Tag: statistics

JMIRx Med. 2022 May 24;3(2):e32935. doi: 10.2196/32935. eCollection 2022 Apr-Jun.

ABSTRACT

BACKGROUND: In 2021, new variants of the SARS-CoV-2 virus appeared with increased transmissibility and virulence as compared with the original wild variant. The first variants of concern (VoCs), Alpha (B1.1.7) and Gamma (P.1), first appeared in the United Kingdom and Brazil, respectively. The Delta (B.1.617.2) variant, seen in India in October 2020, dominated COVID-19 infections across all regions through the second half of 2021.

OBJECTIVE: This research explores the degree to which SARS-CoV-2 VoCs generate waves of fluctuations in case-fatality rates (CFRs) across countries in several regions, increase the risk of mortality to persons with certain comorbidities, and decrease the risk of mortality as the percentage of fully vaccinated populations increases.

METHODS: This analysis introduces a measure of the temporal dynamics of COVID-19 infections in the form of a proxy CFR (pCFR), which can be compared among countries. It uses economic and demographic data reported by the World Bank and International Monetary Fund, plus publicly available epidemiological and medical statistics reported to the relevant national and international public health authorities. From these ecological data, pandemic average and daily COVID-19 CFRs and their correlations with potential cofactors were computed for 2021, a year dominated by the spread of World Health Organization-designated VoCs. The study does not investigate disease pathology; rather, it compares the daily case rates and pCFRs to reveal underlying contributing factors that vary from country to country and region to region.

RESULTS: The in-depth global regression analysis of cofactors found that the strongest single correlation with COVID-19 fatality was 0.36 (SD 0.02) with P<.001 for chronic kidney disease. No other single physiological cofactors display positive correlations exceeding 0.26 (SD 0.26), with P=.008 (asthma) and P=.01 (coronary disease). The study confirms that the pCFR is a valuable metric for tracking waves of infection due to different VoCs within countries.

CONCLUSIONS: The influence of social, economic, and medical cofactors on the CFR due to VoCs remains qualitatively similar, albeit strengthened, to the levels found for the wild strain. The strong regional variations of the influence of all cofactors observed for the wild strain persists in infections for all VoCs with very strong correlation coefficients seen in the Middle East for asthma (0.76), coronary heart disease (0.60), lung disease (0.70), and chronic kidney disease (0.52). Strong regional variations emphasize the influence on COVID-19 mortality due to regional differences in national economics, patterns of health care policies, and variations in cultural practices and environment. The pCFR-based analysis reveals clear patterns of the spread of VoCs across regions, but there is little evidence for the spread of the Lambda and Mu (B.1.621) variants of interest outside of South America.

PMID:35969709 | PMC:PMC9364421 | DOI:10.2196/32935

J Anim Sci Technol. 2022 Jul;64(4):800-811. doi: 10.5187/jast.2022.e45. Epub 2022 Jul 31.

ABSTRACT

The integration of metabolomics and transcriptomics may elucidate the correlation between the genotypic and phenotypic patterns in organisms. In equine physiology, various metabolite levels vary during exercise, which may be correlated with a modified gene expression pattern of related genes. Integrated metabolomic and transcriptomic studies in horses have not been conducted to date. The objective of this study was to detect the effect of moderate exercise on the metabolomic and transcriptomic levels in horses. In this study, using nuclear magnetic resonance (NMR) spectroscopy, we analyzed the concentrations of metabolites in muscle and plasma; we also determined the gene expression patterns of branched chain (alpha) keto acid dehydrogenase kinase complex (BCKDK), which encodes the key regulatory enzymes in branched-chain amino acid (BCAA) catabolism, in two breeds of horses, Thoroughbred and Jeju, at different time intervals. The concentrations of metabolites in muscle and plasma were measured by ¹H NMR (nuclear magnetic resonance) spectroscopy, and the relative metabolite levels before and after exercise in the two samples were compared. Subsequently, multivariate data analysis based on the metabolic profiles was performed using orthogonal partial least square discriminant analysis (OPLS-DA), and variable important plots and t-test were used for basic statistical analysis. The stress-induced expression patterns of BCKDK genes in horse muscle-derived cells were examined using quantitative reverse transcription polymerase chain reaction (qPCR) to gain insight into the role of transcript in response to exercise stress. In this study, we found higher concentrations of aspartate, leucine, isoleucine, and lysine in the skeletal muscle of Jeju horses than in Thoroughbred horses. In plasma, compared with Jeju horses, Thoroughbred horses had higher levels of alanine and methionine before exercise; whereas post-exercise, lysine levels were increased. Gene expression analysis revealed a decreased expression level of BCKDK in the post-exercise period in Thoroughbred horses.

