ROI-Finder: machine learning to guide region-of-interest scanning for X-ray fluorescence microscopy

The microscopy research at the Bionanoprobe (currently at beamline 9-ID and later 2-ID after APS-U) of Argonne National Laboratory focuses on applying synchrotron X-ray fluorescence (XRF) techniques to obtain trace elemental mappings of cryogenic biological samples to gain insights about their role in critical biological activities. The elemental mappings and the morphological aspects of the biological samples, in this instance, the bacterium Escherichia coli (E. Coli), also serve as label-free biological fingerprints to identify E. coli cells that have been treated differently. The key limitations of achieving good identification performance are the extraction of cells from raw XRF measurements via binary conversion, definition of features, noise floor and proportion of cells treated differently in the measurement. Automating cell extraction from raw XRF measurements across different types of chemical treatment and the implementation of machine-learning models to distinguish cells from the background and their differing treatments are described. Principal components are calculated from domain knowledge specific features and clustered to distinguish healthy and poisoned cells from the background without manual annotation. The cells are ranked via fuzzy clustering to recommend regions of interest for automated experimentation. The effects of dwell time and the amount of data required on the usability of the software are also discussed.

Evaluating the Short-Term Environmental and Clinical Effects of a Radiation Oncology Department's Response to the COVID-19 Pandemic (STEER COVID-19)

Purpose/Objective(s)

During the COVID-19 pandemic, hypofractionated regimens and virtual care was adopted by our institution to preserve hospital capacity and reduce foot traffic. This study's primary objective was to assess the collective environmental impact of these strategic changes by identifying sources of carbon dioxide equivalents (CO₂e). As sustainable healthcare is only justifiable if the quality of the care is maintained, we also evaluated the rate of radiation-related acute adverse event.

Materials/Methods

All patients treated with external beam radiation therapy from April 1, 2019 to March 31, 2021 at our single institution were identified (n=10,175) along with their radiotherapy visits (176,423 fractions), and visits to the radiation nursing clinic (RNC) or emergency (ER) department. A treatment regimen was considered hypofractionated if the dose per fraction was ≥ 240 cGy. If the dose per fraction was ≥ 600 cGy and the total dose of the treatment regimen was > 2000 cGy, then the treatment regimen was classified as SBRT. Out-patient hospital and virtual visits (n=75,853) during this same period were also analyzed. Environmental impact measures, including linear accelerator power usage, patient travel distances, and personal protection equipment (PPE) consumption were all converted into CO₂e. A waiver of individual patient consent was granted for this study by our institution's Research Ethics Board (REB).

Results

The use of curative hypofractionated regimens increased from 17% to 27% during the pandemic year. Twelve out of 15 cancer sites increased their use of hypofractionated regimens. Carbon footprint was reduced by 39% during the pandemic year (1,332,388 kg CO₂e) as compared to the pre-pandemic year (2,024,823 kg CO₂e). For comparison, the 744 tonnes of CO₂e saved during the pandemic year equates to the CO₂e produced by the annual energy consumption of 182 Canadian households or the CO₂e sequestered by 12,000 seedling trees planted and grown for 10 years. On average 121 kg CO₂e and 100 kg CO₂e were emitted per radiation regimen delivered during the pre-pandemic and pandemic year, respectively. Comparing patients in the pre-pandemic vs. pandemic year, there was a significant reduction in the proportion of hypofractionated patients who needed a visit to either the RNC (39% vs. 25%; p<0.001) or ER (6% vs. 2%; p<0.001) during and within 90 days of radiotherapy.

Conclusion

This study demonstrated the environmental benefits of increased use of hypofractionated regimens and virtual care, while assuring that there was no added acute radiation-related adverse event. Our findings support their continued use as one of many long-term strategies to reduce the environmental footprint of healthcare delivery. Treatment efficacy and side-effects will need to be assessed in subsequent years to further support the sustainability of these strategies.

β-Delayed One and Two Neutron Emission Probabilities Southeast of ^{132}Sn and the Odd-Even Systematics in r-Process Nuclide Abundances

The β-delayed one- and two-neutron emission probabilities (P_{1n} and P_{2n}) of 20 neutron-rich nuclei with N≥82 have been measured at the RIBF facility of the RIKEN Nishina Center. P_{1n} of ^{130,131}Ag, ^{133,134}Cd, ^{135,136}In, and ^{138,139}Sn were determined for the first time, and stringent upper limits were placed on P_{2n} for nearly all cases. β-delayed two-neutron emission (β2n) was unambiguously identified in ^{133}Cd and ^{135,136}In, and their P_{2n} were measured. Weak β2n was also detected from ^{137,138}Sn. Our results highlight the effect of the N=82 and Z=50 shell closures on β-delayed neutron emission probability and provide stringent benchmarks for newly developed macroscopic-microscopic and self-consistent global models with the inclusion of a statistical treatment of neutron and γ emission. The impact of our measurements on r-process nucleosynthesis was studied in a neutron star merger scenario. Our P_{1n} and P_{2n} have a direct impact on the odd-even staggering of the final abundance, improving the agreement between calculated and observed Solar System abundances. The odd isotope fraction of Ba in r-process-enhanced (r-II) stars is also better reproduced using our new data.

