A reverse transcriptase controls prophage genome reduction to promote phage dissemination in Pseudomonas aeruginosa biofilms

Filamentous bacteriophages play a critical role in biofilm formation and virulence in the opportunistic pathogen Pseudomonas aeruginosa. Here, studies of the filamentous Pf4 prophage life cycle within P. aeruginosa biofilms revealed that the prophage-encoded reverse transcriptase (RT) regulates phage genome dynamics. The RT and the non-coding RNA PhrD collaborate to edit the Pf4 phage genome to generate superinfective Pf4 variants capable of rapid propagation within biofilms by preserving genes essential for virion assembly and reconstituting a promoter for the phage excisionase gene. Mutant cells emerge in biofilms where intact Pf4 prophages are replaced by these reduced-genome phage variants, further enhancing virion production. The discovery of RT's role in phage genome reduction expands understanding of RT functions and of the versatility of phage biology and its impact on microbial community dynamics within biofilms.

Convolutional LSTM model for cine image prediction of abdominal motion

Objective.In this study, we tackle the challenge of latency in magnetic resonance linear accelerator (MR-Linac) systems, which compromises target coverage accuracy in gated real-time radiotherapy. Our focus is on enhancing motion prediction precision in abdominal organs to address this issue. We developed a convolutional long short-term memory (convLSTM) model, utilizing 2D cine magnetic resonance (cine-MR) imaging for this purpose.Approach.Our model, featuring a sequence-to-one architecture with six input frames and one output frame, employs structural similarity index measure (SSIM) as loss function. Data was gathered from 17 cine-MRI datasets using the Philips Ingenia MR-sim system and an Elekta Unity MR-Linac equivalent sequence, focusing on regions of interest (ROIs) like the stomach, liver, pancreas, and kidney. The datasets varied in duration from 1 to 10 min.Main results.The study comprised three main phases: hyperparameter optimization, individual training, and transfer learning with or without fine-tuning. Hyperparameters were initially optimized to construct the most effective model. Then, the model was individually applied to each dataset to predict images four frames ahead (1.24-3.28 s). We evaluated the model's performance using metrics such as SSIM, normalized mean square error, normalized correlation coefficient, and peak signal-to-noise ratio, specifically for ROIs with target motion. The average SSIM values achieved were 0.54, 0.64, 0.77, and 0.66 for the stomach, liver, kidney, and pancreas, respectively. In the transfer learning phase with fine-tuning, the model showed improved SSIM values of 0.69 for the liver and 0.78 for the kidney, compared to 0.64 and 0.37 without fine-tuning.Significance. The study's significant contribution is demonstrating the convLSTM model's ability to accurately predict motion for multiple abdominal organs using a Unity-equivalent MR sequence. This advancement is key in mitigating latency issues in MR-Linac radiotherapy, potentially improving the precision and effectiveness of real-time treatment for abdominal cancers.

Dose Constraints and Planning Considerations for Thoracic Radiation Therapy: Delphi Consensus from a National Survey of Experts

PURPOSE/OBJECTIVE(S)

Many physicians refer to trial protocols or published guidelines (NCCN, QUANTEC, HyTEC) for dose-volume histogram (DVH) metrics. However, there may be variation in implementing these metrics during plan optimization. Some studies have suggested better outcomes for patients treated at high-volume, high-expertise centers. These differences may in part be due to greater standardization or center-specific treatment planning processes. We surveyed radiation oncologists with stated thoracic-specific expertise using the Delphi method to formulate consensus DVH metrics that would be considered ideal for high-quality radiation treatment plans.

MATERIALS/METHODS

Thoracic radiation oncology experts were identified using departmental websites of ACGME-accredited radiation oncology programs. After confirming their expertise, panelists were invited to submit their institutional templates and complete three rounds of questions related to normal organ dose constraints, target coverage metrics, prescribing practices, and other planning considerations. Queried radiation schemes included conventional fractionation, twice-daily fractionation, and stereotactic body radiation therapy (3 and 5 fractions). Preliminary consensus statements were generated using median values for DVH metrics and were iteratively refined in subsequent surveys. Consensus was pre-defined as ≥75% agreement among panelists.

