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Bio-protocol Jul 2023Current means to quantify cells, gene expression, and fibrosis of liver histological slides are not standardized in the research community and typically rely upon data...
Current means to quantify cells, gene expression, and fibrosis of liver histological slides are not standardized in the research community and typically rely upon data acquired from a selection of random regions identified in each slide. As such, analyses are subject to selection bias as well as limited subsets of available data elements throughout the slide. A whole-slide analysis of cells and fibrosis would provide for a more accurate and complete quantitative analysis, along with minimization of intra- and inter-experimental variables. Herein, we present , a method for quantifying whole-slide scans of digitized histologic images to render a more comprehensive analysis of presented data elements. After loading images and preparing the project in the QuPath program, researchers are provided with one to two scripts per analysis that generate an average intensity threshold for their staining, automated tissue annotation, and downstream detection of their anticipated cellular matrices. When compared with two standard methodologies for histological quantification, had two significant advantages: increased speed and a 50-fold greater tissue area coverage. Using publicly available open-source code (GitHub), improves the reliability and reproducibility of experimental results while reducing the time scientists require to perform bulk analysis of liver histology. This analytical process is readily adaptable by most laboratories, requires minimal optimization, and its principles and code can be optimized for use in other organs. Graphical overview.
PubMed: 37497459
DOI: 10.21769/BioProtoc.4776 -
Poultry Science Jul 2024Goose circovirus (GoCV), a potential immunosuppressive virus possessing a circular single-stranded DNA genome, is widely distributed in both domesticated and wild geese....
Goose circovirus (GoCV), a potential immunosuppressive virus possessing a circular single-stranded DNA genome, is widely distributed in both domesticated and wild geese. This virus infection causes significant economic losses in the waterfowl industry. The codon usage patterns of viruses reflect the evolutionary history and genetic architecture, allowing them to adapt quickly to changes in the external environment, particularly to their hosts. In this study, we retrieved the coding sequences (Rep and Cap) and the genome of GoCV from GenBank, conducting comprehensive research to explore the codon usage patterns in 144 GoCV strains. The overall codon usage of the GoCV strains was relatively similar and exhibited a slight bias. The effective number of codons (ENC) indicated a low overall extent of codon usage bias (CUB) in GoCV. Combined with the base composition and relative synonymous codon usage (RSCU) analysis, the results revealed a bias toward A- and G-ending codons in the overall codon usage. Analysis of the ENC-GC plot and neutrality plot suggested that natural selection plays an important role in shaping the codon usage pattern of GoCV, with mutation pressure having a minor influence. Furthermore, the correlations between ENC and relative indices, as well as correspondence analysis (COA), showed that hydrophobicity and geographical distribution also contribute to codon usage variation in GoCV, suggesting the possible involvement of natural selection. In conclusion, GoCV exhibits comparatively slight CUB, with natural selection being the major factor shaping the codon usage pattern of GoCV. Our research contributes to a deeper understanding of GoCV evolution and its host adaptation, providing valuable insights for future basic studies and vaccine design related to GoCV.
Topics: Circovirus; Animals; Codon Usage; Geese; Poultry Diseases; Circoviridae Infections; Selection, Genetic; Host Adaptation; Adaptation, Physiological
PubMed: 38713985
DOI: 10.1016/j.psj.2024.103775 -
World Journal of Urology Nov 2023To evaluate the proportions of detected prostate cancer (PCa) and clinically significant PCa (csPCa), as well as identify clinical predictors of PCa, in patients...
OBJECTIVE
To evaluate the proportions of detected prostate cancer (PCa) and clinically significant PCa (csPCa), as well as identify clinical predictors of PCa, in patients with PI-RADS > = 3 lesion at mpMRI and initial negative targeted and systematic biopsy (initial biopsy) who underwent a second MRI and a re-biopsy.
