Category: Statistics

J Math Biol. 2023 Jul 30;87(2):34. doi: 10.1007/s00285-023-01965-x.

ABSTRACT

Inversions, also sometimes called reversals, are a major contributor to variation among bacterial genomes, with studies suggesting that those involving small numbers of regions are more likely than larger inversions. Deletions may arise in bacterial genomes through the same biological mechanism as inversions, and hence a model that incorporates both is desirable. However, while inversion distances between genomes have been well studied, there has yet to be a model which accounts for the combination of both deletions and inversions. To account for both of these operations, we introduce an algebraic model that utilises partial permutations. This leads to an algorithm for calculating the minimum distance to the most recent common ancestor of two bacterial genomes evolving by inversions (of adjacent regions) and deletions. The algebraic model makes the existing short inversion models more complete and realistic by including deletions, and also introduces new algebraic tools into evolutionary distance problems.

PMID:37517046 | DOI:10.1007/s00285-023-01965-x

Fa Yi Xue Za Zhi. 2023 Jun 25;39(3):296-304. doi: 10.12116/j.issn.1004-5619.2022.520602.

ABSTRACT

OBJECTIVES: To provide a guideline for genealogy inference and family lineage investigation through a study of the mismatch tolerance distribution of Y-STR loci in Chinese Han male lineage.

METHODS: Three Han lineages with clear genetic relationships were selected. YFiler Platinum PCR amplification Kit was used to obtain the typing data of 35 Y-STR loci in male samples. The variation of Y-STR haplotypes in generation inheritance and the mismatch tolerance at 1-7 kinship levels were statistically analyzed.

RESULTS: Mutations in Y-STR were family-specific with different mutation loci and numbers of mutation in different lineages. Among all the mutations, 66.03% were observed on rapidly and fast mutating loci. At 1-7 kinship levels, the number of mismatch tolerance ranged from 0 to 5 on all 35 Y-STR loci, with a maximum step size of 6. On medium and slow mutant loci, the number of mismatch tolerance ranged from 0 to 2, with a maximum step size of 3; on rapidly and fast mutant loci, the number of mismatch tolerance ranged from 0 to 3, with a maximum step size of 6.

CONCLUSIONS: Combined use of SNP genealogy inference and Y-STR lineage investigation, both 0 and multiple mismatch tolerance need to be considered. Family lineage with 0-3 mismatch tolerance on all 35 Y-STR loci and 0-1 mismatch tolerance on medium and slow loci can be prioritized for screening. When the number of mismatch tolerance is eligible, family lineages with long steps should be carefully excluded. Meanwhile, adding fast mutant loci should also be handled with caution.

PMID:37517019 | DOI:10.12116/j.issn.1004-5619.2022.520602

Knee Surg Sports Traumatol Arthrosc. 2023 Jul 30. doi: 10.1007/s00167-023-07509-6. Online ahead of print.

ABSTRACT

PURPOSE: The Attune^® total knee arthroplasty system was introduced in 2013 to address lingering issues of patient dissatisfaction. However, recent literature reports concerns of early tibial tray debonding. The aim of this study was to compare the incidence of radiolucent lines, survivorship and patient reported outcome-measures between the Attune^® system and the well-established Triathlon^® system.

METHODS: This retrospective database review was conducted at a single institution in Cork, Ireland. All primary Attune^® (N = 445) and Triathlon^® (N = 285) systems implanted between 2015 and 2016 were reviewed. Radiolucent lines were assessed for those with a minimum two-year radiological follow-up (Attune^® = 338; Triathlon^® = 231). X-rays were taken post op, at 6 months, 2 years and 5 years. Radiolucent lines were documented using the Modern Knee Society Radiographic System. Five-year survival was assessed using Kaplan-Meier analysis with the Log Rank method to determine statistical significance. The Oxford Knee Score and EQ-5D-5L, were collected pre-op, at 6 months, 2 years and 5 years post-operatively and compared using the Kruskal-Wallis Test.