Spontaneous Ferromagnetism Induced Topological Transition in EuB_{6}

The interplay between various symmetries and electronic bands topology is one of the core issues for topological quantum materials. Spontaneous magnetism, which leads to the breaking of time-reversal symmetry, has been proven to be a powerful approach to trigger various exotic topological phases. In this Letter, utilizing the combination of angle-resolved photoemission spectroscopy, magneto-optical Kerr effect microscopy, and first-principles calculations, we present the direct evidence on the realization of the long-sought spontaneous ferromagnetism induced topological transition in soft ferromagnetic EuB_{6}. Explicitly, we reveal the topological transition is from Z_{2}=1 topological insulator in paramagnetic state to χ=1 magnetic topological semimetal in low temperature ferromagnetic state. Our results demonstrate that the simple band structure near the Fermi level and rich topological phases make EuB_{6} an ideal platform to study the topological phase physics.

[Effect of gastroesophageal reflux disease on the clinical characteristics of patients with laryngopharyngeal reflux disease]

Objective: To investigate the effect of gastroesophageal reflux disease (GERD) on the clinical characteristics of patients with laryngopharyngeal reflux disease(LPRD). Methods: The data of 141 patients with symptoms of LPRD, who were admitted to the Department of Pharyngology, Laryngology& Phonosurgery at the Sixth Medical Center of the PLA General Hospital from November 2020 to October 2021, were retrospectively analyzed.There were 118 males and 23 females, aged 28-75 (56.72±10.04) years old. The included patients underwent simultaneous 24-hour hypopharyngeal and esophageal multichannel intraluminal impedance pH monitoring (24h-HEMII-pH), salivary pepsin test at multiple times, Reflux Symptom Index (RSI), and Reflux Finding Score (RFS). One laryngopharyngeal reflux event on 24 h-HEMII-pH monitoring results was used as a diagnostic criterion for LPRD. And the duration of lower esophageal pH<4.0>4.0% at 24 h or DeMeester score>14.7 were used as diagnostic criteria for GERD. Among them, patients with both positive LPRD and GERD were classified as L&G group, patients with positive LPRD and negative GERD were classified as IL group, patients with negative LPRD and positive GERD were classified as IG group, and patients with both negative LPRD and GERD were classified as N group. The differences in the clinical characteristics of reflux and salivary pepsin assay in each group were statistically analyzed. SPSS 23.0 software was applied for statistical analysis. Results: According to the 24 h-HEMII-pH results, 116 (82.3%) patients were diagnosed with LPRD and 45 (31.9%) with GERD, including 82 (58.2%) in the IL group, 34 (24.1%) in the L&G group, 11 (7.8%) in the IG group, and 14 (9.9%) in the N group. Based on the salivary pepsin test, a total of 106 patients had positive results, and the L&G group had a significantly higher rate of positive total salivary pepsin test (94.1%) and positive morning test (70.6%) than the IL group (75.6%, 26.8%), IG group (63.6%, 27.3%) and N group (35.7%, 28.6%), with chi-square values of 19.01 and 20.81, both with P<0.001. The patients in the L&G group had a significantly higher RSI score (14.0) than the IL group (7.0), IG group (1.0) and N group (0), H=52.26,P<0.001. The difference in RFS between the L&G and IL groups was not statistically significant (Z=-0.92,P>0.05). Conclusion: Combined with GERD, LPRD patients have more obvious clinical symptoms and higher positive rate of pepsin test in saliva.

Genetic sensitivity to stress modifies the relationship between socioeconomic status and major adverse cardiovascular events

Background

Lower socioeconomic status (SES) associates with major adverse cardiovascular events (MACE), in part through stress-related neural pathways that elicit inflammation. However, it is unknown whether genes that heighten stress sensitivity modify the association between lower SES and MACE.

Purpose

To assess whether genetic predisposition to stress sensitivity would modify the link between low SES and MACE

Methods

13,154 participants (median age 60 yrs, 41% male) from the Mass General Brigham Biobank were studied. A polygenic risk score for neuroticism (nPRS) was used as a measure of genetic predisposition to stress sensitivity (GSS). Using home addresses, SES was evaluated as median income and area deprivation index (ADI). Stress-related neural activity (SNA) was assessed (N=978) using validated FDG PET/CT imaging methods. MACE, and cardiovascular disease (CVD) risk factors were evaluated. Mediation analyses were employed.

