Diagnostic test accuracy: application and practice using R software

The objective of this paper is to describe general approaches of diagnostic test accuracy (DTA) that are available for the quantitative synthesis of data using R software. We conduct a DTA that summarizes statistics for univariate analysis and bivariate analysis. The package commands of R software were “metaprop” and “metabin” for sensitivity, specificity, and diagnostic odds ratio; forest for forest plot; reitsma of “mada” for a summarized receiver-operating characteristic (ROC) curve; and “metareg” for meta-regression analysis. The estimated total effect sizes, test for heterogeneity and moderator effect, and a summarized ROC curve are reported using R software. In particular, we focus on how to calculate the effect sizes of target studies in DTA. This study focuses on the practical methods of DTA rather than theoretical concepts for researchers whose fields of study were non-statistics related. By performing this study, we hope that many researchers will use R software to determine the DTA more easily, and that there will be greater interest in related research

The association of prior hospitalization with clinical outcomes among patients admitted with pneumonia: a propensity score matching study

Abstract Background Although prior hospitalization (PH) has been considered as a risk factor for infection with potentially drug-resistant (PDR) pathogens in patients admitted with pneumonia, the evidence is limited. We aimed to elucidate the clinical impact of PH on these patients. Methods PH was defined as hospitalization for two or more days in the preceding 90 days. Patients with PH-associated pneumonia (PHAP) or community-acquired pneumonia (CAP) were matched using the propensity score matching method, and the clinical outcomes were compared. We also conducted subgroup analyses based on intravenous antibiotic use during PH, duration of PH, and time to re-admission. Results A total of 704 patients were identified; the PHAP group included 97 patients (13.7%). After matching according to propensity scores, the baseline characteristics of the PHAP group were similar to those of the CAP group. The isolation rate of PDR pathogens as well as the 30-day and total in-hospital mortality did not differ between propensity score-matched PHAP and CAP patients (13.6% vs. 10.2%, P = 0.485; 10.2% vs. 14.8%, P = 0.362; and 13.6% vs. 15.9%, P = 0.671, respectively). In subgroup analyses, only intravenous antibiotic use during PH was associated with the isolation rate of PDR pathogens (adjusted OR: 5.066; 95% CI: 1.231–20.845). Conclusions PH itself might not be related with higher isolation rates of PDR pathogens or mortality in patients admitted with pneumonia. Therefore, it seems reasonable that broad spectrum antibiotic therapy for PDR pathogens should be selectively applied to PHAP patients with intravenous antibiotic use during PH

Confocal nonlinear optical imaging on hexagonal boron nitride nanosheets

Optical microscopy with optimal axial resolution is critical for precise visualization of two-dimensional flat-top structures. Here, we present sub-diffraction-limited ultrafast imaging of hexagonal boron nitride (hBN) nanosheets using a confocal focus-engineered coherent anti-Stokes Raman scattering (cFE-CARS) microscopic system. By incorporating a pinhole with a diameter of approximately 30μm, we effectively minimized the intensity of side lobes induced by circular partial pi-phase shift in the wavefront (diameter, d0) of the probe beam, as well as nonresonant background CARS intensities. Using axial-resolution-improved cFE-CARS (acFE-CARS), the achieved axial resolution is 350nm, exhibiting a 4.3-folded increase in the signal-to-noise ratio compared to the previous case with 0.58 d0 phase mask. This improvement can be accomplished by using a phase mask of 0.24 d0. Additionally, we employed nondegenerate phase matching with three temporally separable incident beams, which facilitated cross-sectional visualization of highly-sample-specific and vibration-sensitive signals in a pump-probe fashion with subpicosecond time resolution. Our observations reveal time-dependent CARS dephasing in hBN nanosheets, induced by Raman-free induction decay (0.66ps) in the 1373cm−1 mode. © 2023, Chinese Society for Optical Engineering.TRU

Proposed risk factors for infection with multidrug-resistant pathogens in hemodialysis patients hospitalized with pneumonia