RESULTS

A total of 194 experts were invited, and 100 agreed to participate. The panel was 28% female and included experts from 29 states with a median of 11 years of clinical experience (IQR 6-19). 89% specialized in 1-2 disease sites. Response rates for the Demographics, round 1, 2, and 3 surveys were 83%, 78%, 57%, and 55%, respectively. 93% of panelists believed that DVH metrics should provide thresholds for both optimal and acceptable criteria for treatment planning. 49 of the 96 proposed normal tissue dose constraint statements were iterated to consensus (Table 1), and 5 of 7 proposed target coverage metric statements achieved consensus.

CONCLUSION

This study highlights the heterogeneity in metrics used by thoracic radiation oncologists and provides levels of consensus on ideal and acceptable dose constraints as guidance for treatment planning. Future directions include using these statements to develop prescription templates and acceptance criteria for treatment planning systems for widespread use as well as extending this Delphi approach to additional disease sites.

Artificial Intelligence-Assisted Evaluation of the Spatial Relationship between Brain Arteriovenous Malformations and the Corticospinal Tract to Predict Postsurgical Motor Defects

BACKGROUND AND PURPOSE

Preoperative evaluation of brain AVMs is crucial for the selection of surgical candidates. Our goal was to use artificial intelligence to predict postsurgical motor defects in patients with brain AVMs involving motor-related areas.

MATERIALS AND METHODS

Eighty-three patients who underwent microsurgical resection of brain AVMs involving motor-related areas were retrospectively reviewed. Four artificial intelligence-based indicators were calculated with artificial intelligence on TOF-MRA and DTI, including FN5mm/50mm (the proportion of fiber numbers within 5-50mm from the lesion border), FN10mm/50mm (the same but within 10-50mm), FP5mm/50mm (the proportion of fiber voxel points within 5-50mm from the lesion border), and FP10mm/50mm (the same but within 10-50mm). The association between the variables and long-term postsurgical motor defects was analyzed using univariate and multivariate analyses. Least absolute shrinkage and selection operator regression with the Pearson correlation coefficient was used to select the optimal features to develop the machine learning model to predict postsurgical motor defects. The area under the curve was calculated to evaluate the predictive performance.

RESULTS

In patients with and without postsurgical motor defects, the mean FN5mm/50mm, FN10mm/50mm, FP5mm/50mm, and FP10mm/50mm were 0.24 (SD, 0.24) and 0.03 (SD, 0.06), 0.37 (SD, 0.27) and 0.06 (SD, 0.08), 0.06 (SD, 0.10) and 0.01 (SD, 0.02), and 0.10 (SD, 0.12) and 0.02 (SD, 0.05), respectively. Univariate and multivariate logistic analyses identified FN10mm/50mm as an independent risk factor for long-term postsurgical motor defects (P = .002). FN10mm/50mm achieved a mean area under the curve of 0.86 (SD, 0.08). The mean area under the curve of the machine learning model consisting of FN10mm/50mm, diffuseness, and the Spetzler-Martin score was 0.88 (SD, 0.07).

CONCLUSIONS

The artificial intelligence-based indicator, FN10mm/50mm, can reflect the lesion-fiber spatial relationship and act as a dominant predictor for postsurgical motor defects in patients with brain AVMs involving motor-related areas.

Radiation Therapy Decision Making Process and Operations for COVID-19 Positive Patients

Purpose/Objective(s)

A challenging clinical dilemma during the COVID-19 pandemic is management of cancer patients who test positive for COVID. Given the need to balance the risk of disease progression with the risk of transmission to other patients and staff, radiation therapy for these patients requires careful consideration and modification of standard workflows. It is also critical to develop processes to mitigate radiation treatment interruption, which can affect patient outcomes. The objective of this study was to report the clinical operations and outcomes for COVID positive patients receiving radiation therapy during the pandemic at a tertiary cancer center including 2 network locations.

Materials/Methods

During March 2020 to March 2022, the Radiation Oncology COVID committee (RO COVID) developed an integrated process to triage patients, provide treatment recommendations, and implement infection control procedures to safely deliver radiation therapy to COVID positive patients. Policies were created for each center with multidisciplinary input from infectious disease, radiation oncology, radiation therapy, and nursing. All COVID positive patients were presented to the RO COVID group and evaluated for clinical urgency, benefit with radiation, and life expectancy. If deemed necessary, a limited planned break or hypofractionated regimen was recommended to minimize staff exposure. We conducted a retrospective review of COVID positive patients with different primary malignancies treated through the COVID positive pathway.

