Category: Statistics

Nat Commun. 2023 Aug 12;14(1):4873. doi: 10.1038/s41467-023-40658-3.

ABSTRACT

Multiplexed DNA fluorescence in situ hybridization (FISH) imaging technologies have been developed to map the folding of chromatin fibers at tens of nanometers and up to several kilobases in resolution in single cells. However, computational methods to reliably identify chromatin loops from such imaging datasets are still lacking. Here we present a Single-Nucleus Analysis Pipeline for multiplexed DNA FISH (SnapFISH), to process the multiplexed DNA FISH data and identify chromatin loops. SnapFISH can identify known chromatin loops from mouse embryonic stem cells with high sensitivity and accuracy. In addition, SnapFISH obtains comparable results of chromatin loops across datasets generated from diverse imaging technologies. SnapFISH is freely available at https://github.com/HuMingLab/SnapFISH .

PMID:37573342 | DOI:10.1038/s41467-023-40658-3

BMC Vet Res. 2023 Aug 12;19(1):123. doi: 10.1186/s12917-023-03673-6.

ABSTRACT

BACKGROUND: Subclinical mastitis (SCM) is one of the most economically important diseases affecting the dairy industry. The SCM does not cause visible changes in the udder or physical changes of the milk as compared to clinical mastitis, and a clear overview of the prevalence and risk factors in the different regions of Africa is still lacking. The objective of this study was to investigate the prevalence of SCM and assess the associated risk factors and dominant bacterial pathogens among cattle in Africa.

MATERIALS AND METHODS: We gathered and systematically reviewed literature concerning SCM, published in English from January 2010 through December 2020 in two databases (PubMed and Web of Science), and meta-analysis was conducted using the ‘meta’ and ‘metafor’ packages in the R statistical software.

RESULTS: A total of 258 studies were retrieved and at the end of the screening, 82 full-texts were eligible for inclusion in the meta-analysis. The prevalence of SCM was reported in 11 countries in five regions of Africa, and the random-effects model showed that the weighted pooled prevalence estimate (PPE) was 48.2% (95% CI: 43.6-52.8%). Heterogeneity was high and statistically significant as I² (proportion of observed variation) was 98.1% (95% CI: 98.0-98.3%), τ² (true between-study variance) was 0.0433 (95% CI: 0.0322-0.0611), and the Cochran Q statistic was 4362.8 (p < 0.0001). Subgroup and meta-regression analyses showed that East Africa had significantly (p = 0.0092) the highest PPE of SCM (67.7%, 95% CI: 55.7-78.7) followed by West Africa (50.5%, 95%CI: 31.4-69.5), and the lowest was in North Africa (40.3%, 95%: 32.2-48.6). Other significant moderators for SCM were age (p < 0.0001), breed (p = 0.0002), lactation stage (p = 0.019) and parity (p = 0.0008) of cattle. Staphylococcus species (prevalence 43.7%) were the most predominant pathogens, followed by Streptococcus (18.2%) and Escherichia species (9.5%).

CONCLUSION: The present study showed a high variation of SCM prevalence in various parts of Africa, although there is a need for more data in some regions. The reported prevalence is a clear sign of inappropriate management practices among cattle herds and an indicator of the threat that SCM poses to the dairy industry. The information about the predisposing factors may guide effective management and control strategies to reduce transmission of the disease.

PMID:37573335 | DOI:10.1186/s12917-023-03673-6

BMC Pregnancy Childbirth. 2023 Aug 12;23(1):583. doi: 10.1186/s12884-023-05894-x.

ABSTRACT

BACKGROUND: This study aimed to investigate the factors associated with the antenatal umbilical cord pitch value by ultrasound measurement in late pregnancy. We investigated the factors associated with the umbilical cord pitch value under prenatal ultrasound measurement.

METHODS: This study included 528 pregnant women who underwent routine antenatal ultrasound examinations in Ningbo Women and Children’s Hospital from December 2020 to August 2021. Their umbilical cord pitch values and diameter, Wharton’s jelly thickness, amniotic fluid indexes, umbilical artery blood flow parameters, and other relevant data, such as ages and gestational ages, were measured. Information about delivery methods, placenta, umbilical cord, and neonatal weight were recorded during follow-up. Statistical analysis was performed on the above data, and the factors associated with the pitch values were analyzed by linear regression.

RESULTS: This study revealed that cord torsion (p < 0.001, 95% confidence interval [CI]=-34.81 to -19.01), cord entanglement (p < 0.001, 95% CI = 10.71 to 20.11), thickening of Wharton’s jelly (p = 0.001, 95% CI = 5.39 to 20.24), and cord edema (p = 0.015, 95%CI = 2.09 to 19.44), gestational age (p = 0.024, 95%CI = 0.14 to 1.89), age of pregnant woman (p = 0.009, 95%CI= -1.15 to -0.16), and neonatal weight (p = 0.011, 95%CI = 0.002 to 0.012) were significantly correlated with the pitch values.