Abstract Background In patients with hemodialysis-associated pneumonia (HDAP), information on both microbiologic features and antimicrobial strategies is limited. The aim of this study is to investigate predictive factors of infection with multidrug-resistant (MDR) pathogens in HDAP patients. Methods This was a multicenter, retrospective, and observational study. Enrolled patients were classified into MDR or non-MDR pathogens groups according to culture results. We examined risk factors of infection with MDR pathogens and created a decision support tool using these risk factors. Results MDR pathogens were identified in 24 (22.8%) out of a total of 105 HDAP patients. The most common MDR pathogens were methicillin-resistant Staphylococcus aureus (10 patients, 9.5%) and the isolation rate of Pseudomonas aeruginosa was 6.6%. Logistic regression showed two variables were associated with the isolation of MDR pathogens: recent hospitalization (adjusted odds ratio [OR]: 2.951, 95% confidence interval [CI]: 1.022–8.518) and PSI (Pneumonia Severity Index) score (adjusted OR: 1.023, 95% CI: 1.005–1.041). The optimal cut-off value for PSI score using a receiver operating characteristic curve analysis was 147. According to the presence of 0, 1, or 2 of the identified risk factors, the prevalence of MDR pathogens was 7.6, 28.2 and 64.2%, respectively (p  147 are risk factors of infection with MDR pathogens in HDAP patients. This simple proposed tool would facilitate more accurate identification of MDR pathogens in these patients

Sub 100 nm resolution confocal focus-engineered coherent anti-Stokes Raman scattering microscopy under non-degenerate pumping condition

For the development of microscopic tools that can resolve non-fluorescent samples beyond the diffraction limit, we propose focus-engineered non-degenerate pumped coherent anti-Stokes Raman scattering (CARS) using spa-tial light modulator (SLM)-based phase shaping, liquid lens focus control, and confocal detection. Non-degenerate pumped CARS (ND-CARS) with frequency-doubled probe pulses resulted in approximately 75% improvement in resolution compared to that of degenerate CARS. Focal adjustment using the liquid lens facilitated the accurate overlapping of three beams. The circular pi-phase modulation at the center of the probe-beam wavefront demar-cated the net CARS focal volume into a sub 100 nm-scale core and surrounding side lobes. The confocal geometry detection setup successfully removed the side lobes, allowing optical imaging of 81 nm-sized zinc oxide particles at 87 nm, and edge-to-edge resolution was determined to be 103 nm.FALS

Aqueous Synthesis of the Tiopronin-Capped Gold Nanoclusters/Nanoparticles with Precise Size Control via Deprotonation of the Ligand

Gold nanoparticles have led to numerous advances in nanomaterial-based sensors and biomedical technologies owing to their chemical inertness and outstanding physiochemical and optical properties. Gold nanoparticles are still considered one of the most promising types of nanomaterials in various biomedical fields, including drug delivery, cancer therapy, biomolecule detection, and high-accuracy diagnosis. Surface functionalization of gold nanoparticles with various ligands modifies the physicochemical properties of the surface, thereby improving the biocompatibility and uptake efficiency of a living system. Tiopronin, one of the most commonly used ligands for gold nanoparticles, has both thiol and carboxyl functional groups that can be easily attached to various biomolecules. However, the conventional method of synthesizing tiopronin-capped gold nanoclusters using methanol and acetic acid as a solvent requires a laborious and time-consuming dialysis process to remove methanol and acetic acid. In this study, we demonstrate a novel and simple aqueous synthesis method to obtain tiopronin-capped gold nanoclusters/nanoparticles with precise size control in the sub-nanometer to nanometer range. The main advantage of our synthesis method is that it does not require a dialysis process because it uses water as a solvent. The boron byproduct produced during the synthesis can be removed with a simple volatilization process. Moreover, we characterized the physical morphologies, photoelectronic properties, hydrodynamic size, and crystal structure of the tiopronin-capped gold nanoclusters/nanoparticles using transmission electron microscopy, spectrophotometry, fluorescence spectrometry, dynamic light scattering, zeta potential, and X-ray diffraction

Metabolically healthy and unhealthy obesity and the development of lung dysfunction

