Tag: statistics

PLoS Genet. 2022 Feb 24;18(2):e1010022. doi: 10.1371/journal.pgen.1010022. eCollection 2022 Feb.

ABSTRACT

The ability to accurately identify and quantify genetic signatures associated with soft selective sweeps based on patterns of nucleotide variation has remained controversial. We here provide counter viewpoints to recent publications in PLOS Genetics that have argued not only for the statistical identifiability of soft selective sweeps, but also for their pervasive evolutionary role in both Drosophila and HIV populations. We present evidence that these claims owe to a lack of consideration of competing evolutionary models, unjustified interpretations of empirical outliers, as well as to new definitions of the processes themselves. Our results highlight the dangers of fitting evolutionary models based on hypothesized and episodic processes without properly first considering common processes and, more generally, of the tendency in certain research areas to view pervasive positive selection as a foregone conclusion.

PMID:35202407 | DOI:10.1371/journal.pgen.1010022

PLoS Comput Biol. 2022 Feb 24;18(2):e1009819. doi: 10.1371/journal.pcbi.1009819. eCollection 2022 Feb.

NO ABSTRACT

PMID:35202399 | DOI:10.1371/journal.pcbi.1009819

MMWR Morb Mortal Wkly Rep. 2022 Feb 25;71(8):326. doi: 10.15585/mmwr.mm7108a7.

NO ABSTRACT

PMID:35202350 | DOI:10.15585/mmwr.mm7108a7

PLoS One. 2022 Feb 24;17(2):e0262502. doi: 10.1371/journal.pone.0262502. eCollection 2022.

ABSTRACT

The analysis of contingency tables is a powerful statistical tool used in experiments with categorical variables. This study improves parts of the theory underlying the use of contingency tables. Specifically, the linkage disequilibrium parameter as a measure of two-way interactions applied to three-way tables makes it possible to quantify Simpson’s paradox by a simple formula. With tests on three-way interactions, there is only one that determines whether the partial interactions of all variables agree or whether there is at least one variable whose partial interactions disagree. To date, there has been no test available that determines whether the partial interactions of a certain variable agree or disagree, and the presented work closes this gap. This work reveals the relation of the multiplicative and the additive measure of a three-way interaction. Another contribution addresses the question of which cells in a contingency table are fixed when the first- and second-order marginal totals are given. The proposed procedure not only detects fixed zero counts but also fixed positive counts. This impacts the determination of the degrees of freedom. Furthermore, limitations of methods that simulate contingency tables with given pairwise associations are addressed.

PMID:35202396 | DOI:10.1371/journal.pone.0262502

Vet Sci. 2022 Feb 17;9(2):85. doi: 10.3390/vetsci9020085.

ABSTRACT

This sequential explanatory mixed-method study consisted of analytical, cross-sectional, and qualitative studies. The research was conducted in the Khao Nor and Khao Kaew areas of the Banphot Pisai districts of Nakhon Sawan Province in 2019. Here, we examined the rodent contact characteristics of villagers in these areas and determined the potential characteristics/risk factors associated with rodents using a semi-structured questionnaire, key informant interview (KII), and focus group discussion (FGD). Results of the quantitative study (N1 = 372) characterized participants that contacted rodents per gender, age, occupation, knowledge, attitude, and practice (KAP), including their cultural contexts, and beliefs. Ninety participants (24.2%) reported contact with rodents, and the reasons for their direct physical rodent contact were hunting (35, 9.4%), killing (41, 11.0%), preparing rodents as food (33, 8.9%), consuming cooked meats (12, 3.2%), feeding food (4, 1.1%), cleaning feces (17, 4.6%), and cleaning carcasses (33, 8.9%). Moreover, logistic regression results showed that males encountering rodents were statistically significant (Adjusted OR = 3.137, 95% CI 1.914-5.139, p < 0.001). Low monthly household income (<THB 15,000 or <USD 450) was also negatively statistically significant with encountering rodents (Adjusted OR = 0.57, 95% CI 0.33-0.99, p = 0.04). Additionally, the villagers had a low level of knowledge toward zoonotic diseases and inappropriate attitudes and practices toward contacting rodents and zoonotic diseases. Thirty-five qualitative study participants (N2) participated in the KIIs and FGDs. Various rodent contact activities were also reported among the qualitative research participants, such as hunting, consumption, and selling them to their friends and neighbors. However, these rodents also destroyed their belongings, crops, and plants. Some participants also reported that rodents accounted for leptospirosis transmission. As a result, communication intervention should be planned to provide appropriate knowledge and attitude to the villagers, especially among those who have close contact with rodents in the understudied area.

