 provider in the Southern portion of Las Vegas, NV and provides non-emergent transport within Henderson, Las Vegas, and Unincorporated Clark County. We are looking for full-time Critical Care Paramedics who are looking to work for a private agency that provides excellent pay and benefits as well as work in one of the most interesting cities in the world. Contact us for additional ...
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EMS Instructor - Lane Community College
EMS Instructor Lane Community College • First applicant review date is March 29, 2018, closes April 6, 2018 • View Job and Apply: https://ift.tt/2Ib3tGB Faculty Schedule: This position is for nine (9) months (1.0 FTE) with the expectation of approximately one (1) month or equivalent work during the summer.(With an outstanding benefits package!) Looking for a new direction for your EMS skills and ...
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A New Method for Monitoring Abnormal Muscle Response in Hemifacial Spasm: A Prospective Study
Hemifacial spasm (HFS) is a neurovascular compression syndrome and microvascular decompression (MVD) is the only curative treatment. An intraoperative abnormal muscle response (AMR) has been a reliable diagnostic tool and indicator of complete facial nerve decompression. An AMR is elicited by stimulation of a facial nerve branch and is recorded from facial muscles innervated by other nerve branches. Typically, it is instantly eliminated on intraoperative facial nerve electromyography (EMG) when the facial nerve is decompressed.
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High Prevalence of CTX-M-15-Type Extended-Spectrum β-Lactamase Among AmpC β-Lactamase-Producing Klebsiella pneumoniae Isolates Causing Bacteremia in Korea
Microbial Drug Resistance, Ahead of Print.
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Prevalence of Pyrazinamide Resistance in Khyber Pakhtunkhwa, Pakistan
Microbial Drug Resistance, Ahead of Print.
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Efficacy of Testosterone plus NASA Exercise Countermeasures during Head-Down Bed Rest
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Exercise Training Mitigates Multi-System Deconditioning during Bed Rest
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Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia [Anthropology]
Population genomic studies of ancient human remains have shown how modern-day European population structure has been shaped by a number of prehistoric migrations. The Neolithization of Europe has been associated with large-scale migrations from Anatolia, which was followed by migrations of herders from the Pontic steppe at the onset of...
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DEC2 modulates orexin expression and regulates sleep [Genetics]
Adequate sleep is essential for physical and mental health. We previously identified a missense mutation in the human DEC2 gene (BHLHE41) leading to the familial natural short sleep behavioral trait. DEC2 is a transcription factor regulating the circadian clock in mammals, although its role in sleep regulation has been unclear....
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Requirement for intron structures in activating the Cd8a locus [Genetics]
During differentiation of CD4+CD8+ double-positive (DP) thymocytes into the CD4−CD8+ single-positive (CD8SP) thymocytes committed to the cytotoxic T cell lineage, Cd8a transcription is temporally terminated after positive selection and is subsequently reinitiated, a process known as coreceptor reversal. Despite the identification of a transcriptional enhancer in the Cd8a gene that...
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Reconstructing a metazoan genetic pathway with transcriptome-wide epistasis measurements [Genetics]
RNA-sequencing (RNA-seq) is commonly used to identify genetic modules that respond to perturbations. In single cells, transcriptomes have been used as phenotypes, but this concept has not been applied to whole-organism RNA-seq. Also, quantifying and interpreting epistatic effects using expression profiles remains a challenge. We developed a single coefficient to...
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The manual pressures of stone tool behaviors and their implications for the evolution of the human hand
Source:Journal of Human Evolution, Volume 119
Author(s): Erin Marie Williams-Hatala, Kevin G. Hatala, McKenzie Gordon, Alastair Key, Margaret Kasper, Tracy L. Kivell
It is widely agreed that biomechanical stresses imposed by stone tool behaviors influenced the evolution of the human hand. Though archaeological evidence suggests that early hominins participated in a variety of tool behaviors, it is unlikely that all behaviors equally influenced modern human hand anatomy. It is more probable that a behavior's likelihood of exerting a selective pressure was a weighted function of the magnitude of stresses associated with that behavior, the benefits received from it, and the amount of time spent performing it. Based on this premise, we focused on the first part of that equation and evaluated magnitudes of stresses associated with stone tool behaviors thought to have been commonly practiced by early hominins, to determine which placed the greatest loads on the digits. Manual pressure data were gathered from 39 human subjects using a Novel Pliance® manual pressure system while they participated in multiple Plio-Pleistocene tool behaviors: nut-cracking, marrow acquisition with a hammerstone, flake production with a hammerstone, and handaxe and flake use. Manual pressure distributions varied significantly according to behavior, though there was a tendency for regions of the hand subject to the lowest pressures (e.g., proximal phalanges) to be affected less by behavior type. Hammerstone use during marrow acquisition and flake production consistently placed the greatest loads on the digits collectively, on each digit and on each phalanx. Our results suggest that, based solely on the magnitudes of stresses, hammerstone use during marrow acquisition and flake production are the most likely of the assessed behaviors to have influenced the anatomical and functional evolution of the human hand.