RESULTS: The Attune^® had a higher proportion of radiolucent lines at the tibial tray [87.1% (54/62) vs 61.4% (27/44); p = 0.001] and at the implant-cement interface [62.9% (39/62) vs 43.2% (19/44); p = 0.02]. Conversely, the Triathlon^® had a higher proportion AT the femur [38.6% (17/44) vs 12.9% (8/62); p = 0.001] and at the cement-bone interface [56.8% (25/44) vs 37.1% (23/62); p = 0.02]. The overall frequency of radiolucent lines was similar in both the Attune^® and Triathlon^® groups [17.8%, (60/338) vs 17.7%, (41/231); p = 0.49]. There was no difference in revision-free survival analysis at 5 years (Attune^® 97.8% vs Triathlon^® 95.8%; p = 0.129). The Attune^® performed better at 5 years in the Oxford Knee Score [Attune^® = 42.6 (SD 5.2) vs Triathlon^® = 41 (SD 6.4); p = 0.001] and in the EQ-5D [Attune^® = 0.773 (SD 0.187) vs Triathlon^® = 0.729 (SD 0.218); p = 0.013]. There was no difference at 5 years in the EQ-VAS [Attune^® = 80.4 (SD 13.7) vs Triathlon^® = 78.5 (SD 15.3); p = 0.25].

CONCLUSION: The Attune^® system exhibited a higher incidence of radiolucent lines at the tibial tray. However, this did not lead to decreased survivorship at medium term follow-up compared to the Triathlon^®. Furthermore, improvements in patient reported outcomes modestly favoured the Attune^® system.

LEVEL OF EVIDENCE: III.

PMID:37516985 | DOI:10.1007/s00167-023-07509-6

J Cancer Res Clin Oncol. 2023 Jul 30. doi: 10.1007/s00432-023-05195-y. Online ahead of print.

ABSTRACT

PURPOSE: In this study, we aimed at profiling of luminal B breast cancer specific gene expression pattern in Indian women using mRNA-seq and validation based on TCGA expression data.

METHODS: RNA isolated from luminal B tumor and adjacent normal tissues was used for library construction and sequencing. Reference-based assemblies of these reads were used for differential gene expression analysis using DeSeq2. The DEGs were evaluated using TCGA expression data. Kaplan-Meier survival method was used to evaluate association between genes showing luminal B specific differential expression pattern and breast cancer prognosis and statistical significance was assessed using log-rank test. Alternate splicing analysis was done using rmats.

RESULTS: Differential expression analysis identified 2371 differentially expressed genes (DEGs) in luminal B breast tumors in comparison with adjacent normal tissues of Indian Women. Of them, 1692 DEGs were validated using TCGA luminal B paired samples. Integration of this data with the DEGs obtained by comparative analysis of unpaired luminal B with luminal A unpaired samples from TCGA resulted in 291 DEGs showing luminal B specific expression pattern. Further, 26 genes of prognostic value were identified. Differential splicing analysis between luminal B tumors and adjacent normal tissues in our cohort led to the identification of 687 genes showing significant differential alternate splicing events.

CONCLUSION: This study profiled gene expression pattern of luminal B tumors of Indian women and identified 26 key genes of prognostic value for luminal B breast cancer. This study also profiled differential alternate splicing and identified important alternate splicing events in luminal B breast cancer.

PMID:37516983 | DOI:10.1007/s00432-023-05195-y

Comput Methods Biomech Biomed Engin. 2023 Jul 30:1-14. doi: 10.1080/10255842.2023.2224912. Online ahead of print.

ABSTRACT

The purpose of this study was to develop a machine learning model to reconstruct time series kinematic and kinetic profiles of the ankle and knee joint across six different tasks using an ankle-mounted IMU. Four male collegiate basketball players performed repeated tasks, including walking, jogging, running, sidestep cutting, max-height jumping, and stop-jumping, resulting in a total of 102 movements. Ankle and knee flexion-extension angles and moments were estimated using motion capture and inverse dynamics and considered ‘actual data’ for the purpose of model fitting. Synchronous acceleration and angular velocity data were collected from right ankle-mounted IMUs. A time-series feature extraction model was used to determine a set of features used as input to a random forest regression model to predict the ankle and knee kinematics and kinetics. Five-fold cross-validation was performed to verify the model accuracy, and statistical parametric mapping was used to determine the difference between the predicted and experimental time series. The random forest regression model predicted the time-series profiles of the ankle and knee flexion-extension angles and moments with high accuracy (Kinematics: R2 ranged from 0.782 to 0.962, RMSE ranged from 2.19° to 11.58°; Kinetics: R2 ranged from 0.711 to 0.966, RMSE ranged from 0.10 Nm/kg to 0.41 Nm/kg). There were differences between predicted and actual time series for the knee flexion-extension moment during stop-jumping and walking. An appropriately trained feature-based regression model can predict time series knee and ankle joint angles and moments across a wide range of tasks using a single ankle-mounted IMU.