METHODS
A total of 290 patients from 10 tertiary referral centers were included. The primary outcome measures were the presence of PCa and csPCa at re-biopsy. Logistic regression analyses were performed to evaluate predictors of PCa and csPCa, adjusting for relevant covariates.
RESULTS
Forty-two percentage of patients exhibited the presence of a new lesion. Furthermore, at the second MRI, patients showed stable, upgrading, and downgrading PI-RADS lesions in 42%, 39%, and 19%, respectively. The interval from the initial to repeated mpMRI and from the initial to repeated biopsy was 16 mo (IQR 12-20) and 18 mo (IQR 12-21), respectively. One hundred and eight patients (37.2%) were diagnosed with PCa and 74 (25.5%) with csPCa at re-biopsy. The presence of ASAP on the initial biopsy strongly predicted the presence of PCa and csPCa at re-biopsy. Furthermore, PI-RADS scores at the first and second MRI and a higher number of systematic biopsy cores at first and second biopsy were independent predictors of the presence of PCa and csPCa. Selection bias cannot be ruled out.
CONCLUSIONS
Persistent PI-RADS ≥ 3 at the second MRI is suggestive of the presence of a not negligible proportion of csPca. These findings contribute to the refinement of risk stratification for men with initial negative MRI-TBx.
Topics: Male; Humans; Magnetic Resonance Imaging; Multiparametric Magnetic Resonance Imaging; Prostatic Neoplasms; Image-Guided Biopsy; Tertiary Care Centers; Retrospective Studies
PubMed: 37755520
DOI: 10.1007/s00345-023-04578-7 -
Diagnostics (Basel, Switzerland) Sep 2023mutation () is the most frequent point mutation in non-small cell lung cancer (NSCLC) and has been proven to be a predictive biomarker for direct inhibitors in... (Review)
Review
mutation () is the most frequent point mutation in non-small cell lung cancer (NSCLC) and has been proven to be a predictive biomarker for direct inhibitors in advanced solid cancers. We sought to determine the prognostic significance of in patients with NSCLC using the meta-analytic approach. A protocol is registered at the International Prospective Register for systematic reviews (CRD42022345868). PubMed, EMBASE, The Cochrane Library, and Clinicaltrials.gov.in were searched for prospective or retrospective studies reporting survival data for tumors with compared with either other mutations or wild-type (-). The hazard ratios (HRs) for overall survival (OS) or Disease-free survival (DFS) of tumors were pooled according to fixed or random-effects models. Sixteen studies enrolling 10,153 participants were included in the final analysis. tumors had poor OS [] but similar DFS [HR 2.36, 95% CI 0.64-8.16] compared to tumors. Compared to other mutations, tumors had poor DFS [] but similar OS [HR, 1.03; 95% CI, 0.84-1.26]. Compared to other mutations, high PD-L1 expression (>50%) [] was associated with tumors. is a promising prognostic factor for patients with NSCLC, negatively impacting survival. Prevailing significant heterogeneity and selection bias might reduce the validity of these findings. Concomitant high PD-L1 expression in these tumors opens doors for exciting therapeutic potential.
PubMed: 37835787
DOI: 10.3390/diagnostics13193043 -
Infection, Genetics and Evolution :... Aug 2024African swine fever (ASF) is a serious animal disease, and has spread to Africa, Europe and Asia, causing massive economic losses. African swine fever virus (ASFV) is...
