Tag: statistics

Brief Bioinform. 2021 May 11:bbab086. doi: 10.1093/bib/bbab086. Online ahead of print.

ABSTRACT

The mechanisms controlling biological process, such as the development of disease or cell differentiation, can be investigated by examining changes in the networks of gene dependencies between states in the process. High-throughput experimental methods, like microarray and RNA sequencing, have been widely used to gather gene expression data, which paves the way to infer gene dependencies based on computational methods. However, most differential network analysis methods are designed to deal with fully observed data, but missing values, such as the dropout events in single-cell RNA-sequencing data, are frequent. New methods are needed to take account of these missing values. Moreover, since the changes of gene dependencies may be driven by certain perturbed genes, considering the changes in gene expression levels may promote the identification of gene network rewiring. In this study, a novel weighted differential network estimation (WDNE) model is proposed to handle multi-platform gene expression data with missing values and take account of changes in gene expression levels. Simulation studies demonstrate that WDNE outperforms state-of-the-art differential network estimation methods. When applied WDNE to infer differential gene networks associated with drug resistance in ovarian tumors, cell differentiation and breast tumor heterogeneity, the hub genes in the estimated differential gene networks can provide important insights into the underlying mechanisms. Furthermore, a Matlab toolbox, differential network analysis toolbox, was developed to implement the WDNE model and visualize the estimated differential networks.

PMID:33975339 | DOI:10.1093/bib/bbab086

Cancer Epidemiol. 2021 May 8;73:101948. doi: 10.1016/j.canep.2021.101948. Online ahead of print.

ABSTRACT

BACKGROUND: Glioblastoma (GBM) is the most common primary brain tumor. Epidemiologic studies on GBM are rarely reported in the special age group of adolescents and young adults (AYA) in comparison to other age groups. We aim to present data on GBM in Jordan, with a focus on the AYA age, including the incidence, gender, location and outcome, as well as long term survival (LTS).

METHODS: Data on GBM was requested from the Jordan Cancer Registry (JCR), and statistical analysis was performed. All data were retrospective and anonymized.

RESULTS: Eight hundred GBM cases were analyzed from 2000 to 2016 including 505 males (63.1 %). Males outnumbered females across are studied years (p-value <0.001). There were 49 pediatrics (0-14 years, 6.1 %), 125 AYA (15-39 years, 15.6 %), 358 adults (40-59 years, 44.8 %) and 268 elderly (60+ years, 33.5 %) cases. Supratentorial location predominated across all age groups (p-value <0.001). The preponderance of males and supratentorial tumors remained across the AYA age group in comparison to others. The median overall survival (OS) was 23.61 months. AYA age group had a better outcome in comparison to the adults/elderly age group (p-value< 0.001). LTS appear to be more common in the AYA age group (p-value 0.021).

CONCLUSIONS: This is the first comparative epidemiologic study of GBM in Jordan, focusing on the AYA age group. The AYA age group appears to be associated with a better outcome compared to older age groups, with more LTS compared to others.

PMID:33975256 | DOI:10.1016/j.canep.2021.101948

Meat Sci. 2021 May 5;179:108538. doi: 10.1016/j.meatsci.2021.108538. Online ahead of print.

ABSTRACT

This study investigated reactions of pigs (N = 148) and sheep (N = 77) to group stunning where animals were present for the slaughter of others. Mock stunning with an isolated animal was used as the control. In both species, there was little evidence to suggest a difference in blood glucose and cortisol with stun order (P ≥ 0.21). In pigs, lactate differed by stun order (P < 0.001). Control pigs had lower lactate than pigs stunned first (P = 0.009) likely due to longer rest time after pre-slaughter handling. Conversely, the control sheep had greater average lactate than other groups. However, due to limited sample size and large variation there was not enough evidence to conclude an effect of stun order on sheep lactate (P = 0.28). Overall, there was limited evidence of an impact of stun order on behavior. The last pigs stunned exhibited a greater likelihood of grunting compared with other stun orders (P ≤ 0.05).

PMID:33975260 | DOI:10.1016/j.meatsci.2021.108538

J Environ Manage. 2021 May 8;291:112664. doi: 10.1016/j.jenvman.2021.112664. Online ahead of print.