PMID:35969708 | PMC:PMC9353351 | DOI:10.5187/jast.2022.e45

J Anim Sci Technol. 2022 Jul;64(4):792-799. doi: 10.5187/jast.2022.e44. Epub 2022 Jul 31.

ABSTRACT

Dopamine (DA) is known to be a key modulator of animal behaviors. Thus, the plasma concentration of DA might be used as a biomarker for the behavioral characteristics of horses. The behavioral characteristics of horses vary depending on the breed, age, and sex. Moreover, the DA receptor genotypes are also related to horse behaviors. Thus, the aim of this study was to investigate the DA concentration variations of horse plasma by breed, age, sex, or genotype of its receptor. The horses were divided by breed into Thoroughbred (n = 13), Pony (n = 9), Warmblood (n = 4), and Haflinger (n = 5). The age variable was divided into three different groups: post-pubertal (2-5 years, n = 6), adult (6-13 years, n = 19), and aged horses (15-24 years, n = 6). The sex variable was divided into geldings (n = 8) and mares (n = 23). Approximately 10 mL of blood was collected, and an ELISA kit was used to measure the plasma concentration of DA. Polymerase chain reaction analysis was performed to identify the genetic variation in the DA D4 receptor gene (DRD4). SPSS statistical software was used for statistical analysis. The DA concentrations in geldings were significantly lower than those in mares. There was no significant difference in DA concentrations among breed and age groups. Horses with the GG and GA genotypes had significantly higher plasma concentrations of DA compared to horses with the AA genotype for the G292A gene. Briefly, the plasma concentration of DA varied depending on the sex and genotype of G292A. These factors should be considered when the concentration of DA is used as a biomarker for the behavioral characteristics of horses. In conclusion, the DA concentration or DRD4 genotype of horse plasma has the potential to be used as a biomarker that can predict the behavioral characteristics of horses.

PMID:35969706 | PMC:PMC9353348 | DOI:10.5187/jast.2022.e44

J Anim Sci Technol. 2022 Jul;64(4):727-739. doi: 10.5187/jast.2022.e54. Epub 2022 Jul 31.

ABSTRACT

Mycotoxin contamination in pig feeds has a negative impact on growth performance, the immune system, and major body organs. Arginine (Arg) plays an important role in animals’ body biochemistry and physiology. This study aimed to determine the effect of dietary Arg supplementation on mitigating the negative effects of mycotoxins in growing pigs. A total of 72 growing pigs (Landrace × Large white) with initial mean body weight (BW) = 55 ± 2.5 kg were allotted to four treatment groups with three replicates per group of six pigs per replicate in a completely randomized design. The treatments included a non-toxin diet with 1.2% Arg (NT1.2) and mycotoxin-challenged treatments supplemented with 1.2% Arg (TX1.2), 1.3% Arg (TX1.3), and 1.4% Arg (TX1.4). Statistical analysis of data included the effects of dietary level of Arg. The results indicated a significantly higher BW (p < 0.05), average daily gain (p < 0.05), and gain-to-feed ratio (p < 0.05) in the NT1.2 group than in the TX1.2, TX1.3, and TX1.4 groups. The relative weight of the liver was higher (p < 0.05) in the TX1.2 compared to that of the NT1.2 group, although it was not different from that of TX1.3 and TX1.4. The level of tumor necrosis factor-alpha was significantly up-regulated (p < 0.05) in the liver tissue of the TX1.2 group compared to that of the other treatments. Overall, dietary Arg supplementation remedied liver injury and alleviated the compromised immune system caused by mycotoxin toxicity.

PMID:35969699 | PMC:PMC9353345 | DOI:10.5187/jast.2022.e54

J Athl Train. 2022 Jun 1;57(6):564-570. doi: 10.4085/1062-6050-733-20.

ABSTRACT

CONTEXT: Individuals with chronic ankle instability (CAI) present with alterations in the compositional structure of their talar articular cartilage. These alterations likely influence how the talar cartilage responds to the loading associated with activities of daily living, such as walking. Ultrasonography has emerged as an alternative imaging modality for assessing the amount of cartilage deformation in response to loading because it is clinically accessible and cost effective for routine measurements.

OBJECTIVES: To (1) compare talar-cartilage deformation in response to a standardized exercise protocol between those with and those without CAI and (2) examine the association between spatiotemporal walking gait parameters and cartilage deformation.

DESIGN: Case-control study.

SETTING: Research laboratory.