African swine fever (ASF) is a serious animal disease, and has spread to Africa, Europe and Asia, causing massive economic losses. African swine fever virus (ASFV) is transmitted from a reservoir host (warthog) to domestic pigs via a sylvatic cycle (transmission between warthogs and soft ticks) and a domestic cycle (transmission between domestic pigs) and survives by expressing a variety of genes related to virus-host interactions. We evaluated differences in codon usage patterns among ASFV genotypes and clades and explored the common and specific evolutionary and genetic characteristics of ASFV sequences. We analysed the evolutionary relationships, nucleotide compositions, codon usage patterns, selection pressures (mutational pressure and natural selection) and viral adaptation to host codon usage based on the coding sequences (CDS) of key functional genes of ASFV. AT bias was detected in the six genes analysed, irrespective of clade. The AT bias of genes (A224L, A179L, EP153R) encoding proteins involved in interaction with host cells after infection was high; among them, the AT bias of EP153R was the greatest at 78.3%. A large number of overrepresented codons were identified in EP153R, whereas there were no overrepresented codons with a relative synonymous codon usage (RSCU) value of ≥3 in B646L. In most genes, the pattern of selection pressure was similar for each clade, but in EP153R, diverse patterns of selection pressure were captured within the same clade and genotype. As a result of evaluating host adaptation based on the codon adaptation index (CAI), for B646L, E183L, CP204L and A179L, the codon usage patterns in all sequences were more similar to tick than domestic pig or wild boar. However, EP153R showed the lowest average CAI value of 0.52 when selecting tick as a reference set. The genes analysed in this study showed different magnitudes of selection pressure at the clade and genotype levels, which is likely to be related to the function of the encoded proteins and may determine key evolutionary traits of viruses, such as the level of genetic variation and host range. The diversity of codon adaptations at the genetic level in ASFV may account for differences in translational selection in ASFV hosts and provides insight into viral host adaptation and co-evolution.
Topics: African Swine Fever Virus; Animals; Swine; Evolution, Molecular; Selection, Genetic; African Swine Fever; Codon Usage; Phylogeny; Genotype
PubMed: 38824981
DOI: 10.1016/j.meegid.2024.105612 -
European Journal of Medical Research Sep 2023Although the role of adjuvant chemotherapy (CT) for resectable biliary tract cancer (BTC) is gradually recognized, the benefit of adjuvant chemoradiotherapy (CRT) is...
BACKGROUND
Although the role of adjuvant chemotherapy (CT) for resectable biliary tract cancer (BTC) is gradually recognized, the benefit of adjuvant chemoradiotherapy (CRT) is still controversial. Our study is designed to compare the prognosis of CRT versus CT in BCT patients.
METHODS
Clinicopathologic characteristics of patients with operable gallbladder cancer (GBCA), intrahepatic bile duct cancer (IHBDC), or extrahepatic bile duct cancer (EHBDC) were obtained from the Surveillance, Epidemiology and End Results (SEER) database (2004-2015). Univariate and multivariate analyses were performed to identify prognostic factors for overall survival (OS). Selection bias were reduced by propensity-score matching (PSM). Kaplan-Meier analysis was used to estimate the survival time.
RESULTS
Within 922 patients, 53.9% received adjuvant CRT, and 46.1% received adjuvant CT. Multivariate analysis showed age, primary tumor site, T stage, N stage, tumor size, number of removed lymph nodes, and treatment were independent risk factors for OS. Similar improvement of CRT on survival was identified by PSM in the matched cohort compared with CT (28.0 months vs. 25.0 months, p = 0.033), particularly in GBCA cohort (25.0 months vs. 19.0 months, p = 0.003). Subgroup analysis indicated CRT improved outcomes of patients with age ≥ 60, female, lymph nodes positive, tumor size ≥ 5 cm, and none removed lymph node diseases.
CONCLUSION
Adjuvant CRT correlated with improved survival in patients with resected BTC compared with adjuvant CT, particularly in GBCAs. In addition, patients with age ≥ 60, female, lymph nodes positive, tumor size ≥ 5 cm, and none removed lymph node diseases may receive more benefits from adjuvant CRT.
Topics: Humans; Female; Chemoradiotherapy, Adjuvant; Propensity Score; Biliary Tract Neoplasms; Gallbladder Neoplasms; Bile Duct Neoplasms
PubMed: 37658421
DOI: 10.1186/s40001-023-01299-w -
BMC Psychiatry Oct 2023Loneliness is one of the major health problems among older adults. Among this population, home and community-based services (HCBS) have become increasingly popular....