Results

A total of 68 COVID positive patients were treated with the COVID positive pathway (HN 15, Breast 9, CNS 8, GU 8, GYN, 7, Thoracic 6, GI 5, HEME 5, PED 3, SARC 2). The median age was 57.1 years (IQR 45.8-63.4) and 47% were female. There were 39 patients (57%) who were asymptomatic and were tested for routine pre-radiation screening or due to concerns of COVID exposure. Twenty-three (34%) patients were treated with palliative intent and 8 (12%) were treated for an emergent indication (i.e., spinal cord compression, bleeding). Thirteen (19%) patients were receiving radiation treatment, had a treatment break (7-21 days), and then resumed their radiation course. All treatments were successfully completed without known nosocomial spread of COVID to staff or other patients. Among this heterogenous group of patients, 58 (85%) were alive with a median follow up of 2 months (IQR 0.5-7.5). COVID infection may have contributed to 3 out of 10 deaths (4% of total cohort). The remaining deaths were due to progression of disease or other non-COVID causes.

Conclusion

In this study, COVID positive patients were safely treated with radiation therapy through a comprehensive decision making and clinical operations pathway taking into account evolving COVID guidelines for three different variant surges. Although limited in follow up, patient outcomes are promising with few COVID-related deaths and low overall mortality rates, even with hypofractionated regimens.

Nectin4 antagonises type I interferon production by targeting TRAF3 for autophagic degradation and disrupting TRAF3-TBK1 complex formation

Autophagy, a conserved cellular degradative process, plays a crucial role in innate immunity during viral infections. Nervous necrosis virus (NNV), a leading cause of fish diseases with morbidity and mortality, triggers cell autophagy to promote viral replication; however, the details of how NNV utilises autophagy to facilitate its own replication remain largely unexplored. Here, we investigated the mechanism by which the sea perch Nectin4 (LjNectin4), a receptor of NNV, regulates autophagy and the innate immune system by targeting TNFR-associated factor 3 (TRAF3). Our data demonstrated that LjNectin4 directly binds to the NNV capsid protein and facilitates NNV entry, indicating that LjNectin4 functions as an NNV receptor. Moreover, LjNectin4 promoted NNV replication by inhibiting key elements of the RLR signalling pathway (MDA5, MAVS, TRAF3, TBK1, and IRF3)-induced IFN response. Mechanistically, LjNectin4 directly interacted with TRAF3 and promoted its autophagy-mediated lysosomal degradation. Domain mapping of the interaction between TRAF3 and LjNectin4 or TBK1 showed that both LjNectin4 and TBK1 interacted with the ZF2 and TRAF-C domains of TRAF3, suggesting that LjNectin4 blocked TRAF3-TBK1 complex formation. Collectively, our study revealed that NNV utilises LjNectin4 to suppress IFN production by mediating TRAF3 autophagic degradation and disrupting the TRAF3-TBK1 complex, thereby promoting NNV replication.

Tongxin formula protects H9c2 cardiomyocytes from cobalt chloride-induced hypoxic injury via inhibition of apoptosis

In this study, the effect of the Tongxin formula (TXF) on the apoptosis of H9c2 cardiomyocytes induced by cobalt chloride (CoCl₂) was investigated, and the potential mechanism was explored. A hypoxic injury model of H9c2 cardiomyocytes was established using CoCl₂. The cell viability was measured using a Cell Counting Kit-8 assay. The lactate dehydrogenase (LDH) release and caspase-3 activity were measured using spectrophotometry. The apoptosis was measured via Annexin V-FITC/PI staining and flow cytometry. The changes in the mitochondrial membrane potential were examined using immunofluorescence microscopy following the loading of JC-1 probes. The expressions of apoptosis-related proteins and key proteins in the phosphatidylinositol 3-kinase/protein kinase B (PI3K/Akt) pathway were examined via immunoblotting. The different TXF concentrations studied significantly improved the percentage of viability of cardiomyocytes with hypoxic injury, and the LDH release, apoptotic rate, caspase-3 activity, and levels of cleaved caspase-3 protein were reduced in the injured cells. Additionally, the TXF group had increased mitochondrial membrane potential, upregulated expression of Bcl-2 and p-Akt proteins, and significantly reduced expression of cleaved caspase-3 protein in the cells with hypoxic injury. Moreover, in the TXF group, the treatment significantly reduced the BAX protein expression, but the difference was not statistically significant compared with the CoCl2 group. In this study, TXF regulated the expression of apoptosis-related proteins, inhibited apoptosis, increased the mitochondrial membrane potential, and alleviated damage to the mitochondrial membrane, thereby protecting the cardiomyocytes from hypoxic injury. The underlying mechanism could be related to activation of the PI3K/Akt signaling pathway and upregulation of the Bcl-2 protein.