PMID:37516980 | DOI:10.1080/10255842.2023.2224912

J Nutr Educ Behav. 2023 Jul 27:S1499-4046(23)00392-5. doi: 10.1016/j.jneb.2023.06.001. Online ahead of print.

ABSTRACT

OBJECTIVE: To determine the effect of Food Sensations for Adults on food literacy behaviors and selected dietary behaviors.

METHODS: A quasi-experimental design using preprogram and postprogram questionnaires over 4 weeks with a control group (n = 75) matched for sex, age group, and socioeconomic disadvantage to program participants (n = 867). General linear mixed models assessed change in food literacy behavior frequency in 3 self-reported domains (plan and manage, selection, and preparation) and fruit and vegetable servings.

RESULTS: Postprogram, Food Sensations for Adults participants reported modest yet statistically significant score improvements in 2 of the 3 domains of food literacy behaviors in the plan and manage (12.4%) and preparation (9.8%) domains, as well as servings of vegetables (22.6% or 0.5 servings).

CONCLUSION AND IMPLICATIONS: Quasi-experimental designs indicate food literacy programs can produce modest short-term changes across a range of food literacy and dietary behaviors.

PMID:37516955 | DOI:10.1016/j.jneb.2023.06.001

J Hand Surg Am. 2023 Jul 29:S0363-5023(23)00296-4. doi: 10.1016/j.jhsa.2023.05.019. Online ahead of print.

ABSTRACT

PURPOSE: Thumb carpometacarpal (CMC) osteoarthritis (OA) causes functional disability and an increased health care burden in the aging population. The role of therapy in thumb CMC OA has been minimally analyzed in the literature. We hypothesized that patients treated with therapy for thumb CMC OA would demonstrate reduced rates of surgery for this diagnosis.

METHODS: We queried a national insurance dataset for all patients with an International Classification of Diseases, Ninth Revision, or International Statistical Classification of Diseases, Tenth Revision, code for thumb CMC OA, with a minimum of 2 years of follow-up. A 2:1 propensity-matched cohort of patients with CMC OA who did not receive therapy versus a therapy cohort was created, with a minimum of two sessions of hand therapy for inclusion. The primary outcome was the rate of thumb CMC OA surgery occurring within 2 years of diagnosis; time to surgery and use of thumb CMC injections were secondary outcomes. Multivariable logistic regression analysis was used to identify the risk factors for undergoing surgical treatment.

RESULTS: After matching, the therapy cohort comprised 14,548 patients, with a matched group of 28,930 patients who did not undergo therapy. In the overall sample, the rate of surgery within 2 years was 22.5%. Two-year surgical treatment rates were significantly higher for those who did not undergo therapy when compared with those who did (29.3% vs 13.1%). Patients treated with therapy had a significantly longer time to surgery, with no difference in the rate of surgery after one year. In multivariable regression of all included variables, lack of therapy intervention had the highest odds of surgery for thumb CMC OA (odds ratio 4.3).

CONCLUSIONS: We present the findings of a large insurance database evaluating the association of therapy with rates of surgical treatment for thumb CMC arthritis. On average, those treated with therapy had longer times to surgery, and the 2-year surgery rates for patients diagnosed with thumb CMC arthritis were significantly higher in those who did not undergo therapy treatment.

TYPE OF STUDY/LEVEL OF EVIDENCE: Prognostic II.

PMID:37516939 | DOI:10.1016/j.jhsa.2023.05.019

West Afr J Med. 2023 Jul 28;40(7):761-768.

ABSTRACT

BACKGROUND: Globally, female-perpetrated IPV has been well studied among various groups but little is known about IPV against heterosexual men living with HIV. This study sought to identify the prevalence and determinants of female-perpetrated IPV among heterosexual HIV-positive men in Birnin Kudu, Jigawa State, Nigeria.