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Kanapoi revisited: Paleoecological and biogeographical inferences from the fossil fish
Source:Journal of Human Evolution
Author(s): Kathlyn M. Stewart, Scott J. Rufolo
Fish fossils were recovered from three different depositional contexts at the Pliocene Kanapoi site to: 1) test the assumption that habitat and ecology of modern fish taxa can predict habitat and ecology of fossil taxa; 2) reconstruct the lake and river environments in the Kanapoi Formation, with reference to fish fossils from the nearby Lothagam site deposits; and 3) investigate biogeographical inferences from the fossils. We compare the Kanapoi fish taxa and their depositional environments with the taxa and environments in modern Lake Turkana, and with another Plio-Pleistocene fauna from the eastern Turkana Basin. Taphonomic caveats are discussed. Our results support the use of ecological preferences of modern fish to predict past preferences. Our analysis of the Kanapoi fossils also indicates that the Pliocene Lonyumun Lake had a diverse fauna, with an unusual mix of taxa compared to the modern lake. The presence of possibly endemic species in the Pliocene lake may additionally represent a period of isolation during this epoch. Few fish fossils were recovered in the deposits of the ancestral Kerio River, a primary affluent of Lonyumun Lake then as now, but those present indicate a different ecology than that interpreted for the modern lake. Previously unknown fish taxa which enter the lake during the Pliocene suggest the existence of a connection between the Nile River and the Turkana Basin, which may have been viable for other vertebrates, including hominins.
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The Importance of the Saphenous Nerve Block for Analgesia Following Major Ankle Surgery: A Randomized, Controlled, Double-Blind Study
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Too Deep or Not Too Deep?: A Propensity-Matched Comparison of the Analgesic Effects of a Superficial Versus Deep Serratus Fascial Plane Block for Ambulatory Breast Cancer Surgery
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What do randomized controlled trials say about virtual rehabilitation in stroke? A systematic literature review and meta-analysis of upper-limb and cognitive outcomes
Virtual-reality based rehabilitation (VR) shows potential as an engaging and effective way to improve upper-limb function and cognitive abilities following a stroke. However, an updated synthesis of the litera...
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The clinical relevance of advanced artificial feedback in the control of a multi-functional myoelectric prosthesis
To effectively replace the human hand, a prosthesis should seamlessly respond to user intentions but also convey sensory information back to the user. Restoration of sensory feedback is rated highly by the pro...
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EMT - Basic - First Response Ambulance
Emergency Medical Technicians-Basic (EMT-B) respond to emergency calls to provide efficient and immediate care to the critically ill and injured, and to transport the patient to a medical facility. After receiving the call from the dispatcher, the EMT-B drives the ambulance to address or location given, using the most expeditious route, depending on traffic and weather conditions. The EMT-B must observe ...
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Optimized Target-AID system efficiently induces single base changes in zebrafish
Source:Journal of Genetics and Genomics
Author(s): Xiaochan Lu, Yunxing Liu, Guanrong Yan, Song Li, Wei Qin, Shuo Lin
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Modelling Movement Energetics Using Global Positioning System Devices in Contact Team Sports: Limitations and Solutions
Abstract
Quantifying the training and competition loads of players in contact team sports can be performed in a variety of ways, including kinematic, perceptual, heart rate or biochemical monitoring methods. Whilst these approaches provide data relevant for team sports practitioners and athletes, their application to a contact team sport setting can sometimes be challenging or illogical. Furthermore, these methods can generate large fragmented datasets, do not provide a single global measure of training load and cannot adequately quantify all key elements of performance in contact team sports. A previous attempt to address these limitations via the estimation of metabolic energy demand (global energy measurement) has been criticised for its inability to fully quantify the energetic costs of team sports, particularly during collisions. This is despite the seemingly unintentional misapplication of the model's principles to settings outside of its intended use. There are other hindrances to the application of such models, which are discussed herein, such as the data-handling procedures of Global Position System manufacturers and the unrealistic expectations of end users. Nevertheless, we propose an alternative energetic approach, based on Global Positioning System-derived data, to improve the assessment of mechanical load in contact team sports. We present a framework for the estimation of mechanical work performed during locomotor and contact events with the capacity to globally quantify the work done during training and matches.