CONCLUSION: The umbilical cord pitch value significantly correlated with cord entanglement, cord torsion, cord edema, Wharton’s jelly thickening, gestational age, age of the pregnant woman, and neonatal weight. Notably, the pitch value by prenatal ultrasound measurement is predictive of cord morphological abnormalities such as cord entanglement, cord torsion, cord edema, and Wharton’s jelly thickening.

PMID:37573329 | DOI:10.1186/s12884-023-05894-x

Mol Autism. 2023 Aug 12;14(1):30. doi: 10.1186/s13229-023-00562-5.

ABSTRACT

BACKGROUND: Prenatal exposure to maternal metabolic conditions associated with inflammation and steroid dysregulation has previously been linked to increased autism risk. Steroid-related maternal serum biomarkers have also provided insight into the in utero steroid environment for offspring who develop autism.

OBJECTIVE: This study examines the link between autism among offspring and early second trimester maternal steroid-related serum biomarkers from pregnancies enriched for prenatal metabolic syndrome (PNMS) exposure.

STUDY DESIGN: Early second trimester maternal steroid-related serum biomarkers (i.e., estradiol, free testosterone, total testosterone, and sex hormone binding globulin) were compared between pregnancies corresponding to offspring with (N = 68) and without (N = 68) autism. Multiple logistic regression analyses were stratified by sex and gestational duration. One-way ANCOVA with post hoc tests was performed for groups defined by autism status and PNMS exposure.

RESULTS: Increased estradiol was significantly associated with autism only in males (AOR = 1.13 per 100 pg/ml, 95% CI 1.01-1.27, p = 0.036) and only term pregnancies (AOR = 1.17 per 100 pg/ml, 95% CI 1.04-1.32, p = 0.010). Autism status was significantly associated with decreased sex hormone binding globulin (AOR = 0.65 per 50 nmol/L, 95% CI 0.55-0.78, p < 0.001) overall and when stratified by sex and term pregnancy status. The inverse association between sex hormone binding globulin and autism was independent of PNMS exposure.

LIMITATIONS: The relative racial and ethnic homogeneity of Utah’s population limits the generalizability of study results. Although significant differences by autism status were identified in concentrations of sex hormone binding globulin overall and of estradiol in participant subgroups, differences by PNMS exposure failed to reach statistical significance, which may reflect insufficient statistical power.

CONCLUSION: Both elevated maternal serum estradiol in males only and low maternal serum sex hormone binding globulin in both sexes are associated with increased autism risk. Further investigation is merited to identify how steroid, metabolic, and inflammatory processes can interact to influence neurodevelopment in early second trimester.

PMID:37573326 | DOI:10.1186/s13229-023-00562-5

Nat Commun. 2023 Aug 12;14(1):4869. doi: 10.1038/s41467-023-40585-3.

ABSTRACT

While perovskite solar cells have reached competitive efficiency values during the last decade, stability issues remain a critical challenge to be addressed for pushing this technology towards commercialisation. In this study, we analyse a large homogeneous dataset of Maximum Power Point Tracking (MPPT) operational ageing data that we collected with a custom-built High-throughput Ageing System in the past 3 years. In total, 2,245 MPPT ageing curves are analysed which were obtained under controlled conditions (continuous illumination, controlled temperature and atmosphere) from devices comprising various lead-halide perovskite absorbers, charge selective layers, contact layers, and architectures. In a high-level statistical analysis, we find a correlation between the maximum reached power conversion efficiency (PCE) and the relative PCE loss observed after 150-hours of ageing, with more efficient cells statistically also showing higher stability. Additionally, using the unsupervised machine learning method self-organising map, we cluster this dataset based on the degradation curve shapes. We find a correlation between the frequency of particular shapes of degradation curves and the maximum reached PCE.

PMID:37573324 | DOI:10.1038/s41467-023-40585-3

BMC Public Health. 2023 Aug 12;23(1):1541. doi: 10.1186/s12889-023-16477-y.

ABSTRACT

BACKGROUND: The objectives of this study were to investigate the proportion of treatment-resistant depression (TRD) among patients with diagnosed major depressive disorder (MDD) and undergoing antidepressant treatment, to estimate the economic cost of MDD, TRD, and non-treatment-resistant depression (non-TRD), and to examine the differences between TRD and non-TRD MDD in a Thai public tertiary hospital.