PATIENTS OR OTHER PARTICIPANTS: A volunteer sample of 24 participants with self-reported CAI (age = 23.2 ± 3.9 years, body mass index [BMI] = 25.1 ± 3.7 kg/m2) and 24 uninjured controls (age = 24.3 ± 2.9 years, BMI = 22.9 ± 2.8 kg/m2).

MAIN OUTCOME MEASURE(S): Spatiotemporal walking gait was first assessed from 5 self-selected trials using an electronic walkway with data sampled at 120 Hz. An 8- to 13-MHz linear-array ultrasound transducer placed transversely in line with the medial and lateral malleoli captured 3 images before and after a standardized loading protocol consisting of 30 single- and double-limb squats, 2-minute single-limb balance, and 10 single-legged drops from a 40-cm-height box.

RESULTS: After controlling for BMI, we found that the participants with CAI had greater deformation than the uninjured control participants (P = .034). No other between-groups differences were observed (P values > .05). No significant partial correlations were noted between talar-cartilage deformation and spatiotemporal gait parameters when controlling for BMI (P > .05).

CONCLUSIONS: Individuals with CAI had greater talar-cartilage deformation in response to a standardized exercise protocol than control individuals. The amount of talar-cartilage deformation was not associated with the spatiotemporal walking gait.

PMID:35969663 | DOI:10.4085/1062-6050-733-20

Global Spine J. 2022 Aug 15:21925682221117139. doi: 10.1177/21925682221117139. Online ahead of print.

ABSTRACT

STUDY DESIGN: Retrospective Cohort.

OBJECTIVES: To validate the most concise risk stratification system to date, the 5-item modified frailty index (mFI-5), and compare its effectiveness with the established 11-item modified frailty index (mFI-11) in the elderly population undergoing posterior instrumented spine surgery.

METHODS: A single centre retrospective review of posterior instrumented spine surgeries in patients aged 65 years and older was conducted. The primary outcome was rate of post-operative major complications (Clavien-Dindo Classification ≥ 4). Secondary outcome measures included rate of all complications, 6-month mortality and surgical site infection. Multi-variate analysis was performed and adjusted receiver operating characteristic curves were generated and compared by DeLong’s test. The indices were correlated with Spearman’s rho.

RESULTS: 272 cases were identified. The risk of major complications was independently associated with both the mFI-5 (OR 1.89, 95% CI 1.01-3.55, P = .047) and mFI-11 (OR 3.73, 95% CI 1.90-7.30, P = .000). Both the mFI-5 and mFI-11 were statistically significant predictors of risk of all complications (P = .007 and P = .003), surgical site infection (P = .011 and P = .003) and 6-month mortality (P = .031 and P = .000). Adjusted ROC curves determined statistically similar c-statistics for major complications (.68 vs .68, P = .64), all complications (.66 vs .64, P = .10), surgical site infection (.75 vs .75, P = .76) and 6-month mortality (.83 vs .81, P = .21). The 2 indices correlated very well with a Spearman’s rho of .944.

CONCLUSIONS: The mFI-5 and mFI-11 are equally effective predictors of postoperative morbidity and mortality in this population. The brevity of the mFI-5 is advantageous in facilitating its daily clinical use.

PMID:35969642 | DOI:10.1177/21925682221117139

PLoS One. 2022 Aug 15;17(8):e0273069. doi: 10.1371/journal.pone.0273069. eCollection 2022.

ABSTRACT

BACKGROUND: Eritrea has achieved the global target (90%) for tuberculosis (TB) treatment success rate. Though, events of unsuccessful TB treatment outcomes (death, treatment failure, lost to follow up and not evaluated) could lead to further TB transmission and the development of resistant strains. Hence, factors related to these events should be explored and addressed. This study aims to fill the gap in evidence by identifying the determinants of unsuccessful TB treatment outcomes in Eritrea’s Northern Red Sea region.

METHODS: A retrospective cohort study was conducted in Eritrea’s Northern Red Sea region. Data collected using a data extraction tool was analyzed using Stata version 13. Frequencies, proportions, median and standard deviations were used to describe the data. Furthermore, univariable and multivariable logistic regression analysis were performed to determine the risk factors for unsuccessful TB treatment outcomes. Crude odds ratio (COR) and adjusted odds ratio (AOR) with their 95% confidence interval (CI) presented and p-value < 0.05 was considered statistically significant.