ABSTRACT

Reliable estimates of wildlife mortality due to wildlife-vehicle collisions are key to understanding its impact on wildlife populations and developing strategies to prevent or reduce collisions. Standardised approaches for monitoring roadkill are needed to derive robust and unbiased estimates of mortality that are comparable across different study systems and ecological contexts. When designing surveys, there is a trade-off between survey frequency (and hence logistical effort and financial cost) and carcass detection. In this regard, carcass persistence (the period a carcass remains detectable before being removed by decomposition or scavengers) is important; the longer a carcass persists, the greater the likelihood it will be detected with lower survey effort by conducting more infrequent surveys. Using multi-taxon carcass data collected over a month of repeated driven surveys, combined with five covariates (species functional group, body weight, carcass position on road, carcass condition [either flattened or not after impact], and rainfall prior to each survey), we explored the drivers of carcass persistence with the overall aim of providing information to optimise the design of carcass surveys along linear infrastructure. Our methodological approach included a survival analysis to determine carcass persistence, linear regressions to test the effect of covariates, a subsampling analysis (using field data and a simulation exercise) to assess how the proportion of carcasses detected changes according to survey frequency, and an analysis to compare the costs of surveys based on study duration, transect length and survey frequency. Mean overall carcass persistence was 2.7 days and was significantly correlated with position on road and within-functional group body weight. There was no evidence for a significant effect of rainfall, while the effect of carcass condition was weakly non-significant. The proportion of carcasses detected decreased sharply when survey intervals were longer than three days. However, we showed that survey costs can be reduced by up to 80% by conducting non-daily surveys. Expanding on the call for a standardised methodology for roadkill surveys, we propose that carcass persistence be explicitly considered during survey design. By carefully considering the objectives of the survey and characteristics of the focal taxa, researchers can substantially reduce logistical costs. In addition, we developed an R Shiny web app that can be used by practitioners to compare survey costs across a variety of survey characteristics. This web app will allow practitioners to easily assess the trade-off between carcass detection and logistical effort.

PMID:33975269 | DOI:10.1016/j.jenvman.2021.112664

Growth Horm IGF Res. 2021 Apr 30;57-58:101392. doi: 10.1016/j.ghir.2021.101392. Online ahead of print.

ABSTRACT

OBJECTIVE: We sought to obtain a better understanding of the burden of short stature using a systematic literature review.

METHODS: Studies of the burden of short stature, of any cause in adults and children, were searched using Embase, MEDLINE and Cochrane databases in April 2020, capturing publications from 2008 onwards. Case series and populations with adult-onset growth hormone deficiency (GHD) were excluded.

RESULTS: Of 1684 publications identified, 41 studies (33 in children, 8 in adults) were included. All studies assessed human burden. Most study populations in children included short stature due to GHD, idiopathic short stature (ISS) and short stature after being born small for gestational age (SGA). In these populations, four studies showed that quality of life (QoL) in children with short stature was significantly worse than in children with normal stature. A significant association between QoL and short stature was observed in children with chronic kidney disease (CKD) (3 studies), achondroplasia (1 study) and transfusion-dependent β-thalassaemia (1 study), and in samples with mixed causes of short stature (3 studies). Three studies (one in GHD/ISS/SGA and two in CKD) found no significant association between short stature and QoL, and several studies did not report statistical significance. Approximately half of adult studies showed that QoL was reduced with short stature, and the other half showed no association. Two studies, one in adults with Prader-Willi syndrome and one in children with GHD, suggested a potential association between short stature and poorer cognitive outcomes. Three studies demonstrated an increased caregiver burden in parents of children with short stature.

CONCLUSIONS: Evidence suggests that, compared with those with normal stature, children and adults with short stature of any cause may experience poorer QoL. Further research could extend our understanding of the human burden in this field.

PMID:33975197 | DOI:10.1016/j.ghir.2021.101392

Comput Biol Med. 2021 May 4;134:104465. doi: 10.1016/j.compbiomed.2021.104465. Online ahead of print.