Results

Over median (IQR) 4.9 (4.1–5.9) years of follow-up, 1,030 (7.8%) individuals had MACE. Lower SES (as low income, or alternatively as high ADI) associated with incident MACE among individuals with higher GSS (nPRS ≥ median) but not lower GSS (Fig. 1A and 1B). Similarly, lower SES associated with SNA among individuals with higher but not lower GSS (Fig. 1C). SNA mediated the relationship between income and MACE (P&lt;0.05**) among those with higher GSS.

Conclusions

Genetic predisposition to stress sensitivity appears to heighten CVD risk associated with lower SES. This relationship may result from differential activation of stress-related neural pathways.

Funding Acknowledgement

Type of funding sources: None.

[RHPN2 is highly expressed in osteosarcoma cells to promote cell proliferation and migration and inhibit apoptosis]

OBJECTIVE

To screen for aberrantly expressed genes in osteosarcoma cells and investigate the role of RHPN2 in regulating the proliferation, apoptosis, migration and tumorigenic abilities of osteosarcoma cells.

METHODS

We used GEO2R to analyze the differential gene expression profile between osteosarcoma cells and normal cells in the GSE70414 dataset. RTqPCR and Western blotting were performed to detect RHPN2 expression in osteosarcoma cell lines MG-63, 143B and SAOS2. Two RHPN2-shRNA and a control NC-shRNA were designed to silence the expression of RHPN2 in 143B cells, and CCK8 assay, colony-forming assay, annexin V-FITC/PI staining and scratch assays were carried out to examine the changes in proliferation, apoptosis and migration of the cells. We also established nude mouse models bearing osteosarcoma xenografts derived 143B cells and RHPN2-shRNA-transfected 143B cells, and assessed the effect of RHPN2 silencing on osteosarcoma cell tumorigenesis using HE staining. Kaplan-Meier survival curves were used to analyze the correlation between RHPN2 expression and survival outcomes of patients with osteosarcoma.

RESULTS

RHPN2 expression was significantly upregulated in osteosarcoma cell lines MG-63, 143B and SAOS2 (P < 0.01). Silencing of RHPN2 significantly inhibited the proliferation and migration of 143B cells in vitro, promoted cell apoptosis (P < 0.01), and suppressed tumorigenic capacity of the cells in nude mice. A high expression of RHPN2 was significantly correlated with a poor prognosis of patients with osteosarcoma (P < 0.05).

CONCLUSION

RHPN2 is highly expressed in osteosarcoma cells to promote cell proliferation and migration and inhibits cell apoptosis. A high expression of RHPN2 is associated with a poorer prognosis of the patients with osteosarcoma.

Optimising diffusion-weighted imaging of the thyroid gland using dedicated surface coil

AIM

To assess the feasibility of applying field-of-view (FOV) optimised and constrained undistorted single-shot (FOCUS) diffusion-weighted imaging (DWI) in the thyroid gland by comparing its image quality with conventional DWI (C-DWI) qualitatively and quantitatively using a dedicated surface coil exclusively designed for the thyroid gland at 3 T magnetic resonance imaging (MRI).

MATERIALS AND METHODS

In this prospective study, 32 healthy volunteers who had undergone 3 T the thyroid gland MRI with FOCUS-DWI and C-DWI were enrolled. Two independent reviewers assessed the overall image quality, artefacts, sharpness, and geometric distortion based on a five-point Likert scale. The signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and apparent diffusion coefficient (ADC) were quantified for both sequences. Interobserver agreement, qualitative scores, and quantitative parameters were compared between two sequences.

RESULTS

Agreement between the two readers was good for FOCUS-DWI (κ = 0.714-0.778) and moderate to good for C-DWI (κ = 0.525-0.672) in qualitative image quality assessment. Qualitatively, image quality (overall image quality, artefacts, sharpness, and geometric distortion) was significantly better in FOCUS-DWI than that in the C-DWI (all p<0.05); however, quantitatively, FOCUS-DWI had significantly lower SNRs (p<0.001) and CNRs (p=0.012) compared with C-DWI. The ADC value on FOCUS-DWI was significantly higher than that on C-DWI (p<0.001).

CONCLUSION

FOCUS-DWI depicted the thyroid gland with significantly better image quality qualitatively and less ghost artefacts, but had significantly lower SNR and CNR quantitatively, compared with C-DWI, suggesting that both DWI sequences have advantages and could be chosen for different purposes.