Category: Statistics

Theor Popul Biol. 2023 Aug 4:S0040-5809(23)00049-7. doi: 10.1016/j.tpb.2023.07.004. Online ahead of print.

ABSTRACT

Recombination is a powerful evolutionary process that shapes the genetic diversity observed in the populations of many species. Reconstructing genealogies in the presence of recombination from sequencing data is a very challenging problem, as this relies on mutations having occurred on the correct lineages in order to detect the recombination and resolve the ordering of coalescence events in the local trees. We investigate the probability of reconstructing the true topology of ancestral recombination graphs (ARGs) under the coalescent with recombination and gene conversion. We explore how sample size and mutation rate affect the inherent uncertainty in reconstructed ARGs, which sheds light on the theoretical limitations of ARG reconstruction methods. We illustrate our results using estimates of evolutionary rates for several organisms; in particular, we find that for parameter values that are realistic for SARS-CoV-2, the probability of reconstructing genealogies that are close to the truth is low.

PMID:37544486 | DOI:10.1016/j.tpb.2023.07.004

J Affect Disord. 2023 Aug 4:S0165-0327(23)00989-8. doi: 10.1016/j.jad.2023.08.013. Online ahead of print.

ABSTRACT

BACKGROUND: People with mental illness have a reduced life expectancy, but the extent of the mortality gap and the contribution of natural and unnatural causes to excess mortality among people with mental illness in South Africa are unknown.

METHODS: We analysed reimbursement claims from South African medical insurance scheme beneficiaries aged 15-85 years. We estimated excess life years lost (LYL) associated with organic, substance use, psychotic, mood, anxiety, eating, personality, developmental or any mental disorders.

RESULTS: We followed 1,070,183 beneficiaries for a median of three years, of whom 282,926 (26.4 %) received mental health diagnoses. Men with a mental health diagnosis lost 3.83 life years (95 % CI 3.58-4.10) compared to men without. Women with a mental health diagnosis lost 2.19 life years (1.97-2.41) compared to women without. Excess mortality varied by sex and diagnosis, from 11.50 LYL (95 % CI 9.79-13.07) among men with alcohol use disorder to 0.87 LYL (0.40-1.43) among women with generalised anxiety disorder. Most LYL were attributable to natural causes (men: 3.42, women: 1.94). A considerable number of LYL were attributable to unnatural causes among men with bipolar (1.52) or substance use (2.45) disorder.

LIMITATIONS: Mental diagnoses are based on reimbursement claims.

CONCLUSIONS: Premature mortality among South African individuals with mental disorders is high. Our findings support interventions for the prevention, early detection, and treatment of physical comorbidities in this population. Targeted programs for suicide prevention and substance use treatment, particularly among men, can help reduce excess mortality from unnatural causes.

PMID:37544483 | DOI:10.1016/j.jad.2023.08.013

J Fluency Disord. 2023 Jul 26;77:105996. doi: 10.1016/j.jfludis.2023.105996. Online ahead of print.

ABSTRACT

PURPOSE: Using word- and nonword-reading passages in Kannada, which has a transparent orthography, we attempted to determine (a) whether orthographic differences between English and Kannada may explain the observed differences in stutter rates on nonwords, and (b) whether longer nonwords, like words, incur higher rates of stutters.

METHODS: Stutters are defined as sound or syllable repetitions, sound prolongations, broken words or nonwords (a pause within a word or nonword), abnormal pauses, and intrusive vowel-like sounds. Twenty-six persons, who stutter, read the word and nonword passages. The nonwords were created by changing the first syllable of each word; otherwise words and nonwords were equivalent in length and syllable structure. Stutters were counted from audio-recordings and statistically analyzed.

RESULTS: PWS stuttered on words in varying amounts and in significantly larger amounts on nonwords. Stutter frequency increased roughly in proportion to the increase in the length of phonological words (previously known) and nonwords (reported for the first time here).