RESULTS: Among 1227 TB patients included in this study, 9.6% had unsuccessful TB treatment outcomes. In multivariable logistic regression analysis, TB cases 55-64 years old (AOR: 2.75[CI: 1.21-6.32], p = 0.016) and those ≥ 65 years old (AOR: 4.02[CI: 1.72-9.45], p = 0.001) had 2.7 and 4 times higher likelihood of unsuccessful TB treatment outcome respectively. In addition, HIV positive TB patients (AOR: 5.13[CI: 1.87-14.06], p = 0.002) were 5 times more likely to have unsuccessful TB treatment outcome. TB treatment in Ghindae Regional Referral Hospital (AOR: 5.01[2.61-9.61], p < 0.001), Massawa Hospital (AOR: 4.35[2.28-8.30], p< 0.001) and Nakfa Hospital (AOR: 2.53[1.15-5.53], p = 0.021) was associated with 5, 4 and 2.5 higher odds of unsuccessful TB treatment outcome respectively.

CONCLUSION: In this setting, old age, HIV co-infection and health facility were the independent predictors of unsuccessful TB treatment outcome.

PMID:35969629 | DOI:10.1371/journal.pone.0273069

PLoS One. 2022 Aug 15;17(8):e0268339. doi: 10.1371/journal.pone.0268339. eCollection 2022.

ABSTRACT

The stretch-shortening cycle (SSC) motor execution ability of the lower limb was measured using the rebound jump index (RJ-index) in RJ test; this performance is influenced by the interaction of the forces exerted by the three joints of the lower limb.We aimed to determine RJ performance variables and identify the lower limb kinetic variables that affect them. One hundred two female university students (age, 20.1±1.0 years; height, 164.6±7.2 cm; mass, 58.9±7.3 kg) for whom RJ performance variables (RJ-index, jump height, and contact time) and joint kinetics (torque, power, and work) were measured. Statistical analysis showed a strong correlation between the RJ-index and jump height or contact time (r = 0.920, -0.726, p < 0.05) but a weak correlation between the jump height and contact time (r = -0.384, p < 0.05). Furthermore, positive ankle power was the most influential factor for RJ performance variables; additionally, positive knee power and hip work and eccentric knee torque significantly influenced jump height, and positive ankle power, negative work and power, and concentric torque significantly influenced the contact time. The acquisition of the jump height and a shorter contact time requires different kinetic variables. Furthermore, the characteristics of the force exerted by the three joints of the lower limb that compose the RJ-index may be different even if the RJ-index has the same value. Therefore, by assessing not only the RJ-index but also the jump height, contact time, and characteristics of lower limb joint kinetics in the RJ test, it is possible to conduct effective training to improve lower limb SSC motor execution performance according to individual characteristics.

PMID:35969620 | DOI:10.1371/journal.pone.0268339

PLoS Comput Biol. 2022 Aug 15;18(8):e1010392. doi: 10.1371/journal.pcbi.1010392. Online ahead of print.

ABSTRACT

Inside the nucleus, chromosomes are subjected to direct physical interaction between different components, active forces, and thermal noise, leading to the formation of an ensemble of three-dimensional structures. However, it is still not well understood to what extent and how the structural ensemble varies from one chromosome region or cell-type to another. We designed a statistical analysis technique and applied it to single-cell chromosome imaging data to reveal the heterogeneity of individual chromosome structures. By analyzing the resulting structural landscape, we find that the largest dynamic variation is the overall radius of gyration of the chromatin region, followed by domain reorganization within the region. By comparing different human cell-lines and experimental perturbation data using this statistical analysis technique and a network-based similarity quantification approach, we identify both cell-type and condition-specific features of the structural landscapes. We identify a relationship between epigenetic state and the properties of chromosome structure fluctuation and validate this relationship through polymer simulations. Overall, our study suggests that the types of variation in a chromosome structure ensemble are cell-type as well as region-specific and can be attributed to constraints placed on the structure by factors such as variation in epigenetic state.

PMID:35969616 | DOI:10.1371/journal.pcbi.1010392

PLoS One. 2022 Aug 15;17(8):e0272225. doi: 10.1371/journal.pone.0272225. eCollection 2022.

ABSTRACT

We present a database that classifies all patent applications filed at either the United States Patent and Trademark Office (USPTO) or the European Patent Office (EPO) as being either product patents, process patents or ‘mixed patents’. We use the share of claims that refer to either product or process inventions which allows to classify all patent applications along a continuum of pure process patents and pure product patents. We find that process-oriented patents draw more on previous knowledge, are more original and more radical than product patents. Lower breadth of protection is positively associated with pure process patenting, whereas product and mixed variants can be protected more broadly. This characterisation uncovers heterogeneity of patented inventions that allows for a more sophisticated use of patent statistics. It can improve the accuracy of analyses, but also reveal new aspects related to property rights.

PMID:35969608 | DOI:10.1371/journal.pone.0272225