PMID:35202338 | DOI:10.3390/vetsci9020085

Vet Sci. 2022 Feb 17;9(2):87. doi: 10.3390/vetsci9020087.

ABSTRACT

Neosporosis is recognized as one of the major causes of bovine abortion worldwide. Canids are the main definitive host for this parasite and the presence of dogs in the farm is an important factor for the Neospora caninum infection in bovines. Since, in the province of Lecce, located in the Apulia region of Southern Italy, there are no studies showing the presence of the infection in farm animals, the objective was to perform a serological evaluation for anti-N. caninum antibodiesin serum from 706 dairy cattle and 21 farm dogs located in 40 farms uniformlydistributed over the territory.The presence of N. caninum infection was confirmed in 90.0% (36/40) of the 40 farms examined. The results obtained on all serum samples by an enzyme-linked immunosorbent assay (ID Screen^®Neospora caninum competition ELISA kit) for anti-N. caninum antibodies showed a seropositivity rate of 21.1% (149/706) among dairy cows, with a statistically significant higher percentage of positive subjects in the animals over two years old and a positivity rate of 42.9% (9/21) in tested dogs. The obtained data confirmed the presence of neosporosis even in the Lecce area, where it could therefore represent an important cause of abortion and economic losses.

PMID:35202340 | DOI:10.3390/vetsci9020087

Vet Sci. 2022 Feb 17;9(2):84. doi: 10.3390/vetsci9020084.

ABSTRACT

The purpose of the study was to quantify serum and fecal amino acids (AA) in cats with chronic kidney disease (CKD) and compare to healthy cats. Thirty-five cats with International Renal Interest Society Stage 1-4 CKD and 16 healthy mature adult and senior client-owned cats were included in this prospective cross-sectional study. Sera were analyzed for 25 AA concentrations using an ion exchange chromatography AA analyzer with post column ninhydrin derivatization. Voided fecal samples were analyzed for 22 AA concentrations using liquid chromatography with tandem mass spectrometry. CKD cats had lower serum concentrations of phenylalanine (mean difference ± standard error of the mean: 12.7 ± 4.3 µM; p = 0.03), threonine (29.6 ± 9.2 µM; p = 0.03), tryptophan (18.4 ± 5.4 µM; p = 0.005), serine (29.8 ± 12.6 µM; p = 0.03), and tyrosine (11.6 ± 3.8 µM; p = 0.01) and higher serum concentrations of aspartic acid (4.7 ± 2.0 µM; p = 0.01), β-alanine (3.4 ± 1.2 µM; p = 0.01), citrulline (5.7 ± 1.6 µM; p = 0.01), and taurine (109.9 ± 29.6 µM; p = 0.01) when compared to healthy cats. Fecal AA concentrations did not differ between healthy cats and CKD cats. 3-Methylhistidine-to-creatinine did not differ between healthy cats with and without muscle loss. Cats with CKD IRIS Stages 1-4 have a deranged serum amino acid profile compared to healthy cats.

PMID:35202337 | DOI:10.3390/vetsci9020084

Vet Sci. 2022 Jan 27;9(2):51. doi: 10.3390/vetsci9020051.

