Category: Statistics

Forensic Sci Int. 2021 Aug 30;327:110987. doi: 10.1016/j.forsciint.2021.110987. Online ahead of print.

ABSTRACT

Human gaits are the patterns of limb movements which involve both the upper and lower body parts. These patterns in terms of step rate, gait speed, stance widening, stride, and bipedal forces are influenced by different factors including environmental (such as social, cultural, and behavioral traits) and physical changes (such as age and health status). These factors are reflected on the imprinted shoeprints generated with body forces, which in turn can be used to predict age, a problem not systematically addressed using any computational approach. We collected 100,000 shoeprints of subjects ranging from 7 to 80 years old and used the data to develop a deep learning end-to-end model ShoeNet to analyze age-related patterns and predict age. The model integrates various convolutional neural network models together using a skip mechanism to extract age-related features, especially in pressure and abrasion regions from pair-wise shoeprints. The results show that 40.23% of the subjects had prediction errors within 5-years of age and the prediction accuracy for gender/sex classification reached 86.07%. Interestingly, the age-related features mostly reside in the asymmetric differences between left and right shoeprints. The analysis also reveals interesting age-related and gender-related patterns in the pressure distributions on shoeprints; in particular, the pressure forces spread from the middle of the toe toward outside regions over age with gender-specific variations of forces on heel regions. Such statistics provide insight into new methods for forensic investigations, medical studies of gait pattern disorders, biometrics, and sport studies.

PMID:34555663 | DOI:10.1016/j.forsciint.2021.110987

J Mech Behav Biomed Mater. 2021 Sep 15;124:104838. doi: 10.1016/j.jmbbm.2021.104838. Online ahead of print.

ABSTRACT

To develop antimicrobial restorative materials for root caries, we assessed a 4-META/MMA-TBB resin (Bondfill SB Plus, Sun Medical) containing benzalkonium chloride (BAC) or cetylpyridinium chloride (CPC) at 1.25, 2.5, and 5.0 wt%. The same resin without antibacterial agent was used as control. The degree of conversion was measured by attenuated total reflectance-Fourier transform infrared spectroscopy. The 3-point flexural strength test was conducted according to ISO 4049. The antimicrobial effect against three oral bacteria (Streptococcus mutans, S. sobrinus, and Actinomyces naeslundii) was assessed using agar diffusion tests. The shear bond strength to root dentin was assessed after 24 h of storage in water with or without 10,000 thermal cycles. The shear bond strength data were statistically compared using a linear mixed-effects model (α = 0.05). The specimen with 5.0 wt% BAC showed a significantly higher degree of conversion than the control, but it also had significantly lower flexural strength and lower shear bond strength after thermal cycling than the other specimens. When BAC or CPC was added at ≥ 2.5 wt%, the resins inhibited the growth of the three investigated microbes. In conclusion, both BAC and CPC showed significant antimicrobial effects when added at 5.0 wt% to the 4-META/MMA-TBB resin. Up to 2.5 wt%, neither antimicrobial agent affected the degree of conversion, flexural strength, or shear bond strength of the resin.

PMID:34555621 | DOI:10.1016/j.jmbbm.2021.104838

Eur J Cancer. 2021 Sep 20;157:278-290. doi: 10.1016/j.ejca.2021.08.014. Online ahead of print.

ABSTRACT

INTRODUCTION: Which neoadjuvant treatment for locally advanced thoracic oesophagus (TE) or gastro-oesophageal junction carcinoma is best remains an open question. Randomised controlled trials variously accrued patients with adenocarcinoma and squamous cell carcinoma, making strong conclusions hard to obtain. The primary objective of this individual participant data meta-analysis was to investigate the effect of neoadjuvant chemotherapy on overall survival (OS).

PATIENTS AND METHODS: Eligible trials should have closed to accrual before 2016 and compared neoadjuvant chemotherapy and surgery (CS) to surgery alone. All relevant published and unpublished trials were identified via searches of electronic databases, conference proceedings and clinical trial registers. The main end-point was OS. Investigators were contacted to obtain the individual patient data, which was recorded, harmonised and checked. A random-effects Cox model, stratified by trial, was used for meta-analysis and subgroup analyses were preplanned.

