Abstract
Motivation
Nuclear magnetic resonance spectroscopy (NMR) is widely used to analyze metabolites in biological samples, but the analysis requires specific expertise, it is time-consuming, and ...can be inaccurate. Here, we present a powerful automate tool, SPatial clustering Algorithm-Statistical TOtal Correlation SpectroscopY (SPA-STOCSY), which overcomes challenges faced when analyzing NMR data and identifies metabolites in a sample with high accuracy.
Results
As a data-driven method, SPA-STOCSY estimates all parameters from the input dataset. It first investigates the covariance pattern among datapoints and then calculates the optimal threshold with which to cluster datapoints belonging to the same structural unit, i.e. the metabolite. Generated clusters are then automatically linked to a metabolite library to identify candidates. To assess SPA-STOCSY’s efficiency and accuracy, we applied it to synthesized spectra and spectra acquired on Drosophila melanogaster tissue and human embryonic stem cells. In the synthesized spectra, SPA outperformed Statistical Recoupling of Variables (SRV), an existing method for clustering spectral peaks, by capturing a higher percentage of the signal regions and the close-to-zero noise regions. In the biological data, SPA-STOCSY performed comparably to the operator-based Chenomx analysis while avoiding operator bias, and it required <7 min of total computation time. Overall, SPA-STOCSY is a fast, accurate, and unbiased tool for untargeted analysis of metabolites in the NMR spectra. It may thus accelerate the use of NMR for scientific discoveries, medical diagnostics, and patient-specific decision making.
Availability and implementation
The codes of SPA-STOCSY are available at https://github.com/LiuzLab/SPA-STOCSY.
Cancer and other noncommunicable diseases (NCDs) are now widely recognized as a threat to global development. The latest United Nations high-level meeting on NCDs reaffirmed this observation and also ...highlighted the slow progress in meeting the 2011 Political Declaration on the Prevention and Control of Noncommunicable Diseases and the third Sustainable Development Goal. Lack of situational analyses, priority setting, and budgeting have been identified as major obstacles in achieving these goals. All of these have in common that they require information on the local cancer epidemiology. The Global Burden of Disease (GBD) study is uniquely poised to provide these crucial data.
To describe cancer burden for 29 cancer groups in 195 countries from 1990 through 2017 to provide data needed for cancer control planning.
We used the GBD study estimation methods to describe cancer incidence, mortality, years lived with disability, years of life lost, and disability-adjusted life-years (DALYs). Results are presented at the national level as well as by Socio-demographic Index (SDI), a composite indicator of income, educational attainment, and total fertility rate. We also analyzed the influence of the epidemiological vs the demographic transition on cancer incidence.
In 2017, there were 24.5 million incident cancer cases worldwide (16.8 million without nonmelanoma skin cancer NMSC) and 9.6 million cancer deaths. The majority of cancer DALYs came from years of life lost (97%), and only 3% came from years lived with disability. The odds of developing cancer were the lowest in the low SDI quintile (1 in 7) and the highest in the high SDI quintile (1 in 2) for both sexes. In 2017, the most common incident cancers in men were NMSC (4.3 million incident cases); tracheal, bronchus, and lung (TBL) cancer (1.5 million incident cases); and prostate cancer (1.3 million incident cases). The most common causes of cancer deaths and DALYs for men were TBL cancer (1.3 million deaths and 28.4 million DALYs), liver cancer (572 000 deaths and 15.2 million DALYs), and stomach cancer (542 000 deaths and 12.2 million DALYs). For women in 2017, the most common incident cancers were NMSC (3.3 million incident cases), breast cancer (1.9 million incident cases), and colorectal cancer (819 000 incident cases). The leading causes of cancer deaths and DALYs for women were breast cancer (601 000 deaths and 17.4 million DALYs), TBL cancer (596 000 deaths and 12.6 million DALYs), and colorectal cancer (414 000 deaths and 8.3 million DALYs).
The national epidemiological profiles of cancer burden in the GBD study show large heterogeneities, which are a reflection of different exposures to risk factors, economic settings, lifestyles, and access to care and screening. The GBD study can be used by policy makers and other stakeholders to develop and improve national and local cancer control in order to achieve the global targets and improve equity in cancer care.