CONCLUSION: The results cannot be attributed to the difficulty of pronouncing nonwords because Kannada orthography has a one-to-one relationship between the written and spoken forms of words. Speech production is a multi-stage process consisting of ideation, lemma selection, phonological word creation, and the articulatory planning and execution. Because nonwords lack meaning and clearly identifiable part of speech, it appears that stutters arise late in the speech production process at the phonological word formation and articulatory planning stages. Meaning, lexicality, and morphosyntax may not contribute significantly to the occurrence of stutters.

PMID:37544029 | DOI:10.1016/j.jfludis.2023.105996

J Med Virol. 2023 Aug;95(8):e29023. doi: 10.1002/jmv.29023.

ABSTRACT

An increasing trend of sapovirus (SaV) infections in Japanese children during 2009-2019, particularly after the introduction of the voluntary rotavirus (RV)-vaccination program has been observed. Herein, we investigated the epidemiological situation of SaV infections from 2019 to 2022 when people adopted a precautionary lifestyle due to the emergence of the COVID-19 pandemic, and RV vaccines had been implemented as routine vaccines. Stool samples were collected from children who attended outpatient clinics with acute gastroenteritis and analyzed by reverse transcriptase-polymerase chain reaction to determine viral etiology. Among 961 stool samples, 80 (8.3%) were positive for SaV: 2019-2020 (6.5%), 2020-2021 (0%), and 2021-2022 (12.8%). The trend of SaV infection in Japanese children yet remained upward with statistical significance (p = 0.000). The major genotype was GI.1 (75%) which caused a large outbreak in Kyoto between December 2021 and February 2022. Phylogenetic, gene sequence and deduced amino acid sequence analyses suggested that these GI.1 strains detected in the outbreak and other places during 2021-2022 or 2019-2020 remained genetically identical and widely spread. This study reveals that SaV infection is increasing among Japanese children which is a grave concern and demands immediate attention to be paid before SaV attains a serious public health problem.

PMID:37543991 | DOI:10.1002/jmv.29023

J Appl Clin Med Phys. 2023 Aug 6:e14112. doi: 10.1002/acm2.14112. Online ahead of print.

ABSTRACT

PURPOSE: To develop a prediction model (PM) for target positioning using diaphragm waveforms extracted from CBCT projection images.

METHODS: Nineteen patients with lung cancer underwent orthogonal rotational kV x-ray imaging lasting 70 s. IR markers placed on their abdominal surfaces and an implanted gold marker located nearest to the tumor were considered as external surrogates and the target, respectively. Four different types of regression-based PM were trained using surrogate motions and target positions for the first 60 s, as follows: Scenario A: Based on the clinical scenario, 3D target positions extracted from projection images were used as they were (PM_CL ). Scenario B: The short-arc 4D-CBCT waveform exhibiting eight target positions was obtained by averaging the target positions in Scenario A. The waveform was repeated for 60 s (W_4D-CBCT ) by adapting to the respiratory phase of the external surrogate. W_4D-CBCT was used as the target positions (PM_4D-CBCT ). Scenario C: The Amsterdam Shroud (AS) signal, which depicted the diaphragm motion in the superior-inferior direction was extracted from the orthogonal projection images. The amplitude and phase of W_4D-CBCT were corrected based on the AS signal. The AS-corrected W_4D-CBCT was used as the target positions (PM_AS-4D-CBCT ). Scenario D: The AS signal was extracted from single projection images. Other processes were the same as in Scenario C. The prediction errors were calculated for the remaining 10 s.

RESULTS: The 3D prediction error within 3 mm was 77.3% for PM_4D-CBCT , which was 12.8% lower than that for PM_CL . Using the diaphragm waveforms, the percentage of errors within 3 mm improved by approximately 7% to 84.0%-85.3% for PM_AS-4D-CBCT in Scenarios C and D, respectively. Statistically significant differences were observed between the prediction errors of PM_4D-CBCT and PM_AS-4D-CBCT .

CONCLUSION: PM_AS-4D-CBCT outperformed PM_4D-CBCT , proving the efficacy of the AS signal-based correction. PM_AS-4D-CBCT would make it possible to predict target positions from 4D-CBCT images without gold markers.