RESULTS: 16 trials were identified as eligible. Individual patient data were obtained from 12 trial and 2478 patients. CS was associated with an improved OS versus surgery, hazard ratio (HR) = 0.83 [0.72-0.96], p < 0.0001, translating to an absolute benefit of 5.7% at 5-years from 16.8% to 22.5%. Treatment effects did not vary substantially between adenocarcinoma (HR = 0.73 [0.62-0.87]) and squamous cell carcinoma (HR = 0.91 [0.76-1.08], interaction p = 0.26). A somewhat more pronounced effect was observed in gastro-oesophageal junction (HR = 0.68 [0.50-0.93]) versus TE (HR = 0.87 [0.75-1.00], interaction p = 0.07). CS was also associated with a greater disease-free survival (HR = 0.74 [0.64-0.85], p < 0.001).

CONCLUSIONS: Neoadjuvant chemotherapy conferred a better OS than surgery alone and should be considered in all anatomical location and histological subtypes.

PMID:34555647 | DOI:10.1016/j.ejca.2021.08.014

Redox Biol. 2021 Sep 16;47:102138. doi: 10.1016/j.redox.2021.102138. Online ahead of print.

ABSTRACT

Growing evidence implicates an association between psychosocial stress and oxidative stress (OxSt) although there are not yet reliable biomarkers to study this association. We used a Trier Social Stress Test (TSST) and compared the response of a healthy control group (HC; N=10) against the response of a schizophrenia group (SCZ; N=10) that is expected to have higher levels of OxSt. Because our previous study showed inconsistent changes in conventional molecular markers for stress responses in the neuroendocrine and immune systems, we analyzed the same serum samples using a separate reducing capacity assay that provides a more global measurement of OxSt. This assay uses the moderately strong oxidizing agent iridium (Ir) to probe a sample’s reducing capacity. Specifically, we characterized OxSt by this Ir-reducing capacity assay (Ir-RCA) using two measurement modalities (optical and electrochemical) and we tuned this assay by imposing an input voltage sequence that generates multiple output metrics for data-driven analysis. We defined five OxSt metrics (one optical and four electrochemical metrics) and showed: (i) internal consistency among each metric in the measurements of all 40 samples (baseline and post TSST for N=20); (ii) all five metrics were consistent with expectations of higher levels of OxSt for the SCZ group (three individual metrics showed statistically significant differences); and (iii) all five metrics showed higher levels of OxSt Post-TSST (one metric showed statistically significant difference). Using multivariant analysis, we showed that combinations of OxSt metrics could discern statistically significant increases in OxSt for both the SCZ and HC groups 90 min after the imposed acute psychosocial stress.

PMID:34555595 | DOI:10.1016/j.redox.2021.102138

Comput Methods Programs Biomed. 2021 Sep 16;211:106420. doi: 10.1016/j.cmpb.2021.106420. Online ahead of print.

ABSTRACT

OBJECTIVE: Hepatic encephalopathy (HE) is among the most common complications of cirrhosis. Data for cirrhosis with HE is typically unbalanced. Traditional statistical methods and machine learning algorithms thus cannot identify a few classes. In this paper, we use machine learning algorithms to construct a risk prediction model for liver cirrhosis complicated by HE to improve the efficiency of its prediction.

METHOD: We collected medical data from 1,256 patients with cirrhosis and performed preprocessing to extract 81 features from these irregular data. To predict HE in cirrhotic patients, we compared several classification methods: logistic regression, weighted random forest (WRF), SVM, and weighted SVM (WSVM). We also used an additional 722 patients with cirrhosis for external validation of the model.

RESULTS: The WRF, WSVM, and logistic regression models exhibited better recognition ability for patients with HE than traditional machine learning models (sensitivity> 0.70), but their ability to identify patients with uncomplicated HE was slightly lower (specificity approximately 85%). The comprehensive evaluation index of the traditional model was higher than those of other models (G-means> 0.80 and F-measure> 0.40). For the WRF, the G-means (0.82), F-measure (0.46), and AUC (0.82) were superior to those of the logistic regression and WSVM models, which means that it can better predict the incidence of HE in patients.

CONCLUSION: The WRF model is more suitable for the classification of unbalanced medical data and can be used to construct a risk prediction and evaluation system for liver cirrhosis complicated with HE. The probabilistic prediction models of WRF can help clinicians identify high-risk patients with HE.

PMID:34555589 | DOI:10.1016/j.cmpb.2021.106420

Comput Methods Programs Biomed. 2021 Sep 16;211:106418. doi: 10.1016/j.cmpb.2021.106418. Online ahead of print.