METHODS: This was a combined study between retrospective review of medical records and a cross-sectional survey. The sample size was 500 dyads of antidepressant-treated MDD patients and their unpaid caregivers. MDD patients’ medical records, the concept of healthcare resource utilization, the Work Productivity and Activity Impairment Questionnaire: depression and mood & mental state versions (WPAI: D, MM), the Class Impairment Questionnaire (CIQ), and the Family Experiences Interview Schedule (FEIS) were applied as the tools of the study. Pearson Chi’s square, Fisher’s Exact test, and independent T-test were employed for statistical analysis.

RESULTS: The proportion of TRD was 19.6% among antidepressant-treated MDD patients in a Thai tertiary public hospital. The results of the study indicated that several factors showed a statistically significant association with TRD criteria. These factors included younger age of MDD patients, a younger age of onset of MDD, lower body mass index (BMI), a history of suicide attempts and self-harm, as well as frequent smoking behavior. The annualized economic cost of TRD was 276,059.97 baht per person ($7,668.33), which was significantly higher than that of cost of non-TRD (173,487.04 baht or $4,819.08). The aggregated economic costs of MDD were 96.8 million baht annually ($2.69 M) if calculated from 500 MDD patients and unpaid caregivers. This contributed to the economic cost of TRD 27.05 million baht (98 respondents) and the economic cost of non-TRD 69.74 million baht (402 respondents).

CONCLUSIONS: The economic burden associated with TRD was significantly higher compared to non-TRD among antidepressant-treated MDD patients. Specifically, both direct medical costs and indirect costs were notably elevated in the TRD group.

PMID:37573321 | DOI:10.1186/s12889-023-16477-y

BMC Med Educ. 2023 Aug 12;23(1):572. doi: 10.1186/s12909-023-04550-4.

ABSTRACT

BACKGROUND: This study explores the impacts of the Council on Medical Student Education in Pediatrics (COMSEP) Journal Club, a unique means of providing monthly professional development for a large international community of pediatric undergraduate medical educators. In particular, we sought to establish member engagement with the Journal Club, identify factors impacting member contributions to the Journal Club, and determine perceived benefits of and barriers to participation as a Journal Club reviewer.

METHODS: Using an established Annual Survey as a study instrument, six survey questions were distributed to members of COMSEP. Items were pilot tested prior to inclusion. Quantitative data were analyzed using descriptive statistics and chi-square analysis..

RESULTS: Of 125 respondents who completed the survey, 38% reported reading the Journal Club most months or always. Level of engagement varied. Reasons for reading included a topic of interest, keeping up to date on medical education literature, gaining practical tips for teaching and implementing new curricula. Motivators for writing a review included keeping up to date, contributing to a professional organization, and developing skill in analyzing medical education literature, with a minority citing reasons of enhancing their educational portfolio or academic promotion. The most commonly cited barriers were lack of time and lack of confidence or training in ability to analyze medical education literature.

CONCLUSION: As a strategy to disseminate the latest evidence in medical education to its membership, the COMSEP Journal Club is effective. Its format is ideally suited for busy educators and may help in members’ professional development and in the development of a community of practice.

PMID:37573320 | DOI:10.1186/s12909-023-04550-4

BMC Oral Health. 2023 Aug 12;23(1):557. doi: 10.1186/s12903-023-03266-7.

ABSTRACT

BACKGROUND: Many scholars have proven cervical vertebral maturation (CVM) method can predict the growth and development and assist in choosing the best time for treatment. However, assessing CVM is a complex process. The experience and seniority of the clinicians have an enormous impact on judgment. This study aims to establish a fully automated, high-accuracy CVM assessment system called the psc-CVM assessment system, based on deep learning, to provide valuable reference information for the growth period determination.

METHODS: This study used 10,200 lateral cephalograms as the data set (7111 in train set, 1544 in validation set and 1545 in test set) to train the system. The psc-CVM assessment system is designed as three parts with different roles, each operating in a specific order. 1) Position Network for locating the position of cervical vertebrae; 2) Shape Recognition Network for recognizing and extracting the shapes of cervical vertebrae; and 3) CVM Assessment Network for assessing CVM according to the shapes of cervical vertebrae. Statistical analysis was conducted to detect the performance of the system and the agreement of CVM assessment between the system and the expert panel. Heat maps were analyzed to understand better what the system had learned. The area of the third (C3), fourth (C4) cervical vertebrae and the lower edge of second (C2) cervical vertebrae were activated when the system was assessing the images.