IntroductionLow dietary calcium intake is a risk factor for pre-eclampsia, a major contributor to maternal and perinatal mortality and morbidity worldwide. Calcium supplementation can prevent ...pre-eclampsia in women with low dietary calcium. However, the optimal dose and timing of calcium supplementation are not known. We plan to undertake an individual participant data (IPD) meta-analysis of randomised trials to determine the effects of various calcium supplementation regimens in preventing pre-eclampsia and its complications and rank these by effectiveness. We also aim to evaluate the cost-effectiveness of calcium supplementation to prevent pre-eclampsia.Methods and analysisWe will identify randomised trials on calcium supplementation before and during pregnancy by searching major electronic databases including Embase, CINAHL, MEDLINE, CENTRAL, PubMed, Scopus, AMED, LILACS, POPLINE, AIM, IMSEAR, ClinicalTrials.gov and the WHO International Clinical Trials Registry Platform, without language restrictions, from inception to February 2022. Primary researchers of the identified trials will be invited to join the International Calcium in Pregnancy Collaborative Network and share their IPD. We will check each study’s IPD for consistency with the original authors before standardising and harmonising the data. We will perform a series of one-stage and two-stage IPD random-effect meta-analyses to obtain the summary intervention effects on pre-eclampsia with 95% CIs and summary treatment–covariate interactions (maternal risk status, dietary intake, timing of intervention, daily dose of calcium prescribed and total intake of calcium). Heterogeneity will be summarised using tau2, I2 and 95% prediction intervals for effect in a new study. Sensitivity analysis to explore robustness of statistical and clinical assumptions will be carried out. Minor study effects (potential publication bias) will be investigated using funnel plots. A decision analytical model for use in low-income and middle-income countries will assess the cost-effectiveness of calcium supplementation to prevent pre-eclampsia.Ethics and disseminationNo ethical approvals are required. We will store the data in a secure repository in an anonymised format. The results will be published in peer-reviewed journals.PROSPERO registration numberCRD42021231276.
To review the imaging findings of laryngeal amyloidosis and to identify radiological findings suggestive of this disease.
Retrospective case series.
A retrospective chart review of patients with ...pathologically confirmed laryngeal amyloidosis was performed from 2009-2022. Clinical and demographic factors were collected. A fellowship-trained head and neck radiologist reviewed all computed tomography (CT) scans and magnetic resonance imaging (MRI) findings within this cohort.
12 patients were identified and a total of 36 imaging studies analyzed. Localized amyloidosis was found in the supraglottic region (n=6), glottic region (n=7), and subglottic region (n=5); 6 patients had disease spanning two subsites. The most common finding on CT scan was a homogeneous and well-defined submucosal soft tissue mass. Punctate calcifications were present in three cases. Presence of contrast enhancement was identified in the majority of patients who underwent MRI (4/5). MRI showed consistent signal intensity, hypointense or isointense on both T1-weighted and T2-weighted images. Diffusion-weighted sequences were obtained in every patient and did not demonstrate diffusion restriction.
This is the largest series searching for unifying imaging characteristics of laryngeal amyloidosis. This research suggests that characteristics from CT and MR provide both similar and unique features of laryngeal amyloidosis on imaging. Both modalities identify a submucosal mass. CT is the preferred modality to demonstrate punctate calcifications, while MRI identifies enhancement and altered signal characteristics. The main benefit of serial imaging is correlation with patient symptoms, identification of the extent of disease, and assisting in delineating appropriate timing for surgery.
E-cigarette (e-cig) aerosols are complex mixtures of various chemicals including humectants (propylene glycol (PG) and vegetable glycerin (VG)), nicotine, and various flavoring additives. Emerging ...research is beginning to challenge the “relatively safe” perception of e-cigarettes. Recent studies suggest e-cig aerosols provoke oxidative stress; however, details of the underlying molecular mechanisms remain unclear. Here we used a redox proteomics assay of thiol total oxidation to identify signatures of site-specific protein thiol modifications in Sprague-Dawley rat lungs following in vivo e-cig aerosol exposures. Histologic evaluation of rat lungs exposed acutely to e-cig aerosols revealed mild perturbations in lung structure. Bronchoalveolar lavage (BAL) fluid analysis demonstrated no significant change in cell count or differential. Conversely, total lung glutathione decreased significantly in rats exposed to e-cig aerosol compared to air controls. Redox proteomics quantified the levels of total oxidation for 6682 cysteine sites representing 2865 proteins. Protein thiol oxidation and alterations by e-cig exposure induced perturbations of protein quality control, inflammatory responses and redox homeostasis. Perturbations of protein quality control were confirmed with semi-quantification of total lung polyubiquitination and 20S proteasome activity. Our study highlights the importance of redox control in the pulmonary response to e-cig exposure and the utility of thiol-based redox proteomics as a tool for elucidating the molecular mechanisms underlying this response.