ABSTRACT

The COVID-19 pandemic and lockdown brought numerous teaching challenges requiring innovative approaches to teaching and learning, including novel modes of content delivery, virtual classrooms, and online assessment schemes. The aim of this study is to describe and assess the efficacy of the methods implemented at the University of León (Spain) to adapt to lockdowns in the context of the Cytology and Histology (CH) course for veterinary medicine undergraduate students. To evaluate the success of lockdown-adapted methodologies, we used inferential statistical analysis to compare the academic outcomes of two cohorts: 2018-2019 (traditional face-to-face-presential-learning and evaluation) and 2019-2020 (some face-to-face and some online lockdown-adapted learning and online lockdown-adapted evaluation). This analysis considered scores in both theoretical and practical exams and students’ final subject score. We also evaluated the number of logs onto the Moodle platform throughout the 2019-2020 period, as well as performing a student satisfaction survey in both courses. The use of explanatory pre-recorded lectures, continuous online self-assessment tests, and virtual microscopy (VM) may have produced significant improvements in the acquisition of histology competencies among students in the lockdown cohort. However, we need to implement further strategies to improve the assessment of students’ true level of knowledge acquisition. According to the student feedback, VM is a well-accepted resource that is perceived as a flexible and enjoyable tool to use. However, while students found that the resource enhances their ability to learn about microscopic structures, they felt that it should not completely replace optical microscopy.

PMID:35202304 | DOI:10.3390/vetsci9020051

Toxics. 2022 Feb 14;10(2):86. doi: 10.3390/toxics10020086.

ABSTRACT

Bisphenol A (BPA), which is contained in numerous plastic products, is known to act as an endocrine-disruptive, toxic, and carcinogenic chemical. This experimental series sought to determine the influence of BPA exposure on the femoral bone architecture and biomechanical properties of male and female Wistar rats. BPA was applied subcutaneously by using osmotic pumps. After 12 weeks, the bones were analyzed by micro-computed tomography (micro-CT) and a three-point bending test. Comparing the female low- and high-dose groups, a significantly greater marrow area (p = 0.047) was identified in the group exposed to a higher BPA concentration. In addition, the trabecular number tended to be higher in the female high-dose group when compared to the low-dose group (p > 0.05). The area moment of inertia also tended to be higher in the male high-dose group when compared to the male low-dose group (p > 0.05). Considering our results, BPA-related effects on the bone morphology in female Wistar rats are osteoanabolic after high-dose exposure, while, in male rats, a tendency toward negative effects on the bone morphology in terms of a reduced cross-sectional cortical area and total area could be demonstrated.

PMID:35202272 | DOI:10.3390/toxics10020086

Vet Sci. 2022 Jan 18;9(2):33. doi: 10.3390/vetsci9020033.

ABSTRACT

(1) Background: Systemic inflammatory response syndrome (SIRS) can occur due to a large number of traumatic or non-traumatic diseases. Hyperbaric oxygen therapy (HBOT) may be used as a main or adjuvant treatment for inflammation, leading to the main aim of this study, which was to verify the applicability of HBOT as a safe and tolerable tool in SIRS-positive dogs. (2) Methods: This prospective cohort study included 49 dogs who showed two or more parameters of SIRS, divided into the Traumatic Study Group (n = 32) and the Non-Traumatic Study Group (n = 17). All dogs were submitted to HBOT for 60-90 min sessions, with 2.4-2.8 ATA. (3) Results: This study revealed that 73.5% (36/49) of dogs showed improvement, and the minimum number of HBOT sessions was two, with a mean of 12.73. The number of days between diagnosis and the beginning of HBOT showed statistical significance (p = 0.031) relative to the clinical outcome. No dogs showed any major side effects. (4) Conclusions: We concluded that HBOT may be safe and tolerable for SIRS-positive dogs, and that it should be applied as early as possible.

PMID:35202287 | DOI:10.3390/vetsci9020033