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Video: Self-flying drones could serve as emergency responders
"Swarm drones" can navigate themselves and coordinate with each other, making them potentially useful for high-level rescue missions and more
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Does Your SOP Need Updating?
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Does Your SOP Need Updating?
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Does Your SOP Need Updating?
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Does Your SOP Need Updating?
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Hepatocellular adenoma in a woman who was undergoing testosterone treatment for gender identity disorder
Abstract
A 32-year-old Japanese woman was admitted to our hospital for the diagnosis and treatment of multiple liver tumors. She had been receiving 125 mg testosterone enanthate every 2 weeks following female-to-male gender identity disorder (GID) diagnosis at 20 years of age. Ultrasonography, computed tomography, and magnetic resonance imaging showed 11 hepatic nodular tumors with a maximum diameter of 28 mm. Liver tumors with hepatocellular adenoma (HCA) were diagnosed with needle biopsy. Segmentectomy of the left lateral lobe including two lesions, subsegmentectomy of S6 including two lesions, enucleation of each tumor in S5 and S7, and open surgical radiofrequency ablation for each tumor in S4 and S7 were performed. Immunohistochemical specimens showed that the tumor cells were diffusely and strongly positive for glutamine synthetase and that the nuclei were ectopically positive for β-catenin. Thus, the tumors were diagnosed as β-catenin-activated HCA (b-HCA). Transcatheter arterial chemoembolization plus subsequent radiofrequency ablation was performed for the 3 residual lesions in S4 and S8. Although testosterone enanthate was being continued for GID, no recurrence was observed until at least 22 months after the intensive treatments. HCA development in such patients receiving testosterone should be closely monitored using image inspection.
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Corticosterone level and central dopaminergic activity involved in agile and exploratory behaviours in formosan wood mice ( Apodemus semotus )
Abstract
The native Formosan wood mouse (Apodemus semotus) is the dominant rodent in Taiwan. In their natural environment, Formosan wood mice exhibit high locomotor activity, including searching and exploratory behaviours, which is observed similarly in the laboratory environment. How the behavioural responses of Formosan wood mice exhibit in elevated plus maze and marble burying tests remains unclear. How corticosterone levels and central dopaminergic activities are related to the behaviours in these tests is also unclear. This study compared the behaviours of Formosan wood mice with that of C57BL/6J mice using the elevated plus maze and marble burying tests, and measured the corticosterone levels and central dopaminergic activities. Formosan wood mice showed greater locomotor and exploratory activity than the C57BL/6J mice. Similarly, the marble burying and rearing numbers were higher for Formosan wood mice. High locomotor and exploratory behaviours were strongly correlated with corticosterone levels after acute mild restraint stress in Formosan wood mice. The anxiolytic, diazepam, reduced the high exploratory activity, corticosterone levels and central dopaminergic activities. The high locomotor and exploratory behaviours of Formosan wood mice are related to the corticosterone levels and central dopaminergic activities. These data may explain Formosan wood mice dominance in the intermediate altitude of Taiwan.
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Protective effects of mitochondrion-targeted peptide SS-31 against hind limb ischemia-reperfusion injury
Abstract
Hind limb ischemia-reperfusion injury is an important pathology in vascular surgery. Reactive oxygen species are thought to be involved in the pathogenesis of hind limb ischemia-reperfusion injury. SS-31, which belongs to a family of mitochondrion-targeted peptide antioxidants, was shown to reduce mitochondrial reactive oxygen species production. In this study, we investigated whether the treatment of SS-31 could protect hind limb from ischemia-reperfusion injury in a mouse model. The results showed that SS-31 treatment either before or after ischemia exhibited similar protective effects. Histopathologically, SS-31 treatment prevented the IR-induced histological deterioration compared with the corresponding vehicle control. SS-31 treatment diminished oxidative stress revealed by the reduced malondialdehyde level and increased activities and protein levels of Sod and catalase. Cellular ATP contents and mitochondrial membrane potential increased and the level of cytosolic cytC was decreased after SS-31 treatment in this IR model, demonstrating that mitochondria were protected. The IR-induced increase of levels of inflammatory factors, such as Tnf-α and Il-1β, was prevented by SS-31 treatment. In agreement with the reduced cytosolic cytC, cleaved-caspase 3 was kept at a very low level after SS-31 treatment. Overall, the effect of SS-31 treatment before ischemia is mildly more effective than that after ischemia. In conclusion, our results demonstrate that SS-31 confers a protective effect in the mouse model of hind limb ischemia-reperfusion injury preventatively and therapeutically.