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•Acute exposure to electronic cigarettes (e-cig) aerosols decreased total lung glutathione in rats.•E-cig exposures induced alterations in site-specific thiol oxidation and perturbated redox hemostasis.•Acute e-cig exposures increased proteasome 20S activity in rat lungs following persistent e-cig oxidative stress.
Benchmark comparisons in surgery allow identification of gaps in the quality of care provided. The aim of this study was to determine quality thresholds for high (HAR) and low (LAR) anterior ...resections in colorectal cancer surgery by applying the concept of benchmarking.
This 5-year multinational retrospective study included patients who underwent anterior resection for cancer in 19 high-volume centres on five continents. Benchmarks were defined for 11 relevant postoperative variables at discharge, 3 months, and 6 months (for LAR). Benchmarks were calculated for two separate cohorts: patients without (ideal) and those with (non-ideal) outcome-relevant co-morbidities. Benchmark cut-offs were defined as the 75th percentile of each centre's median value.
A total of 3903 patients who underwent HAR and 3726 who had LAR for cancer were analysed. After 3 months' follow-up, the mortality benchmark in HAR for ideal and non-ideal patients was 0.0 versus 3.0 per cent, and in LAR it was 0.0 versus 2.2 per cent. Benchmark results for anastomotic leakage were 5.0 versus 6.9 per cent for HAR, and 13.6 versus 11.8 per cent for LAR. The overall morbidity benchmark in HAR was a Comprehensive Complication Index (CCI®) score of 8.6 versus 14.7, and that for LAR was CCI® score 11.9 versus 18.3.
Regular comparison of individual-surgeon or -unit outcome data against benchmark thresholds may identify gaps in care quality that can improve patient outcome.
We estimated the particle number distributions (PNDs), particle number concentrations (PNCs), physicochemical characteristics, meteorological effects, and respiratory deposition doses (RDD) in the ...human respiratory tract for three different particle modes: nucleation (N6–30), accumulation (N30–300), and coarse (N300–10,000) modes. This study was conducted in three different microenvironments (MEs) in London (indoor, IN; traffic intersection, TI; park, PK) measuring particles in the range of 6 nm–10,000 nm using an electrical low-pressure impactor (ELPI+). Mean PNCs were 1.68 ± 1.03 × 104 #cm−3, 7.00 ± 18.96 × 104 #cm−3, and 0.76 ± 0.95 × 104 #cm−3 at IN, TI, and PK, respectively. The PNDs were high for nucleation-mode particles at the TI site, especially during peak traffic hours. Wind speeds ranging from 0 to 6 ms−1 exhibit higher PNCs for nucleation- and accumulation-mode particles at TI and PK sites. Physicochemical characterisation shows trace metals, including Fe, O, and inorganic elements, that were embedded in a matrix of organic material in some samples. Alveolar RDD was higher for the nucleation and accumulation modes than the coarse-mode particles. The chemical signatures from the physicochemical characterisation indicate the varied sources at different MEs. These findings enhance our understanding of the different particle profiles at each ME and should help devise ways of reducing personal exposure at each ME.
The off-line estimation of the parameters of continuous-time, linear, time-invariant transfer function models can be achieved straightforwardly using linear prefilters on the measured input and ...output of the system. The on-line estimation of continuous-time models with time-varying parameters is less straightforward because it requires the updating of the continuous-time prefilter parameters. This paper shows how such on-line estimation is possible by using recursive instrumental variable approaches. The proposed methods are presented in detail and also evaluated on a numerical example using both single experiment and Monte Carlo simulation analysis. In addition, the proposed recursive algorithms are tested using data from two real-life systems.
•Recursive instrumental variable methods for identifying continuous-time linear time-varying models are presented.•A robust implementation of the algorithms is presented.•For the proposed algorithms, guidelines are provided for the choice of hyperparameters.•Two examples based on real data are presented, namely, an electrical circuit benchmark and a hydrological system example.
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