QuPath, originally created at the Centre for Cancer Research & Cell Biology at Queen’s University Belfast as part of a research programme in digital pathology (DP) funded by Invest Northern Ireland ...and Cancer Research UK, is arguably the most wildly used image analysis software program in the world. On the back of the explosion of DP and a need to comprehensively visualise and analyse whole slides images (WSI), QuPath was developed to address the many needs associated with tissue based image analysis; these were several fold and, predominantly, translational in nature: from the requirement to visualise images containing billions of pixels from files several GBs in size, to the demand for high-throughput reproducible analysis, which the paradigm of routine visual pathological assessment continues to struggle to deliver. Resultantly, large-scale biomarker quantification must increasingly be augmented with DP. Here we highlight the impact of the open source Quantitative Pathology & Bioimage Analysis DP system since its inception, by discussing the scope of scientific research in which QuPath has been cited, as the system of choice for researchers.
Background
With increasing prevalence of methicillin-resistant
Staphylococcus aureus
(MRSA) in patients undergoing hip and knee arthroplasty, some have advocated a dual-antibiotic regimen including ...vancomycin as prophylaxis against surgical site infections. However, routine administration of vancomycin may result in impaired renal functions in susceptible patients.
Questions/purposes
The purpose of this study was to determine whether patients receiving antibiotic prophylaxis with cefazolin and vancomycin have a higher risk of postoperative acute kidney injury (AKI) compared with patients receiving cefazolin alone before elective primary hip and knee arthroplasty. We also aimed to compare severity and recovery of AKI in these two cohorts and to determine independent risk factors for AKI.
Methods
We retrospectively evaluated a series of 1828 patients undergoing primary hip and knee arthroplasty over a 2-year period who received either cefazolin (n = 500) or cefazolin and vancomycin (n = 1328) as perioperative antibiotic prophylaxis. During the study period, a perceived high prevalence of MRSA infections at our institution led some surgeons to add vancomycin to the prophylactic antibiotic regimen. The patient characteristics, case mix, and preoperative renal function and baseline creatinine clearance were similar between the two groups. We defined AKI according to the published Acute Kidney Injury Network (AKIN) criteria, and the risk of AKI in both groups was compared. We also compared the proportions of patients by AKIN severity stage and assessed recovery as defined by creatinine levels showing kidney function reaching 50% baseline. The American Society of Anesthesiologists (ASA) classification, preoperative chronic kidney disease, intraoperative fluid requirements, and estimated blood loss were recorded. We analyzed the data using a multivariate logistic regression model to identify potential independent risk factors, including dual antibiotic therapy.
Results
Patients receiving dual antibiotics were more likely to develop AKI compared with those receiving cefazolin alone (13% versus 8%, p = 0.002). Dual-antibiotic prophylaxis also was associated with greater severity; patients in the dual antibiotic group had higher rates of Grade II and III acute kidney injury (3% versus 0%, p = 0.003). There was no difference in the rate of return to baseline renal function (2 ± 1.4 days versus 3 ± 3.4 days; mean difference, 0.5 days; 95% confidence interval CI, −0.2 to 1.2 days; p = 0.155). Controlling for confounding variables, dual antibiotic prophylaxis (adjusted odds ratio OR, 1.82; 95% CI, 1.25–2.64; p = 0.002), ASA class (adjusted OR, 1.64; 95% CI, 1.24–2.17; p = 0.001), and preoperative kidney disease (adjusted OR, 1.81; 95% CI, 1.30–2.52; p = 0.001) were independent risk factors for AKI after primary total joint arthroplasty.
Conclusions
Without a clear advantage in reducing surgical site infections, the utility and safety of routine addition of vancomycin to the prophylactic regimen in all patients undergoing primary hip and knee arthroplasty should be avoided. Further prospective studies should look at the efficacy of preoperative MRSA screening, decolonization, and selective use of vancomycin in high-risk patients.
Level of Evidence
Level III, therapeutic study.
Epigenetic information is characterized by its stable transmission during mitotic cell divisions and plasticity during development and differentiation. This duality is in contrast to genetic ...information, which is stable and identical in all cells in an organism with exception of immunoglobulin gene rearrangements in lymphocytes and somatic mutations in cancer cells. Allele-specific analysis of gene expression and epigenetic modifications provides a unique approach to studying epigenetic regulation in normal and cancer cells. Extension of Knudson's two-hits theory to include epigenetic alteration as a means to inactivate tumor suppressor genes provides better understanding of how genetic mutations and epigenetic alterations jointly contribute to cancer development. High-throughput technology has greatly accelerated cancer discovery. Large initiatives such as TCGA have shown that epigenetic components are frequent targets of mutations in cancer and these discoveries provide new insights into understanding cancer etiology and generate new opportunities for cancer therapeutics.