RESULTS: The system has achieved good performance for CVM assessment with an average AUC (the area under the curve) of 0.94 and total accuracy of 70.42%, as evaluated on the test set. The Cohen’s Kappa between the system and the expert panel is 0.645. The weighted Kappa between the system and the expert panel is 0.844. The overall ICC between the psc-CVM assessment system and the expert panel was 0.946. The F1 score rank for the psc-CVM assessment system was: CVS (cervical vertebral maturation stage) 6 > CVS1 > CVS4 > CVS5 > CVS3 > CVS2.

CONCLUSIONS: The results showed that the psc-CVM assessment system achieved high accuracy in CVM assessment. The system in this study was significantly consistent with expert panels in CVM assessment, indicating that the system can be used as an efficient, accurate, and stable diagnostic aid to provide a clinical aid for determining growth and developmental stages by CVM.

PMID:37573308 | DOI:10.1186/s12903-023-03266-7

BMC Oral Health. 2023 Aug 12;23(1):562. doi: 10.1186/s12903-023-03195-5.

ABSTRACT

BACKGROUND: Pain is usually subjective and thus it is challenging to describe its characteristics such as nature, intensity, and origin. Non-invasive methods such as assessing salivary alpha-amylase (SAA) may aid the practitioner to evaluate the pain intensity. Hence, the current study aimed to correlate the levels of SAA with the pain intensity in patients presenting with varied endodontic pain levels.

METHODS: Sixty patients who presented with varied intensities of endodontic pain were selected for the present study out of which seven patients were excluded/dropped, leaving a total sample of fifty-five patients for assessment. Mandibular molar with symptomatic irreversible pulpitis without periapical pathology were included in the study. A 5ml of un-stimulated was obtained from the patients, following which the local anesthesia was administered. Root canal treatment was then performed and the pain scores at pre-operative and post-operative were recorded. Additionally, salivary samples were collected after emergency endodontic treatment and sent for sialochemical analysis. IBM.SPSS statistics software 23.0 was employed to assess the obtained data.

RESULTS: A statistically significant drop in the pain score (P < 0.001) and SAA levels (P < 0.001) were observed post-operatively in the contract to pre-operative state. A strong positive correlation was reported between SAA levels and pain scores in patients undergoing emergency endodontic treatment at both time intervals namely pre-operative (P < 0.001) and post-operative (P < 0.001).

CONCLUSION: The results of this preliminary showed a strong association between the pain score and SAA levels in patients undergoing an emergency endodontic treatment.

PMID:37573306 | DOI:10.1186/s12903-023-03195-5

J Transl Med. 2023 Aug 12;21(1):536. doi: 10.1186/s12967-023-04397-9.

ABSTRACT

BACKGROUND: Studies have examined the effect of weight change on osteoporosis, but the results were controversial. Among them, few had looked at weight change over the life span. This study aimed to fill this gap and investigate the association between lifetime body mass index (BMI) trajectories and bone loss.

METHODS: In this cross-sectional study, participants at age 50 and above were selected from the National Health and Nutrition Examination Survey (NHANES) 2005-2018. Dual-energy X-ray Absorptiometry was used to measure the bone mineral density at the femoral neck and lumbar spine. Standard BMI criteria were used, with < 25 kg/m² for normal, 25-29.9 kg/m² for overweight, and ≥ 30 kg/m² for obesity. The latent class trajectory model (LCTM) was used to identify BMI trajectories. Multinomial logistic regression models were fitted to evaluate the association between different BMI trajectories and osteoporosis or osteopenia.

RESULTS: For the 9,706 eligible participants, we identified four BMI trajectories, including stable (n = 7,681, 70.14%), slight increase (n = 1253, 12.91%), increase to decrease (n = 195, 2.01%), and rapid increase (n = 577, 5.94%). Compared with individuals in the stable trajectory, individuals in the rapid increase trajectory had higher odds of osteoporosis (OR = 2.25, 95% CI 1.19-4.23) and osteopenia (OR = 1.49, 95% CI 1.02-2.17). This association was only found in the lumbar spine (OR = 2.11, 95% CI 1.06-4.2) but not in the femoral neck. In early-stage (age 25-10 years ago) weight change, staying an obesity and stable weight seemed to have protective effects on osteoporosis (OR = 0.26, 95% CI 0.08-0.77) and osteopenia (OR = 0.46, 95% CI 0.25-0.84). Meanwhile, keeping an early-stage stable and overweight was related to lower odds of osteopenia (OR = 0.53, 95% CI 0.34-0.83). No statistically significant association between recent (10 years ago to baseline) weight change and osteoporosis was found.

CONCLUSIONS: Rapid and excess weight gain during adulthood is associated with a higher risk of osteoporosis. But this association varies by skeletal sites. Maintaining stable overweight and obesity at an early stage may have potentially beneficial effects on bone health.

PMID:37573305 | DOI:10.1186/s12967-023-04397-9