ABSTRACT

Backgound and Objective: Detecting differentially expressed genes is an important step in genome wide analysis and expression profiling. There are a wide array of algorithms used in today’s research based on statistical approaches. Even though the current algorithms work, they sometimes miss-predict. There is no framework available for measuring the quality of current algorithms. New machine learning methods (like gradient boost and deep neural networks) were not used to solve this problem. The Gene-Bench open source python package addresses these issues by providing an evaluation and data handling system for differentially expressed genes detection algorithms on microarray data. We also provide MIDGET, a new group of algorithms based on state of the art machine learning approaches Methods: The Gene-Bench package provides data collected from real experiments that consists of 73 transcription-factor perturbation experiments with validation data from Chip-seq experiments and 129 drug perturbation experiments, synthetic data generated with our own method and three evaluation metrics (Kolmogorov, F1 and AUC/ROC). Besides the data and metrics, Gene-Bench also contains well-known algorithms and a new method to identify differentially expressed genes, called MIDGET: Machine learning Identification Differential Gene Expression Tool that is using big-data and machine learning methods to identify differentially expressed genes. The two new groups of machine learning algorithms provided in our package use extreme gradient boosting and deep neural networks to achieve their results. Results: The Gene-Bench package is highly flexible, allows fast prototyping and evaluating of new and old algorithms and provides multiple new machine-learning algorithms (called MIDGET) that perform better on all evaluation metrics than all the other tested alternatives. While everything provided in Gene-Bench is algorithm independent, the user can also use algorithms implemented in the R language even though the package is written in Python. Conclusions: The Gene-Bench package fills a gap in evaluating and benchmarking differential gene detection algorithms. It also provides machine learning methods that perform detection with higher accuracy in all tested metrics. It is available at https://github.com/raduangelescu/GeneBench/ and can be directly installed from the Python Package Index using pip install genebench.

PMID:34555591 | DOI:10.1016/j.cmpb.2021.106418

Chemosphere. 2021 Sep 16;287(Pt 3):132268. doi: 10.1016/j.chemosphere.2021.132268. Online ahead of print.

ABSTRACT

Dissolved salts, colloidal particles, and active microorganisms in brackish surface water distribution systems (BSWD) cause multiple fouling, poses potential threat to the environmental pollution, and raising technical and economic issues as well. So far, the co-occurrence and interactions of multiple fouling remains largely unknown. Multiple fouling behaviors were assessed in agriculture BSWD under different nitrogen (N) fertilizers. X-ray diffraction, Rietveld refinement analysis, 16S rRNA, and microbial network analysis were conducted to determine the fouling characteristics. Statistical analysis was applied to reveal the relative contributions and interaction of multiple fouling. Our results demonstrated, multiple fouling of precipitates, particulates and biofoulings were co-occurred. Fouling growth was largely attributed to the strong interactions of different fouling. The binary interactions of precipitates – particulates contributed 51.1%, and ternary interactions of precipitates – particulates – biofouling contributed 25.4% to explain the decline of system performance, while the contribution of each single type fouling was minimal. Thereby indicating the significant role of calcium silica, biomineralization and bio-silicates in fouling. The lower acid N fertilizer broken the interaction of multiple fouling by increasing the precipitate crystal parameters and repulsive forces amongst particulates, as well as destroyed microbial interactions in biofouling. Overall, this study open frontier for multiple fouling in-depth profiling and antifouling guidance for effective utilization of BSWD.

PMID:34555585 | DOI:10.1016/j.chemosphere.2021.132268

BJOG. 2021 Sep 23. doi: 10.1111/1471-0528.16943. Online ahead of print.

ABSTRACT

OBJECTIVE: To investigate the association between hysterectomy with conservation of one or both adnexa and ovarian and tubal cancer.

DESIGN: Prospective cohort study.

SETTING: 13 NHS Trusts in England, Wales and Northern Ireland.

POPULATION: 202,506 postmenopausal women recruited between 2001-2005 to the UK Collaborative Trial of Ovarian Cancer Screening (UKCTOCS) and followed up until 31 December 2014.

METHODS: Multiple sources (questionnaires, hospital notes, Hospital Episodes Statistics, national cancer/death registries, ultrasound reports) were used to obtain accurate data on hysterectomy (with conservation of one or both adnexa) and outcomes censored at bilateral oophorectomy, death, ovarian/tubal cancer diagnosis, loss to follow-up or 31 December 2014. Cox proportional hazards regression models were used to assess the association.

MAIN OUTCOME MEASURES: Invasive epithelial ovarian and tubal cancer (WHO 2014) on independent outcome review.