Abstract We investigated the association of metabolically healthy (MH) and unhealthy (MU) obesity with incident lung dysfunction. This cohort study included 253,698 Korean lung disease-free adults (mean age, 37.4 years) at baseline. Spirometry-defined lung dysfunction was classified as a restrictive pattern (RP) or obstructive pattern (OP). We defined obesity as BMI ≥ 25 kg/m2 and MH as the absence of any metabolic syndrome components with a homeostasis model assessment of insulin resistance < 2.5: otherwise, participants were considered MU. During a median follow-up of 4.9 years, 10,775 RP cases and 7140 OP cases develped. Both MH and MU obesity showed a positive association with incident RP, with a stronger association in the MU than in the MH group (P interaction = 0.001). Multivariable-adjusted hazard ratios (95% CI) for incident RP comparing obesity to the normal-weight category was 1.15 (1.05–1.25) among the MH group and 1.38 (1.30–1.47) among MU group. Conversely, obesity was inversely associated with OP because of a greater decline in forced vital capacity than forced expiratory volume in 1 s. Both MH and MU obesity were positively associated with RP. However, the associations between obesity, metabolic health, and lung functions might vary depending on the type of lung disease

Activation strain model: Rational design of catalysts

Funnel plot for publication bias assessment of studies for (a) positive qSOFA score and (b) positive SIRS criteria score for the prediction of in-hospital mortality. (PDF 97 kb

Diagnostic Performance of Antigen Rapid Diagnostic Tests, Chest Computed Tomography, and Lung Point-of-Care-Ultrasonography for SARS-CoV-2 Compared with RT-PCR Testing: A Systematic Review and Network Meta-Analysis

(1) Background: The comparative performance of various diagnostic methods for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection remains unclear. This study aimed to investigate the comparison of the 3 index test performances of rapid antigen diagnostic tests (RDTs), chest computed tomography (CT), and lung point-of-care-ultrasonography (US) with reverse transcription-polymerase chain reaction (RT-PCR), the reference standard, to provide more evidence-based data on the appropriate use of these index tests. (2) Methods: We retrieved data from electronic literature searches of PubMed, Cochrane Library, and EMBASE from 1 January 2020, to 1 April 2021. Diagnostic performance was examined using bivariate random-effects diagnostic test accuracy (DTA) and Bayesian network meta-analysis (NMA) models. (3) Results: Of the 3992 studies identified in our search, 118 including 69,445 participants met our selection criteria. Among these, 69 RDT, 38 CT, and 15 US studies in the pairwise meta-analysis were included for DTA with NMA. CT and US had high sensitivity of 0.852 (95% credible interval (CrI), 0.791&ndash;0.914) and 0.879 (95% CrI, 0.784&ndash;0.973), respectively. RDT had high specificity, 0.978 (95% CrI, 0.960&ndash;0.996). In accuracy assessment, RDT and CT had a relatively higher than US. However, there was no significant difference in accuracy between the 3 index tests. (4) Conclusions: This meta-analysis suggests that, compared with the reference standard RT-PCR, the 3 index tests (RDTs, chest CT, and lung US) had similar and complementary performances for diagnosis of SARS-CoV-2 infection. To manage and control COVID-19 effectively, future large-scale prospective studies could be used to obtain an optimal timely diagnostic process that identifies the condition of the patient accurately

Simultaneous Extraction of the Grain Size, Single-Crystalline Grain Sheet Resistance, and Grain Boundary Resistivity of Polycrystalline Monolayer Graphene

The electrical properties of polycrystalline graphene grown by chemical vapor deposition (CVD) are determined by grain-related parameters&mdash;average grain size, single-crystalline grain sheet resistance, and grain boundary (GB) resistivity. However, extracting these parameters still remains challenging because of the difficulty in observing graphene GBs and decoupling the grain sheet resistance and GB resistivity. In this work, we developed an electrical characterization method that can extract the average grain size, single-crystalline grain sheet resistance, and GB resistivity simultaneously. We observed that the material property, graphene sheet resistance, could depend on the device dimension and developed an analytical resistance model based on the cumulative distribution function of the gamma distribution, explaining the effect of the GB density and distribution in the graphene channel. We applied this model to CVD-grown monolayer graphene by characterizing transmission-line model patterns and simultaneously extracted the average grain size (~5.95 &mu;m), single-crystalline grain sheet resistance (~321 &Omega;/sq), and GB resistivity (~18.16 k&Omega;-&mu;m) of the CVD-graphene layer. The extracted values agreed well with those obtained from scanning electron microscopy images of ultraviolet/ozone-treated GBs and the electrical characterization of graphene devices with sub-micrometer channel lengths