RETRACTED: Modulation of macrophage phenotype through controlled release of interleukin-4 from gelatine coatings on titanium surfaces

Pro-inflammatory phenotype (M1) macrophages initiate angiogenesis, while their prolonged activation can induce chronic inflammation. Anti-inflammatory phenotype (M2) macrophages promote vessel maturation and tissue regeneration. Biomaterials which can promote M2 polarisation after appropriate inflammation should enhance angiogenesis and wound healing. Herein, Interleukin-4 (IL-4), an anti-inflammatory cytokine, was adsorbed onto a titanium surface. Then, a genipin cross-linked gelatine hydrogel was coated onto the surface to delay IL-4 release. The cross-linking degree of the hydrogel was modulated by the different amount of genipin to control release of IL-4. When 0.7 wt% (weight %) genipin was used as a cross-linker, the sample (GG07-I) released less IL-4 within the first several days, followed by a sustained release time to 14 d. Meanwhile, the release rate of IL-4 in GG07-I reached a peak between 3 d and 7 d. In culture with macrophages in vitro, GG07-I and GG07 exhibited good cytocompatibility. The phenotypical switch of macrophages stimulated by the samples was determined by FACS, ELISA and PCR. Macrophages cultured with GG07-I, GG07 and PT were firstly activated to the M1 phenotype by interferon-gamma (IFN-γ). Then, due to the release of IL-4 in 5 to 7 d, GG07-I enhanced CD206, increased the secretion and gene expression of M2 marker, such as interleukin-10 (IL-10), arginase-1 (ARG-1) and platelet derived growth factor-BB (PDGF- BB). GG07-I prompted the switch from M1 to M2 phenotype. Those appropriate secretion of cytokines would benefit both vascularisation and osseointegration. Thus, the biomaterial directing inflammatory reaction has good prospects for clinical treatments.

Metabolic changes in methomyl poisoned rats treated by vitamin E

In this study, we developed a serum and urine metabolomic method based on gas chromatography-mass spectrometry (GC-MS) combination with biomedical results to evaluate the effect of vitamin E treatment on methomyl poisoning rats. The rats were divided into three groups: the control group, methomyl poisoning group, and vitamin E treatment group. Partial least squares discriminate analysis (PLS-DA) showed that methomyl poisoning induced metabolic perturbations. Compared to the control group, based on the urinary metabolomics data, the level of ribitol, l-proline, xylitol, hydrocinnamic acid, 11-cis-octadecenoic acid, octadecanoic acid, and hexadecanoic acid of methomyl poisoning group increased, while the level of 2,3,4-trihydroxybutyric acid, ethanimidic acid, pantothenic acid, and retinoic acid decreased. Vitamin E pretreatment effectively normalized the levels of metabolites in rat urine in vitamin E treatment group. There was no significant difference in rat plasma metabolomic data after acute methomyl poisoning. The results indicate that metabolomic method based on GC-MS may be useful to elucidate the vitamin E treatment for methomyl poisoning.

Preliminary Study on HA Coating Percutaneously Implanted in Bone

A comparative investigation on the possibility of hydroxyapatite (HA) coating and pure Ti column to form biological sealing with skin tissue was completed in this study. HA coating and pure Ti column were percutaneously implanted in the tibia of rabbits. Compared with titanium (Ti) implant, HA coating forms epithelial sealing with skin tissue at 6 weeks postoperatively, while the Ti implant may loosen from the implanted site and be lost. The Ti column loosing rate at this time was 50%. However, once the Ti implant becomes fixed with the bone tissue, it can form epithelial sealing with skin tissue just like the HA coating, at 8 weeks postoperatively. At 8 weeks postoperatively, the epithelial sealing is not destroyed in spite of the fact that the HA coating is biodegraded. Our results show that the HA coating can become fixed with the bone faster than the Ti, which is beneficial for epithelial sealing formation. The main role of HA coating for epithelial sealing is beneficial for sealing at the initial period after it is implanted.