BACKGROUND
Loneliness is one of the major health problems among older adults. Among this population, home and community-based services (HCBS) have become increasingly popular. Despite its health benefits, little is known about the relationship between HCBS use and loneliness in older people with functional limitations. We aim to explore the characteristics of loneliness among older people with functional limitations and examine the association between HCBS use and loneliness in China.
METHODS
We used a cross-sectional data from the 2018 China Health and Retirement Longitudinal Study, which includes a nationally representative sample of Chinese residents aged 65 and older with functional limitations. Logistic regression models were used to examine the associations between HCBS use and loneliness, and we further used propensity score matching to address potential sample selection bias.
RESULT
In China, 46% of older people with functional limitations felt lonely and only 22% of older people with functional limitations reported using HCBS in 2018. Compared with participants who did not receive HCBS, those who received HCBS were less likely to report loneliness (OR = 0.81, 95% CI = 0.63, 0.99, p = 0.048), and the results remained significant after addressing sample selection bias using propensity score matching.
CONCLUSION
Our results showed that loneliness was common among Chinese older people with functional limitations, and the proportion of HCBS use was low. There was robust evidence to support that among older people with functional limitations, HCBS use was associated with decreased loneliness. Further policies should promote the development of broader HCBS use for older people with functional limitations to reduce their loneliness.
Topics: Humans; Aged; Loneliness; Cross-Sectional Studies; Community Health Services; Longitudinal Studies; Logistic Models
PubMed: 37794343
DOI: 10.1186/s12888-023-05225-6 -
Scandinavian Journal of Trauma,... Nov 2023Sepsis is a life-threatening condition that contributes significantly to protracted hospitalisations globally. The unique positioning of paramedics and other emergency...
BACKGROUND
Sepsis is a life-threatening condition that contributes significantly to protracted hospitalisations globally. The unique positioning of paramedics and other emergency care cadres in emergency contexts enable the prospect of early identification and management of sepsis, however, a standardised screening tool still does not exist in the emergency setting. The objective of this review was to identify and recommend the most clinically ideal sepsis screening tool for emergency contexts such as emergency departments and out-of-hospital emergency contexts.
METHODS
A rapid review of five databases (Medline, Embase, the Cochrane Library, CINAHL, and ProQuest Central) was undertaken, with searches performed on February 10, 2022. Covidence software was used by two authors for initial screening, and full text review was undertaken independently by each reviewer, with conflicts resolved by consensus-finding and a mediator. Systematic reviews, meta-analyses, randomised controlled trials, and prospective observational studies were eligible for inclusion. Data extraction used an a priori template and focused on sensitivity and specificity, with ROBINS-I and ROBIS bias assessment tools employed to assess risk of bias in included studies. Study details and key findings were summarised in tables. The a priori review protocol was registered on Open Science Framework ( https://doi.org/10.17605/OSF.IO/3XQ5T ).
RESULTS
The literature search identified 362 results. After review, 18 studies met the inclusion criteria and were included for analysis. There were five systematic reviews, with three including meta-analysis, eleven prospective observational studies, one randomised controlled trial, and one validation study.
CONCLUSIONS
The review recognised that a paucity of evidence exists surrounding standardised sepsis screening tools in the emergency context. The use of a sepsis screening tool in the emergency environment may be prudent, however there is currently insufficient evidence to recommend a single screening tool for this context. A combination of the qSOFA and SIRS may be employed to avoid 'practice paralysis' in the interim. The authors acknowledge the inherent potential for publication and selection bias within the review due to the inclusion criteria.
Topics: Humans; Bias; Mass Screening; Observational Studies as Topic; Paramedicine; Sensitivity and Specificity; Sepsis
PubMed: 37946312
DOI: 10.1186/s13049-023-01111-y -
BMJ Open Nov 2023This study aims to assess sample selection bias in mobile phone survey estimates of fertility and under-5 mortality.