MATERIALS AND METHODS: This was a descriptive crosssectional study carried out at one secondary and tertiary health facility respectively, both situated in Birnin Kudu. Using an intervieweradministered pre-tested questionnaire, the prevalence and determinants of female-perpetrated IPV was assessed among 322 heterosexual HIV-positive men attending the anti-retroviral therapy clinics at the two health facilities. Data was entered into and analyzed using statistical package for social sciences version 25.

RESULTS: The prevalence of IPV in the last year was 45% (145D 322). Out of the survivors of IPV, 143 (98.6%), 75 (51.7%), and 51 (35.2%) had experienced psychological aggression, physical assault and sexual coercion respectively. The number of children fathered, experience of childhood violence, and marital status were significantly associated with IPV (p< 0.05) However, they remained significant determinants of IPV after controlling for confounders (ethnicity, marital status, educational status ) {Adjusted Odds ratio (aOR) = 7.34 and 95% confidence interval (C.I.) = 1.49 – 35.4; aOR= 1.84 C.I. 1.33 – 2.80; aOR = O.51 (0.29 – 0.90) respectively}.

CONCLUSION: This study identified a high prevalence of femaleperpetrated IPV against heterosexual men living with HIV and emphasizes that exposure to childhood violence and being childless are determinants of IPV. Efforts should be made to screen for IPV among men living with HIV so as to optimize their health and wellbeing.

PMID:37516936

West Afr J Med. 2023 Jul 28;40(7):748-752.

ABSTRACT

BACKGROUND: Gallstones detected incidentally during imaging are termed ‘silent’ or asymptomatic gallstones and they account for 80% of all gallstones. About 1-2% of patients with silent gallstones develop symptoms yearly; however, determining those who will develop symptoms is a major challenge. Ultrasonography is the most sensitive and specific method of detecting gallstones with an accuracy greater than 95%. The study aims to determine the prevalence of ultrasound-diagnosed silent gallstones in a Nigerian population and to determine its association with age and gender.

METHODS: This was a retrospective analysis of abdominal ultrasound scans performed at the Radiology department of a tertiary institution between January 2013 and December 2015. Data retrieved included age, sex, and sonographic findings. Data analysis was done by simple proportions and percentages using the Statistical Package for Social Sciences version 20.0 software.

RESULTS: Two thousand, one hundred and thirty-eight patients had abdominal ultrasound scans for various reasons during the study period. These included 915 males and 1223 females. Incidental findings of gallstones were observed in 52 patients, giving a prevalence of 2.4%. The prevalence of gallstones increased with age (p=0.051) with the highest prevalence seen in the 5th decade. Gallstones prevalence was higher in females with a male-to-female ratio of 1:3.5.

CONCLUSION: The prevalence of silent gallstones is low in our environment, but given the complications that may arise, follow-up for early detection of complications in the patients is therefore strongly recommended.

PMID:37516927

West Afr J Med. 2023 Jul 28;40(7):742-747.

ABSTRACT

BACKGROUND: Covid-19 vaccination is recommended for the prevention of Covid-19 infection. However, there is paucity of studies assessing post-vaccination side effects, especially in Africa, and thus, the need for this study.

OBJECTIVES: To determine the prevalence of post-covid-19 vaccination side effects; the frequency of occurrence of each side effect and the willingness to receive the second dose of the vaccine.

METHODS: A descriptive cross-sectional study was conducted among Corp members undergoing the three-week compulsory orientation course in a National Youth Service Corps (NYSC) orientation camp in Keffi, North-Central Nigeria. A total of 552 Corp members received the Covid-19 vaccine (AstraZeneca), 268 consented and were enrolled in the study. Data were obtained through online Google forms and were analyzed using SPSS version 26.

RESULTS: The mean age of the respondents was 25 years (SD = 2.5). The prevalence of post-covid-19 vaccination side effects was 90.7%, 95% CI (86.8 – 93.8). The most common side effects were weakness (53.5%), pain at the injection site (52.7%), and headache (52.7%). There was a weak association between the duration of symptoms and intake of medications (Cramer’s V = 0.148) which was not statistically significant. About a quarter, 62 (24.0%), of the respondents who received the first dose of the vaccine, were unwilling to accept the second dose, mainly due to their fear of the side effects – 53 (85.5%).

CONCLUSION: Our study population had a high prevalence of post-covid-19 vaccination side effects. Thus, the need to educate recipients on possible side effects and remedies.

PMID:37516926