PMID:37543990 | DOI:10.1002/acm2.14112

J Endocrinol Invest. 2023 Aug 6. doi: 10.1007/s40618-023-02159-4. Online ahead of print.

ABSTRACT

PURPOSE: The risk of cardiovascular diseases’ death (CVD) in patients with differentiated thyroid cancer (DTC) treated with radioactive iodine (RAI) after surgery has not been adequately studied.

METHODS: Data of DTC patients who received RAI after surgery were retrieved from the Surveillance, Epidemiology, and End Result (SEER) database (2004-2015). Standardized mortality rate (SMR) analysis was used to evaluate the CVD risk in patients with RAI vs general population. A 1:1 propensity score matching (PSM) was applied to balance inter-group bias, and Pearson’s correlation coefficient was used to detect collinearity between variables. The Cox proportional hazard model and multivariate competing risk model were utilized to evaluate the impact of RAI on CVD. At last, we curved forest plots to compare differences in factors significantly associated with CVD or cancer-related deaths.

RESULTS: DTC patients with RAI treatment showed lower SMR for CVD than general population (RAI: SMR = 0.66, 95% CI 0.62-0.71, P < 0.05). After PSM, Cox proportional hazard regression demonstrated a decreased risk of CVD among patients with RAI compared to patients without (HR = 0.76, 95% CI 0.6-0.97, P = 0.029). However, in competing risk regression analysis, there was no significant difference (adjusted HR = 0.82, 95% CI 0.66-1.01, P = 0.11). The independent risk factors associated with CVD were different from those associated with cancer-related deaths.

CONCLUSION: The CVD risk between DTC patients treated with RAI and those who did not was no statistical difference. Noteworthy, they had decreased CVD risk compared with the general population.

PMID:37543985 | DOI:10.1007/s40618-023-02159-4

Arch Iran Med. 2023 Jan 1;26(1):8-15. doi: 10.34172/aim.2023.02.

ABSTRACT

BACKGROUND: The co-existence of chronic diseases (CDs), a condition defined as multimorbidity (MM), is becoming a major public health issue. Therefore, we aimed to determine the patterns and predictors of MM in the Azar Cohort.

METHODS: We evaluated the prevalence of MM in 15,006 (35-70-year old) subjects of the Azar Cohort Study. MM was defined as the co-existence of two or more CDs. Data on the subjects’ socioeconomic status, demographics, sleeping habits, and physical activity were collected using questionnaires.

RESULTS: The overall prevalence of MM was 28.1%. The most prevalent CDs, in decreasing order, were obesity, hypertension, depression, and diabetes. Obesity, depression, and diabetes were the most co-occurring CDs. The MM risk increased significantly with age, illiteracy, and in females. Also, the subjects within the lowest tertile of physical activity level (OR=1.89; 95% CI: 1.75-2.05) showed higher MM risk than those with the highest level of physical activity. Findings regarding current smoking status indicated that being an ex-smoker or smoker of other types of tobacco significantly increased the risk of MM.

CONCLUSION: The reduction of MM is possible by promoting public health from an early age among people of various socioeconomic conditions. It is vital to offer the necessary health support to the aging population of Iran.

PMID:37543916 | DOI:10.34172/aim.2023.02

Arch Iran Med. 2022 Nov 1;25(11):737-741. doi: 10.34172/aim.2022.116.

ABSTRACT

BACKGROUND: In December 2019, a cluster of viral pneumonia cases, later identified as coronavirus disease 2019 (COVID-19), was first reported in Wuhan, China, and then continued to spread to other parts of the world. COVID-19 is thought to be more prevalent in adults than children; therefore, information about COVID-19 burden and characteristics in children is lacking.

METHODS: We gathered data on the profile and transmission in children with COVID-19 from data collected by the North Sumatera Provincial Health Office team. Data were presented as mean±SD and percentage. Statistical analysis was performed using STATA version 15.0.