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Contemporary Management of Ulcerative Colitis
Abstract
Purpose of Review
We discuss the newest evidence-based data on management of ulcerative colitis (UC). We emphasize risk-stratification, optimizing medical therapies, and surgical outcomes of UC.
Recent Findings
Recent medical advances include introduction of novel agents for UC. Vedolizumab, an anti-adhesion molecule, has demonstrated efficacy in moderate to severe UC. Tofacitinib, a small molecule, has also demonstrated efficacy. Data on optimization of infliximab show the superiority of combination therapy with azathioprine over monotherapy with infliximab or azathioprine alone. Data on anti-tumor necrosis factor-alpha (anti-TNF) therapeutic drug monitoring also hold promise, as do preliminary data on the dose escalation of infliximab in severe hospitalized UC. Surgical outcome data are reassuring, with new fertility data showing the effectiveness of in vitro fertilization.
Summary
UC management is multi-disciplinary and changing. While novel therapies hold promise, better optimization of our current arsenal will also improve outcomes.
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Prevalence and associated factors of preoperative functional disability in elective surgical patients over 55 years old: a prospective cohort study
Abstract
Purpose
In preoperative settings, patients may have functional disabilities due to the disease for which surgery is being performed or comorbidities, but the associated and predictive factors remain unknown. This study examined the prevalence of preoperative functional disability and clarified the associated factors.
Methods
Individuals aged ≥ 55 years who were scheduled to undergo surgery in a tertiary-care hospital in Japan between April 2016 and September 2016 were eligible for enrolment in the study. Patients with the diseases requiring psychiatric treatment and patients unable to complete the questionnaire without help were excluded. After obtaining informed consent, each patient was asked to complete the 12-item World Health Organization Disability Assessment Schedule-2.0, which is a standardized evaluation tool for assessing comprehensive living function. Data from these questionnaires and the patients' characteristics were evaluated. Multiple logistic regression analysis was conducted to determine independent factors associated with preoperative functional disability.
Results
Of 1201 recruited patients, 912 (75.9%) were included in our analysis. The prevalence of preoperative functional disability was 29.2%. Regression analysis identified six independent associated factors for preoperative functional disability: body mass index ≥ 30 kg m−2, mixed lung disease, serum albumin values, malnutrition, risk of malnutrition, and preoperative use of corticosteroids.
Conclusions
In total, 29.2% of preoperative patients had functional disability. Obesity, nutritional deficiency, respiratory complications, and low serum albumin values were determined as potentially modifiable factors.
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Effects of resistance training on MRI-derived epicardial fat volume and arterial stiffness in women with obesity: a randomized pilot study
Abstract
Aim
To date, few studies have analyzed the effects of exercise on cardiac adipose tissue. Overall, exercise programs did not meet the recommendations for significant weight loss, the utilization of resistance training was minimal, and the conclusions derived from these studies have diminished exercise as a strategy for cardiac fat loss.
Purpose
The objective of this pilot study was to analyze the effects of 3-week high-intensity, moderate-volume muscular endurance resistance training (RT) on cardiac fat and arterial stiffness.
Methods
A total of 11 young females with obesity, BMI = 34.13 (± 3.16) kg/m2 (n = 5 control, n = 6 intervention) completed the study. Absolute strength was assessed using one repetition maximum test (1RM) for bench press (BP) and leg press (LP), and relative strength was calculated using body weight (BW) as BP-to-BW and LP-to-BW ratio. Magnetic resonance was used to quantify epicardial and paracardial adipose tissue (EAT and PAT) volume, and applanation tonometry was used to assess arterial stiffness by estimating pulse wave velocity (PWV).
Results
EAT and PAT volumes (ml) showed significant interaction effects (p = 0.037 and p = 0.031), and very large changes (d > 1) of EAT (p = 0.006) and PAT (p = 0.036) in the intervention group. In addition, strength was significantly improved, including BP (p = 0.003), LP (p = 0.001), BP-to-BW ratio (p = 0.001), and LP-to-BW ratio (p = 0.002), while no changes were found in PWV.
Conclusions
High-intensity, moderate-volume RT, designed to enhance muscular endurance following the recommendations reduces EAT and PAT volumes, improves physical fitness in females with obesity, and has no negative effects on arterial stiffness.
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