ABSTRACT

The application of 3D imaging is at its cusp in craniofacial diagnosis and treatment planning. However, most applications are limited to simple subjective superimposition-based analysis. As the diagnostic accuracy dictates the precision in operability, we propose a novel method that enables objective clinical decision making for patients with mandibular asymmetry. We analyzed cone-beam computed tomography (CBCT) scans of 34 patients who underwent surgical correction for mandibular asymmetry using a high-throughput computing algorithm. Radiomic segmentation of quantitative features of surface and volume followed by exploration resulted in identification of a computed modified absolute mandibular midsagittal plane (cmAMP). Tomographic similarity scan (ToSS) curves were generated via bilateral equidistant scanning in an antero-posterior direction with cmAMP as the reference. ToSS comprised of a comprehensive similarity index (SI) score curve and a segment-wise volume curve. The SI score was computed using the Sørensen-Dice similarity coefficient ranging from 0 to 1. The volumetric analysis was represented as the non-overlapping volume (NOV) and overlapping volume (OV) for each segment, with two segmentation lines, at the mental foramen anteriorly and the intraoral vertical ramus osteotomy region posteriorly. Statistical analysis showed strong negative correlation between the NOV and SI scores for the anterior, middle, and total mandible (P < 0.001). Additionally, a significant correlation was observed between the change in the SI scores for anterior (P = 0.044) and middle segments (P < 0.001) to the total mandible when comparing the data before and after the surgery. This work demonstrated the potential of incorporating ToSS curves in surgical simulation software to improve precision in the clinical decision-making process.

PMID:33975208 | DOI:10.1016/j.compbiomed.2021.104465

J Hazard Mater. 2021 Apr 15;417:125882. doi: 10.1016/j.jhazmat.2021.125882. Online ahead of print.

ABSTRACT

Organophosphorus flame retardants (PFRs) are a group of emerging contaminants which have been detected in worldwide waters. However, source of various PFRs in the large-scale area like coastal water environment have not been clearly revealed. In this study, fifteen PFRs in coast of Guangdong-Hong Kong-Macao Greater Bay area (GBA), China were investigated, and a method of spatial pattern analysis was firstly used for pollution source identification. Seawater samples from different segments of GBA coast were analyzed and thirteen PFRs were quantified with total concentrations ranging from 32.7 to 1032.7 ng L^-1. GBA coasts have been seriously polluted by PFRs. A hierarchical cluster analysis of the PFR concentrations in different GBA sites showed significant spatial distributions for different types of PFRs. A series of correlation analysis between PFRs distributions and spatial pattern of GBA socio-economic indicators were performed, and multiple sources including human settlement, wastewater, manufacture, construction industry, vehicles, and shipping transport were found to be correlated to PFRs pollutions in the coasts. This study indicates that spatial pattern analysis based on statistical analysis would be a promising method of analyzing environmental data and exploring pollution source in large-scale area.

PMID:33975162 | DOI:10.1016/j.jhazmat.2021.125882

Addict Behav. 2021 Mar 26;120:106936. doi: 10.1016/j.addbeh.2021.106936. Online ahead of print.

ABSTRACT

BACKGROUND: Exposure to childhood adversity has been linked to long-term negative mental health consequences in adulthood.

PURPOSE: This review examined the association between exposure to the death of a family member (i.e., parent or sibling) during childhood or adolescence and the subsequent diagnosis of a substance use disorder.

METHODS: Electronic databases (Scopus, Medline (for Ovid), EMBASE, and PsychINFO) were searched for cohort and case-control studies in the English language. Studies were retained if it was demonstrable that exposure to death occurred before age 18, and that disorder was diagnosed subsequently. Sensitivity analyses were performed for the meta-analysis, and study quality assessed using the Newcastle-Ottawa Scale.

RESULTS: Nine studies, seven cohort and two case-control, were retained. Due to differential metrics (hazard ratios [HRs] versus odds/risk ratios [ORs/RRs]), only one meta-analysis was possible. Individuals experiencing familial death had 1.42 (95% CI = 0.96, 2.09) times the odds of developing a substance use disorder compared to those non-exposed. Where there was a statistically significant effect in other studies, these were mostly studies using National Registers (1.4 ≤ HR ≤ 2.51).