OBJECTIVES
This study aims to assess sample selection bias in mobile phone survey estimates of fertility and under-5 mortality.
DESIGN
With data from the Demographic and Health Surveys, we use logistic regressions to identify sociodemographic correlates of mobile phone ownership and access, and Poisson regressions to estimate the association between mobile phone ownership (or access) and fertility and under-5 mortality estimates. We evaluate the potential reasons why estimates by mobile phone ownership differ using a set of behavioural characteristics.
SETTING
34 low-income and middle-income countries, mostly in sub-Saharan Africa.
PARTICIPANTS
534 536 women between the ages of 15 and 49.
OUTCOME MEASURES
Under-5 mortality rate (U5MR) and total fertility rate (TFR).
RESULTS
Mobile phone ownership ranges from 23.6% in Burundi to 96.7% in Armenia. The median TFR ratio and U5MR ratio between the non-owners and the owners of a mobile phone are 1.48 and 1.29, respectively. Fertility and mortality rates would be biased downwards if estimates are only based on women who own or have access to mobile phones. Estimates of U5MR can be adjusted through poststratification using age, educational level, area of residence, wealth and marital status as weights. However, estimates of TFR remain biased even after adjusting for these covariates. This difference is associated with behavioural factors (eg, contraceptive use) that are not captured by the poststratification variables, but for which there are also differences between mobile phone owners and non-owners.
CONCLUSIONS
Mobile phone surveys need to collect data on sociodemographic background characteristics to be able to weight and adjust mortality estimates ex post facto. Fertility estimates from mobile phone surveys will be biased unless further research uncovers the mechanisms driving the bias.
Topics: Humans; Female; Adolescent; Young Adult; Adult; Middle Aged; Selection Bias; Developing Countries; Surveys and Questionnaires; Cell Phone; Fertility
PubMed: 37977863
DOI: 10.1136/bmjopen-2023-071791 -
Human Brain Mapping Apr 2024The goal of this study was to examine what happens to established associations between attention deficit hyperactivity disorder (ADHD) symptoms and cortical surface and...
The goal of this study was to examine what happens to established associations between attention deficit hyperactivity disorder (ADHD) symptoms and cortical surface and thickness regions once we apply inverse probability of censoring weighting (IPCW) to address potential selection bias. Moreover, we illustrate how different factors that predict participation contribute to potential selection bias. Participants were 9- to 11-year-old children from the Generation R study (N = 2707). Cortical area and thickness were measured with magnetic resonance imaging (MRI) and ADHD symptoms with the Child Behavior Checklist. We examined how associations between ADHD symptoms and brain morphology change when we weight our sample back to either follow-up (ages 9-11), baseline (cohort at birth), or eligible (population of Rotterdam at time of recruitment). Weights were derived using IPCW or raking and missing predictors of participation used to estimate weights were imputed. Weighting analyses to baseline and eligible increased beta coefficients for the middle temporal gyrus surface area, as well as fusiform gyrus cortical thickness. Alternatively, the beta coefficient for the rostral anterior cingulate decreased. Removing one group of variables used for estimating weights resulted in the weighted regression coefficient moving closer to the unweighted regression coefficient. In addition, we found considerably different beta coefficients for most surface area regions and all thickness measures when we did not impute missing covariate data. Our findings highlight the importance of using inverse probability weighting (IPW) in the neuroimaging field, especially in the context of mental health-related research. We found that including all variables related to exposure-outcome in the IPW model and combining IPW with multiple imputations can help reduce bias. We encourage future psychiatric neuroimaging studies to define their target population, collect information on eligible but not included participants and use inverse probability of censoring weighting (IPCW) to reduce selection bias.
Topics: Child; Infant, Newborn; Humans; Selection Bias; Attention Deficit Disorder with Hyperactivity; Probability; Bias; Temporal Lobe
PubMed: 38590154
DOI: 10.1002/hbm.26562