RESULTS: Hysterectomy with conservation of one or both adnexa was reported in 41,912 (20.7%; 41,912/202,506) women. Median follow up was 11.1years (IQR 9.96-12.04), totalling >2.17million women-years. Among women who had undergone hysterectomy, 0.55% (231/41912) were diagnosed with ovarian/tubal cancer, compared with 0.59% (945/160594) of those with intact uterus. Multivariable analysis showed no evidence of an association between hysterectomy and invasive epithelial ovarian/tubal cancer (RR=0.98, 95%CI 0.85-1.13, p=0.765).

CONCLUSIONS: This large cohort study provides further independent validation that hysterectomy is not associated with alteration of invasive epithelial ovarian and tubal cancer risk. This data is important both for clinical counselling and for refining risk prediction models.

PMID:34555263 | DOI:10.1111/1471-0528.16943

J Vet Emerg Crit Care (San Antonio). 2021 Sep 23. doi: 10.1111/vec.13129. Online ahead of print.

ABSTRACT

OBJECTIVE: To measure and compare viscoelastic coagulation in 2 canine blood donor populations using a novel, point-of-care device (VCM Vet Analyzer, VCM).

DESIGN: Cohort study.

SETTING: Academic and commercial veterinary blood banks.

ANIMALS: Non-Greyhounds from community-based blood donor program and Greyhounds from a blood bank colony.

INTERVENTION: Blood was collected from all dogs via direct venipuncture for a complete hemogram, biochemistry, and point-of-care viscoelastic coagulation.

MEASUREMENT AND MAIN RESULTS: All biochemical measurements for all dogs in Group NG (n = 38, non-Greyhounds) and Group G (n = 53, Greyhounds) were within local reference intervals. Hematology data showed significant statistical differences between groups in hemoglobin, RBC, platelet, and WBC concentrations. Group G demonstrated lower maximum clot firmness (MCF) with 17 VCM units (26 VCM units in Group NG), increased lysis with 30 VCM units at 30 minutes (LI30) and 27 VCM units at 45 minutes (LI45) (86 VCM units LI30 and 85 VCM units LI45 in Group NG), and decreased amplitude of 13 VCM units 10 minutes (A10) after clot time (CT) and 6 VCM units 20 minutes after CT (A20) (18 VCM units [A10] and 22 VCM units [A20] in Group NG).

CONCLUSION: This study found differences between healthy Greyhound and non-Greyhound blood donors in measures of clot strength and fibrinolysis as measured by the VCM. Whereas Greyhound have unique hematologic and hemostatic profiles, these measured viscoelastic differences are important to note prior to and following surgical intervention to aid in clinical decision-making if bleeding complications develop.

PMID:34555256 | DOI:10.1111/vec.13129

BJOG. 2021 Sep 23. doi: 10.1111/1471-0528.16944. Online ahead of print.

ABSTRACT

OBJECTIVE: The My Baby’s Movements (MBM) trial aimed to evaluate the impact on stillbirth rates of a multifaceted awareness package (MBM intervention).

DESIGN: Stepped-wedge cluster-randomised controlled trial.

SETTING: Twenty-seven maternity hospitals in Australia and New Zealand.

POPULATION/SAMPLE: Women with a singleton pregnancy without major fetal anomaly at ≥28 weeks’ gestation from August 2016-May 2019.

METHODS: The MBM intervention was implemented at randomly assigned time points with sequential introduction into 8 groups of 3-5 hospitals at four-monthly intervals. Using generalised linear mixed models, the stillbirth rate was compared in the control and intervention periods adjusting for calendar time, study population characteristics, and hospital effects.

OUTCOME MEASURES: Stillbirth at ≥28 weeks’ gestation.

RESULTS: There were 304,850 births with 290,105 meeting inclusion criteria: 150,053 in control and 140,052 in intervention periods. The stillbirth rate was lower (although not statistically significantly) during the intervention compared with the control period (2.2 versus 2.4/1000 births; aOR 1.18, 95% CI 0.93-1.50; p=0.18) The decrease in stillbirth rates was larger across calendar time: 2.7/1000 in the first versus 2.0/1000 in the last 18 months. No increase in secondary outcomes, including obstetric intervention or adverse neonatal outcome, was evident.

CONCLUSION: The MBM intervention did not reduce stillbirths beyond the downward trend over time. Due to low uptake, the role of the intervention remains unclear, though the downward trend across time suggests some benefit in lowering the stillbirth rate. In this study setting, awareness of fetal movements may have reached pregnant women and clinicians prior to implementation of the intervention.

PMID:34555257 | DOI:10.1111/1471-0528.16944