Diabetic nephropathy is a serious complication of diabetes mellitus and is associated with considerable morbidity and high mortality. There is increasing evidence to suggest that dysregulation of the ...epigenome is involved in diabetic nephropathy. We assessed whether epigenetic modification of DNA methylation is associated with diabetic nephropathy in a case-control study of 192 Irish patients with type 1 diabetes mellitus (T1D). Cases had T1D and nephropathy whereas controls had T1D but no evidence of renal disease.
We performed DNA methylation profiling in bisulphite converted DNA from cases and controls using the recently developed Illumina Infinium HumanMethylation27 BeadChip, that enables the direct investigation of 27,578 individual cytosines at CpG loci throughout the genome, which are focused on the promoter regions of 14,495 genes.
Singular Value Decomposition (SVD) analysis indicated that significant components of DNA methylation variation correlated with patient age, time to onset of diabetic nephropathy, and sex. Adjusting for confounding factors using multivariate Cox-regression analyses, and with a false discovery rate (FDR) of 0.05, we observed 19 CpG sites that demonstrated correlations with time to development of diabetic nephropathy. Of note, this included one CpG site located 18 bp upstream of the transcription start site of UNC13B, a gene in which the first intronic SNP rs13293564 has recently been reported to be associated with diabetic nephropathy.
This high throughput platform was able to successfully interrogate the methylation state of individual cytosines and identified 19 prospective CpG sites associated with risk of diabetic nephropathy. These differences in DNA methylation are worthy of further follow-up in replication studies using larger cohorts of diabetic patients with and without nephropathy.
Background
Alternative payment models, such as the Centers for Medicare & Medicaid Services (CMS) Bundled Payment for Care Improvement (BPCI) initiative, aim to decrease overall costs for hip and ...knee arthroplasties.
Questions/purposes
We asked: (1) Is there any difference in the CMS episode-of-care costs, hospital length of stay, and readmission rate from before and after implementation of our bundled-payment program? (2) Is there any difference in reimbursements and resource utilization between revision THA and TKA at our institution? (3) Are there any independent risk factors for patients with high costs who may not be appropriate for a bundled-payment system for revision total joint arthroplasty (TJA)?
Methods
Between October 2013 and March 2015, 218 patients underwent revision TKA or THA in one health system. Two hundred seventeen patients were reviewed as part of this study, and one patient with hemophilia was excluded from the analysis as an outlier. Our institution began a BPCI program for revision TJA during this study period. Patients’ procedures done before January 1, 2014 at one hospital and January 1, 2015 at another hospital were not included in the bundled-care arrangement (70 revision TKAs and 56 revision THAs), whereas 50 revision TKAs and 41 revision THAs were performed under the BPCI initiative. Patient demographics, medical comorbidities, episode-of-care reimbursement data derived directly from CMS, length of stay, and readmission proportions were compared between the bundled and nonbundled groups.
Results
Length of stay in the group that underwent surgery before the bundled-care arrangement was longer than for patients whose procedures were done under the BPCI (mean 4.02 SD, 3.0 days versus mean 5.27 days SD, 3.6 days; p = 0.001). Index hospitalization reimbursement for the bundled group was less than for the nonbundled group (mean USD 17,754 SD, USD 2741 versus mean USD 18,316 SD, USD 4732; p = 0.030). There was no difference, with the numbers available, in total episode-of-care CMS costs between the two groups (mean USD 38,107 SD, USD 18,328 versus mean USD 37,851 SD, USD 17,208; p = 0.984). There was no difference, with the numbers available, in the total episode-of-care CMS costs between revision hip arthroplasties and revision knee arthroplasties (mean USD 38,627 SD, USD 18,607 versus mean USD 37,414 SD, USD 16,884; p = 0.904). Disposition to rehabilitation (odds ratio OR, 5.49; 95% CI, 1.97–15.15; p = 0.001), length of stay 4 days or greater (OR, 3.66; 95% CI, 1.60–8.38; p = 0.002), and readmission within 90 days (OR, 6.99; 95% CI, 2.58–18.91; p < 0.001) were independent risk factors for high-cost episodes.
Conclusions
Bundled payments have the potential to be a viable reimbursement model for revision TJA. Owing to the unpredictable nature of the surgical procedures, inherent high risks of complications, and varying degrees of surgical complexity, future studies are needed to determine whether bundling patients having revision TJA will result in improved care and decreased costs.
Level of Evidence
Level IV, economic and decision analysis.