LIMITATIONS: Meta-analysis options were limited by the variety of study designs.

CONCLUSIONS: Evidence for a significant association between familial death and subsequent disorder appears to be an artefact of the study design. Implications of key findings. Further studies are required to better understand and estimate the association between familial death and substance use disorders. Registration and funding. The review was pre-registered (PROSPERO Reg No: CRD42020192892) and funded by the Irish Research Council (COALESCE/2019/61).

PMID:33975176 | DOI:10.1016/j.addbeh.2021.106936

J Forensic Leg Med. 2021 May 6;80:102176. doi: 10.1016/j.jflm.2021.102176. Online ahead of print.

ABSTRACT

OBJECTIVE: To investigate the difference in selected variables between children with and without hymenal transection, which is a healed defect that extends through the entire depth of the posterior hymenal membrane to the vaginal wall.

MATERIALS AND METHODS: All female children from Southern Denmark who were examined by photocolposcopy in a six-year period were included in a retrospective cohort study. Statistical analyses included a chi-square test and a logistic regression analysis.

RESULTS: Eighty girls under 15 years of age who were suspected to have been sexually abused were included. Sixteen of the girls had hymenal transections. There was a statistically significant correlation between the presence of hymenal transections and reported fresh bleeding after the assault.

CONCLUSION: Bleeding after an assault could indicate more severe lesions, which might explain why these patients did not heal completely.

PMID:33975177 | DOI:10.1016/j.jflm.2021.102176

Am J Emerg Med. 2021 May 6;48:203-208. doi: 10.1016/j.ajem.2021.05.007. Online ahead of print.

ABSTRACT

BACKGROUND: The effect of early vasopressin initiation on clinical outcomes in patients with septic shock is uncertain. A systematic review and meta-analysis was performed to evaluate the impact of early start of vasopressin support within 6 h after the diagnosis on clinical outcomes in septic shock patients.

METHODS: We searched the PubMed, Cochrane, and Embase databases for randomized controlled trials (RCTs) and cohort studies from inception to the 1st of February 2021. We included studies involving adult patients (> 16 years)with septic shock. All authors reported our primary outcome of short-term mortality and in the experimental group patients in the studies receiving vasopressin infusion within 6 h after diagnosis of septic shock and in the control group patients in the studies receiving no vasopressin infusion or vasopressin infusion 6 h after diagnosis of septic shock, clearly comparing with clinically relevant secondary outcomes(use of renal replacement therapy(RRT),new onset arrhythmias, ICU length of stay and length of hospitalization). Results were expressed as odds ratio (OR) and mean difference (MD) with accompanying 95% confidence interval (CI).

RESULTS: Five studies including 788 patients were included. The primary outcome of this meta-analysis showed that short-term mortality between the two groups was no difference (odds ratio [OR] = 1.09; 95% CI, 0.8 to 1.48; P = 0.6; χ2 = 0.83; I2 = 0%). Secondary outcomes demonstrated that the use of RRT was less in the experimental group than that of the control group (OR = 0.63; 95% CI, 0.44 to 0.88; P = 0.007; χ2 = 3.15; I2 = 36%).The new onset arrhythmias between the two groups was no statistically significant difference (OR = 0.59; 95% CI, 0.31 to 1.1; P = 0.10; χ2 = 4.7; I2 = 36%). There was no statistically significant difference in the ICU length of stay(mean difference = 0.16; 95% CI, – 0.91 to 1.22; P = 0.77; χ2 = 6.08; I2 = 34%) and length of hospitalization (mean difference = -2.41; 95% CI, -6.61 to 1.78; P = 0.26; χ2 = 8.57; I2 = 53%) between the two groups.

CONCLUSIONS: Early initiation of vasopressin in patients within 6 h of septic shock onset was not associated with decreased short-term mortality, new onset arrhythmias, shorter ICU length of stay and length of hospitalization, but can reduce the use of RRT. Further large-scale RCTs are still needed to evaluate the benefit of starting vasopressin in the early phase of septic shock.

PMID:33975132 | DOI:10.1016/j.ajem.2021.05.007