RESULTS: From April to October 2020, there were 1125 confirmed COVID-19 cases in children in North Sumatera, representing approximately 8.9% of all cases. Death occurred in 0.62% of the patients, and the children who died had underlying diseases. Four major clusters of COVID-19 infection in children were found in three Islamic boarding schools and one refugee shelter.

CONCLUSION: A high number of children in North Sumatera were affected by COVID-19, and mortality was found to be higher in children with underlying diseases. Major clusters were found in places with prolonged and repeated activities in close contact, such as boarding schools and a refugee shelter.

PMID:37543898 | DOI:10.34172/aim.2022.116

Arch Iran Med. 2022 Sep 1;25(9):617-623. doi: 10.34172/aim.2022.97.

ABSTRACT

BACKGROUND: Organ preservation solutions are not easily accessible in Iran, similar to many resource-limited countries. We aimed to evaluate the efficacy of a locally-produced HTK solution among adult liver transplantation candidates in a pilot clinical trial study.

METHODS: Adult patients undergoing liver transplantation were randomly allocated into two groups. One received the HTK solution (PharMedCina Inc., Shiraz, Iran), and the second received the commercially available HTK solution (Custodiol ^®).

RESULTS: Overall, 28 individuals entered the study, including 11 and 9 males (78.6% and 64.3%) in the Custodiol^® and local HTK groups, respectively. Clinical characteristics, including postoperative biliary complications, reperfusion syndrome, infection and primary non-function (PNF) rates, amount of intraoperative bleeding, length of hospital and ICU stay, peak aspartate aminotransferase (AST) and alanine aminotransferase (ALT), and duration of follow-up were similar between the two groups (P>0.05). One patient died in the locally-produced HTK group. The patient underwent re-transplantation 20 days after his first liver transplantation due to PNF. Two patients died in the Custodiol group, both due to PNF of the liver, which occurred five and three days after transplantation. The two groups did not show any difference regarding serum levels of AST, ALT, alkaline phosphatase (ALP), bilirubin, platelet count, prothrombin time and international normalized ratio, white blood cell count, blood urea nitrogen, and creatinine on the first postoperative day and on the day of discharge (P>0.05).

CONCLUSION: Based on the findings of this pilot study with the current sample size, no statistically significant difference was found between our locally-produced HTK solution and Custodiol^® regarding clinical outcomes.

PMID:37543887 | DOI:10.34172/aim.2022.97

Arch Iran Med. 2022 Aug 1;25(8):552-556. doi: 10.34172/aim.2022.88.

ABSTRACT

BACKGROUND: The accuracy and reliability of noninvasive methods of neonatal jaundice assessment are not completely obvious, including which area of the body is more suitable to estimate actual bilirubin with transcutaneous bilirubinometry (TCB).

METHODS: This cross-sectional study compares the accuracy of three noninvasive methods for neonatal jaundice estimation included visual estimation, TCB on the forehead, and TCB on the sternum. The mean and standard deviation describe quantitative variables. In addition to analytical analysis, we used the linear regression test to evaluate the association of different variables with the accuracy of TCB as well as paired t test for comparing the TCB results on the sternum with the forehead before and after phototherapy. For all statistical tests, a P value less than 0.05 was considered as significant.

RESULTS: We enrolled 100 neonates with a mean age (±SD, standard deviation) of 6.5±1.9 days (range 2-11 days) in our study. The mean gestational age (GA) of the participants was 38.94 weeks±1.00 w SD, and their mean (±SD) weight was 3302 g (±315.60). The mean (mg/dL)±SD for bilirubin level by clinical estimation of jaundice, TCB on the forehead and TCB on the sternum were 17.35±2.88, 17.23±1.63, and 17.77±1.58, respectively. Also, comparing mean differences before and after phototherapy showed that TCB on the sternum is a good predictor for neonatal jaundice before phototherapy (0.539 vs. 0.348).

CONCLUSION: TCB on the sternum is more predictive than the forehead, especially before phototherapy, to assess the need for treatment in outpatient settings.

PMID:37543878 | DOI:10.34172/aim.2022.88