Stress granules (SGs) are cytoplasmic condensates that often form as part of the cellular antiviral response. Despite the growing interest in understanding the interplay between SGs and other ...biological condensates and viral replication, the role of SG formation during coronavirus infection remains poorly understood. Several proteins from different coronaviruses have been shown to suppress SG formation upon overexpression, but there are only a handful of studies analyzing SG formation in coronavirus-infected cells. To better understand SG inhibition by coronaviruses, we analyzed SG formation during infection with the human common cold coronavirus OC43 (HCoV-OC43) and the pandemic SARS-CoV2. We did not observe SG induction in infected cells and both viruses inhibited eukaryotic translation initiation factor 2α (eIF2α) phosphorylation and SG formation induced by exogenous stress. Furthermore, in SARS-CoV2 infected cells we observed a sharp decrease in the levels of SG-nucleating protein G3BP1. Ectopic overexpression of nucleocapsid (N) and non-structural protein 1 (Nsp1) from both HCoV-OC43 and SARS-CoV2 inhibited SG formation. The Nsp1 proteins of both viruses inhibited arsenite-induced eIF2α phosphorylation, and the Nsp1 of SARS-CoV2 alone was sufficient to cause a decrease in G3BP1 levels. This phenotype was dependent on the depletion of cytoplasmic mRNA mediated by Nsp1 and associated with nuclear accumulation of the SG-nucleating protein TIAR. To test the role of G3BP1 in coronavirus replication, we infected cells overexpressing EGFP-tagged G3BP1 with HCoV-OC43 and observed a significant decrease in virus replication compared to control cells expressing EGFP. The antiviral role of G3BP1 and the existence of multiple SG suppression mechanisms that are conserved between HCoV-OC43 and SARS-CoV2 suggest that SG formation may represent an important antiviral host defense that coronaviruses target to ensure efficient replication.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Besides the cytochrome c pathway, plant mitochondria have an alternative respiratory pathway that is comprised of a single homodimeric protein, alternative oxidase (AOX). Transgenic cultured tobacco ...cells with altered levels of AOX were used to test the hypothesis that the alternative pathway in plant mitochondria functions as a mechanism to decrease the formation of reactive oxygen species (ROS) produced during respiratory electron transport. Using the ROS-sensitive probe 2',7'-dichlorofluorescein diacetate, we found that antisense suppression of AOX resulted in cells with a significantly higher level of ROS compared with wild-type cells, whereas the overexpression of AOX resulted in cells with lower ROS abundance. Laser-scanning confocal microscopy showed that the difference in ROS abundance among wild-type and AOX transgenic cells was caused by changes in mitochondrial-specific ROS formation. Mitochondrial ROS production was exacerbated by the use of antimycin A, which inhibited normal cytochrome electron transport. In addition, cells overexpressing AOX were found to have consistently lower expression of genes encoding ROS-scavenging enzymes, including the superoxide dismutase genes SodA and SodB, as well as glutathione peroxidase. Also, the abundance of mRNAs encoding salicylic acid-binding catalase and a pathogenesis-related protein were significantly higher in cells deficient in AOX. These results are evidence that AOX plays a role in lowering mitochondrial ROS formation in plant cells.
Recent cross-sectional studies have identified differences in autobiographical memory (AM) among individuals with chronic pain, but the temporal relationship between the 2 is unknown. Moreover, AM ...has yet to be studied in patients undergoing major surgery. This study addressed these gaps by conducting a prospective, longitudinal study of memory performance, postsurgical pain, and psychosocial factors in 97 adult participants scheduled for major surgery. Memories were evaluated using the Autobiographical Memory Test before and one month after surgery when participants were asked to recall personal events related to positive and pain-related word cues. Responses were coded for level of specificity, emotional valence, and surgery-related content. Questionnaires assessing presence/absence of pain and psychological functioning were administered before and at 1-, 3-, 6-, and 12-month follow-ups. Generalized estimating equations modelled pain at each postsurgical time point with memory variables as predictors. As hypothesized, higher numbers of specific pain memories recalled before surgery predicted lower odds of pain across all time points (OR = 0.58, 95% CI 0.37-0.91). Participants who took longer to recall pain memories before surgery (OR = 2.65, 95% CI 1.31-5.37)) and those who produced more surgery-related content at the one-month assessment (OR = 1.31, 95% CI 1.02-1.68) had greater odds of reporting postsurgical pain up to 12 months later. These findings indicate that presurgical AM biases are risk factors for development and maintenance of postsurgical pain. To the extent that these biases are causal, presurgical interventions that modify the quality and content of patients' memories may prove to be promising strategies in the prevention of chronic postsurgical pain.
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